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
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
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
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
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
ad21323c96
gnu: cpuid: Update to 20180519.
...
* gnu/packages/linux.scm (cpuid): Update to 20180519.
2018-06-15 09:57:17 +02:00
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
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
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
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
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
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
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
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
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
657bed34f4
gnu: fcitx: Use HTTPS home page.
...
* gnu/packages/fcitx.scm (fcitx)[home-page]: Use HTTPS.
2018-06-15 09:57:15 +02:00
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
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
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
beb2d4be84
gnu: nickle: Update to 2.81.
...
* gnu/packages/nickle.scm (nickle): Update to 2.81.
2018-06-15 09:57:14 +02:00
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
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
cf9a29b24c
gnu: Add r-genomicinteractions.
...
* gnu/packages/bioconductor.scm (r-genomicinteractions): New variable.
2018-06-15 09:14:01 +02:00
a32279ffb6
gnu: Add r-interactionset.
...
* gnu/packages/bioconductor.scm (r-interactionset): New variable.
2018-06-15 09:14:01 +02:00
056402220e
gnu: innoextract: Update to 1.7.
...
* gnu/packages/compression.scm (innoextract): Update to 1.7.
2018-06-15 09:10:35 +02:00
6ffdfe6a01
gnu: Add r-riboseqr.
...
* gnu/packages/bioconductor.scm (r-riboseqr): New variable.
2018-06-15 07:43:23 +02:00
0490f9de88
gnu: Add r-riboprofiling.
...
* gnu/packages/bioconductor.scm (r-riboprofiling): New variable.
2018-06-15 07:43:22 +02:00
609f4ad12f
gnu: Add r-chipcomp.
...
* gnu/packages/bioconductor.scm (r-chipcomp): New variable.
2018-06-15 07:43:22 +02:00
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
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
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
bb15b581f7
gnu: Add r-bayseq.
...
* gnu/packages/bioconductor.scm (r-bayseq): New variable.
2018-06-15 07:43:22 +02:00
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
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
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
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
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
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
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
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
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
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
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
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
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
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
d518261f05
gnu: cppcheck: Update to 1.84.
...
* gnu/packages/check.scm (cppcheck): Update to 1.84.
2018-06-14 18:55:51 +02:00
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
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
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
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
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
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
f715f102e0
gnu: fio: Update to 3.7.
...
* gnu/packages/benchmark.scm (fio): Update to 3.7.
2018-06-14 15:41:09 +02:00
53131eab2d
gnu: Add minimap2.
...
* gnu/packages/bioinformatics.scm (minimap2): New variable.
2018-06-14 13:51:15 +02:00
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
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
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
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
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
b863b50d80
gnu: Add python-pynamecheap.
...
* gnu/packages/python.scm (python-pynamecheap, python2-pynamecheap): New
variables.
2018-06-14 08:18:02 +02:00
f4adbe7405
gnu: Add python-tldextract.
...
* gnu/packages/python.scm (python-tldextract, python2-tldextract): New
variables.
2018-06-14 08:17:59 +02:00
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
40c1b61aac
gnu: Add tmate.
...
* gnu/packages/terminals.scm (tmate): New variable.
2018-06-14 11:20:31 +05:30
0b5c16c07f
Fix typo in (gnu packages gtk) header.
...
* gnu/packages/gtk.scm: Fix ‘Coypright’ typo.
2018-06-14 04:30:50 +02:00
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
846325a8d8
gnu: Add r-writexl.
...
* gnu/packages/cran.scm (r-writexl): New variable.
2018-06-13 15:14:37 +02:00
546fc4aa55
gnu: Add r-hdf5r.
...
* gnu/packages/cran.scm (r-hdf5r): New variable.
2018-06-13 15:14:37 +02:00
0c9868aa5b
gnu: Add r-nbclust.
...
* gnu/packages/cran.scm (r-nbclust): New variable.
2018-06-13 11:51:28 +02:00
f22bfee945
gnu: Add r-factoextra.
...
* gnu/packages/cran.scm (r-factoextra): New variable.
2018-06-13 11:51:28 +02:00
e83841a296
gnu: Add r-factominer.
...
* gnu/packages/cran.scm (r-factominer): New variable.
2018-06-13 11:51:28 +02:00
Ricardo Wurmus