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39281 Commits

Author SHA1 Message Date
Ludovic Courtès 7a54b2281d
gnu: guix-daemon: Install 'guix-authenticate'. 
Fixes <https://bugs.gnu.org/33368>.
Reported by Konrad Hinsen <konrad.hinsen@fastmail.net>.

* gnu/packages/package-management.scm (guix-daemon)[arguments]: In
'install' phase, build "install-nodist_libexecSCRIPTS" target to install
'guix-authenticate'.
 2018-11-14 21:34:08 +01:00
Ludovic Courtès 89f1fee8e7
download: Access content-addressed mirrors over HTTPS. 
Bug <http://bugs.gnu.org/22774> is no longer relevant now that we use
"builtin:download" exclusively.

* guix/download.scm (%content-addressed-mirrors): Use "https", not
"http".
 2018-11-14 21:34:08 +01:00
Ludovic Courtès ee2cfdfe86
download: Add Software Heritage as a content-addressed mirror. 
* guix/download.scm (%content-addressed-mirrors): Add Software
Heritage.
 2018-11-14 21:34:07 +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
Leo Famulari 8263b9f71f
gnu: certbot, python-acme: Update to 0.28.0. 
* gnu/packages/tls.scm (certbot, python-acme): Update to 0.28.0.
 2018-11-13 10:10:42 -05:00
Ludovic Courtès 3483f82413
gnu: guix: Update to f5a2724. 
* gnu/packages/package-management.scm (guix): Update to f5a2724.
 2018-11-13 15:44:25 +01:00
Ludovic Courtès f5a2724ae4
deduplication: Restore directory mtime and permissions after deduplication. 
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
Ludovic Courtès 8390869811
tests: Check file canonicalization for 'restore-file-set'. 
* 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
Ludovic Courtès 3ed56ad09b
tests: Remove check for a feature that appeared in Guile 2.0.10. 
* tests/nar.scm: Remove test for 'open-sha256-input-port'.
 2018-11-13 14:59:45 +01:00
Ludovic Courtès d3f75179e5
services: nscd: Add 'invalidate' and 'statistics' actions. 
* 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
Ludovic Courtès 190877748e
services: mcron: Fix typo in comment. 
* gnu/services/mcron.scm (shepherd-schedule-action): Fix typo in comment.
 2018-11-13 14:59:45 +01:00
Ludovic Courtès 1afe1985f5
nar: Access the database instead of connecting to the daemon. 
* guix/store/database.scm (%default-database-file): New variable.
(path-id): Export.
* guix/nar.scm (finalize-store-file): Use 'with-database' instead of
'with-store', and use 'path-id' instead of 'valid-path?'.
 2018-11-13 14:59:45 +01:00
Oleg Pykhalov 155956449a
gnu: restic: Fix build phase. 
* gnu/packages/backup.scm (restic)[arguments]: Set "HOME" environment variable
in build phase.
 2018-11-13 15:03:15 +03:00
Ricardo Wurmus 6018683683
gnu: c-toxcore: Fetch sources from git. 
* gnu/packages/messaging.scm (c-toxcore)[source]: Fetch from git.
 2018-11-13 10:51:41 +01:00
Ricardo Wurmus 05a5721f06
build-system/dub: Let all phases return #T unconditionally. 
* guix/build/dub-build-system.scm (configure, build, check): Return #T
unconditionally; use INVOKE.
 2018-11-13 10:46:00 +01:00
Rutger Helling 7fed5481fe
gnu: wine-staging: Update to 3.20. 
* gnu/packages/wine.scm (wine-staging-patchset-data): Update to 3.20.
* gnu/packages/wine.scm (wine-staging): Update to 3.20.
 2018-11-13 10:24:42 +01:00
Julien Lepiller 0dd60c1c9b
gnu: php: Update to 7.2.12. 
* gnu/packages/php.scm (php): Update to 7.2.12.
 2018-11-12 23:57:42 +01:00
Ludovic Courtès c6080c3249
store: Add a functional object cache and use it in 'lower-object'. 
This leads to ~25% improvements on things like:

  guix system build desktop.tmpl --no-grafts -d

* guix/store.scm (<nix-server>)[object-cache]: New field.
* guix/store.scm (open-connection): Initialize it.
(cache-object-mapping, lookup-cached-object, %mcached): New procedures.
(mcached): New macro.
* guix/gexp.scm (lower-object): Use it.
* guix/grafts.scm (grafting?): New procedure.
 2018-11-12 23:37:13 +01:00
Ludovic Courtès 9ed86fe175
tests: Add 'test-assertm' to (guix tests). 
* guix/tests.scm (test-assertm): New macro.
* tests/gexp.scm (test-assertm): Remove.
* tests/profiles.scm (test-assertm): Remove.
* tests/challenge.scm (%store, test-assertm): Remove.
* tests/debug-link.scm (%store, test-assertm): Remove.
* tests/size.scm (%store, test-assertm): Remove.
 2018-11-12 23:37:13 +01:00
Ricardo Wurmus 1767581fb5
build-system/haskell: Fix register phase. 
This is a follow-up to commit a7e231a2a3.

Reported by Marius Bakke <mbakke@fastmail.com>.

* guix/build/haskell-build-system.scm (register): Use "when" instead of
"unless".
 2018-11-12 18:21:04 +01:00
Arun Isaac e740a90228
gnu: youtube-dl: Update to 2018.11.07. 
* gnu/packages/video.scm (youtube-dl): Update to 2018.11.07.
 2018-11-12 22:09:12 +05:30