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Author SHA1 Message Date
Ludovic Courtès 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
Ludovic Courtès 36d654fa54
channels: Tweak test. 
* 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
Clément Lassieur 88e8b807d6
gnu: torbrowser: Copy buildID from the official build. 
* 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
Sharlatan Hellseher c4687f5437
Revert "gnu: Add minify." 
This reverts commit f8c2d8141e.

Fixes: error: go-github-com-tdewolff-minify-v2: unbound variable
<https://ci.guix.gnu.org/eval/1086875/log/raw>

Change-Id: I26e02842980cf09e924ac1cae8f3a6421a005276
 2024-01-30 23:56:11 +00:00
Sharlatan Hellseher 7a63fba807
teams: go: Add golang-xyz.scm to scope. 
* etc/teams.scm (go): Add "gnu/packages/golang-xyz.scm".

Change-Id: I580eadf52b631c6582e256a2900786b53483a466
 2024-01-30 22:58:22 +00:00
Thomas Ieong f8c2d8141e
gnu: Add minify. 
* 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
Thomas Ieong aab6ea6f41
gnu: Add go-github-com-matryer-try. 
* 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
Thomas Ieong b998d58221
gnu: Add go-github-com-djherbis-atime. 
* 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
Sharlatan Hellseher 376bba6030
gnu: Add (gnu packages golang-xyz) module. 
* 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
Sharlatan Hellseher fb2b72a5f3
gnu: go-github-com-go-jose-go-jose-v3: Move to (gnu packages golang-web). 
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
Ricardo Wurmus f6bbee5f05
gnu: axoloti-patcher: Add missing headers. 
* gnu/packages/axoloti.scm (axoloti-patcher)[arguments]: Include generic
headers in search paths.

Change-Id: I2e1819966eb657ba4a7e0c823e6686de8599dd9a
 2024-01-30 22:44:43 +01:00
Ricardo Wurmus c2dc19aecc
gnu: axoloti-patcher: Use G-expression. 
* 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
Artyom V. Poptsov bed3a0b547
gnu: yggdrasil: Update to 0.5.5. 
* 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
David Thompson a901e950dd
gnu: guile-hoot: Update to 0.3.0. 
* gnu/packages/guile-xyz.scm (guile-hoot): Update to 0.3.0.

Change-Id: I355d4b11bdd45bf87e3d7227f259907b1e7d57bd
 2024-01-30 11:08:37 -05:00
Ricardo Wurmus 7cdad00e30
gnu: r-scran: Update to 1.30.2. 
* gnu/packages/bioconductor.scm (r-scran): Update to 1.30.2.

Change-Id: I49388f6307f88cb671b0a721cc4c82a4804312c6
 2024-01-30 16:59:52 +01:00
Ricardo Wurmus aa7950070b
gnu: r-bioccheck: Update to 1.38.2. 
* 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
Ricardo Wurmus 8d8eec7f9d
gnu: r-flowcore: Update to 2.14.1. 
* gnu/packages/bioconductor.scm (r-flowcore): Update to 2.14.1.

Change-Id: I7a8002206aaab85a722463a81939d7cea7d61644
 2024-01-30 16:59:51 +01:00
Ricardo Wurmus 9e1e462746
gnu: r-rsubread: Update to 2.16.1. 
* gnu/packages/bioconductor.scm (r-rsubread): Update to 2.16.1.

Change-Id: Id01d956d2f76347270d05961dba13f65b268862a
 2024-01-30 16:59:51 +01:00
Ricardo Wurmus ca6e432089
gnu: r-edger: Update to 4.0.12. 
* gnu/packages/bioconductor.scm (r-edger): Update to 4.0.12.

Change-Id: If99f10f80fb7c085863d2da79cfce2b94af71543
 2024-01-30 16:59:51 +01:00
Ricardo Wurmus 4df162962d
gnu: r-biostrings: Update to 2.70.2. 
* gnu/packages/bioconductor.scm (r-biostrings): Update to 2.70.2.

Change-Id: Id43796f35c5afe6fbe3a37d72e111d28937254a2
 2024-01-30 16:59:51 +01:00
Ricardo Wurmus 1c27a3a8a8
gnu: r-biomart: Update to 2.58.1. 
* gnu/packages/bioconductor.scm (r-biomart): Update to 2.58.1.

Change-Id: I6304e3be6919367f5d9d99ddb7aae75ab39b9985
 2024-01-30 16:59:51 +01:00
Ricardo Wurmus 6f11ca52f1
gnu: r-robustbase: Update to 0.99-2. 
* gnu/packages/statistics.scm (r-robustbase): Update to 0.99-2.

Change-Id: Ic6a248fd55b6b4467742040a884ed25e9d090f47
 2024-01-30 15:48:57 +01:00
Ricardo Wurmus ef5640f763
gnu: r-viridis: Update to 0.6.5. 
* gnu/packages/statistics.scm (r-viridis): Update to 0.6.5.

Change-Id: Iaa83edbc2a304e0327f8815967f2e28b686691a0
 2024-01-30 15:48:57 +01:00
Ricardo Wurmus c72ceba47f
gnu: r-commonmark: Update to 1.9.1. 
* gnu/packages/statistics.scm (r-commonmark): Update to 1.9.1.

Change-Id: Ifccd39448f0d6181bfcede089aa922cd60c5293c
 2024-01-30 15:48:57 +01:00
Ricardo Wurmus e6847d7a2f
gnu: r-data-table: Update to 1.15.0. 
* gnu/packages/statistics.scm (r-data-table): Update to 1.15.0.

Change-Id: I2187d368fb461d72b07e3445bad0240ecc5cd6f1
 2024-01-30 15:48:57 +01:00
Ricardo Wurmus 71936c6145
gnu: r-tfruns: Update to 1.5.2. 
* gnu/packages/cran.scm (r-tfruns): Update to 1.5.2.

Change-Id: Iefffe073fb7d2d54e190b3d0433dcb760dad9a10
 2024-01-30 15:48:57 +01:00
Ricardo Wurmus 08d6f49857
gnu: r-spatstat-geom: Update to 3.2-8. 
* gnu/packages/cran.scm (r-spatstat-geom): Update to 3.2-8.

Change-Id: Iab7190ff6dbe409cc1b400f6a69001a8c13ac1bc
 2024-01-30 15:48:57 +01:00
Ricardo Wurmus 281db78112
gnu: r-iheatmapr: Update to 0.7.1. 
* gnu/packages/cran.scm (r-iheatmapr): Update to 0.7.1.

Change-Id: I83046a2d71d29a18dc15a7a568d0212947b936dd
 2024-01-30 15:48:57 +01:00
Ricardo Wurmus 2435d457e8
gnu: r-emoa: Update to 0.5-2. 
* gnu/packages/cran.scm (r-emoa): Update to 0.5-2.

Change-Id: Ia1138543ad4a2acf104c4fc19e2d75cfa07eed81
 2024-01-30 15:48:56 +01:00
Ricardo Wurmus 6bde30b814
gnu: r-tidygraph: Update to 1.3.1. 
* gnu/packages/cran.scm (r-tidygraph): Update to 1.3.1.

Change-Id: I597eaa3eb3afba90462b5ca0a7fed262ecf1aa60
 2024-01-30 15:48:56 +01:00
Ricardo Wurmus a03ad38b2f
gnu: r-xgboost: Update to 1.7.7.1. 
* gnu/packages/cran.scm (r-xgboost): Update to 1.7.7.1.

Change-Id: I949455d58c1fdbb878a77d82e8501c5a615ed441
 2024-01-30 15:48:56 +01:00
Ricardo Wurmus 50e728fbab
gnu: r-yulab-utils: Update to 0.1.4. 
* gnu/packages/cran.scm (r-yulab-utils): Update to 0.1.4.

Change-Id: Ic7e6288859a857ecbd23566b9e5bd1796206764c
 2024-01-30 15:48:56 +01:00
Ricardo Wurmus 48f41d06e8
gnu: r-bqtl: Update to 1.0-36. 
* gnu/packages/cran.scm (r-bqtl): Update to 1.0-36.

Change-Id: I598ad41402e05e8ed628aaf57eac4a1e47689228
 2024-01-30 15:48:56 +01:00
Ricardo Wurmus 2bb1d89f97
gnu: r-listenv: Update to 0.9.1. 
* gnu/packages/cran.scm (r-listenv): Update to 0.9.1.

Change-Id: I998a9d35b176ed8dd038fd6392f46b4052e56dd7
 2024-01-30 15:48:56 +01:00
Ricardo Wurmus 8bad30c244
gnu: r-phylobase: Update to 0.8.12. 
* gnu/packages/cran.scm (r-phylobase): Update to 0.8.12.

Change-Id: I4d022d85cdb6f79fae167bfd7c52a0c2620b0092
 2024-01-30 15:48:55 +01:00
Ricardo Wurmus b7e3c82000
gnu: r-densityclust: Update to 0.3.3. 
* 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
Ricardo Wurmus 02931399e8
gnu: r-interp: Update to 1.1-6. 
* gnu/packages/cran.scm (r-interp): Update to 1.1-6.

Change-Id: I846729e1637fc0f8762cf8a235cc78df2c1eb810
 2024-01-30 15:48:55 +01:00
Ricardo Wurmus 8b0a49ad4e
gnu: r-zip: Update to 2.3.1. 
* gnu/packages/cran.scm (r-zip): Update to 2.3.1.

Change-Id: I20ff34e492271063d6baf37f59f6da181c1d7805
 2024-01-30 15:48:55 +01:00
Ricardo Wurmus 51d7fae43a
gnu: r-nestedcv: Update to 0.7.4. 
* 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
Ricardo Wurmus 775ae73c3d
gnu: r-laeken: Update to 0.5.3. 
* gnu/packages/cran.scm (r-laeken): Update to 0.5.3.

Change-Id: I9ab9a89d88511b80efb912119ec81a24fafceb84
 2024-01-30 15:48:55 +01:00
Ricardo Wurmus f3af65b8d0
gnu: r-sp: Update to 2.1-3. 
* gnu/packages/cran.scm (r-sp): Update to 2.1-3.

Change-Id: I111d108e6f144ecfdecf5e5ff94b6b11110a9395
 2024-01-30 15:48:54 +01:00
Ricardo Wurmus 5701d13103
gnu: r-powerlaw: Update to 0.80.0. 
* gnu/packages/cran.scm (r-powerlaw): Update to 0.80.0.

Change-Id: I1b3c185ac4a8748698fe9218c262620b42f5f06d
 2024-01-30 15:48:54 +01:00
Ricardo Wurmus 854d1be754
gnu: r-httpuv: Update to 1.6.14. 
* gnu/packages/cran.scm (r-httpuv): Update to 1.6.14.

Change-Id: I1f650010cce97020f7b563adfcd74d7e4dec4981
 2024-01-30 15:48:54 +01:00
Ricardo Wurmus 51ca656726
gnu: r-ga: Update to 3.2.4. 
* gnu/packages/cran.scm (r-ga): Update to 3.2.4.

Change-Id: I698d5c3eda6598c435fcf37b5e7eaaf5c4e15e63
 2024-01-30 15:48:54 +01:00
Ricardo Wurmus cd9e88c9d0
gnu: r-ggm: Update to 2.5.1. 
* 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
Ricardo Wurmus 1541c1bb17
gnu: r-rjava: Update to 1.0-11. 
* 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
Ricardo Wurmus 1bb0d6355c
gnu: r-catdata: Update to 1.2.4. 
* 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
Ricardo Wurmus c3e2892558
gnu: r-r-devices: Update to 2.17.2. 
* 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
Ricardo Wurmus 67c1a96196
gnu: r-igraph: Update to 2.0.1.1. 
* 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
Ricardo Wurmus 788657b62d
gnu: r-antiword: Update to 1.3.3. 
* gnu/packages/cran.scm (r-antiword): Update to 1.3.3.
[properties]: Tell updater not to remove "antiword" input.
[arguments]: Use G-expression.

Change-Id: Ifdbf80f546b0ab3abfc3b8002ba01b46c9105a1c
 2024-01-30 15:31:07 +01:00