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* gnu: perl-xml-simple: Update to 2.25.Tobias Geerinckx-Rice2018-03-19
| | | | * gnu/packages/xml.scm (perl-xml-simple): Update to 2.25.
* gnu: perl-math-random-secure: Fix typo.Tobias Geerinckx-Rice2018-03-19
| | | | | * gnu/packages/crypto.scm (perl-math-random-secure)[description]: Fix the spelling of ‘millennia’.
* gnu: pigx-bsseq: Update to 0.0.7.Ricardo Wurmus2018-03-19
| | | | | * gnu/packages/bioinformatics.scm (pigx-bsseq): Update to 0.0.7. [inputs]: Add coreutils, sed, and grep.
* gnu: bismark: Fix references to gunzip.Ricardo Wurmus2018-03-19
| | | | | | * gnu/packages/bioinformatics.scm (bismark)[arguments]: Keep reference to gunzip executable. [inputs]: Add gzip.
* gnu: pigx-scrnaseq: Update to 0.0.3.Ricardo Wurmus2018-03-19
| | | | | * gnu/packages/bioinformatics.scm (pigx-scrnaseq): Update to 0.0.3. [inputs]: Add coreutils and perl.
* patchelf: Use 'https' for source uri.Efraim Flashner2018-03-19
| | | | * gnu/packages/elf.scm (patchelf)[source]: Use 'https' for source uri.
* gnu: python-paramiko: Update to 2.1.5.Leo Famulari2018-03-19
| | | | | * gnu/packages/python-crypto.scm (python-paramiko, python2-paramiko): Update to 2.1.5.
* gnu: python-pynacl: Update to 1.2.0.Leo Famulari2018-03-19
| | | | | * gnu/packages/python-crypto.scm (python-pynacl): Update to 1.2.0. [native-inputs]: Add python-hypothesis.
* gnu: pigx: Update to 0.0.2.Ricardo Wurmus2018-03-19
| | | | * gnu/packages/bioinformatics.scm (pigx): Update to 0.0.2.
* gnu: r-rcas: Use ghc-pandoc-citeproc-with-pandoc-1.Ricardo Wurmus2018-03-19
| | | | | * gnu/packages/bioinformatics.scm (r-rcas)[inputs]: Replace ghc-pandoc-citeproc with ghc-pandoc-citeproc-with-pandoc-1.
* gnu: bash-completion: Update to 2.8.Tobias Geerinckx-Rice2018-03-19
| | | | | * gnu/packages/bash.scm (bash-completion): Update to 2.8. * gnu/packages/patches/bash-completion-directories.patch: Update context.
* gnu: hdparm: Update to 9.55.Tobias Geerinckx-Rice2018-03-19
| | | | * gnu/packages/linux.scm (hdparm): Update to 9.55.
* gnu: libtirpc: Update to 1.0.3.Tobias Geerinckx-Rice2018-03-19
| | | | | | | * 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.
* gnu: libtirpc: Always return #t from phases.Tobias Geerinckx-Rice2018-03-19
| | | | * gnu/packages/onc-rpc.scm (libtirpc)[arguments]: End phase with #t.
* gnu: perl-file-basedir: Update to 0.08.Tobias Geerinckx-Rice2018-03-19
| | | | * gnu/packages/freedesktop.scm (perl-file-basedir): Update to 0.08.
* gnu: enlightenment: Update to 0.22.2.Tobias Geerinckx-Rice2018-03-19
| | | | * gnu/packages/enlightenment.scm (enlightenment): Update to 0.22.2.
* gnu: python-oslo.utils: Update to 3.36.0.Tobias Geerinckx-Rice2018-03-19
| | | | * gnu/packages/openstack.scm (python-oslo.utils): Update to 3.36.0.
* gnu: python-oslo.i18n: Update to 3.20.0.Tobias Geerinckx-Rice2018-03-19
| | | | * gnu/packages/openstack.scm (python-oslo.i18n): Update to 3.20.0.
* gnu: r-withr: Update to 2.1.2.Tobias Geerinckx-Rice2018-03-19
| | | | * gnu/packages/statistics.scm (r-withr): Update to 2.1.2.
* gnu: tilda: Update to 1.4.1.Efraim Flashner2018-03-19
| | | | | | * gnu/packages/terminals.scm (tilda): Update to 1.4.1. [arguments]: Rename 'autogen phase to 'bootstrap. Clean up 'bootstrap phase.
* gnu: pigx-chipseq: Update to 0.0.8.Ricardo Wurmus2018-03-19
| | | | | | * gnu/packages/bioinformatics.scm (pigx-chipseq): Update to 0.0.8. [inputs]: Add python-magic, python-xlrd, and trim-galore. [arguments]: Disable tests.
* gnu: pigx-scrnaseq: Use pandoc-1.Ricardo Wurmus2018-03-19
| | | | | | * 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.
* gnu: pigx-bsseq: Use pandoc-1.Ricardo Wurmus2018-03-19
| | | | | | * 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.
* gnu: pigx-chipseq: Use pandoc-1.Ricardo Wurmus2018-03-19
| | | | | | * 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.
* gnu: pigx-rnaseq: Use pandoc-1.Ricardo Wurmus2018-03-19
| | | | | | * 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.
* gnu: Add ghc-pandoc-citeproc-with-pandoc-1.Ricardo Wurmus2018-03-19
| | | | * gnu/packages/haskell.scm (ghc-pandoc-citeproc-with-pandoc-1): New variable.
* git-download: Fix recursive checkouts.Eric Bavier2018-03-18
| | | | | * guix/git-download.scm (git-fetch)<build>: Fix match on INPUTS, which may contain package outputs.
* gnu: Add r-abbyyr.Vijayalakshmi Vedantham2018-03-19
| | | | | | * gnu/packages/cran.scm (r-abbyyr): New variable. Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
* glob: Add an extra glob pattern compilation stage.Ludovic Courtès2018-03-18
| | | | | | | | | | | | | * 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'.
* glob: Support square brackets in patterns.Ludovic Courtès2018-03-18
| | | | | | | | | | | * 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.
* linux-modules: 'load-linux-module*' honors BLACK-LIST in recursive calls.Ludovic Courtès2018-03-18
| | | | | * gnu/build/linux-modules.scm (load-linux-module*): Pass BLACK-LIST in recursive call.
* linux-modules: Add 'current-kernel-directory'.Ludovic Courtès2018-03-18
| | | | | * gnu/build/linux-modules.scm (current-kernel-directory): New procedure. (current-alias-file): Use it.
* vm: Display a backtrace upon error by default.Ludovic Courtès2018-03-18
| | | | | * gnu/system/vm.scm (expression->derivation-in-linux-vm): Pass #:on-error to 'base-initrd'.
* tests: elpa: Don't actually download files.Ludovic Courtès2018-03-18
| | | | * tests/elpa.scm (eval-test-with-elpa): Mock 'url-fetch'.
* import: elpa: Return 'license:gpl3+ for ELPA only.Ludovic Courtès2018-03-18
| | | | | | | | | Fixes <https://bugs.gnu.org/30836>. Reported by Konrad Hinsen <konrad.hinsen@fastmail.net>. * guix/import/elpa.scm (elpa-package->sexp): Add LICENSE parameter and honor it. (elpa->guix-package): Pass 'license:gpl3+ only when REPO is 'gnu.
* import: elpa: Adjust test for HTTPS URLs.Ludovic Courtès2018-03-18
| | | | | | This is a followup to 44dd3d579db3aa467e41d0b431029e46cae8e12d. * tests/elpa.scm (eval-test-with-elpa): Use https.
* gnu: youtube-dl: Update to 2018.03.14.Sohom Bhattacharjee2018-03-18
| | | | | | * gnu/packages/video.scm (youtube-dl): Update to 2018.03.14. Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
* gnu: shotwell: Update to 0.28.0.Christopher Baines2018-03-18
| | | | * gnu/packages/gnome.scm (shotwell): Update to 0.28.0.
* gnu: Add ruby-ruby-engine.Ben Woodcroft2018-03-18
| | | | * gnu/packages/ruby.scm (ruby-ruby-engine): New variable.
* gnu: Add ruby-rake.Ben Woodcroft2018-03-18
| | | | * gnu/packages/ruby.scm (ruby-rake): New variable.
* gnu: Add ruby-erubis.Ben Woodcroft2018-03-18
| | | | * gnu/packages/ruby.scm (ruby-erubis): New variable.
* gnu: Add ruby-sporkmonger-rack-mount.Ben Woodcroft2018-03-18
| | | | * gnu/packages/ruby.scm (ruby-sporkmonger-rack-mount): New variable.
* gnu: Add ruby-creole.Ben Woodcroft2018-03-18
| | | | * gnu/packages/ruby.scm (ruby-creole): New variable.
* gnu: Add ruby-contest.Ben Woodcroft2018-03-18
| | | | * gnu/packages/ruby.scm (ruby-contest): New variable.
* gnu: Add ruby-rack-protection.Ben Woodcroft2018-03-18
| | | | * gnu/packages/ruby.scm (ruby-rack-protection): New variable.
* gnu: Add ruby-rack-test.Ben Woodcroft2018-03-18
| | | | * gnu/packages/ruby.scm (ruby-rack-test): New variable.
* gnu: Add ruby-asciidoctor.Ben Woodcroft2018-03-18
| | | | * gnu/packages/ruby.scm (ruby-asciidoctor): New variable.
* gnu: Add ruby-asciimath.Ben Woodcroft2018-03-18
| | | | * gnu/packages/maths.scm (ruby-asciimath): New variable.
* gnu: icecat: Fix CVE-2018-{5146,5147}, etc.Mark H Weaver2018-03-17
| | | | | | | Includes fixes for CVE-2018-5146 and CVE-2018-5147. * gnu/packages/gnuzilla.scm (icecat)[source]: Add selected fixes from the upstream mozilla-esr52 repository.
* gnu: Add terraform-docs.Christopher Baines2018-03-17
| | | | | * gnu/packages/terraform.scm: New file. * gnu/local.mk (GNU_SYSTEM_MODULES): Add it.
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