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2020-04-27file-systems: mount the PID cgroup filesystem.Jakub Kądziołka
* gnu/system/file-systems.scm (%control-groups): Add "pids". * gnu/services/docker.scm (docker-shepherd-service): Resolve a TODO. This has allowed me to make a specific configuration of nsjail work.
2020-04-27gnu: Add python-scikit-rebate.Roel Janssen
* gnu/packages/machine-learning.scm (python-scikit-rebate): New variable.
2020-04-27gnu: Add python-deeptools.Roel Janssen
* gnu/packages/bioinformatics.scm (python-deeptools): New variable.
2020-04-27gnu: Add python-deeptoolsintervals.Roel Janssen
* gnu/packages/bioinformatics.scm (python-deeptoolsintervals): New variable.
2020-04-27gnu: Add python-bitarray.Roel Janssen
* gnu/packages/python-xyz.scm (python-bitarray): New variable.
2020-04-27gnu: Add r-cummerbund.Roel Janssen
* gnu/packages/bioconductor.scm (r-cummerbund): New variable.
2020-04-27gnu: Add r-inum.Roel Janssen
* gnu/packages/cran.scm (r-inum): New variable.
2020-04-27gnu: Add r-ggpmisc.Roel Janssen
* gnu/packages/cran.scm (r-ggpmisc): New variable.
2020-04-27gnu: Add r-coverageview.Roel Janssen
* gnu/packages/bioconductor.scm (r-coverageview): New variable.
2020-04-27gnu: Add peek.Ricardo Wurmus
* gnu/packages/video.scm (peek): New variable.
2020-04-27gnu: emacs-org-reveal: Fix syntax error in description.Ricardo Wurmus
* gnu/packages/emacs-xyz.scm (emacs-org-reveal)[description]: Fix Texinfo syntax error.
2020-04-27gnu: Add texlive-inconsolata.Ricardo Wurmus
* gnu/packages/tex.scm (texlive-inconsolata): New variable.
2020-04-27gnu: Add r-bsgenome-hsapiens-ucsc-hg38.Roel Janssen
* gnu/packages/bioconductor.scm (r-bsgenome-hsapiens-ucsc-hg38): New variable.
2020-04-27gnu: Add r-karyoploter.Roel Janssen
* gnu/packages/bioconductor.scm (r-karyoploter): New variable.
2020-04-27gnu: Add r-bezier.Roel Janssen
* gnu/packages/cran.scm (r-bezier): New variable.
2020-04-27gnu: Add r-ideoviz.Roel Janssen
* gnu/packages/bioconductor.scm (r-ideoviz): New variable.
2020-04-27gnu: Add r-ecp.Roel Janssen
* gnu/packages/cran.scm (r-ecp): New variable.
2020-04-27gnu: Add r-reordercluster.Roel Janssen
* gnu/packages/cran.scm (r-reordercluster): New variable.
2020-04-27gnu: liblinphone: Move documentation and tester to separate outputs.Maxim Cournoyer
* gnu/packages/linphone.scm (liblinphone)[outputs]: Add a "doc" and "tester" outputs. [phases]: Add a separate-outputs phase. Move the glib-or-gtk-compile-schemas and glib-or-gtk-wrap phases after it.
2020-04-27gnu: liblinphone: Fix the input type of some dependencies.Maxim Cournoyer
Libraries being linked to such as libxml2, libiconv and zlib should appear as 'inputs' rather than 'native-inputs'. * gnu/packages/linphone.scm (liblinphone)[native-inputs]: Move libiconv, libxml2 and zlib to... [inputs]: ...here. Move eudev, python-pystache and python-six to native-inputs.
2020-04-27gnu: liblinphone: Remove hicolor-icon-theme and murrine inputs.Maxim Cournoyer
Icon themes and theme engines are best left for the users to select and install themselves. * gnu/packages/linphone.scm (liblinphone)[inputs]: Remove hicolor-icon-theme. [propagated-inputs]: Remove murrine.
2020-04-26gnu: Add loadable module to wireguard-linux-compat.Brice Waegeneire
* gnu/packages/vpn.scm (wireguard-linux-compat)[build-system]: Replace 'gnu-build-system' by 'linux-module-build-system'. [outputs]: Add 'kernel-patch'. [arguments]: Adjust the build system. Add phases 'change-directory' and 'reset-cwd'. Rename phases 'build' to 'build-patch' and 'install' to 'install-patch'. [description]: Mention the loadable module. Signed-off-by: Leo Famulari <leo@famulari.name>
2020-04-26channels: Use a declarative profile.Ludovic Courtès
* guix/channels.scm (package-cache-file): Use 'profile' instead of 'profile-derivation'.
2020-04-26services: system: Initial entries are non-monadic.Ludovic Courtès
* gnu/system.scm (operating-system-directory-base-entries): Return a regular, non-monadic value. * gnu/services.scm (system-derivation): Adjust accordingly. * gnu/system/linux-container.scm (container-essential-services): Likewise.
2020-04-26pack: Use a declarative profile.Ludovic Courtès
* guix/scripts/pack.scm (guix-pack): Use a declarative profile instead of 'profile-derivation'.
2020-04-26services: profile: Use a declarative profile.Ludovic Courtès
* gnu/services.scm (packages->profile-entry): Use 'profile' instead of 'profile-derivation'.
2020-04-26system: 'operating-system-directory-base-entries' uses 'profile'.Ludovic Courtès
* gnu/system.scm (operating-system-directory-base-entries): Use a declarative profile instead of 'profile-derivation'.
2020-04-26profiles: Add lowerable <profile> record type.Ludovic Courtès
* guix/profiles.scm (<profile>): New record type. * tests/profiles.scm ("<profile>"): New test.
2020-04-26gnu: r-snplocs-hsapiens-dbsnp144-grch37: Fix description.Roel Janssen
* gnu/packages/bioconductor.scm: Use two spaces after ending a sentence.
2020-04-26gnu: Add r-snplocs-hsapiens-dbsnp144-grch37.Roel Janssen
* gnu/packages/bioconductor.scm (r-snplocs-hsapiens-dbsnp144-grch37): New variable.
2020-04-26gnu: Add hackneyed-x11-cursors.Maxim Cournoyer
* gnu/packages/xorg.scm (hackneyed-x11-cursors): New variable.
2020-04-26gnu: Add r-motifbreakr.Roel Janssen
* gnu/packages/bioconductor.scm (r-motifbreakr): New variable.
2020-04-26gnu: Add r-motifdb.Roel Janssen
* gnu/packages/bioconductor.scm (r-motifdb): New variable.
2020-04-26gnu: Add r-pasilla.Roel Janssen
* gnu/packages/bioconductor.scm (r-pasilla): New variable.
2020-04-26gnu: guile3.0-chickadee: Rename to guile3.0-chickadee.Christopher Baines
This avoids having to packages, both called guile-chickadee. * gnu/packages/game-development.scm (guile3.0-chickadee)[name]: Change from guile-chickadee to guile3.0-chickadee.
2020-04-26reconfigure: Don't call build-derivations for upgrade-services testChristopher Baines
This commit adjusts the upgrade-services system test to not build anything when computing the derivation for the system test. I came across this when looking at issues computing the system test derivations to store in the Guix Data Service. * gnu/tests/reconfigure.scm (run-upgrade-services-test): Remove the use of, and definition for ensure-service-file.
2020-04-26substitute: Close port at the end of http-multiple-get.Christopher Baines
* guix/scripts/substitute.scm (http-multiple-get): Add close-port call.
2020-04-26substitute: Make http-multiple-get batch size configurable.Christopher Baines
* guix/scripts/substitute.scm (http-multiple-get): Add batch-size parameter.
2020-04-26substitute: Use the same port for multiple request batches.Christopher Baines
In http-multiple-get. * guix/scripts/substitute.scm (http-multiple-get): Switch port to p in one occurrence.
2020-04-26gnu: Add tarsplitter.Lars-Dominik Braun
* gnu/packages/compression.scm (tarsplitter): New variable. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2020-04-26gnu: Add rav1e.Leo Famulari
* gnu/packages/video.scm (rav1e): New variable. * gnu/packages/rust-apps.scm (rust-cbindgen-0.12, rust-cargo-c): New variables. * gnu/packages/crates-io.scm: Various new packages and upgrades. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2020-04-26gnu: python-scanpy: Update to 1.4.6.Efraim Flashner
* gnu/packages/bioinformatics.scm (python-scanpy): Update to 1.4.6. [arguments]: Add another network based test to skip. [propagated-inputs]: Add python-tqdm.
2020-04-26gnu: python-publicsuffix2: Adjust for Guile 3.0.Marius Bakke
* gnu/packages/python-web.scm (python-publicsuffix2): Provide explicit destination in calls to FORMAT.
2020-04-26gnu: nim: Adjust for Guile 3.0.Marius Bakke
* gnu/packages/nim.scm (nim)[arguments]: Provide explicit destination in calls to FORMAT.
2020-04-26gnu: tpacpi-bat: Adjust for Guile 3.0.Marius Bakke
* gnu/packages/linux.scm (tpacpi-bat)[arguments]: Provide explicit destination in calls to FORMAT.
2020-04-26gnu: nmoldyn: Adjust for Guile 3.0.Marius Bakke
* gnu/packages/chemistry.scm (nmoldyn)[arguments]: Provide explicit destination in calls to FORMAT.
2020-04-26gnu: calcurse: Adjust for Guile 3.0.Marius Bakke
* gnu/packages/calcurse.scm (calcurse)[arguments]: Provide explicit destination in calls to FORMAT.
2020-04-26gnu: thinkfan: Adjust for Guile 3.0.Marius Bakke
* gnu/packages/linux.scm (thinkfan)[arguments]: Provide explicit destination in calls to FORMAT (destination is no longer optional with Guile 3).
2020-04-26gnu: Add sylpheed.Eric Brown
* gnu/packages/mail.scm (sylpheed): New variable. Signed-off-by: Mathieu Othacehe <m.othacehe@gmail.com>
2020-04-26gnu: Add xarchiver.Raghav Gururajan
* gnu/packages/compression (xarchiver): New variable. Signed-off-by: Mathieu Othacehe <m.othacehe@gmail.com>
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