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20651 Commits

Author SHA1 Message Date
Ricardo Wurmus 701111989e
gnu: ncbi-vdb: Use modify-phases syntax. 
* gnu/packages/bioinformatics.scm (ncbi-vdb)[arguments]: Use modify-phases
syntax.
 2017-03-16 10:20:56 +01:00
Ricardo Wurmus 5021f54787
gnu: ncbi-vdb: Update to 2.8.2. 
* gnu/packages/bioinformatics.scm (ncbi-vdb): Update to 2.8.2.
 2017-03-16 10:19:25 +01:00
Ricardo Wurmus 6c4ccf3228
gnu: ngs-sdk: Update to 1.3.0. 
* gnu/packages/bioinformatics.scm (ngs-sdk): Update to 1.3.0.
 2017-03-16 10:18:48 +01:00
Ricardo Wurmus 56f76b08be
gnu: jack-2: Fix build by patching fast_rand. 
* gnu/packages/audio.scm (jack-2)[arguments]: Add phase "patch-fast_rand" to
apply upstream fixes.
 2017-03-16 09:41:20 +01:00
Leo Famulari 5707ce6e4b
Revert "gnu: bdftopcf: Use libxfont2." 
Building with libxfont2 leads to an error in the configure phase:

"No package 'xfont' found"

This reverts commit 2060b4d95f.
 2017-03-16 02:06:56 -04:00
Tobias Geerinckx-Rice 0f03c53168
gnu: Add pzstd. 
* gnu/packages/compression.scm (pzstd): New variable.
 2017-03-16 05:44:02 +01:00
Tobias Geerinckx-Rice f6ac3101ff
gnu: Add zstd. 
* gnu/packages/compression.scm (zstd): New variable.
 2017-03-16 05:44:02 +01:00
Tobias Geerinckx-Rice 9186216268
gnu: python-publicsuffix2: Update to 2.20160818. 
* gnu/packages/python.scm (python-publicsuffix2): Update to 2.20160818.
 2017-03-16 05:44:02 +01:00
Tobias Geerinckx-Rice 192b887a03
gnu: awscli: Update to 1.11.63. 
* gnu/packages/python.scm (awscli): Update to 1.11.63.
 2017-03-16 05:44:01 +01:00
Tobias Geerinckx-Rice d93985fe22
gnu: python-botocore: Update to 1.5.26. 
* gnu/packages/python.scm (python-botocore): Update to 1.5.26.
 2017-03-16 05:44:01 +01:00
Tobias Geerinckx-Rice 70fc93cb28
gnu: python-ptyprocess: Update to 0.5.1. 
* gnu/packages/python.scm (python-ptyprocess): Update to 0.5.1.
 2017-03-16 05:44:01 +01:00
Kei Kebreau 26a657f06a
gnu: Add prboom-plus. 
* gnu/packages/games.scm (prboom-plus): New variable.
 2017-03-15 23:14:42 -04:00
Gábor Boskovits 5b5cf3c765
gnu: Add tftp-hpa. 
* gnu/packages/networking.scm (tftp-hpa): New variable.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2017-03-15 18:24:30 -04:00
Andy Wingo 80a725726d
gnu: guile-next: Update to 2.2.0. 
* gnu/packages/guile.scm (guile-next): Update to 2.2.0.
 2017-03-15 22:59:40 +01:00
Leo Famulari dce8ac54b4
gnu: profanity: Make the source URL version-agnostic. 
* gnu/packages/messaging.scm (profanity)[source]: Use (version) in the source
URL.
 2017-03-15 17:20:27 -04:00
Tobias Geerinckx-Rice cf8d068775
gnu: units: Update to 2.14. 
* gnu/packages/maths.scm (units): Update to 2.14.
 2017-03-15 22:19:40 +01:00
Tobias Geerinckx-Rice 3d602acb13
gnu: no-more-secrets: Update to 0.3.2. 
* gnu/packages/games.scm (no-more-secrets): Update to 0.3.2.
 2017-03-15 22:19:40 +01:00
Tobias Geerinckx-Rice 7ea523853c
gnu: mailutils: Update to 3.2. 
* gnu/packages/mail.scm (mailutils): Update to 3.2.
 2017-03-15 22:19:40 +01:00
Tobias Geerinckx-Rice f38607536e
gnu: Use INSTALL-FILE where appropriate. 
* 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.
 2017-03-15 22:19:39 +01:00
Tobias Geerinckx-Rice 618e4bfbad
gnu: cryptsetup: Update to 1.7.4. 
* gnu/packages/cryptsetup.scm (cryptsetup): Update to 1.7.4.
 2017-03-15 22:19:39 +01:00
Tobias Geerinckx-Rice 4e128dd582
gnu: man-pages: Update to 4.10. 
* gnu/packages/man.scm (man-pages): Update to 4.10.
[home-page]: Use HTTPS.
 2017-03-15 22:19:38 +01:00
Mekeor Melire a829c6501b
gnu: Add profanity. 
* gnu/packages/messaging.scm (profanity): New variable.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2017-03-15 17:17:06 -04:00
Mekeor Melire 781d3b070c
gnu: Add libstrophe. 
* gnu/packages/messaging.scm (libstrophe): New variable.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2017-03-15 17:17:06 -04:00
Mekeor Melire 13292ee570
gnu: Add libmesode. 
* gnu/packages/messaging.scm (libmesode): New variable.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2017-03-15 17:17:06 -04:00
Leo Famulari 9e61d1534a
gnu: bitcoin-core: Update to 0.14.0. 
* gnu/packages/finance.scm (bitcoin-core): Update to 0.14.0.
 2017-03-15 15:48:43 -04:00
Marius Bakke b8f99f4ae3
gnu: nss, nss-certs: Update to 3.29.3. 
* gnu/packages/gnuzilla.scm (nss): Update to 3.29.3.
* gnu/packages/certs.scm (nss-certs): Update to 3.29.3.
 2017-03-15 17:57:51 +01:00
Marius Bakke d027b0011f
gnu: nss: Increase test timeouts. 
* gnu/packages/patches/nss-increase-test-timeout.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/gnuzilla.scm (nss)[source]: Use it.
 2017-03-15 17:56:05 +01:00
Marius Bakke 1461dd2410
Revert "Revert "gnu: nss: Build for aarch64-linux with 64-bit support."" 
This reverts commit adb984d23c.
 2017-03-15 17:53:27 +01:00
Marius Bakke db3c06d511
gnu: nss: Use 'modify-phases' syntax. 
* gnu/packages/gnuzilla.scm (nss)[arguments]: Use 'modify-phases'.
 2017-03-15 17:53:24 +01:00
Marius Bakke 4b7e5c1131
Merge branch 'master' into core-updates 2017-03-15 17:52:26 +01:00
Marius Bakke adb984d23c
Revert "gnu: nss: Build for aarch64-linux with 64-bit support." 
Temporary revert to fix messy merge conflict!

This reverts commit 568004c3c9.
 2017-03-15 17:51:23 +01:00
Ludovic Courtès 608e42e7c9
build: Prefer Guile 2.2 over 2.0. 
* 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.
 2017-03-15 15:19:54 +01:00
Ludovic Courtès 13159c68ef
tests: Expect less accurate location info in 2.2.0. 
* tests/guix-system.sh: Work around inaccurate location info in 2.2.0.
 2017-03-15 15:19:54 +01:00
Ludovic Courtès a9a0227c01
store: Adjust UTF-8 test to Guile 2.2. 
* tests/store.scm ("current-build-output-port, UTF-8 + garbage"): On
Guile 2.2, expect REPLACEMENT CHARACTER instead of '?'.
 2017-03-15 15:19:53 +01:00
Ludovic Courtès 70dfdd501a
syscalls: Adjust 'clone' to Guile 2.2. 
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'.
 2017-03-15 15:19:53 +01:00
Ludovic Courtès 81a0f1cdf1
zlib: Don't rely on EBADF being ignored by 'fport_close'. 
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.
 2017-03-15 15:19:53 +01:00
Ludovic Courtès bc551cf32b
maint: Mention guix-patches@gnu.org in 'HACKING'. 
Fixes <http://bugs.gnu.org/25899>.

* HACKING: Mention guix-patches@gnu.org.
 2017-03-15 15:19:53 +01:00
Marius Bakke bd102157a1
gnu: mariadb: Update to 10.1.22 [fixes CVE-2017-3302 and CVE-2017-3313]. 
* gnu/packages/databases.scm (mariadb): Update to 10.1.22.
 2017-03-15 15:08:31 +01:00
Efraim Flashner 378640ec37
gnu: qemu-minimal: Add aarch64 to target list. 
* gnu/packages/qemu.scm (qemu-minimal)[arguments]: Add 'aarch64-softmmu'
to the target list.
 2017-03-15 15:58:02 +02:00
Efraim Flashner 27bf00e691
gnu: python-waf: Update to 1.9.8. 
* gnu/packages/python.scm (python-waf, python2-waf): Update to 1.9.8.
[home-page]: Use https.
 2017-03-15 13:08:56 +02:00
Tobias Geerinckx-Rice 283234a309
gnu: direnv: Update to 2.11.3. 
* gnu/packages/shellutils.scm (direnv): Update to 2.11.3.
 2017-03-15 03:45:57 +01:00
Tobias Geerinckx-Rice 68c10f31f9
gnu: conky: Update to 1.10.6. 
* gnu/packages/conky.scm (conky): Update to 1.10.6.
 2017-03-15 03:45:56 +01:00
Tobias Geerinckx-Rice 708e76287c
gnu: obs: Update to 18.0.1. 
* gnu/packages/video.scm (obs): Update to 18.0.1.
 2017-03-15 03:45:56 +01:00
Tobias Geerinckx-Rice 17753e6edb
gnu: youtube-dl: Update to 2017.03.15. 
* gnu/packages/video.scm (youtube-dl): Update to 2017.03.15.
 2017-03-15 03:45:55 +01:00
Tobias Geerinckx-Rice a988cbb766
gnu: stress-make: Fix description. 
* gnu/packages/debug.scm (stress-make)[description]: Fix typo.
Avoid ambiguous use of ‘in order’.
 2017-03-15 03:45:55 +01:00
Tobias Geerinckx-Rice d540156c69
gnu: znc: Update to 1.6.5. 
* gnu/packages/messaging.scm (znc): Update to 1.6.5.
 2017-03-15 03:43:21 +01:00
Tobias Geerinckx-Rice 6d57723ac8
gnu: grue-hunter: Correctly install documentation. 
* gnu/packages/games.scm (grue-hunter)[arguments]: Install and populate
‘/share/doc/grue-hunter’ as a directory, not a plain file.
 2017-03-15 01:10:31 +01:00
Tobias Geerinckx-Rice b2d748edff
gnu: samtools: End installation phases with truth. 
* gnu/packages/bioinformatics.scm (samtools, samtools-0.1)[arguments]:
Return #T instead of the undefined results of COPY-FILE or INSTALL-FILE.
 2017-03-15 01:10:30 +01:00
Leo Famulari 35dcfed370
gnu: w3m: Update to 0.5.3+git20170102 [security fixes]. 
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.
 2017-03-14 18:26:28 -04:00
Leo Famulari 2eab5db300
Revert "gnu: gitolite: Fix shebangs in hooks." 
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 d0c16adb19.
 2017-03-14 18:26:28 -04:00