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* Merge branch 'nix'.Ludovic Courtès2015-07-03
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 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.
* scripts: environment: Return the exit status of the command.Cyril Roelandt2015-07-02
| | | | | * guix/scripts/environment.scm (guix-environment): Return the exit status of the command.
* gnu: gnupg: Enable TLS support.Mark H Weaver2015-07-02
| | | | | | * 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 '().
* gnu: gnupg: Update to 2.1.6.Mark H Weaver2015-07-02
| | | | * gnu/packages/gnupg.scm (gnupg): Update to 2.1.6.
* gnu: Add WarpedLMM.Ricardo Wurmus2015-07-02
| | | | * gnu/packages/bioinformatics.scm (python2-warpedlmm): New variable.
* gnu: r: Set default pager.Ricardo Wurmus2015-07-02
| | | | | * gnu/packages/statistics.scm (r)[arguments]: Add phase "set-default-pager" to avoid "false" as a default pager.
* environment: Define 'GUIX_ENVIRONMENT'.Ludovic Courtès2015-07-01
| | | | | | | * 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.
* doc: Mention .bashrc vs. .bash_profile for 'guix environment'.Ludovic Courtès2015-07-01
| | | | | * doc/guix.texi (Invoking guix environment): Add footnote about .bashrc vs. .bash_profile.
* environment: Improve error reporting for '-l'.Ludovic Courtès2015-07-01
| | | | | | | | | | | 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'.
* environment: For --ad-hoc, allow users to specify an output.Ludovic Courtès2015-07-01
| | | | | | | | | | | | * 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.
* environment: Add --system.Ludovic Courtès2015-07-01
| | | | | | | * 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.
* environment: Add only the specified outputs of the dependencies.Ludovic Courtès2015-07-01
| | | | | | | | | | | | | | | | | | | | 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.
* tests: Add tests for 'guix environment'.Ludovic Courtès2015-07-01
| | | | | * tests/guix-environment.sh: New file. * Makefile.am (SH_TESTS): Add it.
* gnu: powertabeditor: Replace "gcc" with "libiberty".Ricardo Wurmus2015-07-01
| | | | | * gnu/packages/music.scm (powertabeditor)[inputs]: Replace "gcc" with "libiberty".
* gnu: Add Hydrogen.Ricardo Wurmus2015-07-01
| | | | * gnu/packages/music.scm (hydrogen): New variable.
* gnu: linux-libre: Update to 4.1.1.Mark H Weaver2015-07-01
| | | | * gnu/packages/linux.scm (linux-libre): Update to 4.1.1.
* gnu: git: Add inputs for send-email.Eric Bavier2015-06-30
| | | | | | | | | * 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.
* gnu: Add perl-authen-sasl.Eric Bavier2015-06-30
| | | | * gnu/packages/web.scm (perl-authen-sasl): New variable.
* gnu: Add perl-gssapi.Eric Bavier2015-06-30
| | | | * gnu/packages/web.scm (perl-gssapi): New variable.
* gnu: Add perl-net-smtp-ssl.Eric Bavier2015-06-30
| | | | * gnu/packages/web.scm (perl-net-smtp-ssl): New variable.
* gnu: curl: Disable test that fails on Hydra.Mark H Weaver2015-06-30
| | | | * gnu/packages/curl.scm (arguments): Disable test 1510.
* gnu: curl: Update to 7.43.0.Mark H Weaver2015-06-30
| | | | * gnu/packages/curl.scm (curl): Update to 7.43.0.
* gnu: Add deal.II.Eric Bavier2015-06-29
| | | | | | * 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.
* gnu: Add SLEPc.Eric Bavier2015-06-29
| | | | | * gnu/packages/maths.scm (slepc, slepc-complex, slepc-openmpi) (slepc-complex-openmpi): New variables.
* gnu: Add arpack-ng-openmpi.Eric Bavier2015-06-29
| | | | * gnu/packages/maths.scm (arpack-ng-openmpi): New variable.
* gnu: petsc: Upgrade to 3.6.0.Eric Bavier2015-06-29
| | | | | | * 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.
* gnu: Add MUMPS.Eric Bavier2015-06-29
| | | | | | | * 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.
* gnu: Add METIS.Eric Bavier2015-06-29
| | | | * gnu/packages/maths.scm (metis): New variable.
* gnu: Add p4est.Eric Bavier2015-06-29
| | | | * gnu/packages/maths.scm (p4est, p4est-openmpi): New variables.
* gnu: Add ScaLAPACK.Eric Bavier2015-06-29
| | | | * gnu/packages/maths.scm (scalapack): New variable.
* gnu: scotch, pt-scotch: Build esmumps libraries.Eric Bavier2015-06-29
| | | | | | | * 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.
* gnu: scotch, pt-scotch: Use modify-phases.Eric Bavier2015-06-29
| | | | * gnu/packages/maths.scm (scotch, pt-scotch)[arguments]: Use modify-phases.
* gnu: Update scotch to 6.0.4.Eric Bavier2015-06-29
| | | | | | | | | * 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.
* gnu: openmpi: Upgrade to 1.8.5.Eric Bavier2015-06-29
| | | | | | * gnu/packages/mpi.scm (openmpi): Upgrade to 1.8.5. [native-inputs]: Add perl. [arguments]: Add configure flags for thread support.
* gnu: hwloc: Move numactl to inputs.Eric Bavier2015-06-29
| | | | | | * gnu/packages/mpi.scm (hwloc)[propagated-inputs]: Move numactl from here... [inputs]: ...to here. [arguments]: New 'refine-libnuma' phase.
* gnu: hwloc: Upgrade to 1.10.1.Eric Bavier2015-06-29
| | | | | | | | | * 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.
* gnu: python-mccabe: Fix license field.Eric Bavier2015-06-29
| | | | | * gnu/packages/python.scm (python-mccabe)[license]: 'expat' -> 'license:expat'.
* gnu: Add python-flake8.Cyril Roelandt2015-06-30
| | | | * gnu/packages/python.scm (python-flake8, python2-flake8): New variables.
* gnu: Add python-mccabe.Cyril Roelandt2015-06-30
| | | | * gnu/packages/python.scm (python-mccabe, python2-mccabe): New variables.
* gnu: Add python-pyflakes.Cyril Roelandt2015-06-30
| | | | * gnu/packages/python.scm (python-pyflakes, python2-pyflakes): New variables.
* gnu: Add python-pep8.Cyril Roelandt2015-06-30
| | | | * gnu/packages/python.scm (python-pep8, python2-pep8): New variables.
* doc: Add 'guix environment' examples.Ludovic Courtès2015-06-29
| | | | | | | | * 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'.
* gnu: withershins: Use new "libiberty" package.Ricardo Wurmus2015-06-29
| | | | | * gnu/packages/code.scm (withershins)[inputs]: Replace "gcc" with "libiberty". [arguments]: Simplify "find-libiberty" phase.
* gnu: Add libiberty.Ricardo Wurmus2015-06-29
| | | | * gnu/packages/gcc.scm (make-libiberty, libiberty): New variables.
* gnu: r: Update to 3.2.1.Ricardo Wurmus2015-06-29
| | | | | | * 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.
* gnu: Add Blast+.Ricardo Wurmus2015-06-29
| | | | * gnu/packages/bioinformatics.scm (blast+): New variable.
* gnu: global: Update to 6.5.Ludovic Courtès2015-06-29
| | | | * gnu/packages/code.scm (global): Update to 6.5.
* gnu: help2man: Update to 1.47.1.Ludovic Courtès2015-06-29
| | | | * gnu/packages/man.scm (help2man): Update to 1.47.1.
* gnu: parallel: Update to 20150622.Ludovic Courtès2015-06-29
| | | | * gnu/packages/parallel.scm (parallel): Update to 20150622.
* gnu: screen: Update to 4.3.1.Ludovic Courtès2015-06-29
| | | | * gnu/packages/screen.scm (screen): Update to 4.3.1.
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