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2018-03-20Revert "Revert "gnu: patchelf: Update argument phase.""Marius Bakke
This change only affects armhf, which doesn't use PatchELF. My bad! This reverts commit b1d096f869ed53b84486855d73c7e9070fdf3ae2.
2018-03-20Revert "build-system/meson: Use 'target-arm32?' for armhf-linux case."Marius Bakke
This requires adding (guix utils) to the build inputs, and causes too many rebuilds for now. This reverts commit 24a2e9172a2d8970d57865c6130f2184385183a3.
2018-03-20Revert "gnu: patchelf: Update argument phase."Marius Bakke
It causes too many rebuilds this late in the 'staging' cycle. This reverts commit c1d1cd817c7ab8d99e962e286c207943765a8e8f.
2018-03-19gnu: uwsgi: Update to 2.0.17 [fixes CVE-2018-7490].Leo Famulari
* gnu/packages/web.scm (uwsgi): Update to 2.0.17. [source]: Use HTTPS URL.
2018-03-19gnu: mcron: Update to 1.1 and deprecate "mcron2".Ludovic Courtès
* gnu/packages/guile.scm (mcron): Update to 1.1. [native-inputs]: Add TZDATA-FOR-TESTS. [arguments]: New field. (mcron2): Define using 'deprecated-package'. * gnu/services/mcron.scm: Replace 'mcron2' with 'mcron'. * doc/guix.texi (Scheduled Job Execution): Likewise. * gnu/tests/base.scm (%mcron-os): Remove comment about mcron2.
2018-03-19gnu: linux-libre: Update to 4.15.11.Mark H Weaver
* gnu/packages/linux.scm (%linux-libre-version): Update to 4.15.11. (%linux-libre-hash): Update hash.
2018-03-19gnu: linux-libre@4.14: Update to 4.14.28.Mark H Weaver
* gnu/packages/linux.scm (%linux-libre-4.14-version): Update to 4.14.28. (%linux-libre-4.14-hash): Update hash.
2018-03-19gnu: linux-libre@4.9: Update to 4.9.88.Mark H Weaver
* gnu/packages/linux.scm (linux-libre-4.9): Update to 4.9.88.
2018-03-19gnu: linux-libre@4.4: Update to 4.4.122.Mark H Weaver
* gnu/packages/linux.scm (linux-libre-4.4): Update to 4.4.122.
2018-03-19gnu: weechat: Update to 2.1.Tobias Geerinckx-Rice
* gnu/packages/irc.scm (weechat): Update to 2.1.
2018-03-19gnu: perl-xml-compile-soap: Update to 3.24.Tobias Geerinckx-Rice
* gnu/packages/xml.scm (perl-xml-compile-soap): Update to 3.24.
2018-03-19gnu: perl-xml-simple: Update to 2.25.Tobias Geerinckx-Rice
* gnu/packages/xml.scm (perl-xml-simple): Update to 2.25.
2018-03-19gnu: perl-math-random-secure: Fix typo.Tobias Geerinckx-Rice
* gnu/packages/crypto.scm (perl-math-random-secure)[description]: Fix the spelling of ‘millennia’.
2018-03-19build-system/meson: Use 'target-arm32?' for armhf-linux case.Efraim Flashner
* guix/build-system/meson.scm (lower, meson-build): Replace armhf-linux detection with 'target-arm32?' macro.
2018-03-19gnu: pigx-bsseq: Update to 0.0.7.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (pigx-bsseq): Update to 0.0.7. [inputs]: Add coreutils, sed, and grep.
2018-03-19gnu: bismark: Fix references to gunzip.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (bismark)[arguments]: Keep reference to gunzip executable. [inputs]: Add gzip.
2018-03-19gnu: pigx-scrnaseq: Update to 0.0.3.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (pigx-scrnaseq): Update to 0.0.3. [inputs]: Add coreutils and perl.
2018-03-19patchelf: Use 'https' for source uri.Efraim Flashner
* gnu/packages/elf.scm (patchelf)[source]: Use 'https' for source uri.
2018-03-19patchelf: Use 'https' for source uri.Efraim Flashner
* gnu/packages/elf.scm (patchelf)[source]: Use 'https' for source uri.
2018-03-19gnu: patchelf: Update argument phase.Efraim Flashner
* gnu/packages/elf.scm (patchelf)[arguments]: Use 'modify-phases' syntax. Replace 'system*' with 'invoke'.
2018-03-19gnu: patchelf: Use 'target-arm32?' for armhf-linux case.Efraim Flashner
* gnu/packages/elf.scm (patchelf)[inputs]: Replace armhf-linux detection logic with 'target-arm32?' macro. [arguments]: Same.
2018-03-19gnu: python-paramiko: Update to 2.1.5.Leo Famulari
* gnu/packages/python-crypto.scm (python-paramiko, python2-paramiko): Update to 2.1.5.
2018-03-19gnu: python-pynacl: Update to 1.2.0.Leo Famulari
* gnu/packages/python-crypto.scm (python-pynacl): Update to 1.2.0. [native-inputs]: Add python-hypothesis.
2018-03-19gnu: pigx: Update to 0.0.2.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (pigx): Update to 0.0.2.
2018-03-19gnu: r-rcas: Use ghc-pandoc-citeproc-with-pandoc-1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-rcas)[inputs]: Replace ghc-pandoc-citeproc with ghc-pandoc-citeproc-with-pandoc-1.
2018-03-19gnu: bash-completion: Update to 2.8.Tobias Geerinckx-Rice
* gnu/packages/bash.scm (bash-completion): Update to 2.8. * gnu/packages/patches/bash-completion-directories.patch: Update context.
2018-03-19gnu: hdparm: Update to 9.55.Tobias Geerinckx-Rice
* gnu/packages/linux.scm (hdparm): Update to 9.55.
2018-03-19gnu: libtirpc: Update to 1.0.3.Tobias Geerinckx-Rice
* gnu/packages/onc-rpc.scm (libtirpc): Update to 1.0.3. [source]: Remove patch. * gnu/packages/patches/libtirpc-missing-headers.patch: Delete file. * gnu/local.mk (dist_patch_DATA): Remove it.
2018-03-19gnu: libtirpc: Always return #t from phases.Tobias Geerinckx-Rice
* gnu/packages/onc-rpc.scm (libtirpc)[arguments]: End phase with #t.
2018-03-19gnu: perl-file-basedir: Update to 0.08.Tobias Geerinckx-Rice
* gnu/packages/freedesktop.scm (perl-file-basedir): Update to 0.08.
2018-03-19gnu: enlightenment: Update to 0.22.2.Tobias Geerinckx-Rice
* gnu/packages/enlightenment.scm (enlightenment): Update to 0.22.2.
2018-03-19gnu: python-oslo.utils: Update to 3.36.0.Tobias Geerinckx-Rice
* gnu/packages/openstack.scm (python-oslo.utils): Update to 3.36.0.
2018-03-19gnu: python-oslo.i18n: Update to 3.20.0.Tobias Geerinckx-Rice
* gnu/packages/openstack.scm (python-oslo.i18n): Update to 3.20.0.
2018-03-19gnu: r-withr: Update to 2.1.2.Tobias Geerinckx-Rice
* gnu/packages/statistics.scm (r-withr): Update to 2.1.2.
2018-03-19gnu: tilda: Update to 1.4.1.Efraim Flashner
* gnu/packages/terminals.scm (tilda): Update to 1.4.1. [arguments]: Rename 'autogen phase to 'bootstrap. Clean up 'bootstrap phase.
2018-03-19gnu: pigx-chipseq: Update to 0.0.8.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (pigx-chipseq): Update to 0.0.8. [inputs]: Add python-magic, python-xlrd, and trim-galore. [arguments]: Disable tests.
2018-03-19gnu: pigx-scrnaseq: Use pandoc-1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (pigx-scrnaseq)[inputs]: Replace ghc-pandoc with ghc-pandoc-1, and ghc-pandoc-citeproc with ghc-pandoc-citeproc-with-pandoc-1.
2018-03-19gnu: pigx-bsseq: Use pandoc-1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (pigx-bsseq)[inputs]: Replace ghc-pandoc with ghc-pandoc-1, and ghc-pandoc-citeproc with ghc-pandoc-citeproc-with-pandoc-1.
2018-03-19gnu: pigx-chipseq: Use pandoc-1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (pigx-chipseq)[inputs]: Replace ghc-pandoc with ghc-pandoc-1, and ghc-pandoc-citeproc with ghc-pandoc-citeproc-with-pandoc-1.
2018-03-19gnu: pigx-rnaseq: Use pandoc-1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (pigx-rnaseq)[inputs]: Replace ghc-pandoc with ghc-pandoc-1, and ghc-pandoc-citeproc with ghc-pandoc-citeproc-with-pandoc-1.
2018-03-19gnu: Add ghc-pandoc-citeproc-with-pandoc-1.Ricardo Wurmus
* gnu/packages/haskell.scm (ghc-pandoc-citeproc-with-pandoc-1): New variable.
2018-03-19Merge branch 'master' into stagingMarius Bakke
2018-03-18git-download: Fix recursive checkouts.Eric Bavier
* guix/git-download.scm (git-fetch)<build>: Fix match on INPUTS, which may contain package outputs.
2018-03-19gnu: Add r-abbyyr.Vijayalakshmi Vedantham
* gnu/packages/cran.scm (r-abbyyr): New variable. Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2018-03-18glob: Add an extra glob pattern compilation stage.Ludovic Courtès
* guix/glob.scm (compile-glob-pattern): Rename to... (string->sglob): ... this. (compile-sglob, string->compiled-sglob): New procedures. (glob-match?): Replace '?, 'range, and 'set with a single clause. * tests/glob.scm (test-compile-glob-pattern): Rename to... (test-string->sglob): ... this. Adjust accordingly. (test-glob-match): Use 'string->compiled-sglob' instead of 'compile-glob-pattern'. * gnu/build/linux-modules.scm (read-module-aliases): Use 'string->compiled-sglob' instead of 'compile-glob-pattern'.
2018-03-18glob: Support square brackets in patterns.Ludovic Courtès
* guix/glob.scm (wildcard-indices): Remove. (parse-bracket): New procedure. (compile-glob-pattern): Rewrite. Support square brackets for sets and ranges. (glob-match?): Support sets and ranges. * tests/glob.scm (test-compile-glob-pattern) (test-glob-match): New macros. Use them to rewrite the existing tests, and add new tests.
2018-03-18linux-modules: 'load-linux-module*' honors BLACK-LIST in recursive calls.Ludovic Courtès
* gnu/build/linux-modules.scm (load-linux-module*): Pass BLACK-LIST in recursive call.
2018-03-18linux-modules: Add 'current-kernel-directory'.Ludovic Courtès
* gnu/build/linux-modules.scm (current-kernel-directory): New procedure. (current-alias-file): Use it.
2018-03-18vm: Display a backtrace upon error by default.Ludovic Courtès
* gnu/system/vm.scm (expression->derivation-in-linux-vm): Pass #:on-error to 'base-initrd'.
2018-03-18tests: elpa: Don't actually download files.Ludovic Courtès
* tests/elpa.scm (eval-test-with-elpa): Mock 'url-fetch'.
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