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Author SHA1 Message Date
Mark H Weaver
230a59d418
gnu: linux-libre@4.14: Update to 4.14.173. 
* gnu/packages/linux.scm (linux-libre-4.14-version): Update to 4.14.173.
(linux-libre-4.14-pristine-source): Update hash.
 2020-03-12 20:50:52 -04:00
Mark H Weaver
e0d5a43e51
gnu: linux-libre@4.9: Update to 4.9.216. 
* gnu/packages/linux.scm (linux-libre-4.9-version): Update to 4.9.216.
(linux-libre-4.9-pristine-source): Update hash.
 2020-03-12 20:50:24 -04:00
Mark H Weaver
dcd7a97b8c
gnu: linux-libre@4.4: Update to 4.4.216. 
* gnu/packages/linux.scm (linux-libre-4.4-version): Update to 4.4.216.
(linux-libre-4.4-pristine-source): Update hash.
 2020-03-12 20:49:19 -04:00
Carl Dong
0f864175dc
gnu: mingw-w64-*: Update to 7.0.0. 
* gnu/packages/mingw.scm (make-mingw-w64): Update to 7.0.0.
 2020-03-12 15:45:28 -04:00
Alexandru-Sergiu Marton
b431f6c9cc
gnu: ghc-extra: Update to 1.7.1. 
* gnu/packages/haskell-xyz.scm (ghc-extra): Update to 1.7.1.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2020-03-12 14:10:41 -04:00
Ludovic Courtès
2843fed0e9
weather: Allow for multiple '--manifest' options. 
* guix/scripts/weather.scm (guix-weather)[package-list]: Account for all
the 'manifest entries in OPTS.
* doc/guix.texi (Invoking guix weather): Document it.
 2020-03-12 18:32:16 +01:00
Ludovic Courtès
71bb485541
weather: Add '--display-missing'. 
* guix/scripts/weather.scm (report-server-coverage): Add
 #:display-missing? and honor it.
(show-help, %options): Add "--display-missing".
(guix-weather): Pass #:display-missing? to 'report-server-coverage'.
* doc/guix.texi (Invoking guix weather): Document it.
 2020-03-12 18:32:16 +01:00
Ludovic Courtès
e0dbed64c5
gnu: singularity: Do not use the "errors=remount-ro" squashfs option. 
This mount option stopped being supported with Linux-libre 5.4.5:

  http://ci.guix.gnu.org/build/2056359/details

* gnu/packages/linux.scm (singularity)[source]: Remove
"errors=remount-ro" mount option from source code.
 2020-03-12 18:32:16 +01:00
Ludovic Courtès
22464cf32a
gnu: singularity: Wrap programs so they find Coreutils. 
* gnu/packages/linux.scm (singularity)[arguments]: Add 'set-PATH' phase.
 2020-03-12 18:32:16 +01:00
Ludovic Courtès
cf2ac04f13
gexp: Add 'with-parameters'. 
* guix/gexp.scm (<parameterized>): New record type.
(with-parameters): New macro.
(compile-parameterized): New gexp compiler.
* tests/gexp.scm ("with-parameters for %current-system")
("with-parameters for %current-target-system")
("with-parameters + file-append"): New tests.
* doc/guix.texi (G-Expressions): Document it.
 2020-03-12 18:32:15 +01:00
Amar Singh
be78906592
gnu: Add guile-torrent. 
* gnu/packages/guile-xyz.scm (guile-torrent): New variable.

Signed-off-by: Mathieu Othacehe <m.othacehe@gmail.com>
 2020-03-12 15:52:41 +01:00
Efraim Flashner
0c08e4bfa1
gnu: edirect: Update to 13.3.20200128. 
* gnu/packages/bioinformatics.scm (edirect): Update to 13.3.20200128.
[source]: Remove bundled certificate authority tarball.
 2020-03-12 16:50:23 +02:00
Ricardo Wurmus
72e76113f7
gnu: r-car: Update to 3.0-7. 
* gnu/packages/statistics.scm (r-car): Update to 3.0-7.
[native-inputs]: Add r-knitr.
 2020-03-12 15:15:04 +01:00
Ricardo Wurmus
92d6c94a16
gnu: r-nloptr: Update to 1.2.2.1. 
* gnu/packages/statistics.scm (r-nloptr): Update to 1.2.2.1.
 2020-03-12 15:15:04 +01:00
Ricardo Wurmus
66f1fead63
gnu: r-roxygen2: Update to 7.1.0. 
* gnu/packages/statistics.scm (r-roxygen2): Update to 7.1.0.
[native-inputs]: Move r-knitr from here...
[propagated-inputs]: ...to here.
 2020-03-12 15:15:04 +01:00
Ricardo Wurmus
09583a0f79
gnu: r-xml2: Update to 1.2.5. 
* gnu/packages/statistics.scm (r-xml2): Update to 1.2.5.
[native-inputs]: Add r-knitr.
 2020-03-12 15:15:04 +01:00
Ricardo Wurmus
defbaab3f8
gnu: r-tam: Update to 3.4-26. 
* gnu/packages/cran.scm (r-tam): Update to 3.4-26.
 2020-03-12 15:15:03 +01:00
Ricardo Wurmus
4dab179de2
gnu: r-cdm: Update to 7.5-15. 
* gnu/packages/cran.scm (r-cdm): Update to 7.5-15.
 2020-03-12 15:15:03 +01:00
Ricardo Wurmus
ca29e40dac
gnu: r-parameters: Update to 0.6.0. 
* gnu/packages/cran.scm (r-parameters): Update to 0.6.0.
[native-inputs]: Add r-knitr.
 2020-03-12 15:15:03 +01:00
Ricardo Wurmus
40ac3dc394
gnu: r-graphlayouts: Update to 0.6.0. 
* gnu/packages/cran.scm (r-graphlayouts): Update to 0.6.0.
 2020-03-12 15:15:03 +01:00
Ricardo Wurmus
9d3d3d1bd5
gnu: r-ggfortify: Update to 0.4.9. 
* gnu/packages/cran.scm (r-ggfortify): Update to  0.4.9.
[native-inputs]: Add r-knitr.
 2020-03-12 15:15:03 +01:00
Ricardo Wurmus
0cc0e7e370
gnu: r-ggplotify: Update to 0.0.5. 
* gnu/packages/cran.scm (r-ggplotify): Update to 0.0.5.
[native-inputs]: Add r-knitr.
 2020-03-12 15:15:03 +01:00
Ricardo Wurmus
f718c28cc6
gnu: r-pegas: Update to 0.13. 
* gnu/packages/cran.scm (r-pegas): Update to 0.13.
 2020-03-12 15:15:03 +01:00
Ricardo Wurmus
a85aef2d75
gnu: r-spatialextremes: Update to 2.0-8. 
* gnu/packages/cran.scm (r-spatialextremes): Update to 2.0-8.
 2020-03-12 15:15:03 +01:00
Ricardo Wurmus
dca5a8143f
gnu: r-tidytree: Update to 0.3.2. 
* gnu/packages/cran.scm (r-tidytree): Update to 0.3.2.
[native-inputs]: Add r-knitr.
 2020-03-12 15:15:03 +01:00
Ricardo Wurmus
d520e4c942
gnu: r-rcppparallel: Update to 5.0.0. 
* gnu/packages/cran.scm (r-rcppparallel): Update to 5.0.0.
 2020-03-12 15:15:03 +01:00
Ricardo Wurmus
69a3c4ce51
gnu: r-sjplot: Update to 2.8.3. 
* gnu/packages/cran.scm (r-sjplot): Update to 2.8.3.
[propagated-inputs]: Remove r-forcats.
[native-inputs]: Remove r-knitr.
 2020-03-12 15:15:03 +01:00
Ricardo Wurmus
cd26e5dee8
gnu: r-catdap: Update to 1.3.5. 
* gnu/packages/cran.scm (r-catdap): Update to 1.3.5.
 2020-03-12 15:15:03 +01:00
Ricardo Wurmus
f7306e465e
gnu: r-vim: Update to 5.1.1. 
* gnu/packages/cran.scm (r-vim): Update to 5.1.1.
 2020-03-12 15:15:03 +01:00
Ricardo Wurmus
117270fb51
gnu: r-vctrs: Update to 0.2.4. 
* gnu/packages/cran.scm (r-vctrs): Update to 0.2.4.
[native-inputs]: Add r-knitr.
 2020-03-12 15:15:03 +01:00
Ricardo Wurmus
6bd6097ed5
gnu: r-cicero: Update to 1.4.4. 
* gnu/packages/bioconductor.scm (r-cicero): Update to 1.4.4.
[native-inputs]: Add r-knitr.
 2020-03-12 15:15:02 +01:00
Ricardo Wurmus
0754fefb75
gnu: r-ggcyto: Update to 1.14.1. 
* gnu/packages/bioconductor.scm (r-ggcyto): Update to 1.14.1.
[native-inputs]: Add r-knitr.
 2020-03-12 15:15:02 +01:00
Ricardo Wurmus
e0061f5125
gnu: r-mlinterfaces: Update to 1.66.5. 
* gnu/packages/bioconductor.scm (r-mlinterfaces): Update to 1.66.5.
 2020-03-12 15:15:02 +01:00
Ricardo Wurmus
0b692ef2c6
gnu: r-qtl: Update to 1.46-2. 
* gnu/packages/bioinformatics.scm (r-qtl): Update to 1.46-2.
 2020-03-12 15:15:02 +01:00
Pierre Neidhardt
04ff192ec4
gnu: Add hyperledger-iroha. 
This package was co-authored with Efraim Flashner <efraim@flashner.co.il>

* gnu/packages/hyperledger.scm (hyperledger-iroha): New variable.
 2020-03-12 15:34:28 +02:00
Efraim Flashner
f204d155e3
gnu: Add boost-1.69. 
* gnu/packages/boost.scm (boost-1.69): New hidden package.
 2020-03-12 15:34:28 +02:00
Pierre Neidhardt
37109658a5
gnu: Add hyperledger-iroha-ed25519. 
* gnu/packages/hyperledger.scm (hyperledger-iroha-ed25519): New variable.
 2020-03-12 15:34:28 +02:00
Efraim Flashner
d56d3ae704
gnu: grpc: Build shared libraries. 
* gnu/packages/machine-learning.scm (grpc)[outputs]: Add static.
[arguments]: Copy configure-flags from cmake-build-system. Add custom
phases 'configure-shared, 'install-shared-libraries and 'move-static-libs
to build shared libs and move static libs to their own output.
(tensorflow)[native-inputs]: Add grpc:static.
 2020-03-12 15:34:28 +02:00
Efraim Flashner
b0aa58d8f1
gnu: python2-jupyter-console: Build with python2. 
* gnu/packages/python-xyz.scm (python2-jupyter-console)[arguments]: Add
python keyword, set to python-2.
 2020-03-12 15:34:28 +02:00
Efraim Flashner
e8588a7847
gnu: python-jupyter-console: Specify python2 variant. 
* gnu/packages/python-xyz.scm (python-jupyter-console)[properties]: New
field. Specify python2-jupyter-console as python2 variant.
 2020-03-12 15:34:27 +02:00
Ricardo Wurmus
a595399230
services: mumi-service-type: Update to latest version of mumi. 
* gnu/services/web.scm (%mumi-activation): Create /var/mumi/db.
(mumi-shepherd-services): Add service for mumi worker.
 2020-03-12 12:47:45 +01:00
Ricardo Wurmus
c107e50a0e
gnu: mumi: Update to 0.0.0-7.6653e2d. 
* gnu/packages/mail.scm (mumi): Update to 0.0.0-7.6653e2d.
[inputs]: Add guile-sqlite3.
 2020-03-12 12:47:45 +01:00
Ricardo Wurmus
e4cdadc18d
gnu: r-cairo: Update to 1.5-11. 
* gnu/packages/statistics.scm (r-cairo): Update to 1.5-11.
 2020-03-12 12:47:45 +01:00
Felix Gruber
0a703c0486
gnu: dune-istl: Build with suitesparse 
* gnu/packages/maths.scm (dune-istl)[inputs]: Add suitesparse to build
additional solvers in dune-istl.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2020-03-12 11:52:38 +01:00
Felix Gruber
f1f9466e33
gnu: Add dune-subgrid 
* gnu/packages/maths.scm (dune-subgrid): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2020-03-12 11:52:38 +01:00
Felix Gruber
07ebb75d17
gnu: Add dune-uggrid. 
* gnu/packages/maths.scm (dune-uggrid): New variable.
(dune-grid)[propagated-inputs]: Add dune-uggrid dependency, so
that the UGGrid class in dune-grid can be used by packages that
have dune-grid as input.
(dune-functions)[arguments]: Enable tests that previously weren't
built as they require dune-uggrid.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2020-03-12 11:52:38 +01:00
Felix Gruber
a669f6e27b
gnu: dune-*: set up MPI for tests 
* gnu/packages/maths.scm (dune-common, dune-grid, dune-istl,
dune-alugrid): [arguments]: correctly set up MPI instead of disabling
tests that require MPI.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2020-03-12 11:52:38 +01:00
Ludovic Courtès
f7537e30b8
inferior: Distinguish inferior exceptions. 
This avoids ambiguities when looking at a backtrace where the exception
was actually thrown by an inferior in a very different context.

* guix/inferior.scm (&inferior-exception): New condition type.
(read-repl-response): Add optional 'inferior' parameter.  Raise
'&inferior-exception' instead of rethrowing to KEY when receiving an
'exception' message.
(read-inferior-response): Pass INFERIOR to 'read-repl-response'.
* tests/inferior.scm ("&inferior-exception"): New test.
 2020-03-12 11:52:38 +01:00
Ludovic Courtès
c00ae79cca
import: cpan: Gracefully handle missing projects. 
* guix/import/cpan.scm (cpan-fetch): Check whether 'json-fetch' returns #f.
 2020-03-12 11:52:38 +01:00
Ludovic Courtès
2d0409a4a2
import: utils: Remove 'assoc-ref*'. 
* guix/import/utils.scm (assoc-ref*): Remove.
 2020-03-12 11:52:37 +01:00