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2018-09-24gnu: Add r-xbioc.•••* gnu/packages/bioinformatics.scm (r-xbioc): New variable. Ricardo Wurmus
2018-09-24gnu: Prefix all Emacs packages with "emacs-".•••* gnu/packages/emacs.scm: Prefix all Emacs packages with "emacs-". This is to enforce consistency and so that `emacs-packages?' can reliably detect Emacs packages based on the "emacs-" prefix. Pierre Neidhardt
2018-09-24gnu: python-networkx: Use HTTPS home page.•••* gnu/packages/python.scm (python-networkx)[home-page]: Use HTTPS. Tobias Geerinckx-Rice
2018-09-24gnu: python-networkx: Update to 2.2.•••* gnu/packages/python.scm (python-networkx): Update to 2.2. Tobias Geerinckx-Rice
2018-09-24gnu: python-decorator: Update to 4.3.0.•••* gnu/packages/python.scm (python-decorator): Update to 4.3.0. [arguments]: Run the test suite. Tobias Geerinckx-Rice
2018-09-24gnu: python-marshmallow: Update to 3.0.0b14.•••* gnu/packages/python.scm (python-marshmallow): Update to 3.0.0b14. Tobias Geerinckx-Rice
2018-09-24gnu: libiptcdata: Update to 1.0.5.•••* gnu/packages/image.scm (libiptcdata): Update to 1.0.5. [home-page]: Follow Debian's maintained upstream. Tobias Geerinckx-Rice
2018-09-24gnu: virtualgl: Update to 2.6.•••* gnu/packages/gl.scm (virtualgl): Update to 2.6. [inputs]: Add libxtst. Tobias Geerinckx-Rice
2018-09-24gnu: parallel: Update to 20180922.•••* gnu/packages/parallel.scm (parallel): Update to 20180922. Tobias Geerinckx-Rice
2018-09-24gnu: workrave: Use Guix's built-in bootstrap phase.•••* gnu/packages/gnome.scm (workrave)[arguments]: Remove 'autoconf' phase. Tobias Geerinckx-Rice
2018-09-24gnu: python-gitdb: Update to 2.0.4.•••* gnu/packages/version-control.scm (python-gitdb): Update to 2.0.4. [arguments]: Replace AND with equivalent but more 'accurate' BEGIN. Tobias Geerinckx-Rice
2018-09-24gnu: nano: Update to 3.1.•••* gnu/packages/nano.scm (nano): Update to 3.1. Tobias Geerinckx-Rice
2018-09-24gnu: fping: Use HTTPS home page.•••* gnu/packages/networking.scm (fping)[home-page]: Use HTTPS. Tobias Geerinckx-Rice
2018-09-24gnu: fping: Update to 4.1.•••* gnu/packages/networking.scm (fping): Update to 4.1. Tobias Geerinckx-Rice
2018-09-23vm: Use "cache=loose" for all 9p mounts.•••This significantly improves read throughput when running things like "guix hash -r ...". * gnu/system/vm.scm (%linux-vm-file-systems): Add 'flags' for "store". Add "cache=loose" to every file system. Ludovic Courtès
2018-09-23vm: Disable deduplication for 'guix system vm-image'.•••* gnu/system/vm.scm (qemu-image): Pass #:deduplicate? #f to 'root-partition-initializer'. Ludovic Courtès
2018-09-23database: Register each store item only once.•••Fixes <https://bugs.gnu.org/32600>. Reported by Leo Famulari. * guix/store/database.scm (register-items): Check whether TO-REGISTER is in DB by calling 'path-id', and skip the reset-timestamps, registration, and deduplication phases when it is. Ludovic Courtès
2018-09-23database: 'register-items' shows a progress bar.•••* guix/store/database.scm (register-items): Add #:log-port. Use 'progress-reporter/bar' to show a progress report. (register-path): Pass #:log-port to 'register-items'. Ludovic Courtès
2018-09-23store-copy: Display a progress bar when copying store items.•••* guix/build/store-copy.scm (populate-store): Add #:log-port parameter. Use 'progress-reporter/bar' to report progress. Ludovic Courtès
2018-09-23serialization: Remove redundancy in 'write-file'.•••* guix/serialization.scm (write-file): Remove redundant 'member' call. Ludovic Courtès
2018-09-23system: Mention '--skip-checks' in initrd diagnostics.•••* gnu/system/mapped-devices.scm (check-device-initrd-modules): Add note about '--skip-checks'. Ludovic Courtès
2018-09-23gnu: Add emacs-synosaurus.•••* gnu/packages/emacs.scm (emacs-synosaurus): New variable. Pierre Neidhardt
2018-09-23gnu: xpra: Update to 2.3.4.•••* gnu/packages/xorg.scm (xpra): Update to 2.3.4. Rutger Helling
2018-09-23gnu: eolie: Use webkitgtk-2.22.•••* gnu/packages/gnome.scm (eolie)[native-inputs]: Add gcc-7:lib. [inputs]: Replace webkitgtk with webkitgtk-2.22. [arguments]: Add "gcc:lib" to the list of libraries to add to LD_LIBRARY_PATH. Use invoke. Mark H Weaver
2018-09-23gnu: epiphany: Use webkitgtk-2.22.•••* gnu/packages/gnome.scm (epiphany)[native-inputs]: Add gcc-7. [inputs]: Replace webkitgtk with webkitgtk-2.22. Mark H Weaver
2018-09-23gnu: webkitgtk: Add version 2.22.2.•••* gnu/packages/webkit.scm (webkitgtk-2.22): New variable. Mark H Weaver
2018-09-22gnu: Add Go 1.11.•••* gnu/packages/golang.scm (go-1.11): New variable. Signed-off-by: Leo Famulari <leo@famulari.name> Katherine Cox-Buday
2018-09-22gnu: icecat: Add fixes from upstream mozilla-esr60 [security fixes].•••Includes fixes for CVE-2018-12383 and CVE-2018-12385. * gnu/packages/patches/icecat-CVE-2018-12383.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. * gnu/packages/patches/icecat-avoid-bundled-libraries.patch: Adapt to apply cleanly to IceCat 60. * gnu/packages/gnuzilla.scm (mozilla-patch): Update to fetch from mozilla-esr60. (icecat): Add selected changesets from upstream mozilla-esr60. Mark H Weaver
2018-09-22Revert 'gnu: rust: Remove unused "ar" setting.'.•••Some versions of Rust do need it and others complain about it. For now, revert the removal entirely. This reverts commit ec944a1de97c8a523d6e1089b8c4430424297f93. Danny Milosavljevic
2018-09-22gnu: hmmer: Update to 3.2.1.•••* gnu/packages/bioinformatics.scm (hmmer): Update to 3.2.1. [origin]: Remove patch. [license]: Change to BSD-3. [supported-systems]: New field. * gnu/packages/patches/hmmer-remove-cpu-specificity.patch: Delete file. * gnu/local.mk (dist_patch_DATA): Remove it. Ben Woodcroft
2018-09-21gnu: snap: Update to 4.2.1.4.•••* gnu/packages/education.scm (snap): Update to 4.2.1.4. Nicolas Goaziou
2018-09-21gnu: emacs-org: Update to 9.1.14.•••* gnu/packages/emacs.scm (emacs-org): Update to 9.1.14. Nicolas Goaziou
2018-09-21gnu: workrave: Update to 1.10.21.•••* gnu/packages/gnome.scm (workrave): Update to 1.10.21. [source]: Use GIT-FILE-NAME. Tobias Geerinckx-Rice
2018-09-21gnu: emacs-password-store: Update to 1.7.3.•••* gnu/packages/emacs.scm (emacs-password-store): Update to 1.7.3. Tobias Geerinckx-Rice
2018-09-21gnu: filezilla: Update to 3.37.1.•••* gnu/packages/ftp.scm (filezilla): Update to 3.37.1. Tobias Geerinckx-Rice
2018-09-21gnu: wxwidgets: Update to 3.0.4.•••* gnu/packages/wxwidgets.scm (wxwidgets): Update to 3.0.4. Tobias Geerinckx-Rice
2018-09-21gnu: python-pyparsing: Update to 2.2.1.•••* gnu/packages/python.scm (python-pyparsing): Update to 2.2.1. [source]: Use PYPI-URI. Tobias Geerinckx-Rice
2018-09-21gnu: rust: Remove unused "ar" setting.•••* gnu/packages/rust.scm (rust-1.20)[arguments]<#:phases>[configure]: Remove unused "ar" setting. Danny Milosavljevic
2018-09-21doc: Add section about inferiors.•••* doc/guix.texi (Inferiors): New node. (Channels): Add xref to "Inferiors". Ludovic Courtès
2018-09-21inferior: Add 'inferior-for-channels'.•••* guix/inferior.scm (%inferior-cache-directory): New variable. (inferior-for-channels): New procedure. Ludovic Courtès
2018-09-21channels: Add 'channel-instances->derivation'.•••* guix/channels.scm (channel-instances->derivation): New procedure. (latest-channel-derivation): Use it. (channel-instance-derivations): Make private. Ludovic Courtès
2018-09-21profiles: 'packages->manifest' now accepts inferior packages.•••* guix/profiles.scm (packages->manifest)[inferiors-loaded?]: New variable. [inferior->entry]: New procedure. Accept inferior packages when INFERIORS-LOADED? is true. * tests/guix-package.sh: Add test using a manifest with an inferior. * tests/inferior.scm ("packages->manifest"): New test. Ludovic Courtès
2018-09-21inferior: Add 'inferior-package->manifest-entry'.•••* guix/inferior.scm (inferior-package->manifest-entry): New procedure. * tests/inferior.scm (manifest-entry->list): New procedure. ("inferior-package->manifest-entry"): New test. Ludovic Courtès
2018-09-21inferior: Add 'inferior-package-search-paths' & co.•••* guix/inferior.scm (%inferior-package-search-paths) (inferior-package-native-search-paths) (inferior-package-search-paths) (inferior-package-transitive-native-search-paths): New procedures. * tests/inferior.scm ("inferior-package-search-paths"): New test. Ludovic Courtès
2018-09-21inferior: Add 'inferior-package-inputs' & co.•••* guix/inferior.scm (open-inferior): Use (ice-9 match). (inferior-package-input-field, inferior-package-inputs): (inferior-package-native-inputs) (inferior-package-propagated-inputs) (inferior-package-transitive-propagated-inputs): New procedures. * tests/inferior.scm ("inferior-package-inputs"): New test. inputs fixlet Ludovic Courtès
2018-09-21inferior: Add 'lookup-inferior-packages'.•••* guix/inferior.scm (<inferior>)[packages, table]: New fields. (open-inferior): Initialize these new fields. (inferior-packages): Rename to... (%inferior-packages): ... this. (inferior-packages): New procedure; force the promise. (%inferior-package-table, lookup-inferior-packages): New procedures. * tests/inferior.scm ("lookup-inferior-packages") ("lookup-inferior-packages and eq?-ness"): New tests. Ludovic Courtès
2018-09-21inferior: Add 'inferior-package-derivation'.•••* guix/inferior.scm (read-inferior-response) (send-inferior-request): New procedures. (inferior-eval): Rewrite in terms of these. (proxy, inferior-package-derivation, inferior-package->derivation) (package-compiler): New procedures. * tests/inferior.scm ("inferior-package-derivation"): New test. Ludovic Courtès
2018-09-21gnu: Add r-pore.•••* gnu/packages/bioinformatics.scm (r-pore): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org> pimi
2018-09-21gnu: hdf5-parallel-openmpi: Really enable parallel build.•••This fix ensures that the H5_HAVE_PARALLEL identifier is correctly set in the file H5pubconf.h. * gnu/packages/maths.scm (hdf5-parallel-openmpi)[arguments]: Add the "--enable-parallel" flag to the list of configure flags. Remove the incompatible "--enable-cxx" flag. Add 'mpi-setup' phase. Signed-off-by: Ludovic Courtès <ludovic.courtes@inria.fr> Paul Garlick
2018-09-21gnu: hdf5: Allow for absence of utility script.•••* gnu/packages/maths.scm (hdf5)[arguments]: Add condition to 'split' phase to check for existence of h5fc script. Signed-off-by: Ludovic Courtès <ludo@gnu.org> Paul Garlick
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