From 6212146f887327b0ef017702982194f2d8180178 Mon Sep 17 00:00:00 2001 From: Ludovic Courtès Date: Thu, 12 Dec 2019 22:18:37 +0100 Subject: import: utils: Update docstring of 'recursive-import'. This is a followup to 70a8e13277d4a44b89dd9ee2290b98105f0235f1. * guix/import/utils.scm (recursive-import): Update docstring. --- guix/import/utils.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/guix/import/utils.scm b/guix/import/utils.scm index 47fc8276a9..d17d400ddf 100644 --- a/guix/import/utils.scm +++ b/guix/import/utils.scm @@ -402,7 +402,7 @@ obtain a node's uniquely identifying \"key\"." (define* (recursive-import package-name repo #:key repo->guix-package guix-name #:allow-other-keys) - "Return a stream of package expressions for PACKAGE-NAME and all its + "Return a list of package expressions for PACKAGE-NAME and all its dependencies, sorted in topological order. For each package, call (REPO->GUIX-PACKAGE NAME REPO), which should return a package expression and a list of dependencies; call (GUIX-NAME NAME) to obtain the Guix package -- cgit v1.2.3 From 94fea21b214a9111c5c8155bfebdad13114df95f Mon Sep 17 00:00:00 2001 From: Ludovic Courtès Date: Fri, 13 Dec 2019 13:44:51 +0100 Subject: gnu: hdf5@1.10: Update to 1.10.5. * gnu/packages/maths.scm (hdf5-1.10): Update to 1.10.5. Remove "hdf5-mpi-deprecations.patch". * gnu/packages/patches/hdf5-mpi-deprecations.patch: Remove. * gnu/local.mk (dist_patch_DATA): Remove it. --- gnu/local.mk | 1 - gnu/packages/maths.scm | 7 ++- gnu/packages/patches/hdf5-mpi-deprecations.patch | 61 ------------------------ 3 files changed, 3 insertions(+), 66 deletions(-) delete mode 100644 gnu/packages/patches/hdf5-mpi-deprecations.patch diff --git a/gnu/local.mk b/gnu/local.mk index 7f8715235d..32b2c141fa 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -969,7 +969,6 @@ dist_patch_DATA = \ %D%/packages/patches/hdf4-shared-fortran.patch \ %D%/packages/patches/hdf4-tirpc.patch \ %D%/packages/patches/hdf5-config-date.patch \ - %D%/packages/patches/hdf5-mpi-deprecations.patch \ %D%/packages/patches/hdf5-1.8-mpi-deprecations.patch \ %D%/packages/patches/hdf-eos2-build-shared.patch \ %D%/packages/patches/hdf-eos2-remove-gctp.patch \ diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index 8364d528fd..0ed61ad4a1 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -925,7 +925,7 @@ extremely large and complex data collections.") (define-public hdf5-1.10 (package (inherit hdf5) - (version "1.10.4") + (version "1.10.5") (source (origin (method url-fetch) @@ -939,9 +939,8 @@ extremely large and complex data collections.") (take (string-split version #\.) 2)) "/src/hdf5-" version ".tar.bz2"))) (sha256 - (base32 "1pr85fa1sh2ky6ai2hs3f21lp252grl2cq3wbyi4rh7dm83gyrqj")) - (patches (search-patches "hdf5-config-date.patch" - "hdf5-mpi-deprecations.patch")))))) + (base32 "0i3g6v521vigzbx8wpd32ibsiiw92r65ca3qdbn0d8fj8f4fmmk8")) + (patches (search-patches "hdf5-config-date.patch")))))) (define-public hdf-java (package diff --git a/gnu/packages/patches/hdf5-mpi-deprecations.patch b/gnu/packages/patches/hdf5-mpi-deprecations.patch deleted file mode 100644 index eb5d1cb681..0000000000 --- a/gnu/packages/patches/hdf5-mpi-deprecations.patch +++ /dev/null @@ -1,61 +0,0 @@ ---- a/src/H5.c -+++ b/src/H5.c -@@ -138,7 +138,7 @@ - if (mpi_initialized && !mpi_finalized) { - int key_val; - -- if(MPI_SUCCESS != (mpi_code = MPI_Comm_create_keyval(MPI_NULL_COPY_FN, -+ if(MPI_SUCCESS != (mpi_code = MPI_Comm_create_keyval(MPI_COMM_NULL_COPY_FN, - (MPI_Comm_delete_attr_function *)H5_mpi_delete_cb, - &key_val, NULL))) - HMPI_GOTO_ERROR(FAIL, "MPI_Comm_create_keyval failed", mpi_code) ---- hdf5-1.10.4/testpar/t_cache.c -+++ hdf5-1.10.4/testpar/t_cache.c -@@ -1217,20 +1217,20 @@ - struct mssg_t sample; /* used to compute displacements */ - - /* setup the displacements array */ -- if ( ( MPI_SUCCESS != MPI_Address(&sample.req, &displs[0]) ) || -- ( MPI_SUCCESS != MPI_Address(&sample.src, &displs[1]) ) || -- ( MPI_SUCCESS != MPI_Address(&sample.dest, &displs[2]) ) || -- ( MPI_SUCCESS != MPI_Address(&sample.mssg_num, &displs[3]) ) || -- ( MPI_SUCCESS != MPI_Address(&sample.base_addr, &displs[4]) ) || -- ( MPI_SUCCESS != MPI_Address(&sample.len, &displs[5]) ) || -- ( MPI_SUCCESS != MPI_Address(&sample.ver, &displs[6]) ) || -- ( MPI_SUCCESS != MPI_Address(&sample.count, &displs[7]) ) || -- ( MPI_SUCCESS != MPI_Address(&sample.magic, &displs[8]) ) ) { -+ if ( ( MPI_SUCCESS != MPI_Get_address(&sample.req, &displs[0]) ) || -+ ( MPI_SUCCESS != MPI_Get_address(&sample.src, &displs[1]) ) || -+ ( MPI_SUCCESS != MPI_Get_address(&sample.dest, &displs[2]) ) || -+ ( MPI_SUCCESS != MPI_Get_address(&sample.mssg_num, &displs[3]) ) || -+ ( MPI_SUCCESS != MPI_Get_address(&sample.base_addr, &displs[4]) ) || -+ ( MPI_SUCCESS != MPI_Get_address(&sample.len, &displs[5]) ) || -+ ( MPI_SUCCESS != MPI_Get_address(&sample.ver, &displs[6]) ) || -+ ( MPI_SUCCESS != MPI_Get_address(&sample.count, &displs[7]) ) || -+ ( MPI_SUCCESS != MPI_Get_address(&sample.magic, &displs[8]) ) ) { - - nerrors++; - success = FALSE; - if ( verbose ) { -- HDfprintf(stdout, "%d:%s: MPI_Address() call failed.\n", -+ HDfprintf(stdout, "%d:%s: MPI_Get_address() call failed.\n", - world_mpi_rank, FUNC); - } - -@@ -1245,14 +1245,14 @@ - - if ( success ) { - -- result = MPI_Type_struct(9, block_len, displs, mpi_types, &mpi_mssg_t); -+ result = MPI_Type_create_struct(9, block_len, displs, mpi_types, &mpi_mssg_t); - - if ( result != MPI_SUCCESS ) { - - nerrors++; - success = FALSE; - if ( verbose ) { -- HDfprintf(stdout, "%d:%s: MPI_Type_struct() call failed.\n", -+ HDfprintf(stdout, "%d:%s: MPI_Type_create_struct() call failed.\n", - world_mpi_rank, FUNC); - } - } -- cgit v1.2.3 From 085bdfd09266cc0a6255c75821feb2b2ee58f761 Mon Sep 17 00:00:00 2001 From: Ludovic Courtès Date: Fri, 13 Dec 2019 18:00:44 +0100 Subject: gnu: guile-next: Update to 2.9.7. * gnu/packages/guile.scm (guile-next): Update to 2.9.7. --- gnu/packages/guile.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/guile.scm b/gnu/packages/guile.scm index 9df008c413..5a5d1af56a 100644 --- a/gnu/packages/guile.scm +++ b/gnu/packages/guile.scm @@ -288,14 +288,14 @@ without requiring the source code to be rewritten.") (package (inherit guile-2.2) (name "guile-next") - (version "2.9.6") + (version "2.9.7") (source (origin (inherit (package-source guile-2.2)) (uri (string-append "ftp://alpha.gnu.org/gnu/guile/guile-" version ".tar.xz")) (sha256 (base32 - "09rihg5bhzhdk6hfkpav6ajny69dflabgvnm8r7lran723gy5vbf")))) + "1dskpj8a2gl3h8si4virq8z4y06v9ywyadfa92gn2fiip2qmkw0d")))) (native-search-paths (list (search-path-specification (variable "GUILE_LOAD_PATH") -- cgit v1.2.3 From 5f12df7ea6dd8422aaf5b27f07b27897073a65bd Mon Sep 17 00:00:00 2001 From: Leo Prikler Date: Fri, 13 Dec 2019 14:05:24 +0100 Subject: gnu: emacs-telega: Patch `ffplay` instead of propagating. * gnu/packages/emacs-xyz.scm (emacs-telega) [phases]: : Rename to telega-paths-patch. : Substitute ffplay path for patching. [propagated-inputs] : Remove. [inputs] : Add. Fixes: #38590 Signed-off-by: Brett Gilio Co-authored-by: Brett Gilio --- gnu/packages/emacs-xyz.scm | 20 ++++++++++++++------ 1 file changed, 14 insertions(+), 6 deletions(-) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index ae7e7a64cc..86e0ad1108 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -20113,10 +20113,18 @@ fish-completion. It can be used in both Eshell and M-x shell.") (("python3 run_tests.py") "")) #t)) - ;; Modify telega-util to reflect unique dir name in - ;; `telega-install-data' phase. - (add-after 'unpack 'telega-data-patch - (lambda _ + (add-after 'unpack 'telega-paths-patch + (lambda* (#:key inputs #:allow-other-keys) + ;; Hard-code path to `ffplay`. + (let ((ffplay-bin (string-append (assoc-ref inputs "ffmpeg") + "/bin/ffplay"))) + (substitute* "telega-ffplay.el" + (("\\(executable-find \"ffplay\"\\)") + (string-append + "(and (file-executable-p \"" ffplay-bin "\")" + "\"" ffplay-bin "\")")))) + ;; Modify telega-util to reflect unique dir name in + ;; `telega-install-data' phase. (substitute* "telega-util.el" (("\\(concat \"etc/\" filename\\) telega--lib-directory") "(concat \"telega-data/\" filename) @@ -20149,7 +20157,6 @@ fish-completion. It can be used in both Eshell and M-x shell.") (invoke "python3" "server/run_tests.py") #t)) (delete 'configure) - ;; Build emacs-side using `emacs-build-system' (add-after 'compress-documentation 'emacs-add-source-to-load-path (assoc-ref emacs:%standard-phases 'add-source-to-load-path)) @@ -20168,9 +20175,10 @@ fish-completion. It can be used in both Eshell and M-x shell.") (assoc-ref emacs:%standard-phases 'build)) (add-after 'emacs-build 'emacs-make-autoloads (assoc-ref emacs:%standard-phases 'make-autoloads))))) + (inputs + `(("ffmpeg" ,ffmpeg))) ; mp4/gif support. (propagated-inputs `(("emacs-visual-fill-column" ,emacs-visual-fill-column) - ("ffmpeg" ,ffmpeg) ; mp4/gif support. ("libwebp" ,libwebp))) ; sticker support. (native-inputs `(("tdlib" ,tdlib) -- cgit v1.2.3 From e19a53938875cbe53a00daa0501846e53656d1af Mon Sep 17 00:00:00 2001 From: Brett Gilio Date: Fri, 13 Dec 2019 12:37:15 -0600 Subject: gnu: emacs-telega: Correct path coding for `ffmpeg`. * gnu/packages/emacs-xyz.scm (emacs-telega)[arguments]: Continuation of the previous patch. Adds a hard-coded path from NAME `ffmpeg-bin` to work around issue of ffmpeg not being found on the system PATH. --- gnu/packages/emacs-xyz.scm | 12 +++++++++--- 1 file changed, 9 insertions(+), 3 deletions(-) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 86e0ad1108..0480b1b33f 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -20115,14 +20115,20 @@ fish-completion. It can be used in both Eshell and M-x shell.") #t)) (add-after 'unpack 'telega-paths-patch (lambda* (#:key inputs #:allow-other-keys) - ;; Hard-code path to `ffplay`. + ;; Hard-code paths to `ffplay` and `ffmpeg`. (let ((ffplay-bin (string-append (assoc-ref inputs "ffmpeg") - "/bin/ffplay"))) + "/bin/ffplay")) + (ffmpeg-bin (string-append (assoc-ref inputs "ffmpeg") + "/bin/ffmpeg"))) (substitute* "telega-ffplay.el" (("\\(executable-find \"ffplay\"\\)") (string-append "(and (file-executable-p \"" ffplay-bin "\")" - "\"" ffplay-bin "\")")))) + "\"" ffplay-bin "\")")) + (("\\(executable-find \"ffmpeg\"\\)") + (string-append + "(and (file-executable-p \"" ffmpeg-bin "\")" + "\"" ffmpeg-bin "\")")))) ;; Modify telega-util to reflect unique dir name in ;; `telega-install-data' phase. (substitute* "telega-util.el" -- cgit v1.2.3 From c45fdf90a9cb9eb4a13695f110404957940f1f7d Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Fri, 13 Dec 2019 22:57:31 +0200 Subject: gnu: imlib2: Update to 1.6.1. * gnu/packages/image.scm (imlib2): Update to 1.6.1. --- gnu/packages/image.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/image.scm b/gnu/packages/image.scm index 0536779b64..e07ab15aec 100644 --- a/gnu/packages/image.scm +++ b/gnu/packages/image.scm @@ -852,7 +852,7 @@ compose, and analyze GIF images.") (define-public imlib2 (package (name "imlib2") - (version "1.6.0") + (version "1.6.1") (source (origin (method url-fetch) (uri (string-append @@ -860,7 +860,7 @@ compose, and analyze GIF images.") "/imlib2-" version ".tar.bz2")) (sha256 (base32 - "07b9v3ycwhici35fnczvpyjpgkc7gbcdhajpl9dwhpzdzbfl1i6g")))) + "0v8n3dswx7rxqfd0q03xwc7j2w1mv8lv18rdxv487a1xw5vklfad")))) (build-system gnu-build-system) (native-inputs `(("pkgconfig" ,pkg-config))) -- cgit v1.2.3 From ba4fcea499c74515925f2bc6a414ba64fff7754c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 13 Dec 2019 13:26:01 +0100 Subject: gnu: r-desolve: Update description. * gnu/packages/cran.scm (r-desolve)[description]: Use texinfo syntax. --- gnu/packages/cran.scm | 21 +++++++++++---------- 1 file changed, 11 insertions(+), 10 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index ad8c6ebe67..c2f0e156bd 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -15940,16 +15940,17 @@ programming problems.") `(("gfortran" ,gfortran))) (home-page "https://desolve.r-forge.r-project.org/") (synopsis "Solvers for initial value problems of differential equations") - (description "This package provides functions that solve initial -value problems of a system of first-order ordinary differential equations (ODE), -of partial differential equations (PDE), of differential algebraic equations -(DAE), and of delay differential equations. The functions provide an interface -to the FORTRAN functions lsoda, lsodar, lsode, lsodes of the ODEPACK collection, -to the FORTRAN functions dvode and daspk and a C-implementation of solvers of -the Runge-Kutta family with fixed or variable time steps. The package contains -routines designed for solving ODEs resulting from 1-D, 2-D and 3-D partial -differential equations (PDE) that have been converted to ODEs by numerical -differencing.") + (description "This package provides functions that solve initial value +problems of a system of first-order @dfn{ordinary differential +equations} (ODE), of @dfn{partial differential equations} (PDE), of +@dfn{differential algebraic equations} (DAE), and of delay differential +equations. The functions provide an interface to the FORTRAN functions +@code{lsoda}, @code{lsodar}, @code{lsode}, @code{lsodes} of the ODEPACK +collection, to the FORTRAN functions @code{dvode} and @code{daspk} and a +C-implementation of solvers of the Runge-Kutta family with fixed or variable +time steps. The package contains routines designed for solving ODEs resulting +from 1-D, 2-D and 3-D partial differential equations that have been converted +to ODEs by numerical differencing.") (license license:gpl2+))) (define-public r-pracma -- cgit v1.2.3 From e44c4cd73cfb256c97a0f14f8b3731b35b024dd8 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 13 Dec 2019 13:30:58 +0100 Subject: gnu: Add r-bio3d. * gnu/packages/cran.scm (r-bio3d): 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 c2f0e156bd..1c3d40d76c 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -16013,3 +16013,34 @@ graphics directly in the terminal window. This package provides a basic plotting function (and equivalents of curve, density, acf and barplot) as well as a boxplot function.") (license license:lgpl3+))) + +(define-public r-bio3d + (package + (name "r-bio3d") + (version "2.4-0") + (source + (origin + (method url-fetch) + (uri (cran-uri "bio3d" version)) + (sha256 + (base32 + "0ikpk1ppdp50m9kd289z616i382j9i7ji1zchyd4xqfyk8lnxf4s")))) + (properties `((upstream-name . "bio3d"))) + (build-system r-build-system) + (inputs `(("zlib" ,zlib))) + (propagated-inputs `(("r-rcpp" ,r-rcpp))) + (home-page "http://thegrantlab.org/bio3d/") + (synopsis "Biological structure analysis") + (description + "This package provides utilities to process, organize and explore protein +structure, sequence and dynamics data. Features include the ability to read +and write structure, sequence and dynamic trajectory data, perform sequence +and structure database searches, data summaries, atom selection, alignment, +superposition, rigid core identification, clustering, torsion analysis, +distance matrix analysis, structure and sequence conservation analysis, normal +mode analysis, principal component analysis of heterogeneous structure data, +and correlation network analysis from normal mode and molecular dynamics data. +In addition, various utility functions are provided to enable the statistical +and graphical power of the R environment to work with biological sequence and +structural data.") + (license license:gpl2+))) -- cgit v1.2.3 From db07641a676cf057597fb2e08bac7e391cb846d6 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 13 Dec 2019 13:31:20 +0100 Subject: gnu: Add r-bios2cor. * gnu/packages/cran.scm (r-bios2cor): New variable. --- gnu/packages/cran.scm | 33 +++++++++++++++++++++++++++++++++ 1 file changed, 33 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 1c3d40d76c..d6013d3b9f 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -16044,3 +16044,36 @@ In addition, various utility functions are provided to enable the statistical and graphical power of the R environment to work with biological sequence and structural data.") (license license:gpl2+))) + +(define-public r-bios2cor + (package + (name "r-bios2cor") + (version "2.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "Bios2cor" version)) + (sha256 + (base32 + "1rrz0vs6wbkwys3l5jv1rdnlhyb4r1q9pv7jlnmsx6c1b4f4vz5n")))) + (properties `((upstream-name . "Bios2cor"))) + (build-system r-build-system) + (propagated-inputs + `(("r-bigmemory" ,r-bigmemory) + ("r-bio3d" ,r-bio3d) + ("r-circular" ,r-circular) + ("r-igraph" ,r-igraph))) + (home-page "https://cran.r-project.org/web/packages/Bios2cor/") + (synopsis "From biological sequences and simulations to correlation analysis") + (description + "This package provides utilities for computation and analysis of +correlation/covariation in multiple sequence alignments and in side chain +motions during molecular dynamics simulations. Features include the +computation of correlation/covariation scores using a variety of scoring +functions between either sequence positions in alignments or side chain +dihedral angles in molecular dynamics simulations and utilities to analyze the +correlation/covariation matrix through a variety of tools including network +representation and principal components analysis. In addition, several +utility functions are based on the R graphical environment to provide friendly +tools for help in data interpretation.") + (license license:gpl2+))) -- cgit v1.2.3 From 59beb0d23feaa046646bfcc84acb121d10fb2fb0 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 13 Dec 2019 13:49:24 +0100 Subject: gnu: Add r-networkd3. * gnu/packages/cran.scm (r-networkd3): New variable. --- gnu/packages/cran.scm | 66 +++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 66 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index d6013d3b9f..984b8b8858 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -16077,3 +16077,69 @@ representation and principal components analysis. In addition, several utility functions are based on the R graphical environment to provide friendly tools for help in data interpretation.") (license license:gpl2+))) + +;; This package includes minified JavaScript files. When upgrading please +;; check that there are no new minified JavaScript files. +(define-public r-networkd3 + (package + (name "r-networkd3") + (version "0.4") + (source + (origin + (method url-fetch) + (uri (cran-uri "networkD3" version)) + (sha256 + (base32 + "02wxki67drppgfka1is1ykg1f2rxf0x0657c0crj7ipfy62jbf1k")) + (snippet + '(begin + (delete-file "inst/htmlwidgets/lib/d3-4.5.0/d3.min.js") + #t)))) + (properties `((upstream-name . "networkD3"))) + (build-system r-build-system) + (arguments + `(#:modules ((guix build utils) + (guix build r-build-system) + (srfi srfi-1) + (ice-9 popen)) + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'process-javascript + (lambda* (#:key inputs #:allow-other-keys) + (with-directory-excursion "inst/htmlwidgets/lib/" + (call-with-values + (lambda () + (unzip2 + `((,(assoc-ref inputs "d3.v4.js") + "d3-4.5.0/d3.min.js")))) + (lambda (sources targets) + (for-each (lambda (source target) + (format #t "Processing ~a --> ~a~%" + source target) + (let ((minified (open-pipe* OPEN_READ "uglify-js" source))) + (call-with-output-file target + (lambda (port) + (dump-port minified port))))) + sources targets)))) + #t))))) + (native-inputs + `(("uglify-js" ,uglify-js) + ;; NOTE: Make sure that this version of d3 is still valid when + ;; upgrading the package. + ("d3.v4.js" + ,(origin + (method url-fetch) + (uri "https://d3js.org/d3.v4.js") + (sha256 + (base32 + "0y7byf6kcinfz9ac59jxc4v6kppdazmnyqfav0dm4h550fzfqqlg")))))) + (propagated-inputs + `(("r-htmlwidgets" ,r-htmlwidgets) + ("r-igraph" ,r-igraph) + ("r-magrittr" ,r-magrittr))) + (home-page "https://cran.r-project.org/package=networkD3") + (synopsis "D3 JavaScript network graphs from R") + (description + "This package creates D3 JavaScript network, tree, dendrogram, and Sankey +graphs from R.") + (license license:gpl3+))) -- cgit v1.2.3 From 303c7d1dff7e0a2f91591489c83fb0dfa15ca8a8 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 13 Dec 2019 13:57:37 +0100 Subject: gnu: Add r-aasea. * gnu/packages/cran.scm (r-aasea): New variable. --- gnu/packages/cran.scm | 32 ++++++++++++++++++++++++++++++++ 1 file changed, 32 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 984b8b8858..3b7cb48038 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -16143,3 +16143,35 @@ tools for help in data interpretation.") "This package creates D3 JavaScript network, tree, dendrogram, and Sankey graphs from R.") (license license:gpl3+))) + +(define-public r-aasea + (package + (name "r-aasea") + (version "1.1.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "aaSEA" version)) + (sha256 + (base32 + "0him4r8qyp0xssgrmdxjs45yn4d28h5anv4jyxxbbs9phb0m6j3h")))) + (properties `((upstream-name . "aaSEA"))) + (build-system r-build-system) + (propagated-inputs + `(("r-bios2cor" ,r-bios2cor) + ("r-dt" ,r-dt) + ("r-hmisc" ,r-hmisc) + ("r-magrittr" ,r-magrittr) + ("r-networkd3" ,r-networkd3) + ("r-plotly" ,r-plotly) + ("r-seqinr" ,r-seqinr) + ("r-shiny" ,r-shiny) + ("r-shinydashboard" ,r-shinydashboard))) + (home-page "https://cran.r-project.org/web/packages/aaSEA/") + (synopsis "Amino acid substitution effect analyzer") + (description + "Given a protein multiple sequence alignment, it is a daunting task to +assess the effects of substitutions along sequence length. The aaSEA package +is intended to help researchers to rapidly analyze property changes caused by +single, multiple and correlated amino acid substitutions in proteins.") + (license license:gpl3))) -- cgit v1.2.3 From c20a81eed1b22b4cec136f78925bcc4d2be2393f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 13 Dec 2019 15:22:10 +0100 Subject: gnu: Add r-fastmap. * gnu/packages/cran.scm (r-fastmap): 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 3b7cb48038..de66afcabc 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -729,6 +729,30 @@ objects in HTML format.") and vice-versa.") (license license:gpl2+))) +(define-public r-fastmap + (package + (name "r-fastmap") + (version "1.0.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "fastmap" version)) + (sha256 + (base32 + "1v7sp56xiha0bh78g3w92k52p9vkp7ryzpw0z66nyddxzrfv0y27")))) + (properties `((upstream-name . "fastmap"))) + (build-system r-build-system) + (home-page "https://r-lib.github.io/fastmap/") + (synopsis "Fast implementation of a key-value store") + (description + "This package provides a fast implementation of a key-value store. +Environments are commonly used as key-value stores, but every time a new key +is used, it is added to R's global symbol table, causing a small amount of +memory leakage. This can be problematic in cases where many different keys +are used. Fastmap avoids this memory leak issue by implementing the map using +data structures in C++.") + (license license:expat))) + (define-public r-shiny (package (name "r-shiny") -- cgit v1.2.3 From 6e6fa954af3515c093821362450dc4e94db65ead Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 13 Dec 2019 15:22:30 +0100 Subject: gnu: r-shiny: Update to 1.4.0. * gnu/packages/cran.scm (r-shiny): Update to 1.4.0. [arguments]: Update list of JavaScript files to replace. [propagated-inputs]: Add r-fastmap. --- gnu/packages/cran.scm | 13 +++++++++---- 1 file changed, 9 insertions(+), 4 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index de66afcabc..ad7cff55a5 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -756,7 +756,7 @@ data structures in C++.") (define-public r-shiny (package (name "r-shiny") - (version "1.2.0") + (version "1.4.0") (source (origin (method git-fetch) @@ -766,7 +766,7 @@ data structures in C++.") (file-name (git-file-name name version)) (sha256 (base32 - "1kl3dh68h4cnrm3rqn9pddk5n6bsmr5x0626bkfv0qqi0q92zin4")))) + "17ac48g414h9dhi0k4wrah4gyik0q5r0xw3kc01c02qfjwimqsx7")))) (build-system r-build-system) (arguments `(#:modules ((guix build r-build-system) @@ -795,7 +795,7 @@ data structures in C++.") "/share/javascript/html5shiv.min.js")) (replace-file "json2-min.js" (string-append (assoc-ref inputs "js-json2") - "/share/javascript/json2.min.js")) + "/share/javascript/json2-min.js")) (replace-file "strftime/strftime-min.js" (string-append (assoc-ref inputs "js-strftime") "/share/javascript/strftime.min.js")) @@ -826,10 +826,15 @@ data structures in C++.") ("shiny.js" . "shiny.min.js") ("jquery.js" . - "jquery.min.js"))))) + "jquery.min.js") + ("legacy/jquery.js" . + "legacy/jquery.min.js") + ("showdown/src/showdown.js" . + "showdown/compressed/showdown.js"))))) #t))))) (propagated-inputs `(("r-crayon" ,r-crayon) + ("r-fastmap" ,r-fastmap) ("r-httpuv" ,r-httpuv) ("r-mime" ,r-mime) ("r-jsonlite" ,r-jsonlite) -- cgit v1.2.3 From 595d9502238947e276eb49c63b74b519537a81d5 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 13 Dec 2019 15:14:01 +0100 Subject: gnu: Add r-abacus. * gnu/packages/cran.scm (r-abacus): 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 ad7cff55a5..d06d1d2d5d 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -16204,3 +16204,28 @@ assess the effects of substitutions along sequence length. The aaSEA package is intended to help researchers to rapidly analyze property changes caused by single, multiple and correlated amino acid substitutions in proteins.") (license license:gpl3))) + +(define-public r-abacus + (package + (name "r-abacus") + (version "1.0.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "ABACUS" version)) + (sha256 + (base32 + "0m1dnkwjr1522l9ddbzzx7ayxvli17sbmk6s28adpmzzjwh2kd1i")))) + (properties `((upstream-name . "ABACUS"))) + (build-system r-build-system) + (propagated-inputs + `(("r-ggplot2" ,r-ggplot2) + ("r-shiny" ,r-shiny))) + (home-page "https://shiny.abdn.ac.uk/Stats/apps/") + (synopsis "Apps-based activities for communicating and understanding statistics") + (description + "This package provides a set of Shiny apps for effective communication +and understanding in statistics. The current version includes properties of +normal distribution, properties of sampling distribution, one-sample z and t +tests, two samples independent (unpaired) t test and analysis of variance.") + (license license:gpl3))) -- cgit v1.2.3 From 8fed766a7d3988ec39861c546507b945da9c84d9 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 13 Dec 2019 16:38:43 +0100 Subject: gnu: Add r-abc-rap. * gnu/packages/cran.scm (r-abc-rap): 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 d06d1d2d5d..8916e50f10 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -16229,3 +16229,24 @@ and understanding in statistics. The current version includes properties of normal distribution, properties of sampling distribution, one-sample z and t tests, two samples independent (unpaired) t test and analysis of variance.") (license license:gpl3))) + +(define-public r-abc-rap + (package + (name "r-abc-rap") + (version "0.9.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "ABC.RAP" version)) + (sha256 + (base32 + "1kdspln17v0krvahcd55vib4dv5azp60b3r1zf489x10qqbp1mxk")))) + (properties `((upstream-name . "ABC.RAP"))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/web/packages/ABC.RAP/") + (synopsis "Array-based CpG region analysis pipeline") + (description + "This package aims to identify candidate genes that are differentially +methylated between cases and controls. It applies Student's t-test and delta +beta analysis to identify candidate genes containing multiple CpG sites.") + (license license:gpl3))) -- cgit v1.2.3 From 647ff4a98b422028c162fb4f861ad9d323a4cadf Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 13 Dec 2019 16:40:40 +0100 Subject: gnu: Add r-abcadm. * gnu/packages/cran.scm (r-abcadm): 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 8916e50f10..b7555f959c 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -16250,3 +16250,28 @@ tests, two samples independent (unpaired) t test and analysis of variance.") methylated between cases and controls. It applies Student's t-test and delta beta analysis to identify candidate genes containing multiple CpG sites.") (license license:gpl3))) + +(define-public r-abcadm + (package + (name "r-abcadm") + (version "1.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "abcADM" version)) + (sha256 + (base32 + "0vcabnnnwc0psv9v3rda5aap9s8cq1pjh02zva3ki64hlavf2a10")))) + (properties `((upstream-name . "abcADM"))) + (build-system r-build-system) + (propagated-inputs + `(("r-bh" ,r-bh) + ("r-rcpp" ,r-rcpp))) + (home-page "https://cran.r-project.org/web/packages/abcADM/") + (synopsis "Fit accumulated damage models and estimate reliability using ABC") + (description + "This package provides tools to estimate parameters of accumulated +damage (load duration) models based on failure time data under a Bayesian +framework, using @dfn{Approximate Bayesian Computation} (ABC), and to assess +long-term reliability under stochastic load profiles.") + (license license:gpl3))) -- cgit v1.2.3 From 72e5c6e95f1b16b08a8d69680833f7ce15b8e50f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 13 Dec 2019 16:42:35 +0100 Subject: gnu: Add r-rglpk. * gnu/packages/cran.scm (r-rglpk): New variable. --- gnu/packages/cran.scm | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index b7555f959c..d6891ce6c3 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -16275,3 +16275,29 @@ damage (load duration) models based on failure time data under a Bayesian framework, using @dfn{Approximate Bayesian Computation} (ABC), and to assess long-term reliability under stochastic load profiles.") (license license:gpl3))) + +(define-public r-rglpk + (package + (name "r-rglpk") + (version "0.6-4") + (source + (origin + (method url-fetch) + (uri (cran-uri "Rglpk" version)) + (sha256 + (base32 + "19mzpyimzq9zqnbi05j79b2di3nzaln8swggs9p8sqdr60qvr3d2")))) + (properties `((upstream-name . "Rglpk"))) + (build-system r-build-system) + (propagated-inputs + `(("r-slam" ,r-slam))) + (inputs + `(("glpk" ,glpk))) + (home-page "http://R-Forge.R-project.org/projects/rglp/") + (synopsis "R interface to the GNU Linear Programming Kit") + (description + "This package provides an R interface to the GNU Linear Programming Kit, +software for solving large-scale @dfn{linear programming} (LP), @dfn{mixed +integer linear programming} (MILP) and other related problems.") + ;; Either license + (license (list license:gpl2 license:gpl3)))) -- cgit v1.2.3 From 84822497c2b7854ab16c35599c11edba3fa84b7a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 13 Dec 2019 16:43:02 +0100 Subject: gnu: Add r-abcdefba. * gnu/packages/cran.scm (r-abcdefba): New variable. --- gnu/packages/cran.scm | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index d6891ce6c3..c3b9a56c81 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -16301,3 +16301,29 @@ software for solving large-scale @dfn{linear programming} (LP), @dfn{mixed integer linear programming} (MILP) and other related problems.") ;; Either license (license (list license:gpl2 license:gpl3)))) + +(define-public r-abcdefba + (package + (name "r-abcdefba") + (version "0.4") + (source + (origin + (method url-fetch) + (uri (cran-uri "abcdeFBA" version)) + (sha256 + (base32 + "1rxjripy8v6bxi25vdfjnbk24zkmf752qbl73cin6nvnqflwxkx4")))) + (properties `((upstream-name . "abcdeFBA"))) + (build-system r-build-system) + (propagated-inputs + `(("r-corrplot" ,r-corrplot) + ("r-lattice" ,r-lattice) + ("r-rgl" ,r-rgl) + ("r-rglpk" ,r-rglpk))) + (home-page "https://cran.r-project.org/web/packages/abcdeFBA/") + (synopsis "A-Biologist-Can-Do-Everything of Flux Balance Analysis with this package") + (description + "This package provides functions for Constraint Based Simulation using +Flux Balance Analysis and informative analysis of the data generated during +simulation.") + (license license:gpl2))) -- cgit v1.2.3 From ae07172c659796f07d9ad878c33be6a7c79ec6ee Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 13 Dec 2019 16:45:50 +0100 Subject: gnu: Add r-abcrlda. * gnu/packages/cran.scm (r-abcrlda): New variable. --- gnu/packages/cran.scm | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index c3b9a56c81..6432af9392 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -16327,3 +16327,26 @@ integer linear programming} (MILP) and other related problems.") Flux Balance Analysis and informative analysis of the data generated during simulation.") (license license:gpl2))) + +(define-public r-abcrlda + (package + (name "r-abcrlda") + (version "1.0.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "abcrlda" version)) + (sha256 + (base32 + "0j29ifsvmxfx2g6v4bpbb4s6miwfpf4vlkpbgj6f2q078s4clc85")))) + (properties `((upstream-name . "abcrlda"))) + (build-system r-build-system) + (home-page "https://ieeexplore.ieee.org/document/8720003/") + (synopsis "Asymptotically bias-corrected regularized linear discriminant analysis") + (description + "This package offers methods to perform @dfn{asymptotically +bias-corrected regularized linear discriminant analysis} (ABC_RLDA) for +cost-sensitive binary classification. The bias-correction is an estimate of +the bias term added to regularized discriminant analysis that minimizes the +overall risk.") + (license license:gpl3))) -- cgit v1.2.3 From 3e33377767b9b2cd3a37724cae364c317698317d Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 13 Dec 2019 16:47:10 +0100 Subject: gnu: Add r-abemus. * gnu/packages/cran.scm (r-abemus): 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 6432af9392..21a51a6d9f 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -16350,3 +16350,28 @@ cost-sensitive binary classification. The bias-correction is an estimate of the bias term added to regularized discriminant analysis that minimizes the overall risk.") (license license:gpl3))) + +(define-public r-abemus + (package + (name "r-abemus") + (version "1.0.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "abemus" version)) + (sha256 + (base32 + "1dhllb184byp1yl15rg2w02zgw3iajag7cxshirg47mnmm7n70bb")))) + (properties `((upstream-name . "abemus"))) + (build-system r-build-system) + (propagated-inputs + `(("r-data-table" ,r-data-table))) + (home-page "https://cran.r-project.org/web/packages/abemus/") + (synopsis "Adaptive base error model in ultra-deep sequencing data") + (description + "This package provides an implementation of @dfn{Adaptive Base Error +Model in Ultra-deep Sequencing data} (ABEMUS), which combines +platform-specific genetic knowledge and empirical signal to readily detect and +quantify somatic @dfn{single nucleotide variants} (SNVs) in @dfn{circulating +cell free DNA} (cfDNA).") + (license license:gpl3))) -- cgit v1.2.3 From 8990fc1584ce2270063774e098ebf2ac8090c32d Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 13 Dec 2019 18:26:01 +0100 Subject: gnu: Add r-rintrojs. * gnu/packages/cran.scm (r-rintrojs): New variable. --- gnu/packages/cran.scm | 62 +++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 62 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 21a51a6d9f..d4bfcfaaa0 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -16375,3 +16375,65 @@ platform-specific genetic knowledge and empirical signal to readily detect and quantify somatic @dfn{single nucleotide variants} (SNVs) in @dfn{circulating cell free DNA} (cfDNA).") (license license:gpl3))) + +;; This package includes minified JavaScript files. When upgrading please +;; check that there are no new minified JavaScript files. +(define-public r-rintrojs + (package + (name "r-rintrojs") + (version "0.2.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "rintrojs" version)) + (sha256 + (base32 + "0vyqb3pyrh12saddar71ac9csn2vkd2j8ln6ygpqys8ky1lc3427")))) + (properties `((upstream-name . "rintrojs"))) + (build-system r-build-system) + (arguments + `(#:modules ((guix build utils) + (guix build r-build-system) + (srfi srfi-1) + (ice-9 popen)) + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'process-javascript + (lambda* (#:key inputs #:allow-other-keys) + (with-directory-excursion "inst/javascript/introjs/" + (call-with-values + (lambda () + (unzip2 + `((,(assoc-ref inputs "intro.js") + "intro.min.js")))) + (lambda (sources targets) + (for-each (lambda (source target) + (format #t "Processing ~a --> ~a~%" + source target) + (let ((minified (open-pipe* OPEN_READ "uglify-js" source))) + (call-with-output-file target + (lambda (port) + (dump-port minified port))))) + sources targets)))) + #t))))) + (native-inputs + `(("uglify-js" ,uglify-js) + ("intro.js" + ,(origin + (method url-fetch) + (uri "https://raw.githubusercontent.com/usablica/intro.js/v2.9.3/intro.js") + (sha256 + (base32 + "1qf8n1sfy9qkiqqnfgg0xbhmfgh0g3mqsjas8qhz230h3zzlzxj8")))))) + (propagated-inputs + `(("r-jsonlite" ,r-jsonlite) + ("r-shiny" ,r-shiny))) + (home-page "https://github.com/carlganz/rintrojs") + (synopsis "Wrapper for the Intro.js library") + (description + "This package provides a wrapper for the @url{http://www.introjs.com, +Intro.js} library. This package makes it easy to include step-by-step +introductions, and clickable hints in a Shiny application. It supports both +static introductions in the UI, and programmatic introductions from the +server-side.") + (license license:agpl3+))) -- cgit v1.2.3 From 322e8d85798f32bc0a4f5bf30d4896931046780d Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 13 Dec 2019 18:26:59 +0100 Subject: gnu: Add r-sysfonts. * gnu/packages/cran.scm (r-sysfonts): New variable. --- gnu/packages/cran.scm | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index d4bfcfaaa0..2838dcb37a 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -16437,3 +16437,29 @@ introductions, and clickable hints in a Shiny application. It supports both static introductions in the UI, and programmatic introductions from the server-side.") (license license:agpl3+))) + +(define-public r-sysfonts + (package + (name "r-sysfonts") + (version "0.8") + (source + (origin + (method url-fetch) + (uri (cran-uri "sysfonts" version)) + (sha256 + (base32 + "0wng902plryf2d8fc7k7m3jx11acz51kb2d91cqbyhq7xpk06z43")))) + (properties `((upstream-name . "sysfonts"))) + (build-system r-build-system) + (inputs + `(("freetype" ,freetype) + ("libpng" ,libpng) + ("zlib" ,zlib))) + (native-inputs + `(("pkg-config" ,pkg-config))) + (home-page "https://github.com/yixuan/sysfonts") + (synopsis "Loading fonts into R") + (description + "This is a package to simplify loading of system fonts and Google Fonts +into R, in order to support other packages.") + (license license:gpl2))) -- cgit v1.2.3 From 369e1bb6a89695280b4a47acdd3ac9eb4f935085 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 13 Dec 2019 18:28:36 +0100 Subject: gnu: Add r-showtextdb. * gnu/packages/cran.scm (r-showtextdb): 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 2838dcb37a..c4f1586f64 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -16463,3 +16463,25 @@ server-side.") "This is a package to simplify loading of system fonts and Google Fonts into R, in order to support other packages.") (license license:gpl2))) + +(define-public r-showtextdb + (package + (name "r-showtextdb") + (version "2.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "showtextdb" version)) + (sha256 + (base32 + "1qwwj9x2jvadvwn60h75k99c9xi7yhqjsgaakahz5paxgj583bsh")))) + (properties `((upstream-name . "showtextdb"))) + (build-system r-build-system) + (propagated-inputs + `(("r-sysfonts" ,r-sysfonts))) + (home-page "https://cran.r-project.org/web/packages/showtextdb/") + (synopsis "Font files for the 'showtext' package") + (description + "This package provides font files that can be used by the @code{showtext} +package.") + (license license:asl2.0))) -- cgit v1.2.3 From d7937243bad6ffb204b98521c8cdda0f7864bf5a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 13 Dec 2019 18:28:53 +0100 Subject: gnu: Add r-showtext. * gnu/packages/cran.scm (r-showtext): New variable. --- gnu/packages/cran.scm | 32 ++++++++++++++++++++++++++++++++ 1 file changed, 32 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index c4f1586f64..cddf78951d 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -16485,3 +16485,35 @@ into R, in order to support other packages.") "This package provides font files that can be used by the @code{showtext} package.") (license license:asl2.0))) + +(define-public r-showtext + (package + (name "r-showtext") + (version "0.7") + (source + (origin + (method url-fetch) + (uri (cran-uri "showtext" version)) + (sha256 + (base32 + "1ihgqzfia36b0n9aa41p1w98wxxvs1lxh1zz0570hbfqmph1sk73")))) + (properties `((upstream-name . "showtext"))) + (build-system r-build-system) + (inputs + `(("freetype" ,freetype) + ("libpng" ,libpng) + ("zlib" ,zlib))) + (propagated-inputs + `(("r-showtextdb" ,r-showtextdb) + ("r-sysfonts" ,r-sysfonts))) + (native-inputs `(("pkg-config" ,pkg-config))) + (home-page "https://github.com/yixuan/showtext") + (synopsis "Using fonts more easily in R graphs") + (description + "This package aims to make it easy to use various types of +fonts (TrueType, OpenType, Type 1, web fonts, etc.) in R graphs, and supports +most output formats of R graphics including PNG, PDF and SVG. Text glyphs +will be converted into polygons or raster images, hence after the plot has +been created, it no longer relies on the font files. No external software +such as Ghostscript is needed to use this package.") + (license license:asl2.0))) -- cgit v1.2.3 From 2ecd4e3bfdd6fe2d2ca3acbf50d6917af905fee0 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 13 Dec 2019 18:29:58 +0100 Subject: gnu: Add r-emojifont. * gnu/packages/cran.scm (r-emojifont): 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 cddf78951d..2101489577 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -16517,3 +16517,28 @@ will be converted into polygons or raster images, hence after the plot has been created, it no longer relies on the font files. No external software such as Ghostscript is needed to use this package.") (license license:asl2.0))) + +(define-public r-emojifont + (package + (name "r-emojifont") + (version "0.5.3") + (source + (origin + (method url-fetch) + (uri (cran-uri "emojifont" version)) + (sha256 + (base32 + "1cdrrl3hvrs8rskyy6zgr7q2mmg8yb9k8sld1m64zsp7y009g19k")))) + (properties `((upstream-name . "emojifont"))) + (build-system r-build-system) + (propagated-inputs + `(("r-ggplot2" ,r-ggplot2) + ("r-proto" ,r-proto) + ("r-showtext" ,r-showtext) + ("r-sysfonts" ,r-sysfonts))) + (home-page "https://guangchuangyu.github.io/emojifont") + (synopsis "Emoji and Font Awesome in R graphics") + (description + "This package enables the use of emoji and the Font Awesome glyphs in +both base and ggplot2 graphics.") + (license license:artistic2.0))) -- cgit v1.2.3 From a99c4c7584fc7e16df0fe3f55d640fa8e1bbed03 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 13 Dec 2019 18:30:32 +0100 Subject: gnu: Add r-abstractr. * gnu/packages/cran.scm (r-abstractr): 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 2101489577..2b318e6090 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -16542,3 +16542,32 @@ such as Ghostscript is needed to use this package.") "This package enables the use of emoji and the Font Awesome glyphs in both base and ggplot2 graphics.") (license license:artistic2.0))) + +(define-public r-abstractr + (package + (name "r-abstractr") + (version "0.1.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "abstractr" version)) + (sha256 + (base32 + "1ymwp7syrynwd4i8aj2x5n8jdi9d96fjzl6jb09n0bnr5fgl7vig")))) + (properties `((upstream-name . "abstractr"))) + (build-system r-build-system) + (propagated-inputs + `(("r-colourpicker" ,r-colourpicker) + ("r-emojifont" ,r-emojifont) + ("r-ggplot2" ,r-ggplot2) + ("r-gridextra" ,r-gridextra) + ("r-rintrojs" ,r-rintrojs) + ("r-shiny" ,r-shiny) + ("r-shinythemes" ,r-shinythemes))) + (home-page "https://matt-kumar.shinyapps.io/portfolio") + (synopsis "R-Shiny application for creating visual abstracts") + (description + "This package provides an R Shiny application to create visual abstracts +for original research. A variety of user defined options and formatting are +included.") + (license license:gpl3))) -- cgit v1.2.3 From bd74d7e6fc0e4b0c282a3a202b3dbfb4858368d0 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 13 Dec 2019 18:31:07 +0100 Subject: gnu: Add r-abtest. * gnu/packages/cran.scm (r-abtest): 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 2b318e6090..f931aa67e3 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -16571,3 +16571,33 @@ both base and ggplot2 graphics.") for original research. A variety of user defined options and formatting are included.") (license license:gpl3))) + +(define-public r-abtest + (package + (name "r-abtest") + (version "0.2.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "abtest" version)) + (sha256 + (base32 + "1ky3cf827kj24bhcpk00v5zl5jdkii1gca0x81ay1cjkzfispgws")))) + (properties `((upstream-name . "abtest"))) + (build-system r-build-system) + (propagated-inputs + `(("r-matrix" ,r-matrix) + ("r-mvtnorm" ,r-mvtnorm) + ("r-plotrix" ,r-plotrix) + ("r-rcolorbrewer" ,r-rcolorbrewer) + ("r-rcpp" ,r-rcpp) + ("r-sn" ,r-sn) + ("r-truncnorm" ,r-truncnorm) + ("r-vgam" ,r-vgam))) + (home-page "https://cran.r-project.org/web/packages/abtest/") + (synopsis "Bayesian A/B testing") + (description + "This package provides functions for Bayesian A/B testing including prior +elicitation options based on Kass and Vaidyanathan (1992) +@url{doi:10.1111/j.2517-6161.1992.tb01868.x}.") + (license license:gpl2+))) -- cgit v1.2.3 From 72b67e0b36cd472c893f99f4a3ab9a491e41000b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 13 Dec 2019 18:40:58 +0100 Subject: gnu: Add r-activedriverwgs. * gnu/packages/bioconductor.scm (r-activedriverwgs): 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 e584a7bced..ca29fb5a3e 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6059,3 +6059,37 @@ features (e.g. genes, microRNAs).") data. This modified test allows for testing differential expression in qPCR data.") (license license:gpl2+))) + +;; This is a CRAN package, but it depends on Bioconductor packages, so we put +;; it here. +(define-public r-activedriverwgs + (package + (name "r-activedriverwgs") + (version "1.0.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "ActiveDriverWGS" version)) + (sha256 + (base32 + "08l9dj8d3cd74z1dqn8n4yqykwvqjxsfa067wnxyh7xnfvvnm5v1")))) + (properties + `((upstream-name . "ActiveDriverWGS"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biostrings" ,r-biostrings) + ("r-bsgenome" ,r-bsgenome) + ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicranges" ,r-genomicranges) + ("r-iranges" ,r-iranges) + ("r-plyr" ,r-plyr) + ("r-s4vectors" ,r-s4vectors))) + (home-page "https://cran.r-project.org/web/packages/ActiveDriverWGS/") + (synopsis "Driver discovery tool for cancer whole genomes") + (description + "This package provides a method for finding an enrichment of cancer +simple somatic mutations (SNVs and Indels) in functional elements across the +human genome. ActiveDriverWGS detects coding and noncoding driver elements +using whole genome sequencing data.") + (license license:gpl3))) -- cgit v1.2.3 From 0379a167612f40e525251f4c1b92c9150405af7d Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 13 Dec 2019 18:41:48 +0100 Subject: gnu: Add r-accept. * gnu/packages/cran.scm (r-accept): 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 f931aa67e3..385b97adfc 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -16601,3 +16601,32 @@ included.") elicitation options based on Kass and Vaidyanathan (1992) @url{doi:10.1111/j.2517-6161.1992.tb01868.x}.") (license license:gpl2+))) + +(define-public r-accept + (package + (name "r-accept") + (version "0.7.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "accept" version)) + (sha256 + (base32 + "1r4mhy9g4wjcjgdd0gwdarmr09292il3vdkmx0hz7vh9mffyr9kx")))) + (properties `((upstream-name . "accept"))) + (build-system r-build-system) + (propagated-inputs + `(("r-dplyr" ,r-dplyr) + ("r-extrafont" ,r-extrafont) + ("r-mass" ,r-mass) + ("r-plotly" ,r-plotly) + ("r-stringr" ,r-stringr) + ("r-viridis" ,r-viridis))) + (home-page "https://cran.r-project.org/web/packages/accept/") + (synopsis "Acute COPD Exacerbation Prediction Tool (ACCEPT)") + (description + "This package allows clinicians to predict the rate and severity of +future acute exacerbation in @dfn{Chronic Obstructive Pulmonary +Disease} (COPD) patients, based on the clinical prediction model published in +Adibi et al. (2019) @url{doi:10.1101/651901}.") + (license license:gpl3))) -- cgit v1.2.3 From bba4ec62e36a6071d978cdb2e5d267f9bc2068c7 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 13 Dec 2019 18:42:45 +0100 Subject: gnu: Add r-smpracticals. * gnu/packages/cran.scm (r-smpracticals): 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 385b97adfc..2de143ca13 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -16630,3 +16630,30 @@ future acute exacerbation in @dfn{Chronic Obstructive Pulmonary Disease} (COPD) patients, based on the clinical prediction model published in Adibi et al. (2019) @url{doi:10.1101/651901}.") (license license:gpl3))) + +(define-public r-smpracticals + (package + (name "r-smpracticals") + (version "1.4-3") + (source + (origin + (method url-fetch) + (uri (cran-uri "SMPracticals" version)) + (sha256 + (base32 + "0zxq84f9i3b86xx6msb25b61gyj9k09iab2b7wg4d93yas9qzayf")))) + (properties `((upstream-name . "SMPracticals"))) + (build-system r-build-system) + (propagated-inputs + `(("r-ellipse" ,r-ellipse) + ("r-mass" ,r-mass) + ("r-nlme" ,r-nlme) + ("r-survival" ,r-survival))) + (home-page "http://statwww.epfl.ch/davison/SM/") + (synopsis "Practicals for use with Davison (2003) Statistical Models") + (description + "This package contains the datasets and a few functions for use with the +practicals outlined in Appendix A of the book Statistical Models (Davison, +2003, Cambridge University Press). The practicals themselves can be found at +@url{http://statwww.epfl.ch/davison/SM/}.") + (license license:gpl2+))) -- cgit v1.2.3 From 5a5431e406fb75fef1d80a937e1b4ed605ed30fa Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 13 Dec 2019 18:48:12 +0100 Subject: gnu: Add r-fgui. * gnu/packages/cran.scm (r-fgui): 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 2de143ca13..ea9994915d 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -16657,3 +16657,30 @@ practicals outlined in Appendix A of the book Statistical Models (Davison, 2003, Cambridge University Press). The practicals themselves can be found at @url{http://statwww.epfl.ch/davison/SM/}.") (license license:gpl2+))) + +(define-public r-fgui + (package + (name "r-fgui") + (version "1.0-8") + (source + (origin + (method url-fetch) + (uri (cran-uri "fgui" version)) + (sha256 + (base32 + "024fzd1c7iwqprn26hwjb9l2qlvvyzl449d7iixy0x69djwsrysv")))) + (properties `((upstream-name . "fgui"))) + (build-system r-build-system) + (home-page + "https://sites.google.com/site/thomashoffmannproject/software/fgui") + (synopsis "Create GUI for R functions") + (description + "Rapidly create a GUI for a function you created by automatically +creating widgets for arguments of the function. This package automatically +parses help routines for context-sensitive help to these arguments. The +interface is essentially a wrapper to some Tcl/Tk routines to both simplify +and facilitate GUI creation. More advanced Tcl/Tk routines/GUI objects can be +incorporated into the interface for greater customization for the more +experienced.") + ;; Any version of the GPL. + (license (list license:gpl2+ license:gpl3+)))) -- cgit v1.2.3 From f9d9c83183c02a6d50fa0b277ec69a897def73bb Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 13 Dec 2019 18:48:33 +0100 Subject: gnu: Add r-tcltk2. * gnu/packages/cran.scm (r-tcltk2): 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 ea9994915d..82403e5b42 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -73,6 +73,7 @@ #:use-module (gnu packages python) #:use-module (gnu packages python-xyz) #:use-module (gnu packages statistics) + #:use-module (gnu packages tcl) #:use-module (gnu packages tls) #:use-module (gnu packages web) #:use-module (gnu packages xorg)) @@ -16684,3 +16685,26 @@ incorporated into the interface for greater customization for the more experienced.") ;; Any version of the GPL. (license (list license:gpl2+ license:gpl3+)))) + +(define-public r-tcltk2 + (package + (name "r-tcltk2") + (version "1.2-11") + (source + (origin + (method url-fetch) + (uri (cran-uri "tcltk2" version)) + (sha256 + (base32 + "1ibxld379600xx7kiqq3fck083s8psry12859980218rnzikl65d")))) + (properties `((upstream-name . "tcltk2"))) + (build-system r-build-system) + (inputs + `(("tcl" ,tcl) + ("tk" ,tk))) + (home-page "http://www.sciviews.org/SciViews-R") + (synopsis "Tcl/Tk additions") + (description + "This package provides a series of additional Tcl commands and Tk widgets +with style and various functions to supplement the tcltk package") + (license license:lgpl3))) -- cgit v1.2.3 From c5b86d3a18fc671ee645dc8bfdaaced1a995ab2f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 13 Dec 2019 18:49:05 +0100 Subject: gnu: Add r-accrual. * gnu/packages/cran.scm (r-accrual): 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 82403e5b42..0186fe7a52 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -16708,3 +16708,33 @@ experienced.") "This package provides a series of additional Tcl commands and Tk widgets with style and various functions to supplement the tcltk package") (license license:lgpl3))) + +(define-public r-accrual + (package + (name "r-accrual") + (version "1.3") + (source + (origin + (method url-fetch) + (uri (cran-uri "accrual" version)) + (sha256 + (base32 + "11clm9s5c5518nmp6hd6pjnp0s28y92b2i2x0xgj4j5g816p4j3z")))) + (properties `((upstream-name . "accrual"))) + (build-system r-build-system) + (propagated-inputs + `(("r-fgui" ,r-fgui) + ("r-smpracticals" ,r-smpracticals) + ("r-tcltk2" ,r-tcltk2))) + (home-page "https://cran.r-project.org/web/packages/accrual/") + (synopsis "Bayesian accrual prediction") + (description + "Subject recruitment for medical research is challenging. Slow patient +accrual leads to delay in research. Accrual monitoring during the process of +recruitment is critical. Researchers need reliable tools to manage the +accrual rate. This package provides an implementation of a Bayesian method +that integrates researcher's experience on previous trials and data from the +current study, providing reliable prediction on accrual rate for clinical +studies. It provides functions for Bayesian accrual prediction which can be +easily used by statisticians and clinical researchers.") + (license license:gpl2))) -- cgit v1.2.3 From 592d423ca5d751d4dc6beb6b7500228ec6103937 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 13 Dec 2019 18:49:29 +0100 Subject: gnu: Add r-accrued. * gnu/packages/cran.scm (r-accrued): New variable. --- gnu/packages/cran.scm | 20 ++++++++++++++++++++ 1 file changed, 20 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 0186fe7a52..7547b176fc 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -16738,3 +16738,23 @@ current study, providing reliable prediction on accrual rate for clinical studies. It provides functions for Bayesian accrual prediction which can be easily used by statisticians and clinical researchers.") (license license:gpl2))) + +(define-public r-accrued + (package + (name "r-accrued") + (version "1.4.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "accrued" version)) + (sha256 + (base32 + "05g1jb5914z18rcai1ahn7nihn27vr2rnadwv94gc1j7ivvikvs5")))) + (properties `((upstream-name . "accrued"))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/web/packages/accrued/") + (synopsis "Data quality visualization tools for partially accruing data") + (description + "This is a package for visualizing data quality of partially accruing +data.") + (license license:gpl3))) -- cgit v1.2.3 From 7e2e46cbe2dd2fe9f90f61dfffdd89e66172ce8e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 13 Dec 2019 18:49:53 +0100 Subject: gnu: Add r-mda. * gnu/packages/cran.scm (r-mda): 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 7547b176fc..dcbad9cb12 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -16758,3 +16758,25 @@ easily used by statisticians and clinical researchers.") "This is a package for visualizing data quality of partially accruing data.") (license license:gpl3))) + +(define-public r-mda + (package + (name "r-mda") + (version "0.4-10") + (source + (origin + (method url-fetch) + (uri (cran-uri "mda" version)) + (sha256 + (base32 + "19g6kn6g0shidrjfffklbmzc5w7mcimrxhagx4nmpslg59ibqdkh")))) + (properties `((upstream-name . "mda"))) + (build-system r-build-system) + (propagated-inputs `(("r-class" ,r-class))) + (native-inputs `(("gfortran" ,gfortran))) + (home-page "https://cran.r-project.org/web/packages/mda/") + (synopsis "Mixture and flexible discriminant analysis") + (description + "This is a package for mixture and flexible discriminant analysis, +@dfn{multivariate adaptive regression splines} (MARS), BRUTO, and so on.") + (license license:gpl2))) -- cgit v1.2.3 From c909b710a4ee5021268fc0abbaf324771d6dd63c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 13 Dec 2019 18:50:09 +0100 Subject: gnu: Add r-elasticnet. * gnu/packages/cran.scm (r-elasticnet): New variable. --- gnu/packages/cran.scm | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index dcbad9cb12..a92a487059 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -16780,3 +16780,26 @@ data.") "This is a package for mixture and flexible discriminant analysis, @dfn{multivariate adaptive regression splines} (MARS), BRUTO, and so on.") (license license:gpl2))) + +(define-public r-elasticnet + (package + (name "r-elasticnet") + (version "1.1.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "elasticnet" version)) + (sha256 + (base32 + "0p9dplnsp28z4s2fl6afbwrgd0aj339fak8mmndicmrh7bb7rpmb")))) + (properties `((upstream-name . "elasticnet"))) + (build-system r-build-system) + (propagated-inputs + `(("r-lars" ,r-lars))) + (home-page "http://www.stat.umn.edu/~hzou") + (synopsis "Elastic-Net for sparse estimation and sparse PCA") + (description + "This package provides functions for fitting the entire solution path of +the Elastic-Net and also provides functions for estimating sparse Principal +Components. The Lasso solution paths can be computed by the same function.") + (license license:gpl2+))) -- cgit v1.2.3 From 7199d2a5fcd4db00314086947285bbe3f5ea8fc3 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 13 Dec 2019 18:50:26 +0100 Subject: gnu: Add r-sparselda. * gnu/packages/cran.scm (r-sparselda): 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 a92a487059..5c0d44ebf7 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -16803,3 +16803,27 @@ data.") the Elastic-Net and also provides functions for estimating sparse Principal Components. The Lasso solution paths can be computed by the same function.") (license license:gpl2+))) + +(define-public r-sparselda + (package + (name "r-sparselda") + (version "0.1-9") + (source + (origin + (method url-fetch) + (uri (cran-uri "sparseLDA" version)) + (sha256 + (base32 + "1k3sw9kc40yxnfss4vrsx34qxmv8ssddyhbfjhxrdldvblhbwchb")))) + (properties `((upstream-name . "sparseLDA"))) + (build-system r-build-system) + (propagated-inputs + `(("r-elasticnet" ,r-elasticnet) + ("r-mass" ,r-mass) + ("r-mda" ,r-mda))) + (home-page "http://www.imm.dtu.dk/~lhc") + (synopsis "Sparse discriminant analysis") + (description + "This package performs sparse linear discriminant analysis for Gaussians +and mixture of Gaussian models.") + (license license:gpl2+))) -- cgit v1.2.3 From b8d52fe2771220742bf7e55700d0a91e05d8536c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 13 Dec 2019 18:50:49 +0100 Subject: gnu: Add r-accsda. * gnu/packages/cran.scm (r-accsda): New variable. --- gnu/packages/cran.scm | 33 +++++++++++++++++++++++++++++++++ 1 file changed, 33 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 5c0d44ebf7..5c530a6a36 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -16827,3 +16827,36 @@ Components. The Lasso solution paths can be computed by the same function.") "This package performs sparse linear discriminant analysis for Gaussians and mixture of Gaussian models.") (license license:gpl2+))) + +(define-public r-accsda + (package + (name "r-accsda") + (version "1.0.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "accSDA" version)) + (sha256 + (base32 + "0sgxy5y8kkc1n35657kifwfjsba7y5m1vbr7rkk5lmbpkzahqm61")))) + (properties `((upstream-name . "accSDA"))) + (build-system r-build-system) + (propagated-inputs + `(("r-ggplot2" ,r-ggplot2) + ("r-ggthemes" ,r-ggthemes) + ("r-gridextra" ,r-gridextra) + ("r-mass" ,r-mass) + ("r-rarpack" ,r-rarpack) + ("r-sparselda" ,r-sparselda))) + (home-page "https://github.com/gumeo/accSDA/wiki") + (synopsis "Accelerated sparse discriminant analysis") + (description + "This package provides an implementation of sparse linear discriminant +analysis, which is a supervised classification method for multiple classes. +Various novel optimization approaches to this problem are implemented +including @dfn{alternating direction method of multipliers} (ADMM), +@dfn{proximal gradient} (PG) and @dfn{accelerated proximal gradient} (APG). +Functions for performing cross validation are also supplied along with basic +prediction and plotting functions. @dfn{Sparse zero variance +discriminant} (SZVD) analysis is also included in the package.") + (license license:gpl2+))) -- cgit v1.2.3 From b441dac7af3f6fbf8b0a7def117abc0181b52f33 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 13 Dec 2019 18:51:11 +0100 Subject: gnu: Add r-ace2fastq. * gnu/packages/cran.scm (r-ace2fastq): New variable. --- gnu/packages/cran.scm | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 5c530a6a36..4b4d1996b7 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -16860,3 +16860,29 @@ Functions for performing cross validation are also supplied along with basic prediction and plotting functions. @dfn{Sparse zero variance discriminant} (SZVD) analysis is also included in the package.") (license license:gpl2+))) + +(define-public r-ace2fastq + (package + (name "r-ace2fastq") + (version "0.6.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "ace2fastq" version)) + (sha256 + (base32 + "09kk3yyqnr2xp820g0p3aai9a21figigjr9lxkr3zjq2d8gzwfic")))) + (properties `((upstream-name . "ace2fastq"))) + (build-system r-build-system) + (propagated-inputs + `(("r-stringr" ,r-stringr))) + (home-page "https://github.com/c5sire/ace2fastq") + (synopsis "ACE file to FASTQ converter") + (description + "The ACE file format is used in genomics to store contigs from sequencing +machines. This tools converts it into FASTQ format. Both formats contain the +sequence characters and their corresponding quality information. Unlike the +FASTQ file, the ACE file stores the quality values numerically. The +conversion algorithm uses the standard Sanger formula. The package +facilitates insertion into pipelines, and content inspection.") + (license license:gpl3))) -- cgit v1.2.3 From ca1bc50cad56b45e3db9c42bb9ac3fde288986c0 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 13 Dec 2019 18:51:44 +0100 Subject: gnu: Add r-rngwell. * gnu/packages/cran.scm (r-rngwell): 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 4b4d1996b7..e823b82e0e 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -16886,3 +16886,24 @@ FASTQ file, the ACE file stores the quality values numerically. The conversion algorithm uses the standard Sanger formula. The package facilitates insertion into pipelines, and content inspection.") (license license:gpl3))) + +(define-public r-rngwell + (package + (name "r-rngwell") + (version "0.10-5") + (source + (origin + (method url-fetch) + (uri (cran-uri "rngWELL" version)) + (sha256 + (base32 + "0b4ys525gksgqwqx9id4bdgyi9mwj6n3r87xdzf4fc9hp3cc16jb")))) + (properties `((upstream-name . "rngWELL"))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/web/packages/rngWELL/") + (synopsis "Toolbox for WELL random number generators") + (description + "This is a dedicated package to WELL pseudo random generators, which were +introduced in Panneton et al. (2006), ``Improved Long-Period Generators Based +on Linear Recurrences Modulo 2'', ACM Transactions on Mathematical Software.") + (license license:bsd-3))) -- cgit v1.2.3 From e6bf147293e8cf36aa4090e5b4aa5d653201c9a9 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 13 Dec 2019 18:52:39 +0100 Subject: gnu: Add r-randtoolbox. * gnu/packages/cran.scm (r-randtoolbox): New variable. --- gnu/packages/cran.scm | 37 +++++++++++++++++++++++++++++++++++++ 1 file changed, 37 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index e823b82e0e..ed47472583 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -16907,3 +16907,40 @@ facilitates insertion into pipelines, and content inspection.") introduced in Panneton et al. (2006), ``Improved Long-Period Generators Based on Linear Recurrences Modulo 2'', ACM Transactions on Mathematical Software.") (license license:bsd-3))) + +(define-public r-randtoolbox + (package + (name "r-randtoolbox") + (version "1.30.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "randtoolbox" version)) + (sha256 + (base32 + "141p13ajgzmb2s89rlac7zrra92mi1izvpfrngb4kqzlf3igdsqd")))) + (properties `((upstream-name . "randtoolbox"))) + (build-system r-build-system) + (propagated-inputs + `(("r-rngwell" ,r-rngwell))) + (native-inputs + `(("gfortran" ,gfortran))) + (home-page "https://cran.r-project.org/web/packages/randtoolbox/") + (synopsis "Toolbox for pseudo and quasi random number generation") + (description + "This package provides + +@enumerate +@item pseudo random generators, such as general linear +congruential generators, multiple recursive generators and generalized +feedback shift register (SF-Mersenne Twister algorithm and WELL +generators) + +@item quasi random generators, such as the Torus algorithm, the Sobol +sequence, the Halton sequence (including the Van der Corput sequence), and + +@item some generator tests: the gap test, the serial test, the poker test. +@end enumerate + +See e.g. Gentle (2003) @url{doi:10.1007/b97336}.") + (license license:bsd-3))) -- cgit v1.2.3 From 390bc8726bbd9625557f1cd02b3853995de34b8f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 13 Dec 2019 18:53:00 +0100 Subject: gnu: Add r-lhs. * gnu/packages/cran.scm (r-lhs): 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 ed47472583..1a09342180 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -16944,3 +16944,24 @@ sequence, the Halton sequence (including the Van der Corput sequence), and See e.g. Gentle (2003) @url{doi:10.1007/b97336}.") (license license:bsd-3))) + +(define-public r-lhs + (package + (name "r-lhs") + (version "1.0.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "lhs" version)) + (sha256 + (base32 + "0lzaqr7xi3ckln5nglv5xf5njm359slpz1jc6s02hpsqdw6armd4")))) + (properties `((upstream-name . "lhs"))) + (build-system r-build-system) + (propagated-inputs `(("r-rcpp" ,r-rcpp))) + (home-page "https://github.com/bertcarnell/lhs") + (synopsis "Latin Hypercube Samples") + (description + "This package provides a number of methods for creating and augmenting +Latin Hypercube Samples.") + (license license:gpl3))) -- cgit v1.2.3 From 1442ca73402ba7904830204e59aa2d76bd85af46 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 13 Dec 2019 18:53:16 +0100 Subject: gnu: Add r-acebayes. * gnu/packages/cran.scm (r-acebayes): 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 1a09342180..91f842e8f4 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -16965,3 +16965,34 @@ See e.g. Gentle (2003) @url{doi:10.1007/b97336}.") "This package provides a number of methods for creating and augmenting Latin Hypercube Samples.") (license license:gpl3))) + +(define-public r-acebayes + (package + (name "r-acebayes") + (version "1.8") + (source + (origin + (method url-fetch) + (uri (cran-uri "acebayes" version)) + (sha256 + (base32 + "1xm6bw0qm2vlcrk274x0bawzb2lnacb1wsmzba5mg3i75a55pqln")))) + (properties `((upstream-name . "acebayes"))) + (build-system r-build-system) + (propagated-inputs + `(("r-compare" ,r-compare) + ("r-lhs" ,r-lhs) + ("r-randtoolbox" ,r-randtoolbox) + ("r-rcpp" ,r-rcpp) + ("r-rcpparmadillo" ,r-rcpparmadillo))) + (home-page "https://cran.r-project.org/web/packages/acebayes/") + (synopsis "Optimal Bayesian experimental design using the ACE algorithm") + (description + "Finding an optimal Bayesian experimental design involves maximizing an +objective function given by the expectation of some appropriately chosen +utility function with respect to the joint distribution of unknown +quantities (including responses). This objective function is usually not +available in closed form and the design space can be continuous and of high +dimensionality. This package uses @dfn{Approximate Coordinate Exchange} (ACE) +to maximise an approximation to the expectation of the utility function.") + (license license:gpl2))) -- cgit v1.2.3 From 43a70edc291de476d705805230f61458de992f70 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 13 Dec 2019 18:56:16 +0100 Subject: gnu: Add r-acet. * gnu/packages/cran.scm (r-acet): New variable. --- gnu/packages/cran.scm | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 91f842e8f4..8c7fe23667 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -16996,3 +16996,29 @@ available in closed form and the design space can be continuous and of high dimensionality. This package uses @dfn{Approximate Coordinate Exchange} (ACE) to maximise an approximation to the expectation of the utility function.") (license license:gpl2))) + +(define-public r-acet + (package + (name "r-acet") + (version "1.8.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "ACEt" version)) + (sha256 + (base32 + "0626d6kg485xjya164wagrr5z223jvi93ywbwpdns7fkm03c0dlq")))) + (properties `((upstream-name . "ACEt"))) + (build-system r-build-system) + (propagated-inputs + `(("r-bh" ,r-bh) + ("r-mass" ,r-mass) + ("r-rcpp" ,r-rcpp) + ("r-rcpparmadillo" ,r-rcpparmadillo))) + (home-page "https://cran.r-project.org/web/packages/ACEt/") + (synopsis "Estimating dynamic heritability and twin model comparison") + (description + "This package supports twin models that are able to estimate the dynamic +behaviour of the variance components in the classical twin models with respect +to age using B-splines and P-splines.") + (license license:gpl2+))) -- cgit v1.2.3 From a8a7ba9acb5108f710a89e6e79c686ee5979c209 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 13 Dec 2019 18:56:39 +0100 Subject: gnu: Add r-acfmperiod. * gnu/packages/cran.scm (r-acfmperiod): 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 8c7fe23667..ece356e7cd 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -17022,3 +17022,32 @@ to maximise an approximation to the expectation of the utility function.") behaviour of the variance components in the classical twin models with respect to age using B-splines and P-splines.") (license license:gpl2+))) + +(define-public r-acfmperiod + (package + (name "r-acfmperiod") + (version "1.0.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "acfMPeriod" version)) + (sha256 + (base32 + "1yww8isfrbs2v9s94hx7p2imyszcgadwafdgpj438n2ik0q6p9d5")))) + (properties `((upstream-name . "acfMPeriod"))) + (build-system r-build-system) + (propagated-inputs + `(("r-mass" ,r-mass))) + (home-page "https://cran.r-project.org/web/packages/acfMPeriod/") + (synopsis "Estimation of the ACF from the M-periodogram") + (description + "This package support non-robust and robust computations of the sample +autocovariance (ACOVF) and sample autocorrelation functions (ACF) of +univariate and multivariate processes. The methodology consists in reversing +the diagonalization procedure involving the periodogram or the +cross-periodogram and the Fourier transform vectors, and, thus, obtaining the +ACOVF or the ACF as discussed in Fuller (1995) +@url{doi:10.1002/9780470316917}. The robust version is obtained by fitting +robust M-regressors to obtain the M-periodogram or M-cross-periodogram as +discussed in Reisen et al. (2017) @url{doi:10.1016/j.jspi.2017.02.008}.") + (license license:gpl2+))) -- cgit v1.2.3 From 3b89a8af7a8cf873b8712aecce7ac1335adb9856 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 13 Dec 2019 18:56:55 +0100 Subject: gnu: Add r-gamlss-data. * gnu/packages/cran.scm (r-gamlss-data): 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 ece356e7cd..280810f929 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -17051,3 +17051,24 @@ ACOVF or the ACF as discussed in Fuller (1995) robust M-regressors to obtain the M-periodogram or M-cross-periodogram as discussed in Reisen et al. (2017) @url{doi:10.1016/j.jspi.2017.02.008}.") (license license:gpl2+))) + +(define-public r-gamlss-data + (package + (name "r-gamlss-data") + (version "5.1-4") + (source + (origin + (method url-fetch) + (uri (cran-uri "gamlss.data" version)) + (sha256 + (base32 + "1dgfspbmps6ipzcmw681wjdp320nm50dwsxafgrcwxndqgc7fdqd")))) + (properties `((upstream-name . "gamlss.data"))) + (build-system r-build-system) + (home-page "http://www.gamlss.org/") + (synopsis "GAMLSS data") + (description + "This package provides data used as examples to demonstrate GAMLSS +models.") + ;; Either version of the license + (license (list license:gpl2 license:gpl3)))) -- cgit v1.2.3 From 6cc356c3535cd5b16b7a6929903d62beded8e732 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 13 Dec 2019 18:59:02 +0100 Subject: gnu: Add r-gamlss. * gnu/packages/cran.scm (r-gamlss): 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 280810f929..ed705145c7 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -17072,3 +17072,34 @@ discussed in Reisen et al. (2017) @url{doi:10.1016/j.jspi.2017.02.008}.") models.") ;; Either version of the license (license (list license:gpl2 license:gpl3)))) + +(define-public r-gamlss + (package + (name "r-gamlss") + (version "5.1-5") + (source + (origin + (method url-fetch) + (uri (cran-uri "gamlss" version)) + (sha256 + (base32 + "0gcngfck0dk2rhjg0z1fnc61dqs0s049jy2rkywaf57531s2k8bc")))) + (properties `((upstream-name . "gamlss"))) + (build-system r-build-system) + (propagated-inputs + `(("r-gamlss-data" ,r-gamlss-data) + ("r-gamlss-dist" ,r-gamlss-dist) + ("r-mass" ,r-mass) + ("r-nlme" ,r-nlme) + ("r-survival" ,r-survival))) + (home-page "http://www.gamlss.org/") + (synopsis "Generalized additive models for location scale and shape") + (description + "This package provides functions for fitting the generalized additive +models for location scale and shape introduced by Rigby and +Stasinopoulos (2005), @url{doi:10.1111/j.1467-9876.2005.00510.x}. The models +use a distributional regression approach where all the parameters of the +conditional distribution of the response variable are modelled using +explanatory variables.") + ;; Either version of the license + (license (list license:gpl2 license:gpl3)))) -- cgit v1.2.3 From 220557a7f3e9468682dda5f4b3efe1e2e9203920 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 13 Dec 2019 18:59:33 +0100 Subject: gnu: Add r-acid. * gnu/packages/cran.scm (r-acid): 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 ed705145c7..c2ea959234 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -17103,3 +17103,32 @@ conditional distribution of the response variable are modelled using explanatory variables.") ;; Either version of the license (license (list license:gpl2 license:gpl3)))) + +(define-public r-acid + (package + (name "r-acid") + (version "1.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "acid" version)) + (sha256 + (base32 + "030i0y8s283ivbsmjccpbv9v7mgbcg2jk9df7vgcbbns74swf9hd")))) + (properties `((upstream-name . "acid"))) + (build-system r-build-system) + (propagated-inputs + `(("r-gamlss" ,r-gamlss) + ("r-gamlss-dist" ,r-gamlss-dist) + ("r-hmisc" ,r-hmisc))) + (home-page "https://cran.r-project.org/web/packages/acid/") + (synopsis "Analysing conditional income distributions") + (description + "This package provides functions for the analysis of income distributions +for subgroups of the population as defined by a set of variables like age, +gender, region, etc. This entails a Kolmogorov-Smirnov test for a mixture +distribution as well as functions for moments, inequality measures, entropy +measures and polarisation measures of income distributions. This package thus +aides the analysis of income inequality by offering tools for the exploratory +analysis of income distributions at the disaggregated level.") + (license license:gpl3))) -- cgit v1.2.3 From 542590c5a3714a06bd364b54763fcfd78826c245 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 13 Dec 2019 19:10:05 +0100 Subject: gnu: Add r-acm4r. * gnu/packages/cran.scm (r-acm4r): 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 c2ea959234..b491484508 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -17132,3 +17132,27 @@ measures and polarisation measures of income distributions. This package thus aides the analysis of income inequality by offering tools for the exploratory analysis of income distributions at the disaggregated level.") (license license:gpl3))) + +(define-public r-acm4r + (package + (name "r-acm4r") + (version "1.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "acm4r" version)) + (sha256 + (base32 + "1wqzc35i1rshx0zlmas8y4qkkvy6h9r4i4apscjjv1xg2wjflzxa")))) + (properties `((upstream-name . "acm4r"))) + (build-system r-build-system) + (propagated-inputs `(("r-mass" ,r-mass))) + (home-page "https://cran.r-project.org/web/packages/acm4r/") + (synopsis "Align-and-count method comparisons of RFLP data") + (description + "This is a package to compare sequence fragment lengths or molecular +weights from pairs of lanes. The number of matching bands in the +@dfn{Restriction Fragment Length Polymorphism} (RFLP) data is calculated using +the align-and-count method.") + ;; Any version of the GPL + (license (list license:gpl2+ license:gpl3+)))) -- cgit v1.2.3 From fa82997feac8636464bcf92571236105e1719999 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 13 Dec 2019 19:10:33 +0100 Subject: gnu: Add r-filematrix. * gnu/packages/cran.scm (r-filematrix): 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 b491484508..ddbd8dec25 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -17156,3 +17156,33 @@ weights from pairs of lanes. The number of matching bands in the the align-and-count method.") ;; Any version of the GPL (license (list license:gpl2+ license:gpl3+)))) + +(define-public r-filematrix + (package + (name "r-filematrix") + (version "1.3") + (source + (origin + (method url-fetch) + (uri (cran-uri "filematrix" version)) + (sha256 + (base32 + "1v3aj1ng742msb0sfdnjsbqb508mqjf8jlq2v33vxldhradw5w0b")))) + (properties `((upstream-name . "filematrix"))) + (build-system r-build-system) + ;; These inputs are needed for vignettes + (native-inputs + `(("r-knitr" ,r-knitr) + ("r-rmarkdown" ,r-rmarkdown) + ("pandoc-citeproc" ,ghc-pandoc-citeproc))) + (home-page "https://github.com/andreyshabalin/filematrix") + (synopsis "File-backed matrix class with convenient read and write access") + (description + "This package provides an interface for working with large matrices +stored in files, not in computer memory. It supports multiple non-character +data types (double, integer, logical and raw) of various sizes (e.g. 8 and 4 +byte real values). Access to parts of the matrix is done by indexing, exactly +as with usual R matrices. It supports very large matrices; the package has +been tested on multi-terabyte matrices. It allows for more than 2^32 rows or +columns, ad allows for quick addition of extra columns to a filematrix.") + (license license:lgpl3))) -- cgit v1.2.3 From 73f055df34b1d174544e0232b5aaf1d735f90d9e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 13 Dec 2019 19:24:31 +0100 Subject: gnu: Add r-acmeeqtl. * gnu/packages/cran.scm (r-acmeeqtl): 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 ddbd8dec25..943a1b629f 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -17186,3 +17186,28 @@ as with usual R matrices. It supports very large matrices; the package has been tested on multi-terabyte matrices. It allows for more than 2^32 rows or columns, ad allows for quick addition of extra columns to a filematrix.") (license license:lgpl3))) + +(define-public r-acmeeqtl + (package + (name "r-acmeeqtl") + (version "1.6") + (source + (origin + (method url-fetch) + (uri (cran-uri "ACMEeqtl" version)) + (sha256 + (base32 + "049xjv2ym35bbn43zwi68cq27fwdh404vp0r2ca5gxgmmx8kj1cz")))) + (properties `((upstream-name . "ACMEeqtl"))) + (build-system r-build-system) + (propagated-inputs + `(("r-filematrix" ,r-filematrix))) + (home-page "https://github.com/andreyshabalin/ACMEeqtl") + (synopsis "Estimation of interpretable eQTL effect sizes") + (description + "This package provides a non-linear model, termed ACME, that reflects a +parsimonious biological model for allelic contributions of cis-acting eQTLs. +With non-linear least-squares algorithm the maximum likelihood parameters can +be estimated. The ACME model provides interpretable effect size estimates and +p-values with well controlled Type-I error.") + (license license:lgpl3))) -- cgit v1.2.3 From 2dc8723abd724d2fac491511a27102c6e5b8e61c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 13 Dec 2019 19:25:07 +0100 Subject: gnu: Add r-acmer. * gnu/packages/cran.scm (r-acmer): 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 943a1b629f..ce34315b03 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -17211,3 +17211,30 @@ With non-linear least-squares algorithm the maximum likelihood parameters can be estimated. The ACME model provides interpretable effect size estimates and p-values with well controlled Type-I error.") (license license:lgpl3))) + +(define-public r-acmer + (package + (name "r-acmer") + (version "1.1.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "acmeR" version)) + (sha256 + (base32 + "000b2hqlhj93958nddw0fqb15ahigs08najv2miivym046x04mf7")))) + (properties `((upstream-name . "acmeR"))) + (build-system r-build-system) + (propagated-inputs `(("r-foreign" ,r-foreign))) + (home-page "https://cran.r-project.org/web/packages/acmeR/") + (synopsis "ACME estimator of bird and bat mortality by wind turbines") + (description + "This package provides an implementation of the ACME estimator, described +in Wolpert (2015), ACME: A Partially Periodic Estimator of Avian & Chiropteran +Mortality at Wind Turbines. Unlike most other models, this estimator supports +decreasing-hazard Weibull model for persistence; decreasing search proficiency +as carcasses age; variable bleed-through at successive searches; and interval +mortality estimates. The package provides, based on search data, functions +for estimating the mortality inflation factor in Frequentist and Bayesian +settings.") + (license license:expat))) -- cgit v1.2.3 From 1c2e3d7d316573b3fd51d2a37af19a27df20be97 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 13 Dec 2019 19:26:05 +0100 Subject: gnu: Add r-r-huge. * gnu/packages/cran.scm (r-r-huge): New variable. --- gnu/packages/cran.scm | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index ce34315b03..413211f363 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -17238,3 +17238,29 @@ mortality estimates. The package provides, based on search data, functions for estimating the mortality inflation factor in Frequentist and Bayesian settings.") (license license:expat))) + +(define-public r-r-huge + (package + (name "r-r-huge") + (version "0.9.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "R.huge" version)) + (sha256 + (base32 + "13p558qalv60pgr24nsm6mi92ryj65rsbqa6pgdwy0snjqx12bgi")))) + (properties `((upstream-name . "R.huge"))) + (build-system r-build-system) + (propagated-inputs + `(("r-r-methodss3" ,r-r-methodss3) + ("r-r-oo" ,r-r-oo) + ("r-r-utils" ,r-r-utils))) + (home-page "https://github.com/HenrikBengtsson/R.huge") + (synopsis "Methods for accessing huge amounts of data") + (description + "This is a deprecated package for accessing huge amounts of data. + Cross-platform alternatives are the following packages: bigmemory (CRAN), +ff (CRAN), or BufferedMatrix (Bioconductor). The main usage of it was inside +the @code{aroma.affymetrix} package.") + (license license:lgpl2.1+))) -- cgit v1.2.3 From 9f9520a1299fccd8508d03ce0c9280c6e0030207 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 13 Dec 2019 22:53:19 +0100 Subject: gnu: bluez-alsa: Update to 2.0.0. * gnu/packages/audio.scm (bluez-alsa): Update to 2.0.0. [source]: Use git-file-name. [arguments]: Override ALSA plugin directory and dbus configuration directory. [inputs]: Add dbus. --- gnu/packages/audio.scm | 15 ++++++++++++--- 1 file changed, 12 insertions(+), 3 deletions(-) diff --git a/gnu/packages/audio.scm b/gnu/packages/audio.scm index 24c294b8e2..e6e89c0064 100644 --- a/gnu/packages/audio.scm +++ b/gnu/packages/audio.scm @@ -3331,7 +3331,7 @@ mixers.") (define-public bluez-alsa (package (name "bluez-alsa") - (version "1.2.0") + (version "2.0.0") (source (origin ;; The tarballs are mere snapshots and don't contain a ;; bootstrapped build system. @@ -3339,11 +3339,19 @@ mixers.") (uri (git-reference (url "https://github.com/Arkq/bluez-alsa.git") (commit (string-append "v" version)))) - (file-name (string-append name "-" version "-checkout")) + (file-name (git-file-name name version)) (sha256 (base32 - "1qinf41wl2ihx54zmmhanycihwjkn7dn1cicq6pp4rqbiv79b95x")))) + "08mppgnjf1j2733bk9yf0cny6rfxxwiys0s62lz2zd2lpdl6d9lz")))) (build-system gnu-build-system) + (arguments + `(#:configure-flags + (list (string-append "--with-alsaplugindir=" + (assoc-ref %outputs "out") + "/lib/alsa-lib") + (string-append "--with-dbusconfdir=" + (assoc-ref %outputs "out") + "/etc/dbus-1")))) (native-inputs `(("autoconf" ,autoconf) ("automake" ,automake) @@ -3352,6 +3360,7 @@ mixers.") (inputs `(("alsa-lib" ,alsa-lib) ("bluez" ,bluez) + ("dbus" ,dbus) ("glib" ,glib) ("libbsd" ,libbsd) ("ncurses" ,ncurses) -- cgit v1.2.3 From 4e410c9d23c96b7b5c94e2e68f3ad7daedd08771 Mon Sep 17 00:00:00 2001 From: Mark H Weaver Date: Fri, 13 Dec 2019 23:08:25 -0500 Subject: gnu: linux-libre@4.19: Update to 4.19.89. * gnu/packages/linux.scm (linux-libre-4.19-version): Update to 4.19.89. (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 0a3f7957c5..3bb68397c7 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -364,10 +364,10 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." (%upstream-linux-source version hash) deblob-scripts-5.3))) -(define-public linux-libre-4.19-version "4.19.88") +(define-public linux-libre-4.19-version "4.19.89") (define-public linux-libre-4.19-pristine-source (let ((version linux-libre-4.19-version) - (hash (base32 "1gizkdmq46ykw7ya3hibd6lalww2kvsia346pq3xvrk6s5mkp4n1"))) + (hash (base32 "0ijx8ih91p4g95zpwz6ga3q2x9lf1948xf2v5mz4348byf5hdwv8"))) (make-linux-libre-source version (%upstream-linux-source version hash) deblob-scripts-4.19))) -- cgit v1.2.3 From 3e9e242aa52d4f3b462052cacf3f7ab47a44b72a Mon Sep 17 00:00:00 2001 From: Mark H Weaver Date: Fri, 13 Dec 2019 23:09:39 -0500 Subject: gnu: linux-libre: Update to 5.3.16. * gnu/packages/linux.scm (linux-libre-5.3-version): Update to 5.3.16. (linux-libre-5.3-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 3bb68397c7..c70aa6c815 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -356,10 +356,10 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." "linux-" version ".tar.xz")) (sha256 hash))) -(define-public linux-libre-5.3-version "5.3.15") +(define-public linux-libre-5.3-version "5.3.16") (define-public linux-libre-5.3-pristine-source (let ((version linux-libre-5.3-version) - (hash (base32 "15qidl06lyfylx1b43b4wz2zfkr4000bkr7ialslmb7yi7mamj6f"))) + (hash (base32 "19asdv08rzp33f0zxa2swsfnbhy4zwg06agj7sdnfy4wfkrfwx49"))) (make-linux-libre-source version (%upstream-linux-source version hash) deblob-scripts-5.3))) -- cgit v1.2.3 From 8e6f63dd83b06962e155a88f101eda9c18f3ca7e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 13 Dec 2019 22:57:59 +0100 Subject: gnu: Add r-activepathways. * gnu/packages/bioconductor.scm (r-activepathways): New variable. --- gnu/packages/bioconductor.scm | 30 ++++++++++++++++++++++++++++++ 1 file changed, 30 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index ca29fb5a3e..1ef636d7f6 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6093,3 +6093,33 @@ simple somatic mutations (SNVs and Indels) in functional elements across the human genome. ActiveDriverWGS detects coding and noncoding driver elements using whole genome sequencing data.") (license license:gpl3))) + +;; This is a CRAN package, but it depends on Bioconductor packages, so we put +;; it here. +(define-public r-activepathways + (package + (name "r-activepathways") + (version "1.0.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "ActivePathways" version)) + (sha256 + (base32 + "1xb0d1svmzw404pv8ja6wr4773k7x2lxkrzrayilvzqbfzj1wx20")))) + (properties + `((upstream-name . "ActivePathways"))) + (build-system r-build-system) + (propagated-inputs + `(("r-data-table" ,r-data-table) + ("r-ggplot2" ,r-ggplot2) + ("r-metap" ,r-metap))) + (home-page "https://cran.r-project.org/web/packages/ActivePathways/") + (synopsis "Multivariate pathway enrichment analysis") + (description + "This package represents an integrative method of analyzing multi omics +data that conducts enrichment analysis of annotated gene sets. ActivePathways +uses a statistical data fusion approach, rationalizes contributing evidence +and highlights associated genes, improving systems-level understanding of +cellular organization in health and disease.") + (license license:gpl3))) -- cgit v1.2.3 From 2fe1e66c4d2cab9922a6c98680c8d71bfc05654c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 13 Dec 2019 23:01:20 +0100 Subject: gnu: Add r-r-filesets. * gnu/packages/cran.scm (r-r-filesets): New variable. --- gnu/packages/cran.scm | 32 ++++++++++++++++++++++++++++++++ 1 file changed, 32 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 413211f363..495ef13628 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -17264,3 +17264,35 @@ settings.") ff (CRAN), or BufferedMatrix (Bioconductor). The main usage of it was inside the @code{aroma.affymetrix} package.") (license license:lgpl2.1+))) + +(define-public r-r-filesets + (package + (name "r-r-filesets") + (version "2.13.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "R.filesets" version)) + (sha256 + (base32 + "124rygq0bl9n4akxcm868nl30cyk3rz0iprb98zlpk62gci9f5fg")))) + (properties `((upstream-name . "R.filesets"))) + (build-system r-build-system) + (propagated-inputs + `(("r-digest" ,r-digest) + ("r-r-cache" ,r-r-cache) + ("r-r-methodss3" ,r-r-methodss3) + ("r-r-oo" ,r-r-oo) + ("r-r-utils" ,r-r-utils))) + (home-page "https://github.com/HenrikBengtsson/R.filesets") + (synopsis "Easy handling of and access to files") + (description + "This package provides classes and methods to locate, setup, subset, +navigate and iterate file sets, i.e. sets of files located in one or more +directories on the file system. The API is designed such that these classes +can be extended via inheritance to provide a richer API for special file +formats. Moreover, a specific name format is defined such that filenames and +directories can be considered to have full names which consists of a name +followed by comma-separated tags. This adds additional flexibility to +identify file sets and individual files.") + (license license:lgpl2.1+))) -- cgit v1.2.3 From 217cd2e3ee6b04ed2ac0ab4548106f8708367aa5 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 13 Dec 2019 23:02:28 +0100 Subject: gnu: Add r-r-devices. * gnu/packages/cran.scm (r-r-devices): 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 495ef13628..ec001ab383 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -17296,3 +17296,33 @@ directories can be considered to have full names which consists of a name followed by comma-separated tags. This adds additional flexibility to identify file sets and individual files.") (license license:lgpl2.1+))) + +(define-public r-r-devices + (package + (name "r-r-devices") + (version "2.16.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "R.devices" version)) + (sha256 + (base32 + "15zlnq3g27whq26fbcy5zfl5hiddm256h4rga4frblg6wqlbkvdd")))) + (properties `((upstream-name . "R.devices"))) + (build-system r-build-system) + (propagated-inputs + `(("r-base64enc" ,r-base64enc) + ("r-r-methodss3" ,r-r-methodss3) + ("r-r-oo" ,r-r-oo) + ("r-r-utils" ,r-r-utils))) + (home-page "https://github.com/HenrikBengtsson/R.devices") + (synopsis "Unified handling of graphics devices") + (description + "This package provides functions for creating plots and image files in a +unified way regardless of output format (EPS, PDF, PNG, SVG, TIFF, WMF, etc.). +Default device options as well as scales and aspect ratios are controlled in a +uniform way across all device types. Switching output format requires minimal +changes in code. This package is ideal for large-scale batch processing, +because it will never leave open graphics devices or incomplete image files +behind, even on errors or user interrupts.") + (license license:lgpl2.1+))) -- cgit v1.2.3 From eff3e8a471e4ca7a449f6acd338a4db0c4c95a0e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 13 Dec 2019 23:03:13 +0100 Subject: gnu: Add r-acnr. * gnu/packages/cran.scm (r-acnr): 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 ec001ab383..207bb13bcd 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -17326,3 +17326,24 @@ changes in code. This package is ideal for large-scale batch processing, because it will never leave open graphics devices or incomplete image files behind, even on errors or user interrupts.") (license license:lgpl2.1+))) + +(define-public r-acnr + (package + (name "r-acnr") + (version "1.0.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "acnr" version)) + (sha256 + (base32 + "087hq4i7jp67ba2finzsqjfnqbiprl33na6ryjv9zqzsdawj9cym")))) + (properties `((upstream-name . "acnr"))) + (build-system r-build-system) + (home-page "https://github.com/mpierrejean/acnr") + (synopsis "Annotated copy-number regions") + (description + "This package provides SNP array data from different types of copy-number +regions. These regions were identified manually by the authors of the package +and may be used to generate realistic data sets with known truth.") + (license license:lgpl2.1+))) -- cgit v1.2.3 From 5d887a03551a24228a4cf5519bcd27a5ae6a123b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 13 Dec 2019 23:03:31 +0100 Subject: gnu: Add r-acopula. * gnu/packages/cran.scm (r-acopula): New variable. --- gnu/packages/cran.scm | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 207bb13bcd..6f2eb07951 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -17347,3 +17347,29 @@ behind, even on errors or user interrupts.") regions. These regions were identified manually by the authors of the package and may be used to generate realistic data sets with known truth.") (license license:lgpl2.1+))) + +(define-public r-acopula + (package + (name "r-acopula") + (version "0.9.3") + (source + (origin + (method url-fetch) + (uri (cran-uri "acopula" version)) + (sha256 + (base32 + "0vvbbw8pfs9jwfz5c57lw48pr0qj661r0ys007q6zf9jmlrhx1ln")))) + (properties `((upstream-name . "acopula"))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/web/packages/acopula/") + (synopsis "Modelling dependence with multivariate Archimax copulas") + (description + "Archimax copulas are a mixture of Archimedean and EV copulas. This +package provides definitions of several parametric families of generator and +dependence function, computes CDF and PDF, estimates parameters, tests for +goodness of fit, generates random sample and checks copula properties for +custom constructs. In the 2-dimensional case explicit formulas for density +are used, contrary to higher dimensions when all derivatives are linearly +approximated. Several non-archimax families (normal, FGM, Plackett) are +provided as well.") + (license license:gpl2))) -- cgit v1.2.3 From cb350053dab549e9bbd85aec651e3662a9f68062 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 13 Dec 2019 23:05:18 +0100 Subject: gnu: Add r-tuner. * gnu/packages/cran.scm (r-tuner): 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 6f2eb07951..b1217ad992 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -17373,3 +17373,27 @@ are used, contrary to higher dimensions when all derivatives are linearly approximated. Several non-archimax families (normal, FGM, Plackett) are provided as well.") (license license:gpl2))) + +(define-public r-tuner + (package + (name "r-tuner") + (version "1.3.3") + (source + (origin + (method url-fetch) + (uri (cran-uri "tuneR" version)) + (sha256 + (base32 + "0av978m4h2iqazyfq6n2cgkh4wpllihh7s29lah2nb8ngc0w5hxx")))) + (properties `((upstream-name . "tuneR"))) + (build-system r-build-system) + (propagated-inputs `(("r-signal" ,r-signal))) + (home-page "https://cran.r-project.org/web/packages/tuneR/") + (synopsis "Analysis of music and speech") + (description + "This is a package for the analysis of music and speech. Analyze music +and speech, extract features like MFCCs, handle wave files and their +representation in various ways, read MP3, read MIDI, perform steps of a +transcription, ...") + ;; Either of these versions. + (license (list license:gpl2 license:gpl3)))) -- cgit v1.2.3 From 19172e12ef990f9c7527a90fe24ab3e38a348974 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 13 Dec 2019 23:05:27 +0100 Subject: gnu: Add r-seewave. * gnu/packages/cran.scm (r-seewave): New variable. --- gnu/packages/cran.scm | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index b1217ad992..0f0ecb6829 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -17397,3 +17397,29 @@ representation in various ways, read MP3, read MIDI, perform steps of a transcription, ...") ;; Either of these versions. (license (list license:gpl2 license:gpl3)))) + +(define-public r-seewave + (package + (name "r-seewave") + (version "2.1.5") + (source + (origin + (method url-fetch) + (uri (cran-uri "seewave" version)) + (sha256 + (base32 + "1qg8f5gik9pw6f9mcxqmrc9x3003s8vdm6g01pjjpyc9qaqiz2vi")))) + (properties `((upstream-name . "seewave"))) + (build-system r-build-system) + (propagated-inputs + `(("r-tuner" ,r-tuner))) + (home-page "http://rug.mnhn.fr/seewave") + (synopsis "Sound analysis and synthesis") + (description + "This package provides functions for analysing, manipulating, displaying, +editing and synthesizing time waves (particularly sound). This package +processes time analysis (oscillograms and envelopes), spectral content, +resonance quality factor, entropy, cross correlation and autocorrelation, +zero-crossing, dominant frequency, analytic signal, frequency coherence, 2D +and 3D spectrograms and many other analyses.") + (license license:gpl2+))) -- cgit v1.2.3 From c12227d9719898dd1bd405ef0141747bd90e53b4 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 13 Dec 2019 23:08:25 +0100 Subject: gnu: Add r-acousticndlcoder. * gnu/packages/cran.scm (r-acousticndlcoder): 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 0f0ecb6829..a07cfbe153 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -17423,3 +17423,32 @@ resonance quality factor, entropy, cross correlation and autocorrelation, zero-crossing, dominant frequency, analytic signal, frequency coherence, 2D and 3D spectrograms and many other analyses.") (license license:gpl2+))) + +(define-public r-acousticndlcoder + (package + (name "r-acousticndlcoder") + (version "1.0.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "AcousticNDLCodeR" version)) + (sha256 + (base32 + "1fgzgwanpv2pzy74xdk3hamc44p8qch467wh163dxby8jr9ik0sb")))) + (properties + `((upstream-name . "AcousticNDLCodeR"))) + (build-system r-build-system) + (propagated-inputs + `(("r-seewave" ,r-seewave) + ("r-tuner" ,r-tuner) + ("r-zoo" ,r-zoo))) + (home-page "https://cran.r-project.org/web/packages/AcousticNDLCodeR/") + (synopsis "Coding sound files for use with NDL") + (description + "Make acoustic cues to use with the R package @code{ndl}. +The package implements functions used in the PLoS ONE paper \"Words from +spontaneous conversational speech can be recognized with human-like accuracy +by an error-driven learning algorithm that discriminates between meanings +straight from smart acoustic features, bypassing the phoneme as recognition +unit.\" @url{doi:10.1371/journal.pone.0174623}") + (license license:gpl2+))) -- cgit v1.2.3 From 56cba940c3e56d0c811652e638408d098894ae8e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 13 Dec 2019 23:08:51 +0100 Subject: gnu: Add r-acp. * gnu/packages/cran.scm (r-acp): 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 a07cfbe153..d09bc22e19 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -17452,3 +17452,27 @@ by an error-driven learning algorithm that discriminates between meanings straight from smart acoustic features, bypassing the phoneme as recognition unit.\" @url{doi:10.1371/journal.pone.0174623}") (license license:gpl2+))) + +(define-public r-acp + (package + (name "r-acp") + (version "2.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "acp" version)) + (sha256 + (base32 + "0lcwbjcyyr32m6qjmjqh25qjwrbyqj1n092xhgbhxzd8fslppnmn")))) + (properties `((upstream-name . "acp"))) + (build-system r-build-system) + (propagated-inputs + `(("r-quantmod" ,r-quantmod) + ("r-tseries" ,r-tseries))) + (home-page "https://cran.r-project.org/web/packages/acp/") + (synopsis "Autoregressive conditional Poisson") + (description + "This package supports the analysis of count data exhibiting +autoregressive properties, using the @dfn{Autoregressive Conditional Poisson} +model (ACP(p,q)) proposed by Heinen (2003).") + (license license:gpl2))) -- cgit v1.2.3 From f18c0544f6dd48aee582d95a0d6400939fa8b441 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 13 Dec 2019 23:09:24 +0100 Subject: gnu: Add r-ada. * gnu/packages/cran.scm (r-ada): 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 d09bc22e19..d7b8e866d6 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -17476,3 +17476,27 @@ unit.\" @url{doi:10.1371/journal.pone.0174623}") autoregressive properties, using the @dfn{Autoregressive Conditional Poisson} model (ACP(p,q)) proposed by Heinen (2003).") (license license:gpl2))) + +(define-public r-ada + (package + (name "r-ada") + (version "2.0-5") + (source + (origin + (method url-fetch) + (uri (cran-uri "ada" version)) + (sha256 + (base32 + "1h3a07czp0w3hrhjcg1fz721y8vsfclzqi3rq8qfzgpfb4h1f06r")))) + (properties `((upstream-name . "ada"))) + (build-system r-build-system) + (propagated-inputs `(("r-rpart" ,r-rpart))) + (home-page "https://cran.r-project.org/web/packages/ada/") + (synopsis "Stochastic boosting") + (description + "This package provides a straightforward, well-documented, and broad +boosting routine for classification, ideally suited for small to +moderate-sized data sets. It performs discrete, real, and gentle boost under +both exponential and logistic loss on a given data set.") + ;; Any version of the GPL. + (license (list license:gpl2+ license:gpl3+)))) -- cgit v1.2.3 From 270529f633e3636bc10cc00ae5081093bb2e95cb Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 13 Dec 2019 23:09:40 +0100 Subject: gnu: Add r-genalg. * gnu/packages/cran.scm (r-genalg): New variable. --- gnu/packages/cran.scm | 20 ++++++++++++++++++++ 1 file changed, 20 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index d7b8e866d6..9edf9eaf7f 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -17500,3 +17500,23 @@ moderate-sized data sets. It performs discrete, real, and gentle boost under both exponential and logistic loss on a given data set.") ;; Any version of the GPL. (license (list license:gpl2+ license:gpl3+)))) + +(define-public r-genalg + (package + (name "r-genalg") + (version "0.2.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "genalg" version)) + (sha256 + (base32 + "1wzfamq8k5yhwbdx0wy1w5bks93brj0p890xxc4yqrja4w38ja3s")))) + (properties `((upstream-name . "genalg"))) + (build-system r-build-system) + (home-page "https://github.com/egonw/genalg") + (synopsis "R based genetic algorithm") + (description + "This package provides an R based genetic algorithm for binary and +floating point chromosomes.") + (license license:gpl2))) -- cgit v1.2.3 From 6afc037e74a2bc92adde2ffecb2c3722f9113b6b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 13 Dec 2019 23:09:52 +0100 Subject: gnu: Add r-kernelfactory. * gnu/packages/cran.scm (r-kernelfactory): 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 9edf9eaf7f..1b03627a8a 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -17520,3 +17520,28 @@ both exponential and logistic loss on a given data set.") "This package provides an R based genetic algorithm for binary and floating point chromosomes.") (license license:gpl2))) + +(define-public r-kernelfactory + (package + (name "r-kernelfactory") + (version "0.3.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "kernelFactory" version)) + (sha256 + (base32 + "001kw9k3ivd4drd4mwqapkkk3f4jgljiaprhg2630hmll064s89j")))) + (properties `((upstream-name . "kernelFactory"))) + (build-system r-build-system) + (propagated-inputs + `(("r-auc" ,r-auc) + ("r-genalg" ,r-genalg) + ("r-kernlab" ,r-kernlab) + ("r-randomforest" ,r-randomforest))) + (home-page "https://cran.r-project.org/web/packages/kernelFactory/") + (synopsis "Ensemble of kernel machines") + (description + "Kernel factory is an ensemble method where each base classifier (random +forest) is fit on the kernel matrix of a subset of the training data.") + (license license:gpl2+))) -- cgit v1.2.3 From 6c2dcba99df361cdbb3f1b1beeff5b3cf34330b9 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 13 Dec 2019 23:10:09 +0100 Subject: gnu: Add r-dummies. * gnu/packages/cran.scm (r-dummies): New variable. --- gnu/packages/cran.scm | 20 ++++++++++++++++++++ 1 file changed, 20 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 1b03627a8a..3a332a428e 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -17545,3 +17545,23 @@ floating point chromosomes.") "Kernel factory is an ensemble method where each base classifier (random forest) is fit on the kernel matrix of a subset of the training data.") (license license:gpl2+))) + +(define-public r-dummies + (package + (name "r-dummies") + (version "1.5.6") + (source + (origin + (method url-fetch) + (uri (cran-uri "dummies" version)) + (sha256 + (base32 + "01f84crqx17xd6xy55qxlvsj3knm8lhw7jl26p2rh2w3y0nvqlbm")))) + (properties `((upstream-name . "dummies"))) + (build-system r-build-system) + (home-page "http://www.decisionpatterns.com") + (synopsis "Create dummy/indicator variables flexibly and efficiently") + (description + "This package lets you expand factors, characters and other eligible +classes into dummy/indicator variables.") + (license license:gpl2+))) -- cgit v1.2.3 From 3bc2c210431720d75c3a0eb786d4b4ff14a19061 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 13 Dec 2019 23:10:23 +0100 Subject: gnu: Add r-acrm. * gnu/packages/cran.scm (r-acrm): New variable. --- gnu/packages/cran.scm | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 3a332a428e..d3db6b0ca4 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -17565,3 +17565,29 @@ forest) is fit on the kernel matrix of a subset of the training data.") "This package lets you expand factors, characters and other eligible classes into dummy/indicator variables.") (license license:gpl2+))) + +(define-public r-acrm + (package + (name "r-acrm") + (version "0.1.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "aCRM" version)) + (sha256 + (base32 + "0kzp568hd9c9a9qgniia5s5gv0q5f89xfvvwpzb197gqhs3x092v")))) + (properties `((upstream-name . "aCRM"))) + (build-system r-build-system) + (propagated-inputs + `(("r-ada" ,r-ada) + ("r-dummies" ,r-dummies) + ("r-kernelfactory" ,r-kernelfactory) + ("r-randomforest" ,r-randomforest))) + (home-page "https://cran.r-project.org/web/packages/aCRM/") + (synopsis "Convenience functions for analytical customer relationship management") + (description + "This package provides convenience functions for data preparation and +modeling often used in @dfn{analytical customer relationship +management} (aCRM).") + (license license:gpl2+))) -- cgit v1.2.3 From c3f5989c8f92de1693610c5237e0794991d7534d Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 13 Dec 2019 23:11:26 +0100 Subject: gnu: Add r-treeclust. * gnu/packages/cran.scm (r-treeclust): 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 d3db6b0ca4..6dd36c36ce 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -17591,3 +17591,27 @@ classes into dummy/indicator variables.") modeling often used in @dfn{analytical customer relationship management} (aCRM).") (license license:gpl2+))) + +(define-public r-treeclust + (package + (name "r-treeclust") + (version "1.1-7") + (source + (origin + (method url-fetch) + (uri (cran-uri "treeClust" version)) + (sha256 + (base32 + "1s7kh6q0bkixsygrip95zf1bi10ihddsa5lq9dfxd68yh8rsby6z")))) + (properties `((upstream-name . "treeClust"))) + (build-system r-build-system) + (propagated-inputs + `(("r-cluster" ,r-cluster) + ("r-rpart" ,r-rpart))) + (home-page "https://cran.r-project.org/web/packages/treeClust/") + (synopsis "Cluster distances through trees") + (description + "This package provides tools to create a measure of inter-point +dissimilarity useful for clustering mixed data, and, optionally, perform the +clustering.") + (license license:gpl2+))) -- cgit v1.2.3 From 4b44bfb6ec86fd51bc7d3bac31adcb6731592578 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 13 Dec 2019 23:11:55 +0100 Subject: gnu: Add r-acrosstic. * gnu/packages/cran.scm (r-acrosstic): 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 6dd36c36ce..ebff9de29c 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -17615,3 +17615,27 @@ management} (aCRM).") dissimilarity useful for clustering mixed data, and, optionally, perform the clustering.") (license license:gpl2+))) + +(define-public r-acrosstic + (package + (name "r-acrosstic") + (version "1.0-3") + (source + (origin + (method url-fetch) + (uri (cran-uri "AcrossTic" version)) + (sha256 + (base32 + "03180h79jhjd66ibrnsfp3yyp2jlfysp7cymw46phzj2palghsc0")))) + (properties `((upstream-name . "AcrossTic"))) + (build-system r-build-system) + (propagated-inputs + `(("r-lpsolve" ,r-lpsolve) + ("r-treeclust" ,r-treeclust))) + (home-page "https://cran.r-project.org/web/packages/AcrossTic/") + (synopsis "Cost-minimal regular spanning subgraph with TreeClust") + (description + "This is a package for constructing minimum-cost regular spanning +subgraph as part of a non-parametric two-sample test for equality of +distribution.") + (license license:gpl2+))) -- cgit v1.2.3 From d015db6f57888c5573dfb276121971cb7d44f4b7 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 13 Dec 2019 23:12:12 +0100 Subject: gnu: Add r-acrt. * gnu/packages/cran.scm (r-acrt): 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 ebff9de29c..6c0bc01df0 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -17639,3 +17639,28 @@ clustering.") subgraph as part of a non-parametric two-sample test for equality of distribution.") (license license:gpl2+))) + +(define-public r-acrt + (package + (name "r-acrt") + (version "1.0.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "acrt" version)) + (sha256 + (base32 + "0y9ndcq8ffpfrv7w9rikm4zn68jpsj6baqisq9kp2433xrwzdb6s")))) + (properties `((upstream-name . "acrt"))) + (build-system r-build-system) + (propagated-inputs + `(("r-rcpp" ,r-rcpp) + ("r-rcppeigen" ,r-rcppeigen) + ("r-sandwich" ,r-sandwich))) + (home-page "https://cran.r-project.org/web/packages/acrt/") + (synopsis "Autocorrelation robust testing") + (description + "This package provides functions for testing affine hypotheses on the +regression coefficient vector in regression models with autocorrelated +errors.") + (license license:gpl2))) -- cgit v1.2.3 From 49e9a9aea2131f39c44689aebf02a87887cc0f87 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 13 Dec 2019 23:12:24 +0100 Subject: gnu: Add r-acs. * gnu/packages/cran.scm (r-acs): New variable. --- gnu/packages/cran.scm | 33 +++++++++++++++++++++++++++++++++ 1 file changed, 33 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 6c0bc01df0..76bae8ec93 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -17664,3 +17664,36 @@ distribution.") regression coefficient vector in regression models with autocorrelated errors.") (license license:gpl2))) + +(define-public r-acs + (package + (name "r-acs") + (version "2.1.4") + (source + (origin + (method url-fetch) + (uri (cran-uri "acs" version)) + (sha256 + (base32 + "0ajw9rf8l8akcvgqvbxjvryc6wjx74521xyxswz2b0bky3m6kah5")))) + (properties `((upstream-name . "acs"))) + (build-system r-build-system) + (propagated-inputs + `(("r-httr" ,r-httr) + ("r-plyr" ,r-plyr) + ("r-rcpp" ,r-rcpp) + ("r-stringr" ,r-stringr) + ("r-xml" ,r-xml))) + (home-page "http://dusp.mit.edu/faculty/ezra-glenn") + (synopsis "Work with data from the US Census") + (description + "This package provides a general toolkit for downloading, managing, +analyzing, and presenting data from the +@url{https://www.census.gov/data/developers/data-sets.html, U.S. Census}, +including SF1 (Decennial short-form), SF3 (Decennial long-form), and the +American Community Survey (ACS). Confidence intervals provided with ACS data +are converted to standard errors to be bundled with estimates in complex +@code{acs} objects. The package provides new methods to conduct standard +operations on @code{acs} objects and present/plot data in statistically +appropriate ways.") + (license license:gpl3))) -- cgit v1.2.3 From 07d958fe0edb21df38541cc3a9eabf0ae1ab9f84 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 14 Dec 2019 09:22:21 +0100 Subject: gnu: Add r-acss-data. * gnu/packages/cran.scm (r-acss-data): 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 76bae8ec93..37f8e8d877 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -17697,3 +17697,30 @@ are converted to standard errors to be bundled with estimates in complex operations on @code{acs} objects and present/plot data in statistically appropriate ways.") (license license:gpl3))) + +(define-public r-acss-data + (package + (name "r-acss-data") + (version "1.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "acss.data" version)) + (sha256 + (base32 + "09kl4179ipr8bq19g89xcdi1xxs397zcx5cvgp6viy8gn687ilgv")))) + (properties `((upstream-name . "acss.data"))) + (build-system r-build-system) + (home-page "http://complexitycalculator.com/methodology.html") + (synopsis "Data for algorithmic complexity of short strings") + (description + "This is a data only package providing the algorithmic complexity of +short strings, computed using the coding theorem method. For a given set of +symbols in a string, all possible or a large number of random samples of +Turing machines with a given number of states (e.g., 5) and number of symbols +corresponding to the number of symbols in the strings were simulated until +they reached a halting state or failed to end. This package contains data on +4.5 million strings from length 1 to 12 simulated on Turing machines with 2, +4, 5, 6, and 9 symbols. The complexity of the string corresponds to the +distribution of the halting states.") + (license license:gpl2+))) -- cgit v1.2.3 From 0ea0b2dd46014fdfef14614d582d60ce29c65a1f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 14 Dec 2019 09:22:36 +0100 Subject: gnu: Add r-acss. * gnu/packages/cran.scm (r-acss): 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 37f8e8d877..b588d6e9f0 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -17724,3 +17724,32 @@ they reached a halting state or failed to end. This package contains data on 4, 5, 6, and 9 symbols. The complexity of the string corresponds to the distribution of the halting states.") (license license:gpl2+))) + +(define-public r-acss + (package + (name "r-acss") + (version "0.2-5") + (source + (origin + (method url-fetch) + (uri (cran-uri "acss" version)) + (sha256 + (base32 + "0cqa60544f58l5qd7h6xmsir40b9hqnq6pqgd5hfx2j2l5n7qhmk")))) + (properties `((upstream-name . "acss"))) + (build-system r-build-system) + (propagated-inputs + `(("r-acss-data" ,r-acss-data) + ("r-zoo" ,r-zoo))) + (home-page "http://complexitycalculator.com/methodology.html") + (synopsis "Algorithmic complexity for short strings") + (description + "The main purpose of this package is to provide the algorithmic +complexity for short strings, an approximation of the Kolmogorov Complexity of +a short string using the coding theorem method. While the database containing +the complexity is provided in the data only package @code{acss.data}, this +package provides functions accessing the data such as @code{prob_random} +returning the posterior probability that a given string was produced by a +random process. In addition, two traditional (but problematic) measures of +complexity are also provided: entropy and change complexity.") + (license license:gpl2+))) -- cgit v1.2.3 From ffecbcbf517b78f31e2289ea067e9825a76a489b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 14 Dec 2019 10:07:08 +0100 Subject: gnu: Add r-acswr. * gnu/packages/cran.scm (r-acswr): 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 b588d6e9f0..6059acdddd 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -17753,3 +17753,25 @@ returning the posterior probability that a given string was produced by a random process. In addition, two traditional (but problematic) measures of complexity are also provided: entropy and change complexity.") (license license:gpl2+))) + +(define-public r-acswr + (package + (name "r-acswr") + (version "1.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "ACSWR" version)) + (sha256 + (base32 + "195vjrkang5cl7gwsna0aq4p0h4jym9xg9yh94bnf8vq6wf8j83n")))) + (properties `((upstream-name . "ACSWR"))) + (build-system r-build-system) + (propagated-inputs + `(("r-mass" ,r-mass))) + (home-page "https://cran.r-project.org/web/packages/ACSWR/") + (synopsis "Companion package for the book \"A Course in Statistics with R\"") + (description + "This is a companion package for the book \"A Course in Statistics with +R\" (ISBN 978-1-119-15272-9.)") + (license license:gpl2))) -- cgit v1.2.3 From 6f0a5ab09819d1237d7434f1565db3016d785c8a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 14 Dec 2019 10:07:18 +0100 Subject: gnu: Add r-alabama. * gnu/packages/cran.scm (r-alabama): New variable. --- gnu/packages/cran.scm | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 6059acdddd..22e994059b 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -17775,3 +17775,26 @@ complexity are also provided: entropy and change complexity.") "This is a companion package for the book \"A Course in Statistics with R\" (ISBN 978-1-119-15272-9.)") (license license:gpl2))) + +(define-public r-alabama + (package + (name "r-alabama") + (version "2015.3-1") + (source + (origin + (method url-fetch) + (uri (cran-uri "alabama" version)) + (sha256 + (base32 + "0mlgk929gdismikwx4k2ndqq57nnqj7mlgvd3479b214hksgq036")))) + (properties `((upstream-name . "alabama"))) + (build-system r-build-system) + (propagated-inputs `(("r-numderiv" ,r-numderiv))) + (home-page "https://cran.r-project.org/web/packages/alabama/") + (synopsis "Constrained nonlinear optimization") + (description + "Alabama stands for Augmented Lagrangian Adaptive Barrier Minimization +Algorithm; it is used for optimizing smooth nonlinear objective functions with +constraints. Linear or nonlinear equality and inequality constraints are +allowed.") + (license license:gpl2+))) -- cgit v1.2.3 From 70c0dbe73fa099cd7bebccb3bffba3dfe3c3137b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 14 Dec 2019 10:07:26 +0100 Subject: gnu: Add r-gdina. * gnu/packages/cran.scm (r-gdina): New variable. --- gnu/packages/cran.scm | 40 ++++++++++++++++++++++++++++++++++++++++ 1 file changed, 40 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 22e994059b..cb68994565 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -17798,3 +17798,43 @@ Algorithm; it is used for optimizing smooth nonlinear objective functions with constraints. Linear or nonlinear equality and inequality constraints are allowed.") (license license:gpl2+))) + +(define-public r-gdina + (package + (name "r-gdina") + (version "2.7.3") + (source + (origin + (method url-fetch) + (uri (cran-uri "GDINA" version)) + (sha256 + (base32 + "0875xfbm36gqzr0116xzlbm8rlff85rybr4s4hjzfflfvjdhgvfx")))) + (properties `((upstream-name . "GDINA"))) + (build-system r-build-system) + (propagated-inputs + `(("r-alabama" ,r-alabama) + ("r-ggplot2" ,r-ggplot2) + ("r-mass" ,r-mass) + ("r-nloptr" ,r-nloptr) + ("r-numderiv" ,r-numderiv) + ("r-rcpp" ,r-rcpp) + ("r-rcpparmadillo" ,r-rcpparmadillo) + ("r-rsolnp" ,r-rsolnp) + ("r-shiny" ,r-shiny) + ("r-shinydashboard" ,r-shinydashboard))) + (home-page "https://github.com/Wenchao-Ma/GDINA") + (synopsis "Generalized DINA model framework") + (description + "This package provides a set of psychometric tools for cognitive +diagnosis modeling based on the generalized deterministic inputs, noisy and +gate (G-DINA) model by de la Torre (2011) @url{doi:10.1007/s11336-011-9207-7} +and its extensions, including the sequential G-DINA model by Ma and de la +Torre (2016) @url{doi:10.1111/bmsp.12070} for polytomous responses, and the +polytomous G-DINA model by Chen and de la Torre +@url{doi:10.1177/0146621613479818} for polytomous attributes. Joint attribute +distribution can be independent, saturated, higher-order, loglinear smoothed +or structured. Q-matrix validation, item and model fit statistics, model +comparison at test and item level and differential item functioning can also +be conducted. A graphical user interface is also provided.") + (license license:gpl3))) -- cgit v1.2.3 From d024207e7bfaba0453e34de48510378ddd2dff4d Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 14 Dec 2019 10:07:48 +0100 Subject: gnu: Add r-actcd. * gnu/packages/cran.scm (r-actcd): 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 cb68994565..dd30ba3fbe 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -17838,3 +17838,33 @@ or structured. Q-matrix validation, item and model fit statistics, model comparison at test and item level and differential item functioning can also be conducted. A graphical user interface is also provided.") (license license:gpl3))) + +(define-public r-actcd + (package + (name "r-actcd") + (version "1.2-0") + (source + (origin + (method url-fetch) + (uri (cran-uri "ACTCD" version)) + (sha256 + (base32 + "0mzjxxr2zfdidw8ibh6w8mvpkw3q3nvngqi05g9ind26ckvk053p")))) + (properties `((upstream-name . "ACTCD"))) + (build-system r-build-system) + (propagated-inputs + `(("r-gdina" ,r-gdina) + ("r-r-methodss3" ,r-r-methodss3))) + (native-inputs + `(("gfortran" ,gfortran))) + (home-page "https://cran.r-project.org/web/packages/ACTCD/") + (synopsis "Asymptotic classification theory for cognitive diagnosis") + (description + "This is a package supporting cluster analysis for cognitive diagnosis +based on the Asymptotic Classification Theory (Chiu, Douglas & Li, 2009; +@url{doi:10.1007/s11336-009-9125-0}). Given the sample statistic of +sum-scores, cluster analysis techniques can be used to classify examinees into +latent classes based on their attribute patterns. In addition to the +algorithms used to classify data, three labeling approaches are proposed to +label clusters so that examinees' attribute profiles can be obtained.") + (license license:gpl2+))) -- cgit v1.2.3 From 6790adf338a1e3606d451135cec244f737c96156 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 14 Dec 2019 10:10:38 +0100 Subject: gnu: Add r-ineq. * gnu/packages/cran.scm (r-ineq): 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 dd30ba3fbe..f01df24bb2 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -17868,3 +17868,24 @@ latent classes based on their attribute patterns. In addition to the algorithms used to classify data, three labeling approaches are proposed to label clusters so that examinees' attribute profiles can be obtained.") (license license:gpl2+))) + +(define-public r-ineq + (package + (name "r-ineq") + (version "0.2-13") + (source + (origin + (method url-fetch) + (uri (cran-uri "ineq" version)) + (sha256 + (base32 + "09fsxyrh0j7mwmb5hkhmrzgcy7kf85jxkh7zlwpgqgcsyl1n91z0")))) + (properties `((upstream-name . "ineq"))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/web/packages/ineq/") + (synopsis "Measuring inequality, concentration, and poverty") + (description + "This package provides tools for measuring inequality, concentration, and +poverty measures. It provides both empirical and theoretical Lorenz curves.") + ;; Either of these two versions. + (license (list license:gpl2 license:gpl3)))) -- cgit v1.2.3 From c090b9977c22854c23a5e3f6c5352263c67713f6 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 14 Dec 2019 10:10:56 +0100 Subject: gnu: Add r-actfrag. * gnu/packages/cran.scm (r-actfrag): 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 f01df24bb2..c36328c896 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -17889,3 +17889,30 @@ label clusters so that examinees' attribute profiles can be obtained.") poverty measures. It provides both empirical and theoretical Lorenz curves.") ;; Either of these two versions. (license (list license:gpl2 license:gpl3)))) + +(define-public r-actfrag + (package + (name "r-actfrag") + (version "0.1.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "ActFrag" version)) + (sha256 + (base32 + "06l5a679j6289008ls57v420mnzpq9a4ln7svi5bh0vpvws7sr9d")))) + (properties `((upstream-name . "ActFrag"))) + (build-system r-build-system) + (propagated-inputs + `(("r-accelerometry" ,r-accelerometry) + ("r-dplyr" ,r-dplyr) + ("r-ineq" ,r-ineq) + ("r-survival" ,r-survival) + ("r-tidyr" ,r-tidyr))) + (home-page "https://github.com/junruidi/ActFrag") + (synopsis "Activity fragmentation metrics extraction") + (description + "This package provides functions to extract commonly used fragmentation +metrics to quantify time accumulation strategies based on minute level +actigraphy-measured activity counts data.") + (license license:gpl3))) -- cgit v1.2.3 From 77a5bf938febc580d972e02c89fe27a691a53445 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 14 Dec 2019 10:11:09 +0100 Subject: gnu: Add r-fda. * gnu/packages/cran.scm (r-fda): 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 c36328c896..a1a64c0ec2 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -17916,3 +17916,27 @@ poverty measures. It provides both empirical and theoretical Lorenz curves.") metrics to quantify time accumulation strategies based on minute level actigraphy-measured activity counts data.") (license license:gpl3))) + +(define-public r-fda + (package + (name "r-fda") + (version "2.4.8") + (source + (origin + (method url-fetch) + (uri (cran-uri "fda" version)) + (sha256 + (base32 + "0n39rzbhg1hipzn51rzmbchn2358qgapg08iv7lmiqj5y7i9qns2")))) + (properties `((upstream-name . "fda"))) + (build-system r-build-system) + (propagated-inputs + `(("r-matrix" ,r-matrix))) + (home-page "http://www.functionaldata.org") + (synopsis "Functional data analysis") + (description + "These functions were developed to support functional data analysis as +described in Ramsay, J. O. and Silverman, B. W. (2005) Functional Data +Analysis. The package includes data sets and script files working many +examples.") + (license license:gpl2+))) -- cgit v1.2.3 From 402dae07b5a8baa5d99d6d8e39b3917d0706b9b7 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 14 Dec 2019 10:52:27 +0100 Subject: gnu: Add r-actigraphy. * gnu/packages/cran.scm (r-actigraphy): New variable. --- gnu/packages/cran.scm | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index a1a64c0ec2..6efd1a66c2 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -17940,3 +17940,26 @@ described in Ramsay, J. O. and Silverman, B. W. (2005) Functional Data Analysis. The package includes data sets and script files working many examples.") (license license:gpl2+))) + +(define-public r-actigraphy + (package + (name "r-actigraphy") + (version "1.3.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "Actigraphy" version)) + (sha256 + (base32 + "0y0ccmxhdfhdmi4k6pbfvnqknkqbgvfsf2qf7z7rc4xpfgym6574")))) + (properties `((upstream-name . "Actigraphy"))) + (build-system r-build-system) + (propagated-inputs + `(("r-fda" ,r-fda) + ("r-sdmtools" ,r-sdmtools))) + (home-page "https://cran.r-project.org/web/packages/Actigraphy/") + (synopsis "Actigraphy data analysis") + (description + "This package provides tools for functional linear modeling and analysis +of actigraphy data.") + (license license:asl2.0))) -- cgit v1.2.3 From 7f960d81fb8685e707b6805e1ac00da63f39407c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 14 Dec 2019 10:54:34 +0100 Subject: gnu: Add r-activedriver. * gnu/packages/cran.scm (r-activedriver): 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 6efd1a66c2..00ce9ad934 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -17963,3 +17963,31 @@ examples.") "This package provides tools for functional linear modeling and analysis of actigraphy data.") (license license:asl2.0))) + +(define-public r-activedriver + (package + (name "r-activedriver") + (version "1.0.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "ActiveDriver" version)) + (sha256 + (base32 + "10c7ga48fwvpd5mc4dqiyw4kc2l0iz5qn4hg7xk15r1qmm5rsipa")))) + (properties `((upstream-name . "ActiveDriver"))) + (build-system r-build-system) + (propagated-inputs + `(("r-mass" ,r-mass))) + (home-page "https://cran.r-project.org/web/packages/ActiveDriver/") + (synopsis "Tools for finding cancer driver proteins") + (description + "This package provides a mutation analysis tool that discovers cancer +driver genes with frequent mutations in protein signalling sites such as +post-translational modifications (phosphorylation, ubiquitination, etc). The +Poisson generalized linear regression model identifies genes where cancer +mutations in signalling sites are more frequent than expected from the +sequence of the entire gene. Integration of mutations with signalling +information helps find new driver genes and propose candidate mechanisms to +known drivers.") + (license license:gpl2+))) -- cgit v1.2.3 From 89d4f154b982a83ded18cbae801fd41f56cbada8 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 14 Dec 2019 10:54:49 +0100 Subject: gnu: Add r-activitycounts. * gnu/packages/cran.scm (r-activitycounts): New variable. --- gnu/packages/cran.scm | 32 ++++++++++++++++++++++++++++++++ 1 file changed, 32 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 00ce9ad934..259fa1d3e9 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -17991,3 +17991,35 @@ sequence of the entire gene. Integration of mutations with signalling information helps find new driver genes and propose candidate mechanisms to known drivers.") (license license:gpl2+))) + +(define-public r-activitycounts + (package + (name "r-activitycounts") + (version "0.1.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "activityCounts" version)) + (sha256 + (base32 + "0zgxr2sk3a8kmygfxx1p5hnrfwdkxx7php6jlrhm8wv6052ck8jz")))) + (properties + `((upstream-name . "activityCounts"))) + (build-system r-build-system) + (propagated-inputs + `(("r-lubridate" ,r-lubridate) + ("r-magrittr" ,r-magrittr) + ("r-seewave" ,r-seewave) + ("r-signal" ,r-signal) + ("r-tibble" ,r-tibble))) + (home-page "https://github.com/walkabillylab/activityCounts") + (synopsis "Generate ActiLife counts") + (description + "ActiLife generates activity counts from data collected by Actigraph +accelerometers. Actigraph is one of the most common research-grade +accelerometers. There is considerable research validating and developing +algorithms for human activity using ActiLife counts. Unfortunately, ActiLife +counts are proprietary and difficult to implement if researchers use different +accelerometer brands. The code creates ActiLife counts from raw acceleration +data for different accelerometer brands.") + (license license:gpl3))) -- cgit v1.2.3 From 6f94a3e5f599d2fb1a70ed8297576b39658ebed2 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 14 Dec 2019 10:55:01 +0100 Subject: gnu: Add r-activityindex. * gnu/packages/cran.scm (r-activityindex): 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 259fa1d3e9..4ff97d350c 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -18023,3 +18023,28 @@ counts are proprietary and difficult to implement if researchers use different accelerometer brands. The code creates ActiLife counts from raw acceleration data for different accelerometer brands.") (license license:gpl3))) + +(define-public r-activityindex + (package + (name "r-activityindex") + (version "0.3.6") + (source + (origin + (method url-fetch) + (uri (cran-uri "ActivityIndex" version)) + (sha256 + (base32 + "14k6d78s15j7kb7jhixf4msrdjdl28d0r264cbvy41p8dkq7ysvk")))) + (properties `((upstream-name . "ActivityIndex"))) + (build-system r-build-system) + (propagated-inputs + `(("r-data-table" ,r-data-table) + ("r-matrixstats" ,r-matrixstats) + ("r-r-utils" ,r-r-utils))) + (home-page "https://cran.r-project.org/web/packages/ActivityIndex/") + (synopsis "Activity Index calculation using raw accelerometry data") + (description + "This is a package to read raw accelerometry from GT3X+ accelerometry +data and plain table data to calculate the Activity Index from Bai et +al. (2016) @url{doi:10.1371/journal.pone.0160644}.") + (license license:gpl3))) -- cgit v1.2.3 From bbaab253966522abb74d8b3937d69f158de360f9 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 14 Dec 2019 10:55:14 +0100 Subject: gnu: Add r-activpal. * gnu/packages/cran.scm (r-activpal): 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 4ff97d350c..2c83e70563 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -18048,3 +18048,34 @@ data for different accelerometer brands.") data and plain table data to calculate the Activity Index from Bai et al. (2016) @url{doi:10.1371/journal.pone.0160644}.") (license license:gpl3))) + +(define-public r-activpal + (package + (name "r-activpal") + (version "0.1.3") + (source + (origin + (method url-fetch) + (uri (cran-uri "activPAL" version)) + (sha256 + (base32 + "1h6hp5z89ji73gdzxy1dgbfwjysiy5lvcqh90xagpb7sa7ahs3na")))) + (properties `((upstream-name . "activPAL"))) + (build-system r-build-system) + (propagated-inputs + `(("r-devtools" ,r-devtools) + ("r-dplyr" ,r-dplyr) + ("r-ggplot2" ,r-ggplot2) + ("r-lubridate" ,r-lubridate) + ("r-magrittr" ,r-magrittr) + ("r-tidyr" ,r-tidyr))) + (home-page "https://cran.r-project.org/web/packages/activPAL") + (synopsis "Processing and chart generation from activPAL events files") + (description + "This package contains functions to generate pre-defined summary +statistics from activPAL events files. The package also contains functions to +produce informative graphics that visualize physical activity behaviour and +trends. This includes generating graphs that align physical activity +behaviour with additional time based observations described by other data +sets, such as sleep diaries and continuous glucose monitoring data.") + (license license:gpl3))) -- cgit v1.2.3 From a5d4dc7efb2b1bf01fe7bbbf18d91f8b6c63e7aa Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 14 Dec 2019 10:56:03 +0100 Subject: gnu: Add r-activpalprocessing. * gnu/packages/cran.scm (r-activpalprocessing): 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 2c83e70563..7020725983 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -18079,3 +18079,27 @@ trends. This includes generating graphs that align physical activity behaviour with additional time based observations described by other data sets, such as sleep diaries and continuous glucose monitoring data.") (license license:gpl3))) + +(define-public r-activpalprocessing + (package + (name "r-activpalprocessing") + (version "1.0.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "activpalProcessing" version)) + (sha256 + (base32 + "1y0bjx2qx53iy930y9iww4q1yzjj8y16cwgixk1mq3w4g1f116d1")))) + (properties + `((upstream-name . "activpalProcessing"))) + (build-system r-build-system) + (propagated-inputs + `(("r-chron" ,r-chron))) + (home-page "https://cran.r-project.org/web/packages/activpalProcessing/") + (synopsis "Process activPAL events files") + (description + "This package performs estimation of physical activity and sedentary +behavior variables from activPAL events files.") + ;; Either version of the GPL. + (license (list license:gpl2 license:gpl3)))) -- cgit v1.2.3 From 5f08fa64f023192c1aef0b34afb00b17bdd591de Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 14 Dec 2019 10:56:22 +0100 Subject: gnu: Add r-actogrammr. * gnu/packages/cran.scm (r-actogrammr): 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 7020725983..ba322ee220 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -18103,3 +18103,32 @@ sets, such as sleep diaries and continuous glucose monitoring data.") behavior variables from activPAL events files.") ;; Either version of the GPL. (license (list license:gpl2 license:gpl3)))) + +(define-public r-actogrammr + (package + (name "r-actogrammr") + (version "0.2.3") + (source + (origin + (method url-fetch) + (uri (cran-uri "actogrammr" version)) + (sha256 + (base32 + "1jzvarmd41yqlrkagzlc8m19n5mn0w0b36fy50lyvgrfsafjfbqa")))) + (properties `((upstream-name . "actogrammr"))) + (build-system r-build-system) + (propagated-inputs + `(("r-dplyr" ,r-dplyr) + ("r-ggplot2" ,r-ggplot2) + ("r-lubridate" ,r-lubridate) + ("r-readr" ,r-readr) + ("r-tidyr" ,r-tidyr))) + (home-page "https://cran.r-project.org/web/packages/actogrammr/") + (synopsis "Read in activity data and plot actograms") + (description + "Read in activity measurements from standard file formats used by +circadian rhythm researchers, currently only ClockLab format, and process and +plot the data. The central type of plot is the actogram, as first described +in \"Activity and distribution of certain wild mice in relation to biotic +communities\" by MS Johnson (1926) @url{doi:10.2307/1373575}.") + (license license:gpl3))) -- cgit v1.2.3 From 1830e0383b808a1a1b943f714335cf36efc38795 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 14 Dec 2019 10:56:41 +0100 Subject: gnu: Add r-expint. * gnu/packages/cran.scm (r-expint): New variable. --- gnu/packages/cran.scm | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index ba322ee220..7bb4726fd1 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -18132,3 +18132,26 @@ plot the data. The central type of plot is the actogram, as first described in \"Activity and distribution of certain wild mice in relation to biotic communities\" by MS Johnson (1926) @url{doi:10.2307/1373575}.") (license license:gpl3))) + +(define-public r-expint + (package + (name "r-expint") + (version "0.1-6") + (source + (origin + (method url-fetch) + (uri (cran-uri "expint" version)) + (sha256 + (base32 + "0iai25cglcdnf44d2d1fz1xpw4q600my4zq4493fk4cs5673mlf7")))) + (properties `((upstream-name . "expint"))) + (build-system r-build-system) + (home-page "https://gitlab.com/vigou3/expint") + (synopsis "Exponential integral and incomplete Gamma function") + (description + "This package provides the exponential integrals @code{E_1(x)}, +@code{E_2(x)}, @code{E_n(x)} and @code{Ei(x)}, and the incomplete gamma +function @code{G(a, x)} defined for negative values of its first argument. +The package also gives easy access to the underlying C routines through an +API; see the package vignette for details.") + (license license:gpl2+))) -- cgit v1.2.3 From 7faa05377eda6b7ec5d9292da435f1534285f3dd Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 14 Dec 2019 10:56:56 +0100 Subject: gnu: Add r-actuar. * gnu/packages/cran.scm (r-actuar): 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 7bb4726fd1..1f0ebea2c1 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -18155,3 +18155,31 @@ function @code{G(a, x)} defined for negative values of its first argument. The package also gives easy access to the underlying C routines through an API; see the package vignette for details.") (license license:gpl2+))) + +(define-public r-actuar + (package + (name "r-actuar") + (version "2.3-3") + (source + (origin + (method url-fetch) + (uri (cran-uri "actuar" version)) + (sha256 + (base32 + "0aw3hlan5y22mdqk1wvnw9ksqhwp4yy5hi0dpv21p7s0hyxhphih")))) + (properties `((upstream-name . "actuar"))) + (build-system r-build-system) + (propagated-inputs `(("r-expint" ,r-expint))) + (home-page "https://gitlab.com/vigou3/actuar") + (synopsis "Actuarial functions and heavy tailed distributions") + (description + "This package provides functions and data sets for actuarial science: +modeling of loss distributions; risk theory and ruin theory; simulation of +compound models, discrete mixtures and compound hierarchical models; +credibility theory. It boasts support for many additional probability +distributions to model insurance loss amounts and loss frequency: 19 +continuous heavy tailed distributions; the Poisson-inverse Gaussian discrete +distribution; zero-truncated and zero-modified extensions of the standard +discrete distributions. It also supports phase-type distributions commonly +used to compute ruin probabilities.") + (license license:gpl2+))) -- cgit v1.2.3 From 6968aa2fe71a5f5ee63b453d43d3b6d00b1b0f22 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 14 Dec 2019 10:57:13 +0100 Subject: gnu: Add r-bmp. * gnu/packages/cran.scm (r-bmp): New variable. --- gnu/packages/cran.scm | 20 ++++++++++++++++++++ 1 file changed, 20 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 1f0ebea2c1..58d9a7f69f 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -18183,3 +18183,23 @@ distribution; zero-truncated and zero-modified extensions of the standard discrete distributions. It also supports phase-type distributions commonly used to compute ruin probabilities.") (license license:gpl2+))) + +(define-public r-bmp + (package + (name "r-bmp") + (version "0.3") + (source + (origin + (method url-fetch) + (uri (cran-uri "bmp" version)) + (sha256 + (base32 + "0jd67r11bn98hjwgyr6gas423787xy7ji2hq7ay80blkkcj91xxx")))) + (properties `((upstream-name . "bmp"))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/web/packages/bmp/") + (synopsis "Read Bitmap (BMP) images") + (description + "This package provides pure R tools to read BMP format images. It is +currently limited to 8 bit greyscale images and 24, 32 bit (A)RGB images.") + (license license:gpl2+))) -- cgit v1.2.3 From 7dd1fbf9ee14dd534bbd7ce2b629d1a2f6333341 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 14 Dec 2019 10:57:29 +0100 Subject: gnu: Add r-readbitmap. * gnu/packages/cran.scm (r-readbitmap): 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 58d9a7f69f..1699abb85d 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -18203,3 +18203,32 @@ used to compute ruin probabilities.") "This package provides pure R tools to read BMP format images. It is currently limited to 8 bit greyscale images and 24, 32 bit (A)RGB images.") (license license:gpl2+))) + +(define-public r-readbitmap + (package + (name "r-readbitmap") + (version "0.1.5") + (source + (origin + (method url-fetch) + (uri (cran-uri "readbitmap" version)) + (sha256 + (base32 + "14825906l326w59g6apy00j55jg3h5kx2r6s031f4gdkbrc7szbk")))) + (properties `((upstream-name . "readbitmap"))) + (build-system r-build-system) + (inputs + `(("libjpeg" ,libjpeg) + ("libpng" ,libpng))) + (propagated-inputs + `(("r-bmp" ,r-bmp) + ("r-jpeg" ,r-jpeg) + ("r-png" ,r-png) + ("r-tiff" ,r-tiff))) + (home-page "https://github.com/jefferis/readbitmap") + (synopsis "Unified interface to read bitmap images (BMP, JPEG, PNG, TIFF)") + (description + "This package provides tools to identify and read BMP, JPEG, PNG, and +TIFF format bitmap images. Identification defaults to the use of the magic +number embedded in the file rather than the file extension.") + (license license:gpl2+))) -- cgit v1.2.3 From 5e2ad376848845ce114e97b24901a90a222ef939 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 14 Dec 2019 11:28:11 +0100 Subject: gnu: Add r-imager. * gnu/packages/cran.scm (r-imager): New variable. --- gnu/packages/cran.scm | 42 ++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 42 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 1699abb85d..f5eaf88c1b 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -18232,3 +18232,45 @@ currently limited to 8 bit greyscale images and 24, 32 bit (A)RGB images.") TIFF format bitmap images. Identification defaults to the use of the magic number embedded in the file rather than the file extension.") (license license:gpl2+))) + +(define-public r-imager + (package + (name "r-imager") + (version "0.41.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "imager" version)) + (sha256 + (base32 + "19fqgjhg04garbipx20g72h9dd6k0jj4ac48nby6km4h665vrs4v")))) + (properties `((upstream-name . "imager"))) + (build-system r-build-system) + (inputs + `(("fftw" ,fftw) + ("libtiff" ,libtiff) + ("libx11" ,libx11) + ("zlib" ,zlib))) + (propagated-inputs + `(("r-cairo" ,r-cairo) + ("r-downloader" ,r-downloader) + ("r-igraph" ,r-igraph) + ("r-jpeg" ,r-jpeg) + ("r-magrittr" ,r-magrittr) + ("r-plyr" ,r-plyr) + ("r-png" ,r-png) + ("r-purrr" ,r-purrr) + ("r-rcpp" ,r-rcpp) + ("r-readbitmap" ,r-readbitmap) + ("r-stringr" ,r-stringr))) + (native-inputs `(("pkg-config" ,pkg-config))) + (home-page "http://dahtah.github.io/imager") + (synopsis "Image processing library") + (description + "This is a package for fast image processing for images in up to 4 +dimensions (two spatial dimensions, one time/depth dimension, one color +dimension). It provides most traditional image processing tools (filtering, +morphology, transformations, etc.) as well as various functions for easily +analyzing image data using R. The package wraps @url{http://cimg.eu, CImg}, a +simple, modern C++ library for image processing.") + (license license:lgpl3))) -- cgit v1.2.3 From 154555e42fafbbeb45ebc44a2f4de19b41adc2cd Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 14 Dec 2019 11:28:35 +0100 Subject: gnu: Add r-acuityview. * gnu/packages/cran.scm (r-acuityview): 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 f5eaf88c1b..64b6ed9c10 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -18274,3 +18274,27 @@ morphology, transformations, etc.) as well as various functions for easily analyzing image data using R. The package wraps @url{http://cimg.eu, CImg}, a simple, modern C++ library for image processing.") (license license:lgpl3))) + +(define-public r-acuityview + (package + (name "r-acuityview") + (version "0.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "AcuityView" version)) + (sha256 + (base32 + "0f0iclmnwdc8ixiiai4svk4x1g3pjy7dhm3cm58fv6ckx12d3d2l")))) + (properties `((upstream-name . "AcuityView"))) + (build-system r-build-system) + (propagated-inputs + `(("r-fftwtools" ,r-fftwtools) + ("r-imager" ,r-imager) + ("r-plotrix" ,r-plotrix))) + (home-page "https://cran.r-project.org/web/packages/AcuityView/") + (synopsis "Display scenes as seen by an animal with less acute vision") + (description + "This package provides a simple method for representing a visual scene as +it may be seen by an animal with less acute vision.") + (license license:gpl2+))) -- cgit v1.2.3 From 2a1fd51864826dd983194a16a49a9e0220f02454 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 14 Dec 2019 11:28:50 +0100 Subject: gnu: Add r-adabag. * gnu/packages/cran.scm (r-adabag): 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 64b6ed9c10..6b64e797ea 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -18298,3 +18298,31 @@ simple, modern C++ library for image processing.") "This package provides a simple method for representing a visual scene as it may be seen by an animal with less acute vision.") (license license:gpl2+))) + +(define-public r-adabag + (package + (name "r-adabag") + (version "4.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "adabag" version)) + (sha256 + (base32 + "109wrl1pwvmyv2l909hrvk7dg4aa9pv449mvdycp50zwrsw9w0a7")))) + (properties `((upstream-name . "adabag"))) + (build-system r-build-system) + (propagated-inputs + `(("r-caret" ,r-caret) + ("r-doparallel" ,r-doparallel) + ("r-foreach" ,r-foreach) + ("r-rpart" ,r-rpart))) + (home-page "https://cran.r-project.org/web/packages/adabag/") + (synopsis "Multiclass AdaBoost.M1, SAMME and Bagging") + (description + "This package implements Freund and Schapire's Adaboost.M1 algorithm and +Breiman's Bagging algorithm using classification trees as individual +classifiers. Once these classifiers have been trained, they can be used to +predict on new data. Also, cross validation estimation of the error can be +done.") + (license license:gpl2+))) -- cgit v1.2.3 From 0b13a75716136aac6ffee5f1f10bec77393a1ca7 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 14 Dec 2019 11:29:24 +0100 Subject: gnu: Add r-adagio. * gnu/packages/cran.scm (r-adagio): New variable. --- gnu/packages/cran.scm | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 6b64e797ea..bebf4acbe4 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -18326,3 +18326,26 @@ classifiers. Once these classifiers have been trained, they can be used to predict on new data. Also, cross validation estimation of the error can be done.") (license license:gpl2+))) + +(define-public r-adagio + (package + (name "r-adagio") + (version "0.7.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "adagio" version)) + (sha256 + (base32 + "1h9l0ddrxq8y35iy9hdkxdvdwsqpnpkzzbkbwwhm4380lq1m7a3k")))) + (properties `((upstream-name . "adagio"))) + (build-system r-build-system) + (native-inputs `(("gfortran" ,gfortran))) + (home-page "https://cran.r-project.org/web/packages/adagio/") + (synopsis "Discrete and global optimization routines") + (description + "This package provides methods and algorithms for discrete optimization, +e.g. knapsack and subset sum procedures, derivative-free Nelder-Mead and +Hooke-Jeeves minimization, and some (evolutionary) global optimization +functions.") + (license license:gpl3+))) -- cgit v1.2.3 From 09e9ad334ac15ddea7e440cb1737f2c687f5c43a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 14 Dec 2019 11:29:40 +0100 Subject: gnu: Add r-univoutl. * gnu/packages/cran.scm (r-univoutl): New variable. --- gnu/packages/cran.scm | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index bebf4acbe4..855a3c956e 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -18349,3 +18349,29 @@ e.g. knapsack and subset sum procedures, derivative-free Nelder-Mead and Hooke-Jeeves minimization, and some (evolutionary) global optimization functions.") (license license:gpl3+))) + +(define-public r-univoutl + (package + (name "r-univoutl") + (version "0.1-5") + (source + (origin + (method url-fetch) + (uri (cran-uri "univOutl" version)) + (sha256 + (base32 + "193wrpkvgmlrx43nag8w3ivrlqm37nm6g86wcvd3bgw3hchs70gi")))) + (properties `((upstream-name . "univOutl"))) + (build-system r-build-system) + (propagated-inputs + `(("r-hmisc" ,r-hmisc) + ("r-robustbase" ,r-robustbase))) + (home-page "https://github.com/marcellodo/univOutl") + (synopsis "Detection of univariate outliers") + (description + "This package provides well-known outlier detection techniques in the +univariate case. Methods to deal with skewed distribution are included too. +The Hidiroglou-Berthelot (1986) method to search for outliers in ratios of +historical data is implemented as well. When available, survey weights can be +used in outliers detection.") + (license license:gpl2+))) -- cgit v1.2.3 From 5458490ebb2aa5fbb5d72ce8468791669bc634ca Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 14 Dec 2019 11:29:56 +0100 Subject: gnu: Add r-tolerance. * gnu/packages/cran.scm (r-tolerance): 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 855a3c956e..cc0f876d85 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -18375,3 +18375,33 @@ The Hidiroglou-Berthelot (1986) method to search for outliers in ratios of historical data is implemented as well. When available, survey weights can be used in outliers detection.") (license license:gpl2+))) + +(define-public r-tolerance + (package + (name "r-tolerance") + (version "1.3.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "tolerance" version)) + (sha256 + (base32 + "17qh4ad1f3fbcpwlxxqh8qr9bnwjcl4yxk0l3fkbr6b2l4rc5p86")))) + (properties `((upstream-name . "tolerance"))) + (build-system r-build-system) + (propagated-inputs + `(("r-rgl" ,r-rgl))) + (home-page "https://cran.r-project.org/web/packages/tolerance/") + (synopsis "Statistical tolerance intervals and regions") + (description + "This package provides functions for estimating tolerance +limits (intervals) for various univariate distributions (binomial, Cauchy, +discrete Pareto, exponential, two-parameter exponential, extreme value, +hypergeometric, Laplace, logistic, negative binomial, negative hypergeometric, +normal, Pareto, Poisson-Lindley, Poisson, uniform, and Zipf-Mandelbrot), +Bayesian normal tolerance limits, multivariate normal tolerance regions, +nonparametric tolerance intervals, tolerance bands for regression +settings (linear regression, nonlinear regression, nonparametric regression, +and multivariate regression), and analysis of variance tolerance intervals. +Visualizations are also available for most of these settings.") + (license license:gpl2+))) -- cgit v1.2.3 From 94ecf71344bc55fa2610d45f391a21befdfb54f7 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 14 Dec 2019 13:30:50 +0100 Subject: gnu: Add r-additivitytests. * gnu/packages/cran.scm (r-additivitytests): 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 cc0f876d85..0aa20b8e6e 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -18405,3 +18405,24 @@ settings (linear regression, nonlinear regression, nonparametric regression, and multivariate regression), and analysis of variance tolerance intervals. Visualizations are also available for most of these settings.") (license license:gpl2+))) + +(define-public r-additivitytests + (package + (name "r-additivitytests") + (version "1.1-4") + (source + (origin + (method url-fetch) + (uri (cran-uri "additivityTests" version)) + (sha256 + (base32 + "048ds90wqjdjy1nyhna3m06asdklbh8sx1n556kss2j1r1pma1sw")))) + (properties + `((upstream-name . "additivityTests"))) + (build-system r-build-system) + (home-page "https://github.com/simecek/additivityTests") + (synopsis "Additivity tests in the two way Anova with single sub-class numbers") + (description + "This package provides an implementation of the Tukey, Mandel, +Johnson-Graybill, LBI, Tusell and modified Tukey non-additivity tests.") + (license license:gpl3))) -- cgit v1.2.3 From 9906cb80de8e2bcfc55507d6c6f00fc3a89000b3 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 14 Dec 2019 13:31:21 +0100 Subject: gnu: Add r-flexclust. * gnu/packages/cran.scm (r-flexclust): 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 0aa20b8e6e..3cd12d185c 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -18426,3 +18426,32 @@ Visualizations are also available for most of these settings.") "This package provides an implementation of the Tukey, Mandel, Johnson-Graybill, LBI, Tusell and modified Tukey non-additivity tests.") (license license:gpl3))) + +(define-public r-flexclust + (package + (name "r-flexclust") + (version "1.4-0") + (source + (origin + (method url-fetch) + (uri (cran-uri "flexclust" version)) + (sha256 + (base32 + "0x7wxk8y46ndyz6fdacym0rd6p9wh3pcfr28chjcg5d7fm849zl2")))) + (properties `((upstream-name . "flexclust"))) + (build-system r-build-system) + (propagated-inputs + `(("r-class" ,r-class) + ("r-lattice" ,r-lattice) + ("r-modeltools" ,r-modeltools))) + (home-page "https://cran.r-project.org/web/packages/flexclust/") + (synopsis "Flexible cluster algorithms") + (description + "The main function @code{kcca} implements a general framework for +k-centroids cluster analysis supporting arbitrary distance measures and +centroid computation. Further cluster methods include hard competitive +learning, neural gas, and QT clustering. There are numerous visualization +methods for cluster results (neighborhood graphs, convex cluster hulls, +barcharts of centroids, ...), and bootstrap methods for the analysis of +cluster stability.") + (license license:gpl2))) -- cgit v1.2.3 From 86a760cc67170331abcb1f0bdf73af4716effad5 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 14 Dec 2019 13:31:40 +0100 Subject: gnu: Add r-biclust. * gnu/packages/cran.scm (r-biclust): 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 3cd12d185c..354837823b 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -18455,3 +18455,34 @@ methods for cluster results (neighborhood graphs, convex cluster hulls, barcharts of centroids, ...), and bootstrap methods for the analysis of cluster stability.") (license license:gpl2))) + +(define-public r-biclust + (package + (name "r-biclust") + (version "2.0.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "biclust" version)) + (sha256 + (base32 + "1y5n6wfa1lx88ck3x09rcg0dh3pw89225h85hmq2la1s1fpa48i0")))) + (properties `((upstream-name . "biclust"))) + (build-system r-build-system) + (propagated-inputs + `(("r-additivitytests" ,r-additivitytests) + ("r-colorspace" ,r-colorspace) + ("r-flexclust" ,r-flexclust) + ("r-ggplot2" ,r-ggplot2) + ("r-lattice" ,r-lattice) + ("r-mass" ,r-mass) + ("r-tidyr" ,r-tidyr))) + (home-page "https://cran.r-project.org/web/packages/biclust/") + (synopsis "BiCluster algorithms") + (description + "The main function @code{biclust()} provides several algorithms to find +biclusters in two-dimensional data, spectral, plaid model, xmotifs, and bimax. +In addition, the package provides methods for data +preprocessing (normalization and discretization), visualization, and +validation of bicluster solutions.") + (license license:gpl3))) -- cgit v1.2.3 From 9cd3ae8620ed27fb54da1face9ec1a4265746602 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 14 Dec 2019 13:32:02 +0100 Subject: gnu: Add r-icge. * gnu/packages/cran.scm (r-icge): 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 354837823b..8482f274b6 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -18486,3 +18486,27 @@ In addition, the package provides methods for data preprocessing (normalization and discretization), visualization, and validation of bicluster solutions.") (license license:gpl3))) + +(define-public r-icge + (package + (name "r-icge") + (version "0.3") + (source + (origin + (method url-fetch) + (uri (cran-uri "ICGE" version)) + (sha256 + (base32 + "0xin7zml1nbygyi08hhg3wwr2jr1zcsvrlgia89zp4xanxlzgaqa")))) + (properties `((upstream-name . "ICGE"))) + (build-system r-build-system) + (propagated-inputs + `(("r-cluster" ,r-cluster) + ("r-mass" ,r-mass))) + (home-page "https://cran.r-project.org/web/packages/ICGE/") + (synopsis "Cluster estimation and identification of atypical units") + (description + "ICGE is a package that helps to estimate the number of real clusters in +data as well as to identify atypical units. The underlying methods are based +on distances rather than on unit x variables.") + (license license:gpl2+))) -- cgit v1.2.3 From 9fd2d4fdb17ad70b8e94a388546eab59642faecd Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 14 Dec 2019 13:32:19 +0100 Subject: gnu: Add r-depth. * gnu/packages/cran.scm (r-depth): 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 8482f274b6..7688e90f23 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -18510,3 +18510,32 @@ validation of bicluster solutions.") data as well as to identify atypical units. The underlying methods are based on distances rather than on unit x variables.") (license license:gpl2+))) + +(define-public r-depth + (package + (name "r-depth") + (version "2.1-1.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "depth" version)) + (sha256 + (base32 + "0szy0027nh4ps1z919i740i50app5q7cfyg1fj7pdyl45nbl8k6m")))) + (properties `((upstream-name . "depth"))) + (build-system r-build-system) + (propagated-inputs + `(("r-abind" ,r-abind) + ("r-circular" ,r-circular) + ("r-rgl" ,r-rgl))) + (native-inputs + `(("gfortran" ,gfortran))) + (home-page "https://cran.r-project.org/web/packages/depth/") + (synopsis "Nonparametric depth functions for multivariate analysis") + (description + "This package provides tools for depth functions methodology applied to +multivariate analysis. Besides allowing calculation of depth values and +depth-based location estimators, the package includes functions or drawing +contour plots and perspective plots of depth functions. Euclidian and +spherical depths are supported.") + (license license:gpl2))) -- cgit v1.2.3 From ccc2c19b02ef2a5b71ea67719a0d57b34e2622b7 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 14 Dec 2019 13:32:39 +0100 Subject: gnu: Add r-archetypes. * gnu/packages/cran.scm (r-archetypes): 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 7688e90f23..dbaf4f88af 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -18539,3 +18539,27 @@ depth-based location estimators, the package includes functions or drawing contour plots and perspective plots of depth functions. Euclidian and spherical depths are supported.") (license license:gpl2))) + +(define-public r-archetypes + (package + (name "r-archetypes") + (version "2.2-0.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "archetypes" version)) + (sha256 + (base32 + "0ibxsr173ib77gjhid91m85s8gjii4mi2w3d52q5301igv20p7r0")))) + (properties `((upstream-name . "archetypes"))) + (build-system r-build-system) + (propagated-inputs + `(("r-modeltools" ,r-modeltools) + ("r-nnls" ,r-nnls))) + (home-page "https://cran.r-project.org/web/packages/archetypes") + (synopsis "Archetypal analysis") + (description + "The main function @code{archetypes} implements a framework for +archetypal analysis supporting arbitrary problem solving mechanisms for the +different conceptual parts of the algorithm.") + (license license:gpl2+))) -- cgit v1.2.3 From c71724653ab2b75ef533e9b9920e7b3f735154ad Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 14 Dec 2019 13:32:49 +0100 Subject: gnu: Add r-shapes. * gnu/packages/cran.scm (r-shapes): 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 dbaf4f88af..6ef9f2e680 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -18563,3 +18563,32 @@ spherical depths are supported.") archetypal analysis supporting arbitrary problem solving mechanisms for the different conceptual parts of the algorithm.") (license license:gpl2+))) + +(define-public r-shapes + (package + (name "r-shapes") + (version "1.2.5") + (source + (origin + (method url-fetch) + (uri (cran-uri "shapes" version)) + (sha256 + (base32 + "0gfpdydfysp5mwg7qmkn73s67gvh2szb40mzqrx97h41ijgcgd8s")))) + (properties `((upstream-name . "shapes"))) + (build-system r-build-system) + (propagated-inputs + `(("r-mass" ,r-mass) + ("r-minpack-lm" ,r-minpack-lm) + ("r-rgl" ,r-rgl) + ("r-scatterplot3d" ,r-scatterplot3d))) + (home-page "http://www.maths.nottingham.ac.uk/~ild/shapes") + (synopsis "Statistical shape analysis") + (description + "This package provides routines for the statistical analysis of landmark +shapes, including Procrustes analysis, graphical displays, principal +components analysis, permutation and bootstrap tests, thin-plate spline +transformation grids and comparing covariance matrices. See Dryden, I.L. and +Mardia, K.V. (2016). Statistical shape analysis, with Applications in R (2nd +Edition), John Wiley and Sons.") + (license license:gpl2))) -- cgit v1.2.3 From c67508079d2abf9b286812c3b2889f4bbbcf2735 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 14 Dec 2019 13:34:09 +0100 Subject: gnu: Add r-anthropometry. * gnu/packages/cran.scm (r-anthropometry): New variable. --- gnu/packages/cran.scm | 33 +++++++++++++++++++++++++++++++++ 1 file changed, 33 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 6ef9f2e680..9e11802224 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -18592,3 +18592,36 @@ transformation grids and comparing covariance matrices. See Dryden, I.L. and Mardia, K.V. (2016). Statistical shape analysis, with Applications in R (2nd Edition), John Wiley and Sons.") (license license:gpl2))) + +(define-public r-anthropometry + (package + (name "r-anthropometry") + (version "1.13") + (source + (origin + (method url-fetch) + (uri (cran-uri "Anthropometry" version)) + (sha256 + (base32 + "1f568ri1s6psaby8y737vrkarbjg64v89d4jyw23hy17apdmszr8")))) + (properties `((upstream-name . "Anthropometry"))) + (build-system r-build-system) + (propagated-inputs + `(("r-archetypes" ,r-archetypes) + ("r-biclust" ,r-biclust) + ("r-cluster" ,r-cluster) + ("r-depth" ,r-depth) + ("r-fnn" ,r-fnn) + ("r-icge" ,r-icge) + ("r-nnls" ,r-nnls) + ("r-rgl" ,r-rgl) + ("r-shapes" ,r-shapes))) + (home-page "https://cran.r-project.org/web/packages/Anthropometry/") + (synopsis "Statistical methods for anthropometric data") + (description + "This package provides statistical methods especially developed to +analyze anthropometric data. These methods are aimed at providing effective +solutions to some commons problems related to Ergonomics and Anthropometry. +They are based on clustering, the statistical concept of data depth, +statistical shape analysis and archetypal analysis.") + (license license:gpl2+))) -- cgit v1.2.3 From 5c0b5b8ad7351a0d951ee2227093aacefdae28e4 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 14 Dec 2019 13:34:32 +0100 Subject: gnu: Add r-adamethods. * gnu/packages/cran.scm (r-adamethods): 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 9e11802224..bbe44d60b8 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -18625,3 +18625,33 @@ solutions to some commons problems related to Ergonomics and Anthropometry. They are based on clustering, the statistical concept of data depth, statistical shape analysis and archetypal analysis.") (license license:gpl2+))) + +(define-public r-adamethods + (package + (name "r-adamethods") + (version "1.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "adamethods" version)) + (sha256 + (base32 + "0mp73zh5x6h18gv29v981kb9n632kb58lvlcxwr6vcvrx393nrxh")))) + (properties `((upstream-name . "adamethods"))) + (build-system r-build-system) + (propagated-inputs + `(("r-anthropometry" ,r-anthropometry) + ("r-archetypes" ,r-archetypes) + ("r-fnn" ,r-fnn) + ("r-foreach" ,r-foreach) + ("r-nnls" ,r-nnls) + ("r-tolerance" ,r-tolerance) + ("r-univoutl" ,r-univoutl))) + (home-page "https://cran.r-project.org/web/packages/adamethods/") + (synopsis "Archetypoid algorithms and anomaly detection") + (description + "This package is a collection of several algorithms to obtain +archetypoids with small and large databases and with both classical +multivariate data and functional data (univariate and multivariate). Some of +these algorithms also allow to detect anomalies (outliers).") + (license license:gpl2+))) -- cgit v1.2.3 From e31ec53ed808ad7c949ec23521c87ed29b74c5e0 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 14 Dec 2019 13:34:53 +0100 Subject: import: cran: Recognize LGPL 2.1+. * guix/import/cran.scm (string->license): Add case for lgpl2.1+. --- guix/import/cran.scm | 1 + 1 file changed, 1 insertion(+) diff --git a/guix/import/cran.scm b/guix/import/cran.scm index d9018cc7da..0aee0c7cd7 100644 --- a/guix/import/cran.scm +++ b/guix/import/cran.scm @@ -82,6 +82,7 @@ ("LGPL-2.1" 'lgpl2.1) ("LGPL-3" 'lgpl3) ("LGPL (>= 2)" 'lgpl2.0+) + ("LGPL (>= 2.1)" 'lgpl2.1+) ("LGPL (>= 3)" 'lgpl3+) ("MIT" 'expat) ("MIT + file LICENSE" 'expat) -- cgit v1.2.3 From af58b275c95410dca556f91760e293535f9eb511 Mon Sep 17 00:00:00 2001 From: Mathieu Othacehe Date: Sat, 14 Dec 2019 17:34:28 +0100 Subject: gnu: Add u-boot-pine64-lts. * gnu/packages/bootloaders.scm (u-boot-pine64-lts): New variable. --- gnu/packages/bootloaders.scm | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/gnu/packages/bootloaders.scm b/gnu/packages/bootloaders.scm index 156e4c4cdd..55b4abbda5 100644 --- a/gnu/packages/bootloaders.scm +++ b/gnu/packages/bootloaders.scm @@ -9,6 +9,7 @@ ;;; Copyright © 2017, 2018 Efraim Flashner ;;; Copyright © 2018, 2019 Tobias Geerinckx-Rice ;;; Copyright © 2019 nee +;;; Copyright © 2019 Mathieu Othacehe ;;; ;;; This file is part of GNU Guix. ;;; @@ -677,6 +678,9 @@ it fits within common partitioning schemes.") (define-public u-boot-pine64-plus (make-u-boot-sunxi64-package "pine64_plus" "aarch64-linux-gnu")) +(define-public u-boot-pine64-lts + (make-u-boot-sunxi64-package "pine64-lts" "aarch64-linux-gnu")) + (define-public u-boot-pinebook (make-u-boot-sunxi64-package "pinebook" "aarch64-linux-gnu")) -- cgit v1.2.3 From db78fc0679945e37e5ee3bfc28a363cabfda6800 Mon Sep 17 00:00:00 2001 From: Mathieu Othacehe Date: Sat, 14 Dec 2019 17:35:02 +0100 Subject: gnu: bootloaders: Fix make-u-boot-sunxi64-package cross-compilation. * gnu/packages/bootloaders.scm (make-u-boot-sunxi64-package)[arguments]: Search in native-inputs to fix cross-compilation. --- gnu/packages/bootloaders.scm | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/gnu/packages/bootloaders.scm b/gnu/packages/bootloaders.scm index 55b4abbda5..91d567288f 100644 --- a/gnu/packages/bootloaders.scm +++ b/gnu/packages/bootloaders.scm @@ -662,9 +662,11 @@ it fits within common partitioning schemes.") ((#:phases phases) `(modify-phases ,phases (add-after 'unpack 'set-environment - (lambda* (#:key inputs #:allow-other-keys) - (let ((bl31 (string-append (assoc-ref inputs "firmware") - "/bl31.bin"))) + (lambda* (#:key native-inputs inputs #:allow-other-keys) + (let ((bl31 + (string-append + (assoc-ref (or native-inputs inputs) "firmware") + "/bl31.bin"))) (setenv "BL31" bl31) ;; This is necessary when we're using the bundled dtc. ;(setenv "PATH" (string-append (getenv "PATH") ":" -- cgit v1.2.3 From 94de8d0a7f54de4396b9a5954126460278a4c808 Mon Sep 17 00:00:00 2001 From: Mathieu Othacehe Date: Sat, 14 Dec 2019 17:37:23 +0100 Subject: gnu: Add u-boot-pine64-lts-bootloader. * gnu/bootloader/u-boot.scm (u-boot-pine64-lts-bootloader): New variable. --- gnu/bootloader/u-boot.scm | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/gnu/bootloader/u-boot.scm b/gnu/bootloader/u-boot.scm index e21526eb7e..3e892c5475 100644 --- a/gnu/bootloader/u-boot.scm +++ b/gnu/bootloader/u-boot.scm @@ -1,6 +1,6 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2017 David Craven -;;; Copyright © 2017 Mathieu Othacehe +;;; Copyright © 2017, 2019 Mathieu Othacehe ;;; ;;; This file is part of GNU Guix. ;;; @@ -33,6 +33,7 @@ u-boot-nintendo-nes-classic-edition-bootloader u-boot-novena-bootloader u-boot-pine64-plus-bootloader + u-boot-pine64-lts-bootloader u-boot-pinebook-bootloader u-boot-puma-rk3399-bootloader u-boot-rock64-rk3328-bootloader @@ -206,6 +207,11 @@ (inherit u-boot-allwinner64-bootloader) (package u-boot-pine64-plus))) +(define u-boot-pine64-lts-bootloader + (bootloader + (inherit u-boot-allwinner-bootloader) + (package u-boot-pine64-lts))) + (define u-boot-pinebook-bootloader (bootloader (inherit u-boot-allwinner64-bootloader) -- cgit v1.2.3 From 5c1bd7b8d1f1f0e436147baf6ed100e96189366d Mon Sep 17 00:00:00 2001 From: Julien Lepiller Date: Sat, 14 Dec 2019 17:42:33 +0100 Subject: gnu: josm: Update to 15553. * gnu/packages/geo.scm (josm): Update to 15553. --- gnu/packages/geo.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/geo.scm b/gnu/packages/geo.scm index 41801ed0e6..278ece094c 100644 --- a/gnu/packages/geo.scm +++ b/gnu/packages/geo.scm @@ -1081,7 +1081,7 @@ an independent project by the JOSM team.") (define-public josm (package (name "josm") - (version "15492") + (version "15553") (source (origin (method svn-fetch) (uri (svn-reference @@ -1090,7 +1090,7 @@ an independent project by the JOSM team.") (recursive? #f))) (sha256 (base32 - "12xkwcv77as30a61w1c8a0i2b0kiiks71d487gbdfv7azlj4vqia")) + "091pbcn4fnmk42fmxplhis3nw5dbljf6ws8acyhx5dflyn49xzmx")) (file-name (string-append name "-" version "-checkout")) (modules '((guix build utils))) (snippet -- cgit v1.2.3 From e9d8dee6c3d6e2ddff74841a3ab3a2ba2816bf27 Mon Sep 17 00:00:00 2001 From: Brett Gilio Date: Sat, 14 Dec 2019 13:06:07 -0600 Subject: gnu: emacs-doom-themes: Update to 2.1.6-2. * gnu/packages/emacs-xyz.scm (emacs-doom-themes): Update to 2.1.6-2. [arguments]: Disable byte-compilation regarding issue in upstream. . --- gnu/packages/emacs-xyz.scm | 71 ++++++++++++++++++++++++++-------------------- 1 file changed, 40 insertions(+), 31 deletions(-) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 0480b1b33f..30b62588dc 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -19783,38 +19783,47 @@ contrast and few colors.") (license license:gpl3+)))) (define-public emacs-doom-themes - (package - (name "emacs-doom-themes") - (version "2.1.6") - (source (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/hlissner/emacs-doom-themes.git") - (commit (string-append "v" version)))) - (file-name (git-file-name name version)) - (sha256 - (base32 "042pzcdhxi2z07jcscgjbaki9nrrm0cbgbbrnymd1r4q8ckkn8l9")))) - (build-system emacs-build-system) - (native-inputs - `(("emacs-ert-runner" ,emacs-ert-runner))) - (arguments - `(#:tests? #t - #:test-command '("ert-runner") - #:phases - (modify-phases %standard-phases - (add-after 'unpack 'move-themes - (lambda _ - ;; Move the source files to the top level, which is in the - ;; EMACSLOADPATH. - (for-each (lambda (f) - (rename-file f (basename f))) - (find-files "./themes" ".*\\.el$")) - #t))))) - (synopsis "Wide collection of color themes for Emacs") - (description "Emacs-doom-themes contains numerous popular color themes for + (let ((commit "088bfad9a6983c42016da33cd11b9ee855451dcb") + (revision "2") + (version "2.1.6")) + (package + (name "emacs-doom-themes") + (version (git-version version revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/hlissner/emacs-doom-themes.git") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1dmq0vja1k907id56y4012cm3f49vf106v3gglk9sf4kbi9cash2")))) + (build-system emacs-build-system) + (native-inputs + `(("emacs-ert-runner" ,emacs-ert-runner))) + (arguments + `(#:tests? #t + #:test-command '("ert-runner") + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'move-themes + (lambda _ + ;; Move the source files to the top level, which is in the + ;; EMACSLOADPATH. + (for-each (lambda (f) + (rename-file f (basename f))) + (find-files "./themes" ".*\\.el$")) + #t)) + ;; XXX: There is a byte-code overflow issue in the latest + ;; checkout which affects byte-compilation for several theme + ;; files. The easiest way to work around this is to disable + ;; byte-compilation until the issue is resolved. + ;; + (delete 'build)))) + (synopsis "Wide collection of color themes for Emacs") + (description "Emacs-doom-themes contains numerous popular color themes for Emacs that integrate with major modes like Org-mode.") - (home-page "https://github.com/hlissner/emacs-doom-themes") - (license license:expat))) + (home-page "https://github.com/hlissner/emacs-doom-themes") + (license license:expat)))) (define-public emacs-modus-themes (package -- cgit v1.2.3 From d900e1f675d9332bc585ced375d7cc1478b10b21 Mon Sep 17 00:00:00 2001 From: Alex Griffin Date: Sat, 14 Dec 2019 12:34:59 -0600 Subject: gnu: Add htmlcxx. * gnu/packages/web.scm (htmlcxx): New variable. --- gnu/packages/web.scm | 33 +++++++++++++++++++++++++++++++++ 1 file changed, 33 insertions(+) diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm index 749bc06fa9..0536f3089d 100644 --- a/gnu/packages/web.scm +++ b/gnu/packages/web.scm @@ -7011,3 +7011,36 @@ endpoint that will be used to trigger the task. Poussetaches makes HTTP requests with the registered payload until the right status code is returned.") (license license:isc))) + +(define-public htmlcxx + (package + (name "htmlcxx") + (version "0.87") + (source + (origin + (method url-fetch) + (uri + (string-append "mirror://sourceforge/htmlcxx/v" + version "/htmlcxx-" version ".tar.gz")) + (sha256 + (base32 "1j3mzjlczjrk4ahc43s6kzpvzypzjmqz4sillnca5yadrwwgjf2x")))) + (build-system gnu-build-system) + (home-page "http://htmlcxx.sourceforge.net/") + (synopsis "Simple non-validating CSS1 and HTML parser for C++") + (description "htmlcxx is a simple non-validating CSS1 and HTML parser for +C++. Although there are several other HTML parsers available, htmlcxx has some +characteristics that make it unique: +@itemize +@item STL like navigation of DOM tree, using excelent's tree.hh library from +Kasper Peeters +@item It is possible to reproduce exactly, character by character, the original +document from the parse tree +@item Bundled CSS parser +@item Optional parsing of attributes +@item C++ code that looks like C++ (not so true anymore) +@item Offsets of tags/elements in the original document are stored in the nodes +of the DOM tree +@end itemize") + (license (list license:lgpl2.0 + license:gpl2 + license:asl2.0)))) -- cgit v1.2.3 From 9d97a11f04548b8b4f9865b4fa4173a119aa9985 Mon Sep 17 00:00:00 2001 From: Brett Gilio Date: Sat, 14 Dec 2019 14:07:22 -0600 Subject: gnu: emacs-telega: Update to 0.5.3-1. * gnu/packages/emacs-xyz.scm (emacs-telega): Update to 0.5.3-1. [version]: Correct the version number used in the package elisp code itself. --- 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 30b62588dc..505594aa0d 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -20083,8 +20083,8 @@ fish-completion. It can be used in both Eshell and M-x shell.") (define-public emacs-telega (let ((commit "6184e76990db395bea02f7b5d3169e746111e1ad") - (revision "2") - (version "0.5.2")) + (revision "1") + (version "0.5.3")) (package (name "emacs-telega") (version (git-version version revision commit)) -- cgit v1.2.3 From 428561aa63e7ddcafdd80a50e2b147fc97f77662 Mon Sep 17 00:00:00 2001 From: Ludovic Courtès Date: Sat, 14 Dec 2019 14:59:32 +0100 Subject: challenge: Fix type mismatch when comparing to a local hash. * guix/scripts/challenge.scm (call-with-mismatches)[narinfo1]: When LOCAL-HASH is true, call 'narinfo-hash->sha256' and use 'bytevector=?' instead of 'string=?'. --- guix/scripts/challenge.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/guix/scripts/challenge.scm b/guix/scripts/challenge.scm index 51e8d3e4e3..ebeebd5cbe 100644 --- a/guix/scripts/challenge.scm +++ b/guix/scripts/challenge.scm @@ -321,8 +321,9 @@ specified in COMPARISON-REPORT." (define narinfo1 (if local-hash (find (lambda (narinfo) - (not (string=? (narinfo-hash narinfo) - local-hash))) + (not (bytevector=? (narinfo-hash->sha256 + (narinfo-hash narinfo)) + local-hash))) narinfos) (first (comparison-report-narinfos comparison-report)))) -- cgit v1.2.3 From 5f9cd63eb0d803966ce645c9d1db3438370e5505 Mon Sep 17 00:00:00 2001 From: Ludovic Courtès Date: Sun, 15 Dec 2019 00:11:30 +0100 Subject: base64: Do not use (rnrs). * guix/base64.scm: Remove #:use-module clauses for (rnrs) and (srfi srfi-13). Add other #:use-module clauses. (fxbit-field): Define as an alias for 'bit-field. (fx=?, fx+, mod): New aliases. (assert): New macro. --- guix/base64.scm | 18 ++++++++++++------ 1 file changed, 12 insertions(+), 6 deletions(-) diff --git a/guix/base64.scm b/guix/base64.scm index 0fa501eca0..c4fdd9c390 100644 --- a/guix/base64.scm +++ b/guix/base64.scm @@ -52,11 +52,10 @@ base64url-alphabet get-delimited-base64 put-delimited-base64) - #:use-module (rnrs) - #:use-module ((srfi srfi-13) - #:select (string-index - string-prefix? string-suffix? - string-concatenate string-trim-both))) + #:use-module (srfi srfi-11) + #:use-module (srfi srfi-60) + #:use-module (rnrs bytevectors) + #:use-module (rnrs io ports)) (define-syntax define-alias @@ -67,12 +66,19 @@ ;; Force the use of Guile's own primitives to avoid the overhead of its 'fx' ;; procedures. -(define-alias fxbit-field bitwise-bit-field) +(define-alias fxbit-field bit-field) (define-alias fxarithmetic-shift ash) (define-alias fxarithmetic-shift-left ash) (define-alias fxand logand) (define-alias fxior logior) (define-alias fxxor logxor) +(define-alias fx=? =) +(define-alias fx+ +) +(define-alias mod modulo) + +(define-syntax-rule (assert exp) + (unless exp + (throw 'assertion-failure 'exp))) (define base64-alphabet "ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz0123456789+/") -- cgit v1.2.3 From 178e5500347ec25e777207310e44d5f598a3ddef Mon Sep 17 00:00:00 2001 From: Ludovic Courtès Date: Sun, 15 Dec 2019 00:19:17 +0100 Subject: gnu: bootloaders: Avoid #:select on (gnu packages …) module. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/bootloaders.scm: Remove use of #:select. --- gnu/packages/bootloaders.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/bootloaders.scm b/gnu/packages/bootloaders.scm index 91d567288f..21b32a1ab1 100644 --- a/gnu/packages/bootloaders.scm +++ b/gnu/packages/bootloaders.scm @@ -29,7 +29,7 @@ (define-module (gnu packages bootloaders) #:use-module (gnu packages) #:use-module (gnu packages admin) - #:use-module ((gnu packages algebra) #:select (bc)) + #:use-module (gnu packages algebra) #:use-module (gnu packages assembly) #:use-module (gnu packages base) #:use-module (gnu packages disk) -- cgit v1.2.3 From 4ac5d4fee19aad08289ed10da15e32d937ea595d Mon Sep 17 00:00:00 2001 From: Konrad Hinsen Date: Fri, 13 Dec 2019 13:53:47 +0100 Subject: gnu: Add gfortran-toolchain MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/commencement.scm: (gfortran-toolchain): New variable. Signed-off-by: Ludovic Courtès --- gnu/packages/commencement.scm | 13 +++++++++++++ 1 file changed, 13 insertions(+) diff --git a/gnu/packages/commencement.scm b/gnu/packages/commencement.scm index 68030376fc..14ecf246d4 100644 --- a/gnu/packages/commencement.scm +++ b/gnu/packages/commencement.scm @@ -2601,4 +2601,17 @@ an d binaries, plus debugging symbols in the @code{debug} output), and Binutils (define-public gcc-toolchain-9 (make-gcc-toolchain gcc-9)) +;; Provide the Fortran toolchain package only for the version of gfortran that +;; is used by Guix internally to build Fortran libraries, because combining +;; code compiled with different versions can cause problems. + +(define-public gfortran-toolchain + (package (inherit (make-gcc-toolchain gfortran)) + (synopsis "Complete GCC tool chain for Fortran development") + (description "This package provides a complete GCC tool chain for +Fortran development to be installed in user profiles. This includes +gfortran, as well as libc (headers and binaries, plus debugging symbols +in the @code{debug} output), and binutils."))) + + ;;; commencement.scm ends here -- cgit v1.2.3 From 586e1611b9562248ab32903fd3d98211de445533 Mon Sep 17 00:00:00 2001 From: Brett Gilio Date: Sat, 14 Dec 2019 18:44:25 -0600 Subject: gnu: Add emacs-parseclj. * gnu/packages/emacs-xyz.scm (emacs-parseclj): 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 505594aa0d..9f5a5b9cbb 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -20522,3 +20522,27 @@ on removable volumes in Linux.") data, including buffers, window configuration, variables, and more.") (home-page "https://github.com/thierryvolpiatto/psession") (license license:gpl3+)))) + +(define-public emacs-parseclj + (package + (name "emacs-parseclj") + (version "0.1.0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/clojure-emacs/parseclj.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "03bm5dm4hmkqimv4wqxjjh5814pxysmm7z54bv2rf7zwv1x7dggr")))) + (build-system emacs-build-system) + (propagated-inputs `(("emacs-a" ,emacs-a))) + (home-page "https://cider.mx") + (synopsis "Clojure parser for Emacs Lisp") + (description + "An Emacs Lisp library for parsing Clojure code and EDN data. +It supports several input and output formats, all powered by the +same shift-reduce parser function.") + (license license:gpl3+))) -- cgit v1.2.3 From 47a9a59270dae9991f43e7cef662bc872b54e5b6 Mon Sep 17 00:00:00 2001 From: Brett Gilio Date: Sat, 14 Dec 2019 18:44:50 -0600 Subject: gnu: Add emacs-parseedn. * gnu/packages/emacs-xyz.scm (emacs-parseedn): New variable. --- gnu/packages/emacs-xyz.scm | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 9f5a5b9cbb..6ffd9e176f 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -20523,6 +20523,31 @@ data, including buffers, window configuration, variables, and more.") (home-page "https://github.com/thierryvolpiatto/psession") (license license:gpl3+)))) +(define-public emacs-parseedn + (package + (name "emacs-parseedn") + (version "0.1.0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/clojure-emacs/parseedn.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "11wi3hwcgmy54p6ivpijqm7v0hj6j75a19qk5z779bqfrp79b4pc")))) + (build-system emacs-build-system) + (propagated-inputs + `(("emacs-a" ,emacs-a) + ("emacs-parseclj" ,emacs-parseclj))) + (home-page "https://cider.mx") + (synopsis "EDN parser for Emacs Lisp") + (description + "An Emacs Lisp library for parsing EDN (Clojure) data. +It uses parseclj's shift-reduce parser internally.") + (license license:gpl3+))) + (define-public emacs-parseclj (package (name "emacs-parseclj") -- cgit v1.2.3 From 7d4d881266a4992e2f596ebef53e64be3861f3d6 Mon Sep 17 00:00:00 2001 From: Brett Gilio Date: Sat, 14 Dec 2019 18:45:22 -0600 Subject: gnu: emacs-cider: Update to 0.23.0. * gnu/packages/emacs-xyz.scm (emacs-cider): Update to 0.23.0. [propagated-inputs]: Add emacs-seq, emacs-parseedn. --- gnu/packages/emacs-xyz.scm | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 6ffd9e176f..2e6e027479 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -7146,7 +7146,7 @@ target will call @code{compile} on it.") (define-public emacs-cider (package (name "emacs-cider") - (version "0.21.0") + (version "0.23.0") (source (origin (method git-fetch) @@ -7156,7 +7156,7 @@ target will call @code{compile} on it.") (file-name (git-file-name name version)) (sha256 (base32 - "0lbrwj67fnvynkdkzvnzp3p8vqlz0ldrcs317vg60bqfhx7hvqkj")))) + "05yjkqc6d4grq9z5pxmv3anqh4zlhfg4v46jlccp6ynh030g7axs")))) (build-system emacs-build-system) (arguments '(#:exclude ; Don't exclude 'cider-test.el'. @@ -7164,7 +7164,9 @@ target will call @code{compile} on it.") (propagated-inputs `(("emacs-clojure-mode" ,emacs-clojure-mode) ("emacs-sesman" ,emacs-sesman) + ("emacs-seq" ,emacs-seq) ("emacs-spinner" ,emacs-spinner) + ("emacs-parseedn" ,emacs-parseedn) ("emacs-pkg-info" ,emacs-pkg-info) ("emacs-queue" ,emacs-queue))) (home-page "https://cider.readthedocs.io/") -- cgit v1.2.3 From 4fb8e2744a62a7124521f8fa7fb160fa56e5d41d Mon Sep 17 00:00:00 2001 From: Brett Gilio Date: Sat, 14 Dec 2019 18:46:06 -0600 Subject: gnu: emacs-cider: Update home-page. * gnu/packages/emacs-xyz.scm (emacs-cider)[home-page]: Change to https://cider.mx/. --- gnu/packages/emacs-xyz.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 2e6e027479..9e4edf282f 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -7169,7 +7169,7 @@ target will call @code{compile} on it.") ("emacs-parseedn" ,emacs-parseedn) ("emacs-pkg-info" ,emacs-pkg-info) ("emacs-queue" ,emacs-queue))) - (home-page "https://cider.readthedocs.io/") + (home-page "https://cider.mx/") (synopsis "Clojure development environment for Emacs") (description "CIDER (Clojure Interactive Development Environment that Rocks) aims to -- cgit v1.2.3 From 58c3a4f5969977402d83452f70d10289e0cd7305 Mon Sep 17 00:00:00 2001 From: Björn Höfling Date: Sun, 15 Dec 2019 12:31:35 +0100 Subject: gnu: java-svg-salamander: Return #t from snippet. * gnu/packages/java.scm (java-svg-salamander)[origin]: Return #t from snippet. --- gnu/packages/java.scm | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/gnu/packages/java.scm b/gnu/packages/java.scm index cc63ccf19a..6550463fa5 100644 --- a/gnu/packages/java.scm +++ b/gnu/packages/java.scm @@ -1,3 +1,4 @@ + ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2015, 2016, 2017, 2018, 2019 Ricardo Wurmus ;;; Copyright © 2016 Leo Famulari @@ -11680,7 +11681,9 @@ IPTC, XMP, ICC and more formats.") "1zv3kjdkf6iqf02x6ln76254y634j2ji448y706a65lsbfjmmicf")) (modules '((guix build utils))) (snippet - `(for-each delete-file (find-files "." ".*.jar"))) + '(begin + (for-each delete-file (find-files "." ".*.jar")) + #t)) (patches (search-patches "java-svg-salamander-Fix-non-det.patch")))) (build-system ant-build-system) -- cgit v1.2.3 From b5b6e74e150469e48111f0e6e5a83ab9f6b40cd8 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 14 Dec 2019 15:52:29 +0100 Subject: gnu: Add r-idpmisc. * gnu/packages/cran.scm (r-idpmisc): 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 bbe44d60b8..b12d984387 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -18655,3 +18655,32 @@ archetypoids with small and large databases and with both classical multivariate data and functional data (univariate and multivariate). Some of these algorithms also allow to detect anomalies (outliers).") (license license:gpl2+))) + +(define-public r-idpmisc + (package + (name "r-idpmisc") + (version "1.1.19") + (source + (origin + (method url-fetch) + (uri (cran-uri "IDPmisc" version)) + (sha256 + (base32 + "13qcvfm703frs367paddz1wq9k3p17f9p5347m56bhky5hjkaphd")))) + (properties `((upstream-name . "IDPmisc"))) + (build-system r-build-system) + (propagated-inputs + `(("r-lattice" ,r-lattice))) + (home-page "https://cran.r-project.org/web/packages/IDPmisc/") + (synopsis "Functions for data analyses and visualization") + (description + "This package provides different high-level graphics functions for +displaying large datasets, displaying circular data in a very flexible way, +finding local maxima, brewing color ramps, drawing nice arrows, zooming +2D-plots, creating figures with differently colored margin and plot region. +In addition, the package contains auxiliary functions for data manipulation +like omitting observations with irregular values or selecting data by logical +vectors, which include NAs. Other functions are especially useful in +spectroscopy and analyses of environmental data: robust baseline fitting, +finding peaks in spectra, converting humidity measures.") + (license license:gpl3+))) -- cgit v1.2.3 From f431d5e299b9e00c22b02e9d5464e6d4196561ba Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 14 Dec 2019 15:54:50 +0100 Subject: guix: Upgrade to Bioconductor 3.10. * guix/build-system/r.scm (bioconductor-uri): Switch to version 3.10. * guix/import/cran.scm (%bioconductor-version): Same. --- 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 dd2a9fe8de..2d328764b0 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/3.9" + (string-append "https://bioconductor.org/packages/3.10" type-url-part "/src/contrib/Archive/" name "_" version ".tar.gz")))) diff --git a/guix/import/cran.scm b/guix/import/cran.scm index 0aee0c7cd7..f3f1747e43 100644 --- a/guix/import/cran.scm +++ b/guix/import/cran.scm @@ -133,9 +133,9 @@ package definition." (define %cran-url "https://cran.r-project.org/web/packages/") (define %bioconductor-url "https://bioconductor.org/packages/") -;; The latest Bioconductor release is 3.9. Bioconductor packages should be +;; The latest Bioconductor release is 3.10. Bioconductor packages should be ;; updated together. -(define %bioconductor-version "3.9") +(define %bioconductor-version "3.10") (define* (bioconductor-packages-list-url #:optional type) (string-append "https://bioconductor.org/packages/" -- cgit v1.2.3 From eb15df8deab4f8a1560389dc41dc51c7270779d8 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 14 Dec 2019 16:36:05 +0100 Subject: gnu: Add r-qqman. * gnu/packages/cran.scm (r-qqman): 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 b12d984387..c9dfafa9b1 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -18684,3 +18684,25 @@ vectors, which include NAs. Other functions are especially useful in spectroscopy and analyses of environmental data: robust baseline fitting, finding peaks in spectra, converting humidity measures.") (license license:gpl3+))) + +(define-public r-qqman + (package + (name "r-qqman") + (version "0.1.4") + (source + (origin + (method url-fetch) + (uri (cran-uri "qqman" version)) + (sha256 + (base32 + "1v9s9ag1hfb47py87wb2nad4mbsfx35832hdmrh5kxrb2f11zl1s")))) + (properties `((upstream-name . "qqman"))) + (build-system r-build-system) + (propagated-inputs + `(("r-calibrate" ,r-calibrate))) + (home-page "https://cran.r-project.org/web/packages/qqman/") + (synopsis "Q-Q and Manhattan plots for GWAS data") + (description + "This package allows you to create Q-Q and Manhattan plots for GWAS data +from PLINK results.") + (license license:gpl3))) -- cgit v1.2.3 From e5d722fb4c606bcc0d15e788464d6962a9ff8817 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 14 Dec 2019 16:37:03 +0100 Subject: gnu: Add r-biocversion. * gnu/packages/bioconductor.scm (r-biocversion): New variable. --- gnu/packages/bioconductor.scm | 20 ++++++++++++++++++++ 1 file changed, 20 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 1ef636d7f6..dd52f66918 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -879,6 +879,26 @@ package @code{affy}.") ;;; Packages +(define-public r-biocversion + (package + (name "r-biocversion") + (version "3.10.1") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "BiocVersion" version)) + (sha256 + (base32 + "0mfqjqfvrwwglldq3g7nbic5hf3nwzv02nbfxnl2cfvf9gznlh5f")))) + (properties `((upstream-name . "BiocVersion"))) + (build-system r-build-system) + (home-page "https://bioconductor.org/packages/BiocVersion/") + (synopsis "Set the appropriate version of Bioconductor packages") + (description + "This package provides repository information for the appropriate version +of Bioconductor.") + (license license:artistic2.0))) + (define-public r-biocgenerics (package (name "r-biocgenerics") -- cgit v1.2.3 From b4a22ccaaadb0934e4a44aeb25609d8abdac998b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 14 Dec 2019 16:37:36 +0100 Subject: gnu: Add r-multidataset. * gnu/packages/bioconductor.scm (r-multidataset): New variable. --- gnu/packages/bioconductor.scm | 35 +++++++++++++++++++++++++++++++++++ 1 file changed, 35 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index dd52f66918..894a150624 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5044,6 +5044,41 @@ conditions. A Bayesian network is used to model the regulatory structure and Markov-Chain-Monte-Carlo is applied to sample the activity states.") (license license:gpl2+))) +(define-public r-multidataset + (package + (name "r-multidataset") + (version "1.14.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "MultiDataSet" version)) + (sha256 + (base32 + "0iw99ymrv3ls023mpmgyagmb5simgsgadpj0k4bnssfaqnklywlj")))) + (properties `((upstream-name . "MultiDataSet"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-genomicranges" ,r-genomicranges) + ("r-ggplot2" ,r-ggplot2) + ("r-ggrepel" ,r-ggrepel) + ("r-iranges" ,r-iranges) + ("r-limma" ,r-limma) + ("r-qqman" ,r-qqman) + ("r-s4vectors" ,r-s4vectors) + ("r-summarizedexperiment" ,r-summarizedexperiment))) + (home-page "https://bioconductor.org/packages/MultiDataSet/") + (synopsis "Implementation of MultiDataSet and ResultSet") + (description + "This package provides an implementation of the BRGE's (Bioinformatic +Research Group in Epidemiology from Center for Research in Environmental +Epidemiology) MultiDataSet and ResultSet. MultiDataSet is designed for +integrating multi omics data sets and ResultSet is a container for omics +results. This package contains base classes for MEAL and rexposome +packages.") + (license license:expat))) + (define-public r-ropls (package (name "r-ropls") -- cgit v1.2.3 From b4aee31dcb3a926109a185df055e780116867fcc Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 14 Dec 2019 16:38:06 +0100 Subject: gnu: Add r-cytolib. * gnu/packages/bioconductor.scm (r-cytolib): New variable. --- gnu/packages/bioconductor.scm | 20 ++++++++++++++++++++ 1 file changed, 20 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 894a150624..796543f7c0 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5264,6 +5264,26 @@ and to both short and long sequence reads.") cluster count and membership by stability evidence in unsupervised analysis.") (license license:gpl2))) +(define-public r-cytolib + (package + (name "r-cytolib") + (version "1.8.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "cytolib" version)) + (sha256 + (base32 + "1zk5i09k782lw6297gl3rh0g4fxswr2ang8dgqj7p0814l7h15k9")))) + (properties `((upstream-name . "cytolib"))) + (build-system r-build-system) + (home-page "https://bioconductor.org/packages/cytolib/") + (synopsis "C++ infrastructure for working with gated cytometry") + (description + "This package provides the core data structure and API to represent and +interact with gated cytometry data.") + (license license:artistic2.0))) + (define-public r-flowcore (package (name "r-flowcore") -- cgit v1.2.3 From 15ac0c195c45c5376560617510c4a5da9758af62 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 14 Dec 2019 16:39:31 +0100 Subject: gnu: Add r-ncdfflow. * gnu/packages/bioconductor.scm (r-ncdfflow): 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 796543f7c0..1488252f61 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5340,6 +5340,37 @@ Cytometry data using non-parametric clustering and segmented-regression-based change point detection.") (license license:artistic2.0))) +(define-public r-ncdfflow + (package + (name "r-ncdfflow") + (version "2.32.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "ncdfFlow" version)) + (sha256 + (base32 + "06lscx6h4rg80ifi90rj7z2497b8w1fjipm3l8s3230rkizhh02i")))) + (properties `((upstream-name . "ncdfFlow"))) + (build-system r-build-system) + (inputs + `(("zlib" ,zlib))) + (propagated-inputs + `(("r-bh" ,r-bh) + ("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-flowcore" ,r-flowcore) + ("r-rcpp" ,r-rcpp) + ("r-rcpparmadillo" ,r-rcpparmadillo) + ("r-rhdf5lib" ,r-rhdf5lib) + ("r-zlibbioc" ,r-zlibbioc))) + (home-page "https://bioconductor.org/packages/ncdfFlow/") + (synopsis "HDF5 based storage for flow cytometry data") + (description + "This package provides HDF5 storage based methods and functions for +manipulation of flow cytometry data.") + (license license:artistic2.0))) + (define-public r-flowsom (package (name "r-flowsom") -- cgit v1.2.3 From f5f440312d848e12463f0c6f7510a86b623a9e27 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 14 Dec 2019 16:38:34 +0100 Subject: gnu: Add r-ggcyto. * gnu/packages/bioconductor.scm (r-ggcyto): 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 1488252f61..65ce365eef 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5371,6 +5371,40 @@ change point detection.") manipulation of flow cytometry data.") (license license:artistic2.0))) +(define-public r-ggcyto + (package + (name "r-ggcyto") + (version "1.14.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "ggcyto" version)) + (sha256 + (base32 + "165qszvy5z176h1l3dnjb5dcm279b6bjl5n5gzz8wfn4xpn8anc8")))) + (properties `((upstream-name . "ggcyto"))) + (build-system r-build-system) + (propagated-inputs + `(("r-data-table" ,r-data-table) + ("r-flowcore" ,r-flowcore) + ("r-flowworkspace" ,r-flowworkspace) + ("r-ggplot2" ,r-ggplot2) + ("r-gridextra" ,r-gridextra) + ("r-ncdfflow" ,r-ncdfflow) + ("r-plyr" ,r-plyr) + ("r-rcolorbrewer" ,r-rcolorbrewer) + ("r-rlang" ,r-rlang) + ("r-scales" ,r-scales))) + (home-page "https://github.com/RGLab/ggcyto/issues") + (synopsis "Visualize Cytometry data with ggplot") + (description + "With the dedicated fortify method implemented for @code{flowSet}, +@code{ncdfFlowSet} and @code{GatingSet} classes, both raw and gated flow +cytometry data can be plotted directly with ggplot. The @code{ggcyto} wrapper +and some custom layers also make it easy to add gates and population +statistics to the plot.") + (license license:artistic2.0))) + (define-public r-flowsom (package (name "r-flowsom") -- cgit v1.2.3 From 5aa7e882fa3f198fa8e108827162d71b0229033c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 14 Dec 2019 16:46:12 +0100 Subject: gnu: Add r-ggplot-multistats. * gnu/packages/cran.scm (r-ggplot-multistats): 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 c9dfafa9b1..3190cee592 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -18706,3 +18706,31 @@ finding peaks in spectra, converting humidity measures.") "This package allows you to create Q-Q and Manhattan plots for GWAS data from PLINK results.") (license license:gpl3))) + +(define-public r-ggplot-multistats + (package + (name "r-ggplot-multistats") + (version "1.0.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "ggplot.multistats" version)) + (sha256 + (base32 + "1afzfa86vc484bcwpg7m1ky03jpax584rigzgai8w06pifkmz0il")))) + (properties + `((upstream-name . "ggplot.multistats"))) + (build-system r-build-system) + (propagated-inputs + `(("r-ggplot2" ,r-ggplot2) + ("r-hexbin" ,r-hexbin) + ("r-rlang" ,r-rlang) + ("r-scales" ,r-scales))) + (home-page "https://github.com/flying-sheep/ggplot.multistats") + (synopsis "Multiple summary statistics for binned stats/geometries") + (description + "This package provides the ggplot binning layer @code{stat_summaries_hex()}, +which functions similar to its singular form, but allows the use of multiple +statistics per bin. Those statistics can be mapped to multiple bin +aesthetics.") + (license license:gpl3))) -- cgit v1.2.3 From 257b3b812ce5ef605090c079e6e59cb5383a2100 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 14 Dec 2019 19:34:06 +0100 Subject: gnu: Add r-knn-covertree. * gnu/packages/cran.scm (r-knn-covertree): New variable. --- gnu/packages/cran.scm | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 3190cee592..349ea62e6b 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -18734,3 +18734,29 @@ which functions similar to its singular form, but allows the use of multiple statistics per bin. Those statistics can be mapped to multiple bin aesthetics.") (license license:gpl3))) + +(define-public r-knn-covertree + (package + (name "r-knn-covertree") + (version "1.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "knn.covertree" version)) + (sha256 + (base32 + "0msfcmwydws7q7m5jdb0dxab0nkbl7mq5llg6v3r4qrnlvrdggvz")))) + (properties `((upstream-name . "knn.covertree"))) + (build-system r-build-system) + (propagated-inputs + `(("r-matrix" ,r-matrix) + ("r-rcpp" ,r-rcpp) + ("r-rcppeigen" ,r-rcppeigen))) + (home-page "https://github.com/flying-sheep/knn.covertree") + (synopsis "Accurate kNN Implementation with multiple distance measures") + (description + "Similarly to the FNN package, this package allows calculation of the k +nearest neighbors (kNN) of a data matrix. The implementation is based on +cover trees introduced by Alina Beygelzimer, Sham Kakade, and John +Langford (2006) @url{doi:10.1145/1143844.1143857}.") + (license license:agpl3+))) -- cgit v1.2.3 From 9d1099eb073e562386d815c2ff76bcbcb208ff52 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 14 Dec 2019 19:35:03 +0100 Subject: gnu: r-preprocesscore: Update to 1.48.0. * gnu/packages/statistics.scm (r-preprocesscore): Update to 1.48.0. --- 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 81ff0107b4..811033f0c3 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -4080,14 +4080,14 @@ hierarchical clustering dendrograms.") (define-public r-preprocesscore (package (name "r-preprocesscore") - (version "1.46.0") + (version "1.48.0") (source (origin (method url-fetch) (uri (bioconductor-uri "preprocessCore" version)) (sha256 (base32 - "0iiyn42hlvmc5vabg5x15mls11124i23sh4qijwk0narh438cqm0")))) + "0zrb9hx60vppkg0priczdb301nhq5f0dj8lkc8rcc4xrqqr915qm")))) (properties `((upstream-name . "preprocessCore"))) (build-system r-build-system) -- cgit v1.2.3 From dbfce8ff5b76700da34753d302f8aae0a2c114c4 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 14 Dec 2019 19:36:04 +0100 Subject: gnu: r-rgraphviz: Update to 2.30.0. * gnu/packages/graph.scm (r-rgraphviz): Update to 2.30.0. --- gnu/packages/graph.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/graph.scm b/gnu/packages/graph.scm index 52db619fb3..4095926af3 100644 --- a/gnu/packages/graph.scm +++ b/gnu/packages/graph.scm @@ -165,14 +165,14 @@ model.") (define-public r-rgraphviz (package (name "r-rgraphviz") - (version "2.28.0") + (version "2.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rgraphviz" version)) (sha256 (base32 - "0nivz8fshaqig6ynjqbya2gmxsy4hm7jnd8fhb853z5g0ydp7g0c")))) + "00lrkbgbb4payybckcmazsv8skysgdlglyqbl7yjb37vv3gnfc6c")))) (properties `((upstream-name . "Rgraphviz"))) (build-system r-build-system) ;; FIXME: Rgraphviz bundles the sources of an older variant of -- cgit v1.2.3 From 0dd4b7d73278ca0b90b2b74f8e64eb86fbb69d69 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 14:24:25 +0100 Subject: gnu: Add r-flowviz. * gnu/packages/bioconductor.scm (r-flowviz): 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 65ce365eef..cbb79da2d1 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5405,6 +5405,35 @@ and some custom layers also make it easy to add gates and population statistics to the plot.") (license license:artistic2.0))) +(define-public r-flowviz + (package + (name "r-flowviz") + (version "1.50.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "flowViz" version)) + (sha256 + (base32 + "0ik16bxcfcg3q26ra3055718kskid64aaazcbqsxalca9ppdm4k7")))) + (properties `((upstream-name . "flowViz"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biobase" ,r-biobase) + ("r-flowcore" ,r-flowcore) + ("r-hexbin" ,r-hexbin) + ("r-idpmisc" ,r-idpmisc) + ("r-kernsmooth" ,r-kernsmooth) + ("r-lattice" ,r-lattice) + ("r-latticeextra" ,r-latticeextra) + ("r-mass" ,r-mass) + ("r-rcolorbrewer" ,r-rcolorbrewer))) + (home-page "https://bioconductor.org/packages/flowViz/") + (synopsis "Visualization for flow cytometry") + (description + "This package provides visualization tools for flow cytometry data.") + (license license:artistic2.0))) + (define-public r-flowsom (package (name "r-flowsom") -- cgit v1.2.3 From c8ab9eb1b4d9af156d8008d43e6a7520e8718683 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 14:24:42 +0100 Subject: gnu: Add r-flowclust. * gnu/packages/bioconductor.scm (r-flowclust): New variable. --- gnu/packages/bioconductor.scm | 37 +++++++++++++++++++++++++++++++++++++ 1 file changed, 37 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index cbb79da2d1..c59d799cc0 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5434,6 +5434,43 @@ statistics to the plot.") "This package provides visualization tools for flow cytometry data.") (license license:artistic2.0))) +(define-public r-flowclust + (package + (name "r-flowclust") + (version "3.24.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "flowClust" version)) + (sha256 + (base32 + "0k4bgc4mf512njfdfg5ld9l7slgfxyfh766jab87j96zrrgcnj8s")))) + (properties `((upstream-name . "flowClust"))) + (build-system r-build-system) + (arguments + `(#:configure-flags + (list "--configure-args=--enable-bundled-gsl=no"))) + (propagated-inputs + `(("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-clue" ,r-clue) + ("r-corpcor" ,r-corpcor) + ("r-ellipse" ,r-ellipse) + ("r-flowcore" ,r-flowcore) + ("r-flowviz" ,r-flowviz) + ("r-graph" ,r-graph) + ("r-mnormt" ,r-mnormt))) + (inputs + `(("gsl" ,gsl))) + (native-inputs + `(("pkg-config" ,pkg-config))) + (home-page "https://bioconductor.org/packages/flowClust") + (synopsis "Clustering for flow cytometry") + (description + "This package provides robust model-based clustering using a t-mixture +model with Box-Cox transformation.") + (license license:artistic2.0))) + (define-public r-flowsom (package (name "r-flowsom") -- cgit v1.2.3 From f1964519e748cda1703ec874ce8e33bcd85ddcb9 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 14:24:56 +0100 Subject: gnu: Add r-rprotobuflib. * gnu/packages/bioconductor.scm (r-rprotobuflib): New variable. --- gnu/packages/bioconductor.scm | 30 ++++++++++++++++++++++++++++++ 1 file changed, 30 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index c59d799cc0..8d0861a5f3 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5471,6 +5471,36 @@ statistics to the plot.") model with Box-Cox transformation.") (license license:artistic2.0))) +;; TODO: this package bundles an old version of protobuf. It's not easy to +;; make it use our protobuf package instead. +(define-public r-rprotobuflib + (package + (name "r-rprotobuflib") + (version "1.8.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "RProtoBufLib" version)) + (sha256 + (base32 + "0dlgki21a37bxqh3cf83vl5zqxm86472g8a9plvhrjzzsn3mwnrm")))) + (properties `((upstream-name . "RProtoBufLib"))) + (build-system r-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'unpack-bundled-sources + (lambda _ + (with-directory-excursion "src" + (invoke "tar" "xf" "protobuf-2.6.0.tgz")) + #t))))) + (home-page "https://bioconductor.org/packages/RProtoBufLib/") + (synopsis "C++ headers and static libraries of Protocol buffers") + (description + "This package provides the headers and static library of Protocol buffers +for other R packages to compile and link against.") + (license license:bsd-3))) + (define-public r-flowsom (package (name "r-flowsom") -- cgit v1.2.3 From 82c1111745828a9595f129360198229f1a108263 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 14:25:11 +0100 Subject: gnu: Add r-flowworkspace. * gnu/packages/bioconductor.scm (r-flowworkspace): New variable. --- gnu/packages/bioconductor.scm | 48 +++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 48 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 8d0861a5f3..babb553640 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5501,6 +5501,54 @@ model with Box-Cox transformation.") for other R packages to compile and link against.") (license license:bsd-3))) +(define-public r-flowworkspace + (package + (name "r-flowworkspace") + (version "3.34.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "flowWorkspace" version)) + (sha256 + (base32 + "0hvbkxyylsygra31l1lxyvbsr5hc50lqy1y7gwrfgrfil4a2m762")))) + (properties `((upstream-name . "flowWorkspace"))) + (build-system r-build-system) + (propagated-inputs + `(("r-bh" ,r-bh) + ("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-cytolib" ,r-cytolib) + ("r-data-table" ,r-data-table) + ("r-digest" ,r-digest) + ("r-dplyr" ,r-dplyr) + ("r-flowcore" ,r-flowcore) + ("r-flowviz" ,r-flowviz) + ("r-graph" ,r-graph) + ("r-gridextra" ,r-gridextra) + ("r-lattice" ,r-lattice) + ("r-latticeextra" ,r-latticeextra) + ("r-matrixstats" ,r-matrixstats) + ("r-ncdfflow" ,r-ncdfflow) + ("r-rbgl" ,r-rbgl) + ("r-rcolorbrewer" ,r-rcolorbrewer) + ("r-rcpp" ,r-rcpp) + ("r-rcppparallel" ,r-rcppparallel) + ("r-rgraphviz" ,r-rgraphviz) + ("r-rprotobuflib" ,r-rprotobuflib) + ("r-scales" ,r-scales) + ("r-stringr" ,r-stringr))) + (home-page "https://bioconductor.org/packages/flowWorkspace/") + (synopsis "Infrastructure for working with cytometry data") + (description + "This package is designed to facilitate comparison of automated gating +methods against manual gating done in flowJo. This package allows you to +import basic flowJo workspaces into BioConductor and replicate the gating from +flowJo using the @code{flowCore} functionality. Gating hierarchies, groups of +samples, compensation, and transformation are performed so that the output +matches the flowJo analysis.") + (license license:artistic2.0))) + (define-public r-flowsom (package (name "r-flowsom") -- cgit v1.2.3 From b700b9ec21d5fb7664860a777c51f07015af5339 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 14:25:30 +0100 Subject: gnu: Add r-flowstats. * gnu/packages/bioconductor.scm (r-flowstats): 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 babb553640..d5eca996ac 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5549,6 +5549,42 @@ samples, compensation, and transformation are performed so that the output matches the flowJo analysis.") (license license:artistic2.0))) +(define-public r-flowstats + (package + (name "r-flowstats") + (version "3.44.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "flowStats" version)) + (sha256 + (base32 + "0pql0lpf90nra7w6z6nd8l9cgjlsg2pxysfravnbzfhl3pjvd96w")))) + (properties `((upstream-name . "flowStats"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-cluster" ,r-cluster) + ("r-fda" ,r-fda) + ("r-flowcore" ,r-flowcore) + ("r-flowviz" ,r-flowviz) + ("r-flowworkspace" ,r-flowworkspace) + ("r-kernsmooth" ,r-kernsmooth) + ("r-ks" ,r-ks) + ("r-lattice" ,r-lattice) + ("r-mass" ,r-mass) + ("r-ncdfflow" ,r-ncdfflow) + ("r-rcolorbrewer" ,r-rcolorbrewer) + ("r-rrcov" ,r-rrcov))) + (home-page "http://www.github.com/RGLab/flowStats") + (synopsis "Statistical methods for the analysis of flow cytometry data") + (description + "This package provides methods and functionality to analyze flow data +that is beyond the basic infrastructure provided by the @code{flowCore} +package.") + (license license:artistic2.0))) + (define-public r-flowsom (package (name "r-flowsom") -- cgit v1.2.3 From 6aedc805146986e6fe8c8191fcf321b8fbe555ca Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 14:25:45 +0100 Subject: gnu: Add r-opencyto. * gnu/packages/bioconductor.scm (r-opencyto): New variable. --- gnu/packages/bioconductor.scm | 42 ++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 42 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index d5eca996ac..56d32ed0d9 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5585,6 +5585,48 @@ that is beyond the basic infrastructure provided by the @code{flowCore} package.") (license license:artistic2.0))) +(define-public r-opencyto + (package + (name "r-opencyto") + (version "1.24.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "openCyto" version)) + (sha256 + (base32 + "0h25nhvq1zq624wsgb55wjcgri9rcd2fnqkb31h9jdakr01dw2sb")))) + (properties `((upstream-name . "openCyto"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-clue" ,r-clue) + ("r-data-table" ,r-data-table) + ("r-flowclust" ,r-flowclust) + ("r-flowcore" ,r-flowcore) + ("r-flowstats" ,r-flowstats) + ("r-flowviz" ,r-flowviz) + ("r-flowworkspace" ,r-flowworkspace) + ("r-graph" ,r-graph) + ("r-gtools" ,r-gtools) + ("r-ks" ,r-ks) + ("r-lattice" ,r-lattice) + ("r-mass" ,r-mass) + ("r-ncdfflow" ,r-ncdfflow) + ("r-plyr" ,r-plyr) + ("r-r-utils" ,r-r-utils) + ("r-rbgl" ,r-rbgl) + ("r-rcolorbrewer" ,r-rcolorbrewer) + ("r-rcpp" ,r-rcpp) + ("r-rrcov" ,r-rrcov))) + (home-page "https://bioconductor.org/packages/openCyto") + (synopsis "Hierarchical gating pipeline for flow cytometry data") + (description + "This package is designed to facilitate the automated gating methods in a +sequential way to mimic the manual gating strategy.") + (license license:artistic2.0))) + (define-public r-flowsom (package (name "r-flowsom") -- cgit v1.2.3 From 7a62d5e0c233738b387bfa9544f741dad5823146 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 14:26:31 +0100 Subject: gnu: Add r-cytoml. * gnu/packages/bioconductor.scm (r-cytoml): New variable. --- gnu/packages/bioconductor.scm | 48 +++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 48 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 56d32ed0d9..73f415541a 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -40,6 +40,7 @@ #:use-module (gnu packages pkg-config) #:use-module (gnu packages statistics) #:use-module (gnu packages web) + #:use-module (gnu packages xml) #:use-module (srfi srfi-1)) @@ -5627,6 +5628,53 @@ package.") sequential way to mimic the manual gating strategy.") (license license:artistic2.0))) +(define-public r-cytoml + (package + (name "r-cytoml") + (version "1.12.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "CytoML" version)) + (sha256 + (base32 + "0m8x18wkvis85cawv7j07pk59w76wnzy93ia99gd24j82z4h97p1")))) + (properties `((upstream-name . "CytoML"))) + (build-system r-build-system) + (inputs + `(("libxml2" ,libxml2))) + (propagated-inputs + `(("r-base64enc" ,r-base64enc) + ("r-bh" ,r-bh) + ("r-biobase" ,r-biobase) + ("r-corpcor" ,r-corpcor) + ("r-cytolib" ,r-cytolib) + ("r-data-table" ,r-data-table) + ("r-dplyr" ,r-dplyr) + ("r-flowcore" ,r-flowcore) + ("r-flowworkspace" ,r-flowworkspace) + ("r-ggcyto" ,r-ggcyto) + ("r-graph" ,r-graph) + ("r-jsonlite" ,r-jsonlite) + ("r-lattice" ,r-lattice) + ("r-ncdfflow" ,r-ncdfflow) + ("r-opencyto" ,r-opencyto) + ("r-plyr" ,r-plyr) + ("r-rbgl" ,r-rbgl) + ("r-rcpp" ,r-rcpp) + ("r-rcppparallel" ,r-rcppparallel) + ("r-rgraphviz" ,r-rgraphviz) + ("r-rprotobuflib" ,r-rprotobuflib) + ("r-runit" ,r-runit) + ("r-xml" ,r-xml) + ("r-yaml" ,r-yaml))) + (home-page "https://github.com/RGLab/CytoML") + (synopsis "GatingML interface for cross platform cytometry data sharing") + (description + "This package provides an interface to implementations of the GatingML2.0 +standard to exchange gated cytometry data with other software platforms.") + (license license:artistic2.0))) + (define-public r-flowsom (package (name "r-flowsom") -- cgit v1.2.3 From 2c8433ca0a51d24b84af0942fdcc82934e2054a7 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 14:27:30 +0100 Subject: gnu: r-depecher: Update to 1.2.0. * gnu/packages/bioconductor.scm (r-depecher): Update to 1.2.0. [arguments]: Remove field. [propagated-inputs]: Remove r-biocparallel; add r-fnn and r-robustbase. --- gnu/packages/bioconductor.scm | 15 ++++----------- 1 file changed, 4 insertions(+), 11 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 73f415541a..48c0e27f61 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5748,29 +5748,21 @@ delete entire rows with missing data.") (define-public r-depecher (package (name "r-depecher") - (version "1.0.3") + (version "1.2.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DepecheR" version)) (sha256 (base32 - "0qj2h2a50fncppvi2phh0mbivxkn1mv702mqpi9mvvkf3bzq8m0h")))) + "1f6zbc0fq7xjflh3mkjx1n83mpppw663dj22rlpxzwp1kpmf6wm5")))) (properties `((upstream-name . "DepecheR"))) (build-system r-build-system) - (arguments - `(#:phases - (modify-phases %standard-phases - (add-after 'unpack 'fix-syntax-error - (lambda _ - (substitute* "src/Makevars" - ((" & ") " && ")) - #t))))) (propagated-inputs `(("r-beanplot" ,r-beanplot) - ("r-biocparallel" ,r-biocparallel) ("r-dosnow" ,r-dosnow) ("r-dplyr" ,r-dplyr) + ("r-fnn" ,r-fnn) ("r-foreach" ,r-foreach) ("r-ggplot2" ,r-ggplot2) ("r-gplots" ,r-gplots) @@ -5781,6 +5773,7 @@ delete entire rows with missing data.") ("r-rcpp" ,r-rcpp) ("r-rcppeigen" ,r-rcppeigen) ("r-reshape2" ,r-reshape2) + ("r-robustbase" ,r-robustbase) ("r-viridis" ,r-viridis))) (home-page "https://bioconductor.org/packages/DepecheR/") (synopsis "Identify traits of clusters in high-dimensional entities") -- cgit v1.2.3 From be5e4e96158dc9b7c8f283174a9144876c5d608a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 14:29:28 +0100 Subject: gnu: r-biocgenerics: Update to 0.32.0. * gnu/packages/bioconductor.scm (r-biocgenerics): 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 48c0e27f61..600812d462 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -903,13 +903,13 @@ of Bioconductor.") (define-public r-biocgenerics (package (name "r-biocgenerics") - (version "0.30.0") + (version "0.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocGenerics" version)) (sha256 (base32 - "1n87686bg5nmpqdpzwv1h551dkbxp9wk6wbmzpkgm71qxnk2yv9f")))) + "1np8y442zyakm4axpinbw1qsgc6wd3zjsnirbhc8lcii4ky9j0rn")))) (properties `((upstream-name . "BiocGenerics"))) (build-system r-build-system) -- cgit v1.2.3 From 5d87f1261536cdd0579c92243dc046b2693805f3 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 14:29:43 +0100 Subject: gnu: r-affycomp: Update to 1.62.0. * gnu/packages/bioconductor.scm (r-affycomp): 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 600812d462..3baa863a8d 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -923,14 +923,14 @@ packages.") (define-public r-affycomp (package (name "r-affycomp") - (version "1.60.0") + (version "1.62.0") (source (origin (method url-fetch) (uri (bioconductor-uri "affycomp" version)) (sha256 (base32 - "1nijqljg5r3qj1y6an0i58sby76hqacj3a3nvainxic4n5wlzh0n")))) + "0cl7c3m2lz2w8g2k7z7wjd0dyj0dkssvms99qpg8a1v3hx1xs6js")))) (properties `((upstream-name . "affycomp"))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase))) -- cgit v1.2.3 From c2fa63e9058d6c90cfe209bb65ee7abd59e6cc72 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 14:29:56 +0100 Subject: gnu: r-affycompatible: Update to 1.46.0. * gnu/packages/bioconductor.scm (r-affycompatible): Update to 1.46.0. --- 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 3baa863a8d..0a0b01ab40 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -944,14 +944,14 @@ measures for Affymetrix Oligonucleotide Arrays.") (define-public r-affycompatible (package (name "r-affycompatible") - (version "1.44.0") + (version "1.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AffyCompatible" version)) (sha256 (base32 - "1zi96qa6vkgwvvy5cn6c3p1kbfsaz74zsw2kjxarz5qs744f0xvs")))) + "10ahrdlifp1i7rd58zb10w75y5bnigs7xp5gv4fhb5y7p7dvb0ks")))) (properties `((upstream-name . "AffyCompatible"))) (build-system r-build-system) -- cgit v1.2.3 From f561421d0406f8e42250baab7323273346993144 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 14:30:10 +0100 Subject: gnu: r-affycontam: Update to 1.44.0. * gnu/packages/bioconductor.scm (r-affycontam): 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 0a0b01ab40..f26363d27f 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -972,14 +972,14 @@ Command Console} (AGCC)-compatible sample annotation files.") (define-public r-affycontam (package (name "r-affycontam") - (version "1.42.0") + (version "1.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "affyContam" version)) (sha256 (base32 - "0nzk1cm26rhmym753wyhn35hqnz5lvavi3i5qfgdvhxgjy3m1jgp")))) + "0yd1prgv5zfkg22ski73mvg96qknwz8v6ji6s4qy8p4wrqyj7b7l")))) (properties `((upstream-name . "affyContam"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 1693534f76264d6e4e6d472dae16f1c4547ed591 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 14:30:22 +0100 Subject: gnu: r-affycoretools: Update to 1.58.2. * gnu/packages/bioconductor.scm (r-affycoretools): Update to 1.58.2. --- 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 f26363d27f..f45adaf66a 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -997,14 +997,14 @@ problems in CEL-level data to help evaluate performance of quality metrics.") (define-public r-affycoretools (package (name "r-affycoretools") - (version "1.56.0") + (version "1.58.2") (source (origin (method url-fetch) (uri (bioconductor-uri "affycoretools" version)) (sha256 (base32 - "17dxpzhwwdwnxkdpmyjwdnacg41hw60mlc71w4nzlvs28sfsy09s")))) + "0cgy9phwdk4x9lr11xh6zs7v8r5xq959fmsmzwrpnd50dr7hzkvd")))) (properties `((upstream-name . "affycoretools"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From ce5162d09dc015d5be232290ff22e0e93d5d691c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 14:30:36 +0100 Subject: gnu: r-affxparser: Update to 1.58.0. * gnu/packages/bioconductor.scm (r-affxparser): 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 f45adaf66a..1ad29a773b 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1036,14 +1036,14 @@ to streamline the more common analyses that a Biostatistician might see.") (define-public r-affxparser (package (name "r-affxparser") - (version "1.56.0") + (version "1.58.0") (source (origin (method url-fetch) (uri (bioconductor-uri "affxparser" version)) (sha256 (base32 - "1jv7k9pn4c7szi3ma2f2xsd58pkrkvjpk5wra73r6kc607qgrv33")))) + "03h4lxr48p84f6i7zb2rm10ma3k4d1nmvdw5yhxcmzqbmd12lk40")))) (properties `((upstream-name . "affxparser"))) (build-system r-build-system) (home-page "https://github.com/HenrikBengtsson/affxparser") -- cgit v1.2.3 From 7a111924ee027266a448fae68e56bf2da6e5b525 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 14:30:49 +0100 Subject: gnu: r-annotate: Update to 1.64.0. * gnu/packages/bioconductor.scm (r-annotate): 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 1ad29a773b..530af292ff 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1064,14 +1064,14 @@ structure.") (define-public r-annotate (package (name "r-annotate") - (version "1.62.0") + (version "1.64.0") (source (origin (method url-fetch) (uri (bioconductor-uri "annotate" version)) (sha256 (base32 - "0hww0h4b7bv37mnjviazy247mnzj72z5linwm1gvljrgqv3bagcs")))) + "0rcmdy6hs6m4d6wxgi52c0bhdsbf2sm9f155qbcb05sn0nh8pxwy")))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) -- cgit v1.2.3 From ddd36739284e8afa6e13a43887a8fe2f1c63f9f6 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 14:31:02 +0100 Subject: gnu: r-hpar: Update to 1.28.0. * gnu/packages/bioconductor.scm (r-hpar): 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 530af292ff..f6b2fbb89f 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1091,14 +1091,14 @@ microarrays.") (define-public r-hpar (package (name "r-hpar") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "hpar" version)) (sha256 (base32 - "1mnld60nrn6qpb24sz2sy8vlw3wkhfc3z726gi67l8b5mdmkxgg5")))) + "1yhay1ryrgj9cqa1x136cw40ca93afyvg0sarm30jsbj8nc1rm5m")))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/hpar/") (synopsis "Human Protein Atlas in R") -- cgit v1.2.3 From 2e73ea955bedff76388748e576be320d27ba13a4 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 14:31:14 +0100 Subject: gnu: r-regioner: Update to 1.18.0. * gnu/packages/bioconductor.scm (r-regioner): 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 f6b2fbb89f..7834b680d3 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1109,14 +1109,14 @@ the Human Protein Atlas project.") (define-public r-regioner (package (name "r-regioner") - (version "1.16.5") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "regioneR" version)) (sha256 (base32 - "12x7sh5d8y549hqz4qjb2j3ak22l79w9l0vdbv4gn0bwi5206k8h")))) + "0m073hrqp62zpd2blnqm5ka539hcilir05m8av14vdhzhjzp13ya")))) (properties `((upstream-name . "regioneR"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 7ccbaf1b6e4998abab05e0056f06ac39881d0973 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 14:31:27 +0100 Subject: gnu: r-reportingtools: Update to 2.26.0. * gnu/packages/bioconductor.scm (r-reportingtools): 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 7834b680d3..ff703f26ed 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1138,14 +1138,14 @@ region sets and other genomic features.") (define-public r-reportingtools (package (name "r-reportingtools") - (version "2.24.0") + (version "2.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ReportingTools" version)) (sha256 (base32 - "16ska7mlacka0xi8x2icy8v42vaxccb3a1x73szmfvcrwr592qsc")))) + "0wmi2219wydyzc07rz3azsrksa7wiacfh9pr5x2fsmj9f0w3n15w")))) (properties `((upstream-name . "ReportingTools"))) (build-system r-build-system) -- cgit v1.2.3 From 7778e91a2d577ae0a8c1651a559ffe7516a25f96 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 14:31:40 +0100 Subject: gnu: r-geneplotter: Update to 1.64.0. * gnu/packages/bioconductor.scm (r-geneplotter): 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 ff703f26ed..4958093955 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1186,14 +1186,14 @@ browser.") (define-public r-geneplotter (package (name "r-geneplotter") - (version "1.62.0") + (version "1.64.0") (source (origin (method url-fetch) (uri (bioconductor-uri "geneplotter" version)) (sha256 (base32 - "0jlqs20mqr0wgmjgzkzaynp3cy1z3xjzpz7055c1qi42fhimmimb")))) + "1k6780fn1kkghpm1prhhsyw621441a3bmnqfl9ns0zbc1zdq39nx")))) (build-system r-build-system) (propagated-inputs `(("r-annotate" ,r-annotate) -- cgit v1.2.3 From 79820b9fe90c435e969583590f218ba76fa4162a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 14:31:53 +0100 Subject: gnu: r-oligoclasses: Update to 1.48.0. * gnu/packages/bioconductor.scm (r-oligoclasses): 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 4958093955..4d228804af 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1211,14 +1211,14 @@ browser.") (define-public r-oligoclasses (package (name "r-oligoclasses") - (version "1.46.0") + (version "1.48.0") (source (origin (method url-fetch) (uri (bioconductor-uri "oligoClasses" version)) (sha256 (base32 - "0z86zrmn80kcy6fgb9i9zs82vhim73n8hlkqy7y8sbb2jwksdr72")))) + "02m1m3dkiyywalphw3i5n6y3bs8zp24xh59v9cz6jgjpah811skf")))) (properties `((upstream-name . "oligoClasses"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 084c651cbf5a7086e810c0e8f9593b0bd27e32d0 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 14:32:05 +0100 Subject: gnu: r-oligo: Update to 1.50.0. * gnu/packages/bioconductor.scm (r-oligo): 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 4d228804af..4207047a5f 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1246,14 +1246,14 @@ packages.") (define-public r-oligo (package (name "r-oligo") - (version "1.48.0") + (version "1.50.0") (source (origin (method url-fetch) (uri (bioconductor-uri "oligo" version)) (sha256 (base32 - "0qkyz65zvry0syibjkvkshwijccna18jy0hlib0n5x4c8x9zs5df")))) + "01icfyy82f9k0m7ngrppz1ckq3wpq7zp6kgf8ppc55j6582c5jh3")))) (properties `((upstream-name . "oligo"))) (build-system r-build-system) (inputs `(("zlib" ,zlib))) -- cgit v1.2.3 From bcf711b58bef401d2f5ea10854c25ca6b0eb9025 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 14:32:17 +0100 Subject: gnu: r-qvalue: Update to 2.18.0. * gnu/packages/bioconductor.scm (r-qvalue): 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 4207047a5f..763159a36d 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1280,14 +1280,14 @@ Affymetrix (CEL files) and NimbleGen arrays (XYS files).") (define-public r-qvalue (package (name "r-qvalue") - (version "2.16.0") + (version "2.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "qvalue" version)) (sha256 (base32 - "00mahhwb4n2s6nycwkdkjs2qgyyyi7hyrby3qr269krprr6q3lh5")))) + "0njnidyncm3g3712mnp77cs4kghn596ss1pz6fhp1cr0wxcayp6j")))) (build-system r-build-system) (propagated-inputs `(("r-ggplot2" ,r-ggplot2) -- cgit v1.2.3 From 73883f0f146ecfdace9276010dcef20400343302 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 14:32:46 +0100 Subject: gnu: r-diffbind: Update to 2.14.0. * gnu/packages/bioconductor.scm (r-diffbind): 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 763159a36d..ff01e1e25f 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1309,14 +1309,14 @@ problems in genomics, brain imaging, astrophysics, and data mining.") (define-public r-diffbind (package (name "r-diffbind") - (version "2.12.0") + (version "2.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DiffBind" version)) (sha256 (base32 - "1ialb1j2xa21a8dzss76qky83rg8y6jwdwi0mhy8b088zvxavich")))) + "1729wyi2l4480yrkp5wg3ryirrmlk0j3njqs1qyckq3c8bjk12h2")))) (properties `((upstream-name . "DiffBind"))) (build-system r-build-system) (inputs -- cgit v1.2.3 From ba74434fc4f3159578b2b8123197e7a6c3c45bb1 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 14:32:58 +0100 Subject: gnu: r-ripseeker: Update to 1.26.0. * gnu/packages/bioconductor.scm (r-ripseeker): 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 ff01e1e25f..5a3819f6ef 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1354,14 +1354,14 @@ occupancy (overlap) analysis and plotting functions.") (define-public r-ripseeker (package (name "r-ripseeker") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RIPSeeker" version)) (sha256 (base32 - "0rfff4wal51iji0m74mgnrlcq6i41nq5b79mv5brv7mab3g0cv43")))) + "1wyv9mfrbxzklysfjcnwb8yils71janyyxa982jn0zxx4p9cl3vs")))) (properties `((upstream-name . "RIPSeeker"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 16d49c2a7c0d821b3fce11507fd4cd2fb74a95ed Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 14:33:13 +0100 Subject: gnu: r-multtest: Update to 2.42.0. * gnu/packages/bioconductor.scm (r-multtest): 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 5a3819f6ef..2812ef04d2 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1387,14 +1387,14 @@ processing to visualization and annotation.") (define-public r-multtest (package (name "r-multtest") - (version "2.40.0") + (version "2.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "multtest" version)) (sha256 (base32 - "0vy9wk1111qm69xy4r4n01b9rw60dsrcj2169jd45yiq63cdq7bv")))) + "0qna9lx76ldsfy8qf5xmhl4ymqfkj29m1gdqhph06s470c8mwari")))) (build-system r-build-system) (propagated-inputs `(("r-survival" ,r-survival) -- cgit v1.2.3 From 70eb483a28973b9795217d7c0932db1650319828 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 14:33:25 +0100 Subject: gnu: r-graph: Update to 1.64.0. * gnu/packages/bioconductor.scm (r-graph): 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 2812ef04d2..944613a792 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1425,13 +1425,13 @@ expressed genes in DNA microarray experiments.") (define-public r-graph (package (name "r-graph") - (version "1.62.0") + (version "1.64.0") (source (origin (method url-fetch) (uri (bioconductor-uri "graph" version)) (sha256 (base32 - "0rs81a8kp7nfzsfy2d11mlrjf4z156075p52wvz9nvi3vc6l348w")))) + "1ivf59k7k552m7zd8g3wwazd71dq3xmgmhcq435738i02h0fqnyc")))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics))) -- cgit v1.2.3 From cf8968d7e6c42dc85998c4640cfd3fa1f8df85de Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 14:33:38 +0100 Subject: gnu: r-chippeakanno: Update to 3.20.0. * gnu/packages/bioconductor.scm (r-chippeakanno): Update to 3.20.0. --- 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 944613a792..d816c25157 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1472,14 +1472,14 @@ determining dependencies between variables, code improvement suggestions.") (define-public r-chippeakanno (package (name "r-chippeakanno") - (version "3.18.2") + (version "3.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ChIPpeakAnno" version)) (sha256 (base32 - "0wzwdxvvr7wknz5jnan0wsp81c1gv4d2qx0mrb1yybqf4z068779")))) + "0hp3s3shnrb55cxvx9wrdl67wqw9f55gdgx7262s4mahpxjswfsa")))) (properties `((upstream-name . "ChIPpeakAnno"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From b6c2f098ba16d688696facb6a0cfe112409c91d9 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 14:33:50 +0100 Subject: gnu: r-marray: Update to 1.64.0. * gnu/packages/bioconductor.scm (r-marray): 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 d816c25157..02cdbb9d43 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1528,12 +1528,12 @@ enrichedGO (addGeneIDs).") (define-public r-marray (package (name "r-marray") - (version "1.62.0") + (version "1.64.0") (source (origin (method url-fetch) (uri (bioconductor-uri "marray" version)) (sha256 - (base32 "000745d7gxka8cx4jwxf0p128jk90dw6wi3y8dkrkyz2arkl29yz")))) + (base32 "1mbs9rk279hnm9yz34za3xz3hb88ll1d0abw4m2pgjgbh4kkhdrl")))) (build-system r-build-system) (propagated-inputs `(("r-limma" ,r-limma))) -- cgit v1.2.3 From 8341f7062e6a2a4fbb173074f3c413a54dbb73a0 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 14:34:02 +0100 Subject: gnu: r-cghbase: Update to 1.46.0. * gnu/packages/bioconductor.scm (r-cghbase): Update to 1.46.0. --- 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 02cdbb9d43..5c3f86b0cc 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1547,12 +1547,12 @@ normalization and quality checking.") (define-public r-cghbase (package (name "r-cghbase") - (version "1.44.0") + (version "1.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "CGHbase" version)) (sha256 - (base32 "0z9lvn5dxym6kc8ak5fsqkipv2p4z49va3cyz1ch8rw477k2iwvm")))) + (base32 "0136pk6pfwpiiy9vca4pgg4wh74jfb5ssglpdszzhamljpvg765x")))) (properties `((upstream-name . "CGHbase"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 8f2a4ea18b9d00e32592f746a5c134bcabe422cf Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 14:34:15 +0100 Subject: gnu: r-cghcall: Update to 2.48.0. * gnu/packages/bioconductor.scm (r-cghcall): 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 5c3f86b0cc..3fb412086f 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1567,12 +1567,12 @@ the @code{arrayCGH} packages.") (define-public r-cghcall (package (name "r-cghcall") - (version "2.46.0") + (version "2.48.0") (source (origin (method url-fetch) (uri (bioconductor-uri "CGHcall" version)) (sha256 - (base32 "13vzk4myizs94hyak4iyxdrqyxyq1g85hwsmd13892g8pww6ga93")))) + (base32 "1x8pz7zhw2nabik1vgdhlivndqvil3s7vnl5070k493v6gza0p3s")))) (properties `((upstream-name . "CGHcall"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 23ce5ad1d697b52854d5415c4049d85d9e76019e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 14:34:28 +0100 Subject: gnu: r-qdnaseq: Update to 1.22.0. * gnu/packages/bioconductor.scm (r-qdnaseq): Update to 1.22.0. [propagated-inputs]: Remove r-biocparallel; add r-future and r-future-apply. --- 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 3fb412086f..44a64b319c 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1590,20 +1590,21 @@ the @code{arrayCGH} packages.") (define-public r-qdnaseq (package (name "r-qdnaseq") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "QDNAseq" version)) (sha256 - (base32 "02afy5bpj35981q1qm59jx399hksk6a9v1jfwy7x888rn86gfcfz")))) + (base32 "0xcqdpv9a47zpxx0q9sif5y4s1yzx3pig0kywy961kh5xgl5bcrq")))) (properties `((upstream-name . "QDNAseq"))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) - ("r-biocparallel" ,r-biocparallel) ("r-cghbase" ,r-cghbase) ("r-cghcall" ,r-cghcall) ("r-dnacopy" ,r-dnacopy) + ("r-future" ,r-future) + ("r-future-apply" ,r-future-apply) ("r-genomicranges" ,r-genomicranges) ("r-iranges" ,r-iranges) ("r-matrixstats" ,r-matrixstats) -- cgit v1.2.3 From d77228232d7a95652eb04b8604c750b2b7b8906e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 14:34:52 +0100 Subject: gnu: r-bayseq: Update to 2.20.0. * gnu/packages/bioconductor.scm (r-bayseq): Update to 2.20.0. --- 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 44a64b319c..b938de7c0c 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1623,14 +1623,14 @@ respectively.") (define-public r-bayseq (package (name "r-bayseq") - (version "2.18.0") + (version "2.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "baySeq" version)) (sha256 (base32 - "13lm7n5zqw8yg5sqb92h6ppcnr0l32qdgmv7i16pn32fb6z41p0w")))) + "040s1d3756spyzblkyx2vcy7bn3vf87mhsp3is35yxkj55n3myjk")))) (properties `((upstream-name . "baySeq"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From b0897fbf950c61502ad70c413084802e99e275fc Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 14:35:04 +0100 Subject: gnu: r-chipcomp: Update to 1.16.0. * gnu/packages/bioconductor.scm (r-chipcomp): 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 b938de7c0c..cfef7df345 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1649,14 +1649,14 @@ more complex hypotheses) via empirical Bayesian methods.") (define-public r-chipcomp (package (name "r-chipcomp") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ChIPComp" version)) (sha256 (base32 - "0ragyl9dhg0ymgkh4z9d1cbwhbpcwh6x4985laaw6wmq2sjm732y")))) + "0wk0vvg6dk9wk60lzbadrnqar75dppvyr4hiwrhv9rhhah2mg2mg")))) (properties `((upstream-name . "ChIPComp"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 88af7049ea8e69166bb46941d8e1a3dcc46d7002 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 14:35:16 +0100 Subject: gnu: r-riboprofiling: Update to 1.16.0. * gnu/packages/bioconductor.scm (r-riboprofiling): 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 cfef7df345..23fe4af380 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1683,14 +1683,14 @@ datasets.") (define-public r-riboprofiling (package (name "r-riboprofiling") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RiboProfiling" version)) (sha256 (base32 - "1si8zkznm0slvghk786qsp0wd6sns6hggrnz88ww9fcfvsqvzsy9")))) + "0nfzyiq7cd6fs5agzl1zyfg8s631wi7kjngiyvd3vxlhi8wsjicx")))) (properties `((upstream-name . "RiboProfiling"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 595b6c9a89bd0a403e212326cf0b262ec60a09a2 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 14:35:29 +0100 Subject: gnu: r-riboseqr: Update to 1.20.0. * gnu/packages/bioconductor.scm (r-riboseqr): 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 23fe4af380..64e56deb5c 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1722,14 +1722,14 @@ assessment, principal component analysis on codon coverage.") (define-public r-riboseqr (package (name "r-riboseqr") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "riboSeqR" version)) (sha256 (base32 - "1d1v098w7fmnsmxfg3l7yndyyr7ajig00axiwg413lyg255is1ga")))) + "1jr7h64hyhyf9gf15lah6iqwyljfc8mraf9kya4lql6lcjjkjiqm")))) (properties `((upstream-name . "riboSeqR"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From bb841742ddae5313fd8ff1f6f9cdce2952bb810f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 14:35:41 +0100 Subject: gnu: r-interactionset: Update to 1.14.0. * gnu/packages/bioconductor.scm (r-interactionset): 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 64e56deb5c..1abd69ada5 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1750,14 +1750,14 @@ parsing of genetic sequencing data from ribosome profiling experiments.") (define-public r-interactionset (package (name "r-interactionset") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "InteractionSet" version)) (sha256 (base32 - "0djgfpp34l6w8mk5b8s4wh0l12s4nn0f9ifvc3dq4970f6hb55z6")))) + "0n2l95h56x5g68p10cap8p4x3a6vaph2hjlk09vmi3j48lrzb2kh")))) (properties `((upstream-name . "InteractionSet"))) (build-system r-build-system) -- cgit v1.2.3 From b701ed6e83242c25ff76851d68b949e1ef7351b8 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 14:35:53 +0100 Subject: gnu: r-genomicinteractions: Update to 1.20.0. * gnu/packages/bioconductor.scm (r-genomicinteractions): 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 1abd69ada5..c271a6e8be 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1782,14 +1782,14 @@ experiments.") (define-public r-genomicinteractions (package (name "r-genomicinteractions") - (version "1.18.1") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicInteractions" version)) (sha256 (base32 - "0hq2n5yfr9h2ayn10dy9lz08gd2q0awrm5cy2kqdmz4d8ss4r94p")))) + "10kwb70c9aq0bfqpq48h186lsbwgrg18m14r9z8x6n8l7cds5azc")))) (properties `((upstream-name . "GenomicInteractions"))) (build-system r-build-system) -- cgit v1.2.3 From b2b5b03115a2ec4bb93b178c4f567d30dafdb4cf Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 14:36:06 +0100 Subject: gnu: r-ctc: Update to 1.60.0. * gnu/packages/bioconductor.scm (r-ctc): Update to 1.60.0. --- 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 c271a6e8be..1ec4394b8e 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1821,14 +1821,14 @@ information and producing various plots and statistics.") (define-public r-ctc (package (name "r-ctc") - (version "1.58.0") + (version "1.60.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ctc" version)) (sha256 (base32 - "15n5b6i18x14km5rdqiydxcak5cr5dr3adwwwc5kcqf5gkwmi3am")))) + "0wh27izkyr1j26nznisw654mb5c94xpwjjkx7r6bhwg9ihxxcl6d")))) (build-system r-build-system) (propagated-inputs `(("r-amap" ,r-amap))) (home-page "https://bioconductor.org/packages/ctc/") -- cgit v1.2.3 From ab7f3cbbeb5e98e371c080f802807e54c5327641 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 14:36:17 +0100 Subject: gnu: r-goseq: Update to 1.38.0. * gnu/packages/bioconductor.scm (r-goseq): 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 1ec4394b8e..d16d3731d3 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1841,14 +1841,14 @@ trees and clusters to other programs.") (define-public r-goseq (package (name "r-goseq") - (version "1.36.0") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "goseq" version)) (sha256 (base32 - "0h8kd3d7yfdq8padfb0k92crwxi5h9gvgv4l3pa8k8wn4kczvciw")))) + "11ypa41qv1nx3cncxlwlbhdxqlwq95rb9byv2z3crrf9nfp24byv")))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) -- cgit v1.2.3 From 728571fbc65b39525c773382c08ed04653e8c5f6 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 14:36:30 +0100 Subject: gnu: r-glimma: Update to 1.14.0. * gnu/packages/bioconductor.scm (r-glimma): 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 d16d3731d3..c6cb1d4940 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1867,14 +1867,14 @@ defined categories which are over/under represented in RNA-seq data.") (define-public r-glimma (package (name "r-glimma") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Glimma" version)) (sha256 (base32 - "11qg5khqspxldfgg6p3xsxys472ab8wwi2snwc6bdxczv1f2p56x")))) + "1rjrqgl96iz4b3xqpc174wgz7bqmc8gbm9ljag0y27kz29fwng8r")))) (properties `((upstream-name . "Glimma"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 9c071144a85280443e05c14edbde5aa15a1e5a68 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 14:36:44 +0100 Subject: gnu: r-rots: Update to 1.14.0. * gnu/packages/bioconductor.scm (r-rots): 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 c6cb1d4940..e5e8b4a478 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1894,14 +1894,14 @@ information.") (define-public r-rots (package (name "r-rots") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ROTS" version)) (sha256 (base32 - "1j29pfyv2pn0wp544m5a568b3yd31kzavwwiwqylcjwvq5lfzy77")))) + "08mwlb0lpprys2b7vif8aj5bnprmn09mm79zz158gbhrv9j9d1qm")))) (properties `((upstream-name . "ROTS"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 565bb84b315420dad5032becf3b0272f1fc820bb Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 14:36:55 +0100 Subject: gnu: r-plgem: Update to 1.58.0. * gnu/packages/bioconductor.scm (r-plgem): 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 e5e8b4a478..c63fa60f50 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1918,14 +1918,14 @@ in omics data.") (define-public r-plgem (package (name "r-plgem") - (version "1.56.0") + (version "1.58.0") (source (origin (method url-fetch) (uri (bioconductor-uri "plgem" version)) (sha256 (base32 - "0y6gp5rlkvlv435qps7zhih84g5wrdvg6myj74ywnpl5a773nfqp")))) + "0fkyvcw2qxp4g527s9rzia45yapi0r6gbij7svisil8rbgfdp45v")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) -- cgit v1.2.3 From 74bb4cdf57f5de7fdcf7ccd29fc1334fd75d638b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 14:37:15 +0100 Subject: gnu: r-inspect: Update to 1.16.0. * gnu/packages/bioconductor.scm (r-inspect): Update to 1.16.0. [propagated-inputs]: Remove r-preprocesscore; add r-genomeinfodb and r-kernsmooth. --- 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 c63fa60f50..aa12fd66da 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1943,14 +1943,14 @@ genes or proteins in these datasets.") (define-public r-inspect (package (name "r-inspect") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "INSPEcT" version)) (sha256 (base32 - "1a7smljndiyahgpj6vl079pvi3n0rfk1vkdkp799y4nm2wnhn93r")))) + "043066zygf2y2jp6dvfwl56hkzcdvkmymhjx3gh4mhi48l71zqv9")))) (properties `((upstream-name . "INSPEcT"))) (build-system r-build-system) (propagated-inputs @@ -1959,12 +1959,13 @@ genes or proteins in these datasets.") ("r-biocparallel" ,r-biocparallel) ("r-deseq2" ,r-deseq2) ("r-desolve" ,r-desolve) + ("r-genomeinfodb" ,r-genomeinfodb) ("r-genomicalignments" ,r-genomicalignments) ("r-genomicfeatures" ,r-genomicfeatures) ("r-genomicranges" ,r-genomicranges) ("r-iranges" ,r-iranges) + ("r-kernsmooth" ,r-kernsmooth) ("r-plgem" ,r-plgem) - ("r-preprocesscore" ,r-preprocesscore) ("r-proc" ,r-proc) ("r-rootsolve" ,r-rootsolve) ("r-rsamtools" ,r-rsamtools) -- cgit v1.2.3 From 2d86dc2062a8ffbe8cc9168026780a0b3801121b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 14:37:41 +0100 Subject: gnu: r-dnabarcodes: Update to 1.16.0. * gnu/packages/bioconductor.scm (r-dnabarcodes): 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 aa12fd66da..87bdd78412 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1986,14 +1986,14 @@ modeling the rates that determines changes in mature mRNA levels.") (define-public r-dnabarcodes (package (name "r-dnabarcodes") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DNABarcodes" version)) (sha256 (base32 - "1a0c9ag9n41cs0da9lfvpkxf7n5vbrfypaygdv66mw73aibix6v0")))) + "0r2r9qc2qvf7rfl1h5ynvv3xd7n444zbc697s85qxqdpr4sxqmfd")))) (properties `((upstream-name . "DNABarcodes"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From efd0934733ab8e04572fc26a05d5bee52aa9802c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 14:37:54 +0100 Subject: gnu: r-ruvseq: Update to 1.20.0. * gnu/packages/bioconductor.scm (r-ruvseq): 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 87bdd78412..235c2aba00 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2013,14 +2013,14 @@ demultiplexed, i.e. assigned to their original reference barcode.") (define-public r-ruvseq (package (name "r-ruvseq") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RUVSeq" version)) (sha256 (base32 - "0ln4qc9d5r15zlhazx6annx97c0wrx3jqpcvk7yj1jnwh349lw33")))) + "1ipbbzpngx988lsmwqv7vbmqm65m43xvsmipayfppkrr6jipzxrj")))) (properties `((upstream-name . "RUVSeq"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 12e2aa96dceae5d09a2f5a3ffe25fdcf479f502a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 14:38:18 +0100 Subject: gnu: r-biocneighbors: Update to 1.4.1. * gnu/packages/bioconductor.scm (r-biocneighbors): Update to 1.4.1. [propagated-inputs]: Remove r-biocgenerics; add r-matrix. --- 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 235c2aba00..39eccc05b6 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2039,19 +2039,19 @@ samples.") (define-public r-biocneighbors (package (name "r-biocneighbors") - (version "1.2.0") + (version "1.4.1") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocNeighbors" version)) (sha256 (base32 - "08ak72y6mafzkhzfkx6b7waljpa0f1nxcrvyspd88sgzxgxjnkmg")))) + "05vi1cij37s8wgj92k3l6a3f3dwldj8jvijdp4695zczka6kypdf")))) (properties `((upstream-name . "BiocNeighbors"))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-biocparallel" ,r-biocparallel) + `(("r-biocparallel" ,r-biocparallel) + ("r-matrix" ,r-matrix) ("r-rcpp" ,r-rcpp) ("r-rcppannoy" ,r-rcppannoy) ("r-rcpphnsw" ,r-rcpphnsw) -- cgit v1.2.3 From c88448d4b81978111e2ded8e5af97196fafbf9da Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 14:38:42 +0100 Subject: gnu: r-biocsingular: Update to 1.2.0. * gnu/packages/bioconductor.scm (r-biocsingular): Update to 1.2.0. --- 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 39eccc05b6..494cd9ad5e 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2070,14 +2070,14 @@ achieved for all methods using the BiocParallel framework.") (define-public r-biocsingular (package (name "r-biocsingular") - (version "1.0.0") + (version "1.2.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocSingular" version)) (sha256 (base32 - "129z6bkdhm5wlvrjiwrr8yl2jj9chh4i6dm6firlj4c4ql3jp4f5")))) + "0qd7r2k56ym7ivjgapxbk7fyj2d7396f1ad1hkgnicgyw1an5q1r")))) (properties `((upstream-name . "BiocSingular"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 2e17cbd7333613ed81291f635133784243194e94 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 14:39:01 +0100 Subject: gnu: r-savr: Update to 1.24.0. * gnu/packages/bioconductor.scm (r-savr): 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 494cd9ad5e..fa89f3a060 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2136,14 +2136,14 @@ maps.") (define-public r-savr (package (name "r-savr") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "savR" version)) (sha256 (base32 - "101p0c07p49c50lfnbfanyyikdypmqkvwclqifq32js9phqwhf6h")))) + "1lsnqjl6qxbj0wai05qb2wrxrhxq5iarv2livmvwiwv70iigqygf")))) (properties `((upstream-name . "savR"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 84825e55236efeee648abefc5477c7ab78823be8 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 14:39:12 +0100 Subject: gnu: r-chipexoqual: Update to 1.10.0. * gnu/packages/bioconductor.scm (r-chipexoqual): 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 fa89f3a060..31e931ce25 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2162,14 +2162,14 @@ Viewer (SAV) files, access data, and generate QC plots.") (define-public r-chipexoqual (package (name "r-chipexoqual") - (version "1.8.0") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ChIPexoQual" version)) (sha256 (base32 - "02341i3lg74czgapf5qc6zvi2321af3rp85qavbg209fyc219acj")))) + "044n6kn16qczpdhp0w0z5x8xpr0rfs9s8q70rafgnvj7a2q1xdd0")))) (properties `((upstream-name . "ChIPexoQual"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From eb3fd3825c25fcc90af856e8d59d61a60870f2d6 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 14:39:26 +0100 Subject: gnu: r-copynumber: Update to 1.26.0. * gnu/packages/bioconductor.scm (r-copynumber): 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 31e931ce25..2fd26bd9ef 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2200,13 +2200,13 @@ sequencing data.") (define-public r-copynumber (package (name "r-copynumber") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "copynumber" version)) (sha256 (base32 - "0gmxi7w776pjqv3v0pkdihb167zzrnr9hw64yfvzgjhkhrc6a4rp")))) + "0r6r1adj20x3ckm0dlipxlf1rzngr92xsxxpy81mqxf4jpmyr8gj")))) (build-system r-build-system) (propagated-inputs `(("r-s4vectors" ,r-s4vectors) -- cgit v1.2.3 From bba70cda0a5b1e5a1db76807656ab1129e530fc2 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 14:39:38 +0100 Subject: gnu: r-dnacopy: Update to 1.60.0. * gnu/packages/bioconductor.scm (r-dnacopy): Update to 1.60.0. --- 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 2fd26bd9ef..a8385acbf8 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2223,14 +2223,14 @@ penalized least squares regression method.") (define-public r-dnacopy (package (name "r-dnacopy") - (version "1.58.0") + (version "1.60.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DNAcopy" version)) (sha256 (base32 - "1gybr3cbsrqjgz00n4l5kb2nrmh302xpvzk5zk957ijj5qbfwmxa")))) + "119z5lqhhw9ppg6s4dvbxk1kxf3wc55ibpm9b88c91s04yd7m9yw")))) (properties `((upstream-name . "DNAcopy"))) (build-system r-build-system) (native-inputs `(("gfortran" ,gfortran))) -- cgit v1.2.3 From 96030bf71882e964d3f526f806798a9825067e83 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 14:39:51 +0100 Subject: gnu: r-deds: Update to 1.60.0. * gnu/packages/bioconductor.scm (r-deds): Update to 1.60.0. --- 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 a8385acbf8..5892e7a23d 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2274,14 +2274,14 @@ clusters).") (define-public r-deds (package (name "r-deds") - (version "1.58.0") + (version "1.60.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DEDS" version)) (sha256 (base32 - "029g7wgxc7yp1cdyalbi8gipkskrgp7nyl1s2whhjy5dqpfcpigs")))) + "0vzsmah2lhxf8k6n4d0i4j609sbvygmb6ii2ridg9z3nskwkrhp8")))) (properties `((upstream-name . "DEDS"))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/DEDS/") -- cgit v1.2.3 From a9649c41380b59dea4800b3d256c3fda232f932a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 14:40:04 +0100 Subject: gnu: r-ebseq: Update to 1.26.0. * gnu/packages/bioconductor.scm (r-ebseq): 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 5892e7a23d..80828dd855 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2323,14 +2323,14 @@ and regression inferences from RNA-sequencing data.") (define-public r-ebseq (package (name "r-ebseq") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "EBSeq" version)) (sha256 (base32 - "13rf85gffqn86r5gqibla3gqrnnag2zinrfawpcsgn3fk7hl3v83")))) + "0ay1vcccpc29r3vinlnwp9256345bfb346kg2y11kib4bnrabjb6")))) (properties `((upstream-name . "EBSeq"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 153dc51bfe102bb7bb9034c8d5e25fd754c36c7f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 14:40:15 +0100 Subject: gnu: r-lpsymphony: Update to 1.14.0. * gnu/packages/bioconductor.scm (r-lpsymphony): 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 80828dd855..c788797bd8 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2347,14 +2347,14 @@ gene and isoform level using RNA-seq data") (define-public r-lpsymphony (package (name "r-lpsymphony") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "lpsymphony" version)) (sha256 (base32 - "13wvq4ip8nkyxmpncs6fzcf3vphra1n0fd5vz9kspbch0k1z6bsv")))) + "0j5j9kggh3l61vp6hpnqf45d5kzifksaj0sqhvs1zahmx2c1gfdv")))) (build-system r-build-system) (inputs `(("gfortran" ,gfortran) -- cgit v1.2.3 From 0383bd05cec997496d9c189d0ce5dae2beffb377 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 14:40:29 +0100 Subject: gnu: r-ihw: Update to 1.14.0. * gnu/packages/bioconductor.scm (r-ihw): 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 c788797bd8..f8686a6fa1 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2377,14 +2377,14 @@ to install interface to SYMPHONY.") (define-public r-ihw (package (name "r-ihw") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "IHW" version)) (sha256 (base32 - "05hs6w1albkbyqzkid0bchb5zs41f31a7vhfbcswryhc86cxwzkz")))) + "0rnw7r9pylpj3a5graavcpiqv2v67rv2a4dlcynkf4ihpxs4bg8x")))) (properties `((upstream-name . "IHW"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From a5cc1f104b0112656f920a40205d8666b1a6eacc Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 14:40:42 +0100 Subject: gnu: r-icobra: Update to 1.14.0. * gnu/packages/bioconductor.scm (r-icobra): 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 f8686a6fa1..40a71c9637 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2407,14 +2407,14 @@ independent of the p-value under the null hypothesis.") (define-public r-icobra (package (name "r-icobra") - (version "1.12.1") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "iCOBRA" version)) (sha256 (base32 - "1wj0vqyb6h4rddmn4va3182yap9bv4m1r1jlzyjfyrqxhl2sqb1q")))) + "1l0yr2grpwmr3pc5h50p1j4nxyb1ddmc55l7rhxpp4igh4fq1avz")))) (properties `((upstream-name . "iCOBRA"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From dc5237f85e4ad46ac72cdf5f45ef8ab8bd59f250 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 14:40:57 +0100 Subject: gnu: r-mast: Update to 1.12.0. * gnu/packages/bioconductor.scm (r-mast): Update to 1.12.0. [propagated-inputs]: Remove r-blme. --- 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 40a71c9637..bb082c9ddb 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2441,19 +2441,18 @@ interactive exploration of results.") (define-public r-mast (package (name "r-mast") - (version "1.10.0") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MAST" version)) (sha256 (base32 - "0f2qkp346095k9m45frpd3bivrvaps9wlm0m3n0z8j0aj7w1kqlx")))) + "1l78rrwkzyswpj6pgc9z8290fqrk4akba76invkkazpyh91r8gga")))) (properties `((upstream-name . "MAST"))) (build-system r-build-system) (propagated-inputs `(("r-abind" ,r-abind) - ("r-blme" ,r-blme) ("r-biobase" ,r-biobase) ("r-biocgenerics" ,r-biocgenerics) ("r-data-table" ,r-data-table) -- cgit v1.2.3 From 9732e690a5835096ff7110431f04ee0932768600 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 14:41:17 +0100 Subject: gnu: r-monocle: Update to 2.14.0. * gnu/packages/bioconductor.scm (r-monocle): 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 bb082c9ddb..635d008928 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2474,14 +2474,14 @@ single cell assay data.") (define-public r-monocle (package (name "r-monocle") - (version "2.12.0") + (version "2.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "monocle" version)) (sha256 (base32 - "1rnr3k0wc61a806w9flapni91wz5xm0l66jabjzx0vbiwgczs32z")))) + "18b9y592q48mbcp5w095qs1kaklq64v6dcnlpqhv3rwxvywygsz2")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) -- cgit v1.2.3 From 81a125cdb638b68f74ddc968d70a97e9e0e68668 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 14:41:29 +0100 Subject: gnu: r-noiseq: Update to 2.30.0. * gnu/packages/bioconductor.scm (r-noiseq): 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 635d008928..0874a4af1b 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2591,14 +2591,14 @@ qPCR data, but could be used with other types as well.") (define-public r-noiseq (package (name "r-noiseq") - (version "2.28.0") + (version "2.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "NOISeq" version)) (sha256 (base32 - "1k7k0xqa0lxj6mfsvbmd6x6glv9wynbwl87w5d3bilbq4dpc139j")))) + "1a8p66hhnwmay0rjabwq7356wr93yn33nqgr9rr7whpp9nls1hg4")))) (properties `((upstream-name . "NOISeq"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 2f223b21154fe0591d9d974069b309d46973212e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 14:41:43 +0100 Subject: gnu: r-scdd: Update to 1.10.0. * gnu/packages/bioconductor.scm (r-scdd): 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 0874a4af1b..350b79ba4d 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2618,14 +2618,14 @@ assumptions.") (define-public r-scdd (package (name "r-scdd") - (version "1.8.0") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "scDD" version)) (sha256 (base32 - "01hp6xxxap7541yi5dv596xvamqyyihvgkdy224ixa0n2cxyrhyf")))) + "0nk0qq664zs7dnlcamdkrrhvll01p7f96jj3igbxxlzj3dvr58w4")))) (properties `((upstream-name . "scDD"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 048a43d6a5a3840f8fb5888eb21a483dc2909d62 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 14:41:56 +0100 Subject: gnu: r-scone: Update to 1.10.0. * gnu/packages/bioconductor.scm (r-scone): 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 350b79ba4d..7dcc146ba1 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2654,14 +2654,14 @@ distributions.") (define-public r-scone (package (name "r-scone") - (version "1.8.0") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "scone" version)) (sha256 (base32 - "00cr0jp1ywxygf2pryw7mmcmn7cp1500fvifkbwgg2qxbkq5zqck")))) + "1hfsbnix0y9ad6bj0d8q2aw13pb3vjcaa0dfwxxapzl90zwbsjhp")))) (build-system r-build-system) (propagated-inputs `(("r-aroma-light" ,r-aroma-light) -- cgit v1.2.3 From db85744ef3400c47f0bfeaaa6c566601ab498ec5 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 14:42:18 +0100 Subject: gnu: r-geoquery: Update to 2.54.1. * gnu/packages/bioconductor.scm (r-geoquery): Update to 2.54.1. --- 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 7dcc146ba1..8c65afa403 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2694,14 +2694,14 @@ high-throughput analyses.") (define-public r-geoquery (package (name "r-geoquery") - (version "2.52.0") + (version "2.54.1") (source (origin (method url-fetch) (uri (bioconductor-uri "GEOquery" version)) (sha256 (base32 - "1r8x4jsl1mr9j7wyyqlj0zgwd80vkqhxxqrcgbb78ksryzq45jkr")))) + "0j8mlldy7dc38fx5zwj6z6l4b9bhvrn8sil3z8asnd4ic7w9ifx5")))) (properties `((upstream-name . "GEOquery"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 418d72142c0502179c10101833849c427457123a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 14:42:32 +0100 Subject: gnu: r-illuminaio: Update to 0.28.0. * gnu/packages/bioconductor.scm (r-illuminaio): Update to 0.28.0. --- 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 8c65afa403..bf1a5e5cc2 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2725,14 +2725,14 @@ the bridge between GEO and BioConductor.") (define-public r-illuminaio (package (name "r-illuminaio") - (version "0.26.0") + (version "0.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "illuminaio" version)) (sha256 (base32 - "18plm8p40gfzfmqflxssrdj8az3xvmnmh9i9dafl3af3bxwv03l8")))) + "1psza8jq6h8fv2rm91ah67dgjlnj1l80yracwgdl1agd0ycv90sh")))) (build-system r-build-system) (propagated-inputs `(("r-base64" ,r-base64))) -- cgit v1.2.3 From 3381dc4b5c11ca60ef9ae00164a8563fc3ba3bd4 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 14:57:50 +0100 Subject: gnu: r-mzr: Update to 2.20.0. * gnu/packages/bioinformatics.scm (r-mzr): Update to 2.20.0. --- 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 bdb3ff761b..abc83f3f84 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9202,14 +9202,14 @@ proteomics packages.") (define-public r-mzr (package (name "r-mzr") - (version "2.18.1") + (version "2.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "mzR" version)) (sha256 (base32 - "1pr1pcrg3r3pccm5ag6l8ic6rpqbk9jnlb9mm7g4ak5jwrajbzjq")) + "1cwd7phlc5jbx6r6cznyfbdpvcin5fvsaasbbi65zn0s92a80r13")) (modules '((guix build utils))) (snippet '(begin @@ -9231,7 +9231,7 @@ proteomics packages.") #t))))) (inputs `(;; Our default boost package won't work here, unfortunately, even with - ;; mzR version 2.18.1. + ;; mzR version 2.20.0. ("boost" ,boost-for-mysql) ; use this instead of the bundled boost sources ("zlib" ,zlib))) (propagated-inputs -- cgit v1.2.3 From d12328f9fe222d930f5e7ba5e71afc4c24f124bc Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 14:58:07 +0100 Subject: gnu: r-protgenerics: Update to 1.18.0. * gnu/packages/bioinformatics.scm (r-protgenerics): 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 abc83f3f84..cbb050c216 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9182,14 +9182,14 @@ as allowing spectra with different resolutions.") (define-public r-protgenerics (package (name "r-protgenerics") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ProtGenerics" version)) (sha256 (base32 - "12jjwmg58b4xbivxlw4pffq0qfi2c1c5hyrci0sfyphrc99fvx0i")))) + "1k1ggjgx2la8b21841a4ngkp6xfxwz0czv7x960r7i1jqif8y48z")))) (properties `((upstream-name . "ProtGenerics"))) (build-system r-build-system) (home-page "https://github.com/lgatto/ProtGenerics") -- cgit v1.2.3 From 2a6ce98b1721ac7655bac15057ef5ae021cefdfa Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 14:58:20 +0100 Subject: gnu: r-sva: Update to 3.34.0. * gnu/packages/bioinformatics.scm (r-sva): Update to 3.34.0. --- 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 cbb050c216..e340fbe484 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9072,14 +9072,14 @@ TAB-Seq.") (define-public r-sva (package (name "r-sva") - (version "3.32.1") + (version "3.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "sva" version)) (sha256 (base32 - "0jj6klfha5v5qmx2sjblf1an6s2zqd7mmgsp7sfmh4k2jpqi3jm9")))) + "1bzms6idx30s4nxl610zwa8rjxsyxb5pf3vxsdfmxg8j4pab9gh1")))) (build-system r-build-system) (propagated-inputs `(("r-genefilter" ,r-genefilter) -- cgit v1.2.3 From 065c305ca5e89c7b643e0a2342ff34bfb3be529e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 14:58:33 +0100 Subject: gnu: r-methylkit: Update to 1.12.0. * gnu/packages/bioinformatics.scm (r-methylkit): Update to 1.12.0. --- 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 e340fbe484..7b17e72f40 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9025,13 +9025,13 @@ number detection tools.") (define-public r-methylkit (package (name "r-methylkit") - (version "1.10.0") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "methylKit" version)) (sha256 (base32 - "1z687vpi5kwcqpnd6r74c5y72hcsbqlwg0bk95kksgpi81q710qj")))) + "0klwc0sbmrxj1lxbz16pl39rxjm0pi57gjw547hlgnac1p9fspzy")))) (properties `((upstream-name . "methylKit"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 51ca216bdf0c1a67205830996a88c0449dcc54f5 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 14:58:45 +0100 Subject: gnu: r-affyio: Update to 1.56.0. * gnu/packages/bioinformatics.scm (r-affyio): Update to 1.56.0. --- 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 7b17e72f40..4e8fd0fc65 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9256,14 +9256,14 @@ previously been used in XCMS.") (define-public r-affyio (package (name "r-affyio") - (version "1.54.0") + (version "1.56.0") (source (origin (method url-fetch) (uri (bioconductor-uri "affyio" version)) (sha256 (base32 - "1s78hm51fgac3i2j4bbdy0z6g14370154s6km8lldc9zpahx8b6p")))) + "0sbkadxdlx7qzxc8z8iv90y6j9b2f62mk3i54dijjh56x3hjy3hb")))) (build-system r-build-system) (propagated-inputs `(("r-zlibbioc" ,r-zlibbioc))) -- cgit v1.2.3 From 32f6059635b35152261b487e2d98028c1d902076 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 14:58:59 +0100 Subject: gnu: r-affy: Update to 1.64.0. * gnu/packages/bioinformatics.scm (r-affy): 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 4e8fd0fc65..89271ef17e 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9280,14 +9280,14 @@ CDF file formats.") (define-public r-affy (package (name "r-affy") - (version "1.62.0") + (version "1.64.0") (source (origin (method url-fetch) (uri (bioconductor-uri "affy" version)) (sha256 (base32 - "05vz0vf3472s1ivfhc0gc8yz98y4rvvp7cf6kfbxhy1b23im1bgk")))) + "131za66wbaz9y86gvjqcc2yd1f2ngl2b796xw726g75djhdgxgap")))) (build-system r-build-system) (propagated-inputs `(("r-affyio" ,r-affyio) -- cgit v1.2.3 From 746e1f062e8370c5e2fecba1e79d9518e9679796 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 14:59:12 +0100 Subject: gnu: r-copywriter: Update to 2.18.0. * gnu/packages/bioinformatics.scm (r-copywriter): 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 89271ef17e..51ae421da7 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8985,14 +8985,14 @@ GenomicRanges Bioconductor package.") (define-public r-copywriter (package (name "r-copywriter") - (version "2.16.0") + (version "2.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "CopywriteR" version)) (sha256 (base32 - "0kv3k58wyyicq1hhq7bddh0v3b2ksz6fa47skvnp8f193csza9g6")))) + "0llg1zpxg7qnvja5f5w1z1xic0jdg6zc4mfn97h2sm44skxxcyl1")))) (properties `((upstream-name . "CopywriteR"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 43058ca65681dd412eaa6a02a5fe1dfce0b76a0d Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 14:59:26 +0100 Subject: gnu: r-chipseq: Update to 1.36.0. * gnu/packages/bioinformatics.scm (r-chipseq): 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 51ae421da7..c58325d540 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8933,14 +8933,14 @@ common bioinformatics tools.") (define-public r-chipseq (package (name "r-chipseq") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "chipseq" version)) (sha256 (base32 - "1835nhrxcaqpqf1kxrsk1js8bf7x33z1n3bqjvm8404091acqyma")))) + "1ln6bn08xig3j6ryak1xfkjhvpnlm2vf1czz9hlj6f02299nbs6l")))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) -- cgit v1.2.3 From af87ac3aa76a2d7623ce84d7c1145e9631c438f8 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 14:59:38 +0100 Subject: gnu: r-annotationfilter: Update to 1.10.0. * gnu/packages/bioinformatics.scm (r-annotationfilter): Update to 1.10.0. --- 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 c58325d540..d554e4d4ca 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8628,13 +8628,13 @@ the available RAM.") (define-public r-annotationfilter (package (name "r-annotationfilter") - (version "1.8.0") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AnnotationFilter" version)) (sha256 (base32 - "15qh4jwxxqsnb308nxzj99gckfk18rhp8g26q1xwgkr57zc5kcrx")))) + "1l9sxhlvnwn6327vgg02h11ppmqr2zr07ff8wmcng0i1jbqwa8q5")))) (properties `((upstream-name . "AnnotationFilter"))) (build-system r-build-system) -- cgit v1.2.3 From dc9d4832b961c13f141a6de825e78c7888530c60 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 14:59:52 +0100 Subject: gnu: r-vsn: Update to 3.54.0. * gnu/packages/bioinformatics.scm (r-vsn): Update to 3.54.0. --- 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 d554e4d4ca..42dd4908be 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9308,14 +9308,14 @@ analysis.") (define-public r-vsn (package (name "r-vsn") - (version "3.52.0") + (version "3.54.0") (source (origin (method url-fetch) (uri (bioconductor-uri "vsn" version)) (sha256 (base32 - "1vqmyxg06kgq9m3w6n0jykqm4jgsjw879r4s216wlcq4xc94dh1r")))) + "1naqzb2m0km8fzr6chf9z71sisrwviy1fdi9b3hn4i8p18b4kqzh")))) (build-system r-build-system) (propagated-inputs `(("r-affy" ,r-affy) -- cgit v1.2.3 From 758dfc61ee5e042a9aaa746e4d432a2e0a7f49ce Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:00:07 +0100 Subject: gnu: r-mzid: Update to 1.24.0. * gnu/packages/bioinformatics.scm (r-mzid): 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 42dd4908be..ff37536095 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9342,14 +9342,14 @@ and specific in detecting differential transcription.") (define-public r-mzid (package (name "r-mzid") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "mzID" version)) (sha256 (base32 - "0vnyg7jlmy7ain7gmjwhqyqr664znrvrdlh7zd63563vhb87qarn")))) + "1glcv096bn6pxlw89dlij1nzpwnjvrbxysvw2gm6qgm7rhxlaxrw")))) (properties `((upstream-name . "mzID"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From c81ccd307608684c0732c852772d6221ac9b8245 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:00:29 +0100 Subject: gnu: r-delayedmatrixstats: Update to 1.8.0. * gnu/packages/bioinformatics.scm (r-delayedmatrixstats): Update to 1.8.0. --- 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 ff37536095..29d0bb84e2 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10683,14 +10683,14 @@ variable and significantly correlated genes.") (define-public r-delayedmatrixstats (package (name "r-delayedmatrixstats") - (version "1.6.1") + (version "1.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DelayedMatrixStats" version)) (sha256 (base32 - "1riyzfsq4bd513hidkw3cfkx3jywk3x87j89q70v459xsdfdc95b")))) + "0mv2rl6a6l404piabcazxz1s6ars016pxhjf5v40hhr6y1r0wbqy")))) (properties `((upstream-name . "DelayedMatrixStats"))) (build-system r-build-system) -- cgit v1.2.3 From 964634fa44b7476f1611e9ac201f937c50ba794a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:00:51 +0100 Subject: gnu: r-scran: Update to 1.14.5. * gnu/packages/bioinformatics.scm (r-scran): Update to 1.14.5. [propagated-inputs]: Remove r-dynamictreecut. --- 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 29d0bb84e2..8c1efae335 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10642,14 +10642,14 @@ quality control.") (define-public r-scran (package (name "r-scran") - (version "1.12.1") + (version "1.14.5") (source (origin (method url-fetch) (uri (bioconductor-uri "scran" version)) (sha256 (base32 - "17mknpkvs7mgnlbf2hv9k7rwbx2vlg60yrwfyb8nn3nxsb6vm7yn")))) + "0ydy6gvpgpvrs4ryk1qvmmxp6cpaizs294jwg42jawxndkds1l3y")))) (build-system r-build-system) (propagated-inputs `(("r-beachmat" ,r-beachmat) @@ -10661,7 +10661,6 @@ quality control.") ("r-delayedarray" ,r-delayedarray) ("r-delayedmatrixstats" ,r-delayedmatrixstats) ("r-dqrng" ,r-dqrng) - ("r-dynamictreecut" ,r-dynamictreecut) ("r-edger" ,r-edger) ("r-igraph" ,r-igraph) ("r-limma" ,r-limma) -- cgit v1.2.3 From bf23416fe1a3fecbadb195d31af1f27a2e2c7d7b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:01:21 +0100 Subject: gnu: r-scater: Update to 1.14.5. * gnu/packages/bioinformatics.scm (r-scater): Update to 1.14.5. [propagated-inputs]: Remove r-dplyr. --- 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 8c1efae335..fe42c4ee9b 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10607,13 +10607,13 @@ libraries.") (define-public r-scater (package (name "r-scater") - (version "1.12.2") + (version "1.14.5") (source (origin (method url-fetch) (uri (bioconductor-uri "scater" version)) (sha256 (base32 - "16a17161xlhh6qpna9qxph3anlc7ydgyrczmy4alfiw8si7pzmxa")))) + "1c2p1dqz4lckk657v5g0labxrf0i21l0wa3rvszslmrszn60mkif")))) (build-system r-build-system) (propagated-inputs `(("r-beachmat" ,r-beachmat) @@ -10623,7 +10623,6 @@ libraries.") ("r-biocsingular" ,r-biocsingular) ("r-delayedarray" ,r-delayedarray) ("r-delayedmatrixstats" ,r-delayedmatrixstats) - ("r-dplyr" ,r-dplyr) ("r-ggbeeswarm" ,r-ggbeeswarm) ("r-ggplot2" ,r-ggplot2) ("r-matrix" ,r-matrix) -- cgit v1.2.3 From 376f2f35b60d1a187e63811631367e21be9240ec Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:01:40 +0100 Subject: gnu: r-singlecellexperiment: Update to 1.8.0. * gnu/packages/bioinformatics.scm (r-singlecellexperiment): Update to 1.8.0. --- 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 fe42c4ee9b..dc15aa75a8 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10580,14 +10580,14 @@ matrices.") (define-public r-singlecellexperiment (package (name "r-singlecellexperiment") - (version "1.6.0") + (version "1.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "SingleCellExperiment" version)) (sha256 (base32 - "0m3yjnv1njb4gyzcjfk7a0lz2vgggp2wjz382gqrb0qhhwcgfkj5")))) + "11pqb3cigi9xbhxq2k3n7z23v1ibd03ws1lcrh5c5ffgb33nlyw5")))) (properties `((upstream-name . "SingleCellExperiment"))) (build-system r-build-system) -- cgit v1.2.3 From 8804e4b48e925c4f22bd2fa5b9e8a2b141274eea Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:01:53 +0100 Subject: gnu: r-beachmat: Update to 2.2.1. * gnu/packages/bioinformatics.scm (r-beachmat): Update to 2.2.1. [propagated-inputs]: Add r-matrix. --- 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 dc15aa75a8..95967fdff2 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10558,18 +10558,19 @@ packages.") (define-public r-beachmat (package (name "r-beachmat") - (version "2.0.0") + (version "2.2.1") (source (origin (method url-fetch) (uri (bioconductor-uri "beachmat" version)) (sha256 (base32 - "14cz19fw97s8mhm9r2n5li44vckx069k8nqsyy64c3lkfm4vy4zx")))) + "1bpnlw2kdy9yc2vq948k980r0j25ipb80llhvn0j3kxjiwyfgs3i")))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) - ("r-delayedarray" ,r-delayedarray))) + ("r-delayedarray" ,r-delayedarray) + ("r-matrix" ,r-matrix))) (home-page "https://bioconductor.org/packages/beachmat") (synopsis "Compiling Bioconductor to handle each matrix type") (description "This package provides a consistent C++ class interface for a -- cgit v1.2.3 From 1f5d262cfd7f00c950d698cc22390ea383d485e7 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:02:29 +0100 Subject: gnu: r-rhdf5lib: Update to 1.8.0. * gnu/packages/bioinformatics.scm (r-rhdf5lib): Update to 1.8.0. [arguments]: Update patches. --- gnu/packages/bioinformatics.scm | 24 ++++++++++++++++++------ 1 file changed, 18 insertions(+), 6 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 95967fdff2..743f593a13 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10487,14 +10487,14 @@ block processing.") (define-public r-rhdf5lib (package (name "r-rhdf5lib") - (version "1.6.3") + (version "1.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rhdf5lib" version)) (sha256 (base32 - "0q68n5jm7w99paibj8vkxbdksbyrxilzwc9dkp3zf8zrdc5qfxzy")) + "17lhwnm9rqsvbqkvwp0m07vjrk63a4389p2y39zffv8fgznxqzd7")) (modules '((guix build utils))) (snippet '(begin @@ -10511,10 +10511,14 @@ block processing.") (for-each delete-file '("configure" "configure.ac")) ;; Do not make other packages link with the proprietary libsz. (substitute* "R/zzz.R" - (("'%s/libhdf5_cpp.a %s/libhdf5.a %s/libsz.a -lz'") - "'%s/libhdf5_cpp.a %s/libhdf5.a %s/libhdf5.a -lz'") - (("'%s/libhdf5.a %s/libsz.a -lz'") - "'%s/libhdf5.a %s/libhdf5.a -lz'")) + (("'\"%s/libhdf5.a\" \"%s/libsz.a\" -lz'") + "'\"%s/libhdf5.a\" \"%s/libhdf5.a\" -lz'") + (("'\"%s/libhdf5_cpp.a\" \"%s/libhdf5.a\" \"%s/libsz.a\" -lz'") + "'\"%s/libhdf5_cpp.a\" \"%s/libhdf5.a\" \"%s/libhdf5.a\" -lz'") + (("'%s/libhdf5_hl.a %s/libhdf5.a %s/libsz.a -lz'") + "'%s/libhdf5_hl.a %s/libhdf5.a %s/libhdf5.a -lz'") + (("'%s/libhdf5_hl_cpp.a %s/libhdf5_hl.a %s/libhdf5_cpp.a %s/libhdf5.a %s/libsz.a -lz'") + "'%s/libhdf5_hl_cpp.a %s/libhdf5_hl.a %s/libhdf5_cpp.a %s/libhdf5.a %s/libhdf5.a -lz'")) (with-directory-excursion "src" (invoke "tar" "xvf" (assoc-ref inputs "hdf5-source")) (rename-file (string-append "hdf5-" ,(package-version hdf5-1.10)) @@ -10539,6 +10543,14 @@ block processing.") (assoc-ref inputs "hdf5") "/lib/libhdf5.a\n")) (("HDF5_CXX_INCLUDE=.*") "HDF5_CXX_INCLUDE=./hdf5/c++/src\n") (("HDF5_INCLUDE=.*") "HDF5_INCLUDE=./hdf5/src\n") + (("HDF5_HL_INCLUDE=.*") "HDF5_HL_INCLUDE=./hdf5/hl/src\n") + (("HDF5_HL_CXX_INCLUDE=.*") "HDF5_HL_CXX_INCLUDE=./hdf5/hl/c++/src\n") + (("HDF5_HL_LIB=.*") + (string-append "HDF5_HL_LIB=" + (assoc-ref inputs "hdf5") "/lib/libhdf5_hl.a\n")) + (("HDF5_HL_CXX_LIB=.*") + (string-append "HDF5_HL_CXX_LIB=" + (assoc-ref inputs "hdf5") "/lib/libhdf5_hl_cpp.a\n")) ;; szip is non-free software (("cp \"\\$\\{SZIP_LIB\\}.*") "") (("PKG_LIBS =.*") "PKG_LIBS = -lz -lhdf5\n"))) -- cgit v1.2.3 From 7557bd0cce20340929d8536399ef8bbcc1bb90c6 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:03:00 +0100 Subject: gnu: r-hdf5array: Update to 1.14.1. * gnu/packages/bioinformatics.scm (r-hdf5array): Update to 1.14.1. [propagated-inputs]: Add r-matrix. --- 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 743f593a13..669d8aa70b 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10458,14 +10458,14 @@ provided.") (define-public r-hdf5array (package (name "r-hdf5array") - (version "1.12.3") + (version "1.14.1") (source (origin (method url-fetch) (uri (bioconductor-uri "HDF5Array" version)) (sha256 (base32 - "1037j6f0yyw4cf6p051810qamxi1sji5w4d0fgq5lyzyl5d36fm6")))) + "04hd02zd5jix5p2zg10asmwjg1fynqgmclbhbmk7fb6arx5hm11f")))) (properties `((upstream-name . "HDF5Array"))) (build-system r-build-system) (inputs @@ -10474,6 +10474,7 @@ provided.") `(("r-biocgenerics" ,r-biocgenerics) ("r-delayedarray" ,r-delayedarray) ("r-iranges" ,r-iranges) + ("r-matrix" ,r-matrix) ("r-rhdf5" ,r-rhdf5) ("r-rhdf5lib" ,r-rhdf5lib) ("r-s4vectors" ,r-s4vectors))) -- cgit v1.2.3 From 8db291590065f13b45389008680b763b0612e7c3 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:03:18 +0100 Subject: gnu: r-fithic: Update to 1.12.0. * gnu/packages/bioinformatics.scm (r-fithic): Update to 1.12.0. --- 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 669d8aa70b..60b226e0fc 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10405,13 +10405,13 @@ visualizations for publication-quality multi-panel figures.") (define-public r-fithic (package (name "r-fithic") - (version "1.10.0") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "FitHiC" version)) (sha256 (base32 - "1qrxy4v8vmykrk8y6g3bs5wh5xhbs6pxyydbxy3vnj2mjirnxr6d")))) + "1irwkwi4afdj395134k31mvx7c2vpdd0rv8zrblnldascdsb04kc")))) (properties `((upstream-name . "FitHiC"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 0a1602124108d8985de31f14c28e01bf91807d8d Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:03:30 +0100 Subject: gnu: r-hitc: Update to 1.30.0. * gnu/packages/bioinformatics.scm (r-hitc): 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 60b226e0fc..6ec904e7b3 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10429,13 +10429,13 @@ assays such as Hi-C.") (define-public r-hitc (package (name "r-hitc") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "HiTC" version)) (sha256 (base32 - "059a1xxv2kb0bb32flymg2s8ylhavnv3j8l4125rfidagcgxgzjq")))) + "0byahi0fz0dzjyklz8v9whax9ygg7gwb4pl1j3zbl6z8a9qx8pps")))) (properties `((upstream-name . "HiTC"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 28329991b063692aabd21f0372fffd053766f292 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:03:41 +0100 Subject: gnu: r-gwascat: Update to 2.18.0. * gnu/packages/bioinformatics.scm (r-gwascat): 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 6ec904e7b3..37b35c5aec 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10352,14 +10352,14 @@ with your data.") (define-public r-gwascat (package (name "r-gwascat") - (version "2.16.1") + (version "2.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "gwascat" version)) (sha256 (base32 - "0d4krqx8zjniwp6k2vzwqgfws39w03x51kqiwd5dks1fp05sw4xh")))) + "038vhfsk2vs7inn5di093cmjbb81k7j0af385sg7l01jj70bdqq1")))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) -- cgit v1.2.3 From 2e13f10e8901e6c20cd942c80a5b9b516cc2bc48 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:03:53 +0100 Subject: gnu: r-sushi: Update to 1.24.0. * gnu/packages/bioinformatics.scm (r-sushi): 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 37b35c5aec..7d1082061d 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10383,13 +10383,13 @@ EMBL-EBI GWAS catalog.") (define-public r-sushi (package (name "r-sushi") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Sushi" version)) (sha256 (base32 - "1hgh3jfcx0bh3fyvp85v7435hvsk3ah1hxx5117ss93v03iwjf1g")))) + "15xng21hd09fb234ravrry3b872zg82w8x9lijxab9n96xihcpz5")))) (properties `((upstream-name . "Sushi"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From d57b6b4bae0d8df17926f77116f292be377a69d3 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:04:06 +0100 Subject: gnu: r-gviz: Update to 1.30.0. * gnu/packages/bioinformatics.scm (r-gviz): 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 7d1082061d..4c3b3a34ca 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10306,14 +10306,14 @@ family of feature/genome hypotheses.") (define-public r-gviz (package (name "r-gviz") - (version "1.28.3") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Gviz" version)) (sha256 (base32 - "0347r1ly0vzpilflzbyzsjdf4cday294lw3fxzx61clblrmws1ki")))) + "1p7n4yc77272rd8ybsim3rcg6kf6wmc95pwwav40b754imxn263z")))) (properties `((upstream-name . "Gviz"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From cfa93a30b4981dbce9b41f172dcea6ec9f56098d Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:04:18 +0100 Subject: gnu: r-gqtlstats: Update to 1.18.0. * gnu/packages/bioinformatics.scm (r-gqtlstats): 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 4c3b3a34ca..e78e3fad10 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10252,14 +10252,14 @@ defining LD blocks.") (define-public r-gqtlstats (package (name "r-gqtlstats") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "gQTLstats" version)) (sha256 (base32 - "17xadfn8qh1pwzlpcbds5wrjr9bzhsnmv90wffxmp02hq20qkrh5")))) + "1dly4p9r4231hf31xg1nzqiyvjbcfjljfmhb88ic1jxwnvniyv2f")))) (properties `((upstream-name . "gQTLstats"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 6fff104191651c8d506b793c050ead5cdb85c6de Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:04:35 +0100 Subject: gnu: r-ldblock: Update to 1.16.0. * gnu/packages/bioinformatics.scm (r-ldblock): Update to 1.16.0. [propagated-inputs]: Remove r-go-db and r-homo-sapiens. --- gnu/packages/bioinformatics.scm | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index e78e3fad10..6ac1f37bdd 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10218,14 +10218,14 @@ by Ernst and Kellis.") (define-public r-ldblock (package (name "r-ldblock") - (version "1.14.3") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ldblock" version)) (sha256 (base32 - "154yvrvs8ik7ifcny1681cmqra0i163j00k4vbvkvl701p5gsp5q")))) + "0xpigfidmylfawy6vzshqnsw1lzjs4qms8q7zffij6bkvkv7920x")))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) @@ -10233,8 +10233,6 @@ by Ernst and Kellis.") ("r-ensembldb" ,r-ensembldb) ("r-genomeinfodb" ,r-genomeinfodb) ("r-genomicfiles" ,r-genomicfiles) - ("r-go-db" ,r-go-db) - ("r-homo-sapiens" ,r-homo-sapiens) ("r-httr" ,r-httr) ("r-matrix" ,r-matrix) ("r-rsamtools" ,r-rsamtools) -- cgit v1.2.3 From 14eb0978a8b24b329bbb1bbda87e01b243ab9f6f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:04:55 +0100 Subject: gnu: r-snpstats: Update to 1.36.0. * gnu/packages/bioinformatics.scm (r-snpstats): 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 6ac1f37bdd..18bc7d021c 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10121,14 +10121,14 @@ and more.") (define-public r-snpstats (package (name "r-snpstats") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "snpStats" version)) (sha256 (base32 - "0drfd24a5pkrhzmpidlh717bgh2dm68mpn6vj1vlpkilfbkifl34")))) + "1xq1rjljg70h5mshdza56dis0iv1a20sivs6dav3w5jbdd1l5qkh")))) (properties `((upstream-name . "snpStats"))) (build-system r-build-system) (inputs `(("zlib" ,zlib))) -- cgit v1.2.3 From 67d4fd523ddfae27a99ad63d43882869b66f7ec5 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:05:07 +0100 Subject: gnu: r-erma: Update to 1.2.0. * gnu/packages/bioinformatics.scm (r-erma): Update to 1.2.0. --- 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 18bc7d021c..a7450284ba 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10180,14 +10180,14 @@ several related annotation packages.") (define-public r-erma (package (name "r-erma") - (version "1.0.0") + (version "1.2.0") (source (origin (method url-fetch) (uri (bioconductor-uri "erma" version)) (sha256 (base32 - "0j7ggp63m5y88cxgi49vcql1s1avzifwvvd2hydj4lj3yrmzib48")))) + "085qsr73p8nyp435f15l4l1jkfd64bfd9gl4z496nfxdnqn95srz")))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) -- cgit v1.2.3 From 89a41696abb3e1d4c2e9ab61d588780b30e537d6 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:05:19 +0100 Subject: gnu: r-gqtlbase: Update to 1.18.0. * gnu/packages/bioinformatics.scm (r-gqtlbase): 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 a7450284ba..b862cb706f 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10086,14 +10086,14 @@ organisms via the @code{g:Profiler} toolkit.") (define-public r-gqtlbase (package (name "r-gqtlbase") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "gQTLBase" version)) (sha256 (base32 - "1n2cizb88g2ankngvhxv377gizg80y3fhlx67sgm0z4ilm6a30ql")))) + "1qr8dqjbmj1mdjbzbnxwzfrm8f02wqfsgic8ws5kv7pmsby63y4x")))) (properties `((upstream-name . "gQTLBase"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 81600df30206833b68799a324a574f0b3390006f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:05:32 +0100 Subject: gnu: r-ggbio: Update to 1.34.0. * gnu/packages/bioinformatics.scm (r-ggbio): 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 b862cb706f..983de2f894 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9999,14 +9999,14 @@ effort and encourages consistency.") (define-public r-ggbio (package (name "r-ggbio") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ggbio" version)) (sha256 (base32 - "10s6hnffnrrsx3896adqdc5g55fzd5y6qhnp1mq0c641nw833rwd")))) + "13wzwh40anh8l53yp19bg4w5cpxykcaf228dc8cxvjndyib711qb")))) (build-system r-build-system) (arguments `(#:phases -- cgit v1.2.3 From 866810e68609a39344a4ccd613ffcedc9d7dc921 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:05:43 +0100 Subject: gnu: r-biovizbase: Update to 1.34.1. * gnu/packages/bioinformatics.scm (r-biovizbase): Update to 1.34.1. --- 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 983de2f894..1e1c2fa015 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9957,14 +9957,14 @@ the fact that each of these packages implements a select methods.") (define-public r-biovizbase (package (name "r-biovizbase") - (version "1.32.0") + (version "1.34.1") (source (origin (method url-fetch) (uri (bioconductor-uri "biovizBase" version)) (sha256 (base32 - "1lba1801ak0a4vz6f8jffp9d525q27p0dhi2bp4f68mvdwwl2994")))) + "04vvj907bgs67w8rb7n1haf80p6cd0qj5fdxw0dwryb455y35vir")))) (properties `((upstream-name . "biovizBase"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From e89032667d059a2b23f7a68f587b813eb7ba1b5f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:05:54 +0100 Subject: gnu: r-organismdbi: Update to 1.28.0. * gnu/packages/bioinformatics.scm (r-organismdbi): 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 1e1c2fa015..3a306656f9 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9925,14 +9925,14 @@ chromosome region or transcript models of lincRNA genes.") (define-public r-organismdbi (package (name "r-organismdbi") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "OrganismDbi" version)) (sha256 (base32 - "14azk69pmwlhza0mhsxigsg127w3mgsx9hhrbdcdqmy3vzfbfaqq")))) + "1bvfyh733mhka9zd00hrzpalgjs255c2blnxyf60ipzk5jg7yllb")))) (properties `((upstream-name . "OrganismDbi"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From e107f3df54e74ada7f25d522cf62286bcf5e8660 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:06:06 +0100 Subject: gnu: r-ensembldb: Update to 2.10.2. * gnu/packages/bioinformatics.scm (r-ensembldb): Update to 2.10.2. --- 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 3a306656f9..87c32ad922 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9882,14 +9882,14 @@ originally made available by Holmes, Harris, and Quince, 2012, PLoS ONE 7(2): (define-public r-ensembldb (package (name "r-ensembldb") - (version "2.8.1") + (version "2.10.2") (source (origin (method url-fetch) (uri (bioconductor-uri "ensembldb" version)) (sha256 (base32 - "103z902104ljdp6s9y2dmgrl5wkdz8vvlbbqgk8r4drkg7m3d4lj")))) + "02lnpyp85zchmz404hr5381zmihvq4x9zgxdrbn2afi352vg0vab")))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) -- cgit v1.2.3 From 2edb116c1ca4abaa8cc0d3d2db0e594ce3e842d3 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:06:17 +0100 Subject: gnu: r-dirichletmultinomial: Update to 1.28.0. * gnu/packages/bioinformatics.scm (r-dirichletmultinomial): 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 87c32ad922..e423081106 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9853,14 +9853,14 @@ self-defined annotation graphics.") (define-public r-dirichletmultinomial (package (name "r-dirichletmultinomial") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DirichletMultinomial" version)) (sha256 (base32 - "0qirvhnbv4wd50ln4pqbk4dj6h2935ipf9p4sw1x62qqhwxidqk4")))) + "0knmncmkkf2ypyqfcl5s8nmyyf9nrzkqprzn9w3w8182c0v49r0s")))) (properties `((upstream-name . "DirichletMultinomial"))) (build-system r-build-system) -- cgit v1.2.3 From dac706c3221ff190acd66108fb15787f87322044 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:06:28 +0100 Subject: gnu: r-complexheatmap: Update to 2.2.0. * gnu/packages/bioinformatics.scm (r-complexheatmap): Update to 2.2.0. --- 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 e423081106..9851c30e08 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9821,14 +9821,14 @@ provide added flexibility for data combination and manipulation.") (define-public r-complexheatmap (package (name "r-complexheatmap") - (version "2.0.0") + (version "2.2.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ComplexHeatmap" version)) (sha256 (base32 - "1imnb72r10csl2h12sckic7hcsb8v2z0y3dyw1ax2fpykmsmq776")))) + "1pj6a6rmqckk033pkklk6hr4066rzavamy6w194rfdhind90rk0p")))) (properties `((upstream-name . "ComplexHeatmap"))) (build-system r-build-system) -- cgit v1.2.3 From 48c7ee93b73ff20c08624635b94c1fa9bce405c4 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:06:39 +0100 Subject: gnu: r-genomicfiles: Update to 1.22.0. * gnu/packages/bioinformatics.scm (r-genomicfiles): 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 9851c30e08..01cd91ceb1 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9788,14 +9788,14 @@ analysis using other methods.") (define-public r-genomicfiles (package (name "r-genomicfiles") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicFiles" version)) (sha256 (base32 - "122g0yhpsm6fyvv38agp57clagl13h324rk06mlgb2xz104a1j4i")))) + "1x6q827ms2l5lwzha1vsgfrshh35n9f19jq57xagrqlafxgpz86s")))) (properties `((upstream-name . "GenomicFiles"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From b342b20a24429b1c5e28ca598c52beac1428d24e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:06:53 +0100 Subject: gnu: r-gage: Update to 2.36.0. * gnu/packages/bioinformatics.scm (r-gage): Update to 2.36.0. --- 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 01cd91ceb1..2ef86dae9e 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9759,14 +9759,14 @@ microarrays or GRanges for sequencing data.") (define-public r-gage (package (name "r-gage") - (version "2.34.0") + (version "2.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "gage" version)) (sha256 (base32 - "08d5yg7n4rx4xsginc8bx0sycpj06pi1k7i44ff757444p20srwq")))) + "1qxfmg0id19iy3ia8h5nrvk3d1azqb28kl7m08i23654wb6b45c6")))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) -- cgit v1.2.3 From fedba48bb54a94f29054a553e45bca8fb9b460d9 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:07:05 +0100 Subject: gnu: r-keggrest: Update to 1.26.1. * gnu/packages/bioinformatics.scm (r-keggrest): Update to 1.26.1. --- 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 2ef86dae9e..25f50b99af 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9735,14 +9735,14 @@ microarrays or GRanges for sequencing data.") (define-public r-keggrest (package (name "r-keggrest") - (version "1.24.1") + (version "1.26.1") (source (origin (method url-fetch) (uri (bioconductor-uri "KEGGREST" version)) (sha256 (base32 - "0yxp3iajdy61q6mjgp1nxdgmf2yb58cvqmdgab7lqxr0ky1wkfkr")))) + "1cgjvv9n88y3ah21356mh8z2l08vjn42hjy8hcljsibknzc4v247")))) (properties `((upstream-name . "KEGGREST"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From c21bf901e284af219029a209b3261fe8d9c98cf2 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:07:17 +0100 Subject: gnu: r-fastseg: Update to 1.32.0. * gnu/packages/bioinformatics.scm (r-fastseg): 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 25f50b99af..03e189eec5 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9705,14 +9705,14 @@ by the user, helping with quick and reproducible access.") (define-public r-fastseg (package (name "r-fastseg") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "fastseg" version)) (sha256 (base32 - "03gggz29nf8kyy9clkifqr0xm8v0yb0kl0gjfb5c0vrjmwkfqvdf")))) + "1cys6frmbizc8bf933mwvvnr31sfya9ahcc0wm66pbd1x3mygkmk")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) -- cgit v1.2.3 From 6339ea22f1674466b00161bab259f1288c28b1bb Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:07:34 +0100 Subject: gnu: r-annotationhub: Update to 2.18.0. * gnu/packages/bioinformatics.scm (r-annotationhub): Update to 2.18.0. [propagated-inputs]: Add r-biocversion. --- 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 03e189eec5..9ac2c5a946 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9667,14 +9667,14 @@ Shiny-based display methods for Bioconductor objects.") (define-public r-annotationhub (package (name "r-annotationhub") - (version "2.16.1") + (version "2.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AnnotationHub" version)) (sha256 (base32 - "0c773cmhng907839f0bq161jky7362lxxny36ac55qxiz1giqi8j")))) + "19vj3bk8jz68q84g3j8xs1s9bqz90lbwbciig1h45zvn2zc6087m")))) (properties `((upstream-name . "AnnotationHub"))) (build-system r-build-system) (propagated-inputs @@ -9682,6 +9682,7 @@ Shiny-based display methods for Bioconductor objects.") ("r-biocfilecache" ,r-biocfilecache) ("r-biocgenerics" ,r-biocgenerics) ("r-biocmanager" ,r-biocmanager) + ("r-biocversion" ,r-biocversion) ("r-curl" ,r-curl) ("r-dplyr" ,r-dplyr) ("r-httr" ,r-httr) -- cgit v1.2.3 From 2beffcb5585a860b2144807fbbdc92bbb00dbd86 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:07:52 +0100 Subject: gnu: r-interactivedisplaybase: Update to 1.24.0. * gnu/packages/bioinformatics.scm (r-interactivedisplaybase): 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 9ac2c5a946..2427fb3bfe 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9643,14 +9643,14 @@ global-scaling and full-quantile normalization.") (define-public r-interactivedisplaybase (package (name "r-interactivedisplaybase") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "interactiveDisplayBase" version)) (sha256 (base32 - "1kkyv7hkygacmksvld9gs3ycf6wlblqcwi11nny0hq3l0ha265v5")))) + "0zwf3ma6wf4zypl6bgjp0n72k2hmp0g16gzl4v3y4157rxcbpl0n")))) (properties `((upstream-name . "interactiveDisplayBase"))) (build-system r-build-system) -- cgit v1.2.3 From 0a6704e226e58ef4d117177046af8d4499cba943 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:08:03 +0100 Subject: gnu: r-edaseq: Update to 2.20.0. * gnu/packages/bioinformatics.scm (r-edaseq): Update to 2.20.0. --- 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 2427fb3bfe..fd2ac20dad 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9604,14 +9604,14 @@ distribution.") (define-public r-edaseq (package (name "r-edaseq") - (version "2.18.0") + (version "2.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "EDASeq" version)) (sha256 (base32 - "0mmc9bij17w4mfwcc566zbj5fvqgl8gfqs0qvj6ri4mbcql9jxb3")))) + "19mgzbv8yxgvw86wpq401l27q55ygawlngl775yavwccz1zbhjnj")))) (properties `((upstream-name . "EDASeq"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 783bbe3aceb80cb9b0feec2bf3e11ca36ccbf589 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:08:13 +0100 Subject: gnu: r-deseq: Update to 1.38.0. * gnu/packages/bioinformatics.scm (r-deseq): 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 fd2ac20dad..e4b26e753e 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9573,14 +9573,14 @@ classes.") (define-public r-deseq (package (name "r-deseq") - (version "1.36.0") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DESeq" version)) (sha256 (base32 - "0jppqrikg9qfqcfw5qd3m5c7bag9g23bc0kcpk5zfkk1wv09mnlm")))) + "14pys93gsl50xmq5pc7pp1g20v3ywlg0yzkkhwb3kiy8573xn9nc")))) (properties `((upstream-name . "DESeq"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 3ccf1e3c20cef02b578e8db0ad4e8de1f0a6d7f7 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:08:24 +0100 Subject: gnu: r-aroma-light: Update to 3.16.0. * gnu/packages/bioinformatics.scm (r-aroma-light): Update to 3.16.0. --- 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 e4b26e753e..0bae0a5a39 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9546,14 +9546,14 @@ discovery of differentially expressed genes and markers.") (define-public r-aroma-light (package (name "r-aroma-light") - (version "3.14.0") + (version "3.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "aroma.light" version)) (sha256 (base32 - "0a1prl4jhbqpa85i2vyia1ks9iippzl8np50fvm9wx8kbjxna5l6")))) + "0cgdg650j4dl0b45pwaw49ib97dwjazrv9sqzkygrjmcnnfxry8x")))) (properties `((upstream-name . "aroma.light"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 597aeb8a345ae42234f8c01816c0a95ef12126ba Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:08:35 +0100 Subject: gnu: r-msnid: Update to 1.20.0. * gnu/packages/bioinformatics.scm (r-msnid): 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 0bae0a5a39..bd48d2bb1f 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9445,14 +9445,14 @@ of mass spectrometry based proteomics data.") (define-public r-msnid (package (name "r-msnid") - (version "1.18.1") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MSnID" version)) (sha256 (base32 - "1n49l5mjdz7p4g2nwsbhm1jcj42sv6lsriq77n2imvacsvk0qfmb")))) + "0m71f2y12hmwvng45kzz4r4qrgc2jbd7j9gprmw8y5laawpdaifg")))) (properties `((upstream-name . "MSnID"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 589939937de29d40c2e0ef03abf83fdd9a64546e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:08:45 +0100 Subject: gnu: r-msnbase: Update to 2.12.0. * gnu/packages/bioinformatics.scm (r-msnbase): Update to 2.12.0. --- 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 bd48d2bb1f..5a209e0389 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9402,14 +9402,14 @@ structure (pcaRes) to provide a common interface to the PCA results.") (define-public r-msnbase (package (name "r-msnbase") - (version "2.10.1") + (version "2.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MSnbase" version)) (sha256 (base32 - "0z63yqazkycq0zbbarq9ida6al35hv3g7g9g7s7bss4gh0hk7lhd")))) + "1z889xkfphqqmv31i8hh5xqyclv660ic26rfck5bjpgk3s2zzwi6")))) (properties `((upstream-name . "MSnbase"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 4e5c21768403e71970822deedc2f8413a672c19f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:08:55 +0100 Subject: gnu: r-pcamethods: Update to 1.78.0. * gnu/packages/bioinformatics.scm (r-pcamethods): Update to 1.78.0. --- 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 5a209e0389..63574b9b22 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9372,14 +9372,14 @@ specific parser.") (define-public r-pcamethods (package (name "r-pcamethods") - (version "1.76.0") + (version "1.78.0") (source (origin (method url-fetch) (uri (bioconductor-uri "pcaMethods" version)) (sha256 (base32 - "0svf4n7l0afy4wwgs6x8x4dm330r3311l5vmsxw2f0r4axkh3bzk")))) + "1wir67kfjm0m9gf0ki8qmvh45n4gx2k0wfl9pd1hp4g62fbrj1pj")))) (properties `((upstream-name . "pcaMethods"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 126539d1ae060c7f312ad60811b0c9814818acac Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:09:06 +0100 Subject: gnu: r-rhdf5: Update to 2.30.1. * gnu/packages/bioinformatics.scm (r-rhdf5): Update to 2.30.1. --- 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 63574b9b22..b6217e2a74 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8601,13 +8601,13 @@ of gene-level counts.") (define-public r-rhdf5 (package (name "r-rhdf5") - (version "2.28.1") + (version "2.30.1") (source (origin (method url-fetch) (uri (bioconductor-uri "rhdf5" version)) (sha256 (base32 - "027cv1kh3xl66lrrahv2jgfmvgcwfpcj9dpgdj5fd9ybf5nyjcwb")))) + "18pv74jj4wr1981r92ss10qkgf5g1b09dsbz3im3j70a4l5l0df0")))) (build-system r-build-system) (propagated-inputs `(("r-rhdf5lib" ,r-rhdf5lib))) -- cgit v1.2.3 From 3a0229eba01463d68183c0272e237e206997a002 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:09:17 +0100 Subject: gnu: r-tximport: Update to 1.14.0. * gnu/packages/bioinformatics.scm (r-tximport): 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 b6217e2a74..53793a107b 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8579,13 +8579,13 @@ factors bound at the specific regions.") (define-public r-tximport (package (name "r-tximport") - (version "1.12.3") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "tximport" version)) (sha256 (base32 - "070nx0blvvfhsnkbb5j899wy7dgalrh4xfcciir9l2xl67lna1zf")))) + "09r23n2812q89by0r0cz2fx1gfnmn3jb3hwbg61m52bika82pakj")))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/tximport") (synopsis "Import and summarize transcript-level estimates for gene-level analysis") -- cgit v1.2.3 From 3964f2c24e9ea94e9dfefb616c5b32cc78d0fdd7 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:09:27 +0100 Subject: gnu: r-mutationalpatterns: Update to 1.12.0. * gnu/packages/bioinformatics.scm (r-mutationalpatterns): Update to 1.12.0. --- 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 53793a107b..dde45d40ee 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8474,14 +8474,14 @@ library implementing most of the pipeline's features.") (define-public r-mutationalpatterns (package (name "r-mutationalpatterns") - (version "1.10.0") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MutationalPatterns" version)) (sha256 (base32 - "1k3r06xj1nim1s8as1i7fykfa6fbb4x456kslbzdvbf83ppx34z3")))) + "08715l6swrlccviw7932v5hyrd2x4c6049vy9qnxk0lw3sp1zvsf")))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) -- cgit v1.2.3 From f375d7407247fd5cb1e60f69cf3e6a2bf983a5f1 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:09:38 +0100 Subject: gnu: r-rcas: Update to 1.12.0. * gnu/packages/bioinformatics.scm (r-rcas): Update to 1.12.0. --- 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 dde45d40ee..3cf308ff02 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8373,13 +8373,13 @@ paired-end data.") (define-public r-rcas (package (name "r-rcas") - (version "1.10.1") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RCAS" version)) (sha256 (base32 - "06z5zmdi34jblw37z6ff8hb6lvvi0chwr37acwqfn8d27ax9lakz")))) + "1s3gvvxi1029d1vfwnjh21nnw3mlx08kcwz63891hml9y850cvsn")))) (properties `((upstream-name . "RCAS"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 7b6c008960985e5b90531cc1999e4b671e88b966 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:09:50 +0100 Subject: gnu: r-bamsignals: Update to 1.18.0. * gnu/packages/bioinformatics.scm (r-bamsignals): 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 3cf308ff02..9da6fe8580 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8343,14 +8343,14 @@ of other R packages who wish to make use of HTSlib.") (define-public r-bamsignals (package (name "r-bamsignals") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bamsignals" version)) (sha256 (base32 - "15q1q51dwl9qxfkf10yppw4m194ba03nq9plsrbj8fqj00v4729i")))) + "0699b0pqbs0dvs91yjibcjc90lxj9mg8rcml4a6wchfr9md7n74w")))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) -- cgit v1.2.3 From 108c03a8eb1907b2ad2f9e055f896a6e91962c87 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:10:02 +0100 Subject: gnu: r-rhtslib: Update to 1.18.0. * gnu/packages/bioinformatics.scm (r-rhtslib): Update to 1.18.0. [propagated-inputs]: Add curl. --- 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 9da6fe8580..c545b81002 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8313,21 +8313,22 @@ secondary structure and comparative analysis in R.") (define-public r-rhtslib (package (name "r-rhtslib") - (version "1.16.3") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rhtslib" version)) (sha256 (base32 - "1lmrfr32nrz36abn440kvzzck53y2320xjxqzs2jw7m2a9h3ryak")))) + "04inkq44lxwymqv51mxgaphasqjcdc9rl5p58imnrdm0kszs8prm")))) (properties `((upstream-name . "Rhtslib"))) (build-system r-build-system) ;; Without this a temporary directory ends up in the Rhtslib.so binary, ;; which makes R abort the build. (arguments '(#:configure-flags '("--no-staged-install"))) (propagated-inputs - `(("r-zlibbioc" ,r-zlibbioc))) + `(("curl" ,curl) + ("r-zlibbioc" ,r-zlibbioc))) (inputs `(("zlib" ,zlib))) (native-inputs -- cgit v1.2.3 From 2f15045400da6649aa9bda0d649a46ff400807cf Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:10:24 +0100 Subject: gnu: r-zlibbioc: Update to 1.32.0. * gnu/packages/bioinformatics.scm (r-zlibbioc): 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 c545b81002..3410ddd4d1 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8271,13 +8271,13 @@ R/qtl, to better handle high-dimensional data and complex cross designs.") (define-public r-zlibbioc (package (name "r-zlibbioc") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "zlibbioc" version)) (sha256 (base32 - "1h0a2ps2rfk9azzps7p23sxj5z1giv8gcx0ypzgyz7fkr4xi9z7k")))) + "1xh7qan0w62mzsmanbx9vcj6ygdfhzw1abaxijkq7f4nh5w87idj")))) (properties `((upstream-name . "zlibbioc"))) (build-system r-build-system) -- cgit v1.2.3 From a5f9b30338f5d8014c4a7bdc321ae0ce55be7459 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:10:35 +0100 Subject: gnu: r-motifrg: Update to 1.30.0. * gnu/packages/bioinformatics.scm (r-motifrg): 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 3410ddd4d1..15670006b7 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8190,14 +8190,14 @@ Stephens (1990).") (define-public r-motifrg (package (name "r-motifrg") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "motifRG" version)) (sha256 (base32 - "02c7fbjwdq7pk96bd2rn07l9r2hqy00s3hfpli5ybmwgvc9h9z4z")))) + "0s6wdr036lra9x93r9k8wvicbkgzypjh3jp46h92yacw8d829k0d")))) (properties `((upstream-name . "motifRG"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From a9790190d17dada618dd3036e254fbbccb61648f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:10:44 +0100 Subject: gnu: r-seqlogo: Update to 1.52.0. * gnu/packages/bioinformatics.scm (r-seqlogo): 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 15670006b7..06853e1235 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8169,14 +8169,14 @@ downloaded from Encode.") (define-public r-seqlogo (package (name "r-seqlogo") - (version "1.50.0") + (version "1.52.0") (source (origin (method url-fetch) (uri (bioconductor-uri "seqLogo" version)) (sha256 (base32 - "1z63imr1a24nqijpvxaxlakykcsadfqyxl2b3vlllncxnjjvb52b")))) + "0s94aahp8ma1crmp83dz65ifjwrx6wqi3q6005lmbp8yk2x1rkj4")))) (properties `((upstream-name . "seqLogo"))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/seqLogo") -- cgit v1.2.3 From e06b34e8c68929da4c1d61b77040361dfb1c427c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:10:55 +0100 Subject: gnu: r-genomation: Update to 1.18.0. * gnu/packages/bioinformatics.scm (r-genomation): 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 06853e1235..f69b34bbc0 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8095,13 +8095,13 @@ reference point and sorted by a user defined feature.") (define-public r-genomation (package (name "r-genomation") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "genomation" version)) (sha256 (base32 - "06i711pwq9znd7plh0p25skxnnh5dyl61c33k9gma243wvlzmlkj")))) + "1sba928h23b67gr3i4yj1bg655g24l3bcgsf5gvymzrv5idrss1l")))) (build-system r-build-system) (propagated-inputs `(("r-biostrings" ,r-biostrings) -- cgit v1.2.3 From b590742362b670852fc781153bc333ffe4227746 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:11:06 +0100 Subject: gnu: r-seqpattern: Update to 1.18.0. * gnu/packages/bioinformatics.scm (r-seqpattern): 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 f69b34bbc0..380826a53f 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8068,13 +8068,13 @@ microarray data, using nearest neighbor averaging.") (define-public r-seqpattern (package (name "r-seqpattern") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "seqPattern" version)) (sha256 (base32 - "1ljqscbmrmi5d4lzzvg2d86sqzch26yxw57d33qyid300wm60db2")))) + "1gxrq6s2hiyac69idh5r1nbr1s69n0hg4ap2skm4g6857av9pwqf")))) (properties `((upstream-name . "seqPattern"))) (build-system r-build-system) -- cgit v1.2.3 From bca1c45e4e23eb90a835f29876267e69a0f0bcb1 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:11:17 +0100 Subject: gnu: r-impute: Update to 1.60.0. * gnu/packages/bioinformatics.scm (r-impute): 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 380826a53f..a6656f9de0 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8048,13 +8048,13 @@ genome data packages and support for efficient SNP representation.") (define-public r-impute (package (name "r-impute") - (version "1.58.0") + (version "1.60.0") (source (origin (method url-fetch) (uri (bioconductor-uri "impute" version)) (sha256 (base32 - "144jb889979cv3il2zxqk724v3sj1wnzjm3lkspxcvk29dbb9q8j")))) + "0igz1phjd1j9bg9z4kyy7j8v9bxi9sdwz4df26r51i2vavlbrf4q")))) (native-inputs `(("gfortran" ,gfortran))) (build-system r-build-system) -- cgit v1.2.3 From e3a2b96c800bd60d214d3126d26e91cacd653918 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:11:27 +0100 Subject: gnu: r-bsgenome: Update to 1.54.0. * gnu/packages/bioinformatics.scm (r-bsgenome): Update to 1.54.0. --- 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 a6656f9de0..68274f17ed 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8018,13 +8018,13 @@ dependencies between GO terms can be implemented and applied.") (define-public r-bsgenome (package (name "r-bsgenome") - (version "1.52.0") + (version "1.54.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BSgenome" version)) (sha256 (base32 - "0zwx42s73hc1vhn0v82i67mcixdwwc6n6q5h5vpnhpxlm4qwgqzp")))) + "0nn1b3h4hmnx5whf2cmzmyxdrcf4myj8c38rwr0sw4rc07xfzndy")))) (properties `((upstream-name . "BSgenome"))) (build-system r-build-system) -- cgit v1.2.3 From 323f42b2ca58b380c08a9fabbcecb2acb648af17 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:11:37 +0100 Subject: gnu: r-topgo: Update to 2.37.0. * gnu/packages/bioinformatics.scm (r-topgo): Update to 2.37.0. --- 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 68274f17ed..e6a2b69727 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7985,13 +7985,13 @@ information about the latest version of the Gene Ontologies.") (define-public r-topgo (package (name "r-topgo") - (version "2.36.0") + (version "2.37.0") (source (origin (method url-fetch) (uri (bioconductor-uri "topGO" version)) (sha256 (base32 - "09z42jwz5vh289ijz3x68zv5vmgkgcbhlp73vvmna1gld5lh5kz1")))) + "1cplr92aq3pa266ilvmg9xfmc95gag89b5jka04a5mh88j24y2ca")))) (properties `((upstream-name . "topGO"))) (build-system r-build-system) -- cgit v1.2.3 From 9fec34039189bd240b77aae2798fd93c945076c5 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:11:46 +0100 Subject: gnu: r-genomicfeatures: Update to 1.38.0. * gnu/packages/bioinformatics.scm (r-genomicfeatures): 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 e6a2b69727..1163652656 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7920,13 +7920,13 @@ as well as query and modify the browser state, such as the current viewport.") (define-public r-genomicfeatures (package (name "r-genomicfeatures") - (version "1.36.4") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicFeatures" version)) (sha256 (base32 - "0mzqv8pyxx5nwchyx3radym9ws2f9hb50xc9abjsjs4w4pv91j3k")))) + "0xd9rlsicycbanbcfhc97cj8b8vk94g7lkbmhk37w1511bq35wz5")))) (properties `((upstream-name . "GenomicFeatures"))) (build-system r-build-system) -- cgit v1.2.3 From 15187da9e7f5c3bafb586b292e12a1112dd48c1e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:11:56 +0100 Subject: gnu: r-rtracklayer: Update to 1.46.0. * gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.46.0. --- 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 1163652656..0561972768 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7873,13 +7873,13 @@ alignments.") (define-public r-rtracklayer (package (name "r-rtracklayer") - (version "1.44.4") + (version "1.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "rtracklayer" version)) (sha256 (base32 - "0dnifr58j2si2qbnvap2wslz3xgjv3h4l7a6v7nmmc57hq6kdbym")))) + "0lp9xsm8kqrgpwgwj7qaqcv1z6qynbz084grlpwp94zsp2ppf0n6")))) (build-system r-build-system) (arguments `(#:phases -- cgit v1.2.3 From 55e515d2069c6533eac7816cf07cb43b7249b342 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:12:06 +0100 Subject: gnu: r-genomicalignments: Update to 1.22.1. * gnu/packages/bioinformatics.scm (r-genomicalignments): Update to 1.22.1. --- 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 0561972768..5b57d16123 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7840,13 +7840,13 @@ samples.") (define-public r-genomicalignments (package (name "r-genomicalignments") - (version "1.20.1") + (version "1.22.1") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicAlignments" version)) (sha256 (base32 - "0s3q97q4pgj5jwn4g95al44rahrwsncsf45v01v4071msx3xmjxq")))) + "065xvy4pkda0ajvl1b75iski95k1pnbhxwdq7vkfl8v55915vqh6")))) (properties `((upstream-name . "GenomicAlignments"))) (build-system r-build-system) -- cgit v1.2.3 From 264db038c693ae952f11b8b78c28bc1414e083a7 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:12:16 +0100 Subject: gnu: r-summarizedexperiment: Update to 1.16.0. * gnu/packages/bioinformatics.scm (r-summarizedexperiment): 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 5b57d16123..349d619e20 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7809,13 +7809,13 @@ array-like objects like @code{DataFrame} objects (typically with Rle columns), (define-public r-summarizedexperiment (package (name "r-summarizedexperiment") - (version "1.14.1") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "SummarizedExperiment" version)) (sha256 (base32 - "0bhwgzrdipr0qjzc4j0qspqprx3v1rvshmx4j6506dv43pqlgp3f")))) + "04ljfw49ydgshrjv71qv9xr6y23a9vb8kp5fdjvpa8f6gzlb2a8m")))) (properties `((upstream-name . "SummarizedExperiment"))) (build-system r-build-system) -- cgit v1.2.3 From 4ada4fb7453fbad4fb5acf90d966e111e6dda237 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:12:26 +0100 Subject: gnu: r-delayedarray: Update to 0.12.0. * gnu/packages/bioinformatics.scm (r-delayedarray): Update to 0.12.0. --- 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 349d619e20..0253230ca6 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7777,13 +7777,13 @@ tab-delimited (tabix) files.") (define-public r-delayedarray (package (name "r-delayedarray") - (version "0.10.0") + (version "0.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DelayedArray" version)) (sha256 (base32 - "0l907ggxndn3f29zvsd5pppmp4c31rb22r6zkhvgph7xdxahyy6z")))) + "0329n1gbg2bq2vjhxfqqgakg75cdzcrcrgcwafjbg5zhkq86lc0q")))) (properties `((upstream-name . "DelayedArray"))) (build-system r-build-system) -- cgit v1.2.3 From e1d681e2af58510133369b9999505b4116956b4b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:12:35 +0100 Subject: gnu: r-rsamtools: Update to 2.2.1. * gnu/packages/bioinformatics.scm (r-rsamtools): Update to 2.2.1. --- 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 0253230ca6..9d43eb3aea 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7732,13 +7732,13 @@ biological sequences or sets of sequences.") (define-public r-rsamtools (package (name "r-rsamtools") - (version "2.0.3") + (version "2.2.1") (source (origin (method url-fetch) (uri (bioconductor-uri "Rsamtools" version)) (sha256 (base32 - "03qfpaqbffirpnby88mv6h45njfapli28crdvg35h2zi2jkkmhvp")))) + "0hpdc88prpq1gcja89n5s1ndcg81523qrkbkm9gbhm7rm8wmi8cl")))) (properties `((upstream-name . "Rsamtools"))) (build-system r-build-system) -- cgit v1.2.3 From 15cd3f6ef5a69bfb4a264759b3d607cb92eb521c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:12:45 +0100 Subject: gnu: r-biostrings: Update to 2.54.0. * gnu/packages/bioinformatics.scm (r-biostrings): Update to 2.54.0. --- 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 9d43eb3aea..ac002a56f5 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7706,13 +7706,13 @@ objects.") (define-public r-biostrings (package (name "r-biostrings") - (version "2.52.0") + (version "2.54.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Biostrings" version)) (sha256 (base32 - "0inrl97hli3qz6cfxcikc4picmbrqc8phdgqi18ynlvxy5ql64h4")))) + "0pq7g2hflx2cjlpwdj6mscw9hnxvlf5y50dxf48lbrf9r3q9kmyp")))) (properties `((upstream-name . "Biostrings"))) (build-system r-build-system) -- cgit v1.2.3 From 5854a4a265eef5523404ffe754bd3ecfbd575344 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:12:54 +0100 Subject: gnu: r-biocparallel: Update to 1.20.0. * gnu/packages/bioinformatics.scm (r-biocparallel): 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 ac002a56f5..b14289e764 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7681,13 +7681,13 @@ powerful online queries from gene annotation to database mining.") (define-public r-biocparallel (package (name "r-biocparallel") - (version "1.18.1") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocParallel" version)) (sha256 (base32 - "1j6wbls4qgvi5gj99c51r00jhxrzxk3x3258wg7dcjzbfqypvyw3")))) + "1wgnad4089xn8yxl9md7xprgh3vswcbyxg7di0931ik6x54m9zws")))) (properties `((upstream-name . "BiocParallel"))) (build-system r-build-system) -- cgit v1.2.3 From 68a9d9f26a306a54c79536a832d35d856f7179d3 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:13:05 +0100 Subject: gnu: r-biomart: Update to 2.42.0. * gnu/packages/bioinformatics.scm (r-biomart): Update to 2.42.0. [propagated-inputs]: Add r-biocfilecache, r-openssl, and r-rappdirs; remove r-rcurl. --- gnu/packages/bioinformatics.scm | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index b14289e764..e85ccade8e 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7648,21 +7648,23 @@ annotation data packages using SQLite data storage.") (define-public r-biomart (package (name "r-biomart") - (version "2.40.5") + (version "2.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biomaRt" version)) (sha256 (base32 - "1kjvxnkpsx3j2hji3cg3ka2gv8a9mg117lzzxyqjb7qa4zw7dipx")))) + "0difh4dsccjzhpfkvajy2adh98ym9164gd6clnsnic6qr6sk86ss")))) (properties `((upstream-name . "biomaRt"))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) + ("r-biocfilecache" ,r-biocfilecache) ("r-httr" ,r-httr) + ("r-openssl" ,r-openssl) ("r-progress" ,r-progress) - ("r-rcurl" ,r-rcurl) + ("r-rappdirs" ,r-rappdirs) ("r-stringr" ,r-stringr) ("r-xml" ,r-xml))) (home-page "https://bioconductor.org/packages/biomaRt") -- cgit v1.2.3 From de9ae3e7b1d8860dc0affbb9b7278392649452e0 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:13:34 +0100 Subject: gnu: r-annotationdbi: Update to 1.48.0. * gnu/packages/bioinformatics.scm (r-annotationdbi): Update to 1.48.0. --- 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 e85ccade8e..dfc37ea28f 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7621,13 +7621,13 @@ on Bioconductor or which replace R functions.") (define-public r-annotationdbi (package (name "r-annotationdbi") - (version "1.46.1") + (version "1.48.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AnnotationDbi" version)) (sha256 (base32 - "13nanz4nzy0mcda8ljz2g8d81hpqfz6jky7ydz5hpk0g2264b9ga")))) + "09piz1f0xpbb4amskx4ilby6lfrn27hhwk75il2c4lq6m3hr4w8s")))) (properties `((upstream-name . "AnnotationDbi"))) (build-system r-build-system) -- cgit v1.2.3 From 8d1c3666d7b87322a8232e237b343a202c0eb787 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:13:44 +0100 Subject: gnu: r-biobase: Update to 2.46.0. * gnu/packages/bioinformatics.scm (r-biobase): Update to 2.46.0. --- 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 dfc37ea28f..2698dad314 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7599,13 +7599,13 @@ manipulating genomic intervals and variables defined along a genome.") (define-public r-biobase (package (name "r-biobase") - (version "2.44.0") + (version "2.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Biobase" version)) (sha256 (base32 - "15yl92niqamx3lmwd11zlk0xniibqnh1gi280iadxicmchi83npc")))) + "1gx41083dqlm59vwqdxvc4ny31x91j48mda9n3scg0f2zwasvqgl")))) (properties `((upstream-name . "Biobase"))) (build-system r-build-system) -- cgit v1.2.3 From 0202b13e8bfc65a0d0c64b2b13f5497e7134c7f2 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:13:54 +0100 Subject: gnu: r-genomicranges: Update to 1.38.0. * gnu/packages/bioinformatics.scm (r-genomicranges): 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 2698dad314..c409d7e409 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7570,13 +7570,13 @@ different technologies, including microarrays, RNA-seq, and quantitative PCR.") (define-public r-genomicranges (package (name "r-genomicranges") - (version "1.36.1") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicRanges" version)) (sha256 (base32 - "1yid84gn0052v52h84685lvk854grl1wl65psmlmxx9yyykgc0jn")))) + "0xdds6ws7jjdfy4x3mb0qhy43kpxdmifmpw0jdk4wgw999zabb50")))) (properties `((upstream-name . "GenomicRanges"))) (build-system r-build-system) -- cgit v1.2.3 From da6edb199def379b1ae40bc426646be67a025d5d Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:14:03 +0100 Subject: gnu: r-xvector: Update to 0.26.0. * gnu/packages/bioinformatics.scm (r-xvector): Update to 0.26.0. --- 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 c409d7e409..efb6e33083 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7534,13 +7534,13 @@ different technologies, including microarrays, RNA-seq, and quantitative PCR.") (define-public r-xvector (package (name "r-xvector") - (version "0.24.0") + (version "0.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "XVector" version)) (sha256 (base32 - "12y09pwy86h1za6cmaxs960r7fs0vjzhl0li8jn59vqq9liza1ap")))) + "0s2gg84yzl5ffkzp6n7kh0jjk1vd90z189f5hkfn18rn67cy2nv7")))) (properties `((upstream-name . "XVector"))) (build-system r-build-system) -- cgit v1.2.3 From eea491e5c6d3bf879d620f6f9d5b442df920c8c5 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:14:13 +0100 Subject: gnu: r-limma: Update to 3.42.0. * gnu/packages/bioinformatics.scm (r-limma): Update to 3.42.0. --- 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 efb6e33083..2c004d28c7 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7515,13 +7515,13 @@ coding changes and predict coding outcomes.") (define-public r-limma (package (name "r-limma") - (version "3.40.6") + (version "3.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "limma" version)) (sha256 (base32 - "166z8cdh6w90rldqqaar7hyaskwiy4smawjfbn4sn58clv6q3mp8")))) + "0cfynv6qbnar5rl7vjh5lvddd381g9wqx1zd6a7l130hf59mwswn")))) (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 8f5d2c3abcee3b89954a2f5799fad8353454d979 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:14:22 +0100 Subject: gnu: r-variantannotation: Update to 1.32.0. * gnu/packages/bioinformatics.scm (r-variantannotation): 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 2c004d28c7..ba94ac9b55 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7476,13 +7476,13 @@ CAGE.") (define-public r-variantannotation (package (name "r-variantannotation") - (version "1.30.1") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "VariantAnnotation" version)) (sha256 (base32 - "144x3d3b9a3q5jy4aqrk1nf2yavwjhwlf71s7qyr4x3ms3wmvf8i")))) + "009s7rzp78s2w6iybizina42qx2w8qv3xwjbkpqphmm451maykgs")))) (properties `((upstream-name . "VariantAnnotation"))) (inputs -- cgit v1.2.3 From da03fa3c908ffe6c1082e03d5cdfdf071269304f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:14:31 +0100 Subject: gnu: r-edger: Update to 3.28.0. * gnu/packages/bioinformatics.scm (r-edger): Update to 3.28.0. --- 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 ba94ac9b55..f036e9137e 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7448,13 +7448,13 @@ names in their natural, rather than lexicographic, order.") (define-public r-edger (package (name "r-edger") - (version "3.26.8") + (version "3.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "edgeR" version)) (sha256 (base32 - "1wwimzviy2vklp80faz7sbbp74qcw2csbmlfgvzj7b785vwarpwg")))) + "1m7l6fbyik1b79v0h9qkmpa39svij1yiw24gxahbdqjg7fzsavh3")))) (properties `((upstream-name . "edgeR"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 937f3a46eb95ad6da9568ed63f91a53d9c95e748 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:14:41 +0100 Subject: gnu: r-genomeinfodb: Update to 1.22.0. * gnu/packages/bioinformatics.scm (r-genomeinfodb): 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 f036e9137e..06fd215492 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7420,13 +7420,13 @@ ID and species. It is used by functions in the GenomeInfoDb package.") (define-public r-genomeinfodb (package (name "r-genomeinfodb") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomeInfoDb" version)) (sha256 (base32 - "0zkhms81b3jz30q7ag81a1mq1rgqg4izyfdvcni68gvn8gm7kdyk")))) + "07zljs2mfi8rf31g903f43v2f7767xbnflfrx9qjnmgf7bm039x0")))) (properties `((upstream-name . "GenomeInfoDb"))) (build-system r-build-system) -- cgit v1.2.3 From d2723484f637888fe858d85fda93886df596ebcd Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:14:50 +0100 Subject: gnu: r-iranges: Update to 2.20.1. * gnu/packages/bioinformatics.scm (r-iranges): Update to 2.20.1. --- 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 06fd215492..736bd6d842 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7368,13 +7368,13 @@ S4Vectors package itself.") (define-public r-iranges (package (name "r-iranges") - (version "2.18.3") + (version "2.20.1") (source (origin (method url-fetch) (uri (bioconductor-uri "IRanges" version)) (sha256 (base32 - "05rw2b2bwns443n7d6lf97zdv1jbqdii2nprhs6x852w73m2a2g3")))) + "0qssp04wfrc1r92hd3szy03n8sdz8vrqjdxa2mcrsc0k0n9bchz5")))) (properties `((upstream-name . "IRanges"))) (build-system r-build-system) -- cgit v1.2.3 From d37daf89290ecfe4a5cd8d63bcf199fa8bbe4799 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:15:00 +0100 Subject: gnu: r-s4vectors: Update to 0.24.1. * gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.24.1. --- 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 736bd6d842..02b5b9a7f8 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7341,13 +7341,13 @@ checks on R packages that are to be submitted to the Bioconductor repository.") (define-public r-s4vectors (package (name "r-s4vectors") - (version "0.22.1") + (version "0.24.1") (source (origin (method url-fetch) (uri (bioconductor-uri "S4Vectors" version)) (sha256 (base32 - "0cpxqb18wd3pjd7bi8lry13sm5ffqahcvvxpk5pwm5xcj30cdlm9")))) + "1rr7ml3gn83g8fbvhgvryyzlh4p3qgpwcrsz6ii4y7gh1hqxggpx")))) (properties `((upstream-name . "S4Vectors"))) (build-system r-build-system) -- cgit v1.2.3 From 7758d5205c79a29d0d95ca03b08db548d1be12df Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:15:09 +0100 Subject: gnu: r-bioccheck: Update to 1.22.0. * gnu/packages/bioinformatics.scm (r-bioccheck): 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 02b5b9a7f8..922beb8175 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7294,13 +7294,13 @@ functionality.") (define-public r-bioccheck (package (name "r-bioccheck") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocCheck" version)) (sha256 (base32 - "1gkw9s6dhdryga9ap5yhvcqg9jsy4cn417ayqk1qiv6fy91fd124")))) + "1qnvl5yajgh67ijkq6gdsafri1k5hyw5gzn2ccqk9ymx6i2xd80g")))) (properties `((upstream-name . "BiocCheck"))) (build-system r-build-system) -- cgit v1.2.3 From ef961544336610c256ddc2150cbd72a6dc7bd486 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:15:19 +0100 Subject: gnu: r-biocstyle: Update to 2.14.2. * gnu/packages/bioinformatics.scm (r-biocstyle): Update to 2.14.2. --- 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 922beb8175..8104cf4d2c 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7268,13 +7268,13 @@ also known as views, in a controlled vocabulary.") (define-public r-biocstyle (package (name "r-biocstyle") - (version "2.12.0") + (version "2.14.2") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocStyle" version)) (sha256 (base32 - "029x8r9rcx6zy0xixdpwxai4jv4ynb161821fzac6z4r8k418398")))) + "0nc1cbzp5zdwc0rss4r6v7cpgynmmnj3sczwmajr58nabkndwsvf")))) (properties `((upstream-name . "BiocStyle"))) (build-system r-build-system) -- cgit v1.2.3 From 74d59b67482e0ec5f2644e4b861fa84491a1d402 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:15:30 +0100 Subject: gnu: r-biocviews: Update to 1.54.0. * gnu/packages/bioinformatics.scm (r-biocviews): Update to 1.54.0. --- 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 8104cf4d2c..ac56940aaa 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7240,13 +7240,13 @@ BLAST, KEGG, GenBank, MEDLINE and GO.") (define-public r-biocviews (package (name "r-biocviews") - (version "1.52.2") + (version "1.54.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biocViews" version)) (sha256 (base32 - "0qwrsd9fcpkv7hhzy1scnj7ahdxi6cjary28kqk6b36gkzmnrw4r")))) + "0yn8jys1900d31haayz0ppqk5y79mwjajwp4alz6pln3dbs70f3g")))) (properties `((upstream-name . "biocViews"))) (build-system r-build-system) -- cgit v1.2.3 From f8f815667d3f7f70f71dee4ef997dcefc9f8fe1a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:15:39 +0100 Subject: gnu: r-grohmm: Update to 1.20.0. * gnu/packages/bioinformatics.scm (r-grohmm): 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 ac56940aaa..cac08b9951 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7007,14 +7007,14 @@ annotation infrastructure.") (define-public r-grohmm (package (name "r-grohmm") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "groHMM" version)) (sha256 (base32 - "1p368qf8ab1vy8gl2j7rx0l7bvva4m7w06i364rqzs0sdyzlbm3y")))) + "0ywr8f6bfhg2ia3n4rmsxr4v1xqmlyhkwh0rvkgh3yqgnbvihndg")))) (properties `((upstream-name . "groHMM"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 58fd68b2992c4ed900e43e9b977168785f0f8b4a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:15:48 +0100 Subject: gnu: r-systempiper: Update to 1.20.0. * gnu/packages/bioinformatics.scm (r-systempiper): 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 cac08b9951..422106fc21 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -6960,14 +6960,14 @@ ungapped alignment formats.") (define-public r-systempiper (package (name "r-systempiper") - (version "1.18.2") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "systemPipeR" version)) (sha256 (base32 - "18s5vpmw766pm64w7bwwfgpsv9yzhwclf0ya1rpqz8qslw7bbdjf")))) + "17r25v9wcglyma2v1c8fka80dm7fx86saxlsb2aprmwi4h3dhb0j")))) (properties `((upstream-name . "systemPipeR"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From f29c9f0d33d20a2179ae11d309a9cea64f86fedd Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:15:57 +0100 Subject: gnu: r-shortread: Update to 1.44.0. * gnu/packages/bioinformatics.scm (r-shortread): Update to 1.44.0. --- 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 422106fc21..c69506910e 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -6918,14 +6918,14 @@ testing and other simple calculations.") (define-public r-shortread (package (name "r-shortread") - (version "1.42.0") + (version "1.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ShortRead" version)) (sha256 (base32 - "1irqzdgsavjqsq0vva4966qh8qgn7xn9382dmhahm1hxb94qmi59")))) + "18v2khq53za1m8i9va1z4wynah55gccbb42nq769vdcw7bl80wpa")))) (properties `((upstream-name . "ShortRead"))) (build-system r-build-system) (inputs -- cgit v1.2.3 From 545730891e33745dd0ab6e33705f32746a0642dd Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:16:06 +0100 Subject: gnu: r-gostats: Update to 2.52.0. * gnu/packages/bioinformatics.scm (r-gostats): Update to 2.52.0. --- 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 c69506910e..f77dab258e 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -6887,14 +6887,14 @@ analysis.") (define-public r-gostats (package (name "r-gostats") - (version "2.50.0") + (version "2.52.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GOstats" version)) (sha256 (base32 - "1a95i6awm2a8xv42fg2z3n29fg9z29i45kd80hxf6mvqqgzj80xp")))) + "19f4gxm3sbprqrnwzvskvywv6j4ibm8xkrbgg4h0fvh2b5331nwc")))) (properties `((upstream-name . "GOstats"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 4afcf941d2bdcf909bc41b248a5041b93cf0b67c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:16:17 +0100 Subject: gnu: r-category: Update to 2.52.1. * gnu/packages/bioinformatics.scm (r-category): Update to 2.52.1. --- 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 f77dab258e..9b6ed372c1 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -6856,14 +6856,14 @@ Enrichment Analysis} (GSEA).") (define-public r-category (package (name "r-category") - (version "2.50.0") + (version "2.52.1") (source (origin (method url-fetch) (uri (bioconductor-uri "Category" version)) (sha256 (base32 - "1n36xfnwn2np5f0lix9abvv9w6jb25jqz3xzvqzklz9s1af4k6x4")))) + "0ga0ij9hyzsxa5pavwmv35i8xggia2wygrk4m4z8an0qcvgy3v5g")))) (properties `((upstream-name . "Category"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From d2661841be8f58ef70dbf57b5ac53562e71a4e06 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:16:29 +0100 Subject: gnu: r-gseabase: Update to 1.48.0. * gnu/packages/bioinformatics.scm (r-gseabase): Update to 1.48.0. --- 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 9b6ed372c1..bd100bd47a 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -6829,14 +6829,14 @@ the graph algorithms contained in the Boost library.") (define-public r-gseabase (package (name "r-gseabase") - (version "1.46.0") + (version "1.48.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GSEABase" version)) (sha256 (base32 - "0vh53xk2prjbdkbr3hwfiflx1gh7ilrqs3j1p3lyd6syy3rn9n83")))) + "0kcb90sxlf19d5dxhdbqk9x62svky4262cccl0wxarbq6gf3bd57")))) (properties `((upstream-name . "GSEABase"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 33a2acb75708b12d9f02153d2220991a7c0b91d4 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:16:39 +0100 Subject: gnu: r-rbgl: Update to 1.62.1. * gnu/packages/bioinformatics.scm (r-rbgl): Update to 1.62.1. --- 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 bd100bd47a..ce31050942 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -6806,14 +6806,14 @@ databases. Packages produced are intended to be used with AnnotationDbi.") (define-public r-rbgl (package (name "r-rbgl") - (version "1.60.0") + (version "1.62.1") (source (origin (method url-fetch) (uri (bioconductor-uri "RBGL" version)) (sha256 (base32 - "06brn9hl6lybx6hdfp1sycwj6wn1bjfi8xyhpy0v122v1z8d5mbz")))) + "0ixbkdirf08i400db587r262j52sdwdgk3884nxk5xkbhx2m6vg0")))) (properties `((upstream-name . "RBGL"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 12c4555d446c7f20eadd0f3ee20068cd493779cb Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:16:49 +0100 Subject: gnu: r-annotationforge: Update to 1.28.0. * gnu/packages/bioinformatics.scm (r-annotationforge): 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 ce31050942..5236877dbc 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -6776,14 +6776,14 @@ exploration of the results.") (define-public r-annotationforge (package (name "r-annotationforge") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AnnotationForge" version)) (sha256 (base32 - "0m4w8n2711wr28znv646cfc7m5jqlr8friz334zdyjmhg7m2xkb7")))) + "0h2r60v339ajk5r6xq4iwwcpihdvf12fi8255byr2dhglzrd8xl7")))) (properties `((upstream-name . "AnnotationForge"))) (build-system r-build-system) -- cgit v1.2.3 From ebc81e300cabb88c906592fbeb046b5ecb35e25f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:17:00 +0100 Subject: gnu: r-dexseq: Update to 1.32.0. * gnu/packages/bioinformatics.scm (r-dexseq): 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 5236877dbc..19a25175ed 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -6733,14 +6733,14 @@ distribution.") (define-public r-dexseq (package (name "r-dexseq") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DEXSeq" version)) (sha256 (base32 - "1b2s0vwm97g0wgm4ms0f4pqkqiqmxscnhg700aybl5vx0m2fa8xm")))) + "0sqqb65ckliif2nmvlvc7w49id59z0nvqcdz5gry8l2mn6azrf6a")))) (properties `((upstream-name . "DEXSeq"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 867018e1384cb778e92db48557ebd48f3181d1ef Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:17:09 +0100 Subject: gnu: r-deseq2: Update to 1.26.0. * gnu/packages/bioinformatics.scm (r-deseq2): 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 19a25175ed..cf149e02ff 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -6696,14 +6696,14 @@ high-throughput sequencing experiments.") (define-public r-deseq2 (package (name "r-deseq2") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DESeq2" version)) (sha256 (base32 - "0fkk326addm2cw688gnmdzsmri5qx8j6ldnr4xin6kjnwicqhlqd")))) + "1lmbhznfs8dz9ipd53z4ccwvwxqwzx1ayw56jlrvlsambaj8fash")))) (properties `((upstream-name . "DESeq2"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 0726645eca3963ebae223aa263817fc7ad71b3da Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:17:24 +0100 Subject: gnu: r-genefilter: Update to 1.68.0. * gnu/packages/bioinformatics.scm (r-genefilter): Update to 1.68.0. [propagated-inputs]: Remove r-s4vectors and add r-biocgenerics. --- 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 cf149e02ff..8a007dca4d 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -6669,14 +6669,14 @@ information as possible.") (define-public r-genefilter (package (name "r-genefilter") - (version "1.66.0") + (version "1.68.0") (source (origin (method url-fetch) (uri (bioconductor-uri "genefilter" version)) (sha256 (base32 - "1jq7lam4dnbvz55lx93kcl9afl8xfjd6xs374d35m21bkay418kj")))) + "1xjr02qhldspjwd6y374wgik18fgywb6408wsz471i8b4ik98ckc")))) (build-system r-build-system) (native-inputs `(("gfortran" ,gfortran))) @@ -6684,7 +6684,7 @@ information as possible.") `(("r-annotate" ,r-annotate) ("r-annotationdbi" ,r-annotationdbi) ("r-biobase" ,r-biobase) - ("r-s4vectors" ,r-s4vectors) + ("r-biocgenerics" ,r-biocgenerics) ("r-survival" ,r-survival))) (home-page "https://bioconductor.org/packages/genefilter") (synopsis "Filter genes from high-throughput experiments") -- cgit v1.2.3 From 989be6df996eb4e99b9be91057a2aed3a5492750 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:17:47 +0100 Subject: gnu: r-unifiedwmwqpcr: Update to 1.22.0. * gnu/packages/bioconductor.scm (r-unifiedwmwqpcr): 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 bf1a5e5cc2..8eb1142f87 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6442,14 +6442,14 @@ features (e.g. genes, microRNAs).") (define-public r-unifiedwmwqpcr (package (name "r-unifiedwmwqpcr") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "unifiedWMWqPCR" version)) (sha256 (base32 - "10j70bp5y1x2prz2iagqmwf04y79yqinq08wz4ilh8wggb9f7l8a")))) + "1l6rf7scxxyz4x0m4li54y6905sqj4jrx481zb9h3vqhcfcmn8lj")))) (properties `((upstream-name . "unifiedWMWqPCR"))) (build-system r-build-system) -- cgit v1.2.3 From 0b0906c845deea89fdda5e7868b845367dc98821 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:17:57 +0100 Subject: gnu: r-htqpcr: Update to 1.40.0. * gnu/packages/bioconductor.scm (r-htqpcr): 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 8eb1142f87..25bb0bd95a 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6409,14 +6409,14 @@ measures.") (define-public r-htqpcr (package (name "r-htqpcr") - (version "1.38.0") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "HTqPCR" version)) (sha256 (base32 - "09xgj797f0qsbm4jswxw7ijjwa4jxg06bfkq66xfhbvascyyrhg7")))) + "008iczqaa0wn5nw144vfg3qylg7qa1q963nq9mqhgj3sxlg4rmjx")))) (properties `((upstream-name . "HTqPCR"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From e2f481dad0fedd325e5191e0dfc87e922cc6a01e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:18:06 +0100 Subject: gnu: r-variancepartition: Update to 1.16.0. * gnu/packages/bioconductor.scm (r-variancepartition): 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 25bb0bd95a..e387180684 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6367,14 +6367,14 @@ arrays based on fast wavelet-based functional models.") (define-public r-variancepartition (package (name "r-variancepartition") - (version "1.14.1") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "variancePartition" version)) (sha256 (base32 - "0w4kri2389x1082xppx7l6xl1a5g74fyp02iwb4938x3gzwqwbjd")))) + "1ygx7f2sp4b7ilgspm6vqcbjxs7br9s6g3gwcdb978kx03ymp4i8")))) (properties `((upstream-name . "variancePartition"))) (build-system r-build-system) -- cgit v1.2.3 From e13f977312948449c0e8aa806983690ec19cfa48 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:18:16 +0100 Subject: gnu: r-wavetiling: Update to 1.28.0. * gnu/packages/bioconductor.scm (r-wavetiling): 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 e387180684..ff9a3c1451 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6336,14 +6336,14 @@ same genome coordinate system.") (define-public r-wavetiling (package (name "r-wavetiling") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "waveTiling" version)) (sha256 (base32 - "0l0saa0myabpq2rl9dq70zff8jpxr3mkanxlj65hc41f0m5xllir")))) + "0d7l559zlmly8mncmh1zhkqmsml0bwwfpm7ccp8l26y852vwf7hf")))) (properties `((upstream-name . "waveTiling"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 053a2127bcdb2f47de244909d1255129d0342946 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:18:24 +0100 Subject: gnu: r-genomegraphs: Update to 1.46.0. * gnu/packages/bioconductor.scm (r-genomegraphs): Update to 1.46.0. --- 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 ff9a3c1451..b933ecf999 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6308,14 +6308,14 @@ populations, splice site strength, conservation, etc.") (define-public r-genomegraphs (package (name "r-genomegraphs") - (version "1.44.0") + (version "1.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomeGraphs" version)) (sha256 (base32 - "026skcn2cqchlzaqsnk11gb8d8aq1rz7lrnx4mmsba234mh4j7kd")))) + "05vavhz936v7cknig2f2mn3fd9fiy54r3swlvifpawramblp1ags")))) (properties `((upstream-name . "GenomeGraphs"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 6f5415d5f67c4b6d489b3d1133cbc821e69b4dd7 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:18:34 +0100 Subject: gnu: r-variantfiltering: Update to 1.22.0. * gnu/packages/bioconductor.scm (r-variantfiltering): 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 b933ecf999..65f70c061b 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6261,14 +6261,14 @@ provides methods for retrieving enriched pathways.") (define-public r-variantfiltering (package (name "r-variantfiltering") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "VariantFiltering" version)) (sha256 (base32 - "0vpghxacqcbaxx2scb5gfhcmfpw1lkls7h6qnbwbnmjwy01q2p17")))) + "13pgfk2mbffd9smmxnwz7g0jrwng78711053wfzadr107zbyn4r8")))) (properties `((upstream-name . "VariantFiltering"))) (build-system r-build-system) -- cgit v1.2.3 From cb734c60dc4ac1e9c0c3733a41e19811cf3d3b08 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:18:42 +0100 Subject: gnu: r-timeseriesexperiment: Update to 1.4.0. * gnu/packages/bioconductor.scm (r-timeseriesexperiment): Update to 1.4.0. --- 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 65f70c061b..3875a88584 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6222,14 +6222,14 @@ procedures that induce nucleotide substitutions (e.g. BisSeq).") (define-public r-timeseriesexperiment (package (name "r-timeseriesexperiment") - (version "1.2.0") + (version "1.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "TimeSeriesExperiment" version)) (sha256 (base32 - "1j11g7a2p0yk38fx6wd6152l1xynghj01pfxihalw601jwf1bl0y")))) + "0xqa6hzknnci20zx2f6mw5cpqx8pq0v6fzf053hh51p1l2ikvgqm")))) (properties `((upstream-name . "TimeSeriesExperiment"))) (build-system r-build-system) -- cgit v1.2.3 From c0cba4b5429bbbb0dab7a290bbfa81a63d080191 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:18:52 +0100 Subject: gnu: r-wavcluster: Update to 2.20.0. * gnu/packages/bioconductor.scm (r-wavcluster): Update to 2.20.0. --- 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 3875a88584..8cba68214d 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6176,14 +6176,14 @@ format.") (define-public r-wavcluster (package (name "r-wavcluster") - (version "2.18.0") + (version "2.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "wavClusteR" version)) (sha256 (base32 - "02i53dskirzr9nls3dsmv7dqhvy3vikkpx7247zpy2qd9r5yvhy2")))) + "0vq3xxsvwq86rlya7xc92sc4i6b48sib0pcina3xivg3ky2j3z7y")))) (properties `((upstream-name . "wavClusteR"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 02c18abe6264381b2c272a340f007a08a99bb1ac Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:19:01 +0100 Subject: gnu: r-reqon: Update to 1.32.0. * gnu/packages/bioconductor.scm (r-reqon): 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 8cba68214d..e33e64db09 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6151,14 +6151,14 @@ genome sequence.") (define-public r-reqon (package (name "r-reqon") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ReQON" version)) (sha256 (base32 - "04bljr8vgb9z9800d9v8w7a4rvjkwq48zd8n5divq30zj9k2na7a")))) + "10p6l2zxijqyypdm970jyfqyrnfhaq3nf7cg2q6mgd1srggfa0cx")))) (properties `((upstream-name . "ReQON"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 2223bbc7263bfa48216fb6715cf1a8f4eec9e1cf Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:19:09 +0100 Subject: gnu: r-seqbias: Update to 1.34.0. * gnu/packages/bioconductor.scm (r-seqbias): 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 e33e64db09..f0265d7d73 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6123,14 +6123,14 @@ with multiple R processes supported by the package @code{parallel}.") (define-public r-seqbias (package (name "r-seqbias") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "seqbias" version)) (sha256 (base32 - "1pk97jsq0rxijsdm5wnmlw79mhy19skdq1h3mmfbdjh560md47lw")))) + "19vbdyjblij2533ibmrw1n0rkqfrbflma6cg5b79ghks0mg7z8hq")))) (properties `((upstream-name . "seqbias"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 8b941a50efac6caafd92e2be2715d46a7a554d9e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:19:18 +0100 Subject: gnu: r-bigmelon: Update to 1.12.0. * gnu/packages/bioconductor.scm (r-bigmelon): 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 f0265d7d73..c92aa943a6 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6095,14 +6095,14 @@ with multiple R processes supported by the package @code{parallel}.") (define-public r-bigmelon (package (name "r-bigmelon") - (version "1.10.0") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bigmelon" version)) (sha256 (base32 - "0269kf3d34dbng3swk7pclpk02vy4k3askygmzi5my3fqyfzdkj9")))) + "0sw7rp4p03m1s72b4j06jfb7as3v1n2w2z4ppk8s4f80fb05bcls")))) (properties `((upstream-name . "bigmelon"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From f5ef7dd6b77fa2b9c80c96f2630bc0fc57511349 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:19:26 +0100 Subject: gnu: r-gdsfmt: Update to 1.22.0. * gnu/packages/bioconductor.scm (r-gdsfmt): 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 c92aa943a6..a079244c35 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6038,14 +6038,14 @@ metrics, with methods for objects produced by the @code{methylumi} and (define-public r-gdsfmt (package (name "r-gdsfmt") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "gdsfmt" version)) (sha256 (base32 - "0h3hgwxq26dg09fyxqg545v9dg1dizsj58cf05rncr3jj4f8g0xy")) + "0zc9v62imd0ykz4h30pxa64q0y45qijmkwdk2pd4ncsg8fc2jlz9")) (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 9eade2294efe19ab52725273cce3c4dc45bc02aa Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:19:36 +0100 Subject: gnu: r-watermelon: Update to 1.30.0. * gnu/packages/bioconductor.scm (r-watermelon): 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 a079244c35..88421dfca8 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6001,14 +6001,14 @@ data.") (define-public r-watermelon (package (name "r-watermelon") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "wateRmelon" version)) (sha256 (base32 - "0354ahmfvhqw3yfp17rmz35vlgjp262n4q3hr8qyccyrnk2dz17z")))) + "0a66fq04yph9dis91lzjk9kh134zy6fj98yklrwf24r1080qngx0")))) (properties `((upstream-name . "wateRmelon"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 3672b74f6f860681819233bdd180452a447015c0 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:19:46 +0100 Subject: gnu: r-roc: Update to 1.62.0. * gnu/packages/bioconductor.scm (r-roc): Update to 1.62.0. [propagated-inputs]: Add r-knitr. --- 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 88421dfca8..4ae1516f2e 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5955,16 +5955,18 @@ regulatory networks from expression data.") (define-public r-roc (package (name "r-roc") - (version "1.60.0") + (version "1.62.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ROC" version)) (sha256 (base32 - "1sapnl8kyaldgvdc657wqcmyjb24nvrnaw7v94bbs8yf5pmfm71c")))) + "1aqpyc28czagg3nbybh55vf152nbar61jjw79w04326d97mc3j3y")))) (properties `((upstream-name . "ROC"))) (build-system r-build-system) + (propagated-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://www.bioconductor.org/packages/ROC/") (synopsis "Utilities for ROC curves") (description -- cgit v1.2.3 From 33ce50e322f4fbaf4b3af962e8298cceafa23806 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:20:01 +0100 Subject: gnu: r-genie3: Update to 1.8.0. * gnu/packages/bioconductor.scm (r-genie3): 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 4ae1516f2e..d34963e55b 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5934,14 +5934,14 @@ cisTopics and explore the nature and regulatory proteins driving them.") (define-public r-genie3 (package (name "r-genie3") - (version "1.6.0") + (version "1.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GENIE3" version)) (sha256 (base32 - "0lvrpw4xn7xyinmn13f65i0vkzfzwdj5y8gsa8vyy8kcn83d28fx")))) + "0p67lhgy3lb4nc958s51hx7rvgwhzwfic9xhpsrask40k43spv7l")))) (properties `((upstream-name . "GENIE3"))) (build-system r-build-system) (propagated-inputs `(("r-reshape2" ,r-reshape2))) -- cgit v1.2.3 From 42b06298efbda1ff10c904a04413ecc4d4552403 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:20:09 +0100 Subject: gnu: r-cicero: Update to 1.4.0. * gnu/packages/bioconductor.scm (r-cicero): Update to 1.4.0. --- 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 d34963e55b..cc17d653a9 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5827,14 +5827,14 @@ genes in the gene-set that are ranked above the leading edge).") (define-public r-cicero (package (name "r-cicero") - (version "1.2.0") + (version "1.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "cicero" version)) (sha256 (base32 - "0f15l8zrh7l7nnvznb66116hvfk15djb9q240vbscm2w0y5fvkcr")))) + "0mmm7vvzq50b5fayid0bw82b5lar3xm9fwl2ya30q0p4db2y6wnz")))) (build-system r-build-system) (propagated-inputs `(("r-assertthat" ,r-assertthat) -- cgit v1.2.3 From 51ffac455ebb62d39a13dba268c34f5342444435 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:20:18 +0100 Subject: gnu: r-rcistarget: Update to 1.6.0. * gnu/packages/bioconductor.scm (r-rcistarget): 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 cc17d653a9..022c9b7f79 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5792,14 +5792,14 @@ data, to only emphasize the data that actually matters.") (define-public r-rcistarget (package (name "r-rcistarget") - (version "1.4.0") + (version "1.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RcisTarget" version)) (sha256 (base32 - "133x2vr86ifbk82q08x1c8q19zsk5za7b6qrzz77dhsyf4bhcvpd")))) + "1nnah7s0jd24fpfyxsf76jas8dm23c3266aps124wdlqsp9q5qjw")))) (properties `((upstream-name . "RcisTarget"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 4930a89ad5b546bbd4b31c7c0489273fc7fae3a6 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:20:28 +0100 Subject: gnu: r-mixomics: Update to 6.10.6. * gnu/packages/bioconductor.scm (r-mixomics): Update to 6.10.6. --- 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 022c9b7f79..1cc8b4f54b 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5707,14 +5707,14 @@ self-organizing map clustering and minimal spanning trees.") (define-public r-mixomics (package (name "r-mixomics") - (version "6.8.5") + (version "6.10.6") (source (origin (method url-fetch) (uri (bioconductor-uri "mixOmics" version)) (sha256 (base32 - "0s93ai5d7li8pnxd87n12j9gypvac5zfahsk68j7zjv68dglj8s7")))) + "18jwrdyc4pnx917y1kskxz3fqvlrkyy4ny0xqrfcidz0j7p0b7wr")))) (properties `((upstream-name . "mixOmics"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From ba71567acd56ba20103b14705cb15fbf4d192c59 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:20:37 +0100 Subject: gnu: r-flowsom: Update to 1.18.0. * gnu/packages/bioconductor.scm (r-flowsom): Update to 1.18.0. [propagated-inputs]: Add r-cytoml, r-flowworkspace, and r-rcolorbrewer; remove r-flowutils. --- 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 1cc8b4f54b..f3bf10b375 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5679,22 +5679,24 @@ standard to exchange gated cytometry data with other software platforms.") (define-public r-flowsom (package (name "r-flowsom") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "FlowSOM" version)) (sha256 (base32 - "03wl3xk7g7vajc4kkrqa0gsbjfxlqr918qi849h5nir31963398l")))) + "0265sq4zvj6d6h5ghqj9xzm4b0z9v65kgyl88cgdcpdkzfnfcvd5")))) (properties `((upstream-name . "FlowSOM"))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) ("r-consensusclusterplus" ,r-consensusclusterplus) + ("r-cytoml" ,r-cytoml) ("r-flowcore" ,r-flowcore) - ("r-flowutils" ,r-flowutils) + ("r-flowworkspace" ,r-flowworkspace) ("r-igraph" ,r-igraph) + ("r-rcolorbrewer" ,r-rcolorbrewer) ("r-tsne" ,r-tsne) ("r-xml" ,r-xml))) (home-page "https://bioconductor.org/packages/FlowSOM/") -- cgit v1.2.3 From 8042087804b748cc2a1f0c773b569a39d0fbc358 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:21:06 +0100 Subject: gnu: r-flowmeans: Update to 1.46.0. * gnu/packages/bioconductor.scm (r-flowmeans): Update to 1.46.0. --- 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 f3bf10b375..ef55cd5193 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5319,14 +5319,14 @@ with flow cytometry data.") (define-public r-flowmeans (package (name "r-flowmeans") - (version "1.44.0") + (version "1.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "flowMeans" version)) (sha256 (base32 - "0yp6y3mq5h4nf1d7ybqnriigwfmwanrqavpj3ry482sgiaip1hp2")))) + "1yisrikaafmpb4sig2c5l0wcz4idrs4as7i9x90v6z2v94iq0m8h")))) (properties `((upstream-name . "flowMeans"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From b2a2f3213065aa5d4f63df3631140a4dd8b358fd Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:21:15 +0100 Subject: gnu: r-flowcore: Update to 1.52.1. * gnu/packages/bioconductor.scm (r-flowcore): Update to 1.52.1. [propagated-inputs]: Remove r-corpcor, r-graph, r-mass, and r-rrcov; add r-cytolib. --- gnu/packages/bioconductor.scm | 11 ++++------- 1 file changed, 4 insertions(+), 7 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index ef55cd5193..a53dcf5ed1 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5289,26 +5289,23 @@ interact with gated cytometry data.") (define-public r-flowcore (package (name "r-flowcore") - (version "1.50.0") + (version "1.52.1") (source (origin (method url-fetch) (uri (bioconductor-uri "flowCore" version)) (sha256 (base32 - "0pvcyzycsmgc8iw60q9xnhllfan6ihwpz3gvk8h1n9jmhpxzylan")))) + "08kvxc187iwlixibx1860jcp5g9bsw8abkv06x2qv1w83fas4pp2")))) (properties `((upstream-name . "flowCore"))) (build-system r-build-system) (propagated-inputs `(("r-bh" ,r-bh) ("r-biobase" ,r-biobase) ("r-biocgenerics" ,r-biocgenerics) - ("r-corpcor" ,r-corpcor) - ("r-graph" ,r-graph) - ("r-mass" ,r-mass) + ("r-cytolib" ,r-cytolib) ("r-matrixstats" ,r-matrixstats) - ("r-rcpp" ,r-rcpp) - ("r-rrcov" ,r-rrcov))) + ("r-rcpp" ,r-rcpp))) (home-page "https://bioconductor.org/packages/flowCore") (synopsis "Basic structures for flow cytometry data") (description -- cgit v1.2.3 From 8ad6b23f68fbb9f12f0ad53df2e53688b88959fc Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:21:44 +0100 Subject: gnu: r-consensusclusterplus: Update to 1.50.0. * gnu/packages/bioconductor.scm (r-consensusclusterplus): 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 a53dcf5ed1..ae662b45b2 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5244,14 +5244,14 @@ and to both short and long sequence reads.") (define-public r-consensusclusterplus (package (name "r-consensusclusterplus") - (version "1.48.0") + (version "1.50.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ConsensusClusterPlus" version)) (sha256 (base32 - "1mlcm3wq5n8s0gxs35j0ph9576fhbrbrrsj2xy84fy20prcfs4w8")))) + "0pnh5zy6d3c364xxjdn5zp3kf5afhsxv6yzkdn1qspny0pmqlrp4")))) (properties `((upstream-name . "ConsensusClusterPlus"))) (build-system r-build-system) -- cgit v1.2.3 From 482ba0b3ed3bec20e42a5b04dc205f7c6532dc16 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:21:52 +0100 Subject: gnu: r-flowutils: Update to 1.50.0. * gnu/packages/bioconductor.scm (r-flowutils): 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 ae662b45b2..d481c38192 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5218,14 +5218,14 @@ and to both short and long sequence reads.") (define-public r-flowutils (package (name "r-flowutils") - (version "1.48.0") + (version "1.50.0") (source (origin (method url-fetch) (uri (bioconductor-uri "flowUtils" version)) (sha256 (base32 - "1r7b0rszdzjq7jphh65p5m4x5ps0zbbagxl26gn2mapbjdyb47rm")))) + "1xcs19j9p3izvksyy5wzsbicwby0dsa9g2w7gjzwynzgj5dpfr81")))) (properties `((upstream-name . "flowUtils"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 4390788ea2dc74d6a6590bc4bf3a0d7d3f44ef02 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:22:02 +0100 Subject: gnu: r-rsubread: Update to 2.0.0. * gnu/packages/bioconductor.scm (r-rsubread): Update to 2.0.0. --- 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 d481c38192..300bf0c030 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5194,14 +5194,14 @@ annotations.") (define-public r-rsubread (package (name "r-rsubread") - (version "1.34.7") + (version "2.0.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rsubread" version)) (sha256 (base32 - "0z4ydk9296bp76ah5y6a7za5jyn4h238xngb789zragly902x83y")))) + "0l8q9y2a4m1di0w5nlxhq9jgliinhgr2fwjpm5ixnqx5j3iprlwd")))) (properties `((upstream-name . "Rsubread"))) (build-system r-build-system) (inputs `(("zlib" ,zlib))) -- cgit v1.2.3 From 700072565f765b51491b147d40ae9a038cd822be Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:22:13 +0100 Subject: gnu: r-annotatr: Update to 1.12.1. * gnu/packages/bioconductor.scm (r-annotatr): Update to 1.12.1. --- 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 300bf0c030..ea718f8751 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5155,14 +5155,14 @@ datasets.") (define-public r-annotatr (package (name "r-annotatr") - (version "1.10.0") + (version "1.12.1") (source (origin (method url-fetch) (uri (bioconductor-uri "annotatr" version)) (sha256 (base32 - "1zlhy6swfgqjhhcqn8c6akxd4c4z8p85swfh095imji7hxnlhh1f")))) + "1bibk3p1q4cavqy11xs6rqqhqdjsq2dd7lf7blwcr27s5ajcd6dj")))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) -- cgit v1.2.3 From 7d29dc9c7b753f2f70318129544611fc175c60aa Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:22:22 +0100 Subject: gnu: r-biosigner: Update to 1.14.0. * gnu/packages/bioconductor.scm (r-biosigner): Update to 1.14.0. [propagated-inputs]: Add r-multidataset. --- 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 ea718f8751..65479c7cae 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5120,18 +5120,19 @@ coefficients).") (define-public r-biosigner (package (name "r-biosigner") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biosigner" version)) (sha256 (base32 - "1643iya40v6whb7lw7y34w5sanbasvj4yhvcygbip667yhphyv5b")))) + "1kdfhw629qczrfms0jmphqz0ksjzi8js00xj92h1lnv092npfk0j")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) ("r-e1071" ,r-e1071) + ("r-multidataset" ,r-multidataset) ("r-randomforest" ,r-randomforest) ("r-ropls" ,r-ropls))) (native-inputs -- cgit v1.2.3 From 643aaf7eaf937f1ae862384ee10c9a736efc1776 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:22:37 +0100 Subject: gnu: r-ropls: Update to 1.18.0. * gnu/packages/bioconductor.scm (r-ropls): Update to 1.18.0. [propagated-inputs]: Add r-multidataset. --- 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 65479c7cae..f8c2fc64be 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5084,16 +5084,18 @@ packages.") (define-public r-ropls (package (name "r-ropls") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ropls" version)) (sha256 (base32 - "099nv9dgmw3avkxv7cd27r16yj56svjlp5q4i389yp1n0r5zhyl2")))) + "05w1zrq92w3jfwq5sdyj27m5qjg4zv7acywia8vd6y5fbgcnyzlp")))) (build-system r-build-system) - (propagated-inputs `(("r-biobase" ,r-biobase))) + (propagated-inputs + `(("r-biobase" ,r-biobase) + ("r-multidataset" ,r-multidataset))) (native-inputs `(("r-knitr" ,r-knitr))) ; for vignettes (home-page "https://dx.doi.org/10.1021/acs.jproteome.5b00354") -- cgit v1.2.3 From 8d766270c4c31ce2324e7f903467c7c85227fac8 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:22:54 +0100 Subject: gnu: r-birta: Update to 1.30.0. * gnu/packages/bioconductor.scm (r-birta): 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 f8c2fc64be..759cfb48c5 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5020,14 +5020,14 @@ routines to analyse the resulting networks and their natural projections.") (define-public r-birta (package (name "r-birta") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "birta" version)) (sha256 (base32 - "12xjyvgmh4h0b7hi4qg50kcpb9003gnh2xyfgncb8l9mzvsbkxc2")))) + "1zhlwapdgkz0fpv5bqfxh9aw6ymnmxnnm1r0n0kfzn5izyjavslg")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) -- cgit v1.2.3 From a9e5145c323dc9fc3ced68e3ae4188eaf56265b2 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:23:03 +0100 Subject: gnu: r-birewire: Update to 3.18.0. * gnu/packages/bioconductor.scm (r-birewire): 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 759cfb48c5..6cf84c249b 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4991,14 +4991,14 @@ graphics.") (define-public r-birewire (package (name "r-birewire") - (version "3.16.0") + (version "3.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiRewire" version)) (sha256 (base32 - "1gjb18l3gq3w8zl6r5d49hw0r1kfh9f7ghv9hz6y86aniprvb518")))) + "1074cp422ail72yajn8p0bg26h6zzz07nzypnwfyv86qrpvpdw9q")))) (properties `((upstream-name . "BiRewire"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 11db82b07c7fac1d62a7d9a2f6c89131b18f83ef Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:23:11 +0100 Subject: gnu: r-rqc: Update to 1.20.0. * gnu/packages/bioconductor.scm (r-rqc): 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 6cf84c249b..1c0d3b9df0 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4950,14 +4950,14 @@ quantification of genomic regions of interest.") (define-public r-rqc (package (name "r-rqc") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rqc" version)) (sha256 (base32 - "09kyn5nc2fqfdm3q07h0x2jyh24vsq5sxxm63ir1lvv250lmal4g")))) + "1nxkrb9kx41g050yz935yrl9pjkakhr8v6whxcvr72gg4r9m2x3m")))) (properties `((upstream-name . "Rqc"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From a15e52ec7862f9952edfe398bea6bd8ef7775ae8 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:23:21 +0100 Subject: gnu: r-quasr: Update to 1.26.0. * gnu/packages/bioconductor.scm (r-quasr): 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 1c0d3b9df0..ec72db0e4a 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4905,14 +4905,14 @@ index.") (define-public r-quasr (package (name "r-quasr") - (version "1.24.2") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "QuasR" version)) (sha256 (base32 - "1pshm41iba9nfq2pigk4dyldn5434w83rhgj99cdjnd0rszj7ajx")))) + "07m5q7wasapj2984kwy897510flbhvz7x0fgs7q2vm5wjhfzdrgv")))) (properties `((upstream-name . "QuasR"))) (build-system r-build-system) (inputs -- cgit v1.2.3 From 3dd2450e651cbf8faddf08095b36e511d4d8e2de Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:23:31 +0100 Subject: gnu: r-rhisat2: Update to 1.2.0. * gnu/packages/bioconductor.scm (r-rhisat2): Update to 1.2.0. [arguments]: Add phase to make package reproducible and to avoid shelling out to 'which'. [native-inputs]: Remove which. --- gnu/packages/bioconductor.scm | 18 ++++++++++++++---- 1 file changed, 14 insertions(+), 4 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index ec72db0e4a..07800d636b 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4877,18 +4877,28 @@ interpretation.") (define-public r-rhisat2 (package (name "r-rhisat2") - (version "1.0.3") + (version "1.2.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rhisat2" version)) (sha256 (base32 - "02ig9qci18n93vmya7q6bijrqsbfh69fyg8iqysf89ym2vd3x3c5")))) + "02fn5cm8sj2s9x00505y3iyipn1r3lpvpwpjy2pdxdbpmhb5hy49")))) (properties `((upstream-name . "Rhisat2"))) (build-system r-build-system) - (native-inputs - `(("which" ,which))) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'make-reproducible + (lambda _ + (substitute* "src/Makefile" + (("`hostname`") "guix") + (("`date`") "0") + ;; Avoid shelling out to "which". + (("^CC =.*") (which "gcc")) + (("^CPP =.*") (which "g++"))) + #t))))) (propagated-inputs `(("r-genomicfeatures" ,r-genomicfeatures) ("r-genomicranges" ,r-genomicranges) -- cgit v1.2.3 From 2cebc5d13517fa0810753e24732f990698a87b55 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:24:10 +0100 Subject: gnu: r-sgseq: Update to 1.20.0. * gnu/packages/bioconductor.scm (r-sgseq): 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 07800d636b..2ba67c6ee1 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4836,14 +4836,14 @@ alignment tool.") (define-public r-sgseq (package (name "r-sgseq") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "SGSeq" version)) (sha256 (base32 - "09c0hv74pl310wahyyp4x50g6sz30bvrg24p2j9h7glla5dh2z4s")))) + "0950iv08wd0kjaw55rjn7m6syklvrabwr2zqq74wzyc5afyk2mrw")))) (properties `((upstream-name . "SGSeq"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 02684becc98cca1f01ff671901f3c3667d928c58 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:24:19 +0100 Subject: gnu: r-rbowtie: Update to 1.26.0. * gnu/packages/bioconductor.scm (r-rbowtie): 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 2ba67c6ee1..5cdcfee99a 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4813,14 +4813,14 @@ Gaussian distributions.") (define-public r-rbowtie (package (name "r-rbowtie") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rbowtie" version)) (sha256 (base32 - "1p8gbd2zn677lq8d009p2cplg1jm2jhn81lppipj638i9ynjh44f")))) + "0yy31xhdmf6xb21wlhmxxwfqpm0nil39pb2cs3pq5ia758lb88z4")))) (properties `((upstream-name . "Rbowtie"))) (build-system r-build-system) (inputs -- cgit v1.2.3 From 049de95de73570f6415bb880b7008bebb58fa143 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:24:26 +0100 Subject: gnu: r-iclusterplus: Update to 1.22.0. * gnu/packages/bioconductor.scm (r-iclusterplus): 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 5cdcfee99a..17aa7631c9 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4783,14 +4783,14 @@ and data files used across sessions.") (define-public r-iclusterplus (package (name "r-iclusterplus") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "iClusterPlus" version)) (sha256 (base32 - "14x43jjhbp4zwb4dv9rwrm5l5p7h76bc1zkdbiikqip9bzph0viq")))) + "1dzgfzf2x8m62hssvsn1zzag7m444kyxj2vpdxl9nk859dr5pf37")))) (properties `((upstream-name . "iClusterPlus"))) (build-system r-build-system) (native-inputs `(("gfortran" ,gfortran))) -- cgit v1.2.3 From 97e317007c4bcf58984d3fbf09935abdda6315db Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:24:34 +0100 Subject: gnu: r-biocfilecache: Update to 1.10.2. * gnu/packages/bioconductor.scm (r-biocfilecache): Update to 1.10.2. --- 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 17aa7631c9..9cb281c410 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4753,14 +4753,14 @@ Infinium HumanMethylation 450k assay.") (define-public r-biocfilecache (package (name "r-biocfilecache") - (version "1.8.0") + (version "1.10.2") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocFileCache" version)) (sha256 (base32 - "1mi8p8hvrdxim8lqsid2cb7284imyjf9rlzsrdlzdjac7dp9bpdb")))) + "0jivhn95y6zv5ryamqk6nyd4l8nlskq64j362l9ml9qw746v0ja6")))) (properties `((upstream-name . "BiocFileCache"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 4f0d858841ecc2e7e209122b92f762cf04d23d54 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:24:43 +0100 Subject: gnu: r-arrmnormalization: Update to 1.26.0. * gnu/packages/bioconductor.scm (r-arrmnormalization): 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 9cb281c410..8521c2da78 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4730,14 +4730,14 @@ expression\".") (define-public r-arrmnormalization (package (name "r-arrmnormalization") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ARRmNormalization" version)) (sha256 (base32 - "05m7hy1qd4lr1ylb0ld30dirdl9jfp1zhvifl6wvj40x74b6h2d1")))) + "0jj81q454nyh4hr5c56q1hv7i4ynx3rwnvpv08w34a6m77122bi1")))) (properties `((upstream-name . "ARRmNormalization"))) (build-system r-build-system) -- cgit v1.2.3 From 82d87ce02a3a4633901b21423322c52a264b96e4 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:24:50 +0100 Subject: gnu: r-progeny: Update to 1.8.0. * gnu/packages/bioconductor.scm (r-progeny): 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 8521c2da78..eb947de2f3 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4708,14 +4708,14 @@ rapid adapter trimming, identification, and read merging.") (define-public r-progeny (package (name "r-progeny") - (version "1.6.0") + (version "1.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "progeny" version)) (sha256 (base32 - "03rm90vfb9ivxhapvs3h5yggfazf8bf5vh1krknvb3xyw27br9dw")))) + "0j3kxjj7xmmwb29p87n3bw7bl38gcb94jrpw32126a578rf1pfrq")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase))) (home-page "https://github.com/saezlab/progeny") -- cgit v1.2.3 From c5a4c5a1ce1304a33e2242966278c0d2efaf4d1b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:24:58 +0100 Subject: gnu: r-rbowtie2: Update to 1.8.0. * gnu/packages/bioconductor.scm (r-rbowtie2): 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 eb947de2f3..6c9a4f907d 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4685,14 +4685,14 @@ This algorithm is based on the publication by Hart et al., 2013 (Pubmed ID (define-public r-rbowtie2 (package (name "r-rbowtie2") - (version "1.6.0") + (version "1.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rbowtie2" version)) (sha256 (base32 - "1yphnrk5j52gzvy9g6mw05dzh9sm8xxvhyja59ak68nrs1bh3lq4")))) + "1b7x42n9zisi2w2wwfc0c39j8s9868imyr0ysqgswf6l5mv9ivc5")))) (properties `((upstream-name . "Rbowtie2"))) (build-system r-build-system) (inputs -- cgit v1.2.3 From 18b93e035071ba4aa0b8331266d6846f457e9c69 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:25:06 +0100 Subject: gnu: r-zfpkm: Update to 1.8.0. * gnu/packages/bioconductor.scm (r-zfpkm): 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 6c9a4f907d..c80bd0a1e0 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4658,14 +4658,14 @@ Currently only Affymetrix oligonucleotide analysis is supported.") (define-public r-zfpkm (package (name "r-zfpkm") - (version "1.6.0") + (version "1.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "zFPKM" version)) (sha256 (base32 - "14knxp8cjjp9fhc6py66c7hrckf112jamz3gl1v60l1f2l1hmfvz")))) + "1hg0vc0ns8d4jpddn1v5a5m13a033b0wf1al01pb1lvmx5mzzr2n")))) (properties `((upstream-name . "zFPKM"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 316bcd07a8ebb25fcf91350de4fe926f6a0b373f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:25:14 +0100 Subject: gnu: r-webbioc: Update to 1.58.0. * gnu/packages/bioconductor.scm (r-webbioc): 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 c80bd0a1e0..f423713cdf 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4625,14 +4625,14 @@ widgets in R.") (define-public r-webbioc (package (name "r-webbioc") - (version "1.56.0") + (version "1.58.0") (source (origin (method url-fetch) (uri (bioconductor-uri "webbioc" version)) (sha256 (base32 - "0ilrwzbk0v41p6hwng7jmr3hwwb4skdcjqml1mc3xmh99lcvw8hz")))) + "1cwrmvh1l603k6j1r425c4vrqp0zf0x7bgx7y1wnbq4r7yc5sp62")))) (build-system r-build-system) (inputs `(("netpbm" ,netpbm) -- cgit v1.2.3 From 1a2569e4cc71a4060a46d2a5ee45b3d26b0e7608 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:25:23 +0100 Subject: gnu: r-widgettools: Update to 1.64.0. * gnu/packages/bioconductor.scm (r-widgettools): 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 f423713cdf..f6dd76285d 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4604,14 +4604,14 @@ visualization of exonic read coverage.") (define-public r-widgettools (package (name "r-widgettools") - (version "1.62.0") + (version "1.64.0") (source (origin (method url-fetch) (uri (bioconductor-uri "widgetTools" version)) (sha256 (base32 - "021b4s5vcy68p95p8rrcz8a8b1gyk4k8zq06snn32k2dqr91xi1a")))) + "1nqy3icayacv5mlv5s5xgfli0dqzancs6zpffrl5p237c994nyr5")))) (properties `((upstream-name . "widgetTools"))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/widgetTools/") -- cgit v1.2.3 From 25db5611e26c4cbf5b4fdff1b7da4ed7c63abf44 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:25:33 +0100 Subject: gnu: r-wiggleplotr: Update to 1.10.1. * gnu/packages/bioconductor.scm (r-wiggleplotr): Update to 1.10.1. --- 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 f6dd76285d..31d7cf6cd9 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4572,14 +4572,14 @@ that arising from 16s metagenomic surveys.") (define-public r-wiggleplotr (package (name "r-wiggleplotr") - (version "1.8.0") + (version "1.10.1") (source (origin (method url-fetch) (uri (bioconductor-uri "wiggleplotr" version)) (sha256 (base32 - "0yl3ymsk5iijbypjg7lf6mkjgb54893vml2v5aqp2q4l8q0ld7l0")))) + "1pj2bsn5azs18mp5hr4g7c6rnds2y2rjjnak2785kaj7xi8jly4m")))) (build-system r-build-system) (propagated-inputs `(("r-assertthat" ,r-assertthat) -- cgit v1.2.3 From 92f40538d34b1ca0ccb21e96a12559dbde68a00c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:25:41 +0100 Subject: gnu: r-wrench: Update to 1.4.0. * gnu/packages/bioconductor.scm (r-wrench): Update to 1.4.0. --- 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 31d7cf6cd9..e81a7042e3 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4548,14 +4548,14 @@ data for high-throughput, untargeted analyte profiling.") (define-public r-wrench (package (name "r-wrench") - (version "1.2.0") + (version "1.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Wrench" version)) (sha256 (base32 - "1js4dsgpgwq552r4ay78awd5vhzlmva0v8xvn3dy9v18y4j9k94i")))) + "1s8d7jn0dk5zk2fhvsd4sgicypz4c41nzf19nqzcwb9bd6asgrwm")))) (properties `((upstream-name . "Wrench"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 4fb52345b259d8e0bc240c407800dcbaa69080c6 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:25:49 +0100 Subject: gnu: r-xcms: Update to 3.8.1. * gnu/packages/bioconductor.scm (r-xcms): Update to 3.8.1. [propagated-inputs]: Add r-iranges. --- 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 e81a7042e3..5a7ee8c720 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4512,19 +4512,20 @@ based on @dfn{Continuous Wavelet Transform} (CWT).") (define-public r-xcms (package (name "r-xcms") - (version "3.6.2") + (version "3.8.1") (source (origin (method url-fetch) (uri (bioconductor-uri "xcms" version)) (sha256 (base32 - "0icww3f1kahyk96mc07yhsbyiranzm2614n509as09jf8bdhq23v")))) + "18iglvlvlxrdwn2apdvihj9jxmx0kwm5z37rml67xcj9sfdi3bjb")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) ("r-biocgenerics" ,r-biocgenerics) ("r-biocparallel" ,r-biocparallel) + ("r-iranges" ,r-iranges) ("r-lattice" ,r-lattice) ("r-massspecwavelet" ,r-massspecwavelet) ("r-msnbase" ,r-msnbase) -- cgit v1.2.3 From a07ee2584abef35e55155d3fc5c06631d4eae061 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:26:10 +0100 Subject: gnu: r-massspecwavelet: Update to 1.52.0. * gnu/packages/bioconductor.scm (r-massspecwavelet): 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 5a7ee8c720..6b0a411ff1 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4488,14 +4488,14 @@ genes.") (define-public r-massspecwavelet (package (name "r-massspecwavelet") - (version "1.50.0") + (version "1.52.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MassSpecWavelet" version)) (sha256 (base32 - "1qg73qv69fvf2al7znkh9lmyx5qmkqv2mpl33lahdwzkm0lh6n72")))) + "0xnj3ncrwvr2b8msi3g77mgzj0zaksn3lgqdn1abh0ww5wgk83v7")))) (properties `((upstream-name . "MassSpecWavelet"))) (build-system r-build-system) -- cgit v1.2.3 From 1f0101ae01a9e84e2c21d72444157a3f5052b16b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:26:19 +0100 Subject: gnu: r-xbseq: Update to 1.18.0. * gnu/packages/bioconductor.scm (r-xbseq): 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 6b0a411ff1..423fec0608 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4451,14 +4451,14 @@ sites and alignments obtained from standard RNA-seq experiments.") (define-public r-xbseq (package (name "r-xbseq") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "XBSeq" version)) (sha256 (base32 - "12l5qnkg6iahwyfmcsf18hys2i9cjn486sacvsqqfcjj3m88w1gy")))) + "1qr5gvf8jcx6r0ac7d2wmnikswmp3k71lirnw7dyr6fndzrdz9lp")))) (properties `((upstream-name . "XBSeq"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From f0dd0fec401daa7acd65d559dd70dce8048448b5 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:28:16 +0100 Subject: gnu: r-roar: Update to 1.22.0. * gnu/packages/bioconductor.scm (r-roar): 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 423fec0608..b5ac035be3 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4422,14 +4422,14 @@ large RNA-seq experiments.") (define-public r-roar (package (name "r-roar") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "roar" version)) (sha256 (base32 - "11ib5vr2vrrqsqcikph528c56bp52myyfdlwkklp8m0r15kwpxr7")))) + "1nqw0agx9x8ycdf0gw17fdlnmzpw9x3zig1wcy10xpyhyjdbbi06")))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) -- cgit v1.2.3 From 94fdea1267608d3fd4dd831f7d491fb9de5ab26d Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:28:24 +0100 Subject: gnu: r-yarn: Update to 1.12.0. * gnu/packages/bioconductor.scm (r-yarn): 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 b5ac035be3..a411a6fb84 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4387,14 +4387,14 @@ groups.") (define-public r-yarn (package (name "r-yarn") - (version "1.10.0") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "yarn" version)) (sha256 (base32 - "00gmwylpdmssz8xpd91d8fsiyglr7f9vc9bdalpa7w5vg4c6d2f6")))) + "0891a10adkhm1zpm7fpcxc2xfxjf9yrpckaz87b2wdjdiwivc4cp")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) -- cgit v1.2.3 From eb697ff5bbf018aa7a24987b13670737261be1cb Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:28:32 +0100 Subject: gnu: r-quantro: Update to 1.20.0. * gnu/packages/bioconductor.scm (r-quantro): 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 a411a6fb84..b9b8ef95d2 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4356,14 +4356,14 @@ chips with the MAQC reference datasets.") (define-public r-quantro (package (name "r-quantro") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "quantro" version)) (sha256 (base32 - "0zfb2s410ijp0didapnq7q4gn2d26wy785cygxyvg8sq6mlw2cab")))) + "09f3x1j50ll5hhn3qwys5x06mii3fqsrk6dkvsxai0kdxv9cjz9m")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) -- cgit v1.2.3 From 87942b74c66c27363a8455e32808bd04401f93f4 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:29:27 +0100 Subject: gnu: r-yaqcaffy: Update to 1.46.0. * gnu/packages/bioconductor.scm (r-yaqcaffy): Update to 1.46.0. --- 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 b9b8ef95d2..8cda3163e3 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4334,14 +4334,14 @@ generating high resolution journal figures.") (define-public r-yaqcaffy (package (name "r-yaqcaffy") - (version "1.44.0") + (version "1.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "yaqcaffy" version)) (sha256 (base32 - "1v12mbai6gf7wpxbyz4clvr7w1mlbv3scjf4kydfin8wwrrzq670")))) + "0kzzqsf1lfbcmy95w2z0c9qrvp7mbwm50k2l9wvz3xa5wz6xa7gz")))) (build-system r-build-system) (propagated-inputs `(("r-simpleaffy" ,r-simpleaffy))) -- cgit v1.2.3 From a87aa2ff5a145444ed45b8724e4676a32fd8bfa9 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:30:31 +0100 Subject: gnu: r-simpleaffy: Update to 2.62.0. * gnu/packages/bioconductor.scm (r-simpleaffy): 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 8cda3163e3..cf123c8796 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4306,14 +4306,14 @@ gene-specific bidning is expected.") (define-public r-simpleaffy (package (name "r-simpleaffy") - (version "2.60.0") + (version "2.62.0") (source (origin (method url-fetch) (uri (bioconductor-uri "simpleaffy" version)) (sha256 (base32 - "0zjpbjkk27w56mrxsxynkqc298xxsarsnzbd7injg6zakhlmhy6a")))) + "18bz3pfgp0f7906flrljx97ann8s71pnb8gpw7nah46n8vqc0xcs")))) (build-system r-build-system) (propagated-inputs `(("r-affy" ,r-affy) -- cgit v1.2.3 From 2f90bab8d13a17f8504e815b674d776dfca44015 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:30:40 +0100 Subject: gnu: r-gcrma: Update to 2.58.0. * gnu/packages/bioconductor.scm (r-gcrma): 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 cf123c8796..c7e5c772a2 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4270,14 +4270,14 @@ provided.") (define-public r-gcrma (package (name "r-gcrma") - (version "2.56.0") + (version "2.58.0") (source (origin (method url-fetch) (uri (bioconductor-uri "gcrma" version)) (sha256 (base32 - "1wazr3f4hwzpd0cjs2nlnzifr2g1r8a692pxap9xnmrw66zq94s4")))) + "0c9sa9ldlcpdcjdan8m4ndnyaisr6wbarq486sl44ikh7wf1csfx")))) (build-system r-build-system) (propagated-inputs `(("r-affy" ,r-affy) -- cgit v1.2.3 From 580e434267e613f39c13723829c13542462ba502 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:30:47 +0100 Subject: gnu: r-yapsa: Update to 1.12.0. * gnu/packages/bioconductor.scm (r-yapsa): 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 c7e5c772a2..952cfb16d1 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4230,14 +4230,14 @@ decomposition algorithms.") (define-public r-yapsa (package (name "r-yapsa") - (version "1.10.0") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "YAPSA" version)) (sha256 (base32 - "0rfjn2x6hsqiigd53bnl7z5ix5s2mbpr9glsyihsa7i6iazh3n1q")))) + "132x51f8k8zyx6j8jk05x4lr9q1hlblgvr69wkhn0q3f8mhaj926")))) (properties `((upstream-name . "YAPSA"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 4f8e0487fc17a9c227c64844ccab29f912fc7ede Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:30:55 +0100 Subject: gnu: r-somaticsignatures: Update to 2.22.0. * gnu/packages/bioconductor.scm (r-somaticsignatures): 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 952cfb16d1..6c8ba04b85 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4193,14 +4193,14 @@ genomic categories and to add self-defined graphics in the plot.") (define-public r-somaticsignatures (package (name "r-somaticsignatures") - (version "2.20.0") + (version "2.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "SomaticSignatures" version)) (sha256 (base32 - "0wc4ddwngvkc9jhihzaxx8yazqncl1kbgkx8vqn5gd4w2hx0h5bx")))) + "1gvrkahllwz38g3hn9pjlikhfqz19a4qglcqmyrxk7h9ybx5zy5z")))) (properties `((upstream-name . "SomaticSignatures"))) (build-system r-build-system) -- cgit v1.2.3 From cf0a1cb3b4a94f472ab03c2eff366aff58621eb3 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:31:16 +0100 Subject: gnu: r-gtrellis: Update to 1.18.0. * gnu/packages/bioconductor.scm (r-gtrellis): 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 6c8ba04b85..4e5bd8973a 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4166,14 +4166,14 @@ analysis.") (define-public r-gtrellis (package (name "r-gtrellis") - (version "1.16.1") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "gtrellis" version)) (sha256 (base32 - "069hln9vflyxic24bxrlmdmz9h3jdd2qaqy898rgk5bn0gqwcjix")))) + "0mgspmv6p1a2k98jyy2dfl0wpa2vh7bhnjfm2xaqmcsxzmbjhh9z")))) (build-system r-build-system) (propagated-inputs `(("r-circlize" ,r-circlize) -- cgit v1.2.3 From 3796e2442b3b5c34ba3eea760b7632067c573279 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:31:39 +0100 Subject: gnu: r-yamss: Update to 1.12.0. * gnu/packages/bioconductor.scm (r-yamss): 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 4e5bd8973a..ea4f07e3bb 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4134,14 +4134,14 @@ visualization with image data.") (define-public r-yamss (package (name "r-yamss") - (version "1.10.0") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "yamss" version)) (sha256 (base32 - "00756szrmfm1jdayl90jgblydn6sick9nagdf77pn7wzh6wlaj23")))) + "1n49a2vg1667wycrjww29xfafngllvpb5nq5wy6pgn0akva91nky")))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) -- cgit v1.2.3 From ca7192a1c93634d0f2b507cce761d3ae59e3bc3e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:31:47 +0100 Subject: gnu: r-ebimage: Update to 4.28.1. * gnu/packages/bioconductor.scm (r-ebimage): Update to 4.28.1. --- 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 ea4f07e3bb..8ca2737678 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4095,14 +4095,14 @@ needed.") (define-public r-ebimage (package (name "r-ebimage") - (version "4.26.0") + (version "4.28.1") (source (origin (method url-fetch) (uri (bioconductor-uri "EBImage" version)) (sha256 (base32 - "0c8rfi40959rbpbizpiizkq21az3lfwf2azlj55yz5m61qp7mgsq")))) + "0q54q2nw6p1s4nrj1l8qz78m67xcysj2x82zs43my8iv2g9iifgs")))) (properties `((upstream-name . "EBImage"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 3a35d274500b0db7dd485a880e74e96c9a8ddc92 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:31:57 +0100 Subject: gnu: r-aucell: Update to 1.8.0. * gnu/packages/bioconductor.scm (r-aucell): Update to 1.8.0. [propagated-inputs]: Add r-biocgenerics and r-s4vectors. --- 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 8ca2737678..bb1a99d372 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4060,21 +4060,23 @@ investigation using RNA-seq data.") (define-public r-aucell (package (name "r-aucell") - (version "1.6.1") + (version "1.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AUCell" version)) (sha256 (base32 - "1vd8w6dygn1b5bwlha09mm6fbwyj07pmawpv53agcg1y7jlxs31b")))) + "1g4mdq8z29fjxrfjng0fb3cvbph49mwds4ijsa2bn2k6f75dnzky")))) (properties `((upstream-name . "AUCell"))) (build-system r-build-system) (propagated-inputs - `(("r-data-table" ,r-data-table) + `(("r-biocgenerics" ,r-biocgenerics) + ("r-data-table" ,r-data-table) ("r-gseabase" ,r-gseabase) ("r-mixtools" ,r-mixtools) ("r-r-utils" ,r-r-utils) + ("r-s4vectors" ,r-s4vectors) ("r-shiny" ,r-shiny) ("r-summarizedexperiment" ,r-summarizedexperiment))) (home-page "https://bioconductor.org/packages/AUCell/") -- cgit v1.2.3 From 50e6f76278cd647423b7fab59330c33bc427e3b5 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:32:17 +0100 Subject: gnu: r-allelicimbalance: Update to 1.24.0. * gnu/packages/bioconductor.scm (r-allelicimbalance): 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 bb1a99d372..a1c4379765 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4019,14 +4019,14 @@ text files).") (define-public r-allelicimbalance (package (name "r-allelicimbalance") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AllelicImbalance" version)) (sha256 (base32 - "1f51y8zjgz0wdd33qbs1gpnadbprixr4wcfvff6v3s09rmnr8fng")))) + "0vy8w7ii2qljsmq8lr21lygkcrsshc7syyqhadlbxyj3scgi7kyc")))) (properties `((upstream-name . "AllelicImbalance"))) (build-system r-build-system) -- cgit v1.2.3 From eda490855679c87480846c0d161cc474d15e4c83 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:32:24 +0100 Subject: gnu: r-annotationtools: Update to 1.60.0. * gnu/packages/bioconductor.scm (r-annotationtools): Update to 1.60.0. --- 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 a1c4379765..9ed78a470a 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3994,14 +3994,14 @@ different identifieres using the Biocore Data Team data-packages (e.g. (define-public r-annotationtools (package (name "r-annotationtools") - (version "1.58.0") + (version "1.60.0") (source (origin (method url-fetch) (uri (bioconductor-uri "annotationTools" version)) (sha256 (base32 - "148fi8bv1m0y81psm0jv1nqvjhvr461drnl0krqd7skcf0mb0fc1")))) + "1cq7ayq2swp2ahlphz74nh5mb869rgyyr0kkqy1mxyilk8k2g44i")))) (properties `((upstream-name . "annotationTools"))) (build-system r-build-system) -- cgit v1.2.3 From 3a731c8334a5da49a22621ee09c49850e37351b1 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:32:31 +0100 Subject: gnu: r-annotationfuncs: Update to 1.36.0. * gnu/packages/bioconductor.scm (r-annotationfuncs): 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 9ed78a470a..65f3b2f658 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3969,14 +3969,14 @@ the brain using an ontology, both provided by the Allen Brain Atlas project.") (define-public r-annotationfuncs (package (name "r-annotationfuncs") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AnnotationFuncs" version)) (sha256 (base32 - "12vh07x8s9y74h65q1pnjlma752pz29bmyyhlnqaiy83gsg26hm3")))) + "0ws14b1ibqml7w8kj0gi7wdp6wd8dcdpnrmcxldjzsyawf17q0yq")))) (properties `((upstream-name . "AnnotationFuncs"))) (build-system r-build-system) -- cgit v1.2.3 From 307667c4ef427ee3975f8f80fe12ac1c61ab0f50 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:32:39 +0100 Subject: gnu: r-abaenrichment: Update to 1.16.0. * gnu/packages/bioconductor.scm (r-abaenrichment): 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 65f3b2f658..4201460a96 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3939,14 +3939,14 @@ annotations and ontologies.") (define-public r-abaenrichment (package (name "r-abaenrichment") - (version "1.14.1") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ABAEnrichment" version)) (sha256 (base32 - "1w322wsp6bd3gyfwzgdf088cvfmpq774knr57d0dj420ljf4xn48")))) + "128ik28j8kmdkycffhxajv5h174zdq9sfn2gz6ai90wgkdadbzwp")))) (properties `((upstream-name . "ABAEnrichment"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 4997e0254a414c3cceba9ac251db822835fc2bbd Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:32:46 +0100 Subject: gnu: r-gofuncr: Update to 1.6.0. * gnu/packages/bioconductor.scm (r-gofuncr): 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 4201460a96..1f89f79aea 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3892,14 +3892,14 @@ footprints.") (define-public r-gofuncr (package (name "r-gofuncr") - (version "1.4.0") + (version "1.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GOfuncR" version)) (sha256 (base32 - "1znnkh96yyv6rkbjxx2942nixw4ixdll1f72v92wzsxdcbwkgqdm")))) + "0hmi13pz923fm95asys615rih63b1i2nvynfczr1zcsc9fzn4h35")))) (properties `((upstream-name . "GOfuncR"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 36aecb2105f9bd9743a089f3348ad04e36aaca08 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:32:53 +0100 Subject: gnu: r-atacseqqc: Update to 1.10.1. * gnu/packages/bioconductor.scm (r-atacseqqc): Update to 1.10.1. --- 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 1f89f79aea..bc8a22bc9d 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3847,14 +3847,14 @@ position-specific scores within R and Bioconductor.") (define-public r-atacseqqc (package (name "r-atacseqqc") - (version "1.8.5") + (version "1.10.1") (source (origin (method url-fetch) (uri (bioconductor-uri "ATACseqQC" version)) (sha256 (base32 - "1i8f0vs0z4jbc2yvj1diay7jhcmb1a82zv96xllk771f25nvmmxp")))) + "12ix0bvwk50d48z85f3453k7szm1j27gk4qgw56az4fxra472rlh")))) (properties `((upstream-name . "ATACseqQC"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From e89f16e646fdc47e8d9a922f740ee878391995fb Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:33:01 +0100 Subject: gnu: r-genomicscores: Update to 1.10.0. * gnu/packages/bioconductor.scm (r-genomicscores): 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 bc8a22bc9d..3947c1ce3c 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3816,14 +3816,14 @@ type and symbol colors.") (define-public r-genomicscores (package (name "r-genomicscores") - (version "1.8.1") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicScores" version)) (sha256 (base32 - "0xgv5h6hwr4p2p05z8vzhivy97gfirm4rj1ihb5c8fhgc5vp85dy")))) + "175iaqv7npa11yw48vmqpgx0qqs3g44c3dsya7ccwd1lg97fznkj")))) (properties `((upstream-name . "GenomicScores"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From dda936ca9aab984797a1bde8a4481177cf98ecab Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:33:09 +0100 Subject: gnu: r-motifstack: Update to 1.30.0. * gnu/packages/bioconductor.scm (r-motifstack): Update to 1.30.0. [propagated-inputs]: Add r-ggplot2. --- 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 3947c1ce3c..1657d1fd34 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3785,19 +3785,20 @@ distributions, modules and filter motifs.") (define-public r-motifstack (package (name "r-motifstack") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "motifStack" version)) (sha256 (base32 - "0qbv5pvn1g9xfn221vqjmp9vfxpkda1wxkn0kyn2nqyb80d4jf9f")))) + "00rafqs1gqlcxlbsdn9qnq9xb7wjphiksb3hsx76viqjbjzi14wg")))) (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) -- cgit v1.2.3 From 35a1b3ec4cc1f75ff300c6aa50f1b2b5bee1adc4 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:33:30 +0100 Subject: gnu: r-motiv: Update to 1.42.0. * gnu/packages/bioconductor.scm (r-motiv): Update to 1.42.0. [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 1657d1fd34..72d2bb36bf 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3754,14 +3754,14 @@ genomic sequence data.") (define-public r-motiv (package (name "r-motiv") - (version "1.40.0") + (version "1.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MotIV" version)) (sha256 (base32 - "088z3vyx5h2c4ll4sway01cd4h0x2ayhbv55f6l2kss71v6k6byf")))) + "07k4rw4nhcn4sg43psv1h7qr064gws22m2yyr7x8sy3f1i1c954k")))) (properties `((upstream-name . "MotIV"))) (build-system r-build-system) (inputs @@ -3769,6 +3769,7 @@ genomic sequence data.") (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) ("r-biostrings" ,r-biostrings) + ("r-genomicranges" ,r-genomicranges) ("r-iranges" ,r-iranges) ("r-lattice" ,r-lattice) ("r-rgadem" ,r-rgadem) -- cgit v1.2.3 From 6dfe5056c9c3aa107448d9a17783c275a5deb0b9 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:33:58 +0100 Subject: gnu: r-rgadem: Update to 2.34.0. * gnu/packages/bioconductor.scm (r-rgadem): 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 72d2bb36bf..f18825bc0a 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3729,14 +3729,14 @@ fitting a three-component normal mixture on z-scores.") (define-public r-rgadem (package (name "r-rgadem") - (version "2.32.0") + (version "2.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "rGADEM" version)) (sha256 (base32 - "1zf8ayllf1i79wc39vyln2hii1bgg88sw6h1hngkqx4phyvl9q18")))) + "14ylbrzb9haqwfdd9g813mzhll6gwvqf2r7cmbaxz5lkl0j0nglx")))) (properties `((upstream-name . "rGADEM"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 32b471f4a7e003f887aeaa0831779764e562bf25 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:34:20 +0100 Subject: gnu: r-bacon: Update to 1.14.0. * gnu/packages/bioconductor.scm (r-bacon): 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 f18825bc0a..5b078e8a5d 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3704,14 +3704,14 @@ further downstream analysis on its output.") (define-public r-bacon (package (name "r-bacon") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bacon" version)) (sha256 (base32 - "1p6h348kwbsan6dwviclwxx02jcdmf580g5f95w2sgn4jnfv7q1q")))) + "1q18vm4znl47v56cnvx9y5ygrial2mdjpl8x1043jq00kyygrc86")))) (build-system r-build-system) (propagated-inputs `(("r-biocparallel" ,r-biocparallel) -- cgit v1.2.3 From aef4b34669cb4bbb1b0cb4c724a2955e7b25e8db Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:34:28 +0100 Subject: gnu: r-abseqr: Update to 1.4.0. * gnu/packages/bioconductor.scm (r-abseqr): Update to 1.4.0. --- 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 5b078e8a5d..ff24741b94 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3658,14 +3658,14 @@ Affymetrix arrays.") (define-public r-abseqr (package (name "r-abseqr") - (version "1.2.0") + (version "1.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "abseqR" version)) (sha256 (base32 - "0cbjm7cxjfrkwqhcrrh93w0zf3skmi2p9hyx7acg0ym5fz0ic51r")))) + "1n9h5qkj4njr1f8fvhg9sj9wxcd7hljnnk8m80zwswzs2n9ivppa")))) (properties `((upstream-name . "abseqR"))) (build-system r-build-system) (inputs -- cgit v1.2.3 From 344eb4c404f92ced894779f27455417ba597f35d Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:34:35 +0100 Subject: gnu: r-a4: Update to 1.34.0. * gnu/packages/bioconductor.scm (r-a4): 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 ff24741b94..0206d77103 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3633,14 +3633,14 @@ Affymetrix arrays.") (define-public r-a4 (package (name "r-a4") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "a4" version)) (sha256 (base32 - "08146qzsr6mjblmh08g83063nnyrfl35z6p65v71isprkydgxyhy")))) + "14yipy6s2wqr9q0yp09x1mm17npknrhs6yd34i3wrb5id64ywnq4")))) (build-system r-build-system) (propagated-inputs `(("r-a4base" ,r-a4base) -- cgit v1.2.3 From 85c945aa97d89fdc17ec5d64c3ffa7f99ba1184b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:34:43 +0100 Subject: gnu: r-a4base: Update to 1.34.0. * gnu/packages/bioconductor.scm (r-a4base): 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 0206d77103..d533e30c3e 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3601,14 +3601,14 @@ provides reporting features.") (define-public r-a4base (package (name "r-a4base") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "a4Base" version)) (sha256 (base32 - "0yd8gkg3dlkijnms88bxkqsghhc9i32pgd9yaq6hzr67wk879wa1")))) + "0dgqyq4dnlcik5qqygnhxlhfr98sh6kmdcj2qllhrwyk0lmsfk01")))) (properties `((upstream-name . "a4Base"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 977a7802c13f67e8d3c7bc627e87d1e7474a3546 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:34:50 +0100 Subject: gnu: r-a4reporting: Update to 1.34.0. * gnu/packages/bioconductor.scm (r-a4reporting): 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 d533e30c3e..6bc382b92f 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3578,14 +3578,14 @@ is used for preprocessing the arrays.") (define-public r-a4reporting (package (name "r-a4reporting") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "a4Reporting" version)) (sha256 (base32 - "1lail2iw8jmvfdq9brv7i41k6vmbhx2kp21jxq2cj1zva5rcqssj")))) + "15nd4pa5hkdzkhinvqw5ijdqb7k5gk37v2hmk3jsg2d6m0jqphi5")))) (properties `((upstream-name . "a4Reporting"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From d6859c7c9bd653547bba108aa3c02c2a348c0d7e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:34:56 +0100 Subject: gnu: r-a4preproc: Update to 1.34.0. * gnu/packages/bioconductor.scm (r-a4preproc): 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 6bc382b92f..a207270f3b 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3556,14 +3556,14 @@ Affymetrix arrays.") (define-public r-a4preproc (package (name "r-a4preproc") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "a4Preproc" version)) (sha256 (base32 - "13sj4zriq1mian2xcjwkbmmpdjh3h6dgjslar2hc8nmd34cb9xjr")))) + "11j5nc33gd6yis1fyagr0y39g21bzkc59kq8b8sd6b3pfc84zrjd")))) (properties `((upstream-name . "a4Preproc"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 102b982cbe970095373f34345f7b3babc3334f17 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:35:04 +0100 Subject: gnu: r-a4classif: Update to 1.34.0. * gnu/packages/bioconductor.scm (r-a4classif): 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 a207270f3b..18a592f0f3 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3528,14 +3528,14 @@ arrays.") (define-public r-a4classif (package (name "r-a4classif") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "a4Classif" version)) (sha256 (base32 - "1jif0w3hx020zzwkaza1a26mf34343y7a3v80ic93in6n53yjhj0")))) + "0gj3hdflfs1ybc2kshl9w1dzy0rfzppfj08hx3wa2chjsm0m9brn")))) (properties `((upstream-name . "a4Classif"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 4ed18ddc0f73f8f2a04464bd7031c68eae063c73 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:35:11 +0100 Subject: gnu: r-a4core: Update to 1.34.0. * gnu/packages/bioconductor.scm (r-a4core): 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 18a592f0f3..96263c48de 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3505,14 +3505,14 @@ It allows searching of biological metadata using various criteria.") (define-public r-a4core (package (name "r-a4core") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "a4Core" version)) (sha256 (base32 - "1cr0d1w81iygil3pygqzigfb1a0hc248qd9vqvs0n537cxrxq7i7")))) + "0xcs9wl2yrprl4yc0z5s4zrkil3752k9xc1fi8fcx7zab1mm80df")))) (properties `((upstream-name . "a4Core"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From fc4a9dd579667ee10528dfcdb82034486d2e5e89 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:35:18 +0100 Subject: gnu: r-annaffy: Update to 1.58.0. * gnu/packages/bioconductor.scm (r-annaffy): 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 96263c48de..f41f6ec0e2 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3469,14 +3469,14 @@ data in R and Bioconductor containers.") (define-public r-annaffy (package (name "r-annaffy") - (version "1.56.0") + (version "1.58.0") (source (origin (method url-fetch) (uri (bioconductor-uri "annaffy" version)) (sha256 (base32 - "0sz96lcw0xc4bw1h3x0j40yh5ragmybsq6zwd0adlwzkhvriqjn9")))) + "1jrf4bq2wky4ay1jrcy60si6hxdcn4j05w5vgs38yfb92gq77i16")))) (build-system r-build-system) (arguments `(#:phases -- cgit v1.2.3 From 6374984a205b7e3d64118a7265125de9aff41a84 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:35:26 +0100 Subject: gnu: r-mlinterfaces: Update to 1.66.0. * gnu/packages/bioconductor.scm (r-mlinterfaces): 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 f41f6ec0e2..3b078a23c2 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3428,14 +3428,14 @@ profiles (GO and KEGG) of gene and gene clusters.") (define-public r-mlinterfaces (package (name "r-mlinterfaces") - (version "1.64.1") + (version "1.66.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MLInterfaces" version)) (sha256 (base32 - "1c1hciwy37zpr5bzdjj2xxx2r4jdfmr5w0zmg010lm2985z41gqh")))) + "1vnzqd3y3jk1wgxybckzrcgwk0ly7zgcz5ki1ib0bk1jwv6xk5x8")))) (properties `((upstream-name . "MLInterfaces"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 08c01b7e0efe2a87ec8de6c280c701825ce9b534 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:35:35 +0100 Subject: gnu: r-clusterprofiler: Update to 3.14.0. * gnu/packages/bioconductor.scm (r-clusterprofiler): Update to 3.14.0. --- 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 3b078a23c2..65fbb7098d 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3395,14 +3395,14 @@ All the visualization methods are developed based on ggplot2 graphics.") (define-public r-clusterprofiler (package (name "r-clusterprofiler") - (version "3.12.0") + (version "3.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "clusterProfiler" version)) (sha256 (base32 - "1jw8h6nlcgd86qhqlcgi3icylb7amcqimlvzg29gay3bf3grwfhq")))) + "0mm9iafrsjb8sj27k9mg40ab13vq4rmrzhaajm6g1wdkb2jqikjk")))) (properties `((upstream-name . "clusterProfiler"))) (build-system r-build-system) -- cgit v1.2.3 From 0654a9bc3bd07d8ddd6f337400a77c5c95726b85 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:35:45 +0100 Subject: gnu: r-enrichplot: Update to 1.6.0. * gnu/packages/bioconductor.scm (r-enrichplot): Update to 1.6.0. [propagated-inputs]: Remove r-upsetr. --- 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 65fbb7098d..2a38311b89 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3359,14 +3359,14 @@ data.") (define-public r-enrichplot (package (name "r-enrichplot") - (version "1.4.0") + (version "1.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "enrichplot" version)) (sha256 (base32 - "1i9psakvvdc6jn7k7zwpbdhwvf9r8s7649w05mwh1hy978x4rh6h")))) + "1jblx00b869xhx1c4n9m2g1hqr00rm9ywr1hrlx42bdd8k5ax1xh")))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) @@ -3382,8 +3382,7 @@ data.") ("r-igraph" ,r-igraph) ("r-purrr" ,r-purrr) ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-reshape2" ,r-reshape2) - ("r-upsetr" ,r-upsetr))) + ("r-reshape2" ,r-reshape2))) (home-page "https://github.com/GuangchuangYu/enrichplot") (synopsis "Visualization of functional enrichment result") (description -- cgit v1.2.3 From 166b3c2da65a30b38928129d86fc291243de5a57 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:35:59 +0100 Subject: gnu: r-dose: Update to 3.12.0. * gnu/packages/bioconductor.scm (r-dose): 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 2a38311b89..37a22b67d9 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3325,14 +3325,14 @@ to multiple hypothesis correction.") (define-public r-dose (package (name "r-dose") - (version "3.10.2") + (version "3.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DOSE" version)) (sha256 (base32 - "06jm1mnfd92s84f21562vsmj6jfkravfqf4lcxx2lk7s4ll66znj")))) + "0ss8mr28q0vswxjmhcas0aqag5nl099jbyn5w3ypbbxqwfvf9jj5")))) (properties `((upstream-name . "DOSE"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From b4e1268c7b14bf0aaf5b479920076c4a378475c4 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:36:09 +0100 Subject: gnu: r-fgsea: Update to 1.12.0. * gnu/packages/bioconductor.scm (r-fgsea): 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 37a22b67d9..9d9077a7c4 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3295,14 +3295,14 @@ phenotype of interest.") (define-public r-fgsea (package (name "r-fgsea") - (version "1.10.1") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "fgsea" version)) (sha256 (base32 - "1k2f9hkp1mvc9fpqzhbf08jd0yg4xaa312v9vy37fxd9pyrwp5a6")))) + "0pbq3g515kcbi4wvfx8m09p01h2f8vwsi1qqsyahxz4r1fasz4c1")))) (build-system r-build-system) (propagated-inputs `(("r-bh" ,r-bh) -- cgit v1.2.3 From 869965df1c9ccfe89706fe2861ab396b231434a4 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:36:16 +0100 Subject: gnu: r-sigpathway: Update to 1.54.0. * gnu/packages/bioconductor.scm (r-sigpathway): 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 9d9077a7c4..adce05e247 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3273,14 +3273,14 @@ the data set is suitable for such analysis.") (define-public r-sigpathway (package (name "r-sigpathway") - (version "1.52.0") + (version "1.54.0") (source (origin (method url-fetch) (uri (bioconductor-uri "sigPathway" version)) (sha256 (base32 - "1mc4lb78rcmpihzjiy4w738cbalw5zxms30z8kyy12s6vbxi6hx7")))) + "057qdkbfldpy6hsysk9mrs1vvsqgyl9yx2s6c2f26jz1pardkbqb")))) (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 5ed767521c47cca56fb8d5ef06609673bb4d49c5 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:36:23 +0100 Subject: gnu: r-anota: Update to 1.34.0. * gnu/packages/bioconductor.scm (r-anota): 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 adce05e247..018afce1ab 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3242,14 +3242,14 @@ sets of GO terms, gene products and gene clusters.") (define-public r-anota (package (name "r-anota") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "anota" version)) (sha256 (base32 - "0jchhyf9gqyj0k0fn5zp319griy32cckqpldq9x58z69l2ix2s2c")))) + "1bkavzrxy1bjz0bwapwa9i3ysln7gljgziwd8c05fmg2f46j1z6m")))) (build-system r-build-system) (propagated-inputs `(("r-multtest" ,r-multtest) -- cgit v1.2.3 From c245ec3d49dc254636255f6dd22038ff353188ec Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:36:30 +0100 Subject: gnu: r-gosemsim: Update to 2.12.0. * gnu/packages/bioconductor.scm (r-gosemsim): Update to 2.12.0. --- 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 018afce1ab..9a3148fc03 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3215,14 +3215,14 @@ information about samples and features can be added to the plot.") (define-public r-gosemsim (package (name "r-gosemsim") - (version "2.10.0") + (version "2.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GOSemSim" version)) (sha256 (base32 - "035jbm14rb1rjp2n00dp5bm88ad8a9afv4lvzpkv39nil98nzbdg")))) + "0pqnlgdvh5szjhwc1mw1snjgpj9lrsnk44bn164cl3zwvdayccya")))) (properties `((upstream-name . "GOSemSim"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 9f218627d6eb44b030182d3a612fab35f3fb65bc Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:36:36 +0100 Subject: gnu: r-heatplus: Update to 2.32.0. * gnu/packages/bioconductor.scm (r-heatplus): 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 9a3148fc03..cef38f6839 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3190,14 +3190,14 @@ gmapR.") (define-public r-heatplus (package (name "r-heatplus") - (version "2.30.0") + (version "2.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Heatplus" version)) (sha256 (base32 - "18b0zy12przp88sj1smvfdd39m17nhhnqzk656bs5pjls2ifmcm6")))) + "0hx5gqgh4xrkx37ccprq7azj9jziff137bdk0gvrixcx52ws6h89")))) (properties `((upstream-name . "Heatplus"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 9b72bbf784bee388b9484d15cf929a2068329b32 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:36:43 +0100 Subject: gnu: r-varianttools: Update to 1.28.0. * gnu/packages/bioconductor.scm (r-varianttools): 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 cef38f6839..d0f02bad3a 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3150,14 +3150,14 @@ peak definition in combination with known profile characteristics.") (define-public r-varianttools (package (name "r-varianttools") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "VariantTools" version)) (sha256 (base32 - "0y37nziipwikg47x4jhhsx0dyv15rrih4a4z43jbzv4jgq4krzql")))) + "0aafcprsqbn1xl8jqnxfl8r2d0lmzhssqpr26lam2cprh3yk0xiv")))) (properties `((upstream-name . "VariantTools"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From a18f325e0a2c13cfe53eac6fcc9e9e983b0f1fec Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:36:50 +0100 Subject: gnu: r-triform: Update to 1.28.0. * gnu/packages/bioconductor.scm (r-triform): 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 d0f02bad3a..e79282ef26 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3126,14 +3126,14 @@ published results; and a routine for graphical display.") (define-public r-triform (package (name "r-triform") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "triform" version)) (sha256 (base32 - "0bsxkn386kfx4gg19p6smy5fi3k7xdw89r5hvfsks8hsdpdz3hya")))) + "12qdyrcw2mcawqdw65v0hjaghzlwa10xl6j8458izcrm5k6dlvz9")))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) -- cgit v1.2.3 From 1b890c3231a7748622c2e8766184bab0d432658f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:36:57 +0100 Subject: gnu: r-ioniser: Update to 2.10.0. * gnu/packages/bioconductor.scm (r-ioniser): Update to 2.10.0. --- 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 e79282ef26..4bba4f9689 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2997,14 +2997,14 @@ evaluation of DEG analysis methods.") (define-public r-ioniser (package (name "r-ioniser") - (version "2.8.0") + (version "2.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "IONiseR" version)) (sha256 (base32 - "0kznyqqpm0zbah537p197z1cgrgh9w82whmq0aydfxzgs2vxdw2y")))) + "1c265bzh923i9mw83mjpj0bzbkixbs6sg1h1z51y9xjkakdgg90f")))) (properties `((upstream-name . "IONiseR"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From a2877d6970ad113b2ffc8adb4fd46bceca1d9f3a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:37:04 +0100 Subject: gnu: r-linnorm: Update to 2.10.0. * gnu/packages/bioconductor.scm (r-linnorm): Update to 2.10.0. --- 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 4bba4f9689..d05970f7ec 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2938,14 +2938,14 @@ especially Illumina Infinium methylation microarrays.") (define-public r-linnorm (package (name "r-linnorm") - (version "2.8.0") + (version "2.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Linnorm" version)) (sha256 (base32 - "1rv3ljdwb71364qd2p8za3jpk08agvzwas6f63s5d8wjlapzm3i5")))) + "15mhwiqmp9m65zvrdbr2hhy3x81lf4jbwgjsf75g41if2v2g8x67")))) (properties `((upstream-name . "Linnorm"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 8f7bc872e1253071c5c04d59fc90a2083c0fd479 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:37:11 +0100 Subject: gnu: r-lumi: Update to 2.38.0. * gnu/packages/bioconductor.scm (r-lumi): 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 d05970f7ec..3824c83263 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2899,14 +2899,14 @@ and Infinium HD arrays are also included.") (define-public r-lumi (package (name "r-lumi") - (version "2.36.0") + (version "2.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "lumi" version)) (sha256 (base32 - "1rf6xmd2wnajjvnl50q63agakzjf4hrzn2chdsnhapi7fh7bcjba")))) + "0lgrqbdvp7ykcafc0bpnbcsf396na3jj5c35x9ysf5bpcas23nmm")))) (build-system r-build-system) (propagated-inputs `(("r-affy" ,r-affy) -- cgit v1.2.3 From b57cffb974128585094c86c021113361d1f6424b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:37:17 +0100 Subject: gnu: r-methylumi: Update to 2.32.0. * gnu/packages/bioconductor.scm (r-methylumi): 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 3824c83263..29d55db042 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2855,14 +2855,14 @@ methylation arrays.") (define-public r-methylumi (package (name "r-methylumi") - (version "2.30.0") + (version "2.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "methylumi" version)) (sha256 (base32 - "13acn771ybi10v50x123bq5yqd62b8sr4gz77lpgaj192sxq9d9f")))) + "0zd4h6n37v3z0mas69z2xsf5s0naih828987m8v0g9hhq4f6hf5w")))) (build-system r-build-system) (propagated-inputs `(("r-annotate" ,r-annotate) -- cgit v1.2.3 From dfd4287cba9304941fe0f4d397d87c436b8e647a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:37:24 +0100 Subject: gnu: r-minfi: Update to 1.32.0. * gnu/packages/bioconductor.scm (r-minfi): 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 29d55db042..bcb6b29207 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2806,14 +2806,14 @@ studies.") (define-public r-minfi (package (name "r-minfi") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "minfi" version)) (sha256 (base32 - "0qir0zd0qa97fzm33v10nyrsjp8nmzhn7mn20dnlpsg7rwlf60pd")))) + "177isdvcq2476xybvfbh7x11qsj5nzckgh3b6p156wlx9ap9dvl3")))) (build-system r-build-system) (propagated-inputs `(("r-beanplot" ,r-beanplot) -- cgit v1.2.3 From 4efdac562b2a52dde224a9f9a309674ec99a5bbb Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:37:30 +0100 Subject: gnu: r-bumphunter: Update to 1.28.0. * gnu/packages/bioconductor.scm (r-bumphunter): 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 bcb6b29207..c5da9d8abd 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2772,14 +2772,14 @@ Bayes Analyses of Microarrays} (EBAM).") (define-public r-bumphunter (package (name "r-bumphunter") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bumphunter" version)) (sha256 (base32 - "1dkyicwqdaahnxcxj6kmivkqb47yccx51lb1q0yar3xpw91vwlfx")))) + "1p3gwb954zns61d1pwgkplxnvgk2lixrl93kkkf439wa3vlgsnjv")))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) -- cgit v1.2.3 From b4ee414880d4b375492e3599677a934653f783c8 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:37:38 +0100 Subject: gnu: r-siggenes: Update to 1.60.0. * gnu/packages/bioconductor.scm (r-siggenes): Update to 1.60.0. --- 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 c5da9d8abd..9714e84b6d 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2746,14 +2746,14 @@ files, including IDAT.") (define-public r-siggenes (package (name "r-siggenes") - (version "1.58.0") + (version "1.60.0") (source (origin (method url-fetch) (uri (bioconductor-uri "siggenes" version)) (sha256 (base32 - "178jmmdxsv3rd71a9w5yrvg5aplak40hb42vna15g1d55c2yv1ib")))) + "03lmq3hqprwps4miynl2vhqi3v4als5vqmz4lb19lk5a4zja72b4")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) -- cgit v1.2.3 From 6e10ac0780203e5efd0469ed9d8be4f76cfb8303 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:37:46 +0100 Subject: gnu: r-destiny: Update to 3.0.0. * gnu/packages/bioconductor.scm (r-destiny): Update to 3.0.0. [propagated-inputs]: Add r-ggplot-multistats, r-irlba, r-knn-covertree, r-pcamethods, r-rcpphnsw, r-rspectra, r-singlecellexperiment, r-tidyr, and r-tidyselect; remove r-igraph. --- gnu/packages/bioconductor.scm | 14 +++++++++++--- 1 file changed, 11 insertions(+), 3 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 9714e84b6d..cb748df6c2 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2102,29 +2102,37 @@ possible, parallelization is achieved using the BiocParallel framework.") (define-public r-destiny (package (name "r-destiny") - (version "2.14.0") + (version "3.0.0") (source (origin (method url-fetch) (uri (bioconductor-uri "destiny" version)) (sha256 (base32 - "1bpa114fgrknn6415g4d1jrvb924nkwi18jzfqribpvcf1vlgrf3")))) + "0vj9nk8g6i4vzm6cnzvbsqcvyk6fhmx0a0nxxrciarffyhqk81yz")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) ("r-biocgenerics" ,r-biocgenerics) + ("r-ggplot-multistats" ,r-ggplot-multistats) ("r-ggplot2" ,r-ggplot2) ("r-ggthemes" ,r-ggthemes) - ("r-igraph" ,r-igraph) + ("r-irlba" ,r-irlba) + ("r-knn-covertree" ,r-knn-covertree) ("r-matrix" ,r-matrix) + ("r-pcamethods" ,r-pcamethods) ("r-proxy" ,r-proxy) ("r-rcpp" ,r-rcpp) ("r-rcppeigen" ,r-rcppeigen) + ("r-rcpphnsw" ,r-rcpphnsw) + ("r-rspectra" ,r-rspectra) ("r-scales" ,r-scales) ("r-scatterplot3d" ,r-scatterplot3d) + ("r-singlecellexperiment" ,r-singlecellexperiment) ("r-smoother" ,r-smoother) ("r-summarizedexperiment" ,r-summarizedexperiment) + ("r-tidyr" ,r-tidyr) + ("r-tidyselect" ,r-tidyselect) ("r-vim" ,r-vim))) (home-page "https://bioconductor.org/packages/destiny/") (synopsis "Create and plot diffusion maps") -- cgit v1.2.3 From 614a1e3fa2d731d4719f03912b1b87fb4fd309cb Mon Sep 17 00:00:00 2001 From: Mathieu Othacehe Date: Sat, 14 Dec 2019 17:46:27 +0100 Subject: gnu: info-reader: Fix cross-compilation. * gnu/packages/texinfo.scm (info-reader)[arguments]: Add keep-only-info-reader phase to inherited texinfo package phases, so that fix-cross-configure phase is preserved. --- gnu/packages/texinfo.scm | 49 ++++++++++++++++++++++++------------------------ 1 file changed, 25 insertions(+), 24 deletions(-) diff --git a/gnu/packages/texinfo.scm b/gnu/packages/texinfo.scm index 1edeea2425..3d0894b84f 100644 --- a/gnu/packages/texinfo.scm +++ b/gnu/packages/texinfo.scm @@ -3,6 +3,7 @@ ;;; Copyright © 2014, 2016 Eric Bavier ;;; Copyright © 2015 Mark H Weaver ;;; Copyright © 2017 Efraim Flashner +;;; Copyright © 2019 Mathieu Othacehe ;;; ;;; This file is part of GNU Guix. ;;; @@ -108,32 +109,32 @@ is on expressing the content semantically, avoiding physical markup commands.") (inherit texinfo) (name "info-reader") (arguments - `(#:disallowed-references ,(assoc-ref (package-inputs texinfo) - "perl") + `(,@(substitute-keyword-arguments (package-arguments texinfo) + ((#:phases phases) + `(modify-phases ,phases + (add-after 'install 'keep-only-info-reader + (lambda* (#:key outputs #:allow-other-keys) + ;; Remove everything but 'bin/info' and associated + ;; files. + (define (files) + (scandir "." (lambda (file) + (not (member file '("." "..")))))) + (let ((out (assoc-ref outputs "out"))) + (with-directory-excursion out + (for-each delete-file-recursively + (fold delete (files) '("bin" "share")))) + (with-directory-excursion (string-append out "/bin") + (for-each delete-file (delete "info" (files)))) + (with-directory-excursion (string-append out "/share") + (for-each delete-file-recursively + (fold delete (files) + '("info" "locale")))) + #t)))))) + #:disallowed-references ,(assoc-ref (package-inputs texinfo) + "perl") #:modules ((ice-9 ftw) (srfi srfi-1) - ,@%gnu-build-system-modules) - - #:phases (modify-phases %standard-phases - (add-after 'install 'keep-only-info-reader - (lambda* (#:key outputs #:allow-other-keys) - ;; Remove everything but 'bin/info' and associated - ;; files. - (define (files) - (scandir "." (lambda (file) - (not (member file '("." "..")))))) - - (let ((out (assoc-ref outputs "out"))) - (with-directory-excursion out - (for-each delete-file-recursively - (fold delete (files) '("bin" "share")))) - (with-directory-excursion (string-append out "/bin") - (for-each delete-file (delete "info" (files)))) - (with-directory-excursion (string-append out "/share") - (for-each delete-file-recursively - (fold delete (files) - '("info" "locale")))) - #t)))))) + ,@%gnu-build-system-modules))) (synopsis "Standalone Info documentation reader"))) (define-public texi2html -- cgit v1.2.3 From 97115892b9661e396afddc515e7f8f948167f0c5 Mon Sep 17 00:00:00 2001 From: Pierre Neidhardt Date: Sat, 14 Dec 2019 14:34:55 +0100 Subject: gnu: Add theorafile. * gnu/packages/video.scm (theorafile): New variable. --- gnu/packages/video.scm | 41 ++++++++++++++++++++++++++++++++++++++++- 1 file changed, 40 insertions(+), 1 deletion(-) diff --git a/gnu/packages/video.scm b/gnu/packages/video.scm index 3280114878..ef60767236 100644 --- a/gnu/packages/video.scm +++ b/gnu/packages/video.scm @@ -24,7 +24,7 @@ ;;; Copyright © 2017, 2018, 2019 Rutger Helling ;;; Copyright © 2018 Roel Janssen ;;; Copyright © 2018, 2019 Marius Bakke -;;; Copyright © 2018 Pierre Neidhardt +;;; Copyright © 2018, 2019 Pierre Neidhardt ;;; Copyright © 2018, 2019 Leo Famulari ;;; Copyright © 2018 Brendan Tildesley ;;; Copyright © 2018 Arun Isaac @@ -3677,3 +3677,42 @@ user interface features a builtin video player and is designed with attention to convenience of translating and batch processing of multiple documents.") (home-page "https://otsaloma.io/gaupol/") (license license:gpl3+))) + +(define-public theorafile + (let ((commit "404b14d7602b5918d117eaa64e8aa6601ede8593")) + (package + (name "theorafile") + (version (git-version "0.0.0" "1" commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/FNA-XNA/Theorafile.git") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "128c3pjzqbgrj020glm5jd6ss18vl19471lj615w2brjwb7c1f0z")))) + (build-system gnu-build-system) + (arguments + '(#:make-flags '("CC=gcc") + #:phases + (modify-phases %standard-phases + (delete 'configure) + (replace 'check + (lambda _ + (setenv "CC" "gcc") + (invoke "make" "test"))) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let ((out (assoc-ref outputs "out"))) + (install-file "libtheorafile.so" (string-append out "/lib")) + (install-file "theorafile.h" (string-append out "/include"))) + #t))))) + (native-inputs + ;; For tests. + `(("sdl2" ,sdl2))) + (home-page "https://github.com/FNA-XNA/Theorafile") + (synopsis "Ogg Theora Video Decoder Library") + (description "Theorafile is a library for quickly and easily decoding Ogg +Theora videos. Theorafile was written to be used for FNA's VideoPlayer.") + (license license:zlib)))) -- cgit v1.2.3 From a13116b60c803d8ba7ee99197bed16d7bdf2eaa5 Mon Sep 17 00:00:00 2001 From: Mathieu Othacehe Date: Sun, 15 Dec 2019 17:10:19 +0100 Subject: gnu: texinfo: Add missing include. * gnu/packages/texinfo.scm (info-reader): Fix missing include, introduced by f5d670606354728a453b8cc962c4f85516007d13. --- gnu/packages/texinfo.scm | 1 + 1 file changed, 1 insertion(+) diff --git a/gnu/packages/texinfo.scm b/gnu/packages/texinfo.scm index 3d0894b84f..7f95c29b9e 100644 --- a/gnu/packages/texinfo.scm +++ b/gnu/packages/texinfo.scm @@ -23,6 +23,7 @@ (define-module (gnu packages texinfo) #:use-module (guix licenses) #:use-module (guix packages) + #:use-module (guix utils) #:use-module (guix download) #:use-module (guix build-system gnu) #:use-module (gnu packages) -- cgit v1.2.3 From 514001e9cee0cc65a887de09cb7588987648322c Mon Sep 17 00:00:00 2001 From: Carlo Zancanaro Date: Sat, 14 Dec 2019 22:18:44 +1100 Subject: gnu: abcl: Update to 1.6.0. * gnu/packages/java.scm (abcl): Update to 1.6.0. Signed-off-by: Efraim Flashner --- gnu/packages/java.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/java.scm b/gnu/packages/java.scm index 6550463fa5..d0e3fd8d33 100644 --- a/gnu/packages/java.scm +++ b/gnu/packages/java.scm @@ -11479,7 +11479,7 @@ network protocols, and core version control algorithms.") (define-public abcl (package (name "abcl") - (version "1.5.0") + (version "1.6.0") (source (origin (method url-fetch) @@ -11487,7 +11487,7 @@ network protocols, and core version control algorithms.") version "/abcl-src-" version ".tar.gz")) (sha256 (base32 - "1hhvcg050nfpjbdmskc1cv2j38qi6qfl77a61b5cxx576kbff3lj")) + "0hvbcsffr8n2xwdixc8wyw1bfl9fxn2gyy0c4nma7j9zbn0wwgw9")) (patches (search-patches "abcl-fix-build-xml.patch")))) -- cgit v1.2.3 From 6a65185ee46babca0630db1d64eaa8c1447d1cd6 Mon Sep 17 00:00:00 2001 From: Vagrant Cascadian Date: Sun, 15 Dec 2019 16:13:41 +0000 Subject: gnu: diffoscope: Update to 133. * gnu/packages/diffoscope (diffoscope): Update to 133. --- gnu/packages/diffoscope.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/diffoscope.scm b/gnu/packages/diffoscope.scm index 7fe7766a15..821dc8aff9 100644 --- a/gnu/packages/diffoscope.scm +++ b/gnu/packages/diffoscope.scm @@ -67,7 +67,7 @@ #:use-module (ice-9 match)) (define-public diffoscope - (let ((version "131")) + (let ((version "133")) (package (name "diffoscope") (version version) @@ -79,7 +79,7 @@ (file-name (git-file-name name version)) (sha256 (base32 - "0jai3kycjlrc64f4vg8yklri6ds1451qy6r6sw2646bhjr0gs233")))) + "0mvg5iyd3zjxsm66vax3qb89214j3wxcklvbhfrr8jlbzaw9pznh")))) (build-system python-build-system) (arguments `(#:phases (modify-phases %standard-phases -- cgit v1.2.3 From 9a27551b397722db704683e3a5f7c3bc9eeda417 Mon Sep 17 00:00:00 2001 From: Brett Gilio Date: Sun, 15 Dec 2019 13:43:46 -0600 Subject: gnu: emacs-doom-modeline: Update to 2.8.2. * gnu/packages/emacs-xyz.scm (emacs-doom-modeline): Update to 2.8.2. --- 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 9e4edf282f..12584c87ac 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -20211,7 +20211,7 @@ Telegram messaging platform.") (define-public emacs-doom-modeline (package (name "emacs-doom-modeline") - (version "2.8.0") + (version "2.8.2") (source (origin (method git-fetch) (uri (git-reference @@ -20219,7 +20219,7 @@ Telegram messaging platform.") (commit (string-append "v" version)))) (sha256 (base32 - "12zksk0rwpgpdc00km3z0hmc8wm1j1r8lbwn4kivniw56mgy0n22")) + "11srz1mr821axggs2jcmdhihxx09a2dniqv3n039wbdfaimfaidz")) (file-name (git-file-name name version)))) (build-system emacs-build-system) (arguments -- cgit v1.2.3 From b425426236a7953131e4c252c04c2423818a300d Mon Sep 17 00:00:00 2001 From: Brett Gilio Date: Sun, 15 Dec 2019 13:50:19 -0600 Subject: gnu: emacs-async: Update to 1.9.4. * gnu/packages/emacs-xyz.scm (emacs-async): Update to 1.9.4. --- 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 12584c87ac..16a06b9e45 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -1586,7 +1586,7 @@ rather than the contents of files.") (package (name "emacs-async") (home-page "https://github.com/jwiegley/emacs-async") - (version "1.9.3") + (version "1.9.4") (source (origin (method git-fetch) (uri (git-reference @@ -1595,7 +1595,7 @@ rather than the contents of files.") (file-name (git-file-name name version)) (sha256 (base32 - "1zsnb6dy8p6y68xgidv3dfxaga4biramfw8fq7wac0sc50vc98vq")))) + "0hhpyxb3d531jb2f3wvzx25183f0anm8nxv6mh0p825q2gkm6ly7")))) (build-system emacs-build-system) (synopsis "Asynchronous processing in Emacs") (description -- cgit v1.2.3 From 00895524ec80c6c2e813a57667136f93dc5f4475 Mon Sep 17 00:00:00 2001 From: Brett Gilio Date: Sun, 15 Dec 2019 13:52:58 -0600 Subject: gnu: emacs-direnv: Update to 2.0.0. * gnu/packages/emacs-xyz.scm (emacs-direnv): Update to 2.0.0. --- 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 16a06b9e45..1eff125d1e 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -1720,7 +1720,7 @@ Emacs buffer.") (define-public emacs-direnv (package (name "emacs-direnv") - (version "1.5.0") + (version "2.0.0") (source (origin (method git-fetch) @@ -1730,7 +1730,7 @@ Emacs buffer.") (file-name (git-file-name name version)) (sha256 (base32 - "02blhinkkfh3iai6j1k5swplf5mkwijy3p7wy38rnd1gnyj2z4la")))) + "005ibyzsx1fdyrl5iyhqpb1bg83mphzahq7zvw58x00syyqi2z49")))) (build-system emacs-build-system) (propagated-inputs `(("dash" ,emacs-dash) -- cgit v1.2.3 From 12bf15ffe4ed50b0af9a6dc08e39481d7e5b7ecc Mon Sep 17 00:00:00 2001 From: Brett Gilio Date: Sun, 15 Dec 2019 14:00:06 -0600 Subject: gnu: emacs-fill-column-indicator: Update to 1.90. * gnu/packages/emacs-xyz.scm (emacs-fill-column-indicator): Update to 1.90. --- 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 1eff125d1e..ee934315bf 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -2682,16 +2682,16 @@ keep pressing the key until it selects what you want. There's also (define-public emacs-fill-column-indicator (package (name "emacs-fill-column-indicator") - (version "1.89") + (version "1.90") (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/alpaker/Fill-Column-Indicator.git") - (commit (string-append "v" version)))) + (commit version))) (file-name (git-file-name name version)) (sha256 - (base32 "010kf8jsly74y7m6mmkn1h6y205kz23zphs50zgy2nag2p88rz9y")))) + (base32 "0snjznxdwwfdgccdcvrnk467416r244r2r5qcm2sga8l0ha9gw9z")))) (build-system emacs-build-system) (home-page "https://www.emacswiki.org/emacs/FillColumnIndicator") (synopsis "Graphically indicate the fill column") -- cgit v1.2.3 From 6694b67f4fa6dfdc87f0f89f62020ef2c8ac2c5f Mon Sep 17 00:00:00 2001 From: Brett Gilio Date: Sun, 15 Dec 2019 14:07:26 -0600 Subject: gnu: emacs-undercover: Update to 0.6.1. * gnu/packages/emacs-xyz.scm (emacs-undercover): Update to 0.6.1. --- 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 ee934315bf..5aeb326d9f 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -2786,16 +2786,16 @@ Emacs shell script.") (define-public emacs-undercover (package (name "emacs-undercover") - (version "0.6.0") + (version "0.6.1") (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/sviridov/undercover.el.git") - (commit (string-append "v" version)))) + (commit version))) (file-name (git-file-name name version)) (sha256 - (base32 "06qcvbp5rd0kh3ibrxj5p6r578lwsrgd7yj5c6slwmkdmna2fj33")))) + (base32 "080bmfwyfi8663y8x594770hqz7mff7zvj2v03qdfwbhdr9w9y29")))) (build-system emacs-build-system) (propagated-inputs `(("emacs-dash" ,emacs-dash) -- cgit v1.2.3 From 44e7222bf71110aaba50eed897e867575356a993 Mon Sep 17 00:00:00 2001 From: Brett Gilio Date: Sun, 15 Dec 2019 14:09:25 -0600 Subject: gnu: emacs-paren-face: Update to 1.0.4. * gnu/packages/emacs-xyz.scm (emacs-paren-face): Update to 1.0.4. --- gnu/packages/emacs-xyz.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 5aeb326d9f..8d45367ed2 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -2810,7 +2810,7 @@ Lisp.") (define-public emacs-paren-face (package (name "emacs-paren-face") - (version "1.0.0") + (version "1.0.4") (source (origin (method git-fetch) @@ -2819,7 +2819,8 @@ Lisp.") (commit version))) (file-name (git-file-name name version)) (sha256 - (base32 "0f128gqn170s6hl62n44i9asais75ns1mpvb4l8vzy1sc0v16c0k")))) + (base32 + "1cr0vnm57lxs48z17ddcv7qlfvks7wdsp01zsw0c7i3h5ajl8myp")))) (build-system emacs-build-system) (home-page "https://github.com/tarsius/paren-face") (synopsis "Face for parentheses in lisp modes") -- cgit v1.2.3 From 1bd94e3a656f4e59e866de403fce0ff8918be63a Mon Sep 17 00:00:00 2001 From: Brett Gilio Date: Sun, 15 Dec 2019 14:11:39 -0600 Subject: gnu: emacs-rich-minority: Update to 1.0.3. * gnu/packages/emacs-xyz.scm (emacs-rich-minority): Update to 1.0.3. --- gnu/packages/emacs-xyz.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 8d45367ed2..fcbf92f7ab 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -3054,7 +3054,7 @@ their original location with another.") (define-public emacs-rich-minority (package (name "emacs-rich-minority") - (version "1.0.1") + (version "1.0.3") (source (origin (method git-fetch) @@ -3063,7 +3063,8 @@ their original location with another.") (commit version))) (file-name (git-file-name name version)) (sha256 - (base32 "11hwf9y5ax207w6rwrsmi3pmn7pn7ap6iys0z8hni2f5zzxjrmx3")))) + (base32 + "1kn7c9qr9ykj68iqffzzmjsr6aazwac8cxb7j960sjb282rq0yyj")))) (build-system emacs-build-system) (home-page "https://github.com/Malabarba/rich-minority") (synopsis "Clean-up and beautify the list of minor modes") -- cgit v1.2.3 From 0da921dce73afa06f4f98e936df310919437ca18 Mon Sep 17 00:00:00 2001 From: Brett Gilio Date: Sun, 15 Dec 2019 14:15:52 -0600 Subject: gnu: emacs-ob-ipython: Update to 20180224. * gnu/packages/emacs-xyz.scm (emacs-ob-ipython): Update to 20180224. --- 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 fcbf92f7ab..7715d57f4e 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -3470,16 +3470,16 @@ minibuffer to enable editing the minibuffer input in another buffer with (define-public emacs-ob-ipython (package (name "emacs-ob-ipython") - (version "20150704.8807064693") + (version "20180224") (source (origin (method git-fetch) (uri (git-reference - (commit "880706469338ab59b5bb7dbe8460016f89755364") + (commit "7147455230841744fb5b95dcbe03320313a77124") (url "https://github.com/gregsexton/ob-ipython.git"))) (file-name (git-file-name name version)) (sha256 (base32 - "1scf25snbds9ymagpny30ijbsg479r3nm0ih01dy4m9d0g7qryb7")))) + "1a10fc2jk37ni5sjjvf87s5nyaz2a6h2mlj5dxh4dhv5sd3bb85p")))) (build-system emacs-build-system) (propagated-inputs `(("emacs-f" ,emacs-f))) -- cgit v1.2.3 From 503f9aadc4daf218af244bf4a5a950e5d85850e6 Mon Sep 17 00:00:00 2001 From: Brett Gilio Date: Sun, 15 Dec 2019 14:32:48 -0600 Subject: gnu: emacs-jedi: Update to 0.2.8. * gnu/packages/emacs-xyz.scm (emacs-jedi): Update to 0.2.8. --- 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 7715d57f4e..4c30bdf872 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -4365,7 +4365,7 @@ and popup menus.") (define-public emacs-jedi (package (name "emacs-jedi") - (version "0.2.7") + (version "0.2.8") (source (origin (method git-fetch) (uri (git-reference @@ -4374,7 +4374,7 @@ and popup menus.") (file-name (git-file-name name version)) (sha256 (base32 - "0xbp9fcxgbf298w05hvf52z41kk7r52975ailgdn8sg60xc98fa7")))) + "1bckxppfzd5gwn0aw4h86igb7igal9axqncq7j8zmflg7zppncf1")))) (build-system emacs-build-system) (native-inputs `(("emacs-mocker" ,emacs-mocker))) -- cgit v1.2.3 From e3c4fcaae3876063d414a57f8c5845dabcb1dc9c Mon Sep 17 00:00:00 2001 From: Brett Gilio Date: Sun, 15 Dec 2019 14:33:08 -0600 Subject: gnu: emacs-org-trello: Update to 0.8.1. * gnu/packages/emacs-xyz.scm (emacs-org-trello): Update to 0.8.1. --- gnu/packages/emacs-xyz.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 4c30bdf872..8c330e144c 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -4671,7 +4671,7 @@ overview of tasks in a subtree.") (define-public emacs-org-trello (package (name "emacs-org-trello") - (version "0.8.0") + (version "0.8.1") (source (origin (method git-fetch) @@ -4680,7 +4680,8 @@ overview of tasks in a subtree.") (commit version))) (file-name (git-file-name name version)) (sha256 - (base32 "0m5hyhb6211hdmyp1bq6f3fklfgw3957knd96bfdafj727vdnlzm")))) + (base32 + "02gx3kv4mkij69ln8x8wf9n28x17pbb4kv85v78d3lxph7ykqimc")))) (build-system emacs-build-system) (propagated-inputs `(("emacs-dash" ,emacs-dash) -- cgit v1.2.3 From 317cc181809bfed3e32588010d6c5901987b9f8c Mon Sep 17 00:00:00 2001 From: Brett Gilio Date: Sun, 15 Dec 2019 14:44:35 -0600 Subject: gnu: emacs-elfeed: Update to 3.3.0. * gnu/packages/emacs-xyz.scm (emacs-elfeed): Update to 3.3.0. --- 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 8c330e144c..eb3996d6e3 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -6355,7 +6355,7 @@ and tooling.") (define-public emacs-elfeed (package (name "emacs-elfeed") - (version "3.2.0") + (version "3.3.0") (source (origin (method git-fetch) @@ -6364,7 +6364,7 @@ and tooling.") (commit version))) (file-name (git-file-name name version)) (sha256 - (base32 "0m0a35210pb4yf6m8mzaq6nkl9x6fphjjqyl3dzygnmmzxkc8aw2")))) + (base32 "0j8a94val4ml7g1vcjgzk1w89h55sxfdrwnncmz6qbh1y2xsz8c5")))) (build-system emacs-build-system) (arguments `(#:tests? #t -- cgit v1.2.3 From 5487ddac2279d7d1200d558864d7c063a39de1c6 Mon Sep 17 00:00:00 2001 From: Brett Gilio Date: Sun, 15 Dec 2019 14:58:18 -0600 Subject: gnu: emacs-find-file-in-project: Update to 5.7.7. * gnu/packages/emacs-xyz.scm (emacs-find-file-in-project): Update to 5.7.7. [arguments]: Modify tests to use ert. --- gnu/packages/emacs-xyz.scm | 18 ++++++------------ 1 file changed, 6 insertions(+), 12 deletions(-) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index eb3996d6e3..917dd57a3a 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -6482,7 +6482,7 @@ maximizes flexibility (at the expense of conciseness).") (define-public emacs-find-file-in-project (package (name "emacs-find-file-in-project") - (version "5.4.7") + (version "5.7.7") (source (origin (method git-fetch) (uri (git-reference @@ -6491,19 +6491,13 @@ maximizes flexibility (at the expense of conciseness).") (file-name (git-file-name name version)) (sha256 (base32 - "1sdnyqv69mipbgs9yax88m9b6crsa59rjhwrih197pifl4089awr")))) + "1skjbh7m0cck2rwmgzrrds51gipqf1jqghyfx15drc1n6kwivx3h")))) (build-system emacs-build-system) (arguments - `(#:phases - (modify-phases %standard-phases - (add-before 'check 'set-shell - ;; Otherwise Emacs shell-file-name is set to "/bin/sh", which doesn't - ;; work. - (lambda _ - (setenv "SHELL" (which "sh")) - #t))) - #:tests? #t - #:test-command '("./tests/test.sh"))) + `(#:tests? #t + #:test-command '("ert-runner" "tests"))) + (native-inputs + `(("ert-runner" ,emacs-ert-runner))) (home-page "https://github.com/technomancy/find-file-in-project") (synopsis "File/directory finder for Emacs") (description "@code{find-file-in-project} allows to find files or -- cgit v1.2.3 From bc685e1ca3516a218c083da206d3d1c354733073 Mon Sep 17 00:00:00 2001 From: Vagrant Cascadian Date: Sun, 15 Dec 2019 20:42:15 +0000 Subject: gnu: diffoscope: Add support for zstd compression. * gnu/packages/diffoscope (diffoscope)[native-inputs]: Add zstd. [arguments]: Add add-known-tools phase with support for zstd. --- gnu/packages/diffoscope.scm | 9 ++++++++- 1 file changed, 8 insertions(+), 1 deletion(-) diff --git a/gnu/packages/diffoscope.scm b/gnu/packages/diffoscope.scm index 821dc8aff9..93630f3bb6 100644 --- a/gnu/packages/diffoscope.scm +++ b/gnu/packages/diffoscope.scm @@ -90,6 +90,12 @@ (lambda _ (substitute* "setup.py" (("'python-magic',") "")))) + ;; Patch in support for known tools + (add-after 'unpack 'add-known-tools + (lambda _ + (substitute* "diffoscope/external_tools.py" + (("'debian': 'zstd'") + "'debian': 'zstd', 'guix': 'zstd'")))) ;; This test is broken because our `file` package has a ;; bug in berkeley-db file type detection. (add-after 'unpack 'remove-berkeley-test @@ -209,7 +215,8 @@ ("wabt" ,wabt) ("xxd" ,xxd) ("xz" ,xz) - ("zip" ,zip))) + ("zip" ,zip) + ("zstd" ,zstd))) (home-page "https://diffoscope.org/") (synopsis "Compare files, archives, and directories in depth") (description -- cgit v1.2.3 From 467ad2120af092ece123c35519cc417c8729d4b2 Mon Sep 17 00:00:00 2001 From: Brett Gilio Date: Sun, 15 Dec 2019 15:13:42 -0600 Subject: gnu: emacs-rainbow-delimiters: Update to 2.1.4. * gnu/packages/emacs-xyz.scm (emacs-rainbow-delimiters): Update to 2.1.4. --- 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 917dd57a3a..04e91c4628 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -6643,7 +6643,7 @@ completion, interactive development and more.") (define-public emacs-rainbow-delimiters (package (name "emacs-rainbow-delimiters") - (version "2.1.3") + (version "2.1.4") (source (origin (method git-fetch) (uri (git-reference @@ -6652,7 +6652,7 @@ completion, interactive development and more.") (file-name (git-file-name name version)) (sha256 (base32 - "0vs9pf8lqq5p5qz1770pxgw47ym4xj8axxmwamn66br59mykdhv0")))) + "1zr2669savnmkc68hiqsq9wccm6bs1j6jbmlac1xqh6nq7xgq36g")))) (build-system emacs-build-system) (home-page "https://github.com/Fanael/rainbow-delimiters") (arguments -- cgit v1.2.3 From fb4b5d2ea9cdac300e5f3a0e4ca72b4f935f5703 Mon Sep 17 00:00:00 2001 From: Brett Gilio Date: Sun, 15 Dec 2019 15:15:22 -0600 Subject: gnu: emacs-writeroom: Update to 3.9. * gnu/packages/emacs-xyz.scm (emacs-writeroom): Update to 3.9. --- gnu/packages/emacs-xyz.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 04e91c4628..a739af8ef7 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -6737,7 +6737,7 @@ window edge.") (define-public emacs-writeroom (package (name "emacs-writeroom") - (version "3.7") + (version "3.9") (source (origin (method git-fetch) @@ -6746,7 +6746,8 @@ window edge.") (commit version))) (file-name (git-file-name name version)) (sha256 - (base32 "13nbls5qxz5z8firjxaip8m9vzfbbpxmwrmr01njbk4axpwrpj0z")))) + (base32 + "1nrppnfqsaki6myp58w8jhmzb94rzskh5n98glcn4ghr8sqnafi8")))) (build-system emacs-build-system) (propagated-inputs `(("emacs-visual-fill-column" ,emacs-visual-fill-column))) -- cgit v1.2.3 From 426ab00aae1d15ec34c41c8df9ede30b999c9664 Mon Sep 17 00:00:00 2001 From: Brett Gilio Date: Sun, 15 Dec 2019 15:19:31 -0600 Subject: gnu: emacs-helm: Update to 3.6.0. * gnu/packages/emacs-xyz.scm (emacs-helm): Update to 3.6.0. --- 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 a739af8ef7..ad983d2ebc 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -6907,7 +6907,7 @@ ack, ag, helm and pt.") (define-public emacs-helm (package (name "emacs-helm") - (version "3.5.0") + (version "3.6.0") (source (origin (method git-fetch) @@ -6916,7 +6916,7 @@ ack, ag, helm and pt.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "07bijcnfkv60l3swasxv53x32l6glds05mxnbb3xbnmkgm1pm9if")))) + (base32 "0miq2q52pbicijp7pmj0widk252qixswywc03d120s4hya2b7vd7")))) (build-system emacs-build-system) (propagated-inputs `(("emacs-async" ,emacs-async) -- cgit v1.2.3 From 638850e68cb7d4fd48e11e59f1cf70eb25c65fe6 Mon Sep 17 00:00:00 2001 From: Brett Gilio Date: Sun, 15 Dec 2019 15:22:21 -0600 Subject: gnu: emacs-helm-org: Update to 1.0-2. * gnu/packages/emacs-xyz.scm (emacs-helm-org): Update to 1.0-2. --- 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 ad983d2ebc..2207261e5b 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -6934,8 +6934,8 @@ not tied in the trap of backward compatibility.") (license license:gpl3+))) (define-public emacs-helm-org - (let ((commit "542dda7bc9a3b9dfb439e4f8a1e5f60cfb6cc256") - (revision "1")) + (let ((commit "b9a1167b0716a22a69670f4c35e0ac59d2e0b220") + (revision "2")) (package (name "emacs-helm-org") (version (git-version "1.0" revision commit)) @@ -6947,7 +6947,7 @@ not tied in the trap of backward compatibility.") (commit commit))) (file-name (git-file-name name version)) (sha256 - (base32 "1xa32w80icrykpyfb89fhb0s4l7ysi0sc7f7lfwqz5najwbgqipl")))) + (base32 "1gc27i4azqpgijva1f4ckfdp4s52mc9pnfcmzhkwhknr6pd6jlcr")))) (build-system emacs-build-system) (propagated-inputs `(("emacs-helm" ,emacs-helm))) -- cgit v1.2.3 From 6b714d8d148050f51359d7dd69a6f06ba9054a68 Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Sun, 15 Dec 2019 22:25:41 +0100 Subject: gnu: emacs-htmlize: Update to 1.55. * gnu/packages/emacs-xyz.scm (emacs-htmlize): Update to 1.55. --- 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 2207261e5b..9d60e48733 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -9134,7 +9134,7 @@ to the home page or read the comments in the source file, (define-public emacs-htmlize (package (name "emacs-htmlize") - (version "1.53") + (version "1.55") (source (origin (method git-fetch) @@ -9143,7 +9143,7 @@ to the home page or read the comments in the source file, (commit (string-append "release/" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "0dr235c0z8is3pi5xdgqyqljg6px0b2aya6qb79zkyi477bmz4ip")))) + (base32 "0gi3xshscpa53qrj8yplfsqahcilc2ybcc2p7gnh5nbnf2n1n97x")))) (build-system emacs-build-system) (home-page "https://github.com/hniksic/emacs-htmlize") (synopsis "Convert buffer text and decorations to HTML") -- cgit v1.2.3 From 0fce0b2eef617204c70548c5dce2002bde4110f9 Mon Sep 17 00:00:00 2001 From: Brett Gilio Date: Sun, 15 Dec 2019 15:30:16 -0600 Subject: gnu: emacs-telega: Add comment about obtaining version. * gnu/packages/emacs-xyz.scm (emacs-telega): Add comment about obtaining version. --- gnu/packages/emacs-xyz.scm | 3 +++ 1 file changed, 3 insertions(+) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 9d60e48733..7ea8032b79 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -20082,6 +20082,9 @@ fish-completion. It can be used in both Eshell and M-x shell.") (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. + ;; or by running M-x telega-version. (let ((commit "6184e76990db395bea02f7b5d3169e746111e1ad") (revision "1") (version "0.5.3")) -- cgit v1.2.3 From 6704e88d42b7c13e39975bd9c1790c079df57305 Mon Sep 17 00:00:00 2001 From: Ludovic Courtès Date: Sun, 15 Dec 2019 21:34:09 +0100 Subject: gnu: guile-gcrypt: Update to 0.2.1. * gnu/packages/gnupg.scm (guile-gcrypt): Update to 0.2.1. --- gnu/packages/gnupg.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/gnupg.scm b/gnu/packages/gnupg.scm index 9576f79333..b31280e39b 100644 --- a/gnu/packages/gnupg.scm +++ b/gnu/packages/gnupg.scm @@ -456,7 +456,7 @@ gpgpme starting with version 1.7.") (define-public guile-gcrypt (package (name "guile-gcrypt") - (version "0.2.0") + (version "0.2.1") (home-page "https://notabug.org/cwebber/guile-gcrypt") (source (origin (method git-fetch) @@ -465,7 +465,7 @@ gpgpme starting with version 1.7.") (commit (string-append "v" version)))) (sha256 (base32 - "1mhc5m4xygkfj7x18f8apiqpfdn9mrql0am5sk13cf5xn8x1r63z")) + "0n232iyayc46f7hywmjw0jr7pbmmz5h4b04jskhkzz9gxz0ci99c")) (file-name (string-append name "-" version "-checkout")))) (build-system gnu-build-system) (native-inputs -- cgit v1.2.3 From 4dbd704d5dcfdb753b3308102cfcbad1311dcb63 Mon Sep 17 00:00:00 2001 From: Leo Prikler Date: Wed, 4 Dec 2019 02:46:44 +0100 Subject: gnu: Add lolcat MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/games.scm (lolcat): New package. Signed-off-by: Ludovic Courtès --- gnu/packages/games.scm | 39 +++++++++++++++++++++++++++++++++++++++ 1 file changed, 39 insertions(+) diff --git a/gnu/packages/games.scm b/gnu/packages/games.scm index ded27c1f63..c8d671bbdc 100644 --- a/gnu/packages/games.scm +++ b/gnu/packages/games.scm @@ -502,6 +502,45 @@ cows can think too: all you have to do is run @command{cowthink}. If you're tired of cows, a variety of other ASCII-art messengers are available.") (license license:gpl3+))) +(define-public lolcat + (let ((commit "35dca3d0a381496d7195cd78f5b24aa7b62f2154") + (revision "0")) + (package + (name "lolcat") + (version (git-version "1.0" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/jaseg/lolcat.git") + (commit commit))) + (sha256 + (base32 + "0jjbkqcc2ikjxd1xgdyv4rb0vsw218181h89f2ywg29ffs3ypd8g")) + (file-name (git-file-name name version)))) + (build-system gnu-build-system) + (arguments + `(#:tests? #f ;; no check target + #:make-flags (list "CC=gcc") + #:phases + (modify-phases %standard-phases + (delete 'bootstrap) + (delete 'configure) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (dest (string-append out "/bin"))) + (mkdir-p dest) + (install-file "lolcat" dest) + (install-file "censor" dest) + #t)))))) + (home-page "https://github.com/jaseg/lolcat") + (synopsis "Rainbow coloring effect for text console display") + (description "@command{lolcat} concatenates files and streams like +regular @command{cat}, but it also adds terminal escape codes between +characters and lines resulting in a rainbow effect.") + (license license:wtfpl2)))) + (define-public freedoom (package (name "freedoom") -- cgit v1.2.3 From 5d1601eab5dcc1a9c3a15a6e49f06c65e22c3f84 Mon Sep 17 00:00:00 2001 From: nixo Date: Wed, 11 Dec 2019 13:31:09 +0100 Subject: gnu: criu: Update to 3.13. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/virtualization.scm (criu): Update to 3.13. Signed-off-by: Ludovic Courtès --- gnu/packages/virtualization.scm | 38 ++++++++++++++++++++------------------ 1 file changed, 20 insertions(+), 18 deletions(-) diff --git a/gnu/packages/virtualization.scm b/gnu/packages/virtualization.scm index e83ae43da2..f5ccfcb593 100644 --- a/gnu/packages/virtualization.scm +++ b/gnu/packages/virtualization.scm @@ -57,6 +57,7 @@ #:use-module (gnu packages golang) #:use-module (gnu packages gtk) #:use-module (gnu packages image) + #:use-module (gnu packages libbsd) #:use-module (gnu packages libusb) #:use-module (gnu packages linux) #:use-module (gnu packages ncurses) @@ -690,14 +691,14 @@ domains, their live performance and resource utilization statistics.") (define-public criu (package (name "criu") - (version "3.11") + (version "3.13") (source (origin (method url-fetch) (uri (string-append "http://download.openvz.org/criu/criu-" version ".tar.bz2")) (sha256 (base32 - "03nimyn3wy5mlw30gq7bvlzvvprqjv8f25240yj5arzlld8mhsw8")))) + "1yn9ix9lqvqvjrs3a3g6g1wqfniyf9n7giy0mr3jvijmrcm7y0pa")))) (build-system gnu-build-system) (arguments `(#:test-target "test" @@ -705,7 +706,11 @@ domains, their live performance and resource utilization statistics.") #:make-flags (list (string-append "PREFIX=" (assoc-ref %outputs "out")) (string-append "LIBDIR=" (assoc-ref %outputs "out") - "/lib")) + "/lib") + (string-append "ASCIIDOC=" (assoc-ref %build-inputs "asciidoc") + "/bin/asciidoc") + (string-append "XMLTO=" (assoc-ref %build-inputs "xmlto") + "/bin/xmlto")) #:phases (modify-phases %standard-phases (replace 'configure @@ -721,21 +726,17 @@ domains, their live performance and resource utilization statistics.") ;; which define some of the same constants. (assoc-ref inputs "kernel-headers") "/include")) - ;; Prevent xmlto from failing the install phase. + #t)) + (add-after 'configure 'fix-documentation + (lambda* (#:key inputs outputs #:allow-other-keys) (substitute* "Documentation/Makefile" - (("XMLTO.*:=.*") - (string-append "XMLTO:=" - (assoc-ref inputs "xmlto") - "/bin/xmlto" - " --skip-validation " - " -x " - (assoc-ref inputs "docbook-xsl") - "/xml/xsl/docbook-xsl-" - ,(package-version docbook-xsl) - "/manpages/docbook.xsl")) - (("\\$\\(XMLTO\\);") - (string-append (assoc-ref inputs "xmlto") - "/bin/xmlto;"))) + (("-m custom.xsl") + (string-append + "-m custom.xsl --skip-validation -x " + (assoc-ref inputs "docbook-xsl") "/xml/xsl/" + ,(package-name docbook-xsl) "-" + ,(package-version docbook-xsl) + "/manpages/docbook.xsl"))) #t)) (add-after 'unpack 'hardcode-variables (lambda* (#:key inputs #:allow-other-keys) @@ -783,7 +784,8 @@ domains, their live performance and resource utilization statistics.") ("libaio" ,libaio) ("libcap" ,libcap) ("libnet" ,libnet) - ("libnl" ,libnl))) + ("libnl" ,libnl) + ("libbsd" ,libbsd))) (native-inputs `(("pkg-config" ,pkg-config) ("perl" ,perl) -- cgit v1.2.3 From 099ce5d4901706dc2c5be888a5c8cbf8fcd0d576 Mon Sep 17 00:00:00 2001 From: Giacomo Leidi Date: Thu, 12 Dec 2019 23:21:35 +0100 Subject: gnu: Add papirus-icon-theme. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/gnome-xyz.scm (papirus-icon-theme): New variable. Signed-off-by: Ludovic Courtès --- gnu/packages/gnome-xyz.scm | 34 ++++++++++++++++++++++++++++++++++ 1 file changed, 34 insertions(+) diff --git a/gnu/packages/gnome-xyz.scm b/gnu/packages/gnome-xyz.scm index d05bdf0ac0..00ad701ad8 100644 --- a/gnu/packages/gnome-xyz.scm +++ b/gnu/packages/gnome-xyz.scm @@ -213,3 +213,37 @@ It uses ES6 syntax and claims to be more actively maintained than others.") dark elements. It supports GNOME, Unity, Xfce, and Openbox.") (home-page "https://numixproject.github.io") (license license:gpl3+))) + +(define-public papirus-icon-theme + (let ((version "0.0.0") ;; The package does not use semver + (revision "0") + (tag "20191201")) + (package + (name "papirus-icon-theme") + (version (git-version version revision tag)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/PapirusDevelopmentTeam/papirus-icon-theme.git") + (commit tag))) + (sha256 + (base32 + "0lnz1kmz28xh1f4slbsx7ycji5hgszyiyprbf5w5fbjhvi5gzw1h")) + (file-name (git-file-name name version)))) + (build-system gnu-build-system) + (arguments + '(#:tests? #f + #:make-flags (list (string-append "PREFIX=" (assoc-ref %outputs "out"))) + #:phases + (modify-phases %standard-phases + (delete 'bootstrap) + (delete 'configure) + (delete 'build)))) + (native-inputs + `(("gtk+:bin" ,gtk+ "bin"))) + (home-page "https://git.io/papirus-icon-theme") + (synopsis "Fork of Paper icon theme with a lot of new icons and a few extras") + (description "Papirus is a fork of the icon theme Paper with a lot of new icons +and a few extra features.") + (license license:gpl3)))) -- cgit v1.2.3 From e67118adb4a6faf4d442ccc1d3042be522b8d0c5 Mon Sep 17 00:00:00 2001 From: Brett Gilio Date: Sun, 15 Dec 2019 16:02:43 -0600 Subject: gnu: Add emacs-hide-mode-line. * gnu/packages/emacs-xyz.scm (emacs-hide-mode-line): New variable. --- gnu/packages/emacs-xyz.scm | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 7ea8032b79..8212e4d5b9 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -20574,3 +20574,24 @@ It uses parseclj's shift-reduce parser internally.") It supports several input and output formats, all powered by the same shift-reduce parser function.") (license license:gpl3+))) + +(define-public emacs-hide-mode-line + (package + (name "emacs-hide-mode-line") + (version "1.0.2") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/hlissner/emacs-hide-mode-line.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0dfzjgxfkcw4wisbyldsm1km18pfp9j8xgadn6qnsz11l55bpgyp")))) + (build-system emacs-build-system) + (synopsis "Emacs plugin that hides the mode-line") + (description "A minor mode that hides the mode-line in your current +buffer. It can be used to toggle an alternative mode-line, toggle its visibility, +or simply disable the mode-line in buffers where it is not very useful.") + (home-page "https://github.com/hlissner/emacs-hide-mode-line") + (license license:expat))) -- cgit v1.2.3 From 0128a9df8f896e011ceb6b44781ed1521492bf45 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:49:20 +0100 Subject: gnu: r-rgooglemaps: Update to 1.4.5. * gnu/packages/cran.scm (r-rgooglemaps): Update to 1.4.5. --- 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 349ea62e6b..b9d75ae0b9 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -1292,14 +1292,14 @@ coordinates.") (define-public r-rgooglemaps (package (name "r-rgooglemaps") - (version "1.4.4") + (version "1.4.5") (source (origin (method url-fetch) (uri (cran-uri "RgoogleMaps" version)) (sha256 (base32 - "0sbklacc4jl5524ixhc11mh6smrzdz4l9pji6cn402i6zdn9z05x")))) + "1acf0qc9597apcidjzrpvwhg9ihypr38jigc10jvqn33qbn1i9s7")))) (properties `((upstream-name . "RgoogleMaps"))) (build-system r-build-system) (propagated-inputs `(("r-png" ,r-png))) -- cgit v1.2.3 From 3dc1d4330056acd9540e6aa9542e1927e8bb2755 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:49:37 +0100 Subject: gnu: r-amap: Update to 0.8-18. * gnu/packages/cran.scm (r-amap): Update to 0.8-18. --- 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 b9d75ae0b9..8ab15957e1 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -1424,13 +1424,13 @@ embedded @url{https://github.com/WizardMac/ReadStat,ReadStat} C library.") (define-public r-amap (package (name "r-amap") - (version "0.8-17") + (version "0.8-18") (source (origin (method url-fetch) (uri (cran-uri "amap" version)) (sha256 (base32 - "1il94bkhl8192vawq4gr2gwyhqhid27jr2312rhvr72ssg8p713b")))) + "0zpcb73w413na23f6giml9311jh0j0y766w2fh9i40d2h7bbvyvs")))) (build-system r-build-system) (native-inputs `(("gfortran" ,gfortran))) -- cgit v1.2.3 From c9a0f6106912905ad814549764731e659715f4ec Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:49:44 +0100 Subject: gnu: r-rmysql: Update to 0.10.18. * gnu/packages/cran.scm (r-rmysql): Update to 0.10.18. --- 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 8ab15957e1..713f4375eb 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -2777,14 +2777,14 @@ dimensioned arrays.") (define-public r-rmysql (package (name "r-rmysql") - (version "0.10.17") + (version "0.10.18") (source (origin (method url-fetch) (uri (cran-uri "RMySQL" version)) (sha256 (base32 - "1xamf99ih44dvaxg5x4ivj0hkqssmabgqd7gh8b8q1srw7yg8kbm")))) + "0r4626sk78fhlgivr0c7mwg9mj29ayr0iz5x90rdl4d5nc2r6kq4")))) (properties `((upstream-name . "RMySQL"))) (build-system r-build-system) (inputs -- cgit v1.2.3 From a3b51a34f448c1986f2625f90a32ca71663bfb69 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:49:52 +0100 Subject: gnu: r-broom: Update to 0.5.3. * gnu/packages/cran.scm (r-broom): Update to 0.5.3. --- 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 713f4375eb..1a2d7f9622 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -3045,14 +3045,14 @@ by base R methods related to model fitting.") (define-public r-broom (package (name "r-broom") - (version "0.5.2") + (version "0.5.3") (source (origin (method url-fetch) (uri (cran-uri "broom" version)) (sha256 (base32 - "0qmclih5dm5sqzy4hplcfy677kr12pm9pnpv3r319g14dd27pbqn")))) + "177m249dxbf9pf249610qrl58v025ws41ipfihy66751pwsv2n8d")))) (build-system r-build-system) (propagated-inputs `(("r-backports" ,r-backports) -- cgit v1.2.3 From c79e80f81b5c4e9dde4b86bbba720aa29ff5e91b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:50:00 +0100 Subject: gnu: r-mice: Update to 3.7.0. * gnu/packages/cran.scm (r-mice): Update to 3.7.0. --- 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 1a2d7f9622..458d5130e8 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -3336,14 +3336,14 @@ analysis of multiply imputed data sets.") (define-public r-mice (package (name "r-mice") - (version "3.6.0") + (version "3.7.0") (source (origin (method url-fetch) (uri (cran-uri "mice" version)) (sha256 (base32 - "0pgcxdmp77604h6f4x8hhs6j4xdjgf5b9zvnixyzdj8vcgdjpivv")))) + "1wx1s1gc07iz63w4m8z0i1n5mc273f89grp5d3hfla7ypicjkasf")))) (build-system r-build-system) (propagated-inputs `(("r-broom" ,r-broom) -- cgit v1.2.3 From a8e8a10a762477b94e3c8ae554d1362d7d755e42 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:50:07 +0100 Subject: gnu: r-tinytex: Update to 0.18. * gnu/packages/cran.scm (r-tinytex): Update to 0.18. --- 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 458d5130e8..c6861abbf8 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -4132,14 +4132,14 @@ terminals.") (define-public r-tinytex (package (name "r-tinytex") - (version "0.17") + (version "0.18") (source (origin (method url-fetch) (uri (cran-uri "tinytex" version)) (sha256 (base32 - "0mgxrbj4gam2gvxfk26nq820vsfjggj81m2l7j9m8vp361k15r0w")))) + "04mpbhadixbxmnazj0q6cj973cajchscvyh1k6a5b3qk26dp5krr")))) (build-system r-build-system) (propagated-inputs `(("r-xfun" ,r-xfun))) -- cgit v1.2.3 From 2beb585c8d4318f09f32364c988d875432347f5d Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:50:15 +0100 Subject: gnu: r-sna: Update to 2.5. * gnu/packages/cran.scm (r-sna): Update to 2.5. --- 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 c6861abbf8..7cccb09bb6 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -4225,14 +4225,14 @@ detect possible inconsistencies.") (define-public r-sna (package (name "r-sna") - (version "2.4") + (version "2.5") (source (origin (method url-fetch) (uri (cran-uri "sna" version)) (sha256 (base32 - "1ks8819qvpdfansfqj9p32s1rhvl26frvbi78m4rx1wd1qcv74i2")))) + "1j3i6300m686qqfmyvadim377cd3mplzgj6mandygw8brg50id8k")))) (build-system r-build-system) (propagated-inputs `(("r-network" ,r-network) -- cgit v1.2.3 From 98ce8a31f0d78ff84361decc1d8ae5f6db91723a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:50:22 +0100 Subject: gnu: r-renv: Update to 0.9.2. * gnu/packages/cran.scm (r-renv): Update to 0.9.2. --- 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 7cccb09bb6..229402f58c 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -5628,14 +5628,14 @@ Python's @url{https://github.com/ActiveState/appdirs,Appdirs} to R.") (define-public r-renv (package (name "r-renv") - (version "0.9.1") + (version "0.9.2") (source (origin (method url-fetch) (uri (cran-uri "renv" version)) (sha256 (base32 - "0mwqpcay6v1hnvhggsrn1chvdlhi9hwvsswas8ysygfy5wxxz1sm")))) + "1jwnabryn77s29ybwdfzlnd7c8m05xmi69kp5qbvdxy2gjwjzcdr")))) (properties `((upstream-name . "renv"))) (build-system r-build-system) (home-page "https://rstudio.github.io/renv") -- cgit v1.2.3 From cceb86f98263c5420784a9f9b4ad54955f1ca637 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:50:28 +0100 Subject: gnu: r-rdpack: Update to 0.11-1. * gnu/packages/cran.scm (r-rdpack): 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 229402f58c..6239909792 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -6148,14 +6148,14 @@ hierarchical models using Markov Chain Monte Carlo (MCMC) simulation.") (define-public r-rdpack (package (name "r-rdpack") - (version "0.11-0") + (version "0.11-1") (source (origin (method url-fetch) (uri (cran-uri "Rdpack" version)) (sha256 (base32 - "11cd27s6zp5cxnwxcvz6rjf00y0r7aq8ywhzwpf1r4xy1z44kd4g")))) + "080y15p2hl4jsq91ak2f1y2kx1iqq5c5wzyx3zyhjwp01cahy0jq")))) (properties `((upstream-name . "Rdpack"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 31fa45b679bca1731eebde64b993f3cc758151c7 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:50:35 +0100 Subject: gnu: r-deriv: Update to 4.0. * gnu/packages/cran.scm (r-deriv): Update to 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 6239909792..865d0ece74 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -6716,14 +6716,14 @@ Group (Non-)Overlap considerations.") (define-public r-deriv (package (name "r-deriv") - (version "3.9.0") + (version "4.0") (source (origin (method url-fetch) (uri (cran-uri "Deriv" version)) (sha256 (base32 - "0hlqm216bg3l79gq6m0am0xz6vd3l2hgjnjm6lym3mkmgkka4kxw")))) + "03mlfy8jzzzbh2l18gnmw0a71n9savx4cw72yhkxq93v2xj8fy3n")))) (properties `((upstream-name . "Deriv"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/Deriv") -- cgit v1.2.3 From f92c0c1efcb978c32445d9f3bc184d20950a6a2e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:50:45 +0100 Subject: gnu: r-multcomp: Update to 1.4-11. * gnu/packages/cran.scm (r-multcomp): Update to 1.4-11. --- 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 865d0ece74..5c7eb2547a 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -8148,14 +8148,14 @@ packages maintained by Torsten Hothorn.") (define-public r-multcomp (package (name "r-multcomp") - (version "1.4-10") + (version "1.4-11") (source (origin (method url-fetch) (uri (cran-uri "multcomp" version)) (sha256 (base32 - "1kzmdn9jmz5bmhf3wsfr12ljbasmwsgcsfdia52k0bi6q0swdg19")))) + "0jw9661hs4396wz9vflk3rak0ryzj1cg2pnndsn1gb4fjyf2vlhb")))) (build-system r-build-system) (propagated-inputs `(("r-codetools" ,r-codetools) -- cgit v1.2.3 From afc1ff2f0811fc7f81e2c60ab63cc4dba4a19e94 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:50:54 +0100 Subject: gnu: r-performance: Update to 0.4.2. * gnu/packages/cran.scm (r-performance): Update to 0.4.2. --- 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 5c7eb2547a..d677ecb4ee 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -8433,14 +8433,14 @@ ROPE percentage and pd).") (define-public r-performance (package (name "r-performance") - (version "0.4.0") + (version "0.4.2") (source (origin (method url-fetch) (uri (cran-uri "performance" version)) (sha256 (base32 - "0lxpmp9smn5r3xvfik36nr608wcpmmximjh0v2sckyvjf7hnb4s0")))) + "1pcjmqqm178dvdcpzkv5p4sj7glsppcny7znljb2nqkxh539a59p")))) (build-system r-build-system) (propagated-inputs `(("r-bayestestr" ,r-bayestestr) -- cgit v1.2.3 From d4e8f2070504466ef4ec8d458f7c91dec052d615 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:51:01 +0100 Subject: gnu: r-lmertest: Update to 3.1-1. * gnu/packages/cran.scm (r-lmertest): Update to 3.1-1. --- 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 d677ecb4ee..0265d508da 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -9041,14 +9041,14 @@ experiments using ANOVA or mixed models.") (define-public r-lmertest (package (name "r-lmertest") - (version "3.1-0") + (version "3.1-1") (source (origin (method url-fetch) (uri (cran-uri "lmerTest" version)) (sha256 (base32 - "1nkz8cmxa5yb8q4i65bmhnn5pd4bhwcyjplyscynb24z3f64xp9b")))) + "0r2vvs3nl6p8xla3gd943khb4ixp0alvspqpnz2y6n3wk8zgh3jj")))) (properties `((upstream-name . "lmerTest"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From b744174e7dc02f41075a53acbadf7a66d37e2925 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:51:07 +0100 Subject: gnu: r-fmsb: Update to 0.7.0. * gnu/packages/cran.scm (r-fmsb): Update to 0.7.0. --- 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 0265d508da..c3ac14ddc0 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -9486,14 +9486,14 @@ for evolution along a phylogenetic tree.") (define-public r-fmsb (package (name "r-fmsb") - (version "0.6.3") + (version "0.7.0") (source (origin (method url-fetch) (uri (cran-uri "fmsb" version)) (sha256 (base32 - "1n29bnyp20pvpk2lsa9fblsj5w7amp14snc74pk5w3yr5y6rj0s5")))) + "0x1wkzfdvv4s5xmr0whcwjz4aac71gacwymj2c3mzj2bbswwlw45")))) (build-system r-build-system) (home-page "http://minato.sip21c.org/msb/") (synopsis "Functions for medical statistics book with demographic data") -- cgit v1.2.3 From 5f99ffb013ca3766c691f666539ba6759790f361 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:51:19 +0100 Subject: gnu: r-tm: Update to 0.7-7. * gnu/packages/cran.scm (r-tm): Update to 0.7-7. --- 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 c3ac14ddc0..8d579b364d 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -9667,14 +9667,14 @@ Processing.") (define-public r-tm (package (name "r-tm") - (version "0.7-6") + (version "0.7-7") (source (origin (method url-fetch) (uri (cran-uri "tm" version)) (sha256 (base32 - "0spv43kjbpxq3rdxx8ysgrncjyc35ydiwk7gp8n4sig45iqyz59r")))) + "0pyics8j7a4wkh5gzin46l0qars5vgbb1886xqpdqjs1z0gy9nyh")))) (properties `((upstream-name . "tm"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 126f027b99d0f3620fbca0f9ca402e7efe4f9d5f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:51:25 +0100 Subject: gnu: r-tidytree: Update to 0.3.1. * gnu/packages/cran.scm (r-tidytree): Update to 0.3.1. --- 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 8d579b364d..11f98ed893 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -9763,13 +9763,13 @@ maps.") (define-public r-tidytree (package (name "r-tidytree") - (version "0.3.0") + (version "0.3.1") (source (origin (method url-fetch) (uri (cran-uri "tidytree" version)) (sha256 - (base32 "1sbfwcxf9v1lhpa0392b49b6qfjrq7nlqz2djqzk5aknj9j64zvy")))) + (base32 "1bnzs62z2l8ck2h9gabmxvayizv4nfn8dmyzry83fv0cspjbyiv7")))) (build-system r-build-system) (propagated-inputs `(("r-ape" ,r-ape) -- cgit v1.2.3 From 074c698e724265c256162dfd7a1c4c8249b9a08a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:51:33 +0100 Subject: gnu: r-spam: Update to 2.5-1. * gnu/packages/cran.scm (r-spam): Update to 2.5-1. --- 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 11f98ed893..06c793d3cb 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -11083,13 +11083,13 @@ This makes it a convenient and fast interface to C/C++ and Fortran code.") (define-public r-spam (package (name "r-spam") - (version "2.5-0") + (version "2.5-1") (source (origin (method url-fetch) (uri (cran-uri "spam" version)) (sha256 - (base32 "1wfv45jq8zy8kyjr308zicc1461y1777qll1cy6lw4071f9rvba2")))) + (base32 "0ry0a76cljlmilrzcriiizcidxyhq1i7i9bqhvl1qda81ld8hifi")))) (build-system r-build-system) (propagated-inputs `(("r-dotcall64" ,r-dotcall64))) -- cgit v1.2.3 From a2e3f27e1f46f3b0f0a8902bb5b5f9a04148cbfd Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:51:39 +0100 Subject: gnu: r-nlme: Update to 3.1-143. * gnu/packages/statistics.scm (r-nlme): Update to 3.1-143. --- 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 811033f0c3..3b6abbace7 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -590,13 +590,13 @@ and operations on them using LAPACK and SuiteSparse.") (define-public r-nlme (package (name "r-nlme") - (version "3.1-142") + (version "3.1-143") (source (origin (method url-fetch) (uri (cran-uri "nlme" version)) (sha256 - (base32 "0figfb1i22hfkkhzpprmpp723s01r43x725a1ab0pc9gsxqg90nx")))) + (base32 "13iixbs2ibldc75rl7rav5n5kx33zwm33xnfw1yvlkpcqf38bd22")))) (build-system r-build-system) (propagated-inputs `(("r-lattice" ,r-lattice))) -- cgit v1.2.3 From 2947e330dacd181ba5543294691e216e9341a601 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:51:46 +0100 Subject: gnu: r-plyr: Update to 1.8.5. * gnu/packages/statistics.scm (r-plyr): Update to 1.8.5. [native-inputs]: Move r-rcpp from here... [propagated-inputs]: ...to here. --- gnu/packages/statistics.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 3b6abbace7..95cf8c2f07 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -933,15 +933,15 @@ in which the whole-plots or split-plots or both can be freely exchangeable.") (define-public r-plyr (package (name "r-plyr") - (version "1.8.4") + (version "1.8.5") (source (origin (method url-fetch) (uri (cran-uri "plyr" version)) (sha256 - (base32 "1igar5pcjqh0jyxv0z3jah8rz617vfa86vw0r5c7c031b7bj5db0")))) + (base32 "0x4mbb3rgv1ayxqidw0p9i10khbg51fz5r62vw4il8d7licqq07a")))) (build-system r-build-system) - (native-inputs `(("r-rcpp" ,r-rcpp))) + (propagated-inputs `(("r-rcpp" ,r-rcpp))) (home-page "http://had.co.nz/plyr") (synopsis "Tools for Splitting, Applying and Combining Data") (description -- cgit v1.2.3 From 6c2887e6b22fcdb2bf0de71d866f2c0c3dfd4d9f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:52:08 +0100 Subject: gnu: r-dbi: Update to 1.1.0. * gnu/packages/statistics.scm (r-dbi): Update to 1.1.0. --- 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 95cf8c2f07..6b81b06f53 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -1240,13 +1240,13 @@ evaluation (NSE) in R.") (define-public r-dbi (package (name "r-dbi") - (version "1.0.0") + (version "1.1.0") (source (origin (method url-fetch) (uri (cran-uri "DBI" version)) (sha256 (base32 - "1x8wy2vg2gcgd9bww04qmf0dsn3kp0rfjd8q8j1r2x9zxccg25pz")))) + "1r03j9rdcxb9bhxk40dkmy10ikz4yzsxhy3f9k9ix3x577xbfvd9")))) (build-system r-build-system) (home-page "https://github.com/rstats-db/DBI") (synopsis "R database interface") -- cgit v1.2.3 From d2d7259b4781f5e308d1896cb4cea2151ce7249b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:52:14 +0100 Subject: gnu: r-rmarkdown: Update to 2.0. * gnu/packages/statistics.scm (r-rmarkdown): Update to 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 6b81b06f53..309eb57a56 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -2662,13 +2662,13 @@ certain criterion, e.g., it contains a certain regular file.") (define-public r-rmarkdown (package (name "r-rmarkdown") - (version "1.18") + (version "2.0") (source (origin (method url-fetch) (uri (cran-uri "rmarkdown" version)) (sha256 - (base32 "0fykzbb5kjsqc8v6gjcdma7rmq0gailp30qij6plgna4d8nhjw3w")))) + (base32 "1bm3n17wa0pf1cq7qmwhbnn02x2pld7zzmmzjcvwy6apanch9fl7")))) (properties `((upstream-name . "rmarkdown"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 804e0682bf657b5f897435cfb2beb6ba0b4b386c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:52:20 +0100 Subject: gnu: r-segmented: Update to 1.1-0. * gnu/packages/statistics.scm (r-segmented): Update to 1.1-0. --- 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 309eb57a56..9fb3604831 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -2972,14 +2972,14 @@ statements.") (define-public r-segmented (package (name "r-segmented") - (version "1.0-0") + (version "1.1-0") (source (origin (method url-fetch) (uri (cran-uri "segmented" version)) (sha256 (base32 - "1igsfkffpa60zn6j45lhw1zgr5pz6rjknv2f3sylnx5l9fdwibgf")))) + "06cxdrqgnpk5fvbam5i7qa4n71wry0yvlj0jpwbxf267mvpx10fh")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/segmented") (synopsis "Regression models with breakpoints estimation") -- cgit v1.2.3 From 468fb90fdd991038c0c948ad7934a4489876a807 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:52:31 +0100 Subject: gnu: r-sparsem: Update to 1.78. * gnu/packages/statistics.scm (r-sparsem): Update to 1.78. [inputs]: Move gfortran from here... [native-inputs]: ...to here. --- gnu/packages/statistics.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 9fb3604831..ba0148b452 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -3013,16 +3013,16 @@ worker processes and collect and return the results on the master.") (define-public r-sparsem (package (name "r-sparsem") - (version "1.77") + (version "1.78") (source (origin (method url-fetch) (uri (cran-uri "SparseM" version)) (sha256 (base32 - "0p6ljma2h12cq1xmy0cxb48ih8dhxxbnwkqzvx3cckxf2kprycm9")))) + "0cmlm0lps3daalvp5jzjnjfys388hgkyc8yw0g5r2351h749xdyn")))) (properties `((upstream-name . "SparseM"))) - (inputs + (native-inputs `(("gfortran" ,gfortran))) (build-system r-build-system) (home-page "http://www.econ.uiuc.edu/~roger/research/sparse/sparse.html") -- cgit v1.2.3 From 155d48f6c6f396be7f7f9fc4be17e77168297360 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:52:51 +0100 Subject: gnu: r-glmnet: Update to 3.0-2. * gnu/packages/statistics.scm (r-glmnet): Update to 3.0-2. --- 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 ba0148b452..3b76030159 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -3207,13 +3207,13 @@ analysis of large sparse or dense matrices.") (define-public r-glmnet (package (name "r-glmnet") - (version "3.0-1") + (version "3.0-2") (source (origin (method url-fetch) (uri (cran-uri "glmnet" version)) (sha256 - (base32 "04wa926mnss53p1fhx0mjgxnmwmmqls12sc0sy7w09kbmyqa3fq7")))) + (base32 "0b3nnfzp8dxcdkvxr0yvy6d58yk3xg4kz1wqa42bxqppbakmd2gl")))) (build-system r-build-system) (native-inputs `(("gfortran" ,gfortran))) -- cgit v1.2.3 From 34982a46225d03191f87752d760d54f4782751fd Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 15:52:58 +0100 Subject: gnu: r-quantreg: Update to 5.54. * gnu/packages/statistics.scm (r-quantreg): Update to 5.54. --- 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 3b76030159..188e03f979 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -5107,13 +5107,13 @@ using modular prediction and response module classes.") (define-public r-quantreg (package (name "r-quantreg") - (version "5.52") + (version "5.54") (source (origin (method url-fetch) (uri (cran-uri "quantreg" version)) (sha256 - (base32 "0rq9as31wiz41lmi9hmdq3gknpcbpwqzfcn065ysjdxzjdb57dcy")))) + (base32 "19nh79qrkb75q348nk148l8wqjwnq5jgq29wpzqym5cfv1kjqfvh")))) (build-system r-build-system) (native-inputs `(("gfortran" ,gfortran))) -- cgit v1.2.3 From e703f6d8ef354d2c394c4f68bde5b9bf66237f70 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Dec 2019 23:10:49 +0100 Subject: gnu: Add pinfo. * gnu/packages/texinfo.scm (pinfo): New variable. --- gnu/packages/texinfo.scm | 55 +++++++++++++++++++++++++++++++++++++++++++++++- 1 file changed, 54 insertions(+), 1 deletion(-) diff --git a/gnu/packages/texinfo.scm b/gnu/packages/texinfo.scm index 7f95c29b9e..de3f7c5d35 100644 --- a/gnu/packages/texinfo.scm +++ b/gnu/packages/texinfo.scm @@ -4,6 +4,7 @@ ;;; Copyright © 2015 Mark H Weaver ;;; Copyright © 2017 Efraim Flashner ;;; Copyright © 2019 Mathieu Othacehe +;;; Copyright © 2019 Ricardo Wurmus ;;; ;;; This file is part of GNU Guix. ;;; @@ -25,11 +26,15 @@ #:use-module (guix packages) #:use-module (guix utils) #:use-module (guix download) + #:use-module (guix git-download) #:use-module (guix build-system gnu) #:use-module (gnu packages) + #:use-module (gnu packages autotools) #:use-module (gnu packages compression) + #:use-module (gnu packages gettext) #:use-module (gnu packages ncurses) - #:use-module (gnu packages perl)) + #:use-module (gnu packages perl) + #:use-module (gnu packages readline)) (define-public texinfo (package @@ -183,3 +188,51 @@ of the GNU Texinfo implementation) do not intend to make further releases of Texi2HTML.") ;; Files in /lib under lgpl2.1+ and x11 (license gpl2+))) + +(define-public pinfo + (package + (name "pinfo") + (version "0.6.13") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/baszoetekouw/pinfo.git") + (commit (string-append "v" version)))) + (sha256 + (base32 + "173d2p22irwiabvr4z6qvr6zpr6ysfkhmadjlyhyiwd7z62larvy")))) + (build-system gnu-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'remove-Werror + (lambda _ + (substitute* "configure.ac" + (("-Werror") "")) + #t)) + (add-after 'unpack 'embed-reference-to-clear + (lambda* (#:key inputs #:allow-other-keys) + (substitute* '("src/manual.c" + "src/mainfunction.c" + "src/utils.c") + (("\"clear\"") + (string-append "\"" (which "clear") "\""))) + #t))))) + (inputs + `(("ncurses" ,ncurses) + ("readline" ,readline))) + (native-inputs + `(("autoconf" ,autoconf) + ("automake" ,automake) + ("gettext" ,gnu-gettext) + ("libtool" ,libtool) + ("texinfo" ,texinfo))) + (home-page "https://github.com/baszoetekouw/pinfo") + (synopsis "Lynx-style Info file and man page reader") + (description + "Pinfo is an Info file viewer. Pinfo is similar in use to the Lynx web +browser. You just move across info nodes, and select links, follow them, etc. +It supports many colors. Pinfo also supports viewing of manual pages -- they +are colorized like in the midnight commander's viewer, and additionaly they +are hypertextualized.") + (license gpl2+))) -- cgit v1.2.3 From 00386d3430f12710997f17091a55c07323ff138c Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Sun, 15 Dec 2019 23:33:06 +0100 Subject: gnu: Add emacs-eww-lnum. * gnu/packages/emacs-xyz.scm (emacs-eww-lnum): 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 8212e4d5b9..a27000ddac 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -1241,6 +1241,30 @@ or unexpected behavior inside an elisp configuration file (typically "Emacs-wget is an emacs interface for the wget file downloader.") (license license:gpl2+))) +(define-public emacs-eww-lnum + (package + (name "emacs-eww-lnum") + (version "1.1") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/m00natic/eww-lnum.git") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0gs6bi3s2sszc6v2b26929azmn5513kvyin99n4d0ark1jdbjmv2")))) + (build-system emacs-build-system) + (home-page "https://github.com/m00natic/eww-lnum") + (synopsis "Conkeror-like functionality for Eww") + (description "This is extension to the Emacs browser Eww that adds +Conkeror-like functionality. In short, currently visible links, forms, +buttons are temporarily assigned numbers with which the former can be +immediately activated. Also filtering can be applied so selection can be +incrementally confined in Isearch manner.") + (license license:gpl3+))) + + ;;; ;;; Multimedia. -- cgit v1.2.3 From 90ee17cdac77e48603b93ab30b71c4ba7ce2db42 Mon Sep 17 00:00:00 2001 From: Alexandros Theodotou Date: Mon, 16 Dec 2019 04:42:22 +0000 Subject: gnu: Add python-sphinx-intl * gnu/packages/sphinx.scm (python-sphinx-intl): New variable. Signed-off-by: Brett Gilio --- gnu/packages/sphinx.scm | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) diff --git a/gnu/packages/sphinx.scm b/gnu/packages/sphinx.scm index b74137362c..a3958d2c9b 100644 --- a/gnu/packages/sphinx.scm +++ b/gnu/packages/sphinx.scm @@ -11,6 +11,7 @@ ;;; Copyright © 2017 Julien Lepiller ;;; Copyright © 2019 Efraim Flashner ;;; Copyright © 2019 Nicolas Goaziou +;;; Copyright © 2019 Alexandros Theodotou ;;; ;;; This file is part of GNU Guix. ;;; @@ -565,3 +566,26 @@ and several other projects.") (description "This package is an extension to reStructuredText and Sphinx to be able to read and render the Doxygen xml output.") (license license:bsd-3))) + +(define-public python-sphinx-intl + (package + (name "python-sphinx-intl") + (version "2.0.0") + (source + (origin + (method url-fetch) + (uri (pypi-uri "sphinx-intl" version)) + (sha256 + (base32 + "0zbf1bh23b3kza8bnjykmv2k21xmmr4gamhi3lnicnr6ypnrphr5")))) + (build-system python-build-system) + (propagated-inputs + `(("python-sphinx" ,python-sphinx) + ("python-click" ,python-click))) + (home-page "https://github.com/sphinx-doc/sphinx-intl") + (synopsis + "Sphinx utility that makes it easy to translate and to apply translation") + (description + "A utility tool that provides several features that make it easy to +translate and to apply translation to Sphinx generated document.") + (license license:bsd-2))) -- cgit v1.2.3 From 2c82d4ad10de8e0ba462d81401385c5e7499f6e2 Mon Sep 17 00:00:00 2001 From: Brett Gilio Date: Mon, 16 Dec 2019 00:06:05 -0600 Subject: gnu: ccls: Configure using -isystem for header files. * gnu/packages/cpp.scm (ccls): Configure using -isystem for header files. [arguments]: Use GCC as a build input for preprocessing and searching GCC subdirectories, this provides better support for header file completion on runtime. [inputs]: Add ncurses for command-line support. Remove LLVM, it is not needed. [native-inputs]: Move rapidjson from inputs to native-inputs, add GCC. --- gnu/packages/cpp.scm | 18 +++++++++++++----- 1 file changed, 13 insertions(+), 5 deletions(-) diff --git a/gnu/packages/cpp.scm b/gnu/packages/cpp.scm index 335f9a65cd..7870184a52 100644 --- a/gnu/packages/cpp.scm +++ b/gnu/packages/cpp.scm @@ -6,6 +6,7 @@ ;;; Copyright © 2019 Mathieu Othacehe ;;; Copyright © 2019 Pierre Neidhardt ;;; Copyright © 2019 Jan Wielkiewicz +;;; Copyright © 2019 Brett Gilio ;;; ;;; This file is part of GNU Guix. ;;; @@ -35,7 +36,9 @@ #:use-module (gnu packages check) #:use-module (gnu packages code) #:use-module (gnu packages compression) + #:use-module (gnu packages gcc) #:use-module (gnu packages llvm) + #:use-module (gnu packages ncurses) #:use-module (gnu packages perl) #:use-module (gnu packages pkg-config) #:use-module (gnu packages tls) @@ -305,12 +308,17 @@ tools (containers, algorithms) used by other QuantStack packages.") (file-name (git-file-name name version)))) (build-system cmake-build-system) (arguments - '(#:tests? #f)) ; no check target. - (inputs - `(("rapidjson" ,rapidjson))) - (native-inputs + `(#:tests? #f ; no check target. + #:configure-flags + (list (string-append "-DCMAKE_CXX_FLAGS='-isystem " + (assoc-ref %build-inputs "gcc") + "/include/c++'")))) + (inputs `(("clang" ,clang) - ("llvm" ,llvm))) + ("ncurses" ,ncurses))) + (native-inputs + `(("rapidjson" ,rapidjson) + ("gcc" ,gcc))) (home-page "https://github.com/MaskRay/ccls") (synopsis "C/C++/Objective-C language server") (description -- cgit v1.2.3 From 3c80b07a0b4a2f1c2702acd6896f94892c516709 Mon Sep 17 00:00:00 2001 From: Brett Gilio Date: Mon, 16 Dec 2019 00:10:14 -0600 Subject: gnu: ccls: Adjust indentation * gnu/packages/cpp.scm (ccls): Adjust indentation. --- gnu/packages/cpp.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/cpp.scm b/gnu/packages/cpp.scm index 7870184a52..f30da0e043 100644 --- a/gnu/packages/cpp.scm +++ b/gnu/packages/cpp.scm @@ -313,7 +313,7 @@ tools (containers, algorithms) used by other QuantStack packages.") (list (string-append "-DCMAKE_CXX_FLAGS='-isystem " (assoc-ref %build-inputs "gcc") "/include/c++'")))) - (inputs + (inputs `(("clang" ,clang) ("ncurses" ,ncurses))) (native-inputs -- cgit v1.2.3 From 223236f6c2f8ee8eb6bf3b95b25185365d258767 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 16 Dec 2019 08:03:20 +0100 Subject: gnu: guile-studio: Update to 0.0.2. * gnu/packages/guile-xyz.scm (guile-studio): Update to 0.0.2. [arguments]: Only include emacs inputs in INPUTS make flag. --- gnu/packages/guile-xyz.scm | 108 ++++++++++++++++++++++++--------------------- 1 file changed, 58 insertions(+), 50 deletions(-) diff --git a/gnu/packages/guile-xyz.scm b/gnu/packages/guile-xyz.scm index 674b24e594..f0a022be2d 100644 --- a/gnu/packages/guile-xyz.scm +++ b/gnu/packages/guile-xyz.scm @@ -2002,59 +2002,67 @@ The picture values can directly be displayed in Geiser.") (license license:lgpl3+)))) (define-public guile-studio - (let ((commit "98fbbbd08de396cd8a0e45f2a4badf1c733a5772") - (revision "3")) - (package - (name "guile-studio") - (version (git-version "0.0.1" revision commit)) - (source (origin - (method git-fetch) - (uri (git-reference - (url "https://git.elephly.net/software/guile-studio.git") - (commit commit))) - (file-name (git-file-name name version)) - (sha256 - (base32 - "0rxl5gv2mavycwkl33lcwyb3z71j2f4zyzk60k7vl3hzszpr08iq")))) - (build-system gnu-build-system) - (arguments - `(#:tests? #f ; there are none - #:make-flags - (list (string-append "ICONS_DIR=" - (assoc-ref %build-inputs "adwaita-icon-theme") - "/share/icons/Adwaita/") - (string-append "PICT_DIR=" - (assoc-ref %build-inputs "guile-picture-language")) - (string-append "EMACS_DIR=" - (assoc-ref %build-inputs "emacs")) - (string-append "GUILE_DIR=" - (assoc-ref %build-inputs "guile")) - (string-join (cons "INPUTS=" (map cdr %build-inputs))) - (string-append "PREFIX=" (assoc-ref %outputs "out"))) - #:phases - (modify-phases %standard-phases - (delete 'configure) - (delete 'install)))) - (inputs - `(("guile" ,guile-2.2) - ("guile-picture-language" ,guile-picture-language) - ("emacs" ,emacs) - ("emacs-geiser" ,emacs-geiser) - ("emacs-company" ,emacs-company) - ("emacs-flycheck" ,emacs-flycheck) - ("emacs-smart-mode-line" ,emacs-smart-mode-line) - ("emacs-paren-face" ,emacs-paren-face) - ("adwaita-icon-theme" ,adwaita-icon-theme))) - (native-inputs - `(("texinfo" ,texinfo))) - (home-page "https://gnu.org/software/guile") - (synopsis "IDE for Guile") - (description - "This is Emacs with a few settings that make working with Guile easier + (package + (name "guile-studio") + (version "0.0.2") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://git.elephly.net/software/guile-studio.git") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "10ls4ra148hd9ra7sin4kh9vv0am5pwk48p7dsjhrlg2l1hsh4hi")))) + (build-system gnu-build-system) + (arguments + `(#:modules + ((ice-9 match) + (srfi srfi-1) + ,@%gnu-build-system-modules) + #:tests? #f ; there are none + #:make-flags + (list (string-append "ICONS_DIR=" + (assoc-ref %build-inputs "adwaita-icon-theme") + "/share/icons/Adwaita/") + (string-append "PICT_DIR=" + (assoc-ref %build-inputs "guile-picture-language")) + (string-append "EMACS_DIR=" + (assoc-ref %build-inputs "emacs")) + (string-append "GUILE_DIR=" + (assoc-ref %build-inputs "guile")) + (string-join (cons "INPUTS=" + (filter-map + (lambda (input) + (match input + ((label . pkg) + (and (string-prefix? "emacs" label) pkg)))) + %build-inputs))) + (string-append "PREFIX=" (assoc-ref %outputs "out"))) + #:phases + (modify-phases %standard-phases + (delete 'configure) + (delete 'install)))) + (inputs + `(("guile" ,guile-2.2) + ("guile-picture-language" ,guile-picture-language) + ("emacs" ,emacs) + ("emacs-geiser" ,emacs-geiser) + ("emacs-company" ,emacs-company) + ("emacs-flycheck" ,emacs-flycheck) + ("emacs-smart-mode-line" ,emacs-smart-mode-line) + ("emacs-paren-face" ,emacs-paren-face) + ("adwaita-icon-theme" ,adwaita-icon-theme))) + (native-inputs + `(("texinfo" ,texinfo))) + (home-page "https://gnu.org/software/guile") + (synopsis "IDE for Guile") + (description + "This is Emacs with a few settings that make working with Guile easier for people new to Emacs. Features include: CUA mode, Geiser, tool bar icons to evaluate Guile buffers, support for Guile's very own picture language, code completion, a simple mode line, etc.") - (license license:gpl3+)))) + (license license:gpl3+))) (define-public guile-stis-parser (let ((commit "6e85d37ffc333b722f4413a6c648263701eb75bd") -- cgit v1.2.3 From d0ef3a00486a868ff490257013650fa60928214d Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Mon, 16 Dec 2019 14:13:16 +0200 Subject: gnu: libreoffice: Update to 6.3.4.2. * gnu/packages/libreoffice.scm (libreoffice): Update to 6.3.4.2. --- gnu/packages/libreoffice.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/libreoffice.scm b/gnu/packages/libreoffice.scm index 761e75072d..038031b800 100644 --- a/gnu/packages/libreoffice.scm +++ b/gnu/packages/libreoffice.scm @@ -929,7 +929,7 @@ converting QuarkXPress file format. It supports versions 3.1 to 4.1.") (define-public libreoffice (package (name "libreoffice") - (version "6.3.3.2") + (version "6.3.4.2") (source (origin (method url-fetch) @@ -939,7 +939,7 @@ converting QuarkXPress file format. It supports versions 3.1 to 4.1.") (version-prefix version 3) "/libreoffice-" version ".tar.xz")) (sha256 (base32 - "1kz5950vhjc33rx7pyl5sw9lxxm90hxrj7v8y86jy34skjrfa3nl")) + "1774vmf3lr5x24ikpn1z5vqcdwrhiwfkjy7sx09jqkvpm6d5awnb")) (patches (search-patches "libreoffice-icu.patch" "libreoffice-glm.patch")) (modules '((guix build utils))) -- cgit v1.2.3 From 8c4c5bf86ac57e2923f51f9dcc5794dedb85ed3c Mon Sep 17 00:00:00 2001 From: Mathieu Othacehe Date: Mon, 16 Dec 2019 15:08:01 +0100 Subject: Revert "gnu: info-reader: Fix cross-compilation." This reverts commit 614a1e3fa2d731d4719f03912b1b87fb4fd309cb. This is broken on master with the following error: output (`/gnu/store/6rnhfi8zrdajbahbq9ii8bpj7mwfcjba-info-reader-6.6') is not allowed to refer to path `/gnu/store/ziinjmbnq004866mwjrczsk12wf35qb8-perl-5.30.0' build of /gnu/store/nnfvr10713khxp1bkbpwi5wxbj8cm4wb-info-reader-6.6.drv failed View build log at '/var/log/guix/drvs/nn/fvr10713khxp1bkbpwi5wxbj8cm4wb-info-reader-6.6.drv.bz2'. --- gnu/packages/texinfo.scm | 49 ++++++++++++++++++++++++------------------------ 1 file changed, 24 insertions(+), 25 deletions(-) diff --git a/gnu/packages/texinfo.scm b/gnu/packages/texinfo.scm index de3f7c5d35..1162e77b07 100644 --- a/gnu/packages/texinfo.scm +++ b/gnu/packages/texinfo.scm @@ -3,7 +3,6 @@ ;;; Copyright © 2014, 2016 Eric Bavier ;;; Copyright © 2015 Mark H Weaver ;;; Copyright © 2017 Efraim Flashner -;;; Copyright © 2019 Mathieu Othacehe ;;; Copyright © 2019 Ricardo Wurmus ;;; ;;; This file is part of GNU Guix. @@ -115,32 +114,32 @@ is on expressing the content semantically, avoiding physical markup commands.") (inherit texinfo) (name "info-reader") (arguments - `(,@(substitute-keyword-arguments (package-arguments texinfo) - ((#:phases phases) - `(modify-phases ,phases - (add-after 'install 'keep-only-info-reader - (lambda* (#:key outputs #:allow-other-keys) - ;; Remove everything but 'bin/info' and associated - ;; files. - (define (files) - (scandir "." (lambda (file) - (not (member file '("." "..")))))) - - (let ((out (assoc-ref outputs "out"))) - (with-directory-excursion out - (for-each delete-file-recursively - (fold delete (files) '("bin" "share")))) - (with-directory-excursion (string-append out "/bin") - (for-each delete-file (delete "info" (files)))) - (with-directory-excursion (string-append out "/share") - (for-each delete-file-recursively - (fold delete (files) - '("info" "locale")))) - #t)))))) - #:disallowed-references ,(assoc-ref (package-inputs texinfo) + `(#:disallowed-references ,(assoc-ref (package-inputs texinfo) "perl") + #:modules ((ice-9 ftw) (srfi srfi-1) - ,@%gnu-build-system-modules))) + ,@%gnu-build-system-modules) + + #:phases (modify-phases %standard-phases + (add-after 'install 'keep-only-info-reader + (lambda* (#:key outputs #:allow-other-keys) + ;; Remove everything but 'bin/info' and associated + ;; files. + (define (files) + (scandir "." (lambda (file) + (not (member file '("." "..")))))) + + (let ((out (assoc-ref outputs "out"))) + (with-directory-excursion out + (for-each delete-file-recursively + (fold delete (files) '("bin" "share")))) + (with-directory-excursion (string-append out "/bin") + (for-each delete-file (delete "info" (files)))) + (with-directory-excursion (string-append out "/share") + (for-each delete-file-recursively + (fold delete (files) + '("info" "locale")))) + #t)))))) (synopsis "Standalone Info documentation reader"))) (define-public texi2html -- cgit v1.2.3 From 709f839c20e1b985f81a262ca6a97eb79a9da6ed Mon Sep 17 00:00:00 2001 From: Pierre Neidhardt Date: Mon, 16 Dec 2019 15:34:51 +0100 Subject: gnu: emacs-helm-fish-completion: Update to 0.2. * gnu/packages/emacs-xyz.scm (emacs-helm-fish-completion): Update to 0.2. --- gnu/packages/emacs-xyz.scm | 42 ++++++++++++++++++++---------------------- 1 file changed, 20 insertions(+), 22 deletions(-) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index a27000ddac..1fd75a8240 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -20081,29 +20081,27 @@ Google guidelines.") (license license:gpl3+)))) (define-public emacs-helm-fish-completion - (let ((commit "ef764dd123040fe67ef8b62a1c13842e940b0963") - (revision "1")) - (package - (name "emacs-helm-fish-completion") - (version (git-version "0.1" revision commit)) - (home-page "https://github.com/emacs-helm/helm-fish-completion") - (source - (origin - (method git-fetch) - (uri (git-reference - (url home-page) - (commit commit))) - (file-name (git-file-name name version)) - (sha256 - (base32 "0k80kpapwfq2rv1lb0r994d0w6czl92xrmnkmrg0a05f4b3q0lb4")))) - (build-system emacs-build-system) - (propagated-inputs - `(("helm" ,emacs-helm) - ("fish-completion" ,emacs-fish-completion))) - (synopsis "Helm interface for Emacs fish-completion") - (description "Helm Fish Completion is a Helm interface for Emacs + (package + (name "emacs-helm-fish-completion") + (version "0.2") + (home-page "https://github.com/emacs-helm/helm-fish-completion") + (source + (origin + (method git-fetch) + (uri (git-reference + (url home-page) + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 "089gp2k22xwn33z8brpyb7r18vpyralq2cwxj1xsc8b2sj9s4896")))) + (build-system emacs-build-system) + (propagated-inputs + `(("helm" ,emacs-helm) + ("fish-completion" ,emacs-fish-completion))) + (synopsis "Helm interface for Emacs fish-completion") + (description "Helm Fish Completion is a Helm interface for Emacs fish-completion. It can be used in both Eshell and M-x shell.") - (license license:gpl3+)))) + (license license:gpl3+))) (define-public emacs-telega ;; This package has versions newer than indicated on MELPA. -- cgit v1.2.3 From c6a7fe7937a3db3ade7ced40c08dd674fbf5cf9c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 16 Dec 2019 15:01:39 +0100 Subject: gnu: yoshimi: Update to 1.6.1. * gnu/packages/music.scm (yoshimi): Update to 1.6.1. --- gnu/packages/music.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/music.scm b/gnu/packages/music.scm index 134fe7ed51..f80fb067e8 100644 --- a/gnu/packages/music.scm +++ b/gnu/packages/music.scm @@ -2185,7 +2185,7 @@ capabilities, custom envelopes, effects, etc.") (define-public yoshimi (package (name "yoshimi") - (version "1.6.0.3") + (version "1.6.1") (source (origin (method url-fetch) (uri (string-append "mirror://sourceforge/yoshimi/" @@ -2193,7 +2193,7 @@ capabilities, custom envelopes, effects, etc.") "/yoshimi-" version ".tar.bz2")) (sha256 (base32 - "1z2mnmm299ng6jcwa61dzr1ilwa5fjgsggxl2wa5smji6b4npmx7")))) + "1shnz429zgl0b4y5bpb61frk1747jwqfahq4hx44c972580zghzh")))) (build-system cmake-build-system) (arguments `(#:tests? #f ; there are no tests -- cgit v1.2.3 From 88ca4029a676a99325085a7ecede63d8b011de8f Mon Sep 17 00:00:00 2001 From: Mathieu Othacehe Date: Mon, 16 Dec 2019 12:39:18 +0100 Subject: gnu: iw: Fix cross-compilation. * gnu/packages/linux.scm (iw)[arguments]: Set PKG_CONFIG and CC variables correctly for cross-compilation. --- gnu/packages/linux.scm | 14 ++++++++++++-- 1 file changed, 12 insertions(+), 2 deletions(-) diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index c70aa6c815..a062e2ba55 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -2071,8 +2071,18 @@ configuration and monitoring interfaces.") (native-inputs `(("pkg-config" ,pkg-config))) (inputs `(("libnl" ,libnl))) (arguments - `(#:make-flags (list (string-append "PREFIX=" (assoc-ref %outputs "out")) - "CC=gcc") + `(#:make-flags + (let* ((target ,(%current-target-system)) + (gcc (if target (string-append target "-gcc") "gcc")) + (pkg-config (if target + (string-append target "-pkg-config") + "pkg-config"))) + (list + (string-append "CC=" gcc) + (string-append "PKG_CONFIG=" + (assoc-ref %build-inputs "pkg-config") + "/bin/" pkg-config) + (string-append "PREFIX=" (assoc-ref %outputs "out")))) #:phases (modify-phases %standard-phases (delete 'configure)))) (home-page "https://wireless.wiki.kernel.org/") (synopsis "Tool for configuring wireless devices") -- cgit v1.2.3 From 46429444d6dcec58690cdfeb9080cd9a4c7c7181 Mon Sep 17 00:00:00 2001 From: Mathieu Othacehe Date: Mon, 16 Dec 2019 16:41:01 +0100 Subject: gnu: psmisc: Fix cross-compilation. * gnu/packages/linux.scm (psmisc)[arguments]: Pass ac_cv_func_malloc_0_nonnull=yes and ac_cv_func_realloc_0_nonnull=yes options that are required when cross-compiling. --- gnu/packages/linux.scm | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index a062e2ba55..55a5ceb93c 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -1078,6 +1078,13 @@ at login. Local and dynamic reconfiguration are its key features.") (sha256 (base32 "16i7qzjmm6g0lzha8yzpfrlcxnvkgh95hkq9gdjd4zmzb8d0wxa1")))) (build-system gnu-build-system) + (arguments + `(,@(if (%current-target-system) + '(#:configure-flags + (list + "ac_cv_func_malloc_0_nonnull=yes" + "ac_cv_func_realloc_0_nonnull=yes")) + '()))) (inputs `(("ncurses" ,ncurses))) (home-page "https://gitlab.com/psmisc/psmisc") (synopsis "Small utilities that use the proc file system") -- cgit v1.2.3 From d0a26d0be9b1bdf00cfc20ddac6236e840707d27 Mon Sep 17 00:00:00 2001 From: Jan Nieuwenhuizen Date: Mon, 16 Dec 2019 11:42:37 +0100 Subject: gnu: gash: Update to 0.2.0. * gnu/packages/shells.scm (gash): Update to 0.2.0. --- gnu/packages/shells.scm | 19 ++++++------------- 1 file changed, 6 insertions(+), 13 deletions(-) diff --git a/gnu/packages/shells.scm b/gnu/packages/shells.scm index 40a59635b1..1d2f754e4a 100644 --- a/gnu/packages/shells.scm +++ b/gnu/packages/shells.scm @@ -11,6 +11,7 @@ ;;; Copyright © 2017 Arun Isaac ;;; Copyright © 2019 Meiyo Peng ;;; Copyright © 2019 Timothy Sample +;;; Copyright © 2019 Jan (janneke) Nieuwenhuizen ;;; ;;; This file is part of GNU Guix. ;;; @@ -794,30 +795,22 @@ is commonly written.") (define-public gash (package (name "gash") - (version "0.1") + (version "0.2.0") (source (origin (method url-fetch) (uri (string-append "mirror://savannah/gash/gash-" version ".tar.gz")) (sha256 (base32 - "00m3lif64zyxd41cnk208kc81nl6qz659676qgiaqgwrw0brzrid")) - (modules '((guix build utils))) - (snippet - '(begin - (substitute* "Makefile.in" - (("^moddir = (.*)/guile/(.*)" _ before after) - (string-append "moddir = " before "/guile/site/" - after)) - (("^ccachedir = (.*)/ccache/(.*)" _ before after) - (string-append "ccachedir = " before - "/site-ccache/" after))) - #t)))) + "13m0yz5h9nj3x40mr6wr5xcpq1lscndfwcicw3skrz801025hhgf")) + (modules '((guix build utils))))) (build-system gnu-build-system) (native-inputs `(("pkg-config" ,pkg-config))) (inputs `(("guile" ,guile-2.2))) + (arguments + '(#:make-flags '("XFAIL_TESTS=tests/redirects.org"))) (home-page "https://savannah.nongnu.org/projects/gash/") (synopsis "POSIX-compatible shell written in Guile Scheme") (description "Gash is a POSIX-compatible shell written in Guile -- cgit v1.2.3 From dbcef44a0bdc5472cd49cd02d9d11a9c5ff037c9 Mon Sep 17 00:00:00 2001 From: Mădălin Ionel Patrașcu Date: Mon, 16 Dec 2019 16:25:16 +0100 Subject: gnu: Add python-iocapture. * gnu/packages/python-xyz.scm (python-iocapture): New variable. Co-authored-by: Ricardo Wurmus Signed-off-by: Ricardo Wurmus --- gnu/packages/python-xyz.scm | 40 ++++++++++++++++++++++++++++++++++++++++ 1 file changed, 40 insertions(+) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 9fac87648a..2ec13b7c15 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -67,6 +67,7 @@ ;;; Copyright © 2019 Giacomo Leidi ;;; Copyright © 2019 Wiktor Żelazny ;;; Copyright © 2019 Tanguy Le Carrour +;;; Copyright © 2019 Mădălin Ionel Patrașcu ;;; ;;; This file is part of GNU Guix. ;;; @@ -16786,3 +16787,42 @@ services to what you expect in your tests.") (define-public python2-ujson (package-with-python2 python-ujson)) + +(define-public python-iocapture + ;; The latest release is more than a year older than this commit. + (let ((commit "fdc021c431d0840303908dfc3ca8769db383595c") + (revision "1")) + (package + (name "python-iocapture") + (version "0.1.2") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/oinume/iocapture.git") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1mkbhqibxvgwg0p7slr8dfraa3g2s6bsayladhax2jccwj4kcndz")))) + (build-system python-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (delete 'check) + (add-after 'install 'check + (lambda* (#:key inputs outputs #:allow-other-keys) + (add-installed-pythonpath inputs outputs) + (invoke "py.test" "-v" "tests") + #t))))) + (propagated-inputs + `(("python-flexmock" ,python-flexmock) + ("python-pytest" ,python-pytest) + ("python-pytest-cov" ,python-pytest-cov) + ("python-six" ,python-six))) + (home-page "https://github.com/oinume/iocapture") + (synopsis "Python capturing tool for stdout and stderr") + (description + "This package helps you to capture the standard out (stdout) and the +standard error channel (stderr) in your program.") + (license license:expat)))) -- cgit v1.2.3 From db6bd842aa4a6254b185740bda36f01c83cd9779 Mon Sep 17 00:00:00 2001 From: Mădălin Ionel Patrașcu Date: Mon, 16 Dec 2019 16:25:17 +0100 Subject: gnu: Add python-argh. * gnu/packages/python-xyz.scm (python-argh): New variable. Signed-off-by: Ricardo Wurmus --- gnu/packages/python-xyz.scm | 36 ++++++++++++++++++++++++++++++++++++ 1 file changed, 36 insertions(+) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 2ec13b7c15..e1c5c60f10 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -16826,3 +16826,39 @@ services to what you expect in your tests.") "This package helps you to capture the standard out (stdout) and the standard error channel (stderr) in your program.") (license license:expat)))) + +(define-public python-argh + ;; There are 21 commits since the latest release containing important + ;; improvements. + (let ((commit "dcd3253f2994400a6a58a700c118c53765bc50a4") + (revision "1")) + (package + (name "python-argh") + (version (git-version "0.26.2" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/neithere/argh.git") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1p5h3dnpbsjmqrvil96s71asc6i3gpinmbrabqmwnrsxprz7r3ns")))) + (build-system python-build-system) + (propagated-inputs + `(("python-iocapture" ,python-iocapture) + ("python-mock" ,python-mock) + ("python-pytest" ,python-pytest) + ("python-pytest-cov" ,python-pytest-cov) + ("python-pytest-xdist" ,python-pytest-xdist) + ("python-tox" ,python-tox))) + (home-page "https://github.com/neithere/argh/") + (synopsis "Argparse wrapper with natural syntax") + (description + "python-argh is a small library that provides several layers of +abstraction on top of @code{python-argparse}. The layers can be mixed. It is +always possible to declare a command with the highest possible (and least +flexible) layer and then tune the behaviour with any of the lower layers +including the native API of @code{python-argparse}.") + (license license:lgpl3+)))) -- cgit v1.2.3 From 792c3db553a02714f32fdfad639c6e168b30033b Mon Sep 17 00:00:00 2001 From: Brett Gilio Date: Mon, 16 Dec 2019 14:04:59 -0600 Subject: Revert "gnu: ccls: Adjust indentation" This reverts commit 3c80b07a0b4a2f1c2702acd6896f94892c516709. --- gnu/packages/cpp.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/cpp.scm b/gnu/packages/cpp.scm index f30da0e043..7870184a52 100644 --- a/gnu/packages/cpp.scm +++ b/gnu/packages/cpp.scm @@ -313,7 +313,7 @@ tools (containers, algorithms) used by other QuantStack packages.") (list (string-append "-DCMAKE_CXX_FLAGS='-isystem " (assoc-ref %build-inputs "gcc") "/include/c++'")))) - (inputs + (inputs `(("clang" ,clang) ("ncurses" ,ncurses))) (native-inputs -- cgit v1.2.3 From 1171c4b3c03399061b786c24a239ff69cb00eeea Mon Sep 17 00:00:00 2001 From: Brett Gilio Date: Mon, 16 Dec 2019 14:05:17 -0600 Subject: Revert "gnu: ccls: Configure using -isystem for header files." This reverts commit 2c82d4ad10de8e0ba462d81401385c5e7499f6e2. --- gnu/packages/cpp.scm | 18 +++++------------- 1 file changed, 5 insertions(+), 13 deletions(-) diff --git a/gnu/packages/cpp.scm b/gnu/packages/cpp.scm index 7870184a52..335f9a65cd 100644 --- a/gnu/packages/cpp.scm +++ b/gnu/packages/cpp.scm @@ -6,7 +6,6 @@ ;;; Copyright © 2019 Mathieu Othacehe ;;; Copyright © 2019 Pierre Neidhardt ;;; Copyright © 2019 Jan Wielkiewicz -;;; Copyright © 2019 Brett Gilio ;;; ;;; This file is part of GNU Guix. ;;; @@ -36,9 +35,7 @@ #:use-module (gnu packages check) #:use-module (gnu packages code) #:use-module (gnu packages compression) - #:use-module (gnu packages gcc) #:use-module (gnu packages llvm) - #:use-module (gnu packages ncurses) #:use-module (gnu packages perl) #:use-module (gnu packages pkg-config) #:use-module (gnu packages tls) @@ -308,17 +305,12 @@ tools (containers, algorithms) used by other QuantStack packages.") (file-name (git-file-name name version)))) (build-system cmake-build-system) (arguments - `(#:tests? #f ; no check target. - #:configure-flags - (list (string-append "-DCMAKE_CXX_FLAGS='-isystem " - (assoc-ref %build-inputs "gcc") - "/include/c++'")))) - (inputs - `(("clang" ,clang) - ("ncurses" ,ncurses))) + '(#:tests? #f)) ; no check target. + (inputs + `(("rapidjson" ,rapidjson))) (native-inputs - `(("rapidjson" ,rapidjson) - ("gcc" ,gcc))) + `(("clang" ,clang) + ("llvm" ,llvm))) (home-page "https://github.com/MaskRay/ccls") (synopsis "C/C++/Objective-C language server") (description -- cgit v1.2.3 From 27d083433a0426c2bde54684e72ed5de14c18175 Mon Sep 17 00:00:00 2001 From: Christopher Baines Date: Mon, 16 Dec 2019 21:00:46 +0000 Subject: gnu: guix-data-service: Update to 0.0.1-8.a019a5e. * gnu/packages/web.scm (guix-data-service): Update to 0.0.1-8.a019a5e. --- gnu/packages/web.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm index 0536f3089d..19017fb9ea 100644 --- a/gnu/packages/web.scm +++ b/gnu/packages/web.scm @@ -4194,8 +4194,8 @@ CDF, Atom 0.3, and Atom 1.0 feeds.") (package-with-python2 python-feedparser)) (define-public guix-data-service - (let ((commit "156b7eea7e7d538e332d8cfcf482c5ebec0a25c0") - (revision "7")) + (let ((commit "a019a5ed821cf1b7b2c2b0e1bd2dc25a51bbcb84") + (revision "8")) (package (name "guix-data-service") (version (string-append "0.0.1-" revision "." (string-take commit 7))) @@ -4207,7 +4207,7 @@ CDF, Atom 0.3, and Atom 1.0 feeds.") (file-name (git-file-name name version)) (sha256 (base32 - "1cg7jzk7pabfp3mgnkpycasv7fs522xp3nqdvna1y76aif3pd3zh")))) + "1kckfdgh8v9mmxxrsz6n2ibs78jr821qpbqh4mz8fyavm28c7h3f")))) (build-system gnu-build-system) (arguments '(#:modules ((guix build utils) -- cgit v1.2.3 From 4ade2dd9d2c64912d6a57c05c799fa512c82dd5d Mon Sep 17 00:00:00 2001 From: Mădălin Ionel Patrașcu Date: Mon, 16 Dec 2019 16:25:18 +0100 Subject: gnu: python-pyfaidx: Update to 0.5.7. * gnu/packages/bioinformatics.scm (python-pyfaidx): Update to 0.5.7. --- 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 8a007dca4d..eb2d6f1be3 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -13433,14 +13433,14 @@ bgzipped text file that contains a pair of genomic coordinates per line.") (define-public python-pyfaidx (package (name "python-pyfaidx") - (version "0.5.4.2") + (version "0.5.7") (source (origin (method url-fetch) (uri (pypi-uri "pyfaidx" version)) (sha256 (base32 - "0y5zyjksj1rdglj601xd2bbni5abhdh622y3ck76chyzxz9z4rx8")))) + "02jvdx3ksy6w5gd29i1d0g0zsabbz7c14qg482ff7pza6sdl0b2i")))) (build-system python-build-system) (propagated-inputs `(("python-six" ,python-six))) -- cgit v1.2.3 From c70a019137a74a0013013e82594a9954b4f8a523 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 16 Dec 2019 23:00:43 +0100 Subject: gnu: Add python-fsspec. * gnu/packages/python-xyz.scm (python-fsspec): New variable. --- gnu/packages/python-xyz.scm | 22 ++++++++++++++++++++++ 1 file changed, 22 insertions(+) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index e1c5c60f10..4a5f1a1289 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -15890,6 +15890,28 @@ append on old values. Partd excels at shuffling operations.") (define-public python2-partd (package-with-python2 python-partd)) +(define-public python-fsspec + (package + (name "python-fsspec") + (version "0.6.1") + (source + (origin + (method url-fetch) + (uri (pypi-uri "fsspec" version)) + (sha256 + (base32 + "1g9ba8v04s1nrh7pvzfm2md7ivl2mrz3hcq3y9d1a44gd62h17zj")))) + (build-system python-build-system) + (arguments '(#:tests? #f)) ; there are none + (home-page "https://github.com/intake/filesystem_spec") + (synopsis "File-system specification") + (description "The purpose of this package is to produce a template or +specification for a file-system interface, that specific implementations +should follow, so that applications making use of them can rely on a common +behavior and not have to worry about the specific internal implementation +decisions with any given backend.") + (license license:bsd-3))) + (define-public python-dask (package (name "python-dask") -- cgit v1.2.3 From 86c7ca07aaf7c2af642089e00bcd9d0e7d64304d Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 16 Dec 2019 23:11:41 +0100 Subject: gnu: python-dask: Update to 2.9.0. * gnu/packages/python-xyz.scm (python-dask): Update to 2.9.0. [arguments]: Adjust phase to disable broken tests. [propagated-inputs]: Add python-fsspec and python-packaging. --- gnu/packages/python-xyz.scm | 24 ++++++++++++------------ 1 file changed, 12 insertions(+), 12 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 4a5f1a1289..aa75837e5f 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -15915,38 +15915,38 @@ decisions with any given backend.") (define-public python-dask (package (name "python-dask") - (version "1.2.2") + (version "2.9.0") (source (origin (method url-fetch) (uri (pypi-uri "dask" version)) (sha256 - (base32 "0b29gvf96gmp20wicly3v3mhyc93zbm3mdv935fka6x0wax7cy2y")))) + (base32 "1w1hqr8vyx6ygwflj2737dcy0mmgvrc0s602gnny8pzlcbs9m76b")))) (build-system python-build-system) - ;; A single test out of 5000+ fails. This test is marked as xfail when - ;; pytest-xdist is used. (arguments `(#:phases (modify-phases %standard-phases - (add-after 'unpack 'disable-broken-test + (add-after 'unpack 'disable-broken-tests (lambda _ + ;; This test is marked as xfail when pytest-xdist is used. (substitute* "dask/tests/test_threaded.py" (("def test_interrupt\\(\\)" m) (string-append "@pytest.mark.skip(reason=\"Disabled by Guix\")\n" m))) - (when (which "python2") - ;; This test fails with recent Pandas: - ;; . - (substitute* "dask/dataframe/tests/test_dataframe.py" - (("def test_info\\(\\)" m) - (string-append "@pytest.mark.skip(reason=\"Disabled by Guix\")\n" - m)))) + ;; This one fails with a type error: + ;; TypeError: Already tz-aware, use tz_convert to convert. + (substitute* "dask/dataframe/tests/test_shuffle.py" + (("def test_set_index_timestamp\\(\\)" m) + (string-append "@pytest.mark.skip(reason=\"Disabled by Guix\")\n" + m))) #t)) (replace 'check (lambda _ (invoke "pytest" "-vv")))))) (propagated-inputs `(("python-cloudpickle" ,python-cloudpickle) + ("python-fsspec" ,python-fsspec) ("python-numpy" ,python-numpy) + ("python-packaging" ,python-packaging) ("python-pandas" ,python-pandas) ("python-partd" ,python-partd) ("python-toolz" ,python-toolz) -- cgit v1.2.3 From b7716f1b39b596f74fe0f41009ef506d242c5ece Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 16 Dec 2019 23:12:25 +0100 Subject: gnu: Remove python2-dask. This package can no longer be built with Python 2. * gnu/packages/python-xyz.scm (python2-dask): Remove variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index aa75837e5f..f0490f248c 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -15965,9 +15965,6 @@ larger-than-memory or distributed environments. These parallel collections run on top of the dynamic task schedulers. ") (license license:bsd-3))) -(define-public python2-dask - (package-with-python2 python-dask)) - (define-public python-ilinkedlist (package (name "python-ilinkedlist") -- cgit v1.2.3 From cfd83f3282ed1c416e0e99bdfc334d9be0d1856b Mon Sep 17 00:00:00 2001 From: Mădălin Ionel Patrașcu Date: Mon, 16 Dec 2019 16:25:19 +0100 Subject: gnu: Add python-gffutils. * gnu/packages/bioinformatics.scm (python-gffutils): New variable. Co-authored-by: Ricardo Wurmus --- gnu/packages/bioinformatics.scm | 51 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 51 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index eb2d6f1be3..7bbdcae149 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -15384,3 +15384,54 @@ methylation metrics from them. MethylDackel requires an indexed fasta file containing the reference genome as well.") ;; See https://github.com/dpryan79/MethylDackel/issues/85 (license license:expat))) + +(define-public python-gffutils + ;; The latest release is older more than a year than the latest commit + (let ((commit "4034c54600813b1402945e12faa91b3a53162cf1") + (revision "1")) + (package + (name "python-gffutils") + (version (git-version "0.9" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/daler/gffutils.git") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1rwafjdnbir5wnk0ap06ww4lra3p5frhy7mfs03rlldgfnwxymsn")))) + (build-system python-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (replace 'check + (lambda _ + ;; Tests need to access the HOME directory + (setenv "HOME" "/tmp") + (invoke "nosetests" "-a" "!slow"))) + (add-after 'unpack 'make-gz-files-writable + (lambda _ + (for-each make-file-writable + (find-files "." "\\.gz")) + #t))))) + (propagated-inputs + `(("python-argcomplete" ,python-argcomplete) + ("python-argh" ,python-argh) + ("python-biopython" ,python-biopython) + ("python-pybedtools" ,python-pybedtools) + ("python-pyfaidx" ,python-pyfaidx) + ("python-simplejson" ,python-simplejson) + ("python-six" ,python-six))) + (native-inputs + `(("python-nose" , python-nose))) + (home-page "https://github.com/daler/gffutils") + (synopsis "Tool for manipulation of GFF and GTF files") + (description + "python-gffutils is a Python package for working with and manipulating the +GFF and GTF format files typically used for genomic annotations. The files are +loaded into a sqlite3 database, allowing much more complex manipulation of +hierarchical features (e.g., genes, transcripts, and exons) than is possible +with plain-text methods alone.") + (license license:expat)))) ;; MIT license -- cgit v1.2.3 From 94f9c0cdc402b87ec3e21b633d92496fa1e3f066 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 16 Dec 2019 23:31:53 +0100 Subject: gnu: python-gffutils: Update description. * gnu/packages/bioinformatics.scm (python-gffutils)[description]: Reflow paragraph and fix spelling of SQLite. --- gnu/packages/bioinformatics.scm | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 7bbdcae149..961344198f 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -15429,9 +15429,9 @@ containing the reference genome as well.") (home-page "https://github.com/daler/gffutils") (synopsis "Tool for manipulation of GFF and GTF files") (description - "python-gffutils is a Python package for working with and manipulating the -GFF and GTF format files typically used for genomic annotations. The files are -loaded into a sqlite3 database, allowing much more complex manipulation of -hierarchical features (e.g., genes, transcripts, and exons) than is possible -with plain-text methods alone.") - (license license:expat)))) ;; MIT license + "python-gffutils is a Python package for working with and manipulating +the GFF and GTF format files typically used for genomic annotations. The +files are loaded into a SQLite database, allowing much more complex +manipulation of hierarchical features (e.g., genes, transcripts, and exons) +than is possible with plain-text methods alone.") + (license license:expat)))) -- cgit v1.2.3 From b9676a4bbb201f32970818cc8cbbe2bcfc61e829 Mon Sep 17 00:00:00 2001 From: Vagrant Cascadian Date: Mon, 16 Dec 2019 21:50:55 +0000 Subject: gnu: libsecp256k1: Update to 20191213. * gnu/packages/crypto (libsecp256k1): Update to 20191213. --- gnu/packages/crypto.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/crypto.scm b/gnu/packages/crypto.scm index e63823de2c..db39166d45 100644 --- a/gnu/packages/crypto.scm +++ b/gnu/packages/crypto.scm @@ -884,10 +884,10 @@ trivial to build for local use. Portability is emphasized over performance.") (license license:unlicense))) (define-public libsecp256k1 - (let ((commit "e34ceb333b1c0e6f4115ecbb80c632ac1042fa49")) + (let ((commit "d644dda5c9dbdecee52d1aa259235510fdc2d4ee")) (package (name "libsecp256k1") - (version (git-version "20181126" "1" commit)) + (version (git-version "20191213" "1" commit)) (source (origin (method git-fetch) (uri (git-reference @@ -895,7 +895,7 @@ trivial to build for local use. Portability is emphasized over performance.") (commit commit))) (sha256 (base32 - "0as78s179hcr3ysk3fw98k5wzabgnwri7vkkc17wg31lyz6ids6c")) + "0zmx32746khsm2cx0p3pdy3j2vkwmafvf7axiixijhgcg0xjv93i")) (file-name (git-file-name name version)))) (build-system gnu-build-system) (native-inputs -- cgit v1.2.3 From d08c3e51ab62575e722aec24fba42a0cb84198cc Mon Sep 17 00:00:00 2001 From: Vagrant Cascadian Date: Mon, 16 Dec 2019 21:20:53 +0000 Subject: gnu: electron-cash: Update to 4.0.12. * gnu/packages/finanace (electron-cash): Update to 4.0.12. [source] switch to git. [inputs] Add libsecp256k1. [arguments] Add phase patching to use libsecp256k1 from inputs. --- gnu/packages/finance.scm | 36 ++++++++++++++++++++++-------------- 1 file changed, 22 insertions(+), 14 deletions(-) diff --git a/gnu/packages/finance.scm b/gnu/packages/finance.scm index 5588fe00ea..637a4dc522 100644 --- a/gnu/packages/finance.scm +++ b/gnu/packages/finance.scm @@ -445,28 +445,36 @@ other machines/servers. Electrum does not download the Bitcoin blockchain.") (package (inherit electrum) (name "electron-cash") - (version "4.0.10") + (version "4.0.12") (source (origin - (method url-fetch) - (uri (string-append "https://electroncash.org/downloads/" - version - "/win-linux/Electron-Cash-" - version - ".tar.gz")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/Electron-Cash/Electron-Cash.git") + (commit version))) + (file-name (git-file-name name version)) (sha256 (base32 - "1rcywlma6hk52ymisx536jvkdwa73rhn1jxhsbs4wbvajl90w9s8")) - (modules '((guix build utils))) - (snippet - '(begin - ;; Delete the bundled dependencies. - (delete-file-recursively "packages") - #t)))) + "0gidrx8499v7rig7ljhd70wssshs1qm0gp1553g70i323hcbf62x")))) (inputs `(,@(package-inputs electrum) + ("libsecp256k1", libsecp256k1) ("python-dateutil", python-dateutil) ("python-dnspython", python-dnspython))) + (arguments + `(#:tests? #f ;; package doesn't have any tests + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'use-libsecp256k1-input + (lambda* (#:key inputs #:allow-other-keys) + (substitute* "lib/secp256k1.py" + (("library_paths = .* 'libsecp256k1.so.0'.") + (string-append "library_paths = ('" (assoc-ref inputs "libsecp256k1") "/lib/libsecp256k1.so.0'"))))) + (add-before 'build 'patch-home + (lambda* (#:key outputs #:allow-other-keys) + (substitute* "setup.py" + (("~/.local/share") + (string-append (assoc-ref outputs "out") "/local/share")))))))) (home-page "https://electroncash.org/") (synopsis "Bitcoin Cash wallet") (description -- cgit v1.2.3 From e5c32a3afa4b3b24fa8e93d8453b0977e492a27e Mon Sep 17 00:00:00 2001 From: Vagrant Cascadian Date: Mon, 16 Dec 2019 23:16:52 +0000 Subject: gnu: electron-cash: Use substitute-keyword-arguments from electrum. * gnu/packages/finance (electron-cash)[arguments]: Use substitute-keyword-arguments to re-use arguments from electrum. --- gnu/packages/finance.scm | 21 ++++++++------------- 1 file changed, 8 insertions(+), 13 deletions(-) diff --git a/gnu/packages/finance.scm b/gnu/packages/finance.scm index 637a4dc522..ce3033c054 100644 --- a/gnu/packages/finance.scm +++ b/gnu/packages/finance.scm @@ -462,19 +462,14 @@ other machines/servers. Electrum does not download the Bitcoin blockchain.") ("python-dateutil", python-dateutil) ("python-dnspython", python-dnspython))) (arguments - `(#:tests? #f ;; package doesn't have any tests - #:phases - (modify-phases %standard-phases - (add-after 'unpack 'use-libsecp256k1-input - (lambda* (#:key inputs #:allow-other-keys) - (substitute* "lib/secp256k1.py" - (("library_paths = .* 'libsecp256k1.so.0'.") - (string-append "library_paths = ('" (assoc-ref inputs "libsecp256k1") "/lib/libsecp256k1.so.0'"))))) - (add-before 'build 'patch-home - (lambda* (#:key outputs #:allow-other-keys) - (substitute* "setup.py" - (("~/.local/share") - (string-append (assoc-ref outputs "out") "/local/share")))))))) + (substitute-keyword-arguments (package-arguments electrum) + ((#:phases phases) + `(modify-phases ,phases + (add-after 'unpack 'use-libsecp256k1-input + (lambda* (#:key inputs #:allow-other-keys) + (substitute* "lib/secp256k1.py" + (("library_paths = .* 'libsecp256k1.so.0'.") + (string-append "library_paths = ('" (assoc-ref inputs "libsecp256k1") "/lib/libsecp256k1.so.0'"))))))))) (home-page "https://electroncash.org/") (synopsis "Bitcoin Cash wallet") (description -- cgit v1.2.3 From ca825070e49cd7239fa80762cf2e64bc8c45858c Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Tue, 17 Dec 2019 09:17:27 +0200 Subject: gnu: pinfo: Use a source file name. * gnu/packages/texinfo.scm (pinfo)[source]: Add 'file-name'. --- gnu/packages/texinfo.scm | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/gnu/packages/texinfo.scm b/gnu/packages/texinfo.scm index 1162e77b07..44800b3961 100644 --- a/gnu/packages/texinfo.scm +++ b/gnu/packages/texinfo.scm @@ -2,7 +2,7 @@ ;;; Copyright © 2012, 2013, 2015, 2016, 2017, 2019 Ludovic Courtès ;;; Copyright © 2014, 2016 Eric Bavier ;;; Copyright © 2015 Mark H Weaver -;;; Copyright © 2017 Efraim Flashner +;;; Copyright © 2017, 2019 Efraim Flashner ;;; Copyright © 2019 Ricardo Wurmus ;;; ;;; This file is part of GNU Guix. @@ -197,6 +197,7 @@ Texi2HTML.") (uri (git-reference (url "https://github.com/baszoetekouw/pinfo.git") (commit (string-append "v" version)))) + (file-name (git-file-name name version)) (sha256 (base32 "173d2p22irwiabvr4z6qvr6zpr6ysfkhmadjlyhyiwd7z62larvy")))) -- cgit v1.2.3 From d1df75543556be079cbcd658adb86d9bf281e10a Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Tue, 17 Dec 2019 09:30:40 +0200 Subject: gnu: brasero: Hard-code name in source uri. * gnu/packages/gnome.scm (brasero)[source]: Hard-code name. --- 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 1d4d7563a5..a98e2fe160 100644 --- a/gnu/packages/gnome.scm +++ b/gnu/packages/gnome.scm @@ -193,9 +193,9 @@ (version "3.12.2") (source (origin (method url-fetch) - (uri (string-append "mirror://gnome/sources/" name "/" + (uri (string-append "mirror://gnome/sources/brasero/" (version-major+minor version) "/" - name "-" version ".tar.xz")) + "brasero-" version ".tar.xz")) (sha256 (base32 "0h90y674j26rvjahb8cc0w79zx477rb6zaqcj26wzvq8kmpic8k8")))) -- cgit v1.2.3 From ba549e17facaa65dc68b6c6eddfb8d8a2bf0e4f4 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Tue, 17 Dec 2019 09:31:21 +0200 Subject: gnu: brasero: Fix-up inputs. * gnu/packages/gnome.scm (brasero)[inputs]: Move itstool ... [native-inputs]: ... to here. --- gnu/packages/gnome.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/gnome.scm b/gnu/packages/gnome.scm index a98e2fe160..beb847cfd7 100644 --- a/gnu/packages/gnome.scm +++ b/gnu/packages/gnome.scm @@ -219,6 +219,7 @@ `(("hicolor-icon-theme" ,hicolor-icon-theme))) (native-inputs `(("intltool" ,intltool) + ("itstool" ,itstool) ("glib" ,glib "bin") ; glib-compile-schemas, etc. ("gobject-introspection" ,gobject-introspection) ("pkg-config" ,pkg-config))) @@ -229,7 +230,6 @@ ("gstreamer" ,gstreamer) ("gst-plugins-base" ,gst-plugins-base) ("gtk+" ,gtk+) - ("itstool" ,itstool) ("libcanberra" ,libcanberra) ("libice" ,libice) ("libnotify" ,libnotify) -- cgit v1.2.3 From fb9399e93f30b4ec302941f651dce9d3ed1d1056 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Tue, 17 Dec 2019 09:31:47 +0200 Subject: gnu: brasero: Update home-page. * gnu/packages/gnome.scm (brasero)[home-page]: Use new home-page. --- gnu/packages/gnome.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/gnome.scm b/gnu/packages/gnome.scm index beb847cfd7..5371bcaa57 100644 --- a/gnu/packages/gnome.scm +++ b/gnu/packages/gnome.scm @@ -236,7 +236,7 @@ ("libsm" ,libsm) ("libxml2" ,libxml2) ("totem-pl-parser" ,totem-pl-parser))) - (home-page "https://projects.gnome.org/brasero/") + (home-page "https://wiki.gnome.org/Apps/Brasero") (synopsis "CD/DVD burning tool for Gnome") (description "Brasero is an application to burn CD/DVD for the Gnome Desktop. It is designed to be as simple as possible and has some unique -- cgit v1.2.3 From ef2c55bbcfc6660e5e6e4a3550c1968e88dd02ed Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Tue, 17 Dec 2019 09:36:31 +0200 Subject: gnu: libidl: Set upstream name. * gnu/packages/gnome.scm (libidl)[properties]: New field. --- gnu/packages/gnome.scm | 1 + 1 file changed, 1 insertion(+) diff --git a/gnu/packages/gnome.scm b/gnu/packages/gnome.scm index 5371bcaa57..ea4fe95658 100644 --- a/gnu/packages/gnome.scm +++ b/gnu/packages/gnome.scm @@ -1799,6 +1799,7 @@ Definition Language (idl) files, which is a specification for defining portable interfaces. libidl was initially written for orbit (the orb from the GNOME project, and the primary means of libidl distribution). However, the functionality was designed to be as reusable and portable as possible.") + (properties `((upstream-name . "libIDL"))) (license license:lgpl2.0+))) -- cgit v1.2.3 From 80a06e62063e9e10b1e1618f4a849580d2254b16 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Tue, 17 Dec 2019 09:37:11 +0200 Subject: gnu: libidl: Hard-code name in source uri. * gnu/packages/gnome.scm (libidl)[source]: Hard-code name. --- gnu/packages/gnome.scm | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/gnu/packages/gnome.scm b/gnu/packages/gnome.scm index ea4fe95658..c8cc119f3e 100644 --- a/gnu/packages/gnome.scm +++ b/gnu/packages/gnome.scm @@ -1779,10 +1779,9 @@ library.") (version "0.8.14") (source (origin (method url-fetch) - (uri (let ((upstream-name "libIDL")) - (string-append "mirror://gnome/sources/" upstream-name "/" - (version-major+minor version) "/" - upstream-name "-" version ".tar.bz2"))) + (uri (string-append "mirror://gnome/sources/libIDL/" + (version-major+minor version) "/" + "libIDL-" version ".tar.bz2")) (sha256 (base32 "08129my8s9fbrk0vqvnmx6ph4nid744g5vbwphzkaik51664vln5")))) -- cgit v1.2.3 From a315afa35b9772f995d0b5f87b7ca9d4726cb1af Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Tue, 17 Dec 2019 09:49:41 +0200 Subject: gnu: dia: Fix-up inputs. * gnu/packages/gnome.scm (dia)[inputs]: Sort alphabetically. Move glib:bin ... [native-inputs]: ... to here. Sort alphabetically. --- gnu/packages/gnome.scm | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/gnu/packages/gnome.scm b/gnu/packages/gnome.scm index c8cc119f3e..a54c23d1be 100644 --- a/gnu/packages/gnome.scm +++ b/gnu/packages/gnome.scm @@ -340,20 +340,20 @@ either on a local, or remote machine via a number of methods.") "1b4bba0k8ph4cwgw8xjglss0p6n111bpd5app67lrq79mp0ad06l")))) (build-system gnu-build-system) (inputs - `(("glib" ,glib "bin") - ("pango" ,pango) + `(("freetype" ,freetype) ("gdk-pixbuf" ,gdk-pixbuf) ("gtk+" ,gtk+-2) + ("libart-lgpl" ,libart-lgpl) ("libxml2" ,libxml2) - ("freetype" ,freetype) - ("libart-lgpl" ,libart-lgpl))) + ("pango" ,pango))) (native-inputs - `(("intltool" ,intltool) - ("pkg-config" ,pkg-config) + `(("autoconf" ,autoconf) ("automake" ,automake) - ("autoconf" ,autoconf) + ("intltool" ,intltool) + ("glib" ,glib "bin") ("libtool" ,libtool) ("perl" ,perl) + ("pkg-config" ,pkg-config) ("python-wrapper" ,python-wrapper))) (arguments `(#:phases -- cgit v1.2.3 From 4b3e91de2dbcd61575d888b97896cb5a64724410 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Tue, 17 Dec 2019 09:51:45 +0200 Subject: gnu: dia: Don't override bootstrap phase. * gnu/packages/gnome.scm (dia)[arguments]: Remove custom 'run-autogen phgase. Add phase before 'bootstrap to not run configure. --- gnu/packages/gnome.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/gnu/packages/gnome.scm b/gnu/packages/gnome.scm index a54c23d1be..9bc37f7a81 100644 --- a/gnu/packages/gnome.scm +++ b/gnu/packages/gnome.scm @@ -358,9 +358,10 @@ either on a local, or remote machine via a number of methods.") (arguments `(#:phases (modify-phases %standard-phases - (add-after 'unpack 'run-autogen + (add-before 'bootstrap 'dont-configure-during-bootstrap (lambda _ - (system* "sh" "autogen.sh")))))) + (setenv "NOCONFIGURE" "true") + #t))))) (home-page "https://wiki.gnome.org/Apps/Dia") (synopsis "Diagram creation for GNOME") (description "Dia can be used to draw different types of diagrams, and -- cgit v1.2.3 From 914c8cdf07944123312cef30020b991d0726c432 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Tue, 17 Dec 2019 09:57:21 +0200 Subject: gnu: dia: Fix version number. This commit is actually after to 0.97.3 release. * gnu/packages/gnome.scm (dia)[version]: Use git-version. [source]: Update to new source uri. Use git-file-name. --- gnu/packages/gnome.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/gnome.scm b/gnu/packages/gnome.scm index 9bc37f7a81..82c86b65cc 100644 --- a/gnu/packages/gnome.scm +++ b/gnu/packages/gnome.scm @@ -328,13 +328,13 @@ either on a local, or remote machine via a number of methods.") (let ((commit "fbc306168edab63db80b904956117cbbdc514ee4")) (package (name "dia") - (version (string-append "0.97.2-" (string-take commit 7))) + (version (git-version "0.97.3" "1" commit)) (source (origin (method git-fetch) (uri (git-reference - (url "https://git.gnome.org/browse/dia") + (url "https://gitlab.gnome.org/GNOME/dia.git/") (commit commit))) - (file-name (string-append name "-" version "-checkout")) + (file-name (git-file-name name version)) (sha256 (base32 "1b4bba0k8ph4cwgw8xjglss0p6n111bpd5app67lrq79mp0ad06l")))) -- cgit v1.2.3 From 5a0beca3aac7d22325229c8c044d23f9b038c20b Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Tue, 17 Dec 2019 10:23:02 +0200 Subject: gnu: shotwell: Clean-up inputs. * gnu/packages/gnome.scm (shotwell)[arguments]: Add phase to skip gtk-update-icon-cache. [inputs]: Sort alphabetically. Move glib:bin ... [native-inputs]: ... to here. Remove desktop-file-utils, gtk+:bin. --- gnu/packages/gnome.scm | 32 +++++++++++++++++++------------- 1 file changed, 19 insertions(+), 13 deletions(-) diff --git a/gnu/packages/gnome.scm b/gnu/packages/gnome.scm index 82c86b65cc..0a9087eaff 100644 --- a/gnu/packages/gnome.scm +++ b/gnu/packages/gnome.scm @@ -5093,32 +5093,38 @@ metadata in photo and video files of various formats.") "1m9i8r4gyd2hzlxjjwfyck4kz7gdg2vz2k6l6d0ga9hdfq2l4p9l")))) (build-system meson-build-system) (arguments - '(#:glib-or-gtk? #t)) + '(#:glib-or-gtk? #t + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'skip-gtk-update-icon-cache + (lambda _ + (substitute* "build-aux/meson/postinstall.py" + (("gtk-update-icon-cache") (which "true")) + (("update-desktop-database") (which "true"))) + #t))))) (propagated-inputs `(("dconf" ,dconf))) (native-inputs - `(("desktop-file-utils" ,desktop-file-utils) ; for update-desktop-database - ("gettext" ,gettext-minimal) - ("gtk+" ,gtk+ "bin") ; gtk-update-icon-cache + `(("gettext" ,gettext-minimal) + ("glib:bin" ,glib "bin") ("itstool" ,itstool) ("pkg-config" ,pkg-config) ("vala" ,vala))) (inputs - `(("glib:bin" ,glib "bin") - ("gstreamer" ,gstreamer) + `(("gcr" ,gcr) + ("gexiv2" ,gexiv2) ("gst-plugins-base" ,gst-plugins-base) + ("gstreamer" ,gstreamer) + ("json-glib" ,json-glib) ("libgdata" ,libgdata) ("libgee" ,libgee) - ("gexiv2" ,gexiv2) + ("libgphoto2" ,libgphoto2) + ("libgudev" ,libgudev) ("libraw" ,libraw) - ("json-glib" ,json-glib) - ("webkitgtk" ,webkitgtk) - ("sqlite" ,sqlite) ("libsoup" ,libsoup) ("libxml2" ,libxml2) - ("libgudev" ,libgudev) - ("libgphoto2" ,libgphoto2) - ("gcr" ,gcr))) + ("sqlite" ,sqlite) + ("webkitgtk" ,webkitgtk))) (home-page "https://wiki.gnome.org/Apps/Shotwell") (synopsis "Photo manager for GNOME 3") (description -- cgit v1.2.3 From 5ba865a73fbb1a23b2b82b3015a4171b3d9fe3c4 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 17 Dec 2019 14:55:18 +0100 Subject: gnu: Add r-gee. * gnu/packages/cran.scm (r-gee): 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 06c793d3cb..2101cd51c6 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -7851,6 +7851,27 @@ analysis.") ;; Either version of the GPL. (license (list license:gpl2 license:gpl3)))) +(define-public r-gee + (package + (name "r-gee") + (version "4.13-20") + (source + (origin + (method url-fetch) + (uri (cran-uri "gee" version)) + (sha256 + (base32 + "167pzgnmj4cjc41ykps1mfwi6s7y32zxyycn5z17vn4v0pp4q0ak")))) + (properties `((upstream-name . "gee"))) + (build-system r-build-system) + (native-inputs + `(("gfortran" ,gfortran))) + (home-page "https://cran.r-project.org/web/packages/gee/") + (synopsis "Generalized estimation equation solver") + (description + "This package provides a solver for generalized estimation equations.") + (license license:gpl2))) + (define-public r-dvmisc (package (name "r-dvmisc") -- cgit v1.2.3 From 3b21f5814c14604d8e940415e27b8d4aa25baf93 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 17 Dec 2019 14:55:29 +0100 Subject: gnu: Add r-tab. * gnu/packages/cran.scm (r-tab): 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 2101cd51c6..68b9c50d2f 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -7872,6 +7872,37 @@ analysis.") "This package provides a solver for generalized estimation equations.") (license license:gpl2))) +(define-public r-tab + (package + (name "r-tab") + (version "4.1.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "tab" version)) + (sha256 + (base32 + "0ds8n6gncidb66in7hlqkcmil5yfsf7ihqvmls789hrm2iz9xlfm")))) + (properties `((upstream-name . "tab"))) + (build-system r-build-system) + (propagated-inputs + `(("r-dplyr" ,r-dplyr) + ("r-gee" ,r-gee) + ("r-knitr" ,r-knitr) + ("r-mass" ,r-mass) + ("r-survey" ,r-survey) + ("r-survival" ,r-survival) + ("r-xtable" ,r-xtable))) + (home-page "https://cran.r-project.org/web/packages/tab/") + (synopsis "Create summary tables for statistical reports") + (description + "This package contains functions for creating various types of summary +tables, e.g. comparing characteristics across levels of a categorical variable +and summarizing fitted generalized linear models, generalized estimating +equations, and Cox proportional hazards models. Functions are available to +handle data from simple random samples as well as complex surveys.") + (license license:gpl3+))) + (define-public r-dvmisc (package (name "r-dvmisc") -- cgit v1.2.3 From 8a51ddce25bc38db0d7fe0954975881ff826efc1 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 17 Dec 2019 14:55:42 +0100 Subject: gnu: r-bh: Update to 1.72.0-1. * gnu/packages/statistics.scm (r-bh): Update to 1.72.0-1. --- 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 188e03f979..9056d656fb 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -1260,13 +1260,13 @@ R/DBMS implementations.") (define-public r-bh (package (name "r-bh") - (version "1.69.0-1") + (version "1.72.0-1") (source (origin (method url-fetch) (uri (cran-uri "BH" version)) (sha256 (base32 - "18mckfwxxv8m8rzaz03mg2h6vhaj7y131h6yasfg0s73nxj47zd0")))) + "1cm3gawky0dlfj8awv356j3f5pfv732rz10wlfnix2s2xf5cdz4a")))) (build-system r-build-system) (home-page "https://github.com/eddelbuettel/bh") (synopsis "R package providing subset of Boost headers") -- cgit v1.2.3 From f98480a975996068d24830990a2dbdb62e357211 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 17 Dec 2019 14:55:50 +0100 Subject: gnu: r-seurat: Update to 3.1.2. * gnu/packages/bioinformatics.scm (r-seurat): Update to 3.1.2. --- 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 961344198f..3215a155f1 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9487,13 +9487,13 @@ and irregular enzymatic cleavages, mass measurement accuracy, etc.") (define-public r-seurat (package (name "r-seurat") - (version "3.1.1") + (version "3.1.2") (source (origin (method url-fetch) (uri (cran-uri "Seurat" version)) (sha256 (base32 - "084lr2fjdksshsmv1ww82bgn3a9mml7kswsidjrs89snabgvn360")))) + "0m1qi39snbmkkv1p07bzg1r7snc9x6a1y0dghvpk1nzgcfpmnsj4")))) (properties `((upstream-name . "Seurat"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From f87c6727899a181a904a624e8e9fff13c5ccd229 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 17 Dec 2019 14:55:54 +0100 Subject: gnu: r-ordinal: Update to 2019.12-10. * gnu/packages/cran.scm (r-ordinal): Update to 2019.12-10. --- 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 68b9c50d2f..7c7710efb0 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -3236,14 +3236,14 @@ with the package @code{optim}.") (define-public r-ordinal (package (name "r-ordinal") - (version "2019.4-25") + (version "2019.12-10") (source (origin (method url-fetch) (uri (cran-uri "ordinal" version)) (sha256 (base32 - "1pvrkly4x12w32n7w1qljdwzqnlkv7rfa7rx0nz5vbiw29xas4i8")))) + "09bpmjmbf4x82kgf6bm4bkncq2apdv9mk20zj4zgma2jx2vyfhbs")))) (build-system r-build-system) (propagated-inputs `(("r-mass" ,r-mass) -- cgit v1.2.3 From 4d6ccb000008435fbc815bd9ea49b8d66c8b305e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 17 Dec 2019 14:56:00 +0100 Subject: gnu: r-argparser: Update to 0.6. * gnu/packages/cran.scm (r-argparser): Update to 0.6. --- 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 7c7710efb0..b726944dad 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -3799,14 +3799,14 @@ rules, boxes, trees, and Unicode symbols with ASCII alternatives.") (define-public r-argparser (package (name "r-argparser") - (version "0.4") + (version "0.6") (source (origin (method url-fetch) (uri (cran-uri "argparser" version)) (sha256 (base32 - "0s1wxshx4jk69wfxhycx973q6y8cmqrfymyjklhq1i8xrj0kmmx9")))) + "1pxiz9jlhlnpzqn1lz349r07i7glw708w202x6dlnxp112fg7k4x")))) (build-system r-build-system) (home-page "https://bitbucket.org/djhshih/argparser") (synopsis "Command-line argument parser") -- cgit v1.2.3 From 6e963260ae1665d06bc7c9011ec6d69931ab1443 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 17 Dec 2019 14:56:05 +0100 Subject: gnu: r-ttr: Update to 0.23-6. * gnu/packages/cran.scm (r-ttr): Update to 0.23-6. --- 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 b726944dad..85b689fc9b 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -4278,14 +4278,14 @@ of these tests are also included.") (define-public r-ttr (package (name "r-ttr") - (version "0.23-5") + (version "0.23-6") (source (origin (method url-fetch) (uri (cran-uri "TTR" version)) (sha256 (base32 - "0fxipnyxaz55n4camrk9cs71x9w4dsmjrihysv8i1s6khf825rg6")))) + "0rg22ma3x07s9djlxscfw5jcq1gbir05cwhgvwfi53x1sf4hmhdg")))) (properties `((upstream-name . "TTR"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From f6e75823bd3f4438a1fbe14f4f1d35f8d58c4ce8 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 17 Dec 2019 14:56:17 +0100 Subject: gnu: r-dvmisc: Update to 1.1.4. * gnu/packages/cran.scm (r-dvmisc): Update to 1.1.4. [propagated-inputs]: Add r-tab; remove r-purrr. --- 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 85b689fc9b..2980641102 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -7906,13 +7906,13 @@ handle data from simple random samples as well as complex surveys.") (define-public r-dvmisc (package (name "r-dvmisc") - (version "1.1.3") + (version "1.1.4") (source (origin (method url-fetch) (uri (cran-uri "dvmisc" version)) (sha256 - (base32 "0x391pxg5mqgp5xxc8qwhwxky8ds7d9gr9iwmsb12c92kxfk00bv")))) + (base32 "01v6sixx0f3nrn6ymfifb3pvd2msfrwm21kmdv38laxq29vc4rsi")))) (build-system r-build-system) (propagated-inputs `(("r-cubature" ,r-cubature) @@ -7922,10 +7922,10 @@ handle data from simple random samples as well as complex surveys.") ("r-mass" ,r-mass) ("r-mvtnorm" ,r-mvtnorm) ("r-pracma" ,r-pracma) - ("r-purrr" ,r-purrr) ("r-rbenchmark" ,r-rbenchmark) ("r-rcpp" ,r-rcpp) - ("r-survey" ,r-survey))) + ("r-survey" ,r-survey) + ("r-tab" ,r-tab))) (home-page "https://cran.r-project.org/web/packages/dvmisc/") (synopsis "Faster computation of common statistics and miscellaneous functions") (description -- cgit v1.2.3 From cd0e2815d5730969cafdcea031e5ccd32547ede4 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 17 Dec 2019 14:57:51 +0100 Subject: gnu: r-ggeffects: Update to 0.14.0. * gnu/packages/cran.scm (r-ggeffects): Update to 0.14.0. [propagated-inputs]: Remove r-dplyr and r-rlang. --- gnu/packages/cran.scm | 8 +++----- 1 file changed, 3 insertions(+), 5 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 2980641102..88c1a4bf74 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -8512,22 +8512,20 @@ effects models and Bayesian models.") (define-public r-ggeffects (package (name "r-ggeffects") - (version "0.13.0") + (version "0.14.0") (source (origin (method url-fetch) (uri (cran-uri "ggeffects" version)) (sha256 (base32 - "0ryfbaav0k874kbwmhbiv7fan93dmkpaimm1iw5kryjhhs3917lb")))) + "1djz82xww86h8f33m2vm40lliicppgyhm6hyn3h6rzrqjrlrsmdw")))) (build-system r-build-system) (propagated-inputs - `(("r-dplyr" ,r-dplyr) - ("r-insight" ,r-insight) + `(("r-insight" ,r-insight) ("r-magrittr" ,r-magrittr) ("r-mass" ,r-mass) ("r-purrr" ,r-purrr) - ("r-rlang" ,r-rlang) ("r-sjlabelled" ,r-sjlabelled) ("r-sjmisc" ,r-sjmisc))) (home-page "https://github.com/strengejacke/ggeffects") -- cgit v1.2.3 From 5722022f888cfd1947d8835029f094e9b32a8d75 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 17 Dec 2019 14:58:07 +0100 Subject: gnu: r-repr: Update to 1.0.2. * gnu/packages/cran.scm (r-repr): Update to 1.0.2. --- 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 88c1a4bf74..2bf238f2a1 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -12482,14 +12482,14 @@ compatible with @code{rzmq} are also provided.") (define-public r-repr (package (name "r-repr") - (version "1.0.1") + (version "1.0.2") (source (origin (method url-fetch) (uri (cran-uri "repr" version)) (sha256 (base32 - "0jy43g34r38fqprcdys0p9pliahrj5l64a9bbkzy206qgz0j5ppc")))) + "0wn9fdddqjgn0bdfl75x89rcxahbgqs324bhg0pfq6va5q2mlbbw")))) (build-system r-build-system) (propagated-inputs `(("r-base64enc" ,r-base64enc) -- cgit v1.2.3 From aaa74ee57d51537e1c7a768978fec91fdc5b9d35 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 17 Dec 2019 14:58:12 +0100 Subject: gnu: r-pracma: Update to 2.2.9. * gnu/packages/cran.scm (r-pracma): Update to 2.2.9. --- 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 2bf238f2a1..795e5db4f1 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -16036,12 +16036,12 @@ to ODEs by numerical differencing.") (define-public r-pracma (package (name "r-pracma") - (version "2.2.5") + (version "2.2.9") (source (origin (method url-fetch) (uri (cran-uri "pracma" version)) (sha256 - (base32 "0isd3s0i4mzmva8lkh0j76hwjy1w50q7d1n9lhxsnnkgalx3xs1g")))) + (base32 "07mzhzz73wsjjw1q05l024gcd13hwnzsxf873q9dyhw6x3shzshc")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/pracma/") (synopsis "Practical numerical math functions") -- cgit v1.2.3 From 3e313792aad45e8351f128f950ca1c96b58ea417 Mon Sep 17 00:00:00 2001 From: Ludovic Courtès Date: Tue, 17 Dec 2019 15:25:15 +0100 Subject: gnu: python-elasticsearch: Update to 7.1.0. * gnu/packages/python-web.scm (python-elasticsearch): Update to 7.1.0. --- 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 1632d7ade5..179e64e0a1 100644 --- a/gnu/packages/python-web.scm +++ b/gnu/packages/python-web.scm @@ -2532,14 +2532,14 @@ CSS tidy. Also supports URL rewriting in CSS files.") (define-public python-elasticsearch (package (name "python-elasticsearch") - (version "6.1.1") + (version "7.1.0") (source (origin (method url-fetch) (uri (pypi-uri "elasticsearch" version)) (sha256 (base32 - "1kjxl45yvvgfb5fmamx0kfsfg9pzphiqrwbkns3s28r1w7ya74cd")))) + "0rnjvlhw4v3vg14l519qliy1s1zpmx3827q0xfviwvk42rr7hh01")))) (build-system python-build-system) (native-inputs `(("python-mock" ,python-mock) -- cgit v1.2.3 From a7c75b8dbfd812571ba803b089d081671085e4d3 Mon Sep 17 00:00:00 2001 From: Konrad Hinsen Date: Mon, 16 Dec 2019 12:18:52 +0100 Subject: gnu: gfortran: change to a hidden package MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/gcc.scm (gfortran-4.8, gfortran-4.9) (gfortran-5, gfortran-6, gfortran-7, gfortran-8) (gfortran-9): Wrap in 'hidden-package'. Signed-off-by: Ludovic Courtès --- gnu/packages/gcc.scm | 35 +++++++++++++++++++++-------------- 1 file changed, 21 insertions(+), 14 deletions(-) diff --git a/gnu/packages/gcc.scm b/gnu/packages/gcc.scm index bda6a2b48a..29b9d34569 100644 --- a/gnu/packages/gcc.scm +++ b/gnu/packages/gcc.scm @@ -649,32 +649,39 @@ as the 'native-search-paths' field." (files '("lib" "lib64"))))) (define-public gfortran-4.8 - (custom-gcc gcc-4.8 "gfortran" '("fortran") - %generic-search-paths)) + (hidden-package + (custom-gcc gcc-4.8 "gfortran" '("fortran") + %generic-search-paths))) (define-public gfortran-4.9 - (custom-gcc gcc-4.9 "gfortran" '("fortran") - %generic-search-paths)) + (hidden-package + (custom-gcc gcc-4.9 "gfortran" '("fortran") + %generic-search-paths))) (define-public gfortran-5 - (custom-gcc gcc-5 "gfortran" '("fortran") - %generic-search-paths)) + (hidden-package + (custom-gcc gcc-5 "gfortran" '("fortran") + %generic-search-paths))) (define-public gfortran-6 - (custom-gcc gcc-6 "gfortran" '("fortran") - %generic-search-paths)) + (hidden-package + (custom-gcc gcc-6 "gfortran" '("fortran") + %generic-search-paths))) (define-public gfortran-7 - (custom-gcc gcc-7 "gfortran" '("fortran") - %generic-search-paths)) + (hidden-package + (custom-gcc gcc-7 "gfortran" '("fortran") + %generic-search-paths))) (define-public gfortran-8 - (custom-gcc gcc-8 "gfortran" '("fortran") - %generic-search-paths)) + (hidden-package + (custom-gcc gcc-8 "gfortran" '("fortran") + %generic-search-paths))) (define-public gfortran-9 - (custom-gcc gcc-9 "gfortran" '("fortran") - %generic-search-paths)) + (hidden-package + (custom-gcc gcc-9 "gfortran" '("fortran") + %generic-search-paths))) (define-public gfortran ;; Note: Update this when GCC changes! We cannot use -- cgit v1.2.3 From 2963ae8e4adcc6be06a7b3052ea23fd220612dae Mon Sep 17 00:00:00 2001 From: Guillaume Le Vaillant Date: Mon, 16 Dec 2019 12:00:04 +0100 Subject: gnu: txr: Update to 229. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/lisp.scm (txr): Update to 229. Signed-off-by: Ludovic Courtès --- gnu/packages/lisp.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/lisp.scm b/gnu/packages/lisp.scm index d51b9a3662..e2732a478d 100644 --- a/gnu/packages/lisp.scm +++ b/gnu/packages/lisp.scm @@ -741,7 +741,7 @@ enough to play the original mainframe Zork all the way through.") (define-public txr (package (name "txr") - (version "224") + (version "229") (source (origin (method git-fetch) @@ -752,7 +752,7 @@ enough to play the original mainframe Zork all the way through.") (patches (search-patches "txr-shell.patch")) (sha256 (base32 - "1036k71f6mffy9rjwzmhr5nnp1n0wzb0rqvilpzvb8jc5yxv0810")))) + "070lqckhbcq3wn5ajyaa41hh0gypaa48wnxkk6mc5mxvmv76ml46")))) (build-system gnu-build-system) (arguments '(#:configure-flags '("cc=gcc") -- cgit v1.2.3 From 328dd9b7c2030dfb66013e12f055b5b449c94007 Mon Sep 17 00:00:00 2001 From: Jethro Cao Date: Wed, 11 Dec 2019 21:33:44 +0700 Subject: gnu: Add love-nuklear. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/game-development.scm (love-nuklear): New variable. Signed-off-by: Ludovic Courtès --- gnu/packages/game-development.scm | 32 ++++++++++++++++++++++++++++++++ 1 file changed, 32 insertions(+) diff --git a/gnu/packages/game-development.scm b/gnu/packages/game-development.scm index 833f00b77c..febe15fa57 100644 --- a/gnu/packages/game-development.scm +++ b/gnu/packages/game-development.scm @@ -16,6 +16,7 @@ ;;; Copyright © 2018 Marius Bakke ;;; Copyright © 2019 Pierre Neidhardt ;;; Copyright © 2019 Leo Prikler +;;; Copyright © 2019 Jethro Cao ;;; ;;; This file is part of GNU Guix. ;;; @@ -653,6 +654,37 @@ programming language.") (home-page "https://love2d.org/") (license license:zlib))) +(define-public love-nuklear + (let ((version "v2.6") + (commit "fef4e00a602efb16c57ae962850b6e7a01f7a29a")) + (package + (name "love-nuklear") + (version (git-version version "1" commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/keharriso/love-nuklear/") + (commit commit) + (recursive? #t))) + ;; NOTE: the HEAD of the Nuklear git-submodule is at commit + ;; "adc52d710fe3c87194b99f540c53e82eb75c2521" of Oct 1 2019 + (file-name (git-file-name name version)) + (sha256 + (base32 + "15qmy8mfwkxy2x9rmxs6f9cyvjvwwj6yf78bs863xmc56dmjzzbn")))) + (build-system cmake-build-system) + (arguments + `(#:build-type "Release" + #:tests? #f)) + (inputs + `(("luajit" ,luajit))) + (synopsis "Lightweight immediate mode GUI for LÖVE games") + (description "LÖVE is a Lua framework for making 2D games. Nuklear +is a minimal state immediate mode graphical user interface toolkit. This +package is the Nuklear bindings for LÖVE created by Kevin Harrison.") + (home-page "https://github.com/keharriso/love-nuklear/") + (license license:expat)))) + (define-public allegro-4 (package (name "allegro") -- cgit v1.2.3 From 595036d9f9242ffe7adf6a20a2833342ba35a041 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 17 Dec 2019 19:13:42 +0100 Subject: gnu: Add libsbml. * gnu/packages/bioinformatics.scm (libsbml): New variable. --- gnu/packages/bioinformatics.scm | 38 ++++++++++++++++++++++++++++++++++++++ 1 file changed, 38 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 3215a155f1..528b603476 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -15435,3 +15435,41 @@ files are loaded into a SQLite database, allowing much more complex manipulation of hierarchical features (e.g., genes, transcripts, and exons) than is possible with plain-text methods alone.") (license license:expat)))) + +(define-public libsbml + (package + (name "libsbml") + (version "5.18.0") + (source (origin + (method url-fetch) + (uri (string-append "mirror://sourceforge/sbml/libsbml/" + version "/stable/libSBML-" + version "-core-src.tar.gz")) + (sha256 + (base32 + "0slkagrk3nfi2qsksv6b1brj6zhx4bj4bkib2sdycvrcd10ql2lh")))) + (build-system cmake-build-system) + (arguments + `(#:test-target "test" + #:configure-flags + (list "-DWITH_CHECK=ON" + (string-append "-DLIBXML_LIBRARY=" + (assoc-ref %build-inputs "libxml2") + "/lib/libxml2.so") + (string-append "-DLIBXML_INCLUDE_DIR=" + (assoc-ref %build-inputs "libxml2") + "/include/libxml2")))) + (propagated-inputs + `(("libxml2" ,libxml2))) + (native-inputs + `(("check" ,check) + ("swig" ,swig))) + (home-page "http://sbml.org/Software/libSBML") + (synopsis "Process SBML files and data streams") + (description "LibSBML is a library to help you read, write, manipulate, +translate, and validate SBML files and data streams. The @dfn{Systems Biology +Markup Language} (SBML) is an interchange format for computer models of +biological processes. SBML is useful for models of metabolism, cell +signaling, and more. It continues to be evolved and expanded by an +international community.") + (license license:lgpl2.1+))) -- cgit v1.2.3 From 5828dd030b4cf3920573f7982420999aa5743100 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 17 Dec 2019 19:18:11 +0100 Subject: gnu: Add r-poibin. * gnu/packages/cran.scm (r-poibin): New variable. --- gnu/packages/cran.scm | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 795e5db4f1..24eade12ec 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -18810,3 +18810,26 @@ nearest neighbors (kNN) of a data matrix. The implementation is based on cover trees introduced by Alina Beygelzimer, Sham Kakade, and John Langford (2006) @url{doi:10.1145/1143844.1143857}.") (license license:agpl3+))) + +(define-public r-poibin + (package + (name "r-poibin") + (version "1.4") + (source + (origin + (method url-fetch) + (uri (cran-uri "poibin" version)) + (sha256 + (base32 + "1rllgmk7yanb5amysl33kmi11lx86q5kqblyb8qqb3ckj2w4jhm2")))) + (properties `((upstream-name . "poibin"))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/web/packages/poibin/") + (synopsis "Poisson binomial distribution") + (description + "This package provides an implementation of both the exact and +approximation methods for computing the @dfn{cumulative distribution +function} (CDF) of the Poisson binomial distribution. It also provides the +@dfn{probability mass function} (PMF), quantile function, and random number +generation for the Poisson binomial distribution.") + (license license:gpl2))) -- cgit v1.2.3 From c686e53afe184f086576901ee1d2f8a45a474606 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 17 Dec 2019 19:18:26 +0100 Subject: gnu: Add r-diagram. * gnu/packages/cran.scm (r-diagram): 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 24eade12ec..117362cd9f 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -18833,3 +18833,30 @@ function} (CDF) of the Poisson binomial distribution. It also provides the @dfn{probability mass function} (PMF), quantile function, and random number generation for the Poisson binomial distribution.") (license license:gpl2))) + +(define-public r-diagram + (package + (name "r-diagram") + (version "1.6.4") + (source + (origin + (method url-fetch) + (uri (cran-uri "diagram" version)) + (sha256 + (base32 + "0f6ffprn5k0ir1s7m9s7izc64aa17r3gnygagz5bihrlsvawaavw")))) + (properties `((upstream-name . "diagram"))) + (build-system r-build-system) + (propagated-inputs + `(("r-shape" ,r-shape))) + (home-page "https://cran.r-project.org/web/packages/diagram/") + (synopsis "Visualize simple graphs (networks) and plot flow diagrams") + (description + "This package provides tools to visualize simple graphs (networks) based +on a transition matrix, utilities to plot flow diagrams, visualizing webs, +electrical networks, etc. It also includes supporting material for the book +\"A practical guide to ecological modelling - using R as a simulation +platform\" by Karline Soetaert and Peter M.J. Herman (2009) and the book +\"Solving Differential Equations in R\" by Karline Soetaert, Jeff Cash and +Francesca Mazzia (2012).") + (license license:gpl2+))) -- cgit v1.2.3 From 96afb6c683175b0f0474cd7589ad6ca44dac4a5b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 17 Dec 2019 19:18:36 +0100 Subject: gnu: Add r-lim. * gnu/packages/cran.scm (r-lim): New variable. --- gnu/packages/cran.scm | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 117362cd9f..3a342bc903 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -18860,3 +18860,26 @@ platform\" by Karline Soetaert and Peter M.J. Herman (2009) and the book \"Solving Differential Equations in R\" by Karline Soetaert, Jeff Cash and Francesca Mazzia (2012).") (license license:gpl2+))) + +(define-public r-lim + (package + (name "r-lim") + (version "1.4.6") + (source + (origin + (method url-fetch) + (uri (cran-uri "LIM" version)) + (sha256 + (base32 + "03x1gnm06bw1wrzc01110bjzd2mvjdzbc2mbrazh22jrmb32w5d8")))) + (properties `((upstream-name . "LIM"))) + (build-system r-build-system) + (propagated-inputs + `(("r-diagram" ,r-diagram) + ("r-limsolve" ,r-limsolve))) + (home-page "https://cran.r-project.org/web/packages/LIM/") + (synopsis "Linear inverse model examples and solution methods") + (description + "This package provides functions that read and solve linear inverse +problems (food web problems, linear programming problems).") + (license license:gpl2+))) -- cgit v1.2.3 From 59d485e118fab91c36937704396d1045f2e0815a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 17 Dec 2019 19:18:46 +0100 Subject: gnu: Add r-shinycssloaders. * gnu/packages/cran.scm (r-shinycssloaders): 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 3a342bc903..c5e6b96f67 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -18883,3 +18883,30 @@ Francesca Mazzia (2012).") "This package provides functions that read and solve linear inverse problems (food web problems, linear programming problems).") (license license:gpl2+))) + +(define-public r-shinycssloaders + (package + (name "r-shinycssloaders") + (version "0.2.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "shinycssloaders" version)) + (sha256 + (base32 + "1bpzsm7m7c366sjl1qndp4m5dg2vlm68rjgdy9n1ija9xbp0r2g4")))) + (properties + `((upstream-name . "shinycssloaders"))) + (build-system r-build-system) + (propagated-inputs + `(("r-digest" ,r-digest) + ("r-glue" ,r-glue) + ("r-shiny" ,r-shiny))) + (home-page "https://github.com/andrewsali/shinycssloaders") + (synopsis "Add CSS loading animations to Shiny outputs") + (description + "This package provides tools to create a lightweight Shiny wrapper for +the css-loaders created by Luke Hass +@url{https://github.com/lukehaas/css-loaders}. Wrapping a Shiny output will +automatically show a loader when the output is (re)calculating.") + (license license:gpl3))) -- cgit v1.2.3 From 1028bf0a05ee2f44d41f56eecd5ae6f72f150e05 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 17 Dec 2019 19:18:54 +0100 Subject: gnu: Add r-rsvg. * gnu/packages/cran.scm (r-rsvg): 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 c5e6b96f67..1f15e29b06 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -18910,3 +18910,31 @@ the css-loaders created by Luke Hass @url{https://github.com/lukehaas/css-loaders}. Wrapping a Shiny output will automatically show a loader when the output is (re)calculating.") (license license:gpl3))) + +(define-public r-rsvg + (package + (name "r-rsvg") + (version "1.3") + (source + (origin + (method url-fetch) + (uri (cran-uri "rsvg" version)) + (sha256 + (base32 + "11mccgf6hfskg45wqc114sx3qy2r494y6axdf73z6xwhs1wpm97g")))) + (properties `((upstream-name . "rsvg"))) + (build-system r-build-system) + (inputs + `(("librsvg" ,librsvg) + ("zlib" ,zlib))) + (native-inputs + `(("pkg-config" ,pkg-config))) + (home-page "https://github.com/jeroen/rsvg#readme") + (synopsis "Render SVG images into PDF, PNG, PostScript, or Bitmap arrays") + (description + "This package allows you to render vector-based SVG images into +high-quality custom-size bitmap arrays using the librsvg2 library. The +resulting bitmap can be written to e.g. PNG, JPEG or WEBP format. In +addition, the package can convert images directly to various formats such as +PDF or PostScript.") + (license license:expat))) -- cgit v1.2.3 From d11d6feafaff1a91bf9e24221432356c6828e93a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 17 Dec 2019 19:46:18 +0100 Subject: gnu: Add r-bgmix. * gnu/packages/bioconductor.scm (r-bgmix): New variable. --- gnu/packages/bioconductor.scm | 22 ++++++++++++++++++++++ 1 file changed, 22 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index cb748df6c2..9e3aaf7fe2 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6553,3 +6553,25 @@ uses a statistical data fusion approach, rationalizes contributing evidence and highlights associated genes, improving systems-level understanding of cellular organization in health and disease.") (license license:gpl3))) + +(define-public r-bgmix + (package + (name "r-bgmix") + (version "1.46.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "BGmix" version)) + (sha256 + (base32 + "1bwqqhkh4m3hhpd71grwjrg7n07lzvys4y7aghmw2gw5ibnk5683")))) + (properties `((upstream-name . "BGmix"))) + (build-system r-build-system) + (propagated-inputs + `(("r-kernsmooth" ,r-kernsmooth))) + (home-page "https://bioconductor.org/packages/BGmix/") + (synopsis "Bayesian models for differential gene expression") + (description + "This package provides fully Bayesian mixture models for differential +gene expression.") + (license license:gpl2))) -- cgit v1.2.3 From 75eb1149f3feb7b786455c09866611d54ccd4fc4 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 17 Dec 2019 19:46:30 +0100 Subject: gnu: Add r-bgx. * gnu/packages/bioconductor.scm (r-bgx): New variable. --- gnu/packages/bioconductor.scm | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 9e3aaf7fe2..0f3342007f 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6575,3 +6575,28 @@ cellular organization in health and disease.") "This package provides fully Bayesian mixture models for differential gene expression.") (license license:gpl2))) + +(define-public r-bgx + (package + (name "r-bgx") + (version "1.52.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "bgx" version)) + (sha256 + (base32 + "0fiqqv6pin0zhxaw67hzfjccq2qkl9qfqjf10nx2zmpxm2licavm")))) + (properties `((upstream-name . "bgx"))) + (build-system r-build-system) + (propagated-inputs + `(("r-affy" ,r-affy) + ("r-biobase" ,r-biobase) + ("r-gcrma" ,r-gcrma) + ("r-rcpp" ,r-rcpp))) + (home-page "https://bioconductor.org/packages/bgx/") + (synopsis "Bayesian gene expression") + (description + "This package provides tools for Bayesian integrated analysis of +Affymetrix GeneChips.") + (license license:gpl2))) -- cgit v1.2.3 From 6bd50acf41ef0a44703e7f7cb0d6065696ade69d Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 17 Dec 2019 19:47:00 +0100 Subject: gnu: Add r-bhc. * gnu/packages/bioconductor.scm (r-bhc): 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 0f3342007f..f84b609f56 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6600,3 +6600,29 @@ gene expression.") "This package provides tools for Bayesian integrated analysis of Affymetrix GeneChips.") (license license:gpl2))) + +(define-public r-bhc + (package + (name "r-bhc") + (version "1.38.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "BHC" version)) + (sha256 + (base32 + "1bxx3jak8mgvay3j1xd59bb9j86pzl6hh5abxww9x1b7rswmy1jh")))) + (properties `((upstream-name . "BHC"))) + (build-system r-build-system) + (home-page "https://bioconductor.org/packages/BHC/") + (synopsis "Bayesian hierarchical clustering") + (description + "The method implemented in this package performs bottom-up hierarchical +clustering, using a Dirichlet Process (infinite mixture) to model uncertainty +in the data and Bayesian model selection to decide at each step which clusters +to merge. This avoids several limitations of traditional methods, for example +how many clusters there should be and how to choose a principled distance +metric. This implementation accepts multinomial (i.e. discrete, with 2+ +categories) or time-series data. This version also includes a randomised +algorithm which is more efficient for larger data sets.") + (license license:gpl3))) -- cgit v1.2.3 From de9374b73cc14245d41d4944c0632a804fe52efb Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 17 Dec 2019 19:47:11 +0100 Subject: gnu: Add r-bicare. * gnu/packages/bioconductor.scm (r-bicare): 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 f84b609f56..896d451bac 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6626,3 +6626,27 @@ metric. This implementation accepts multinomial (i.e. discrete, with 2+ categories) or time-series data. This version also includes a randomised algorithm which is more efficient for larger data sets.") (license license:gpl3))) + +(define-public r-bicare + (package + (name "r-bicare") + (version "1.44.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "BicARE" version)) + (sha256 + (base32 + "1gia5vzmvbk4k1vx3bh9nld1ws9s3c0y11qfbzqhfnfjbd7n8qcs")))) + (properties `((upstream-name . "BicARE"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biobase" ,r-biobase) + ("r-gseabase" ,r-gseabase) + ("r-multtest" ,r-multtest))) + (home-page "http://bioinfo.curie.fr") + (synopsis "Biclustering analysis and results exploration") + (description + "This is a package for biclustering analysis and exploration of +results.") + (license license:gpl2))) -- cgit v1.2.3 From 40fe63ad8a3578a2a7090ee18fcb3d35096ba8c8 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 17 Dec 2019 19:47:19 +0100 Subject: gnu: Add r-bifet. * gnu/packages/bioconductor.scm (r-bifet): 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 896d451bac..beb46c9ded 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6650,3 +6650,31 @@ algorithm which is more efficient for larger data sets.") "This is a package for biclustering analysis and exploration of results.") (license license:gpl2))) + +(define-public r-bifet + (package + (name "r-bifet") + (version "1.6.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "BiFET" version)) + (sha256 + (base32 + "0ck1d6hxd4f40hfz8p2z5xmjbz79yhrf6fisjka2xzk5v9fm4p4k")))) + (properties `((upstream-name . "BiFET"))) + (build-system r-build-system) + (propagated-inputs + `(("r-genomicranges" ,r-genomicranges) + ("r-poibin" ,r-poibin))) + (home-page "https://bioconductor.org/packages/BiFET") + (synopsis "Bias-free footprint enrichment test") + (description + "BiFET identifies @dfn{transcription factors} (TFs) whose footprints are +over-represented in target regions compared to background regions after +correcting for the bias arising from the imbalance in read counts and GC +contents between the target and background regions. For a given TF k, BiFET +tests the null hypothesis that the target regions have the same probability of +having footprints for the TF k as the background regions while correcting for +the read count and GC content bias.") + (license license:gpl3))) -- cgit v1.2.3 From e823337c6eb9ab99e0e3311d4c8024cb220afd08 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 17 Dec 2019 19:47:27 +0100 Subject: gnu: Add r-rsbml. * gnu/packages/bioconductor.scm (r-rsbml): 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 beb46c9ded..4e7bfc582a 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6678,3 +6678,31 @@ tests the null hypothesis that the target regions have the same probability of having footprints for the TF k as the background regions while correcting for the read count and GC content bias.") (license license:gpl3))) + +(define-public r-rsbml + (package + (name "r-rsbml") + (version "2.44.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "rsbml" version)) + (sha256 + (base32 + "1dbp0aaijxn3na26b68ws0v9qzvml61ifb9z4i8pz7q6h48n7lxa")))) + (properties `((upstream-name . "rsbml"))) + (build-system r-build-system) + (inputs + `(("libsbml" ,libsbml) + ("zlib" ,zlib))) + (propagated-inputs + `(("r-biocgenerics" ,r-biocgenerics) + ("r-graph" ,r-graph))) + (native-inputs + `(("pkg-config" ,pkg-config))) + (home-page "http://www.sbml.org") + (synopsis "R support for SBML") + (description + "This package provides an R interface to libsbml for SBML parsing, +validating output, provides an S4 SBML DOM, converts SBML to R graph objects.") + (license license:artistic2.0))) -- cgit v1.2.3 From 75a8bb31859b217e4864c96ecde0019b69c17280 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 17 Dec 2019 19:47:42 +0100 Subject: gnu: Add r-hypergraph. * gnu/packages/bioconductor.scm (r-hypergraph): New variable. --- gnu/packages/bioconductor.scm | 22 ++++++++++++++++++++++ 1 file changed, 22 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 4e7bfc582a..eeffafc51c 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6706,3 +6706,25 @@ the read count and GC content bias.") "This package provides an R interface to libsbml for SBML parsing, validating output, provides an S4 SBML DOM, converts SBML to R graph objects.") (license license:artistic2.0))) + +(define-public r-hypergraph + (package + (name "r-hypergraph") + (version "1.58.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "hypergraph" version)) + (sha256 + (base32 + "1bixmslxy7r987zw1vf4dg72hfi04lf4vj03n7ygym2g8nfhbh7m")))) + (properties `((upstream-name . "hypergraph"))) + (build-system r-build-system) + (propagated-inputs + `(("r-graph" ,r-graph))) + (home-page "https://bioconductor.org/packages/hypergraph") + (synopsis "Hypergraph data structures") + (description + "This package implements some simple capabilities for representing and +manipulating hypergraphs.") + (license license:artistic2.0))) -- cgit v1.2.3 From 5aef09bd0ed72f8fec820eb7080bd68c735a39be Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 17 Dec 2019 19:48:04 +0100 Subject: gnu: Add r-hyperdraw. * gnu/packages/bioconductor.scm (r-hyperdraw): New variable. --- gnu/packages/bioconductor.scm | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index eeffafc51c..f506bb4690 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -32,6 +32,7 @@ #:use-module (gnu packages compression) #:use-module (gnu packages gcc) #:use-module (gnu packages graph) + #:use-module (gnu packages graphviz) #:use-module (gnu packages haskell-xyz) #:use-module (gnu packages image) #:use-module (gnu packages maths) @@ -6728,3 +6729,27 @@ validating output, provides an S4 SBML DOM, converts SBML to R graph objects.") "This package implements some simple capabilities for representing and manipulating hypergraphs.") (license license:artistic2.0))) + +(define-public r-hyperdraw + (package + (name "r-hyperdraw") + (version "1.38.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "hyperdraw" version)) + (sha256 + (base32 + "0a8h3pb7196qi49ady8ni92m5wqb1hvxw6khk9j63mwj3h7jinbj")))) + (properties `((upstream-name . "hyperdraw"))) + (build-system r-build-system) + (inputs `(("graphviz" ,graphviz))) + (propagated-inputs + `(("r-graph" ,r-graph) + ("r-hypergraph" ,r-hypergraph) + ("r-rgraphviz" ,r-rgraphviz))) + (home-page "https://bioconductor.org/packages/hyperdraw") + (synopsis "Visualizing hypergraphs") + (description + "This package provides functions for visualizing hypergraphs.") + (license license:gpl2+))) -- cgit v1.2.3 From 6ca6f8663b1d7b5d0e6c8f33bd9420d1ade832db Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 17 Dec 2019 19:48:13 +0100 Subject: gnu: Add r-biggr. * gnu/packages/bioconductor.scm (r-biggr): New variable. --- gnu/packages/bioconductor.scm | 30 ++++++++++++++++++++++++++++++ 1 file changed, 30 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index f506bb4690..f388f16e23 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6753,3 +6753,33 @@ manipulating hypergraphs.") (description "This package provides functions for visualizing hypergraphs.") (license license:gpl2+))) + +(define-public r-biggr + (package + (name "r-biggr") + (version "1.22.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "BiGGR" version)) + (sha256 + (base32 + "1n2ypc84abmhn6br0yi87k7lvjc11k7abzhgvzdabc2ai1qgcqif")))) + (properties `((upstream-name . "BiGGR"))) + (build-system r-build-system) + (propagated-inputs + `(("r-hyperdraw" ,r-hyperdraw) + ("r-hypergraph" ,r-hypergraph) + ("r-lim" ,r-lim) + ("r-limsolve" ,r-limsolve) + ("r-rsbml" ,r-rsbml) + ("r-stringr" ,r-stringr))) + (home-page "https://bioconductor.org/packages/BiGGR/") + (synopsis "Constraint based modeling using metabolic reconstruction databases") + (description + "This package provides an interface to simulate metabolic reconstruction +from the @url{http://bigg.ucsd.edu/, BiGG database} and other metabolic +reconstruction databases. The package facilitates @dfn{flux balance +analysis} (FBA) and the sampling of feasible flux distributions. Metabolic +networks and estimated fluxes can be visualized with hypergraphs.") + (license license:gpl3+))) -- cgit v1.2.3 From 820373dbc82dfccf0edd779a4ab4b68672432a2d Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 17 Dec 2019 19:48:21 +0100 Subject: gnu: Add r-bigmemoryextras. * gnu/packages/bioconductor.scm (r-bigmemoryextras): 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 f388f16e23..0e817a1fb6 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6783,3 +6783,35 @@ reconstruction databases. The package facilitates @dfn{flux balance analysis} (FBA) and the sampling of feasible flux distributions. Metabolic networks and estimated fluxes can be visualized with hypergraphs.") (license license:gpl3+))) + +(define-public r-bigmemoryextras + (package + (name "r-bigmemoryextras") + (version "1.34.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "bigmemoryExtras" version)) + (sha256 + (base32 + "17dk7c44ikphcrpi8hnxyvlmj30qmj098kc0ihfi69bp9rw1cibq")))) + (properties + `((upstream-name . "bigmemoryExtras"))) + (build-system r-build-system) + (propagated-inputs + `(("r-bigmemory" ,r-bigmemory))) + (home-page "https://github.com/phaverty/bigmemoryExtras") + (synopsis "Extension of the bigmemory package") + (description + "This package defines a @code{BigMatrix} @code{ReferenceClass} which adds +safety and convenience features to the @code{filebacked.big.matrix} class from +the @code{bigmemory} package. @code{BigMatrix} protects against segfaults by +monitoring and gracefully restoring the connection to on-disk data and it also +protects against accidental data modification with a filesystem-based +permissions system. Utilities are provided for using @code{BigMatrix}-derived +classes as @code{assayData} matrices within the @code{Biobase} package's +@code{eSet} family of classes. @code{BigMatrix} provides some optimizations +related to attaching to, and indexing into, file-backed matrices with +dimnames. Additionally, the package provides a @code{BigMatrixFactor} class, +a file-backed matrix with factor properties.") + (license license:artistic2.0))) -- cgit v1.2.3 From d38775b13fa24dd9e2bc3e4e48a69a9e83cbdc6a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 17 Dec 2019 19:48:29 +0100 Subject: gnu: Add r-bigpint. * gnu/packages/bioconductor.scm (r-bigpint): New variable. --- gnu/packages/bioconductor.scm | 39 +++++++++++++++++++++++++++++++++++++++ 1 file changed, 39 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 0e817a1fb6..743a96754f 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6815,3 +6815,42 @@ related to attaching to, and indexing into, file-backed matrices with dimnames. Additionally, the package provides a @code{BigMatrixFactor} class, a file-backed matrix with factor properties.") (license license:artistic2.0))) + +(define-public r-bigpint + (package + (name "r-bigpint") + (version "1.2.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "bigPint" version)) + (sha256 + (base32 + "10vs0lzfyxp6sm4r9pxfwipjvzmmaqnvwn1hc5q37s5qz44fg0hk")))) + (properties `((upstream-name . "bigPint"))) + (build-system r-build-system) + (propagated-inputs + `(("r-dplyr" ,r-dplyr) + ("r-ggally" ,r-ggally) + ("r-ggplot2" ,r-ggplot2) + ("r-gridextra" ,r-gridextra) + ("r-hexbin" ,r-hexbin) + ("r-hmisc" ,r-hmisc) + ("r-htmlwidgets" ,r-htmlwidgets) + ("r-plotly" ,r-plotly) + ("r-plyr" ,r-plyr) + ("r-rcolorbrewer" ,r-rcolorbrewer) + ("r-reshape" ,r-reshape) + ("r-shiny" ,r-shiny) + ("r-shinycssloaders" ,r-shinycssloaders) + ("r-shinydashboard" ,r-shinydashboard) + ("r-stringr" ,r-stringr) + ("r-tidyr" ,r-tidyr))) + (home-page "https://github.com/lindsayrutter/bigPint") + (synopsis "Big multivariate data plotted interactively") + (description + "This package provides methods for visualizing large multivariate +datasets using static and interactive scatterplot matrices, parallel +coordinate plots, volcano plots, and litre plots. It includes examples for +visualizing RNA-sequencing datasets and differentially expressed genes.") + (license license:gpl3))) -- cgit v1.2.3 From 991554fc920b5cc09e6d005f7d649fde9f4de2c5 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 17 Dec 2019 19:48:38 +0100 Subject: gnu: Add r-chemminer. * gnu/packages/bioconductor.scm (r-chemminer): New variable. --- gnu/packages/bioconductor.scm | 39 +++++++++++++++++++++++++++++++++++++++ 1 file changed, 39 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 743a96754f..2423e74b3f 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6854,3 +6854,42 @@ datasets using static and interactive scatterplot matrices, parallel coordinate plots, volcano plots, and litre plots. It includes examples for visualizing RNA-sequencing datasets and differentially expressed genes.") (license license:gpl3))) + +(define-public r-chemminer + (package + (name "r-chemminer") + (version "3.38.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "ChemmineR" version)) + (sha256 + (base32 + "1j6vmkhc03dmmkm5wgbcv62pw5dclp49f906xkx1pwg27bdldbga")))) + (properties `((upstream-name . "ChemmineR"))) + (build-system r-build-system) + (propagated-inputs + `(("r-base64enc" ,r-base64enc) + ("r-bh" ,r-bh) + ("r-biocgenerics" ,r-biocgenerics) + ("r-dbi" ,r-dbi) + ("r-digest" ,r-digest) + ("r-dt" ,r-dt) + ("r-ggplot2" ,r-ggplot2) + ("r-gridextra" ,r-gridextra) + ("r-png" ,r-png) + ("r-rcpp" ,r-rcpp) + ("r-rcurl" ,r-rcurl) + ("r-rjson" ,r-rjson) + ("r-rsvg" ,r-rsvg))) + (home-page "https://github.com/girke-lab/ChemmineR") + (synopsis "Cheminformatics toolkit for R") + (description + "ChemmineR is a cheminformatics package for analyzing drug-like small +molecule data in R. It contains functions for efficient processing of large +numbers of molecules, physicochemical/structural property predictions, +structural similarity searching, classification and clustering of compound +libraries with a wide spectrum of algorithms. In addition, it offers +visualization functions for compound clustering results and chemical +structures.") + (license license:artistic2.0))) -- cgit v1.2.3 From 48bcbef07a773ad4f0b8a07caec2ba1eb6b8bab0 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 17 Dec 2019 19:48:50 +0100 Subject: gnu: Add r-bioassayr. * gnu/packages/bioconductor.scm (r-bioassayr): New variable. --- gnu/packages/bioconductor.scm | 33 +++++++++++++++++++++++++++++++++ 1 file changed, 33 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 2423e74b3f..0b3df4f59c 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6893,3 +6893,36 @@ libraries with a wide spectrum of algorithms. In addition, it offers visualization functions for compound clustering results and chemical structures.") (license license:artistic2.0))) + +(define-public r-bioassayr + (package + (name "r-bioassayr") + (version "1.24.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "bioassayR" version)) + (sha256 + (base32 + "08vxkvxhqnryfbj4dwk3ifb9pn544www9zk2pj9fjbh5xfpwi7zw")))) + (properties `((upstream-name . "bioassayR"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biocgenerics" ,r-biocgenerics) + ("r-chemminer" ,r-chemminer) + ("r-dbi" ,r-dbi) + ("r-matrix" ,r-matrix) + ("r-rjson" ,r-rjson) + ("r-rsqlite" ,r-rsqlite) + ("r-xml" ,r-xml))) + (home-page "https://github.com/TylerBackman/bioassayR") + (synopsis "Cross-target analysis of small molecule bioactivity") + (description + "bioassayR is a computational tool that enables simultaneous analysis of +thousands of bioassay experiments performed over a diverse set of compounds +and biological targets. Unique features include support for large-scale +cross-target analyses of both public and custom bioassays, generation of +@dfn{high throughput screening fingerprints} (HTSFPs), and an optional +preloaded database that provides access to a substantial portion of publicly +available bioactivity data.") + (license license:artistic2.0))) -- cgit v1.2.3 From 29fd736a66bd503c325f95625871d0ebcad6dd69 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 17 Dec 2019 19:48:58 +0100 Subject: gnu: Add r-biobroom. * gnu/packages/bioconductor.scm (r-biobroom): New variable. --- gnu/packages/bioconductor.scm | 30 ++++++++++++++++++++++++++++++ 1 file changed, 30 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 0b3df4f59c..577a43c87c 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6926,3 +6926,33 @@ cross-target analyses of both public and custom bioassays, generation of preloaded database that provides access to a substantial portion of publicly available bioactivity data.") (license license:artistic2.0))) + +(define-public r-biobroom + (package + (name "r-biobroom") + (version "1.18.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "biobroom" version)) + (sha256 + (base32 + "1480ycdsh9xdhbpr47vdw5g6m8arqsnp8hc19wwhzm8npxh4qqlb")))) + (properties `((upstream-name . "biobroom"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biobase" ,r-biobase) + ("r-broom" ,r-broom) + ("r-dplyr" ,r-dplyr) + ("r-tidyr" ,r-tidyr))) + (home-page "https://github.com/StoreyLab/biobroom") + (synopsis "Turn Bioconductor objects into tidy data frames") + (description + "This package contains methods for converting standard objects +constructed by bioinformatics packages, especially those in Bioconductor, and +converting them to @code{tidy} data. It thus serves as a complement to the +@code{broom} package, and follows the same tidy, augment, glance division of +tidying methods. Tidying data makes it easy to recombine, reshape and +visualize bioinformatics analyses.") + ;; Any version of the LGPL. + (license license:lgpl3+))) -- cgit v1.2.3 From 0bb64e1796b7ae99de8026b7928d8d85ae96602b Mon Sep 17 00:00:00 2001 From: Mark H Weaver Date: Tue, 17 Dec 2019 17:22:36 -0500 Subject: gnu: linux-libre@4.14: Update to 4.14.159. * gnu/packages/linux.scm (linux-libre-4.14-version): Update to 4.14.159. (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 55a5ceb93c..dae0df715f 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -372,10 +372,10 @@ 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 "4.14.158") +(define-public linux-libre-4.14-version "4.14.159") (define-public linux-libre-4.14-pristine-source (let ((version linux-libre-4.14-version) - (hash (base32 "1cqvr8pgqx005a9qyphqykakzwc54adq8mmdc9sgrxkkw9rfqj8d"))) + (hash (base32 "1wi6m3w40z0v9krb12g9q09s9y471r51rhcv3qa81lc53cx2vm78"))) (make-linux-libre-source version (%upstream-linux-source version hash) deblob-scripts-4.14))) -- cgit v1.2.3 From a15adacb5214040efe619065bbe7688a34d829d2 Mon Sep 17 00:00:00 2001 From: Mark H Weaver Date: Tue, 17 Dec 2019 17:23:42 -0500 Subject: gnu: linux-libre@4.19: Update to 4.19.90. * gnu/packages/linux.scm (linux-libre-4.19-version): Update to 4.19.90. (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 dae0df715f..292af23673 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -364,10 +364,10 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." (%upstream-linux-source version hash) deblob-scripts-5.3))) -(define-public linux-libre-4.19-version "4.19.89") +(define-public linux-libre-4.19-version "4.19.90") (define-public linux-libre-4.19-pristine-source (let ((version linux-libre-4.19-version) - (hash (base32 "0ijx8ih91p4g95zpwz6ga3q2x9lf1948xf2v5mz4348byf5hdwv8"))) + (hash (base32 "1zgpbim9019aymvgh0fr5g2r9j2xspw14amlnk09w5mgdl56rn19"))) (make-linux-libre-source version (%upstream-linux-source version hash) deblob-scripts-4.19))) -- cgit v1.2.3 From ef6856ea7244912a79d7890d93bfc480588d09e5 Mon Sep 17 00:00:00 2001 From: Mark H Weaver Date: Tue, 17 Dec 2019 17:24:23 -0500 Subject: gnu: linux-libre: Update to 5.3.17. * gnu/packages/linux.scm (linux-libre-5.3-version): Update to 5.3.17. (linux-libre-5.3-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 292af23673..7f094be422 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -356,10 +356,10 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." "linux-" version ".tar.xz")) (sha256 hash))) -(define-public linux-libre-5.3-version "5.3.16") +(define-public linux-libre-5.3-version "5.3.17") (define-public linux-libre-5.3-pristine-source (let ((version linux-libre-5.3-version) - (hash (base32 "19asdv08rzp33f0zxa2swsfnbhy4zwg06agj7sdnfy4wfkrfwx49"))) + (hash (base32 "10igr1dm9pazmhpi3arsyywj4757531nal003dn9rhs2xc8pkx5c"))) (make-linux-libre-source version (%upstream-linux-source version hash) deblob-scripts-5.3))) -- cgit v1.2.3 From 356a79becc4061d158c68718ad169abac1ab672f Mon Sep 17 00:00:00 2001 From: Björn Höfling Date: Sun, 15 Dec 2019 22:00:56 +0100 Subject: swh: Fix API call for getting origin. When using the archival linter, git origins already in the archive where not recognized due to an API change and where repeatedly asked for archival. This is fixed here. * guix/swh.scm (lookup-origin): Fix API URI for getting origin. (): Fix comment with API URI example. --- guix/swh.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/guix/swh.scm b/guix/swh.scm index 7acad05928..372e4c84d1 100644 --- a/guix/swh.scm +++ b/guix/swh.scm @@ -244,7 +244,7 @@ FALSE-IF-404? is true, return #f upon 404 responses." docstring (call (swh-url components ...) json->value))))) -;; +;; (define-json-mapping make-origin origin? json->origin (id origin-id) @@ -365,7 +365,7 @@ FALSE-IF-404? is true, return #f upon 404 responses." (define-query (lookup-origin url) "Return an origin for URL." - (path "/api/1/origin/git/url" url) + (path "/api/1/origin" url "get") json->origin) (define-query (lookup-content hash type) -- cgit v1.2.3 From c57b8419f4b9ccd4ee27ed052346f192b9e28366 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Wed, 18 Dec 2019 09:53:48 +0200 Subject: gnu: python-ecdsa: Update to 0.14.1. * gnu/packages/python-crypto.scm (python-ecdsa): Update to 0.14.1. [inputs]: Move openssl ... [native-inputs]: ... to here. [propagated-inputs]: Add python-six. --- gnu/packages/python-crypto.scm | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/gnu/packages/python-crypto.scm b/gnu/packages/python-crypto.scm index af51ae04b6..65594a5aa6 100644 --- a/gnu/packages/python-crypto.scm +++ b/gnu/packages/python-crypto.scm @@ -232,15 +232,17 @@ Python interface around SSH networking concepts.") (define-public python-ecdsa (package (name "python-ecdsa") - (version "0.13.3") + (version "0.14.1") (source (origin (method url-fetch) (uri (pypi-uri "ecdsa" version)) (sha256 - (base32 "0k9xxklf865g6x43gkfarwb25ffrkmpvkzkh71rylqx7cjq80g0n")))) + (base32 "13nx5cbfxc0gnax5zwdmp9xc40qd1llk62mv85jyrvqkbw017ik4")))) (build-system python-build-system) - (inputs + (propagated-inputs + `(("python-six" ,python-six))) + (native-inputs `(("openssl" ,openssl))) (home-page "https://github.com/warner/python-ecdsa") (synopsis "ECDSA cryptographic signature library (pure python)") -- cgit v1.2.3 From 92fe25130c1521d3976e1053fc50be38b72ecc55 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Wed, 18 Dec 2019 09:54:47 +0200 Subject: gnu: python-ecdsa: Actually run the test suite. * gnu/packages/python-crypto.scm (python-ecdsa)[arguments]: Replace 'check phase. [native-inputs]: Add python-pytest. --- gnu/packages/python-crypto.scm | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/gnu/packages/python-crypto.scm b/gnu/packages/python-crypto.scm index 65594a5aa6..63d3be17c2 100644 --- a/gnu/packages/python-crypto.scm +++ b/gnu/packages/python-crypto.scm @@ -240,10 +240,16 @@ Python interface around SSH networking concepts.") (sha256 (base32 "13nx5cbfxc0gnax5zwdmp9xc40qd1llk62mv85jyrvqkbw017ik4")))) (build-system python-build-system) + (arguments + '(#:phases + (modify-phases %standard-phases + (replace 'check + (lambda _ (invoke "pytest")))))) (propagated-inputs `(("python-six" ,python-six))) (native-inputs - `(("openssl" ,openssl))) + `(("openssl" ,openssl) + ("python-pytest" ,python-pytest))) (home-page "https://github.com/warner/python-ecdsa") (synopsis "ECDSA cryptographic signature library (pure python)") (description -- cgit v1.2.3 From 8fd60494030c3e8e948bd2452253ce936fb445ba Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Wed, 18 Dec 2019 10:29:28 +0200 Subject: gnu: cmst: Update to 2019.01.13. * gnu/packages/connman.scm (cmst): Update to 2019.01.13. --- gnu/packages/connman.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/connman.scm b/gnu/packages/connman.scm index 1185561bc4..0098cb8dc7 100644 --- a/gnu/packages/connman.scm +++ b/gnu/packages/connman.scm @@ -137,7 +137,7 @@ sharing) to clients via USB, ethernet, WiFi, cellular and Bluetooth.") (define-public cmst (package (name "cmst") - (version "2017.09.19") + (version "2019.01.13") (source (origin (method url-fetch) @@ -145,7 +145,7 @@ sharing) to clients via USB, ethernet, WiFi, cellular and Bluetooth.") "https://github.com/andrew-bibb/cmst/releases/download/cmst-" version "/cmst-" version ".tar.xz")) (sha256 - (base32 "0dh4639n3l8a19svaagib41hdq5q7x70bnc28dmnwy4jflf38yrm")))) + (base32 "1cn6xz2rpkf5kx5d6p2x2lh85zppjacp59l6gj3n6x12p90al1vl")))) (inputs `(("qtbase" ,qtbase))) (native-inputs -- cgit v1.2.3 From 7e9d6f0f3f018a85c951ebae0669ace9f80fc053 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Wed, 18 Dec 2019 10:34:27 +0200 Subject: gnu: libmicrohttpd: Update to 0.9.69. * gnu/packages/gnunet.scm (libmicrohttpd): Update to 0.9.69. --- gnu/packages/gnunet.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/gnunet.scm b/gnu/packages/gnunet.scm index 9d53ca5b80..8a9597a68c 100644 --- a/gnu/packages/gnunet.scm +++ b/gnu/packages/gnunet.scm @@ -149,14 +149,14 @@ tool to extract metadata from a file and print the results.") (define-public libmicrohttpd (package (name "libmicrohttpd") - (version "0.9.68") + (version "0.9.69") (source (origin (method url-fetch) (uri (string-append "mirror://gnu/libmicrohttpd/libmicrohttpd-" version ".tar.gz")) (sha256 (base32 - "0q8bc4hrxn6llml7w2vam6n833x8injs39wgdkhwkawr50m6wwf5")))) + "0zp34zgcahym5kp2r83gfb5wnr8yf643a26k6zk96x3qica6p6zv")))) (build-system gnu-build-system) (inputs `(("curl" ,curl) -- cgit v1.2.3 From 6f15ea24158aac4c265bb0a93d199123dad9c02e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 18 Dec 2019 15:23:15 +0100 Subject: gnu: Add r-reactome-db. * gnu/packages/bioconductor.scm (r-reactome-db): New variable. --- gnu/packages/bioconductor.scm | 22 ++++++++++++++++++++++ 1 file changed, 22 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 577a43c87c..b9ee81a560 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -47,6 +47,28 @@ ;;; Annotations +(define-public r-reactome-db + (package + (name "r-reactome-db") + (version "1.70.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "reactome.db" version 'annotation)) + (sha256 + (base32 + "05wc4fp0faq6h3kq5rwafnips043as31yq11mrjngfxvf5i10srg")))) + (properties `((upstream-name . "reactome.db"))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotationdbi" ,r-annotationdbi))) + (home-page "https://bioconductor.org/packages/reactome.db/") + (synopsis "Annotation maps for reactome") + (description + "This package provides a set of annotation maps for the REACTOME +database, assembled using data from REACTOME.") + (license license:cc-by4.0))) + (define-public r-bsgenome-celegans-ucsc-ce6 (package (name "r-bsgenome-celegans-ucsc-ce6") -- cgit v1.2.3 From ff1146b9b1ade0692c82cf0135790d7796134a99 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 18 Dec 2019 15:23:27 +0100 Subject: gnu: Add r-curatedtcgadata. * gnu/packages/bioconductor.scm (r-curatedtcgadata): New variable. --- gnu/packages/bioconductor.scm | 33 +++++++++++++++++++++++++++++++++ 1 file changed, 33 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index b9ee81a560..2ca1679f8b 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -900,6 +900,39 @@ examples' of Affymetrix data, unlike the artificial examples included in the package @code{affy}.") (license license:gpl2+))) +(define-public r-curatedtcgadata + (package + (name "r-curatedtcgadata") + (version "1.8.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "curatedTCGAData" version 'experiment)) + (sha256 + (base32 + "02y6cgihmsl9b4a9mmcdjjgjp06lpz04biyvxd3n5lk5gnqd9r3y")))) + (properties + `((upstream-name . "curatedTCGAData"))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotationhub" ,r-annotationhub) + ("r-experimenthub" ,r-experimenthub) + ("r-hdf5array" ,r-hdf5array) + ("r-multiassayexperiment" ,r-multiassayexperiment) + ("r-s4vectors" ,r-s4vectors) + ("r-summarizedexperiment" ,r-summarizedexperiment))) + (home-page "https://bioconductor.org/packages/curatedTCGAData/") + (synopsis "Curated data from The Cancer Genome Atlas") + (description + "This package provides publicly available data from The Cancer Genome +Atlas (TCGA) as @code{MultiAssayExperiment} objects. +@code{MultiAssayExperiment} integrates multiple assays (e.g., RNA-seq, copy +number, mutation, microRNA, protein, and others) with clinical / pathological +data. It also links assay barcodes with patient identifiers, enabling +harmonized subsetting of rows (features) and columns (patients / samples) +across the entire multi-'omics experiment.") + (license license:artistic2.0))) + ;;; Packages -- cgit v1.2.3 From 3eacc8fa8f9625427cbc07f27e5249c7b24fcb62 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 18 Dec 2019 15:24:05 +0100 Subject: gnu: Add r-influencer. * gnu/packages/cran.scm (r-influencer): 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 1f15e29b06..040c2ead4a 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -18938,3 +18938,31 @@ resulting bitmap can be written to e.g. PNG, JPEG or WEBP format. In addition, the package can convert images directly to various formats such as PDF or PostScript.") (license license:expat))) + +(define-public r-influencer + (package + (name "r-influencer") + (version "0.1.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "influenceR" version)) + (sha256 + (base32 + "12p9362hkndlnz1rd8j2rykg57kbm6l7ks60by3rd25xg50k5jag")))) + (properties `((upstream-name . "influenceR"))) + (build-system r-build-system) + (propagated-inputs + `(("r-igraph" ,r-igraph) + ("r-matrix" ,r-matrix))) + (home-page "https://github.com/rcc-uchicago/influenceR") + (synopsis "Tools to quantify structural importance of nodes in a network") + (description + "This package provides functionality to compute various node centrality +measures on networks. Included are functions to compute betweenness +centrality (by utilizing Madduri and Bader's SNAP library), implementations of +Burt's constraint and @dfn{effective network size} (ENS) metrics, Borgatti's +algorithm to identify key players, and Valente's bridging metric. The +betweenness, Key Players, and bridging implementations are parallelized with +OpenMP.") + (license license:gpl2))) -- cgit v1.2.3 From c373223e635cd8f5f2770dd0b05f3a310fc7f7dd Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 18 Dec 2019 15:24:13 +0100 Subject: gnu: Add r-graphite. * gnu/packages/bioconductor.scm (r-graphite): 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 2ca1679f8b..89cdda25d9 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7011,3 +7011,30 @@ tidying methods. Tidying data makes it easy to recombine, reshape and visualize bioinformatics analyses.") ;; Any version of the LGPL. (license license:lgpl3+))) + +(define-public r-graphite + (package + (name "r-graphite") + (version "1.32.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "graphite" version)) + (sha256 + (base32 + "1r9fk0cpdwm7012pa85dkjcpkml2j89zcznpf4hfdz66anfyyycd")))) + (properties `((upstream-name . "graphite"))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotationdbi" ,r-annotationdbi) + ("r-checkmate" ,r-checkmate) + ("r-graph" ,r-graph) + ("r-httr" ,r-httr) + ("r-rappdirs" ,r-rappdirs))) + (home-page "https://bioconductor.org/packages/graphite/") + (synopsis "Networks from pathway databases") + (description + "Graphite provides networks derived from eight public pathway databases, +and automates the conversion of node identifiers (e.g. from Entrez IDs to gene +symbols).") + (license license:agpl3+))) -- cgit v1.2.3 From f388834e1152e18463d64d9b3d2499c4f939bdda Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 18 Dec 2019 15:24:21 +0100 Subject: gnu: Add r-reactomepa. * gnu/packages/bioconductor.scm (r-reactomepa): New variable. --- gnu/packages/bioconductor.scm | 30 ++++++++++++++++++++++++++++++ 1 file changed, 30 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 89cdda25d9..25481d5b1d 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7038,3 +7038,33 @@ visualize bioinformatics analyses.") and automates the conversion of node identifiers (e.g. from Entrez IDs to gene symbols).") (license license:agpl3+))) + +(define-public r-reactomepa + (package + (name "r-reactomepa") + (version "1.30.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "ReactomePA" version)) + (sha256 + (base32 + "1vwc9kj1l4yi7c4f4lnq0i3wl2nrmmhcxyakz8qak122fi92z3j1")))) + (properties `((upstream-name . "ReactomePA"))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotationdbi" ,r-annotationdbi) + ("r-dose" ,r-dose) + ("r-enrichplot" ,r-enrichplot) + ("r-ggplot2" ,r-ggplot2) + ("r-ggraph" ,r-ggraph) + ("r-graphite" ,r-graphite) + ("r-igraph" ,r-igraph) + ("r-reactome-db" ,r-reactome-db))) + (home-page "https://guangchuangyu.github.io/software/ReactomePA") + (synopsis "Reactome pathway analysis") + (description + "This package provides functions for pathway analysis based on the +REACTOME pathway database. It implements enrichment analysis, gene set +enrichment analysis and several functions for visualization.") + (license license:gpl2))) -- cgit v1.2.3 From 21afe920f13d8bdebb25759be0b3decb48e4a9d2 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 18 Dec 2019 15:24:27 +0100 Subject: gnu: Add r-ebarrays. * gnu/packages/bioconductor.scm (r-ebarrays): 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 25481d5b1d..5ae80f0502 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7068,3 +7068,27 @@ symbols).") REACTOME pathway database. It implements enrichment analysis, gene set enrichment analysis and several functions for visualization.") (license license:gpl2))) + +(define-public r-ebarrays + (package + (name "r-ebarrays") + (version "2.50.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "EBarrays" version)) + (sha256 + (base32 + "063rhsdp8x0f881kslq06zxfp6b2qabrz4vmfrn8a4v3pd3n7s13")))) + (properties `((upstream-name . "EBarrays"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biobase" ,r-biobase) + ("r-cluster" ,r-cluster) + ("r-lattice" ,r-lattice))) + (home-page "https://bioconductor.org/packages/EBarrays/") + (synopsis "Gene clustering and differential expression identification") + (description + "EBarrays provides tools for the analysis of replicated/unreplicated +microarray data.") + (license license:gpl2+))) -- cgit v1.2.3 From f180be2923e7685854493b9385fe70392cd7d286 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 18 Dec 2019 15:24:46 +0100 Subject: gnu: Add r-bioccasestudies. * gnu/packages/bioconductor.scm (r-bioccasestudies): New variable. --- gnu/packages/bioconductor.scm | 22 ++++++++++++++++++++++ 1 file changed, 22 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 5ae80f0502..d54444438c 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7092,3 +7092,25 @@ enrichment analysis and several functions for visualization.") "EBarrays provides tools for the analysis of replicated/unreplicated microarray data.") (license license:gpl2+))) + +(define-public r-bioccasestudies + (package + (name "r-bioccasestudies") + (version "1.48.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "BiocCaseStudies" version)) + (sha256 + (base32 + "1sg9vxs24zfz3dg9y0qlrdsq43y0pbahbvcfxzlxjzjw80xzxpbd")))) + (properties + `((upstream-name . "BiocCaseStudies"))) + (build-system r-build-system) + (propagated-inputs `(("r-biobase" ,r-biobase))) + (home-page "https://bioconductor.org/packages/BiocCaseStudies") + (synopsis "Support for the case studies monograph") + (description + "This package provides software and data to support the case studies +monograph.") + (license license:artistic2.0))) -- cgit v1.2.3 From 49f0860be0067990ac93cae2982e0ecbb0efb634 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 18 Dec 2019 15:24:53 +0100 Subject: gnu: Add r-biocgraph. * gnu/packages/bioconductor.scm (r-biocgraph): New variable. --- gnu/packages/bioconductor.scm | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index d54444438c..abba62d659 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7114,3 +7114,28 @@ microarray data.") "This package provides software and data to support the case studies monograph.") (license license:artistic2.0))) + +(define-public r-biocgraph + (package + (name "r-biocgraph") + (version "1.48.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "biocGraph" version)) + (sha256 + (base32 + "1rv2lwiqwg7h7za23n896fs4dpla3xhw6kzwghb6iw5nlm2m61yw")))) + (properties `((upstream-name . "biocGraph"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biocgenerics" ,r-biocgenerics) + ("r-geneplotter" ,r-geneplotter) + ("r-graph" ,r-graph) + ("r-rgraphviz" ,r-rgraphviz))) + (home-page "https://bioconductor.org/packages/biocGraph/") + (synopsis "Graph examples and use cases in Bioinformatics") + (description + "This package provides examples and code that make use of the +different graph related packages produced by Bioconductor.") + (license license:artistic2.0))) -- cgit v1.2.3 From 244270e6ae2d44ab6f06ffa6061660c85d3f357c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 18 Dec 2019 15:25:00 +0100 Subject: gnu: Add r-experimenthub. * gnu/packages/bioconductor.scm (r-experimenthub): 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 abba62d659..70ad6edc2f 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7139,3 +7139,35 @@ monograph.") "This package provides examples and code that make use of the different graph related packages produced by Bioconductor.") (license license:artistic2.0))) + +(define-public r-experimenthub + (package + (name "r-experimenthub") + (version "1.12.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "ExperimentHub" version)) + (sha256 + (base32 + "054w2lkyirbmhgia0rp4nk9zzw3zphz6jxg6fc9zlarp90g64z24")))) + (properties `((upstream-name . "ExperimentHub"))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotationhub" ,r-annotationhub) + ("r-biocfilecache" ,r-biocfilecache) + ("r-biocgenerics" ,r-biocgenerics) + ("r-biocmanager" ,r-biocmanager) + ("r-curl" ,r-curl) + ("r-rappdirs" ,r-rappdirs) + ("r-s4vectors" ,r-s4vectors))) + (home-page "https://bioconductor.org/packages/ExperimentHub/") + (synopsis "Client to access ExperimentHub resources") + (description + "This package provides a client for the Bioconductor ExperimentHub web +resource. ExperimentHub provides a central location where curated data from +experiments, publications or training courses can be accessed. Each resource +has associated metadata, tags and date of modification. The client creates +and manages a local cache of files retrieved enabling quick and reproducible +access.") + (license license:artistic2.0))) -- cgit v1.2.3 From 06784793913c771512e1e095b57dd6d57b4144f7 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 18 Dec 2019 15:25:08 +0100 Subject: gnu: Add r-multiassayexperiment. * gnu/packages/bioconductor.scm (r-multiassayexperiment): New variable. --- gnu/packages/bioconductor.scm | 33 +++++++++++++++++++++++++++++++++ 1 file changed, 33 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 70ad6edc2f..6590f6eb5b 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7171,3 +7171,36 @@ has associated metadata, tags and date of modification. The client creates and manages a local cache of files retrieved enabling quick and reproducible access.") (license license:artistic2.0))) + +(define-public r-multiassayexperiment + (package + (name "r-multiassayexperiment") + (version "1.12.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "MultiAssayExperiment" version)) + (sha256 + (base32 + "0hqg0b0hd5msnb4jcn1nbfyy1n1llfkipy2ivwncivkmbdn8psp4")))) + (properties + `((upstream-name . "MultiAssayExperiment"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-genomicranges" ,r-genomicranges) + ("r-iranges" ,r-iranges) + ("r-s4vectors" ,r-s4vectors) + ("r-summarizedexperiment" ,r-summarizedexperiment) + ("r-tidyr" ,r-tidyr))) + (home-page "http://waldronlab.io/MultiAssayExperiment/") + (synopsis "Integration of multi-omics experiments in Bioconductor") + (description + "MultiAssayExperiment harmonizes data management of multiple assays +performed on an overlapping set of specimens. It provides a familiar +Bioconductor user experience by extending concepts from +@code{SummarizedExperiment}, supporting an open-ended mix of standard data +classes for individual assays, and allowing subsetting by genomic ranges or +rownames.") + (license license:artistic2.0))) -- cgit v1.2.3 From c2b36a044140a2f1a186b85002e5c8ed98163a25 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 18 Dec 2019 15:25:17 +0100 Subject: gnu: Add r-bioconcotk. * gnu/packages/bioconductor.scm (r-bioconcotk): New variable. --- gnu/packages/bioconductor.scm | 43 +++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 43 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 6590f6eb5b..2bc453dcaa 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7204,3 +7204,46 @@ Bioconductor user experience by extending concepts from classes for individual assays, and allowing subsetting by genomic ranges or rownames.") (license license:artistic2.0))) + +(define-public r-bioconcotk + (package + (name "r-bioconcotk") + (version "1.6.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "BiocOncoTK" version)) + (sha256 + (base32 + "0rnah6c01a33yb9663jim9iclan61rpcwprb56mykgn1pf5hywbj")))) + (properties `((upstream-name . "BiocOncoTK"))) + (build-system r-build-system) + (propagated-inputs + `(("r-bigrquery" ,r-bigrquery) + ("r-car" ,r-car) + ("r-complexheatmap" ,r-complexheatmap) + ("r-curatedtcgadata" ,r-curatedtcgadata) + ("r-dbi" ,r-dbi) + ("r-dplyr" ,r-dplyr) + ("r-dt" ,r-dt) + ("r-genomicfeatures" ,r-genomicfeatures) + ("r-genomicranges" ,r-genomicranges) + ("r-ggplot2" ,r-ggplot2) + ("r-ggpubr" ,r-ggpubr) + ("r-graph" ,r-graph) + ("r-httr" ,r-httr) + ("r-iranges" ,r-iranges) + ("r-magrittr" ,r-magrittr) + ("r-plyr" ,r-plyr) + ("r-rgraphviz" ,r-rgraphviz) + ("r-rjson" ,r-rjson) + ("r-s4vectors" ,r-s4vectors) + ("r-scales" ,r-scales) + ("r-shiny" ,r-shiny) + ("r-summarizedexperiment" ,r-summarizedexperiment))) + (home-page "https://bioconductor.org/packages/BiocOncoTK") + (synopsis "Bioconductor components for general cancer genomics") + (description + "The purpose of this package is to provide a central interface to various +tools for genome-scale analysis of cancer studies.") + (license license:artistic2.0))) -- cgit v1.2.3 From 4d12c1e335e3949c451b045a1f128200432fdde9 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 18 Dec 2019 15:25:23 +0100 Subject: gnu: Add r-biocor. * gnu/packages/bioconductor.scm (r-biocor): 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 2bc453dcaa..62ec80397c 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7247,3 +7247,30 @@ rownames.") "The purpose of this package is to provide a central interface to various tools for genome-scale analysis of cancer studies.") (license license:artistic2.0))) + +(define-public r-biocor + (package + (name "r-biocor") + (version "1.10.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "BioCor" version)) + (sha256 + (base32 + "1bjw02rwmz2d715sgpfp08njb15200ch7cmipsf9hd5835ppg1jl")))) + (properties `((upstream-name . "BioCor"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biocparallel" ,r-biocparallel) + ("r-gseabase" ,r-gseabase) + ("r-matrix" ,r-matrix))) + (home-page "https://llrs.github.io/BioCor/") + (synopsis "Functional similarities") + (description + "This package provides tools to calculate functional similarities based +on the pathways described on KEGG and REACTOME or in gene sets. These +similarities can be calculated for pathways or gene sets, genes, or clusters +and combined with other similarities. They can be used to improve networks, +gene selection, testing relationships, and so on.") + (license license:expat))) -- cgit v1.2.3 From 4a18112dfb738c325f9ef0145e9480df642ec9b8 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 18 Dec 2019 15:25:31 +0100 Subject: gnu: Add r-biocpkgtools. * gnu/packages/bioconductor.scm (r-biocpkgtools): New variable. --- gnu/packages/bioconductor.scm | 44 +++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 44 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 62ec80397c..c5ad29297c 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7274,3 +7274,47 @@ similarities can be calculated for pathways or gene sets, genes, or clusters and combined with other similarities. They can be used to improve networks, gene selection, testing relationships, and so on.") (license license:expat))) + +(define-public r-biocpkgtools + (package + (name "r-biocpkgtools") + (version "1.4.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "BiocPkgTools" version)) + (sha256 + (base32 + "0gyhb3071pxmvaxla7cxy9k97s3z3ynl62jnqz9jnkd53c7jnd53")))) + (properties `((upstream-name . "BiocPkgTools"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biocmanager" ,r-biocmanager) + ("r-biocviews" ,r-biocviews) + ("r-dplyr" ,r-dplyr) + ("r-dt" ,r-dt) + ("r-gh" ,r-gh) + ("r-graph" ,r-graph) + ("r-htmltools" ,r-htmltools) + ("r-htmlwidgets" ,r-htmlwidgets) + ("r-httr" ,r-httr) + ("r-igraph" ,r-igraph) + ("r-jsonlite" ,r-jsonlite) + ("r-magrittr" ,r-magrittr) + ("r-rbgl" ,r-rbgl) + ("r-readr" ,r-readr) + ("r-rex" ,r-rex) + ("r-rvest" ,r-rvest) + ("r-stringr" ,r-stringr) + ("r-tibble" ,r-tibble) + ("r-tidyr" ,r-tidyr) + ("r-xml2" ,r-xml2))) + (home-page "https://github.com/seandavi/BiocPkgTools") + (synopsis "Collection of tools for learning about Bioconductor packages") + (description + "Bioconductor has a rich ecosystem of metadata around packages, usage, +and build status. This package is a simple collection of functions to access +that metadata from R. The goal is to expose metadata for data mining and +value-added functionality such as package searching, text mining, and +analytics on packages.") + (license license:expat))) -- cgit v1.2.3 From 43b66e3f7c7628804faf0f336c903458d319f412 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 18 Dec 2019 15:25:38 +0100 Subject: gnu: Add r-biocset. * gnu/packages/bioconductor.scm (r-biocset): New variable. --- gnu/packages/bioconductor.scm | 33 +++++++++++++++++++++++++++++++++ 1 file changed, 33 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index c5ad29297c..8bd6bfe7af 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7318,3 +7318,36 @@ that metadata from R. The goal is to expose metadata for data mining and value-added functionality such as package searching, text mining, and analytics on packages.") (license license:expat))) + +(define-public r-biocset + (package + (name "r-biocset") + (version "1.0.1") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "BiocSet" version)) + (sha256 + (base32 + "1xcksnvjflrdarn8xqmgf0n6wbsjkq9jazqwp35i52vqcq4ic1j9")))) + (properties `((upstream-name . "BiocSet"))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotationdbi" ,r-annotationdbi) + ("r-dplyr" ,r-dplyr) + ("r-keggrest" ,r-keggrest) + ("r-plyr" ,r-plyr) + ("r-rlang" ,r-rlang) + ("r-rtracklayer" ,r-rtracklayer) + ("r-tibble" ,r-tibble))) + (home-page + "https://bioconductor.org/packages/BiocSet") + (synopsis + "Representing Different Biological Sets") + (description + "BiocSet displays different biological sets in a triple tibble format. +These three tibbles are @code{element}, @code{set}, and @code{elementset}. +The user has the abilty to activate one of these three tibbles to perform +common functions from the @code{dplyr} package. Mapping functionality and +accessing web references for elements/sets are also available in BiocSet.") + (license license:artistic2.0))) -- cgit v1.2.3 From 0156297f2920a036a7060586ea3286ed5ecbab26 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 18 Dec 2019 15:25:45 +0100 Subject: gnu: Add r-biocworkflowtools. * gnu/packages/bioconductor.scm (r-biocworkflowtools): 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 8bd6bfe7af..7d45a26579 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7351,3 +7351,34 @@ The user has the abilty to activate one of these three tibbles to perform common functions from the @code{dplyr} package. Mapping functionality and accessing web references for elements/sets are also available in BiocSet.") (license license:artistic2.0))) + +(define-public r-biocworkflowtools + (package + (name "r-biocworkflowtools") + (version "1.12.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "BiocWorkflowTools" version)) + (sha256 + (base32 + "1v4bhnpdkmllm7aghms9b7369hkrgz7mn69wbrqg1x42pgkf30ad")))) + (properties + `((upstream-name . "BiocWorkflowTools"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biocstyle" ,r-biocstyle) + ("r-bookdown" ,r-bookdown) + ("r-git2r" ,r-git2r) + ("r-httr" ,r-httr) + ("r-knitr" ,r-knitr) + ("r-rmarkdown" ,r-rmarkdown) + ("r-rstudioapi" ,r-rstudioapi) + ("r-stringr" ,r-stringr) + ("r-usethis" ,r-usethis))) + (home-page "https://bioconductor.org/packages/BiocWorkflowTools/") + (synopsis "Tools to aid the development of Bioconductor Workflow packages") + (description + "This package provides functions to ease the transition between +Rmarkdown and LaTeX documents when authoring a Bioconductor Workflow.") + (license license:expat))) -- cgit v1.2.3 From 77e2de365497bf4c8b81cbd78624f78293490485 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 18 Dec 2019 15:25:50 +0100 Subject: gnu: Add r-biodist. * gnu/packages/bioconductor.scm (r-biodist): New variable. --- gnu/packages/bioconductor.scm | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 7d45a26579..6d91dcf2e4 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7382,3 +7382,26 @@ accessing web references for elements/sets are also available in BiocSet.") "This package provides functions to ease the transition between Rmarkdown and LaTeX documents when authoring a Bioconductor Workflow.") (license license:expat))) + +(define-public r-biodist + (package + (name "r-biodist") + (version "1.58.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "bioDist" version)) + (sha256 + (base32 + "0iabw07px3ybdgbbab0vv350051cm4aq8w47rz9dnmzx4kil9h5q")))) + (properties `((upstream-name . "bioDist"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biobase" ,r-biobase) + ("r-kernsmooth" ,r-kernsmooth))) + (home-page "https://bioconductor.org/packages/bioDist/") + (synopsis "Different distance measures") + (description + "This package provides a collection of software tools for calculating +distance measures.") + (license license:artistic2.0))) -- cgit v1.2.3 From 96c158be1b4340cefa7a66d781c21f2c5ca4691a Mon Sep 17 00:00:00 2001 From: Mark H Weaver Date: Wed, 18 Dec 2019 15:08:42 -0500 Subject: gnu: linux-libre: Update deblob scripts. * gnu/packages/linux.scm (deblob-scripts-4.19): Update to 4.19.90. (deblob-scripts-4.14): Update to 4.14.159. (deblob-scripts-5.3, deblob-scripts-4.9, deblob-scripts-4.4): Update version numbers to 5.3.17, 4.9.206, and 4.4.206, respectively, although the scripts themselves have not changed. --- gnu/packages/linux.scm | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index 7f094be422..c07a6cc1dd 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -188,31 +188,31 @@ defconfig. Return the appropriate make target if applicable, otherwise return (define deblob-scripts-5.3 (linux-libre-deblob-scripts - "5.3.11" + "5.3.17" (base32 "15n09zq38d69y1wl28s3nasf3377qp2yil5b887zpqrm00dif7i4") (base32 "1xk3gzgnl9m29avka32zkggl36sdxyvps40hr12hjy42l1ysfshm"))) (define deblob-scripts-4.19 (linux-libre-deblob-scripts - "4.19.84" + "4.19.90" (base32 "02zs405awaxydbapka4nz8h6lmnc0dahgczqsrs5s2bmzjyyqkcy") - (base32 "1s89hmy4ihd65by2p1xxkxj476f6c9s5g9r9yvqncb50xlhilk50"))) + (base32 "0xpcl6pd1280gm81bivz45dfhy6v16j0hghxhjynmcbasgnx8vpd"))) (define deblob-scripts-4.14 (linux-libre-deblob-scripts - "4.14.154" + "4.14.159" (base32 "091jk9jkn9jf39bxpc7395bhcb7p96nkg3a8047380ki06lnfxh6") - (base32 "1pcsfzpcv3bs30iyhwpk1x64r0gyv7wi22spnq6avzj1ayva10kw"))) + (base32 "0yd0c3qxk5rm686j4kd5v4zppjj3k9ivqnv46z4p3xh1gqmhv7cz"))) (define deblob-scripts-4.9 (linux-libre-deblob-scripts - "4.9.201" + "4.9.206" (base32 "1wvldzlv7q2xdbadas87dh593nxr4a8p5n0f8zpm72lja6w18hmg") (base32 "0is8gn4qdd7h5l6lacvhqdch26lmrbgxfm8ab7fx8n85ha7y358w"))) (define deblob-scripts-4.4 (linux-libre-deblob-scripts - "4.4.201" + "4.4.206" (base32 "0x2j1i88am54ih2mk7gyl79g25l9zz4r08xhl482l3fvjj2irwbw") (base32 "12ac4g3ky8yma8sylmxvvysqvd4hnaqjiwmxrxb6wlxggfd7zkbx"))) -- cgit v1.2.3 From 7ebf4c40f178449b8ace9a42791baa5e8647124a Mon Sep 17 00:00:00 2001 From: Mark H Weaver Date: Wed, 18 Dec 2019 14:57:30 -0500 Subject: gnu: linux-libre: Update to 5.3.18. * gnu/packages/linux.scm (linux-libre-5.3-version): Update to 5.3.18. (linux-libre-5.3-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 c07a6cc1dd..5c5f930485 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -356,10 +356,10 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." "linux-" version ".tar.xz")) (sha256 hash))) -(define-public linux-libre-5.3-version "5.3.17") +(define-public linux-libre-5.3-version "5.3.18") (define-public linux-libre-5.3-pristine-source (let ((version linux-libre-5.3-version) - (hash (base32 "10igr1dm9pazmhpi3arsyywj4757531nal003dn9rhs2xc8pkx5c"))) + (hash (base32 "133342nv9ddjad2rizmcbilg9rhg339sfqr9l77j4cgkqhblkw90"))) (make-linux-libre-source version (%upstream-linux-source version hash) deblob-scripts-5.3))) -- cgit v1.2.3 From 8e53fe2b91d2776bc1529e7b34967c8f1d9edc32 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Fri, 6 Dec 2019 20:53:08 +0100 Subject: gnu: Remove uses of deprecated Qemu network configuration. * gnu/build/vm.scm (load-in-linux-vm): Move Qemu network configuration from ARCH-SPECIFIC-FLAGS to the Qemu command line. Use the "-nic" option of Qemu instead of "-device" and "-net". * gnu/system/vm.scm (common-qemu-options): Do not add a '-net' command. (virtual-machine-compiler): Use "-nic user,..." instead of "-net". * doc/guix.texi (Installing Guix in a VM, Invoking guix system, Running Guix in a VM): Do the same for examples. --- doc/guix.texi | 28 +++++++++++++--------------- gnu/build/vm.scm | 10 ++-------- gnu/system/vm.scm | 5 ++--- 3 files changed, 17 insertions(+), 26 deletions(-) diff --git a/doc/guix.texi b/doc/guix.texi index a5cff4cab2..7fa1eca097 100644 --- a/doc/guix.texi +++ b/doc/guix.texi @@ -46,7 +46,7 @@ Copyright @copyright{} 2017, 2018 Carlo Zancanaro@* Copyright @copyright{} 2017 Thomas Danckaert@* Copyright @copyright{} 2017 humanitiesNerd@* Copyright @copyright{} 2017 Christopher Allan Webber@* -Copyright @copyright{} 2017, 2018 Marius Bakke@* +Copyright @copyright{} 2017, 2018, 2019 Marius Bakke@* Copyright @copyright{} 2017, 2019 Hartmut Goebel@* Copyright @copyright{} 2017, 2019 Maxim Cournoyer@* Copyright @copyright{} 2017, 2018, 2019 Tobias Geerinckx-Rice@* @@ -2472,7 +2472,7 @@ Boot the USB installation image in an VM: @example qemu-system-x86_64 -m 1024 -smp 1 -enable-kvm \ - -net user -net nic,model=virtio -boot menu=on,order=d \ + -nic user,model=virtio-net-pci -boot menu=on,order=d \ -drive file=guix-system.img \ -drive media=cdrom,file=guix-system-install-@value{VERSION}.@var{system}.iso @end example @@ -26156,7 +26156,7 @@ below, which enables networking and requests 1@tie{}GiB of RAM for the emulated machine: @example -$ /gnu/store/@dots{}-run-vm.sh -m 1024 -net user +$ /gnu/store/@dots{}-run-vm.sh -m 1024 -smp 2 -net user,model=virtio-net-pci @end example The VM shares its store with the host system. @@ -26642,7 +26642,7 @@ vm-image} on x86_64 hardware: @example $ qemu-system-x86_64 \ - -net user -net nic,model=virtio \ + -nic user,model=virtio-net-pci \ -enable-kvm -m 1024 \ -device virtio-blk,drive=myhd \ -drive if=none,file=/tmp/qemu-image,id=myhd @@ -26655,16 +26655,14 @@ Here is what each of these options means: This specifies the hardware platform to emulate. This should match the host. -@item -net user +@item -nic user,model=virtio-net-pci Enable the unprivileged user-mode network stack. The guest OS can access the host but not vice versa. This is the simplest way to get the -guest OS online. - -@item -net nic,model=virtio -You must create a network interface of a given model. If you do not -create a NIC, the boot will fail. Assuming your hardware platform is +guest OS online. @code{model} specifies which network device to emulate: +@code{virtio-net-pci} is a special device made for virtualized operating +systems and recommended for most uses. Assuming your hardware platform is x86_64, you can get a list of available NIC models by running -@command{qemu-system-x86_64 -net nic,model=help}. +@command{qemu-system-x86_64 -nic model=help}. @item -enable-kvm If your system has hardware virtualization extensions, enabling the @@ -26688,11 +26686,11 @@ the ``myhd'' drive. @end table The default @command{run-vm.sh} script that is returned by an invocation of -@command{guix system vm} does not add a @command{-net user} flag by default. +@command{guix system vm} does not add a @command{-nic user} flag by default. To get network access from within the vm add the @code{(dhcp-client-service)} to your system definition and start the VM using -@command{`guix system vm config.scm` -net user}. An important caveat of using -@command{-net user} for networking is that @command{ping} will not work, because +@command{`guix system vm config.scm` -nic user}. An important caveat of using +@command{-nic user} for networking is that @command{ping} will not work, because it uses the ICMP protocol. You'll have to use a different command to check for network connectivity, for example @command{guix download}. @@ -26706,7 +26704,7 @@ To enable SSH inside a VM you need to add an SSH server like 22 by default, to the host. You can do this with @example -`guix system vm config.scm` -net user,hostfwd=tcp::10022-:22 +`guix system vm config.scm` -nic user,model=virtio-net-pci,hostfwd=tcp::10022-:22 @end example To connect to the VM you can run diff --git a/gnu/build/vm.scm b/gnu/build/vm.scm index 89d685b352..9a9e5bd001 100644 --- a/gnu/build/vm.scm +++ b/gnu/build/vm.scm @@ -131,14 +131,7 @@ the #:references-graphs parameter of 'derivation'." ;; The serial port name differs between emulated ;; architectures/machines. " console=" - (if target-arm? "ttyAMA0" "ttyS0")) - - ;; NIC is not supported on ARM "virt" machine, so use a user mode - ;; network stack instead. - ,@(if target-arm? - '("-device" "virtio-net-pci,netdev=mynet" - "-netdev" "user,id=mynet") - '("-net" "nic,model=virtio")))) + (if target-arm? "ttyAMA0" "ttyS0")))) (when make-disk-image? (format #t "creating ~a image of ~,2f MiB...~%" @@ -163,6 +156,7 @@ the #:references-graphs parameter of 'derivation'." ;; CPU with the maximum possible feature set otherwise. "-cpu" "max" "-m" (number->string memory-size) + "-nic" "user,model=virtio-net-pci" "-object" "rng-random,filename=/dev/urandom,id=guixsd-vm-rng" "-device" "virtio-rng-pci,rng=guixsd-vm-rng" "-virtfs" diff --git a/gnu/system/vm.scm b/gnu/system/vm.scm index 8609bd2ace..81b2e06ba2 100644 --- a/gnu/system/vm.scm +++ b/gnu/system/vm.scm @@ -927,7 +927,6 @@ with '-virtfs' options for the host file systems listed in SHARED-FS." '()) "-no-reboot" - "-net nic,model=virtio" "-object" "rng-random,filename=/dev/urandom,id=guixsd-vm-rng" "-device" "virtio-rng-pci,rng=guixsd-vm-rng" @@ -1046,8 +1045,8 @@ FORWARDINGS is a list of host-port/guest-port pairs." (($ os qemu graphic? memory-size disk-image-size forwardings) (let ((options - `("-net" ,(string-append - "user," + `("-nic" ,(string-append + "user,model=virtio-net-pci," (port-forwardings->qemu-options forwardings))))) (system-qemu-image/shared-store-script os #:qemu qemu -- cgit v1.2.3 From 17ac8bb67038608547801aa2563b04526fee9932 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Thu, 12 Dec 2019 01:24:32 +0100 Subject: gnu: darktable: Fix build failure. * gnu/packages/photo.scm (darktable)[arguments]: Move CPATH override from #:make-flags to a phase, so the GETENV call returns useful data. --- gnu/packages/photo.scm | 13 +++++++------ 1 file changed, 7 insertions(+), 6 deletions(-) diff --git a/gnu/packages/photo.scm b/gnu/packages/photo.scm index f6d86f0857..20af5cc7f5 100644 --- a/gnu/packages/photo.scm +++ b/gnu/packages/photo.scm @@ -374,18 +374,19 @@ photographic equipment.") (arguments `(#:tests? #f ; there are no tests #:configure-flags '("-DBINARY_PACKAGE_BUILD=On") - #:make-flags - (list - (string-append "CPATH=" (assoc-ref %build-inputs "ilmbase") - "/include/OpenEXR:" (or (getenv "CPATH") ""))) #:phases (modify-phases %standard-phases - (add-before 'configure 'set-ldflags - (lambda* (#:key outputs #:allow-other-keys) + (add-before 'configure 'set-LDFLAGS-and-CPATH + (lambda* (#:key inputs outputs #:allow-other-keys) (setenv "LDFLAGS" (string-append "-Wl,-rpath=" (assoc-ref outputs "out") "/lib/darktable")) + + ;; Ensure the OpenEXR headers are found. + (setenv "CPATH" + (string-append (assoc-ref inputs "ilmbase") + "/include/OpenEXR:" (or (getenv "CPATH") ""))) #t))))) (native-inputs `(("llvm" ,llvm-3.9.1) -- cgit v1.2.3 From 6b1e6b5c421fdd56e5f8dfefa030d6a95d835cac Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Thu, 12 Dec 2019 01:27:37 +0100 Subject: gnu: darktable: Remove redundant inputs. * gnu/packages/photo.scm (darktable)[native-inputs]: Remove. --- gnu/packages/photo.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/photo.scm b/gnu/packages/photo.scm index 20af5cc7f5..d511ad1eda 100644 --- a/gnu/packages/photo.scm +++ b/gnu/packages/photo.scm @@ -388,9 +388,6 @@ photographic equipment.") (string-append (assoc-ref inputs "ilmbase") "/include/OpenEXR:" (or (getenv "CPATH") ""))) #t))))) - (native-inputs - `(("llvm" ,llvm-3.9.1) - ("clang" ,clang-3.9.1))) (inputs `(("libxslt" ,libxslt) ("libxml2" ,libxml2) -- cgit v1.2.3 From fe3110ac58364aceff71391b984e8056a6db9395 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Thu, 12 Dec 2019 01:28:11 +0100 Subject: gnu: darktable: Update to 2.6.3. * gnu/packages/photo.scm (darktable): Update to 2.6.3. --- gnu/packages/photo.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/photo.scm b/gnu/packages/photo.scm index d511ad1eda..0867433245 100644 --- a/gnu/packages/photo.scm +++ b/gnu/packages/photo.scm @@ -361,7 +361,7 @@ photographic equipment.") (define-public darktable (package (name "darktable") - (version "2.6.2") + (version "2.6.3") (source (origin (method url-fetch) @@ -369,7 +369,7 @@ photographic equipment.") "https://github.com/darktable-org/darktable/releases/" "download/release-" version "/darktable-" version ".tar.xz")) (sha256 - (base32 "0igvgyd042j7hm4y8fcm6dc1qqjs4d1r7y6f0pzpa0x416xyzfcw")))) + (base32 "1w3q3dhcxa0bs590zbsj61ap8z84wmn04xs5q3gjwisqhjf9j655")))) (build-system cmake-build-system) (arguments `(#:tests? #f ; there are no tests -- cgit v1.2.3 From ab7010af1f1077c056529769a53a380147c3933f Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Sun, 15 Dec 2019 21:27:31 +0100 Subject: gexp: Allow character literals in GEXP->SEXP. Fixes . * tests/gexp.scm ("lower-gexp, character literal"): New test. * guix/gexp.scm (gexp->sexp)[self-quoting?]: Add CHAR? to the tested types. * guix/repl.scm (self-quoting?): Likewise. * gnu/tests.scm (marionette-shepherd-service)[self-quoting?]: Likewise. --- gnu/tests.scm | 2 +- guix/gexp.scm | 2 +- guix/repl.scm | 2 +- tests/gexp.scm | 6 ++++++ 4 files changed, 9 insertions(+), 3 deletions(-) diff --git a/gnu/tests.scm b/gnu/tests.scm index 27cb39c2b9..cc72e56858 100644 --- a/gnu/tests.scm +++ b/gnu/tests.scm @@ -98,7 +98,7 @@ (or (pred x) (one-of rest ...)))))) (one-of symbol? string? keyword? pair? null? array? - number? boolean?))) + number? boolean? char?))) (match (primitive-fork) (0 diff --git a/guix/gexp.scm b/guix/gexp.scm index a96592ac76..411f0844ff 100644 --- a/guix/gexp.scm +++ b/guix/gexp.scm @@ -1028,7 +1028,7 @@ and in the current monad setting (system type, etc.)" (or (pred x) (one-of rest ...)))))) (one-of symbol? string? keyword? pair? null? array? - number? boolean?))) + number? boolean? char?))) (define* (reference->sexp ref #:optional native?) (with-monad %store-monad diff --git a/guix/repl.scm b/guix/repl.scm index 1ead18c53b..0f75f9cd0b 100644 --- a/guix/repl.scm +++ b/guix/repl.scm @@ -37,7 +37,7 @@ (or (pred x) (one-of rest ...)))))) (one-of symbol? string? keyword? pair? null? array? - number? boolean?))) + number? boolean? char?))) (define (send-repl-response exp output) "Write the response corresponding to the evaluation of EXP to PORT, an diff --git a/tests/gexp.scm b/tests/gexp.scm index 84c16422c2..8b1596f66d 100644 --- a/tests/gexp.scm +++ b/tests/gexp.scm @@ -886,6 +886,12 @@ (run-with-store %store (lower-gexp #~(foo #$+))))) +(test-equal "lower-gexp, character literal" + '(#\+) + (lowered-gexp-sexp + (run-with-store %store + (lower-gexp #~(#\+))))) + (test-assertm "gexp->derivation #:references-graphs" (mlet* %store-monad ((one (text-file "one" (random-text))) -- cgit v1.2.3 From 9077cf68ec57c0303ef7746e203c3fe5ed041add Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Wed, 18 Dec 2019 22:20:07 +0100 Subject: gnu: libdbi-drivers: Adapt to multiple-output MariaDB. * gnu/packages/databases.scm (mariadb/fixed-install-db): New public variable. (libdbi-drivers)[inputs]: Add MARIADB:DEV and MARIADB:LIB. Remove MARIADB. [native-inputs]: Add MARIADB/FIXED-INSTALL-DB. [arguments]: Adjust accordingly. --- gnu/packages/databases.scm | 48 ++++++++++++++++++++++++++++++++++++++-------- 1 file changed, 40 insertions(+), 8 deletions(-) diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm index cb843672af..0a1a7ecefa 100644 --- a/gnu/packages/databases.scm +++ b/gnu/packages/databases.scm @@ -17,7 +17,7 @@ ;;; Copyright © 2016 Jan Nieuwenhuizen ;;; Copyright © 2016 Andy Patterson ;;; Copyright © 2016 Danny Milosavljevic -;;; Copyright © 2016, 2017, 2018 Marius Bakke +;;; Copyright © 2016, 2017, 2018, 2019 Marius Bakke ;;; Copyright © 2017, 2018 Julien Lepiller ;;; Copyright © 2017 Thomas Danckaert ;;; Copyright © 2017 Jelle Licht @@ -125,6 +125,7 @@ #:use-module (guix build-system ruby) #:use-module (guix build-system cmake) #:use-module (guix build-system scons) + #:use-module (guix build-system trivial) #:use-module ((guix build utils) #:hide (which)) #:use-module (guix utils) #:use-module (srfi srfi-1) @@ -899,6 +900,33 @@ Language.") as a drop-in replacement of MySQL.") (license license:gpl2))) +;; TODO: mysql_install_db is broken in MariaDB. This package is here as +;; a workaround for packages that need it. Merge with 'mariadb' in the next +;; rebuild cycle. +(define-public mariadb/fixed-install-db + (hidden-package + (package/inherit + mariadb + (name "mariadb-fixed") + (native-inputs '()) + (inputs + `(("mariadb" ,mariadb) + ("mariadb:lib" ,mariadb "lib"))) + (outputs '("out")) + (build-system trivial-build-system) + (arguments + `(#:modules ((guix build utils)) + #:builder + (begin + (use-modules ((guix build utils))) + (let ((out (assoc-ref %outputs "out"))) + (copy-recursively (assoc-ref %build-inputs "mariadb") out) + (substitute* (string-append out "/bin/mysql_install_db") + (("\\$basedir/share/mysql") + (string-append (assoc-ref %build-inputs "mariadb:lib") + "/share/mysql"))) + #t))))))) + ;; Don't forget to update the other postgresql packages when upgrading this one. (define-public postgresql (package @@ -3233,25 +3261,29 @@ simultaneous database connections by using this framework.") "0m680h8cc4428xin4p733azysamzgzcmv4psjvraykrsaz6ymlj3")))) (build-system gnu-build-system) (native-inputs - `(("inetutils" ,inetutils) - ("glibc-locales" ,glibc-locales))) + `(;; For tests. + ("inetutils" ,inetutils) + ("glibc-locales" ,glibc-locales) + ("mariadb" ,mariadb/fixed-install-db))) (inputs `(("libdbi" ,libdbi) - ("mysql" ,mariadb) + ("mariadb:dev" ,mariadb "dev") + ("mariadb:lib" ,mariadb "lib") ("postgresql" ,postgresql) ("sqlite" ,sqlite))) (arguments `(#:configure-flags (let ((libdbi (assoc-ref %build-inputs "libdbi")) - (mysql (assoc-ref %build-inputs "mysql")) + (mysql:inc (assoc-ref %build-inputs "mariadb:dev")) + (mysql:lib (assoc-ref %build-inputs "mariadb:lib")) (postgresql (assoc-ref %build-inputs "postgresql")) (sqlite (assoc-ref %build-inputs "sqlite"))) (list "--disable-docs" (string-append "--with-dbi-incdir=" libdbi "/include") (string-append "--with-dbi-libdir=" libdbi "/lib") "--with-mysql" - (string-append "--with-mysql-incdir=" mysql "/include/mysql") - (string-append "--with-mysql-libdir=" mysql "/lib") + (string-append "--with-mysql-incdir=" mysql:inc "/include/mysql") + (string-append "--with-mysql-libdir=" mysql:lib "/lib") "--with-pgsql" (string-append "--with-pgsql-incdir=" postgresql "/include") (string-append "--with-pgsql-libdir=" postgresql "/lib") @@ -3265,7 +3297,7 @@ simultaneous database connections by using this framework.") (substitute* "tests/test_mysql.sh" (("^MYMYSQLD=.*") (string-append "MYMYSQLD=" - (assoc-ref inputs "mysql") + (assoc-ref inputs "mariadb") "/bin/mysqld"))) #t)) (add-after 'install 'remove-empty-directories -- cgit v1.2.3 From 6afea7489b76c8db58d4f389fdbedc7c2b8992bd Mon Sep 17 00:00:00 2001 From: Björn Höfling Date: Wed, 18 Dec 2019 22:31:05 +0100 Subject: guix: swh: Fix example URI in comment for . This is a one-character follow-up to 356a79becc4061d158c68718ad169abac1ab672f Reported by Jonathan Brielmaier . * guix/swh.scm(): Remove a slash from example URI witin a comment. --- guix/swh.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/guix/swh.scm b/guix/swh.scm index 372e4c84d1..70eeef5c6b 100644 --- a/guix/swh.scm +++ b/guix/swh.scm @@ -244,7 +244,7 @@ FALSE-IF-404? is true, return #f upon 404 responses." docstring (call (swh-url components ...) json->value))))) -;; +;; (define-json-mapping make-origin origin? json->origin (id origin-id) -- cgit v1.2.3