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135676 Commits (76805a574417f7b7c33df50f4c4ac8a2e022eddb)

Author SHA1 Message Date
Ricardo Wurmus 76805a5744
gnu: r-flowsorted-blood-epic: Update to 2.8.0. 
* gnu/packages/bioconductor.scm (r-flowsorted-blood-epic): Update to 2.8.0.

Change-Id: I000d233d1a78f36e8daed08f0112cc592b2f99f6
 2024-05-08 12:53:16 +02:00
Ricardo Wurmus aded842e92
gnu: r-flowsorted-blood-450k: Update to 1.42.0. 
* gnu/packages/bioconductor.scm (r-flowsorted-blood-450k): Update to 1.42.0.

Change-Id: I07c3a8640e8b7ca9e36b0a3e81d9831fc4d7299e
 2024-05-08 12:53:16 +02:00
Ricardo Wurmus f5a724eb16
gnu: r-copyhelper: Update to 1.36.0. 
* gnu/packages/bioconductor.scm (r-copyhelper): Update to 1.36.0.

Change-Id: I4726f8bf6c654b03ee4eb84ae697e7844d06e164
 2024-05-08 12:53:16 +02:00
Ricardo Wurmus b53302805e
gnu: r-chromstardata: Update to 1.30.0. 
* gnu/packages/bioconductor.scm (r-chromstardata): Update to 1.30.0.

Change-Id: I19aa49ac9d6499d2cea91b0d45fd04f10511b18f
 2024-05-08 12:53:16 +02:00
Ricardo Wurmus cfb000d7e5
gnu: r-champdata: Update to 2.36.0. 
* gnu/packages/bioconductor.scm (r-champdata): Update to 2.36.0.

Change-Id: I5387b2e3722e95911a5355cc56d83086ef205a4c
 2024-05-08 12:53:16 +02:00
Ricardo Wurmus 9e2ac92d2f
gnu: r-celldex: Update to 1.14.0. 
* gnu/packages/bioconductor.scm (r-celldex): Update to 1.14.0.
[propagated-inputs]: Add r-alabaster-base, r-alabaster-matrix, r-alabaster-se, r-dbi,
r-gypsum, r-jsonlite, r-matrix, and r-rsqlite.

Change-Id: Iba166c14dae781e14a9762dc3480ece5ba12a802
 2024-05-08 12:53:16 +02:00
Ricardo Wurmus 4bcc9c836d
gnu: r-breastcancervdx: Update to 1.42.0. 
* gnu/packages/bioconductor.scm (r-breastcancervdx): Update to 1.42.0.

Change-Id: I52de3659b7d07d03491091ef0de4ee5d305ec4eb
 2024-05-08 12:53:16 +02:00
Ricardo Wurmus 0e2bfbce09
gnu: r-breakpointrdata: Update to 1.22.0. 
* gnu/packages/bioconductor.scm (r-breakpointrdata): Update to 1.22.0.

Change-Id: I111126dae913bd01e5a3f87551108e6ba1733b89
 2024-05-08 12:53:16 +02:00
Ricardo Wurmus 9d1c351076
gnu: r-biscuiteerdata: Update to 1.18.0. 
* gnu/packages/bioconductor.scm (r-biscuiteerdata): Update to 1.18.0.

Change-Id: Icc31cf376b8f2f085cc045c02383164128f0f009
 2024-05-08 12:53:16 +02:00
Ricardo Wurmus a4e4f9cf21
gnu: r-bodymaprat: Update to 1.20.0. 
* gnu/packages/bioconductor.scm (r-bodymaprat): Update to 1.20.0.

Change-Id: I8eb8b9e71cb1068e058b3e827096f25607ac5f01
 2024-05-08 12:53:15 +02:00
Ricardo Wurmus 62e7c74453
gnu: r-bladderbatch: Update to 1.42.0. 
* gnu/packages/bioconductor.scm (r-bladderbatch): Update to 1.42.0.

Change-Id: I49350259fef502e59368e4dc0894dcf52db33917
 2024-05-08 12:53:15 +02:00
Ricardo Wurmus 5b87013c93
gnu: r-bcellviper: Update to 1.40.0. 
* gnu/packages/bioconductor.scm (r-bcellviper): Update to 1.40.0.

Change-Id: I5d7af04599d79147eaa2626aead238179e78cfde
 2024-05-08 12:53:15 +02:00
Ricardo Wurmus 6ac2448400
gnu: r-arrmdata: Update to 1.40.0. 
* gnu/packages/bioconductor.scm (r-arrmdata): Update to 1.40.0.

Change-Id: I4695eec74200dd5deac20a71c020a9517e56f9a7
 2024-05-08 12:53:15 +02:00
Ricardo Wurmus fa4635d3ad
gnu: r-aneufinderdata: Update to 1.32.0. 
* gnu/packages/bioconductor.scm (r-aneufinderdata): Update to 1.32.0.

Change-Id: I91727bf7974078374a2bf9ca935b9df2ca60201f
 2024-05-08 12:53:15 +02:00
Ricardo Wurmus 4add20468d
gnu: r-adductdata: Update to 1.20.0. 
* gnu/packages/bioconductor.scm (r-adductdata): Update to 1.20.0.

Change-Id: I9f795cf931e90fa5f8331a5d3ffa855b56355ca6
 2024-05-08 12:53:15 +02:00
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