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2021-12-04gnu: emacs-org-roam-bibtex: Update to 0.6.1.Nicolas Goaziou
* gnu/packages/emacs-xyz.scm (emacs-org-roam-bibtex): Update to 0.6.1.
2021-12-04gnu: janet: Update to 1.19.0.jgart
* gnu/packages/lisp.scm (janet): Update to 1.19.0. Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>
2021-12-04gnu: tinmop: Update to 0.9.2.cage
* 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>
2021-12-04gnu: pigx-sars-cov2-ww: Update to 0.0.4.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (pigx-sars-cov2-ww): Update to 0.0.4. [inputs]: Add bbmap, bedtools, fastp, ivar, and r-r-utils.
2021-12-03gnu: imp: Update to 2.15.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (imp): Update to 2.15.0. [arguments]: Disable one more test.
2021-12-03gnu: Add r-fpeek.Ricardo Wurmus
* gnu/packages/cran.scm (r-fpeek): New variable.
2021-12-03gnu: emacs: Load package descriptors from packages referenced by subdirs.elLiliana Marie Prikler
* 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’.
2021-12-03gnu: emacs: Make DocView PDF work out of the box.Liliana Marie Prikler
* gnu/packages/emacs.scm (emacs)[patch-program-file-names]: Add patches for the programs “gs”, “dvipdf”, “ps2pdf” and “pdftotext”. [inputs]: Add ghostscript and poppler.
2021-12-03gnu: emacs: Find real GVFS processes.Liliana Marie Prikler
* 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.
2021-12-03gnu: Add valeronoi.phodina
* gnu/packages/engineering.scm (valeronoi): New variable. Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
2021-12-03gnu: st: Install terminfo files.jgart
* 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>
2021-12-03gnu: emacs-org: Preserve version information.Morgan Smith
* gnu/packages/emacs-xyz.scm (emacs-org)[#:phases]: Prevent install phase from deleting the version information. Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
2021-12-03gnu: emacs-consult-notmuch: Update to 0.6.Nicolas Goaziou
* gnu/packages/emacs-xyz.scm (emacs-consult-notmuch): Update to 0.6.
2021-12-03gnu: emacs-helm: Update to 3.8.2.Nicolas Goaziou
* gnu/packages/emacs-xyz.scm (emacs-helm): Update to 3.8.2.
2021-12-03gnu: emacs-vertico: Update to 0.17.Nicolas Goaziou
* gnu/packages/emacs-xyz.scm (emacs-vertico): Update to 0.17.
2021-12-03gnu: python-ont-fast5-api: Update to 4.0.0.Ricardo Wurmus
* 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.
2021-12-03gnu: Add vbz-compression.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (vbz-compression): New variable.
2021-12-03system: vm: Remove the vga argument.Mathieu Othacehe
* gnu/system/vm.scm (common-qemu-options): Remove the "-vga std" argument that is the default since QEMU 2.2. Suggested-by: Attila Lendvai <attila@lendvai.name>
2021-12-03guix system vm: Add --no-graphic CLI argument.Attila Lendvai
It configures QEMU to use the tty it was started in for IO (as opposed to opening a separate graphical window). This enables copy-pasting and scrollback. Exit QEMU with C-a x. * gnu/system/vm.scm (system-qemu-image/shared-store-script): Also add the '-nographic' QEMU argument when called with #:graphic? #false. * guix/scripts/system.scm (system-derivation-for-action): Propagate the #:graphic? keyword arg. (perform-action): Add and propagate the #:graphic? keyword arg. (show-help): Add --no-graphic CLI arg. (%options): Process the new --no-graphic CLI arg. (process-action): Feed in the CLI arg through the #:graphic? keyword arg. * doc/guix.texi (Invoking guix system): Add example to combine guix system and invoking the vm start script into one command. Split the description of the various options into separate paragraphs. Add a paragraph to describe --no-graphic. Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
2021-12-03gnu: cl-coalton: Update to 0.0.1-2.012f6c8.Charles
* gnu/packages/lisp-xyz.scm (sbcl-coalton): Update to 0.0.1-2.012f6c8. Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>
2021-12-03gnu: cl-float-features: Update to 1.0.0-2.c1f86ae.Charles
* gnu/packages/lisp-xyz.scm (sbcl-float-features): Update to 1.0.0-2.c1f86ae. Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>
2021-12-03gnu: ivar: Disable parallel tests.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (ivar)[arguments]: Disable parallel tests.
2021-12-03gnu: Remove python2-biom-format.Ricardo Wurmus
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.
2021-12-03gnu: r-flowclust: Add gsl.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-flowclust)[inputs]: Remove accidentally committed comment character.
2021-12-03gnu: icecat: Remove vestigial icecat-78-makeicecat.patch.Mark H Weaver
This is a followup to commit a63231003e7bbeafb0110b077788e47e78685f20. * gnu/packages/patches/icecat-78-makeicecat.patch: Delete file. * gnu/local.mk (dist_patch_DATA): Remove it.
2021-12-03gnu: cuirass: Update to 1.1.0-6.df8837c.Mathieu Othacehe
* gnu/packages/ci.scm (cuirass): Update to 1.1.0-6.df8837c.
2021-12-03gnu: python-pandocfilters: Update to 1.5.0.jgart
* gnu/packages/textutils.scm (python-pandocfilters): Update to 1.5.0. Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
2021-12-03gnu: icecat: Fix CVE-2021-43527.Mark H Weaver
* 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.
2021-12-03gnu: nss: Fix CVE-2021-43527 via graft.Mark H Weaver
* 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.
2021-12-02gnu: openjdk16: Use MAKE-FILE-WRITABLE.Ricardo Wurmus
* gnu/packages/java.scm (openjdk16)[arguments]: Do not shell out to "chmod".
2021-12-02gnu: Add openjdk17.Arne Babenhauserheide
* gnu/packages/java.scm (openjdk17): New variable. Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2021-12-02gnu: python2-decorator: Downgrade to 4.3.0Ricardo Wurmus
* gnu/packages/python-xyz.scm (python2-decorator): Keep at 4.3.0. (python-decorator)[properties]: Add python2-variant.
2021-12-02gnu: ribodiff: Remove trailing #T.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (ribodiff)[arguments]: Remove trailing #T from build phase.
2021-12-02gnu: ribodiff: Disable broken test.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (ribodiff)[arguments]: Add build phase 'disable-plot-test.
2021-12-02gnu: python2-statsmodels: Downgrade to 0.9.0.Ricardo Wurmus
* gnu/packages/statistics.scm (python2-statsmodels): Downgrade to 0.9.0.
2021-12-02gnu: khmer: Fix build with Python 3.8.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (khmer)[source]: Remove trailing #T. [arguments]: Remove trailing #T from build phases; add build phase 'python-3.8-compatibility.
2021-12-02gnu: python-biom-format: Update to 2.1.10.Ricardo Wurmus
* 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.
2021-12-02gnu: Add trayer-srg.jgart
* gnu/packages/wm.scm (trayer-srg): New variable. Co-authored-by: Disseminate Dissent <disseminatedissent@protonmail.com> Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
2021-12-02gnu: pardre: Update to 2.2.5.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (pardre): Update to 2.2.5. [arguments]: Remove trailing #T and update comment about tests.
2021-12-02gnu: pardre: Use C++ bindings for MPI.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (pardre)[inputs]: Replace openmpi with openmpi-c++.
2021-12-02gnu: Add openmpi-c++.Ricardo Wurmus
* gnu/packages/mpi.scm (openmpi-c++): New variable.
2021-12-02gnu: Add libconfini.Liliana Marie Prikler
* gnu/packages/cpp.scm (libconfini): New variable. Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
2021-12-02gnu: shotcut: Update to 21.10.31.Vinicius Monego
* gnu/packages/video.scm (shotcut): Update to 21.10.31. Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
2021-12-02gnu: kdenlive: Update to 21.08.3.Vinicius Monego
* 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>
2021-12-02gnu: mlt: Update to 7.2.0.Vinicius Monego
* gnu/packages/video.scm (mlt): Update to 7.2.0. Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
2021-12-02gnu: ccls: Update to 0.20210330.jgart
* gnu/packages/cpp.scm (ccls): Update to 0.20210330. Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
2021-12-02gnu: guile-udev: Update to 0.2.0Artyom V. Poptsov
* gnu/packages/guile-xyz.scm (guile-udev): Update to 0.2.0. Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
2021-12-02gnu: python-ipython: Update to 7.20.0.Ricardo Wurmus
* gnu/packages/python-xyz.scm (python-ipython): Update to 7.20.0.
2021-12-02gnu: python-ipython: Remove trailing #T.Ricardo Wurmus
* gnu/packages/python-xyz.scm (python-ipython)[arguments]: Remove trailing #T from build phases.
2021-12-02gnu: yggdrasil: Simplify build phases.Efraim Flashner
* gnu/packages/networking.scm (yggdrasil)[arguments]: Rewrite custom 'build phase reusing go-build-system 'build phase. Remove custom 'install phase.
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