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46753 Commits

Author SHA1 Message Date
Ricardo Wurmus c2847323d8
gnu: freebayes: Simplify and enable tests. 
* 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.
 2019-08-09 12:15:26 +02:00
Ricardo Wurmus 7cd98e868e
gnu: freebayes: Move bamtools to inputs. 
* gnu/packages/bioinformatics.scm (freebayes)[native-inputs]: Move bamtools
from here...
[inputs]: ...to here.
 2019-08-09 12:15:26 +02:00
Arun Isaac db18d87ac3
gnu: guile-email: Update to 0.2.0. 
* 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.
 2019-08-09 14:45:33 +05:30
Efraim Flashner 32c517a327
gnu: 4store: Remove unneeded build phase. 
* gnu/packages/databases.scm (4store)[arguments]: Remove unneeded
'generate-configure phase.
 2019-08-09 12:13:18 +03:00
Efraim Flashner 50e20b8fee
gnu: 4store: Don't use unstable tarball. 
* gnu/packages/databases.scm (4store)[source]: Download using
'git-fetch'.
 2019-08-09 12:12:08 +03:00
Pierre Neidhardt 8803dbdad8
gnu: Add freebayes. 
* gnu/packages/bioinformatics.scm (freebayes): New variable.
 2019-08-09 10:47:25 +03:00
Pierre Neidhardt 95fb1a1851
gnu: Add vcflib. 
* gnu/packages/bioinformatics.scm (vcflib): New variable.
(tabixpp-freebayes): New private variable.
 2019-08-09 10:43:40 +03:00
Mark H Weaver f7780fdf61
gnu: isc-dhcp: Update bundled BIND to 9.11.9. 
* 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.
 2019-08-08 17:24:21 -04:00
Jovany Leandro G.C 5cded306f9
gnu: Add cutter. 
* gnu/packages/engineering.scm (cutter): New variable.

Signed-off-by: Marius Bakke <mbakke@fastmail.com>
 2019-08-08 20:14:14 +02:00
Dimakakos Dimos via Guix-patches ae54a4c0ef
gnu: Add emacs-ox-hugo. 
gnu/packages/emacs-xyz.scm (emacs-ox-hugo): New variable

Signed-off-by: Marius Bakke <mbakke@fastmail.com>
 2019-08-08 20:14:14 +02:00
Kyle Meyer a4a41a7ba8
gnu: git-annex: Update to 7.20190708. 
* 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>
 2019-08-08 20:14:14 +02:00
Kyle Meyer 3d45d8f14b
gnu: git-annex: Don't patch shebang used in hooks. 
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>
 2019-08-08 20:14:14 +02:00
Brian Leung deccffb264
gnu: emacs-helpful: Update to 0.17. 
* gnu/packages/emacs-xyz.scm (emacs-helpful): Update to 0.17.

Signed-off-by: Marius Bakke <mbakke@fastmail.com>
 2019-08-08 20:14:14 +02:00
Marius Bakke 36f400f616
Merge branch 'master' into staging 2019-08-08 18:14:45 +02:00
Marius Bakke ffc4869e45
gnu: ruby-pg: Update to 1.1.4. 
* gnu/packages/ruby.scm (ruby-pg): Update to 1.1.4.
[inputs]: Change from POSTGRESQL-9.6 to POSTGRESQL.
 2019-08-08 17:48:46 +02:00
Marius Bakke c96ec77198
gnu: exempi: Update home page. 
* gnu/packages/freedesktop.scm (exempi)[home-page]: Update to current.
 2019-08-08 17:48:46 +02:00
Marius Bakke 14b80bf6ca
gnu: postgresql@9: Update to 9.6.15 [fixes CVE-2019-10208]. 
* gnu/packages/databases.scm (postgresql-9.6): Update to 9.6.15.
 2019-08-08 17:48:46 +02:00
Marius Bakke cbfddc2f33
gnu: postgresql@11: Update to 11.5 [fixes CVE-2019-10208, CVE-2019-10209]. 
* gnu/packages/databases.scm (postgresql-11): Update to 11.5.
 2019-08-08 17:48:46 +02:00
Marius Bakke df3db97587
gnu: exempi: Update to 2.5.1. 
* gnu/packages/freedesktop.scm (exempi): Update to 2.5.1.
 2019-08-08 17:48:45 +02:00
Marius Bakke bd12be346b
gnu: LibRaw: Update to 0.19.4. 
* gnu/packages/photo.scm (libraw): Update to 0.19.4.
 2019-08-08 17:48:45 +02:00
Marius Bakke c8f5827a56
gnu: postgresql: Udpate to 10.10 [fixes CVE-2019-10208]. 
* gnu/packages/databases.scm (postgresql): Update to 10.10.
 2019-08-08 17:32:18 +02:00
Ricardo Wurmus 7ef25083f0
gnu: r-modelr: Update to 0.1.5. 
* gnu/packages/cran.scm (r-modelr): Update to 0.1.5.
[propagated-inputs]: Remove r-lazyeval; add r-rlang.
 2019-08-08 17:20:46 +02:00
Ricardo Wurmus eb8963d989
gnu: r-quantreg: Update to 5.51. 
* gnu/packages/statistics.scm (r-quantreg): Update to 5.51.
 2019-08-08 16:47:05 +02:00
Ricardo Wurmus eaca771e88
gnu: r-knitr: Update to 1.24. 
* gnu/packages/statistics.scm (r-knitr): Update to 1.24.
 2019-08-08 16:47:05 +02:00
Ricardo Wurmus 9649072cbd
gnu: r-markdown: Update to 1.1. 
* gnu/packages/statistics.scm (r-markdown): Update to 1.1.
[propagated-inputs]: Add r-xfun.
 2019-08-08 16:47:05 +02:00
Ricardo Wurmus d099499e0b
gnu: r-ggsignif: Update to 0.6.0. 
* gnu/packages/cran.scm (r-ggsignif): Update to 0.6.0.
 2019-08-08 16:47:05 +02:00
Ricardo Wurmus 90060e2071
gnu: r-hdf5array: Update to 1.12.2. 
* gnu/packages/bioinformatics.scm (r-hdf5array): Update to 1.12.2.
 2019-08-08 16:47:05 +02:00
Ricardo Wurmus a39f2e4cea
gnu: r-biocparallel: Update to 1.18.1. 
* gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.18.1.
 2019-08-08 16:47:02 +02:00
Marius Bakke ba73c434e0
gnu: ToME4: Disable parallel build. 
* gnu/packages/games.scm (tome4)[arguments]: Add <#:parallel-build?>.
 2019-08-08 16:45:14 +02:00
Efraim Flashner 1a069a170c
Revert "gnu: Add vcflib." 
This reverts commit 194e45f90a.

This commit does not have a good commit message, and it breaks master
 2019-08-08 15:34:05 +03:00
Efraim Flashner 6bc63fd8a7
Revert "gnu: Add freebayes." 
This reverts commit 173e046950.
 2019-08-08 15:32:51 +03:00
Pierre Neidhardt 173e046950
gnu: Add freebayes. 
* gnu/packages/bioinformatics.scm (freebayes): New variable.
 2019-08-08 15:18:34 +03:00
Pierre Neidhardt 194e45f90a
gnu: Add vcflib. 
* gnu/packages/bioinformatics.scm (vcflib): New variable.
 2019-08-08 15:18:33 +03:00
Pierre Neidhardt 7d71557d4d
gnu: Add fastahack. 
* gnu/packages/bioinformatics.scm (fastahack): New variable.
 2019-08-08 15:18:32 +03:00
Pierre Neidhardt 70782dddff
gnu: Add fsom. 
* gnu/packages/bioinformatics.scm (fsom): New variable.
 2019-08-08 15:18:31 +03:00
Pierre Neidhardt 8cd51276e5
gnu: Add multichoose. 
* gnu/packages/bioinformatics.scm (multichoose): New variable.
 2019-08-08 15:18:30 +03:00
Pierre Neidhardt 7faa70cf2b
gnu: Add smithwaterman. 
* gnu/packages/bioinformatics.scm (smithwaterman): New variable.
 2019-08-08 15:18:29 +03:00
Pierre Neidhardt 62a031afc4
gnu: Add tabixpp. 
* gnu/packages/bioinformatics.scm (tabixpp): New variable.
 2019-08-08 15:18:14 +03:00
Efraim Flashner 8378c87a59
gnu: Add network-manager-openconnect. 
* gnu/packages/gnome.scm (network-manager-openconnect): New variable.
 2019-08-08 10:08:00 +03:00
Robert Vollmert caa366ec23
gnu: ghc-trifecta: Disable tests. 
* gnu/packages/haskell.scm (ghc-trifecta)[arguments]: Disable tests.
 2019-08-07 22:05:34 -04:00
Robert Vollmert dbfaac113a
gnu: ghc-yaml: Disable tests. 
* gnu/packages/haskell.scm (ghc-yaml)[arguments]: Disable tests.
 2019-08-07 22:05:34 -04:00
Robert Vollmert 9ec2d6f84c
gnu: ghc-libmpd-haskell: Disable tests. 
* gnu/packages/haskell.scm (ghc-libmpd-haskell)[arguments]: Disable
tests.
 2019-08-07 22:05:33 -04:00
Robert Vollmert 3755088b54
gnu: Remove ghc-packedstring. 
The package has no reverse dependencies and is deprecated upstream.

* gnu/packages/haskell.scm (ghc-packedstring): Remove variable.
 2019-08-07 22:05:33 -04:00
Robert Vollmert 63edeca773
gnu: Remove ghc-haddock-test. 
The package doesn't build, has no reverse dependencies, and is
deprecated upstream.

* gnu/packages/haskell.scm (ghc-haddock-test): Remove variable.
 2019-08-07 22:05:33 -04:00
Robert Vollmert 0d59302eba
gnu: Remove ghc-regex-tdfa-rc. 
The package doesn't build, has no reverse dependencies, and is deprecated
upstream.

* gnu/packages/haskell.scm (ghc-regex-tdfa-rc): Remove variable.
 2019-08-07 22:05:33 -04:00
Robert Vollmert 8ede1021c8
gnu: Add ghc-snap-server. 
* gnu/packages/haskell-web.scm (ghc-snap-server): New variable.
 2019-08-07 22:05:33 -04:00
Robert Vollmert 4f1793a2be
gnu: Add ghc-snap-core. 
* gnu/packages/haskell-web.scm (ghc-snap-core): New variable.
 2019-08-07 22:05:32 -04:00
Robert Vollmert 4ccd679f25
gnu: Add ghc-http-streams. 
* gnu/packages/haskell-web.scm (ghc-http-streams): New variable.
 2019-08-07 22:05:32 -04:00
Robert Vollmert 0173cdd31d
gnu: Add ghc-http-common. 
* gnu/packages/haskell-web.scm (ghc-http-common): New variable.
 2019-08-07 22:05:32 -04:00
Robert Vollmert 4ba66e6f16
gnu: Add ghc-openssl-streams. 
* gnu/packages/haskell-crypto.scm (ghc-openssl-streams): New variable.
 2019-08-07 22:05:32 -04:00