gnu: obs: Update to 0.14.2.
* gnu/packages/video.scm (obs): Update to 0.14.2.
gnu: emacs-better-defaults: Specify source file name.
* gnu/packages/emacs.scm (emacs-better-defaults)[source]: Specify a
useful file name, as usual with tarballs from GitHub.
gnu: imagemagick: Fix CVE-2016-5118.
* gnu/packages/patches/imagemagick-CVE-2016-5118.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/imagemagick.scm (imagemagick): Use it.
gnu: graphicsmagick: Update to 1.3.24 [security update].
Fixes CVE-2016-{2317, 2318, 5118} and many other security issues
described in 'NEWS.txt'.
* gnu/packages/patches/graphicsmagick-CVE-2016-5118.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Remove it.
* gnu/packages/imagemagick.scm (graphicsmagick): Update to 1.3.24.
[source]: Remove patch.
daemon: Substitute queries return immediately when substitutes are disabled.
Reported by Federico Beffa <beffa@ieee.org>
at <https://lists.gnu.org/archive/html/guix-devel/2016-05/msg00928.html>.
* nix/libstore/local-store.cc (LocalStore::querySubstitutablePaths)
(LocalStore::querySubstitutablePathInfos): Return when
'settings.useSubstitutes' is false.
* tests/store.scm ("references/substitutes missing reference info"):
Make sure to return #f on failure.
* tests/store.scm ("substitutable-path-info when substitutes are turned off"):
("substitutable-paths when substitutes are turned off"): New tests.
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.
gnu: Add ghmm.
* gnu/packages/machine-learning.scm (ghmm): New variable.
gnu: gimp: Update to 2.8.16.
* gnu/packages/gimp.scm (gimp): Update to 2.8.16.
gnu: Add r-genomationdata.
* gnu/packages/bioinformatics.scm (r-genomationdata): New variable.
gnu: Add r-runit.
* gnu/packages/statistics.scm (r-runit): New variable.
gnu: julia: Update to 0.4.5.
* gnu/packages/julia.scm (julia): Update to 0.4.5.
(libuv-julia): Update commit.
gnu: Add r-knitrbootstrap.
* gnu/packages/statistics.scm (r-knitrbootstrap): New variable.
daemon: rounds: Keep the differing output if -K is given.
Regardless of -K, we now also print which output differs.
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.
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>
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.
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.
daemon: When repairing, rebuild if there is no substituter.