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27773 Commits

Author SHA1 Message Date
Leo Famulari dacd8cf2e8
gnu: links: Fix-CVE-2017-11114. 
* gnu/packages/patches/links-CVE-2017-11114.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/web-browsers.scm (links)[source]: Use it.
 2017-12-20 20:08:35 -05:00
Mark H Weaver 66df43b9ae
gnu: linux-libre: Update to 4.14.8. 
* gnu/packages/linux.scm (%linux-libre-version): Update to 4.14.8.
(%linux-libre-hash): Update hash.
 2017-12-20 18:28:36 -05:00
Mark H Weaver 0786e4bd12
gnu: linux-libre@4.9: Update to 4.9.71. 
* gnu/packages/linux.scm (linux-libre-4.9): Update to 4.9.71.
 2017-12-20 18:27:48 -05:00
Mark H Weaver 770635e11d
gnu: linux-libre@4.4: Update to 4.4.107. 
* gnu/packages/linux.scm (linux-libre-4.4): Update to 4.4.107.
 2017-12-20 18:27:08 -05:00
Ludovic Courtès 8d6cd08573
gnu: diffutils: Fix Gnulib/getopt cross-compilation issue. 
Previously cross-compilation would fail:

     CC       xvasprintf.o
   xstrtol-error.c:50:16: warning: 'struct rpl_option' declared inside parameter list
		   int exit_status)
		   ^
   xstrtol-error.c: In function 'xstrtol_error':
   xstrtol-error.c:84:5: error: invalid use of undefined type 'struct rpl_option'

* gnu/packages/patches/diffutils-getopt.patch: New file.
* gnu/packages/base.scm (diffutils)[source]: Use it.
* gnu/local.mk (dist_patch_DATA): Add it.
 2017-12-20 23:19:31 +01:00
Ricardo Wurmus 4305176096
gnu: microscheme: Fix home page. 
* gnu/packages/avr.scm (microscheme)[home-page]: Use GitHub project page.

Fixes <https://bugs.gnu.org/29791>.
 2017-12-20 23:18:24 +01:00
Leo Famulari 0e06bec250
gnu: gpgme: Build with the latest GnuPG. 
* gnu/packages/gnupg.scm (gpgme)[inputs]: Use the latest gnupg package.
[arguments]: Keep a reference to the gnupg package used for build.
 2017-12-20 16:41:41 -05:00
Ludovic Courtès 066ccc2c69
gnu: gcc: Fix cross-compilation. 
Previously "guix build gcc@5 --target=TRIPLET" would fail like this:

   checking for exported symbols... /tmp/guix-build-gcc-5.5.0.drv-0/gcc-5.5.0/libcc1/configure: line 14531: -T: command not found
   yes
   checking for -rdynamic... /tmp/guix-build-gcc-5.5.0.drv-0/gcc-5.5.0/libcc1/configure: line 14541: -T: command not found
   no
   checking for library containing dlopen... -ldl
   checking for -fPIC -shared... yes
   configure: error:
      Building GCC with plugin support requires a host that supports
      -fPIC, -shared, -ldl and -rdynamic.

* gnu/packages/gcc.scm (gcc-4.7)[maybe-target-tools]: Add "OBJDUMP".
(gcc-5)[source](snippet, modules): New fields.
 2017-12-20 22:21:16 +01:00
Leo Famulari e6f63412c9
gnu: python-pygpgme: Use GnuPG 1 for the test suite. 
* gnu/packages/gnupg.scm (python-pygpgme, python2-pygpgme)[inputs]: Use gnupg-1
and make it a native-input.
 2017-12-20 15:13:22 -05:00
Leo Famulari 5965b08307
gnu: libassuan: Update to 2.5.1. 
* gnu/packages/gnupg.scm (libassuan): Update to 2.5.1.
 2017-12-20 15:11:27 -05:00
Tobias Geerinckx-Rice 48a9654ad6
gnu: exim: Update to 4.90. 
* gnu/packages/mail.scm (exim): Update to 4.90.
 2017-12-20 16:50:28 +01:00
Ludovic Courtès 614fffe427
build-system/gnu: Add the "static" output of libc in cross environments. 
Fixes a regression whereby the host libc.a would be missing when
cross-compiling.

This is a followup to commit 6dff905e51.

* guix/build-system/gnu.scm (standard-cross-packages): Add the
"cross-libc:static".
 2017-12-20 14:56:47 +01:00
Leo Famulari 8bc6956bbd
gnu: rng-tools: Update to 6.1. 
Rng-tools development appears to have moved to GitHub [0]:

"NOTE: The rng-tools project hasn't seen updates in some time, but is
still in active use. To facilitate ongoing development, the rng-tools
project is moved to here:
https://github.com/nhorman/rng-tools"

[0]
https://sourceforge.net/p/gkernel/wiki/Home/

* gnu/packages/linux.scm (rng-tools): Update to 6.1.
[source]: Use new upstream URL and give a descriptive file-name.
[arguments]: Add a 'bootstrap' phase.
[native-inputs]: Add autoconf, automake, and pkg-config.
[inputs]: Add sysfsutils.
 2017-12-20 03:53:52 -05:00
Rutger Helling 09a91adcf8
gnu: libressl: Update to 2.6.4. 
* gnu/packages/tls.scm (libressl): Update to 2.6.4.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2017-12-20 02:56:55 -05:00
Leo Famulari afcbc348a3
gnu: babl: Update to 0.1.38. 
* gnu/packages/gimp.scm (babl): Update to 0.1.38.
 2017-12-20 01:40:14 -05:00
Marius Bakke 1b0f65dc99
gnu: icu4c: Update to 60.2. 
* gnu/packages/icu4c.scm (icu4c): Update to 60.2.
 2017-12-19 23:34:10 +01:00
Marius Bakke b8e607bcf4
gnu: gtk+: Update to 3.22.26. 
* gnu/packages/gtk.scm (gtk+): Update to 3.22.26.
 2017-12-19 23:34:10 +01:00
Marius Bakke 31d170f381
gnu: harfbuzz: Update to 1.7.3. 
* gnu/packages/gtk.scm (harfbuzz): Update to 1.7.3.
 2017-12-19 23:34:09 +01:00
Leo Famulari 74c96b0b09
gnu: webkitgtk: Update to 2.18.4 [fixes CVE-2017-{7156,13856,13866,13870}]. 
* gnu/packages/webkit.scm (webkitgtk): Update to 2.18.4.
 2017-12-19 14:52:15 -05:00
Ricardo Wurmus 57ae890fb3
gnu: r-htmltable: Update to 1.11.0. 
* gnu/packages/web.scm (r-htmltable): Update to 1.11.0.
[propagated-inputs]: Add r-dplyr, r-htmltools, r-rstudioapi, and r-tidyr.
 2017-12-19 20:35:08 +01:00
Ricardo Wurmus aead9e1bc5
gnu: r-testthat: Update to 2.0.0. 
* gnu/packages/statistics.scm (r-testthat): Update to 2.0.0.
[propagated-inputs]: Add r-cli, r-rlang, and r-withr.
 2017-12-19 20:35:08 +01:00
Ricardo Wurmus 2976f304e2
gnu: Add r-cli. 
* gnu/packages/cran.scm (r-cli): New variable.
 2017-12-19 20:35:08 +01:00
Ricardo Wurmus d03949449a
gnu: r-hardyweinberg: Update to 1.5.9. 
* gnu/packages/cran.scm (r-hardyweinberg): Update to 1.5.9.
[propagated-inputs]: Add r-rsolnp.
 2017-12-19 20:35:08 +01:00
Ricardo Wurmus cb8b4c1196
gnu: Add r-rsolnp. 
* gnu/packages/cran.scm (r-rsolnp): New variable.
 2017-12-19 20:35:07 +01:00
Ricardo Wurmus 02cdb45f34
gnu: Add r-truncnorm. 
* gnu/packages/cran.scm (r-truncnorm): New variable.
 2017-12-19 20:35:07 +01:00
Ricardo Wurmus 5378f38332
gnu: r-curl: Update to 3.1. 
* gnu/packages/web.scm (r-curl): Update to 3.1.
 2017-12-19 20:35:07 +01:00
Ricardo Wurmus f9f1291bc0
gnu: r-ade4: Update to 1.7-10. 
* gnu/packages/statistics.scm (r-ade4): Update to 1.7-10.
[propagated-inputs]: Add r-mass.
 2017-12-19 20:35:07 +01:00
Ricardo Wurmus 83b0e1d53f
gnu: r-registry: Update to 0.5. 
* gnu/packages/statistics.scm (r-registry): Update to 0.5.
 2017-12-19 20:35:07 +01:00
Ricardo Wurmus d2dc69b8be
gnu: r-iterators: Update to 1.0.9. 
* gnu/packages/statistics.scm (r-iterators): Update to 1.0.9.
 2017-12-19 20:35:07 +01:00
Ricardo Wurmus 4a1945da16
gnu: r-segmented: Update to 0.5-3.0. 
* gnu/packages/statistics.scm (r-segmented): Update to 0.5-3.0.
 2017-12-19 20:35:06 +01:00
Ricardo Wurmus 0a1b447e2b
gnu: r-rprojroot: Update to 1.3-1. 
* gnu/packages/statistics.scm (r-rprojroot): Update to 1.3-1.
 2017-12-19 20:35:06 +01:00
Ricardo Wurmus 102a271870
gnu: r-rcpparmadillo: Update to 0.8.300.1.0. 
* gnu/packages/statistics.scm (r-rcpparmadillo): Update to 0.8.300.1.0.
 2017-12-19 20:35:06 +01:00
Ricardo Wurmus 0300cacae1
gnu: r-plotrix: Update to 3.7. 
* gnu/packages/statistics.scm (r-plotrix): Update to 3.7.
 2017-12-19 20:35:06 +01:00
Ricardo Wurmus 004e108aad
gnu: r-git2r: Update to 0.20.0. 
* gnu/packages/statistics.scm (r-git2r): Update to 0.20.0.
 2017-12-19 20:35:06 +01:00
Ricardo Wurmus 069e3b5c09
gnu: r-backports: Update to 1.1.2. 
* gnu/packages/statistics.scm (r-backports): Update to 1.1.2.
 2017-12-19 20:35:05 +01:00
Ricardo Wurmus 1028f9ef11
gnu: r-yaml: Update to 2.1.16. 
* gnu/packages/statistics.scm (r-yaml): Update to 2.1.16.
 2017-12-19 20:35:05 +01:00
Ricardo Wurmus de3fd9253f
gnu: r-reshape2: Update to 1.4.3. 
* gnu/packages/statistics.scm (r-reshape2): Update to 1.4.3.
 2017-12-19 20:35:05 +01:00
Ricardo Wurmus d0c1a402db
gnu: r-digest: Update to 0.6.13. 
* gnu/packages/statistics.scm (r-digest): Update to 0.6.13.
 2017-12-19 20:35:05 +01:00
Ricardo Wurmus 2960f9658f
gnu: r-vcd: Update to 1.4-4. 
* gnu/packages/cran.scm (r-vcd): Update to 1.4-4.
 2017-12-19 20:35:05 +01:00
Ricardo Wurmus f46a74e9f0
gnu: r-proxy: Update to 0.4-20. 
* gnu/packages/cran.scm (r-proxy): Update to 0.4-20.
 2017-12-19 20:35:04 +01:00
Ricardo Wurmus b9e8a5c594
gnu: r-biomart: Update to 2.34.1. 
* gnu/packages/bioinformatics.scm (r-biomart): Update to 2.34.1.
[propagated-inputs]: Add r-httr.
 2017-12-19 20:35:04 +01:00
Ricardo Wurmus 11e42209a8
gnu: r-gviz: Update to 1.22.2. 
* gnu/packages/bioinformatics.scm (r-gviz): Update to 1.22.2.
 2017-12-19 20:35:04 +01:00
Ricardo Wurmus 2ccd850192
gnu: r-gqtlstats: Update to 1.10.1. 
* gnu/packages/bioinformatics.scm (r-gqtlstats): Update to 1.10.1.
 2017-12-19 20:35:04 +01:00
Ricardo Wurmus 28d25d037e
gnu: r-rtracklayer: Update to 1.38.2. 
* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.38.2.
 2017-12-19 20:35:04 +01:00
Ricardo Wurmus d41f678420
gnu: r-limma: Update to 3.34.4. 
* gnu/packages/bioinformatics.scm (r-limma): Update to 3.34.4.
 2017-12-19 20:35:03 +01:00
Ricardo Wurmus ab0dd8ac10
gnu: r-edger: Update to 3.20.2. 
* gnu/packages/bioinformatics.scm (r-edger): Update to 3.20.2.
 2017-12-19 20:35:03 +01:00
Ricardo Wurmus 7665fb39f5
gnu: r-biocstyle: Update to 2.6.1. 
* gnu/packages/bioinformatics.scm (r-biocstyle): Update to 2.6.1.
 2017-12-19 20:35:03 +01:00
Ricardo Wurmus 756ac7254c
gnu: r-dexseq: Update to 1.24.2. 
* gnu/packages/bioinformatics.scm (r-dexseq): Update to 1.24.2.
 2017-12-19 20:35:03 +01:00
Ricardo Wurmus 8d11ef4470
gnu: r-vegan: Update to 2.4-5. 
* gnu/packages/bioinformatics.scm (r-vegan): Update to 2.4-5.
 2017-12-19 20:35:02 +01:00
Efraim Flashner 677bc34d5b
gnu: Remove redundant cmake libdir configure flags. 
* gnu/packages/bioinformatics.scm (imp)[arguments]: Remove
CMAKE_INSTALL_LIBDIR flag.
* gnu/packages/calendar.scm (libical): Same.
* gnu/packages/engineering.scm (kicad): Same.
* gnu/packages/games.scm (openrct2, mgba): Same.
* gnu/packages/gl.scm (virtualgl): Same.
* gnu/packages/image-processing.scm (mia): Same.
* gnu/packages/linux.scm (rdma-core): Same.
* gnu/packages/machine-learning.scm (dlib): Same.
* gnu/packages/maths.scm (lapack, superlu, z3): Same.
* gnu/packages/password-utils.scm (keepassxc): Same.
* gnu/packages/photo.scm (darktable): Same.
* gnu/packages/rdesktop.scm (freerdp): Same.
 2017-12-19 19:52:01 +02:00