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Author SHA1 Message Date
Mark H Weaver d5ce3594f6
gnu: linux-libre@4.9: Update to 4.9.109. 
* gnu/packages/linux.scm (linux-libre-4.9): Update to 4.9.109.
 2018-06-18 03:38:11 -04:00
Mark H Weaver 021d6296d8
gnu: linux-libre@4.4: Update to 4.4.138. 
* gnu/packages/linux.scm (linux-libre-4.4): Update to 4.4.138.
 2018-06-18 03:37:14 -04:00
Tobias Geerinckx-Rice 69e0aac3a7
gnu: zathura-pdf-mupdf: Link to JPEG libraries. 
* gnu/packages/pdf.scm (zathura-pdf-mupdf)[source]: Add patch.
* gnu/packages/patches/zathura-pdf-mupdf-link-to-jpeg-libraries.patch:
New file.
* gnu/local.mk (dist_patch_DATA): Add it.
 2018-06-18 04:04:41 +02:00
Pierre Neidhardt 47de00af16
gnu: encfs: Update to 1.9.5. 
* gnu/packages/crypto.scm (encfs): Update to 1.9.5.
[source](snippet): Adjust paths.  Remove two bundled libraries.
[native-inputs]: Add googletest-source.
[arguments]: Add 'unpack-googletest' and 'make-unittests' phases.

Signed-off-by: Kei Kebreau <kkebreau@posteo.net>
 2018-06-17 21:59:51 -04:00
Tobias Geerinckx-Rice 6321610d41
gnu: zathura: Fix plugin path regression. 
eb6a5dab5c (gnu: zathura: Update to 0.3.9)
silently broke Zathura's (Guix-specific) ZATHURA_PLUGIN_PATH mechanism.

My environment was so filthy that all happened to work just fine, but as
usual Marius was right and the patch needed tweaking.

* gnu/packages/patches/zathura-plugindir-environment-variable.patch:
Tweak.
 2018-06-18 03:59:46 +02:00
Arun Isaac b4eae997fe
gnu: texlive-bin: Use absolute path to ghostscript executable "gs". 
* gnu/packages/tex.scm (texlive-bin)[arguments]: Rename fix-unix-detection
phase to configure-ghostscript-executable. Replace "gs" in epstopdf.pl with
the absolute path to "gs" in the store.
 2018-06-17 21:29:07 +05:30
Gábor Boskovits 3b6ba18bab
gnu: ant: Add missing dependencies. 
* gnu/packages/java.scm (ant)[native-inputs]: Add zip and unzip.
 2018-06-17 14:30:26 +02:00
宋文武 33f61dc1b5
gnu: Remove Mr. Rescue. 
It's not compatible with love-11.1.

* gnu/packages/game.scm (mrrescue): Remove variable.
 2018-06-17 20:23:42 +08:00
Gábor Boskovits 1c7ef07ea1
gnu: ant/java8: Add missing dependencies. 
* gnu/packages/java.scm (ant/java8)[native-inputs]: Add zip and unzip.
 2018-06-17 14:18:34 +02:00
Kei Kebreau c5829179ca
gnu: clusterssh: Update to 4.13.2. 
* gnu/packages/admin.scm (clusterssh): Update to 4.13.2.
[build-system]: Switch to perl-build-system.
[arguments]: Remove 'set-load-paths' phase.
[inputs]: Remove perl.
[native-inputs]: Add perl-cpan-changes, perl-file-slurp, perl-file-which,
perl-module-build, perl-readonly, perl-test-differences,
perl-test-distmanifest, perl-test-perltidy, perl-test-pod,
perl-test-pod-coverage, perl-test-trap and perltidy.
[propagated-inputs]: Add perl-exception-class, perl-try-tiny and
perl-x11-protocol-other.
 2018-06-16 20:52:43 -04:00
Kei Kebreau 469e82715e
gnu: perltidy: Update to 20180220. 
* gnu/packages/perl.scm (perltidy): Update to 20180220.
 2018-06-16 20:52:43 -04:00
Kei Kebreau 0943b0b534
gnu: Add perl-test-perltidy. 
* gnu/packages/perl-check.scm (perl-test-perltidy): New variable.
 2018-06-16 20:52:37 -04:00
Kei Kebreau 32315df9c7
gnu: Add perl-file-finder. 
* gnu/packages/perl.scm (perl-file-finder): New variable.
 2018-06-16 20:42:27 -04:00
Kei Kebreau 52b1551bff
gnu: Add perl-test-distmanifest. 
* gnu/packages/perl-check.scm (perl-test-distmanifest): New variable.
 2018-06-16 20:41:16 -04:00
Kei Kebreau 048657cccd
gnu: Add perl-module-manifest. 
* gnu/packages/perl.scm (perl-module-manifest): New variable.
 2018-06-16 20:40:25 -04:00
Kei Kebreau b2d5b00d42
gnu: Add perl-cpan-changes. 
* gnu/packages/perl.scm (perl-cpan-changes): New variable.
 2018-06-16 20:39:35 -04:00
Kei Kebreau f82fe68f99
gnu: Add perl-x11-protocol-other. 
* gnu/packages/xorg.scm (perl-x11-protocol-other): New variable.
 2018-06-16 20:38:32 -04:00
Ludovic Courtès f3a34b9de8
gnu: gsl: Update to 2.5. 
* gnu/packages/maths.scm (gsl): Update to 2.5.
 2018-06-17 01:40:14 +02:00
Ludovic Courtès 554eaae4a0
gnu: diffoscope: Update to 96. 
* gnu/packages/package-management.scm (diffoscope): Update to 96.
 2018-06-17 01:40:14 +02:00
Ludovic Courtès 6710206881
gnu: magit: Update to 2.13.0. 
* gnu/packages/emacs.scm (magit): Update to 2.13.0.
 2018-06-17 01:40:14 +02:00
Pierre Neidhardt 3348e9f371
gnu: emacs-fish-completion: Don't propagate inputs. 
* gnu/packages/emacs.scm (emacs-fish-completion)[propagated-inputs]: Remove fish
[inputs]: Add fish.
[arguments]: New field.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-06-17 01:40:14 +02:00
Pierre Neidhardt a14de83213
gnu: upx: Fix CVE-2017-15056. 
* gnu/packages/patches/upx-protect-against-bad-crafted-input.patch: New file.
* gnu/packages/compression.scm (upx)[source]: Use it.
* gnu/local.mk (dist_patch_DATA): Add it.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-06-17 01:40:13 +02:00
Marius Bakke ed2ae0dc7f
gnu: strace: Update to 4.23. 
* gnu/packages/linux.scm (strace): Update to 4.23.
[source]: Remove obsolete patch.
* gnu/packages/patches/strace-kernel-4.16.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Remove it.
 2018-06-16 21:35:26 +02:00
Marius Bakke 4c0df1a870
gnu: offlineimap: Update to 7.2.1. 
* gnu/packages/mail.scm (offlineimap): Update to 7.2.1.
 2018-06-16 21:35:26 +02:00
Marius Bakke ec8cdd0ec6
gnu: maim: Update to 5.5.2. 
* gnu/packages/xdisorg.scm (maim): Update to 5.5.2.
 2018-06-16 21:35:26 +02:00
Marius Bakke 30e26b6af3
gnu: ffmpeg: Update to 4.0.1. 
* gnu/packages/video.scm (ffmpeg): Update to 4.0.1.
 2018-06-16 21:35:25 +02:00
Marius Bakke 259341cf93
gnu: ldb: Fix build on 32-bit systems. 
* guix/utils.scm (target-64bit?): New procedure.
* gnu/packages/samba.scm (ldb)[inputs]: Only add LMDB on 64-bit systems.
[arguments]: Make #:tests? conditional on LMDB availability.
 2018-06-16 21:35:25 +02:00
Marius Bakke 406c83f78d
gnu: perl: Fix CVE-2018-12015. 
* gnu/packages/patches/perl-archive-tar-CVE-2018-12015.patch: New file.
* gnu/local.mk (dist_patch_DATA): Register it.
* gnu/packages/perl.scm (perl-5.26.2)[source](patches): Use it.
 2018-06-16 21:35:25 +02:00
Marius Bakke 57b1dba116
gnu: libedit: Update to 20180525-3.1. 
* gnu/packages/libedit.scm (libedit): Update to 20180525-3.1.
 2018-06-16 21:35:25 +02:00
Marius Bakke 7727f91f44
gnu: openal: Update to 0.18.2. 
* gnu/packages/audio.scm (openal): Update to 0.18.2.
 2018-06-16 21:35:25 +02:00
Marius Bakke cdbcfc113b
gnu: linux-libre: Fix build on AArch64. 
* gnu/packages/patches/binutils-aarch64-symbol-relocation.patch: New file.
* gnu/local.mk (dist_patch_DATA): Register it.
* gnu/packages/base.scm (binutils/fixed): New public variable.
* gnu/packages/linux.scm (make-linux-libre)[native-inputs]: On aarch64, define
new ld-wrapper with the above binutils and use it.
 2018-06-16 21:35:24 +02:00
Oleg Pykhalov f77886c1c5
gnu: Add restic. 
* gnu/packages/backup.scm (restic): New variable.
 2018-06-16 21:52:40 +03:00
Clément Lassieur e8b3a15849
gnu: Add dehydrated. 
* gnu/packages/tls.scm (dehydrated): New variable.
 2018-06-16 20:45:56 +02:00
Gábor Boskovits cded3a7593
gnu: ant-bootstrap: Make build reproducible. 
* gnu/packages/java.scm (ant-bootstrap)[arguments]<#:phases>[strip-jar-timestamps]:
New phase to reset jar file timestamps.
<#:imported-modules>: Import guix build syscalls, gnu-build-system-modules.
<#:modules>: Import guix build: gnu-build-system, utils, syscalls.
[native-inputs]: Add unzip, zip.
 2018-06-16 19:58:41 +02:00
宋文武 806f599c5b
gnu: wesnoth: Update to 1.14.3. 
* gnu/packages/games.scm (wesnoth): Update to 1.14.3.
 2018-06-16 22:16:39 +08:00
Julien Lepiller 697a9d0d06
gnu: groovy: Add groovy-xml to the closure. 
* gnu/packages/groovy.scm (groovy)[inputs]: Add groovy-xml.
[arguments]: Add groovy-xml to the list of classes available for class
loading.
 2018-06-16 14:09:40 +02:00
Julien Lepiller 8c2c105c12
gnu: Add maven. 
* gnu/packages/maven.scm (maven): New variable.
 2018-06-16 13:18:25 +02:00
Julien Lepiller 0c1e98eb92
gnu: Add maven-compat. 
* gnu/packages/maven.scm (maven-compat): New variable.
 2018-06-16 13:18:19 +02:00
Julien Lepiller 19126bba4e
gnu: Add maven-resolver-transport-wagon. 
* gnu/packages/maven.scm (maven-resolver-transport-wagon): New variable.
 2018-06-16 13:18:17 +02:00
Julien Lepiller aa06dd0f7d
gnu: Add maven-wagon-http. 
* gnu/packages/maven.scm (maven-wagon-http): New variable.
 2018-06-16 13:18:15 +02:00
Julien Lepiller c3f5ec6ec7
gnu: Add maven-wagon-http-shared. 
* gnu/packages/maven.scm (maven-wagon-http-shared): New variable.
 2018-06-16 13:18:13 +02:00
Julien Lepiller 53360e488d
gnu: Add maven-wagon-tck-http. 
* gnu/packages/maven.scm (maven-wagon-tck-http): New variable.
 2018-06-16 13:18:11 +02:00
Julien Lepiller 0d1b3b39bc
gnu: Add maven-wagon-file. 
* gnu/packages/maven.scm (maven-wagon-file): New variable.
 2018-06-16 13:18:09 +02:00
Julien Lepiller f216a9f99a
gnu: Add maven-wagon-provider-test. 
* gnu/packages/maven.scm (maven-wagon-provider-test): New variable.
 2018-06-16 13:18:07 +02:00
Julien Lepiller ff7a0fcff3
gnu: Add maven-wagon-provider-api. 
* gnu/packages/maven.scm (maven-wagon-provider-api): New variable.
 2018-06-16 13:18:04 +02:00
Julien Lepiller e2c7d32995
gnu: Add maven-embedder. 
* gnu/packages/maven.scm (maven-embedder): New variable.
 2018-06-16 13:18:02 +02:00
Julien Lepiller b822544cfe
gnu: Add maven-core. 
* gnu/packages/maven.scm (maven-core): New variable.
 2018-06-16 13:18:00 +02:00
Julien Lepiller 9f25cba65a
gnu: Add java-plexus-component-metadata. 
* gnu/packages/maven.scm (java-plexus-component-metadata): New variable.
 2018-06-16 13:17:58 +02:00
Julien Lepiller a59d5f3542
gnu: Add maven-plugin-annotations. 
* gnu/packages/maven.scm (maven-plugin-annotations): New variable.
 2018-06-16 13:17:56 +02:00
Julien Lepiller 7a42f05869
gnu: Add maven-core-bootstrap. 2018-06-16 13:17:54 +02:00
Julien Lepiller 8f5caf9366
gnu: Add maven-plugin-api. 
* gnu/packages/maven.scm (maven-plugin-api): New variable.
 2018-06-16 13:17:52 +02:00
Julien Lepiller ab621bf142
gnu: Add java-qdox. 
* gnu/packages/java.scm (java-qdox): New variable.
 2018-06-16 13:17:50 +02:00
Julien Lepiller 7d65489ffe
gnu: Add java-plexus-cli. 
* gnu/packages/java.scm (java-plexus-cli): New variable.
 2018-06-16 13:17:48 +02:00
Julien Lepiller 087583a7db
gnu: Add java-eclipse-jetty-webapp-9.2. 
* gnu/packages/web.scm (java-eclipse-jetty-webapp-9.2): New variable.
 2018-06-16 13:17:46 +02:00
Julien Lepiller d736511864
gnu: Add java-eclipse-jetty-webapp. 
* gnu/packages/web.scm (java-eclipse-jetty-webapp): New variable.
 2018-06-16 13:17:44 +02:00
Julien Lepiller 38b57575c1
gnu. Add java-eclipse-jetty-xml-9.2. 
* gnu/packages/web.scm (java-eclipse-jetty-xml-9.2): New variable.
 2018-06-16 13:17:42 +02:00
Julien Lepiller f69a1d04a1
gnu: Add java-eclipse-jetty-xml. 
* gnu/packages/web.scm (java-eclipse-jetty-xml): New variable.
 2018-06-16 13:17:39 +02:00
Julien Lepiller c099f6a716
gnu: java-eclipse-jetty-security-9.2: Ignore test error. 
* gnu/packages/web.scm (java-eclipse-jetty-security-9.2)[arguments]:
Ignore one failing test.
 2018-06-16 13:17:19 +02:00
Ricardo Wurmus 901bcb7815
gnu: pigx-chipseq: Update to 0.0.16. 
* gnu/packages/bioinformatics.scm (pigx-chipseq): Update to 0.0.16.
 2018-06-16 12:11:09 +02:00
Rutger Helling 3e3fa14faa
gnu: mesa: Update to 18.1.2. 
* gnu/packages/gl.scm (mesa): Update to 18.1.2.
 2018-06-16 09:40:50 +02:00
Leo Famulari 12e530ba63
gnu: BIND: Fix CVE-2018-5738. 
* gnu/packages/patches/bind-CVE-2018-5738.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/dns.scm (isc-bind)[source]: Use it.
 2018-06-15 16:41:16 -04:00
Mark H Weaver a7c8716928
gnu: grub: Fix build on i686. 
Fixes <https://bugs.gnu.org/31380>.

* gnu/packages/bootloaders.scm (grub)[native-inputs]: Add "ld-wrapper"
and "binutils".

Co-authored-by: Ludovic Courtès <ludo@gnu.org>
 2018-06-15 16:41:52 +02:00
Danny Milosavljevic 4ce4fc5010
system: Add os-with-u-boot. 
* gnu/system/install.scm (os-with-u-boot): New procedure.
* gnu/packages/bootloaders.scm (make-u-boot-package): Export.
* doc/guix.texi (Building the Installation Image for ARM Boards): New
subsection.
 2018-06-15 14:16:37 +02:00
fis 0017e55f89
gnu: Add shadowsocks. 
* gnu/packages/networking.scm (shadowsocks): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-06-15 10:04:59 +02:00
Tobias Geerinckx-Rice ad21323c96
gnu: cpuid: Update to 20180519. 
* gnu/packages/linux.scm (cpuid): Update to 20180519.
 2018-06-15 09:57:17 +02:00
Tobias Geerinckx-Rice d41a5f826d
gnu: light: Return #t from phase. 
* gnu/packages/linux.scm (light)[arguments]: End ‘patch-makefile’ phase
with #t.
 2018-06-15 09:57:17 +02:00
Tobias Geerinckx-Rice a756fa5ac0
gnu: light: Update to 1.1. 
* gnu/packages/linux.scm (light): Update to 1.1.
[source]: Switch to GIT-FETCH.
 2018-06-15 09:57:17 +02:00
Tobias Geerinckx-Rice 14b0c49670
gnu: f2fs-tools: Update to 1.10.0. 
* gnu/packages/linux.scm (f2fs-tools): Update to 1.10.0.
 2018-06-15 09:57:16 +02:00
Tobias Geerinckx-Rice 52d5b73fc4
gnu: spice-protocol: Update to 0.12.14. 
* gnu/packages/spice.scm (spice-protocol): Update to 0.12.14.
 2018-06-15 09:57:16 +02:00
Tobias Geerinckx-Rice 0ce92d74a2
gnu: python-pyrfc3339: Update to 1.1. 
* gnu/packages/time.scm (python-pyrfc3339): Update to 1.1.
 2018-06-15 09:57:16 +02:00
Tobias Geerinckx-Rice 5bc4188ffd
gnu: gource: Update to 0.49. 
* gnu/packages/version-control.scm (gource): Update to 0.49.
 2018-06-15 09:57:16 +02:00
Tobias Geerinckx-Rice d21fb90a27
gnu: perl-xml-libxml-simple: Update to 0.99. 
* gnu/packages/xml.scm (perl-xml-libxml-simple): Update to 0.99.
 2018-06-15 09:57:16 +02:00
Tobias Geerinckx-Rice 914c6f621e
gnu: fcitx-configtool: Update to 0.4.10. 
* gnu/packages/fcitx.scm (fcitx-configtool): Update to 0.4.10.
 2018-06-15 09:57:15 +02:00
Tobias Geerinckx-Rice 50ca5fb332
gnu: fcitx: Update to 4.2.9.6. 
* gnu/packages/fcitx.scm (fcitx): Update to 4.2.9.6.
[native-inputs]: Add extra-cmake-modules.
 2018-06-15 09:57:15 +02:00
Tobias Geerinckx-Rice 657bed34f4
gnu: fcitx: Use HTTPS home page. 
* gnu/packages/fcitx.scm (fcitx)[home-page]: Use HTTPS.
 2018-06-15 09:57:15 +02:00
Tobias Geerinckx-Rice 26d66a518c
gnu: perl-xml-xpath: Update to 1.42. 
* gnu/packages/xml.scm (perl-xml-xpath): Update to 1.42.
 2018-06-15 09:57:15 +02:00
Tobias Geerinckx-Rice 9332d70602
gnu: perl-xml-xpath: Propagate inputs. 
* gnu/packages/xml.scm (perl-xml-xpath)[inputs]: Rename this...
[propagated-inputs]: ...to this.
 2018-06-15 09:57:14 +02:00
Tobias Geerinckx-Rice 50632f0a8d
gnu: perl-xml-atom: Propagate inputs. 
* gnu/packages/xml.scm (perl-xml-atom)[inputs]: Rename to...
[propagated-inputs]: ...this, and...
[native-inputs]: ...remove duplicate packages from here.
 2018-06-15 09:57:14 +02:00
Tobias Geerinckx-Rice beb2d4be84
gnu: nickle: Update to 2.81. 
* gnu/packages/nickle.scm (nickle): Update to 2.81.
 2018-06-15 09:57:14 +02:00
Tobias Geerinckx-Rice 752ff6e9aa
gnu: r-cubature: Update to 1.4. 
* gnu/packages/cran.scm (r-cubature): Update to 1.4.
 2018-06-15 09:57:14 +02:00
Rutger Helling abde01f27d
gnu: neofetch: Update to 4.0.2. 
* gnu/packages/admin.scm (neofetch): Update to 4.0.2.
 2018-06-15 09:18:13 +02:00
Ricardo Wurmus cf9a29b24c
gnu: Add r-genomicinteractions. 
* gnu/packages/bioconductor.scm (r-genomicinteractions): New variable.
 2018-06-15 09:14:01 +02:00
Ricardo Wurmus a32279ffb6
gnu: Add r-interactionset. 
* gnu/packages/bioconductor.scm (r-interactionset): New variable.
 2018-06-15 09:14:01 +02:00
Rutger Helling 056402220e
gnu: innoextract: Update to 1.7. 
* gnu/packages/compression.scm (innoextract): Update to 1.7.
 2018-06-15 09:10:35 +02:00
Ricardo Wurmus 6ffdfe6a01
gnu: Add r-riboseqr. 
* gnu/packages/bioconductor.scm (r-riboseqr): New variable.
 2018-06-15 07:43:23 +02:00
Ricardo Wurmus 0490f9de88
gnu: Add r-riboprofiling. 
* gnu/packages/bioconductor.scm (r-riboprofiling): New variable.
 2018-06-15 07:43:22 +02:00
Ricardo Wurmus 609f4ad12f
gnu: Add r-chipcomp. 
* gnu/packages/bioconductor.scm (r-chipcomp): New variable.
 2018-06-15 07:43:22 +02:00
Ricardo Wurmus 2bece692a6
gnu: Add r-bsgenome-mmusculus-ucsc-mm9-masked. 
* gnu/packages/bioconductor.scm (r-bsgenome-mmusculus-ucsc-mm9-masked): New
variable.
 2018-06-15 07:43:22 +02:00
Ricardo Wurmus 6fbd759b13
gnu: Add r-bsgenome-hsapiens-ucsc-hg19-masked. 
* gnu/packages/bioconductor.scm (r-bsgenome-hsapiens-ucsc-hg19-masked): New
variable.
 2018-06-15 07:43:22 +02:00
Ricardo Wurmus dfac7eb917
gnu: Add r-bsgenome-dmelanogaster-ucsc-dm3-masked. 
* gnu/packages/bioconductor.scm (r-bsgenome-dmelanogaster-ucsc-dm3-masked):
New variable.
 2018-06-15 07:43:22 +02:00
Ricardo Wurmus bb15b581f7
gnu: Add r-bayseq. 
* gnu/packages/bioconductor.scm (r-bayseq): New variable.
 2018-06-15 07:43:22 +02:00
Leo Famulari b494bbe466
gnu: certbot, python-acme: Update to 0.25.1. 
* gnu/packages/tls.scm (certbot): Update 0.25.1.
(python-acme): Update to 0.25.1.
[native-inputs]: Add python-pytest.
[propagated-inputs]: Add python-requests-toolbelt.
 2018-06-14 19:38:56 -04:00
Leo Famulari 9297fc61cc
gnu: Go 1.10: Update to 1.10.3. 
* gnu/packages/golang.scm (go-1.10): Update to 1.10.3.
 2018-06-14 17:49:56 -04:00
Leo Famulari 96fd9a0e62
gnu: Go 1.9: Update to 1.9.7. 
* gnu/packages/golang.scm (go-1.9): Update to 1.9.7.
 2018-06-14 17:49:53 -04:00
Konrad Hinsen 565af91acc
gnu: emacs-racket-mode: Update and bug fix. 
* gnu/packages/emacs.scm (emacs-racket-mode): Update and bug fix.

- Update to the current commit
- Bug fix: include Racket files in addition to Emacs Lisp files

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-06-14 23:34:59 +02:00
Fis Trivial a8fb82a8ab
gnu: Add vowpal-wabbit. 
* gnu/packages/machine-learning.scm (vowpal-wabbit): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-06-14 23:34:59 +02:00
Fis Trivial 112c2c010b
gnu: Add lightgbm. 
* gnu/packages/machine-learning.scm (lightgbm): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-06-14 23:34:59 +02:00
Ludovic Courtès baed923682
self: Add 'guix-daemon' to the result. 
* gnu/packages/package-management.scm (guix-daemon): New variable.
* guix/self.scm (whole-package): Add #:daemon and honor it.
(compiled-guix): Pass #:daemon to 'whole-package'.
 2018-06-14 23:34:59 +02:00
Gábor Boskovits 0effadcad5
gnu: libressl: Update to 2.7.4 [fixes CVE-2018-{0495,0732}]. 
* gnu/packages/tls.scm (libressl): Update to 2.7.4.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2018-06-14 17:11:17 -04:00
Leo Famulari e3173fe18e
gnu: botan: Update to 2.6.0 [fixes CVE-2018-{9127,9860}]. 
* gnu/packages/crypto.scm (botan): Update to 2.6.0.
 2018-06-14 16:02:52 -04:00
Leo Famulari a4bae9af00
gnu: vdirsyncer: Update to 0.6.6. 
* gnu/packages/dav.scm (vdirsyncer): Update to 0.6.6.
[arguments]: Simplify the man-page building.
 2018-06-14 15:51:57 -04:00
Leo Famulari 44d1b9569b
gnu: python-click-log: Update to 0.3.2. 
* gnu/packages/python.scm (python-click-log): Update to 0.3.2.
 2018-06-14 15:51:56 -04:00
Leo Famulari b6c675c693
gnu: GnuPG 1.4: Update to 1.4.23. 
* gnu/packages/gnupg.scm (gnupg-1): Update to 1.4.23.
[source]: Remove patch.
* gnu/packages/patches/gnupg-1.4-CVE-2018-12020.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Remove it.
 2018-06-14 15:35:23 -04:00
Tobias Geerinckx-Rice ef0d765605
gnu: python-freezegun: Update to 0.3.10. 
* gnu/packages/check.scm (python-freezegun): Update to 0.3.10.
 2018-06-14 18:55:52 +02:00
Tobias Geerinckx-Rice 19611b7a0a
gnu: python-freezegun: Return #t from phase. 
* gnu/packages/check.scm (python-freezegun)[arguments]: Substitute
INVOKE for SYSTEM*.
 2018-06-14 18:55:52 +02:00
Tobias Geerinckx-Rice d518261f05
gnu: cppcheck: Update to 1.84. 
* gnu/packages/check.scm (cppcheck): Update to 1.84.
 2018-06-14 18:55:51 +02:00
Tobias Geerinckx-Rice 6dd5f2ea63
gnu: qrencode: Update to 4.0.2. 
* gnu/packages/aidc.scm (qrencode): Update to 4.0.2.
 2018-06-14 18:55:51 +02:00
Tobias Geerinckx-Rice f71619648c
gnu: perl-dbi: Update to 1.641. 
* gnu/packages/databases.scm (perl-dbi): Update to 1.641.
 2018-06-14 18:55:51 +02:00
Tobias Geerinckx-Rice 1ba7a62362
gnu: python-nose-timer: Update to 0.7.2. 
* gnu/packages/check.scm (python-nose-timer): Update to 0.7.2.
[source]: Remove patch...
* gnu/packages/patches/python-nose-timer-drop-ordereddict.patch:
...delete file...
* gnu/local.mk (dist_patch_DATA): ...and remove it.
 2018-06-14 18:55:46 +02:00
Rutger Helling ecbac51a0c
gnu: openrct2: Downgrade to 0.1.1. 
* gnu/packages/games.scm (openrct2): Downgrade to 0.1.1 due to audio not
working on 0.1.2+. Needs fixing before upgrade.
[arguments]: Add "-DDOWNLOAD_TITLE_SEQUENCES=OFF" configure-flag. Remove
'fixgcc7 and 'get-rid-of-errors phases.
[native-inputs]: Remove gcc@7.
 2018-06-14 18:14:30 +02:00
Clément Lassieur 43fa239717
gnu: emacs-password-store: Update to 1.7.2. 
* gnu/packages/emacs.scm (emacs-password-store): Update to 1.7.2.
[propagated-inputs]: Add emacs-with-editor.
 2018-06-14 17:37:04 +02:00
Clément Lassieur ab6f400531
gnu: password-store: Update to 1.7.2. 
* gnu/packages/password-utils.scm (password-store): Update to 1.7.2.
[source]: Remove 'password-store-gnupg-compat.patch'.
* gnu/packages/patches/password-store-gnupg-compat.patch: Remove file.
* gnu/local.mk (dist_patch_DATA): Remove it.
 2018-06-14 17:36:59 +02:00
Ricardo Wurmus f715f102e0
gnu: fio: Update to 3.7. 
* gnu/packages/benchmark.scm (fio): Update to 3.7.
 2018-06-14 15:41:09 +02:00
Ricardo Wurmus 53131eab2d
gnu: Add minimap2. 
* gnu/packages/bioinformatics.scm (minimap2): New variable.
 2018-06-14 13:51:15 +02:00
Ricardo Wurmus ce573b1128
gnu: pigx-bsseq: Update to 0.0.9. 
* gnu/packages/bioinformatics.scm (pigx-bsseq): Update to 0.0.9.
 2018-06-14 12:56:49 +02:00
Ludovic Courtès ea0a06cee2
Remove 'guix-register' and its traces. 
* Makefile.am (SH_TESTS): Remove tests/guix-register.sh.
* build-aux/pre-inst-env.in (GUIX_REGISTER): Remove.
* gnu/build/install.scm (directives): Remove outdated comment.
* gnu/build/vm.scm (root-partition-initializer): Update comment.
* gnu/packages/package-management.scm (guix-register): Remove.
* guix/config.scm.in (%sbindir, %guix-register-program): Remove.
* guix/scripts/system.scm (install): Adjust docstring.
* guix/self.scm (make-config.scm): Remove #:guix.  Do not generate
%sbindir and %guix-register-program.
(specification->package): Remove "guix".
* nix/guix-register/guix-register.cc: Remove.
* nix/libstore/store-api.cc (decodeValidPathInfo): Remove.
* nix/libstore/store-api.hh (decodeValidPathInfo): Remove declaration.
* nix/local.mk (sbin_PROGRAMS, guix_register_SOURCES)
(guix_register_CPPFLAGS, guix_register_LDFLAGS): Remove.
* tests/guix-register.sh: Remove.
 2018-06-14 11:17:00 +02:00
Ludovic Courtès c5a2e1ffcb
build: Require Guile-SQLite3. 
The next commits make (sqlite3) an indirect dependency of (gnu build
install), which is itself used by (guix scripts system), hence this new
requirement.

* configure.ac: Error out when $guix_cv_have_recent_guile_sqlite3 is
false.  Remove HAVE_GUILE_SQLITE3 Automake conditional.
* Makefile.am (MODULES, SCM_TESTS): Remove HAVE_GUILE_SQLITE3 conditions.
* doc/guix.texi (Requirements): Add Guile-SQLite3.
* README: Ditto.
* gnu/packages/package-management.scm (guix)[propagated-inputs]: Add
GUILE-SQLITE3.
[arguments]: In 'wrap-program' phase, take guile-sqlite3 into account.
 2018-06-14 11:16:58 +02:00
Efraim Flashner 03439df66f
gnu: libgcrypt: Fix CVE-2018-0495. 
* gnu/packages/gnupg.scm (libgcrypt)[replacement]: New field.
(libgcrypt/fixed): New package.
 2018-06-14 11:06:48 +03:00
Clément Lassieur 85d79a79e4
gnu: Add python-dns-lexicon. 
* gnu/packages/python.scm (python-dns-lexicon, python2-dns-lexicon): New
variables.
 2018-06-14 08:18:06 +02:00
Clément Lassieur b863b50d80
gnu: Add python-pynamecheap. 
* gnu/packages/python.scm (python-pynamecheap, python2-pynamecheap): New
variables.
 2018-06-14 08:18:02 +02:00
Clément Lassieur f4adbe7405
gnu: Add python-tldextract. 
* gnu/packages/python.scm (python-tldextract, python2-tldextract): New
variables.
 2018-06-14 08:17:59 +02:00
Clément Lassieur 0dc572380b
gnu: Add python-requests-file. 
* gnu/packages/python.scm (python-requests-file, python2-requests-file): New
variables.
 2018-06-14 08:17:55 +02:00
Arun Isaac 40c1b61aac
gnu: Add tmate. 
* gnu/packages/terminals.scm (tmate): New variable.
 2018-06-14 11:20:31 +05:30
Tobias Geerinckx-Rice 0b5c16c07f
Fix typo in (gnu packages gtk) header. 
* gnu/packages/gtk.scm: Fix ‘Coypright’ typo.
 2018-06-14 04:30:50 +02:00
Tobias Geerinckx-Rice b262aba733
gnu: python-gnupg: Return #t from phase. 
* gnu/packages/gnupg.scm (python-gnupg)[arguments]: Substitute INVOKE
for SYSTEM*.
 2018-06-14 04:02:14 +02:00
Tobias Geerinckx-Rice ff76a1e9ca
gnu: python-gnupg: Update to 0.4.3. 
* gnu/packages/gnupg.scm (python-gnupg): Update to 0.4.3.
[arguments]: Remove obsolete substitution.
 2018-06-14 04:01:21 +02:00
Alex Vong a1a3b25dfe
gnu: custom-gcc: Fix regex used for matching executables. 
Fixes <https://bugs.gnu.org/31561>.

* gnu/packages/gcc.scm (custom-gcc)[arguments]: Fix regex used for matching
broken or conflicting executables.

Signed-off-by: Danny Milosavljevic <dannym@scratchpost.org>
 2018-06-14 01:30:44 +02:00
Tobias Geerinckx-Rice 2b78360138
gnu: sssd: Update to 1.16.2. 
* gnu/packages/sssd.scm (sssd): Update to 1.16.2.
[native-inputs]: Add libxml2.
 2018-06-14 00:52:30 +02:00
Ricardo Wurmus 844cc1c8f3
gnu: pigx-scrnaseq: Update to 0.0.5. 
* gnu/packages/bioinformatics.scm (pigx-scrnaseq): Update to 0.0.5.
[inputs]: Add python-magic.
 2018-06-13 22:30:55 +02:00
Nicolas Goaziou 4bf474b243
gnu: emacs-orgalist: Update to 1.8. 
* gnu/packages/emacs.scm (emacs-orgalist): Update to 1.8.
 2018-06-13 21:38:18 +02:00
Kei Kebreau 935cb931b5
gnu: emacspeak: Update to 48.0. 
* gnu/packages/emacs.scm (emacspeak): Update to 48.0.
[arguments]: Use 'invoke'.  In the 'install' phase, add additional
installation directories and fix the launch script substitution.
[inputs]: Add emacs and perl.
[native-inputs]: Remove emacs-minimal.
 2018-06-13 14:44:13 -04:00
Efraim Flashner a8ef66f94d
gnu: mesa: Build tegra driver on arm systems. 
* gnu/packages/gl.scm (mesa)[arguments]: Add 'tegra' to the
gallium-drivers list for armhf-linux and aarch64-linux.
 2018-06-13 19:37:04 +03:00
Ricardo Wurmus 6ccd88e8cb
gnu: r-factoextra: Fix syntax error. 
* gnu/packages/cran.scm (r-factoextra)[description]: Fix syntax error.
 2018-06-13 16:42:29 +02:00
Ricardo Wurmus 13b8dcf589
gnu: r-seurat: Update to 2.3.2. 
* gnu/packages/bioinformatics.scm (r-seurat): Update to 2.3.2.
[propagated-inputs]: Add r-hdf5r.
 2018-06-13 15:14:37 +02:00
Ricardo Wurmus 5b2a339e19
gnu: r-s4vectors: Update to 0.18.3. 
* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.18.3.
 2018-06-13 15:14:37 +02:00
Ricardo Wurmus 5b730eba3e
gnu: r-biocviews: Update to 1.48.1. 
* gnu/packages/bioinformatics.scm (r-biocviews): Update to 1.48.1.
 2018-06-13 15:14:37 +02:00
Ricardo Wurmus c812f46817
gnu: r-rjson: Update to 0.2.20. 
* gnu/packages/web.scm (r-rjson): Update to 0.2.20.
 2018-06-13 15:14:37 +02:00
Ricardo Wurmus 242ffd6c80
gnu: r-zoo: Update to 1.8-2. 
* gnu/packages/statistics.scm (r-zoo): Update to 1.8-2.
 2018-06-13 15:14:37 +02:00
Ricardo Wurmus 6221de1879
gnu: r-rmarkdown: Update to 1.10. 
* gnu/packages/statistics.scm (r-rmarkdown): Update to 1.10.
[propagated-inputs]: Add r-tinytex.
 2018-06-13 15:14:37 +02:00
Ricardo Wurmus d086829d39
gnu: r-highr: Update to 0.7. 
* gnu/packages/statistics.scm (r-highr): Update to 0.7.
 2018-06-13 15:14:37 +02:00
Ricardo Wurmus 26a53dd957
gnu: r-stringi: Update to 1.2.3. 
* gnu/packages/statistics.scm (r-stringi): Update to 1.2.3.
 2018-06-13 15:14:37 +02:00
Ricardo Wurmus 3399dc97fc
gnu: r-munsell: Update to 0.5.0. 
* gnu/packages/statistics.scm (r-munsell): Update to 0.5.0.
 2018-06-13 15:14:37 +02:00
Ricardo Wurmus 0357db53c8
gnu: r-rgooglemaps: Update to 1.4.2. 
* gnu/packages/geo.scm (r-rgooglemaps): Update to 1.4.2.
 2018-06-13 15:14:37 +02:00
Ricardo Wurmus 1df9a0cf47
gnu: r-reticulate: Update to 1.8. 
* gnu/packages/cran.scm (r-reticulate): Update to 1.8.
 2018-06-13 15:14:37 +02:00
Ricardo Wurmus fa7236f1b3
gnu: r-later: Update to 0.7.3. 
* gnu/packages/cran.scm (r-later): Update to 0.7.3.
 2018-06-13 15:14:37 +02:00
Ricardo Wurmus 36dc359186
gnu: r-radiant-data: Update to 0.9.5. 
* gnu/packages/cran.scm (r-radiant-data): Update to 0.9.5.
[propagated-inputs]: Remove r-plyr; add r-glue, r-plotly, r-readxl, r-rlang,
and r-writexl.
 2018-06-13 15:14:37 +02:00
Ricardo Wurmus 014818b691
gnu: r-cubature: Update to 1.3-13. 
* gnu/packages/cran.scm (r-cubature): Update to 1.3-13.
 2018-06-13 15:14:37 +02:00
Ricardo Wurmus 8d2f8aeddf
gnu: r-extradistr: Update to 1.8.9. 
* gnu/packages/cran.scm (r-extradistr): Update to 1.8.9.
 2018-06-13 15:14:37 +02:00
Ricardo Wurmus 1268a995da
gnu: r-statnet-common: Update to 4.1.2. 
* gnu/packages/cran.scm (r-statnet-common): Update to 4.1.2.
[propagated-inputs]: Add r-coda.
 2018-06-13 15:14:37 +02:00
Ricardo Wurmus 2bce7795c1
gnu: r-stringdist: Update to 0.9.5.1. 
* gnu/packages/cran.scm (r-stringdist): Update to 0.9.5.1.
 2018-06-13 15:14:37 +02:00