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2021-12-10gnu: Add rust-atty-0.2.11.•••* gnu/packages/crates-io.scm (rust-atty-0.2.11): New variable. Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr> Petr Hodina
2021-12-10gnu: rust-anyhow-1: Update to 1.0.46.•••* gnu/packages/crates-io.scm (rust-anyhow-1): Update to 1.0.46. Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr> Petr Hodina
2021-12-10gnu: Add rust-tree-magic-0.2.•••* gnu/packages/crates-io.scm (rust-tree-magic-0.2): New variable. Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr> Petr Hodina
2021-12-10gnu: Add rust-x11rb-0.8.•••* gnu/packages/crates-graphics.scm (rust-x11rb-0.8): New variable. Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr> Petr Hodina
2021-12-10gnu: Add rust-winapi-wsapoll-0.1.•••* gnu/packages/crates-io.scm (rust-winapi-wsapoll-0.1): New variable. Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr> Petr Hodina
2021-12-10gnu: Add rust-rspotify-0.10.•••* gnu/packages/crates-io.scm (rust-rspotify-0.10): New variable. Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr> Petr Hodina
2021-12-10gnu: Add rust-derive-builder-0.7.•••* gnu/packages/crates-io.scm (rust-derive-builder-0.7): New variable. Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr> Petr Hodina
2021-12-10gnu: Add rust-derive-builder-core-0.5.•••* gnu/packages/crates-io.scm (rust-derive-builder-core-0.5): New variable. Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr> Petr Hodina
2021-12-10gnu: Add rust-dotenv-0.13•••* gnu/packages/crates-io.scm (rust-dotenv-0.13): New variable. Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr> Petr Hodina
2021-12-10gnu: Add rust-tui-0.16.•••* gnu/packages/crates-io.scm (rust-tui-0.16): New variable. (rust-tui-0.15): Inherit from above. Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr> Petr Hodina
2021-12-10gnu: Add rust-argh-0.1.•••* gnu/packages/crates-io.scm (rust-argh-0.1): New variable. Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr> Petr Hodina
2021-12-10gnu: Add rust-argh-derive-0.1.•••* gnu/packages/crates-io (rust-argh-derive-0.1): New variable. Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr> Petr Hodina
2021-12-10gnu: Add rust-argh-shared-0.1.•••* gnu/packages/crates-io.scm (rust-argh-shared-0.1): New variable. Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr> Petr Hodina
2021-12-09gnu: opam: Update to 2.1.2.•••* gnu/packages/ocaml.scm (opam): Update to 2.1.2. Julien Lepiller
2021-12-09gnu: pplacer: Fix build.•••* gnu/packages/bioinformatics.scm (pplacer)[inputs]: Replace gsl with gsl-static. * gnu/packages/ocaml.scm (ocaml4.07-gsl-1)[inputs]: Same. Efraim Flashner
2021-12-09gnu: Add gsl-static.•••* gnu/packages/maths.scm (gsl-static): New variable. Efraim Flashner
2021-12-09gnu: python-dendropy: Skip additional test.•••* gnu/packages/bioinformatics.scm (python-dendropy)[arguments]: Adjust custom 'skip-broken-tests phase to skip additional test. Efraim Flashner
2021-12-09gnu: mumi: Update to 0.0.1-6.8a45281.•••* gnu/packages/mail.scm (mumi): Update to 0.0.1-6.8a45281. [arguments]: Remove trailing #T. Ricardo Wurmus
2021-12-09gnu: python-rich: Remove optional input ipywidgets.•••* gnu/packages/python-xyz.scm (python-rich)[propagated-inputs]: Remove python-ipywidgets. Ricardo Wurmus
2021-12-09gnu: r-minimal: Remove extraneous references.•••* gnu/packages/statistics.scm (r-minimal)[arguments]: Remove references to native build-time tools. Ricardo Wurmus
2021-12-09gnu: uBlock Origin: Update to 1.39.2.•••* gnu/packages/browser-extensions.scm (ublock-origin): Update to 1.39.2. Marius Bakke
2021-12-09gnu: ungoogled-chromium: Update to 96.0.4664.93-1.•••* gnu/packages/chromium.scm (%chromium-version): Set to 96.0.4664.93. (%ungoogled-origin, ungoogled-chromium): Update hashes. Marius Bakke
2021-12-09gnu: imp: Build with default cmake.•••* gnu/packages/bioinformatics.scm (imp)[arguments]: Remove cmake flag. Efraim Flashner
2021-12-09gnu: repeat-masker: Update to 4.1.2-p1.•••* gnu/packages/bioinformatics.scm (repeat-masker): Update to 4.1.2-p1. Ricardo Wurmus
2021-12-09gnu: metabat: Update to 2.15.•••* gnu/packages/bioinformatics.scm (metabat): Update to 2.15. [source]: Remove patch. [build-system]: Use cmake-build-system. [arguments]: Adjust to new build system. * gnu/packages/patches/metabat-fix-compilation.patch: Remove file. * gnu/local.mk (dist_patch_DATA): Remove it. Ricardo Wurmus
2021-12-09gnu: python2-scikit-learn: Disable one more test.•••* gnu/packages/machine-learning.scm (python2-scikit-learn)[arguments]: Do not inherit; remove obsolete 'make-files-writable phase; disable one more failing test in 'check phase. Ricardo Wurmus
2021-12-09gnu: seek: Update to 1-1.196ed4c.•••* gnu/packages/bioinformatics.scm (seek): Update to 1-1.196ed4c. [source]: Fetch from github. [build-system]: Use cmake-build-system. [arguments]: Remove all custom phases; replace 'check phase; disable tests; set configure flags. [inputs]: Add apache-thrift:include, apache-thrift:lib, and python. [native-inputs]: Remove autoconf, automake, and perl; add pkg-config. Ricardo Wurmus
2021-12-09gnu: libsvm: Install header and library.•••* gnu/packages/machine-learning.scm (libsvm)[arguments]: Add build phase 'build-lib; also install header file and shared library in the 'install phase. Ricardo Wurmus
2021-12-09gnu: miso: Update to 0.5.4-1.b714021.•••* gnu/packages/bioinformatics.scm (miso): Update to 0.5.4-1.b714021. [source]: Fetch via git; simplify snippet. [inputs]: Replace samtools with samtools-1.2. [home-page]: Update to new location. Ricardo Wurmus
2021-12-09gnu: Add samtools-1.2.•••* gnu/packages/bioinformatics.scm (samtools-1.2): New variable. Ricardo Wurmus
2021-12-09gnu: Add htslib-for-samtools-1.2.•••* gnu/packages/bioinformatics.scm (htslib-for-samtools-1.2): New variable. Ricardo Wurmus
2021-12-09gnu: python2-scipy: Override native inputs.•••* gnu/packages/python-science.scm (python2-scipy)[native-inputs]: Override; replace gfortran with gfortran-7; add gcc-7. Ricardo Wurmus
2021-12-09gnu: python2-matplotlib: Fix mpl_toolkits module.•••* gnu/packages/python-xyz.scm (python2-matplotlib)[arguments]: Add phase 'create-init-file; restore 'sanity-check phase. Ricardo Wurmus
2021-12-09gnu: Add gfortran-7.•••* gnu/packages/gcc.scm (gfortran-7): New variable. Ricardo Wurmus
2021-12-09gnu: emacs-evil-magit: Remove deprecated package.•••* gnu/packages/emacs-xyz.scm (emacs-evil-magit): Delete variable. evil-magit has been consolidated into evil-collection. The package has been removed from MELPA since February. See here: <https://github.com/emacs-evil/evil-magit>. Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr> jgart via Guix-patches via
2021-12-09gnu: Add emacs-dpd.•••* gnu/packages/emacs-xyz.scm (emacs-dpd): New variable. Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr> Andrew Tropin
2021-12-09gnu: valeronoi: Update to 0.1.6.•••* gnu/packages/engineering.scm (valeronoi): Update to 0.1.6. Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr> Petr Hodina
2021-12-08gnu: tiramisu: Update to 2.0.20211107.•••* gnu/packages/gnome-xyz.scm (tiramisu): Update to 2.0.20211107. [native-inputs]: Add vala. Signed-off-by: Leo Famulari <leo@famulari.name> terramorpha
2021-12-09gnu: isc-dhcp: Update bundled BIND to 9.11.36 [fixes CVE-2021-25219].•••* gnu/packages/admin.scm (isc-dhcp)[inputs]: Update bundled BIND to 9.11.36. Signed-off-by: Tobias Geerinckx-Rice <me@tobias.gr> Leo Famulari
2021-12-09gnu: bind: Update to 9.16.23 [fixes CVE-2021-25218, CVE-2021-25219].•••* gnu/packages/dns.scm (isc-bind): Update to 9.16.23. [source]: Add patch. * gnu/packages/patches/bind-re-add-attr-constructor-priority.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. Tobias Geerinckx-Rice
2021-12-08gnu: python-slepc4py: Update to 3.16.1.•••This is a followup 5b4d1e57b6d4931f6ee2a50abf84222fe015d045. * gnu/packages/maths.scm (slepc-openmpi)[inputs]: Move ARPACK-NG-OPENMPI to... [propagated-inputs]: ... here. (python-slepc4py): Update to 3.16.1. Ludovic Courtès
2021-12-08gnu: python-petsc4py: Update to 3.16.1.•••This is a followup to 07ac13a26a0d7c8319afb42c55fc2116ec44668f. * gnu/packages/maths.scm (python-petsc4py): Update to 3.16.1. Ludovic Courtès
2021-12-08gnu: geeqie: Fix X11 error at startup.•••Fixes <https://issues.guix.gnu.org/52089>. Reported by Maxim Cournoyer <maxim.cournoyer@gmail.com>. Patch provided by John Kehayias <john.kehayias@protonmail.com>. * gnu/packages/patches/geeqie-clutter.patch: New file. * gnu/packages/image-viewers.scm (geeqie)[sources]: Use it. * gnu/local.mk (dist_patch_DATA): Add it. Ludovic Courtès
2021-12-08gnu: Add realmd.•••* gnu/packages/admin.scm (realmd): New variable. Signed-off-by: Leo Famulari <leo@famulari.name> Petr Hodina
2021-12-08gnu: go-github-com-alcortesm-tgz: Don't reset gzip timestamps.•••The tgz files are committed test fixtures, so don't reset their timestamps. * gnu/packages/golang.scm (go-github-com-alcortesm-tgz)[arguments]: Remove 'make-git-checkout-writable' phase. Delete 'reset-gzip-timestamps' phase instead. Signed-off-by: Leo Famulari <leo@famulari.name> Sarah Morgensen
2021-12-08gnu: Remove go-gopkg.in-check.v1.•••This package is a duplicate of go-gopkg-in-check-v1 in golang.scm, has no binaries, and has no dependents, so remove it. * gnu/packages/check.scm (go-gopkg.in-check.v1): Remove variable. Signed-off-by: Leo Famulari <leo@famulari.name> Sarah Morgensen
2021-12-08gnu: mumps: Allow compilation with GCC 10.•••Following the suggestion at <https://community.freefem.org/t/compline-on-macos-10-15-6/543>. * gnu/packages/maths.scm (mumps)[arguments]: In 'configure' phase, add '-fallow-argument-mismatch' to 'OPTF'. Ludovic Courtès
2021-12-08gnu: idutils: Fix build with glibc 2.33.•••* gnu/packages/idutils.scm (idutils)[source]: Remove reference to 'gets' from "lib/stdio.in.h". Ludovic Courtès
2021-12-08gnu: fzf: Wrap with a compliant find(1).•••* gnu/packages/terminals.scm (fzf)[inputs]: Add findutils. [arguments]: Wrap the ‘fzf’ executable with its /bin directory in $PATH. Addresses <https://issues.guix.gnu.org/52372>. Tobias Geerinckx-Rice
2021-12-08gnu: libtorrent-rasterbar: Build with default cmake.•••* gnu/packages/bittorrent.scm (libtorrent-rasterbar)[arguments]: Remove cmake flag. Efraim Flashner
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