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2019-06-29gnu: r-genomicfeatures: Update to 1.36.3....* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.36.3. Ricardo Wurmus
2019-06-29gnu: r-genomicalignments: Update to 1.20.1....* gnu/packages/bioinformatics.scm (r-genomicalignments): Update to 1.20.1. Ricardo Wurmus
2019-06-29gnu: r-biomart: Update to 2.40.1....* gnu/packages/bioinformatics.scm (r-biomart): Update to 2.40.1. Ricardo Wurmus
2019-06-29gnu: r-edger: Update to 3.26.5....* gnu/packages/bioinformatics.scm (r-edger): Update to 3.26.5. Ricardo Wurmus
2019-06-29gnu: r-systempiper: Update to 1.18.2....* gnu/packages/bioinformatics.scm (r-systempiper): Update to 1.18.2. Ricardo Wurmus
2019-06-29gnu: r-rsubread: Update to 1.34.4....* gnu/packages/bioconductor.scm (r-rsubread): Update to 1.34.4. Ricardo Wurmus
2019-06-29gnu: r-genomicscores: Update to 1.8.1....* gnu/packages/bioconductor.scm (r-genomicscores): Update to 1.8.1. Ricardo Wurmus
2019-06-29gnu: r-dose: Update to 3.10.2....* gnu/packages/bioconductor.scm (r-dose): Update to 3.10.2. Ricardo Wurmus
2019-06-28gnu: python-llvmlite: Build against LLVM 7....This is a follow-up to commit c5296e205b65a9b53553cf45be2ab223d5e82df5. * gnu/packages/llvm.scm (llvm-7, clang-runtime-7, clang-7): New public variables. (python-llvmlite)[inputs]: Inherit from LLVM-7 instead of LLVM. Marius Bakke
2019-06-28gnu: Add beets-bandcamp....* gnu/packages/music.scm (beets-bandcamp): New variable. Signed-off-by: Tobias Geerinckx-Rice <me@tobias.gr> Jakob L. Kreuze
2019-06-28gnu: musescore: Update to 3.2....* gnu/packages/music.scm (musescore): Update to 3.2. Nicolas Goaziou
2019-06-28gnu: snap: Update to 5....* gnu/packages/education.scm (snap): Update to 5. Nicolas Goaziou
2019-06-28gnu: atlas: All phases return #t....* gnu/packages/maths.scm (atlas)[arguments]: Ensure all custom phases return #t. Efraim Flashner
2019-06-28gnu: krita: Update to 4.2.2....* gnu/packages/kde.scm (krita): Update to 4.2.2. [source]: Don't use NAME in source URI. [arguments]: Remove obsolete configure flags. [native-inputs]: Add pkg-config. [inputs]: Add quazip, reorder alphabetically. Nicolas Goaziou
2019-06-28gnu: Add quazip....* gnu/packages/compression.scm (quazip): New variable. Nicolas Goaziou
2019-06-27gnu: linux-libre@4.14: Update to 4.14.131....* gnu/packages/linux.scm (%linux-libre-4.14-version): Update to 4.14.131. (%linux-libre-4.14-hash): Update hash. Mark H Weaver
2019-06-27gnu: linux-libre@4.9: Update to 4.9.184....* gnu/packages/linux.scm (linux-libre-4.9): Update to 4.9.184. Mark H Weaver
2019-06-27gnu: linux-libre@4.4: Update to 4.4.184....* gnu/packages/linux.scm (linux-libre-4.4): Update to 4.4.184. Mark H Weaver
2019-06-27gnu: pigx-scrnaseq: Update to 0.0.8....* gnu/packages/bioinformatics.scm (pigx-scrnaseq): Update to 0.0.8. Ricardo Wurmus
2019-06-27gnu: mame: Update to 0.211....* gnu/packages/emulators.scm (mame): Update to 0.211. Rutger Helling
2019-06-27tests: Avoid TCP port collision between lint.scm and guix-daemon.sh....This could lead to random deadlocks in one of these two tests when running "make check -j5". * tests/guix-daemon.sh (tcp_socket): Change port to 9998 to avoid collision with tests/lint.scm. Ludovic Courtès
2019-06-27ui: 'show-derivation-outputs' accepts <derivation-input> records....* guix/ui.scm (show-derivation-outputs): Handle <derivation-input> records. Ludovic Courtès
2019-06-27ui: 'show-what-to-build' accepts derivation inputs....This is a followup to f8a9f99cd602ce1dc5307cb0c21ae718ad8796bb. * guix/ui.scm (show-what-to-build)[inputs]: New variables. [substitutable-info]: Build the derivation list from INPUTS. Pass INPUTS to 'derivation-build-plan'. Ludovic Courtès
2019-06-27packages: 'specification->package+output' distinguishes "no output specified"....Until now the caller couldn't tell the different between a spec like "foo:out" and one like "foo". This change allows users to distinguish between these two cases. * gnu/packages.scm (specification->package+output): Disable output membership test when OUTPUT = #f and SUB-DRV = #f. * tests/packages.scm ("specification->package+output") ("specification->package+output invalid output") ("specification->package+output no default output") ("specification->package+output invalid output, no default"): New tests. Ludovic Courtès
2019-06-27derivations: 'build-derivations' can be passed derivation inputs....* guix/derivations.scm (build-derivations): Accept <derivation-input> records among DERIVATIONS. * tests/derivations.scm ("build-derivations with specific output"): Test it. Ludovic Courtès
2019-06-27derivations: 'derivation' preserves pointer equality....* guix/derivations.scm (derivation): Check if FILE is already in %DERIVATION-CACHE and return it if it is. Ludovic Courtès
2019-06-27derivations: <derivation-input> now aggregates a <derivation>....Consequently, the whole graph of <derivation> object is readily available without having to go through 'read-derivation-from-file', which could have cache misses if the requested <derivation> object had been GC'd in the meantime. This is an important property for the performance of things like 'derivation-build-plan' that traverse the derivation graph. * guix/derivations.scm (<derivation-input>): Replace 'path' field by 'derivation'. (derivation-input-path): Adjust accordingly. (derivation-input-key): New procedure. (derivation-input-output-paths): Adjust accordingly. (coalesce-duplicate-inputs): Likewise. (derivation-prerequisites): Use 'derivation-input-key' to compute keys for INPUT-SET. (derivation-build-plan): Likewise. (read-derivation): Add optional 'read-derivation-from-file' parameter. [make-input-drvs]: Call it. (write-derivation)[write-input]: Adjust to new <derivation-input>. (derivation/masked-inputs): Likewise, and remove redundant 'coalesce-duplicate-inputs' call. (derivation)[input->derivation-input]: Change to consider only the derivation case. Update call to 'make-derivation-input'. [input->source]: New procedure. Separate sources from inputs. (map-derivation): Adjust to new <derivation-input>. * tests/derivations.scm ("parse & export"): Pass a second argument to 'read-derivation'. ("build-expression->derivation and derivation-prerequisites") ("derivation-prerequisites and valid-derivation-input?"): Adjust to new <derivation-input>. Ludovic Courtès
2019-06-27graph: Use 'derivation-input-derivation'....* guix/scripts/graph.scm (derivation-dependencies): Use 'derivation-input-derivation'. Ludovic Courtès
2019-06-27ui: 'show-what-to-build' uses 'derivation-build-plan'....* guix/ui.scm (show-what-to-build)[build-or-substitutable?]: Remove. Use 'derivation-build-plan' instead of 'derivation-prerequisites-to-build', passing it all of DRV at once, and remove 'fold2' shenanigans and postprocessing of BUILD. Ludovic Courtès
2019-06-27derivations: Rewrite and replace 'derivations-prerequisites-to-build'....The new 'derivation-build-plan' procedure has a more appropriate signature: it takes a list of <derivation-inputs> instead of taking one <derivation>. Its body is also much simpler. * guix/derivations.scm (derivation-build-plan): New procedure. (derivation-prerequisites-to-build): Express in terms of 'derivation-build-plan' and mark as deprecated. * tests/derivations.scm: Change 'derivation-prerequisites-to-build' tests to 'derivation-build-plan' and adjust accordingly. Ludovic Courtès
2019-06-27derivations: Add 'derivation-input'....* guix/derivations.scm (derivation-input): New procedure. * tests/grafts.scm (make-derivation-input): Remove. ("graft-derivation, unused outputs not depended on"): Use 'derivation-input'. Ludovic Courtès
2019-06-27ui: Add 'display-search-results' and use it....* guix/ui.scm (display-search-results): New procedure. * guix/scripts/package.scm (find-packages-by-description): Remove 'unzip2' call and return a list of pairs. (process-query): Change to use 'display-search-results'. * guix/scripts/system/search.scm (find-service-types): Remove 'unzip2' call and return a list of pairs. (guix-system-search): Use 'display-search-results'. Ludovic Courtès
2019-06-27syscalls: Add 'terminal-rows'....* guix/build/syscalls.scm (terminal-dimension): New procedure. (terminal-columns): Rewrite in terms of 'terminal-dimension'. (terminal-rows): New procedure. * tests/syscalls.scm ("terminal-rows"): New test. Ludovic Courtès
2019-06-27ui: 'relevance' considers regexps connected with a logical and....* guix/ui.scm (relevance)[score]: Change to return 0 when one of REGEXPS doesn't match. * tests/ui.scm ("package-relevance"): New test. Ludovic Courtès
2019-06-27accounts: Use 'fsync' instead of 'fdatasync'....* gnu/build/accounts.scm (catch-ENOSYS): Remove. (database-writer): Use 'fsync' instead of 'fdatasync'. Ludovic Courtès
2019-06-27gnu: dosbox: Update to 0.74-3....* gnu/packages/emulators.scm (dosbox): Update to 0.74-3. Rutger Helling
2019-06-27gnu: rep-gtk: Update to 0.90.8.3....* gnu/packages/sawfish.scm (rep-gtk): Update to 0.90.8.3. [source]: Use HTTPS URI. [arguments]: Add remove-autogen phase. [native-inputs]: Add autoconf, automake and libtool. [home-page]: Update URI. Arun Isaac
2019-06-27gnu: sawfish: Update to 1.12.0....* gnu/packages/sawfish.scm (sawfish): Update to 1.12.0. [source]: Use HTTPS URI. [home-page]: Update URI. Signed-off-by: Arun Isaac <arunisaac@systemreboot.net> Benjamin Slade
2019-06-26gnu: electron-cash: Update to 4.0.7....* gnu/packages/finance (electron-cash): Update to 4.0.7. Vagrant Cascadian
2019-06-27Revert "gnu: openssh: Don't create the PRIVSEP_PATH directory."...This reverts commit 46475f72ab6127e7818fdea4a0ea9cc07c60a5f4. Tobias Geerinckx-Rice
2019-06-27Revert "gnu: openssh: Clean-up custom install phase."...This reverts commit 7754136e464e02284624ad05c196d9ec26099143. Tobias Geerinckx-Rice
2019-06-26gnu: supertux: Fix homepage....* gnu/packages/games.scm (supertux)[homepage]: Fix URL. Nicolas Goaziou
2019-06-26gnu: Add texmacs....* gnu/packages/text-editors.scm (texmacs): New variable. Andreas Enge
2019-06-26gnu: python-pathpy: Update to 11.5.0....* gnu/packages/python-xyz.scm (python-pathpy): Update to 11.5.0. [outputs]: Add separate "doc" output. [native-inputs]: Add python-jaraco-packaging. [arguments]: Enable tests; uncomment "build-doc" and "install-doc" phases; replace "check" phase to skip flaky test. Ricardo Wurmus
2019-06-26gnu: Add python-jaraco-packaging....* gnu/packages/python-xyz.scm (python-jaraco-packaging): New variable. Ricardo Wurmus
2019-06-26gnu: Add python-pytest-virtualenv....* gnu/packages/python-check.scm (python-pytest-virtualenv): New variable. Ricardo Wurmus
2019-06-26gnu: Add python-pytest-fixture-config....* gnu/packages/python-check.scm (python-pytest-fixture-config): New variable. Ricardo Wurmus
2019-06-26gnu: Add python-pytest-shutil....* gnu/packages/python-check.scm (python-pytest-shutil): New variable. Ricardo Wurmus
2019-06-26gnu: Add python-pytest-flake8....* gnu/packages/python-check.scm (python-pytest-flake8): New variable. Ricardo Wurmus
2019-06-26gnu: Add python-pytest-checkdocs....* gnu/packages/python-check.scm (python-pytest-checkdocs): New variable. Ricardo Wurmus