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* gnu: epiphany: Use webkitgtk-2.22.Mark H Weaver2018-09-23
| | | | | * gnu/packages/gnome.scm (epiphany)[native-inputs]: Add gcc-7. [inputs]: Replace webkitgtk with webkitgtk-2.22.
* gnu: webkitgtk: Add version 2.22.2.Mark H Weaver2018-09-23
| | | | * gnu/packages/webkit.scm (webkitgtk-2.22): New variable.
* gnu: Add Go 1.11.Katherine Cox-Buday2018-09-22
| | | | | | * gnu/packages/golang.scm (go-1.11): New variable. Signed-off-by: Leo Famulari <leo@famulari.name>
* gnu: icecat: Add fixes from upstream mozilla-esr60 [security fixes].Mark H Weaver2018-09-22
| | | | | | | | | | | | Includes fixes for CVE-2018-12383 and CVE-2018-12385. * gnu/packages/patches/icecat-CVE-2018-12383.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. * gnu/packages/patches/icecat-avoid-bundled-libraries.patch: Adapt to apply cleanly to IceCat 60. * gnu/packages/gnuzilla.scm (mozilla-patch): Update to fetch from mozilla-esr60. (icecat): Add selected changesets from upstream mozilla-esr60.
* Revert 'gnu: rust: Remove unused "ar" setting.'.Danny Milosavljevic2018-09-22
| | | | | | | Some versions of Rust do need it and others complain about it. For now, revert the removal entirely. This reverts commit ec944a1de97c8a523d6e1089b8c4430424297f93.
* gnu: hmmer: Update to 3.2.1.Ben Woodcroft2018-09-22
| | | | | | | | | * gnu/packages/bioinformatics.scm (hmmer): Update to 3.2.1. [origin]: Remove patch. [license]: Change to BSD-3. [supported-systems]: New field. * gnu/packages/patches/hmmer-remove-cpu-specificity.patch: Delete file. * gnu/local.mk (dist_patch_DATA): Remove it.
* gnu: snap: Update to 4.2.1.4.Nicolas Goaziou2018-09-21
| | | | * gnu/packages/education.scm (snap): Update to 4.2.1.4.
* gnu: emacs-org: Update to 9.1.14.Nicolas Goaziou2018-09-21
| | | | * gnu/packages/emacs.scm (emacs-org): Update to 9.1.14.
* gnu: workrave: Update to 1.10.21.Tobias Geerinckx-Rice2018-09-21
| | | | | * gnu/packages/gnome.scm (workrave): Update to 1.10.21. [source]: Use GIT-FILE-NAME.
* gnu: emacs-password-store: Update to 1.7.3.Tobias Geerinckx-Rice2018-09-21
| | | | * gnu/packages/emacs.scm (emacs-password-store): Update to 1.7.3.
* gnu: filezilla: Update to 3.37.1.Tobias Geerinckx-Rice2018-09-21
| | | | * gnu/packages/ftp.scm (filezilla): Update to 3.37.1.
* gnu: wxwidgets: Update to 3.0.4.Tobias Geerinckx-Rice2018-09-21
| | | | * gnu/packages/wxwidgets.scm (wxwidgets): Update to 3.0.4.
* gnu: python-pyparsing: Update to 2.2.1.Tobias Geerinckx-Rice2018-09-21
| | | | | * gnu/packages/python.scm (python-pyparsing): Update to 2.2.1. [source]: Use PYPI-URI.
* gnu: rust: Remove unused "ar" setting.Danny Milosavljevic2018-09-21
| | | | | * gnu/packages/rust.scm (rust-1.20)[arguments]<#:phases>[configure]: Remove unused "ar" setting.
* gnu: Add r-pore.pimi2018-09-21
| | | | | | * gnu/packages/bioinformatics.scm (r-pore): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
* gnu: hdf5-parallel-openmpi: Really enable parallel build.Paul Garlick2018-09-21
| | | | | | | | | | | 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>
* gnu: hdf5: Allow for absence of utility script.Paul Garlick2018-09-21
| | | | | | | * 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>
* gnu: rust: Remove unused "localstatedir" setting.Danny Milosavljevic2018-09-21
| | | | | * gnu/packages/rust.scm (rust-1.20)[arguments]<#:phases>[configure]: Remove unused "localstatedir" setting.
* gnu: libfilezilla: Update to 0.13.2.Tobias Geerinckx-Rice2018-09-21
| | | | | * gnu/packages/ftp.scm (libfilezilla): Update to 0.13.2. [source]: Use HTTPS.
* gnu: python-pyparsing: Update home page.Tobias Geerinckx-Rice2018-09-21
| | | | * gnu/packages/python.scm (python-pyparsing)[home-page]: Update.
* gnu: emacs-mu4e-conversation: Fix typo in description.Tobias Geerinckx-Rice2018-09-21
| | | | | * gnu/packages/emacs.scm (emacs-mu4e-conversation)[description]: Fix 'correspondant' typo.
* gnu: kodi: Use INVOKE.Tobias Geerinckx-Rice2018-09-21
| | | | * gnu/packages/kodi.scm (kodi)[arguments]: Substitute INVOKE for SYSTEM*.
* gnu: crossguid: Use INVOKE.Tobias Geerinckx-Rice2018-09-21
| | | | * gnu/packages/kodi.scm (crossguid)[arguments]: Substitute INVOKE for SYSTEM*.
* gnu: icecat: Update to 60.2.0-gnu1 (pre-release).Mark H Weaver2018-09-21
| | | | | | | | | | | | | | | | * 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.
* gnu: libvpx: Add upstream security fix.Mark H Weaver2018-09-21
| | | | | | * 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.
* gnu: python-paramiko: Update to 2.4.2 [security fixes].Tobias Geerinckx-Rice2018-09-21
| | | | * gnu/packages/python-crypto.scm (python-paramiko): Update to 2.4.2.
* gnu: python-paramiko: Use HTTPS home page.Tobias Geerinckx-Rice2018-09-21
| | | | * gnu/packages/python-crypto.scm (python-paramiko)[home-page]: Use HTTPS.
* gnu: python-rencode: Update to 1.0.5.Tobias Geerinckx-Rice2018-09-21
| | | | | * gnu/packages/python.scm (python-rencode): Update to 1.0.5. [arguments]: Add a 'delete-bogus-test' phase.
* gnu: python-hdf4: Use INVOKE.Tobias Geerinckx-Rice2018-09-21
| | | | | * gnu/packages/python.scm (python-hdf4)[arguments]: Substitute INVOKE for SYSTEM*.
* gnu: s6: Update to 2.7.2.1.Tobias Geerinckx-Rice2018-09-21
| | | | * gnu/packages/skarnet.scm (s6): Update to 2.7.2.1.
* gnu: perl-xml-compile: Update to 1.60.Tobias Geerinckx-Rice2018-09-21
| | | | | | * gnu/packages/xml.scm (perl-xml-compile): Update to 1.60. [propagated-inputs]: Add perl-carp, perl-scalar-list-utils, and perl-types-serialiser.
* gnu: emacs-orgalist: Update to 1.9.Nicolas Goaziou2018-09-21
| | | | * gnu/packages/emacs.scm (emacs-orgalist): Update to 1.9.
* gnu: openscenegraph: Update to 3.6.3.Tobias Geerinckx-Rice2018-09-21
| | | | | | * gnu/packages/graphics.scm (openscenegraph): Update to 3.6.3. [source]: Use GIT-FILE-NAME. [inputs]: Remove unused pth and qtbase.
* gnu: python-pydot: Update to 1.2.4.Tobias Geerinckx-Rice2018-09-21
| | | | | | * gnu/packages/graphviz.scm (python-pydot): Update to 1.2.4. [arguments]: Run the test suite. [native-inputs]: Add python-chardet.
* Add 'GNU Guix' comment to all (gnu packages) headers.Tobias Geerinckx-Rice2018-09-21
| | | | * gnu/packages/debian.scm, gnu/packages/syndication.scm: Add comments.
* gnu: ubuntu-keyring: Update to 2018.09.18.1.Tobias Geerinckx-Rice2018-09-21
| | | | * gnu/packages/debian.scm (ubuntu-keyring): Update to 2018.09.18.1.
* gnu: perl-dbd-mysql: Update to 4.048.Tobias Geerinckx-Rice2018-09-21
| | | | * gnu/packages/databases.scm (perl-dbd-mysql): Update to 4.048.
* gnu: rust: Work around mtime bug in rust build helpers.Danny Milosavljevic2018-09-21
| | | | | | | | * 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.
* gnu: rust@1.20.0: Fix tests.Danny Milosavljevic2018-09-21
| | | | | | | * 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.
* gnu: linux-libre: Update to 4.18.9.Mark H Weaver2018-09-20
| | | | | * gnu/packages/linux.scm (%linux-libre-version): Update to 4.18.9. (%linux-libre-hash): Update hash.
* gnu: linux-libre@4.14: Update to 4.14.71.Mark H Weaver2018-09-20
| | | | | * gnu/packages/linux.scm (%linux-libre-4.14-version): Update to 4.14.71. (%linux-libre-4.14-hash): Update hash.
* gnu: linux-libre@4.9: Update to 4.9.128.Mark H Weaver2018-09-20
| | | | * gnu/packages/linux.scm (linux-libre-4.9): Update to 4.9.128.
* gnu: linux-libre@4.4: Update to 4.4.157.Mark H Weaver2018-09-20
| | | | * gnu/packages/linux.scm (linux-libre-4.4): Update to 4.4.157.
* gnu: qbittorrent: Update to 4.1.3.fis trivial2018-09-20
| | | | | | | * 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>
* gnu: gprolog: Update to 1.4.5.fis trivial2018-09-20
| | | | | | | * gnu/packages/gprolog.scm (gprolog): Update to 1.4.5. [source]: Add an alternate source URL. Signed-off-by: Leo Famulari <leo@famulari.name>
* gnu: rsem: Update to 1.3.1.Ricardo Wurmus2018-09-20
| | | | | | | | | * 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.
* gnu: ghc-pandoc-citeproc: Update to 0.14.3.1.Ricardo Wurmus2018-09-20
| | | | * gnu/packages/haskell.scm (ghc-pandoc-citeproc): Update to 0.14.3.1.
* gnu: ghc-xml-conduit: Update to 1.8.0.1.Ricardo Wurmus2018-09-20
| | | | | * gnu/packages/haskell.scm (ghc-xml-conduit): Update to 1.8.0.1. [inputs]: Add ghc-doctest.
* gnu: python2-scikit-learn: Fix check phase.Ricardo Wurmus2018-09-20
| | | | | * gnu/packages/machine-learning.scm (python2-scikit-learn)[arguments]: Override check phase to disable broken tests and pass environment variables.
* gnu: Add r-parmigene.Ricardo Wurmus2018-09-20
| | | | * gnu/packages/cran.scm (r-parmigene): New variable.
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