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2018-09-24gnu: Add r-bseqsc.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-bseqsc): New variable.
2018-09-24gnu: Add r-cssam.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-cssam): New variable.
2018-09-24gnu: Add r-xbioc.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-xbioc): New variable.
2018-09-24gnu: Prefix all Emacs packages with "emacs-".Pierre Neidhardt
* gnu/packages/emacs.scm: Prefix all Emacs packages with "emacs-". This is to enforce consistency and so that `emacs-packages?' can reliably detect Emacs packages based on the "emacs-" prefix.
2018-09-24gnu: python-networkx: Use HTTPS home page.Tobias Geerinckx-Rice
* gnu/packages/python.scm (python-networkx)[home-page]: Use HTTPS.
2018-09-24gnu: python-networkx: Update to 2.2.Tobias Geerinckx-Rice
* gnu/packages/python.scm (python-networkx): Update to 2.2.
2018-09-24gnu: python-decorator: Update to 4.3.0.Tobias Geerinckx-Rice
* gnu/packages/python.scm (python-decorator): Update to 4.3.0. [arguments]: Run the test suite.
2018-09-24gnu: python-marshmallow: Update to 3.0.0b14.Tobias Geerinckx-Rice
* gnu/packages/python.scm (python-marshmallow): Update to 3.0.0b14.
2018-09-24gnu: libiptcdata: Update to 1.0.5.Tobias Geerinckx-Rice
* gnu/packages/image.scm (libiptcdata): Update to 1.0.5. [home-page]: Follow Debian's maintained upstream.
2018-09-24gnu: virtualgl: Update to 2.6.Tobias Geerinckx-Rice
* gnu/packages/gl.scm (virtualgl): Update to 2.6. [inputs]: Add libxtst.
2018-09-24gnu: parallel: Update to 20180922.Tobias Geerinckx-Rice
* gnu/packages/parallel.scm (parallel): Update to 20180922.
2018-09-24gnu: workrave: Use Guix's built-in bootstrap phase.Tobias Geerinckx-Rice
* gnu/packages/gnome.scm (workrave)[arguments]: Remove 'autoconf' phase.
2018-09-24gnu: python-gitdb: Update to 2.0.4.Tobias Geerinckx-Rice
* gnu/packages/version-control.scm (python-gitdb): Update to 2.0.4. [arguments]: Replace AND with equivalent but more 'accurate' BEGIN.
2018-09-24gnu: nano: Update to 3.1.Tobias Geerinckx-Rice
* gnu/packages/nano.scm (nano): Update to 3.1.
2018-09-24gnu: fping: Use HTTPS home page.Tobias Geerinckx-Rice
* gnu/packages/networking.scm (fping)[home-page]: Use HTTPS.
2018-09-24gnu: fping: Update to 4.1.Tobias Geerinckx-Rice
* gnu/packages/networking.scm (fping): Update to 4.1.
2018-09-23vm: Use "cache=loose" for all 9p mounts.Ludovic Courtès
This significantly improves read throughput when running things like "guix hash -r ...". * gnu/system/vm.scm (%linux-vm-file-systems): Add 'flags' for "store". Add "cache=loose" to every file system.
2018-09-23vm: Disable deduplication for 'guix system vm-image'.Ludovic Courtès
* gnu/system/vm.scm (qemu-image): Pass #:deduplicate? #f to 'root-partition-initializer'.
2018-09-23system: Mention '--skip-checks' in initrd diagnostics.Ludovic Courtès
* gnu/system/mapped-devices.scm (check-device-initrd-modules): Add note about '--skip-checks'.
2018-09-23gnu: Add emacs-synosaurus.Pierre Neidhardt
* gnu/packages/emacs.scm (emacs-synosaurus): New variable.
2018-09-23gnu: xpra: Update to 2.3.4.Rutger Helling
* gnu/packages/xorg.scm (xpra): Update to 2.3.4.
2018-09-23gnu: eolie: Use webkitgtk-2.22.Mark H Weaver
* gnu/packages/gnome.scm (eolie)[native-inputs]: Add gcc-7:lib. [inputs]: Replace webkitgtk with webkitgtk-2.22. [arguments]: Add "gcc:lib" to the list of libraries to add to LD_LIBRARY_PATH. Use invoke.
2018-09-23gnu: epiphany: Use webkitgtk-2.22.Mark H Weaver
* gnu/packages/gnome.scm (epiphany)[native-inputs]: Add gcc-7. [inputs]: Replace webkitgtk with webkitgtk-2.22.
2018-09-23gnu: webkitgtk: Add version 2.22.2.Mark H Weaver
* gnu/packages/webkit.scm (webkitgtk-2.22): New variable.
2018-09-22gnu: Add Go 1.11.Katherine Cox-Buday
* gnu/packages/golang.scm (go-1.11): New variable. Signed-off-by: Leo Famulari <leo@famulari.name>
2018-09-22gnu: icecat: Add fixes from upstream mozilla-esr60 [security fixes].Mark H Weaver
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.
2018-09-22Revert 'gnu: rust: Remove unused "ar" setting.'.Danny Milosavljevic
Some versions of Rust do need it and others complain about it. For now, revert the removal entirely. This reverts commit ec944a1de97c8a523d6e1089b8c4430424297f93.
2018-09-22gnu: hmmer: Update to 3.2.1.Ben Woodcroft
* 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.
2018-09-21gnu: snap: Update to 4.2.1.4.Nicolas Goaziou
* gnu/packages/education.scm (snap): Update to 4.2.1.4.
2018-09-21gnu: emacs-org: Update to 9.1.14.Nicolas Goaziou
* gnu/packages/emacs.scm (emacs-org): Update to 9.1.14.
2018-09-21gnu: workrave: Update to 1.10.21.Tobias Geerinckx-Rice
* gnu/packages/gnome.scm (workrave): Update to 1.10.21. [source]: Use GIT-FILE-NAME.
2018-09-21gnu: emacs-password-store: Update to 1.7.3.Tobias Geerinckx-Rice
* gnu/packages/emacs.scm (emacs-password-store): Update to 1.7.3.
2018-09-21gnu: filezilla: Update to 3.37.1.Tobias Geerinckx-Rice
* gnu/packages/ftp.scm (filezilla): Update to 3.37.1.
2018-09-21gnu: wxwidgets: Update to 3.0.4.Tobias Geerinckx-Rice
* gnu/packages/wxwidgets.scm (wxwidgets): Update to 3.0.4.
2018-09-21gnu: python-pyparsing: Update to 2.2.1.Tobias Geerinckx-Rice
* gnu/packages/python.scm (python-pyparsing): Update to 2.2.1. [source]: Use PYPI-URI.
2018-09-21gnu: rust: Remove unused "ar" setting.Danny Milosavljevic
* gnu/packages/rust.scm (rust-1.20)[arguments]<#:phases>[configure]: Remove unused "ar" setting.
2018-09-21gnu: Add r-pore.pimi
* gnu/packages/bioinformatics.scm (r-pore): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2018-09-21gnu: hdf5-parallel-openmpi: Really enable parallel build.Paul Garlick
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>
2018-09-21gnu: hdf5: Allow for absence of utility script.Paul Garlick
* 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>
2018-09-21gnu: rust: Remove unused "localstatedir" setting.Danny Milosavljevic
* gnu/packages/rust.scm (rust-1.20)[arguments]<#:phases>[configure]: Remove unused "localstatedir" setting.
2018-09-21gnu: libfilezilla: Update to 0.13.2.Tobias Geerinckx-Rice
* gnu/packages/ftp.scm (libfilezilla): Update to 0.13.2. [source]: Use HTTPS.
2018-09-21gnu: python-pyparsing: Update home page.Tobias Geerinckx-Rice
* gnu/packages/python.scm (python-pyparsing)[home-page]: Update.
2018-09-21gnu: emacs-mu4e-conversation: Fix typo in description.Tobias Geerinckx-Rice
* gnu/packages/emacs.scm (emacs-mu4e-conversation)[description]: Fix 'correspondant' typo.
2018-09-21gnu: kodi: Use INVOKE.Tobias Geerinckx-Rice
* gnu/packages/kodi.scm (kodi)[arguments]: Substitute INVOKE for SYSTEM*.
2018-09-21gnu: crossguid: Use INVOKE.Tobias Geerinckx-Rice
* gnu/packages/kodi.scm (crossguid)[arguments]: Substitute INVOKE for SYSTEM*.
2018-09-21gnu: icecat: Update to 60.2.0-gnu1 (pre-release).Mark H Weaver
* 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.
2018-09-21gnu: libvpx: Add upstream security fix.Mark H Weaver
* 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.
2018-09-21gnu: python-paramiko: Update to 2.4.2 [security fixes].Tobias Geerinckx-Rice
* gnu/packages/python-crypto.scm (python-paramiko): Update to 2.4.2.
2018-09-21gnu: python-paramiko: Use HTTPS home page.Tobias Geerinckx-Rice
* gnu/packages/python-crypto.scm (python-paramiko)[home-page]: Use HTTPS.
2018-09-21gnu: python-rencode: Update to 1.0.5.Tobias Geerinckx-Rice
* gnu/packages/python.scm (python-rencode): Update to 1.0.5. [arguments]: Add a 'delete-bogus-test' phase.
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