7a14f9365a
guix: Upgrade to Bioconductor 3.18.
...
* guix/build-system/r.scm (bioconductor-uri): Bump Bioconductor version to
3.18.
* guix/import/cran.scm (%bioconductor-version): Same.
Change-Id: Ic3fc2e6ab6b5f6f6e55662f81baee67391158c5b
2023-11-03 22:49:10 +01:00
ec52655ce6
guix: Upgrade to Bioconductor 3.16.
...
* guix/build-system/r.scm (bioconductor-uri): Bump Bioconductor version to
3.17.
* guix/import/cran.scm (%bioconductor-version): Same.
2023-04-29 20:09:30 +02:00
ae587c2ef0
guix: Strip #:use-module lists.
...
This was obtained by setting up this environment:
guix shell -D guix --with-input=guile@3.0.9=guile-next \
--with-commit=guile-next=e2ed33ef0445c867fe56c247054aa67e834861f2
-- make -j5
then adding 'unused-module' to (@@ (guix build compiler) %warnings),
building, and checking all the "unused module" warnings and removing
those that were definitely unused.
2023-03-13 15:08:33 +01:00
f4a7ccc976
guix: Upgrade to Bioconductor 3.16.
...
* guix/build-system/r.scm (bioconductor-uri): Bump Bioconductor version to
3.16.
* guix/import/cran.scm (%bioconductor-version): Same.
2022-11-24 12:31:11 +01:00
556ca8ba21
guix: Upgrade to Bioconductor 3.15.
...
* guix/build-system/r.scm (bioconductor-uri): Bump Bioconductor version to
3.15.
* guix/import/cran.scm (%bioconductor-version): Same.
2022-05-28 23:19:05 +02:00
1c94392a13
Merge remote-tracking branch 'origin/master' into core-updates-frozen
2021-11-08 09:06:14 +02:00
22b568de43
guix: Upgrade to Bioconductor 3.14.
...
* guix/build-system/r.scm (bioconductor-uri): Bump Bioconductor version to
3.14.
* guix/import/cran.scm (%bioconductor-version): Same.
2021-11-07 22:34:34 +00:00
8d59c262ad
Merge branch 'master' into core-updates
...
Conflicts:
gnu/local.mk
gnu/packages/algebra.scm
gnu/packages/bioinformatics.scm
gnu/packages/curl.scm
gnu/packages/docbook.scm
gnu/packages/emacs-xyz.scm
gnu/packages/maths.scm
gnu/packages/plotutils.scm
gnu/packages/python-web.scm
gnu/packages/python-xyz.scm
gnu/packages/radio.scm
gnu/packages/readline.scm
gnu/packages/tls.scm
gnu/packages/xml.scm
gnu/packages/xorg.scm
2021-06-06 21:16:32 +02:00
c343c3bc1f
guix: Update to Bioconductor 3.13.
...
* guix/build-system/r.scm (bioconductor-uri): Update version.
* guix/import/cran.scm (%bioconductor-version): Update.
2021-06-05 09:12:39 +02:00
f95fc73248
build-system: Use 'sexp->gexp' for plain sexps.
...
This reduces memory allocations and list traversals during 'gexp->sexp',
'gexp-inputs', etc.
* guix/build-system/cargo.scm (cargo-build): Use 'sexp->gexp' for sexps
known to not contain file-like objects. Change default #:phases to a
symbol.
* guix/build-system/cmake.scm (cmake-build, cmake-cross-build): Likewise.
* guix/build-system/copy.scm (copy-build): Likewise.
* guix/build-system/font.scm (font-build): Likewise.
* guix/build-system/glib-or-gtk.scm (glib-or-gtk-build): Likewise.
* guix/build-system/gnu.scm (%strip-flags, %strip-directories): New
variables.
(gnu-build): Use them. Use 'sexp->gexp' where appropriate.
(gnu-cross-build): Likewise.
* guix/build-system/meson.scm (meson-build): Likewise.
* guix/build-system/perl.scm (perl-build): Likewise.
* guix/build-system/python.scm (python-build): Likewise.
* guix/build-system/ruby.scm (ruby-build): Likewise.
* guix/build-system/scons.scm (scons-build): Likewise.
* guix/build-system/texlive.scm (texlive-build): Likewise.
* guix/build-system/trivial.scm (trivial-build): Likewise.
* guix/build-system/waf.scm (waf-build): Likewise.
* guix/build-system/android-ndk.scm (android-ndk-build): Likewise.
* guix/build-system/ant.scm (ant-build): Likewise.
* guix/build-system/asdf.scm (asdf-build/source, asdf-build): Likewise.
* guix/build-system/chicken.scm (chicken-build): Likewise.
* guix/build-system/clojure.scm (clojure-build): Likewise.
(source->output-path, maybe-guile->guile): Remove.
* guix/build-system/dub.scm (dub-build): Likewise.
* guix/build-system/emacs.scm (emacs-build): Likewise.
* guix/build-system/go.scm (go-build): Likewise.
* guix/build-system/haskell.scm (haskell-build): Likewise.
* guix/build-system/julia.scm (julia-build): Likewise.
* guix/build-system/linux-module.scm (linux-module-build)
(linux-module-build-cross): Likewise.
* guix/build-system/maven.scm (maven-build): Likewise.
* guix/build-system/minify.scm (minify-build): Likewise.
* guix/build-system/node.scm (node-build): Likewise.
* guix/build-system/qt.scm (qt-build, qt-cross-build): Likewise.
* guix/build-system/r.scm (r-build): Likewise.
* guix/build-system/rakudo.scm (rakudo-build): Likewise.
* guix/build-system/renpy.scm (renpy-build): Likewise.
* guix/packages.scm (patch-and-repack): Use 'sexp->gexp' when SNIPPET is
a pair.
* guix/svn-download.scm (svn-multi-fetch): Use 'sexp->gexp' for
'svn-multi-reference-locations'.
2021-03-30 22:48:44 +02:00
7d873f194c
build-system: Rewrite using gexps.
...
* guix/packages.scm (expand-input): Remove 'store', 'system', and
'cross-system' parameters; add #:native?. Rewrite to return
name/gexp-input tuples.
(bag->derivation): Adjust accordingly. Lower (bag-build bag).
(bag->cross-derivation): Ditto. Instead of #:native-drvs and
#:target-drvs, pass #:build-inputs, #:host-inputs, and #:target-inputs.
(%derivation-cache): Remove.
* gnu/packages/bootstrap.scm (raw-build): Turn into a monadic procedure.
* gnu/packages/commencement.scm (glibc-final)[arguments]: Use
'gexp-input' for the #:allowed-references argument.
* guix/build-system/cmake.scm (cmake-build): Remove 'store' parameter.
Switch to the use of gexps and 'gexp->derivation'.
(lower): Remove #:source from 'private-keywords'.
* guix/build-system/glib-or-gtk.scm (glib-or-gtk-build, lower):
Likewise.
* guix/build-system/font.scm (font-build): Likewise.
* guix/build-system/gnu.scm (gnu-build): Likewise, and remove
'canonicalize-reference'.
(gnu-cross-build): Likewise, and expect #:build-inputs, #:host-inputs,
and #:target-inputs instead of #:native-drvs and #:target-drvs.
(lower): Likewise.
* guix/build-system/perl.scm (perl-build, lower): Likewise.
* guix/build-system/python.scm (python-build, lower): Likewise.
* guix/build-system/ruby.scm (ruby-build, lower): Likewise.
* guix/build-system/waf.scm (waf-build, lower): Likewise.
* guix/build-system/trivial.scm (guile-for-build): Remove.
(trivial-build): Remove 'store' parameter, change to gexps.
(trivial-cross-build): Ditto, and change to #:build-inputs & co.
* guix/build-system/cargo.scm (cargo-build): Change to 'gexp->derivation'.
* guix/build-system/copy.scm (copy-build): Likewise.
* guix/build-system/dune.scm (dune-build): Likewise.
* guix/build-system/guile.scm (guile-build, guile-cross-build):
Likewise.
* guix/build-system/meson.scm (meson-build): Likewise.
* guix/build-system/ocaml.scm (ocaml-build): Likewise.
* guix/build-system/scons.scm (scons-build): Likewise.
* guix/build-system/texlive.scm (texlive-build): Likewise.
* guix/build-system/android-ndk.scm (android-ndk-build): Likewise.
* guix/build-system/ant.scm (ant-build): Likewise.
* guix/build-system/asdf.scm (asdf-build/source, asdf-build): Likewise.
* guix/build-system/chicken.scm (chicken-build): Likewise.
* guix/build-system/clojure.scm (clojure-build): Likewise.
(source->output-path, maybe-guile->guile): Remove.
* guix/build-system/dub.scm (dub-build): Likewise.
* guix/build-system/emacs.scm (emacs-build): Likewise.
* guix/build-system/go.scm (go-build): Likewise.
* guix/build-system/haskell.scm (haskell-build): Likewise.
* guix/build-system/julia.scm (julia-build): Likewise.
* guix/build-system/linux-module.scm (linux-module-build)
(linux-module-build-cross): Likewise.
* guix/build-system/maven.scm (maven-build): Likewise.
* guix/build-system/minify.scm (minify-build): Likewise.
* guix/build-system/node.scm (node-build): Likewise.
* guix/build-system/qt.scm (qt-build, qt-cross-build): Likewise.
* guix/build-system/r.scm (r-build): Likewise.
* guix/build-system/rakudo.scm (rakudo-build): Likewise.
* guix/build-system/renpy.scm (renpy-build): Likewise.
* tests/builders.scm ("gnu-build"): Call 'store-lower' on 'gnu-build'.
Pass #:source parameter.
* tests/packages.scm ("search paths"): Use 'abort-to-prompt' instead of
a normal return from the 'build' method.
("package->bag, sensitivity to %current-target-system"): Change 'build'
to match the new build system signature.
squash! build-system: Rewrite using gexps.
squash! build-system: Rewrite using gexps.
2021-03-30 22:48:43 +02:00
0a79b24506
import: cran: Update the Bioconductor version to 3.12.
...
* guix/import/cran.scm (%bioconductor-version): Set to 3.12.
* guix/build-system/r.scm (bioconductor-uri): Update to 3.12.
2020-12-09 12:12:19 +01:00
b032d14ebd
build-system/r: bioconductor-uri: Fix archive URL.
...
* guix/build-system/r.scm (bioconductor-uri): Fix archive URL.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2020-06-30 00:18:27 +02:00
8e518d4802
guix: Update to Bioconductor 3.11.
...
* guix/build-system/r.scm (bioconductor-uri): Use new URL.
* guix/import/cran.scm (%bioconductor-version): Update to 3.11.
2020-06-13 01:19:38 +02:00
f431d5e299
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.
2019-12-15 15:38:51 +01:00
74e7465c9b
Revert "build-system/r: Use %bioconductor-version."
...
This reverts commit 41ca406fa5
2019-09-16 14:34:15 +03:00
41ca406fa5
build-system/r: Use %bioconductor-version.
...
* guix/build-system/r.scm (bioconductor-uri): Use %bioconductor-version
instead of hard-coding the version string.
2019-09-16 12:26:25 +02:00
c586f427b4
build-system/r: bioconductor-uri: Take optional package type.
...
* guix/build-system/r.scm (bioconductor-uri): Take optional TYPE argument to
return annotation or experiment URLs.
2019-08-16 15:07:22 +02:00
6490cd31cc
guix: Update to Bioconductor 3.9.
...
* guix/build-system/r.scm (bioconductor-uri): Use 3.9 archive URL.
* guix/import/cran.scm (%bioconductor-version): Update to 3.9.
2019-05-06 00:14:27 +02:00
9da4848632
guix: Update to Bioconductor 3.8.
...
* guix/import/cran.scm (%bioconductor-version): Update to 3.8.
* guix/build-system/r.scm (bioconductor-uri): Update archive URL.
2018-11-06 18:21:24 +01:00
32eb44240d
build-system/r: Accept #:r argument.
...
* guix/build-system/r.scm (lower): Add #:r to private-keywords.
2018-06-18 13:51:28 +02:00
0ebef06dbe
build-system/r: Update to Bioconductor 3.7.
...
This is a follow-up to 41f17554d8
2018-06-05 09:58:52 +02:00
25e51b1c45
guix: Add archive support for bioconductor-uri.
...
* guix/build-system/r.scm (bioconductor-uri): Also return the archive URL.
* guix/import/cran.scm (latest-bioconductor-release, fetch-description):
Adjust because bioconductor-uri now returns a list.
2017-11-07 08:14:09 +01:00
5713bbf157
Use HTTPS for bioconductor.org.
...
* doc/guix.texi (Invoking guix import, Invoking guix refresh): Use HTTPS for
bioconductor.org URLs.
* gnu/packages/bioinformatics.scm (r-annotate, r-geneplotter, r-genefilter)
(r-deseq2, r-dexseq, r-annotationforge, r-rbgl, r-gseabase, r-category)
(r-gostats, r-shortread, r-biocgenerics, r-biocinstaller, r-biocviews)
(r-biocstyle, r-bioccheck, r-s4vectors, r-iranges, r-genomeinfodbdata)
(r-genomeinfodb, r-xvector, r-genomicranges, r-biobase, r-annotationdbi)
(r-biomart, r-biocparallel, r-biostrings, r-rsamtools, r-delayedarray)
(r-summarizedexperiment, r-genomicalignments, r-rtracklayer)
(r-genomicfeatures, r-graph, r-topgo, r-bsgenome, r-impute, r-seqpattern)
(r-seqlogo, r-motifrg, r-bamsignals, r-mutationalpatterns, r-tximport)
(r-rhdf5, r-chipseq, r-sva, r-affy, r-vsn, r-mzid, r-msnid)
(r-interactivedisplaybase, r-annotationhub)[home-page]: Likewise.
* gnu/packages/bioinformatics.scm (r-txdb-hsapiens-ucsc-hg19-knowngene)
(r-go-db, r-bsgenome-hsapiens-1000genomes-hs37d5, r-org-hs-eg-db)
(r-org-ce-eg-db, r-org-dm-eg-db, r-org-mm-eg-db)
(r-bsgenome-hsapiens-ucsc-hg19, r-bsgenome-mmusculus-ucsc-mm9)
(r-bsgenome-mmusculus-ucsc-mm10, r-txdb-mmusculus-ucsc-mm10-knowngene)
(r-bsgenome-celegans-ucsc-ce6, r-bsgenome-celegans-ucsc-ce10)
(r-bsgenome-dmelanogaster-ucsc-dm3, r-copyhelper)[source, home-page]:
Likewise.
* gnu/packages/statistics.scm (r-rcurl)[source]: Likewise.
* guix/build-system/r.scm (bioconductor-uri): Likewise.
* guix/import/cran.scm (%cran-url, bioconductor-package?)
(bioconductor-data-package?, bioconductor-experiment-package?): Likewise.
2017-10-21 17:43:40 +02:00
2d7c4ae3ee
gnu: r: Rename to r-minimal.
...
* gnu/packages/statistics.scm (r): Rename to...
(r-minimal): ...this new variable.
(r-with-recommended-packages): Rename to...
(r): ...this.
* guix/build-system/r.scm (default-r): Reference r-minimal.
* gnu/packages/emacs.scm (emacs-ess)[inputs],
gnu/packages/machine-learning.scm (shogun)[inputs],
gnu/packages/python.scm (python-rpy2)[inputs],
gnu/packages/bioinformatics.scm (ribotaper)[inputs],
(couger)[propagated-inputs],
(roary)[inputs],
(rsem)[inputs],
(rcas-web)[inputs]: Change "r" to "r-minimal".
2017-03-17 10:14:02 +01:00
cb6ce89e21
build-system/r: Support "substitutable?" flag.
...
* guix/build-system/r.scm (r-build): Support the "substitutable?" flag.
2016-03-31 15:47:19 +02:00
12d38e8d43
build: Add bioconductor-uri procedure.
...
* guix/build-system/r.scm (bioconductor-uri): New procedure.
2015-12-21 22:32:01 +01:00
5546114e73
build: Add cran-uri procedure.
...
* guix/build-system/r.scm (cran-uri): New procedure.
2015-09-21 10:48:26 +02:00
f8f3bef6aa
build: Add R build system.
...
* guix/build-system/r.scm: New file.
* guix/build/r-build-system: New file.
* Makefile.am (MODULES): Add new files.
* doc/guix.texi (Build Systems): Document r-build-system.
2015-08-31 15:39:34 +02:00
Ricardo Wurmus
Ludovic Courtès
zimoun
Efraim Flashner
Marius Bakke
Roel Janssen
Tobias Geerinckx-Rice
Ricardo Wurmus