66dd088d3c
maint: Add gnupg to the manifest.
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* manifest.scm: Add gnupg.
Change-Id: Id5e90f87e5c3a07aa3e49afa97cc0b6d3ce71b41
2024-01-31 09:07:25 +01:00
323b58ac18
channels: ‘latest-channel-instances’ traverses user-provided channels first.
...
Previously, ‘latest-channel-instances’ would perform a depth-first
traversal of channels. Since dependencies specified in ‘.guix-channel’
are usually less specific that those provided by the user, this would
lead to the use of instances corresponding to those less specific specs,
which in turn might declare dependencies that do not exist for the more
specific instances.
This commit changes ‘latest-channel-instances’ to perform a
breadth-first traversal, thereby giving user-supplied channels higher
precedence over dependencies found via ‘.guix-channel’.
Fixes <https://issues.guix.gnu.org/68822 >.
* guix/channels.scm (latest-channel-instances)[ignore?]: Remove.
[instance-name, same-named?, more-specific?]: New procedures.
Rewrite as a breadth-first traversal using a regular loop.
* tests/channels.scm ("latest-channel-instances reads dependencies from most-specific instance"):
New test.
Change-Id: Iba518145cfd209f04293a56246dbfee3b714650b
2024-01-31 09:07:25 +01:00
36d654fa54
channels: Tweak test.
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* tests/channels.scm ("latest-channel-instances excludes duplicate channel dependencies"):
Use ‘equal?’ rather than ‘string=?’ since we can get #f.
Change-Id: I437b9d7e23200cf0c98b1593e68b1d355bc2de01
2024-01-31 09:07:25 +01:00
88e8b807d6
gnu: torbrowser: Copy buildID from the official build.
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* gnu/packages/tor.scm (%moz-build-date): Update to 20240115174022.
Reported-by: André Batista <nandre@riseup.net>
Change-Id: Ia057d6efe9db9e04ece03d994ee226ecdbc6cc04
2024-01-31 03:02:07 +01:00
c4687f5437
Revert "gnu: Add minify."
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This reverts commit f8c2d8141ehttps://ci.guix.gnu.org/eval/1086875/log/raw >
Change-Id: I26e02842980cf09e924ac1cae8f3a6421a005276
2024-01-30 23:56:11 +00:00
7a63fba807
teams: go: Add golang-xyz.scm to scope.
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* etc/teams.scm (go): Add "gnu/packages/golang-xyz.scm".
Change-Id: I580eadf52b631c6582e256a2900786b53483a466
2024-01-30 22:58:22 +00:00
f8c2d8141e
gnu: Add minify.
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* gnu/packages/web.scm (minify): New variable.
Co-authored-by: Sharlatan Hellseher <sharlatanus@gmail.com>
Co-authored-by: Hilton Chain <hako@ultrarare.space>
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
Change-Id: I7289c77a17f63501b6c7771606d396241333ac3a
2024-01-30 22:58:22 +00:00
aab6ea6f41
gnu: Add go-github-com-matryer-try.
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* gnu/packages/golang-check.scm (go-github-com-matryer-try): New variable.
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
Change-Id: Ic354425938374fcd29e871a597da63a7a390cfa1
2024-01-30 22:58:22 +00:00
b998d58221
gnu: Add go-github-com-djherbis-atime.
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* gnu/packages/golang-xyz.scm (go-github-com-djherbis-atime): New variable.
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
Change-Id: I320070d68e7f590f830060904f5cbdf59d839d1d
2024-01-30 22:58:22 +00:00
376bba6030
gnu: Add (gnu packages golang-xyz) module.
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* gnu/packages/golang-xyz.scm: New file.
* gnu/local.mk: Add to gnu/packages/golang-xyz.scm scope.
Change-Id: I25e434de1adc29c2f08146f040755287c63632d6
2024-01-30 22:58:22 +00:00
fb2b72a5f3
gnu: go-github-com-go-jose-go-jose-v3: Move to (gnu packages golang-web).
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Drop inheritance from go-gopkg-in-square-go-jose-v2 as it's archived by
the owner on Feb 27, 2023.
* gnu/packages/golang.scm (go-github-com-go-jose-go-jose-v3): Move from
here ...
* gnu/packages/golang-web.scm: ... to here.
Change-Id: I67838e18a43d93e5ae3b62e9645b7d22cf474103
2024-01-30 22:58:22 +00:00
f6bbee5f05
gnu: axoloti-patcher: Add missing headers.
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* gnu/packages/axoloti.scm (axoloti-patcher)[arguments]: Include generic
headers in search paths.
Change-Id: I2e1819966eb657ba4a7e0c823e6686de8599dd9a
2024-01-30 22:44:43 +01:00
c2dc19aecc
gnu: axoloti-patcher: Use G-expression.
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* gnu/packages/axoloti.scm (axoloti-patcher)[arguments]: Use G-expression;
delete 'make-git-checkout-writable phase.
Change-Id: I4f9b98351f1752391211f1aed84d484184d32771
2024-01-30 22:44:09 +01:00
bed3a0b547
gnu: yggdrasil: Update to 0.5.5.
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* gnu/packages/networking.scm (yggdrasil): Update to 0.5.5.
Change-Id: Iba086d544e8225ec1b08de80f0fc3f01aa1f17b3
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2024-01-30 17:11:54 +01:00
a901e950dd
gnu: guile-hoot: Update to 0.3.0.
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* gnu/packages/guile-xyz.scm (guile-hoot): Update to 0.3.0.
Change-Id: I355d4b11bdd45bf87e3d7227f259907b1e7d57bd
2024-01-30 11:08:37 -05:00
7cdad00e30
gnu: r-scran: Update to 1.30.2.
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* gnu/packages/bioconductor.scm (r-scran): Update to 1.30.2.
Change-Id: I49388f6307f88cb671b0a721cc4c82a4804312c6
2024-01-30 16:59:52 +01:00
aa7950070b
gnu: r-bioccheck: Update to 1.38.2.
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* gnu/packages/bioconductor.scm (r-bioccheck): Update to 1.38.2.
[propagated-inputs]: Remove r-httr; add r-httr2 and r-rvest.
Change-Id: I5bcf99f2e3e93141fe502f061c2f347d4f0783bc
2024-01-30 16:59:51 +01:00
8d8eec7f9d
gnu: r-flowcore: Update to 2.14.1.
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* gnu/packages/bioconductor.scm (r-flowcore): Update to 2.14.1.
Change-Id: I7a8002206aaab85a722463a81939d7cea7d61644
2024-01-30 16:59:51 +01:00
9e1e462746
gnu: r-rsubread: Update to 2.16.1.
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* gnu/packages/bioconductor.scm (r-rsubread): Update to 2.16.1.
Change-Id: Id01d956d2f76347270d05961dba13f65b268862a
2024-01-30 16:59:51 +01:00
ca6e432089
gnu: r-edger: Update to 4.0.12.
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* gnu/packages/bioconductor.scm (r-edger): Update to 4.0.12.
Change-Id: If99f10f80fb7c085863d2da79cfce2b94af71543
2024-01-30 16:59:51 +01:00
4df162962d
gnu: r-biostrings: Update to 2.70.2.
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* gnu/packages/bioconductor.scm (r-biostrings): Update to 2.70.2.
Change-Id: Id43796f35c5afe6fbe3a37d72e111d28937254a2
2024-01-30 16:59:51 +01:00
1c27a3a8a8
gnu: r-biomart: Update to 2.58.1.
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* gnu/packages/bioconductor.scm (r-biomart): Update to 2.58.1.
Change-Id: I6304e3be6919367f5d9d99ddb7aae75ab39b9985
2024-01-30 16:59:51 +01:00
6f11ca52f1
gnu: r-robustbase: Update to 0.99-2.
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* gnu/packages/statistics.scm (r-robustbase): Update to 0.99-2.
Change-Id: Ic6a248fd55b6b4467742040a884ed25e9d090f47
2024-01-30 15:48:57 +01:00
ef5640f763
gnu: r-viridis: Update to 0.6.5.
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* gnu/packages/statistics.scm (r-viridis): Update to 0.6.5.
Change-Id: Iaa83edbc2a304e0327f8815967f2e28b686691a0
2024-01-30 15:48:57 +01:00
c72ceba47f
gnu: r-commonmark: Update to 1.9.1.
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* gnu/packages/statistics.scm (r-commonmark): Update to 1.9.1.
Change-Id: Ifccd39448f0d6181bfcede089aa922cd60c5293c
2024-01-30 15:48:57 +01:00
e6847d7a2f
gnu: r-data-table: Update to 1.15.0.
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* gnu/packages/statistics.scm (r-data-table): Update to 1.15.0.
Change-Id: I2187d368fb461d72b07e3445bad0240ecc5cd6f1
2024-01-30 15:48:57 +01:00
71936c6145
gnu: r-tfruns: Update to 1.5.2.
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* gnu/packages/cran.scm (r-tfruns): Update to 1.5.2.
Change-Id: Iefffe073fb7d2d54e190b3d0433dcb760dad9a10
2024-01-30 15:48:57 +01:00
08d6f49857
gnu: r-spatstat-geom: Update to 3.2-8.
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* gnu/packages/cran.scm (r-spatstat-geom): Update to 3.2-8.
Change-Id: Iab7190ff6dbe409cc1b400f6a69001a8c13ac1bc
2024-01-30 15:48:57 +01:00
281db78112
gnu: r-iheatmapr: Update to 0.7.1.
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* gnu/packages/cran.scm (r-iheatmapr): Update to 0.7.1.
Change-Id: I83046a2d71d29a18dc15a7a568d0212947b936dd
2024-01-30 15:48:57 +01:00
2435d457e8
gnu: r-emoa: Update to 0.5-2.
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* gnu/packages/cran.scm (r-emoa): Update to 0.5-2.
Change-Id: Ia1138543ad4a2acf104c4fc19e2d75cfa07eed81
2024-01-30 15:48:56 +01:00
6bde30b814
gnu: r-tidygraph: Update to 1.3.1.
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* gnu/packages/cran.scm (r-tidygraph): Update to 1.3.1.
Change-Id: I597eaa3eb3afba90462b5ca0a7fed262ecf1aa60
2024-01-30 15:48:56 +01:00
a03ad38b2f
gnu: r-xgboost: Update to 1.7.7.1.
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* gnu/packages/cran.scm (r-xgboost): Update to 1.7.7.1.
Change-Id: I949455d58c1fdbb878a77d82e8501c5a615ed441
2024-01-30 15:48:56 +01:00
50e728fbab
gnu: r-yulab-utils: Update to 0.1.4.
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* gnu/packages/cran.scm (r-yulab-utils): Update to 0.1.4.
Change-Id: Ic7e6288859a857ecbd23566b9e5bd1796206764c
2024-01-30 15:48:56 +01:00
48f41d06e8
gnu: r-bqtl: Update to 1.0-36.
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* gnu/packages/cran.scm (r-bqtl): Update to 1.0-36.
Change-Id: I598ad41402e05e8ed628aaf57eac4a1e47689228
2024-01-30 15:48:56 +01:00
2bb1d89f97
gnu: r-listenv: Update to 0.9.1.
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* gnu/packages/cran.scm (r-listenv): Update to 0.9.1.
Change-Id: I998a9d35b176ed8dd038fd6392f46b4052e56dd7
2024-01-30 15:48:56 +01:00
8bad30c244
gnu: r-phylobase: Update to 0.8.12.
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* gnu/packages/cran.scm (r-phylobase): Update to 0.8.12.
Change-Id: I4d022d85cdb6f79fae167bfd7c52a0c2620b0092
2024-01-30 15:48:55 +01:00
b7e3c82000
gnu: r-densityclust: Update to 0.3.3.
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* gnu/packages/cran.scm (r-densityclust): Update to 0.3.3.
[propagated-inputs]: Remove r-rcpp; add r-cpp11.
Change-Id: Ia6b5737e2225e67fa064f031d985c076694ec9ce
2024-01-30 15:48:55 +01:00
02931399e8
gnu: r-interp: Update to 1.1-6.
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* gnu/packages/cran.scm (r-interp): Update to 1.1-6.
Change-Id: I846729e1637fc0f8762cf8a235cc78df2c1eb810
2024-01-30 15:48:55 +01:00
8b0a49ad4e
gnu: r-zip: Update to 2.3.1.
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* gnu/packages/cran.scm (r-zip): Update to 2.3.1.
Change-Id: I20ff34e492271063d6baf37f59f6da181c1d7805
2024-01-30 15:48:55 +01:00
51d7fae43a
gnu: r-nestedcv: Update to 0.7.4.
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* gnu/packages/cran.scm (r-nestedcv): Update to 0.7.4.
[propagated-inputs]: Add r-rhpcblasctl.
Change-Id: Ica97cf7c960125543210c48851861d7826a8f8aa
2024-01-30 15:48:55 +01:00
775ae73c3d
gnu: r-laeken: Update to 0.5.3.
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* gnu/packages/cran.scm (r-laeken): Update to 0.5.3.
Change-Id: I9ab9a89d88511b80efb912119ec81a24fafceb84
2024-01-30 15:48:55 +01:00
f3af65b8d0
gnu: r-sp: Update to 2.1-3.
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* gnu/packages/cran.scm (r-sp): Update to 2.1-3.
Change-Id: I111d108e6f144ecfdecf5e5ff94b6b11110a9395
2024-01-30 15:48:54 +01:00
5701d13103
gnu: r-powerlaw: Update to 0.80.0.
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* gnu/packages/cran.scm (r-powerlaw): Update to 0.80.0.
Change-Id: I1b3c185ac4a8748698fe9218c262620b42f5f06d
2024-01-30 15:48:54 +01:00
854d1be754
gnu: r-httpuv: Update to 1.6.14.
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* gnu/packages/cran.scm (r-httpuv): Update to 1.6.14.
Change-Id: I1f650010cce97020f7b563adfcd74d7e4dec4981
2024-01-30 15:48:54 +01:00
51ca656726
gnu: r-ga: Update to 3.2.4.
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* gnu/packages/cran.scm (r-ga): Update to 3.2.4.
Change-Id: I698d5c3eda6598c435fcf37b5e7eaaf5c4e15e63
2024-01-30 15:48:54 +01:00
cd9e88c9d0
gnu: r-ggm: Update to 2.5.1.
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* gnu/packages/bioconductor.scm (r-ggm): Update to 2.5.1.
[propagated-inputs]: Add r-biocmanager.
Change-Id: I8db7e517b96c3c42cb05246378b4190c9c954a47
2024-01-30 15:48:54 +01:00
1541c1bb17
gnu: r-rjava: Update to 1.0-11.
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* gnu/packages/cran.scm (r-rjava): Update to 1.0-11.
[source]: Remove snippet.
[arguments]: Remove 'replace-bundled-minified-JavaScript phase.
[native-inputs]: Remove esbuild.
Change-Id: I008810b6919412023fc419d9cbadfea0fe2892bb
2024-01-30 15:48:08 +01:00
1bb0d6355c
gnu: r-catdata: Update to 1.2.4.
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* gnu/packages/cran.scm (r-catdata): Update to 1.2.4.
[native-inputs]: Add r-knitr.
Change-Id: I7e2873a612f114d7124d5787ff70a8bf0ffefe93
2024-01-30 15:41:54 +01:00
c3e2892558
gnu: r-r-devices: Update to 2.17.2.
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* gnu/packages/cran.scm (r-r-devices): Update to 2.17.2.
[arguments]: Add 'set-HOME phase.
[native-inputs]: Add r-r-rsp.
Change-Id: Iaaead01e690e95971148ae063aa7af589969d39c
2024-01-30 15:41:07 +01:00
67c1a96196
gnu: r-igraph: Update to 2.0.1.1.
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* gnu/packages/cran.scm (r-igraph): Update to 2.0.1.1.
[properties]: Tell updater to keep extra native input "which".
[native-inputs]: Add pkg-config and which.
Change-Id: Id56c68784d192f7a3031a338fe63a4c17799c605
2024-01-30 15:36:03 +01:00
Ludovic Courtès
Ludovic Courtès
Clément Lassieur
Sharlatan Hellseher
Thomas Ieong
Ricardo Wurmus
Artyom V. Poptsov
David Thompson