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Author SHA1 Message Date
Maxim Cournoyer 1d837aaa32
tests: lightdm: Bump timeout waiting for screen text to 60 seconds. 
This is to avoid non-deterministic failures on slower machines.

* gnu/tests/lightdm.scm (run-lightdm-test) <wait-for-screen-text>: Bump
timeout to 60 s (from the default 30 s).
 2023-07-19 10:38:15 -04:00
Maxim Cournoyer 1edbadc6b4
tests: xvnc: Fix 'gdm auto-suspend is disabled' test. 
This failure is another collateral from commit a09c7da ("tests: Fork and exec
a new Guile for the marionette REPL."), which isolated the marionette
evaluation environment from that of the host.

* gnu/tests/vnc.scm (run-xvnc-test): Move the (guix build utils) import to...
["gdm auto-suspend is disabled"]: ... inside the marionette-eval of this
test.  Complete comment.

Reported-by: Bruno Victal <mirai@makinata.eu>
 2023-07-19 10:38:15 -04:00
Bruno Victal 9542429299
tests: xvnc: Group up GDM test and use GNU Ocrad instead of Tesseract. 
* gnu/tests/vnc.scm (run-xvnc-test): Group up GDM test.  Use GNU Ocrad.

Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
Modified-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
 2023-07-19 10:38:15 -04:00
Bruno Victal ab2abe16de
tests: gdm: Prefer OCR to delay. 
* gnu/tests/gdm.scm (run-gdm-test): Use wait-for-screen-text instead of sleep.

Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
Modified-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
 2023-07-19 10:38:15 -04:00
Bruno Victal 6a86e2d13a
marionette: Allow passing custom OCR arguments. 
* gnu/build/marionette.scm (%default-ocrad-arguments): New variable.
(invoke-ocrad-ocr, invoke-tesseract-ocr, marionette-screen-text)
[ocr-arguments]: New argument.

Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
 2023-07-19 10:38:15 -04:00
Ricardo Wurmus b9bd1bcce9
import/utils: beautify-description: Wrap class names in @code{...}. 
* guix/import/utils.scm (beautify-description): Add procedure to wrap words in
@code{...} markup.
* tests/import-utils.scm: Add two tests.
 2023-07-19 15:53:28 +02:00
Ricardo Wurmus 5566f691a2
gnu: Add r-qfeatures. 
* gnu/packages/bioconductor.scm (r-qfeatures): New variable.
 2023-07-19 15:29:23 +02:00
Ricardo Wurmus 16a05db0ac
gnu: Add r-spectra. 
* gnu/packages/bioconductor.scm (r-spectra): New variable.
 2023-07-19 15:29:23 +02:00
Ricardo Wurmus 3fa6c2b1cb
gnu: Add r-rtcgatoolbox. 
* gnu/packages/bioconductor.scm (r-rtcgatoolbox): New variable.
 2023-07-19 15:29:23 +02:00
Ricardo Wurmus 45bf1a9a6b
import/utils: Add more initial words to beautify-description. 
* guix/import/utils.scm (beautify-description): Add "Classes" and "Tools" to
initial words to be prefixed with "This package provides".
 2023-07-19 15:29:22 +02:00
Ricardo Wurmus 571ad39628
gnu: Add r-gwastools. 
* gnu/packages/bioconductor.scm (r-gwastools): New variable.
 2023-07-19 15:29:22 +02:00
Ricardo Wurmus 5be6946e19
gnu: Add r-beadarray. 
* gnu/packages/bioconductor.scm (r-beadarray): New variable.
 2023-07-19 15:29:22 +02:00
Ricardo Wurmus a4dc8edced
gnu: Add r-beaddatapackr. 
* gnu/packages/bioconductor.scm (r-beaddatapackr): New variable.
 2023-07-19 15:29:22 +02:00
Ricardo Wurmus 9cf4d48850
gnu: Add r-ucell. 
* gnu/packages/bioconductor.scm (r-ucell): New variable.
 2023-07-19 15:29:22 +02:00
Ricardo Wurmus 91b1367e90
gnu: Add r-tcgautils. 
* gnu/packages/bioconductor.scm (r-tcgautils): New variable.
 2023-07-19 15:29:22 +02:00
Ricardo Wurmus 3132fcf7f8
gnu: Add r-globalancova. 
* gnu/packages/bioconductor.scm (r-globalancova): New variable.
 2023-07-19 15:29:22 +02:00
Ricardo Wurmus 72e6324b4a
gnu: Add r-seqarray. 
* gnu/packages/bioconductor.scm (r-seqarray): New variable.
 2023-07-19 15:29:22 +02:00
Ricardo Wurmus 1f80d41735
gnu: Add r-nebulosa. 
* gnu/packages/bioconductor.scm (r-nebulosa): New variable.
 2023-07-19 15:29:22 +02:00
Ricardo Wurmus 15b35874b1
gnu: Add r-ggtreeextra. 
* gnu/packages/bioconductor.scm (r-ggtreeextra): New variable.
 2023-07-19 15:29:22 +02:00
Ricardo Wurmus c63da4eb52
gnu: Add r-survcomp. 
* gnu/packages/bioconductor.scm (r-survcomp): New variable.
 2023-07-19 15:29:22 +02:00
Ricardo Wurmus 2edbfd43aa
gnu: r-missmethyl: Move out of experiments section. 
* gnu/packages/bioconductor.scm (r-missmethyl): Move from experiments section
to packages section.
 2023-07-19 15:29:14 +02:00
Ricardo Wurmus e74e9f6240
gnu: r-cellid: Move out of experiments section. 
* gnu/packages/bioconductor.scm (r-cellid): Move from experiments section to
packages section.
 2023-07-19 15:29:14 +02:00
Ricardo Wurmus efec1a8453
gnu: Add r-mfuzz. 
* gnu/packages/bioconductor.scm (r-mfuzz): New variable.
 2023-07-19 15:29:14 +02:00
Ricardo Wurmus 5a20a14c3e
gnu: Add r-raggedexperiment. 
* gnu/packages/bioconductor.scm (r-raggedexperiment): New variable.
 2023-07-19 15:29:14 +02:00
Ricardo Wurmus 9d45783d77
gnu: Add r-spatialexperiment. 
* gnu/packages/bioconductor.scm (r-spatialexperiment): New variable.
 2023-07-19 15:29:14 +02:00
Ricardo Wurmus c5f9e435da
gnu: Add r-singscore. 
* gnu/packages/bioconductor.scm (r-singscore): New variable.
 2023-07-19 15:29:14 +02:00
Ricardo Wurmus f77216721e
gnu: Add r-plyranges. 
* gnu/packages/bioconductor.scm (r-plyranges): New variable.
 2023-07-19 14:57:07 +02:00
Ricardo Wurmus b7d3a9e2f5
gnu: Add r-tkwidgets. 
* gnu/packages/bioconductor.scm (r-tkwidgets): New variable.
 2023-07-19 14:56:11 +02:00
Ricardo Wurmus dc889e85a9
gnu: Add r-dyndoc. 
* gnu/packages/bioconductor.scm (r-dyndoc): New variable.
 2023-07-19 14:55:11 +02:00
Ricardo Wurmus d0c96a78ed
gnu: Add r-genomicdatacommons. 
* gnu/packages/bioconductor.scm (r-genomicdatacommons): New variable.
 2023-07-19 14:54:02 +02:00
Ricardo Wurmus 46cae56dfe
gnu: Add r-snprelate. 
* gnu/packages/bioconductor.scm (r-snprelate): New variable.
 2023-07-19 14:53:06 +02:00
Ricardo Wurmus b4cfd40aae
gnu: Add r-enhancedvolcano. 
* gnu/packages/bioconductor.scm (r-enhancedvolcano): New variable.
 2023-07-19 14:37:54 +02:00
Ricardo Wurmus 1b48d723bd
gnu: Add r-logistf. 
* gnu/packages/cran.scm (r-logistf): New variable.
 2023-07-19 13:09:32 +02:00
Ricardo Wurmus c31eea21dd
gnu: Add r-formula-tools. 
* gnu/packages/cran.scm (r-formula-tools): New variable.
 2023-07-19 13:09:25 +02:00
Ricardo Wurmus 5f6daad3c8
gnu: Add r-operator-tools. 
* gnu/packages/cran.scm (r-operator-tools): New variable.
 2023-07-19 13:09:03 +02:00
Ricardo Wurmus 4415a421c4
gnu: Add r-uchardet. 
* gnu/packages/cran.scm (r-uchardet): New variable.
 2023-07-19 13:08:47 +02:00
Ricardo Wurmus ff6b2a88c4
gnu: Add r-gwasexacthw. 
* gnu/packages/cran.scm (r-gwasexacthw): New variable.
 2023-07-19 13:08:02 +02:00
Ricardo Wurmus b2750695f7
gnu: Add r-gsva. 
* gnu/packages/bioconductor.scm (r-gsva): New variable.
 2023-07-19 09:56:55 +02:00
Andre A. Gomes 1f53bfb7d7
gnu: cl-usocket: Update to 0.8.6. 
* gnu/packages/lisp-xyz.scm (sbcl-usocket): Update to 0.8.6.

Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>
 2023-07-19 09:14:25 +02:00
Andre A. Gomes 324f56927b
gnu: cl-ndebug: Update to 0.2.0. 
* gnu/packages/lisp-xyz.scm (sbcl-ndebug): Update to 0.2.0.

Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>
 2023-07-19 09:12:01 +02:00
Andre A. Gomes 54a49cf1cc
gnu: cl-lisp-unit2: Update to 0.9.4-0.b5aa17b. 
* gnu/packages/lisp-check.scm (sbcl-lisp-unit2): Update to 0.9.4-0.b5aa17b.

Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>
 2023-07-19 09:10:10 +02:00
Andre A. Gomes 2d298564e3
gnu: cl-array-utils: Update to 1.2.0-0.29da8fc. 
* gnu/packages/lisp-xyz.scm (sbcl-array-utils): Update to 1.2.0-0.29da8fc.

Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>
 2023-07-19 09:10:04 +02:00
Janneke Nieuwenhuizen 8831d3ba9f
gnu: commencement: hurd-minimal-boot0: Update to 0.9.git20230216. 
* gnu/packages/commencement.scm (hurd-minimal-boot0): Remove redundant let
and package-with-bootstrap-guile.
[name]: New field; give proper name.
[version]: New field.
[source]: Update to 0.9.git20230216, using hurd-headers-boot0' source.
[inputs]: Add autoconf-boot0, automake-boot0, gnumach-headers-boot0.
[native-inputs]: Add autoconf-boot0, automake-boot0, and
gnumach-headers-boot0.
* gnu/packages/commencement.scm (hurd-version-boot0, hurd-source-boot0):
Remove.
 2023-07-19 07:33:58 +02:00
Janneke Nieuwenhuizen e9c23e2c8e
gnu: commencement: hurd-headers-boot0: Update to 0.9.git20230216. 
* gnu/packages/commencement.scm (hurd-headers-boot0): Remove redundant outer
let and package-with-bootstrap-guile.
[name]: New field; give proper name.
[version]: New field.
[source]: Update to 0.9.git20230216, using git-fetch-from-tarball.
[inputs]: Add autoconf-boot0, automake-boot0, gnumach-headers-boot0.
 2023-07-19 07:33:58 +02:00
Josselin Poiret 72dbad505a
gnu: mig: Use git-fetch. 
Now that we have `git-fetch-from-tarball' to break the cycle in commencement
for git-fetch sources, we can finally update mig to use git-fetch to allow
`--with-commit' builds.

* gnu/packages/hurd.scm (mig)[source]: Use git-fetch again.
* gnu/packages/commencement.scm (mig-boot0)[source]: Use
git-fetch-from-tarball accordingly.
 2023-07-19 07:33:55 +02:00
Janneke Nieuwenhuizen c1840e9442
gnu: commencement: mig-boot0: Update to 1.8+git20230520. 
* gnu/packages/commencement.scm (mig-boot0): Remove redundant
outer let.
[name]: New field, give proper name.
[version]: New field
[source]: Update to 1.8+git20230520.
[native-inputs]: Add autoconf-boot0, automake-boot0.
[inputs]: Add gnumach-headers-boot0.
 2023-07-19 07:32:33 +02:00
Janneke Nieuwenhuizen 5315c23702
gnu: commencement: gnumach-headers-boot0: Update to 1.8+git20221224. 
* gnu/packages/commencement.scm (gnumach-headers-boot0)[name]: New field; give
proper name.
[source]: Update to 1.8+git20221224, using git-fetch-from-tarball.
[native-inputs]: Add autoconf-boot0, automake-boot0, texinfo-boot0.
[arguments]: Add 'patch-compat' phase to allow building hurd-minimal etc, with
our out-of-date bootstsrap binaries.
 2023-07-19 07:32:32 +02:00
Ludovic Courtès ed88588931
gnu: commencement: Add git-fetch-from-tarball utility. 
* gnu/packages/commencement.scm (git-fetch-from-tarball): New procedure.
 2023-07-19 07:32:32 +02:00
Janneke Nieuwenhuizen 85f940b0e7
gnu: commencement: Add automake-boot0. 
* gnu/packages/commencement.scm (automake-boot0): New variable.
 2023-07-19 07:32:32 +02:00
Janneke Nieuwenhuizen 9c6081c705
gnu: commencement: Add autoconf-boot0. 
* gnu/packages/commencement.scm (autoconf-boot0): New variable.
 2023-07-19 07:32:29 +02:00