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2017-03-28Replace (compose not PROC) with simpler idioms.Ludovic Courtès
* 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) ...)'.
2017-03-28import cran: Automatically add gfortran and zlib when needed.Ricardo Wurmus
* guix/import/cran.scm (needs-fortran?, needs-zlib?): New procedures. (description->package): Use them.
2017-03-17gnu: r: Do not build recommended packages.Ricardo Wurmus
* 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.
2017-01-28Add (guix memoization).Ludovic Courtès
* 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.
2016-12-17import cran: Handle HTTP errors.Ricardo Wurmus
Fixes <http://bugs.gnu.org/23479>. * guix/import/cran.scm (fetch-description): Return #f in case of HTTP errors.
2016-12-17import cran: Add recursive importer.Ricardo Wurmus
* guix/import/cran.scm (recursive-import): New variable. (cran->guix-package): Memoize the procedure.
2016-12-17import cran: Ignore default R packages.Ricardo Wurmus
* guix/import/cran.scm (default-r-packages): New variable. (description->package): Drop default R packages from list of inputs.
2016-12-17import cran: description->package: Also return package dependencies.Ricardo Wurmus
* guix/import/cran.scm (description->package): Return package dependencies in addition to generated package expression.
2016-12-17import cran: Move guix-name to top-level.Ricardo Wurmus
* guix/import/cran.scm (guix-name): Move to top-level.
2016-12-17import cran: Remove more invalid characters from package names.Ricardo Wurmus
* guix/import/cran.scm (guix-name): Replace period and underscore with dash; always prepend package names with "r-".
2016-12-17import cran: Handle BSD licenses with LICENSE file.Ricardo Wurmus
* guix/import/cran.scm (string->license): Add cases for BSD licenses with LICENSE file.
2016-12-17import cran: Translate MIT to the Expat license.Ricardo Wurmus
* guix/import/cran.scm (string->license): Translate "MIT" license to Expat license.
2016-12-17import cran: Do not use "or later" licenses by default.Ricardo Wurmus
* guix/import/cran.scm (string->license): Use exact license versions.
2016-11-03import: cran: Fix off-by-one error.Ricardo Wurmus
* guix/import/cran.scm (package->upstream-name): Do not include leading slash in upstream name URL.
2016-10-26import cran: Use URL for Bioconductor 3.4.Ricardo Wurmus
* guix/import/cran.scm (%bioconductor-svn-url): Update to release URL for version 3.4.
2016-05-16import cran: latest-bioconductor-release: Wrap Bioconductor URL in list.Ricardo Wurmus
* guix/import/cran.scm (latest-bioconductor-release): Wrap Bioconductor URL in list in the "urls" field of the "upstream-source" value.
2016-05-16import cran: Use URL for Bioconductor 3.3.Ricardo Wurmus
* guix/import/cran.scm (%bioconductor-svn-url): Update to release URL for version 3.3.
2016-04-15upstream: Pass a package object to updaters.Ludovic Courtès
* 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.
2016-03-22import: cran: Accept single URL in addition to single URL.Ricardo Wurmus
* guix/import/cran.scm (package->upstream-name): Match single URL in addition to list of URLs.
2016-01-20import: Add Bioconductor importer and updater.Ricardo Wurmus
* 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.
2016-01-14import: cran: Move beautify-description to utils module.Ben Woodcroft
* guix/import/cran.scm (beautify-description): Move from here... * guix/import/utils.scm: ... to here.
2016-01-07import: Rename "cran-fetch" to "fetch-description".Ricardo Wurmus
* guix/import/cran.scm (cran-fetch): Rename procedure ... (fetch-description): ... to this.
2016-01-07import: Add package->upstream-name procedure.Ricardo Wurmus
* guix/import/cran.scm (package->upstream-name): New procedure.
2015-12-21import: Drop empty list items.Ricardo Wurmus
* guix/import/cran.scm (listify): Remove empty strings from result list.
2015-12-11import: cran: Parse DESCRIPTION instead of HTML.Ricardo Wurmus
* 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.
2015-12-11import: cran: Match more license strings.Ricardo Wurmus
* guix/import/cran.scm (string->license): Match more license strings to license symbols.
2015-10-27upstream: Add 'description' field to 'upstream-updater'.Alex Kost
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.
2015-10-21import: cran: Add copyright notice.Ludovic Courtès
Add notice for commit d882c23.
2015-10-21import: cran: Avoid HTTP redirect.Ludovic Courtès
* guix/import/cran.scm (cran-fetch): Add trailing slash in URL to avoid HTTP redirect.
2015-10-21import: cran: Add updater.Ludovic Courtès
* 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.
2015-09-21import: cran-sxml->sexp: Use cran-uri in package expression.Ricardo Wurmus
* guix/import/cran.scm (cran-sxml->sexp): Use the cran-uri procedure in the generated package expression.
2015-08-31import: Add 'cran' importer.Ricardo Wurmus
* 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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