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2018-03-30gnu: ao: Update to 0-2.9d857d1.Ricardo Wurmus
* gnu/packages/engineering.scm (ao): Rename... (libfive): ...to this new variable; update to 0-2.9d857d1. [inputs]: Remove glfw, libepoxy, glm, guile-2.0; add qtbase, guile-2.2. [home-page]: Use new libfive home page. [description]: Adjust. (ao): Redefine using 'deprecated-package'.
2018-03-30gnu: emacs-org: Change source and naming scheme.Nicolas Goaziou
* gnu/packages/emacs.scm (emacs-org): Switch back to ELPA. Adopt its naming scheme.
2018-03-30gnu: emacs-org-contrib: Fix build.Nicolas Goaziou
* gnu/packages/emacs.scm (emacs-org-contrib): Update SHA256. [version]: Add keyword. [arguments]: Use new keyword.
2018-03-30gnu: Add delly.Roel Janssen
* gnu/packages/bioinformatics.scm (delly): New variable. * gnu/packages/patches/delly-use-system-libraries.patch: New file. * gnu/local.mk: Include delly-use-system-libraries.patch. Signed-off-by: Leo Famulari <leo@famulari.name>
2018-03-30gnu: Add r-regioner.Roel Janssen
* gnu/packages/bioconductor.scm (r-regioner): New variable. Signed-off-by: Leo Famulari <leo@famulari.name>
2018-03-30gnu: rust: Update rust to 1.24.1.Nikolai Merinov
* gnu/packages/rust.scm (rust-bootstrap): Freeze bootstrap version to 1.22.1. Reorganize bootstrap binaries to match new "rust" package structure with two ouputs "out" with Rust compiler and "cargo" with Cargo package manager. Replace all "system*" by "invoke". (rust-1.23): Rename "rustc" to "rust". Update sha256 for tarball. Add cargo related dependencies. Install "cargo" as separate "rust" output. Remove substitutes for parts that were fixed in "rustc" source code. Install documentation to separate "doc" output. Update configuration according to changes in "rustc" source code. Replace all "system*" by "invoke". (rust): Create package for 1.24.1 rust release based on rust-1.23 release. * guix/build-system/cargo.scm (default-rust): Replace "default-cargo" and "default-rustc" functions with "default-rust" function. (cargo-build-system): Take only one package as "rust" source. Use "rustc" of default output of "rust" package, use "cargo" as "cargo" output of "rust" package.
2018-03-30gnu: ruby-2.2: Update to 2.2.10.Ben Woodcroft
* gnu/packages/ruby.scm (ruby-2.2): Update to 2.2.10.
2018-03-30gnu: ruby-2.3: Update to 2.3.7.Ben Woodcroft
* gnu/packages/ruby.scm (ruby-2.3): Update to 2.3.7.
2018-03-30gnu: mash: Update to 2.0.Ben Woodcroft
* gnu/packages/bioinformatics.scm (mash): Update to 2.0.
2018-03-30gnu: mafft: Update to 7.394.Ben Woodcroft
* gnu/packages/bioinformatics.scm (mafft): Update to 7.394.
2018-03-30gnu: diamond: Update to 0.9.19.Ben Woodcroft
* gnu/packages/bioinformatics.scm (diamond): Update to 0.9.19.
2018-03-29gnu: pybitmessage: Update to 0.6.3.2 [security fixes].Ricardo Wurmus
* gnu/packages/messaging.scm (pybitmessage): Update to 0.6.3.2. [source]: Fetch from git.
2018-03-29gnu: hydrogen: Update to 1.0.0-beta1.Ricardo Wurmus
* gnu/packages/music.scm (hydrogen): Update to 1.0.0-beta1. [source]: Fetch from git. [arguments]: Add phase to fix installation directory for pixmaps. [inputs]: Remove qt-4; add qtbase and qtxmlpatterns.
2018-03-29gnu: mod-host: Update to 0.10.6-3.1726ad06b.Ricardo Wurmus
* gnu/packages/music.scm (mod-host): Update to 0.10.6-3.1726ad06b.
2018-03-29gnu: drumkv1: Update to 0.9.0.Ricardo Wurmus
* gnu/packages/music.scm (drumkv1): Update to 0.9.0.
2018-03-29gnu: samplv1: Update to 0.9.0.Ricardo Wurmus
* gnu/packages/music.scm (samplv1): Update to 0.9.0.
2018-03-29gnu: padthv1: Update to 0.9.0.Ricardo Wurmus
* gnu/packages/music.scm (padthv1): Update to 0.9.0.
2018-03-29gnu: synthv1: Update to 0.9.0.Ricardo Wurmus
* gnu/packages/music.scm (synthv1): Update to 0.9.0.
2018-03-29gnu: qtractor: Update to 0.9.0.Ricardo Wurmus
* gnu/packages/music.scm (qtractor): Update to 0.9.0.
2018-03-29gnu: awesome: Remove obsolete snippet.Marius Bakke
* gnu/packages/wm.scm (awesome)[source](snippet): Remove.
2018-03-29gnu: xcb-util-xrm: Update to 1.3.Marius Bakke
* gnu/packages/xdisorg.scm (xcb-util-xrm): Update to 1.3.
2018-03-29gnu: mbedtls-apache: Update to 2.7.2.Marius Bakke
* gnu/packages/tls.scm (mbedtls-apache): Update to 2.7.2. [source](snippet): Remove.
2018-03-29gnu: Add botan.Leo Famulari
* gnu/packages/crypto.scm (botan): New variable.
2018-03-29gnu: Add fpm2.Tonton
* gnu/packages/password-utils.scm (fpm2): New variable. Signed-off-by: Tonton <tonton@riseup.net> Signed-off-by: Marius Bakke <mbakke@fastmail.com>
2018-03-29gnu: Add screen-message.Tonton
* gnu/packages/xdisorg.scm (screen-message): New variable. Signed-off-by: Tonton <tonton@riseup.net> Signed-off-by: Marius Bakke <mbakke@fastmail.com>
2018-03-29gnu: r-lme4: Update to 1.1-16.Tobias Geerinckx-Rice
* gnu/packages/statistics.scm (r-lme4): Update to 1.1-16.
2018-03-29gnu: r-curl: Update to 3.2.Tobias Geerinckx-Rice
* gnu/packages/web.scm (r-curl): Update to 3.2.
2018-03-29gnu: bspwm: Update to 0.9.4.Tobias Geerinckx-Rice
* gnu/packages/wm.scm (bspwm): Update to 0.9.4.
2018-03-29gnu: rss-bridge: Update to 2018-03-11.Tobias Geerinckx-Rice
* gnu/packages/web.scm (rss-bridge): Update to 2018-03-11.
2018-03-29gnu: r-mutationalpatterns: Update to 1.4.3.Roel Janssen
* gnu/packages/bioinformatics.scm (r-mutationalpatterns): Update to 1.4.3; [propagated-inputs]: Remove r-gridextra.
2018-03-29gnu: kaiju: Update to 1.6.2.Roel Janssen
* gnu/packages/bioinformatics.scm (kaiju): Update to 1.6.2; [inputs]: Add zlib.
2018-03-29gnu: Add duperemove.Vasile Dumitrascu
* gnu/packages/disk.scm (duperemove): New variable. Co-authored-by: Ludovic Courtès <ludovic.courtes@inria.fr>
2018-03-29gnu: Add python-debug.Ludovic Courtès
Suggested by Pjotr Prins <pjotr.public12@thebird.nl>. * gnu/packages/python.scm (python-debug): New variable.
2018-03-29gnu: nano: Update to 2.9.5.Efraim Flashner
* gnu/packages/nano.scm (nano): Update to 2.9.5.
2018-03-29gnu: Add r-idr.Roel Janssen
* gnu/packages/cran.scm (r-idr): New variable.
2018-03-29gnu: Add r-amap.Roel Janssen
* gnu/packages/cran.scm (r-amap): New variable.
2018-03-29gnu: Add r-venndiagram.Roel Janssen
* gnu/packages/cran.scm (r-venndiagram): New variable.
2018-03-29gnu: Add r-pastecs.Roel Janssen
* gnu/packages/cran.scm (r-pastecs): New variable.
2018-03-29gnu: libusb4java: Adjust for building with libusb 1.0.22.Ricardo Wurmus
* gnu/packages/libusb.scm (libusb4java)[arguments]: Add phase to remove "-Werror" flag.
2018-03-29gnu: libusb-for-axoloti: Update patch.Ricardo Wurmus
* gnu/packages/patches/libusb-for-axoloti.patch: Update context for libusb 1.0.22.
2018-03-28gnu: node: Update to 9.10.0.Jelle Licht
* gnu/packages/node.scm (node): Update to 9.10.0.
2018-03-28gnu: http-parser: Update to 2.8.0.Jelle Licht
* gnu/packages/web.scm (http-parser): Update to 2.8.0.
2018-03-28gnu: xf86-video-ati: Update to 18.0.1.Marius Bakke
* gnu/packages/xorg.scm (xf86-video-ati): Update to 18.0.1.
2018-03-28gnu: xf86-input-libinput: Update to 0.27.0.Marius Bakke
* gnu/packages/xorg.scm (xf86-input-libinput): Update to 0.27.0.
2018-03-28gnu: ntp: Update to 4.2.8p11 [security-fixes].Leo Famulari
Fixes CVE-2016-1549 and CVE-2018-{7170,7182,7183,7184,7185}. * gnu/packages/ntp.scm (ntp): Update to 4.2.8p11.
2018-03-28gnu: openssl: Replace with OpenSSL 1.0.2o [fixes CVE-2018-0739].Leo Famulari
* gnu/packages/tls.scm (openssl)[replacement]: New field. (openssl-1.0.2o): New variable.
2018-03-28gnu: Add r-parsedate.Konrad Hinsen
* gnu/packages/cran.scm (r-parsedate): New variable. Signed-off-by: Ludovic Courtès <ludovic.courtes@inria.fr>
2018-03-28gnu: mu: Fix tests failures triggered by DST.Maxim Cournoyer
* gnu/packages/mail.scm (mu)[phases]: Add 'fix-date-tests. Signed-off-by: Ludovic Courtès <ludovic.courtes@inria.fr>
2018-03-28gnu: Add tcalc.Nadya Voronova
* gnu/packages/maths.scm (tcalc): New variables. Signed-off-by: Ludovic Courtès <ludovic.courtes@inria.fr>
2018-03-28gnu: culmus: Rename to font-culmus.Arun Isaac
* gnu/packages/fonts.scm (culmus): Rename to... (font-culmus): ...this. Re-indent.
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