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2020-06-13Merge branch 'staging'Marius Bakke
2020-06-13gnu: Add r-pcatools.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-pcatools): New variable.
2020-06-13gnu: libnode: Delete unused phase.Ricardo Wurmus
This is a follow-up to commit bb310a1976198eacdc67e0712e19735cd656b21d. * gnu/packages/node.scm (libnode)[arguments]: Delete phase "patch-npm-shebang".
2020-06-13gnu: Add meshlab.Ekaitz Zarraga
* gnu/packages/engineering.scm (meshlab): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2020-06-13gnu: perf: Set 'CC'.Ludovic Courtès
* gnu/packages/linux.scm (perf)[arguments]: Add "CC=gcc" to #:make-flags. This fixes a (harmless?) error message during the 'configure' phase.
2020-06-13gnu: perf: Restore use of dependencies.Ludovic Courtès
* gnu/packages/linux.scm (perf)[arguments]: Remove C_INCLUDE_PATH from #:make-flags. It is no longer needed since the switch to C_INCLUDE_PATH in 2073b55e6b964cb8ca15e8c74cb32dac00f05f0d and would prevent dependencies from being found.
2020-06-13gnu: guile-sqlite3: Update to 0.1.2.Danny Milosavljevic
* gnu/packages/guile.scm (guile-sqlite3): Update to 0.1.2.
2020-06-13Revert "gnu: node: Build shared library."Ricardo Wurmus
This reverts commit f9311eaa7cb7849e9b17162c93b874c74d8fcbbd. Adding "--shared" replaces the executable with the shared library, breaking all users of the nodejs executable.
2020-06-13gnu: r-v8: Use libnode instead of node.Ricardo Wurmus
* gnu/packages/cran.scm (r-v8)[inputs]: Replace node with libnode.
2020-06-13gnu: Add libnode.Ricardo Wurmus
* gnu/packages/node.scm (libnode): New variable.
2020-06-13image: Remove 'maybe-with-target'.Mathieu Othacehe
* gnu/system/image.scm (maybe-with-target): Remove, (system-image): adapt accordingly.
2020-06-13install: final: Add some logging.Mathieu Othacehe
* gnu/installer/final.scm (umount-cow-store): Add some logging.
2020-06-13image: Add 'target' support.Mathieu Othacehe
* gnu/image.scm (<image>)[target]: New field, (image-target): new public method. * gnu/system/image.scm (hurd-disk-image): Set "i586-pc-gnu" as image 'target' field, (maybe-with-target): new procedure, (system-image): honor image 'target' field using the above procedure.
2020-06-13image: Make 'find-image' non-monadic.Jan (janneke) Nieuwenhuizen
* gnu/system/image.scm (find-image): Make non-monadic. Add 'target' parameter. * gnu/tests/install.scm (run-install): Update caller, passing (%current-target-system). * guix/scripts/system.scm (perform-action): Likewise.
2020-06-13gnome: gnome-desktop: Add bubblewrap as an input.Christopher Baines
This is expected to be available, oddly as libseccomp is available. These changes fix thumbnails for Nautilus. * gnu/packages/gnome.scm (gnome-desktop)[arguments]: Add 'patch-bubblewrap phase. [inputs]: Add bubblewrap.
2020-06-13gnu: emacs-debbugs: Update to 0.23.Michael Rohleder
* gnu/packages/emacs-xyz.scm (emacs-debbugs): Update to 0.23. Signed-off-by: 宋文武 <iyzsong@member.fsf.org>
2020-06-13services: hurd: Remove deprecated 'hurd-getty-service' wrapper.Jan (janneke) Nieuwenhuizen
* gnu/services/hurd.scm (hurd-getty-service): Remove.
2020-06-13system: hurd: Remove 'cross-hurd-image' hack.Jan (janneke) Nieuwenhuizen
The initial guix build -f gnu/system/hurd.scm hack has been superseded by regular guix system (cross) build. * gnu/system/hurd.scm (compile-manifest, cross-hurd-image): Remove.
2020-06-13system: bare-hurd.tmpl: Add openssh-sans-x client and service.Jan (janneke) Nieuwenhuizen
* gnu/system/examples/bare-hurd.tmpl (%hurd-os)[packages]: Add openssh-sans-x. [services]: Add openssh-service. Add example usage.
2020-06-13gnu: r-mzr: Update to 2.22.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-mzr): Update to 2.22.0. [native-inputs]: Add r-knitr.
2020-06-13gnu: r-biodist: Update to 1.60.0.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-biodist): Update to 1.60.0.
2020-06-13gnu: r-biocworkflowtools: Update to 1.14.0.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-biocworkflowtools): Update to 1.14.0.
2020-06-13gnu: r-biocset: Update to 1.2.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-biocset): Update to 1.2.1. [native-inputs]: Add r-knitr.
2020-06-13gnu: r-biocpkgtools: Update to 1.6.0.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-biocpkgtools): Update to 1.6.0.
2020-06-13gnu: r-biocor: Update to 1.12.0.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-biocor): Update to 1.12.0. [native-inputs]: Add r-knitr.
2020-06-13gnu: r-bioconcotk: Update to 1.8.0.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-bioconcotk): Update to 1.8.0. [native-inputs]: Add r-knitr.
2020-06-13gnu: r-multiassayexperiment: Update to 1.14.0.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-multiassayexperiment): Update to 1.14.0.
2020-06-13gnu: r-experimenthub: Update to 1.14.0.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-experimenthub): Update to 1.14.0. [native-inputs]: Add r-knitr.
2020-06-13gnu: r-biocgraph: Update to 1.50.0.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-biocgraph): Update to 1.50.0.
2020-06-13gnu: r-bioccasestudies: Update to 1.50.0.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-bioccasestudies): Update to 1.50.0.
2020-06-13gnu: r-ebarrays: Update to 2.52.0.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-ebarrays): Update to 2.52.0.
2020-06-13gnu: r-reactomepa: Update to 1.32.0.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-reactomepa): Update to 1.32.0. [native-inputs]: Add r-knitr.
2020-06-13gnu: r-graphite: Update to 1.34.0.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-graphite): Update to 1.34.0.
2020-06-13gnu: r-biobroom: Update to 1.20.0.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-biobroom): Update to 1.20.0. [native-inputs]: Add r-knitr.
2020-06-13gnu: r-bioassayr: Update to 1.26.0.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-bioassayr): Update to 1.26.0.
2020-06-13gnu: r-chemminer: Update to 3.40.0.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-chemminer): Update to 3.40.0. [native-inputs]: Add r-knitr.
2020-06-13gnu: r-bigpint: Update to 1.4.0.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-bigpint): Update to 1.4.0. [propagated-inputs]: Add r-delayedarray and r-summarizedexperiment.
2020-06-13gnu: r-bigmemoryextras: Update to 1.36.0.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-bigmemoryextras): Update to 1.36.0. [native-inputs]: Add r-knitr.
2020-06-13gnu: r-biggr: Update to 1.24.0.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-biggr): Update to 1.24.0.
2020-06-13gnu: r-hyperdraw: Update to 1.40.0.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-hyperdraw): Update to 1.40.0.
2020-06-13gnu: r-hypergraph: Update to 1.60.0.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-hypergraph): Update to 1.60.0.
2020-06-13gnu: r-rsbml: Update to 2.46.0.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-rsbml): Update to 2.46.0.
2020-06-13gnu: r-bifet: Update to 1.8.0.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-bifet): Update to 1.8.0. [native-inputs]: Add r-knitr.
2020-06-13gnu: r-bicare: Update to 1.46.0.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-bicare): Update to 1.46.0.
2020-06-13gnu: r-bhc: Update to 1.40.0.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-bhc): Update to 1.40.0.
2020-06-13gnu: r-bgx: Update to 1.54.0.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-bgx): Update to 1.54.0.
2020-06-13gnu: r-bgmix: Update to 1.48.0.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-bgmix): Update to 1.48.0.
2020-06-13gnu: r-unifiedwmwqpcr: Update to 1.24.0.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-unifiedwmwqpcr): Update to 1.24.0.
2020-06-13gnu: r-htqpcr: Update to 1.42.0.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-htqpcr): Update to 1.42.0.
2020-06-13gnu: r-variancepartition: Update to 1.18.0.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-variancepartition): Update to 1.18.0. [native-inputs]: Add r-knitr.
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