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46837 Commits

Author SHA1 Message Date
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
Robert Vollmert 0925b80409
gnu: Add ghc-hsopenssl. 
* gnu/packages/haskell-crypto.scm (ghc-hsopenssl): New variable.
 2019-08-07 22:05:32 -04:00
Robert Vollmert 7b01a977e4
gnu: Add ghc-io-streams-haproxy. 
* gnu/packages/haskell-xyz.scm (ghc-io-streams-haproxy): New variable.
 2019-08-07 22:05:32 -04:00
Robert Vollmert 658dbc7ff2
gnu: Add ghc-io-streams. 
* gnu/packages/haskell-xyz.scm (ghc-io-streams): New variable.
 2019-08-07 22:05:31 -04:00
Robert Vollmert 14e4199646
gnu: Add ghc-zlib-bindings. 
* gnu/packages/haskell-xyz.scm (ghc-zlib-bindings): New variable.
 2019-08-07 22:05:31 -04:00
Robert Vollmert bbf8bf31e4
gnu: Add ghc-threads. 
* gnu/packages/haskell-xyz.scm (ghc-threads): New variable.
 2019-08-07 22:05:31 -04:00
Robert Vollmert b57e99f574
gnu: Add ghc-readable. 
* gnu/packages/haskell-xyz.scm (ghc-readable): New variable.
 2019-08-07 22:05:31 -04:00
Robert Vollmert efb96749a2
gnu: Add ghc-concurrent-extra. 
* gnu/packages/haskell-xyz.scm (ghc-concurrent-extra): New variable.
 2019-08-07 22:05:31 -04:00
Robert Vollmert 79fcc5e59b
gnu: Add ghc-language-glsl. 
* gnu/packages/haskell-xyz.scm (ghc-language-glsl): New variable.
 2019-08-07 22:05:30 -04:00
Robert Vollmert 6b34d01cbf
gnu: Add ghc-prettyclass. 
* gnu/package/haskell-xyz.scm: New file.
* gnu/local.mk: Add it.
* gnu/packages/haskell-xyz.scm (ghc-prettyclass): New variable.
 2019-08-07 22:05:30 -04:00
Robert Vollmert 91732735f6
gnu: ghc-ansi-terminal: Downgrade to 0.8.0.4. 
This reverts commits

    cbff89d126,
    5a499d0f7d, and
    4e3ebbfb16.

* gnu/packages/haskell.scm (ghc-ansi-terminal): Downgrade to 0.8.0.4.
(ghc-ansi-terminal-0.8): Delete variable.
(ghc-ansi-wl-pprint, ghc-concurrent-output)[inputs]: Replace
'ghc-ansi-terminal-0.8' with 'ghc-ansi-terminal'.
* gnu/packages/haskell-check.scm (ghc-hedgehog)[inputs]: Likewise.
 2019-08-07 22:05:30 -04:00
Robert Vollmert e8aea9018b
gnu: ghc-validation: Downgrade to 1. 
This is the Stackage LTS version, which is compatible with
ansi-terminal 0.8.

* gnu/packages/haskell.scm (ghc-validation): Downgrade to 1.
 2019-08-07 22:05:30 -04:00
Robert Vollmert f74aa98ed7
gnu: ghc-concurrent-output: Downgrade to 1.10.9. 
This is the Stackage LTS version, which is compatible with
ansi-terminal 0.8.

* gnu/packages/haskell.scm (ghc-concurrent-output): Downgrade to 1.10.9
and use ghc-ansi-terminal-0.8.
 2019-08-07 22:05:30 -04:00
Robert Vollmert 1c54c30d9c
gnu: ghc-validation: Do not generate 'Setup.hs'. 
This is handled by the build system.

* gnu/packages/haskell.scm (ghc-validation): Remove 'arguments'.
 2019-08-07 22:05:30 -04:00
Robert Vollmert a1eb8be8ca
gnu: Remove ghc-parsec, ghc-stm, ghc-text, ghc-xhtml. 
These are ghc-8.4-bundled packages, removing to avoid build
conflicts.

* gnu/packages/haskell.scm (ghc-parsec, ghc-stm, ghc-text): Remove.
* gnu/packages/haskell-web.scm (ghc-xhtml): Remove.
* gnu/packages/agda.scm (agda)[inputs]: Remove ghc-stm and ghc-text.
* gnu/packages/bioinformatics.scm (ngless)[inputs]: Remove ghc-parsec and
ghc-text.
* gnu/packages/haskell-apps.scm (darcs)[inputs]: Remove ghc-parsec.
(git-annex)[inputs]: Remove ghc-stm and ghc-text.
(ghc-sdl2)[inputs]: Remove ghc-text.
(ghc-sdl2-image)[inputs]: Remove ghc-text.
* gnu/packages/haskell-check.scm (ghc-tasty-ant-xml)[inputs]: Remove ghc-stm.
(ghc-tasty)[inputs]: Remove ghc-stm.
(ghc-tasty-rerun)[inputs]: Same.
(ghc-quickcheck-instances)[inputs]: Remove ghc-text.
(ghc-hedgehog)[inputs]: Remove ghc-stm.
* gnu/packages/haskell-crypto.scm (ghc-asn1-encoding)[inputs]: Remove
ghc-text.
* gnu/packages/haskell-web.scm (ghc-tagsoup)[inputs]: Remove ghc-text.
(ghc-cookie)[inputs]: Same.
(ghc-http-types)[inputs]: Same.
(ghc-http)[inputs]: Remove ghc-parsec.
(ghc-http-client)[inputs]: Remove ghc-text.
(ghc-http2)[inputs]: Remove ghc-stm.
(ghc-http-conduit)[native-inputs]: Remove ghc-text.
(ghc-wai)[inputs]: Same.
(ghc-wai-extra)[inputs]: Same.
(ghc-warp)[inputs]: Remove ghc-stm and ghc-text.
(ghc-xss-sanitize)[native-inputs]: Remove ghc-text.
(ghc-css-text)[inputs]: Same.
(ghc-mime-types)[inputs]: Same.
(ghc-blaze-html)[inputs]: Same.
(ghc-aeson)[inputs]: Same.
(ghc-aeson-pretty)[inputs]: Same.
(ghc-aeson-qq)[inputs]: Remove ghc-text and ghc-parsec.
(ghc-multipart)[inputs]: Remove ghc-parsec.
(ghc-uri-encode)[inputs]: Remove ghc-text.
(ghc-path-pieces)[inputs]: Same.
(ghc-yesod-core)[inputs]: Remove ghc-text and ghc-parsec.
(ghc-yesod-persistent)[inputs]: Remove ghc-text.
(ghc-yesod-form)[inputs]: Same.
(ghc-yesod)[inputs]: Same.
(ghc-hxt-regex-xmlschema)[inputs]: Remove ghc-parsec and ghc-text.
(ghc-hxt)[inputs]: Remove ghc-parsec.
* gnu/packages/haskell.scm (ghc-convertible)[inputs]: Remove ghc-text.
(ghc-double-conversion)[inputs]: Same.
(ghc-tree-diff)[inputs]: Remove ghc-parsec and ghc-text.
[native-inputs]: Remove ghc-parsec.
(ghc-cgi)[inputs]: Remove ghc-parsec.
(hlint)[inputs]: Remove ghc-text.
(ghc-openglraw)[inputs]: Remove ghc-text.
(ghc-opengl)[inputs]: Same.
(ghc-streaming-commons)[inputs]: Remove ghc-stm and ghc-text.
(ghc-hackage-security)[inputs]: Remove ghc-parsec.
(cabal-install)[inputs]: Remove ghc-stm.
(ghc-parsec-numbers)[inputs]: Remove ghc-parsec.
(ghc-safesemaphore)[inputs]: Remove ghc-stm.
(ghc-text-binary)[inputs]: Remove ghc-text.
(ghc-hashable)[inputs]: Remove ghc-text.
(ghc-transformers-base)[inputs]: Remove ghc-stm.
(ghc-indents)[inputs]: Remove ghc-parsec.
(ghc-regex-tdfa-rc)[inputs]: Same.
(ghc-regex-tdfa-text)[inputs]: Same.
(ghc-regex)[inputs]: Remove ghc-text.
(ghc-parsers)[inputs]: Remove ghc-parsec and ghc-text.
(ghc-attoparsec)[inputs]: Remove ghc-text.
(ghc-attoparsec-bootstrap)[inputs]: Same.
(ghc-zip-archive)[inputs]: Same.
(ghc-polyparse)[inputs]: Same.
(ghc-reducers)[inputs]: Same.
(ghc-xml)[inputs]: Same.
(ghc-feed)[inputs]: Same.
(ghc-exceptions)[inputs]: Remove ghc-stm.
(ghc-case-insensitive)[inputs]: Remove ghc-text.
(ghc-megaparsec)[inputs]: Same.
(ghc-network-uri)[inputs]: Remove ghc-parsec.
(ghc-monad-control)[inputs]: Remove ghc-stm.
(ghc-blaze-builder)[inputs]: Remove ghc-text.
(ghc-blaze-markup)[inputs]: Same.
(ghc-async)[inputs]: Remove ghc-stm.
(ghc-invariant)[inputs]: Same.
(ghc-statevar)[inputs]: Same.
(ghc-lens)[inputs]: Remove ghc-text.
(ghc-cheapskate)[inputs]: Same.
(ghc-semigroups)[inputs]: Same.
(ghc-semigroups-bootstrap)[inputs]: Same.
(ghc-fast-logger)[inputs]: Same.
(ghc-scientific)[inputs]: Same.
(ghc-scientific-bootstrap)[inputs]: Same.
(ghc-texmath)[inputs]: Remove ghc-parsec.
(ghc-highlighting-kate)[inputs]: Same.
(ghc-cmark)[inputs]: Remove ghc-text.
(ghc-cmark-gfm)[inputs]: Same.
(ghc-th-lift-instances)[inputs]: Same.
(ghc-yaml)[inputs]: Same.
(ghc-hslua)[inputs]: Same.
(ghc-hslua-module-text)[inputs]: Same.
(ghc-skylighting-core)[inputs]: Same.
(ghc-doctemplates)[inputs]: Remove ghc-text and ghc-parsec.
(ghc-pandoc)[inputs]: Same.
(ghc-typed-process)[inputs]: Remove ghc-stm.
(ghc-conduit-extra)[inputs]: Remove ghc-stm and ghc-text.
(ghc-xml-types)[inputs]: Remove ghc-text.
(ghc-xml-conduit)[inputs]: Same.
(ghc-pandoc-citeproc)[inputs]: Remove ghc-text and ghc-parsec.
(ghc-regex-tdfa)[inputs]: Remove ghc-parsec.
(ghc-wl-pprint-text)[inputs]: Remove ghc-text.
(ghc-graphviz)[inputs]: Same.
(ghc-system-filepath-bootstrap)[inputs]: Same.
(ghc-system-fileio-bootstrap)[inputs]: Same.
(ghc-shelly)[inputs]: Same.
(ghc-chell)[inputs]: Same.
(ghc-system-filepath)[inputs]: Same.
(ghc-system-fileio)[inputs]: Same.
(ghc-fsnotify)[inputs]: Same.
(ghc-json)[inputs]: Remove ghc-text and ghc-parsec.
(ghc-esqueleto)[inputs]: Remove ghc-text.
(shellcheck)[inputs]: Remove ghc-parsec.
(ghc-errors)[inputs]: Remove ghc-text.
(ghc-chunked-data)[inputs]: Same.
(ghc-uuid-types)[inputs]: Same.
(ghc-uuid)[inputs]: Same.
(ghc-rebase)[inputs]: Remove ghc-stm and ghc-text.
(ghc-foldl)[inputs]: Remove ghc-text.
(ghc-mono-traversable)[inputs]: Same.
(ghc-conduit-combinators)[inputs]: Same.
(ghc-aws)[inputs]: Same.
(ghc-stm-chans)[inputs]: Remove ghc-stm.
(ghc-monad-logger)[inputs]: Remove ghc-text and ghc-stm.
(ghc-shakespeare)[inputs]: Remove ghc-parsec and ghc-text.
(ghc-resource-pool)[inputs]: Remove ghc-stm.
(ghc-attoparsec-iso8601)[inputs]: Remove ghc-text.
(ghc-http-api-data)[inputs]: Same.
(ghc-persistent)[inputs]: Same.
(ghc-aeson-compat)[inputs]: Same.
(ghc-persistent-template)[inputs]: Same.
(ghc-unliftio)[inputs]: Remove ghc-stm.
(ghc-persistent-sqlite)[native-inputs]: Remove ghc-text.
(ghc-bytes)[inputs]: Same.
(ghc-missingh)[inputs]: Remove ghc-parsec.
(ghc-rio)[inputs]: Remove ghc-text.
(ghc-cairo)[inputs]: Same.
(ghc-atomic-write)[inputs]: Remove ghc-text.
[native-inputs]: Same.
(ghc-stm-conduit)[inputs]: Remove ghc-stm.
(ghc-conduit-algorithms)[inputs]: Same.
(ghc-interpolate)[native-inputs]: Remove ghc-text.
(ghc-hpack)[inputs]: Same.
(ghc-inline-c)[inputs]: Remove ghc-parsec.
(ghc-configurator)[inputs]: Remove ghc-text.
(ghc-c2hs)[native-inputs]: Same.
(ghc-libmpd)[inputs]: Same.
(ghc-concurrent-output)[inputs]: Remove ghc-stm.
* gnu/packages/idris.scm (idris)[inputs]: Remove ghc-text.
* gnu/packages/wm.scm (xmobar)[inputs]: Remove ghc-parsec and ghc-stm.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2019-08-07 22:05:29 -04:00
Robert Vollmert e07f765558
import: hackage: Update list of ghc-included packages. 
It turns out the list in the release notes is incomplete.
This updates the list from /gnu/store/<hash>-ghc-8.4.3/lib/ghc-8.4.3.

* guix/import/hackage.scm (ghc-standard-libraries): Update list.
 2019-08-07 22:05:29 -04:00
Robert Vollmert cce84c34cd
gnu: Add ghc-8.6. 
* gnu/packages/haskell.scm (ghc-8.6): New variable.

Co-authored-by: Timothy Sample <samplet@ngyro.com>
 2019-08-07 22:05:29 -04:00