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2024-12-03gnu: Add r-hgu95a-db.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-hgu95a-db): New variable. Change-Id: I9eb2e8182689a2e1ba38c180d476dd60363f3c51
2024-12-03gnu: r-curatedtcgadata: Add missing input.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-curatedtcgadata)[native-inputs]: Add r-testthat. Change-Id: I9379295f854ab66a88321326c25f8d7a15fe2e26
2024-12-03gnu: r-pando: Add missing inputs and disable tests.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-pando)[native-inputs]: Add r-bsgenome-hsapiens-ucsc-hg38, r-devtools, r-doparallel, and r-ensdb-hsapiens-v86. [arguments]: Disable tests. Change-Id: Ic66679e2b8c4cdb9835ce08dc4dbb0a42e35e291
2024-12-03gnu: r-anpan: Add missing input.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-anpan)[native-inputs]: Add r-testthat. Change-Id: I69be3fa82db5f9c4e1302c9a3bd2d4f5253bde13
2024-12-03gnu: r-caretensemble: Add missing inputs.Ricardo Wurmus
* gnu/packages/cran.scm (r-caretensemble)[native-inputs]: Add r-catools, r-earth, r-glmnet, r-mlbench, and r-randomforest. Change-Id: I66037e22d86b1cadc5e57f84bfebb4e37396c705
2024-12-03gnu: r-parsnip: Add missing input.Ricardo Wurmus
* gnu/packages/cran.scm (r-parsnip)[native-inputs]: Add r-earth. [arguments]: Remove phase 'delete-bad-tests. Change-Id: I64f4000afc59ab838476f6f08cc331f9121e802b
2024-12-03gnu: Add r-earth.Ricardo Wurmus
* gnu/packages/cran.scm (r-earth): New variable. Change-Id: If6ae39912cade13d0d81c1e5178eb20c5017ccb3
2024-12-03gnu: r-openmx: Add missing input.Ricardo Wurmus
* gnu/packages/cran.scm (r-openmx)[native-inputs]: Add r-numderiv. Change-Id: I7ed2872021b5f164d256704180076bf4618f5e8f
2024-12-03gnu: Add r-plotmo.Ricardo Wurmus
* gnu/packages/cran.scm (r-plotmo): New variable. Change-Id: Id0803e02acc72f1f98429f023b1d673453fde302
2024-12-03gnu: r-kmer: Add missing input.Ricardo Wurmus
* gnu/packages/cran.scm (r-kmer)[native-inputs]: Add r-knitr. Change-Id: Ia28f582637d27c87413af1169ae816ee05377652
2024-12-03gnu: r-devtools: Add missing input.Ricardo Wurmus
* gnu/packages/statistics.scm (r-devtools)[native-inputs]: Add r-mockery. Change-Id: I2d67a549e9eaee339b5362dac54d417deec850b9
2024-12-03gnu: r-hdwgcna: Add missing inputs.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-hdwgcna)[native-inputs]: Add r-devtools and r-testthat. Change-Id: I553d4fc2f1a682e5d552862c5e50a31140528073
2024-12-03gnu: r-rcmdcheck: Add missing inputs.Ricardo Wurmus
* gnu/packages/cran.scm (r-rcmdcheck)[native-inputs]: Add r-mockery and r-webfakes. Change-Id: Id4389d7c6d1c8bce5af67bcbf6d3e04956f58c9b
2024-12-03gnu: r-haplo-stats: Fix vignettes.Ricardo Wurmus
* gnu/packages/cran.scm (r-haplo-stats)[arguments]: Add phase 'set-HOME. Change-Id: Ia1f5e5c33753b2261c7b4dc2ffa40322e9c840a9
2024-12-03gnu: r-celldex: Disable tests.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-celldex)[arguments]: Disable tests. Change-Id: I1881b1793f2fe8bc870697976a5c3434147760ca
2024-12-03gnu: r-ihw: Add missing inputs.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-ihw)[native-inputs]: Add r-ggplot2 and r-scales. Change-Id: Ib52a30442b00ae4303d307a816578012563aa612
2024-12-03gnu: r-ewastools: Add missing inputs.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-ewastools)[native-inputs]: Add r-enmix, r-illuminahumanmethylationepicanno-ilm10b4-hg19, r-minfi, r-stringi, and r-testthat. Change-Id: I8ba2b1c46a4898b27874a7dc8648bb142f4b5a70
2024-12-03gnu: r-enmix: Add missing inputs.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-enmix)[native-inputs]: Add r-minfidata. Change-Id: I0afa8a677c1b91ffec7463b2ed11aadd01a16797
2024-12-03gnu: r-untb: Add missing inputs and disable vignettes.Ricardo Wurmus
* gnu/packages/cran.scm (r-untb)[arguments]: Skip building vignettes. [native-inputs]: Add r-vdiffr. Change-Id: I0e3a8a075fd34f28cee1a76a443c215f500e5012
2024-12-03gnu: r-dalex: Add test inputs.Ricardo Wurmus
* gnu/packages/cran.scm (r-dalex)[native-inputs]: Add r-gower and r-ranger. Change-Id: I2a2de0275dff4a664fbfb660f7cbf065928dddc0
2024-12-03gnu: r-minfi: Disable tests.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-minfi)[arguments]: Disable tests. Change-Id: I6fdb8d78c176c2ebbfbd9289a00833b79448c7a2
2024-12-03gnu: r-bamutils: Add test inputs and disable tests.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-bamutils)[arguments]: Disable tests. [native-inputs]: Add r-testthat and samtools. Change-Id: I781c38fb59355a51f2cd27a833d7ed5dbe5277ab
2024-12-03gnu: r-bamutils: Update to 0.0.0.9000-2.0a7d2d9.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-bamutils): Update to 0.0.0.9000-2.0a7d2d9. Change-Id: I04e86c2ff1059f23a34615ac6067926cdd9cb355
2024-12-03gnu: r-rbamtools: Disable tests.Ricardo Wurmus
* gnu/packages/cran.scm (r-rbamtools)[arguments]: Disable tests. Change-Id: I6a16095454d3d58de23786bec21b54245dc5a462
2024-12-03gnu: r-chippeakanno: Add missing inputs.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-chippeakanno)[native-inputs]: Add r-biomart, r-bsgenome-celegans-ucsc-ce10, r-bsgenome-drerio-ucsc-danrer7, r-bsgenome-hsapiens-ucsc-hg19, r-ensdb-hsapiens-v79, r-org-ce-eg-db, r-org-hs-eg-db, r-reactome-db, and r-txdb-hsapiens-ucsc-hg38-knowngene. Change-Id: Ifd3e71dcca3297c03c9cc93da6c677a274c58b2c
2024-12-03gnu: r-arrow: Add missing input.Ricardo Wurmus
* gnu/packages/cran.scm (r-arrow)[native-inputs]: Add glibc-utf8-locales, r-dplyr, r-hms, r-lubridate, r-stringr, r-tibble, and tzdata-for-tests. [arguments]: Add phases 'delete-bad-tests, 'set-test-locale, and 'set-timezone. Change-Id: Iece4e463ebe73d41a42594eff7850f2efa96b26f
2024-12-03gnu: r-annotatr: Disable tests.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-annotatr)[arguments]: Disable tests. Change-Id: I819fe4bc651c39315ba6d42e34d36b505979003d
2024-12-03gnu: r-lpsymphony: Add missing input.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-lpsymphony)[native-inputs]: Add gfortran. Change-Id: Id5bcbdb1bf19364fc8cbee905efb18698893f771
2024-12-03gnu: r-multiassayexperiment: Add missing inputs.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-multiassayexperiment)[native-inputs]: Add r-hdf5array, r-raggedexperiment, and r-reshape2. [arguments]: Add phase 'set-HOME. Change-Id: Ifafc630ebd32cc255a4d7fd1c190a885e2f7020f
2024-12-03gnu: r-phylogram: Add missing input.Ricardo Wurmus
* gnu/packages/cran.scm (r-phylogram)[native-inputs]: Add r-knitr. Change-Id: Ib2e4816c516cc5af9f9495c925e9e244453d30c9
2024-12-03gnu: r-dicekriging: Add missing inputs.Ricardo Wurmus
* gnu/packages/cran.scm (r-dicekriging)[native-inputs]: Add r-numderiv. Change-Id: Ie5ac8b8e7d9c809ee06d26988c582d91d78fdfe6
2024-12-03gnu: r-mvnfast: Disable tests.Ricardo Wurmus
* gnu/packages/cran.scm (r-mvnfast)[arguments]: Disable tests. Change-Id: I2c4ad28984200081faa328fbd606aff22c2bd0cb
2024-12-03gnu: r-janitor: Fix tests.Ricardo Wurmus
* gnu/packages/cran.scm (r-janitor)[native-inputs]: Add tzdata-for-tests. [arguments]: Add phases 'set-timezone and 'delete-bad-tests. Change-Id: Ibbea9ef585d6697e93c31d46b1ff7cc4e23e0e17
2024-12-03gnu: r-trajectoryutils: Add missing inputs.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-trajectoryutils)[native-inputs]: Add r-biocneighbors and r-delayedmatrixstats. Change-Id: Id49b6e481ebae657f40aba4692dda4de4e2d5bd1
2024-12-03gnu: r-reinforcelearn: Add missing inputs.Ricardo Wurmus
* gnu/packages/cran.scm (r-reinforcelearn)[native-inputs]: Add r-knitr and r-testthat. Change-Id: I71965722253610030cce43e34d299891760cdc9f
2024-12-03gnu: r-bigmemoryextras: Add missing input.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-bigmemoryextras)[native-inputs]: Add r-testthat. Change-Id: Iafc29855c30e74c055f157303e3c2f351f0e7aeb
2024-12-03gnu: r-leidenbase: Add missing inputs.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-leidenbase)[native-inputs]: Add r-knitr and r-testthat. Change-Id: I35e5aebbe6a5e44dea1743f011e4a3a362f6efb1
2024-12-03gnu: r-spacyr: Fix tests.Ricardo Wurmus
* gnu/packages/cran.scm (r-spacyr)[argumenst]: Add phase 'set-HOME. Change-Id: I990c80dd94388da09aa1592e3cc0dd8d14a65d94
2024-12-03gnu: r-quantmod: Disable tests.Ricardo Wurmus
* gnu/packages/cran.scm (r-quantmod)[arguments]: Disable tests. Change-Id: If5ef32ec14ef1bfaca5f5ef983ad0b0e8971837b
2024-12-03gnu: r-partitions: Skip vignettes.Ricardo Wurmus
* gnu/packages/cran.scm (r-partitions)[arguments]: Skip building vignettes. Change-Id: I66d86a439d4ce0922dc74a86c3e4c53a0c632e07
2024-12-03gnu: r-nnlm: Add missing input.Ricardo Wurmus
* gnu/packages/statistics.scm (r-nnlm)[native-inputs]: Add r-testthat. Change-Id: Id0acc0730f43e87d764b2938a299e3a0734358d5
2024-12-03gnu: r-arsenal: Add missing input.Ricardo Wurmus
* gnu/packages/cran.scm (r-arsenal)[native-inputs]: Add r-broom. Change-Id: I442b99b481b73d401e178a69d593fa7a4566fe6a
2024-12-03gnu: r-tester: Disable tests.Ricardo Wurmus
* gnu/packages/cran.scm (r-tester)[arguments]: Disable tests. Change-Id: I85ffcd3735018e267d020df95c9ceeef05a18e30
2024-12-03gnu: r-tclust: Add missing inputs.Ricardo Wurmus
* gnu/packages/statistics.scm (r-tclust)[native-inputs]: Add r-cluster, r-mclust, and r-sn. Change-Id: I029d0fb895b24ecc796c76b93055e8203c7dfaae
2024-12-03gnu: r-illuminaio: Add missing inputs.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-illuminaio)[native-inputs]: Add r-biocstyle and r-illuminadatatestfiles. Change-Id: I2a0cea6faf2f67e2b851944e442a2a541328349a
2024-12-03gnu: Add r-illuminadatatestfiles.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-illuminadatatestfiles): New variable. Change-Id: I6d1d3f342c8f6587557b18d5071d19e1e4e6aa28
2024-12-03gnu: r-gypsum: Disable tests.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-gypsum)[arguments]: Disable tests. Change-Id: Ibec4e3986a6257b20e6a01a8286f1d6ce682171e
2024-12-03gnu: r-rpf: Add missing input.Ricardo Wurmus
* gnu/packages/cran.scm (r-rpf)[native-inputs]: Add r-mirt and r-numderiv. Change-Id: Ib4a36600ca7c24897d7c8745ae0e387c22fe2998
2024-12-03gnu: r-cgdsr: Disable tests.Ricardo Wurmus
* gnu/packages/cran.scm (r-cgdsr)[arguments]: Disable tests. [native-inputs]: Add r-testthat. Change-Id: I66ef4d375c0f23f2271d56f9b424fee3ed6aa2da
2024-12-03gnu: Add r-mirt.Ricardo Wurmus
* gnu/packages/cran.scm (r-mirt): New variable. Change-Id: I2c4155632c0df6cc293e14470acbb7974e4511db
generated by cgit
s='msg-avail'>...* gnu/bootloader/grub.scm (keyboard-layout-file): New procedure. (grub-configuration-file)[keyboard-layout-file]: New variable. [builder]: Use it. * gnu/bootloader.scm (<bootloader-configuration>)[keyboard-layout]: New field. * doc/guix.texi (Bootloader Configuration): Document it. Co-authored-by: nee <nee-git@hidamari.blue> Ludovic Courtès 2019-03-16bootloader: Use 'invoke/quiet' when running 'grub-install' and co....This hides potentially confusing GRUB messages from the user, such as "Installing for i386-pc platform." * gnu/bootloader/extlinux.scm (install-extlinux): Use 'invoke/quiet' instead of 'system*' and 'error'. * gnu/bootloader/grub.scm (install-grub, install-grub-efi): Likewise. * guix/scripts/system.scm (bootloader-installer-script): Guard against 'message-condition?' and handle them properly. Ludovic Courtès 2019-03-13Remove traces of "GuixSD"....* gnu/bootloader/extlinux.scm (extlinux-configuration-file): Remove mentions of "GuixSD". * gnu/bootloader/grub.scm (install-grub-efi): Likewise. * gnu/build/vm.scm (make-iso9660-image): Change default #:volume-id to "Guix_image". (initialize-hard-disk): Search for the "Guix_image" label. * gnu/ci.scm (system-test-jobs, tarball-jobs): Remove "GuixSD". * gnu/installer/newt/welcome.scm (run-welcome-page): Likewise. * gnu/packages/audio.scm (supercollider)[description]: Likewise. * gnu/packages/curl.scm (curl): Likewise. * gnu/packages/emacs.scm (emacs): Likewise. * gnu/packages/gnome.scm (network-manager): Likewise. * gnu/packages/julia.scm (julia): Likewise. * gnu/packages/linux.scm (alsa-plugins): Likewise. (powertop, wireless-regdb): Likewise. * gnu/packages/package-management.scm (guix): Likewise. * gnu/packages/polkit.scm (polkit): Likewise. * gnu/packages/tex.scm (texlive-bin): Likewise. * gnu/services/base.scm (file-systems->fstab): Likewise. * gnu/services/cups.scm (%cups-activation): Likewise. * gnu/services/mail.scm (%dovecot-activation): Likewise. * gnu/services/messaging.scm (prosody-configuration)[log]: Likewise. * gnu/system/examples/vm-image.tmpl (vm-image-motd): Likewise. * gnu/system/install.scm (installation-os)[file-systems]: Change root file system label to "Guix_image". * gnu/system/mapped-devices.scm (check-device-initrd-modules): Remove "GuixSD". * gnu/system/vm.scm (system-docker-image): Likewise. (system-disk-image)[root-label]: Change to "Guix_image". * gnu/tests/install.scm (run-install): Remove "GuixSD". * guix/modules.scm (guix-module-name?): Likewise. * nix/libstore/optimise-store.cc: Likewise. Ludovic Courtès 2018-11-18bootloader: De-monadify configuration file generators....* gnu/bootloader/extlinux.scm: Remove unneeded imports. (extlinux-configuration-file): Use 'computed-file' instead of 'gexp->derivation'. * gnu/bootloader/grub.scm (svg->png): Likewise. (grub-background-image, eye-candy): Adjust accordingly, return non-monadically. (grub-configuration-file): Likewise, and use 'computed-file' instead of 'gexp->derivation'. * gnu/bootloader/u-boot.scm: Remove unneeded imports. * gnu/system.scm: Add 'lower-object' call. Ludovic Courtès 2018-06-26bootloader: grub-efi: Identify as "GuixSD" instead of "grub"....* gnu/bootloader/grub.scm (install-grub-efi): Pass "--bootloader-id" to grub-install. Marius Bakke 2018-06-26bootloader: grub-efi: Support EFI directories relative to MOUNT-POINT....* gnu/bootloader/grub.scm (install-grub-efi): When MOUNT-POINT/EFI-DIR exists, install there rather than EFI-DIR directly. Marius Bakke 2018-06-01bootloader: grub: Use 'with-extensions'....* gnu/bootloader/grub.scm (svg->png): Use 'with-extensions'. Remove 'add-to-load-path' calls. * gnu/build/svg.scm: Use (rsvg) and (cairo) the normal way. Remove 'module-autoload!' calls. Ludovic Courtès 2018-06-01bootloader: grub: Simplify 'svg->png'....* gnu/bootloader/grub.scm (svg->png): Remove now unneeded #:guile-for-build argument. Ludovic Courtès 2018-05-28file-systems: Remove 'title' field and add <file-system-label>....The 'title' field was easily overlooked and was an endless source of confusion. Now, the value of the 'device' field is self-contained. * gnu/system/file-systems.scm (<file-system>): Change constructor name to '%file-system'. [title]: Remove. (<file-system-label>): New record type with printer. (report-deprecation, device-expression) (process-file-system-declaration, file-system): New macros. (file-system-title): New procedure. (file-system->spec, spec->file-system): Adjust to handle <file-system-label>. * gnu/system.scm (bootable-kernel-arguments): Add case for 'file-system-label?'. (read-boot-parameters): Likewise. (mapped-device-user): Avoid 'file-system-title'. (fs->boot-device): Remove. (operating-system-boot-parameters): Use 'file-system-device' instead of 'fs->boot-device'. (device->sexp): Add case for 'file-system-label?'. * gnu/bootloader/grub.scm (grub-root-search): Add case for 'file-system-label?'. * gnu/system/examples/bare-bones.tmpl, gnu/system/examples/beaglebone-black.tmpl, gnu/system/examples/lightweight-desktop.tmpl, gnu/system/examples/vm-image.tmpl: Remove uses of 'title'. * gnu/system/vm.scm (virtualized-operating-system): Remove uses of 'file-system-title'. * guix/scripts/system.scm (check-file-system-availability): Likewise, and adjust fix-it hint. (check-initrd-modules)[file-system-/dev]: Likewise. * gnu/build/file-systems.scm (canonicalize-device-spec): Remove 'title' parameter. [canonical-title]: Remove. Match on SPEC's type rather than on CANONICAL-TITLE. (mount-file-system): Adjust caller. * gnu/build/linux-boot.scm (boot-system): Interpret ROOT here. * gnu/services/base.scm (file-system->fstab-entry): Remove use of 'file-system-title'. * doc/guix.texi (File Systems): Remove documentation of the 'title' field. Rewrite documentation of 'device' and document 'file-system-label'. Ludovic Courtès