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29159 Commits

Author SHA1 Message Date
Nicolas Goaziou a255142af3
gnu: emacs-org: Update to 9.1.14. 
* gnu/packages/emacs.scm (emacs-org): Update to 9.1.14.
 2018-09-21 21:55:28 +02:00
Tobias Geerinckx-Rice 1302837f6b
gnu: workrave: Update to 1.10.21. 
* gnu/packages/gnome.scm (workrave): Update to 1.10.21.
[source]: Use GIT-FILE-NAME.
 2018-09-21 20:32:27 +02:00
Tobias Geerinckx-Rice 43726c522f
gnu: emacs-password-store: Update to 1.7.3. 
* gnu/packages/emacs.scm (emacs-password-store): Update to 1.7.3.
 2018-09-21 20:32:27 +02:00
Tobias Geerinckx-Rice 10fadd1e3d
gnu: filezilla: Update to 3.37.1. 
* gnu/packages/ftp.scm (filezilla): Update to 3.37.1.
 2018-09-21 19:52:27 +02:00
Tobias Geerinckx-Rice 9a32bdf8a9
gnu: wxwidgets: Update to 3.0.4. 
* gnu/packages/wxwidgets.scm (wxwidgets): Update to 3.0.4.
 2018-09-21 19:52:26 +02:00
Tobias Geerinckx-Rice 199d72e327
gnu: python-pyparsing: Update to 2.2.1. 
* gnu/packages/python.scm (python-pyparsing): Update to 2.2.1.
[source]: Use PYPI-URI.
 2018-09-21 19:52:26 +02:00
Danny Milosavljevic ec944a1de9
gnu: rust: Remove unused "ar" setting. 
* gnu/packages/rust.scm (rust-1.20)[arguments]<#:phases>[configure]: Remove
unused "ar" setting.
 2018-09-21 17:59:09 +02:00
pimi 7e27393f82
gnu: Add r-pore. 
* gnu/packages/bioinformatics.scm (r-pore): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-09-21 17:04:37 +02:00
Paul Garlick 45201bf245
gnu: hdf5-parallel-openmpi: Really enable parallel build. 
This fix ensures that the H5_HAVE_PARALLEL identifier is correctly set
in the file H5pubconf.h.

* gnu/packages/maths.scm (hdf5-parallel-openmpi)[arguments]: Add
the "--enable-parallel" flag to the list of configure flags.  Remove
the incompatible "--enable-cxx" flag.  Add 'mpi-setup' phase.

Signed-off-by: Ludovic Courtès <ludovic.courtes@inria.fr>
 2018-09-21 17:04:37 +02:00
Paul Garlick b0d1e60fff
gnu: hdf5: Allow for absence of utility script. 
* gnu/packages/maths.scm (hdf5)[arguments]: Add condition to 'split'
phase to check for existence of h5fc script.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-09-21 17:04:37 +02:00
Danny Milosavljevic 10e066f410
gnu: rust: Remove unused "localstatedir" setting. 
* gnu/packages/rust.scm (rust-1.20)[arguments]<#:phases>[configure]: Remove
unused "localstatedir" setting.
 2018-09-21 15:21:24 +02:00
Tobias Geerinckx-Rice 118a084531
gnu: libfilezilla: Update to 0.13.2. 
* gnu/packages/ftp.scm (libfilezilla): Update to 0.13.2.
[source]: Use HTTPS.
 2018-09-21 15:04:29 +02:00
Tobias Geerinckx-Rice 41e551b2d3
gnu: python-pyparsing: Update home page. 
* gnu/packages/python.scm (python-pyparsing)[home-page]: Update.
 2018-09-21 15:03:49 +02:00
Tobias Geerinckx-Rice eacb5dc487
gnu: emacs-mu4e-conversation: Fix typo in description. 
* gnu/packages/emacs.scm (emacs-mu4e-conversation)[description]:
Fix 'correspondant' typo.
 2018-09-21 15:03:49 +02:00
Tobias Geerinckx-Rice 93ab9a5d76
gnu: kodi: Use INVOKE. 
* gnu/packages/kodi.scm (kodi)[arguments]: Substitute INVOKE for SYSTEM*.
 2018-09-21 15:03:48 +02:00
Tobias Geerinckx-Rice 2aa137e261
gnu: crossguid: Use INVOKE. 
* gnu/packages/kodi.scm (crossguid)[arguments]: Substitute INVOKE for SYSTEM*.
 2018-09-21 15:03:48 +02:00
Mark H Weaver e67ad5532f
gnu: icecat: Update to 60.2.0-gnu1 (pre-release). 
* gnu/packages/gnuzilla.scm (icecat): Update to 60.2.0-gnu1.
[source]: Download pre-release from alpha.gnu.org.  Remove obsolete patches.
Comment out the code to delete the bundled copies of libevent, cairo,
harfbuzz, and graphite2.
[inputs]: Use the latest ffmpeg.  Comment out libevent, cairo, harfbuzz, and
graphite2.
[native-inputs]: Add rust and cargo.
[arguments]: Remove --enable-gio and --disable-gnomeui.  Add --disable-stylo.
Comment out --with-system-{libevent,harfbuzz,graphite2}, --enable-system-cairo.
Import %cargo-build-system-modules.  Add 'patch-cargo-checksums' phase.
* gnu/packages/patches/icecat-CVE-2018-5157-and-CVE-2018-5158.patch,
gnu/packages/patches/icecat-bug-1413868-pt1.patch: Delete files.
* gnu/local.mk (dist_patch_DATA): Remove them.
 2018-09-21 07:16:02 -04:00
Mark H Weaver c5327efb97
gnu: libvpx: Add upstream security fix. 
* gnu/packages/patches/libvpx-use-after-free-in-postproc.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/video.scm (libvpx)[source]: Add patch.
 2018-09-21 07:15:59 -04:00
Tobias Geerinckx-Rice 6569549dfa
gnu: python-paramiko: Update to 2.4.2 [security fixes]. 
* gnu/packages/python-crypto.scm (python-paramiko): Update to 2.4.2.
 2018-09-21 13:18:42 +02:00
Tobias Geerinckx-Rice 101ad242be
gnu: python-paramiko: Use HTTPS home page. 
* gnu/packages/python-crypto.scm (python-paramiko)[home-page]: Use HTTPS.
 2018-09-21 13:18:42 +02:00
Tobias Geerinckx-Rice a1d6610e84
gnu: python-rencode: Update to 1.0.5. 
* gnu/packages/python.scm (python-rencode): Update to 1.0.5.
[arguments]: Add a 'delete-bogus-test' phase.
 2018-09-21 13:18:42 +02:00
Tobias Geerinckx-Rice e36058634d
gnu: python-hdf4: Use INVOKE. 
* gnu/packages/python.scm (python-hdf4)[arguments]: Substitute INVOKE
for SYSTEM*.
 2018-09-21 13:18:42 +02:00
Tobias Geerinckx-Rice 6f05556ba7
gnu: s6: Update to 2.7.2.1. 
* gnu/packages/skarnet.scm (s6): Update to 2.7.2.1.
 2018-09-21 13:18:41 +02:00
Tobias Geerinckx-Rice 174988fa05
gnu: perl-xml-compile: Update to 1.60. 
* gnu/packages/xml.scm (perl-xml-compile): Update to 1.60.
[propagated-inputs]: Add perl-carp, perl-scalar-list-utils, and
perl-types-serialiser.
 2018-09-21 13:18:41 +02:00
Nicolas Goaziou 1df40d3dbf
gnu: emacs-orgalist: Update to 1.9. 
* gnu/packages/emacs.scm (emacs-orgalist): Update to 1.9.
 2018-09-21 11:52:12 +02:00
Tobias Geerinckx-Rice 3752b683dc
gnu: openscenegraph: Update to 3.6.3. 
* gnu/packages/graphics.scm (openscenegraph): Update to 3.6.3.
[source]: Use GIT-FILE-NAME.
[inputs]: Remove unused pth and qtbase.
 2018-09-21 10:25:33 +02:00
Tobias Geerinckx-Rice 29ddbc5607
gnu: python-pydot: Update to 1.2.4. 
* gnu/packages/graphviz.scm (python-pydot): Update to 1.2.4.
[arguments]: Run the test suite.
[native-inputs]: Add python-chardet.
 2018-09-21 10:25:32 +02:00
Tobias Geerinckx-Rice 1779aaa09a
Add 'GNU Guix' comment to all (gnu packages) headers. 
* gnu/packages/debian.scm, gnu/packages/syndication.scm: Add comments.
 2018-09-21 10:25:32 +02:00
Tobias Geerinckx-Rice 4aa64e3a81
gnu: ubuntu-keyring: Update to 2018.09.18.1. 
* gnu/packages/debian.scm (ubuntu-keyring): Update to 2018.09.18.1.
 2018-09-21 10:25:32 +02:00
Tobias Geerinckx-Rice eeecbe09cc
gnu: perl-dbd-mysql: Update to 4.048. 
* gnu/packages/databases.scm (perl-dbd-mysql): Update to 4.048.
 2018-09-21 10:25:31 +02:00
Danny Milosavljevic e0b07ccc1a
gnu: rust: Work around mtime bug in rust build helpers. 
* gnu/packages/rust.scm (rust-1.20)[arguments]<#:phases>[fix-mtime-bug]:
Delete.
[reset-timestamps-after-changes]: Modify.
(rust-1.24): Don't delete "fix-mtime-bug" since now it doesn't ever
get created.
 2018-09-21 01:35:00 +02:00
Danny Milosavljevic 1bfaae25fa
gnu: rust@1.20.0: Fix tests. 
* gnu/packages/rust.scm (rust-1.23)[arguments]<#:phases>
[patch-cargo-tests, ignore-glibc-2.27-incompatible-test,fix-mtime-bug]: Move
to...
(rust-1.20): ... here.
 2018-09-21 01:31:10 +02:00
Mark H Weaver 83e8b1d794
gnu: linux-libre: Update to 4.18.9. 
* gnu/packages/linux.scm (%linux-libre-version): Update to 4.18.9.
(%linux-libre-hash): Update hash.
 2018-09-20 18:04:56 -04:00
Mark H Weaver c57a2a12b1
gnu: linux-libre@4.14: Update to 4.14.71. 
* gnu/packages/linux.scm (%linux-libre-4.14-version): Update to 4.14.71.
(%linux-libre-4.14-hash): Update hash.
 2018-09-20 18:04:48 -04:00
Mark H Weaver 41d6afb266
gnu: linux-libre@4.9: Update to 4.9.128. 
* gnu/packages/linux.scm (linux-libre-4.9): Update to 4.9.128.
 2018-09-20 18:04:42 -04:00
Mark H Weaver c6ede267e6
gnu: linux-libre@4.4: Update to 4.4.157. 
* gnu/packages/linux.scm (linux-libre-4.4): Update to 4.4.157.
 2018-09-20 18:04:35 -04:00
fis trivial ea2364621a
gnu: qbittorrent: Update to 4.1.3. 
* gnu/packages/bittorrent.scm (qbittorrent): Update to 4.1.3.
[inputs]: Use python-wrapper instead of python.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2018-09-20 15:31:17 -04:00
fis trivial f5c10a94ef
gnu: gprolog: Update to 1.4.5. 
* gnu/packages/gprolog.scm (gprolog): Update to 1.4.5.
[source]: Add an alternate source URL.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2018-09-20 15:27:43 -04:00
Ricardo Wurmus 89ee8a6edf
gnu: rsem: Update to 1.3.1. 
* gnu/packages/bioinformatics.scm (rsem): Update to 1.3.1.
[source]: Fetch from git; remove patch; delete bundled samtools.
[arguments]: Pass make flags; adjust phases.
[inputs]: Remove ncurses and samtools-0.1; add htslib-1.3.
* gnu/packages/patches/rsem-makefile.patch: Remove patch.
* gnu/local.mk (dist_patch_DATA): Remove it.
 2018-09-20 17:55:26 +02:00
Ricardo Wurmus a235ea4f30
gnu: ghc-pandoc-citeproc: Update to 0.14.3.1. 
* gnu/packages/haskell.scm (ghc-pandoc-citeproc): Update to 0.14.3.1.
 2018-09-20 17:20:07 +02:00
Ricardo Wurmus e30397dddb
gnu: ghc-xml-conduit: Update to 1.8.0.1. 
* gnu/packages/haskell.scm (ghc-xml-conduit): Update to 1.8.0.1.
[inputs]: Add ghc-doctest.
 2018-09-20 17:20:02 +02:00
Ricardo Wurmus 391fc11f0e
gnu: python2-scikit-learn: Fix check phase. 
* gnu/packages/machine-learning.scm (python2-scikit-learn)[arguments]:
Override check phase to disable broken tests and pass environment variables.
 2018-09-20 15:56:59 +02:00
Ricardo Wurmus 26358ac5ab
gnu: Add r-parmigene. 
* gnu/packages/cran.scm (r-parmigene): New variable.
 2018-09-20 15:56:30 +02:00
Marius Bakke 985d542e02
gnu: gstreamer: Update to 1.14.3. 
* gnu/packages/gstreamer.scm (gstreamer, gst-plugins-base, gst-plugins-good,
gst-plugins-bad, gst-plugins-ugly, gst-libav, python-gst): Update to 1.14.3.
 2018-09-20 14:00:02 +02:00
Marius Bakke 2817ac3c18
Merge branch 'master' into core-updates 2018-09-20 13:37:58 +02:00
Marius Bakke 3e12df7d71
gnu: Add emacs-dired-sidebar. 
* gnu/packages/emacs.scm (emacs-dired-sidebar): New public variable.
 2018-09-20 13:29:29 +02:00
Marius Bakke 166b2c970e
gnu: eolie: Update home page. 
* gnu/packages/gnome.scm (eolie)[home-page]: Set to wiki.gnome.org/Apps/Eolie.
 2018-09-20 13:29:29 +02:00
Tobias Geerinckx-Rice 3e63a83c0f
gnu: u-boot: Use HTTPS home page. 
* gnu/packages/bootloaders.scm (u-boot)[home-page]: Use HTTPS.
 2018-09-20 04:50:34 +02:00
Tobias Geerinckx-Rice 84c7fbfd6d
gnu: ccid: Update to 1.4.30. 
* gnu/packages/security-token.scm (ccid): Update to 1.4.30.
 2018-09-20 04:50:34 +02:00
Tobias Geerinckx-Rice 4eb161962f
gnu: opusfile: Update to 0.11. 
* gnu/packages/xiph.scm (opusfile): Update to 0.11.
 2018-09-20 04:50:33 +02:00
Tobias Geerinckx-Rice e61c2991e4
Use INVOKE in (gnu packages xdisorg). 
* gnu/packages/xdisorg.scm (scrot, unclutter, xautolock, nxbelld)
[arguments]: Use INVOKE.
 2018-09-20 04:17:04 +02:00
Tobias Geerinckx-Rice 2385ecb224
Use INVOKE in (gnu packages shells). 
* gnu/packages/shells.scm (mksh)[arguments]: Use INVOKE...
(scsh)[arguments]: ...and also return #t from all phases.
 2018-09-20 04:17:04 +02:00
Tobias Geerinckx-Rice 9923d5a40f
gnu: Use INVOKE & return #t from Ruby package phases. 
* gnu/packages/maths.scm (ruby-asciimath)[arguments]: Return #t from
all phases.
* gnu/packages/rails.scm (ruby-debug-inspector)[arguments]: Substitute
INVOKE for SYSTEM*.
* gnu/packages/ruby.scm (ruby-permutation, ruby-blankslate)
(ruby-minitest-pretty-diff, ruby-guard, ruby-rb-inotify, ruby-tins)
(ruby-gem-hadar, ruby-term-ansicolor, ruby-json-pure)
(ruby-activesupport, ruby-redcloth, ruby-netrc, ruby-unf-ext, ruby-yard)
(ruby-turn, ruby-sqlite3, ruby-shoulda-context, ruby-shoulda-matchers)
(ruby-shoulda, ruby-httpclient, ruby-ansi, ruby-bio-commandeer)
(ruby-rubytest, ruby-brass, ruby-qed, ruby-ae, ruby-lemon, ruby-hashery)
(ruby-rc4, ruby-concurrent)[arguments]: Likewise.
 2018-09-20 04:17:04 +02:00
Tobias Geerinckx-Rice 4f66ae2899
gnu: ruby-heredoc-unindent: Fix typo in description. 
* gnu/packages/ruby.scm (ruby-heredoc-unindent)[description]: Fix typo.
 2018-09-20 04:17:03 +02:00
Tobias Geerinckx-Rice 7616d75fd6
Use INVOKE in (gnu packages telephony). 
* gnu/packages/telephony.scm (libiax2, mumble)[arguments]: Use INVOKE.
 2018-09-20 04:17:03 +02:00
Tobias Geerinckx-Rice e564d33ce8
gnu: gourmet: Use HTTPS home page. 
* gnu/packages/nutrition.scm (gourmet)[home-page]: Use HTTPS.
 2018-09-20 04:17:03 +02:00
Tobias Geerinckx-Rice 29a000b602
gnu: sg3-utils: Update to 1.44. 
* gnu/packages/scsi.scm (sg3-utils): Update to 1.44.
 2018-09-20 04:17:02 +02:00
Leo Famulari e266043e67
gnu: shotwell: Update to 0.28.4. 
* gnu/packages/gnome.scm (shotwell): Update to 0.28.4.
 2018-09-19 17:31:49 -04:00
Leo Famulari 508d5c5fa8
gnu: OpenSC: Update to 0.19.0 [security fixes]. 
Fixes CVE-2018-{16391,16392,16393,16418,16419,16420,16421,16422,16423,16424,
16425,16426,16427}.

* gnu/packages/security-token.scm (opensc): Update to 0.19.0.
 2018-09-19 15:08:00 -04:00
Andy Patterson 1d98b44ea6
gnu: sbcl-slynk: Fix the build. 
* gnu/packages/lisp.scm (sbcl-slynk-boot0): Update to commit
cbf84c36c4eca8b032e3fd16177a7bc02df3ec4c.
[origin]<snippet>: Replace slynk/util references with the built system name
slynk-util. Remove compile-time invocations of slynk-require.
(sbcl-slynk-util): Inherit from sbcl-slynk-boot0.
[inputs]: Add sbcl-slynk-boot0.
[arguments]: Set an appropriate asd-file and asd-system-name.
(sbcl-slynk-arglists)[arguments]: Set an appropriate asdf-system-name.
(sbcl-slynk-fancy-inspector)[arguments]: Likewise.
(sbcl-slynk-package-fu)[arguments]: Likewise.
(sbcl-slynk-mrepl)[arguments]: Likewise.
(sbcl-slynk-trace-dialog)[arguments]: Likewise.
(sbcl-slynk-profiler)[arguments]: Likewise.
(sbcl-slynk-indentation)[arguments]: Likewise.
(sbcl-slynk-retro)[arguments]: Likewise.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-09-19 18:25:28 +02:00
Marius Bakke 4d679255da
gnu: glm: Update to 0.9.9.2. 
* gnu/packages/maths.scm (glm): Update to 0.9.9.2.
 2018-09-19 15:20:21 +02:00
Marius Bakke f6ae59c2e0
gnu: feh: Update to 2.28. 
* gnu/packages/image-viewers.scm (feh): Update to 2.28.
 2018-09-19 15:20:21 +02:00
Marius Bakke f03c4ec649
gnu: arpack-ng: Update to 3.6.3. 
* gnu/packages/maths.scm (arpack-ng): Update to 3.6.3.
 2018-09-19 15:20:21 +02:00
Marius Bakke 622ef2b90a
gnu: arpack-ng: Don't use unstable tarball. 
* gnu/packages/maths.scm (arpack-ng)[source]: Use GIT-FETCH.
 2018-09-19 15:20:21 +02:00
Marius Bakke c5c1e410cf
gnu: Reinstate xf86-video-ast. 
* gnu/packages/patches/xf86-video-ast-remove-mibstore.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Remove it.
* gnu/packages/xorg.scm (xf86-video-ast): New public variable.
 2018-09-19 15:20:21 +02:00
Danny Milosavljevic 6c1a658414
gnu: rust@1.19.0: Install libtest. 
* gnu/packages/rust.scm (rust-1.19)[arguments]<#:phases>[build]: Build
libtest.
 2018-09-19 14:41:01 +02:00
Danny Milosavljevic 4a90fcf9e7
gnu: mrustc: Enable tests. 
* gnu/packages/rust.scm (mrustc)[arguments]: Add #:test-target.
<#:phases>[install]: Don't install test output.
 2018-09-19 14:41:01 +02:00
Pierre Neidhardt 1cfcb841ed
gnu: git-credential-netrc: Add Git.pm to PERL5LIB. 
* gnu/packages/version-control.scm (git)[credential-netrc]: Add Git.pm to PERL5LIB.
 2018-09-19 09:07:12 +02:00
Ludovic Courtès 0058888c7e
gnu: Add guile-debbugs. 
* gnu/packages/guile.scm (guile-debbugs): New variable.
 2018-09-18 23:23:44 +02:00
Leo Famulari 32b3611375
gnu: Go 1.10: Update to 1.10.4. 
* gnu/packages/golang.scm (go-1.10): Update to 1.10.4.
 2018-09-18 15:30:03 -04:00
Tobias Geerinckx-Rice 56c180750c
gnu: busybox: Update to 1.29.3. 
* gnu/packages/busybox.scm (busybox): Update to 1.29.3.
 2018-09-18 14:18:43 +02:00
Tobias Geerinckx-Rice d99051715a
gnu: xorriso: Update to 1.5.0. 
* gnu/packages/cdrom.scm (xorriso): Update to 1.5.0.
 2018-09-18 13:50:32 +02:00
Tobias Geerinckx-Rice 8190578fa0
gnu: libisofs: Update to 1.5.0. 
* gnu/packages/cdrom.scm (libisofs): Update to 1.5.0.
 2018-09-18 13:50:32 +02:00
Tobias Geerinckx-Rice 4999f45ea9
gnu: libburn: Update to 1.5.0. 
* gnu/packages/cdrom.scm (libburn): Update to 1.5.0.
 2018-09-18 13:50:32 +02:00
Tobias Geerinckx-Rice 487cf5aaf6
gnu: rc: Simplify. 
* gnu/packages/shells.scm (rc)[source]: Replace magic commit ID with the
tagged release. Use GIT-FILE-NAME.
[arguments]: Remove 'autoreconf' phase (relying on Guix's built-in
'bootstrap' phase instead) and adjust the ordering of 'patch-trip.rc'
accordingly.
 2018-09-18 13:50:09 +02:00
Tobias Geerinckx-Rice 7c0ed27a8b
gnu: ncmpc: Update to 0.30. 
* gnu/packages/mpd.scm (ncmpc): Update to 0.30.
[arguments]: Add 'expand-C++-include-path' phase.
[inputs]: Add gcc-8.
 2018-09-18 13:50:09 +02:00
Tobias Geerinckx-Rice 8ecd843df5
gnu: exfat-utils: Update to 1.3.0. 
* gnu/packages/mtools.scm (exfat-utils): Update to 1.3.0.
 2018-09-18 13:50:09 +02:00
Tobias Geerinckx-Rice b22c44f1ea
gnu: cinnamon-desktop: Use Guix's built-in bootstrap phase. 
* gnu/packages/cinnamon.scm (cinnamon-desktop)[arguments]: Remove
'autoconf' phase. Add 'skip-premature-configure' phase.
 2018-09-18 13:49:23 +02:00
Tobias Geerinckx-Rice 0edc232be9
gnu: gourmet: Use INVOKE. 
* gnu/packages/nutrition.scm (gourmet)[arguments]: Substitute INVOKE for
SYSTEM*.
 2018-09-18 13:49:23 +02:00
Ludovic Courtès 56c240ba8c
gnu: Add confusion-mdl. 
* gnu/packages/lisp.scm (confusion-mdl): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-09-17 23:19:45 +02:00
Tobias Geerinckx-Rice d68aa41573
gnu: enlightenment: Update to 0.22.4. 
* gnu/packages/enlightenment.scm (enlightenment): Update to 0.22.4.
 2018-09-17 12:50:21 +02:00
Tobias Geerinckx-Rice ee127549a3
gnu: efl: Update to 1.21.1. 
* gnu/packages/enlightenment.scm (efl): Update to 1.21.1.
 2018-09-17 12:50:21 +02:00
Tobias Geerinckx-Rice f6a4d57e06
gnu: foo2zjs: Update to 20180910. 
* gnu/packages/cups.scm (foo2zjs): Update to 20180910.
 2018-09-17 12:50:21 +02:00
Tobias Geerinckx-Rice a09a21190f
gnu: libiptcdata: Mark up description. 
* gnu/packages/image.scm (libiptcdata)[description]: Use @dfn{}.
 2018-09-17 12:50:20 +02:00
Tobias Geerinckx-Rice 99d386a71f
gnu: powwow: Update to 1.2.18. 
* gnu/packages/games.scm (powwow): Update to 1.2.18.
 2018-09-17 12:50:20 +02:00
Tobias Geerinckx-Rice 36aff81aa3
gnu: powwow: Use HTTPS home page. 
* gnu/packages/games.scm (powwow)[home-page]: Use HTTPS.
 2018-09-17 12:50:20 +02:00
Tobias Geerinckx-Rice 956bcc8ed2
gnu: python-dirsync: Update to 2.2.3. 
* gnu/packages/python.scm (python-dirsync): Update to 2.2.3.
[native-inputs]: Remove unzip.
 2018-09-17 12:50:20 +02:00
Leo Famulari 4fed15fba3
gnu: mbedtls-apache: Update to 2.7.6. 
* gnu/packages/tls.scm (mbedtls-apache): Update to 2.7.6.
 2018-09-17 01:14:15 -04:00
Mark H Weaver ad99df3990
gnu: linux-libre: Update to 4.18.8. 
* gnu/packages/linux.scm (%linux-libre-version): Update to 4.18.8.
(%linux-libre-hash): Update hash.
 2018-09-16 19:13:42 -04:00
Mark H Weaver c333c8b6f1
gnu: linux-libre@4.14: Update to 4.14.70. 
* gnu/packages/linux.scm (%linux-libre-4.14-version): Update to 4.14.70.
(%linux-libre-4.14-hash): Update hash.
 2018-09-16 19:12:53 -04:00
Mark H Weaver bf9d141a65
gnu: linux-libre@4.9: Update to 4.9.127. 
* gnu/packages/linux.scm (linux-libre-4.9): Update to 4.9.127.
 2018-09-16 19:12:10 -04:00
Mark H Weaver b55d75f133
gnu: linux-libre@4.4: Update to 4.4.156. 
* gnu/packages/linux.scm (linux-libre-4.4): Update to 4.4.156.
 2018-09-16 19:11:33 -04:00
Tobias Geerinckx-Rice 31fdfc0cdd
gnu: dmidecode: Update to 3.2. 
* gnu/packages/admin.scm (dmidecode): Update to 3.2.
 2018-09-16 23:44:46 +02:00
Ben Woodcroft 5edef88b88
gnu: Add ruby-multi-test. 
* gnu/packages/ruby.scm (ruby-multi-test): New variable.

Signed-off-by: Christopher Baines <mail@cbaines.net>
 2018-09-16 18:29:45 +01:00
Ben Woodcroft 1b6f5475a1
gnu: Enable tests for ruby-multi-json. 
* gnu/packages/ruby.scm (ruby-multi-json)[version]: Update to 1.13.1.
[source]: Switch to GitHub, so that the tests can be run.
[arguments]: Enable running the tests, and add a patch to fix an issue running
the tests.
[native-inputs]: Add native-inputs required for running the tests.
[home-page]: Use HTTPS.

Signed-off-by: Christopher Baines <mail@cbaines.net>
 2018-09-16 18:29:45 +01:00
Ben Woodcroft ed4b6b1840
gnu: Add ruby-oj. 
* gnu/packages/ruby.scm (ruby-oj): New variable.

Signed-off-by: Christopher Baines <mail@cbaines.net>
 2018-09-16 18:29:45 +01:00
Ben Woodcroft 2db0f9c82d
gnu: Add ruby-yajl-ruby. 
* gnu/packages/ruby.scm (ruby-yajl-ruby): New variable.

Signed-off-by: Christopher Baines <mail@cbaines.net>
 2018-09-16 18:29:45 +01:00
Roel Janssen cbb1b16865
admin: python-pyudev: Add dependency on python-six. 
* gnu/packages/admin.scm (python-pyudev): Add dependency on python-six.
 2018-09-15 21:26:50 +02:00
Julien Lepiller 636579210f
gnu: php: Update to 7.2.10. 
* gnu/packages/php.scm (php): Update to 7.2.10.
 2018-09-15 21:06:08 +02:00
Rutger Helling e8079dd9e4
gnu: wine-staging: Update to 3.16. 
* gnu/packages/wine.scm (wine-staging): Update to 3.16.
 2018-09-15 15:09:01 +02:00
Rutger Helling b947c614df
gnu: wine-staging-patchset-data: Update to 3.16. 
* gnu/packages/wine.scm (wine-staging-patchset-data): Update to 3.16.
 2018-09-15 15:09:01 +02:00
Rutger Helling 85a349787b
gnu: wine: Update to 3.0.3. 
* gnu/packages/wine.scm (wine): Update to 3.0.3.
 2018-09-15 15:09:00 +02:00
Tobias Geerinckx-Rice 4be83af427
gnu: gambit-c: Update to 4.9.0. 
The tests makefile still contains the offending lines, but I was unable
to reproduce the failure across 3 different machines.

* gnu/packages/scheme.scm (gambit-c): Update to 4.9.0.
[arguments]: Remove 'fix-tests' phase.
 2018-09-15 12:15:28 +02:00
Tobias Geerinckx-Rice 4e9832dd38
gnu: gambit-c: Update home page. 
* gnu/packages/scheme.scm (gambit-c)[home-page]: Update.
 2018-09-15 12:15:05 +02:00
Maxim Cournoyer 511f3be695
gnu: Add python-user-agents. 
* gnu/packages/python.scm (python-user-agents, python2-user-agents): New
variables.

Signed-off-by: 宋文武 <iyzsong@member.fsf.org>
 2018-09-15 12:19:06 +08:00
Maxim Cournoyer 2ee67781ff
gnu: Add python-ua-parser. 
* gnu/packages/python.scm (python-ua-parser, python2-ua-parser): New variables.

Signed-off-by: 宋文武 <iyzsong@member.fsf.org>
 2018-09-15 12:19:06 +08:00
Maxim Cournoyer 935d5ceb9b
gnu: Add python-pycountry. 
* gnu/packages/python.scm (python-pycountry, python2-pycountry): New variables.

Signed-off-by: 宋文武 <iyzsong@member.fsf.org>
 2018-09-15 12:19:06 +08:00
Tobias Geerinckx-Rice 021b42f5e7
gnu: zsh: Update to 5.6.2. 
* gnu/packages/shells.scm (zsh): Update to 5.6.2.
 2018-09-15 05:17:51 +02:00
Tobias Geerinckx-Rice 81fb037f5a
gnu: libetpan: Use HTTPS home page. 
* gnu/packages/mail.scm (libetpan)[home-page]: Use HTTPS.
 2018-09-15 05:17:50 +02:00
Tobias Geerinckx-Rice 483be9bda6
gnu: ocaml-ounit: Update to 2.0.8. 
* gnu/packages/ocaml.scm (ocaml-ounit): Update to 2.0.8.
 2018-09-15 05:17:50 +02:00
Tobias Geerinckx-Rice 3319817174
gnu: pybind11: Update to 2.2.4. 
* gnu/packages/python.scm (pybind11): Update to 2.2.4.
 2018-09-15 05:17:50 +02:00
Tobias Geerinckx-Rice 5c34d97187
gnu: pybind11: Don't use unstable tarball. 
* gnu/packages/python.scm (pybind11)[source]: Use GIT-FETCH and
GIT-FILE-NAME.
 2018-09-15 05:17:50 +02:00
Maxim Cournoyer 61853b7447
gnu: libjpeg: Improve description. 
* gnu/packages/image.scm (libjpeg)[description]: Add the list of the programs
it provides.

Signed-off-by: 宋文武 <iyzsong@member.fsf.org>
 2018-09-15 10:49:50 +08:00
Tobias Geerinckx-Rice 25bc6370a4
gnu: snakemake: Update to 5.2.4. 
* gnu/packages/python.scm (snakemake): Update to 5.2.4.
[propagated-inputs]: Add python-gitpython.
 2018-09-15 03:38:31 +02:00
Tobias Geerinckx-Rice bbe2a94799
gnu: libsigrokdecode: Update to 0.5.2. 
* gnu/packages/electronics.scm (libsigrokdecode): Update to 0.5.2.
 2018-09-15 03:38:31 +02:00
Tobias Geerinckx-Rice 9f1b186afc
gnu: libetpan: Update to 1.9.1. 
* gnu/packages/mail.scm (libetpan): Update to 1.9.1.
 2018-09-15 03:38:31 +02:00
Tobias Geerinckx-Rice aae96f8fac
gnu: libetpan: Don't use unstable tarball. 
* gnu/packages/mail.scm (libetpan)[source]: Use GIT-FETCH and
GIT-FILE-NAME.
 2018-09-15 03:38:31 +02:00
Tobias Geerinckx-Rice f9fe94c1f6
gnu: emacs-magit-popup: Don't use unstable tarball. 
* gnu/packages/emacs.scm (emacs-magit-popup)[source]: Use GIT-FETCH and
GIT-FILE-NAME.
 2018-09-15 03:38:30 +02:00
Tobias Geerinckx-Rice e1bf455cee
gnu: emacs-magit-popup: Update to 2.12.4. 
* gnu/packages/emacs.scm (emacs-magit-popup): Update to 2.12.4.
 2018-09-15 03:38:30 +02:00
Tobias Geerinckx-Rice 49c941b43b
gnu: libmwaw: Update to 0.3.14. 
* gnu/packages/libreoffice.scm (libmwaw): Update to 0.3.14.
 2018-09-15 03:38:30 +02:00
Tobias Geerinckx-Rice 002d73a01f
gnu: libwps: Update to 0.4.10. 
* gnu/packages/libreoffice.scm (libwps): Update to 0.4.10.
 2018-09-15 03:38:30 +02:00
Tobias Geerinckx-Rice c924fe38dc
gnu: umoci: Update to 0.4.2. 
* gnu/packages/virtualization.scm (umoci): Update to 0.4.2.
 2018-09-15 03:36:36 +02:00
Tobias Geerinckx-Rice 56f3b85bd3
gnu: python-iso8601: Update to 0.1.12. 
* gnu/packages/time.scm (python-iso8601): Update to 0.1.12.
 2018-09-15 03:36:36 +02:00
Tobias Geerinckx-Rice ed017a78be
gnu: coq: Update to 8.8.1. 
* gnu/packages/ocaml.scm (coq): Update to 8.8.1.
 2018-09-15 03:36:36 +02:00
Tobias Geerinckx-Rice 1d7cc6841e
gnu: coq: INVOKE. 
* gnu/packages/ocaml.scm (coq)[arguments]: Substitute INVOKE for
SYSTEM*.
 2018-09-15 03:36:35 +02:00
Leo Famulari 9e9e5d5a26
gnu: OpenSSL 1.1: Update to 1.1.1. 
* gnu/packages/tls.scm (openssl-next): Update to 1.1.1.
[arguments]: Patch a `/usr/bin/env` invocation in the 'config' script.
Adjust the documentation output.
* gnu/packages/patches/openssl-1.1.0-c-rehash-in.patch: Rename and ...
* gnu/packages/patches/openssl-1.1-c-rehash-in.patch: ... adjust patch.
* gnu/local.mk (dist_patch_DATA): Adjust accordingly.
 2018-09-14 16:51:49 -04:00
Danny Milosavljevic e830c9d0b0
gnu: Rename "banana-pi" to "bananapi". 
* gnu/bootloader/u-boot.scm (u-boot-banana-pi-m2-ultra-bootloader): Rename
to...
(u-boot-bananapi-m2-ultra-bootloader): ...this.
* gnu/packages/bootloaders.scm (u-boot-banana-pi-m2-ultra): Rename to...
(u-boot-bananapi-m2-ultra): ...this.
* gnu/system/install.scm (banana-pi-m2-ultra-installation-os): Rename to...
(bananapi-m2-ultra-installation-os): ...this.
 2018-09-14 21:31:24 +02:00
Ricardo Wurmus 7a20877a18
gnu: python-llvmlite: Remove obsolete patch. 
* gnu/packages/llvm.scm (python-llvmlite)[inputs]: Remove patch that is
obsolete since the upgrade to LLVM 6.0.1.
 2018-09-14 15:12:03 +02:00
Eric Brown daa6036fda
gnu: Add openblas-ilp64. 
* gnu/packages/maths.scm (openblas-ilp64): New variable.

Co-authored-by: Ludovic Courtès <ludovic.courtes@inria.fr>
 2018-09-14 11:23:07 +02:00
Ricardo Wurmus 1dd153b3aa
gnu: Add python-hic2cool. 
* gnu/packages/bioinformatics.scm (python-hic2cool): New variable.
 2018-09-14 09:15:49 +02:00
pimi 03c95f0414
gnu: Add r-abps. 
* gnu/packages/cran.scm (r-abps): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2018-09-14 07:46:19 +02:00
pimi 016cabf7be
gnu: Add r-abodoutlier. 
* gnu/packages/cran.scm (r-abodoutlier): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2018-09-14 07:46:19 +02:00
Danny Milosavljevic 317b139c5d
gnu: rust: Update to 1.27.2. 
* gnu/packages/rust.scm (rust): Update to 1.27.2.
 2018-09-13 22:37:55 +02:00
pimi b6afe7b7f5
gnu: Add r-abnormality. 
* gnu/packages/cran.scm (r-abnormality): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2018-09-13 22:16:01 +02:00
Tobias Geerinckx-Rice f0314f65df
gnu: Add perl-devel-checklib. 
* gnu/packages/perl.scm (perl-devel-checklib): New public variable.
 2018-09-13 19:53:08 +02:00
Tobias Geerinckx-Rice 7ec4f648e5
gnu: sg3_utils: Mark up description. 
* gnu/packages/scsi.scm (sg3_utils)[description]: Use @dfn{}.
Wrap commands in @command{} rather than @code{}, and @itemize them.
 2018-09-13 19:53:08 +02:00
Tobias Geerinckx-Rice 581b6f5e96
gnu: sudo: Update to 1.8.25p1. 
* gnu/packages/admin.scm (sudo): Update to 1.8.25p1.
 2018-09-13 19:53:07 +02:00
Tobias Geerinckx-Rice 0b0b43ed7a
gnu: youtube-viewer: Update to 3.4.1. 
* gnu/packages/video.scm (youtube-viewer): Update to 3.4.1.
 2018-09-13 19:53:07 +02:00
Tobias Geerinckx-Rice 6be445785a
gnu: youtube-viewer: Don't use unstable tarball. 
* gnu/packages/video.scm (youtube-viewer)[source]: Use GIT-FETCH and
GIT-FILE-NAME.
 2018-09-13 19:53:07 +02:00
Leo Famulari ecd1301651
gnu: libinput: Update to 1.12.0. 
* gnu/packages/freedesktop.scm (libinput): Update to 1.12.0.
 2018-09-13 13:33:10 -04:00
Leo Famulari d763940711
Merge branch 'master' into core-updates 2018-09-13 13:32:39 -04:00
Leo Famulari 7d1cc61293
Revert "gnu: libinput: Update to 1.12.0." 
Libinput-minimal has a lot of dependent packages, and this isn't reported by
`guix refresh --list-dependent`. We'll save this commit for another time.

This reverts commit 38dc3d6f17.
 2018-09-13 13:28:10 -04:00
pimi ebb3cdb1ea
gnu: Add r-abjutils. 
* gnu/packages/cran.scm (r-abjutils): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2018-09-13 19:18:47 +02:00
pimi 1efcd0f1ea
gnu: Add r-abhgenotyper. 
* gnu/packages/cran.scm (r-abhgenotyper): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2018-09-13 19:13:43 +02:00
Manuel Graf ae72b8f55b
gnu: Add ClusterShell. 
* gnu/packages/ssh.scm (clustershell): New variable.

Co-authored-by: Ludovic Courtès <ludovic.courtes@inria.fr>
 2018-09-13 19:12:25 +02:00
Leo Famulari 38dc3d6f17
gnu: libinput: Update to 1.12.0. 
* gnu/packages/freedesktop.scm (libinput): Update to 1.12.0.
 2018-09-13 13:08:24 -04:00
pimi ef26400b66
gnu: Add r-abf2. 
gnu/packages/cran.scm (r-abf2): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2018-09-13 19:05:35 +02:00
Efraim Flashner f21967a44b
gnu: retroarch: Fix building on armhf-linux. 
* gnu/packages/emulators.scm (retroarch)[arguments]: Add custom flags
when building for armhf-linux.
 2018-09-13 18:40:32 +03:00
Efraim Flashner fade67ab75
gnu: retroarch: Use shared zlib. 
* gnu/packages/emulators.scm (retroarch)[arguments]: In custom
'configure phase, use our zlib instead of vendor's zlib.
 2018-09-13 18:40:30 +03:00
Danny Milosavljevic 060366f6b3
gnu: rust@1.23.0: Inherit outputs. 
* gnu/packages/rust.scm (rust-1.23)[outputs]: Inherit.
 2018-09-13 17:19:04 +02:00
Danny Milosavljevic b78fe27b31
gnu: rust@1.25.0: Disable pedantic test. 
* gnu/packages/rust.scm (rust-1.25)[arguments]<#:phases>
[disable-nil-enum-test]: New phase.
 2018-09-13 17:17:15 +02:00
Danny Milosavljevic 6fe73b487b
gnu: rust: Accept more detailed gdb responses. 
* gnu/packages/patches/rust-1.25-accept-more-detailed-gdb-lines.patch: New
file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/rust.scm (rust-1.25): Use it.
(rust-1.26): Use it.
(rust): Use it.
 2018-09-13 17:17:15 +02:00
pimi 3cadd3ce93
gnu: Add r-abe. 
gnu/packages/cran.scm (r-abe): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2018-09-13 15:21:40 +02:00
pimi d1ca3d7297
gnu: Add r-svdialogs. 
gnu/packages/cran.scm (r-svdialogs): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2018-09-13 15:07:45 +02:00
宋文武 26700caed9
gnu: racket: Fix incompatibility with libedit. 
The former patching made racket detecting libedit as the old 2.11 version,
which leads to failure:
<https://lists.gnu.org/archive/html/help-guix/2018-09/msg00027.html>.

* gnu/packages/scheme.scm (racket)[arguments]: Patch the 'ffi-lib' call of
libedit using 'PLT_READLINE_LIB'.
 2018-09-13 20:20:41 +08:00
Danny Milosavljevic 73dc7834de
gnu: rust@1.20.0: Replace "default-ar" by "ar". 
* gnu/packages/rust.scm (rust-1.20)[arguments]<#:phases>[configure]: Replace
"default-ar" by "ar".
 2018-09-13 10:10:49 +02:00
Danny Milosavljevic 1ab3e1dd98
gnu: Add rust@1.22.1. 
* gnu/packages/rust.scm (rust-1.22): New variable.
 2018-09-13 10:10:49 +02:00
Danny Milosavljevic 05ebff92bd
gnu: Add rust@1.21.0. 
* gnu/packages/rust.scm (rust-1.21): New variable.
 2018-09-13 10:10:49 +02:00
Danny Milosavljevic e69b1a7c6e
gnu: rust-bootstrap: Clean up comments. 
* gnu/packages/rust.scm (rust-bootstrap): Clean up comments.
 2018-09-13 10:10:49 +02:00
Danny Milosavljevic bfdc0e4d45
gnu: rust: Move "cc" from rust-bootstrap to rust proper. 
* gnu/packages/rust.scm (rust-bootstrap)[arguments]<#:phases>[install]:
Delete "cc".
(rust-1.23)[arguments]<#:phases>: Delete "provide-cc" deletion.
 2018-09-13 10:10:49 +02:00
Danny Milosavljevic 333c0ca966
gnu: rust@1.23.0: Use rust@1.20.0 as template. 
* gnu/packages/rust.scm (rust-1.23)[inherit]: Use rust-1.20.
[arguments]<#:phases>: Delete "patch-cargo-tomls" phase deletion.
Add "provide-cc" phase deletion.
Add "configure-archiver" phase deletion.
[configure]: Inherit phase.
[reset-timestamps-after-changes]: Inherit phase.
[build]: Inherit phase.
[check]: Inherit phase.
[install]: Inherit phase.
[wrap-rustc]: Inherit phase.
 2018-09-13 10:10:48 +02:00
Maxim Cournoyer f309671c28
gnu: Add emacs-org-reveal. 
* gnu/packages/emacs.scm (emacs-org-reveal): New variable.
 2018-09-12 22:48:04 -04:00
Maxim Cournoyer 82baeea297
gnu: Add emacs-elpy. 
* gnu/packages/emacs.scm (emacs-elpy): New variable.
 2018-09-12 22:16:25 -04:00
Maxim Cournoyer dcc31d7f41
gnu: Add emacs-highlight-indentation. 
* gnu/packages/emacs.scm (emacs-highlight-indentation): New variable.
 2018-09-12 22:16:25 -04:00
Maxim Cournoyer 87e9fb5753
gnu: Add emacs-pyvenv. 
* gnu/packages/emacs.scm (emacs-pyvenv): New variable.
 2018-09-12 22:16:24 -04:00
Maxim Cournoyer 2c6ff3a2bc
gnu: Add emacs-find-file-in-project. 
* gnu/packages/emacs.scm (emacs-find-file-in-project): New variable.
 2018-09-12 22:16:24 -04:00
Maxim Cournoyer 563f151bd4
gnu: Add emacs-mocker. 
* gnu/packages/emacs.scm (emacs-mocker): New variable.
 2018-09-12 22:16:24 -04:00
Maxim Cournoyer aaf10fa7d8
gnu: Add emacs-el-x. 
* gnu/packages/emacs.scm (emacs-el-x): New variable.
 2018-09-12 22:16:23 -04:00
Maxim Cournoyer 8795ce8673
gnu: Add python-black. 
* gnu/packages/python.scm (python-black): New variable.
 2018-09-12 22:16:23 -04:00
Maxim Cournoyer 7e846d07e8
gnu: Add python-toml. 
* gnu/packages/python.scm (python-toml): New variables.
 2018-09-12 22:16:23 -04:00
Maxim Cournoyer 4bd8f4f302
gnu: python-jedi: Update to 0.12.1. 
* gnu/packages/python.scm (python-jedi): Update to 0.12.1.
[propagated-inputs]: Move python-parso here, as it is required at run time.
 2018-09-12 22:16:18 -04:00
Danny Milosavljevic 614cfd5c54
gnu: Add rust@1.20.0. 
* gnu/packages/rust.scm (rust-1.20): New variable.
 2018-09-13 00:25:01 +02:00
Danny Milosavljevic 3763e7716c
gnu: rust@1.19.0: Remove superfluous install-file call. 
* gnu/packages/rust.scm (rust-1.19)[arguments]<#:phases>[build]: Remove
superfluous install-file call.
 2018-09-12 23:17:42 +02:00
Danny Milosavljevic 5a3fcf5b44
gnu: rust@1.19.0: Install rustdoc. 
* gnu/packages/rust.scm (rust-1.19)[arguments]<#:phases>[install]: Install
rustdoc.
 2018-09-12 23:17:42 +02:00
Danny Milosavljevic 0bcd1bc778
gnu: rust@1.19.0: Use match-lambda directly. 
Follow-up to 3159ef7c99.

* gnu/packages/rust.scm (rust-1.19)[arguments]<#:phases>[build]: Use
match-lambda directly.
 2018-09-12 23:17:42 +02:00
Nils Gillmann f006237c54
gnu: gnurl: Update to 7.61.1. 
* gnu/packages/gnunet.scm (gnurl): Update to 7.61.1.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2018-09-12 16:02:39 -04:00
Leo Famulari ff9008d8de
gnu: Zsh: Remove workaround required for Zsh 5.6. 
This is a followup to commit 5a5d3e3563.

* gnu/packages/shells.scm (zsh)[arguments]: Remove substitutions in 'patch-test'
phase.
 2018-09-12 15:21:42 -04:00
Pierre Neidhardt 4fa7f29f2a
gnu: emacs-hl-todo: Update to 1.9.0. 
* gnu/packages/emacs.scm (emacs-hl-todo): Update to 1.9.0.
 2018-09-12 19:51:26 +02:00
Ricardo Wurmus 4a89bdd196
gnu: python-scikit-learn: Update to 0.19.2. 
* gnu/packages/machine-learning.scm (python-scikit-learn): Update to 0.19.2.
[source]: Fetch from git.
[arguments]: Run tests before installation; replace "check" phase, add
"build-ext" phase; delete "reset-gzip-timestamps" phase.
[native-inputs]: Add python-pytest and python-pandas; remove python-nose.
 2018-09-12 19:35:02 +02:00
Pierre Neidhardt b002809f84
gnu: Add emacs-blimp. 
* gnu/packages/emacs.scm (emacs-blimp): New variable.
 2018-09-12 19:34:17 +02:00
Pierre Neidhardt 320105eadb
gnu: Add emacs-org-web-tools. 
* gnu/packages/emacs.scm (emacs-org-web-tools): New variable.
 2018-09-12 19:34:17 +02:00
Pierre Neidhardt 9c208f38f2
gnu: Add emacs-youtube-dl. 
* gnu/packages/emacs.scm (emacs-youtube-dl): New variable.
 2018-09-12 19:34:14 +02:00
Tobias Geerinckx-Rice acd4da3f29
gnu: libfilezilla: Update to 0.13.1. 
* gnu/packages/ftp.scm (libfilezilla): Update to 0.13.1.
 2018-09-12 16:44:08 +02:00
Tobias Geerinckx-Rice bec13d872d
gnu: sg3-utils: Update to 1.43. 
* gnu/packages/scsi.scm (sg3-utils): Update to 1.43.
[license]: Add bsd-2.
 2018-09-12 16:44:08 +02:00
Tobias Geerinckx-Rice 0f304ba73e
gnu: syslinux: Use HTTPS home page. 
* gnu/packages/bootloaders.scm (syslinux)[home-page]: Use HTTPS.
 2018-09-12 16:09:38 +02:00
Tobias Geerinckx-Rice 60d8db74c6
gnu: syslinux: Use INVOKE. 
* gnu/packages/bootloaders.scm (syslinux)[arguments]: Substitute INVOKE
for SYSTEM*.
 2018-09-12 16:09:38 +02:00
Tobias Geerinckx-Rice 5a5d3e3563
gnu: zsh: Update to 5.6.1. 
* gnu/packages/shells.scm (zsh): Update to 5.6.1.
 2018-09-12 16:09:38 +02:00
Tobias Geerinckx-Rice 4dbef67102
gnu: zsh: Use HTTPS. 
* gnu/packages/shells.scm (zsh)[source, home-page]: Use HTTPS.
 2018-09-12 16:09:37 +02:00
Tobias Geerinckx-Rice c8749b0250
gnu: Add perl-mock-config. 
* gnu/packages/perl-check.scm (perl-mock-config): New public variable.
 2018-09-12 16:09:37 +02:00
Efraim Flashner b2c8d31ff6
gnu: perl-moosex-getopt: Update to 0.73. 
* gnu/packages/perl.scm (perl-moosex-getopt): Update to 0.73.
[native-inputs]: Add perl-module-build-tiny, perl-path-tiny,
perl-test-needs.
 2018-09-12 10:28:47 +03:00
Eric Bavier bbe46a4af5
mpi: Factorize openmpi setup build phase. 
* gnu/packages/mpi.scm (%openmpi-setup): New variable.
* gnu/packages/maths.scm (scalapack, slepc-openmpi, mumps-openmpi)
(superlu-dist, p4est, petsc-openmpi, hypre-openmpi, elemental)
(sundials-openmpi, arpack-ng-openmpi)[arguments]: Use it in #:phases.
 2018-09-11 20:29:04 -05:00
Eric Bavier 5882078e8c
font-fantasque-sans: Upgrade to 1.7.2. 
* gnu/packages/fonts.scm (font-fantasque-sans): Upgrade to 1.7.2.
[native-inputs]: Add zip.
[arguments]: Add 'xrange->range phase for python3 compatibility.  Adjust
install phase to work with newly generated font variants.
 2018-09-11 20:29:03 -05:00
Pierre Neidhardt 2b0820bf0d
gnu: emacs-helm: Update to 3.0. 
* gnu/packages/emacs.scm (emacs-helm): Update to 3.0.
 2018-09-11 23:53:35 +02:00
Pierre Neidhardt ee0d184502
gnu: Add emacs-hackernews. 
* gnu/packages/emacs.scm (emacs-hackernews): New variable.
 2018-09-11 23:53:35 +02:00
Pierre Neidhardt bd8f74dfbe
gnu: emacs-evil-collection: Update to 20180911. 
* gnu/packages/emacs.scm (emacs-evil-collection): Update to 20180911.
 2018-09-11 23:53:35 +02:00
Pierre Neidhardt ac9e307740
gnu: emacs-magit-todos: Update to 1.1. 
* gnu/packages/emacs.scm (emacs-magit-todos): Update to 1.1.
 2018-09-11 23:53:35 +02:00
Pierre Neidhardt 475e16578f
gnu: emacs-helm-system-packages: Update to 1.10.1. 
* gnu/packages/emacs.scm (emacs-helm-system-packages): Update to 1.10.1.
 2018-09-11 23:53:35 +02:00
Jan Nieuwenhuizen 4a67079f71
gnu: mes: Oops, use mirror://gnu download url. 
* gnu/packages/mes.scm (mes): Oops, use mirror://gnu download url.
 2018-09-11 22:34:02 +02:00
Tobias Geerinckx-Rice a855117c59
gnu: snakemake: Update home page. 
* gnu/packages/python.scm (snakemake)[home-page]: Update.
 2018-09-11 21:12:43 +02:00
Tobias Geerinckx-Rice 9b83c15afe
gnu: snakemake: Update to 5.2.2. 
* gnu/packages/python.scm (snakemake): Update to 5.2.2.
 2018-09-11 21:03:08 +02:00
Tobias Geerinckx-Rice a93de1ae9e
gnu: obnam: Add deprecation warning. 
* gnu/packages/backup.scm (obnam)[synopsis, description]: Note its
retirement.
 2018-09-11 21:03:07 +02:00
Tobias Geerinckx-Rice cd1e138cc6
gnu: unbound: Update to 1.8.0. 
* gnu/packages/dns.scm (unbound): Update to 1.8.0.
 2018-09-11 21:03:07 +02:00
Tobias Geerinckx-Rice 702a87f2d1
gnu: perl-dbd-mysql: Update to 4.047. 
* gnu/packages/databases.scm (perl-dbd-mysql): Update to 4.047.
[arguments]: Add 'skip-library-detection' phase.
 2018-09-11 21:03:07 +02:00
Jonathan Brielmaier 52b0a352c3
gnu: libreoffice: Update to 6.1.0.3. 
* gnu/packages/libreoffice.scm (libreoffice): Update to 6.1.0.3.
[source]: Correct indenting.
[inputs]: Add libnumbertext and python-lxml.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-09-11 17:46:30 +02:00
Jonathan Brielmaier aeba7d4650
gnu: Add libnumbertext. 
* gnu/packages/libreoffice.scm (libnumbertext): New public variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-09-11 17:46:30 +02:00
Paul Garlick aa82260bc0
gnu: arpack-ng-openmpi: Fix build. 
* gnu/packages/maths.scm (arpack-ng-openmpi)[arguments]: Add
'set-test-environment phase.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-09-11 17:46:29 +02:00
Tim Gesthuizen d2fe71b04d
gnu: Add emacs-irony-mode. 
* gnu/packages/emacs.scm (emacs-irony-mode): New variable.
(emacs-irony-mode-server): New variable.

Co-authored-by: Ludovic Courtès <ludo@gnu.org>
 2018-09-11 17:46:28 +02:00
Ludovic Courtès 8539eb5c46
gnu: jupyter-guile-kernel: Add dependencies to the search path. 
This allows:

  guix environment --ad-hoc jupyter jupyter-guile-kernel \
    -- jupyter notebook

to work out-of-the-box.

* gnu/packages/guile.scm (jupyter-guile-kernel)[arguments]: In
'install-kernel' phase, add '-L' and '-C' flags to 'kernel.json'.
[propagated-inputs]: Remove.
[inputs]: Add GUILE-JSON and GUILE-SIMPLE-ZMQ.
 2018-09-11 17:46:28 +02:00
Ludovic Courtès 828fa94d7a
gnu: guile-simple-zmq, jupyter-guile-kernel: Update to 5bb66a0 and a7db924. 
* gnu/packages/guile.scm (guile-simple-zmq): Update to 5bb66a0.
(jupyter-guile-kernel): Update to a7db924.
 2018-09-11 17:46:28 +02:00
Mădălin Ionel Patrașcu 01af264dcb
gnu: Add r-svgui. 
* gnu/packages/cran.scm (r-svgui): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2018-09-11 17:27:10 +02:00
Marius Bakke f6b7ccc9f9
gnu: spice: Update to 0.14.1 [fixes CVE-2018-10873]. 
* gnu/packages/spice.scm (spice): Update to 0.14.1.
[source](uri): Update to new "spice-server" subdirectory.
[native-inputs]: Add GLIB-NETWORKING and GSETTINGS-DESKTOP-SCHEMAS.
[arguments]: Remove configure-flag which is now off even when celt is
available.  Add phase to set $SSL_CERT_FILE.
 2018-09-11 14:12:53 +02:00
Marius Bakke 41a659d2ec
gnu: usbredir: Update to 0.8.0. 
* gnu/packages/spice.scm (usbredir): Update to 0.8.0.
[source]: Use URL-FETCH.
[native-inputs]: Remove AUTOCONF, AUTOMAKE and LIBTOOL.
[arguments]: Remove.
 2018-09-11 14:12:53 +02:00
Marius Bakke 36e8185667
gnu: lv2: Use Python 2 for building. 
* gnu/packages/audio.scm (lv2)[arguments]: Set #:python.
 2018-09-11 14:00:20 +02:00
Marius Bakke f659e5e379
gnu: python-waf: Update to 2.0.11. 
* gnu/packages/python.scm (python-waf): Update to 2.0.11.
 2018-09-11 13:43:03 +02:00
Leo Famulari b4ff75b507
gnu: syncthing: Update to 0.14.50. 
* gnu/packages/syncthing.scm (syncthing): Update to 0.14.50.
 2018-09-11 03:24:46 -04:00
Leo Famulari e76709f71f
gnu: go-github-com-syncthing-notify: Update to 0.0.0-2.b76b458. 
* gnu/packages/syncthing.scm (go-github-com-syncthing-notify): Update to
0.0.0-2.b76b458.
 2018-09-11 03:24:42 -04:00
Leo Famulari 091ef8c97e
gnu: VLC: Update to 3.0.4. 
* gnu/packages/video.scm (vlc): Update to 3.0.4.
 2018-09-10 19:24:51 -04:00
Leo Famulari 5d9c28f117
gnu: git: Update to 2.19.0. 
* gnu/packages/version-control.scm (git): Update to 2.19.0.
(cgit)[inputs]: Use the source of Git 2.18.0.
 2018-09-10 19:02:45 -04:00
pimi cbb0edd1be
gnu: Add r-abd. 
* gnu/packages/cran.scm (r-abd): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-09-11 00:14:58 +02:00
pimi 6c6ce2d088
gnu: Add r-mosaic. 
* gnu/packages/cran.scm (r-mosaic): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-09-11 00:14:58 +02:00
pimi 2f195b6f23
gnu: Add r-mosaicdata. 
* gnu/packages/cran.scm (r-mosaicdata): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-09-11 00:14:58 +02:00
Ricardo Wurmus d54145c38a
gnu: guitarix: Update to 0.37.3. 
* gnu/packages/audio.scm (guitarix): Update to 0.37.3.
[inputs]: Add curl.
 2018-09-10 23:58:14 +02:00
Thorsten Wilms 029de52fe9
gnu: guitarix-lv2: Use correct configure flag. 
* gnu/packages/audio.scm (guitarix-lv2)[arguments]: Change configure flag.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2018-09-10 23:58:14 +02:00
Tobias Geerinckx-Rice 2740549754
gnu: kakoune: Use HTTPS home page. 
* gnu/packages/text-editors.scm (kakoune)[home-page]: Use HTTPS.
 2018-09-10 22:54:36 +02:00
Tobias Geerinckx-Rice b38827096f
gnu: mcrl2: Use HTTPS home page. 
* gnu/packages/maths.scm (mcrl2)[home-page]: Use HTTPS.
 2018-09-10 22:54:36 +02:00
Tobias Geerinckx-Rice 4105f13bb5
gnu: tor: Update to 0.3.4.8. 
* gnu/packages/tor.scm (tor): Update to 0.3.4.8.
 2018-09-10 22:54:35 +02:00
Tobias Geerinckx-Rice 695775b138
gnu: kakoune: Update to 2018.09.04. 
* gnu/packages/text-editors.scm (kakoune): Update to 2018.09.04.
 2018-09-10 22:15:20 +02:00
Tobias Geerinckx-Rice 4b41568fa5
gnu: python-binaryornot: Update to 0.4.4. 
* gnu/packages/python.scm (python-binaryornot): Update to 0.4.4.
 2018-09-10 22:15:20 +02:00
Tobias Geerinckx-Rice 86788cb0c9
gnu: python-parse: Update to 1.8.4. 
* gnu/packages/python.scm (python-parse): Update to 1.8.4.
 2018-09-10 22:15:20 +02:00
Tobias Geerinckx-Rice c0ea7f5ff4
gnu: python-parse: Mark up description. 
* gnu/packages/python.scm (python-parse)[description]: Use @code{}.
 2018-09-10 22:15:20 +02:00
Tobias Geerinckx-Rice cc12ac58a2
gnu: python-jedi: Update to 0.12.1. 
* gnu/packages/python.scm (python-jedi): Update to 0.12.1.
[synopsis, description]: Adjust to expanded functionality.
 2018-09-10 22:15:19 +02:00
Tobias Geerinckx-Rice 7a6eaf5ca9
gnu: python-parso: Update to 0.3.1. 
* gnu/packages/python.scm (python-parso): Update to 0.3.1.
 2018-09-10 22:15:19 +02:00
Tobias Geerinckx-Rice d56eee862b
gnu: qtractor: Update to 0.9.2. 
* gnu/packages/music.scm (qtractor): Update to 0.9.2.
[arguments]: Remove obsolete Qt 5.11 workaround.
 2018-09-10 22:15:19 +02:00
Leo Famulari 875d068176
Adjust all users of (gnu packages ldc) to use (gnu packages dlang). 
This is a followup to commit 98d6543f86.

* gnu/packages/bioinformatics.scm, guix/build-system/dub.scm: Adjust
accordingly.
 2018-09-10 15:44:32 -04:00
Marius Bakke 242f2711bd
gnu: python-pyzmq: Update to 17.1.2. 
* gnu/packages/python.scm (python-pyzmq): Update to 17.1.2.
 2018-09-10 20:38:48 +02:00
Marius Bakke b8d165b18a
gnu: python-traitlets: Update to 4.3.2. 
* gnu/packages/python.scm (python-traitlets): Update to 4.3.2.
[native-inputs]: Remove PYTHON-NOSE and PYTHON-MOCK.  Add PYTHON-PYTEST.
[arguments]: Adjust check phase accordingly.
[properties]: New field.
(python2-traitlets)[propagated-inputs]: Add PYTHON2-ENUM34.
 2018-09-10 20:38:48 +02:00
Marius Bakke 9fc445b1a5
gnu: python-pexpect: Update to 4.6.0. 
* gnu/packages/python.scm (python-pexpect): Update to 4.6.0.
 2018-09-10 20:38:48 +02:00
Marius Bakke c5e4b4cc8f
gnu: Add libabigail. 
* gnu/packages/elf.scm (libabigail): New public variable.
 2018-09-10 20:27:42 +02:00
Marius Bakke fc449407fe
gnu: python-debian: Update home page. 
* gnu/packages/python.scm (python-debian)[home-page]: Set to source
repository.
 2018-09-10 20:27:42 +02:00
Marius Bakke 418ec0adc9
gnu: python-libarchive-c: Update to 2.8. 
* gnu/packages/python.scm (python-libarchive-c): Update to 2.8.
[arguments]: Replace 'check' phase.
[native-inputs]: Add PYTHON-MOCK and PYTHON-PYTEST.
 2018-09-10 20:27:42 +02:00
Marius Bakke ba0052e8ae
gnu: python-tlsh: Update to 3.4.5. 
* gnu/packages/python.scm (python-tlsh): Update to 3.4.5.
 2018-09-10 20:27:42 +02:00
Marius Bakke 8fe059bf6c
gnu: python-cryptography: Update to 2.3.1. 
* gnu/packages/python-crypto.scm (python-cryptography-vectors,
python-cryptography): Update to 2.3.1.
 2018-09-10 20:27:42 +02:00
Tobias Geerinckx-Rice 2424d5e56c
gnu: cloc: Update source hash. 
The upstream tarball was modified in place. The only changes are:

  --- /gnu/store/5v39h6zjs33hj5dm2yggz5qk0mva00bs-cloc-1.78.tar.gz
  +++ /gnu/store/pm5ghks76vv6awv3969yvi7qxqfnfs1l-cloc-1.78.tar.gz
  ├── filetype from file(1)
  │ @@ -1 +1 @@
  │ -gzip compressed data, last modified: Fri Sep  7 18:22:49 2018, from Unix
  │ +gzip compressed data, last modified: Sat Sep  8 14:09:43 2018, from Unix
  │   --- 5v39h6zjs33hj5dm2yggz5qk0mva00bs-cloc-1.78.tar
  ├── +++ pm5ghks76vv6awv3969yvi7qxqfnfs1l-cloc-1.78.tar
  │ ├── file list
  │ │ @@ -1,13 +1,13 @@
  │ │  -rwxrwxr-x 0 al (1000) al (1000) 545021 2018-09-07 18:21:22 cloc-1.78/cloc
  │ │  -rwxrwxr-x 0 al (1000) al (1000)   1818 2018-09-07 18:21:22 cloc-1.78/sqlite_formatter
  │ │ -drwxrwxr-x 0 al (1000) al (1000)      0 2018-09-07 18:21:22 cloc-1.78/Unix/
  │ │ --rwxrwxr-x 0 al (1000) al (1000) 498571 2018-09-07 18:21:22 cloc-1.78/Unix/cloc
  │ │ +drwxrwxr-x 0 al (1000) al (1000)      0 2018-09-08 14:09:23 cloc-1.78/Unix/
  │ │ +-rwxrwxr-x 0 al (1000) al (1000) 498537 2018-09-08 14:09:22 cloc-1.78/Unix/cloc
  │ │  -rwxrwxr-x 0 al (1000) al (1000)  32382 2018-09-07 18:21:22 cloc-1.78/Unix/t/00_C.t
  │ │  -rwxrwxr-x 0 al (1000) al (1000)  12614 2018-09-07 18:21:22 cloc-1.78/Unix/t/01_opts.t
  │ │  -rw-rw-r-- 0 al (1000) al (1000)    862 2018-09-07 18:21:22 cloc-1.78/Unix/README
  │ ├── cloc-1.78/Unix/cloc
  │ │ @@ -1,8 +1,7 @@
  │ │ -#!/usr/local/perl/5.28.0/bin/perl
  │ │  #!/usr/bin/env perl

* gnu/packages/code.scm (cloc)[source]: Update sha256 hash.
 2018-09-10 20:20:00 +02:00
Leo Famulari 254844f22d
gnu: nano: Update to 3.0. 
* gnu/packages/nano.scm (nano): Update to 3.0.
 2018-09-10 13:54:29 -04:00
Mark H Weaver eb07a6f898
gnu: linux-libre: Update to 4.18.7. 
* gnu/packages/linux.scm (%linux-libre-version): Update to 4.18.7.
(%linux-libre-hash): Update hash.
 2018-09-10 13:25:54 -04:00
Mark H Weaver c727ed05ac
gnu: linux-libre@4.14: Update to 4.14.69. 
* gnu/packages/linux.scm (%linux-libre-4.14-version): Update to 4.14.69.
(%linux-libre-4.14-hash): Update hash.
 2018-09-10 13:24:01 -04:00
Mark H Weaver 176999f18e
gnu: linux-libre@4.9: Update to 4.9.126. 
* gnu/packages/linux.scm (linux-libre-4.9): Update to 4.9.126.
 2018-09-10 13:23:20 -04:00
Mark H Weaver d7e9bd15fa
gnu: linux-libre@4.4: Update to 4.4.155. 
* gnu/packages/linux.scm (linux-libre-4.4): Update to 4.4.155.
 2018-09-10 13:22:35 -04:00
Tobias Geerinckx-Rice 98184e566c
gnu: gnome-mpv: Update to 0.15. 
* gnu/packages/video.scm (gnome-mpv): Update to 0.15.
 2018-09-10 18:22:00 +02:00
Tobias Geerinckx-Rice 37a2ea118d
gnu: fortify-headers: Update to 1.0. 
* gnu/packages/suckless.scm (fortify-headers): Update to 1.0.
 2018-09-10 18:22:00 +02:00
Tobias Geerinckx-Rice 7c8b1bf664
gnu: python-genshi: Update to 0.7.1. 
* gnu/packages/python-web.scm (python-genshi): Update to 0.7.1.
[source]: Use GIT-FETCH and GIT-FILE-NAME. Remove patches.
* gnu/packages/patches/python-genshi-add-support-for-python-3.4-AST.patch,
gnu/packages/patches/python-genshi-buildable-on-python-2.7.patch,
gnu/packages/patches/python-genshi-disable-speedups-on-python-3.3.patch,
gnu/packages/patches/python-genshi-fix-tests-on-python-3.5.patch,
gnu/packages/patches/python-genshi-isstring-helper.patch,
gnu/packages/patches/python-genshi-stripping-of-unsafe-script-tags.patch:
Delete files.
* gnu/local.mk (dist_patch_DATA): Remove them.
 2018-09-10 18:21:59 +02:00
Tobias Geerinckx-Rice 83397e0786
gnu: python-sockjs-tornado: Update to 1.0.5. 
* gnu/packages/python-web.scm (python-sockjs-tornado): Update to 1.0.5.
 2018-09-10 18:21:59 +02:00
Tobias Geerinckx-Rice 1f7fe26f83
gnu: python-sockjs-tornado: Edit synopsis & description. 
* gnu/packages/python-web.scm (python-sockjs-tornado)[synopsis]
[description]: Pick nits.
 2018-09-10 18:21:59 +02:00
Pjotr Prins 98d6543f86
gnu: Rename ldc.scm to dlang.scm. 
* gnu/packages/ldc.scm: Rename to...
* gnu/packages/dlang.scm: ... this.
* gnu/local.mk (GNU_SYSTEM_MODULES): Adjust accordingly.
 2018-09-10 17:47:52 +02:00
Pjotr Prins 633e8aab69
gnu: ldc: Update to 1.10.0. 
* gnu/packages/ldc.scm (ldc): Update to 1.10.0.
[native-inputs]: Switch to LLVM and CLANG.
(ldc-bootstrap)[synopsis, description]: Tweak.
* gnu/packages/patches/ldc-disable-phobos-tests.patch: New file.
* gnu/packages/patches/ldc-1.7.0-disable-phobos-tests.patch: Remove.
* gnu/local.mk (dist_patch_DATA): Adjust accordingly.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-09-10 17:47:52 +02:00
Benjamin Slade f80d6ea251
gnu: Add hstr. 
* gnu/packages/shellutils.scm (hstr): New variable.
 2018-09-10 17:47:52 +02:00
Alex Kost 8a8662d286
gnu: emacs-guix: Update to 0.5. 
* gnu/packages/emacs.scm (emacs-guix): Update to 0.5.
[propagated-inputs]: Add 'guile-gcrypt'.
[arguments]: Adjust #:configure-flags accordingly.
 2018-09-10 18:38:32 +03:00
Alex Kost fdf68c232d
gnu: emacs-build-farm: Update to 0.2.1. 
* gnu/packages/emacs.scm (emacs-build-farm): Update to 0.2.1.
Change source from gitlab to notabug.
 2018-09-10 18:38:32 +03:00
Alex Kost 5d78cf0b6c
gnu: emacs-bui: Update to 1.2.0. 
* gnu/packages/emacs.scm (emacs-bui): Update to 1.2.0.
Change source from github to notabug.
 2018-09-10 18:38:32 +03:00
Ricardo Wurmus 5bfa7510d1
gnu: Add python-pygenometracks. 
* gnu/packages/bioinformatics.scm (python-pygenometracks): New variable.
 2018-09-10 16:50:26 +02:00
Ricardo Wurmus 1189c7f1b0
gnu: Add python-hicexplorer. 
* gnu/packages/bioinformatics.scm (python-hicexplorer): New variable.
 2018-09-10 16:50:26 +02:00
Ricardo Wurmus 5bb9e0af8d
gnu: Add python-cooler. 
* gnu/packages/bioinformatics.scm (python-cooler): New variable.
 2018-09-10 16:50:26 +02:00
Ricardo Wurmus 80f4db91b1
gnu: Add python-pyfaidx. 
* gnu/packages/bioinformatics.scm (python-pyfaidx): New variable.
 2018-09-10 16:50:26 +02:00
Ricardo Wurmus 1f41f01c14
gnu: Add python-pypairix. 
* gnu/packages/bioinformatics.scm (python-pypairix): New variable.
 2018-09-10 16:50:26 +02:00
Ricardo Wurmus a9d496b353
gnu: Add python-intervaltree. 
* gnu/packages/bioinformatics.scm (python-intervaltree): New variable.
 2018-09-10 16:50:26 +02:00
Ricardo Wurmus a6a7156aa9
gnu: Add python-dask. 
* gnu/packages/python.scm (python-dask): New variable.
 2018-09-10 16:50:26 +02:00
Ricardo Wurmus 035989c403
gnu: Add python-partd. 
* gnu/packages/python.scm (python-partd): New variable.
 2018-09-10 16:50:26 +02:00
Ricardo Wurmus c27a9d8a88
gnu: Add python-blosc. 
* gnu/packages/python.scm (python-blosc): New variable.
 2018-09-10 16:50:26 +02:00
Ricardo Wurmus b2b8226244
gnu: Add python-locket. 
* gnu/packages/python.scm (python-locket): New variable.
 2018-09-10 16:50:26 +02:00
Ricardo Wurmus 930ba31d20
gnu: Add python-cloudpickle. 
* gnu/packages/python.scm (python-cloudpickle): New variable.
 2018-09-10 16:50:26 +02:00
Ricardo Wurmus 3d352cb9cf
gnu: Add python-sortedcontainers. 
* gnu/packages/python.scm (python-sortedcontainers): New variable.
 2018-09-10 16:50:26 +02:00
Ricardo Wurmus 098cb1e9c4
gnu: Add python-cytoolz. 
* gnu/packages/python.scm (python-cytoolz): New variable.
 2018-09-10 16:50:26 +02:00
Ricardo Wurmus 7cd51cd28e
gnu: Add python-toolz. 
* gnu/packages/python.scm (python-toolz): New variable.
 2018-09-10 16:50:25 +02:00
Ricardo Wurmus 943a4cb601
gnu: Add python-multiprocess. 
* gnu/packages/python.scm (python-multiprocess): New variable.
 2018-09-10 16:50:25 +02:00
Ricardo Wurmus fc62567251
gnu: Add python-dill. 
* gnu/packages/python.scm (python-dill): New variable.
 2018-09-10 16:50:25 +02:00
Tobias Geerinckx-Rice 82d5c7c6de
gnu: python-typing: Update to 3.6.6. 
* gnu/packages/python.scm (python-typing): Update to 3.6.6.
 2018-09-10 15:29:13 +02:00
Tobias Geerinckx-Rice 419aa05e1b
gnu: tinyproxy: Update to 1.10.0. 
* gnu/packages/web.scm (tinyproxy): Update to 1.10.0.
[native-inputs]: Remove asciidoc.
 2018-09-10 15:29:12 +02:00
Tobias Geerinckx-Rice f6c8a97a04
gnu: spectrwm: Update to 3.2.0. 
* gnu/packages/wm.scm (spectrwm): Update to 3.2.0.
[arguments]: Remove 'fix-freetype-include' phase.
 2018-09-10 15:29:12 +02:00
Marius Bakke f2d4944086
gnu: guile-xcb: Install compiled files to "lib" instead of "share". 
This follows up commit b03f270e3d which removes
the previous install location from Guiles search path.

* gnu/packages/guile-wm.scm (guile-xcb)[arguments]: Amend #:configure-flags.
 2018-09-10 14:49:46 +02:00
Mădălin Ionel Patrașcu 57d70dbabc
gnu: Add yad. 
* gnu/packages/gtk.scm (yad): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2018-09-10 14:45:15 +02:00
Marius Bakke 4d19a14e77
gnu: python-llfuse: Update to 1.3.5. 
* gnu/packages/python.scm (python-llfuse): Update to 1.3.5.
 2018-09-10 14:29:40 +02:00
Marius Bakke 073705e725
gnu: python2-contextlib2: Use 'invoke' instead of 'system*'. 
* gnu/packages/python.scm (python2-contextlib2)[arguments]: Use INVOKE.
 2018-09-10 14:28:42 +02:00
Marius Bakke d06940882d
gnu: python2-contextlib2: Update to 0.5.5. 
* gnu/packages/python.scm (python2-contextlib2): Update to 0.5.5.
[native-inputs]: Add PYTHON2-UNITTEST2.
 2018-09-10 14:25:25 +02:00
Marius Bakke d4c04e509b
gnu: Remove python-contextlib2. 
This package is part of the Python standard library since version 3.2.

* gnu/packages/python.scm (python-contextlib2): Rename to ...
(python2-contextlib2): ... this.  Remove previous incarnation.
[arguments]: Set #:python.
 2018-09-10 14:24:34 +02:00
Marius Bakke e5eef32445
gnu: perl-module-runtime: Update to 0.016. 
* gnu/packages/perl.scm (perl-module-runtime): Update to 0.016.
 2018-09-10 14:13:36 +02:00
Ludovic Courtès 94b3b6041d
gnu: hpcguix-web: Update to 53e09ea. 
* gnu/packages/web.scm (hpcguix-web): Update to 53e09ea.
 2018-09-10 12:18:14 +02:00
Alex Vong d930374014
gnu: youtube-dl: Update to 2018.08.04. 
* gnu/packages/video.scm (youtube-dl): Update to 2018.08.04.
 2018-09-10 11:31:34 +02:00
Leo Famulari de15ff1a6c
gnu: Add asignify. 
* gnu/packages/crypto.scm (asignify): New variable.
 2018-09-09 20:05:47 -04:00
Marius Bakke 02107081da
gnu: double-conversion: Update to 3.1.0. 
* gnu/packages/maths.scm (double-conversion): Update to 3.1.0.
 2018-09-10 01:41:29 +02:00
Marius Bakke 2bdc73fb26
gnu: double-conversion: Don't use unstable tarball. 
* gnu/packages/maths.scm (double-conversion)[source]: Use GIT-FETCH.
 2018-09-10 01:41:29 +02:00
Marius Bakke 68a08dfbe5
gnu: libgd: Incorporate grafted changes. 
* gnu/packages/gd.scm (gd)[replacement]: Remove field.
[source](patches): Add "gd-CVE-2018-5711.patch" and
"gd-CVE-2018-1000222.patch".
(gd/fixed): Remove variable.
* gnu/packages/php.scm (gd-for-php): Remove variable.
(php)[inputs]: Change GD-FOR-PHP to GD.
 2018-09-10 01:39:01 +02:00
Marius Bakke fe79ce3b1f
Merge branch 'master' into core-updates 2018-09-10 01:37:32 +02:00
Marius Bakke fb94354a69
gnu: jbig2dec: Remove graft for 0.15. 
* gnu/packages/image.scm (jbig2dec): Update to 0.15.
[source]: Reindent.
(jbig2dec-0.15): Remove variable.
 2018-09-10 01:00:26 +02:00
Marius Bakke 18784d8f11
gnu: OpenSSL: Remove obsolete workaround. 
* gnu/packages/tls.scm (openssl)[arguments]: Remove workaround that is not
needed for GCC version 5.3 and later.
 2018-09-10 00:54:03 +02:00
Leo Famulari d4bd2453ec
gnu: certbot: Update to 0.27.1. 
* gnu/packages/tls.scm (python-acme): Update to 0.27.1.
[arguments]: Use invoke.
(certbot): Update to 0.27.1.
[native-inputs]: Use python-sphinx-1.6.
 2018-09-09 18:52:04 -04:00
Leo Famulari ced98c7e89
gnu: libgd: Fix CVE-2018-{5711,1000222}. 
* gnu/packages/patches/gd-CVE-2018-1000222.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/gd.scm (gd/fixed): New variable.
* gnu/packages/php.scm (gd-for-php)[source]: Use 'gd-CVE-2018-1000222.patch'.
 2018-09-09 18:13:19 -04:00
Ricardo Wurmus 45350539aa
gnu: r-chron: Update to 2.3-53. 
* gnu/packages/statistics.scm (r-chron): Update to 2.3-53.
 2018-09-09 22:26:02 +02:00
Ricardo Wurmus ab50580a9d
gnu: r-annotationhub: Update to 2.12.1. 
* gnu/packages/bioinformatics.scm (r-annotationhub): Update to 2.12.1.
 2018-09-09 22:26:02 +02:00
Ricardo Wurmus 35c076e619
gnu: r-chippeakanno: Update to 3.14.2. 
* gnu/packages/bioconductor.scm (r-chippeakanno): Update to 3.14.2.
 2018-09-09 22:26:02 +02:00
Roel Janssen c36d972531
gnu: Update texmaker to 5.0.2. 
* gnu/packages/tex.scm (texmaker): Update to 5.0.2.
 2018-09-09 21:59:08 +02:00
Marius Bakke 4333d48a82
gnu: mariadb: Move unbundle substitutions to source snippet. 
* gnu/packages/databases.scm (mariadb)[source](snippet): Add two substitutions
from ...
[arguments]: The 'unbundle' phase here.  Rename to 'fix-pcre-detection.
 2018-09-09 17:59:37 +02:00
Marius Bakke 1d957c79b6
gnu: mariadb: Update to 10.1.36. 
* gnu/packages/databases.scm (mariadb): Update to 10.1.36.
[arguments]: Disable one new test.
 2018-09-09 17:59:36 +02:00
Marius Bakke 5e53722249
gnu: jbig2dec: Don't build libjbig2dec.a. 
* gnu/packages/image.scm (jbig2dec)[arguments]: New field.
 2018-09-09 17:59:36 +02:00
Marius Bakke de781c05e7
gnu: util-linux: Remove static library reference from '.la' files. 
* gnu/packages/linux.scm (util-linux)[arguments]: Substitute all '.la' files.
 2018-09-09 17:59:36 +02:00
Marius Bakke 334bd08c42
gnu: cmake: Update to 3.12.2. 
* gnu/packages/cmake.scm (cmake): Update to 3.12.2.
 2018-09-09 17:59:36 +02:00
Marius Bakke a34ce3308e
gnu: gdk-pixbuf: Update to 2.38.0. 
* gnu/packages/gtk.scm (gdk-pixbuf): Update to 2.38.0.
[build-system]: Switch to MESON-BUILD-SYSTEM.
[arguments]: Don't explicitly enable x11 in #:configure-flags.  Prevent tests
from getting installed.  Adjust test substitutions.  Add phase to fix install.
[native-inputs]: Add GETTEXT-MINIMAL.
(gdk-pixbuf+svg)[arguments]: Adjust accordingly.
 2018-09-09 17:59:36 +02:00
Marius Bakke 7b1ad8b1d9
gnu: gtk+: Update to 3.24.0. 
* gnu/packages/gtk.scm (gtk+): Update to 3.24.0.
 2018-09-09 17:59:36 +02:00
Marius Bakke 2246c19218
gnu: mesa: Update to 18.1.8. 
* gnu/packages/gl.scm (mesa): Update to 18.1.8.
 2018-09-09 17:59:36 +02:00
Marius Bakke 589aca1c18
gnu: Python: Delete broken test. 
* gnu/packages/python.scm (python-3.7)[source](snippet): Delete test which
may crash some systems.
 2018-09-09 17:59:36 +02:00
Marius Bakke 9adaf1f408
gnu: OpenBLAS: Update to 0.3.3. 
* gnu/packages/maths.scm (openblas): Update to 0.3.3.
 2018-09-09 17:59:35 +02:00
Marius Bakke 9bb8b563a8
gnu: meson: Update to 0.47.2. 
* gnu/packages/build-tools.scm (meson): Update to 0.47.2.
 2018-09-09 17:59:35 +02:00
Marius Bakke 5d948c0c5d
gnu: python-hypothesis: Update to 3.70.3. 
* gnu/packages/check.scm (python-hypothesis): Update to 3.70.3.
 2018-09-09 17:59:35 +02:00
Marius Bakke ad8ae693c8
gnu: python-pytest: Update to 3.8.0. 
* gnu/packages/check.scm (python-pytest): Update to 3.8.0.
 2018-09-09 17:59:35 +02:00
Marius Bakke 529c36225a
gnu: fontconfig: Update to 2.13.1. 
* gnu/packages/fontutils.scm (fontconfig): Update to 2.13.1.
 2018-09-09 17:59:35 +02:00
Marius Bakke 6cd715adef
gnu: python-scipy: Update to 1.1.0. 
* gnu/packages/python.scm (python-scipy): Update to 1.1.0.
 2018-09-09 17:59:35 +02:00
Marius Bakke f6f8645cc9
gnu: libcmis: Fix FTBFS with Boost >= 1.68.0. 
* gnu/packages/libreoffice.scm (libcmis)[arguments]: Add phase to substitute
header file name.
 2018-09-09 17:59:35 +02:00
Marius Bakke 436969904c
gnu: vigra: Fix FTBFS with Numpy >= 1.15. 
* gnu/packages/image.scm (vigra)[arguments]: Disable one more test.
 2018-09-09 17:59:34 +02:00
Marius Bakke 6bbbdb1a34
gnu: oath-toolkit: Fix FTBFS with Glibc >= 2.28. 
* gnu/packages/patches/oath-toolkit-glibc-compat.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/authentication.scm (oath-toolkit)[source](patches): New field.
 2018-09-09 17:59:34 +02:00
Marius Bakke 0171019418
gnu: openssl: Update to 1.0.2p. 
* gnu/packages/patches/openssl-1.0.2-CVE-2018-0495.patch,
gnu/packages/patches/openssl-1.0.2-CVE-2018-0732.patch: Delete files.
* gnu/local.mk (dist_patch_DATA): Remove them.
* gnu/packages/tls.scm (openssl): Update to 1.0.2p.
[source](patches): Remove obsolete.
 2018-09-09 17:57:39 +02:00
Marius Bakke 16676fc3b1
gnu: curl: Remove graft for 7.61.1. 
* gnu/packages/curl.scm (curl): Update to 7.61.1.
(curl-7.61.1): Remove variable.
 2018-09-09 17:55:33 +02:00
Marius Bakke 842c44c974
gnu: ghostscript: Remove graft for 9.24. 
* gnu/packages/patches/ghostscript-CVE-2018-10194.patch,
gnu/packages/patches/ghostscript-runpath.patch: Delete files.
* gnu/local.mk (dist_patch_DATA): Remove them.
* gnu/packages/ghostscript.scm (ghostscript): Update to 9.24.
(ghostscript/fixed): Remove variable.
 2018-09-09 17:54:32 +02:00
Marius Bakke 0aeb134850
Merge branch 'master' into core-updates 2018-09-09 17:40:35 +02:00
Marius Bakke 0084744b3a
gnu: ghostscript: Update replacement to 9.24 [security fixes]. 
The following CVEs are fixed with this release: CVE-2018-15908,
CVE-2018-15909, CVE-2018-15910, CVE-2018-15911, CVE-2018-16509,
CVE-2018-16510, CVE-2018-16511, CVE-2018-16513, CVE-2018-16539,
CVE-2018-16540, CVE-2018-16541, CVE-2018-16542, CVE-2018-16543.

* gnu/packages/patches/ghostscript-CVE-2018-10194.patch: Delete file.
* gnu/packages/patches/ghostscript-CVE-2018-16509.patch,
gnu/packages/patches/ghostscript-bug-699708.patch: New files.
* gnu/local.mk (dist_patch_DATA): Adjust accordingly.
* gnu/packages/ghostscript.scm (ghostscript/fixed): Update to 9.24.
[source](patches): Remove 'ghostscript-CVE-2018-10194.patch' and
'ghostscript-runpath.patch'.  Add 'ghostscript-CVE-2018-16509.patch' and
'ghostscript-bug-699708.patch'.
[arguments]: Add LDFLAGS to #:configure-flags, and a phase to create output
directory.
 2018-09-09 16:43:11 +02:00
Marius Bakke 910a20e2b8
gnu: jbig2dec: Replace with 0.15 [security fixes]. 
* gnu/packages/image.scm (jbig2dec-0.15): New public variable.
(jbig2dec)[replacement]: New field.
 2018-09-09 16:43:11 +02:00
Marius Bakke a617fd55df
gnu: OpenBLAS: Update source URI. 
* gnu/packages/maths.scm (openblas)[source](uri): Use the more stable
SourceForge mirror.
 2018-09-09 16:43:11 +02:00
Marius Bakke 1448fa2547
gnu: openal: Update to 1.19.0. 
* gnu/packages/audio.scm (openal): Update to 1.19.0.
 2018-09-09 16:43:11 +02:00
Marius Bakke e9c1492f66
gnu: glm: Update to 0.9.9.1. 
* gnu/packages/maths.scm (glm): Update to 0.9.9.1.
 2018-09-09 16:43:10 +02:00
Marius Bakke 91b3a6d4db
gnu: msmtp: Remove unneeded input. 
* gnu/packages/mail.scm (msmtp)[inputs]: Remove LIBIDN, which is only required
when using OpenSSL (or GnuTLS sans IDN support).
 2018-09-09 16:43:10 +02:00
Marius Bakke 37f9cfae43
gnu: msmtp: Update to 1.8.0. 
* gnu/packages/mail.scm (msmtp): Update to 1.8.0.
 2018-09-09 16:43:10 +02:00
Marius Bakke 249846bfde
gnu: libsoup: Update to 2.64.0. 
* gnu/packages/gnome.scm (libsoup): Update to 2.64.0.
[inputs]: Add LIBPSL.
 2018-09-09 16:43:10 +02:00
Marius Bakke 617cf5de92
gnu: mpfr: Update home page. 
* gnu/packages/multiprecision.scm (mpfr)[home-page]: Use HTTPS.
 2018-09-09 16:43:10 +02:00
Marius Bakke 81bf0fd0d4
gnu: julia: Update objconv input. 
* gnu/packages/julia.scm (julia)[inputs]: Update the hash of "objconv", which
does not have a stable URL.  Add a file name and use HTTPS while at it.
 2018-09-09 16:43:10 +02:00
Tobias Geerinckx-Rice b64e67ad40
gnu: cloc: Update to 1.78. 
* gnu/packages/code.scm (cloc): Update to 1.78.
[source]: Update URI.
 2018-09-09 15:01:55 +02:00
Tobias Geerinckx-Rice c2311644a5
gnu: signify: Update to 24. 
* gnu/packages/crypto.scm (signify): Update to 24.
 2018-09-09 15:01:54 +02:00
Tobias Geerinckx-Rice bb105673b8
gnu: musl: Update to 1.1.20. 
* gnu/packages/musl.scm (musl): Update to 1.1.20.
 2018-09-09 15:01:54 +02:00
Tobias Geerinckx-Rice bb5e06a35e
gnu: perl-pegex: Update to 0.67. 
* gnu/packages/perl.scm (perl-pegex): Update to 0.67.
 2018-09-09 15:01:54 +02:00
Tobias Geerinckx-Rice 9ad80992d0
gnu: perl-config-autoconf: Update to 0.317. 
* gnu/packages/perl.scm (perl-config-autoconf): Update to 0.317.
 2018-09-09 15:01:53 +02:00
Tobias Geerinckx-Rice 15dbc911f6
gnu: perl-extutils-installpaths: Update to 0.012. 
* gnu/packages/perl.scm (perl-extutils-installpaths): Update to 0.012.
 2018-09-09 15:01:53 +02:00
Tobias Geerinckx-Rice 4e77b75e11
gnu: perl-extutils-helpers: Update to 0.026. 
* gnu/packages/perl.scm (perl-extutils-helpers): Update to 0.026.
 2018-09-09 15:01:53 +02:00
Tobias Geerinckx-Rice 748e6e1271
gnu: perl-getopt-long-descriptive: Update to 0.103. 
* gnu/packages/perl.scm (perl-getopt-long-descriptive): Update to 0.103.
 2018-09-09 15:01:53 +02:00
Tobias Geerinckx-Rice 04fc0b9489
gnu: perl-namespace-clean: Update to 0.27. 
* gnu/packages/perl.scm (perl-namespace-clean): Update to 0.27.
 2018-09-09 15:01:52 +02:00
Tobias Geerinckx-Rice 49e63e3884
gnu: perl-datetime: Update to 1.50. 
* gnu/packages/perl.scm (perl-datetime): Update to 1.50.
 2018-09-09 15:01:52 +02:00
Tobias Geerinckx-Rice 2d32a6572d
gnu: perl-params-validate: Update to 1.29. 
* gnu/packages/perl.scm (perl-params-validate): Update to 1.29.
 2018-09-09 15:01:52 +02:00
Tobias Geerinckx-Rice a0fad0374e
gnu: links: Update to 2.17. 
* gnu/packages/web-browsers.scm (links): Update to 2.17.
 2018-09-09 15:01:52 +02:00
Tobias Geerinckx-Rice b9114ccbad
gnu: aircrack-ng: Update to 1.3. 
* gnu/packages/networking.scm (aircrack-ng): Update to 1.3.
[native-inputs]: Add autoconf, automake, libtool, and which.
[inputs]: Add libpcap.
[arguments]: Use conventional --options in #:configure-flags.
Restore ‘configure’ phase. Add ‘patch-evalrev’ and customise ‘bootstrap’
phases. Simplify ‘absolutize-tools’ phase.
 2018-09-09 14:50:34 +02:00
Tobias Geerinckx-Rice 6930ea33c9
gnu: aircrack-ng: Use HTTPS. 
* gnu/packages/networking.scm (aircrack-ng)[source, home-page]: Use HTTPS.
 2018-09-09 14:50:34 +02:00
宋文武 d7f99b3b76
gnu: perl: Improve description. 
Fixes <https://bug.gnu.org/32650>.

* gnu/packages/perl.scm (perl)[description]: Use description from 'perlintro'.
 2018-09-09 19:11:52 +08:00
Jan Nieuwenhuizen c665774a1c
gnu: mes: Update to 0.17.1. 
* gnu/packages/patches/mes-nyacc-0.86.0.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/mes.scm (mes): Update to 0.17.1, depend on latest Nyacc 0.86.0.
(nyacc-for-mes): Remove.
 2018-09-08 20:36:30 +02:00
Jan Nieuwenhuizen 445ecce923
gnu: nyacc: Update to 0.86.0. 
* gnu/packages/patches/nyacc-binary-literals.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/mes.scm (nyacc): Update to 0.86.0, add patch.
 2018-09-08 20:36:30 +02:00
Benjamin Slade 39b5d8fd9d
gnu: Add frotz, frotz-dumb-terminal, and frotz-sdl. 
* gnu/packages/games.scm (frotz, frotz-dumb-terminal, frotz-sdl): New
variables.

Signed-off-by: Kei Kebreau <kkebreau@posteo.net>
 2018-09-08 13:41:10 -04:00
Mark H Weaver 090e3768e8
gnu: linux-libre: Update to 4.18.6. 
* gnu/packages/linux.scm (%linux-libre-version): Update to 4.18.6.
(%linux-libre-hash): Update hash.
 2018-09-07 21:05:14 -04:00
Mark H Weaver 4be8fdd3cc
gnu: linux-libre@4.14: Update to 4.14.68. 
* gnu/packages/linux.scm (%linux-libre-4.14-version): Update to 4.14.68.
(%linux-libre-4.14-hash): Update hash.
 2018-09-07 21:03:03 -04:00
Mark H Weaver ddb419ce04
gnu: linux-libre@4.9: Update to 4.9.125. 
* gnu/packages/linux.scm (linux-libre-4.9): Update to 4.9.125.
 2018-09-07 21:02:30 -04:00
Mark H Weaver 48d17ba1d3
gnu: linux-libre@4.4: Update to 4.4.154. 
* gnu/packages/linux.scm (linux-libre-4.4): Update to 4.4.154.
 2018-09-07 21:01:48 -04:00
Ludovic Courtès 9f1f200c04
gnu: diffoscope: Update to 100. 
* gnu/packages/package-management.scm (diffoscope): Update to 100.
 2018-09-07 17:59:16 +02:00
Ludovic Courtès afdd1555c4
gnu: indent: Add version 2.2.12. 
* gnu/packages/code.scm (indent-2.2.12): New variable.
 2018-09-07 17:57:04 +02:00
Ludovic Courtès 6b4f99102c
gnu: gdb: Update to 8.2. 
* gnu/packages/gdb.scm (gdb): Update to 8.2.
 2018-09-07 17:55:55 +02:00
Ludovic Courtès 15214828a5
gnu: guile-json: Update to 1.2.0. 
* gnu/packages/guile.scm (guile-json): Update to 1.2.0.
[license]: Change to GPL3+.
 2018-09-07 17:55:51 +02:00
pimi 214452ffd3
gnu: Add r-ggformula. 
* gnu/packages/cran.scm (r-ggformula): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-09-07 11:40:06 +02:00
pimi c61f7bc543
gnu: Add r-mosaiccore. 
* gnu/packages/cran.scm (r-mosaiccore): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-09-07 11:40:06 +02:00
pimi 77b33e0ede
gnu: Add r-ggstance. 
gnu/packages/cran.scm (r-ggstance): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-09-07 11:40:06 +02:00
pimi 12da2a5e58
gnu: Add r-abctools. 
* gnu/packages/cran.scm (r-abctools): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-09-07 11:40:06 +02:00
pimi cadc10a513
gnu: Add r-abcrf. 
* gnu/packages/cran.scm (r-abcrf): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-09-07 11:40:06 +02:00
pimi 40c10917bc
gnu: Add r-abcp2. 
* gnu/packages/cran.scm (r-abcp2): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-09-07 11:40:06 +02:00
Alex Branham 12498b59e7
gnu: emacs-ess: Update to 17.11. 
* gnu/packages/emacs.scm (emacs-ess): Update to 17.11
[url]: Use github for https
[snippet]: update julia-mode substitution, only build info doc, bypass failing test
[propagated-inputs]: Add emacs-julia-mode
[description]: Mention that ESS supports Julia and JAGS (which replaces OpenBUGS)
[arguments]: Remove 'set-home' phase.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-09-07 11:40:06 +02:00
Ludovic Courtès b03f270e3d
gnu: guile: Remove "share/guile/site" from GUILE_LOAD_COMPILED_PATH. 
.go files should always go to lib/guile/2.x/site-ccache, and in
practice, we no longer have packages that don't do that.

* gnu/packages/guile.scm (guile-2.2)[native-search-paths]: Remove
"share/guile/site/2.2" from GUILE_LOAD_COMPILED_PATH spec.
(guile-2.0)[native-search-paths]: Likewise.
 2018-09-07 10:47:52 +02:00
Tobias Geerinckx-Rice 0012e0dd56
gnu: knot: Update to 2.7.2. 
* gnu/packages/dns.scm (knot): Update to 2.7.2.
 2018-09-07 03:01:40 +02:00
Leo Famulari 91cc2a38de
gnu: Wireshark: Update to 2.6.3 [fixes CVE-2018-{14994,16056,16057,16058}]. 
* gnu/packages/networking.scm (wireshark): Update to 2.6.3.
 2018-09-06 17:05:42 -04:00
Leo Famulari 1e066f0706
gnu: curl: Update replacement to 7.61.1 [fixes CVE-2018-14618]. 
* gnu/packages/curl.scm (curl)[replacement]: Update to 7.61.1.
(curl-7.61.0): Replace variable with ...
(curl-7.61.1): ... new variable.
 2018-09-06 17:02:52 -04:00
Kei Kebreau 21f5f351fb
gnu: libgme: Update to 0.6.2. 
* gnu/packages/music.scm (libgme): Update to 0.6.2.
[native-inputs]: Add gcc-4.9.
 2018-09-06 11:01:52 -04:00
Eric Brown f66be84d08
gnu: gfortran, gcc-objc, gcc-objc++: Add version 8. 
* gnu/packages/gcc.scm (gfortran-8, gcc-objc-8, gcc-objc++-8): New
variables.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-09-06 11:12:40 +02:00
Ludovic Courtès b290a631a0
gnu: guile-present: Install .go files to libdir. 
* gnu/packages/plotutils.scm (guile-present)[source](modules, snippet):
Remove.
 2018-09-06 10:49:42 +02:00
Ludovic Courtès 89874fd156
gnu: guile-charting: Install .go files to libdir. 
* gnu/packages/plotutils.scm (guile-charting)[source](modules, snippet):
Remove.
 2018-09-06 10:48:44 +02:00
Ludovic Courtès b3ca2d8883
gnu: hpcguix-web: Update to 9ff40fc. 
* gnu/packages/web.scm (hpcguix-web): Update to 9ff40fc.
[arguments]: In 'wrap-program' phase, add guile-gcrypt, guile-git, and
guile-bytestructures to DEPS.
 2018-09-06 10:46:07 +02:00
Ludovic Courtès 96d6c41dfa
gnu: guile-commonmark: Install .go files to libdir. 
* gnu/packages/guile.scm (guile-commonmark)[source](snippet): Change the
"modir = " and "godir = " line separately, allowing .go files to be
installed to $(libdir).
 2018-09-06 10:43:01 +02:00
Ricardo Wurmus d53aeeafcc
Add missing use-modules clause. 
This is a follow-up to commit 5dfe491290.
Sorry!

* gnu/packages/bioinformatics.scm, gnu/packages/graph.scm: Use (gnu packages
bioconductor).
 2018-09-06 04:53:32 +02:00
Tobias Geerinckx-Rice 79b283e433
gnu: ccache: Update to 3.4.3. 
* gnu/packages/ccache.scm (ccache): Update to 3.4.3.
[arguments]: Remove obsolete 'munge-failing-test' phase.
 2018-09-06 02:33:47 +02:00
Tobias Geerinckx-Rice d83477adf9
gnu: font-fira-code: Update to 1.205. 
* gnu/packages/fonts.scm (font-fira-code): Update to 1.205.
 2018-09-06 02:33:47 +02:00
Tobias Geerinckx-Rice a5c70c2e0e
gnu: libmpdclient: Update to 2.15. 
* gnu/packages/mpd.scm (libmpdclient): Update to 2.15.
 2018-09-06 02:33:47 +02:00
Ricardo Wurmus 00a43cb81c
gnu: pigx-scrnaseq: Use latest version of Pandoc. 
* gnu/packages/bioinformatics.scm (pigx-scrnaseq)[inputs]: Replace
"ghc-pandoc-citeproc-with-pandoc-1" with "ghc-pandoc-citeproc", and
"ghc-pandoc-1" with "ghc-pandoc".
 2018-09-05 20:03:09 +02:00
Ricardo Wurmus c2b4f81e51
gnu: pigx-bsseq: Use latest version of Pandoc. 
* gnu/packages/bioinformatics.scm (pigx-bsseq)[inputs]: Replace
"ghc-pandoc-citeproc-with-pandoc-1" with "ghc-pandoc-citeproc", and
"ghc-pandoc-1" with "ghc-pandoc".
 2018-09-05 20:03:09 +02:00
Ricardo Wurmus 7cd40c8c5d
gnu: pigx-chipseq: Use latest version of Pandoc. 
* gnu/packages/bioinformatics.scm (pigx-chipseq)[inputs]: Replace
"ghc-pandoc-citeproc-with-pandoc-1" with "ghc-pandoc-citeproc", and
"ghc-pandoc-1" with "ghc-pandoc".
 2018-09-05 20:03:09 +02:00
Ricardo Wurmus ca248f1db9
gnu: pigx-rnaseq: Use latest version of Pandoc. 
* gnu/packages/bioinformatics.scm (pigx-rnaseq)[inputs]: Replace
"ghc-pandoc-citeproc-with-pandoc-1" with "ghc-pandoc-citeproc", and
"ghc-pandoc-1" with "ghc-pandoc".
 2018-09-05 20:03:09 +02:00
Ricardo Wurmus dff5640a59
gnu: r-rcas: Use standard version of ghc-pandoc-citeproc. 
* gnu/packages/bioinformatics.scm (r-rcas)[native-inputs]: Replace
"ghc-pandoc-citeproc-with-pandoc-1" with "ghc-pandoc-citeproc".
 2018-09-05 20:03:09 +02:00
Ricardo Wurmus f33a4748b7
gnu: r-modelmetrics: Update to 1.2.0. 
* gnu/packages/statistics.scm (r-modelmetrics): Update to 1.2.0.
[propagated-inputs]: Add r-data-table.
 2018-09-05 20:03:09 +02:00
Ricardo Wurmus 0d279d607a
gnu: r-robustbase: Update to 0.93-2. 
* gnu/packages/statistics.scm (r-robustbase): Update to 0.93-2.
 2018-09-05 20:03:09 +02:00
Ricardo Wurmus 8e499d756a
gnu: r-rann: Update to 2.6. 
* gnu/packages/statistics.scm (r-rann): Update to 2.6.
 2018-09-05 20:03:09 +02:00
Ricardo Wurmus 314e8e763f
gnu: r-ggthemes: Update to 4.0.1. 
* gnu/packages/statistics.scm (r-ggthemes): Update to 4.0.1.
[propagated-inputs]: Remove r-assertthat and r-colorspace; add r-purrr,
r-stringr, and r-tibble.
 2018-09-05 20:03:09 +02:00
Ricardo Wurmus e5db6890ad
gnu: r-ztable: Update to 0.2.0. 
* gnu/packages/statistics.scm (r-ztable): Update to 0.2.0.
[propagated-inputs]: Add r-flextable, r-magrittr, r-moonbook, r-officer,
r-rcolorbrewer, r-scales, and r-stringr.
 2018-09-05 20:03:08 +02:00
Ricardo Wurmus f0519c8fae
gnu: r-zoo: Update to 1.8-3. 
* gnu/packages/statistics.scm (r-zoo): Update to 1.8-3.
 2018-09-05 20:03:08 +02:00
Ricardo Wurmus 8da236a377
gnu: r-gtools: Update to 3.8.1. 
* gnu/packages/statistics.scm (r-gtools): Update to 3.8.1.
 2018-09-05 20:03:08 +02:00
Ricardo Wurmus c28d8d8db0
gnu: r-kernlab: Update to 0.9-27. 
* gnu/packages/machine-learning.scm (r-kernlab): Update to 0.9-27.
 2018-09-05 20:03:08 +02:00
Ricardo Wurmus c0608f815c
gnu: r-adaptivesparsity: Update to 1.6. 
* gnu/packages/machine-learning.scm (r-adaptivesparsity): Update to 1.6.
[propagated-inputs]: Add r-mass and r-matrix.
 2018-09-05 20:03:08 +02:00
Ricardo Wurmus a207bca2ad
gnu: r-codedepends: Move from cran to bioconductor. 
* gnu/packages/cran.scm (r-codedepends): Move from here...
* gnu/packages/bioconductor.scm (r-codedepends): ...to here.
 2018-09-05 20:03:08 +02:00
Ricardo Wurmus 5dfe491290
gnu: r-graph: Move from bioinformatics to bioconductor. 
* gnu/packages/bioinformatics.scm (r-graph): Move from here...
* gnu/packages/bioconductor.scm (r-graph): ...to here.
 2018-09-05 20:03:08 +02:00
Ricardo Wurmus caaec88651
gnu: r-ggpubr: Update to 0.1.8. 
* gnu/packages/cran.scm (r-ggpubr): Update to 0.1.8.
[propagated-inputs]: Add r-glue and r-polynom.
 2018-09-05 20:03:08 +02:00
Ricardo Wurmus a9b02ddd73
gnu: r-codedepends: Update to 0.6.5. 
* gnu/packages/cran.scm (r-codedepends): Update to 0.6.5.
[propagated-inputs]: Add r-graph.
 2018-09-05 20:03:08 +02:00
Ricardo Wurmus 2e6909baf0
gnu: r-later: Update to 0.7.4. 
* gnu/packages/cran.scm (r-later): Update to 0.7.4.
 2018-09-05 20:03:08 +02:00
Ricardo Wurmus 12132229b0
gnu: r-maptools: Update to 0.9-3. 
* gnu/packages/cran.scm (r-maptools): Update to 0.9-3.
 2018-09-05 20:03:08 +02:00
Ricardo Wurmus 7a96c4e0a0
gnu: r-fnn: Update to 1.1.2.1. 
* gnu/packages/cran.scm (r-fnn): Update to 1.1.2.1.
 2018-09-05 20:03:08 +02:00
Ricardo Wurmus 19950821d7
gnu: r-heatmaply: Update to 0.15.2. 
* gnu/packages/cran.scm (r-heatmaply): Update to 0.15.2.
 2018-09-05 20:03:08 +02:00
Ricardo Wurmus 1fe9919a57
gnu: r-tsa: Update to 1.2. 
* gnu/packages/cran.scm (r-tsa): Update to 1.2.
[propagated-inputs]: Remove r-tseries.
 2018-09-05 20:03:08 +02:00
Ricardo Wurmus be5642eb69
gnu: r-statnet-common: Update to 4.1.4. 
* gnu/packages/cran.scm (r-statnet-common): Update to 4.1.4.
 2018-09-05 20:03:08 +02:00
Ricardo Wurmus e32368c130
gnu: r-metap: Update to 1.0. 
* gnu/packages/cran.scm (r-metap): Update to 1.0.
[propagated-inputs]: Add r-rdpack.
 2018-09-05 20:03:07 +02:00
Ricardo Wurmus d97d98e142
gnu: r-tinytex: Update to 0.8. 
* gnu/packages/cran.scm (r-tinytex): Update to 0.8.
 2018-09-05 20:03:07 +02:00
Ricardo Wurmus 6f5b157e3d
gnu: r-pillar: Update to 1.3.0. 
* gnu/packages/cran.scm (r-pillar): Update to 1.3.0.
[propagated-inputs]: Add r-fansi.
 2018-09-05 20:03:07 +02:00
Ricardo Wurmus 69bf449bf1
gnu: r-xts: Update to 0.11-0. 
* gnu/packages/cran.scm (r-xts): Update to 0.11-0.
[native-inputs]: Remove.
 2018-09-05 20:03:07 +02:00
Ricardo Wurmus 1b3b2a72ee
gnu: r-mice: Update to 3.3.0. 
* gnu/packages/cran.scm (r-mice): Update to 3.3.0.
 2018-09-05 20:03:07 +02:00
Ricardo Wurmus a7265593d3
gnu: r-pan: Update to 1.6. 
* gnu/packages/cran.scm (r-pan): Update to 1.6.
 2018-09-05 20:03:07 +02:00
Ricardo Wurmus e7630cc931
gnu: r-jomo: Update to 2.6-4. 
* gnu/packages/cran.scm (r-jomo): Update to 2.6-4.
[propagated-inputs]: Add r-ordinal.
 2018-09-05 20:03:07 +02:00
Ricardo Wurmus b8f6e2f82a
gnu: Add r-ordinal. 
* gnu/packages/cran.scm (r-ordinal): New variable.
 2018-09-05 20:03:07 +02:00
Ricardo Wurmus dc66835226
gnu: Add r-ucminf. 
* gnu/packages/cran.scm (r-ucminf): New variable.
 2018-09-05 20:03:07 +02:00
Ricardo Wurmus 45c156bf81
gnu: r-broom: Update to 0.5.0. 
* gnu/packages/cran.scm (r-broom): Update to 0.5.0.
[propagated-inputs]: Add r-backports, r-dplyr, r-purrr, and r-tibble; remove
r-plyr and r-psych.
 2018-09-05 20:03:07 +02:00
Ricardo Wurmus 2d2b95d151
gnu: r-ipred: Update to 0.9-7. 
* gnu/packages/cran.scm (r-ipred): Update to 0.9-7.
 2018-09-05 20:03:07 +02:00
Ricardo Wurmus c73752cac5
gnu: r-pls: Update to 2.7-0. 
* gnu/packages/cran.scm (r-pls): Update to 2.7-0.
 2018-09-05 20:03:07 +02:00
Ricardo Wurmus b00e8ae771
gnu: r-glue: Update to 1.3.0. 
* gnu/packages/cran.scm (r-glue): Update to 1.3.0.
 2018-09-05 20:03:07 +02:00
Ricardo Wurmus b72de5b3f6
gnu: r-callr: Update to 3.0.0. 
* gnu/packages/cran.scm (r-callr): Update to 3.0.0.
[propagated-inputs]: Add r-base64enc.
 2018-09-05 20:03:07 +02:00
Ricardo Wurmus e3c1e93e35
gnu: r-reprex: Update to 0.2.0. 
* gnu/packages/cran.scm (r-reprex): Update to 0.2.0.
[propagated-inputs]: Add r-clipr, r-rlang, and r-withr.
 2018-09-05 20:03:07 +02:00
Ricardo Wurmus 2cdd9d4f83
gnu: r-reticulate: Update to 1.10. 
* gnu/packages/cran.scm (r-reticulate): Update to 1.10.
 2018-09-05 20:03:07 +02:00
Ricardo Wurmus cb96d81be4
gnu: r-doby: Update to 4.6-2. 
* gnu/packages/cran.scm (r-doby): Update to 4.6-2.
 2018-09-05 20:03:07 +02:00
Ricardo Wurmus 589bd1c426
gnu: Add r-flextable. 
* gnu/packages/cran.scm (r-flextable): New variable.
 2018-09-05 20:03:06 +02:00
Ricardo Wurmus 78f2c08c0b
gnu: r-rmarkdown: Use latest version of Pandoc. 
* gnu/packages/statistics.scm (r-rmarkdown)[propagated-inputs]: Replace
"ghc-pandoc-1" with "ghc-pandoc".
 2018-09-05 20:03:06 +02:00
Ricardo Wurmus f9f4578ba0
Revert "gnu: ghc-tasty: Update to 1.1.0.3." 
This reverts commit 3ad6b89090.
 2018-09-05 20:03:06 +02:00
Ricardo Wurmus 90708323a1
Revert "gnu: ghc-base-compat: Update to 0.10.4." 
This reverts commit 0fa2c552fc.

We may not upgrade base-compat at this point because we haven't upgraded the
default GHC yet.
 2018-09-05 20:03:06 +02:00
Ricardo Wurmus 0fd7d59dc3
gnu: Add r-moonbook. 
* gnu/packages/cran.scm (r-moonbook): New variable.
 2018-09-05 20:03:06 +02:00
Ricardo Wurmus aaed237d1b
gnu: Add r-nortest. 
* gnu/packages/cran.scm (r-nortest): New variable.
 2018-09-05 20:03:06 +02:00
Ricardo Wurmus 1f560b9cdb
gnu: Add r-sjmisc. 
* gnu/packages/cran.scm (r-sjmisc): New variable.
 2018-09-05 20:03:06 +02:00
Ricardo Wurmus cfc0631433
gnu: Add r-sjlabelled. 
* gnu/packages/cran.scm (r-sjlabelled): New variable.
 2018-09-05 20:03:06 +02:00
Ricardo Wurmus de059e4bd3
gnu: Add r-prediction. 
* gnu/packages/cran.scm (r-prediction): New variable.
 2018-09-05 20:03:06 +02:00
Ricardo Wurmus bfee9ce88f
gnu: Add r-snakecase. 
* gnu/packages/cran.scm (r-snakecase): New variable.
 2018-09-05 20:03:06 +02:00
Ricardo Wurmus c183fa2688
gnu: Add r-officer. 
* gnu/packages/cran.scm (r-officer): New variable.
 2018-09-05 20:03:06 +02:00
Ricardo Wurmus 5dbe7aa920
gnu: r-googlesheets: Update to 0.3.0. 
* gnu/packages/statistics.scm (r-googlesheets): Update to 0.3.0.
[propagated-inputs]: Add r-tibble.
 2018-09-05 20:03:06 +02:00
Ricardo Wurmus 88cb7aa9e7
gnu: r-plotly: Update to 4.8.0. 
* gnu/packages/statistics.scm (r-plotly): Update to 4.8.0.
[propagated-inputs]: Add r-promises and r-rlang.
 2018-09-05 20:03:06 +02:00
Ricardo Wurmus 195eec737c
gnu: r-matrixstats: Update to 0.54.0. 
* gnu/packages/statistics.scm (r-matrixstats): Update to 0.54.0.
 2018-09-05 20:03:06 +02:00
Ricardo Wurmus e2a2c3378e
gnu: r-r-rsp: Update to 0.43.0. 
* gnu/packages/statistics.scm (r-r-rsp): Update to 0.43.0.
 2018-09-05 20:03:06 +02:00
Ricardo Wurmus eefa7c7f3d
gnu: r-r-utils: Update to 2.7.0. 
* gnu/packages/statistics.scm (r-r-utils): Update to 2.7.0.
 2018-09-05 20:03:06 +02:00
Ricardo Wurmus e926159eb3
gnu: r-e1071: Update to 1.7-0. 
* gnu/packages/statistics.scm (r-e1071): Update to 1.7-0.
 2018-09-05 20:03:05 +02:00
Ricardo Wurmus 2aafa73a94
gnu: r-xml: Update to 3.98-1.16. 
* gnu/packages/statistics.scm (r-xml): Update to 3.98-1.16.
 2018-09-05 20:03:05 +02:00
Ricardo Wurmus 41f6685388
gnu: r-rcpparmadillo: Update to 0.9.100.5.0. 
* gnu/packages/statistics.scm (r-rcpparmadillo): Update to 0.9.100.5.0.
 2018-09-05 20:03:05 +02:00
Ricardo Wurmus 19cb93be55
gnu: r-git2r: Update to 0.23.0. 
* gnu/packages/statistics.scm (r-git2r): Update to 0.23.0.
[native-inputs]: Add pkg-config.
 2018-09-05 20:03:05 +02:00
Ricardo Wurmus 2848c52c5e
gnu: r-roxygen2: Update to 6.1.0. 
* gnu/packages/statistics.scm (r-roxygen2): Update to 6.1.0.
[propagated-inputs]: Add r-pkgload and r-purrr.
[native-inputs]: Add r-knitr.
 2018-09-05 20:03:05 +02:00
Ricardo Wurmus 9b7e8df85b
gnu: r-ade4: Update to 1.7-13. 
* gnu/packages/statistics.scm (r-ade4): Update to 1.7-13.
 2018-09-05 20:03:05 +02:00
Ricardo Wurmus 7f38b31ecb
gnu: r-xtable: Update to 1.8-3. 
* gnu/packages/statistics.scm (r-xtable): Update to 1.8-3.
 2018-09-05 20:03:05 +02:00
Ricardo Wurmus 6b02569f1d
gnu: r-dbplyr: Update to 1.2.2. 
* gnu/packages/statistics.scm (r-dbplyr): Update to 1.2.2.
 2018-09-05 20:03:05 +02:00
Ricardo Wurmus 3299bc1c5e
gnu: r-yaml: Update to 2.2.0. 
* gnu/packages/statistics.scm (r-yaml): Update to 2.2.0.
 2018-09-05 20:03:05 +02:00
Ricardo Wurmus 2a96a093ec
gnu: r-evaluate: Update to 0.11. 
* gnu/packages/statistics.scm (r-evaluate): Update to 0.11.
 2018-09-05 20:03:05 +02:00
Ricardo Wurmus 3bf390279d
gnu: r-scales: Update to 1.0.0. 
* gnu/packages/statistics.scm (r-scales): Update to 1.0.0.
[propagated-inputs]: Remove r-dichromat and r-plyr.
 2018-09-05 20:03:05 +02:00
Ricardo Wurmus 97c81cc174
gnu: r-stringi: Update to 1.2.4. 
* gnu/packages/statistics.scm (r-stringi): Update to 1.2.4.
 2018-09-05 20:03:05 +02:00
Ricardo Wurmus e362be8e89
gnu: Add r-pkgload. 
* gnu/packages/cran.scm (r-pkgload): New variable.
 2018-09-05 20:03:05 +02:00
Ricardo Wurmus 4f8247b54b
gnu: Add r-pkgbuild. 
* gnu/packages/cran.scm (r-pkgbuild): New variable.
 2018-09-05 20:03:05 +02:00
Ricardo Wurmus 1ec1989f80
gnu: r-httpuv: Update to 1.4.5. 
* gnu/packages/web.scm (r-httpuv): Update to 1.4.5.
[native-inputs]: Add pkg-config.
 2018-09-05 20:03:05 +02:00
Ricardo Wurmus f077174178
gnu: r-scran: Update to 1.8.4. 
* gnu/packages/bioinformatics.scm (r-scran): Update to 1.8.4.
 2018-09-05 20:03:05 +02:00
Ricardo Wurmus 8e44ff0c0d
gnu: r-scater: Update to 1.8.4. 
* gnu/packages/bioinformatics.scm (r-scater): Update to 1.8.4.
 2018-09-05 20:03:05 +02:00
Ricardo Wurmus e69c07e61a
gnu: r-hdf5array: Update to 1.8.1. 
* gnu/packages/bioinformatics.scm (r-hdf5array): Update to 1.8.1.
 2018-09-05 20:03:04 +02:00
Ricardo Wurmus 16527f1cbc
gnu: r-ggbio: Update to 1.28.5. 
* gnu/packages/bioinformatics.scm (r-ggbio): Update to 1.28.5.
[propagated-inputs]: Add r-rlang.
 2018-09-05 20:03:04 +02:00
Ricardo Wurmus 70daf9362b
gnu: r-biovizbase: Update to 1.28.2. 
* gnu/packages/bioinformatics.scm (r-biovizbase): Update to 1.28.2.
[propagated-inputs]: Add r-rlang.
 2018-09-05 20:03:04 +02:00
Ricardo Wurmus ff7c7d62f4
gnu: r-keggrest: Update to 1.20.1. 
* gnu/packages/bioinformatics.scm (r-keggrest): Update to 1.20.1.
 2018-09-05 20:03:04 +02:00
Ricardo Wurmus 3c55304688
gnu: r-edaseq: Update to 2.14.1. 
* gnu/packages/bioinformatics.scm (r-edaseq): Update to 2.14.1.
 2018-09-05 20:03:04 +02:00
Ricardo Wurmus eb251fe524
gnu: r-igraph: Update to 1.2.2. 
* gnu/packages/graph.scm (r-igraph): Update to 1.2.2.
 2018-09-05 20:03:04 +02:00
Ricardo Wurmus c273bcdfce
gnu: r-diffusionmap: Update to 1.1-0.1. 
* gnu/packages/graph.scm (r-diffusionmap): Update to 1.1-0.1.
 2018-09-05 20:03:04 +02:00
Ricardo Wurmus 6f6aef80e3
gnu: r-seurat: Update to 2.3.4. 
* gnu/packages/bioinformatics.scm (r-seurat): Update to 2.3.4.
[source]: Remove snippet.
[arguments]: Remove.
[native-inputs]: Remove.
[propagated-inputs]: Remove r-caret, r-diffusionmap, r-fnn, r-gdata, r-ranger,
r-stringr, r-tclust, and rvgam; add r-httr.
 2018-09-05 20:03:04 +02:00
Ricardo Wurmus 07bd90ce90
gnu: r-msnbase: Update to 2.6.3. 
* gnu/packages/bioinformatics.scm (r-msnbase): Update to 2.6.3.
 2018-09-05 20:03:04 +02:00
Ricardo Wurmus 4ee8c37cca
gnu: r-maldiquant: Update to 1.18. 
* gnu/packages/bioinformatics.scm (r-maldiquant): Update to 1.18.
 2018-09-05 20:03:04 +02:00
Ricardo Wurmus 48b21f8b6b
gnu: r-seqminer: Update to 6.1. 
* gnu/packages/bioinformatics.scm (r-seqminer): Update to 6.1.
 2018-09-05 20:03:04 +02:00
Ricardo Wurmus ad2ed8d01f
gnu: r-genomicfeatures: Update to 1.32.2. 
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.32.2.
 2018-09-05 20:03:04 +02:00
Ricardo Wurmus f2e79823c6
gnu: r-rtracklayer: Update to 1.40.6. 
* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.40.6.
 2018-09-05 20:03:04 +02:00
Ricardo Wurmus aea1b6fb8a
gnu: r-delayedarray: Update to 0.6.5. 
* gnu/packages/bioinformatics.scm (r-delayedarray): Update to 0.6.5.
 2018-09-05 20:03:04 +02:00
Ricardo Wurmus 3e61c2a8b1
gnu: r-rsamtools: Update to 1.32.3. 
* gnu/packages/bioinformatics.scm (r-rsamtools): Update to 1.32.3.
 2018-09-05 20:03:04 +02:00
Ricardo Wurmus a02340058c
gnu: r-biocparallel: Update to 1.14.2. 
* gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.14.2.
 2018-09-05 20:03:04 +02:00
Ricardo Wurmus 1d56c79f86
gnu: r-genomicranges: Update to 1.32.6. 
* gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.32.6.
 2018-09-05 20:03:04 +02:00
Ricardo Wurmus 688cb08527
gnu: r-limma: Update to 3.36.3. 
* gnu/packages/bioinformatics.scm (r-limma): Update to 3.36.3.
 2018-09-05 20:03:03 +02:00
Ricardo Wurmus 33a103a543
gnu: r-variantannotation: Update to 1.26.1. 
* gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.26.1.
 2018-09-05 20:03:03 +02:00
Ricardo Wurmus 1adf4596a6
gnu: r-edger: Update to 3.22.3. 
* gnu/packages/bioinformatics.scm (r-edger): Update to 3.22.3.
 2018-09-05 20:03:03 +02:00
Ricardo Wurmus 5728d9c6c0
gnu: r-iranges: Update to 2.14.11. 
* gnu/packages/bioinformatics.scm (r-iranges): Update to 2.14.11.
 2018-09-05 20:03:03 +02:00
Ricardo Wurmus 3c04375614
gnu: r-biocviews: Update to 1.48.3. 
* gnu/packages/bioinformatics.scm (r-biocviews): Update to 1.48.3.
 2018-09-05 20:03:03 +02:00
Ricardo Wurmus ce0e762bf9
gnu: r-annotationforge: Update to 1.22.2. 
* gnu/packages/bioinformatics.scm (r-annotationforge): Update to 1.22.2.
 2018-09-05 20:03:03 +02:00
Ricardo Wurmus 65050163e0
gnu: r-chippeakanno: Update to 3.14.1. 
* gnu/packages/bioconductor.scm (r-chippeakanno): Update to 3.14.1.
 2018-09-05 20:03:03 +02:00
Ricardo Wurmus 88e4ed55d6
gnu: Add r-clipr. 
* gnu/packages/cran.scm (r-clipr): New variable.
 2018-09-05 20:03:03 +02:00
Ricardo Wurmus 6a8469755c
gnu: Add r-rdpack. 
* gnu/packages/cran.scm (r-rdpack): New variable.
 2018-09-05 20:03:03 +02:00
Ricardo Wurmus dd954dd743
gnu: Add r-gbrd. 
* gnu/packages/cran.scm (r-gbrd): New variable.
 2018-09-05 20:03:03 +02:00
Ricardo Wurmus 53718658d2
gnu: Add r-polynom. 
* gnu/packages/cran.scm (r-polynom): New variable.
 2018-09-05 20:03:03 +02:00
Ricardo Wurmus 356230da4a
gnu: Add r-fansi. 
* gnu/packages/cran.scm (r-fansi): New variable.
 2018-09-05 20:03:03 +02:00
Ludovic Courtès 3b0153bd82
gnu: guix-daemon: Add dependency on Guile-Gcrypt. 
This is a followup to 53166aec98, which
made Guile-Gcrypt a hard dependency.

* gnu/packages/package-management.scm (guix-daemon)[inputs]: Add
GUILE-GCRYPT.
 2018-09-05 15:48:04 +02:00
Ludovic Courtès 7903f00a74
gnu: cuirass: Add dependency on Guile-Gcrypt. 
This is a followup to 53166aec98, which
added a hard dependency of Guix on Guile-Gcrypt.

* gnu/packages/ci.scm (cuirass)[inputs]: Add GUILE-GCRYPT.
[arguments]: In 'wrap-program' phase, use 'string-join' to compute
'mods'.  Define 'objs' for use in GUILE_LOAD_COMPILED_PATH, and take
objects from lib/guile/X.Y/site-ccache.
 2018-09-05 15:35:54 +02:00
Ludovic Courtès 5e3082df1c
gnu: guile-fibers: Install .go files to "…/site-ccache". 
* gnu/packages/guile.scm (guile-fibers)[arguments]: New field.
 2018-09-05 15:35:54 +02:00
Eric Bavier 3f5e6ccf9b
slepc: Upgrade to 3.9.2. 
* gnu/packages/maths.scm (slepc): Upgrade to 3.9.2.
 2018-09-05 08:10:38 -05:00
Eric Bavier c15be1280e
petsc: Upgrade to 3.9.3. 
* gnu/packages/maths.scm (petsc): Upgrade to 3.9.3.
[arguments]: Remove unnecessary configure flags.
 2018-09-05 08:10:37 -05:00
Eric Bavier a3a99e27bb
petsc: Move example code to "examples" output. 
* gnu/packages/maths.scm (petsc)[arguments]: New 'move-examples' phase.
 2018-09-05 08:10:37 -05:00
Eric Bavier b26e4f26ff
gnu: Add SUNDIALS. 
* gnu/packages/maths.scm (sundials, sundials-openmpi): New variables.
 2018-09-05 08:10:31 -05:00
Alex Vong 296f091b48
gnu: packages: mp3: Use HTTPS where possible. 
* gnu/packages/mp3.scm (libmad)[home-page]: Use HTTPS.
(libid3tag)[home-page]: Likewise.
(mp3info)[source, home-page]: Likewise.
(mpg123)[source]: Likewise.
(libmpcdec)[source, home-page]: Likewise.

Signed-off-by: 宋文武 <iyzsong@member.fsf.org>
 2018-09-05 20:56:55 +08:00
Alex Vong 998100e6e8
gnu: eyed3: Update home page. 
* gnu/packages/mp3.scm (eyed3)[home-page]: Update to redirected HTTPS URL.

Signed-off-by: 宋文武 <iyzsong@member.fsf.org>
 2018-09-05 20:56:55 +08:00
Ludovic Courtès 53166aec98
gnu: guix: Update to 3d43017. 
* gnu/packages/package-management.scm (guix): Update to 3d43017.
 2018-09-05 14:31:48 +02:00
Ludovic Courtès 185948b8a8
gnu: xorg: Fix typo. 
* gnu/packages/xorg.scm: Fix typo in Benjamin's email address.
 2018-09-05 13:57:43 +02:00
Ricardo Wurmus 4fd2622df8
gnu: python-tables: Update to 3.4.4. 
* gnu/packages/python.scm (python-tables): Update to 3.4.4.
 2018-09-05 12:01:23 +02:00
Ricardo Wurmus 8afdeb8751
gnu: python-pybigwig: Update to 0.3.12. 
* gnu/packages/bioinformatics.scm (python-pybigwig): Update to 0.3.12.
[propagated-inputs]: Add python-numpy.
 2018-09-05 12:01:23 +02:00
Ricardo Wurmus 0d7974c376
gnu: libbigwig: Update to 0.4.2. 
* gnu/packages/bioinformatics.scm (libbigwig): Update to 0.4.2.
[source]: Fetch from git.
[arguments]: Disable tests; remove build phases "disable-curl-test" and
"create-target-dirs".
[native-inputs]: Add python-2.
 2018-09-05 12:01:23 +02:00
Ricardo Wurmus ca1dc4c76a
gnu: nss-pam-ldapd: Update to 0.9.10. 
* gnu/packages/openldap.scm (nss-pam-ldapd): Update to 0.9.10.
 2018-09-05 11:44:52 +02:00
Rutger Helling fefe17b088
gnu: dolphin-emu: Update to commit 5f0d825. 
* gnu/packages/emulators.scm (dolphin-emu): Update to commit 5f0d825.
 2018-09-05 10:23:20 +02:00
Leo Famulari fcf4841c0e
gnu: Zsh: Patch some tests that began failing in 5.6. 
* gnu/packages/shells.scm (zsh)[arguments]: Patch the tests rather than deleting
them.
 2018-09-04 18:34:01 -04:00
Leo Famulari 95681e5586
gnu: Zsh: Update to 5.6 [fixes CVE-2018-{0502,13259}]. 
* gnu/packages/shells.scm (zsh): Update to 5.6.
[arguments]: Skip some tests.
 2018-09-04 18:10:53 -04:00
Ludovic Courtès ca71942445
Switch to Guile-Gcrypt. 
This removes (guix hash) and (guix pk-crypto), which now live as part of
Guile-Gcrypt (version 0.1.0.)

* guix/gcrypt.scm, guix/hash.scm, guix/pk-crypto.scm,
tests/hash.scm, tests/pk-crypto.scm: Remove.
* configure.ac: Test for Guile-Gcrypt.  Remove LIBGCRYPT and
LIBGCRYPT_LIBDIR assignments.
* m4/guix.m4 (GUIX_ASSERT_LIBGCRYPT_USABLE): Remove.
* README: Add Guile-Gcrypt to the dependencies; move libgcrypt as
"required unless --disable-daemon".
* doc/guix.texi (Requirements): Likewise.
* gnu/packages/bash.scm, guix/derivations.scm, guix/docker.scm,
guix/git.scm, guix/http-client.scm, guix/import/cpan.scm,
guix/import/cran.scm, guix/import/crate.scm, guix/import/elpa.scm,
guix/import/gnu.scm, guix/import/hackage.scm,
guix/import/texlive.scm, guix/import/utils.scm, guix/nar.scm,
guix/pki.scm, guix/scripts/archive.scm,
guix/scripts/authenticate.scm, guix/scripts/download.scm,
guix/scripts/hash.scm, guix/scripts/pack.scm,
guix/scripts/publish.scm, guix/scripts/refresh.scm,
guix/scripts/substitute.scm, guix/store.scm,
guix/store/deduplication.scm, guix/tests.scm, tests/base32.scm,
tests/builders.scm, tests/challenge.scm, tests/cpan.scm,
tests/crate.scm, tests/derivations.scm, tests/gem.scm,
tests/nar.scm, tests/opam.scm, tests/pki.scm,
tests/publish.scm, tests/pypi.scm, tests/store-deduplication.scm,
tests/store.scm, tests/substitute.scm: Adjust imports.
* gnu/system/vm.scm: Likewise.
(guile-sqlite3&co): Rename to...
(gcrypt-sqlite3&co): ... this.  Add GUILE-GCRYPT.
(expression->derivation-in-linux-vm)[config]: Remove.
(iso9660-image)[config]: Remove.
(qemu-image)[config]: Remove.
(system-docker-image)[config]: Remove.
* guix/scripts/pack.scm: Adjust imports.
(guile-sqlite3&co): Rename to...
(gcrypt-sqlite3&co): ... this.  Add GUILE-GCRYPT.
(self-contained-tarball)[build]: Call 'make-config.scm' without
 #:libgcrypt argument.
(squashfs-image)[libgcrypt]: Remove.
[build]: Call 'make-config.scm' without #:libgcrypt.
(docker-image)[config, json]: Remove.
[build]: Add GUILE-GCRYPT to the extensions  Remove (guix config) from
the imported modules.
* guix/self.scm (specification->package): Remove "libgcrypt", add
"guile-gcrypt".
(compiled-guix): Remove #:libgcrypt.
[guile-gcrypt]: New variable.
[dependencies]: Add it.
[*core-modules*]: Remove #:libgcrypt from 'make-config.scm' call.
Add #:extensions.
[*config*]: Remove #:libgcrypt from 'make-config.scm' call.
(%dependency-variables): Remove %libgcrypt.
(make-config.scm): Remove #:libgcrypt.
* build-aux/build-self.scm (guile-gcrypt): New variable.
(make-config.scm): Remove #:libgcrypt.
(build-program)[fake-gcrypt-hash]: New variable.
Add (gcrypt hash) to the imported modules.  Adjust load path
assignments.
* gnu/packages/package-management.scm (guix)[propagated-inputs]: Add
GUILE-GCRYPT.
[arguments]: In 'wrap-program' phase, add GUILE-GCRYPT to the search
path.
 2018-09-04 17:25:11 +02:00
Alex Vong 1bf758767d
gnu: Add emacs-picpocket. 
* gnu/packages/emacs.scm (emacs-picpocket): New public variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-09-04 15:39:43 +02:00
Paul Garlick 71ca16b58d
gnu: petsc-openmpi: Configure with support for hdf5 data format. 
* gnu/packages/maths.scm (petsc-openmpi)[inputs]: Add
hdf5-parallel-openmpi.
[arguments]: Add '--with-hdf5-include' and '--with-hdf5-lib'
flags.  Add 'set-test-environment' phase.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-09-04 15:22:48 +02:00
Jonathan Brielmaier b50658fe8a
gnu: kicad: Update to 5.0.0. 
* gnu/packages/engineering.scm (kicad): Update to 5.0.0.
[source]: Change from git to url-fetch.
[arguments]: Remove now unneeded build version parameter.
[inputs]: Add opencascade-oce.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-09-04 15:02:59 +02:00
Arun Isaac 906a396bff
gnu: ghc-zlib: Enable tests. 
* gnu/packages/haskell.scm (ghc-zlib)[arguments]: Enable tests. Allow building
with newer tasty.
[native-inputs]: Add ghc-quickcheck, ghc-tasty, ghc-tasty-hunit and
ghc-tasty-quickcheck.
 2018-09-04 17:31:09 +05:30
Arun Isaac 6300ba5b66
gnu: ghc-integer-logarithms: Allow building with newer tasty. 
* gnu/packages/haskell.scm (ghc-integer-logarithms)[arguments]: Allow building
with newer tasty.
 2018-09-04 15:24:32 +05:30
Arun Isaac 8374cc4b05
gnu: ghc-tasty-ant-xml: Update to 1.1.4. 
* gnu/packages/haskell-check.scm (ghc-tasty-ant-xml): Update to 1.1.4.
 2018-09-04 15:21:56 +05:30
Arun Isaac 3ad6b89090
gnu: ghc-tasty: Update to 1.1.0.3. 
* gnu/packages/haskell-check.scm (ghc-tasty): Update to 1.1.0.3.
[inputs]: Add ghc-wcwidth.
(ghc-attoparsec-bootstrap, ghc-integer-logarithms-bootstrap,
ghc-scientific-bootstrap): New variables.
(ghc-wcwidth)[inputs]: Replace ghc-attoparsec with ghc-attoparsec-bootstrap.
(ghc-scientific)[inputs]: Replace ghc-integer-logarithms with
ghc-integer-logarithms-bootstrap.
(ghc-attoparsec)[inputs]: Replace ghc-scientific with
ghc-scientific-bootstrap.
 2018-09-04 12:15:17 +05:30
Arun Isaac 9c4b522f15
gnu: Add ghc-wcwidth. 
* gnu/packages/haskell.scm (ghc-wcwidth): New variable.
 2018-09-04 12:15:10 +05:30
Ludovic Courtès fd95f37f36
Revert "gnu: perl: Add support for cross-compilation" 
This reverts commit 5108c18e7e, which was
accidentally committed.
 2018-09-03 23:49:12 +02:00
Raphaël Mélotte 5108c18e7e
gnu: perl: Add support for cross-compilation 
* gnu/packages/perl.scm (perl): use cross-libc when cross-compiling

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-09-03 23:41:08 +02:00
Benjamin Slade 38fe6449c0
gnu: Add transset-df. 
* gnu/packages/xorg.scm (transset-df): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-09-03 23:40:23 +02:00
Marius Bakke 65a58f3907
gnu: ppp: Use OpenSSL for cryptography. 
* gnu/packages/samba.scm (ppp)[source](patches): Add upstream patch.
[inputs]: Add OPENSSL.
[arguments]: Add substitution for OpenSSL headers.
 2018-09-03 19:25:28 +02:00
Marius Bakke 70dc8db8e7
Merge branch 'master' into core-updates 2018-09-03 19:20:06 +02:00
Marius Bakke c702749dfd
gnu: arpack-ng: Update to 3.6.2. 
* gnu/packages/maths.scm (arpack-ng): Update to 3.6.2.
 2018-09-03 19:09:01 +02:00
Marius Bakke 91bb495b85
gnu: arpack-ng: Drop redundant phase. 
* gnu/packages/maths.scm (arpack-ng)[arguments]: Remove.
 2018-09-03 19:09:01 +02:00
Marius Bakke 1f7d142000
gnu: python-matplotlib: Update to 2.2.3. 
* gnu/packages/python.scm (python-matplotlib): Update to 2.2.3.
 2018-09-03 19:09:00 +02:00
Marius Bakke cbd7c65709
gnu: ppp: Return #t from all phases. 
* gnu/packages/samba.scm (ppp)[arguments]: Return #t from phase.
 2018-09-03 18:58:47 +02:00
Marius Bakke 84aa18ff7f
gnu: re2: Update to 2018-09-01. 
* gnu/packages/regex.scm (re2): Update to 2018-09-01.
 2018-09-03 18:58:47 +02:00
Marius Bakke fcde1d27bb
gnu: openexr: Update to 2.3.0. 
* gnu/packages/graphics.scm (openexr): Update to 2.3.0.
[source](uri): Change to new download location.
[source](snippet): Remove workaround.
[source](patches): Remove.
* gnu/packages/patches/openexr-missing-samples.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Remove it.
 2018-09-03 18:58:47 +02:00
Marius Bakke 1ae2c577a6
gnu: ilmbase: Update to 2.3.0. 
* gnu/packages/graphics.scm (ilmbase): Update to 2.3.0.
[source](uri): Change to new download location.
 2018-09-03 18:58:46 +02:00
Marius Bakke 9156206199
gnu: simplescreenrecorder: Build against modular Qt. 
* gnu/packages/video.scm (simplescreenrecorder)[inputs]: Remove QT.  Add
QTBASE and QTX11EXTRAS.
 2018-09-03 18:58:46 +02:00
Marius Bakke 65e686d6cb
Merge branch 'security-updates' 2018-09-03 18:58:20 +02:00
Efraim Flashner a5896da34e
gnu: gnu-pw-mgr: Update to 2.4.2. 
* gnu/packages/gnu-pw-mgr.scm (gnu-pw-mgr): Update to 2.4.2.
 2018-09-03 19:34:24 +03:00
Tobias Geerinckx-Rice 38a8cd329d
gnu: python-nbxmpp: Update to 0.6.7. 
* gnu/packages/messaging.scm (python-nbxmpp): Update to 0.6.7.
 2018-09-03 18:21:43 +02:00
Tobias Geerinckx-Rice b619b7f67b
gnu: libircclient: Update to 1.10. 
* gnu/packages/messaging.scm (libircclient): Update to 1.10.
 2018-09-03 18:21:43 +02:00
Tobias Geerinckx-Rice cfcfc6ab62
Fix some typos. 
* doc/guix.texi (Sound Services, DNS Services): Fix typos.
* gnu/packages/cpp.scm (json-modern-cxx)[description]: Likewise.
* gnu/packages/emacs.scm (emacs-fancy-narrow)[synopsis, description]:
Likewise. Edit & mark up while we're here.
* gnu/packages/mail.scm (alot)[synopsis, description]: Ditto.
 2018-09-03 18:21:43 +02:00
Tobias Geerinckx-Rice fb458bf3bc
gnu: sudo: Update to 1.8.25. 
* gnu/packages/admin.scm (sudo): Update to 1.8.25.
 2018-09-03 18:21:42 +02:00
Efraim Flashner 0cc6447669
gnu: python-efl: Update to 1.21.0. 
* gnu/packages/enlightenment.scm (python-efl): Update to 1.21.0.
[source]: Don't use pypi source.
[arguments]: Delete network tests.
 2018-09-03 17:32:44 +03:00
Efraim Flashner 290bef39f6
gnu: efl: Update to 1.21.0. 
* gnu/packages/enlightenment.scm (efl): Update to 1.21.0.
 2018-09-03 17:32:44 +03:00
Ricardo Wurmus 02ddafef55
gnu: python-scipy: Disable broken tests. 
* gnu/packages/python.scm (python-scipy)[arguments]: Skip two broken tests.
 2018-09-03 13:49:32 +02:00
Rutger Helling 26baaaf49b
gnu: c-toxcore: Update to 0.2.7. 
* gnu/packages/messaging.scm (c-toxcore): Update to 0.2.7.
 2018-09-03 08:22:51 +02:00
Rutger Helling aa613d71ec
gnu: openrct2: Update to 0.2.1. 
* gnu/packages/games.scm (openrct2-objects): Update to 1.0.6.
* gnu/packages/games.scm (openrct2): Update to 0.2.1.
 2018-09-03 08:22:50 +02:00
Efraim Flashner 647465ace9
gnu: jellyfish: Update to 2.2.10. 
* gnu/packages/bioinformatics.scm (jellyfish): Update to 2.2.10.
[supported-systems]: Add aarch64-linux, mips64el-linux.
 2018-09-03 08:32:33 +03:00
Oleg Pykhalov 3910977823
gnu: monitoring.scm: Fix copyright line. 
This is a follow-up to ead46692ec.
 2018-09-02 19:18:16 +03:00
Alex Vong 2bd6ed9e4c
gnu: haskell-mode: Fix test failure. 
Fixes <https://bugs.gnu.org/31726>.

Thanks to Jack Hill <jackhill@jackhill.us> for exploring different solutions
at <https://debbugs.gnu.org/cgi/bugreport.cgi?bug=31726>.

* gnu/packages/patches/haskell-mode-unused-variables.patch,
gnu/packages/patches/haskell-mode-make-check.patch: New files.
* gnu/local.mk (dist_patch_DATA): Add them.
* gnu/packages/emacs.scm (haskell-mode)[source]: Use them.
[arguments]: Adjust 'pre-build' phase to embed file name.

Co-authored-by: Ludovic Courtès <ludo@gnu.org>
 2018-09-02 17:06:43 +02:00
Konrad Hinsen b21a55a9f2
gnu: emacs-helpful: Update to 0.13. 
* gnu/packages/emacs.scm (emacs-helpful): Update to 0.13.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-09-02 16:58:06 +02:00
Konrad Hinsen 351b6463af
gnu: emacs-elisp-refs: Update to 1.3. 
* gnu/packages/emacs.scm (emacs-elisp-refs): Update to 1.3.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-09-02 16:56:22 +02:00
Rutger Helling 87284c6b48
gnu: wine-staging: Update to 3.15. 
* gnu/packages/wine.scm (wine-staging): Update to 3.15.
 2018-09-02 08:53:03 +02:00
Rutger Helling ab2e38e206
gnu: wine-staging-patchset-data: Update to 3.15. 
* gnu/packages/wine.scm (wine-staging-patchset-data): Update to 3.15.
 2018-09-02 08:53:03 +02:00
宋文武 9bf98520f2
gnu: rosegarden: Update to 18.06. 
* gnu/packages/music.scm (rosegarden): Update to 18.06.
[home-page]: Use HTTPS.
 2018-09-02 13:18:28 +08:00
Danny Milosavljevic 24d298b459
gnu: rust: Move rust-1.19 down. 2018-09-02 00:22:53 +02:00
Danny Milosavljevic 3159ef7c99
gnu: rust: Bootstrap (only) Rust 1.19.0 by mrustc. 
* gnu/packages/patches/rust-1.19-mrustc.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/rust.scm (rust-1.19)[source]: Add patch
"rust-1.19-mrustc.patch".
[arguments]<#:modules>: New field.
<#:phases>[patch-cargo-tomls]: New phase.
<#:phases>[build]: Modify.
<#:phases>[install]: Modify.
[native-inputs]: Replace rust-bootstrap by mrustc.
(rust-1.23)[native-inputs]: New field.
[arguments]<#:phases>: Delete phase "patch-cargo-tomls".
 2018-09-02 00:09:34 +02:00
Manuel Graf a0a273c1ee
gnu: Add perftest. 
* gnu/packages/linux.scm (perftest): New variable.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2018-09-01 17:51:29 -04:00
Julien Lepiller 37a0f47073
gnu: Add ruby-jekyll-paginate-v2. 
* gnu/packages/ruby.scm (ruby-jekyll-paginate-v2): New variable.
 2018-09-01 23:09:14 +02:00
Julien Lepiller 49e1dde53f
gnu: Add jekyll. 
* gnu/packages/ruby.scm (jekyll): New variable.
 2018-09-01 23:09:09 +02:00
Julien Lepiller 3729611379
gnu: Add ruby-pathutil. 
* gnu/packages/ruby.scm (ruby-pathutil): New variable.
 2018-09-01 23:09:06 +02:00
Julien Lepiller 49395112c4
gnu: Add ruby-forwardable-extended. 
* gnu/packages/ruby.scm (ruby-forwardable-extended): New variable.
 2018-09-01 23:09:04 +02:00
Julien Lepiller a13d451e18
gnu: Add ruby-liquid. 
* gnu/packages/ruby.scm (ruby-liquid): New variable.
 2018-09-01 23:09:02 +02:00
Julien Lepiller f1ec4d7611
gnu: Add ruby-mercenary. 
* gnu/packages/ruby.scm (ruby-mercenary): New variable.
 2018-09-01 23:09:00 +02:00
Julien Lepiller f8ae2ee528
gnu: Add ruby-safe-yaml. 
* gnu/packages/ruby.scm (ruby-safe-yaml): New variable.
 2018-09-01 23:08:58 +02:00
Julien Lepiller 73bfc125ef
gnu: Add ruby-heredoc-unindent. 
* gnu/packages/ruby.scm (ruby-heredoc-unindent): New variable.
 2018-09-01 23:08:56 +02:00
Julien Lepiller 2e072e37aa
gnu: Add ruby-hashie. 
* gnu/packages/ruby.scm (ruby-hashie): New variable.
 2018-09-01 23:08:55 +02:00
Julien Lepiller 2c5028bd97
gnu: Add ruby-rouge-2. 
* gnu/packages/ruby.scm (ruby-rouge-2): New variable.
 2018-09-01 23:08:53 +02:00
Julien Lepiller 4ce0414bca
gnu: Add ruby-rouge. 
* gnu/packages/ruby.scm (ruby-rouge): New variable.
 2018-09-01 23:08:46 +02:00
Julien Lepiller 5e2f74bdb8
gnu: Add ruby-em-websocket. 
* gnu/packages/ruby.scm (ruby-em-websocket): New variable.
 2018-09-01 23:08:44 +02:00
Julien Lepiller fa0063bcf4
gnu: Add ruby-http-parser.rb. 
* gnu/packages/ruby.scm (ruby-http-parser.rb): New variable.
 2018-09-01 23:08:42 +02:00
Julien Lepiller 0312706955
gnu: Add ruby-kramdown. 
* gnu/packages/ruby.scm (ruby-kramdown): New variable.
 2018-09-01 23:08:40 +02:00
Julien Lepiller 197ca8ecd2
gnu: Add ruby-prawn-table. 
* gnu/packages/ruby.scm (ruby-prawn-table): New variable.
 2018-09-01 23:08:38 +02:00
Julien Lepiller 7ad8dd086c
gnu: Add ruby-prawn. 
* gnu/packages/ruby.scm (ruby-prawn): New variable.
 2018-09-01 23:08:36 +02:00
Julien Lepiller 37fbced73c
gnu: Add ruby-yard. 
* gnu/packages/ruby.scm (ruby-yard): New variable.
 2018-09-01 23:08:34 +02:00
Julien Lepiller 770e3b535e
gnu: Add ruby-pdf-core. 
* gnu/packages/ruby.scm (ruby-pdf-core): New variable.
 2018-09-01 23:08:31 +02:00
Julien Lepiller 461fb8598e
gnu: Add ruby-pdf-inspector. 
* gnu/packages/ruby.scm (ruby-pdf-inspector): New variable.
 2018-09-01 23:08:29 +02:00
Julien Lepiller abbe629c6a
gnu: Add ruby-pdf-reader. 
* gnu/packages/ruby.scm (ruby-pdf-reader): New variable.
 2018-09-01 23:08:27 +02:00
Julien Lepiller 00d71efca6
gnu: Add ruby-morecane. 
* gnu/packages/ruby.scm (ruby-morecane): New variable.
 2018-09-01 23:08:10 +02:00
Julien Lepiller 83d9f67221
gnu: Add ruby-cane. 
* gnu/packages/ruby.scm (ruby-cane): New variable.
 2018-09-01 23:08:06 +02:00
Julien Lepiller 3224a5a84a
gnu: Add ruby-parallel. 
* gnu/packages/ruby.scm (ruby-parallel): New variable.
 2018-09-01 23:08:04 +02:00
Julien Lepiller ceac6f6f5b
gnu: Add ruby-jekyll-watch. 
* gnu/packages/ruby.scm (ruby-jekyll-watch): New variable.
 2018-09-01 23:08:02 +02:00
Julien Lepiller 88ed727fc5
gnu: Add ruby-listen-3.0. 
* gnu/packages/ruby.scm (ruby-listen-3.0): New variable.
 2018-09-01 23:08:00 +02:00
Julien Lepiller 5e242cb44c
gnu: Add ruby-jekyll-sass-converter. 
* gnu/packages/ruby.scm (ruby-jekyll-sass-converter): New variable.
 2018-09-01 23:07:58 +02:00
Julien Lepiller f00f449223
gnu: Add ruby-sass. 
* gnu/packages/ruby.scm (ruby-sass): New variable.
 2018-09-01 23:07:56 +02:00
Julien Lepiller 6456beef01
gnu: Add ruby-sass-spec. 
* gnu/packages/ruby.scm (ruby-sass-spec): New variable.
 2018-09-01 23:07:54 +02:00
Julien Lepiller ddc3a66798
gnu: Add ruby-diffy. 
* gnu/packages/ruby.scm (ruby-diffy): New variable.
 2018-09-01 23:07:52 +02:00
Julien Lepiller 0c8eedc153
gnu: Add ruby-terminfo. 
* gnu/packages/ruby.scm (ruby-terminfo): New variable.
 2018-09-01 23:07:50 +02:00
Julien Lepiller 18077ffc46
gnu: Add ruby-sass-listen. 
* gnu/packages/ruby.scm (ruby-sass-listen): New variable.
 2018-09-01 23:07:48 +02:00
Julien Lepiller 6bba8ecf7b
gnu: Add ruby-rdoc. 
* gnu/packages/ruby.scm (ruby-rdoc): New variable.
 2018-09-01 23:07:46 +02:00
Julien Lepiller f22c038799
gnu: Add ruby-command-line-reporter-3. 
* gnu/packages/ruby.scm (ruby-command-line-reporter-3): New variable.
 2018-09-01 23:07:44 +02:00
Julien Lepiller 78b9c291f6
gnu: Add ruby-command-line-reporter. 
* gnu/packages/ruby.scm (ruby-command-line-reporter): New variable.
 2018-09-01 23:07:42 +02:00
Julien Lepiller 9c7f15c048
gnu: Add ruby-colorator. 
* gnu/packages/ruby.scm (ruby-colorator): New variable.
 2018-09-01 23:07:39 +02:00
Julien Lepiller 6f2c4efb56
gnu: Add ruby-addressable. 
* gnu/package/ruby.scm (ruby-addressable): New variable.
 2018-09-01 23:07:37 +02:00
Julien Lepiller 0d16905b60
gnu: Add ruby-public-suffix. 
* gnu/packages/ruby.scm (ruby-public-suffix): New variable.
 2018-09-01 23:07:35 +02:00
Julien Lepiller afb7a3e8d5
gnu: ruby-ttfunk: Update to 1.5.1. 
* gnu/packages/ruby.scm (ruby-ttfunk): Update to 1.5.1.
 2018-09-01 23:07:32 +02:00
Julien Lepiller ef381322d5
gnu: ruby-activesupport: Update to 5.2.1. 
* gnu/packages/ruby.scm (ruby-activesupport): Update to 5.2.1.
 2018-09-01 23:07:30 +02:00
Julien Lepiller cbb50182ad
gnu: ruby-i18n: Update to 1.1.0. 
* gnu/packages/ruby.scm (ruby-i18n): Update to 1.1.0.
 2018-09-01 23:07:28 +02:00
Julien Lepiller 352b5d7e74
gnu: Add ruby-concurrent. 
* gnu/packages/ruby.scm (ruby-concurrent): New variable.
 2018-09-01 23:07:06 +02:00
Oleg Pykhalov ead46692ec
gnu: Add zabbix-agentd and zabbix-server. 
* gnu/packages/monitoring.scm (zabbix-agentd, zabbix-server): New variables.
 2018-09-01 19:01:36 +03:00
Marius Bakke e59588482b
gnu: nss, nss-certs: Update to 3.39 [fixes CVE-2018-12384]. 
* gnu/packages/gnuzilla.scm (nss): Update to 3.39.
* gnu/packages/certs.scm (nss-certs): Likewise.
 2018-09-01 13:26:13 +02:00
Marius Bakke 7ea90c217f
gnu: nspr: Update to 4.20. 
* gnu/packages/gnuzilla.scm (nspr): Update to 4.20.
 2018-09-01 13:23:39 +02:00
Marius Bakke 279ed3efee
gnu: qtbase: Fix build with glibc >= 2.28. 
* gnu/packages/patches/qtbase-glibc-compat.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/qt.scm (qtbase)[source](patches): Use it.
[arguments]: Remove "--no-feature-renameat2" from #:configure-flags.
 2018-09-01 13:00:01 +02:00
Marius Bakke 53b7c9716e
gnu: python-waf: Update to 2.0.10. 
* gnu/packages/python.scm (python-waf): Update to 2.0.10.
 2018-09-01 12:59:00 +02:00
Marius Bakke 3469a5ea47
gnu: gcc@4.9: Fix FTBFS with Glibc >= 2.28. 
* gnu/packages/commencement.scm (gcc-for-libstdc++): New variable.
(libstdc++-boot0): Inherit from GCC-FOR-LIBSTDC++ instead of GCC-4.9.
* gnu/packages/gcc.scm (gcc-4.9)[source](patches): Add
"gcc-4.9-libsanitizer-ustat.patch".
* gnu/packages/patches/gcc-4.9-libsanitizer-ustat.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
 2018-09-01 12:58:47 +02:00
Marius Bakke a446cf26d7
gnu: texinfo@5: Fix FTBFS with Perl >= 5.28. 
* gnu/packages/patches/texinfo-5-perl-compat.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/texinfo.scm (texinfo-5)[source](patches): New field.
 2018-09-01 12:56:52 +02:00
Leo Famulari ea59f0487b
gnu: Remove Krita 3. 
Krita 3 fails to build with Qt 5.11.1. Since it's also unmaintained upstream,
remove it.

* gnu/packages/kde.scm (krita-3): Remove variable.
 2018-09-01 02:09:53 -04:00
Leo Famulari fd67d793c2
gnu: Krita: Build with libraw 0.18. 
Fixes <https://bugs.gnu.org/32467>.

Reported by Björn Höfling <bjoern.hoefling@bjoernhoefling.de>.

* gnu/packages/photo.scm (libraw-0.18): New variable.
* gnu/packages/kde.scm (krita)[inputs]: Use libraw-0.18.
 2018-09-01 02:09:52 -04:00
Leo Famulari 7ce9eaf013
gnu: Krita: Update to 4.1.1. 
* gnu/packages/kde.scm (krita): Update to 4.1.1.
 2018-09-01 02:09:52 -04:00
Leo Famulari d84a887a5f
gnu: libksysguard: Update to 5.13.4. 
* gnu/packages/kde.scm (libksysguard): Update to 5.13.4.
 2018-09-01 02:09:52 -04:00
Leo Famulari 600f1ad8e6
gnu: KDE: Update to 5.49.0. 
Fixes <https://bugs.gnu.org/32013>.

* gnu/packages/kde-frameworks.scm (attica, baloo, bluez-qt, breeze-icons,
extra-cmake-modules, kactivities, kactivities-stats, kapidox, karchive, kauth,
kbookmarks, kcmutils, kcodecs, kcompletion, kconfig, kconfigwidgets,
kcoreaddons, kcrash, kdbusaddons, kde-framework-integration, kdeclarative, kded,
kdesignerplugin, kdesu, kdewebkit, kdnssd, kdoctools, kemoticons, kfilemetadata,
kglobalaccel, kguiaddons, ki18n, kiconthemes, kidletime, kimageformats, kinit,
kio, kirigami, kitemmodels, kitemview, kjobwidgets, knewstuff, knotification,
knotifyconfig, kpackage, kparts, kpeople, kplotting, kpty, krunner, kservice,
ksyntaxhighlighting, ktexteditor, ktextwidgets, kunitcoversion, kwallet,
kwayland, kwidgetsaddons, kwindowsystem, kxmlgui, kxmlrpcclient,
modemmanager-qt, networkmanager-qt, oxygen-icons, plasma-framework, prison,
qqc2-desktop-style, solid, sonnet, threadweaver): Update to 5.49.0.
(extra-cmake-modules)[arguments]: Remove obsolete workaround.
(attica)[arguments]: Disable some new tests.

Co-authored-by: Björn Höfling <bjoern.hoefling@bjoernhoefling.de>
 2018-09-01 02:09:49 -04:00
Eric Bavier 220458b098
gnu: hypre: Update to 2.14.0. 
* gnu/packages/maths.scm (hypre): Update to 2.14.0
 2018-08-31 10:08:00 -05:00
Ricardo Wurmus 9ce2f07ab6
gnu: python-matplotlib: Use python-pyqt-without-qtwebkit. 
* gnu/packages/python.scm (python-matplotlib)[propagated-inputs]: Replace
python-pyqt with python-pyqt-without-qtwebkit.
 2018-08-31 16:37:56 +02:00
Ricardo Wurmus 0e2d6d2698
gnu: Add python-pyqt-without-qtwebkit. 
* gnu/packages/qt.scm (python-pyqt-without-qtwebkit): New variable.
 2018-08-31 16:37:56 +02:00
Rutger Helling 0b6678cd44
gnu: retroarch: Update to 1.7.4. 
* gnu/packages/emulators.scm (retroarch): Update to 1.7.4.
 2018-08-31 08:25:45 +02:00
Nicolas Goaziou be4c63f484
gnu: mame: Update to 0.201. 
* gnu/packages/emulators.scm (mame): Update to 0.201.
[arguments]: Remove unnecessary fix.
 2018-08-31 07:04:17 +02:00
Tobias Geerinckx-Rice 0c048c11a4
gnu: cmocka: Update to 1.1.2. 
* gnu/packages/check.scm (cmocka): Update to 1.1.2.
 2018-08-30 19:29:08 +02:00
Tobias Geerinckx-Rice 8a68b71d99
gnu: keyutils: Update to 1.5.11. 
* gnu/packages/crypto.scm (keyutils): Update to 1.5.11.
[inputs]: Add mit-krb5.
 2018-08-30 19:28:11 +02:00
Tobias Geerinckx-Rice d6d9ca1017
gnu: Don't use unstable tarballs in (packages opencl). 
* gnu/packages/opencl.scm (opencl-clhpp, clinfo, beignet, pocl)
[source]: Use GIT-FETCH and GIT-FILE-NAME.
(pocl)[arguments]: Remove ‘remove-headers’ phase.
(make-opencl-headers)[source]: Use GIT-FILE-NAME.
 2018-08-30 19:28:11 +02:00
Tobias Geerinckx-Rice 8294362688
gnu: Add pipewalker. 
* gnu/packages/games.scm (pipewalker): New public variable.
 2018-08-30 19:28:11 +02:00
Tobias Geerinckx-Rice 6e8c75b884
gnu: Add msr-tools. 
* gnu/packages/hardware.scm (msr-tools): New public variable.
 2018-08-30 19:28:10 +02:00
Tobias Geerinckx-Rice aadd1d241c
gnu: Add ddcutil. 
* gnu/packages/hardware.scm: New file.
(ddcutil): New public variable.
* gnu/local.mk (GNU_SYSTEM_MODULES): Add the new file.
 2018-08-30 19:28:10 +02:00
Marius Bakke 7693f678d1
gnu: pango: Replace with 1.42.4. 
Fixes <https://bugs.gnu.org/32594>.

* gnu/packages/gtk.scm (pango)[replacement]: New field.
(pango-1.42.4): New public variable.
 2018-08-30 18:57:10 +02:00
Marius Bakke 883832b480
gnu: appstream-glib: Update to 0.7.12. 
* gnu/packages/glib.scm (appstream-glib): Update to 0.7.12.
 2018-08-30 18:44:57 +02:00
Marius Bakke 4c13cb36f8
gnu: GnuPG: Update to 2.2.10. 
* gnu/packages/gnupg.scm (gnupg): Update to 2.2.10.
 2018-08-30 18:44:57 +02:00
Marius Bakke e50c727878
gnu: rng-tools: Update to 6.4. 
* gnu/packages/linux.scm (rng-tools): Update to 6.4.
 2018-08-30 18:44:57 +02:00
Marius Bakke d3c1075c14
gnu: samba: Update to 4.8.5. 
* gnu/packages/samba.scm (samba): Update to 4.8.5.
 2018-08-30 18:44:57 +02:00
Marius Bakke 652940d060
gnu: ldb: Update to 1.3.6. 
* gnu/packages/samba.scm (ldb): Update to 1.3.6.
 2018-08-30 18:44:57 +02:00
Marius Bakke 99088aa751
gnu: p11-kit: Update to 0.23.14. 
* gnu/packages/tls.scm (p11-kit): Update to 0.23.14.
 2018-08-30 18:44:56 +02:00
Marius Bakke 471884ed11
gnu: lilv: Propagate LV2. 
* gnu/packages/audio.scm (lilv)[propagated-inputs]: Add LV2.
[inputs]: Remove.
 2018-08-30 18:44:51 +02:00
Oleg Pykhalov b5d1286f2d
gnu: net-snmp: Specify '--with-openssl' configuration flag. 
* gnu/packages/networking.scm (net-snmp)[arguments]: Add '--with-openssl'
flag.
 2018-08-30 14:46:15 +03:00
Eric Bavier f9e140a243
netsurf: Upgrade to 3.8. 
* gnu/packages/patches/netsurf-message-timestamp.patch: New patch.
* gnu/packages/patches/netsurf-system-utf8proc.patch: Adjust to new source.
* gnu/packages/web.scm (netsurf): Upgrade to 3.8.
[source]: Add the new patch.
 2018-08-30 00:44:40 -05:00
Eric Bavier c558113fb9
nsgenbind: Upgrade to 0.6. 
* gnu/packages/web.scm (nsgenbind): Upgrade to 0.6.
 2018-08-30 00:44:40 -05:00
Eric Bavier 1be7077572
libnspsl: Upgrade to 0.1.3. 
* gnu/packages/web.scm (libnspsl): Upgrade to 0.1.3.
 2018-08-30 00:44:40 -05:00
Eric Bavier 3e1035d738
libnsutils: Upgrade to 0.0.5. 
* gnu/packages/web.scm (libnsutils): Upgrade to 0.0.5.
 2018-08-30 00:44:40 -05:00
Eric Bavier 1dc02e727b
libnsgif: Upgrade to 0.2.1. 
* gnu/packages/web.scm (libnsgif): Upgrade to 0.2.1.
 2018-08-30 00:44:39 -05:00
Eric Bavier ef2198ac5b
libnsbmp: Upgrade to 0.1.5. 
* gnu/packages/web.scm (libnsbmp): Upgrade to 0.1.5.
 2018-08-30 00:44:39 -05:00
Eric Bavier bb38628fab
libsvgtiny: Upgrade to 0.1.7. 
* gnu/packages/web.scm (libsvgtiny): Upgrade to 0.1.7.
 2018-08-30 00:44:39 -05:00
Eric Bavier f8311c0fee
libdom: Upgrade to 0.3.3. 
* gnu/packages/web.scm (libdom): Upgrade to 0.3.3.
 2018-08-30 00:44:39 -05:00
Eric Bavier 2bb1752b7d
libcss: Upgrade to 0.8.0. 
* gnu/packages/web.scm (libcss): Upgrade to 0.8.0.
 2018-08-30 00:44:39 -05:00
Eric Bavier 60e411fc94
libwapcaplet: Upgrade to 0.4.1. 
* gnu/packages/web.scm (libwapcaplet): Upgrade to 0.4.1.
 2018-08-30 00:44:39 -05:00
Eric Bavier b06bf74b41
hubbub: Upgrade to 0.3.5. 
* gnu/packages/web.scm (hubbub): Upgrade to 0.3.5.
 2018-08-30 00:44:39 -05:00
Eric Bavier ea9b34c2f5
libparserutils: Upgrade to 0.2.4. 
* gnu/packages/web.scm (libparserutils): Upgrade to 0.2.4.
 2018-08-30 00:44:38 -05:00
Eric Bavier fa4131f2aa
netsurf-buildsystem: Upgrade to 1.7. 
* gnu/packages/web.scm (netsurf-buildsystem): Upgrade to 1.7.
 2018-08-30 00:44:33 -05:00
Mark H Weaver a28604ee81
gnu: linux-libre@4.4: Update to 4.4.153. 
* gnu/packages/linux.scm (linux-libre-4.4): Update to 4.4.153.
 2018-08-30 00:53:01 -04:00
Tobias Geerinckx-Rice 9986316618
gnu: mujs: Update to 1.0.4. 
* gnu/packages/javascript.scm (mujs): Update to 1.0.4.
 2018-08-30 04:42:54 +02:00
Tobias Geerinckx-Rice bfb994d8be
gnu: r-car: Update to 3.0-2. 
* gnu/packages/statistics.scm (r-car): Update to 3.0-2.
 2018-08-30 04:42:52 +02:00
Tobias Geerinckx-Rice ad3306f62f
gnu: perl-gd: Update to 2.69. 
* gnu/packages/gd.scm (perl-gd): Update to 2.69.
 2018-08-30 04:42:51 +02:00
Tobias Geerinckx-Rice 33eea5c439
gnu: perl-sub-identify: Update to 0.14. 
* gnu/packages/perl.scm (perl-sub-identify): Update to 0.14.
 2018-08-30 04:42:51 +02:00
Tobias Geerinckx-Rice a82b561fef
gnu: robocut: Don't use unstable tarball. 
* gnu/packages/printers.scm (robocut)[source]: Use GIT-FETCH and
GIT-FILE-NAME.
 2018-08-30 04:42:38 +02:00
Tobias Geerinckx-Rice 1f0f9514eb
gnu: gparted: Update to 0.32.0. 
* gnu/packages/disk.scm (gparted): Update to 0.32.0.
 2018-08-30 04:40:31 +02:00
Tobias Geerinckx-Rice 7bb7920f64
gnu: duplicity: Update to 0.7.18.1. 
* gnu/packages/backup.scm (duplicity): Update to 0.7.18.1.
[arguments]: Remove upstreamed '--ignore-mdc-error' kluge.
Rename 'patch-source' phase to 'use-store-file-names'.
 2018-08-30 03:51:00 +02:00
Kei Kebreau 99e0fb24fb
gnu: audacity: Fix GtkFileChooserDialog. 
* gnu/packages/audio.scm (audacity)[arguments]: Add 'wrap-program' phase to fix
GtkFileChooserDialog.
[inputs]: Rename "gtk" to "gtk+".
 2018-08-29 20:56:35 -04:00
Tobias Geerinckx-Rice 16de7f15cb
gnu: snappy: Optimise. 
* gnu/packages/compression.scm (snappy)[source]: Build with ‘-O2’.
* gnu/package/patches/snappy-add-O2-flag-in-CmakeLists.txt.patch:
New file.
* gnu/local.mk (dist_patch_DATA): Add it.
 2018-08-30 00:51:11 +02:00
Christopher Lemmer Webber caf8a003b3
gnu: emacs-racket-mode: Update to commit 92c3348. 
* gnu/packages/emacs.scm (emacs-racket-mode): Update to commit 92c3348.
 2018-08-29 15:52:20 -04:00
Vagrant Cascadian b4c698c8c9
gnu: python-trezor: Update to 0.10.2. 
* gnu/packages/finance.scm (python-trezor): Update to 0.10.2.
[arguments]: Replace check with tests that do not require hardware device.
[propagated-inputs]: Add python-click, python-libusb1, python-pyblake2 and
python-typing.
[native-inputs]: Add python-mock and python-pytest.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2018-08-29 14:52:56 -04:00
pimi 4f9355c360
gnu: Add gffcompare. 
gnu/packages/bioinformatics.scm (gffcompare): New variable.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2018-08-29 14:13:49 -04:00
pimi 9e21f2170e
gnu: Add r-abcoptim. 
gnu/packages/cran.scm (r-abcoptim): New variable.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2018-08-29 14:13:46 -04:00
Danny Milosavljevic 15c56e8273
gnu: Add solaar. 
* gnu/packages/admin.scm (solaar): New variable.
 2018-08-29 17:18:30 +02:00
Danny Milosavljevic ac94ccb9b4
gnu: Add python-pyudev. 
* gnu/packages/admin.scm (python-pyudev): New variable.
 2018-08-29 17:18:28 +02:00
Ricardo Wurmus c7fe888b42
gnu: Add python-scanpy. 
* gnu/packages/bioinformatics.scm (python-scanpy): New variable.
 2018-08-29 17:06:13 +02:00
Ricardo Wurmus 22b770ce00
gnu: Add python-anndata. 
* gnu/packages/python.scm (python-anndata): New variable.
 2018-08-29 17:06:13 +02:00
Ricardo Wurmus d8b8eb3ff5
gnu: Add python-numba. 
* gnu/packages/python.scm (python-numba): New variable.
 2018-08-29 17:06:13 +02:00
Ricardo Wurmus 8892cac329
gnu: Add python-llvmlite. 
* gnu/packages/llvm.scm (python-llvmlite): New variable.
 2018-08-29 17:06:13 +02:00
Marius Bakke 9e17757ff5
Revert "gnu: snappy: Optimise." 
This causes too many rebuilds for the master branch.

This reverts commit f96ed06805.
 2018-08-29 16:58:54 +02:00
Ricardo Wurmus 9587544b44
gnu: Add ghc 8.4.3. 
* gnu/packages/haskell.scm (ghc-8): Rename this...
(ghc-8.0): ...to this.
(ghc): Point at ghc-8.0.
(ghc-8): New variable for GHC 8.4.3.

Co-authored-by: Timothy Samplet <samplet@ngyro.com>
 2018-08-29 16:56:35 +02:00
Ricardo Wurmus 59b55def00
gnu: Add r-infotheo. 
* gnu/packages/cran.scm (r-infotheo): New variable.
 2018-08-29 13:11:17 +02:00
Tobias Geerinckx-Rice acf18cb190
gnu: capstone: Use HTTPS home page. 
* gnu/packages/engineering.scm (capstone)[home-page]: Use HTTPS.
 2018-08-28 22:46:38 +02:00
Tobias Geerinckx-Rice 2c3d30ef51
gnu: r-plotrix: Update to 3.7-3. 
* gnu/packages/statistics.scm (r-plotrix): Update to 3.7-3.
 2018-08-28 22:31:00 +02:00
Tobias Geerinckx-Rice f882d7c7c5
gnu: python-apipkg: Update home page. 
* gnu/packages/python.scm (python-apipkg)[home-page]: Update.
 2018-08-28 22:31:00 +02:00
Tobias Geerinckx-Rice e29bb27d88
gnu: r-pracma: Update to 2.1.5. 
* gnu/packages/maths.scm (r-pracma): Update to 2.1.5.
 2018-08-28 22:31:00 +02:00
Tobias Geerinckx-Rice 7bbdd943e7
gnu: claws-mail: Update to 3.17.1. 
* gnu/packages/mail.scm (claws-mail): Update to 3.17.1.
 2018-08-28 22:31:00 +02:00
Tobias Geerinckx-Rice 4fca5a44f6
gnu: libntlm: Update to 1.5. 
* gnu/packages/gsasl.scm (libntlm): Update to 1.5.
[source]: Use HTTPS.
 2018-08-28 22:31:00 +02:00
Tobias Geerinckx-Rice f96ed06805
gnu: snappy: Optimise. 
* gnu/packages/compression.scm (snappy)[source]: Build with ‘-O2’.
* gnu/package/patches/snappy-add-O2-flag-in-CmakeLists.txt.patch:
New file.
* gnu/local.mk (dist_patch_DATA): Add it.
 2018-08-28 22:30:59 +02:00
Efraim Flashner dc8675afa7
gnu: Add urlscan. 
* gnu/packages/mail.scm (urlscan): New variable.
 2018-08-28 22:48:32 +03:00
Efraim Flashner 967de7c5b0
gnu: Add ephoto. 
* gnu/packages/enlightenment.scm (ephoto): New variable.
 2018-08-28 22:45:55 +03:00
Vagrant Cascadian 84fbb4b223
gnu: electron-cash: Update to 3.3.1. 
* gnu/packages/finance.scm (electron-cash): Update to 3.3.1.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2018-08-28 15:30:13 -04:00
Leo Famulari 8a5a1eff42
gnu: dropbear: Fix CVE-2018-15599. 
* gnu/packages/patches/dropbear-CVE-2018-15599.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/ssh.scm (dropbear)[source]: Use it.
 2018-08-28 14:44:11 -04:00
Ludovic Courtès 1ae29e3f5a
gnu: dico: Update to 2.6. 
* gnu/packages/dico.scm (dico): Update to 2.6.
[inputs]: Switch to GUILE-2.2.
 2018-08-28 12:35:02 +02:00
Ison111 d2434b6966
gnu: Add SpaceFM. 
* gnu/packages/lxde.scm (spacefm): New variable.

Co-authored-by: Ludovic Courtès <ludo@gnu.org>
 2018-08-28 12:35:02 +02:00
Alex Kost 40f7ebac66
gnu: Add emacs-build-farm. 
* gnu/packages/emacs.scm (emacs-build-farm): New variable.
 2018-08-28 12:23:52 +03:00
Alex Kost 8b1f8f64c8
gnu: openmw: Update to 0.44.0. 
* gnu/packages/game-development.scm (openmw): Update to 0.44.0.
 2018-08-28 12:23:52 +03:00
Marius Bakke d9362003b6
gnu: GRUB: Adjust to recent binutils changes. 
* gnu/packages/patches/grub-binutils-compat.patch: New file.
* gnu/local.mk (dist_patch_DATA): Register it.
* gnu/packages/bootloaders.scm (grub)[source](patches): Add it.
 2018-08-28 01:23:12 +02:00
Marius Bakke 8f1022d0a8
gnu: vala: Update to 0.40.9. 
* gnu/packages/gnome.scm (vala): Update to 0.40.9.
 2018-08-28 01:23:12 +02:00
Marius Bakke 61fca0fd22
Merge branch 'master' into core-updates 2018-08-28 01:22:24 +02:00
Marius Bakke 526ce41930
gnu: GRUB: Check for errors from efibootmgr. 
* gnu/packages/patches/grub-check-error-efibootmgr.patch: New file.
* gnu/local.mk (dist_patch_DATA): Register it.
* gnu/packages/bootloaders.scm (grub)[source](patches): New field.
 2018-08-28 01:19:28 +02:00
Marius Bakke 2987b2e0d2
gnu: seabios: Update source URI. 
* gnu/packages/firmware.scm (seabios)[source](uri): Download from seabios.org.
 2018-08-28 01:19:28 +02:00
Marius Bakke eb87b634a7
gnu: slang: Update to 2.3.2. 
* gnu/packages/slang.scm (slang): Update to 2.3.2.
 2018-08-28 01:19:28 +02:00
Marius Bakke 3c3c3d1d92
gnu: emacs-async: Download using git. 
The MELPA tarball hash changed.  Prevent this problem in the future
by downloading a git checkout.

* gnu/packages/emacs.scm (emacs-async)[home-page]: Update to actual.
[source]: Use GIT-FETCH.
 2018-08-28 01:19:28 +02:00
Leo Famulari 0de33cb364
gnu: feh: Enable EXIF support. 
* gnu/packages/image-viewers.scm (feh)[arguments]: Enable EXIF support.
(inputs): Add libexif.
 2018-08-27 17:04:57 -04:00
Leo Famulari f2d2dc70fc
gnu: libexif: Update home-page URL. 
* gnu/packages/photo.scm (libexif)[home-page]: Update URL.
 2018-08-27 17:04:57 -04:00
Leo Famulari 6635a3cc7f
gnu: python-pygit2: Update to 0.26.4. 
* gnu/packages/python.scm (python-pygit2, python2-pygit2): Update to 0.26.4.
[source]: Remove 'python-pygit2-disable-network-tests.patch'.
* gnu/packages/patches/python-pygit2-disable-network-tests.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Remove it.
 2018-08-27 15:13:46 -04:00
Marius Bakke 57dac1ee93
gnu: python-cairocffi: Update to 0.9.0. 
* gnu/packages/python.scm (python-cairocffi): Update to 0.9.0.
[source](uri): Use PYPI-URI.
[native-inputs]: Add PYTHON-PYTEST-COV and PYTHON-PYTEST-RUNNER.
[arguments]: Remove #:tests? and outdated comment.
 2018-08-27 20:40:17 +02:00
Marius Bakke a1d3874293
gnu: python-xcffib: Update to 0.6.0. 
* gnu/packages/python.scm (python-xcffib): Update to 0.6.0.
 2018-08-27 20:40:16 +02:00
Marius Bakke 1abe0554a4
gnu: poppler: Update to 0.68.0. 
* gnu/packages/pdf.scm (poppler): Update to 0.68.0.
[inputs]: Change LIBJPEG to LIBJPEG-TURBO.
 2018-08-27 20:40:16 +02:00
Marius Bakke eb637c64fe
gnu: poppler: Propagate Glib. 
* gnu/packages/pdf.scm (poppler)[inputs]: Move GLIB ...
[propagated-inputs]: ... here.  New field.
 2018-08-27 20:40:16 +02:00
Marius Bakke cbc8a92011
gnu: cairo: Fix undefined behaviour. 
This fixes <https://bugs.freedesktop.org/show_bug.cgi?id=104325> which showed
up in Guix as an infinite loop during cairocffi tests.

* gnu/packages/patches/cairo-setjmp-wrapper.patch: New file.
* gnu/local.mk (dist_patch_DATA): Register it.
* gnu/packages/gtk.scm (cairo)[source](patches): Add it.
 2018-08-27 20:17:16 +02:00
Marius Bakke b651a5ab35
gnu: python-pandas: Update to 0.23.4. 
* gnu/packages/python.scm (python-pandas): Update to 0.23.4.
[arguments]: Disable "--strict-data-files" pytest option.  Delete one more
test.  Adjust pytest invocation to be more verbose and skip very slow tests.
 2018-08-27 18:28:29 +02:00
Marius Bakke 4053585e3f
gnu: python-beautifulsoup4: Update to 4.6.3. 
* gnu/packages/python.scm (python-beautifulsoup4): Update to 4.6.3.
 2018-08-27 17:13:07 +02:00
Marius Bakke 397334d977
gnu: python-pillow: Update to 5.2.0. 
* gnu/packages/patches/python-pillow-fix-failing-tests.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Remove it.
* gnu/packages/python.scm (python-pillow): Update to 5.2.0.
[source](patches, patch-flags): Remove.
[native-inputs]: Replace PYTHON-NOSE with PYTHON-PYTEST.
[arguments]: Adjust custom check phase accordingly.
 2018-08-27 16:49:05 +02:00
Marius Bakke b49e1e81db
gnu: python-pycairo: Update to 1.17.1. 
* gnu/packages/gtk.scm (python-pycairo): Update to 1.17.1.
 2018-08-27 16:33:48 +02:00
Marius Bakke 74f3fdbdb3
gnu: python-pygobject: Update to 3.28.3. 
* gnu/packages/glib.scm (python-pygobject): Update to 3.28.3.
 2018-08-27 16:30:02 +02:00
Marius Bakke e30fc54637
gnu: python-dateutil: Update to 2.7.3. 
* gnu/packages/time.scm (python-dateutil): Update to 2.7.3.
[native-inputs]: Add PYTHON-SETUPTOOLS-SCM.
[license]: Add ASL2.0.
 2018-08-27 16:28:06 +02:00
Clément Lassieur a30cbd5dfb
gnu: cuirass: Update to 8d40c49. 
* gnu/packages/ci.scm (cuirass): Update to 8d40c49.
 2018-08-27 16:12:56 +02:00
Marius Bakke d7c82e8e03
gnu: python-numpy: Update to 1.15.1. 
* gnu/packages/python.scm (python-numpy): Update to 1.15.1.
[native-inputs]: Replace PYTHON-NOSE with PYTHON-PYTEST.
[arguments]: Set PATH before running tests.  Use INVOKE.
 2018-08-27 16:05:11 +02:00
Pierre Neidhardt 4715f92ef0
Update email for Pierre Neidhardt. 
* .mailmap: Add name and email for Pierre Neidhardt.
* gnu/packages/c.scm, gnu/packages/code.scm, gnu/packages/compression.scm,
gnu/packages/disk.scm, gnu/packages/emacs.scm, gnu/packages/freedesktop.scm,
gnu/packages/golang.scm, gnu/packages/image.scm, gnu/packages/music.scm,
gnu/packages/networking.scm, gnu/packages/password-utils.scm,
gnu/packages/perl-check.scm, gnu/packages/perl.scm,
gnu/packages/textutils.scm, gnu/packages/video.scm, gnu/packages/xdisorg.scm:
Update email for Pierre Neidhardt.
 2018-08-27 14:46:26 +02:00
Rutger Helling c0fdc5a53d
gnu: wayland: Update to 1.16.0. 
* gnu/packages/freedesktop.scm (wayland): Update to 1.16.0.
 2018-08-27 10:16:51 +02:00
Rutger Helling 2aeee872a6
gnu: weston: Update to 5.0.0. 
* gnu/packages/freedesktop.scm (weston): Update to 5.0.0.
 2018-08-27 10:11:30 +02:00
Ludovic Courtès 1ca54999db
gnu: Add Lepton-EDA. 
* gnu/packages/engineering.scm (lepton-eda): New variable.
 2018-08-27 01:13:23 +02:00
Ludovic Courtès 69502b5eb4
gnu: Add guile-aa-tree. 
* gnu/packages/guile.scm (guile-aa-tree): New variable.
 2018-08-27 01:13:23 +02:00
Marius Bakke 45c78bf924
gnu: gcc: Include libsanitizer patch for versions 6 and 7. 
* gnu/packages/gcc.scm (gcc-6, gcc-7)[source](patches): Add
"gcc-libsanitizer-ustat.patch".
 2018-08-26 16:50:39 +02:00
Marius Bakke 8d48f358e9
gnu: parted: Fix build with glibc >= 2.28. 
* gnu/packages/patches/parted-glibc-compat.patch: New file.
* gnu/local.mk (dist_patch_DATA): Register it.
* gnu/packages/disk.scm (parted)[source](patches): New field.
 2018-08-26 16:20:04 +02:00
Marius Bakke 60ecc10f18
gnu: xorg-server@1.19.3: Rename to "xorg-server-for-tests". 
...and update to the latest xorg-server.

* gnu/packages/gtk.scm (gtk+, gtkmm, girara): Change XORG-SERVER-1.19.3
references to XORG-SERVER-FOR-TESTS.
* gnu/packages/pdf.scm (zathura)[native-inputs]: Likewise.
* gnu/packages/xorg.scm (xorg-server-1.19.3): Rename to ...
(xorg-server-for-tests): ... this.
 2018-08-26 16:17:31 +02:00
Christopher Lemmer Webber 6948fa0875
gnu: emacs-racket-mode: Update to commit add0190. 
* gnu/packages/emacs.scm (emacs-racket-mode): Update to commit add0190.
 2018-08-26 07:02:04 -04:00
Arun Isaac 2cad58ca6f
gnu: ghc-scientific: Update to 0.3.6.2. 
* gnu/packages/haskell.scm (ghc-scientific): Update to 0.3.6.2.
[inputs]: Move ghc-tasty ...
[native-inputs]: ... to here.
 2018-08-26 11:48:22 +05:30
Arun Isaac 7550f4b0ef
gnu: ghc-integer-logarithms: Update to 1.0.2.1. 
* gnu/packages/haskell.scm (ghc-integer-logarithms): Update to 1.0.2.1.
[inputs]: Move ghc-quickcheck, ghc-smallcheck, ghc-tasty, ghc-tasty-hunit,
ghc-tasty-quickcheck, ghc-tasty-smallcheck ...
[native-inputs]: ... to here.
[home-page]: Update URI.
 2018-08-26 11:37:25 +05:30
Arun Isaac b625f3a5fb
gnu: ghc-smallcheck: Update to 1.1.5. 
* gnu/packages/haskell.scm (ghc-smallcheck): Update to 1.1.5.
 2018-08-26 11:33:48 +05:30
Arun Isaac 3c30054290
gnu: ghc-optparse-applicative: Update to 0.14.2.0. 
* gnu/packages/haskell.scm (ghc-optparse-applicative): Update to 0.14.2.0.
[arguments]: Enable tests.
 2018-08-26 11:27:00 +05:30
Mark H Weaver cfb15a5163
gnu: linux-libre: Update to 4.18.5. 
* gnu/packages/linux.scm (%linux-libre-version): Update to 4.18.5.
(%linux-libre-hash): Update hash.
 2018-08-26 00:38:41 -04:00
Mark H Weaver fabe2c7354
gnu: linux-libre@4.14: Update to 4.14.67. 
* gnu/packages/linux.scm (%linux-libre-4.14-version): Update to 4.14.67.
(%linux-libre-4.14-hash): Update hash.
 2018-08-26 00:36:42 -04:00
Mark H Weaver 8d55adfa67
gnu: linux-libre@4.9: Update to 4.9.124. 
* gnu/packages/linux.scm (linux-libre-4.9): Update to 4.9.124.
 2018-08-26 00:36:11 -04:00
Mark H Weaver 032712f621
gnu: linux-libre@4.4: Update to 4.4.152. 
* gnu/packages/linux.scm (linux-libre-4.4): Update to 4.4.152.
 2018-08-26 00:35:30 -04:00
Ludovic Courtès 64daf2177f
gnu: emacs-recent-addresses: Switch to a branch that works with Helm. 
* gnu/packages/emacs.scm (emacs-recent-addresses)[source]: Change URL
and update to afbbfdc.
 2018-08-26 01:47:41 +02:00
Kyle Meyer bff861ece5
gnu: Add emacs-git-annex. 
* gnu/packages/emacs.scm (emacs-git-annex): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-08-26 01:47:40 +02:00
Kyle Meyer 8a9e0b6ebf
gnu: emacs-recent-addresses: Add missing words to description. 
* gnu/packages/emacs.scm (emacs-recent-addresses)[description]: Add missing
words.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-08-26 01:47:40 +02:00
Marius Bakke 8ad6584103
gnu: mesa: Update to 18.1.7. 
* gnu/packages/gl.scm (mesa): Update to 18.1.7.
 2018-08-26 01:04:45 +02:00
Kei Kebreau 7d01ee66d4
gnu: Add avogadro. 
* gnu/packages/chemistry.scm (avogadro): New variable.
* gnu/packages/patches/avogadro-boost148.patch,
gnu/packages/patches/avogadro-eigen3-update.patch,
gnu/packages/patches/avogadro-python-eigen-lib.patch: New files.
* gnu/local.mk (dist_patch_DATA): Add them.
 2018-08-25 17:05:30 -04:00
Marius Bakke fa2146f769
gnu: xkeyboard-config: Update to 2.24. 
* gnu/packages/xorg.scm (xkeyboard-config): Update to 2.24.
 2018-08-25 20:13:08 +02:00
Marius Bakke c37e932764
gnu: gdb: Remove obsolete patch. 
* gnu/packages/patches/gdb-python-3.7.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Remove it.
* gnu/packages/gdb.scm (gdb)[source](patches): Remove field.
 2018-08-25 19:23:35 +02:00
Marius Bakke 65ba72d749
gnu: libx11: Remove graft for 1.6.6. 
* gnu/packages/xorg.scm (libx11): Update to 1.6.6.
[replacement]: Remove field.
(libx11-1.6.6): Remove variable.
 2018-08-25 16:57:35 +02:00
Marius Bakke 839167ff9d
Merge branch 'staging' into core-updates 2018-08-25 16:44:07 +02:00
Marius Bakke 030c912616
gnu: libdrm: Update to 2.4.93. 
* gnu/packages/xdisorg.scm (libdrm): Update to 2.4.93.
 2018-08-25 16:40:31 +02:00
Marius Bakke 9b3b4c05a0
gnu: mesa: Build against elfutils instead of libelf. 
* gnu/packages/gl.scm (mesa)[inputs]: Change from LIBELF to ELFUTILS.
 2018-08-25 16:40:31 +02:00
Marius Bakke 173d291466
Merge branch 'master' into staging 2018-08-25 16:38:51 +02:00
Marius Bakke 94e9d750a2
gnu: libx11: Replace with 1.6.6 [security fixes]. 
This fixes CVE-2018-14599, CVE-2018-14600, and CVE-2018-14598.

* gnu/packages/xorg.scm (libx11)[replacement]: New field.
(libx11-1.6.6): New public variable.
 2018-08-25 16:32:06 +02:00
Marius Bakke 27c1df05a8
gnu: linux-libre-headers: Update to 4.14.67. 
* gnu/packages/linux.scm (linux-libre-headers): Update to 4.14.67.
 2018-08-25 16:27:46 +02:00
Marius Bakke cf59c62853
gnu: Remove bison@2.7. 
* gnu/packages/bison.scm (bison-2.7): Remove variable.
 2018-08-25 16:23:37 +02:00
Marius Bakke 34f4c214b6
gnu: flex: Update bison-for-tests to 3.0.5. 
* gnu/packages/flex.scm (flex)[inputs]: Make BISON-FOR-TESTS inherit source
from BISON, and disable tests on it since they require flex.
 2018-08-25 16:23:36 +02:00
Marius Bakke 2fa4066c0a
gnu: findutils: Fix build with glibc 2.28. 
* gnu/packages/patches/findutils-gnulib-libio.patch,
gnu/packages/patches/findutils-makedev.patch: New files.
* gnu/local.mk (dist_patch_DATA): Register it.
* gnu/packages/base.scm (findutils)[source](patches): Use them.
 2018-08-25 16:23:36 +02:00
Marius Bakke 8c8ded2cc9
gnu: grep: Work around test failure with glibc 2.28. 
* gnu/packages/base.scm (grep)[arguments]: Add phase 'disable-failing-tests'.
 2018-08-25 16:23:36 +02:00
Marius Bakke a8dcf6cec7
gnu: coreutils: Update to 8.30. 
* gnu/packages/base.scm (coreutils): Update to 8.30.
[arguments]: Add phase to skip broken test.
 2018-08-25 16:23:36 +02:00
Marius Bakke c7b87eeda2
gnu: gzip: Fix FTBFS with glibc >= 2.28. 
* gnu/packages/compression.scm (gzip)[arguments]: Add phase
'patch-for-glibc-2.28'.
 2018-08-25 16:23:36 +02:00
Marius Bakke 95895d53b0
gnu: m4: Fix FTBFS with glibc >= 2.28. 
* gnu/packages/patches/m4-gnulib-libio.patch: New file.
* gnu/local.mk (dist_patch_DATA): Register it.
* gnu/packages/m4.scm (m4)[source](patches): New field.
 2018-08-25 16:23:36 +02:00
Marius Bakke 1aef659e86
gnu: gcc: Fix build with glibc >= 2.28. 
* gnu/packages/patches/gcc-libsanitizer-ustat.patch: New file.
* gnu/local.mk (dist_patch_DATA): Register it.
* gnu/packages/gcc.scm (gcc-5)[source](patches): Add it.
 2018-08-25 16:23:36 +02:00
Marius Bakke e13b547407
gnu: glibc: Update to 2.28. 
* gnu/packages/patches/glibc-2.28-git-fixes.patch: New file.
* gnu/local.mk (dist_patch_DATA): Register it.
* gnu/packages/base.scm (glibc/linux): Update to 2.28.
[source](patches): Add 'glibc-2.28-git-fixes.patch'.  Remove 2.27 equivalent.
(glibc-2.28): Remove variable.
(glibc-2.27): New public variable
 2018-08-25 16:23:35 +02:00
宋文武 7789bf9531
gnu: dante: Disable preloading to make 'sockd' work. 
* gnu/packages/networking.scm (dante)[arguments]: Pass '--disable-preload'
to #:configure-flags.
 2018-08-25 16:40:21 +08:00
Leo Famulari 36a8d5cdf4
gnu: OpenSSH: Update to 7.8p1. 
* gnu/packages/ssh.scm (openssh): Update to 7.8p1.
[source]: Remove 'openssh-CVE-2018-15473.patch'.
* gnu/packages/patches/openssh-CVE-2018-15473.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Remove it.
 2018-08-24 17:04:58 -04:00
Ludovic Courtès c1352b4bad
gnu: font-gnu-unifont: Update to 11.0.02. 
* gnu/packages/fonts.scm (font-gnu-unifont): Update to 11.0.02.
[arguments]: Adjust code to install 'unifont.info.gz' in 'install'
phase.
 2018-08-24 17:54:10 +02:00
Ludovic Courtès bf0bb925ea
gnu: gdb: Update to 8.1.1. 
* gnu/packages/gdb.scm (gdb): Update to 8.1.1.
 2018-08-24 17:50:52 +02:00
Ricardo Wurmus 079cdd9c15
gnu: Add find-circ. 
* gnu/packages/bioinformatics.scm (find-circ): New variable.
 2018-08-24 11:20:19 +02:00
Tobias Geerinckx-Rice 4a3cf8929f
gnu: r-catools: Update to 1.17.1.1. 
* gnu/packages/statistics.scm (r-catools): Update to 1.17.1.1.
 2018-08-24 04:25:50 +02:00
Tobias Geerinckx-Rice 0e5d66abf6
gnu: keepassxc: Update to 2.3.4. 
* gnu/packages/password-utils.scm (keepassxc): Update to 2.3.4.
[arguments]: Remove obsolete ‘patch-sources’ phase.
 2018-08-24 04:25:50 +02:00
Tobias Geerinckx-Rice a7b14a1b39
gnu: capstone: Update to 3.0.5. 
* gnu/packages/engineering.scm (capstone): Update to 3.0.5.
[arguments]: Set cstool's LDFLAGS in the environment instead of
SUBSTITUTE*ing the Makefile.
 2018-08-24 03:04:56 +02:00
Tobias Geerinckx-Rice 77c027b98b
gnu: r-trimcluster: Update to 0.1-2.1. 
* gnu/packages/statistics.scm (r-trimcluster): Update to 0.1-2.1.
 2018-08-24 02:30:43 +02:00
Tobias Geerinckx-Rice 6d83cd1f9a
gnu: r-synchronicity: Update to 1.3.5. 
* gnu/packages/statistics.scm (r-synchronicity): Update to 1.3.5.
 2018-08-24 02:30:42 +02:00
Tobias Geerinckx-Rice 6a9a50fd2f
gnu: guile-lib: Update to 0.2.6.1. 
* gnu/packages/guile.scm (guile-lib): Update to 0.2.6.1.
[source]: Remove obsolete snippet.
 2018-08-24 02:30:42 +02:00
Tobias Geerinckx-Rice a0a7e42500
gnu: tuxguitar: Update to 1.5.2. 
* gnu/packages/music.scm (tuxguitar): Update to 1.5.2.
[source]: Remove obsolete snippet.
 2018-08-24 02:30:41 +02:00
Tobias Geerinckx-Rice 38146797e6
gnu: libgig: Update to 4.1.0. 
* gnu/packages/music.scm (libgig): Update to 4.1.0.
 2018-08-24 02:30:41 +02:00
Tobias Geerinckx-Rice f6181921e5
gnu: denemo: Use INVOKE. 
* gnu/packages/music.scm (denemo)[arguments]: Substitute INVOKE for
SYSTEM*.
 2018-08-24 02:30:41 +02:00
Tobias Geerinckx-Rice fbde7b08e5
gnu: ncmpc: Update to 0.29. 
* gnu/packages/mpd.scm (ncmpc): Update to 0.29.
[build-system]: Switch to Meson.
[arguments]: Find ncurses.h.
[native-inputs]: Add gettext.
 2018-08-24 02:30:41 +02:00
Ludovic Courtès 0b4e5f7e5b
gnu: parallel: Update to 20180822. 
* gnu/packages/parallel.scm (parallel): Update to 20180822.
 2018-08-24 00:40:09 +02:00
Ludovic Courtès 444488fc1b
gnu: boost: Move 1.59.0 definition to boost.scm. 
Fixes a regression introduced in commit
7cbf06d8c2 where the top-level code of
these two modules would depend on each other, leading to "boost: unbound
variable" kind of errors in some circumstances.

* gnu/packages/databases.scm (boost-for-mysql): Move to...
* gnu/packages/boost.scm (boost-for-mysql): ... here.  Make public and
add 'properties' field.
 2018-08-24 00:36:04 +02:00
Tobias Geerinckx-Rice d32da49c76
gnu: r-devtools: Update to 1.13.6. 
* gnu/packages/statistics.scm (r-devtools): Update to 1.13.6.
 2018-08-23 23:11:52 +02:00
Tobias Geerinckx-Rice c95f9f09a7
gnu: drumkv1: Update to 0.9.2. 
* gnu/packages/music.scm (drumkv1): Update to 0.9.2.
 2018-08-23 23:01:56 +02:00
Tobias Geerinckx-Rice 69b4d24871
gnu: synthv1: Update to 0.9.2. 
* gnu/packages/music.scm (synthv1): Update to 0.9.2.
 2018-08-23 23:01:56 +02:00
Tobias Geerinckx-Rice 29618d6722
gnu: samplv1: Update to 0.9.2. 
* gnu/packages/music.scm (samplv1): Update to 0.9.2.
 2018-08-23 23:01:56 +02:00
Tobias Geerinckx-Rice 2c59066f6a
gnu: padthv1: Update to 0.9.2. 
* gnu/packages/music.scm (padthv1): Update to 0.9.2.
 2018-08-23 23:01:56 +02:00
Tobias Geerinckx-Rice 9459216aa1
gnu: Update home pages for the V1 synth family. 
* gnu/packages/music.scm (synthv1, drumkv1, samplv1, padthv1)
[home-page]: Update & use HTTPS.
 2018-08-23 23:01:55 +02:00
pimi 16b0e8da48
gnu: Add r-a3. 
gnu/packages/cran.scm (r-a3): New variable.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2018-08-23 16:26:40 -04:00
pimi 881cc61c1b
gnu: Add r-manipulatewidget. 
gnu/packages/cran.scm (r-manipulatewidget): New variable.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2018-08-23 16:26:40 -04:00
pimi 87b576aa8b
gnu: Add r-slam. 
gnu/packages/cran.scm (r-slam): New variable.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2018-08-23 16:26:40 -04:00
pimi c994418b8c
gnu: Add r-abcanalysis. 
gnu/packages/cran.scm (r-abcanalysis): New variable.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2018-08-23 16:26:40 -04:00
pimi 67cf070239
gnu: Add r-miniui. 
gnu/packages/web.scm (r-miniui): New variable.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2018-08-23 16:26:40 -04:00
Tobias Geerinckx-Rice 694765e1d6
gnu: qjackctl: Update to 0.5.3. 
* gnu/packages/audio.scm (qjackctl): Update to 0.5.3.
 2018-08-23 17:16:42 +02:00
Tobias Geerinckx-Rice 97353dfb69
gnu: byobu: Update home page. 
* gnu/packages/screen.scm (byobu)[home-page]: Update & use HTTPS.
 2018-08-23 17:16:41 +02:00
Tobias Geerinckx-Rice 9e29921162
gnu: byobu: Update to 5.127. 
* gnu/packages/screen.scm (byobu): Update to 5.127.
* gnu/packages/patches/byobu-writable-status.patch: Adjust context
accordingly.
 2018-08-23 17:16:41 +02:00
Tobias Geerinckx-Rice f868276b8a
gnu: wine-staging-patchset-data: Don't use unstable archive. 
* gnu/packages/wine.scm (wine-staging-patchset-data)[source]:
Use GIT-FETCH and GIT-FILE-NAME.
[native-inputs]: Remove unzip.
[arguments]: Adjust and refactor accordingly.
 2018-08-23 17:16:41 +02:00
Tobias Geerinckx-Rice 574e2ee8ea
gnu: yubico-piv-tool: Update to 1.6.1. 
* gnu/packages/security-token.scm (yubico-piv-tool): Update to 1.6.1.
 2018-08-23 17:16:41 +02:00
Tobias Geerinckx-Rice fa5511b6e9
gnu: r-car: Update to 3.0-1. 
* gnu/packages/statistics.scm (r-car): Update to 3.0-1.
 2018-08-23 17:16:40 +02:00
Tobias Geerinckx-Rice 39bb1cc77a
gnu: r-digest: Update to 0.6.16. 
* gnu/packages/statistics.scm (r-digest): Update to 0.6.16.
 2018-08-23 17:16:40 +02:00
Tobias Geerinckx-Rice ed61c44895
gnu: r-dplyr: Update to 0.7.6. 
* gnu/packages/statistics.scm (r-dplyr): Update to 0.7.6.
 2018-08-23 17:16:40 +02:00
Tobias Geerinckx-Rice 51dbad04c5
gnu: r-rcpp: Update to 0.12.18. 
* gnu/packages/cran.scm (r-rcpp): Update to 0.12.18.
 2018-08-23 17:16:40 +02:00
Tobias Geerinckx-Rice 02489a6646
gnu: duplicity: Update to 0.7.18. 
* gnu/packages/backup.scm (duplicity): Update to 0.7.18.
 2018-08-23 17:16:39 +02:00
Marius Bakke 3ea66dadf6
gnu: boost: Update to 1.68.0. 
* gnu/packages/boost.scm (boost): Update to 1.68.0.
[arguments]: Remove /bin/sh substitution.
 2018-08-23 14:56:03 +02:00
Marius Bakke bd65ecf460
gnu: boost: Provide libboost_python compatibility symlink. 
* gnu/packages/boost.scm (boost)[arguments]: Add phase 'provide-libboost_python'.
 2018-08-23 14:56:02 +02:00
Arun Isaac 72816ebed2
gnu: darcs: Update to 2.14.1. 
* gnu/packages/version-control.scm (darcs): Update to 2.14.1.
[arguments]: Add patch-sh phase. Enable tests.
 2018-08-23 15:51:43 +05:30
Arun Isaac d3c7e70858
gnu: ghc-zlib: Update to 0.6.2. 
* gnu/packages/haskell.scm (ghc-zlib): Update to 0.6.2.
 2018-08-23 14:43:48 +05:30
Arun Isaac cdccdec1f2
gnu: ghc-quickcheck-instances: Update to 0.3.18. 
* gnu/packages/haskell-check.scm (ghc-quickcheck-instances): Update to 0.3.18.
[arguments]: Allow building with newer base-compat.
 2018-08-23 14:37:57 +05:30
Arun Isaac f797a0e987
gnu: ghc-graphviz: Update to 2999.20.0.2. 
* gnu/packages/haskell.scm (ghc-graphviz): Update to 2999.20.0.2.
[native-inputs]: Add ghc-hspec, graphviz and hspec-discover.
 2018-08-23 13:21:23 +05:30
Arun Isaac e173a95ffa
gnu: ghc-wl-pprint-text: Update to 1.2.0.0. 
* gnu/packages/haskell.scm (ghc-wl-pprint-text): Update to 1.2.0.0.
[inputs]: Add ghc-base-compat.
 2018-08-23 13:21:23 +05:30
Arun Isaac 0fa2c552fc
gnu: ghc-base-compat: Update to 0.10.4. 
* gnu/packages/haskell.scm (ghc-base-compat): Update to 0.10.4.
 2018-08-23 13:21:23 +05:30
Arun Isaac a3ab433a14
gnu: ghc-fgl-arbitrary: Allow building with newer hspec. 
* gnu/packages/haskell.scm (ghc-fgl-arbitrary)[arguments]: Allow building with
newer hspec.
 2018-08-23 13:00:53 +05:30
Arun Isaac c4348ca72c
gnu: ghc-shelly: Update to 1.8.1. 
* gnu/packages/haskell.scm (ghc-shelly): Update to 1.8.1.
[inputs]: Add ghc-hspec-contrib.
 2018-08-23 12:53:47 +05:30
Arun Isaac 66dbe158cf
gnu: ghc-sandi: Update to 0.4.2. 
* gnu/packages/haskell.scm (ghc-sandi): Update to 0.4.2.
 2018-08-23 12:44:00 +05:30
Arun Isaac b1a1600030
gnu: ghc-fgl: Update to 5.6.0.0. 
* gnu/packages/haskell.scm (ghc-fgl): Update to 5.6.0.0.
[arguments]: Allow building with newer hspec.
 2018-08-23 12:32:46 +05:30
Mark H Weaver 4e51d3e9ae
gnu: guile-redis: Remove duplicate 'home-page' field. 
* gnu/packages/guile.scm (guile-redis): Remove duplicate 'home-page' field.
 2018-08-23 02:30:30 -04:00
Mark H Weaver efe2e7506e
gnu: guile-gcrypt: Remove duplicate 'home-page' field. 
This is a followup to commit b0cb92b2d4.

* gnu/packages/gnupg.scm (guile-gcrypt): Remove duplicate 'home-page' field.
 2018-08-23 02:29:31 -04:00
Mark H Weaver 12dc04d0b4
gnu: linux-libre: Update to 4.18.4. 
* gnu/packages/linux.scm (%linux-libre-version): Update to 4.18.4.
(%linux-libre-hash): Update hash.
 2018-08-23 02:22:57 -04:00
Mark H Weaver 98dfe06e3e
gnu: linux-libre@4.14: Update to 4.14.66. 
* gnu/packages/linux.scm (%linux-libre-4.14-version): Update to 4.14.66.
(%linux-libre-4.14-hash): Update hash.
 2018-08-23 02:21:28 -04:00
Mark H Weaver bb2efc0384
gnu: linux-libre@4.9: Update to 4.9.123. 
* gnu/packages/linux.scm (linux-libre-4.9): Update to 4.9.123.
 2018-08-23 02:20:44 -04:00
Mark H Weaver 435722f72c
gnu: linux-libre@4.4: Update to 4.4.151. 
* gnu/packages/linux.scm (linux-libre-4.4): Update to 4.4.151.
 2018-08-23 02:20:00 -04:00
Ludovic Courtès b0cb92b2d4
gnu: Add guile-gcrypt. 
* gnu/packages/gnupg.scm (guile-gcrypt): New variable.
 2018-08-23 00:44:55 +02:00
Leo Famulari 58927996d9
gnu: perl-dbd-mysql: Update to 4.046. 
* gnu/packages/databases.scm (perl-dbd-mysql): Update to 4.046.
[source]: Update URL. Remove 'perl-dbd-mysql-CVE-2017-10788.patch'.
* gnu/packages/patches/perl-dbd-mysql-CVE-2017-10788.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Remove it.
 2018-08-22 15:40:08 -04:00
Paul Garlick 414f620fbb
gnu: python-pkgconfig: Enable tests. 
* gnu/packages/python.scm (python-pkgconfig)[arguments]: Replace 'check' phase.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2018-08-22 15:13:52 -04:00
Paul Garlick 5fab62527c
gnu: python-pkgconfig: Update to 1.3.1. 
* gnu/packages/python.scm (python-pkgconfig): Update to 1.3.1.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2018-08-22 15:13:49 -04:00
Leo Famulari 373a9fd4db
gnu: soundtouch: Fix CVE-2018-{1000223,14044,14045}. 
* gnu/packages/patches/soundtouch-CVE-2018-14044-14045.patch,
gnu/packages/patches/soundtouch-CVE-2018-1000223.patch: New files.
* gnu/local.mk (dist_patch_DATA): Add them.
* gnu/packages/audio.scm (soundtouch)[source]: Use them.
 2018-08-22 13:38:39 -04:00
Leo Famulari eb88ccf711
gnu: soundtouch: Update to 2.0.0. 
* gnu/packages/audio.scm (soundtouch): Update to 2.0.0.
 2018-08-22 13:38:39 -04:00
Marius Bakke 233df51ebc
Merge branch 'master' into staging 2018-08-22 18:14:04 +02:00
Marius Bakke 22cf2f4abf
gnu: python-cffi: Update to 1.11.5. 
* gnu/packages/libffi.scm (python-cffi): Update to 1.11.5.
 2018-08-22 18:01:10 +02:00
Marius Bakke a20016e15a
gnu: python-urllib3: Update to 1.23. 
* gnu/packages/python-web.scm (python-urllib3): Update to 1.23.
 2018-08-22 18:01:10 +02:00
Marius Bakke 064732bd0c
gnu: python-certifi: Update to 2018.8.13. 
* gnu/packages/python-crypto.scm (python-certifi): Update to 2018.8.13.
 2018-08-22 18:01:10 +02:00
Marius Bakke 00ffbfd394
gnu: python-idna: Update to 2.7. 
* gnu/packages/python.scm (python-idna): Update to 2.7.
 2018-08-22 18:01:10 +02:00
Marius Bakke fb76ef8477
gnu: Remove GCC ICE workarounds. 
* gnu/packages/patches/doxygen-gcc-ice.patch,
gnu/packages/patches/mariadb-gcc-ice.patch,
gnu/packages/patches/perf-gcc-ice.patch: Delete files
* gnu/local.mk (dist_patch_DATA): Adjust accordingly.
* gnu/packages/databases.scm (mariadb)[source](patches): Likewise.
* gnu/packages/linux.scm (perf)[source](patches): Likewise.
* gnu/packages/documentation.scm (doxygen)[inputs, arguments]: Likewise.
 2018-08-22 18:01:09 +02:00
Marius Bakke 43cec3fb1e
gnu: mariadb: Remove huge mysql_embedded executable. 
* gnu/packages/databases.scm (mariadb)[arguments]: Adjust deletion regex.
 2018-08-22 17:52:40 +02:00
Marius Bakke 22f5c07624
gnu: mariadb: Propagate OpenSSL. 
* gnu/packages/databases.scm (mariadb)[inputs]: Move OPENSSL ...
[propagated-inputs]: ... here.
(r-rmysql)[inputs]: Remove OPENSSL.
 2018-08-22 17:50:07 +02:00
Leo Famulari 180a8986e5
gnu: ImageMagick: Update to 6.9.10-10. 
* gnu/packages/imagemagick.scm (imagemagick): Update to 6.9.10-10.
 2018-08-22 03:25:47 -04:00
Leo Famulari 09efe9af2d
gnu: GraphicsMagick: Update to 1.3.30. 
* gnu/packages/imagemagick.scm (graphicsmagick): Update to 1.3.30.
 2018-08-22 03:25:46 -04:00
Tobias Geerinckx-Rice dc695341f7
gnu: r-fpc: Update to 2.1-11.1. 
* gnu/packages/statistics.scm (r-fpc): Update to 2.1-11.1.
 2018-08-22 00:03:44 +02:00
Tobias Geerinckx-Rice 7138c48e6e
gnu: r-survival: Update to 2.42-6. 
* gnu/packages/statistics.scm (r-survival): Update to 2.42-6.
 2018-08-22 00:03:44 +02:00
Tobias Geerinckx-Rice 311f06c94a
gnu: Add sqlcrush. 
* gnu/packages/databases.smc (sqlcrush): New public variable.
 2018-08-22 00:03:43 +02:00
Tobias Geerinckx-Rice 9763102bd7
gnu: Add python-pymysql. 
* gnu/packages/databases.scm (python-pymysql, python2-pymysql): New
public variables.
 2018-08-22 00:03:43 +02:00
Raphaël Mélotte f998453559
gnu: luakit: Fix crash on startup. 
* gnu/packages/web-browsers.scm (luakit): add XDG_CONFIG_DIRS to the
  wrapping phase.

This fixes a crash when no configuration file is present in the user's home
directory. It allows luakit to use it's own default configuration files.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-08-21 23:27:09 +02:00
Ludovic Courtès c305ac30c3
gnu: guile-ssh: Don't build libguile-ssh.a. 
* gnu/packages/ssh.scm (guile-ssh)[arguments]: Add #:configure-flags.
 2018-08-21 23:27:08 +02:00
Marius Bakke fdb222033c
gnu: gdbm: Update to 1.18. 
* gnu/packages/databases.scm (gdbm): Update to 1.18.
 2018-08-21 17:25:23 +02:00
Marius Bakke 25febeedc6
gnu: python-numpydoc: Update to 0.8.0. 
* gnu/packages/python.scm (python-numpydoc): Update to 0.8.0.
[source](uri): Use PYPI-URI.
[source](snippet): Remove.
 2018-08-21 17:24:31 +02:00
Marius Bakke 7eab5e7377
gnu: python-greenlet: Update to 0.4.14. 
* gnu/packages/python.scm (python-greenlet): Update to 0.4.14.
 2018-08-21 17:24:31 +02:00
Marius Bakke a8c9321368
gnu: cups-filters: Update to 1.21.0. 
* gnu/packages/cups.scm (cups-filters): Update to 1.21.0.
 2018-08-21 17:24:31 +02:00
Marius Bakke 3bbfc451ed
gnu: python-sphinx: Update to 1.7.7. 
* gnu/packages/openstack.scm (python-mox3, python-openstackdocstheme,
  python-stevedore, python-oslo.config)[native-inputs]: Change
PYTHON-SPHINX-1.6 to PYTHON-SPHINX.
* gnu/packages/python.scm (python-sphinx): Update to 1.7.7.
[arguments]: Incorporate changes from the 1.6 variant.  Disable two tests.
[propagated-inputs]: Add PYTHON-PACKAGING and PYTHON-SPHINXCONTRIB-WEBSUPPORT.
[native-inputs]: Add IMAGEMAGICK and PYTHON-PYTEST.
(python2-sphinx)[propagated-inputs]: Add PYTHON2-TYPING.
(python-sphinx-1.6, python2-sphinx-1.6, python-sphinx-1.5.3): Remove variables.
(python-matplotlib-documentation)[native-inputs]: Change from
PYTHON-SPHINX-1.6 to PYTHON-SPHINX.
 2018-08-21 17:24:31 +02:00
Marius Bakke f70785a4c0
gnu: python-sphinxcontrib-websupport: Add a python2 variant. 
* gnu/packages/python.scm (python2-sphinxcontrib-websupport): New public variable.
 2018-08-21 17:24:31 +02:00
Marius Bakke f65ef00556
gnu: python-sphinxcontrib-websupport: Update to 1.1.0. 
* gnu/packages/python.scm (python-sphinxcontrib-websupport): Update to 1.1.0.
 2018-08-21 17:24:31 +02:00
Marius Bakke 5f2707a255
gnu: python-sphinxcontrib-websupport: Disable tests. 
* gnu/packages/python.scm (python-sphinxcontrib-websupport)[arguments]: New
field.
[native-inputs, inputs]: Remove.
 2018-08-21 17:24:31 +02:00
Marius Bakke efada0946d
gnu: python-jinja2: Update to 2.10. 
* gnu/packages/python.scm (python-jinja2): Update to 2.10.
 2018-08-21 17:24:30 +02:00
Marius Bakke 88166588a0
gnu: python-babel: Run the tests. 
* gnu/packages/python.scm (python-babel)[native-inputs]: Add PYTHON-FREEZEGUN
and PYTHON-PYTEST.
[arguments]: Replace 'check' phase.  Remove #:tests?.
 2018-08-21 17:24:30 +02:00
Marius Bakke b3a21b2cf9
gnu: python-babel: Update to 2.6.0. 
* gnu/packages/python.scm (python-babel): Update to 2.6.0.
 2018-08-21 17:24:30 +02:00
Marius Bakke cb5ba282cc
gnu: python-pytz: Update to 2018.5. 
* gnu/packages/time.scm (python-pytz): Update to 2018.5.
[source](uri): Update file extension.
[native-inputs]: Remove.
 2018-08-21 17:24:30 +02:00
Marius Bakke 2be1b754ba
gnu: python-sqlalchemy: Update to 1.2.11. 
* gnu/packages/databases.scm (python-sqlalchemy): Update to 1.2.11.
 2018-08-21 17:24:30 +02:00
Marius Bakke 9871a896aa
gnu: python-sqlalchemy: Use 'invoke'. 
* gnu/packages/databases.scm (python-sqlalchemy)[arguments]: Use INVOKE
instead of SYSTEM*.
 2018-08-21 17:24:30 +02:00
Marius Bakke 632900f586
gnu: python-packaging: Run the tests. 
* gnu/packages/python.scm (python-packaging)[arguments]: Override 'check' phase.
 2018-08-21 17:24:30 +02:00
Marius Bakke c52ff2ed76
gnu: python-packaging: Update to 17.1. 
* gnu/packages/python.scm (python-packaging): Update to 17.1.
 2018-08-21 17:24:30 +02:00
Marius Bakke 26aef5e956
gnu: python-imagesize: Fix typo. 
* gnu/packages/python.scm (python-imagesize)[synopsis]: Remove stray character.
 2018-08-21 17:24:29 +02:00
Marius Bakke 4c36fc7051
gnu: python-imagesize: Update to 1.0.0. 
* gnu/packages/python.scm (python-imagesize): Update to 1.0.0.
[arguments]: Remove.
 2018-08-21 17:24:29 +02:00
Marius Bakke 9764dac511
gnu: python-markupsafe: Update to 1.0. 
* gnu/packages/python.scm (python-markupsafe): Update to 1.0.
 2018-08-21 17:24:29 +02:00
Marius Bakke 4750b3a268
gnu: python-pytest: Run the tests again. 
"python setup.py test" is ineffective since 3.6.x.  The circle is complete.

* gnu/packages/check.scm (python-pytest)[arguments]: Override 'check' phase.
[native-inputs]: Add PYTHON-PYTEST-BOOTSTRAP.
 2018-08-21 17:24:29 +02:00
Marius Bakke e2c7b7bb68
gnu: libssh2: MIPS workaround no longer is. 
* gnu/packages/ssh.scm (libssh2)[arguments]: Override the 'bootstrap' phase
regardless of target system.  Remove 'autoreconf' phase.
 2018-08-21 17:24:29 +02:00
Marius Bakke 7b0faf32e9
gnu: pango: Update to 1.42.4. 
* gnu/packages/gtk.scm (pango): Update to 1.42.4.
 2018-08-21 17:24:29 +02:00
Marius Bakke 1935b8d56a
gnu: libffi: Don't optimize for the build machine CPU. 
* gnu/packages/libffi.scm (libffi)[arguments]: Add #:configure-flags.
 2018-08-21 17:24:29 +02:00
Marius Bakke e63199ec68
gnu: libatomic-ops: Update to 7.6.6. 
* gnu/packages/bdw-gc.scm (libatomic-ops): Update to 7.6.6.
 2018-08-21 17:24:29 +02:00
Marius Bakke 827509a30c
gnu: python-olefile: Update to 0.45.1. 
* gnu/packages/python.scm (python-olefile): Update to 0.45.1.
 2018-08-21 17:24:28 +02:00
Marius Bakke d76cd3defd
gnu: python-lxml: Update to 4.2.4. 
* gnu/packages/python.scm (python-lxml): Update to 4.2.4.
 2018-08-21 17:24:28 +02:00
Marius Bakke f6cd3f7970
gnu: python-ipaddress: Update to 1.0.22. 
* gnu/packages/python.scm (python-ipaddress): Update to 1.0.22.
 2018-08-21 17:24:28 +02:00
Marius Bakke c69d231c2a
gnu: python-pycparser: Update to 2.18. 
* gnu/packages/python.scm (python-pycparser): Update to 2.18.
 2018-08-21 17:24:28 +02:00
Marius Bakke b3751f9cea
gnu: python-setuptools-scm: Update to 3.1.0. 
* gnu/packages/python.scm (python-setuptools-scm): Update to 3.1.0.
 2018-08-21 17:24:28 +02:00
Marius Bakke 67a7da1f31
gnu: python-hypothesis: Update to 3.68.2. 
* gnu/packages/check.scm (python-hypothesis): Update to 3.68.2.
 2018-08-21 17:24:28 +02:00
Marius Bakke e241f9a020
gnu: python-more-itertools: Update to 4.3.0. 
* gnu/packages/python.scm (python-more-itertools): Update to 4.3.0.
 2018-08-21 17:24:28 +02:00
Marius Bakke 7f5d3445af
gnu: python-scandir: Update to 1.9.0. 
* gnu/packages/python.scm (python-scandir): Update to 1.9.0.
 2018-08-21 17:24:28 +02:00
Marius Bakke e2da8bcd9e
gnu: python-pytest: Update to 3.7.2. 
* gnu/packages/check.scm (python-pytest): Update to 3.7.2.
(python2-pytest)[propagated-inputs]: Add PYTHON2-PATHLIB.
(python2-pytest-bootstrap)[propagated-inputs]: Add PYTHON-PATHLIB2-BOOTSTRAP.
* gnu/packages/python.scm (python2-pathlib2-bootstrap): New public variable.
 2018-08-21 17:24:28 +02:00
Marius Bakke 27885fcc26
gnu: python-pluggy: Update to 0.7.1. 
* gnu/packages/python.scm (python-pluggy): Update to 0.7.1.
[native-inputs]: Add PYTHON-SETUPTOOLS-SCM.
 2018-08-21 17:24:27 +02:00
Marius Bakke fdf16a81b2
gnu: graphite2: Update to 1.3.12. 
* gnu/packages/fontutils.scm (graphite2): Update to 1.3.12.
 2018-08-21 17:24:27 +02:00
Marius Bakke 85932a7b8e
gnu: libuv: Update to 1.23.0. 
* gnu/packages/libevent.scm (libuv): Update to 1.23.0.
 2018-08-21 17:24:27 +02:00
Marius Bakke 1c61a086bc
gnu: expat: Update to 2.2.6. 
* gnu/packages/xml.scm (expat): Update to 2.2.6.
 2018-08-21 17:24:27 +02:00
Marius Bakke f203e53386
gnu: cmake: Update to 3.12.1. 
* gnu/packages/cmake.scm (cmake): Update to 3.12.1.
 2018-08-21 17:24:27 +02:00
Marius Bakke 09118c58da
gnu: glib: Update to 2.56.2. 
* gnu/packages/glib.scm (glib): Update to 2.56.2.
 2018-08-21 17:24:27 +02:00
Marius Bakke a5dae0c03c
gnu: dbus: Update to 1.12.10. 
* gnu/packages/glib.scm (dbus): Update to 1.12.10.
 2018-08-21 17:24:27 +02:00
Marius Bakke 11e5bf70d5
gnu: harfbuzz: Update to 1.8.8. 
* gnu/packages/gtk.scm (harfbuzz): Update to 1.8.8.
 2018-08-21 17:24:27 +02:00
Marius Bakke 3f35e0da86
gnu: bootstrap-tarballs: Adjust to static outputs of zlib and libunistring. 
* gnu/packages/make-bootstrap.scm (%gcc-static)[inputs]: Add ZLIB:STATIC.
(%guile-static)[inputs]: Add LIBUNISTRING:STATIC.
 2018-08-21 17:24:26 +02:00
Marius Bakke c0b3867c21
gnu: libunistring: Do install static library. 
...but do so to a separate output.  This reverts commit
1f2d64e4a8.

* gnu/packages/libunistring.scm (libunistring)[outputs]: New field.
[arguments]: Add phase for moving libunistring.a.  Remove #:configure-flags.
 2018-08-21 17:24:26 +02:00
Leo Famulari 6cd2c4a83c
gnu: openssh: Don't allow remote username enumeration [fixes CVE-2018-15473]. 
* gnu/packages/patches/openssh-CVE-2018-15473.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/ssh.scm (openssh)[source]: Use it.
 2018-08-21 11:16:30 -04:00
Leo Famulari 2fbc38e33b
gnu: python-paramiko: Add some missing dependencies. 
* gnu/packages/python-crypto.scm (python-paramiko,
python2-paramiko)[propagated-inputs]: Add python-bcrypt and python-pynacl.
 2018-08-21 11:04:47 -04:00
Pierre Neidhardt 15e57838c6
gnu: asymptote: Use minimal texlive-union. 
* gnu/packages/plotutils.scm (asymptote)[native-inputs]: Replace texlive with texlive-union.
 2018-08-21 16:32:22 +02:00
Pierre Neidhardt 756fc3e1ef
gnu: texlive-latex-base: Include support files. 
* gnu/packages/tex.scm (texlive-latex-base)[native-inputs]: Include support files.
 2018-08-21 16:32:22 +02:00
Pierre Neidhardt 9b02a79bb0
gnu: mit-scheme: Use minimal texlive-union. 
* gnu/packages/scheme.scm (mit-scheme)[native-inputs]: Replace texlive with texlive-union.
 2018-08-21 16:30:22 +02:00
Tobias Geerinckx-Rice 49dcfb5045
gnu: sl: Don't use unstable tarball. 
* gnu/packages/toys.scm (sl)[source]: Use GIT-FETCH and GIT-FILE-NAME.
 2018-08-21 07:17:06 +02:00
Tobias Geerinckx-Rice 20b5b97381
gnu: python-rpy2: Update to 2.9.4. 
* gnu/packages/python.scm (python-rpy2): Update to 2.9.4.
[arguments]: Remove obsolete phases and substitute INVOKE for SYSTEM*
now that we can.
 2018-08-21 07:17:06 +02:00
Tobias Geerinckx-Rice db09a450d2
gnu: python-rpy2: Update home page. 
* gnu/packages/python.scm (python-rpy2)[home-page]: Update URI.
 2018-08-21 07:17:05 +02:00
Tobias Geerinckx-Rice 93f9e0d9e9
gnu: r-iterators: Update to 1.0.10. 
* gnu/packages/statistics.scm (r-iterators): Update to 1.0.10.
 2018-08-21 07:17:05 +02:00
Tobias Geerinckx-Rice 4370881631
gnu: r-foreign: Update to 0.8-71. 
* gnu/packages/statistics.scm (r-foreign): Update to 0.8-71.
 2018-08-21 07:17:05 +02:00
Tobias Geerinckx-Rice aaaede49c1
gnu: r-with-tests: Return #t from all phases. 
* gnu/packages/statistics.scm (r-with-tests)[arguments]: Substitute
INVOKE for SYSTEM*.
 2018-08-21 07:04:06 +02:00
Tobias Geerinckx-Rice bdb7447843
gnu: fftw: Update to 3.3.8. 
* gnu/packages/algebra.scm (fftw): Update to 3.3.8.
 2018-08-21 07:04:06 +02:00
Tobias Geerinckx-Rice 4fb0871e77
gnu: at-spi2-atk: Update to 2.26.2. 
* gnu/packages/gtk.scm (at-spi2-atk): Update to 2.26.2.
 2018-08-21 07:04:06 +02:00
Tobias Geerinckx-Rice 8327ffcc7f
gnu: unixodbc: Update to 2.3.7. 
* gnu/packages/databases.scm (unixodbc): Update to 2.3.7.
 2018-08-21 07:04:05 +02:00
Tobias Geerinckx-Rice 6d863cdedd
gnu: r-openssl: Update to 1.0.2. 
* gnu/packages/statistics.scm (r-openssl): Update to 1.0.2.
 2018-08-21 03:25:42 +02:00
Tobias Geerinckx-Rice 4481004fa4
gnu: r-modeltools: Update to 0.2-22. 
* gnu/packages/statistics.scm (r-modeltools): Update to 0.2-22.
 2018-08-21 03:25:41 +02:00
Tobias Geerinckx-Rice 8ecf3f7ea5
gnu: mysql: Update to 5.7.23. 
* gnu/packages/databases.scm (mysql): Update to 5.7.23.
 2018-08-20 20:17:20 +02:00
Tobias Geerinckx-Rice 7cbf06d8c2
gnu: mysql: Fix build. 
MySQL demands boost@1.59.0, and lying about it no longer works:

sql/item_geofunc_internal.cc: In function ‘void handle_gis_exception(const char*)’:
sql/item_geofunc_internal.cc:37:81: error: expected unqualified-id before ‘&’ token
   catch (const boost::geometry::detail::self_get_turn_points::self_ip_exception &)
                                                                                 ^
[...]

* gnu/packages/databases.scm (boost-for-mysql): New variable.
(mysql)[inputs]: Use that instead of the regular boost.
[arguments]: Remove now-unnecessary ‘patch-boost-version’ phase.
 2018-08-20 20:17:20 +02:00
Tobias Geerinckx-Rice 725449bd7a
gnu: python-pyodbc: Update to 4.0.24. 
* gnu/packages/databases.scm (python-pyodbc): Update to 4.0.24.
 2018-08-20 20:17:19 +02:00
Tobias Geerinckx-Rice 28635e5266
gnu: python-mysqlclient: Update to 1.3.13. 
* gnu/packages/databases.scm (python-mysqlclient): Update to 1.3.13.
 2018-08-20 20:17:19 +02:00
Tobias Geerinckx-Rice db4e76416c
gnu: perl-dbd-sqlite: Update to 1.58. 
* gnu/packages/databases.scm (perl-dbd-sqlite): Update to 1.58.
 2018-08-20 20:17:19 +02:00
Tobias Geerinckx-Rice 9c112bee91
gnu: r-energy: Update to 1.7-5. 
* gnu/packages/cran.scm (r-energy): Update to 1.7-5.
 2018-08-20 20:17:19 +02:00
Tobias Geerinckx-Rice 8b0701d97a
gnu: r-tinytex: Update to 0.6. 
* gnu/packages/cran.scm (r-tinytex): Update to 0.6.
[propagated-inputs]: Add r-xfun.
 2018-08-20 20:17:18 +02:00
Tobias Geerinckx-Rice 2045af8035
gnu: r-xfun: Update to 0.3. 
* gnu/packages/cran.scm (r-xfun): Update to 0.3.
 2018-08-20 20:17:18 +02:00
Tobias Geerinckx-Rice 9b77f724c0
gnu: r-jomo: Update to 2.6-3. 
* gnu/packages/cran.scm (r-jomo): Update to 2.6-3.
 2018-08-20 20:17:18 +02:00
Tobias Geerinckx-Rice cd4abb6d4a
gnu: r-trend: Update to 1.1.1. 
* gnu/packages/cran.scm (r-trend): Update to 1.1.1.
 2018-08-20 20:17:18 +02:00
Tobias Geerinckx-Rice dc98bbcad4
gnu: r-lava: Update to 1.6.3. 
* gnu/packages/cran.scm (r-lava): Update to 1.6.3.
 2018-08-20 20:17:17 +02:00
Tobias Geerinckx-Rice 632cefdac9
gnu: r-mitml: Update to 0.3-6. 
* gnu/packages/cran.scm (r-mitml): Update to 0.3-6.
 2018-08-20 20:17:17 +02:00
Tobias Geerinckx-Rice 658e37b6e8
gnu: r-vgam: Update to 1.0-6. 
* gnu/packages/statistics.scm (r-vgam): Update to 1.0-6.
 2018-08-20 20:17:17 +02:00
Tobias Geerinckx-Rice 52773e5cf4
gnu: python-py: Use HTTPS home page. 
* gnu/packages/python.scm (python-py)[home-page]: Use HTTPS.
 2018-08-20 16:36:20 +02:00
Tobias Geerinckx-Rice c85626bb0f
gnu: xpad: Update to 5.1.0. 
* gnu/packages/gnome.scm (xpad): Update to 5.1.0.
[arguments]: Remove obsolete ‘run-autogen’ phase.
 2018-08-20 16:35:55 +02:00
Tobias Geerinckx-Rice bc2f9dc3ce
gnu: emacs-f: Update to 0.20.0. 
* gnu/packages/emacs.scm (emacs-f): Update to 0.20.0.
 2018-08-20 16:35:55 +02:00
Tobias Geerinckx-Rice bd0570f21d
gnu: emacs-f: Don't use unstable tarball. 
* gnu/packages/emacs.scm (emacs-f)[source]: Use GIT-FETCH and
GIT-FILE-NAME.
 2018-08-20 16:35:55 +02:00
Tobias Geerinckx-Rice cb4baa4da6
gnu: gimp: Report bugs to Guix. 
Upstream prints this when running ./configure. Take the hint.

  NOTE: if you plan on packaging GIMP for distribution, it is
        recommended to override the bug report URL with option:
          --with-bug-report-url=https://example.com/
        so that you can filter packaging bugs from core bugs before
        reporting upstream.

* gnu/packages/gimp.scm (gimp)[arguments]: Customise bug report URI.
 2018-08-20 16:35:54 +02:00
Tobias Geerinckx-Rice 0f83d6029e
gnu: gimp: Update to 2.10.6. 
* gnu/packages/gimp.scm (gimp): Update to 2.10.6.
 2018-08-20 16:35:54 +02:00
Tobias Geerinckx-Rice 901888a854
gnu: gegl: Update to 0.4.8. 
* gnu/packages/gimp.scm (gegl): Update to 0.4.8.
 2018-08-20 16:35:54 +02:00
Tobias Geerinckx-Rice 3cae7f582e
gnu: babl: Update to 0.1.56. 
* gnu/packages/gimp.scm (babl): Update to 0.1.56.
 2018-08-20 16:35:54 +02:00
Ludovic Courtès 64bcc76c00
gnu: guile-ssh: Update to 0.11.3. 
* gnu/packages/ssh.scm (guile-ssh): Update to 0.11.3.
 2018-08-20 16:32:18 +02:00
Ludovic Courtès 0ec3800274
gnu: guile-json: Update to 1.1.1. 
* gnu/packages/guile.scm (guile-json): Update to 1.1.1.
[source]: Remove snippet.
[native-inputs]: Add PKG-CONFIG.
 2018-08-20 16:32:18 +02:00
Ludovic Courtès a50eed201b
gnu: guile-redis: Update to 1.0.0. 
* gnu/packages/guile.scm (guile-redis): Update to 1.0.0.
[source]: Fetch from github.com.  Remove snippet.
[native-inputs]: Add AUTOCONF, AUTOMAKE, and PKG-CONFIG.
 2018-08-20 16:32:17 +02:00
Roel Janssen e63da346cf
gnu: Update virtuoso-ose to 7.2.5. 
* gnu/packages/databases.scm (virtuoso-ose): Update to 7.2.5.
 2018-08-20 16:13:45 +02:00
Rutger Helling f307a9eca5
gnu: xpra: Update to 2.3.3. 
* gnu/packages/xorg.scm (xpra): Update to 2.3.3.
 2018-08-20 08:48:53 +02:00
Rutger Helling 346c146f7f
gnu: wine-staging: Update to 3.14. 
* gnu/packages/wine.scm (wine-staging): Update to 3.14.
 2018-08-20 08:17:49 +02:00
Rutger Helling 56d4b2163a
gnu: wine-staging-patchset-data: Update to 3.14. 
* gnu/packages/wine.scm (wine-staging-patchset-data): Update to 3.14.
 2018-08-20 08:17:49 +02:00
Leo Famulari 1feaca62d3
gnu: syncthing: Invoke build steps with INVOKE. 
* gnu/packages/syncthing.scm (syncthing)[arguments]: Use INVOKE.
 2018-08-19 17:50:48 -04:00
Marius Bakke 146c3b2160
gnu: libconfuse: Update to 3.2.2 [fixes CVE-2018-14447]. 
* gnu/packages/wm.scm (libconfuse): Update to 3.2.2.
 2018-08-19 18:40:30 +02:00
Ludovic Courtès 0b93d04ac5
gnu: gcc@4.8: Fix libsanitizer build issue. 
Fixes <https://bugs.gnu.org/32397>.
Reported by fis trivial <ybbs.daans@hotmail.com>.

* gnu/packages/patches/gcc-4.8-libsanitizer-fix.patch: New file.
* gnu/packages/gcc.scm (gcc-4.8)[source]: Use it.
* gnu/local.mk (dist_patch_DATA): Add it.
 2018-08-19 18:21:24 +02:00
Ludovic Courtès 6d1a7ce8ea
gnu: libchop: Fix build and test errors. 
* gnu/packages/backup.scm (libchop)[arguments]: New field.
 2018-08-19 18:21:24 +02:00