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2019-07-25gnu: exim: Update to 4.92.1 [fixes CVE-2019-13917].Tobias Geerinckx-Rice
* gnu/packages/mail.scm (exim): Update to 4.92.1.
2019-07-25gnu: xpra: Update to 2.5.3.Rutger Helling
* gnu/packages/xorg.scm (xpra): Update to 2.5.3.
2019-07-25gnu: Add xchm.Jovany Leandro G.C
* gnu/packages/ebook.scm (xchm): New variable. Signed-off-by: Ricardo Wurmus <rekado@elephly.net> Co-authored-by: Ricardo Wurmus <rekado@elephly.net>
2019-07-24gnu: starfighter: Update to 2.0.0.3.Kei Kebreau
* gnu/packages/games.scm (starfighter): Update to 2.0.0.3. [source]: Use url-fetch and remove 'file-name' field. [native-inputs]: Remove autoconf and automake.
2019-07-25gnu: Explicitly refer to 'guile-json-1' when needed.Ludovic Courtès
* gnu/packages/bioinformatics.scm (rcas-web)[inputs]: Change 'guile-json' to 'guile-json-1'. * gnu/packages/ci.scm (cuirass)[inputs]: Likewise. * gnu/packages/guile-xyz.scm (artanis)[inputs]: Likewise. * gnu/packages/guile-xyz.scm (jupyter-guile-kernel)[inputs]: Likewise. * gnu/packages/guile-xyz.scm (guile-mastodon)[inputs]: Likewise. * gnu/packages/mail.scm (mumi)[inputs]: Likewise. * gnu/packages/package-management.scm (guix)[inputs]: Likewise. * gnu/packages/package-management.scm (guix-daemon)[inputs]: Likewise. * gnu/packages/web.scm (hpcguix-web)[inputs]: Likewise.
2019-07-25gnu: guile-json: Define 'guile-json-1'.Ludovic Courtès
* gnu/packages/guile.scm (guile-json-1): New variable.
2019-07-25maint: Switch to Guile-JSON 3.x.Ludovic Courtès
Guile-JSON 3.x is incompatible with Guile-JSON 1.x, which we relied on until now: it maps JSON dictionaries to alists (instead of hash tables), and JSON arrays to vectors (instead of lists). This commit is about adjusting all the existing code to this new mapping. * m4/guix.m4 (GUIX_CHECK_GUILE_JSON): New macro. * configure.ac: Use it. * doc/guix.texi (Requirements): Mention the Guile-JSON version. * guix/git-download.scm (git-fetch)[guile-json]: Use GUILE-JSON-3. * guix/import/cpan.scm (string->license): Expect vectors instead of lists. (module->dist-name): Use 'json-fetch' instead of 'json-fetch-alist'. (cpan-fetch): Likewise. * guix/import/crate.scm (crate-fetch): Likewise, and call 'vector->list' for DEPS. * guix/import/gem.scm (rubygems-fetch): Likewise. * guix/import/json.scm (json-fetch-alist): Remove. * guix/import/pypi.scm (pypi-fetch): Use 'json-fetch' instead of 'json-fetch-alist'. (latest-source-release, latest-wheel-release): Call 'vector->list' on RELEASES. * guix/import/stackage.scm (stackage-lts-info-fetch): Use 'json-fetch' instead of 'json-fetch-alist'. (lts-package-version): Use 'vector->list'. * guix/import/utils.scm (hash-table->alist): Remove. (alist->package): Pass 'vector->list' on the inputs fields, and default to the empty vector. * guix/scripts/import/json.scm (guix-import-json): Remove call to 'hash-table->alist'. * guix/swh.scm (define-json-reader): Expect pair? or null? instead of hash-table?. [extract-field]: Use 'assoc-ref' instead of 'hash-ref'. (json->branches): Use 'map' instead of 'hash-map->list'. (json->checksums): Likewise. (json->directory-entries, origin-visits): Call 'vector->list' on the result of 'json->scm'. * tests/import-utils.scm ("alist->package with dependencies"): New test. * gnu/installer.scm (build-compiled-file)[builder]: Use GUILE-JSON-3. * gnu/installer.scm (installer-program)[installer-builder]: Likewise. * gnu/installer/locale.scm (iso639->iso639-languages): Use 'assoc-ref' instead of 'hash-ref', and pass vectors through 'vector->list'. (iso3166->iso3166-territories): Likewise. * gnu/system/vm.scm (system-docker-image)[build]: Use GUILE-JSON-3. * guix/docker.scm (manifest, config): Adjust for Guile-JSON 3. * guix/scripts/pack.scm (docker-image)[build]: Use GUILE-JSON-3. * guix/import/github.scm (fetch-releases-or-tags): Update docstring. (latest-released-version): Use 'assoc-ref' instead of 'hash-ref'. Pass the result of 'fetch-releases-or-tags' to 'vector->list'. * guix/import/launchpad.scm (latest-released-version): Likewise.
2019-07-24gnu: Add r-depecher.zimoun
* gnu/packages/bioconductor.scm (r-depecher): New variable. Co-authored-by: Ricardo Wurmus <rekado@elephly.net> Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2019-07-24gnu: Add r-mixomics.zimoun
* gnu/packages/bioconductor.scm (r-mixomics): New variable. Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2019-07-24gnu: Add r-flowsom.zimoun
* gnu/packages/bioconductor.scm (r-flowsom): New variable. Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2019-07-24gnu: Add r-flowmeans.zimoun
* gnu/packages/bioconductor.scm (r-flowmeans): New variable. Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2019-07-24gnu: Add r-consensusclusterplus.zimoun
* gnu/packages/bioconductor.scm (r-consensusclusterplus): New variable. Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2019-07-24gnu: Add r-flowutils.zimoun
* gnu/packages/bioconductor.scm (r-flowutils): New variable. Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2019-07-24gnu: Add r-flowcore.zimoun
* gnu/packages/bioconductor.scm (r-flowcore): New variable. Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2019-07-24gnu: Add r-all.zimoun
* gnu/packages/bioconductor.scm (r-all): New variable. Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2019-07-24gnu: Add r-kableextra.zimoun
* gnu/packages/cran.scm (r-kableextra): New variable. Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2019-07-24gnu: Add r-umap.zimoun
* gnu/packages/cran.scm (r-umap): New variable. Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2019-07-24gnu: emacs-gitpatch: Update to 0.5.1.Jelle Licht
* gnu/packages/emacs-xyz.scm (emacs-gitpatch): Update to 0.5.1.
2019-07-24gnu: terminator: Propagate gsettings-desktop-schemas.Tobias Geerinckx-Rice
* gnu/packages/gnome.scm (terminator)[propagated-inputs]: Add gsettings-desktop-schemas.
2019-07-24gnu: spice-gtk: Update to 0.37.Tobias Geerinckx-Rice
* gnu/packages/spice.scm (spice-gtk): Update to 0.37. [propagated-inputs]: Use latest spice-protocol. (spice-protocol-0.12): Remove unused variable.
2019-07-24gnu: libvirt-glib: Propagate pkg-config requirements.Tobias Geerinckx-Rice
* gnu/packages/virtualization.scm (libvirt-glib)[inputs]: Move glib, libvirt, libxml2, and gobject-introspection… [native-inputs]: …here.
2019-07-24gnu: libvirt-glib: Update to 2.0.0.Tobias Geerinckx-Rice
* gnu/packages/virtualization.scm (libvirt-glib): Update to 2.0.0. [arguments]: Remove ‘fix-tests’ phase.
2019-07-24gnu: julia: Update to 1.1.1.Nicolò Balzarotti
* gnu/packages/julia.scm (libuv-julia): Update to commit 26dbe56. (libunwind-for-julia): Remove. (llvm-patch-url, llvm-patch): New procedures. (llvm-julia): New variable. (julia): Update to 1.1.1. [arguments]: Adjust 'prepare-deps' to new set of dependencies. Adjust 'hardcode-soname-map': remove openlibm and libfftw handling. Update file names in 'fix-include-and-link-paths' and 'hardcode-paths'. Adjust 'disable-broken-tests'. Pass PREFIX, LIBFLAS, and LIBBLASNAME in #:make-flags; update other flags. [inputs]: Replace LLVM-3.9.1 with LLVM-JULIA. Replace LIBUNWIND-FOR-JULIA with LIBUNWIND. Add "rmath" and "libwhich". [native-inputs]: Remove "unicode-data". Co-authored-by: Ludovic Courtès <ludo@gnu.org>
2019-07-24gnu: llvm: Add 'system->llvm-target' procedure.Ludovic Courtès
* gnu/packages/llvm.scm (system->llvm-target): New procedure.
2019-07-23gnu: terminology: Update to 1.5.0.Efraim Flashner
* gnu/packages/enlightenment.scm (terminology): Update to 1.5.0.
2019-07-23gnu: emacs-request: Update to 0.3.1.Mathieu Lirzin
* gnu/packages/emacs-xyz.scm (emacs-request): Update to 0.3.1. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2019-07-23gnu: emacs-google-translate: Update to 0.11.18.Mathieu Lirzin
* gnu/packages/emacs-xyz.scm (emacs-google-translate): Update to 0.11.18. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2019-07-23gnu: mallard-ducktype: Update to 1.0.2.Jack Hill
* gnu/packages/python-xyz.scm (mallard-ducktype) Update to 1.0.2. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2019-07-22gnu: harmonist: Update to 0.2.Julien Lepiller
* gnu/packages/games.scm (harmonist): Update to 0.2.
2019-07-22gnu: vlc: Build against libvpx@1.8.Marius Bakke
* gnu/packages/video.scm (vlc)[inputs]: Change LIBVPX-1.7 to LIBVPX.
2019-07-22gnu: libvpx: Update to 1.8.1.Marius Bakke
* gnu/packages/video.scm (libvpx): Update to 1.8.1.
2019-07-22gnu: zstd: Update to 1.4.1.Marius Bakke
* gnu/packages/compression.scm (zstd): Update to 1.4.1.
2019-07-22gnu: zstd: Move libraries to separate outputs.Marius Bakke
* gnu/packages/compression.scm (zstd)[outputs]: New field. [arguments]: Add phase 'adjust-libary-locations'. Pass LIBDIR and INCLUDEDIR in <#:make-flags>. * gnu/packages/backup.scm (borg)[inputs]: Change ZSTD to ZSTD:LIB. * gnu/packages/sync.scm (casync)[inputs]: Likewise. * gnu/packages/tor.scm (tor)[inputs]: Likewise. * gnu/packages/linux.scm (btrfs-progs)[inputs]: Likewise. Add ZSTD:STATIC.
2019-07-22gnu: whois: Update to 5.5.0.Marius Bakke
* gnu/packages/networking.scm (whois): Update to 5.5.0.
2019-07-22gnu: jsoncpp: Update to 1.9.1.Marius Bakke
* gnu/packages/serialization.scm (jsoncpp): Update to 1.9.1.
2019-07-22gnu: ffmpeg: Update to 4.1.4.Marius Bakke
* gnu/packages/video.scm (ffmpeg): Update to 4.1.4.
2019-07-22gnu: x265: Update to 3.1.1.Marius Bakke
* gnu/packages/video.scm (x265): Update to 3.1.1.
2019-07-22gnu: ungoogled-chromium: Enable parallel build.Marius Bakke
...but limit the memory usage. Tested with --cores=8 on a 16 GiB RAM machine. * gnu/packages/chromium.scm (ungoogled-chromium)[arguments]: Remove <#:parallel-build?>. Add "jumbo_file_merge_limit=8" in <#:configure-flags>.
2019-07-22gnu: htslib: Propagate zlib.Ricardo Wurmus
Reported by Vedran Franke <Vedran.Franke@mdc-berlin.de>. * gnu/packages/bioinformatics.scm (htslib)[inputs]: Move zlib from here... [propagated-inputs]: ...to here.
2019-07-22gnu: perl-net-http: Update to 6.19.Efraim Flashner
* gnu/packages/web.scm (perl-net-httpd): Update to 6.19.
2019-07-22gnu: perl-test-simple: Update to 1.302164.Efraim Flashner
* gnu/packages/perl-check.scm (perl-test-simple): Update to 1.302164.
2019-07-22gnu: perl-cpan-meta: Update to 2.150010.Efraim Flashner
* gnu/packages/perl.scm (perl-cpan-meta): Update to 2.150010.
2019-07-22gnu: perl-clone: Update to 0.42.Efraim Flashner
* gnu/packages/perl.scm (perl-clone): Update to 0.42.
2019-07-22gnu: perl-hash-merge: Update to 0.300.Efraim Flashner
* gnu/packages/perl.scm (perl-hash-merge): Update to 0.300. [inputs]: Add perl-clone-choose.
2019-07-22gnu: mallard-ducktype: Run tests.Efraim Flashner
* gnu/packages/python-xyz.scm (mallard-ducktype)[arguments]: Replace 'check phase to run test suite.
2019-07-22gnu: oil-shell: Update to 0.6.0Robert Vollmert
* gnu/packages/shells.scm (oil-shell): Update to 0.6.0. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2019-07-21gnu: libreoffice: Fix xdg-open absolute paths.Chris Marusich
Fixes: <https://bugs.gnu.org/36728>. * gnu/packages/libreoffice.scm (libreoffice) [inputs]: Add xdg-utils. [arguments][#:phases][prepare-src]: Replace hard-coded absolute paths to xdg-open in the source with the path to xdg-open in the xdg-utils input.
2019-07-21gnu: libosinfo: Update to 1.5.0.Tobias Geerinckx-Rice
* gnu/packages/virtualization.scm (libosinfo): Update to 1.5.0. [arguments]: Remove ‘disable-broken-test’ phase. [native-inputs]: Remove check.
2019-07-21gnu: linux-libre: Update to 5.2.2.Mark H Weaver
* gnu/packages/linux.scm (linux-libre-5.2-version): Update to 5.2.2. (linux-libre-5.2-pristine-source): Update hash.
2019-07-21gnu: linux-libre@4.19: Update to 4.19.60.Mark H Weaver
* gnu/packages/linux.scm (linux-libre-4.19-version): Update to 4.19.60. (linux-libre-4.19-pristine-source): Update hash.
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