From 2dd4f389c7f436144941c9adfb0be7dddd22c73e Mon Sep 17 00:00:00 2001 From: Mathieu Othacehe Date: Tue, 8 Dec 2020 11:48:31 +0100 Subject: gnu: cuirass: Update to 0.0.1-56.697fa14. * gnu/packages/ci.scm (cuirass): Update to 0.0.1-56.697fa14. --- gnu/packages/ci.scm | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/gnu/packages/ci.scm b/gnu/packages/ci.scm index 2fb9822fb5..161b45846e 100644 --- a/gnu/packages/ci.scm +++ b/gnu/packages/ci.scm @@ -68,8 +68,8 @@ (file-name (string-append name "-" version "-checkout"))))))) (define-public cuirass - (let ((commit "fd432b8e8f449d691773e96e7d90f44761e01aa3") - (revision "55")) + (let ((commit "697fa14584551d9595cd042f1ffeba240e45a127") + (revision "56")) (package (name "cuirass") (version (git-version "0.0.1" revision commit)) @@ -81,7 +81,7 @@ (file-name (git-file-name name version)) (sha256 (base32 - "10j3w3px0250avwry2x8wsa0m0plvm957g4qqgnajsbc9gvka554")))) + "0gw9cja8fiyra9vnn3y384gwanvsqdq6gwjcvmz91sy5lvfwv34m")))) (build-system gnu-build-system) (arguments '(#:modules ((guix build utils) @@ -94,7 +94,7 @@ #:phases (modify-phases %standard-phases (add-after 'unpack 'disable-repo-tests - (λ _ + (lambda _ ;; Disable tests that use a connection to the Guix daemon. (substitute* "Makefile.am" (("tests/repo.scm \\\\") "\\")) -- cgit v1.2.3 From 770fb659a62d8adab9a4ba7b44e2760722703879 Mon Sep 17 00:00:00 2001 From: Mathieu Othacehe Date: Tue, 8 Dec 2020 11:53:25 +0100 Subject: services: cuirass: Add queue-size option. * gnu/services/cuirass.scm (): Add "queue-size" field. (cuirass-shepherd-service): Honor it. * doc/guix.texi (Continuous Integration): Document it. --- doc/guix.texi | 3 +++ gnu/services/cuirass.scm | 4 ++++ 2 files changed, 7 insertions(+) diff --git a/doc/guix.texi b/doc/guix.texi index fc57f4f537..0e647a284c 100644 --- a/doc/guix.texi +++ b/doc/guix.texi @@ -25695,6 +25695,9 @@ Owner's group of the @code{cuirass} process. Number of seconds between the poll of the repositories followed by the Cuirass jobs. +@item @code{queue-size} (default: @code{1}) +Size of the database writer queue. + @item @code{database} (default: @code{"/var/lib/cuirass/cuirass.db"}) Location of sqlite database which contains the build results and previously added specifications. diff --git a/gnu/services/cuirass.scm b/gnu/services/cuirass.scm index a50f583807..7706ed41c6 100644 --- a/gnu/services/cuirass.scm +++ b/gnu/services/cuirass.scm @@ -69,6 +69,8 @@ (default "cuirass")) (interval cuirass-configuration-interval ;integer (seconds) (default 60)) + (queue-size cuirass-configuration-queue-size + (default 1)) (database cuirass-configuration-database ;string (file-name) (default "/var/lib/cuirass/cuirass.db")) (port cuirass-configuration-port ;integer (port) @@ -98,6 +100,7 @@ (user (cuirass-configuration-user config)) (group (cuirass-configuration-group config)) (interval (cuirass-configuration-interval config)) + (queue-size (cuirass-configuration-queue-size config)) (database (cuirass-configuration-database config)) (ttl (cuirass-configuration-ttl config)) (port (cuirass-configuration-port config)) @@ -119,6 +122,7 @@ "--database" #$database "--ttl" #$(string-append (number->string ttl) "s") "--interval" #$(number->string interval) + "--queue-size" #$(number->string queue-size) #$@(if queries-log-file (list (string-append "--log-queries=" queries-log-file)) -- cgit v1.2.3 From ad6cf3d4adddf39fbd8318b96756abd933ff6735 Mon Sep 17 00:00:00 2001 From: Zhu Zihao Date: Mon, 7 Dec 2020 22:29:58 +0800 Subject: gnu: Add xcb-imdkit. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/fcitx5.scm: New file. * gnu/local.mk (GNU_SYSTEM_MODULES): Add it. Signed-off-by: 宋文武 --- gnu/local.mk | 1 + gnu/packages/fcitx5.scm | 62 +++++++++++++++++++++++++++++++++++++++++++++++++ 2 files changed, 63 insertions(+) create mode 100644 gnu/packages/fcitx5.scm diff --git a/gnu/local.mk b/gnu/local.mk index f59d2543cd..90df6f3966 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -205,6 +205,7 @@ GNU_SYSTEM_MODULES = \ %D%/packages/erlang.scm \ %D%/packages/fabric-management.scm \ %D%/packages/fcitx.scm \ + %D%/packages/fcitx5.scm \ %D%/packages/figlet.scm \ %D%/packages/file.scm \ %D%/packages/file-systems.scm \ diff --git a/gnu/packages/fcitx5.scm b/gnu/packages/fcitx5.scm new file mode 100644 index 0000000000..1c81e35862 --- /dev/null +++ b/gnu/packages/fcitx5.scm @@ -0,0 +1,62 @@ +;;; GNU Guix --- Functional package management for GNU +;;; Copyright © 2020 Zhu Zihao +;;; +;;; This file is part of GNU Guix. +;;; +;;; GNU Guix is free software; you can redistribute it and/or modify it +;;; under the terms of the GNU General Public License as published by +;;; the Free Software Foundation; either version 3 of the License, or (at +;;; your option) any later version. +;;; +;;; GNU Guix is distributed in the hope that it will be useful, but +;;; WITHOUT ANY WARRANTY; without even the implied warranty of +;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +;;; GNU General Public License for more details. +;;; +;;; You should have received a copy of the GNU General Public License +;;; along with GNU Guix. If not, see . + +(define-module (gnu packages fcitx5) + #:use-module (guix packages) + #:use-module (guix download) + #:use-module (guix build-system cmake) + #:use-module ((guix licenses) #:prefix license:) + #:use-module (gnu packages datastructures) + #:use-module (gnu packages kde-frameworks) + #:use-module (gnu packages pkg-config) + #:use-module (gnu packages xorg)) + +(define-public xcb-imdkit + (package + (name "xcb-imdkit") + (version "1.0.1") + (source + (origin + (method url-fetch) + (uri (string-append + "https://download.fcitx-im.org/fcitx5/xcb-imdkit/xcb-imdkit-" + version ".tar.xz")) + (sha256 + (base32 "1qgbbp8y8ci7haz99vgbrgpjsbrwwyjianyhdvxcirnbm5bybvmz")) + (modules '((guix build utils))) + (snippet + '(begin + ;; Remove bundled uthash. + (delete-file-recursively "uthash") + #t)))) + (build-system cmake-build-system) + (inputs + `(("uthash" ,uthash) + ("libxcb" ,libxcb) + ("xcb-util" ,xcb-util) + ("xcb-util-keysyms" ,xcb-util-keysyms))) + (native-inputs + `(("extra-cmake-modules" ,extra-cmake-modules) + ("pkg-config" ,pkg-config))) + (home-page "https://github.com/fcitx/xcb-imdkit") + (synopsis "Input method development support for XCB") + (description "Xcb-imdkit is an implementation of xim protocol in XCB, +comparing with the implementation of IMDkit with Xlib, and xim inside Xlib, it +has less memory foot print, better performance, and safer on malformed +client.") + (license license:lgpl2.1))) -- cgit v1.2.3 From aa5cfb39a5e4d2c5d394d013d222e0d56bb6b0a1 Mon Sep 17 00:00:00 2001 From: Zhu Zihao Date: Mon, 7 Dec 2020 22:38:35 +0800 Subject: gnu: Add fcitx5. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/fcitx5.scm (fcitx5): New variable. Signed-off-by: 宋文武 --- gnu/packages/fcitx5.scm | 73 +++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 73 insertions(+) diff --git a/gnu/packages/fcitx5.scm b/gnu/packages/fcitx5.scm index 1c81e35862..41d163c45b 100644 --- a/gnu/packages/fcitx5.scm +++ b/gnu/packages/fcitx5.scm @@ -22,8 +22,21 @@ #:use-module (guix build-system cmake) #:use-module ((guix licenses) #:prefix license:) #:use-module (gnu packages datastructures) + #:use-module (gnu packages enchant) + #:use-module (gnu packages freedesktop) + #:use-module (gnu packages gettext) + #:use-module (gnu packages glib) + #:use-module (gnu packages gtk) + #:use-module (gnu packages iso-codes) #:use-module (gnu packages kde-frameworks) + #:use-module (gnu packages libevent) + #:use-module (gnu packages linux) #:use-module (gnu packages pkg-config) + #:use-module (gnu packages pretty-print) + #:use-module (gnu packages unicode) + #:use-module (gnu packages web) + #:use-module (gnu packages xdisorg) + #:use-module (gnu packages xml) #:use-module (gnu packages xorg)) (define-public xcb-imdkit @@ -60,3 +73,63 @@ comparing with the implementation of IMDkit with Xlib, and xim inside Xlib, it has less memory foot print, better performance, and safer on malformed client.") (license license:lgpl2.1))) + +(define-public fcitx5 + (package + (name "fcitx5") + (version "5.0.3") + (source + (origin + (method url-fetch) + (uri (string-append + "https://download.fcitx-im.org/fcitx5/fcitx5/fcitx5-" + version "_dict.tar.xz")) + (sha256 + (base32 "06zkb33m2rnhg385iy79n3r4svz5jbav74di61xqa3lhbv7534s3")))) + (build-system cmake-build-system) + (arguments + `(#:configure-flags + (list (string-append "-DCLDR_DIR=" + (assoc-ref %build-inputs "unicode-cldr-common") + "/share/unicode/cldr")))) + (inputs + `(("cairo" ,cairo) + ("cairo-xcb" ,cairo-xcb) + ("dbus" ,dbus) + ("enchant" ,enchant) + ("expat" ,expat) + ("fmt" ,fmt) + ("gdk-pixbuf" ,gdk-pixbuf) + ("gettext" ,gettext-minimal) + ("glib" ,glib) + ("iso-codes" ,iso-codes) + ("json-c" ,json-c) + ("libevent" ,libevent) + ("libpthread-stubs" ,libpthread-stubs) + ("libuuid" ,util-linux "lib") + ("libx11" ,libx11) + ("libxcb" ,libxcb) + ("libxfixes" ,libxfixes) + ("libxinerama" ,libxinerama) + ("libxkbcommon" ,libxkbcommon) + ("libxkbfile" ,libxkbfile) + ("pango" ,pango) + ("unicode-cldr-common" ,unicode-cldr-common) + ("wayland" ,wayland) + ("wayland-protocols" ,wayland-protocols) + ("xcb-imdkit" ,xcb-imdkit) + ("xcb-util" ,xcb-util) + ("xcb-util-keysyms" ,xcb-util-keysyms) + ("xcb-util-wm" ,xcb-util-wm) + ("xkeyboard-config" ,xkeyboard-config))) + (native-inputs + `(("extra-cmake-modules" ,extra-cmake-modules) + ("pkg-config" ,pkg-config))) + (native-search-paths + (list (search-path-specification + (variable "FCITX_ADDON_DIRS") + (files '("lib/fcitx5"))))) + (home-page "https://github.com/fcitx/fcitx5") + (synopsis "Input method framework") + (description "Fcitx 5 is a generic input method framework.") + (license license:lgpl2.1+))) -- cgit v1.2.3 From 2d07803be80d36c90fcc9ec44a796e4f09a37ebd Mon Sep 17 00:00:00 2001 From: Zhu Zihao Date: Mon, 7 Dec 2020 22:39:29 +0800 Subject: gnu: Add fcitx5-lua. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/fcitx5.scm (fcitx5-lua): New variable. Signed-off-by: 宋文武 --- gnu/packages/fcitx5.scm | 45 +++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 45 insertions(+) diff --git a/gnu/packages/fcitx5.scm b/gnu/packages/fcitx5.scm index 41d163c45b..0a71f68534 100644 --- a/gnu/packages/fcitx5.scm +++ b/gnu/packages/fcitx5.scm @@ -31,6 +31,7 @@ #:use-module (gnu packages kde-frameworks) #:use-module (gnu packages libevent) #:use-module (gnu packages linux) + #:use-module (gnu packages lua) #:use-module (gnu packages pkg-config) #:use-module (gnu packages pretty-print) #:use-module (gnu packages unicode) @@ -133,3 +134,47 @@ client.") (synopsis "Input method framework") (description "Fcitx 5 is a generic input method framework.") (license license:lgpl2.1+))) + +(define-public fcitx5-lua + (package + (name "fcitx5-lua") + (version "5.0.1") + (source + (origin + (method url-fetch) + (uri (string-append + "https://download.fcitx-im.org/fcitx5/fcitx5-lua/fcitx5-lua-" + version ".tar.xz")) + (sha256 + (base32 "177mj56j8yrl79hvk7bbrifvm137np23pwalv83ibgk4l51z92hf")))) + (build-system cmake-build-system) + (arguments + `(#:configure-flags + (list + (string-append "-DFEM_INCLUDE_INSTALL_DIR=" %output "/include") + (string-append "-DFEM_LIB_INSTALL_DIR=" %output "/lib")) + #:phases + (modify-phases %standard-phases + (add-before 'configure 'patch-install-prefix + (lambda* (#:key outputs #:allow-other-keys) + (for-each + (lambda (x) + (format #t "patch-install-prefix: Fixing install prefix in ~a~%" + x) + (substitute* x + (("\\$\\{FCITX_INSTALL_PKGDATADIR\\}") + (string-append (assoc-ref outputs "out") + "/share/fcitx5")))) + '("src/addonloader/CMakeLists.txt" + "src/imeapi/CMakeLists.txt"))))))) + (inputs + `(("fcitx5" ,fcitx5) + ("lua" ,lua) + ("gettext" ,gettext-minimal) + ("libpthread-stubs" ,libpthread-stubs))) + (native-inputs + `(("extra-cmake-modules" ,extra-cmake-modules))) + (home-page "https://github.com/fcitx/fcitx5-lua") + (synopsis "Lua support for Fcitx 5") + (description "Fcitx5-lua allows writing Fcitx5 extension in Lua.") + (license license:lgpl2.1+))) -- cgit v1.2.3 From 69d3419ca3b60f4f7edfbd424edbcbd0a73cd976 Mon Sep 17 00:00:00 2001 From: Zhu Zihao Date: Mon, 7 Dec 2020 22:40:41 +0800 Subject: gnu: Add libime. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/fcitx5.scm (libime): New variable. Signed-off-by: 宋文武 --- gnu/packages/fcitx5.scm | 28 ++++++++++++++++++++++++++++ 1 file changed, 28 insertions(+) diff --git a/gnu/packages/fcitx5.scm b/gnu/packages/fcitx5.scm index 0a71f68534..d9d98b4794 100644 --- a/gnu/packages/fcitx5.scm +++ b/gnu/packages/fcitx5.scm @@ -21,9 +21,11 @@ #:use-module (guix download) #:use-module (guix build-system cmake) #:use-module ((guix licenses) #:prefix license:) + #:use-module (gnu packages boost) #:use-module (gnu packages datastructures) #:use-module (gnu packages enchant) #:use-module (gnu packages freedesktop) + #:use-module (gnu packages gcc) #:use-module (gnu packages gettext) #:use-module (gnu packages glib) #:use-module (gnu packages gtk) @@ -34,6 +36,7 @@ #:use-module (gnu packages lua) #:use-module (gnu packages pkg-config) #:use-module (gnu packages pretty-print) + #:use-module (gnu packages python) #:use-module (gnu packages unicode) #:use-module (gnu packages web) #:use-module (gnu packages xdisorg) @@ -178,3 +181,28 @@ client.") (synopsis "Lua support for Fcitx 5") (description "Fcitx5-lua allows writing Fcitx5 extension in Lua.") (license license:lgpl2.1+))) + +(define-public libime + (package + (name "libime") + (version "1.0.2") + (source + (origin + (method url-fetch) + (uri (string-append "https://download.fcitx-im.org/fcitx5/libime/libime-" + version "_dict.tar.xz")) + (sha256 + (base32 "006pncby7p6h3rnicckzjwi6jzsrqiqbj6p9bpic80lanlllgw31")))) + (build-system cmake-build-system) + (inputs + `(("fcitx5" ,fcitx5) + ("boost" ,boost))) + (native-inputs + `(("gcc" ,gcc-9) ;for #include and ld support + ("extra-cmake-modules" ,extra-cmake-modules) + ("python" ,python))) ;needed to run test + (home-page "https://github.com/fcitx/libime") + (synopsis "Library for implementing generic input method") + (description "Libime is a library for implmenting various input methods +editors.") + (license license:lgpl2.1+))) -- cgit v1.2.3 From 4394d3721a25eb103bff24404e90e1a6c7049166 Mon Sep 17 00:00:00 2001 From: Zhu Zihao Date: Mon, 7 Dec 2020 22:42:43 +0800 Subject: gnu: Add fcitx5-qt. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/fcitx5.scm (fcitx5-qt): New variable. Signed-off-by: 宋文武 --- gnu/packages/fcitx5.scm | 36 ++++++++++++++++++++++++++++++++++++ 1 file changed, 36 insertions(+) diff --git a/gnu/packages/fcitx5.scm b/gnu/packages/fcitx5.scm index d9d98b4794..ee479156b9 100644 --- a/gnu/packages/fcitx5.scm +++ b/gnu/packages/fcitx5.scm @@ -37,6 +37,7 @@ #:use-module (gnu packages pkg-config) #:use-module (gnu packages pretty-print) #:use-module (gnu packages python) + #:use-module (gnu packages qt) #:use-module (gnu packages unicode) #:use-module (gnu packages web) #:use-module (gnu packages xdisorg) @@ -206,3 +207,38 @@ client.") (description "Libime is a library for implmenting various input methods editors.") (license license:lgpl2.1+))) + +(define-public fcitx5-qt + (package + (name "fcitx5-qt") + (version "5.0.1") + (source + (origin + (method url-fetch) + (uri (string-append "https://download.fcitx-im.org/fcitx5" + "/fcitx5-qt/fcitx5-qt-" + version ".tar.xz")) + (sha256 + (base32 "0ilhb4yw9k3m1c4fidnv3nd5dgm9xxds11dgdys6gswjjnmcgqqm")))) + (build-system cmake-build-system) + (arguments + `(#:configure-flags + (list (string-append "-DCMAKE_INSTALL_QT5PLUGINDIR=" + %output "/lib/qt5/plugins") + "-DENABLE_QT4=Off"))) + (inputs + `(("fcitx5" ,fcitx5) + ("libxcb" ,libxcb) + ("libxkbcommon" ,libxkbcommon) + ("qtbase" ,qtbase) + ("gettext" ,gettext-minimal))) + (native-inputs + `(("extra-cmake-modules" ,extra-cmake-modules))) + (home-page "https://github.com/fcitx/fcitx5-qt") + (synopsis "Qt library and IM module for Fcitx 5") + (description "Fcitx5-qt provides Qt library for development and IM module +for Qt based application.") + (license (list license:lgpl2.1+ + ;; Files under qt4(Fcitx5Qt4DBusAddons), qt5/dbusaddons + ;; and qt5/platforminputcontext. + license:bsd-3)))) -- cgit v1.2.3 From d4aca38b50d75cff9bd065a855e7368a51843db4 Mon Sep 17 00:00:00 2001 From: Zhu Zihao Date: Mon, 7 Dec 2020 22:43:47 +0800 Subject: gnu: Add fcitx5-gtk. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/fcitx5.scm (fcitx5-gtk): New variable. Signed-off-by: 宋文武 --- gnu/packages/fcitx5.scm | 51 +++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 51 insertions(+) diff --git a/gnu/packages/fcitx5.scm b/gnu/packages/fcitx5.scm index ee479156b9..bdebe579a9 100644 --- a/gnu/packages/fcitx5.scm +++ b/gnu/packages/fcitx5.scm @@ -208,6 +208,57 @@ client.") editors.") (license license:lgpl2.1+))) +(define-public fcitx5-gtk + (package + (name "fcitx5-gtk") + (version "5.0.1") + (source + (origin + (method url-fetch) + (uri (string-append "https://download.fcitx-im.org/fcitx5" + "/fcitx5-gtk/fcitx5-gtk-" + version ".tar.xz")) + (sha256 + (base32 "0h53liraqc5nz4nyi3ixdfdw3zzkdcsiff7j25acc3gmaa5gyij7")))) + (build-system cmake-build-system) + (arguments + `(#:tests? #f ;No test + #:configure-flags + (list (string-append "-DGOBJECT_INTROSPECTION_GIRDIR=" + %output "/share/gir-1.0") + (string-append "-DGOBJECT_INTROSPECTION_TYPELIBDIR=" + %output "/lib/girepository-1.0")) + #:phases + (modify-phases %standard-phases + (add-before 'configure 'patch-install-prefix + (lambda* (#:key outputs #:allow-other-keys) + (let ((out (assoc-ref outputs "out")) + (gtk2 (assoc-ref outputs "gtk2"))) + ;; Install GTK+ 2 input method module to its own output. + (substitute* "gtk2/CMakeLists.txt" + (("\\$\\{CMAKE_INSTALL_LIBDIR\\}") + (string-append gtk2 "/lib"))))))))) + (inputs + `(("fcitx5" ,fcitx5) + ("libxkbcommon" ,libxkbcommon) + ("gobject-introspection" ,gobject-introspection) + ("gtk2" ,gtk+-2) + ("gtk3" ,gtk+) + ("glib" ,glib) + ("libx11" ,libx11) + ("gettext" ,gettext-minimal))) + (native-inputs + `(("extra-cmake-modules" ,extra-cmake-modules) + ("pkg-config" ,pkg-config) + ("glib" ,glib "bin"))) ;for glib-genmarshal + ;; TODO: Add "lib" output to reduce the closure size of "gtk2". + (outputs '("out" "gtk2")) + (home-page "https://github.com/fcitx/fcitx5-gtk") + (synopsis "Glib based D-Bus client and GTK IM module for Fcitx 5") + (description "Fcitx5-gtk provides a Glib based D-Bus client and IM module +for GTK+2/GTK+3 application.") + (license license:lgpl2.1+))) + (define-public fcitx5-qt (package (name "fcitx5-qt") -- cgit v1.2.3 From 9a23698ecd1f444bb63a3829f6a69ec8b3c5ea8e Mon Sep 17 00:00:00 2001 From: Zhu Zihao Date: Sat, 28 Nov 2020 13:25:37 +0800 Subject: gnu: Add fcitx5-chinese-addons. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/fcitx5.scm (fcitx5-chinese-addons): New variable. Signed-off-by: 宋文武 --- gnu/packages/fcitx5.scm | 78 +++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 78 insertions(+) diff --git a/gnu/packages/fcitx5.scm b/gnu/packages/fcitx5.scm index bdebe579a9..5de32e3c71 100644 --- a/gnu/packages/fcitx5.scm +++ b/gnu/packages/fcitx5.scm @@ -22,6 +22,7 @@ #:use-module (guix build-system cmake) #:use-module ((guix licenses) #:prefix license:) #:use-module (gnu packages boost) + #:use-module (gnu packages curl) #:use-module (gnu packages datastructures) #:use-module (gnu packages enchant) #:use-module (gnu packages freedesktop) @@ -38,6 +39,7 @@ #:use-module (gnu packages pretty-print) #:use-module (gnu packages python) #:use-module (gnu packages qt) + #:use-module (gnu packages textutils) #:use-module (gnu packages unicode) #:use-module (gnu packages web) #:use-module (gnu packages xdisorg) @@ -293,3 +295,79 @@ for Qt based application.") ;; Files under qt4(Fcitx5Qt4DBusAddons), qt5/dbusaddons ;; and qt5/platforminputcontext. license:bsd-3)))) + +(define-public fcitx5-chinese-addons + (package + (name "fcitx5-chinese-addons") + (version "5.0.2") + (source + (origin + (method url-fetch) + (uri (string-append "https://download.fcitx-im.org/fcitx5" + "/fcitx5-chinese-addons/fcitx5-chinese-addons-" + version "_dict.tar.xz")) + (sha256 + (base32 "0mf91gzwzhfci0jn6g3l516xjw8r4v40ginnbl70h1zx6vr24rfp")))) + (build-system cmake-build-system) + (arguments + `(#:configure-flags + (list + (string-append "-DFEM_INCLUDE_INSTALL_DIR=" %output "/include") + (string-append "-DFEM_LIB_INSTALL_DIR=" %output "/lib")) + #:phases + (modify-phases %standard-phases + (add-before 'configure 'patch-install-prefix + (lambda* (#:key outputs #:allow-other-keys) + (for-each + (lambda (x) + (format #t "patch-install-prefix: Fixing install prefix in ~a~%" + x) + (substitute* x + (("\\$\\{FCITX_INSTALL_PKGDATADIR\\}") + (string-append (assoc-ref outputs "out") + "/share/fcitx5")))) + (find-files "." "CMakeLists\\.txt$")))) + (add-before 'configure 'split-outputs + ;; Build with GUI supports requires Qt and increase package closure + ;; by 800M on x86_64, so place it under another output. + (lambda* (#:key outputs #:allow-other-keys) + (substitute* "gui/pinyindictmanager/CMakeLists.txt" + (("\\$\\{CMAKE_INSTALL_LIBDIR\\}" _) + (string-append (assoc-ref outputs "gui") "/lib")))))))) + (inputs + `(("fcitx5" ,fcitx5) + ("fcitx5-lua" ,fcitx5-lua) + ("boost" ,boost) + ("libime",libime) + ("curl" ,curl) + ("gettext" ,gettext-minimal) + ("fmt" ,fmt) + ("libpthread-stubs" ,libpthread-stubs) + ("opencc" ,opencc) + ("qtbase" ,qtbase) + ("fcitx5-qt" ,fcitx5-qt) + ("qtwebkit" ,qtwebkit))) + (native-inputs + `(("extra-cmake-modules" ,extra-cmake-modules) + ("pkg-config" ,pkg-config))) + (outputs '("out" "gui")) + (home-page "https://github.com/fcitx/fcitx5-chinese-addons") + (synopsis "Chinese related addons for Fcitx 5") + (description "Fcitx5-chinese-addons provides Chinese related addons, +including input methods previous bundled inside Fcitx 4: + +@itemize +@item Bingchan +@item Cangjie +@item Erbi +@item Pinyin +@item Shuangpin +@item Wanfeng +@item Wubi +@item Wubi Pinyin +@item Ziranma +@end itemize\n") + (license (list license:lgpl2.1+ + license:gpl2+ + ;; im/pinyin/emoji.txt + license:unicode)))) -- cgit v1.2.3 From ac1c7530d84aa80dedae60ca0737c270852d8d07 Mon Sep 17 00:00:00 2001 From: Zhu Zihao Date: Mon, 7 Dec 2020 22:46:03 +0800 Subject: gnu: Add fcitx5-configtool. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/fcitx5.scm (fcitx5-configtool): New variable. Signed-off-by: 宋文武 --- gnu/packages/fcitx5.scm | 39 +++++++++++++++++++++++++++++++++++++++ 1 file changed, 39 insertions(+) diff --git a/gnu/packages/fcitx5.scm b/gnu/packages/fcitx5.scm index 5de32e3c71..69632d8511 100644 --- a/gnu/packages/fcitx5.scm +++ b/gnu/packages/fcitx5.scm @@ -371,3 +371,42 @@ including input methods previous bundled inside Fcitx 4: license:gpl2+ ;; im/pinyin/emoji.txt license:unicode)))) + +(define-public fcitx5-configtool + (package + (name "fcitx5-configtool") + (version "5.0.1") + (source + (origin + (method url-fetch) + (uri (string-append + "https://download.fcitx-im.org/fcitx5" + "/fcitx5-configtool/fcitx5-configtool-" version ".tar.xz")) + (sha256 + (base32 "0mrqhzvab41hkvhkz7vkb8d2mv5bgx4aqp9jpz4kf3kskwm1q14b")))) + (build-system cmake-build-system) + (arguments + `(#:configure-flags + ;; KDE is currently not working on Guix, KCM supports doesn't make sense. + '("-DENABLE_KCM=Off"))) + (inputs + `(("fcitx5" ,fcitx5) + ("fcitx5-qt" ,fcitx5-qt) + ("qtbase" ,qtbase) + ("qtx11extras" ,qtx11extras) + ("kitemviews" ,kitemviews) + ("kwidgetsaddons" ,kwidgetsaddons) + ("libx11" ,libx11) + ("xkeyboard-config" ,xkeyboard-config) + ("libxkbfile" ,libxkbfile) + ("gettext" ,gettext-minimal) + ("iso-codes" ,iso-codes))) + (native-inputs + `(("gcc" ,gcc-9) + ("extra-cmake-modules" ,extra-cmake-modules) + ("pkg-config" ,pkg-config))) + (home-page "https://github.com/fcitx/fcitx5-configtool") + (synopsis "Graphical configuration tool for Fcitx 5") + (description "Fcitx5-configtool is a graphical configuration tool +to manage different input methods in Fcitx 5.") + (license license:gpl2+))) -- cgit v1.2.3 From af34f757ced016956cc73e1d9ddc52d4d79620f2 Mon Sep 17 00:00:00 2001 From: Zhu Zihao Date: Mon, 7 Dec 2020 22:45:06 +0800 Subject: gnu: Add fcitx5-material-color-theme. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/fcitx5.scm (fcitx5-material-color-theme): New variable. Signed-off-by: 宋文武 --- gnu/packages/fcitx5.scm | 71 +++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 71 insertions(+) diff --git a/gnu/packages/fcitx5.scm b/gnu/packages/fcitx5.scm index 69632d8511..b14385d9b2 100644 --- a/gnu/packages/fcitx5.scm +++ b/gnu/packages/fcitx5.scm @@ -19,7 +19,9 @@ (define-module (gnu packages fcitx5) #:use-module (guix packages) #:use-module (guix download) + #:use-module (guix git-download) #:use-module (guix build-system cmake) + #:use-module (guix build-system copy) #:use-module ((guix licenses) #:prefix license:) #:use-module (gnu packages boost) #:use-module (gnu packages curl) @@ -410,3 +412,72 @@ including input methods previous bundled inside Fcitx 4: (description "Fcitx5-configtool is a graphical configuration tool to manage different input methods in Fcitx 5.") (license license:gpl2+))) + +(define-public fcitx5-material-color-theme + (package + (name "fcitx5-material-color-theme") + (version "0.1") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/hosxy/Fcitx5-Material-Color") + (commit version))) + (sha256 + (base32 "1mgc722521jmfx0xc3ibmiycd3q2w7xg2956xcpc07kz90gcdjaa")))) + (build-system copy-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (use-modules (srfi srfi-26)) + + (let* ((out (assoc-ref outputs "out")) + (assets-dir (string-append + out "/share/fcitx5-material-color-theme")) + (themes-prefix (string-append out "/share/fcitx5/themes"))) + + (define (install-theme-variant variant target) + (let ((dir (string-append themes-prefix "/" target)) + (png (string-append "panel-" variant ".png")) + (conf (string-append "theme-" variant ".conf"))) + (format #t "install: Installing color variant \"~a\" to ~a~%" + variant dir) + (substitute* conf + (("^Name=.*") + (string-append "Name=" target "\n"))) + (mkdir-p dir) + (install-file png dir) + (copy-file conf (string-append dir "/theme.conf")) + (symlink (string-append assets-dir "/arrow.png") + (string-append dir "/arrow.png")))) + + (mkdir-p assets-dir) + (install-file "arrow.png" assets-dir) + (for-each + (lambda (x) + (install-theme-variant + x (string-append "Material-Color-" (string-capitalize x)))) + '("black" "blue" "brown" "indigo" + "orange" "pink" "red" "teal")) + + (install-theme-variant + "deepPurple" "Material-Color-DeepPurple"))))))) + (home-page "https://github.com/hosxy/Fcitx5-Material-Color") + (synopsis "Material Design for Fcitx 5") + (description "Fcitx5-material-color-theme is a Material Design theme +for Fcitx 5 with following color variants: + +@itemize +@item Black +@item Blue +@item Brown +@item Indigo +@item Orange +@item Pink +@item Red +@item teal +@item DeepPurple +@end itemize\n") + (license license:asl2.0))) -- cgit v1.2.3 From 4e110f61ac43ead1230f7cf18b8d8cc70c8bfe88 Mon Sep 17 00:00:00 2001 From: Julien Lepiller Date: Tue, 8 Dec 2020 13:44:53 +0100 Subject: guix: opam: Remove stray `pk'. * guix/import/opam.scm (opam->guix-package): Remove stray `pk'. --- guix/import/opam.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/guix/import/opam.scm b/guix/import/opam.scm index 867812124d..78d72df2ce 100644 --- a/guix/import/opam.scm +++ b/guix/import/opam.scm @@ -267,7 +267,7 @@ REPOSITORY is #f, from the official OPAM repository. Return a 'package' sexp or #f on failure." (and-let* ((opam-file (opam-fetch name repository)) (version (assoc-ref opam-file "version")) - (opam-content (pk (assoc-ref opam-file "metadata"))) + (opam-content (assoc-ref opam-file "metadata")) (url-dict (metadata-ref opam-content "url")) (source-url (or (metadata-ref url-dict "src") (metadata-ref url-dict "archive"))) -- cgit v1.2.3 From 59873d94ceb97b5ca95d3dc7ea91332c66c753d2 Mon Sep 17 00:00:00 2001 From: Julien Lepiller Date: Tue, 8 Dec 2020 13:41:47 +0100 Subject: guix: opam: Filter implicit inputs. * guix/import/opam.scm (opam->guix-package, depends->inputs): Filter out implicit inputs. --- guix/import/opam.scm | 21 +++++++++++---------- 1 file changed, 11 insertions(+), 10 deletions(-) diff --git a/guix/import/opam.scm b/guix/import/opam.scm index 78d72df2ce..4f366a9384 100644 --- a/guix/import/opam.scm +++ b/guix/import/opam.scm @@ -235,12 +235,15 @@ path to the repository." (equal? "ocaml" name)) names))) -(define (depends->inputs depends) +(define (filter-dependencies depends) + "Remove implicit dependencies from the list of dependencies in @var{depends}." (filter (lambda (name) - (and (not (equal? "" name)) - (not (equal? "ocaml" name)) - (not (equal? "ocamlfind" name)))) - (map dependency->input depends))) + (and (not (member name '("" "ocaml" "ocamlfind" "dune" "jbuilder"))) + (not (string-prefix? "base-" name)))) + depends)) + +(define (depends->inputs depends) + (filter-dependencies (map dependency->input depends))) (define (depends->native-inputs depends) (filter (lambda (name) (not (equal? "" name))) @@ -272,7 +275,8 @@ or #f on failure." (source-url (or (metadata-ref url-dict "src") (metadata-ref url-dict "archive"))) (requirements (metadata-ref opam-content "depends")) - (dependencies (dependency-list->names requirements)) + (names (dependency-list->names requirements)) + (dependencies (filter-dependencies names)) (native-dependencies (depends->native-inputs requirements)) (inputs (dependency-list->inputs (depends->inputs requirements))) (native-inputs (dependency-list->inputs @@ -282,10 +286,7 @@ or #f on failure." (lambda (name) (not (member name '("dune" "jbuilder")))) native-dependencies)))) - ;; If one of these are required at build time, it means we - ;; can use the much nicer dune-build-system. - (let ((use-dune? (or (member "dune" (append dependencies native-dependencies)) - (member "jbuilder" (append dependencies native-dependencies))))) + (let ((use-dune? (member "dune" names))) (call-with-temporary-output-file (lambda (temp port) (and (url-fetch source-url temp) -- cgit v1.2.3 From 15ee1b8317adeb74938f3bb7f0c7cb635a818292 Mon Sep 17 00:00:00 2001 From: Julien Lepiller Date: Tue, 8 Dec 2020 13:58:49 +0100 Subject: guix: opam: Pass default repository to recursive importer. * guix/import/opam.scm (opam->guix-package): Rename #:repository key to #:repo. (opam-recursive-import): Pass #:repo keyword. * tests/opam.scm (opam->guix-package): Rename #:repository to #:repo. --- guix/import/opam.scm | 9 +++++---- tests/opam.scm | 2 +- 2 files changed, 6 insertions(+), 5 deletions(-) diff --git a/guix/import/opam.scm b/guix/import/opam.scm index 4f366a9384..6e98822104 100644 --- a/guix/import/opam.scm +++ b/guix/import/opam.scm @@ -264,11 +264,11 @@ path to the repository." (substring version 1) version))))) -(define* (opam->guix-package name #:key (repository (get-opam-repository)) version) +(define* (opam->guix-package name #:key (repo (get-opam-repository)) version) "Import OPAM package NAME from REPOSITORY (a directory name) or, if REPOSITORY is #f, from the official OPAM repository. Return a 'package' sexp or #f on failure." - (and-let* ((opam-file (opam-fetch name repository)) + (and-let* ((opam-file (opam-fetch name repo)) (version (assoc-ref opam-file "version")) (opam-content (assoc-ref opam-file "metadata")) (url-dict (metadata-ref opam-content "url")) @@ -323,10 +323,11 @@ or #f on failure." (not (member name '("dune" "jbuilder")))) dependencies)))))))) -(define (opam-recursive-import package-name) +(define* (opam-recursive-import package-name #:repo (get-opam-repository)) (recursive-import package-name #:repo->guix-package opam->guix-package - #:guix-name ocaml-name->guix-name)) + #:guix-name ocaml-name->guix-name + #:repo repo)) (define (guix-name->opam-name name) (if (string-prefix? "ocaml-" name) diff --git a/tests/opam.scm b/tests/opam.scm index ec2a668307..8d43e2ce70 100644 --- a/tests/opam.scm +++ b/tests/opam.scm @@ -85,7 +85,7 @@ url { (with-output-to-file (string-append my-package "/opam") (lambda _ (format #t "~a" test-opam-file)))) - (match (opam->guix-package "foo" #:repository test-repo) + (match (opam->guix-package "foo" #:repo test-repo) (('package ('name "ocaml-foo") ('version "1.0.0") -- cgit v1.2.3 From a8dccd4bdc1e58219d4ba08fe1649bf0b8325f44 Mon Sep 17 00:00:00 2001 From: Julien Lepiller Date: Tue, 8 Dec 2020 14:58:39 +0100 Subject: guix: opam: Add --repo argument to importer. * guix/scripts/import/opam.scm (guix-import-opam): Pass --repo argument to recursive and non-recursive importers. * guix/import/opam.scm (get-opam-repository): Select proper repository location depending on a new repo argument. (opam->guix-package): Use get-opam-repository in the procedure body. --- guix/import/opam.scm | 21 ++++++++++++++------- guix/scripts/import/opam.scm | 10 ++++++++-- 2 files changed, 22 insertions(+), 9 deletions(-) diff --git a/guix/import/opam.scm b/guix/import/opam.scm index 6e98822104..6f5c95df3b 100644 --- a/guix/import/opam.scm +++ b/guix/import/opam.scm @@ -120,12 +120,19 @@ (define-peg-pattern condition-string all (and QUOTE (* STRCHR) QUOTE)) (define-peg-pattern condition-var all (+ (or (range #\a #\z) "-" ":"))) -(define (get-opam-repository) +(define* (get-opam-repository #:optional repo) "Update or fetch the latest version of the opam repository and return the path to the repository." - (receive (location commit _) - (update-cached-checkout "https://github.com/ocaml/opam-repository") - location)) + (let ((url (cond + ((or (not repo) (equal? repo 'opam)) + "https://github.com/ocaml/opam-repository") + (else (throw 'unknown-repository repo))))) + (receive (location commit _) + (update-cached-checkout url) + (cond + ((or (not repo) (equal? repo 'opam)) + location) + (else location))))) (define (latest-version versions) "Find the most recent version from a list of versions." @@ -264,11 +271,11 @@ path to the repository." (substring version 1) version))))) -(define* (opam->guix-package name #:key (repo (get-opam-repository)) version) +(define* (opam->guix-package name #:key (repo 'opam) version) "Import OPAM package NAME from REPOSITORY (a directory name) or, if REPOSITORY is #f, from the official OPAM repository. Return a 'package' sexp or #f on failure." - (and-let* ((opam-file (opam-fetch name repo)) + (and-let* ((opam-file (opam-fetch name (get-opam-repository repo))) (version (assoc-ref opam-file "version")) (opam-content (assoc-ref opam-file "metadata")) (url-dict (metadata-ref opam-content "url")) @@ -323,7 +330,7 @@ or #f on failure." (not (member name '("dune" "jbuilder")))) dependencies)))))))) -(define* (opam-recursive-import package-name #:repo (get-opam-repository)) +(define* (opam-recursive-import package-name #:key repo) (recursive-import package-name #:repo->guix-package opam->guix-package #:guix-name ocaml-name->guix-name diff --git a/guix/scripts/import/opam.scm b/guix/scripts/import/opam.scm index 20da1437fe..da9392821c 100644 --- a/guix/scripts/import/opam.scm +++ b/guix/scripts/import/opam.scm @@ -44,6 +44,8 @@ Import and convert the opam package for PACKAGE-NAME.\n")) -h, --help display this help and exit")) (display (G_ " -r, --recursive import packages recursively")) + (display (G_ " + --repo import packages from this opam repository")) (display (G_ " -V, --version display version information and exit")) (newline) @@ -58,6 +60,9 @@ Import and convert the opam package for PACKAGE-NAME.\n")) (option '(#\V "version") #f #f (lambda args (show-version-and-exit "guix import opam"))) + (option '(#f "repo") #t #f + (lambda (opt name arg result) + (alist-cons 'repo arg result))) (option '(#\r "recursive") #f #f (lambda (opt name arg result) (alist-cons 'recursive #t result))) @@ -79,6 +84,7 @@ Import and convert the opam package for PACKAGE-NAME.\n")) %default-options)) (let* ((opts (parse-options)) + (repo (and=> (assoc-ref opts 'repo) string->symbol)) (args (filter-map (match-lambda (('argument . value) value) @@ -93,9 +99,9 @@ Import and convert the opam package for PACKAGE-NAME.\n")) `(define-public ,(string->symbol name) ,pkg)) (_ #f)) - (opam-recursive-import package-name)) + (opam-recursive-import package-name #:repo repo)) ;; Single import - (let ((sexp (opam->guix-package package-name))) + (let ((sexp (opam->guix-package package-name #:repo repo))) (unless sexp (leave (G_ "failed to download meta-data for package '~a'~%") package-name)) -- cgit v1.2.3 From ccc4d287b7bd2a3ddea7b7f2c1ea2a722e68115c Mon Sep 17 00:00:00 2001 From: Julien Lepiller Date: Tue, 8 Dec 2020 15:03:47 +0100 Subject: guix: opam: Add coq support in the importer. * guix/import/opam.scm (get-opam-repository): Add support for coq repositories. (ocaml-name->guix-name): Properly name coq package. * doc/guix.texi (Invoking guix import): Document it. --- doc/guix.texi | 19 +++++++++++++++++++ guix/import/opam.scm | 8 ++++++++ 2 files changed, 27 insertions(+) diff --git a/doc/guix.texi b/doc/guix.texi index 0e647a284c..7960143723 100644 --- a/doc/guix.texi +++ b/doc/guix.texi @@ -11291,6 +11291,25 @@ in Guix. @cindex OCaml Import metadata from the @uref{https://opam.ocaml.org/, OPAM} package repository used by the OCaml community. + +Additional options include: + +@table @code +@item --recursive +@itemx -r +Traverse the dependency graph of the given upstream package recursively +and generate package expressions for all those packages that are not yet +in Guix. +@item --repo +Select the given repository (a repository name). Possible values include: +@itemize +@item @code{opam}, the default opam repository, +@item @code{coq} or @code{coq-released}, the stable repository for coq packages, +@item @code{coq-core-dev}, the repository that contains development versions of coq, +@item @code{coq-extra-dev}, the repository that contains development versions + of coq packages. +@end itemize +@end table @end table The structure of the @command{guix import} code is modular. It would be diff --git a/guix/import/opam.scm b/guix/import/opam.scm index 6f5c95df3b..54143f83ca 100644 --- a/guix/import/opam.scm +++ b/guix/import/opam.scm @@ -126,12 +126,19 @@ path to the repository." (let ((url (cond ((or (not repo) (equal? repo 'opam)) "https://github.com/ocaml/opam-repository") + ((string-prefix? "coq-" (symbol->string repo)) + "https://github.com/coq/opam-coq-archive") + ((equal? repo 'coq) "https://github.com/coq/opam-coq-archive") (else (throw 'unknown-repository repo))))) (receive (location commit _) (update-cached-checkout url) (cond ((or (not repo) (equal? repo 'opam)) location) + ((equal? repo 'coq) + (string-append location "/released")) + ((string-prefix? "coq-" (symbol->string repo)) + (string-append location "/" (substring (symbol->string repo) 4))) (else location))))) (define (latest-version versions) @@ -168,6 +175,7 @@ path to the repository." (substitute-char (cond ((equal? name "ocamlfind") "ocaml-findlib") + ((equal? name "coq") name) ((string-prefix? "ocaml" name) name) ((string-prefix? "conf-" name) (substring name 5)) (else (string-append "ocaml-" name))) -- cgit v1.2.3 From adbb62f16e09f219c465dcaffc321eb311eaed86 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Tue, 8 Dec 2020 18:14:31 +0200 Subject: gnu: fcitx5-material-color-theme: Add source file-name. * gnu/packages/fcitx5.scm (fcitx5-material-color-theme)[source]: Add file-name field. --- gnu/packages/fcitx5.scm | 1 + 1 file changed, 1 insertion(+) diff --git a/gnu/packages/fcitx5.scm b/gnu/packages/fcitx5.scm index b14385d9b2..89de7b4dcf 100644 --- a/gnu/packages/fcitx5.scm +++ b/gnu/packages/fcitx5.scm @@ -423,6 +423,7 @@ to manage different input methods in Fcitx 5.") (uri (git-reference (url "https://github.com/hosxy/Fcitx5-Material-Color") (commit version))) + (file-name (git-file-name name version)) (sha256 (base32 "1mgc722521jmfx0xc3ibmiycd3q2w7xg2956xcpc07kz90gcdjaa")))) (build-system copy-build-system) -- cgit v1.2.3 From e1d3b07ffc137bdbc7a244064180ec5aa61a2040 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Tue, 8 Dec 2020 13:21:23 -0500 Subject: gnu: isync: Use OpenSSL 1.1. * gnu/packages/mail.scm (isync)[inputs]: Replace openssl-1.0 with openssl. --- gnu/packages/mail.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/mail.scm b/gnu/packages/mail.scm index a2d6b71377..6e3ee4c46a 100644 --- a/gnu/packages/mail.scm +++ b/gnu/packages/mail.scm @@ -1993,7 +1993,7 @@ hashing scheme (such as scrypt) plug-in for @code{Dovecot}.") (inputs `(("bdb" ,bdb) ("cyrus-sasl" ,cyrus-sasl) - ("openssl" ,openssl-1.0) + ("openssl" ,openssl) ("zlib" ,zlib))) (home-page "https://isync.sourceforge.io/") (synopsis "Mailbox synchronization program") -- cgit v1.2.3 From c9c3569ad98f5cf7054ae529056000093f85c2ae Mon Sep 17 00:00:00 2001 From: Christopher Baines Date: Tue, 8 Dec 2020 20:05:48 +0000 Subject: gnu: libmypaint: Update to 1.6.1. Needed by mypaint@2.0.1. * gnu/packages/gimp.scm (libmypaint): Update to 1.6.1. --- gnu/packages/gimp.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/gimp.scm b/gnu/packages/gimp.scm index a47de30ae4..da19939679 100644 --- a/gnu/packages/gimp.scm +++ b/gnu/packages/gimp.scm @@ -409,7 +409,7 @@ inverse fourier transform.") (define-public libmypaint (package (name "libmypaint") - (version "1.5.1") + (version "1.6.1") (source (origin (method url-fetch) (uri (string-append "https://github.com/mypaint/libmypaint/" @@ -417,7 +417,7 @@ inverse fourier transform.") version ".tar.xz")) (sha256 (base32 - "0aqcv4fyscpfhknxgfpq0v84aj2nzigqvpi4zgv2zkl41h51by5f")))) + "0priwpmc7dizccqvn21ig6d649bprl3xl1hmjj7nddznjgr585vl")))) (build-system gnu-build-system) (native-inputs `(("intltool" ,intltool) -- cgit v1.2.3 From 8a55a3994c805aa2d4f5d04433908b206c294d47 Mon Sep 17 00:00:00 2001 From: L p R n d n Date: Fri, 1 May 2020 12:21:55 +0200 Subject: gnu: Add mypaint. * gnu/packages/image.scm (mypaint): New variable. Signed-off-by: Christopher Baines --- gnu/packages/image.scm | 63 ++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 63 insertions(+) diff --git a/gnu/packages/image.scm b/gnu/packages/image.scm index 750be166c9..979b069415 100644 --- a/gnu/packages/image.scm +++ b/gnu/packages/image.scm @@ -59,8 +59,10 @@ #:use-module (gnu packages freedesktop) #:use-module (gnu packages gettext) #:use-module (gnu packages ghostscript) + #:use-module (gnu packages gimp) #:use-module (gnu packages gl) #:use-module (gnu packages glib) + #:use-module (gnu packages gnome) #:use-module (gnu packages graphics) #:use-module (gnu packages gtk) #:use-module (gnu packages lua) @@ -76,6 +78,7 @@ #:use-module (gnu packages python-xyz) #:use-module (gnu packages qt) #:use-module (gnu packages sphinx) + #:use-module (gnu packages swig) #:use-module (gnu packages textutils) #:use-module (gnu packages video) #:use-module (gnu packages web) @@ -2163,6 +2166,66 @@ painting and palette manipulation tools. It also handles JPEG, JPEG2000, GIF, TIFF, WEBP, BMP, PNG, XPM formats.") (license license:gpl3+))) +(define-public mypaint + (package + (name "mypaint") + (version "2.0.1") + (source (origin + (method url-fetch) + (uri (string-append "https://github.com/mypaint/mypaint/" + "releases/download/v" version "/mypaint-" + version ".tar.xz")) + (sha256 + (base32 + "05mvay73vb9d2sh1ckv4vny45n059dmsps1jcppjizfmrpbkgr7k")))) + (build-system python-build-system) + (arguments + `(#:imported-modules ((guix build glib-or-gtk-build-system) + ,@%python-build-system-modules) + #:modules ((guix build python-build-system) + ((guix build glib-or-gtk-build-system) #:prefix glib-or-gtk:) + (guix build utils)) + #:phases + (modify-phases %standard-phases + (add-after 'install 'glib-or-gtk-wrap + (assoc-ref glib-or-gtk:%standard-phases 'glib-or-gtk-wrap)) + (add-after 'install 'wrap-program + (lambda* (#:key outputs inputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (gdk-pixbuf (assoc-ref inputs "gdk-pixbuf")) + (gtk+ (assoc-ref inputs "gtk+"))) + (wrap-program (string-append out "/bin/mypaint") + `("GI_TYPELIB_PATH" ":" prefix + (,(getenv "GI_TYPELIB_PATH")))) + #t))) + (add-before 'check 'pre-check + (lambda _ + ;; Tests need writing access + (setenv "HOME" "/tmp") + #t))))) + (native-inputs + `(("pkg-config" ,pkg-config) + ("gobject-introspection" ,gobject-introspection) + ("swig" ,swig) + ("gettext" ,gettext-minimal))) + (inputs + `(("gtk+" ,gtk+) + ("gdk-pixbuf" ,gdk-pixbuf+svg) + ("hicolor-icon-theme" ,hicolor-icon-theme) + ("libmypaint" ,libmypaint) + ("mypaint-brushes" ,mypaint-brushes) + ("json-c" ,json-c) + ("lcms" ,lcms) + ("python-numpy" ,python-numpy) + ("python-pycairo" ,python-pycairo) + ("python-pygobject" ,python-pygobject))) + (home-page "http://mypaint.org/") + (synopsis "Fast and simple painting app for artists") + (description + "MyPaint is a simple drawing and painting program that works well with +Wacom-style graphics tablets.") + (license license:gpl2+))) + (define-public phockup (package (name "phockup") -- cgit v1.2.3 From 2d1a621b8dc39f7903b47b84c1f8de253ae4fc43 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Tue, 8 Dec 2020 22:09:14 +0200 Subject: gnu: mruby: Update to 2.1.2. * gnu/packages/ruby.scm (mruby): Update to 2.1.2. --- gnu/packages/ruby.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/ruby.scm b/gnu/packages/ruby.scm index f48685be22..4c16f84099 100644 --- a/gnu/packages/ruby.scm +++ b/gnu/packages/ruby.scm @@ -228,7 +228,7 @@ a focus on simplicity and productivity.") (define-public mruby (package (name "mruby") - (version "2.0.0") + (version "2.1.2") (source (origin (method git-fetch) @@ -238,7 +238,7 @@ a focus on simplicity and productivity.") (file-name (git-file-name name version)) (sha256 (base32 - "1r6w1asjshff43ymdwa6xmrkggza99mi2kw88k7ic6ag2j81hcj5")))) + "0fhfv8pi7i8jn2vgk2n2rjnbnfa12nhj514v8i4k353n7q4pmkh3")))) (build-system gnu-build-system) (arguments `(#:test-target "test" -- cgit v1.2.3 From 20e5658c0471c76cc297cfd30ad49f0585310e27 Mon Sep 17 00:00:00 2001 From: Vincent Legoll Date: Mon, 16 Mar 2020 16:32:25 +0100 Subject: gnu: ocaml-menhir: Update to 20200211. * gnu/packages/ocaml.scm (ocaml-menhir): Update to 20200211. [build-system]: Switch from gnu to dune. [arguments]: Remove phases and make-flags. [native-inputs]: Remove field. Signed-off-by: Christopher Baines --- gnu/packages/ocaml.scm | 16 ++++------------ 1 file changed, 4 insertions(+), 12 deletions(-) diff --git a/gnu/packages/ocaml.scm b/gnu/packages/ocaml.scm index 369e819573..2bfda7307e 100644 --- a/gnu/packages/ocaml.scm +++ b/gnu/packages/ocaml.scm @@ -739,8 +739,7 @@ Emacs.") (define-public ocaml-menhir (package (name "ocaml-menhir") - ;; More recent versions can be built after we have dune >= 2.0 - (version "20190626") + (version "20200211") (source (origin (method git-fetch) @@ -749,19 +748,12 @@ Emacs.") (commit version))) (file-name (git-file-name name version)) (sha256 - (base32 "0v8av4pw6rykzb7wx54xhbsx0jhh8xyb4x0k4yrxi0w5ylkck6mb")))) - (build-system ocaml-build-system) + (base32 "019izf51kdc7pzkw68zg8a2alc8lxw1gwdp7in970mr90n16b5zj")))) + (build-system dune-build-system) (inputs `(("ocaml" ,ocaml))) - (native-inputs - `(("ocamlbuild" ,ocamlbuild))) (arguments - `(#:make-flags `("USE_OCAMLFIND=true" - ,(string-append "PREFIX=" (assoc-ref %outputs "out"))) - #:tests? #f ; No check target - #:phases - (modify-phases %standard-phases - (delete 'configure)))) + `(#:tests? #f)) ; No check target (home-page "http://gallium.inria.fr/~fpottier/menhir/") (synopsis "Parser generator") (description "Menhir is a parser generator. It turns high-level grammar -- cgit v1.2.3 From e9edaf3639ecf9d4fdaf7901d60a87c582be1c44 Mon Sep 17 00:00:00 2001 From: Ludovic Courtès Date: Mon, 7 Dec 2020 22:32:04 +0100 Subject: database: Remove unnecessary module imports. * guix/store/database.scm: Remove unnecessary imports added in 4b9eecd322e566783369795ebea63a479b51f486. --- guix/store/database.scm | 2 -- 1 file changed, 2 deletions(-) diff --git a/guix/store/database.scm b/guix/store/database.scm index 2ea63b17aa..b36b127630 100644 --- a/guix/store/database.scm +++ b/guix/store/database.scm @@ -21,7 +21,6 @@ (define-module (guix store database) #:use-module (sqlite3) #:use-module (guix config) - #:use-module (guix gexp) #:use-module (guix serialization) #:use-module (guix store deduplication) #:use-module (guix base16) @@ -29,7 +28,6 @@ #:use-module (guix build syscalls) #:use-module ((guix build utils) #:select (mkdir-p executable-file?)) - #:use-module (guix utils) #:use-module (guix build store-copy) #:use-module (srfi srfi-1) #:use-module (srfi srfi-11) -- cgit v1.2.3 From 4a9873529758f07869aede8057099a0f23144f8b Mon Sep 17 00:00:00 2001 From: Ludovic Courtès Date: Tue, 8 Dec 2020 22:28:00 +0100 Subject: gnu: autotools: Add version 2.70. * gnu/packages/autotools.scm (autoconf): Rename to... (autoconf-2.69): ... this. (autoconf): Define as an alias for AUTOCONF-2.69. (autoconf-2.70): New variable. --- gnu/packages/autotools.scm | 35 ++++++++++++++++++++++++++++++++++- 1 file changed, 34 insertions(+), 1 deletion(-) diff --git a/gnu/packages/autotools.scm b/gnu/packages/autotools.scm index 775576ff5d..203f1bfb52 100644 --- a/gnu/packages/autotools.scm +++ b/gnu/packages/autotools.scm @@ -43,7 +43,7 @@ #:use-module (ice-9 match) #:export (autoconf-wrapper)) -(define-public autoconf +(define-public autoconf-2.69 (package (name "autoconf") (version "2.69") @@ -103,6 +103,39 @@ scripts are self-contained and portable, freeing the user from needing to know anything about Autoconf or M4.") (license gpl3+))) ; some files are under GPLv2+ +(define-public autoconf-2.70 + (package + (inherit autoconf-2.69) + (version "2.70") + (source + (origin + (method url-fetch) + (uri (string-append "mirror://gnu/autoconf/autoconf-" + version ".tar.xz")) + (sha256 + (base32 + "1ipckz0wr2mvhj9n3ys54fmf2aksin6bhqvzl304bn6rc1w257ps")))) + (arguments + (substitute-keyword-arguments (package-arguments autoconf-2.69) + ((#:tests? _ #f) + ;; FIXME: To run the test suite, fix all the instances where scripts + ;; generates "#! /bin/sh" shebangs. + #f) + ((#:phases phases '%standard-phases) + `(modify-phases ,phases + (add-before 'check 'prepare-tests + (lambda _ + (for-each patch-shebang + (append (find-files "tests" + (lambda (file stat) + (executable-file? file))) + (find-files "bin" + (lambda (file stat) + (executable-file? file))))) + #t)))))))) + +(define-public autoconf autoconf-2.69) + (define-public autoconf-2.68 (package (inherit autoconf) (version "2.68") -- cgit v1.2.3 From 2e308238ad09e9527f9b8c3ec4a90b6b05a93367 Mon Sep 17 00:00:00 2001 From: Ludovic Courtès Date: Tue, 1 Dec 2020 15:00:14 +0100 Subject: daemon: 'Agent' constructor takes a list of environment variables. * nix/libutil/util.hh (struct Agent)[Agent]: Add 'env' parameter. * nix/libutil/util.cc (Agent::Agent): Honor it. --- nix/libutil/util.cc | 6 +++++- nix/libutil/util.hh | 7 +++++-- 2 files changed, 10 insertions(+), 3 deletions(-) diff --git a/nix/libutil/util.cc b/nix/libutil/util.cc index 59a2981359..69f1c634a9 100644 --- a/nix/libutil/util.cc +++ b/nix/libutil/util.cc @@ -1173,7 +1173,7 @@ void commonChildInit(Pipe & logPipe) ////////////////////////////////////////////////////////////////////// -Agent::Agent(const string &command, const Strings &args) +Agent::Agent(const string &command, const Strings &args, const std::map &env) { debug(format("starting agent '%1%'") % command); @@ -1191,6 +1191,10 @@ Agent::Agent(const string &command, const Strings &args) commonChildInit(fromAgent); + for (auto pair: env) { + setenv(pair.first.c_str(), pair.second.c_str(), 1); + } + if (chdir("/") == -1) throw SysError("changing into `/"); /* Dup the communication pipes. */ diff --git a/nix/libutil/util.hh b/nix/libutil/util.hh index 13cff44316..880b0e93b2 100644 --- a/nix/libutil/util.hh +++ b/nix/libutil/util.hh @@ -7,6 +7,7 @@ #include #include #include +#include #include #include @@ -281,8 +282,10 @@ struct Agent /* The process ID of the agent. */ Pid pid; - /* The command and arguments passed to the agent. */ - Agent(const string &command, const Strings &args); + /* The command and arguments passed to the agent along with a list of + environment variable name/value pairs. */ + Agent(const string &command, const Strings &args, + const std::map &env = std::map()); ~Agent(); }; -- cgit v1.2.3 From 79c6614f58a57b985daf8940766319e440311db0 Mon Sep 17 00:00:00 2001 From: Ludovic Courtès Date: Tue, 1 Dec 2020 15:01:40 +0100 Subject: daemon: Use 'Agent' to spawn 'guix substitute --query'. * nix/libstore/local-store.hh (RunningSubstituter): Remove. (LocalStore)[runningSubstituter]: Change to unique_ptr. [setSubstituterEnv, didSetSubstituterEnv]: Remove. [getLineFromSubstituter, getIntLineFromSubstituter]: Take an 'Agent'. * nix/libstore/local-store.cc (LocalStore::~LocalStore): Remove reference to 'runningSubstituter'. (LocalStore::setSubstituterEnv, LocalStore::startSubstituter): Remove. (LocalStore::getLineFromSubstituter): Adjust to 'run' being an 'Agent'. (LocalStore::querySubstitutablePaths): Spawn substituter agent if needed. Adjust to 'Agent' interface. (LocalStore::querySubstitutablePathInfos): Likewise. * nix/libstore/build.cc (SubstitutionGoal::tryToRun): Remove call to 'setSubstituterEnv' and add 'setenv' call for "_NIX_OPTIONS" instead. (SubstitutionGoal::finished): Remove 'readLine' call for 'dummy'. * guix/scripts/substitute.scm (%allow-unauthenticated-substitutes?): Remove second argument to 'make-parameter'. (process-query): Call 'warn-about-missing-authentication' when (%allow-unauthenticated-substitutes?) is #t. (guix-substitute): Wrap body in 'parameterize'. Set 'guix-warning-port' too. No longer exit when 'substitute-urls' returns the empty list. No longer print newline initially. * tests/substitute.scm (test-quit): Parameterize 'current-error-port' to account for the port changes in 'guix-substitute'. --- guix/scripts/substitute.scm | 132 ++++++++++++++++++------------------ nix/libstore/build.cc | 6 +- nix/libstore/local-store.cc | 159 +++++++++++--------------------------------- nix/libstore/local-store.hh | 22 +----- tests/substitute.scm | 3 +- 5 files changed, 110 insertions(+), 212 deletions(-) diff --git a/guix/scripts/substitute.scm b/guix/scripts/substitute.scm index feae2df9cb..5e392eaa8b 100755 --- a/guix/scripts/substitute.scm +++ b/guix/scripts/substitute.scm @@ -124,11 +124,7 @@ disabled!~%")) ;; purposes, and should be avoided otherwise. (make-parameter (and=> (getenv "GUIX_ALLOW_UNAUTHENTICATED_SUBSTITUTES") - (cut string-ci=? <> "yes")) - (lambda (value) - (when value - (warn-about-missing-authentication)) - value))) + (cut string-ci=? <> "yes")))) (define %narinfo-ttl ;; Number of seconds during which cached narinfo lookups are considered @@ -893,6 +889,9 @@ authorized substitutes." (define (valid? obj) (valid-narinfo? obj acl)) + (when (%allow-unauthenticated-substitutes?) + (warn-about-missing-authentication)) + (match (string-tokenize command) (("have" paths ..1) ;; Return the subset of PATHS available in CACHE-URLS. @@ -1139,68 +1138,67 @@ default value." ((= string->number number) (> number 0)) (_ #f))) - (mkdir-p %narinfo-cache-directory) - (maybe-remove-expired-cache-entries %narinfo-cache-directory - cached-narinfo-files - #:entry-expiration - cached-narinfo-expiration-time - #:cleanup-period - %narinfo-expired-cache-entry-removal-delay) - (check-acl-initialized) - - ;; Starting from commit 22144afa in Nix, we are allowed to bail out directly - ;; when we know we cannot substitute, but we must emit a newline on stdout - ;; when everything is alright. - (when (null? (substitute-urls)) - (exit 0)) - - ;; Say hello (see above.) - (newline) - (force-output (current-output-port)) - - ;; Sanity-check SUBSTITUTE-URLS so we can provide a meaningful error message. - (for-each validate-uri (substitute-urls)) - - ;; Attempt to install the client's locale so that messages are suitably - ;; translated. LC_CTYPE must be a UTF-8 locale; it's the case by default so - ;; don't change it. - (match (or (find-daemon-option "untrusted-locale") - (find-daemon-option "locale")) - (#f #f) - (locale (false-if-exception (setlocale LC_MESSAGES locale)))) - - (catch 'system-error - (lambda () - (set-thread-name "guix substitute")) - (const #t)) ;GNU/Hurd lacks 'prctl' - - (with-networking - (with-error-handling ; for signature errors - (match args - (("--query") - (let ((acl (current-acl))) - (let loop ((command (read-line))) - (or (eof-object? command) - (begin - (process-query command - #:cache-urls (substitute-urls) - #:acl acl) - (loop (read-line))))))) - (("--substitute" store-path destination) - ;; Download STORE-PATH and add store it as a Nar in file DESTINATION. - ;; Specify the number of columns of the terminal so the progress - ;; report displays nicely. - (parameterize ((current-terminal-columns (client-terminal-columns))) - (process-substitution store-path destination - #:cache-urls (substitute-urls) - #:acl (current-acl) - #:print-build-trace? print-build-trace?))) - ((or ("-V") ("--version")) - (show-version-and-exit "guix substitute")) - (("--help") - (show-help)) - (opts - (leave (G_ "~a: unrecognized options~%") opts)))))) + ;; The daemon's agent code opens file descriptor 4 for us and this is where + ;; stderr should go. + (parameterize ((current-error-port (match args + (("--query") (fdopen 4 "wl")) + (_ (current-error-port))))) + ;; Redirect diagnostics to file descriptor 4 as well. + (guix-warning-port (current-error-port)) + + (mkdir-p %narinfo-cache-directory) + (maybe-remove-expired-cache-entries %narinfo-cache-directory + cached-narinfo-files + #:entry-expiration + cached-narinfo-expiration-time + #:cleanup-period + %narinfo-expired-cache-entry-removal-delay) + (check-acl-initialized) + + ;; Sanity-check SUBSTITUTE-URLS so we can provide a meaningful error + ;; message. + (for-each validate-uri (substitute-urls)) + + ;; Attempt to install the client's locale so that messages are suitably + ;; translated. LC_CTYPE must be a UTF-8 locale; it's the case by default + ;; so don't change it. + (match (or (find-daemon-option "untrusted-locale") + (find-daemon-option "locale")) + (#f #f) + (locale (false-if-exception (setlocale LC_MESSAGES locale)))) + + (catch 'system-error + (lambda () + (set-thread-name "guix substitute")) + (const #t)) ;GNU/Hurd lacks 'prctl' + + (with-networking + (with-error-handling ; for signature errors + (match args + (("--query") + (let ((acl (current-acl))) + (let loop ((command (read-line))) + (or (eof-object? command) + (begin + (process-query command + #:cache-urls (substitute-urls) + #:acl acl) + (loop (read-line))))))) + (("--substitute" store-path destination) + ;; Download STORE-PATH and store it as a Nar in file DESTINATION. + ;; Specify the number of columns of the terminal so the progress + ;; report displays nicely. + (parameterize ((current-terminal-columns (client-terminal-columns))) + (process-substitution store-path destination + #:cache-urls (substitute-urls) + #:acl (current-acl) + #:print-build-trace? print-build-trace?))) + ((or ("-V") ("--version")) + (show-version-and-exit "guix substitute")) + (("--help") + (show-help)) + (opts + (leave (G_ "~a: unrecognized options~%") opts))))))) ;;; Local Variables: ;;; eval: (put 'with-timeout 'scheme-indent-function 1) diff --git a/nix/libstore/build.cc b/nix/libstore/build.cc index 8413819114..7e9ab3f39c 100644 --- a/nix/libstore/build.cc +++ b/nix/libstore/build.cc @@ -2986,8 +2986,6 @@ void SubstitutionGoal::tryToRun() if (pathExists(destPath)) deletePath(destPath); - worker.store.setSubstituterEnv(); - /* Fill in the arguments. */ Strings args; args.push_back("guix"); @@ -2999,6 +2997,9 @@ void SubstitutionGoal::tryToRun() /* Fork the substitute program. */ pid = startProcess([&]() { + /* Communicate substitute-urls & co. to 'guix substitute'. */ + setenv("_NIX_OPTIONS", settings.pack().c_str(), 1); + commonChildInit(logPipe); if (dup2(outPipe.writeSide, STDOUT_FILENO) == -1) @@ -3041,7 +3042,6 @@ void SubstitutionGoal::finished() logPipe.readSide.close(); /* Get the hash info from stdout. */ - string dummy = readLine(outPipe.readSide); string expectedHashStr = statusOk(status) ? readLine(outPipe.readSide) : ""; outPipe.readSide.close(); diff --git a/nix/libstore/local-store.cc b/nix/libstore/local-store.cc index 8c479002ec..4219573a56 100644 --- a/nix/libstore/local-store.cc +++ b/nix/libstore/local-store.cc @@ -57,7 +57,6 @@ void checkStoreNotSymlink() LocalStore::LocalStore(bool reserveSpace) - : didSetSubstituterEnv(false) { schemaPath = settings.nixDBPath + "/schema"; @@ -182,21 +181,6 @@ LocalStore::LocalStore(bool reserveSpace) LocalStore::~LocalStore() { - try { - if (runningSubstituter) { - RunningSubstituter &i = *runningSubstituter; - if (!i.disabled) { - i.to.close(); - i.from.close(); - i.error.close(); - if (i.pid != -1) - i.pid.wait(true); - } - } - } catch (...) { - ignoreException(); - } - try { if (fdTempRoots != -1) { fdTempRoots.close(); @@ -796,96 +780,31 @@ Path LocalStore::queryPathFromHashPart(const string & hashPart) }); } - -void LocalStore::setSubstituterEnv() -{ - if (didSetSubstituterEnv) return; - - /* Pass configuration options (including those overridden with - --option) to substituters. */ - setenv("_NIX_OPTIONS", settings.pack().c_str(), 1); - - didSetSubstituterEnv = true; -} - - -void LocalStore::startSubstituter(RunningSubstituter & run) -{ - if (run.disabled || run.pid != -1) return; - - debug(format("starting substituter program `%1% substitute'") - % settings.guixProgram); - - Pipe toPipe, fromPipe, errorPipe; - - toPipe.create(); - fromPipe.create(); - errorPipe.create(); - - setSubstituterEnv(); - - run.pid = startProcess([&]() { - if (dup2(toPipe.readSide, STDIN_FILENO) == -1) - throw SysError("dupping stdin"); - if (dup2(fromPipe.writeSide, STDOUT_FILENO) == -1) - throw SysError("dupping stdout"); - if (dup2(errorPipe.writeSide, STDERR_FILENO) == -1) - throw SysError("dupping stderr"); - execl(settings.guixProgram.c_str(), "guix", "substitute", "--query", NULL); - throw SysError(format("executing `%1%'") % settings.guixProgram); - }); - - run.to = toPipe.writeSide.borrow(); - run.from = run.fromBuf.fd = fromPipe.readSide.borrow(); - run.error = errorPipe.readSide.borrow(); - - toPipe.readSide.close(); - fromPipe.writeSide.close(); - errorPipe.writeSide.close(); - - /* The substituter may exit right away if it's disabled in any way - (e.g. copy-from-other-stores.pl will exit if no other stores - are configured). */ - try { - getLineFromSubstituter(run); - } catch (EndOfFile & e) { - run.to.close(); - run.from.close(); - run.error.close(); - run.disabled = true; - if (run.pid.wait(true) != 0) throw; - } -} - - /* Read a line from the substituter's stdout, while also processing its stderr. */ -string LocalStore::getLineFromSubstituter(RunningSubstituter & run) +string LocalStore::getLineFromSubstituter(Agent & run) { string res, err; - /* We might have stdout data left over from the last time. */ - if (run.fromBuf.hasData()) goto haveData; - while (1) { checkInterrupt(); fd_set fds; FD_ZERO(&fds); - FD_SET(run.from, &fds); - FD_SET(run.error, &fds); + FD_SET(run.fromAgent.readSide, &fds); + FD_SET(run.builderOut.readSide, &fds); /* Wait for data to appear on the substituter's stdout or stderr. */ - if (select(run.from > run.error ? run.from + 1 : run.error + 1, &fds, 0, 0, 0) == -1) { + if (select(std::max(run.fromAgent.readSide, run.builderOut.readSide) + 1, &fds, 0, 0, 0) == -1) { if (errno == EINTR) continue; throw SysError("waiting for input from the substituter"); } /* Completely drain stderr before dealing with stdout. */ - if (FD_ISSET(run.error, &fds)) { + if (FD_ISSET(run.builderOut.readSide, &fds)) { char buf[4096]; - ssize_t n = read(run.error, (unsigned char *) buf, sizeof(buf)); + ssize_t n = read(run.builderOut.readSide, (unsigned char *) buf, sizeof(buf)); if (n == -1) { if (errno == EINTR) continue; throw SysError("reading from substituter's stderr"); @@ -903,23 +822,20 @@ string LocalStore::getLineFromSubstituter(RunningSubstituter & run) } /* Read from stdout until we get a newline or the buffer is empty. */ - else if (run.fromBuf.hasData() || FD_ISSET(run.from, &fds)) { - haveData: - do { - unsigned char c; - run.fromBuf(&c, 1); - if (c == '\n') { - if (!err.empty()) printMsg(lvlError, "substitute: " + err); - return res; - } - res += c; - } while (run.fromBuf.hasData()); + else if (FD_ISSET(run.fromAgent.readSide, &fds)) { + unsigned char c; + readFull(run.fromAgent.readSide, (unsigned char *) &c, 1); + if (c == '\n') { + if (!err.empty()) printMsg(lvlError, "substitute: " + err); + return res; + } + res += c; } } } -template T LocalStore::getIntLineFromSubstituter(RunningSubstituter & run) +template T LocalStore::getIntLineFromSubstituter(Agent & run) { string s = getLineFromSubstituter(run); T res; @@ -935,27 +851,26 @@ PathSet LocalStore::querySubstitutablePaths(const PathSet & paths) if (!settings.useSubstitutes || paths.empty()) return res; if (!runningSubstituter) { - std::unique_ptrfresh(new RunningSubstituter); + const Strings args = { "substitute", "--query" }; + const std::map env = { { "_NIX_OPTIONS", settings.pack() } }; + std::unique_ptr fresh(new Agent(settings.guixProgram, args, env)); runningSubstituter.swap(fresh); } - RunningSubstituter & run = *runningSubstituter; - startSubstituter(run); - - if (!run.disabled) { - string s = "have "; - foreach (PathSet::const_iterator, j, paths) - if (res.find(*j) == res.end()) { s += *j; s += " "; } - writeLine(run.to, s); - while (true) { - /* FIXME: we only read stderr when an error occurs, so - substituters should only write (short) messages to - stderr when they fail. I.e. they shouldn't write debug - output. */ - Path path = getLineFromSubstituter(run); - if (path == "") break; - res.insert(path); - } + Agent & run = *runningSubstituter; + + string s = "have "; + foreach (PathSet::const_iterator, j, paths) + if (res.find(*j) == res.end()) { s += *j; s += " "; } + writeLine(run.toAgent.writeSide, s); + while (true) { + /* FIXME: we only read stderr when an error occurs, so + substituters should only write (short) messages to + stderr when they fail. I.e. they shouldn't write debug + output. */ + Path path = getLineFromSubstituter(run); + if (path == "") break; + res.insert(path); } return res; @@ -967,18 +882,18 @@ void LocalStore::querySubstitutablePathInfos(PathSet & paths, SubstitutablePathI if (!settings.useSubstitutes) return; if (!runningSubstituter) { - std::unique_ptrfresh(new RunningSubstituter); + const Strings args = { "substitute", "--query" }; + const std::map env = { { "_NIX_OPTIONS", settings.pack() } }; + std::unique_ptr fresh(new Agent(settings.guixProgram, args, env)); runningSubstituter.swap(fresh); } - RunningSubstituter & run = *runningSubstituter; - startSubstituter(run); - if (run.disabled) return; + Agent & run = *runningSubstituter; string s = "info "; foreach (PathSet::const_iterator, i, paths) if (infos.find(*i) == infos.end()) { s += *i; s += " "; } - writeLine(run.to, s); + writeLine(run.toAgent.writeSide, s); while (true) { Path path = getLineFromSubstituter(run); diff --git a/nix/libstore/local-store.hh b/nix/libstore/local-store.hh index 2e48cf03e6..57d15bac7e 100644 --- a/nix/libstore/local-store.hh +++ b/nix/libstore/local-store.hh @@ -38,21 +38,11 @@ struct OptimiseStats }; -struct RunningSubstituter -{ - Pid pid; - AutoCloseFD to, from, error; - FdSource fromBuf; - bool disabled; - RunningSubstituter() : disabled(false) { }; -}; - - class LocalStore : public StoreAPI { private: /* The currently running substituter or empty. */ - std::unique_ptr runningSubstituter; + std::unique_ptr runningSubstituter; Path linksDir; @@ -178,8 +168,6 @@ public: void markContentsGood(const Path & path); - void setSubstituterEnv(); - void createUser(const std::string & userName, uid_t userId); private: @@ -213,8 +201,6 @@ private: /* Cache for pathContentsGood(). */ std::map pathContentsGoodCache; - bool didSetSubstituterEnv; - /* The file to which we write our temporary roots. */ Path fnTempRoots; AutoCloseFD fdTempRoots; @@ -262,11 +248,9 @@ private: void removeUnusedLinks(const GCState & state); - void startSubstituter(RunningSubstituter & runningSubstituter); - - string getLineFromSubstituter(RunningSubstituter & run); + string getLineFromSubstituter(Agent & run); - template T getIntLineFromSubstituter(RunningSubstituter & run); + template T getIntLineFromSubstituter(Agent & run); Path createTempDirInStore(); diff --git a/tests/substitute.scm b/tests/substitute.scm index 6560612c40..bd5b6305b0 100644 --- a/tests/substitute.scm +++ b/tests/substitute.scm @@ -47,7 +47,8 @@ it writes to GUIX-WARNING-PORT a messages that matches ERROR-RX." (test-equal name '(1 #t) (let ((error-output (open-output-string))) - (parameterize ((guix-warning-port error-output)) + (parameterize ((current-error-port error-output) + (guix-warning-port error-output)) (catch 'quit (lambda () exp -- cgit v1.2.3 From a618a8c6203d4cf57f12873a86797b8685b11e14 Mon Sep 17 00:00:00 2001 From: Ludovic Courtès Date: Tue, 1 Dec 2020 15:55:57 +0100 Subject: daemon: Factorize substituter agent spawning. * nix/libstore/local-store.hh (class LocalStore)[substituter]: New method. [runningSubstituter]: Turn into a shared_ptr. * nix/libstore/local-store.cc (LocalStore::querySubstitutablePaths): Call 'substituter' instead of using inline code. (LocalStore::querySubstitutablePathInfos): Likewise. (LocalStore::substituter): New method. --- nix/libstore/local-store.cc | 25 +++++++++++-------------- nix/libstore/local-store.hh | 5 ++++- 2 files changed, 15 insertions(+), 15 deletions(-) diff --git a/nix/libstore/local-store.cc b/nix/libstore/local-store.cc index 4219573a56..c304e2ddd1 100644 --- a/nix/libstore/local-store.cc +++ b/nix/libstore/local-store.cc @@ -850,14 +850,7 @@ PathSet LocalStore::querySubstitutablePaths(const PathSet & paths) if (!settings.useSubstitutes || paths.empty()) return res; - if (!runningSubstituter) { - const Strings args = { "substitute", "--query" }; - const std::map env = { { "_NIX_OPTIONS", settings.pack() } }; - std::unique_ptr fresh(new Agent(settings.guixProgram, args, env)); - runningSubstituter.swap(fresh); - } - - Agent & run = *runningSubstituter; + Agent & run = *substituter(); string s = "have "; foreach (PathSet::const_iterator, j, paths) @@ -877,18 +870,22 @@ PathSet LocalStore::querySubstitutablePaths(const PathSet & paths) } -void LocalStore::querySubstitutablePathInfos(PathSet & paths, SubstitutablePathInfos & infos) +std::shared_ptr LocalStore::substituter() { - if (!settings.useSubstitutes) return; - if (!runningSubstituter) { const Strings args = { "substitute", "--query" }; const std::map env = { { "_NIX_OPTIONS", settings.pack() } }; - std::unique_ptr fresh(new Agent(settings.guixProgram, args, env)); - runningSubstituter.swap(fresh); + runningSubstituter = std::make_shared(settings.guixProgram, args, env); } - Agent & run = *runningSubstituter; + return runningSubstituter; +} + +void LocalStore::querySubstitutablePathInfos(PathSet & paths, SubstitutablePathInfos & infos) +{ + if (!settings.useSubstitutes) return; + + Agent & run = *substituter(); string s = "info "; foreach (PathSet::const_iterator, i, paths) diff --git a/nix/libstore/local-store.hh b/nix/libstore/local-store.hh index 57d15bac7e..9ba37219da 100644 --- a/nix/libstore/local-store.hh +++ b/nix/libstore/local-store.hh @@ -42,7 +42,10 @@ class LocalStore : public StoreAPI { private: /* The currently running substituter or empty. */ - std::unique_ptr runningSubstituter; + std::shared_ptr runningSubstituter; + + /* Ensure the substituter is running and return it. */ + std::shared_ptr substituter(); Path linksDir; -- cgit v1.2.3 From 711df9ef3c04a0e0d7e844bed4c6b260ea1f65c1 Mon Sep 17 00:00:00 2001 From: Ludovic Courtès Date: Wed, 2 Dec 2020 16:27:34 +0100 Subject: daemon: Run 'guix substitute --substitute' as an agent. This avoids spawning one substitute process per substitution. * nix/libstore/build.cc (class Worker)[substituter]: New field. [outPipe, logPipe, pid]: Remove. (class SubstitutionGoal)[expectedHashStr, status, substituter]: New fields. (SubstitutionGoal::timedOut): Adjust to check 'substituter'. (SubstitutionGoal::tryToRun): Remove references to 'outPipe' and 'logPipe'. Run "guix substitute --substitute" as an 'Agent'. Send the request with 'writeLine'. (SubstitutionGoal::finished): Likewise. (SubstitutionGoal::handleChildOutput): Change to fill in 'expectedHashStr' and 'status'. (SubstitutionGoal::handleEOF): Call 'wakeUp' unconditionally. (SubstitutionGoal::~SubstitutionGoal): Adjust to check 'substituter'. * guix/scripts/substitute.scm (process-substitution): Write "success\n" to stdout upon success. (%error-to-file-descriptor-4?): New variable. (guix-substitute): Set 'current-error-port' to file descriptor 4 unless (%error-to-file-descriptor-4?) is false. Remove "--substitute" arguments. Loop reading line from stdin. * tests/substitute.scm : Call '%error-to-file-descriptor-4?'. (request-substitution): New procedure. ("substitute, no signature") ("substitute, invalid hash") ("substitute, unauthorized key") ("substitute, authorized key") ("substitute, unauthorized narinfo comes first") ("substitute, unsigned narinfo comes first") ("substitute, first narinfo is unsigned and has wrong hash") ("substitute, first narinfo is unsigned and has wrong refs") ("substitute, two invalid narinfos") ("substitute, narinfo with several URLs"): Adjust to new "guix substitute --substitute" calling convention. --- guix/scripts/substitute.scm | 34 ++++++++---- nix/libstore/build.cc | 129 ++++++++++++++++++++++---------------------- tests/substitute.scm | 95 ++++++++++++++++++-------------- 3 files changed, 145 insertions(+), 113 deletions(-) diff --git a/guix/scripts/substitute.scm b/guix/scripts/substitute.scm index 5e392eaa8b..73abd3f029 100755 --- a/guix/scripts/substitute.scm +++ b/guix/scripts/substitute.scm @@ -88,6 +88,7 @@ write-narinfo %allow-unauthenticated-substitutes? + %error-to-file-descriptor-4? substitute-urls guix-substitute)) @@ -1016,7 +1017,10 @@ DESTINATION as a nar file. Verify the substitute against ACL." ;; Skip a line after what 'progress-reporter/file' printed, and another ;; one to visually separate substitutions. - (display "\n\n" (current-error-port))))) + (display "\n\n" (current-error-port)) + + ;; Tell the daemon that we're done. + (display "success\n" (current-output-port))))) ;;; @@ -1127,6 +1131,11 @@ default value." (unless (string->uri uri) (leave (G_ "~a: invalid URI~%") uri))) +(define %error-to-file-descriptor-4? + ;; Whether to direct 'current-error-port' to file descriptor 4 like + ;; 'guix-daemon' expects. + (make-parameter #t)) + (define-command (guix-substitute . args) (category internal) (synopsis "implement the build daemon's substituter protocol") @@ -1140,9 +1149,9 @@ default value." ;; The daemon's agent code opens file descriptor 4 for us and this is where ;; stderr should go. - (parameterize ((current-error-port (match args - (("--query") (fdopen 4 "wl")) - (_ (current-error-port))))) + (parameterize ((current-error-port (if (%error-to-file-descriptor-4?) + (fdopen 4 "wl") + (current-error-port)))) ;; Redirect diagnostics to file descriptor 4 as well. (guix-warning-port (current-error-port)) @@ -1184,15 +1193,22 @@ default value." #:cache-urls (substitute-urls) #:acl acl) (loop (read-line))))))) - (("--substitute" store-path destination) + (("--substitute") ;; Download STORE-PATH and store it as a Nar in file DESTINATION. ;; Specify the number of columns of the terminal so the progress ;; report displays nicely. (parameterize ((current-terminal-columns (client-terminal-columns))) - (process-substitution store-path destination - #:cache-urls (substitute-urls) - #:acl (current-acl) - #:print-build-trace? print-build-trace?))) + (let loop () + (match (read-line) + ((? eof-object?) + #t) + ((= string-tokenize ("substitute" store-path destination)) + (process-substitution store-path destination + #:cache-urls (substitute-urls) + #:acl (current-acl) + #:print-build-trace? + print-build-trace?) + (loop)))))) ((or ("-V") ("--version")) (show-version-and-exit "guix substitute")) (("--help") diff --git a/nix/libstore/build.cc b/nix/libstore/build.cc index 7e9ab3f39c..50d300253d 100644 --- a/nix/libstore/build.cc +++ b/nix/libstore/build.cc @@ -262,6 +262,7 @@ public: LocalStore & store; std::shared_ptr hook; + std::shared_ptr substituter; Worker(LocalStore & store); ~Worker(); @@ -2773,15 +2774,6 @@ private: /* Path info returned by the substituter's query info operation. */ SubstitutablePathInfo info; - /* Pipe for the substituter's standard output. */ - Pipe outPipe; - - /* Pipe for the substituter's standard error. */ - Pipe logPipe; - - /* The process ID of the builder. */ - Pid pid; - /* Lock on the store path. */ std::shared_ptr outputLock; @@ -2795,6 +2787,17 @@ private: typedef void (SubstitutionGoal::*GoalState)(); GoalState state; + /* The substituter. */ + std::shared_ptr substituter; + + /* Either the empty string, or the expected hash as returned by the + substituter. */ + string expectedHashStr; + + /* Either the empty string, or the status phrase returned by the + substituter. */ + string status; + void tryNext(); public: @@ -2840,7 +2843,7 @@ SubstitutionGoal::SubstitutionGoal(const Path & storePath, Worker & worker, bool SubstitutionGoal::~SubstitutionGoal() { - if (pid != -1) worker.childTerminated(pid); + if (substituter) worker.childTerminated(substituter->pid); } @@ -2848,9 +2851,9 @@ void SubstitutionGoal::timedOut() { if (settings.printBuildTrace) printMsg(lvlError, format("@ substituter-failed %1% timeout") % storePath); - if (pid != -1) { - pid_t savedPid = pid; - pid.kill(); + if (substituter) { + pid_t savedPid = substituter->pid; + substituter.reset(); worker.childTerminated(savedPid); } amDone(ecFailed); @@ -2977,45 +2980,29 @@ void SubstitutionGoal::tryToRun() printMsg(lvlInfo, format("fetching path `%1%'...") % storePath); - outPipe.create(); - logPipe.create(); - destPath = repair ? storePath + ".tmp" : storePath; /* Remove the (stale) output path if it exists. */ if (pathExists(destPath)) deletePath(destPath); - /* Fill in the arguments. */ - Strings args; - args.push_back("guix"); - args.push_back("substitute"); - args.push_back("--substitute"); - args.push_back(storePath); - args.push_back(destPath); - - /* Fork the substitute program. */ - pid = startProcess([&]() { - - /* Communicate substitute-urls & co. to 'guix substitute'. */ - setenv("_NIX_OPTIONS", settings.pack().c_str(), 1); - - commonChildInit(logPipe); - - if (dup2(outPipe.writeSide, STDOUT_FILENO) == -1) - throw SysError("cannot dup output pipe into stdout"); + if (!worker.substituter) { + const Strings args = { "substitute", "--substitute" }; + const std::map env = { { "_NIX_OPTIONS", settings.pack() } }; + worker.substituter = std::make_shared(settings.guixProgram, args, env); + } - execv(settings.guixProgram.c_str(), stringsToCharPtrs(args).data()); + /* Borrow the worker's substituter. */ + if (!substituter) substituter.swap(worker.substituter); - throw SysError(format("executing `%1% substitute'") % settings.guixProgram); - }); + /* Send the request to the substituter. */ + writeLine(substituter->toAgent.writeSide, + (format("substitute %1% %2%") % storePath % destPath).str()); - pid.setSeparatePG(true); - pid.setKillSignal(SIGTERM); - outPipe.writeSide.close(); - logPipe.writeSide.close(); - worker.childStarted(shared_from_this(), - pid, singleton >(logPipe.readSide), true, true); + set fds; + fds.insert(substituter->fromAgent.readSide); + fds.insert(substituter->builderOut.readSide); + worker.childStarted(shared_from_this(), substituter->pid, fds, true, true); state = &SubstitutionGoal::finished; @@ -3030,28 +3017,25 @@ void SubstitutionGoal::finished() { trace("substitute finished"); - /* Since we got an EOF on the logger pipe, the substitute is - presumed to have terminated. */ - pid_t savedPid = pid; - int status = pid.wait(true); - - /* So the child is gone now. */ - worker.childTerminated(savedPid); - - /* Close the read side of the logger pipe. */ - logPipe.readSide.close(); + /* Remove the 'guix substitute' process from the list of children. */ + worker.childTerminated(substituter->pid); - /* Get the hash info from stdout. */ - string expectedHashStr = statusOk(status) ? readLine(outPipe.readSide) : ""; - outPipe.readSide.close(); + /* If max-jobs > 1, the worker might have created a new 'substitute' + process in the meantime. If that is the case, terminate ours; + otherwise, give it back to the worker. */ + if (worker.substituter) { + substituter.reset (); + } else { + worker.substituter.swap(substituter); + } /* Check the exit status and the build result. */ HashResult hash; try { - if (!statusOk(status)) - throw SubstError(format("fetching path `%1%' %2%") - % storePath % statusToString(status)); + if (status != "success") + throw SubstError(format("fetching path `%1%' (status: '%2%')") + % storePath % status); if (!pathExists(destPath)) throw SubstError(format("substitute did not produce path `%1%'") % destPath); @@ -3122,16 +3106,33 @@ void SubstitutionGoal::finished() void SubstitutionGoal::handleChildOutput(int fd, const string & data) { - assert(fd == logPipe.readSide); - if (verbosity >= settings.buildVerbosity) writeToStderr(data); - /* Don't write substitution output to a log file for now. We - probably should, though. */ + if (verbosity >= settings.buildVerbosity + && fd == substituter->builderOut.readSide) { + writeToStderr(data); + /* Don't write substitution output to a log file for now. We + probably should, though. */ + } + + if (fd == substituter->fromAgent.readSide) { + /* Trim whitespace to the right. */ + size_t end = data.find_last_not_of(" \t\n"); + string trimmed = (end != string::npos) ? data.substr(0, end + 1) : data; + + if (expectedHashStr == "") { + expectedHashStr = trimmed; + } else if (status == "") { + status = trimmed; + worker.wakeUp(shared_from_this()); + } else { + printMsg(lvlError, format("unexpected substituter message '%1%'") % data); + } + } } void SubstitutionGoal::handleEOF(int fd) { - if (fd == logPipe.readSide) worker.wakeUp(shared_from_this()); + worker.wakeUp(shared_from_this()); } diff --git a/tests/substitute.scm b/tests/substitute.scm index bd5b6305b0..b86ce09425 100644 --- a/tests/substitute.scm +++ b/tests/substitute.scm @@ -58,6 +58,14 @@ it writes to GUIX-WARNING-PORT a messages that matches ERROR-RX." (let ((message (get-output-string error-output))) (->bool (string-match error-rx message)))))))))) +(define (request-substitution item destination) + "Run 'guix substitute --substitute' to fetch ITEM to DESTINATION." + (parameterize ((guix-warning-port (current-error-port))) + (with-input-from-string (string-append "substitute " item " " + destination "\n") + (lambda () + (guix-substitute "--substitute"))))) + (define %public-key ;; This key is known to be in the ACL by default. (call-with-input-file (string-append %config-directory "/signing-key.pub") @@ -184,6 +192,11 @@ a file for NARINFO." ;; Transmit these options to 'guix substitute'. (substitute-urls (list (getenv "GUIX_BINARY_SUBSTITUTE_URL"))) +;; Never use file descriptor 4, unlike what happens when invoked by the +;; daemon. +(%error-to-file-descriptor-4? #f) + + (test-equal "query narinfo without signature" "" ; not substitutable @@ -284,10 +297,12 @@ System: mips64el-linux\n") (test-quit "substitute, no signature" "no valid substitute" (with-narinfo %narinfo - (guix-substitute "--substitute" - (string-append (%store-prefix) - "/aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa-foo") - "foo"))) + (with-input-from-string (string-append "substitute " + (%store-prefix) + "/aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa-foo" + " foo\n") + (lambda () + (guix-substitute "--substitute"))))) (test-quit "substitute, invalid hash" "no valid substitute" @@ -295,10 +310,12 @@ System: mips64el-linux\n") (with-narinfo (string-append %narinfo "Signature: " (signature-field "different body") "\n") - (guix-substitute "--substitute" - (string-append (%store-prefix) - "/aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa-foo") - "foo"))) + (with-input-from-string (string-append "substitute " + (%store-prefix) + "/aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa-foo" + " foo\n") + (lambda () + (guix-substitute "--substitute"))))) (test-quit "substitute, unauthorized key" "no valid substitute" @@ -307,10 +324,12 @@ System: mips64el-linux\n") %narinfo #:public-key %wrong-public-key) "\n") - (guix-substitute "--substitute" - (string-append (%store-prefix) - "/aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa-foo") - "foo"))) + (with-input-from-string (string-append "substitute " + (%store-prefix) + "/aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa-foo" + " foo\n") + (lambda () + (guix-substitute "--substitute"))))) (test-equal "substitute, authorized key" "Substitutable data." @@ -319,10 +338,9 @@ System: mips64el-linux\n") (dynamic-wind (const #t) (lambda () - (guix-substitute "--substitute" - (string-append (%store-prefix) - "/aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa-foo") - "substitute-retrieved") + (request-substitution (string-append (%store-prefix) + "/aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa-foo") + "substitute-retrieved") (call-with-input-file "substitute-retrieved" get-string-all)) (lambda () (false-if-exception (delete-file "substitute-retrieved")))))) @@ -352,10 +370,9 @@ System: mips64el-linux\n") (map (cut string-append "file://" <>) (list %alternate-substitute-directory %main-substitute-directory)))) - (guix-substitute "--substitute" - (string-append (%store-prefix) - "/aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa-foo") - "substitute-retrieved")) + (request-substitution (string-append (%store-prefix) + "/aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa-foo") + "substitute-retrieved")) (call-with-input-file "substitute-retrieved" get-string-all)) (lambda () (false-if-exception (delete-file "substitute-retrieved"))))))) @@ -381,10 +398,9 @@ System: mips64el-linux\n") (map (cut string-append "file://" <>) (list %alternate-substitute-directory %main-substitute-directory)))) - (guix-substitute "--substitute" - (string-append (%store-prefix) - "/aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa-foo") - "substitute-retrieved")) + (request-substitution (string-append (%store-prefix) + "/aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa-foo") + "substitute-retrieved")) (call-with-input-file "substitute-retrieved" get-string-all)) (lambda () (false-if-exception (delete-file "substitute-retrieved"))))))) @@ -417,10 +433,9 @@ System: mips64el-linux\n") (map (cut string-append "file://" <>) (list %alternate-substitute-directory %main-substitute-directory)))) - (guix-substitute "--substitute" - (string-append (%store-prefix) - "/aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa-foo") - "substitute-retrieved")) + (request-substitution (string-append (%store-prefix) + "/aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa-foo") + "substitute-retrieved")) (call-with-input-file "substitute-retrieved" get-string-all)) (lambda () (false-if-exception (delete-file "substitute-retrieved"))))))) @@ -451,10 +466,9 @@ System: mips64el-linux\n") (map (cut string-append "file://" <>) (list %alternate-substitute-directory %main-substitute-directory)))) - (guix-substitute "--substitute" - (string-append (%store-prefix) - "/aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa-foo") - "substitute-retrieved")) + (request-substitution (string-append (%store-prefix) + "/aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa-foo") + "substitute-retrieved")) (call-with-input-file "substitute-retrieved" get-string-all)) (lambda () (false-if-exception (delete-file "substitute-retrieved"))))))) @@ -470,10 +484,12 @@ System: mips64el-linux\n") #:public-key %wrong-public-key)) %main-substitute-directory - (guix-substitute "--substitute" - (string-append (%store-prefix) - "/aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa-foo") - "substitute-retrieved")))) + (with-input-from-string (string-append "substitute " + (%store-prefix) + "/aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa-foo" + " substitute-retrieved\n") + (lambda () + (guix-substitute "--substitute")))))) (test-equal "substitute, narinfo with several URLs" "Substitutable data." @@ -513,10 +529,9 @@ System: mips64el-linux\n"))) (parameterize ((substitute-urls (list (string-append "file://" %main-substitute-directory)))) - (guix-substitute "--substitute" - (string-append (%store-prefix) - "/aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa-foo") - "substitute-retrieved")) + (request-substitution (string-append (%store-prefix) + "/aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa-foo") + "substitute-retrieved")) (call-with-input-file "substitute-retrieved" get-string-all)) (lambda () (false-if-exception (delete-file "substitute-retrieved"))))))) -- cgit v1.2.3 From 5ff521452b9ec2aae9ed8e4bb7bdc250a581f203 Mon Sep 17 00:00:00 2001 From: Ludovic Courtès Date: Wed, 2 Dec 2020 22:49:39 +0100 Subject: substitute: Cache and reuse connections while substituting. That way, when fetching a series of substitutes from the same server(s), the connection is reused instead of being closed/opened for each substitutes, which saves on network round trips and TLS handshakes. * guix/http-client.scm (http-fetch): Add #:keep-alive? and honor it. * guix/progress.scm (progress-report-port): Add #:close? parameter and honor it. * guix/scripts/substitute.scm (at-most): Return the tail as a second value. (fetch): Add #:port and #:keep-alive? and honor them. (%max-cached-connections): New variable. (open-connection-for-uri/cached, call-with-cached-connection): New procedures. (with-cached-connection): New macro. (process-substitution): Wrap 'fetch' call in 'with-cached-connection'. Pass #:close? to 'progress-report-port'. --- guix/http-client.scm | 12 +++--- guix/progress.scm | 8 ++-- guix/scripts/substitute.scm | 103 +++++++++++++++++++++++++++++++++++++------- nix/libstore/build.cc | 29 ++++++++----- 4 files changed, 117 insertions(+), 35 deletions(-) diff --git a/guix/http-client.scm b/guix/http-client.scm index a767175d67..553640fe9e 100644 --- a/guix/http-client.scm +++ b/guix/http-client.scm @@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2012, 2013, 2014, 2015, 2016, 2017, 2018 Ludovic Courtès +;;; Copyright © 2012, 2013, 2014, 2015, 2016, 2017, 2018, 2020 Ludovic Courtès ;;; Copyright © 2015 Mark H Weaver ;;; Copyright © 2012, 2015 Free Software Foundation, Inc. ;;; Copyright © 2017 Tobias Geerinckx-Rice @@ -70,6 +70,7 @@ (define* (http-fetch uri #:key port (text? #f) (buffered? #t) + (keep-alive? #f) (verify-certificate? #t) (headers '((user-agent . "GNU Guile"))) timeout) @@ -79,6 +80,9 @@ textual. Follow any HTTP redirection. When BUFFERED? is #f, return an unbuffered port, suitable for use in `filtered-port'. HEADERS is an alist of extra HTTP headers. +When KEEP-ALIVE? is true, the connection is marked as 'keep-alive' and PORT is +not closed upon completion. + When VERIFY-CERTIFICATE? is true, verify HTTPS server certificates. TIMEOUT specifies the timeout in seconds for connection establishment; when @@ -104,11 +108,7 @@ Raise an '&http-get-error' condition if downloading fails." (setvbuf port 'none)) (let*-values (((resp data) (http-get uri #:streaming? #t #:port port - ;; XXX: When #:keep-alive? is true, if DATA is - ;; a chunked-encoding port, closing DATA won't - ;; close PORT, leading to a file descriptor - ;; leak. - #:keep-alive? #f + #:keep-alive? keep-alive? #:headers headers)) ((code) (response-code resp))) diff --git a/guix/progress.scm b/guix/progress.scm index fec65b424c..cd80ae620a 100644 --- a/guix/progress.scm +++ b/guix/progress.scm @@ -337,9 +337,10 @@ should be a object." (report total) (loop total (get-bytevector-n! in buffer 0 buffer-size)))))))) -(define (progress-report-port reporter port) +(define* (progress-report-port reporter port #:key (close? #t)) "Return a port that continuously reports the bytes read from PORT using -REPORTER, which should be a object." +REPORTER, which should be a object. When CLOSE? is true, +PORT is closed when the returned port is closed." (match reporter (($ start report stop) (let* ((total 0) @@ -364,5 +365,6 @@ REPORTER, which should be a object." ;; trace. (unless (zero? total) (stop)) - (close-port port))))))) + (when close? + (close-port port)))))))) diff --git a/guix/scripts/substitute.scm b/guix/scripts/substitute.scm index 73abd3f029..25075eedff 100755 --- a/guix/scripts/substitute.scm +++ b/guix/scripts/substitute.scm @@ -188,9 +188,14 @@ again." (sigaction SIGALRM SIG_DFL) (apply values result))))) -(define* (fetch uri #:key (buffered? #t) (timeout? #t)) +(define* (fetch uri #:key (buffered? #t) (timeout? #t) + (keep-alive? #f) (port #f)) "Return a binary input port to URI and the number of bytes it's expected to -provide." +provide. + +When PORT is true, use it as the underlying I/O port for HTTP transfers; when +PORT is false, open a new connection for URI. When KEEP-ALIVE? is true, the +connection (typically PORT) is kept open once data has been fetched from URI." (case (uri-scheme uri) ((file) (let ((port (open-file (uri-path uri) @@ -206,7 +211,7 @@ provide." ;; sudo tc qdisc add dev eth0 root netem delay 1500ms ;; and then cancel with: ;; sudo tc qdisc del dev eth0 root - (let ((port #f)) + (let ((port port)) (with-timeout (if timeout? %fetch-timeout 0) @@ -217,10 +222,11 @@ provide." (begin (when (or (not port) (port-closed? port)) (set! port (guix:open-connection-for-uri - uri #:verify-certificate? #f)) - (unless (or buffered? (not (file-port? port))) - (setvbuf port 'none))) + uri #:verify-certificate? #f))) + (unless (or buffered? (not (file-port? port))) + (setvbuf port 'none)) (http-fetch uri #:text? #f #:port port + #:keep-alive? keep-alive? #:verify-certificate? #f)))))) (else (leave (G_ "unsupported substitute URI scheme: ~a~%") @@ -478,17 +484,17 @@ indicates that PATH is unavailable at CACHE-URL." (build-request (string->uri url) #:method 'GET #:headers headers))) (define (at-most max-length lst) - "If LST is shorter than MAX-LENGTH, return it; otherwise return its -MAX-LENGTH first elements." + "If LST is shorter than MAX-LENGTH, return it and the empty list; otherwise +return its MAX-LENGTH first elements and its tail." (let loop ((len 0) (lst lst) (result '())) (match lst (() - (reverse result)) + (values (reverse result) '())) ((head . tail) (if (>= len max-length) - (reverse result) + (values (reverse result) lst) (loop (+ 1 len) tail (cons head result))))))) (define* (http-multiple-get base-uri proc seed requests @@ -962,6 +968,68 @@ the URI, its compression method (a string), and the compressed file size." (((uri compression file-size) _ ...) (values uri compression file-size)))) +(define %max-cached-connections + ;; Maximum number of connections kept in cache by + ;; 'open-connection-for-uri/cached'. + 16) + +(define open-connection-for-uri/cached + (let ((cache '())) + (lambda* (uri #:key fresh?) + "Return a connection for URI, possibly reusing a cached connection. +When FRESH? is true, delete any cached connections for URI and open a new +one. Return #f if URI's scheme is 'file' or #f." + (define host (uri-host uri)) + (define scheme (uri-scheme uri)) + (define key (list host scheme (uri-port uri))) + + (and (not (memq scheme '(file #f))) + (match (assoc-ref cache key) + (#f + ;; Open a new connection to URI and evict old entries from + ;; CACHE, if any. + (let-values (((socket) + (guix:open-connection-for-uri + uri #:verify-certificate? #f)) + ((new-cache evicted) + (at-most (- %max-cached-connections 1) cache))) + (for-each (match-lambda + ((_ . port) + (false-if-exception (close-port port)))) + evicted) + (set! cache (alist-cons key socket new-cache)) + socket)) + (socket + (if (or fresh? (port-closed? socket)) + (begin + (false-if-exception (close-port socket)) + (set! cache (alist-delete key cache)) + (open-connection-for-uri/cached uri)) + (begin + ;; Drain input left from the previous use. + (drain-input socket) + socket)))))))) + +(define (call-with-cached-connection uri proc) + (let ((port (open-connection-for-uri/cached uri))) + (catch #t + (lambda () + (proc port)) + (lambda (key . args) + ;; If PORT was cached and the server closed the connection in the + ;; meantime, we get EPIPE. In that case, open a fresh connection and + ;; retry. We might also get 'bad-response or a similar exception from + ;; (web response) later on, once we've sent the request. + (if (or (and (eq? key 'system-error) + (= EPIPE (system-error-errno `(,key ,@args)))) + (memq key '(bad-response bad-header bad-header-component))) + (proc (open-connection-for-uri/cached uri #:fresh? #t)) + (apply throw key args)))))) + +(define-syntax-rule (with-cached-connection uri port exp ...) + "Bind PORT with EXP... to a socket connected to URI." + (call-with-cached-connection uri (lambda (port) exp ...))) + (define* (process-substitution store-item destination #:key cache-urls acl print-build-trace?) "Substitute STORE-ITEM (a store file name) from CACHE-URLS, and write it to @@ -984,10 +1052,12 @@ DESTINATION as a nar file. Verify the substitute against ACL." (G_ "Downloading ~a...~%") (uri->string uri))) (let*-values (((raw download-size) - ;; Note that Hydra currently generates Nars on the fly - ;; and doesn't specify a Content-Length, so - ;; DOWNLOAD-SIZE is #f in practice. - (fetch uri #:buffered? #f #:timeout? #f)) + ;; 'guix publish' without '--cache' doesn't specify a + ;; Content-Length, so DOWNLOAD-SIZE is #f in this case. + (with-cached-connection uri port + (fetch uri #:buffered? #f #:timeout? #f + #:port port + #:keep-alive? #t))) ((progress) (let* ((dl-size (or download-size (and (equal? compression "none") @@ -1001,7 +1071,9 @@ DESTINATION as a nar file. Verify the substitute against ACL." (uri->string uri) dl-size (current-error-port) #:abbreviation nar-uri-abbreviation)))) - (progress-report-port reporter raw))) + ;; Keep RAW open upon completion so we can later reuse + ;; the underlying connection. + (progress-report-port reporter raw #:close? #f))) ((input pids) ;; NOTE: This 'progress' port of current process will be ;; closed here, while the child process doing the @@ -1218,6 +1290,7 @@ default value." ;;; Local Variables: ;;; eval: (put 'with-timeout 'scheme-indent-function 1) +;;; eval: (put 'with-cached-connection 'scheme-indent-function 2) ;;; End: ;;; substitute.scm ends here diff --git a/nix/libstore/build.cc b/nix/libstore/build.cc index 50d300253d..6cfe7aba7e 100644 --- a/nix/libstore/build.cc +++ b/nix/libstore/build.cc @@ -3114,17 +3114,24 @@ void SubstitutionGoal::handleChildOutput(int fd, const string & data) } if (fd == substituter->fromAgent.readSide) { - /* Trim whitespace to the right. */ - size_t end = data.find_last_not_of(" \t\n"); - string trimmed = (end != string::npos) ? data.substr(0, end + 1) : data; - - if (expectedHashStr == "") { - expectedHashStr = trimmed; - } else if (status == "") { - status = trimmed; - worker.wakeUp(shared_from_this()); - } else { - printMsg(lvlError, format("unexpected substituter message '%1%'") % data); + /* DATA may consist of several lines. Process them one by one. */ + string input = data; + while (!input.empty()) { + /* Process up to the first newline. */ + size_t end = input.find_first_of("\n"); + string trimmed = (end != string::npos) ? input.substr(0, end) : input; + + /* Update the goal's state accordingly. */ + if (expectedHashStr == "") { + expectedHashStr = trimmed; + } else if (status == "") { + status = trimmed; + worker.wakeUp(shared_from_this()); + } else { + printMsg(lvlError, format("unexpected substituter message '%1%'") % input); + } + + input = (end != string::npos) ? input.substr(end + 1) : ""; } } } -- cgit v1.2.3 From bfe4cdf88ee3e88910d22291a4c745462f2d6417 Mon Sep 17 00:00:00 2001 From: Ludovic Courtès Date: Thu, 3 Dec 2020 09:44:22 +0100 Subject: daemon: Raise an error if substituter doesn't send the expected hash. It was already impossible in practice for 'expectedHashStr' to be empty if 'status' == "success". * nix/libstore/build.cc (SubstitutionGoal::finished): Throw 'SubstError' when 'expectedHashStr' is empty. --- nix/libstore/build.cc | 37 +++++++++++++++++++------------------ 1 file changed, 19 insertions(+), 18 deletions(-) diff --git a/nix/libstore/build.cc b/nix/libstore/build.cc index 6cfe7aba7e..b5551b87ae 100644 --- a/nix/libstore/build.cc +++ b/nix/libstore/build.cc @@ -3040,27 +3040,28 @@ void SubstitutionGoal::finished() if (!pathExists(destPath)) throw SubstError(format("substitute did not produce path `%1%'") % destPath); + if (expectedHashStr == "") + throw SubstError(format("substituter did not communicate hash for `%1'") % storePath); + hash = hashPath(htSHA256, destPath); /* Verify the expected hash we got from the substituer. */ - if (expectedHashStr != "") { - size_t n = expectedHashStr.find(':'); - if (n == string::npos) - throw Error(format("bad hash from substituter: %1%") % expectedHashStr); - HashType hashType = parseHashType(string(expectedHashStr, 0, n)); - if (hashType == htUnknown) - throw Error(format("unknown hash algorithm in `%1%'") % expectedHashStr); - Hash expectedHash = parseHash16or32(hashType, string(expectedHashStr, n + 1)); - Hash actualHash = hashType == htSHA256 ? hash.first : hashPath(hashType, destPath).first; - if (expectedHash != actualHash) { - if (settings.printBuildTrace) - printMsg(lvlError, format("@ hash-mismatch %1% %2% %3% %4%") - % storePath % "sha256" - % printHash16or32(expectedHash) - % printHash16or32(actualHash)); - throw SubstError(format("hash mismatch for substituted item `%1%'") % storePath); - } - } + size_t n = expectedHashStr.find(':'); + if (n == string::npos) + throw Error(format("bad hash from substituter: %1%") % expectedHashStr); + HashType hashType = parseHashType(string(expectedHashStr, 0, n)); + if (hashType == htUnknown) + throw Error(format("unknown hash algorithm in `%1%'") % expectedHashStr); + Hash expectedHash = parseHash16or32(hashType, string(expectedHashStr, n + 1)); + Hash actualHash = hashType == htSHA256 ? hash.first : hashPath(hashType, destPath).first; + if (expectedHash != actualHash) { + if (settings.printBuildTrace) + printMsg(lvlError, format("@ hash-mismatch %1% %2% %3% %4%") + % storePath % "sha256" + % printHash16or32(expectedHash) + % printHash16or32(actualHash)); + throw SubstError(format("hash mismatch for substituted item `%1%'") % storePath); + } } catch (SubstError & e) { -- cgit v1.2.3 From 799f066768bacb321ebad84c75b2bbfd269e7cd8 Mon Sep 17 00:00:00 2001 From: Ludovic Courtès Date: Tue, 8 Dec 2020 22:58:37 +0100 Subject: import: opam: Adjust test to latest 'opam->guix-package' changes. This is a followup to a8dccd4bdc1e58219d4ba08fe1649bf0b8325f44, which broke the test. * guix/import/opam.scm (get-opam-repository): Prevent inlining. * tests/opam.scm ("opam->guix-package"): Mock 'get-opam-repository'. --- guix/import/opam.scm | 3 +++ tests/opam.scm | 67 +++++++++++++++++++++++++++------------------------- 2 files changed, 38 insertions(+), 32 deletions(-) diff --git a/guix/import/opam.scm b/guix/import/opam.scm index 54143f83ca..670973b193 100644 --- a/guix/import/opam.scm +++ b/guix/import/opam.scm @@ -141,6 +141,9 @@ path to the repository." (string-append location "/" (substring (symbol->string repo) 4))) (else location))))) +;; Prevent Guile 3 from inlining this procedure so we can mock it in tests. +(set! get-opam-repository get-opam-repository) + (define (latest-version versions) "Find the most recent version from a list of versions." (fold (lambda (a b) (if (version>? a b) a b)) (car versions) versions)) diff --git a/tests/opam.scm b/tests/opam.scm index 8d43e2ce70..11984b56a6 100644 --- a/tests/opam.scm +++ b/tests/opam.scm @@ -80,38 +80,41 @@ url { (set! test-source-hash (call-with-input-file file-name port-sha256)))) (_ (error "Unexpected URL: " url))))) - (let ((my-package (string-append test-repo "/packages/foo/foo.1.0.0"))) - (mkdir-p my-package) - (with-output-to-file (string-append my-package "/opam") - (lambda _ - (format #t "~a" test-opam-file)))) - (match (opam->guix-package "foo" #:repo test-repo) - (('package - ('name "ocaml-foo") - ('version "1.0.0") - ('source ('origin - ('method 'url-fetch) - ('uri "https://example.org/foo-1.0.0.tar.gz") - ('sha256 - ('base32 - (? string? hash))))) - ('build-system 'ocaml-build-system) - ('propagated-inputs - ('quasiquote - (("ocaml-zarith" ('unquote 'ocaml-zarith))))) - ('native-inputs - ('quasiquote - (("ocaml-alcotest" ('unquote 'ocaml-alcotest)) - ("ocamlbuild" ('unquote 'ocamlbuild))))) - ('home-page "https://example.org/") - ('synopsis "Some example package") - ('description "This package is just an example.") - ('license #f)) - (string=? (bytevector->nix-base32-string - test-source-hash) - hash)) - (x - (pk 'fail x #f))))) + (mock ((guix import opam) get-opam-repository + (const test-repo)) + (let ((my-package (string-append test-repo + "/packages/foo/foo.1.0.0"))) + (mkdir-p my-package) + (with-output-to-file (string-append my-package "/opam") + (lambda _ + (format #t "~a" test-opam-file)))) + (match (opam->guix-package "foo" #:repo test-repo) + (('package + ('name "ocaml-foo") + ('version "1.0.0") + ('source ('origin + ('method 'url-fetch) + ('uri "https://example.org/foo-1.0.0.tar.gz") + ('sha256 + ('base32 + (? string? hash))))) + ('build-system 'ocaml-build-system) + ('propagated-inputs + ('quasiquote + (("ocaml-zarith" ('unquote 'ocaml-zarith))))) + ('native-inputs + ('quasiquote + (("ocaml-alcotest" ('unquote 'ocaml-alcotest)) + ("ocamlbuild" ('unquote 'ocamlbuild))))) + ('home-page "https://example.org/") + ('synopsis "Some example package") + ('description "This package is just an example.") + ('license #f)) + (string=? (bytevector->nix-base32-string + test-source-hash) + hash)) + (x + (pk 'fail x #f)))))) ;; Test the opam file parser ;; We fold over some test cases. Each case is a pair of the string to parse and the -- cgit v1.2.3 From 456421fc0f6ab7b6929d7c23a6ff957d9243f6e6 Mon Sep 17 00:00:00 2001 From: Ludovic Courtès Date: Tue, 8 Dec 2020 23:38:04 +0100 Subject: gnu: guix: Update to 799f066. * gnu/packages/package-management.scm (guix): Update to 799f066. --- gnu/packages/package-management.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/package-management.scm b/gnu/packages/package-management.scm index 9e8f9df76d..96cf2c47ca 100644 --- a/gnu/packages/package-management.scm +++ b/gnu/packages/package-management.scm @@ -131,8 +131,8 @@ ;; Note: the 'update-guix-package.scm' script expects this definition to ;; start precisely like this. (let ((version "1.2.0") - (commit "c952a9312a94bb236495ec654bf184685cf9fe79") - (revision 5)) + (commit "799f066768bacb321ebad84c75b2bbfd269e7cd8") + (revision 6)) (package (name "guix") @@ -148,7 +148,7 @@ (commit commit))) (sha256 (base32 - "1k32p37ikwls086mgxjhz9qhrbc7lgvfpbnk0ikfg4p40rxjp4w8")) + "04k8q5yjmxazskl13ap210jki2zh73zlzd0xdx06v08liskgz10q")) (file-name (string-append "guix-" version "-checkout")))) (build-system gnu-build-system) (arguments -- cgit v1.2.3 From 02b21f35cc610216bc9b71f4970a00759aa8b14e Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Tue, 8 Dec 2020 13:04:29 -0500 Subject: gnu: OpenSSL: Update to 1.1.1i [fixes CVE-2020-1971]. * gnu/packages/tls.scm (openssl)[replacement]: Update replacement to 1.1.1i (openssl-1.1.1g): Replace with ... (openssl-1.1.1i): ... new variable. --- gnu/packages/tls.scm | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/gnu/packages/tls.scm b/gnu/packages/tls.scm index 28c6d8c392..008578cd8f 100644 --- a/gnu/packages/tls.scm +++ b/gnu/packages/tls.scm @@ -307,7 +307,7 @@ required structures.") (package (name "openssl") (version "1.1.1f") - (replacement openssl-1.1.1g) + (replacement openssl-1.1.1i) (source (origin (method url-fetch) (uri (list (string-append "https://www.openssl.org/source/openssl-" @@ -439,10 +439,10 @@ required structures.") (license license:openssl) (home-page "https://www.openssl.org/"))) -(define openssl-1.1.1g +(define openssl-1.1.1i (package (inherit openssl) - (version "1.1.1g") + (version "1.1.1i") (source (origin (method url-fetch) (uri (list (string-append "https://www.openssl.org/source/openssl-" @@ -455,7 +455,7 @@ required structures.") (patches (search-patches "openssl-1.1-c-rehash-in.patch")) (sha256 (base32 - "0ikdcc038i7jk8h7asq5xcn8b1xc2rrbc88yfm4hqbz3y5s4gc6x")))))) + "0hjj1phcwkz69lx1lrvr9grhpl4y529mwqycqc1hdla1zqsnmgp8")))))) (define-public openssl-1.0 (package -- cgit v1.2.3 From 54f777ca4e0935dd408d5cc0445d82e72325a989 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Tue, 8 Dec 2020 22:10:33 -0500 Subject: gnu: linux-libre: Update to 5.9.13. * gnu/packages/linux.scm (linux-libre-5.9-version): Update to 5.9.13. (linux-libre-5.9-pristine-source): Update hash. --- gnu/packages/linux.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index 3d36468172..7325083581 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -352,7 +352,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." ;; The current "stable" kernel. That is, the most recently released major ;; version. -(define-public linux-libre-5.9-version "5.9.12") +(define-public linux-libre-5.9-version "5.9.13") (define deblob-scripts-5.9 (linux-libre-deblob-scripts linux-libre-5.9-version @@ -360,7 +360,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." (base32 "0yb04a4j2wq3mwvks3cj7kcm2pscmfs29lrz3falkxpbvjxbbgq2"))) (define-public linux-libre-5.9-pristine-source (let ((version linux-libre-5.9-version) - (hash (base32 "1gfrn3sz3h4cbsf3r8f9jxja400qsmbrk8sclk4cjx1l5qcmczyr"))) + (hash (base32 "0ancdbfmrhq7wnvzrrnayiw8j4k1pjjnmvjxkl12lal7bjdahdml"))) (make-linux-libre-source version (%upstream-linux-source version hash) deblob-scripts-5.9))) -- cgit v1.2.3 From 66b1b55148f03bac5bf6d5f7d747f60bb254ce61 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Tue, 8 Dec 2020 22:11:05 -0500 Subject: gnu: linux-libre 5.4: Update to 5.4.82. * gnu/packages/linux.scm (linux-libre-5.4-version): Update to 5.4.82. (linux-libre-5.4-pristine-source): Update hash. --- gnu/packages/linux.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index 7325083581..6226cb6b3d 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -368,7 +368,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." ;; The "longterm" kernels — the older releases with long-term upstream support. ;; Here are the support timelines: ;; -(define-public linux-libre-5.4-version "5.4.81") +(define-public linux-libre-5.4-version "5.4.82") (define deblob-scripts-5.4 (linux-libre-deblob-scripts linux-libre-5.4-version @@ -376,7 +376,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." (base32 "167zcfkw62pm6nv1xdvvhxw0ca724sywcywnv3z00189f8f8p3vg"))) (define-public linux-libre-5.4-pristine-source (let ((version linux-libre-5.4-version) - (hash (base32 "09w4bpr3v9rzcvxics5wddabplwbpk1mynl45lh9csbjfpjbsw4l"))) + (hash (base32 "1byx163v83aw0ixphwz20znml2s2n3cy1kp89vgwbdiqxbj5hi7v"))) (make-linux-libre-source version (%upstream-linux-source version hash) deblob-scripts-5.4))) -- cgit v1.2.3 From a2eae5ec4a6ac2df9c6d92f13b49cbfb8469fde2 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Tue, 8 Dec 2020 22:11:40 -0500 Subject: gnu: linux-libre 4.19: Update to 4.19.162. * gnu/packages/linux.scm (linux-libre-4.19-version): Update to 4.19.162. (linux-libre-4.19-pristine-source): Update hash. --- gnu/packages/linux.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index 6226cb6b3d..6cf55bdc25 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -381,7 +381,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." (%upstream-linux-source version hash) deblob-scripts-5.4))) -(define-public linux-libre-4.19-version "4.19.161") +(define-public linux-libre-4.19-version "4.19.162") (define deblob-scripts-4.19 (linux-libre-deblob-scripts linux-libre-4.19-version @@ -389,7 +389,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." (base32 "1jiaw0as1ippkrjdpd52657w5mz9qczg3y2hlra7m9k0xawwiqlf"))) (define-public linux-libre-4.19-pristine-source (let ((version linux-libre-4.19-version) - (hash (base32 "0h9wskmz9wridwnicnjlcmj1112qnlvqk01bhjkxv6b8jsajjh87"))) + (hash (base32 "052nk889fcvw7p4vll5dky6dcr1g6mvn1i93xykhch6yxkl26ds5"))) (make-linux-libre-source version (%upstream-linux-source version hash) deblob-scripts-4.19))) -- cgit v1.2.3 From 2b0185a74bfae4adde46142ea0fc5fb02c4b1c4a Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Tue, 8 Dec 2020 22:12:23 -0500 Subject: gnu: linux-libre 4.14: Update to 4.14.211. * gnu/packages/linux.scm (linux-libre-4.14-version): Update to 4.14.211. (linux-libre-4.14-pristine-source): Update hash. --- gnu/packages/linux.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index 6cf55bdc25..ee460c38b2 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -394,7 +394,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." (%upstream-linux-source version hash) deblob-scripts-4.19))) -(define-public linux-libre-4.14-version "4.14.210") +(define-public linux-libre-4.14-version "4.14.211") (define deblob-scripts-4.14 (linux-libre-deblob-scripts linux-libre-4.14-version @@ -402,7 +402,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." (base32 "1qij18inijj6c3ma8hv98yjagnzxdxyn134da9fd23ky8q6hbvky"))) (define-public linux-libre-4.14-pristine-source (let ((version linux-libre-4.14-version) - (hash (base32 "067xqi6sgf50p7s3n6y77cgf5bj5062s3bz3kqpp6f9wnk85267r"))) + (hash (base32 "0hp9457m0hal2d3bf5fs3ghp59s6hlc9bwl0s1apjgqa8fmkjdss"))) (make-linux-libre-source version (%upstream-linux-source version hash) deblob-scripts-4.14))) -- cgit v1.2.3 From f7c2896e528fa5d1821eae36cc7d8e54d313daec Mon Sep 17 00:00:00 2001 From: Ryan Prior Date: Sun, 4 Oct 2020 05:22:23 +0000 Subject: gnu: Add go-github-com-go-sql-driver-mysql. * gnu/packages/golang.scm (go-github-com-go-sql-driver-mysql): New variable. Signed-off-by: Efraim Flashner --- gnu/packages/golang.scm | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) diff --git a/gnu/packages/golang.scm b/gnu/packages/golang.scm index bacb835dec..12561c0a32 100644 --- a/gnu/packages/golang.scm +++ b/gnu/packages/golang.scm @@ -3582,6 +3582,31 @@ without requiring a real database connection.") (home-page "https://github.com/DATA-DOG/go-sqlmock") (license license:expat)))) +(define-public go-github-com-go-sql-driver-mysql + (package + (name "go-github-com-go-sql-driver-mysql") + (version "1.5.0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/go-sql-driver/mysql") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "11x0m9yf3kdnf6981182r824psgxwfaqhn3x3in4yiidp0w0hk3v")))) + (build-system go-build-system) + (arguments + '(#:tests? #f ;; tests require a network connection + #:import-path "github.com/go-sql-driver/mysql")) + (home-page "https://github.com/go-sql-driver/mysql") + (synopsis "MySQL driver for golang") + (description + "This is a pure Go implementaton of the MySQL API, compatible with +golang's database/sql package.") + (license license:mpl2.0))) + (define-public go-golang-org-colorful (package (name "go-golang-org-colorful") -- cgit v1.2.3 From 016501aec6d27ea5eda8cd7a8531418c26d867b9 Mon Sep 17 00:00:00 2001 From: Ryan Prior Date: Sun, 4 Oct 2020 05:22:35 +0000 Subject: gnu: Add go-github-com-jmespath-go-jmespath. * gnu/packages/golang.scm (go-github-com-jmespath-go-jmespath): New variable. Signed-off-by: Efraim Flashner --- gnu/packages/golang.scm | 28 ++++++++++++++++++++++++++++ 1 file changed, 28 insertions(+) diff --git a/gnu/packages/golang.scm b/gnu/packages/golang.scm index 12561c0a32..dc431b173a 100644 --- a/gnu/packages/golang.scm +++ b/gnu/packages/golang.scm @@ -5129,6 +5129,34 @@ the parse trees produced by the html package.") to jQuery to the Go language.") (license license:bsd-3))) +(define-public go-github-com-jmespath-go-jmespath + (package + (name "go-github-com-jmespath-go-jmespath") + (version "0.4.0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/jmespath/go-jmespath") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "18zyr9nlywmwp3wpzcjxrgq9s9d2mmc6zg6xhsna00m663nkyc3n")))) + (build-system go-build-system) + (arguments + '(#:import-path "github.com/jmespath/go-jmespath")) + (native-inputs + `(("go-github-com-davecgh-go-spew" ,go-github-com-davecgh-go-spew) + ("go-github-com-pmezard-go-difflib" ,go-github-com-pmezard-go-difflib) + ("go-gopkg-in-yaml-v2" ,go-gopkg-in-yaml-v2))) + (home-page "https://github.com/jmespath/go-jmespath") + (synopsis "Golang implementation of JMESPath") + (description + "This package implements JMESPath, a query language for JSON. It +transforms one JSON document into another through a JMESPath expression.") + (license license:asl2.0))) + (define-public go-github-com-aymerick-douceur (package (name "go-github-com-aymerick-douceur") -- cgit v1.2.3 From 994103655930ba46a6fffb7be7f9648d89ea5a7b Mon Sep 17 00:00:00 2001 From: Ryan Prior Date: Sun, 4 Oct 2020 05:22:41 +0000 Subject: gnu: Add go-github-com-aws-sdk. * gnu/packages/golang.scm (go-github-com-aws-sdk): New variable. Signed-off-by: Efraim Flashner --- gnu/packages/golang.scm | 29 +++++++++++++++++++++++++++++ 1 file changed, 29 insertions(+) diff --git a/gnu/packages/golang.scm b/gnu/packages/golang.scm index dc431b173a..3b42bf3c8f 100644 --- a/gnu/packages/golang.scm +++ b/gnu/packages/golang.scm @@ -512,6 +512,35 @@ way of specifying command line options.") (home-page "https://github.com/jessevdk/go-flags") (license license:bsd-3))) +(define-public go-github-com-aws-sdk + (package + (name "go-github-com-aws-sdk") + (version "1.35.2") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/aws/aws-sdk-go") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1ky5lw2s2zpslnnqcs6hgsrwvwbxwgflb5jwf16dd4aga3vrg10c")))) + (build-system go-build-system) + (arguments + '(#:import-path "github.com/aws/aws-sdk-go/aws" + #:unpack-path "github.com/aws/aws-sdk-go")) + (propagated-inputs + `(("go-github-com-go-sql-driver-mysql" ,go-github-com-go-sql-driver-mysql) + ("go-github-com-jmespath-go-jmespath" ,go-github-com-jmespath-go-jmespath) + ("go-github-com-pkg-errors" ,go-github-com-pkg-errors) + ("go-golang-org-x-net" ,go-golang-org-x-net))) + (home-page "https://github.com/aws/aws-sdk-go") + (synopsis "Library to access Amazon Web Services (AWS)") + (description + "This is the official AWS SDK for the Go programming language.") + (license license:asl2.0))) + (define-public go-gopkg.in-tomb.v2 (let ((commit "d5d1b5820637886def9eef33e03a27a9f166942c") (revision "0")) -- cgit v1.2.3 From 8e2aad26ae9b7365db83d4f6c74e9e79c57766a6 Mon Sep 17 00:00:00 2001 From: "elaexuotee@wilsonb.com" Date: Wed, 9 Dec 2020 15:53:44 +0900 Subject: gnu: Add lemonbar-xft. * gnu/packages/wm.scm (lemonbar-xft): New variable. Signed-off-by: Christopher Baines --- gnu/packages/wm.scm | 47 +++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 47 insertions(+) diff --git a/gnu/packages/wm.scm b/gnu/packages/wm.scm index 653af37de7..73a83c3411 100644 --- a/gnu/packages/wm.scm +++ b/gnu/packages/wm.scm @@ -38,6 +38,7 @@ ;;; Copyright © 2020 EuAndreh ;;; Copyright © 2020 Michael Rohleder ;;; Copyright © 2020 Guillaume Le Vaillant +;;; Copyright © 2020 B. Wilson ;;; ;;; This file is part of GNU Guix. ;;; @@ -2029,6 +2030,52 @@ formatting, RandR and Xinerama support and EWMH compliance without wasting your precious memory.") (license license:x11)))) +(define-public lemonbar-xft + ;; Upstream v2.0 tag is several years behind HEAD + (let ((commit "481e12363e2a0fe0ddd2176a8e003392be90ed02")) + (package + (inherit lemonbar) + (name "lemonbar-xft") + (version (string-append "2.0." (string-take commit 7))) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/drscream/lemonbar-xft") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0588g37h18lv50h7w8vfbwhvc3iajh7sdr53848spaif99nh3mh4")))) + (inputs + `(("freetype" ,freetype) + ("libxft" ,libxft) + ("libx11" ,libx11) + ,@(package-inputs lemonbar))) + (arguments + (substitute-keyword-arguments (package-arguments lemonbar) + ((#:make-flags make-flags) + `(append + ,make-flags + (list (string-append + "CFLAGS=" + (string-join + (list (string-append + "-I" (assoc-ref %build-inputs "freetype") + "/include/freetype2") + (string-append + "-D" "VERSION=" + (format #f "'~s'" ,version)))))))))) + (home-page "https://github.com/drscream/lemonbar-xft") + (synopsis + (string-append + (package-synopsis lemonbar) + " with fontconfig support")) + (description + (string-append + (package-description lemonbar) + "This is a fork of the @code{lemonbar} package that adds fontconfig +support, for easier unicode usage."))))) + (define-public xclickroot (package (name "xclickroot") -- cgit v1.2.3 From 5560bd7b6b42f7241212f1ee63ff95770faf4023 Mon Sep 17 00:00:00 2001 From: Guillaume Le Vaillant Date: Wed, 9 Dec 2020 10:34:35 +0100 Subject: gnu: monero: Update to 0.17.1.6. * gnu/packages/finance.scm (monero): Update to 0.17.1.6. --- gnu/packages/finance.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/finance.scm b/gnu/packages/finance.scm index df6d6fa424..a1becff413 100644 --- a/gnu/packages/finance.scm +++ b/gnu/packages/finance.scm @@ -625,7 +625,7 @@ other machines/servers. Electroncash does not download the Bitcoin Cash blockch ;; the system's dynamically linked library. (package (name "monero") - (version "0.17.1.5") + (version "0.17.1.6") (source (origin (method git-fetch) @@ -645,7 +645,7 @@ other machines/servers. Electroncash does not download the Bitcoin Cash blockch "external/unbound")) #t)) (sha256 - (base32 "0yy9n2qng02j314h8fh5n0mcy6vpdks0yk4d8ifn8hj03f3g2c8b")))) + (base32 "0b6zyr3mzqvcxf48i2g45gr649x6nhppik5598jsvg0z7i2hxb9q")))) (build-system cmake-build-system) (native-inputs `(("doxygen" ,doxygen) -- cgit v1.2.3 From 53c480006b50e93b80bf61d6a3ebfbe4a9ef91bf Mon Sep 17 00:00:00 2001 From: Guillaume Le Vaillant Date: Wed, 9 Dec 2020 11:23:28 +0100 Subject: gnu: monero-gui: Update to 0.17.1.6. * gnu/packages/finance.scm (monero-gui): Update to 0.17.1.6. --- gnu/packages/finance.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/finance.scm b/gnu/packages/finance.scm index a1becff413..579e060d26 100644 --- a/gnu/packages/finance.scm +++ b/gnu/packages/finance.scm @@ -735,7 +735,7 @@ the Monero command line client and daemon.") (define-public monero-gui (package (name "monero-gui") - (version "0.17.1.5") + (version "0.17.1.6") (source (origin (method git-fetch) @@ -744,7 +744,7 @@ the Monero command line client and daemon.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "0qlcqli0wvrjfy89mbgh1hpmk60dxgn5sws93h8lhgyfwx557iw0")))) + (base32 "0kn5wvx2psbdaqmy1cxlbf5l1mdpvh0b6hh9drah3s7nj3654a3r")))) (build-system qt-build-system) (native-inputs `(,@(package-native-inputs monero) -- cgit v1.2.3 From 533935ccf71bef93f2f146fba1b2bb6402559965 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Wed, 9 Dec 2020 12:55:02 +0200 Subject: services: science.scm: Add missing copyright headers. This module was always supposed to have the GPL3 header in place. Follow-up to 8f19e63f760fe02f9969225da2f3f3c36801218f. * gnu/services/science.scm: Add Copyright headers. --- gnu/services/science.scm | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) diff --git a/gnu/services/science.scm b/gnu/services/science.scm index 94ff0f36f2..6f7ac91154 100644 --- a/gnu/services/science.scm +++ b/gnu/services/science.scm @@ -1,3 +1,21 @@ +;;; GNU Guix --- Functional package management for GNU +;;; Copyright © 2020 Efraim Flashner +;;; +;;; This file is part of GNU Guix. +;;; +;;; GNU Guix is free software; you can redistribute it and/or modify it +;;; under the terms of the GNU General Public License as published by +;;; the Free Software Foundation; either version 3 of the License, or (at +;;; your option) any later version. +;;; +;;; GNU Guix is distributed in the hope that it will be useful, but +;;; WITHOUT ANY WARRANTY; without even the implied warranty of +;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +;;; GNU General Public License for more details. +;;; +;;; You should have received a copy of the GNU General Public License +;;; along with GNU Guix. If not, see . + (define-module (gnu services science) #:export ( rshiny-configuration -- cgit v1.2.3 From 0a79b24506054574e17e2d7772a8fd5da878bc32 Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Wed, 18 Nov 2020 15:27:20 +0100 Subject: import: cran: Update the Bioconductor version to 3.12. * guix/import/cran.scm (%bioconductor-version): Set to 3.12. * guix/build-system/r.scm (bioconductor-uri): Update to 3.12. --- guix/build-system/r.scm | 2 +- guix/import/cran.scm | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/guix/build-system/r.scm b/guix/build-system/r.scm index 5ef982d66a..e2bf41f18d 100644 --- a/guix/build-system/r.scm +++ b/guix/build-system/r.scm @@ -59,7 +59,7 @@ release corresponding to NAME and VERSION." "/src/contrib/" name "_" version ".tar.gz") ;; TODO: use %bioconductor-version from (guix import cran) - (string-append "https://bioconductor.org/packages/3.11" + (string-append "https://bioconductor.org/packages/3.12" type-url-part "/src/contrib/" name "_" version ".tar.gz")))) diff --git a/guix/import/cran.scm b/guix/import/cran.scm index d6baa6b5e5..6c1fbd7ba3 100644 --- a/guix/import/cran.scm +++ b/guix/import/cran.scm @@ -142,9 +142,9 @@ package definition." (define %cran-url "https://cran.r-project.org/web/packages/") (define %bioconductor-url "https://bioconductor.org/packages/") -;; The latest Bioconductor release is 3.11. Bioconductor packages should be +;; The latest Bioconductor release is 3.12. Bioconductor packages should be ;; updated together. -(define %bioconductor-version "3.11") +(define %bioconductor-version "3.12") (define* (bioconductor-packages-list-url #:optional type) (string-append "https://bioconductor.org/packages/" -- cgit v1.2.3 From 25f4e6520e96efd8afc32c11e90f4493a197e088 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:46:56 +0100 Subject: gnu: r-ideoviz: Update to 1.26.0. * gnu/packages/bioconductor.scm (r-ideoviz): Update to 1.26.0. --- gnu/packages/bioconductor.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index eac9c074a9..e5d382a94f 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2,7 +2,7 @@ ;;; Copyright © 2016, 2017, 2018, 2019, 2020 Ricardo Wurmus ;;; Copyright © 2016, 2017, 2018, 2020 Roel Janssen ;;; Copyright © 2017, 2018, 2019 Tobias Geerinckx-Rice -;;; Copyright © 2019 Simon Tournier +;;; Copyright © 2019, 2020 Simon Tournier ;;; Copyright © 2020 Peter Lo ;;; Copyright © 2020 Mădălin Ionel Patrașcu ;;; Copyright © 2020 Jakub Kądziołka @@ -748,13 +748,13 @@ annotations.") (define-public r-ideoviz (package (name "r-ideoviz") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "IdeoViz" version)) (sha256 (base32 - "1ndj14qhpgidjb4qsga80ghqzz1x8kvy2gy1bvvgwlkfxa62rn50")))) + "1k5c0skr6pvpcvkak9f0a088w5wsx4fl3jb9a76gyyni4nkj7djq")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) -- cgit v1.2.3 From 5ef637ddc7d3b1173f46104b1a739c12a4653fc3 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:47:00 +0100 Subject: gnu: r-coverageview: Update to 1.28.0. * gnu/packages/bioconductor.scm (r-coverageview): Update to 1.28.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index e5d382a94f..d665138ec2 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1077,13 +1077,13 @@ package @code{affy}.") (define-public r-coverageview (package (name "r-coverageview") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "CoverageView" version)) (sha256 (base32 - "1fcz7pkffz5l3jdxb9glji2zdmr6nx67h6vfpr2yi8n3slg2hrrj")))) + "1k89gzqhd8ca8s9gk5bfzringnc5nayqbwzwwy35fls1cg96qmsj")))) (build-system r-build-system) (propagated-inputs `(("r-s4vectors" ,r-s4vectors) -- cgit v1.2.3 From a3e2e538373f96366985d926536271ec7b4e7806 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:47:03 +0100 Subject: gnu: r-cummerbund: Update to 2.32.0. * gnu/packages/bioconductor.scm (r-cummerbund): Update to 2.32.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index d665138ec2..be07169eab 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1104,13 +1104,13 @@ how the coverage distributed across the genome.") (define-public r-cummerbund (package (name "r-cummerbund") - (version "2.30.0") + (version "2.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "cummeRbund" version)) (sha256 (base32 - "1av7yfxcq1wwbqfqcz7caiz5kf6kg5wq9qcg5v6yccihclzwvxjc")))) + "1x7rby50api1c66al6a0i92q82ydjmh3h8l2k7hj0ffpn8c5pdgj")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) -- cgit v1.2.3 From 70ab99096d2950936e1c8f843c1d067925473752 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:47:06 +0100 Subject: gnu: r-biocversion: Update to 3.12.0. * gnu/packages/bioconductor.scm (r-biocversion): Update to 3.12.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index be07169eab..58cd8507d0 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1170,14 +1170,14 @@ across the entire multi-'omics experiment.") (define-public r-biocversion (package (name "r-biocversion") - (version "3.11.1") + (version "3.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocVersion" version)) (sha256 (base32 - "1rrzx3dqds0jlj1bmjc744wiamb2hssbh3jfxz1s9jp4cvnwrpmz")))) + "1cj9swyf4zbkdq45bhw0kymh2aghkwimxjlfj5r2j7kdiyh6n3rk")))) (properties `((upstream-name . "BiocVersion"))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/BiocVersion/") -- cgit v1.2.3 From aa311eaa741b5787e3292fb55c8c6aa043a9f4dc Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:47:09 +0100 Subject: gnu: r-biocgenerics: Update to 0.36.0. * gnu/packages/bioconductor.scm (r-biocgenerics): Update to 0.36.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 58cd8507d0..bbb8459a37 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1190,13 +1190,13 @@ of Bioconductor.") (define-public r-biocgenerics (package (name "r-biocgenerics") - (version "0.34.0") + (version "0.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocGenerics" version)) (sha256 (base32 - "15nvqyh2gx5zkn1krbs5c4rhw5642bijdfsf2rgic70gzr05cksk")))) + "1y9pgangz2f0n9v3zj8brz8bv7a1yjsncdnd5h1l7zv0c0j9fh9q")))) (properties `((upstream-name . "BiocGenerics"))) (build-system r-build-system) -- cgit v1.2.3 From c472549f67728545cc5e51d451ecee104e4938e4 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:47:12 +0100 Subject: gnu: r-affycomp: Update to 1.66.0. * gnu/packages/bioconductor.scm (r-affycomp): Update to 1.66.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index bbb8459a37..4fca231d8a 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1210,14 +1210,14 @@ packages.") (define-public r-affycomp (package (name "r-affycomp") - (version "1.64.0") + (version "1.66.0") (source (origin (method url-fetch) (uri (bioconductor-uri "affycomp" version)) (sha256 (base32 - "0zg8dshas5b2ny4pnxxxqihnr4l20666ivrgglb939a23mplgps0")))) + "106gz4rami04r0ffc7rxkrv92s3yrcnlqnyykd5s8lrkndbihrpk")))) (properties `((upstream-name . "affycomp"))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase))) -- cgit v1.2.3 From fa2d16cc276de02d434ebad8b8a4ad1939025872 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:47:16 +0100 Subject: gnu: r-affycompatible: Update to 1.50.0. * gnu/packages/bioconductor.scm (r-affycompatible): Update to 1.50.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 4fca231d8a..6f95238d1c 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1231,14 +1231,14 @@ measures for Affymetrix Oligonucleotide Arrays.") (define-public r-affycompatible (package (name "r-affycompatible") - (version "1.48.0") + (version "1.50.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AffyCompatible" version)) (sha256 (base32 - "0394sr4spafhfypjsafwjr0y0zsgv52ajdcyvsmkdk7375898lqd")))) + "0pcs51miy45bky26i1d4iarbjh569gssb5g4fr26bzgjmq19yl7x")))) (properties `((upstream-name . "AffyCompatible"))) (build-system r-build-system) -- cgit v1.2.3 From 3e82f9ccaf969d31a6b6f36ae0494463c359840b Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:47:19 +0100 Subject: gnu: r-affycontam: Update to 1.48.0. * gnu/packages/bioconductor.scm (r-affycontam): Update to 1.48.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 6f95238d1c..67c57dd1fd 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1259,14 +1259,14 @@ Command Console} (AGCC)-compatible sample annotation files.") (define-public r-affycontam (package (name "r-affycontam") - (version "1.46.0") + (version "1.48.0") (source (origin (method url-fetch) (uri (bioconductor-uri "affyContam" version)) (sha256 (base32 - "1dh5c3blk2dl9kg13y6snplnx61x2f9hvp5lc7jmg25xk916517i")))) + "0pi5fll5868sb80vb9kbymz6gkjv58f0abk6zwn407cnyjhr342b")))) (properties `((upstream-name . "affyContam"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From a92219b45fc98e13392e41ab824fb036c913bbe5 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:47:22 +0100 Subject: gnu: r-affycoretools: Update to 1.62.0. * gnu/packages/bioconductor.scm (r-affycoretools): Update to 1.62.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 67c57dd1fd..fd603c8a98 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1284,14 +1284,14 @@ problems in CEL-level data to help evaluate performance of quality metrics.") (define-public r-affycoretools (package (name "r-affycoretools") - (version "1.60.1") + (version "1.62.0") (source (origin (method url-fetch) (uri (bioconductor-uri "affycoretools" version)) (sha256 (base32 - "0cnb54b3kmg9rnycvaz949bdali9n98qzrw7gwka6abmg1lv232s")))) + "0jacgwylg7wjw3xk3ga2sb1wkdklm5glamhbmqgvzm5kdjnl0rv0")))) (properties `((upstream-name . "affycoretools"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 8e6a2c328f4ac97951525b305023cadaa5f1e949 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:47:25 +0100 Subject: gnu: r-affxparser: Update to 1.62.0. * gnu/packages/bioconductor.scm (r-affxparser): Update to 1.62.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index fd603c8a98..aaa463045d 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1326,14 +1326,14 @@ to streamline the more common analyses that a Biostatistician might see.") (define-public r-affxparser (package (name "r-affxparser") - (version "1.60.0") + (version "1.62.0") (source (origin (method url-fetch) (uri (bioconductor-uri "affxparser" version)) (sha256 (base32 - "0d4hq1w0a3dm4bg9qsv7wqrbv2y7b9gllxfmnqs9n2nnwmvgi8yq")))) + "13h4iwskvgwgxid9f60gzb1zndgbhdlbn9ixv5waihy1jkcbn24p")))) (properties `((upstream-name . "affxparser"))) (build-system r-build-system) (home-page "https://github.com/HenrikBengtsson/affxparser") -- cgit v1.2.3 From 7d56302332b25859b60aaf0cbae916e9e67069f2 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:47:28 +0100 Subject: gnu: r-annotate: Update to 1.68.0. * gnu/packages/bioconductor.scm (r-annotate): Update to 1.68.0. [propagated-inputs]: Remove 'r-rcurl', add 'r-httr'. --- gnu/packages/bioconductor.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index aaa463045d..880998d5ef 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1354,21 +1354,21 @@ structure.") (define-public r-annotate (package (name "r-annotate") - (version "1.66.0") + (version "1.68.0") (source (origin (method url-fetch) (uri (bioconductor-uri "annotate" version)) (sha256 (base32 - "1ivszqknryq6n5a85z8zj12fvgcs6zz3zlza8q08pl6cs4m5rm4w")))) + "1rql591x56532m8n4axdkfkhkbcsz5hfrf7271s0lmkvy84i7z6l")))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) ("r-biobase" ,r-biobase) ("r-biocgenerics" ,r-biocgenerics) ("r-dbi" ,r-dbi) - ("r-rcurl" ,r-rcurl) + ("r-httr" ,r-httr) ("r-xml" ,r-xml) ("r-xtable" ,r-xtable))) (home-page -- cgit v1.2.3 From fa7578b32f634e01342f47b59fe517f033c70827 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:47:31 +0100 Subject: gnu: r-hpar: Update to 1.32.1. * gnu/packages/bioconductor.scm (r-hpar): Update to 1.32.1. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 880998d5ef..f421bab236 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1381,14 +1381,14 @@ microarrays.") (define-public r-hpar (package (name "r-hpar") - (version "1.30.0") + (version "1.32.1") (source (origin (method url-fetch) (uri (bioconductor-uri "hpar" version)) (sha256 (base32 - "1jq0qw7wq3426cp004divywjm3ryixkykcmwlhrri13agz6rx3r9")))) + "0h10b0fyblpsnxj60rpbk99z7snrkkb5jssmf0v27s6d445jq2zr")))) (build-system r-build-system) (native-inputs `(("r-knitr" ,r-knitr))) -- cgit v1.2.3 From d1ff3604b7a5eb8f5e3f3bbf1aa891f3834468cc Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:47:34 +0100 Subject: gnu: r-regioner: Update to 1.22.0. * gnu/packages/bioconductor.scm (r-regioner): Update to 1.22.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index f421bab236..3e47a84a80 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1401,14 +1401,14 @@ the Human Protein Atlas project.") (define-public r-regioner (package (name "r-regioner") - (version "1.20.1") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "regioneR" version)) (sha256 (base32 - "0bzjwzj5mvb49wgvs3gd3jfpm7s0zfkca763i65i7m994lgvz33c")))) + "0c2khfyrgy3y68cj6b07s91hplabbj70xwdgwrf2bsd9h6gknjdi")))) (properties `((upstream-name . "regioneR"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From c03c76344ece26aec06608dfc729e173448d66e9 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:47:37 +0100 Subject: gnu: r-reportingtools: Update to 2.30.0. * gnu/packages/bioconductor.scm (r-reportingtools): Update to 2.30.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 3e47a84a80..a85d9fa5ff 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1432,14 +1432,14 @@ region sets and other genomic features.") (define-public r-reportingtools (package (name "r-reportingtools") - (version "2.28.0") + (version "2.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ReportingTools" version)) (sha256 (base32 - "1ig1h224silbdbdr0j9j9sysp9l9dzpcsjzn8jp57h3gh4pdqbfx")))) + "0gkshdhx44yjffqf1xmvik7j5hlhszp1n9ckanaws9ky3iia8j31")))) (properties `((upstream-name . "ReportingTools"))) (build-system r-build-system) -- cgit v1.2.3 From d72c4c98c840846cc1e73e111b6c9f3de3905623 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:47:40 +0100 Subject: gnu: r-geneplotter: Update to 1.68.0. * gnu/packages/bioconductor.scm (r-geneplotter): Update to 1.68.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index a85d9fa5ff..5851d0a104 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1482,14 +1482,14 @@ browser.") (define-public r-geneplotter (package (name "r-geneplotter") - (version "1.66.0") + (version "1.68.0") (source (origin (method url-fetch) (uri (bioconductor-uri "geneplotter" version)) (sha256 (base32 - "1y494da1llmrvn3qm7akwgwjazvpffabi8llw3fbday14cay1br5")))) + "1f8nr60n1nig1gdy85wqdhpzxvp9r4chygxm8xpy882mdvfv6rqx")))) (build-system r-build-system) (propagated-inputs `(("r-annotate" ,r-annotate) -- cgit v1.2.3 From 464df5ccbb7c65678c0eb76533a07a1b0e88d964 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:47:44 +0100 Subject: gnu: r-oligoclasses: Update to 1.52.0. * gnu/packages/bioconductor.scm (r-oligoclasses): Update to 1.52.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 5851d0a104..b0bbb5f776 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1507,14 +1507,14 @@ browser.") (define-public r-oligoclasses (package (name "r-oligoclasses") - (version "1.50.4") + (version "1.52.0") (source (origin (method url-fetch) (uri (bioconductor-uri "oligoClasses" version)) (sha256 (base32 - "1d8c3i8v8kcm1afgpz6zc1iysip7993y8456cqxl37f7n6n0ax67")))) + "19p6h0cgnma5md5mm9bn6rxfhr0a9znljgdbvsqybms6asvh18gy")))) (properties `((upstream-name . "oligoClasses"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 9af6fdf861b06b7d1be9911ea19f9cb97c2689e4 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:47:47 +0100 Subject: gnu: r-oligo: Update to 1.54.0. * gnu/packages/bioconductor.scm (r-oligo): Update to 1.54.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index b0bbb5f776..34633962f5 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1542,14 +1542,14 @@ packages.") (define-public r-oligo (package (name "r-oligo") - (version "1.52.1") + (version "1.54.1") (source (origin (method url-fetch) (uri (bioconductor-uri "oligo" version)) (sha256 (base32 - "1gpvr33pwzz1glzajcipvjcplb7yxvjj00q0ybqcc3wa47bhfkwd")))) + "0cpfkvxpni7an361li0k0qlfcraj7z9zv71r25dbly5kp3dql7k3")))) (properties `((upstream-name . "oligo"))) (build-system r-build-system) (inputs `(("zlib" ,zlib))) -- cgit v1.2.3 From e9b60a290183d30bbd835e9281fab75d90d62780 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:47:50 +0100 Subject: gnu: r-qvalue: Update to 2.22.0. * gnu/packages/bioconductor.scm (r-qvalue): Update to 2.22.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 34633962f5..4323fe9d0a 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1578,14 +1578,14 @@ Affymetrix (CEL files) and NimbleGen arrays (XYS files).") (define-public r-qvalue (package (name "r-qvalue") - (version "2.20.0") + (version "2.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "qvalue" version)) (sha256 (base32 - "1hndmdr9niagbr4ry0vbhffvjzjg9im27kdbn0sa774k6r5b4z3f")))) + "0xbww16lz0k2p4mmq1aqd7iz7d8rvzgw1gm55jy6xbx19ymj64i5")))) (build-system r-build-system) (propagated-inputs `(("r-ggplot2" ,r-ggplot2) -- cgit v1.2.3 From a0df9b93ef6777fc549f102c703f307512618995 Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Wed, 18 Nov 2020 16:25:15 +0100 Subject: gnu: Add r-rcppnumerical. * gnu/packages/bioconductor.scm (r-rcppnumerical): New variable. --- gnu/packages/bioconductor.scm | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 4323fe9d0a..482a930586 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1606,6 +1606,30 @@ problems in genomics, brain imaging, astrophysics, and data mining.") ;; Any version of the LGPL. (license license:lgpl3+))) +(define r-rcppnumerical + (package + (name "r-rcppnumerical") + (version "0.4-0") + (source (origin + (method url-fetch) + (uri (cran-uri "RcppNumerical" version)) + (sha256 + (base32 + "1a92fql6mijhnr1kxkcxwivf95pk9lhgmhzkshs51h0ybfv5krik")))) + (properties `((upstream-name . "RcppNumerical"))) + (build-system r-build-system) + (propagated-inputs + `(("r-rcpp" ,r-rcpp) + ("r-rcppeigen" ,r-rcppeigen))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://github.com/yixuan/RcppNumerical") + (synopsis "Rcpp integration for numerical computing libraries") + (description "This package provides a collection of open source libraries +for numerical computing (numerical integration, optimization, etc.) and their +integration with @code{Rcpp}.") + (license license:gpl2+))) + (define-public r-diffbind (package (name "r-diffbind") -- cgit v1.2.3 From 3b399e514f55d2a9700a64f86462e071b5bb993d Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Wed, 18 Nov 2020 16:25:46 +0100 Subject: gnu: Add r-apeglm. * gnu/packages/bioconductor.scm (r-apeglm): New variable. --- gnu/packages/bioconductor.scm | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 482a930586..56d8036899 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1630,6 +1630,33 @@ for numerical computing (numerical integration, optimization, etc.) and their integration with @code{Rcpp}.") (license license:gpl2+))) +(define-public r-apeglm + (package + (name "r-apeglm") + (version "1.12.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "apeglm" version)) + (sha256 + (base32 + "0pix1fhxk2q89p2745fgsmxwics9rf10l392qhw3rw6v6ynhims2")))) + (properties `((upstream-name . "apeglm"))) + (build-system r-build-system) + (propagated-inputs + `(("r-emdbook" ,r-emdbook) + ("r-genomicranges" ,r-genomicranges) + ("r-rcpp" ,r-rcpp) + ("r-rcppeigen" ,r-rcppeigen) + ("r-rcppnumerical" ,r-rcppnumerical) + ("r-summarizedexperiment" ,r-summarizedexperiment))) + (native-inputs `(("r-knitr" ,r-knitr))) + (home-page "https://bioconductor.org/packages/apeglm") + (synopsis "Approximate posterior estimation for GLM coefficients") + (description "This package provides Bayesian shrinkage estimators for +effect sizes for a variety of GLM models, using approximation of the +posterior for individual coefficients.") + (license license:gpl2))) + (define-public r-diffbind (package (name "r-diffbind") -- cgit v1.2.3 From a7f4a8b4d0d7fb98b1c8839b7d0c2600364e39c1 Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Wed, 18 Nov 2020 16:34:45 +0100 Subject: gnu: Add r-invgamma. * gnu/packages/cran.scm (r-invgamma): New variable. --- gnu/packages/cran.scm | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index adb1bf421b..ee4e484cd0 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -2878,6 +2878,24 @@ and S4 methods with inlined C, C++ or Fortran code supporting @code{.C} and representation of intervals, including a method of coercing variables in data frames.") (license license:gpl2))) +(define-public r-invgamma + (package + (name "r-invgamma") + (version "1.1") + (source (origin + (method url-fetch) + (uri (cran-uri "invgamma" version)) + (sha256 + (base32 + "12ga2y4wc9bc5zz6vimvxwgjpsx3ys3209nq63gscbw559ydxa5a")))) + (properties `((upstream-name . "invgamma"))) + (build-system r-build-system) + (home-page "https://github.com/dkahle/invgamma") + (synopsis "Inverse gamma distribution") + (description "This package provides a light weight implementation of the +standard distribution functions for the inverse gamma distribution, wrapping +those for the gamma distribution in the @code{stats} package.") + (license license:gpl2))) (define-public r-bdsmatrix (package -- cgit v1.2.3 From deda2319f7f2ab0038311b847e31d5f6b5877f6e Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Wed, 18 Nov 2020 16:32:25 +0100 Subject: gnu: Add r-etrunct. * gnu/packages/cran.scm (r-etrunct): New variable. --- gnu/packages/cran.scm | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index ee4e484cd0..855b45e597 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -2769,6 +2769,25 @@ complex object; primarily used in common with the packages extRemes and SpatialVx.") (license license:gpl2+))) +(define-public r-etrunct + (package + (name "r-etrunct") + (version "0.1") + (source (origin + (method url-fetch) + (uri (cran-uri "etrunct" version)) + (sha256 + (base32 + "0ayazgyqlc8jcqr03cwfmfhm4pck6xri1r6vkgqy4arqkrrnrcqr")))) + (properties `((upstream-name . "etrunct"))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/web/packages/etrunct") + (synopsis "Computes moments of univariate truncated T distribution") + (description "This package computes moments of univariate truncated +T distribution. There is only one exported function, @code{e_trunct}, +which should be seen for details.") + (license license:expat))) + (define-public r-extremes (package (name "r-extremes") -- cgit v1.2.3 From 755d16a3b0494fcddfa46e40bcf494abbd278509 Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Wed, 18 Nov 2020 16:40:13 +0100 Subject: gnu: Add r-mixsqp. * gnu/packages/cran.scm (r-mixsqp): New variable. --- gnu/packages/cran.scm | 31 +++++++++++++++++++++++++++++++ 1 file changed, 31 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 855b45e597..60fac20c03 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -8636,6 +8636,37 @@ conveniently wrapped into a data frame.") multiple-imputation datasets.") (license license:gpl2))) +(define-public r-mixsqp + (package + (name "r-mixsqp") + (version "0.3-43") + (source (origin + (method url-fetch) + (uri (cran-uri "mixsqp" version)) + (sha256 + (base32 + "1qics04w0swyp216d6g8dmsph8q2kpadpacp66h2qih3521js12q")))) + (properties `((upstream-name . "mixsqp"))) + (build-system r-build-system) + (propagated-inputs + `(("r-irlba" ,r-irlba) + ("r-rcpp" ,r-rcpp) + ("r-rcpparmadillo" ,r-rcpparmadillo))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://github.com/stephenslab/mixsqp") + (synopsis + "Sequential quadratic programming for maximum-likelihood estimation") + (description + "This package provides an optimization method based on sequential +quadratic programming for maximum likelihood estimation of the mixture +proportions in a finite mixture model where the component densities are +known. The algorithm is expected to obtain solutions that are at least +as accurate as the state-of-the-art MOSEK interior-point solver, and they +are expected to arrive at solutions more quickly when the number of +samples is large and the number of mixture components is not too large.") + (license license:expat))) + (define-public r-magick (package (name "r-magick") -- cgit v1.2.3 From c84762c446bb2c98aecc1d94009fcc3137d5fd04 Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Wed, 18 Nov 2020 16:41:54 +0100 Subject: gnu: Add r-ashr. * gnu/packages/cran.scm (r-ashr): New variable. --- gnu/packages/cran.scm | 28 ++++++++++++++++++++++++++++ 1 file changed, 28 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 60fac20c03..25bb9d75ec 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -585,6 +585,34 @@ interrupts and timeouts. This provides the basis for a sandboxing mechanism.") (license license:expat))) +(define-public r-ashr + (package + (name "r-ashr") + (version "2.2-47") + (source (origin + (method url-fetch) + (uri (cran-uri "ashr" version)) + (sha256 + (base32 + "1rqb5j30ylaf1h4l66x4jxyn5inrvhc42d90qd5mgkxsq0ghdlr4")))) + (properties `((upstream-name . "ashr"))) + (build-system r-build-system) + (propagated-inputs + `(("r-etrunct" ,r-etrunct) + ("r-invgamma" ,r-invgamma) + ("r-matrix" ,r-matrix) + ("r-mixsqp" ,r-mixsqp) + ("r-rcpp" ,r-rcpp) + ("r-squarem" ,r-squarem) + ("r-truncnorm" ,r-truncnorm))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://github.com/stephens999/ashr") + (synopsis "Methods for adaptive shrinkage, using empirical bayes") + (description "This package implements an empirical Bayes approach for +large-scale hypothesis testing and false discovery rate estimation.") + (license license:gpl3+))) + (define-public r-askpass (package (name "r-askpass") -- cgit v1.2.3 From 6e396c4bff6c79befdc3e255b7d21c6af1774c5e Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Wed, 18 Nov 2020 16:47:44 +0100 Subject: gnu: Add r-greylistchip. * gnu/packages/bioconductor.scm (r-greylistchip): New variable. --- gnu/packages/bioconductor.scm | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 56d8036899..d8db2ba83b 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1657,6 +1657,33 @@ effect sizes for a variety of GLM models, using approximation of the posterior for individual coefficients.") (license license:gpl2))) +(define-public r-greylistchip + (package + (name "r-greylistchip") + (version "1.22.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "GreyListChIP" version)) + (sha256 + (base32 + "1d1yvza1aw3vs3di6mrra5l52ig0p9bpzprrqvknjaz5i4yb8ma6")))) + (properties `((upstream-name . "GreyListChIP"))) + (build-system r-build-system) + (propagated-inputs + `(("r-bsgenome" ,r-bsgenome) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicalignments" ,r-genomicalignments) + ("r-genomicranges" ,r-genomicranges) + ("r-mass" ,r-mass) + ("r-rsamtools" ,r-rsamtools) + ("r-rtracklayer" ,r-rtracklayer) + ("r-summarizedexperiment" ,r-summarizedexperiment))) + (home-page "https://bioconductor.org/packages/GreyListChIP") + (synopsis "Greylist artefact regions based on ChIP inputs") + (description "This package identifies regions of ChIP experiments with high +signal in the input, that lead to spurious peaks during peak calling.") + (license license:artistic2.0))) + (define-public r-diffbind (package (name "r-diffbind") -- cgit v1.2.3 From 341ebaaa0172a3f17b6dbbba1717e4e31374445a Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Wed, 18 Nov 2020 16:48:25 +0100 Subject: gnu: r-diffbind: Update to 3.0.7. * gnu/packages/bioconductor.scm (r-diffbind): Update to 3.0.7. [propagated-inputs]: Add r-apeglm, r-ashr, and r-greylistchip; remove r-edger. --- gnu/packages/bioconductor.scm | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index d8db2ba83b..ec2273ce10 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1687,29 +1687,31 @@ signal in the input, that lead to spurious peaks during peak calling.") (define-public r-diffbind (package (name "r-diffbind") - (version "2.16.2") + (version "3.0.7") (source (origin (method url-fetch) (uri (bioconductor-uri "DiffBind" version)) (sha256 (base32 - "11y9kigdikqcd0cnksh306nsaadak0kgivk7773mv3yszrxxwzj1")))) + "0irhqsi6rrkrkc7dhwmfpqfd0mnigs17027czcx8vgbrbra4lcvd")))) (properties `((upstream-name . "DiffBind"))) (build-system r-build-system) (inputs `(("zlib" ,zlib))) (propagated-inputs `(("r-amap" ,r-amap) + ("r-apeglm" ,r-apeglm) + ("r-ashr" ,r-ashr) ("r-biocparallel" ,r-biocparallel) ("r-deseq2" ,r-deseq2) ("r-dplyr" ,r-dplyr) - ("r-edger" ,r-edger) ("r-genomicalignments" ,r-genomicalignments) ("r-genomicranges" ,r-genomicranges) ("r-ggplot2" ,r-ggplot2) ("r-ggrepel" ,r-ggrepel) ("r-gplots" ,r-gplots) + ("r-greylistchip" ,r-greylistchip) ("r-iranges" ,r-iranges) ("r-lattice" ,r-lattice) ("r-limma" ,r-limma) -- cgit v1.2.3 From 1e6920c521b682dd5847fc8d8e7ec4c422add135 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:47:56 +0100 Subject: gnu: r-multtest: Update to 2.46.0. * gnu/packages/bioconductor.scm (r-multtest): Update to 2.46.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index ec2273ce10..f008badbcb 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1767,14 +1767,14 @@ processing to visualization and annotation.") (define-public r-multtest (package (name "r-multtest") - (version "2.44.0") + (version "2.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "multtest" version)) (sha256 (base32 - "12li7nzzygm3sjfx472095irqpawixk48d0k591wlnrms6sxchx2")))) + "06vixd81nh3nxrc6km73p7c4bwln1zm39fa9gp7gj272vsxkx53q")))) (build-system r-build-system) (propagated-inputs `(("r-survival" ,r-survival) -- cgit v1.2.3 From f519b4dc010311e69488421798c8b11fbc28693b Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:47:59 +0100 Subject: gnu: r-graph: Update to 1.68.0. * gnu/packages/bioconductor.scm (r-graph): Update to 1.68.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index f008badbcb..bb63d84f94 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1805,13 +1805,13 @@ expressed genes in DNA microarray experiments.") (define-public r-graph (package (name "r-graph") - (version "1.66.0") + (version "1.68.0") (source (origin (method url-fetch) (uri (bioconductor-uri "graph" version)) (sha256 (base32 - "15v0nx9gzpszmdn5lil1s1y8qfmsirlznh56wcyqq4sxwjbyjn9g")))) + "0wr7j2pasvi3srvg9z3n034ljk8mldcixny6b3kmqbqm8dqy9py4")))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics))) -- cgit v1.2.3 From d068d96743430a38d39db79f486907da675ae188 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:48:02 +0100 Subject: gnu: r-chippeakanno: Update to 3.24.0. * gnu/packages/bioconductor.scm (r-chippeakanno): Update to 3.24.0. --- gnu/packages/bioconductor.scm | 14 ++++---------- 1 file changed, 4 insertions(+), 10 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index bb63d84f94..dbd4d06d2a 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1903,36 +1903,31 @@ determining dependencies between variables, code improvement suggestions.") (define-public r-chippeakanno (package (name "r-chippeakanno") - (version "3.22.4") + (version "3.24.1") (source (origin (method url-fetch) (uri (bioconductor-uri "ChIPpeakAnno" version)) (sha256 (base32 - "0wxgjdikinkqj7jvs2725ak0291q6zhikyf1c93w8cngwvd9i1gq")))) + "0qdkwjv8s46d1kmgg2chijv7yzy9sv49kiks18w8x2z89prn15gj")))) (properties `((upstream-name . "ChIPpeakAnno"))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) - ("r-biobase" ,r-biobase) ("r-biocgenerics" ,r-biocgenerics) - ("r-biocmanager" ,r-biocmanager) ("r-biomart" ,r-biomart) ("r-biostrings" ,r-biostrings) - ("r-bsgenome" ,r-bsgenome) ("r-dbi" ,r-dbi) - ("r-delayedarray" ,r-delayedarray) ("r-ensembldb" ,r-ensembldb) ("r-genomeinfodb" ,r-genomeinfodb) ("r-genomicalignments" ,r-genomicalignments) ("r-genomicfeatures" ,r-genomicfeatures) ("r-genomicranges" ,r-genomicranges) - ("r-go-db" ,r-go-db) + ("r-ggplot2" ,r-ggplot2) ("r-graph" ,r-graph) - ("r-idr" ,r-idr) ("r-iranges" ,r-iranges) - ("r-limma" ,r-limma) + ("r-keggrest" ,r-keggrest) ("r-matrixstats" ,r-matrixstats) ("r-multtest" ,r-multtest) ("r-rbgl" ,r-rbgl) @@ -1940,7 +1935,6 @@ determining dependencies between variables, code improvement suggestions.") ("r-rsamtools" ,r-rsamtools) ("r-rtracklayer" ,r-rtracklayer) ("r-s4vectors" ,r-s4vectors) - ("r-seqinr" ,r-seqinr) ("r-summarizedexperiment" ,r-summarizedexperiment) ("r-venndiagram" ,r-venndiagram))) (native-inputs -- cgit v1.2.3 From 6e6c6272306e01a11ae79786e0ee86e4e2c8df5e Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:48:05 +0100 Subject: gnu: r-marray: Update to 1.68.0. * gnu/packages/bioconductor.scm (r-marray): Update to 1.68.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index dbd4d06d2a..086ad5b474 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1955,12 +1955,12 @@ enrichedGO (addGeneIDs).") (define-public r-marray (package (name "r-marray") - (version "1.66.0") + (version "1.68.0") (source (origin (method url-fetch) (uri (bioconductor-uri "marray" version)) (sha256 - (base32 "1sym3nis5qzg05b2in83xr019mvz8czy8qvispc0hzsq42yng6kd")))) + (base32 "1kkgv166gzvlj8p58vzam3hcaz8mypi3hhpdsjhaszwg6nav4ray")))) (build-system r-build-system) (propagated-inputs `(("r-limma" ,r-limma))) -- cgit v1.2.3 From ee052d05f17d8a50056922e5fae7253dfcf903be Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:48:08 +0100 Subject: gnu: r-cghbase: Update to 1.50.0. * gnu/packages/bioconductor.scm (r-cghbase): Update to 1.50.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 086ad5b474..22b1b590f5 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1974,12 +1974,12 @@ normalization and quality checking.") (define-public r-cghbase (package (name "r-cghbase") - (version "1.48.0") + (version "1.50.0") (source (origin (method url-fetch) (uri (bioconductor-uri "CGHbase" version)) (sha256 - (base32 "0gfqqa9rs5hid53ihlky88qndgrwxxz0s6j7s505f660dd5nzlkf")))) + (base32 "10zhjmls3f63cj0bnywjb97zhrj7x3xsq6yjhvf5cclxc4kcrcx4")))) (properties `((upstream-name . "CGHbase"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 724000356ec545c372c7a2b41ae84099db65150f Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:48:11 +0100 Subject: gnu: r-cghcall: Update to 2.52.0. * gnu/packages/bioconductor.scm (r-cghcall): Update to 2.52.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 22b1b590f5..5f1a4083bb 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1994,12 +1994,12 @@ the @code{arrayCGH} packages.") (define-public r-cghcall (package (name "r-cghcall") - (version "2.50.0") + (version "2.52.0") (source (origin (method url-fetch) (uri (bioconductor-uri "CGHcall" version)) (sha256 - (base32 "1dz6sag8khl18vkb97b5w6fk6k9s7s9xxnc467dd3bmhmajlmrrg")))) + (base32 "1a6k87xfm79wnsc30k5aziakv51h4dd9zqw81q8bd72hc3fpz8ba")))) (properties `((upstream-name . "CGHcall"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 3b6484097ca9d4678b4b4c1a0d3c225d8811a360 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:48:14 +0100 Subject: gnu: r-qdnaseq: Update to 1.26.0. * gnu/packages/bioconductor.scm (r-qdnaseq): Update to 1.26.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 5f1a4083bb..0ba17fbfdd 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2017,12 +2017,12 @@ the @code{arrayCGH} packages.") (define-public r-qdnaseq (package (name "r-qdnaseq") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "QDNAseq" version)) (sha256 - (base32 "1ji9pl2r1idyj3qzggj7qd2kqx31i6b3igwk2hqjb8qzkyb37p86")))) + (base32 "1njka1ldaj12id3m2z8ghlrm2lg0n5pxsxyv5gpjnsiabnnaw6ph")))) (properties `((upstream-name . "QDNAseq"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 63572b0c12da0465fcee3ebda0baa5792a2920af Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:48:18 +0100 Subject: gnu: r-bayseq: Update to 2.24.0. * gnu/packages/bioconductor.scm (r-bayseq): Update to 2.24.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 0ba17fbfdd..b603b7cdc7 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2050,14 +2050,14 @@ respectively.") (define-public r-bayseq (package (name "r-bayseq") - (version "2.22.0") + (version "2.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "baySeq" version)) (sha256 (base32 - "1x0d34pqv9s15nmmxsfbw0ycxbf5348mi30ahycarjkjsyzycymj")))) + "1496inlw0x4mfy3g2v7j9ips96sf7576ydnfn6hvn2m6rz2ls215")))) (properties `((upstream-name . "baySeq"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 03b655c5246f4f5b37fb45dc5be9ce4a235d50f8 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:48:24 +0100 Subject: gnu: r-riboprofiling: Update to 1.20.0. * gnu/packages/bioconductor.scm (r-riboprofiling): Update to 1.20.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index b603b7cdc7..6accb9549a 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2110,14 +2110,14 @@ datasets.") (define-public r-riboprofiling (package (name "r-riboprofiling") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RiboProfiling" version)) (sha256 (base32 - "0s30m96dbbrzbywz3wai5ar0nsshb16lq101nyl20w1bk7sk2bha")))) + "112071w7aw7cwckipq0dll1lssl7pwafma4v9jj9sx12rjcj57xg")))) (properties `((upstream-name . "RiboProfiling"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 3813c9fe5658873bc59bcca30717f38b12fbdb8a Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:48:27 +0100 Subject: gnu: r-riboseqr: Update to 1.24.0. * gnu/packages/bioconductor.scm (r-riboseqr): Update to 1.24.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 6accb9549a..773cba7eb6 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2151,14 +2151,14 @@ assessment, principal component analysis on codon coverage.") (define-public r-riboseqr (package (name "r-riboseqr") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "riboSeqR" version)) (sha256 (base32 - "04a4dkmacd6xy55m84amxa0fspbc4kgg9r9k7bc3wrxswk77ccxk")))) + "07i64gch14rsbjlfv17s689wzlqbi7hcqhcw21pp6cw8bvhvd5xr")))) (properties `((upstream-name . "riboSeqR"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From d27dfbf7f91f88786043b157c24ad3bf351a53e4 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:48:36 +0100 Subject: gnu: r-ctc: Update to 1.64.0. * gnu/packages/bioconductor.scm (r-ctc): Update to 1.64.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 773cba7eb6..e5235d6289 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2254,14 +2254,14 @@ information and producing various plots and statistics.") (define-public r-ctc (package (name "r-ctc") - (version "1.62.0") + (version "1.64.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ctc" version)) (sha256 (base32 - "0lv126xj092hps3f3dsv7hasdyy26wcx8npl9idq2l4h9addk6v6")))) + "1nwlphbfba3w8ixck02k5c84qm4flnp9fd68li0jn5a08qi9gmyp")))) (build-system r-build-system) (propagated-inputs `(("r-amap" ,r-amap))) (home-page "https://bioconductor.org/packages/ctc/") -- cgit v1.2.3 From c97bcfbd787926c39805c959997e5081a98547e4 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:48:39 +0100 Subject: gnu: r-goseq: Update to 1.42.0. * gnu/packages/bioconductor.scm (r-goseq): Update to 1.42.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index e5235d6289..81c0f078fc 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2274,14 +2274,14 @@ trees and clusters to other programs.") (define-public r-goseq (package (name "r-goseq") - (version "1.40.0") + (version "1.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "goseq" version)) (sha256 (base32 - "1iyri4rrchzsn8p6wjxr4k30d3cqx3km5mnd9hkfm5d0s7fjzlym")))) + "18fs3m4kl3zahn42j20rjvxy83irscgqx0dvid7va4majvsib509")))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) -- cgit v1.2.3 From 3dab4570fab4aed88b6e6d01983ebee80a50199b Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:48:42 +0100 Subject: gnu: r-glimma: Update to 2.0.0. * gnu/packages/bioconductor.scm (r-glimma): Update to 2.0.0. --- gnu/packages/bioconductor.scm | 12 ++++++++---- 1 file changed, 8 insertions(+), 4 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 81c0f078fc..16ab91c7b3 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2300,20 +2300,24 @@ defined categories which are over/under represented in RNA-seq data.") (define-public r-glimma (package (name "r-glimma") - (version "1.16.0") + (version "2.0.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Glimma" version)) (sha256 (base32 - "1bxfgwjqb9p400a5a5q6p17kcnl3ddz090llihkfih9kyxii9n4y")))) + "0gy30v30lw27frhmw39pzacqzrv2vwj5rsp6gb3yifllrahdiffv")))) (properties `((upstream-name . "Glimma"))) (build-system r-build-system) (propagated-inputs - `(("r-edger" ,r-edger) + `(("r-deseq2" ,r-deseq2) + ("r-edger" ,r-edger) + ("r-htmlwidgets" ,r-htmlwidgets) ("r-jsonlite" ,r-jsonlite) - ("r-s4vectors" ,r-s4vectors))) + ("r-limma" ,r-limma) + ("r-s4vectors" ,r-s4vectors) + ("r-summarizedexperiment" ,r-summarizedexperiment))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://github.com/Shians/Glimma") -- cgit v1.2.3 From 0ef40b23b60990fecc049c9cc8b5fe977da71f87 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:48:45 +0100 Subject: gnu: r-rots: Update to 1.18.0. * gnu/packages/bioconductor.scm (r-rots): Update to 1.18.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 16ab91c7b3..c70d5a5788 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2333,14 +2333,14 @@ information.") (define-public r-rots (package (name "r-rots") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ROTS" version)) (sha256 (base32 - "1mqhi1rfiw7mhiyify7vm3w17p7sc76wjda3ak6690hrc3gsm3cm")))) + "0qk0gfhgr14g13zlfyf5101b5s8cma7j3r8a92q93h0axy8ka23n")))) (properties `((upstream-name . "ROTS"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 1c9bdfcf3c6cd59781a1380e6ef6ffa0e5759cec Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:48:48 +0100 Subject: gnu: r-plgem: Update to 1.62.0. * gnu/packages/bioconductor.scm (r-plgem): Update to 1.62.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index c70d5a5788..05336e9e26 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2357,14 +2357,14 @@ in omics data.") (define-public r-plgem (package (name "r-plgem") - (version "1.60.0") + (version "1.62.0") (source (origin (method url-fetch) (uri (bioconductor-uri "plgem" version)) (sha256 (base32 - "1fs5nbjnrm7x23y7d9krq56r1kzxka40ca1rs6sq70mn6syhj90a")))) + "039gqwsm1v6q8v8b248nm8g9gnsk379mfx65rbgdmh3chsd8pm8a")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) -- cgit v1.2.3 From 41d6b41feb62fee4892315932d83013a5bf9518d Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:48:52 +0100 Subject: gnu: r-inspect: Update to 1.20.0. * gnu/packages/bioconductor.scm (r-inspect): Update to 1.20.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 05336e9e26..11e0335dd4 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2382,14 +2382,14 @@ genes or proteins in these datasets.") (define-public r-inspect (package (name "r-inspect") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "INSPEcT" version)) (sha256 (base32 - "1yyglkdc3ww2jzswhcxk9g1imydfm39krl87as5l9fbm7mv3vd4z")))) + "1jymvi5mf7vhs58zfh290pacfswgvkw09rmbirmr24kxcgl30483")))) (properties `((upstream-name . "INSPEcT"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 874a774fccc6d8a3cf8a2b1814c4f76d516cdd3d Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:48:55 +0100 Subject: gnu: r-dnabarcodes: Update to 1.20.0. * gnu/packages/bioconductor.scm (r-dnabarcodes): Update to 1.20.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 11e0335dd4..6d0540825c 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2429,14 +2429,14 @@ modeling the rates that determines changes in mature mRNA levels.") (define-public r-dnabarcodes (package (name "r-dnabarcodes") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DNABarcodes" version)) (sha256 (base32 - "03y39hjpkb05fnawy3k797bph1iydi1blmpgyy4244zjgk6rs5x7")))) + "0zzf6xgg6k1gdig8zvpawck2bgmamsc0k43j4pl4xsz9an6dmzbg")))) (properties `((upstream-name . "DNABarcodes"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From a55b1622c5a234509a9d07464535554e4c3f0596 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:48:58 +0100 Subject: gnu: r-ruvseq: Update to 1.24.0. * gnu/packages/bioconductor.scm (r-ruvseq): Update to 1.24.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 6d0540825c..b15759b977 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2458,14 +2458,14 @@ demultiplexed, i.e. assigned to their original reference barcode.") (define-public r-ruvseq (package (name "r-ruvseq") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RUVSeq" version)) (sha256 (base32 - "0yqs9xgyzw3cwb4l7zjl1cjgbsjp05qrqnwyvh7q81wdp7x5p55x")))) + "1anrybyrzpajr5434svyfbaypjai6x0ifsmqvjgimmxq3xqhv0jh")))) (properties `((upstream-name . "RUVSeq"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From bbae34aae7dd202a7fbdb5faad01d47d69929aa4 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:49:01 +0100 Subject: gnu: r-biocneighbors: Update to 1.8.0. * gnu/packages/bioconductor.scm (r-biocneighbors): Update to 1.8.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index b15759b977..b032a12a84 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2486,14 +2486,14 @@ samples.") (define-public r-biocneighbors (package (name "r-biocneighbors") - (version "1.6.0") + (version "1.8.1") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocNeighbors" version)) (sha256 (base32 - "14cyyrwxi82xm5wy6bb1176zg322ll67wjrw9vvi4fhfs1k4wqxy")))) + "0hip1sgi3zkrf8g9bw12alaszivja3difalnybr5s7gvh8qd5sf4")))) (properties `((upstream-name . "BiocNeighbors"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 4217307fb3efb8720cfdde5c97f0d2729a529e9d Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:49:07 +0100 Subject: gnu: r-destiny: Update to 3.4.0. * gnu/packages/bioconductor.scm (r-destiny): Update to 3.4.0. [propagated-inputs]: Remove r-nbconvertr. --- gnu/packages/bioconductor.scm | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index b032a12a84..04a6c16b28 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2553,14 +2553,14 @@ possible, parallelization is achieved using the BiocParallel framework.") (define-public r-destiny (package (name "r-destiny") - (version "3.2.0") + (version "3.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "destiny" version)) (sha256 (base32 - "0ik5vwxz9cci3glwgb5ff03sfyr4sjcp8ckfymlgmlm6fz8cp21n")))) + "1i7f5q02zvpfaxhd76fbw0h1wfgjphyn5hrmrjpvlnv4ardzsir2")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) @@ -2571,7 +2571,6 @@ possible, parallelization is achieved using the BiocParallel framework.") ("r-irlba" ,r-irlba) ("r-knn-covertree" ,r-knn-covertree) ("r-matrix" ,r-matrix) - ("r-nbconvertr" ,r-nbconvertr) ("r-pcamethods" ,r-pcamethods) ("r-proxy" ,r-proxy) ("r-rcpp" ,r-rcpp) -- cgit v1.2.3 From 967fc583929e6494e9e14b9797071a46d3084277 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:49:11 +0100 Subject: gnu: r-savr: Update to 1.28.0. * gnu/packages/bioconductor.scm (r-savr): Update to 1.28.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 04a6c16b28..79e72a48b7 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2597,14 +2597,14 @@ maps.") (define-public r-savr (package (name "r-savr") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "savR" version)) (sha256 (base32 - "17jdnr47ivblfspr4b32z9fds1fqiiwsi2z6r524g1v4944p8w5a")))) + "1vha9b7gndwjzvrzr1hdhv3wc6a1s2n9grxwfd78yb2lkysf4hic")))) (properties `((upstream-name . "savR"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From ff4d080422b334a9d348b84aea9e36ecc9ab47f7 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:49:14 +0100 Subject: gnu: r-chipexoqual: Update to 1.14.0. * gnu/packages/bioconductor.scm (r-chipexoqual): Update to 1.14.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 79e72a48b7..861d647906 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2623,14 +2623,14 @@ Viewer (SAV) files, access data, and generate QC plots.") (define-public r-chipexoqual (package (name "r-chipexoqual") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ChIPexoQual" version)) (sha256 (base32 - "02rsf1rvm0p6dn18zq2a4hpvpd9m2i5rziyi4zm8j43qvs8xhafp")))) + "15r5jgkfwwfqpw4v4q2ddmglm3bfw002nnbnzn1s0v2b1w3bgiag")))) (properties `((upstream-name . "ChIPexoQual"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 43d8db0462321b547837ef23142a57438eb6ab42 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:49:17 +0100 Subject: gnu: r-copynumber: Update to 1.30.0. * gnu/packages/bioconductor.scm (r-copynumber): Update to 1.30.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 861d647906..4a8cab5829 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2663,13 +2663,13 @@ sequencing data.") (define-public r-copynumber (package (name "r-copynumber") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "copynumber" version)) (sha256 (base32 - "1b7v6xijpi2mir49cf83gpadhxm5pnbs6d8q8qga7y06hn9jx6my")))) + "00fyfy3kpz33v1hqisd5m5xdazwjmjrfj8ssbf6p9m3am2ar23gm")))) (build-system r-build-system) (propagated-inputs `(("r-s4vectors" ,r-s4vectors) -- cgit v1.2.3 From 850f4c2a36397fe7e339773dcc859cfcf2b6090e Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:49:20 +0100 Subject: gnu: r-dnacopy: Update to 1.64.0. * gnu/packages/bioconductor.scm (r-dnacopy): Update to 1.64.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 4a8cab5829..bcece712f9 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2686,14 +2686,14 @@ penalized least squares regression method.") (define-public r-dnacopy (package (name "r-dnacopy") - (version "1.62.0") + (version "1.64.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DNAcopy" version)) (sha256 (base32 - "0jg8lr83drzfs5h73c7mk7x99vj99a2p2s1sqjc4gicn927xvhza")))) + "0km5af4iw8a0m6by933lgdi5246jafyfxk6fsqdiwg07v9wxw5hc")))) (properties `((upstream-name . "DNAcopy"))) (build-system r-build-system) (native-inputs `(("gfortran" ,gfortran))) -- cgit v1.2.3 From 939c888dac51c9676bd13a85a8bdd381e1040e1b Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:49:23 +0100 Subject: gnu: r-ebseq: Update to 1.30.0. * gnu/packages/bioconductor.scm (r-ebseq): Update to 1.30.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index bcece712f9..df9cd50d1e 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2786,14 +2786,14 @@ and regression inferences from RNA-sequencing data.") (define-public r-ebseq (package (name "r-ebseq") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "EBSeq" version)) (sha256 (base32 - "0s9r1xxpfm5794ipjm5a5c8gfxicc6arma6f74aaz8zi5y5q9x5f")))) + "1x2489xaqg85v7n3yhqs0nh9ha6dn4m167dkc6akzig4xivwjjny")))) (properties `((upstream-name . "EBSeq"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 37da451316fcc25764cbab7cb371beb75b681d47 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:49:26 +0100 Subject: gnu: r-karyoploter: Update to 1.16.0. * gnu/packages/bioconductor.scm (r-karyoploter): Update to 1.16.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index df9cd50d1e..695bd380db 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2810,13 +2810,13 @@ gene and isoform level using RNA-seq data") (define-public r-karyoploter (package (name "r-karyoploter") - (version "1.14.1") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "karyoploteR" version)) (sha256 (base32 - "1wlnzkq58baqj9854nzf5rbglchb2xy4wsp3s0q8xfq8v0p3baxf")))) + "1agw49mckm3g33igqdp9lr8a4ky8nhivaxrs7d00dvzk0diqwdb2")))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) -- cgit v1.2.3 From 378d67c950f7462430012b924f3a1bd32af7cc7b Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:49:29 +0100 Subject: gnu: r-lpsymphony: Update to 1.18.0. * gnu/packages/bioconductor.scm (r-lpsymphony): Update to 1.18.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 695bd380db..8153775218 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2848,14 +2848,14 @@ coordinates.") (define-public r-lpsymphony (package (name "r-lpsymphony") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "lpsymphony" version)) (sha256 (base32 - "072ikmd267n18hrj7dip4dp1vb5dinj82p3h95n2jaf04h9hwfn4")))) + "0f9qjfv7rp1y3mwscnjz3pph7m40zgz55xcdhyii6k1iw2vyaxx9")))) (build-system r-build-system) (inputs `(("zlib" ,zlib))) -- cgit v1.2.3 From 95b1f3507a4e2ea1ab0acd82e65ab6fc06202a8b Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:49:33 +0100 Subject: gnu: r-ihw: Update to 1.18.0. * gnu/packages/bioconductor.scm (r-ihw): Update to 1.18.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 8153775218..1389b38462 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2878,14 +2878,14 @@ to install interface to SYMPHONY.") (define-public r-ihw (package (name "r-ihw") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "IHW" version)) (sha256 (base32 - "169ir0k1gygdh1wybwa0drdxnhrdrlyzzy0rkygi7jsirn69m74j")))) + "04szg3bj5cjixxcp8j3inmj0fzk2mg8gp2w2b33x0im8ik24qiw0")))) (properties `((upstream-name . "IHW"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From e26b5eefdae5a1ea0ecbb29b630132fbac2d35da Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:49:36 +0100 Subject: gnu: r-icobra: Update to 1.18.0. * gnu/packages/bioconductor.scm (r-icobra): Update to 1.18.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 1389b38462..38b768abbb 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2910,14 +2910,14 @@ independent of the p-value under the null hypothesis.") (define-public r-icobra (package (name "r-icobra") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "iCOBRA" version)) (sha256 (base32 - "0cvklagby3i221dlhyb51cciv0b3ch4a8z0wpm67q5n6n3k0cil1")))) + "0knqvvfi5y53jk8s2g2bqgxnh2pbdf38676fk7pkdp1r2j6cbi3s")))) (properties `((upstream-name . "iCOBRA"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 532b1068563326c5a2279346bd80412e80e39d23 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:49:39 +0100 Subject: gnu: r-mast: Update to 1.16.0. * gnu/packages/bioconductor.scm (r-mast): Update to 1.16.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 38b768abbb..091ba62ed4 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2946,14 +2946,14 @@ interactive exploration of results.") (define-public r-mast (package (name "r-mast") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MAST" version)) (sha256 (base32 - "12d0q2fbq9d5jgyccmfv0cghv282s0j86wjfbnjpdf73fdrp6brr")))) + "11qr7n9i4masqz0yzikddchyn223m8dy6zv461dly07fd43qi9mn")))) (properties `((upstream-name . "MAST"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 38bc0bf808c26f1c6c26234eed6e9ce472de1b24 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:49:42 +0100 Subject: gnu: r-monocle: Update to 2.18.0. * gnu/packages/bioconductor.scm (r-monocle): Update to 2.18.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 091ba62ed4..c03f83f630 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2981,14 +2981,14 @@ single cell assay data.") (define-public r-monocle (package (name "r-monocle") - (version "2.16.0") + (version "2.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "monocle" version)) (sha256 (base32 - "1vziidavlyhixmx6j7lf29qx8xcjwrc9q3x2f63gcff41q3jf9xd")))) + "1k3hwi9aspjy75arigg7i1w7ygf112y12cndibf2bhpz2phzwslx")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) -- cgit v1.2.3 From 8396c45eda8ae61f8ffe404c6a8c7af027c19c48 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:49:45 +0100 Subject: gnu: r-noiseq: Update to 2.34.0. * gnu/packages/bioconductor.scm (r-noiseq): Update to 2.34.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index c03f83f630..20338ee12a 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3100,14 +3100,14 @@ qPCR data, but could be used with other types as well.") (define-public r-noiseq (package (name "r-noiseq") - (version "2.31.0") + (version "2.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "NOISeq" version)) (sha256 (base32 - "0lg3za0km6v9l6dxigbxx6nsx9y6m3dyzh9srngi53s8387vhj33")))) + "08qlavakclgzk345bliam4cfjhsy39n4s6m1biqpq94n9qp00x8f")))) (properties `((upstream-name . "NOISeq"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From bde9dc5b9726eb754612b10648042ab5dee3fab9 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:49:51 +0100 Subject: gnu: r-scone: Update to 1.14.0. * gnu/packages/bioconductor.scm (r-scone): Update to 1.14.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 20338ee12a..97b9f55184 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3165,14 +3165,14 @@ distributions.") (define-public r-scone (package (name "r-scone") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "scone" version)) (sha256 (base32 - "12hcmbpncm0l1yxhm3sgkqqfri7s5qc46ikv5qcj8pw5a42rkx3g")))) + "1lnyxcrw3kn5gi3n59dwdhkqps58cjxfknsjsj53qz5rv8iiqz73")))) (build-system r-build-system) (propagated-inputs `(("r-aroma-light" ,r-aroma-light) -- cgit v1.2.3 From 5c4edeef02552c0e53d7c6ed0a62401b1e8e4f9b Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:49:54 +0100 Subject: gnu: r-geoquery: Update to 2.58.0. * gnu/packages/bioconductor.scm (r-geoquery): Update to 2.58.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 97b9f55184..2164985a8f 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3207,14 +3207,14 @@ high-throughput analyses.") (define-public r-geoquery (package (name "r-geoquery") - (version "2.56.0") + (version "2.58.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GEOquery" version)) (sha256 (base32 - "0sap1dsa3k3qpv5z5y3cimxyhbm8qai87gqn3g1w3hwlcqsss92m")))) + "1jzhgnd404wkz978vbqzwbgixr7yk98c7s9q1fzlyax4f8l0cpi4")))) (properties `((upstream-name . "GEOquery"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From e89966e977693297e513bb03f9a637f5ba7a9e20 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:49:57 +0100 Subject: gnu: r-illuminaio: Update to 0.32.0. * gnu/packages/bioconductor.scm (r-illuminaio): Update to 0.32.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 2164985a8f..dd64a52fcc 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3240,14 +3240,14 @@ the bridge between GEO and BioConductor.") (define-public r-illuminaio (package (name "r-illuminaio") - (version "0.30.0") + (version "0.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "illuminaio" version)) (sha256 (base32 - "0i587r1v5aa25w0jm1zvh7spc1gqmvza49i2kv00g1qzj8whq67c")))) + "1yqm2fqw5ka7qywbal3p7axlwm1r0wibsr33n5xjma1dl9pi8fay")))) (build-system r-build-system) (propagated-inputs `(("r-base64" ,r-base64))) -- cgit v1.2.3 From 0fd830feaacd0fc9e11b253932adb98f9e12e2c0 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:50:00 +0100 Subject: gnu: r-siggenes: Update to 1.64.0. * gnu/packages/bioconductor.scm (r-siggenes): Update to 1.64.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index dd64a52fcc..688395e6dc 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3261,14 +3261,14 @@ files, including IDAT.") (define-public r-siggenes (package (name "r-siggenes") - (version "1.62.0") + (version "1.64.0") (source (origin (method url-fetch) (uri (bioconductor-uri "siggenes" version)) (sha256 (base32 - "0i4y1hgq1ljxkf6sypb6c8yp412a8q5v5z68cx1zrgxnccvp0mfy")))) + "08wi2i6pqx06v13533y3mpli5fb637h0xfwcwy67ya9j2ygypv7w")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) -- cgit v1.2.3 From 50c5fee6b5f11ef3f65f401c1d737b2126b7c587 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:50:03 +0100 Subject: gnu: r-bumphunter: Update to 1.32.0. * gnu/packages/bioconductor.scm (r-bumphunter): Update to 1.32.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 688395e6dc..c36f782549 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3287,14 +3287,14 @@ Bayes Analyses of Microarrays} (EBAM).") (define-public r-bumphunter (package (name "r-bumphunter") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bumphunter" version)) (sha256 (base32 - "04y6spdx89j3bsq2xniqd3sbfmakwc0klbpzjlp1q2xs9kywr4dq")))) + "0hfl820kfxydv5kpgyly7sibv2sp6dqsmc78qm33n81w4z4j0mkk")))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) -- cgit v1.2.3 From 37e09611f2057d2c5a4ca5c337b8bc5513a77d96 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:50:16 +0100 Subject: gnu: r-linnorm: Update to 2.14.0. * gnu/packages/bioconductor.scm (r-linnorm): Update to 2.14.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index c36f782549..127ae364f6 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3457,14 +3457,14 @@ especially Illumina Infinium methylation microarrays.") (define-public r-linnorm (package (name "r-linnorm") - (version "2.12.0") + (version "2.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Linnorm" version)) (sha256 (base32 - "143hdfswp5sda5al1igrm5gyn7a6mp1j7hjm5jsc300335lm3kgp")))) + "1is1kp5av01kqqph16xl7w1dqbyd0q85pgqfv9gqkk8m53635cz3")))) (properties `((upstream-name . "Linnorm"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 2a1a6d74d644adb8867c0d50e4c1e242b9d8f2f6 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:50:19 +0100 Subject: gnu: r-ioniser: Update to 2.14.0. * gnu/packages/bioconductor.scm (r-ioniser): Update to 2.14.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 127ae364f6..62d9ba327f 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3518,14 +3518,14 @@ evaluation of DEG analysis methods.") (define-public r-ioniser (package (name "r-ioniser") - (version "2.12.0") + (version "2.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "IONiseR" version)) (sha256 (base32 - "05fndlblczabva60gn6h0dijqxyn0wknrv8a925fgc4bn415g31w")))) + "0cfa64d3qv881sa9d665rfki91jaz2spg0zfrb24m37948qzk1lx")))) (properties `((upstream-name . "IONiseR"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 67837d4afe96a78b8ef6da829a41a26cb75b3c17 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:50:22 +0100 Subject: gnu: r-varianttools: Update to 1.32.0. * gnu/packages/bioconductor.scm (r-varianttools): Update to 1.32.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 62d9ba327f..5d917b1a70 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3666,14 +3666,14 @@ peak definition in combination with known profile characteristics.") (define-public r-varianttools (package (name "r-varianttools") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "VariantTools" version)) (sha256 (base32 - "0g93rljlmhk1d53z0bgi84i2cn5c3r1dpm8id2pv0nk9ncdh3yxx")))) + "1im4g9p419mikkh4v585yf5f23d13chy67znk4g2mii2i1cd1c89")))) (properties `((upstream-name . "VariantTools"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 9813d24ddf2a512e5893e994c47e0c5e90509a12 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:50:25 +0100 Subject: gnu: r-heatplus: Update to 2.36.0. * gnu/packages/bioconductor.scm (r-heatplus): Update to 2.36.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 5d917b1a70..1e1597960d 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3706,14 +3706,14 @@ gmapR.") (define-public r-heatplus (package (name "r-heatplus") - (version "2.34.0") + (version "2.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Heatplus" version)) (sha256 (base32 - "12nd0h8svx7qydv1shk0gdpvnbixf7qi6zh06881wsmxf5s970rw")))) + "0vp8y0242k6q07yjk4sg2w7mlk5pgzhjgqkxa79c5ypkyp095a8n")))) (properties `((upstream-name . "Heatplus"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From b2084e4d2162813ab3319dcbb43feedaa074710a Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:50:28 +0100 Subject: gnu: r-gosemsim: Update to 2.16.1. * gnu/packages/bioconductor.scm (r-gosemsim): Update to 2.16.1. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 1e1597960d..da5ccf4efb 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3731,14 +3731,14 @@ information about samples and features can be added to the plot.") (define-public r-gosemsim (package (name "r-gosemsim") - (version "2.14.2") + (version "2.16.1") (source (origin (method url-fetch) (uri (bioconductor-uri "GOSemSim" version)) (sha256 (base32 - "02r7m1x6g8bb7q8l0hpvakdzdv5v1nplhx5lbiy798a7c3xg895b")))) + "1hk1626172scja2gr6axy98czblz0zljiqgqaknsv2xj6frhxcgs")))) (properties `((upstream-name . "GOSemSim"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 33c905b9c07ce815beb8bfffff1e695bfbdf90ec Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:50:31 +0100 Subject: gnu: r-anota: Update to 1.38.0. * gnu/packages/bioconductor.scm (r-anota): Update to 1.38.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index da5ccf4efb..8af709e280 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3760,14 +3760,14 @@ sets of GO terms, gene products and gene clusters.") (define-public r-anota (package (name "r-anota") - (version "1.36.0") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "anota" version)) (sha256 (base32 - "1ind5cyq85l63xpqmg2n9rg805s5amh48iiw05zqr8kih6hlilpm")))) + "02s061q6dfw1czppqiklb0fz6q0mjyqgxg6926b2dpqpz8hv690x")))) (build-system r-build-system) (propagated-inputs `(("r-multtest" ,r-multtest) -- cgit v1.2.3 From 7dabc6298f279b3853100c79272d896190b05114 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:50:34 +0100 Subject: gnu: r-sigpathway: Update to 1.58.0. * gnu/packages/bioconductor.scm (r-sigpathway): Update to 1.58.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 8af709e280..d7a942266c 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3791,14 +3791,14 @@ the data set is suitable for such analysis.") (define-public r-sigpathway (package (name "r-sigpathway") - (version "1.56.0") + (version "1.58.0") (source (origin (method url-fetch) (uri (bioconductor-uri "sigPathway" version)) (sha256 (base32 - "0a79sdvag80p7xcdz8mp8wiby36yxmappzycfd2rp36v9drjk0h5")))) + "1fkw0ss471pllqxyjyif5lr35cr8sqpx31x0ccjp85lm3blws72l")))) (properties `((upstream-name . "sigPathway"))) (build-system r-build-system) (home-page "https://www.pnas.org/cgi/doi/10.1073/pnas.0506577102") -- cgit v1.2.3 From d68a9ffa68e49fdd6f3413804b0cfa6963191faf Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:50:37 +0100 Subject: gnu: r-fgsea: Update to 1.16.0. * gnu/packages/bioconductor.scm (r-fgsea): Update to 1.16.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index d7a942266c..ea497d1808 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3813,14 +3813,14 @@ phenotype of interest.") (define-public r-fgsea (package (name "r-fgsea") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "fgsea" version)) (sha256 (base32 - "0zbjj8al1ps7immxixsn5g8lvbmpmxvqwqbpdgsicxp00gb9bybc")))) + "0jmkkayabx3m0lyyc2mxd4vdvv7gv7fbk1r884gplnf2zgsx068n")))) (build-system r-build-system) (propagated-inputs `(("r-bh" ,r-bh) -- cgit v1.2.3 From aeb1d56f8f5855ed13fa3c11658d618b80ca0725 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:50:40 +0100 Subject: gnu: r-dose: Update to 3.16.0. * gnu/packages/bioconductor.scm (r-dose): Update to 3.16.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index ea497d1808..53cdcedd77 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3845,14 +3845,14 @@ to multiple hypothesis correction.") (define-public r-dose (package (name "r-dose") - (version "3.14.0") + (version "3.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DOSE" version)) (sha256 (base32 - "1j0wcg7w2ns3ag9d272cqlg3j62ag2xnc5gfsjl6g2ij5xkvylb8")))) + "149hpf690jls5r5g84sh2hqs10qbqi94syhxfv8n2f800fk7lgy4")))) (properties `((upstream-name . "DOSE"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From b7d1ea7bfac41425620b293c40c242f765f69d51 Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Wed, 18 Nov 2020 16:59:15 +0100 Subject: gnu: Add r-shadowtext. * gnu/packages/cran.scm (r-shadowtext): New variable. --- gnu/packages/cran.scm | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 25bb9d75ec..0d5256a996 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -560,6 +560,30 @@ generalized linear, additive and interaction models to potentially high-dimensional data.") (license license:gpl2))) +(define-public r-shadowtext + (package + (name "r-shadowtext") + (version "0.0.7") + (source (origin + (method url-fetch) + (uri (cran-uri "shadowtext" version)) + (sha256 + (base32 + "1s1ip8zfr684a3ld7hvf524bhn2j31k6d1wbhh1ni0flsggv2ckf")))) + (properties `((upstream-name . "shadowtext"))) + (build-system r-build-system) + (propagated-inputs + `(("r-ggplot2" ,r-ggplot2) + ("r-scales" ,r-scales))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://github.com/GuangchuangYu/shadowtext/") + (synopsis "Shadow text grob and layer") + (description "This package implements @code{shadowtextGrob()} for +@code{grid} and @code{geom_shadowtext()} layer for @code{ggplot2}. +These functions draw text grob with background shadow.") + (license license:artistic2.0))) + (define-public r-sys (package (name "r-sys") -- cgit v1.2.3 From eb3d17eb99dad918ceba8317eb050a45f9b9eaa5 Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Wed, 18 Nov 2020 16:59:45 +0100 Subject: gnu: r-enrichplot: Update to 1.10.1. * gnu/packages/bioconductor.scm (r-enrichplot): Update to 1.10.1. [propagated-inputs]: Remove r-annotationdbi, r-europepmc, r-ggplotify, r-ggridges, and r-gridextra; add r-magrittr and r-shadowtext. --- gnu/packages/bioconductor.scm | 15 ++++++--------- 1 file changed, 6 insertions(+), 9 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 53cdcedd77..7a06e20446 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3880,32 +3880,29 @@ data.") (define-public r-enrichplot (package (name "r-enrichplot") - (version "1.8.1") + (version "1.10.1") (source (origin (method url-fetch) (uri (bioconductor-uri "enrichplot" version)) (sha256 (base32 - "01m3cp717ldfbz5w3yfywvjg6sfjzz7s3vlk7w268lmmcg6g6bz7")))) + "0h0455plh8bxnpizgfxij9625ff32rs1a51yzpnrf5hl27xbfkdd")))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-cowplot" ,r-cowplot) + `(("r-cowplot" ,r-cowplot) ("r-dose" ,r-dose) - ("r-europepmc" ,r-europepmc) ("r-ggplot2" ,r-ggplot2) - ("r-ggplotify" ,r-ggplotify) ("r-ggraph" ,r-ggraph) - ("r-ggridges" ,r-ggridges) ("r-gosemsim" ,r-gosemsim) - ("r-gridextra" ,r-gridextra) ("r-igraph" ,r-igraph) + ("r-magrittr" ,r-magrittr) ("r-plyr" ,r-plyr) ("r-purrr" ,r-purrr) ("r-rcolorbrewer" ,r-rcolorbrewer) ("r-reshape2" ,r-reshape2) - ("r-scatterpie" ,r-scatterpie))) + ("r-scatterpie" ,r-scatterpie) + ("r-shadowtext" ,r-shadowtext))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://github.com/GuangchuangYu/enrichplot") -- cgit v1.2.3 From 3fd84a461d60429f6a7f3efd4a4067292decb6aa Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:50:46 +0100 Subject: gnu: r-clusterprofiler: Update to 3.18.0. * gnu/packages/bioconductor.scm (r-clusterprofiler): Update to 3.18.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 7a06e20446..6b23933dbc 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3916,14 +3916,14 @@ All the visualization methods are developed based on ggplot2 graphics.") (define-public r-clusterprofiler (package (name "r-clusterprofiler") - (version "3.16.1") + (version "3.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "clusterProfiler" version)) (sha256 (base32 - "11zsgb8wbdv8r4c04iczz4aala4yw4ai7rz8igdzz87c0940nxkb")))) + "07xkc515gp9j4axg0qh39ni65mcbjgxmzjh5wxd86w64lz7xh8b9")))) (properties `((upstream-name . "clusterProfiler"))) (build-system r-build-system) -- cgit v1.2.3 From 4f82931de4634cee6a07fb024b961ed8284ab3d8 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:50:50 +0100 Subject: gnu: r-mlinterfaces: Update to 1.70.0. * gnu/packages/bioconductor.scm (r-mlinterfaces): Update to 1.70.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 6b23933dbc..ac1da656c4 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3953,14 +3953,14 @@ profiles (GO and KEGG) of gene and gene clusters.") (define-public r-mlinterfaces (package (name "r-mlinterfaces") - (version "1.68.0") + (version "1.70.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MLInterfaces" version)) (sha256 (base32 - "0x3mnvb5a6kri4q5w0wfmx02v79my08zhmkaik9pqlprd7y5wynq")))) + "1j920h1657rc5agd1vrkzk126npfhw7pzr7p7gwg4i0h0wv25q3r")))) (properties `((upstream-name . "MLInterfaces"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From c47a8cd9e1a0ade649853e9344dbd7881830c9e5 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:50:56 +0100 Subject: gnu: r-a4core: Update to 1.38.0. * gnu/packages/bioconductor.scm (r-a4core): Update to 1.38.0. --- gnu/packages/bioconductor.scm | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index ac1da656c4..4edc615c6c 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4030,19 +4030,21 @@ It allows searching of biological metadata using various criteria.") (define-public r-a4core (package (name "r-a4core") - (version "1.36.0") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "a4Core" version)) (sha256 (base32 - "1hn9lkaib1bx5n52as882f8zwsln8w40sx8hxbrnimjvgfxrbvnp")))) + "13mzhn92kqpbn58zmh96f6frkm85sv9137mldfzaljf6snk0spg2")))) (properties `((upstream-name . "a4Core"))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) ("r-glmnet" ,r-glmnet))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/a4Core") (synopsis "Automated Affymetrix array analysis core package") (description -- cgit v1.2.3 From fa51705f19a6190f81a0b479871864b9f055cef8 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:50:59 +0100 Subject: gnu: r-a4classif: Update to 1.38.0. * gnu/packages/bioconductor.scm (r-a4classif): Update to 1.38.0. --- gnu/packages/bioconductor.scm | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 4edc615c6c..ac19230b9d 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4055,24 +4055,26 @@ arrays.") (define-public r-a4classif (package (name "r-a4classif") - (version "1.36.0") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "a4Classif" version)) (sha256 (base32 - "0bj8m4nprw3maahd1qx9jjdxfip9ihbbpydbzwjxn6dlgw2i8mcr")))) + "03fln0x1am5fqhj4fpkx1yq58paqha086bhhr8az8j0vsq1r7wcz")))) (properties `((upstream-name . "a4Classif"))) (build-system r-build-system) (propagated-inputs `(("r-a4core" ,r-a4core) ("r-a4preproc" ,r-a4preproc) + ("r-biobase" ,r-biobase) ("r-glmnet" ,r-glmnet) - ("r-mlinterfaces" ,r-mlinterfaces) ("r-pamr" ,r-pamr) ("r-rocr" ,r-rocr) ("r-varselrf" ,r-varselrf))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/a4Classif/") (synopsis "Automated Affymetrix array analysis classification package") (description -- cgit v1.2.3 From 85155e2ed9ed12d8955507b0a860af27ba7bb84b Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:51:02 +0100 Subject: gnu: r-a4preproc: Update to 1.38.0. * gnu/packages/bioconductor.scm (r-a4preproc): Update to 1.38.0. --- gnu/packages/bioconductor.scm | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index ac19230b9d..bae7932b5d 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4085,18 +4085,21 @@ Affymetrix arrays.") (define-public r-a4preproc (package (name "r-a4preproc") - (version "1.36.0") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "a4Preproc" version)) (sha256 (base32 - "1hy3jvhdjyjzzmw5wkil3cs26hvqnb056r09x0p2bjg5sc9hh8b8")))) + "1j8jhal83x1xpmsaw8iwv2r32i1ghzm6n0ipjk06yqa9f6zb7f7i")))) (properties `((upstream-name . "a4Preproc"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi))) + `(("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/a4Preproc/") (synopsis "Automated Affymetrix array analysis preprocessing package") (description -- cgit v1.2.3 From 2fb8298c801087d93c7ea8349864b7886b2b8981 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:51:05 +0100 Subject: gnu: r-a4reporting: Update to 1.38.0. * gnu/packages/bioconductor.scm (r-a4reporting): Update to 1.38.0. --- gnu/packages/bioconductor.scm | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index bae7932b5d..b3f203c42d 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4110,19 +4110,20 @@ is used for preprocessing the arrays.") (define-public r-a4reporting (package (name "r-a4reporting") - (version "1.36.0") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "a4Reporting" version)) (sha256 (base32 - "1jhlxqwfbgflcyzy9gyxznzcadj9zxchl3lfdlc4ffm0hwz5jl2f")))) + "1jx4ym3hyix8gwr8d2r38w1wj7siv6ynzhwanczcjf1naws3dqpy")))) (properties `((upstream-name . "a4Reporting"))) (build-system r-build-system) (propagated-inputs - `(("r-annaffy" ,r-annaffy) - ("r-xtable" ,r-xtable))) + `(("r-xtable" ,r-xtable))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/a4Reporting/") (synopsis "Automated Affymetrix array analysis reporting package") (description -- cgit v1.2.3 From 564d4279f227fa1c5d865fe30ba50e726a806c3a Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:51:08 +0100 Subject: gnu: r-a4base: Update to 1.38.0. * gnu/packages/bioconductor.scm (r-a4base): Update to 1.38.0. --- gnu/packages/bioconductor.scm | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index b3f203c42d..9f641ec37a 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4134,21 +4134,20 @@ provides reporting features.") (define-public r-a4base (package (name "r-a4base") - (version "1.36.0") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "a4Base" version)) (sha256 (base32 - "0b7fy1wcydb9z43wb1663skswvhivn7ji15g00gqcshwkkiq4x02")))) + "0bqagjmg3yjmdzxv4j7685jjhgb261pq60b5qkfffr1lfnz27lsp")))) (properties `((upstream-name . "a4Base"))) (build-system r-build-system) (propagated-inputs `(("r-a4core" ,r-a4core) ("r-a4preproc" ,r-a4preproc) ("r-annaffy" ,r-annaffy) - ("r-annotationdbi" ,r-annotationdbi) ("r-biobase" ,r-biobase) ("r-genefilter" ,r-genefilter) ("r-glmnet" ,r-glmnet) -- cgit v1.2.3 From 68efaafe328a941ecd8a9870926eb931cb624442 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:51:11 +0100 Subject: gnu: r-a4: Update to 1.38.0. * gnu/packages/bioconductor.scm (r-a4): Update to 1.38.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 9f641ec37a..b394ffce43 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4165,14 +4165,14 @@ Affymetrix arrays.") (define-public r-a4 (package (name "r-a4") - (version "1.36.0") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "a4" version)) (sha256 (base32 - "1rzxg1h48jnlwqfjyyqzz6i3zlkfzc0i714rfplry7dyni6asgr7")))) + "12q09dhxjl7yrd5m2y7a03kv5614dp144ajmskp5q9x2gvz30f79")))) (build-system r-build-system) (propagated-inputs `(("r-a4base" ,r-a4base) -- cgit v1.2.3 From 8816139e8422063eaba9b8022b667445fac73aa7 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:51:14 +0100 Subject: gnu: r-abseqr: Update to 1.8.0. * gnu/packages/bioconductor.scm (r-abseqr): Update to 1.8.0. --- gnu/packages/bioconductor.scm | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index b394ffce43..011cc0fdd0 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4190,19 +4190,18 @@ Affymetrix arrays.") (define-public r-abseqr (package (name "r-abseqr") - (version "1.6.0") + (version "1.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "abseqR" version)) (sha256 (base32 - "0pzyfn0jv41rja6l4jbgwgsqy0q1d3kz23m9m6pc67p2a231i9c5")))) + "0lh7kcsp3yb3s8s8j6w9k1by8i16q7r2a49z8y1xjmkcb2klsi3f")))) (properties `((upstream-name . "abseqR"))) (build-system r-build-system) (inputs - `(("pandoc" ,pandoc) - ("pandoc-citeproc" ,pandoc-citeproc))) + `(("pandoc" ,pandoc))) (propagated-inputs `(("r-biocparallel" ,r-biocparallel) ("r-biocstyle" ,r-biocstyle) -- cgit v1.2.3 From d5dcf1bb4bdd13cfaaaf526c8f62ea410a90bea8 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:51:17 +0100 Subject: gnu: r-bacon: Update to 1.18.0. * gnu/packages/bioconductor.scm (r-bacon): Update to 1.18.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 011cc0fdd0..344c0dfdfa 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4238,14 +4238,14 @@ further downstream analysis on its output.") (define-public r-bacon (package (name "r-bacon") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bacon" version)) (sha256 (base32 - "066b9vyp8ivnzm9741mb5z763a7z40ar9m8w31yw84fjiv01v3dl")))) + "0cv4zhs075mz8c5gdwhr45v14fb1lyi3rlwjfqyz15dmmnzlxw47")))) (build-system r-build-system) (propagated-inputs `(("r-biocparallel" ,r-biocparallel) -- cgit v1.2.3 From 41071edcac219ee17b2d5a4e76b92468c182bf68 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:51:21 +0100 Subject: gnu: r-rgadem: Update to 2.38.0. * gnu/packages/bioconductor.scm (r-rgadem): Update to 2.38.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 344c0dfdfa..a32a81a46e 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4265,14 +4265,14 @@ fitting a three-component normal mixture on z-scores.") (define-public r-rgadem (package (name "r-rgadem") - (version "2.36.0") + (version "2.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "rGADEM" version)) (sha256 (base32 - "14mflbwhhj9f3b05zdlsdjwxmpb120r23fy306qkvxjprdqn4sz8")))) + "0x13glgkcnjg4qsn0v0qgzy6bgmghqpvgwfww2ha641p0c5i9qzw")))) (properties `((upstream-name . "rGADEM"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From a2bae167801cb9cc8f29300709b0463ac98dc099 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:51:24 +0100 Subject: gnu: r-motifdb: Update to 1.32.0. * gnu/packages/bioconductor.scm (r-motifdb): Update to 1.32.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index a32a81a46e..0b33e11d93 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4323,12 +4323,12 @@ distributions, modules and filter motifs.") (define-public r-motifdb (package (name "r-motifdb") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MotifDb" version)) (sha256 - (base32 "0ixmdqp0s0xv9ar85n2wirbbssrzlk8a892wam55jdsf9y8aabkm")))) + (base32 "0gfk1dgw7gd2y4cnmfdzpzjqkvvikcwx20h0fp7aiq8f0zfwlav5")))) (properties `((upstream-name . "MotifDb"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 301e549c223e9af89b2c7ccbca73ce3edacd6b9b Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:51:27 +0100 Subject: gnu: r-motifbreakr: Update to 2.4.0. * gnu/packages/bioconductor.scm (r-motifbreakr): Update to 2.4.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 0b33e11d93..a30053c996 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4350,12 +4350,12 @@ frequency matrices from nine public sources, for multiple organisms.") (define-public r-motifbreakr (package (name "r-motifbreakr") - (version "2.2.0") + (version "2.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "motifbreakR" version)) (sha256 - (base32 "09czgmyjcycsvyvadpjddwwvqvxzd0ba3zhczh4mqc09gwa6vhlm")))) + (base32 "0nni6i7h51kz0ch8ls9c9jzd7fjmc9wsavp11hx6w6bmhnh3k4n7")))) (properties `((upstream-name . "motifbreakR"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 4b4cd2b8a2293076fbdcb23ec0ffa618ebd5f1aa Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:51:31 +0100 Subject: gnu: r-motifstack: Update to 1.34.0. * gnu/packages/bioconductor.scm (r-motifstack): Update to 1.34.0. --- gnu/packages/bioconductor.scm | 7 ++----- 1 file changed, 2 insertions(+), 5 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index a30053c996..684916643c 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4401,24 +4401,21 @@ Bioconductor.") (define-public r-motifstack (package (name "r-motifstack") - (version "1.32.1") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "motifStack" version)) (sha256 (base32 - "02vmkgn36n5xpmizy33znlzgmi3w5hnhsibgisbnhwwgxpkrwpcd")))) + "1psqpdbgbad31bd8hg5bl62qi5s9rl75nzm85igfpxar3zwwxjlb")))) (properties `((upstream-name . "motifStack"))) (build-system r-build-system) (propagated-inputs `(("r-ade4" ,r-ade4) ("r-biostrings" ,r-biostrings) ("r-ggplot2" ,r-ggplot2) - ("r-grimport2" ,r-grimport2) ("r-htmlwidgets" ,r-htmlwidgets) - ("r-motiv" ,r-motiv) - ("r-scales" ,r-scales) ("r-xml" ,r-xml))) (native-inputs `(("r-knitr" ,r-knitr))) -- cgit v1.2.3 From 392806183d3dc055adacefe3a62dd9bf524d9db9 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:51:33 +0100 Subject: gnu: r-genomicscores: Update to 2.2.0. * gnu/packages/bioconductor.scm (r-genomicscores): Update to 2.2.0. --- gnu/packages/bioconductor.scm | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 684916643c..718e2d0c00 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4432,20 +4432,22 @@ type and symbol colors.") (define-public r-genomicscores (package (name "r-genomicscores") - (version "2.0.0") + (version "2.2.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicScores" version)) (sha256 (base32 - "0si2lgc37mkah4w990q1q2bf8xmshxj7cbx92bcrp0zaipjr96bb")))) + "1492xirsgag2dsr6ys9wm3a65sq826p9hcdg3b4dm1wbxgdfx6jr")))) (properties `((upstream-name . "GenomicScores"))) (build-system r-build-system) (propagated-inputs `(("r-annotationhub" ,r-annotationhub) ("r-biobase" ,r-biobase) + ("r-biocfilecache" ,r-biocfilecache) ("r-biocgenerics" ,r-biocgenerics) + ("r-biocmanager" ,r-biocmanager) ("r-biostrings" ,r-biostrings) ("r-delayedarray" ,r-delayedarray) ("r-genomeinfodb" ,r-genomeinfodb) -- cgit v1.2.3 From 2ba61c67aa61994910ef22ee14179b4a1a5aaf2a Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:51:36 +0100 Subject: gnu: r-atacseqqc: Update to 1.14.4. * gnu/packages/bioconductor.scm (r-atacseqqc): Update to 1.14.4. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 718e2d0c00..8441a84be2 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4469,14 +4469,14 @@ position-specific scores within R and Bioconductor.") (define-public r-atacseqqc (package (name "r-atacseqqc") - (version "1.12.5") + (version "1.14.4") (source (origin (method url-fetch) (uri (bioconductor-uri "ATACseqQC" version)) (sha256 (base32 - "1103daz82k97vzmxjmf7jwm2nd3w8i0jwplrsi9996bkih11qwbf")))) + "04sn0zl4m60i5jvqz5rmhc4qwcgrhk6rhznrygmm93k9v363mbn9")))) (properties `((upstream-name . "ATACseqQC"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From c3b69d63334acae645cb635ea024b4ecab4c7966 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:51:39 +0100 Subject: gnu: r-gofuncr: Update to 1.10.0. * gnu/packages/bioconductor.scm (r-gofuncr): Update to 1.10.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 8441a84be2..b0256999fd 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4516,14 +4516,14 @@ footprints.") (define-public r-gofuncr (package (name "r-gofuncr") - (version "1.8.0") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GOfuncR" version)) (sha256 (base32 - "1ixjkqb9wpwqfzxsg0h96c6fa63wrk72sfh6x4pq0kpyrcc0ind1")))) + "1ah4v2jj508wjsmrncw58wjq2cyris7bnzfw6kr7jp9n4dvn33mq")))) (properties `((upstream-name . "GOfuncR"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 8a7f7112f1b6ec126e7e18b6fdad4b6ab62ab431 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:51:43 +0100 Subject: gnu: r-abaenrichment: Update to 1.20.0. * gnu/packages/bioconductor.scm (r-abaenrichment): Update to 1.20.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index b0256999fd..6920c230f5 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4565,14 +4565,14 @@ annotations and ontologies.") (define-public r-abaenrichment (package (name "r-abaenrichment") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ABAEnrichment" version)) (sha256 (base32 - "09ihbgxrhpcz2q7svldhm710a0yrhiqk9p0q0myv11c2w50ymwkw")))) + "0i0214ap9f6lnyawdgcdsds6g3g9qqji3wbn6ln6rs698gjs9w9c")))) (properties `((upstream-name . "ABAEnrichment"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From bc12a4b6604fe71ea784f6d6f20aa37ecd9f2c5d Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:51:46 +0100 Subject: gnu: r-annotationfuncs: Update to 1.40.0. * gnu/packages/bioconductor.scm (r-annotationfuncs): Update to 1.40.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 6920c230f5..f0832c0cfc 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4597,14 +4597,14 @@ the brain using an ontology, both provided by the Allen Brain Atlas project.") (define-public r-annotationfuncs (package (name "r-annotationfuncs") - (version "1.38.0") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AnnotationFuncs" version)) (sha256 (base32 - "1yfsxzn7s1nlc3xz2yj39j6hmdfapc9qj9h0cd71gkaxj53ial7d")))) + "0xsm7741zm81bi4c9hy0zaacnk8a6bahdpc6srqzrbsz0pfzdyhr")))) (properties `((upstream-name . "AnnotationFuncs"))) (build-system r-build-system) -- cgit v1.2.3 From 577915421da9ef5adaa46a1289db63815602bb0b Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:51:49 +0100 Subject: gnu: r-annotationtools: Update to 1.64.0. * gnu/packages/bioconductor.scm (r-annotationtools): Update to 1.64.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index f0832c0cfc..7838a4ae37 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4622,14 +4622,14 @@ different identifieres using the Biocore Data Team data-packages (e.g. (define-public r-annotationtools (package (name "r-annotationtools") - (version "1.62.0") + (version "1.64.0") (source (origin (method url-fetch) (uri (bioconductor-uri "annotationTools" version)) (sha256 (base32 - "1b1yfnknr9vbn4y2mxdfyx57i5jbabhp9pwx8axlg2a7lawkfmdk")))) + "1q3c30hqxjgar3gm8d7h4rw3m7cgc11cgv9q0fwv5abj075cj224")))) (properties `((upstream-name . "annotationTools"))) (build-system r-build-system) -- cgit v1.2.3 From 85c6636bacae4ebe050b2f93b2efef177ef32507 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:51:52 +0100 Subject: gnu: r-allelicimbalance: Update to 1.28.0. * gnu/packages/bioconductor.scm (r-allelicimbalance): Update to 1.28.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 7838a4ae37..a2562fae36 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4647,14 +4647,14 @@ text files).") (define-public r-allelicimbalance (package (name "r-allelicimbalance") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AllelicImbalance" version)) (sha256 (base32 - "0irn4xdlvazdkv0055f45693y6zvqaz7j3vml5xscnh45ls6vmqr")))) + "1hk08kwxjlg2jb59bwv9fbc446pyf6knkscfj757nl6yjf11akbl")))) (properties `((upstream-name . "AllelicImbalance"))) (build-system r-build-system) -- cgit v1.2.3 From ff8b915377ba4f354d7316ef26c934e715e4eeb8 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:51:55 +0100 Subject: gnu: r-aucell: Update to 1.12.0. * gnu/packages/bioconductor.scm (r-aucell): Update to 1.12.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index a2562fae36..5e4bcd00d9 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4690,14 +4690,14 @@ investigation using RNA-seq data.") (define-public r-aucell (package (name "r-aucell") - (version "1.10.0") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AUCell" version)) (sha256 (base32 - "0fgqkgjhf92vkljkwn44lm8cjvzq1lvk80nk6xhsp5q6s5isbmns")))) + "0ibsf3nid27hipr03z7phh0yzwfj8bqza6n6g7wfghpls4l12ipx")))) (properties `((upstream-name . "AUCell"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From ba0bf98dff6823ab6b912d2228c54050828fd421 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:51:58 +0100 Subject: gnu: r-ebimage: Update to 4.32.0. * gnu/packages/bioconductor.scm (r-ebimage): Update to 4.32.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 5e4bcd00d9..886077530e 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4729,14 +4729,14 @@ needed.") (define-public r-ebimage (package (name "r-ebimage") - (version "4.30.0") + (version "4.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "EBImage" version)) (sha256 (base32 - "13amrbh545hwk7sygndzyv7wpa0m2y0lzlwj89jm1xm62x577w9v")))) + "0qi8bbix5bjahs73ljhfvidlbj8hz5m5j0sb9cjxlngnnldbh4ww")))) (properties `((upstream-name . "EBImage"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 65ba4ba5f1c69469df6ca5b8b4907bd4f5f2db25 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:52:01 +0100 Subject: gnu: r-yamss: Update to 1.16.0. * gnu/packages/bioconductor.scm (r-yamss): Update to 1.16.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 886077530e..129f6edede 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4768,14 +4768,14 @@ visualization with image data.") (define-public r-yamss (package (name "r-yamss") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "yamss" version)) (sha256 (base32 - "00x2lnssgzbmhy5bb2m0f8rq2nsz3lb5xlp2vhkcagza39h3xb0c")))) + "0cxzn7j9apjcabbvvii16kn4whwd9khcyz867w5ag3zdxwvg7l7w")))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) -- cgit v1.2.3 From 0836ef6b69a1fb4d26ad3b33bb1d4e32a6f872bd Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:52:04 +0100 Subject: gnu: r-gtrellis: Update to 1.22.0. * gnu/packages/bioconductor.scm (r-gtrellis): Update to 1.22.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 129f6edede..6ca58021fb 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4802,14 +4802,14 @@ analysis.") (define-public r-gtrellis (package (name "r-gtrellis") - (version "1.20.1") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "gtrellis" version)) (sha256 (base32 - "1v2l7r945xx4cf9s8m19csj7716n2ayxy05adkl8zqgxk0gxzqm1")))) + "14mpavkxlp9d1kccwi4b9hi7x8md5j4s1g17ivqsj38lxqjvg5gw")))) (build-system r-build-system) (propagated-inputs `(("r-circlize" ,r-circlize) -- cgit v1.2.3 From 36f3a19ae681af6aa543619349bf93874d9d2c98 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:52:07 +0100 Subject: gnu: r-somaticsignatures: Update to 2.26.0. * gnu/packages/bioconductor.scm (r-somaticsignatures): Update to 2.26.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 6ca58021fb..119ed04345 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4831,14 +4831,14 @@ genomic categories and to add self-defined graphics in the plot.") (define-public r-somaticsignatures (package (name "r-somaticsignatures") - (version "2.24.0") + (version "2.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "SomaticSignatures" version)) (sha256 (base32 - "0d34mss73w1jdnmilk060a1fywlfmqbnlir089q9m3q1p3x0j4c1")))) + "1pwf9ws0klcij27w22p0nh924yp5h2jsidp54ppp7mnx08iv0801")))) (properties `((upstream-name . "SomaticSignatures"))) (build-system r-build-system) -- cgit v1.2.3 From 3d41f0c29724c44dc5315a0e2758b08f89ce2643 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:52:13 +0100 Subject: gnu: r-gcrma: Update to 2.62.0. * gnu/packages/bioconductor.scm (r-gcrma): Update to 2.62.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 119ed04345..12e8d23ca0 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4919,14 +4919,14 @@ provided.") (define-public r-gcrma (package (name "r-gcrma") - (version "2.60.0") + (version "2.62.0") (source (origin (method url-fetch) (uri (bioconductor-uri "gcrma" version)) (sha256 (base32 - "1klbnygc1i5ac1x00bsk0rjw5h5dn6pn65fa3y9r09q47gpy1c5g")))) + "1v1x13iwcv6c9x7r1iz2598rwlyzic67jbqcajg24ib6lcfn9f00")))) (build-system r-build-system) (propagated-inputs `(("r-affy" ,r-affy) -- cgit v1.2.3 From 48aaef23b31b52867791e0666a9ef672841ec2d5 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:52:17 +0100 Subject: gnu: r-simpleaffy: Update to 2.66.0. * gnu/packages/bioconductor.scm (r-simpleaffy): Update to 2.66.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 12e8d23ca0..0a4258f753 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4955,14 +4955,14 @@ gene-specific binding is expected.") (define-public r-simpleaffy (package (name "r-simpleaffy") - (version "2.64.0") + (version "2.66.0") (source (origin (method url-fetch) (uri (bioconductor-uri "simpleaffy" version)) (sha256 (base32 - "040043spblr8v67lkn3nnxhgfmfh2iwaizph4fnms1ik6qz662x7")))) + "04a11dsqd5y4b39nny94acnh0qhdazjc6d1803izza4vrgmw2csb")))) (build-system r-build-system) (propagated-inputs `(("r-affy" ,r-affy) -- cgit v1.2.3 From 94dee0af25a48b0551677d410bfc71dfd77118d7 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:52:20 +0100 Subject: gnu: r-yaqcaffy: Update to 1.50.0. * gnu/packages/bioconductor.scm (r-yaqcaffy): Update to 1.50.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 0a4258f753..bb0714d5d3 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4983,14 +4983,14 @@ generating high resolution journal figures.") (define-public r-yaqcaffy (package (name "r-yaqcaffy") - (version "1.48.0") + (version "1.50.0") (source (origin (method url-fetch) (uri (bioconductor-uri "yaqcaffy" version)) (sha256 (base32 - "1l0cblh9sfrsil15bjya7d8kkas8bj6klj2w3c4384njdsjsjcf0")))) + "18gphcjj15iivrahp52186bvdg07yd2dvrykfjdd4r1vyf33im96")))) (build-system r-build-system) (propagated-inputs `(("r-simpleaffy" ,r-simpleaffy))) -- cgit v1.2.3 From 72476adef557d3d52e837b64b7eb71b79453bccc Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:52:29 +0100 Subject: gnu: r-roar: Update to 1.26.0. * gnu/packages/bioconductor.scm (r-roar): Update to 1.26.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index bb0714d5d3..fcd9b799d1 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5075,14 +5075,14 @@ large RNA-seq experiments.") (define-public r-roar (package (name "r-roar") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "roar" version)) (sha256 (base32 - "069g887migvk70n0377dqr0fk7wjbz3w0asgk42bwhp8xpjfym6f")))) + "0spidrcjnrcli0whkf6h8pa1i9dg9arjbm7b1skxbs6dn2k4yyqw")))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) -- cgit v1.2.3 From 7f71341e5daa3f638f46d81beb6619ee105da239 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:52:32 +0100 Subject: gnu: r-xbseq: Update to 1.22.0. * gnu/packages/bioconductor.scm (r-xbseq): Update to 1.22.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index fcd9b799d1..9c8fbc207a 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5104,14 +5104,14 @@ sites and alignments obtained from standard RNA-seq experiments.") (define-public r-xbseq (package (name "r-xbseq") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "XBSeq" version)) (sha256 (base32 - "13br7x1q6dg8daxahskwq24f09wbxr8kyszl1z7dhc26bid2pvy0")))) + "1dvk2jpsdynqw5071z54yd5j0ddprhc1ppk834cz9liibd72d7vz")))) (properties `((upstream-name . "XBSeq"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From f4e19e62bb54d88c7c8b7e9c67d43929c97a8e48 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:52:35 +0100 Subject: gnu: r-massspecwavelet: Update to 1.56.0. * gnu/packages/bioconductor.scm (r-massspecwavelet): Update to 1.56.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 9c8fbc207a..22cbf14099 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5143,14 +5143,14 @@ genes.") (define-public r-massspecwavelet (package (name "r-massspecwavelet") - (version "1.54.0") + (version "1.56.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MassSpecWavelet" version)) (sha256 (base32 - "0nv1r68g7f1rps6sqaccd4n4x0i19wklvyabhp4b03cdk22gl3nq")))) + "1vvxbxc538raqdsy0x9ln41vjhp2aw1nrh4k35y3s9mhb1jlzzv3")))) (properties `((upstream-name . "MassSpecWavelet"))) (build-system r-build-system) -- cgit v1.2.3 From 1e536c307c5e1652c5276e8b610c9950cdf08ab7 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 3 Dec 2020 02:54:46 +0100 Subject: gnu: Update r-msnbase to 2.16.0. * gnu/packages/bioinformatics.scm (r-msnbase): Update to 2.16.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 5efcfdea11..792640faee 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9870,14 +9870,14 @@ structure (pcaRes) to provide a common interface to the PCA results.") (define-public r-msnbase (package (name "r-msnbase") - (version "2.14.2") + (version "2.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MSnbase" version)) (sha256 (base32 - "17vlv9gh41s1hp043b7j1jfqiw52alh1misjzy1kxl0g90rld00l")))) + "0cvcdmq1glifga5qwv9j3lgj31dcrcc6ql4kkk83jy4y43v2zxlx")))) (properties `((upstream-name . "MSnbase"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From fa2201c10837d06b727b2d9bce37ad04e9fe3dfd Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 3 Dec 2020 22:23:46 +0100 Subject: gnu: Add r-mscoreutils. * gnu/packages/bioconductor.scm (r-mscoreutils): New variable. --- gnu/packages/bioconductor.scm | 31 +++++++++++++++++++++++++++++++ 1 file changed, 31 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 22cbf14099..99f3c467d1 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8829,3 +8829,34 @@ contains high-performing functions operating on rows and columns of are optimized per data type and for subsetted calculations such that both memory usage and processing time is minimized.") (license license:expat))) + +(define-public r-mscoreutils + (package + (name "r-mscoreutils") + (version "1.2.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "MsCoreUtils" version)) + (sha256 + (base32 + "0fa3bcf2cmzf5y8wjs7pnzs26qwgqnrrl4hj4sa4fp9kv8z80630")))) + (properties `((upstream-name . "MsCoreUtils"))) + (build-system r-build-system) + (propagated-inputs + `(("r-mass" ,r-mass) + ("r-rcpp" ,r-rcpp) + ("r-s4vectors" ,r-s4vectors))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://github.com/RforMassSpectrometry/MsCoreUtils") + (synopsis "Core utils for mass spectrometry data") + (description + "This package defines low-level functions for mass spectrometry data and +is independent of any high-level data structures. These functions include +mass spectra processing functions (noise estimation, smoothing, binning), +quantitative aggregation functions (median polish, robust summarisation, +etc.), missing data imputation, data normalisation (quantiles, vsn, etc.) as +well as misc helper functions, that are used across high-level data structure +within the R for Mass Spectrometry packages.") + (license license:artistic2.0))) -- cgit v1.2.3 From a3af40eaf57d4f707c6f6ec2ad346de10201ea63 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:52:38 +0100 Subject: gnu: r-xcms: Update to 3.12.0. * gnu/packages/bioconductor.scm (r-xcms): Update to 3.12.0. [propagated-inputs]: Add r-mscoreutils. --- gnu/packages/bioconductor.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 99f3c467d1..029000fd90 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5167,14 +5167,14 @@ based on @dfn{Continuous Wavelet Transform} (CWT).") (define-public r-xcms (package (name "r-xcms") - (version "3.10.2") + (version "3.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "xcms" version)) (sha256 (base32 - "0sk53jcl7sjrpw2ncdpl8sw1b1j9mizlrj517rinr1qrbm6lsn8f")))) + "17kyybj093mj0g2sbfmjp19mmkww4w025n6zc0hbznqb94vkc8fv")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) @@ -5183,6 +5183,7 @@ based on @dfn{Continuous Wavelet Transform} (CWT).") ("r-iranges" ,r-iranges) ("r-lattice" ,r-lattice) ("r-massspecwavelet" ,r-massspecwavelet) + ("r-mscoreutils" ,r-mscoreutils) ("r-msnbase" ,r-msnbase) ("r-mzr" ,r-mzr) ("r-plyr" ,r-plyr) -- cgit v1.2.3 From dc7c6368edd3441705e44162b9b8e7e3cc780dc9 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:52:41 +0100 Subject: gnu: r-wrench: Update to 1.8.0. * gnu/packages/bioconductor.scm (r-wrench): Update to 1.8.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 029000fd90..f9ac706ffa 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5207,14 +5207,14 @@ data for high-throughput, untargeted analyte profiling.") (define-public r-wrench (package (name "r-wrench") - (version "1.6.0") + (version "1.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Wrench" version)) (sha256 (base32 - "05dyk3yvbqrzvinv3ig8ad9wffwr14z715cicsbxwxpv5lq84wx6")))) + "01z7rd9fn6cpab3dxgwfpfjlq6vsqb8jhbzvhcqn9v2vqc2pridx")))) (properties `((upstream-name . "Wrench"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 397bcd2ccdd3f7265030acd046a75c7e0e322365 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:52:44 +0100 Subject: gnu: r-wiggleplotr: Update to 1.14.0. * gnu/packages/bioconductor.scm (r-wiggleplotr): Update to 1.14.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index f9ac706ffa..39d8998b72 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5233,14 +5233,14 @@ that arising from 16s metagenomic surveys.") (define-public r-wiggleplotr (package (name "r-wiggleplotr") - (version "1.12.1") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "wiggleplotr" version)) (sha256 (base32 - "1wknigh1md3w4h68caqlpq945maipdkpmw10hc2rlx4nbbpcnawp")))) + "1k4wlh5ayb1w4dr6dydqfgm3415qhsfmshmi6zjyyhhkd2626vad")))) (build-system r-build-system) (propagated-inputs `(("r-assertthat" ,r-assertthat) -- cgit v1.2.3 From ba53681a469aad12235652ecfd8693bc77d2435c Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:52:47 +0100 Subject: gnu: r-widgettools: Update to 1.68.0. * gnu/packages/bioconductor.scm (r-widgettools): Update to 1.68.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 39d8998b72..2496ff36ab 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5267,14 +5267,14 @@ visualization of exonic read coverage.") (define-public r-widgettools (package (name "r-widgettools") - (version "1.66.0") + (version "1.68.0") (source (origin (method url-fetch) (uri (bioconductor-uri "widgetTools" version)) (sha256 (base32 - "0lrdpsgm9r7yfyyj5crvb7px4hrghxhmiic4iissz40slbfyvilx")))) + "172f0pmsspd9lss557cmxzjfsbansimjyhwdiahg8pqrayhwvf2w")))) (properties `((upstream-name . "widgetTools"))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/widgetTools/") -- cgit v1.2.3 From d176ad34d757d5f8bc26ab3399075b32bbcbe298 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:52:50 +0100 Subject: gnu: r-webbioc: Update to 1.62.0. * gnu/packages/bioconductor.scm (r-webbioc): Update to 1.62.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 2496ff36ab..2a730502ea 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5288,14 +5288,14 @@ widgets in R.") (define-public r-webbioc (package (name "r-webbioc") - (version "1.60.0") + (version "1.62.0") (source (origin (method url-fetch) (uri (bioconductor-uri "webbioc" version)) (sha256 (base32 - "16376ya5a5x2hwkl1v9y4r7np1drdwm912knnqg2dn90zmrdwr5f")))) + "1nnmr4ddi07x7sy89fgdn7iwz5k4l8n5ca3xjnlbpwxycza793vj")))) (build-system r-build-system) (inputs `(("netpbm" ,netpbm) -- cgit v1.2.3 From 59fafa19f5d3cae3c50c8b67e46215ee88ca7767 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:52:53 +0100 Subject: gnu: r-zfpkm: Update to 1.12.0. * gnu/packages/bioconductor.scm (r-zfpkm): Update to 1.12.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 2a730502ea..d2ef9c8ae2 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5321,14 +5321,14 @@ Currently only Affymetrix oligonucleotide analysis is supported.") (define-public r-zfpkm (package (name "r-zfpkm") - (version "1.10.0") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "zFPKM" version)) (sha256 (base32 - "0scszhfqrgzhglz1a6kxfydq9dx8fqx28j3dypp91y5ah2w6mdys")))) + "1sa7m7mzzr92c9ickial5701414rab233lq1il1sm9yfdkf8s9fm")))) (properties `((upstream-name . "zFPKM"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 9834d1ab3836730cf3308603019b736d0a653013 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:52:57 +0100 Subject: gnu: r-rbowtie2: Update to 1.12.0. * gnu/packages/bioconductor.scm (r-rbowtie2): Update to 1.12.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index d2ef9c8ae2..5205a43dd9 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5350,14 +5350,14 @@ This algorithm is based on the publication by Hart et al., 2013 (Pubmed ID (define-public r-rbowtie2 (package (name "r-rbowtie2") - (version "1.10.1") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rbowtie2" version)) (sha256 (base32 - "19v7wfvrd53j618c1xbiqnlsf2kxw697myryx0vb9s2aspknyzz7")))) + "1pcdcqn82ray73bajjnx5zgs98m56acviq3adbzga0cfqf6wiqx5")))) (properties `((upstream-name . "Rbowtie2"))) (build-system r-build-system) (inputs -- cgit v1.2.3 From d115db7f7d05ddf63ab3b2cc2d503d9135b2e20e Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:53:00 +0100 Subject: gnu: r-progeny: Update to 1.12.0. * gnu/packages/bioconductor.scm (r-progeny): Update to 1.12.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 5205a43dd9..62569063ba 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5375,14 +5375,14 @@ rapid adapter trimming, identification, and read merging.") (define-public r-progeny (package (name "r-progeny") - (version "1.10.0") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "progeny" version)) (sha256 (base32 - "09rq3nf9zm7w9djmx8xc8j3win3597p2v36zqgkhgkjwq5rkjgsh")))) + "00lhzz4plmx5128khs298n6zv9204mhqv548lxxdhaw18b16vwm7")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) -- cgit v1.2.3 From 0067589a9ebeb6d0af2e4e037a36d074b6da9f88 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:53:03 +0100 Subject: gnu: r-arrmnormalization: Update to 1.30.0. * gnu/packages/bioconductor.scm (r-arrmnormalization): Update to 1.30.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 62569063ba..1a499912b7 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5405,14 +5405,14 @@ expression\".") (define-public r-arrmnormalization (package (name "r-arrmnormalization") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ARRmNormalization" version)) (sha256 (base32 - "0zhhvr051fmh6g0bqrl525mkf094j1jnc57j201jlzmvdpkydlpv")))) + "1ximvi0jbwmymx6iy70qfyr9j26x5arlarra9fzs5hq05jif6q95")))) (properties `((upstream-name . "ARRmNormalization"))) (build-system r-build-system) -- cgit v1.2.3 From e65e81d28546dcaa841e3c4cb4354ece003efefa Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:53:06 +0100 Subject: gnu: r-biocfilecache: Update to 1.14.0. * gnu/packages/bioconductor.scm (r-biocfilecache): Update to 1.14.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 1a499912b7..3f46251126 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5428,14 +5428,14 @@ Infinium HumanMethylation 450k assay.") (define-public r-biocfilecache (package (name "r-biocfilecache") - (version "1.12.1") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocFileCache" version)) (sha256 (base32 - "02yayjyliaqxcwqa0n2ccmsfflskqzf0gvdibh2r3nz5bi66imkf")))) + "0r032a033636bxap0vvb02jvjqiynzj9npqd8603qnwmhvvfi5z1")))) (properties `((upstream-name . "BiocFileCache"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 4bc0675de04cbd764c34b09c9237f520e336711a Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:53:09 +0100 Subject: gnu: r-iclusterplus: Update to 1.26.0. * gnu/packages/bioconductor.scm (r-iclusterplus): Update to 1.26.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 3f46251126..02f18b713f 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5460,14 +5460,14 @@ and data files used across sessions.") (define-public r-iclusterplus (package (name "r-iclusterplus") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "iClusterPlus" version)) (sha256 (base32 - "0j987xvxixdz0wnhgp4kgfcgz5jffrcdhmldrgpgv582qmf4r94w")))) + "02ji84dsbn4wir8sim4qy8h57524mnrsq51wxc7n8ybp5x7n9k9q")))) (properties `((upstream-name . "iClusterPlus"))) (build-system r-build-system) (native-inputs `(("gfortran" ,gfortran))) -- cgit v1.2.3 From ea86d93e8c2cc0871d063c6f6b372072929f024a Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:53:12 +0100 Subject: gnu: r-rbowtie: Update to 1.30.0. * gnu/packages/bioconductor.scm (r-rbowtie): Update to 1.30.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 02f18b713f..a6b02deb86 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5490,14 +5490,14 @@ Gaussian distributions.") (define-public r-rbowtie (package (name "r-rbowtie") - (version "1.28.1") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rbowtie" version)) (sha256 (base32 - "0589ggbfx6di42wvqyhnzgrhmb52swr3r5z22w6b8x0z2y7hl8b3")))) + "0rgxqc3sbq7phnrn9a6z361725h4zi2mi985i43n7fi3csif7507")))) (properties `((upstream-name . "Rbowtie"))) (build-system r-build-system) (inputs -- cgit v1.2.3 From ca0271c55064b684dfdba01dcbc6155c6a13e7d3 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:53:15 +0100 Subject: gnu: r-sgseq: Update to 1.24.0. * gnu/packages/bioconductor.scm (r-sgseq): Update to 1.24.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index a6b02deb86..c32700387b 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5515,14 +5515,14 @@ alignment tool.") (define-public r-sgseq (package (name "r-sgseq") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "SGSeq" version)) (sha256 (base32 - "11rxx7abjyga2sdcp4x4z3n8xjx6973sckyzmh9ax6r46kwhxq8c")))) + "1nfhy5kgyz56b6pyxcq8kflqwnhl9nlffszwpqb5fdh5ibz8xbjx")))) (properties `((upstream-name . "SGSeq"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From c36d888f42aa4895fbe14f5a6d9709ef4c8af8e9 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:53:18 +0100 Subject: gnu: r-rhisat2: Update to 1.6.0. * gnu/packages/bioconductor.scm (r-rhisat2): Update to 1.6.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index c32700387b..c049e1dcc6 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5558,14 +5558,14 @@ interpretation.") (define-public r-rhisat2 (package (name "r-rhisat2") - (version "1.4.0") + (version "1.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rhisat2" version)) (sha256 (base32 - "0hhmcdnixkaqx9x9cl2vjaba3ri8m6wkbnbhxjmy51jwqzy2223a")))) + "0f9x2qcazml0zjcgyy0kdphnww4d1m62rn0ijcqlhy1bng6ihwwb")))) (properties `((upstream-name . "Rhisat2"))) (build-system r-build-system) (arguments -- cgit v1.2.3 From 1b4c271970287e4b37390f5bcb4644259b0a383d Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:53:21 +0100 Subject: gnu: r-quasr: Update to 1.30.0. * gnu/packages/bioconductor.scm (r-quasr): Update to 1.30.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index c049e1dcc6..158c10645e 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5598,14 +5598,14 @@ index.") (define-public r-quasr (package (name "r-quasr") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "QuasR" version)) (sha256 (base32 - "0d87ajaaq8a7xgzl820qx5bvxw86ppab8clqk77sj02rfijnvjn8")))) + "032m01q34nnmvbhcb2g3pz2fqmgcw5464m74m1m0h7x9bl04a5k8")))) (properties `((upstream-name . "QuasR"))) (build-system r-build-system) (inputs -- cgit v1.2.3 From d8a7bf768f667562f1186928e273fe122894a8e3 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:53:24 +0100 Subject: gnu: r-rqc: Update to 1.24.0. * gnu/packages/bioconductor.scm (r-rqc): Update to 1.24.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 158c10645e..0b01b90c98 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5645,14 +5645,14 @@ quantification of genomic regions of interest.") (define-public r-rqc (package (name "r-rqc") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rqc" version)) (sha256 (base32 - "1qsm9r6xfsplk8zpf7p0k7fi86l8a74nx963sna8gzig5qgrvnm3")))) + "083c3ql0gndb6y7m9d3rpbkimyw8cj8jyv77mwwjhq49lzwsg6n9")))) (properties `((upstream-name . "Rqc"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 979b1edc526516024cf15248e843e6a070990dc2 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:53:28 +0100 Subject: gnu: r-birewire: Update to 3.22.0. * gnu/packages/bioconductor.scm (r-birewire): Update to 3.22.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 0b01b90c98..16348fbce8 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5688,14 +5688,14 @@ graphics.") (define-public r-birewire (package (name "r-birewire") - (version "3.20.0") + (version "3.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiRewire" version)) (sha256 (base32 - "0y7jb1abnik2y4ivpyqrgfl77rml6fhz88isd54l646ghslwxj0g")))) + "1h9zjjd5krsjpbxlmsbzwx7kbishn0z6mpm8zmrcpmbfrprp38qw")))) (properties `((upstream-name . "BiRewire"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From e78e04d2eea6341a6738261af09f5e7838d6399e Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:53:31 +0100 Subject: gnu: r-multidataset: Update to 1.18.0. * gnu/packages/bioconductor.scm (r-multidataset): Update to 1.18.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 16348fbce8..db6178794c 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5746,14 +5746,14 @@ Markov-Chain-Monte-Carlo is applied to sample the activity states.") (define-public r-multidataset (package (name "r-multidataset") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MultiDataSet" version)) (sha256 (base32 - "0hjnj32m9wwlh2krdpdyl5jk1cakvlgki80z51mabhc62pajzf39")))) + "025gfgn83ancp0khdmq2y4lwm97v5zqnjksi79rr0w175syznx5w")))) (properties `((upstream-name . "MultiDataSet"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 59daf6ed1262b4e44ef68817af204f0e265eed10 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:53:34 +0100 Subject: gnu: r-ropls: Update to 1.22.0. * gnu/packages/bioconductor.scm (r-ropls): Update to 1.22.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index db6178794c..16cb41e03a 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5783,14 +5783,14 @@ packages.") (define-public r-ropls (package (name "r-ropls") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ropls" version)) (sha256 (base32 - "1drww1mr0nira3qplyga6s3mljpjxshjgbn524kzxi0nrfbcvmnx")))) + "1h76s89hsafrkshpkx7vjinfni9lzfpnbfyg3fhkkrwpp1fnwyj5")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) -- cgit v1.2.3 From 26e417063f03ee7cff9841f6c31048ac62239f74 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:53:37 +0100 Subject: gnu: r-biosigner: Update to 1.18.0. * gnu/packages/bioconductor.scm (r-biosigner): Update to 1.18.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 16cb41e03a..7416e3e054 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5821,14 +5821,14 @@ coefficients).") (define-public r-biosigner (package (name "r-biosigner") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biosigner" version)) (sha256 (base32 - "1v760q7hzaybkf2q9230rmr4phi8hglm59qwsjzvncxrhs3dpj06")))) + "1rqfmn9lpaajij9p302dfwv57pm4hw7xn2p7lx7hvpb3psa719xm")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) -- cgit v1.2.3 From 458aa446220eaea7202a965f417cfdea315e0998 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:53:40 +0100 Subject: gnu: r-annotatr: Update to 1.16.0. * gnu/packages/bioconductor.scm (r-annotatr): Update to 1.16.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 7416e3e054..eda4d0c8fb 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5854,14 +5854,14 @@ datasets.") (define-public r-annotatr (package (name "r-annotatr") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "annotatr" version)) (sha256 (base32 - "0z3ydcybd81w543fw8fiblghndx5m28w8qsphh5vqj726i0nj8cl")))) + "0dq67snpqxl9mifljm6zlnkdb0ghjwday0fvcn3i7zmrfszgzyf9")))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) -- cgit v1.2.3 From d764f1e7fef44a577be7c90f7efdd7d399d448b3 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:53:43 +0100 Subject: gnu: r-rsubread: Update to 2.4.2. * gnu/packages/bioconductor.scm (r-rsubread): Update to 2.4.2. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index eda4d0c8fb..c4c7b8ba31 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5895,14 +5895,14 @@ annotations.") (define-public r-rsubread (package (name "r-rsubread") - (version "2.2.6") + (version "2.4.2") (source (origin (method url-fetch) (uri (bioconductor-uri "Rsubread" version)) (sha256 (base32 - "04h79qhq93d8id0rr5xnj9vf82ygwxzdlnck78yv738xd0jjvnpm")))) + "1wczrw5jb69x45hd3rdqqs9vkysdqwlxn9h3kjzn57r4x5q7jrra")))) (properties `((upstream-name . "Rsubread"))) (build-system r-build-system) (inputs `(("zlib" ,zlib))) -- cgit v1.2.3 From d361222d8f60e82ab4da5c99a3ae23b18d35cf2b Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:53:46 +0100 Subject: gnu: r-flowutils: Update to 1.54.0. * gnu/packages/bioconductor.scm (r-flowutils): Update to 1.54.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index c4c7b8ba31..5a1dc09c2b 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5921,14 +5921,14 @@ and to both short and long sequence reads.") (define-public r-flowutils (package (name "r-flowutils") - (version "1.52.0") + (version "1.54.0") (source (origin (method url-fetch) (uri (bioconductor-uri "flowUtils" version)) (sha256 (base32 - "03jj4zyffm9kwzrg4vbsk6clc2v2m95wgalgqwzi31n9a2zyaza4")))) + "1q4g666nd51j24hcp2wxla1bdi77kbfd4i0pxgp7rs2jf7200k09")))) (properties `((upstream-name . "flowUtils"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From a49024e6afad920964a70507f2539edf2b135cfa Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:53:49 +0100 Subject: gnu: r-consensusclusterplus: Update to 1.54.0. * gnu/packages/bioconductor.scm (r-consensusclusterplus): Update to 1.54.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 5a1dc09c2b..54f6b3adb5 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5947,14 +5947,14 @@ and to both short and long sequence reads.") (define-public r-consensusclusterplus (package (name "r-consensusclusterplus") - (version "1.52.0") + (version "1.54.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ConsensusClusterPlus" version)) (sha256 (base32 - "06gq3a95h0km1hzbx1za8q0l7kla3jdzvn6cnfz43ijx4n3dzzcq")))) + "06h85l1mg2kpjprylzz44nhxp64k211plhch5qhg39wp0fk34lfp")))) (properties `((upstream-name . "ConsensusClusterPlus"))) (build-system r-build-system) -- cgit v1.2.3 From c6ccd4fcb1770e2168c66f956d6f071eb5d77719 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:53:52 +0100 Subject: gnu: r-cytolib: Update to 2.2.0. * gnu/packages/bioconductor.scm (r-cytolib): Update to 2.2.0. [native-inputs]: Add pkg-config. --- gnu/packages/bioconductor.scm | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 54f6b3adb5..8e33e27060 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5972,20 +5972,21 @@ cluster count and membership by stability evidence in unsupervised analysis.") (define-public r-cytolib (package (name "r-cytolib") - (version "2.0.3") + (version "2.2.0") (source (origin (method url-fetch) (uri (bioconductor-uri "cytolib" version)) (sha256 (base32 - "123d1wlymq8r8d83as380h1dgw6v4s317acyvp1lsg2cpfp3gslj")))) + "1wylzps7wbvm64k62w5bbi8l74gaqca96psfapxfg6mcac5yz4qw")))) (properties `((upstream-name . "cytolib"))) (build-system r-build-system) (inputs `(("zlib" ,zlib))) (native-inputs - `(("r-knitr" ,r-knitr))) + `(("r-knitr" ,r-knitr) + ("pkg-config" ,pkg-config))) (propagated-inputs `(("r-bh" ,r-bh) ("r-rcpp" ,r-rcpp) -- cgit v1.2.3 From 3f0e93b47b73db8e565bd4182310b9c59229e497 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:53:55 +0100 Subject: gnu: r-flowcore: Update to 2.2.0. * gnu/packages/bioconductor.scm (r-flowcore): Update to 2.2.0. [propagated-inputs]: Add r-s4vectors. --- gnu/packages/bioconductor.scm | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 8e33e27060..d4fb0b2a7e 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6004,14 +6004,14 @@ interact with gated cytometry data.") (define-public r-flowcore (package (name "r-flowcore") - (version "2.0.1") + (version "2.2.0") (source (origin (method url-fetch) (uri (bioconductor-uri "flowCore" version)) (sha256 (base32 - "1xalndmfidfzqwlppdanx7cnm4ysznq21ingmykhxni86s42kd8p")))) + "001ickrl2asdl0zwpdjqkl1w7137nzxbryamxihgya394jw73xr8")))) (properties `((upstream-name . "flowCore"))) (build-system r-build-system) (propagated-inputs @@ -6022,7 +6022,8 @@ interact with gated cytometry data.") ("r-matrixstats" ,r-matrixstats) ("r-rcpp" ,r-rcpp) ("r-rcpparmadillo" ,r-rcpparmadillo) - ("r-rprotobuflib" ,r-rprotobuflib))) + ("r-rprotobuflib" ,r-rprotobuflib) + ("r-s4vectors" ,r-s4vectors))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/flowCore") -- cgit v1.2.3 From 2cd78131cc9e1bf1c861fae27f8cef2f035cf432 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:53:58 +0100 Subject: gnu: r-flowmeans: Update to 1.50.0. * gnu/packages/bioconductor.scm (r-flowmeans): Update to 1.50.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index d4fb0b2a7e..1432f6b867 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6036,14 +6036,14 @@ with flow cytometry data.") (define-public r-flowmeans (package (name "r-flowmeans") - (version "1.48.0") + (version "1.50.0") (source (origin (method url-fetch) (uri (bioconductor-uri "flowMeans" version)) (sha256 (base32 - "1sv5vpwm3qdhkn1gdrk3n674harjcni91g63sqzfmybiwq8dlym7")))) + "02y5b3iqjlqjlxrqq0l24dr68sjaniz26jqf14cnnwz1xg5hz734")))) (properties `((upstream-name . "flowMeans"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From eac1eaaa0fbc7aa13ba6c8eb94687c48d3e3786f Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:54:01 +0100 Subject: gnu: r-ncdfflow: Update to 2.36.0. * gnu/packages/bioconductor.scm (r-ncdfflow): Update to 2.36.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 1432f6b867..e72b6c380a 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6062,14 +6062,14 @@ change point detection.") (define-public r-ncdfflow (package (name "r-ncdfflow") - (version "2.34.0") + (version "2.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ncdfFlow" version)) (sha256 (base32 - "0avxn2abh4fk1gkncrxz7jwzgvd90m3m0ly318q0z38cjhsw3j9f")))) + "1knqc3ic2vpck7n7m7adxjz3ac70ra89d5gvlgp9r2q3kgaciwac")))) (properties `((upstream-name . "ncdfFlow"))) (build-system r-build-system) (inputs -- cgit v1.2.3 From d5a53ab76bb35fe0f05435e6cc38acdf5d0fce9d Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:54:07 +0100 Subject: gnu: r-flowviz: Update to 1.54.0. * gnu/packages/bioconductor.scm (r-flowviz): Update to 1.54.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index e72b6c380a..0d7c705dd4 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6132,14 +6132,14 @@ statistics to the plot.") (define-public r-flowviz (package (name "r-flowviz") - (version "1.52.0") + (version "1.54.0") (source (origin (method url-fetch) (uri (bioconductor-uri "flowViz" version)) (sha256 (base32 - "0f3jfwdmaq9wrgl737blk5gmpc29l9kb6nadqhxpvbjwqsnzx0yq")))) + "1s6jrn2a7hv984xvm6gyn8k3hnma8qidrw9kgj9z5128hv330z7k")))) (properties `((upstream-name . "flowViz"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 33c5b6d7ca3feb68f05d55e67adc904d49f780f8 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:54:10 +0100 Subject: gnu: r-flowclust: Update to 3.28.0. * gnu/packages/bioconductor.scm (r-flowclust): Update to 3.28.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 0d7c705dd4..15503f5390 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6163,14 +6163,14 @@ statistics to the plot.") (define-public r-flowclust (package (name "r-flowclust") - (version "3.26.0") + (version "3.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "flowClust" version)) (sha256 (base32 - "06mkq9y41jax07x4knhvhzgrkgqdvpvcw604bxdk6bv9wx3ipq5b")))) + "1ml3y5wq68jbyr7l5j4zs79bj5bbwzmn5gx41yi88hq78iwkscrq")))) (properties `((upstream-name . "flowClust"))) (build-system r-build-system) (arguments -- cgit v1.2.3 From 5bab0b7eee003225935b695cde96ea64f2775f79 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:54:14 +0100 Subject: gnu: r-rprotobuflib: Update to 2.2.0. * gnu/packages/bioconductor.scm (r-rprotobuflib): Update to 2.2.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 15503f5390..300229d44c 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6203,14 +6203,14 @@ model with Box-Cox transformation.") (define-public r-rprotobuflib (package (name "r-rprotobuflib") - (version "2.0.0") + (version "2.2.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RProtoBufLib" version)) (sha256 (base32 - "0kfinf9vzc1i5qxmaw832id557gr1vqdi1m8yiaxz83g37wh8vps")))) + "09n4ny3ymfkja2br4rrr2n9dzw3hs7qijhcq4mj0avr86i27llqz")))) (properties `((upstream-name . "RProtoBufLib"))) (build-system r-build-system) (arguments -- cgit v1.2.3 From 7f940bd09397a13dfde158baa2ad8ed9943b587a Mon Sep 17 00:00:00 2001 From: zimoun Date: Wed, 2 Dec 2020 16:21:59 +0100 Subject: gnu: Add r-aws-signature. * gnu/packages/cran.scm (r-aws-signature): New variable. --- gnu/packages/cran.scm | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 0d5256a996..cbe9ac9bf8 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -31,6 +31,7 @@ ;;; Copyright © 2020 Antoine Côté ;;; Copyright © 2020 Arun Isaac ;;; Copyright © 2020 Magali Lemes +;;; Copyright © 2020 Simon Tournier ;;; ;;; This file is part of GNU Guix. ;;; @@ -24776,3 +24777,27 @@ orthogonal coordinate systems: cartesian, polar, spherical, cylindrical, parabolic or user defined by custom scale factors.") (license license:gpl3))) +(define-public r-aws-signature + (package + (name "r-aws-signature") + (version "0.6.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "aws.signature" version)) + (sha256 + (base32 + "15llpcnrdq4y6jsn7079yjmgbr5d1wgy2ymsm3jj3gkrd5l4zzpp")))) + (properties `((upstream-name . "aws.signature"))) + (build-system r-build-system) + (propagated-inputs + `(("r-base64enc" ,r-base64enc) + ("r-digest" ,r-digest))) + (home-page "https://github.com/cloudyr/aws.signature") + (synopsis "Amazon Web Services Request Signatures") + (description + "This package generates version 2 and 4 request signatures for Amazon Web +Services (AWS) and provides a mechanism for retrieving credentials from +environment variables, AWS credentials files, and EC2 instance metadata. For +use on EC2 instances, the package 'aws.ec2metadata' is suggested.") + (license license:gpl2+))) -- cgit v1.2.3 From ffa42c77416c6d6f5f3be2faa6b6e0d8bae9b0ed Mon Sep 17 00:00:00 2001 From: zimoun Date: Wed, 2 Dec 2020 16:25:30 +0100 Subject: gnu: Add r-aws-s3. * gnu/packages/cran.scm (r-aws-s3): New variable. --- gnu/packages/cran.scm | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index cbe9ac9bf8..9533006a26 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -24801,3 +24801,30 @@ Services (AWS) and provides a mechanism for retrieving credentials from environment variables, AWS credentials files, and EC2 instance metadata. For use on EC2 instances, the package 'aws.ec2metadata' is suggested.") (license license:gpl2+))) + +(define-public r-aws-s3 + (package + (name "r-aws-s3") + (version "0.3.21") + (source + (origin + (method url-fetch) + (uri (cran-uri "aws.s3" version)) + (sha256 + (base32 + "132cczq0ml7lpp2yl6l4p99dn1zihrncnpa6wyad4m9mnr50a8dx")))) + (properties `((upstream-name . "aws.s3"))) + (build-system r-build-system) + (propagated-inputs + `(("r-aws-signature" ,r-aws-signature) + ("r-base64enc" ,r-base64enc) + ("r-curl" ,r-curl) + ("r-digest" ,r-digest) + ("r-httr" ,r-httr) + ("r-xml2" ,r-xml2))) + (home-page "https://github.com/cloudyr/aws.s3") + (synopsis "AWS S3 Client Package") + (description + "This package provides a simple client package for the Amazon Web +Services (AWS) Simple Storage Service (S3) REST API.") + (license license:gpl2+))) -- cgit v1.2.3 From 1b347814f806afa4f7cb3c530172b675a895dd32 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:54:17 +0100 Subject: gnu: r-flowworkspace: Update to 4.2.0. * gnu/packages/bioconductor.scm (r-flowworkspace): Update to 4.2.0. [inputs]: Add zlib. [propagated-inputs]: Add r-aws-s3 and r-aws-signature. Remove r-stringr. --- gnu/packages/bioconductor.scm | 11 +++++++---- 1 file changed, 7 insertions(+), 4 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 300229d44c..73acf40a6b 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6233,18 +6233,22 @@ for other R packages to compile and link against.") (define-public r-flowworkspace (package (name "r-flowworkspace") - (version "4.0.6") + (version "4.2.0") (source (origin (method url-fetch) (uri (bioconductor-uri "flowWorkspace" version)) (sha256 (base32 - "123ny8n3jjgmsnpghk1dafxkwmcyr513gxi8y4h4qszq4s6ai15v")))) + "19svh32jq1dpq3ayhpd5r8bw0iax8d9kdvpvc23gx2pf16g1j5ag")))) (properties `((upstream-name . "flowWorkspace"))) (build-system r-build-system) + (inputs + `(("zlib" ,zlib))) (propagated-inputs - `(("r-bh" ,r-bh) + `(("r-aws-s3" ,r-aws-s3) + ("r-aws-signature" ,r-aws-signature) + ("r-bh" ,r-bh) ("r-biobase" ,r-biobase) ("r-biocgenerics" ,r-biocgenerics) ("r-cytolib" ,r-cytolib) @@ -6266,7 +6270,6 @@ for other R packages to compile and link against.") ("r-rhdf5lib" ,r-rhdf5lib) ("r-rprotobuflib" ,r-rprotobuflib) ("r-scales" ,r-scales) - ("r-stringr" ,r-stringr) ("r-xml" ,r-xml))) (native-inputs `(("r-knitr" ,r-knitr))) -- cgit v1.2.3 From fd11c7b80ff35f866d3e750456a75a79814d0114 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:54:20 +0100 Subject: gnu: r-flowstats: Update to 4.2.0. * gnu/packages/bioconductor.scm (r-flowstats): Update to 4.2.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 73acf40a6b..ae6b133765 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6287,14 +6287,14 @@ matches the flowJo analysis.") (define-public r-flowstats (package (name "r-flowstats") - (version "4.0.0") + (version "4.2.0") (source (origin (method url-fetch) (uri (bioconductor-uri "flowStats" version)) (sha256 (base32 - "1ygvxvd7y6jp907y0h3hycdwvw1fch16w84g06nk4f4g4kvrzdir")))) + "1i6nrwc55k4bn4qprgs6npy7wf8537m429yncqsygsv47z21ix6x")))) (properties `((upstream-name . "flowStats"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 5abf0a0dd25e7ccc81e1f534795803e1375bf824 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:54:23 +0100 Subject: gnu: r-opencyto: Update to 2.2.0. * gnu/packages/bioconductor.scm (r-opencyto): Update to 2.2.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index ae6b133765..522ddb0ad8 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6323,14 +6323,14 @@ package.") (define-public r-opencyto (package (name "r-opencyto") - (version "2.0.0") + (version "2.2.0") (source (origin (method url-fetch) (uri (bioconductor-uri "openCyto" version)) (sha256 (base32 - "10dyd6dddskv70vhpwfbsqdb8pb9i3ka0fgvl1h51wqlckbsj89m")))) + "02dymy5fa0wjd4pql3jdv1d65mak7ra4il96va7c0km8s87rn40v")))) (properties `((upstream-name . "openCyto"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 63033b159a748935c55df4f12deea4c496544bb8 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:54:26 +0100 Subject: gnu: r-cytoml: Update to 2.2.1. * gnu/packages/bioconductor.scm (r-cytoml): Update to 2.2.1. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 522ddb0ad8..b3f60171a1 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6367,14 +6367,14 @@ sequential way to mimic the manual gating strategy.") (define-public r-cytoml (package (name "r-cytoml") - (version "2.0.5") + (version "2.2.1") (source (origin (method url-fetch) (uri (bioconductor-uri "CytoML" version)) (sha256 (base32 - "174brv027mm90lydfg6hnhazwh8jy4vf6ial4hpsfalwa5jrz55n")))) + "1d8x49aqc95x1vx456hya5r7mal80pj9l6wmr5x5pb5r8qyzz6yq")))) (properties `((upstream-name . "CytoML"))) (build-system r-build-system) (inputs -- cgit v1.2.3 From 1f7ddaf0fb0f480e335f40a8537c24d2ed94e787 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:54:29 +0100 Subject: gnu: r-flowsom: Update to 1.22.0. * gnu/packages/bioconductor.scm (r-flowsom): Update to 1.22.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index b3f60171a1..e4274a2de2 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6419,14 +6419,14 @@ standard to exchange gated cytometry data with other software platforms.") (define-public r-flowsom (package (name "r-flowsom") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "FlowSOM" version)) (sha256 (base32 - "1p17jv4q1dbcc47jpjy9hbcvzpwrx8waq7qpcj778jsyz6z6jh78")))) + "0gydp6q6zqkadw356k9br646zfynz8gk9ckbx9d297x503j5sgwf")))) (properties `((upstream-name . "FlowSOM"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 0e78ce36f0ad66801aae5559ed3468133051e051 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:54:32 +0100 Subject: gnu: r-mixomics: Update to 6.14.0. * gnu/packages/bioconductor.scm (r-mixomics): Update to 6.14.0. --- gnu/packages/bioconductor.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index e4274a2de2..cec29541b7 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6449,20 +6449,21 @@ self-organizing map clustering and minimal spanning trees.") (define-public r-mixomics (package (name "r-mixomics") - (version "6.12.2") + (version "6.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "mixOmics" version)) (sha256 (base32 - "1nkqlvm9j1f4vfj3f3kyxqgan38rpa9imimvl9pwivvsfl647vvc")))) + "0q43ay5r0qsx0zjjnrq24fk6pq5cimviky5lm4w2mbjclqf0gv0q")))) (properties `((upstream-name . "mixOmics"))) (build-system r-build-system) (propagated-inputs `(("r-corpcor" ,r-corpcor) ("r-dplyr" ,r-dplyr) ("r-ellipse" ,r-ellipse) + ("r-ggrepel" ,r-ggrepel) ("r-ggplot2" ,r-ggplot2) ("r-gridextra" ,r-gridextra) ("r-igraph" ,r-igraph) -- cgit v1.2.3 From fafaeab48b91ca5d5e9cb153c06a7d4babef1353 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:54:35 +0100 Subject: gnu: r-depecher: Update to 1.6.0. * gnu/packages/bioconductor.scm (r-depecher): Update to 1.6.0. --- gnu/packages/bioconductor.scm | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index cec29541b7..dbd7e2aa20 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6492,16 +6492,16 @@ delete entire rows with missing data.") (license license:gpl2+))) (define-public r-depecher - (package + (package ;Source/Weave error (name "r-depecher") - (version "1.4.1") + (version "1.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DepecheR" version)) (sha256 (base32 - "0dscfl6wxpl5538jzkrwisdwbr873d38rzd19vl6z5br71jvpv3v")))) + "0c7yv3a7k22nhhw3601n8jdl61cjmlny9b3nfrzsp78mkxi0h469")))) (properties `((upstream-name . "DepecheR"))) (build-system r-build-system) (propagated-inputs @@ -6511,6 +6511,7 @@ delete entire rows with missing data.") ("r-fnn" ,r-fnn) ("r-foreach" ,r-foreach) ("r-ggplot2" ,r-ggplot2) + ("r-gmodels" ,r-gmodels) ("r-gplots" ,r-gplots) ("r-mass" ,r-mass) ("r-matrixstats" ,r-matrixstats) -- cgit v1.2.3 From 6481357330a9e577359cd009c70c5128845aa3d6 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:54:38 +0100 Subject: gnu: r-rcistarget: Update to 1.10.0. * gnu/packages/bioconductor.scm (r-rcistarget): Update to 1.10.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index dbd7e2aa20..d96f2c7423 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6540,14 +6540,14 @@ data, to only emphasize the data that actually matters.") (define-public r-rcistarget (package (name "r-rcistarget") - (version "1.8.0") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RcisTarget" version)) (sha256 (base32 - "1lvi873dv0vhw53s1pmcilw8qwlywm9p2ybphcl168nzh6w31r4i")))) + "0a711jzxl1kggpk3ln68xzc5y30my4nbs1mxx8951pyi3jvzjfyf")))) (properties `((upstream-name . "RcisTarget"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 7954fe16a0e52a2ef344e50f7b69a0a69dc15931 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:54:41 +0100 Subject: gnu: r-cicero: Update to 1.8.0. * gnu/packages/bioconductor.scm (r-cicero): Update to 1.8.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index d96f2c7423..10dc0b232b 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6577,14 +6577,14 @@ genes in the gene-set that are ranked above the leading edge).") (define-public r-cicero (package (name "r-cicero") - (version "1.6.2") + (version "1.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "cicero" version)) (sha256 (base32 - "042ba6yfa7fksij2v7cwnp2sca3vmz7izn6fsxx9xswnncrkgcqh")))) + "0hrra9ngpzmd57dwm0058zy0g7ymsil4pmvi3sgppfzimgviqiwf")))) (build-system r-build-system) (propagated-inputs `(("r-assertthat" ,r-assertthat) -- cgit v1.2.3 From 5d1bd61137746808dc0d2593a07e6d7467117a65 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:54:44 +0100 Subject: gnu: r-genie3: Update to 1.12.0. * gnu/packages/bioconductor.scm (r-genie3): Update to 1.12.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 10dc0b232b..ea616a2cbd 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6688,14 +6688,14 @@ cisTopics and explore the nature and regulatory proteins driving them.") (define-public r-genie3 (package (name "r-genie3") - (version "1.10.0") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GENIE3" version)) (sha256 (base32 - "1bsm0gxracsyg1wnaw3whvskghfpbgbm9navr8wdmxj2hjp3dqs7")))) + "1z7qkv0cgdx2plhc7xdz6s7vwdjhzcdadi35wg3fl6xpids5njf5")))) (properties `((upstream-name . "GENIE3"))) (build-system r-build-system) (propagated-inputs `(("r-reshape2" ,r-reshape2))) -- cgit v1.2.3 From e7b61ba7f6456388f2590429055ae7934b28492b Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:54:47 +0100 Subject: gnu: r-roc: Update to 1.66.0. * gnu/packages/bioconductor.scm (r-roc): Update to 1.66.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index ea616a2cbd..52dec9c42b 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6711,14 +6711,14 @@ regulatory networks from expression data.") (define-public r-roc (package (name "r-roc") - (version "1.64.0") + (version "1.66.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ROC" version)) (sha256 (base32 - "0gmx3r77yl5fqrj5j2hamwynbis75qd62q28964kx16z33xfgx89")))) + "02b9n42z3kjrfxpdf3glqvimd79nhnycq00mb09fzhkpp5zl43c9")))) (properties `((upstream-name . "ROC"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From a50779b8a3cad111f5d73699f3683df30776591f Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:54:53 +0100 Subject: gnu: r-gdsfmt: Update to 1.26.0. * gnu/packages/bioconductor.scm (r-gdsfmt): Update to 1.26.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 52dec9c42b..5de8a7e730 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6796,14 +6796,14 @@ metrics, with methods for objects produced by the @code{methylumi} and (define-public r-gdsfmt (package (name "r-gdsfmt") - (version "1.24.1") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "gdsfmt" version)) (sha256 (base32 - "0ipf60wylbhvwk9q3mbnak0f1n6k7spfh90s1c1c0b47ryxsri67")) + "0x8ik179sf38ihx2y24cvsa9d8isdmx2z27sjhcwq0r3xpjxpz1a")) (modules '((guix build utils))) ;; Remove bundled sources of zlib, lz4, and xz. Don't attempt to build ;; them and link with system libraries instead. -- cgit v1.2.3 From 42e00c09232ae1747dcfbf7015074511233ec38a Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:55:00 +0100 Subject: gnu: r-seqbias: Update to 1.38.0. * gnu/packages/bioconductor.scm (r-seqbias): Update to 1.38.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 5de8a7e730..59a239f614 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6883,14 +6883,14 @@ with multiple R processes supported by the package @code{parallel}.") (define-public r-seqbias (package (name "r-seqbias") - (version "1.36.0") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "seqbias" version)) (sha256 (base32 - "0sy2fv98x4qfz9llns28jh1n4bi991jj856y8a5fbzpx7y990lai")))) + "1m634sidmk6c603k2gflyiddkns9vr6ij591nmab523xk5r2f4b2")))) (properties `((upstream-name . "seqbias"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 0c53f27dd653210e7267b88482c802cc20239ced Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:55:03 +0100 Subject: gnu: r-reqon: Update to 1.36.0. * gnu/packages/bioconductor.scm (r-reqon): Update to 1.36.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 59a239f614..b798d3b478 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6949,14 +6949,14 @@ injected in that sequence).") (define-public r-reqon (package (name "r-reqon") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ReQON" version)) (sha256 (base32 - "06m0hd4aqsxjyzhs8b1zys7lz8289qgwn7jp2dpln1j7cf02q4bz")))) + "1yz0r0rrk4n6dnqbdq41lvs5z8l6vkx729m0a7f29svw4dbc6mdq")))) (properties `((upstream-name . "ReQON"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From fd7e23b5512a0437755f175852dfeb2dfbb2e4e3 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:55:06 +0100 Subject: gnu: r-wavcluster: Update to 2.24.0. * gnu/packages/bioconductor.scm (r-wavcluster): Update to 2.24.0. --- gnu/packages/bioconductor.scm | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index b798d3b478..5bdf8a0795 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6974,14 +6974,14 @@ format.") (define-public r-wavcluster (package (name "r-wavcluster") - (version "2.22.0") + (version "2.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "wavClusteR" version)) (sha256 (base32 - "0204czqjmkwhd6gznwxzb0vj3dg3aif628g8c30085aa2jljn9bk")))) + "18cg0jbr3rjyx31wwyag1n5gams55pbd2rvb99i3g80q9hvswawi")))) (properties `((upstream-name . "wavClusteR"))) (build-system r-build-system) (propagated-inputs @@ -6998,8 +6998,7 @@ format.") ("r-rtracklayer" ,r-rtracklayer) ("r-s4vectors" ,r-s4vectors) ("r-seqinr" ,r-seqinr) - ("r-stringr" ,r-stringr) - ("r-wmtsa" ,r-wmtsa))) + ("r-stringr" ,r-stringr))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/wavClusteR/") -- cgit v1.2.3 From 87f704b43c03e7f5f6c622ed8905deb4eb3691b8 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:55:09 +0100 Subject: gnu: r-timeseriesexperiment: Update to 1.8.0. * gnu/packages/bioconductor.scm (r-timeseriesexperiment): Update to 1.8.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 5bdf8a0795..ca3fc95547 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7021,14 +7021,14 @@ procedures that induce nucleotide substitutions (e.g. BisSeq).") (define-public r-timeseriesexperiment (package (name "r-timeseriesexperiment") - (version "1.6.0") + (version "1.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "TimeSeriesExperiment" version)) (sha256 (base32 - "1k0djvcsyjj1ayncvmi8nlqi3jdn5qp41y3fwsqg1cp0qsvx7zv3")))) + "1jx0rk660mfzk7rfhamnp0disx3bv456cqi9hyaz2wcbcdrlvcjn")))) (properties `((upstream-name . "TimeSeriesExperiment"))) (build-system r-build-system) -- cgit v1.2.3 From 45ea773f946685b0fb4bd965da302556163c5970 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:55:12 +0100 Subject: gnu: r-variantfiltering: Update to 1.26.0. * gnu/packages/bioconductor.scm (r-variantfiltering): Update to 1.26.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index ca3fc95547..8e304b6bff 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7062,14 +7062,14 @@ provides methods for retrieving enriched pathways.") (define-public r-variantfiltering (package (name "r-variantfiltering") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "VariantFiltering" version)) (sha256 (base32 - "0lsrnybsbm9siyjv4nal6bmprj8ynwgk4n1145f4h52g78wq3br4")))) + "0zy53knvyk8wy3hmnsxc0w9qkhvx6xhviskvx7rwmrsi7pz531l5")))) (properties `((upstream-name . "VariantFiltering"))) (build-system r-build-system) -- cgit v1.2.3 From 44ecd5f77f01eaf3142fd5ca9d3a8daa34a52df3 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:55:15 +0100 Subject: gnu: r-variancepartition: Update to 1.20.0. * gnu/packages/bioconductor.scm (r-variancepartition): Update to 1.20.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 8e304b6bff..67960dd979 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7168,14 +7168,14 @@ arrays based on fast wavelet-based functional models.") (define-public r-variancepartition (package (name "r-variancepartition") - (version "1.18.3") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "variancePartition" version)) (sha256 (base32 - "1jrlhi2c5ibvq8a41g5hwdq4kk4rdd7m464rz5767zaaci7l2ay0")))) + "0fisaqd5v8xy9rz9l1zs62k1n2h4k1irzgwj46ci947l52x1qhah")))) (properties `((upstream-name . "variancePartition"))) (build-system r-build-system) -- cgit v1.2.3 From 949626f2098f4cf69cd66c56f99030057a692c0b Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:55:18 +0100 Subject: gnu: r-htqpcr: Update to 1.44.0. * gnu/packages/bioconductor.scm (r-htqpcr): Update to 1.44.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 67960dd979..a95acbfc46 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7212,14 +7212,14 @@ measures.") (define-public r-htqpcr (package (name "r-htqpcr") - (version "1.42.0") + (version "1.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "HTqPCR" version)) (sha256 (base32 - "08bd5zkjdnz726s03bvvzv03va0xbrr818ipp6737z9g3nk9m81j")))) + "1fzjx6psr41naq9ycpnv3lxlgkiyrpn7r2wl1i4gz45f3lax0yji")))) (properties `((upstream-name . "HTqPCR"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From fa7e24291082dd6b12faf72e765d2cd098af409a Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:55:21 +0100 Subject: gnu: r-unifiedwmwqpcr: Update to 1.26.0. * gnu/packages/bioconductor.scm (r-unifiedwmwqpcr): Update to 1.26.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index a95acbfc46..b4b5e38509 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7246,14 +7246,14 @@ features (e.g. genes, microRNAs).") (define-public r-unifiedwmwqpcr (package (name "r-unifiedwmwqpcr") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "unifiedWMWqPCR" version)) (sha256 (base32 - "1l9gxq3askr3cz2a4bqsw7vjr1agivzvx651cblkygv57x08zf81")))) + "1ad5a7gy43l8x1rf5lgqiy2bv6fgah7cbnp4lrqwshphlnr30ndv")))) (properties `((upstream-name . "unifiedWMWqPCR"))) (build-system r-build-system) -- cgit v1.2.3 From fad5da32dc923a85c9eef38f0802d4c349e9fe35 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:55:24 +0100 Subject: gnu: r-bgmix: Update to 1.50.0. * gnu/packages/bioconductor.scm (r-bgmix): Update to 1.50.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index b4b5e38509..f2f5a9d876 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7337,14 +7337,14 @@ cellular organization in health and disease.") (define-public r-bgmix (package (name "r-bgmix") - (version "1.48.0") + (version "1.50.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BGmix" version)) (sha256 (base32 - "1pfi3hinjn6ymikadgj8dqm59h7mapf01wj86dbbvf8y1xqp8y8n")))) + "0r9gjqajarg5mivxhqdzn8m8hmfarmzbplp3zqyyznccri03pv50")))) (properties `((upstream-name . "BGmix"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 3cebe2745acefd09e56ee6383882cda3c307bc3a Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:55:27 +0100 Subject: gnu: r-bgx: Update to 1.56.0. * gnu/packages/bioconductor.scm (r-bgx): Update to 1.56.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index f2f5a9d876..f38ae38af0 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7359,14 +7359,14 @@ gene expression.") (define-public r-bgx (package (name "r-bgx") - (version "1.54.1") + (version "1.56.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bgx" version)) (sha256 (base32 - "0a10fg9n5p024jrmbis102gqpbz23sc6vdn1sal2697hlxikzb46")))) + "0gm4wv9drqvg9r4f0id1ivrfgv0nvh0hb6hp63b3jd14092777im")))) (properties `((upstream-name . "bgx"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 2219bef12f4e106a7963ca14b294df38f1739899 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:55:30 +0100 Subject: gnu: r-bhc: Update to 1.42.0. * gnu/packages/bioconductor.scm (r-bhc): Update to 1.42.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index f38ae38af0..6bad8ec8df 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7384,14 +7384,14 @@ Affymetrix GeneChips.") (define-public r-bhc (package (name "r-bhc") - (version "1.40.0") + (version "1.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BHC" version)) (sha256 (base32 - "06milqjg2nl3ra47sxi7a2p2d3mbrx3wk168pqgimvs8snldd2xr")))) + "1n2rkbj8j10f38d40wvi6mwjxnrlfx71a48ab07bp2s0hwhxd7yn")))) (properties `((upstream-name . "BHC"))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/BHC/") -- cgit v1.2.3 From 4ec665693dfdf1d323ce7e88e5d30ae78fa4ff67 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:55:33 +0100 Subject: gnu: r-bicare: Update to 1.48.0. * gnu/packages/bioconductor.scm (r-bicare): Update to 1.48.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 6bad8ec8df..1ff44a0751 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7410,14 +7410,14 @@ algorithm which is more efficient for larger data sets.") (define-public r-bicare (package (name "r-bicare") - (version "1.46.0") + (version "1.48.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BicARE" version)) (sha256 (base32 - "0llckbl3l26lf6wgjg7rxs8k1yrk043vvdhnkc6ncg33sydj383y")))) + "1np3967rjx54hbjsynvya75lcsqa6zic6frw5fjwqybwv2pzzw2k")))) (properties `((upstream-name . "BicARE"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From d57be633236674358eb3c17c89014fa40319c463 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:55:36 +0100 Subject: gnu: r-bifet: Update to 1.10.0. * gnu/packages/bioconductor.scm (r-bifet): Update to 1.10.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 1ff44a0751..28521e277e 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7434,14 +7434,14 @@ results.") (define-public r-bifet (package (name "r-bifet") - (version "1.8.0") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiFET" version)) (sha256 (base32 - "1v2dshs09iy2glzq0vwxmr83x867j844i1ixsfcamvfq33fwbbr5")))) + "191m1xhsj4l64rrh67hqiz1rdkfhw0gfd5aymf3x0xm710l3rh4a")))) (properties `((upstream-name . "BiFET"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 3320f044a39fa57d523961ad3f6c27082b23c795 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:55:39 +0100 Subject: gnu: r-rsbml: Update to 2.48.0. * gnu/packages/bioconductor.scm (r-rsbml): Update to 2.48.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 28521e277e..86199f26e2 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7464,14 +7464,14 @@ the read count and GC content bias.") (define-public r-rsbml (package (name "r-rsbml") - (version "2.46.0") + (version "2.48.0") (source (origin (method url-fetch) (uri (bioconductor-uri "rsbml" version)) (sha256 (base32 - "1i1izznnwzrc6m7s3hblfff466icfvxl2gjdqaln8qfg9v87rslx")))) + "0vrjfhwcpc699sq78pkm022fam3ahar8h3lx3fr879dd21k02g61")))) (properties `((upstream-name . "rsbml"))) (build-system r-build-system) (inputs -- cgit v1.2.3 From 294fd58a42e2e651966fc5b21f68fb29111774fb Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:55:43 +0100 Subject: gnu: r-hypergraph: Update to 1.62.0. * gnu/packages/bioconductor.scm (r-hypergraph): Update to 1.62.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 86199f26e2..15a613197f 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7492,14 +7492,14 @@ validating output, provides an S4 SBML DOM, converts SBML to R graph objects.") (define-public r-hypergraph (package (name "r-hypergraph") - (version "1.60.0") + (version "1.62.0") (source (origin (method url-fetch) (uri (bioconductor-uri "hypergraph" version)) (sha256 (base32 - "1iq9b9rzy3ikx8xszsjiv3p8l702n2h2s9w33797wcmkg4apslb7")))) + "1p5mzr2aiqqc1j2inh45abjvqhid9jqv6wiym1xxnz16mpaa7q97")))) (properties `((upstream-name . "hypergraph"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 249b703056b19ba3a2a11e1a583a592a3e015c6c Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:55:46 +0100 Subject: gnu: r-hyperdraw: Update to 1.42.0. * gnu/packages/bioconductor.scm (r-hyperdraw): Update to 1.42.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 15a613197f..85794daad6 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7514,14 +7514,14 @@ manipulating hypergraphs.") (define-public r-hyperdraw (package (name "r-hyperdraw") - (version "1.40.0") + (version "1.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "hyperdraw" version)) (sha256 (base32 - "1qzx5sqp7rpspk8g1j34p03ds1vmw0h7hpzb2ijpbvmsja5drzvf")))) + "0z3a3lpz7s0fw023fxldkgxvl2dl1wn8agnyj09sky11ainxdayz")))) (properties `((upstream-name . "hyperdraw"))) (build-system r-build-system) (inputs `(("graphviz" ,graphviz))) -- cgit v1.2.3 From 0f94a9edb01100a45f3898ee2cc41fb08c2ee8f9 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:55:49 +0100 Subject: gnu: r-biggr: Update to 1.26.0. * gnu/packages/bioconductor.scm (r-biggr): Update to 1.26.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 85794daad6..89d7a79418 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7538,14 +7538,14 @@ manipulating hypergraphs.") (define-public r-biggr (package (name "r-biggr") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiGGR" version)) (sha256 (base32 - "05afi6hsh1dv6lc6l0dfhvvi8k34wyzf1k1jimam7a6pbrhyy5dk")))) + "1hlsnss6071ck4ky1akxp1dnv3vmd8f85drdziqmm4nc2dfrr14y")))) (properties `((upstream-name . "BiGGR"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From e80f8262f6ab8ba1a8ca4af6479868af3d2a6f27 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:55:52 +0100 Subject: gnu: r-bigmemoryextras: Update to 1.38.0. * gnu/packages/bioconductor.scm (r-bigmemoryextras): Update to 1.38.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 89d7a79418..f963f08a76 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7568,14 +7568,14 @@ networks and estimated fluxes can be visualized with hypergraphs.") (define-public r-bigmemoryextras (package (name "r-bigmemoryextras") - (version "1.36.0") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bigmemoryExtras" version)) (sha256 (base32 - "053bqcd3p4i7agj43ccjxfz40a1sxrymd49vdpfq8ypslkwk7g0g")))) + "1k31h746j8r3f92vj62s38fw12qjkv5814ipcqfbswnxgaan17zj")))) (properties `((upstream-name . "bigmemoryExtras"))) (build-system r-build-system) -- cgit v1.2.3 From 1e288678031810dbc07a7da902c330173391253b Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:55:55 +0100 Subject: gnu: r-bigpint: Update to 1.6.0. * gnu/packages/bioconductor.scm (r-bigpint): Update to 1.6.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index f963f08a76..f9238b62e0 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7602,14 +7602,14 @@ a file-backed matrix with factor properties.") (define-public r-bigpint (package (name "r-bigpint") - (version "1.4.0") + (version "1.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bigPint" version)) (sha256 (base32 - "1m92ngkzimcc37byf0ziphrby8wmjd5hfa53gvfphgaakyj9bjg8")))) + "1axgapy4iyx059777m9faczwwj03h3i5dyrs0rlc84axzhzd2kis")))) (properties `((upstream-name . "bigPint"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 95ef2681425d64e33b3f581b26b55cfe536f9ba3 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:55:58 +0100 Subject: gnu: r-chemminer: Update to 3.42.0. * gnu/packages/bioconductor.scm (r-chemminer): Update to 3.42.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index f9238b62e0..302361585e 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7645,14 +7645,14 @@ visualizing RNA-sequencing datasets and differentially expressed genes.") (define-public r-chemminer (package (name "r-chemminer") - (version "3.40.0") + (version "3.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ChemmineR" version)) (sha256 (base32 - "0cna5xsqflvhlp2k47asxyv3w4ympmz2wy2cwjyzlal6936fjikf")))) + "14q9zhhxgkx5skj424i2rbjdbp5j8jfkxspkhnkwv5i45cvkgh19")))) (properties `((upstream-name . "ChemmineR"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 2f36b0406e01a54d3f72bc8d6bac6798ff138859 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:56:01 +0100 Subject: gnu: r-bioassayr: Update to 1.28.0. * gnu/packages/bioconductor.scm (r-bioassayr): Update to 1.28.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 302361585e..4a773a24ef 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7686,14 +7686,14 @@ structures.") (define-public r-bioassayr (package (name "r-bioassayr") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bioassayR" version)) (sha256 (base32 - "1n0gsnxcl0lplqk8rs5ygxrxpx389ddl6wv3ciyz9g2xry5biyfy")))) + "0vxnd8wnhjdfqh47nc6y1ffiy5r9a6n3g2hyk1r9bv6vhrd0ns3f")))) (properties `((upstream-name . "bioassayR"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 95e30d8f6e0e1bf958c394f87cbd8db381177d21 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:56:04 +0100 Subject: gnu: r-biobroom: Update to 1.22.0. * gnu/packages/bioconductor.scm (r-biobroom): Update to 1.22.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 4a773a24ef..58eaea4bf8 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7721,14 +7721,14 @@ available bioactivity data.") (define-public r-biobroom (package (name "r-biobroom") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biobroom" version)) (sha256 (base32 - "06qcrprn58kbrr5kyw1jl6z88b9w9g8xs6rkhrbnz8k7rv373fhf")))) + "07wzamwl07p20s932aym2jkf6c1zz7d9h7kyby5ka4pw4abynlrv")))) (properties `((upstream-name . "biobroom"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 26224e09ae4f014777ced1fe10f065caf658775e Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:56:07 +0100 Subject: gnu: r-graphite: Update to 1.36.0. * gnu/packages/bioconductor.scm (r-graphite): Update to 1.36.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 58eaea4bf8..bfb6bcd98a 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7753,14 +7753,14 @@ visualize bioinformatics analyses.") (define-public r-graphite (package (name "r-graphite") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "graphite" version)) (sha256 (base32 - "0rc9cw3picz1y0lwhbzpk03ciij8kij74m15qgzh2ykla7zprb2p")))) + "1ihza8m397qfvr79fhghs2knmw862hwz2akysy39r8hndv6lc7wk")))) (properties `((upstream-name . "graphite"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From a4f4a55283c306c6c0b50430b3c85af6330314ca Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:56:10 +0100 Subject: gnu: r-reactomepa: Update to 1.34.0. * gnu/packages/bioconductor.scm (r-reactomepa): Update to 1.34.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index bfb6bcd98a..f8856c452d 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7780,14 +7780,14 @@ symbols).") (define-public r-reactomepa (package (name "r-reactomepa") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ReactomePA" version)) (sha256 (base32 - "1ngilyn1mihwxs4sh5gk9y829xghdmh277cfw3vfgflz9sgwy21x")))) + "04b2ng9jp2bsfbg3wnbg6m6a5c3szcmbypk1lx34i63228g8z98m")))) (properties `((upstream-name . "ReactomePA"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From b0f3bfe4ae536d2527167d2c590495568a16fc71 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:56:13 +0100 Subject: gnu: r-ebarrays: Update to 2.54.0. * gnu/packages/bioconductor.scm (r-ebarrays): Update to 2.54.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index f8856c452d..f67b3c29a2 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7812,14 +7812,14 @@ enrichment analysis and several functions for visualization.") (define-public r-ebarrays (package (name "r-ebarrays") - (version "2.52.0") + (version "2.54.0") (source (origin (method url-fetch) (uri (bioconductor-uri "EBarrays" version)) (sha256 (base32 - "00ld26bld8xgin9zqwxybahvhmqbrvr09jfphg0yr4j4zck6sqgf")))) + "1r2dl19my1hqkq01fqk48pk3agb98vgrplj56kb4srhz2xm0w9pd")))) (properties `((upstream-name . "EBarrays"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 7dced9ad0171e534214096ee0d807e8c2a045e86 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:56:16 +0100 Subject: gnu: r-bioccasestudies: Update to 1.52.0. * gnu/packages/bioconductor.scm (r-bioccasestudies): Update to 1.52.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index f67b3c29a2..8c07f99363 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7836,14 +7836,14 @@ microarray data.") (define-public r-bioccasestudies (package (name "r-bioccasestudies") - (version "1.50.0") + (version "1.52.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocCaseStudies" version)) (sha256 (base32 - "0fadck1dk1zavpn9yrcwx6zgfi18fw5xfs8svgzipns6bq41j8ix")))) + "03n49b6fvyyzmvdy4yif3cl7yv21c09c8xdx4cvvax5zz4v4sab1")))) (properties `((upstream-name . "BiocCaseStudies"))) (build-system r-build-system) -- cgit v1.2.3 From abc18fc596b81acf2eb6ac02d11be97c521cee04 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:56:20 +0100 Subject: gnu: r-biocgraph: Update to 1.52.0. * gnu/packages/bioconductor.scm (r-biocgraph): Update to 1.52.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 8c07f99363..7996cdd5bc 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7858,14 +7858,14 @@ monograph.") (define-public r-biocgraph (package (name "r-biocgraph") - (version "1.50.0") + (version "1.52.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biocGraph" version)) (sha256 (base32 - "1372bm4y3czqhpki10pnprxfkfncfcsy59zzvf8wj6q03acaavrj")))) + "02y7vizc6jv8y9r8chsda4yysim0ch45i3rasqvv7m85zqsskf75")))) (properties `((upstream-name . "biocGraph"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 49a728581f33430f75dc1f7b6150108cc539828f Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:56:23 +0100 Subject: gnu: r-experimenthub: Update to 1.16.0. * gnu/packages/bioconductor.scm (r-experimenthub): Update to 1.16.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 7996cdd5bc..69b242209a 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7883,14 +7883,14 @@ different graph related packages produced by Bioconductor.") (define-public r-experimenthub (package (name "r-experimenthub") - (version "1.14.2") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ExperimentHub" version)) (sha256 (base32 - "1kgvprchz1fg8pl1irj62mk2gyb4jcc9iimpypv4c2iccy5bp84x")))) + "1zi7vsrhf1hj27rlzrxl4jd81fqh1yhn0svp2d9w71fizsi71akg")))) (properties `((upstream-name . "ExperimentHub"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 13d0b780c12efa2c5f0d144773c5d40982d6d65d Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:56:26 +0100 Subject: gnu: r-multiassayexperiment: Update to 1.16.0. * gnu/packages/bioconductor.scm (r-multiassayexperiment): Update to 1.16.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 69b242209a..043abece1e 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7917,14 +7917,14 @@ access.") (define-public r-multiassayexperiment (package (name "r-multiassayexperiment") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MultiAssayExperiment" version)) (sha256 (base32 - "0qlfnd86999jqv2nd0ikixi2sfd449dyg3ml4nbs8ycs57c2irgh")))) + "1nx3gikl8vr54862h6wl0q30arnpynla085219lhh61ziswdffrs")))) (properties `((upstream-name . "MultiAssayExperiment"))) (build-system r-build-system) -- cgit v1.2.3 From e29b15ee9747f94fa1ae064ca44f2dce24f3be3f Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:56:29 +0100 Subject: gnu: r-bioconcotk: Update to 1.10.0. * gnu/packages/bioconductor.scm (r-bioconcotk): Update to 1.10.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 043abece1e..a34a6b7224 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7952,14 +7952,14 @@ rownames.") (define-public r-bioconcotk (package (name "r-bioconcotk") - (version "1.8.0") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocOncoTK" version)) (sha256 (base32 - "021qzygfwdnd3naz1iqq01zr3zxv3k7wm1lklik24vc7axshxbmk")))) + "1jwp0gww2xyx8qfv5h4y0v3g66mmlyrd1v64xn91si4fsymk4108")))) (properties `((upstream-name . "BiocOncoTK"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 072f722f8e147b5c4b254a237d33353e76dc1bba Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:56:32 +0100 Subject: gnu: r-biocor: Update to 1.14.0. * gnu/packages/bioconductor.scm (r-biocor): Update to 1.14.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index a34a6b7224..e5ac9c5096 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7997,14 +7997,14 @@ tools for genome-scale analysis of cancer studies.") (define-public r-biocor (package (name "r-biocor") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BioCor" version)) (sha256 (base32 - "1xghclfqv8d23g72g8914br5zjx4sz9zihzczwwmpl15lghpnqwy")))) + "12slrdn98h43j3y7klk3chrwa2ycwm4krhz3l3kfzbxr834mhy19")))) (properties `((upstream-name . "BioCor"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 6a5d8cadeed9c6b26fffb8db300679245da77e05 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:56:35 +0100 Subject: gnu: r-biocpkgtools: Update to 1.8.0. * gnu/packages/bioconductor.scm (r-biocpkgtools): Update to 1.8.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index e5ac9c5096..6adce2500b 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8026,14 +8026,14 @@ gene selection, testing relationships, and so on.") (define-public r-biocpkgtools (package (name "r-biocpkgtools") - (version "1.6.0") + (version "1.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocPkgTools" version)) (sha256 (base32 - "0l5fvi1m4834n4h0iswbap135s9mpaiabw9czzn1r72ssz86vrcr")))) + "12j4vag40zdgrxfzaqvf3ly7776qyziryz04c3jqzgsqfvzvzz8m")))) (properties `((upstream-name . "BiocPkgTools"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From ff4834c065a3b0d90021fbbba2f8306ade9ce691 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 3 Dec 2020 14:33:05 +0100 Subject: gnu: Add r-biocio. * gnu/packages/bioconductor.scm (r-biocio): New variable. --- gnu/packages/bioconductor.scm | 36 ++++++++++++++++++++++++++++++++++++ 1 file changed, 36 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 6adce2500b..a854fef82e 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8867,3 +8867,39 @@ etc.), missing data imputation, data normalisation (quantiles, vsn, etc.) as well as misc helper functions, that are used across high-level data structure within the R for Mass Spectrometry packages.") (license license:artistic2.0))) + +(define-public r-biocio + (package + (name "r-biocio") + (version "1.0.1") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "BiocIO" version)) + (sha256 + (base32 + "06gg5ra3r7q4b6mz14c2s9d453cnh1lxh517ffl9f8dr8vwv5s18")))) + (properties `((upstream-name . "BiocIO"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biocgenerics" ,r-biocgenerics) + ("r-genomicranges" ,r-genomicranges) + ("r-rcurl" ,r-rcurl) + ("r-s4vectors" ,r-s4vectors))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://bioconductor.org/packages/BiocIO") + (synopsis "Standard input and output for Bioconductor packages") + (description + "This package implements `import()` and `export()` standard generics for +importing and exporting biological data formats. `import()` supports +whole-file as well as chunk-wise iterative import. The `import()` interface +optionally provides a standard mechanism for 'lazy' access via `filter()` (on +row or element-like components of the file resource), `select()` (on +column-like components of the file resource) and `collect()`. The `import()` +interface optionally provides transparent access to remote (e.g. via https) +as well as local access. Developers can register a file extension, e.g., +`.loom` for dispatch from character-based URIs to specific `import()` / +`export()` methods based on classes representing file types, e.g., +`LoomFile()`.") + (license license:artistic2.0))) -- cgit v1.2.3 From feb0cbf402e33880e74eb0576dd51083462519d9 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:56:38 +0100 Subject: gnu: r-biocset: Update to 1.4.0. * gnu/packages/bioconductor.scm (r-biocset): Update to 1.4.0. [propagated-inputs]: Add r-s4vectors; remove r-rtracklayer. --- gnu/packages/bioconductor.scm | 11 +++++++---- 1 file changed, 7 insertions(+), 4 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index a854fef82e..b938729b0e 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8076,24 +8076,27 @@ analytics on packages.") (define-public r-biocset (package (name "r-biocset") - (version "1.2.2") + (version "1.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocSet" version)) (sha256 (base32 - "041hq3rp0kv7kjwcjjrksk8lw3sj6j1v3wdcr8z611k0g0z6p0cj")))) + "16pjg09i0j5qk9s9qzm6fq5q0bgwb4wgqvp6scs06ajgrr07qjqg")))) (properties `((upstream-name . "BiocSet"))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) + ("r-biocio" ,r-biocio) ("r-dplyr" ,r-dplyr) ("r-keggrest" ,r-keggrest) + ("r-ontologyindex" ,r-ontologyindex) ("r-plyr" ,r-plyr) ("r-rlang" ,r-rlang) - ("r-rtracklayer" ,r-rtracklayer) - ("r-tibble" ,r-tibble))) + ("r-s4vectors" ,r-s4vectors) + ("r-tibble" ,r-tibble) + ("r-tidyr" ,r-tidyr))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page -- cgit v1.2.3 From 7891c83c3edadbd0c832512050a59a8eb9e27ea3 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:56:41 +0100 Subject: gnu: r-biocworkflowtools: Update to 1.16.0. * gnu/packages/bioconductor.scm (r-biocworkflowtools): Update to 1.16.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index b938729b0e..fdb7599789 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8114,14 +8114,14 @@ accessing web references for elements/sets are also available in BiocSet.") (define-public r-biocworkflowtools (package (name "r-biocworkflowtools") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocWorkflowTools" version)) (sha256 (base32 - "0p9r71ql67sdlgd5pv118lhz8b85pr5y4ijfwzcy8wrr8jwlbddy")))) + "0lvckdy20bhgyhqbccp0rdfi2p6vvip694r27qwpyi5092nfmqh6")))) (properties `((upstream-name . "BiocWorkflowTools"))) (build-system r-build-system) -- cgit v1.2.3 From 15be98c136acb6c8f7a3c12d8db427d2f6032b6e Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:56:44 +0100 Subject: gnu: r-biodist: Update to 1.62.0. * gnu/packages/bioconductor.scm (r-biodist): Update to 1.62.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index fdb7599789..5d8ca54812 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8147,14 +8147,14 @@ Rmarkdown and LaTeX documents when authoring a Bioconductor Workflow.") (define-public r-biodist (package (name "r-biodist") - (version "1.60.0") + (version "1.62.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bioDist" version)) (sha256 (base32 - "17bvxk0anvsp29j5nbblvaymf8qgbj3sz4ir2l7wj8kb8jfi19cp")))) + "10p4iajpyqgqb35743jm1a33lwbsmax2g4vz9fbbhn2cpiq3chap")))) (properties `((upstream-name . "bioDist"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 7a242042ae8db8894a8345b355c283c360afb6af Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:56:50 +0100 Subject: gnu: r-rgreat: Update to 1.22.0. * gnu/packages/bioconductor.scm (r-rgreat): Update to 1.22.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 5d8ca54812..96cf277bb1 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8216,14 +8216,14 @@ dimensional mass cytometry data.") (define-public r-rgreat (package (name "r-rgreat") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "rGREAT" version)) (sha256 (base32 - "0n8dw9ibb2klsczcxvvinpi9l53w8cs436i0c8w2jmramayl593v")))) + "0p2b8cqxibxxmsh687y7yvlvr2a5ipiz53jb4wsr8ddypynb1asj")))) (properties `((upstream-name . "rGREAT"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 126846a0da12cab28b84b073d36e375cfa7b4dbc Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:56:53 +0100 Subject: gnu: r-m3c: Update to 1.12.0. * gnu/packages/bioconductor.scm (r-m3c): Update to 1.12.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 96cf277bb1..ff002c1296 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8244,14 +8244,14 @@ user's input and automatically retrieving results from GREAT web server.") (define-public r-m3c (package (name "r-m3c") - (version "1.10.0") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "M3C" version)) (sha256 (base32 - "0zq8lm4280p8h65i7myscwa4srs5ajh944xv6zni2f5sjyp7ij2y")))) + "05ygi4fd85hh17mlww5wcww8d5z5zvkn2r46s4n6g18mcbv8snv5")))) (properties `((upstream-name . "M3C"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 3cacc3bdceaae80da74bb2055d01f40e2c5553b3 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:56:56 +0100 Subject: gnu: r-icens: Update to 1.62.0. * gnu/packages/bioconductor.scm (r-icens): Update to 1.62.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index ff002c1296..f7986ac057 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8277,14 +8277,14 @@ hypothesis @code{K=1}.") (define-public r-icens (package (name "r-icens") - (version "1.60.0") + (version "1.62.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Icens" version)) (sha256 (base32 - "0fh7wgkrw20f61p06i87nccnbig9wv4m0jcg7cx1rw7g2ndnabgp")))) + "1w94mvh8pai77h4fcaiyacmzs58n4kbiq6bm4z0hk24j1ywph3dr")))) (properties `((upstream-name . "Icens"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From e5b2c80dc296fc6e05f92aeb3a2b4dc1eb717faa Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:56:59 +0100 Subject: gnu: r-fourcseq: Update to 1.24.0. * gnu/packages/bioconductor.scm (r-fourcseq): Update to 1.24.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index f7986ac057..bf67276aa0 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8363,13 +8363,13 @@ with: (define-public r-fourcseq (package (name "r-fourcseq") - (version "1.22.1") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "FourCSeq" version)) (sha256 - (base32 "14q1ijnqnbd9xs60sfvyqjfiypjrvhacpwp2v85yfhcxw870cx5b")))) + (base32 "1rwdphcj26xis47n8j1fiyc3k3qbsgn0bhf5bhgy5vm11yqyvicb")))) (properties `((upstream-name . "FourCSeq"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 8fa30df02a9cf01d313d4f757b5ec37d18964b81 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:57:03 +0100 Subject: gnu: r-preprocesscore: Update to 1.52.0. * gnu/packages/bioconductor.scm (r-preprocesscore): Update to 1.52.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index bf67276aa0..3bdaf3ff3b 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8407,14 +8407,14 @@ generated.") (define-public r-preprocesscore (package (name "r-preprocesscore") - (version "1.50.0") + (version "1.52.0") (source (origin (method url-fetch) (uri (bioconductor-uri "preprocessCore" version)) (sha256 (base32 - "0q1406kswylc8zn5k3wyd34p34pfzbhi1ggkfsh30zcjp6adbwjl")))) + "1i5ky3bfbkrz4lgfs72fkckr8q3wq48p38mp05cjmnmh1chmdw38")))) (properties `((upstream-name . "preprocessCore"))) (build-system r-build-system) -- cgit v1.2.3 From b6348b0edfe021196d8e0c83cdd56b963e9304fa Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:57:06 +0100 Subject: gnu: r-rgraphviz: Update to 2.34.0. * gnu/packages/bioconductor.scm (r-rgraphviz): Update to 2.34.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 3bdaf3ff3b..b1a73c4cf8 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8468,14 +8468,14 @@ data manipulation and visualization.") (define-public r-rgraphviz (package (name "r-rgraphviz") - (version "2.32.0") + (version "2.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rgraphviz" version)) (sha256 (base32 - "1calpvzgcz6v7s4x6bf35kj83sga95zjp7x87p5d3qnbv7q2wz5y")))) + "1k0nrskak2v5xv7za226r3wypja3zxxmmc0cxz2imjhlgnkbha77")))) (properties `((upstream-name . "Rgraphviz"))) (build-system r-build-system) (arguments -- cgit v1.2.3 From 724b7706785136d4a22e15b27c89dd1ae109be8b Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:58:38 +0100 Subject: gnu: r-xvector: Update to 0.30.0. * gnu/packages/bioinformatics.scm (r-xvector): Update to 0.30.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 792640faee..84b036c781 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8027,13 +8027,13 @@ different technologies, including microarrays, RNA-seq, and quantitative PCR.") (define-public r-xvector (package (name "r-xvector") - (version "0.28.0") + (version "0.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "XVector" version)) (sha256 (base32 - "11h1hszv4798q1gbx8r6zf8vlaqx4v9ql0lbh2xaxybp66a03pvc")))) + "1pqljikg4f6jb7wgm5537zwgq5b013nyz1agjrwfq2cljb0ym6lq")))) (properties `((upstream-name . "XVector"))) (build-system r-build-system) -- cgit v1.2.3 From 7105658e9c07d5f46fbdac12db2b0b61ab550a71 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:57:09 +0100 Subject: gnu: r-fithic: Update to 1.16.0. * gnu/packages/bioconductor.scm (r-fithic): Update to 1.16.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index b1a73c4cf8..9bcd95c7da 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8506,13 +8506,13 @@ objects from the @code{graph} package.") (define-public r-fithic (package (name "r-fithic") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "FitHiC" version)) (sha256 (base32 - "1dffkdxm08wq4kjd9j2v2625x3p6vbrk33a2zx94pwpgkghr72yp")))) + "1sdfkqc6s7m9whkzr0mllzzfjzhj2g54ncjwxj8q0azjgszrfwd2")))) (properties `((upstream-name . "FitHiC"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From ed44a72acfde4840acbefdc5ed1759871dadcdbd Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:57:12 +0100 Subject: gnu: r-hitc: Update to 1.34.0. * gnu/packages/bioconductor.scm (r-hitc): Update to 1.34.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 9bcd95c7da..7793f927be 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8532,13 +8532,13 @@ assays such as Hi-C.") (define-public r-hitc (package (name "r-hitc") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "HiTC" version)) (sha256 (base32 - "1jx2pfa7sbdz7xi466lz1h5xv126g56z73n0a5l2wrq28k47qaxy")))) + "1xbh36qgmzl8b6xq0hnl41li2x18yma50fq0v4dglh2ddn7as9iy")))) (properties `((upstream-name . "HiTC"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 57820475dba2508bde5b9b787e8251ec969dffca Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:58:20 +0100 Subject: gnu: r-s4vectors: Update to 0.28.0. * gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.28.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 84b036c781..04919d6d81 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7832,13 +7832,13 @@ checks on R packages that are to be submitted to the Bioconductor repository.") (define-public r-s4vectors (package (name "r-s4vectors") - (version "0.26.1") + (version "0.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "S4Vectors" version)) (sha256 (base32 - "1ddr3ngyczx332zw9ai1a6h7442lgrbfcj8vrhvbkdkzqwj14xmb")))) + "0rfn46g2mfda01s75vpcfn5jc7xkp0jrl5v79gyd40jm37p4j1zv")))) (properties `((upstream-name . "S4Vectors"))) (build-system r-build-system) -- cgit v1.2.3 From cf6033ee6e45bb56c913b31289d61620971ca3be Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:58:23 +0100 Subject: gnu: r-iranges: Update to 2.24.0. * gnu/packages/bioinformatics.scm (r-iranges): Update to 2.24.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 04919d6d81..33ee7ce144 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7859,13 +7859,13 @@ S4Vectors package itself.") (define-public r-iranges (package (name "r-iranges") - (version "2.22.2") + (version "2.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "IRanges" version)) (sha256 (base32 - "1y24jw62806wp2afiyj1x6n00gj7d3323klqdypra9q43pg1w49d")))) + "1lfc8xz45v63y3q40im00i944hi0p9idwhx50w3nzkwdpk79315b")))) (properties `((upstream-name . "IRanges"))) (build-system r-build-system) -- cgit v1.2.3 From 47f6fd802e463c3a6d76a1960d0a40f30c8e58c5 Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Wed, 18 Nov 2020 15:45:14 +0100 Subject: gnu: Add r-ggalluvial. * gnu/packages/cran.scm (r-ggalluvial): New variable. --- gnu/packages/cran.scm | 29 +++++++++++++++++++++++++++++ 1 file changed, 29 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 9533006a26..05b1541ec7 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -256,6 +256,35 @@ ordered indexed observations. It is particularly aimed at irregular time series of numeric vectors/matrices and factors.") (license license:gpl2+))) +(define-public r-ggalluvial + (package + (name "r-ggalluvial") + (version "0.12.2") + (source (origin + (method url-fetch) + (uri (cran-uri "ggalluvial" version)) + (sha256 + (base32 + "1qcpbb6h2znsq246n1291rxgfryiw24caghbk8acjzzfbdhdj8x1")))) + (properties `((upstream-name . "ggalluvial"))) + (build-system r-build-system) + (propagated-inputs + `(("r-dplyr" ,r-dplyr) + ("r-ggplot2" ,r-ggplot2) + ("r-lazyeval" ,r-lazyeval) + ("r-rlang" ,r-rlang) + ("r-tidyr" ,r-tidyr) + ("r-tidyselect" ,r-tidyselect))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "http://corybrunson.github.io/ggalluvial/") + (synopsis "Alluvial plots for ggplot2") + (description "This package provides alluvial plots for @code{ggplot2}. +Alluvial plots use variable-width ribbons and stacked bar plots to represent +multi-dimensional or repeated-measures data with categorical or ordinal +variables.") + (license license:gpl3))) + (define-public r-ggpmisc (package (name "r-ggpmisc") -- cgit v1.2.3 From c8da013780711fa58832fedaa7956c4d2e08c8cd Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Wed, 18 Nov 2020 15:51:14 +0100 Subject: gnu: Add r-matrixgenerics. * gnu/packages/bioconductor.scm (r-matrixgenerics): New variable. --- gnu/packages/bioconductor.scm | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 7793f927be..97dcdfed3e 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1952,6 +1952,33 @@ for finding the peaks with bi-directional promoters with summary statistics enrichedGO (addGeneIDs).") (license license:gpl2+))) +(define-public r-matrixgenerics + (package + (name "r-matrixgenerics") + (version "1.2.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "MatrixGenerics" version)) + (sha256 + (base32 + "1a3sw79185d6rld3wlrynkzcbp754a7jkracrmvn0ra964ia8zvc")))) + (properties + `((upstream-name . "MatrixGenerics"))) + (build-system r-build-system) + (propagated-inputs + `(("r-matrixstats" ,r-matrixstats))) + (home-page "https://bioconductor.org/packages/MatrixGenerics") + (synopsis "S4 generic summary statistic functions for matrix-like objects") + (description + "This package provides S4 generic functions modeled after the +@code{matrixStats} API for alternative matrix implementations. Packages with +alternative matrix implementation can depend on this package and implement the +generic functions that are defined here for a useful set of row and column +summary statistics. Other package developers can import this package and +handle a different matrix implementations without worrying about +incompatibilities.") + (license license:artistic2.0))) + (define-public r-marray (package (name "r-marray") -- cgit v1.2.3 From fafa94b065aa20e62d139acbe4f2db30593ebd0e Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:59:03 +0100 Subject: gnu: r-delayedarray: Update to 0.16.0. * gnu/packages/bioinformatics.scm (r-delayedarray): Update to 0.16.0. [propagated-inputs]: Add r-matrixgenerics; remove r-matrixstats. --- gnu/packages/bioinformatics.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 33ee7ce144..a0912832d3 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8281,13 +8281,13 @@ tab-delimited (tabix) files.") (define-public r-delayedarray (package (name "r-delayedarray") - (version "0.14.1") + (version "0.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DelayedArray" version)) (sha256 (base32 - "0xi0i621hrl7k9rsc8x8nc3ib74sk8hxhbyr2lxqclw45pk95s7v")))) + "1564wnradxw15nsnv6w2wd3xngcs3xa1mlibbq3hygi5fcx4fk3g")))) (properties `((upstream-name . "DelayedArray"))) (build-system r-build-system) @@ -8296,7 +8296,7 @@ tab-delimited (tabix) files.") ("r-s4vectors" ,r-s4vectors) ("r-iranges" ,r-iranges) ("r-matrix" ,r-matrix) - ("r-matrixstats" ,r-matrixstats))) + ("r-matrixgenerics" ,r-matrixgenerics))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/DelayedArray") -- cgit v1.2.3 From 5992c25e7fa9c71f3c08642d62b58a544a7fa11f Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:57:15 +0100 Subject: gnu: r-hdf5array: Update to 1.18.0. * gnu/packages/bioconductor.scm (r-hdf5array): Update to 1.18.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 97dcdfed3e..3e4e2e9cbc 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8588,14 +8588,14 @@ provided.") (define-public r-hdf5array (package (name "r-hdf5array") - (version "1.16.1") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "HDF5Array" version)) (sha256 (base32 - "01767v90nl0499jcicpxngbbs0af5p9c5aasi5va01w3v5bnqddn")))) + "1hr149q03p09y1cjnx8av854j53041wfyq66xpsjw4mypzjf6f28")))) (properties `((upstream-name . "HDF5Array"))) (build-system r-build-system) (inputs -- cgit v1.2.3 From 79cb6af375a1a1778d5b053b693b6c19df0c4bb0 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:57:18 +0100 Subject: gnu: r-rhdf5lib: Update to 1.12.0. * gnu/packages/bioconductor.scm (r-rhdf5lib): Update to 1.12.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 3e4e2e9cbc..49fd547528 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8618,14 +8618,14 @@ block processing.") (define-public r-rhdf5lib (package (name "r-rhdf5lib") - (version "1.10.1") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rhdf5lib" version)) (sha256 (base32 - "0f45sqrvzj6x4mckalyp8366hm8v0rrmzklx3xd4gs6l2wallcn9")) + "0wia85a6dkgibsjcmpqas5068msck3h3bqpgw2x07bk189z4vay2")) (modules '((guix build utils))) (snippet '(begin -- cgit v1.2.3 From c5ae5c1c40bfa0299e728f31934ab4a45f9b8197 Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Thu, 19 Nov 2020 15:31:09 +0100 Subject: gnu: r-rhdf5lib: Fix build. * gnu/packages/bioconductor.scm (r-rhdf5lib)[arguments]: Fix build. --- gnu/packages/bioconductor.scm | 2 ++ 1 file changed, 2 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 49fd547528..840f937c2b 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8660,6 +8660,8 @@ block processing.") ;; Remove unnecessary store reference. (("C Compiler:.*") "C Compiler: GCC\n")) + (rename-file "hdf5/src/libhdf5.settings.in" + "hdf5/src/libhdf5.settings") (rename-file "Makevars.in" "Makevars") (substitute* "Makevars" (("@ZLIB_LIB@") "-lz") -- cgit v1.2.3 From b58c4e7613bc3e3602042dbf340f5116f4cae4bb Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 4 Dec 2020 03:06:21 +0100 Subject: gnu: r-cytolib: Fix r-rhdf5libs linking. * gnu/packages/bioconductor.scm (r-cytolib): [arguments]: Avoid to have a plain directory on the list of libraries to link. Co-authored-by: Ricardo Wurmus . --- gnu/packages/bioconductor.scm | 11 +++++++++++ 1 file changed, 11 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 840f937c2b..ab2595b229 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6009,6 +6009,17 @@ cluster count and membership by stability evidence in unsupervised analysis.") "1wylzps7wbvm64k62w5bbi8l74gaqca96psfapxfg6mcac5yz4qw")))) (properties `((upstream-name . "cytolib"))) (build-system r-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'fix-linking + (lambda _ + (substitute* "src/Makevars.in" + ;; This is to avoid having a plain directory on the list of + ;; libraries to link. + (("\\(RHDF5_LIBS\\)" match) + (string-append match "/libhdf5.a"))) + #t))))) (inputs `(("zlib" ,zlib))) (native-inputs -- cgit v1.2.3 From 26cf5eb5686b9a0464fc886f7219c6b9e8f2a889 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 4 Dec 2020 03:20:55 +0100 Subject: gnu: r-hdf5array: Fix r-rhdf5libs linking. * gnu/packages/bioconductor.scm (r-hdf5array): [arguments]: Avoid to have a plain directory on the list of libraries to link. Co-authored-by: Ricardo Wurmus . --- gnu/packages/bioconductor.scm | 11 +++++++++++ 1 file changed, 11 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index ab2595b229..0989d1bff4 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8609,6 +8609,17 @@ provided.") "1hr149q03p09y1cjnx8av854j53041wfyq66xpsjw4mypzjf6f28")))) (properties `((upstream-name . "HDF5Array"))) (build-system r-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'fix-linking + (lambda _ + (substitute* "src/Makevars" + ;; This is to avoid having a plain directory on the list of + ;; libraries to link. + (("\\(RHDF5LIB_LIBS\\)" match) + (string-append match "/libhdf5.a"))) + #t))))) (inputs `(("zlib" ,zlib))) (propagated-inputs -- cgit v1.2.3 From ece564f07dc7398ff9739555708c9bda31262ceb Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 4 Dec 2020 04:55:45 +0100 Subject: gnu: r-flowworkspace: Fix r-rhdf5libs linking. * gnu/packages/bioconductor.scm (r-flowworkspace): [arguments]: Avoid to have a plain directory on the list of libraries to link. --- gnu/packages/bioconductor.scm | 11 +++++++++++ 1 file changed, 11 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 0989d1bff4..ce831af6d4 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6281,6 +6281,17 @@ for other R packages to compile and link against.") "19svh32jq1dpq3ayhpd5r8bw0iax8d9kdvpvc23gx2pf16g1j5ag")))) (properties `((upstream-name . "flowWorkspace"))) (build-system r-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'fix-linking + (lambda _ + (substitute* "src/Makevars" + ;; This is to avoid having a plain directory on the list of + ;; libraries to link. + (("\\{h5lib\\}" match) + (string-append match "/libhdf5.a"))) + #t))))) (inputs `(("zlib" ,zlib))) (propagated-inputs -- cgit v1.2.3 From 2b224f904a18bd84080119ee57d4f2750a0da732 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 4 Dec 2020 05:07:38 +0100 Subject: gnu: r-cytoml: Fix r-rhdf5libs linking. * gnu/packages/bioconductor.scm (r-cytoml): [arguments]: Avoid to have a plain directory on the list of libraries to link. --- gnu/packages/bioconductor.scm | 11 +++++++++++ 1 file changed, 11 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index ce831af6d4..299204540d 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6426,6 +6426,17 @@ sequential way to mimic the manual gating strategy.") "1d8x49aqc95x1vx456hya5r7mal80pj9l6wmr5x5pb5r8qyzz6yq")))) (properties `((upstream-name . "CytoML"))) (build-system r-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'fix-linking + (lambda _ + (substitute* "src/Makevars.in" + ;; This is to avoid having a plain directory on the list of + ;; libraries to link. + (("\\{h5lib\\}" match) + (string-append match "/libhdf5.a"))) + #t))))) (inputs `(("libxml2" ,libxml2))) (propagated-inputs -- cgit v1.2.3 From 0022e9f4c000f2b8054b470a06d75f62b2b8cafb Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 4 Dec 2020 03:35:34 +0100 Subject: gnu: r-ncdfflow: Fix r-rhdf5libs link. * gnu/packages/bioconductor.scm (r-ncdfflow): [arguments]: Avoid to have a plain directory on the list of libraries to link. Co-authored-by: Ricardo Wurmus . --- gnu/packages/bioconductor.scm | 11 +++++++++++ 1 file changed, 11 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 299204540d..76a82ffd67 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6110,6 +6110,17 @@ change point detection.") "1knqc3ic2vpck7n7m7adxjz3ac70ra89d5gvlgp9r2q3kgaciwac")))) (properties `((upstream-name . "ncdfFlow"))) (build-system r-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'fix-linking + (lambda _ + (substitute* "src/Makevars" + ;; This is to avoid having a plain directory on the list of + ;; libraries to link. + (("\\(RHDF5_LIBS\\)" match) + (string-append match "/libhdf5.a"))) + #t))))) (inputs `(("zlib" ,zlib))) (propagated-inputs -- cgit v1.2.3 From fe4ce29a5c21387a66a87bf76cf479414a9147c5 Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Wed, 18 Nov 2020 17:20:48 +0100 Subject: gnu: r-beachmat: Update to 2.6.1. * gnu/packages/bioconductor.scm (r-beachmat): Update to 2.6.1. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 76a82ffd67..867dc7083f 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8757,14 +8757,14 @@ packages.") (define-public r-beachmat (package (name "r-beachmat") - (version "2.4.0") + (version "2.6.1") (source (origin (method url-fetch) (uri (bioconductor-uri "beachmat" version)) (sha256 (base32 - "1vl6jbf9ia78cm4ikdb8vz04jv4b46zhvg5i006c63a9pzw7zhxi")))) + "0dkh3igvwbvir4p0y6x4q07mcv51b35qhva63vrjd6bbkdjn9brr")))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) -- cgit v1.2.3 From 64cf667e98c9eae83589750d4112302b6ffac1bf Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:57:36 +0100 Subject: gnu: r-genefilter: Update to 1.72.0. * gnu/packages/bioinformatics.scm (r-genefilter): Update to 1.72.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index a0912832d3..b911ef4e64 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7142,14 +7142,14 @@ information as possible.") (define-public r-genefilter (package (name "r-genefilter") - (version "1.70.0") + (version "1.72.0") (source (origin (method url-fetch) (uri (bioconductor-uri "genefilter" version)) (sha256 (base32 - "1sbbrnq6p90fri0ik6aq2zw26kasw63nyiy7xkzrj6vgyq7x258g")))) + "0929g6c4v2qhgipgrh1a5gv6444sm2dp52x9c3qbk03i8wzc6633")))) (build-system r-build-system) (native-inputs `(("gfortran" ,gfortran) -- cgit v1.2.3 From 936227f1440bb17f2168552e990fa8bc7521ce39 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:57:39 +0100 Subject: gnu: r-deseq2: Update to 1.30.0. * gnu/packages/bioinformatics.scm (r-deseq2): Update to 1.30.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index b911ef4e64..d72f8b87b1 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7170,14 +7170,14 @@ high-throughput sequencing experiments.") (define-public r-deseq2 (package (name "r-deseq2") - (version "1.28.1") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DESeq2" version)) (sha256 (base32 - "0xh12c2skr0bbv893p05gvbismkcnqw8zwh7yz4wmycgajfzg2pp")))) + "0q2f9cywrcmp1p7ii8f45g4dk4hsnjflq3yqhsxgnpv9fw338qpp")))) (properties `((upstream-name . "DESeq2"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From a323c1e9b4069905ee27df5a16729b2c1e252f1e Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:57:43 +0100 Subject: gnu: r-dexseq: Update to 1.36.0. * gnu/packages/bioinformatics.scm (r-dexseq): Update to 1.36.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index d72f8b87b1..ff869bd06b 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7208,14 +7208,14 @@ distribution.") (define-public r-dexseq (package (name "r-dexseq") - (version "1.34.1") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DEXSeq" version)) (sha256 (base32 - "1m03awaw06mfv5gszq23k5apsqqzjqa5rcwp20y4xbpl7bywpsyl")))) + "0wfjb42xcr4wjy8a654b74411dky8hp6sp8xdwf0sxqgsxy106qi")))) (properties `((upstream-name . "DEXSeq"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 4451918e3a1db84a8f4c51e7b42590c9ed34589e Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:57:46 +0100 Subject: gnu: r-annotationforge: Update to 1.32.0. * gnu/packages/bioinformatics.scm (r-annotationforge): Update to 1.32.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index ff869bd06b..1c080d72d9 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7253,14 +7253,14 @@ exploration of the results.") (define-public r-annotationforge (package (name "r-annotationforge") - (version "1.30.1") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AnnotationForge" version)) (sha256 (base32 - "1a2155jxbwc6qr3dcyvp850grhdr7czc7bs3s87ff4sgdl0jp3jw")))) + "0y3820dkvwz09wlmz9drx6gqpsr9cwppaiz40zafwfxbz65y8px7")))) (properties `((upstream-name . "AnnotationForge"))) (build-system r-build-system) -- cgit v1.2.3 From 7a57b229b6d778dd4d37c2a22d570007fffe77cd Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:57:49 +0100 Subject: gnu: r-rbgl: Update to 1.66.0. * gnu/packages/bioinformatics.scm (r-rbgl): Update to 1.66.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 1c080d72d9..b01e92e1b9 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7285,14 +7285,14 @@ databases. Packages produced are intended to be used with AnnotationDbi.") (define-public r-rbgl (package (name "r-rbgl") - (version "1.64.0") + (version "1.66.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RBGL" version)) (sha256 (base32 - "079599a6xn2i7snfn2vgshkw0c00rrfhj44pvi03ap8id29bkayy")))) + "016vyzgixb3gjpzi21rbs6ngnnqcxr77krwjjf1ldnzzj8vqrqsz")))) (properties `((upstream-name . "RBGL"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 03312f052afd7d0113c7165a7b026b69245c64b0 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:57:52 +0100 Subject: gnu: r-gseabase: Update to 1.52.0. * gnu/packages/bioinformatics.scm (r-gseabase): Update to 1.52.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index b01e92e1b9..fdd2d1a50b 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7308,14 +7308,14 @@ the graph algorithms contained in the Boost library.") (define-public r-gseabase (package (name "r-gseabase") - (version "1.50.1") + (version "1.52.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GSEABase" version)) (sha256 (base32 - "1k4faj53cwvqijad8cf7fcghzxcv9shlbpl8n73bsncc8k192y2j")))) + "0lcxbxfg62zdf2nql49asn3555cqrrxpjm2xsxf7vlxv84dl6r44")))) (properties `((upstream-name . "GSEABase"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From afbc8e143359f70330cc7578da805787b373bd5f Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:57:55 +0100 Subject: gnu: r-category: Update to 2.56.0. * gnu/packages/bioinformatics.scm (r-category): Update to 2.56.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index fdd2d1a50b..c5109a3e4f 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7337,14 +7337,14 @@ Enrichment Analysis} (GSEA).") (define-public r-category (package (name "r-category") - (version "2.54.0") + (version "2.56.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Category" version)) (sha256 (base32 - "1grspdzk5a4vidnxwcd1jmy1vcn494aydsp3vydx235yv7iqac1b")))) + "0m77wpnica0h2ia9ajdaiga4plgz1s9wls6pdnxzk7kwl8a68wkr")))) (properties `((upstream-name . "Category"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 74204b48eb28d9c7bbceefff0832a5c373b2f7e3 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:57:58 +0100 Subject: gnu: r-gostats: Update to 2.56.0. * gnu/packages/bioinformatics.scm (r-gostats): Update to 2.56.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index c5109a3e4f..5fe661da0f 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7368,14 +7368,14 @@ analysis.") (define-public r-gostats (package (name "r-gostats") - (version "2.54.0") + (version "2.56.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GOstats" version)) (sha256 (base32 - "00q39cyv4l28r6s9gjnd0qhl7h80vmwp4lpmchisqzj44xzyics9")))) + "18q8p0fv9fl2r6zjxknfjwqxr69dlyxy6c8amzn6c6dwjq1cxk6j")))) (properties `((upstream-name . "GOstats"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From a05bb428e470f2a908895249365ce0cb178e2471 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:58:01 +0100 Subject: gnu: r-shortread: Update to 1.48.0. * gnu/packages/bioinformatics.scm (r-shortread): Update to 1.48.0. --- gnu/packages/bioinformatics.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 5fe661da0f..db410b63c3 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7399,14 +7399,14 @@ testing and other simple calculations.") (define-public r-shortread (package (name "r-shortread") - (version "1.46.0") + (version "1.48.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ShortRead" version)) (sha256 (base32 - "0l4kdln69y6yhln0xiv2jmpxg05fjcglln406p43a2bqvk2lr03d")))) + "0w4m8d3h660mmr2ymp206r1n4aqssxmkv8yxkbr5y1swrahxzfk9")))) (properties `((upstream-name . "ShortRead"))) (build-system r-build-system) (inputs @@ -7419,6 +7419,7 @@ testing and other simple calculations.") ("r-genomeinfodb" ,r-genomeinfodb) ("r-genomicalignments" ,r-genomicalignments) ("r-genomicranges" ,r-genomicranges) + ("r-rhtslib" ,r-rhtslib) ("r-hwriter" ,r-hwriter) ("r-iranges" ,r-iranges) ("r-lattice" ,r-lattice) -- cgit v1.2.3 From 5598f53497407871d124cc2f74e375ed6d99e026 Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Wed, 18 Nov 2020 15:59:02 +0100 Subject: gnu: r-systempiper: Update to 1.24.2. * gnu/packages/bioinformatics.scm (r-systempiper): Update to 1.24.2. [propagated-inputs]: Add r-iranges. --- gnu/packages/bioinformatics.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index db410b63c3..ac31c38a1c 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7442,14 +7442,14 @@ ungapped alignment formats.") (define-public r-systempiper (package (name "r-systempiper") - (version "1.22.0") + (version "1.24.2") (source (origin (method url-fetch) (uri (bioconductor-uri "systemPipeR" version)) (sha256 (base32 - "01ilhlrvy28jfdyxjria4024yryj5zgympgqznw17g3y3az78kk2")))) + "0blvvci57q12sl18yvw07233rfnj47mfadzm0pdpig1ll5z6ld2j")))) (properties `((upstream-name . "systemPipeR"))) (build-system r-build-system) (propagated-inputs @@ -7465,6 +7465,7 @@ ungapped alignment formats.") ("r-ggplot2" ,r-ggplot2) ("r-go-db" ,r-go-db) ("r-gostats" ,r-gostats) + ("r-iranges" ,r-iranges) ("r-limma" ,r-limma) ("r-magrittr" ,r-magrittr) ("r-pheatmap" ,r-pheatmap) -- cgit v1.2.3 From 16a4822a07644a30dcd9aabf404434da1105d05f Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:58:07 +0100 Subject: gnu: r-grohmm: Update to 1.24.0. * gnu/packages/bioinformatics.scm (r-grohmm): Update to 1.24.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index ac31c38a1c..12bc10c892 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7496,14 +7496,14 @@ annotation infrastructure.") (define-public r-grohmm (package (name "r-grohmm") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "groHMM" version)) (sha256 (base32 - "04z9qq1xwdsaxbqhyld37w0ybvzly9pc1hcyrnwdbyjwd7n1fncb")))) + "08pap9wsaxl4jjlc1py0rc019gmi6daa0f9cr3ih1d97wybncanx")))) (properties `((upstream-name . "groHMM"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 182a080127f0905ed59b212622919a2878315a84 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:58:10 +0100 Subject: gnu: r-biocviews: Update to 1.58.0. * gnu/packages/bioinformatics.scm (r-biocviews): Update to 1.58.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 12bc10c892..745cbb8fd7 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7729,13 +7729,13 @@ BLAST, KEGG, GenBank, MEDLINE and GO.") (define-public r-biocviews (package (name "r-biocviews") - (version "1.56.2") + (version "1.58.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biocViews" version)) (sha256 (base32 - "0kw0qfm1fw5yv2rbz6x23431rh0fnzj66f2bls7j285biyjmmx7w")))) + "0f0aa51h9x8n114zz6q6iw45d78i9wzl4ycbpiy0bdn23167pd84")))) (properties `((upstream-name . "biocViews"))) (build-system r-build-system) -- cgit v1.2.3 From 1160c83cafc605178b2377d137d62d02430c9fea Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:58:13 +0100 Subject: gnu: r-biocstyle: Update to 2.18.0. * gnu/packages/bioinformatics.scm (r-biocstyle): Update to 2.18.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 745cbb8fd7..e3f345f4ea 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7757,13 +7757,13 @@ also known as views, in a controlled vocabulary.") (define-public r-biocstyle (package (name "r-biocstyle") - (version "2.16.1") + (version "2.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocStyle" version)) (sha256 (base32 - "09sz2bnbfbj8wz16k0q8xrvag9fldxqyp5vbg9pvd9skh28hv7c7")))) + "1hfdvld0n9py45mxm05kbb0sq0s9p8yky3s6jb02gzhlxkk3q4fs")))) (properties `((upstream-name . "BiocStyle"))) (build-system r-build-system) -- cgit v1.2.3 From 2ae3b7db24d39104eec9b75099bb6572a3409d76 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:58:17 +0100 Subject: gnu: r-bioccheck: Update to 1.26.0. * gnu/packages/bioinformatics.scm (r-bioccheck): Update to 1.26.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index e3f345f4ea..06b1736558 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7785,13 +7785,13 @@ functionality.") (define-public r-bioccheck (package (name "r-bioccheck") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocCheck" version)) (sha256 (base32 - "1p9ys18sn1crxw1iac2jdgqvwpb5hjd9nfxx0qn0ncrv0b550mny")))) + "1hyncn9zqj432da95k86rm5b28nbwrvzm52jbhisifkxj1j43cib")))) (properties `((upstream-name . "BiocCheck"))) (build-system r-build-system) -- cgit v1.2.3 From cde7fcedf9d67fca18436fbe01e16d21f6822a66 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:58:26 +0100 Subject: gnu: r-genomeinfodb: Update to 1.26.0. * gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.26.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 06b1736558..be71cad7ff 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7913,13 +7913,13 @@ ID and species. It is used by functions in the GenomeInfoDb package.") (define-public r-genomeinfodb (package (name "r-genomeinfodb") - (version "1.24.2") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomeInfoDb" version)) (sha256 (base32 - "1cqs53p4m5q1dr59war72bccphy01ilw4xra24fmngrv4x32rznd")))) + "1xfhz7gmccijy2z015w07lh04g0ijh7zi6k7q6m4lripgban93g9")))) (properties `((upstream-name . "GenomeInfoDb"))) (build-system r-build-system) -- cgit v1.2.3 From 5996929b361279bc2fa409feb0f1fb8b9d0b305c Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:58:29 +0100 Subject: gnu: r-edger: Update to 3.32.0. * gnu/packages/bioinformatics.scm (r-edger): Update to 3.32.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index be71cad7ff..5589055b48 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7943,13 +7943,13 @@ names in their natural, rather than lexicographic, order.") (define-public r-edger (package (name "r-edger") - (version "3.30.3") + (version "3.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "edgeR" version)) (sha256 (base32 - "1z9bkg08rgqn3jm2s4ndbj641w33wl8jd3j6m5if6h2nnw6011ic")))) + "0dkjd6li270icy1x5qbzpakk9bx712mdm5k32lrr3yrggq92jhjg")))) (properties `((upstream-name . "edgeR"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From d972ab690ee9e70da8df246c6163cbbeec7a239f Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:58:35 +0100 Subject: gnu: r-limma: Update to 3.46.0. * gnu/packages/bioinformatics.scm (r-limma): Update to 3.46.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 5589055b48..fc0085ef38 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8010,13 +8010,13 @@ coding changes and predict coding outcomes.") (define-public r-limma (package (name "r-limma") - (version "3.44.3") + (version "3.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "limma" version)) (sha256 (base32 - "09fnqxx4rzq5n447aqg2l6y0idfwgz2jxz99sifxsr2q8afzbcj6")))) + "1xxv493q1kip9bjfv7v7k5dnq7hz7gvl80i983v4mvwavhgnbxfz")))) (build-system r-build-system) (home-page "http://bioinf.wehi.edu.au/limma") (synopsis "Package for linear models for microarray and RNA-seq data") -- cgit v1.2.3 From 7641dba3e6ae8b09af23e7de8adb254954cd5800 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:58:41 +0100 Subject: gnu: r-genomicranges: Update to 1.42.0. * gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.42.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index fc0085ef38..4a2d124b7a 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8065,13 +8065,13 @@ different technologies, including microarrays, RNA-seq, and quantitative PCR.") (define-public r-genomicranges (package (name "r-genomicranges") - (version "1.40.0") + (version "1.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicRanges" version)) (sha256 (base32 - "0wn1zr2qq0rpv9z2wialgizn6xzdlcjg1w2kif67n53svz6vk2x1")))) + "0j4py5g6pdj35xhlaqhxxhg55j9l4mcdk3yck4dgyavv5f2dh24i")))) (properties `((upstream-name . "GenomicRanges"))) (build-system r-build-system) -- cgit v1.2.3 From 9103041d1305f6c923f013487085825d9e546940 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:58:44 +0100 Subject: gnu: r-biobase: Update to 2.50.0. * gnu/packages/bioinformatics.scm (r-biobase): Update to 2.50.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 4a2d124b7a..1f867f3981 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8096,13 +8096,13 @@ manipulating genomic intervals and variables defined along a genome.") (define-public r-biobase (package (name "r-biobase") - (version "2.48.0") + (version "2.50.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Biobase" version)) (sha256 (base32 - "13p3kgnxm7hbn8cy289kbhaiyfa6rxx7l1pbvajwqzbay3cxznqp")))) + "11kgc4flywlm3i18603558l8ksv91c24vkc5fnnbcd375i2dhhd4")))) (properties `((upstream-name . "Biobase"))) (build-system r-build-system) -- cgit v1.2.3 From f517365cef5ba849b6704a5c3b4af81273bf9de0 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:58:48 +0100 Subject: gnu: r-annotationdbi: Update to 1.52.0. * gnu/packages/bioinformatics.scm (r-annotationdbi): Update to 1.52.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 1f867f3981..9a97c2e127 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8118,13 +8118,13 @@ on Bioconductor or which replace R functions.") (define-public r-annotationdbi (package (name "r-annotationdbi") - (version "1.50.3") + (version "1.52.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AnnotationDbi" version)) (sha256 (base32 - "0qcxfn4pvaksna0nvxr74ysn2wzaxn732pkhd6ffrj8pwhkhy5p3")))) + "0zqxgh3nx6y8ry12s2vss2f4axz5vpqxha1y4ifhhcx4zhpzsglr")))) (properties `((upstream-name . "AnnotationDbi"))) (build-system r-build-system) -- cgit v1.2.3 From 4fac3fe67dbdc2858584f1ed8adfe09c5526e9ef Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:58:51 +0100 Subject: gnu: r-biomart: Update to 2.46.0. * gnu/packages/bioinformatics.scm (r-biomart): Update to 2.46.0. --- gnu/packages/bioinformatics.scm | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 9a97c2e127..55189cc5a2 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8147,13 +8147,13 @@ annotation data packages using SQLite data storage.") (define-public r-biomart (package (name "r-biomart") - (version "2.44.1") + (version "2.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biomaRt" version)) (sha256 (base32 - "0np4nh3gj60mgb6312z7x0z9fg5bhrhw872sp3dzgmqc8q8b84iz")))) + "1zpdm8nw1d0m31pdmzw1dccbd6iczfhiklhm4d325zkzf3jrkvxf")))) (properties `((upstream-name . "biomaRt"))) (build-system r-build-system) @@ -8165,7 +8165,8 @@ annotation data packages using SQLite data storage.") ("r-progress" ,r-progress) ("r-rappdirs" ,r-rappdirs) ("r-stringr" ,r-stringr) - ("r-xml" ,r-xml))) + ("r-xml" ,r-xml) + ("r-xml2" ,r-xml2))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/biomaRt") -- cgit v1.2.3 From 444b101dc2ef3da7e4c04284b6c42ab4c6eb3beb Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Wed, 18 Nov 2020 16:01:34 +0100 Subject: gnu: r-biocparallel: Update to 1.24.1. * gnu/packages/bioconductor.scm (r-biocparallel): Update to 1.24.1. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 55189cc5a2..2607b6444f 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8185,13 +8185,13 @@ powerful online queries from gene annotation to database mining.") (define-public r-biocparallel (package (name "r-biocparallel") - (version "1.22.0") + (version "1.24.1") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocParallel" version)) (sha256 (base32 - "1lsg5xm5j3ly5k60fidzhkgqc9jgscyfkqngjvd9qp6yfzvsb82g")))) + "1iryicvmcagcrj29kp49mqhiq2kn72j4idj380hi9illmdrg9ism")))) (properties `((upstream-name . "BiocParallel"))) (build-system r-build-system) -- cgit v1.2.3 From 5d60273b7749523f653f2060a178dc35b03de35b Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:58:57 +0100 Subject: gnu: r-biostrings: Update to 2.58.0. * gnu/packages/bioinformatics.scm (r-biostrings): Update to 2.58.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 2607b6444f..a59c39a237 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8212,13 +8212,13 @@ objects.") (define-public r-biostrings (package (name "r-biostrings") - (version "2.56.0") + (version "2.58.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Biostrings" version)) (sha256 (base32 - "0imhfz7dg8b3l5qzipjranqqshdsg2x6zc49drlhn8sc7j40cvi8")))) + "1rbqhs73mhfr1gi0rx28jiyan7i3hb45ai3jpl1656fnrhgjfxq5")))) (properties `((upstream-name . "Biostrings"))) (build-system r-build-system) -- cgit v1.2.3 From 9168ab09112fb0204a6c90d90aea5cf422a74ccc Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:59:00 +0100 Subject: gnu: r-rsamtools: Update to 2.6.0. * gnu/packages/bioinformatics.scm (r-rsamtools): Update to 2.6.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index a59c39a237..b9c1813460 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8239,13 +8239,13 @@ biological sequences or sets of sequences.") (define-public r-rsamtools (package (name "r-rsamtools") - (version "2.4.0") + (version "2.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rsamtools" version)) (sha256 (base32 - "0z01z0s71f941k7sns46nyabps28c69d6jxx6sppjpc6h4vrw0vq")))) + "040pggkwglc6wy90qnc7xcdnaj0v3iqlykvvsl74241409qly554")))) (properties `((upstream-name . "Rsamtools"))) (build-system r-build-system) -- cgit v1.2.3 From 8607a5394b4fa44334ba909d190cb97acb13191c Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:59:06 +0100 Subject: gnu: r-summarizedexperiment: Update to 1.20.0. * gnu/packages/bioinformatics.scm (r-summarizedexperiment): Update to 1.20.0. [propagated-inputs]: Add r-matrixgenerics. --- gnu/packages/bioinformatics.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index b9c1813460..25d574b716 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8317,13 +8317,13 @@ array-like objects like @code{DataFrame} objects (typically with Rle columns), (define-public r-summarizedexperiment (package (name "r-summarizedexperiment") - (version "1.18.2") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "SummarizedExperiment" version)) (sha256 (base32 - "1raw5ycigr6gjgzn3kx3jls5hzww10fhnwd8c17c20hmhirf13rw")))) + "04x6d4mcsnvz6glkmf6k2cv3fs8zk03i9rvv0ahpl793n8l411ps")))) (properties `((upstream-name . "SummarizedExperiment"))) (build-system r-build-system) @@ -8335,6 +8335,7 @@ array-like objects like @code{DataFrame} objects (typically with Rle columns), ("r-genomicranges" ,r-genomicranges) ("r-iranges" ,r-iranges) ("r-matrix" ,r-matrix) + ("r-matrixgenerics" ,r-matrixgenerics) ("r-s4vectors" ,r-s4vectors))) (native-inputs `(("r-knitr" ,r-knitr))) -- cgit v1.2.3 From 3ca5b0547460c8866b63931b9ea355191b64b2d2 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:58:32 +0100 Subject: gnu: r-variantannotation: Update to 1.36.0. * gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.36.0. [propagated-inputs]: Add r-matrixgenerics. --- gnu/packages/bioinformatics.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 25d574b716..ab33194543 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7971,13 +7971,13 @@ CAGE.") (define-public r-variantannotation (package (name "r-variantannotation") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "VariantAnnotation" version)) (sha256 (base32 - "09y6ymwky839nb0y7y93w810hk9mvwqn7595q1276c28dkddiqvw")))) + "1sl0l6v05lfglj281nszma0h5k234md7rn2pdah8vs2d4iq3kimw")))) (properties `((upstream-name . "VariantAnnotation"))) (inputs @@ -7993,6 +7993,7 @@ CAGE.") ("r-genomicfeatures" ,r-genomicfeatures) ("r-genomicranges" ,r-genomicranges) ("r-iranges" ,r-iranges) + ("r-matrixgenerics" ,r-matrixgenerics) ("r-summarizedexperiment" ,r-summarizedexperiment) ("r-rhtslib" ,r-rhtslib) ("r-rsamtools" ,r-rsamtools) -- cgit v1.2.3 From 077e813657b46dff06bdb80a9cd1e6411be7eb91 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:59:09 +0100 Subject: gnu: r-genomicalignments: Update to 1.26.0. * gnu/packages/bioinformatics.scm (r-genomicalignments): Update to 1.26.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index ab33194543..174a52dccf 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8352,13 +8352,13 @@ samples.") (define-public r-genomicalignments (package (name "r-genomicalignments") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicAlignments" version)) (sha256 (base32 - "0v8k6d7frm5p48cmk4zik78cw9abz4inx0zhl4zrmmx31ifyvk8d")))) + "1q95px6s6snsax4ax955zzpdlrwp5liwf70wqq0lrk9mp6lq0hbr")))) (properties `((upstream-name . "GenomicAlignments"))) (build-system r-build-system) -- cgit v1.2.3 From 92377e7fea9f5222607267aa5e3057f8b3113477 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:59:12 +0100 Subject: gnu: r-rtracklayer: Update to 1.50.0. * gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.50.0. --- gnu/packages/bioinformatics.scm | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 174a52dccf..976626e6d4 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8385,13 +8385,13 @@ alignments.") (define-public r-rtracklayer (package (name "r-rtracklayer") - (version "1.48.0") + (version "1.50.0") (source (origin (method url-fetch) (uri (bioconductor-uri "rtracklayer" version)) (sha256 (base32 - "1zcgk92sidhy4y7ws9ms4nkkh2hnccfhfh53qgna0kma9jy4v5xf")))) + "12zimhpdzjyzd81wrzz5hdbzvlgzcs22x1nnaf2jq4cba3ch5px8")))) (build-system r-build-system) (arguments `(#:phases @@ -8418,7 +8418,8 @@ alignments.") ("r-rsamtools" ,r-rsamtools) ("r-s4vectors" ,r-s4vectors) ("r-xml" ,r-xml) - ("r-xvector" ,r-xvector))) + ("r-xvector" ,r-xvector) + ("r-zlibbioc" ,r-zlibbioc))) (home-page "https://bioconductor.org/packages/rtracklayer") (synopsis "R interface to genome browsers and their annotation tracks") (description -- cgit v1.2.3 From 26e2184fc13558630f3f6fae3874fdc1d6880d9a Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Wed, 18 Nov 2020 16:03:39 +0100 Subject: gnu: r-genomicfeatures: Update to 1.42.1. * gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.42.1. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 976626e6d4..f6b860c6b9 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8433,13 +8433,13 @@ as well as query and modify the browser state, such as the current viewport.") (define-public r-genomicfeatures (package (name "r-genomicfeatures") - (version "1.40.1") + (version "1.42.1") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicFeatures" version)) (sha256 (base32 - "0zm7q957g952qyfqmvf27sldsnq6sqd0wlgnqzvmxayg9pxh0l0z")))) + "17dyd9hcw6pw16y353dh55wfhxmkxka99lbsxsp9xyrhffwrxi0s")))) (properties `((upstream-name . "GenomicFeatures"))) (build-system r-build-system) -- cgit v1.2.3 From 6a7de43a5858b7969c3a96e34f849ec074a3a1fc Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Wed, 18 Nov 2020 16:04:40 +0100 Subject: gnu: r-topgo: Update to 2.42.0. * gnu/packages/bioinformatics.scm (r-topgo): Update to 2.42.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index f6b860c6b9..79a7c1b1c4 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8500,13 +8500,13 @@ information about the latest version of the Gene Ontologies.") (define-public r-topgo (package (name "r-topgo") - (version "2.40.0") + (version "2.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "topGO" version)) (sha256 (base32 - "13rhbvn27sj75fklf1cnjaazacx8yyjlhqlnbp5zk157q6y5cwdr")))) + "0vr3l9gvd3dhy446k3fkj6rm7z1abxi56rbnrs64297yzxaz1ngl")))) (properties `((upstream-name . "topGO"))) (build-system r-build-system) -- cgit v1.2.3 From e2e11f095f5e18f0d61b20b293e1ac55fd8f5906 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:59:22 +0100 Subject: gnu: r-bsgenome: Update to 1.58.0. * gnu/packages/bioinformatics.scm (r-bsgenome): Update to 1.58.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 79a7c1b1c4..3b4dd9bc7e 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8533,13 +8533,13 @@ dependencies between GO terms can be implemented and applied.") (define-public r-bsgenome (package (name "r-bsgenome") - (version "1.56.0") + (version "1.58.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BSgenome" version)) (sha256 (base32 - "1jw8r1qm9fpg2s1cw2y4np243jjxm65j2xdy2785h8fc1b02msf6")))) + "1gbvmxr6r57smgvhqgwspbcnwyk4hsfkxkpzzcs6470q03zfb4wq")))) (properties `((upstream-name . "BSgenome"))) (build-system r-build-system) -- cgit v1.2.3 From a180744b378aa72c24d6c92c4b3955f44694e9c6 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:59:25 +0100 Subject: gnu: r-impute: Update to 1.64.0. * gnu/packages/bioinformatics.scm (r-impute): Update to 1.64.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 3b4dd9bc7e..586d149abd 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8564,13 +8564,13 @@ genome data packages and support for efficient SNP representation.") (define-public r-impute (package (name "r-impute") - (version "1.62.0") + (version "1.64.0") (source (origin (method url-fetch) (uri (bioconductor-uri "impute" version)) (sha256 (base32 - "161p6l1cp3wwdynkxwvg0yhrh6yv20brdlplw5w5mavn4hf1nm0h")))) + "1pnjasw9i19nmxwjzrd9jbln31yc5jilfvwk414ya5zbqfsazvxa")))) (native-inputs `(("gfortran" ,gfortran))) (build-system r-build-system) -- cgit v1.2.3 From 44bf116f033a0abf5dba904008c4f82951a0c4dc Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:59:28 +0100 Subject: gnu: r-seqpattern: Update to 1.22.0. * gnu/packages/bioinformatics.scm (r-seqpattern): Update to 1.22.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 586d149abd..8433a23771 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8584,13 +8584,13 @@ microarray data, using nearest neighbor averaging.") (define-public r-seqpattern (package (name "r-seqpattern") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "seqPattern" version)) (sha256 (base32 - "0f1yvx2ri1557rzjx08q5bgml1cvkm8hjl8xn1qi4rjs64sy6mci")))) + "0j68n6fwycxjpl2va5fw7ajb123n758s2pq997d76dysxghmrlzq")))) (properties `((upstream-name . "seqPattern"))) (build-system r-build-system) -- cgit v1.2.3 From 2a70c96e3dc1a1393da478f0e533bdab84e510e5 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:59:31 +0100 Subject: gnu: r-genomation: Update to 1.22.0. * gnu/packages/bioinformatics.scm (r-genomation): Update to 1.22.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 8433a23771..ff9b3f41ed 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8611,13 +8611,13 @@ reference point and sorted by a user defined feature.") (define-public r-genomation (package (name "r-genomation") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "genomation" version)) (sha256 (base32 - "1cy8kqwddiha5jy6nda1al956i4wncbgjkrxwijdb08cmka2sfwh")))) + "1ana06irlpdgnmk8mb329nws9sm8n6max4qargf1xdcdf3rnk45g")))) (build-system r-build-system) (propagated-inputs `(("r-biostrings" ,r-biostrings) -- cgit v1.2.3 From 329879b70cd93ab7ae1caa8cb0067dc8b3d39a02 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:59:34 +0100 Subject: gnu: r-seqlogo: Update to 1.56.0. * gnu/packages/bioinformatics.scm (r-seqlogo): Update to 1.56.0. --- gnu/packages/bioinformatics.scm | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index ff9b3f41ed..aa1f21e4ba 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8687,16 +8687,18 @@ downloaded from Encode.") (define-public r-seqlogo (package (name "r-seqlogo") - (version "1.54.3") + (version "1.56.0") (source (origin (method url-fetch) (uri (bioconductor-uri "seqLogo" version)) (sha256 (base32 - "09kkxir305fv8z2yyihvspkrzclxbw1cx5mvhfkrhl10rap6662j")))) + "02rpzjjfg5chlwwfbvv72cm78cg2vfmdwzars0cin9hz1hd7rnq1")))) (properties `((upstream-name . "seqLogo"))) (build-system r-build-system) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/seqLogo") (synopsis "Sequence logos for DNA sequence alignments") (description -- cgit v1.2.3 From b0d85e36f1258e2a5bed5cf00f09065e193a9cd1 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:59:37 +0100 Subject: gnu: r-zlibbioc: Update to 1.36.0. * gnu/packages/bioinformatics.scm (r-zlibbioc): Update to 1.36.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index aa1f21e4ba..c1f2e8d010 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8737,13 +8737,13 @@ throughput genetic sequencing data sets using regression methods.") (define-public r-zlibbioc (package (name "r-zlibbioc") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "zlibbioc" version)) (sha256 (base32 - "0j1l052jb2cwc1nifxzwknc9csagf4f2d092zs0i95dz0rma89l0")))) + "0m36ddss0znvm19dhnxcclxjhgjplw8ajk8v419h20ab8an6khxg")))) (properties `((upstream-name . "zlibbioc"))) (build-system r-build-system) -- cgit v1.2.3 From 728369634f8ad4f658a17a169a3b9e236c15ff07 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:59:40 +0100 Subject: gnu: r-rhtslib: Update to 1.22.0. * gnu/packages/bioinformatics.scm (r-rhtslib): Update to 1.22.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index c1f2e8d010..211930fef1 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8779,14 +8779,14 @@ secondary structure and comparative analysis in R.") (define-public r-rhtslib (package (name "r-rhtslib") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rhtslib" version)) (sha256 (base32 - "186r7icrkzrni1c4n33ip7dlsfgys7hnqf0simvxrpl3yhh3ygdi")))) + "18wag2jnpda6078xjkpfdvar1gkb2myhw83gg03l39sabh35qya4")))) (properties `((upstream-name . "Rhtslib"))) (build-system r-build-system) ;; Without this a temporary directory ends up in the Rhtslib.so binary, -- cgit v1.2.3 From 2c15a1c5022e578e98ac6ae0c8477d334b4f4ca2 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:59:43 +0100 Subject: gnu: r-bamsignals: Update to 1.22.0. * gnu/packages/bioinformatics.scm (r-bamsignals): Update to 1.22.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 211930fef1..5cc3562311 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8811,14 +8811,14 @@ of other R packages who wish to make use of HTSlib.") (define-public r-bamsignals (package (name "r-bamsignals") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bamsignals" version)) (sha256 (base32 - "0p858xxfv79yc8b3lq58zl9f00irvbn3czsd8wdi5040xg42m402")))) + "0p3r9z9z5sfkd0b951cgr751k4z0yviyn1jfw9d4fcnyld7g1jxv")))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) -- cgit v1.2.3 From a823a745251db4905dde1bf426f03fcd70fc0cb5 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:59:46 +0100 Subject: gnu: r-rcas: Update to 1.16.0. * gnu/packages/bioinformatics.scm (r-rcas): Update to 1.16.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 5cc3562311..9d098fffb6 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8843,13 +8843,13 @@ paired-end data.") (define-public r-rcas (package (name "r-rcas") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RCAS" version)) (sha256 (base32 - "0f812pgv3ys1zv4n9sqkgm01hj4cdd0i0h85dqbhkwd94zl6cavl")))) + "0vdxml618vqvf8xyh0zxs307p9zby0cj9dqyiiz625ilyq1hkw2m")))) (properties `((upstream-name . "RCAS"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 6d5a4dd0a7c808e1318a8c8da88def7196027f94 Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Wed, 18 Nov 2020 16:06:22 +0100 Subject: gnu: r-mutationalpatterns: Update to 3.0.1. * gnu/packages/bioinformatics.scm (r-mutationalpatterns): Update to 3.0.1. [native-inputs]: Add r-knitr. [propagated-inputs]: Add r-bsgenome, r-dplyr, r-ggalluvial, r-magrittr, r-purrr, r-stringr, r-tibble, and r-tidyr; remove r-reshape2 and r-summarizedexperiment. --- gnu/packages/bioinformatics.scm | 23 +++++++++++++++-------- 1 file changed, 15 insertions(+), 8 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 9d098fffb6..b2625342b0 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8943,33 +8943,40 @@ library implementing most of the pipeline's features.") (define-public r-mutationalpatterns (package (name "r-mutationalpatterns") - (version "2.0.0") + (version "3.0.1") (source (origin (method url-fetch) (uri (bioconductor-uri "MutationalPatterns" version)) (sha256 (base32 - "02lyjiabyhmifycksvpcx29a0pb7z9xjw0hgg8n0sd0dy3afqhcm")))) + "1988kjjgq8af0hj7chhpxi88717wwmzs9qgrwapjh0hm2hjwhn35")))) (build-system r-build-system) + (native-inputs + `(("r-knitr" ,r-knitr))) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) ("r-biostrings" ,r-biostrings) + ("r-bsgenome" ,r-bsgenome) ;; These two packages are suggested packages ("r-bsgenome-hsapiens-1000g" ,r-bsgenome-hsapiens-1000genomes-hs37d5) ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19) - ("r-genomicranges" ,r-genomicranges) + ("r-cowplot" ,r-cowplot) + ("r-dplyr" ,r-dplyr) ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicranges" ,r-genomicranges) + ("r-ggalluvial" ,r-ggalluvial) + ("r-ggdendro" ,r-ggdendro) ("r-ggplot2" ,r-ggplot2) ("r-iranges" ,r-iranges) + ("r-magrittr" ,r-magrittr) ("r-nmf" ,r-nmf) - ("r-plyr" ,r-plyr) ("r-pracma" ,r-pracma) - ("r-reshape2" ,r-reshape2) - ("r-cowplot" ,r-cowplot) - ("r-ggdendro" ,r-ggdendro) + ("r-purrr" ,r-purrr) ("r-s4vectors" ,r-s4vectors) - ("r-summarizedexperiment" ,r-summarizedexperiment) + ("r-stringr" ,r-stringr) + ("r-tibble" ,r-tibble) + ("r-tidyr" ,r-tidyr) ("r-variantannotation" ,r-variantannotation))) (home-page "https://bioconductor.org/packages/MutationalPatterns/") (synopsis "Extract and visualize mutational patterns in genomic data") -- cgit v1.2.3 From ec0050c0a92ee5f4c39b3b37222a3f72901e4164 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:59:53 +0100 Subject: gnu: r-tximport: Update to 1.18.0. * gnu/packages/bioinformatics.scm (r-tximport): Update to 1.18.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index b2625342b0..b60eea560b 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9055,13 +9055,13 @@ factors bound at the specific regions.") (define-public r-tximport (package (name "r-tximport") - (version "1.16.1") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "tximport" version)) (sha256 (base32 - "1x9959lkjl2h869rgd1b30q1idxzjkr1fyqbpndqk3kbi4q2gr40")))) + "1nxnlvl4iv2392xa72j0lzy2xnb3vrvyhfrdj9l54znwkrryyq34")))) (build-system r-build-system) (native-inputs `(("r-knitr" ,r-knitr))) -- cgit v1.2.3 From cad3eb4eb455afd34f5cdb40fc371bb85dce2040 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:59:59 +0100 Subject: gnu: r-annotationfilter: Update to 1.14.0. * gnu/packages/bioinformatics.scm (r-annotationfilter): Update to 1.14.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index b60eea560b..d6f6e87065 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9108,13 +9108,13 @@ the available RAM.") (define-public r-annotationfilter (package (name "r-annotationfilter") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AnnotationFilter" version)) (sha256 (base32 - "18kh1xrhpwb48s1qj4f1v8af3jmw49pnbp5afi2myn9894hxg0cs")))) + "0npk0laa2rc93rsh6yikj886zf2fl53a050j07fj9w67j0q0h3s9")))) (properties `((upstream-name . "AnnotationFilter"))) (build-system r-build-system) -- cgit v1.2.3 From 36fd725b6f3f55e8ffa10410c742f561ae36a3da Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 16:00:02 +0100 Subject: gnu: r-chipseq: Update to 1.40.0. * gnu/packages/bioinformatics.scm (r-chipseq): Update to 1.40.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index d6f6e87065..3c66c5fede 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9455,14 +9455,14 @@ manipulate and analyze genetic variants.") (define-public r-chipseq (package (name "r-chipseq") - (version "1.38.0") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "chipseq" version)) (sha256 (base32 - "0lh859s0aq73vac1phcgagf6n000qgq2xsk0bmfr61n5swifml2a")))) + "12pzq24aarvgxfmhcad0l5g951xqdvvi7bspgbsvlvmfkqd74j2v")))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) -- cgit v1.2.3 From 2ed79a0a42a4c99511747580a6eccc87db9b38ab Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 16:00:05 +0100 Subject: gnu: r-copywriter: Update to 2.22.0. * gnu/packages/bioinformatics.scm (r-copywriter): Update to 2.22.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 3c66c5fede..26cdc4553a 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9507,14 +9507,14 @@ GenomicRanges Bioconductor package.") (define-public r-copywriter (package (name "r-copywriter") - (version "2.20.0") + (version "2.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "CopywriteR" version)) (sha256 (base32 - "0c36wpv0rygkbqpf3dwh5xmc3lr7p8lrdzsq2fbbpw04skl6i7m2")))) + "060p6l6l8i6b15hyyz5v5kkxih3h4wcciixii51m9mn82z23xr2f")))) (properties `((upstream-name . "CopywriteR"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 99bd4f2d7c86771cba4cb38443c3e71d9082631a Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 16:00:08 +0100 Subject: gnu: r-methylkit: Update to 1.16.0. * gnu/packages/bioinformatics.scm (r-methylkit): Update to 1.16.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 26cdc4553a..ec5cdbba31 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9547,13 +9547,13 @@ number detection tools.") (define-public r-methylkit (package (name "r-methylkit") - (version "1.14.2") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "methylKit" version)) (sha256 (base32 - "1qr13d2712ypbn96ijic2z5adr5dsd61kzscx7shw6vyj360rlm5")))) + "11pmn191n0ga28x1w20cm2cmw8kddl29q6h2xfjjba5bspp2g613")))) (properties `((upstream-name . "methylKit"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 858eb988a066d8d40d827313fe0edf9c836c5866 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 16:00:11 +0100 Subject: gnu: r-sva: Update to 3.38.0. * gnu/packages/bioinformatics.scm (r-sva): Update to 3.38.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index ec5cdbba31..fb88cbc16e 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9596,14 +9596,14 @@ TAB-Seq.") (define-public r-sva (package (name "r-sva") - (version "3.36.0") + (version "3.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "sva" version)) (sha256 (base32 - "0xa1lm0k1a6nig90mab6xh4gln88rbs5l1cdr6ik6agg7jhs7ji4")))) + "1hpzzg3qrgkd8kwg1m5gq94cikjgk9j4l1wk58fxl49s6fmd13zy")))) (build-system r-build-system) (propagated-inputs `(("r-edger" ,r-edger) -- cgit v1.2.3 From 4d9e168db89e2c642df0c285b534a580a507ee95 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 16:00:14 +0100 Subject: gnu: r-protgenerics: Update to 1.22.0. * gnu/packages/bioinformatics.scm (r-protgenerics): Update to 1.22.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index fb88cbc16e..bf48504d72 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9659,14 +9659,14 @@ trait.") (define-public r-protgenerics (package (name "r-protgenerics") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ProtGenerics" version)) (sha256 (base32 - "14xzdh7vxss8vmrw91hcwrszdn3ikm71mah8875b2lkrkrfzbl73")))) + "0yihxphgkshvfv1sn67wc4zvr2zlzws2j7ki3zabm6vyfkfdkfiz")))) (properties `((upstream-name . "ProtGenerics"))) (build-system r-build-system) (home-page "https://github.com/lgatto/ProtGenerics") -- cgit v1.2.3 From badb4678bdc20a78812efadb6112e72949ed4487 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 21 Nov 2020 07:37:49 +0100 Subject: gnu: r-mzr: Update to 2.24.1. * gnu/packages/bioinformatics.scm (r-mzr): Update to 2.24.1. --- gnu/packages/bioinformatics.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index bf48504d72..788a947347 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9679,14 +9679,14 @@ proteomics packages.") (define-public r-mzr (package (name "r-mzr") - (version "2.22.0") + (version "2.24.1") (source (origin (method url-fetch) (uri (bioconductor-uri "mzR" version)) (sha256 (base32 - "1r8j8yiz5lcan7j4h37sza2kwczl48dxvld3da3ghjjq67cdc2cm")) + "0ik0yrjhvk8r5pm990chn2aadp0gqzzkkm0027682ky34xp142sg")) (modules '((guix build utils))) (snippet '(begin @@ -9708,7 +9708,7 @@ proteomics packages.") #t))))) (inputs `(;; Our default boost package won't work here, unfortunately, even with - ;; mzR version 2.22.0. + ;; mzR version 2.24.1. ("boost" ,boost-for-mysql) ; use this instead of the bundled boost sources ("zlib" ,zlib))) (propagated-inputs -- cgit v1.2.3 From 471ceb5e5e809af3fa398a14cd402480c9c293cd Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 21 Nov 2020 07:36:40 +0100 Subject: gnu: r-mzr: Fix linking. * gnu/packages/bioinformatics.scm (r-mzr)[arguments]: Fix linking with rhdf5 libraries. --- gnu/packages/bioinformatics.scm | 9 +++++++-- 1 file changed, 7 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 788a947347..14a9775323 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9701,9 +9701,14 @@ proteomics packages.") (lambda _ (substitute* "src/Makevars" (("\\./boost/libs.*") "") - (("ARCH_OBJS=" line) + ;; This is to avoid having a plain directory on the list of + ;; libraries to link. + (("\\(RHDF5_LIBS\\)" match) + (string-append match "/libhdf5.a")) + (("PKG_LIBS=") "PKG_LIBS=$(BOOST_LIBS) ") + (("\\ARCH_OBJS=" line) (string-append line - "\nARCH_LIBS=-lboost_system -lboost_regex \ + "\nBOOST_LIBS=-lboost_system -lboost_regex \ -lboost_iostreams -lboost_thread -lboost_filesystem -lboost_chrono\n"))) #t))))) (inputs -- cgit v1.2.3 From d6750c6587b5f8aea327b7a6c00198d0df0c5880 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 16:00:21 +0100 Subject: gnu: r-affyio: Update to 1.60.0. * gnu/packages/bioinformatics.scm (r-affyio): Update to 1.60.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 14a9775323..c015bd8f94 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9740,14 +9740,14 @@ previously been used in XCMS.") (define-public r-affyio (package (name "r-affyio") - (version "1.58.0") + (version "1.60.0") (source (origin (method url-fetch) (uri (bioconductor-uri "affyio" version)) (sha256 (base32 - "0j1f61409yq6hmkqrpzamfm7dx35rlq33ccs7wb1qcqx3d3nb75q")))) + "14xnzrxrvgxgixjhq5a9fdgcmrxam2j74hwidkc9if92ffv6s83h")))) (build-system r-build-system) (propagated-inputs `(("r-zlibbioc" ,r-zlibbioc))) -- cgit v1.2.3 From 6a6f38b89e5f1c90b176f266ca51155f7352527f Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 16:00:25 +0100 Subject: gnu: r-affy: Update to 1.68.0. * gnu/packages/bioinformatics.scm (r-affy): Update to 1.68.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index c015bd8f94..4c3fe86e52 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9764,14 +9764,14 @@ CDF file formats.") (define-public r-affy (package (name "r-affy") - (version "1.66.0") + (version "1.68.0") (source (origin (method url-fetch) (uri (bioconductor-uri "affy" version)) (sha256 (base32 - "0m6hkyjxmsf80n3anhwh9k26csxczv6v92fkb7klnchdski61pyc")))) + "0ywz548cbzk2k1njnxhlk5ydzvz2dk78ka8kx53gwrmdc4sc2b06")))) (build-system r-build-system) (propagated-inputs `(("r-affyio" ,r-affyio) -- cgit v1.2.3 From 75bdab83ccdaab3faa9c3b8942d50f8e4a69dec7 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 16:00:28 +0100 Subject: gnu: r-vsn: Update to 3.58.0. * gnu/packages/bioinformatics.scm (r-vsn): Update to 3.58.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 4c3fe86e52..df70f750de 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9792,14 +9792,14 @@ analysis.") (define-public r-vsn (package (name "r-vsn") - (version "3.56.0") + (version "3.58.0") (source (origin (method url-fetch) (uri (bioconductor-uri "vsn" version)) (sha256 (base32 - "1k82dikrv1gcync5y1131wg7z1kxv2z2jl4nndg20bixc3398h58")))) + "0dfrfflidpnphwyqzmmfiz9blfqv6qa09xlwgfabhpfsf3ml2rlb")))) (build-system r-build-system) (propagated-inputs `(("r-affy" ,r-affy) -- cgit v1.2.3 From b47560c1cf6ece6f72ce9fba02df181ad89cb551 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 16:00:31 +0100 Subject: gnu: r-mzid: Update to 1.28.0. * gnu/packages/bioinformatics.scm (r-mzid): Update to 1.28.0. [propagated-inputs]: Remove r-rcpp. --- gnu/packages/bioinformatics.scm | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index df70f750de..ac0cf5b574 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9828,14 +9828,14 @@ and specific in detecting differential transcription.") (define-public r-mzid (package (name "r-mzid") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "mzID" version)) (sha256 (base32 - "0y50lzkdamkpz67f6r5whp246qsxpbammjil7g8vjprx0c4jk5n5")))) + "0s7d6cz1li7v3ni6n6hrdspl93yiyr283kmbbd3hhkfgzgx6kpq2")))) (properties `((upstream-name . "mzID"))) (build-system r-build-system) (propagated-inputs @@ -9844,7 +9844,6 @@ and specific in detecting differential transcription.") ("r-iterators" ,r-iterators) ("r-plyr" ,r-plyr) ("r-protgenerics" ,r-protgenerics) - ("r-rcpp" ,r-rcpp) ("r-xml" ,r-xml))) (native-inputs `(("r-knitr" ,r-knitr))) -- cgit v1.2.3 From 2ed937e0aa02a788a569468cf83dd3762231bed3 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 16:00:34 +0100 Subject: gnu: r-pcamethods: Update to 1.82.0. * gnu/packages/bioinformatics.scm (r-pcamethods): Update to 1.82.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index ac0cf5b574..eb0c1dee18 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9859,14 +9859,14 @@ specific parser.") (define-public r-pcamethods (package (name "r-pcamethods") - (version "1.80.0") + (version "1.82.0") (source (origin (method url-fetch) (uri (bioconductor-uri "pcaMethods" version)) (sha256 (base32 - "10cww4jxyynkwxbbsx804nwac31j0hh8dgisygld0q663gaxkgni")))) + "04xb4vjky6hq58l30i1iq9rv5gzjdxnidjxpnzg7pvg67vz8pgf0")))) (properties `((upstream-name . "pcaMethods"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From e520c68fa9a9fcc5cf018cec15b05ee9ece5eb0a Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 4 Dec 2020 02:07:45 +0100 Subject: gnu: Add r-msmseda. * gnu/packages/bioconductor.scm (r-msmseq): New variable. --- gnu/packages/bioconductor.scm | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 867dc7083f..cfb59fc884 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8990,3 +8990,29 @@ as well as local access. Developers can register a file extension, e.g., `export()` methods based on classes representing file types, e.g., `LoomFile()`.") (license license:artistic2.0))) + +(define-public r-msmseda + (package + (name "r-msmseda") + (version "1.28.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "msmsEDA" version)) + (sha256 + (base32 + "1llmy8msxmrqik3s3439wffma1662vwvvcaz8q0a4g5ridkmdbrx")))) + (properties `((upstream-name . "msmsEDA"))) + (build-system r-build-system) + (propagated-inputs + `(("r-gplots" ,r-gplots) + ("r-mass" ,r-mass) + ("r-msnbase" ,r-msnbase) + ("r-rcolorbrewer" ,r-rcolorbrewer))) + (home-page + "https://bioconductor.org/packages/msmsEDA") + (synopsis "Exploratory data analysis of LC-MS/MS data by spectral counts") + (description + "Exploratory data analysis to assess the quality of a set of LC-MS/MS +experiments, and visualize de influence of the involved factors.") + (license license:gpl2))) -- cgit v1.2.3 From 16f16b5e2149eff4fd785c3680ee007b059343b1 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 4 Dec 2020 02:08:41 +0100 Subject: gnu: Add r-msmstests. * gnu/packages/bioconductor.scm (r-msmstests): New variable. --- gnu/packages/bioconductor.scm | 32 ++++++++++++++++++++++++++++++++ 1 file changed, 32 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index cfb59fc884..3ad28e16aa 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9016,3 +9016,35 @@ as well as local access. Developers can register a file extension, e.g., "Exploratory data analysis to assess the quality of a set of LC-MS/MS experiments, and visualize de influence of the involved factors.") (license license:gpl2))) + +(define-public r-msmstests + (package + (name "r-msmstests") + (version "1.28.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "msmsTests" version)) + (sha256 + (base32 + "1zsnmzj1qvjdwz7mwg9wrsk5iskpqs0f6jccqn8mxy9dgkskmp0j")))) + (properties `((upstream-name . "msmsTests"))) + (build-system r-build-system) + (propagated-inputs + `(("r-edger" ,r-edger) + ("r-msmseda" ,r-msmseda) + ("r-msnbase" ,r-msnbase) + ("r-qvalue" ,r-qvalue))) + (home-page + "https://bioconductor.org/packages/msmsTests") + (synopsis "Differential LC-MS/MS expression tests") + (description + "This packages provides statistical tests for label-free LC-MS/MS data +by spectral counts, to discover differentially expressed proteins between two +biological conditions. Three tests are available: Poisson GLM regression, +quasi-likelihood GLM regression, and the negative binomial of the edgeR +package.The three models admit blocking factors to control for nuissance +variables.To assure a good level of reproducibility a post-test filter is +available, where we may set the minimum effect size considered biologicaly +relevant, and the minimum expression of the most abundant condition.") + (license license:gpl2))) -- cgit v1.2.3 From 971f3a377c0613bb898b1ddfd533b7cb3ab8a10e Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 16:00:40 +0100 Subject: gnu: r-msnid: Update to 1.24.0. * gnu/packages/bioinformatics.scm (r-msnid): Update to 1.24.0. [propagated-inputs]: Add r-annotationdbi, r-annotationhub, r-biocgenerics, r-biocstyle, r-biostrings, r-ggplot2, r-msmstests, r-purrr, r-rlang, r-runit, r-stringr, r-tibble, and r-xtable. --- gnu/packages/bioinformatics.scm | 21 +++++++++++++++++---- 1 file changed, 17 insertions(+), 4 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index eb0c1dee18..b86194e82c 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9934,30 +9934,43 @@ of mass spectrometry based proteomics data.") (define-public r-msnid (package (name "r-msnid") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MSnID" version)) (sha256 (base32 - "0dwa6j2nqb3223a8g4f453aznjh69wngrpvdi12iy69j1psbbjcc")))) + "05bncy7lw2a3h8xgnavjiz56pc6mk8q7l6qdd81197nawxs3j02d")))) (properties `((upstream-name . "MSnID"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) + `(("r-annotationdbi" ,r-annotationdbi) + ("r-annotationhub" ,r-annotationhub) + ("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-biocstyle" ,r-biocstyle) + ("r-biostrings" ,r-biostrings) ("r-data-table" ,r-data-table) ("r-doparallel" ,r-doparallel) ("r-dplyr" ,r-dplyr) ("r-foreach" ,r-foreach) + ("r-ggplot2" ,r-ggplot2) ("r-iterators" ,r-iterators) ("r-msnbase" ,r-msnbase) + ("r-msmstests" ,r-msmstests) ("r-mzid" ,r-mzid) ("r-mzr" ,r-mzr) ("r-protgenerics" ,r-protgenerics) + ("r-purrr" ,r-purrr) ("r-r-cache" ,r-r-cache) ("r-rcpp" ,r-rcpp) - ("r-reshape2" ,r-reshape2))) + ("r-reshape2" ,r-reshape2) + ("r-rlang" ,r-rlang) + ("r-runit" ,r-runit) + ("r-stringr" ,r-stringr) + ("r-tibble" ,r-tibble) + ("r-xtable" ,r-xtable))) (home-page "https://bioconductor.org/packages/MSnID") (synopsis "Utilities for LC-MSn proteomics identifications") (description -- cgit v1.2.3 From 8db8a683b9a75d72886a50dbf8d3a2824785d8b2 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 16:00:43 +0100 Subject: gnu: r-aroma-light: Update to 3.20.0. * gnu/packages/bioinformatics.scm (r-aroma-light): Update to 3.20.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index b86194e82c..d128e16097 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9986,14 +9986,14 @@ and irregular enzymatic cleavages, mass measurement accuracy, etc.") (define-public r-aroma-light (package (name "r-aroma-light") - (version "3.18.0") + (version "3.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "aroma.light" version)) (sha256 (base32 - "19y5f2minx2pp73zdh43v1qkwpkaxygkl8cwlnwja15i46s0bcyc")))) + "0pi37rlfqh24p9wd7l1xb3f7c7938xdscgcc5agp8c9qhajq25a0")))) (properties `((upstream-name . "aroma.light"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 8e55b9f50207ed5c3ed5a4ae9f780b2c4474245e Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 16:00:46 +0100 Subject: gnu: r-edaseq: Update to 2.24.0. * gnu/packages/bioinformatics.scm (r-edaseq): Update to 2.24.0. --- gnu/packages/bioinformatics.scm | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index d128e16097..30bef47a5a 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10044,14 +10044,14 @@ distribution.") (define-public r-edaseq (package (name "r-edaseq") - (version "2.22.0") + (version "2.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "EDASeq" version)) (sha256 (base32 - "12gzxjh73qshlwvsf92lbrf4bi199kxg2snrkprh1z4yqf7bjfm4")))) + "0fznj7lsgkss1svv4rq8g87s1gmnbd7hccim41dv1c2w2nl0n2ip")))) (properties `((upstream-name . "EDASeq"))) (build-system r-build-system) (propagated-inputs @@ -10062,7 +10062,6 @@ distribution.") ("r-biocmanager" ,r-biocmanager) ("r-biomart" ,r-biomart) ("r-biostrings" ,r-biostrings) - ("r-deseq" ,r-deseq) ("r-genomicfeatures" ,r-genomicfeatures) ("r-genomicranges" ,r-genomicranges) ("r-iranges" ,r-iranges) -- cgit v1.2.3 From 3becce3ff3e3f7b8df46ba0b3534b5b946f1e810 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 16:00:49 +0100 Subject: gnu: r-interactivedisplaybase: Update to 1.28.0. * gnu/packages/bioinformatics.scm (r-interactivedisplaybase): Update to 1.28.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 30bef47a5a..8f0a67328e 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10084,14 +10084,14 @@ global-scaling and full-quantile normalization.") (define-public r-interactivedisplaybase (package (name "r-interactivedisplaybase") - (version "1.26.3") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "interactiveDisplayBase" version)) (sha256 (base32 - "1x5vipqa4pgwpd62c1c58shnlpv3zyzzpf4wdwr00q1swkdb7wv3")))) + "08id2hkx4ssxj34dildx00a4j3z0nv171b7b0wl6xjks7wk6lv01")))) (properties `((upstream-name . "interactiveDisplayBase"))) (build-system r-build-system) -- cgit v1.2.3 From a9dc755e670b61281944cca5f80c77738736cec5 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 16:00:52 +0100 Subject: gnu: r-annotationhub: Update to 2.22.0. * gnu/packages/bioinformatics.scm (r-annotationhub): Update to 2.22.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 8f0a67328e..7b498f2fbf 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10111,14 +10111,14 @@ Shiny-based display methods for Bioconductor objects.") (define-public r-annotationhub (package (name "r-annotationhub") - (version "2.20.2") + (version "2.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AnnotationHub" version)) (sha256 (base32 - "04bz91m2wx1zm61rvpr0syyklz232fw74wrl73d965wi3x8fyda5")))) + "1950x654ffqx53b154kbph808zdh2xm5vmj9vzmc5nxc28fi2z5g")))) (properties `((upstream-name . "AnnotationHub"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From b6dd0722c8875b9a4c5847725b23492446dcc27e Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 16:00:55 +0100 Subject: gnu: r-fastseg: Update to 1.36.0. * gnu/packages/bioinformatics.scm (r-fastseg): Update to 1.36.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 7b498f2fbf..7034623afb 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10152,14 +10152,14 @@ by the user, helping with quick and reproducible access.") (define-public r-fastseg (package (name "r-fastseg") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "fastseg" version)) (sha256 (base32 - "1d48n245pzmvcpsz93lxb4frqh222gfhpmlvm0sb74skn16way63")))) + "1ln6w93ag4wanp0nrm0pqngbfc88w95zq2kcj583hbxy885dkg4f")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) -- cgit v1.2.3 From 143437c6233a50a52540266eaf60700147c7b589 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 16:00:59 +0100 Subject: gnu: r-keggrest: Update to 1.30.0. * gnu/packages/bioinformatics.scm (r-keggrest): Update to 1.30.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 7034623afb..3a49e68031 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10182,14 +10182,14 @@ microarrays or GRanges for sequencing data.") (define-public r-keggrest (package (name "r-keggrest") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "KEGGREST" version)) (sha256 (base32 - "0q76w17fya2x0z7mvyhkk5kqh07flldgih13ma44vhcy1bdlm6j1")))) + "0awg0hmxj25rpmqyf6jz6kbkswmimz3h352xx15xhkamwcxykng6")))) (properties `((upstream-name . "KEGGREST"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 78cadd0fefdf8389e22e5e0918bd50844dc1d07a Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 16:01:02 +0100 Subject: gnu: r-gage: Update to 2.40.0. * gnu/packages/bioinformatics.scm (r-gage): Update to 2.40.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 3a49e68031..198b71421e 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10208,14 +10208,14 @@ microarrays or GRanges for sequencing data.") (define-public r-gage (package (name "r-gage") - (version "2.38.3") + (version "2.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "gage" version)) (sha256 (base32 - "1bqmvjiya1df0b3h491lp1jxahiyidvaf9n094z0sk84x5y3xh2p")))) + "0xm50wgjjjymv71mbv1clnhx4m12nrd1pc6vfplpdqr5q49v3yd5")))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) -- cgit v1.2.3 From 0fde2f9ad2fa86a7ada50766c1bde922974b8aa4 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 16:01:05 +0100 Subject: gnu: r-genomicfiles: Update to 1.26.0. * gnu/packages/bioinformatics.scm (r-genomicfiles): Update to 1.26.0. [propagated-inputs]: Add r-matrixgenerics. --- gnu/packages/bioinformatics.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 198b71421e..b5c5a04ead 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10239,14 +10239,14 @@ analysis using other methods.") (define-public r-genomicfiles (package (name "r-genomicfiles") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicFiles" version)) (sha256 (base32 - "1k3824pzf9fdqvcv6cz2742q3mabpmncrc72hwa21ac8wy1b04n4")))) + "0awnf0m1pz7cw9wvh9cfxz9k7xm6wnvjm7xbxf139lrhd4nlyqjz")))) (properties `((upstream-name . "GenomicFiles"))) (build-system r-build-system) (propagated-inputs @@ -10256,6 +10256,7 @@ analysis using other methods.") ("r-genomicalignments" ,r-genomicalignments) ("r-genomicranges" ,r-genomicranges) ("r-iranges" ,r-iranges) + ("r-matrixgenerics" ,r-matrixgenerics) ("r-rsamtools" ,r-rsamtools) ("r-rtracklayer" ,r-rtracklayer) ("r-s4vectors" ,r-s4vectors) -- cgit v1.2.3 From 4ef1e375b459ac93bc7c3d55bb7c2815fe1bbb03 Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Wed, 18 Nov 2020 16:15:14 +0100 Subject: gnu: r-complexheatmap: Update to 2.6.2. * gnu/packages/bioinformatics.scm (r-complexheatmap): Update to 2.6.2; [propagated-inputs]: Add r-cairo, r-digest, r-iranges, r-matrixstats, and r-s4vectors. --- gnu/packages/bioinformatics.scm | 13 +++++++++---- 1 file changed, 9 insertions(+), 4 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index b5c5a04ead..2da3cc8ed2 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10273,25 +10273,30 @@ provide added flexibility for data combination and manipulation.") (define-public r-complexheatmap (package (name "r-complexheatmap") - (version "2.4.3") + (version "2.6.2") (source (origin (method url-fetch) (uri (bioconductor-uri "ComplexHeatmap" version)) (sha256 (base32 - "1gx0hzrkla92pgmfkrm2zp0ccnhizq6rs26zgzpi5x8a5lvghh5q")))) + "1nx1xxpq8zrvi990v9fmvx3msl85pdz5dp1gp6m78q6i4s2alg5x")))) (properties `((upstream-name . "ComplexHeatmap"))) (build-system r-build-system) (propagated-inputs - `(("r-circlize" ,r-circlize) + `(("r-cairo" ,r-cairo) + ("r-circlize" ,r-circlize) ("r-clue" ,r-clue) ("r-colorspace" ,r-colorspace) + ("r-digest" ,r-digest) ("r-getoptlong" ,r-getoptlong) ("r-globaloptions" ,r-globaloptions) + ("r-iranges" ,r-iranges) + ("r-matrixstats" ,r-matrixstats) ("r-png" ,r-png) - ("r-rcolorbrewer" ,r-rcolorbrewer))) + ("r-rcolorbrewer" ,r-rcolorbrewer) + ("r-s4vectors" ,r-s4vectors))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page -- cgit v1.2.3 From 8962a13afe052b69a6c0f03731002e18d017065d Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 16:01:11 +0100 Subject: gnu: r-dirichletmultinomial: Update to 1.32.0. * gnu/packages/bioinformatics.scm (r-dirichletmultinomial): Update to 1.32.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 2da3cc8ed2..c824153350 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10312,14 +10312,14 @@ self-defined annotation graphics.") (define-public r-dirichletmultinomial (package (name "r-dirichletmultinomial") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DirichletMultinomial" version)) (sha256 (base32 - "1m9dsrddrllb2i88qzik1867iv9mggrgdkn0dlp8sq7gl69vmalb")))) + "098zql6ryd1b0gkq4cjybblyh0x8xidxxfygqq5a5x9asl8y4vsk")))) (properties `((upstream-name . "DirichletMultinomial"))) (build-system r-build-system) -- cgit v1.2.3 From 06fe3b7a53018b50322fa5fb16817218e254e6e3 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 16:01:14 +0100 Subject: gnu: r-ensembldb: Update to 2.14.0. * gnu/packages/bioinformatics.scm (r-ensembldb): Update to 2.14.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index c824153350..4d55ca8310 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10341,14 +10341,14 @@ originally made available by Holmes, Harris, and Quince, 2012, PLoS ONE 7(2): (define-public r-ensembldb (package (name "r-ensembldb") - (version "2.12.1") + (version "2.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ensembldb" version)) (sha256 (base32 - "1vvchc04nshxc768fp31rxb603aj3hmq8xlh5qabcwf2c3z9719g")))) + "04il99gcrqzakvc0bxchdp9gghkn1sp9lpiian0iz4y7r67z3wpy")))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) -- cgit v1.2.3 From 6e182c237af03f0697e6692e9d98b9b0ff35df7c Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 16:01:17 +0100 Subject: gnu: r-organismdbi: Update to 1.32.0. * gnu/packages/bioinformatics.scm (r-organismdbi): Update to 1.32.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 4d55ca8310..0ca41516c0 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10386,14 +10386,14 @@ chromosome region or transcript models of lincRNA genes.") (define-public r-organismdbi (package (name "r-organismdbi") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "OrganismDbi" version)) (sha256 (base32 - "194h5576inq44qr666snzq0ygnc77rk5ljkn9bn8zs6x6gb3cwaw")))) + "1mklnzs0d0ygcdibwfnk5xqr8ln6wpa00qcaw9c68m342kql0jqw")))) (properties `((upstream-name . "OrganismDbi"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 3c6eecdeed6d90232a2615e5ba7adfbaa135a1ac Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 16:01:20 +0100 Subject: gnu: r-biovizbase: Update to 1.38.0. * gnu/packages/bioinformatics.scm (r-biovizbase): Update to 1.38.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 0ca41516c0..272bf6465d 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10418,14 +10418,14 @@ the fact that each of these packages implements a select methods.") (define-public r-biovizbase (package (name "r-biovizbase") - (version "1.36.0") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biovizBase" version)) (sha256 (base32 - "1vq2mxa2jkljgw75zqjdkyml0ppi5dspvwj4cznfhi31cq8ds0qh")))) + "10jflvadfcgxq2jnfxkpn417xd8ibh3zllz9rsqnq5w3wgfr4fhq")))) (properties `((upstream-name . "biovizBase"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 74a11b21be4f3bc632e437b60eb8ba1152f3e7e1 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 16:01:23 +0100 Subject: gnu: r-ggbio: Update to 1.38.0. * gnu/packages/bioinformatics.scm (r-ggbio): Update to 1.38.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 272bf6465d..211f8c2802 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10460,14 +10460,14 @@ effort and encourages consistency.") (define-public r-ggbio (package (name "r-ggbio") - (version "1.36.0") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ggbio" version)) (sha256 (base32 - "11ggnqjq42fi2hm9xlvrrlr2xhy4kglvl1a0mycp1s4v67lxw5h5")))) + "0vabil4jzrlv01aibqjhdkvrv2bf2kkpsidrkjj06isqr5fz54lw")))) (build-system r-build-system) (arguments `(#:phases -- cgit v1.2.3 From 6e338901bfd27da75a34bf89d15ab7efa388cc7f Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 16:01:30 +0100 Subject: gnu: r-snpstats: Update to 1.40.0. * gnu/packages/bioinformatics.scm (r-snpstats): Update to 1.40.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 211f8c2802..0adaf7004b 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10562,14 +10562,14 @@ and more.") (define-public r-snpstats (package (name "r-snpstats") - (version "1.38.0") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "snpStats" version)) (sha256 (base32 - "1qv3nqqr30d3n66mawqd9dbl95dl89r4bcjvkc5iassy1yrwr8wq")))) + "1298a71swwav53yf9kfqkdpach3818plqcbw0lgb6sibs8y8ff24")))) (properties `((upstream-name . "snpStats"))) (build-system r-build-system) (inputs `(("zlib" ,zlib))) -- cgit v1.2.3 From 494010ad3eb01d3f487143c78e8aabb8037e7af0 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 16:01:33 +0100 Subject: gnu: r-erma: Update to 1.6.0. * gnu/packages/bioinformatics.scm (r-erma): Update to 1.6.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 0adaf7004b..229bfbff54 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10621,14 +10621,14 @@ several related annotation packages.") (define-public r-erma (package (name "r-erma") - (version "1.4.0") + (version "1.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "erma" version)) (sha256 (base32 - "1ccfbq0r48sr3h8050w8zv8402h7nx09adr0xdyqlg7kwp9vd2l3")))) + "1k2j1xhv0vwn45xmh8ds0gz812px5hnpgzvp37ngsdn4j5ai1l0k")))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) -- cgit v1.2.3 From 0a8d08e887ddeeb48c2cb8bed0158e7017812e54 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 16:01:36 +0100 Subject: gnu: r-ldblock: Update to 1.20.0. * gnu/packages/bioinformatics.scm (r-ldblock): Update to 1.20.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 229bfbff54..aeef64b454 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10661,14 +10661,14 @@ by Ernst and Kellis.") (define-public r-ldblock (package (name "r-ldblock") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ldblock" version)) (sha256 (base32 - "0plw00n2zfgh029ab41dnydzgv2yxrapjp770147rx9pff4dngrv")))) + "09i3ikv0axks9g842z1pjsc8x0fba51zyyc218h0bylbi1n9cdkm")))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) -- cgit v1.2.3 From 717e53fdc085e3a7b71b9f37da2358282289add4 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 16:01:42 +0100 Subject: gnu: r-gviz: Update to 1.34.0. * gnu/packages/bioinformatics.scm (r-gviz): Update to 1.34.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index aeef64b454..c49dec1b7e 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10751,14 +10751,14 @@ family of feature/genome hypotheses.") (define-public r-gviz (package (name "r-gviz") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Gviz" version)) (sha256 (base32 - "0cgkp0ciyy2qykqgh3vzp5mx9b4vsvacjh2jnsj3wldiapzlz08a")))) + "0v7bz46b91dnrr55ah42ljj1i2xs3090s4w0lw8098pag00p4vh2")))) (properties `((upstream-name . "Gviz"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 83129edfb7a7c3af71c05040253acec9fdb1c801 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 16:01:45 +0100 Subject: gnu: r-gwascat: Update to 2.22.0. * gnu/packages/bioinformatics.scm (r-gwascat): Update to 2.22.0. [propagated-inputs]: Add r-biocfilecache, r-readr, r-snpstats, and r-variantannotation; remove r-biocgenerics, r-ggplot2, r-rsamtools, and r-rtracklayer. --- gnu/packages/bioinformatics.scm | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index c49dec1b7e..43571a4644 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10800,27 +10800,27 @@ with your data.") (define-public r-gwascat (package (name "r-gwascat") - (version "2.20.1") + (version "2.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "gwascat" version)) (sha256 (base32 - "1cq5cmdrf0a0arr841yvkh6d8drc15p7mif1afr215l1s3y2dwd4")))) + "1aqi1ny93virnzsxkh9ccx3mws70bgv0r8nwgla09vffb7f16nna")))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) - ("r-biocgenerics" ,r-biocgenerics) + ("r-biocfilecache" ,r-biocfilecache) ("r-biostrings" ,r-biostrings) ("r-genomeinfodb" ,r-genomeinfodb) ("r-genomicfeatures" ,r-genomicfeatures) ("r-genomicranges" ,r-genomicranges) - ("r-ggplot2" ,r-ggplot2) ("r-iranges" ,r-iranges) - ("r-rsamtools" ,r-rsamtools) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors))) + ("r-readr" ,r-readr) + ("r-s4vectors" ,r-s4vectors) + ("r-snpstats" ,r-snpstats) + ("r-variantannotation" ,r-variantannotation))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/gwascat") -- cgit v1.2.3 From e7078204425fa3d4b78e0765b1b1b230c43fa308 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 16:01:48 +0100 Subject: gnu: r-sushi: Update to 1.28.0. * gnu/packages/bioinformatics.scm (r-sushi): Update to 1.28.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 43571a4644..ec7dd71b3d 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10833,13 +10833,13 @@ EMBL-EBI GWAS catalog.") (define-public r-sushi (package (name "r-sushi") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Sushi" version)) (sha256 (base32 - "17j3d5qjq5nbv99by5mq8rwr0jgh2jyyfn2nwxmwgzlmk3lgi1rb")))) + "0ksj4f9z14mjsv6ssg5dwhpldw4r7wpdsln2if5g486mm1c56r8p")))) (properties `((upstream-name . "Sushi"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From aca4ebe40ae4b4e280ecb093382daa9ab5bd0ef9 Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Wed, 18 Nov 2020 17:01:03 +0100 Subject: gnu: r-annaffy: Update to 1.62.0. * gnu/packages/bioconductor.scm (r-annaffy): Update to 1.62.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 3ad28e16aa..ce64a3052f 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4021,14 +4021,14 @@ data in R and Bioconductor containers.") (define-public r-annaffy (package (name "r-annaffy") - (version "1.60.0") + (version "1.62.0") (source (origin (method url-fetch) (uri (bioconductor-uri "annaffy" version)) (sha256 (base32 - "1rc9fb83by9jfgwfj2zhhbj93v296blwd8jl2rh7jj200mrpznn4")))) + "1szlr33lq98pd3kx6n9l07lhr93swbk6vjpvb2n9f7716k39mi4i")))) (build-system r-build-system) (arguments `(#:phases -- cgit v1.2.3 From a23310ffc24f077dac9c1bd6c93d57791f583b55 Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Wed, 18 Nov 2020 17:24:59 +0100 Subject: gnu: Add r-bluster. * gnu/packages/bioconductor.scm (r-bluster): New variable. --- gnu/packages/bioconductor.scm | 29 +++++++++++++++++++++++++++++ 1 file changed, 29 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index ce64a3052f..78ad278893 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -72,6 +72,35 @@ database, assembled using data from REACTOME.") (license license:cc-by4.0))) +(define-public r-bluster + (package + (name "r-bluster") + (version "1.0.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "bluster" version)) + (sha256 + (base32 + "0izrf82m5znyrgai5y5jss4k2brabh4ajxdvnlwwc92l5bw7jp61")))) + (properties `((upstream-name . "bluster"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biocneighbors" ,r-biocneighbors) + ("r-biocparallel" ,r-biocparallel) + ("r-igraph" ,r-igraph) + ("r-matrix" ,r-matrix) + ("r-rcpp" ,r-rcpp) + ("r-s4vectors" ,r-s4vectors))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://bioconductor.org/packages/bluster") + (synopsis "Clustering algorithms for Bioconductor") + (description"This package wraps common clustering algorithms in an easily +extended S4 framework. Backends are implemented for hierarchical, k-means +and graph-based clustering. Several utilities are also provided to compare +and evaluate clustering results.") + (license license:gpl3))) + (define-public r-bsgenome-celegans-ucsc-ce6 (package (name "r-bsgenome-celegans-ucsc-ce6") -- cgit v1.2.3 From 5e719988f2718397440719b76161f4217a6ff223 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 21 Nov 2020 10:24:12 +0100 Subject: gnu: Add r-sparsematrixstats. * gnu/packages/bioconductor.scm (r-sparsematrixstats): New variable. --- gnu/packages/bioconductor.scm | 28 ++++++++++++++++++++++++++++ 1 file changed, 28 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 78ad278893..bec37aa1d6 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8917,6 +8917,34 @@ cell-specific biases, assignment of cell cycle phase, and detection of highly variable and significantly correlated genes.") (license license:gpl3))) +(define-public r-sparsematrixstats + (package + (name "r-sparsematrixstats") + (version "1.2.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "sparseMatrixStats" version)) + (sha256 + (base32 + "0d1idbda1pzhdam9m0i5rn0c6pl7gwv0v3mcrv4wi5760v9qd5qh")))) + (properties + `((upstream-name . "sparseMatrixStats"))) + (build-system r-build-system) + (propagated-inputs + `(("r-matrix" ,r-matrix) + ("r-matrixgenerics" ,r-matrixgenerics) + ("r-matrixstats" ,r-matrixstats) + ("r-rcpp" ,r-rcpp))) + (native-inputs `(("r-knitr" ,r-knitr))) + (home-page "https://bioconductor.org/packages/sparseMatrixStats/") + (synopsis "Summary statistics for rows and columns of sparse matrices") + (description + "This package provides high performance functions for row and column +operations on sparse matrices. Currently, the optimizations are limited to +data in the column sparse format.") + (license license:expat))) + (define-public r-delayedmatrixstats (package (name "r-delayedmatrixstats") -- cgit v1.2.3 From 60ad3c7b3b918246f7c8b692d476e204afca55ec Mon Sep 17 00:00:00 2001 From: zimoun Date: Wed, 2 Dec 2020 16:10:10 +0100 Subject: gnu: r-genomationdata: Update to 1.22.0. * gnu/packages/bioinformatics.scm (r-genomationdata): Update to 1.22.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index ec7dd71b3d..20acf63bc1 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8659,7 +8659,7 @@ genomic intervals. In addition, it can use BAM or BigWig files as input.") (define-public r-genomationdata (package (name "r-genomationdata") - (version "1.14.0") + (version "1.22.0") (source (origin (method url-fetch) ;; We cannot use bioconductor-uri here because this tarball is @@ -8669,7 +8669,7 @@ genomic intervals. In addition, it can use BAM or BigWig files as input.") "genomationData_" version ".tar.gz")) (sha256 (base32 - "10xyb8akjrhmak2i0mnv1agny2ipy364q9nlibyplpzc7vdb6bw7")))) + "0igjsvfnws3498j65ifniw0kbxfqpfr59rcjddqvq4zsj453fx1g")))) (build-system r-build-system) ;; As this package provides little more than large data files, it doesn't ;; make sense to build substitutes. -- cgit v1.2.3 From 35dae95110c2724f445b1e3f407b66d57b9c1ce5 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:48:30 +0100 Subject: gnu: r-interactionset: Update to 1.18.0. * gnu/packages/bioconductor.scm (r-interactionset): Update to 1.18.0. --- gnu/packages/bioconductor.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index bec37aa1d6..5e6a87218c 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2233,16 +2233,16 @@ parsing of genetic sequencing data from ribosome profiling experiments.") (license license:gpl3))) (define-public r-interactionset - (package + (package ;BROKEN (name "r-interactionset") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "InteractionSet" version)) (sha256 (base32 - "1nsivm9j0mzkfhwqsa2y9gxxdbaplg4z8vn5dfvls3nrihnqpk4v")))) + "14lp23b298wr3r7ggcfvas0xlf1866cpla0rv7dz589f50z6bj31")))) (properties `((upstream-name . "InteractionSet"))) (build-system r-build-system) -- cgit v1.2.3 From dd9341ffa337d9f53ca5748901540146c58b05cc Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:48:33 +0100 Subject: gnu: r-genomicinteractions: Update to 1.24.0. * gnu/packages/bioconductor.scm (r-genomicinteractions): Update to 1.24.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 5e6a87218c..3d04c8eb2d 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2269,14 +2269,14 @@ experiments.") (define-public r-genomicinteractions (package (name "r-genomicinteractions") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicInteractions" version)) (sha256 (base32 - "0fg66v31nfajb40da6gxpigm2z11ywkdijs7npvc1mr62ynx9qmy")))) + "0ad0a5cadchx1rkqj4cc8k0y1zf34jgp1406hvik5zabr7xijkbd")))) (properties `((upstream-name . "GenomicInteractions"))) (build-system r-build-system) -- cgit v1.2.3 From 798ec28916c87f961174bde384fbd26b675bd1e5 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:49:04 +0100 Subject: gnu: r-biocsingular: Update to 1.6.0. * gnu/packages/bioconductor.scm (r-biocsingular): Update to 1.6.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 3d04c8eb2d..1b0e69c282 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2575,14 +2575,14 @@ achieved for all methods using the BiocParallel framework.") (define-public r-biocsingular (package (name "r-biocsingular") - (version "1.4.0") + (version "1.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocSingular" version)) (sha256 (base32 - "0368a9xj4cvicqkxmhh12ln46q9gnxla70s1dqrxxfn3b6k525ih")))) + "1hczix1h14d19hzcsngqkqqnqkprs41phzlcird8haxnw9bs03ni")))) (properties `((upstream-name . "BiocSingular"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From d0db04fcaf9103b1f092f3b09df6b937dda7a8ef Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:52:10 +0100 Subject: gnu: r-yapsa: Update to 1.16.0. * gnu/packages/bioconductor.scm (r-yapsa): Update to 1.16.0. --- gnu/packages/bioconductor.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 1b0e69c282..dcdfdd4a02 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4926,14 +4926,14 @@ decomposition algorithms.") (define-public r-yapsa (package (name "r-yapsa") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "YAPSA" version)) (sha256 (base32 - "06lkf01vl4fyhj82srx8k870fhw76a1han0kp4jglh43b1c19c1k")))) + "1vwccrp01p8i42axbaz1bqq173la18ldrzmrjawr5nkjjkvddbpb")))) (properties `((upstream-name . "YAPSA"))) (build-system r-build-system) (propagated-inputs @@ -4953,7 +4953,7 @@ decomposition algorithms.") ("r-gridextra" ,r-gridextra) ("r-gtrellis" ,r-gtrellis) ("r-keggrest" ,r-keggrest) - ("r-lsei" ,r-lsei) + ("r-limsolve" ,r-limsolve) ("r-magrittr" ,r-magrittr) ("r-pmcmr" ,r-pmcmr) ("r-pracma" ,r-pracma) -- cgit v1.2.3 From 4ef898d449a4f894056264ec9722565f274acef4 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:57:24 +0100 Subject: gnu: r-singlecellexperiment: Update to 1.12.0. * gnu/packages/bioconductor.scm (r-singlecellexperiment): Update to 1.12.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index dcdfdd4a02..4822fcad47 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8811,14 +8811,14 @@ matrices.") (define-public r-singlecellexperiment (package (name "r-singlecellexperiment") - (version "1.10.1") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "SingleCellExperiment" version)) (sha256 (base32 - "092wvk11n7pa234vlwhxm3gdi4k3sbnz1splhxalbdhz3jf02zfp")))) + "0wpgb2rhxxlclpmwl08iyfy204f7gpj8ijd0qdy4j41c58bl4qm2")))) (properties `((upstream-name . "SingleCellExperiment"))) (build-system r-build-system) -- cgit v1.2.3 From 86fcceeae1f551ddb9bc692e46245c8291ed3984 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 21 Nov 2020 10:23:27 +0100 Subject: gnu: Add r-rhdf5filters. * gnu/packages/bioinformatics.scm (r-rhdf5filters): New variable. --- gnu/packages/bioinformatics.scm | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 20acf63bc1..1438fc3f9b 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9076,6 +9076,32 @@ provided as a matrix which can be used as an offset for different expression of gene-level counts.") (license license:gpl2+))) +(define-public r-rhdf5filters + (package + (name "r-rhdf5filters") + (version "1.2.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "rhdf5filters" version)) + (sha256 + (base32 + "1jvnss44liapbc6hk93yg1gknv0ahd5x86dydqiwq9l65jd03psq")))) + (properties `((upstream-name . "rhdf5filters"))) + (build-system r-build-system) + (propagated-inputs + `(("r-rhdf5lib" ,r-rhdf5lib))) + (inputs + `(("zlib" ,zlib))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://github.com/grimbough/rhdf5filters") + (synopsis "HDF5 compression filters") + (description + "This package provides a collection of compression filters for use with +HDF5 datasets.") + (license license:bsd-2))) + (define-public r-rhdf5 (package (name "r-rhdf5") -- cgit v1.2.3 From 53affb349aa0d7d09fa2acedddfb58548f2e0747 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:59:56 +0100 Subject: gnu: r-rhdf5: Update to 2.34.0. * gnu/packages/bioinformatics.scm (r-rhdf5): Update to 2.34.0. [propagated-inputs]: Add r-rhdf5filters. [arguments]: Avoid to have a plain directory on the list of libraries to link. Co-authored-by: Ricardo Wurmus . --- gnu/packages/bioinformatics.scm | 18 +++++++++++++++--- 1 file changed, 15 insertions(+), 3 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 1438fc3f9b..af42f5f5e6 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9105,16 +9105,28 @@ HDF5 datasets.") (define-public r-rhdf5 (package (name "r-rhdf5") - (version "2.32.3") + (version "2.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "rhdf5" version)) (sha256 (base32 - "0fnx60dpf6s2qwq48lg98g18g8k7wgm66pw0kamlbb7l2hnwycvf")))) + "0almr1vscrgj5g4dyrags131wia2pmdbdidlpskbgm44ha6hpmqi")))) (build-system r-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'fix-linking + (lambda _ + (substitute* "src/Makevars" + ;; This is to avoid having a plain directory on the list of + ;; libraries to link. + (("\\(RHDF5_LIBS\\)" match) + (string-append match "/libhdf5.a"))) + #t))))) (propagated-inputs - `(("r-rhdf5lib" ,r-rhdf5lib))) + `(("r-rhdf5filters" ,r-rhdf5filters) + ("r-rhdf5lib" ,r-rhdf5lib))) (inputs `(("zlib" ,zlib))) (native-inputs -- cgit v1.2.3 From 10c87ecf777af2c2aebe0775fba75237c20df279 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:57:33 +0100 Subject: gnu: r-delayedmatrixstats: Update to 1.12.0. * gnu/packages/bioconductor.scm (r-delayedmatrixstats): Update to 1.12.0. Co-authored-by: Ricardo Wurmus . --- gnu/packages/bioconductor.scm | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 4822fcad47..7f188a4115 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8948,14 +8948,14 @@ data in the column sparse format.") (define-public r-delayedmatrixstats (package (name "r-delayedmatrixstats") - (version "1.10.1") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DelayedMatrixStats" version)) (sha256 (base32 - "046sam0rz42ph0m7jz7v3bck7d3h2mp45gzywh5dvc1qkjq6fdxx")))) + "0xgjamxwf9wwy6dc138mxx5xgjhq5d2z7irliyxbmpaf5kicnwyi")))) (properties `((upstream-name . "DelayedMatrixStats"))) (build-system r-build-system) @@ -8966,7 +8966,8 @@ data in the column sparse format.") ("r-iranges" ,r-iranges) ("r-matrix" ,r-matrix) ("r-matrixstats" ,r-matrixstats) - ("r-s4vectors" ,r-s4vectors))) + ("r-s4vectors" ,r-s4vectors) + ("r-sparsematrixstats" ,r-sparsematrixstats))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://github.com/PeteHaitch/DelayedMatrixStats") -- cgit v1.2.3 From 0e60dda0ae235044e692626d7b4532f63c591c5a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 21 Nov 2020 10:23:56 +0100 Subject: gnu: Add r-scuttle. * gnu/packages/bioconductor.scm (r-scuttle): New variable. --- gnu/packages/bioconductor.scm | 34 ++++++++++++++++++++++++++++++++++ 1 file changed, 34 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 7f188a4115..3572b605c6 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8837,6 +8837,40 @@ factors for each cell, along with the usual metadata for genes and libraries.") (license license:gpl3))) +(define-public r-scuttle + (package + (name "r-scuttle") + (version "1.0.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "scuttle" version)) + (sha256 + (base32 + "1k8q3wzq6f6j6wkjp9fy9j214rv98kyvcxnpavk6blqgaxjqwdr6")))) + (properties `((upstream-name . "scuttle"))) + (build-system r-build-system) + (propagated-inputs + `(("r-beachmat" ,r-beachmat) + ("r-biocgenerics" ,r-biocgenerics) + ("r-biocparallel" ,r-biocparallel) + ("r-delayedarray" ,r-delayedarray) + ("r-delayedmatrixstats" ,r-delayedmatrixstats) + ("r-matrix" ,r-matrix) + ("r-rcpp" ,r-rcpp) + ("r-s4vectors" ,r-s4vectors) + ("r-singlecellexperiment" ,r-singlecellexperiment) + ("r-summarizedexperiment" ,r-summarizedexperiment))) + (native-inputs `(("r-knitr" ,r-knitr))) + (home-page "https://bioconductor.org/packages/scuttle") + (synopsis "Single-cell RNA-Seq analysis utilities") + (description + "This package provides basic utility functions for performing single-cell +analyses, focusing on simple normalization, quality control and data +transformations. It also provides some helper functions to assist development +of other packages.") + (license license:gpl3))) + (define-public r-scater (package (name "r-scater") -- cgit v1.2.3 From d4b5d18684aaa4e462a6036a7622cf74b3250bed Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:57:27 +0100 Subject: gnu: r-scater: Update to 1.18.3. * gnu/packages/bioconductor.scm (r-scater): Update to 1.18.3. [propagated-inputs]: Add r-gridextra, r-scutlle. Remove r-beachmat, r-rcpp. Co-authored-by: Ricardo Wurmus . --- gnu/packages/bioconductor.scm | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 3572b605c6..5b10bfda18 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8874,17 +8874,16 @@ of other packages.") (define-public r-scater (package (name "r-scater") - (version "1.16.2") + (version "1.18.3") (source (origin (method url-fetch) (uri (bioconductor-uri "scater" version)) (sha256 (base32 - "1pa5wvgjb30rw1vsjwbnn07ss3sc5n8ck5d7khdby4r2s9177s33")))) + "14f7yw277nykxmcm7wlhlsf3nizpwzz24hax1icx73lavfxmc535")))) (build-system r-build-system) (propagated-inputs - `(("r-beachmat" ,r-beachmat) - ("r-biocgenerics" ,r-biocgenerics) + `(("r-biocgenerics" ,r-biocgenerics) ("r-biocneighbors" ,r-biocneighbors) ("r-biocparallel" ,r-biocparallel) ("r-biocsingular" ,r-biocsingular) @@ -8892,10 +8891,11 @@ of other packages.") ("r-delayedmatrixstats" ,r-delayedmatrixstats) ("r-ggbeeswarm" ,r-ggbeeswarm) ("r-ggplot2" ,r-ggplot2) + ("r-gridextra" ,r-gridextra) ("r-matrix" ,r-matrix) - ("r-rcpp" ,r-rcpp) ("r-rlang" ,r-rlang) ("r-s4vectors" ,r-s4vectors) + ("r-scuttle" ,r-scuttle) ("r-singlecellexperiment" ,r-singlecellexperiment) ("r-summarizedexperiment" ,r-summarizedexperiment) ("r-viridis" ,r-viridis))) -- cgit v1.2.3 From b03c955c6f009e764b05018b399afe1eca8c1a7a Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:57:30 +0100 Subject: gnu: r-scran: Update to 1.18.0. * gnu/packages/bioconductor.scm (r-scran): Update to 1.18.0. [propagated-inputs]: Add r-bluster, r-scuttle. Remove r-iranges. Co-authored-by: Ricardo Wurmus . --- gnu/packages/bioconductor.scm | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 5b10bfda18..c172f15ec4 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8911,14 +8911,14 @@ quality control.") (define-public r-scran (package (name "r-scran") - (version "1.16.0") + (version "1.18.1") (source (origin (method url-fetch) (uri (bioconductor-uri "scran" version)) (sha256 (base32 - "1gm4ys4aq8h1pn45k1rxk384wjyf55izivw8kgxbrflj6j4xvvsv")))) + "1zap12rm61z2hg6ykknbif478nr7g468v8mp50bj5hqgi69ywcww")))) (build-system r-build-system) (propagated-inputs `(("r-beachmat" ,r-beachmat) @@ -8927,17 +8927,17 @@ quality control.") ("r-biocneighbors" ,r-biocneighbors) ("r-biocparallel" ,r-biocparallel) ("r-biocsingular" ,r-biocsingular) + ("r-bluster" ,r-bluster) ("r-delayedarray" ,r-delayedarray) ("r-delayedmatrixstats" ,r-delayedmatrixstats) ("r-dqrng" ,r-dqrng) ("r-edger" ,r-edger) ("r-igraph" ,r-igraph) - ("r-iranges" ,r-iranges) ("r-limma" ,r-limma) ("r-matrix" ,r-matrix) ("r-rcpp" ,r-rcpp) ("r-s4vectors" ,r-s4vectors) - ("r-scater" ,r-scater) + ("r-scuttle" ,r-scuttle) ("r-singlecellexperiment" ,r-singlecellexperiment) ("r-statmod" ,r-statmod) ("r-summarizedexperiment" ,r-summarizedexperiment))) -- cgit v1.2.3 From 970984237a071314571f3e2e2445601f43896aab Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 4 Dec 2020 03:57:20 +0100 Subject: gnu: r-biocviews: Update to 1.58.1. * gnu/packages/bioinformatics.scm (r-biocviews): Update to 1.58.1. Co-authored-by: Ricardo Wurmus . --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index af42f5f5e6..42ebbe7cbc 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7729,13 +7729,13 @@ BLAST, KEGG, GenBank, MEDLINE and GO.") (define-public r-biocviews (package (name "r-biocviews") - (version "1.58.0") + (version "1.58.1") (source (origin (method url-fetch) (uri (bioconductor-uri "biocViews" version)) (sha256 (base32 - "0f0aa51h9x8n114zz6q6iw45d78i9wzl4ycbpiy0bdn23167pd84")))) + "1by2639z7n62z84dr8rj9jz12gsd1k8q42zsnxacxbwfwp6h0cl4")))) (properties `((upstream-name . "biocViews"))) (build-system r-build-system) -- cgit v1.2.3 From 1174317e030ba5a5ba19844f79235db7748daecc Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:56:47 +0100 Subject: gnu: r-pcatools: Update to 2.2.0. * gnu/packages/bioconductor.scm (r-pcatools): Update to 2.2.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index c172f15ec4..fc040b4eb8 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8270,14 +8270,14 @@ distance measures.") (define-public r-pcatools (package (name "r-pcatools") - (version "2.0.0") + (version "2.2.0") (source (origin (method url-fetch) (uri (bioconductor-uri "PCAtools" version)) (sha256 (base32 - "0mnwqrhm1hmhzwrpidf6z207w1ycpm572snvpp5swlg6hnxq6bnc")))) + "1fz9h99yyn49b5rcnkg2kjdfmczfwnc44fpwbia0izj6gx192phb")))) (properties `((upstream-name . "PCAtools"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 3f04b8167b5359026e9c27c3123852a27fe7650a Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:48:21 +0100 Subject: gnu: r-chipcomp: Update to 1.20.0. * gnu/packages/bioconductor.scm (r-chipcomp): Update to 1.20.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index fc040b4eb8..8e2888fb34 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2132,14 +2132,14 @@ more complex hypotheses) via empirical Bayesian methods.") (define-public r-chipcomp (package (name "r-chipcomp") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ChIPComp" version)) (sha256 (base32 - "0780kj9vbzdhf2jkfb1my8m58pcdwk6jqw6zfng82g46jias98cp")))) + "0dbypfgys74snmyf982183ilzg6vamfw1d5y0lp5p8zxbffh2xl7")))) (properties `((upstream-name . "ChIPComp"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From b856a48768be469ec2e4fc3e7de058b5c70d8372 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:49:48 +0100 Subject: gnu: r-scdd: Update to 1.14.0. * gnu/packages/bioconductor.scm (r-scdd): Update to 1.14.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 8e2888fb34..e96cefca65 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3183,14 +3183,14 @@ assumptions.") (define-public r-scdd (package (name "r-scdd") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "scDD" version)) (sha256 (base32 - "19q01jksxpv4p26wp2c6faa4fffkjnqlbcds2x955pk35jkqknxx")))) + "07l07fq5633ccq5d3l35dm34pwvaqfa3b3qwpn5v5xn99f5hfz0g")))) (properties `((upstream-name . "scDD"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 43bf50ecae79d4e875fe5b6772470b65903d007c Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:54:04 +0100 Subject: gnu: r-ggcyto: Update to 1.18.0. * gnu/packages/bioconductor.scm (r-ggcyto): Update to 1.18.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index e96cefca65..e890542b31 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6173,14 +6173,14 @@ manipulation of flow cytometry data.") (define-public r-ggcyto (package (name "r-ggcyto") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ggcyto" version)) (sha256 (base32 - "1ih6ggay7jjxnx8blc2sk95g8d40gkim145jllkk8sqwl02g44p0")))) + "0myjvhm9jjb9cih5nlka3f9zg5ncy8gy3krpdpa0618jdglvgr1m")))) (properties `((upstream-name . "ggcyto"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 45dfb7516656a977fb8998b535b658062249a4ce Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 4 Dec 2020 05:16:13 +0100 Subject: gnu: Add r-catalyst. * gnu/packages/bioconductor.scm (r-catalyst): New variable. --- gnu/packages/bioconductor.scm | 58 +++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 58 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index e890542b31..43f33721df 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9140,3 +9140,61 @@ variables.To assure a good level of reproducibility a post-test filter is available, where we may set the minimum effect size considered biologicaly relevant, and the minimum expression of the most abundant condition.") (license license:gpl2))) + +(define-public r-catalyst + (package + (name "r-catalyst") + (version "1.14.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "CATALYST" version)) + (sha256 + (base32 + "13af7c4irx1f5yqi32k7kj661vzg32wn3dnps7r9pjijfl4drhrh")))) + (properties `((upstream-name . "CATALYST"))) + (build-system r-build-system) + (propagated-inputs + `(("r-circlize" ,r-circlize) + ("r-complexheatmap" ,r-complexheatmap) + ("r-consensusclusterplus" ,r-consensusclusterplus) + ("r-cowplot" ,r-cowplot) + ("r-data-table" ,r-data-table) + ("r-dplyr" ,r-dplyr) + ("r-drc" ,r-drc) + ("r-flowcore" ,r-flowcore) + ("r-flowsom" ,r-flowsom) + ("r-ggplot2" ,r-ggplot2) + ("r-ggrepel" ,r-ggrepel) + ("r-ggridges" ,r-ggridges) + ("r-gridextra" ,r-gridextra) + ("r-magrittr" ,r-magrittr) + ("r-matrix" ,r-matrix) + ("r-matrixstats" ,r-matrixstats) + ("r-nnls" ,r-nnls) + ("r-purrr" ,r-purrr) + ("r-rcolorbrewer" ,r-rcolorbrewer) + ("r-reshape2" ,r-reshape2) + ("r-rtsne" ,r-rtsne) + ("r-s4vectors" ,r-s4vectors) + ("r-scales" ,r-scales) + ("r-scater" ,r-scater) + ("r-singlecellexperiment" ,r-singlecellexperiment) + ("r-summarizedexperiment" ,r-summarizedexperiment))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page + "https://github.com/HelenaLC/CATALYST") + (synopsis "Cytometry data analysis tools") + (description + "This package is Cytometry dATa anALYSis Tools (CATALYST). Mass +cytometry (CyTOF) uses heavy metal isotopes rather than fluorescent tags as +reporters to label antibodies, thereby substantially decreasing spectral +overlap and allowing for examination of over 50 parameters at the single cell +level. While spectral overlap is significantly less pronounced in CyTOF than +flow cytometry, spillover due to detection sensitivity, isotopic impurities, +and oxide formation can impede data interpretability. We designed +CATALYST (Cytometry dATa anALYSis Tools) to provide a pipeline for +preprocessing of cytometry data, including i) normalization using bead +standards, ii) single-cell deconvolution, and iii) bead-based compensation.") + (license license:gpl2+))) -- cgit v1.2.3 From e5a4198bc314061ea9dea5d3573386f939f44dea Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:50:06 +0100 Subject: gnu: r-minfi: Update to 1.36.0. * gnu/packages/bioconductor.scm (r-minfi): Update to 1.36.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 43f33721df..b30680752b 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3377,14 +3377,14 @@ studies.") (define-public r-minfi (package (name "r-minfi") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "minfi" version)) (sha256 (base32 - "0bl1sk9syy770d5wqa0k1y0wrs5x8sbj13px1v03v3693pdj081w")))) + "1x3ksp6syl54hds7wgm4p9yj4mznhhhhk20ijn3i2jc3k8xqcqfi")))) (build-system r-build-system) (propagated-inputs `(("r-beanplot" ,r-beanplot) -- cgit v1.2.3 From 0b7dd447066b5eb1b305e593d8198a7d0e3759f6 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:50:10 +0100 Subject: gnu: r-methylumi: Update to 2.36.0. * gnu/packages/bioconductor.scm (r-methylumi): Update to 2.36.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index b30680752b..684c2c3069 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3428,14 +3428,14 @@ methylation arrays.") (define-public r-methylumi (package (name "r-methylumi") - (version "2.34.0") + (version "2.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "methylumi" version)) (sha256 (base32 - "0phb2dyndnk9rv79nx246cn1sc9wbzdqqbgl6402knc7dgh799wr")))) + "00w5affxzirf6ffiznk33papwwvwsk2zgy6xvsx7iaf5kvnak2nh")))) (build-system r-build-system) (propagated-inputs `(("r-annotate" ,r-annotate) -- cgit v1.2.3 From 4eeaa159d27edb816d1f90e68c6029ac24753a28 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:50:13 +0100 Subject: gnu: r-lumi: Update to 2.42.0. * gnu/packages/bioconductor.scm (r-lumi): Update to 2.42.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 684c2c3069..58eac8e11a 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3474,14 +3474,14 @@ and Infinium HD arrays are also included.") (define-public r-lumi (package (name "r-lumi") - (version "2.40.0") + (version "2.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "lumi" version)) (sha256 (base32 - "196izc4mdh8j4f04fsf8cqm99w1inzpwy34kwvhz6zvxj2ywn1i9")))) + "19asap8vhm3g8hyvpr8l7mw071dsa1d95wx46lh8m6achffngqv3")))) (build-system r-build-system) (propagated-inputs `(("r-affy" ,r-affy) -- cgit v1.2.3 From adf6edc750c75de4e5b592ca74035326ce4871cf Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:52:23 +0100 Subject: gnu: r-quantro: Update to 1.24.0. * gnu/packages/bioconductor.scm (r-quantro): Update to 1.24.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 58eac8e11a..e33ad56388 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5061,14 +5061,14 @@ chips with the MAQC reference datasets.") (define-public r-quantro (package (name "r-quantro") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "quantro" version)) (sha256 (base32 - "0ap9cl5z79wg44mnagjsk8py3kngb4f0ddnx85cbnwqkvb769zbz")))) + "1mq4hda73idkq0lkfrhcmiz4kkalfn47dh3i75br5fi33mdgc0k2")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) -- cgit v1.2.3 From 8db36c1f688fa5e201db2cf648830e493d2babf2 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:52:26 +0100 Subject: gnu: r-yarn: Update to 1.16.0. * gnu/packages/bioconductor.scm (r-yarn): Update to 1.16.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index e33ad56388..f8cc275ce4 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5094,14 +5094,14 @@ groups.") (define-public r-yarn (package (name "r-yarn") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "yarn" version)) (sha256 (base32 - "1xdjwy1gkfg8lhgq4iwwmbi01903qljjs7yd96cvacmvgn8z6qvx")))) + "0p8wz5jn601vxbbxkm73ps3fx0j1y56nr2qf6y8k80vgrk7bv5gp")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) -- cgit v1.2.3 From 9f6e2bfe1febe9ea0f763bb928d60f44508df9ab Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:54:50 +0100 Subject: gnu: r-watermelon: Update to 1.34.0. * gnu/packages/bioconductor.scm (r-watermelon): Update to 1.34.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index f8cc275ce4..6d3804d62d 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6859,14 +6859,14 @@ data.") (define-public r-watermelon (package (name "r-watermelon") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "wateRmelon" version)) (sha256 (base32 - "1c3a6bq3ggmv8kmdfrgiar6nwgircgzjrbgd9z9dqiin7j13gxwn")))) + "1sc2nxg9bafpvlwqhky2p5b6fkimkk9v3xcab9kvwnj6szrb6p3f")))) (properties `((upstream-name . "wateRmelon"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 64f9fb308f776fbc5e8b3fe39f06bc34fec01c2a Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 15:54:56 +0100 Subject: gnu: r-bigmelon: Update to 1.16.0. * gnu/packages/bioconductor.scm (r-bigmelon): Update to 1.16.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 6d3804d62d..89ebbe530a 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6955,14 +6955,14 @@ with multiple R processes supported by the package @code{parallel}.") (define-public r-bigmelon (package (name "r-bigmelon") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bigmelon" version)) (sha256 (base32 - "1cryjhbiacm45g097rpqgbva49hs5vdx4y4h5h2v1gw4k78hwb4y")))) + "0hj5njwx7n681vigkq4560f9dm7mdjgvcwbgp5nbdn1fb2z24bk7")))) (properties `((upstream-name . "bigmelon"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 6a4818716d16613d56f0a4c7c8745ae75da8edb6 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 16:01:26 +0100 Subject: gnu: r-gqtlbase: Update to 1.21.1. Co-authored-by: Ricardo Wurmus * gnu/packages/bioinformatics.scm (r-gqtlbase): Update to 1.21.1. [arguments]: Add phase to patch broken NAMESPACE file. --- gnu/packages/bioinformatics.scm | 14 ++++++++++++-- 1 file changed, 12 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 42ebbe7cbc..c758724552 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10563,16 +10563,26 @@ interval to data view, mismatch pileup, and several splicing summaries.") (define-public r-gqtlbase (package (name "r-gqtlbase") - (version "1.20.4") + (version "1.21.1") (source (origin (method url-fetch) (uri (bioconductor-uri "gQTLBase" version)) (sha256 (base32 - "1ly14vhhqxjpbxjypi6ppd37dycabdhf4ny4nsvp9969k418zv41")))) + "0nipibm1bk9k70ajbw1f6vjmz0dh7gk21l17q3m54bnawxsggrfh")))) (properties `((upstream-name . "gQTLBase"))) (build-system r-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + ;; This is an upstream bug. + (add-after 'unpack 'fix-imports + (lambda _ + (substitute* "NAMESPACE" + ((".*maxffmode.*") "") + (("importFrom\\(ff,.*") "import(ff)\n")) + #t))))) (propagated-inputs `(("r-batchjobs" ,r-batchjobs) ("r-bbmisc" ,r-bbmisc) -- cgit v1.2.3 From cde035e67f3f5aba866c64b895b8a6aa234692ad Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 30 Oct 2020 16:01:39 +0100 Subject: gnu: r-gqtlstats: Update to 1.21.3. * gnu/packages/bioinformatics.scm (r-gqtlstats): Update to 1.21.3. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index c758724552..9cf5c0acab 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10743,14 +10743,14 @@ defining LD blocks.") (define-public r-gqtlstats (package (name "r-gqtlstats") - (version "1.20.0") + (version "1.21.3") (source (origin (method url-fetch) (uri (bioconductor-uri "gQTLstats" version)) (sha256 (base32 - "1jjqfpjp93nmxjn757j5mzcax96bzcqdd1gr3rsdxg7ap008l2w7")))) + "1h78l23idf867djmdk97b02jxgmz4vfr2dai01fp648d0lsx5mkl")))) (properties `((upstream-name . "gQTLstats"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 7601015fc9d51a2f2ecdd676bcae51ed7121d30d Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 7 Dec 2020 16:01:24 +0100 Subject: gnu: r-delayedmatrixstats: Update to 1.12.1. * gnu/packages/bioconductor.scm (r-delayedmatrixstats): Update to 1.12.1. [propagated-inputs]: Add r-matrixgenerics. --- gnu/packages/bioconductor.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 89ebbe530a..5f524f310c 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8982,14 +8982,14 @@ data in the column sparse format.") (define-public r-delayedmatrixstats (package (name "r-delayedmatrixstats") - (version "1.12.0") + (version "1.12.1") (source (origin (method url-fetch) (uri (bioconductor-uri "DelayedMatrixStats" version)) (sha256 (base32 - "0xgjamxwf9wwy6dc138mxx5xgjhq5d2z7irliyxbmpaf5kicnwyi")))) + "1cyvj6ffl10vaiip146dldc1w8if854kpz9nhi50ndhpkmdb8sa0")))) (properties `((upstream-name . "DelayedMatrixStats"))) (build-system r-build-system) @@ -8999,6 +8999,7 @@ data in the column sparse format.") ("r-hdf5array" ,r-hdf5array) ("r-iranges" ,r-iranges) ("r-matrix" ,r-matrix) + ("r-matrixgenerics" ,r-matrixgenerics) ("r-matrixstats" ,r-matrixstats) ("r-s4vectors" ,r-s4vectors) ("r-sparsematrixstats" ,r-sparsematrixstats))) -- cgit v1.2.3 From 4617cc7fd509cc73703e5b273c634f995bb69a5d Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 7 Dec 2020 16:44:23 +0100 Subject: gnu: r-rhtslib: Propagate zlib. * gnu/packages/bioinformatics.scm (r-rhtslib)[inputs]: Move zlib from here... [propagated-inputs]: ...to here. (r-variantannotation, r-rsamtools, r-bamsignals, r-rhdf5, r-methylkit)[inputs]: Remove zlib. * gnu/packages/bioconductor.scm (r-diffbind, r-quasr, r-cytolib, r-ncdfflow, r-flowworkspace, r-seqbias)[inputs]: Remove zlib. --- gnu/packages/bioconductor.scm | 12 ------------ gnu/packages/bioinformatics.scm | 13 +------------ 2 files changed, 1 insertion(+), 24 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 5f524f310c..5a3d638434 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1726,8 +1726,6 @@ signal in the input, that lead to spurious peaks during peak calling.") "0irhqsi6rrkrkc7dhwmfpqfd0mnigs17027czcx8vgbrbra4lcvd")))) (properties `((upstream-name . "DiffBind"))) (build-system r-build-system) - (inputs - `(("zlib" ,zlib))) (propagated-inputs `(("r-amap" ,r-amap) ("r-apeglm" ,r-apeglm) @@ -5664,8 +5662,6 @@ index.") "032m01q34nnmvbhcb2g3pz2fqmgcw5464m74m1m0h7x9bl04a5k8")))) (properties `((upstream-name . "QuasR"))) (build-system r-build-system) - (inputs - `(("zlib" ,zlib))) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) ("r-biobase" ,r-biobase) @@ -6049,8 +6045,6 @@ cluster count and membership by stability evidence in unsupervised analysis.") (("\\(RHDF5_LIBS\\)" match) (string-append match "/libhdf5.a"))) #t))))) - (inputs - `(("zlib" ,zlib))) (native-inputs `(("r-knitr" ,r-knitr) ("pkg-config" ,pkg-config))) @@ -6150,8 +6144,6 @@ change point detection.") (("\\(RHDF5_LIBS\\)" match) (string-append match "/libhdf5.a"))) #t))))) - (inputs - `(("zlib" ,zlib))) (propagated-inputs `(("r-bh" ,r-bh) ("r-biobase" ,r-biobase) @@ -6332,8 +6324,6 @@ for other R packages to compile and link against.") (("\\{h5lib\\}" match) (string-append match "/libhdf5.a"))) #t))))) - (inputs - `(("zlib" ,zlib))) (propagated-inputs `(("r-aws-s3" ,r-aws-s3) ("r-aws-signature" ,r-aws-signature) @@ -6997,8 +6987,6 @@ with multiple R processes supported by the package @code{parallel}.") `(("r-biostrings" ,r-biostrings) ("r-genomicranges" ,r-genomicranges) ("r-rhtslib" ,r-rhtslib))) - (inputs - `(("zlib" ,zlib))) ; This comes from rhtslib. (home-page "https://bioconductor.org/packages/seqbias/") (synopsis "Estimation of per-position bias in high-throughput sequencing data") (description diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 9cf5c0acab..9edf75a82c 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7980,8 +7980,6 @@ CAGE.") "1sl0l6v05lfglj281nszma0h5k234md7rn2pdah8vs2d4iq3kimw")))) (properties `((upstream-name . "VariantAnnotation"))) - (inputs - `(("zlib" ,zlib))) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) ("r-biobase" ,r-biobase) @@ -8260,8 +8258,6 @@ biological sequences or sets of sequences.") (substitute* "NAMESPACE" (("import\\(zlibbioc\\)") "")) #t))))) - (inputs - `(("zlib" ,zlib))) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) ("r-biocparallel" ,r-biocparallel) @@ -8794,9 +8790,8 @@ secondary structure and comparative analysis in R.") (arguments '(#:configure-flags '("--no-staged-install"))) (propagated-inputs `(("curl" ,curl) + ("zlib" ,zlib) ; packages using rhtslib need to link with zlib ("r-zlibbioc" ,r-zlibbioc))) - (inputs - `(("zlib" ,zlib))) (native-inputs `(("pkg-config" ,pkg-config) ("r-knitr" ,r-knitr))) @@ -8827,8 +8822,6 @@ of other R packages who wish to make use of HTSlib.") ("r-rcpp" ,r-rcpp) ("r-rhtslib" ,r-rhtslib) ("r-zlibbioc" ,r-zlibbioc))) - (inputs - `(("zlib" ,zlib))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/bamsignals") @@ -9127,8 +9120,6 @@ HDF5 datasets.") (propagated-inputs `(("r-rhdf5filters" ,r-rhdf5filters) ("r-rhdf5lib" ,r-rhdf5lib))) - (inputs - `(("zlib" ,zlib))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/rhdf5") @@ -9616,8 +9607,6 @@ number detection tools.") ("r-zlibbioc" ,r-zlibbioc))) (native-inputs `(("r-knitr" ,r-knitr))) ; for vignettes - (inputs - `(("zlib" ,zlib))) (home-page "https://github.com/al2na/methylKit") (synopsis "DNA methylation analysis from high-throughput bisulfite sequencing results") -- cgit v1.2.3 From ebf11de4e32a5c2ff03a55a81892ff42ca547c14 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 7 Dec 2020 16:46:44 +0100 Subject: gnu: r-diffbind: Update to 3.0.8. * gnu/packages/bioconductor.scm (r-diffbind): Update to 3.0.8. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 5a3d638434..bd7df29378 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1716,14 +1716,14 @@ signal in the input, that lead to spurious peaks during peak calling.") (define-public r-diffbind (package (name "r-diffbind") - (version "3.0.7") + (version "3.0.8") (source (origin (method url-fetch) (uri (bioconductor-uri "DiffBind" version)) (sha256 (base32 - "0irhqsi6rrkrkc7dhwmfpqfd0mnigs17027czcx8vgbrbra4lcvd")))) + "11svdfjp4faswrmzwkryzhd0ji2pl9vwsd35lvbfjgakbpxnyn8a")))) (properties `((upstream-name . "DiffBind"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 59a6780f70e138a515dfe9c3b5b5399dbd91c228 Mon Sep 17 00:00:00 2001 From: Ludovic Courtès Date: Wed, 9 Dec 2020 11:55:13 +0100 Subject: services: avahi: Depend on 'user-processes'. * gnu/services/avahi.scm (avahi-shepherd-service): Add 'user-processes' to 'requirement'. --- gnu/services/avahi.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/services/avahi.scm b/gnu/services/avahi.scm index 54656708ca..7812191cb2 100644 --- a/gnu/services/avahi.scm +++ b/gnu/services/avahi.scm @@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2014, 2015, 2016, 2017, 2018, 2019 Ludovic Courtès +;;; Copyright © 2014, 2015, 2016, 2017, 2018, 2019, 2020 Ludovic Courtès ;;; ;;; This file is part of GNU Guix. ;;; @@ -130,7 +130,7 @@ (list (shepherd-service (documentation "Run the Avahi mDNS/DNS-SD responder.") (provision '(avahi-daemon)) - (requirement '(dbus-system networking)) + (requirement '(user-processes dbus-system networking)) (start #~(make-forkexec-constructor (list #$(file-append avahi "/sbin/avahi-daemon") -- cgit v1.2.3 From f066e657132461519de897e695e91e8d381a7a4b Mon Sep 17 00:00:00 2001 From: Ludovic Courtès Date: Wed, 9 Dec 2020 11:56:09 +0100 Subject: services: guix-publish: Depend on 'avahi-daemon' when needed. * gnu/services/base.scm (guix-publish-shepherd-service): Add 'user-processes' to 'requirement'. When ADVERTISE? is true, also add 'avahi-daemon'. --- gnu/services/base.scm | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/gnu/services/base.scm b/gnu/services/base.scm index 709d011f53..8449d924af 100644 --- a/gnu/services/base.scm +++ b/gnu/services/base.scm @@ -1825,7 +1825,9 @@ raise a deprecation warning if the 'compression-level' field was used." advertise?) (list (shepherd-service (provision '(guix-publish)) - (requirement '(guix-daemon)) + (requirement `(user-processes + guix-daemon + ,@(if advertise? '(avahi-daemon) '()))) (start #~(make-forkexec-constructor (list #$(file-append guix "/bin/guix") "publish" "-u" "guix-publish" -- cgit v1.2.3 From 69a0440a02945b3fb8d156b7f9d96628059d5f67 Mon Sep 17 00:00:00 2001 From: Ludovic Courtès Date: Wed, 9 Dec 2020 11:58:01 +0100 Subject: doc: Document 'advertise?' for 'guix-publish-configuration'. * doc/guix.texi (Base Services): Document the 'advertise?' field of 'guix-publish-configuration'. --- doc/guix.texi | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/doc/guix.texi b/doc/guix.texi index 7960143723..38927bc0b5 100644 --- a/doc/guix.texi +++ b/doc/guix.texi @@ -15353,6 +15353,14 @@ The TCP port to listen for connections. The host (and thus, network interface) to listen to. Use @code{"0.0.0.0"} to listen on all the network interfaces. +@item @code{advertise?} (default: @code{#f}) +When true, advertise the service on the local network @i{via} the DNS-SD +protocol, using Avahi. + +This allows neighboring Guix devices with discovery on (see +@code{guix-configuration} above) to discover this @command{guix publish} +instance and to automatically download substitutes from it. + @item @code{compression} (default: @code{'(("gzip" 3))}) This is a list of compression method/level tuple used when compressing substitutes. For example, to compress all substitutes with @emph{both} lzip -- cgit v1.2.3 From 3d85c3ec652feb22824f355538b51e6955ded361 Mon Sep 17 00:00:00 2001 From: Ludovic Courtès Date: Wed, 9 Dec 2020 13:55:46 +0100 Subject: gnu: pciutils: Fix compilation error on GNU/Hurd. * gnu/packages/patches/pciutils-hurd-fix.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. * gnu/packages/pciutils.scm (pciutils)[arguments]: Add 'apply-hurd-patch' phase when (hurd-target?) is true. [inputs]: Add "hurd-patch" entry when (hurd-target?) is true. --- gnu/local.mk | 1 + gnu/packages/patches/pciutils-hurd-fix.patch | 23 +++++++++++++++++++++++ gnu/packages/pciutils.scm | 15 +++++++++++++-- 3 files changed, 37 insertions(+), 2 deletions(-) create mode 100644 gnu/packages/patches/pciutils-hurd-fix.patch diff --git a/gnu/local.mk b/gnu/local.mk index 90df6f3966..67482b8226 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -1435,6 +1435,7 @@ dist_patch_DATA = \ %D%/packages/patches/pam-krb5-CVE-2020-10595.patch \ %D%/packages/patches/pango-skip-libthai-test.patch \ %D%/packages/patches/pciutils-hurd-configure.patch \ + %D%/packages/patches/pciutils-hurd-fix.patch \ %D%/packages/patches/plasma-framework-fix-KF5PlasmaMacros.cmake.patch \ %D%/packages/patches/ppsspp-disable-upgrade-and-gold.patch \ %D%/packages/patches/samba-fix-fcntl-hint-detection.patch \ diff --git a/gnu/packages/patches/pciutils-hurd-fix.patch b/gnu/packages/patches/pciutils-hurd-fix.patch new file mode 100644 index 0000000000..f1979d4352 --- /dev/null +++ b/gnu/packages/patches/pciutils-hurd-fix.patch @@ -0,0 +1,23 @@ +Fix a build error on GNU/Hurd for pciutils 3.7.0. + +commit 053cf6c8b2acafadf828912828336d90fe9b8696 +Author: Martin Mares +Date: Sun May 31 11:53:28 2020 +0200 + + HURD backend should compile again + + Fixes a bug introduced by commit 82c06b47dea5a38075ce9d56f743360bc47b4c78. + +diff --git a/lib/hurd.c b/lib/hurd.c +index 7b3b2ae..ccd92f6 100644 +--- a/lib/hurd.c ++++ b/lib/hurd.c +@@ -307,7 +307,6 @@ hurd_fill_regions(struct pci_dev *d) + d->base_addr[i] |= regions[i].is_64 << 2; + d->base_addr[i] |= regions[i].is_prefetchable << 3; + +- if (flags & PCI_FILL_SIZES) +- d->size[i] = regions[i].size; ++ d->size[i] = regions[i].size; + } + } diff --git a/gnu/packages/pciutils.scm b/gnu/packages/pciutils.scm index a5ed121c85..d7d224b292 100644 --- a/gnu/packages/pciutils.scm +++ b/gnu/packages/pciutils.scm @@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2014, 2015, 2017 Ludovic Courtès +;;; Copyright © 2014, 2015, 2017, 2020 Ludovic Courtès ;;; Copyright © 2016 Efraim Flashner ;;; Copyright © 2018 Tobias Geerinckx-Rice ;;; Copyright © 2019 Mathieu Othacehe @@ -92,7 +92,15 @@ (replace 'install (lambda* (#:key outputs #:allow-other-keys) ;; Install the commands, library, and .pc files. - (invoke "make" "install" "install-lib")))) + (invoke "make" "install" "install-lib"))) + + ,@(if (hurd-target?) + '((add-after 'unpack 'apply-hurd-patch + (lambda* (#:key inputs #:allow-other-keys) + (let ((patch (assoc-ref inputs "hurd-patch"))) + (invoke "patch" "-p1" "--batch" "-i" + patch))))) + '())) ;; Make sure programs have an RPATH so they can find libpciutils.so. #:make-flags (list (string-append "LDFLAGS=-Wl,-rpath=" @@ -109,6 +117,9 @@ (package-supported-systems kmod)) `(("kmod" ,kmod)) '()) + ,@(if (hurd-target?) + `(("hurd-patch" ,(search-patch "pciutils-hurd-fix.patch"))) + '()) ("zlib" ,zlib))) (home-page "https://mj.ucw.cz/sw/pciutils/") (synopsis "Programs for inspecting and manipulating PCI devices") -- cgit v1.2.3 From 51034596643a36ccbf87081736437eaef078d9cb Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Wed, 9 Dec 2020 14:54:27 +0100 Subject: gnu: emacs-debbugs: Update to 0.27. * gnu/packages/emacs-xyz.scm (emacs-debbugs): Update to 0.27. --- gnu/packages/emacs-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index e2658b4547..dcf05c909d 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -4840,14 +4840,14 @@ source code using IPython.") (define-public emacs-debbugs (package (name "emacs-debbugs") - (version "0.26") + (version "0.27") (source (origin (method url-fetch) (uri (string-append "https://elpa.gnu.org/packages/debbugs-" version ".tar")) (sha256 - (base32 "14n2rrs3ccvlp8fhxs08awlqdfawxwbj8nq1xpa0wwlbfvxnf24c")))) + (base32 "1zn9p9vmfv5ihrp8d06b6abs48q225v42cgwa01s39hld6zg6wbv")))) (build-system emacs-build-system) (arguments '(#:include '("\\.el$" "\\.wsdl$" "\\.info$"))) (propagated-inputs -- cgit v1.2.3 From a294eecd98c8237781ab0c80c3b7695b77f7ec35 Mon Sep 17 00:00:00 2001 From: Pierre Neidhardt Date: Wed, 9 Dec 2020 17:27:51 +0100 Subject: gnu: Add emacs-helm-switch-to-repl. * gnu/packages/emacs-xyz.scm (emacs-helm-switch-to-repl): New variable. --- gnu/packages/emacs-xyz.scm | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index dcf05c909d..9407a4fdc2 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -23536,6 +23536,30 @@ Google guidelines.") fish-completion. It can be used in both Eshell and M-x shell.") (license license:gpl3+))) +(define-public emacs-helm-switch-to-repl + (package + (name "emacs-helm-switch-to-repl") + (version "0.1.0") + (home-page "https://github.com/emacs-helm/helm-switch-to-repl") + (source + (origin + (method git-fetch) + (uri (git-reference + (url home-page) + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0n19brymwnawhi0y10m54cas3qg64pmkqq1ajvjw1rfibmw3n6nk")))) + (build-system emacs-build-system) + (propagated-inputs + `(("helm" ,emacs-helm))) + (synopsis "Helm action to switch directory in Emacs REPLs") + (description "Helm \"Switch-to-REPL\" offers the +@code{helm-switch-to-repl} action, a generalized and extensible version of +@code{helm-ff-switch-to-shell}. It can be added to @code{helm-find-files} and +other @code{helm-type-file} sources such as @code{helm-locate}.") + (license license:gpl3+))) + (define-public emacs-telega ;; This package has versions newer than indicated on MELPA. ;; Get the current version from `telega-version` in telega.el. -- cgit v1.2.3 From 44308c8c5fcf881a4d29ee0abc38b09fcbafb0b4 Mon Sep 17 00:00:00 2001 From: Pierre Neidhardt Date: Wed, 9 Dec 2020 18:08:28 +0100 Subject: gnu: Add libzim. * gnu/packages/web.scm (libzim): New variable. --- gnu/packages/web.scm | 41 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 41 insertions(+) diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm index ff40743832..4e5595cb5c 100644 --- a/gnu/packages/web.scm +++ b/gnu/packages/web.scm @@ -79,8 +79,10 @@ #:use-module (guix build-system glib-or-gtk) #:use-module (guix build-system gnu) #:use-module (guix build-system go) + #:use-module (guix build-system meson) #:use-module (guix build-system perl) #:use-module (guix build-system python) + #:use-module (guix build-system qt) #:use-module (guix build-system scons) #:use-module (guix build-system trivial) #:use-module (gnu packages) @@ -90,6 +92,7 @@ #:use-module (gnu packages autotools) #:use-module (gnu packages base) #:use-module (gnu packages bison) + #:use-module (gnu packages bittorrent) #:use-module (gnu packages boost) #:use-module (gnu packages check) #:use-module (gnu packages compression) @@ -111,6 +114,7 @@ #:use-module (gnu packages glib) #:use-module (gnu packages gnome) #:use-module (gnu packages gnu-doc) + #:use-module (gnu packages gnunet) #:use-module (gnu packages gnupg) #:use-module (gnu packages golang) #:use-module (gnu packages gperf) @@ -118,6 +122,7 @@ #:use-module (gnu packages guile) #:use-module (gnu packages guile-xyz) #:use-module (gnu packages hurd) + #:use-module (gnu packages icu4c) #:use-module (gnu packages image) #:use-module (gnu packages java) #:use-module (gnu packages jemalloc) @@ -152,6 +157,7 @@ #:use-module (gnu packages qt) #:use-module (gnu packages re2c) #:use-module (gnu packages readline) + #:use-module (gnu packages search) #:use-module (gnu packages sphinx) #:use-module (gnu packages texinfo) #:use-module (gnu packages textutils) @@ -7854,3 +7860,38 @@ solution for any project's interface needs: (description "gmnisrv is a simple Gemini protocol server written in C.") (license (list license:gpl3+ license:bsd-3))))) ;; for ini.c and ini.h + +(define-public libzim + (package + (name "libzim") + (version "6.2.2") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/openzim/libzim") + (commit version))) + (sha256 + (base32 + "0p2317cp19lx0hw9n4fsb3nw2vc4hc1yyi98k3yrs41pkr840kwa")) + (file-name (git-file-name name version)))) + (build-system meson-build-system) + (arguments + ;; TODO: Find out why tests fail. + '(#:tests? #f)) + (inputs + `(("icu4c" ,icu4c) + ("liblzma" ,xz) + ("libuuid" ,util-linux "lib") + ("xapian" ,xapian) + ("zlib" ,zlib) + ("zstd" ,zstd "lib"))) + (native-inputs + `(("pkg-config" ,pkg-config) + ("googletest" ,googletest))) + (home-page "https://wiki.openzim.org/wiki/Main_Page") + (synopsis "Reference implementation of the ZIM specification") + (description "The openZIM project proposes offline storage solutions for +content coming from the Web. The zimlib is the standard implementation of the +ZIM specification. It is a library which implements the read and write method +for ZIM files.") + (license license:gpl2))) -- cgit v1.2.3 From acbf47a0676cad4d56801845047118e3fcd1c5f2 Mon Sep 17 00:00:00 2001 From: Pierre Neidhardt Date: Wed, 9 Dec 2020 18:09:47 +0100 Subject: gnu: Add kiwix-lib. * gnu/packages/web.scm (kiwix-lib): New variable. --- gnu/packages/web.scm | 54 ++++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 54 insertions(+) diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm index 4e5595cb5c..97bff39718 100644 --- a/gnu/packages/web.scm +++ b/gnu/packages/web.scm @@ -7895,3 +7895,57 @@ content coming from the Web. The zimlib is the standard implementation of the ZIM specification. It is a library which implements the read and write method for ZIM files.") (license license:gpl2))) + +(define-public kiwix-lib + (package + (name "kiwix-lib") + (version "9.4.0") + (home-page "https://github.com/kiwix/kiwix-lib/") + (source (origin + (method git-fetch) + (uri (git-reference + (url home-page) + (commit version))) + (sha256 + (base32 + "0nsm4qgl0cb6wv983n0px1kf217k4kykb8q56b8j6ikp061lzamm")) + (file-name (git-file-name name version)))) + (build-system meson-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-before 'configure 'fix-paths-and-includes + (lambda* (#:key inputs #:allow-other-keys) + (setenv "CPPFLAGS" (string-append "-I" (assoc-ref inputs "mustache"))) + (substitute* "src/aria2.cpp" + (("ARIA2_CMD \"aria2c\"") + (string-append "ARIA2_CMD \"" + (assoc-ref inputs "aria2") + "/bin/aria2c\""))) + #t))))) + (inputs + `(("aria2" ,aria2) + ("curl" ,curl) + ("icu4c" ,icu4c) + ("libmicrohttpd" ,libmicrohttpd) + ("libzim" ,libzim) + ("pugixml" ,pugixml) + ("xapian" ,xapian) + ("zlib" ,zlib) + ("zstd" ,zstd "lib"))) + (native-inputs + `(("mustache" ,(origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/kainjow/Mustache") + ;; XXX: Readme says to use version 3. Can we use 3.2.1? + (commit "v4.1"))) + (file-name (git-file-name "mustache" "4.1")) + (sha256 + (base32 + "0r9rbk6v1wpld2ismfsk2lkhbyv3dkf0p03hkjivbj05qkfhvlbb")))) + ("pkg-config" ,pkg-config))) + (synopsis "Common code base for all Kiwix ports") + (description "The Kiwix library provides the Kiwix software suite core. +It contains the code shared by all Kiwix ports.") + (license license:gpl3))) -- cgit v1.2.3 From 5f6a0019339d8ee06a3f0a9bbb5df672179fe57a Mon Sep 17 00:00:00 2001 From: Pierre Neidhardt Date: Wed, 9 Dec 2020 18:20:26 +0100 Subject: gnu: Add kiwix-desktop. * gnu/packages/web.scm (kiwix-desktop): New variable. --- gnu/packages/web.scm | 56 ++++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 56 insertions(+) diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm index 97bff39718..6be6011c4e 100644 --- a/gnu/packages/web.scm +++ b/gnu/packages/web.scm @@ -7949,3 +7949,59 @@ for ZIM files.") (description "The Kiwix library provides the Kiwix software suite core. It contains the code shared by all Kiwix ports.") (license license:gpl3))) + +(define-public kiwix-desktop + (package + (name "kiwix-desktop") + (version "2.0.5") + (source (origin + (method url-fetch) + (uri (string-append + "https://download.kiwix.org/release/kiwix-desktop/kiwix-desktop-" + version + ".tar.gz")) + (sha256 + (base32 + "1a9h4qmh6fkfscyp6lax0ri07dvvzw2wp4kr1sm86n0bdk3cwwha")))) + (build-system gnu-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (replace 'configure + (lambda* (#:key outputs #:allow-other-keys) + (invoke "qmake" + (string-append "PREFIX=" + (assoc-ref outputs "out"))))) + (add-before 'configrue 'enable-print-support + (lambda _ + (substitute* "kiwix-desktop.pro" + (("webenginewidgets") "webenginewidgets printsupport")) + #t)) + (add-before 'configure 'substitute-source + ;; Looks like .pro file is missing a feature. + ;; See https://github.com/kiwix/kiwix-desktop/issues/556. + (lambda* (#:key inputs #:allow-other-keys) + (substitute* "kiwix-desktop.pro" + (("webenginewidgets" all) (string-append all " printsupport"))) + #t))))) + (inputs + `(("curl" ,curl) + ("icu4c" ,icu4c) + ("kiwix-lib" ,kiwix-lib) + ("libzim" ,libzim) + ("pugixml" ,pugixml) + ("qtbase" ,qtbase) + ("qtdeclarative" ,qtdeclarative) + ("qtwebchannel" ,qtwebchannel) + ("qtwebengine" ,qtwebengine) + ("xapian" ,xapian) + ("zlib" ,zlib) + ("zstd" ,zstd "lib"))) + (native-inputs + `(("pkg-config" ,pkg-config) + ("qmake" ,qtbase))) + (home-page "https://wiki.kiwix.org/wiki/Software") + (synopsis "Viewer and manager of ZIM files") + (description "Kiwix Desktop allows you to enjoy a lot of different content +offline (such as Wikipedia), without any access to Internet.") + (license license:gpl3))) -- cgit v1.2.3 From e36291ef52a30b1c667b78ef76c1980363f8c138 Mon Sep 17 00:00:00 2001 From: Eric Brown Date: Wed, 22 Apr 2020 06:07:14 -0500 Subject: gnu: Add r-restrserve. * gnu/packages/cran.scm (r-restrserve): New variable. Signed-off-by: Christopher Baines --- gnu/packages/cran.scm | 30 ++++++++++++++++++++++++++++++ 1 file changed, 30 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 05b1541ec7..fb6507b674 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -2632,6 +2632,36 @@ quantities.") @code{melt} and @code{cast}. This package provides them.") (license license:expat))) +(define-public r-restrserve + (package + (name "r-restrserve") + (version "0.4.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "RestRserve" version)) + (sha256 + (base32 "07mm65yxzpwlg6x3lsggj41v8nl4m6v9mszhqjpgj19v3yxvwgi0")))) + (build-system r-build-system) + (propagated-inputs + `(("r-checkmate" ,r-checkmate) + ("r-jsonlite" ,r-jsonlite) + ("r-mime" ,r-mime) + ("r-r6" ,r-r6) + ("r-rcpp" ,r-rcpp) + ("r-rserve" ,r-rserve) + ("r-uuid" ,r-uuid))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://restrserve.org") + (synopsis "R web API framework") + (description + "RestRserve is an R web API framework for building high-performance AND +robust microservices and app backends. With Rserve backend on UNIX-like +systems it is parallel by design. It will handle incoming requests in +parallel - each request in a separate fork.") + (license license:gpl2+))) + (define-public r-progress (package (name "r-progress") -- cgit v1.2.3 From 2a23e3f582941aee3461aa7b52e0ccb78c9e540d Mon Sep 17 00:00:00 2001 From: Eric Bavier Date: Wed, 9 Dec 2020 11:50:20 -0600 Subject: gnu: dealii: Update to 9.2.0. * gnu/packages/maths.scm (dealii): Update to 9.2.0. --- gnu/packages/maths.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index 47cc8216dd..2ab9621c7f 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -4194,7 +4194,7 @@ revised simplex and the branch-and-bound methods.") (define-public dealii (package (name "dealii") - (version "9.1.1") + (version "9.2.0") (source (origin (method url-fetch) @@ -4202,7 +4202,7 @@ revised simplex and the branch-and-bound methods.") "download/v" version "/dealii-" version ".tar.gz")) (sha256 (base32 - "0xhjv0gzswpjbc43xbrpwfc5848g508l01855nszx3g5gwzlhnzw")) + "0fm4xzrnb7dfn4415j24d8v3jkh0lssi86250x2f5wgi83xq4nnh")) (modules '((guix build utils))) (snippet ;; Remove bundled sources: UMFPACK, TBB, muParser, and boost -- cgit v1.2.3 From eaca440b659c7367a7a3fc689bdac9fa15726c9f Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Mon, 7 Dec 2020 16:43:28 -0500 Subject: gnu: python-llfuse: Update to 1.3.8. * gnu/packages/python-xyz.scm (python-llfuse): Update to 1.3.8. --- gnu/packages/python-xyz.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index d07c91121a..8891db3c50 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -8813,13 +8813,13 @@ third-party code.") (define-public python-llfuse (package (name "python-llfuse") - (version "1.3.6") + (version "1.3.8") (source (origin (method url-fetch) - (uri (pypi-uri "llfuse" version ".tar.bz2")) + (uri (pypi-uri "llfuse" version)) (sha256 (base32 - "1j9fzxpgmb4rxxyl9jcf84zvznhgi3hnh4hg5vb0qaslxkvng8ii")))) + "1g2cdhdqrb6m7655qp61pn61pwj1ql61cdzhr2jvl3w4i8877ddr")))) (build-system python-build-system) (inputs `(("fuse" ,fuse) -- cgit v1.2.3 From bd5f75125925e423f4585bcb4cc36d15bfb97daa Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Dec 2020 17:44:53 +0100 Subject: gnu: Add r-brio. * gnu/packages/cran.scm (r-brio): New variable. --- gnu/packages/cran.scm | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index fb6507b674..b2cd3059e7 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -100,6 +100,27 @@ #:use-module (gnu packages xml) #:use-module (gnu packages xorg)) +(define-public r-brio + (package + (name "r-brio") + (version "1.1.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "brio" version)) + (sha256 + (base32 + "0f7amcd2cjm09aiq39209cz680l5d2gqpp6wwfhz24zagfsa7cvb")))) + (properties `((upstream-name . "brio"))) + (build-system r-build-system) + (home-page "https://github.com/r-lib/brio") + (synopsis "Basic R input output") + (description + "This package provides functions to handle basic input output. These +functions always read and write UTF-8 (8-bit Unicode Transformation Format) +files and provide more explicit control over line endings.") + (license license:expat))) + (define-public r-rticles (package (name "r-rticles") -- cgit v1.2.3 From 24cf213edb125dca292013332830cf33679bfd90 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Dec 2020 17:45:11 +0100 Subject: gnu: Add r-diffobj. * gnu/packages/cran.scm (r-diffobj): New variable. --- gnu/packages/cran.scm | 22 ++++++++++++++++++++++ 1 file changed, 22 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index b2cd3059e7..19e78c2bcd 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -121,6 +121,28 @@ functions always read and write UTF-8 (8-bit Unicode Transformation Format) files and provide more explicit control over line endings.") (license license:expat))) +(define-public r-diffobj + (package + (name "r-diffobj") + (version "0.3.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "diffobj" version)) + (sha256 + (base32 + "0v18zz14g8ppzmj1d997rdmsfh327ml4wvpmfx168lravdsk5ym2")))) + (properties `((upstream-name . "diffobj"))) + (build-system r-build-system) + (propagated-inputs `(("r-crayon" ,r-crayon))) + (native-inputs `(("r-knitr" ,r-knitr))) + (home-page "https://github.com/brodieG/diffobj") + (synopsis "Diffs for R objects") + (description + "Generate a colorized diff of two R objects for an intuitive +visualization of their differences.") + (license license:gpl2+))) + (define-public r-rticles (package (name "r-rticles") -- cgit v1.2.3 From 71a732c35d18cf627c50209c9615ed886f59de66 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Dec 2020 17:45:24 +0100 Subject: gnu: Add r-waldo. * gnu/packages/cran.scm (r-waldo): New variable. --- gnu/packages/cran.scm | 30 ++++++++++++++++++++++++++++++ 1 file changed, 30 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 19e78c2bcd..526eba0e5d 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -143,6 +143,36 @@ files and provide more explicit control over line endings.") visualization of their differences.") (license license:gpl2+))) +(define-public r-waldo + (package + (name "r-waldo") + (version "0.2.3") + (source + (origin + (method url-fetch) + (uri (cran-uri "waldo" version)) + (sha256 + (base32 + "0lsw8p4wiggqm9fvh5vgmf0ms0npcg3hcwyzlg5ahv5yx4pv5fhz")))) + (properties `((upstream-name . "waldo"))) + (build-system r-build-system) + (propagated-inputs + `(("r-cli" ,r-cli) + ("r-diffobj" ,r-diffobj) + ("r-fansi" ,r-fansi) + ("r-glue" ,r-glue) + ("r-rematch2" ,r-rematch2) + ("r-rlang" ,r-rlang) + ("r-tibble" ,r-tibble))) + (home-page "https://github.com/r-lib/waldo") + (synopsis "Find differences between R objects") + (description + "Compare complex R objects and reveal the key differences. This package +was designed particularly for use in testing packages where being able to +quickly isolate key differences makes understanding test failures much +easier.") + (license license:expat))) + (define-public r-rticles (package (name "r-rticles") -- cgit v1.2.3 From 9c3f5b2fa0e57d21c68bda70b5f7b57cd2982ced Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Dec 2020 17:46:02 +0100 Subject: gnu: Add r-gitcreds. * gnu/packages/cran.scm (r-gitcreds): New variable. --- gnu/packages/cran.scm | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 526eba0e5d..13e3de2b84 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -96,6 +96,7 @@ #:use-module (gnu packages statistics) #:use-module (gnu packages tcl) #:use-module (gnu packages tls) + #:use-module (gnu packages version-control) #:use-module (gnu packages web) #:use-module (gnu packages xml) #:use-module (gnu packages xorg)) @@ -9707,6 +9708,30 @@ files to an structured list. Users can manipulate this resulting list with back to file after modifications.") (license license:gpl3))) +(define-public r-gitcreds + (package + (name "r-gitcreds") + (version "0.1.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "gitcreds" version)) + (sha256 + (base32 + "1snzn7nxy0rwz0bzjsg6k04c0n811dgn8gn9cmn2v78aj57ayjmi")))) + (properties `((upstream-name . "gitcreds"))) + (build-system r-build-system) + (inputs `(("git" ,git-minimal))) + (native-inputs `(("r-knitr" ,r-knitr))) + (home-page "https://github.com/r-lib/gitcreds") + (synopsis "Query git credentials from R") + (description + "Query, set, and delete credentials from the git credential store. +Manage GitHub tokens and other git credentials. This package is to be used by +other packages that need to authenticate to GitHub and/or other git +repositories.") + (license license:expat))) + (define-public r-gh (package (name "r-gh") -- cgit v1.2.3 From 73545fde4249b160e0c7d0f6da9e55ae0c9f8c47 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Dec 2020 17:46:25 +0100 Subject: gnu: Add r-parallelly. * gnu/packages/cran.scm (r-parallelly): New variable. --- gnu/packages/cran.scm | 28 ++++++++++++++++++++++++++++ 1 file changed, 28 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 13e3de2b84..14a2bd751c 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -12738,6 +12738,34 @@ simple as possible to identify global objects for the purpose of exporting them in distributed compute environments.") (license license:lgpl2.1+))) +(define-public r-parallelly + (package + (name "r-parallelly") + (version "1.21.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "parallelly" version)) + (sha256 + (base32 + "1hlr81khr7z4x9gprymdh19mdq3nw6wm8d2795sd2pa3ya6phnb0")))) + (properties `((upstream-name . "parallelly"))) + (build-system r-build-system) + (home-page "https://github.com/HenrikBengtsson/parallelly") + (synopsis "Enhancements of the parallel package") + (description + "This package provides utility functions that enhance the @code{parallel} +package and support the built-in parallel backends of the @code{future} +package. For example, @code{availableCores} gives the number of CPU cores +available to your R process as given by R options and environment variables, +including those set by job schedulers on high-performance compute clusters. +If none is set, it will fall back to @code{parallel::detectCores}. Another +example is @code{makeClusterPSOCK}, which is backward compatible with +@code{parallel::makePSOCKcluster} while doing a better job in setting up +remote cluster workers without the need for configuring the firewall to do +port-forwarding to your local computer.") + (license license:lgpl2.1+))) + (define-public r-future (package (name "r-future") -- cgit v1.2.3 From feb7c4f6cabc270b34894c54fbdbaffc782e3c60 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Dec 2020 17:46:45 +0100 Subject: gnu: Add r-ash. * gnu/packages/cran.scm (r-ash): New variable. --- gnu/packages/cran.scm | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 14a2bd751c..ddf34ea439 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -19334,6 +19334,27 @@ metrics to quantify time accumulation strategies based on minute level actigraphy-measured activity counts data.") (license license:gpl3))) +(define-public r-ash + (package + (name "r-ash") + (version "1.0-15") + (source + (origin + (method url-fetch) + (uri (cran-uri "ash" version)) + (sha256 + (base32 + "1ay2a2agdmiz7zzvn26mli0x0iwk09g5pp4yy1r23knhkp1pn2lb")))) + (properties `((upstream-name . "ash"))) + (build-system r-build-system) + (native-inputs `(("gfortran" ,gfortran))) + (home-page "https://cran.r-project.org/web/packages/ash/") + (synopsis "David Scott's ASH routines") + (description + "This package provides David Scott's ASH routines ported from S-PLUS to +R.") + (license license:gpl2+))) + (define-public r-fda (package (name "r-fda") -- cgit v1.2.3 From 14caba7eeb55310794c13ffe0da8a9691354b587 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Dec 2020 17:47:00 +0100 Subject: gnu: Add r-hdrcde. * gnu/packages/cran.scm (r-hdrcde): New variable. --- gnu/packages/cran.scm | 29 +++++++++++++++++++++++++++++ 1 file changed, 29 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index ddf34ea439..e3451d9a56 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -19355,6 +19355,35 @@ actigraphy-measured activity counts data.") R.") (license license:gpl2+))) +(define-public r-hdrcde + (package + (name "r-hdrcde") + (version "3.3") + (source + (origin + (method url-fetch) + (uri (cran-uri "hdrcde" version)) + (sha256 + (base32 + "0c2qbw4c3mq1cb068kjs72rxlbibz8svwcrx853jyr8ybs23z7ab")))) + (properties `((upstream-name . "hdrcde"))) + (build-system r-build-system) + (propagated-inputs + `(("r-ash" ,r-ash) + ("r-ggplot2" ,r-ggplot2) + ("r-kernsmooth" ,r-kernsmooth) + ("r-ks" ,r-ks) + ("r-locfit" ,r-locfit) + ("r-rcolorbrewer" ,r-rcolorbrewer))) + (native-inputs `(("gfortran" ,gfortran))) + (home-page "http://pkg.robjhyndman.com/hdrcde") + (synopsis "Highest density regions and conditional density estimation") + (description + "This is a package for the computation of highest density regions in one +and two dimensions, kernel estimation of univariate density functions +conditional on one covariate, and multimodal regression.") + (license license:gpl3))) + (define-public r-fda (package (name "r-fda") -- cgit v1.2.3 From 6279d2b6dd1216573e51e25b4479820b81c01a54 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Dec 2020 17:47:13 +0100 Subject: gnu: Add r-rainbow. * gnu/packages/cran.scm (r-rainbow): New variable. --- gnu/packages/cran.scm | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index e3451d9a56..5aa2b0d040 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -19384,6 +19384,33 @@ and two dimensions, kernel estimation of univariate density functions conditional on one covariate, and multimodal regression.") (license license:gpl3))) +(define-public r-rainbow + (package + (name "r-rainbow") + (version "3.6") + (source + (origin + (method url-fetch) + (uri (cran-uri "rainbow" version)) + (sha256 + (base32 + "11vfcck17d2xjc049ci5i8l1nqv345anmd110gdz7654i1pj9lb3")))) + (properties `((upstream-name . "rainbow"))) + (build-system r-build-system) + (propagated-inputs + `(("r-cluster" ,r-cluster) + ("r-colorspace" ,r-colorspace) + ("r-hdrcde" ,r-hdrcde) + ("r-ks" ,r-ks) + ("r-mass" ,r-mass) + ("r-pcapp" ,r-pcapp))) + (home-page "https://cran.r-project.org/web/packages/rainbow/") + (synopsis "Bagplots, boxplots and rainbow plots for functional data") + (description + "This is a package for visualizing functional data and identifying +functional outliers with bagplots, boxplots and rainbow plots.") + (license license:gpl3))) + (define-public r-fda (package (name "r-fda") -- cgit v1.2.3 From f0862a357810895dd8759331daeebf9ee5b22d49 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Dec 2020 17:47:28 +0100 Subject: gnu: Add r-fds. * gnu/packages/cran.scm (r-fds): New variable. --- gnu/packages/cran.scm | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 5aa2b0d040..f7ecdfae4b 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -19411,6 +19411,31 @@ conditional on one covariate, and multimodal regression.") functional outliers with bagplots, boxplots and rainbow plots.") (license license:gpl3))) +(define-public r-fds + (package + (name "r-fds") + (version "1.8") + (source + (origin + (method url-fetch) + (uri (cran-uri "fds" version)) + (sha256 + (base32 + "1284vncixrzrz9x6b52gslrbrbia07sd0xac7nwdqhp5f5v5wfi0")))) + (properties `((upstream-name . "fds"))) + (build-system r-build-system) + (propagated-inputs + `(("r-rainbow" ,r-rainbow) + ("r-rcurl" ,r-rcurl))) + (home-page "https://cran.r-project.org/web/packages/fds/") + (synopsis "Functional data sets") + (description "This package contains a list of functional time series, +sliced functional time series, and functional data sets. Functional time +series is a special type of functional data observed over time. Sliced +functional time series is a special type of functional time series with a time +variable observed over time.") + (license license:gpl2+))) + (define-public r-fda (package (name "r-fda") -- cgit v1.2.3 From 8d15940f3c77144ad19e9c6a1d5604d67fe1a91c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Dec 2020 17:47:48 +0100 Subject: gnu: Add r-gamm4. * gnu/packages/cran.scm (r-gamm4): New variable. --- gnu/packages/cran.scm | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index f7ecdfae4b..b7d3d4cdbd 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -22836,6 +22836,31 @@ connection, user authentication and file transfer. A simple R client is included in this package as well.") (license license:gpl2))) +(define-public r-gamm4 + (package + (name "r-gamm4") + (version "0.2-6") + (source + (origin + (method url-fetch) + (uri (cran-uri "gamm4" version)) + (sha256 + (base32 + "128c725y9s07c1m9cvd9hgi9hldrymcs5divd8pw7bdjh9jvdiap")))) + (properties `((upstream-name . "gamm4"))) + (build-system r-build-system) + (propagated-inputs + `(("r-lme4" ,r-lme4) + ("r-matrix" ,r-matrix) + ("r-mgcv" ,r-mgcv))) + (home-page "https://cran.r-project.org/web/packages/gamm4/") + (synopsis "Generalized additive mixed models using mgcv and lme4") + (description + "Estimate generalized additive mixed models via a version of function +@code{gamm} from the @code{mgcv} package, using the @code{lme4} packagefor +estimation.") + (license license:gpl2+))) + (define-public r-brms (package (name "r-brms") -- cgit v1.2.3 From fab49665bbeba23dff45beafbab34a1413ae77e7 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Dec 2020 17:48:04 +0100 Subject: gnu: Add r-optimx. * gnu/packages/cran.scm (r-optimx): New variable. --- gnu/packages/cran.scm | 28 ++++++++++++++++++++++++++++ 1 file changed, 28 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index b7d3d4cdbd..85b1dec362 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -22861,6 +22861,34 @@ included in this package as well.") estimation.") (license license:gpl2+))) +(define-public r-optimx + (package + (name "r-optimx") + (version "2020-4.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "optimx" version)) + (sha256 + (base32 + "00bi2sr2hr7x6cfwlsn7hz2r56lcyv9naa8vmfcgr1r269fc50b3")))) + (properties `((upstream-name . "optimx"))) + (build-system r-build-system) + (propagated-inputs `(("r-numderiv" ,r-numderiv))) + (native-inputs `(("r-knitr" ,r-knitr))) + (home-page "https://cran.r-project.org/web/packages/optimx/") + (synopsis "Expanded replacement and extension of the optim function") + (description + "This package provides a replacement and extension of the @code{optim} +function to call to several function minimization codes in R in a single +statement. These methods handle smooth, possibly box constrained functions of +several or many parameters. Note that the function @code{optimr} was prepared +to simplify the incorporation of minimization codes going forward. This +package also implements some utility codes and some extra solvers, including +safeguarded Newton methods. Many methods previously separate are now included +here.") + (license license:gpl2))) + (define-public r-brms (package (name "r-brms") -- cgit v1.2.3 From d106e3e7f6247a9a54cc5b8ea17da5aaf591889e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Dec 2020 17:48:23 +0100 Subject: gnu: Add r-projpred. * gnu/packages/cran.scm (r-projpred): New variable. --- gnu/packages/cran.scm | 39 +++++++++++++++++++++++++++++++++++++++ 1 file changed, 39 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 85b1dec362..cf09080855 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -22889,6 +22889,45 @@ safeguarded Newton methods. Many methods previously separate are now included here.") (license license:gpl2))) +(define-public r-projpred + (package + (name "r-projpred") + (version "2.0.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "projpred" version)) + (sha256 + (base32 + "0nx514mrfh3gv854pr71w5x3zgdnn0kinf5nh7z90q3h7ysry2mg")))) + (properties `((upstream-name . "projpred"))) + (build-system r-build-system) + (propagated-inputs + `(("r-dplyr" ,r-dplyr) + ("r-gamm4" ,r-gamm4) + ("r-ggplot2" ,r-ggplot2) + ("r-lme4" ,r-lme4) + ("r-loo" ,r-loo) + ("r-magrittr" ,r-magrittr) + ("r-mass" ,r-mass) + ("r-mgcv" ,r-mgcv) + ("r-optimx" ,r-optimx) + ("r-rcpp" ,r-rcpp) + ("r-rcpparmadillo" ,r-rcpparmadillo) + ("r-rngtools" ,r-rngtools) + ("r-rstantools" ,r-rstantools) + ("r-tidyverse" ,r-tidyverse))) + (native-inputs `(("r-knitr" ,r-knitr))) + (home-page "https://mc-stan.org/projpred/") + (synopsis "Projection predictive feature selection") + (description + "This package performs projection predictive feature selection for +generalized linear models and generalized linear and additive multilevel +models. The package is compatible with the @code{rstanarm} and @code{brms} +packages, but other reference models can also be used. See the package +vignette for more information and examples.") + (license license:gpl3))) + (define-public r-brms (package (name "r-brms") -- cgit v1.2.3 From 18ddbd474b49fb00a50dfdc0d6dfb0185cd7b8fd Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Dec 2020 19:47:40 +0100 Subject: gnu: r-d3r: Update to 0.9.1. * gnu/packages/cran.scm (r-d3r): Update to 0.9.1. [arguments]: Use esbuild for minification. [native-inputs]: Add source for D3 version 6; replace uglify-js with esbuild. --- gnu/packages/cran.scm | 28 +++++++++++++++++----------- 1 file changed, 17 insertions(+), 11 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index cf09080855..5fbbe7a71d 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -1607,20 +1607,19 @@ Bootstrap themes, which are packaged for use with Shiny applications.") (define-public r-d3r (package (name "r-d3r") - (version "0.9.0") + (version "0.9.1") (source (origin (method url-fetch) (uri (cran-uri "d3r" version)) (sha256 (base32 - "0vd1qk8yr18xdfkv5ybhqvf0mmccpi721wqa7c881nzm9nnlzc4y")))) + "0kc82vvyfxhxvqfalngn36prn3sxdiinsx04rn99ha6zdc27zp5k")))) (build-system r-build-system) (arguments `(#:modules ((guix build utils) (guix build r-build-system) - (srfi srfi-1) - (ice-9 popen)) + (srfi srfi-1)) #:phases (modify-phases %standard-phases (add-after 'unpack 'process-javascript @@ -1634,16 +1633,16 @@ Bootstrap themes, which are packaged for use with Shiny applications.") (,(assoc-ref inputs "d3.v4.js") "v4/dist/d3.min.js") (,(assoc-ref inputs "d3.v5.js") - "v5/dist/d3.min.js")))) + "v5/dist/d3.min.js") + (,(assoc-ref inputs "d3.v6.js") + "v6/dist/d3.min.js")))) (lambda (sources targets) (for-each (lambda (source target) (format #t "Processing ~a --> ~a~%" source target) (delete-file target) - (let ((minified (open-pipe* OPEN_READ "uglify-js" source))) - (call-with-output-file target - (lambda (port) - (dump-port minified port))))) + (invoke "esbuild" source "--minify" + (string-append "--outfile=" target))) sources targets)))) #t))))) (propagated-inputs @@ -1652,7 +1651,7 @@ Bootstrap themes, which are packaged for use with Shiny applications.") ("r-rlang" ,r-rlang) ("r-tidyr" ,r-tidyr))) (native-inputs - `(("uglify-js" ,uglify-js) + `(("esbuild" ,esbuild) ("d3.v3.js" ,(origin (method url-fetch) @@ -1673,7 +1672,14 @@ Bootstrap themes, which are packaged for use with Shiny applications.") (uri "https://d3js.org/d3.v5.js") (sha256 (base32 - "0kxvx5pfagxn6nhavdwsdnzyd26g0z5dsfi1pi5dvcmb0c8ipcdn")))))) + "0kxvx5pfagxn6nhavdwsdnzyd26g0z5dsfi1pi5dvcmb0c8ipcdn")))) + ("d3.v6.js" + ,(origin + (method url-fetch) + (uri "https://d3js.org/d3.v6.js") + (sha256 + (base32 + "1x6432ca7p1pfxhz3airzw943fincn9izzxkclc1wmphcvv2n2p9")))))) (home-page "https://github.com/timelyportfolio/d3r") (synopsis "d3.js utilities for R") (description -- cgit v1.2.3 From 6c148eaae7ed0688e1e42b092f02ba8a4a870edf Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Dec 2020 19:49:00 +0100 Subject: import/utils: Fix conditional. This is a follow-up to commit 45584061a9ebe961e2be08ee94c3fe8ad74e2713. * guix/import/utils.scm (package->definition): Use EQ? instead of = to compare truthiness; use ELSE instead of (#T). --- guix/import/utils.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/guix/import/utils.scm b/guix/import/utils.scm index 7de95349cd..e227c2e42d 100644 --- a/guix/import/utils.scm +++ b/guix/import/utils.scm @@ -275,9 +275,9 @@ version. If APPEND-VERSION?/string is a string, append this string." (cond ((string? append-version?/string) (string-append name "-" append-version?/string)) - ((= append-version?/string #t) + ((eq? append-version?/string #t) (string-append name "-" (version-major+minor version))) - ((#t) version))) + (else name))) ,guix-package)))) (define (build-system-modules) -- cgit v1.2.3 From 00a275fbf427027592838bdd7217a7bd6e24994f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Dec 2020 19:50:12 +0100 Subject: gnu: r-magrittr: Update to 2.0.1. * gnu/packages/statistics.scm (r-magrittr): Update to 2.0.1. --- gnu/packages/statistics.scm | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 314a11e429..9a9eb436c1 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -889,14 +889,18 @@ algorithms.") (define-public r-magrittr (package (name "r-magrittr") - (version "1.5") + (version "2.0.1") (source (origin (method url-fetch) (uri (cran-uri "magrittr" version)) (sha256 - (base32 "1s1ar6rag8m277qcqmdp02gn4awn9bdj9ax0r8s32i59mm1mki05")))) + (base32 "0pxd99fvg406whqsk9wh756rayrwh84xn3h44zmlpcy23kanbhkm")))) (build-system r-build-system) + ;; knitr needs magrittr + #; + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://cran.r-project.org/web/packages/magrittr/index.html") (synopsis "A forward-pipe operator for R") (description -- cgit v1.2.3 From 3e337d9bb74bfd0e56ce06d9757332e7d1660a0f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Dec 2020 21:56:00 +0100 Subject: gnu: r-rticles: Update to 0.17. * gnu/packages/cran.scm (r-rticles): Update to 0.17. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 5fbbe7a71d..039c52bbf6 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -177,14 +177,14 @@ easier.") (define-public r-rticles (package (name "r-rticles") - (version "0.16") + (version "0.17") (source (origin (method url-fetch) (uri (cran-uri "rticles" version)) (sha256 (base32 - "1ca3k5sdy9mnm6frcimqwf5k18j14wn69x5iagjnjwhq711l8dv0")))) + "1wbwva5n88dw3vvhcrlzkr58cv03hyx0dqgfmxj7d0dgf4ichr3c")))) (properties `((upstream-name . "rticles"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From d856813829318b24b9bc58a0ca814f53065ee805 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Dec 2020 21:56:07 +0100 Subject: gnu: r-v8: Update to 3.4.0. * gnu/packages/cran.scm (r-v8): Update to 3.4.0. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 039c52bbf6..14922cc2ae 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -222,14 +222,14 @@ degree elevation and curve fitting.") (define-public r-v8 (package (name "r-v8") - (version "3.3.1") + (version "3.4.0") (source (origin (method url-fetch) (uri (cran-uri "V8" version)) (sha256 (base32 - "1d2j9p1fsz9hp8n8lrywyrkwivhfa3qx5ha5f24vin8b6l04xy67")))) + "1g9z22pc8ydx1yhv57ww2d2jg5hvrl7ilwa79x89zgn17jha5j7m")))) (properties `((upstream-name . "V8"))) (build-system r-build-system) (arguments -- cgit v1.2.3 From 17fa0953a82f70b7dbd4d2af18f08e3dae7b4802 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Dec 2020 21:56:11 +0100 Subject: gnu: r-ggalluvial: Update to 0.12.3. * gnu/packages/cran.scm (r-ggalluvial): Update to 0.12.3. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 14922cc2ae..70b9d85f17 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -333,13 +333,13 @@ series of numeric vectors/matrices and factors.") (define-public r-ggalluvial (package (name "r-ggalluvial") - (version "0.12.2") + (version "0.12.3") (source (origin (method url-fetch) (uri (cran-uri "ggalluvial" version)) (sha256 (base32 - "1qcpbb6h2znsq246n1291rxgfryiw24caghbk8acjzzfbdhdj8x1")))) + "0mkan9gxg3yxjism22yxbhvlh2lh7wpbrqpb355za790prcmjbh3")))) (properties `((upstream-name . "ggalluvial"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 9bf316fcaf88b9bb691aa1ef02d5fe4fbf23772a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Dec 2020 21:56:14 +0100 Subject: gnu: r-ggpmisc: Update to 0.3.7. * gnu/packages/cran.scm (r-ggpmisc): Update to 0.3.7. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 70b9d85f17..f6b978a9ee 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -362,13 +362,13 @@ variables.") (define-public r-ggpmisc (package (name "r-ggpmisc") - (version "0.3.6") + (version "0.3.7") (source (origin (method url-fetch) (uri (cran-uri "ggpmisc" version)) (sha256 (base32 - "05i81q9rg8zf35vgcxhn3yhkc9dlvcpwpxncq1q3zs0rxhfkf208")))) + "121s6c9k4fn3rcz2myc1kxczllq2826c8zllaii58q8lica7dsyn")))) (build-system r-build-system) (propagated-inputs `(("r-broom" ,r-broom) -- cgit v1.2.3 From 2b1abb4f435ed0fca722f75c990a4a2d3807975f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Dec 2020 21:56:19 +0100 Subject: gnu: r-vegan: Update to 2.5-7. * gnu/packages/cran.scm (r-vegan): Update to 2.5-7. [propagated-inputs]: Remove r-knitr. [native-inputs]: Add r-knitr. --- gnu/packages/cran.scm | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index f6b978a9ee..d08f710dfe 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -765,20 +765,20 @@ read a protected key.") (define-public r-vegan (package (name "r-vegan") - (version "2.5-6") + (version "2.5-7") (source (origin (method url-fetch) (uri (cran-uri "vegan" version)) (sha256 (base32 - "0g60rgn1i7wqf9pf5m1yki1m45gcp7i5hmjic0ci0f6vng70mh5k")))) + "0aj6m9l1vkh32sar6fyvq4p8j4h2f2f347w1300qnzgaa5lmhfz6")))) (build-system r-build-system) (native-inputs - `(("gfortran" ,gfortran))) + `(("r-knitr" ,r-knitr) ; needed for vignettes + ("gfortran" ,gfortran))) (propagated-inputs `(("r-cluster" ,r-cluster) - ("r-knitr" ,r-knitr) ; needed for vignettes ("r-lattice" ,r-lattice) ("r-mass" ,r-mass) ("r-mgcv" ,r-mgcv) -- cgit v1.2.3 From 0415a46fd989553fe97f0d514f1ba6d3417fc6a1 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Dec 2020 21:56:22 +0100 Subject: gnu: r-shinyfiles: Update to 0.9.0. * gnu/packages/cran.scm (r-shinyfiles): Update to 0.9.0. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index d08f710dfe..6dcf0de6a3 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -1552,13 +1552,13 @@ application framework for R, making it easy to create attractive dashboards.") (define-public r-shinyfiles (package (name "r-shinyfiles") - (version "0.8.0") + (version "0.9.0") (source (origin (method url-fetch) (uri (cran-uri "shinyFiles" version)) (sha256 - (base32 "0gwyx37f2r86cldsyknws9pafpj8g5mg3mchlyl9ymgnk5f4b88w")))) + (base32 "0rsijlx16vd74r7bd8s9zipy71kgpw19v9s85kxj5bmwc6njmbai")))) (properties `((upstream-name . "shinyFiles"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 327167bd508604e1ec0644e2148a3cb9df9f3017 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Dec 2020 21:56:26 +0100 Subject: gnu: r-colorspace: Update to 2.0-0. * gnu/packages/cran.scm (r-colorspace): Update to 2.0-0. [native-inputs]: Add r-knitr. --- gnu/packages/cran.scm | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 6dcf0de6a3..ee51bc334a 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -2074,14 +2074,16 @@ XML. To learn more about the Abbyy OCR API, see @url{http://ocrsdk.com/}.") (define-public r-colorspace (package (name "r-colorspace") - (version "1.4-1") + (version "2.0-0") (source (origin (method url-fetch) (uri (cran-uri "colorspace" version)) (sha256 - (base32 "0wyny3ah2d74hqv80s6imrarpna09gq3j9rjnz6zx2qg0lx72gb9")))) + (base32 "13h1hara0s6xn16bgkrbd0flszah1yiylwfwxwn2inqqk6pm6sjf")))) (build-system r-build-system) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://cran.r-project.org/web/packages/colorspace") (synopsis "Color space manipulation") (description -- cgit v1.2.3 From b1ad80e284791a4d2c7541d49795a70224650474 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Dec 2020 21:56:30 +0100 Subject: gnu: r-ps: Update to 1.5.0. * gnu/packages/cran.scm (r-ps): Update to 1.5.0. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index ee51bc334a..6e6ff916ac 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -2222,13 +2222,13 @@ print, summary, plot, update, etc. (define-public r-ps (package (name "r-ps") - (version "1.4.0") + (version "1.5.0") (source (origin (method url-fetch) (uri (cran-uri "ps" version)) (sha256 - (base32 "0yns03ffd2a2cs4b6dsjjlqhv46vq2g094m8psmhf3h9i52awyaz")))) + (base32 "15pyz94b0z6ibrjp25np5nd4z20whnnr35wsavdgwmsmynba2qbl")))) (build-system r-build-system) (home-page "https://ps.r-lib.org") (synopsis "List, query, and manipulate system processes") -- cgit v1.2.3 From bd69b54a559095dad8ca4e8700d18c92e6e55811 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Dec 2020 21:56:33 +0100 Subject: gnu: r-circlize: Update to 0.4.11. * gnu/packages/cran.scm (r-circlize): Update to 0.4.11. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 6e6ff916ac..af05c7b31b 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -2472,14 +2472,14 @@ validation and filtering on the values, making options invisible or private.") (define-public r-circlize (package (name "r-circlize") - (version "0.4.10") + (version "0.4.11") (source (origin (method url-fetch) (uri (cran-uri "circlize" version)) (sha256 (base32 - "1xb1jq3mg4kw1513zv1i09vhn7rj7f8vp0bnms2qml74s47wxsgk")))) + "1s84xl7kv3qc1261xxaq4aqh64gwywhacsf5nh6yf8djw0d1w42d")))) (build-system r-build-system) (propagated-inputs `(("r-colorspace" ,r-colorspace) -- cgit v1.2.3 From 07cb3171732dca80d3cc137237292d2d26343d48 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Dec 2020 21:56:36 +0100 Subject: gnu: r-distillery: Update to 1.2. * gnu/packages/cran.scm (r-distillery): Update to 1.2. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index af05c7b31b..7e8b360542 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -2945,14 +2945,14 @@ quantile mixture from L-moments and trimmed L-moments.") (define-public r-distillery (package (name "r-distillery") - (version "1.1") + (version "1.2") (source (origin (method url-fetch) (uri (cran-uri "distillery" version)) (sha256 (base32 - "15qhvhg6wmvlxrvvw70sk8pv76z5pd04vyasgczvxa0599ih7bzh")))) + "10nhh9p0hp294pp4aav0y0zsmir2qbn05sf3k52rmzmm36q2kc8y")))) (build-system r-build-system) (home-page "https://ral.ucar.edu/staff/ericg/") (synopsis "Functions for confidence intervals and object information") -- cgit v1.2.3 From 882d699ff22eebbc37585bf5fbce200ec1c18fcc Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Dec 2020 21:56:39 +0100 Subject: gnu: r-extremes: Update to 2.1. * gnu/packages/cran.scm (r-extremes): Update to 2.1. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 7e8b360542..e55b5f4b61 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -2985,14 +2985,14 @@ which should be seen for details.") (define-public r-extremes (package (name "r-extremes") - (version "2.0-12") + (version "2.1") (source (origin (method url-fetch) (uri (cran-uri "extRemes" version)) (sha256 (base32 - "0wldzvj1h93jksq31dw9zgnr1wrqwmfr9qwmg7qk7nznsn2yy1h2")))) + "1b69r3mzl6hp3g3rqxyc77m8r40jyq7c2d87q85af7xqkn6hnxid")))) (properties `((upstream-name . "extRemes"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 89088dc1bbc72eab2a9dddff5df46da345013e5e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Dec 2020 21:56:42 +0100 Subject: gnu: r-inline: Update to 0.3.17. * gnu/packages/cran.scm (r-inline): Update to 0.3.17. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index e55b5f4b61..cc08dea765 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -3054,13 +3054,13 @@ by Li, Brown, Huang, and Bickel") (define-public r-inline (package (name "r-inline") - (version "0.3.16") + (version "0.3.17") (source (origin (method url-fetch) (uri (cran-uri "inline" version)) (sha256 (base32 - "0x9m2hwin6anfhkf61cnsbqn4qp1pr2gy1pbwbdgbdz2cmns85nj")))) + "1wslsn60q959yrr27cwanba43qlpfaxzdli46i9dc26lxfr5fa3r")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/inline") (synopsis "Functions to inline C, C++, Fortran function calls from R") -- cgit v1.2.3 From 54dd6ce673ae65733ee812c33676eb7af56903b9 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Dec 2020 21:56:45 +0100 Subject: gnu: r-fitdistrplus: Update to 1.1-3. * gnu/packages/cran.scm (r-fitdistrplus): Update to 1.1-3. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index cc08dea765..dafa8e1712 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -3244,14 +3244,14 @@ functions from LINPACK.") (define-public r-fitdistrplus (package (name "r-fitdistrplus") - (version "1.1-1") + (version "1.1-3") (source (origin (method url-fetch) (uri (cran-uri "fitdistrplus" version)) (sha256 (base32 - "1rnfnwmxa495fql7q0h9018cnwygwhj8gfh6ryz1vbf474570vjl")))) + "1pjnqx0j26dai2fa4ip56wspmfsrcm9dpmxkg15y9623w5b58vbp")))) (build-system r-build-system) (propagated-inputs `(("r-mass" ,r-mass) -- cgit v1.2.3 From 1d8b53164e6c2455ab0e6dcfbe3098232e7c2d19 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Dec 2020 21:56:48 +0100 Subject: gnu: r-lava: Update to 1.6.8.1. * gnu/packages/cran.scm (r-lava): Update to 1.6.8.1. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index dafa8e1712..20b784ad13 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -3409,14 +3409,14 @@ available in a vignette.") (define-public r-lava (package (name "r-lava") - (version "1.6.8") + (version "1.6.8.1") (source (origin (method url-fetch) (uri (cran-uri "lava" version)) (sha256 (base32 - "0jdmjjs894mfncswmzz7sa6cy7hqbqii5fcvl3zqkmzpbadb2za2")))) + "1yiz8y3jhxkszgz9m9fialp9r27hy97xh0imfvs8ziv7dk43y93d")))) (build-system r-build-system) (propagated-inputs `(("r-numderiv" ,r-numderiv) -- cgit v1.2.3 From 9597dc08b397529126e86c59b3ec06b77aba1129 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Dec 2020 21:56:52 +0100 Subject: gnu: r-generics: Update to 0.1.0. * gnu/packages/cran.scm (r-generics): Update to 0.1.0. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 20b784ad13..43c46b70d7 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -3797,14 +3797,14 @@ created using basic graphics.") (define-public r-generics (package (name "r-generics") - (version "0.0.2") + (version "0.1.0") (source (origin (method url-fetch) (uri (cran-uri "generics" version)) (sha256 (base32 - "0xk1xhpy7gpv3pvaygzhpfdxj72zmb38pb4nscfyg2ff36vx3cvi")))) + "0qw7r0d2qvlj1pvrlpv30d6akml624ydxkk19hv85iv6pfyx2wdb")))) (build-system r-build-system) (home-page "https://github.com/r-lib/generics") (synopsis "Common S3 generics not provided by base R methods") -- cgit v1.2.3 From cfd8779b2299eb9194ba83cacf18caaa5fc4562c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Dec 2020 21:56:55 +0100 Subject: gnu: r-recipes: Update to 0.1.15. * gnu/packages/cran.scm (r-recipes): Update to 0.1.15. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 43c46b70d7..7a9979df5a 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -3855,14 +3855,14 @@ provides a one-row summary of model-level statistics.") (define-public r-recipes (package (name "r-recipes") - (version "0.1.14") + (version "0.1.15") (source (origin (method url-fetch) (uri (cran-uri "recipes" version)) (sha256 (base32 - "0ix678aj71ml5cmfhy1j0b2ddhf5wlb1d74bjc9djr6r86xsqmcz")))) + "0xif0ak3w90xmfzlxvb5pnzc3scpfl1pyhrjffi3mq4asvsd52l0")))) (build-system r-build-system) (propagated-inputs `(("r-dplyr" ,r-dplyr) -- cgit v1.2.3 From 55a090deb4652a8567c7e0583dd4a9444369eada Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Dec 2020 21:57:00 +0100 Subject: gnu: r-mice: Update to 3.12.0. * gnu/packages/cran.scm (r-mice): Update to 3.12.0. [propagated-inputs]: Add r-cpp11 and r-rlang. --- gnu/packages/cran.scm | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 7a9979df5a..e65a4d1c3e 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -4146,21 +4146,23 @@ analysis of multiply imputed data sets.") (define-public r-mice (package (name "r-mice") - (version "3.11.0") + (version "3.12.0") (source (origin (method url-fetch) (uri (cran-uri "mice" version)) (sha256 (base32 - "1gawccw32l00rcriyxys0mzbxh44x04rziy0cbycc3i1qm39d4fq")))) + "0i7i9r0ipn7fypzp5xv1dnr54l30b7kg38mmq1kcvj2z1mjrwpap")))) (build-system r-build-system) (propagated-inputs `(("r-broom" ,r-broom) + ("r-cpp11" ,r-cpp11) ("r-dplyr" ,r-dplyr) ("r-generics" ,r-generics) ("r-lattice" ,r-lattice) ("r-rcpp" ,r-rcpp) + ("r-rlang" ,r-rlang) ("r-tidyr" ,r-tidyr))) (home-page "https://cran.r-project.org/web/packages/mice/") (synopsis "Multivariate imputation by chained equations") -- cgit v1.2.3 From 841c3edf3cca03bd9e046f1fdb3d249933f4f230 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Dec 2020 21:57:03 +0100 Subject: gnu: r-hardyweinberg: Update to 1.6.9. * gnu/packages/cran.scm (r-hardyweinberg): Update to 1.6.9. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index e65a4d1c3e..af9c193cdc 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -4227,14 +4227,14 @@ programming} (SQP) based solver).") (define-public r-hardyweinberg (package (name "r-hardyweinberg") - (version "1.6.8") + (version "1.6.9") (source (origin (method url-fetch) (uri (cran-uri "HardyWeinberg" version)) (sha256 (base32 - "0b6j1mkpr7ck2nr9fmpnsjdv29jc6vg4b91cg50skmcgky1j0zi7")))) + "0l93r1hkr483hp4yd7rm7mdkgl5lp0nkvv0inahj3r1cplgfxpvs")))) (properties `((upstream-name . "HardyWeinberg"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 86572c35c4304c169bccabb87af73986cc5b2f23 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Dec 2020 21:57:06 +0100 Subject: gnu: r-cli: Update to 2.2.0. * gnu/packages/cran.scm (r-cli): Update to 2.2.0. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index af9c193cdc..44a0fccbf1 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -4585,14 +4585,14 @@ plots in @code{ggplot2}.") (define-public r-cli (package (name "r-cli") - (version "2.1.0") + (version "2.2.0") (source (origin (method url-fetch) (uri (cran-uri "cli" version)) (sha256 (base32 - "03zaq9yhz6gw49qdnhc66b3sw9i916ahkzyg2cgh17dhf31d2acq")))) + "1f20mk9pb9kqn0ni2z0sqsx8qj1apcbiw08pa4gwry142zv7m9rr")))) (build-system r-build-system) (propagated-inputs `(("r-assertthat" ,r-assertthat) -- cgit v1.2.3 From d4e67f37deef69c9e35a2746087605fe7ce45e4c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Dec 2020 21:57:10 +0100 Subject: gnu: r-processx: Update to 3.4.5. * gnu/packages/cran.scm (r-processx): Update to 3.4.5. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 44a0fccbf1..895edf4686 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -4650,13 +4650,13 @@ constants, and control debugging of packages via environment variables.") (define-public r-processx (package (name "r-processx") - (version "3.4.4") + (version "3.4.5") (source (origin (method url-fetch) (uri (cran-uri "processx" version)) (sha256 - (base32 "0as8lzfpbz5rcpcpczvrrgd67whngkmw12q33r2yn3k7lq80z95a")))) + (base32 "055v2gdrgqsfy8s672wsq79bqr44b4jjmcbqivx4p2d6lqx10s73")))) (build-system r-build-system) (propagated-inputs `(("r-ps" ,r-ps) -- cgit v1.2.3 From bb70fae499bbecafba88ec2dd73f2a845a956756 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Dec 2020 21:57:13 +0100 Subject: gnu: r-vctrs: Update to 0.3.5. * gnu/packages/cran.scm (r-vctrs): Update to 0.3.5. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 895edf4686..4cbbdcf2ab 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -4860,14 +4860,14 @@ to variables on the left-hand side of the assignment.") (define-public r-vctrs (package (name "r-vctrs") - (version "0.3.4") + (version "0.3.5") (source (origin (method url-fetch) (uri (cran-uri "vctrs" version)) (sha256 (base32 - "0xvqgc36zhd9y1xsm7kwrbr5sxwnd3jbr9qrb1gma2lqkqf42izb")))) + "1k1mcq7jkpc55dsm0wb4k8asc1irvmi5884v3ap4sabf22c5sq0i")))) (build-system r-build-system) (propagated-inputs `(("r-digest" ,r-digest) -- cgit v1.2.3 From e0c8fc46238740c2b3b1106d21f0dcabac0d58d4 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Dec 2020 21:57:16 +0100 Subject: gnu: r-pillar: Update to 1.4.7. * gnu/packages/cran.scm (r-pillar): Update to 1.4.7. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 4cbbdcf2ab..1879850b89 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -4899,14 +4899,14 @@ to variables on the left-hand side of the assignment.") (define-public r-pillar (package (name "r-pillar") - (version "1.4.6") + (version "1.4.7") (source (origin (method url-fetch) (uri (cran-uri "pillar" version)) (sha256 (base32 - "01ck8ziqzjc9ibbj3g88siz1iw263dgl8jx6ryw2v50rjrr3y7fj")))) + "167ji21fx04s2niw5pjq9vzxgagxzsg3gimh8dzr2kl5ljrb5vfd")))) (build-system r-build-system) (propagated-inputs `(("r-cli" ,r-cli) -- cgit v1.2.3 From d2be197fa54e4177a53b42f42f7c4f07fee05b4d Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Dec 2020 21:57:19 +0100 Subject: gnu: r-tinytex: Update to 0.27. * gnu/packages/cran.scm (r-tinytex): Update to 0.27. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 1879850b89..da72d3855c 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -4947,14 +4947,14 @@ terminals.") (define-public r-tinytex (package (name "r-tinytex") - (version "0.26") + (version "0.27") (source (origin (method url-fetch) (uri (cran-uri "tinytex" version)) (sha256 (base32 - "02b0v8ydbfspma3rgsdpkf2cm6jl9qm3l9jsrl0xng482b06bb0q")))) + "10hbc9h1fsw91w5f4fjcaqy68b3n1wr6pml01fnkf3pdjiri5sj0")))) (build-system r-build-system) (propagated-inputs `(("r-xfun" ,r-xfun))) -- cgit v1.2.3 From 514848aebcc8ca5b13e11ff77c55c60ab80eb05f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Dec 2020 21:57:22 +0100 Subject: gnu: r-ifultools: Update to 2.0-22. * gnu/packages/cran.scm (r-ifultools): Update to 2.0-22. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index da72d3855c..5229e9885b 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -5205,14 +5205,14 @@ provides some missing S-PLUS functionality in R.") (define-public r-ifultools (package (name "r-ifultools") - (version "2.0-5") + (version "2.0-22") (source (origin (method url-fetch) (uri (cran-uri "ifultools" version)) (sha256 (base32 - "040kvbczcmmbaiaz0k0pdq9af541pjj6iwzh1a3w4szh9w6b5a3j")))) + "0f95vqc47dgssqngznk0rclr72ndbyxc7gdq2cmbksvq7qpn3gg1")))) (build-system r-build-system) (propagated-inputs `(("r-mass" ,r-mass) -- cgit v1.2.3 From 114a0fb5a53daf73373f690db0ede051488c329a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Dec 2020 21:57:25 +0100 Subject: gnu: r-quantmod: Update to 0.4.18. * gnu/packages/cran.scm (r-quantmod): Update to 0.4.18. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 5229e9885b..5b41918727 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -5268,14 +5268,14 @@ Fisher's method), and Sidak correction.") (define-public r-quantmod (package (name "r-quantmod") - (version "0.4.17") + (version "0.4.18") (source (origin (method url-fetch) (uri (cran-uri "quantmod" version)) (sha256 (base32 - "1ss441rwlr88kz212m0wgx0hwgwi41rhy1jncg2lgqzqfvr5dzqa")))) + "0dbcrncv06iqcbkky95dd7l32xq0hhbnkb0kj8wwzym1jf748h5a")))) (build-system r-build-system) (propagated-inputs `(("r-curl" ,r-curl) -- cgit v1.2.3 From e836f28835b08f3de7f558ad776f3383841a734e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Dec 2020 21:57:29 +0100 Subject: gnu: r-tseries: Update to 0.10-48. * gnu/packages/cran.scm (r-tseries): Update to 0.10-48. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 5b41918727..b729e725d6 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -5292,14 +5292,14 @@ financial trading strategies.") (define-public r-tseries (package (name "r-tseries") - (version "0.10-47") + (version "0.10-48") (source (origin (method url-fetch) (uri (cran-uri "tseries" version)) (sha256 (base32 - "0yzvc9djp3angvxdxqi60wi726y76ablsb71q88ycvw0avgpf8r0")))) + "0wa4rcf0igayi1yrwc6wak6d491560p0z89rz32haqlkiiq25gak")))) (build-system r-build-system) (propagated-inputs `(("r-quadprog" ,r-quadprog) -- cgit v1.2.3 From 964d8a8494204a086ccbd19b83f38efb36861ca6 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Dec 2020 21:57:32 +0100 Subject: gnu: r-radiant-data: Update to 1.3.12. * gnu/packages/cran.scm (r-radiant-data): Update to 1.3.12. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index b729e725d6..0797e0e189 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -5832,14 +5832,14 @@ systems.") (define-public r-radiant-data (package (name "r-radiant-data") - (version "1.3.10") + (version "1.3.12") (source (origin (method url-fetch) (uri (cran-uri "radiant.data" version)) (sha256 (base32 - "09a3wn3gl1zjq5zsc5zaxyq71dg5qnpk57bmwd6qy8w99g2clm8c")) + "08bqqrfvpgyf613ikihwfnzb23l23f5nfs7zynnxbjxc1zfhbpny")) (modules '((guix build utils))) (snippet '(begin -- cgit v1.2.3 From df6c02d6886406c29763314ff8045d6badf684c4 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Dec 2020 21:57:35 +0100 Subject: gnu: r-renv: Update to 0.12.3. * gnu/packages/cran.scm (r-renv): Update to 0.12.3. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 0797e0e189..18f974f7a1 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -6529,14 +6529,14 @@ Python's @url{https://github.com/ActiveState/appdirs,Appdirs} to R.") (define-public r-renv (package (name "r-renv") - (version "0.12.0") + (version "0.12.3") (source (origin (method url-fetch) (uri (cran-uri "renv" version)) (sha256 (base32 - "1jwm1ik600xswb53i1swjsnfrjjdffmmyk5k9hjc7kc8nlfl0ay5")))) + "0k31x19gzpffb701c76p840cip10c0dh8yv3wcs30gqi0ag1g77l")))) (properties `((upstream-name . "renv"))) (build-system r-build-system) (native-inputs -- cgit v1.2.3 From bc08f4f41e39e8f6aa03b3af292b6647838ad188 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Dec 2020 21:57:39 +0100 Subject: gnu: r-rbibutils: Update to 2.0. * gnu/packages/cran.scm (r-rbibutils): Update to 2.0. [propagated-inputs]: Remove r-xml2. --- gnu/packages/cran.scm | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 18f974f7a1..ec51c1c19e 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -7097,17 +7097,16 @@ hierarchical models using Markov Chain Monte Carlo (MCMC) simulation.") (define-public r-rbibutils (package (name "r-rbibutils") - (version "1.3") + (version "2.0") (source (origin (method url-fetch) (uri (cran-uri "rbibutils" version)) (sha256 (base32 - "1i000czyd059dczd2nn1cb0d4n0bjykrfh51rs85s8r2zlaydn6i")))) + "1vfg2188i4dyhrmvnwpsh2la8qkd4wkryz2fpj4cppi1wfz3ml83")))) (properties `((upstream-name . "rbibutils"))) (build-system r-build-system) - (propagated-inputs `(("r-xml2" ,r-xml2))) (home-page "https://geobosh.github.io/rbibutils/") (synopsis "Convert between bibliography formats") (description -- cgit v1.2.3 From e0c6ecf2fc88897ab2eace8d438c91a3f6e4a371 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Dec 2020 21:57:42 +0100 Subject: gnu: r-rdpack: Update to 2.1. * gnu/packages/cran.scm (r-rdpack): Update to 2.1. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index ec51c1c19e..b527066b01 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -7119,14 +7119,14 @@ implemented in bibutils.") (define-public r-rdpack (package (name "r-rdpack") - (version "2.0") + (version "2.1") (source (origin (method url-fetch) (uri (cran-uri "Rdpack" version)) (sha256 (base32 - "04gk68y3cxlqhfl1aarjwz2mvx934ka0yxfgzrnw03ykhvb47fpi")))) + "1kmz0kq2z1xl55w22paz98x9jpss06abvicmkslv4zq77kz99q16")))) (properties `((upstream-name . "Rdpack"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 624d3887a578136a9cfa0cdd58dca0136c43a0ef Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Dec 2020 21:57:45 +0100 Subject: gnu: r-officer: Update to 0.3.15. * gnu/packages/cran.scm (r-officer): Update to 0.3.15. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index b527066b01..0e3290611b 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -7146,14 +7146,14 @@ references and Rd files.") (define-public r-officer (package (name "r-officer") - (version "0.3.14") + (version "0.3.15") (source (origin (method url-fetch) (uri (cran-uri "officer" version)) (sha256 (base32 - "1nyv4710bcd2afh1l1qiy5zrspjcdvc7mrzz5189dwy9xvgxi31h")))) + "1s9hrkdx105c1plpxywv68bmp8hvvxbdizhwx81fxr79fhj62x5j")))) (build-system r-build-system) (propagated-inputs `(("r-magrittr" ,r-magrittr) -- cgit v1.2.3 From 2ed2e1d58c925088c2b2750cc2162bbd3f180768 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Dec 2020 21:57:49 +0100 Subject: gnu: r-insight: Update to 0.11.1. * gnu/packages/cran.scm (r-insight): Update to 0.11.1. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 0e3290611b..1b6994b82c 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -7408,14 +7408,14 @@ other add-on packages.") (define-public r-insight (package (name "r-insight") - (version "0.10.0") + (version "0.11.1") (source (origin (method url-fetch) (uri (cran-uri "insight" version)) (sha256 (base32 - "1r4val3hvc43zailfmq6wcbg366s0bi0ysib476a49k1x6h8b6ji")))) + "1m95xfvai1kbzqxdggjvdbk6ax2dg4v2lrfpqn7v607g2n77n2k0")))) (build-system r-build-system) (native-inputs `(("r-knitr" ,r-knitr))) -- cgit v1.2.3 From 7b5443d2d98fb5b5ad84370d200d3f8d4745bd8c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Dec 2020 21:57:53 +0100 Subject: gnu: r-flextable: Update to 0.6.1. * gnu/packages/cran.scm (r-flextable): Update to 0.6.1. [native-inputs]: Add r-knitr. --- gnu/packages/cran.scm | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 1b6994b82c..5085196434 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -7542,14 +7542,14 @@ functions.") (define-public r-flextable (package (name "r-flextable") - (version "0.5.11") + (version "0.6.1") (source (origin (method url-fetch) (uri (cran-uri "flextable" version)) (sha256 (base32 - "1yb872izzr9yja7q2vfqm0imcbcgs0fvi4b19arhdlwwa42figj4")))) + "06nzyd2a9yaf9hmn740xrgxw0448z5dvlplcj3kizz9sm23aw9li")))) (build-system r-build-system) (propagated-inputs `(("r-base64enc" ,r-base64enc) @@ -7562,6 +7562,8 @@ functions.") ("r-rmarkdown" ,r-rmarkdown) ("r-uuid" ,r-uuid) ("r-xml2" ,r-xml2))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://davidgohel.github.io/flextable") (synopsis "Functions for tabular reporting") (description -- cgit v1.2.3 From f836bc870ed635e9ca87621e353e13f22cc31952 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Dec 2020 21:57:56 +0100 Subject: gnu: r-doby: Update to 4.6.8. * gnu/packages/cran.scm (r-doby): Update to 4.6.8. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 5085196434..f34912959a 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -7790,14 +7790,14 @@ the work.") (define-public r-doby (package (name "r-doby") - (version "4.6.7") + (version "4.6.8") (source (origin (method url-fetch) (uri (cran-uri "doBy" version)) (sha256 (base32 - "16vg1aa272sfzyqxfb63fyis9hv6g5m3nmxxa6mk1gy0irqnl3jk")))) + "0r97kwsj6g87m7shgnjc5c9y71jkhiq4xd9q0s2bxl0vl92qqwvg")))) (properties `((upstream-name . "doBy"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From e99a124b72220869d8a8c925ee064eebaf3e9eea Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Dec 2020 21:57:59 +0100 Subject: gnu: r-blockfest: Update to 1.8. * gnu/packages/cran.scm (r-blockfest): Update to 1.8. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index f34912959a..79f749dc60 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -7876,14 +7876,14 @@ procedures to speed up calculations in R.") (define-public r-blockfest (package (name "r-blockfest") - (version "1.6") + (version "1.8") (source (origin (method url-fetch) (uri (cran-uri "BlockFeST" version)) (sha256 (base32 - "0hj7a5as7nxbgjac7lbj6qfwffx3g8x8phpf9a55f1c9cdzi73a5")))) + "12cbrmgqszlj729zrn9d1d7drbr0iay43knnmrzcxs6v7lfszsx5")))) (properties `((upstream-name . "BlockFeST"))) (build-system r-build-system) (propagated-inputs `(("r-basix" ,r-basix))) -- cgit v1.2.3 From 925b72fd6d9f1ae691aaf8a31ffe5468f5ff705d Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Dec 2020 21:58:02 +0100 Subject: gnu: r-slam: Update to 0.1-48. * gnu/packages/cran.scm (r-slam): Update to 0.1-48. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 79f749dc60..007dcc622e 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -7983,13 +7983,13 @@ the analyzed items.") (define-public r-slam (package (name "r-slam") - (version "0.1-47") + (version "0.1-48") (source (origin (method url-fetch) (uri (cran-uri "slam" version)) (sha256 - (base32 "12fggw2c7hz3bpvsaqm24g3r6lbpq6jgli24g7x5j859iak5cqv9")))) + (base32 "1ppsvkph4v1dffxgp12a4wnr9arj7pkmh4qv0and3f6nbz9k42qa")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/slam/") (synopsis "Sparse lightweight arrays and matrices") -- cgit v1.2.3 From f76cc34b4f44ad53c68e201e35362e3fe61cc352 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Dec 2020 21:58:05 +0100 Subject: gnu: r-raster: Update to 3.4-5. * gnu/packages/cran.scm (r-raster): Update to 3.4-5. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 007dcc622e..4e9e0f28be 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -8272,14 +8272,14 @@ used to teach mathematics, statistics, computation and modeling.") (define-public r-raster (package (name "r-raster") - (version "3.3-13") + (version "3.4-5") (source (origin (method url-fetch) (uri (cran-uri "raster" version)) (sha256 (base32 - "1s6457rq94qvm3s2lqscs2c2gn5kzcpxa13i8nhlgb1klx5kams7")))) + "19g4chd0nyhnz6hc2j0v9ahjcgz64vvja4y3mrj1pfis1dwhsqn6")))) (build-system r-build-system) (propagated-inputs `(("r-rcpp" ,r-rcpp) -- cgit v1.2.3 From e0ba249568b6f177b68299df76044ca56b3ce919 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Dec 2020 21:58:09 +0100 Subject: gnu: r-magick: Update to 2.5.2. * gnu/packages/cran.scm (r-magick): Update to 2.5.2. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 4e9e0f28be..cc59307b53 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -8867,14 +8867,14 @@ samples is large and the number of mixture components is not too large.") (define-public r-magick (package (name "r-magick") - (version "2.5.0") + (version "2.5.2") (source (origin (method url-fetch) (uri (cran-uri "magick" version)) (sha256 (base32 - "1fhwr34xff6793ifbzqmij8b8qg7hrnr4birqpg33ib0mdd6flkf")))) + "0myvryya7b4bbw0hs4jqflrbdffmg78kz28gbybw3yc7zwc7sqxx")))) (build-system r-build-system) (inputs `(("imagemagick" ,imagemagick) -- cgit v1.2.3 From 2424da94f65d89645ea082d98bfd690422fbf23e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Dec 2020 21:58:12 +0100 Subject: gnu: r-multcomp: Update to 1.4-15. * gnu/packages/cran.scm (r-multcomp): Update to 1.4-15. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index cc59307b53..9df9004795 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -9281,14 +9281,14 @@ packages maintained by Torsten Hothorn.") (define-public r-multcomp (package (name "r-multcomp") - (version "1.4-14") + (version "1.4-15") (source (origin (method url-fetch) (uri (cran-uri "multcomp" version)) (sha256 (base32 - "14a55isy1sp745s109nirlk5fryy144cri6dl8y9d9wjhfxz336a")))) + "1klvn4a1rlrzwhy1cjrkbbh6jspgzbrdm0jxsb1lmf1yzdz609wr")))) (build-system r-build-system) (propagated-inputs `(("r-codetools" ,r-codetools) -- cgit v1.2.3 From 2c9a5c0620ca271e1f1caba8ea9a9442a96870c3 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Dec 2020 21:58:15 +0100 Subject: gnu: r-bayestestr: Update to 0.8.0. * gnu/packages/cran.scm (r-bayestestr): Update to 0.8.0. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 9df9004795..7760ac8093 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -9545,14 +9545,14 @@ differentiation.") (define-public r-bayestestr (package (name "r-bayestestr") - (version "0.7.5") + (version "0.8.0") (source (origin (method url-fetch) (uri (cran-uri "bayestestR" version)) (sha256 (base32 - "0l6q7v96m9asqa0p55k0gpzy8hddf8srkhc9r7zf4hv0dscbi9dv")))) + "11mxnpqc85y13wf8mnnrh0k8d3jqdsr99hkv4cgvwav38qpvjhhw")))) (properties `((upstream-name . "bayestestR"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 5af35b3acff2e9122cc47d90d5bf592c9d4f39d7 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Dec 2020 21:58:18 +0100 Subject: gnu: r-performance: Update to 0.6.0. * gnu/packages/cran.scm (r-performance): Update to 0.6.0. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 7760ac8093..af9524b095 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -9572,14 +9572,14 @@ ROPE percentage and pd).") (define-public r-performance (package (name "r-performance") - (version "0.5.1") + (version "0.6.0") (source (origin (method url-fetch) (uri (cran-uri "performance" version)) (sha256 (base32 - "1vkc87vbhw7l626pdnpiravnpsa5j0iv73lbwy3m309lnfvv0cqx")))) + "0ai1pp6k0pmmjgpj7hc53s0h258c4mljln8lv3nd9r7kzrmic0gc")))) (build-system r-build-system) (propagated-inputs `(("r-bayestestr" ,r-bayestestr) -- cgit v1.2.3 From 620c01b76d85102e5c0035f2811cbc850e2115f6 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Dec 2020 21:58:21 +0100 Subject: gnu: r-ggeffects: Update to 1.0.0. * gnu/packages/cran.scm (r-ggeffects): Update to 1.0.0. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index af9524b095..cdd7970e70 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -9599,14 +9599,14 @@ effects models and Bayesian models.") (define-public r-ggeffects (package (name "r-ggeffects") - (version "0.16.0") + (version "1.0.0") (source (origin (method url-fetch) (uri (cran-uri "ggeffects" version)) (sha256 (base32 - "0v8n8jmp6x1iagbyc5jgf1d29yz5hd3ibnyl9n9f73vqq5bzj0p5")))) + "18diwssc5vij5g7zh9mv0ppcv3xgfi2jqzfx9srxfahg05sr1xdq")))) (build-system r-build-system) (propagated-inputs `(("r-insight" ,r-insight) -- cgit v1.2.3 From 2ccaac5519042d3302834d995459a0b24028cda6 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Dec 2020 21:58:24 +0100 Subject: gnu: r-effectsize: Update to 0.4.1. * gnu/packages/cran.scm (r-effectsize): Update to 0.4.1. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index cdd7970e70..bd1fe9152b 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -9629,14 +9629,14 @@ results using @code{ggplot2}.") (define-public r-effectsize (package (name "r-effectsize") - (version "0.4.0") + (version "0.4.1") (source (origin (method url-fetch) (uri (cran-uri "effectsize" version)) (sha256 (base32 - "0shx19ahw13wrn7jlyyvzvngqk66d6jiw9i51mx3psdn3hdnhy9s")))) + "1rbl63b1c7z9llznnwvclqrcgdd4hfmc7y66v7raqqf2a4nadqa5")))) (properties `((upstream-name . "effectsize"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 5f68a11ea2f1417ee952f5c60f1abd5d1eea5f17 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Dec 2020 21:58:30 +0100 Subject: gnu: r-gh: Update to 1.2.0. * gnu/packages/cran.scm (r-gh): Update to 1.2.0. [propagated-inputs]: Add r-gitcreds. [native-inputs]: Add r-knitr. --- gnu/packages/cran.scm | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index bd1fe9152b..dc10240943 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -9746,20 +9746,23 @@ repositories.") (define-public r-gh (package (name "r-gh") - (version "1.1.0") + (version "1.2.0") (source (origin (method url-fetch) (uri (cran-uri "gh" version)) (sha256 (base32 - "1bc9bn1078s664hc806dh0y1ncxif77q479rfmxfir9z7hwaz7yy")))) + "1zvy3ylxvni10lhvmbm9h14mg4wlsbdbzbzviwf28jxss8749219")))) (build-system r-build-system) (propagated-inputs `(("r-cli" ,r-cli) + ("r-gitcreds" ,r-gitcreds) ("r-httr" ,r-httr) ("r-ini" ,r-ini) ("r-jsonlite" ,r-jsonlite))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://github.com/r-lib/gh#readme") (synopsis "Access the GitHub API via R") (description -- cgit v1.2.3 From a2a6466db8e10690fb24a3637aa6c893f33f008f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Dec 2020 21:58:33 +0100 Subject: gnu: r-rcppannoy: Update to 0.0.17. * gnu/packages/cran.scm (r-rcppannoy): Update to 0.0.17. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index dc10240943..aab6e6d7dc 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -10293,14 +10293,14 @@ address a bug.") (define-public r-rcppannoy (package (name "r-rcppannoy") - (version "0.0.16") + (version "0.0.17") (source (origin (method url-fetch) (uri (cran-uri "RcppAnnoy" version)) (sha256 (base32 - "0bfa35lp6vc4b0h3ymvdx50br233q8vvyjml34ngi81rj0imz3fr")))) + "0z4dpvk2hmh817709l70jdl1vvnzn0vb9wlr5m8jza24sn9w14ac")))) (properties `((upstream-name . "RcppAnnoy"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 7fc054b0501e7e68e7fbcda14789ba00af971a5e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Dec 2020 21:58:36 +0100 Subject: gnu: r-tiff: Update to 0.1-6. * gnu/packages/cran.scm (r-tiff): Update to 0.1-6. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index aab6e6d7dc..a77cc12f25 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -10783,14 +10783,14 @@ redundant complex conjugate when the input is real data.") (define-public r-tiff (package (name "r-tiff") - (version "0.1-5") + (version "0.1-6") (source (origin (method url-fetch) (uri (cran-uri "tiff" version)) (sha256 (base32 - "0asf2bws3x3yd3g3ixvk0f86b0mdf882pl8xrqlxrkbgjalyc54m")))) + "1yy4im2lwzhjnnkfwxgkknsajvm83pcwaf370pkgfva2db0xjfv2")))) (build-system r-build-system) (inputs `(("libtiff" ,libtiff) -- cgit v1.2.3 From 7e205beddf17c98c5652c2b946b93022464b5bf3 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Dec 2020 21:58:39 +0100 Subject: gnu: r-tm: Update to 0.7-8. * gnu/packages/cran.scm (r-tm): Update to 0.7-8. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index a77cc12f25..62725ca18f 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -10828,14 +10828,14 @@ Processing.") (define-public r-tm (package (name "r-tm") - (version "0.7-7") + (version "0.7-8") (source (origin (method url-fetch) (uri (cran-uri "tm" version)) (sha256 (base32 - "0pyics8j7a4wkh5gzin46l0qars5vgbb1886xqpdqjs1z0gy9nyh")))) + "0mk2lsplynms15nw92vbdgsafg4bw1m0ik31gch1mnsnv61idsxi")))) (properties `((upstream-name . "tm"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From c148d5afbc4d2b4a88f2d15aaf0de38bf03a38d9 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Dec 2020 21:58:42 +0100 Subject: gnu: r-flare: Update to 1.7.0. * gnu/packages/cran.scm (r-flare): Update to 1.7.0. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 62725ca18f..29c43314d6 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -11215,14 +11215,14 @@ diagnostics for controlling type-1 errors are also provided.") (define-public r-flare (package (name "r-flare") - (version "1.6.0.2") + (version "1.7.0") (source (origin (method url-fetch) (uri (cran-uri "flare" version)) (sha256 (base32 - "1ybrsx1djqldw0l5l1iz4pfh6xxb8ckkg1ric7wnsr51wm9ljlh5")))) + "0f992dmgnr6s8g3386i9bjfyf08q8srgw7sjz2yx7snj8znq7251")))) (build-system r-build-system) (propagated-inputs `(("r-igraph" ,r-igraph) -- cgit v1.2.3 From 68b720ec4ab4106024a71139d90e07a19c072e24 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Dec 2020 21:58:45 +0100 Subject: gnu: r-rnifti: Update to 1.3.0. * gnu/packages/cran.scm (r-rnifti): Update to 1.3.0. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 29c43314d6..395bd1b6fb 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -11315,14 +11315,14 @@ Touzet and Varre (2007).") (define-public r-rnifti (package (name "r-rnifti") - (version "1.2.3") + (version "1.3.0") (source (origin (method url-fetch) (uri (cran-uri "RNifti" version)) (sha256 (base32 - "02jdxz3w423k9b5wldky4pnnq0cs2zlfi52jxjw1mk24z756j692")))) + "1zr0q79id62csmc30c7gs4hbmavk8n6p50a981sfz51dczhjj5ny")))) (properties `((upstream-name . "RNifti"))) (build-system r-build-system) (propagated-inputs `(("r-rcpp" ,r-rcpp))) -- cgit v1.2.3 From 319a408e08e5d10ebb4e7fec0198ff45c3bff99d Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Dec 2020 21:58:49 +0100 Subject: gnu: r-rmpfr: Update to 0.8-2. * gnu/packages/cran.scm (r-rmpfr): Update to 0.8-2. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 395bd1b6fb..a3aefb89fb 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -11784,14 +11784,14 @@ limitations\" using the GNU Multiple Precision library.") (define-public r-rmpfr (package (name "r-rmpfr") - (version "0.8-1") + (version "0.8-2") (source (origin (method url-fetch) (uri (cran-uri "Rmpfr" version)) (sha256 (base32 - "09kw7hyca8xc09r2d88qj81cclar8acaq5q9q5rw9f49iffda0rr")))) + "007pc7fpzl2mcg3qxa2vfjip6m2dr314qjsnybkj3kdj70bszxkl")))) (properties `((upstream-name . "Rmpfr"))) (build-system r-build-system) (inputs -- cgit v1.2.3 From c91d1a75e9e7c29d9a89ed6c694b0cad1275fa5d Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Dec 2020 21:58:53 +0100 Subject: gnu: r-epi: Update to 2.42. * gnu/packages/cran.scm (r-epi): Update to 2.42. [propagated-inputs]: Add r-dplyr. --- gnu/packages/cran.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index a3aefb89fb..d790f5ef0b 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -12573,19 +12573,20 @@ model with finite state space using the Aalen-Johansen estimator.") (define-public r-epi (package (name "r-epi") - (version "2.41") + (version "2.42") (source (origin (method url-fetch) (uri (cran-uri "Epi" version)) (sha256 (base32 - "09miba6zk63bwc79n3030kgzlvy3whkq968pgqyghxnsjfh5ckp5")))) + "1vsyxlxl6n5y3wr8w7ji17hnhvbr0xsawqbdl1ajcfg5faizm9sl")))) (properties `((upstream-name . "Epi"))) (build-system r-build-system) (propagated-inputs `(("r-cmprsk" ,r-cmprsk) ("r-data-table" ,r-data-table) + ("r-dplyr" ,r-dplyr) ("r-etm" ,r-etm) ("r-mass" ,r-mass) ("r-matrix" ,r-matrix) -- cgit v1.2.3 From d1d42fa5c08243374ed1f73a99356883f3a84824 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Dec 2020 21:58:56 +0100 Subject: gnu: r-globals: Update to 0.14.0. * gnu/packages/cran.scm (r-globals): Update to 0.14.0. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index d790f5ef0b..bc372a5308 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -12732,14 +12732,14 @@ subsetting.") (define-public r-globals (package (name "r-globals") - (version "0.13.1") + (version "0.14.0") (source (origin (method url-fetch) (uri (cran-uri "globals" version)) (sha256 (base32 - "1ch9m7fxclfhfa38b743wcm7w1bkx9kmivc6l7phpbgs6h9jhrcc")))) + "1wrjiiif6rpc268zz79pvpw33si6n6ffgxdnxmmcracwhb5vqg90")))) (build-system r-build-system) (propagated-inputs `(("r-codetools" ,r-codetools))) -- cgit v1.2.3 From bb9e6860883c05363cf8fc960bdff6274c7ee7c9 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Dec 2020 21:59:00 +0100 Subject: gnu: r-future: Update to 1.20.1. * gnu/packages/cran.scm (r-future): Update to 1.20.1. [propagated-inputs]: Add r-parallelly. --- gnu/packages/cran.scm | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index bc372a5308..6758efc365 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -12784,19 +12784,20 @@ port-forwarding to your local computer.") (define-public r-future (package (name "r-future") - (version "1.19.1") + (version "1.20.1") (source (origin (method url-fetch) (uri (cran-uri "future" version)) (sha256 (base32 - "12f483h7g172ygafbg7h43vykv0f7xz9miwqf5q8dyv7gpgqi5fl")))) + "14k00g8c9zgf77d6q7x2vibvlivzk2rzj7lwn7v7d9nr6prqzlb6")))) (build-system r-build-system) (propagated-inputs `(("r-digest" ,r-digest) ("r-globals" ,r-globals) - ("r-listenv" ,r-listenv))) + ("r-listenv" ,r-listenv) + ("r-parallelly" ,r-parallelly))) (native-inputs `(("r-r-rsp" ,r-r-rsp))) ; vignette builder (home-page "https://github.com/HenrikBengtsson/future") -- cgit v1.2.3 From d5204d6bb4be4f2f5ac7817715432821f8d3e47c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Dec 2020 21:59:03 +0100 Subject: gnu: r-tensora: Update to 0.36.2. * gnu/packages/cran.scm (r-tensora): Update to 0.36.2. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 6758efc365..1327290a86 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -13083,14 +13083,14 @@ Coefficient Logit Models.") (define-public r-tensora (package (name "r-tensora") - (version "0.36.1") + (version "0.36.2") (source (origin (method url-fetch) (uri (cran-uri "tensorA" version)) (sha256 (base32 - "176hjy3bvg3in62r97wxbhq187sjz6c1gwy9x6spaxl6k4my3zy7")))) + "19wwh654qlja4z1n7afjpzsrrm53p8ddysa2vra5mdnkddb4g2cf")))) (properties `((upstream-name . "tensorA"))) (build-system r-build-system) (home-page "http://www.stat.boogaart.de/tensorA") -- cgit v1.2.3 From e3d06628735e1f296a1cc6c45cffe9421cfc74ac Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Dec 2020 21:59:06 +0100 Subject: gnu: r-deldir: Update to 0.2-3. * gnu/packages/cran.scm (r-deldir): Update to 0.2-3. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 1327290a86..b7ae902c56 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -14269,14 +14269,14 @@ sampling.") (define-public r-deldir (package (name "r-deldir") - (version "0.1-29") + (version "0.2-3") (source (origin (method url-fetch) (uri (cran-uri "deldir" version)) (sha256 (base32 - "1vwh8c8zxspyls05q9kgzz5p85i8k8aax5ir45np2bmg0pjvh6kv")))) + "0kin1hsd6dj36kkg7n328mzp21wwn9jm69lvgg2rvbf6bq7q091d")))) (build-system r-build-system) (native-inputs `(("gfortran" ,gfortran))) (home-page "https://cran.r-project.org/web/packages/deldir") -- cgit v1.2.3 From 77eb8216cc4f0275a6627959ddf7431f9f38b862 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Dec 2020 21:59:10 +0100 Subject: gnu: r-rms: Update to 6.1-0. * gnu/packages/cran.scm (r-rms): Update to 6.1-0. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index b7ae902c56..fe97c9d3b6 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -14533,13 +14533,13 @@ lspec, polyclass, and polymars.") (define-public r-rms (package (name "r-rms") - (version "6.0-1") + (version "6.1-0") (source (origin (method url-fetch) (uri (cran-uri "rms" version)) (sha256 - (base32 "1zkcsqcvldfj4kyn0346vi51igq951qrnpxlv2pfvap6n2v5wbxq")))) + (base32 "0llz519rgnc7v2jqhfrjgixkpkmmi5wi1a52hgz3n28s46ww77mq")))) (build-system r-build-system) (propagated-inputs `(("r-cluster" ,r-cluster) -- cgit v1.2.3 From 91e1961659f50006d3862eef85b795979a6312b3 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Dec 2020 21:59:14 +0100 Subject: gnu: r-ggraph: Update to 2.0.4. * gnu/packages/cran.scm (r-ggraph): Update to 2.0.4. [propagated-inputs]: Add r-withr. --- gnu/packages/cran.scm | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index fe97c9d3b6..fd98f105b0 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -15454,14 +15454,14 @@ databases, including ENA, PDB or ChEMBL are also accessible.") (define-public r-ggraph (package (name "r-ggraph") - (version "2.0.3") + (version "2.0.4") (source (origin (method url-fetch) (uri (cran-uri "ggraph" version)) (sha256 (base32 - "1pz06j0za4p6dc3fqjzcw8bpym70bmnfcvpv1q34r74rnwzjdyvq")))) + "1j3xf4fsv0i0gbppdrw4yprfyk53wx6s8nvnkipi2ywbm7cr4q4w")))) (build-system r-build-system) (propagated-inputs `(("r-digest" ,r-digest) @@ -15477,7 +15477,8 @@ databases, including ENA, PDB or ChEMBL are also accessible.") ("r-rlang" ,r-rlang) ("r-scales" ,r-scales) ("r-tidygraph" ,r-tidygraph) - ("r-viridis" ,r-viridis))) + ("r-viridis" ,r-viridis) + ("r-withr" ,r-withr))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://cran.r-project.org/web/packages/ggraph/") -- cgit v1.2.3 From a80b912c87b972ef03ccfcc432c40957babe61db Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Dec 2020 21:59:19 +0100 Subject: gnu: r-ggvis: Update to 0.4.7. * gnu/packages/cran.scm (r-ggvis): Update to 0.4.7. [propagated-inputs]: Remove r-lazyeval; add r-rlang. --- gnu/packages/cran.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index fd98f105b0..61dced9f7c 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -15563,22 +15563,22 @@ discriminant analysis for the purpose of classifying high dimensional data.") (define-public r-ggvis (package (name "r-ggvis") - (version "0.4.6") + (version "0.4.7") (source (origin (method url-fetch) (uri (cran-uri "ggvis" version)) (sha256 (base32 - "1k40mkfxj66qvwbsp849maihv6vxkdprhhzjkwffwn0lwl78lsz1")))) + "1qv512pd4x5vmx15y9nvqmabbbw14h75fmi1sjbcg5yl25z0cswy")))) (build-system r-build-system) (propagated-inputs `(("r-assertthat" ,r-assertthat) ("r-dplyr" ,r-dplyr) ("r-htmltools" ,r-htmltools) ("r-jsonlite" ,r-jsonlite) - ("r-lazyeval" ,r-lazyeval) ("r-magrittr" ,r-magrittr) + ("r-rlang" ,r-rlang) ("r-shiny" ,r-shiny))) (home-page "https://ggvis.rstudio.com/") (synopsis "Interactive grammar of graphics") -- cgit v1.2.3 From c1ba4adf8f424a2f30159a5d4d3e6087390c7d4c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Dec 2020 21:59:22 +0100 Subject: gnu: r-clue: Update to 0.3-58. * gnu/packages/cran.scm (r-clue): Update to 0.3-58. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 61dced9f7c..7b3329a5e4 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -16264,14 +16264,14 @@ experiments in a well-organized and reproducible way.") (define-public r-clue (package (name "r-clue") - (version "0.3-57") + (version "0.3-58") (source (origin (method url-fetch) (uri (cran-uri "clue" version)) (sha256 (base32 - "05rdcahawxlxci3fjxihjvvh33wqpxw50sx015165ab4nh3rsdkf")))) + "1rwwxlnpl1k0n4k96vxc9zajw9kb4syqwzj76fvaf0qim8p6ddia")))) (build-system r-build-system) (propagated-inputs `(("r-cluster" ,r-cluster))) (home-page "https://cran.r-project.org/web/packages/clue/") -- cgit v1.2.3 From 9b398a03328441ecc45d60db746b9ed2432d84c8 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Dec 2020 21:59:25 +0100 Subject: gnu: r-dae: Update to 3.1-32. * gnu/packages/cran.scm (r-dae): Update to 3.1-32. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 7b3329a5e4..63dbc06c07 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -16407,14 +16407,14 @@ classification and regression models.") (define-public r-dae (package (name "r-dae") - (version "3.1-27") + (version "3.1-32") (source (origin (method url-fetch) (uri (cran-uri "dae" version)) (sha256 (base32 - "14q3cxhcz0zqjdkas0dl71k2bp5qwvb60gha47s78hdr38r46kml")))) + "126w1lb9pz8mb2ajl2vz5dj798nbifp0dypnzfgcwixif5g5bpqi")))) (build-system r-build-system) (propagated-inputs `(("r-ggplot2" ,r-ggplot2) -- cgit v1.2.3 From 8d459d27e04345217257a0e9fe9a46f699b9a786 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Dec 2020 21:59:31 +0100 Subject: gnu: r-refmanager: Update to 1.3.0. * gnu/packages/cran.scm (r-refmanager): Update to 1.3.0. [propagated-inputs]: Remove r-bibtex. [native-inputs]: Add r-knitr. --- gnu/packages/cran.scm | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 63dbc06c07..96038a9f5d 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -16552,24 +16552,25 @@ results and plots in a unified style using the @code{ggplot2} package.") (define-public r-refmanager (package (name "r-refmanager") - (version "1.2.12") + (version "1.3.0") (source (origin (method url-fetch) (uri (cran-uri "RefManageR" version)) (sha256 (base32 - "1hfxa1qacfryk36mpaqdhdgws5jwxiyy489ikd3wa18bp1wz8dkp")))) + "1spzdp5ni52dybcaxqnhwdphh27wjyrsfy4hsxsplpg9rqwfqfps")))) (properties `((upstream-name . "RefManageR"))) (build-system r-build-system) (propagated-inputs - `(("r-bibtex" ,r-bibtex) - ("r-httr" ,r-httr) + `(("r-httr" ,r-httr) ("r-jsonlite" ,r-jsonlite) ("r-lubridate" ,r-lubridate) ("r-plyr" ,r-plyr) ("r-stringr" ,r-stringr) ("r-xml2" ,r-xml2))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://github.com/ropensci/RefManageR/") (synopsis "Straightforward BibTeX and BibLaTeX bibliography management") (description -- cgit v1.2.3 From e458d7b533363d611eb999e5c6e8f3ab52a5128f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Dec 2020 21:59:34 +0100 Subject: gnu: r-umap: Update to 0.2.7.0. * gnu/packages/cran.scm (r-umap): Update to 0.2.7.0. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 96038a9f5d..e6834aa50e 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -16650,14 +16650,14 @@ easily.") (define-public r-umap (package (name "r-umap") - (version "0.2.6.0") + (version "0.2.7.0") (source (origin (method url-fetch) (uri (cran-uri "umap" version)) (sha256 (base32 - "0zajn2sk705sckljxl5vz4q2sxpsqim2grmjq2jwwc8ysr1h2s9f")))) + "191vpy84s0bar06y9z1qx43x2kc4qp7lmrcmd0cvz2pnzq722jab")))) (build-system r-build-system) (propagated-inputs `(("r-openssl" ,r-openssl) -- cgit v1.2.3 From b71e9344787ec2b34f9b64ed76bc9b45b2bb3725 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Dec 2020 21:59:37 +0100 Subject: gnu: r-uwot: Update to 0.1.9. * gnu/packages/cran.scm (r-uwot): Update to 0.1.9. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index e6834aa50e..76182348a3 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -16677,14 +16677,14 @@ in R, including a translation of the original algorithm into R.") (define-public r-uwot (package (name "r-uwot") - (version "0.1.8") + (version "0.1.9") (source (origin (method url-fetch) (uri (cran-uri "uwot" version)) (sha256 (base32 - "1jzh8r1h6f7pw7pb1fr32vn6ai9g10s56ahkq0vi77iznihy1rpd")))) + "1iqvircvlxyd68n5279a0cwn5rc3pshxs7w1gqrns9c602xd6mhy")))) (build-system r-build-system) (propagated-inputs `(("r-dqrng" ,r-dqrng) -- cgit v1.2.3 From 010deb276ff6557704332a9717789e92713cc462 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Dec 2020 21:59:40 +0100 Subject: gnu: r-leiden: Update to 0.3.6. * gnu/packages/cran.scm (r-leiden): Update to 0.3.6. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 76182348a3..6e350c5978 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -16836,14 +16836,14 @@ computed using the L1 (Manhattan, taxicab) metric.") (define-public r-leiden (package (name "r-leiden") - (version "0.3.4") + (version "0.3.6") (source (origin (method url-fetch) (uri (cran-uri "leiden" version)) (sha256 (base32 - "0cj98s1d9771dahn2xwdb1hpkw51jsfmgvzpam34c7i57fj37hn2")))) + "1k1250bjgf2cb1whp2sl1r6b88156qwi2zkamw5iy2q1qhw6w2d7")))) (properties `((upstream-name . "leiden"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 2213fe7b3ecde43ecd0e954c713ad5ef8e76ade6 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Dec 2020 21:59:43 +0100 Subject: gnu: r-patchwork: Update to 1.1.0. * gnu/packages/cran.scm (r-patchwork): Update to 1.1.0. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 6e350c5978..0ad9584b30 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -16864,14 +16864,14 @@ guaranteeing well-connected communities.\" .") (define-public r-patchwork (package (name "r-patchwork") - (version "1.0.1") + (version "1.1.0") (source (origin (method url-fetch) (uri (cran-uri "patchwork" version)) (sha256 (base32 - "0wm93a40idrkzn5hpnykhznvh7hdbfqw0dkzzn0zk83qlwyc9g02")))) + "13vswvcfmadmjz7pw0qdqdr6x85zbza4gljx2nx3a39hldj71yck")))) (build-system r-build-system) (propagated-inputs `(("r-ggplot2" ,r-ggplot2) -- cgit v1.2.3 From af3385c9c353648bce78576e8102ce68cfed8014 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Dec 2020 21:59:46 +0100 Subject: gnu: r-parameters: Update to 0.10.1. * gnu/packages/cran.scm (r-parameters): Update to 0.10.1. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 0ad9584b30..acfdbee043 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -17189,14 +17189,14 @@ in pipelines.") (define-public r-parameters (package (name "r-parameters") - (version "0.9.0") + (version "0.10.1") (source (origin (method url-fetch) (uri (cran-uri "parameters" version)) (sha256 (base32 - "17jjmy1qnx25ldvasrwhmal45nl1sr8qjxprbi8fcjwra9af6cr6")))) + "1xvjvsdd0hql209f7v2l1nw7gy8jkj5qp0699p5m2h55a01jl778")))) (properties `((upstream-name . "parameters"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 98d69d6f58224dcbd7056cfd9910ce620ca283cd Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Dec 2020 21:59:50 +0100 Subject: gnu: r-sysfonts: Update to 0.8.2. * gnu/packages/cran.scm (r-sysfonts): Update to 0.8.2. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index acfdbee043..43bde09cae 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -17836,14 +17836,14 @@ server-side.") (define-public r-sysfonts (package (name "r-sysfonts") - (version "0.8.1") + (version "0.8.2") (source (origin (method url-fetch) (uri (cran-uri "sysfonts" version)) (sha256 (base32 - "1xp40hchjfif80a6jj210ghrjcvjjf66vqcssdy7a1j53nl1n994")))) + "1gapsiva0vjd2myxgm1avav6my5x00rmy2hx0qll7dm7v1isznbv")))) (properties `((upstream-name . "sysfonts"))) (build-system r-build-system) (inputs -- cgit v1.2.3 From 6ad24c2b0970b2a51c87ae8bf305ea87a69a2034 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Dec 2020 21:59:53 +0100 Subject: gnu: r-showtext: Update to 0.9-1. * gnu/packages/cran.scm (r-showtext): Update to 0.9-1. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 43bde09cae..2d8ef6e34c 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -17884,14 +17884,14 @@ package.") (define-public r-showtext (package (name "r-showtext") - (version "0.9") + (version "0.9-1") (source (origin (method url-fetch) (uri (cran-uri "showtext" version)) (sha256 (base32 - "11fx2vv8jlvcnybh18y7v4bn2c67aqsqwfq7y8dpywbwr4zg8jid")))) + "1hq346k2lm7rv49hw7srn3ab5gcp6b0r4zc1kgsdmswyh3q1asra")))) (properties `((upstream-name . "showtext"))) (build-system r-build-system) (inputs -- cgit v1.2.3 From 3e44c41bcb7abf35a84c3750266c91f40aea9457 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Dec 2020 21:59:56 +0100 Subject: gnu: r-abtest: Update to 0.2.2. * gnu/packages/cran.scm (r-abtest): Update to 0.2.2. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 2d8ef6e34c..f97e056631 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -18005,14 +18005,14 @@ regression models.") (define-public r-abtest (package (name "r-abtest") - (version "0.2.1") + (version "0.2.2") (source (origin (method url-fetch) (uri (cran-uri "abtest" version)) (sha256 (base32 - "1zfd13d7dplawk24dbdr1ka8cbdp5w6sxb0zlm7k4dhvn6ksi8h0")))) + "1ak0m4jd1grriwg4pn3aqf1468qma6rjn5kqjh8izx7zl29jd07v")))) (properties `((upstream-name . "abtest"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From b937197a14e3204da63abad356fb362632bbfb39 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Dec 2020 21:59:59 +0100 Subject: gnu: r-r-filesets: Update to 2.14.0. * gnu/packages/cran.scm (r-r-filesets): Update to 2.14.0. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index f97e056631..1b178da612 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -18699,14 +18699,14 @@ the @code{aroma.affymetrix} package.") (define-public r-r-filesets (package (name "r-r-filesets") - (version "2.13.0") + (version "2.14.0") (source (origin (method url-fetch) (uri (cran-uri "R.filesets" version)) (sha256 (base32 - "124rygq0bl9n4akxcm868nl30cyk3rz0iprb98zlpk62gci9f5fg")))) + "08xv8b3c81nf54viyr3w912al18483k5gfnjpg7bxbdfk70dfzbh")))) (properties `((upstream-name . "R.filesets"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 5a4b3d642c40490f98b3e8cc8631139bc88feb90 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Dec 2020 22:00:03 +0100 Subject: gnu: r-fda: Update to 5.1.7. * gnu/packages/cran.scm (r-fda): Update to 5.1.7. [propagated-inputs]: Add r-fds. --- gnu/packages/cran.scm | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 1b178da612..f7f83950a4 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -19457,18 +19457,19 @@ variable observed over time.") (define-public r-fda (package (name "r-fda") - (version "5.1.5.1") + (version "5.1.7") (source (origin (method url-fetch) (uri (cran-uri "fda" version)) (sha256 (base32 - "0zi001cw5536x6rgr4l0skva7fk53663zf6ggnsa8znml090sihm")))) + "1r8hfi6x1maw5zz8k95wfcr7v69lg4zl3mcj69cvvq2mkg4y3158")))) (properties `((upstream-name . "fda"))) (build-system r-build-system) (propagated-inputs - `(("r-matrix" ,r-matrix))) + `(("r-fds" ,r-fds) + ("r-matrix" ,r-matrix))) (home-page "https://www.functionaldata.org") (synopsis "Functional data analysis") (description -- cgit v1.2.3 From cdbe38c682bbc86dcd3bd407e8d27dc1abeb8df7 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Dec 2020 22:00:06 +0100 Subject: gnu: r-isocodes: Update to 2020.12.04. * gnu/packages/cran.scm (r-isocodes): Update to 2020.12.04. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index f7f83950a4..48d83b2e1e 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -20845,14 +20845,14 @@ and Euclidean distance is particularly fast.") (define-public r-isocodes (package (name "r-isocodes") - (version "2020.03.16") + (version "2020.12.04") (source (origin (method url-fetch) (uri (cran-uri "ISOcodes" version)) (sha256 (base32 - "1hz1sj57qkkkrgn8slsz2n4jv1fkyp40503j9rg30lxy4gmb83hn")))) + "18373rkhmwm7y2drvfbhrxkqw9d23avf0ndvh0fg00z4djvddkjx")))) (properties `((upstream-name . "ISOcodes"))) (build-system r-build-system) (home-page "https://cran.r-project.org/package=ISOcodes") -- cgit v1.2.3 From fccc5ac29a36fd35822a5bee5cf447119001bd6a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Dec 2020 22:00:10 +0100 Subject: gnu: r-stopwords: Update to 2.1. * gnu/packages/cran.scm (r-stopwords): Update to 2.1. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 48d83b2e1e..95f6256b33 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -20867,14 +20867,14 @@ character codes as well as the UN M.49 area codes.") (define-public r-stopwords (package (name "r-stopwords") - (version "2.0") + (version "2.1") (source (origin (method url-fetch) (uri (cran-uri "stopwords" version)) (sha256 (base32 - "155g00ansyqfpp1mzd2q6mn0k214xinf78nww2368h24kz761jjw")))) + "1g2p8gsj7xjck7idcwczgc7fmv72lzwjw00qarrj0cv44kypmiq8")))) (properties `((upstream-name . "stopwords"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From b19230386d4248e93daaeef67a5ed97ad63bf420 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Dec 2020 22:00:13 +0100 Subject: gnu: r-loo: Update to 2.4.0. * gnu/packages/cran.scm (r-loo): Update to 2.4.0. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 95f6256b33..16e4efe084 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -21937,13 +21937,13 @@ recommendations for developers.") (define-public r-loo (package (name "r-loo") - (version "2.3.1") + (version "2.4.0") (source (origin (method url-fetch) (uri (cran-uri "loo" version)) (sha256 - (base32 "12z0k8lhz0rxygs5lc7076nw6qhk0pda8nxf65hkinfrf4dy53fr")))) + (base32 "01a15ikfnyxhjhrgvy3ag929rg45dxp3wji1j38r4hg4q1yz4ma9")))) (properties `((upstream-name . "loo"))) (build-system r-build-system) (inputs -- cgit v1.2.3 From 2847297e88bbb5f6c6242054b7068d77853eb51b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Dec 2020 22:00:16 +0100 Subject: gnu: r-isoband: Update to 0.2.3. * gnu/packages/cran.scm (r-isoband): Update to 0.2.3. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 16e4efe084..99015cfb84 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -22239,14 +22239,14 @@ Encyclopedia of Integer Sequences} (OEIS) in the function help page.") (define-public r-isoband (package (name "r-isoband") - (version "0.2.2") + (version "0.2.3") (source (origin (method url-fetch) (uri (cran-uri "isoband" version)) (sha256 (base32 - "044fg014gb6v6v11gm7ivfipz45iqw9cpahjhaacw6kyahyb66zx")))) + "1zkzdc39dpw2z59bjck27nimz9a2vskmw0f7wb17s53dvy7k3lzr")))) (properties `((upstream-name . "isoband"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From f694850d38f3963ef10b14068b6ae9435f1cd7bd Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Dec 2020 22:00:20 +0100 Subject: gnu: r-brms: Update to 2.14.4. * gnu/packages/cran.scm (r-brms): Update to 2.14.4. [propagated-inputs]: Add r-projpred. --- gnu/packages/cran.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 99015cfb84..2ef2b7912f 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -22950,14 +22950,14 @@ vignette for more information and examples.") (define-public r-brms (package (name "r-brms") - (version "2.14.0") + (version "2.14.4") (source (origin (method url-fetch) (uri (cran-uri "brms" version)) (sha256 (base32 - "0s8dl1xm3bpivfv3hw94zv9cifjg8cgs5137yd8d755kc2v0fdmf")))) + "0mzwihhgmn405l6zq11a180q4k3chggj9qj0j7q838b9vrszg59j")))) (properties `((upstream-name . "brms"))) (build-system r-build-system) (propagated-inputs @@ -22975,6 +22975,7 @@ vignette for more information and examples.") ("r-mgcv" ,r-mgcv) ("r-nleqslv" ,r-nleqslv) ("r-nlme" ,r-nlme) + ("r-projpred" ,r-projpred) ("r-rcpp" ,r-rcpp) ("r-rstan" ,r-rstan) ("r-rstantools" ,r-rstantools) -- cgit v1.2.3 From aa486bbc2fe086ea57bbf2fe38a33f076de6d098 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Dec 2020 22:00:23 +0100 Subject: gnu: r-hardhat: Update to 0.1.5. * gnu/packages/cran.scm (r-hardhat): Update to 0.1.5. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 2ef2b7912f..2ea200c3d0 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -23175,14 +23175,14 @@ counting and recursive k-means partitioning.") (define-public r-hardhat (package (name "r-hardhat") - (version "0.1.4") + (version "0.1.5") (source (origin (method url-fetch) (uri (cran-uri "hardhat" version)) (sha256 (base32 - "0gaj4hr4dj27jaasp7v0hzaivipplvq746ajsyz4yd1in03hfjvs")))) + "1b7f9i9fy39j9n03g40vd6nzgq9fgq914xg3svf84najlknvjzly")))) (properties `((upstream-name . "hardhat"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 80a279b118fcbe4db4964e991d091da303964a42 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Dec 2020 22:00:26 +0100 Subject: gnu: r-spatstat-data: Update to 1.5-2. * gnu/packages/cran.scm (r-spatstat-data): Update to 1.5-2. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 2ea200c3d0..d15a46d68d 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -23580,14 +23580,14 @@ which may also be useful for other purposes.") (define-public r-spatstat-data (package (name "r-spatstat-data") - (version "1.4-3") + (version "1.5-2") (source (origin (method url-fetch) (uri (cran-uri "spatstat.data" version)) (sha256 (base32 - "18lfj5vkwxgf5w9qz0g5al3zy8y2yi3bnd13w24hszfc82nbcmc9")))) + "17vbf48g1mh8iigzzlaa9j4mw087hib7f1kkbl3c50xjcrr5iw6b")))) (properties `((upstream-name . "spatstat.data"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 94ebe64f198250fb8c644fe8aae11417d9c47b1e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Dec 2020 22:00:29 +0100 Subject: gnu: r-cpp11: Update to 0.2.4. * gnu/packages/cran.scm (r-cpp11): Update to 0.2.4. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index d15a46d68d..dc7f7d62eb 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -23670,14 +23670,14 @@ for linear mixed models (AIREML).") (define-public r-cpp11 (package (name "r-cpp11") - (version "0.2.3") + (version "0.2.4") (source (origin (method url-fetch) (uri (cran-uri "cpp11" version)) (sha256 (base32 - "1avcip33bldzz0rhkl43b4sljrbb8i24684xxmr9il5bijcpyy97")))) + "08lrmpfkwh1w290a5ikhs9yn1vn32wbgvbzb4n3zb2indb8s5g69")))) (properties `((upstream-name . "cpp11"))) (build-system r-build-system) (native-inputs `(("r-knitr" ,r-knitr))) -- cgit v1.2.3 From 29ebaf068ec154afe8ada325c22e04efdb5fac58 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Dec 2020 22:00:36 +0100 Subject: gnu: r-tune: Update to 0.1.2. * gnu/packages/cran.scm (r-tune): Update to 0.1.2. [propagated-inputs]: Remove r-crayon and r-lifecycle; add r-generics. --- gnu/packages/cran.scm | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index dc7f7d62eb..e90f242e37 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -24484,27 +24484,26 @@ for creating, simulating, or validating values for such parameters.") (define-public r-tune (package (name "r-tune") - (version "0.1.1") + (version "0.1.2") (source (origin (method url-fetch) (uri (cran-uri "tune" version)) (sha256 (base32 - "0293xkmv1nyvm72wxznnlm3qpf6475xzl2sf52mnrjxxr7i447p1")))) + "0ja7rjkjj88v3ngrc6izcz2qh9qv4s8abgcafmvx2ihgz99hds37")))) (properties `((upstream-name . "tune"))) (build-system r-build-system) (propagated-inputs `(("r-cli" ,r-cli) - ("r-crayon" ,r-crayon) ("r-dials" ,r-dials) ("r-dplyr" ,r-dplyr) ("r-foreach" ,r-foreach) + ("r-generics" ,r-generics) ("r-ggplot2" ,r-ggplot2) ("r-glue" ,r-glue) ("r-gpfit" ,r-gpfit) ("r-hardhat" ,r-hardhat) - ("r-lifecycle" ,r-lifecycle) ("r-parsnip" ,r-parsnip) ("r-purrr" ,r-purrr) ("r-recipes" ,r-recipes) -- cgit v1.2.3 From 48504a231aff17dc7bb4cc22e2a41d4135704a32 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Dec 2020 22:00:40 +0100 Subject: gnu: r-tidymodels: Update to 0.1.2. * gnu/packages/cran.scm (r-tidymodels): Update to 0.1.2. [propagated-inputs]: Remove r-crayon. --- gnu/packages/cran.scm | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index e90f242e37..8fc8be6a18 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -24805,20 +24805,19 @@ model-related packages.") (define-public r-tidymodels (package (name "r-tidymodels") - (version "0.1.1") + (version "0.1.2") (source (origin (method url-fetch) (uri (cran-uri "tidymodels" version)) (sha256 (base32 - "0w2xnr642klmqlflkw6rkvqcrgs01i8f34nk9wdax3fsl1yx2wi4")))) + "09njrl655sh82xrzckgg56a6ndfrjla5fy8675wj4jsj14jpv0fw")))) (properties `((upstream-name . "tidymodels"))) (build-system r-build-system) (propagated-inputs `(("r-broom" ,r-broom) ("r-cli" ,r-cli) - ("r-crayon" ,r-crayon) ("r-dials" ,r-dials) ("r-dplyr" ,r-dplyr) ("r-ggplot2" ,r-ggplot2) -- cgit v1.2.3 From 1f2ceaccf14fbc5be72d0d12c4573560d09a824f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Dec 2020 22:00:43 +0100 Subject: gnu: r-diversitree: Update to 0.9-15. * gnu/packages/cran.scm (r-diversitree): Update to 0.9-15. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 8fc8be6a18..45703792ed 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -25091,14 +25091,14 @@ Maximum Parsimony, distance methods and Hadamard conjugation.") (define-public r-diversitree (package (name "r-diversitree") - (version "0.9-14") + (version "0.9-15") (source (origin (method url-fetch) (uri (cran-uri "diversitree" version)) (sha256 (base32 - "0xkxw4n1rsagip51smh9k0h0lmnnvsajqcxma7yh95ifdkyrcyy4")))) + "1sk3sgn5hi04978s5s7gy6pzp28g3v9rglmiamlgs96c9wyyyff7")))) (build-system r-build-system) (native-inputs `(("gfortran" ,gfortran))) -- cgit v1.2.3 From 59771643deacfe19676f526f3c7e51f80056d796 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Dec 2020 22:00:46 +0100 Subject: gnu: r-codetools: Update to 0.2-18. * gnu/packages/statistics.scm (r-codetools): Update to 0.2-18. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 9a9eb436c1..f1d2fcd98c 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -503,14 +503,14 @@ Hubert, based on Kaufman and Rousseeuw (1990) \"Finding Groups in Data\".") (define-public r-codetools (package (name "r-codetools") - (version "0.2-16") + (version "0.2-18") (source (origin (method url-fetch) (uri (cran-uri "codetools" version)) (sha256 (base32 - "00bmhzqprqfn3w6ghx7sakai6s7il8gbksfiawj8in5mbhbncypn")))) + "0a2c115glq8jxixwfigrpvjabhxchn9r4mc40y41dg9dg6wsd7hs")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/codetools") (synopsis "Code analysis tools for R") -- cgit v1.2.3 From ff34dbb5423cf80e2c2f2bfe746101d389198ae8 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Dec 2020 22:00:55 +0100 Subject: gnu: r-testthat: Update to 3.0.0. * gnu/packages/statistics.scm (r-testthat): Update to 3.0.0. [propagated-inputs]: Add r-brio, r-callr, r-desc, r-jsonlite, r-lifecycle, r-processx, r-ps, and r-waldo. [native-inputs]: Add r-knitr. --- gnu/packages/statistics.scm | 16 +++++++++++++--- 1 file changed, 13 insertions(+), 3 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index f1d2fcd98c..359f52a7f2 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -1583,26 +1583,36 @@ R packages that praise their users.") (define-public r-testthat (package (name "r-testthat") - (version "2.3.2") + (version "3.0.0") (source (origin (method url-fetch) (uri (cran-uri "testthat" version)) (sha256 (base32 - "0v70v2fs0f2ir962z9csbjlj8snrq9mbjfyhhb9dhz3zy26qs9hs")))) + "069ixg03r1s85my9dbc9c1261i4gz8fc1mv67whi2l6kpbp4cjzh")))) (build-system r-build-system) (propagated-inputs - `(("r-cli" ,r-cli) + `(("r-brio" ,r-brio) + ("r-callr" ,r-callr) + ("r-cli" ,r-cli) ("r-crayon" ,r-crayon) + ("r-desc" ,r-desc) ("r-digest" ,r-digest) ("r-ellipsis" ,r-ellipsis) ("r-evaluate" ,r-evaluate) + ("r-jsonlite" ,r-jsonlite) + ("r-lifecycle" ,r-lifecycle) ("r-magrittr" ,r-magrittr) ("r-pkgload" ,r-pkgload) ("r-praise" ,r-praise) + ("r-processx" ,r-processx) + ("r-ps" ,r-ps) ("r-r6" ,r-r6) ("r-rlang" ,r-rlang) + ("r-waldo" ,r-waldo) ("r-withr" ,r-withr))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://github.com/hadley/testthat") (synopsis "Unit testing for R") (description -- cgit v1.2.3 From 0bc87a52823eaf9faf57e0b1c600f8584338027a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Dec 2020 22:00:59 +0100 Subject: gnu: r-rlang: Update to 0.4.9. * gnu/packages/statistics.scm (r-rlang): Update to 0.4.9. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 359f52a7f2..509fddc4b0 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -1645,13 +1645,13 @@ defined in different packages.") (define-public r-rlang (package (name "r-rlang") - (version "0.4.8") + (version "0.4.9") (source (origin (method url-fetch) (uri (cran-uri "rlang" version)) (sha256 (base32 - "0z8hnwbzpwal66svwp04csjm49vdb9rmwzvn8hyqn93qy6pd9015")))) + "0qix6jigz3qqjx151fpv1k5hq2miqyakvm3jql2qqsyr9d1028yr")))) (build-system r-build-system) (home-page "http://rlang.tidyverse.org") (synopsis "Functions for base types, core R and Tidyverse features") -- cgit v1.2.3 From 348c21eafc37da1e198fdca778ac7d8fce0e75dd Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Dec 2020 22:01:03 +0100 Subject: gnu: r-dbplyr: Update to 2.0.0. * gnu/packages/statistics.scm (r-dbplyr): Update to 2.0.0. [propagated-inputs]: Add r-withr. --- gnu/packages/statistics.scm | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 509fddc4b0..6a9194c861 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -1731,14 +1731,14 @@ database.") (define-public r-dbplyr (package (name "r-dbplyr") - (version "1.4.4") + (version "2.0.0") (source (origin (method url-fetch) (uri (cran-uri "dbplyr" version)) (sha256 (base32 - "1v0p0557n6bz84nq9jc4182k00mdd1hvz7h4w3bbg81z0fmpj0d8")))) + "0sa0ggirvfn8j9y4cvhj04z93h6979jm4knjzahdvyzyxhv1kmzc")))) (build-system r-build-system) (propagated-inputs `(("r-assertthat" ,r-assertthat) @@ -1752,7 +1752,8 @@ database.") ("r-r6" ,r-r6) ("r-rlang" ,r-rlang) ("r-tibble" ,r-tibble) - ("r-tidyselect" ,r-tidyselect))) + ("r-tidyselect" ,r-tidyselect) + ("r-withr" ,r-withr))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://github.com/tidyverse/dbplyr") -- cgit v1.2.3 From aed99e0c7d9cf6b1379a21557367025d029d09e8 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Dec 2020 22:01:06 +0100 Subject: gnu: r-data-table: Update to 1.13.4. * gnu/packages/statistics.scm (r-data-table): Update to 1.13.4. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 6a9194c861..88851939ee 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -1850,13 +1850,13 @@ times.") (define-public r-data-table (package (name "r-data-table") - (version "1.13.2") + (version "1.13.4") (source (origin (method url-fetch) (uri (cran-uri "data.table" version)) (sha256 (base32 - "011qsjfybvlpy2sjn9b6hfkcgwx2xrnpxlaqq3y3baps8n1lgnr7")))) + "0jrvl5b8qbzmiymhjgbj4l2nai87ijvv33aw24xvzjx0rkys9dv1")))) (build-system r-build-system) (inputs `(("zlib" ,zlib))) -- cgit v1.2.3 From e4ce58424e08be63ba81a9bb5e72cc7c1230838f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Dec 2020 22:01:09 +0100 Subject: gnu: r-backports: Update to 1.2.0. * gnu/packages/statistics.scm (r-backports): Update to 1.2.0. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 88851939ee..607d699b95 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -2125,14 +2125,14 @@ limited to R.") (define-public r-backports (package (name "r-backports") - (version "1.1.10") + (version "1.2.0") (source (origin (method url-fetch) (uri (cran-uri "backports" version)) (sha256 (base32 - "1pq16bf40zx441ylmqqqilj3xp39r707h56kwqp5yqklq9yln2z1")))) + "1xgp4i6yxkh2viia96hlf004hn47yrhfivwf8wv63xdldqa8yj9v")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/backports") (synopsis "Reimplementations of functions introduced since R 3.0.0") -- cgit v1.2.3 From 48af6aa1cb30bec60f83cf75ceb6894d1c7b6b83 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Dec 2020 22:01:13 +0100 Subject: gnu: r-rstudioapi: Update to 0.13. * gnu/packages/statistics.scm (r-rstudioapi): Update to 0.13. [native-inputs]: Add r-knitr. --- gnu/packages/statistics.scm | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 607d699b95..32c741739c 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -2433,14 +2433,16 @@ pure C implementation of the Git core methods.") (define-public r-rstudioapi (package (name "r-rstudioapi") - (version "0.11") + (version "0.13") (source (origin (method url-fetch) (uri (cran-uri "rstudioapi" version)) (sha256 (base32 - "0srh0m4mw4k6s7spwb84l4cx4xnn04cp5cjxi0fwza7bwavpzq0k")))) + "12vdfzzjc6mv4h105l8cp108j3hjk0mqmg23m6mqr3jarfymphxa")))) (build-system r-build-system) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://cran.r-project.org/web/packages/rstudioapi") (synopsis "Safely access the RStudio API") (description -- cgit v1.2.3 From da290237fbaff45de868e082e08ff291d94465b6 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Dec 2020 22:01:16 +0100 Subject: gnu: r-rcpparmadillo: Update to 0.10.1.2.0. * gnu/packages/statistics.scm (r-rcpparmadillo): Update to 0.10.1.2.0. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 32c741739c..fa49de8e5d 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -2630,13 +2630,13 @@ well as additional utilities such as panel and axis annotation functions.") (define-public r-rcpparmadillo (package (name "r-rcpparmadillo") - (version "0.10.1.0.0") + (version "0.10.1.2.0") (source (origin (method url-fetch) (uri (cran-uri "RcppArmadillo" version)) (sha256 (base32 - "0m0f4viw3r6zfk85b7v7h5dqydhdkjdacpl0bqxkmcndlzq8jnsb")))) + "0nzi6plhdijx3khavmywzw9wbch0hj8kygphw35wdlslm4cnqcj1")))) (properties `((upstream-name . "RcppArmadillo"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 5d0ccf888f4136fe92756b32c0d57bf4c5feca0b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Dec 2020 22:01:20 +0100 Subject: gnu: r-rprojroot: Update to 2.0.2. * gnu/packages/statistics.scm (r-rprojroot): Update to 2.0.2. [propagated-inputs]: Remove r-backports. [native-inputs]: Add r-knitr. --- gnu/packages/statistics.scm | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index fa49de8e5d..a3e7162471 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -2699,17 +2699,17 @@ encoder/decoder, round-off-error-free sum and cumsum, etc.") (define-public r-rprojroot (package (name "r-rprojroot") - (version "1.3-2") + (version "2.0.2") (source (origin (method url-fetch) (uri (cran-uri "rprojroot" version)) (sha256 (base32 - "12r3fdxmi2pmwn6ic3rhg0b20ll5z420m0d8fziv1n21961namnz")))) + "07wy07yhms8zln9qb0iwx69dq08h4lrdi8kavjcplfxcskq638az")))) (build-system r-build-system) - (propagated-inputs - `(("r-backports" ,r-backports))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://github.com/krlmlr/rprojroot") (synopsis "Finding files in project subdirectories") (description -- cgit v1.2.3 From 3ffc5515db95c04ef9174538ed849c14111289fb Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Dec 2020 22:01:23 +0100 Subject: gnu: r-hmisc: Update to 4.4-2. * gnu/packages/statistics.scm (r-hmisc): Update to 4.4-2. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index a3e7162471..ba096c080a 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -4029,13 +4029,13 @@ package instead.") (define-public r-hmisc (package (name "r-hmisc") - (version "4.4-1") + (version "4.4-2") (source (origin (method url-fetch) (uri (cran-uri "Hmisc" version)) (sha256 - (base32 "0mm3r2kv0kgrhg7salk2hw0s37d4i2mghwk0l0qxaw2ny0w8w5z6")))) + (base32 "1j7vkckmahdh90ndcl646sjpxq82y4x55ngxqvkni22mv16wc2j9")))) (properties `((upstream-name . "Hmisc"))) (build-system r-build-system) (native-inputs -- cgit v1.2.3 From 31a6a60576dc708abd15a8e85eb8c142aa673416 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Dec 2020 22:01:26 +0100 Subject: gnu: r-gplots: Update to 3.1.1. * gnu/packages/statistics.scm (r-gplots): Update to 3.1.1. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index ba096c080a..43c7a8c946 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -4225,14 +4225,14 @@ including: (define-public r-gplots (package (name "r-gplots") - (version "3.1.0") + (version "3.1.1") (source (origin (method url-fetch) (uri (cran-uri "gplots" version)) (sha256 (base32 - "05rislwgaw6v5dmhcwyvc04hi1fgaxrpb61f66kx483px45w6f24")))) + "0f8khaymz383w2ksnk80d4kpnvgmdk37pbycpsnl2vabaz11kbpr")))) (build-system r-build-system) (propagated-inputs `(("r-catools" ,r-catools) -- cgit v1.2.3 From 61d24175b6ae3166884203ce678df4d6a8bac72a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Dec 2020 22:01:29 +0100 Subject: gnu: r-mclust: Update to 5.4.7. * gnu/packages/statistics.scm (r-mclust): Update to 5.4.7. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 43c7a8c946..284e1c4b19 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -4717,14 +4717,14 @@ models, generalized linear models and model-based clustering.") (define-public r-mclust (package (name "r-mclust") - (version "5.4.6") + (version "5.4.7") (source (origin (method url-fetch) (uri (cran-uri "mclust" version)) (sha256 (base32 - "1z46qask09x3xpv0wzvhn09218vwyrip4f5jrhnx96khpwvczzyl")))) + "08scl72llpinfijiyx14yqvmx8lma9jvh8h92v9ynnzfr9kadxa5")))) (build-system r-build-system) (native-inputs `(("gfortran" ,gfortran) -- cgit v1.2.3 From d6d29848696891b73a3ff114400f39ccb2c9940c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Dec 2020 22:01:33 +0100 Subject: gnu: r-fpc: Update to 2.2-9. * gnu/packages/statistics.scm (r-fpc): Update to 2.2-9. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 284e1c4b19..e2fded49c9 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -4936,14 +4936,14 @@ of the points.") (define-public r-fpc (package (name "r-fpc") - (version "2.2-8") + (version "2.2-9") (source (origin (method url-fetch) (uri (cran-uri "fpc" version)) (sha256 (base32 - "07a125pji1flmybn6iidcnizwnqyl6chnrckxa5jp4qxxfdqx658")))) + "0f7sfmpcycr9y7cy5gasyjm2ardxa62kglqms92mcr68jrp01c19")))) (build-system r-build-system) (propagated-inputs `(("r-class" ,r-class) -- cgit v1.2.3 From d0c7b9f718252d4208434437e5e36666d2d881f8 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Dec 2020 22:01:36 +0100 Subject: gnu: r-lme4: Update to 1.1-26. * gnu/packages/statistics.scm (r-lme4): Update to 1.1-26. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index e2fded49c9..a4c7d37750 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -5161,14 +5161,14 @@ algorithms.") (define-public r-lme4 (package (name "r-lme4") - (version "1.1-25") + (version "1.1-26") (source (origin (method url-fetch) (uri (cran-uri "lme4" version)) (sha256 (base32 - "0vvjac7hnn5lfbyl92zi8qxyc8kkjcwsg94z0p2s2q311in4gnp4")))) + "0ls2krph4pfjn45vf9fn3ln3x98s85wxrkvm5pnxyx55n1pnsjrn")))) (build-system r-build-system) (propagated-inputs `(("r-boot" ,r-boot) -- cgit v1.2.3 From 52e14cb7988f1f5e5f52ef8487388540fb3e1ae0 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Dec 2020 22:01:39 +0100 Subject: gnu: r-lubridate: Update to 1.7.9.2. * gnu/packages/statistics.scm (r-lubridate): Update to 1.7.9.2. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index a4c7d37750..5d51efff18 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -5497,14 +5497,14 @@ is supported.") (define-public r-lubridate (package (name "r-lubridate") - (version "1.7.9") + (version "1.7.9.2") (source (origin (method url-fetch) (uri (cran-uri "lubridate" version)) (sha256 (base32 - "0wnjzvfkrgp2hkr8g5r5vcgcxmsq8bhdmkzkk0m93wr3fgh5xyfb")))) + "0yfvlgksasmia7rsp83lsipjpgvlly5qkldcfxj68lfaz9l2sspf")))) (build-system r-build-system) (propagated-inputs `(("r-generics" ,r-generics) -- cgit v1.2.3 From 371ba7b4be81895d202519824bf19893bfdb2526 Mon Sep 17 00:00:00 2001 From: Giacomo Leidi Date: Tue, 12 May 2020 23:31:30 +0200 Subject: guix: Add globstar support. * guix/glob.scm (string->sglob) (glob-match?): Add globstar support. * tests/glob.scm: Update accordingly. Signed-off-by: Jelle Licht --- guix/glob.scm | 15 +++++++++++++++ tests/glob.scm | 8 ++++++-- 2 files changed, 21 insertions(+), 2 deletions(-) diff --git a/guix/glob.scm b/guix/glob.scm index a9fc744802..d73783cd30 100644 --- a/guix/glob.scm +++ b/guix/glob.scm @@ -1,5 +1,6 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2018 Ludovic Courtès +;;; Copyright © 2020 Giacomo Leidi ;;; ;;; This file is part of GNU Guix. ;;; @@ -61,6 +62,11 @@ STR, a glob pattern such as \"foo*\" or \"foo??bar\"." (flatten (reverse (if (null? pending) result (cons-string pending result))))) + ((#\* #\* #\/ . rest) + (if (zero? brackets) + (loop rest '() 0 + (cons* '**/ (cons-string pending result))) + (loop rest (cons '**/ pending) brackets result))) (((and chr (or #\? #\*)) . rest) (let ((wildcard (match chr (#\? '?) @@ -121,6 +127,15 @@ STR, a glob pattern such as \"foo*\" or \"foo??bar\"." (string-null? str)) (('*) #t) + (('**/) + #t) + (('**/ suffix . rest) + (let ((rest (if (eq? '* suffix) (cdr rest) rest)) + (suffix (if (eq? '* suffix) (car rest) suffix))) + (match (string-contains str suffix) + (#f #f) + (index (loop rest (string-drop str + (+ index (string-length suffix)))))))) (('* suffix . rest) (match (string-contains str suffix) (#f #f) diff --git a/tests/glob.scm b/tests/glob.scm index 3134069789..2a5a40c3c6 100644 --- a/tests/glob.scm +++ b/tests/glob.scm @@ -1,5 +1,6 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2018 Ludovic Courtès +;;; Copyright © 2020 Giacomo Leidi ;;; ;;; This file is part of GNU Guix. ;;; @@ -53,7 +54,8 @@ "foo[abc]bar" => '("foo" (set #\a #\b #\c) "bar") "foo[a[b]c]bar" => '("foo" (set #\a #\[ #\b #\] #\c) "bar") "[123]x" => '((set #\1 #\2 #\3) "x") - "[a-z]" => '((range #\a #\z))) + "[a-z]" => '((range #\a #\z)) + "**/*.scm" => '(**/ * ".scm")) (test-glob-match ("foo" matches "foo" (and not "foobar" "barfoo")) @@ -64,6 +66,8 @@ ("ab[0-9]c" matches "ab0c" "ab7c" "ab9c" (and not "ab-c" "ab00c" "ab3")) ("ab[cdefg]" matches "abc" "abd" "abg" - (and not "abh" "abcd" "ab["))) + (and not "abh" "abcd" "ab[")) + ("foo/**/*.scm" matches "foo/bar/baz.scm" "foo/bar.scm" "foo/bar/baz/zab.scm" + (and not "foo/bar/baz.java" "foo/bar.smc"))) (test-end "glob") -- cgit v1.2.3 From 471478779306ba345c545eea8fa602a0a966f140 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Dec 2020 23:27:59 +0100 Subject: gnu: r-biocneighbors: Update to 1.8.2. * gnu/packages/bioconductor.scm (r-biocneighbors): Update to 1.8.2. [propagated-inputs]: Remove r-rcppannoy. --- gnu/packages/bioconductor.scm | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index bd7df29378..84ff2dac0b 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2540,21 +2540,20 @@ samples.") (define-public r-biocneighbors (package (name "r-biocneighbors") - (version "1.8.1") + (version "1.8.2") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocNeighbors" version)) (sha256 (base32 - "0hip1sgi3zkrf8g9bw12alaszivja3difalnybr5s7gvh8qd5sf4")))) + "19gyl917lf5ydy5hgj0hnc388rw5sbj83awav9js2yr2zmbgn4d7")))) (properties `((upstream-name . "BiocNeighbors"))) (build-system r-build-system) (propagated-inputs `(("r-biocparallel" ,r-biocparallel) ("r-matrix" ,r-matrix) ("r-rcpp" ,r-rcpp) - ("r-rcppannoy" ,r-rcppannoy) ("r-rcpphnsw" ,r-rcpphnsw) ("r-s4vectors" ,r-s4vectors))) (native-inputs -- cgit v1.2.3 From 7cda2d415fdb606bfada1d0db083ee9f5dcfcbcd Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Dec 2020 23:28:08 +0100 Subject: gnu: r-biosigner: Update to 1.18.2. * gnu/packages/bioconductor.scm (r-biosigner): Update to 1.18.2. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 84ff2dac0b..9df3724da7 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5872,14 +5872,14 @@ coefficients).") (define-public r-biosigner (package (name "r-biosigner") - (version "1.18.0") + (version "1.18.2") (source (origin (method url-fetch) (uri (bioconductor-uri "biosigner" version)) (sha256 (base32 - "1rqfmn9lpaajij9p302dfwv57pm4hw7xn2p7lx7hvpb3psa719xm")))) + "0i18j4fk91x5017yk1l35c58k5aby22yh81zkp59irphpv9akvjn")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) -- cgit v1.2.3 From 589ac42212daa513ed7dd8c74390e273d0d263cb Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Dec 2020 23:28:11 +0100 Subject: gnu: r-cicero: Update to 1.8.1. * gnu/packages/bioconductor.scm (r-cicero): Update to 1.8.1. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 9df3724da7..c646c88408 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6666,14 +6666,14 @@ genes in the gene-set that are ranked above the leading edge).") (define-public r-cicero (package (name "r-cicero") - (version "1.8.0") + (version "1.8.1") (source (origin (method url-fetch) (uri (bioconductor-uri "cicero" version)) (sha256 (base32 - "0hrra9ngpzmd57dwm0058zy0g7ymsil4pmvi3sgppfzimgviqiwf")))) + "12y857p4p0m7k72bimli8wjn9cd0gxjwcs3n7ri9pn9l9d42krqr")))) (build-system r-build-system) (propagated-inputs `(("r-assertthat" ,r-assertthat) -- cgit v1.2.3 From eed728951c2d98371902eb29e8c0a8d93cd20849 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Dec 2020 23:28:14 +0100 Subject: gnu: r-beachmat: Update to 2.6.2. * gnu/packages/bioconductor.scm (r-beachmat): Update to 2.6.2. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index c646c88408..d5f9760ead 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8773,14 +8773,14 @@ packages.") (define-public r-beachmat (package (name "r-beachmat") - (version "2.6.1") + (version "2.6.2") (source (origin (method url-fetch) (uri (bioconductor-uri "beachmat" version)) (sha256 (base32 - "0dkh3igvwbvir4p0y6x4q07mcv51b35qhva63vrjd6bbkdjn9brr")))) + "1yxm5andf4hsxxsmwrn5vl79707yfqkhzzajq6fvhsmaad3f97n7")))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) -- cgit v1.2.3 From 3872153a2ffe9610f79161814deacfdd9f3f3283 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Dec 2020 23:28:18 +0100 Subject: gnu: r-scuttle: Update to 1.0.3. * gnu/packages/bioconductor.scm (r-scuttle): Update to 1.0.3. [propagated-inputs]: Add r-genomicranges. --- gnu/packages/bioconductor.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index d5f9760ead..85ee56c539 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8827,14 +8827,14 @@ libraries.") (define-public r-scuttle (package (name "r-scuttle") - (version "1.0.0") + (version "1.0.3") (source (origin (method url-fetch) (uri (bioconductor-uri "scuttle" version)) (sha256 (base32 - "1k8q3wzq6f6j6wkjp9fy9j214rv98kyvcxnpavk6blqgaxjqwdr6")))) + "0l2r6fhyd33dllf2mc5a1pd5sawfvcin54pgh9l1nafqzg3sdv2m")))) (properties `((upstream-name . "scuttle"))) (build-system r-build-system) (propagated-inputs @@ -8843,6 +8843,7 @@ libraries.") ("r-biocparallel" ,r-biocparallel) ("r-delayedarray" ,r-delayedarray) ("r-delayedmatrixstats" ,r-delayedmatrixstats) + ("r-genomicranges" ,r-genomicranges) ("r-matrix" ,r-matrix) ("r-rcpp" ,r-rcpp) ("r-s4vectors" ,r-s4vectors) -- cgit v1.2.3 From baeaa02e75cdbed970d8bcc22f90b87435b7f91d Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Dec 2020 23:28:21 +0100 Subject: gnu: r-biocstyle: Update to 2.18.1. * gnu/packages/bioinformatics.scm (r-biocstyle): Update to 2.18.1. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 9edf75a82c..8dce352cba 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7757,13 +7757,13 @@ also known as views, in a controlled vocabulary.") (define-public r-biocstyle (package (name "r-biocstyle") - (version "2.18.0") + (version "2.18.1") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocStyle" version)) (sha256 (base32 - "1hfdvld0n9py45mxm05kbb0sq0s9p8yky3s6jb02gzhlxkk3q4fs")))) + "0rsxyna4dd99x42vc82mlkxx774vb9375llpakg53max1hhwkrqp")))) (properties `((upstream-name . "BiocStyle"))) (build-system r-build-system) -- cgit v1.2.3 From 4745f0dfca433112e373b9e22af0147eb958931a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Dec 2020 23:28:24 +0100 Subject: gnu: r-genomeinfodb: Update to 1.26.2. * gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.26.2. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 8dce352cba..35275493ad 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7913,13 +7913,13 @@ ID and species. It is used by functions in the GenomeInfoDb package.") (define-public r-genomeinfodb (package (name "r-genomeinfodb") - (version "1.26.0") + (version "1.26.2") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomeInfoDb" version)) (sha256 (base32 - "1xfhz7gmccijy2z015w07lh04g0ijh7zi6k7q6m4lripgban93g9")))) + "092izc49maxjhf6m4b0qx21ad16dz7bmxy5pysp3vkyhdrfa2f7v")))) (properties `((upstream-name . "GenomeInfoDb"))) (build-system r-build-system) -- cgit v1.2.3 From 48f77ecbb1a12129dda78c240775f3ad3051c423 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Dec 2020 23:28:28 +0100 Subject: gnu: r-keggrest: Update to 1.30.1. * gnu/packages/bioinformatics.scm (r-keggrest): Update to 1.30.1. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 35275493ad..172bb85791 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10209,14 +10209,14 @@ microarrays or GRanges for sequencing data.") (define-public r-keggrest (package (name "r-keggrest") - (version "1.30.0") + (version "1.30.1") (source (origin (method url-fetch) (uri (bioconductor-uri "KEGGREST" version)) (sha256 (base32 - "0awg0hmxj25rpmqyf6jz6kbkswmimz3h352xx15xhkamwcxykng6")))) + "0k9z85xf9la2y98xqmdmjb8mci9fh2fdybkl77x1yl26hyalip0s")))) (properties `((upstream-name . "KEGGREST"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 15c4e135a7999dc7701ab4f3fafae4f1f1cd383d Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Wed, 9 Dec 2020 18:16:08 -0500 Subject: gnu: Remove Attic. This package was superseded by Borg in 2016, and hasn't built successfully for a while. * gnu/packages/backup.scm (attic): Remove variable. --- gnu/packages/backup.scm | 44 -------------------------------------------- 1 file changed, 44 deletions(-) diff --git a/gnu/packages/backup.scm b/gnu/packages/backup.scm index a403224480..892b92dc2f 100644 --- a/gnu/packages/backup.scm +++ b/gnu/packages/backup.scm @@ -696,50 +696,6 @@ to not fully trusted targets. Borg is a fork of Attic.") (home-page "https://www.borgbackup.org/") (license license:bsd-3))) -(define-public attic - (package - (name "attic") - (version "0.16") - (source (origin - (method url-fetch) - (uri (pypi-uri "Attic" version)) - (sha256 - (base32 - "0b5skd36r4c0915lwpkqg5hxm49gls9pprs1b7hc40910wlcsl36")))) - (build-system python-build-system) - (arguments - `(;; The tests assume they are run as root: - ;; https://github.com/jborg/attic/issues/7 - #:tests? #f - #:phases - (modify-phases %standard-phases - (add-before - 'build 'set-openssl-prefix - (lambda* (#:key inputs #:allow-other-keys) - (setenv "ATTIC_OPENSSL_PREFIX" (assoc-ref inputs "openssl")) - #t))))) - (inputs - `(("acl" ,acl) - ("openssl" ,openssl) - ("python-msgpack" ,python-msgpack) - - ;; Attic is probably incompatible with llfuse > 0.41. - ;; These links are to discussions of llfuse compatibility from - ;; the borg project. Borg is a recent fork of attic, and attic - ;; has not been updated since the fork, so it's likely that - ;; llfuse compatibility requirements are still the same. - ;; https://github.com/borgbackup/borg/issues/642 - ;; https://github.com/borgbackup/borg/issues/643 - ("python-llfuse" ,python-llfuse-0.41))) - (synopsis "Deduplicating backup program") - (description "Attic is a deduplicating backup program. The main goal of -Attic is to provide an efficient and secure way to backup data. The data -deduplication technique used makes Attic suitable for daily backups since only -changes are stored.") - (home-page "https://attic-backup.org/") - (license license:bsd-3) - (properties `((superseded . ,borg))))) - (define-public wimlib (package (name "wimlib") -- cgit v1.2.3 From ec2eccbf3d1a6378c5ebf1e3d17ec72b4b2a4cd0 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Wed, 9 Dec 2020 18:17:20 -0500 Subject: gnu: Remove python-llfuse-0.41. * gnu/packages/python-xyz.scm (python-llfuse-0.41): Remove variable. --- gnu/packages/python-xyz.scm | 16 ---------------- 1 file changed, 16 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 8891db3c50..d312e3172a 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -8838,22 +8838,6 @@ third-party code.") (strip-python2-variant python-llfuse))) (propagated-inputs `(("python2-contextlib2" ,python2-contextlib2))))) -;; For attic-0.16 -(define-public python-llfuse-0.41 - (package (inherit python-llfuse) - (version "0.41.1") - (source (origin - (method url-fetch) - (uri (string-append - "https://bitbucket.org/nikratio/python-llfuse/downloads/" - "llfuse-" version ".tar.bz2")) - (sha256 - (base32 - "1imlqw9b73086y97izr036f58pgc5akv4ihc2rrf8j5h75jbrlaa")))) - ;; Python-LLFUSE < 0.42 includes underscore.js, which is MIT (expat) - ;; licensed. The rest of the package is licensed under LGPL2.0 or later. - (license (list license:expat license:lgpl2.0+)))) - (define-public python-msgpack (package (name "python-msgpack") -- cgit v1.2.3 From 11456ba8d7ec08c7c563c719eac8c5c9c58e92bd Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Thu, 10 Dec 2020 08:23:33 +0100 Subject: gnu: emacs-chess: Update to 2.0.5. * gnu/packages/emacs-xyz.scm (emacs-chess): Update to 2.0.5. --- gnu/packages/emacs-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 9407a4fdc2..a231f5697e 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -6624,14 +6624,14 @@ board and goal value can be customized.") (define-public emacs-chess (package (name "emacs-chess") - (version "2.0.4") + (version "2.0.5") (source (origin (method url-fetch) (uri (string-append "https://elpa.gnu.org/packages/" "chess-" version ".tar")) (sha256 - (base32 "1sq1bjmp513vldfh7hc2bbfc54665abqiz0kqgqq3gijckaxn5js")))) + (base32 "1a4iwjdh6k348df6qywjws9z9f862d62m0b2sz57z4xhywiyxpr7")))) (build-system emacs-build-system) (arguments `(#:phases -- cgit v1.2.3 From 1781d35364d8c06c3d879f5b6d5cc69f70d7ae05 Mon Sep 17 00:00:00 2001 From: Michael Rohleder Date: Wed, 9 Dec 2020 19:12:45 +0100 Subject: gnu: emacs-dash-docs: Update to 1.4.0-2.dafc8fc. * gnu/packages/emacs-xyz.scm (emacs-dash-docs): Update to 1.4.0-2.dafc8fc. Signed-off-by: Nicolas Goaziou --- gnu/packages/emacs-xyz.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index a231f5697e..99d5db186f 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -21946,8 +21946,8 @@ copied into @code{org-mode} buffers.") (license license:gpl3+)))) (define-public emacs-dash-docs - (let ((commit "111fd9b97001f1ad887b45e5308a14ddd68ce70a") - (revision "1")) + (let ((commit "dafc8fc9f1ddb2e4e39e0b8d066c42d5d7ce8d06") + (revision "2")) (package (name "emacs-dash-docs") (version (git-version "1.4.0" revision commit)) @@ -21960,7 +21960,7 @@ copied into @code{org-mode} buffers.") (file-name (git-file-name name version)) (sha256 (base32 - "0sckb7z0ylflva212bns7iq9mfnffgjghi0qspsbfwra35zb9xng")))) + "0n6d3mm43gj16v8kjjradcfik93wb89dsqnfcbskb28bvcamafid")))) (build-system emacs-build-system) (propagated-inputs `(("emacs-async" ,emacs-async))) -- cgit v1.2.3 From ef24052f88838fc036052c933541964e8b9b9958 Mon Sep 17 00:00:00 2001 From: Morgan Smith Date: Wed, 9 Dec 2020 12:38:24 -0500 Subject: gnu: Add emacs-org-pretty-table. * gnu/packages/emacs-xyz.scm (emacs-org-pretty-table): New variable. Signed-off-by: Nicolas Goaziou --- gnu/packages/emacs-xyz.scm | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 99d5db186f..71453cb0c3 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -10264,6 +10264,30 @@ lists, and project planning with a fast and effective plain-text system. This package is equivalent to org-plus-contrib, but only includes additional files that you would find in @file{contrib/} from the git repository."))) +(define-public emacs-org-pretty-table + ;; There is no release yet. + (let ((commit "1331c600b83d95b28730b1bfcb48369ac1cf12ef") + (revision "0")) + (package + (name "emacs-org-pretty-table") + (version (git-version "0.0.1" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/Fuco1/org-pretty-table") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0yvqxh66y400n2n5ykmb1zrzd80bakffpwn6nmf37728x4cj8krh")))) + (build-system emacs-build-system) + (home-page "https://github.com/Fuco1/org-pretty-table") + (synopsis "Make tables in Org mode and OrgTbl mode prettier") + (description + "This package displays tables in Org mode and OrgTbl mode using Unicode +characters.") + (license license:gpl3+)))) + (define-public emacs-ob-sclang (package (inherit emacs-org-contrib) -- cgit v1.2.3 From 38b05e7d3071d35bba6f2259b58b2ee8bedd04ca Mon Sep 17 00:00:00 2001 From: Michael Rohleder Date: Wed, 9 Dec 2020 18:53:47 +0100 Subject: gnu: emacs-company-emoji: Update to 2.6.0. * gnu/packages/emacs-xyz.scm (emacs-company-emoji): Update to 2.6.0. Signed-off-by: Nicolas Goaziou --- gnu/packages/emacs-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 71453cb0c3..ae6e10ddae 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -24864,7 +24864,7 @@ variables.") (define-public emacs-company-emoji (package (name "emacs-company-emoji") - (version "2.5.2") + (version "2.6.0") (source (origin (method git-fetch) @@ -24873,7 +24873,7 @@ variables.") (commit version))) (file-name (git-file-name name version)) (sha256 - (base32 "0r9zcbm3nb3zw5cwrkl098v5b49jbga5404bj7j55g6k4rwkjar2")))) + (base32 "0pa67yfcr8lrxdbvln8hs663gsxz38ggwpva7121ngascqgx42wp")))) (build-system emacs-build-system) (propagated-inputs `(("emacs-company" ,emacs-company))) -- cgit v1.2.3 From 71dd1be597f320ee89ea68bac5e898d1f4026c7f Mon Sep 17 00:00:00 2001 From: Michael Rohleder Date: Wed, 9 Dec 2020 23:24:46 +0100 Subject: gnu: emacs-lsp-ivy: Update to 0.4. * gnu/packages/emacs-xyz.scm (emacs-lsp-ivy): Update to 0.4. Signed-off-by: Nicolas Goaziou --- gnu/packages/emacs-xyz.scm | 46 ++++++++++++++++++++++------------------------ 1 file changed, 22 insertions(+), 24 deletions(-) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index ae6e10ddae..33b21f7fe3 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -21035,31 +21035,29 @@ and code peeking.") (license license:gpl3+)))) (define-public emacs-lsp-ivy - (let ((commit "caf1e1d7e22ed0b5fe18dd508d1a6f83dd163288") - (revision "2")) - (package - (name "emacs-lsp-ivy") - (version (git-version "0.1" revision commit)) - (source (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/emacs-lsp/lsp-ivy") - (commit commit))) - (file-name (git-file-name name version)) - (sha256 - (base32 - "084ds4qhzhivfnicy3h7z4mblxgcqx8pfnkbjr9qjrfng7cisy4z")))) - (build-system emacs-build-system) - (propagated-inputs - `(("emacs-ivy" ,emacs-ivy) - ("emacs-lsp-mode" ,emacs-lsp-mode) - ("emacs-dash" ,emacs-dash))) - (home-page "https://github.com/emacs-lsp/lsp-ivy") - (synopsis "Provide LSP-enhanced completion for symbols") - (description - "This package enhances @code{ivy} with completion for symbols from + (package + (name "emacs-lsp-ivy") + (version "0.4") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/emacs-lsp/lsp-ivy") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 "08dpn0vcfdwwysijwdpnnj91m69yw0q464i0wmp51zpj3dyd4kb1")))) + (build-system emacs-build-system) + (propagated-inputs + `(("emacs-dash" ,emacs-dash) + ("emacs-ivy" ,emacs-ivy) + ("emacs-lsp-mode" ,emacs-lsp-mode))) + (home-page "https://github.com/emacs-lsp/lsp-ivy") + (synopsis "Provide LSP-enhanced completion for symbols") + (description + "This package enhances @code{ivy} with completion for symbols from workspaces with a LSP-compliant server running.") - (license license:gpl3+)))) + (license license:gpl3+))) (define-public emacs-helm-lsp (let ((commit "3a58ca4cfd94b9ab1e15e819d3b16ef568e8889b") -- cgit v1.2.3 From 0faef871784f4f88e622dd36b492f020387f7a5e Mon Sep 17 00:00:00 2001 From: Mathieu Othacehe Date: Thu, 10 Dec 2020 09:46:50 +0100 Subject: avahi: Ignore local services. * guix/avahi.scm (avahi-browse-service-thread): Add "ignore-local?" argument and honor it. --- guix/avahi.scm | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/guix/avahi.scm b/guix/avahi.scm index 8a82fd3beb..aa90a5cdd4 100644 --- a/guix/avahi.scm +++ b/guix/avahi.scm @@ -92,6 +92,7 @@ when STOP-LOOP? procedure returns true." (define* (avahi-browse-service-thread proc #:key types + (ignore-local? #t) (family AF_INET) (stop-loop? (const #f)) (timeout 100)) @@ -116,7 +117,9 @@ when STOP-LOOP? procedure returns true." ;; Add the service if the host is unknown. This means that if a ;; service is available on multiple network interfaces for a single ;; host, only the first interface found will be considered. - (unless (hash-ref %known-hosts service-name) + (unless (or (hash-ref %known-hosts service-name) + (and ignore-local? + (member lookup-result-flag/local flags))) (let* ((address (inet-ntop family address)) (local-address (interface->ip-address interface)) (service* (avahi-service @@ -144,8 +147,8 @@ when STOP-LOOP? procedure returns true." ((eq? event browser-event/remove) (let ((service (hash-ref %known-hosts service-name))) (when service - (proc 'remove-service service) - (hash-remove! %known-hosts service-name)))))) + (proc 'remove-service service) + (hash-remove! %known-hosts service-name)))))) (define client-callback (lambda (client state) -- cgit v1.2.3 From 3fdb01f1f5a5f7cdf347a43ecc00a62df3a5ca8d Mon Sep 17 00:00:00 2001 From: Christopher Baines Date: Thu, 10 Dec 2020 09:28:25 +0000 Subject: gnu: guile-prometheus: Update to 0-4.f661edf. * gnu/packages/guile-xyz.scm (guile-prometheus): Update to 0-4.f661edf. --- gnu/packages/guile-xyz.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/guile-xyz.scm b/gnu/packages/guile-xyz.scm index f49ddf9216..bd12b7b240 100644 --- a/gnu/packages/guile-xyz.scm +++ b/gnu/packages/guile-xyz.scm @@ -886,8 +886,8 @@ Vicare Scheme and IronScheme. Right now it contains: (license license:bsd-3))) (define-public guile-prometheus - (let ((commit "2549c482fb04db84481d595f0bf99a1c8bb97c4c") - (revision "3")) + (let ((commit "f661edf72d2dd711dffe4313c2a9360e79b36dd1") + (revision "4")) (package (name "guile-prometheus") (version (git-version "0" revision commit)) @@ -898,7 +898,7 @@ Vicare Scheme and IronScheme. Right now it contains: (commit commit))) (sha256 (base32 - "0wfaspy3gvn2bkfzlvgx9ncz6114ldxxj25vnj4frcgbzqbdsair")) + "1556rv3b72wxba7yz4nn681k2l8fp70dwx32whyyxg755ma4r76f")) (file-name (string-append name "-" version "-checkout")))) (build-system gnu-build-system) (native-inputs -- cgit v1.2.3 From 8e344e36771e35702ab3e4bef72529dcd3498809 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Thu, 10 Dec 2020 14:22:20 +0200 Subject: gnu: singularity: Update command substitutions. Reported by Hao Chen . * gnu/packages/linux.scm (singularity)[arguments]: Update 'patch-references phase to actually patch mksquashfs calls and to patch sed calls. --- gnu/packages/linux.scm | 18 +++++++++--------- 1 file changed, 9 insertions(+), 9 deletions(-) diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index ee460c38b2..4b1fe7e15a 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -4045,18 +4045,18 @@ thanks to the use of namespaces.") (modify-phases %standard-phases (add-after 'unpack 'patch-references (lambda _ - (substitute* "libexec/cli/build.exec" - (("if ! singularity_which mksquashfs") "if 0") - (("if ! mksquashfs") - (string-append "if ! " (which "mksquashfs")))) - (substitute* (list "libexec/cli/help.exec" - "libexec/bootstrap-scripts/functions" - "libexec/bootstrap-scripts/post.sh" - "libexec/functions") + (substitute* "libexec/cli/build.exec.in" + (("-mksquashfs") (string-append "-" (which "mksquashfs")))) + (substitute* (append + (find-files "libexec" "functions") + (find-files "libexec/bootstrap-scripts" ".*sh$") + (find-files "libexec/cli" ".*exec$")) (("\\| grep ") (string-append "| " (which "grep") " ")) (("egrep ") - (string-append (which "egrep") " "))) + (string-append (which "egrep") " ")) + ((" sed ") + (string-append " " (which "sed") " "))) #t)) (add-after 'install 'set-PATH (lambda* (#:key inputs outputs #:allow-other-keys) -- cgit v1.2.3 From 793713dc3f227cf3b3a22bf45f6da682fa9165ed Mon Sep 17 00:00:00 2001 From: divoplade Date: Tue, 10 Nov 2020 14:21:17 +0100 Subject: gnu: exim: Enable authenticators. * gnu/packages/mail.scm (exim)[arguments]: Enable cram_md5, dovecot, external, plaintext, spa and tls authenticators in configure phase. Signed-off-by: Arun Isaac --- gnu/packages/mail.scm | 9 ++++++++- 1 file changed, 8 insertions(+), 1 deletion(-) diff --git a/gnu/packages/mail.scm b/gnu/packages/mail.scm index 6e3ee4c46a..f85713433e 100644 --- a/gnu/packages/mail.scm +++ b/gnu/packages/mail.scm @@ -39,6 +39,7 @@ ;;; Copyright © 2020 Alexandru-Sergiu Marton ;;; Copyright © 2020 Oleg Pykhalov ;;; Copyright © 2020 B. Wilson +;;; Copyright © 2020 divoplade ;;; ;;; This file is part of GNU Guix. ;;; @@ -1700,7 +1701,13 @@ delivery.") (("(ZCAT_COMMAND=).*" all var) (string-append var gzip "/bin/zcat\n")) (("# (USE_GNUTLS(|_PC)=.*)" all line) - (string-append line "\n"))) + (string-append line "\n")) + (("# (AUTH_CRAM_MD5=yes)" all line) line) + (("# (AUTH_DOVECOT=yes)" all line) line) + (("# (AUTH_EXTERNAL=yes)" all line) line) + (("# (AUTH_PLAINTEXT=yes)" all line) line) + (("# (AUTH_SPA=yes)" all line) line) + (("# (AUTH_TLS=yes)" all line) line)) ;; This file has hard-coded relative file names for tools despite ;; the zcat configuration above. (substitute* '("src/exigrep.src") -- cgit v1.2.3 From 3138e4a75b401ceb2231055c9e4952d000baa12d Mon Sep 17 00:00:00 2001 From: Niklas Eklund Date: Sun, 6 Dec 2020 21:40:38 +0100 Subject: gnu: stumpwm-with-slynk: Fix build error. * gnu/packages/wm.scm (stumpwm-with-slynk)[arguments]: Provide a writable directory to use as $HOME during building. Signed-off-by: Efraim Flashner --- gnu/packages/wm.scm | 2 ++ 1 file changed, 2 insertions(+) diff --git a/gnu/packages/wm.scm b/gnu/packages/wm.scm index 73a83c3411..3569d7f057 100644 --- a/gnu/packages/wm.scm +++ b/gnu/packages/wm.scm @@ -39,6 +39,7 @@ ;;; Copyright © 2020 Michael Rohleder ;;; Copyright © 2020 Guillaume Le Vaillant ;;; Copyright © 2020 B. Wilson +;; Copyright © 2020 Niklas Eklund ;;; ;;; This file is part of GNU Guix. ;;; @@ -1680,6 +1681,7 @@ productive, customizable lisp based systems.") (lambda* (#:key inputs outputs #:allow-other-keys) (let* ((out (assoc-ref outputs "out")) (program (string-append out "/bin/stumpwm"))) + (setenv "HOME" "/tmp") (build-program program outputs #:entry-program '((stumpwm:stumpwm) 0) #:dependencies '("stumpwm" "slynk") -- cgit v1.2.3 From d4e3527f78d22d77a62d6e00e179526c37831bc8 Mon Sep 17 00:00:00 2001 From: Ryan Prior Date: Mon, 7 Dec 2020 06:47:58 +0000 Subject: gnu: visidata: Update to 2.1. * gnu/packages/visidata.scm (visidata): Update to 2.1. Signed-off-by: Efraim Flashner --- gnu/packages/visidata.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/visidata.scm b/gnu/packages/visidata.scm index 6ba2939b4f..db126eb4ff 100644 --- a/gnu/packages/visidata.scm +++ b/gnu/packages/visidata.scm @@ -31,14 +31,14 @@ (define-public visidata (package (name "visidata") - (version "2.0.1") + (version "2.1") (source (origin (method url-fetch) (uri (pypi-uri "visidata" version)) (sha256 (base32 - "1p4x9fz59ablyjvp18y50zdsapavhzx7w5hk2v8rsar5ill8947v")))) + "15y6yif0h610ill57ck85l8n5faw849caw6rhf95rd0x67hkikaa")))) (build-system python-build-system) (arguments '(#:phases -- cgit v1.2.3 From 64098437081d8752d95ca9d065bf8367bd5ffb08 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Thu, 10 Dec 2020 16:59:06 +0100 Subject: gnu: nfs-utils: Fix location of external util-linux binaries. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Fixes: ~ λ sudo mount -t nfs 1.2.3.4:/ /mnt /gnu/store/aaa-nfs-utils-2.4.3/sbin/start-statd: line 10: /gnu/store/bbb-util-linux-2.35.1-lib/bin/flock: No such file or directory mount.nfs: rpc.statd is not running but is required for remote locking. * gnu/packages/nfs.scm (nfs-utils)[inputs]: Point the util-linux label at util-linux:out and add util-linux:lib as a separate input. --- gnu/packages/nfs.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/gnu/packages/nfs.scm b/gnu/packages/nfs.scm index ba50ca5e01..8370107939 100644 --- a/gnu/packages/nfs.scm +++ b/gnu/packages/nfs.scm @@ -117,10 +117,11 @@ `(("keyutils" ,keyutils) ("libevent" ,libevent) ("libnfsidmap" ,libnfsidmap) - ("rpcsvc-proto" ,rpcsvc-proto) ;for 'rpcgen' + ("rpcsvc-proto" ,rpcsvc-proto) ;for 'rpcgen' ("sqlite" ,sqlite) ("lvm2" ,lvm2) - ("util-linux" ,util-linux "lib") + ("util-linux" ,util-linux) ; only for above substitutions + ("util-linux:lib" ,util-linux "lib") ; for libblkid ("mit-krb5" ,mit-krb5) ("libtirpc" ,libtirpc) ("python-wrapper" ,python-wrapper))) ;for the Python based tools -- cgit v1.2.3 From 77667e2e6307851637f3b7e1373feb778da1e46f Mon Sep 17 00:00:00 2001 From: Christopher Baines Date: Thu, 10 Dec 2020 19:57:16 +0000 Subject: gnu: guile-prometheus: Update to 0-5.35dc26c. * gnu/packages/guile-xyz.scm (guile-prometheus): Update to 0-5.35dc26c. --- gnu/packages/guile-xyz.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/guile-xyz.scm b/gnu/packages/guile-xyz.scm index bd12b7b240..edee85f527 100644 --- a/gnu/packages/guile-xyz.scm +++ b/gnu/packages/guile-xyz.scm @@ -886,8 +886,8 @@ Vicare Scheme and IronScheme. Right now it contains: (license license:bsd-3))) (define-public guile-prometheus - (let ((commit "f661edf72d2dd711dffe4313c2a9360e79b36dd1") - (revision "4")) + (let ((commit "35dc26c0ea44c3d70f1819f240d84e2cbb4b7b4c") + (revision "5")) (package (name "guile-prometheus") (version (git-version "0" revision commit)) @@ -898,7 +898,7 @@ Vicare Scheme and IronScheme. Right now it contains: (commit commit))) (sha256 (base32 - "1556rv3b72wxba7yz4nn681k2l8fp70dwx32whyyxg755ma4r76f")) + "07822jj4appw37lf444kc4xlgl7nm64mgldag56072l55kwashgb")) (file-name (string-append name "-" version "-checkout")))) (build-system gnu-build-system) (native-inputs -- cgit v1.2.3 From 73817f711baf5c26f10690b6df4d802b3434f70d Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Tue, 8 Dec 2020 00:56:24 +0100 Subject: gnu: qoauth: Fix wrong URL in comment. * gnu/packages/web.scm (qoauth)[arguments]: Adjust comment. --- gnu/packages/web.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm index 6be6011c4e..82d5df3a75 100644 --- a/gnu/packages/web.scm +++ b/gnu/packages/web.scm @@ -1082,7 +1082,7 @@ instances, while JSON's objects will be mapped to @code{QVariantMap}.") (lambda* (#:key outputs #:allow-other-keys) (substitute* "src/src.pro" ;; Do not attempt to install the .prf file into qtbase - ;; "lib/mkspecs/features", ref . + ;; "lib/qt5/mkspecs/features", ref . (("\\$\\$\\[QMAKE_MKSPECS\\]") (string-append (assoc-ref outputs "out") "/lib/qt5/mkspecs"))) #t)) -- cgit v1.2.3 From d677f3d6231d352fdb65b70f67d85fb5744e912c Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Thu, 10 Dec 2020 23:42:48 +0100 Subject: etc: Add more SELinux permissions for the daemon. * etc/guix-daemon.cil.in (guix_daemon): Permit file write, getattr, link and unlink for the guix_daemon_exec_t type. --- etc/guix-daemon.cil.in | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/etc/guix-daemon.cil.in b/etc/guix-daemon.cil.in index cc8999d9a8..4f52157354 100644 --- a/etc/guix-daemon.cil.in +++ b/etc/guix-daemon.cil.in @@ -167,7 +167,9 @@ (process (fork execmem setrlimit setpgid setsched))) (allow guix_daemon_t guix_daemon_exec_t - (file (execute execute_no_trans read open entrypoint map))) + (file (execute + execute_no_trans read write open entrypoint map + getattr link unlink))) ;; TODO: unknown (allow guix_daemon_t -- cgit v1.2.3 From e530fb41287f8d048643c74fb349bd602abbf3e5 Mon Sep 17 00:00:00 2001 From: Mark Meyer Date: Fri, 15 Dec 2017 12:35:38 +0100 Subject: gnu: Add virtaal. * gnu/packages/text-editors.scm (virtaal): New variable. Signed-off-by: Arun Isaac --- gnu/packages/text-editors.scm | 41 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 41 insertions(+) diff --git a/gnu/packages/text-editors.scm b/gnu/packages/text-editors.scm index 878cbb669d..749b93e29f 100644 --- a/gnu/packages/text-editors.scm +++ b/gnu/packages/text-editors.scm @@ -11,6 +11,7 @@ ;;; Copyright © 2019, 2020 Nicolas Goaziou ;;; Copyright © 2020 Marius Bakke ;;; Copyright © 2020 Tom Zander +;;; Copyright © 2020 Mark Meyer ;;; ;;; This file is part of GNU Guix. ;;; @@ -62,6 +63,7 @@ #:use-module (gnu packages perl) #:use-module (gnu packages pkg-config) #:use-module (gnu packages python) + #:use-module (gnu packages python-web) #:use-module (gnu packages python-xyz) #:use-module (gnu packages qt) #:use-module (gnu packages regex) @@ -1029,3 +1031,42 @@ files. It was originally developed on the Amiga 3000T.") systems that displays its buffer(s) as a hex dump. The user interface is kept similar to vi/ex.") (license license:bsd-3))) + +(define-public virtaal + (package + (name "virtaal") + (version "0.7.1") + (source (origin + (method url-fetch) + (uri (string-append "mirror://sourceforge/translate/Virtaal/" + version "/virtaal-" version ".tar.bz2")) + (sha256 + (base32 + "0cyimjp3191qlmw6n0ipqdr9xr0cq4f6dqvz4rl9q31h6l3kywf9")))) + (build-system python-build-system) + (arguments + `(#:python ,python-2 + #:use-setuptools? #f + #:tests? #f ;; Failing tests + #:phases + (modify-phases %standard-phases + (add-before 'build 'configure + (lambda* (#:key outputs #:allow-other-keys) + ;; Set data file path to absolute store path. + (substitute* "virtaal/common/pan_app.py" + (("file_discovery\\.get_abs_data_filename.*") + (string-append "os.path.join('" + (assoc-ref outputs "out") + "/share', *path_parts)")))))))) + (inputs + `(("python2-lxml" ,python2-lxml) + ("python2-pygtk" ,python2-pygtk) + ("python2-simplejson" ,python2-simplejson) + ("python2-translate-toolkit" ,python2-translate-toolkit) + ("python2-pycurl" ,python2-pycurl))) + (synopsis "Graphical translation tool") + (description "Virtaal is a powerful yet simple translation tool with an +uncluttered user interface. It supports a multitude of translation formats +provided by the Translate Toolkit, including XLIFF and PO.") + (home-page "https://virtaal.translatehouse.org/") + (license license:gpl2+))) -- cgit v1.2.3 From f3bfeef5406ee39834f97f3f9555a1da68fa460c Mon Sep 17 00:00:00 2001 From: Nicolò Balzarotti Date: Fri, 1 Mar 2019 09:07:51 +0100 Subject: gnu: Add emacs-smart-hungry-delete. * gnu/packages/emacs-xyz.scm (emacs-smart-hungry-delete): New variable. Signed-off-by: Arun Isaac --- gnu/packages/emacs-xyz.scm | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 33b21f7fe3..24cd0173ce 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -25814,3 +25814,26 @@ anymore. In this way, it's like a lightweight \"workspace\" manager, allowing you to easily restore one or more frames, including their windows, the windows' layout, and their buffers.") (license license:gpl3+))) + +(define-public emacs-smart-hungry-delete + (let ((commit "7c1d56a92481594e14d40b5fdf6c48657a0108a0")) + (package + (name "emacs-smart-hungry-delete") + (version "0.1") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/hrehfeld/emacs-smart-hungry-delete") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0mxaslx5823s68a8ggbbnmfk1jiswjvip5s4sg7ihfagnci72wni")))) + (build-system emacs-build-system) + (home-page "https://github.com/hrehfeld/emacs-smart-hungry-delete") + (synopsis "Smart hungry deletion of whitespace") + (description "@code{emacs-smart-hungry-delete} hungrily deletes whitespace +between cursor and next word, parenthesis or delimiter while honoring some +rules about where space should be left to separate words and parentheses.") + (license license:gpl2+)))) -- cgit v1.2.3 From 72e3614666b8ffb7ecc568cbf4ba18874b9d8750 Mon Sep 17 00:00:00 2001 From: Kyle Meyer Date: Thu, 10 Dec 2020 23:56:45 +0000 Subject: gnu: emacs-elpher: Mention gemini in synopsis and description. * gnu/packages/emacs-xyz.scm (emacs-elpher)[synopsis, description]: Mention gemini support to help those searching for gemini clients. Signed-off-by: Arun Isaac --- gnu/packages/emacs-xyz.scm | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 24cd0173ce..1f6deb75e4 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -22702,10 +22702,10 @@ it forcibly (lambda _ (invoke "makeinfo" "elpher.texi")))))) (home-page "gopher://thelambdalab.xyz/1/projects/elpher/") - (synopsis "Gopher client for Emacs") - (description "Elpher is a full-featured gopher client for Emacs. Its -features include intuitive keyboard and mouse-driven browsing, out-of-the-box -compatibility with evil-mode, clickable web and gopher links in plain text, + (synopsis "Gopher and gemini client for Emacs") + (description "Elpher is a full-featured gopher and gemini client for +Emacs. Its features include intuitive keyboard and mouse-driven browsing, +out-of-the-box compatibility with evil-mode, clickable links in plain text, caching of visited sites, pleasant and configurable visualization of Gopher directories, direct visualisation of image files, jumping directly to links by name (with autocompletion), a simple bookmark management system and -- cgit v1.2.3 From f765577dec0340d035021d030f17b54a3a5fd6b1 Mon Sep 17 00:00:00 2001 From: Brett Gilio Date: Sat, 10 Nov 2018 15:04:51 -0600 Subject: gnu: Add emacs-webpaste. * gnu/packages/emacs-xyz.com (emacs-webpaste): New variable. Signed-off-by: Arun Isaac --- gnu/packages/emacs-xyz.scm | 41 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 41 insertions(+) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 1f6deb75e4..2318027c58 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -25837,3 +25837,44 @@ windows' layout, and their buffers.") between cursor and next word, parenthesis or delimiter while honoring some rules about where space should be left to separate words and parentheses.") (license license:gpl2+)))) + +(define-public emacs-webpaste + (package + (name "emacs-webpaste") + (version "3.2.0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/etu/webpaste.el") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "08545ihkzflw80rwklnxiswrpdrl8kr74xzxm5wsgrf36fkj9rn2")))) + (build-system emacs-build-system) + (arguments + `(#:tests? #t + #:test-command '("make" "unit" "integration") + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'fix-tests + (lambda _ + ;; Do not use cask to run tests. + (substitute* "Makefile" + (("\\$\\{CASK\\} exec ") "")) + ;; Disable tests that need network access. + (substitute* (list "tests/unit/test-webpaste-provider-creation.el" + "tests/integration/test-webpaste-providers.el") + (("describe") "xdescribe"))))))) + (native-inputs + `(("emacs-buttercup" ,emacs-buttercup))) + (propagated-inputs + `(("emacs-request" ,emacs-request))) + (home-page "https://github.com/etu/webpaste.el") + (synopsis "Paste to pastebin-like services") + (description "This mode allows to paste whole buffers or parts of buffers +to pastebin-like services. It supports more than one service and will +failover if one service fails. More services can easily be added over time +and prefered services can easily be configured.") + (license license:gpl3+))) -- cgit v1.2.3 From 8f330aebee504269d4d7188daa85e95503f71888 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Fri, 11 Dec 2020 12:04:15 +0200 Subject: gnu: busybox: Update to 1.32.0. * gnu/packages/busybox.scm (busybox): Update to 1.32.0. [source]: Remove patch. * gnu/packates/patches/busybox-1.31.1-fix-build-with-glibc-2.31.patch: Remove file. * gnu/local.mk (dist_patch_DATA): Remove it. --- gnu/local.mk | 1 - gnu/packages/busybox.scm | 11 ++-- .../busybox-1.31.1-fix-build-with-glibc-2.31.patch | 68 ---------------------- 3 files changed, 4 insertions(+), 76 deletions(-) delete mode 100644 gnu/packages/patches/busybox-1.31.1-fix-build-with-glibc-2.31.patch diff --git a/gnu/local.mk b/gnu/local.mk index 67482b8226..b32ebf4e3b 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -857,7 +857,6 @@ dist_patch_DATA = \ %D%/packages/patches/blender-2.79-python-3.7-fix.patch \ %D%/packages/patches/blender-2.79-python-3.8-fix.patch \ %D%/packages/patches/bpftrace-disable-bfd-disasm.patch \ - %D%/packages/patches/busybox-1.31.1-fix-build-with-glibc-2.31.patch \ %D%/packages/patches/byobu-writable-status.patch \ %D%/packages/patches/calibre-no-updates-dialog.patch \ %D%/packages/patches/calibre-remove-test-sqlite.patch \ diff --git a/gnu/packages/busybox.scm b/gnu/packages/busybox.scm index 0a93c6475e..c931a2f2f7 100644 --- a/gnu/packages/busybox.scm +++ b/gnu/packages/busybox.scm @@ -1,6 +1,6 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2014 John Darrington -;;; Copyright © 2016, 2017, 2018, 2019 Efraim Flashner +;;; Copyright © 2016, 2017, 2018, 2019, 2020 Efraim Flashner ;;; Copyright © 2018, 2019, 2020 Tobias Geerinckx-Rice ;;; ;;; This file is part of GNU Guix. @@ -32,7 +32,7 @@ (define-public busybox (package (name "busybox") - (version "1.31.1") + (version "1.32.0") (source (origin (method url-fetch) (uri (string-append @@ -40,10 +40,7 @@ version ".tar.bz2")) (sha256 (base32 - "1659aabzp8w4hayr4z8kcpbk2z1q2wqhw7i1yb0l72b45ykl1yfh")) - (patches - (search-patches - "busybox-1.31.1-fix-build-with-glibc-2.31.patch")))) + "12g63zsvzfz04wbyga8riyl8ils05riw4xf26cyiaasbs3qqfpf3")))) (build-system gnu-build-system) (arguments '(#:phases @@ -90,7 +87,7 @@ ;; true in guix build environment (substitute* "testsuite/pidof.tests" (("-s init") "-s $(cat /proc/1/comm)")) - + ;; This test cannot possibly pass. ;; It is trying to test that "which ls" returns "/bin/ls" when PATH is not set. ;; However, this relies on /bin/ls existing. Which it does not in guix. diff --git a/gnu/packages/patches/busybox-1.31.1-fix-build-with-glibc-2.31.patch b/gnu/packages/patches/busybox-1.31.1-fix-build-with-glibc-2.31.patch deleted file mode 100644 index 1518df067f..0000000000 --- a/gnu/packages/patches/busybox-1.31.1-fix-build-with-glibc-2.31.patch +++ /dev/null @@ -1,68 +0,0 @@ -See: https://bugs.gentoo.org/708350 -Author: Patrick McLean -Date: 2020-02-06 23:06:22 +0000 -diff --git a/coreutils/date.c b/coreutils/date.c -index 3414d38ae..4ade6abb4 100644 ---- a/coreutils/date.c -+++ b/coreutils/date.c -@@ -279,6 +279,9 @@ int date_main(int argc UNUSED_PARAM, char **argv) - time(&ts.tv_sec); - #endif - } -+#if !ENABLE_FEATURE_DATE_NANO -+ ts.tv_nsec = 0; -+#endif - localtime_r(&ts.tv_sec, &tm_time); - - /* If date string is given, update tm_time, and maybe set date */ -@@ -301,9 +304,10 @@ int date_main(int argc UNUSED_PARAM, char **argv) - if (date_str[0] != '@') - tm_time.tm_isdst = -1; - ts.tv_sec = validate_tm_time(date_str, &tm_time); -+ ts.tv_nsec = 0; - - /* if setting time, set it */ -- if ((opt & OPT_SET) && stime(&ts.tv_sec) < 0) { -+ if ((opt & OPT_SET) && clock_settime(CLOCK_REALTIME, &ts) < 0) { - bb_perror_msg("can't set date"); - } - } -diff --git a/libbb/missing_syscalls.c b/libbb/missing_syscalls.c -index 87cf59b3d..dc40d9155 100644 ---- a/libbb/missing_syscalls.c -+++ b/libbb/missing_syscalls.c -@@ -15,14 +15,6 @@ pid_t getsid(pid_t pid) - return syscall(__NR_getsid, pid); - } - --int stime(const time_t *t) --{ -- struct timeval tv; -- tv.tv_sec = *t; -- tv.tv_usec = 0; -- return settimeofday(&tv, NULL); --} -- - int sethostname(const char *name, size_t len) - { - return syscall(__NR_sethostname, name, len); -diff --git a/util-linux/rdate.c b/util-linux/rdate.c -index 70f829e7f..878375d78 100644 ---- a/util-linux/rdate.c -+++ b/util-linux/rdate.c -@@ -95,9 +95,13 @@ int rdate_main(int argc UNUSED_PARAM, char **argv) - if (!(flags & 2)) { /* no -p (-s may be present) */ - if (time(NULL) == remote_time) - bb_error_msg("current time matches remote time"); -- else -- if (stime(&remote_time) < 0) -+ else { -+ struct timespec ts; -+ ts.tv_sec = remote_time; -+ ts.tv_nsec = 0; -+ if (clock_settime(CLOCK_REALTIME, &ts) < 0) - bb_perror_msg_and_die("can't set time of day"); -+ } - } - - if (flags != 1) /* not lone -s */ -- cgit v1.2.3 From f769ad12f1b7834a5fb6c870a6737d2eea495744 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Fri, 11 Dec 2020 12:17:51 +0200 Subject: gnu: toybox: Cross compile. * gnu/packages/busybox.scm (toybox)[arguments]: Use cc-for-target. --- gnu/packages/busybox.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/gnu/packages/busybox.scm b/gnu/packages/busybox.scm index c931a2f2f7..7fc065f7ac 100644 --- a/gnu/packages/busybox.scm +++ b/gnu/packages/busybox.scm @@ -22,6 +22,7 @@ #:use-module (guix licenses) #:use-module (guix packages) #:use-module (guix download) + #:use-module (guix utils) #:use-module (guix build-system gnu) #:use-module (gnu packages) #:use-module (gnu packages admin) @@ -132,11 +133,11 @@ any small or embedded system.") "00aw9d809wj1bqlb2fsssdgz7rj0363ya14py0gfdm0rkp98zcpa")))) (build-system gnu-build-system) (arguments - '(#:phases + `(#:phases (modify-phases %standard-phases (add-before 'configure 'set-environment-variables (lambda _ - (setenv "CC" (which "gcc")) + (setenv "CC" ,(cc-for-target)) (setenv "HOSTCC" (which "gcc")) #t)) (replace 'configure -- cgit v1.2.3 From 2639a99cf31e3ce2970645badf11f15679c893b5 Mon Sep 17 00:00:00 2001 From: Zhu Zihao Date: Tue, 8 Dec 2020 21:44:38 +0800 Subject: gnu: fcitx5-lua: Remove stale build steps. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/fcitx5.scm (fcitx-lua)[arguments]: Remove it. Signed-off-by: 宋文武 --- gnu/packages/fcitx5.scm | 19 ------------------- 1 file changed, 19 deletions(-) diff --git a/gnu/packages/fcitx5.scm b/gnu/packages/fcitx5.scm index 89de7b4dcf..431aeceb02 100644 --- a/gnu/packages/fcitx5.scm +++ b/gnu/packages/fcitx5.scm @@ -156,25 +156,6 @@ client.") (sha256 (base32 "177mj56j8yrl79hvk7bbrifvm137np23pwalv83ibgk4l51z92hf")))) (build-system cmake-build-system) - (arguments - `(#:configure-flags - (list - (string-append "-DFEM_INCLUDE_INSTALL_DIR=" %output "/include") - (string-append "-DFEM_LIB_INSTALL_DIR=" %output "/lib")) - #:phases - (modify-phases %standard-phases - (add-before 'configure 'patch-install-prefix - (lambda* (#:key outputs #:allow-other-keys) - (for-each - (lambda (x) - (format #t "patch-install-prefix: Fixing install prefix in ~a~%" - x) - (substitute* x - (("\\$\\{FCITX_INSTALL_PKGDATADIR\\}") - (string-append (assoc-ref outputs "out") - "/share/fcitx5")))) - '("src/addonloader/CMakeLists.txt" - "src/imeapi/CMakeLists.txt"))))))) (inputs `(("fcitx5" ,fcitx5) ("lua" ,lua) -- cgit v1.2.3 From 91e35e32a4938e0e37499c64fa8ed3e7cf51dce3 Mon Sep 17 00:00:00 2001 From: Zhu Zihao Date: Tue, 8 Dec 2020 21:45:56 +0800 Subject: gnu: fcitx5-chinese-addons: Remove stale build steps. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/fcitx5.scm (fcitx5-chinese-addons)[arguments] : Remove it. : Remove phase 'patch-install-prefix'. Signed-off-by: 宋文武 --- gnu/packages/fcitx5.scm | 17 +---------------- 1 file changed, 1 insertion(+), 16 deletions(-) diff --git a/gnu/packages/fcitx5.scm b/gnu/packages/fcitx5.scm index 431aeceb02..ed0d928fc7 100644 --- a/gnu/packages/fcitx5.scm +++ b/gnu/packages/fcitx5.scm @@ -293,23 +293,8 @@ for Qt based application.") (base32 "0mf91gzwzhfci0jn6g3l516xjw8r4v40ginnbl70h1zx6vr24rfp")))) (build-system cmake-build-system) (arguments - `(#:configure-flags - (list - (string-append "-DFEM_INCLUDE_INSTALL_DIR=" %output "/include") - (string-append "-DFEM_LIB_INSTALL_DIR=" %output "/lib")) - #:phases + `(#:phases (modify-phases %standard-phases - (add-before 'configure 'patch-install-prefix - (lambda* (#:key outputs #:allow-other-keys) - (for-each - (lambda (x) - (format #t "patch-install-prefix: Fixing install prefix in ~a~%" - x) - (substitute* x - (("\\$\\{FCITX_INSTALL_PKGDATADIR\\}") - (string-append (assoc-ref outputs "out") - "/share/fcitx5")))) - (find-files "." "CMakeLists\\.txt$")))) (add-before 'configure 'split-outputs ;; Build with GUI supports requires Qt and increase package closure ;; by 800M on x86_64, so place it under another output. -- cgit v1.2.3 From edc2acb7796a9f1c6d3a6caea54bad3a17cd988b Mon Sep 17 00:00:00 2001 From: Mathieu Othacehe Date: Fri, 11 Dec 2020 17:52:36 +0100 Subject: gnu: guile-simple-zmq: Update to 0.0.0-5.f8b7d81. * gnu/packages/guile-xyz.scm (guile-simple-zmq): Update to 0.0.0-5.f8b7d81. --- gnu/packages/guile-xyz.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/guile-xyz.scm b/gnu/packages/guile-xyz.scm index edee85f527..a844ab7b08 100644 --- a/gnu/packages/guile-xyz.scm +++ b/gnu/packages/guile-xyz.scm @@ -966,8 +966,8 @@ convenient nested tree operations.") (license license:gpl3+))) (define-public guile-simple-zmq - (let ((commit "5fc3b7190d31c258ce969c2a5d2ad38c66a09d09") - (revision "4")) + (let ((commit "f8b7d81afb38525750f8818ed2956ca18c828ee8") + (revision "5")) (package (name "guile-simple-zmq") (version (git-version "0.0.0" revision commit)) @@ -979,7 +979,7 @@ convenient nested tree operations.") (commit commit))) (sha256 (base32 - "0inhvl5jssvbw3nd129wdahfwyvy1iciq403wzf0algbvl1fqs7z")) + "1gpzlpcq7bxw7sxyrg8zslwb3631vizw56lgg1aavw4gafh0hxb3")) (file-name (git-file-name name version)))) (build-system guile-build-system) (arguments -- cgit v1.2.3 From dbdae9f96f11a006993b659e0e7fd5cbf467f844 Mon Sep 17 00:00:00 2001 From: Ludovic Courtès Date: Fri, 11 Dec 2020 16:24:53 +0100 Subject: maint: Avoid macros obsolete in Autoconf 2.70. * configure.ac: Require Autoconf 2.69. Use 'AS_HELP_STRING' instead of 'AC_HELP_STRING'. * m4/guix.m4: Likewise. * config-daemon.ac: Use 'AC_CONFIG_HEADERS' instead of the singular variant. --- config-daemon.ac | 2 +- configure.ac | 12 ++++++------ m4/guix.m4 | 4 ++-- 3 files changed, 9 insertions(+), 9 deletions(-) diff --git a/config-daemon.ac b/config-daemon.ac index 50ead355a8..19958d331b 100644 --- a/config-daemon.ac +++ b/config-daemon.ac @@ -13,7 +13,7 @@ if test "x$guix_build_daemon" = "xyes"; then GUIX_ASSERT_CXX11 AC_PROG_RANLIB - AC_CONFIG_HEADER([nix/config.h]) + AC_CONFIG_HEADERS([nix/config.h]) dnl Use 64-bit file system calls so that we can support files > 2 GiB. AC_SYS_LARGEFILE diff --git a/configure.ac b/configure.ac index 942e84164a..a5bdf24e93 100644 --- a/configure.ac +++ b/configure.ac @@ -1,7 +1,7 @@ # -*- Autoconf -*- # Process this file with autoconf to produce a configure script. -AC_PREREQ(2.68) +AC_PREREQ([2.69]) AC_INIT([GNU Guix], [m4_esyscmd([build-aux/git-version-gen .tarball-version])], [bug-guix@gnu.org], [guix], @@ -29,35 +29,35 @@ GUIX_ASSERT_SUPPORTED_SYSTEM AM_CONDITIONAL([CROSS_COMPILING], [test "x$cross_compiling" = "xyes"]) AC_ARG_WITH(store-dir, - AC_HELP_STRING([--with-store-dir=PATH], + AS_HELP_STRING([--with-store-dir=PATH], [file name of the store (defaults to /gnu/store)]), [storedir="$withval"], [storedir="/gnu/store"]) AC_SUBST(storedir) AC_ARG_WITH([bash-completion-dir], - AC_HELP_STRING([--with-bash-completion-dir=DIR], + AS_HELP_STRING([--with-bash-completion-dir=DIR], [name of the Bash completion directory]), [bashcompletiondir="$withval"], [bashcompletiondir='${sysconfdir}/bash_completion.d']) AC_SUBST([bashcompletiondir]) AC_ARG_WITH([zsh-completion-dir], - AC_HELP_STRING([--with-zsh-completion-dir=DIR], + AS_HELP_STRING([--with-zsh-completion-dir=DIR], [name of the Zsh completion directory]), [zshcompletiondir="$withval"], [zshcompletiondir='${datadir}/zsh/site-functions']) AC_SUBST([zshcompletiondir]) AC_ARG_WITH([fish-completion-dir], - AC_HELP_STRING([--with-fish-completion-dir=DIR], + AS_HELP_STRING([--with-fish-completion-dir=DIR], [name of the Fish completion directory]), [fishcompletiondir="$withval"], [fishcompletiondir='${datadir}/fish/vendor_completions.d']) AC_SUBST([fishcompletiondir]) AC_ARG_WITH([selinux-policy-dir], - AC_HELP_STRING([--with-selinux-policy-dir=DIR], + AS_HELP_STRING([--with-selinux-policy-dir=DIR], [name of the SELinux policy directory]), [selinux_policydir="$withval"], [selinux_policydir='${datadir}/selinux/']) diff --git a/m4/guix.m4 b/m4/guix.m4 index 4fa7cdf737..f8eb5aaf51 100644 --- a/m4/guix.m4 +++ b/m4/guix.m4 @@ -26,7 +26,7 @@ AC_DEFUN([GUIX_SYSTEM_TYPE], [ AC_REQUIRE([AC_CANONICAL_HOST]) AC_PATH_PROG([SED], [sed]) - AC_ARG_WITH(system, AC_HELP_STRING([--with-system=SYSTEM], + AC_ARG_WITH(system, AS_HELP_STRING([--with-system=SYSTEM], [Platform identifier (e.g., `i686-linux').]), [guix_system="$withval"], [case "$host_cpu" in @@ -78,7 +78,7 @@ dnl Assert that this is a system to which the distro is ported. AC_DEFUN([GUIX_ASSERT_SUPPORTED_SYSTEM], [ AC_REQUIRE([GUIX_SYSTEM_TYPE]) - AC_ARG_WITH([courage], [AC_HELP_STRING([--with-courage], + AC_ARG_WITH([courage], [AS_HELP_STRING([--with-courage], [Assert that even if this platform is unsupported, you will be courageous and port the GNU System distribution to it (see "GNU Distribution" in the manual.)])], -- cgit v1.2.3 From 26b1030012837ff3f91d2a39971358180324d730 Mon Sep 17 00:00:00 2001 From: Ludovic Courtès Date: Fri, 11 Dec 2020 16:26:50 +0100 Subject: maint: Remove unused 'NIX_VERSION' macro. * config-daemon.ac: Do not define NIX_VERSION. --- config-daemon.ac | 1 - 1 file changed, 1 deletion(-) diff --git a/config-daemon.ac b/config-daemon.ac index 19958d331b..85caee269b 100644 --- a/config-daemon.ac +++ b/config-daemon.ac @@ -34,7 +34,6 @@ if test "x$guix_build_daemon" = "xyes"; then dnl Look for SQLite, a required dependency. PKG_CHECK_MODULES([SQLITE3], [sqlite3 >= 3.6.19]) - AC_DEFINE([NIX_VERSION], ["0.0.0"], [Fake Nix version number.]) AC_DEFINE_UNQUOTED([SYSTEM], ["$guix_system"], [Guix host system type--i.e., platform and OS kernel tuple.]) -- cgit v1.2.3 From d8051557aee9fa252b015ff67cc15681e8540777 Mon Sep 17 00:00:00 2001 From: Ludovic Courtès Date: Fri, 11 Dec 2020 17:26:03 +0100 Subject: Revert "services: openssh: Warn about 'password-authentication?' default." This reverts commit aecd2a13cbd8301d0fdeafcacbf69e12cc3f6138 for two reasons: 1. The warning would fire every time (gnu services ssh) is loaded; 2. There's still no clear consensus on the approach to follow as discussed in . --- gnu/installer/services.scm | 8 ++------ gnu/services/ssh.scm | 18 ++---------------- 2 files changed, 4 insertions(+), 22 deletions(-) diff --git a/gnu/installer/services.scm b/gnu/installer/services.scm index 14a3bb9be6..ec5ea30594 100644 --- a/gnu/installer/services.scm +++ b/gnu/installer/services.scm @@ -1,6 +1,6 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2018 Mathieu Othacehe -;;; Copyright © 2019, 2020 Ludovic Courtès +;;; Copyright © 2019 Ludovic Courtès ;;; Copyright © 2020 Jan (janneke) Nieuwenhuizen ;;; ;;; This file is part of GNU Guix. @@ -93,11 +93,7 @@ (system-service (name (G_ "OpenSSH secure shell daemon (sshd)")) (type 'networking) - (snippet '((service openssh-service-type - (openssh-configuration - ;; Currently the default is #t but it's considered - ;; unsafe. Explicitly pass #f. - (password-authentication? #f)))))) + (snippet '((service openssh-service-type)))) (system-service (name (G_ "Tor anonymous network router")) (type 'networking) diff --git a/gnu/services/ssh.scm b/gnu/services/ssh.scm index 1e45495e1b..1891db0487 100644 --- a/gnu/services/ssh.scm +++ b/gnu/services/ssh.scm @@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2014, 2015, 2016, 2017, 2018, 2019, 2020 Ludovic Courtès +;;; Copyright © 2014, 2015, 2016, 2017, 2018, 2019 Ludovic Courtès ;;; Copyright © 2016 David Craven ;;; Copyright © 2016 Julien Lepiller ;;; Copyright © 2017 Clément Lassieur @@ -33,9 +33,6 @@ #:use-module (guix gexp) #:use-module (guix records) #:use-module (guix modules) - #:use-module ((guix i18n) #:select (G_)) - #:use-module ((guix diagnostics) #:select (warning source-properties->location)) - #:use-module ((guix memoization) #:select (mlambda)) #:use-module (srfi srfi-1) #:use-module (srfi srfi-26) #:use-module (ice-9 match) @@ -279,16 +276,6 @@ The other options should be self-descriptive." ;;; OpenSSH. ;;; -(define true-but-soon-false - (mlambda (loc) - ;; The plan is to change the default 'password-authentication?' to #f in - ;; Guix 1.3.0 or so. See . - (warning (source-properties->location loc) - (G_ "The default value of the 'password-authentication?' -field of 'openssh-configuration' will change from #true to #false in the -future. Explicitly set it to #true to allow password authentication.~%")) - #t)) - (define-record-type* openssh-configuration make-openssh-configuration openssh-configuration? @@ -309,8 +296,7 @@ future. Explicitly set it to #true to allow password authentication.~%")) (default #f)) ;; Boolean (password-authentication? openssh-configuration-password-authentication? - (default (true-but-soon-false - (current-source-location)))) + (default #t)) ;; Boolean (public-key-authentication? openssh-configuration-public-key-authentication? (default #t)) -- cgit v1.2.3 From fd247542215fbd10f28980f3d5255014b150e95a Mon Sep 17 00:00:00 2001 From: Ludovic Courtès Date: Mon, 7 Dec 2020 15:17:22 +0100 Subject: build: 'script/guix' uses our own 'guile' executable. * Makefile.am (do_subst): Substitute @abs_top_builddir@. * scripts/guix.in: Use it. --- Makefile.am | 1 + scripts/guix.in | 2 +- 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/Makefile.am b/Makefile.am index 1a3ca227a4..9803ba5dc7 100644 --- a/Makefile.am +++ b/Makefile.am @@ -39,6 +39,7 @@ do_subst = $(SED) \ -e 's,[@]GUILE[@],$(GUILE),g' \ -e 's,[@]guilemoduledir[@],$(guilemoduledir),g' \ -e 's,[@]guileobjectdir[@],$(guileobjectdir),g' \ + -e 's,[@]abs_top_builddir[@],$(abs_top_builddir),g' \ -e 's,[@]localedir[@],$(localedir),g' scripts/guix: scripts/guix.in Makefile diff --git a/scripts/guix.in b/scripts/guix.in index 0a3ab1f64d..e0194d6ea2 100644 --- a/scripts/guix.in +++ b/scripts/guix.in @@ -1,4 +1,4 @@ -#!@GUILE@ \ +#!@abs_top_builddir@/guile \ --no-auto-compile -e main -s !# ;;; GNU Guix --- Functional package management for GNU -- cgit v1.2.3 From 459f0d07a1b0f76802a8b7deec8488f5956bce86 Mon Sep 17 00:00:00 2001 From: Ludovic Courtès Date: Mon, 7 Dec 2020 15:18:20 +0100 Subject: self: Move Guile early in the module search path. Until now, Guile modules would first be searched for in MODULE-DIRECTORY, then in each $GUILE_LOAD_PATH entry, and finally in Guile itself. * guix/self.scm (guix-command): Make GUILE the second entry in the %LOAD-PATH and %LOAD-COMPILED-PATH. --- guix/self.scm | 23 ++++++++++++++--------- 1 file changed, 14 insertions(+), 9 deletions(-) diff --git a/guix/self.scm b/guix/self.scm index c0de14b79a..ca67f653fa 100644 --- a/guix/self.scm +++ b/guix/self.scm @@ -650,17 +650,22 @@ load path." (program-file "guix-command" #~(begin (set! %load-path - (cons (string-append #$module-directory - "/share/guile/site/" - (effective-version)) - %load-path)) + (append (list (string-append #$module-directory + "/share/guile/site/" + (effective-version)) + (string-append #$guile "/share/guile/" + (effective-version))) + %load-path)) (set! %load-compiled-path - (cons (string-append #$module-directory - "/lib/guile/" - (effective-version) - "/site-ccache") - %load-compiled-path)) + (append (list (string-append #$module-directory + "/lib/guile/" + (effective-version) + "/site-ccache") + (string-append #$guile "/lib/guile/" + (effective-version) + "/ccache")) + %load-compiled-path)) ;; To maximize the chances that locales are set up right ;; out-of-the-box, bundle "common" UTF-8 locales. -- cgit v1.2.3 From d20665ecbfe7278f550a1ed4cd76565013feab59 Mon Sep 17 00:00:00 2001 From: Ludovic Courtès Date: Mon, 7 Dec 2020 15:20:11 +0100 Subject: guix: 'guile' executable ignores GUILE_LOAD_PATH during startup. When starting the 'guix' command, this ensures Guile modules are immediately found instead of being search for in other directories. This reduces the number of 'stat' calls during startup when GUILE_LOAD_PATH is set to (almost) that of "env -i $(type -P guix)". * gnu/packages/aux-files/guile-launcher.c (load_path) (load_compiled_path): New variables. (inner_main): Restore GUILE_LOAD_PATH and GUILE_LOAD_COMPILED_PATH and set %load-path and %load-compiled-path accordingly. (main): Save GUILE_LOAD_PATH and GUILE_LOAD_COMPILED_PATH and unset them. --- gnu/packages/aux-files/guile-launcher.c | 46 +++++++++++++++++++++++++++++++-- 1 file changed, 44 insertions(+), 2 deletions(-) diff --git a/gnu/packages/aux-files/guile-launcher.c b/gnu/packages/aux-files/guile-launcher.c index 886ede2846..1dd5d77e66 100644 --- a/gnu/packages/aux-files/guile-launcher.c +++ b/gnu/packages/aux-files/guile-launcher.c @@ -1,5 +1,5 @@ /* GNU Guix --- Functional package management for GNU - Copyright 1996-1997,2000-2001,2006,2008,2011,2013,2018 + Copyright 1996-1997,2000-2001,2006,2008,2011,2013,2018,2020 Free Software Foundation, Inc. Copyright (C) 2020 Ludovic Courtès @@ -19,14 +19,47 @@ along with GNU Guix. If not, see . */ /* This file implements a variant of the 'guile' executable that does not - complain about locale issues. */ + complain about locale issues and arranges to reduce startup time by + ignoring GUILE_LOAD_PATH and GUILE_LOAD_COMPILED_PATH until it has + booted. */ +#include +#include #include #include +/* Saved values of GUILE_LOAD_PATH and GUILE_LOAD_COMPILED_PATH. */ +static const char *load_path, *load_compiled_path; + static void inner_main (void *unused, int argc, char **argv) { + if (load_path != NULL) + { + setenv ("GUILE_LOAD_PATH", load_path, 1); + SCM load_path_var = + scm_c_public_lookup ("guile", "%load-path"); + SCM addition = + scm_parse_path (scm_from_locale_string (load_path), SCM_EOL); + scm_variable_set_x (load_path_var, + scm_append + (scm_list_2 (scm_variable_ref (load_path_var), + addition))); + } + + if (load_compiled_path != NULL) + { + setenv ("GUILE_LOAD_COMPILED_PATH", load_compiled_path, 1); + SCM load_compiled_path_var = + scm_c_public_lookup ("guile", "%load-compiled-path"); + SCM addition = + scm_parse_path (scm_from_locale_string (load_compiled_path), SCM_EOL); + scm_variable_set_x (load_compiled_path_var, + scm_append + (scm_list_2 (scm_variable_ref (load_compiled_path_var), + addition))); + } + scm_shell (argc, argv); } @@ -40,6 +73,15 @@ main (int argc, char **argv) which is always preferable over the C locale. */ setlocale (LC_ALL, "en_US.utf8"); + const char *str; + str = getenv ("GUILE_LOAD_PATH"); + load_path = str != NULL ? strdup (str) : NULL; + str = getenv ("GUILE_LOAD_COMPILED_PATH"); + load_compiled_path = str ? strdup (str) : NULL; + + unsetenv ("GUILE_LOAD_PATH"); + unsetenv ("GUILE_LOAD_COMPILED_PATH"); + scm_install_gmp_memory_functions = 1; scm_boot_guile (argc, argv, inner_main, 0); return 0; /* never reached */ -- cgit v1.2.3 From 41d01b4e2e74a3e655bac03c241f0de7cb34b75f Mon Sep 17 00:00:00 2001 From: Ludovic Courtès Date: Mon, 7 Dec 2020 16:01:36 +0100 Subject: self: Remove the empty string from '%load-extensions'. * guix/self.scm (guix-command): Set '%load-extensions'. --- guix/self.scm | 3 +++ 1 file changed, 3 insertions(+) diff --git a/guix/self.scm b/guix/self.scm index ca67f653fa..7cda6656c9 100644 --- a/guix/self.scm +++ b/guix/self.scm @@ -649,6 +649,9 @@ load path." (program-file "guix-command" #~(begin + ;; Remove the empty extension from the search path. + (set! %load-extensions '(".scm")) + (set! %load-path (append (list (string-append #$module-directory "/share/guile/site/" -- cgit v1.2.3 From 382e0fee7f1cf982e33cf70d43e078e0b8572547 Mon Sep 17 00:00:00 2001 From: Zheng Junjie <873216071@qq.com> Date: Sun, 6 Dec 2020 21:36:11 +0800 Subject: gnu: Add hsetroot. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/xdisorg.scm (hsetroot): New variable. Co-authored-by: Ludovic Courtès --- gnu/packages/xdisorg.scm | 41 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 41 insertions(+) diff --git a/gnu/packages/xdisorg.scm b/gnu/packages/xdisorg.scm index 7c4148c87f..93f23d6722 100644 --- a/gnu/packages/xdisorg.scm +++ b/gnu/packages/xdisorg.scm @@ -42,6 +42,7 @@ ;;; Copyright © 2020 Gabriel Arazas ;;; Copyright © 2020 James Smith ;;; Copyright © 2020 B. Wilson +;;; Copyright © 2020 Zheng Junjie <873216071@qq.com> ;;; ;;; This file is part of GNU Guix. ;;; @@ -2618,3 +2619,43 @@ and execute @file{.desktop} files of the Application type.") "@command{sx} is a simple alternative to both @command{xinit} and @command{startx} for starting an Xorg server.") (license license:x11))) + +(define-public hsetroot + (package + (name "hsetroot") + (version "1.0.5") + (home-page "https://github.com/himdel/hsetroot") + (source (origin + (method git-fetch) + (file-name (git-file-name name version)) + (uri (git-reference + (url home-page) + (commit version))) + (sha256 + (base32 + "1jbk5hlxm48zmjzkaq5946s58rqwg1v1ds2sdyd2ba029hmvr722")))) + (build-system gnu-build-system) + (arguments + `(#:tests? #f + #:make-flags + (list + "CC=gcc" + (string-append "PREFIX=" (assoc-ref %outputs "out"))) + #:phases + (modify-phases %standard-phases + (delete 'configure) + (add-before 'install 'mkdir-install-path + (lambda* (#:key outputs #:allow-other-keys) + (let ((out (assoc-ref outputs "out"))) + (mkdir-p (string-append out "/bin")))))))) + (inputs + `(("libx11" ,libx11) + ("imlib2" ,imlib2) + ("libxinerama" ,libxinerama))) + (native-inputs + `(("pkg-config" ,pkg-config))) + (synopsis "Imlib2-based wallpaper changer") + (description + "The @command{hsetroot} command composes wallpapers for X. +This package is the fork of hsetroot by Hyriand.") + (license license:gpl2+))) -- cgit v1.2.3 From eee3af86c74bd9f90e8888ad7a0180dc609eaa9d Mon Sep 17 00:00:00 2001 From: Ryan Prior Date: Fri, 11 Dec 2020 03:59:02 +0000 Subject: gnu: esbuild: Update to 0.8.21. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/web.scm (esbuild): Update to 0.8.21. Signed-off-by: Ludovic Courtès --- gnu/packages/web.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm index 82d5df3a75..f26b114d1a 100644 --- a/gnu/packages/web.scm +++ b/gnu/packages/web.scm @@ -1485,7 +1485,7 @@ used to validate and fix HTML data.") (define-public esbuild (package (name "esbuild") - (version "0.8.19") + (version "0.8.21") (source (origin (method git-fetch) @@ -1494,7 +1494,7 @@ used to validate and fix HTML data.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "19y4g0wjkvrqzl4ngnlkb1giqjyx35gwz4zfk8pw4szsy85z6mli")) + (base32 "1gkh3ka7gfdqvzymj6vh9w2d0cp7n2vih42y7ghg7y8x6ry4c6mi")) (modules '((guix build utils))) (snippet '(begin -- cgit v1.2.3 From 4a084c7a7b8e64e4598fd7149b77c8b79d5b5c56 Mon Sep 17 00:00:00 2001 From: Guillaume Le Vaillant Date: Fri, 11 Dec 2020 16:37:29 +0100 Subject: gnu: Add simple-neural-network. * gnu/packages/lisp-xyz.scm (cl-simple-neural-network, ecl-simple-neural-network, sbcl-simple-neural-network): New variables. --- gnu/packages/lisp-xyz.scm | 41 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 41 insertions(+) diff --git a/gnu/packages/lisp-xyz.scm b/gnu/packages/lisp-xyz.scm index 6fd4ec5b2d..68adff3169 100644 --- a/gnu/packages/lisp-xyz.scm +++ b/gnu/packages/lisp-xyz.scm @@ -12405,3 +12405,44 @@ Service (S3) and CloudFront service from Common Lisp.") (define-public ecl-zs3 (sbcl-package->ecl-package sbcl-zs3)) + +(define-public sbcl-simple-neural-network + (package + (name "sbcl-simple-neural-network") + (version "3.1") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/glv2/simple-neural-network") + (commit (string-append "v" version)))) + (file-name (git-file-name "simple-neural-network" version)) + (sha256 + (base32 "1jj1c90fr5clwka0jv32hv6xp1bkdlpa6x5jh19an13rhx8ll4zr")))) + (build-system asdf-build-system/sbcl) + (native-inputs + `(("chipz" ,sbcl-chipz) + ("fiveam" ,sbcl-fiveam))) + (inputs + `(("cl-store" ,sbcl-cl-store) + ("lparallel" ,sbcl-lparallel))) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'check 'remove-test-data + (lambda* (#:key outputs #:allow-other-keys) + (let ((out (assoc-ref outputs "out"))) + (for-each delete-file (find-files out "\\.gz$")))))))) + (synopsis "Simple neural network in Common Lisp") + (description + "@code{simple-neural-network} is a Common Lisp library for creating, +training and using basic neural networks. The networks created by this +library are feedforward neural networks trained using backpropagation.") + (home-page "https://github.com/glv2/simple-neural-network") + (license license:gpl3+))) + +(define-public cl-simple-neural-network + (sbcl-package->cl-source-package sbcl-simple-neural-network)) + +(define-public ecl-simple-neural-network + (sbcl-package->ecl-package sbcl-simple-neural-network)) -- cgit v1.2.3 From 6e301c3a53270301bf2685f59b470a88b521105f Mon Sep 17 00:00:00 2001 From: Guillaume Le Vaillant Date: Fri, 11 Dec 2020 18:08:00 +0100 Subject: gnu: sbcl-geco: Update to 2.1.1. * gnu/packages/lisp-xyz.scm (sbcl-geco): Update to 2.1.1. [source]: Fetch from Github. [home-page]: Update to author's page. * gnu/packages/patches/sbcl-geco-fix-organism-class.patch: Remove file. * gnu/local.mk (dist_patch_DATA): Remove it. --- gnu/local.mk | 1 - gnu/packages/lisp-xyz.scm | 15 ++++++++------- gnu/packages/patches/sbcl-geco-fix-organism-class.patch | 13 ------------- 3 files changed, 8 insertions(+), 21 deletions(-) delete mode 100644 gnu/packages/patches/sbcl-geco-fix-organism-class.patch diff --git a/gnu/local.mk b/gnu/local.mk index b32ebf4e3b..f94725b1e5 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -1596,7 +1596,6 @@ dist_patch_DATA = \ %D%/packages/patches/rust-openssl-sys-no-vendor.patch \ %D%/packages/patches/rxvt-unicode-escape-sequences.patch \ %D%/packages/patches/sbcl-clml-fix-types.patch \ - %D%/packages/patches/sbcl-geco-fix-organism-class.patch \ %D%/packages/patches/scalapack-blacs-mpi-deprecations.patch \ %D%/packages/patches/scheme48-tests.patch \ %D%/packages/patches/scotch-build-parallelism.patch \ diff --git a/gnu/packages/lisp-xyz.scm b/gnu/packages/lisp-xyz.scm index 68adff3169..747617fdda 100644 --- a/gnu/packages/lisp-xyz.scm +++ b/gnu/packages/lisp-xyz.scm @@ -11234,17 +11234,18 @@ XML to Lisp structures or s-expressions and back.") (define-public sbcl-geco (package (name "sbcl-geco") - (version "2.01a") + (version "2.1.1") (source (origin - (method url-fetch) - (uri (string-append "https://common-lisp.net/project/geco/download/" - "geco-" version ".tar.gz")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/gpwwjr/GECO") + (commit (string-append "v" version)))) + (file-name (git-file-name "geco" version)) (sha256 - (base32 "0kk0bzr1019cfmf2b1jl1rk9shv3gx5z1znifxllg9mb98yqsgw0")) - (patches (search-patches "sbcl-geco-fix-organism-class.patch")))) + (base32 "1rc8a4mk40hjx5qy980hjylv6xxqdbq38hg8c4w30y93abfd519s")))) (build-system asdf-build-system/sbcl) - (home-page "https://common-lisp.net/project/geco/") + (home-page "http://hiwaay.net/~gpw/geco/geco.html") (synopsis "Genetic algorithm toolkit for Common Lisp") (description "GECO (Genetic Evolution through Combination of Objects) is an extensible, diff --git a/gnu/packages/patches/sbcl-geco-fix-organism-class.patch b/gnu/packages/patches/sbcl-geco-fix-organism-class.patch deleted file mode 100644 index 817596241e..0000000000 --- a/gnu/packages/patches/sbcl-geco-fix-organism-class.patch +++ /dev/null @@ -1,13 +0,0 @@ -Fix the ORGANISM class so that SBCL >= 2.0.9 can compile it without error. - ---- a/classes.lisp 2020-10-28 12:11:10.725659464 +0100 -+++ b/classes.lisp 2020-10-31 17:34:36.822752447 +0100 -@@ -148,7 +148,7 @@ - :accessor score - :initarg :score - :initform 'nil -- :type number) -+ :type (or number null)) - (NORMALIZED-SCORE - :accessor normalized-score - :initarg :normalized-score -- cgit v1.2.3 From 703cdbbd33cc7ae4b00f82fc2418317cdec4bd52 Mon Sep 17 00:00:00 2001 From: Adam Kandur Date: Wed, 2 Dec 2020 17:23:33 +0100 Subject: gnu: Add cl-autowrap. * gnu/packages/lisp-xyz.scm (cl-autowrap, ecl-cl-autowrap, sbcl-cl-autowrap): New variable. Signed-off-by: Guillaume Le Vaillant --- gnu/packages/lisp-xyz.scm | 35 +++++++++++++++++++++++++++++++++++ 1 file changed, 35 insertions(+) diff --git a/gnu/packages/lisp-xyz.scm b/gnu/packages/lisp-xyz.scm index 747617fdda..c8b5e84322 100644 --- a/gnu/packages/lisp-xyz.scm +++ b/gnu/packages/lisp-xyz.scm @@ -5638,6 +5638,41 @@ extension-points via the concept of hooks.") (define-public ecl-cl-hooks (sbcl-package->ecl-package sbcl-cl-hooks)) +(define-public sbcl-cl-autowrap + (let ((revision "1") + (commit "ae846d6968fc0d000de0c541638929a157f3009e")) + ;; no taged branches + (package + (name "sbcl-cl-autowrap") + (version (git-version "1.0" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/rpav/cl-autowrap") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1gisldp2zns92kdcaikghm7c38ldy2d884n8bfg0wcjvbz78p3ar")))) + (build-system asdf-build-system/sbcl) + (inputs + `(("alexandria" ,sbcl-alexandria) + ("cffi" ,sbcl-cffi) + ("cl-json" ,sbcl-cl-json) + ("cl-ppcre" ,sbcl-cl-ppcre) + ("defpackage-plus" ,sbcl-defpackage-plus) + ("trivial-features" ,sbcl-trivial-features))) + (home-page "https://github.com/rpav/cl-autowrap") + (synopsis "FFI wrapper generator for Common Lisp") + (description "This is a c2ffi-based wrapper generator for Common Lisp.") + (license license:bsd-2)))) + +(define-public cl-autowrap + (sbcl-package->cl-source-package sbcl-cl-autowrap)) + +(define-public ecl-cl-autowrap + (sbcl-package->ecl-package sbcl-cl-autowrap)) + (define-public sbcl-s-sysdeps ;; No release since 2013. (let ((commit "9aa23bbdceb24bcdbe0e7c39fa1901858f823106") -- cgit v1.2.3 From 2ae3033449a6ee803fc3ead77c5f26967e9dc34c Mon Sep 17 00:00:00 2001 From: Sharlatan Hellseher Date: Mon, 7 Dec 2020 21:22:50 +0000 Subject: gnu: Add cl-abnf. * gnu/packages/lisp-xyz.scm (cl-abnf, ecl-cl-abnf, sbcl-cl-abnf): New variables. Signed-off-by: Guillaume Le Vaillant --- gnu/packages/lisp-xyz.scm | 39 +++++++++++++++++++++++++++++++++++++++ 1 file changed, 39 insertions(+) diff --git a/gnu/packages/lisp-xyz.scm b/gnu/packages/lisp-xyz.scm index c8b5e84322..7ec625c8bf 100644 --- a/gnu/packages/lisp-xyz.scm +++ b/gnu/packages/lisp-xyz.scm @@ -309,6 +309,45 @@ streams which are similar to string streams.") (define-public ecl-flexi-streams (sbcl-package->ecl-package sbcl-flexi-streams)) +(define-public sbcl-cl-abnf + ;; There are no releases + (let ((commit "ba1fbb104dedbdaddb1ef93d2e4da711bd96cd70") + (revision "1")) + (package + (name "sbcl-cl-abnf") + (version (git-version "0.0.0" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/dimitri/cl-abnf") + (commit commit))) + (file-name (git-file-name "cl-abnf" version)) + (sha256 + (base32 "0f09nsndxa90acm71zd4qdnp40v705a4sqm04mnv9x76h6dlggmz")))) + (build-system asdf-build-system/sbcl) + (inputs + `(("cl-ppcre" ,sbcl-cl-ppcre) + ("esrap" ,sbcl-esrap))) + (arguments + `(#:asd-systems '("abnf"))) + (home-page "https://github.com/dimitri/cl-abnf") + (synopsis "ABNF parser generator for Common Lisp") + (description "This Common Lisp library implements a parser generator for +the ABNF grammar format as described in RFC2234. The generated parser is a +regular expression scanner provided by the cl-ppcre lib, which means that we +can't parse recursive grammar definition. One such definition is the ABNF +definition as given by the RFC. Fortunately, as you have this lib, you most +probably don't need to generate another parser to handle that particular ABNF +grammar.") + (license license:expat)))) + +(define-public cl-abnf + (sbcl-package->cl-source-package sbcl-cl-abnf)) + +(define-public ecl-cl-abnf + (sbcl-package->ecl-package sbcl-cl-abnf)) + (define-public sbcl-cl-ppcre (package (name "sbcl-cl-ppcre") -- cgit v1.2.3 From 6ca66f641485cc5a06ba7d34b9c36b738ea1d654 Mon Sep 17 00:00:00 2001 From: Guillaume Le Vaillant Date: Fri, 11 Dec 2020 18:49:55 +0100 Subject: gnu: ecl-lparallel: Disable never ending tests. * gnu/packages/lisp-xyz.scm (ecl-lparallel)[arguments]: Disable tests. --- gnu/packages/lisp-xyz.scm | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/gnu/packages/lisp-xyz.scm b/gnu/packages/lisp-xyz.scm index 7ec625c8bf..f77e949fea 100644 --- a/gnu/packages/lisp-xyz.scm +++ b/gnu/packages/lisp-xyz.scm @@ -2764,7 +2764,11 @@ Lisp, featuring: (sbcl-package->cl-source-package sbcl-lparallel)) (define-public ecl-lparallel - (sbcl-package->ecl-package sbcl-lparallel)) + (package + (inherit (sbcl-package->ecl-package sbcl-lparallel)) + (arguments + ;; TODO: Find why the tests get stuck forever; disable them for now. + `(#:tests? #f)))) (define-public sbcl-cl-markup (let ((commit "e0eb7debf4bdff98d1f49d0f811321a6a637b390")) -- cgit v1.2.3 From 8361817bf693742757b096468198626f297bb09e Mon Sep 17 00:00:00 2001 From: Mathieu Othacehe Date: Fri, 4 Dec 2020 11:33:16 +0100 Subject: install: Discover local substitute servers. * gnu/installer/substitutes.scm: New file. * gnu/installer/newt/substitutes.scm: New file. * gnu/local.mk (INSTALLER_MODULES): Add them. * po/guix/POTFILES.in: Add gnu/installer/newt/substitutes.scm. * gnu/installer/proxy.scm (with-silent-shepherd): Move to ... * gnu/installer/utils.scm: ... here. * gnu/installer/record.scm ()[substitutes-page]: New field. * gnu/installer/newt.scm (substitutes-page): New procedure, (newt-installer): register it. * gnu/installer.scm (installer-steps): Add "substitutes-page" step. * gnu/system/install.scm (%installation-services): Add avahi-service-type and enable substitute server discover in guix-service-type. []: Set it to %mdns-host-lookup-nss. --- gnu/installer.scm | 7 +++++++ gnu/installer/newt.scm | 5 +++++ gnu/installer/newt/substitutes.scm | 43 ++++++++++++++++++++++++++++++++++++++ gnu/installer/proxy.scm | 6 +----- gnu/installer/record.scm | 3 +++ gnu/installer/substitutes.scm | 41 ++++++++++++++++++++++++++++++++++++ gnu/installer/utils.scm | 11 +++++++++- gnu/local.mk | 2 ++ gnu/system/install.scm | 6 ++++++ po/guix/POTFILES.in | 1 + 10 files changed, 119 insertions(+), 6 deletions(-) create mode 100644 gnu/installer/newt/substitutes.scm create mode 100644 gnu/installer/substitutes.scm diff --git a/gnu/installer.scm b/gnu/installer.scm index f401b242f8..7863edbb67 100644 --- a/gnu/installer.scm +++ b/gnu/installer.scm @@ -266,6 +266,13 @@ selected keymap." (compute (lambda _ ((installer-network-page current-installer))))) + ;; Ask whether to enable substitute server discovery. + (installer-step + (id 'substitutes) + (description (G_ "Substitute server discovery")) + (compute (lambda _ + ((installer-substitutes-page current-installer))))) + ;; Prompt for users (name, group and home directory). (installer-step (id 'user) diff --git a/gnu/installer/newt.scm b/gnu/installer/newt.scm index a1cbeca49a..4f7fc6f4dc 100644 --- a/gnu/installer/newt.scm +++ b/gnu/installer/newt.scm @@ -30,6 +30,7 @@ #:use-module (gnu installer newt page) #:use-module (gnu installer newt partition) #:use-module (gnu installer newt services) + #:use-module (gnu installer newt substitutes) #:use-module (gnu installer newt timezone) #:use-module (gnu installer newt user) #:use-module (gnu installer newt utils) @@ -101,6 +102,9 @@ problem. The backtrace is displayed below. Please report it by email to \ (define (network-page) (run-network-page)) +(define (substitutes-page) + (run-substitutes-page)) + (define (hostname-page) (run-hostname-page)) @@ -130,6 +134,7 @@ problem. The backtrace is displayed below. Please report it by email to \ (locale-page locale-page) (menu-page menu-page) (network-page network-page) + (substitutes-page substitutes-page) (timezone-page timezone-page) (hostname-page hostname-page) (user-page user-page) diff --git a/gnu/installer/newt/substitutes.scm b/gnu/installer/newt/substitutes.scm new file mode 100644 index 0000000000..938cb1a53b --- /dev/null +++ b/gnu/installer/newt/substitutes.scm @@ -0,0 +1,43 @@ +;;; GNU Guix --- Functional package management for GNU +;;; Copyright © 2020 Mathieu Othacehe +;;; +;;; This file is part of GNU Guix. +;;; +;;; GNU Guix is free software; you can redistribute it and/or modify it +;;; under the terms of the GNU General Public License as published by +;;; the Free Software Foundation; either version 3 of the License, or (at +;;; your option) any later version. +;;; +;;; GNU Guix is distributed in the hope that it will be useful, but +;;; WITHOUT ANY WARRANTY; without even the implied warranty of +;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +;;; GNU General Public License for more details. +;;; +;;; You should have received a copy of the GNU General Public License +;;; along with GNU Guix. If not, see . + +(define-module (gnu installer newt substitutes) + #:use-module (gnu installer substitutes) + #:use-module (gnu installer utils) + #:use-module (guix i18n) + #:use-module (newt) + #:use-module (ice-9 match) + #:export (run-substitutes-page)) + +(define* (run-substitutes-page) + (match (current-clients) + (() + (case (choice-window + (G_ "Substitute server discovery.") + (G_ "Enable") (G_ "Disable") + (G_ " By turning this option on, you allow Guix to fetch \ +substitutes (pre-built binaries) during installation from servers \ +discovered on your local area network (LAN) in addition to the official \ +server. This can increase download throughput. + + There are no security risks: only genuine substitutes may be retrieved from \ +those servers. However, eavesdroppers on your LAN may be able to see what \ +software you are installing.")) + ((1) (enable-discovery)) + ((2) (disable-discovery)))) + (_ #f))) diff --git a/gnu/installer/proxy.scm b/gnu/installer/proxy.scm index befaf3ab0a..86c827294e 100644 --- a/gnu/installer/proxy.scm +++ b/gnu/installer/proxy.scm @@ -17,15 +17,11 @@ ;;; along with GNU Guix. If not, see . (define-module (gnu installer proxy) + #:use-module (gnu installer utils) #:use-module (gnu services herd) #:export (set-http-proxy clear-http-proxy)) -(define-syntax-rule (with-silent-shepherd exp ...) - (parameterize ((shepherd-message-port - (%make-void-port "w"))) - exp ...)) - (define (set-http-proxy proxy) (with-silent-shepherd (with-shepherd-action 'guix-daemon diff --git a/gnu/installer/record.scm b/gnu/installer/record.scm index 6ebd87f6a6..0b34318c45 100644 --- a/gnu/installer/record.scm +++ b/gnu/installer/record.scm @@ -33,6 +33,7 @@ installer-locale-page installer-menu-page installer-network-page + installer-substitutes-page installer-timezone-page installer-hostname-page installer-user-page @@ -73,6 +74,8 @@ (menu-page installer-menu-page) ;; procedure void -> void (network-page installer-network-page) + ;; procedure void -> void + (substitutes-page installer-substitutes-page) ;; procedure (zonetab) -> posix-timezone (timezone-page installer-timezone-page) ;; procedure void -> void diff --git a/gnu/installer/substitutes.scm b/gnu/installer/substitutes.scm new file mode 100644 index 0000000000..c9a7418f89 --- /dev/null +++ b/gnu/installer/substitutes.scm @@ -0,0 +1,41 @@ +;;; GNU Guix --- Functional package management for GNU +;;; Copyright © 2020 Mathieu Othacehe +;;; +;;; This file is part of GNU Guix. +;;; +;;; GNU Guix is free software; you can redistribute it and/or modify it +;;; under the terms of the GNU General Public License as published by +;;; the Free Software Foundation; either version 3 of the License, or (at +;;; your option) any later version. +;;; +;;; GNU Guix is distributed in the hope that it will be useful, but +;;; WITHOUT ANY WARRANTY; without even the implied warranty of +;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +;;; GNU General Public License for more details. +;;; +;;; You should have received a copy of the GNU General Public License +;;; along with GNU Guix. If not, see . + +(define-module (gnu installer substitutes) + #:use-module (gnu installer utils) + #:use-module (gnu services herd) + #:export (enable-discovery + disable-discovery)) + +(define (enable-discovery) + (with-silent-shepherd + (with-shepherd-action 'guix-daemon + ('discover "on") + result + result))) + +(define (disable-discovery) + (with-silent-shepherd + (with-shepherd-action 'guix-daemon + ('discover "off") + result + result))) + +;; Local Variables: +;; eval: (put 'with-silent-shepherd 'scheme-indent-function 0) +;; End: diff --git a/gnu/installer/utils.scm b/gnu/installer/utils.scm index a7fa66a199..bb97bc5560 100644 --- a/gnu/installer/utils.scm +++ b/gnu/installer/utils.scm @@ -18,6 +18,7 @@ ;;; along with GNU Guix. If not, see . (define-module (gnu installer utils) + #:use-module (gnu services herd) #:use-module (guix utils) #:use-module (guix build utils) #:use-module (guix i18n) @@ -43,7 +44,9 @@ with-server-socket current-server-socket current-clients - send-to-clients)) + send-to-clients + + with-silent-shepherd)) (define* (read-lines #:optional (port (current-input-port))) "Read lines from PORT and return them as a list." @@ -233,3 +236,9 @@ accepting socket." (current-clients (reverse remainder)) exp) + +(define-syntax-rule (with-silent-shepherd exp ...) + "Evaluate EXP while discarding shepherd messages." + (parameterize ((shepherd-message-port + (%make-void-port "w"))) + exp ...)) diff --git a/gnu/local.mk b/gnu/local.mk index f94725b1e5..4cca7671a8 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -717,6 +717,7 @@ INSTALLER_MODULES = \ %D%/installer/record.scm \ %D%/installer/services.scm \ %D%/installer/steps.scm \ + %D%/installer/substitutes.scm \ %D%/installer/tests.scm \ %D%/installer/timezone.scm \ %D%/installer/user.scm \ @@ -733,6 +734,7 @@ INSTALLER_MODULES = \ %D%/installer/newt/page.scm \ %D%/installer/newt/partition.scm \ %D%/installer/newt/services.scm \ + %D%/installer/newt/substitutes.scm \ %D%/installer/newt/timezone.scm \ %D%/installer/newt/user.scm \ %D%/installer/newt/utils.scm \ diff --git a/gnu/system/install.scm b/gnu/system/install.scm index 7701297411..a6b9e3d952 100644 --- a/gnu/system/install.scm +++ b/gnu/system/install.scm @@ -34,6 +34,7 @@ #:use-module ((guix store) #:select (%store-prefix)) #:use-module (gnu installer) #:use-module (gnu system locale) + #:use-module (gnu services avahi) #:use-module (gnu services dbus) #:use-module (gnu services networking) #:use-module (gnu services shepherd) @@ -335,6 +336,10 @@ Access documentation at any time by pressing Alt-F2.\x1b[0m ;; The usual services. (syslog-service) + ;; Use the Avahi daemon to discover substitute servers on the local + ;; network. It can be faster than fetching from remote servers. + (service avahi-service-type) + ;; The build daemon. Register the default substitute server key(s) ;; as trusted to allow the installation process to use substitutes by ;; default. @@ -435,6 +440,7 @@ Access documentation at any time by pressing Alt-F2.\x1b[0m (host-name "gnu") (timezone "Europe/Paris") (locale "en_US.utf8") + (name-service-switch %mdns-host-lookup-nss) (bootloader (bootloader-configuration (bootloader grub-bootloader) (target "/dev/sda"))) diff --git a/po/guix/POTFILES.in b/po/guix/POTFILES.in index 5afb13ffdb..1aec3bef3c 100644 --- a/po/guix/POTFILES.in +++ b/po/guix/POTFILES.in @@ -25,6 +25,7 @@ gnu/installer/newt/network.scm gnu/installer/newt/page.scm gnu/installer/newt/partition.scm gnu/installer/newt/services.scm +gnu/installer/newt/substitutes.scm gnu/installer/newt/timezone.scm gnu/installer/newt/user.scm gnu/installer/newt/utils.scm -- cgit v1.2.3 From 7eb920351abc7757ee9711ac147e63d6936e5ee8 Mon Sep 17 00:00:00 2001 From: Simon South Date: Fri, 11 Dec 2020 15:16:47 -0500 Subject: gnu: knot-resolver: Update to 5.2.1. * gnu/packages/dns.scm (knot-resolver): Update to 5.2.1. [source]: Remove obsolete patch. * gnu/packages/patches/knot-resolver-fix-map-command-on-32-bit.patch: Delete file. * gnu/local.mk (dist_patch_DATA): Remove it. Signed-off-by: Tobias Geerinckx-Rice --- gnu/local.mk | 1 - gnu/packages/dns.scm | 7 +- .../knot-resolver-fix-map-command-on-32-bit.patch | 146 --------------------- 3 files changed, 2 insertions(+), 152 deletions(-) delete mode 100644 gnu/packages/patches/knot-resolver-fix-map-command-on-32-bit.patch diff --git a/gnu/local.mk b/gnu/local.mk index 4cca7671a8..f8c615a83d 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -1223,7 +1223,6 @@ dist_patch_DATA = \ %D%/packages/patches/kmail-Fix-missing-link-libraries.patch \ %D%/packages/patches/kmod-module-directory.patch \ %D%/packages/patches/kmscon-runtime-keymap-switch.patch \ - %D%/packages/patches/knot-resolver-fix-map-command-on-32-bit.patch \ %D%/packages/patches/kpackage-allow-external-paths.patch \ %D%/packages/patches/kpackage-fix-KF5PackageMacros.cmake.patch \ %D%/packages/patches/kmplayer-aarch64.patch \ diff --git a/gnu/packages/dns.scm b/gnu/packages/dns.scm index d59fe57ade..403ebd3d8b 100644 --- a/gnu/packages/dns.scm +++ b/gnu/packages/dns.scm @@ -937,17 +937,14 @@ synthesis, and on-the-fly re-configuration.") (define-public knot-resolver (package (name "knot-resolver") - (version "5.2.0") + (version "5.2.1") (source (origin (method url-fetch) (uri (string-append "https://secure.nic.cz/files/knot-resolver/" "knot-resolver-" version ".tar.xz")) (sha256 (base32 - "0cwlipib3x88dr6cijqv2aps13b4ijv524wc85ns07rkldy2c948")) - (patches - (search-patches - "knot-resolver-fix-map-command-on-32-bit.patch")))) + "09jqy23q1pgj76y2qd1xfk72wwmypnyawm3span3gx00qi2bfdxa")))) (build-system meson-build-system) (outputs '("out" "doc")) (arguments diff --git a/gnu/packages/patches/knot-resolver-fix-map-command-on-32-bit.patch b/gnu/packages/patches/knot-resolver-fix-map-command-on-32-bit.patch deleted file mode 100644 index 02c0fbcb70..0000000000 --- a/gnu/packages/patches/knot-resolver-fix-map-command-on-32-bit.patch +++ /dev/null @@ -1,146 +0,0 @@ -commit e01979620025666633250b3e2d545fe59c629f73 -Author: Vladimír Čunát -Date: Fri Nov 13 14:16:32 2020 +0100 - - fix map() command on 32-bit platforms; regressed in 5.2.0 - - LuaJIT FFI was using opendir() (etc.) variants with 32-bit inodes - but the C parts was using them as 64-bit inode variants. - Consequently the `struct dirent` layout didn't match and we were getting - filenames shifted by eight bytes. - - Now the whole dir-listing lua function is written in C. - -diff --git a/.luacheckrc b/.luacheckrc -index 0cf0b884..67bc18f6 100644 ---- a/.luacheckrc -+++ b/.luacheckrc -@@ -20,6 +20,7 @@ new_read_globals = { - 'user', - 'verbose', - 'worker', -+ 'kluautil_list_dir', - -- Sandbox declarations - 'kB', - 'MB', -diff --git a/NEWS b/NEWS -index 2eae3082..9d8cde99 100644 ---- a/NEWS -+++ b/NEWS -@@ -1,6 +1,10 @@ - Knot Resolver X.Y.X (yyyy-mm-dd) - ================================ - -+Bugfixes -+-------- -+- fix map() command on 32-bit platforms; regressed in 5.2.0 (!1093) -+ - - Knot Resolver 5.2.0 (2020-11-11) - ================================ -diff --git a/daemon/bindings/impl.c b/daemon/bindings/impl.c -index d10f4525..d9ad0774 100644 ---- a/daemon/bindings/impl.c -+++ b/daemon/bindings/impl.c -@@ -2,6 +2,7 @@ - * SPDX-License-Identifier: GPL-3.0-or-later - */ - -+#include - #include - #include - #include -@@ -29,6 +30,29 @@ const char * lua_table_checkindices(lua_State *L, const char *keys[]) - return NULL; - } - -+/** Return table listing filenames in a given directory (ls -A). */ -+static int kluautil_list_dir(lua_State *L) -+{ -+ lua_newtable(L); // empty table even on errors -+ -+ const char *path = lua_tolstring(L, 1, NULL); -+ if (!path) return 1; -+ DIR *dir = opendir(path); -+ if (!dir) return 1; -+ -+ struct dirent *entry; -+ int lua_i = 1; -+ while ((entry = readdir(dir)) != NULL) { -+ if (strcmp(entry->d_name, ".") && strcmp(entry->d_name, "..")) { -+ lua_pushstring(L, entry->d_name); -+ lua_rawseti(L, -2, lua_i++); -+ } -+ } -+ -+ closedir(dir); -+ return 1; -+} -+ - - /* Each of these just creates the correspondingly named lua table of functions. */ - int kr_bindings_cache (lua_State *L); /* ./cache.c */ -@@ -44,6 +68,9 @@ void kr_bindings_register(lua_State *L) - kr_bindings_modules(L); - kr_bindings_net(L); - kr_bindings_worker(L); -+ -+ /* Finally some lua utils *written in C*, not really a binding. */ -+ lua_register(L, "kluautil_list_dir", kluautil_list_dir); - } - - void lua_error_p(lua_State *L, const char *fmt, ...) -diff --git a/daemon/lua/kluautil.lua b/daemon/lua/kluautil.lua -index 57912e7b..e73e952c 100644 ---- a/daemon/lua/kluautil.lua -+++ b/daemon/lua/kluautil.lua -@@ -1,6 +1,5 @@ - -- SPDX-License-Identifier: GPL-3.0-or-later - --local ffi = require('ffi') - local kluautil = {} - - -- Get length of table -@@ -28,14 +27,6 @@ function kluautil.kr_table_unpack(tab) - return unpack(tab, 1, tab.n) - end - --ffi.cdef([[ -- typedef struct __dirstream DIR; -- DIR *opendir(const char *name); -- struct dirent *readdir(DIR *dirp); -- int closedir(DIR *dirp); -- char *strerror(int errnum); --]]) -- - -- Fetch over HTTPS - function kluautil.kr_https_fetch(url, out_file, ca_file) - local http_ok, http_request = pcall(require, 'http.request') -@@ -88,26 +79,6 @@ function kluautil.kr_https_fetch(url, out_file, ca_file) - return true - end - ---- List directory --function kluautil.list_dir (path) -- local results = {} -- local dir = ffi.C.opendir(path) -- if dir == nil then -- return results -- end -- -- local entry = ffi.C.readdir(dir) -- while entry ~= nil do -- local entry_name = ffi.string(ffi.C.kr_dirent_name(entry)) -- if entry_name ~= '.' and entry_name ~= '..' then -- table.insert(results, entry_name) -- end -- entry = ffi.C.readdir(dir) -- end -- -- ffi.C.closedir(dir) -- -- return results --end -+kluautil.list_dir = kluautil_list_dir - - return kluautil -- cgit v1.2.3 From 482b8ae2cd3f126a1300178e317df8993bf75b16 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 12 Dec 2020 00:06:18 +0100 Subject: import/cran: Abort with error message when recursive import fails. Previously, after a failed recursive import "guix import" would signal success. * guix/import/cran.scm (cran->guix-package): Raise a condition when all repositories have been exhausted. * guix/scripts/import/cran.scm (guix-import-cran): Handle errors. --- guix/import/cran.scm | 6 +++++- guix/scripts/import/cran.scm | 9 +++++---- 2 files changed, 10 insertions(+), 5 deletions(-) diff --git a/guix/import/cran.scm b/guix/import/cran.scm index 6c1fbd7ba3..1d25a5125e 100644 --- a/guix/import/cran.scm +++ b/guix/import/cran.scm @@ -29,6 +29,7 @@ #:use-module (srfi srfi-11) #:use-module (srfi srfi-26) #:use-module (srfi srfi-34) + #:use-module (srfi srfi-35) #:use-module (ice-9 receive) #:use-module (web uri) #:use-module (guix memoization) @@ -585,7 +586,10 @@ s-expression corresponding to that package, or #f on failure." ((bioconductor) ;; Retry import from CRAN (cran->guix-package package-name #:repo 'cran)) - (else (values #f '())))))))) + (else + (raise (condition + (&message + (message "couldn't find meta-data for R package"))))))))))) (define* (cran-recursive-import package-name #:key (repo 'cran)) (recursive-import package-name diff --git a/guix/scripts/import/cran.scm b/guix/scripts/import/cran.scm index 33944c4a3f..20e82ae2ca 100644 --- a/guix/scripts/import/cran.scm +++ b/guix/scripts/import/cran.scm @@ -97,10 +97,11 @@ Import and convert the CRAN package for PACKAGE-NAME.\n")) ((package-name) (if (assoc-ref opts 'recursive) ;; Recursive import - (map package->definition - (filter identity - (cran-recursive-import package-name - #:repo (or (assoc-ref opts 'repo) 'cran)))) + (with-error-handling + (map package->definition + (filter identity + (cran-recursive-import package-name + #:repo (or (assoc-ref opts 'repo) 'cran))))) ;; Single import (let ((sexp (cran->guix-package package-name #:repo (or (assoc-ref opts 'repo) 'cran)))) -- cgit v1.2.3 From 6718ce446c3904214697cde8eb666fe86368d034 Mon Sep 17 00:00:00 2001 From: Miguel Ángel Arruga Vivas Date: Sat, 12 Dec 2020 02:27:58 +0100 Subject: news: Add 'es' translation. --- etc/news.scm | 26 ++++++++++++++++++++++++-- 1 file changed, 24 insertions(+), 2 deletions(-) diff --git a/etc/news.scm b/etc/news.scm index 16bcd0450b..8cd1c89837 100644 --- a/etc/news.scm +++ b/etc/news.scm @@ -20,6 +20,7 @@ (entry (commit "79f9dee3c4c0e6d21066f142116a537207ae7ba4") (title (en "Local substitute servers discovery is now supported") (de "Substitutserver können jetzt im lokalen Netz erkannt werden") + (es "Los servidores de sustituciones se pueden descubrir localmente") (fr "La découverte des serveurs de substituts locaux est désormais supportée")) (body (en "The @command{guix-daemon} can now discover local substitute @@ -34,6 +35,12 @@ gefunden, die mit der Befehlszeilenoption @option{--advertise} gestartet wurden. Die Ermittlung im Netzwerk verfügbarer Substitutserver baut auf den Protokollen mDNS und DNS-SD auf. Derzeit wird dazu die Bibliothek Guile-Avahi benutzt.") + (es "El daemon @command{guix-daemon} ahora puede descubrir servidores +de sustituciones locales cuando se le proporciona la opción +@option{--discover}. Únicamente se descubrirán los servidores de +sustituciones que se hayan arrancado con la opción @option{--advertise}. La +búsqueda en la red se basa en los protocolos mDNS y DNS-SD, actualmente +mediante el uso de la biblioteca Guile-Avahi.") (fr "Le @command{guix-daemon} peut désormais découvrir les serveurs de substituts locaux lorsque l'option @option{--discover} est passée. Seuls les serveurs de substituts démarrés avec l'option @option{--advertise} seront @@ -42,7 +49,8 @@ l'instant grâce à la librairie Guile-Avahi."))) (entry (commit "a9a2fdaabcc78e7a54d9a6bcfa4ee3de308e9a90") (title (en "Logical Volume Manager (LVM) now supported on Guix System") - (de "Logical Volume Manager (LVM) wird jetzt auf Guix System unterstützt")) + (de "Logical Volume Manager (LVM) wird jetzt auf Guix System unterstützt") + (es "El sistema Guix ahora implementa también volúmenes lógicos LVM")) (body (en "On Guix System, the new @code{lvm-device-mapping} variable allows you to declare ``mapped devices'' for LVM, the Linux Logical Volume @@ -70,7 +78,21 @@ Datenträgergruppe (Volume Group) „vg0“ wie folgt deklariert werden: (type lvm-device-mapping)) @end lisp -Siehe @command{info \"(guix.de) Zugeordnete Geräte\"} für nähere Informationen."))) +Siehe @command{info \"(guix.de) Zugeordnete Geräte\"} für nähere Informationen.") + (es "En el sistema Guix, la nueva variable @code{lvm-device-mapping} +le permite declarar «dispositivos traducidos» para LVM, el gestor de volúmenes +lógicos de Linux. A continuación se muestra un ejemplo con la declaración de +los volúmenes lógicos «alfa» y «beta» del grupo de volúmenes «vg0»: + +@lisp +(mapped-device + (source \"vg0\") + (target (list \"vg0-alfa\" \"vg0-beta\")) + (type lvm-device-mapping)) +@end lisp + +Véase @command{info \"(guix.es) Dispositivos traducidos\"} para obtener más +información."))) (entry (commit "3b6e4e5fd05e72b8a32ff1a2d5e21464260e21e6") (title (en "List of substitute keys is now declarative on Guix System") -- cgit v1.2.3 From 92d99bf2c4bb65bae72a93f70c9e32eda9c85075 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Sat, 12 Dec 2020 00:36:23 -0500 Subject: gnu: linux-libre: Update to 5.9.14. * gnu/packages/linux.scm (linux-libre-5.9-version): Update to 5.9.14. (linux-libre-5.9-pristine-source): Update hash. --- gnu/packages/linux.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index 4b1fe7e15a..002f1581ca 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -352,7 +352,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." ;; The current "stable" kernel. That is, the most recently released major ;; version. -(define-public linux-libre-5.9-version "5.9.13") +(define-public linux-libre-5.9-version "5.9.14") (define deblob-scripts-5.9 (linux-libre-deblob-scripts linux-libre-5.9-version @@ -360,7 +360,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." (base32 "0yb04a4j2wq3mwvks3cj7kcm2pscmfs29lrz3falkxpbvjxbbgq2"))) (define-public linux-libre-5.9-pristine-source (let ((version linux-libre-5.9-version) - (hash (base32 "0ancdbfmrhq7wnvzrrnayiw8j4k1pjjnmvjxkl12lal7bjdahdml"))) + (hash (base32 "0jbb3rzbkh0l75zq9bnc60w55ryvrvcg7vw85fsbcwfzvi0zpz1r"))) (make-linux-libre-source version (%upstream-linux-source version hash) deblob-scripts-5.9))) -- cgit v1.2.3 From 0fae07917ba33c314ae2db601d20db2473a20bca Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Sat, 12 Dec 2020 00:36:53 -0500 Subject: gnu: linux-libre 5.4: Update to 5.4.83. * gnu/packages/linux.scm (linux-libre-5.4-version): Update to 5.4.83. (linux-libre-5.4-pristine-source): Update hash. --- gnu/packages/linux.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index 002f1581ca..6d2b8582e1 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -368,7 +368,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." ;; The "longterm" kernels — the older releases with long-term upstream support. ;; Here are the support timelines: ;; -(define-public linux-libre-5.4-version "5.4.82") +(define-public linux-libre-5.4-version "5.4.83") (define deblob-scripts-5.4 (linux-libre-deblob-scripts linux-libre-5.4-version @@ -376,7 +376,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." (base32 "167zcfkw62pm6nv1xdvvhxw0ca724sywcywnv3z00189f8f8p3vg"))) (define-public linux-libre-5.4-pristine-source (let ((version linux-libre-5.4-version) - (hash (base32 "1byx163v83aw0ixphwz20znml2s2n3cy1kp89vgwbdiqxbj5hi7v"))) + (hash (base32 "1ik14pfgynkn1sjhgyhgmxjvviq0mgvk0ygj76w8mplkpc5rgv5y"))) (make-linux-libre-source version (%upstream-linux-source version hash) deblob-scripts-5.4))) -- cgit v1.2.3 From a3a81a8703295b6ac2f0ffde5a2e8e72196178bb Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Sat, 12 Dec 2020 00:37:29 -0500 Subject: gnu: linux-libre 4.19: Update to 4.19.163. * gnu/packages/linux.scm (linux-libre-4.19-version): Update to 4.19.163. (linux-libre-4.19-pristine-source): Update hash. --- gnu/packages/linux.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index 6d2b8582e1..c9377cc8f5 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -381,7 +381,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." (%upstream-linux-source version hash) deblob-scripts-5.4))) -(define-public linux-libre-4.19-version "4.19.162") +(define-public linux-libre-4.19-version "4.19.163") (define deblob-scripts-4.19 (linux-libre-deblob-scripts linux-libre-4.19-version @@ -389,7 +389,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." (base32 "1jiaw0as1ippkrjdpd52657w5mz9qczg3y2hlra7m9k0xawwiqlf"))) (define-public linux-libre-4.19-pristine-source (let ((version linux-libre-4.19-version) - (hash (base32 "052nk889fcvw7p4vll5dky6dcr1g6mvn1i93xykhch6yxkl26ds5"))) + (hash (base32 "1z65iwwyx2b01fncygckmhpxirzs52qfqmv3agirn4laxgjw9viy"))) (make-linux-libre-source version (%upstream-linux-source version hash) deblob-scripts-4.19))) -- cgit v1.2.3 From 4c327e025277dd59b864200d5ecf671b5656e7c9 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Sat, 12 Dec 2020 00:38:00 -0500 Subject: gnu: linux-libre 4.14: Update to 4.14.212. * gnu/packages/linux.scm (linux-libre-4.14-version): Update to 4.14.212. (linux-libre-4.14-pristine-source): Update hash. --- gnu/packages/linux.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index c9377cc8f5..f67545b033 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -394,7 +394,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." (%upstream-linux-source version hash) deblob-scripts-4.19))) -(define-public linux-libre-4.14-version "4.14.211") +(define-public linux-libre-4.14-version "4.14.212") (define deblob-scripts-4.14 (linux-libre-deblob-scripts linux-libre-4.14-version @@ -402,7 +402,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." (base32 "1qij18inijj6c3ma8hv98yjagnzxdxyn134da9fd23ky8q6hbvky"))) (define-public linux-libre-4.14-pristine-source (let ((version linux-libre-4.14-version) - (hash (base32 "0hp9457m0hal2d3bf5fs3ghp59s6hlc9bwl0s1apjgqa8fmkjdss"))) + (hash (base32 "0y8ck8pfxm8862wi4cz8qp9x9b18yl448i8m7bpbphs290nc66qf"))) (make-linux-libre-source version (%upstream-linux-source version hash) deblob-scripts-4.14))) -- cgit v1.2.3 From b7b9ee75885426a6ed27a78f351c6cdd9cf7f952 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Sat, 12 Dec 2020 00:38:34 -0500 Subject: gnu: linux-libre 4.9: Update to 4.9.248. * gnu/packages/linux.scm (linux-libre-4.9-version): Update to 4.9.248. (linux-libre-4.9-pristine-source): Update hash. --- gnu/packages/linux.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index f67545b033..4c5917bc59 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -407,7 +407,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." (%upstream-linux-source version hash) deblob-scripts-4.14))) -(define-public linux-libre-4.9-version "4.9.247") +(define-public linux-libre-4.9-version "4.9.248") (define deblob-scripts-4.9 (linux-libre-deblob-scripts linux-libre-4.9-version @@ -415,7 +415,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." (base32 "0fxajshb75siq39lj5h8xvhdj8lcmddkslwlyj65rhlwk6g2r4b2"))) (define-public linux-libre-4.9-pristine-source (let ((version linux-libre-4.9-version) - (hash (base32 "1mngdbsq8pdzd0x9hif4715cc7wzc3ahgp1yrknnqk598q0fnfpp"))) + (hash (base32 "1kzczy0lz3lnjkhvx90dgjmzn3d3y55qxlihiclkr4y9c602d1s6"))) (make-linux-libre-source version (%upstream-linux-source version hash) deblob-scripts-4.9))) -- cgit v1.2.3 From ea50795d7f54582d5c439f60e836ff2ee5d8aed2 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Sat, 12 Dec 2020 00:39:26 -0500 Subject: gnu: linux-libre 4.4: Update to 4.4.248. * gnu/packages/linux.scm (linux-libre-4.4-version): Update to 4.4.248. (linux-libre-4.4-pristine-source): Update hash. --- gnu/packages/linux.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index 4c5917bc59..73dec7d1b7 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -420,7 +420,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." (%upstream-linux-source version hash) deblob-scripts-4.9))) -(define-public linux-libre-4.4-version "4.4.247") +(define-public linux-libre-4.4-version "4.4.248") (define deblob-scripts-4.4 (linux-libre-deblob-scripts linux-libre-4.4-version @@ -428,7 +428,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." (base32 "0hhin1jpfkd6nwrb6xqxjzl3hdxy4pn8a15hy2d3d83yw6pflbsf"))) (define-public linux-libre-4.4-pristine-source (let ((version linux-libre-4.4-version) - (hash (base32 "1jh7vmyx55krk6y2r9v48liifs5wwkgns3gp8rs5sm4klfm36r2a"))) + (hash (base32 "1z1xbkm0z0v6k3scszii5hi24pn391332g0li93p3n1rnv74jap5"))) (make-linux-libre-source version (%upstream-linux-source version hash) deblob-scripts-4.4))) -- cgit v1.2.3 From b828057ea4c096898da8c9810e7a6607359f2aa3 Mon Sep 17 00:00:00 2001 From: Hartmut Goebel Date: Sat, 12 Dec 2020 18:22:37 +0100 Subject: gnu: KDE: Fix old cgit home-pages. Fix all home-pages pointing to git-repos a cgit.kde.org, which is gone, to now use the correct repo at invent.kde.org. * gnu/packages/kde.scm (grantleetheme, kdiagram): Update home-page. * gnu/packages/kde-frameworks.scm (kholidays): Likewise. * gnu/packages/kde-internet.scm (libgravatar, libktorrent): Likewise. * gnu/packages/kde-multimedia.scm (libkcddb, libkcompactdisc): Likewise. * gnu/packages/kde-pim.scm (kblog, kdav, kdepim-apps-libs, kdepim-runtime, keventviews, kincidenceeditor, kmailcommon, kmailimporter, kmessagelib, kpimcommon, ksmtp, libkdepim, libkgapi, libkleo, libksieve): Likewise. * gnu/packages/kde-plasma.scm (kdecoration, kscreenlocker): Likewise. --- gnu/packages/kde-frameworks.scm | 2 +- gnu/packages/kde-internet.scm | 4 ++-- gnu/packages/kde-multimedia.scm | 4 ++-- gnu/packages/kde-pim.scm | 30 +++++++++++++++--------------- gnu/packages/kde-plasma.scm | 4 ++-- gnu/packages/kde.scm | 4 ++-- 6 files changed, 24 insertions(+), 24 deletions(-) diff --git a/gnu/packages/kde-frameworks.scm b/gnu/packages/kde-frameworks.scm index febdb1f4f0..951a2f8554 100644 --- a/gnu/packages/kde-frameworks.scm +++ b/gnu/packages/kde-frameworks.scm @@ -811,7 +811,7 @@ interfaces in the areas of colors, fonts, text, images, keyboard input.") (inputs `(("qtbase" ,qtbase) ("qtdeclarative" ,qtdeclarative))) - (home-page "https://cgit.kde.org/kholidays.git") + (home-page "https://invent.kde.org/frameworks/kholidays") (synopsis "Library for regional holiday information") (description "This library provides a C++ API that determines holiday and other special events for a geographical region.") diff --git a/gnu/packages/kde-internet.scm b/gnu/packages/kde-internet.scm index 4203ffbaec..617937002e 100644 --- a/gnu/packages/kde-internet.scm +++ b/gnu/packages/kde-internet.scm @@ -450,7 +450,7 @@ a full-featured client for BitTorrent.") ("qtbase" ,qtbase))) (arguments `(#:tests? #f)) ;; 2/7 tests fail (due to network issues?) - (home-page "https://cgit.kde.org/libgravatar.git") + (home-page "https://invent.kde.org/pim/libgravatar") (synopsis "Online avatar lookup library") (description "This library retrieves avatar images based on a hash from a person's email address, as well as local caching to avoid @@ -484,7 +484,7 @@ unnecessary network operations.") ("qca" ,qca) ("qtbase" ,qtbase) ("solid" ,solid))) - (home-page "https://cgit.kde.org/libktorrent.git") + (home-page "https://invent.kde.org/network/libktorrent") (synopsis "BitTorrent protocol library for C++ / Qt 5 / KDE Frameworks") (description "The KTorrent library supports connectivity to HTTP and UDP trackers, mainline DHT and the new generation Micro Transport diff --git a/gnu/packages/kde-multimedia.scm b/gnu/packages/kde-multimedia.scm index 23417a982d..cc312b6c40 100644 --- a/gnu/packages/kde-multimedia.scm +++ b/gnu/packages/kde-multimedia.scm @@ -695,7 +695,7 @@ Its features include: ("qtbase" ,qtbase))) (arguments `(#:tests? #f)) ; Most tests require network - (home-page "https://cgit.kde.org/libkcddb.git") + (home-page "https://invent.kde.org/multimedia/libkcddb") (synopsis "CDDB library for KDE Platform (runtime)") (description "A library for retrieving and sending cddb information.") (license ;; GPL for programs, LGPL for libraries, FDL for documentation @@ -722,7 +722,7 @@ Its features include: ("phonon" ,phonon) ("qtbase" ,qtbase) ("solid" ,solid))) - (home-page "https://cgit.kde.org/libkcompactdisc.git/") + (home-page "https://invent.kde.org/multimedia/libkcompactdisc") (synopsis "KDE library for playing & ripping CDs") (description "The KDE Compact Disc library provides an API for applications using the KDE Platform to interface with the CD drives for audio diff --git a/gnu/packages/kde-pim.scm b/gnu/packages/kde-pim.scm index 4ef49743fe..b0a2e565ed 100644 --- a/gnu/packages/kde-pim.scm +++ b/gnu/packages/kde-pim.scm @@ -391,7 +391,7 @@ Akonadi PIM data server. It uses Xapian for indexing and querying.") ("kwallat" ,kwallet) ("libkdepim" ,libkdepim) ("qtbase" ,qtbase))) - (home-page "https://cgit.kde.org/incidenceeditor.git") + (home-page "https://invent.kde.org/pim/incidenceeditor") (synopsis "KDE PIM library for editing incidences") (description "This library provides an incidence editor for KDE PIM.") (license ;; GPL for programs, LGPL for libraries @@ -518,7 +518,7 @@ calendar data.") ("qtbase" ,qtbase) ("syndication" ,syndication))) ;; Note: Some tests take up to 90 sec. - (home-page "https://cgit.kde.org/kblog.git") + (home-page "https://invent.kde.org/pim/kblog") (synopsis "Client-side support library for web application remote blogging APIs") (description "KBlog is a library for calling functions on Blogger 1.0, @@ -634,7 +634,7 @@ functions for accessing calendar data using the kcalcore API.") ("kio" ,kio) ("qtbase" ,qtbase) ("qtxmlpatterns" ,qtxmlpatterns))) - (home-page "https://cgit.kde.org/kdav.git") + (home-page "https://invent.kde.org/frameworks/kdav") (synopsis "DAV protocol implementation with KJobs") (description "This is a DAV protocol implementation with KJobs. Calendars and todos are supported, using either GroupDAV or CalDAV, and contacts are @@ -679,7 +679,7 @@ supported using GroupDAV or CardDAV.") ("prison" ,prison) ("qgpgme" ,qgpgme) ("qtbase" ,qtbase))) - (home-page "https://cgit.kde.org/kdepim-apps-libs.git") + (home-page "https://invent.kde.org/pim/kdepim-apps-libs") (synopsis "KDE PIM mail related libraries and data files") (description "This package provides mail related libraries and data files for KDE PIM.") @@ -761,7 +761,7 @@ for KDE PIM.") "/include/KF5:" (or (getenv "CPLUS_INCLUDE_PATH") ""))) #t))))) - (home-page "https://cgit.kde.org/kdepim-runtime.git") + (home-page "https://invent.kde.org/pim/kdepim-runtime") (synopsis "Runtime components for Akonadi KDE") (description "This package contains Akonadi agents written using KDE Development Platform libraries. Any package that uses Akonadi should probably @@ -816,7 +816,7 @@ package.") ("kxmlgui" ,kxmlgui) ("libkdepim" ,libkdepim) ("qtbase" ,qtbase))) - (home-page "https://cgit.kde.org/eventviews.git") + (home-page "https://invent.kde.org/pim/eventviews") (synopsis "KDE PIM library for creating events") (description "This library provides an event creator for KDE PIM.") (license ;; GPL for programs, LGPL for libraries @@ -1180,7 +1180,7 @@ manager from KDE.") ("qtbase" ,qtbase))) (arguments `(#:tests? #f)) ;; TODO: 4/56 tests fail, even with "offscreen" and dbus - (home-page "https://cgit.kde.org/mailcommon.git") + (home-page "https://invent.kde.org/pim/mailcommon") (synopsis "KDE email utility library") (description "The mail common library provides utility functions for dealing with email.") @@ -1219,7 +1219,7 @@ dealing with email.") ("kxmlgui" ,kxmlgui) ("libkdepim" ,libkdepim) ("qtbase" ,qtbase))) - (home-page "https://cgit.kde.org/mailimporter.git") + (home-page "https://invent.kde.org/pim/mailimporter") (synopsis "KDE mail importer library") (description "This package provides libraries for importing mails other e-mail client programs into KMail and KDE PIM.") @@ -1373,7 +1373,7 @@ using a Qt/KMime C++ API.") "/include/KF5:" (or (getenv "CPLUS_INCLUDE_PATH") ""))) #t))))) - (home-page "https://cgit.kde.org/messagelib.git") + (home-page "https://invent.kde.org/pim/messagelib") (synopsis "KDE PIM messaging libraries") (description "This package provides several libraries for messages, e.g. a message list, a mime tree parse, a template parser and the @@ -1701,7 +1701,7 @@ Virtual Contact File}) files to the KPeople contact management library.") ("qtwebengine" ,qtwebengine))) (arguments `(#:tests? #f)) ;; TODO tests hang - (home-page "https://cgit.kde.org/pimcommon.git") + (home-page "https://invent.kde.org/pim/pimcommon") (synopsis "Common libraries for KDE PIM") (description "This package provides common libraries for KDE PIM.") (license ;; GPL for programs, LGPL for libraries @@ -1782,7 +1782,7 @@ text in the text edit to all kinds of markup, like HTML or BBCODE.") _ prefix) (string-append prefix "${KDE_INSTALL_TARGETS_DEFAULT_ARGS})"))) #t))))) - (home-page "https://cgit.kde.org/ksmtp.git") + (home-page "https://invent.kde.org/pim/ksmtp") (synopsis "Library for sending email through an SMTP server") (description "This library provides an API for handling SMTP services. SMTP (Simple Mail Transfer Protocol) is the most prevalent Internet @@ -1863,7 +1863,7 @@ and allows one to view/extract message formatted text in Rich Text Format.") ("kwallet" ,kwallet) ("kwidgetsaddons" ,kwidgetsaddons) ("qtbase" ,qtbase))) - (home-page "https://cgit.kde.org/libkdepim.git") + (home-page "https://invent.kde.org/pim/libkdepim") (synopsis "Libraries for common KDE PIM apps") (description "This package provided libraries for common KDE PIM apps.") (license ;; GPL for programs, LGPL for libraries @@ -1898,7 +1898,7 @@ and allows one to view/extract message formatted text in Rich Text Format.") ("qtwebengine" ,qtwebengine))) (arguments `(#:tests? #f)) ;; TODO 6/48 tests fail - (home-page "https://cgit.kde.org/libkgapi.git") + (home-page "https://invent.kde.org/pim/libkgapi") (synopsis "Library for accessing various Google services via their public API") (description "@code{LibKGAPI} is a C++ library that implements APIs for @@ -1936,7 +1936,7 @@ various Google services.") ("kpimtextedit" ,kpimtextedit) ("qgpgme" ,qgpgme) ("qtbase" ,qtbase))) - (home-page "https://cgit.kde.org/libkleo.git/") + (home-page "https://invent.kde.org/pim/libkleo") (synopsis "KDE PIM cryptographic library") (description "@code{libkleo} is a library for Kleopatra and other parts of KDE using certificate-based crypto.") @@ -1999,7 +1999,7 @@ KDE using certificate-based crypto.") ((".*sieveeditorgraphicalmodewidgettest\\.cpp.*") "")) #t))))) - (home-page "https://cgit.kde.org/libksieve.git") + (home-page "https://invent.kde.org/pim/libksieve") (synopsis "KDE Sieve library") (description "Sieve is a language that can be used filter emails. KSieve is a Sieve parser and interpreter library for KDE.") diff --git a/gnu/packages/kde-plasma.scm b/gnu/packages/kde-plasma.scm index c53f6b29c7..e18d521ad2 100644 --- a/gnu/packages/kde-plasma.scm +++ b/gnu/packages/kde-plasma.scm @@ -52,7 +52,7 @@ (inputs `(("ki18n" ,ki18n) ("qtbase" ,qtbase))) - (home-page "https://cgit.kde.org/kdecoration.git") + (home-page "https://invent.kde.org/plasma/kdecoration") (synopsis "Plugin based library to create window decorations") (description "KDecoration is a library to create window decorations. These window decorations can be used by for example an X11 based window @@ -119,7 +119,7 @@ manager which re-parents a Client window to a window decoration frame.") ("solid" ,solid) ("wayland" ,wayland) ("xcb-util-keysyms" ,xcb-util-keysyms))) - (home-page "https://cgit.kde.org/kscreenlocker.git") + (home-page "https://invent.kde.org/plasma/kscreenlocker") (synopsis "Screen locking library") (description "@code{kscreenlocker} is a library for creating secure lock screens.") diff --git a/gnu/packages/kde.scm b/gnu/packages/kde.scm index 1f747ecfd4..601b2bba8b 100644 --- a/gnu/packages/kde.scm +++ b/gnu/packages/kde.scm @@ -130,7 +130,7 @@ This package contains GUI widgets for baloo.") ("kiconthemes" ,kiconthemes) ("knewstuff" ,knewstuff) ("qtbase" ,qtbase))) - (home-page "https://cgit.kde.org/grantleetheme.git") + (home-page "https://invent.kde.org/pim/grantleetheme") (synopsis "Library providing Grantlee theme support") (description "This library provides Grantlee theme support.") (license ;; LGPL for libraries, FDL for documentation @@ -362,7 +362,7 @@ for some KDevelop language plugins (Ruby, PHP, CSS...).") (inputs `(("qtbase" ,qtbase) ("qtsvg" ,qtsvg))) - (home-page "https://cgit.kde.org/kdiagram.git/") + (home-page "https://invent.kde.org/graphics/kdiagram") (synopsis "Libraries for creating business diagrams") (description "This package provides libraries for integrating business diagrams in Qt-based applications. -- cgit v1.2.3 From 2a951e87c5122c2941eac58fe5edac7dbe005209 Mon Sep 17 00:00:00 2001 From: Leo Prikler Date: Thu, 10 Dec 2020 20:03:11 +0100 Subject: gnu: pygame-sdl2-for-renpy: Drop generated sources in snippet. * gnu/packages/game-development.scm (pygame-sdl2-for-renpy)[source]: Add (guix build utils). [#:phases]: Move from here... [source]: ... to here. Signed-off-by: Nicolas Goaziou --- gnu/packages/game-development.scm | 14 ++++++++------ 1 file changed, 8 insertions(+), 6 deletions(-) diff --git a/gnu/packages/game-development.scm b/gnu/packages/game-development.scm index c57ea5a908..557f02f564 100644 --- a/gnu/packages/game-development.scm +++ b/gnu/packages/game-development.scm @@ -1071,7 +1071,14 @@ to create fully featured games and multimedia programs in the python language.") (method url-fetch) (uri (string-append "https://www.renpy.org/dl/" renpy-version "/pygame_sdl2-" version ".tar.gz")) - (sha256 (base32 "1bmr7j9mlsc4czpgw70ld15ymyp4wxrk9hdsqad40wjwdxvvg2dr")))) + (sha256 (base32 "1bmr7j9mlsc4czpgw70ld15ymyp4wxrk9hdsqad40wjwdxvvg2dr")) + (modules '((guix build utils))) + (snippet + '(begin + ;; drop generated sources + (delete-file-recursively "gen") + (delete-file-recursively "gen3") + #t)))) (build-system python-build-system) (arguments `(#:tests? #f ; tests require pygame to be installed first @@ -1090,11 +1097,6 @@ to create fully featured games and multimedia programs in the python language.") "/lib -Wl,-rpath," (assoc-ref inputs "sdl-union") "/lib -Wl,--enable-new-dtags -lSDL2")) - #t)) - (add-before 'build 'drop-generated-files - (lambda args - (delete-file-recursively "gen") - (delete-file-recursively "gen3") #t))))) (inputs `(("sdl-union" -- cgit v1.2.3 From 1592491c39af02a2f651ccd4d0d9cf97104e352f Mon Sep 17 00:00:00 2001 From: Leo Prikler Date: Thu, 10 Dec 2020 20:03:12 +0100 Subject: gnu: renpy: Use system fribidi and drop generated sources. * gnu/packages/patches/renpy-use-system-fribidi.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it here. * gnu/packages/game-development.scm (renpy)[source] Use it here. : Add (guix build utils). : Drop generated sources and fribidi sources. (arguments)[phases]: Add fix-include-paths. (inputs): Add fribidi. Signed-off-by: Nicolas Goaziou --- gnu/local.mk | 1 + gnu/packages/game-development.scm | 21 ++++++++- .../patches/renpy-use-system-fribidi.patch | 52 ++++++++++++++++++++++ 3 files changed, 73 insertions(+), 1 deletion(-) create mode 100644 gnu/packages/patches/renpy-use-system-fribidi.patch diff --git a/gnu/local.mk b/gnu/local.mk index f8c615a83d..18a2389514 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -1569,6 +1569,7 @@ dist_patch_DATA = \ %D%/packages/patches/rct-add-missing-headers.patch \ %D%/packages/patches/readline-link-ncurses.patch \ %D%/packages/patches/readline-6.2-CVE-2014-2524.patch \ + %D%/packages/patches/renpy-use-system-fribidi.patch \ %D%/packages/patches/reposurgeon-add-missing-docbook-files.patch \ %D%/packages/patches/r-httpuv-1.5.4-unvendor-libuv.patch \ %D%/packages/patches/ri-li-modernize_cpp.patch \ diff --git a/gnu/packages/game-development.scm b/gnu/packages/game-development.scm index 557f02f564..21f7f7e880 100644 --- a/gnu/packages/game-development.scm +++ b/gnu/packages/game-development.scm @@ -1120,7 +1120,18 @@ developed mainly for Ren'py.") (method url-fetch) (uri (string-append "https://www.renpy.org/dl/" version "/renpy-" version "-source.tar.bz2")) - (sha256 (base32 "1anr5cfbvbsbik4v4rvrkdkciwhg700k4lydfbs4n85raimz9mw4")))) + (sha256 (base32 "1anr5cfbvbsbik4v4rvrkdkciwhg700k4lydfbs4n85raimz9mw4")) + (modules '((guix build utils))) + (patches + (search-patches + "renpy-use-system-fribidi.patch")) + (snippet + '(with-directory-excursion "module" + ;; drop generated sources + (delete-file-recursively "gen") + ;; drop fribidi sources + (delete-file-recursively "fribidi-src") + #t)))) (build-system python-build-system) (arguments `(#:tests? #f ; Ren'py doesn't seem to package tests @@ -1133,6 +1144,13 @@ developed mainly for Ren'py.") (("xdg-open") (which "xdg-open"))) #t)) + (add-after 'unpack 'fix-include-paths + (lambda* (#:key inputs #:allow-other-keys) + (substitute* "module/setup.py" + (("/usr/include/fribidi") + (string-append (assoc-ref inputs "fribidi") + "/include/fribidi"))) + #t)) (add-after 'set-paths 'set-build-vars (lambda* (#:key inputs #:allow-other-keys) (setenv "RENPY_CYTHON" @@ -1170,6 +1188,7 @@ developed mainly for Ren'py.") (inputs `(("ffmpeg" ,ffmpeg) ("freetype" ,freetype) + ("fribidi" ,fribidi) ("glew" ,glew) ("libpng" ,libpng) ("python2-pygame" ,python2-pygame-sdl2) diff --git a/gnu/packages/patches/renpy-use-system-fribidi.patch b/gnu/packages/patches/renpy-use-system-fribidi.patch new file mode 100644 index 0000000000..1437274bcc --- /dev/null +++ b/gnu/packages/patches/renpy-use-system-fribidi.patch @@ -0,0 +1,52 @@ +See also [Arch] and [Gentoo] for similar patches in other distros. +[Arch] https://github.com/archlinux/svntogit-community/blob/packages/renpy/trunk/renpy-system-fribidi.patch +[Gentoo] https://gitweb.gentoo.org/repo/gentoo.git/tree/games-engines/renpy/files/renpy-7.3.5-use-system-fribidi.patch + +Index: renpy-7.3.5-source/module/renpybidicore.c +=================================================================== +--- renpy-7.3.5-source.orig/module/renpybidicore.c ++++ renpy-7.3.5-source/module/renpybidicore.c +@@ -1,5 +1,5 @@ + #include +-#include ++#include + #include + + #ifndef alloca +Index: renpy-7.3.5-source/module/setup.py +=================================================================== +--- renpy-7.3.5-source.orig/module/setup.py ++++ renpy-7.3.5-source/module/setup.py +@@ -119,30 +119,13 @@ cython( + sdl + [ png, 'z', 'm' ]) + + FRIBIDI_SOURCES = """ +-fribidi-src/lib/fribidi.c +-fribidi-src/lib/fribidi-arabic.c +-fribidi-src/lib/fribidi-bidi.c +-fribidi-src/lib/fribidi-bidi-types.c +-fribidi-src/lib/fribidi-deprecated.c +-fribidi-src/lib/fribidi-joining.c +-fribidi-src/lib/fribidi-joining-types.c +-fribidi-src/lib/fribidi-mem.c +-fribidi-src/lib/fribidi-mirroring.c +-fribidi-src/lib/fribidi-run.c +-fribidi-src/lib/fribidi-shape.c + renpybidicore.c + """.split() + cython( + "_renpybidi", + FRIBIDI_SOURCES, +- includes=[ +- BASE + "/fribidi-src/", +- BASE + "/fribidi-src/lib/", +- ], +- define_macros=[ +- ("FRIBIDI_ENTRY", ""), +- ("HAVE_CONFIG_H", "1"), +- ]) ++ includes=["/usr/include/fribidi"], ++ libs=["fribidi"]) + + + cython("_renpysteam", language="c++", compile_if=steam_sdk, libs=["steam_api"]) -- cgit v1.2.3 From 6760578c89bfbc32b55f860dc63a0b1513dd95d3 Mon Sep 17 00:00:00 2001 From: Christopher Lam Date: Fri, 11 Dec 2020 13:23:38 +0000 Subject: gnu: GnuCash: Update to 4.2. * gnu/packages/gnucash.scm (gnucash): Update to 4.2. [inputs]: Replace guile-2.0 with guile-3.0. Remove libgnomecanvas. Add swig. [arguments]: Adjust the 'fix-finance-quote-check' substitution. (gnucash-docs)[source]: Update hash. Signed-off-by: Leo Famulari --- gnu/packages/gnucash.scm | 18 ++++++++++-------- 1 file changed, 10 insertions(+), 8 deletions(-) diff --git a/gnu/packages/gnucash.scm b/gnu/packages/gnucash.scm index dcee4dc166..455c791816 100644 --- a/gnu/packages/gnucash.scm +++ b/gnu/packages/gnucash.scm @@ -7,6 +7,7 @@ ;;; Copyright © 2019 Maxim Cournoyer ;;; Copyright © 2019 Guillaume Le Vaillant ;;; Copyright © 2020 Prafulla Giri +;;; Copyright © 2020 Christopher Lam ;;; ;;; This file is part of GNU Guix. ;;; @@ -51,6 +52,7 @@ #:use-module (gnu packages perl) #:use-module (gnu packages pkg-config) #:use-module (gnu packages python) + #:use-module (gnu packages swig) #:use-module (gnu packages tls) #:use-module (gnu packages web) #:use-module (gnu packages webkit) @@ -61,28 +63,28 @@ ;; directory. (package (name "gnucash") - (version "3.8") + (version "4.2") (source (origin (method url-fetch) (uri (string-append "mirror://sourceforge/gnucash/gnucash%20%28stable%29/" - version "/gnucash-" version "b" ".tar.bz2")) + version "/gnucash-" version ".tar.bz2")) (sha256 (base32 - "0dvzm3bib7jcj685sklpzyy9mrak9mxyvih2k9fk4sl3v21wlphg")))) + "020k1mm909dcgs52ls4v7xx3yn8gqazi9awyr81l6y7pkq1spn2n")))) (build-system cmake-build-system) (inputs - `(("guile" ,guile-2.2) + `(("guile" ,guile-3.0) ("boost" ,boost) ("icu4c" ,icu4c) ("glib" ,glib) ("gtk" ,gtk+) ("libdbi" ,libdbi) ("libdbi-drivers" ,libdbi-drivers) - ("libgnomecanvas" ,libgnomecanvas) ("libofx" ,libofx) ("libxml2" ,libxml2) ("libxslt" ,libxslt) + ("swig" ,swig) ("webkitgtk" ,webkitgtk) ("aqbanking" ,aqbanking) ("python" ,python) @@ -134,8 +136,8 @@ ;; execute them with perl, so execute them directly instead. (add-after 'unpack 'fix-finance-quote-check (lambda _ - (substitute* "libgnucash/scm/price-quotes.scm" - (("\"perl\" \"-w\" ") "")) + (substitute* "gnucash/price-quotes.scm" + (("\"perl\" \"-w\" ") "")) #t)) ;; The qof test requires the en_US, en_GB, and fr_FR locales. (add-before 'check 'install-locales @@ -230,7 +232,7 @@ installed as well as Yelp, the Gnome help browser.") version "/gnucash-docs-" version revision ".tar.gz")) (sha256 (base32 - "19v6kchda724xkkgwlw5rg21jcpirhch12j9sr6ibnv61sd4ql52")))) + "1p1rbv0gyi07nh5pzhk3xm46w66kjyaipb6rpaq9yb9gil1nl7q5")))) (build-system gnu-build-system) ;; These are native-inputs because they are only required for building the ;; documentation. -- cgit v1.2.3 From f98e3adcd533a4a4c5482343a26d01076e946f92 Mon Sep 17 00:00:00 2001 From: John Soo Date: Thu, 12 Nov 2020 23:04:27 -0800 Subject: gnu: emacs-guix: Update to 0.5.2.3-a694fdb. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Fixes . * gnu/packages/emacs-xyz.scm (emacs-guix): Update to a694fdb. [inputs]: Use guile from guix. Signed-off-by: Ludovic Courtès --- gnu/packages/emacs-xyz.scm | 12 +++++++----- 1 file changed, 7 insertions(+), 5 deletions(-) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 2318027c58..69b05048e4 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -2764,20 +2764,21 @@ type, for example: packages, buffers, files, etc.") (license license:gpl3+))) (define-public emacs-guix - (let ((commit "58a840d0671091e3064e36244790ef8839da87d6") - (revision "2")) + (let* ((commit "a694fdbcedb6edd2239a31d326e475c763ee32f8") + (revision "3")) (package (name "emacs-guix") (version (git-version "0.5.2" revision commit)) (source (origin (method git-fetch) (uri (git-reference - (url "https://gitlab.com/emacs-guix/emacs-guix") + ;; TODO: Use the official version when it has a new home + (url "https://github.com/jsoo1/guix.el") (commit commit))) (file-name (git-file-name name version)) (sha256 (base32 - "1qnr5sixmvrhr9rinrhfy7sy20mikjvvwbdixwkbx30qpcdwgwj1")))) + "1pqw7zbgxzwpig4xr0izc3z8h80c72i6bl5yi12br0d7aq6dbkvj")))) (build-system gnu-build-system) (native-inputs `(("autoconf" ,autoconf) @@ -2786,7 +2787,8 @@ type, for example: packages, buffers, files, etc.") ("texinfo" ,texinfo) ("emacs" ,emacs-minimal))) (inputs - `(("guile" ,@(assoc-ref (package-native-inputs guix) "guile")) + `(("guile" + ,@(assoc-ref (package-native-inputs guix) "guile")) ("guix" ,guix))) (propagated-inputs `(("geiser" ,emacs-geiser) -- cgit v1.2.3 From b52d37daed2084564004b64f76b0d11e94f73068 Mon Sep 17 00:00:00 2001 From: Michael Rohleder Date: Fri, 11 Dec 2020 05:29:32 +0100 Subject: gnu: synapse: Update to 1.24.0. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/matrix.scm (synapse): Update to 1.24.0. Signed-off-by: Ludovic Courtès --- gnu/packages/matrix.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/matrix.scm b/gnu/packages/matrix.scm index 6a6cc628ca..426f26d1e1 100644 --- a/gnu/packages/matrix.scm +++ b/gnu/packages/matrix.scm @@ -61,13 +61,13 @@ an LDAP server.") (define-public synapse (package (name "synapse") - (version "1.22.1") + (version "1.24.0") (source (origin (method url-fetch) (uri (pypi-uri "matrix-synapse" version)) (sha256 (base32 - "1pbxdqpfa7wzdz61p6x58x7841vng1g65qayxgcw73bn1shl50jb")))) + "0pmn8aqc7jj2xdrwljjz2vwg58hlyxp9axac471pcmg2vqais5yb")))) (build-system python-build-system) ;; TODO Run tests with ‘PYTHONPATH=. trial3 tests’. (propagated-inputs -- cgit v1.2.3 From f49746c38a0c58a051cd871d15aef774d6768699 Mon Sep 17 00:00:00 2001 From: Robert Smith Date: Fri, 11 Dec 2020 15:11:29 -0800 Subject: gnu: Add wlr-randr MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/wm.scm (wlr-randr): New variable. Signed-off-by: Ludovic Courtès --- gnu/packages/wm.scm | 22 ++++++++++++++++++++++ 1 file changed, 22 insertions(+) diff --git a/gnu/packages/wm.scm b/gnu/packages/wm.scm index 3569d7f057..6c4f2c6960 100644 --- a/gnu/packages/wm.scm +++ b/gnu/packages/wm.scm @@ -40,6 +40,7 @@ ;;; Copyright © 2020 Guillaume Le Vaillant ;;; Copyright © 2020 B. Wilson ;; Copyright © 2020 Niklas Eklund +;;; Copyright © 2020 Robert Smith ;;; ;;; This file is part of GNU Guix. ;;; @@ -1559,6 +1560,27 @@ modules for building a Wayland compositor.") Wlroots based compositors.") (license license:expat))) ; MIT license +(define-public wlr-randr + (package + (name "wlr-randr") + (version "0.1.0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/emersion/wlr-randr") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "10c8zzp78s5bw34vvjhilipa28bsdx3jbyhnxgp8f8kawh3cvgsc")))) + (build-system meson-build-system) + (inputs `(("wayland" ,wayland))) + (native-inputs `(("pkg-config" ,pkg-config))) + (home-page "https://github.com/emersion/wlr-randr") + (synopsis "Utility to manage Wayland compositor outputs") + (description "wlr-randr is a utility to manage outputs of a Wayland compositor.") + (license license:expat))) ; MIT license + (define-public mako (package (name "mako") -- cgit v1.2.3 From f53c1005248963dfe8765c8c8c3489a156066ef8 Mon Sep 17 00:00:00 2001 From: pukkamustard Date: Mon, 7 Dec 2020 12:55:37 +0100 Subject: gnu: Add guile-sodium. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/guile-xyz.scm (guile-sodium): New variable. Signed-off-by: Ludovic Courtès --- gnu/packages/guile-xyz.scm | 31 +++++++++++++++++++++++++++++++ 1 file changed, 31 insertions(+) diff --git a/gnu/packages/guile-xyz.scm b/gnu/packages/guile-xyz.scm index a844ab7b08..77819f5b01 100644 --- a/gnu/packages/guile-xyz.scm +++ b/gnu/packages/guile-xyz.scm @@ -32,6 +32,7 @@ ;;; Copyright © 2020 Jesse Gibbons ;;; Copyright © 2020 Mike Rosset ;;; Copyright © 2020 Leo Prikler +;;; Copyright © 2020 pukkamustard ;;; ;;; This file is part of GNU Guix. ;;; @@ -58,6 +59,7 @@ #:use-module (gnu packages base) #:use-module (gnu packages bash) #:use-module (gnu packages compression) + #:use-module (gnu packages crypto) #:use-module (gnu packages databases) #:use-module (gnu packages disk) #:use-module (gnu packages emacs) @@ -4176,3 +4178,32 @@ recursively. It also provides new versions of @code{open-output-file}, directory of its argument if it does not exist.") (home-page "https://mkdir-p.divoplade.fr") (license license:asl2.0))) + +(define-public guile-sodium + (package + (name "guile-sodium") + (version "0.1.0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://inqlab.net/git/guile-sodium.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 (base32 "189jsj87hycs57a54x0b9lifwvhr63nypb9vfxdrq7rwrpcvi5f8")))) + (build-system gnu-build-system) + (arguments `()) + (native-inputs + `(("autoconf" ,autoconf) + ("automake" ,automake) + ("pkg-config" ,pkg-config) + ("texinfo" ,texinfo))) + (inputs `(("guile" ,guile-3.0))) + (propagated-inputs `(("libsodium" ,libsodium))) + (synopsis "Guile bindings to the libsodium cryptographic library") + (description + "This package provides Guile bindings to the libsodium cryptographic library +which provides core cryptographic primitives needed to build higher-level +tools.") + (home-page "https://inqlab.net/git/guile-sodium.git") + (license license:gpl3+))) -- cgit v1.2.3 From 208cb960672ccb6b36b82070ae8346d23159a469 Mon Sep 17 00:00:00 2001 From: pukkamustard Date: Mon, 7 Dec 2020 12:55:38 +0100 Subject: gnu: Add guile-eris. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/guile-xyz.scm (guile-eris): New variable. Signed-off-by: Ludovic Courtès --- gnu/packages/guile-xyz.scm | 33 +++++++++++++++++++++++++++++++++ 1 file changed, 33 insertions(+) diff --git a/gnu/packages/guile-xyz.scm b/gnu/packages/guile-xyz.scm index 77819f5b01..dfffbfc62f 100644 --- a/gnu/packages/guile-xyz.scm +++ b/gnu/packages/guile-xyz.scm @@ -4207,3 +4207,36 @@ which provides core cryptographic primitives needed to build higher-level tools.") (home-page "https://inqlab.net/git/guile-sodium.git") (license license:gpl3+))) + +(define-public guile-eris + (package + (name "guile-eris") + (version "0.2.0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://inqlab.net/git/eris.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 (base32 "1ijglmwkdy1l87gj429qfjis0v8b1zlxhbyfhx5za8664h68nqka")))) + (build-system gnu-build-system) + (arguments '()) + (native-inputs + `(("autoconf" ,autoconf) + ("automake" ,automake) + ("pkg-config" ,pkg-config) + ("texinfo" ,texinfo) + ;; test dependency + ("guile-srfi-180" ,guile-srfi-180))) + (inputs `(("guile" ,guile-3.0))) + (propagated-inputs + `(("guile-sodium" ,guile-sodium))) + (synopsis "Guile implementation of the Encoding for Robust Immutable Storage (ERIS)") + (description + "Guile-ERIS is the reference implementation of the Encoding for Robust +Immutable Storage (ERIS). ERIS allows arbirtary content to be encoded into +uniformly sized, encrypted blocks that can be reassembled using a short +read-capability.") + (home-page "https://inqlab.net/git/eris.git") + (license license:gpl3+))) -- cgit v1.2.3 From 18de9e395ff8e67b673f519fe44a849d42aa26ad Mon Sep 17 00:00:00 2001 From: Lars-Dominik Braun Date: Mon, 7 Dec 2020 11:23:19 +0100 Subject: gnu: r-rmarkdown: Add missing propagated input. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/statistics.scm (r-rmarkdown) [propagated-inputs]: Add pandoc-citeproc. Signed-off-by: Ludovic Courtès --- gnu/packages/statistics.scm | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 5d51efff18..c45544f52e 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -2740,7 +2740,8 @@ certain criterion, e.g., it contains a certain regular file.") ("r-tinytex" ,r-tinytex) ("r-xfun" ,r-xfun) ("r-yaml" ,r-yaml) - ("pandoc" ,pandoc))) + ("pandoc" ,pandoc) + ("pandoc-citeproc" ,pandoc-citeproc))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://rmarkdown.rstudio.com") -- cgit v1.2.3 From f765b88cb7ca3a7a28ed5200bd63cafc839646a2 Mon Sep 17 00:00:00 2001 From: Ludovic Courtès Date: Sat, 12 Dec 2020 20:58:36 +0100 Subject: gnu: gnucash: Make SWIG a native input. * gnu/packages/gnucash.scm (gnucash)[inputs]: Move SWIG to... [native-inputs]: ... here. --- gnu/packages/gnucash.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/gnucash.scm b/gnu/packages/gnucash.scm index 455c791816..f71e8209fa 100644 --- a/gnu/packages/gnucash.scm +++ b/gnu/packages/gnucash.scm @@ -84,7 +84,6 @@ ("libofx" ,libofx) ("libxml2" ,libxml2) ("libxslt" ,libxslt) - ("swig" ,swig) ("webkitgtk" ,webkitgtk) ("aqbanking" ,aqbanking) ("python" ,python) @@ -97,6 +96,7 @@ ("googlemock" ,(package-source googletest)) ("googletest" ,googletest) ("gnucash-docs" ,gnucash-docs) + ("swig" ,swig) ("pkg-config" ,pkg-config))) (propagated-inputs ;; dconf is required at runtime according to README.dependencies. -- cgit v1.2.3 From 853c5790d6cbbef68904134d993e41b8618fa430 Mon Sep 17 00:00:00 2001 From: Vinicius Monego Date: Sat, 12 Dec 2020 17:06:12 -0300 Subject: gnu: emacs-fountain-mode: Update to 3.3.3. * gnu/packages/emacs-xyz.scm (emacs-fountain-mode): Update to 3.3.3. Signed-off-by: Nicolas Goaziou --- gnu/packages/emacs-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 69b05048e4..aab881d43b 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -3247,7 +3247,7 @@ files and directories.") (define-public emacs-fountain-mode (package (name "emacs-fountain-mode") - (version "3.3.0") + (version "3.3.3") (source (origin (method git-fetch) @@ -3256,7 +3256,7 @@ files and directories.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "04jrv6i4ah3i8c9hcd9wyaw2vrxr46f50qb9qwna2v7qa5vaway3")))) + (base32 "095nrkg2bap6rcg9hy3bh0nis4v2f8w8d9hnahkzsa3njlpqa4ka")))) (build-system emacs-build-system) (home-page "https://github.com/rnkn/fountain-mode") (synopsis "Major mode for screenwriting in Fountain markup") -- cgit v1.2.3 From 7ae66d9c12b50a2e152b9276865381557f7d3d3f Mon Sep 17 00:00:00 2001 From: Vinicius Monego Date: Sat, 12 Dec 2020 17:13:26 -0300 Subject: gnu: python-onnx: Update to 1.8.0. * gnu/packages/machine-learning.scm (python-onnx): Update to 1.8.0. Signed-off-by: Nicolas Goaziou --- gnu/packages/machine-learning.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm index f1d0922ef2..920b5d82ed 100644 --- a/gnu/packages/machine-learning.scm +++ b/gnu/packages/machine-learning.scm @@ -582,7 +582,7 @@ in terms of new algorithms.") (define-public python-onnx (package (name "python-onnx") - (version "1.7.0") + (version "1.8.0") (source (origin (method url-fetch) @@ -591,7 +591,7 @@ in terms of new algorithms.") ;; to use googletest from Guix and enable tests by default. (patches (search-patches "python-onnx-use-system-googletest.patch")) (sha256 - (base32 "0j6rgfbhsw3a8id8pyg18y93k68lbjbj1kq6qia36h69f6pvlyjy")))) + (base32 "0365zkikq6v3cl5hh2daa5z1alhij8xpn8rmlcny340jrv9pyy2z")))) (build-system python-build-system) (native-inputs `(("cmake" ,cmake) -- cgit v1.2.3 From 5f40ad9ae2a199609ee28640288a69769532dbf0 Mon Sep 17 00:00:00 2001 From: Vinicius Monego Date: Sat, 12 Dec 2020 17:15:28 -0300 Subject: gnu: sleef: Update to 3.5.1. * gnu/packages/maths.scm (sleef): Update to 3.5.1. Signed-off-by: Nicolas Goaziou --- gnu/packages/maths.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index 2ab9621c7f..5c90a4f5c0 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -518,7 +518,7 @@ numbers.") (define-public sleef (package (name "sleef") - (version "3.4.1") + (version "3.5.1") (source (origin (method git-fetch) @@ -527,7 +527,7 @@ numbers.") (commit version))) (file-name (git-file-name name version)) (sha256 - (base32 "1gvf7cfvszmgjrsqivwmyy1jnp3hy80dmszxx827lhjz8yqq5019")))) + (base32 "1jybqrl2dvjxzg30xrhh847s375n2jr1pix644wi6hb5wh5mx3f7")))) (build-system cmake-build-system) (arguments '(#:configure-flags (list "-DCMAKE_BUILD_TYPE=Release" -- cgit v1.2.3 From 4060df28d6c121f5541f2c47c54923df7354ab42 Mon Sep 17 00:00:00 2001 From: Michael Rohleder Date: Sat, 12 Dec 2020 04:05:49 +0100 Subject: gnu: python-parse: Update to 1.18.0. * gnu/packages/python-xyz.scm (python-parse): Update to 1.18.0. Signed-off-by: Nicolas Goaziou --- gnu/packages/python-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index d312e3172a..1f9321c184 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -2184,14 +2184,14 @@ backported for previous versions of Python from 2.4 to 3.3.") (define-public python-parse (package (name "python-parse") - (version "1.8.4") + (version "1.18.0") (source (origin (method url-fetch) (uri (pypi-uri "parse" version)) (sha256 (base32 - "0f8997xr8nq2nq35iiviq8ningd1zvy59fg503xfpbi2dwhgdkf3")))) + "19063x4xdjpaf7rfxai6jpgm2k4yvkq7wha8aa8cagbjsqr60rli")))) (build-system python-build-system) (arguments `(#:phases -- cgit v1.2.3 From 036df7468c49a123d607581138dcee65291c7c6b Mon Sep 17 00:00:00 2001 From: Michael Rohleder Date: Sun, 6 Dec 2020 16:15:26 +0100 Subject: gnu: emacs-list-utils: Suppress warning "Package cl is deprecated". * gnu/packages/emacs-xyz.scm (emacs-list-utils)[arguments]: Add phase patch-require-cl to substitute "(require 'cl)" in a autoload section. Signed-off-by: Nicolas Goaziou --- gnu/packages/emacs-xyz.scm | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index aab881d43b..004c293f52 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -15261,6 +15261,14 @@ and @code{erc-send-modify-hook} to download and show images.") (sha256 (base32 "07hbz2md52ccy95gv4d5n6szrfmpfqf3w4kwqdg2cf54c7kgf7hw")))) (build-system emacs-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'patch-require-cl + (lambda _ + (substitute* "list-utils.el" + (("\\(require 'cl\\)") "(require 'cl-lib)")) + #t))))) (home-page "https://github.com/rolandwalker/list-utils") (synopsis "List-manipulation utility functions") (description "This package provides a list manipulation library for Emacs.") -- cgit v1.2.3 From e799da33ee069e3b6ade08eb72a09499742155f8 Mon Sep 17 00:00:00 2001 From: Morgan Smith Date: Wed, 9 Dec 2020 10:48:03 -0500 Subject: gnu: emacs-bluetooth: Add dbus to inputs * gnu/packages/emacs-xyz.scm (emacs-bluetooth)[inputs, arguments]: Add dbus Signed-off-by: Nicolas Goaziou --- gnu/packages/emacs-xyz.scm | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 004c293f52..ef2c891a27 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -1810,7 +1810,8 @@ mode, Rmail, Gnus, MH-E, and VM). BBDB is fully customizable.") (base32 "1dq04p6ms0zx4awlypp4crkz7dzal4xg8ac7p8fqacz196rczssp")))) (build-system emacs-build-system) (inputs - `(("bluez" ,bluez))) + `(("bluez" ,bluez) + ("dbus" ,dbus))) (propagated-inputs `(("emacs-dash" ,emacs-dash))) (home-page "https://gitlab.com/rstocker/emacs-bluetooth") -- cgit v1.2.3 From e1da617a2037fd3eae073f1e0b8c28d8f8a49469 Mon Sep 17 00:00:00 2001 From: Vinicius Monego Date: Sat, 12 Dec 2020 17:10:46 -0300 Subject: gnu: libredwg: Update to 0.11.1. * gnu/packages/engineering.scm (libredwg): Update to 0.11.1. [native-inputs]: Change python to python-wrapper, add perl. Signed-off-by: Nicolas Goaziou --- gnu/packages/engineering.scm | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/gnu/packages/engineering.scm b/gnu/packages/engineering.scm index e436994492..7eb8bbf893 100644 --- a/gnu/packages/engineering.scm +++ b/gnu/packages/engineering.scm @@ -1133,22 +1133,23 @@ use on a given system.") (define-public libredwg (package (name "libredwg") - (version "0.11") + (version "0.11.1") (source (origin (method url-fetch) (uri (string-append "mirror://gnu/libredwg/libredwg-" version ".tar.xz")) (sha256 - (base32 "1vd7ii32k5447z7k4w9s005hv1ffpj6dyf1w40x6c53qksrblny2")))) + (base32 "1xx6y6ckm4mzqln8y8lqf5frcn2b32ypc0d0h9dzpz6363zh7pdn")))) (build-system gnu-build-system) (arguments `(#:configure-flags '("--disable-bindings"))) (native-inputs `(("libxml2" ,libxml2) ("parallel" ,parallel) + ("perl" ,perl) ("pkg-config" ,pkg-config) - ("python" ,python) + ("python" ,python-wrapper) ("python-libxml2" ,python-libxml2))) (inputs `(("pcre2" ,pcre2))) -- cgit v1.2.3 From 3a87b299257cda788e4955575d6ed829390e1764 Mon Sep 17 00:00:00 2001 From: Joseph LaFreniere Date: Fri, 20 Nov 2020 08:26:40 -0600 Subject: gnu: Add rust-hashbrown-0.1. * gnu/packages/crates-io.scm (rust-hashbrown-0.1): New variable. Signed-off-by: Efraim Flashner --- gnu/packages/crates-io.scm | 33 +++++++++++++++++++++++++++++++++ 1 file changed, 33 insertions(+) diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index a0c31be751..933337ec3a 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -11395,6 +11395,39 @@ hash map.") ("rust-rustc-hash" ,rust-rustc-hash-1) ("rust-serde-test" ,rust-serde-test-1)))))) +(define-public rust-hashbrown-0.1 + (package + (inherit rust-hashbrown-0.5) + (name "rust-hashbrown") + (version "0.1.8") + (source + (origin + (method url-fetch) + (uri (crate-uri "hashbrown" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "1np350nrzysy021ndn2135q5vpzrp5nli78ywz114d1vcnv2kbiv")) + (modules '((guix build utils))) + (snippet + '(begin + (substitute* "Cargo.toml" + (("~1.2") "1.2")) + #t)))) + (arguments + `(#:cargo-inputs + (("rust-byteorder" ,rust-byteorder-1) + ("rust-rayon" ,rust-rayon-1) + ("rust-scopeguard" ,rust-scopeguard-0.3) + ("rust-serde" ,rust-serde-1)) + #:cargo-development-inputs + (("rust-lazy-static" ,rust-lazy-static-1) + ("rust-rand" ,rust-rand-0.5) + ("rust-rayon" ,rust-rayon-1) + ("rust-rustc-hash" ,rust-rustc-hash-1) + ("rust-serde-test" ,rust-serde-test-1)))))) + (define-public rust-hashlink-0.6 (package (name "rust-hashlink") -- cgit v1.2.3 From cd0ce4ab44f8fdf7681d2a0d66019134eb02d66f Mon Sep 17 00:00:00 2001 From: Joseph LaFreniere Date: Fri, 20 Nov 2020 08:26:42 -0600 Subject: gnu: Add rust-escargot-0.3. * gnu/packages/crates-io.scm (rust-escargot-0.3): New variable. Signed-off-by: Efraim Flashner --- gnu/packages/crates-io.scm | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index 933337ec3a..52d6336b94 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -8306,6 +8306,25 @@ variables.") (description "Cargo API written in Paris.") (license (list license:expat license:asl2.0)))) +(define-public rust-escargot-0.3 + (package + (inherit rust-escargot-0.5) + (name "rust-escargot") + (version "0.3.1") + (source + (origin + (method url-fetch) + (uri (crate-uri "escargot" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "19fmn7bz1h6nlqy0mp825xwjwnrjn4xjdpwc06jl51j3fiz1znqr")))) + (arguments + `(#:cargo-inputs + (("rust-serde" ,rust-serde-1) + ("rust-serde-json" ,rust-serde-json-1)))))) + (define-public rust-expat-sys-2.1 (package (name "rust-expat-sys") -- cgit v1.2.3 From 14819a725277e026c95a3db7238469d1251448da Mon Sep 17 00:00:00 2001 From: Joseph LaFreniere Date: Fri, 20 Nov 2020 08:26:43 -0600 Subject: gnu: Add rust-predicates-core-0.9. * gnu/packages/crates-io.scm (rust-predicates-core-0.9): New variable. Signed-off-by: Efraim Flashner --- gnu/packages/crates-io.scm | 15 +++++++++++++++ 1 file changed, 15 insertions(+) diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index 52d6336b94..d907040a5b 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -20351,6 +20351,21 @@ functions.") "An API for boolean-valued predicate functions.") (license (list license:expat license:asl2.0)))) +(define-public rust-predicates-core-0.9 + (package + (inherit rust-predicates-core-1) + (name "rust-predicates-core") + (version "0.9.0") + (source + (origin + (method url-fetch) + (uri (crate-uri "predicates-core" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "1ig5wi3j2faxss6kshv5xdwnchiwbkq2fgx6v962mh6ij31hpy45")))))) + (define-public rust-predicates-tree-1 (package (name "rust-predicates-tree") -- cgit v1.2.3 From aa2da2a31e1472315890cde6f21fc2ed124e2525 Mon Sep 17 00:00:00 2001 From: Joseph LaFreniere Date: Fri, 20 Nov 2020 08:26:44 -0600 Subject: gnu: Add rust-predicates-tree-0.9. * gnu/packages/crates-io.scm (rust-predicates-tree-0.9): New variable. Signed-off-by: Efraim Flashner --- gnu/packages/crates-io.scm | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index d907040a5b..fc6b3bab61 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -20392,6 +20392,25 @@ functions.") "Render boolean-valued predicate functions results as a tree.") (license (list license:expat license:asl2.0)))) +(define-public rust-predicates-tree-0.9 + (package + (inherit rust-predicates-tree-1) + (name "rust-predicates-tree") + (version "0.9.0") + (source + (origin + (method url-fetch) + (uri (crate-uri "predicates-tree" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "1ga0yyfmqbwi28naxlr6cvpmiig0qnwx5adc858hmjxxh6dxz1if")))) + (arguments + `(#:cargo-inputs + (("rust-predicates-core" ,rust-predicates-core-0.9) + ("rust-treeline" ,rust-treeline-0.1)))))) + (define-public rust-pretty-assertions-0.6 (package (name "rust-pretty-assertions") -- cgit v1.2.3 From eb6064a4181edea9df627dc3f6dc57ba6fef583b Mon Sep 17 00:00:00 2001 From: Joseph LaFreniere Date: Fri, 20 Nov 2020 08:26:45 -0600 Subject: gnu: Add rust-normalize-line-endings-0.2. * gnu/packages/crates-io.scm (rust-normalize-line-endings-0.2): New variable. Signed-off-by: Efraim Flashner --- gnu/packages/crates-io.scm | 15 +++++++++++++++ 1 file changed, 15 insertions(+) diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index fc6b3bab61..6639e4cfef 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -17011,6 +17011,21 @@ combinators library.") with all line endings.") (license license:asl2.0))) +(define-public rust-normalize-line-endings-0.2 + (package + (inherit rust-normalize-line-endings-0.3) + (name "rust-normalize-line-endings") + (version "0.2.2") + (source + (origin + (method url-fetch) + (uri (crate-uri "normalize-line-endings" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "1a1knz9j1w5a1pl2q6whmjphm3z6p64r5njnam7syp5rx8wil2if")))))) + (define-public rust-notify-4 (package (name "rust-notify") -- cgit v1.2.3 From 05bec9f68a6b80c52709d8378aa2c99ea89a57bb Mon Sep 17 00:00:00 2001 From: Joseph LaFreniere Date: Fri, 20 Nov 2020 08:26:46 -0600 Subject: gnu: Add rust-predicates-0.9. * gnu/packages/crates-io.scm (rust-predicates-0.9): New variable. Signed-off-by: Efraim Flashner --- gnu/packages/crates-io.scm | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index 6639e4cfef..05e684855b 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -20345,6 +20345,30 @@ dependency to expose a precomputed hash.") functions.") (license (list license:expat license:asl2.0)))) +(define-public rust-predicates-0.9 + (package + (inherit rust-predicates-1) + (name "rust-predicates") + (version "0.9.1") + (source + (origin + (method url-fetch) + (uri (crate-uri "predicates" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "085ysw5iigw9l7fdy0pxqs7h165m9hxaxdknmkyq868izivpj7pk")))) + (arguments + `(#:cargo-inputs + (("rust-difference" ,rust-difference-2) + ("rust-float-cmp" ,rust-float-cmp-0.4) + ("rust-normalize-line-endings" ,rust-normalize-line-endings-0.2) + ("rust-predicates-core" ,rust-predicates-core-0.9) + ("rust-regex" ,rust-regex-1)) + #:cargo-development-inputs + (("rust-predicates-tree" ,rust-predicates-tree-0.9)))))) + (define-public rust-predicates-core-1 (package (name "rust-predicates-core") -- cgit v1.2.3 From 3faab12d4958eb789e18f093c3cde9153609af58 Mon Sep 17 00:00:00 2001 From: Joseph LaFreniere Date: Fri, 20 Nov 2020 08:26:47 -0600 Subject: gnu: Add rust-assert-cmd-0.9. * gnu/packages/crates-io.scm (rust-assert-cmd-0.9): New variable. Signed-off-by: Efraim Flashner --- gnu/packages/crates-io.scm | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index 05e684855b..4dcc06a2d1 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -1081,6 +1081,29 @@ standard library.") (description "Test CLI Applications.") (license (list license:expat license:asl2.0)))) +(define-public rust-assert-cmd-0.9 + (package + (inherit rust-assert-cmd-1) + (name "rust-assert-cmd") + (version "0.9.1") + (source + (origin + (method url-fetch) + (uri (crate-uri "assert-cmd" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "02gq7j9qzjkbyq4hk18cih3kylk3dyxwa2gc5k7lah9kdwkhrdn5")))) + (arguments + `(#:cargo-inputs + (("rust-escargot" ,rust-escargot-0.3) + ("rust-predicates" ,rust-predicates-0.9) + ("rust-predicates-core" ,rust-predicates-core-0.9) + ("rust-predicates-tree" ,rust-predicates-tree-0.9)) + #:cargo-development-inputs + (("rust-docmatic" ,rust-docmatic-0.1)))))) + (define-public rust-assert-fs-0.11 (package (name "rust-assert-fs") -- cgit v1.2.3 From 9bc75a2be9cffd1f5141590ffbf386db1d5083ae Mon Sep 17 00:00:00 2001 From: Joseph LaFreniere Date: Fri, 20 Nov 2020 08:26:48 -0600 Subject: gnu: Add rust-automod-1. * gnu/packages/crates-io.scm (rust-automod-1): New variable. Signed-off-by: Efraim Flashner --- gnu/packages/crates-io.scm | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index 4dcc06a2d1..85d51ba0d6 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -1330,6 +1330,32 @@ methods.") "1chwgimpx5z7xbag7krr9d8asxfqbh683qhgl9kn3hxk2l0djj8x")))) (arguments '(#:skip-build? #t)))) +(define-public rust-automod-1 + (package + (name "rust-automod") + (version "1.0.0") + (source + (origin + (method url-fetch) + (uri (crate-uri "automod" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "1z8kdbvvz0k8mfs45mvs16lr9xj59cdcp0sm45fawfh93gai4mhg")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-inputs + (("rust-proc-macro2" ,rust-proc-macro2-1) + ("rust-quote" ,rust-quote-1) + ("rust-syn" ,rust-syn-1)) + ;; Tests not included in tar. + #:tests? #f)) + (home-page "https://github.com/dtolnay/automod") + (synopsis "Pull in every source file in a directory as a module") + (description "Pull in every source file in a directory as a module.") + (license (list license:expat license:asl2.0)))) + (define-public rust-average-0.10 (package (name "rust-average") -- cgit v1.2.3 From 46ab6c48f0a43a82292edf7f312e484212f04674 Mon Sep 17 00:00:00 2001 From: Joseph LaFreniere Date: Fri, 20 Nov 2020 08:26:49 -0600 Subject: gnu: Add rust-bincode-0.8. * gnu/packages/crates-io.scm (rust-bincode-0.8): New variable. Signed-off-by: Efraim Flashner --- gnu/packages/crates-io.scm | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index 85d51ba0d6..fe564ba176 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -1777,6 +1777,29 @@ tracebacks.") that uses Serde for transforming structs into bytes and vice versa!") (license license:expat))) +(define-public rust-bincode-0.8 + (package + (inherit rust-bincode-1) + (name "rust-bincode") + (version "0.8.1") + (source + (origin + (method url-fetch) + (uri (crate-uri "bincode" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "0nbj0lwykwa1a7sa4303rxgpng9p2hcz9s5d5qcrckrpmcxjsjkf")))) + (arguments + `(#:cargo-inputs + (("rust-byteorder" ,rust-byteorder-1) + ("rust-num-traits" ,rust-num-traits-0.1) + ("rust-serde" ,rust-serde-1)) + #:cargo-development-inputs + (("rust-serde-bytes" ,rust-serde-bytes-0.10) + ("rust-serde-derive" ,rust-serde-derive-1)))))) + (define-public rust-bindgen-0.55 (package (name "rust-bindgen") -- cgit v1.2.3 From 44d233d74d16486cbce02cbfe5defbdc86637c3c Mon Sep 17 00:00:00 2001 From: Joseph LaFreniere Date: Fri, 20 Nov 2020 08:26:50 -0600 Subject: gnu: Add rust-bindgen-0.46. * gnu/packages/crates-io.scm (rust-bindgen-0.46): New variable. Signed-off-by: Efraim Flashner --- gnu/packages/crates-io.scm | 35 +++++++++++++++++++++++++++++++++++ 1 file changed, 35 insertions(+) diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index fe564ba176..6e4be1c810 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -2039,6 +2039,41 @@ bindings to C and C++ libraries.") ("rust-diff" ,rust-diff-0.1) ("rust-shlex" ,rust-shlex-0.1)))))) +(define-public rust-bindgen-0.46 + (package + (inherit rust-bindgen-0.50) + (name "rust-bindgen") + (version "0.46.0") + (source + (origin + (method url-fetch) + (uri (crate-uri "bindgen" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "1qclvj5pydn5camw396b0r3nz4nn3p5wpxg4fgg1favp043pyzwg")))) + (arguments + `(#:cargo-inputs + (("rust-bitflags" ,rust-bitflags-1) + ("rust-cexpr" ,rust-cexpr-0.3) + ("rust-cfg-if" ,rust-cfg-if-0.1) + ("rust-clang-sys" ,rust-clang-sys-0.26) + ("rust-clap" ,rust-clap-2) + ("rust-env-logger" ,rust-env-logger-0.6) + ("rust-hashbrown" ,rust-hashbrown-0.1) + ("rust-lazy-static" ,rust-lazy-static-1) + ("rust-log" ,rust-log-0.4) + ("rust-peeking-take-while" ,rust-peeking-take-while-0.1) + ("rust-proc-macro2" ,rust-proc-macro2-0.4) + ("rust-quote" ,rust-quote-0.6) + ("rust-regex" ,rust-regex-1) + ("rust-which" ,rust-which-2.0)) + #:cargo-development-inputs + (("rust-clap" ,rust-clap-2) + ("rust-diff" ,rust-diff-0.1) + ("rust-shlex" ,rust-shlex-0.1))))) ) + (define-public rust-bindgen-0.37 (package (inherit rust-bindgen-0.50) -- cgit v1.2.3 From 4964b17e38153a5f23bc61910754d9bb38aa5c27 Mon Sep 17 00:00:00 2001 From: Joseph LaFreniere Date: Fri, 20 Nov 2020 08:26:52 -0600 Subject: gnu: Add rust-cachedir-0.1. * gnu/packages/crates-io.scm (rust-cachedir-0.1): New variable. Signed-off-by: Efraim Flashner --- gnu/packages/crates-io.scm | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index 6e4be1c810..51f31ce1e8 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -3324,6 +3324,32 @@ exposed as Reader/Writer streams.") "The ChaCha family of stream ciphers.") (license (list license:asl2.0 license:expat)))) +(define-public rust-cachedir-0.1 + (package + (name "rust-cachedir") + (version "0.1.1") + (source + (origin + (method url-fetch) + (uri (crate-uri "cachedir" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "1j18j73fxrr82marcdrn86123vr9v5n0fgyjkf9mi9pzyk8hjrf0")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-inputs + (("rust-tempfile" ,rust-tempfile-3)) + ;; Tests require a mutable home directory and access to /var/tmp. + #:tests? #f)) + (home-page "https://github.com/lilianmoraru/cachedir") + (synopsis "Interact with cache directories and @file{CACHEDIR.TAG} files") + (description + "This package provides a library to help interacting with cache +directories and @code{CACHEDIR.TAG} files.") + (license (list license:expat license:asl2.0)))) + (define-public rust-calloop-0.4 (package (name "rust-calloop") -- cgit v1.2.3 From fb7f184af4779bf516b55782c393a7330b3ea770 Mon Sep 17 00:00:00 2001 From: Joseph LaFreniere Date: Fri, 20 Nov 2020 08:26:53 -0600 Subject: gnu: Add rust-cfg-if-1. * gnu/packages/crates-io.scm (rust-cfg-if-1): New variable. Signed-off-by: Efraim Flashner --- gnu/packages/crates-io.scm | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index 51f31ce1e8..8d176ea18e 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -3732,6 +3732,32 @@ archive to be linked into Rustcode.") #:cargo-development-inputs (("rust-clang-sys" ,rust-clang-sys-0.11)))))) +(define-public rust-cfg-if-1 + (package + (name "rust-cfg-if") + (version "1.0.0") + (source + (origin + (method url-fetch) + (uri (crate-uri "cfg-if" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "1za0vb97n4brpzpv8lsbnzmq5r8f2b0cpqqr0sy8h5bn751xxwds")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-inputs + (("rust-compiler-builtins" ,rust-compiler-builtins-0.1) + ("rust-rustc-std-workspace-core" ,rust-rustc-std-workspace-core-1)))) + (home-page "https://github.com/alexcrichton/cfg-if") + (synopsis "Define an item depending on parameters") + (description "This package provides a macro to ergonomically define an +item depending on a large number of @code{#[cfg]} parameters. Structured like +an @code{if-else} chain, the first matching branch is the item that gets +emitted.") + (license (list license:asl2.0 license:expat)))) + (define-public rust-cfg-if-0.1 (package (name "rust-cfg-if") -- cgit v1.2.3 From 24e6f5a2a974be09a3029c51b5b9220235237cfb Mon Sep 17 00:00:00 2001 From: Joseph LaFreniere Date: Fri, 20 Nov 2020 08:26:54 -0600 Subject: gnu: rust-chrono-0.4: Update to 0.4.19. * gnu/packages/crates-io.scm (rust-chrono-0.4): Update to 0.4.19. [arguments]: In cargo-inputs add rust-libc-0.2, rust-pure-rust-locales-0.5. In cargo-development-inputs replace rust-criterion-0.2 with 0.3, rust-wasm-bindgen-test-0.2 with 0.3. Don't skip build, skip tests. Build with 'unstable-locales' features. Signed-off-by: Efraim Flashner --- gnu/packages/crates-io.scm | 24 +++++++++++++----------- 1 file changed, 13 insertions(+), 11 deletions(-) diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index 8d176ea18e..b0362c9f4e 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -3786,7 +3786,7 @@ depending on a large number of #[cfg] parameters. Structured like an (define-public rust-chrono-0.4 (package (name "rust-chrono") - (version "0.4.13") + (version "0.4.19") (source (origin (method url-fetch) @@ -3795,28 +3795,30 @@ depending on a large number of #[cfg] parameters. Structured like an (string-append name "-" version ".tar.gz")) (sha256 (base32 - "1dm0q1kmk2vq5djwhp1j9cm4aa38wr9vy1i1w19p2y0nj4188kf7")))) + "0wyfl6c00vhfl562spnfcna3zkw8jqvcp652m9iskhl8j26dc2k7")))) (build-system cargo-build-system) (arguments - `(#:skip-build? #t - #:cargo-inputs - (("rust-num-integer" ,rust-num-integer-0.1) + `(#:cargo-inputs + (("rust-js-sys" ,rust-js-sys-0.3) + ("rust-libc" ,rust-libc-0.2) + ("rust-num-integer" ,rust-num-integer-0.1) ("rust-num-traits" ,rust-num-traits-0.2) - ("rust-js-sys" ,rust-js-sys-0.3) + ("rust-pure-rust-locales" ,rust-pure-rust-locales-0.5) ("rust-rustc-serialize" ,rust-rustc-serialize-0.3) ("rust-serde" ,rust-serde-1) ("rust-time" ,rust-time-0.1) ("rust-wasm-bindgen" ,rust-wasm-bindgen-0.2)) #:cargo-development-inputs - (;("rust-bincode" ,rust-bincode-0.8) - ("rust-criterion" ,rust-criterion-0.2) + (("rust-bincode" ,rust-bincode-0.8) + ("rust-criterion" ,rust-criterion-0.3) ("rust-doc-comment" ,rust-doc-comment-0.3) ("rust-num-iter" ,rust-num-iter-0.1) ("rust-serde-derive" ,rust-serde-derive-1) ("rust-serde-json" ,rust-serde-json-1) - ("rust-wasm-bindgen-test" ,rust-wasm-bindgen-test-0.2)))) - (home-page - "https://github.com/chronotope/chrono") + ("rust-wasm-bindgen-test" ,rust-wasm-bindgen-test-0.3)) + #:features '("unstable-locales") + #:tests? #f)) + (home-page "https://github.com/chronotope/chrono") (synopsis "Date and time library for Rust") (description "Date and time library for Rust.") (license (list license:expat license:asl2.0)))) -- cgit v1.2.3 From 5ef65f0e61ab0051d44ad9dce995052a5b7a7367 Mon Sep 17 00:00:00 2001 From: Joseph LaFreniere Date: Fri, 20 Nov 2020 08:26:55 -0600 Subject: gnu: rust-derive-more-0.99: Update to 0.99.11. * gnu/packages/crates-io.scm (rust-derive-more-0.99): Update to 0.99.11. Signed-off-by: Efraim Flashner --- gnu/packages/crates-io.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index b0362c9f4e..98d8ca25bc 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -6690,7 +6690,7 @@ error-chain.") (define-public rust-derive-more-0.99 (package (name "rust-derive-more") - (version "0.99.9") + (version "0.99.11") (source (origin (method url-fetch) @@ -6699,7 +6699,7 @@ error-chain.") (string-append name "-" version ".tar.gz")) (sha256 (base32 - "0xizcpj39rx0474mbbx8m0xww98qh92zsg82gf52qnvbryqri299")))) + "131xrz5nmnh8zq3vcvv0wfpcaflypbxp3fin984fsqddc5hhxjs1")))) (build-system cargo-build-system) (arguments `(#:tests? #f ; Some test files missing. -- cgit v1.2.3 From 799a91fec4211ad916dade3bf421f353d0e26497 Mon Sep 17 00:00:00 2001 From: Joseph LaFreniere Date: Fri, 20 Nov 2020 08:26:56 -0600 Subject: gnu: Add rust-dirs-sys-next-0.1. * gnu/packages/crates-io.scm (rust-dirs-sys-next-0.1): New variable. Signed-off-by: Efraim Flashner --- gnu/packages/crates-io.scm | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index 98d8ca25bc..237405210c 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -7144,6 +7144,27 @@ standard locations of directories for config, cache and other data.") and @code{directories} crates.") (license (list license:asl2.0 license:expat)))) +(define-public rust-dirs-sys-next-0.1 + (package + (inherit rust-dirs-sys-0.3) + (name "rust-dirs-sys-next") + (version "0.1.1") + (source + (origin + (method url-fetch) + (uri (crate-uri "dirs-sys-next" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "0zgy7is3h2dyf1l4sa7k065w2kvx0l12l40my4rswm2mc1gkdplr")))) + (arguments + `(#:cargo-inputs + (("rust-libc" ,rust-libc-0.2) + ("rust-redox-users" ,rust-redox-users-0.3) + ("rust-winapi" ,rust-winapi-0.3)))) + (home-page "https://github.com/xdg-rs/dirs/tree/master/dirs-sys"))) + (define-public rust-discard-1.0 (package (name "rust-discard") -- cgit v1.2.3 From 70f3d89bb9f7515e10fff60533aee39c9249703f Mon Sep 17 00:00:00 2001 From: Joseph LaFreniere Date: Fri, 20 Nov 2020 08:26:57 -0600 Subject: gnu: Add rust-dirs-next-1. * gnu/packages/crates-io.scm (rust-dirs-next-1): New variable. Signed-off-by: Efraim Flashner --- gnu/packages/crates-io.scm | 22 ++++++++++++++++++++++ 1 file changed, 22 insertions(+) diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index 237405210c..1fcc5cafbd 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -7116,6 +7116,28 @@ standard locations of directories for config, cache and other data.") ("rust-redox-users" ,rust-redox-users-0.3) ("rust-winapi" ,rust-winapi-0.3)))))) +(define-public rust-dirs-next-1 + (package + (inherit rust-dirs-1.0) + (name "rust-dirs-next") + (version "1.0.2") + (source + (origin + (method url-fetch) + (uri (crate-uri "dirs-next" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "1dl2dqzsrcb7qigfiwpdpakhdkpz0629pvylbj2ylyrkh1dfcdng")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-inputs + (("rust-cfg-if" ,rust-cfg-if-1) + ("rust-dirs-sys" ,rust-dirs-sys-next-0.1)))) + (home-page "https://github.com/xdg-rs/dirs") + (license (list license:expat license:asl2.0)))) + (define-public rust-dirs-sys-0.3 (package (name "rust-dirs-sys") -- cgit v1.2.3 From f431cad053fe5e08027b96b75f1bb2bd53d1fa7d Mon Sep 17 00:00:00 2001 From: Joseph LaFreniere Date: Fri, 20 Nov 2020 08:26:58 -0600 Subject: gnu: Add rust-directories-next-1. * gnu/packages/crates-io.scm (rust-directories-next-1): New variable. Signed-off-by: Efraim Flashner --- gnu/packages/crates-io.scm | 22 ++++++++++++++++++++++ 1 file changed, 22 insertions(+) diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index 1fcc5cafbd..527a847b3f 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -7057,6 +7057,28 @@ on Linux, the Known Folder API on Windows, and the Standard Directory guidelines on macOS.") (license (list license:expat license:asl2.0)))) +(define-public rust-directories-next-1 + (package + (inherit rust-directories-3) + (name "rust-directories-next") + (version "1.0.3") + (source + (origin + (method url-fetch) + (uri (crate-uri "directories-next" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "0mmym1h9vlyapwlzygfas3q9mx03mki8cnf5y1bmr713q7mwqa4a")))) + (arguments + `(#:cargo-inputs + (("rust-cfg-if" ,rust-cfg-if-1) + ("rust-dirs-sys" ,rust-dirs-sys-next-0.1)) + #:cargo-development-inputs + (("rust-bencher" ,rust-bencher-0.1)))) + (home-page "https://github.com/xdg-rs/dirs/tree/master/directories"))) + (define-public rust-dirs-3 (package (name "rust-dirs") -- cgit v1.2.3 From 59eb35fb3d673f6a0351a579c47836a7bb101512 Mon Sep 17 00:00:00 2001 From: Joseph LaFreniere Date: Fri, 20 Nov 2020 08:26:59 -0600 Subject: gnu: Add rust-exitfailure-0.5. * gnu/packages/crates-io.scm (rust-exitfailure-0.5): New variable. Signed-off-by: Efraim Flashner --- gnu/packages/crates-io.scm | 29 +++++++++++++++++++++++++++++ 1 file changed, 29 insertions(+) diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index 527a847b3f..dc6296e3a7 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -8551,6 +8551,35 @@ variables.") (("rust-serde" ,rust-serde-1) ("rust-serde-json" ,rust-serde-json-1)))))) +(define-public rust-exitfailure-0.5 + (package + (name "rust-exitfailure") + (version "0.5.1") + (source + (origin + (method url-fetch) + (uri (crate-uri "exitfailure" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "0585wix3b3pjjj90fkqj9x4ar46d24x82k8rdin3czzk5a1vvx9g")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-inputs + (("rust-failure" ,rust-failure-0.1)) + #:cargo-development-inputs + (("rust-assert-cmd" ,rust-assert-cmd-0.9) + ("rust-predicates" ,rust-predicates-0.9)) + ;; Tests fail with "No such file or directory". + #:tests? #f)) + (home-page "https://github.com/tismith/exitfailure") + (synopsis "Provide @code{newtype} wrappers for using @code{?} in @code{main}") + (description + "This package provides a basic @code{newtype} wrappers to help with using +@code{?} in @code{main}.") + (license (list license:expat license:asl2.0)))) + (define-public rust-expat-sys-2.1 (package (name "rust-expat-sys") -- cgit v1.2.3 From 33b11ea782d3be6ac071b2f2b8ded79ddf9572d6 Mon Sep 17 00:00:00 2001 From: Joseph LaFreniere Date: Fri, 20 Nov 2020 08:27:00 -0600 Subject: gnu: Add rust-float-cmp-0.4. * gnu/packages/crates-io.scm (rust-float-cmp-0.4): New variable. Signed-off-by: Efraim Flashner --- gnu/packages/crates-io.scm | 15 +++++++++++++++ 1 file changed, 15 insertions(+) diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index dc6296e3a7..f84faa8e7a 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -9117,6 +9117,21 @@ streams.") (base32 "03hmx3n48hjm0x1ig84n1j87kzp75lzr6cj1sgi6a6pykgn4n8km")))))) +(define-public rust-float-cmp-0.4 + (package + (inherit rust-float-cmp-0.5) + (name "rust-float-cmp") + (version "0.4.0") + (source + (origin + (method url-fetch) + (uri (crate-uri "float-cmp" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "0036jb8ry4h83n319jb20b5yvyfyq8mx8dkxnyjm22nq8fl8yjhk")))))) + (define-public rust-float-cmp-0.3 (package (inherit rust-float-cmp-0.5) -- cgit v1.2.3 From 95f55fecf1a02387cea2f5108fbe2b73bfcdb25b Mon Sep 17 00:00:00 2001 From: Joseph LaFreniere Date: Fri, 20 Nov 2020 08:27:11 -0600 Subject: gnu: Add rust-pure-rust-locales-0.5. * gnu/packages/crates-io.scm (rust-pure-rust-locales-0.5): New variable. Signed-off-by: Efraim Flashner --- gnu/packages/crates-io.scm | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index f84faa8e7a..6f71cf6398 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -21527,6 +21527,31 @@ compliant email address validation.") (description "This package provides a library for async wake signals.") (license license:asl2.0))) +(define-public rust-pure-rust-locales-0.5 + (package + (name "rust-pure-rust-locales") + (version "0.5.3") + (source + (origin + (method url-fetch) + (uri (crate-uri "pure-rust-locales" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "0ryjj0gs4hfadqx9vl4sgi32zyb2dlvwpxca1m1kmrw9hk1g7gv5")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-inputs + (("rust-itertools" ,rust-itertools-0.8) + ("rust-nom" ,rust-nom-5)))) + (home-page "https://github.com/cecton/pure-rust-locales") + (synopsis "Pure Rust locales imported directly from the GNU C Library") + (description + "Pure Rust locales imported directly from the GNU C Library. +@code{LC_COLLATE} and @code{LC_CTYPE} are not yet supported.") + (license license:expat))) + (define-public rust-quantiles-0.7 (package (name "rust-quantiles") -- cgit v1.2.3 From bc49b009bf08326b55aea3508a6b677a065d5a31 Mon Sep 17 00:00:00 2001 From: Vinicius Monego Date: Sat, 12 Dec 2020 17:36:56 -0300 Subject: gnu: python-httpx: Update to 0.16.1. * gnu/packages/python-web.scm (python-httpx): Update to 0.16.1. Signed-off-by: Nicolas Goaziou --- gnu/packages/python-web.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm index 107f579ad6..9195b8328c 100644 --- a/gnu/packages/python-web.scm +++ b/gnu/packages/python-web.scm @@ -4989,7 +4989,7 @@ Some things HTTP Core does do: (define-public python-httpx (package (name "python-httpx") - (version "0.15.4") + (version "0.16.1") (source (origin ;; PyPI tarball does not contain tests. @@ -4999,7 +4999,7 @@ Some things HTTP Core does do: (commit version))) (file-name (git-file-name name version)) (sha256 - (base32 "1qr91xw6jxynvihmw953bi5446ssm9ffmb2c4nhfa77v7883sp21")))) + (base32 "00gmq45fckcqkj910bvd7pyqz1mvgsdvz4s0k7dzbnc5czzq1f4a")))) (build-system python-build-system) (arguments `(#:phases -- cgit v1.2.3 From f3340338d56c2596cc1ed48f05462e333b7cce5e Mon Sep 17 00:00:00 2001 From: Vinicius Monego Date: Sat, 12 Dec 2020 17:12:05 -0300 Subject: gnu: setzer: Update to 0.3.8. * gnu/packages/gnome.scm (setzer): Update to 0.3.8. Signed-off-by: Nicolas Goaziou --- gnu/packages/gnome.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/gnome.scm b/gnu/packages/gnome.scm index 623732d8bc..64fded105a 100644 --- a/gnu/packages/gnome.scm +++ b/gnu/packages/gnome.scm @@ -11504,7 +11504,7 @@ and toolbars.") (define-public setzer (package (name "setzer") - (version "0.3.6") + (version "0.3.8") (source (origin (method git-fetch) @@ -11513,7 +11513,7 @@ and toolbars.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "118gip6bv4mcsq4nrai7kl0vmqqbyzpsd4ky9vhxb1x2cvg048s8")))) + (base32 "1f5qmkz4hzn54sh56z3hw8zrvg93xlz62ggzlzyg7vgsr83kpns9")))) (build-system meson-build-system) (arguments `(#:glib-or-gtk? #t -- cgit v1.2.3 From 18918ebeeb152731e06634a003e8cf3edd24f6a3 Mon Sep 17 00:00:00 2001 From: David Dashyan Date: Sat, 12 Dec 2020 23:03:03 +0300 Subject: gnu: Add openfortivpn * gnu/packages/vpn.scm (openfortivpn): New variable. Signed-off-by: Leo Famulari --- gnu/packages/vpn.scm | 29 +++++++++++++++++++++++++++++ 1 file changed, 29 insertions(+) diff --git a/gnu/packages/vpn.scm b/gnu/packages/vpn.scm index 04c34c3d4d..0c504ca6cc 100644 --- a/gnu/packages/vpn.scm +++ b/gnu/packages/vpn.scm @@ -14,6 +14,7 @@ ;;; Copyright © 2020 Brice Waegeneire ;;; Copyright © 2020 Ryan Prior ;;; Copyright © 2020 Ivan Kozlov +;;; Copyright © 2020 David Dashyan ;;; ;;; This file is part of GNU Guix. ;;; @@ -287,6 +288,34 @@ and probably others.") (license license:lgpl2.1) (home-page "https://www.infradead.org/openconnect/"))) +(define-public openfortivpn + (package + (name "openfortivpn") + (version "1.15.0") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/adrienverge/openfortivpn") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1qsfgpxg553s8rc9cyrc4k96z0pislxsdxb9wyhp8fdprkak2mw2")))) + (build-system gnu-build-system) + (native-inputs + `(("autoconf" ,autoconf) + ("autotools" ,automake) + ("pkg-config" ,pkg-config))) + (inputs + `(("openssl" ,openssl) + ("ppp" ,ppp))) + (home-page "https://github.com/adrienverge/openfortivpn") + (synopsis "Client for PPP+SSL VPN tunnel services") + (description "Openfortivpn is a client for PPP+SSL VPN tunnel services. It +spawns a pppd process and operates the communication between the gateway and +this process. It is compatible with Fortinet VPNs.") + (license license:gpl3+))) + (define-public openvpn (package (name "openvpn") -- cgit v1.2.3 From 8f2656f1debffe92ea088f4c88cfe8ec560b2ba3 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sat, 12 Dec 2020 22:57:16 +0100 Subject: services: pcscd-shepherd-service: Fix PID file location. Fixes . * gnu/services/security-token.scm (pcscd-shepherd-service): Look for pcscd.pid in /run instead of /var/run. Reported by Raffael Stocker . --- gnu/services/security-token.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/services/security-token.scm b/gnu/services/security-token.scm index 354549b33c..da5314e7d5 100644 --- a/gnu/services/security-token.scm +++ b/gnu/services/security-token.scm @@ -57,7 +57,7 @@ (modules '((gnu build shepherd))) (start #~(lambda _ (invoke #$(file-append pcsc-lite "/sbin/pcscd")) - (call-with-input-file "/var/run/pcscd/pcscd.pid" read))) + (call-with-input-file "/run/pcscd/pcscd.pid" read))) (stop #~(make-kill-destructor))))))) (define pcscd-activation -- cgit v1.2.3 From 4c9a4079945c983bfdd7e9ff1ec998451e7ba292 Mon Sep 17 00:00:00 2001 From: Zheng Junjie <873216071@qq.com> Date: Sat, 12 Dec 2020 14:37:27 -0500 Subject: gnu: Add ebook-tools. * gnu/packages/ebook.scm (ebook-tools): New variable. Signed-off-by: Leo Famulari --- gnu/packages/ebook.scm | 28 ++++++++++++++++++++++++++++ 1 file changed, 28 insertions(+) diff --git a/gnu/packages/ebook.scm b/gnu/packages/ebook.scm index a23c677880..f1e2bd49cb 100644 --- a/gnu/packages/ebook.scm +++ b/gnu/packages/ebook.scm @@ -7,6 +7,7 @@ ;;; Copyright © 2018, 2019, 2020 Tobias Geerinckx-Rice ;;; Copyright © 2020 Marius Bakke ;;; Copyright © 2020 Vinicius Monego +;;; Copyright © 2020 Zheng Junjie <873216071@qq.com> ;;; ;;; This file is part of GNU Guix. ;;; @@ -29,6 +30,7 @@ #:use-module (guix download) #:use-module (guix utils) #:use-module (guix git-download) + #:use-module (guix build-system cmake) #:use-module (guix build-system gnu) #:use-module (guix build-system meson) #:use-module (guix build-system python) @@ -314,6 +316,32 @@ e-books for convenient reading.") license:silofl1.1 license:cc-by-sa3.0)))) +(define-public ebook-tools + (package + (name "ebook-tools") + (version "0.2.2") + (source + (origin + (method url-fetch) + (uri (string-append "mirror://sourceforge/ebook-tools/ebook-tools/" + version "/ebook-tools-" version ".tar.gz")) + (sha256 + (base32 + "1bi7wsz3p5slb43kj7lgb3r6lb91lvb6ldi556k4y50ix6b5khyb")))) + (arguments + `(#:tests? #f)) ; No 'test' target + (build-system cmake-build-system) + (native-inputs + `(("pkg-config" ,pkg-config))) + (inputs + `(("libzip" ,libzip) + ("libxml2" ,libxml2))) + (home-page "http://ebook-tools.sourceforge.net") + (synopsis "Tools and library for dealing with various ebook file formats") + (description "This package provides command-line tools and a library for +accessing and converting various ebook file formats.") + (license license:expat))) + (define-public liblinebreak (package (name "liblinebreak") -- cgit v1.2.3 From 7a8d4557593461a69ab2380bec4d2a07a2c08c1e Mon Sep 17 00:00:00 2001 From: Zheng Junjie <873216071@qq.com> Date: Sat, 12 Dec 2020 14:38:08 -0500 Subject: gnu: Add kdegraphics-mobipocket. * gnu/packages/kde.scm (kdegraphics-mobipocket): New variable. Signed-off-by: Leo Famulari --- gnu/packages/kde.scm | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) diff --git a/gnu/packages/kde.scm b/gnu/packages/kde.scm index 601b2bba8b..fff84bafad 100644 --- a/gnu/packages/kde.scm +++ b/gnu/packages/kde.scm @@ -11,6 +11,7 @@ ;;; Copyright © 2020 Marius Bakke ;;; Copyright © 2020 Michael Rohleder ;;; Copyright © 2020 Prafulla Giri +;;; Copyright © 2020 Zheng Junjie <873216071@qq.com> ;;; ;;; This file is part of GNU Guix. ;;; @@ -765,6 +766,28 @@ Python, PHP, and Perl.") (description "Runtime library for kdegames") (license (list license:gpl2+ license:fdl1.2+)))) +(define-public kdegraphics-mobipocket + (package + (name "kdegraphics-mobipocket") + (version "20.12.0") + (source + (origin + (method url-fetch) + (uri (string-append "mirror://kde/stable/release-service/" version + "/src/" name "-" version ".tar.xz")) + (sha256 + (base32 "0fm880lp9g60zgrkjyh4jxws6x0s77l9ia4f8pza3w8sxcbbswk5")))) + (build-system cmake-build-system) + (native-inputs + `(("extra-cmake-modules" ,extra-cmake-modules))) + (inputs + `(("kio" ,kio) + ("qtbase" ,qtbase))) + (home-page "https://apps.kde.org/en/kdegraphics_mobipocket") + (synopsis "KDE thumbnailer for Mobipocket files") + (description "This package provides a KDE plugin that shows thumbnails of +Mobipocket e-books in Dolphin and other KDE apps.") + (license license:gpl2+))) (define-public zeroconf-ioslave (package (name "zeroconf-ioslave") -- cgit v1.2.3 From fdfa25ed7b993597993f0afb355d1da928143e17 Mon Sep 17 00:00:00 2001 From: Zheng Junjie <873216071@qq.com> Date: Sat, 12 Dec 2020 14:38:20 -0500 Subject: gnu: Add libkexiv2. * gnu/packages/kde.scm (libkexiv2): New variable. Signed-off-by: Leo Famulari --- gnu/packages/kde.scm | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) diff --git a/gnu/packages/kde.scm b/gnu/packages/kde.scm index fff84bafad..3a15aa6554 100644 --- a/gnu/packages/kde.scm +++ b/gnu/packages/kde.scm @@ -788,6 +788,30 @@ Python, PHP, and Perl.") (description "This package provides a KDE plugin that shows thumbnails of Mobipocket e-books in Dolphin and other KDE apps.") (license license:gpl2+))) + +(define-public libkexiv2 + (package + (name "libkexiv2") + (version "20.12.0") + (source + (origin + (method url-fetch) + (uri (string-append "mirror://kde/stable/release-service/" version + "/src/" name "-" version ".tar.xz")) + (sha256 + (base32 "0k0iinf7s8qlk3fwvq7iic1b4zn2gm65rfd58q7d3wb1i1j2hjjk")))) + (build-system cmake-build-system) + (native-inputs + `(("extra-cmake-modules" ,extra-cmake-modules))) + (inputs + `(("exiv2" ,exiv2) + ("qtbase" ,qtbase))) + (home-page "https://invent.kde.org/graphics/libkexiv2") + (synopsis "Manipulate the metadata of images") + (description "Libkexiv2 wraps the Exiv2 library, allowing to manipulate +picture metadata as EXIF/IPTC and XMP.") + (license license:gpl2+))) + (define-public zeroconf-ioslave (package (name "zeroconf-ioslave") -- cgit v1.2.3 From 0313617f6585bc41cfab1c6f4455cffca0b4597d Mon Sep 17 00:00:00 2001 From: Vinicius Monego Date: Sat, 12 Dec 2020 17:09:49 -0300 Subject: gnu: veusz: Update to 3.3.1. * gnu/packages/maths.scm (veusz): Update to 3.3.1. Signed-off-by: Nicolas Goaziou --- gnu/packages/maths.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index 5c90a4f5c0..c118e9e25c 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -2211,13 +2211,13 @@ ASCII text files using Gmsh's own scripting language.") (define-public veusz (package (name "veusz") - (version "3.2.1") + (version "3.3.1") (source (origin (method url-fetch) (uri (pypi-uri "veusz" version)) (sha256 - (base32 "00vmfpvyd6f33l5awlf02qdik3gmbhzyfizfwwbx7qnam2i9bbwy")))) + (base32 "1q7hi1qwwg4pgiz62isvv1pia85m13bspdpp1q3mrnwl11in0ag0")))) (build-system python-build-system) (arguments `(;; Tests will fail because they depend on optional packages like -- cgit v1.2.3 From a4cd86ff4b7a9dd4bf1a5320b8121b470e381b67 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sat, 12 Dec 2020 23:24:22 +0100 Subject: gnu: htop: Update to 3.0.3. * gnu/packages/admin.scm (htop): Update to 3.0.3. --- gnu/packages/admin.scm | 4 ++-- gnu/services/security-token.scm | 1 + 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/gnu/packages/admin.scm b/gnu/packages/admin.scm index 9df14b5ca0..d8083d6f7c 100644 --- a/gnu/packages/admin.scm +++ b/gnu/packages/admin.scm @@ -515,7 +515,7 @@ or via the @code{facter} Ruby library.") (define-public htop (package (name "htop") - (version "3.0.2") + (version "3.0.3") (source (origin (method git-fetch) @@ -523,7 +523,7 @@ or via the @code{facter} Ruby library.") (url "https://github.com/htop-dev/htop") (commit version))) (sha256 - (base32 "1qmqhbnc5yw4brd24yrp85k09770c1c00nl03mkv5pdz2bvqivk7")) + (base32 "0ylig6g2w4r3qfb16cf922iriqyn64frkzpk87vpga16kclvf08y")) (file-name (git-file-name name version)))) (build-system gnu-build-system) (inputs diff --git a/gnu/services/security-token.scm b/gnu/services/security-token.scm index da5314e7d5..ec26006538 100644 --- a/gnu/services/security-token.scm +++ b/gnu/services/security-token.scm @@ -1,5 +1,6 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2018 Arun Isaac +;;; Copyright © 2020 Tobias Geerinckx-Rice ;;; ;;; This file is part of GNU Guix. ;;; -- cgit v1.2.3 From 593b3a9da67c15e9bdcbe52d6cbfaa2f7f8ff74a Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sat, 12 Dec 2020 23:28:04 +0100 Subject: gnu: youtube-dl: Update to 2020.12.12. * gnu/packages/video.scm (youtube-dl): Update to 2020.12.12. --- gnu/packages/video.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/video.scm b/gnu/packages/video.scm index 58703d3274..f4c7174c03 100644 --- a/gnu/packages/video.scm +++ b/gnu/packages/video.scm @@ -2190,14 +2190,14 @@ To load this plugin, specify the following option when starting mpv: (define-public youtube-dl (package (name "youtube-dl") - (version "2020.12.07") + (version "2020.12.12") (source (origin (method url-fetch) (uri (string-append "https://youtube-dl.org/downloads/latest/" "youtube-dl-" version ".tar.gz")) (sha256 (base32 - "0sbrwak9c0pbacg15q2wj5fcsj5k5k1sx9jm7rcjwkjdhqcjqrsi")))) + "0iv4l78ylzx8q6myv4v7xq6r5y0hacz6l30bqk1szncfikvfc3cf")))) (build-system python-build-system) (arguments ;; The problem here is that the directory for the man page and completion -- cgit v1.2.3 From 9faee1e64585e99ff2a93fe65ed26a0a28c46ca1 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sat, 12 Dec 2020 23:32:34 +0100 Subject: gnu: openntpd: Update to 6.8p1. * gnu/packages/ntp.scm (openntpd): Update to 6.8p1. --- gnu/packages/ntp.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/ntp.scm b/gnu/packages/ntp.scm index 95d784c62a..6d046eed1b 100644 --- a/gnu/packages/ntp.scm +++ b/gnu/packages/ntp.scm @@ -166,14 +166,14 @@ computers over a network.") (define-public openntpd (package (name "openntpd") - (version "6.2p3") + (version "6.8p1") (source (origin (method url-fetch) (uri (string-append "mirror://openbsd/OpenNTPD/openntpd-" version ".tar.gz")) (sha256 (base32 - "0fn12i4kzsi0zkr4qp3dp9bycmirnfapajqvdfx02zhr4hanj0kv")))) + "0ijsylc7a4jlpxsqa0jq1w1c7333id8pcakzl7a5749ria1xp0l5")))) (build-system gnu-build-system) (arguments '(#:configure-flags `( "--with-privsep-user=ntpd" -- cgit v1.2.3 From 4de58a4b81d47db2e3bc84f5ce728d82aa83c54a Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Sat, 12 Dec 2020 16:36:26 +0100 Subject: download: Update ImageMagick mirror list. * guix/download.scm (%mirrors): Remove defunct ImageMagick mirrors, update URLs for directory structure changes (/releases instead of /legacy). Move official site last. --- guix/download.scm | 21 ++++++--------------- 1 file changed, 6 insertions(+), 15 deletions(-) diff --git a/guix/download.scm b/guix/download.scm index c24e0132c7..494825860e 100644 --- a/guix/download.scm +++ b/guix/download.scm @@ -248,22 +248,13 @@ (imagemagick ;; from http://www.imagemagick.org/script/download.php ;; (without mirrors that are unavailable or not up to date) - ;; mirrors keeping old versions at the top level - "https://sunsite.icm.edu.pl/packages/ImageMagick/" - ;; mirrors moving old versions to "legacy" - "http://mirror.checkdomain.de/imagemagick/" - "http://ftp.surfnet.nl/pub/ImageMagick/" - "http://mirror.searchdaimon.com/ImageMagick" - "http://mirror.is.co.za/pub/imagemagick/" - "http://www.imagemagick.org/download/" - "ftp://mirror.aarnet.edu.au/pub/imagemagick/" - "ftp://ftp.kddlabs.co.jp/graphics/ImageMagick/" - "ftp://ftp.u-aizu.ac.jp/pub/graphics/image/ImageMagick/imagemagick.org/" + "https://sunsite.icm.edu.pl/packages/ImageMagick/releases" + "http://mirror.checkdomain.de/imagemagick/releases" + "ftp://ftp.u-aizu.ac.jp/pub/graphics/image/ImageMagick/imagemagick.org/releases" "ftp://ftp.nluug.nl/pub/ImageMagick/" - "ftp://ftp.tpnet.pl/pub/graphics/ImageMagick/" - "ftp://ftp.fifi.org/pub/ImageMagick/" - ;; one legacy location as a last resort - "http://www.imagemagick.org/download/legacy/") + "http://www.imagemagick.org/download/releases/" + ;; Try this if all else fails (normally contains just the latest version). + "http://www.imagemagick.org/download/") (debian "http://ftp.de.debian.org/debian/" "http://ftp.fr.debian.org/debian/" -- cgit v1.2.3 From 9e78ec5d2459b5b74caa4fd98a68029b4d8c1697 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Sat, 12 Dec 2020 16:58:08 +0100 Subject: gnu: multipath-tools: Use the latest json-c. * gnu/packages/linux.scm (multipath-tools)[inputs]: Change from JSON-C-0.13 to JSON-C. --- gnu/packages/linux.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index 73dec7d1b7..0e9932785d 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -4544,7 +4544,7 @@ arrays when needed.") ;; For tests. ("cmocka" ,cmocka))) (inputs - `(("json-c" ,json-c-0.13) + `(("json-c" ,json-c) ("libaio" ,libaio) ("liburcu" ,liburcu) ("lvm2" ,lvm2) -- cgit v1.2.3 From 38438ea90995a32637b9cc2a481d59150b013612 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Sat, 12 Dec 2020 19:29:45 +0100 Subject: gnu: Remove python2-babel@2.6. * gnu/packages/python-xyz.scm (python2-babel-2.6): Remove variable. --- gnu/packages/python-xyz.scm | 12 ------------ 1 file changed, 12 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 1f9321c184..bfe005dc30 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -719,18 +719,6 @@ etc. ") (define-public python2-babel (package-with-python2 python-babel)) -;; Sphinx < 2.0 requires this version. Remove once no longer needed. -(define-public python2-babel-2.6 - (package - (inherit python2-babel) - (version "2.6.0") - (source (origin - (method url-fetch) - (uri (pypi-uri "Babel" version)) - (sha256 - (base32 - "08rxmbx2s4irp0w0gmn498vns5xy0fagm0fg33xa772jiks51flc")))))) - (define-public python2-backport-ssl-match-hostname (package (name "python2-backport-ssl-match-hostname") -- cgit v1.2.3 From ddeec8cad3c32358f16a326b2f1fe2126aca0158 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Sat, 12 Dec 2020 19:46:23 +0100 Subject: gnu: postgresql: Add 13.1. * gnu/packages/databases.scm (postgresql-13): New public variable. --- gnu/packages/databases.scm | 12 ++++++++++++ 1 file changed, 12 insertions(+) diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm index bfa78556bc..4b1a1ff09d 100644 --- a/gnu/packages/databases.scm +++ b/gnu/packages/databases.scm @@ -1206,6 +1206,18 @@ pictures, sounds, or video.") (define-public postgresql-10 postgresql) +(define-public postgresql-13 + (package + (inherit postgresql) + (version "13.1") + (source (origin + (inherit (package-source postgresql)) + (uri (string-append "https://ftp.postgresql.org/pub/source/v" + version "/postgresql-" version ".tar.bz2")) + (sha256 + (base32 + "07z6zwr58dckaa97yl9ml240z83d1lhgaxw9aq49i8lsp21mqd0j")))))) + (define-public postgresql-11 (package (inherit postgresql) -- cgit v1.2.3 From 1adeb744560af94687eb7c3780c7145c52674070 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Sat, 12 Dec 2020 22:03:37 +0100 Subject: gnu: cURL: Update replacement to 7.74.0 [security fixes]. This fixes CVE-2020-8284, CVE-2020-8285, and CVE-2020-8286. * gnu/packages/curl.scm (curl-7.71.0): Rename to ... (curl-7.74.0): ... this. Update to 7.74.0. (curl)[replacement]: Adjust accordingly. --- gnu/packages/curl.scm | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/gnu/packages/curl.scm b/gnu/packages/curl.scm index 55b7e4393b..33a2188d70 100644 --- a/gnu/packages/curl.scm +++ b/gnu/packages/curl.scm @@ -54,7 +54,7 @@ (package (name "curl") (version "7.69.1") - (replacement curl-7.71.0) + (replacement curl-7.74.0) (source (origin (method url-fetch) (uri (string-append "https://curl.haxx.se/download/curl-" @@ -171,18 +171,18 @@ tunneling, and so on.") (name "curl-minimal") (inputs (alist-delete "openldap" (package-inputs curl)))))) -;; Replacement package to fix CVE-2020-8169 and CVE-2020-8177. -(define curl-7.71.0 +;; Replacement package to fix multiple security vulnerabilities. +(define curl-7.74.0 (package (inherit curl) - (version "7.71.0") + (version "7.74.0") (source (origin (inherit (package-source curl)) (uri (string-append "https://curl.haxx.se/download/curl-" version ".tar.xz")) (sha256 (base32 - "0wlppmx9iry8slh4pqcxj7lwc6fqwnlhh9ri2pcym2rx76a8gwfd")))) + "12w7gskrglg6qrmp822j37fmbr0icrcxv7rib1fy5xiw80n5z7cr")))) (arguments (substitute-keyword-arguments (package-arguments curl) ((#:phases phases) -- cgit v1.2.3