* 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.
* guix/monad-repl.scm (store-monad-language): Add 'store' parameter and
use it. Remove call to 'open-connection'.
(enter-store-monad): Use 'with-store' and pass the store to
'store-monad-language.
The .gem file stored in GEM_HOME after install is both redundant and an
archive that stores timestamped files which makes builds
non-deterministic, so delete it after 'gem install'.
* guix/build/ruby-build-system.scm (install): Remove cached gem after
install.
* guix/scripts/package.scm (find-packages-by-description): Change 'rx'
parameter to 'regexps'.
[matches-all?, matches-one?]: New procedures.
Use them.
(process-query): Collect regexps from all 'search' queries, and pass
them to 'find-packages-by-description'.
* tests/guix-package.sh: Add tests.
* doc/guix.texi (Invoking guix package): Document it.
Previously, the 'git checkout' invocation would remove sub-modules that
had been initialized by 'git clone --recursive'.
* guix/build/git.scm (git-fetch): Never use "git clone --recursive".
Invoke "git submodule update --init --recursive" after "git checkout".
Remove '.git' directories as the last step.
Before that it would include #f for most origins since that the default
value of 'origin-patch-guile'.
* guix/scripts/graph.scm (bag-node-edges): When 'origin-patch-guile'
returns #f, use (default-guile).
* tests/graph.scm ("bag DAG, including origins"): Check for an edge from
O to (default-guile).
Fixes <http://bugs.gnu.org/22280>.
Reported by Leo Famulari <leo@famulari.name>.
* guix/scripts/graph.scm (%bag-emerged-node-type)[edges]: Mimic
%BAG-NODE-TYPE. This is a followup to 38b92da.
* guix/packages.scm (package-transitive-native-search-paths): New
procedure.
* tests/packages.scm ("package-transitive-native-search-paths"): New
test.
Reported by Efraim Flashner <efraim@flashner.co.il>
at <https://lists.gnu.org/archive/html/guix-devel/2015-12/msg00202.html>.
* guix/gnu-maintenance.scm (latest-ftp-release): Call KEEP-FILE? on
directories too.
(latest-gnome-release)[even-minor-version?]: Protect again MINOR being
false; change pattern to match VERSION with two or more numbers. Remove
use of 'version-major+minor'.
[even-numbered-tarball?]: Rename to...
[even-numbered?]: ... this. Use 'package-name->name+version'. When
VERSION is #f, check NAME.
* guix/derivations.scm (substitution-oracle): Add #:mode parameter and
honor it.
(derivation-prerequisites-to-build): Likewise.
[derivation-built?]: Take it into account.
* guix/ui.scm (show-what-to-build): Add #:mode parameter. Pass it to
'substitute-oracle' and 'derivations-prerequisites-to-build'.
* tests/derivations.scm ("derivation-prerequisites-to-build in 'check'
mode"): New test.
Suggested by Efraim Flashner <efraim@flashner.co.il>.
* guix/gnu-maintenance.scm (latest-ftp-release): Add #:keep-file?
parameter and honor it.
(latest-gnome-release)[%not-dot]: New variable.
[even-minor-version?, even-numbered-tarball?]: New procedures.
Pass EVEN-NUMBERED-TARBALL? as #:keep-file? argument.
* guix/gnu-maintenance.scm (latest-ftp-release): Add #:file->signature
parameter. Honor it.
(latest-gnome-release): Pass #:file->signature.
* guix/upstream.scm (coalesce-sources): Keep 'signature-urls' as #f
unless both sources provide it.
Eric Bavier