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Author SHA1 Message Date
Ludovic Courtès 7750f220be
gnu: tor: Record the file name of 'torsocks' in 'torify'. 
* gnu/packages/tor.scm (tor)[arguments]: Add 'adjust-torify' phase.
[inputs]: Add TORSOCKS.
 2022-05-30 16:34:39 +02:00
Ludovic Courtès 61d4f9e89d
tests: Adjust crate importer test to spdx changes. 
This is a followup to 95b0544fcf.

* tests/crate.scm ("licenses: MIT/Apache-2.0 AND BSD-2-Clause"): Adjust
expected result.
 2022-05-30 16:34:39 +02:00
Ludovic Courtès 1ae0e1dc29
store: 'map/accumulate-builds' preserves caches. 
Fixes <https://issues.guix.gnu.org/55721>.

Starting from the switch to functional object caches ca.
9e5812ac59, we would be losing accumulated
caches when aborting to the build handler.  This patch fixes that.

In particular, by preserving '%reference-cache-id', we avoid redundant
'query-references' RPCs, which accounted for a large part of the extra
processing time.

* guix/store.scm (build-accumulator): When returning an <unresolved>
node, call 'set-store-connection-caches!' before and after to preserve
caches.
(map/accumulate-builds): Pass STORE as the first argument to
the <unresolved> continuation.
 2022-05-30 16:34:39 +02:00
Ricardo Wurmus 281bf72745
gnu: r-lmom: Update to 2.9. 
* gnu/packages/statistics.scm (r-lmom): Update to 2.9.
 2022-05-30 15:35:04 +02:00
Ricardo Wurmus eba783130f
gnu: r-chron: Update to 2.3-57. 
* gnu/packages/statistics.scm (r-chron): Update to 2.3-57.
 2022-05-30 15:34:59 +02:00
Ricardo Wurmus 85e77d93ac
gnu: r-tree: Update to 1.0-42. 
* gnu/packages/cran.scm (r-tree): Update to 1.0-42.
 2022-05-30 15:34:52 +02:00
Ricardo Wurmus 440bd1b617
gnu: r-parameters: Update to 0.18.1. 
* gnu/packages/cran.scm (r-parameters): Update to 0.18.1.
 2022-05-30 15:34:46 +02:00
Ricardo Wurmus 0880acbcb5
gnu: r-clue: Update to 0.3-61. 
* gnu/packages/cran.scm (r-clue): Update to 0.3-61.
 2022-05-30 15:34:39 +02:00
Ricardo Wurmus 7815efe731
gnu: r-cobs: Update to 1.3-5. 
* gnu/packages/cran.scm (r-cobs): Update to 1.3-5.
 2022-05-30 15:34:34 +02:00
Ricardo Wurmus 56373df33a
gnu: r-gee: Update to 4.13-23. 
* gnu/packages/cran.scm (r-gee): Update to 4.13-23.
 2022-05-30 15:34:28 +02:00
Ricardo Wurmus d3cb071050
gnu: r-qpdf: Update to 1.2.0. 
* gnu/packages/cran.scm (r-qpdf): Update to 1.2.0.
[source]: Remove trailing #T from snippet.
[arguments]: Remove trailing #T from 'configure phase.
[inputs]: Add libjpeg-turbo.
 2022-05-30 15:30:47 +02:00
Ricardo Wurmus bfcae1efbb
gnu: r-batchelor: Update to 1.12.1. 
* gnu/packages/bioconductor.scm (r-batchelor): Update to 1.12.1.
 2022-05-30 15:16:35 +02:00
Efraim Flashner d2a9142852
gnu: gcc-9: Update to 9.5.0. 
* gnu/packages/gcc.scm (gcc-9): Update to 9.5.0.
 2022-05-30 15:28:04 +03:00
Efraim Flashner dc26d0f94e
gnu: hello: Update to 2.12.1. 
* gnu/packages/base.scm (hello): Update to 2.12.1.
 2022-05-30 15:28:04 +03:00
Efraim Flashner a037815f62
gnu: nss: Skip tests on riscv64-linux. 
* gnu/packages/nss.scm (nss)[arguments]: Skip tests when building for
riscv64-linux.
 2022-05-30 15:26:17 +03:00
Efraim Flashner 19e1045352
gnu: nss: Adjust make-flags for riscv64-linux. 
* gnu/packages/nss.scm (nss)[arguments]: When building for riscv64-linux
don't build the binaries with gtest.
 2022-05-30 15:18:17 +03:00
Evgenii Lepikhin 69b27be15d
gnu: Add rust-serde-regex-1. 
* gnu/packages/crates-io.scm (rust-serde-regex-1): New variable.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2022-05-30 11:13:53 +03:00
Evgenii Lepikhin 6ec464ced7
gnu: rust-nom-7: Update to 7.1.1. 
* gnu/packages/crates-io.scm (rust-nom-7): Update to 7.1.1.
[arguments]: In cargo-inputs replace rust-minimal-lexical-0.1 with 0.2.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2022-05-30 11:13:52 +03:00
Evgenii Lepikhin 4f5a71d5b7
gnu: Add rust-minimal-lexical-0.2. 
* gnu/packages/crates-io.scm (rust-minimal-lexical-0.2): New variable.
(rust-minimal-lexical-0.1): Inherit from rust-minimal-lexical-0.2.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2022-05-30 11:13:52 +03:00
Evgenii Lepikhin 4b18cb437a
gnu: Add rust-located-yaml-0.2. 
* gnu/packages/crates-io.scm (rust-located-yaml-0.2) New variable.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2022-05-30 11:13:51 +03:00
Evgenii Lepikhin 30cf5284b2
gnu: Add rust-pretty-0.11. 
* gnu/packages/crates-io.scm (rust-pretty-0.11) New variable.
(rust-pretty-0.5): Inherit from rust-pretty-0.11.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2022-05-30 11:13:51 +03:00
Evgenii Lepikhin acada2580f
gnu: Add rust-nom-locate-4. 
* gnu/packages/crates-io.scm (rust-nom-locate-4): New variable.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2022-05-30 11:13:50 +03:00
Efraim Flashner 4259a6516a
gnu: virtuoso-ose: Register patch. 
This is a follow-up to 48efbde7a9.

* gnu/local.mk (dist_patch_DATA): Register patch.
 2022-05-30 10:42:47 +03:00
Efraim Flashner 1a8519dd01
gnu: yt-dlp: Remove trailing #t. 
* gnu/packages/video.scm (yt-dlp)[source]: Remove trailing #t from
snippet.
[arguments]: Remove trailing #t from phases.
 2022-05-30 10:41:28 +03:00
Efraim Flashner d56506aad5
gnu: yt-dlp: Update to 2022.05.18. 
* gnu/packages/video.scm (yt-dlp): Update to 2022.05.18.
[inputs]: Add python-brotli and python-certifi.
 2022-05-30 10:41:28 +03:00
Efraim Flashner e5dd864e68
gnu: links: Update to 2.27. 
* gnu/packages/web-browsers.scm (links): Update to 2.27.
 2022-05-30 10:41:25 +03:00
Roel Janssen 48efbde7a9
gnu: virtuoso-ose: Update to 7.2.7. 
* gnu/packages/databases.scm (virtuoso-ose): Update to 7.2.7; Run autogen
  after applying the patch below.
* gnu/packages/patches/virtuoso-ose-remove-pre-built-jar-files.patch:
  New file.
 2022-05-30 09:03:02 +02:00
Mark H Weaver 7f63a6aefc
gnu: icecat: Update to 91.9.1-guix0-preview1 [security fixes]. 
Includes fixes for CVE-2022-1529 and CVE-2022-1802.

* gnu/packages/gnuzilla.scm (%icecat-version, %icecat-build-id): Update.
(icecat-source): Update gnuzilla commit, base version, and hashes.
 2022-05-29 23:21:41 -04:00
Wiktor Zelazny acb08304c8
gnu: Add python-gpy. 
* gnu/packages/python-science.scm (python-gpy): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-05-29 23:56:06 +02:00
Wiktor Zelazny 6400f08d07
gnu: Add python-paramz. 
* gnu/packages/python-science.scm (python-paramz): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-05-29 23:56:05 +02:00
Wiktor Zelazny 6dacd15381
gnu: Add python-climin. 
* gnu/packages/python-science.scm (python-climin): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-05-29 23:56:05 +02:00
Felix Gruber 3d1b2bc740
gnu: wla-dx: Update to 10.1. 
* gnu/packages/assembly.scm (wla-dx): Update to 10.1.
[native-inputs]: Use new style.
[arguments]: Add custom 'check phase to run run_tests.sh.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-05-29 23:56:05 +02:00
Ludovic Courtès 40530ffd15
store: Record cache lookups in 'references/cached'. 
* guix/store.scm (references/cached): Add call to
'record-cache-lookup!'.
 2022-05-29 23:56:01 +02:00
Danny Milosavljevic 98e2f4fbeb
gnu: openjdk: Update to 17.0.3. 
* gnu/packages/java.scm (openjdk17): Update to 17.0.3.
 2022-05-29 22:57:19 +02:00
Julien Lepiller d1f4b6dc83
gnu: python-translate-toolkit: Update to 3.6.2. 
* gnu/packages/python-xyz.scm (python-translate-toolkit): Update to
  3.6.2.
 2022-05-29 22:20:15 +02:00
Julien Lepiller 31a9d8677c
gnu: python-user-agents: Update to 2.2.0. 
* gnu/packages/python-xyz.scm (python-user-agents): Update to 2.2.0.
 2022-05-29 21:30:45 +02:00
Julien Lepiller 92a83f38b5
gnu: python-ua-parser: Update to 0.10.0. 
* gnu/packages/python-xyz.scm (python-ua-parser): Update to 0.10.0.
 2022-05-29 21:30:16 +02:00
Efraim Flashner e8b2219152
gnu: lagrange: Update to 1.13.6. 
* gnu/packages/web-browsers.scm (lagrange): Update to 1.13.6.
[source]: Adjust snippet to remove another bundled library.
 2022-05-29 19:26:47 +03:00
Efraim Flashner 9cd22702b8
gnu: wget: Update to 1.21.3. 
* gnu/packages/wget.scm (wget): Update to 1.21.3.
 2022-05-29 16:31:59 +03:00
Efraim Flashner 1ed40eee39
gnu: mutt: Update to 2.2.5. 
* gnu/packages/mail.scm (mutt): Update to 2.2.5.
 2022-05-29 16:31:59 +03:00
Efraim Flashner 46ed423e28
gnu: git-annex: Update to 10.20220525. 
* gnu/packages/haskell-apps.scm (git-annex): Update to 10.20220525.
 2022-05-29 16:31:59 +03:00
Efraim Flashner e4fe344a5c
gnu: nmap: Honor tests? flag. 
* gnu/packages/admin.scm (nmap)[arguments]: In custom 'check phase honor
the #:tests? flag.
 2022-05-29 16:31:09 +03:00
Efraim Flashner 50970a28b7
gnu: wgetpaste: Remove trailing #t from phases. 
* gnu/packages/wget.scm (wgetpaste)[arguments]: Remove trailing #t from
phases.
 2022-05-29 16:31:09 +03:00
Efraim Flashner c62be7d530
gnu: wgetpaste: Add missing input. 
* gnu/packages/wget.scm (wgetpaste)[inputs]: Add bash-minimal.
 2022-05-29 16:23:48 +03:00
cage 69af8a6837
gnu: telescope: Update to 0.8.1. 
* gnu/packages/web-browsers.scm (telescope): Update to 0.8.1.
[home-page]: Update to new upstream home-page.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2022-05-29 16:10:34 +03:00
Efraim Flashner d540e686ef
gnu: Add pbuilder. 
* gnu/packages/debian.scm (pbuilder): New variable.
 2022-05-29 16:01:02 +03:00
Rene Saavedra b456086c65
gnu: apostrophe: Build with correct webkitgtk. 
* gnu/packages/gnome.scm (apostrophe)[inputs]: Replace webkitgtk with
webkitgtk-with-libsoup2.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2022-05-29 15:53:48 +03:00
Ricardo Wurmus e640da33f3
Merge branch 'wip-r' 2022-05-29 11:49:03 +02:00
Ricardo Wurmus 89e9262012
gnu: r-bsgenome-hsapiens-ucsc-hg19-masked: Update to 1.3.993. 
* gnu/packages/bioconductor.scm (r-bsgenome-hsapiens-ucsc-hg19-masked): Update to 1.3.993.
 2022-05-29 11:44:09 +02:00
Efraim Flashner 926fcb488b
gnu: clang-from-llvm: Fix building on riscv64-linux. 
* gnu/packages/llvm.scm (clang-from-llvm)[arguments]: When building for
riscv64-linux add configure-flags and make-flags to ensure linking with
'-latomic'.
 2022-05-29 08:46:17 +03:00