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2019-03-08activation: Shared system home directories are now 555 and root-owned.Ludovic Courtès
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.
2019-03-08gnu: Add java-eclipse-jdt-compiler-apt.Ricardo Wurmus
* gnu/packages/java.scm (java-eclipse-jdt-compiler-apt): New variable.
2019-03-08gnu: blast+: Update to 2.7.1.Ricardo Wurmus
* 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.
2019-03-08gnu: Add texlive-latex-pdfx.Ricardo Wurmus
* gnu/packages/tex.scm (texlive-latex-pdfx): New variable.
2019-03-08gnu: Add texlive-latex-xmpincl.Ricardo Wurmus
* gnu/packages/tex.scm (texlive-latex-xmpincl): New variable.
2019-03-08gnu: Add translate2geda.Ricardo Wurmus
* gnu/packages/engineering.scm (translate2geda): New variable.
2019-03-08gnu: Add rkrlv2.Ricardo Wurmus
* gnu/packages/music.scm (rkrlv2): New variable.
2019-03-08gnu: fc-host-tools: Update to 10.Danny Milosavljevic
* gnu/packages/embedded.scm (fc-host-tools): Update to 10. [arguments]<:make-flags>: Change INSTBIN to INSTALL_PREFIX.
2019-03-08gnu: crawl: Find all the included headers.Efraim Flashner
* gnu/packages/games.scm (crawl)[arguments]: Add a custom phase to change the path for some headers.
2019-03-08gnu: crawl: Don't assume system architecture.Efraim Flashner
This allows crawl to build on non-Intel architectures. * gnu/packages/games.scm (crawl)[arguments]: Add a custom phase to remove x86* specific CFLAGS.
2019-03-08gnu: crawl: Build with python3-wrapper.Efraim Flashner
* gnu/packages/games.scm (crawl)[native-inputs replace python with python-wrapper. [arguments]: Remove custom 'patch-python phase.
2019-03-08gnu: u-boot: Remove openssl input.Vagrant Cascadian
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>
2019-03-08gnu: flatpak: Add more dependencies.Rutger Helling
* gnu/packages/package-management.scm (flatpak)[propagated-inputs]: Add "glib-networking", "gnupg" and "gsettings-desktop-schemas".
2019-03-08gnu: r-genelendatabase: Update to 1.18.0.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-genelendatabase): Update to 1.18.0.
2019-03-08gnu: r-mzr: Update to 2.16.2.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-mzr): Update to 2.16.2. [inputs]: Replace "boost" with "boost-for-mysql".
2019-03-08gnu: r-gviz: Update to 1.26.5.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-gviz): Update to 1.26.5.
2019-03-08gnu: r-ensembldb: Update to 2.6.7.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-ensembldb): Update to 2.6.7.
2019-03-08gnu: r-annotationhub: Update to 2.14.4.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-annotationhub): Update to 2.14.4.
2019-03-08gnu: r-rhtslib: Update to 1.14.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-rhtslib): Update to 1.14.1.
2019-03-08gnu: r-genomicfeatures: Update to 1.34.4.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.34.4.
2019-03-08gnu: r-rtracklayer: Update to 1.42.2.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.42.2.
2019-03-08gnu: r-rsamtools: Update to 1.34.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-rsamtools): Update to 1.34.1.
2019-03-08gnu: r-biocparallel: Update to 1.16.6.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.16.6.
2019-03-08gnu: r-variantannotation: Update to 1.28.11.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.28.11.
2019-03-08gnu: r-genomeinfodb: Update to 1.18.2.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.18.2.
2019-03-08gnu: r-dexseq: Update to 1.28.2.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-dexseq): Update to 1.28.2.
2019-03-08gnu: man-pages: Update to 5.00.Tobias Geerinckx-Rice
* gnu/packages/man.scm (man-pages): Update to 5.00. [source]: Re-format.
2019-03-08gnu: dovecot: Update to 2.3.5.Tobias Geerinckx-Rice
* 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’.
2019-03-08gnu: dovecot: Don't use NAME in source URI.Tobias Geerinckx-Rice
* gnu/packages/mail.scm (dovecot)[source]: Hard-code NAME.
2019-03-08gnu: Add mruby.Ricardo Wurmus
* gnu/packages/ruby.scm (mruby): New variable.
2019-03-07gnu: r-ggmap: Update to 3.0.0.Ricardo Wurmus
* 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.
2019-03-07gnu: r-readxl: Update to 1.3.0.Ricardo Wurmus
* gnu/packages/cran.scm (r-readxl): Update to 1.3.0.
2019-03-07gnu: r-sys: Update to 3.0.Ricardo Wurmus
* gnu/packages/cran.scm (r-sys): Update to 3.0.
2019-03-07gnu: r-servr: Update to 0.13.Ricardo Wurmus
* gnu/packages/cran.scm (r-servr): Update to 0.13.
2019-03-07gnu: r-flextable: Update to 0.5.1.Ricardo Wurmus
* 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.
2019-03-07gnu: r-proxy: Update to 0.4-23.Ricardo Wurmus
* gnu/packages/cran.scm (r-proxy): Update to 0.4-23.
2019-03-07gnu: r-haven: Update to 2.1.0.Ricardo Wurmus
* gnu/packages/cran.scm (r-haven): Update to 2.1.0.
2019-03-07gnu: r-emdbook: Update to 1.3.11.Ricardo Wurmus
* gnu/packages/cran.scm (r-emdbook): Update to 1.3.11.
2019-03-07gnu: r-rmysql: Update to 0.10.17.Ricardo Wurmus
* gnu/packages/cran.scm (r-rmysql): Update to 0.10.17. [native-inputs]: Remove pkg-config.
2019-03-07gnu: r-gower: Update to 0.2.0.Ricardo Wurmus
* gnu/packages/cran.scm (r-gower): Update to 0.2.0. [native-inputs]: Remove r-knitr.
2019-03-07gnu: r-ggsignif: Update to 0.5.0.Ricardo Wurmus
* gnu/packages/cran.scm (r-ggsignif): Update to 0.5.0.
2019-03-07gnu: r-jomo: Update to 2.6-7.Ricardo Wurmus
* gnu/packages/cran.scm (r-jomo): Update to 2.6-7.
2019-03-07gnu: r-mice: Update to 3.4.0.Ricardo Wurmus
* gnu/packages/cran.scm (r-mice): Update to 3.4.0.
2019-03-07gnu: r-xfun: Update to 0.5.Ricardo Wurmus
* gnu/packages/cran.scm (r-xfun): Update to 0.5.
2019-03-07gnu: r-metap: Update to 1.1.Ricardo Wurmus
* gnu/packages/cran.scm (r-metap): Update to 1.1.
2019-03-07gnu: r-ifultools: Update to 2.0-5.Ricardo Wurmus
* gnu/packages/cran.scm (r-ifultools): Update to 2.0-5.
2019-03-07gnu: r-radiant-data: Update to 0.9.9.Ricardo Wurmus
* gnu/packages/cran.scm (r-radiant-data): Update to 0.9.9. [propagated-inputs]: Add r-stringi; remove r-summarytools.
2019-03-07gnu: r-later: Update to 0.8.0.Ricardo Wurmus
* gnu/packages/cran.scm (r-later): Update to 0.8.0.
2019-03-07gnu: r-vim: Update to 4.8.0.Ricardo Wurmus
* gnu/packages/cran.scm (r-vim): Update to 4.8.0. [propagated-inputs]: Add r-ranger.
2019-03-07gnu: r-fnn: Update to 1.1.3.Ricardo Wurmus
* gnu/packages/cran.scm (r-fnn): Update to 1.1.3.
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