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130298 Commits (aea3c44027eab1bcd4fe2c881dff0e54d78368f5)

Author SHA1 Message Date
Ricardo Wurmus 8369898fb0
gnu: r-genelendatabase: Update to 1.38.0. 
* gnu/packages/bioconductor.scm (r-genelendatabase): Update to 1.38.0.

Change-Id: Idf120599c34af21cd3c5c854d434c93c702f0cd4
 2024-01-22 13:54:45 +01:00
Ricardo Wurmus 95c3baf59f
gnu: r-flowsorted-blood-epic: Update to 2.6.0. 
* gnu/packages/bioconductor.scm (r-flowsorted-blood-epic): Update to 2.6.0.

Change-Id: I458aa7c0ac482d1e60d6afb66b236ea6886d7ce6
 2024-01-22 13:54:45 +01:00
Ricardo Wurmus 43e6cc3189
gnu: r-flowsorted-blood-450k: Update to 1.40.0. 
* gnu/packages/bioconductor.scm (r-flowsorted-blood-450k): Update to 1.40.0.

Change-Id: Ia2d2ae18c80d3a4a7858026a424da1537d657782
 2024-01-22 13:54:45 +01:00
Ricardo Wurmus 4c4f07ca26
gnu: r-copyhelper: Update to 1.34.0. 
* gnu/packages/bioconductor.scm (r-copyhelper): Update to 1.34.0.

Change-Id: I2cfa340e85fb723615295949ef614db1761f9c6e
 2024-01-22 13:54:45 +01:00
Ricardo Wurmus f0591739ce
gnu: r-chromstardata: Update to 1.28.0. 
* gnu/packages/bioconductor.scm (r-chromstardata): Update to 1.28.0.

Change-Id: I5146185d21a589b93152fe67df4e4a100a0b0a33
 2024-01-22 13:54:45 +01:00
Ricardo Wurmus 225f49fb30
gnu: r-champdata: Update to 2.34.0. 
* gnu/packages/bioconductor.scm (r-champdata): Update to 2.34.0.

Change-Id: I658aab6c78df1fcbd7fb4d34df144635a2a10347
 2024-01-22 13:54:45 +01:00
Ricardo Wurmus 7b5db44490
gnu: r-celldex: Update to 1.12.0. 
* gnu/packages/bioconductor.scm (r-celldex): Update to 1.12.0.

Change-Id: I565b21aafa46cb710a8acc3ab16b7905614e6838
 2024-01-22 13:54:45 +01:00
Ricardo Wurmus 1aac5e7bc8
gnu: r-breakpointrdata: Update to 1.20.0. 
* gnu/packages/bioconductor.scm (r-breakpointrdata): Update to 1.20.0.

Change-Id: I1fe98a2e5fd8bf4b3106c7315dda8dee906c5152
 2024-01-22 13:54:45 +01:00
Ricardo Wurmus 6c1bb9047e
gnu: r-biscuiteerdata: Update to 1.16.0. 
* gnu/packages/bioconductor.scm (r-biscuiteerdata): Update to 1.16.0.
[propagated-inputs]: Add r-genomicranges.

Change-Id: I5459630b266f04bbac50562cb134e9ca28bbc2d7
 2024-01-22 13:54:45 +01:00
Ricardo Wurmus cd5a4ac6df
gnu: r-bladderbatch: Update to 1.40.0. 
* gnu/packages/bioconductor.scm (r-bladderbatch): Update to 1.40.0.

Change-Id: I2d5ec797815dd0101da8692b1fa320020c33ab85
 2024-01-22 13:54:45 +01:00
Ricardo Wurmus 09ee801fe9
gnu: r-bcellviper: Update to 1.38.0. 
* gnu/packages/bioconductor.scm (r-bcellviper): Update to 1.38.0.

Change-Id: Iaac28d6376364c0d0e30c29deb6df22c40b18b29
 2024-01-22 13:54:45 +01:00
Ricardo Wurmus ee966f03d5
gnu: r-arrmdata: Update to 1.38.0. 
* gnu/packages/bioconductor.scm (r-arrmdata): Update to 1.38.0.

Change-Id: Id1c900cd1a058057d18129c7f2d373bc4772d5cd
 2024-01-22 13:54:45 +01:00
Ricardo Wurmus 9512db59ab
gnu: r-aneufinderdata: Update to 1.30.0. 
* gnu/packages/bioconductor.scm (r-aneufinderdata): Update to 1.30.0.

Change-Id: I94049747ac40bfe1926bfe6a34727c35e1fb6578
 2024-01-22 13:54:45 +01:00
Ricardo Wurmus 8f70c2352d
gnu: r-adductdata: Update to 1.18.0. 
* gnu/packages/bioconductor.scm (r-adductdata): Update to 1.18.0.

Change-Id: I268b9dde5e1913d17e195a77005e3c28b41f6aca
 2024-01-22 13:54:45 +01:00
Ricardo Wurmus b6fb97a250
gnu: r-pfam-db: Update to 3.18.0. 
* gnu/packages/bioconductor.scm (r-pfam-db): Update to 3.18.0.

Change-Id: Iee6ad8fe9188cb6eb5df5f163e5af228a783b682
 2024-01-22 13:54:45 +01:00
Ricardo Wurmus f16f8105e8
gnu: r-txdb-hsapiens-ucsc-hg38-knowngene: Update to 3.18.0. 
* gnu/packages/bioconductor.scm (r-txdb-hsapiens-ucsc-hg38-knowngene): Update to 3.18.0.

Change-Id: Ic11773dbb44ba5c90ea69142c03bbe7292ca03a6
 2024-01-22 13:54:45 +01:00
Ricardo Wurmus 5265421826
gnu: r-bsgenome-hsapiens-ucsc-hg38: Update to 1.4.5. 
* gnu/packages/bioconductor.scm (r-bsgenome-hsapiens-ucsc-hg38): Update to 1.4.5.
[propagated-inputs]: Add r-genomeinfodb.

Change-Id: I77c7e216286314619c05272a0baffb68dcd5a3e6
 2024-01-22 13:54:45 +01:00
Ricardo Wurmus 505aac07c4
gnu: r-org-mm-eg-db: Update to 3.18.0. 
* gnu/packages/bioconductor.scm (r-org-mm-eg-db): Update to 3.18.0.

Change-Id: Idee9907070a23dd79bf77e2d4a7e8ac17419826a
 2024-01-22 13:54:45 +01:00
Ricardo Wurmus f13e407689
gnu: r-org-dr-eg-db: Update to 3.18.0. 
* gnu/packages/bioconductor.scm (r-org-dr-eg-db): Update to 3.18.0.

Change-Id: Icb7f74c83ff7189c7b02964fcb25bac6610fd790
 2024-01-22 13:54:44 +01:00
Ricardo Wurmus 8445ad15ec
gnu: r-org-dm-eg-db: Update to 3.18.0. 
* gnu/packages/bioconductor.scm (r-org-dm-eg-db): Update to 3.18.0.

Change-Id: Ic50a64af9d5b76a4c7cb8864e8e723c533218e19
 2024-01-22 13:54:44 +01:00
Ricardo Wurmus 0adeabcf53
gnu: r-org-ce-eg-db: Update to 3.18.0. 
* gnu/packages/bioconductor.scm (r-org-ce-eg-db): Update to 3.18.0.

Change-Id: Id83d4e64b80ce01abdb2fe06735e0af6b7ebac10
 2024-01-22 13:54:44 +01:00
Ricardo Wurmus 297fc0d76c
gnu: r-illuminahumanmethylation450kanno-ilmn12-hg19: Update to 0.6.1. 
* gnu/packages/bioconductor.scm (r-illuminahumanmethylation450kanno-ilmn12-hg19): Update to 0.6.1.

Change-Id: I142318c4854c75f27bcd1bfe4bfc389cbc8b3725
 2024-01-22 13:54:44 +01:00
Ricardo Wurmus c5a934df85
gnu: r-go-db: Update to 3.18.0. 
* gnu/packages/bioconductor.scm (r-go-db): Update to 3.18.0.

Change-Id: I90ff2421b742369847353aaf32cf8bc4651afda7
 2024-01-22 13:54:44 +01:00
Ricardo Wurmus d9de950ac6
gnu: r-genomeinfodbdata: Update to 1.2.11. 
* gnu/packages/bioconductor.scm (r-genomeinfodbdata): Update to 1.2.11.

Change-Id: Iacb39950f70c8affe457330df8b43260e71ab548
 2024-01-22 13:54:44 +01:00
Ricardo Wurmus 2ee9cce50f
gnu: r-bsgenome-mmusculus-ucsc-mm10: Update to 1.4.3. 
* gnu/packages/bioconductor.scm (r-bsgenome-mmusculus-ucsc-mm10): Update to 1.4.3.

Change-Id: Idbf573d2b4931550122119eed67879c2b13ed52f
 2024-01-22 13:54:44 +01:00
Ricardo Wurmus 6ee0d63dfc
gnu: r-reactome-db: Update to 1.86.2. 
* gnu/packages/bioconductor.scm (r-reactome-db): Update to 1.86.2.

Change-Id: I8312c151f89ef27c5f75adbdf27c098e77f05453
 2024-01-22 13:54:44 +01:00
Ricardo Wurmus 287c5b085b
gnu: r-org-sc-sgd-db: Update to 3.18.0. 
* gnu/packages/bioconductor.scm (r-org-sc-sgd-db): Update to 3.18.0.

Change-Id: I1f7a497f0b36b1fe336343e215fe5c3f179b11ed
 2024-01-22 13:54:44 +01:00
Ricardo Wurmus 8ec5a25eff
gnu: r-org-bt-eg-db: Update to 3.18.0. 
* gnu/packages/bioconductor.scm (r-org-bt-eg-db): Update to 3.18.0.

Change-Id: I4385882eeb83326af88141b301f892632f6cf678
 2024-01-22 13:54:44 +01:00
Ricardo Wurmus d2573f4e28
gnu: r-org-eck12-eg-db: Update to 3.18.0. 
* gnu/packages/bioconductor.scm (r-org-eck12-eg-db): Update to 3.18.0.

Change-Id: Ic8b25521c9a735522c69e3d696d8a514f8d6d17c
 2024-01-22 13:54:44 +01:00
Ricardo Wurmus 389c6082a4
import/cran: Set HOME when ExperimentHub is among the inputs. 
* guix/import/cran.scm (phases-for-inputs): Add 'set-HOME phase when
ExperimentHub is among inputs.

Change-Id: Ie3a2443934704eed8694a76a651b806209722421
 2024-01-22 13:54:44 +01:00
Ricardo Wurmus 29353820f2
import/cran: Also update annotation and experiment packages. 
* guix/import/cran.scm (latest-bioconductor-release): Determine package type
and pass it to LATEST-BIOCONDUCTOR-PACKAGE-VERSION and BIOCONDUCTOR-URI.
(%bioconductor-updater): Compose all bioconductor predicates.

Change-Id: Icef3ae05e28ed0f2796d9abf90e51821d2dfcc4c
 2024-01-22 13:54:44 +01:00
Jean-Pierre De Jesus DIAZ d264237d55
gnu: make-crust-package: Unite firmware and tools. 
* gnu/packages/firmware.scm (make-crust-package): Perform union of
make-crust-firmware and make-crust-tools.
* gnu/packages/firmware.scm (make-crust-firmware): New procedure.

Change-Id: I687bb6d53aae9bd60ed988baf9d17e92f31faa7b
 2024-01-22 11:26:57 +01:00
Jean-Pierre De Jesus DIAZ 938f153784
gnu: Add make-crust-tools. 
* gnu/packages/firmware.scm (make-crust-tools): New procedure.

Change-Id: Iac05ecf1796e4c10692a423c12423ea9b078d141
 2024-01-22 11:26:57 +01:00
Jean-Pierre De Jesus DIAZ dde246ed41
gnu: make-crust-package: Use or1k-elf as target. 
* gnu/packages/firmware.scm (make-crust-package): Use or1k-elf as the
target.

Change-Id: I6c8bf053527f1e12e35402f18cebf8e75557c788
 2024-01-22 11:26:56 +01:00
Jean-Pierre De Jesus DIAZ fa0b2cdab3
gnu: make-crust-package: Update to 0.6. 
* gnu/packages/firmware.scm (make-crust-package): Update to 0.6.  Do not
install host tool as it is not built by default.

Change-Id: Ia79ae8208589601d32235f6d8ace9dce3f8d74f9
 2024-01-22 11:26:56 +01:00
Jean-Pierre De Jesus DIAZ e5a00639aa
gnu: make-crust-package: Memoize. 
* gnu/packages/firmware.scm (make-crust-package): Use mlambda.

Change-Id: I2d916b96bc650f3731a69505e086cf8f8f470809
 2024-01-22 11:26:56 +01:00
Jean-Pierre De Jesus DIAZ ae7da5cbf0
gnu: make-crust-package: Use shorter synopsis. 
* gnu/packages/firmware.scm (make-crust-package) <synopsis>: Make it
short.

Change-Id: I8b93b25a9a6a75aaa92ffa590d0fd46a5511fd49
 2024-01-22 11:26:56 +01:00
Jean-Pierre De Jesus DIAZ 937e64537e
gnu: Add gcc-cross-or1k-elf-toolchain. 
* gnu/packages/cross-toolchain.scm (gcc-cross-or1k-elf-toolchain): New
variable.

Change-Id: Iaf7ed60dbbe116a5efbad8e94be9b2dee51faf15
 2024-01-22 11:26:56 +01:00
Jean-Pierre De Jesus DIAZ 82aef470ce
gnu: cross-gcc-toolchain: Use fixed name. 
* gnu/packages/cross-base.scm (cross-gcc-toolchain) <name>: Always use
gcc-cross- prefix regardless of TARGET having a C standard library or not.

Change-Id: I5cbe89c61e5bd324a385db17c27131ea5ef75669
 2024-01-22 11:26:56 +01:00
Jean-Pierre De Jesus DIAZ 2a43692aa7
guix: Add ork1-elf platform. 
* doc/guix.texi: Document or1k-elf platform.
* guix/platforms/or1k.scm (or1k-elf): New variable.
* Makefile.am (MODULES): Add guix/platforms/or1k.scm.

Change-Id: I3f71a0fa97f1ebd2bbdbf6cd00a93b477a123648
 2024-01-22 11:26:56 +01:00
Nicolas Goaziou 9f6aab9591
gnu: emacs-orgalist: Fix build. 
* gnu/packages/emacs-xyz.scm (emacs-orgalist)[source]<origin>: Use correct extension.

Change-Id: Idea5aa97de9838b4a7bfabd7e7609727bd925a71
 2024-01-22 09:49:45 +01:00
Nicolas Goaziou 9b65b60b97
gnu: notmuch: Update to 0.38.2. 
* gnu/packages/mail.scm (notmuch): Update to 0.38.2.
* gnu/packages/patches/notmuch-emacs-test-output.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Apply file deletion.

Change-Id: I60d0487f2258ed5ef8602de7a624686c5f012a4f
 2024-01-22 09:32:57 +01:00
Nicolas Goaziou 48c52ed486
gnu: emacs-ebdb: Fix build. 
* gnu/packages/emacs-xyz.scm (emacs-ebdb)[propagated-inputs]: Add
EMACS-ORG-ROAM.

Change-Id: I77c2373dcc50ed4a832bf1d493c44eb0b96ebc7b
 2024-01-22 09:14:37 +01:00
Sharlatan Hellseher 17e0b03824
gnu: cambalache: Fix buld. 
As seen in http://ci.guix.gnu.org/build/3338535/log/raw.

* gnu/packages/gnome.scm (cambalache): Fix build.
[inputs]: Swap duplicated webkitgtk to webkitgtk-for-gtk3.

Change-Id: I9604159d3aa343e0bcb539cfade520ddd97cb489
 2024-01-21 23:30:20 +00:00
Nicolas Goaziou 9e9c1613dd
gnu: emacs-org-fc: Update to 0.4.0. 
* gnu/packages/emacs-xyz.scm (emacs-org-fc): Update to 0.4.0.
[arguments]<#:phases>: Fix build error by adding missing (require 'eieio).
<#:test-command>: Load more tests.
[native-inputs]: Add EMACS-EL-MOCK.

Change-Id: Ibdaf38f3dd8f3018bf2b7b53cd94626b983fc953
 2024-01-22 00:20:56 +01:00
Nicolas Goaziou a9d5628f5b
gnu: emacs-el-mock: Update to 1.25.1-1.6cfbc9d. 
* gnu/packages/emacs-xyz.scm (emacs-el-mock): Update to 1.25.1-1.6cfbc9d.

Change-Id: I2e13b8854f9089f68f1ec9eb0fa671e760ea9ec3
 2024-01-22 00:20:56 +01:00
Nicolas Goaziou b63b53b64e
gnu: emacs-plz: Update to 0.7.2. 
* gnu/packages/emacs-xyz.scm (emacs-plz): Update to 0.7.2.

Change-Id: I24ef66998d9a8b83169c185974f2ce2b3697dd4c
 2024-01-22 00:20:55 +01:00
Nicolas Goaziou c3d8f39b5b
gnu: emacs-pg: Update to 0.27. 
* gnu/packages/emacs-xyz.scm (emacs-pg): Update to 0.27.

Change-Id: I10c65f30e790d461c925352b993aa4dc3d6696dd
 2024-01-22 00:20:55 +01:00
Nicolas Goaziou 1c17b444c6
gnu: emacs-org-re-reveal: Update to 3.25.1. 
* gnu/packages/emacs-xyz.scm (emacs-org-re-reveal): Update to 3.25.1.

Change-Id: I79a195184b5d2ad842e4738862086c0b595b967c
 2024-01-22 00:20:55 +01:00
Nicolas Goaziou 396d84071f
gnu: emacs-org-ql: Update to 0.8.4. 
* gnu/packages/emacs-xyz.scm (emacs-org-ql): Update to 0.8.4.

Change-Id: Idb2e25155a62cbf699367a749194dce1852339ec
 2024-01-22 00:20:55 +01:00