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38885 Commits

Author SHA1 Message Date
Tobias Geerinckx-Rice ccbd1648f4
gnu: exim: Update to 4.92.2 [fixes CVE-2019-15846]. 
* gnu/packages/mail.scm (exim): Update to 4.92.2.
 2019-09-06 17:36:04 +02:00
Efraim Flashner cae5312758
gnu: crates-io.scm: Fix several home-pages. 
* gnu/packages/crates-io.scm (rust-constant-time-eq, rust-fixedbitset,
rust-futures, rust-pico-sys, rust-pkg-config, rust-quick-error,
rust-remove-dir-all, rust-spin, rust-tempdir, rust-traitobject,
rust-void)[home-page]: Update to correct home-page.
 2019-09-06 17:25:03 +03:00
Ricardo Wurmus 8205534569
gnu: Add samblaster. 
* gnu/packages/bioinformatics.scm (samblaster): New variable.
 2019-09-06 15:00:49 +02:00
Ricardo Wurmus 7cd446fd3f
gnu: Add r-txdb-celegans-ucsc-ce6-ensgene. 
* gnu/packages/bioconductor.scm (r-txdb-celegans-ucsc-ce6-ensgene): New
variable.
 2019-09-06 15:00:49 +02:00
Efraim Flashner 41ba4cf150
gnu: Add rust-parity-wasm. 
* gnu/packages/crates-io.scm (rust-parity-wasm): New variable.
 2019-09-06 15:46:04 +03:00
Efraim Flashner 540d830edc
gnu: Add rust-time. 
* gnu/packages/crates-io.scm (rust-time): New variable.
 2019-09-06 15:46:03 +03:00
Efraim Flashner 4282cbe9b0
gnu: Add rust-semver-parser-0.7. 
* gnu/packages/crates-io.scm (rust-semver-parser-0.7): New variable.
 2019-09-06 15:46:03 +03:00
Efraim Flashner 516b2f1a3b
gnu: Add rust-getopts. 
* gnu/packages/crates-io.scm (rust-getopts): New variable.
 2019-09-06 15:46:03 +03:00
Efraim Flashner 9a5ee9928a
gnu: Add rust-clang-sys. 
* gnu/packages/crates-io.scm (rust-clang-sys): New variable.
 2019-09-06 15:46:03 +03:00
Efraim Flashner cef7de6fa6
gnu: Add rust-glob-0.2. 
* gnu/packages/crates-io.scm (rust-glob-0.2): New variable.
 2019-09-06 15:46:03 +03:00
Efraim Flashner b79eab74a1
gnu: Add rust-glob. 
* gnu/packages/crates-io.scm (rust-glob): New variable.
 2019-09-06 15:46:03 +03:00
Efraim Flashner 01519b3d9f
gnu: Add rust-sourcefile. 
* gnu/packages/crates-io.scm (rust-sourcefile): New variable.
 2019-09-06 15:46:02 +03:00
Efraim Flashner 61322df019
gnu: Add rust-miow-0.2. 
* gnu/packages/crates-io.scm (rust-miow-0.2): New variable.
 2019-09-06 15:46:02 +03:00
Efraim Flashner 5ae8c1fba3
gnu: Add rust-miow. 
* gnu/packages/crates-io.scm (rust-miow): New variable.
 2019-09-06 15:46:02 +03:00
Efraim Flashner 1241007f16
gnu: Add rust-ansi-term. 
* gnu/packages/crates-io.scm (rust-ansi-term): New variable.
 2019-09-06 15:46:02 +03:00
Efraim Flashner fbf37a7bff
gnu: Add rust-socket2. 
* gnu/packages/crates-io.scm (rust-socket2): New variable.
 2019-09-06 15:46:02 +03:00
Efraim Flashner 3494be3515
gnu: Add rust-tar. 
* gnu/packages/crates-io.scm (rust-tar): New variable.
 2019-09-06 15:46:01 +03:00
Efraim Flashner 27438eb817
gnu: Add rust-filetime. 
* gnu/packages/crates-io.scm (rust-filetime): New variable.
 2019-09-06 15:46:01 +03:00
Efraim Flashner 1a9ce2a252
gnu: Add rust-xattr. 
* gnu/packages/crates-io.scm (rust-xattr): New variable.
 2019-09-06 15:46:01 +03:00
Efraim Flashner 5ef6549e12
gnu: Add rust-tempfile. 
* gnu/packages/crates-io.scm (rust-tempfile): New variable.
 2019-09-06 15:46:01 +03:00
Efraim Flashner 1515ecae21
gnu: Add rust-lzma-sys. 
* gnu/packages/crates-io.scm (rust-lzma-sys): New variable.
 2019-09-06 15:46:01 +03:00
Efraim Flashner f32a4ba746
gnu: Add rust-jemalloc-sys. 
* gnu/packages/crates-io.scm (rust-jemalloc-sys): New variable.
 2019-09-06 15:46:01 +03:00
Efraim Flashner c891c7f174
gnu: Add rust-cargon. 
* gnu/packages/crates-io.scm (rust-cargon): New variable.
 2019-09-06 15:46:00 +03:00
Efraim Flashner f007411308
gnu: Add rust-rustc-demangle. 
* gnu/packages/crates-io.scm (rust-rustc-demangle): New variable.
 2019-09-06 15:46:00 +03:00
Efraim Flashner eda57f4834
gnu: Add rust-pico-sys. 
* gnu/packages/crates-io.scm (rust-pico-sys): New variable.
 2019-09-06 15:46:00 +03:00
Efraim Flashner 02f66e9022
gnu: Add rust-gcc. 
* gnu/packages/crates-io.scm (rust-gcc): New variable.
 2019-09-06 15:46:00 +03:00
Efraim Flashner f51c47b528
gnu: Add rust-openssl-probe. 
* gnu/packages/crates-io.scm (rust-openssl-probe): New variable.
 2019-09-06 15:46:00 +03:00
Efraim Flashner 5b15d635ed
gnu: Add rust-netlib-src. 
* gnu/packages/crates-io.scm (rust-netlib-src): New variable.
 2019-09-06 15:45:59 +03:00
Efraim Flashner e81e48ef29
gnu: Add rust-miniz-sys. 
* gnu/packages/crates-io.scm (rust-miniz-sys): New variable.
 2019-09-06 15:45:59 +03:00
Efraim Flashner 3a3c72e6b1
gnu: Add rust-miniz-oxide. 
* gnu/packages/crates-io.scm (rust-miniz-oxide): New variable.
 2019-09-06 15:45:59 +03:00
Efraim Flashner 94c715e613
gnu: Add rust-memmap-0.6. 
* gnu/packages/crates-io.scm (rust-memmap@0.6): New variable.
 2019-09-06 15:45:59 +03:00
Efraim Flashner 701eaebc66
gnu: Add rust-memmap. 
* gnu/packages/crates-io.scm (rust-memmap): New variable.
 2019-09-06 15:45:59 +03:00
Efraim Flashner aeaa601260
gnu: Add rust-vcpkg. 
* gnu/packages/crates-io.scm (rust-vcpkg): New variable.
 2019-09-06 15:45:59 +03:00
Efraim Flashner 6f5cd37a60
gnu: Add rust-libloading. 
* gnu/packages/crates-io.scm (rust-libloading): New variable.
 2019-09-06 15:45:58 +03:00
Efraim Flashner 412c43b423
gnu: Add rust-compiler-builtins. 
* gnu/packages/crates-io.scm (rust-compiler-builtins): New hidden variable.
 2019-09-06 15:45:58 +03:00
Efraim Flashner e78973f45b
gnu: Add rust-stacker. 
* gnu/packages/crates-io.scm (rust-stacker): New variable.
 2019-09-06 15:45:58 +03:00
Efraim Flashner 2446b451e2
gnu: Add rust-cmake. 
* gnu/packages/crates-io.scm (rust-cmake): New variable.
 2019-09-06 15:45:58 +03:00
Efraim Flashner 5bd7965e11
gnu: Add rust-cc. 
* gnu/packages/crates-io.scm (rust-cc): New variable.
 2019-09-06 15:45:58 +03:00
Efraim Flashner 313778655e
gnu: Add rust-log. 
* gnu/packages/crates-io.scm (rust-log): New variable.
 2019-09-06 15:45:58 +03:00
Efraim Flashner c2c0ac1451
gnu: Add rust-rustc-serialize. 
* gnu/packages/crates-io.scm (rust-rustc-serialize): New variable.
 2019-09-06 15:45:57 +03:00
Efraim Flashner c988c9bb85
gnu: Add rust-base-x. 
* gnu/packages/crates-io.scm (rust-base-x): New variable.
 2019-09-06 15:45:57 +03:00
Efraim Flashner 90c48ddd76
gnu: Add rust-adler32. 
* gnu/packages/crates-io.scm (rust-adler32): New variable.
 2019-09-06 15:45:57 +03:00
Efraim Flashner f81d58b8b3
gnu: Add rust-tempdir. 
* gnu/packages/crates-io.scm (rust-tempdir): New variable.
 2019-09-06 15:45:57 +03:00
Efraim Flashner 2f8e436a29
gnu: Add rust-rand-0.3. 
* gnu/packages/crates-io.scm (rust-rand-0.3): New variable.
 2019-09-06 15:45:57 +03:00
Efraim Flashner 5ef82ec8ba
gnu: Add rust-rand. 
* gnu/packages/crates-io.scm (rust-rand): New variable.
 2019-09-06 15:45:56 +03:00
Brian Leung 43931643a6
gnu: Add emacs-leetcode. 
* gnu/packages/emacs-xyz.scm (emacs-leetcode): New variable.

Signed-off-by: Oleg Pykhalov <go.wigust@gmail.com>
 2019-09-06 12:37:41 +03:00
Brian Leung 14c9c456c7
gnu: emacs-robe: Update to 0.8.2. 
* gnu/packages/emacs-xyz.scm (emacs-robe): Update to 0.8.2.

Signed-off-by: Oleg Pykhalov <go.wigust@gmail.com>
 2019-09-06 12:36:35 +03:00
Brian Leung 141d8a896f
gnu: emacs-flycheck-haskell: Include .hs file. 
* gnu/packages/emacs-xyz.scm (emacs-flycheck-haskell): Include package file.

Signed-off-by: Oleg Pykhalov <go.wigust@gmail.com>
 2019-09-06 12:32:56 +03:00
Brian Leung a9ca0325b5
gnu: emacs-evil-traces: Enable tests. 
* gnu/packages/emacs-xyz.scm (emacs-evil-traces): Enable tests.

Signed-off-by: Oleg Pykhalov <go.wigust@gmail.com>
 2019-09-06 12:26:29 +03:00
Brian Leung 4278537e85
gnu: emacs-org-ql: Enable tests. 
* gnu/packages/emacs-xyz.scm (emacs-org-ql): Enable tests.

Signed-off-by: Oleg Pykhalov <go.wigust@gmail.com>
 2019-09-06 12:26:19 +03:00
Brian Leung d6ac801591
gnu: emacs-sudo-edit: Enable tests. 
* gnu/packages/emacs-xyz.scm (emacs-sudo-edit): Enable tests.
[native-inputs]: Add emacs-undercover.

Signed-off-by: Oleg Pykhalov <go.wigust@gmail.com>
 2019-09-06 12:26:11 +03:00
Brian Leung 1acf8e7ea8
gnu: emacs-evil-exchange: Enable tests. 
* gnu/packages/emacs-xyz.scm (emacs-evil-exchange): Enable tests.
[native-inputs]: Add emacs-ert-runner.

Signed-off-by: Oleg Pykhalov <go.wigust@gmail.com>
 2019-09-06 12:26:02 +03:00
Brian Leung a8afeb058e
gnu: emacs-evil-expat: Enable tests. 
* gnu/packages/emacs-xyz.scm (emacs-evil-expat): Enable tests.

Signed-off-by: Oleg Pykhalov <go.wigust@gmail.com>
 2019-09-06 12:25:47 +03:00
Brian Leung 8deabdba58
gnu: emacs-elisp-demos: Enable tests. 
* gnu/packages/emacs-xyz.scm (emacs-elisp-demos): Enable tests.

Signed-off-by: Oleg Pykhalov <go.wigust@gmail.com>
 2019-09-06 12:25:27 +03:00
Brian Leung 9b4ea95bbe
gnu: emacs-evil-owl: Update to 0.0.1-3.24e5f43. 
* gnu/packages/emacs-xyz.scm (emacs-evil-owl): Update to 0.0.1-3.24e5f43.
[source]: Enable tests.

Signed-off-by: Oleg Pykhalov <go.wigust@gmail.com>
 2019-09-06 12:25:19 +03:00
Brian Leung 473d636072
gnu: emacs-evil-multiedit: Enable tests. 
* gnu/packages/emacs-xyz.scm (emacs-evil-multiedit): Enable tests.
[inputs]: Add emacs-ert-runner.

Signed-off-by: Oleg Pykhalov <go.wigust@gmail.com>
 2019-09-06 12:24:59 +03:00
Ricardo Wurmus 66d2133500
gnu: Add texlive-booktabs. 
* gnu/packages/tex.scm (texlive-booktabs): New variable.
 2019-09-05 22:45:42 +02:00
Ricardo Wurmus 69f0c8cf55
gnu: Add texlive-siunitx. 
* gnu/packages/tex.scm (texlive-siunitx): New variable.
 2019-09-05 22:45:42 +02:00
Ricardo Wurmus 11ecf9f48f
gnu: Add texlive-standalone. 
* gnu/packages/tex.scm (texlive-standalone): New variable.
 2019-09-05 22:45:42 +02:00
Ricardo Wurmus f16e09487b
gnu: texlive-latex-xkeyval: Fix build. 
* gnu/packages/tex.scm (texlive-latex-xkeyval)[arguments]: Add various custom
build phases to fix the build.
[native-inputs]: Add texlive-latex-base, texlive-cm, texlive-lm, texlive-url,
texlive-graphics-def, texlive-xcolor, texlive-latex-footmisc,
texlive-latex-listings, texlive-iftex, texlive-pstricks, texlive-pst-text,
texlive-tools, and texlive-latex-pgf.
 2019-09-05 22:45:41 +02:00
Ricardo Wurmus 99b143655b
gnu: Add texlive-tools. 
* gnu/packages/tex.scm (texlive-tools): New variable.
 2019-09-05 22:45:41 +02:00
Ricardo Wurmus 51bf1c5188
gnu: Add texlive-iftex. 
* gnu/packages/tex.scm (texlive-iftex): New variable.
 2019-09-05 22:45:41 +02:00
Ricardo Wurmus a72d343aea
gnu: Add texlive-pst-text. 
* gnu/packages/tex.scm (texlive-pst-text): New variable.
 2019-09-05 22:45:41 +02:00
Ricardo Wurmus e5c081291e
gnu: Add texlive-pstricks. 
* gnu/packages/tex.scm (texlive-pstricks): New variable.
 2019-09-05 22:45:41 +02:00
Ricardo Wurmus 73ce44218b
gnu: Add texlive-ydoc. 
* gnu/packages/tex.scm (texlive-ydoc): New variable.
 2019-09-05 22:45:41 +02:00
Ricardo Wurmus 266e07421e
gnu: Add texlive-xcolor. 
* gnu/packages/tex.scm (texlive-latex-xcolor): Bind to deprecated package
pointing...
(texlive-color): ...to this variable; implement in terms of
simple-texlive-package.
[arguments]: Add phase "move-files" to install xcolor.pro to the expected
location.
 2019-09-05 22:45:41 +02:00
Ricardo Wurmus f1a46c9025
gnu: texlive-fonts-iwona: Use double spacing in description. 
* gnu/packages/tex.scm (texlive-fonts-iwona)[description]: Use double spacing.
 2019-09-05 22:45:41 +02:00
Ricardo Wurmus 4526bd07f7
gnu: vigra-c: Update to 0.0.0-1.66ff4fa. 
* gnu/packages/image.scm (vigra-c): Update to 0.0.0-1.66ff4fa.
[inputs]: Add hdf5.
 2019-09-05 22:45:41 +02:00
Ricardo Wurmus f480133c4e
gnu: libbigwig: Update to 0.4.4. 
* gnu/packages/bioinformatics.scm (libbigwig): Update to 0.4.4.
 2019-09-05 22:45:41 +02:00
Christopher Baines 067ea2989f
gnu: python-pyfaidx: Remove python-setuptools as an input. 
As this is provided by the build system, and I'm assuming that it's not
necessary to have it as a propagated input.

* gnu/packages/bioinformatics.scm (python-pyfaidx)[propagated-inputs]: Remove
python-setuptools.
 2019-09-05 18:35:47 +02:00
Christopher Baines 5f9fe21d49
gnu: umi-tools: Remove python-setuptools as an input. 
As this is provided by the build system.

* gnu/packages/bioinformatics.scm (umi-tools)[inputs,native-inputs]: Remove
python-setuptools.
 2019-09-05 18:35:42 +02:00
Leo Famulari d550845840
gnu: Syncthing: Update to 1.2.2. 
* gnu/packages/syncthing.scm (syncthing): Update to 1.2.2.
[inputs]: Remove go-github-com-calmh-du and add go-github-com-shirou-gopsutil.
 2019-09-05 11:09:36 -04:00
Leo Famulari 9a2f23341d
gnu: Add go-github-com-shirou-gopsutil. 
* gnu/packages/syncthing.scm (go-github-com-shirou-gopsutil): New variable.
 2019-09-05 11:09:36 -04:00
Leo Famulari a8ad05d40c
gnu: go-github-com-urfave-cli: Update to 1.21.0. 
* gnu/packages/golang.scm (go-github-com-urfave-cli): Update to 1.21.0.
 2019-09-05 11:09:32 -04:00
Nicolas Goaziou 31885f444f
gnu: emacs-org-contrib: Update to 20190904. 
* gnu/packages/emacs-xyz.scm (emacs-org-contrib): Update to 20190904.
 2019-09-05 16:02:27 +02:00
Nicolas Goaziou be285c3dc0
gnu: emacs-org: Update to 9.2.6. 
* gnu/packages/emacs-xyz.scm (emacs-org): Update to 9.2.6.
 2019-09-05 15:57:02 +02:00
Nicolas Goaziou 51072ed8ac
gnu: emacs-org-caldav: Update to 0.0.0-1. 
* gnu/packages/emacs-xyz.scm (emacs-org-caldav): Update to latest commit,
since there is no release yet.
[description]: Remove alpha status, no longer specified in README.
 2019-09-05 15:55:50 +02:00
Pierre Neidhardt 0575fe681c
Revert "gnu: next: Compress the executable." 
Some essential references (e.g. libfixposix) are lost in the process.

This reverts commit 0e8b91dbc4.
 2019-09-05 14:52:48 +02:00
Efraim Flashner 6b4ed9ad97
gnu: gama: Update to 2.07. 
* gnu/packages/gps.scm (gama): Update to 2.07.
 2019-09-05 14:46:42 +03:00
Ricardo Wurmus 79c6d8781b
gnu: bwa-meth: Capture one more reference to "bwa". 
Reported by: Alexander.Blume <Alexander.Blume@mdc-berlin.de>

* gnu/packages/bioinformatics.scm (bwa-meth)[arguments]: Capture invocation of
"bwa index" to retain reference to "bwa" package.
 2019-09-05 12:06:43 +02:00
Pierre Neidhardt 0e8b91dbc4
gnu: next: Compress the executable. 
* gnu/packages/web-browsers.scm (next)[arguments]: Compressing the executable
  brings it from about 95 MiB to 22 MiB.
 2019-09-05 11:55:58 +02:00
Pierre Neidhardt 33a42f67ce
gnu: emacs-evil-collection: Update to 0.0.2. 
* gnu/packages/emacs-xyz.scm (emacs-evil-collection): Update to 0.0.2.
 2019-09-05 11:55:58 +02:00
Ricardo Wurmus 6b5f59c7a6
gnu: Add r-bigmelon. 
* gnu/packages/bioconductor.scm (r-bigmelon): New variable.
 2019-09-05 11:46:29 +02:00
Ricardo Wurmus 7d2cb646f7
gnu: Add r-gdsfmt. 
* gnu/packages/bioconductor.scm (r-gdsfmt): New variable.
 2019-09-05 11:46:29 +02:00
Ricardo Wurmus 38babeaaa4
gnu: Add r-watermelon. 
* gnu/packages/bioconductor.scm (r-watermelon): New variable.
 2019-09-05 11:46:29 +02:00
Ricardo Wurmus 46721deaf8
gnu: Add r-illuminahumanmethylation450kanno-ilmn12-hg19. 
* gnu/packages/bioconductor.scm
(r-illuminahumanmethylation450kanno-ilmn12-hg19): New variable.
 2019-09-05 11:46:29 +02:00
Ricardo Wurmus db316d7376
gnu: Add r-roc. 
* gnu/packages/bioconductor.scm (r-roc): New variable.
 2019-09-05 11:46:29 +02:00
Efraim Flashner 7d57bc4d0d
gnu: efl: Update to 1.22.4. 
* gnu/packages/enlightenment.scm (efl): Update to 1.22.4.
 2019-09-05 12:42:50 +03:00
Pierre Neidhardt a3439b0c70
gnu: sbcl: Use CLISP instead of unboostrappable CCL to build. 
* gnu/packages/lisp.scm (sbcl)[arguments]: Build with CLISP.
 2019-09-05 11:41:35 +02:00
Pierre Neidhardt 9e737b31cb
gnu: sbcl: Update to 1.5.6. 
* gnu/packages/lisp.scm (sbcl): Update to 1.5.6.
 2019-09-05 10:25:02 +02:00
Rutger Helling 2b332c51db
gnu: dolphin-emu: Update to commit a974540. 
* gnu/packages/emulators.scm (dolphin-emu): Update to commit a974540.
[source]: Delete unneeded MoltenVK map.
[arguments]: Properly hardcode libvulkan path.
 2019-09-05 08:22:34 +02:00
Maxim Cournoyer b8e7e20841
gnu: docker: Add support for tini. 
* gnu/packages/docker.scm (docker)[inputs]: Add tini.
[phases]{patch-paths}: Patch the path of the default init binary.
 2019-09-05 09:38:23 +09:00
Maxim Cournoyer 92086eeda3
gnu: Add tini. 
* gnu/packages/docker.scm (tini): New variable.
 2019-09-05 09:38:22 +09:00
Marius Bakke 9bf589867b
gnu: nginx: Update to 1.17.3 [security fixes]. 
This release fixes CVE-2019-9511, CVE-2019-9513, and CVE-2019-9516.

* gnu/packages/web.scm (nginx): Update to 1.17.3.
 2019-09-05 00:21:43 +02:00
Marius Bakke fbcbafdcaa
gnu: miniupnpc: Update to 2.1.20190824. 
* gnu/packages/upnp.scm (miniupnpc): Update to 2.1.20190824.
 2019-09-05 00:21:43 +02:00
Marius Bakke 56ac8ca3c8
gnu: varnish: Update to 6.2.1. 
* gnu/packages/web.scm (varnish): Update to 6.2.1.
 2019-09-05 00:21:43 +02:00
Marius Bakke 276e7739b9
gnu: libnl: Update to 3.5.0. 
* gnu/packages/linux.scm (libnl): Update to 3.5.0.
 2019-09-05 00:21:43 +02:00
Marius Bakke 309721b324
gnu: samba: Update to 4.10.8 [fixes CVE-2019-10197]. 
* gnu/packages/samba.scm (samba): Update to 4.10.8.
 2019-09-05 00:21:42 +02:00
Marius Bakke 173cced751
gnu: tevent: Update to 0.10.1. 
* gnu/packages/samba.scm (tevent): Update to 0.10.1.
 2019-09-05 00:21:42 +02:00
Marius Bakke 1068bdcfe8
gnu: talloc: Update to 2.3.0. 
* gnu/packages/samba.scm (talloc): Update to 2.3.0.
 2019-09-05 00:21:42 +02:00