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2018-03-30gnu: Add delly.•••* 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> Roel Janssen
2018-03-30gnu: Add r-regioner.•••* gnu/packages/bioconductor.scm (r-regioner): New variable. Signed-off-by: Leo Famulari <leo@famulari.name> Roel Janssen
2018-03-30gnu: rust: Update rust to 1.24.1.•••* 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. Nikolai Merinov
2018-03-30gnu: ruby-2.2: Update to 2.2.10.•••* gnu/packages/ruby.scm (ruby-2.2): Update to 2.2.10. Ben Woodcroft
2018-03-30gnu: ruby-2.3: Update to 2.3.7.•••* gnu/packages/ruby.scm (ruby-2.3): Update to 2.3.7. Ben Woodcroft
2018-03-30gnu: mash: Update to 2.0.•••* gnu/packages/bioinformatics.scm (mash): Update to 2.0. Ben Woodcroft
2018-03-30gnu: mafft: Update to 7.394.•••* gnu/packages/bioinformatics.scm (mafft): Update to 7.394. Ben Woodcroft
2018-03-30gnu: diamond: Update to 0.9.19.•••* gnu/packages/bioinformatics.scm (diamond): Update to 0.9.19. Ben Woodcroft
2018-03-29gnu: pybitmessage: Update to 0.6.3.2 [security fixes].•••* gnu/packages/messaging.scm (pybitmessage): Update to 0.6.3.2. [source]: Fetch from git. Ricardo Wurmus
2018-03-29gnu: hydrogen: Update to 1.0.0-beta1.•••* 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. Ricardo Wurmus
2018-03-29gnu: mod-host: Update to 0.10.6-3.1726ad06b.•••* gnu/packages/music.scm (mod-host): Update to 0.10.6-3.1726ad06b. Ricardo Wurmus
2018-03-29gnu: drumkv1: Update to 0.9.0.•••* gnu/packages/music.scm (drumkv1): Update to 0.9.0. Ricardo Wurmus
2018-03-29gnu: samplv1: Update to 0.9.0.•••* gnu/packages/music.scm (samplv1): Update to 0.9.0. Ricardo Wurmus
2018-03-29gnu: padthv1: Update to 0.9.0.•••* gnu/packages/music.scm (padthv1): Update to 0.9.0. Ricardo Wurmus
2018-03-29gnu: synthv1: Update to 0.9.0.•••* gnu/packages/music.scm (synthv1): Update to 0.9.0. Ricardo Wurmus
2018-03-29gnu: qtractor: Update to 0.9.0.•••* gnu/packages/music.scm (qtractor): Update to 0.9.0. Ricardo Wurmus
2018-03-29gnu: awesome: Remove obsolete snippet.•••* gnu/packages/wm.scm (awesome)[source](snippet): Remove. Marius Bakke
2018-03-29gnu: xcb-util-xrm: Update to 1.3.•••* gnu/packages/xdisorg.scm (xcb-util-xrm): Update to 1.3. Marius Bakke
2018-03-29gnu: mbedtls-apache: Update to 2.7.2.•••* gnu/packages/tls.scm (mbedtls-apache): Update to 2.7.2. [source](snippet): Remove. Marius Bakke
2018-03-29gnu: Add botan.•••* gnu/packages/crypto.scm (botan): New variable. Leo Famulari
2018-03-29gnu: Add fpm2.•••* gnu/packages/password-utils.scm (fpm2): New variable. Signed-off-by: Tonton <tonton@riseup.net> Signed-off-by: Marius Bakke <mbakke@fastmail.com> Tonton
2018-03-29gnu: Add screen-message.•••* gnu/packages/xdisorg.scm (screen-message): New variable. Signed-off-by: Tonton <tonton@riseup.net> Signed-off-by: Marius Bakke <mbakke@fastmail.com> Tonton
2018-03-29gnu: r-lme4: Update to 1.1-16.•••* gnu/packages/statistics.scm (r-lme4): Update to 1.1-16. Tobias Geerinckx-Rice
2018-03-29gnu: r-curl: Update to 3.2.•••* gnu/packages/web.scm (r-curl): Update to 3.2. Tobias Geerinckx-Rice
2018-03-29gnu: bspwm: Update to 0.9.4.•••* gnu/packages/wm.scm (bspwm): Update to 0.9.4. Tobias Geerinckx-Rice
2018-03-29gnu: rss-bridge: Update to 2018-03-11.•••* gnu/packages/web.scm (rss-bridge): Update to 2018-03-11. Tobias Geerinckx-Rice
2018-03-29gnu: r-mutationalpatterns: Update to 1.4.3.•••* gnu/packages/bioinformatics.scm (r-mutationalpatterns): Update to 1.4.3; [propagated-inputs]: Remove r-gridextra. Roel Janssen
2018-03-29gnu: kaiju: Update to 1.6.2.•••* gnu/packages/bioinformatics.scm (kaiju): Update to 1.6.2; [inputs]: Add zlib. Roel Janssen
2018-03-29gnu: Add duperemove.•••* gnu/packages/disk.scm (duperemove): New variable. Co-authored-by: Ludovic Courtès <ludovic.courtes@inria.fr> Vasile Dumitrascu
2018-03-29gnu: Add python-debug.•••Suggested by Pjotr Prins <pjotr.public12@thebird.nl>. * gnu/packages/python.scm (python-debug): New variable. Ludovic Courtès
2018-03-29gnu: nano: Update to 2.9.5.•••* gnu/packages/nano.scm (nano): Update to 2.9.5. Efraim Flashner
2018-03-29gnu: Add r-idr.•••* gnu/packages/cran.scm (r-idr): New variable. Roel Janssen
2018-03-29gnu: Add r-amap.•••* gnu/packages/cran.scm (r-amap): New variable. Roel Janssen
2018-03-29gnu: Add r-venndiagram.•••* gnu/packages/cran.scm (r-venndiagram): New variable. Roel Janssen
2018-03-29gnu: Add r-pastecs.•••* gnu/packages/cran.scm (r-pastecs): New variable. Roel Janssen
2018-03-29gnu: libusb4java: Adjust for building with libusb 1.0.22.•••* gnu/packages/libusb.scm (libusb4java)[arguments]: Add phase to remove "-Werror" flag. Ricardo Wurmus
2018-03-29gnu: libusb-for-axoloti: Update patch.•••* gnu/packages/patches/libusb-for-axoloti.patch: Update context for libusb 1.0.22. Ricardo Wurmus
2018-03-29gnu: Refactor boot-service-type and activation-service-type.•••* gnu/services.scm (boot-service-type) <compose>: Use the "identity" procedure instead of the "append" procedure because it more accurately reflects the intent, which is to simply return the single list of extensions to which fold-services applies the "compose" procedure. (activation-service-type) <compose>: Likewise. Chris Marusich
2018-03-29doc: Improve <service-type> documentation.•••* doc/guix.texi (Service Reference): Correct and clarify some statements regarding the "compose" and "extend" procedures of <service-type>. Chris Marusich
2018-03-29guix-install.sh: Explicitly set root's home directory.•••* etc/guix-install.sh (ROOT_HOME): New variable. (sys_create_store, sys_enable_guix_daemon, sys_authorize_build_farms): Use ROOT_HOME instead of ~root or the HOME environment variable. * doc/guix.texi (Binary Installation): Instead of assuming that ~ and $HOME refer to root's directory simply because commands are being run as root, explicilty refer to it via ~root. Fixes: <https://bugs.gnu.org/30728> Chris Marusich
2018-03-28gnu: node: Update to 9.10.0.•••* gnu/packages/node.scm (node): Update to 9.10.0. Jelle Licht
2018-03-28gnu: http-parser: Update to 2.8.0.•••* gnu/packages/web.scm (http-parser): Update to 2.8.0. Jelle Licht
2018-03-28gnu: xf86-video-ati: Update to 18.0.1.•••* gnu/packages/xorg.scm (xf86-video-ati): Update to 18.0.1. Marius Bakke
2018-03-28gnu: xf86-input-libinput: Update to 0.27.0.•••* gnu/packages/xorg.scm (xf86-input-libinput): Update to 0.27.0. Marius Bakke
2018-03-28gnu: ntp: Update to 4.2.8p11 [security-fixes].•••Fixes CVE-2016-1549 and CVE-2018-{7170,7182,7183,7184,7185}. * gnu/packages/ntp.scm (ntp): Update to 4.2.8p11. Leo Famulari
2018-03-28gnu: openssl: Replace with OpenSSL 1.0.2o [fixes CVE-2018-0739].•••* gnu/packages/tls.scm (openssl)[replacement]: New field. (openssl-1.0.2o): New variable. Leo Famulari
2018-03-28gnu: Add r-parsedate.•••* gnu/packages/cran.scm (r-parsedate): New variable. Signed-off-by: Ludovic Courtès <ludovic.courtes@inria.fr> Konrad Hinsen
2018-03-28gnu: mu: Fix tests failures triggered by DST.•••* gnu/packages/mail.scm (mu)[phases]: Add 'fix-date-tests. Signed-off-by: Ludovic Courtès <ludovic.courtes@inria.fr> Maxim Cournoyer
2018-03-28gnu: Add tcalc.•••* gnu/packages/maths.scm (tcalc): New variables. Signed-off-by: Ludovic Courtès <ludovic.courtes@inria.fr> Nadya Voronova
2018-03-28build: Build (guix ci) and (guix scripts weather) when HAVE_GUILE_JSON.•••* Makefile.am (MODULES): Move guix/ci.scm and guix/scripts/weather.scm to the HAVE_GUILE_JSON-guarded block. Ludovic Courtès
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