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Author SHA1 Message Date
Alex Vong
eea5530c9f
gnu: Add clojure-algo-generic. 
* gnu/packages/lisp.scm (clojure-algo-generic): New public variable.
 2018-11-19 12:09:39 +01:00
Alex Vong
c784ffa0c4
gnu: Add clojure-core-match. 
* gnu/packages/lisp.scm (clojure-core-match): New public variable.
 2018-11-19 12:09:15 +01:00
Alex Vong
d2a659e5bf
gnu: Add clojure-instaparse. 
* gnu/packages/lisp.scm (clojure-instaparse): New public variable.
 2018-11-19 12:08:26 +01:00
Alex Vong
53f316ab90
guix: Add clojure-utils. 
* guix/build/clojure-utils.scm: New file.
* gnu/packages/lisp.scm (clojure)[arguments]: Use it.
* Makefile.am (MODULES): Add it.
 2018-11-19 12:05:19 +01:00
Alex Vong
d0ad97115a
gnu: clojure: Use (guix build java-utils) to simplify build phases. 
* gnu/packages/lisp.scm (clojure)[arguments]: Use 'ant-build-javadoc',
'install-jars' and 'install-javadoc' in build phases.
 2018-11-19 12:02:26 +01:00
Alex Vong
8da9187a5a
gnu: clojure: Refactor to ensure there's a single list of libraries. 
This avoids having to update multiple lists.

* gnu/packages/lisp.scm (clojure)[native-inputs]: Use new local variable.
[arguments]: Adjust build phases accordingly.
 2018-11-19 12:02:09 +01:00
Alex Vong
df0a180421
gnu: clojure: Remove 'remove-archives' snippet. 
This is no longer needed since clojure now makes official source releases
in github.

* gnu/packages/lisp.scm (clojure)[source]: Remove it.
[native-inputs]: Remove it in 'submodule'.
[arguments]: Adjust 'unpack-submodule-sources' phase accordingly.
 2018-11-19 12:01:48 +01:00
Alex Vong
28e32b14e4
gnu: clojure: Move from java to lisp. 
* gnu/packages/java.scm (clojure): Move from here...
* gnu/packages/lisp.scm (clojure): ...to here.
 2018-11-19 12:01:25 +01:00
Jovany Leandro G.C
f4ee41c960
gnu: python-kivy: Update to 1.10.1 
* gnu/packages/python.scm (python-kivy): Update to 1.10.1.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-11-19 09:59:08 +01:00
Ludovic Courtès
5e9ce98af7
gnu: help2man: Add 1.47.8. 
* gnu/packages/man.scm (help2man/latest): New variable.
 2018-11-19 09:59:08 +01:00
Ludovic Courtès
1372754dc0
gnu: fuse-exfat: Update to 1.3.0. 
* gnu/packages/linux.scm (fuse-exfat): Update to 1.3.0.
 2018-11-19 09:59:08 +01:00
Ludovic Courtès
c39f3e1c43
gnu: diffoscope: Update to 105. 
* gnu/packages/package-management.scm (diffoscope): Update to 105.
 2018-11-19 09:59:07 +01:00
Leo Famulari
5c40a69f71
gnu: Add libfdk 'FDK AAC' library. 
* gnu/packages/audio.scm (libfdk): New variable.
 2018-11-18 18:19:34 -05:00
Julien Lepiller
564cf93f2a
gnu: ocaml: Update to 4.7.0. 
Update ocaml to the latest version and fixes dependent packages by
updating them or by adding new inputs, such as ocaml-num and ocamlbuild,
that were removed from the core ocaml package. Rename packages that
cannot be built with the new compiler with an ocaml4.02 prefix. Add
ocaml4.02 dependencies.

* gnu/packages/ocaml.scm (ocaml): Update to 4.7.0.
(ocaml-4.02, ocamlbuild, camlp4-4.02, ocaml-num, ocaml4.02-menhir)
(ocaml4.02-lablgtk, ocaml4.02-findlib, ocaml4.02-ounit, ocaml4.02-camlzip)
(ocaml4.02-ocamlmod, ocaml4.02-zarith, ocaml4.02-qcheck, ocaml4.02-qtest)
(ocaml4.02-stringext, ocaml4.02-bisect, dune, ocaml-migrate-parsetree)
(ocaml-ppx-tools-versioned, ocaml-ppx-tools-versioned)
(ocaml4.02-bitstring, ocaml4.02-result, ocaml4.02-topkg, ocaml4.02-rresult)
(ocaml4.02-sqlite3, ocaml4.02-csv, ocaml4.02-mtime, ocaml4.02-cmdliner)
(ocaml4.02-fmt, ocaml4.02-astring, ocaml4.02-alcotest, ocaml4.02-ppx-tools)
(ocaml4.02-react, ocaml4.02-ssl, ocaml4.02-lwt, ocaml-lwt-log)
(ocaml4.02-lwt-log, ocaml4.02-logs, ocaml4.02-fpath, ocaml4.02-bos)
(ocaml4.02-xmlm, ocaml4.02-ulex, ocaml4.02-uchar, ocaml4.02-uutf)
(ocaml4.02-jsonm, ocaml4.02-ocurl, ocaml4.02-base64, ocaml4.02-omake)
(ocaml4.02-batteries, ocaml4.02-pcre, ocaml4.02-oasis)
(ocaml4.02-js-build-tools, ocaml4.02-cppo, ocaml-seq, ocaml4.02-seq)
(ocaml4.02-re, ocaml4.02-ocplib-endian, ocaml4.02-easy-format)
(ocaml4.02-piqilib, ocaml4.02-uuidm, ocaml4.02-graph, ocaml4.02-piqi)
(ocaml4.02-camomile, ocaml4.02-zed, ocaml4.02-lambda-term): New packages.
(opam): Update to 2.0.0.
(camlp4): Update to 4.07+1.
(camlp5): Update to 7.06.
(hevea): Update to 2.32.
(coq)[inputs]: Add ocaml-num.
(emacs-tuareg): Update to 2.2.0.
(ocaml-menhir)[native-inputs]: Add ocamlbuild.
(ocaml-lablgtk): Update to 2.18.6.
(unison)[inputs]: Use ocaml-4.02.
(ocaml-findlib): Update to 1.8.0.
(ocaml-ounit)[native-inputs]: Add ocamlbuild.
(ocamlmod): Update to 0.0.9.
(ocaml-frontc)[arguments]: Use ocaml-4.02.
(ocaml-qcheck)[native-inputs]: Add ocamlbuild.
(ocaml-qtest)[native-inputs]: Remove ocaml-findlib and add ocamlbuild.
(ocaml-stringext)[native-inputs]: Add ocamlbuild.
(ocaml-bisect): Update to 1.3.1.
(ocaml4.01-bisect): Downgrade to 1.3.
(ocaml-bitstring): Update to 3.1.0.
(ocaml-topkg)[native-inputs]: Add ocamlbuild.
(ocaml-rresult)[native-inputs]: Add ocamlbuild.
(ocaml-sqlite3)[native-inputs]: Add ocamlbuild.
(ocaml-csv)[native-inputs]: Add ocamlbuild.
(ocaml-mtime)[native-inputs]: Add ocamlbuild.
(ocaml-cmdliner)[native-inputs]: Add ocamlbuild.
(ocaml-fmt)[native-inputs]: Add ocamlbuild.
(ocaml-astring)[native-inputs]: Add ocamlbuild.
(ocaml-alcotest)[native-inputs]: Add ocamlbuild.
(ocaml-ppx-tools)[native-inputs]: Add ocamlbuild.
(ocaml-react)[native-inputs]: Add ocamlbuild.
(ocaml-ssl)[arguments]: Return #t in phases.
(ocaml-lwt): Update to 4.1.0.
(ocaml-logs)[native-inputs]: Add ocamlbuild.
(ocaml-fpath)[native-inputs]: Add ocamlbuild.
(ocaml-bos)[native-inputs]: Add ocamlbuild.
(ocaml-xmlm): Update to 1.3.0.
(ocaml-ulex): Update to 1.2.0.
(ocaml-uchar)[native-inputs]: Add ocamlbuild.
(ocaml-uutf): Update to 1.0.1.
(ocaml-jsonm): Update to 1.0.1.
(ocaml-ocurl): Update to 0.8.2.
(ocaml-base64)[native-inputs]: Add ocamlbuild.
(ocamlify)[native-inputs]: Use ocaml-4.02.
(omake): Update to 0.10.3.
(ocaml-batteries): Update to 2.9.0.
(ocaml-pcre)[native-inputs]: Add ocamlbuild.
(ocaml-expect): Update 0.0.6.
(ocaml4.02-fileutils): Update to 0.5.3.
(ocaml-oasis): Update 0.4.11.
(ocaml-js-build-tools)[native-inputs]: Add ocamlbuild.
(ocaml-bin-prot): Rename to ocaml4.02-bin-prot.
(ocaml-fieldslib): Rename to ocaml4.02-fieldslib.
(ocaml-ppx-core): Rename to ocaml4.02-ppx-core.
(ocaml-ppx-optcomp): Rename to ocaml4.02-ppx-optcomp.
(ocaml-ppx-driver): Rename to ocaml4.02-ppx-driver.
(ocaml-cppo): Update to 1.6.5.
(ocaml-ppx-deriving): Rename to ocaml4.02-ppx-deriving.
(ocaml-ppx-type-conv): Rename to ocaml4.02-ppx-type-conv.
(ocaml-ppx-inline-test): Rename to ocaml4.02-ppx-inline-test.
(ocaml-ppx-bench): Rename to ocaml4.02-ppx-bench.
(ocaml-ppx-compare): Rename to ocaml4.02-ppx-compare.
(ocaml-sexplib): Rename to ocaml4.02-sexplib.
(ocaml-typerep): Rename to ocaml4.02-typerep.
(ocaml-variantslib): Rename to ocaml4.02-variantslib.
(ocaml-ppx-sexp-conv): Rename to ocaml4.02-ppx-sexp-conv.
(ocaml-ppx-variants-conv): Rename to ocaml4.02-ppx-variants-conv.
(ocaml-ppx-here): Rename to ocaml4.02-ppx-here.
(ocaml-ppx-assert): Rename to ocaml4.02-ppx-assert.
(ocaml-ppx-enumerate): Rename to ocaml4.02-ppx-enumerate.
(ocaml-ppx-let): Rename to ocaml4.02-ppx-let.
(ocaml-ppx-typerep-conv): Rename to ocaml4.02-ppx-typerep-conv.
(ocaml-ppx-sexp-value): Rename to ocaml4.02-ppx-sexp-value.
(ocaml-ppx-pipebang): Rename to ocaml4.02-ppx-pipebang.
(ocaml-ppx-bin-prot): Rename to ocaml4.02-ppx-bin-prot.
(ocaml-ppx-fail): Rename to ocaml4.02-ppx-fail.
(ocaml-ppx-custom-printf): Rename to ocaml4.02-ppx-custom-printf.
(ocaml-ppx-sexp-message): Rename to ocaml4.02-ppx-sexp-message.
(ocaml-ppx-fields-conv): Rename to ocaml4.02-ppx-fields-conv.
(ocaml-re): Update to 1.8.0.
(ocaml-ppx-expect): Rename to ocaml4.02-ppx-expect.
(ocaml-ppx-jane): Rename to ocaml4.02-ppx-jane.
(ocaml-core-kernel): Rename to ocaml4.02-core-kernel.
(ocaml-async-kernel): Rename to ocaml4.02-async-kernel.
(ocaml-async-rpc-kernel): Rename to ocaml4.02-async-rpc-kernel.
(ocaml-core): Rename to ocaml4.02-core.
(ocaml-async-unix): Rename to ocaml4.02-async-unix.
(ocaml-async-extra): Rename to ocaml4.02-async-extra.
(ocaml-async): Rename to ocaml4.02-async.
(ocaml-ocplib-endian)[native-inputs]: Update to 1.0.
(ocaml-cstruct): Rename to ocaml4.02-cstruct.
(ocaml-hex): Rename to ocaml4.02-hex.
(ocaml-ezjsonm): Rename to ocaml4.02-ezjsonm.
(ocaml-uri): Rename to ocaml4.02-uri.
(optcomp): Use ocaml-4.02.
(ocaml-piqilib): Update to 0.6.14.
(ocaml-uuidm)[native-inputs]: Add ocamlbuild.
(ocaml-graph): Update to 1.8.8.
(ocaml-piqi): Update to 0.7.6.
(bap): Update to 1.3.0.
(ocaml-camomile): Update to 1.0.1.
(ocaml-jbuilder): Use ocaml-4.02.
(ocaml-lambda-term): Update to 1.13.
(ocaml-utop): Update to 2.2.0.
(ocaml-integers)[native-inputs]: Add ocamlbuild.
(ocaml-ctypes): Update to 0.14.0.
(ocaml-ocb-stubblr)[native-inputs]: Add ocamlbuild.
(ocaml-tsdl)[native-inputs]: Add ocamlbuild.
* gnu/packages/machine-learning.scm (ocaml-mcl): Use ocaml-4.02.
* gnu/packages/maths.scm (cubicle): Update to 1.1.2.
* gnu/packages/patches/ocaml-bisect-fix-camlp4-in-another-directory.patch:
Update patch.
* guix/build-system/ocaml.scm: (default-ocaml4.02, default-ocaml4.02-findlib)
(package-with-ocaml4.02, strip-ocaml4.02-variant): New variables.
 2018-11-18 18:51:08 +01:00
Kei Kebreau
1472d19abf
gnu: maxima: Fix tests on i686 and x86_64. 
* gnu/packages/maths.scm (maxima)[arguments]: Replace check phase.
 2018-11-18 11:58:38 -05:00
Pierre Neidhardt
d22ba64276
gnu: ccl: Include x86-headers and remove missing "contrib" folder. 
* gnu/packages/lisp.scm (ccl): Include x86-headers and remove missing "contrib" folder.
 2018-11-18 10:39:47 +01:00
Marius Bakke
f8cba3ff4f
gnu: mesa: Stay on RTTI-less LLVM. 
* gnu/packages/llvm.scm (llvm-without-rtti): New public variable.
* gnu/packages/gl.scm (mesa)[inputs]: Use that instead of LLVM.
 2018-11-17 22:54:03 +01:00
Eric Bavier
0a41123f01
gnu: Add ClamAV. 
* gnu/packages/antivirus.scm: New file.
* gnu/packages/patches/clamav-system-tomsfastmath.patch,
gnu/packages/patches/clamav-config-llvm-libs.patch: New files.
* gnu/local.mk (GNU_SYSTEM_MODULES): Add new module.
(dist_patch_DATA): Add patches.

Co-authored-by: Christopher Baines <mail@cbaines.net>
 2018-11-17 00:20:44 -06:00
Eric Bavier
7ed018e8a2
gnu: Add TomsFastMath. 
* gnu/packages/multiprecision.scm (tomsfastmath): New variable.
* gnu/packages/patches/tomsfastmath-constness.patch: New patch.
* gnu/local.mk (dist_patch_DATA): Add it.
 2018-11-17 00:20:44 -06:00
Eric Bavier
fc9dbf4131
llvm: Build with RTTI by default. 
Increases size of llvm@6 by 2.5MiB (2.5%), but saves building specialized
llvm's with rtti enabled for packages that require RTTI when linking with the
llvm libraries.

* gnu/packages/llvm.scm (llvm-3.8-with-rtti): Remove variable.
(llvm)[arguments]: Add '-DLLVM_REQUIRES_RTTI=1' to #:configure-flags.
* gnu/packages/audio.scm (faust-2)[native-inputs]:
'llvm-3.8-with-rtti' -> 'llvm-3.8'.
 2018-11-17 00:19:53 -06:00
Vagrant Cascadian
0c7707d53e
gnu: u-boot: Update to 2018.11. 
* gnu/packages/bootloaders.scm (u-boot): Update to 2018.11.
(u-boot)[native-inputs]: Add lz4.
 2018-11-17 00:16:29 +01:00
Kyle Meyer
243bdcc12e
gnu: Add git-when-merged. 
* gnu/packages/version-control.scm (git-when-merged): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-11-16 23:11:40 +01:00
Thorsten Wilms
7a44e8752e
gnu: Add caps-plugins-lv2. 
* gnu/packages/audio.scm (caps-plugins-lv2): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-11-16 23:09:00 +01:00
David Thompson
a7b7d48cc7
gnu: tiled: Update to 1.2.1. 
* gnu/packages/game-development.scm (tiled): Update to 1.2.1.
 2018-11-16 10:34:29 -05:00
Mathieu Othacehe
2aee2a96b6
guile: newt: Update revision to 2. 
* gnu/packages/guile.scm (guile-newt): Update revision to 2.
 2018-11-16 17:42:07 +09:00
Andreas Enge
eea7cd7519
gnu: Add cmh. 
* gnu/packages/algebra.scm (cmh): New variable.
 2018-11-16 09:06:31 +01:00
Andreas Enge
44ff80fc0e
gnu: gp2c: Update to 0.0.11pl1. 
* gnu/packages/algebra.scm (gp2c): Update to 0.0.11pl1.
 2018-11-16 08:48:47 +01:00
Maxim Cournoyer
03592a6f88
gnu: emacs-realgud: Patch configure.ac to repair the build. 
This fixes https://bugs.gnu.org/33196, a build problem caused by a defective
Elisp snippet in a check in configure.ac.

* gnu/packages/patches/emacs-realgud-fix-configure-ac.patch: Add patch.
* gnu/local.mk (dist_patch_DATA): Register it.
* gnu/packages/emacs.scm (emacs-realgud)[source]: Use it.
 2018-11-15 22:42:35 -05:00
pimi
30f0d21b40
gnu: Add nanopolish. 
* gnu/packages/bioinformatics.scm (nanopolish): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2018-11-15 22:23:57 +01:00
Roel Janssen
2d86eaff5b
gnu: sambamba: Update to 0.6.8. 
* gnu/packages/bioinformatics.scm (sambamba): Update to 0.6.8.
 2018-11-15 13:09:01 +01:00
Mark H Weaver
7413c31693
gnu: linux-libre: Update to 4.19.2. 
* gnu/packages/linux.scm (%linux-libre-version): Update to 4.19.2.
(%linux-libre-hash): Update hash.
 2018-11-14 19:16:24 -05:00
Mark H Weaver
24ba798731
gnu: linux-libre@4.14: Update to 4.14.81. 
* gnu/packages/linux.scm (%linux-libre-4.14-version): Update to 4.14.81.
(%linux-libre-4.14-hash): Update hash.
 2018-11-14 19:14:39 -05:00
Mark H Weaver
6a1cff70bc
gnu: linux-libre@4.9: Update to 4.9.137. 
* gnu/packages/linux.scm (linux-libre-4.9): Update to 4.9.137.
 2018-11-14 19:13:46 -05:00
Paul Garlick
ae0f1dd1a4
gnu: Add fenics. 
* gnu/packages/simulation.scm (fenics): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-11-14 21:34:09 +01:00
Paul Garlick
0ace6c0b84
gnu: Add fenics-dolfin. 
* gnu/packages/simulation.scm (fenics-dolfin): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-11-14 21:34:09 +01:00
Paul Garlick
6b7f1f8afa
gnu: Add python-fenics-ffc. 
* gnu/packages/simulation.scm (python-fenics-ffc): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-11-14 21:34:09 +01:00
Paul Garlick
0fc499834f
gnu: Add python-fenics-fiat. 
* gnu/packages/simulation.scm (python-fenics-fiat): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-11-14 21:34:08 +01:00
Paul Garlick
3941cf5afa
gnu: Add python-fenics-ufl. 
* gnu/packages/simulation.scm (python-fenics-ufl): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-11-14 21:34:08 +01:00
Paul Garlick
f7a4757a4c
gnu: Add python-fenics-dijitso. 
* gnu/packages/simulation.scm (python-fenics-dijitso): New varaible.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-11-14 21:34:08 +01:00
Paul Garlick
6b5687d053
gnu: Add python-slepc4py. 
* gnu/packages/maths.scm (python-slepc4py): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-11-14 21:34:08 +01:00
Paul Garlick
90ff287401
gnu: Add python-petsc4py. 
* gnu/packages/maths.scm (python-petsc4py): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-11-14 21:34:08 +01:00
Paul Garlick
54fcd547b3
gnu: Add python-mpi4py. 
* gnu/packages/mpi.scm (python-mpi4py): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-11-14 21:34:08 +01:00
Ludovic Courtès
7a54b2281d
gnu: guix-daemon: Install 'guix-authenticate'. 
Fixes <https://bugs.gnu.org/33368>.
Reported by Konrad Hinsen <konrad.hinsen@fastmail.net>.

* gnu/packages/package-management.scm (guix-daemon)[arguments]: In
'install' phase, build "install-nodist_libexecSCRIPTS" target to install
'guix-authenticate'.
 2018-11-14 21:34:08 +01:00
Marius Bakke
e921993c25
gnu: xf86-video-r128: Update to 6.12.0. 
* gnu/packages/xorg.scm (xf86-video-r128): Update to 6.12.0.
 2018-11-14 21:05:30 +01:00
Marius Bakke
24dd6ec38a
gnu: mtools: Update to 4.0.20. 
* gnu/packages/mtools.scm (mtools): Update to 4.0.20.
[source](uri): Change to 'bz2' compressed tarball.
 2018-11-14 21:05:30 +01:00
Marius Bakke
7939387da8
gnu: nano: Update to 3.2. 
* gnu/packages/nano.scm (nano): Update to 3.2.
 2018-11-14 21:05:30 +01:00
Marius Bakke
d63f588486
gnu: sudo: Update to 1.8.26. 
* gnu/packages/admin.scm (sudo): Update to 1.8.26.
 2018-11-14 21:05:30 +01:00
Marius Bakke
bac2974e86
gnu: feh: Update to 3.0. 
* gnu/packages/image-viewers.scm (feh): Update to 3.0.
 2018-11-14 21:05:30 +01:00
Ricardo Wurmus
ee66a13563
gnu: Add jamm. 
* gnu/packages/bioinformatics.scm (jamm): New variable.
 2018-11-14 15:13:20 +01:00
Ricardo Wurmus
e4f4a04a51
gnu: Add r-ouch. 
* gnu/packages/cran.scm (r-ouch): New variable.
 2018-11-14 15:13:20 +01:00
Ricardo Wurmus
10483a64ee
gnu: Add r-activity. 
* gnu/packages/cran.scm (r-activity): New variable.
 2018-11-14 15:13:20 +01:00
Ricardo Wurmus
3cef715a46
gnu: Add r-circular. 
* gnu/packages/cran.scm (r-circular): New variable.
 2018-11-14 15:13:20 +01:00
Ricardo Wurmus
08bf097a0b
gnu: Add r-overlap. 
* gnu/packages/cran.scm (r-overlap): New variable.
 2018-11-14 15:13:20 +01:00
Ricardo Wurmus
acbf23da44
gnu: Add r-acdm. 
* gnu/packages/cran.scm (r-acdm): New variable.
 2018-11-14 15:13:20 +01:00
Ricardo Wurmus
ffdeda3ce0
gnu: Add r-acd. 
* gnu/packages/cran.scm (r-acd): New variable.
 2018-11-14 15:13:20 +01:00
Ricardo Wurmus
488dc4e1e2
gnu: Add r-abn. 
* gnu/packages/cran.scm (r-abn): New variable.
 2018-11-14 15:13:20 +01:00
Ricardo Wurmus
0c92f3734e
gnu: Add r-rjags. 
* gnu/packages/cran.scm (r-rjags): New variable.
 2018-11-14 15:13:20 +01:00
Ricardo Wurmus
0bca8643a2
gnu: Add jags. 
* gnu/packages/statistics.scm (jags): New variable.
 2018-11-14 15:13:17 +01:00
Ricardo Wurmus
51b262f310
gnu: r-txdb-mmusculus-ucsc-mm10-knowngene: Update to 3.4.4. 
* gnu/packages/bioinformatics.scm (r-txdb-mmusculus-ucsc-mm10-knowngene):
Update to 3.4.4.
 2018-11-13 23:34:40 +01:00
Ricardo Wurmus
d34959b8d4
gnu: r-org-mm-eg-db: Update to 3.7.0. 
* gnu/packages/bioinformatics.scm (r-org-mm-eg-db): Update to 3.7.0.
 2018-11-13 23:34:40 +01:00
Ricardo Wurmus
314511b862
gnu: r-org-dm-eg-db: Update to 3.7.0. 
* gnu/packages/bioinformatics.scm (r-org-dm-eg-db): Update to 3.7.0.
 2018-11-13 23:34:39 +01:00
Ricardo Wurmus
76bd16bcf6
gnu: r-org-ce-eg-db: Update to 3.7.0. 
* gnu/packages/bioinformatics.scm (r-org-ce-eg-db): Update to 3.7.0.
 2018-11-13 23:34:39 +01:00
Ricardo Wurmus
fc7683fa30
gnu: r-org-hs-eg-db: Update to 3.7.0. 
* gnu/packages/bioinformatics.scm (r-org-hs-eg-db): Update to 3.7.0.
 2018-11-13 23:34:39 +01:00
Ricardo Wurmus
cb9e6ed702
gnu: r-genomationdata: Update to 1.14.0. 
* gnu/packages/bioinformatics.scm (r-genomationdata): Update to 1.14.0.
 2018-11-13 23:34:39 +01:00
Ricardo Wurmus
13e70f6304
gnu: r-go-db: Update to 3.7.0. 
* gnu/packages/bioinformatics.scm (r-go-db): Update to 3.7.0.
 2018-11-13 23:34:39 +01:00
Ricardo Wurmus
13a574652b
gnu: r-genomeinfodbdata: Update to 1.2.0. 
* gnu/packages/bioinformatics.scm (r-genomeinfodbdata): Update to 1.2.0.
 2018-11-13 23:34:39 +01:00
Taegil Bae
3f995aaf21
gnu: spice-vdagent: Fix typo in desktop file. 
Fixes <https://bugs.gnu.org/33346>.

* gnu/packages/spice.scm (spice-vdagent)[arguments]: Fix typo in
'patch-spice-vdagent.desktop' phase.
 2018-11-13 15:26:30 -05:00
Alex Vong
c991806a7d
gnu: ImageMagick: Update to 6.9.10-14. 
* gnu/packages/imagemagick.scm (imagemagick): Update to 6.9.10-14.
 2018-11-14 03:09:37 +08:00
Leo Famulari
d540137509
gnu: libssh: Fetch source over HTTPS. 
* gnu/packages/ssh.scm (libssh)[source]: Use HTTPS URL.
 2018-11-13 11:43:35 -05:00
Leo Famulari
978d59737a
gnu: direnv: Build with Go 1.9. 
* gnu/packages/shellutils.scm (direnv)[native-inputs]: Remove go.
[inputs]: Add go-1.9.
 2018-11-13 11:28:23 -05:00
Leo Famulari
021bf6af18
gnu: Poppler: Fix CVE-2018-19149. 
* gnu/packages/patches/poppler-CVE-2018-19149.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/pdf.scm (poppler)[replacement]: New field.
(poppler/fixed): New variable.
(poppler-qt4, poppler-qt5): Use package/inherit.
 2018-11-13 11:28:23 -05:00
Leo Famulari
8263b9f71f
gnu: certbot, python-acme: Update to 0.28.0. 
* gnu/packages/tls.scm (certbot, python-acme): Update to 0.28.0.
 2018-11-13 10:10:42 -05:00
Ludovic Courtès
3483f82413
gnu: guix: Update to f5a2724. 
* gnu/packages/package-management.scm (guix): Update to f5a2724.
 2018-11-13 15:44:25 +01:00
Oleg Pykhalov
155956449a
gnu: restic: Fix build phase. 
* gnu/packages/backup.scm (restic)[arguments]: Set "HOME" environment variable
in build phase.
 2018-11-13 15:03:15 +03:00
Ricardo Wurmus
6018683683
gnu: c-toxcore: Fetch sources from git. 
* gnu/packages/messaging.scm (c-toxcore)[source]: Fetch from git.
 2018-11-13 10:51:41 +01:00
Rutger Helling
7fed5481fe
gnu: wine-staging: Update to 3.20. 
* gnu/packages/wine.scm (wine-staging-patchset-data): Update to 3.20.
* gnu/packages/wine.scm (wine-staging): Update to 3.20.
 2018-11-13 10:24:42 +01:00
Julien Lepiller
0dd60c1c9b
gnu: php: Update to 7.2.12. 
* gnu/packages/php.scm (php): Update to 7.2.12.
 2018-11-12 23:57:42 +01:00
Arun Isaac
e740a90228
gnu: youtube-dl: Update to 2018.11.07. 
* gnu/packages/video.scm (youtube-dl): Update to 2018.11.07.
 2018-11-12 22:09:12 +05:30
Efraim Flashner
53bcee9ea7
gnu: vifm: Update to 0.10. 
* gnu/packages/vim.scm (vifm): Update to 0.10.
 2018-11-12 12:37:00 +02:00
Pierre Neidhardt
5c4758415d
gnu: go-github-com-aarzilli-golua: Fix for go-1.11. 
* gnu/packages/golang.scm (go-github-com-aarzilli-golua)[arguments]: Fix for go-1.11.
[native-inputs]: Remove lua.
[propagated-inputs]: Add lua.
 2018-11-12 10:31:23 +01:00
Pierre Neidhardt
46a4ae2212
gnu: go-github-com-wtolson-go-taglib: Fix tests and build for go-1.11. 
* gnu/packages/golang.scm (go-github-com-wtolson-go-taglib)[arguments]: Fix tests for go-1.11.
[native-inputs]: Remove pkg-config and taglib.
[propagated-inputs]: Add pkg-config and taglib.
 2018-11-12 10:30:10 +01:00
Pierre Neidhardt
66fa8f0f77
gnu: go-gopkg.in-asn1-ber.v1: Fix tests for go-1.11. 
* gnu/packages/syncthing.scm (go-gopkg.in-asn1-ber.v1): Fix tests for go-1.11.
 2018-11-12 10:29:43 +01:00
Pierre Neidhardt
d4780c8238
gnu: go-github-com-audriusbutkevicius-cli: Fix tests for go-1.11. 
* gnu/packages/syncthing.scm (go-github-com-audriusbutkevicius-cli): Fix tests for go-1.11.
 2018-11-12 10:29:37 +01:00
Pierre Neidhardt
46a37b5966
gnu: go-github-com-prometheus-common-expfmt: Fix tests for go-1.11. 
* gnu/packages/syncthing.scm (go-github-com-prometheus-common-expfmt): Fix tests for go-1.11.
 2018-11-12 10:29:31 +01:00
Pierre Neidhardt
9a65a05201
gnu: go: Update default to 1.11. 
* gnu/packages/golang.scm (go): Update default to 1.11.
 2018-11-12 10:28:46 +01:00
Ricardo Wurmus
5f9b38ba34
gnu: r-s4vectors: Update to 0.20.1. 
* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.20.1.
 2018-11-11 23:13:48 +01:00
Ricardo Wurmus
06910a8689
gnu: r-rcmdcheck: Update to 1.3.2. 
* gnu/packages/cran.scm (r-rcmdcheck): Update to 1.3.2.
 2018-11-11 23:13:48 +01:00
Ricardo Wurmus
2a4c5877a9
gnu: r-ggpubr: Update to 0.1.9. 
* gnu/packages/cran.scm (r-ggpubr): Update to 0.1.9.
 2018-11-11 23:13:48 +01:00
Ricardo Wurmus
441cf11de1
gnu: r-dplyr: Update to 0.7.8. 
* gnu/packages/statistics.scm (r-dplyr): Update to 0.7.8.
 2018-11-11 23:13:48 +01:00
Ricardo Wurmus
41d2c26e67
gnu: r-rcpparmadillo: Update to 0.9.200.4.0. 
* gnu/packages/statistics.scm (r-rcpparmadillo): Update to 0.9.200.4.0.
 2018-11-11 23:13:48 +01:00
Ricardo Wurmus
23dd886a95
gnu: r-rtsne: Update to 0.15. 
* gnu/packages/statistics.scm (r-rtsne): Update to 0.15.
 2018-11-11 23:13:48 +01:00
Ricardo Wurmus
7865c8c460
gnu: r-lme4: Update to 1.1-19. 
* gnu/packages/statistics.scm (r-lme4): Update to 1.1-19.
 2018-11-11 23:13:48 +01:00
Marius Bakke
a509b18087
gnu: webkitgtk@2.22: Adjust to documentation output. 
This is a follow-up to commit 0ead0b4d2c.

* gnu/packages/webkit.scm (webkitgtk)[arguments]: Remove hard coded file list.
(webkitgtk-2.22)[arguments]: Inherit phases using SUBSTITUTE-KEYWORD-ARGUMENTS.
 2018-11-11 22:47:06 +01:00
Ricardo Wurmus
aaf0e47f6d
gnu: libtoxcore: Update to 0.0.0-2.bf69b54. 
* gnu/packages/messaging.scm (libtoxcore): Update to 0.0.0-2.bf69b54.
[native-inputs]: Add check.
 2018-11-11 20:51:51 +01:00
Ricardo Wurmus
e874f34d3f
gnu: mumi: Update to 0.0.0-2.bfd96ce7. 
* gnu/packages/mail.scm (mumi): Update to 0.0.0-2.bfd96ce7.
 2018-11-11 20:51:51 +01:00
Leo Famulari
ec35067631
gnu: PostgreSQL: Update to 10.6 [fixes CVE-2018-16850]. 
* gnu/packages/databases.scm (postgresql): Update to 10.6.
 2018-11-11 14:10:03 -05:00
Pierre Neidhardt
0ead0b4d2c
gnu: webkitgtk: Include documentation. 
* gnu/packages/webkit.scm (webkitgtk): Include documentation.
 2018-11-11 16:44:46 +01:00
Pierre Neidhardt
50ee7e93fc
gnu: gtk-doc: Use local docbook-xsl. 
* gnu/packages/gtk.scm (gtk-doc): Use local docbook-xsl.
 2018-11-11 16:41:45 +01:00
Ricardo Wurmus
89c7894805
gnu: faust-2: Update to 2.5.23. 
* gnu/packages/audio.scm (faust-2): Update to 2.5.23.
[native-inputs]: Replace llvm-with-rtti with llvm-3.8-with-rtti.
* gnu/packages/llvm.scm (llvm-with-rtti): Rename this variable...
(llvm-3.8-with-rtti): ...to this variable; inherit from llvm-3.8.
 2018-11-11 16:19:59 +01:00
Clément Lassieur
37a350ecce
gnu: gajim: Move python-docutils from inputs to native-inputs. 
* gnu/packages/messaging.scm (gajim): Move python-docutils from inputs to
native-inputs.
 2018-11-11 16:00:08 +01:00
Clément Lassieur
60c5b44489
gnu: gajim: Get the second 'wrap-program' phase to return #t. 
* gnu/packages/messaging.scm (gajim)[arguments]: Get the second 'wrap-program'
phase to return #t.
 2018-11-11 16:00:00 +01:00
Clément Lassieur
992a496503
gnu: gajim: Update to 1.1.0. 
* gnu/packages/messaging.scm (gajim): Update to 1.1.0.
[arguments]: Set #:test-target to "test_nogui".  Remove the
'remove-test-resolver' and 'start-xserver' phases.
[inputs]: Remove python-pyasn1.  Add python-cssutils, python-keyring and
python-precis-i18n.
 2018-11-11 15:59:07 +01:00
Clément Lassieur
a311f42e1b
gnu: python-nbxmpp: Update to 0.6.8. 
* gnu/packages/messaging.scm (python-nbxmpp): Update to 0.6.8.
 2018-11-11 15:59:03 +01:00
Clément Lassieur
4ad3786b7b
gnu: Add python-precis-i18n. 
* gnu/packages/messaging.scm (python-precis-i18n): New variable.
 2018-11-11 15:58:50 +01:00
Ricardo Wurmus
902068b436
gnu: tiled: Fetch sources from git. 
* gnu/packages/game-development.scm (tiled)[source]: Fetch from git.
 2018-11-11 13:18:27 +01:00
Ricardo Wurmus
9066424778
gnu: privoxy: Remove custom bootstrap phase. 
* gnu/packages/tor.scm (privoxy)[arguments]: Remove autoconf phase.
 2018-11-11 13:10:56 +01:00
Ricardo Wurmus
2b61cd37b4
gnu: cifs-utils: Remove autoreconf phase. 
* gnu/packages/samba.scm (cifs-utils)[arguments]: Remove autoreconf phase.
 2018-11-11 13:08:56 +01:00
Ricardo Wurmus
cd1f661e82
gnu: libiax2: Fetch sources from git. 
* gnu/packages/telephony.scm (libiax2)[source]: Fetch from git.
 2018-11-11 13:06:31 +01:00
Ricardo Wurmus
5a103bb84e
gnu: libiax2: Remove custom bootstrap phase. 
* gnu/packages/telephony.scm (libiax2)[arguments]: Remove.
 2018-11-11 13:04:08 +01:00
Ricardo Wurmus
6f3dd09f8d
gnu: libharu: Remove custom bootstrap phase. 
* gnu/packages/pdf.scm (libharu)[arguments]: Remove autogen phase.
 2018-11-11 13:00:53 +01:00
Ricardo Wurmus
2b2ab39cfc
gnu: libharu: Fetch sources from git. 
* gnu/packages/pdf.scm (libharu)[source]: Fetch from git.
 2018-11-11 13:00:35 +01:00
Ricardo Wurmus
bc74e9e4cd
gnu: scsh: Remove custom bootstrap phase. 
* gnu/packages/shells.scm (scsh)[arguments]: Remove autoreconf phase.
 2018-11-11 12:56:22 +01:00
Ricardo Wurmus
e5ff963a6d
gnu: xdelta: Remove custom bootstrap phase. 
* gnu/packages/compression.scm (xdelta)[arguments]: Remove autoconf phase.
 2018-11-11 12:52:46 +01:00
Ricardo Wurmus
0633c77b1b
gnu: xdelta: Fetch sources from git. 
* gnu/packages/compression.scm (xdelta)[source]: Fetch from git.
 2018-11-11 12:52:30 +01:00
Ricardo Wurmus
112fcafbae
gnu: libtar: Remove custom bootstrap phase. 
* gnu/packages/compression.scm (libtar)[arguments]: Remove autoconf phase.
 2018-11-11 12:47:51 +01:00
Ricardo Wurmus
3478945948
gnu: minizip: Remove custom bootstrap phase. 
* gnu/packages/compression.scm (minizip)[arguments]: Remove autoreconf phase.
 2018-11-11 12:45:52 +01:00
Ricardo Wurmus
4078beab93
gnu: inotify-tools: Remove custom bootstrap phase. 
* gnu/packages/linux.scm (inotify-tools)[arguments]: Remove.
 2018-11-11 12:36:35 +01:00
Ricardo Wurmus
88f9fea723
gnu: inotify-tools: Fetch sources from git. 
* gnu/packages/linux.scm (inotify-tools)[source]: Fetch from git.
 2018-11-11 12:36:15 +01:00
Ricardo Wurmus
2286107f60
gnu: par2cmdline: Remove custom bootstrap phase. 
* gnu/packages/backup.scm (par2cmdline)[arguments]: Remove.
 2018-11-11 12:31:35 +01:00
Ricardo Wurmus
5cdbdc2b13
gnu: par2cmdline: Fetch sources from git. 
* gnu/packages/backup.scm (par2cmdline)[source]: Fetch from git.
 2018-11-11 12:31:18 +01:00
Ricardo Wurmus
2fef54fd64
gnu: hpcguix-web: Do not re-bootstrap. 
* gnu/packages/web.scm (hpcguix-web)[arguments]: Do not run autoreconf after
the bootstrap phase; remove "autoconf" phase to "set-variables"; end phase
with #T.
 2018-11-11 12:27:01 +01:00
Ricardo Wurmus
cbb6a15056
gnu: schismtracker: Remove custom bootstrap phase. 
* gnu/packages/music.scm (schismtracker)[arguments]: Remove autoconf phase.
 2018-11-11 12:19:23 +01:00
Ricardo Wurmus
8865973848
gnu: lilypond: Use INVOKE. 
* gnu/packages/music.scm (lilypond)[arguments]: Use INVOKE and return #T
unconditionally.
 2018-11-11 12:15:03 +01:00
Ricardo Wurmus
3b9e9415fa
gnu: schismtracker: Fetch sources from git. 
* gnu/packages/music.scm (schismtracker)[source]: Fetch from git.
 2018-11-11 12:07:21 +01:00
Ricardo Wurmus
234a1825b2
gnu: clyrics: Fetch sources from git. 
* gnu/packages/music.scm (clyrics)[source]: Fetch from git.
[native-inputs]: Remove.
[arguments]: Adjust builder.
 2018-11-11 12:01:25 +01:00
Ricardo Wurmus
3a0592ae31
gnu: lmms: Fetch sources from git. 
* gnu/packages/music.scm (lmms)[source]: Fetch from git.
 2018-11-11 12:00:55 +01:00
Ricardo Wurmus
caa39e56f7
gnu: milkytracker: Fetch sources from git. 
* gnu/packages/music.scm (milkytracker)[source]: Fetch from git.
 2018-11-11 11:44:24 +01:00
Ricardo Wurmus
08bc7f2665
gnu: dotconf: Fetch sources from git. 
* gnu/packages/textutils.scm (dotconf)[source]: Fetch from git.
 2018-11-11 11:37:01 +01:00
Ricardo Wurmus
7a52d0e075
gnu: dotconf: Remove custom bootstrap phase. 
* gnu/packages/textutils.scm (dotconf)[arguments]: Remove autoreconf phase.
 2018-11-11 11:36:39 +01:00
Ricardo Wurmus
d68a15806b
gnu: libgtextutils: Remove custom bootstrap phase. 
* gnu/packages/textutils.scm (libgtextutils)[arguments]: Remove.
 2018-11-11 11:34:55 +01:00
Ricardo Wurmus
fab455840e
gnu: libtoxcore: Remove custom bootstrap phase. 
* gnu/packages/messaging.scm (libtoxcore)[arguments]: Remove autoconf phase.
 2018-11-11 11:33:39 +01:00
Ricardo Wurmus
867d9de690
gnu: openocd: Use INVOKE. 
* gnu/packages/embedded.scm (openocd)[arguments]: Use INVOKE and return #T
unconditionally.
 2018-11-11 11:32:12 +01:00
Ricardo Wurmus
4cd6ab1b1f
gnu: libjaylink: Remove custom bootstrap phase. 
* gnu/packages/embedded.scm (libjaylink)[arguments]: Remove.
 2018-11-11 11:23:39 +01:00
Ricardo Wurmus
a69cc70dea
gnu: lrdf: Replace bootstrap phase. 
* gnu/packages/rdf.scm (lrdf)[arguments]: Remove autoreconf phase; replace
bootstrap phase instead.
 2018-11-11 11:22:22 +01:00
Ricardo Wurmus
d212ed2f00
gnu: lrdf: Fetch sources from git. 
* gnu/packages/rdf.scm (lrdf)[source]: Fetch from git.
 2018-11-11 11:21:55 +01:00
Ricardo Wurmus
2cabd29323
gnu: guildhall: Remove custom bootstrap phase. 
* gnu/packages/guile.scm (guildhall)[arguments]: Remove autogen phase.
 2018-11-11 10:38:00 +01:00
Ricardo Wurmus
34da5c394b
gnu: guile-dsv: Remove custom bootstrap phase. 
* gnu/packages/guile.scm (guile-dsv)[arguments]: Remove autoreconf phase.
 2018-11-11 10:22:45 +01:00
Ricardo Wurmus
5ad728e04c
gnu: opendht: Remove custom bootstrap phase. 
* gnu/packages/crypto.scm (opendht)[arguments]: Remove autoconf phase.
 2018-11-11 10:21:02 +01:00
Ricardo Wurmus
974056c05e
gnu: opendht: Fetch sources from git. 
* gnu/packages/crypto.scm (opendht)[source]: Fetch from git.
 2018-11-11 10:20:36 +01:00
Ricardo Wurmus
a49b5322c5
gnu: lxsession: Remove custom bootstrap phase. 
* gnu/packages/lxde.scm (lxsession)[arguments]: Remove autoreconf phase and
end rm-stamp phase with #T.
 2018-11-11 10:16:43 +01:00
Ricardo Wurmus
f1f1cebdd3
gnu: mdbtools: Fetch sources from git. 
* gnu/packages/databases.scm (mdbtools)[source]: Fetch from git.
 2018-11-11 10:09:54 +01:00
Ricardo Wurmus
f626b71923
gnu: mdbtools: Remove custom bootstrap phase. 
* gnu/packages/databases.scm (mdbtools)[arguments]: Remove.
 2018-11-11 10:05:56 +01:00
Ricardo Wurmus
1410e178bb
gnu: pianobar: Fetch sources from git. 
* gnu/packages/music.scm (pianobar)[source]: Fetch from git.
 2018-11-11 10:03:06 +01:00
Ricardo Wurmus
487e3f5a80
gnu: ibus-rime: Fetch sources from git. 
* gnu/packages/ibus.scm (ibus-rime)[source]: Fetch from git.
 2018-11-11 10:03:06 +01:00
Ricardo Wurmus
863742856c
gnu: librime: Fetch sources from git. 
* gnu/packages/ibus.scm (librime)[source]: Fetch from git.
 2018-11-11 10:03:06 +01:00
Efraim Flashner
cab70d4c2a
gnu: perl-autovivification: Update to 0.18. 
* gnu/packages/perl.scm (perl-autovivification): Update to 0.18.
 2018-11-11 08:21:59 +02:00
Mark H Weaver
717d29e25b
gnu: icecat: Add more fixes from mozilla-esr60. 
* gnu/packages/gnuzilla.scm (icecat)[source]: Add selected fixes
from the upstream mozilla-esr60 source repository.
 2018-11-10 20:29:19 -05:00
Mark H Weaver
3b14494616
gnu: icecat: Update to 60.3.0-gnu1. 
* gnu/packages/gnuzilla.scm (icecat): Update to 60.3.0-gnu1.
[source]: Switch back to the normal source URI.  Remove patches that
are no longer applicable.
* gnu/packages/patches/icecat-CVE-2018-12383.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Remove it.
 2018-11-10 20:28:32 -05:00
Mark H Weaver
e22842f5ca
gnu: linux-libre@4.14: Update to 4.14.80. 
* gnu/packages/linux.scm (%linux-libre-4.14-version): Update to 4.14.80.
(%linux-libre-4.14-hash): Update hash.
 2018-11-10 20:23:57 -05:00
Mark H Weaver
62168a5558
gnu: linux-libre@4.9: Update to 4.9.136. 
* gnu/packages/linux.scm (linux-libre-4.9): Update to 4.9.136.
 2018-11-10 20:23:15 -05:00