3941cf5afa
gnu: Add python-fenics-ufl.
...
* gnu/packages/simulation.scm (python-fenics-ufl): New variable.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2018-11-14 21:34:08 +01:00
f7a4757a4c
gnu: Add python-fenics-dijitso.
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* gnu/packages/simulation.scm (python-fenics-dijitso): New varaible.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2018-11-14 21:34:08 +01:00
6b5687d053
gnu: Add python-slepc4py.
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* gnu/packages/maths.scm (python-slepc4py): New variable.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2018-11-14 21:34:08 +01:00
90ff287401
gnu: Add python-petsc4py.
...
* gnu/packages/maths.scm (python-petsc4py): New variable.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2018-11-14 21:34:08 +01:00
54fcd547b3
gnu: Add python-mpi4py.
...
* gnu/packages/mpi.scm (python-mpi4py): New variable.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2018-11-14 21:34:08 +01:00
0fe1fba4af
daemon: Install 'authenticate' script under LIBEXECDIR/guix.
...
That way it is handled in the same way as other helper scripts.
* nix/scripts/guix-authenticate.in: Rename to...
* nix/scripts/authenticate.in: ... this.
* config-daemon.ac: Adjust accordingly.
* nix/local.mk (libstore_a_CPPFLAGS): Remove -DOPENSSL_PATH.
(nodist_libexec_SCRIPTS): Remove.
(nodist_pkglibexec_SCRIPTS): New variable.
* nix/nix-daemon/guix-daemon.cc (main): Remove 'setenv' call for
"PATH".
* nix/libstore/local-store.cc (runAuthenticationProgram): New function.
(LocalStore::exportPath, LocalStore::importPath): Use it instead of
'runProgram' and OPENSSL_PATH.
2018-11-14 21:34:08 +01:00
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
89f1fee8e7
download: Access content-addressed mirrors over HTTPS.
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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
ee2cfdfe86
download: Add Software Heritage as a content-addressed mirror.
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* guix/download.scm (%content-addressed-mirrors): Add Software
Heritage.
2018-11-14 21:34:07 +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.
...
* 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.
...
* gnu/packages/image-viewers.scm (feh): Update to 3.0.
2018-11-14 21:05:30 +01:00
ee66a13563
gnu: Add jamm.
...
* gnu/packages/bioinformatics.scm (jamm): New variable.
2018-11-14 15:13:20 +01:00
e4f4a04a51
gnu: Add r-ouch.
...
* gnu/packages/cran.scm (r-ouch): New variable.
2018-11-14 15:13:20 +01:00
10483a64ee
gnu: Add r-activity.
...
* gnu/packages/cran.scm (r-activity): New variable.
2018-11-14 15:13:20 +01:00
3cef715a46
gnu: Add r-circular.
...
* gnu/packages/cran.scm (r-circular): New variable.
2018-11-14 15:13:20 +01:00
08bf097a0b
gnu: Add r-overlap.
...
* gnu/packages/cran.scm (r-overlap): New variable.
2018-11-14 15:13:20 +01:00
acbf23da44
gnu: Add r-acdm.
...
* gnu/packages/cran.scm (r-acdm): New variable.
2018-11-14 15:13:20 +01:00
ffdeda3ce0
gnu: Add r-acd.
...
* gnu/packages/cran.scm (r-acd): New variable.
2018-11-14 15:13:20 +01:00
488dc4e1e2
gnu: Add r-abn.
...
* gnu/packages/cran.scm (r-abn): New variable.
2018-11-14 15:13:20 +01:00
0c92f3734e
gnu: Add r-rjags.
...
* gnu/packages/cran.scm (r-rjags): New variable.
2018-11-14 15:13:20 +01:00
0bca8643a2
gnu: Add jags.
...
* 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.
...
* 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.
...
* 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.
...
* 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.
...
* 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.
...
* 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.
...
* 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.
...
* 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
190877748e
services: mcron: Fix typo in comment.
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* gnu/services/mcron.scm (shepherd-schedule-action): Fix typo in comment.
2018-11-13 14:59:45 +01:00
1afe1985f5
nar: Access the database instead of connecting to the daemon.
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* 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
155956449a
gnu: restic: Fix build phase.
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* gnu/packages/backup.scm (restic)[arguments]: Set "HOME" environment variable
in build phase.
2018-11-13 15:03:15 +03:00
6018683683
gnu: c-toxcore: Fetch sources from git.
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* gnu/packages/messaging.scm (c-toxcore)[source]: Fetch from git.
2018-11-13 10:51:41 +01:00
7fed5481fe
gnu: wine-staging: Update to 3.20.
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* 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
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
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
Paul Garlick