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7274 Commits

Author SHA1 Message Date
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
Ludovic Courtès 792798f486 records: "options" → "properties". 
* guix/records.scm (define-record-type*): Change "options" to "properties".
 2015-06-11 23:33:32 +02:00
Ludovic Courtès faef3b6a96 records: Factorize field property predicates. 
* guix/records.scm (define-field-property-predicate): New macro.
  (define-record-type*)[thunked-field?, delayed-field?]: Use it.
 2015-06-11 23:33:32 +02:00
Ludovic Courtès b9c8647337 records: Separate default-value handling. 
* guix/records.scm (make-syntactic-constructor)[default-values]: New
  variable.
  [field-default-value]: New procedure.
  Use them.
 2015-06-11 23:33:32 +02:00
Ludovic Courtès 39fc041a7d records: Replace 'eval-when' with a proper 'define-syntax'. 
* guix/records.scm (make-syntactic-constructor): Remove enclosing
  'eval-when'.  Turn into a 'syntax-rules' macro.
 2015-06-11 23:33:32 +02:00
Mark H Weaver b45ce07a8a gnu: gnupg: Update to 2.1.5. 
* gnu/packages/gnupg.scm (gnupg): Update to 2.1.5.
 2015-06-11 14:39:22 -04:00
宋文武 4510b2da3e gnu: Add librest. 
* gnu/packages/gnome.scm (librest): New variable.
 2015-06-11 23:30:54 +08:00
Mark H Weaver 8b1c8e4e27 gnu: inetutils: Update to 1.9.4. 
* gnu/packages/admin.scm (inetutils): Update to 1.9.4.
 2015-06-11 10:08:01 -04:00
Ludovic Courtès a43b55f1a6 guix build: Allow directories to be passed to --with-source. 
* guix/scripts/build.scm (package-with-source)[tarball-base-name]: Gracefully
  handle file names that lack an extension.
  Pass #:recursive? #t to 'download-to-store'.
* guix/download.scm (download-to-store): Add #:recursive? parameter and pass
  it to 'add-to-store'.
* doc/guix.texi (Invoking guix build): Add an example of --with-source with a
  directory.
 2015-06-11 11:19:12 +02:00
Ludovic Courtès c2590362ad environment: Connect to the store after the command line has been parsed. 
* guix/scripts/environment.scm (guix-environment): Call 'parse-command-line'
  outside of 'with-store'.  This allows things like --help to run even if the
  daemon is not running.
 2015-06-11 11:09:12 +02:00
Mark H Weaver 1492801655 Merge branch 'master' into core-updates 2015-06-10 17:50:27 -04:00
Mark H Weaver 1511e02355 gnu: nettle: Update to 3.1.1. 
* gnu/packages/nettle.scm (nettle): Update to 3.1.1.
 2015-06-10 17:49:11 -04:00
Mark H Weaver 70ca2e94d1 gnu: which: Update to 2.21. 
* gnu/packages/base.scm (which): Update to 2.21.
 2015-06-10 17:39:08 -04:00
Ludovic Courtès 2a1552c608 gnu: cross-base: Do not strip cross-gcc. 
Fixes a regression introduced in 9063ef0 whereby #:strip-binaries? would be
left to #t, leading to an invalid cross-built libgcc.a (see
<http://hydra.gnu.org/build/492479/nixlog/1/tail-reload>.)

* gnu/packages/cross-base.scm (cross-gcc-arguments): Add #:strip-binaries? #f
  unconditionally.  Replace 'install' phase to use "make install-strip".
 2015-06-10 23:19:30 +02:00
Ludovic Courtès 57cd353d87 build: Build man pages after the corresponding code. 
* doc.am (doc/guix.1): Remove extraneous $(top_builddir)/.
  (doc/guix-daemon.1): Fix dependency.
  (doc/guix-$(1).1): Remove extraneous $(top_builddir)/.  Depend on the .go
  files instead of the .scm file.  Add dependency on scripts/guix.
 2015-06-10 21:58:16 +02:00
Ludovic Courtès 7887bcbf56 daemon: Internationalize guix-daemon. 
* nix/nix-daemon/guix-daemon.cc (n_, _): New macros.
  (guix_textdomain): New variable.
  (doc): Use 'n_'.
  (options): Likewise, and lowercase messages.
  (argp): Add initializer for 'argp_domain' field.
  (parse_opt): Use '_' for messages.
  (main): Likewise, and add calls to 'setlocale', 'bindtextdomain', and
  'textdomain'.
* daemon.am (guix_daemon_CPPFLAGS): Add -DLOCALEDIR.
* po/guix/Makevars (XGETTEXT_OPTIONS): Remove '--language' option.  Add
  '--keyword=n_'.
* po/guix/POTFILES.in: Add guix-daemon.cc.
 2015-06-10 21:58:16 +02:00
Mark H Weaver 3dbb0e5f8b gnu: qemu: Add fix for CVE-2015-3209. 
* gnu/packages/patches/qemu-CVE-2015-3209.patch: New file.
* gnu-system.am (dist_patch_DATA): Add it.
* gnu/packages/qemu.scm (qemu): Add patch.
 2015-06-10 15:42:16 -04:00
Mark H Weaver e51943f886 gnu: cups: Update to 2.0.3. 
* gnu/packages/cups.scm (cups): Update to 2.0.3.
 2015-06-10 14:50:28 -04:00
Mark H Weaver 63398a25ba gnu: linux-libre: Update to 4.0.5. 
* gnu/packages/linux.scm (linux-libre): Update to 4.0.5.
 2015-06-10 11:37:37 -04:00
Ludovic Courtès 8ac0368e5b guix-register: Use C++11 range 'for' loop instead of 'foreach' macro. 
* nix/guix-register/guix-register.cc (register_validity): Use C++11 range
  'for' loop instead of 'foreach'.
 2015-06-10 13:55:23 +02:00
Ludovic Courtès 369755847b guix-register: Perform deduplication even when --prefix is passed. 
Fixes <http://bugs.gnu.org/19044>.

* nix/guix-register/guix-register.cc (register_validity): Change the (optimize
  && prefix.empty ()) condition to just (optimize).  Change settings.nixStore
  around the loop.  Prepend PREFIX to the argument passed to 'optimisePath'.
* tests/guix-register.sh: Use 'guix-register -p' with duplicate files, and
  make sure they are deduplicated on the target.  Adjust existing tests.
 2015-06-10 13:47:58 +02:00
Ludovic Courtès 4ae1fe14b9 tests: Make the daemon socket explicit in guix-register test. 
* tests/guix-register.sh: Define GUIX_DAEMON_SOCKET.  Pass it explicitly to
  'open-connection'.
 2015-06-10 11:11:52 +02:00
Ludovic Courtès 78acff7c11 guix system: init: Overwrite the items in the target store. 
Fixes <http://bugs.gnu.org/20722>.
Reported by Eric Bavier <ericbavier@openmailbox.org>.

* guix/scripts/system.scm (copy-item): Check whether DEST exists and remove it
  if it does.
 2015-06-10 10:31:47 +02:00
Ludovic Courtès aea9b23213 install: Really overwrite TARGET/var/guix/profiles/system-1-link. 
* gnu/build/install.scm (populate-root-file-system): Delete system-1-link
  under TARGET, not under /.  Use 'catch' and check for EEXIST instead of
  (false-if-exception (delete-file ...)).
 2015-06-10 10:31:25 +02:00
Ludovic Courtès 7522a0160b ui: Replace the global 'symlink' binding. 
* guix/ui.scm (symlink): Set! the global symlink.
 2015-06-10 10:25:16 +02:00
Alex Kost 80cd1d8992 doc: Add 'help2man' to HACKING. 
* HACKING: Mention 'help2man'.
 2015-06-10 10:03:19 +02:00
Ludovic Courtès ab999c2516 gnu: commencement: Remove "debug" output of GCC-FINAL. 
Fixes a regression introduced in 9063ef0.

* gnu/packages/commencement.scm (gcc-final)[outputs]: New field.
 2015-06-10 09:37:36 +02:00
Ludovic Courtès d0b62698c9 gnu: gcc: Build libbacktrace without -Werror. 
* gnu/packages/gcc.scm (gcc-4.7)[arguments] <pre-configure>: Remove -Werror
  from libbacktrace/configure.
 2015-06-09 22:32:15 +02:00
Ludovic Courtès 9063ef0f79 gnu: gcc: Add "debug" output, debugging symbols of libraries. 
* gnu/packages/gcc.scm (gcc-4.7)[install-target]: Remove.
  [outputs]: Add "debug".
  [arguments]: Remove #:strip-binaries?.  Remove 'install' phase.
 2015-06-09 22:32:15 +02:00
Ludovic Courtès 811974925d gnu: gcc: Do not add -rpath=LIBDIR/lib64 to the "lib" spec. 
* gnu/packages/gcc.scm (gcc-4.7): Remove unneeded LIBDIR/lib64 from
  GNU_USER_TARGET_LIB_SPEC.
 2015-06-09 22:32:15 +02:00
Ludovic Courtès e58652502b gnu: make-bootstrap: Adjust gawk patch to 4.1.3. 
* gnu/packages/patches/gawk-shell.patch: Update for gawk 4.1.3.
 2015-06-09 22:32:15 +02:00
Manolis Ragkousis 30347caae7 gnu: guile-static: Use Linux syscalls only on Linux-based systems. 
* gnu/packages/patches/guile-linux-syscalls.patch: Use Linux
  syscalls only on Linux-based systems.
 2015-06-09 22:48:10 +03:00