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48037 Commits

Author SHA1 Message Date
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
Pierre Neidhardt 01e38cc426
build-system/asdf: Add option to compress programs. 
* guix/build/lisp-utils.scm (build-program): Add `compress?' key argument.
(generate-executable-for-system): Same.
(generate-executable): Same.
 2019-09-05 09:56:21 +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
Marius Bakke c0de48c9a5
gnu: tdb: Update to 1.4.2. 
* gnu/packages/databases.scm (tdb): Update to 1.4.2.
 2019-09-05 00:21:42 +02:00
Marius Bakke e25973e18f
gnu: libvisio: Update to 0.1.7. 
* gnu/packages/libreoffice.scm (libvisio): Update to 0.1.7.
 2019-09-05 00:21:42 +02:00
Marius Bakke 558f4a30e2
gnu: libabw: Update to 0.1.3. 
* gnu/packages/libreoffice.scm (libabw): Update to 0.1.3.
[arguments]: Remove.
 2019-09-05 00:21:41 +02:00
Marius Bakke 1a22a234df
gnu: LibRaw: Update to 1.19.5. 
* gnu/packages/photo.scm (libraw): Update to 0.19.5.
 2019-09-05 00:21:41 +02:00
Marius Bakke 5ec7c4a153
gnu: php: Build against Oniguruma 6. 
* gnu/packages/php.scm (php)[inputs]: Change ONIGURUMA-5 to ONIGURUMA.
* gnu/packages/textutils.scm (oniguruma-5): Remove variable.
 2019-09-05 00:21:41 +02:00
Marius Bakke 5ceac3f42b
gnu: oniguruma: Update to 6.9.3 [fixes CVE-2019-13224, CVE-2019-13225]. 
* gnu/packages/textutils.scm (oniguruma): Update to 6.9.3.
 2019-09-05 00:21:41 +02:00
Marius Bakke 56b1977a5d
build-system/julia: Avoid module cycles. 
* guix/build-system/julia.scm: Remove unused imports.
(lower)[julia]: Default to (DEFAULT-JULIA).
 2019-09-05 00:20:41 +02:00
Ricardo Wurmus 458b07ebe0
build-system/julia: Fix syntax error. 
* guix/build-system/julia.scm: Fix invalid module reference.
 2019-09-04 23:56:24 +02:00
L p R n d n 35d4862260
gnu: libxfce4util: Build Vala bindings. 
* gnu/packages/xfce.scm (libxfce4util)[native-inputs]: Add vala.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2019-09-04 23:41:08 +02:00
L p R n d n cb8a5e075a
gnu: libxfce4util: Add gobject-introspection support. 
* gnu/packages/xfce.scm (libxfce4util): Add gobject-introspection to native-inputs.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2019-09-04 23:41:07 +02:00
L p R n d n b45e11dad8
gnu: Add xfce4-screensaver. 
* gnu/packages/xfce.scm (xfce4-screensaver): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2019-09-04 23:41:07 +02:00
L p R n d n d28b6dda86
gnu: Add xfce4-screenshooter. 
* gnu/packages/xfce.scm (xfce4-screenshooter): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2019-09-04 23:41:07 +02:00
Ludovic Courtès f475c6e53e
doc: Update 'README'. 
* README: Update intro a bit.
(Installing Guix as non-root): Remove as it's largely outdated.
(Contact): Update.
 2019-09-04 23:41:07 +02:00
Robert Vollmert c26f562e5e
services: nginx: Pass run-directory on config test. 
Fixes <https://bugs.gnu.org/36388>.
This fixes error logging errors in the activation script.

* gnu/services/web.scm (nginx-activation): Add "-p" flag.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2019-09-04 23:41:07 +02:00
Ludovic Courtès 8161c2d6ce
gnu: ghostscript: Keep the replacement private. 
This avoids having two matches for the "ghostscript" spec.

* gnu/packages/ghostscript.scm (ghostscript/fixed): Keep private.
 2019-09-04 23:41:07 +02:00
Julien Lepiller ce502774b4
gnu: ocaml-easy-format: Update to 1.3.2. 
* gnu/packages/ocaml.scm (ocaml-easy-format): Update to 1.3.2.
 2019-09-04 23:08:49 +02:00
Julien Lepiller e57dd20118
gnu: ocaml-frontc: Update to 3.4.2. 
* gnu/packages/ocaml.scm (ocaml-frontc): Update to 3.4.2.
 2019-09-04 23:08:45 +02:00
Julien Lepiller 4a8a0d8520
gnu: ocaml-ssl: Update to 0.5.9. 
* gnu/packages/ocaml.scm (ocaml-ssl): Update to 0.5.9.
 2019-09-04 23:08:41 +02:00
Julien Lepiller 5a3082eca8
gnu: opam: Update to 2.0.5. 
* gnu/packages/ocaml.scm (opam): Update to 2.0.5.
 2019-09-04 23:08:38 +02:00
Julien Lepiller 69c83817f8
gnu: ocaml-stringext: Update to 1.6.0. 
* gnu/packages/ocaml.scm (ocaml-stringext): Update to 1.6.0.
 2019-09-04 23:08:34 +02:00
Julien Lepiller b3419c4027
gnu: ocaml-markup: Update to 0.8.1. 
* gnu/packages/ocaml.scm (ocaml-markup): Update to 0.8.1.
(ocaml-bisect-ppx): Use propagated-inputs instead of inputs.
 2019-09-04 23:08:25 +02:00
Julien Lepiller 72b2e2ea7a
gnu: ocaml-lwt-log: Update to 1.1.1. 
* gnu/packages/ocaml.scm (ocaml-lwt-log): Update to 1.1.1.
[source]: Use git-fetch.
 2019-09-04 23:08:22 +02:00
Julien Lepiller 8dfe8fee54
gnu: ocaml-biniou: Update to 1.2.1. 
* gnu/packages/ocaml.scm (ocaml-biniou): Update to 1.2.1.
 2019-09-04 23:08:18 +02:00
Julien Lepiller b2f810fe93
import: opam: Use propagated-inputs instead of inputs. 
* guix/import/opam.scm (opam->guix-package): Use propagated-inputs instead of inputs.
 2019-09-04 23:08:16 +02:00
Julien Lepiller d3366a8ee8
import: opam: Remove initial "v" in some version numbers. 
* guix/import/opam.scm (opam-fetch): Remove initial "v" in some version numbers.
 2019-09-04 23:07:55 +02:00
nixo 11d73fb412
gnu: julia: Set search path. 
* gnu/packages/julia.scm (julia)[native-search-paths]: Add
specification for JULIA_LOAD_PATH.

Signed-off-by: Julien Lepiller <julien@lepiller.eu>
 2019-09-04 22:18:07 +02:00
nixo a44a535ebe
build: Add julia-build-system. 
* guix/build/julia-build-system.scm: New file.
* guix/build-system/julia.scm: New file.
* Makefile.am (MODULES): Add them.
* doc/guix.texi (Build Systems): Document julia-build-system.

Signed-off-by: Julien Lepiller <julien@lepiller.eu>
 2019-09-04 22:17:38 +02:00
Marius Bakke 4ab97ef18f
Revert "gnu: texinfo: Fix cross-compilation." 
This causes too many rebuilds for the master branch.

This reverts commit 210b6412ee.
 2019-09-04 19:18:10 +02:00