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* gnu: Add snakemake-4.Ricardo Wurmus2018-07-27
| | | | | | * gnu/packages/python.scm (snakemake-4): New variable. * gnu/packages/bioinformatics.scm (pigx-bsseq, pigx-rnaseq, pigx-scrnaseq, pigx-chipseq)[inputs]: Use it.
* gnu: snakemake: Add missing dependencies.Ricardo Wurmus2018-07-27
| | | | | * gnu/packages/python.scm (snakemake)[propagated-inputs]: Add python-datrie, python-docutils, python-jinja2, python-jsonschema, and python-networkx.
* gnu: Add python-datrie.Ricardo Wurmus2018-07-27
| | | | * gnu/packages/python.scm (python-datrie): New variable.
* gnu: imagemagick: Update to 6.9.10-8.Marius Bakke2018-07-27
| | | | * gnu/packages/imagemagick.scm (imagemagick): Update to 6.9.10-8.
* gnu: mbedtls-apache: Update to 2.7.5.Marius Bakke2018-07-27
| | | | * gnu/packages/tls.scm (mbedtls-apache): Update to 2.7.5.
* gnu: snakemake: Update to 5.2.0.Ricardo Wurmus2018-07-27
| | | | * gnu/packages/python.scm (snakemake): Update to 5.2.0.
* gnu: guile-sdl2: Update to 0.3.0.Ricardo Wurmus2018-07-27
| | | | | * gnu/packages/sdl.scm (guile-sdl2): Update to 0.3.0. [arguments]: Remove "patch-makefile" phase.
* import: hackage: Emit native-inputs in the importer.Danny Milosavljevic2018-07-27
| | | | | | | | | | | | * guix/import/cabal.scm (cabal-custom-setup-dependencies): Export. (cabal-package-custom-setup): Export. (<cabal-package>): New field "custom-setup". (make-cabal-package): Modify. (eval-cabal): Modify. * guix/import/hackage.scm (cabal-dependencies->names): Factor out... (cabal-test-dependencies->names): ...this. (cabal-custom-setup-dependencies->names): New procedure. (hackage-module->sexp): Modify.
* gnu: tiled: Update to 1.1.6.Kei Kebreau2018-07-27
| | | | | * gnu/packages/game-development.scm (tiled): Update to 1.1.6. [arguments]: Substitute invoke for system*.
* gnu: python-xsge: Update to 2018.02.26.Kei Kebreau2018-07-26
| | | | | | * gnu/packages/game-development.scm (python-xsge, python2-xsge): Update to 2018.02.26. [arguments]: Substitute invoke for system*.
* gnu: freeciv: Update to 2.6.0.Kei Kebreau2018-07-26
| | | | * gnu/packages/games.scm (freeciv): Update to 2.6.0.
* gnu: ecryptfs-utils: Patch more hardcoded paths.Brendan Tildesley2018-07-26
| | | | | | | | | * gnu/packages/linux.scm (ecryptfs-utils): [arguments]: Add an additional file to be patched that was missing in the last fix. Ecryptfs will now find the umount binary path as well as mount and others. Re-sort the list of files to be substituted. Signed-off-by: Leo Famulari <leo@famulari.name>
* gnu: cabextract: Delete bundled libmspack.Marius Bakke2018-07-26
| | | | * gnu/packages/compression.scm (cabextract)[source](modules, snippet): New field.
* gnu: cabextract: Update to 1.7.Marius Bakke2018-07-26
| | | | * gnu/packages/compression.scm (cabextract): Update to 1.7.
* gnu: fuse: Update source hash.Marius Bakke2018-07-26
| | | | | | | | The fuse 2.9.8 tarball and signature was modified in place. Both are signed by the same key, at different dates, and the only differences are directory timestamps and a ChangeLog update. * gnu/packages/linux.scm (fuse)[source](sha256): Update.
* gnu: make-u-boot-package: Don't install "sunxi-spl-with-ecc.bin".Danny Milosavljevic2018-07-26
| | | | | * gnu/packages/bootloaders.scm (make-u-boot-package)[arguments]<#:phases> [install]: Don't install "sunxi-spl-with-ecc.bin".
* gnu: Add ruby-net-scp.Danny Milosavljevic2018-07-26
| | | | * gnu/packages/ruby.scm (ruby-net-scp): New variable.
* gnu: translate-shell: Fix .el install directory.Efraim Flashner2018-07-26
| | | | | | * gnu/packages/dictionaries.scm (translate-shell)[arguments]: Change the install directory during the custom 'emacs-install phase to match with other emacs .el packages.
* gnu: java-picard: Fix manifest.Gábor Boskovits2018-07-26
| | | | | * gnu/packages/bioinformatics.scm (java-picard)[arguments]: Adjust phase 'edit-classpath-in-manifest for the new manifest generation code.
* gnu: python-qsintilla: Fix building.Efraim Flashner2018-07-26
| | | | | * gnu/packages/qt.scm (python-qscintilla)[arguments]: Extend custom 'configure phase to also patch the 'installed.txt' file.
* gnu: linux-libre: Update to 4.17.10.Mark H Weaver2018-07-26
| | | | | * gnu/packages/linux.scm (%linux-libre-version): Update to 4.17.10. (%linux-libre-hash): Update hash.
* gnu: linux-libre@4.14: Update to 4.14.58.Mark H Weaver2018-07-26
| | | | | * gnu/packages/linux.scm (%linux-libre-4.14-version): Update to 4.14.58. (%linux-libre-4.14-hash): Update hash.
* gnu: linux-libre@4.9: Update to 4.9.115.Mark H Weaver2018-07-26
| | | | * gnu/packages/linux.scm (linux-libre-4.9): Update to 4.9.115.
* gnu: linux-libre@4.4: Update to 4.4.144.Mark H Weaver2018-07-26
| | | | * gnu/packages/linux.scm (linux-libre-4.4): Update to 4.4.144.
* gnu: Remove dangling variable.Marius Bakke2018-07-25
| | | | * gnu/packages/xml.scm (libxslt/fixed): Remove.
* gnu: Update cabextract.org.uk home pages.Marius Bakke2018-07-25
| | | | | * gnu/packages/compression.scm (libmspack, cabextract)[home-page, source]: Use HTTPS.
* gnu: libmspack: Don't build static library.Marius Bakke2018-07-25
| | | | * gnu/packages/compression.scm (libmspack)[arguments]: Add #:configure-flags.
* gnu: libmspack: Update to 0.7.Marius Bakke2018-07-25
| | | | * gnu/packages/compression.scm (libmspack): Update to 0.7.
* gnu: hplip-minimal: Simplify expression.Marius Bakke2018-07-25
| | | | * gnu/packages/cups.scm (hplip-minimal): Remove unnecessary quotes.
* gnu: libjpeg-turbo: Don't build static libraries.Marius Bakke2018-07-25
| | | | | * gnu/packages/image.scm (libjpeg-turbo)[arguments]: Add "--disable-static" to #:configure-flags.
* gnu: libjpeg-turbo: Update home page.Marius Bakke2018-07-25
| | | | * gnu/packages/image.scm (libjpeg-turbo)[home-page]: Use HTTPS.
* gnu: audit: Don't build static libraries.Marius Bakke2018-07-25
| | | | | * gnu/packages/admin.scm (audit)[arguments]: Add "--disable-static" to #:configure-flags.
* gnu: audit: Update to 2.8.4.Marius Bakke2018-07-25
| | | | | * gnu/packages/admin.scm (audit): Update to 2.8.4. [arguments]: Remove #:phases.
* Merge remote-tracking branch 'origin/master' into qt-updatesEfraim Flashner2018-07-25
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| * gnu: Add pscircle.Oleg Pykhalov2018-07-25
| | | | | | | | * gnu/packages/admin.scm (pscircle): New variable.
| * gnu: Add hplip-minimal.Efraim Flashner2018-07-25
| | | | | | | | | | | | | | | | * gnu/packages/cups.scm (hplip-minimal): New variable. * gnu/packages/scanner.scm (sane-backends)[inputs]: Replace hplip with hplip-minimal. * doc/guix.texi (Printing Services): Change example code to use hplip-minimal in place of hplip. Add note explaining when use hplip.
| * gnu: syncthing: Update to 0.14.49.Leo Famulari2018-07-24
| | | | | | | | | | | | | | | | * gnu/packages/syncthing.scm (syncthing): Update to 0.14.49. [source]: Remove obsolete patch. [inputs]: Remove go-github-com-kardianos-osext. * gnu/packages/patches/syncthing-fix-crash.patch: Delete file. * gnu/local.mk (dist_patch_DATA): Remove it.
| * gnu: go-github-com-syncthing-notify: Update to 0.0.0-1.cdf89c4.Leo Famulari2018-07-24
| | | | | | | | | | * gnu/packages/syncthing.scm (go-github-com-syncthing-notify): Update to 0.0.0-1.cdf89c4.
| * gnu: go-github-com-thejerf-suture: Update to 2.0.3-0.3f1fb62.Leo Famulari2018-07-24
| | | | | | | | | | * gnu/packages/syncthing.scm (go-github-com-thejerf-suture): Update to 2.0.3-0.3f1fb62.
| * gnu: java-tomcat: Strip timestampsBjörn Höfling2018-07-25
| | | | | | | | | | | | | | * gnu/package/web.scm (java-tomcat)[arguments]: Add phase 'strip timestamps. Makes build deterministic. Signed-off-by: Julien Lepiller <julien@lepiller.eu>
| * gnu: java-tomcat: Remove bundled jars.Björn Höfling2018-07-25
| | | | | | | | | | | | * gnu/packages/web.scm (java-tomcat)[source]: Add snippet to remove bundled jars. Signed-off-by: Julien Lepiller <julien@lepiller.eu>
| * gnu: java-tomcat: Update to 8.5.32.Björn Höfling2018-07-25
| | | | | | | | | | | | * gnu/packages/web.scm (java-tomcat): Update to 8.5.32. Signed-off-by: Julien Lepiller <julien@lepiller.eu>
| * gnu: java: Use java-javaee-servletapi instead of java-tomcat.Björn Höfling2018-07-25
| | | | | | | | | | | | | | | | | | | | | | | | | | * gnu/packages/java.scm(java-eclipse-sisu-inject)[inputs]: Remove java-tomcat, add java-javaee-servletapi. (logback-core)[inputs]: Likewise. * gnu/packages/maven.scm (maven-wagon-provider-test)[inputs]: Likewise. * gnu/packages/web.scm (java-eclipse-jetty-webapp)[inputs]: Likewise. (java-eclipse-jetty-server)[inputs]: Likewise. (java-eclipse-jetty-http)[inputs]: Likewise. (java-eclipse-jetty-jmx)[inputs]: Likewise. (java-eclipse-jetty-io)[inputs]: Likewise. Signed-off-by: Julien Lepiller <julien@lepiller.eu>
| * gnu: Add java-javaee-servletapi.Björn Höfling2018-07-25
| | | | | | | | | | | | * gnu/packages/java.scm (java-javaee-servletapi): New variable. Signed-off-by: Julien Lepiller <julien@lepiller.eu>
| * gnu: java: Use java-classpathx-servletapi instead of java-tomcat where possible.Björn Höfling2018-07-25
| | | | | | | | | | | | | | * gnu/package/java.scm (java-commons-jxpath)[inputs]: Remove java-tomcat, add java-classpathx-servletapi. (java-guice-servlet)[inputs]: Likewise. Signed-off-by: Julien Lepiller <julien@lepiller.eu>
| * gnu: java-logback-core: Add file-name field.Björn Höfling2018-07-25
| | | | | | | | | | | | * gnu/package/java.scm (java-logback-core)[source]: Add file-name field. Signed-off-by: Julien Lepiller <julien@lepiller.eu>
| * gnu: java-guice: Remove jars.Björn Höfling2018-07-25
| | | | | | | | | | | | * gnu/packages/java.scm (java-guice)[source]: Add snippet to delete jar-files. Signed-off-by: Julien Lepiller <julien@lepiller.eu>
| * gnu: fuse: Update to 2.9.8 [fixes CVE-2018-10906].Marius Bakke2018-07-24
| | | | | | | | * gnu/packages/linux.scm (fuse): Update to 2.9.8.
| * ruby-build-system: Make phase "replace-git-ls-files" handle more cases.Danny Milosavljevic2018-07-24
| | | | | | | | * guix/build/ruby-build-system.scm (replace-git-ls-files): Modify.
| * gnu: Add ruby-rspec-its.Danny Milosavljevic2018-07-24
| | | | | | | | * gnu/packages/ruby.scm (ruby-rspec-its): New variable.
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