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135711 Commits (fe2f93f9fc491995172b4c9d9cfd432d11060e06)

Author SHA1 Message Date
Ricardo Wurmus 378904acf5
gnu: r-pfam-db: Update to 3.19.1. 
* gnu/packages/bioconductor.scm (r-pfam-db): Update to 3.19.1.

Change-Id: If95fa52bdfeb87ed606b9b7564ce73606a8616c8
 2024-05-08 12:53:15 +02:00
Ricardo Wurmus 7eabe6d69d
gnu: r-escape: Update to 2.0.0. 
* gnu/packages/bioconductor.scm (r-escape): Update to 2.0.0.
[propagated-inputs]: Remove r-broom, r-data-table, r-matrix, and r-rlang; add r-aucell,
r-ggdist, r-ggpointdensity, and r-seuratobject.

Change-Id: I7fa2ea581a85a579feeac50e1e4b32ac4fa83d7b
 2024-05-08 12:53:15 +02:00
Ricardo Wurmus a5729ea6ae
gnu: r-org-mm-eg-db: Update to 3.19.1. 
* gnu/packages/bioconductor.scm (r-org-mm-eg-db): Update to 3.19.1.

Change-Id: I3ae90e3d60941caf901d49c91662f38900588a27
 2024-05-08 12:53:15 +02:00
Ricardo Wurmus afb439ddf1
gnu: r-org-hs-eg-db: Update to 3.19.1. 
* gnu/packages/bioconductor.scm (r-org-hs-eg-db): Update to 3.19.1.

Change-Id: Ib120639d743ba4abd0a129f968bd09a3f9c62775
 2024-05-08 12:53:15 +02:00
Ricardo Wurmus b0cd3610d3
gnu: r-org-dr-eg-db: Update to 3.19.1. 
* gnu/packages/bioconductor.scm (r-org-dr-eg-db): Update to 3.19.1.

Change-Id: Ib5d87389f017f2a4ed106ecaef01f82a689ad46e
 2024-05-08 12:53:15 +02:00
Ricardo Wurmus 1e295ff0d3
gnu: r-org-dm-eg-db: Update to 3.19.1. 
* gnu/packages/bioconductor.scm (r-org-dm-eg-db): Update to 3.19.1.

Change-Id: I3c19de819fe694d9af11c4263132338340fccc47
 2024-05-08 12:53:15 +02:00
Ricardo Wurmus 30be3f2fc8
gnu: r-org-ce-eg-db: Update to 3.19.1. 
* gnu/packages/bioconductor.scm (r-org-ce-eg-db): Update to 3.19.1.

Change-Id: If5ae28c7f68194c7e6dc1b849932417ec1679ec9
 2024-05-08 12:53:15 +02:00
Ricardo Wurmus d85a5a2047
gnu: r-go-db: Update to 3.19.1. 
* gnu/packages/bioconductor.scm (r-go-db): Update to 3.19.1.

Change-Id: I894831796ac3121795d76df059b10680e9545ba0
 2024-05-08 12:53:15 +02:00
Ricardo Wurmus 5cac1ec6c5
gnu: r-genomeinfodbdata: Update to 1.2.12. 
* gnu/packages/bioconductor.scm (r-genomeinfodbdata): Update to 1.2.12.

Change-Id: I185d52161ec45de7d03fedeb51f2a28864df9903
 2024-05-08 12:53:15 +02:00
Ricardo Wurmus 44c5036af2
gnu: r-reactome-db: Update to 1.88.0. 
* gnu/packages/bioconductor.scm (r-reactome-db): Update to 1.88.0.

Change-Id: I80b58a45e8265e82e7a84d8d428fc4339fd926a7
 2024-05-08 12:53:15 +02:00
Ricardo Wurmus 43b32ab2e6
gnu: r-org-sc-sgd-db: Update to 3.19.1. 
* gnu/packages/bioconductor.scm (r-org-sc-sgd-db): Update to 3.19.1.

Change-Id: Iee6d57797bb3dde152ce0e22a3ed25c30c039a09
 2024-05-08 12:53:15 +02:00
Ricardo Wurmus 487cf830ae
gnu: r-org-bt-eg-db: Update to 3.19.1. 
* gnu/packages/bioconductor.scm (r-org-bt-eg-db): Update to 3.19.1.

Change-Id: If37dc4be3287f0729b2e2d4aecef6745700b429c
 2024-05-08 12:53:15 +02:00
Ricardo Wurmus 37696fafac
gnu: r-org-eck12-eg-db: Update to 3.19.1. 
* gnu/packages/bioconductor.scm (r-org-eck12-eg-db): Update to 3.19.1.

Change-Id: I0f3a84abd0dff114231c341e776b542a7b047176
 2024-05-08 12:53:15 +02:00
Ricardo Wurmus a1852df9ff
gnu: r-mafh5-gnomad-v3-1-2-grch38: Update to 3.15.1. 
* gnu/packages/bioconductor.scm (r-mafh5-gnomad-v3-1-2-grch38): Update to 3.15.1.

Change-Id: I6b83a3701c2a4282864bf648677b258c1315598c
 2024-05-08 12:53:15 +02:00
Ricardo Wurmus 8d531f9afb
gnu: Add r-ucsc-utils. 
* gnu/packages/bioconductor.scm (r-ucsc-utils): New variable.

Change-Id: I02eebaa69a57b8bbd97b38ae7d62799971f70d45
 2024-05-08 12:53:15 +02:00
Ricardo Wurmus 61a5676a9d
gnu: r-biocpkgtools: Update to 1.22.0. 
* gnu/packages/bioconductor.scm (r-biocpkgtools): Update to 1.22.0.

Change-Id: I4afb2530597279d9f2b6c01fc7d76c95c88aa629
 2024-05-08 12:53:14 +02:00
Ricardo Wurmus b9040cb312
gnu: r-debcam: Update to 1.22.0. 
* gnu/packages/bioconductor.scm (r-debcam): Update to 1.22.0.

Change-Id: Iec96dd28f8adc4d8c070f2e50098a02a4582ec33
 2024-05-08 12:53:14 +02:00
Ricardo Wurmus 45b4f78687
gnu: Add r-txdbmaker. 
* gnu/packages/bioconductor.scm (r-txdbmaker): New variable.

Change-Id: I2e236b42117525a48917604ea14396ff661b72f7
 2024-05-08 12:53:14 +02:00
Ricardo Wurmus cf3471cc9e
gnu: Add r-pwalign. 
* gnu/packages/bioconductor.scm (r-pwalign): New variable.

Change-Id: I6a12f48c5de948292af7c6888b12e849e1f42db7
 2024-05-08 12:53:14 +02:00
Ricardo Wurmus 155ac301f7
gnu: Add r-psmatch. 
* gnu/packages/bioconductor.scm (r-psmatch): New variable.

Change-Id: I7b3071424563b713912016301f551ce00aceddea
 2024-05-08 12:53:14 +02:00
Ricardo Wurmus 6e126301b4
gnu: Add r-gypsum. 
* gnu/packages/bioconductor.scm (r-gypsum): New variable.

Change-Id: Id3bdf044d9a885605b1b2b2ceba32398da6ddec0
 2024-05-08 12:53:14 +02:00
Ricardo Wurmus 2c6bd40baf
gnu: Add r-alabaster-se. 
* gnu/packages/bioconductor.scm (r-alabaster-se): New variable.

Change-Id: I698a2d678e4819d9ac4b2668a2f7ef2063f8d674
 2024-05-08 12:53:14 +02:00
Ricardo Wurmus 1dd2cce88f
gnu: Add r-alabaster-sce. 
* gnu/packages/bioconductor.scm (r-alabaster-sce): New variable.

Change-Id: I8121614d5b93922555b6cb5fd7a05d68980aff20
 2024-05-08 12:53:14 +02:00
Ricardo Wurmus 092609b36a
gnu: Add r-alabaster-ranges. 
* gnu/packages/bioconductor.scm (r-alabaster-ranges): New variable.

Change-Id: I99e1e6549537acb37de2788961dbd17ef6c1de27
 2024-05-08 12:53:14 +02:00
Ricardo Wurmus ba8fbb89e4
gnu: Add r-alabaster-matrix. 
* gnu/packages/bioconductor.scm (r-alabaster-matrix): New variable.

Change-Id: If5b438983a70f8f81e3442d8a1cb3821f4e3489a
 2024-05-08 12:53:14 +02:00
Ricardo Wurmus 8031162607
gnu: Add r-alabaster-base. 
* gnu/packages/bioconductor.scm (r-alabaster-base): New variable.

Change-Id: Ifb9fe95fb237d12dadf134278f130e614925b5ec
 2024-05-08 12:53:14 +02:00
Ricardo Wurmus 9bd400722d
gnu: Add r-alabaster-schemas. 
* gnu/packages/bioconductor.scm (r-alabaster-schemas): New variable.

Change-Id: I3d9218af9b4408e3375f9ccd98a4c95935b2c273
 2024-05-08 12:53:14 +02:00
Ricardo Wurmus 1117e96d9f
gnu: r-cytoml: Update to 2.16.0. 
* gnu/packages/bioconductor.scm (r-cytoml): Update to 2.16.0.

Change-Id: I14ae3ae0d5ff8d66b964651b6fe3753d934f1554
 2024-05-08 12:53:14 +02:00
Ricardo Wurmus c29bc85ec6
gnu: Add r-jsonvalidate. 
* gnu/packages/cran.scm (r-jsonvalidate): New variable.

Change-Id: I1393fb3b4034f870663dc887be783e8aaf4c9884
 2024-05-08 12:53:14 +02:00
Ricardo Wurmus 53555dac1c
guix: Update Bioconductor version to 3.19. 
* guix/build-system/r.scm (bioconductor-uri): Use 3.19 URL.
* guix/import/cran.scm (%bioconductor-version): Set to 3.19.

Change-Id: I7a2c4dfcdb2c4cdfef581f823d87e73acc163549
 2024-05-08 12:53:14 +02:00
Ricardo Wurmus 66e179ac18
gnu: r-xts: Remove vignette outputs. 
* gnu/packages/cran.scm (r-xts)[source]: Add snippet to remove generated
files.

Change-Id: Iba82b900e632e2cf5a99c9deb807bae6cf3dabcd
 2024-05-08 12:53:14 +02:00
Ricardo Wurmus 628d007b83
gnu: r-desctools: Set HOME variable. 
* gnu/packages/statistics.scm (r-desctools)[argumonts]: Add phase 'pre-check.

Change-Id: Icec222a5cdcb2c95ad7bd600ce5188bd5588bb4e
 2024-05-08 12:53:14 +02:00
Ricardo Wurmus 79c2b32337
gnu: r-with-tests: Update to 4.4.0. 
* gnu/packages/statistics.scm (r-with-tests): Update to 4.4.0.

Change-Id: If77c95867cc16141c397e48c899a9ade3e89876d
 2024-05-08 12:53:14 +02:00
Artyom V. Poptsov 2bea3f2562
gnu: kubo: Unbundle go-cidutil, go-log and go-ipfs-util. 
* gnu/packages/ipfs.scm (kubo) [source]: Delete "go-cidutil", "go-log",
  "go-ipfs-util" from bundled packages.
  [inputs]: Add go-github-com-ipfs-go-cidutil, go-github-com-ipfs-go-log,
  go-github-com-ipfs-go-log-v2, and go-github-com-ipfs-go-ipfs-util.

Change-Id: I3e49deb9572c6ac471210a392a52117fd0b9ce1a
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2024-05-08 00:07:21 +01:00
Artyom V. Poptsov 231ffaf1ac
gnu: Add go-github-com-ipfs-go-cidutil. 
* gnu/packages/ipfs.scm (go-github-com-ipfs-go-cidutil): New variable.

Change-Id: I6077fc00d22b541a959a6623c8666c35288ca105
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2024-05-08 00:05:05 +01:00
Artyom V. Poptsov 6f60f90c15
gnu: Add go-github-com-ipfs-go-log. 
* gnu/packages/ipfs.scm (go-github-com-ipfs-go-log): New variable.

Change-Id: I5b5b1d594b5458a7ca156346c6a6dc3c8d5bd69d
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2024-05-08 00:05:05 +01:00
Artyom V. Poptsov 58cc52f2dc
gnu: Add go-github-com-ipfs-go-log-v2. 
* gnu/packages/ipfs.scm (go-github-com-ipfs-go-log-v2): New variable.

Change-Id: Id6d85bfa883670345420c21937681ae2844f6263
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2024-05-08 00:03:02 +01:00
Artyom V. Poptsov 8cb146a3e6
gnu: Add go-github-com-ipfs-go-detect-race. 
* gnu/packages/ipfs.scm (go-github-com-ipfs-go-detect-race): New variable.

Change-Id: Ic65c12a717a50c4309bc89d29d158a43fbc0c81a
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2024-05-07 23:51:25 +01:00
Artyom V. Poptsov f669a24a95
gnu: Add go-github-com-ipfs-go-ipfs-util. 
* gnu/packages/ipfs.scm (go-github-com-ipfs-go-ipfs-util): New variable.

Change-Id: Ic496282dc62b7c0d5bd9017aff6a3818b2661309
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2024-05-07 23:51:16 +01:00
Sharlatan Hellseher 2795d0f3e7
gnu: kubo: Unbundle go-bazil-org-fuse. 
* gnu/packages/ipfs.scm (kubo) [source]: Remove vendor/bazil.org.
[inputs]: Add go-bazil-org-fuse.

Change-Id: Ie55e609c15a6eaca7ec32521a55620bf674af240
 2024-05-07 23:18:48 +01:00
Sharlatan Hellseher 1f6c4f226d
gnu: Add go-bazil-org-fuse. 
* gnu/packages/golang-xyz.scm (go-bazil-org-fuse): New variable.

Change-Id: I933d90dca50110f53831febc81d587c14973934f
 2024-05-07 23:18:48 +01:00
Sharlatan Hellseher 330a133b85
gnu: go-git-sr-ht-emersion-go-scfg: Move to golang-xyz. 
* gnu/packages/golang.scm: (go-git-sr-ht-emersion-go-scfg): Move from here ...
* gnu/packages/golang-xyz.scm: ... to here

Change-Id: I75cc680543313e41abc86e71d48a9be9e9ce694a
 2024-05-07 23:18:48 +01:00
Sharlatan Hellseher 74b2a9d5a4
gnu: go-git-sr-ht-emersion-gqlclient: Move to golang-web. 
* gnu/packages/golang.scm (go-git-sr-ht-emersion-gqlclient): Move from
here ...
* gnu/packages/golang-web.scm: ... to here.

Change-Id: I2b07dc198f6710680da0430e5f302893060e37b8
 2024-05-07 23:18:47 +01:00
Sharlatan Hellseher 072b06f2f3
gnu: go-git-sr-ht-sircmpwn-getopt: Move to golang-xyz. 
* gnu/packages/golang.scm (go-git-sr-ht-sircmpwn-getopt): Move from here ...
* gnu/packages/golang-xyz.scm: ... to here.

Change-Id: Ic53ec6828f7389326191b659dd16b623e6d1af43
 2024-05-07 23:18:47 +01:00
Sharlatan Hellseher 9716914d4e
gnu: web: Remove syncthing module from used modules. 
There is no more mudule from syncthing which needs to be imported
anymore.

* gnu/packages/web.scm: Remove (gnu packages syncthing) module.

Change-Id: I688e72009e2daa5e75eaeaaeff9026ca888b266b
 2024-05-07 23:17:46 +01:00
Sharlatan Hellseher fb44cd89df
gnu: go-github-com-nbrownus-go-metrics-prometheus: Disable tests. 
* gnu/packages/golang-xyz.scm (go-github-com-nbrownus-go-metrics-prometheus):
Disable all tests.

Change-Id: I7f340fd1e58edc0203068c762a1bbc798003a84b
 2024-05-07 21:33:45 +01:00
Sharlatan Hellseher aa1090713a
gnu: tmsu: Enable test suite. 
* gnu/packages/file-systems.scm (tmsu): Fail over to the project's
Makefile targets.
[arguments]: <#:go>: Use go-1.21.
<#:phases>: Add 'adjust-makefile' phase. Use custom 'build, 'check and
'install phases.

Change-Id: Ice920f2196123f1a1f1561879ab919bc0d4e8512
 2024-05-07 21:33:44 +01:00
Sharlatan Hellseher c7bd735bc4
gnu: sqls: Use go-1.21. 
Merge all inputs into native-inputs since the output result of the
package is an executable that does not require sources from Golang
modules to be available after installation.

* gnu/packages/databases.scm (sqls):
[arguments]: <#:go>: Use go-1.21.
[inputs]: Remove go-github-com-go-sql-driver-mysql,
go-github-com-lib-pq, go-github-com-mattn-go-runewidth,
go-github-com-mattn-go-sqlite3, go-github-com-olekukonko-tablewriter,
go-github-com-pkg-errors, go-github-com-sourcegraph-jsonrpc2,
go-golang-org-x-crypto, go-golang-org-x-xerrors, and
go-gopkg-in-yaml-v2.
[native-inputs]: Add go-github-com-go-sql-driver-mysql,
go-github-com-lib-pq, go-github-com-mattn-go-runewidth,
go-github-com-mattn-go-sqlite3, go-github-com-olekukonko-tablewriter,
go-github-com-pkg-errors, go-github-com-sourcegraph-jsonrpc2,
go-golang-org-x-crypto, go-golang-org-x-xerrors, and
go-gopkg-in-yaml-v2.

Change-Id: I9312a483dfa954b5f0ad4cfac04b5153570bf571
 2024-05-07 21:33:44 +01:00
Sharlatan Hellseher e582f27a53
gnu: Add go-github-com-msteinert-pam-v2. 
* gnu/packages/golang-xyz.scm (go-github-com-msteinert-pam-v2): New variable.

Change-Id: I7dfcb72703722f894eb52c603f02e64e7350f53a
 2024-05-07 21:33:44 +01:00
Jesse Eisses 243ff41195
gnu: Add soju. 
* gnu/packages/irc.scm (soju): New variable..

Modified-by: Sharlatan Hellseher <sharlatanus@gmail.com>
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
Change-Id: I18b7e574339e98fdf2623338aac1635c8e727699
 2024-05-07 21:33:44 +01:00