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Author SHA1 Message Date
Carlo Zancanaro 588a0a335d
gnu: Blender: Use opensubdiv. 
Fixes <https://bugs.gnu.org/36977>.

* gnu/packages/graphics.scm (blender)[inputs]: Add opensubdiv.
[arguments]: Add "-DWITH_OPENSUBDIV=ON" to #:configure-flags.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2019-08-13 14:43:42 -04:00
Carlo Zancanaro 13f30b546d
gnu: Add opensubdiv. 
* gnu/packages/graphics.scm (opensubdiv): New variable.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2019-08-13 14:43:39 -04:00
Marius Bakke 1b1b006afd
Merge branch 'staging' 2019-08-13 18:51:12 +02:00
Marius Bakke fc34abf8c1
gnu: xapian: Update to 1.4.12. 
* gnu/packages/search.scm (xapian, python-xapian-bindings): Update to 1.4.12.
 2019-08-13 18:40:55 +02:00
Marius Bakke da926c2503
gnu: ccid: Update to 1.4.31. 
* gnu/packages/security-token.scm (ccid): Update to 1.4.31.
 2019-08-13 18:40:55 +02:00
Marius Bakke ecfdc95a72
gnu: zathura-pdf-mupdf: Update to 0.3.5. 
* gnu/packages/pdf.scm (zathura-pdf-mupdf): Update to 0.3.5.
 2019-08-13 18:40:54 +02:00
Marius Bakke d08dc99fad
gnu: mupdf: Update to 1.16.1. 
* gnu/packages/pdf.scm (mupdf): Update to 1.16.1.
 2019-08-13 18:40:54 +02:00
Tobias Geerinckx-Rice ecab5e3529
gnu: git: Update to 2.22.1. 
* gnu/packages/version-control.scm (git): Update to 2.22.1.
 2019-08-13 17:09:10 +02:00
Leo Famulari 55fe9abdcc
gnu: tremc: Update to 0.9.1-0.4d50dab. 
* gnu/packages/bittorrent.scm (tremc): Update to 0.9.1-0.4d50dab.
 2019-08-13 11:03:27 -04:00
Nicolas Goaziou 1ae2d3a11b
gnu: emacs-relint: Update to 1.10. 
* gnu/packages/emacs-xyz.scm (emacs-relint): Update to 1.10.
 2019-08-13 12:52:47 +02:00
Nicolas Goaziou 77bdfe2f13
gnu: scribus: Update to 1.5.5. 
* gnu/packages/scribus.scm (scribus): Update to 1.5.5.
[source]: Remove unnecessary patches and snippet.
[description]: Change freetype to FreeType.
* gnu/packages/patches/scribus-poppler.patch: Remove file.
* gnu/local.mk: Apply removal.
 2019-08-13 12:44:06 +02:00
Amin Bandali f9ccde2460
gnu: Add emacs-ebdb. 
* gnu/packages/emacs-xyz.scm (emacs-ebdb): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2019-08-13 12:18:52 +02:00
Brian Leung 39a6852acb
gnu: emacs-inf-ruby: Update to 2.5.2. 
* gnu/packages/emacs-xyz.scm (emacs-inf-ruby): Update to 2.5.2.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2019-08-13 12:13:20 +02:00
Leo Famulari a797e55ca0
gnu: Syncthing: Update to 1.2.1. 
* gnu/packages/syncthing.scm (syncthing): Update to 1.2.1.
 2019-08-12 16:23:12 -04:00
Leo Famulari e9a0e4756f
gnu: go-github-com-syncthing-notify: Update to 0.0.0-5.69c7a95. 
* gnu/packages/syncthing.scm (go-github-com-syncthing-notify): Update to
0.0.0-5.69c7a95.
 2019-08-12 16:23:12 -04:00
Leo Famulari 158e82933c
gnu: go-github-com-lib-pq: Update to 1.2.0. 
* gnu/packages/syncthing.scm (go-github-com-lib-pq): Update to 1.2.0.
 2019-08-12 16:23:12 -04:00
Leo Famulari e7189e0bff
gnu: go-github-com-maruel-panicparse: Update to 1.3.0. 
* gnu/packages/golang.scm (go-github-com-maruel-panicparse): Update to 1.3.0.
 2019-08-12 16:23:11 -04:00
Leo Famulari 8a5073461f
gnu: go-golang-org-x-sys-unix: Update to 0.0.0-4.04f50cd. 
* gnu/packages/golang.scm (go-golang-org-x-sys-unix): Update to 0.0.0-4.04f50cd.
 2019-08-12 16:23:11 -04:00
Leo Famulari 6df4e6899d
gnu: MPD: Update to 0.21.13. 
* gnu/packages/mpd.scm (mpd): Update to 0.21.13.
 2019-08-12 16:21:52 -04:00
Leo Famulari 89ccc9ce91
gnu: dav1d: Update to 0.4.0. 
* gnu/packages/video.scm (dav1d): Update to 0.4.0.
 2019-08-12 16:21:49 -04:00
Nicolas Goaziou 57939283c0
gnu: mame: Fix build. 
* gnu/packages/emulators.scm (mame): Apply upstream patch.
* gnu/packages/patches/mame-rapidjson-fix.patch: New file.
* gnu/local.mk: Register file.
 2019-08-12 15:39:59 +02:00
Efraim Flashner c9093d2794
gnu: Add rust-winapi. 
* gnu/packages/crates-io.scm (rust-winapi): New variable.
 2019-08-12 11:57:33 +03:00
Efraim Flashner 07631e31b1
gnu: Add rust-winapi-x86-64-pc-windows-gnu. 
* gnu/packages/crates-io.scm (rust-winapi-x86-64-pc-windows-gnu): New
variable.
 2019-08-12 11:57:33 +03:00
Efraim Flashner 58fdf6e1f2
gnu: Add rust-winapi-i686-pc-windows-gnu. 
* gnu/packages/crates-io.scm (rust-winapi-i686-pc-windows-gnu): New
variable.
 2019-08-12 11:57:33 +03:00
Efraim Flashner 2a13c9fa5c
gnu: Add rust-wasm-bindgen-shared. 
* gnu/packages/crates-io.scm (rust-wasm-bindgen-shared): New variable.
 2019-08-12 11:57:33 +03:00
Efraim Flashner ede033176a
gnu: Add rust-unindent. 
* gnu/packages/crates-io.scm (rust-unindent): New variable.
 2019-08-12 11:57:32 +03:00
Efraim Flashner 96bb8fd065
gnu: Add rust-unicode-width. 
* gnu/packages/crates-io.scm (rust-unicode-width): New variable.
 2019-08-12 11:57:32 +03:00
Efraim Flashner f706f5dcf0
gnu: Add rust-ucd-util. 
* gnu/packages/crates-io.scm (rust-ucd-util): New variable.
 2019-08-12 11:57:32 +03:00
Efraim Flashner 92a292f14f
gnu: Add rust-typenum. 
* gnu/packages/crates-io.scm (rust-typenum): New variable.
 2019-08-12 11:57:31 +03:00
Efraim Flashner eca548232c
gnu: Add rust-synstructure-test-traits. 
* gnu/packages/crates-io.scm (rust-synstructure-test-traits): New
variable.
 2019-08-12 11:57:31 +03:00
Efraim Flashner 3ded5e3f70
gnu: Add rust-strsim. 
* gnu/packages/crates-io.scm (rust-strsim): New variable.
 2019-08-12 11:57:31 +03:00
Efraim Flashner 0d601e3860
gnu: Add rust-stdweb-internal-runtime. 
* gnu/packages/crates-io.scm (rust-stdweb-internal-runtime): New
variable.
 2019-08-12 11:57:31 +03:00
Efraim Flashner a60f26b24d
gnu: Add rust-spin. 
* gnu/packages/crates-io.scm (rust-spin): New variable.
 2019-08-12 11:57:30 +03:00
Efraim Flashner b158738a04
gnu: Add rust-slab. 
* gnu/packages/crates-io.scm (rust-slab): New variable.
 2019-08-12 11:57:30 +03:00
Efraim Flashner 9cbb0c97ce
gnu: Add rust-shlex. 
* gnu/packages/crates-io.scm (rust-shlex): New variable.
 2019-08-12 11:57:30 +03:00
Efraim Flashner b7ca017ad3
gnu: Add rust-semver-parser. 
* gnu/packages/crates-io.scm (rust-semver-parser): New variable.
 2019-08-12 11:57:29 +03:00
Efraim Flashner ac3e813b84
gnu: Add rust-scopeguard. 
* gnu/packages/crates-io.scm (rust-scopeguard): New variable.
 2019-08-12 11:57:29 +03:00
Efraim Flashner cbfef1f903
gnu: Add rust-scoped-tls. 
* gnu/packages/crates-io.scm (rust-scoped-tls): New variable.
 2019-08-12 11:57:29 +03:00
Efraim Flashner f6a1efbca4
gnu: Add rust-rustc-std-workspace-core. 
* gnu/packages/crates-io.scm (rust-rustc-std-workspace-core): New
variable.
 2019-08-12 11:57:29 +03:00
Efraim Flashner dea7871742
gnu: Add rust-quick-error. 
* gnu/packages/crates-io.scm (rust-quick-error): New variable.
 2019-08-12 11:57:28 +03:00
Efraim Flashner 3bb3a9a021
gnu: Add rust-ppv-lite86. 
* gnu/packages/crates-io.scm (rust-ppv-lite86): New variable.
 2019-08-12 11:57:28 +03:00
Efraim Flashner b7d218d8cb
gnu: Add rust-pocket-resources. 
* gnu/packages/crates-io.scm (rust-pocket-resources): New variable.
 2019-08-12 11:57:28 +03:00
Efraim Flashner b1c3b9e73b
gnu: Add rust-plain. 
* gnu/packages/crates-io.scm (rust-plain): New variable.
 2019-08-12 11:57:27 +03:00
Efraim Flashner b275df9cd3
gnu: Add rust-pin-utils. 
* gnu/packages/creates-io.scm (rust-pin-utils): New variable.
 2019-08-12 11:57:27 +03:00
Efraim Flashner e11365fdad
gnu: Add rust-percent-encoding. 
* gnu/packages/creates-io.scm (rust-percent-encoding): New variable.
 2019-08-12 11:57:27 +03:00
Efraim Flashner f22f05d901
gnu: Add rust-peeking-take-while. 
* gnu/packages/crates-io.scm (rust-peeking-take-while): New variable.
 2019-08-12 11:57:27 +03:00
Efraim Flashner 0c6759d87e
gnu: Add rust-md5. 
* gnu/packages/creates-io.scm (rust-md5): New variable.
 2019-08-12 11:57:26 +03:00
Efraim Flashner e7ffbe2fda
gnu: Add rust-matches. 
* gnu/packages/crates-io.scm (rust-matches): New variable.
 2019-08-12 11:57:26 +03:00
Efraim Flashner 9c6301319e
gnu: Add rust-maplit. 
* gnu/packages/creates-io.scm (rust-maplit): New variable.
 2019-08-12 11:57:26 +03:00
Efraim Flashner bfe256ba2c
gnu: Add rust-json. 
* gnu/packages/creates-io.scm (rust-json): New variable.
 2019-08-12 11:57:25 +03:00
Efraim Flashner 81749732dd
gnu: Add rust-itoa. 
* gnu/packages/creates-io.scm (rust-itoa): New variable.
 2019-08-12 11:57:25 +03:00
Efraim Flashner 1d5c422c4a
gnu: Add rust-hex. 
* gnu/packages/crates-io.scm (rust-hex): New variable.
 2019-08-12 11:57:25 +03:00
Efraim Flashner 1956ba239c
gnu: Add rust-futures. 
* gnu/packages/crates-io.scm (rust-futures): New variable.
 2019-08-12 11:57:25 +03:00
Efraim Flashner 6b69f9f4e3
gnu: Add rust-fs-extra. 
* gnu/packages/creates-io.scm (rust-fs-extra): New variable.
 2019-08-12 11:57:24 +03:00
Efraim Flashner 1816930430
gnu: Add rust-fnv. 
* gnu/packages/crates-io.scm (rust-fnv): New variable.
 2019-08-12 11:57:24 +03:00
Efraim Flashner 7469d541df
gnu: Add rust-fallible-iterator. 
* gnu/packages/crates-io.scm (rust-fallible-iterator): New variable.
 2019-08-12 11:57:24 +03:00
Efraim Flashner f3739ec0c1
gnu: Add rust-dtoa. 
* gnu/packages/crates-io.scm (rust-dtoa): New variable.
 2019-08-12 11:57:23 +03:00
Efraim Flashner f0b9ffcdee
gnu: Add rust-doc-comment. 
* gnu/packages/crates-io.scm (rust-doc-comment): New variable.
 2019-08-12 11:57:23 +03:00
Efraim Flashner b977128212
gnu: Add rust-discard. 
* gnu/packages/crates-io.scm (rust-discard): New variable.
 2019-08-12 11:57:23 +03:00
Efraim Flashner f69bf22334
gnu: Add rust-cfg-if. 
* gnu/packages/crates-io.scm (rust-cfg-if): New variable.
 2019-08-12 11:57:22 +03:00
Efraim Flashner dcc0069932
gnu: Add rust-bitflags. 
* gnu/packages/crates-io.scm (rust-bitflags): New variable.
 2019-08-12 11:57:22 +03:00
Efraim Flashner 242668bdbd
gnu: Add rust-bencher. 
* gnu/packages/crates-io.scm (rust-bencher): New variable.
 2019-08-12 11:57:22 +03:00
Efraim Flashner 060958949a
gnu: Add rust-autocfg. 
* gnu/packages/crates-io.scm (rust-autocfg): New variable.
 2019-08-12 11:57:22 +03:00
Efraim Flashner 96c71bffaa
gnu: crates-io.scm: Sort packages alphabetically. 
* gnu/packages/crates-io.scm: Sort packages alphabetically.
 2019-08-12 11:57:21 +03:00
Efraim Flashner 513a66c932
gnu: vifm: Re-indent package. 
* gnu/packages/vim.scm (vifm)[arguments]: Re-indent section.
 2019-08-12 11:56:55 +03:00
Efraim Flashner b4bd0d86a8
gnu: vifm: Update to 0.10.1. 
* gnu/packages/vim.scm (vifm): Update to 0.10.1.
 2019-08-12 11:56:55 +03:00
Ricardo Wurmus fdc22edb6c
gnu: r-ggplot2: Update to 3.2.1. 
* gnu/packages/statistics.scm (r-ggplot2): Update to 3.2.1.
 2019-08-12 10:25:29 +02:00
Ricardo Wurmus 813b7210aa
gnu: r-with-tests: Update to 3.6.1. 
* gnu/packages/statistics.scm (r-with-tests): Update to 3.6.1.
 2019-08-12 10:25:29 +02:00
Efraim Flashner e203e57b8a
gnu: font-gnu-unifont: Update to 12.1.03. 
* gnu/packages/fonts.scm (font-gnu-unifont): Update to 12.1.03.
 2019-08-12 11:22:40 +03:00
Marius Bakke da7e59ac41
gnu: ungoogled-chromium: Update to 76.0.3809.100-0.8eba5c0 [security fixes]. 
This release fixes CVE-2019-5867 and CVE-2019-5868.

* gnu/packages/chromium.scm (%chromium-version): Set to 76.0.3809.100.
(%ungoogled-revision): Set to 8eba5c0.
(%chromium-origin, %ungoogled-origin): Update hashes.
 2019-08-12 01:50:43 +02:00
Nicolas Goaziou 049915a961
gnu: mame: Update to 0.212. 
* gnu/packages/emulators.scm (mame): Update to 0.212.
 2019-08-11 23:07:20 +02:00
Tobias Geerinckx-Rice c383c36ede
gnu: openconnect: Update to 8.04. 
* gnu/packages/vpn.scm (openconnect): Update to 8.04.
 2019-08-11 19:43:02 +02:00
Mark H Weaver ffb7e5a8e4
gnu: linux-libre@4.9: Update to 4.9.189. 
* gnu/packages/linux.scm (linux-libre-4.9-version): Update to 4.9.189.
(linux-libre-4.9-pristine-source)[hash]: Update hash.
 2019-08-11 13:14:59 -04:00
Mark H Weaver 5e1ab622d9
gnu: linux-libre@4.4: Update to 4.4.189. 
* gnu/packages/linux.scm (linux-libre-4.4-version): Update to 4.4.189.
(linux-libre-4.4-pristine-source)[hash]: Update hash.
 2019-08-11 13:14:05 -04:00
Vagrant Cascadian fae0a777dc
gnu: Update electrum to 3.3.8. 
* gnu/packages/finance (electrum): Update to 3.3.8.
 2019-08-11 08:42:10 -07:00
Vagrant Cascadian c91364d36c
gnu: diffoscope: Update to 120. 
* gnu/packages/package-management (diffoscope): Update to 120.
 2019-08-11 07:45:25 -07:00
Marius Bakke 5e5cdac0ae
Revert "gnu: python-packaging: Update to 19.1." 
The new version fails tests on architectures other than x86_64.

This reverts commit cb16a9fba9.
 2019-08-11 14:58:14 +02:00
Mark H Weaver dbc3f1f8b2
gnu: linux-libre: Update to 5.2.8. 
* gnu/packages/linux.scm (linux-libre-5.2-version): Update to 5.2.8.
(linux-libre-5.2-pristine-source)[hash]: Update hash.
 2019-08-09 14:22:06 -04:00
Mark H Weaver f16109ccef
gnu: linux-libre@4.19: Update to 4.19.66. 
* gnu/packages/linux.scm (linux-libre-4.19-version): Update to 4.19.66.
(linux-libre-4.19-pristine-source)[hash]: Update hash.
 2019-08-09 14:21:21 -04:00
Mark H Weaver 55ebb3ebf6
gnu: linux-libre@4.14: Update to 4.14.138. 
* gnu/packages/linux.scm (linux-libre-4.14-version): Update to 4.14.138.
(linux-libre-4.14-pristine-source)[hash]: Update hash.
 2019-08-09 14:20:12 -04:00
Brian Leung d51f20f9b8
gnu: emacs-deadgrep: Update to 0.8-1.329119c. 
* gnu/packages/emacs-xyz.scm (emacs-deadgrep): Update to 0.8-1.329119c.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2019-08-09 16:32:59 +02:00
Nicolas Goaziou b22e47a1aa
gnu: emacs-xr: Update to 1.13. 
* gnu/packages/emacs-xyz.scm (emacs-xr): Update to 1.13.
 2019-08-09 16:29:21 +02:00
Ricardo Wurmus e33e3a14c5
gnu: r-xml2: Update to 1.2.2. 
* gnu/packages/statistics.scm (r-xml2): Update to 1.2.2.
 2019-08-09 16:03:50 +02:00
Ricardo Wurmus 3ea548290a
gnu: r-ggforce: Update to 0.3.0. 
* gnu/packages/cran.scm (r-ggforce): Update to 0.3.0.
[propagated-inputs]: Add r-tidyselect and r-withr.
 2019-08-09 16:03:34 +02:00
Ricardo Wurmus 179ab67ace
gnu: r-tidytree: Update to 0.2.6. 
* gnu/packages/cran.scm (r-tidytree): Update to 0.2.6.
 2019-08-09 16:03:23 +02:00
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
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 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
Robert Vollmert a62ddb748f
gnu: ghc-8: Rename to 'ghc-8.4'. 
* gnu/packages/haskell.scm (ghc-8): Rename to...
(ghc-8.4): ...this.
(ghc-8): New variable.
 2019-08-07 22:05:23 -04:00
Marius Bakke 8e7f97b9ff
Merge branch 'master' into staging 2019-08-08 00:35:37 +02:00
Marius Bakke ba7ff983d6
gnu: wpa-supplicant: Update to 2.9. 
* gnu/packages/admin.scm (wpa-supplicant-minimal): Update to 2.9.
 2019-08-08 00:30:56 +02:00
Marius Bakke 277faff8ff
gnu: xf86-video-intel: Update to 2.99.917-14.6f4972d. 
* gnu/packages/xorg.scm (xf86-video-intel): Update to 2.99.917-14.6f4972d.
 2019-08-08 00:30:56 +02:00
Jakob L. Kreuze d84e9b75b2
machine: Add 'build-locally?' field for managed hosts. 
* gnu/machine/ssh.scm (machine-ssh-configuration-build-locally?): New
variable.
(managed-host-remote-eval): Pass 'build-locally?' to 'remote-eval'.
 2019-08-07 18:29:07 -04:00
Ricardo Wurmus 9bd1333e58
Merge remote-tracking branch 'origin/master' into wip-texlive 2019-08-07 22:26:55 +02:00
Marius Bakke fa228db78b
gnu: mesa: Update to 19.1.4. 
* gnu/packages/gl.scm (mesa): Update to 19.1.4.
 2019-08-07 22:07:41 +02:00
Jakob L. Kreuze ec12235ce2
reconfigure: Improve tests for system activation. 
* gnu/tests/reconfigure.scm (run-switch-to-system-test): Assert that
'/run/current-system' points to the activated system, and that new user
accounts specified in the operating system declaration are created.
 2019-08-07 15:27:09 -04:00
Efraim Flashner 355ba48c46
gnu: igt-gpu-tools: Rework custom phases. 
* gnu/packages/admin.scm (igt-gpu-tools)[arguments]: Use custom 'autogen
phase to replace 'bootstrap phase.
 2019-08-07 20:06:01 +03:00
Efraim Flashner 72bc58f850
gnu: dosbox: Remove extra build phase. 
* gnu/packages/emulators.scm (dosbox)[arguments]: Remove unneeded
'autogen phase.
 2019-08-07 20:06:00 +03:00
Efraim Flashner 3192f25948
gnu: zimg: Remove extra build phase. 
* gnu/packages/image.scm (zimg)[arguments]: Remove unneeded 'autogen
phase.
 2019-08-07 20:06:00 +03:00
Efraim Flashner 384242adf1
gnu: leptonica: Remove extra build phase. 
* gnu/packages/image.scm (leptonica)[arguments]: Remove unneeded
'autogen phase.
 2019-08-07 20:06:00 +03:00
Efraim Flashner a491856f2a
gnu: ghmm: Remove extra build phase. 
* gnu/packages/machine-learning.scm (ghmm)[arguments]: Remove unneeded
'autogen phase.
 2019-08-07 20:05:59 +03:00
Efraim Flashner e3a699380e
gnu: ghmm: Update source file-name field. 
* gnu/packages/machine-learning.scm (ghmm)[source]: Change 'file-name
field to include '-checkout' string.
 2019-08-07 20:05:59 +03:00
Efraim Flashner 1f53fdae82
gnu: dovecot-libsodium-plugin: Remove extra build phase. 
* gnu/packages/mail.scm (dovecot-libsodium-plugin)[arguments]: Remove
unneeded 'autogen phase.
 2019-08-07 20:05:59 +03:00
Efraim Flashner 7b0efd4c32
gnu: dovecot-trees: Remove extra build phase. 
* gnu/packages/mail.scm (dovecot-trees)[arguments]: Remove unneeded
'autogen phase.
 2019-08-07 20:05:58 +03:00
Efraim Flashner 02abfcca46
gnu: libetpan: Rework custom phases. 
* gnu/packages/mail.scm (libetpan)[arguments]: Use custom 'autogen phase
to replace 'boostrap phase.
 2019-08-07 20:05:58 +03:00
Efraim Flashner 1d05b683ef
gnu: libmediainfo: Remove extra build phase. 
* gnu/packages/video.scm (libmediainfo)[arguments]: Remove unneeded
'autogen phase.
 2019-08-07 20:05:58 +03:00
Efraim Flashner d05e607c9d
gnu: libsmpeg: Remove extra build phase. 
* gnu/packages/video.scm (libsmpeg)[arguments]: Remove unnecessary
'autogen phase.
 2019-08-07 20:05:57 +03:00
Efraim Flashner 2230039427
gnu: vapoursynth: Remove extra build phase. 
* gnu/packages/video.scm (vapoursynth)[arguments]: Remove unneeded
'autogen phase.
 2019-08-07 20:05:57 +03:00
Efraim Flashner fe7023a744
gnu: i3blocks: Remove extra build phase. 
* gnu/packages/wm.scm (i3blocks)[arguments]: Remove unneeded 'autogen
phase.
 2019-08-07 20:05:57 +03:00
Efraim Flashner db736ca20c
gnu: ocproxy: Remove extra build phase. 
* gnu/packages/vpn.scm (ocproxy)[arguments]: Remove unneeded 'autogen
phase.
 2019-08-07 20:05:57 +03:00
Efraim Flashner 0d7f282b02
gnu: openconnect: Fix propagated-inputs. 
* gnu/packages/vpn.scm (openconnect)[inputs]: Move libxml2, gnutls,
zlib ...
[propagated-inputs]: ... to here.
 2019-08-07 20:05:56 +03:00
Ricardo Wurmus 9fa7c20be9
gnu: gnome-maps: Fix runtime error. 
Fixes <https://bugs.gnu.org/35761>.

* gnu/packages/geo.scm (gnome-maps)[arguments]: Add lib output of
gnome-online-accounts and geocode-glib to LD_LIBRARY_PATH.
[inputs]: Add gnome-online-accounts:lib.
 2019-08-07 19:03:19 +02:00
Ricardo Wurmus fdc0688cba
gnu: r-dt: Update to 0.8. 
* gnu/packages/statistics.scm (r-dt): Update to 0.8.
[propagated-inputs]: Add r-jsonlite.
 2019-08-07 12:54:43 +02:00
Ricardo Wurmus 42a8b01d15
gnu: r-epi: Update to 2.38. 
* gnu/packages/cran.scm (r-epi): Update to 2.38.
 2019-08-07 12:54:43 +02:00
Ricardo Wurmus 2132e92261
gnu: r-ggpubr: Update to 0.2.2. 
* gnu/packages/cran.scm (r-ggpubr): Update to 0.2.2.
[propagated-inputs]: Add r-rlang.
 2019-08-07 12:54:43 +02:00
Ricardo Wurmus 33af00eea4
gnu: r-tinytex: Update to 0.15. 
* gnu/packages/cran.scm (r-tinytex): Update to 0.15.
 2019-08-07 12:54:43 +02:00
Ricardo Wurmus f503ed92d2
gnu: r-servr: Update to 0.15. 
* gnu/packages/cran.scm (r-servr): Update to 0.15.
 2019-08-07 12:54:43 +02:00
Rutger Helling 18e700517e
gnu: dolphin-emu: Update to commit 24718c1. 
* gnu/packages/emulators.scm (dolphin-emu): Update to commit 24718c1.
 2019-08-07 08:15:28 +02:00
Mark H Weaver 9d52e3f3d5
gnu: linux-libre: Update to 5.2.7. 
* gnu/packages/linux.scm (linux-libre-5.2-version): Update to 5.2.7.
(linux-libre-5.2-pristine-source)[hash]: Update hash.
 2019-08-07 00:28:32 -04:00
Mark H Weaver 9f90e58c4a
gnu: linux-libre@4.19: Update to 4.19.65. 
* gnu/packages/linux.scm (linux-libre-4.19-version): Update to 4.19.65.
(linux-libre-4.19-pristine-source)[hash]: Update hash.
 2019-08-07 00:28:30 -04:00
Mark H Weaver 7acea31bbc
gnu: linux-libre@4.14: Update to 4.14.137. 
* gnu/packages/linux.scm (linux-libre-4.14-version): Update to 4.14.137.
(linux-libre-4.14-pristine-source)[hash]: Update hash.
 2019-08-07 00:28:28 -04:00
Mark H Weaver 2b6c7a7cbc
gnu: linux-libre@4.9: Update to 4.9.188. 
* gnu/packages/linux.scm (linux-libre-4.9-version): Update to 4.9.188.
(linux-libre-4.9-pristine-source)[hash]: Update hash.
 2019-08-07 00:28:12 -04:00
Mark H Weaver ad6814557e
gnu: linux-libre@4.4: Update to 4.4.188. 
* gnu/packages/linux.scm (linux-libre-4.4-version): Update to 4.4.188.
(linux-libre-4.4-pristine-source)[hash]: Update hash.
 2019-08-07 00:23:20 -04:00
Ricardo Wurmus f2758945fe
gnu: r-ggplotify: Update to 0.0.4. 
* gnu/packages/cran.scm (r-ggplotify): Update to 0.0.4.
 2019-08-06 23:38:22 +02:00
Ricardo Wurmus 5fe9ce982d
gnu: r-bayestestr: Update to 0.2.5. 
* gnu/packages/cran.scm (r-bayestestr): Update to 0.2.5.
 2019-08-06 23:38:22 +02:00
Jakob L. Kreuze fd3119db4f
machine: Implement safety checks. 
* gnu/machine/ssh.scm (machine-check-file-system-availability)
(machine-check-initrd-modules, check-deployment-sanity): New variable.
(deploy-managed-host): Perform safety checks before deploying.
 2019-08-06 16:40:25 -04:00
Jakob L. Kreuze d97ce20400
machine: Rename 'system' field. 
* gnu/machine.scm (machine-system): Delete variable.
(machine-operating-system): New variable.
All callers changed.
* doc/guix.texi (Invoking guix deploy): Use the
'machine-operating-system' accessor rather than 'machine-system'.
 2019-08-06 15:48:51 -04:00
Christopher Baines ec405a4b01
gnu: perl-hash-merge: Change inputs to propagated-inputs. 
Clone::Choose is required at runtime, so this input needs to be
propagated. This change fixes the sqitch package.

* gnu/packages/perl.scm (perl-hash-merge)[inputs]: Change to
propagated-inputs.
 2019-08-06 19:53:51 +01:00
Rutger Helling 86445c8e35
gnu: ffmpeg: Update to 4.2. 
* gnu/packages/video.scm (ffmpeg): Update to 4.2.
[inputs]: Add dav1d.
* gnu/packages/video.scm (ffmpeg-3.4)[arguments]: Adjust inheritance.
 2019-08-06 18:59:28 +02:00
Marius Bakke 58e37b5441
gnu: nss: Fix build failure on armhf-linux. 
Fixes <https://bugs.gnu.org/36930>.

* gnu/packages/patches/nss-freebl-stubs.patch: New file.
* gnu/local.mk (dist_patch_DATA): Adjust accordingly.
* gnu/packages/nss.scm (nss)[source](patches): Add it.
 2019-08-06 17:06:57 +02:00
Ricardo Wurmus b120789193
gnu: r-rsubread: Update to 1.34.6. 
* gnu/packages/bioconductor.scm (r-rsubread): Update to 1.34.6.
 2019-08-06 15:49:00 +02:00
Ricardo Wurmus d6158ecb3b
gnu: r-abaenrichment: Update to 1.14.1. 
* gnu/packages/bioconductor.scm (r-abaenrichment): Update to 1.14.1.
 2019-08-06 15:49:00 +02:00
Ricardo Wurmus fbe5a0872f
gnu: r-atacseqqc: Update to 1.8.5. 
* gnu/packages/bioconductor.scm (r-atacseqqc): Update to 1.8.5.
 2019-08-06 15:49:00 +02:00
Ricardo Wurmus fcbd8960c2
gnu: r-genomicinteractions: Update to 1.18.1. 
* gnu/packages/bioconductor.scm (r-genomicinteractions): Update to 1.18.1.
 2019-08-06 15:49:00 +02:00
Ricardo Wurmus 109b8ad5f9
gnu: r-chippeakanno: Update to 3.18.2. 
* gnu/packages/bioconductor.scm (r-chippeakanno): Update to 3.18.2.
 2019-08-06 15:49:00 +02:00
Ricardo Wurmus c8e141ab02
gnu: r-msnid: Update to 1.18.1. 
* gnu/packages/bioinformatics.scm (r-msnid): Update to 1.18.1.
 2019-08-06 15:49:00 +02:00
Ricardo Wurmus afe4be49f1
gnu: r-rcas: Update to 1.10.1. 
* gnu/packages/bioinformatics.scm (r-rcas): Update to 1.10.1.
 2019-08-06 15:49:00 +02:00
Ricardo Wurmus 76d9b08e1b
gnu: r-genomicfeatures: Update to 1.36.4. 
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.36.4.
 2019-08-06 15:48:59 +02:00
Ricardo Wurmus e16fe0b50a
gnu: r-rtracklayer: Update to 1.44.2. 
* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.44.2.
 2019-08-06 15:48:59 +02:00
Ricardo Wurmus 6f8760d9f8
gnu: r-summarizedexperiment: Update to 1.14.1. 
* gnu/packages/bioinformatics.scm (r-summarizedexperiment): Update to 1.14.1.
 2019-08-06 15:48:59 +02:00
Ricardo Wurmus 2ebd2b440d
gnu: r-biomart: Update to 2.40.3. 
* gnu/packages/bioinformatics.scm (r-biomart): Update to 2.40.3.
 2019-08-06 15:48:59 +02:00
Ricardo Wurmus fbd761fe9b
gnu: r-limma: Update to 3.40.6. 
* gnu/packages/bioinformatics.scm (r-limma): Update to 3.40.6.
 2019-08-06 15:48:59 +02:00
Ricardo Wurmus 8a5f9d3d56
gnu: r-edger: Update to 3.26.6. 
* gnu/packages/bioinformatics.scm (r-edger): Update to 3.26.6.
 2019-08-06 15:48:59 +02:00
Ricardo Wurmus 00300de5d0
gnu: r-xgboost: Update to 0.90.0.2. 
* gnu/packages/cran.scm (r-xgboost): Update to 0.90.0.2.
 2019-08-06 15:48:59 +02:00
Ricardo Wurmus 6fa5987606
gnu: r-citr: Update to 0.3.1. 
* gnu/packages/cran.scm (r-citr): Update to 0.3.1.
[propagated-inputs]: Remove r-bibtex.
 2019-08-06 15:48:59 +02:00
Ricardo Wurmus 5b87fae3f8
gnu: r-enrichr: Update to 2.0. 
* gnu/packages/cran.scm (r-enrichr): Update to 2.0.
 2019-08-06 15:48:59 +02:00
Ricardo Wurmus 006c3dc386
gnu: r-dalex: Update to 0.4.4. 
* gnu/packages/cran.scm (r-dalex): Update to 0.4.4.
 2019-08-06 15:48:58 +02:00
Ricardo Wurmus 22d556a8e1
gnu: r-bookdown: Update to 0.12. 
* gnu/packages/cran.scm (r-bookdown): Update to 0.12.
 2019-08-06 15:48:58 +02:00
Ricardo Wurmus 1a88de187b
gnu: r-ldheatmap: Update to 0.99-7. 
* gnu/packages/cran.scm (r-ldheatmap): Update to 0.99-7.
[propagated-inputs]: Add r-rcpp.
 2019-08-06 15:48:58 +02:00
Ricardo Wurmus 2deb1529a2
gnu: r-sf: Update to 0.7-7. 
* gnu/packages/cran.scm (r-sf): Update to 0.7-7.
 2019-08-06 15:48:58 +02:00
Ricardo Wurmus 4eed03ea41
gnu: r-deldir: Update to 0.1-23. 
* gnu/packages/cran.scm (r-deldir): Update to 0.1-23.
 2019-08-06 15:48:58 +02:00
Ricardo Wurmus 24d439868b
gnu: r-classint: Update to 0.4-1. 
* gnu/packages/cran.scm (r-classint): Update to 0.4-1.
 2019-08-06 15:48:58 +02:00
Ricardo Wurmus 8518744ec4
gnu: r-rematch2: Update to 2.1.0. 
* gnu/packages/cran.scm (r-rematch2): Update to 2.1.0.
 2019-08-06 15:48:58 +02:00
Ricardo Wurmus bd00835630
gnu: r-irkernel: Update to 1.0.2. 
* gnu/packages/cran.scm (r-irkernel): Update to 1.0.2.
 2019-08-06 15:48:58 +02:00
Ricardo Wurmus 51c9504ba6
gnu: r-lavaan: Update to 0.6-4. 
* gnu/packages/cran.scm (r-lavaan): Update to 0.6-4.
 2019-08-06 15:48:58 +02:00
Ricardo Wurmus 01629c665b
gnu: r-bayesm: Update to 3.1-3. 
* gnu/packages/cran.scm (r-bayesm): Update to 3.1-3.
 2019-08-06 15:48:57 +02:00
Ricardo Wurmus eebd93eb6b
gnu: r-rsvd: Update to 1.0.2. 
* gnu/packages/cran.scm (r-rsvd): Update to 1.0.2.
 2019-08-06 15:48:57 +02:00
Ricardo Wurmus d5d631b650
gnu: r-future: Update to 1.14.0. 
* gnu/packages/cran.scm (r-future): Update to 1.14.0.
 2019-08-06 15:48:57 +02:00
Ricardo Wurmus ffb97e695c
gnu: r-spatialextremes: Update to 2.0-7.2. 
* gnu/packages/cran.scm (r-spatialextremes): Update to 2.0-7.2.
 2019-08-06 15:48:57 +02:00
Ricardo Wurmus 504a51369f
gnu: r-bigrquery: Update to 1.2.0. 
* gnu/packages/cran.scm (r-bigrquery): Update to 1.2.0.
[propagated-inputs]: Add r-gargle and r-rlang.
 2019-08-06 15:48:57 +02:00
Ricardo Wurmus 6275418b6f
gnu: Add r-gargle. 
* gnu/packages/cran.scm (r-gargle): New variable.
 2019-08-06 15:48:57 +02:00
Ricardo Wurmus 031afc4890
gnu: r-shades: Update to 1.4.0. 
* gnu/packages/cran.scm (r-shades): Update to 1.4.0.
 2019-08-06 15:48:57 +02:00
Ricardo Wurmus 12618b5080
gnu: r-rnifti: Update to 0.11.1. 
* gnu/packages/cran.scm (r-rnifti): Update to 0.11.1.
 2019-08-06 15:48:57 +02:00
Ricardo Wurmus b154b02620
gnu: r-flare: Update to 1.6.0.2. 
* gnu/packages/cran.scm (r-flare): Update to 1.6.0.2.
 2019-08-06 15:48:57 +02:00
Ricardo Wurmus e0f20dce62
gnu: r-sparsesvd: Update to 0.2. 
* gnu/packages/cran.scm (r-sparsesvd): Update to 0.2.
 2019-08-06 15:48:57 +02:00
Ricardo Wurmus 14148ef1ee
gnu: r-tidytree: Update to 0.2.5. 
* gnu/packages/cran.scm (r-tidytree): Update to 0.2.5.
 2019-08-06 15:48:56 +02:00
Ricardo Wurmus ef93e90fae
gnu: r-rgl: Update to 0.100.26. 
* gnu/packages/cran.scm (r-rgl): Update to 0.100.26.
 2019-08-06 15:48:56 +02:00
Ricardo Wurmus 65555b1d08
gnu: r-afex: Update to 0.24-1. 
* gnu/packages/cran.scm (r-afex): Update to 0.24-1.
 2019-08-06 15:48:56 +02:00
Ricardo Wurmus 99765abb13
gnu: r-usethis: Update to 1.5.1. 
* gnu/packages/cran.scm (r-usethis): Update to 1.5.1.
 2019-08-06 15:48:56 +02:00
Ricardo Wurmus a5a64814b2
gnu: r-sjplot: Update to 2.7.0. 
* gnu/packages/cran.scm (r-sjplot): Update to 2.7.0.
[propagated-inputs]: Add r-ggrepel.
 2019-08-06 15:48:56 +02:00
Ricardo Wurmus 7343fa8ecb
gnu: r-ggeffects: Update to 0.11.0. 
* gnu/packages/cran.scm (r-ggeffects): Update to 0.11.0.
 2019-08-06 15:48:56 +02:00
Ricardo Wurmus 5ae4cbb656
gnu: r-performance: Update to 0.3.0. 
* gnu/packages/cran.scm (r-performance): Update to 0.3.0.
 2019-08-06 15:48:56 +02:00
Ricardo Wurmus 5357c59bf3
gnu: r-emmeans: Update to 1.4. 
* gnu/packages/cran.scm (r-emmeans): Update to 1.4.
 2019-08-06 15:48:56 +02:00
Ricardo Wurmus 332c8df6f0
gnu: r-magick: Update to 2.1. 
* gnu/packages/cran.scm (r-magick): Update to 2.1.
 2019-08-06 15:48:55 +02:00
Ricardo Wurmus 2634febacd
gnu: r-raster: Update to 2.9-23. 
* gnu/packages/cran.scm (r-raster): Update to 2.9-23.
 2019-08-06 15:48:55 +02:00
Ricardo Wurmus a510dc6091
gnu: r-proc: Update to 1.15.3. 
* gnu/packages/cran.scm (r-proc): Update to 1.15.3.
 2019-08-06 15:48:55 +02:00
Ricardo Wurmus 44de742e37
gnu: r-insight: Update to 0.4.1. 
* gnu/packages/cran.scm (r-insight): Update to 0.4.1.
 2019-08-06 15:48:55 +02:00
Ricardo Wurmus 72c967e2ea
gnu: r-abn: Update to 2.1. 
* gnu/packages/cran.scm (r-abn): Update to 2.1.
[propagated-inputs]: Remove r-cairo.
 2019-08-06 15:48:55 +02:00
Ricardo Wurmus c187e8f65d
gnu: r-factominer: Update to 1.42. 
* gnu/packages/cran.scm (r-factominer): Update to 1.42.
 2019-08-06 15:48:55 +02:00
Ricardo Wurmus 2d363778d4
gnu: r-reticulate: Update to 1.13. 
* gnu/packages/cran.scm (r-reticulate): Update to 1.13.
 2019-08-06 15:48:55 +02:00
Ricardo Wurmus e3abc134e8
gnu: r-dosnow: Update to 1.0.18. 
* gnu/packages/cran.scm (r-dosnow): Update to 1.0.18.
 2019-08-06 15:48:55 +02:00
Ricardo Wurmus cc7176cc2c
gnu: r-zip: Update to 2.0.3. 
* gnu/packages/cran.scm (r-zip): Update to 2.0.3.
 2019-08-06 15:48:55 +02:00
Ricardo Wurmus 9c69d79744
gnu: r-radiant-data: Update to 1.0.0. 
* gnu/packages/cran.scm (r-radiant-data): Update to 1.0.0.
 2019-08-06 15:48:54 +02:00
Ricardo Wurmus dbd3950a3f
gnu: r-shinyace: Update to 0.4.0. 
* gnu/packages/cran.scm (r-shinyace): Update to 0.4.0.
 2019-08-06 15:48:54 +02:00
Ricardo Wurmus 9f8f2d9b14
gnu: r-pillar: Update to 1.4.2. 
* gnu/packages/cran.scm (r-pillar): Update to 1.4.2.
 2019-08-06 15:48:54 +02:00
Ricardo Wurmus 56444d1852
gnu: r-vctrs: Update to 0.2.0. 
* gnu/packages/cran.scm (r-vctrs): Update to 0.2.0.
[propagated-inputs]: Add r-ellipsis.
 2019-08-06 15:48:54 +02:00
Ricardo Wurmus 503d5b5a75
gnu: r-processx: Update to 3.4.1. 
* gnu/packages/cran.scm (r-processx): Update to 3.4.1.
 2019-08-06 15:48:54 +02:00
Ricardo Wurmus 70980197aa
gnu: r-vioplot: Update to 0.3.2. 
* gnu/packages/cran.scm (r-vioplot): Update to 0.3.2.
 2019-08-06 15:48:54 +02:00
Ricardo Wurmus 83e3e72a30
gnu: r-hardyweinberg: Update to 1.6.3. 
* gnu/packages/cran.scm (r-hardyweinberg): Update to 1.6.3.
 2019-08-06 15:48:54 +02:00
Ricardo Wurmus 04d42a9de1
gnu: r-mice: Update to 3.6.0. 
* gnu/packages/cran.scm (r-mice): Update to 3.6.0.
 2019-08-06 15:48:54 +02:00
Ricardo Wurmus bed3424619
gnu: r-jomo: Update to 2.6-9. 
* gnu/packages/cran.scm (r-jomo): Update to 2.6-9.
 2019-08-06 15:48:54 +02:00
Ricardo Wurmus 417f7ed58d
gnu: r-recipes: Update to 0.1.6. 
* gnu/packages/cran.scm (r-recipes): Update to 0.1.6.
[propagated-inputs]: Remove r-rcpproll.
 2019-08-06 15:48:54 +02:00
Ricardo Wurmus a80620b96d
gnu: r-geometry: Update to 0.4.2. 
* gnu/packages/cran.scm (r-geometry): Update to 0.4.2.
[propagated-inputs]: Add r-linprog.
 2019-08-06 15:48:54 +02:00
Ricardo Wurmus f3640cee10
gnu: Add r-linprog. 
* gnu/packages/cran.scm (r-linprog): New variable.
 2019-08-06 15:48:53 +02:00
Ricardo Wurmus 099b7c55bb
gnu: r-lava: Update to 1.6.6. 
* gnu/packages/cran.scm (r-lava): Update to 1.6.6.
 2019-08-06 15:48:53 +02:00
Ricardo Wurmus 3337fd1dce
gnu: r-energy: Update to 1.7-6. 
* gnu/packages/cran.scm (r-energy): Update to 1.7-6.
 2019-08-06 15:48:53 +02:00
Ricardo Wurmus 80cdd36fe8
gnu: r-lpsolve: Update to 5.6.13.2. 
* gnu/packages/cran.scm (r-lpsolve): Update to 5.6.13.2.
 2019-08-06 15:48:53 +02:00
Ricardo Wurmus 4522ec869b
gnu: r-rcpp: Update to 1.0.2. 
* gnu/packages/cran.scm (r-rcpp): Update to 1.0.2.
 2019-08-06 15:48:53 +02:00
Ricardo Wurmus cd7e9fb161
gnu: r-pkgbuild: Update to 1.0.4. 
* gnu/packages/cran.scm (r-pkgbuild): Update to 1.0.4.
 2019-08-06 15:48:53 +02:00
Ricardo Wurmus b89805fe14
gnu: r-haven: Update to 2.1.1. 
* gnu/packages/cran.scm (r-haven): Update to 2.1.1.
 2019-08-06 15:48:53 +02:00
Ricardo Wurmus b44c12057b
gnu: r-curl: Update to 4.0. 
* gnu/packages/cran.scm (r-curl): Update to 4.0.
 2019-08-06 15:48:53 +02:00
Ricardo Wurmus 3e0128ec36
gnu: r-callr: Update to 3.3.1. 
* gnu/packages/cran.scm (r-callr): Update to 3.3.1.
 2019-08-06 15:48:53 +02:00
Ricardo Wurmus 6a04f25faf
gnu: r-ellipsis: Update to 0.2.0.1. 
* gnu/packages/cran.scm (r-ellipsis): Update to 0.2.0.1.
 2019-08-06 15:48:53 +02:00
Ricardo Wurmus 710ecc9ceb
gnu: r-clipr: Update to 0.7.0. 
* gnu/packages/cran.scm (r-clipr): Update to 0.7.0.
 2019-08-06 15:48:53 +02:00
Ricardo Wurmus d36430d274
gnu: r-desolve: Update to 1.24. 
* gnu/packages/maths.scm (r-desolve): Update to 1.24.
 2019-08-06 15:48:52 +02:00
Ricardo Wurmus 17e43c425d
gnu: r-quantreg: Update to 5.42.1. 
* gnu/packages/statistics.scm (r-quantreg): Update to 5.42.1.
 2019-08-06 15:48:52 +02:00
Ricardo Wurmus 599fbee5fb
gnu: r-pbapply: Update to 1.4-1. 
* gnu/packages/statistics.scm (r-pbapply): Update to 1.4-1.
 2019-08-06 15:48:52 +02:00
Ricardo Wurmus 0910ff0cfc
gnu: r-robust: Update to 0.4-18.1. 
* gnu/packages/statistics.scm (r-robust): Update to 0.4-18.1.
 2019-08-06 15:48:52 +02:00
Ricardo Wurmus ddfd0afb2a
gnu: r-mclust: Update to 5.4.5. 
* gnu/packages/statistics.scm (r-mclust): Update to 5.4.5.
 2019-08-06 15:48:52 +02:00
Ricardo Wurmus 58aa971fbd
gnu: r-fastica: Update to 1.2-2. 
* gnu/packages/statistics.scm (r-fastica): Update to 1.2-2.
 2019-08-06 15:48:52 +02:00
Ricardo Wurmus db93ef0948
gnu: r-cowplot: Update to 1.0.0. 
* gnu/packages/statistics.scm (r-cowplot): Update to 1.0.0.
[propagated-inputs]: Remove r-plyr; add r-rlang.
 2019-08-06 15:48:52 +02:00
Ricardo Wurmus b2fea05954
gnu: r-rngtools: Update to 1.4. 
* gnu/packages/statistics.scm (r-rngtools): Update to 1.4.
 2019-08-06 15:48:52 +02:00
Ricardo Wurmus 8d84a0ad70
gnu: r-domc: Update to 1.3.6. 
* gnu/packages/statistics.scm (r-domc): Update to 1.3.6.
 2019-08-06 15:48:52 +02:00
Ricardo Wurmus 862959813f
gnu: r-doparallel: Update to 1.0.15. 
* gnu/packages/statistics.scm (r-doparallel): Update to 1.0.15.
 2019-08-06 15:48:52 +02:00
Ricardo Wurmus 5a01128f45
gnu: r-foreach: Update to 1.4.7. 
* gnu/packages/statistics.scm (r-foreach): Update to 1.4.7.
 2019-08-06 15:48:52 +02:00
Ricardo Wurmus b41d03dd35
gnu: r-iterators: Update to 1.0.12. 
* gnu/packages/statistics.scm (r-iterators): Update to 1.0.12.
 2019-08-06 15:48:52 +02:00
Ricardo Wurmus 90752043dd
gnu: r-rsqlite: Update to 2.1.2. 
* gnu/packages/statistics.scm (r-rsqlite): Update to 2.1.2.
 2019-08-06 15:48:52 +02:00
Ricardo Wurmus 2de0f885f4
gnu: r-blob: Update to 1.2.0. 
* gnu/packages/statistics.scm (r-blob): Update to 1.2.0.
[propagated-inputs]: Add r-rlang and r-vctrs; remove r-tibble.
 2019-08-06 15:48:51 +02:00
Ricardo Wurmus feb261ee9b
gnu: r-rmarkdown: Update to 1.14. 
* gnu/packages/statistics.scm (r-rmarkdown): Update to 1.14.
 2019-08-06 15:48:51 +02:00
Ricardo Wurmus 6af62ad50a
gnu: r-rcpparmadillo: Update to 0.9.600.4.0. 
* gnu/packages/statistics.scm (r-rcpparmadillo): Update to 0.9.600.4.0.
 2019-08-06 15:48:51 +02:00
Ricardo Wurmus 9b02d1c836
gnu: r-hms: Update to 0.5.0. 
* gnu/packages/statistics.scm (r-hms): Update to 0.5.0.
[propagated-inputs]: Add r-vctrs.
 2019-08-06 15:48:51 +02:00
Ricardo Wurmus 78896ba23b
gnu: r-devtools: Update to 2.1.0. 
* gnu/packages/statistics.scm (r-devtools): Update to 2.1.0.
[propagated-inputs]: Add r-roxygen2 and r-testthat.
 2019-08-06 15:48:51 +02:00
Ricardo Wurmus 1df87085e3
gnu: r-git2r: Update to 0.26.1. 
* gnu/packages/statistics.scm (r-git2r): Update to 0.26.1.
[inputs]: Remove libssh2 and openssl; add libgit2.
 2019-08-06 15:48:51 +02:00
Ricardo Wurmus 9236b2c144
gnu: r-httr: Update to 1.4.1. 
* gnu/packages/statistics.scm (r-httr): Update to 1.4.1.
 2019-08-06 15:48:51 +02:00
Ricardo Wurmus 3511aff992
gnu: r-openssl: Update to 1.4.1. 
* gnu/packages/statistics.scm (r-openssl): Update to 1.4.1.
 2019-08-06 15:48:51 +02:00
Ricardo Wurmus c02bb7e901
gnu: r-checkmate: Update to 1.9.4. 
* gnu/packages/statistics.scm (r-checkmate): Update to 1.9.4.
 2019-08-06 15:48:51 +02:00
Ricardo Wurmus b29ecb8e37
gnu: r-xml2: Update to 1.2.1. 
* gnu/packages/statistics.scm (r-xml2): Update to 1.2.1.
 2019-08-06 15:48:51 +02:00
Ricardo Wurmus 8d932e71d6
gnu: r-coda: Update to 0.19-3. 
* gnu/packages/statistics.scm (r-coda): Update to 0.19-3.
 2019-08-06 15:48:51 +02:00
Ricardo Wurmus 7d36001bd2
gnu: r-dplyr: Update to 0.8.3. 
* gnu/packages/statistics.scm (r-dplyr): Update to 0.8.3.
 2019-08-06 15:48:50 +02:00
Ricardo Wurmus eae8e56a64
gnu: r-testthat: Update to 2.2.1. 
* gnu/packages/statistics.scm (r-testthat): Update to 2.2.1.
[propagated-inputs]: Add r-evaluate.
 2019-08-06 15:48:50 +02:00
Ricardo Wurmus c2e85d0265
gnu: r-digest: Update to 0.6.20. 
* gnu/packages/statistics.scm (r-digest): Update to 0.6.20.
 2019-08-06 15:48:50 +02:00
Ricardo Wurmus d6e54e7002
gnu: r-nlme: Update to 3.1-141. 
* gnu/packages/statistics.scm (r-nlme): Update to 3.1-141.
 2019-08-06 15:48:50 +02:00
Ricardo Wurmus ecebfe51ce
gnu: r-foreign: Update to 0.8-72. 
* gnu/packages/statistics.scm (r-foreign): Update to 0.8-72.
 2019-08-06 15:48:50 +02:00
Ricardo Wurmus 6eccb0879f
gnu: r-boot: Update to 1.3-23. 
* gnu/packages/statistics.scm (r-boot): Update to 1.3-23.
 2019-08-06 15:48:50 +02:00
Rutger Helling 49fd98bf65
gnu: faudio: Update to 19.08. 
* gnu/packages/audio.scm (faudio): Update to 19.08.
 2019-08-06 13:09:23 +02:00
Rutger Helling 932f795c0e
gnu: kitty: Update to 0.14.3. 
* gnu/packages/terminals.scm (kitty): Update to 0.14.3.
[inputs]: Add libcanberra.
 2019-08-06 13:06:25 +02:00
Ricardo Wurmus 378d94e51b
Merge remote-tracking branch 'origin/master' into wip-texlive 2019-08-06 10:07:36 +02:00
Brian Leung 6a5198170e
gnu: emacs-ivy: Update to 0.12.0-1.d3e4514. 
* gnu/packages/emacs-xyz.scm (emacs-ivy): Update to 0.12.0-1.d3e4514.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2019-08-06 09:41:44 +02:00
Mark H Weaver aac6c53a7b
gnu: libmad: Add more security fixes from Debian. 
Includes fixes for CVE-2017-8372, CVE-2017-8373, and CVE-2017-8374.

Reported by <marit@secmail.pro> in <https://bugs.gnu.org/36909>.

* gnu/packages/patches/libmad-frame-length.patch: Delete file.
* gnu/packages/patches/libmad-length-check.patch,
gnu/packages/patches/libmad-md_size.patch: New files.
* gnu/local.mk (dist_patch_DATA): Update accordingly.
* gnu/packages/mp3.scm (libmad)[source]: Update patches accordingly.
 2019-08-06 03:18:24 -04:00
Rutger Helling b0c48829b6
gnu: flatpak: Update to 1.4.2. 
* gnu/packages/package-management.scm (flatpak): Update to 1.4.2.
 2019-08-06 08:25:35 +02:00
Marius Bakke 2426e2c94c
gnu: strace: Fix test failures on some systems. 
* gnu/packages/patches/strace-ipc-tests.patch: New file.
* gnu/local.mk (dist_patch_DATA): Adjust accordingly.
* gnu/packages/linux.scm (strace)[source](patches): New field.
[arguments]: Add 'regenerate-tests' phase.

Co-Authored-By: Mark H Weaver <mhw@netris.org>
 2019-08-06 02:17:38 -04:00
Tobias Geerinckx-Rice 96681d4be1
gnu: terminator: Wrap instead of propagating GSettings schemas. 
* gnu/packages/gnome.scm (terminator)[inputs]:
Move gsettings-desktop-schemas back here…
[propagated-inputs]: …from here.
[arguments]: Add the glib-or-gtk-build-system's ‘glib-or-gtk-wrap’
phase.
 2019-08-05 22:18:57 +02:00
Tobias Geerinckx-Rice 7b88b71120
gnu: libvirt: Update to 5.6.0. 
* gnu/packages/virtualization.scm (libvirt): Update to 5.6.0.
[source]: Remove patch.
* gnu/packages/patches/libvirt-remove-ATTRIBUTE_UNUSED.patch:
Delete file.
* gnu/local.mk (dist_patch_DATA): Remove it.
 2019-08-05 21:03:31 +02:00
Tobias Geerinckx-Rice d866acca9a
gnu: python-libvirt: Update to 5.6.0. 
* gnu/packages/virtualization.scm (python-libvirt): Update to 5.6.0.
 2019-08-05 21:03:31 +02:00
Mark H Weaver 0fae1b6dee
Revert "gnu: nss: Update to 3.45 [security fixes]." 
This reverts commit 95580bda05.

Note that the security fixes mentioned in that commit were already
present in NSS 3.44.1, which is the version that's now reinstated
by this revert.  The rationale for this revert is that NSS 3.45 fails
to build on armhf-linux.
 2019-08-05 12:45:22 -04:00
Rutger Helling c94884bcc1
gnu: wine: Adapt Intel Vulkan on i686-linux. 
* gnu/packages/wine.scm (wine)[arguments]: Adjust to also provide Vulkan on
i686-linux for Intel.
* gnu/packages/wine.scm (wine64)[arguments]: Adjust to also provide Vulkan on
i686-linux for Intel.
* gnu/packages/wine.scm (wine-staging)[arguments]: Adjust to also provide
Vulkan on i686-linux for Intel.
* gnu/packages/wine.scm (wine64-staging)[arguments]: Adjust to also provide
Vulkan on i686-linux for Intel.
 2019-08-05 16:47:36 +02:00
Brian Leung e15ec8bcec
gnu: emacs-org-super-agenda: Update to 1.1.1-1.375bde4. 
* gnu/packages/emacs-xyz.scm (emacs-org-super-agenda): Update to
1.1.1-1.375bde4.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2019-08-05 16:19:03 +02:00
Brian Leung 4d48e277ca
gnu: Add emacs-org-sidebar. 
* gnu/packages/emacs-xyz.scm (emacs-org-sidebar): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2019-08-05 16:17:46 +02:00
Brian Leung 003d153783
gnu: emacs-dired-hacks: Update to 0.0.1-2.886befe. 
* gnu/packages/emacs-xyz.scm (emacs-dired-hacks): Update to 0.0.1-2.886befe.
[description]: Use full sentences.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2019-08-05 16:16:59 +02:00
Brian Leung f94ae7d472
gnu: Add emacs-nswbuff. 
* gnu/packages/emacs-xyz.scm (emacs-nswbuff): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2019-08-05 16:15:44 +02:00
Brian Leung 12dd1a4838
gnu: Add emacs-company-math. 
* gnu/packages/emacs-xyz.scm (emacs-company-math): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2019-08-05 16:15:00 +02:00
Brian Leung 16fdde79ec
gnu: Add emacs-math-symbol-lists. 
* gnu/packages/emacs-xyz.scm (emacs-math-symbol-lists): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2019-08-05 16:13:58 +02:00
Brian Leung c07f3113d9
gnu: Add emacs-hercules. 
* gnu/packages/emacs-xyz.scm (emacs-hercules): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2019-08-05 16:12:59 +02:00
Brian Leung d052e51b57
gnu: Add emacs-mc-extras. 
* gnu/packages/emacs-xyz.scm (emacs-mc-extras): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2019-08-05 16:12:09 +02:00
Brian Leung 594d60a3f4
gnu: emacs-nodejs-repl: Update to 0.2.2. 
* gnu/packages/emacs-xyz.scm (emacs-nodejs-repl): Update to 0.2.2.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2019-08-05 16:09:52 +02:00
Brian Leung 365e94c019
gnu: emacs-counsel-etags: Update to 1.8.7. 
* gnu/packages/emacs-xyz.scm (emacs-counsel-etags): Update to 1.8.7.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2019-08-05 16:09:37 +02:00
Brian Leung 10989c59cb
gnu: emacs-lua-mode: Update to 20151025-2.95c64bb. 
* gnu/packages/emacs-xyz.scm (emacs-lua-mode): Update to 20151025-2.95c64bb.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2019-08-05 16:08:30 +02:00
Brian Leung f48aa64ea8
gnu: emacs-evil-expat: Update to 0.0.1-1.f4fcd0a. 
* gnu/packages/emacs-xyz.scm (emacs-evil-expat): Update to 0.0.1-1.f4fcd0a.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2019-08-05 16:07:09 +02:00
Brian Leung fef08850b7
gnu: emacs-so-long: Update to 1.0-2.cfae473. 
* gnu/packages/emacs-xyz.scm (emacs-so-long): Update to 1.0-2.cfae473.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2019-08-05 16:05:26 +02:00
Brian Leung aca6091b05
gnu: emacs-highlight-indentation: Update to 0.7.0-1.d03803f. 
* gnu/packages/emacs-xyz.scm (emacs-highlight-indentation): Update to
0.7.0-1.d03803f.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2019-08-05 16:04:27 +02:00
Brian Leung 76c2e51017
gnu: Add emacs-dired-toggle-sudo. 
* gnu/packages/emacs-xyz.scm (emacs-dired-toggle-sudo): New variable.
* gnu/packages/patches/emacs-dired-toggle-sudo-emacs-26.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2019-08-05 16:02:05 +02:00
Brian Leung 1a24d8b347
gnu: Add emacs-helm-org-rifle. 
* gnu/packages/emacs-xyz.scm (emacs-helm-org-rifle): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2019-08-05 15:47:00 +02:00
Brian Leung 1239146613
gnu: emacs-magit-todos: Update to 1.3. 
* gnu/packages/emacs-xyz.scm (emacs-magit-todos): Update to 1.3.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2019-08-05 15:45:54 +02:00
Brian Leung 0074b1e96c
gnu: Add emacs-scroll-on-drag. 
* gnu/packages/emacs-xyz.scm (emacs-scroll-on-drag): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2019-08-05 15:45:24 +02:00
Brian Leung 91b351de53
gnu: Add emacs-evil-traces. 
* gnu/packages/emacs-xyz.scm (emacs-evil-traces): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2019-08-05 15:43:05 +02:00
Brian Leung 7fb91e4f36
gnu: emacs-helm: Update to 3.3. 
* gnu/packages/emacs-xyz.scm (emacs-helm): Update to 3.3.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2019-08-05 15:40:37 +02:00
Jonathan Frederickson 213315d485
gnu: Add libhandy. 
* gnu/packages/gnome.scm (libhandy): New variable.

Co-authored-by: Ricardo Wurmus <rekado@elephly.net>
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2019-08-05 14:06:11 +02:00
Nicolas Goaziou b705b1388f
gnu: emacs-org-contrib: Update to 20190805. 
* gnu/packages/emacs-xyz.scm (emacs-org-contrib): Update to 20190805.
 2019-08-05 13:07:56 +02:00
Nicolas Goaziou dedafb9ccf
gnu: emacs-org: Update to 9.2.5. 
* gnu/packages/emacs-xyz.scm (emacs-org): Update to 9.2.5.
 2019-08-05 13:03:17 +02:00
Brian Leung 71804546b1
gnu: python-scikit-learn: Make gzip timestamps writable. 
* gnu/packages/machine-learning.scm (python-scikit-learn)
[arguments]: Add custom phase to make gzip timestamps writable.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2019-08-05 10:23:02 +03:00
Brian Leung d9340de903
gnu: khmer: Make gzip timestamps writable. 
* gnu/packages/bioinformatics.scm (khmer)[arguments]: Add custom phase
to make gzip timestamps writable.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2019-08-05 10:22:20 +03:00
Rutger Helling 3f14c9135b
gnu: mesa: Enable Intel 32-bit Vulkan drivers. 
* gnu/packages/gl.scm (mesa)[arguments]: Also build Vulkan drivers for Intel
on i686-linux.
 2019-08-05 08:25:04 +02:00
Mark H Weaver 5ee4d11ff4
gnu: linux-libre: Update to 5.2.6. 
* gnu/packages/linux.scm (linux-libre-5.2-version): Update to 5.2.6.
(linux-libre-5.2-pristine-source)[hash]: Update hash.
 2019-08-04 22:02:02 -04:00
Mark H Weaver b4478eb2e3
gnu: linux-libre@4.19: Update to 4.19.64. 
* gnu/packages/linux.scm (linux-libre-4.19-version): Update to 4.19.64.
(linux-libre-4.19-pristine-source)[hash]: Update hash.
 2019-08-04 22:01:59 -04:00
Mark H Weaver cf1941712f
gnu: linux-libre@4.14: Update to 4.14.136. 
* gnu/packages/linux.scm (linux-libre-4.14-version): Update to 4.14.136.
(linux-libre-4.14-pristine-source)[hash]: Update hash.
 2019-08-04 22:01:57 -04:00
Mark H Weaver 8079493c6c
gnu: linux-libre@4.9: Update to 4.9.187. 
* gnu/packages/linux.scm (linux-libre-4.9-version): Update to 4.9.187.
(linux-libre-4.9-pristine-source)[hash]: Update hash.
 2019-08-04 22:01:55 -04:00
Mark H Weaver 71f9016a4f
gnu: linux-libre@4.4: Update to 4.4.187. 
* gnu/packages/linux.scm (linux-libre-4.4-version): Update to 4.4.187.
(linux-libre-4.4-pristine-source)[hash]: Update hash.
 2019-08-04 22:01:52 -04:00
Mark H Weaver 95580bda05
gnu: nss: Update to 3.45 [security fixes]. 
Includes fixes for CVE-2019-11719, CVE-2019-11727, and CVE-2019-11729.

* gnu/packages/nss.scm (nss): Update to 3.45.
 2019-08-04 21:59:38 -04:00
Tobias Geerinckx-Rice 35600cd9a0
gnu: docker-compose: Remove inputs for old Python versions. 
* gnu/packages/docker.scm (docker-compose)[inputs]:
Remove python2-backport-ssl-match-hostname and python-ipaddress.
 2019-08-05 01:06:58 +02:00
Tobias Geerinckx-Rice d12578f2e2
gnu: python-docker-py: Propagate dependencies. 
* gnu/packages/docker.scm (python-docker-py)[inputs]:
Move python-docker-pycreds and python-paramiko from here…
[propagated-inputs]: …to here.
(docker-compose)[inputs]: Remove them.
 2019-08-05 01:06:58 +02:00
Tobias Geerinckx-Rice e643d90f0f
gnu: docker-compose: Remove Windows-specific input. 
* gnu/packages/docker.scm (docker-compose)[inputs]:
Remove python-colorama.
 2019-08-05 01:06:57 +02:00
Marius Bakke 5b689de58d
gnu: x265: Update to 3.1.2. 
* gnu/packages/video.scm (x265): Update to 3.1.2.
 2019-08-05 00:17:09 +02:00
Marius Bakke 621ce95cfe
gnu: x265: Update source URI. 
* gnu/packages/video.scm (x265)[source](uri): Add the canonical upstream at
<https://bitbucket.org/multicoreware/x265>.
 2019-08-05 00:17:09 +02:00
Marius Bakke 15b5963300
gnu: i3-wm: Update to 4.17. 
* gnu/packages/wm.scm (i3-wm): Update to 4.17.
 2019-08-04 17:39:04 +02:00
Marius Bakke cb96d239e6
gnu: i3status: Update to 2.13. 
* gnu/packages/wm.scm (i3status): Update to 2.13.
[arguments]: Remove #:make-flags and #:phases.  Add #:out-of-source?.
[native-inputs]: Add DOCBOOK-XSL, LIBXML2 and XMLTO.
 2019-08-04 17:38:13 +02:00
Marius Bakke 4f868257f3
gnu: samba: Update to 4.10.6. 
* gnu/packages/samba.scm (samba): Update to 4.10.6.
 2019-08-04 16:22:35 +02:00
Marius Bakke 2e2db09280
gnu: strace: Update to 5.2. 
* gnu/packages/linux.scm (strace): Update to 5.2.
 2019-08-04 16:22:20 +02:00
Marius Bakke 16feaeefc9
gnu: libevent: Update to 2.1.11. 
* gnu/packages/libevent.scm (libevent): Update to 2.1.11.
 2019-08-04 16:22:01 +02:00