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* Merge branch 'master' into stagingMarius Bakke2020-03-02
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| * gnu: Add system test for CUPS.Marius Bakke2020-03-02
| | | | | | | | | | * gnu/tests/cups.scm: New file. * gnu/local.mk (GNU_SYSTEM_MODULES): Adjust accordingly.
| * gnu: libgc: Fix replacement inheritance.Marius Bakke2020-03-02
| | | | | | | | | | | | * gnu/packages/bdw-gc.scm (libgc-8.0): Do not use PACKAGE/INHERIT, because it does not make sense to inherit any replacements of LIBGC. (libgc/back-pointers): Use PACKAGE/INHERIT.
| * gnu: Add r-zseq.Ricardo Wurmus2020-03-02
| | | | | | | | * gnu/packages/cran.scm (r-zseq): New variable.
| * gnu: Add r-ztype.Ricardo Wurmus2020-03-02
| | | | | | | | * gnu/packages/cran.scm (r-ztype): New variable.
| * gnu: Add r-zvcv.Ricardo Wurmus2020-03-02
| | | | | | | | * gnu/packages/cran.scm (r-zvcv): New variable.
| * gnu: Add r-zyp.Ricardo Wurmus2020-03-02
| | | | | | | | * gnu/packages/cran.scm (r-zyp): New variable.
| * gnu: Add r-kendall.Ricardo Wurmus2020-03-02
| | | | | | | | * gnu/packages/cran.scm (r-kendall): New variable.
| * gnu: python-smmap: Update to version 3.0.1, deprecate python-smmap2.Maxim Cournoyer2020-03-02
| | | | | | | | | | | | | | | | | | * gnu/packages/python-xyz.scm (python-smmap): Rename from python-smmap2, and update to version 3.0.1. (python-smmap2, python2-smmap2): Preserve original bindings, marked as deprecated. * gnu/packages/version-control.scm (python-gitdb)[propagated-inputs]: Depend on the new python-smmap package.
| * gnu: python-gitpython: Update to 3.1.0.Maxim Cournoyer2020-03-02
| | | | | | | | * gnu/packages/version-control.scm (python-gitpython): Update to 3.1.0.
| * gnu: python-gitdb: Update to 4.0.2.Maxim Cournoyer2020-03-02
| | | | | | | | | | | | | | * gnu/packages/version-control.scm (python-gitdb): Update to 4.0.2. [source]: Correct the PyPI URL to refer to the actual gitdb package, not a mirror. This mirror had a problematic setup.py install requirement that required gitdb>=4.0.1, which would cause run time errors when using snakemake.
| * gnu: python-pyyaml: Update to 5.3.Maxim Cournoyer2020-03-02
| | | | | | | | * gnu/packages/python-xyz.scm (python-pyyaml): Update to 5.3.
| * gnu: python-xenon: Update to 0.7.0.Maxim Cournoyer2020-03-02
| | | | | | | | | | * gnu/packages/python-xyz.scm (python-xenon): Update to 0.7.0. [arguments]: Set #:tests? to #f to disable test suite.
| * gnu: python-radon: Update to 4.1.0.Maxim Cournoyer2020-03-02
| | | | | | | | * gnu/packages/python-xyz.scm (python-radon): Update to 4.1.0.
| * gnu: python-colorama: Update to 0.4.3.Maxim Cournoyer2020-03-02
| | | | | | | | * gnu/packages/python-xyz.scm (python-colorama): Update to 0.4.3.
| * gnu: Add python-wget.Maxim Cournoyer2020-03-02
| | | | | | | | * gnu/packages/python-xyz.scm (python-wget): New variable.
| * gnu: emacs-windower: Fix description.Nicolas Goaziou2020-03-02
| | | | | | | | | | * gnu/packages/emacs-xyz.scm (emacs-windower): Fix Texinfo code for lists in description.
| * gnu: r-forcats: Update to 0.5.0.Ricardo Wurmus2020-03-02
| | | | | | | | * gnu/packages/statistics.scm (r-forcats): Update to 0.5.0.
| * gnu: r-testthat: Update to 2.3.2.Ricardo Wurmus2020-03-02
| | | | | | | | * gnu/packages/statistics.scm (r-testthat): Update to 2.3.2.
| * gnu: r-openmx: Update to 2.17.3.Ricardo Wurmus2020-03-02
| | | | | | | | * gnu/packages/cran.scm (r-openmx): Update to 2.17.3.
| * gnu: r-summarytools: Update to 0.9.6.Ricardo Wurmus2020-03-02
| | | | | | | | * gnu/packages/cran.scm (r-summarytools): Update to 0.9.6.
| * gnu: r-officer: Update to 0.3.7.Ricardo Wurmus2020-03-02
| | | | | | | | | | * gnu/packages/cran.scm (r-officer): Update to 0.3.7. [propagated-inputs]: Remove r-base64enc, r-htmltools, r-rcpp, and r-rlang.
| * gnu: r-seqminer: Update to 8.0.Ricardo Wurmus2020-03-02
| | | | | | | | * gnu/packages/bioinformatics.scm (r-seqminer): Update to 8.0.
| * gnu: ecl-clunit: Use HTTPS home page.Tobias Geerinckx-Rice2020-03-02
| | | | | | | | * gnu/packages/lisp-xyz.scm (ecl-clunit)[home-page]: Use HTTPS.
| * gnu: mapnik: Use HTTPS home page.Tobias Geerinckx-Rice2020-03-02
| | | | | | | | * gnu/packages/geo.scm (mapnik)[home-page]: Use HTTPS.
| * gnu: python-rq: Use HTTPS home page.Tobias Geerinckx-Rice2020-03-02
| | | | | | | | * gnu/packages/databases.scm (python-rq)[home-page]: Use HTTPS.
| * gnu: java-plexus-interpolation: Use HTTPS home page.Tobias Geerinckx-Rice2020-03-02
| | | | | | | | * gnu/packages/java.scm (java-plexus-interpolation)[home-page]: Use HTTPS.
| * gnu: amsynth: Use HTTPS home page.Tobias Geerinckx-Rice2020-03-02
| | | | | | | | * gnu/packages/music.scm (amsynth)[home-page]: Use HTTPS.
| * gnu: pootle: Use HTTPS home page.Tobias Geerinckx-Rice2020-03-02
| | | | | | | | * gnu/packages/django.scm (pootle)[home-page]: Use HTTPS.
| * gnu: muse-sequencer: Update home page.Tobias Geerinckx-Rice2020-03-02
| | | | | | | | | | * gnu/packages/music.scm (muse-sequencer)[home-page]: Follow (HTTPS) redirection.
| * gnu: opensmtpd: Support ECDSA certificates.Tobias Geerinckx-Rice2020-03-02
| | | | | | | | | | | | | | The required libressl version is now stable and more featureful than openssl. * gnu/packages/mail.scm (opensmtpd)[inputs]: Replace openssl with libressl.
| * gnu: libressl: Update to 3.0.2.Tobias Geerinckx-Rice2020-03-02
| | | | | | | | * gnu/packages/tls.scm (libressl): Update to 3.0.2.
| * gnu: r-txdb-mmusculus-ucsc-mm10-knowngene: Update to 3.10.0.Tobias Geerinckx-Rice2020-03-02
| | | | | | | | * gnu/packages/bioconductor.scm (r-txdb-mmusculus-ucsc-mm10-knowngene): Update to 3.10.0.
| * gnu: emacs-modus-themes: Update to 0.6.0.Nicolas Goaziou2020-03-02
| | | | | | | | * gnu/packages/emacs-xyz.scm (emacs-modus-themes): Update to 0.6.0.
| * gnu: Syncthing: Fix installation of the 'util' package output.Leo Famulari2020-03-02
| | | | | | | | * gnu/packages/syncthing.scm (syncthing)[arguments]: Adjust the 'install' phase.
| * gnu: librsvg-next: Fix cargo dependency.Efraim Flashner2020-03-02
| | | | | | | | | | * gnu/packages/gnome.scm (librsvg-next-source): Don't hardcode patch version of cargo inputs.
| * gnu: rust-diff-0.1: Update to 0.1.12.Efraim Flashner2020-03-02
| | | | | | | | | | | | * gnu/packages/crates-io.scm (rust-diff-0.1): Update to 0.1.12. [arguments]: Replace rust-quickcheck-0.8 with 0.9 in cargo-development-inputs.
| * gnu: rust-defmac-0.2: Don't skip build.Efraim Flashner2020-03-02
| | | | | | | | | | * gnu/packages/crates-io.scm (rust-defmac-0.2)[arguments]: Don't skip build.
| * gnu: rust-datetime-0.4: Don't skip build.Efraim Flashner2020-03-02
| | | | | | | | | | * gnu/packages/crates-io.scm (rust-datetime-0.4)[arguments]: Don't skip build. Add rust-regex-0.1 to cargo-development-inputs.
| * gnu: rust-constant-time-eq-0.1: Don't skip build.Efraim Flashner2020-03-02
| | | | | | | | | | * gnu/packages/crates-io.scm (rust-constant-time-eq-0.1)[arguments]: Don't skip build.
| * gnu: debootstrap: Update to 1.0.119.Vincent Legoll2020-03-02
| | | | | | | | | | | | * gnu/packages/debian.scm (debootstrap): Update to 1.0.119. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
| * gnu: vim: Update to 8.2.0343.Efraim Flashner2020-03-02
| | | | | | | | * gnu/packages/vim.scm (vim): Update to 8.2.0343.
| * gnu: r-multiassayexperiment: Update to 1.12.3.Ricardo Wurmus2020-03-01
| | | | | | | | * gnu/packages/bioconductor.scm (r-multiassayexperiment): Update to 1.12.3.
| * gnu: r-cicero: Update to 1.4.2.Ricardo Wurmus2020-03-01
| | | | | | | | * gnu/packages/bioconductor.scm (r-cicero): Update to 1.4.2.
| * gnu: r-mlinterfaces: Update to 1.66.4.Ricardo Wurmus2020-03-01
| | | | | | | | * gnu/packages/bioconductor.scm (r-mlinterfaces): Update to 1.66.4.
| * gnu: r-biocneighbors: Update to 1.4.2.Ricardo Wurmus2020-03-01
| | | | | | | | * gnu/packages/bioconductor.scm (r-biocneighbors): Update to 1.4.2.
| * gnu: r-chippeakanno: Update to 3.20.1.Ricardo Wurmus2020-03-01
| | | | | | | | * gnu/packages/bioconductor.scm (r-chippeakanno): Update to 3.20.1.
| * gnu: r-hdf5array: Update to 1.14.3.Ricardo Wurmus2020-03-01
| | | | | | | | * gnu/packages/bioinformatics.scm (r-hdf5array): Update to 1.14.3.
| * gnu: r-rsamtools: Update to 2.2.3.Ricardo Wurmus2020-03-01
| | | | | | | | * gnu/packages/bioinformatics.scm (r-rsamtools): Update to 2.2.3.
| * gnu: r-edger: Update to 3.28.1.Ricardo Wurmus2020-03-01
| | | | | | | | * gnu/packages/bioinformatics.scm (r-edger): Update to 3.28.1.
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