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7655 Commits

Author SHA1 Message Date
Ricardo Wurmus be0a4c261e gnu: python-scikit-learn: Update to 0.16.1. 
* gnu/packages/python.scm (python-scikit-learn): Update to 0.16.1.
 2015-06-15 10:36:42 +02:00
Ricardo Wurmus a98c6eccf8 gnu: orfm: Update to 0.4.1. 
* gnu/packages/bioinformatics.scm (orfm): Update to 0.4.1.
 2015-06-15 10:36:42 +02:00
Ricardo Wurmus 2f6b3d2e7e gnu: python-scikit-learn: Use OpenBLAS instead of ATLAS. 
* gnu/packages/python.scm (python-scikit-learn)[inputs]: Replace "atlas" with
  "openblas".
* gnu/packages/python.scm (python-scikit-learn)[arguments]: Remove build phase
  'set-environment-variables, which is only needed when ATLAS is used.
 2015-06-15 10:36:42 +02:00
Ricardo Wurmus 719b01c157 gnu: python-scipy: Build with OpenBLAS and lapack. 
* gnu/packages/python.scm (python-scipy)[inputs]: Remove "atlas", add "lapack"
  and "openblas".
* gnu/packages/python.scm (python-scipy)[arguments]: Replace phase
  "set-environment-variables" with "configure-openblas".
 2015-06-15 10:36:42 +02:00
Ricardo Wurmus cba256f8fa gnu: python-numpy-bootstrap: Add lapack to inputs. 
* gnu/packages/python.scm (python-numpy-bootstrap)[inputs]: Add lapack to
  inputs, because OpenBLAS does not include lapack functions.
 2015-06-15 10:36:41 +02:00
Ricardo Wurmus 2e189eb89f gnu: lv2: Update to 1.12.0. 
* gnu/packages/audio.scm (lv2): Update to 1.12.0.
 2015-06-15 08:07:37 +02:00
Ludovic Courtès 86d7043cad gnu: make-bootstrap: Update patching of gawk's configure. 
* gnu/packages/make-bootstrap.scm (%static-inputs)[gawk]: Change
  "-export-dynamic" to "-Wl,-export-dynamic" to account for current
  'configure' file.
 2015-06-15 00:09:25 +02:00
Ludovic Courtès 8dca238b15 gnu: make-bootstrap: Switch to GCC 4.9. 
* gnu/packages/make-bootstrap.scm: Replace all occurrences of "gcc-4.8" with
  "gcc-4.9".
  (%gcc-static): Add --disable-libcilkrts, --disable-libvtv,
  --disable-libbacktrace.
 2015-06-15 00:09:24 +02:00
Mark H Weaver a0d385b052 gnu: screen: Update to 4.3.0. 
* gnu/packages/screen.scm (screen): Update to 4.3.0.
 2015-06-14 12:19:32 -04:00
Mark H Weaver 1a802c7ec2 gnu: openssl: Update to 1.0.2c. 
* gnu/packages/openssl.scm (openssl): Update to 1.0.2c.
 2015-06-14 08:49:50 -04:00
Mark H Weaver bcf2971f6e Merge branch 'master' into core-updates 
Conflicts:
	gnu/packages/commencement.scm
	gnu/packages/xml.scm
 2015-06-14 08:49:42 -04:00
Ludovic Courtès ec29907160 gnu: gcc: Build libsanitizer's bundled libbacktrace without -Werror. 
* gnu/packages/gcc.scm (gcc-4.7)[arguments]: Also patch
  libsanitizer/libbacktrace/Makefile.in.
 2015-06-14 14:41:01 +02:00
Mark H Weaver 7871724df7 gnu: openssl: Update to 1.0.2b. 
* gnu/packages/openssl.scm (openssl): Update to 1.0.2b.
 2015-06-13 23:01:07 -04:00
Mark H Weaver 0ad8f76f7f gnu: perl-net-ssleay: Disable test that fails with openssl-1.0.2b. 
* gnu/packages/patches/perl-net-ssleay-disable-ede-test.patch: New file.
* gnu-system.am (dist_patch_DATA): Add it.
* gnu/packages/openssl.scm (perl-net-ssleay): Add patch.
 2015-06-13 23:01:07 -04:00
Mark H Weaver 4c50e5ab3a gnu: python: Disable ssl test that fails with openssl-1.0.2b. 
* gnu/packages/patches/python-disable-ssl-test.patch: New file.
* gnu-system.am (dist_patch_DATA): Add it.
* gnu/packages/python.scm (python): Add patch.
 2015-06-13 23:01:07 -04:00
Mathieu Lirzin 8c01b9d05a doc: Move most 'HACKING' informations into the manual. 
* HACKING (Contributing): New section.
  (Building from Git, The Perfect Setup, Coding Style, Submitting Patches):
  Move to ...
* doc/guix.texi (Running Guix Before It Is Installed): Likewise.
* doc/contributing.texi: ... here. New file.
* doc.am (EXTRA_DIST): Use it.
* README (Installation): Adapt to it.
* configure.ac (DOT): Likewise.
 2015-06-14 01:44:54 +02:00
Ludovic Courtès b5616bc33d ld-wrapper: Ignore .so files specified after "-plugin" for RUNPATH purposes. 
Reported by Mark H Weaver
at <http://debbugs.gnu.org/cgi/bugreport.cgi?bug=20102#58>.

* gnu/packages/ld-wrapper.in (library-files-linked): Handle "-plugin"
  similarly to "-dynamic-linker".
 2015-06-14 01:00:27 +02:00
Ludovic Courtès 932e7204af gnu: guix: Wrap 'guix' so GUILE_LOAD_PATH includes the dependencies. 
* gnu/packages/package-management.scm (guix-0.8.2)[arguments]: Add
  'wrap-program' phase.
 2015-06-13 22:33:37 +02:00
Ludovic Courtès 02c2cf43ce gnu: guix: Use 'modify-phases'. 
* gnu/packages/package-management.scm (guix-0.8.2)[arguments]: Use
  'modify-phases' instead of 'alist-cons-before'.
 2015-06-13 22:33:37 +02:00
Eric Bavier 0061079a19 gnu: Add hydra. 
* gnu/packages/ci.scm: New file.
* gnu/packages/patches/hydra-automake-1.15.patch,
  gnu/packages/patches/hydra-disable-darcs-test.patch: New files.
* gnu-system.am (GNU_SYSTEM_MODULES): Add file.
  (dist_patch_DATA): Add patches.
 2015-06-13 08:05:01 -05:00
Eric Bavier 6e545bbf55 gnu: Add Catalyst-Authentication-Store-DBIx-Class. 
* gnu/packages/web.scm (perl-catalyst-authentication-store-dbix-class):
  New variable.
 2015-06-13 08:05:00 -05:00
Eric Bavier 514214cbe5 gnu: Add Catalyst-Plugin-Authorization-Roles. 
* gnu/packages/web.scm (perl-catalyst-plugin-authorization-roles): New
  variable.
 2015-06-13 08:05:00 -05:00
Eric Bavier 1937e38d06 gnu: Add Set-Object. 
* gnu/packages/perl.scm (perl-set-object): New variable.
 2015-06-13 08:05:00 -05:00
Ricardo Wurmus 8b9ec354ed gnu: Add powertabeditor. 
* gnu/packages/music.scm (powertabeditor): New variable.
 2015-06-12 23:01:33 +02:00
Ricardo Wurmus 14a17ef6f4 gnu: catch-framework: Update to 1.1.3. 
* gnu/packages/check.scm (catch-framework): Update to 1.1.3.
 2015-06-12 23:01:33 +02:00
Ricardo Wurmus cc45cff83a gnu: Add rtmidi. 
* gnu/packages/audio.scm (rtmidi): New variable.
 2015-06-12 23:01:33 +02:00
Ricardo Wurmus 6ce212b868 gnu: Add pugixml. 
* gnu/packages/xml.scm (pugixml): New variable.
 2015-06-12 23:01:33 +02:00
Ricardo Wurmus ccb8da2654 gnu: Add RapidJSON. 
* gnu/packages/web.scm (rapidjson): New variable.
 2015-06-12 23:01:33 +02:00
Ricardo Wurmus 76e146384c gnu: Add withershins. 
* gnu/packages/code.scm (withershins): New variable.
 2015-06-12 23:01:33 +02:00
Ludovic Courtès e1ad6bfbe1 install: Use udev rules for device-mapper. 
Fixes <http://bugs.gnu.org/20791>.
Reported by Benz Schenk <benz.schenk@uzh.ch>.

* gnu/system/install.scm (installation-services): Add #:rules argument for
  'udev-service'.
 2015-06-12 19:29:52 +02:00
Manolis Ragkousis 16cae799db gnu: patch: Set PATH_MAX for Hurd systems. 
* gnu/packages/patches/patch-hurd-path-max.patch: New file.
* gnu-system.am (dist_patch_DATA): Add it.
 2015-06-12 15:46:25 +03:00
Ben Woodcroft 1e44cf8b0f gnu: Add OrfM. 
* gnu/packages/bioinformatics.scm (orfm): New variable.

Signed-off-by: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
 2015-06-12 12:57:30 +02:00
Ricardo Wurmus 47da6268c4 gnu: icedtea7: Bootstrap with GCJ. 
* gnu/packages/java.scm (icedtea7): Bootstrap with GCJ rather than compile
  with IcedTea6.
 2015-06-12 12:57:30 +02:00
Ricardo Wurmus 36742f4389 gnu: Add Couger. 
* gnu/packages/bioinformatics.scm (couger): New variable.
 2015-06-12 12:57:30 +02:00
Ricardo Wurmus 0931c6091c gnu: Add randomjungle. 
* gnu/packages/machine-learning.scm (randomjungle): New variable.
 2015-06-12 12:57:30 +02:00
Ricardo Wurmus 71f80f5487 gnu: Add python-libsvm. 
* gnu/packages/machine-learning.scm (python-libsvm): New variable.
 2015-06-12 12:57:30 +02:00
Ricardo Wurmus 741115b649 gnu: Add libsvm. 
* gnu/packages/machine-learning.scm: New file.
* gnu-system.am (GNU_SYSTEM_MODULES): Add it.
 2015-06-12 12:57:30 +02:00
Ricardo Wurmus e0a02cb21f gnu: ngs-sdk: Update to version 1.1.1. 
* gnu/packages/bioinformatics.scm (ngs-sdk): Update to version 1.1.1.
 2015-06-12 12:57:29 +02:00
Eric Bavier 48d21d6cd6 gnu: ghc: Patch runtime references to /bin/sh. 
* gnu/packages/haskell.scm (ghc)[arguments]: Rename
  'unpack-and-fix-testsuite' phase to 'unpack-testsuite-and-fix-bins'.
  Patch source files that reference /bin/sh.
 2015-06-11 18:55:49 -05:00
Eric Bavier 6508ce55e9 build-system/haskell: install config for any package that creates it. 
A Cabal package is allowed to declare an "empty" library, in an
otherwise executable-only package, for the purpose of allowing Cabal
to use it as a dependency for other packages.  See e.g. hspec-discover.

* guix/build/haskell-build-system.scm (register): Unconditionally call
  setup script with "register", and install any config file generated.
 2015-06-11 18:55:49 -05:00
Eric Bavier b4b1fe9d2f profiles: Process ghc conf files only once. 
A package may be listed in the manifest inputs multiple times.  Avoid
copying ghc *.conf files twice by deleting duplicates.

* guix/profiles.scm (ghc-package-cache-file)[conf-files]: Delete
  duplicate manifest inputs before copying conf files.
 2015-06-11 18:55:48 -05:00
Eric Bavier 84de458ba8 profiles: Search for ghc conf files only if package db exists. 
This avoids having 'find-files' report warnings about searching in
non-existent directories.

* guix/profiles.scm (ghc-package-cache-file)[conf-files]: Only search
  for *.conf files if the search directory exists.
 2015-06-11 18:55:48 -05:00
Mark H Weaver dc7b1817f6 Revert "gnu: openssl: Update to 1.0.2b." 
This reverts commit 4f467e33de.
 2015-06-12 01:46:03 -04:00
Mark H Weaver 4f467e33de gnu: openssl: Update to 1.0.2b. 
* gnu/packages/openssl.scm (openssl): Update to 1.0.2b.
 2015-06-12 01:25:23 -04:00
Ludovic Courtès 6c35641453 tests: Avoid sequence of zero expressions. 
* tests/records.scm ("define-record-type* with let* behavior"): Add missing
  body for clause.
 2015-06-11 23:33:32 +02:00
Ludovic Courtès ad7c1a2cde records: Remove unnecessary 'begin'. 
* guix/records.scm (define-record-type*): Remove unnecessary 'begin'.
 2015-06-11 23:33:32 +02:00
Ludovic Courtès 79477def6b tests: Write the random seed to the error port. 
* guix/tests.scm (random-seed): New procedure.
  (%seed): Use it, and write the random seed to the error port.
 2015-06-11 23:33:32 +02:00
Ludovic Courtès e21adc768e gnu: guix: Update snapshot. 
* gnu/packages/package-management.scm (guix-devel): Update to a43b55f.
  [source]: Add 'file-name' field.
  [native-inputs]: Add HELP2MAN.
 2015-06-11 23:33:32 +02:00
Ludovic Courtès 0004c5904c packages: Make 'location' field innate. 
* guix/packages.scm (<package>)[location]: Add 'innate' property.
* guix/build-system/gnu.scm (static-package): Remove 'loc' parameter and
  'location' field.
* gnu/packages/autotools.scm (autoconf-wrapper): Remove 'location' field.
* gnu/packages/commencement.scm (gnu-make-boot0, diffutils-boot0, gcc-final):
  Likewise.
* gnu/packages/cross-base.scm (cross): Likewise.
* gnu/packages/emacs.scm (emacs-no-x, emacs-no-x-toolkit): Likewise.
* gnu/packages/make-bootstrap.scm (tarball-package): Likewise.
* gnu/packages/maths.scm (petsc-complex): Likewise.
 2015-06-11 23:33:32 +02:00
Ludovic Courtès 8a16d064fa records: Add support for 'innate' fields. 
* guix/records.scm (make-syntactic-constructor): Add #:innate parameter.
  [record-inheritance]: Honor it.
  [innate-field?]: New procedure.
  (define-record-type*)[innate-field?]: New procedure.
  Pass #:innate to 'make-syntactic-constructor'.
* tests/records.scm ("define-record-type* & inherit & innate",
  "define-record-type* & thunked & innate"): New tests.
 2015-06-11 23:33:32 +02:00