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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>
2021-07-09gnu: 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>
2021-07-09gnu: 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>
2021-07-09gnu: python-arrow: Honor #:tests? in 'check' phase.Ludovic Courtès
* gnu/packages/time.scm (python-arrow)[arguments]: 'check' phase honors #:tests?.
2021-07-09gnu: python-arrow: Update to 1.1.1.Kris Fremen
* gnu/packages/time.scm (python-arrow): Update to 1.1.1.
2021-07-09gnu: Add repo2docker.Hugo Lecomte
* gnu/packages/jupyter.scm (repo2docker): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2021-07-09gnu: Add python-pydata-sphinx-theme.Hugo Lecomte
* gnu/packages/sphinx.scm (python-pydata-sphinx-theme): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2021-07-09gnu: Add python-sphinxcontrib-autoprogram.Hugo Lecomte
* gnu/packages/sphinx.scm (python-sphinxcontrib-autoprogram): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2021-07-09gnu: Add python-jupyter-sphinx.Hugo Lecomte
* gnu/packages/sphinx.scm (python-jupyter-sphinx): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2021-07-09gnu: Add python-pytest-regressions.Hugo Lecomte
* gnu/packages/check.scm (python-pytest-regressions): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2021-07-09gnu: Add python-pytest-datadir.Hugo Lecomte
* gnu/packages/check.scm (python-pytest-datadir): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
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