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7500 commits

Author SHA1 Message Date
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 0dccab9f41
Author: Eelco Dolstra <eelco.dolstra@logicblox.com>
Date:   Thu Jul 2 00:30:16 2015 +0200

    Typo

commit 2cd28517b1
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 6e38685ef6
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 5e0a9ae2e2
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 4e5ab98d6d
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 60bda60fc0
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 5dfea34048
Author: Eelco Dolstra <eelco.dolstra@logicblox.com>
Date:   Thu Jul 2 22:51:33 2015 +0200

    Use std::vector::data()

commit 2459458bc8
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 5558652709 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
Eric Bavier
579f5c8a58 gnu: hwloc: Move numactl to inputs.
* gnu/packages/mpi.scm (hwloc)[propagated-inputs]: Move numactl from here...
  [inputs]: ...to here.
  [arguments]: New 'refine-libnuma' phase.
2015-06-29 15:34:36 -05:00
Eric Bavier
ce7d9c989d gnu: hwloc: Upgrade to 1.10.1.
* gnu/packages/patches/hwloc-gather-topology-lstopo.patch: New patch.
* gnu/packages/mpi.scm (hwloc): Upgrade to 1.10.1.
  [source]: Use patch.
  [propagated-inputs]: Remove libpci.
  [inputs]: Add libpciaccess.
* gnu-system.am (dist_patch_DATA): Add patch.
2015-06-29 15:34:36 -05:00
Eric Bavier
7362371da5 gnu: python-mccabe: Fix license field.
* gnu/packages/python.scm (python-mccabe)[license]: 'expat' ->
  'license:expat'.
2015-06-29 15:34:35 -05:00
Cyril Roelandt
e8df8f476e gnu: Add python-flake8.
* gnu/packages/python.scm (python-flake8, python2-flake8): New variables.
2015-06-30 00:07:56 +02:00
Cyril Roelandt
a59e017cb1 gnu: Add python-mccabe.
* gnu/packages/python.scm (python-mccabe, python2-mccabe): New variables.
2015-06-30 00:07:56 +02:00
Cyril Roelandt
e31d7f4420 gnu: Add python-pyflakes.
* gnu/packages/python.scm (python-pyflakes, python2-pyflakes): New variables.
2015-06-30 00:07:55 +02:00
Cyril Roelandt
d889e6c4d9 gnu: Add python-pep8.
* gnu/packages/python.scm (python-pep8, python2-pep8): New variables.
2015-06-30 00:07:55 +02:00
Ludovic Courtès
fe36d84eae doc: Add 'guix environment' examples.
* doc/environment-gdb.scm: New file.
* doc.am (EXTRA_DIST): Add it.
* doc/guix.texi (Invoking guix environment): Clarify wording of the first
  example.  Add a --ad-hoc example upfront.  Add an example for '-e', and one
  for '-l'.
2015-06-29 23:08:36 +02:00
Ricardo Wurmus
2573410865 gnu: withershins: Use new "libiberty" package.
* gnu/packages/code.scm (withershins)[inputs]: Replace "gcc" with "libiberty".
   [arguments]: Simplify "find-libiberty" phase.
2015-06-29 21:01:13 +02:00
Ricardo Wurmus
2b6b6d13e7 gnu: Add libiberty.
* gnu/packages/gcc.scm (make-libiberty, libiberty): New variables.
2015-06-29 21:01:13 +02:00
Ricardo Wurmus
74e03fccd3 gnu: r: Update to 3.2.1.
* gnu/packages/statistics.scm (r): Update to 3.2.1.
* gnu/packages/patches/r-fix-15899.patch: Remove file.
* gnu-system.am (dist_patch_DATA): Remove it.
2015-06-29 16:13:28 +02:00
Ricardo Wurmus
82c370dea1 gnu: Add Blast+.
* gnu/packages/bioinformatics.scm (blast+): New variable.
2015-06-29 16:13:28 +02:00