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Author SHA1 Message Date
Ricardo Wurmus 564142d25e
gnu: r-catalyst: Update to 1.16.1. 
* gnu/packages/bioconductor.scm (r-catalyst): Update to 1.16.1.
 2021-07-10 21:35:29 +02:00
Ricardo Wurmus c4ffceb0c2
gnu: r-rhdf5lib: Update to 1.14.2. 
* gnu/packages/bioconductor.scm (r-rhdf5lib): Update to 1.14.2.
 2021-07-10 21:35:29 +02:00
Ricardo Wurmus e957d6c93b
gnu: r-bioconcotk: Update to 1.12.1. 
* gnu/packages/bioconductor.scm (r-bioconcotk): Update to 1.12.1.
 2021-07-10 21:35:29 +02:00
Ricardo Wurmus 1cbcf54204
gnu: r-biocstyle: Update to 2.20.2. 
* gnu/packages/bioconductor.scm (r-biocstyle): Update to 2.20.2.
 2021-07-10 21:35:29 +02:00
Ricardo Wurmus 23abd7b6b6
gnu: r-mixomics: Update to 6.16.1. 
* gnu/packages/bioconductor.scm (r-mixomics): Update to 6.16.1.
 2021-07-10 21:35:29 +02:00
Ricardo Wurmus 3d539883ca
gnu: r-rsubread: Update to 2.6.3. 
* gnu/packages/bioconductor.scm (r-rsubread): Update to 2.6.3.
 2021-07-10 21:35:29 +02:00
Ricardo Wurmus a94d1e3b4c
gnu: r-annaffy: Update to 1.64.2. 
* gnu/packages/bioconductor.scm (r-annaffy): Update to 1.64.2.
 2021-07-10 21:35:29 +02:00
Ricardo Wurmus 344c901a4c
gnu: r-clusterprofiler: Update to 4.0.2. 
* gnu/packages/bioconductor.scm (r-clusterprofiler): Update to 4.0.2.
 2021-07-10 21:35:29 +02:00
Ricardo Wurmus a5e6826020
gnu: r-enrichplot: Update to 1.12.2. 
* gnu/packages/bioconductor.scm (r-enrichplot): Update to 1.12.2.
 2021-07-10 21:35:29 +02:00
Ricardo Wurmus 209642912d
gnu: r-dose: Update to 3.18.1. 
* gnu/packages/bioconductor.scm (r-dose): Update to 3.18.1.
 2021-07-10 21:35:29 +02:00
Ricardo Wurmus 072533f579
gnu: r-diffbind: Update to 3.2.4. 
* gnu/packages/bioconductor.scm (r-diffbind): Update to 3.2.4.
 2021-07-10 21:35:28 +02:00
Ricardo Wurmus 9496f34e23
gnu: r-systempiper: Update to 1.26.3. 
* gnu/packages/bioconductor.scm (r-systempiper): Update to 1.26.3.
[propagated-inputs]: Add r-crayon and r-s4vectors.
 2021-07-10 21:35:28 +02:00
Ricardo Wurmus ea52ad7d4f
gnu: r-mzr: Update to 2.26.1. 
* gnu/packages/bioconductor.scm (r-mzr): Update to 2.26.1.
 2021-07-10 21:35:28 +02:00
Ricardo Wurmus 8936e45327
gnu: r-limma: Update to 3.48.1. 
* gnu/packages/bioconductor.scm (r-limma): Update to 3.48.1.
 2021-07-10 21:35:28 +02:00
Ricardo Wurmus dfe8e5cca6
gnu: r-genomeinfodb: Update to 1.28.1. 
* gnu/packages/bioconductor.scm (r-genomeinfodb): Update to 1.28.1.
 2021-07-10 21:35:28 +02:00
Ricardo Wurmus fd00ed8ff8
gnu: r-ensembldb: Update to 2.16.2. 
* gnu/packages/bioconductor.scm (r-ensembldb): Update to 2.16.2.
 2021-07-10 21:35:28 +02:00
Ricardo Wurmus 3c60e8d5e5
gnu: r-edaseq: Update to 2.26.1. 
* gnu/packages/bioconductor.scm (r-edaseq): Update to 2.26.1.
 2021-07-10 21:35:28 +02:00
Ricardo Wurmus f8d7d07679
gnu: r-biocparallel: Update to 1.26.1. 
* gnu/packages/bioconductor.scm (r-biocparallel): Update to 1.26.1.
 2021-07-10 21:35:28 +02:00
Ricardo Wurmus 03c9d86432
gnu: r-biomart: Update to 2.48.2. 
* gnu/packages/bioconductor.scm (r-biomart): Update to 2.48.2.
 2021-07-10 21:35:28 +02:00
Ricardo Wurmus 74bfaf92db
gnu: r-annotationhub: Update to 3.0.1. 
* gnu/packages/bioconductor.scm (r-annotationhub): Update to 3.0.1.
 2021-07-10 21:35:28 +02:00
Ricardo Wurmus bc85faf9a2
gnu: Add r-ggpp. 
* gnu/packages/cran.scm (r-ggpp): New variable.
 2021-07-10 21:35:28 +02:00
Ricardo Wurmus 48abef355d
gnu: Add r-s2. 
* gnu/packages/cran.scm (r-s2): New variable.
 2021-07-10 21:35:28 +02:00
Ricardo Wurmus 9a3f66ee7b
gnu: Add r-wk. 
* gnu/packages/cran.scm (r-wk): New variable.
 2021-07-10 21:35:28 +02:00
Ricardo Wurmus 39e1bc5b02
gnu: Add r-reldist. 
* gnu/packages/cran.scm (r-reldist): New variable.
 2021-07-10 21:35:28 +02:00
Ricardo Wurmus c0e4357043
gnu: r-gtools: Update to 3.9.2. 
* gnu/packages/statistics.scm (r-gtools): Update to 3.9.2.
[arguments]: Remove.
 2021-07-10 21:35:27 +02:00
Ricardo Wurmus ce84ba5bd7
gnu: r-vdiffr: Update to 1.0.2. 
* gnu/packages/cran.scm (r-vdiffr): Update to 1.0.2.
[source]: Remove snippet.
[arguments]: Remove.
[inputs]: Remove freetype and harfbuzz; add libpng and zlib.
[propagated-inputs]: Remove r-bh, r-devtools, r-fontquiver,
r-freetypeharfbuzz, r-gdtools, r-htmlwidgets, r-purrr, r-r6, r-rcpp, r-shiny,
and r-usethis; add r-cpp11 and r-lifecycle.
[native-inputs]: Remove esbuild and js-jquery.
 2021-07-10 21:35:27 +02:00
Ricardo Wurmus 94be433332
gnu: r-rintrojs: Update to 0.3.0. 
* gnu/packages/cran.scm (r-rintrojs): Update to 0.3.0.
[source]: Delete minified JavaScript in snippet.
[arguments]: Minify with esbuild.
[native-inputs]: Replace uglify-js with esbuild; update intro.js to 3.2.1.
[license]: Add license of intro.js.
 2021-07-10 21:35:24 +02:00
Timotej Lazar 5c45ed059c
gnu: qpdfview: Use qt-build-system. 
This fixes compilation after the recent reorganization of qt-build-system. As
a side effect, specifying Qt plugins with environment variables now works.

* gnu/packages/pdf.scm (qpdfview)[build-system]: Use qt-build-system.
[arguments]: Drop #:modules and #:imported-modules, and the 'qt-wrap
phase. Specify that there are no tests.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2021-07-10 14:17:49 -04:00
Pierre Neidhardt 45fdb03500
gnu: sbcl-generic-cl: Update to 0.9. 
* gnu/packages/lisp-xyz.scm (sbcl-generic-cl): Update to 0.9.
 2021-07-10 17:07:17 +02:00
Pierre Neidhardt e1b53728cc
gnu: Add cl-form-types. 
* gnu/packages/lisp-xyz.scm (cl-form-types, ecl-cl-form-types,
sbcl-cl-form-types): New variables.
 2021-07-10 17:07:17 +02:00
Ivan Gankevich c21ccbf14e
gnu: Add ocaml-bibtex2html. 
* gnu/packages/ocaml.scm (ocaml-bibtex2html): New variable.

Signed-off-by: Julien Lepiller <julien@lepiller.eu>
 2021-07-10 15:02:12 +02:00
Julien Lepiller f7f6cbb6b6
gnu: Add texlive-preprint. 
* gnu/packages/tex.scm (texlive-preprint): New variable.
 2021-07-10 15:01:59 +02:00
Ivan Gankevich bfa0df0d61
gnu: hevea: Update to 2.35. 
* gnu/packages/ocaml.scm (hevea): Update to 2.35.

Signed-off-by: Julien Lepiller <julien@lepiller.eu>
 2021-07-10 15:01:31 +02:00
Pierre Neidhardt 4dc0337146
gnu: sbcl-cl-gserver: Update to 1.8.0. 
* gnu/packages/lisp-xyz.scm (sbcl-cl-gserver): Update to 1.8.0.
 2021-07-10 12:18:22 +02:00
Justin Veilleux 24ee1448e8
gnu: Add netdiscover. 
* gnu/packages/networking.scm (netdiscover): New variable.

Signed-off-by: Arun Isaac <arunisaac@systemreboot.net>
 2021-07-10 15:11:26 +05:30
Ludovic Courtès 2ea2bca1dd
services: qemu-binfmt: Preserve argv[0] by default. 
Previously, argv[0] would be replaced by the absolute file name of the
executable.  This could cause discrepancies, for example in the
Coreutils test suite: <https://issues.guix.gnu.org/49485>.

* gnu/services/virtualization.scm (<qemu-platform>)[flags]: Default to "FP".
 2021-07-10 00:24:59 +02:00
Arun Isaac 4ac2e09051
gnu: go-github-com-golang-snappy: Update to 0.0.4. 
* gnu/packages/syncthing.scm (go-github-com-golang-snappy): Update to 0.0.4.
 2021-07-09 21:34:34 +05:30
Andrew Tropin 314beace60
gnu: emacs-dash: Update to 2.19.0. 
* gnu/packages/emacs-xyz.scm (emacs-dash): Update to 2.19.0.

Signed-off-by: Leo Prikler <leo.prikler@student.tugraz.at>
 2021-07-09 17:57:11 +02:00
Zhu Zihao 2086a6a335
gnu: emacs-telega: Fix 'patch-source' phase. 
* gnu/packages/emacs-xyz.scm (emacs-telega)[#:phases]<patch-sources>:
Add missing slash in ‘/bin’ when patching general commands.
Also patch telega-vvnote.el.

Signed-off-by: Leo Prikler <leo.prikler@student.tugraz.at>
 2021-07-09 17:57:10 +02:00
Ludovic Courtès cf88c967af
self: Remove stale comment about "mmap(PROT_NONE) failed" crash. 
This crash was fixed by 0aef94e7bc, itself
a followup to 47d48f0c43.

* guix/self.scm (translate-texi-manuals)[build]: Remove reference to the
PROT_NONE bug.
 2021-07-09 17:33:46 +02:00
Ludovic Courtès 609e66e45f
Revert "self: Build translated manuals with a single process." 
This reverts commit af2d6ec092, which the
parent commit makes unnecessary.
 2021-07-09 17:33:46 +02:00
Ludovic Courtès 580a031e7d
doc: Build manual translations with 'guile-3.0-latest'. 
Fixes <https://bugs.gnu.org/47428>.
Reported by Leo Famulari <leo@famulari.name>.

* doc/build.scm (translated-texi-manuals): Explicitly use 'guile-3.0-latest'.
 2021-07-09 17:33:46 +02:00
Leo Prikler 4236b8586d
gnu: emacs-xyz: Fix indentation. 
* gnu/packages/emacs-xyz.scm: Delete trailing newline.
(emacs-purescript-mode): Delete trailing space.
 2021-07-09 15:08:04 +02:00
Leo Prikler 55d8eca5e9
gnu: emacs-telega-server: Update to 0.7.025. 
* gnu/packages/emacs-xyz.scm (emacs-telega-server): Update to 0.7.025.
 2021-07-09 15:08:04 +02:00
Zhu Zihao cd42e8001a
gnu: emacs-telega-contrib: Update to 0.7.024. 
* gnu/packages/emacs-xyz.scm(emacs-telega-contrib): Update to 0.7.024.
[arguments]<#:phases>: Back to root directory of build before phase
'install-license-files' to properly install licenses.
[propagated-inputs]: Add emacs-dashboard, emacs-transient.

Signed-off-by: Leo Prikler <leo.prikler@student.tugraz.at>
 2021-07-09 15:08:04 +02:00
Zhu Zihao a303be7c3b
gnu: emacs-telega: Update to 0.7.024. 
* gnu/packages/emacs-xyz.scm (emacs-telega): Update to 0.7.024.
[build-system] Use emacs-build-system.
[arguments] Add #:emacs.
Drop outdated phases.
Update ‘patch-sources’ phase to find new occurences of ffmpeg to patch.
Add new ‘configure’ and ‘install-share-files’ phases.

Signed-off-by: Leo Prikler <leo.prikler@student.tugraz.at>
 2021-07-09 15:08:04 +02:00
Zhu Zihao d0ccdd707d
gnu: Add emacs-telega-server. 
* gnu/packages/emacs-xyz.scm (emacs-telega-server): New variable.
* gnu/packages/patches/emacs-telega-path-placeholder.patch: New file.
* gnu/package/patches/emacs-telega-patch-server-functions.patch: Remove stale patch.
* gnu/local.mk (dist_patch_DATA): Update accordingly.

Signed-off-by: Leo Prikler <leo.prikler@student.tugraz.at>
 2021-07-09 15:08:04 +02:00
Mathieu Othacehe 37861f6c29
ci: Add bootstrap packages to the core subset. 
* gnu/ci.scm (%bootstrap-packages): New variable.
(cuirass-jobs): Add it to the core subset.
 2021-07-09 14:12:15 +02:00
Mathieu Othacehe 74168d99bb
system: Provide mg instead of zile. 
Since the update to the 2.6.2 release, the closure size of zile has
increased. Switch to mg which is lighter.

* gnu/system.scm (%base-packages-interactive): Replace zile by mg.
* doc/guix.texi (Proceeding with the Installation,
Using the Configuration System): Adapt those sections.
 2021-07-09 12:08:12 +02:00
Ludovic Courtès b182121458
gnu: python-arrow: Honor #:tests? in 'check' phase. 
* gnu/packages/time.scm (python-arrow)[arguments]: 'check' phase honors
 #:tests?.
 2021-07-09 11:58:52 +02:00