| Age | Commit message (Expand) | Author |
|---|
| 2017-10-21 | 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.
| Tobias Geerinckx-Rice |
| 2017-06-26 | import cran: Generate a valid 'license' field for "GPL"....Fixes <http://bugs.gnu.org/27294>.
Reported by Joshua Sierles <joshua@joshua.si>.
* guix/import/cran.scm (string->license) <"GPL">: Return a quoted list.
| Ludovic Courtès |
| 2017-05-16 | import cran: Check if pkg-config is needed....* guix/import/cran.scm (needs-pkg-config?): New procedure.
(description->package): Use it.
| Ricardo Wurmus |
| 2017-05-16 | import cran: Refactor "needs-zlib?"....* guix/import/cran.scm (tarball-files-match-pattern?): New procedure.
(needs-zlib?): Implement in terms of "tarball-files-match-pattern?".
| Ricardo Wurmus |
| 2017-05-16 | import cran: Export package predicates....* guix/import/cran.scm (cran-package?, bioconductor-package?,
bioconductor-data-package?, bioconductor-experiment-package?): Export
procedures.
| Ricardo Wurmus |
| 2017-05-16 | import cran: Add predicate for Bioconductor experiment packages....* guix/import/cran.scm (bioconductor-experiment-package?): New variable.
| Ricardo Wurmus |
| 2017-05-16 | import cran: Exclude experiment packages in predicate "bioconductor-package?"....* guix/import/cran.scm (bioconductor-package?): Exclude experiment packages,
because they cannot be updated with the default bioconductor updater.
| Ricardo Wurmus |
| 2017-05-16 | import cran: Fetch DESCRIPTION files from Github mirror....* guix/import/cran.scm (%bioconductor-svn-url): Remove variable.
(bioconductor-mirror-url): New procedure.
(fetch-description): Take a REPOSITORY symbol instead of a BASE-URL string.
(cran->guix-package): Pass REPOSITORY symbol to "fetch-description".
(latest-cran-release, latest-bioconductor-release): Adjust accordingly.
(bioconductor-package?): Update comment about SVN.
| Ricardo Wurmus |
| 2017-05-13 | import: cran: Robustify cran-package?....* guix/import/cran.scm (package->upstream-name): Return #f if url
start and end index could not be determined.
(cran-package?): Check if the upstream-name can be extracted from
given package.
* tests/cran.scm: Add "r-minimal is not a cran package" to make sure that
r-minimal is not detected as a cran package.
This fixes a failure of guix refresh on r-minimal because no
upsteam-name can be determined from ".../R-version.tar.gz" uri.
| Mathieu Othacehe |
| 2017-04-28 | import: Update Bioconductor release to 3.5....* guix/import/cran.scm: Change Bioconductor release to 3.5.
| Roel Janssen |
| 2017-04-05 | import cran: Distinguish Bioconductor data packages....* guix/import/cran.scm (bioconductor-package?): Exclude Bioconductor
data packages.
(bioconductor-data-package?): New procedure.
| Ricardo Wurmus |
| 2017-03-28 | Replace (compose not PROC) with simpler idioms....* gnu/packages/bioinformatics.scm (python-pysam)[arguments] <check>:
Use (negate proc) instead of (compose not proc).
* guix/import/cran.scm (recursive-import): Likewise.
* guix/import/elpa.scm (filter-dependencies): Use 'remove' instead of
'(filter (compose not proc) ...)'.
| Ludovic Courtès |
| 2017-03-28 | import cran: Automatically add gfortran and zlib when needed....* guix/import/cran.scm (needs-fortran?, needs-zlib?): New procedures.
(description->package): Use them.
| Ricardo Wurmus |
| 2017-03-17 | gnu: r: Do not build recommended packages....* gnu/packages/statistics.scm (r)[arguments]: Rename phase
"build-recommended-packages-reproducibly" to "build-reproducibly"; add
configure flag "--without-recommended-packages".
* guix/import/cran.scm (default-r-packages): Remove recommended packages.
* gnu/packages/python.scm (python-rpy2)[inputs]: Add r-survival.
* gnu/packages/bioinformatics.scm (r-ape)[propagated-inputs]: Add r-lattice
and r-nlme.
(r-vegan)[propagated-inputs]: Add r-mass.
(r-genefilter)[propagated-inputs]: Add r-survival.
(r-grohmm)[propagated-inputs]: Add r-mass.
(r-bioccheck)[propagated-inputs]: Add r-codetools.
(r-summarizedexperiment)[propagated-inputs]: Add r-matrix.
(r-topgo)[propagated-inputs]: Add r-lattice.
(r-sva)[propagated-inputs]: Add r-mgcv.
(r-raremetals2)[propagated-inputs]: Add r-mass.
(r-vsn)[propagated-inputs]: Add r-lattice.
(r-pcamethods)[propagated-inputs]: Add r-mass.
* gnu/packages/bioinformatics.scm (r-ggplot2)[propagated-inputs]: Add r-mass.
(r-locfit)[propagated-inputs]: Add r-lattice.
(r-coda)[propagated-inputs]: Add r-lattice.
(r-irlba)[propagated-inputs]: Add r-matrix.
(r-glmnet)[propagated-inputs]: Add r-matrix.
(r-e1071)[propagated-inputs]: Add r-class.
(r-spams)[propagated-inputs]: Add r-lattice and r-matrix.
(r-hmisc)[propagated-inputs]: Add r-cluster, r-foreign, r-lattice, r-nnet, and
r-rpart.
(r-zoo)[propagated-inputs]: Add r-lattice.
(r-mixtools)[propagated-inputs]: Add r-boot and r-mass.
(r-flexmix)[propagated-inputs]: Add r-lattice and r-nnet.
(r-prabclus)[propagated-inputs]: Add r-mass.
(r-fpc)[propagated-inputs]: Add r-class, r-cluster, and r-mass.
(r-rcppeigen)[propagated-inputs]: Add r-matrix.
(r-matrixmodels)[propagated-inputs]: Add r-matrix.
(r-lme4)[propagated-inputs]: Add r-mass and r-nlme.
(r-pbkrtest)[propagated-inputs]: Add r-mass and r-matrix.
(r-car)[propagated-inputs]: Add r-mass, r-mgcv, and r-nnet.
(r-tclust)[propagated-inputs]: Add r-cluster.
| Ricardo Wurmus |
| 2017-01-28 | Add (guix memoization)....* guix/combinators.scm (memoize): Remove.
* guix/memoization.scm: New file.
* Makefile.am (MODULES): Add it.
* gnu/packages.scm, gnu/packages/bootstrap.scm,
guix/build-system/gnu.scm, guix/build-system/python.scm,
guix/derivations.scm, guix/gnu-maintenance.scm,
guix/import/cran.scm, guix/import/elpa.scm,
guix/modules.scm, guix/scripts/build.scm,
guix/scripts/graph.scm, guix/scripts/lint.scm,
guix/store.scm, guix/utils.scm: Adjust imports accordingly.
| Ludovic Courtès |
| 2016-12-17 | import cran: Handle HTTP errors....Fixes <http://bugs.gnu.org/23479>.
* guix/import/cran.scm (fetch-description): Return #f in case of HTTP
errors.
| Ricardo Wurmus |
| 2016-12-17 | import cran: Add recursive importer....* guix/import/cran.scm (recursive-import): New variable.
(cran->guix-package): Memoize the procedure.
| Ricardo Wurmus |
| 2016-12-17 | import cran: Ignore default R packages....* guix/import/cran.scm (default-r-packages): New variable.
(description->package): Drop default R packages from list of inputs.
| Ricardo Wurmus |
| 2016-12-17 | import cran: description->package: Also return package dependencies....* guix/import/cran.scm (description->package): Return package
dependencies in addition to generated package expression.
| Ricardo Wurmus |
| 2016-12-17 | import cran: Move guix-name to top-level....* guix/import/cran.scm (guix-name): Move to top-level.
| Ricardo Wurmus |
| 2016-12-17 | import cran: Remove more invalid characters from package names....* guix/import/cran.scm (guix-name): Replace period and underscore with
dash; always prepend package names with "r-".
| Ricardo Wurmus |
| 2016-12-17 | import cran: Handle BSD licenses with LICENSE file....* guix/import/cran.scm (string->license): Add cases for BSD licenses
with LICENSE file.
| Ricardo Wurmus |
| 2016-12-17 | import cran: Translate MIT to the Expat license....* guix/import/cran.scm (string->license): Translate "MIT" license to
Expat license.
| Ricardo Wurmus |
| 2016-12-17 | import cran: Do not use "or later" licenses by default....* guix/import/cran.scm (string->license): Use exact license versions.
| Ricardo Wurmus |
| 2016-11-03 | import: cran: Fix off-by-one error....* guix/import/cran.scm (package->upstream-name): Do not include leading
slash in upstream name URL.
| Ricardo Wurmus |
| 2016-10-26 | import cran: Use URL for Bioconductor 3.4....* guix/import/cran.scm (%bioconductor-svn-url): Update to release URL
for version 3.4.
| Ricardo Wurmus |
| 2016-05-16 | import cran: latest-bioconductor-release: Wrap Bioconductor URL in list....* guix/import/cran.scm (latest-bioconductor-release): Wrap Bioconductor
URL in list in the "urls" field of the "upstream-source" value.
| Ricardo Wurmus |
| 2016-05-16 | import cran: Use URL for Bioconductor 3.3....* guix/import/cran.scm (%bioconductor-svn-url): Update to release URL
for version 3.3.
| Ricardo Wurmus |
| 2016-04-15 | upstream: Pass a package object to updaters....* guix/upstream.scm (package-update-path): Pass PACKAGE to
'latest-release'.
* guix/gnu-maintenance.scm (latest-release*)
(latest-gnome-release, latest-xorg-release): Adjust accordingly.
* guix/import/cran.scm (latest-cran-release):
(latest-bioconductor-release): Likewise.
* guix/import/elpa.scm (latest-release): Likewise.
* guix/import/gem.scm (latest-release): Likewise.
* guix/import/github.scm (latest-release): Likewise.
* guix/import/hackage.scm (latest-release): Likewise.
* guix/import/pypi.scm (latest-release): Likewise.
| Ludovic Courtès |
| 2016-03-22 | import: cran: Accept single URL in addition to single URL....* guix/import/cran.scm (package->upstream-name): Match single URL in
addition to list of URLs.
| Ricardo Wurmus |
| 2016-01-20 | import: Add Bioconductor importer and updater....* guix/import/cran.scm (%bioconductor-updater,
latest-bioconductor-release, bioconductor-package?): New procedures.
(cran->guix-package): Support repositories other than CRAN.
(%bioconductor-url, %bioconductor-svn-url): New variables.
(description->package): Update signature to distinguish between packages
from different repositories.
(latest-release): Rename procedure ...
(latest-cran-release): ... to this.
(cran-package?): Do not assume all R packages are available on CRAN.
* tests/cran.scm: Update tests.
* guix/scripts/import/cran.scm: Add "--archive" option and default to
CRAN.
* guix/scripts/refresh.scm (%updaters): Add "%bioconductor-updater".
* doc/guix.texi: Document Bioconductor importer and updater.
| Ricardo Wurmus |
| 2016-01-14 | import: cran: Move beautify-description to utils module....* guix/import/cran.scm (beautify-description): Move from here...
* guix/import/utils.scm: ... to here.
| Ben Woodcroft |
| 2016-01-07 | import: Rename "cran-fetch" to "fetch-description"....* guix/import/cran.scm (cran-fetch): Rename procedure ...
(fetch-description): ... to this.
| Ricardo Wurmus |
| 2016-01-07 | import: Add package->upstream-name procedure....* guix/import/cran.scm (package->upstream-name): New procedure.
| Ricardo Wurmus |
| 2015-12-21 | import: Drop empty list items....* guix/import/cran.scm (listify): Remove empty strings from result list.
| Ricardo Wurmus |
| 2015-12-11 | import: cran: Parse DESCRIPTION instead of HTML....* guix/import/cran.scm (description->alist, listify,
beautify-description, description->package): New procedures.
(table-datum, downloads->url, nodes->text, cran-sxml->sexp): Remove
proceduces.
(latest-release): Use parsed DESCRIPTION instead of SXML.
* tests/cran.scm: Rewrite to match importer.
| Ricardo Wurmus |
| 2015-12-11 | import: cran: Match more license strings....* guix/import/cran.scm (string->license): Match more license strings to
license symbols.
| Ricardo Wurmus |
| 2015-10-27 | upstream: Add 'description' field to 'upstream-updater'....Suggested by Ludovic Courtès <ludo@gnu.org>.
* guix/upstream.scm (<upstream-updater>): Use 'define-record-type*'.
[description]: New field.
(lookup-updater): Adjust accordingly.
* guix/gnu-maintenance.scm (%gnu-updater): Likewise.
* guix/import/cran.scm (%cran-updater): Likewise.
* guix/import/elpa.scm (%elpa-updater): Likewise.
* po/guix/POTFILES.in: Add guix/scripts/import/cran.scm and
guix/gnu-maintenance.scm.
| Alex Kost |
| 2015-10-21 | import: cran: Add copyright notice....Add notice for commit d882c23.
| Ludovic Courtès |
| 2015-10-21 | import: cran: Avoid HTTP redirect....* guix/import/cran.scm (cran-fetch): Add trailing slash in URL to avoid
HTTP redirect.
| Ludovic Courtès |
| 2015-10-21 | import: cran: Add updater....* guix/import/cran.scm (downloads->url, nodes->text): New procedures.
(cran-sxml->sexp): Use them. Remove equivalent local code.
(latest-release, cran-package?): New procedures.
(%cran-updater): New variable.
* guix/scripts/refresh.scm (%updaters): Add %CRAN-UPDATER.
* doc/guix.texi (Invoking guix refresh): Mention CRAN.
| Ludovic Courtès |
| 2015-09-21 | import: cran-sxml->sexp: Use cran-uri in package expression....* guix/import/cran.scm (cran-sxml->sexp): Use the cran-uri procedure in
the generated package expression.
| Ricardo Wurmus |
| 2015-08-31 | import: Add 'cran' importer....* guix/import/cran.scm: New file.
* guix/scripts/import.scm: Add "cran" to 'importers'.
* guix/scripts/import/cran.scm: New file.
* tests/cran.scm: New file.
* Makefile.am (MODULES): Add 'guix/import/cran.scm' and
'guix/scripts/import/cran.scm'.
(SCM_TESTS): Add 'tests/cran.scm'.
* doc/guix.texi (Invoking guix import): Document it.
* po/guix/POTFILES.in: Add 'guix/scripts/import/cran.scm'.
| Ricardo Wurmus |
