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82 Commits

Author SHA1 Message Date
Ricardo Wurmus
e8a968f89d
import/cran: Add more invalid package names to ignore. 
* guix/import/cran.scm (invalid-packages): Add more names.
 2021-01-20 17:18:59 +01:00
Ricardo Wurmus
5f5e3873d7
import/cran: Add input style "specification". 
* guix/import/cran.scm (%input-style): New parameter.
(format-inputs): Use it.
* guix/scripts/import/cran.scm (guix-import-cran): Set the %input-style
parameter.
 (%options): Add "--style" option.
* doc/guix.texi (Invoking guix import): Document it.
 2020-12-22 14:18:34 +01:00
Lars-Dominik Braun
f14bb29def
import: cran: Use CRAN’s canonical URL as home-page. 
* guix/import/cran.scm (%cran-canonical-url): New variable.
(description->package): Construct home-page using canonical URL.

Signed-off-by: Christopher Baines <mail@cbaines.net>
 2020-12-15 22:34:30 +00:00
Ricardo Wurmus
482b8ae2cd
import/cran: Abort with error message when recursive import fails. 
Previously, after a failed recursive import "guix import" would signal
success.

* guix/import/cran.scm (cran->guix-package): Raise a condition when all
repositories have been exhausted.
* guix/scripts/import/cran.scm (guix-import-cran): Handle errors.
 2020-12-12 00:08:27 +01:00
Roel Janssen
0a79b24506
import: cran: Update the Bioconductor version to 3.12. 
* guix/import/cran.scm (%bioconductor-version): Set to 3.12.
* guix/build-system/r.scm (bioconductor-uri):  Update to 3.12.
 2020-12-09 12:12:19 +01:00
Ricardo Wurmus
a689c85af4
import/cran: Fix calls to CRAN->GUIX-PACKAGE. 
* guix/import/cran.scm (cran->guix-package, latest-bioconductor-release):
Invoke CRAN->GUIX-PACKAGE with #:REPO keyword argument.
 2020-12-04 12:27:29 +01:00
Martin Becze
bea3b17739
import: utils: 'recursive-import' accepts an optional version parameter. 
This adds a key VERSION to 'recursive-import' and moves the parameter REPO to
a key. This also changes all the places that rely on 'recursive-import'.

* guix/import/utils.scm (recursive-import): Add the VERSION key. Make REPO a
  key.
  (package->definition): Add optional 'append-version?'.
* guix/scripts/import/crate.scm (guix-import-crate): Add the VERSION key.
* guix/import/crate.scm (crate->guix-package): Add the VERSION key.
  (crate-recursive-import): Pass VERSION to recursive-import, remove now
  unnecessary code.
* guix/import/cran.scm (cran->guix-package, cran-recursive-import): Change the
  REPO parameter to a key.
* guix/import/elpa.scm (elpa->guix-package, elpa-recursive-import): Likewise.
* guix/import/gem.scm (gem->guix-package, recursive-import): Likewise.
* guix/import/opam.scm (opam-recurive-import): Likewise.
* guix/import/pypi.scm (pypi-recursive-import): Likewise.
* guix/import/stackage.scm (stackage-recursive-import): Likewise.
* guix/scripts/import/cran.scm (guix-import-cran): Likewise.
* guix/scripts/import/elpa.scm (guix-import-elpa): Likewise.
* tests/elpa.scm (eval-test-with-elpa): Likewise.
* tests/import-utils.scm (recursive-import): Likewise.

Co-authored-by: Hartmut Goebel <h.goebel@crazy-compilers.com>
 2020-12-02 22:09:23 +01:00
Ludovic Courtès
00290e7365
upstream: Define 'url-predicate' and use it. 
* guix/upstream.scm (url-predicate): New procedure.
(url-prefix-predicate): Define in terms of 'url-predicate'.
* guix/import/cpan.scm (cpan-package?): Use 'url-predicate'.
* guix/import/cran.scm (cran-package?)
(bioconductor-package?)
(bioconductor-data-package?)
(bioconductor-experiment-package?): Likewise.
* guix/import/crate.scm (crate-package?): Likewise.
* guix/import/elpa.scm (package-from-gnu.org?): Likewise.
* guix/import/hackage.scm (hackage-package?): Likewise.
* guix/import/pypi.scm (pypi-package?): Likewise.
* guix/import/gem.scm (gem-package?): Use 'url-prefix-predicate'.
 2020-07-03 23:53:31 +02:00
Ricardo Wurmus
8e518d4802
guix: Update to Bioconductor 3.11. 
* guix/build-system/r.scm (bioconductor-uri): Use new URL.
* guix/import/cran.scm (%bioconductor-version): Update to 3.11.
 2020-06-13 01:19:38 +02:00
pimi
daf9fa94e2
guix: cran: Add missing default R package. 
* guix/import/cran.scm (default-r-packages): Add "datasets" to the list of
default R packages.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2020-05-13 14:02:58 +02:00
Ricardo Wurmus
9e17989017
import/cran: Import missing module. 
This is a follow-up to commit b005c240bb.

Reported-by: Ludovic Courtès <ludo@gnu.org>

* guix/import/cran.scm: Import (guix ui) module.
 2020-03-25 16:28:57 +01:00
Ricardo Wurmus
b005c240bb
import/cran: Support importing from Mercurial repositories. 
* guix/import/cran.scm (download): Accept keyword #:method; add case for hg
method.
(fetch-description): Handle hg repository.
(description->package): Add cases for hg repositories and update call of
DOWNLOAD procedure.
(cran->guix-package): Retry importing from Bioconductor when hg import failed.
 2020-03-25 09:40:05 +01:00
Ricardo Wurmus
c363722e81
import/cran: Add vignette builder to native inputs. 
* guix/import/cran.scm (needs-knitr?): New procedure.
(description->package): Use it.
 2020-03-07 19:31:47 +01:00
Ludovic Courtès
cfd1ed8401
import: cran: Avoid uses of '@@' in the tests. 
* guix/import/cran.scm (description->alist, description->package): Export.
<top level>: Set! 'listify'.
* tests/cran.scm (description-alist, "description->package"): Remove use
of '@@' to access the relevant bindings.
 2020-01-16 23:14:05 +01:00
Ludovic Courtès
af0aefd8c1
import: cran: Fix file descriptor leak. 
Fixes <https://bugs.gnu.org/38836>.
Reported by Ricardo Wurmus <rekado@elephly.net>.

* guix/import/cran.scm (bioconductor-packages-list): Close the port
returned by 'http-fetch/cached'.
(fetch-description): Likewise.
 2020-01-03 16:06:26 +01:00
Ricardo Wurmus
f431d5e299
guix: Upgrade to Bioconductor 3.10. 
* guix/build-system/r.scm (bioconductor-uri): Switch to version 3.10.
* guix/import/cran.scm (%bioconductor-version): Same.
 2019-12-15 15:38:51 +01:00
Ricardo Wurmus
e31ec53ed8
import: cran: Recognize LGPL 2.1+. 
* guix/import/cran.scm (string->license): Add case for lgpl2.1+.
 2019-12-14 13:35:58 +01:00
Ludovic Courtès
ddd5915900
import: utils: 'recursive-import' returns packages in topological order. 
* guix/import/utils.scm (topological-sort): New procedure.
(recursive-import): Rewrite to use it.
* tests/import-utils.scm ("recursive-import"): New test.
* guix/import/cran.scm (cran->guix-package): Always return two values.
* guix/scripts/import/cran.scm (guix-import-cran): Remove 'reverse' call
on 'cran-recursive-import' result.
* guix/scripts/import/crate.scm (guix-import-crate): Likewise.
* guix/scripts/import/elpa.scm (guix-import-elpa): Likewise.
* guix/scripts/import/gem.scm (guix-import-gem): Likewise.
* guix/scripts/import/hackage.scm (guix-import-hackage): Likewise.
* guix/scripts/import/opam.scm (guix-import-opam): Likewise.
* guix/scripts/import/pypi.scm (guix-import-pypi): Likewise.
* guix/scripts/import/stackage.scm (guix-import-stackage): Likewise.
* tests/gem.scm ("gem-recursive-import"): Change the order of package
expressions accordingly.
 2019-12-11 12:12:58 +01:00
Ricardo Wurmus
76c0b60821
import/cran: Export %bioconductor-version. 
* guix/import/cran.scm (%bioconductor-version): Export it.
 2019-09-16 12:26:25 +02:00
Ricardo Wurmus
8786fec485
import: cran: Only use the git import with what looks like a URL. 
* guix/import/cran.scm (fetch-description): Abort if the argument does not
look like a URL.
 2019-09-02 14:46:04 +02:00
Ricardo Wurmus
c7358ac4fc
import: cran: Retry failed git imports on Bioconductor. 
* guix/import/cran.scm (cran->guix-package): Retry failed git imports on
Bioconductor.
 2019-09-02 14:45:17 +02:00
Ricardo Wurmus
ad553ec4b1
import: cran: Add support for git repositories. 
* guix/import/cran.scm (vcs-file?): New procedure.
(download): Support downloading from git.
(fetch-description): Add a clause for the 'git repository type.
(files-match-pattern?): New procedure.
(tarball-files-match-pattern?): Implement in terms of FILES-MATCH-PATTERN?.
(directory-needs-fortran?, directory-needs-zlib?,
directory-needs-pkg-config?): New procedures.
(needs-fortran?, needs-zlib?, needs-pkg-config?): Rename these procedures...
(tarball-needs-fortran?, tarball-needs-zlib?, tarball-needs-pkg-config?):
...to this, and use them.
(file-hash): New procedure.
(description->package): Handle the 'git repository type.
* guix/import/utils.scm (package->definition): Handle package expression
inside of a let.
* guix/scripts/import.scm (guix-import): Handle let expressions.
* doc/guix.texi (Invoking guix import): Document it.
 2019-08-29 11:38:12 +02:00
Ricardo Wurmus
5063deab08
import: cran: Support experiment and annotation packages. 
* guix/import/cran.scm (%bioconductor-packages-list-url): Replace variable...
(bioconductor-packages-list-url): ...with this procedure.
(bioconductor-packages-list): Accept optional TYPE argument.
(latest-bioconductor-package-version): Same.
(fetch-description): Determine package type and use it in calls to
LATEST-BIOCONDUCTOR-PACKAGE-VERSION and BIOCONDUCTOR-URI.
(description->package): Pass package type to URI helper procedure; include
package type in annotation or experiment packages from Bioconducter.
 2019-08-16 15:07:22 +02:00
Ricardo Wurmus
531940d388
import: cran: Ignore invalid packages from the system requirements. 
* guix/import/cran.scm (description->package): Filter invalid packages from
the list of system requirements.
 2019-05-28 23:56:59 +02:00
Ricardo Wurmus
e96619baf7
import: cran: Ignore invalid packages. 
* guix/import/cran.scm (invalid-packages): New variable.
(description->package): Use it.
 2019-05-23 16:10:32 +02:00
Ricardo Wurmus
6490cd31cc
guix: Update to Bioconductor 3.9. 
* guix/build-system/r.scm (bioconductor-uri): Use 3.9 archive URL.
* guix/import/cran.scm (%bioconductor-version): Update to 3.9.
 2019-05-06 00:14:27 +02:00
Ricardo Wurmus
91e05559bd
import: cran: Suggest input changes. 
* guix/import/cran.scm (latest-cran-release, latest-bioconductor-release):
Return input-changes.
 2019-01-12 23:35:11 +01:00
Ricardo Wurmus
2a13642b65
import: cran: Default to 'cran repo. 
* guix/import/cran.scm (cran-recursive-import): Default to 'cran repo.
 2019-01-03 08:34:41 +01:00
Ricardo Wurmus
7bb6420c5a
import: cran: Abort if no description could be fetched. 
* guix/import/cran.scm (cran->guix-package): Only proceed if a valid
description could be fetched.
 2019-01-03 08:34:41 +01:00
Ricardo Wurmus
632ea817b8
import: cran: Use HTTPS. 
* guix/import/cran.scm (%cran-url): Use HTTPS.
 2019-01-03 08:34:41 +01:00
Ricardo Wurmus
b3d0617a55
import: cran: Download tarballs only once. 
* guix/import/cran.scm (download): New procedure.
(fetch-description, description->package): Use it.
 2019-01-03 08:34:41 +01:00
Ricardo Wurmus
10a1cacb16
import: cran: Try import via CRAN if package is not on Bioconductor. 
* guix/import/cran.scm (fetch-description): Return #F on failure.
(cran->guix-package): Retry from CRAN on failure to fetch description from
bioconductor.
 2018-12-20 09:42:22 +01:00
Ricardo Wurmus
9da4848632
guix: Update to Bioconductor 3.8. 
* guix/import/cran.scm (%bioconductor-version): Update to 3.8.
* guix/build-system/r.scm (bioconductor-uri): Update archive URL.
 2018-11-06 18:21:24 +01:00
Ludovic Courtès
ca71942445
Switch to Guile-Gcrypt. 
This removes (guix hash) and (guix pk-crypto), which now live as part of
Guile-Gcrypt (version 0.1.0.)

* guix/gcrypt.scm, guix/hash.scm, guix/pk-crypto.scm,
tests/hash.scm, tests/pk-crypto.scm: Remove.
* configure.ac: Test for Guile-Gcrypt.  Remove LIBGCRYPT and
LIBGCRYPT_LIBDIR assignments.
* m4/guix.m4 (GUIX_ASSERT_LIBGCRYPT_USABLE): Remove.
* README: Add Guile-Gcrypt to the dependencies; move libgcrypt as
"required unless --disable-daemon".
* doc/guix.texi (Requirements): Likewise.
* gnu/packages/bash.scm, guix/derivations.scm, guix/docker.scm,
guix/git.scm, guix/http-client.scm, guix/import/cpan.scm,
guix/import/cran.scm, guix/import/crate.scm, guix/import/elpa.scm,
guix/import/gnu.scm, guix/import/hackage.scm,
guix/import/texlive.scm, guix/import/utils.scm, guix/nar.scm,
guix/pki.scm, guix/scripts/archive.scm,
guix/scripts/authenticate.scm, guix/scripts/download.scm,
guix/scripts/hash.scm, guix/scripts/pack.scm,
guix/scripts/publish.scm, guix/scripts/refresh.scm,
guix/scripts/substitute.scm, guix/store.scm,
guix/store/deduplication.scm, guix/tests.scm, tests/base32.scm,
tests/builders.scm, tests/challenge.scm, tests/cpan.scm,
tests/crate.scm, tests/derivations.scm, tests/gem.scm,
tests/nar.scm, tests/opam.scm, tests/pki.scm,
tests/publish.scm, tests/pypi.scm, tests/store-deduplication.scm,
tests/store.scm, tests/substitute.scm: Adjust imports.
* gnu/system/vm.scm: Likewise.
(guile-sqlite3&co): Rename to...
(gcrypt-sqlite3&co): ... this.  Add GUILE-GCRYPT.
(expression->derivation-in-linux-vm)[config]: Remove.
(iso9660-image)[config]: Remove.
(qemu-image)[config]: Remove.
(system-docker-image)[config]: Remove.
* guix/scripts/pack.scm: Adjust imports.
(guile-sqlite3&co): Rename to...
(gcrypt-sqlite3&co): ... this.  Add GUILE-GCRYPT.
(self-contained-tarball)[build]: Call 'make-config.scm' without
 #:libgcrypt argument.
(squashfs-image)[libgcrypt]: Remove.
[build]: Call 'make-config.scm' without #:libgcrypt.
(docker-image)[config, json]: Remove.
[build]: Add GUILE-GCRYPT to the extensions  Remove (guix config) from
the imported modules.
* guix/self.scm (specification->package): Remove "libgcrypt", add
"guile-gcrypt".
(compiled-guix): Remove #:libgcrypt.
[guile-gcrypt]: New variable.
[dependencies]: Add it.
[*core-modules*]: Remove #:libgcrypt from 'make-config.scm' call.
Add #:extensions.
[*config*]: Remove #:libgcrypt from 'make-config.scm' call.
(%dependency-variables): Remove %libgcrypt.
(make-config.scm): Remove #:libgcrypt.
* build-aux/build-self.scm (guile-gcrypt): New variable.
(make-config.scm): Remove #:libgcrypt.
(build-program)[fake-gcrypt-hash]: New variable.
Add (gcrypt hash) to the imported modules.  Adjust load path
assignments.
* gnu/packages/package-management.scm (guix)[propagated-inputs]: Add
GUILE-GCRYPT.
[arguments]: In 'wrap-program' phase, add GUILE-GCRYPT to the search
path.
 2018-09-04 17:25:11 +02:00
Oleg Pykhalov
ae9e5d6602
import: utils: Add recursive-import. 
* guix/import/cran.scm (cran-guix-name, cran-recursive-import): New
procedures.
(recursive-import): Remove procedure.
* guix/import/utils.scm (guix-name, recursive-import): New procedures.
* guix/scripts/import/cran.scm (guix-import-cran): Use
'cran-recursive-import' procedure.
 2018-06-08 14:58:33 +03:00
Ricardo Wurmus
41f17554d8
import: cran: Update to Bioconductor 3.7. 
* guix/import/cran.scm (%bioconductor-version): Update to 3.7.
 2018-06-02 13:39:13 +02:00
Ricardo Wurmus
25e51b1c45
guix: Add archive support for bioconductor-uri. 
* 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.
 2017-11-07 08:14:09 +01:00
Ricardo Wurmus
27baf50956
import: cran: Use Bioconductor 3.6 helpers. 
* 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.
 2017-11-07 08:13:35 +01:00
Ricardo Wurmus
84dfdc5759
import: cran: Add support for Bioconductor 3.6. 
* guix/import/cran.scm (%bioconductor-version,
%bioconductor-packages-list-url): New variables.
(bioconductor-packages-list, latest-bioconductor-package-version): New
procedures.
 2017-11-07 08:13:34 +01:00
Tobias Geerinckx-Rice
5713bbf157
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.
 2017-10-21 17:43:40 +02:00
Ludovic Courtès
94a400beba
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.
 2017-06-26 22:52:06 +02:00
Ricardo Wurmus
17a69cf623
import cran: Check if pkg-config is needed. 
* guix/import/cran.scm (needs-pkg-config?): New procedure.
(description->package): Use it.
 2017-05-16 21:43:35 +02:00
Ricardo Wurmus
a0f43208cb
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?".
 2017-05-16 21:43:15 +02:00
Ricardo Wurmus
ff8c179ab6
import cran: Export package predicates. 
* guix/import/cran.scm (cran-package?, bioconductor-package?,
bioconductor-data-package?, bioconductor-experiment-package?): Export
procedures.
 2017-05-16 21:42:18 +02:00
Ricardo Wurmus
daaa270ecc
import cran: Add predicate for Bioconductor experiment packages. 
* guix/import/cran.scm (bioconductor-experiment-package?): New variable.
 2017-05-16 21:40:39 +02:00
Ricardo Wurmus
c9ffa91fd3
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.
 2017-05-16 21:40:03 +02:00
Ricardo Wurmus
7c9fcb0825
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.
 2017-05-16 21:39:06 +02:00
Mathieu Othacehe
db427602d8
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.
 2017-05-13 12:40:20 +02:00
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