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37248 Commits

Author SHA1 Message Date
Efraim Flashner 774f8bbeb1
gnu: linkchecker: Use 'git-file-name' for the source. 
* gnu/packages/web.scm (linkchecker)[source]: Add missing 'file-name'
field.
 2018-11-18 11:57:44 +02:00
Efraim Flashner 74854d11ce
gnu: python-pytest-localserver: Update to 0.5.0. 
* gnu/packages/check.scm (python-pytest-localserver): Update to 0.5.0.
 2018-11-18 11:42:35 +02:00
Efraim Flashner 45a2346f32
gnu: python-pytest-localserver: Fix test suite. 
* gnu/packages/check.scm (python-pytest-localserver): Replace custom
'check phase.
 2018-11-18 11:42:23 +02:00
Efraim Flashner e005ddc223
gnu: libgtextutils: Re-instate custom bootstrap phase. 
The source lacks a standard bootstrap script so the bootstrap phase is
skipped otherwise.

* gnu/packages/textutils.smc (libgtextutils)[arguments]: Replace
'bootstrap phase with upstream's bootstrap phase.
 2018-11-18 10:18:47 +02:00
Ludovic Courtès bc9aa60bd5
gnu: nss: Make tests deterministic. 
Tests would fail once certificates had expired, along these lines:

  chains.sh: Verifying certificate(s)  PayPalEE.cert with flags -d AllDB -pp      -o OID.2.16.840.1.114412.1.1
  vfychain -d AllDB -pp -vv      -o OID.2.16.840.1.114412.1.1  /tmp/guix-build-nss-3.39.drv-0/nss-3.39/nss/tests/libpkix/certs/PayPalEE.cert
  Chain is bad!
  PROBLEM WITH THE CERT CHAIN:
  CERT 0. PayPalEE :
    ERROR -8181: Peer's Certificate has expired.
  Returned value is 1, expected result is pass

Using 'faketime' allows us to get deterministic results.

* gnu/packages/gnuzilla.scm (nss)[arguments]: In 'check' phase, run
'all.sh' under 'faketime'.
[native-inputs]: Add LIBFAKETIME.
 2018-11-17 19:02:18 +01:00
Ludovic Courtès 85b28320d4
gnu: Add libfaketime. 
* gnu/packages/check.scm (libfaketime): New variable.
 2018-11-17 17:40:55 +01:00
Mark H Weaver 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
Mark H Weaver 96272e2822
gnu: databases: Return #t from all phases. 
* 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
Mark H Weaver 9f6f726c7f
gnu: compression: Return #t from all phases. 
* 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
Mark H Weaver 29594404a1
gnu: check: Return #t from all phases. 
* 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
Mark H Weaver ee527187a6
gnu: audio: Return #t from all phases. 
* 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
Mark H Weaver c6bf07d14a
gnu: xorg: Return #t from all phases. 
* 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
Mark H Weaver aa6f87a2b9
gnu: xml: Return #t from all phases. 
* 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
Mark H Weaver 9dcfd6aac9
gnu: video: Return #t from all phases. 
* 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
Mark H Weaver 4851af9ebe
gnu: perl: Return #t from all phases. 
* 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
Mark H Weaver 366c1cbbc6
gnu: networking: Return #t from all phases. 
* 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
Mark H Weaver 9922278b25
gnu: linux: Return #t from all phases. 
* gnu/packages/linux.scm (iproute, ntfs-3g, cpupower, radeontop, tlp):
Return #t from all phases.
 2018-11-14 23:43:57 -05:00
Mark H Weaver fccacffbf4
gnu: image: Return #t from all phases. 
* gnu/packages/image.scm (libpng-apng, pngcrush, leptonica, zimg)
(perceptualdiff): Return #t from all phases.
 2018-11-14 23:43:54 -05:00
Mark H Weaver cb8ba848d2
gnu: admin: Return #t from all phases. 
* 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
Ludovic Courtès 21f7d88e7a
gnu: texlive-bin: Fix substitution regexp. 
This is a followup to commit be200ef316.

* gnu/packages/tex.scm (texlive-bin)[arguments]: In
'disable-failing-test' phase, escape "|" characters.
 2018-11-14 23:49:19 +01:00
Marius Bakke 79ee97a144
Merge branch 'master' into core-updates 2018-11-14 21:20:46 +01:00
Marius Bakke 7d9d521fbc
gnu: aide: Provide libpcre.a and libz.a. 
* gnu/packages/admin.scm (aide)[inputs]: Add PCRE:STATIC and ZLIB:STATIC.
 2018-11-14 21:07:01 +01:00
Marius Bakke e921993c25
gnu: xf86-video-r128: Update to 6.12.0. 
* gnu/packages/xorg.scm (xf86-video-r128): Update to 6.12.0.
 2018-11-14 21:05:30 +01:00
Marius Bakke 24dd6ec38a
gnu: mtools: Update to 4.0.20. 
* 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
Marius Bakke 7939387da8
gnu: nano: Update to 3.2. 
* gnu/packages/nano.scm (nano): Update to 3.2.
 2018-11-14 21:05:30 +01:00
Marius Bakke d63f588486
gnu: sudo: Update to 1.8.26. 
* gnu/packages/admin.scm (sudo): Update to 1.8.26.
 2018-11-14 21:05:30 +01:00
Marius Bakke bac2974e86
gnu: feh: Update to 3.0. 
* gnu/packages/image-viewers.scm (feh): Update to 3.0.
 2018-11-14 21:05:30 +01:00
Ricardo Wurmus ee66a13563
gnu: Add jamm. 
* gnu/packages/bioinformatics.scm (jamm): New variable.
 2018-11-14 15:13:20 +01:00
Ricardo Wurmus e4f4a04a51
gnu: Add r-ouch. 
* gnu/packages/cran.scm (r-ouch): New variable.
 2018-11-14 15:13:20 +01:00
Ricardo Wurmus 10483a64ee
gnu: Add r-activity. 
* gnu/packages/cran.scm (r-activity): New variable.
 2018-11-14 15:13:20 +01:00
Ricardo Wurmus 3cef715a46
gnu: Add r-circular. 
* gnu/packages/cran.scm (r-circular): New variable.
 2018-11-14 15:13:20 +01:00
Ricardo Wurmus 08bf097a0b
gnu: Add r-overlap. 
* gnu/packages/cran.scm (r-overlap): New variable.
 2018-11-14 15:13:20 +01:00
Ricardo Wurmus acbf23da44
gnu: Add r-acdm. 
* gnu/packages/cran.scm (r-acdm): New variable.
 2018-11-14 15:13:20 +01:00
Ricardo Wurmus ffdeda3ce0
gnu: Add r-acd. 
* gnu/packages/cran.scm (r-acd): New variable.
 2018-11-14 15:13:20 +01:00
Ricardo Wurmus 488dc4e1e2
gnu: Add r-abn. 
* gnu/packages/cran.scm (r-abn): New variable.
 2018-11-14 15:13:20 +01:00
Ricardo Wurmus 0c92f3734e
gnu: Add r-rjags. 
* gnu/packages/cran.scm (r-rjags): New variable.
 2018-11-14 15:13:20 +01:00
Ricardo Wurmus 0bca8643a2
gnu: Add jags. 
* gnu/packages/statistics.scm (jags): New variable.
 2018-11-14 15:13:17 +01:00
Ricardo Wurmus 51b262f310
gnu: r-txdb-mmusculus-ucsc-mm10-knowngene: Update to 3.4.4. 
* gnu/packages/bioinformatics.scm (r-txdb-mmusculus-ucsc-mm10-knowngene):
Update to 3.4.4.
 2018-11-13 23:34:40 +01:00
Ricardo Wurmus d34959b8d4
gnu: r-org-mm-eg-db: Update to 3.7.0. 
* gnu/packages/bioinformatics.scm (r-org-mm-eg-db): Update to 3.7.0.
 2018-11-13 23:34:40 +01:00
Ricardo Wurmus 314511b862
gnu: r-org-dm-eg-db: Update to 3.7.0. 
* gnu/packages/bioinformatics.scm (r-org-dm-eg-db): Update to 3.7.0.
 2018-11-13 23:34:39 +01:00
Ricardo Wurmus 76bd16bcf6
gnu: r-org-ce-eg-db: Update to 3.7.0. 
* gnu/packages/bioinformatics.scm (r-org-ce-eg-db): Update to 3.7.0.
 2018-11-13 23:34:39 +01:00
Ricardo Wurmus fc7683fa30
gnu: r-org-hs-eg-db: Update to 3.7.0. 
* gnu/packages/bioinformatics.scm (r-org-hs-eg-db): Update to 3.7.0.
 2018-11-13 23:34:39 +01:00
Ricardo Wurmus cb9e6ed702
gnu: r-genomationdata: Update to 1.14.0. 
* gnu/packages/bioinformatics.scm (r-genomationdata): Update to 1.14.0.
 2018-11-13 23:34:39 +01:00
Ricardo Wurmus 13e70f6304
gnu: r-go-db: Update to 3.7.0. 
* gnu/packages/bioinformatics.scm (r-go-db): Update to 3.7.0.
 2018-11-13 23:34:39 +01:00
Ricardo Wurmus 13a574652b
gnu: r-genomeinfodbdata: Update to 1.2.0. 
* gnu/packages/bioinformatics.scm (r-genomeinfodbdata): Update to 1.2.0.
 2018-11-13 23:34:39 +01:00
Taegil Bae 3f995aaf21
gnu: spice-vdagent: Fix typo in desktop file. 
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
Alex Vong c991806a7d
gnu: ImageMagick: Update to 6.9.10-14. 
* gnu/packages/imagemagick.scm (imagemagick): Update to 6.9.10-14.
 2018-11-14 03:09:37 +08:00
Leo Famulari d540137509
gnu: libssh: Fetch source over HTTPS. 
* gnu/packages/ssh.scm (libssh)[source]: Use HTTPS URL.
 2018-11-13 11:43:35 -05:00
Leo Famulari 978d59737a
gnu: direnv: Build with Go 1.9. 
* gnu/packages/shellutils.scm (direnv)[native-inputs]: Remove go.
[inputs]: Add go-1.9.
 2018-11-13 11:28:23 -05:00
Leo Famulari 021bf6af18
gnu: Poppler: Fix CVE-2018-19149. 
* 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