From 3c52c96ca2828c580986a72944c60ae10b6024c3 Mon Sep 17 00:00:00 2001 From: Alexandr Vityazev Date: Thu, 20 May 2021 14:58:14 +0000 Subject: gnu: Remove unnecessary patches for emacs-geiser. * gnu/packages/patches/emacs-geiser-autoload-activate-implementation.patch: * gnu/packages/patches/emacs-geiser-guile-auto-activate.patch: Delete files. * gnu/local.mk (dist_patch_DATA): Apply file removal. Signed-off-by: Nicolas Goaziou --- gnu/local.mk | 2 -- 1 file changed, 2 deletions(-) (limited to 'gnu/local.mk') diff --git a/gnu/local.mk b/gnu/local.mk index 9dac7ea152..b0df9d582d 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -972,8 +972,6 @@ dist_patch_DATA = \ %D%/packages/patches/emacs-exec-path.patch \ %D%/packages/patches/emacs-exwm-fix-fullscreen-states.patch \ %D%/packages/patches/emacs-fix-scheme-indent-function.patch \ - %D%/packages/patches/emacs-geiser-guile-auto-activate.patch \ - %D%/packages/patches/emacs-geiser-autoload-activate-implementation.patch \ %D%/packages/patches/emacs-ignore-empty-xim-styles.patch \ %D%/packages/patches/emacs-json-reformat-fix-tests.patch \ %D%/packages/patches/emacs-highlight-stages-add-gexp.patch \ -- cgit v1.2.3 From 36a90d0637bb47b113ceda5abb64c50600837436 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Wed, 26 May 2021 13:40:59 +0300 Subject: gnu: minimap2: Update to 2.18. * gnu/packages/bioinformatics.scm (minimap2): Update to 2.18. [source]: Remove patch. * gnu/packages/patches/minimap2-aarch64-support.patch: Remove file. * gnu/local.mk (dist_patch_DATA): Remove it. --- gnu/local.mk | 1 - gnu/packages/bioinformatics.scm | 5 +-- .../patches/minimap2-aarch64-support.patch | 52 ---------------------- 3 files changed, 2 insertions(+), 56 deletions(-) delete mode 100644 gnu/packages/patches/minimap2-aarch64-support.patch (limited to 'gnu/local.mk') diff --git a/gnu/local.mk b/gnu/local.mk index b0df9d582d..8355a208ea 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -1424,7 +1424,6 @@ dist_patch_DATA = \ %D%/packages/patches/mingw-w64-6.0.0-gcc.patch \ %D%/packages/patches/mingw-w64-dlltool-temp-prefix.patch \ %D%/packages/patches/mingw-w64-reproducible-gendef.patch \ - %D%/packages/patches/minimap2-aarch64-support.patch \ %D%/packages/patches/minisat-friend-declaration.patch \ %D%/packages/patches/minisat-install.patch \ %D%/packages/patches/mit-krb5-hurd.patch \ diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 074ff8046f..46092fd589 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -12323,7 +12323,7 @@ version does count multisplits.") (define-public minimap2 (package (name "minimap2") - (version "2.17") + (version "2.18") (source (origin (method url-fetch) @@ -12332,8 +12332,7 @@ version does count multisplits.") "minimap2-" version ".tar.bz2")) (sha256 (base32 - "0hi7i9pzxhvjj44khzzzj1lrn5gb5837arr4wgln7k1k5n4ci2mn")) - (patches (search-patches "minimap2-aarch64-support.patch")))) + "1d7fvdqcqd6wns875rkyd7f34ii15gc9l1sivd2wbbpcb0fi0mbs")))) (build-system gnu-build-system) (arguments `(#:tests? #f ; there are none diff --git a/gnu/packages/patches/minimap2-aarch64-support.patch b/gnu/packages/patches/minimap2-aarch64-support.patch deleted file mode 100644 index 95db8579d6..0000000000 --- a/gnu/packages/patches/minimap2-aarch64-support.patch +++ /dev/null @@ -1,52 +0,0 @@ -This patch should be removed with the next release. There is WIP upstream -support for proper support of more architectures, including aarch64 and powerpc64le. - -diff --git a/Makefile b/Makefile -index ed341f6..94dbd85 100644 ---- a/Makefile -+++ b/Makefile -@@ -6,20 +6,18 @@ PROG= minimap2 - PROG_EXTRA= sdust minimap2-lite - LIBS= -lm -lz -lpthread - --ifeq ($(arm_neon),) # if arm_neon is not defined --ifeq ($(sse2only),) # if sse2only is not defined -- OBJS+=ksw2_extz2_sse41.o ksw2_extd2_sse41.o ksw2_exts2_sse41.o ksw2_extz2_sse2.o ksw2_extd2_sse2.o ksw2_exts2_sse2.o ksw2_dispatch.o --else # if sse2only is defined -- OBJS+=ksw2_extz2_sse.o ksw2_extd2_sse.o ksw2_exts2_sse.o --endif --else # if arm_neon is defined -+ifneq ($(arm_neon),) # if arm_neon is defined - OBJS+=ksw2_extz2_neon.o ksw2_extd2_neon.o ksw2_exts2_neon.o -- INCLUDES+=-Isse2neon --ifeq ($(aarch64),) #if aarch64 is not defined - CFLAGS+=-D_FILE_OFFSET_BITS=64 -mfpu=neon -fsigned-char --else #if aarch64 is defined -+ INCLUDES+=-Isse2neon -+else ifneq ($(aarch64),) #if aarch64 is defined -+ OBJS+=ksw2_extz2_neon.o ksw2_extd2_neon.o ksw2_exts2_neon.o - CFLAGS+=-D_FILE_OFFSET_BITS=64 -fsigned-char --endif -+ INCLUDES+=-Isse2neon -+else ifneq ($(sse2only),) # if sse2only is defined -+ OBJS+=ksw2_extz2_sse.o ksw2_extd2_sse.o ksw2_exts2_sse.o -+else # none of the above -+ OBJS+=ksw2_extz2_sse41.o ksw2_extd2_sse41.o ksw2_exts2_sse41.o ksw2_extz2_sse2.o ksw2_extd2_sse2.o ksw2_exts2_sse2.o ksw2_dispatch.o - endif - - .PHONY:all extra clean depend -@@ -46,9 +44,12 @@ sdust:sdust.c kalloc.o kalloc.h kdq.h kvec.h kseq.h ketopt.h sdust.h - - # SSE-specific targets on x86/x86_64 - --ifeq ($(arm_neon),) # if arm_neon is defined, compile this target with the default setting (i.e. no -msse2) -+ifneq ($(arm_neon),) # if arm_neon is defined, compile this target with the default setting (i.e. no -msse2) -+ksw2_ll_sse.o:ksw2_ll_sse.c ksw2.h kalloc.h -+else ifneq ($(aarch64),) - ksw2_ll_sse.o:ksw2_ll_sse.c ksw2.h kalloc.h -- $(CC) -c $(CFLAGS) -msse2 $(CPPFLAGS) $(INCLUDES) $< -o $@ -+else -+ $(CC) -c $(CFLAGS) -msse2 $(CPPFLAGS) $(INCLUDES) $< -o $@ - endif - - ksw2_extz2_sse41.o:ksw2_extz2_sse.c ksw2.h kalloc.h -- cgit v1.2.3 From 32acea79fa9b87221b95f41b90c7783b8ee04012 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Thu, 27 May 2021 17:34:27 +0200 Subject: gnu: lksctp-tools: Update to 1.0.19. * gnu/packages/networking.scm (lksctp-tools): Update to 1.0.19. [source]: Remove patch. * gnu/packages/patches/lksctp-tools-1.0.18-fix-header-file-name.patch: Delete file. * gnu/local.mk (dist_patch_DATA): Remove it. --- gnu/local.mk | 1 - gnu/packages/networking.scm | 6 ++-- .../lksctp-tools-1.0.18-fix-header-file-name.patch | 32 ---------------------- 3 files changed, 2 insertions(+), 37 deletions(-) delete mode 100644 gnu/packages/patches/lksctp-tools-1.0.18-fix-header-file-name.patch (limited to 'gnu/local.mk') diff --git a/gnu/local.mk b/gnu/local.mk index 8355a208ea..792ebac1e1 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -1278,7 +1278,6 @@ dist_patch_DATA = \ %D%/packages/patches/libffi-float128-powerpc64le.patch \ %D%/packages/patches/libvirt-add-install-prefix.patch \ %D%/packages/patches/libziparchive-add-includes.patch \ - %D%/packages/patches/lksctp-tools-1.0.18-fix-header-file-name.patch \ %D%/packages/patches/localed-xorg-keyboard.patch \ %D%/packages/patches/kdiagram-Fix-missing-link-libraries.patch \ %D%/packages/patches/kiki-level-selection-crash.patch \ diff --git a/gnu/packages/networking.scm b/gnu/packages/networking.scm index 6e2128aa12..3da10a2990 100644 --- a/gnu/packages/networking.scm +++ b/gnu/packages/networking.scm @@ -440,7 +440,7 @@ performance across unpredictable networks, such as the Internet.") (define-public lksctp-tools (package (name "lksctp-tools") - (version "1.0.18") + (version "1.0.19") (source (origin (method git-fetch) @@ -449,10 +449,8 @@ performance across unpredictable networks, such as the Internet.") (url "https://github.com/sctp/lksctp-tools") (commit (string-append "v" version)))) (file-name (git-file-name name version)) - (patches - (search-patches "lksctp-tools-1.0.18-fix-header-file-name.patch")) (sha256 - (base32 "1x4fwzrlzvfa3vcpja97m8w5g9ir2zrh4zs7zksminrnmdrs0dsr")))) + (base32 "1jfq58j365mlgssavyw5wcal42n0xjkr40vmj9b8w265wgs28j20")))) (build-system gnu-build-system) (native-inputs `(("autoconf" ,autoconf) diff --git a/gnu/packages/patches/lksctp-tools-1.0.18-fix-header-file-name.patch b/gnu/packages/patches/lksctp-tools-1.0.18-fix-header-file-name.patch deleted file mode 100644 index 1ebe6c803d..0000000000 --- a/gnu/packages/patches/lksctp-tools-1.0.18-fix-header-file-name.patch +++ /dev/null @@ -1,32 +0,0 @@ -From 378560050a8f93786c590cc99a55461666205b61 Mon Sep 17 00:00:00 2001 -From: Xin Long -Date: Fri, 24 Aug 2018 01:13:32 +0800 -Subject: [PATCH] build: fix netinet/sctp.h not to be installed - -After libcnetinet_HEADERS was set to sctp.h.in, netinet/sctp.h can -no longer be installed into ${includedir}. - -Since "AC_CONFIG_HEADERS([src/include/netinet/sctp.h])" is already -added into configure.ac, there's no need to generate sctp.h by -automake. - -So we simply set libcnetinet_HEADERS back to sctp.h. - -Fixes: 9607dd85e70a ("netinet/sctp.h: dynamically build based on system setup") -Signed-off-by: Xin Long -Signed-off-by: Marcelo Ricardo Leitner ---- - src/include/netinet/Makefile.am | 3 +-- - 1 file changed, 1 insertion(+), 2 deletions(-) - -diff --git a/src/include/netinet/Makefile.am b/src/include/netinet/Makefile.am -index ca0aac2..965db8c 100644 ---- a/src/include/netinet/Makefile.am -+++ b/src/include/netinet/Makefile.am -@@ -11,5 +11,4 @@ libcnetinetdir = $(includedir)/netinet - # API. - include_HEADERS = - --libcnetinet_HEADERS = sctp.h.in --BUILT_SOURCES = sctp.h -+libcnetinet_HEADERS = sctp.h -- cgit v1.2.3 From e3cde9aaf8dfef17299987590db11aa1f4df418b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 29 May 2021 07:25:08 +0200 Subject: gnu: Add mosaicatcher. * gnu/packages/patches/mosaicatcher-unbundle-htslib.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. * gnu/packages/bioinformatics.scm (mosaicatcher): New variable. --- gnu/local.mk | 1 + gnu/packages/bioinformatics.scm | 40 ++++++++++++++++++ .../patches/mosaicatcher-unbundle-htslib.patch | 49 ++++++++++++++++++++++ 3 files changed, 90 insertions(+) create mode 100644 gnu/packages/patches/mosaicatcher-unbundle-htslib.patch (limited to 'gnu/local.mk') diff --git a/gnu/local.mk b/gnu/local.mk index 792ebac1e1..cf13d672bd 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -1432,6 +1432,7 @@ dist_patch_DATA = \ %D%/packages/patches/module-init-tools-moduledir.patch \ %D%/packages/patches/monero-use-system-miniupnpc.patch \ %D%/packages/patches/mono-mdoc-timestamping.patch \ + %D%/packages/patches/mosaicatcher-unbundle-htslib.patch \ %D%/packages/patches/mozjs17-aarch64-support.patch \ %D%/packages/patches/mozjs24-aarch64-support.patch \ %D%/packages/patches/mozjs38-pkg-config-version.patch \ diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index f38c0c07ef..2a7443314a 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -6170,6 +6170,46 @@ Roche 454, Ion Torrent and Pacific BioSciences SMRT.") ;; 2. MD5 implementation - RSA Data Security, RFC 1321 (license (list license:gpl2+ license:public-domain))))) +(define-public mosaicatcher + (package + (name "mosaicatcher") + (version "0.3.1") + (source (origin + ;; There are no release tarballs nor tags. + (method git-fetch) + (uri (git-reference + (url "https://github.com/friendsofstrandseq/mosaicatcher") + (commit (string-append version "-dev")))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1n2s5wvvj2y0vfgjkg1q11xahpbagxz7h2vf5q7qyy25s12kbzbd")) + (patches (search-patches "mosaicatcher-unbundle-htslib.patch")))) + (build-system cmake-build-system) + (arguments + `(#:tests? #false ; there are no tests + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'chdir + (lambda _ (chdir "src"))) + (replace 'install + (lambda* (#:key inputs outputs #:allow-other-keys) + (let* ((target (assoc-ref outputs "out")) + (bin (string-append target "/bin")) + (share (string-append target "/share/mosaicatcher"))) + (install-file "mosaic" bin) + (mkdir-p share) + (copy-recursively "../R" share))))))) + (inputs + `(("boost" ,boost) + ("htslib" ,htslib))) + (home-page "https://github.com/friendsofstrandseq/mosaicatcher") + (synopsis "Count and classify Strand-seq reads") + (description + "Mosaicatcher counts Strand-seq reads and classifies strand states of +each chromosome in each cell using a Hidden Markov Model.") + (license license:expat))) + (define-public ngs-sdk (package (name "ngs-sdk") diff --git a/gnu/packages/patches/mosaicatcher-unbundle-htslib.patch b/gnu/packages/patches/mosaicatcher-unbundle-htslib.patch new file mode 100644 index 0000000000..262895ddcf --- /dev/null +++ b/gnu/packages/patches/mosaicatcher-unbundle-htslib.patch @@ -0,0 +1,49 @@ +--- a/src/CMakeLists.txt 2021-05-28 13:07:25.655107983 +0200 ++++ b/src/CMakeLists.txt 2021-05-28 13:09:55.764025497 +0200 +@@ -21,24 +21,6 @@ + + + +-### Link HTSlib +- +-ExternalProject_Add(htslib +- PREFIX ${CMAKE_BINARY_DIR}/htslib +- GIT_REPOSITORY "https://github.com/samtools/htslib.git" +- GIT_TAG "1.3.1" +- UPDATE_COMMAND "" +- BUILD_IN_SOURCE 1 +- CONFIGURE_COMMAND "" +- BUILD_COMMAND make +- INSTALL_COMMAND make install prefix=${CMAKE_BINARY_DIR}/htslib +- LOG_DOWNLOAD 1 +-) +-link_directories (${CMAKE_BINARY_DIR}/htslib/lib) +-include_directories (${CMAKE_BINARY_DIR}/htslib/include) +- +- +- + ### Set version + + # Get the current working branch +@@ -64,13 +46,6 @@ + + # 2. Boost version from find_package (Boost_VERSION) + +-# 3. Get HTSlib version from git +-execute_process( +- COMMAND git describe --always +- WORKING_DIRECTORY ${PROJECT_BINARY_DIR}/htslib +- OUTPUT_VARIABLE HTSLIB_VERSION +- OUTPUT_STRIP_TRAILING_WHITESPACE +-) + set(HTSLIB_VERSION "1.3.1 ${HTSLIB_VERSION}") + + # 4. write version.hpp file +@@ -105,7 +80,6 @@ + add_executable (mosaic main.cpp ${HEADER_FILES}) + target_link_libraries (mosaic LINK_PUBLIC ${Boost_LIBRARIES}) + target_link_libraries (mosaic LINK_PUBLIC hts) +-add_dependencies (mosaic htslib) + + + ### Doxygen API documentation -- cgit v1.2.3 From 395e20ed0803995244b238dd002edd37bdc4cd00 Mon Sep 17 00:00:00 2001 From: Arun Isaac Date: Sat, 29 May 2021 14:01:56 +0530 Subject: gnu: Register gnu/services/ci.scm and gnu/tests/ci.scm. This is a follow-up to commit eda4bb4f16f74436b0caf1c584888c89b3c4c69b. * gnu/local.mk (GNU_SYSTEM_MODULES): Add gnu/services/ci.scm and gnu/tests/ci.scm. --- gnu/local.mk | 3 +++ 1 file changed, 3 insertions(+) (limited to 'gnu/local.mk') diff --git a/gnu/local.mk b/gnu/local.mk index cf13d672bd..0c0a6b924a 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -41,6 +41,7 @@ # Copyright © 2020 Vinicius Monego # Copyright © 2021 Björn Höfling # Copyright © 2021 Philip McGrath +# Copyright © 2021 Arun Isaac # # This file is part of GNU Guix. # @@ -599,6 +600,7 @@ GNU_SYSTEM_MODULES = \ %D%/services/base.scm \ %D%/services/certbot.scm \ %D%/services/cgit.scm \ + %D%/services/ci.scm \ %D%/services/configuration.scm \ %D%/services/cuirass.scm \ %D%/services/cups.scm \ @@ -690,6 +692,7 @@ GNU_SYSTEM_MODULES = \ %D%/tests.scm \ %D%/tests/audio.scm \ %D%/tests/base.scm \ + %D%/tests/ci.scm \ %D%/tests/cups.scm \ %D%/tests/databases.scm \ %D%/tests/desktop.scm \ -- cgit v1.2.3 From 0f6902ea79963a2c5d931414103de978a86f9dfd Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Sun, 30 May 2021 09:46:34 +0300 Subject: gnu: julia-jllwrappers: Move to (gnu packages julia-jll). * gnu/packages/julia-xyz.scm (julia-jlwrappers): Move to ... * gnu/packages/julia-jll.scm: ... here. * gnu/local.mk (GNU_SYSTEM_MODULES): Register julia-jll.scm --- gnu/local.mk | 1 + gnu/packages/julia-jll.scm | 70 ++++++++++++++++++++++++++++++++++++++++++++++ gnu/packages/julia-xyz.scm | 44 +---------------------------- 3 files changed, 72 insertions(+), 43 deletions(-) create mode 100644 gnu/packages/julia-jll.scm (limited to 'gnu/local.mk') diff --git a/gnu/local.mk b/gnu/local.mk index 0c0a6b924a..a5820b5827 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -308,6 +308,7 @@ GNU_SYSTEM_MODULES = \ %D%/packages/jrnl.scm \ %D%/packages/jose.scm \ %D%/packages/julia.scm \ + %D%/packages/julia-jll.scm \ %D%/packages/julia-xyz.scm \ %D%/packages/jupyter.scm \ %D%/packages/kawa.scm \ diff --git a/gnu/packages/julia-jll.scm b/gnu/packages/julia-jll.scm new file mode 100644 index 0000000000..1b63c06312 --- /dev/null +++ b/gnu/packages/julia-jll.scm @@ -0,0 +1,70 @@ +;;; GNU Guix --- Functional package management for GNU +;;; Copyright © 2021 Nicolò Balzarotti +;;; Copyright © 2021 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 packages julia-jll) + #:use-module ((guix licenses) #:prefix license:) + #:use-module (guix packages) + #:use-module (guix git-download) + #:use-module (guix utils) + #:use-module (guix build-system julia) + #:use-module (gnu packages) + #:use-module (gnu packages julia)) + +(define-public julia-jllwrappers + (package + (name "julia-jllwrappers") + (version "1.3.0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaPackaging/JLLWrappers.jl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0v7xhsv9z16d657yp47vgc86ggc01i1wigqh3n0d7i1s84z7xa0h")))) + (arguments + ;; Wants to download stuff + '(#:tests? #f + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'custom-override-path + (lambda* (#:key inputs #:allow-other-keys) + ;; Make @generate_wrapper_header take an optional argument that + ;; guix packagers can pass to override the default "override" + ;; binary path. This won't be needed when something like + ;; https://github.com/JuliaPackaging/JLLWrappers.jl/pull/27 + ;; will be merged. + (substitute* "src/wrapper_generators.jl" + (("generate_wrapper_header.*") + "generate_wrapper_header(src_name, override_path = nothing)\n") + (("pkg_dir = .*" all) + (string-append + all "\n" "override = something(override_path," + "joinpath(dirname(pkg_dir), \"override\"))\n")) + (("@static if isdir.*") "@static if isdir($override)\n") + (("return joinpath.*") "return $override\n")) + #t))))) + (build-system julia-build-system) + (home-page "https://github.com/JuliaPackaging/JLLWrappers.jl") + (synopsis "Julia macros used by JLL packages") + (description "This package contains Julia macros that enable JLL packages +to generate themselves. It is not intended to be used by users, but rather is +used in autogenerated packages via @code{BinaryBuilder.jl}.") + (license license:expat))) diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm index 551f016929..b8ba5bf93f 100644 --- a/gnu/packages/julia-xyz.scm +++ b/gnu/packages/julia-xyz.scm @@ -27,6 +27,7 @@ #:use-module (gnu packages gcc) #:use-module (gnu packages image) #:use-module (gnu packages imagemagick) + #:use-module (gnu packages julia-jll) #:use-module (gnu packages maths) #:use-module (gnu packages tls) #:use-module (gnu packages web)) @@ -1077,49 +1078,6 @@ external IRs. It can be used with Julia metaprogramming tools such as Cassette.") (license license:expat))) -(define-public julia-jllwrappers - (package - (name "julia-jllwrappers") - (version "1.3.0") - (source - (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/JuliaPackaging/JLLWrappers.jl") - (commit (string-append "v" version)))) - (file-name (git-file-name name version)) - (sha256 - (base32 "0v7xhsv9z16d657yp47vgc86ggc01i1wigqh3n0d7i1s84z7xa0h")))) - (arguments - ;; Wants to download stuff - '(#:tests? #f - #:phases - (modify-phases %standard-phases - (add-after 'unpack 'custom-override-path - (lambda* (#:key inputs #:allow-other-keys) - ;; Make @generate_wrapper_header take an optional argument that - ;; guix packagers can pass to override the default "override" - ;; binary path. This won't be needed when something like - ;; https://github.com/JuliaPackaging/JLLWrappers.jl/pull/27 - ;; will be merged. - (substitute* "src/wrapper_generators.jl" - (("generate_wrapper_header.*") - "generate_wrapper_header(src_name, override_path = nothing)\n") - (("pkg_dir = .*" all) - (string-append - all "\n" "override = something(override_path," - "joinpath(dirname(pkg_dir), \"override\"))\n")) - (("@static if isdir.*") "@static if isdir($override)\n") - (("return joinpath.*") "return $override\n")) - #t))))) - (build-system julia-build-system) - (home-page "https://github.com/JuliaPackaging/JLLWrappers.jl") - (synopsis "Julia macros used by JLL packages") - (description "This package contains Julia macros that enable JLL packages -to generate themselves. It is not intended to be used by users, but rather is -used in autogenerated packages via @code{BinaryBuilder.jl}.") - (license license:expat))) - (define-public julia-jpegturbo-jll (package (name "julia-jpegturbo-jll") -- cgit v1.2.3 From e348436589795c72d5e7007eb64ef0efdbe75726 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Thu, 3 Jun 2021 01:31:27 +0200 Subject: gnu: amule: Update to 2.3.3. * gnu/packages/networking.scm (amule): Update to 2.3.3. [source]: Remove patch. * gnu/packages/patches/amule-crypto-6.patch: Delete file. * gnu/local.mk (dist_patch_DATA): Remove it. --- gnu/local.mk | 1 - gnu/packages/networking.scm | 6 ++--- gnu/packages/patches/amule-crypto-6.patch | 45 ------------------------------- 3 files changed, 2 insertions(+), 50 deletions(-) delete mode 100644 gnu/packages/patches/amule-crypto-6.patch (limited to 'gnu/local.mk') diff --git a/gnu/local.mk b/gnu/local.mk index a5820b5827..8c235f50c8 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -809,7 +809,6 @@ dist_patch_DATA = \ %D%/packages/patches/akonadi-not-relocatable.patch \ %D%/packages/patches/akonadi-timestamps.patch \ %D%/packages/patches/allegro-mesa-18.2.5-and-later.patch \ - %D%/packages/patches/amule-crypto-6.patch \ %D%/packages/patches/anki-mpv-args.patch \ %D%/packages/patches/antiword-CVE-2014-8123.patch \ %D%/packages/patches/antlr3-3_1-fix-java8-compilation.patch \ diff --git a/gnu/packages/networking.scm b/gnu/packages/networking.scm index 945123e600..5be5cfd606 100644 --- a/gnu/packages/networking.scm +++ b/gnu/packages/networking.scm @@ -2947,7 +2947,7 @@ file for more details.") (define-public amule (package (name "amule") - (version "2.3.2") + (version "2.3.3") (source (origin (method git-fetch) (uri (git-reference @@ -2956,9 +2956,7 @@ file for more details.") (file-name (git-file-name name version)) (sha256 (base32 - "010wxm6g9f92x6fympj501zbnjka32rzbx0sk3a2y4zpih5d2nsn")) - ;; Patch for adopting crypto++ >= 6.0. - (patches (search-patches "amule-crypto-6.patch")))) + "1nm4vxgmisn1b6l3drmz0q04x067j2i8lw5rnf0acaapwlp8qwvi")))) (build-system gnu-build-system) (arguments `(#:phases diff --git a/gnu/packages/patches/amule-crypto-6.patch b/gnu/packages/patches/amule-crypto-6.patch deleted file mode 100644 index 21a86ab0fa..0000000000 --- a/gnu/packages/patches/amule-crypto-6.patch +++ /dev/null @@ -1,45 +0,0 @@ -From d1d1368c7909ffd8423730afaa811ce7b6a3a8aa Mon Sep 17 00:00:00 2001 -From: Tommy Jerry Mairo -Date: Sun, 4 Feb 2018 12:42:00 -0800 -Subject: [PATCH 1/2] Bugfix: API mismatch with crypto++ 6.0.0 - ---- - src/ClientCreditsList.cpp | 2 +- - 1 file changed, 1 insertion(+), 1 deletion(-) - -diff --git a/src/ClientCreditsList.cpp b/src/ClientCreditsList.cpp -index 3bea9fe2d..a7ae1e34c 100644 ---- a/src/ClientCreditsList.cpp -+++ b/src/ClientCreditsList.cpp -@@ -312,7 +312,7 @@ void CClientCreditsList::InitalizeCrypting() - // calculate and store public key - CryptoPP::RSASSA_PKCS1v15_SHA_Verifier pubkey(*static_cast(m_pSignkey)); - CryptoPP::ArraySink asink(m_abyMyPublicKey, 80); -- pubkey.DEREncode(asink); -+ pubkey.AccessMaterial().Save(asink); - m_nMyPublicKeyLen = asink.TotalPutLength(); - asink.MessageEnd(); - } catch (const CryptoPP::Exception& e) { - -From 88ba0ac952b78382445f2fff73c6792c0474dc62 Mon Sep 17 00:00:00 2001 -From: Tommy Jerry Mairo -Date: Wed, 21 Mar 2018 11:56:28 -0700 -Subject: [PATCH 2/2] Update: Change AccessMaterial to GetMaterial - ---- - src/ClientCreditsList.cpp | 2 +- - 1 file changed, 1 insertion(+), 1 deletion(-) - -diff --git a/src/ClientCreditsList.cpp b/src/ClientCreditsList.cpp -index a7ae1e34c..69e881fd8 100644 ---- a/src/ClientCreditsList.cpp -+++ b/src/ClientCreditsList.cpp -@@ -312,7 +312,7 @@ void CClientCreditsList::InitalizeCrypting() - // calculate and store public key - CryptoPP::RSASSA_PKCS1v15_SHA_Verifier pubkey(*static_cast(m_pSignkey)); - CryptoPP::ArraySink asink(m_abyMyPublicKey, 80); -- pubkey.AccessMaterial().Save(asink); -+ pubkey.GetMaterial().Save(asink); - m_nMyPublicKeyLen = asink.TotalPutLength(); - asink.MessageEnd(); - } catch (const CryptoPP::Exception& e) { -- cgit v1.2.3 From 20d9535e1bf981a37f39f171ad72f67cdb1e6919 Mon Sep 17 00:00:00 2001 From: Carl Dong Date: Sat, 29 May 2021 01:28:10 -0400 Subject: gnu: nsis: Respect SOURCE-DATE-EPOCH for reproducibility * gnu/packages/patches/nsis-source-date-epoch.patch: New patch. * gnu/local.mk (dist_patch_DATA): Register it. * gnu/packages/installers.scm (make-nsis)[source]: Apply it. --- gnu/local.mk | 1 + gnu/packages/installers.scm | 3 ++- gnu/packages/patches/nsis-source-date-epoch.patch | 23 +++++++++++++++++++++++ 3 files changed, 26 insertions(+), 1 deletion(-) create mode 100644 gnu/packages/patches/nsis-source-date-epoch.patch (limited to 'gnu/local.mk') diff --git a/gnu/local.mk b/gnu/local.mk index 8c235f50c8..870769cffc 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -1468,6 +1468,7 @@ dist_patch_DATA = \ %D%/packages/patches/network-manager-plugin-path.patch \ %D%/packages/patches/nginx-socket-cloexec.patch \ %D%/packages/patches/nsis-env-passthru.patch \ + %D%/packages/patches/nsis-source-date-epoch.patch \ %D%/packages/patches/nss-increase-test-timeout.patch \ %D%/packages/patches/nss-3.56-pkgconfig.patch \ %D%/packages/patches/ntfs-3g-CVE-2019-9755.patch \ diff --git a/gnu/packages/installers.scm b/gnu/packages/installers.scm index 775b91f0f7..c768a367aa 100644 --- a/gnu/packages/installers.scm +++ b/gnu/packages/installers.scm @@ -42,7 +42,8 @@ (sha256 (base32 "1sbwx5vzpddharkb7nj4q5z3i5fbg4lan63ng738cw4hmc4v7qdn")) - (patches (search-patches "nsis-env-passthru.patch")))) + (patches (search-patches "nsis-env-passthru.patch" + "nsis-source-date-epoch.patch")))) (build-system scons-build-system) (native-inputs `(("xgcc" ,xgcc) ("xbinutils" ,xbinutils) diff --git a/gnu/packages/patches/nsis-source-date-epoch.patch b/gnu/packages/patches/nsis-source-date-epoch.patch new file mode 100644 index 0000000000..744c2a8011 --- /dev/null +++ b/gnu/packages/patches/nsis-source-date-epoch.patch @@ -0,0 +1,23 @@ +Honour SOURCE_DATE_EPOCH for VERSION default + +Merged upstream as cd3f1024a37a332f1d4fa96a817ca80dfa2a478c, but not yet in a +release. GitHub PR: https://github.com/kichik/nsis/pull/13 + +Python snippet from: https://reproducible-builds.org/docs/source-date-epoch/#python + + +diff --git a/SConstruct b/SConstruct +index e8252c9..41786f2 100755 +--- a/SConstruct ++++ b/SConstruct +@@ -95,8 +95,8 @@ default_doctype = 'html' + if defenv.WhereIs('hhc', os.environ['PATH']): + default_doctype = 'chm' + +-from time import strftime, gmtime +-cvs_version = strftime('%d-%b-%Y.cvs', gmtime()) ++import time ++cvs_version = time.strftime('%d-%b-%Y.cvs', time.gmtime(int(os.environ.get('SOURCE_DATE_EPOCH', time.time())))) + + opts = Variables() + -- cgit v1.2.3 From bdd2970c087eba1027123f45e358bf4eac295572 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sat, 5 Jun 2021 19:13:39 +0200 Subject: gnu: wgetpaste: Update to 2.32. * gnu/packages/wget.scm (wgetpaste): Update to 2.32. [source]: Remove patch. * gnu/packages/patches/wgetpaste-update-bpaste.patch: Delete file. * gnu/local.mk (dist_patch_DATA): Remove it. --- gnu/local.mk | 1 - gnu/packages/patches/wgetpaste-update-bpaste.patch | 27 ---------------------- gnu/packages/wget.scm | 5 ++-- 3 files changed, 2 insertions(+), 31 deletions(-) delete mode 100644 gnu/packages/patches/wgetpaste-update-bpaste.patch (limited to 'gnu/local.mk') diff --git a/gnu/local.mk b/gnu/local.mk index 870769cffc..1c692e0ce4 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -1805,7 +1805,6 @@ dist_patch_DATA = \ %D%/packages/patches/webkitgtk-share-store.patch \ %D%/packages/patches/webkitgtk-bind-all-fonts.patch \ %D%/packages/patches/websocketpp-fix-for-cmake-3.15.patch \ - %D%/packages/patches/wgetpaste-update-bpaste.patch \ %D%/packages/patches/wicd-bitrate-none-fix.patch \ %D%/packages/patches/wicd-get-selected-profile-fix.patch \ %D%/packages/patches/wicd-urwid-1.3.patch \ diff --git a/gnu/packages/patches/wgetpaste-update-bpaste.patch b/gnu/packages/patches/wgetpaste-update-bpaste.patch deleted file mode 100644 index f92a0c17ed..0000000000 --- a/gnu/packages/patches/wgetpaste-update-bpaste.patch +++ /dev/null @@ -1,27 +0,0 @@ -From: Tobias Geerinckx-Rice -Date: Tue, 01 Sep 2020 04:23:25 +0200 -Subject: [PATCH] Update bpaste URL & regular expressions. - -diff -Naur wgetpaste-2.30/wgetpaste wgetpaste-2.30a/wgetpaste ---- wgetpaste-2.30/wgetpaste 2020-07-31 23:56:05.000000000 +0200 -+++ wgetpaste-2.30a/wgetpaste 2020-09-01 04:22:37.499898403 +0200 -@@ -16,7 +16,7 @@ - SERVICES="codepad bpaste dpaste gists snippets" - # bpaste - ENGINE_bpaste=pinnwand --URL_bpaste="https://bpaste.net/" -+URL_bpaste="https://bpa.st/" - DEFAULT_EXPIRATION_bpaste="1week" - DEFAULT_LANGUAGE_bpaste="text" - # codepad -@@ -194,8 +194,8 @@ - xml+velocity xml xquery xslt xtend yaml" - EXPIRATIONS_pinnwand="1day 1week 1month never" - POST_pinnwand="submit=Paste! % % lexer expiry % code" --REGEX_LOC_pinnwand="\(/show/[^ ]*\).*$|https://bpaste.net\1" --REGEX_RAW_pinnwand='s|^\(https\?://[^/]*/\)show\(/[^ ]*/\?\)$|\1raw\2|' -+REGEX_LOC_pinnwand="\(/[^ ]*\).*$|https://bpa.st\1" -+REGEX_RAW_pinnwand='s|^\(https\?://[^/]*\)\(/[^ ]*/\?\)$|\1/raw\2|' - - ### errors - die() { diff --git a/gnu/packages/wget.scm b/gnu/packages/wget.scm index 3d7f266dd7..8891170e10 100644 --- a/gnu/packages/wget.scm +++ b/gnu/packages/wget.scm @@ -78,7 +78,7 @@ in downloaded documents to relative links.") (define-public wgetpaste (package (name "wgetpaste") - (version "2.30") + (version "2.32") (source (origin (method git-fetch) @@ -87,8 +87,7 @@ in downloaded documents to relative links.") (commit version))) (file-name (git-file-name name version)) (sha256 - (base32 "0fhm0qxdsm4k1m24z4bbb7mdv1x1iaqzgsnwkax6vb8bx9yd1ysi")) - (patches (search-patches "wgetpaste-update-bpaste.patch")))) + (base32 "13zdqfnbpymwz2f04icw92flj50227n5r0dcms84qxswfxrarnas")))) (build-system gnu-build-system) (arguments `(#:modules ((guix build gnu-build-system) -- cgit v1.2.3 From b65c02e2d35af6fbe1d1810d6c69cfab194e13e2 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Sun, 6 Jun 2021 12:07:01 +0300 Subject: gnu: freebayes: Update to 1.3.5. * gnu/packages/bioinformatics.scm (freebayes): Update to 1.3.5. [source]: Remove patch. [arguments]: Adjust custom 'patch-source phase for changes in source. [inputs]: Remove zlib. * gnu/packages/patches/freebayes-devendor-deps.patch: Remove file. * gnu/local.mk (dist_patch_DATA): Remove it. --- gnu/local.mk | 1 - gnu/packages/bioinformatics.scm | 16 +-- gnu/packages/patches/freebayes-devendor-deps.patch | 152 --------------------- 3 files changed, 7 insertions(+), 162 deletions(-) delete mode 100644 gnu/packages/patches/freebayes-devendor-deps.patch (limited to 'gnu/local.mk') diff --git a/gnu/local.mk b/gnu/local.mk index 1c692e0ce4..153f6ee8d7 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -1019,7 +1019,6 @@ dist_patch_DATA = \ %D%/packages/patches/fpc-reproducibility.patch \ %D%/packages/patches/fplll-std-fenv.patch \ %D%/packages/patches/freedink-engine-fix-sdl-hints.patch \ - %D%/packages/patches/freebayes-devendor-deps.patch \ %D%/packages/patches/freeimage-unbundle.patch \ %D%/packages/patches/fuse-overlapping-headers.patch \ %D%/packages/patches/gajim-honour-GAJIM_PLUGIN_PATH.patch \ diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 2de8a59d3c..1e38c6e0e7 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -13572,7 +13572,7 @@ manipulations on VCF files.") (define-public freebayes (package (name "freebayes") - (version "1.3.3") + (version "1.3.5") (source (origin (method git-fetch) (uri (git-reference @@ -13580,8 +13580,7 @@ manipulations on VCF files.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "0myz3giad7jqp6ricdfnig9ymlcps2h67mlivadvx97ngagm85z8")) - (patches (search-patches "freebayes-devendor-deps.patch")) + (base32 "1l0z88gq57kva677a6xri5g9k2d9h9lk5yk1q2xmq64wqhv7dvc3")) (modules '((guix build utils))) (snippet '(begin @@ -13593,8 +13592,7 @@ manipulations on VCF files.") ("htslib" ,htslib) ("smithwaterman" ,smithwaterman) ("tabixpp" ,tabixpp) - ("vcflib" ,vcflib) - ("zlib" ,zlib))) + ("vcflib" ,vcflib))) (native-inputs `(("bash-tap" ,bash-tap) ("bc" ,bc) @@ -13627,13 +13625,13 @@ manipulations on VCF files.") (string-append bash-tap "/bin/bash-tap-bootstrap")) (("source.*bash-tap-bootstrap") (string-append "source " bash-tap "/bin/bash-tap-bootstrap"))) - (substitute* "meson.build" - ;; Some inputs aren't actually needed. - ((".*bamtools/src.*") "") - ((".*multichoose.*") "")) (substitute* '("src/BedReader.cpp" "src/BedReader.h") (("../intervaltree/IntervalTree.h") "IntervalTree.h")) + (substitute* "meson.build" + ;; Our pkg-config file is vcflib.pc + (("libvcflib") "vcflib") + (("vcflib_inc,") "")) #t))) (add-after 'unpack 'unpack-submodule-sources (lambda* (#:key inputs #:allow-other-keys) diff --git a/gnu/packages/patches/freebayes-devendor-deps.patch b/gnu/packages/patches/freebayes-devendor-deps.patch deleted file mode 100644 index 9886de11fb..0000000000 --- a/gnu/packages/patches/freebayes-devendor-deps.patch +++ /dev/null @@ -1,152 +0,0 @@ -This patch is original to Guix, ongoing work to upstream bits as possible. - -From 9acc56db5e7469f5976be38b52ba4993de98ee38 Mon Sep 17 00:00:00 2001 -From: Efraim Flashner -Date: Sun, 17 Jan 2021 13:27:17 +0200 -Subject: [PATCH] devendor-dependants - ---- - meson.build | 84 +++++++++++++++++++++++++++++++++++++++++------------ - 1 file changed, 66 insertions(+), 18 deletions(-) - -diff --git a/meson.build b/meson.build -index f6bf242..bded4af 100644 ---- a/meson.build -+++ b/meson.build -@@ -9,8 +9,13 @@ project('freebayes', ['cpp', 'c'], - - zlib_dep = dependency('zlib') - lzma_dep = dependency('liblzma') -+simde_dep = dependency('simde') - bzip2_dep = dependency('bz2lib', required: false) - htslib_dep = dependency('htslib', required : false) -+tabixpp_dep = dependency('tabixpp', required : false) -+fastahack_dep = dependency('fastahack', required : false) -+smithwaterman_dep = dependency('smithwaterman', required : false) -+vcflib_dep = dependency('vcflib', required: false) - thread_dep = dependency('threads') - - if htslib_dep.found() -@@ -59,6 +64,56 @@ else - ] - endif - -+if tabixpp_dep.found() -+ tabixpp_includes = '' -+ tabixpp_src = [] -+else -+ tabixpp_includes = [ -+ 'vcflib/tabixpp', -+ ] -+ tabixpp_src = [ -+ 'vcflib/tabixpp/tabix.cpp', -+ ] -+endif -+ -+if vcflib_dep.found() -+ vcflib_includes = '' -+ vcflib_src = [] -+else -+ vcflib_includes = [ -+ 'vcflib/src', -+ 'vcflib/multichoose', -+ 'vcflib/filevercmp', -+ ] -+ vcflib_src = [ -+ 'vcflib/src/Variant.cpp', -+ ] -+endif -+ -+if fastahack_dep.found() -+ fastahack_src = [] -+else -+ fastahack_src = [ -+ 'vcflib/fastahack/Fasta.cpp', -+ 'vcflib/src/split.cpp', -+ ] -+endif -+ -+if smithwaterman_dep.found() -+ smithwaterman_includes = '' -+ smithwaterman_src = [] -+else -+ smithwaterman_includes = [ -+ 'vcflib/smithwaterman', -+ ] -+ smithwaterman_src = [ -+ 'vcflib/smithwaterman/SmithWatermanGotoh.cpp', -+ 'vcflib/smithwaterman/disorder.cpp', -+ 'vcflib/smithwaterman/Repeats.cpp', -+ 'vcflib/smithwaterman/LeftAlign.cpp', -+ 'vcflib/smithwaterman/IndelAllele.cpp', -+ ] -+endif - - - # -@@ -105,23 +160,18 @@ seqlib_src = [ - ] - - vcflib_src = [ -- 'vcflib/tabixpp/tabix.cpp', -- 'vcflib/src/Variant.cpp', -- 'vcflib/smithwaterman/SmithWatermanGotoh.cpp', -- 'vcflib/smithwaterman/disorder.cpp', -- 'vcflib/smithwaterman/Repeats.cpp', -- 'vcflib/smithwaterman/LeftAlign.cpp', -- 'vcflib/smithwaterman/IndelAllele.cpp', -+ vcflib_src, -+ tabixpp_src, -+ smithwaterman_src, - ] - - bamleftalign_src = [ - 'src/bamleftalign.cpp', - 'src/IndelAllele.cpp', - 'contrib/SeqLib/src/BamWriter.cpp', -- 'vcflib/fastahack/Fasta.cpp', -- 'vcflib/smithwaterman/LeftAlign.cpp', -- 'vcflib/smithwaterman/IndelAllele.cpp', -- 'vcflib/src/split.cpp', -+ fastahack_src, -+ smithwaterman_src, -+ vcflib_src, - 'src/LeftAlign.cpp', - ] - -@@ -134,11 +184,9 @@ incdir = include_directories( - 'ttmath', - 'contrib', - 'contrib/SeqLib', -- 'vcflib/src', -- 'vcflib/tabixpp', -- 'vcflib/smithwaterman', -- 'vcflib/multichoose', -- 'vcflib/filevercmp') -+ tabixpp_includes, -+ smithwaterman_includes, -+ vcflib_includes) - - c_args = ['-fpermissive','-w'] - cpp_args = ['-fpermissive','-w','-Wc++14-compat'] -@@ -152,7 +200,7 @@ executable('freebayes', - include_directories : incdir, - cpp_args : cpp_args, - c_args : c_args, -- dependencies: [zlib_dep, lzma_dep, htslib_dep, thread_dep], -+ dependencies: [zlib_dep, lzma_dep, simde_dep, htslib_dep, tabixpp_dep, smithwaterman_dep, vcflib_dep, thread_dep], - install: true - ) - -@@ -165,7 +213,7 @@ executable('bamleftalign', - include_directories : incdir, - cpp_args : cpp_args, - c_args : c_args, -- dependencies: [zlib_dep, lzma_dep, htslib_dep, thread_dep], -+ dependencies: [zlib_dep, lzma_dep, simde_dep, htslib_dep, tabixpp_dep, fastahack_dep, smithwaterman_dep, vcflib_dep, thread_dep], - install: true - ) - --- -2.30.0 - -- cgit v1.2.3