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23881 Commits

Author SHA1 Message Date
Kei Kebreau 6b2eafaaa8
Revert "gnu: maxima: Ensure gcc is available at runtime." 
This reverts commit f2fa86cc82.
Commit 5ea8dbf0c9 fixes the underlying
issue in GNU Common Lisp.
 2017-07-25 07:58:46 -04:00
Kei Kebreau 5ea8dbf0c9
gnu: gcl: Ensure gcc and binutils are available at runtime. 
* gnu/packages/lisp.scm (gcl)[arguments]: Add -fgnu89-inline to CFLAGS.
Add GCC path to make-flags. Modify 'pre-conf' phase. Add 'wrap' phase.
 2017-07-25 07:58:06 -04:00
Mark H Weaver ebc9f7050c
gnu: webkitgtk: Update to 2.16.6 [security fixes]. 
Includes fixes for CVE-2017-7039, CVE-2017-7018, CVE-2017-7030, CVE-2017-7037,
CVE-2017-7034, CVE-2017-7055, CVE-2017-7056, CVE-2017-7064, CVE-2017-7061,
CVE-2017-7048, and CVE-2017-7046.

* gnu/packages/webkit.scm (webkitgtk): Update to 2.16.6.
 2017-07-25 07:32:25 -04:00
Ludovic Courtès a84ea2191e
system: Add a default '.guile' skeleton. 
* gnu/system/shadow.scm (default-skeletons): Add ".guile".
 2017-07-25 12:23:26 +02:00
Ludovic Courtès 585347d7aa
Add 'guix weather'. 
* guix/scripts/weather.scm: New file.
* Makefile.am (MODULES): Add it.
* doc/guix.texi (Substitutes, Invoking guix publish): Mention "guix
weather".
(Invoking guix weather): New node.

Co-authored-by: Ricardo Wurmus <rekado@elephly.net>
 2017-07-25 12:15:43 +02:00
Leo Famulari 5b4a6ba044
gnu: xterm: Update to 330. 
* gnu/packages/xorg.scm (xterm): Update to 330.
 2017-07-24 22:54:18 -04:00
Leo Famulari 0e8fed86d8
gnu: dialog: Update to 1.3-20170509. 
* gnu/packages/ncurses.scm (dialog): Update to 1.3-20170509.
 2017-07-24 22:54:15 -04:00
Leo Famulari fce8285e4b
gnu: opus: Update to 1.2.1. 
* gnu/packages/xiph.scm (opus): Update to 1.2.1.
[source]: Use new source URL.
 2017-07-24 17:37:05 -04:00
Efraim Flashner f6062e5432
gnu: perl-data-dumper-concise: Update to 2.023. 
* gnu/packages/perl.scm (perl-data-dumper-concise): Update to 2.023.
[source]: Update source uri.
 2017-07-24 22:35:11 +03:00
Efraim Flashner 1627ca0494
gnu: perl-context-preserve: Update to 0.02. 
* gnu/packages/perl.scm (perl-context-preserve): Update to 0.02.
 2017-07-24 22:35:09 +03:00
Christopher Baines d61a894bfa
gnu: gnome: Add deja-dup. 
* gnu/packages/gnome.scm (deja-dup): New variable.
* gnu/packages/patches/deja-dup-use-ref-keyword-for-iter.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add patch file entry.
 2017-07-24 20:05:49 +01:00
Ludovic Courtès e956ae16a4
import: cpan: Updater returns a list of URLs. 
* guix/import/cpan.scm (latest-release): Return a list in the 'urls'
field of 'upstream-source'.
 2017-07-24 17:35:26 +02:00
Ludovic Courtès dc4f697f01
gnu: python-pexpect: Add dependency on the full Bash. 
Fixes a regression introduced in
704243e0c6.

* gnu/packages/python.scm (python-pexpect)[native-inputs]: Add BASH.
 2017-07-24 17:24:17 +02:00
Ludovic Courtès 3e6add96c5
gnu: gnome-mime-data: Do not use the bundled intltool. 
* gnu/packages/gnome.scm (gnome-mime-data)[arguments]: New field.
 2017-07-24 17:11:30 +02:00
Ludovic Courtès 23212bf9e6
gnu: perl: Work around "dotless @INC" build issues. 
* gnu/packages/perl.scm (perl-task-weaken)[arguments]: New field.
(perl-unicode-normalize): Likewise.
* gnu/packages/web.scm (perl-http-server-simple)[arguments]: Add #:phases.
 2017-07-24 16:36:13 +02:00
Ludovic Courtès e2f24597a9
gnu: perl-regexp-common: Update to 2017060201. 
* gnu/packages/perl.scm (perl-regexp-common): Update to 2017060201.
 2017-07-24 16:33:54 +02:00
Ludovic Courtès c022e11187
gnu: guix: Update snapshot. 
* gnu/packages/package-management.scm (guix): Update to f1ddfe4.
 2017-07-24 12:25:08 +02:00
Ludovic Courtès f1ddfe4f14
gnu: python-flaky: Fix Texinfo markup in description. 
* gnu/packages/python.scm (python-flaky)[description]: Escape "@".
 2017-07-24 12:05:53 +02:00
Leo Famulari e081e2dd0b
Merge branch 'master' into core-updates 2017-07-23 19:06:49 -04:00
Leo Famulari 2472f7a8f1
gnu: isc-dhcp: Update bundled bind to 9.9.10-P3. 
This fixes a regression introduced in the fix for CVE-2017-3142, in BIND
9.9.10-P2, commit ecb232bdfc.

See 'CHANGELOG' in the source distribution for more information.

* gnu/packages/admin.scm (isc-dhcp): Update bundled bind to 9.9.10-P3.
 2017-07-23 19:05:37 -04:00
Leo Famulari 5391c6c9d2
gnu: bind: Update to 9.11.1-P3. 
This fixes a regression introduced in the fix for CVE-2017-3142, in BIND
9.11.1-P2, commit faa1369e3c.

See 'CHANGELOG' in the source distribution for more information.

* gnu/packages/dns.scm (isc-bind): Update to 9.11.1-P3.
 2017-07-23 19:05:37 -04:00
Mark H Weaver c67d80563f
gnu: ncurses/gpm: Move to (gnu packages ncurses). 
This is needed to avoid compilation problems caused by the cyclic dependency
between (gnu packages ncurses) and (gnu packages linux).

* gnu/packages/linux.scm (ncurses/gpm): Move to ...
* gnu/packages/ncurses.scm (ncurses/gpm): ... here.  Fix misleading
indentation.  Add (gnu packages linux) to the module imports.
 2017-07-23 17:04:51 -04:00
Efraim Flashner fd900d68a5
gnu: Add support for aarch64's compiled kernel. 
* gnu/packages/linux.scm (linux-libre)[arguments]: Add to the regex to
find and install the aarch64-linux kernel.
* gnu/system.scm (system-linux-image-file-name): Add entry for aarch64.
 2017-07-23 23:33:18 +03:00
Efraim Flashner 826adfdb37
gnu: Add xf86-video-freedreno. 
* gnu/packages/xorg.scm (xf86-video-freedreno): New variable.
 2017-07-23 23:33:17 +03:00
Efraim Flashner 4adeb3f6e6
gnu: Add u-boot-odroid-c2. 
* gnu/packages/bootloaders.scm (u-boot-odroid-c2): New variable.
 2017-07-23 23:33:16 +03:00
Efraim Flashner 1313628339
gnu: u-boot: Update to 2017.07. 
* gnu/packages/bootloaders.scm (u-boot): Update to 2017.07.
 2017-07-23 23:33:13 +03:00
Marius Bakke 846cb73865
gnu: tevent: Update to 0.9.33. 
* gnu/packages/samba.scm (tevent): Update to 0.9.33.
 2017-07-23 22:01:29 +02:00
Marius Bakke 85a5800e52
gnu: talloc: Update to 2.1.10. 
* gnu/packages/samba.scm (talloc): Update to 2.1.10.
 2017-07-23 22:01:29 +02:00
Marius Bakke fbed150133
gnu: ldb: Update to 1.1.31. 
* gnu/packages/samba.scm (ldb): Update to 1.1.31.
[native-inputs]: Add CMOCKA.
 2017-07-23 22:01:28 +02:00
Marius Bakke 17c3f1fb67
gnu: cmocka: Update to 1.1.1. 
* gnu/packages/check.scm (cmocka): Update to 1.1.1.
 2017-07-23 22:01:28 +02:00
Marius Bakke 38bb9df150
gnu: tdb: Update to 1.3.14. 
* gnu/packages/databases.scm (tdb): Update to 1.3.14.
 2017-07-23 22:01:28 +02:00
Marius Bakke 09efef3384
gnu: python-scipy: Update to 0.19.1. 
* gnu/packages/python.scm (python-scipy): Update to 0.19.1.
[source]: Use 'pypi-uri'.
 2017-07-23 22:01:28 +02:00
Marius Bakke 71d20587a5
gnu: python-matplotlib: Update to 2.0.2. 
* gnu/packages/python.scm (python-matplotlib): Update to 2.0.2.
[source]: Use 'pypi-uri'.
 2017-07-23 22:01:28 +02:00
Marius Bakke 9e5ee6b60c
gnu: python-pyparsing: Update to 2.2.0. 
* gnu/packages/python.scm (python-pyparsing, python2-pyparsing): Update to
2.2.0.
 2017-07-23 22:01:27 +02:00
Marius Bakke 007176e710
gnu: python-pyparsing: Use 'modify-phases' syntax. 
* gnu/packages/python.scm (python-pyparsing)[arguments]<#:phases>: Use
'modify-phases'.
 2017-07-23 22:01:27 +02:00
Oleg Pykhalov 6e864d0081
gnu: Add xmobar. 
gnu/packages/wm.scm (xmobar): New variable.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2017-07-23 15:29:36 -04:00
Ben Woodcroft d3dce32216
gnu: metabat: Fix boost-related compilation issue. 
Reported by Leo Famulari.

* gnu/packages/patches/metabat-fix-boost-issue.patch: New file.
* gnu/packages/bioinformatics.scm (metabat): Use it.
* gnu/local.mk (dist_patch_DATA): Add it.
 2017-07-23 22:35:52 +10:00
Efraim Flashner 8f155e3cff
gnu: bash-completion: Update to 2.7. 
* gnu/packages/bash.scm (bash-completion): Update to 2.7.
 2017-07-23 11:05:54 +03:00
Leo Famulari 6c1a317e29
Merge branch 'master' into core-updates 2017-07-23 03:42:12 -04:00
ng0 9478c05955
gnu: getmail: Update to 5.1. 
* gnu/packages/mail.scm (getmail): Update to 5.1.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2017-07-22 20:34:47 -04:00
Ben Woodcroft f3f68a442c
gnu: metabat: Update to 2.11.1. 
* gnu/packages/bioinformatics.scm (metabat): Update to 2.11.1.
[source]: Add patch to fix compilation.
[arguments]: Adjust regular expressions modifying 'SConstruct'.
* gnu/packages/patches/metabat-fix-compilation.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
 2017-07-23 10:29:36 +10:00
Ben Woodcroft 897ab082b2
gnu: python-plastid: Update to 0.4.8. 
* gnu/packages/bioinformatics.scm (python-plastid): Update to 0.4.8.
 2017-07-23 10:29:36 +10:00
Ben Woodcroft 0620387a59
gnu: bcftools: Update to 1.5. 
* gnu/packages/bioinformatics.scm (bcftools): Update to 1.5.
[origin]: Remove fix-makefile patch.
[arguments]: Add configure flags, add LIBS make flag.  Do not delete
configure phase.
* gnu/packages/patches/bcftools-fix-makefile.patch: Remove file.
* gnu/local.mk (dist_patch_DATA): Remove it.
 2017-07-23 10:29:36 +10:00
Ben Woodcroft 63fa0ffcd4
gnu: samtools: Update to 1.5. 
* gnu/packages/bioinformatics.scm (samtools): Update to 1.5.
 2017-07-23 10:29:36 +10:00
Ben Woodcroft 4fb6d1280e
gnu: htslib: Update to 1.5. 
* gnu/packages/bioinformatics.scm (htslib): Update to 1.5.
 2017-07-23 10:29:35 +10:00
Ben Woodcroft 60739965da
gnu: python-pysam: Update to 0.11.2.2. 
* gnu/packages/bioinformatics.scm (python-pysam): Update to 0.11.2.2.
 2017-07-23 10:29:35 +10:00
Ben Woodcroft bca2c57658
gnu: bamm: Use htslib-1.3. 
* gnu/packages/bioinformatics (htslib-1.3): New variable.
(bamm)[inputs]: Replace htslib with htslib-1.3.
 2017-07-23 10:29:35 +10:00
Ben Woodcroft 98593f9f51
gnu: bcftools: Update to 1.4.1. 
* gnu/packages/bioinformatics.scm (bcftools): Update to 1.4.1.
[arguments]: Move Makefile modifications from here ...
[source]: ... to added patch.  Adjust patch for update to 1.4.
* gnu/packages/patches/bcftools-fix-makefile.patch: New file.
* gnu/local.mk (dist_patch_DATA): Register it.
 2017-07-23 10:29:35 +10:00
Ben Woodcroft 4ab1644049
gnu: samtools: Update to 1.4.1. 
* gnu/packages/bioinformatics.scm (samtools): Update to 1.4.1.
[arguments]: Add '--with-htslib=system' configure flag.
[inputs]: Add htslib.
 2017-07-23 10:29:34 +10:00
Ben Woodcroft a9e4a1e641
gnu: htslib: Update to 1.4.1. 
* gnu/packages/bioinformatics.scm (htslib): Update to 1.4.1.
[inputs]: Add curl, openssl.
 2017-07-23 10:29:34 +10:00