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* machine: Implement safety checks.Jakob L. Kreuze2019-08-06
| | | | | | * gnu/machine/ssh.scm (machine-check-file-system-availability) (machine-check-initrd-modules, check-deployment-sanity): New variable. (deploy-managed-host): Perform safety checks before deploying.
* reconfigure: Fix GC root installation.Jakob L. Kreuze2019-08-06
| | | | | | | | | | Fixes <https://bugs.gnu.org/36942>. Reported by ison <ison@airmail.cc>. guix/scripts/system/reconfigure.scm (install-bootloader-program): Switch new symlink to the canonical bootloader configuration file. Signed-off-by: Danny Milosavljevic <dannym@scratchpost.org>
* machine: Rename 'system' field.Jakob L. Kreuze2019-08-06
| | | | | | | | * gnu/machine.scm (machine-system): Delete variable. (machine-operating-system): New variable. All callers changed. * doc/guix.texi (Invoking guix deploy): Use the 'machine-operating-system' accessor rather than 'machine-system'.
* doc: Add note about signing keys.Jakob L. Kreuze2019-08-06
| | | | | * doc/guix.texi (Invoking guix deploy): Add note explaining that deployment targets must authorize the coordinator machine's signing key.
* gnu: perl-hash-merge: Change inputs to propagated-inputs.Christopher Baines2019-08-06
| | | | | | | | Clone::Choose is required at runtime, so this input needs to be propagated. This change fixes the sqitch package. * gnu/packages/perl.scm (perl-hash-merge)[inputs]: Change to propagated-inputs.
* gnu: ffmpeg: Update to 4.2.Rutger Helling2019-08-06
| | | | | | * gnu/packages/video.scm (ffmpeg): Update to 4.2. [inputs]: Add dav1d. * gnu/packages/video.scm (ffmpeg-3.4)[arguments]: Adjust inheritance.
* gnu: r-rsubread: Update to 1.34.6.Ricardo Wurmus2019-08-06
| | | | * gnu/packages/bioconductor.scm (r-rsubread): Update to 1.34.6.
* gnu: r-abaenrichment: Update to 1.14.1.Ricardo Wurmus2019-08-06
| | | | * gnu/packages/bioconductor.scm (r-abaenrichment): Update to 1.14.1.
* gnu: r-atacseqqc: Update to 1.8.5.Ricardo Wurmus2019-08-06
| | | | * gnu/packages/bioconductor.scm (r-atacseqqc): Update to 1.8.5.
* gnu: r-genomicinteractions: Update to 1.18.1.Ricardo Wurmus2019-08-06
| | | | * gnu/packages/bioconductor.scm (r-genomicinteractions): Update to 1.18.1.
* gnu: r-chippeakanno: Update to 3.18.2.Ricardo Wurmus2019-08-06
| | | | * gnu/packages/bioconductor.scm (r-chippeakanno): Update to 3.18.2.
* gnu: r-msnid: Update to 1.18.1.Ricardo Wurmus2019-08-06
| | | | * gnu/packages/bioinformatics.scm (r-msnid): Update to 1.18.1.
* gnu: r-rcas: Update to 1.10.1.Ricardo Wurmus2019-08-06
| | | | * gnu/packages/bioinformatics.scm (r-rcas): Update to 1.10.1.
* gnu: r-genomicfeatures: Update to 1.36.4.Ricardo Wurmus2019-08-06
| | | | * gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.36.4.
* gnu: r-rtracklayer: Update to 1.44.2.Ricardo Wurmus2019-08-06
| | | | * gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.44.2.
* gnu: r-summarizedexperiment: Update to 1.14.1.Ricardo Wurmus2019-08-06
| | | | * gnu/packages/bioinformatics.scm (r-summarizedexperiment): Update to 1.14.1.
* gnu: r-biomart: Update to 2.40.3.Ricardo Wurmus2019-08-06
| | | | * gnu/packages/bioinformatics.scm (r-biomart): Update to 2.40.3.
* gnu: r-limma: Update to 3.40.6.Ricardo Wurmus2019-08-06
| | | | * gnu/packages/bioinformatics.scm (r-limma): Update to 3.40.6.
* gnu: r-edger: Update to 3.26.6.Ricardo Wurmus2019-08-06
| | | | * gnu/packages/bioinformatics.scm (r-edger): Update to 3.26.6.
* gnu: r-xgboost: Update to 0.90.0.2.Ricardo Wurmus2019-08-06
| | | | * gnu/packages/cran.scm (r-xgboost): Update to 0.90.0.2.
* gnu: r-citr: Update to 0.3.1.Ricardo Wurmus2019-08-06
| | | | | * gnu/packages/cran.scm (r-citr): Update to 0.3.1. [propagated-inputs]: Remove r-bibtex.
* gnu: r-enrichr: Update to 2.0.Ricardo Wurmus2019-08-06
| | | | * gnu/packages/cran.scm (r-enrichr): Update to 2.0.
* gnu: r-dalex: Update to 0.4.4.Ricardo Wurmus2019-08-06
| | | | * gnu/packages/cran.scm (r-dalex): Update to 0.4.4.
* gnu: r-bookdown: Update to 0.12.Ricardo Wurmus2019-08-06
| | | | * gnu/packages/cran.scm (r-bookdown): Update to 0.12.
* gnu: r-ldheatmap: Update to 0.99-7.Ricardo Wurmus2019-08-06
| | | | | * gnu/packages/cran.scm (r-ldheatmap): Update to 0.99-7. [propagated-inputs]: Add r-rcpp.
* gnu: r-sf: Update to 0.7-7.Ricardo Wurmus2019-08-06
| | | | * gnu/packages/cran.scm (r-sf): Update to 0.7-7.
* gnu: r-deldir: Update to 0.1-23.Ricardo Wurmus2019-08-06
| | | | * gnu/packages/cran.scm (r-deldir): Update to 0.1-23.
* gnu: r-classint: Update to 0.4-1.Ricardo Wurmus2019-08-06
| | | | * gnu/packages/cran.scm (r-classint): Update to 0.4-1.
* gnu: r-rematch2: Update to 2.1.0.Ricardo Wurmus2019-08-06
| | | | * gnu/packages/cran.scm (r-rematch2): Update to 2.1.0.
* gnu: r-irkernel: Update to 1.0.2.Ricardo Wurmus2019-08-06
| | | | * gnu/packages/cran.scm (r-irkernel): Update to 1.0.2.
* gnu: r-lavaan: Update to 0.6-4.Ricardo Wurmus2019-08-06
| | | | * gnu/packages/cran.scm (r-lavaan): Update to 0.6-4.
* gnu: r-bayesm: Update to 3.1-3.Ricardo Wurmus2019-08-06
| | | | * gnu/packages/cran.scm (r-bayesm): Update to 3.1-3.
* gnu: r-rsvd: Update to 1.0.2.Ricardo Wurmus2019-08-06
| | | | * gnu/packages/cran.scm (r-rsvd): Update to 1.0.2.
* gnu: r-future: Update to 1.14.0.Ricardo Wurmus2019-08-06
| | | | * gnu/packages/cran.scm (r-future): Update to 1.14.0.
* gnu: r-spatialextremes: Update to 2.0-7.2.Ricardo Wurmus2019-08-06
| | | | * gnu/packages/cran.scm (r-spatialextremes): Update to 2.0-7.2.
* gnu: r-bigrquery: Update to 1.2.0.Ricardo Wurmus2019-08-06
| | | | | * gnu/packages/cran.scm (r-bigrquery): Update to 1.2.0. [propagated-inputs]: Add r-gargle and r-rlang.
* gnu: Add r-gargle.Ricardo Wurmus2019-08-06
| | | | * gnu/packages/cran.scm (r-gargle): New variable.
* gnu: r-shades: Update to 1.4.0.Ricardo Wurmus2019-08-06
| | | | * gnu/packages/cran.scm (r-shades): Update to 1.4.0.
* gnu: r-rnifti: Update to 0.11.1.Ricardo Wurmus2019-08-06
| | | | * gnu/packages/cran.scm (r-rnifti): Update to 0.11.1.
* gnu: r-flare: Update to 1.6.0.2.Ricardo Wurmus2019-08-06
| | | | * gnu/packages/cran.scm (r-flare): Update to 1.6.0.2.
* gnu: r-sparsesvd: Update to 0.2.Ricardo Wurmus2019-08-06
| | | | * gnu/packages/cran.scm (r-sparsesvd): Update to 0.2.
* gnu: r-tidytree: Update to 0.2.5.Ricardo Wurmus2019-08-06
| | | | * gnu/packages/cran.scm (r-tidytree): Update to 0.2.5.
* gnu: r-rgl: Update to 0.100.26.Ricardo Wurmus2019-08-06
| | | | * gnu/packages/cran.scm (r-rgl): Update to 0.100.26.
* gnu: r-afex: Update to 0.24-1.Ricardo Wurmus2019-08-06
| | | | * gnu/packages/cran.scm (r-afex): Update to 0.24-1.
* gnu: r-usethis: Update to 1.5.1.Ricardo Wurmus2019-08-06
| | | | * gnu/packages/cran.scm (r-usethis): Update to 1.5.1.
* gnu: r-sjplot: Update to 2.7.0.Ricardo Wurmus2019-08-06
| | | | | * gnu/packages/cran.scm (r-sjplot): Update to 2.7.0. [propagated-inputs]: Add r-ggrepel.
* gnu: r-ggeffects: Update to 0.11.0.Ricardo Wurmus2019-08-06
| | | | * gnu/packages/cran.scm (r-ggeffects): Update to 0.11.0.
* gnu: r-performance: Update to 0.3.0.Ricardo Wurmus2019-08-06
| | | | * gnu/packages/cran.scm (r-performance): Update to 0.3.0.
* gnu: r-emmeans: Update to 1.4.Ricardo Wurmus2019-08-06
| | | | * gnu/packages/cran.scm (r-emmeans): Update to 1.4.
* gnu: r-magick: Update to 2.1.Ricardo Wurmus2019-08-06
| | | | * gnu/packages/cran.scm (r-magick): Update to 2.1.
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