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* gnu: mingw-w64-*: Update to 7.0.0.Carl Dong2020-03-12
| | | | * gnu/packages/mingw.scm (make-mingw-w64): Update to 7.0.0.
* gnu: ghc-extra: Update to 1.7.1.Alexandru-Sergiu Marton2020-03-12
| | | | | | * gnu/packages/haskell-xyz.scm (ghc-extra): Update to 1.7.1. Signed-off-by: Leo Famulari <leo@famulari.name>
* weather: Allow for multiple '--manifest' options.Ludovic Courtès2020-03-12
| | | | | | * guix/scripts/weather.scm (guix-weather)[package-list]: Account for all the 'manifest entries in OPTS. * doc/guix.texi (Invoking guix weather): Document it.
* weather: Add '--display-missing'.Ludovic Courtès2020-03-12
| | | | | | | | * 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.
* gnu: singularity: Do not use the "errors=remount-ro" squashfs option.Ludovic Courtès2020-03-12
| | | | | | | | | 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.
* gnu: singularity: Wrap programs so they find Coreutils.Ludovic Courtès2020-03-12
| | | | * gnu/packages/linux.scm (singularity)[arguments]: Add 'set-PATH' phase.
* gexp: Add 'with-parameters'.Ludovic Courtès2020-03-12
| | | | | | | | | | * 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.
* gnu: Add guile-torrent.base-for-series-3152base-for-series-3151Amar Singh2020-03-12
| | | | | | * gnu/packages/guile-xyz.scm (guile-torrent): New variable. Signed-off-by: Mathieu Othacehe <m.othacehe@gmail.com>
* gnu: edirect: Update to 13.3.20200128.Efraim Flashner2020-03-12
| | | | | * gnu/packages/bioinformatics.scm (edirect): Update to 13.3.20200128. [source]: Remove bundled certificate authority tarball.
* gnu: r-car: Update to 3.0-7.Ricardo Wurmus2020-03-12
| | | | | * gnu/packages/statistics.scm (r-car): Update to 3.0-7. [native-inputs]: Add r-knitr.
* gnu: r-nloptr: Update to 1.2.2.1.Ricardo Wurmus2020-03-12
| | | | * gnu/packages/statistics.scm (r-nloptr): Update to 1.2.2.1.
* gnu: r-roxygen2: Update to 7.1.0.Ricardo Wurmus2020-03-12
| | | | | | * gnu/packages/statistics.scm (r-roxygen2): Update to 7.1.0. [native-inputs]: Move r-knitr from here... [propagated-inputs]: ...to here.
* gnu: r-xml2: Update to 1.2.5.Ricardo Wurmus2020-03-12
| | | | | * gnu/packages/statistics.scm (r-xml2): Update to 1.2.5. [native-inputs]: Add r-knitr.
* gnu: r-tam: Update to 3.4-26.Ricardo Wurmus2020-03-12
| | | | * gnu/packages/cran.scm (r-tam): Update to 3.4-26.
* gnu: r-cdm: Update to 7.5-15.Ricardo Wurmus2020-03-12
| | | | * gnu/packages/cran.scm (r-cdm): Update to 7.5-15.
* gnu: r-parameters: Update to 0.6.0.Ricardo Wurmus2020-03-12
| | | | | * gnu/packages/cran.scm (r-parameters): Update to 0.6.0. [native-inputs]: Add r-knitr.
* gnu: r-graphlayouts: Update to 0.6.0.Ricardo Wurmus2020-03-12
| | | | * gnu/packages/cran.scm (r-graphlayouts): Update to 0.6.0.
* gnu: r-ggfortify: Update to 0.4.9.Ricardo Wurmus2020-03-12
| | | | | * gnu/packages/cran.scm (r-ggfortify): Update to 0.4.9. [native-inputs]: Add r-knitr.
* gnu: r-ggplotify: Update to 0.0.5.Ricardo Wurmus2020-03-12
| | | | | * gnu/packages/cran.scm (r-ggplotify): Update to 0.0.5. [native-inputs]: Add r-knitr.
* gnu: r-pegas: Update to 0.13.Ricardo Wurmus2020-03-12
| | | | * gnu/packages/cran.scm (r-pegas): Update to 0.13.
* gnu: r-spatialextremes: Update to 2.0-8.Ricardo Wurmus2020-03-12
| | | | * gnu/packages/cran.scm (r-spatialextremes): Update to 2.0-8.
* gnu: r-tidytree: Update to 0.3.2.Ricardo Wurmus2020-03-12
| | | | | * gnu/packages/cran.scm (r-tidytree): Update to 0.3.2. [native-inputs]: Add r-knitr.
* gnu: r-rcppparallel: Update to 5.0.0.Ricardo Wurmus2020-03-12
| | | | * gnu/packages/cran.scm (r-rcppparallel): Update to 5.0.0.
* gnu: r-sjplot: Update to 2.8.3.Ricardo Wurmus2020-03-12
| | | | | | * gnu/packages/cran.scm (r-sjplot): Update to 2.8.3. [propagated-inputs]: Remove r-forcats. [native-inputs]: Remove r-knitr.
* gnu: r-catdap: Update to 1.3.5.Ricardo Wurmus2020-03-12
| | | | * gnu/packages/cran.scm (r-catdap): Update to 1.3.5.
* gnu: r-vim: Update to 5.1.1.Ricardo Wurmus2020-03-12
| | | | * gnu/packages/cran.scm (r-vim): Update to 5.1.1.
* gnu: r-vctrs: Update to 0.2.4.Ricardo Wurmus2020-03-12
| | | | | * gnu/packages/cran.scm (r-vctrs): Update to 0.2.4. [native-inputs]: Add r-knitr.
* gnu: r-cicero: Update to 1.4.4.Ricardo Wurmus2020-03-12
| | | | | * gnu/packages/bioconductor.scm (r-cicero): Update to 1.4.4. [native-inputs]: Add r-knitr.
* gnu: r-ggcyto: Update to 1.14.1.Ricardo Wurmus2020-03-12
| | | | | * gnu/packages/bioconductor.scm (r-ggcyto): Update to 1.14.1. [native-inputs]: Add r-knitr.
* gnu: r-mlinterfaces: Update to 1.66.5.Ricardo Wurmus2020-03-12
| | | | * gnu/packages/bioconductor.scm (r-mlinterfaces): Update to 1.66.5.
* gnu: r-qtl: Update to 1.46-2.Ricardo Wurmus2020-03-12
| | | | * gnu/packages/bioinformatics.scm (r-qtl): Update to 1.46-2.
* gnu: Add hyperledger-iroha.base-for-series-3149Pierre Neidhardt2020-03-12
| | | | | | This package was co-authored with Efraim Flashner <efraim@flashner.co.il> * gnu/packages/hyperledger.scm (hyperledger-iroha): New variable.
* gnu: Add boost-1.69.Efraim Flashner2020-03-12
| | | | * gnu/packages/boost.scm (boost-1.69): New hidden package.
* gnu: Add hyperledger-iroha-ed25519.Pierre Neidhardt2020-03-12
| | | | * gnu/packages/hyperledger.scm (hyperledger-iroha-ed25519): New variable.
* gnu: grpc: Build shared libraries.Efraim Flashner2020-03-12
| | | | | | | | * 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.
* gnu: python2-jupyter-console: Build with python2.Efraim Flashner2020-03-12
| | | | | * gnu/packages/python-xyz.scm (python2-jupyter-console)[arguments]: Add python keyword, set to python-2.
* gnu: python-jupyter-console: Specify python2 variant.Efraim Flashner2020-03-12
| | | | | * gnu/packages/python-xyz.scm (python-jupyter-console)[properties]: New field. Specify python2-jupyter-console as python2 variant.
* services: mumi-service-type: Update to latest version of mumi.Ricardo Wurmus2020-03-12
| | | | | * gnu/services/web.scm (%mumi-activation): Create /var/mumi/db. (mumi-shepherd-services): Add service for mumi worker.
* gnu: mumi: Update to 0.0.0-7.6653e2d.Ricardo Wurmus2020-03-12
| | | | | * gnu/packages/mail.scm (mumi): Update to 0.0.0-7.6653e2d. [inputs]: Add guile-sqlite3.
* gnu: r-cairo: Update to 1.5-11.Ricardo Wurmus2020-03-12
| | | | * gnu/packages/statistics.scm (r-cairo): Update to 1.5-11.
* gnu: dune-istl: Build with suitesparseFelix Gruber2020-03-12
| | | | | | | * gnu/packages/maths.scm (dune-istl)[inputs]: Add suitesparse to build additional solvers in dune-istl. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
* gnu: Add dune-subgridFelix Gruber2020-03-12
| | | | | | * gnu/packages/maths.scm (dune-subgrid): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
* gnu: Add dune-uggrid.Felix Gruber2020-03-12
| | | | | | | | | | | * 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>
* gnu: dune-*: set up MPI for testsFelix Gruber2020-03-12
| | | | | | | | * 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>
* inferior: Distinguish inferior exceptions.Ludovic Courtès2020-03-12
| | | | | | | | | | | | 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.
* import: cpan: Gracefully handle missing projects.Ludovic Courtès2020-03-12
| | | | * guix/import/cpan.scm (cpan-fetch): Check whether 'json-fetch' returns #f.
* import: utils: Remove 'assoc-ref*'.Ludovic Courtès2020-03-12
| | | | * guix/import/utils.scm (assoc-ref*): Remove.
* import: pypi: Rewrite to use 'define-json-mapping'.Ludovic Courtès2020-03-12
| | | | | | | | | | * guix/import/pypi.scm (non-empty-string-or-false): New procedure. (<pypi-project>, <project-info>, <distribution>): New record types. (pypi-fetch): Call 'json->pypi-project'. (latest-source-release, latest-wheel-release): Use the new record accessors instead of 'assoc-ref*'. (pypi->guix-package, latest-release): Likewise. * tests/pypi.scm (test-json): Add mandatory fields.
* gnu: guile-next: Enable JIT on ARMv7.Ludovic Courtès2020-03-12
| | | | | | JIT support on ARMv7 is fixed by "guile-3.0-crash.patch". * gnu/packages/guile.scm (guile-3.0)[arguments]: Remove.
* gnu: Add virtualpg.Guillaume Le Vaillant2020-03-12
| | | | * gnu/packages/geo.scm (virtualpg): New variable.
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