08fa45b190
gnu: gnupg: Enable TLS support.
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* 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
5e5fa28e76
gnu: gnupg: Update to 2.1.6.
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* gnu/packages/gnupg.scm (gnupg): Update to 2.1.6.
2015-07-02 12:35:12 -04:00
c61fe02cc0
gnu: Add WarpedLMM.
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* gnu/packages/bioinformatics.scm (python2-warpedlmm): New variable.
2015-07-02 11:16:46 +02:00
f4f4ced8dc
gnu: r: Set default pager.
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* 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
28de8d258b
environment: Define 'GUIX_ENVIRONMENT'.
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* 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
50500f7cf0
doc: Mention .bashrc vs. .bash_profile for 'guix environment'.
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* doc/guix.texi (Invoking guix environment): Add footnote about .bashrc
vs. .bash_profile.
2015-07-01 23:29:49 +02:00
d70389c423
environment: Improve error reporting for '-l'.
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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
417c39f132
environment: For --ad-hoc, allow users to specify an output.
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* 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
ce367ef3a9
environment: Add --system.
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* 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
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
cad2526449
tests: Add tests for 'guix environment'.
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* tests/guix-environment.sh: New file.
* Makefile.am (SH_TESTS): Add it.
2015-07-01 23:29:49 +02:00
d6902798d1
gnu: powertabeditor: Replace "gcc" with "libiberty".
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* gnu/packages/music.scm (powertabeditor)[inputs]: Replace "gcc" with
"libiberty".
2015-07-01 21:52:08 +02:00
d231bb3575
gnu: Add Hydrogen.
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* gnu/packages/music.scm (hydrogen): New variable.
2015-07-01 21:52:08 +02:00
5135aed92b
gnu: linux-libre: Update to 4.1.1.
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* gnu/packages/linux.scm (linux-libre): Update to 4.1.1.
2015-07-01 00:12:39 -04:00
58c1806908
gnu: git: Add inputs for send-email.
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* 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
c6ee18abb6
gnu: Add perl-authen-sasl.
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* gnu/packages/web.scm (perl-authen-sasl): New variable.
2015-06-30 05:01:42 -05:00
9fe938c19f
gnu: Add perl-gssapi.
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* gnu/packages/web.scm (perl-gssapi): New variable.
2015-06-30 05:01:42 -05:00
b1096f3dbb
gnu: Add perl-net-smtp-ssl.
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* gnu/packages/web.scm (perl-net-smtp-ssl): New variable.
2015-06-30 05:01:42 -05:00
d2e3caba5d
gnu: curl: Disable test that fails on Hydra.
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* gnu/packages/curl.scm (arguments): Disable test 1510.
2015-06-30 00:17:00 -04:00
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
a17d45641b
gnu: Add deal.II.
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* 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
a7f0141452
gnu: Add SLEPc.
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* gnu/packages/maths.scm (slepc, slepc-complex, slepc-openmpi)
(slepc-complex-openmpi): New variables.
2015-06-29 15:34:36 -05:00
8c94c886f6
gnu: Add arpack-ng-openmpi.
...
* gnu/packages/maths.scm (arpack-ng-openmpi): New variable.
2015-06-29 15:34:36 -05:00
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
cec86422b7
gnu: Add MUMPS.
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* 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
aa75ad0097
gnu: Add METIS.
...
* gnu/packages/maths.scm (metis): New variable.
2015-06-29 15:34:36 -05:00
700ff22219
gnu: Add p4est.
...
* gnu/packages/maths.scm (p4est, p4est-openmpi): New variables.
2015-06-29 15:34:36 -05:00
e1ff597a64
gnu: Add ScaLAPACK.
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* gnu/packages/maths.scm (scalapack): New variable.
2015-06-29 15:34:36 -05:00
cf0ec6c46e
gnu: scotch, pt-scotch: Build esmumps libraries.
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* 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
d6602ee9d4
gnu: scotch, pt-scotch: Use modify-phases.
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* gnu/packages/maths.scm (scotch, pt-scotch)[arguments]: Use modify-phases.
2015-06-29 15:34:36 -05:00
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
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
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
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
7362371da5
gnu: python-mccabe: Fix license field.
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* gnu/packages/python.scm (python-mccabe)[license]: 'expat' ->
'license:expat'.
2015-06-29 15:34:35 -05:00
e8df8f476e
gnu: Add python-flake8.
...
* gnu/packages/python.scm (python-flake8, python2-flake8): New variables.
2015-06-30 00:07:56 +02:00
a59e017cb1
gnu: Add python-mccabe.
...
* gnu/packages/python.scm (python-mccabe, python2-mccabe): New variables.
2015-06-30 00:07:56 +02:00
e31d7f4420
gnu: Add python-pyflakes.
...
* gnu/packages/python.scm (python-pyflakes, python2-pyflakes): New variables.
2015-06-30 00:07:55 +02:00
d889e6c4d9
gnu: Add python-pep8.
...
* gnu/packages/python.scm (python-pep8, python2-pep8): New variables.
2015-06-30 00:07:55 +02:00
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
2573410865
gnu: withershins: Use new "libiberty" package.
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* gnu/packages/code.scm (withershins)[inputs]: Replace "gcc" with "libiberty".
[arguments]: Simplify "find-libiberty" phase.
2015-06-29 21:01:13 +02:00
2b6b6d13e7
gnu: Add libiberty.
...
* gnu/packages/gcc.scm (make-libiberty, libiberty): New variables.
2015-06-29 21:01:13 +02:00
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
82c370dea1
gnu: Add Blast+.
...
* gnu/packages/bioinformatics.scm (blast+): New variable.
2015-06-29 16:13:28 +02:00
11906b2c38
gnu: global: Update to 6.5.
...
* gnu/packages/code.scm (global): Update to 6.5.
2015-06-29 14:42:10 +02:00
622a616e33
gnu: help2man: Update to 1.47.1.
...
* gnu/packages/man.scm (help2man): Update to 1.47.1.
2015-06-29 14:42:10 +02:00
b1f5fe0eb7
gnu: parallel: Update to 20150622.
...
* gnu/packages/parallel.scm (parallel): Update to 20150622.
2015-06-29 14:42:10 +02:00
dd138fc856
gnu: screen: Update to 4.3.1.
...
* gnu/packages/screen.scm (screen): Update to 4.3.1.
2015-06-29 14:42:10 +02:00
ce1e4bd58d
gnu: texinfo: Add version 6.0.
...
* gnu/packages/texinfo.scm (texinfo-6): New variable.
2015-06-29 14:42:10 +02:00
ab5f49cf6a
gnu: gcc-4.8: Update to 4.8.5.
...
* gnu/packages/gcc.scm (gcc-4.8): Update to 4.8.5.
2015-06-29 14:42:10 +02:00
Mark H Weaver