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35581 Commits

Author SHA1 Message Date
Ricardo Wurmus 5bb9e0af8d
gnu: Add python-cooler. 
* gnu/packages/bioinformatics.scm (python-cooler): New variable.
 2018-09-10 16:50:26 +02:00
Ricardo Wurmus 80f4db91b1
gnu: Add python-pyfaidx. 
* gnu/packages/bioinformatics.scm (python-pyfaidx): New variable.
 2018-09-10 16:50:26 +02:00
Ricardo Wurmus 1f41f01c14
gnu: Add python-pypairix. 
* gnu/packages/bioinformatics.scm (python-pypairix): New variable.
 2018-09-10 16:50:26 +02:00
Ricardo Wurmus a9d496b353
gnu: Add python-intervaltree. 
* gnu/packages/bioinformatics.scm (python-intervaltree): New variable.
 2018-09-10 16:50:26 +02:00
Ricardo Wurmus a6a7156aa9
gnu: Add python-dask. 
* gnu/packages/python.scm (python-dask): New variable.
 2018-09-10 16:50:26 +02:00
Ricardo Wurmus 035989c403
gnu: Add python-partd. 
* gnu/packages/python.scm (python-partd): New variable.
 2018-09-10 16:50:26 +02:00
Ricardo Wurmus c27a9d8a88
gnu: Add python-blosc. 
* gnu/packages/python.scm (python-blosc): New variable.
 2018-09-10 16:50:26 +02:00
Ricardo Wurmus b2b8226244
gnu: Add python-locket. 
* gnu/packages/python.scm (python-locket): New variable.
 2018-09-10 16:50:26 +02:00
Ricardo Wurmus 930ba31d20
gnu: Add python-cloudpickle. 
* gnu/packages/python.scm (python-cloudpickle): New variable.
 2018-09-10 16:50:26 +02:00
Ricardo Wurmus 3d352cb9cf
gnu: Add python-sortedcontainers. 
* gnu/packages/python.scm (python-sortedcontainers): New variable.
 2018-09-10 16:50:26 +02:00
Ricardo Wurmus 098cb1e9c4
gnu: Add python-cytoolz. 
* gnu/packages/python.scm (python-cytoolz): New variable.
 2018-09-10 16:50:26 +02:00
Ricardo Wurmus 7cd51cd28e
gnu: Add python-toolz. 
* gnu/packages/python.scm (python-toolz): New variable.
 2018-09-10 16:50:25 +02:00
Ricardo Wurmus 943a4cb601
gnu: Add python-multiprocess. 
* gnu/packages/python.scm (python-multiprocess): New variable.
 2018-09-10 16:50:25 +02:00
Ricardo Wurmus fc62567251
gnu: Add python-dill. 
* gnu/packages/python.scm (python-dill): New variable.
 2018-09-10 16:50:25 +02:00
Tobias Geerinckx-Rice 82d5c7c6de
gnu: python-typing: Update to 3.6.6. 
* gnu/packages/python.scm (python-typing): Update to 3.6.6.
 2018-09-10 15:29:13 +02:00
Tobias Geerinckx-Rice 419aa05e1b
gnu: tinyproxy: Update to 1.10.0. 
* gnu/packages/web.scm (tinyproxy): Update to 1.10.0.
[native-inputs]: Remove asciidoc.
 2018-09-10 15:29:12 +02:00
Tobias Geerinckx-Rice f6c8a97a04
gnu: spectrwm: Update to 3.2.0. 
* gnu/packages/wm.scm (spectrwm): Update to 3.2.0.
[arguments]: Remove 'fix-freetype-include' phase.
 2018-09-10 15:29:12 +02:00
Mădălin Ionel Patrașcu 57d70dbabc
gnu: Add yad. 
* gnu/packages/gtk.scm (yad): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2018-09-10 14:45:15 +02:00
Ludovic Courtès 94b3b6041d
gnu: hpcguix-web: Update to 53e09ea. 
* gnu/packages/web.scm (hpcguix-web): Update to 53e09ea.
 2018-09-10 12:18:14 +02:00
Ludovic Courtès 81317071fb
services: hpcguix-web: Produce a log file and rotate it. 
* gnu/services/web.scm (%hpcguix-web-log-file)
(%hpcguix-web-log-rotations): New variables.
(hpcguix-web-shepherd-service): Pass #:log-file.
(hpcguix-web-service-type): Extend ROTTLOG-SERVICE-TYPE.
 2018-09-10 12:12:52 +02:00
Ludovic Courtès 19de8273ee
services: tailon: Move to (gnu services web). 
This allows (gnu services admin) to remain deeper in the module graph
and to be used by (gnu services web).

* gnu/services/admin.scm (<tailon-configuration-file>)
(tailon-configuration-files-string)
(tailon-configuration-file-compiler, <tailon-configuration>)
(tailon-shepherd-service, %tailon-accounts)
(tailon-service-type): Move to...
* gnu/services/web.scm: ... here.
* gnu/tests/admin.scm: Remove.  Move test to...
* gnu/tests/web.scm (%tailon-os)
(run-tailon-test, %test-tailon): ... here.
 2018-09-10 12:12:50 +02:00
Alex Vong d930374014
gnu: youtube-dl: Update to 2018.08.04. 
* gnu/packages/video.scm (youtube-dl): Update to 2018.08.04.
 2018-09-10 11:31:34 +02:00
Leo Famulari de15ff1a6c
gnu: Add asignify. 
* gnu/packages/crypto.scm (asignify): New variable.
 2018-09-09 20:05:47 -04:00
Leo Famulari d4bd2453ec
gnu: certbot: Update to 0.27.1. 
* gnu/packages/tls.scm (python-acme): Update to 0.27.1.
[arguments]: Use invoke.
(certbot): Update to 0.27.1.
[native-inputs]: Use python-sphinx-1.6.
 2018-09-09 18:52:04 -04:00
Leo Famulari ced98c7e89
gnu: libgd: Fix CVE-2018-{5711,1000222}. 
* gnu/packages/patches/gd-CVE-2018-1000222.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/gd.scm (gd/fixed): New variable.
* gnu/packages/php.scm (gd-for-php)[source]: Use 'gd-CVE-2018-1000222.patch'.
 2018-09-09 18:13:19 -04:00
Ricardo Wurmus 15cc7e6adf
ui: Add soft port for styling and filtering build output. 
* guix/ui.scm (build-output-port): New procedure.
* guix/scripts/package.scm (%default-options): Print build trace.
(guix-package): Use build-output-port.
* guix/scripts/build.scm (guix-build): Use build-output-port.

Co-authored-by: Sahithi Yarlagadda <sahi@swecha.net>
 2018-09-09 23:18:21 +02:00
Sahithi Yarlagadda 80ec1b73d2
ui: Add support for colorization. 
* guix/ui.scm (ansi-color-tables): New variable.
(color, colorize-string): New procedures.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2018-09-09 22:26:54 +02:00
Ricardo Wurmus 45350539aa
gnu: r-chron: Update to 2.3-53. 
* gnu/packages/statistics.scm (r-chron): Update to 2.3-53.
 2018-09-09 22:26:02 +02:00
Ricardo Wurmus ab50580a9d
gnu: r-annotationhub: Update to 2.12.1. 
* gnu/packages/bioinformatics.scm (r-annotationhub): Update to 2.12.1.
 2018-09-09 22:26:02 +02:00
Ricardo Wurmus 35c076e619
gnu: r-chippeakanno: Update to 3.14.2. 
* gnu/packages/bioconductor.scm (r-chippeakanno): Update to 3.14.2.
 2018-09-09 22:26:02 +02:00
Roel Janssen c36d972531
gnu: Update texmaker to 5.0.2. 
* gnu/packages/tex.scm (texmaker): Update to 5.0.2.
 2018-09-09 21:59:08 +02:00
Marius Bakke 0084744b3a
gnu: ghostscript: Update replacement to 9.24 [security fixes]. 
The following CVEs are fixed with this release: CVE-2018-15908,
CVE-2018-15909, CVE-2018-15910, CVE-2018-15911, CVE-2018-16509,
CVE-2018-16510, CVE-2018-16511, CVE-2018-16513, CVE-2018-16539,
CVE-2018-16540, CVE-2018-16541, CVE-2018-16542, CVE-2018-16543.

* gnu/packages/patches/ghostscript-CVE-2018-10194.patch: Delete file.
* gnu/packages/patches/ghostscript-CVE-2018-16509.patch,
gnu/packages/patches/ghostscript-bug-699708.patch: New files.
* gnu/local.mk (dist_patch_DATA): Adjust accordingly.
* gnu/packages/ghostscript.scm (ghostscript/fixed): Update to 9.24.
[source](patches): Remove 'ghostscript-CVE-2018-10194.patch' and
'ghostscript-runpath.patch'.  Add 'ghostscript-CVE-2018-16509.patch' and
'ghostscript-bug-699708.patch'.
[arguments]: Add LDFLAGS to #:configure-flags, and a phase to create output
directory.
 2018-09-09 16:43:11 +02:00
Marius Bakke 910a20e2b8
gnu: jbig2dec: Replace with 0.15 [security fixes]. 
* gnu/packages/image.scm (jbig2dec-0.15): New public variable.
(jbig2dec)[replacement]: New field.
 2018-09-09 16:43:11 +02:00
Marius Bakke a617fd55df
gnu: OpenBLAS: Update source URI. 
* gnu/packages/maths.scm (openblas)[source](uri): Use the more stable
SourceForge mirror.
 2018-09-09 16:43:11 +02:00
Marius Bakke 1448fa2547
gnu: openal: Update to 1.19.0. 
* gnu/packages/audio.scm (openal): Update to 1.19.0.
 2018-09-09 16:43:11 +02:00
Marius Bakke e9c1492f66
gnu: glm: Update to 0.9.9.1. 
* gnu/packages/maths.scm (glm): Update to 0.9.9.1.
 2018-09-09 16:43:10 +02:00
Marius Bakke 91b3a6d4db
gnu: msmtp: Remove unneeded input. 
* gnu/packages/mail.scm (msmtp)[inputs]: Remove LIBIDN, which is only required
when using OpenSSL (or GnuTLS sans IDN support).
 2018-09-09 16:43:10 +02:00
Marius Bakke 37f9cfae43
gnu: msmtp: Update to 1.8.0. 
* gnu/packages/mail.scm (msmtp): Update to 1.8.0.
 2018-09-09 16:43:10 +02:00
Marius Bakke 249846bfde
gnu: libsoup: Update to 2.64.0. 
* gnu/packages/gnome.scm (libsoup): Update to 2.64.0.
[inputs]: Add LIBPSL.
 2018-09-09 16:43:10 +02:00
Marius Bakke 617cf5de92
gnu: mpfr: Update home page. 
* gnu/packages/multiprecision.scm (mpfr)[home-page]: Use HTTPS.
 2018-09-09 16:43:10 +02:00
Marius Bakke 81bf0fd0d4
gnu: julia: Update objconv input. 
* gnu/packages/julia.scm (julia)[inputs]: Update the hash of "objconv", which
does not have a stable URL.  Add a file name and use HTTPS while at it.
 2018-09-09 16:43:10 +02:00
Tobias Geerinckx-Rice b64e67ad40
gnu: cloc: Update to 1.78. 
* gnu/packages/code.scm (cloc): Update to 1.78.
[source]: Update URI.
 2018-09-09 15:01:55 +02:00
Tobias Geerinckx-Rice c2311644a5
gnu: signify: Update to 24. 
* gnu/packages/crypto.scm (signify): Update to 24.
 2018-09-09 15:01:54 +02:00
Tobias Geerinckx-Rice bb105673b8
gnu: musl: Update to 1.1.20. 
* gnu/packages/musl.scm (musl): Update to 1.1.20.
 2018-09-09 15:01:54 +02:00
Tobias Geerinckx-Rice bb5e06a35e
gnu: perl-pegex: Update to 0.67. 
* gnu/packages/perl.scm (perl-pegex): Update to 0.67.
 2018-09-09 15:01:54 +02:00
Tobias Geerinckx-Rice 9ad80992d0
gnu: perl-config-autoconf: Update to 0.317. 
* gnu/packages/perl.scm (perl-config-autoconf): Update to 0.317.
 2018-09-09 15:01:53 +02:00
Tobias Geerinckx-Rice 15dbc911f6
gnu: perl-extutils-installpaths: Update to 0.012. 
* gnu/packages/perl.scm (perl-extutils-installpaths): Update to 0.012.
 2018-09-09 15:01:53 +02:00
Tobias Geerinckx-Rice 4e77b75e11
gnu: perl-extutils-helpers: Update to 0.026. 
* gnu/packages/perl.scm (perl-extutils-helpers): Update to 0.026.
 2018-09-09 15:01:53 +02:00
Tobias Geerinckx-Rice 748e6e1271
gnu: perl-getopt-long-descriptive: Update to 0.103. 
* gnu/packages/perl.scm (perl-getopt-long-descriptive): Update to 0.103.
 2018-09-09 15:01:53 +02:00
Tobias Geerinckx-Rice 04fc0b9489
gnu: perl-namespace-clean: Update to 0.27. 
* gnu/packages/perl.scm (perl-namespace-clean): Update to 0.27.
 2018-09-09 15:01:52 +02:00