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* guix: Add archive support for bioconductor-uri.Ricardo Wurmus2017-11-07
| | | | | | * 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.
* import: cran: Use Bioconductor 3.6 helpers.Ricardo Wurmus2017-11-07
| | | | | | | * guix/import/cran.scm (bioconductor-mirror-url): Remove procedure. (fetch-description): Extract DESCRIPTION file from tarball for Bioconductor packages. (latest-bioconductor-release): Use latest-bioconductor-package-version.
* import: cran: Add support for Bioconductor 3.6.Ricardo Wurmus2017-11-07
| | | | | | | * guix/import/cran.scm (%bioconductor-version, %bioconductor-packages-list-url): New variables. (bioconductor-packages-list, latest-bioconductor-package-version): New procedures.
* Use HTTPS for bioconductor.org.Tobias Geerinckx-Rice2017-10-21
| | | | | | | | | | | | | | | | | | | | | | | | | | | | * 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.
* import cran: Generate a valid 'license' field for "GPL".Ludovic Courtès2017-06-26
| | | | | | | Fixes <http://bugs.gnu.org/27294>. Reported by Joshua Sierles <joshua@joshua.si>. * guix/import/cran.scm (string->license) <"GPL">: Return a quoted list.
* import cran: Check if pkg-config is needed.Ricardo Wurmus2017-05-16
| | | | | * guix/import/cran.scm (needs-pkg-config?): New procedure. (description->package): Use it.
* import cran: Refactor "needs-zlib?".Ricardo Wurmus2017-05-16
| | | | | * guix/import/cran.scm (tarball-files-match-pattern?): New procedure. (needs-zlib?): Implement in terms of "tarball-files-match-pattern?".
* import cran: Export package predicates.Ricardo Wurmus2017-05-16
| | | | | | * guix/import/cran.scm (cran-package?, bioconductor-package?, bioconductor-data-package?, bioconductor-experiment-package?): Export procedures.
* import cran: Add predicate for Bioconductor experiment packages.Ricardo Wurmus2017-05-16
| | | | * guix/import/cran.scm (bioconductor-experiment-package?): New variable.
* import cran: Exclude experiment packages in predicate "bioconductor-package?".Ricardo Wurmus2017-05-16
| | | | | * guix/import/cran.scm (bioconductor-package?): Exclude experiment packages, because they cannot be updated with the default bioconductor updater.
* import cran: Fetch DESCRIPTION files from Github mirror.Ricardo Wurmus2017-05-16
| | | | | | | | | * 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.
* import: cran: Robustify cran-package?.Mathieu Othacehe2017-05-13
| | | | | | | | | | | | * 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.
* import: Update Bioconductor release to 3.5.Roel Janssen2017-04-28
| | | | * guix/import/cran.scm: Change Bioconductor release to 3.5.
* import cran: Distinguish Bioconductor data packages.Ricardo Wurmus2017-04-05
| | | | | | * guix/import/cran.scm (bioconductor-package?): Exclude Bioconductor data packages. (bioconductor-data-package?): New procedure.
* Replace (compose not PROC) with simpler idioms.Ludovic Courtès2017-03-28
| | | | | | | | * 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) ...)'.
* import cran: Automatically add gfortran and zlib when needed.Ricardo Wurmus2017-03-28
| | | | | * guix/import/cran.scm (needs-fortran?, needs-zlib?): New procedures. (description->package): Use them.
* gnu: r: Do not build recommended packages.Ricardo Wurmus2017-03-17
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * 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.
* Add (guix memoization).Ludovic Courtès2017-01-28
| | | | | | | | | | | | | * 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.
* import cran: Handle HTTP errors.Ricardo Wurmus2016-12-17
| | | | | | | Fixes <http://bugs.gnu.org/23479>. * guix/import/cran.scm (fetch-description): Return #f in case of HTTP errors.
* import cran: Add recursive importer.Ricardo Wurmus2016-12-17
| | | | | * guix/import/cran.scm (recursive-import): New variable. (cran->guix-package): Memoize the procedure.
* import cran: Ignore default R packages.Ricardo Wurmus2016-12-17
| | | | | * guix/import/cran.scm (default-r-packages): New variable. (description->package): Drop default R packages from list of inputs.
* import cran: description->package: Also return package dependencies.Ricardo Wurmus2016-12-17
| | | | | * guix/import/cran.scm (description->package): Return package dependencies in addition to generated package expression.
* import cran: Move guix-name to top-level.Ricardo Wurmus2016-12-17
| | | | * guix/import/cran.scm (guix-name): Move to top-level.
* import cran: Remove more invalid characters from package names.Ricardo Wurmus2016-12-17
| | | | | * guix/import/cran.scm (guix-name): Replace period and underscore with dash; always prepend package names with "r-".
* import cran: Handle BSD licenses with LICENSE file.Ricardo Wurmus2016-12-17
| | | | | * guix/import/cran.scm (string->license): Add cases for BSD licenses with LICENSE file.
* import cran: Translate MIT to the Expat license.Ricardo Wurmus2016-12-17
| | | | | * guix/import/cran.scm (string->license): Translate "MIT" license to Expat license.
* import cran: Do not use "or later" licenses by default.Ricardo Wurmus2016-12-17
| | | | * guix/import/cran.scm (string->license): Use exact license versions.
* import: cran: Fix off-by-one error.Ricardo Wurmus2016-11-03
| | | | | * guix/import/cran.scm (package->upstream-name): Do not include leading slash in upstream name URL.
* import cran: Use URL for Bioconductor 3.4.Ricardo Wurmus2016-10-26
| | | | | * guix/import/cran.scm (%bioconductor-svn-url): Update to release URL for version 3.4.
* import cran: latest-bioconductor-release: Wrap Bioconductor URL in list.Ricardo Wurmus2016-05-16
| | | | | * guix/import/cran.scm (latest-bioconductor-release): Wrap Bioconductor URL in list in the "urls" field of the "upstream-source" value.
* import cran: Use URL for Bioconductor 3.3.Ricardo Wurmus2016-05-16
| | | | | * guix/import/cran.scm (%bioconductor-svn-url): Update to release URL for version 3.3.
* upstream: Pass a package object to updaters.Ludovic Courtès2016-04-15
| | | | | | | | | | | | | | * 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.
* import: cran: Accept single URL in addition to single URL.Ricardo Wurmus2016-03-22
| | | | | * guix/import/cran.scm (package->upstream-name): Match single URL in addition to list of URLs.
* import: Add Bioconductor importer and updater.Ricardo Wurmus2016-01-20
| | | | | | | | | | | | | | | | | * 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.
* import: cran: Move beautify-description to utils module.Ben Woodcroft2016-01-14
| | | | | * guix/import/cran.scm (beautify-description): Move from here... * guix/import/utils.scm: ... to here.
* import: Rename "cran-fetch" to "fetch-description".Ricardo Wurmus2016-01-07
| | | | | * guix/import/cran.scm (cran-fetch): Rename procedure ... (fetch-description): ... to this.
* import: Add package->upstream-name procedure.Ricardo Wurmus2016-01-07
| | | | * guix/import/cran.scm (package->upstream-name): New procedure.
* import: Drop empty list items.Ricardo Wurmus2015-12-21
| | | | * guix/import/cran.scm (listify): Remove empty strings from result list.
* import: cran: Parse DESCRIPTION instead of HTML.Ricardo Wurmus2015-12-11
| | | | | | | | | * 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.
* import: cran: Match more license strings.Ricardo Wurmus2015-12-11
| | | | | * guix/import/cran.scm (string->license): Match more license strings to license symbols.
* upstream: Add 'description' field to 'upstream-updater'.Alex Kost2015-10-27
| | | | | | | | | | | | | 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.
* import: cran: Add copyright notice.Ludovic Courtès2015-10-21
| | | | Add notice for commit d882c23.
* import: cran: Avoid HTTP redirect.Ludovic Courtès2015-10-21
| | | | | * guix/import/cran.scm (cran-fetch): Add trailing slash in URL to avoid HTTP redirect.
* import: cran: Add updater.Ludovic Courtès2015-10-21
| | | | | | | | | * 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.
* import: cran-sxml->sexp: Use cran-uri in package expression.Ricardo Wurmus2015-09-21
| | | | | * guix/import/cran.scm (cran-sxml->sexp): Use the cran-uri procedure in the generated package expression.
* import: Add 'cran' importer.Ricardo Wurmus2015-08-31
* 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'.
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