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2022-03-17gnu: Add r-mbess.Ricardo Wurmus
* gnu/packages/cran.scm (r-mbess): New variable.
2022-03-17gnu: python-jupyter-sphinx: Run tests.Efraim Flashner
* gnu/packages/sphinx.scm (python-jupyter-sphinx)[source]: Download using git-fetch. [arguments]: Use custom 'check phase. [native-inputs]: Add python-pytest.
2022-03-17gnu: python-scipy: Adjust phases.Efraim Flashner
* gnu/packages/python-science.scm (python-scipy)[arguments]: Replace 'check with custom 'check phase.
2022-03-17gnu: sicp: Update to 20180718-2.bda03f7.jgart
* gnu/packages/scheme.scm (sicp): Update to 20180718-2.bda03f7. [version]: Use git-version function. [source]: Use git-file-name function. [arguments]: Remove trailing `#t`. Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>
2022-03-17gnu: cl-3bmd: Update to 0.0.0-3.4e08d82.jgart
* gnu/packages/lisp-xyz.scm (sbcl-3bmd): Update to 0.0.0-3.4e08d82. [native-inputs]: Add sbcl-fiasco. [inputs]: Add python, python-pygments, and use newer inputs guix style. [arguments]: Add 'fix-python3-path' phase. Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>
2022-03-17gnu: cl-envy: Update to 26a7faa.jgart
* gnu/packages/lisp-xyz.scm (sbcl-envy): Update to 26a7faa. [native-inputs]: Uncomment test inputs and use new style. [arguments]: Add 'asd-systems' parameter, Remove 'fix-tests' phase. Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>
2022-03-17gnu: Add r-ggtern.Ricardo Wurmus
* gnu/packages/cran.scm (r-ggtern): New variable.
2022-03-16gnu: cross-base: Don't specify mingw --with-newlibCarl Dong
Previous to this commit, we added a --with-newlib configure flag to cross-gcc when cross-newlib?, but cross-newlib? is true only when target-mingw?. It turns out that specifying --with-newlib disables the GLIBCXX_CROSSCONFIG check, which is used to detect _GLIBCXX_HAVE__WFOPEN, which is required in C++17 std::filesystem for mingw-w64 systems. Additional context: In gnu/packages/embedded.scm, --with-newlib is specified explicitly when we're actually using newlib, which seems like the correct way of handling it. Situation in other distros: - Debian's gcc-mingw-w64 doesn't specify --with-newlib - Fedora's mingw64-gcc-c++ explicitly specifies --without-newlib Chesterton's fence: Chatting with janneke, who originally added this mechanism, reveals that this flag is not only no longer required, but also that removing it doesn't break his guile-mingw builds. See IRC logs of #guix for 2022-02-15. * gnu/packages/cross-base.scm (cross-gcc-arguments): Don't check for and specify --with-newlib. (cross-libc): Check for mingw and use mingw-w64 directly. (cross-newlib?): Remove, unexport. (native-libc): Remove.
2022-03-13gnu: knot: Update to 3.1.6.Tobias Geerinckx-Rice
* gnu/packages/dns.scm (knot): Update to 3.1.6.
2022-03-16gnu: expat: Update to 2.4.7.Leo Famulari
This fixes some regressions in 2.4.5 and 2.4.6: https://www.xml.com/news/2022-02-expat-246/ https://www.xml.com/news/2022-03-expat-247/ * gnu/packages/xml.scm (expat/fixed): Update to 2.4.7.
2022-03-16gnu: OpenSSL 3: Update to 3.0.2 [fixes CVE-2022-0778].Leo Famulari
For more information about this vulnerability: https://www.openssl.org/news/secadv/20220315.txt * gnu/packages/tls.scm (openssl-3.0): Update to 3.0.2.
2022-03-16gnu: OpenSSL: Update to 1.1.1n [fixes CVE-2022-0778].Leo Famulari
For more information about this vulnerability: https://www.openssl.org/news/secadv/20220315.txt * gnu/packages/tls.scm (openssl/fixed): Update to 1.1.1n.
2022-03-13gnu: isc-dhcp: Update bundled BIND to 9.11.37.Tobias Geerinckx-Rice
* gnu/packages/admin.scm (isc-dhcp)[inputs]: Update bind-source-tarball to 9.11.37.
2022-03-13gnu: bind: Update to 9.16.27 [fixes CVE-2022-0396].Tobias Geerinckx-Rice
* gnu/packages/dns.scm (isc-bind): Update to 9.16.27.
2022-03-13gnu: cdrtools: Don't return #t from snippet.Tobias Geerinckx-Rice
* gnu/packages/cdrom.scm (cdrtools)[source]: Don't return #t from snippet.
2022-03-13gnu: cdrtools: Use G-expressions.Tobias Geerinckx-Rice
* gnu/packages/cdrom.scm (cdrtools)[arguments]: Rewrite as G-expressions. Don't return #t from phases.
2022-03-13gnu: cdrtools: Link dynamically.Tobias Geerinckx-Rice
* gnu/packages/cdrom.scm (cdrtools)[arguments]: Add "LINKMODE=dynamic" to the #:configure-flags.
2022-03-13gnu: cdrtools: Prepare for cross-compilation.Tobias Geerinckx-Rice
* gnu/packages/cdrom.scm (cdrtools)[arguments]: Use CC-FOR-TARGET.
2022-03-16gnu: ruby-stackprof: Adjust skipped test on powerpc-linux.Efraim Flashner
* gnu/packages/ruby.scm (ruby-stackprof)[arguments]: On powerpc-linux adjust the 'skip-dubious-test phase.
2022-03-16gnu: i2pd: Update to 2.41.0.Andrew Tropin
* gnu/packages/i2p.scm (i2pd): Update to 2.41.0. [arguments]: Remove trailing slash to match all libi2pd entries. Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>
2022-03-16gnu: cl-mito: Update to 47ba486.jgart
* gnu/packages/lisp-xyz.scm (sbcl-mito): Update to 47ba486. Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>
2022-03-16gnu: opencpn: Update to 5.6.0.Guillaume Le Vaillant
* gnu/packages/geo.scm (opencpn): Update to 5.6.0. [inputs]: Add alsa-utils, eudev, jasper, libjpeg-turbo and libusb.
2022-03-16gnu: Add tessen.Tanguy Le Carrour
* gnu/packages/password-utils.scm (tessen): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2022-03-16gnu: matterbridge: update to 1.24.0Denis 'GNUtoo' Carikli
* gnu/packages/messaging.scm (matterbridge): Update to 1.24.0. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2022-03-16gnu: Add python-mathlibtools.Pradana AUMARS
* gnu/packages/lean.scm (python-mathlibtools): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2022-03-16gnu: dunst: Update to 1.8.1.Jai Vetrivelan
* gnu/packages/dunst.scm (dunst): Update to 1.8.1. * gnu/packages/patches/dunst-1.7.3-fix-crash.patch: Delete file. * gnu/local.mk (dist_patch_DATA): Remove it. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2022-03-16gnu: python-gitlab: update to 3.2.0Denis 'GNUtoo' Carikli
* gnu/packages/python-web.scm (python-gitlab): Update to 3.2.0 Signed-off-by: Denis 'GNUtoo' Carikli <GNUtoo@cyberdimension.org> Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2022-03-16system: Improve 'read-boot-parameters' incompatibility diagnostic.Ludovic Courtès
Previously, when reading an incompatible "parameters" file, 'guix system' would print a warning and then crash with a wrong-type-arg backtrace because code expects 'read-boot-parameters' to always return a <boot-parameters> record. * gnu/system.scm (read-boot-parameters): Upon incompatibility, raise an error instead of returning #f. Also raise a '&fix-hint' condition. * tests/boot-parameters.scm ("read, construction, mandatory fields"): Define 'test-read-boot-parameters' as a macro; expect 'formatted-message?' exceptions rather than #f returns.
2022-03-16gnu: cryfs: Update to 0.11.2.Brendan Tildesley
* gnu/packages/crypto.scm (cryfs): Update to 0.11.2. [arguments]: Fix build with boost 1.77 Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2022-03-16packages: 'modify-inputs' preserves outputs in 'replace' clauses.Ludovic Courtès
Fixes <https://issues.guix.gnu.org/53915>. Reported by Gordon Quad <gordon@niflheim.info>. * guix/packages.scm (replace-input): Preserve the outputs of INPUT by default. * tests/packages.scm ("modify-inputs, replace, extra output"): New test.
2022-03-16tests: Exercise 'modify-inputs' with a 'replace' clause.Ludovic Courtès
* tests/packages.scm ("modify-inputs, replace") ("modify-inputs, replace, change output"): New tests.
2022-03-16gnu : nicotine+: Update to 3.2.1.Fatima Toothpaste
* gnu/packages/nicotine.scm (nicotine+): Update to 3.2.1. [source]: Delete network requried tests in snippet. [arguments]: Remove trailing #t. Replae 'check phase to run proper test. [inputs]: Add bash-minimal, gspell, libappindicator. [native-inputs]: Remove python-pytest. Add xvfb-run. [home-page]: Update URL. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2022-03-16Revert "gnu: %boot3-inputs: Add missing input."Efraim Flashner
This reverts commit ed2ca2dcb558dcda6ea69c64a0a9e9c0b52f892e. This is no longer needed after the gcc STARTFILE_PREFIX_SPEC commit.
2022-03-16Revert "gnu: Add %final-inputs-riscv64."Efraim Flashner
This reverts commit 0444be868903356a37fc8ffd3cdf820ca038f3e6. This is no longer necessary after the gcc STARTFILE_PREFIX_SPEC commit.
2022-03-16gnu: gcc: For riscv64-linux remove STARTFILE_PREFIX_SPEC.Efraim Flashner
* gnu/packages/gcc.scm (gcc-4.7)[arguments]: When building for riscv64-linux and the 'gcc/configure/riscv' directory exists adjust the STARTFILE_PREFIX_SPEC so it doesn't do anything.
2022-03-15gnu: httpie: Update to 3.1.0 [security fixes].kiasoc5
Fixes CVE-2022-24737 and CVE-2022-0430. * gnu/packages/python-web.scm (httpie): Update to 3.1.0. Signed-off-by: Leo Famulari <leo@famulari.name>
2022-03-15gnu: Add r-diffcyt.zimoun
* gnu/packages/bioconductor.scm (r-diffcyt): New variable.
2022-03-15gnu: Add r-ga.zimoun
* gnu/packages/cran.scm (r-ga): New variable.
2022-03-15gnu: Add r-carrier.zimoun
* gnu/packages/cran.scm (r-carrier): New variable.
2022-03-15gnu: Add r-babelwhale.zimoun
* gnu/packages/cran.scm (r-babelwhale): New variable.
2022-03-15gnu: Add r-polychrome.zimoun
* gnu/packages/cran.scm (r-polychrome): New variable.
2022-03-15gnu: Add r-scannotatr.zimoun
* gnu/packages/bioconductor.scm (r-scannotatr): New variable.
2022-03-15gnu: r-sn: Update to 2.0.2.Ricardo Wurmus
* gnu/packages/statistics.scm (r-sn): Update to 2.0.2.
2022-03-15gnu: r-dt: Update to 0.21.Ricardo Wurmus
* gnu/packages/statistics.scm (r-dt): Update to 0.21.
2022-03-15gnu: r-simr: Update to 1.0.6.Ricardo Wurmus
* gnu/packages/statistics.scm (r-simr): Update to 1.0.6. [propagated-inputs]: Add r-lmertest. [synopsis]: Change case and spelling. [description]: Use complete sentences.
2022-03-15gnu: r-rmarkdown: Update to 2.13.Ricardo Wurmus
* gnu/packages/statistics.scm (r-rmarkdown): Update to 2.13. [propagated-inputs]: Add r-bslib.
2022-03-15gnu: r-withr: Update to 2.5.0.Ricardo Wurmus
* gnu/packages/statistics.scm (r-withr): Update to 2.5.0.
2022-03-15gnu: r-openssl: Update to 2.0.0.Ricardo Wurmus
* gnu/packages/statistics.scm (r-openssl): Update to 2.0.0.
2022-03-15gnu: r-commonmark: Update to 1.8.0.Ricardo Wurmus
* gnu/packages/statistics.scm (r-commonmark): Update to 1.8.0.
2022-03-15gnu: r-desc: Update to 1.4.1.Ricardo Wurmus
* gnu/packages/statistics.scm (r-desc): Update to 1.4.1. [propagated-inputs]: Remove r-crayon; add r-cli.
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