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24834 Commits

Author SHA1 Message Date
Ricardo Wurmus 01d87d3c18
gnu: rcas-web: Update to 0.0.4. 
* gnu/packages/bioinformatics.scm (rcas-web): Update to 0.0.4.
 2017-10-11 21:37:37 +02:00
Ludovic Courtès 85a2b58987
zlib: Fix memory leak due to revealed ports not being GC'd. 
Fixes <https://bugs.gnu.org/28784>.

This mostly reverts 81a0f1cdf1, which
introduced a regression: revealed ports are *never* GC'd (contrary to
what Guile's manual suggests).

In addition to the revert, 'close-procedure' now explicitly swallows
EBADF errors when 'close-port' is called.

* guix/zlib.scm (close-procedure): New procedure.
(make-gzip-input-port)[gzfile]: Use 'fileno' instead of 'port->fdes'.
Use 'close-procedure' instead of 'gzclose'.
(make-gzip-output-port): Likewise.
* tests/zlib.scm ("compression/decompression pipe"): Use 'port-closed?'
to determine whether PARENT has been closed.
 2017-10-11 15:20:50 +02:00
Leo Famulari 5781c7dd27
gnu: mpg123: Update to 1.25.7. 
* gnu/packages/mp3.scm (mpg123): Update to 1.25.7.
 2017-10-11 08:24:13 -04:00
Ludovic Courtès 50fcf37c13
doc: Give an example with a FAT UUID. 
* gnu/system/examples/lightweight-desktop.tmpl <file-systems>: Add a
UUID for the /boot/efi partition.
* doc/guix.texi (Using the Configuration System): Mention it.
 2017-10-11 11:12:33 +02:00
Ludovic Courtès 03f66aea63
uuid: Change "fat32" to "fat". 
* gnu/system/uuid.scm (%fat32-endianness): Rename to...
(%fat-endianness): ... this.
(fat32-uuid->string): Rename to...
(fat-uuid->string): ... this.
(%fat32-uuid-rx): Rename to..
(%fat-uuid-rx): ... this.
(string->fat32-uuid): Rename to...
(string->fat-uuid): ... this.
(%uuid-parsers, %uuid-printers): Add 'fat16.
 2017-10-11 11:12:33 +02:00
Ludovic Courtès 88235675fc
file-systems: Add support for FAT16. 
* gnu/build/file-systems.scm (check-fat32-file-system): Rename to...
(check-fat-file-system): ... this.
(check-file-system): Adjust accordingly.
(fat16-superblock?, read-fat16-superblock)
(fat16-superblock-uuid, fat16-superblock-volume-name): New procedures.
(%partition-label-readers, %partition-uuid-readers): Add FAT16.
 2017-10-11 11:12:33 +02:00
Ludovic Courtès 9976c76aab
file-systems: Preserve UUID types when serializing. 
Reported by Roel Janssen <roel@gnu.org>
at <https://lists.gnu.org/archive/html/help-guix/2017-09/msg00094.html>.

* gnu/system/file-systems.scm (file-system->spec): When DEVICE is a
UUID, serialize it in a way that preserves its type.
(spec->file-system): Adjust accordingly.
* gnu/build/file-systems.scm (canonicalize-device-spec): Add case for
when SPEC is 'uuid?'.
 2017-10-11 11:12:33 +02:00
Ludovic Courtès 1c65cca574
file-systems: 'mount-file-system' now takes a <file-system> object. 
* gnu/build/file-systems.scm (mount-file-system): Rename 'spec' to 'fs'
and assume it's a <file-system>.
* gnu/build/linux-boot.scm (boot-system): Assume MOUNTS is a list of
<file-system> and adjust accordingly.
* gnu/build/linux-container.scm (mount-file-systems): Remove
'file-system->spec' call.
* gnu/services/base.scm (file-system-shepherd-service): Add
'spec->file-system' call.  Add (gnu system file-systems) to 'modules'.
* gnu/system/linux-initrd.scm (raw-initrd): Use (gnu system
file-systems).  Add 'spec->file-system' call for #:mounts.
 2017-10-11 11:12:33 +02:00
Theodoros Foradis f26af33aec
gnu: Add freehdl. 
* gnu/packages/engineering.scm (freehdl): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2017-10-11 11:12:33 +02:00
Theodoros Foradis 91cabd3e58
gnu: Add xyce-parallel. 
* gnu/packages/engineering.scm (trilinos-parallel-xyce)
(xyce-parallel): New variables.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2017-10-11 11:12:33 +02:00
Theodoros Foradis 1da02b6a49
gnu: Add xyce-serial. 
* gnu/packages/engineering.scm (trilinos-serial-xyce)
(xyce-serial): New variables.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2017-10-11 11:12:33 +02:00
Theodoros Foradis b509efb385
gnu: Add lapack-3.5. 
* gnu/packages/maths.scm (lapack-3.5): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2017-10-11 11:12:33 +02:00
Ricardo Wurmus 22d1060eff
gnu: python-rpy2: Ignore test results. 
* gnu/packages/python.scm (python-rpy2)[arguments]: Ignore test failures.
 2017-10-11 11:06:05 +02:00
Roel Janssen 6de897ac5a
gnu: Add r-ggdendro. 
* gnu/packages/statistics.scm (r-ggdendro): New variable.
 2017-10-11 10:02:08 +02:00
Mark H Weaver 2f44e7b036
gnu: linux-libre@4.9: Update to 4.9.54. 
* gnu/packages/linux.scm (linux-libre-4.9): Update to 4.9.54.
 2017-10-11 00:39:27 -04:00
Mark H Weaver dac1d8efd4
gnu: linux-libre@4.4: Update to 4.4.91. 
* gnu/packages/linux.scm (linux-libre-4.4): Update to 4.4.91.
 2017-10-11 00:38:46 -04:00
Eric Bavier 7740228e35
build: Set 'NIX_BUILD_HOOK' only if offloading is configured. 
This prevents libstore/build.cc from executing nix/scripts/offload, which is
always created by config.status, when offload support is not enabled.

* build-aux/pre-inst-env.in: Export 'NIX_BUILD_HOOK' only when
configured; unset it otherwise.
 2017-10-10 23:16:07 -05:00
Tobias Geerinckx-Rice c3bece41b7
gnu: dovecot: Update to 2.2.33. 
* gnu/packages/mail.scm (dovecot): Update to 2.2.33.
 2017-10-10 23:42:35 +02:00
Ludovic Courtès db9c49f499
gnu: games: Remove unneeded import. 
Fixes a regression introduced in
42abb842f6.

* gnu/packages/games.scm: Remove unneeded (guix build utils) import,
which led to a name clash on 'which'.
 2017-10-10 23:12:04 +02:00
Ludovic Courtès 90eaa9419a
import: cpan: Load (gnu packages perl) lazily. 
* guix/import/cpan.scm: Remove dependency on (gnu packages perl).
(perl-package): New procedure.
(%corelist, core-module?): Use it instead of referring to 'perl'.
 2017-10-10 23:12:04 +02:00
Ludovic Courtès b719ddbbbb
import: pypi: Remove unneeded import. 
* guix/import/pypi.scm: Remove unneeded import.
 2017-10-10 23:12:03 +02:00
Ludovic Courtès a6e22d8445
ui: Improve reporting of missing closing parentheses. 
Suggested by Ricardo Wurmus.
Works around <https://bugs.gnu.org/28295>.

* guix/ui.scm (report-load-error): Add case for 'read-error'.
* tests/guix-system.sh: Test missing-closing-paren errors.
 2017-10-10 23:12:03 +02:00
Troy Sankey 3f81ca324b
gnu: alot: Update to 0.5.1. 
* gnu/packages/mail.scm (alot): Update to 0.5.1.
[arguments]: Enable tests.
[native-inputs]: Add python2-mock.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2017-10-10 23:09:41 +02:00
Troy Sankey c1578ad063
gnu: python-twisted: Update to 17.1.0. 
* gnu/packages/python.scm (python-twisted): Update to 17.1.0.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2017-10-10 23:09:41 +02:00
Troy Sankey 0cd83b4e00
gnu: Add python-incremental. 
* gnu/packages/python.scm (python-incremental, python2-incremental): New
variables.

Co-authored-by: Ricardo Wurmus <rekado@elephly.net>
 2017-10-10 23:09:41 +02:00
Troy Sankey 96cb5ca1f2
gnu: Add python-automat. 
* gnu/packages/python.scm (python-automat, python2-automat): New variables.

Co-authored-by: Ricardo Wurmus <rekado@elephly.net>
 2017-10-10 23:09:41 +02:00
Ricardo Wurmus 6414410d7a
gnu: Add python-graphviz. 
* gnu/packages/graphviz.scm (python-graphviz, python2-graphviz): New
variables.
 2017-10-10 23:09:40 +02:00
Troy Sankey fd8ff99aa7
gnu: Add python-m2r. 
* gnu/packages/python.scm (python-m2r, python2-m2r): New variables.

Co-authored-by: Ricardo Wurmus <rekado@elephly.net>
 2017-10-10 23:09:40 +02:00
Troy Sankey 9074bac139
gnu: Add python-constantly. 
* gnu/packages/python.scm (python-constantly, python2-constantly): New
variables.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2017-10-10 23:09:40 +02:00
Troy Sankey bb3b4b4ee9
gnu: Add python-attrs. 
* gnu/packages/python.scm (python-attrs, python2-attrs): New variables.

Co-authored-by: Ricardo Wurmus <rekado@elephly.net>
 2017-10-10 23:09:40 +02:00
Julien Lepiller 4b8b4418e6
services: vpn: Fix default tls-auth configuration. 
* gnu/services/vpn.scm (serialize-tls-auth): Fix serialization error when
tls-auth is disabled.
 2017-10-10 22:06:08 +02:00
Julien Lepiller 262a4d335a
gnu: Add java-fasterxml-jackson-dataformat-xml. 
* gnu/packages/java.scm (java-fasterxml-jackson-dataformat-xml): New
variable.
 2017-10-10 22:05:59 +02:00
Julien Lepiller 40f193f316
gnu: Add java-woodstox-core. 
* gnu/packages/java.scm (java-woodstox-core): New variable.
 2017-10-10 22:05:57 +02:00
Julien Lepiller 6fd07b98b1
gnu: Add java-stax2-api. 
* gnu/packages/java.scm (java-stax2-api): New variable.
 2017-10-10 22:05:55 +02:00
Julien Lepiller 087c8fd2c0
gnu: Add java-fasterxml-jackson-dataformat-yaml. 
* gnu/packages/java.scm (java-fasterxml-jackson-dataformat-yaml): New
variable.
 2017-10-10 22:05:52 +02:00
Julien Lepiller 0f296d3747
gnu: Add java-snakeyaml. 
* gnu/packages/java.scm (java-snakeyaml): New variable.
 2017-10-10 22:05:50 +02:00
Julien Lepiller d57d8b89bb
gnu: Add java-fasterxml-jackson-modules-base-jaxb. 
* gnu/packages/java.scm (java-fasterxml-jackson-modules-base-jaxb): New
variable.
 2017-10-10 22:05:45 +02:00
Julien Lepiller f234c7a065
gnu: Add java-fasterxml-jackson-databind. 
* gnu/packages/java.scm (java-fasterxml-jackson-databind): New variable.
 2017-10-10 22:05:43 +02:00
Julien Lepiller 0b5481dfd3
gnu: Add java-fasterxml-jackson-core. 
* gnu/packages/java.scm (java-fasterxml-jackson-core): New variable.
 2017-10-10 22:05:40 +02:00
Julien Lepiller cb05f60d4a
gnu: Add java-fasterxml-jackson-annotations. 
* gnu/packages/java.scm (java-fasterxml-jackson-annotations): New
variable.
 2017-10-10 22:05:34 +02:00
Julien Lepiller 4496d77fb4
gnu: Add java-ops4j-pax-exam-core-junit. 
* gnu/packages/java.scm (java-ops4j-pax-exam-core-junit): New variable.
 2017-10-10 22:05:31 +02:00
Julien Lepiller 7a7c2b7556
gnu: Add java-ops4j-pax-exam-core-spi. 
* gnu/packages/java.scm (java-ops4j-pax-exam-core-spi): New variable.
 2017-10-10 22:05:29 +02:00
Julien Lepiller e179add07b
gnu: Add java-ops4j-pax-exam-core. 
* gnu/packages/java.scm (java-ops4j-pax-exam-core): New variable.
 2017-10-10 22:05:26 +02:00
Julien Lepiller 25aef81d26
gnu: Add java-ops4j-pax-tinybundles. 
* gnu/packages/java.scm (java-ops4j-pax-tinybundles): New variable.
 2017-10-10 22:05:23 +02:00
Julien Lepiller 5f26a13125
gnu: Add java-aqute-bndlib. 
* gnu/packages/java.scm (java-aqute-bndlib): New variable.
 2017-10-10 22:05:21 +02:00
Julien Lepiller 60ba297861
gnu: Add java-aqute-libg. 
* gnu/packages/java.scm (java-aqute-libg): New variable.
 2017-10-10 22:05:18 +02:00
Julien Lepiller e1edf42e82
gnu: Add java-aqute-bnd-annotation. 
* gnu/packages/java.scm (java-aqute-bnd-annotation): New variable.
 2017-10-10 22:05:16 +02:00
Julien Lepiller 214fcd8a91
gnu: Add java-ops4j-base-spi. 
* gnu/packages/java.scm (java-ops4j-base-spi): New variable.
 2017-10-10 22:05:13 +02:00
Julien Lepiller 0edf8cf086
gnu: Add java-ops4j-base-store. 
* gnu/packages/java.scm (java-ops4j-base-store): New variable.
 2017-10-10 22:05:10 +02:00
Julien Lepiller 60dcec7abb
gnu: Add java-ops4j-base-util-property. 
* gnu/packages/java.scm (java-ops4j-base-util-property): New variable.
 2017-10-10 22:05:08 +02:00