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2018-03-01gnu: r-wgcna: Update to 1.63.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-wgcna): Update to 1.63.
2018-03-01gnu: r-topgo: Update to 2.30.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-topgo): Update to 2.30.1.
2018-03-01gnu: r-genomicranges: Update to 1.30.3.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.30.3.
2018-03-01gnu: r-limma: Update to 3.34.9.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-limma): Update to 3.34.9.
2018-03-01gnu: r-edger: Update to 3.20.9.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-edger): Update to 3.20.9.
2018-03-01gnu: r-shortread: Update to 1.36.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-shortread): Update to 1.36.1.
2018-03-01gnu: r-dexseq: Update to 1.24.3.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-dexseq): Update to 1.24.3.
2018-03-01gnu: efl: Use separate "include" output.Efraim Flashner
* gnu/packages/enlightenment.scm (efl)[outputs]: Add 'include' output.
2018-03-01gnu: efl: Update to 1.20.7.Efraim Flashner
* gnu/packages/enlightenment.scm (efl): Update to 1.20.7.
2018-03-01gnu: Add patchmatrix.Ricardo Wurmus
* gnu/packages/music.scm (patchmatrix): New variable.
2018-03-01gnu: ghc-uuid: Fix build.Ricardo Wurmus
* gnu/packages/haskell.scm (ghc-uuid)[arguments]: Allow building with a newer version of QuickCheck.
2018-03-01gnu: golly: Fix source url.Christopher Lemmer Webber
* gnu/packages/games.scm (golly): Fix source url.
2018-03-01gnu: imagemagick: Update to 6.9.9-36.Marius Bakke
* gnu/packages/imagemagick.scm (imagemagick): Update to 6.9.9-36.
2018-03-01gnu: libe-book: Update to 0.1.3.Marius Bakke
* gnu/packages/libreoffice.scm (libe-book): Update to 0.1.3. [propagated-inputs]: Add LIBLANGTAG.
2018-03-01gnu: libabw: Update to 0.1.2.Marius Bakke
* gnu/packages/libreoffice.scm (libabw): Update to 0.1.2.
2018-03-01gnu: libpagemaker: Update to 0.0.4.Marius Bakke
* gnu/packages/libreoffice.scm (libpagemaker): Update to 0.0.4. [source](uri): Use HTTPS.
2018-03-01gnu: libmspub: Update to 0.1.4.Marius Bakke
* gnu/packages/libreoffice.scm (libmspub): Update to 0.1.4. [source](uri): Use HTTPS.
2018-03-01gnu: xorgproto: Update to 2018.4.Marius Bakke
* gnu/packages/xorg.scm (xorgproto): Update to 2018.4.
2018-03-01gnu: cuirass: Update to aa4c778.Ludovic Courtès
* gnu/packages/ci.scm (cuirass): Update to aa4c778.
2018-03-01gnu: nautilus: Use meson-build-system, update to 3.26.2.Rene
* gnu/packages/gnome.scm (nautilus): Update to 3.26.2. [build-system]: Use meson-build-system. [native-inputs]: Add desktop-file-utils and gtk+:bin. [inputs]: Add libselinux. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2018-02-28gnu: Fix Borg crashes with Python msgpack > 0.5Leo Famulari
The Python msgpack library changed its name, but borg (and possibly other packages) still uses the old name. Fixes <https://bugs.gnu.org/30662>. * gnu/packages/python.scm (python-msgpack-transitional): New variable. * gnu/packages/backup.scm (borg)[inputs]: Use it.
2018-02-28gnu: Remove duplicate definition of emacs-esxml.Ricardo Wurmus
* gnu/packages/emacs.scm (emacs-esxml): Remove.
2018-02-28gnu: Remove emacs-nov.Ricardo Wurmus
The package already exists with the name "emacs-nov-el". * gnu/packages/emacs.scm (emacs-nov): Remove.
2018-02-28gnu: java-bouncycastle-bcpkix: Use invoke.Ricardo Wurmus
* gnu/packages/java.scm (java-bouncycastle-bcpkix)[arguments]: Use invoke.
2018-02-28gnu: java-bouncycastle-bcprov: Use invoke.Ricardo Wurmus
* gnu/packages/java.scm (java-bouncycastle-bcprov)[arguments]: Use invoke.
2018-02-28gnu: java-lz4: Use invoke.Ricardo Wurmus
* gnu/packages/java.scm (java-lz4)[arguments]: Use invoke.
2018-02-28gnu: antlr3-3.1: Remove version from package name.Ricardo Wurmus
* gnu/packages/java.scm (antlr3-3.1)[name]: Remove. [arguments]: Adjust accordingly.
2018-02-28gnu: antlr3-3.1: Use invoke.Ricardo Wurmus
* gnu/packages/java.scm (antlr3-3.1)[arguments]: Use invoke.
2018-02-28gnu: java-jansi-native: Simplify.Ricardo Wurmus
* gnu/packages/java.scm (java-jansi-native)[arguments]: Use "invoke"; remove useless "mkdir-p".
2018-02-28gnu: java-jansi-native: Fix description.Ricardo Wurmus
* gnu/packages/java.scm (java-jansi-native)[description]: Replace placeholder text with an actual description.
2018-02-28gnu: java-hawtjni: Simplify build phases.Ricardo Wurmus
* gnu/packages/java.scm (java-hawtjni)[arguments]: Use "invoke" instead of "system*"; use "install-file" instead of "mkdir-p" and "copy-file".
2018-02-28gnu: java-commons-jexl-2: Use invoke.Ricardo Wurmus
* gnu/packages/java.scm (java-commons-jexl-2)[arguments]: Use invoke.
2018-02-28gnu: java-jnacl: Do not prefix jar with "java-".Ricardo Wurmus
* gnu/packages/java.scm (java-jnacl)[arguments]: Rename jar to "jnacl.jar".
2018-02-28gnu: java-jnacl: Update to 0.1.0-2.094e819.Ricardo Wurmus
* gnu/packages/java.scm (java-jnacl): Update to 0.1.0-2.094e819.
2018-02-28gnu: java-jnacl: Simplify build phase.Ricardo Wurmus
* gnu/packages/java.scm (java-jnacl)[arguments]: Simplify "fix-tests" phase.
2018-02-28gnu: java-jnacl: Correct license.Ricardo Wurmus
* gnu/packages/java.scm (java-jnacl)[license]: Change to BSD-2.
2018-02-28gnu: java-jnacl: Use invoke.Ricardo Wurmus
* gnu/packages/java.scm (java-jnacl)[arguments]: Use "invoke".
2018-02-28gnu: Add java-ecj-3.5.Ricardo Wurmus
* gnu/packages/java.scm (java-ecj-3.5): New variable.
2018-02-28gnu: Add java-ecj-3.Ricardo Wurmus
* gnu/packages/java.scm (java-ecj-3): New variable.
2018-02-28gnu: dovecot: Update to 2.3.0.1 [fixes CVE-2017-14461].Tobias Geerinckx-Rice
* gnu/packages/mail.scm (dovecot): Update to 2.3.0.1. [source]: Remove upstreamed patch. * gnu/packages/patches/dovecot-CVE-2017-15132.patch: Delete file. * gnu/local.mk (dist_patch_DATA): Remove it.
2018-02-28gnu: html-xml-utils: Update to 7.6.Tobias Geerinckx-Rice
* gnu/packages/xml.scm (html-xml-utils): Update to 7.6.
2018-02-28gnu: libftdi: Update to 1.4.Tobias Geerinckx-Rice
* gnu/packages/libftdi.scm (libftdi): Update to 1.4.
2018-02-28gnu: git-remote-gcrypt: Update to 1.0.2.Tobias Geerinckx-Rice
* gnu/packages/version-control.scm (git-remote-gcrypt): Update to 1.0.2.
2018-02-28gnu: dropbear: Update to 2018.76.Tobias Geerinckx-Rice
* gnu/packages/ssh.scm (dropbear): Update to 2018.76.
2018-02-28gnu: Add sala.Konrad Hinsen
* gnu/packages/password-utils.scm (sala): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2018-02-28gnu: guile-static-stripped: Add 'finit_module' wrapper.Ludovic Courtès
* gnu/packages/patches/guile-linux-syscalls.patch: Add 'load-linux-module/fd' procedure.
2018-02-28gnu: guile-static-stripped: Remove dependency on bash-minimal.Ludovic Courtès
Previously guile-static-stripped, which is embedded in the initrd, would depend on 'bash-minimal' and 'glibc'; the closure size was 77 MiB. Now the closure size is down to 45.7 MiB. Reported by Danny Milosavljevic <dannym@scratchpost.org> in <https://lists.gnu.org/archive/html/guix-devel/2018-02/msg00505.html>. * gnu/packages/make-bootstrap.scm (%guile-static): Remove the 'pre-configure' phase. (%guile-static-stripped)[arguments]: Add #:allowed-references.
2018-02-28gnu: ccl: Patch absolute file-name.Efraim Flashner
* gnu/packages/lisp.scm (ccl)[arguments]: In 'pre-build add substitution for /bin/pwd.
2018-02-28gnu: keepassxc: Enable various plugins.Efraim Flashner
* gnu/packages/password-utils.scm (keepassxc)[arguments]: Add configure-flags to enable favicons, browser integration and ssh-agent. [inputs]: Add curl, libsodium.
2018-02-28gnu: keepassxc: Update to 2.3.0.Efraim Flashner
* gnu/packages/password-utils.scm (keepassxc): Update to 2.3.0.
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