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2021-07-10gnu: r-googledrive: Update to 2.0.0.Ricardo Wurmus
* gnu/packages/cran.scm (r-googledrive): Update to 2.0.0. [propagated-inputs]: Remove r-curl; add r-cli, r-lifecycle, r-pillar, r-vctrs, and r-withr.
2021-07-10gnu: r-gviz: Update to 1.36.2.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-gviz): Update to 1.36.2.
2021-07-10gnu: r-catalyst: Update to 1.16.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-catalyst): Update to 1.16.1.
2021-07-10gnu: r-rhdf5lib: Update to 1.14.2.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-rhdf5lib): Update to 1.14.2.
2021-07-10gnu: r-bioconcotk: Update to 1.12.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-bioconcotk): Update to 1.12.1.
2021-07-10gnu: r-biocstyle: Update to 2.20.2.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-biocstyle): Update to 2.20.2.
2021-07-10gnu: r-mixomics: Update to 6.16.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-mixomics): Update to 6.16.1.
2021-07-10gnu: r-rsubread: Update to 2.6.3.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-rsubread): Update to 2.6.3.
2021-07-10gnu: r-annaffy: Update to 1.64.2.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-annaffy): Update to 1.64.2.
2021-07-10gnu: r-clusterprofiler: Update to 4.0.2.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-clusterprofiler): Update to 4.0.2.
2021-07-10gnu: r-enrichplot: Update to 1.12.2.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-enrichplot): Update to 1.12.2.
2021-07-10gnu: r-dose: Update to 3.18.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-dose): Update to 3.18.1.
2021-07-10gnu: r-diffbind: Update to 3.2.4.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-diffbind): Update to 3.2.4.
2021-07-10gnu: r-systempiper: Update to 1.26.3.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-systempiper): Update to 1.26.3. [propagated-inputs]: Add r-crayon and r-s4vectors.
2021-07-10gnu: r-mzr: Update to 2.26.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-mzr): Update to 2.26.1.
2021-07-10gnu: r-limma: Update to 3.48.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-limma): Update to 3.48.1.
2021-07-10gnu: r-genomeinfodb: Update to 1.28.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-genomeinfodb): Update to 1.28.1.
2021-07-10gnu: r-ensembldb: Update to 2.16.2.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-ensembldb): Update to 2.16.2.
2021-07-10gnu: r-edaseq: Update to 2.26.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-edaseq): Update to 2.26.1.
2021-07-10gnu: r-biocparallel: Update to 1.26.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-biocparallel): Update to 1.26.1.
2021-07-10gnu: r-biomart: Update to 2.48.2.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-biomart): Update to 2.48.2.
2021-07-10gnu: r-annotationhub: Update to 3.0.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-annotationhub): Update to 3.0.1.
2021-07-10gnu: Add r-ggpp.Ricardo Wurmus
* gnu/packages/cran.scm (r-ggpp): New variable.
2021-07-10gnu: Add r-s2.Ricardo Wurmus
* gnu/packages/cran.scm (r-s2): New variable.
2021-07-10gnu: Add r-wk.Ricardo Wurmus
* gnu/packages/cran.scm (r-wk): New variable.
2021-07-10gnu: Add r-reldist.Ricardo Wurmus
* gnu/packages/cran.scm (r-reldist): New variable.
2021-07-10gnu: r-gtools: Update to 3.9.2.Ricardo Wurmus
* gnu/packages/statistics.scm (r-gtools): Update to 3.9.2. [arguments]: Remove.
2021-07-10gnu: r-vdiffr: Update to 1.0.2.Ricardo Wurmus
* 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.
2021-07-10gnu: r-rintrojs: Update to 0.3.0.Ricardo Wurmus
* 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.
2021-07-10gnu: qpdfview: Use qt-build-system.Timotej Lazar
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>
2021-07-10gnu: sbcl-generic-cl: Update to 0.9.Pierre Neidhardt
* gnu/packages/lisp-xyz.scm (sbcl-generic-cl): Update to 0.9.
2021-07-10gnu: Add cl-form-types.Pierre Neidhardt
* gnu/packages/lisp-xyz.scm (cl-form-types, ecl-cl-form-types, sbcl-cl-form-types): New variables.
2021-07-10gnu: Add ocaml-bibtex2html.Ivan Gankevich
* gnu/packages/ocaml.scm (ocaml-bibtex2html): New variable. Signed-off-by: Julien Lepiller <julien@lepiller.eu>
2021-07-10gnu: Add texlive-preprint.Julien Lepiller
* gnu/packages/tex.scm (texlive-preprint): New variable.
2021-07-10gnu: hevea: Update to 2.35.Ivan Gankevich
* gnu/packages/ocaml.scm (hevea): Update to 2.35. Signed-off-by: Julien Lepiller <julien@lepiller.eu>
2021-07-10gnu: sbcl-cl-gserver: Update to 1.8.0.Pierre Neidhardt
* gnu/packages/lisp-xyz.scm (sbcl-cl-gserver): Update to 1.8.0.
2021-07-10gnu: Add netdiscover.Justin Veilleux
* gnu/packages/networking.scm (netdiscover): New variable. Signed-off-by: Arun Isaac <arunisaac@systemreboot.net>
2021-07-10services: qemu-binfmt: Preserve argv[0] by default.Ludovic Courtès
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".
2021-07-09gnu: go-github-com-golang-snappy: Update to 0.0.4.Arun Isaac
* gnu/packages/syncthing.scm (go-github-com-golang-snappy): Update to 0.0.4.
2021-07-09gnu: emacs-dash: Update to 2.19.0.Andrew Tropin
* gnu/packages/emacs-xyz.scm (emacs-dash): Update to 2.19.0. Signed-off-by: Leo Prikler <leo.prikler@student.tugraz.at>
2021-07-09gnu: emacs-telega: Fix 'patch-source' phase.Zhu Zihao
* 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>
2021-07-09self: Remove stale comment about "mmap(PROT_NONE) failed" crash.Ludovic Courtès
This crash was fixed by 0aef94e7bcbd272720f14c5343f74da5201ef90a, itself a followup to 47d48f0c43c13c0b43bc3e37b6239efd4bf2f74c. * guix/self.scm (translate-texi-manuals)[build]: Remove reference to the PROT_NONE bug.
2021-07-09Revert "self: Build translated manuals with a single process."Ludovic Courtès
This reverts commit af2d6ec092c98ac5f32d8e9e182a141e1268805b, which the parent commit makes unnecessary.
2021-07-09doc: Build manual translations with 'guile-3.0-latest'.Ludovic Courtès
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'.
2021-07-09gnu: emacs-xyz: Fix indentation.Leo Prikler
* gnu/packages/emacs-xyz.scm: Delete trailing newline. (emacs-purescript-mode): Delete trailing space.
2021-07-09gnu: emacs-telega-server: Update to 0.7.025.Leo Prikler
* gnu/packages/emacs-xyz.scm (emacs-telega-server): Update to 0.7.025.
2021-07-09gnu: emacs-telega-contrib: Update to 0.7.024.Zhu Zihao
* 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>
2021-07-09gnu: emacs-telega: Update to 0.7.024.Zhu Zihao
* 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>
2021-07-09gnu: Add emacs-telega-server.Zhu Zihao
* 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>
2021-07-09ci: Add bootstrap packages to the core subset.Mathieu Othacehe
* gnu/ci.scm (%bootstrap-packages): New variable. (cuirass-jobs): Add it to the core subset.
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