2e0f69057a
gnu: bioinformatics: Return #t from all phases and snippets.
...
* gnu/packages/bioinformatics.scm (bamtools, ribotaper, bioawk)
(codingquarry, fraggenescan, minced, pplacer, star, subread, sailfish)
(salmon): Return #t from all phases and snippets, use 'invoke' where
appropriate, and remove vestigal plumbing.
2018-11-14 23:44:18 -05:00
96272e2822
gnu: databases: Return #t from all phases.
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* gnu/packages/databases.scm (4store, go-gopkg.in-mgo.v2, mongodb)
(sparql-query, tdb, sqlcipher, python-sqlparse, mongo-tools): Return #t from
all phases, use invoke where appropriate, and remove vestigial plumbing.
2018-11-14 23:44:16 -05:00
9f6f726c7f
gnu: compression: Return #t from all phases.
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* gnu/packages/compression.scm (perl-compress-raw-zlib, java-snappy)
(java-iq80-snappy, pzstd, java-tukaani-xz): Return #t from all phases.
2018-11-14 23:44:14 -05:00
29594404a1
gnu: check: Return #t from all phases.
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* gnu/packages/check.scm (cmdtest, python-pytest-cov, python-fixtures)
(python-pytest-localserver, python-pytest-flakes)
(python2-coverage-test-runner, python-pylint, python-behave-web-api):
Return #t from all phases, and use invoke where appropriate.
2018-11-14 23:44:12 -05:00
ee527187a6
gnu: audio: Return #t from all phases.
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* gnu/packages/audio.scm (clalsadrv, jack-2, libsbsms, zita-convolver)
(zita-resampler, zita-alsa-pcmi, gsm, cava): Return #t from all phases.
(ladspa): Use 'modify-phases'. Return #t from all phases.
2018-11-14 23:44:10 -05:00
c6bf07d14a
gnu: xorg: Return #t from all phases.
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* gnu/packages/xorg.scm (xcompmgr)
* gnu/packages/xdisorg.scm (xdotool, scrot, unclutter, xscreensaver)
(tint2, nxbelld, xautolock): Return #t from all phases.
2018-11-14 23:44:08 -05:00
aa6f87a2b9
gnu: xml: Return #t from all phases.
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* gnu/packages/xml.scm (python-libxml2, perl-xml-sax, xlsx2csv, libxls)
(java-kxml2): Return #t from all phases.
2018-11-14 23:44:06 -05:00
9dcfd6aac9
gnu: video: Return #t from all phases.
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* gnu/packages/video.scm (youtube-dl-gui, avidemux, xvid, twitchy, aegisub):
Return #t from all phases, use invoke where appropriate, and remove vestigial
plumbing.
2018-11-14 23:44:04 -05:00
4851af9ebe
gnu: perl: Return #t from all phases.
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* gnu/packages/gd.scm (perl-gd-securityimage)
* gnu/packages/libevent.scm (perl-ev)
* gnu/packages/markup.scm (perl-text-markdown-discount)
* gnu/packages/perl-check.scm (perl-test2-bundle-extended)
* gnu/packages/perl.scm (perl-digest-md5, perl-encode-hanextra)
(perl-ipc-run, perl-pathtools)
* gnu/packages/photo.scm (perl-image-exiftool): Return #t from all phases.
2018-11-14 23:44:02 -05:00
366c1cbbc6
gnu: networking: Return #t from all phases.
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* gnu/packages/networking.scm (miredo, tcp-wrappers, librdkafka, ifstatus)
(iodine, httpstat, perl-socket6, perl-netaddr-ip, libproxy, openvswitch)
(libnet, asio): Return #t from all phases.
2018-11-14 23:43:59 -05:00
9922278b25
gnu: linux: Return #t from all phases.
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* gnu/packages/linux.scm (iproute, ntfs-3g, cpupower, radeontop, tlp):
Return #t from all phases.
2018-11-14 23:43:57 -05:00
fccacffbf4
gnu: image: Return #t from all phases.
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* gnu/packages/image.scm (libpng-apng, pngcrush, leptonica, zimg)
(perceptualdiff): Return #t from all phases.
2018-11-14 23:43:54 -05:00
cb8ba848d2
gnu: admin: Return #t from all phases.
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* gnu/packages/admin.scm (daemon-tools, rottlog, wpa-supplicant-minimal)
(wakelan, cpulimit, nmap, sunxi-tools): Return #t from all phases.
2018-11-14 23:43:48 -05:00
21f7d88e7a
gnu: texlive-bin: Fix substitution regexp.
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This is a followup to commit be200ef316
2018-11-14 23:49:19 +01:00
79ee97a144
Merge branch 'master' into core-updates
2018-11-14 21:20:46 +01:00
7d9d521fbc
gnu: aide: Provide libpcre.a and libz.a.
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* gnu/packages/admin.scm (aide)[inputs]: Add PCRE:STATIC and ZLIB:STATIC.
2018-11-14 21:07:01 +01:00
e921993c25
gnu: xf86-video-r128: Update to 6.12.0.
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* gnu/packages/xorg.scm (xf86-video-r128): Update to 6.12.0.
2018-11-14 21:05:30 +01:00
24dd6ec38a
gnu: mtools: Update to 4.0.20.
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* gnu/packages/mtools.scm (mtools): Update to 4.0.20.
[source](uri): Change to 'bz2' compressed tarball.
2018-11-14 21:05:30 +01:00
7939387da8
gnu: nano: Update to 3.2.
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* gnu/packages/nano.scm (nano): Update to 3.2.
2018-11-14 21:05:30 +01:00
d63f588486
gnu: sudo: Update to 1.8.26.
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* gnu/packages/admin.scm (sudo): Update to 1.8.26.
2018-11-14 21:05:30 +01:00
bac2974e86
gnu: feh: Update to 3.0.
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* gnu/packages/image-viewers.scm (feh): Update to 3.0.
2018-11-14 21:05:30 +01:00
ee66a13563
gnu: Add jamm.
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* gnu/packages/bioinformatics.scm (jamm): New variable.
2018-11-14 15:13:20 +01:00
e4f4a04a51
gnu: Add r-ouch.
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* gnu/packages/cran.scm (r-ouch): New variable.
2018-11-14 15:13:20 +01:00
10483a64ee
gnu: Add r-activity.
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* gnu/packages/cran.scm (r-activity): New variable.
2018-11-14 15:13:20 +01:00
3cef715a46
gnu: Add r-circular.
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* gnu/packages/cran.scm (r-circular): New variable.
2018-11-14 15:13:20 +01:00
08bf097a0b
gnu: Add r-overlap.
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* gnu/packages/cran.scm (r-overlap): New variable.
2018-11-14 15:13:20 +01:00
acbf23da44
gnu: Add r-acdm.
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* gnu/packages/cran.scm (r-acdm): New variable.
2018-11-14 15:13:20 +01:00
ffdeda3ce0
gnu: Add r-acd.
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* gnu/packages/cran.scm (r-acd): New variable.
2018-11-14 15:13:20 +01:00
488dc4e1e2
gnu: Add r-abn.
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* gnu/packages/cran.scm (r-abn): New variable.
2018-11-14 15:13:20 +01:00
0c92f3734e
gnu: Add r-rjags.
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* gnu/packages/cran.scm (r-rjags): New variable.
2018-11-14 15:13:20 +01:00
0bca8643a2
gnu: Add jags.
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* gnu/packages/statistics.scm (jags): New variable.
2018-11-14 15:13:17 +01:00
51b262f310
gnu: r-txdb-mmusculus-ucsc-mm10-knowngene: Update to 3.4.4.
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* gnu/packages/bioinformatics.scm (r-txdb-mmusculus-ucsc-mm10-knowngene):
Update to 3.4.4.
2018-11-13 23:34:40 +01:00
d34959b8d4
gnu: r-org-mm-eg-db: Update to 3.7.0.
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* gnu/packages/bioinformatics.scm (r-org-mm-eg-db): Update to 3.7.0.
2018-11-13 23:34:40 +01:00
314511b862
gnu: r-org-dm-eg-db: Update to 3.7.0.
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* gnu/packages/bioinformatics.scm (r-org-dm-eg-db): Update to 3.7.0.
2018-11-13 23:34:39 +01:00
76bd16bcf6
gnu: r-org-ce-eg-db: Update to 3.7.0.
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* gnu/packages/bioinformatics.scm (r-org-ce-eg-db): Update to 3.7.0.
2018-11-13 23:34:39 +01:00
fc7683fa30
gnu: r-org-hs-eg-db: Update to 3.7.0.
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* gnu/packages/bioinformatics.scm (r-org-hs-eg-db): Update to 3.7.0.
2018-11-13 23:34:39 +01:00
cb9e6ed702
gnu: r-genomationdata: Update to 1.14.0.
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* gnu/packages/bioinformatics.scm (r-genomationdata): Update to 1.14.0.
2018-11-13 23:34:39 +01:00
13e70f6304
gnu: r-go-db: Update to 3.7.0.
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* gnu/packages/bioinformatics.scm (r-go-db): Update to 3.7.0.
2018-11-13 23:34:39 +01:00
13a574652b
gnu: r-genomeinfodbdata: Update to 1.2.0.
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* gnu/packages/bioinformatics.scm (r-genomeinfodbdata): Update to 1.2.0.
2018-11-13 23:34:39 +01:00
3f995aaf21
gnu: spice-vdagent: Fix typo in desktop file.
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Fixes <https://bugs.gnu.org/33346 >.
* gnu/packages/spice.scm (spice-vdagent)[arguments]: Fix typo in
'patch-spice-vdagent.desktop' phase.
2018-11-13 15:26:30 -05:00
c991806a7d
gnu: ImageMagick: Update to 6.9.10-14.
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* gnu/packages/imagemagick.scm (imagemagick): Update to 6.9.10-14.
2018-11-14 03:09:37 +08:00
d540137509
gnu: libssh: Fetch source over HTTPS.
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* gnu/packages/ssh.scm (libssh)[source]: Use HTTPS URL.
2018-11-13 11:43:35 -05:00
978d59737a
gnu: direnv: Build with Go 1.9.
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* gnu/packages/shellutils.scm (direnv)[native-inputs]: Remove go.
[inputs]: Add go-1.9.
2018-11-13 11:28:23 -05:00
021bf6af18
gnu: Poppler: Fix CVE-2018-19149.
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* gnu/packages/patches/poppler-CVE-2018-19149.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/pdf.scm (poppler)[replacement]: New field.
(poppler/fixed): New variable.
(poppler-qt4, poppler-qt5): Use package/inherit.
2018-11-13 11:28:23 -05:00
8263b9f71f
gnu: certbot, python-acme: Update to 0.28.0.
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* gnu/packages/tls.scm (certbot, python-acme): Update to 0.28.0.
2018-11-13 10:10:42 -05:00
3483f82413
gnu: guix: Update to f5a2724.
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* gnu/packages/package-management.scm (guix): Update to f5a2724
2018-11-13 15:44:25 +01:00
f5a2724ae4
deduplication: Restore directory mtime and permissions after deduplication.
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Fixes <https://bugs.gnu.org/33361 >.
* guix/store/deduplication.scm (replace-with-link): Call 'set-file-time'
and 'chmod' after 'rename-file'.
* tests/nar.scm ("restore-file-set with directories (signed, valid)"):
New test.
2018-11-13 14:59:46 +01:00
8390869811
tests: Check file canonicalization for 'restore-file-set'.
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* guix/tests.scm (canonical-file?): New procedure.
* tests/nar.scm ("restore-file-set (signed, valid)"): Check that every
item of FILES matches 'canonical-file?'.
2018-11-13 14:59:46 +01:00
3ed56ad09b
tests: Remove check for a feature that appeared in Guile 2.0.10.
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* tests/nar.scm: Remove test for 'open-sha256-input-port'.
2018-11-13 14:59:45 +01:00
d3f75179e5
services: nscd: Add 'invalidate' and 'statistics' actions.
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* gnu/services/base.scm (nscd-action-procedure, nscd-actions): New
procedures.
(nscd-shepherd-service): Add 'modules' and 'actions' fields.
* gnu/tests/base.scm (run-basic-test)["nscd invalidate action"]
["nscd invalidate action, wrong table"]: New tests.
* doc/guix.texi (Services): Mention 'herd doc nscd action'.
(Base Services): Document the actions.
2018-11-13 14:59:45 +01:00
Mark H Weaver