guix-patches - Patches for guix

	Commit message (Collapse)	Author	Age
*	guix: Upgrade to Bioconductor 3.10.	Ricardo Wurmus	2019-12-15
\| \| \| \| \|	* guix/build-system/r.scm (bioconductor-uri): Switch to version 3.10. * guix/import/cran.scm (%bioconductor-version): Same.
*	Revert "build-system/r: Use %bioconductor-version."	Efraim Flashner	2019-09-16
\| \| \| \| \| \|	This reverts commit 41ca406fa54e69f61c55b11ffe5cf465192a907c. This commit breaks 'guix pull', as reported by Hao Chen.
*	build-system/r: Use %bioconductor-version.	Ricardo Wurmus	2019-09-16
\| \| \| \| \|	* guix/build-system/r.scm (bioconductor-uri): Use %bioconductor-version instead of hard-coding the version string.
*	build-system/r: bioconductor-uri: Take optional package type.	Ricardo Wurmus	2019-08-16
\| \| \| \| \|	* guix/build-system/r.scm (bioconductor-uri): Take optional TYPE argument to return annotation or experiment URLs.
*	guix: Update to Bioconductor 3.9.	Ricardo Wurmus	2019-05-06
\| \| \| \| \|	* guix/build-system/r.scm (bioconductor-uri): Use 3.9 archive URL. * guix/import/cran.scm (%bioconductor-version): Update to 3.9.
*	guix: Update to Bioconductor 3.8.	Ricardo Wurmus	2018-11-06
\| \| \| \| \|	* guix/import/cran.scm (%bioconductor-version): Update to 3.8. * guix/build-system/r.scm (bioconductor-uri): Update archive URL.
*	build-system/r: Accept #:r argument.	Ricardo Wurmus	2018-06-18
\| \| \| \|	* guix/build-system/r.scm (lower): Add #:r to private-keywords.
*	build-system/r: Update to Bioconductor 3.7.	Ricardo Wurmus	2018-06-05
\| \| \| \| \| \|	This is a follow-up to 41f17554d88795bf35fbfc3e05301a6d2f64cca0. * guix/build-system/r.scm (bioconductor-uri): Update to version 3.7.
*	guix: Add archive support for bioconductor-uri.	Ricardo Wurmus	2017-11-07
\| \| \| \| \| \|	* 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.
*	Use HTTPS for bioconductor.org.	Tobias Geerinckx-Rice	2017-10-21
\| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \|	* 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.
*	gnu: r: Rename to r-minimal.	Ricardo Wurmus	2017-03-17
\| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \|	* 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".
*	build-system/r: Support "substitutable?" flag.	Ricardo Wurmus	2016-03-31
\| \| \| \|	* guix/build-system/r.scm (r-build): Support the "substitutable?" flag.
*	build: Add bioconductor-uri procedure.	Ricardo Wurmus	2015-12-21
\| \| \| \|	* guix/build-system/r.scm (bioconductor-uri): New procedure.
*	build: Add cran-uri procedure.	Ricardo Wurmus	2015-09-21
\| \| \| \|	* guix/build-system/r.scm (cran-uri): New procedure.
*	build: Add R build system.	Ricardo Wurmus	2015-08-31
	* 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.