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Author SHA1 Message Date
Ricardo Wurmus
c762df5478
etc/committer: Disable diff colors. 
Reported by: morgansmith on IRC.

* etc/committer.scm.in (diff-info): Invoke "git diff" with "--no-color".
 2021-04-08 17:12:06 +02:00
Mathieu Othacehe
2afc79b51d
ci: Introduce new subsets. 
Introduce 'images, 'system-tests and 'tarball subsets.

* gnu/ci.scm (cuirass-jobs): Break the 'all subset into smaller subsets.
 2021-04-08 15:24:03 +02:00
Mathieu Othacehe
14ada96451
ci: Remove the job period argument. 
Cuirass now deals with periodicity directly on specifications.

* gnu/ci.scm (derivation->job): Remove the period argument.
(image-jobs, system-test-jobs, tarball-jobs): Adapt them.
 2021-04-08 15:24:03 +02:00
Ricardo Wurmus
5f0c3535aa
gnu: r-genomicfeatures: Update to 1.42.3. 
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.42.3.
 2021-04-08 13:28:24 +02:00
Ricardo Wurmus
e0147aa46f
gnu: r-gviz: Update to 1.34.1. 
* gnu/packages/bioconductor.scm (r-gviz): Update to 1.34.1.
 2021-04-08 13:28:24 +02:00
Ricardo Wurmus
14a4c30828
gnu: r-universalmotif: Update to 1.8.4. 
* gnu/packages/bioconductor.scm (r-universalmotif): Update to 1.8.4.
 2021-04-08 13:28:24 +02:00
Ricardo Wurmus
8a7933f37e
gnu: r-rsubread: Update to 2.4.3. 
* gnu/packages/bioconductor.scm (r-rsubread): Update to 2.4.3.
 2021-04-08 13:28:24 +02:00
Ricardo Wurmus
215b0ced02
gnu: r-chippeakanno: Update to 3.24.2. 
* gnu/packages/bioconductor.scm (r-chippeakanno): Update to 3.24.2.
[propagated-inputs]: Add r-dplyr.
 2021-04-08 13:28:24 +02:00
Ricardo Wurmus
55185f9b3f
gnu: r-diffbind: Update to 3.0.15. 
* gnu/packages/bioconductor.scm (r-diffbind): Update to 3.0.15.
 2021-04-08 13:28:24 +02:00
Ricardo Wurmus
9d2ca98213
gnu: r-genomeinfodb: Update to 1.26.6. 
* gnu/packages/bioconductor.scm (r-genomeinfodb): Update to 1.26.6.
 2021-04-08 13:28:24 +02:00
Ricardo Wurmus
fb73d7d10d
gnu: r-delayedarray: Update to 0.16.3. 
* gnu/packages/bioconductor.scm (r-delayedarray): Update to 0.16.3.
 2021-04-08 13:28:23 +02:00
Paul Garlick
71ca8fd40b
gnu: Add texlive-mweights. 
* gnu/packages/tex.scm: New variable.
 2021-04-08 11:18:06 +01:00
Morgan Smith
bb4f47a7f6
gnu: axoloti-runtime: Simplify build. 
* gnu/packages/axoloti.scm (axoloti-runtime)[arguments]: Remove
unnecessary environment variable assignments in custom 'build phase.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2021-04-08 11:00:05 +03:00
Morgan Smith
5c9954490c
gnu: gcc-arm-none-eabi: Fix C++ header location. 
Previously the C++ headers where installed in the include folder, overwriting
some C headers.

* gnu/packages/embedded.scm (gcc-arm-none-eabi-4.9)
[native-search-paths]: Add C++ header locations.
(gcc-arm-none-eabi-7-2018-q2-update)[native-search-paths]: Add C++
header locations.
(make-libstdc++-arm-none-eabi)[arguments]: Change C++ header install
location to include/c++.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2021-04-08 10:58:54 +03:00
Ricardo Wurmus
83991a34d5
etc/committer: Recompute hunks before processing changes. 
* etc/committer.scm.in (main): Re-evaluate diff-info after processing
insertions.
 2021-04-08 03:10:14 +02:00
Ricardo Wurmus
43fb6b765d
etc/committer: Record minimal context for hunks to avoid problems. 
With zero context new definitions would be applied to the wrong location in
the file.  More context lines lead to larger hunks, though, so we use just one
line of context.

* etc/committer.scm.in (diff-info): Invoke "git diff" with one line of
context.
[info]: Merge line break and first line.
(lines-to-first-change): New procedure.
(old-sexp, new-sexp): Use it.
 2021-04-08 03:10:14 +02:00
Ricardo Wurmus
56270c1275
etc/committer: Define delay duration as a variable. 
* etc/committer.scm.in (%delay): New variable.
(main): Use it.
 2021-04-08 03:10:14 +02:00
Ricardo Wurmus
c8c3afe848
etc/committer: Handle package additions. 
* etc/committer.scm.in (<hunk>)[diff]: Rename this field...
[diff-lines]: ...to this.
[definition?]: New field.
(hunk->patch): Join diff lines.
(diff-info): Do not join diff lines; record whether a hunk is a new
definition.
(commit-message): Rename this procedure...
(change-commit-message): ...to this.
(add-commit-message): New procedure.
(main): Handle new package definitions before changes.
 2021-04-08 03:10:13 +02:00
Ricardo Wurmus
e1a38cbad8
gnu: r-sn: Update to 2.0.0. 
* gnu/packages/statistics.scm (r-sn): Update to 2.0.0.
 2021-04-08 03:10:13 +02:00
Ricardo Wurmus
2e36f4a1c4
gnu: r-sfsmisc: Update to 1.1-10. 
* gnu/packages/statistics.scm (r-sfsmisc): Update to 1.1-10.
 2021-04-08 03:10:13 +02:00
Ricardo Wurmus
9493b3e9a7
gnu: r-e1071: Update to 1.7-6. 
* gnu/packages/statistics.scm (r-e1071): Update to 1.7-6.
[propagated-inputs]: Add r-proxy.
 2021-04-08 03:10:13 +02:00
Ricardo Wurmus
d98cecdd07
gnu: r-xml: Update to 3.99-0.6. 
* gnu/packages/statistics.scm (r-xml): Update to 3.99-0.6.
 2021-04-08 03:10:13 +02:00
Ricardo Wurmus
d6fd6908c2
gnu: r-rsqlite: Update to 2.2.5. 
* gnu/packages/statistics.scm (r-rsqlite): Update to 2.2.5.
 2021-04-08 03:10:13 +02:00
Ricardo Wurmus
e2851d10db
gnu: r-catools: Update to 1.18.2. 
* gnu/packages/statistics.scm (r-catools): Update to 1.18.2.
 2021-04-08 03:10:13 +02:00
Ricardo Wurmus
63c5888c43
gnu: r-dbplyr: Update to 2.1.1. 
* gnu/packages/statistics.scm (r-dbplyr): Update to 2.1.1.
 2021-04-08 03:10:13 +02:00
Ricardo Wurmus
55378aa21d
gnu: r-survival: Update to 3.2-10. 
* gnu/packages/statistics.scm (r-survival): Update to 3.2-10.
 2021-04-08 03:10:13 +02:00
Ricardo Wurmus
971a997f75
gnu: r-stars: Update to 0.5-2. 
* gnu/packages/cran.scm (r-stars): Update to 0.5-2.
 2021-04-08 03:10:13 +02:00
Ricardo Wurmus
0ec1b08a52
gnu: r-lwgeom: Update to 0.2-6. 
* gnu/packages/cran.scm (r-lwgeom): Update to 0.2-6.
[inputs]: Add zlib.
 2021-04-08 03:10:13 +02:00
Ricardo Wurmus
5a2602032f
gnu: r-ragg: Update to 1.1.2. 
* gnu/packages/cran.scm (r-ragg): Update to 1.1.2.
 2021-04-08 03:10:13 +02:00
Ricardo Wurmus
ded1599829
gnu: r-textshaping: Update to 0.3.3. 
* gnu/packages/cran.scm (r-textshaping): Update to 0.3.3.
 2021-04-08 03:10:13 +02:00
Ricardo Wurmus
2224e02779
gnu: r-bbotk: Update to 0.3.2. 
* gnu/packages/cran.scm (r-bbotk): Update to 0.3.2.
 2021-04-08 03:10:13 +02:00
Ricardo Wurmus
6ec08e19b3
gnu: r-mlr3learners: Update to 0.4.5. 
* gnu/packages/cran.scm (r-mlr3learners): Update to 0.4.5.
 2021-04-08 03:10:12 +02:00
Ricardo Wurmus
ae3df456bb
gnu: r-mlr3misc: Update to 0.8.0. 
* gnu/packages/cran.scm (r-mlr3misc): Update to 0.8.0.
 2021-04-08 03:10:12 +02:00
Ricardo Wurmus
b83b2a3a4b
gnu: r-phangorn: Update to 2.6.3. 
* gnu/packages/cran.scm (r-phangorn): Update to 2.6.3.
[native-inputs]: Add r-knitr.
 2021-04-08 03:10:12 +02:00
Ricardo Wurmus
6e93ab0666
gnu: r-qtl: Update to 1.48-1. 
* gnu/packages/cran.scm (r-qtl): Update to 1.48-1.
 2021-04-08 03:10:12 +02:00
Ricardo Wurmus
3ba3fb71fb
gnu: r-altmeta: Update to 3.3. 
* gnu/packages/cran.scm (r-altmeta): Update to 3.3.
 2021-04-08 03:10:12 +02:00
Ricardo Wurmus
ed5f5f0274
gnu: r-tidyposterior: Update to 0.1.0. 
* gnu/packages/cran.scm (r-tidyposterior): Update to 0.1.0.
[propagated-inputs]: Remove r-lifecycle; add r-tune and r-workflowsets.
 2021-04-08 03:10:12 +02:00
Ricardo Wurmus
7ac3cefc64
gnu: r-slider: Update to 0.2.1. 
* gnu/packages/cran.scm (r-slider): Update to 0.2.1.
[propagated-inputs]: Add r-ellipsis.
 2021-04-08 03:10:12 +02:00
Ricardo Wurmus
47d8e0c1ad
gnu: r-yardstick: Update to 0.0.8. 
* gnu/packages/cran.scm (r-yardstick): Update to 0.0.8.
[propagated-inputs]: Add r-vctrs.
 2021-04-08 03:10:12 +02:00
Ricardo Wurmus
f5c72b2cd7
gnu: r-muhaz: Update to 1.2.6.3. 
* gnu/packages/cran.scm (r-muhaz): Update to 1.2.6.3.
 2021-04-08 03:10:12 +02:00
Ricardo Wurmus
3974902362
gnu: r-cpp11: Update to 0.2.7. 
* gnu/packages/cran.scm (r-cpp11): Update to 0.2.7.
 2021-04-08 03:10:12 +02:00
Ricardo Wurmus
a387de2fa7
gnu: r-spatstat: Update to 2.1-0. 
* gnu/packages/cran.scm (r-spatstat): Update to 2.1-0.
 2021-04-08 03:10:12 +02:00
Ricardo Wurmus
3069514325
gnu: r-spatstat-linnet: Update to 2.1-1. 
* gnu/packages/cran.scm (r-spatstat-linnet): Update to 2.1-1.
 2021-04-08 03:10:11 +02:00
Ricardo Wurmus
2ef03976f3
gnu: r-spatstat-core: Update to 2.0-0. 
* gnu/packages/cran.scm (r-spatstat-core): Update to 2.0-0.
 2021-04-08 03:10:11 +02:00
Ricardo Wurmus
b6aa3ada62
gnu: r-spatstat-geom: Update to 2.0-1. 
* gnu/packages/cran.scm (r-spatstat-geom): Update to 2.0-1.
[propagated-inputs]: Remove r-spatstat-sparse.
 2021-04-08 03:10:11 +02:00
Ricardo Wurmus
8561ce6a8c
gnu: r-spatstat-data: Update to 2.1-0. 
* gnu/packages/cran.scm (r-spatstat-data): Update to 2.1-0.
 2021-04-08 03:10:11 +02:00
Ricardo Wurmus
1134bab6d0
gnu: r-spatstat-sparse: Update to 2.0-0. 
* gnu/packages/cran.scm (r-spatstat-sparse): Update to 2.0-0.
 2021-04-08 03:10:11 +02:00
Ricardo Wurmus
35654c7285
gnu: r-spatstat-utils: Update to 2.1-0. 
* gnu/packages/cran.scm (r-spatstat-utils): Update to 2.1-0.
 2021-04-08 03:10:11 +02:00
Ricardo Wurmus
213d7e7649
gnu: r-shapforxgboost: Update to 0.1.1. 
* gnu/packages/cran.scm (r-shapforxgboost): Update to 0.1.1.
[propagated-inputs]: Remove r-lightgbm.
[native-inputs]: Add r-knitr.
 2021-04-08 03:10:11 +02:00
Ricardo Wurmus
e138e27410
gnu: r-lightgbm: Update to 3.2.0. 
* gnu/packages/cran.scm (r-lightgbm): Update to 3.2.0.
 2021-04-08 03:10:11 +02:00