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49224 Commits

Author SHA1 Message Date
Ricardo Wurmus eb796f53ef
gnu: r-mixomics: Update to 6.8.5. 
* gnu/packages/bioconductor.scm (r-mixomics): Update to 6.8.5.
 2019-10-06 23:08:47 +02:00
Ricardo Wurmus 1c2e573302
gnu: r-regioner: Update to 1.16.5. 
* gnu/packages/bioconductor.scm (r-regioner): Update to 1.16.5.
 2019-10-06 23:08:47 +02:00
Ricardo Wurmus 07d0645b6b
gnu: r-backports: Update to 1.1.5. 
* gnu/packages/statistics.scm (r-backports): Update to 1.1.5.
 2019-10-06 23:08:47 +02:00
Ricardo Wurmus f817005bfe
gnu: r-gargle: Update to 0.4.0. 
* gnu/packages/cran.scm (r-gargle): Update to 0.4.0.
 2019-10-06 23:08:47 +02:00
Ricardo Wurmus 9b112f4030
gnu: r-rcppparallel: Update to 4.4.4. 
* gnu/packages/cran.scm (r-rcppparallel): Update to 4.4.4.
 2019-10-06 23:08:47 +02:00
Ricardo Wurmus 770321180f
gnu: r-hdf5r: Update to 1.3.0. 
* gnu/packages/cran.scm (r-hdf5r): Update to 1.3.0.
 2019-10-06 23:08:47 +02:00
Ricardo Wurmus 2e6ccd6c2d
gnu: r-promises: Update to 1.1.0. 
* gnu/packages/cran.scm (r-promises): Update to 1.1.0.
 2019-10-06 23:08:47 +02:00
Ricardo Wurmus ab99236eba
gnu: r-later: Update to 1.0.0. 
* gnu/packages/cran.scm (r-later): Update to 1.0.0.
 2019-10-06 23:08:47 +02:00
Ricardo Wurmus b7e7c320a2
gnu: r-maptools: Update to 0.9-8. 
* gnu/packages/cran.scm (r-maptools): Update to 0.9-8.
 2019-10-06 23:08:47 +02:00
Ricardo Wurmus ff74344597
gnu: r-htmlwidgets: Update to 1.5. 
* gnu/packages/cran.scm (r-htmlwidgets): Update to 1.5.
 2019-10-06 23:08:47 +02:00
Ricardo Wurmus 82acc94fbf
gnu: r-htmltools: Update to 0.4.0. 
* gnu/packages/cran.scm (r-htmltools): Update to 0.4.0.
[arguments]: Remove field.
[propagated-inputs]: Add r-rlang.
 2019-10-06 23:08:47 +02:00
Ricardo Wurmus 33651044c6
gnu: r-seurat: Update to 3.1.1. 
* gnu/packages/bioinformatics.scm (r-seurat): Update to 3.1.1.
[propagated-inputs]: Add r-httr.
 2019-10-06 23:08:47 +02:00
Ricardo Wurmus 94638cbe77
gnu: r-rsamtools: Update to 2.0.2. 
* gnu/packages/bioinformatics.scm (r-rsamtools): Update to 2.0.2.
 2019-10-06 23:08:47 +02:00
Ricardo Wurmus 122c1b3ce7
gnu: r-biomart: Update to 2.40.5. 
* gnu/packages/bioinformatics.scm (r-biomart): Update to 2.40.5.
 2019-10-06 23:08:46 +02:00
Brian Leung d050fdf4c6
gnu: emacs-helm-ag: Fix version. 
* gnu/packages/emacs-xyz.scm (emacs-helm-ag): Fix version.
 2019-10-06 22:08:27 +02:00
Brian Leung cb2197508a
gnu: Add emacs-helm-org. 
* gnu/packages/emacs-xyz.scm (emacs-helm-org): New variable.
 2019-10-06 22:08:27 +02:00
Brian Leung 45d04b2a7d
gnu: emacs-helm: Update to 3.5.0. 
* gnu/packages/emacs-xyz.scm (emacs-helm): Update to 3.5.0.
 2019-10-06 22:08:27 +02:00
Ricardo Wurmus 4722330d68
gnu: nss-pam-ldapd: Update to 0.9.11. 
* gnu/packages/openldap.scm (nss-pam-ldapd): Update to 0.9.11.
[inputs]: Replace python-2 with python.
 2019-10-06 22:07:07 +02:00
Ricardo Wurmus e08902d3cb
Merge branch 'master' into core-updates 2019-10-06 22:02:20 +02:00
Ricardo Wurmus f58702465d
gnu: Add mloop. 
* gnu/packages/music.scm (mloop): New variable.
 2019-10-06 22:01:01 +02:00
Ricardo Wurmus 4b94e63db6
gnu: guile-studio: Update to 0-2.4d63f3d. 
* gnu/packages/guile-xyz.scm (guile-studio): Update to 0-2.4d63f3d.
 2019-10-06 22:01:01 +02:00
Ricardo Wurmus 1b6f99ea53
gnu: icedtea-7: Fix build on i686-linux. 
* gnu/packages/java.scm (icedtea-7)[arguments]: Use "i386" lib directory when
the system is "i686-linux".
 2019-10-06 22:01:01 +02:00
Ricardo Wurmus fc37b4afb2
gnu: jamvm-1-bootstrap: Fix segfault in bootstrap JVM. 
* gnu/packages/java.scm (jamvm-1-bootstrap)[arguments]: Add configure flags:
--disable-int-caching, --enable-runtime-reloc-checks, and --enable-ffi.
[inputs]: Add libffi.
 2019-10-06 22:01:01 +02:00
Brian Leung ff810d21a5
gnu: emacs-hackernews: Update to 0.5.0-2.2362d7b. 
* gnu/packages/emacs-xyz.scm (emacs-hackernews): Update to 0.5.0-2.2362d7b.
 2019-10-06 20:40:23 +02:00
Brian Leung 9049f28f57
gnu: emacs-undo-propose-el: Update to 3.0.0-3.f80baee. 
* gnu/packages/emacs-xyz.scm (emacs-undo-propose-el): Update to 3.0.0-3.f80baee.
 2019-10-06 20:18:39 +02:00
Brian Leung 1017ba7dd5
gnu: emacs-evil-mc: Update to 0.0.3-2.1cabb86. 
* gnu/packages/emacs-xyz.scm (emacs-evil-mc): Update to 0.0.3-2.1cabb86.
 2019-10-06 19:59:05 +02:00
Pierre Neidhardt cec23736d3
gnu: Add cl-goject-introspection. 
* gnu/packages/lisp.scm (cl-goject-introspection,
  sbcl-cl-gobject-introspection): New variables.
 2019-10-06 19:34:13 +02:00
Marius Bakke 1714edc3d4
gnu: WebKitGTK: Embed absolute file name of libWPEBackend-fdo-1.0.so. 
Fixes <https://bugs.gnu.org/37545>.
Reported by Vagrant Cascadian <vagrant@debian.org>.

* gnu/packages/webkit.scm (webkitgtk)[arguments]: Add phase.
 2019-10-06 18:02:48 +02:00
Marius Bakke c5ceec4150
gnu: linux-libre: Remove glibc from CPATH before the build. 
Fixes <https://bugs.gnu.org/37593>.

* gnu/packages/linux.scm (make-linux-libre*)[arguments]: Drop "libc" from CPATH.
 2019-10-06 18:02:48 +02:00
Marius Bakke dd69897113
gnu: linux-libre: Try to aggressively gather entropy during boot. 
Fixes <https://bugs.gnu.org/37501>.

* gnu/packages/patches/linux-libre-active-entropy.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/linux.scm (linux-libre-5.2-source): Use it.
 2019-10-06 18:02:48 +02:00
Marius Bakke 5157edd885
gnu: perf: Treat kernel headers as system headers. 
* gnu/packages/linux.scm (perf)[arguments]: Instead of disabling -Werror,
set C_INCLUDE_PATH.
 2019-10-06 18:02:48 +02:00
Ludovic Courtès 63b0ce391f
services: shepherd: Compile service files. 
This reduces resident memory for PID 1 from 29.8MiB to 28.7MiB right
after boot on a bare-bones system (x86_64-linux).

* gnu/services/shepherd.scm (scm->go): New procedure.
(shepherd-configuration-file)[config]: Call it and use 'load-compiled'
instead of 'primitive-load'.
 2019-10-06 14:45:35 +02:00
Ludovic Courtès 38b1ea0434
services: udev: Explicitly depend on (gnu build linux-boot). 
* gnu/services/base.scm (udev-shepherd-service): Wrap 'start' method in
'with-imported-modules'.
 2019-10-06 14:45:35 +02:00
Ludovic Courtès 62c2217570
services: agetty: Explicitly depend on (gnu build linux-boot). 
* gnu/services/base.scm (default-serial-port): Wrap in
'with-imported-modules'.
 2019-10-06 14:45:35 +02:00
Ludovic Courtès 1994422752
system: Add 'mount' and 'umount' to '%setuid-programs'. 
Fixes <https://bugs.gnu.org/37569>.
Reported by Diego Nicola Barbato <dnbarbato@posteo.de>.

* gnu/system.scm (%setuid-programs): Add "mount" and "umount" from
util-linux.
 2019-10-06 14:45:35 +02:00
Guillaume Le Vaillant 5a65fede0b
gnu: Add cl-random-forest. 
* gnu/packages/machine-learning.scm (sbcl-cl-random-forest, cl-random-forest,
  ecl-cl-random-forest): New variables.
 2019-10-06 14:37:54 +02:00
Guillaume Le Vaillant 7a15aab836
gnu: Add cl-online-learning. 
* gnu/packages/machine-learning.scm (sbcl-cl-online-learning,
  cl-online-learning, ecl-cl-online-learning): New variables.
 2019-10-06 14:28:55 +02:00
Guillaume Le Vaillant 6e76087223
gnu: Add cl-libsvm-format. 
* gnu/packages/machine-learning.scm (sbcl-cl-libsvm-format, cl-libsvm-format,
  ecl-cl-libsvm-format): New variables.
 2019-10-06 14:28:55 +02:00
Guillaume Le Vaillant 2601da0523
gnu: Add cl-store. 
* gnu/packages/lisp.scm (sbcl-cl-store, cl-store, ecl-cl-store): New
  variables.
 2019-10-06 14:28:51 +02:00
Guillaume Le Vaillant 7273b3b2a6
gnu: sbcl-hu.dwim.asdf: Update to 20190521. 
* gnu/packages/lisp.scm (sbcl-hu.dwim.asdf): Update to 20190521.
  [uri]: Fetch more recent version from Quicklisp.
 2019-10-06 14:19:03 +02:00
Guillaume Le Vaillant f65f713846
gnu: sbcl-alexandria: Update to 1.0.0. 
* gnu/packages/lisp.scm (sbcl-alexandria): Update to 1.0.0.
  [native-inputs]: Add rt.
 2019-10-06 14:19:03 +02:00
Guillaume Le Vaillant fd0f8860ec
gnu: ecl: Do not compile the deprecated MIT-RT. 
Compiling the rt bundled with ECL prevents the ecl-rt package from compiling
properly, as ECL thinks it has already been compiled.

* gnu/packages/lisp.scm (ecl)[arguments]: Add '--without-rt' to
  'configure-flags'.
 2019-10-06 14:19:03 +02:00
Guillaume Le Vaillant d3287fc157
gnu: Add chanl. 
* gnu/packages/lisp.scm (sbcl-chanl, cl-chanl, ecl-chanl): New variables.
 2019-10-06 14:19:03 +02:00
Efraim Flashner d24d980e8e
gnu: Remove rust-clippy. 
This was added by accident in 14f3a7e373.

* gnu/packages/crates-io.scm (rust-clippy): Remove variable.
 2019-10-06 14:38:02 +03:00
Timotej Lazar aa64198492
gnu: endless-sky: Update to 0.9.10. 
* gnu/packages/games.scm (endless-sky): Update to 0.9.10.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2019-10-06 11:58:02 +03:00
Giovanni Biscuolo e7f6d13722
gnu: zabbix: Update to 4.2.7. 
* gnu/packages/monitoring.scm: (zabbix) Update to 4.2.7.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2019-10-06 11:51:16 +03:00
tlecarrour@easter-eggs.com 1e8826bdd3
gnu: Update python-pastel to 0.1.1. 
* gnu/packages/graphics.scm (python-pastel): Update to 0.1.1.
[arguments]: Add custom 'check phase.
[description]: Simplify description.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2019-10-06 11:46:21 +03:00
Efraim Flashner 6792908d6d
gnu: waybar: Update to 0.8.0. 
* gnu/packages/wm.scm (waybar): Update to 0.8.0.
 2019-10-06 11:05:27 +03:00
Tobias Geerinckx-Rice 5a54baf67c
gnu: r-data-table: Update to 1.12.4. 
* gnu/packages/statistics.scm (r-data-table): Update to 1.12.4.
[inputs]: Add zlib.
 2019-10-06 04:46:54 +02:00
Tobias Geerinckx-Rice 011ec062f3
gnu: python-mnemonic: Update to 0.19. 
* gnu/packages/finance.scm (python-mnemonic): Update to 0.19.
 2019-10-06 04:46:54 +02:00