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Author SHA1 Message Date
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
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
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
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
Ricardo Wurmus d0396c8ea1
gnu: r-rcpproll: Update to 0.3.0. 
* gnu/packages/cran.scm (r-rcpproll): Update to 0.3.0.
 2018-06-13 15:14:37 +02:00
Ricardo Wurmus a151f1e60a
gnu: r-extremes: Update to 2.0-9. 
* gnu/packages/cran.scm (r-extremes): Update to 2.0-9.
 2018-06-13 15:14:37 +02:00
Ricardo Wurmus d87130cb2e
gnu: r-sp: Update to 1.3-1. 
* gnu/packages/cran.scm (r-sp): Update to 1.3-1.
 2018-06-13 15:14:37 +02:00
Ricardo Wurmus 5fa9be1118
gnu: r-getoptlong: Update to 0.1.7. 
* gnu/packages/cran.scm (r-getoptlong): Update to 0.1.7.
 2018-06-13 15:14:37 +02:00
Ricardo Wurmus 7b60ab3df7
gnu: r-circlize: Update to 0.4.4. 
* gnu/packages/cran.scm (r-circlize): Update to 0.4.4.
 2018-06-13 15:14:37 +02:00
Ricardo Wurmus 693b4d0ba5
gnu: r-globaloptions: Update to 0.1.0. 
* gnu/packages/cran.scm (r-globaloptions): Update to 0.1.0.
 2018-06-13 15:14:37 +02:00
Ricardo Wurmus 846325a8d8
gnu: Add r-writexl. 
* gnu/packages/cran.scm (r-writexl): New variable.
 2018-06-13 15:14:37 +02:00
Ricardo Wurmus 546fc4aa55
gnu: Add r-hdf5r. 
* gnu/packages/cran.scm (r-hdf5r): New variable.
 2018-06-13 15:14:37 +02:00
Ricardo Wurmus 0c9868aa5b
gnu: Add r-nbclust. 
* gnu/packages/cran.scm (r-nbclust): New variable.
 2018-06-13 11:51:28 +02:00
Ricardo Wurmus f22bfee945
gnu: Add r-factoextra. 
* gnu/packages/cran.scm (r-factoextra): New variable.
 2018-06-13 11:51:28 +02:00
Ricardo Wurmus e83841a296
gnu: Add r-factominer. 
* gnu/packages/cran.scm (r-factominer): New variable.
 2018-06-13 11:51:28 +02:00
Ricardo Wurmus cbf6017d83
gnu: Add r-flashclust. 
* gnu/packages/cran.scm (r-flashclust): New variable.
 2018-06-13 11:51:28 +02:00
Ricardo Wurmus 141e43bd4e
gnu: Add r-ellipse. 
* gnu/packages/cran.scm (r-ellipse): New variable.
 2018-06-13 11:51:28 +02:00
Ricardo Wurmus 5cbaaee83f
gnu: Add r-ggpubr. 
* gnu/packages/cran.scm (r-ggpubr): New variable.
 2018-06-13 11:51:28 +02:00
Ricardo Wurmus 5219c5c585
gnu: Add r-ggsignif. 
* gnu/packages/cran.scm (r-ggsignif): New variable.
 2018-06-13 11:51:28 +02:00
Ricardo Wurmus 85df1a8631
gnu: Add r-ggsci. 
* gnu/packages/cran.scm (r-ggsci): New variable.
 2018-06-13 11:51:28 +02:00
Rutger Helling 0c6ade0be6
gnu: openrct2: Update to 0.2.0. 
* gnu/packages/games.scm (openrct2-title-sequences): New variable.
* gnu/packages/games.scm (openrct2-objects): New variable.
* gnu/packages/games.scm (openrct2): Update to 0.2.0.
[arguments]: Add phases 'fix-usr-share-path&add-data, 'fix-gcc7 and
'get-rid-of-errors.
[inputs]: Add icu4c, openrct2-objects, openrct2-title-sequences.
[native-inputs]: Add gcc@7.
 2018-06-13 11:33:03 +02:00
Rutger Helling 14618a1ebb
gnu: vkquake: Update to 1.00.0. 
* gnu/packages/games.scm (vkquake): Update to 1.00.0.
 2018-06-13 08:47:14 +02:00
Rutger Helling 4b3480d62f
gnu: cheese: Update to 3.28.0. 
* gnu/packages/gnome.scm (cheese): Update to 3.28.0.
 2018-06-13 08:44:02 +02:00
Leo Famulari 3a30ae05ae
gnu: openimageio: Update to 1.7.19. 
* gnu/packages/graphics.scm (openimageio): Update to 1.7.19.
 2018-06-13 00:31:58 -04:00
Tobias Geerinckx-Rice 502a822dfd
gnu: tor: Update to 0.3.3.7. 
* gnu/packages/tor.scm (tor): Update to 0.3.3.7.
 2018-06-12 22:59:29 +02:00
Hartmut Goebel b5792b9cb8
gnu: Add qtwebglplugin. 
* gnu/packages/qt.scm (qtwebglplugin): New variable.

Co-authored-by: 宋文武 <iyzsong@member.fsf.org>
 2018-06-12 22:47:01 +02:00
Hartmut Goebel 359e30c9ea
gnu: Add qtwebview. 
* gnu/packages/qt.scm (qtwebview): New variable.
 2018-06-12 22:47:01 +02:00
Leo Famulari bea07c7f55
gnu: python-llfuse: Update to 1.3.3. 
* gnu/packages/python.scm (python-llfuse, python2-llfuse): Update to 1.3.3.
 2018-06-12 15:30:30 -04:00
Jan Nieuwenhuizen 67cb662a31
gnu: mes: Update to 0.15. 
* gnu/packages/mes.scm (mes): Update to 0.15.
 2018-06-12 19:21:10 +02:00
Efraim Flashner 6921e95ae8
gnu: mame: Fix renaming executable. 
* gnu/packages/emulators.scm (mame)[arguments]: Only rename 'mame64' to
'mame' when 'mame64' exists.
 2018-06-12 19:08:47 +03:00
Mathieu Othacehe a9e7d6564b
gnu: multipath-tools: Fix build. 
(multipath-tools)[arguments]: Pass -n to gzip to avoid timestamp related
warnings causing build failures.
 2018-06-12 16:13:16 +02:00
Ludovic Courtès 90977eb55e
gnu: guile-bytestructures: Update to 1.0.3. 
* gnu/packages/guile.scm (guile-bytestructures): Update to 1.0.3.
(guile-git)[arguments]: Remove.  The workaround for
<https://github.com/TaylanUB/scheme-bytestructures/issues/30> is no
longer needed.
 2018-06-12 15:23:34 +02:00
Ludovic Courtès b5edc47912
gnu: flann: Fix builds with CMake >= 3.11. 
* gnu/packages/patches/flann-cmake-3.11.patch: New file.
* gnu/packages/maths.scm (flann)[source]: Use it.
* gnu/local.mk (dist_patch_DATA): Add it.
 2018-06-12 15:23:34 +02:00
宋文武 feed5194b1
gnu: python-urwid, python2-urwid: Update to 2.0.1. 
* gnu/packages/python.scm (python-urwid, python2-urwird): Update to 2.0.1.
 2018-06-12 20:51:32 +08:00
Leo Famulari 66266d3290
gnu: borg: Update to 1.1.6. 
* gnu/packages/backup.scm (borg): Update to 1.1.6.
[arguments]: Remove the 'adjust-msgpack-dependency' phase because it has been
adopted upstream.
 2018-06-12 08:28:21 -04:00
Ben Sturmfels e68e4a906f
gnu: fabric: Disable problematic tests. 
Reported by Ricardo Wurmus <rekado@elephly.net> at
<https://debbugs.gnu.org/cgi/bugreport.cgi?bug=26647#8>.

* gnu/packages/admin.scm (fabric): Add custom check phase to disable two tests.
 2018-06-12 19:47:12 +08:00
宋文武 7714a06943
gnu: Add skopeo. 
* gnu/packages/virtualization.scm (skopeo): New variable.
 2018-06-12 19:31:18 +08:00
宋文武 efdaf8def0
gnu: Add umoci. 
* gnu/packages/virtualization.scm (umoci): New variable.
 2018-06-12 19:30:52 +08:00
宋文武 3d39130926
gnu: Add libostree. 
* gnu/packages/package-management.scm (libostree): New variable.
 2018-06-12 19:28:18 +08:00
Efraim Flashner c71cc133ec
gnu: vim-syntastic: Update to 3.9.0. 
* gnu/packages/vim.scm (vim-syntastic): Update to 3.9.0.
[source]: Switch to git checkout.
 2018-06-12 11:16:06 +03:00
Efraim Flashner 261348e20d
gnu: vim-fugitive: Update to 2.3. 
* gnu/packages/vim.scm (vim-fugitive): Update to 2.3.
 2018-06-12 11:16:06 +03:00
Efraim Flashner 35a7e5742f
gnu: vim-airline: Update to 0.9. 
* gnu/packages/vim.scm (vim-airline): Update to 0.9.
[source]: Switch to git checkout.
 2018-06-12 11:16:05 +03:00
Efraim Flashner b37404740e
gnu: speedtest-cli: Update to 2.0.2. 
* gnu/packages/networking.scm (speedtest-cli): Update to 2.0.2.
[source]: Switch to a git checkout.
 2018-06-12 11:16:05 +03:00
Efraim Flashner 5b47ea9462
gnu: font-gnu-unifont: Update to 11.0.01. 
* gnu/packages/fonts.scm (font-gnu-unifont): Update to 11.0.01.
 2018-06-12 11:16:02 +03:00
Rutger Helling 14cb7966ba
gnu: wine-staging: Update to 3.10. 
* gnu/packages/wine.scm (wine-staging): Update to 3.10.
 2018-06-12 10:15:03 +02:00
Rutger Helling 32872458a6
gnu: wine-staging-patchset-data: Update to 3.10. 
* gnu/packages/wine.scm (wine-staging-patchset-data): Update to 3.10.
 2018-06-12 10:15:03 +02:00
Mark H Weaver 95d9d95a04
gnu: linux-libre: Update to 4.17.1. 
* gnu/packages/linux.scm (%linux-libre-version): Update to 4.17.1.
(%linux-libre-hash): Update hash.
 2018-06-12 02:57:20 -04:00
Mark H Weaver f3ad05efd9
gnu: linux-libre@4.14: Update to 4.14.49. 
* gnu/packages/linux.scm (%linux-libre-4.14-version): Update to 4.14.49.
(%linux-libre-4.14-hash): Update hash.
 2018-06-12 02:56:19 -04:00
Christopher Baines 2c5f8aad92
gnu: Add emacs-puppet-mode. 
* gnu/packages/emacs.scm (emacs-puppet-mode): New variable.
 2018-06-12 07:49:42 +01:00
Christopher Baines e7a25d2ae7
gnu: elixir: Enable more tests and remove patch. 
Previously, due to issues in the erlang package, many tests would fail, and
the package would also nondeterministically fail to build. This is now
fixed (by patching occurrences of /bin/sh in the erlang package), so all the
tests can be run.

* gnu/packages/elixir.scm (elixir)[source]: Remove patches.
[arguments]: Remove the fix-or-disable-tests phase. Add a new set-home phase
to set the HOME environment variable prior to running the tests.
* gnu/packages/patches/elixir-disable-failing-tests.patch: Delete this file.
* gnu/local.mk: Remove now deleted patch.
 2018-06-12 07:46:18 +01:00
Christopher Baines b5453aa7c3
gnu: erlang: Patch occurrences of /bin/sh in the source. 
Previously, the elixir package would often fail to build, as running :os:cmd
would fail, as /bin/sh doesn't exist when building the elixir package. These
changes fix that issue.

* gnu/packages/erlang.scm (erlang)[arguments]: Add new patch-/bin/sh phase to
replace hardcoded references to /bin/sh with a file in the store.
 2018-06-12 07:44:05 +01:00
Christopher Baines 9b25e1d124
gnu: erlang: Delete the bootstrap phase. 
This fails for the erlang package, as the gnu build system attempts to execute
the bootstrap directory.

* gnu/packages/erlang.scm (erlang)[arguments]: Delete the bootstrap phase.
 2018-06-12 07:43:59 +01:00
Marius Bakke 6321ce42ab
gnu: xf86-video-vmware: Update to 13.3.0. 
* gnu/packages/xorg.scm (xf86-video-vmware): Update to 13.3.0.
 2018-06-11 23:23:10 +02:00
Marius Bakke 4276b0dc1e
gnu: xf86-input-evdev: Update to 2.10.6. 
* gnu/packages/xorg.scm (xf86-input-evdev): Update to 2.10.6.
 2018-06-11 23:15:36 +02:00
Marius Bakke 7b7e30ca29
gnu: xf86-input-synaptics: Update to 1.9.1. 
* gnu/packages/xorg.scm (xf86-input-synaptics): Update to 1.9.1.
 2018-06-11 23:13:26 +02:00
Marius Bakke 8cfcb6ba2a
gnu: xf86-video-fbdev: Update to 0.5.0. 
* gnu/packages/xorg.scm (xf86-video-fbdev): Update to 0.5.0.
 2018-06-11 23:10:04 +02:00
Ludovic Courtès b63f6c0192
gnu: python2: Deprecate "python@2". 
* gnu/packages/python.scm (python2-called-python): New variable.
 2018-06-11 18:23:24 +02:00
Rutger Helling 4d65c1c304
gnu: wine-staging: Add vkd3d support. 
* gnu/packages/wine.scm (wine-staging)[inputs]: Add vkd3d.
 2018-06-11 18:22:10 +02:00
Rutger Helling 85c7f29a25
gnu: Add vkd3d. 
* gnu/packages/vulkan.scm (vkd3d): New variable.
 2018-06-11 18:22:10 +02:00
Rutger Helling 7f54065487
gnu: shaderc: Update to be8e087. 
* gnu/packages/vulkan.scm (shaderc): Update to be8e087.
[arguments]: Enable tests.
[inputs]: Add googletest.
 2018-06-11 18:22:10 +02:00
Rutger Helling fcfef82592
gnu: glslang: Update to 32d3ec3. 
* gnu/packages/vulkan.scm (glslang): Update to 32d3ec3.
 2018-06-11 18:22:10 +02:00
Rutger Helling ba10e0b8e1
gnu: spirv-tools: Update to fe2fbee. 
* gnu/packages/vulkan.scm (spirv-tools): Update to fe2fbee.
[arguments]: Disable tests. Remove "-DCMAKE_INSTALL_LIBDIR" configure-flag.
 2018-06-11 18:22:10 +02:00
Rutger Helling c7c86de669
gnu: spirv-headers: Update to 3ce3e49. 
* gnu/packages/vulkan.scm (spirv-headers): Update to 3ce3e49. Use INVOKE.
 2018-06-11 18:22:10 +02:00
Efraim Flashner 6da97043ea
gnu: Add ovmf-arm. 
* gnu/packages/firmware.scm (ovmf-arm): New variable.
 2018-06-11 19:16:23 +03:00
Efraim Flashner cb97be5f83
gnu: Add ovmf-aarch64. 
* gnu/packages/firmware.scm (ovmf-aarch64): New variable.
 2018-06-11 19:16:23 +03:00
Marius Bakke ff3fd83969
gnu: libraw: Update to 0.18.12 [security fixes]. 
* gnu/packages/photo.scm (libraw): Update to 0.18.12.
 2018-06-11 18:08:21 +02:00
Marius Bakke 9526d86141
gnu: libndp: Update to 1.7. 
* gnu/packages/networking.scm (libndp): Update to 1.7.
 2018-06-11 18:05:54 +02:00
Marius Bakke f24cfb6cc3
gnu: webkitgtk: Update to 2.20.3 [security fixes]. 
Fixes CVE-2018-4190, CVE-2018-4199, CVE-2018-4218, CVE-2018-4222,
CVE-2018-4232, CVE-2018-4233, CVE-2018-4246 and CVE-2018-11646.

* gnu/packages/webkit.scm (webkitgtk): Update to 2.20.3.
 2018-06-11 17:56:56 +02:00
Marius Bakke 6e5a6e641a
gnu: efivar: Update to 36. 
* gnu/packages/linux.scm (efivar): Update to 36.
 2018-06-11 17:54:31 +02:00
Marius Bakke 21a21c20da
gnu: ldb: Delete bundled libraries from the source. 
* gnu/packages/samba.scm (ldb)[source](snippet): New field.
 2018-06-11 17:54:30 +02:00
Marius Bakke 4ee30d6aa2
gnu: ldb: Update to 1.4.0. 
* gnu/packages/samba.scm (ldb): Update to 1.4.0.
[inputs]: Add LMDB.
 2018-06-11 17:54:30 +02:00
Pierre Neidhardt 8bf7f741e9
gnu: Add Add emacs-wgrep-helm. 
* gnu/packages/emacs.scm (emacs-wgrep-helm): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-06-11 15:19:02 +02:00
Pierre Neidhardt 50a1f9264d
gnu: Add emacs-package-lint. 
* gnu/packages/emacs.scm (emacs-package-lint): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-06-11 15:19:02 +02:00
Pierre Neidhardt 00f3774067
gnu: Add emacs-image+. 
* gnu/packages/emacs.scm (emacs-image+): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-06-11 15:19:02 +02:00
Pierre Neidhardt bdfebc4b74
gnu: Add emacs-helm-pass. 
* gnu/packages/emacs.scm (emacs-helm-pass): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-06-11 15:19:02 +02:00
Pierre Neidhardt 2f3aa1d309
gnu: Add emacs-helm-mu. 
* gnu/packages/emacs.scm (emacs-helm-mu): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-06-11 15:19:02 +02:00
Pierre Neidhardt 1e75852629
gnu: Add emacs-helm-ls-git. 
* gnu/packages/emacs.scm (emacs-helm-ls-git): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-06-11 15:19:02 +02:00
Rouby Pierre-Antoine 76a2b27897
gnu: Add go-github-com-spf13-pflag. 
* gnu/packages/golang.scm (go-github-com-spf13-pflag): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-06-11 15:19:01 +02:00
Rouby Pierre-Antoine bcb2179085
gnu: Add go-github-com-jonboulle-clockwork. 
* gnu/packages/golang.scm (go-github-com-jonboulle-clockwork): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-06-11 15:19:01 +02:00
Rouby Pierre-Antoine e8cdf560b0
gnu: Add go-github-com-gorilla-mux. 
* gnu/packages/golang.scm (go-github-com-gorilla-mux): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-06-11 15:19:01 +02:00
Tobias Geerinckx-Rice 14299d21f2
gnu: iproute2: Update to 4.17.0. 
* gnu/packages/linux.scm (iproute): Update to 4.17.0.
 2018-06-11 14:08:31 +02:00
Tobias Geerinckx-Rice 41ea698a4b
gnu: libfilezilla: Update to 0.12.3. 
* gnu/packages/ftp.scm (libfilezilla): Update to 0.12.3.
 2018-06-11 14:08:24 +02:00
Oleg Pykhalov e0cc7f669b
gnu: emacs-emacsql: Replace mysql with mariadb input. 
* gnu/packages/emacs.scm (emacs-emacsql)[inputs]: Replace 'mysql' with
'mariadb'.
 2018-06-11 11:47:50 +03:00
Ludovic Courtès 8b3aea9d9e
gnu: guix: Update to 77a1aac. 
* gnu/packages/package-management.scm (guix): Update to 77a1aac.
 2018-06-10 23:32:00 +02:00
宋文武 670a5e5430
gnu: keepalived: Install info documentation. 
* gnu/packages/cluster.scm (keepalived)[arguments]: Add phases 'build-info'
and 'install-info'.
[native-inputs]: Add texinfo.
 2018-06-10 23:42:14 +08:00
宋文武 af09dabf70
gnu: Add keepalived. 
* gnu/packages/cluster.scm: New file.
* gnu/local.mk (GNU_SYSTEM_MODULES): Add it.
 2018-06-10 22:57:01 +08:00
宋文武 4dd1fb79f7
gnu: Add libnfnetlink. 
* gnu/packages/linux.scm (libnfnetlink): New variable.
 2018-06-10 22:57:01 +08:00
Danny Milosavljevic fc51c11b9d
gnu: mumble: Fix build with Boost 1.66. 
Fixes <https://bugs.gnu.org/31775>.

* gnu/packages/patches/mumble-1.2.19-abs.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/telephony.scm (mumble)[source]: Add it.
 2018-06-10 16:03:35 +02:00
宋文武 e6c8199b66
gnu: nix: Update to 2.0.4. 
* gnu/packages/package-management.scm (nix): Update to 2.0.4.
 2018-06-10 21:38:32 +08:00
Nicolas Goaziou 1bfde769f6
gnu: musescore: Fix build against Qt 5.11. 
* gnu/packages/music.scm (musescore)[arguments]: Remove Webkit support, since
  it is replaced with Qt WebEngine in Qt 5.11.  Add missing include line.
[inputs]: Remove "qtwekbit".
 2018-06-10 13:47:25 +02:00
Alex Vong 09b21b77cc
gnu: heimdal: Update to 7.5.0. 
* gnu/packages/kerberos.scm (heimdal): Update to 7.5.0.
[source]: Update source uri.  Remove patches.
[arguments]: Adjust #:configure-flags and build phases accordingly.
[inputs]: Add sqlite.
[native-inputs]: Add texinfo and unzip.
* gnu/packages/patches/heimdal-CVE-2017-6594.patch,
  gnu/packages/patches/heimdal-CVE-2017-11103.patch: Remove files.
* gnu/local.mk (dist_patch_DATA): Remove them.

Co-authored-by: 宋文武 <iyzsong@member.fsf.org>
 2018-06-10 16:00:45 +08:00
Kei Kebreau b7e2fcf05e
gnu: milkytracker: Update to 1.02.00. 
* gnu/packages/music.scm (milkytracker): Update to 1.02.00.
 2018-06-09 18:32:47 -04:00
Leo Famulari 65956ad352
gnu: GnuPG 1.4: Fix CVE-2018-12020. 
* gnu/packages/patches/gnupg-1.4-CVE-2018-12020.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/gnupg.scm (gnupg-1)[source]: Use it.
 2018-06-09 17:50:03 -04:00
Julien Lepiller 5aa4ea6a2b
gnu: Add maven-resolver-provider. 
* gnu/packages/maven.scm (maven-resolver-provider): New variable.
 2018-06-09 23:25:35 +02:00
Julien Lepiller b218504026
gnu: Add maven-shared-utils. 
gnu/packages/maven.scm (maven-shared-utils): New variable.
 2018-06-09 23:25:26 +02:00
Julien Lepiller 18736663ed
gnu: Add maven-repository-metadata. 
* gnu/packages/maven.scm (maven-repository-metadata): New variable.
 2018-06-09 23:25:24 +02:00
Julien Lepiller 90fe8797cd
gnu: Add maven-resolver-impl. 
* gnu/packages/maven.scm (maven-resolver-impl): New variable.
 2018-06-09 23:25:21 +02:00
Julien Lepiller 516db3b97a
gnu: Add maven-model-builder. 
* gnu/packages/maven.scm (maven-model-builder): New variable.
 2018-06-09 23:25:18 +02:00
Julien Lepiller 3a5572ae76
gnu: Add maven-settings-builder. 
* gnu/packages/maven.scm (maven-settings-builder): New variable.
 2018-06-09 23:25:16 +02:00
Julien Lepiller 18110e45a6
gnu: Add maven-settings. 
* gnu/packages/maven.scm (maven-settings): New variable.
 2018-06-09 23:25:15 +02:00
Julien Lepiller f084641a01
gnu: Add maven-builder-support. 
* gnu/packages/maven.scm (maven-builder-support): New variable.
 2018-06-09 23:25:13 +02:00
Julien Lepiller d55503a6ab
gnu: Add maven-model. 
* gnu/packages/maven.scm (maven-model): New variable.
 2018-06-09 23:25:11 +02:00
Julien Lepiller 458687d586
gnu: Add maven-artifact. 
* gnu/packages/maven.scm (maven-artifact): New variable.
* gnu/packages/patches/maven-generate-component-xml.patch: New file.
* gnu/packages/patches/maven-generate-javax-inject-named.patch: New
file.
* gnu/local.mk (dist_patch_DATA): Add them.
 2018-06-09 23:24:52 +02:00
Julien Lepiller 816db9668c
gnu: po4a: Update to 0.53. 
* gnu/packages/gettext.scm (po4a): Update to 0.53.
[source]: Update to newer github source location.
[arguments]: Disable two failing tests.
 2018-06-09 23:08:13 +02:00
Efraim Flashner 8fc55f36c4
gnu: terminology: Update to 1.2.1. 
* gnu/packages/enlightenment.scm (terminology): Update to 1.2.1.
 2018-06-09 23:01:17 +03:00
Efraim Flashner 216c726673
gnu: gnupg: Update to 2.2.8 (fixes CVE-2018-12020). 
* gnu/packages/gnupg.scm (gnupg): Update to 2.2.8.
 2018-06-09 22:46:22 +03:00
Christopher Baines 5bf37e9c38
gnu: openttd: Add patch to fix compilation. 
* gnu/packages/games.scm (openttd)[source]: Add a unreleased upstream patch to
fix building OpenTTD with ICU 61.
 2018-06-09 12:25:32 +01:00
Christopher Baines aa7587633b
gnu: rhythmbox: Add a unreleased patch from upstream. 
* gnu/packages/gnome.scm (rhythmbox)[source]: Add patch from the upstream Git
repository, as without this, the package fails to build.
 2018-06-09 11:11:28 +01:00
宋文武 d6fb0985a6
gnu: btrfs-progs: Fix build by disabling tests. 
* gnu/packages/linux.scm (btrfs-progs)[#:arguments]: Add '#:tests? #f'.
 2018-06-09 17:18:27 +08:00
宋文武 927846b3ab
gnu: lxc: Update to 3.0.1. 
* gnu/packages/virtualization.scm (lxc): Update to 3.0.1.
 2018-06-09 15:45:16 +08:00
Rutger Helling 945b119fac
gnu: nzbget: Update to 20.0. 
* gnu/packages/networking.scm (nzbget): Update to 20.0.
 2018-06-09 02:30:07 +02:00
Nicolas Goaziou c8b2fd2866
gnu: mame: New variable. 
* gnu/packages/emulators.scm (mame): New variable.
 2018-06-09 00:20:00 +02:00
Nicolas Goaziou d597dda6e0
gnu: asio: New variable. 
* gnu/packages/networking.scm (asio): New variable.
 2018-06-09 00:20:00 +02:00
Oleg Pykhalov da23cc000e
gnu: Add emacs-ivy-yasnippet. 
* gnu/packages/emacs.scm (emacs-ivy-yasnippet): New public variable.
 2018-06-08 23:19:38 +03:00
Gábor Boskovits c315d37058
gnu: exim: Add libnsl input. 
* gnu/packages/mail.scm (exim)[inputs]: Add libnsl.

Signed-off-by: Oleg Pykhalov <go.wigust@gmail.com>
 2018-06-08 22:20:28 +03:00
Oleg Pykhalov ca82bdfdfb
gnu: twitchy: Install 'rofi-twitchy'. 
* gnu/packages/video.scm (twitchy): Install 'rofi-twitchy'.
 2018-06-08 20:30:29 +03:00
Ricardo Wurmus cbc1c27b67
gnu: rcas-web: Update to 0.0.5. 
* gnu/packages/bioinformatics.scm (rcas-web): Update to 0.0.5.
 2018-06-08 17:39:24 +02:00
Kei Kebreau 129948dcbd
gnu: debootstrap: Substitute chroot in 'patch-source' phase. 
* gnu/packages/debian.scm (debootstrap)[arguments]: In 'patch-source' phase,
substitute chroot in the debootstrap script file.
[inputs]: Add coreutils.
 2018-06-08 11:07:51 -04:00
Rouby Pierre-Antoine ad3a580716
gnu: hpcguix-web: Update to commit '87cb516'. 
* gnu/packages/web.scm (hpcguix-web): Update to commit '87cb516'.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-06-08 17:04:24 +02:00
Pierre Neidhardt daa9e89d56
gnu: Add emacs-helm-flycheck. 
* gnu/packages/emacs.scm (emacs-helm-flycheck): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-06-08 17:04:24 +02:00
Pierre Neidhardt 49fd039217
gnu: Add emacs-helm-exwm. 
* gnu/packages/emacs.scm (emacs-helm-exwm): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-06-08 17:04:23 +02:00
Pierre Neidhardt 5a949f5b30
gnu: Add emacs-helm-emms. 
* gnu/packages/emacs.scm (emacs-helm-emms): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-06-08 17:04:23 +02:00
Pierre Neidhardt 0b4e4efe97
gnu: Add emacs-helm-descbinds. 
* gnu/packages/emacs.scm (emacs-helm-descbinds): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-06-08 17:04:23 +02:00
Pierre Neidhardt 3540c6eb2b
gnu: Add emacs-helm-company. 
* gnu/packages/emacs.scm (emacs-helm-company): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-06-08 17:04:23 +02:00
Pierre Neidhardt 2dcea9b446
gnu: Add emacs-google-translate. 
* gnu/packages/emacs.scm (emacs-google-translate): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-06-08 17:04:23 +02:00
Pierre Neidhardt a62d872fdf
gnu: Add emacs-gif-screencast. 
* gnu/packages/emacs.scm (emacs-gif-screencast): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-06-08 17:04:23 +02:00
Tobias Geerinckx-Rice fafeeaa233
gnu: ruby-rack-protection: Update to 2.0.2. 
* gnu/packages/ruby.scm (ruby-rack-protection): Update to 2.0.2.
 2018-06-08 16:00:18 +02:00
Tobias Geerinckx-Rice d2a48984fc
gnu: r-fastcluster: Update to 1.1.25. 
* gnu/packages/statistics.scm (r-fastcluster): Update to 1.1.25.
 2018-06-08 16:00:18 +02:00
Tobias Geerinckx-Rice a1eabab1a3
gnu: opensmtpd: Clarify phase name. 
* gnu/packages/mail.scm (opensmtpd)[arguments]: Rename
‘install-compatibilitymode’ to ‘install-compatibility-links’ and avoid
needless abbrevs while at it.
 2018-06-08 16:00:17 +02:00
Tobias Geerinckx-Rice 19fed04915
gnu: opensmtpd: Patch FHS assumptions. 
This fixes the following failure...

  # smtpctl show message 9275c3fbeccbae93
  execl: No such file or directory

...due to the absence of ‘/bin/cat’ on GuixSD.

* gnu/packages/mail.scm (opensmtpd)[arguments]: Add
‘patch-FHS-file-names’ phase.
 2018-06-08 16:00:17 +02:00
Oleg Pykhalov 2dfb9bbf23
gnu: duplicity: Update to 0.7.17. 
* gnu/packages/backup.scm (duplicity): Update to 0.7.17.
 2018-06-08 16:25:44 +03:00
Oleg Pykhalov c0888cefdf
gnu: Add python-fasteners. 
* gnu/packages/python.scm (python-fasteners, python2-fasteners): New
variables.
 2018-06-08 16:25:44 +03:00
Ludovic Courtès 849a1399ca
gnu: doxygen: Work around GCC ICE on armhf-linux. 
Reported by Mark H Weaver <mhw@netris.org>
at <https://debbugs.gnu.org/cgi/bugreport.cgi?bug=31708#10>.

* gnu/packages/patches/doxygen-gcc-ice.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/documentation.scm (doxygen)[inputs]: Add "gcc-ice-patch"
on armhf-* only.
[arguments]: Add 'apply-gcc-patch' phase on armhf-* only.
 2018-06-08 15:23:39 +02:00
宋文武 cd8ece22bf
gnu: redis: Update to 4.0.9. 
* gnu/packages/database.scm (redis): Update to 4.0.9.
 2018-06-08 20:27:30 +08:00
Paul Garlick 0b88f7e7a7
gnu: ikiwiki: Add inputs for CGI script and remove duplicate input. 
* gnu/packages/web.scm (ikiwiki)[inputs]: Add perl-cgi-formbuilder and
perl-db-file.  Remove perl-uri duplicate.  Sort 'perl-*' inputs
alphabetically.

Signed-off-by: 宋文武 <iyzsong@member.fsf.org>
 2018-06-08 20:27:30 +08:00
Paul Garlick f52de1e17f
gnu: Add perl-cgi-formbuilder. 
* gnu/packages/web.scm (perl-cgi-formbuilder): New variable.

Signed-off-by: 宋文武 <iyzsong@member.fsf.org>
 2018-06-08 20:27:30 +08:00
Mark H Weaver 0b2fd1600f
gnu: linux-libre@4.9: Update to 4.9.107. 
* gnu/packages/linux.scm (linux-libre-4.9): Update to 4.9.107.
 2018-06-07 23:38:28 -04:00
Mark H Weaver b09dc3b911
gnu: linux-libre@4.4: Update to 4.4.136. 
* gnu/packages/linux.scm (linux-libre-4.4): Update to 4.4.136.
 2018-06-07 23:37:46 -04:00
Tobias Geerinckx-Rice 20860819d6
gnu: ruby-asciidoctor: Update description. 
Synchronise with upstream README.

* gnu/packages/ruby.scm (ruby-asciidoctor)[description]: Add PDF.
 2018-06-07 23:58:26 +02:00
Tobias Geerinckx-Rice 4ee41a6ac1
gnu: inxi: Fix up synopsis & description. 
* gnu/packages/admin.scm (inxi)[synopsis]: Fix typo.
[description]: Use @code{}.
 2018-06-07 23:58:26 +02:00
Tobias Geerinckx-Rice 7a83eb37ad
gnu: libngspice: Update to 28. 
* gnu/packages/engineering.scm (libngspice): Update to 28.
 2018-06-07 23:58:25 +02:00
Tobias Geerinckx-Rice ec425ca3a6
gnu: libngspice: Use C-locale date format. 
* gnu/packages/engineering.scm (libngspice): Use a more standard
(C-locale) date format when forging timestamps.
 2018-06-07 23:57:39 +02:00
Tobias Geerinckx-Rice 10ee03c1df
gnu: python-pyxdg: Return #t from phases. 
* gnu/packages/freedesktop.scm (python-pyxdg)[arguments]: Substitute
INVOKE for SYSTEM*.
 2018-06-07 23:57:39 +02:00
Tobias Geerinckx-Rice 5f82a9d5cc
gnu: seabios: Return #t from all phases. 
* gnu/packages/firmware.scm (seabios)[arguments]: Return #t from
the ‘install’ phase.
 2018-06-07 23:57:38 +02:00
Tobias Geerinckx-Rice edf075987c
gnu: gnuastro: Add TIFF support. 
This adds ~3.6 MiB (3.6%) to gnuastro's now-103.9 MiB closure.

* gnu/packages/astronomy.scm (gnuastro)[inputs]: Add libtiff and zlib.
 2018-06-07 23:57:38 +02:00
Tobias Geerinckx-Rice 33031faa4e
gnu: xmlsec: Update to 1.2.26. 
* gnu/packages/xml.scm (xmlsec): Update to 1.2.26.
 2018-06-07 23:57:38 +02:00
Tobias Geerinckx-Rice 6d727bf4c7
gnu: xcalib: Update to 0.10. 
* gnu/packages/xdisorg.scm (xcalib): Update to 0.10.
[home-page]: Switch to new upstream.
[source]: Use GIT-FETCH.  Add xcalib-update-man-page.patch.
[build-system]: Switch to CMAKE-BUILD-SYSTEM.
[arguments]: Remove the old build system's arguments.
[inputs]: Add libxrandr.
 2018-06-07 23:57:38 +02:00
Tobias Geerinckx-Rice d35135fa9e
gnu: perl-net-http: Update to 6.18. 
* gnu/packages/web.scm (perl-net-http): Update to 6.18.
 2018-06-07 23:57:37 +02:00
Tobias Geerinckx-Rice c727262d5f
gnu: perl-cgi: Update to 4.38. 
* gnu/packages/web.scm (perl-cgi): Update to 4.38.
 2018-06-07 23:57:37 +02:00
Danny Milosavljevic 5e88194661
gnu: qucs: Patch bootstrapping scripts. 
* gnu/packages/engineering.scm (qucs)[arguments]<#:phases>[patch-bootstrap]:
New phase.
 2018-06-07 23:23:40 +02:00
Theodoros Foradis 394b89ae04
gnu: qucs-s: Update to 0.0.20. 
* gnu/packages/engineering.scm (qucs-s): Update to 0.0.20.
[arguments]: Modify patch-paths phase to work with version 0.0.20.

Signed-off-by: Danny Milosavljevic <dannym@scratchpost.org>
 2018-06-07 23:23:40 +02:00
Theodoros Foradis fc3c88ec9c
gnu: lapack-3.5: Delete package. 
* gnu/packages/maths.scm (lapack-3.5): Delete package.

Signed-off-by: Danny Milosavljevic <dannym@scratchpost.org>
 2018-06-07 23:23:40 +02:00
Theodoros Foradis ac04601a82
gnu: xyce-serial: Update to 6.8. 
* gnu/packages/engineering.scm (xyce-serial): Update to 6.8.
[inputs]: Replace lapack-3.5 with lapack.
* gnu/packages/engineering.scm (xyce-prallel):
[arguments]: Update configure flags to work with 6.8 version.

Signed-off-by: Danny Milosavljevic <dannym@scratchpost.org>
 2018-06-07 23:23:40 +02:00
Theodoros Foradis d73482b408
gnu: trilinos-serial-xyce: Update to 12.12.1. 
* gnu/packages/engineering.scm (trilinos-serial-xyce): Update to 12.12.1.
[arguments]: Add delete-tribits phase.
[inputs]: Replace lapack-3.5 with lapack.

Signed-off-by: Danny Milosavljevic <dannym@scratchpost.org>
 2018-06-07 23:23:40 +02:00
Theodoros Foradis ecf8d2a935
gnu: libngspice: Update to 27. 
* gnu/packages/engineering.scm (libngspice): Update to 27.

Signed-off-by: Danny Milosavljevic <dannym@scratchpost.org>
 2018-06-07 23:23:40 +02:00
Theodoros Foradis 4f12a62d18
gnu: qucs: Build from git to fix bug. 
* gnu/packages/engineering.scm (qucs): Add TODO comment.
[source]: Use git commit b4f27d9.
[native-inputs]: Add autoconf, automake, flex and bison.

Signed-off-by: Danny Milosavljevic <dannym@scratchpost.org>
 2018-06-07 23:23:34 +02:00
Ricardo Wurmus bcc2e0ed2e
gnu: r-rcas: Update to 1.6.0. 
* gnu/packages/bioinformatics.scm (r-rcas): Update to 1.6.0.
[source]: Fetch from bioconductor.
[native-inputs]: Remove r-knitr.
[propagated-inputs]: Add r-biocgenerics, r-biostrings, r-cowplot, r-dbi,
r-ggseqlogo, r-knitr, r-pheatmap, r-proxy, r-rsqlite, and r-s4vectors.
 2018-06-07 22:51:00 +02:00
Ricardo Wurmus e67acae706
gnu: Add r-ggseqlogo. 
* gnu/packages/cran.scm (r-ggseqlogo): New variable.
 2018-06-07 22:51:00 +02:00
Rutger Helling 8ec919404f
gnu: Add deprecated-package vulkan-icd-loader. 
* gnu/packages/vulkan.scm (vulkan-icd-loader): New variable.
 2018-06-07 13:34:13 +02:00
Efraim Flashner bb63502f0b
gnu: ovmf: Simplify build. 
* gnu/packages/firmware.scm (ovmf)[arguments]: Change custom 'build-ia32
phase to replace 'build. Remove unneeded substitutions in 'configure,
'build and 'build-x64. Shorten 'build and 'build-x64 phases.
 2018-06-07 12:20:47 +03:00
Ricardo Wurmus 6d095c4cab
gnu: star: Update to 2.6.0c. 
* gnu/packages/bioinformatics.scm (star): Update to 2.6.0c.
[source]: Fetch from git.
 2018-06-07 11:09:54 +02:00
Ricardo Wurmus 54179e2463
gnu: libreoffice: Update to 6.0.5.1. 
* gnu/packages/patches/libreoffice-icu.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/libreoffice.scm (libreoffice): Update to 6.0.5.1.
[source]: Add patch.
[inputs]: Add libepubgen and libqxp.
[arguments]: Adjust "prepare-src" phase.
 2018-06-07 11:09:54 +02:00
Ricardo Wurmus e47e1f3311
gnu: orcus: Update to 0.13.4. 
* gnu/packages/libreoffice.scm (orcus): Update to 0.13.4.
 2018-06-07 11:09:54 +02:00
Ricardo Wurmus a3f2425e5d
gnu: ixion: Update to 0.13.0. 
* gnu/packages/libreoffice.scm (ixion): Update to 0.13.0.
 2018-06-07 11:09:54 +02:00
Ricardo Wurmus 4e4dcd476e
gnu: Add libqxp. 
* gnu/packages/libreoffice.scm (libqxp): New variable.
 2018-06-07 11:09:54 +02:00
Ricardo Wurmus 38be0f4245
gnu: Add libepubgen. 
* gnu/packages/libreoffice.scm (libepubgen): New variable.
 2018-06-07 11:09:54 +02:00
Adam Zimmerman d6dd64af37
gnu: opensmtpd: Fix crash on table authentication. 
* gnu/packages/patches/opensmtpd-fix-crash.patch: New patch.
* gnu/packages/mail.scm (opensmtpd)[source]: Use it.
* gnu/local.mk (dist_patch_DATA): Add it.

Signed-off-by: Tobias Geerinckx-Rice <me@tobias.gr>
 2018-06-07 03:57:42 +02:00
Tobias Geerinckx-Rice 6acc671bef
gnu: jbig2dec: Update source and home page URIs. 
The old downloads.ghostscript.com returns a bogus 200 response, while
the new home page lists a different source.

Reported by Gábor Boskovits <boskovits@gmail.com>.

* gnu/packages/image.scm (jbig2dec)[source, home-page]: Update URIs.
 2018-06-07 03:57:41 +02:00
Nicolas Goaziou 4a007e2db9
gnu: scribus: Fix build. 
* gnu/packages/scribus.scm (scribus)[arguments]: Re-introduce fix for
  "ImportError: No module named _sysconfigdata_nd".
 2018-06-07 00:30:13 +02:00
Ricardo Wurmus 116ca65b58
Merge branch 'master' into core-updates 2018-06-06 22:43:37 +02:00
Nicolas Goaziou 25133ca172
gnu: colobot: Update to 0.1.11.1-alpha. 
* gnu/packages/games.scm (colobot): Update to 0.1.11.1-alpha.
[native-inputs]: Update "colobot-data" and "colobot-music" to 0.1.11.1-alpha.
 2018-06-06 19:16:21 +02:00
Nicolas Goaziou 89a651964a
gnu: scribus: Add "libzmf" dependency 
* gnu/packages/scribus.scm (scribus)[inputs]: Add "libzmf".
 2018-06-06 18:34:45 +02:00
Nicolas Goaziou fec8d80cd1
gnu: scribus: Update to 1.5.4. 
* gnu/packages/scribus.scm (scribus): Update to 1.5.4.
[source]: Remove patches.
[arguments]: Remove `patch-source' phase.
 2018-06-06 18:33:38 +02:00
Rutger Helling e6fcf903ec
gnu: vulkan-loader: Update URL and change name. 
* gnu/packages/emulators.scm: Change references from 'vulkan-icd-loader' to
'vulkan-loader'.
* gnu/packages/games.scm: Change references from 'vulkan-icd-loader' to
'vulkan-loader'.
* gnu/packages/video.scm: Change references from 'vulkan-icd-loader' to
'vulkan-loader'.
* gnu/packages/vulkan.scm (vulkan-loader): Rename from 'vulkan-icd-loader' to
'vulkan-loader'. Update URL and hash.
* gnu/packages/wine.scm: Change references from 'vulkan-icd-loader' to
'vulkan-loader'.
 2018-06-06 16:48:47 +02:00
Rutger Helling 7ea56cdec0
gnu: you-get: Update to 0.4.1077. 
* gnu/packages/video.scm (you-get): Update to 0.4.1077.
 2018-06-06 14:39:24 +02:00
Rutger Helling c7a2f7b999
gnu: diffoscope: Update to 95. 
* gnu/packages/package-management.scm (diffoscope): Update to 95.
 2018-06-06 14:39:24 +02:00
Rutger Helling 89fc8aef8c
gnu: epiphany: Update to 3.28.2.1. 
* gnu/packages/gnome.scm (epiphany): Update to 3.28.2.1.
 2018-06-06 14:39:24 +02:00
Rutger Helling f9036105e6
gnu: gnome-disk-utility: Update to 3.28.3. 
* gnu/packages/gnome.scm (gnome-disk-utility): Update to 3.28.3.
 2018-06-06 14:39:23 +02:00
Rutger Helling 9cf329aecc
gnu: gnome-terminal: Update to 3.28.2. 
* gnu/packages/gnome.scm (gnome-terminal): Update to 3.28.2.
 2018-06-06 14:39:23 +02:00
Rutger Helling 6a29c8d344
gnu: gedit: Update to 3.28.1. 
* gnu/packages/gnome.scm (gedit): Update to 3.28.1.
 2018-06-06 14:39:23 +02:00
Ricardo Wurmus e32db0fa0f
gnu: vigra: Disable broken test. 
* gnu/packages/image.scm (vigra)[arguments]: Add phase "disable-broken-test";
enable parallel build.
 2018-06-06 13:15:21 +02:00
Rutger Helling c648781cec
gnu: lynx: Update to 2.8.9dev.19. 
* gnu/packages/web-browsers.scm (lynx): Update to 2.8.9dev.19.
 2018-06-06 12:46:40 +02:00
Efraim Flashner 73c0e477e5
gnu: esmtp: Replace 'bootstrap phase. 
* gnu/packages/mail.scm (esmtp)[arguments]: Use custom 'autoconf phase
to replace default 'bootstrap phase.
 2018-06-06 13:11:50 +03:00
Efraim Flashner a34dfa249c
gnu: can-utils: Remove 'bootstrap phase. 
* gnu/packages/networking.scm (can-utils)[arguments]: Remove unnecessary
'bootstrap phase.
 2018-06-06 13:11:47 +03:00
Tobias Geerinckx-Rice 37b561e4ed
gnu: gerbv: Update to 2.6.2. 
* gnu/packages/engineering.scm (gerbv): Update to 2.6.2.
[arguments]: Remove ‘autoconf’ phase...
[native-inputs]: ...and remove its dependencies.
 2018-06-06 06:12:23 +02:00
Tobias Geerinckx-Rice d193903e0c
gnu: linsmith: Update to 0.99.31. 
* gnu/packages/engineering.scm (linsmith): Update to 0.99.31.
 2018-06-06 06:12:22 +02:00
Tobias Geerinckx-Rice 6e3d48c207
gnu: linsmith: Use HTTPS home page. 
* gnu/packages/engineering.scm (linsmith)[home-page]: Use HTTPS.
 2018-06-06 06:12:22 +02:00
Tobias Geerinckx-Rice 3b295d3f4b
gnu: python-lmdb: Update to 0.94. 
* gnu/packages/databases.scm (python-lmdb): Update to 0.94.
 2018-06-06 06:12:22 +02:00
Tobias Geerinckx-Rice fcf29a7fbb
gnu: debootstrap: Update to 1.0.101. 
* gnu/packages/debian.scm (debootstrap): Update to 1.0.101.
 2018-06-06 06:12:22 +02:00
Tobias Geerinckx-Rice 1a16b925f2
gnu: tomb: Update to 2.5. 
* gnu/packages/crypto.scm (tomb): Update to 2.5.
[inputs, arguments]: Add util-linux for ‘findmnt’.
 2018-06-06 06:12:21 +02:00
Tobias Geerinckx-Rice 115af78e32
gnu: cfitsio: Update to 3.450. 
* gnu/packages/astronomy.scm (cfitsio): Update to 3.450.
 2018-06-06 06:12:21 +02:00
Tobias Geerinckx-Rice 9566bb82e5
gnu: gnuastro: Update to 0.6. 
* gnu/packages/astronomy.scm (gnuastro): Update to 0.6.
 2018-06-06 06:12:21 +02:00
Tobias Geerinckx-Rice 60b0c25222
gnu: wcslib: Fix build. 
* gnu/packages/astronomy.scm (wcslib)[arguments]: Skip the default
‘install-license-files’ phase.  Don't build or test in parallel.
 2018-06-06 06:12:21 +02:00
Tobias Geerinckx-Rice 4f12e5cc7c
gnu: inxi: Update to 3.0.11-1. 
* gnu/packages/admin.scm (inxi): Update to 3.0.11-1.
 2018-06-06 06:12:21 +02:00
Tobias Geerinckx-Rice b740a30527
gnu: inxi: Use GIT-FETCH. 
* gnu/packages/admin.scm (inxi)[source]: Use GIT-FETCH.
[native-inputs]: Remove tar.
[arguments]: Adjust accordingly.
 2018-06-06 06:12:20 +02:00
Tobias Geerinckx-Rice 55f5556e24
gnu: inxi: Fix man page location. 
* gnu/packages/admin.scm (inxi)[arguments]: Install man page to
/share/man instead of /share/doc/man.
 2018-06-06 06:12:20 +02:00
Tobias Geerinckx-Rice bba082a1f8
gnu: ruby-asciidoctor: Use HTTPS home page. 
* gnu/packages/ruby.scm (ruby-asciidoctor)[home-page]: Use HTTPS.
 2018-06-06 06:12:20 +02:00
Tobias Geerinckx-Rice 9933a8e739
gnu: ruby-asciidoctor: Update to 1.5.7.1. 
* gnu/packages/ruby.scm (ruby-asciidoctor): Update to 1.5.7.1.
 2018-06-06 06:12:20 +02:00
Tobias Geerinckx-Rice 24a2622712
gnu: ruby-eventmachine: Use working home page. 
* gnu/packages/ruby.scm (ruby-eventmachine)[home-page]: Update URI.
 2018-06-06 06:12:19 +02:00
Tobias Geerinckx-Rice c207fa5e6c
gnu: ruby-eventmachine: Update to 1.2.7. 
* gnu/packages/ruby.scm (ruby-eventmachine): Update to 1.2.7.
 2018-06-06 06:12:19 +02:00
Tobias Geerinckx-Rice 58021db4d2
gnu: ruby-connection-pool: Update to 2.2.2. 
* gnu/packages/ruby.scm (ruby-connection-pool): Update to 2.2.2.
 2018-06-06 06:12:19 +02:00
Tobias Geerinckx-Rice 15dd85f0c3
gnu: linkchecker: Update to 9.4.0. 
* gnu/packages/web.scm (linkchecker): Update to 9.4.0.
[source]: Use GIT-FETCH.
[inputs]: Add python2-dnspython and python2-pyxdg.
[arguments]: Remove ‘remove-python-requests-version’ phase.
[license]: Remove licences of unbundled inputs.
 2018-06-06 06:12:19 +02:00
Tobias Geerinckx-Rice fe04975281
gnu: xf86-input-wacom: Update to 0.36.1. 
* gnu/packages/xdisorg.scm (xf86-input-wacom): Update to 0.36.1.
[source]: Update URI.
 2018-06-06 06:12:18 +02:00
Tobias Geerinckx-Rice 0ac68e7268
gnu: libwacom: Update to 0.30. 
* gnu/packages/xdisorg.scm (libwacom): Update to 0.30.
[source]: Update URI.
 2018-06-06 06:12:18 +02:00
Tobias Geerinckx-Rice 81dc1d1220
gnu: libwacom, xf86-input-wacom: Update home page. 
‘The Linux Wacom Project has moved.’
-- <http://linuxwacom.sourceforge.net/wiki>

* gnu/packages/xdisorg.scm (libwacom, xf86-input-wacom)[home-page]:
Update URI.
 2018-06-06 06:12:18 +02:00
Leo Famulari d83c9fcb7b
gnu: darktable: Update to 2.4.4. 
* gnu/packages/photo.scm (darktable): Update to 2.4.4.
 2018-06-06 00:05:54 -04:00
Leo Famulari f83eadd2ad
gnu: Update Syncthing to 0.14.48. 
*  gnu/packages/syncthing.scm (syncthing): Update to 0.14.48.
 2018-06-05 20:35:52 -04:00
Leo Famulari a624be49a2
gnu: go-github-com-chmduquesne-rollinghash-adler32: Update to 0.0.0-2.abb8cba. 
* gnu/packages/syncthing.scm (go-github-com-chmduquesne-rollinghash-adler32):
Update to 0.0.0-2.abb8cba.
 2018-06-05 20:35:49 -04:00
Ricardo Wurmus ca8de35e90
Merge branch 'master' into core-updates 2018-06-05 23:44:11 +02:00
Ricardo Wurmus 42639cc980
gnu: qtractor: Update to 0.9.1. 
* gnu/packages/music.scm (qtractor): Update to 0.9.1.
[arguments]: Add phase "fix-build-with-qt-5.11".
 2018-06-05 23:43:12 +02:00
Mark H Weaver db89d31876
gnu: linux-libre: Update to 4.17. 
* gnu/packages/linux.scm (%linux-libre-version): Update to 4.17.
(%linux-libre-hash): Update hash.
* gnu/packages/aux-files/linux-libre/4.16-arm.conf,
gnu/packages/aux-files/linux-libre/4.16-arm64.conf,
gnu/packages/aux-files/linux-libre/4.16-i686.conf,
gnu/packages/aux-files/linux-libre/4.16-x86_64.conf: Delete files.
* gnu/packages/aux-files/linux-libre/4.17-arm.conf,
gnu/packages/aux-files/linux-libre/4.17-arm64.conf,
gnu/packages/aux-files/linux-libre/4.17-i686.conf,
gnu/packages/aux-files/linux-libre/4.17-x86_64.conf: New files.
* Makefile.am (AUX_FILES): Adjust accordingly.
 2018-06-05 17:21:03 -04:00
Mark H Weaver 704051b258
gnu: linux-libre@4.14: Update to 4.14.48. 
* gnu/packages/linux.scm (%linux-libre-4.14-version): Update to 4.14.48.
(%linux-libre-4.14-hash): Update hash.
 2018-06-05 17:20:57 -04:00
Mark H Weaver 4418c59005
gnu: linux-libre@4.9: Update to 4.9.106. 
* gnu/packages/linux.scm (linux-libre-4.9): Update to 4.9.106.
 2018-06-05 17:20:53 -04:00
Ricardo Wurmus b4a145fa71
gnu: yoshimi: Update to 1.5.8. 
* gnu/packages/music.scm (yoshimi): Update to 1.5.8.
 2018-06-05 23:18:10 +02:00
Efraim Flashner 396aab8e69
gnu: freedoom: Fix compilation. 
* gnu/packages/games.scm (freedoom)[arguments]: Remove 'bootstrap phase.
 2018-06-05 22:53:48 +03:00
Efraim Flashner d88884fa3b
gnu: arc-theme: Replace bootstrap phase. 
* gnu/packages/gmome.scm (arc-theme)[arguments]: Replace 'boostrap phase
with a custom phase.
 2018-06-05 22:53:45 +03:00
Efraim Flashner f1c6de3735
gnu: tilda: Replace bootstrap phase. 
* gnu/packages/terminals.scm (tilda)[arguments]: Remove custom
'bootstrap phase and use it to replace default bootstrap phase.
 2018-06-05 22:10:49 +03:00
Ricardo Wurmus 909301591d
gnu: Add sjcount. 
* gnu/packages/bioinformatics.scm (sjcount): New variable.
 2018-06-05 15:42:44 +02:00
Ricardo Wurmus a64e30ed9e
gnu: Remove duplicate definition of r-heatmaply. 
* gnu/packages/cran.scm (r-heatmaply): Remove duplicate.
 2018-06-05 13:59:54 +02:00
Ricardo Wurmus d0f3427433
gnu: Remove duplicate definition of r-heatmaply. 
* gnu/packages/cran.scm (r-heatmaply): Remove duplicate.
 2018-06-05 13:59:15 +02:00
Ricardo Wurmus 1ee581973a
gnu: r-heatmaply: Add r-knitr. 
* gnu/packages/cran.scm (r-heatmaply)[propagated-inputs]: Add r-knitr.
 2018-06-05 13:51:27 +02:00
Ricardo Wurmus 6da3aa3763
gnu: r-heatmaply: Add r-knitr. 
* gnu/packages/cran.scm (r-heatmaply)[propagated-inputs]: Add r-knitr.
 2018-06-05 13:50:29 +02:00
Ricardo Wurmus e53152c72d
gnu: dropseq-tools: Remove failing phase. 
* gnu/packages/bioinformatics.scm (dropseq-tools)[arguments]: Delete
"generate-jar-indices" phase.
 2018-06-05 13:12:13 +02:00
Ricardo Wurmus 0c68f7fd9b
gnu: java-bouncycastle: Disable tests. 
* gnu/packages/java.scm (java-bouncycastle)[arguments]: Disable tests.
 2018-06-05 12:49:41 +02:00
Ricardo Wurmus 9cc66d75a2
gnu: pigx-scrnaseq: Use only one variant of Picard. 
* gnu/packages/bioinformatics.scm (pigx-scrnaseq)[inputs]: Replace
"java-picard" with "java-picard-2.10.3".
 2018-06-05 11:26:34 +02:00
Ricardo Wurmus 1f94ba9408
gnu: java-picard: Delete failing build phase. 
* gnu/packages/bioinformatics.scm (java-picard)[arguments]: Delete
"generate-jar-indices" phase.
 2018-06-05 11:26:08 +02:00
Ricardo Wurmus 1ed386fc26
gnu: java-cisd-jhdf5: Delete failing build phase. 
* gnu/packages/java.scm (java-cisd-jhdf5)[arguments]: Delete build phase
"generate-jar-indices".
 2018-06-05 11:17:03 +02:00
Ricardo Wurmus a993ad833e
gnu: java-picard-1.113: Delete failing build phase. 
* gnu/packages/bioinformatics.scm (java-picard-1.113)[arguments]: Delete
"generate-jar-indices" build phase.
 2018-06-05 11:15:21 +02:00
Ricardo Wurmus e847f402c1
gnu: java-picard-2.10.3: Delete failing build phase. 
* gnu/packages/bioinformatics.scm (java-picard-2.10.3)[arguments]: Delete
generate-jar-indices phase.
 2018-06-05 11:14:38 +02:00
Ricardo Wurmus d7e6fb6d7e
Merge branch 'master' into core-updates 2018-06-05 11:09:39 +02:00
Ricardo Wurmus 71c495c941
gnu: r-rtracklayer: Update to 1.40.3. 
* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.40.3.
 2018-06-05 10:40:42 +02:00
Ricardo Wurmus fb8c17baef
gnu: r-ranger: Update to 0.10.1. 
* gnu/packages/statistics.scm (r-ranger): Update to 0.10.1.
 2018-06-05 10:40:42 +02:00
Ricardo Wurmus c9a879ed54
gnu: r-np: Update to 0.60-8. 
* gnu/packages/cran.scm (r-np): Update to 0.60-8.
 2018-06-05 10:40:42 +02:00
Ricardo Wurmus 83d5c2e106
gnu: t-series: Update to 0.10-45. 
* gnu/packages/cran.scm (t-series): Update to 0.10-45.
 2018-06-05 10:40:42 +02:00
Ricardo Wurmus c152c6b361
gnu: r-ksamples: Update to 1.2-8. 
* gnu/packages/cran.scm (r-ksamples): Update to 1.2-8.
 2018-06-05 10:40:42 +02:00
Ricardo Wurmus d19e0690b9
gnu: r-methylkit: Update to 1.6.1. 
* gnu/packages/bioinformatics.scm (r-methylkit): Update to 1.6.1.
 2018-06-05 10:40:42 +02:00
Ricardo Wurmus 0da6afa286
gnu: r-bamsignals: Update to 1.12.1. 
* gnu/packages/bioinformatics.scm (r-bamsignals): Update to 1.12.1.
 2018-06-05 10:40:42 +02:00
Ricardo Wurmus 66ece08d05
Merge branch 'master' into core-updates 2018-06-05 09:59:27 +02:00
Tobias Geerinckx-Rice 4bf0a1f8d1
gnu: p11-kit: Update to 0.23.12. 
* gnu/packages/tls.scm (p11-kit): Update to 0.23.12.
 2018-06-05 03:19:48 +02:00
Mark H Weaver 8b71684a20
gnu: elfutils: Disable test suite on MIPS. 
* gnu/packages/elf.scm (elfutils)[arguments]: Add (#:tests? #f) on MIPS.
 2018-06-04 21:19:35 -04:00
Tobias Geerinckx-Rice 46fce96881
gnu: beets: Return #t from phases. 
* gnu/packages/music.scm (beets)[arguments]: Substitute INVOKE for
SYSTEM* and return #t from all phases.
 2018-06-05 03:19:26 +02:00
Tobias Geerinckx-Rice 123f86d898
gnu: nano: Update to 2.9.8. 
* gnu/packages/nano.scm (nano): Update to 2.9.8.
 2018-06-05 03:18:46 +02:00
Tobias Geerinckx-Rice 0d35a95417
gnu: python-pycurl: Update to 7.43.0.2. 
* gnu/packages/python-web.scm (python-pycurl): Update to 7.43.0.2.
 2018-06-05 03:18:46 +02:00
Tobias Geerinckx-Rice 4682d48363
gnu: fvwm: Update to 2.6.8. 
* gnu/packages/fvwm.scm (fvwm): Update to 2.6.8.
 2018-06-05 03:01:17 +02:00
Tobias Geerinckx-Rice f7b53e6855
gnu: perl-parse-yapp: Update to 1.21. 
* gnu/packages/perl.scm (perl-parse-yapp): Update to 1.21.
 2018-06-05 03:01:17 +02:00
Tobias Geerinckx-Rice b5dfccd7b6
gnu: perl-text-balanced: Update to 2.03. 
* gnu/packages/perl.scm (perl-text-balanced): Update to 2.03.
[source]: Update URI.
 2018-06-05 03:01:16 +02:00
Tobias Geerinckx-Rice 971b8381ff
gnu: perl-posix-strftime-compiler: Update to 0.42. 
* gnu/packages/perl.scm (perl-posix-strftime-compiler): Update to
0.42.
 2018-06-05 03:01:07 +02:00
Tobias Geerinckx-Rice 27f89be5c9
gnu: perl-moosex-methodattributes: Update to 0.31. 
* gnu/packages/perl.scm (perl-moosex-methodattributes): Update to
0.31.
 2018-06-05 03:00:58 +02:00
Tobias Geerinckx-Rice 91cb6eaf52
gnu: perl-module-install: Update to 1.19. 
* gnu/packages/perl.scm (perl-module-install): Update to 1.19.
[source]: Update URI.
 2018-06-05 01:31:32 +02:00
Tobias Geerinckx-Rice ed2e354b79
gnu: perl-memoize-expirelru: Update to 0.56. 
* gnu/packages/perl.scm (perl-memoize-expirelru): Update to 0.56.
[source]: Update URI.
 2018-06-05 01:31:32 +02:00
Tobias Geerinckx-Rice 01c6607af9
gnu: ccid, pcsc-lite: Move away from alioth.debian.org. 
* gnu/packages/security-token.scm (ccid, pcsc-lite)[source, home-page]:
Update upstream URI.
 2018-06-04 18:27:59 +02:00
Rutger Helling 19b662ea7c
gnu: ranger: Enable image support. 
* gnu/packages/disk.scm (ranger)[inputs]: Add 'w3m'.
[arguments]: Add wrapper for W3MIMGDISPLAY_PATH environment variable.
 2018-06-04 16:35:03 +02:00
Tobias Geerinckx-Rice fd17434249
gnu: lz4: Use HTTPS home page. 
* gnu/packages/compression.scm (lz4)[home-page]: Use HTTPS.
 2018-06-04 15:35:48 +02:00
Tobias Geerinckx-Rice b6315bc0d2
gnu: thermald: Update to 1.7.2. 
* gnu/packages/admin.scm (thermald): Update to 1.7.2.
[arguments]: Remove Upstart kluge as promised.
 2018-06-04 15:35:47 +02:00
Tobias Geerinckx-Rice 49d85a19fb
gnu: pdfgrep: Update to 2.1.1. 
* gnu/packages/pdf.scm (pdfgrep): Update to 2.1.1.
 2018-06-04 15:35:47 +02:00
Tobias Geerinckx-Rice e1345dec67
gnu: lxqt-build-tools: Update to 0.5.0. 
* gnu/packages/lxqt.scm (lxqt-build-tools): Update to 0.5.0.
 2018-06-04 15:35:47 +02:00
Tobias Geerinckx-Rice 12eadf5649
gnu: perl-libintl-perl: Update to 1.29. 
* gnu/packages/perl.scm (perl-libintl-perl): Update to 1.29.
 2018-06-04 15:35:47 +02:00
Tobias Geerinckx-Rice a0b9612fc9
gnu: perl-hash-multivalue: Update to 0.16. 
* gnu/packages/perl.scm (perl-hash-multivalue): Update to 0.16.
[source]: Update URI.
 2018-06-04 15:35:46 +02:00
Tobias Geerinckx-Rice 92299d669a
gnu: perl-file-pushd: Update to 1.016. 
* gnu/packages/perl.scm (perl-file-pushd): Update to 1.016.
 2018-06-04 15:35:46 +02:00
Tobias Geerinckx-Rice cf25329661
gnu: perl-exception-class: Update to 1.44. 
* gnu/packages/perl.scm (perl-exception-class): Update to 1.44.
 2018-06-04 15:35:46 +02:00
Tobias Geerinckx-Rice 4f6c01e78a
gnu: perl-datetime-timezone: Update to 2.19. 
* gnu/packages/perl.scm (perl-datetime-timezone): Update to 2.19.
 2018-06-04 15:35:46 +02:00
Tobias Geerinckx-Rice a1b16662bc
gnu: perl-test-without-module: Update to 0.20. 
* gnu/packages/perl-check.scm (perl-test-without-module): Update to 0.20.
 2018-06-04 15:35:45 +02:00
Tobias Geerinckx-Rice e40ab7382e
gnu: perl-datetime: Update to 1.49. 
* gnu/packages/perl.scm (perl-datetime): Update to 1.49.
 2018-06-04 15:35:45 +02:00
Tobias Geerinckx-Rice 854cf20647
gnu: perl-context-preserve: Update to 0.03. 
* gnu/packages/perl.scm (perl-context-preserve): Update to 0.03.
 2018-06-04 15:35:45 +02:00
Tobias Geerinckx-Rice 30c070d1ae
gnu: perl-class-load-xs: Update to 0.10. 
* gnu/packages/perl.scm (perl-class-load-xs): Update to 0.10.
[native-inputs]: Replace perl-test-requires with perl-test-needs.
Add perl-test-without-module.
 2018-06-04 15:35:45 +02:00
Tobias Geerinckx-Rice d2fe431870
gnu: perl-class-load: Update to 0.24. 
* gnu/packages/perl.scm (perl-class-load): Update to 0.24.
[native-inputs]: Replace perl-test-requires with perl-test-needs.
Add perl-test-without-module.
 2018-06-04 15:35:44 +02:00
Tobias Geerinckx-Rice d017dfaaf3
gnu: sent: Say ‘plain text’. 
‘Plaintext’ is a crypto term.  ‘Slideshow’ is apparently acceptable.

* gnu/packages/suckless.scm (sent)[synopsis, description]: Add spaces.
 2018-06-04 15:35:44 +02:00
Tobias Geerinckx-Rice 4ae9274ae9
gnu: snd: Version documentation directory. 
* gnu/packages/audio.scm (snd)[arguments]: Install documentation to the
conventional location.  Remove redundant MKDIR-P.  Align cosmetically.
 2018-06-04 15:35:44 +02:00
Tobias Geerinckx-Rice 84979374c2
gnu: acpica: Update to 20180531. 
* gnu/packages/admin.scm (acpica): Update to 20180531.
 2018-06-04 15:35:44 +02:00
Tobias Geerinckx-Rice a052d5ab0d
gnu: isync: Add SASL support. 
This adds ~5.5 MiB (7.5%) to isync's now-78.6 MiB closure.

* gnu/packages/mail.scm (isync)[inputs]: Add CYRUS-SASL.
 2018-06-04 15:35:43 +02:00
Ludovic Courtès 7394e264fc
gnu: perf: Work around GCC bug. 
Works around <https://bugs.gnu.org/31708>.

* gnu/packages/patches/perf-gcc-ice.patch: New patch.
* gnu/packages/linux.scm (perf)[source]: Use it.
* gnu/local.mk (dist_patch_DATA): Add it.
 2018-06-04 14:03:54 +02:00
Ludovic Courtès 831f07a009
gnu: signing-party: Update to commit d6f2296. 
* gnu/packages/gnupg.scm (signing-party): Update to commit d6f2296.
[home-page]: Change to salsa.debian.org.
[source]: Use git-fetch.
[arguments]: Remove 'change-directory' phase.  In 'configure' phase,
modify 'gpgwrap/Makefile' instead of 'gpgwrap/src/Makefile'.
 2018-06-04 14:03:54 +02:00
Ricardo Wurmus 32da38d572
Merge branch 'master' into core-updates 2018-06-04 11:25:48 +02:00
Efraim Flashner c0e7a52996
gnu: python-pyqt: Update to 5.10.1. 
* gnu/packages/qt.scm (python-pyqt): Update to 5.10.1.
[inputs]: Remove qtwebkit.
[arguments]: Add custom phase to fix compilation with Qt 5.11.
 2018-06-04 11:06:00 +03:00
Efraim Flashner 9cdd868450
gnu: python-sip: Update to 4.19.8. 
* gnu/packages/qt.scm (python-sip): Update to 4.19.8.
 2018-06-04 11:05:57 +03:00
Efraim Flashner d53e5b366d
gnu: gcompris-qt: Update to 0.91. 
* gnu/packages/education.scm (gcompris-qt): Update to 0.91.
[arguments]: Add custom phase to fix building with Qt 5.11.
 2018-06-03 19:11:27 +03:00
Efraim Flashner 68ddfb2e8d
gnu: quassel: Fix building with Qt 5.11. 
* gnu/packages/irc.scm (quassel)[sources]: Add patch. Return #t from
snippet.
* gnu/packages/patches/quassel-qt-5.11.patch: New file.
* gnu/local.mk (dist_patch_DATA): Register it.
 2018-06-03 15:49:50 +03:00
Rutger Helling 4edc431b0f
gnu: w3m: Enable image support. 
* gnu/packages/w3m.scm (w3m)[inputs]: Add gdk-pixbuf, libx11.
 2018-06-03 13:01:41 +02:00
Efraim Flashner 6f5c67d725
gnu: keepassxc: Fix compilation with Qt 5.11. 
* gnu/packages/password-utils.scm (keepassxc)[arguments]: Add custom
'patch-sources phase to include missing headers.
 2018-06-03 12:46:11 +03:00
Mark H Weaver 0c0431f9ce
Merge branch 'master' into core-updates 2018-06-03 03:36:47 -04:00
Mark H Weaver 2c790226d2
gnu: rust: Fix build for armhf and mips64el. 
This is a followup to commit 514026d7de.

* gnu/packages/rust.scm (nix-system->gnu-triplet-for-rust): New variable.
(rust-bootstrap, mrustc, rust-1.23): Use 'nix-system->gnu-triplet-for-rust'
instead of 'nix-system->gnu-triplet'.
 2018-06-03 03:36:13 -04:00
Efraim Flashner 0ec430f795
gnu: xxd: Remove all inherited inputs. 
* gnu/packages/vim.scm (xxd)[inputs]: New field, don't inherit from vim.
 2018-06-02 23:34:56 +03:00
Efraim Flashner aa75dadab8
gnu: vim: Update to 8.1.0026. 
* gnu/packages/vim.scm (vim): Update to 8.1.0026.
[arguments]: Update substitute list on custom 'patch-config-files phase.
[inputs]: Remove inetutils.
 2018-06-02 23:34:37 +03:00
Efraim Flashner 2d4fdb707e
gnu: xxd: Return true from all phases. 
* gnu/packages/vim.scm (xxd)[arguments]: Return '#t' from custom 'chdir
phase.
 2018-06-02 22:34:23 +03:00
Pierre Neidhardt 15dcd292df
gnu: Add emacs-fish-completion. 
* gnu/packages/emacs.scm (emacs-fish-completion): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-06-02 16:02:52 +02:00
Pierre Neidhardt e374010923
gnu: Add emacs-evil-org. 
* gnu/packages/emacs.scm (emacs-evil-org): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-06-02 16:02:51 +02:00
Pierre Neidhardt ac85107c9f
gnu: Add emacs-evil-multiedit. 
* gnu/packages/emacs.scm (emacs-evil-multiedit): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-06-02 16:02:51 +02:00
Pierre Neidhardt e1e09bcb43
gnu: Add emacs-evil-mu4e. 
* gnu/packages/emacs.scm (emacs-evil-mu4e): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-06-02 16:02:51 +02:00
Pierre Neidhardt c6c1f0bf41
gnu: Add emacs-evil-magit. 
* gnu/packages/emacs.scm (emacs-evil-magit): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-06-02 16:02:51 +02:00
Pierre Neidhardt 22deb03439
gnu: Add emacs-evil-ediff. 
* gnu/packages/emacs.scm (emacs-evil-ediff): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-06-02 16:02:51 +02:00
Ludovic Courtès f52ef55e2b
gnu: guile-json: Update to 1.0.1. 
* gnu/packages/guile.scm (guile-json): Update to 1.0.1.
[source]: Switch to github.com.  Adjust 'snippet' to modify
'configure.ac' and 'Makefile.am'.
[native-inputs]: Add AUTOCONF and AUTOMAKE.
 2018-06-02 15:29:38 +02:00
Ricardo Wurmus e0f8970357
Merge branch 'master' into core-updates 2018-06-02 13:44:43 +02:00
Ricardo Wurmus 92963798a6
gnu: r-scater: Update to 1.8.0. 
* gnu/packages/bioinformatics.scm (r-scater): Update to 1.8.0.
[propagated-inputs]: Add r-delayedarray ad r-delayedmatrixstats; remove
r-matrixstats and r-biomart.
 2018-06-02 13:42:05 +02:00
Ricardo Wurmus 83402242ea
gnu: r-mvtnorm: Update to 1.0-8. 
* gnu/packages/statistics.scm (r-mvtnorm): Update to 1.0-8.
 2018-06-02 13:39:13 +02:00
Ricardo Wurmus 7799a01ef1
gnu: r-rgraphviz: Update to 2.24.0. 
* gnu/packages/graph.scm (r-rgraphviz): Update to 2.24.0.
 2018-06-02 13:39:13 +02:00
Ricardo Wurmus d7e3299987
gnu: r-scran: Update to 1.8.2. 
* gnu/packages/bioinformatics.scm (r-scran): Update to 1.8.2.
[propagated-inputs]: Remove r-zoo; add r-delayedmatrixstats and r-delayedarray.
 2018-06-02 13:39:13 +02:00
Ricardo Wurmus 8ec56b2956
gnu: r-delayedmatrixstats: Update to 1.2.0. 
* gnu/packages/bioinformatics.scm (r-delayedmatrixstats): Update to 1.2.0.
 2018-06-02 13:39:12 +02:00
Ricardo Wurmus d99e0938fa
gnu: r-singlecellexperiment: Update to 1.2.0. 
* gnu/packages/bioinformatics.scm (r-singlecellexperiment): Update to 1.2.0.
 2018-06-02 13:39:12 +02:00
Ricardo Wurmus fd613234b7
gnu: r-beachmat: Update to 1.2.1. 
* gnu/packages/bioinformatics.scm (r-beachmat): Update to 1.2.1.
[inputs]: Add zlib.
 2018-06-02 13:39:12 +02:00
Ricardo Wurmus e9c417361e
gnu: r-rhdf5lib: Update to 1.2.1. 
* gnu/packages/bioinformatics.scm (r-rhdf5lib): Update to 1.2.1.
[arguments]: Adjust substitutions.
 2018-06-02 13:39:12 +02:00
Ricardo Wurmus 0840352835
gnu: r-hdf5array: Update to 1.8.0. 
* gnu/packages/bioinformatics.scm (r-hdf5array): Update to 1.8.0.
 2018-06-02 13:39:12 +02:00
Ricardo Wurmus 5cd725d002
gnu: r-qvalue: Update to 2.12.0. 
* gnu/packages/bioinformatics.scm (r-qvalue): Update to 2.12.0.
 2018-06-02 13:39:12 +02:00
Ricardo Wurmus c6c619c179
gnu: r-hitc: Update to 1.24.0. 
* gnu/packages/bioinformatics.scm (r-hitc): Update to 1.24.0.
 2018-06-02 13:39:12 +02:00
Ricardo Wurmus 4dedecbe70
gnu: r-fithic: Update to 1.6.0. 
* gnu/packages/bioinformatics.scm (r-fithic): Update to 1.6.0.
 2018-06-02 13:39:12 +02:00
Ricardo Wurmus 8db6256f4b
gnu: r-sushi: Update to 1.18.0. 
* gnu/packages/bioinformatics.scm (r-sushi): Update to 1.18.0.
 2018-06-02 13:39:12 +02:00
Ricardo Wurmus 2d3c172b72
gnu: r-gwascat: Update to 2.12.0. 
* gnu/packages/bioinformatics.scm (r-gwascat): Update to 2.12.0.
 2018-06-02 13:39:12 +02:00
Ricardo Wurmus fecbbac286
gnu: r-gviz: Update to 1.24.0. 
* gnu/packages/bioinformatics.scm (r-gviz): Update to 1.24.0.
 2018-06-02 13:39:12 +02:00
Ricardo Wurmus 6929b97583
gnu: r-gqtlstats: Update to 1.12.0. 
* gnu/packages/bioinformatics.scm (r-gqtlstats): Update to 1.12.0.
[propagated-inputs]: Add r-homo-sapiens; remove r-ldblock.
 2018-06-02 13:39:12 +02:00
Ricardo Wurmus 45c29a6e5c
gnu: r-ldblock: Update to 1.10.0. 
* gnu/packages/bioinformatics.scm (r-ldblock): Update to 1.10.0.
[propagated-inputs]: Add r-biocgenerics.
 2018-06-02 13:39:12 +02:00
Ricardo Wurmus 9b0b108ed9
gnu: r-erma: Update to 0.12.0. 
* gnu/packages/bioinformatics.scm (r-erma): Update to 0.12.0.
[propagated-inputs]: Remove r-foreach; add r-biocparallel, r-genomeinfodb, and
r-iranges.
 2018-06-02 13:39:12 +02:00
Ricardo Wurmus d26f95d079
gnu: r-snpstats: Update to 1.30.0. 
* gnu/packages/bioinformatics.scm (r-snpstats): Update to 1.30.0.
 2018-06-02 13:39:12 +02:00
Ricardo Wurmus dcd1f0236c
gnu: r-gqtlbase: Update to 1.12.0. 
* gnu/packages/bioinformatics.scm (r-gqtlbase): Update to 1.12.0.
 2018-06-02 13:39:12 +02:00
Ricardo Wurmus e214a6e6ff
gnu: r-ggbio: Update to 1.28.0. 
* gnu/packages/bioinformatics.scm (r-ggbio): Update to 1.28.0.
 2018-06-02 13:39:11 +02:00
Ricardo Wurmus 34cc18d4de
gnu: r-biovizbase: Update to 1.28.0. 
* gnu/packages/bioinformatics.scm (r-biovizbase): Update to 1.28.0.
 2018-06-02 13:39:11 +02:00
Ricardo Wurmus 94ae875c0a
gnu: r-organismdbi: Update to 1.22.0. 
* gnu/packages/bioinformatics.scm (r-organismdbi): Update to 1.22.0.
 2018-06-02 13:39:11 +02:00
Ricardo Wurmus bbcd19fb4d
gnu: r-ensembldb: Update to 2.4.1. 
* gnu/packages/bioinformatics.scm (r-ensembldb): Update to 2.4.1.
[propagated-inputs]: Remove r-annotationhub.
 2018-06-02 13:39:11 +02:00
Ricardo Wurmus 19adb89854
gnu: r-dirichletmultinomial: Update to 1.22.0. 
* gnu/packages/bioinformatics.scm (r-dirichletmultinomial): Update to 1.22.0.
 2018-06-02 13:39:11 +02:00
Ricardo Wurmus d3fb2ad834
gnu: r-complexheatmap: Update to 1.18.0. 
* gnu/packages/bioinformatics.scm (r-complexheatmap): Update to 1.18.0.
 2018-06-02 13:39:11 +02:00
Ricardo Wurmus d1463f1b0c
gnu: r-genomicfiles: Update to 1.16.0. 
* gnu/packages/bioinformatics.scm (r-genomicfiles): Update to 1.16.0.
 2018-06-02 13:39:11 +02:00
Ricardo Wurmus 1ba126e0e4
gnu: r-gage: Update to 2.30.0. 
* gnu/packages/bioinformatics.scm (r-gage): Update to 2.30.0.
 2018-06-02 13:39:11 +02:00
Ricardo Wurmus 419e438d52
gnu: r-keggrest: Update to 1.20.0. 
* gnu/packages/bioinformatics.scm (r-keggrest): Update to 1.20.0.
 2018-06-02 13:39:11 +02:00
Ricardo Wurmus 15cc1a6867
gnu: r-fastseg: Update to 1.26.0. 
* gnu/packages/bioinformatics.scm (r-fastseg): Update to 1.26.0.
 2018-06-02 13:39:11 +02:00
Ricardo Wurmus 646439c7e3
gnu: r-annotationhub: Update to 2.12.0. 
* gnu/packages/bioinformatics.scm (r-annotationhub): Update to 2.12.0.
 2018-06-02 13:39:11 +02:00
Ricardo Wurmus 420415b057
gnu: r-interactivedisplaybase: Update to 1.18.0. 
* gnu/packages/bioinformatics.scm (r-interactivedisplaybase): Update to 1.18.0.
 2018-06-02 13:39:11 +02:00
Ricardo Wurmus a67dd4c5e9
gnu: r-edaseq: Update to 2.14.0. 
* gnu/packages/bioinformatics.scm (r-edaseq): Update to 2.14.0.
 2018-06-02 13:39:11 +02:00
Ricardo Wurmus 749b712677
gnu: r-deseq: Update to 1.32.0. 
* gnu/packages/bioinformatics.scm (r-deseq): Update to 1.32.0.
 2018-06-02 13:39:11 +02:00
Ricardo Wurmus 0ebd7a4c9f
gnu: r-aroma-light: Update to 3.10.0. 
* gnu/packages/bioinformatics.scm (r-aroma-light): Update to 3.10.0.
 2018-06-02 13:39:11 +02:00
Ricardo Wurmus bdc8b40af2
gnu: r-msnid: Update to 1.14.0. 
* gnu/packages/bioinformatics.scm (r-msnid): Update to 1.14.0.
 2018-06-02 13:39:10 +02:00
Ricardo Wurmus 250d78eac9
gnu: r-msnbase: Update to 2.6.1. 
* gnu/packages/bioinformatics.scm (r-msnbase): Update to 2.6.1.
[propagated-inputs]: Add r-mass and r-scales.
 2018-06-02 13:39:10 +02:00
Ricardo Wurmus 0f773b90db
gnu: r-pcamethods: Update to 1.72.0. 
* gnu/packages/bioinformatics.scm (r-pcamethods): Update to 1.72.0.
 2018-06-02 13:39:10 +02:00
Ricardo Wurmus 7bd2582971
gnu: r-mzid: Update to 1.18.0. 
* gnu/packages/bioinformatics.scm (r-mzid): Update to 1.18.0.
 2018-06-02 13:39:10 +02:00
Ricardo Wurmus af8710624d
gnu: r-vsn: Update to 3.48.1. 
* gnu/packages/bioinformatics.scm (r-vsn): Update to 3.48.1.
 2018-06-02 13:39:10 +02:00
Ricardo Wurmus 5837f1835b
gnu: r-affy: Update to 1.58.0. 
* gnu/packages/bioinformatics.scm (r-affy): Update to 1.58.0.
[inputs]: Add zlib.
 2018-06-02 13:39:10 +02:00
Ricardo Wurmus 82589f7430
gnu: r-affyio: Update to 1.50.0. 
* gnu/packages/bioinformatics.scm (r-affyio): Update to 1.50.0.
 2018-06-02 13:39:10 +02:00
Ricardo Wurmus 39cc491790
gnu: r-mzr: Update to 2.14.0. 
* gnu/packages/bioinformatics.scm (r-mzr): Update to 2.14.0.
[inputs]: Add zlib.
[propagated-inputs]: Add r-rhdf5lib.
 2018-06-02 13:39:10 +02:00
Ricardo Wurmus a02b82088f
gnu: r-protgenerics: Update to 1.12.0. 
* gnu/packages/bioinformatics.scm (r-protgenerics): Update to 1.12.0.
 2018-06-02 13:39:10 +02:00
Ricardo Wurmus 9547dd8613
gnu: r-sva: Update to 3.28.0. 
* gnu/packages/bioinformatics.scm (r-sva): Update to 3.28.0.
 2018-06-02 13:39:10 +02:00
Ricardo Wurmus 19ad568e79
gnu: r-methylkit: Update to 1.6.0. 
* gnu/packages/bioinformatics.scm (r-methylkit): Update to 1.6.0.
 2018-06-02 13:39:10 +02:00
Ricardo Wurmus aae4f716da
gnu: r-copywriter: Update to 2.12.0. 
* gnu/packages/bioinformatics.scm (r-copywriter): Update to 2.12.0.
 2018-06-02 13:39:10 +02:00
Ricardo Wurmus 8f94487da7
gnu: r-chipseq: Update to 1.30.0. 
* gnu/packages/bioinformatics.scm (r-chipseq): Update to 1.30.0.
 2018-06-02 13:39:10 +02:00
Ricardo Wurmus 62509bbc81
gnu: r-annotationfilter: Update to 1.4.0. 
* gnu/packages/bioinformatics.scm (r-annotationfilter): Update to 1.4.0.
 2018-06-02 13:39:10 +02:00
Ricardo Wurmus d73c5728f3
gnu: r-rhdf5: Update to 2.24.0. 
* gnu/packages/bioinformatics.scm (r-rhdf5): Update to 2.24.0.
[arguments]: Remove.
[propagated-inputs]: Remove r-zlibbioc; add r-rhdf5lib.
[inputs]: Remove perl.
 2018-06-02 13:39:10 +02:00
Ricardo Wurmus c76e8baf9e
gnu: r-tximport: Update to 1.8.0. 
* gnu/packages/bioinformatics.scm (r-tximport): Update to 1.8.0.
 2018-06-02 13:39:10 +02:00
Ricardo Wurmus b6c2c8f781
gnu: r-mutationalpatterns: Update to 1.6.1. 
* gnu/packages/bioinformatics.scm (r-mutationalpatterns): Update to 1.6.1.
 2018-06-02 13:39:09 +02:00
Ricardo Wurmus 72f11ff9c5
gnu: r-bamsignals: Update to 1.12.0. 
* gnu/packages/bioinformatics.scm (r-bamsignals): Update to 1.12.0.
 2018-06-02 13:39:09 +02:00
Ricardo Wurmus 1a08bb8a17
gnu: r-rhtslib: Update to 1.12.1. 
* gnu/packages/bioinformatics.scm (r-rhtslib): Update to 1.12.1.
[native-inputs]: Remove autoconf.
 2018-06-02 13:39:09 +02:00
Ricardo Wurmus 2c480bb012
gnu: r-zlibbioc: Update to 1.26.0. 
* gnu/packages/bioinformatics.scm (r-zlibbioc): Update to 1.26.0.
 2018-06-02 13:39:09 +02:00
Ricardo Wurmus 7e6537e257
gnu: r-motifrg: Update to 1.24.0. 
* gnu/packages/bioinformatics.scm (r-motifrg): Update to 1.24.0.
 2018-06-02 13:39:09 +02:00
Ricardo Wurmus 8217c2d0bc
gnu: r-seqlogo: Update to 1.46.0. 
* gnu/packages/bioinformatics.scm (r-seqlogo): Update to 1.46.0.
 2018-06-02 13:39:09 +02:00
Ricardo Wurmus 17d35de73f
gnu: r-genomation: Update to 1.12.0. 
* gnu/packages/bioinformatics.scm (r-genomation): Update to 1.12.0.
 2018-06-02 13:39:09 +02:00
Ricardo Wurmus 5229cedf57
gnu: r-seqpattern: Update to 1.12.0. 
* gnu/packages/bioinformatics.scm (r-seqpattern): Update to 1.12.0.
 2018-06-02 13:39:09 +02:00
Ricardo Wurmus 25d1df5764
gnu: r-impute: Update to 1.54.0. 
* gnu/packages/bioinformatics.scm (r-impute): Update to 1.54.0.
 2018-06-02 13:39:09 +02:00
Ricardo Wurmus 89ef133ebd
gnu: r-bsgenome: Update to 1.48.0. 
* gnu/packages/bioinformatics.scm (r-bsgenome): Update to 1.48.0.
 2018-06-02 13:39:09 +02:00
Ricardo Wurmus f2eb2e453e
gnu: r-topgo: Update to 2.32.0. 
* gnu/packages/bioinformatics.scm (r-topgo): Update to 2.32.0.
 2018-06-02 13:39:09 +02:00
Ricardo Wurmus 2f66fecd89
gnu: r-graph: Update to 1.58.0. 
* gnu/packages/bioinformatics.scm (r-graph): Update to 1.58.0.
 2018-06-02 13:39:09 +02:00
Ricardo Wurmus b4ad4ec6b4
gnu: r-genomicfeatures: Update to 1.32.0. 
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.32.0.
[propagated-inputs]: Remove r-rmysql.
 2018-06-02 13:39:09 +02:00
Ricardo Wurmus a30df29768
gnu: r-rtracklayer: Update to 1.40.2. 
* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.40.2.
[native-inputs]: Add pkg-config.
 2018-06-02 13:39:09 +02:00
Ricardo Wurmus 90102bd06b
gnu: r-genomicalignments: Update to 1.16.0. 
* gnu/packages/bioinformatics.scm (r-genomicalignments): Update to 1.16.0.
 2018-06-02 13:39:09 +02:00
Ricardo Wurmus 9bf4110ea1
gnu: r-summarizedexperiment: Update to 1.10.1. 
* gnu/packages/bioinformatics.scm (r-summarizedexperiment): Update to 1.10.1.
 2018-06-02 13:39:08 +02:00
Ricardo Wurmus 82f593f378
gnu: r-delayedarray: Update to 0.6.0. 
* gnu/packages/bioinformatics.scm (r-delayedarray): Update to 0.6.0.
[propagated-inputs]: Add r-biocparallel.
 2018-06-02 13:39:08 +02:00
Ricardo Wurmus d2367a89dd
gnu: r-rsamtools: Update to 1.32.0. 
* gnu/packages/bioinformatics.scm (r-rsamtools): Update to 1.32.0.
 2018-06-02 13:39:08 +02:00
Ricardo Wurmus 942655add1
gnu: r-biostrings: Update to 2.48.0. 
* gnu/packages/bioinformatics.scm (r-biostrings): Update to 2.48.0.
 2018-06-02 13:39:08 +02:00
Ricardo Wurmus e6eac58d4c
gnu: r-biocparallel: Update to 1.14.1. 
* gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.14.1.
 2018-06-02 13:39:08 +02:00
Ricardo Wurmus 1763cba80e
gnu: r-biomart: Update to 2.36.1. 
* gnu/packages/bioinformatics.scm (r-biomart): Update to 2.36.1.
 2018-06-02 13:39:08 +02:00
Ricardo Wurmus 77f66feee7
gnu: r-annotationdbi: Update to 1.42.1. 
* gnu/packages/bioinformatics.scm (r-annotationdbi): Update to 1.42.1.
 2018-06-02 13:39:08 +02:00