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2016-05-31gnu: Add ghmm.Ricardo Wurmus
* gnu/packages/machine-learning.scm (ghmm): New variable.
2016-05-31gnu: gimp: Update to 2.8.16.Efraim Flashner
* gnu/packages/gimp.scm (gimp): Update to 2.8.16.
2016-05-31gnu: Add r-genomationdata.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-genomationdata): New variable.
2016-05-31gnu: Add r-runit.Ricardo Wurmus
* gnu/packages/statistics.scm (r-runit): New variable.
2016-05-31gnu: julia: Update to 0.4.5.Ricardo Wurmus
* gnu/packages/julia.scm (julia): Update to 0.4.5. (libuv-julia): Update commit.
2016-05-31gnu: Add r-knitrbootstrap.Ricardo Wurmus
* gnu/packages/statistics.scm (r-knitrbootstrap): New variable.
2016-05-31daemon: rounds: Keep the differing output if -K is given.Eelco Dolstra
Regardless of -K, we now also print which output differs.
2016-05-31daemon: Canonicalize gids to 0.Eelco Dolstra
Previously files in the Nix store were owned by root or by nixbld, depending on whether they were created by a substituter or by a builder. This doesn't matter much, but causes spurious diffoscope differences. So use root everywhere.
2016-05-31daemon: check: Keep the differing output if -K is given.Eelco Dolstra
This makes it easier to investigate the non-determinism, e.g. $ nix-build pkgs/stdenv/linux -A stage1.pkgs.zlib --check -K error: derivation ‘/nix/store/l54i8wlw22656i4pk05c52ngv9rpl39q-zlib-1.2.8.drv’ may not be deterministic: output ‘/nix/store/11a27shh6n2ivi4a7s964i65ql80cf27-zlib-1.2.8’ differs from ‘/nix/store/11a27shh6n2ivi4a7s964i65ql80cf27-zlib-1.2.8-check’ $ diffoscope /nix/store/11a27shh6n2ivi4a7s964i65ql80cf27-zlib-1.2.8 /nix/store/11a27shh6n2ivi4a7s964i65ql80cf27-zlib-1.2.8-check ... ├── lib/libz.a │ ├── metadata │ │ @@ -1,15 +1,15 @@ │ │ -rw-r--r-- 30001/30000 3096 Jan 12 15:20 2016 adler32.o ... │ │ +rw-r--r-- 30001/30000 3096 Jan 12 15:28 2016 adler32.o ... Co-authored-by: Ludovic Courtès <ludo@gnu.org>
2016-05-31daemon: check: Fix "failed to produce output path".Eelco Dolstra
This occured when sandbox building is disabled, at least one output exists, and at least one other output does not.
2016-05-31daemon: check: Fix assertion failure when some outputs are missing.Eelco Dolstra
E.g. $ nix-build pkgs/stdenv/linux/ -A stage1.pkgs.perl --check nix-store: src/libstore/build.cc:1323: void nix::DerivationGoal::tryToBuild(): Assertion `buildMode != bmCheck || validPaths.size() == drv->outputs.size()' failed. when perl.out exists but perl.man doesn't. The fix is to only check the outputs that exist. Note that "nix-build -A stage1.pkgs.all --check" will still give a (proper) error in this case.
2016-05-31daemon: When repairing, rebuild if there is no substituter.Eelco Dolstra
2016-05-31daemon: Fix --repair failure on multiple-output derivations.Eelco Dolstra
If repair found a corrupted/missing path that depended on a multiple-output derivation, and some of the outputs of the latter were not present, it failed with a message like error: path ‘/nix/store/cnfn9d5fjys1y93cz9shld2xwaibd7nn-bash-4.3-p42-doc’ is not valid Co-authored-by: Ludovic Courtès <ludo@gnu.org>
2016-05-31daemon: ~PathLocks(): Handle exceptions.Eelco Dolstra
Otherwise, since the call to write a "d" character to the lock file can fail with ENOSPC, we can get an unhandled exception resulting in a call to terminate().
2016-05-31daemon: Handle /tmp being a symlink.Eelco Dolstra
* nix/libstore/build.cc (DerivationGoal::startBuilder): Call 'canonPath' on "/tmp".
2016-05-31services: urandom-seed: Set umask to 077 while shutting down.Leo Famulari
* gnu/services/base.scm (urandom-seed-shepherd-service): Call 'umask'.
2016-05-30gnu: libxml2: Update replacement to 2.9.4 [security fixes].Leo Famulari
This fixes CVE-2016-{1762, 1833, 1834, 1835, 1836, 1837, 1838, 1839, 1840, 3627, 3705, 4483}. * gnu/packages/patches/libxml2-CVE-2016-3627.patch, gnu/packages/patches/libxml2-CVE-2016-3705.patch: Delete files. * gnu/local.mk (dist_patch_DATA): Remove them. * gnu/packages/xml.scm (libxml2/fixed): Update to 2.9.4. [source]: Remove patches.
2016-05-31container: Gracefully report mount errors in the child process.Ludovic Courtès
Fixes <http://bugs.gnu.org/23306>. * gnu/build/linux-container.scm (run-container): Use 'socketpair' instead of 'pipe'. Rename 'in' to 'child' and 'out' to 'parent'. Send a 'ready message or an exception argument list from the child to the parent; adjust the parent accordingly. * tests/containers.scm ("call-with-container, mnt namespace, wrong bind mount"): New test. * tests/guix-environment-container.sh: Add test with --expose=/does-not-exist.
2016-05-31container: Gracefully handle failure to set up user namespaces.Ludovic Courtès
* gnu/build/linux-container.scm (run-container): Exit when the parent process doesn't say 'ready.
2016-05-31download: Update CPAN mirrors.Efraim Flashner
* guix/download.scm (mirrors)[cpan]: Add to mirror list.
2016-05-30gnu: vapoursynth: Update to 32.Efraim Flashner
* gnu/packages/video.scm (vapoursynth): Update to 32.
2016-05-30gnu: Add zimg.Efraim Flashner
* gnu/packages/image.scm (zimg): New variable.
2016-05-30gnu: mcrypt: Fix CVE-2012-4409, CVE-2012-4426, CVE-2012-4527.Efraim Flashner
* gnu/packages/mcrypt.scm (mcrypt)[source]: Add patches. * gnu/packages/patches/mcrypt-CVE-2012-4409.patch, gnu/packages/patches/mcrypt-CVE-2012-4426.patch, gnu/packages/patches/mcrypt-CVE-2012-4527.patch: New variables. * gnu/local.mk (dist_patch_DATA): Add them.
2016-05-30gnu: imagemagick: Update to 6.9.4-5.Leo Famulari
* gnu/packages/imagemagick.scm (imagemagick): Update to 6.9.4-5.
2016-05-30gnu: Remove xgcc-avr.David Thompson
We now have a dedicated package module for the AVR toolchain with important modifications on top of what cross-gcc produces. * gnu/packages/cross-base.scm (xgcc-avr): Delete.
2016-05-30gnu: Add avr-toolchain.David Thompson
* gnu/packages/avr.scm (avr-toolchain): New procedure. (avr-toolchain-4.9, avr-toolchain-5): New variables.
2016-05-30gnu: avr-libc: Update to 2.0.0.David Thompson
* gnu/packages/avr.scm (avr-libc): Update to 2.0.0.
2016-05-30gnu: avr-libc: Fix build.David Thompson
* gnu/packages/avr.scm (avr-libc): Update to 2.0.0. [native-inputs]: Use new avr-gcc and avr-binutils. [arguments]: Add phase to unset C_INCLUDE_PATH.
2016-05-30gnu: Add avr-gcc-5.David Thompson
* gnu/packages/avr.scm (avr-gcc-5): New variable.
2016-05-30gnu: Add avr-gcc.David Thompson
* gnu/packages/avr.scm (avr-gcc): New variable.
2016-05-30gnu: Add avr-binutils.David Thompson
* gnu/packages/avr.scm (avr-binutils): New variable.
2016-05-30gnu: wordnet: Use 'modify-phases'.Efraim Flashner
* gnu/packages/wordnet.scm (wordnet)[arguments]: Use 'modify-phases'.
2016-05-30gnu: wordnet: Fix CVE-2008-2149, CVE-2008-3908.Efraim Flashner
* gnu/packages/wordnet.scm (wordnet)[source]: Add patches. * gnu/packages/patches/wordnet-CVE-2008-2149.patch, gnu/packages/patches/wordnet-CVE-2008-3908-pt1.patch, gnu/packages/patches/wordnet-CVE-2008-3908-pt2.patch: New variables. * gnu/local.mk (dist_patch_DATA): Add them.
2016-05-30gnu: id3lib: Fix CVE-2007-4460.Efraim Flashner
* gnu/packages/mp3.scm (id3lib)[source]: Add patch. * gnu/packages/patches/id3lib-CVE-2007-4460.patch: New variable. * gnu/local.mk (dist_patch_DATA): Add it.
2016-05-30gnu: cyrus-sasl: Update URLs.Leo Famulari
* gnu/packages/cyrus-sasl.scm (cyrus-sasl)[source]: Use HTTPS URL. [home-page]: Update home-page URL.
2016-05-30gnu: devil: Fix CVE-2009-3994.Leo Famulari
* gnu/packages/patches/devil-CVE-2009-3994.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. * gnu/packages/image.scm (devil): Use it.
2016-05-30gnu: iptables: Update to 1.4.21.Leo Famulari
* gnu/packages/linux.scm (iptables): Update to 1.4.21.
2016-05-30gnu: Add emacs-better-defaults.David Thompson
* gnu/packages/emacs.scm (emacs-better-defaults): New variable.
2016-05-30gnu: emacs: Remove uncompressed-file-fetch.David Thompson
* gnu/packages/emacs.scm (uncompressed-file-fetch): Delete. (emacs-rfcview, emacs-ffap-rfc-space, emacs-queue, emacs-spinner): Replace uncompressed-file-fetch with url-fetch.
2016-05-30build: emacs: Handle sources that are a single elisp file.David Thompson
* guix/build/emacs-build-system.scm (gnu:unpack) (store-file->elisp-source-file, unpack): New procedures. (%standard-phases): Use the new unpack procedure.
2016-05-30gnu: Add emacs-seq.humanitiesNerd
* gnu/packages/emacs.scm (emacs-seq): New variable. Signed-off-by: Alex Kost <alezost@gmail.com>
2016-05-30gnu: Add emacs-spinner.humanitiesNerd
* gnu/packages/emacs.scm (emacs-spinner): New variable. Signed-off-by: Alex Kost <alezost@gmail.com>
2016-05-30gnu: Add emacs-pkg-info.humanitiesNerd
* gnu/packages/emacs.scm (emacs-pkg-info): New variable. Signed-off-by: Alex Kost <alezost@gmail.com>
2016-05-30gnu: Add emacs-queue.humanitiesNerd
* gnu/packages/emacs.scm (emacs-queue): New variable. Signed-off-by: Alex Kost <alezost@gmail.com>
2016-05-30gnu: emacs: Fix indentation of scheme keyword lists.Alex Kost
* gnu/packages/patches/emacs-fix-scheme-indent-function.patch: New patch. * gnu/local.mk (dist_patch_DATA): Add it. * gnu/packages/emacs.scm (emacs)[source]: Use it.
2016-05-30gnu: gegl: Fix CVE-2012-4433.Efraim Flashner
* gnu/packages/gimp.scm (gegl)[source]: Add patch. * gnu/packages/patches/gegl-CVE-2012-4433.patch: New variable. * gnu/local.mk (dist_patch_DATA): Add it.
2016-05-30gnu: vte-0.28: Fix CVE-2012-2738.Efraim Flashner
* gnu/packages/gnome.scm (vte-0.28)[source]: Add patches. * gnu/packages/patches/vte-CVE-2012-2738-pt1.patch, gnu/packages/patches/vte-CVE-2012-2738-pt2.patch: New variables. * gnu/local.mk (dist_patch_DATA): Add them.
2016-05-30gnu: t1lib: Fix CVE-2010-2642, CVE-2011-{0764, 1552, 1553, 1554}.Efraim Flashner
* gnu/packages/fontutils.scm (t1lib)[source]: Add patches. * gnu/packages/patches/t1lib-CVE-2010-2642.patch, gnu/packages/patches/t1lib-CVE-2011-0764.patch, gnu/packages/patches/t1lib-CVE-2011-1552+CVE-2011-1553+CVE-2011-1554.patch: New variables. * gnu/local.mk (dist_patch_DATA): Add them.
2016-05-30download: Update Sourceforge mirrors.Efraim Flashner
* guix/download.scm (mirrors)[sourceforge]: Update mirror list.
2016-05-30gnu: dtach: Use 'modify-phases'.Efraim Flashner
* gnu/packages/screen.scm (dtach)[arguments]: Use 'modify-phases'.
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