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2019-03-14gnu: fish: Update to 3.0.2.Meiyo Peng
* gnu/packages/shells.scm (fish): Update to 3.0.2. Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2019-03-14gnu: Add r-rematch2.Nicolò Balzarotti
* gnu/packages/cran.scm (r-rematch2): New variable. Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2019-03-13gnu: w3m: Update to 0.5.3+git20190105.Leo Famulari
* gnu/packages/w3m.scm (w3m): Update to 0.5.3+git20190105.
2019-03-13linux-container: 'containerized-operating-system' removes "useless" services.Ludovic Courtès
Fixes <https://bugs.gnu.org/34211>. Reported by Efraim Flashner <efraim@flashner.co.il>. * gnu/system/linux-container.scm (containerized-operating-system) [useless-services]: New variable. Add 'services' field.
2019-03-13doc: Document the graphical installer some more.Ludovic Courtès
* doc/guix.texi (Preparing for Installation): Rewrite to specify the two installation modes. (Guided Graphical Installation): New node. (Manual Installation): New node, with the former sections. (After System Installation): New node. * doc/images/installer-network.png, doc/images/installer-partitions.png, doc/images/installer-resume.png: New files. * doc/local.mk (dist_infoimage_DATA): Add them.
2019-03-13installer: network: Adjust wording.Ludovic Courtès
* gnu/installer/newt/network.scm (wait-service-online): Adjust wording of the messages.
2019-03-13linux-modules: Factorize 'missing-modules'.Ludovic Courtès
* gnu/build/linux-modules.scm (missing-modules): New procedure. * gnu/system/mapped-devices.scm (check-device-initrd-modules): Use it.
2019-03-13Remove traces of "GuixSD".Ludovic Courtès
* gnu/bootloader/extlinux.scm (extlinux-configuration-file): Remove mentions of "GuixSD". * gnu/bootloader/grub.scm (install-grub-efi): Likewise. * gnu/build/vm.scm (make-iso9660-image): Change default #:volume-id to "Guix_image". (initialize-hard-disk): Search for the "Guix_image" label. * gnu/ci.scm (system-test-jobs, tarball-jobs): Remove "GuixSD". * gnu/installer/newt/welcome.scm (run-welcome-page): Likewise. * gnu/packages/audio.scm (supercollider)[description]: Likewise. * gnu/packages/curl.scm (curl): Likewise. * gnu/packages/emacs.scm (emacs): Likewise. * gnu/packages/gnome.scm (network-manager): Likewise. * gnu/packages/julia.scm (julia): Likewise. * gnu/packages/linux.scm (alsa-plugins): Likewise. (powertop, wireless-regdb): Likewise. * gnu/packages/package-management.scm (guix): Likewise. * gnu/packages/polkit.scm (polkit): Likewise. * gnu/packages/tex.scm (texlive-bin): Likewise. * gnu/services/base.scm (file-systems->fstab): Likewise. * gnu/services/cups.scm (%cups-activation): Likewise. * gnu/services/mail.scm (%dovecot-activation): Likewise. * gnu/services/messaging.scm (prosody-configuration)[log]: Likewise. * gnu/system/examples/vm-image.tmpl (vm-image-motd): Likewise. * gnu/system/install.scm (installation-os)[file-systems]: Change root file system label to "Guix_image". * gnu/system/mapped-devices.scm (check-device-initrd-modules): Remove "GuixSD". * gnu/system/vm.scm (system-docker-image): Likewise. (system-disk-image)[root-label]: Change to "Guix_image". * gnu/tests/install.scm (run-install): Remove "GuixSD". * guix/modules.scm (guix-module-name?): Likewise. * nix/libstore/optimise-store.cc: Likewise.
2019-03-13maint: Change Guix System file names from guixsd-*.Ludovic Courtès
* Makefile.am (GUIXSD_SUPPORTED_SYSTEMS): Rename to... (GUIX_SYSTEM_SUPPORTED_SYSTEMS): ... this. (GUIXSD_VM_SYSTEMS): Rename to... (GUIX_SYSTEM_VM_SYSTEMS): ... this. (GUIXSD_IMAGE_BASE): Rename to... (GUIX_SYSTEM_IMAGE_BASE): ... this. Change "guixsd-" to "guix-system-". (GUIXSD_VM_IMAGE_BASE): Rename to... (GUIX_SYSTEM_VM_IMAGE_BASE): ... this. Change "guixsd-" to "guix-system-". (release): Adjust accordingly. * doc/guix.texi (USB Stick and DVD Installation) (Installing Guix in a VM, Invoking guix system) (Running Guix in a VM): Adjust file names accordingly.
2019-03-13gnu: Add python-velocyto.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-velocyto): New variable.
2019-03-13gnu: python-loompy: Update to 2.0.17.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-loompy): Update to 2.0.17. [source]: Fetch via git. [arguments]: Enable tests, replace "check" phase. [propagated-inputs]: Add python-pandas. [native-inputs]: Add python-pytest.
2019-03-13gnu: Add emacs-dockerfile-mode.Oleg Pykhalov
* gnu/packages/emacs-xyz.scm (emacs-dockerfile-mode): New variable.
2019-03-13gnu: Add emacs-docker.Oleg Pykhalov
* gnu/packages/emacs-xyz.scm (emacs-docker): New variable.
2019-03-13gnu: Add emacs-docker-tramp.Oleg Pykhalov
* gnu/packages/emacs-xyz.scm (emacs-docker-tramp): New variable.
2019-03-13gnu: python-numba: Update to 0.42.0.Ricardo Wurmus
* gnu/packages/python-xyz.scm (python-numba): Update to 0.42.0.
2019-03-13gnu: python-llvmlite: Update to 0.27.1.Ricardo Wurmus
* gnu/packages/llvm.scm (python-llvmlite): Update to 0.27.1. [inputs]: Update patch for custom LLVM variant.
2019-03-13gnu: Add python-on-guile.Ricardo Wurmus
* gnu/packages/guile-xyz.scm (python-on-guile): New variable.
2019-03-13gnu: guile-persist: Install go files to canonical directory.Ricardo Wurmus
* gnu/packages/guile-xyz.scm (guile-persist)[arguments]: Patch target directory for go files in build phase "patch-prefix".
2019-03-13gnu: guile-stis-parser: Install go files to canonical directory.Ricardo Wurmus
* gnu/packages/guile-xyz.scm (guile-stis-parser)[arguments]: Add build phase "use-canonical-directory-for-go-files".
2019-03-13gnu: Add kaldi.Ricardo Wurmus
* gnu/packages/machine-learning.scm (kaldi): New variable.
2019-03-13gnu: Add r-valr.Ricardo Wurmus
* gnu/packages/cran.scm (r-valr): New variable.
2019-03-13gnu: Add r-linnorm.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-linnorm): New variable.
2019-03-13gnu: Add python2-argparse.Ricardo Wurmus
* gnu/packages/python-xyz.scm (python2-argparse): New variable.
2019-03-13gnu: Add r-apcluster.Ricardo Wurmus
* gnu/packages/cran.scm (r-apcluster): New variable.
2019-03-13gnu: Add r-gmodels.Ricardo Wurmus
* gnu/packages/cran.scm (r-gmodels): New variable.
2019-03-13gnu: Add tetoolkit.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (tetoolkit): New variable.
2019-03-13gnu: Add r-irkernel.Ricardo Wurmus
* gnu/packages/cran.scm (r-irkernel): New variable.
2019-03-13gnu: Add r-irdisplay.Ricardo Wurmus
* gnu/packages/cran.scm (r-irdisplay): New variable.
2019-03-13gnu: Add r-repr.Ricardo Wurmus
* gnu/packages/cran.scm (r-repr): New variable.
2019-03-13gnu: Add r-pbdzmq.Ricardo Wurmus
* gnu/packages/cran.scm (r-pbdzmq): New variable.
2019-03-13gnu: Add r-illuminahumanmethylationepicmanifest.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-illuminahumanmethylationepicmanifest): New variable.
2019-03-13gnu: Add r-lumi.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-lumi): New variable.
2019-03-13gnu: Add r-methylumi.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-methylumi): New variable.
2019-03-13gnu: Add r-fdb-infiniummethylation-hg19.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-fdb-infiniummethylation-hg19): New variable.
2019-03-13gnu: portaudio: Build position independent code and install more headers.Ricardo Wurmus
* gnu/packages/audio.scm (portaudio)[arguments]: Pass "--with-pic" and initialize libtool in new build phase "build-only-position-independent-code"; install extra header in new build phase "install-missing-headers".
2019-03-13gnu: Add r-minfi.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-minfi): New variable.
2019-03-13gnu: Add r-bumphunter.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-bumphunter): New variable.
2019-03-13gnu: Add r-siggenes.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-siggenes): New variable.
2019-03-13gnu: Add r-illuminaio.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-illuminaio): New variable.
2019-03-13gnu: Add r-geoquery.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-geoquery): New variable.
2019-03-13gnu: Add r-scone.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-scone): New variable.
2019-03-13gnu: Add r-scdd.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-scdd): New variable.
2019-03-13gnu: Add r-noiseq.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-noiseq): New variable.
2019-03-13gnu: Add r-monocle.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-monocle): New variable.
2019-03-13gnu: Add r-mast.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-mast): New variable.
2019-03-13gnu: Add r-icobra.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-icobra): New variable.
2019-03-13gnu: Add r-beanplot.Ricardo Wurmus
* gnu/packages/cran.scm (r-beanplot): New variable.
2019-03-13gnu: Add r-nor1mix.Ricardo Wurmus
* gnu/packages/cran.scm (r-nor1mix): New variable.
2019-03-13gnu: Add r-ggextra.Ricardo Wurmus
* gnu/packages/cran.scm (r-ggextra): New variable.
2019-03-13gnu: Add r-colourpicker.Ricardo Wurmus
* gnu/packages/cran.scm (r-colourpicker): New variable.
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