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* gnu: i3lock-color: Don't use unstable tarball.Tobias Geerinckx-Rice2019-03-09
| | | | | * gnu/packages/wm.scm (i3lock-color)[source]: Use GIT-FETCH and GIT-FILE-NAME.
* gnu: i3lock-fancy: Don't use unstable tarball.Tobias Geerinckx-Rice2019-03-09
| | | | | * gnu/packages/wm.scm (i3lock-fancy)[source]: Use GIT-FETCH and GIT-FILE-NAME.
* upstream: Correctly report failure to update Git checkouts.Ludovic Courtès2019-03-08
| | | | | | | | | | | | Fixes <https://bugs.gnu.org/34778>. Reported by Gábor Boskovits <boskovits@gmail.com>. * guix/upstream.scm (package-update/url-fetch): New procedure, with code formerly in 'package-update'. (%method-updates): New variable. (package-update): Check the method to download PACKAGE's source, and look up a corresponding update method in %METHOD-UPDATES, and raise an error if none was found.
* activation: Shared system home directories are now 555 and root-owned.Ludovic Courtès2019-03-08
| | | | | | | | | | | | | | | | | | | | Fixes <https://bugs.gnu.org/34788>. Reported by Jack Hill <jackhill@jackhill.us>. Regression introduced by the combination of 8bb76f3d44c1f5ffec8011819494db306a51d801 and 0ae735bcc8ff7fdc89d67b492bdee9091ee19e86: /var/empty would be 700 and owned by one of the system accounts (thus inaccessible to others), and /var/run/dbus would be 700 as well, thereby preventing D-Bus clients from connecting to the daemon. * gnu/build/activation.scm (duplicates): New procedure. (activate-users+groups)[system-accounts]: New variable. Use it. Make shared system account home directories #o555 and root-owned. * gnu/services/dbus.scm (dbus-activation): Make /var/run/dbus #o755. * gnu/tests/base.scm (run-basic-test): Test the ownership and permissions of /var/empty.
* gnu: Add java-eclipse-jdt-compiler-apt.Ricardo Wurmus2019-03-08
| | | | * gnu/packages/java.scm (java-eclipse-jdt-compiler-apt): New variable.
* gnu: Add epl2.0.Ricardo Wurmus2019-03-08
| | | | * guix/licenses.scm (epl2.0): New variable.
* gnu: blast+: Update to 2.7.1.Ricardo Wurmus2019-03-08
| | | | | | | | * gnu/packages/bioinformatics.scm (blast+): Update to 2.7.1. [inputs]: Add lmdb. [source]: Remove obsolete patch. * gnu/package/patches/blast+-fix-makefile.patch: Remove patch. * gnu/local.mk (dist_patch_DATA): Remove it.
* gnu: Add texlive-latex-pdfx.Ricardo Wurmus2019-03-08
| | | | * gnu/packages/tex.scm (texlive-latex-pdfx): New variable.
* gnu: Add texlive-latex-xmpincl.Ricardo Wurmus2019-03-08
| | | | * gnu/packages/tex.scm (texlive-latex-xmpincl): New variable.
* gnu: Add translate2geda.Ricardo Wurmus2019-03-08
| | | | * gnu/packages/engineering.scm (translate2geda): New variable.
* gnu: Add rkrlv2.Ricardo Wurmus2019-03-08
| | | | * gnu/packages/music.scm (rkrlv2): New variable.
* gnu: fc-host-tools: Update to 10.Danny Milosavljevic2019-03-08
| | | | | * gnu/packages/embedded.scm (fc-host-tools): Update to 10. [arguments]<:make-flags>: Change INSTBIN to INSTALL_PREFIX.
* gnu: crawl: Find all the included headers.Efraim Flashner2019-03-08
| | | | | * gnu/packages/games.scm (crawl)[arguments]: Add a custom phase to change the path for some headers.
* gnu: crawl: Don't assume system architecture.Efraim Flashner2019-03-08
| | | | | | | This allows crawl to build on non-Intel architectures. * gnu/packages/games.scm (crawl)[arguments]: Add a custom phase to remove x86* specific CFLAGS.
* gnu: crawl: Build with python3-wrapper.Efraim Flashner2019-03-08
| | | | | | * gnu/packages/games.scm (crawl)[native-inputs replace python with python-wrapper. [arguments]: Remove custom 'patch-python phase.
* channels: Do not fail when the inferior lacks 'guix repl'.Ludovic Courtès2019-03-08
| | | | | | | | | | | | | | | Fixes <https://bugs.gnu.org/34637>. Reported by Martin Flack <martin.flack@gmail.com>. Previously we'd fail to build the package cache for old versions of Guix that lack 'guix repl'. Now we simply ignore the issue and keep going without a cache. * guix/inferior.scm (gexp->derivation-in-inferior): Add #:silent-failure? and honor it. [drop-extra-keyword]: New procedure. Use it. * guix/channels.scm (package-cache-file): Pass #:silent-failure? #t.
* doc: Document references.Ludovic Courtès2019-03-08
| | | | | | | Suggested by "pelzflorian (Florian Pelz)" <pelzflorian@pelzflorian.de>. Fixes <https://bugs.gnu.org/34574>. * doc/guix.texi (Derivations): Document references.
* gnu: u-boot: Remove openssl input.Vagrant Cascadian2019-03-08
| | | | | | | | | Fixes <https://bugs.gnu.org/34717>. * gnu/packages/bootloaders (u-boot): Remove openssl from native-inputs. (u-boot-tools): Disable FIT_SIGNATURES in tests. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
* gnu: flatpak: Add more dependencies.Rutger Helling2019-03-08
| | | | | * gnu/packages/package-management.scm (flatpak)[propagated-inputs]: Add "glib-networking", "gnupg" and "gsettings-desktop-schemas".
* gnu: r-genelendatabase: Update to 1.18.0.Ricardo Wurmus2019-03-08
| | | | * gnu/packages/bioconductor.scm (r-genelendatabase): Update to 1.18.0.
* gnu: r-mzr: Update to 2.16.2.Ricardo Wurmus2019-03-08
| | | | | * gnu/packages/bioinformatics.scm (r-mzr): Update to 2.16.2. [inputs]: Replace "boost" with "boost-for-mysql".
* gnu: r-gviz: Update to 1.26.5.Ricardo Wurmus2019-03-08
| | | | * gnu/packages/bioinformatics.scm (r-gviz): Update to 1.26.5.
* gnu: r-ensembldb: Update to 2.6.7.Ricardo Wurmus2019-03-08
| | | | * gnu/packages/bioinformatics.scm (r-ensembldb): Update to 2.6.7.
* gnu: r-annotationhub: Update to 2.14.4.Ricardo Wurmus2019-03-08
| | | | * gnu/packages/bioinformatics.scm (r-annotationhub): Update to 2.14.4.
* gnu: r-rhtslib: Update to 1.14.1.Ricardo Wurmus2019-03-08
| | | | * gnu/packages/bioinformatics.scm (r-rhtslib): Update to 1.14.1.
* gnu: r-genomicfeatures: Update to 1.34.4.Ricardo Wurmus2019-03-08
| | | | * gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.34.4.
* gnu: r-rtracklayer: Update to 1.42.2.Ricardo Wurmus2019-03-08
| | | | * gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.42.2.
* gnu: r-rsamtools: Update to 1.34.1.Ricardo Wurmus2019-03-08
| | | | * gnu/packages/bioinformatics.scm (r-rsamtools): Update to 1.34.1.
* gnu: r-biocparallel: Update to 1.16.6.Ricardo Wurmus2019-03-08
| | | | * gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.16.6.
* gnu: r-variantannotation: Update to 1.28.11.Ricardo Wurmus2019-03-08
| | | | * gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.28.11.
* gnu: r-genomeinfodb: Update to 1.18.2.Ricardo Wurmus2019-03-08
| | | | * gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.18.2.
* gnu: r-dexseq: Update to 1.28.2.Ricardo Wurmus2019-03-08
| | | | * gnu/packages/bioinformatics.scm (r-dexseq): Update to 1.28.2.
* gnu: man-pages: Update to 5.00.Tobias Geerinckx-Rice2019-03-08
| | | | | * gnu/packages/man.scm (man-pages): Update to 5.00. [source]: Re-format.
* gnu: dovecot: Update to 2.3.5.Tobias Geerinckx-Rice2019-03-08
| | | | | | * gnu/packages/mail.scm (dovecot): Update to 2.3.5. [arguments]: Patch more tests in ‘patch-file-names’ phase, renamed from ‘patch-other-file-names’.
* gnu: dovecot: Don't use NAME in source URI.Tobias Geerinckx-Rice2019-03-08
| | | | * gnu/packages/mail.scm (dovecot)[source]: Hard-code NAME.
* etc: snippets: Prefill package name.Ricardo Wurmus2019-03-08
| | | | | * etc/snippets/text-mode/guix-commit-message-add-package: Extract package name from diff.
* gnu: Add mruby.Ricardo Wurmus2019-03-08
| | | | * gnu/packages/ruby.scm (mruby): New variable.
* etc: snippets: Prefill package name and version.Ricardo Wurmus2019-03-07
| | | | | * etc/snippets/text-mode/guix-commit-message-update-package: Extract package name and version from git diff output.
* gnu: r-ggmap: Update to 3.0.0.Ricardo Wurmus2019-03-07
| | | | | | | * gnu/packages/cran.scm (r-ggmap): Update to 3.0.0. [propagated-inputs]: Add r-bitops, r-dplyr, r-glue, r-httr, r-magrittr, r-purrr, r-stringr, r-tibble, and r-tidyr; remove r-geosphere, r-mapproj, r-proto, and r-reshape2.
* gnu: r-readxl: Update to 1.3.0.Ricardo Wurmus2019-03-07
| | | | * gnu/packages/cran.scm (r-readxl): Update to 1.3.0.
* gnu: r-sys: Update to 3.0.Ricardo Wurmus2019-03-07
| | | | * gnu/packages/cran.scm (r-sys): Update to 3.0.
* gnu: r-servr: Update to 0.13.Ricardo Wurmus2019-03-07
| | | | * gnu/packages/cran.scm (r-servr): Update to 0.13.
* gnu: r-flextable: Update to 0.5.1.Ricardo Wurmus2019-03-07
| | | | | | * gnu/packages/cran.scm (r-flextable): Update to 0.5.1. [propagated-inputs]: Add r-data-table, r-magick, and r-rlang; remove r-r6 and r-stringr.
* gnu: r-proxy: Update to 0.4-23.Ricardo Wurmus2019-03-07
| | | | * gnu/packages/cran.scm (r-proxy): Update to 0.4-23.
* gnu: r-haven: Update to 2.1.0.Ricardo Wurmus2019-03-07
| | | | * gnu/packages/cran.scm (r-haven): Update to 2.1.0.
* gnu: r-emdbook: Update to 1.3.11.Ricardo Wurmus2019-03-07
| | | | * gnu/packages/cran.scm (r-emdbook): Update to 1.3.11.
* gnu: r-rmysql: Update to 0.10.17.Ricardo Wurmus2019-03-07
| | | | | * gnu/packages/cran.scm (r-rmysql): Update to 0.10.17. [native-inputs]: Remove pkg-config.
* gnu: r-gower: Update to 0.2.0.Ricardo Wurmus2019-03-07
| | | | | * gnu/packages/cran.scm (r-gower): Update to 0.2.0. [native-inputs]: Remove r-knitr.
* gnu: r-ggsignif: Update to 0.5.0.Ricardo Wurmus2019-03-07
| | | | * gnu/packages/cran.scm (r-ggsignif): Update to 0.5.0.
* gnu: r-jomo: Update to 2.6-7.Ricardo Wurmus2019-03-07
| | | | * gnu/packages/cran.scm (r-jomo): Update to 2.6-7.
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