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Author SHA1 Message Date
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
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
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
Efraim Flashner
53bcee9ea7
gnu: vifm: Update to 0.10. 
* gnu/packages/vim.scm (vifm): Update to 0.10.
 2018-11-12 12:37:00 +02:00
Pierre Neidhardt
5c4758415d
gnu: go-github-com-aarzilli-golua: Fix for go-1.11. 
* gnu/packages/golang.scm (go-github-com-aarzilli-golua)[arguments]: Fix for go-1.11.
[native-inputs]: Remove lua.
[propagated-inputs]: Add lua.
 2018-11-12 10:31:23 +01:00
Pierre Neidhardt
46a4ae2212
gnu: go-github-com-wtolson-go-taglib: Fix tests and build for go-1.11. 
* gnu/packages/golang.scm (go-github-com-wtolson-go-taglib)[arguments]: Fix tests for go-1.11.
[native-inputs]: Remove pkg-config and taglib.
[propagated-inputs]: Add pkg-config and taglib.
 2018-11-12 10:30:10 +01:00
Pierre Neidhardt
66fa8f0f77
gnu: go-gopkg.in-asn1-ber.v1: Fix tests for go-1.11. 
* gnu/packages/syncthing.scm (go-gopkg.in-asn1-ber.v1): Fix tests for go-1.11.
 2018-11-12 10:29:43 +01:00
Pierre Neidhardt
d4780c8238
gnu: go-github-com-audriusbutkevicius-cli: Fix tests for go-1.11. 
* gnu/packages/syncthing.scm (go-github-com-audriusbutkevicius-cli): Fix tests for go-1.11.
 2018-11-12 10:29:37 +01:00
Pierre Neidhardt
46a37b5966
gnu: go-github-com-prometheus-common-expfmt: Fix tests for go-1.11. 
* gnu/packages/syncthing.scm (go-github-com-prometheus-common-expfmt): Fix tests for go-1.11.
 2018-11-12 10:29:31 +01:00
Pierre Neidhardt
0fd115d536
build-system/go: Plan removal of the pkg folder for go-1.11 onward. 
* guix/build/go-build-system.scm (install): New comment.
 2018-11-12 10:28:46 +01:00
Pierre Neidhardt
9a65a05201
gnu: go: Update default to 1.11. 
* gnu/packages/golang.scm (go): Update default to 1.11.
 2018-11-12 10:28:46 +01:00
Ludovic Courtès
6c843907e9
guix system: Invoking 'guix system init' twice keeps timestamps zeroed. 
Fixes a bug whereby running 'guix system init config.scm /mnt' twice
would, on the second run, change timestamps in /mnt/gnu/store from the
Epoch to now.  This is because the 'register-path' call would bypass the
'reset-timestamps' phase altogether in that case, as a consequence of
commit bb3b6ccb05.

Reported by Christopher Baines.

* guix/scripts/system.scm (install): When TARGET/var/guix exists, delete
it.  As a side-effect, this ensures that later on, the 'register-path'
call invokes 'reset-timestamps' on all the copied store items.
 2018-11-11 23:53:29 +01:00
Ludovic Courtès
652163154c
guix package: '--show' errors when asked for a non-existent package. 
Fixes <https://bugs.gnu.org/33323>.
Reported by swedebugia <swedebugia@riseup.net>.

* guix/scripts/package.scm (process-query): Call 'leave' when
'find-packages-by-name' returns the empty list.
* tests/guix-package.sh: Test it.
 2018-11-11 23:53:29 +01:00
Laura Lazzati
9c001c07d4
doc: Fix typo. 
* doc/guix.texi (Porting to a New Platform): Fix typo.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2018-11-11 23:17:04 +01:00
Ricardo Wurmus
5f9b38ba34
gnu: r-s4vectors: Update to 0.20.1. 
* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.20.1.
 2018-11-11 23:13:48 +01:00
Ricardo Wurmus
06910a8689
gnu: r-rcmdcheck: Update to 1.3.2. 
* gnu/packages/cran.scm (r-rcmdcheck): Update to 1.3.2.
 2018-11-11 23:13:48 +01:00
Ricardo Wurmus
2a4c5877a9
gnu: r-ggpubr: Update to 0.1.9. 
* gnu/packages/cran.scm (r-ggpubr): Update to 0.1.9.
 2018-11-11 23:13:48 +01:00