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13160 Commits

Author SHA1 Message Date
Ludovic Courtès 0a40626fd2
offload: Use (guix build syscalls). 
This is a followup to 4e0ea3eb28.

* guix/scripts/offload.scm: Use (guix build syscalls).
 2016-05-31 18:22:14 +02:00
Ludovic Courtès 75abbd0cbe
daemon: Remove unused XML output code. 
* nix/local.mk (libutil_a_SOURCES): Remove libutil/xml-writer.cc.
(libutil_headers): Remove libutil/xml-writer.hh.
* nix/libutil/xml-writer.hh, nix/libutil/xml-writer.cc: Remove.
 2016-05-31 18:22:14 +02:00
Ricardo Wurmus 23aab4ab2c
gnu: Add ghmm. 
* gnu/packages/machine-learning.scm (ghmm): New variable.
 2016-05-31 17:01:03 +02:00
Efraim Flashner a5dd8db4ff
gnu: gimp: Update to 2.8.16. 
* gnu/packages/gimp.scm (gimp): Update to 2.8.16.
 2016-05-31 17:50:08 +03:00
Ricardo Wurmus 64efa3078a
gnu: Add r-genomationdata. 
* gnu/packages/bioinformatics.scm (r-genomationdata): New variable.
 2016-05-31 16:29:37 +02:00
Ricardo Wurmus aa3b391092
gnu: Add r-runit. 
* gnu/packages/statistics.scm (r-runit): New variable.
 2016-05-31 16:24:59 +02:00
Ricardo Wurmus 8170172502
gnu: julia: Update to 0.4.5. 
* gnu/packages/julia.scm (julia): Update to 0.4.5.
(libuv-julia): Update commit.
 2016-05-31 16:21:31 +02:00
Ricardo Wurmus 4ce3c2872b
gnu: Add r-knitrbootstrap. 
* gnu/packages/statistics.scm (r-knitrbootstrap): New variable.
 2016-05-31 16:18:14 +02:00
Eelco Dolstra b4528110c6
daemon: rounds: Keep the differing output if -K is given. 
Regardless of -K, we now also print which output differs.
 2016-05-31 14:25:28 +02:00
Eelco Dolstra 56b8f56788
daemon: Canonicalize gids to 0. 
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.
 2016-05-31 14:25:28 +02:00
Eelco Dolstra 7f3b2510d6
daemon: check: Keep the differing output if -K is given. 
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>
 2016-05-31 14:25:28 +02:00
Eelco Dolstra 7889e72dad
daemon: check: Fix "failed to produce output path". 
This occured when sandbox building is disabled, at least one output
exists, and at least one other output does not.
 2016-05-31 14:25:28 +02:00
Eelco Dolstra f83e82cd00
daemon: check: Fix assertion failure when some outputs are missing. 
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.
 2016-05-31 14:25:28 +02:00
Eelco Dolstra c56cd90cc9
daemon: When repairing, rebuild if there is no substituter. 2016-05-31 14:25:28 +02:00
Eelco Dolstra 1a9574e3a7
daemon: Fix --repair failure on multiple-output derivations. 
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>
 2016-05-31 14:25:28 +02:00
Eelco Dolstra 63a5be07e2
daemon: ~PathLocks(): Handle exceptions. 
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().
 2016-05-31 14:25:28 +02:00
Eelco Dolstra e08380fb6c
daemon: Handle /tmp being a symlink. 
* nix/libstore/build.cc (DerivationGoal::startBuilder): Call 'canonPath'
on "/tmp".
 2016-05-31 14:25:28 +02:00
Leo Famulari 8fe5d95e66
services: urandom-seed: Set umask to 077 while shutting down. 
* gnu/services/base.scm (urandom-seed-shepherd-service): Call 'umask'.
 2016-05-31 00:03:10 -04:00
Leo Famulari df2dd07b88
gnu: libxml2: Update replacement to 2.9.4 [security fixes]. 
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.
 2016-05-30 21:47:40 -04:00
Ludovic Courtès c06f6db7a4
container: Gracefully report mount errors in the child process. 
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.
 2016-05-31 00:11:04 +02:00
Ludovic Courtès 4c14d4eaa7
container: Gracefully handle failure to set up user namespaces. 
* gnu/build/linux-container.scm (run-container): Exit when the parent
process doesn't say 'ready.
 2016-05-31 00:11:04 +02:00
Efraim Flashner 552ffa021c
download: Update CPAN mirrors. 
* guix/download.scm (mirrors)[cpan]: Add to mirror list.
 2016-05-31 00:05:54 +03:00
Efraim Flashner f80d5fe02e
gnu: vapoursynth: Update to 32. 
* gnu/packages/video.scm (vapoursynth): Update to 32.
 2016-05-30 22:22:26 +03:00
Efraim Flashner 365a4a7f40
gnu: Add zimg. 
* gnu/packages/image.scm (zimg): New variable.
 2016-05-30 22:22:25 +03:00
Efraim Flashner fd1461879c
gnu: mcrypt: Fix CVE-2012-4409, CVE-2012-4426, CVE-2012-4527. 
* 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.
 2016-05-30 21:57:36 +03:00
Leo Famulari 5ae77a6f5a
gnu: imagemagick: Update to 6.9.4-5. 
* gnu/packages/imagemagick.scm (imagemagick): Update to 6.9.4-5.
 2016-05-30 14:08:08 -04:00
David Thompson 503a43f3fc gnu: Remove xgcc-avr. 
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.
 2016-05-30 13:45:21 -04:00
David Thompson 9d2bab09aa gnu: Add avr-toolchain. 
* gnu/packages/avr.scm (avr-toolchain): New procedure.
(avr-toolchain-4.9, avr-toolchain-5): New variables.
 2016-05-30 13:45:21 -04:00
David Thompson 3087b7077c gnu: avr-libc: Update to 2.0.0. 
* gnu/packages/avr.scm (avr-libc): Update to 2.0.0.
 2016-05-30 13:45:21 -04:00
David Thompson e60972f288 gnu: avr-libc: Fix build. 
* 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.
 2016-05-30 13:45:21 -04:00
David Thompson a17eea4ba4 gnu: Add avr-gcc-5. 
* gnu/packages/avr.scm (avr-gcc-5): New variable.
 2016-05-30 13:45:21 -04:00
David Thompson 09b05fc7e9 gnu: Add avr-gcc. 
* gnu/packages/avr.scm (avr-gcc): New variable.
 2016-05-30 13:45:21 -04:00
David Thompson cdc5cfdc4a gnu: Add avr-binutils. 
* gnu/packages/avr.scm (avr-binutils): New variable.
 2016-05-30 13:45:21 -04:00
Efraim Flashner 983911d627
gnu: wordnet: Use 'modify-phases'. 
* gnu/packages/wordnet.scm (wordnet)[arguments]: Use 'modify-phases'.
 2016-05-30 20:19:04 +03:00
Efraim Flashner c1dbd3a870
gnu: wordnet: Fix CVE-2008-2149, CVE-2008-3908. 
* 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.
 2016-05-30 20:14:06 +03:00
Efraim Flashner 1f521b7055
gnu: id3lib: Fix CVE-2007-4460. 
* 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.
 2016-05-30 20:13:24 +03:00
Leo Famulari 3d55d04ab8
gnu: cyrus-sasl: Update URLs. 
* gnu/packages/cyrus-sasl.scm (cyrus-sasl)[source]: Use HTTPS URL.
[home-page]: Update home-page URL.
 2016-05-30 12:53:23 -04:00
Leo Famulari 726f088884
gnu: devil: Fix CVE-2009-3994. 
* 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.
 2016-05-30 12:36:26 -04:00
Leo Famulari ac9fc78ff0
gnu: iptables: Update to 1.4.21. 
* gnu/packages/linux.scm (iptables): Update to 1.4.21.
 2016-05-30 12:18:57 -04:00
David Thompson 6ede256f77 gnu: Add emacs-better-defaults. 
* gnu/packages/emacs.scm (emacs-better-defaults): New variable.
 2016-05-30 11:10:49 -04:00
David Thompson 02736daa8c gnu: emacs: Remove uncompressed-file-fetch. 
* 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.
 2016-05-30 11:06:49 -04:00
David Thompson 578b96af69 build: emacs: Handle sources that are a single elisp file. 
* guix/build/emacs-build-system.scm (gnu:unpack)
(store-file->elisp-source-file, unpack): New procedures.
(%standard-phases): Use the new unpack procedure.
 2016-05-30 10:48:44 -04:00
humanitiesNerd 62a45cb647
gnu: Add emacs-seq. 
* gnu/packages/emacs.scm (emacs-seq): New variable.

Signed-off-by: Alex Kost <alezost@gmail.com>
 2016-05-30 13:11:39 +03:00
humanitiesNerd 565bccc569
gnu: Add emacs-spinner. 
* gnu/packages/emacs.scm (emacs-spinner): New variable.

Signed-off-by: Alex Kost <alezost@gmail.com>
 2016-05-30 13:11:39 +03:00
humanitiesNerd 32abfcf4ee
gnu: Add emacs-pkg-info. 
* gnu/packages/emacs.scm (emacs-pkg-info): New variable.

Signed-off-by: Alex Kost <alezost@gmail.com>
 2016-05-30 13:09:43 +03:00
humanitiesNerd ad6c4bc48a
gnu: Add emacs-queue. 
*  gnu/packages/emacs.scm (emacs-queue): New variable.

Signed-off-by: Alex Kost <alezost@gmail.com>
 2016-05-30 13:09:43 +03:00
Alex Kost 4509ec72a4
gnu: emacs: Fix indentation of scheme keyword lists. 
* 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.
 2016-05-30 13:09:43 +03:00
Efraim Flashner 5f1ba08953
gnu: gegl: Fix CVE-2012-4433. 
* 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.
 2016-05-30 12:09:17 +03:00
Efraim Flashner 7d48938a59
gnu: vte-0.28: Fix CVE-2012-2738. 
* 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.
 2016-05-30 12:09:15 +03:00
Efraim Flashner 4f3e02f198
gnu: t1lib: Fix CVE-2010-2642, CVE-2011-{0764, 1552, 1553, 1554}. 
* 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.
 2016-05-30 12:09:14 +03:00