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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.
2018-03-19gnu: 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.
2018-03-19gnu: 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'.
2018-03-18linux-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'.
2018-03-18gnu: youtube-dl: Update to 2018.03.14.Sohom Bhattacharjee
* gnu/packages/video.scm (youtube-dl): Update to 2018.03.14. Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2018-03-18gnu: shotwell: Update to 0.28.0.Christopher Baines
* gnu/packages/gnome.scm (shotwell): Update to 0.28.0.
2018-03-18gnu: Add ruby-ruby-engine.Ben Woodcroft
* gnu/packages/ruby.scm (ruby-ruby-engine): New variable.
2018-03-18gnu: Add ruby-rake.Ben Woodcroft
* gnu/packages/ruby.scm (ruby-rake): New variable.
2018-03-18gnu: Add ruby-erubis.Ben Woodcroft
* gnu/packages/ruby.scm (ruby-erubis): New variable.
2018-03-18gnu: Add ruby-sporkmonger-rack-mount.Ben Woodcroft
* gnu/packages/ruby.scm (ruby-sporkmonger-rack-mount): New variable.
2018-03-18gnu: Add ruby-creole.Ben Woodcroft
* gnu/packages/ruby.scm (ruby-creole): New variable.
2018-03-18gnu: Add ruby-contest.Ben Woodcroft
* gnu/packages/ruby.scm (ruby-contest): New variable.
2018-03-18gnu: Add ruby-rack-protection.Ben Woodcroft
* gnu/packages/ruby.scm (ruby-rack-protection): New variable.
2018-03-18gnu: Add ruby-rack-test.Ben Woodcroft
* gnu/packages/ruby.scm (ruby-rack-test): New variable.
2018-03-18gnu: Add ruby-asciidoctor.Ben Woodcroft
* gnu/packages/ruby.scm (ruby-asciidoctor): New variable.
2018-03-18gnu: Add ruby-asciimath.Ben Woodcroft
* gnu/packages/maths.scm (ruby-asciimath): New variable.
2018-03-17gnu: icecat: Fix CVE-2018-{5146,5147}, etc.Mark H Weaver
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.
2018-03-17gnu: Add terraform-docs.Christopher Baines
* gnu/packages/terraform.scm: New file. * gnu/local.mk (GNU_SYSTEM_MODULES): Add it.
2018-03-17gnu: Add go-github-com-hashicorp-hcl.Christopher Baines
* gnu/packages/golang.scm (go-github-com-hashicorp-hcl): New variable.
2018-03-17gnu: Add go-github-com-tj-docopt.Christopher Baines
* gnu/packages/golang.scm (go-github-com-tj-docopt): New variable.
2018-03-18gnu: guile-git: Update to 2bb9fbb.Ludovic Courtès
* gnu/packages/guile.scm (guile-git): Update to 2bb9fbb.
2018-03-18gnu: nss-mdns: Adjust Avahi socket file name.Ludovic Courtès
Fixes <https://bugs.gnu.org/30613>. Regression introduced in 550f4509acf2c0f67882260414b0bb2843e07465. Reported by George myglc2 Clemmer <myglc2@gmail.com>. * gnu/packages/avahi.scm (nss-mdns)[arguments]: Remove #:configure-flags. Add #:phases.
2018-03-18gnu: datamash: Update to 1.3.Ludovic Courtès
* gnu/packages/datamash.scm (datamash): Update to 1.3.
2018-03-18gnu: fvwm: Add '.desktop' file.ng0
* gnu/packages/fvwm.scm (fvwm)[arguments]: Add new phase to create '.desktop' file. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2018-03-18services: openssh: Add 'accepted-environment' field.Martin Castillo
* gnu/services/ssh.scm (<openssh-configuration>)[accepted-environment]: New field. (openssh-config-file): Honor 'acccepted-environment'. * doc/guix.texi (Networking Services): Document it. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2018-03-18gnu: java-simple-xml: Fix java8 test failures.Gábor Boskovits
* gnu/packages/patches/javas-simple-xml-fix-tests.patch: New file. * gnu/local.mk (dist_patch_DATA): Register it. * gnu/packages/java.scm (java-simple-xml)[source](patches): Add it. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
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