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2017-03-16gnu: Add r-seurat.Raoul Jean Pierre Bonnal
* gnu/packages/bioinformatics.scm (r-seurat): New variable. Co-authored-by: Ricardo Wurmus <rekado@elephly.net>
2017-03-16gnu: sra-tools: Update to 2.8.2-1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (sra-tools): Update to 2.8.2-1. [arguments]: Add DEFAULT_CRT and DEFAULT_KFG to make flags.
2017-03-16gnu: ncbi-vdb: Install configuration files.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (ncbi-vdb)[arguments]: Add phase "install-configuration-files".
2017-03-16gnu: ncbi-vdb: Override search path for java-ngs.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (ncbi-vdb)[arguments]: Patch "package.prl" to ensure that java-ngs is found by the configure script; remove configure flag "--with-ngs-java-prefix".
2017-03-16gnu: ncbi-vdb: Use modify-phases syntax.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (ncbi-vdb)[arguments]: Use modify-phases syntax.
2017-03-16gnu: ncbi-vdb: Update to 2.8.2.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (ncbi-vdb): Update to 2.8.2.
2017-03-16gnu: ngs-sdk: Update to 1.3.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (ngs-sdk): Update to 1.3.0.
2017-03-16gnu: Add pzstd.Tobias Geerinckx-Rice
* gnu/packages/compression.scm (pzstd): New variable.
2017-03-16gnu: Add zstd.Tobias Geerinckx-Rice
* gnu/packages/compression.scm (zstd): New variable.
2017-03-16gnu: python-publicsuffix2: Update to 2.20160818.Tobias Geerinckx-Rice
* gnu/packages/python.scm (python-publicsuffix2): Update to 2.20160818.
2017-03-16gnu: awscli: Update to 1.11.63.Tobias Geerinckx-Rice
* gnu/packages/python.scm (awscli): Update to 1.11.63.
2017-03-16gnu: python-botocore: Update to 1.5.26.Tobias Geerinckx-Rice
* gnu/packages/python.scm (python-botocore): Update to 1.5.26.
2017-03-16gnu: python-ptyprocess: Update to 0.5.1.Tobias Geerinckx-Rice
* gnu/packages/python.scm (python-ptyprocess): Update to 0.5.1.
2017-03-15gnu: Add prboom-plus.Kei Kebreau
* gnu/packages/games.scm (prboom-plus): New variable.
2017-03-15gnu: Add tftp-hpa.Gábor Boskovits
* gnu/packages/networking.scm (tftp-hpa): New variable. Signed-off-by: Leo Famulari <leo@famulari.name>
2017-03-15gnu: guile-next: Update to 2.2.0.Andy Wingo
* gnu/packages/guile.scm (guile-next): Update to 2.2.0.
2017-03-15gnu: profanity: Make the source URL version-agnostic.Leo Famulari
* gnu/packages/messaging.scm (profanity)[source]: Use (version) in the source URL.
2017-03-15gnu: units: Update to 2.14.Tobias Geerinckx-Rice
* gnu/packages/maths.scm (units): Update to 2.14.
2017-03-15gnu: no-more-secrets: Update to 0.3.2.Tobias Geerinckx-Rice
* gnu/packages/games.scm (no-more-secrets): Update to 0.3.2.
2017-03-15gnu: mailutils: Update to 3.2.Tobias Geerinckx-Rice
* gnu/packages/mail.scm (mailutils): Update to 3.2.
2017-03-15gnu: Use INSTALL-FILE where appropriate.Tobias Geerinckx-Rice
* gnu/packages/admin.scm (wpa-supplicant-minimal): Substitute the simpler INSTALL-FILE for COPY-FILE when invoked with redundant arguments. * gnu/packages/bioinformatics.scm (couger, aragorn, express-beta-diversity, edirect, fasttree, rsem, samtools-0.1): Likewise. * gnu/packages/code.scm (withershins): Likewise. * gnu/packages/conky.scm (conky): Likewise. * gnu/packages/debug.scm (delta, american-fuzzy-lop): Likewise. * gnu/packages/emacs.scm (emacs-mit-scheme-doc): Likewise. * gnu/packages/engineering.scm (librecad): Likewise.
2017-03-15gnu: cryptsetup: Update to 1.7.4.Tobias Geerinckx-Rice
* gnu/packages/cryptsetup.scm (cryptsetup): Update to 1.7.4.
2017-03-15gnu: man-pages: Update to 4.10.Tobias Geerinckx-Rice
* gnu/packages/man.scm (man-pages): Update to 4.10. [home-page]: Use HTTPS.
2017-03-15gnu: Add profanity.Mekeor Melire
* gnu/packages/messaging.scm (profanity): New variable. Signed-off-by: Leo Famulari <leo@famulari.name>
2017-03-15gnu: Add libstrophe.Mekeor Melire
* gnu/packages/messaging.scm (libstrophe): New variable. Signed-off-by: Leo Famulari <leo@famulari.name>
2017-03-15gnu: Add libmesode.Mekeor Melire
* gnu/packages/messaging.scm (libmesode): New variable. Signed-off-by: Leo Famulari <leo@famulari.name>
2017-03-15gnu: bitcoin-core: Update to 0.14.0.Leo Famulari
* gnu/packages/finance.scm (bitcoin-core): Update to 0.14.0.
2017-03-15build: Prefer Guile 2.2 over 2.0.Ludovic Courtès
* configure.ac: In 'GUILE_PKG', prefer 2.2 over 2.0. Remove warning about 2.2 not being fully supported. * doc/guix.texi (Requirements): Mention Guile 2.2.x.
2017-03-15tests: Expect less accurate location info in 2.2.0.Ludovic Courtès
* tests/guix-system.sh: Work around inaccurate location info in 2.2.0.
2017-03-15store: Adjust UTF-8 test to Guile 2.2.Ludovic Courtès
* tests/store.scm ("current-build-output-port, UTF-8 + garbage"): On Guile 2.2, expect REPLACEMENT CHARACTER instead of '?'.
2017-03-15syscalls: Adjust 'clone' to Guile 2.2.Ludovic Courtès
Before that, something like: (call-with-container (lambda () (match (primitive-fork) …))) would hang in 'primitive-fork' as the child process (the one started in the container) would try to pthread_join the finalization thread in 'stop_finalization_thread' in libguile, not knowing that this thread is nonexistent. * guix/build/syscalls.scm (%set-automatic-finalization-enabled?!): New procedure. (without-automatic-finalization): New macro. (clone): Wrap PROC call in 'without-automatic-finalization'.
2017-03-15zlib: Don't rely on EBADF being ignored by 'fport_close'.Ludovic Courtès
In 2.2, 'fport_close' no longer swallows EBADF and instead raises a 'system-error' for this. This commit adjusts for 2.2. * guix/zlib.scm (close-procedure): Remove. (make-gzip-input-port): Use 'port->fdes' instead of 'fileno'. Use 'gzclose' instead of 'close-procedure'. (make-gzip-output-port): Likewise. * tests/zlib.scm ("compression/decompression pipe"): Don't check whether PARENT is closed using 'port-closed?'. Instead, use 'seek' on the underlying FD and check for EBADF.
2017-03-15maint: Mention guix-patches@gnu.org in 'HACKING'.Ludovic Courtès
Fixes <http://bugs.gnu.org/25899>. * HACKING: Mention guix-patches@gnu.org.
2017-03-15gnu: mariadb: Update to 10.1.22 [fixes CVE-2017-3302 and CVE-2017-3313].Marius Bakke
* gnu/packages/databases.scm (mariadb): Update to 10.1.22.
2017-03-15gnu: python-waf: Update to 1.9.8.Efraim Flashner
* gnu/packages/python.scm (python-waf, python2-waf): Update to 1.9.8. [home-page]: Use https.
2017-03-15gnu: direnv: Update to 2.11.3.Tobias Geerinckx-Rice
* gnu/packages/shellutils.scm (direnv): Update to 2.11.3.
2017-03-15gnu: conky: Update to 1.10.6.Tobias Geerinckx-Rice
* gnu/packages/conky.scm (conky): Update to 1.10.6.
2017-03-15gnu: obs: Update to 18.0.1.Tobias Geerinckx-Rice
* gnu/packages/video.scm (obs): Update to 18.0.1.
2017-03-15gnu: youtube-dl: Update to 2017.03.15.Tobias Geerinckx-Rice
* gnu/packages/video.scm (youtube-dl): Update to 2017.03.15.
2017-03-15gnu: stress-make: Fix description.Tobias Geerinckx-Rice
* gnu/packages/debug.scm (stress-make)[description]: Fix typo. Avoid ambiguous use of ‘in order’.
2017-03-15gnu: znc: Update to 1.6.5.Tobias Geerinckx-Rice
* gnu/packages/messaging.scm (znc): Update to 1.6.5.
2017-03-15gnu: grue-hunter: Correctly install documentation.Tobias Geerinckx-Rice
* gnu/packages/games.scm (grue-hunter)[arguments]: Install and populate ‘/share/doc/grue-hunter’ as a directory, not a plain file.
2017-03-15gnu: samtools: End installation phases with truth.Tobias Geerinckx-Rice
* gnu/packages/bioinformatics.scm (samtools, samtools-0.1)[arguments]: Return #T instead of the undefined results of COPY-FILE or INSTALL-FILE.
2017-03-14gnu: w3m: Update to 0.5.3+git20170102 [security fixes].Leo Famulari
See 'NEWS' and 'ChangeLog' in the source distribution for more information about the security-related bug fixes. * gnu/packages/w3m.scm (w3m): Update to 0.5.3+git20170102.
2017-03-14Revert "gnu: gitolite: Fix shebangs in hooks."Leo Famulari
This change embedded store references in the shebangs of scripts that were meant to be copied out of the store. Those scripts would break when the interpreters expected by the shebangs were garbage collected. <https://debbugs.gnu.org/cgi/bugreport.cgi?bug=25966#28> This reverts commit d0c16adb190c7244ee3ef1329cba78a015ae5d10.
2017-03-14pack: Add unit test.Ludovic Courtès
* guix/scripts/pack.scm (self-contained-tarball): Add #:tar option. [build](tar-supports-sort?): New variable. Use it. * tests/pack.scm: New file. * Makefile.am (SCM_TESTS): Add it.
2017-03-14pack: Use maximum compression; use '-n' for gzip.Ludovic Courtès
* guix/scripts/pack.scm (<compressor>)[tar-option]: Remove. [command]: New field. (%compressors): Provide complete commands. Use '-9' or equivalent for each compressor; use '-n' for gzip. (self-contained-tarball)[build]: Adjust accordingly.
2017-03-14Revert "gnu: nss: Use 'modify-phases' syntax."Marius Bakke
This reverts commit 87f1c7efc18f8996b0b2817a5f7b84eebe2ddf5a.
2017-03-14Revert "gnu: nss, nss-certs: Update to 3.29.3."Marius Bakke
Hydra failed to build this version. See discussion at https://lists.gnu.org/archive/html/guix-devel/2017-03/msg00408.html. This reverts commit 4f3dcdd99ba13ab3bdbf1e014afcd076cd95fac7.
2017-03-14gnu: Add ocaml-ppx-typerep-conv.Julien Lepiller
* gnu/packages/ocaml.scm (ocaml-ppx-typerep-conv): New variable.
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