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* gnu: emacs-org-roam-bibtex: Update to 0.6.1.Nicolas Goaziou2021-12-04
| | | | * gnu/packages/emacs-xyz.scm (emacs-org-roam-bibtex): Update to 0.6.1.
* gnu: janet: Update to 1.19.0.jgart2021-12-04
| | | | | | * gnu/packages/lisp.scm (janet): Update to 1.19.0. Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>
* gnu: tinmop: Update to 0.9.2.cage2021-12-04
| | | | | | | | | | * gnu/packages/web-browsers.scm (tinmop): Update to 0.9.2. [inputs]: Move nano, openssl and xdg-utils to... [native-inputs]: ... here. Add automake, autoconf and mandoc. Remove curl and gnupg. [arguments]: Add 'fix-configure.ac' phase. Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>
* gnu: pigx-sars-cov2-ww: Update to 0.0.4.Ricardo Wurmus2021-12-04
| | | | | * gnu/packages/bioinformatics.scm (pigx-sars-cov2-ww): Update to 0.0.4. [inputs]: Add bbmap, bedtools, fastp, ivar, and r-r-utils.
* gnu: imp: Update to 2.15.0.Ricardo Wurmus2021-12-03
| | | | | * gnu/packages/bioinformatics.scm (imp): Update to 2.15.0. [arguments]: Disable one more test.
* gnu: Add r-fpeek.Ricardo Wurmus2021-12-03
| | | | * gnu/packages/cran.scm (r-fpeek): New variable.
* gnu: emacs: Load package descriptors from packages referenced by subdirs.elLiliana Marie Prikler2021-12-03
| | | | | | | | | * gnu/packages/aux-files/emacs/guix-emacs.el (guix-emacs--non-core-load-path): New procedure. (guix-emacs-autoload-packages): Use it here. (guix-emacs-load-package-descriptors): New procedure. * gnu/packages/emacs.scm (emacs)[install-site-start]: Install advice to run ‘guix-emacs-load-package-descriptors’.
* gnu: emacs: Make DocView PDF work out of the box.Liliana Marie Prikler2021-12-03
| | | | | | * gnu/packages/emacs.scm (emacs)[patch-program-file-names]: Add patches for the programs “gs”, “dvipdf”, “ps2pdf” and “pdftotext”. [inputs]: Add ghostscript and poppler.
* gnu: emacs: Find real GVFS processes.Liliana Marie Prikler2021-12-03
| | | | | | * gnu/packages/emacs.scm (emacs)[#:phases]<patch-program-file-names>: Expand calls to “tramp-compat-process-running-p” so that Guix wrappers are also matched.
* gnu: Add valeronoi.phodina2021-12-03
| | | | | | * gnu/packages/engineering.scm (valeronoi): New variable. Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
* gnu: st: Install terminfo files.jgart2021-12-03
| | | | | | | | * gnu/packages/suckless.scm (st)[native-inputs]: Add ncurses. [make-flags](TERMINFO): New flag. [phases](inhibit-terminfo-install): Remove phase. Signed-off-by: Raghav Gururajan <rg@raghavgururajan.name>
* gnu: emacs-org: Preserve version information.Morgan Smith2021-12-03
| | | | | | | * gnu/packages/emacs-xyz.scm (emacs-org)[#:phases]: Prevent install phase from deleting the version information. Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
* gnu: emacs-consult-notmuch: Update to 0.6.Nicolas Goaziou2021-12-03
| | | | * gnu/packages/emacs-xyz.scm (emacs-consult-notmuch): Update to 0.6.
* gnu: emacs-helm: Update to 3.8.2.Nicolas Goaziou2021-12-03
| | | | * gnu/packages/emacs-xyz.scm (emacs-helm): Update to 3.8.2.
* gnu: emacs-vertico: Update to 0.17.Nicolas Goaziou2021-12-03
| | | | * gnu/packages/emacs-xyz.scm (emacs-vertico): Update to 0.17.
* gnu: python-ont-fast5-api: Update to 4.0.0.Ricardo Wurmus2021-12-03
| | | | | | | | * gnu/packages/bioinformatics.scm (python-ont-fast5-api): Update to 4.0.0. [source]: Remove bundled plugin binaries. [arguments]: Install plugin from inputs. [inputs]: Add vbz-compression. [propagated-inputs]: Remove python-six; add python-packaging.
* gnu: Add vbz-compression.Ricardo Wurmus2021-12-03
| | | | * gnu/packages/bioinformatics.scm (vbz-compression): New variable.
* gnu: cl-coalton: Update to 0.0.1-2.012f6c8.Charles2021-12-03
| | | | | | * gnu/packages/lisp-xyz.scm (sbcl-coalton): Update to 0.0.1-2.012f6c8. Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>
* gnu: cl-float-features: Update to 1.0.0-2.c1f86ae.Charles2021-12-03
| | | | | | * gnu/packages/lisp-xyz.scm (sbcl-float-features): Update to 1.0.0-2.c1f86ae. Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>
* gnu: ivar: Disable parallel tests.Ricardo Wurmus2021-12-03
| | | | * gnu/packages/bioinformatics.scm (ivar)[arguments]: Disable parallel tests.
* gnu: Remove python2-biom-format.Ricardo Wurmus2021-12-03
| | | | | | | | There are no users of this variant, and the current version of biom-format does not support Python 2. * gnu/packages/bioinformatics.scm (python2-biom-format): Remove variable. (python-biom-format)[properties]: Remove field.
* gnu: r-flowclust: Add gsl.Ricardo Wurmus2021-12-03
| | | | | * gnu/packages/bioconductor.scm (r-flowclust)[inputs]: Remove accidentally committed comment character.
* gnu: icecat: Remove vestigial icecat-78-makeicecat.patch.Mark H Weaver2021-12-03
| | | | | | | This is a followup to commit a63231003e7bbeafb0110b077788e47e78685f20. * gnu/packages/patches/icecat-78-makeicecat.patch: Delete file. * gnu/local.mk (dist_patch_DATA): Remove it.
* gnu: cuirass: Update to 1.1.0-6.df8837c.Mathieu Othacehe2021-12-03
| | | | * gnu/packages/ci.scm (cuirass): Update to 1.1.0-6.df8837c.
* gnu: python-pandocfilters: Update to 1.5.0.jgart2021-12-03
| | | | | | * gnu/packages/textutils.scm (python-pandocfilters): Update to 1.5.0. Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
* gnu: icecat: Fix CVE-2021-43527.Mark H Weaver2021-12-03
| | | | | | * gnu/packages/patches/icecat-CVE-2021-43527.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. * gnu/packages/gnuzilla.scm (icecat-source): Apply it.
* gnu: nss: Fix CVE-2021-43527 via graft.Mark H Weaver2021-12-03
| | | | | | | * gnu/packages/patches/nss-CVE-2021-43527.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. * gnu/packages/nss.scm (nss/fixed): New variable (nss)[replacement]: New field.
* gnu: openjdk16: Use MAKE-FILE-WRITABLE.Ricardo Wurmus2021-12-02
| | | | * gnu/packages/java.scm (openjdk16)[arguments]: Do not shell out to "chmod".
* gnu: Add openjdk17.Arne Babenhauserheide2021-12-02
| | | | | | * gnu/packages/java.scm (openjdk17): New variable. Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
* gnu: python2-decorator: Downgrade to 4.3.0Ricardo Wurmus2021-12-02
| | | | | * gnu/packages/python-xyz.scm (python2-decorator): Keep at 4.3.0. (python-decorator)[properties]: Add python2-variant.
* gnu: ribodiff: Remove trailing #T.Ricardo Wurmus2021-12-02
| | | | | * gnu/packages/bioinformatics.scm (ribodiff)[arguments]: Remove trailing #T from build phase.
* gnu: ribodiff: Disable broken test.Ricardo Wurmus2021-12-02
| | | | | * gnu/packages/bioinformatics.scm (ribodiff)[arguments]: Add build phase 'disable-plot-test.
* gnu: python2-statsmodels: Downgrade to 0.9.0.Ricardo Wurmus2021-12-02
| | | | * gnu/packages/statistics.scm (python2-statsmodels): Downgrade to 0.9.0.
* gnu: khmer: Fix build with Python 3.8.Ricardo Wurmus2021-12-02
| | | | | | * gnu/packages/bioinformatics.scm (khmer)[source]: Remove trailing #T. [arguments]: Remove trailing #T from build phases; add build phase 'python-3.8-compatibility.
* gnu: python-biom-format: Update to 2.1.10.Ricardo Wurmus2021-12-02
| | | | | | | | * gnu/packages/bioinformatics.scm (python-biom-format): Update to 2.1.10. [source]: Simplify snippet. [arguments]: Add phase 'relax; remove trailing #T from other build phases. [propagated-inputs]: Add python-anndata; replace python-pandas-0.25 with python-pandas.
* gnu: Add trayer-srg.jgart2021-12-02
| | | | | | | * gnu/packages/wm.scm (trayer-srg): New variable. Co-authored-by: Disseminate Dissent <disseminatedissent@protonmail.com> Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
* gnu: pardre: Update to 2.2.5.Ricardo Wurmus2021-12-02
| | | | | * gnu/packages/bioinformatics.scm (pardre): Update to 2.2.5. [arguments]: Remove trailing #T and update comment about tests.
* gnu: pardre: Use C++ bindings for MPI.Ricardo Wurmus2021-12-02
| | | | | * gnu/packages/bioinformatics.scm (pardre)[inputs]: Replace openmpi with openmpi-c++.
* gnu: Add openmpi-c++.Ricardo Wurmus2021-12-02
| | | | * gnu/packages/mpi.scm (openmpi-c++): New variable.
* gnu: Add libconfini.Liliana Marie Prikler2021-12-02
| | | | | | * gnu/packages/cpp.scm (libconfini): New variable. Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
* gnu: shotcut: Update to 21.10.31.Vinicius Monego2021-12-02
| | | | | | * gnu/packages/video.scm (shotcut): Update to 21.10.31. Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
* gnu: kdenlive: Update to 21.08.3.Vinicius Monego2021-12-02
| | | | | | | | * gnu/packages/kde.scm (kdenlive): Update to 21.08.3. [arguments]: Pass "-DBUILD_TESTING=off" to #:configure-flags as tests are currently disabled. Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
* gnu: mlt: Update to 7.2.0.Vinicius Monego2021-12-02
| | | | | | * gnu/packages/video.scm (mlt): Update to 7.2.0. Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
* gnu: ccls: Update to 0.20210330.jgart2021-12-02
| | | | | | * gnu/packages/cpp.scm (ccls): Update to 0.20210330. Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
* gnu: guile-udev: Update to 0.2.0Artyom V. Poptsov2021-12-02
| | | | | | * gnu/packages/guile-xyz.scm (guile-udev): Update to 0.2.0. Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
* gnu: python-ipython: Update to 7.20.0.Ricardo Wurmus2021-12-02
| | | | * gnu/packages/python-xyz.scm (python-ipython): Update to 7.20.0.
* gnu: python-ipython: Remove trailing #T.Ricardo Wurmus2021-12-02
| | | | | * gnu/packages/python-xyz.scm (python-ipython)[arguments]: Remove trailing #T from build phases.
* gnu: yggdrasil: Simplify build phases.Efraim Flashner2021-12-02
| | | | | | * gnu/packages/networking.scm (yggdrasil)[arguments]: Rewrite custom 'build phase reusing go-build-system 'build phase. Remove custom 'install phase.
* gnu: go-golang-zx2c4-com-wireguard: Fix downloading source.Efraim Flashner2021-12-02
| | | | | * gnu/packages/golang.scm (go-golang-zx2c4-com-wireguard)[source]: Adjust commit string in git-reference.
* gnu: go-github-com-vividcortex-ewma: Adjust import-path.Efraim Flashner2021-12-02
| | | | | * gnu/packages/golang.scm (go-github-com-vividcortex-ewma)[arguments]: Adjust import-path to location other go packages expect it to be.
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