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Author SHA1 Message Date
Ricardo Wurmus 02e1acfb2a
gnu: Add vxl. 
* gnu/packages/image-processing.scm (vxl): New variable.
 2019-08-15 14:09:13 +02:00
Ricardo Wurmus 18696f7acf
gnu: Add vtk-6. 
* gnu/packages/image-processing.scm (vtk-6): New variable.
 2019-08-15 14:08:59 +02:00
Jakob L. Kreuze 3033d59ac9
machine: Automatically authorize the coordinator's signing key. 
* guix/ssh.scm (remote-authorize-signing-key): New variable.
* gnu/machine/ssh.scm (deploy-managed-host): Authorize coordinator's
signing key before any invocations of 'remote-eval'.
(deploy-managed-host): Display an error if a signing key does not exist.
* doc/guix.texi (Invoking guix deploy): Remove section describing manual
signing key authorization.
(Invoking guix deploy): Add section describing the 'authorize?' field.
 2019-08-15 07:43:13 -04:00
Jakob L. Kreuze 9c70c460a0
machine: Implement 'roll-back-machine'. 
* gnu/machine.scm (roll-back-machine, &deploy-error, deploy-error?)
(deploy-error-should-roll-back)
(deploy-error-captured-args): New variable.
* gnu/machine/ssh.scm (roll-back-managed-host): New variable.
* guix/scripts/deploy.scm (guix-deploy): Roll-back systems when a
deployment fails.
 2019-08-15 07:43:09 -04:00
Jakob L. Kreuze 5ea7537b9a
machine: Allow non-root users to deploy. 
* doc/guix.texi (Invoking guix deploy): Add section describing
prerequisites for deploying as a non-root user.
* guix/remote.scm (remote-pipe-for-gexp): New optional 'become-command'
argument.
(%remote-eval): New optional 'become-command' argument.
(remote-eval): New 'become-command' keyword argument.
* guix/ssh.scm (remote-inferior): New optional 'become-command'
argument.
(inferior-remote-eval): New optional 'become-command' argument.
(remote-authorize-signing-key): New optional 'become-command' argument.
* gnu/machine/ssh.scm (machine-become-command): New variable.
(managed-host-remote-eval): Invoke 'remote-eval' with the
'#:become-command' keyword.
(deploy-managed-host): Invoke 'remote-authorize-signing-key' with the
'#:become-command' keyword.
 2019-08-15 07:43:03 -04:00
Jakob L. Kreuze 03cbd94d48
remote: Remove '--system' argument. 
* gnu/services.scm (activation-script): Return a <program-file> rather
than a <scheme-file>.
* gnu/deploy.scm (guix-deploy): Remove handling for '--system'.
(show-help): Remove documentation for '--system'.
(%default-options): Remove default setting for 'system'.
 2019-08-14 15:38:13 -04:00
Jakob L. Kreuze 2c8e04f136
remote: Build derivations appropriate for the remote's 
* gnu/machine/ssh.scm (machine-ssh-configuration): Add 'system' field.
(managed-host-remote-eval): Pass 'system' field to 'remote-eval'.
(machine-check-building-for-appropriate-system): New variable.
(check-deployment-sanity): Add call to
'machine-check-building-for-appropriate-system'.
* doc/guix.texi (Invoking guix deploy): Describe new 'system' field.
* guix/ssh.scm (remote-system): New variable.
* guix/remote.scm (remote-eval): Use result of 'remote-system' when
lowering the G-Expression.
(remote-eval): Add 'system' keyword argument.
(trampoline): Return a <program-file> rather than a <scheme-file>.
 2019-08-14 15:38:09 -04:00
Carl Dong 67dac6b892
gnu: mingw: Add x86_64 support. 
This patch parameterizes previously hard-coded instances of
i686-w64-mingw32, adding support for x86_64-w64-mingw32.

* gnu/packages/mingw.scm (make-mingw-w64): New procedure.
(mingw-w64-i686, mingw-w64-x86_64): New variables.
(%mingw-triplet): Remove.
(mingw-w64): Update to point to 'mingw-w64-i686'.
* gnu/packages/cross-base.scm (cross-gcc): Use 'libc' keyword argument
if specified, instead of treating it as a boolean.
(native-libc): Return the correct mingw-w64 depending on machine
specified in target.
* gnu/packages/bootstrap.scm (glibc-dynamic-linker): Add "x86_64-mingw".
* gnu/build/cross-toolchain.scm (set-cross-path/mingw): Replace
hardcoded 'i686-w64-mingw32' instances with 'target' keyword argument.
(cross-gcc-build-phases): Update accordingly; use 'target-mingw?'
implementation of target checking and add commentary.
* gnu/ci.scm (%cross-targets): Add "x86_64-w64-mingw32".
 2019-08-14 21:29:53 +02:00
Eric Bavier 4afdb79249
gnu: onionshare: Upgrade to 2.1. 
* gnu/packages/tor.scm (onionshare): Upgrade to 2.1.
[arguments]: Rename "tests" phase to "check".  Set home directory for tests.
Remove reference to closed upstream bug.
[inputs]: Add python-pycrypto and python-pysocks.
[license]: Remove bsd-3 license; relevant file no longer present.
 2019-08-13 22:34:57 -05:00
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