Commit Graph

7462 Commits

Author SHA1 Message Date
Ricardo Wurmus 80e907fe57 gnu: eigen: Update to 3.2.5.
* gnu/packages/algebra.scm (eigen): Update to 3.2.5.
2015-07-04 13:32:52 +02:00
Mark H Weaver 4463c0d216 gnu: icecat: Fix CVE-2015-{2722,2724,2728,2733,2735,2736,2738,2739,2740,2743}.
* gnu/packages/patches/icecat-CVE-2015-2722-pt1.patch,
  gnu/packages/patches/icecat-CVE-2015-2722-pt2.patch,
  gnu/packages/patches/icecat-CVE-2015-2724-pt1.patch,
  gnu/packages/patches/icecat-CVE-2015-2724-pt2.patch,
  gnu/packages/patches/icecat-CVE-2015-2724-pt3.patch,
  gnu/packages/patches/icecat-CVE-2015-2724-pt4.patch,
  gnu/packages/patches/icecat-CVE-2015-2728-pt1.patch,
  gnu/packages/patches/icecat-CVE-2015-2728-pt2.patch,
  gnu/packages/patches/icecat-CVE-2015-2733-pt1.patch,
  gnu/packages/patches/icecat-CVE-2015-2733-pt2.patch,
  gnu/packages/patches/icecat-CVE-2015-2735.patch,
  gnu/packages/patches/icecat-CVE-2015-2736.patch,
  gnu/packages/patches/icecat-CVE-2015-2738.patch,
  gnu/packages/patches/icecat-CVE-2015-2739.patch,
  gnu/packages/patches/icecat-CVE-2015-2740.patch,
  gnu/packages/patches/icecat-CVE-2015-2743.patch: New files.
* gnu-system.am (dist_patch_DATA): Add them.
* gnu/packages/gnuzilla.scm (icecat)[source]: Add patches.
2015-07-04 05:44:10 -04:00
Alex Kost 4cd86f5d52 Add '.mailmap'.
* .mailmap: New file.
2015-07-04 12:13:02 +03:00
Alex Kost e7c48ee951 Clean up 'THANKS' and 'AUTHORS'.
* THANKS: Add Konrad Hinsen, Cyprien Nicolas, Yakkala Yagnesh Raghava
  and Alexander Shendi.  Remove Federico Beffa, Marek Benc, John
  Darrington, rekado, Cyrill Schenkel and Andy Wingo because they are
  placed in AUTHORS.  Move Amirouche Boubekki and Alex Kost to ...
* AUTHORS: ... here.  Add Arne Babenhauserheide, Ian Denhardt, Kevin
  Lemonnier, Mathieu Lirzin, Pierre-Antoine Rault and Ben Woodcroft.
  Fix some names and emails.
2015-07-04 12:13:01 +03:00
Andreas Enge 257b6c4375 gnu: unrtf: Fix download location.
* gnu/packages/unrtf.scm (unrtf): Fix download location.
2015-07-03 22:54:51 +02:00
Ricardo Wurmus b05d1c68bc gnu: r: Replace "atlas" with "openblas".
* gnu/packages/statistics.scm (r)[inputs]: Replace "atlas" with "openblas".
2015-07-03 18:45:14 +02:00
Ludovic Courtès 606c638016 gnu: gnutls: Move man3 pages to "doc" output.
* gnu/packages/gnutls.scm (gnutls)[arguments]: Add #:phases.
2015-07-03 15:28:07 +02:00
Ludovic Courtès 4b0f2ef743 gnu: qt-4: Remove reference from "out" to "doc".
* gnu/packages/qt.scm (qt-4)[arguments]: Remove '-docdir' configure flag.
  Add 'move-doc' phase.
2015-07-03 15:28:07 +02:00
Ludovic Courtès ff1989a599 gnu: qt-4: Use a more standard directory layout.
* gnu/packages/qt.scm (qt-4)[arguments]: Pass -datadir, -importdir,
  -plugindir, and -translationdir.
2015-07-03 15:28:07 +02:00
Ludovic Courtès cba632c4a8 gnu: qt-4: Use 'modify-phases'.
* gnu/packages/qt.scm (qt-4)[arguments]: Use 'modify-phases' instead of
  'alist-replace'.
2015-07-03 15:28:07 +02:00
Ludovic Courtès ef2f51a445 gnu: cups-filter: Install backends and filters under lib/cups.
This ensures that they are stripped during the 'strip' phase, thereby removing
references to GCC and linux-libre-headers that would otherwise be found in
debugging symbols.

* gnu/packages/cups.scm (cups-filters)[source]: Change pkgbackenddir and
  pkgfilterdir to $(PREFIX)/lib/cups/{filter,backend}.
  (cups)[arguments]: Adjust accordingly.
2015-07-03 15:28:07 +02:00
Ludovic Courtès 6a52df505a gnu: mysql: Remove unnecessary binaries.
This saves ~42 MiB on x86_64.

* gnu/packages/databases.scm (mysql)[arguments]: Add 'remove-extra-binaries'
  phase.
2015-07-03 15:28:06 +02:00
Ludovic Courtès 3f289db69d gnu: mysql: Strip references and GCC and other build-time dependencies.
* gnu/packages/databases.scm (mysql)[arguments]: Add 'strip-extra-references'
  phase.
2015-07-03 15:28:06 +02:00
Ludovic Courtès b5b08878b6 gnu: mutt: Don't retain reference to GCC.
* gnu/packages/patches/mutt-store-references.patch: New file.
* gnu/packages/mail.scm (mutt)[source]: Use it.
* gnu-system.am (dist_patch_DATA): Add it.
2015-07-03 15:28:06 +02:00
Ludovic Courtès 9161ba818d gnu: ghostscript: Add "doc" output.
* gnu/packages/ghostscript.scm (ghostscript)[source](snippet): New field.
  [outputs]: New field.
  [arguments]: Add 'remove-doc-reference' phase.
2015-07-03 15:28:06 +02:00
Ludovic Courtès 4a6aeb670f derivations: Add #:substitutable?, distinguished from #:local-build?.
Fixes <http://bugs.gnu.org/18747>.

* guix/derivations.scm (substitutable-derivation?): Rewrite to check for
  "allowSubstitutes".
  (derivation): Add #:substitutable? parameter.
  [user+system-env-vars]: Honor it.
  (build-expression->derivation): Add #:substitutable? and honor it.
* guix/gexp.scm (gexp->derivation): Likewise.
* tests/derivations.scm ("derivation-prerequisites-to-build and substitutes,
  non-substitutable build"): Use #:substitutable? instead of #:local-build?.
  ("substitutable-derivation?", "derivation-prerequisites-to-build and
  substitutes, local build"): New tests.
* guix/download.scm (url-fetch): Adjust comment.
* guix/git-download.scm (git-fetch): Likewise.
* guix/build-system/gnu.scm (gnu-build, gnu-cross-build): Use #:substitutable?
  instead of #:local-build?.
* doc/guix.texi (Derivations, G-Expressions): Adjust accordingly.
2015-07-03 00:30:55 +02:00
Ludovic Courtès 322eeb87d0 Merge branch 'nix'.
This is a squashed commit of the following:

commit 0dccab9f417b406f5d4aedc81900fc7b2f16c9f6
Author: Eelco Dolstra <eelco.dolstra@logicblox.com>
Date:   Thu Jul 2 00:30:16 2015 +0200

    Typo

commit 2cd28517b13524c242c7758783b0b2d8250fdded
Author: Ludovic Courtès <ludo@gnu.org>
Date:   Wed Jul 1 14:56:34 2015 +0200

    Preserve supplementary groups of build users

    The following patch is an attempt to address this bug (see
    <http://bugs.gnu.org/18994>) by preserving the supplementary groups of
    build users in the build environment.

    In practice, I would expect that supplementary groups would contain only
    one or two groups: the build users group, and possibly the “kvm” group.

    [Changed &at(0) to data() and removed tabs - Eelco]

commit 6e38685ef65284093df79ebe7378bac33b0e7e5d
Author: Eelco Dolstra <eelco.dolstra@logicblox.com>
Date:   Tue Jun 30 21:41:26 2015 +0200

    GC: Handle ENOSPC creating/moving to the trash directory

    Issue #564.

commit 5e0a9ae2e25a1016389f4893a6ed6682aadcf51d
Author: Eelco Dolstra <eelco.dolstra@logicblox.com>
Date:   Mon Jun 22 15:54:55 2015 +0200

    Use posix_fallocate to create /nix/var/nix/db/reserved

commit 4e5ab98d6d14f8b0e3bd1d77b2f4f2354e7a49a8
Author: Eelco Dolstra <eelco.dolstra@logicblox.com>
Date:   Mon Jun 22 15:47:40 2015 +0200

    Make /nix/var/nix/db/reserved bigger

    Issue #564.

commit 60bda60fc06135aa97a93301b1a9e2270768f5b3
Author: Eelco Dolstra <eelco.dolstra@logicblox.com>
Date:   Wed Jun 10 16:17:06 2015 +0200

    Export outputPaths function

    This is useful for the new hydra-queue-runner.

commit 5dfea34048aa8541f20aeb2fbcd163561b609a49
Author: Eelco Dolstra <eelco.dolstra@logicblox.com>
Date:   Thu Jul 2 22:51:33 2015 +0200

    Use std::vector::data()

commit 2459458bc8257734ca78cb7a2db3df20bd730ec0
Author: Eelco Dolstra <eelco.dolstra@logicblox.com>
Date:   Thu Jun 4 16:04:41 2015 +0200

    Allow substitutes for builds that have preferLocalBuild set

    Not substituting builds with "preferLocalBuild = true" was a bad idea,
    because it didn't take the cost of dependencies into account. For
    instance, if we can't substitute a fetchgit call, then we have to
    download/build git and all its dependencies.

    Partially reverts 5558652709f27e8a887580b77b93c705659d7a4b and adds a
    new derivation attribute "allowSubstitutes" to specify whether a
    derivation may be substituted.
2015-07-03 00:30:55 +02:00
Cyril Roelandt d2cef629fd scripts: environment: Return the exit status of the command.
* guix/scripts/environment.scm (guix-environment): Return the exit
  status of the command.
2015-07-02 21:47:24 +02:00
Mark H Weaver 08fa45b190 gnu: gnupg: Enable TLS support.
* gnu/packages/gnupg.scm (gnupg)[native-inputs]: Add pkg-config.
  [inputs]: Add gnutls.
  (gnupg-2.0, gnupg-1)[native-inputs]: Override inherited value to be '().
2015-07-02 12:35:12 -04:00
Mark H Weaver 5e5fa28e76 gnu: gnupg: Update to 2.1.6.
* gnu/packages/gnupg.scm (gnupg): Update to 2.1.6.
2015-07-02 12:35:12 -04:00
Ricardo Wurmus c61fe02cc0 gnu: Add WarpedLMM.
* gnu/packages/bioinformatics.scm (python2-warpedlmm): New variable.
2015-07-02 11:16:46 +02:00
Ricardo Wurmus f4f4ced8dc gnu: r: Set default pager.
* gnu/packages/statistics.scm (r)[arguments]: Add phase "set-default-pager" to
  avoid "false" as a default pager.
2015-07-02 10:50:55 +02:00
Ludovic Courtès 28de8d258b environment: Define 'GUIX_ENVIRONMENT'.
* guix/scripts/environment.scm (create-environment): Define 'GUIX_ENVIRONMENT'.
* doc/guix.texi (Invoking guix environment): Document it.
* gnu/system/shadow.scm (default-skeletons): Adjust 'PS1' depending on whether
  'GUIX_ENVIRONMENT' is defined.
2015-07-01 23:29:49 +02:00
Ludovic Courtès 50500f7cf0 doc: Mention .bashrc vs. .bash_profile for 'guix environment'.
* doc/guix.texi (Invoking guix environment): Add footnote about .bashrc
  vs. .bash_profile.
2015-07-01 23:29:49 +02:00
Ludovic Courtès d70389c423 environment: Improve error reporting for '-l'.
This fixes two problems:

  1. Load errors would print an ugly backtrace.
  2. When FILE was an absolute name, 'load' was passed an incorrect file
     name.

* guix/scripts/environment.scm (options/resolve-packages): Use 'load*' instead
  of 'load'.
2015-07-01 23:29:49 +02:00
Ludovic Courtès 417c39f132 environment: For --ad-hoc, allow users to specify an output.
* guix/scripts/environment.scm (package+propagated-inputs): Add 'output'
  parameter.  Use it in return value.
  (options/resolve-packages): Use 'append-map' instead of 'map'.  For 'load'
  and 'expression', return all the outputs of the resulting package.  For
  'package', use 'specification->package+output' instead of
  'specification->package'.
  (guix-environment): Adjust uses of PACKAGES accordingly.
* doc/guix.texi (Invoking guix environment): Document it.
* tests/guix-environment.sh: Add test for --ad-hoc guile-bootstrap:out.
2015-07-01 23:29:49 +02:00
Ludovic Courtès ce367ef3a9 environment: Add --system.
* guix/scripts/environment.scm (show-help, %options): Add -s/--system.
  (%default-options): Add 'system' pair.
  (guix-environment): Pass 'system' value from OPTS to 'lower-inputs'.
* doc/guix.texi (Invoking guix environment): Document it.
2015-07-01 23:29:49 +02:00
Ludovic Courtès 6b6298ae39 environment: Add only the specified outputs of the dependencies.
Before that, 'guix environment guile' (for instance) would define environment
variables that would refer to the "include" output of Bash, the "debug" output
of libgc, etc., even though these are not listed as inputs in the recipe of
'guile'.

* guix/gexp.scm (lower-inputs): Export.
* guix/scripts/environment.scm (evaluate-input-search-paths): Remove
  'derivations' parameter; add 'search-paths'.  Expect 'inputs' to be
  a list of tuples.  Adjust callers.
  (create-environment): Remove 'derivations' parameter; add 'search-paths'.
  (show-search-paths): Likewise.
  (package+propagated-inputs): New procedure.
  (packages->transitive-inputs, packages+propagated-inputs): Remove.
  (build-inputs): Expect INPUTS to be a list of derivation tuples.
  (guix-environment): Compute INPUTS using 'package+propagated-inputs',
  'package->bag', and 'bag-transitive-inputs'.  Move 'run-with-store' higher.
* tests/guix-environment.sh: Add test with FINDUTILS-BOOT0.
2015-07-01 23:29:49 +02:00
Ludovic Courtès cad2526449 tests: Add tests for 'guix environment'.
* tests/guix-environment.sh: New file.
* Makefile.am (SH_TESTS): Add it.
2015-07-01 23:29:49 +02:00
Ricardo Wurmus d6902798d1 gnu: powertabeditor: Replace "gcc" with "libiberty".
* gnu/packages/music.scm (powertabeditor)[inputs]: Replace "gcc" with
  "libiberty".
2015-07-01 21:52:08 +02:00
Ricardo Wurmus d231bb3575 gnu: Add Hydrogen.
* gnu/packages/music.scm (hydrogen): New variable.
2015-07-01 21:52:08 +02:00
Mark H Weaver 5135aed92b gnu: linux-libre: Update to 4.1.1.
* gnu/packages/linux.scm (linux-libre): Update to 4.1.1.
2015-07-01 00:12:39 -04:00
Eric Bavier 58c1806908 gnu: git: Add inputs for send-email.
* gnu/packages/version-control.scm (package-transitive-propagated-labels*)
  (package-propagated-input-refs): New procedures.
  (git)[inputs]: Add perl-authen-sasl, perl-net-smtp-ssl, and perl-io-socket-ssl.
  [outputs]: Add send-email output.
  [arguments]: Add #:modules argument with srfi-1.  In 'split phase, wrap
  git-send-email.
2015-06-30 05:01:42 -05:00
Eric Bavier c6ee18abb6 gnu: Add perl-authen-sasl.
* gnu/packages/web.scm (perl-authen-sasl): New variable.
2015-06-30 05:01:42 -05:00
Eric Bavier 9fe938c19f gnu: Add perl-gssapi.
* gnu/packages/web.scm (perl-gssapi): New variable.
2015-06-30 05:01:42 -05:00
Eric Bavier b1096f3dbb gnu: Add perl-net-smtp-ssl.
* gnu/packages/web.scm (perl-net-smtp-ssl): New variable.
2015-06-30 05:01:42 -05:00
Mark H Weaver d2e3caba5d gnu: curl: Disable test that fails on Hydra.
* gnu/packages/curl.scm (arguments): Disable test 1510.
2015-06-30 00:17:00 -04:00
Mark H Weaver 4617c2e383 gnu: curl: Update to 7.43.0.
* gnu/packages/curl.scm (curl): Update to 7.43.0.
2015-06-30 00:17:00 -04:00
Eric Bavier a17d45641b gnu: Add deal.II.
* gnu/packages/maths.scm (dealii, dealii-openmpi): New variables.
* gnu/packages/patches/dealii-p4est-interface.patch: New patch.
* gnu-system.am (dist_patch_DATA): Add it.
2015-06-29 15:34:36 -05:00
Eric Bavier a7f0141452 gnu: Add SLEPc.
* gnu/packages/maths.scm (slepc, slepc-complex, slepc-openmpi)
  (slepc-complex-openmpi): New variables.
2015-06-29 15:34:36 -05:00
Eric Bavier 8c94c886f6 gnu: Add arpack-ng-openmpi.
* gnu/packages/maths.scm (arpack-ng-openmpi): New variable.
2015-06-29 15:34:36 -05:00
Eric Bavier 9a899cceab gnu: petsc: Upgrade to 3.6.0.
* gnu/packages/maths.scm (petsc): Upgrade to 3.6.0.
* gnu/packages/patches/petsc-fix-threadcomm.patch: Delete patch.
* gnu-system.am (dist_patch_DATA): Remove it.
2015-06-29 15:34:36 -05:00
Eric Bavier cec86422b7 gnu: Add MUMPS.
* gnu/packages/maths.scm (mumps, mumps-metis, mumps-openmpi)
  (mumps-metis-openmpi): New variables.
* gnu/packages/patches/mumps-build-parallelism.patch: New patch.
* gnu-system.am (dist_patch_DATA): Add it.
2015-06-29 15:34:36 -05:00
Eric Bavier aa75ad0097 gnu: Add METIS.
* gnu/packages/maths.scm (metis): New variable.
2015-06-29 15:34:36 -05:00
Eric Bavier 700ff22219 gnu: Add p4est.
* gnu/packages/maths.scm (p4est, p4est-openmpi): New variables.
2015-06-29 15:34:36 -05:00
Eric Bavier e1ff597a64 gnu: Add ScaLAPACK.
* gnu/packages/maths.scm (scalapack): New variable.
2015-06-29 15:34:36 -05:00
Eric Bavier cf0ec6c46e gnu: scotch, pt-scotch: Build esmumps libraries.
* gnu/packages/maths.scm (scotch)[arguments]: Add 'build-esmumps
  phase.  Install esmumps libraries and headers in 'install phase.
  (pt-scotch)[arguments]: Build ptesmumps in 'build phase.  Add
  make parallelism.
2015-06-29 15:34:36 -05:00
Eric Bavier d6602ee9d4 gnu: scotch, pt-scotch: Use modify-phases.
* gnu/packages/maths.scm (scotch, pt-scotch)[arguments]: Use modify-phases.
2015-06-29 15:34:36 -05:00
Eric Bavier 6c7985408f gnu: Update scotch to 6.0.4.
* gnu/packages/maths.scm (scotch): Update to 6.0.4.
  [arguments]: Add -fPIC to CFLAGS.
* gnu/packages/patches/scotch-test-threading.patch: Adjust patch for a
  new set of test fixes.
* gnu/packages/patches/pt-scotch-build-parallelism.patch: New patch.
* gnu-system.am (dist_patch_DATA): Add it.
2015-06-29 15:34:36 -05:00
Eric Bavier 38f0a2bade gnu: openmpi: Upgrade to 1.8.5.
* gnu/packages/mpi.scm (openmpi): Upgrade to 1.8.5.
  [native-inputs]: Add perl.
  [arguments]: Add configure flags for thread support.
2015-06-29 15:34:36 -05:00