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2019-08-11gnu: diffoscope: Update to 120.Vagrant Cascadian
* gnu/packages/package-management (diffoscope): Update to 120.
2019-08-09gnu: linux-libre: Update to 5.2.8.Mark H Weaver
* gnu/packages/linux.scm (linux-libre-5.2-version): Update to 5.2.8. (linux-libre-5.2-pristine-source)[hash]: Update hash.
2019-08-09gnu: linux-libre@4.19: Update to 4.19.66.Mark H Weaver
* gnu/packages/linux.scm (linux-libre-4.19-version): Update to 4.19.66. (linux-libre-4.19-pristine-source)[hash]: Update hash.
2019-08-09gnu: linux-libre@4.14: Update to 4.14.138.Mark H Weaver
* gnu/packages/linux.scm (linux-libre-4.14-version): Update to 4.14.138. (linux-libre-4.14-pristine-source)[hash]: Update hash.
2019-08-09gnu: emacs-deadgrep: Update to 0.8-1.329119c.Brian Leung
* gnu/packages/emacs-xyz.scm (emacs-deadgrep): Update to 0.8-1.329119c. Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2019-08-09gnu: emacs-xr: Update to 1.13.Nicolas Goaziou
* gnu/packages/emacs-xyz.scm (emacs-xr): Update to 1.13.
2019-08-09gnu: r-xml2: Update to 1.2.2.Ricardo Wurmus
* gnu/packages/statistics.scm (r-xml2): Update to 1.2.2.
2019-08-09gnu: r-ggforce: Update to 0.3.0.Ricardo Wurmus
* gnu/packages/cran.scm (r-ggforce): Update to 0.3.0. [propagated-inputs]: Add r-tidyselect and r-withr.
2019-08-09gnu: r-tidytree: Update to 0.2.6.Ricardo Wurmus
* gnu/packages/cran.scm (r-tidytree): Update to 0.2.6.
2019-08-09gnu: freebayes: Simplify and enable tests.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (freebayes)[arguments]: Enable tests; set make flags; add phase "fix-tests"; fix both Makefiles in "fix-makefiles" phase; move build of tabixpp and vcflib to separate phase "build-tabixpp-and-vcflib"; simplify make invocations; remove custom "build" phase.
2019-08-09gnu: freebayes: Move bamtools to inputs.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (freebayes)[native-inputs]: Move bamtools from here... [inputs]: ...to here.
2019-08-09gnu: guile-email: Update to 0.2.0.Arun Isaac
* gnu/packages/guile-xyz.scm (guile-email): Update to 0.2.0. [source]: Update URI. [native-inputs]: Remove autoconf and automake. Add lzip. [arguments]: Add GUILE_AUTO_COMPILE=0 to #:make-flags. [home-page]: Update URI. [description]: Update description.
2019-08-09gnu: 4store: Remove unneeded build phase.Efraim Flashner
* gnu/packages/databases.scm (4store)[arguments]: Remove unneeded 'generate-configure phase.
2019-08-09gnu: 4store: Don't use unstable tarball.Efraim Flashner
* gnu/packages/databases.scm (4store)[source]: Download using 'git-fetch'.
2019-08-09gnu: Add freebayes.Pierre Neidhardt
* gnu/packages/bioinformatics.scm (freebayes): New variable.
2019-08-09gnu: Add vcflib.Pierre Neidhardt
* gnu/packages/bioinformatics.scm (vcflib): New variable. (tabixpp-freebayes): New private variable.
2019-08-08gnu: isc-dhcp: Update bundled BIND to 9.11.9.Mark H Weaver
* gnu/packages/patches/isc-dhcp-4.4.1-fixes-for-newer-bind.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. * gnu/packages/admin.scm (isc-dhcp): Update BIND version to 9.11.9. [arguments]: In the 'replace-bundled-bind' phase, apply the patch. In the 'post-configure' phase: Refine a substitute* regexp to avoid substituting an instance of "./configure.log" in the BIND Makefile. Substitute /usr/bin/file in the BIND configure script. [native-inputs]: Add 'file', 'patch', and the patch. [inputs]: Update the hash of bind-source-tarball.
2019-08-08gnu: Add cutter.Jovany Leandro G.C
* gnu/packages/engineering.scm (cutter): New variable. Signed-off-by: Marius Bakke <mbakke@fastmail.com>
2019-08-08gnu: Add emacs-ox-hugo.Dimakakos Dimos via Guix-patches
gnu/packages/emacs-xyz.scm (emacs-ox-hugo): New variable Signed-off-by: Marius Bakke <mbakke@fastmail.com>
2019-08-08gnu: git-annex: Update to 7.20190708.Kyle Meyer
* gnu/packages/haskell-apps.scm (git-annex): Update to 7.20190708. [inputs]: Add new dependency, ghc-concurrent-output. Signed-off-by: Marius Bakke <mbakke@fastmail.com>
2019-08-08gnu: git-annex: Don't patch shebang used in hooks.Kyle Meyer
git-annex relies on configuring Git's pre-commit and post-receive hooks. Avoid patching the shebang that git-annex embeds when generating these hooks so that the hooks don't fail if garbage collection claims the bash that was current when the annex repository was initialized. * gnu/packages/haskell-apps.scm (git-annex):[arguments]: Patch hook shebangs only temporarily for tests. Signed-off-by: Marius Bakke <mbakke@fastmail.com>
2019-08-08gnu: emacs-helpful: Update to 0.17.Brian Leung
* gnu/packages/emacs-xyz.scm (emacs-helpful): Update to 0.17. Signed-off-by: Marius Bakke <mbakke@fastmail.com>
2019-08-08gnu: ruby-pg: Update to 1.1.4.Marius Bakke
* gnu/packages/ruby.scm (ruby-pg): Update to 1.1.4. [inputs]: Change from POSTGRESQL-9.6 to POSTGRESQL.
2019-08-08gnu: exempi: Update home page.Marius Bakke
* gnu/packages/freedesktop.scm (exempi)[home-page]: Update to current.
2019-08-08gnu: postgresql@9: Update to 9.6.15 [fixes CVE-2019-10208].Marius Bakke
* gnu/packages/databases.scm (postgresql-9.6): Update to 9.6.15.
2019-08-08gnu: postgresql@11: Update to 11.5 [fixes CVE-2019-10208, CVE-2019-10209].Marius Bakke
* gnu/packages/databases.scm (postgresql-11): Update to 11.5.
2019-08-08gnu: exempi: Update to 2.5.1.Marius Bakke
* gnu/packages/freedesktop.scm (exempi): Update to 2.5.1.
2019-08-08gnu: LibRaw: Update to 0.19.4.Marius Bakke
* gnu/packages/photo.scm (libraw): Update to 0.19.4.
2019-08-08gnu: r-modelr: Update to 0.1.5.Ricardo Wurmus
* gnu/packages/cran.scm (r-modelr): Update to 0.1.5. [propagated-inputs]: Remove r-lazyeval; add r-rlang.
2019-08-08gnu: r-quantreg: Update to 5.51.Ricardo Wurmus
* gnu/packages/statistics.scm (r-quantreg): Update to 5.51.
2019-08-08gnu: r-knitr: Update to 1.24.Ricardo Wurmus
* gnu/packages/statistics.scm (r-knitr): Update to 1.24.
2019-08-08gnu: r-markdown: Update to 1.1.Ricardo Wurmus
* gnu/packages/statistics.scm (r-markdown): Update to 1.1. [propagated-inputs]: Add r-xfun.
2019-08-08gnu: r-ggsignif: Update to 0.6.0.Ricardo Wurmus
* gnu/packages/cran.scm (r-ggsignif): Update to 0.6.0.
2019-08-08gnu: r-hdf5array: Update to 1.12.2.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-hdf5array): Update to 1.12.2.
2019-08-08gnu: r-biocparallel: Update to 1.18.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.18.1.
2019-08-08gnu: ToME4: Disable parallel build.Marius Bakke
* gnu/packages/games.scm (tome4)[arguments]: Add <#:parallel-build?>.
2019-08-08Revert "gnu: Add vcflib."Efraim Flashner
This reverts commit 194e45f90addf5f9bd3e7e2de1dd50b3071f053b. This commit does not have a good commit message, and it breaks master
2019-08-08Revert "gnu: Add freebayes."Efraim Flashner
This reverts commit 173e046950e153477a6aaa0f4860d8f080df6843.
2019-08-08gnu: Add freebayes.Pierre Neidhardt
* gnu/packages/bioinformatics.scm (freebayes): New variable.
2019-08-08gnu: Add vcflib.Pierre Neidhardt
* gnu/packages/bioinformatics.scm (vcflib): New variable.
2019-08-08gnu: Add fastahack.Pierre Neidhardt
* gnu/packages/bioinformatics.scm (fastahack): New variable.
2019-08-08gnu: Add fsom.Pierre Neidhardt
* gnu/packages/bioinformatics.scm (fsom): New variable.
2019-08-08gnu: Add multichoose.Pierre Neidhardt
* gnu/packages/bioinformatics.scm (multichoose): New variable.
2019-08-08gnu: Add smithwaterman.Pierre Neidhardt
* gnu/packages/bioinformatics.scm (smithwaterman): New variable.
2019-08-08gnu: Add tabixpp.Pierre Neidhardt
* gnu/packages/bioinformatics.scm (tabixpp): New variable.
2019-08-08gnu: Add network-manager-openconnect.Efraim Flashner
* gnu/packages/gnome.scm (network-manager-openconnect): New variable.
2019-08-07gnu: ghc-trifecta: Disable tests.Robert Vollmert
* gnu/packages/haskell.scm (ghc-trifecta)[arguments]: Disable tests.
2019-08-07gnu: ghc-yaml: Disable tests.Robert Vollmert
* gnu/packages/haskell.scm (ghc-yaml)[arguments]: Disable tests.
2019-08-07gnu: ghc-libmpd-haskell: Disable tests.Robert Vollmert
* gnu/packages/haskell.scm (ghc-libmpd-haskell)[arguments]: Disable tests.
2019-08-07gnu: Remove ghc-packedstring.Robert Vollmert
The package has no reverse dependencies and is deprecated upstream. * gnu/packages/haskell.scm (ghc-packedstring): Remove variable.
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