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Author SHA1 Message Date
Nicolas Goaziou 1477fdf2b0
gnu: rust-syn-1: Update to 1.0.72. 
* gnu/packages/crates-io.scm (rust-syn-1): Update to 1.0.72.
 2021-06-08 11:04:37 +02:00
Nicolas Goaziou d649c724ae
gnu: rust-proc-macro2-1: Update to 1.0.27. 
* gnu/packages/crates-io.scm (rust-proc-macro2-1): Update to 1.0.27.
 2021-06-08 11:04:36 +02:00
Nicolas Goaziou 3b34218705
gnu: rust-globset-0.4: Update to 0.4.6. 
* gnu/packages/crates-io.scm (rust-globset-0.4): Update to 0.4.6.
 2021-06-08 11:04:36 +02:00
Nicolas Goaziou 9aa1d9e0eb
gnu: rust-walkdir-2: Update to 2.3.2. 
* gnu/packages/crates-io.scm (rust-walkdir-2): Update to 2.3.2.
[arguments]<#:cargo-inputs> Reorder alphabetically.
 2021-06-08 11:04:35 +02:00
nixo 5fe9481d2b
gnu: bsnes: Don't build native binaries. 
* gnu/packages/emulators.scm (bsnes)[arguments]: Add configure-flag to
not build native binaries.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2021-06-08 11:24:31 +03:00
Efraim Flashner df3a60d16f
gnu: Add u-boot-sifive-unmatched. 
* gnu/packages/bootloaders.scm (u-boot-sifive-unmatched): New variable.
 2021-06-08 11:06:42 +03:00
Efraim Flashner 024187c049
gnu: u-boot-2021.07: Update to 2021.07-rc4. 
* gnu/packages/bootloaders.scm (u-boot-2021.07): Update to 2021.07-rc4.
 2021-06-08 11:06:37 +03:00
Ludovic Courtès 0c10902609
grafts: Cache the derivation/graft mapping for the whole session. 
Partly fixes <https://bugs.gnu.org/41702>.
Reported by Lars-Dominik Braun <ldb@leibniz-psychology.org>.

Previously, 'graft-derivation' would start anew at every call.  When
creating a profile with lots of packages, it would potentially do the
same work multiple times.  The per-session cache addresses this.  It
increases the derivation-graft-cache hit rate from 77.9% to 80.1% on:

  GUIX_PROFILING="derivation-graft-cache" ./pre-inst-env \
    guix environment --ad-hoc libreoffice inkscape krita darktable -n

The effect is more visible on the pathological case below, where cache
hit rate goes from 75% to 87% and wall-clock time from 5.0s to 3.5s:

  GUIX_PROFILING="derivation-graft-cache" ./pre-inst-env \
    guix environment --ad-hoc r-learnr --search-paths

* guix/grafts.scm (%graft-cache): New variable.
(graft-derivation): Add calls to 'store-connection-cache' and
'set-store-connection-cache!'.
 2021-06-08 09:25:50 +02:00
Ludovic Courtès fde3c349f5
store: 'references/cached' now uses a per-session cache. 
* guix/store.scm (%reference-cache): Remove.
(%reference-cache-id): New variable.
(references/cached): Rewrite in terms of it.
 2021-06-08 09:25:50 +02:00
Ludovic Courtès 2725f04634
store: Remove 'references/substitutes'. 
This procedure lost its only user in commit
710854304b.

* guix/store.scm (references/substitutes): Remove.
* tests/store.scm ("references/substitutes missing reference info")
("references/substitutes with substitute info"): Remove.
 2021-06-08 09:25:50 +02:00
Ludovic Courtès 4a93fb0595
grafts: Use SRFI-71 instead of SRFI-11. 
* guix/grafts.scm (reference-origins): Use SRFI-71 'let*'.
 2021-06-08 09:25:49 +02:00
Ludovic Courtès 6bd3d4fe06
grafts: Record cache lookups for profiling. 
* guix/grafts.scm (record-cache-lookup!): New procedure.
(with-cache): Use it.
 2021-06-08 09:25:49 +02:00
Ludovic Courtès 0a3c723e07
store: Generalize cache lookup recording. 
* guix/store.scm (cache-lookup-recorder): New procedure.
(record-cache-lookup!): Define in terms of it.
 2021-06-08 09:25:49 +02:00
Ludovic Courtès d9d7b9ec41
store: Support dynamic allocation of per-connection caches. 
* guix/store.scm (<store-connection>)[object-cache]: Remove.
[caches]: New field.
(open-connection, port->connection): Adjust '%make-store-connection'
calls accordingly.
(%store-connection-caches, %object-cache-id): New variables.
(allocate-store-connection-cache, vector-set)
(store-connection-cache, set-store-connection-cache)
(set-store-connection-caches!, set-store-connection-cache!): New
procedures.
(cache-object-mapping): Add #:cache parameter.
(set-store-connection-object-cache!): Remove.
(lookup-cached-object): Use 'store-connection-cache'.
(run-with-store): Use 'store-connection-caches' and
'set-store-connection-caches!'.
 2021-06-08 09:25:49 +02:00
Ludovic Courtès dfed76e4ab
gnu: pantheon: Use modern 'define-module' syntax. 
The :prefix bit introduced in 9f59a9b4bc
led to a test failure in 'tests/graph.scm'.

* gnu/packages/pantheon.scm: Write #:prefix, not :prefix.
 2021-06-08 09:25:49 +02:00
Ludovic Courtès 6b752bd29a
doc: Update minimum Guile-Git version. 
* doc/guix.texi (Requirements): Update Guile-Git version.
 2021-06-08 09:07:36 +02:00
Ludovic Courtès f9d8206e5b
news: Fix typo. 
* etc/news.scm: Remove 'x' introduced by mistake in
dfdcd9d812.
 2021-06-08 09:07:36 +02:00
Efraim Flashner 61bce4d143
gnu: python-mappy: Move to (gnu packages bioinformatics). 
* gnu/packages/python-xyz.scm (python-mappy): Move to ...
* gnu/packages/bioinformatics.scm: ... here.
 2021-06-08 09:50:55 +03:00
Maxim Cournoyer fa43419a0f
gnu: jami: Update to 20210606.1.e2f9490. 
* gnu/packages/jami.scm (jami): Update to 20210606.1.e2f9490.
(pjproject-jami)[0019-ignore-down-interfaces]: Apply new custom patch.
(jami-qt)[source]: Use %jami-sources, which now includes the Qt client.
[phases]{change-directory}: New phase.
 2021-06-08 00:04:07 -04:00
Maxim Cournoyer 6bd47fc826
gnu: jami: Always include the custom Jami patches with the sources. 
Before this change, there was a Jami origin containing the sources with the
patches, and another one containing the sources but with the patches removed.
Unify the source to always contain the patches, which adds just 1 MiB to the
corresponding tarball and simplifies things.

* gnu/packages/jami.scm (%jami-sources): Make it a simple variable.  Move the
docstring to a comment.  Only remove the tarballs, always keeping the patches
with the sources.  Adjust the comments.
(%sfl-patches): Remove variable.
(jami-apply-dependency-patches): Rename to...
(jami-apply-custom-patches): ... this.  Adjust the input label used to
'jami-sources'.
(pjproject-jami): Replace %sfl-patches by %jami-sources.  Adjust following the
renaming of the jami-apply-custom-patches procedure.
(ffmpeg-jami): Likewise.  Do not make a temporary binding, simply call the
unquoted jami-apply-custom-patches procedure.
 2021-06-08 00:03:59 -04:00
Maxim Cournoyer d2686be816
gnu: opendht: Update to 2.2.0rc7-1.c8a0b44. 
* gnu/packages/networking.scm (opendht): Update to 2.2.0rc7-1.c8a0b44.
 2021-06-08 00:02:13 -04:00
Leo Famulari b1372ad8cb
gnu: Add l3afpad. 
* gnu/packages/text-editors.scm (l3afpad): New variable.
 2021-06-07 19:23:39 -04:00
Ricardo Wurmus 4a01e00a13
gnu: pigx-rnaseq: Update to 0.0.17. 
* gnu/packages/bioinformatics.scm (pigx-rnaseq): Update to 0.0.17.
[arguments]: Remove "use-latest-salmon" phase; add "set-timezone" phase.
[inputs]: Replace r-gprofiler with r-gprofiler2; add r-ggpubr and
python-deeptools.
[native-inputs]: Add tzdata.
 2021-06-08 00:53:06 +02:00
Leo Famulari fc58d9ac66
gnu: ghostwriter: Update to 2.0.1. 
* gnu/packages/text-editors.scm (ghostwriter): Update to 2.0.1.
 2021-06-07 18:20:07 -04:00
Nicolas Goaziou 69f56c2767
gnu: python-pikepdf: Update to 2.12.2. 
* gnu/packages/python-xyz.scm (python-pikepdf): Update to 2.12.2.
 2021-06-07 23:29:52 +02:00
Jack Hill 732da2201e
gnu: dino: Update to 0.2.1 [fixes CVE-2021-33896]. 
* gnu/packages/messaging.scm (dino): Update to 0.2.1.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2021-06-07 16:51:38 -04:00
Sergey Trofimov 68dcdf6ea7
gnu: qtwebengine: Enable H.264 WebRTC encoding. 
* gnu/packages/qt.scm (qtwebengine)[inputs]: Add openh264.
[source]: Remove bundled openh264.
[arguments]: Adjust build scripts accordingly in the 'substitute-source' phase.
Pass '-webengine-proprietary-codecs' in the custom 'configure' phase.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2021-06-07 16:51:35 -04:00
Xinglu Chen 920dd34a34
gnu: youtube-dl: Update to 2021.06.06. 
* gnu/packages/video.scm (youtube-dl): Update to 2021.06.06.

Signed-off-by: Tobias Geerinckx-Rice <me@tobias.gr>
 2021-06-07 21:52:37 +02:00
Xinglu Chen 245a65bbe1
gnu: isync: Update to 1.4.2. 
* gnu/packages/mail.scm (isync): Update to 1.4.2.

Signed-off-by: Tobias Geerinckx-Rice <me@tobias.gr>
 2021-06-07 21:52:31 +02:00
Ricardo Wurmus be067c908c
gnu: pigx-rnaseq: Adjust to upgrade of salmon. 
* gnu/packages/bioinformatics.scm (pigx-rnaseq)[arguments]: Add phase
"use-latest-salmon".
 2021-06-07 16:50:33 +02:00
Ricardo Wurmus bb38287570
gnu: salmon: Update to 1.4.0. 
* gnu/packages/bioinformatics.scm (salmon): Update to 1.4.0.
[arguments]: Remove unnecessary flags, add other soon-to-be-unnecessary flags;
remove "prepare-rapmap" phase, add "prepare-pufferfish" phase, add
"fix-error-message-in-tests" phase, simplify "use-system-libraries" phase.
[inputs]: Add curl and pufferfish sources; remove libdivsufsort and rapmap
sources.
 2021-06-07 16:50:33 +02:00
Ricardo Wurmus 483cdf36a5
gnu: cereal: Update to 1.3.0. 
* gnu/packages/serialization.scm (cereal): Update to 1.3.0.
 2021-06-07 16:50:33 +02:00
Ricardo Wurmus 9875dae429
gnu: macs: Update to 2.2.7.1. 
* gnu/packages/bioinformatics.scm (macs): Update to 2.2.7.1.
 2021-06-07 16:50:33 +02:00
Ricardo Wurmus 1ace395f9c
gnu: libgff: Update to 2.0.0. 
* gnu/packages/bioinformatics.scm (libgff): Update to 2.0.0.
[home-page]: Update to new home.
 2021-06-07 16:50:33 +02:00
Ricardo Wurmus 176513f5f3
gnu: jellyfish: Update to 2.3.0. 
* gnu/packages/bioinformatics.scm (jellyfish): Update to 2.3.0.
[arguments]: Disable SSE to avoid tuning to the build node's CPU.
[native-inputs]: Replace python-2 with python-wrapper.
[license]: Update.
 2021-06-07 16:50:33 +02:00
Pierre Neidhardt e3611cc412
gnu: sbcl-fof: Update to 0.2.0. 
* gnu/packages/lisp-xyz.scm (sbcl-fof): Update to 0.2.0.
 2021-06-07 14:00:18 +02:00
Christopher Baines 26499816a9
etc: Add "bordeaux.guix.gnu.org.pub" public key file. 
* etc/substitutes/bordeaux.guix.gnu.org.pub: New file.
* Makefile.am (dist_pkgdata_DATA): Add it.
* guix/self.scm (miscellaneous-files): Add
"share/guix/bordeaux.guix.gnu.org.pub".
 2021-06-07 11:31:17 +01:00
Christopher Baines e536fc1786
gnu: guix-build-coordinator: Update to 0-31.4a47417. 
* gnu/packages/package-management.scm (guix-build-coordinator): Update to
0-31.4a47417.
 2021-06-07 10:35:42 +01:00
Ricardo Wurmus 1ac8f05103
gnu: multiqc: Update to 1.10.1. 
* gnu/packages/bioinformatics.scm (multiqc): Update to 1.10.1.
[arguments]: Remove build phase "relax-requirements"; replace "check" phase.
[propagated-inputs]: Add python-coloredlogs, python-future, python-networkx,
and python-rich; remove python-nose.
[native-inputs]: Add python-pytest and the test suite.
 2021-06-07 10:53:16 +02:00
Ricardo Wurmus 856de4f61c
gnu: Add python-rich. 
* gnu/packages/python-xyz.scm (python-rich): New variable.
 2021-06-07 10:53:16 +02:00
Ricardo Wurmus 17f3194150
gnu: python-dataclasses: Update to 0.8. 
* gnu/packages/python-xyz.scm (python-dataclasses): Update to 0.8.
 2021-06-07 10:53:16 +02:00
Ricardo Wurmus f41e56dcf1
gnu: python-attrs: Update to 21.2.0. 
* gnu/packages/python-xyz.scm (python-attrs): Update to 21.2.0.
(python-attrs-bootstrap): Keep this at 19.3.0 to avoid mass rebuilds.
 2021-06-07 10:53:16 +02:00
Ricardo Wurmus 12964df69a
gnu: python-attrs: Conditionally execute tests. 
* gnu/packages/python-xyz.scm (python-attrs)[arguments]: Wrap "check" phase in
conditional expression.
 2021-06-07 10:53:16 +02:00
Mădălin Ionel Patrașcu a8c653f0fc
gnu: python-hic2cool: Update to 0.8.3. 
* gnu/packages/bioinformatics.scm (python-hic2cool): Update to 0.8.3.
[source]: Download using git-fetch.
[arguments]: Enable tests. Add phase to make test data writable.
[propagated-inputs]: Add python-h5py, python-numpy, python-pandas,
python-scipy.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2021-06-07 10:38:54 +03:00
Vinicius Monego e05100aafd
gnu: gtg: Update to 0.5. 
* gnu/packages/gnome.scm (gtg): Update to 0.5.
[inputs]: Add gdk-pixbuf+svg, pango, python-lxml.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2021-06-07 10:38:54 +03:00
Vinicius Monego 1acc0cfbb9
gnu: srain: Update to 1.2.2. 
* gnu/packages/irc.scm (srain): Update to 1.2.2.
[build-system]: Switch to meson-build-system.
[arguments]: Add #:glib-or-gtk?. Remove 'fix-permissions phase.
[native-inputs]: Add python-sphinx.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2021-06-07 10:38:54 +03:00
Matthew James Kraai d0b3af53e0
gnu: xf86-video-vesa: Update to 2.5.0. 
* gnu/packages/xorg.scm (xf86-video-vesa): Update to 2.5.0.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2021-06-07 10:38:54 +03:00
Lars-Dominik Braun dbe607925a
gnu: xpra: Update to 4.2. 
Fixes <https://issues.guix.gnu.org/issue/48890>.

* gnu/packages/xorg.scm (xpra): Update to 4.2.
[source]: Switch to ".tar.gz" archive and update patch file.
[native-inputs]: Add pandoc.
[arguments]: Adjust custom 'fix-paths phase for changes in source.
* gnu/packages/patches/xpra-4.2-systemd-run.patch: Adapt to new version
and rename file.
* gnu/local.mk (dist_patch_DATA): Rename file.

Signed-off-by: Lars-Dominik Braun <lars@6xq.net>
 2021-06-07 09:33:57 +02:00
Ludovic Courtès 4604d43c0e
gnu: gnutls@3.6.16: Fix cross-compilation. 
Fixes <https://bugs.gnu.org/48771>.
Reported by Eric Brown <ecbrown@ericcbrown.com>.

* gnu/packages/tls.scm (gnutls-3.6.16)[arguments]: New field.
 2021-06-06 23:12:18 +02:00
Vinicius Monego c335fbf3cb
gnu: libheif: Update to 1.12.0. 
* gnu/packages/image.scm (libheif): Update to 1.12.0.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2021-06-06 23:12:18 +02:00