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2020-03-12gnu: singularity: Do not use the "errors=remount-ro" squashfs option.Ludovic Courtès
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.
2020-03-12gnu: singularity: Wrap programs so they find Coreutils.Ludovic Courtès
* gnu/packages/linux.scm (singularity)[arguments]: Add 'set-PATH' phase.
2020-03-12gexp: Add 'with-parameters'.Ludovic Courtès
* 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.
2020-03-12gnu: Add guile-torrent.Amar Singh
* gnu/packages/guile-xyz.scm (guile-torrent): New variable. Signed-off-by: Mathieu Othacehe <m.othacehe@gmail.com>
2020-03-12gnu: edirect: Update to 13.3.20200128.Efraim Flashner
* gnu/packages/bioinformatics.scm (edirect): Update to 13.3.20200128. [source]: Remove bundled certificate authority tarball.
2020-03-12gnu: r-car: Update to 3.0-7.Ricardo Wurmus
* gnu/packages/statistics.scm (r-car): Update to 3.0-7. [native-inputs]: Add r-knitr.
2020-03-12gnu: r-nloptr: Update to 1.2.2.1.Ricardo Wurmus
* gnu/packages/statistics.scm (r-nloptr): Update to 1.2.2.1.
2020-03-12gnu: r-roxygen2: Update to 7.1.0.Ricardo Wurmus
* gnu/packages/statistics.scm (r-roxygen2): Update to 7.1.0. [native-inputs]: Move r-knitr from here... [propagated-inputs]: ...to here.
2020-03-12gnu: r-xml2: Update to 1.2.5.Ricardo Wurmus
* gnu/packages/statistics.scm (r-xml2): Update to 1.2.5. [native-inputs]: Add r-knitr.
2020-03-12gnu: r-tam: Update to 3.4-26.Ricardo Wurmus
* gnu/packages/cran.scm (r-tam): Update to 3.4-26.
2020-03-12gnu: r-cdm: Update to 7.5-15.Ricardo Wurmus
* gnu/packages/cran.scm (r-cdm): Update to 7.5-15.
2020-03-12gnu: r-parameters: Update to 0.6.0.Ricardo Wurmus
* gnu/packages/cran.scm (r-parameters): Update to 0.6.0. [native-inputs]: Add r-knitr.
2020-03-12gnu: r-graphlayouts: Update to 0.6.0.Ricardo Wurmus
* gnu/packages/cran.scm (r-graphlayouts): Update to 0.6.0.
2020-03-12gnu: r-ggfortify: Update to 0.4.9.Ricardo Wurmus
* gnu/packages/cran.scm (r-ggfortify): Update to 0.4.9. [native-inputs]: Add r-knitr.
2020-03-12gnu: r-ggplotify: Update to 0.0.5.Ricardo Wurmus
* gnu/packages/cran.scm (r-ggplotify): Update to 0.0.5. [native-inputs]: Add r-knitr.
2020-03-12gnu: r-pegas: Update to 0.13.Ricardo Wurmus
* gnu/packages/cran.scm (r-pegas): Update to 0.13.
2020-03-12gnu: r-spatialextremes: Update to 2.0-8.Ricardo Wurmus
* gnu/packages/cran.scm (r-spatialextremes): Update to 2.0-8.
2020-03-12gnu: r-tidytree: Update to 0.3.2.Ricardo Wurmus
* gnu/packages/cran.scm (r-tidytree): Update to 0.3.2. [native-inputs]: Add r-knitr.
2020-03-12gnu: r-rcppparallel: Update to 5.0.0.Ricardo Wurmus
* gnu/packages/cran.scm (r-rcppparallel): Update to 5.0.0.
2020-03-12gnu: r-sjplot: Update to 2.8.3.Ricardo Wurmus
* gnu/packages/cran.scm (r-sjplot): Update to 2.8.3. [propagated-inputs]: Remove r-forcats. [native-inputs]: Remove r-knitr.
2020-03-12gnu: r-catdap: Update to 1.3.5.Ricardo Wurmus
* gnu/packages/cran.scm (r-catdap): Update to 1.3.5.
2020-03-12gnu: r-vim: Update to 5.1.1.Ricardo Wurmus
* gnu/packages/cran.scm (r-vim): Update to 5.1.1.
2020-03-12gnu: r-vctrs: Update to 0.2.4.Ricardo Wurmus
* gnu/packages/cran.scm (r-vctrs): Update to 0.2.4. [native-inputs]: Add r-knitr.
2020-03-12gnu: r-cicero: Update to 1.4.4.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-cicero): Update to 1.4.4. [native-inputs]: Add r-knitr.
2020-03-12gnu: r-ggcyto: Update to 1.14.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-ggcyto): Update to 1.14.1. [native-inputs]: Add r-knitr.
2020-03-12gnu: r-mlinterfaces: Update to 1.66.5.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-mlinterfaces): Update to 1.66.5.
2020-03-12gnu: r-qtl: Update to 1.46-2.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-qtl): Update to 1.46-2.
2020-03-12gnu: Add hyperledger-iroha.Pierre Neidhardt
This package was co-authored with Efraim Flashner <efraim@flashner.co.il> * gnu/packages/hyperledger.scm (hyperledger-iroha): New variable.
2020-03-12gnu: Add boost-1.69.Efraim Flashner
* gnu/packages/boost.scm (boost-1.69): New hidden package.
2020-03-12gnu: Add hyperledger-iroha-ed25519.Pierre Neidhardt
* gnu/packages/hyperledger.scm (hyperledger-iroha-ed25519): New variable.
2020-03-12gnu: grpc: Build shared libraries.Efraim Flashner
* 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.
2020-03-12gnu: python2-jupyter-console: Build with python2.Efraim Flashner
* gnu/packages/python-xyz.scm (python2-jupyter-console)[arguments]: Add python keyword, set to python-2.
2020-03-12gnu: python-jupyter-console: Specify python2 variant.Efraim Flashner
* gnu/packages/python-xyz.scm (python-jupyter-console)[properties]: New field. Specify python2-jupyter-console as python2 variant.
2020-03-12services: mumi-service-type: Update to latest version of mumi.Ricardo Wurmus
* gnu/services/web.scm (%mumi-activation): Create /var/mumi/db. (mumi-shepherd-services): Add service for mumi worker.
2020-03-12gnu: mumi: Update to 0.0.0-7.6653e2d.Ricardo Wurmus
* gnu/packages/mail.scm (mumi): Update to 0.0.0-7.6653e2d. [inputs]: Add guile-sqlite3.
2020-03-12gnu: r-cairo: Update to 1.5-11.Ricardo Wurmus
* gnu/packages/statistics.scm (r-cairo): Update to 1.5-11.
2020-03-12gnu: dune-istl: Build with suitesparseFelix Gruber
* gnu/packages/maths.scm (dune-istl)[inputs]: Add suitesparse to build additional solvers in dune-istl. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2020-03-12gnu: Add dune-subgridFelix Gruber
* gnu/packages/maths.scm (dune-subgrid): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2020-03-12gnu: Add dune-uggrid.Felix Gruber
* 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>
2020-03-12gnu: dune-*: set up MPI for testsFelix Gruber
* 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>
2020-03-12inferior: Distinguish inferior exceptions.Ludovic Courtès
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.
2020-03-12import: cpan: Gracefully handle missing projects.Ludovic Courtès
* guix/import/cpan.scm (cpan-fetch): Check whether 'json-fetch' returns #f.
2020-03-12import: utils: Remove 'assoc-ref*'.Ludovic Courtès
* guix/import/utils.scm (assoc-ref*): Remove.
2020-03-12import: pypi: Rewrite to use 'define-json-mapping'.Ludovic Courtès
* 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.
2020-03-12gnu: guile-next: Enable JIT on ARMv7.Ludovic Courtès
JIT support on ARMv7 is fixed by "guile-3.0-crash.patch". * gnu/packages/guile.scm (guile-3.0)[arguments]: Remove.
2020-03-12gnu: Add virtualpg.Guillaume Le Vaillant
* gnu/packages/geo.scm (virtualpg): New variable.
2020-03-12gnu: jgmenu: Update to 4.1.0.Guillaume Le Vaillant
* gnu/packages/xdisorg.scm (jgmenu): Update to 4.1.0.
2020-03-12gnu: udiskie: Update to 2.1.0.Guillaume Le Vaillant
* gnu/packages/freedesktop.scm (udiskie): Update to 2.1.0.
2020-03-12gnu: txr: Update to 233.Guillaume Le Vaillant
* gnu/packages/lisp.scm (txr): Update to 233.
2020-03-12doc: Fix description for "guix package -A".Danny Milosavljevic
* doc/guix.texi (Invoking guix package): Fix description for "guix package -A".
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