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2021-07-28gnu: r-ggpp: Update to 0.4.1.Ricardo Wurmus
* gnu/packages/cran.scm (r-ggpp): Update to 0.4.1. [propagated-inputs]: Remove r-generics and r-plyr.
2021-07-28gnu: r-googlesheets4: Update to 1.0.0.Ricardo Wurmus
* gnu/packages/cran.scm (r-googlesheets4): Update to 1.0.0. [propagated-inputs]: Remove r-lifecycle; add r-cli.
2021-07-28gnu: Add r-lobstr.Ricardo Wurmus
* gnu/packages/cran.scm (r-lobstr): New variable.
2021-07-28gnu: Add r-datawizard.Ricardo Wurmus
* gnu/packages/cran.scm (r-datawizard): New variable.
2021-07-28gnu: r-with-tests: Hardcode path to coreutils’ rmLars-Dominik Braun
When running R in a container like this guix environment --no-cwd -C --ad-hoc r-minimal -- Rscript -e 'Sys.timezone()' it would print an additional line sh: rm: command not found before exiting. * gnu/packages/statistics.scm (r-with-tests) [#:phases]: Add substitute* to patch call to `rm` and rename phase to reflect what it does now.
2021-07-28gnu: Add python-modin.Ricardo Wurmus
* gnu/packages/python-science.scm (python-modin): New variable.
2021-07-28gnu: Add python-distributed.Ricardo Wurmus
* gnu/packages/python-science.scm (python-distributed): New variable.
2021-07-28gnu: Add python-zict.Ricardo Wurmus
* gnu/packages/python-xyz.scm (python-zict): New variable.
2021-07-28gnu: Add python-heapdict.Ricardo Wurmus
* gnu/packages/python-xyz.scm (python-heapdict): New variable.
2021-07-28gnu: python-pyarrow: Fix parquet support.Ricardo Wurmus
Co-authored-by: Phil Beadling <phil@beadling.co.uk>. * gnu/packages/databases.scm (python-pyarrow)[arguments]: Add phases patch-cmake-variables, patch-parquet-library, and set-PYARROW_WITH_PARQUET. [propagated-inputs]: Add "include" output of apache-arrow package.
2021-07-28gnu: python-pandas: Update to 1.3.0.Ricardo Wurmus
* gnu/packages/python-science.scm (python-pandas): Update to 1.3.0. [arguments]: Adjust check phase.
2021-07-28gnu: python-dask: Update to 2021.7.1.Ricardo Wurmus
* gnu/packages/python-xyz.scm (python-dask): Update to 2021.7.1. [arguments]: Do not skip test_shuffle.
2021-07-28gnu: python-partd: Update to 1.2.0.Ricardo Wurmus
* gnu/packages/python-xyz.scm (python-partd): Update to 1.2.0.
2021-07-28gnu: python-numexpr: Update to 2.7.3.Ricardo Wurmus
* gnu/packages/python-xyz.scm (python-numexpr): Update to 2.7.3.
2021-07-28gnu: python-cloudpickle: Update to 1.6.0.Ricardo Wurmus
* gnu/packages/python-xyz.scm (python-cloudpickle-testpkg): New variable. (python-cloudpickle): Update to 1.6.0; inherit from python-cloudpickle-testpkg. [source]: Fetch from git repository. [native-inputs]: Add python-cloudpickle-testpkg; replace python-tornado with python-tornado-6.
2021-07-28gnu: python2-cloudpickle: Override version, source, and native-inputs.Ricardo Wurmus
* gnu/packages/python-xyz.scm (python2-cloudpickle)[version]: Explicitly set to 1.3.0. [source]: Copy from base package. [native-inputs]: Do not inherit; copy.
2021-07-28gnu: cmake: Update to 3.21.1.Ricardo Wurmus
* gnu/packages/cmake.scm (cmake): Update to 3.21.1. [arguments]: Skip one more test.
2021-07-28gnu: julia-distances: Update flakey tests.Efraim Flashner
* gnu/packages/julia-xyz.scm (julia-distances)[arguments]: Adjust the custom 'skip-flakey-tests phase.
2021-07-28gnu: julia-docstringextensions: Skip tests.Efraim Flashner
* gnu/packages/julia-xyz.scm (julia-docstringextensions)[arguments]: Skip tests.
2021-07-28gnu: julia-datavalues: Skip tests.Efraim Flashner
* gnu/packages/julia-xyz.scm (julia-datavalues)[arguments]: Skip tests.
2021-07-28gnu: julia-compat: Update to 3.31.0.Efraim Flashner
* gnu/packages/julia-xyz.scm (julia-compat): Update to 3.31.0.
2021-07-28gnu: global: Update to 6.6.7.Efraim Flashner
* gnu/packages/code.scm (global): Update to 6.6.7.
2021-07-28gnu: julia-jllwrappers: Add julia-preferences.Efraim Flashner
* gnu/packages/julia-jll.scm (julia-jllwrappers)[propagated-inputs]: Add julia-preferences.
2021-07-28gnu: Add julia-preferences.Efraim Flashner
* gnu/packages/julia-xyz.scm (julia-preferences): New variable.
2021-07-28gnu: julia: Skip tests on aarch64-linux.Efraim Flashner
* gnu/packages/julia.scm (julia)[arguments]: Skip tests when building for aarch64-linux.
2021-07-28gnu: llvm-julia: Overide build-type.Efraim Flashner
* gnu/packages/julia.scm (llvm-julia)[arguments]: Move CMAKE_BUILD_TYPE config from configure-flags to build-type.
2021-07-28gnu: libuv-julia: Clean up package definition.Efraim Flashner
* gnu/packages/julia.scm (libuv-julia)[source]: Use git-file-name. [build-system]: Remove field. [arguments]: Remove field.
2021-07-28gnu: julia: Update to 1.6.1.Jean-Baptiste Volatier
* gnu/packages/julia.scm (julia): Update to 1.6.1. [arguments]: Adjust custom 'prepare-deps phase. Remove custom 'fix-precompile phase. Add new 'shared-objects-path phase to fix paths to shared objects. Add new 'adjust-test-suite phase to adjust for differences in bundled vs packaged libraries. Adjust custom 'disable-broken-tests phase for new version. Add symlinks to libs in 'symlink-libraries phase. In make-flags add more finegrained compilation targets for x86_64-linux. Update make-flags for changes since last version. [inputs]: Add nghttp2:lib, gfortran:lib, curl-ssh. Remove arpack-ng, curl. Sort alphabetically. [native-inputs]: Add nss-certs. Sort alphabetically. (libuv-julia): Update to newer revision. (libunwind-julia)[source]: Add new patch. (llvm-julia): Inherit from llvm-11. [source]: Update patch list. [arguments]: Apply minority of the Julia specific patches in 'julia-patches phase. [inputs]: Add julia patches. Co-Authored-By: Nicolò Balzarotti <nicolo@nixo.xyz>. Co-Authored-By: zimoun <zimon.toutoune@gmail.com>. Co-Authored-By: Efraim Flashner <efraim@flashner.co.il>.
2021-07-28gnu: Add curl-ssh.Jean-Baptiste Volatier
* gnu/packages/curl.scm (curl-ssh): New hidden package. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2021-07-28gnu: julia-staticarrays: Update to 1.2.5Jean-Baptiste Volatier
* gnu/packages/julia-xyz.scm (julia-staticarrays): Update to 1.2.5 Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2021-07-28gnu: openlibm: Fix cross-compiling.Jean-Baptiste Volatier
* gnu/packages/maths.scm (openlibm)[arguments]: Add configure-flag to use cc-for-target. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2021-07-28gnu: openlibm: Update to 0.7.4.Jean-Baptiste Volatier
* gnu/packages/maths.scm (openlibm): Update to 0.7.4. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2021-07-28gnu: Add pcre2-10.36.Jean-Baptiste Volatier
* gnu/packages/pcre.scm (pcre2-10.36): New variable. Co-Authored-By: zimoun <zimoun.toutoune@gmail.com>. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2021-07-28gnu: Add utf8proc-2.6.1.Jean-Baptiste Volatier
* gnu/packages/textutils.scm (utf8proc-2.6.1): New variable. Co-Authored-By: zimoun <zimon.toutoune@gmail.com>. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2021-07-28gnu: glibc-for-bootstrap: Update patch.Franz Josef
There was/is something funny going on with the bootstrap glibc. The symbol for posix_spawnp points to getopt_r. Which in turn leads to a lot of crashed in tests later on. I extended the glibc-bootstrap patch to work around this bug. * gnu/packages/patches/glibc-bootstrap-system.patch: Adjust patch to work correctly with new architectures. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2021-07-28gnu: global: Fix lisp install dir.Efraim Flashner
* gnu/packages/code.scm (global)[arguments]: Adjust custom 'post-install phase to move emacs files to the correct directory.
2021-07-27gnu: python-pikepdf: Update to 2.16.0.Nicolas Goaziou
* gnu/packages/python-xyz.scm (python-pikepdf): Update to 2.16.0.
2021-07-27gnu: telescope: Update to 0.4.1.cage
* gnu/packages/web-browsers.scm (telescope): Update to 0.4.1. Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
2021-07-27gnu: emacs-link-hint: Update to 0.1-3.9fbf196.Alexandr Vityazev
* gnu/packages/emacs-xyz.scm (emacs-link-hint): Update to 0.1-3.9fbf196. Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
2021-07-27gnu: emacs-elpher: Update to 2.10.3.Simon South
* gnu/packages/emacs-xyz.scm (emacs-elpher): Update to 2.10.3. Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
2021-07-27gnu: emacs-typit: Update to 0.2.1-2.fa125bf.Morgan Smith
* gnu/packages/emacs-xyz.scm (emacs-typit): Update to 0.2.1-2.fa125bf. Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
2021-07-27gnu: emacs-typit: Fix dictionary location.Morgan Smith
Move the dictionary directory to be next to the lisp files, where it is expected to be. * gnu/packages/emacs-xyz.scm (emacs-typit)[arguments] <#:phases>: Remove install-dictionaries phase. <#:include>: Include dictionaries. Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
2021-07-27gnu: emacs-org-roam-bibtex: Update to 0.6.0.Vinicius Monego
* gnu/packages/emacs-xyz.scm (emacs-org-roam-bibtex): Update to 0.6.0. Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
2021-07-27gnu: emacs-org-roam: Update to 2.0.0.Vinicius Monego
* gnu/packages/emacs-xyz.scm (emacs-org-roam): Update to 2.0.0. [propagated-inputs]: Add emacs-magit. Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
2021-07-27gnu: Add emacs-org-cv.Vinicius Monego
* gnu/packages/emacs-xyz.scm (emacs-org-cv): New variable. Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
2021-07-27gnu: mesa-opencl-icd: Use absolute path for the library.Ivan Gankevich
* gnu/packages/gl.scm (mesa-opencl-icd): Use absolute path for OpenCL platform library in "mesa.icd" file. With this patch setting LD_LIBRARY_PATH=$LIBRARY_PATH is no longer needed to run OpenCL applications. Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>
2021-07-27derivations: Make 'coalesce-duplicate-inputs' linear in the number of inputs.Ludovic Courtès
Partly fixes <https://issues.guix.gnu.org/49439>. Reported by Ricardo Wurmus <rekado@elephly.net>. When running the command: guix environment pigx-scrnaseq --search-paths --no-grafts this change reduces total heap allocations from 1.4GiB to 717MiB (49%) and wall-clock time from 7.5s to 5.7s (24%). Without '--no-grafts', heap allocations go from 2.1GiB to 1.4GiB (33%) and wall-clock time from 12.1s to 10.9s (10%). * guix/derivations.scm (coalesce-duplicate-inputs): Rewrite using a hash table to make it O(N) rather than O(N²).
2021-07-27gnu: sudo: Update to 1.9.7p2.Tobias Geerinckx-Rice
* gnu/packages/admin.scm (sudo): Update to 1.9.7p2.
2021-07-27gnu: WebKitGTK: Update to 2.32.3 [security fixes]Leo Famulari
Fixes CVE-2021-{21775,21779,30663,30665,30689,30724,30749,30795,30797,30799}. https://webkitgtk.org/security/WSA-2021-0004.html * gnu/packages/webkit.scm (webkitgtk): Update to 2.32.2.
2021-07-27gnu: Remove rust-bat-0.17.Nicolas Goaziou
* gnu/packages/crates-io.scm (rust-bat-0.17): Remove variable.
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