kreyren/guix-kreyren
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34 Commits

Author SHA1 Message Date
Roel Janssen
7c3e4660a5
import: Update Bioconductor release to 3.5. 
* guix/import/cran.scm: Change Bioconductor release to 3.5.
 2017-04-28 11:02:26 +02:00
Ricardo Wurmus
5ae63362ae
import cran: Distinguish Bioconductor data packages. 
* guix/import/cran.scm (bioconductor-package?): Exclude Bioconductor
data packages.
(bioconductor-data-package?): New procedure.
 2017-04-05 18:38:51 +02:00
Ludovic Courtès
e1f02f92e9
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) ...)'.
 2017-03-28 22:15:44 +02:00
Ricardo Wurmus
2dca8b2d51
import cran: Automatically add gfortran and zlib when needed. 
* guix/import/cran.scm (needs-fortran?, needs-zlib?): New procedures.
(description->package): Use them.
 2017-03-28 15:37:47 +02:00
Ricardo Wurmus
aeb64f3cb2
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.
 2017-03-17 10:14:02 +01:00
Ludovic Courtès
f9704f179a
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.
 2017-01-28 18:55:20 +01:00
Ricardo Wurmus
fdbc84b056
import cran: Handle HTTP errors. 
Fixes <http://bugs.gnu.org/23479>.

* guix/import/cran.scm (fetch-description): Return #f in case of HTTP
errors.
 2016-12-17 19:13:42 +01:00
Ricardo Wurmus
94e907b962
import cran: Add recursive importer. 
* guix/import/cran.scm (recursive-import): New variable.
(cran->guix-package): Memoize the procedure.
 2016-12-17 19:12:55 +01:00
Ricardo Wurmus
b26abe4f14
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.
 2016-12-17 15:56:48 +01:00
Ricardo Wurmus
ad68f7fa58
import cran: description->package: Also return package dependencies. 
* guix/import/cran.scm (description->package): Return package
  dependencies in addition to generated package expression.
 2016-12-17 15:56:48 +01:00
Ricardo Wurmus
bfa0c752bc
import cran: Move guix-name to top-level. 
* guix/import/cran.scm (guix-name): Move to top-level.
 2016-12-17 15:56:48 +01:00
Ricardo Wurmus
2e5f32ce1b
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-".
 2016-12-17 15:56:47 +01:00
Ricardo Wurmus
576eda6d02
import cran: Handle BSD licenses with LICENSE file. 
* guix/import/cran.scm (string->license): Add cases for BSD licenses
with LICENSE file.
 2016-12-17 15:56:47 +01:00
Ricardo Wurmus
741d68c20d
import cran: Translate MIT to the Expat license. 
* guix/import/cran.scm (string->license): Translate "MIT" license to
Expat license.
 2016-12-17 15:56:47 +01:00
Ricardo Wurmus
13f54d081b
import cran: Do not use "or later" licenses by default. 
* guix/import/cran.scm (string->license): Use exact license versions.
 2016-12-17 15:56:39 +01:00
Ricardo Wurmus
e3100110ce
import: cran: Fix off-by-one error. 
* guix/import/cran.scm (package->upstream-name): Do not include leading
slash in upstream name URL.
 2016-11-03 16:03:28 +01:00
Ricardo Wurmus
a98470b5be
import cran: Use URL for Bioconductor 3.4. 
* guix/import/cran.scm (%bioconductor-svn-url): Update to release URL
for version 3.4.
 2016-10-26 09:28:06 +02:00
Ricardo Wurmus
9916ae15bb
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.
 2016-05-16 21:00:41 +02:00
Ricardo Wurmus
9583e07cae
import cran: Use URL for Bioconductor 3.3. 
* guix/import/cran.scm (%bioconductor-svn-url): Update to release URL
  for version 3.3.
 2016-05-16 20:52:46 +02:00
Ludovic Courtès
7d27a0259b 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.
 2016-04-15 00:32:18 +02:00
Ricardo Wurmus
b98293ebed 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.
 2016-03-22 17:57:40 +01:00
Ricardo Wurmus
d0bd632f89 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.
 2016-01-20 12:41:28 +01:00
Ben Woodcroft
2028a2c960 import: cran: Move beautify-description to utils module. 
* guix/import/cran.scm (beautify-description): Move from here...
* guix/import/utils.scm: ... to here.
 2016-01-14 19:44:36 +10:00
Ricardo Wurmus
34a75d35bb import: Rename "cran-fetch" to "fetch-description". 
* guix/import/cran.scm (cran-fetch): Rename procedure ...
(fetch-description): ... to this.
 2016-01-07 17:18:04 +01:00
Ricardo Wurmus
d1c116089b import: Add package->upstream-name procedure. 
* guix/import/cran.scm (package->upstream-name): New procedure.
 2016-01-07 17:18:02 +01:00
Ricardo Wurmus
be036757bd import: Drop empty list items. 
* guix/import/cran.scm (listify): Remove empty strings from result list.
 2015-12-21 15:24:54 +01:00
Ricardo Wurmus
0f6b9e9828 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.
 2015-12-11 15:35:07 +01:00
Ricardo Wurmus
b6a222757b import: cran: Match more license strings. 
* guix/import/cran.scm (string->license): Match more license strings to
  license symbols.
 2015-12-11 15:35:07 +01:00
Alex Kost
7e6b490d04 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.
 2015-10-27 21:54:57 +03:00
Ludovic Courtès
102eac2a0a import: cran: Add copyright notice. 
Add notice for commit d882c23.
 2015-10-21 14:51:30 +02:00
Ludovic Courtès
053cfdb3d6 import: cran: Avoid HTTP redirect. 
* guix/import/cran.scm (cran-fetch): Add trailing slash in URL to avoid
  HTTP redirect.
 2015-10-21 14:44:41 +02:00
Ludovic Courtès
d882c235d9 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.
 2015-10-21 14:44:41 +02:00
Ricardo Wurmus
a52b625152 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.
 2015-09-21 10:48:26 +02:00
Ricardo Wurmus
e1248602f9 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'.
 2015-08-31 15:39:34 +02:00