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2019-06-29gnu: r-tximport: Update to 1.12.3.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-tximport): Update to 1.12.3.
2019-06-29gnu: r-genomicfeatures: Update to 1.36.3.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.36.3.
2019-06-29gnu: r-genomicalignments: Update to 1.20.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-genomicalignments): Update to 1.20.1.
2019-06-29gnu: r-biomart: Update to 2.40.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-biomart): Update to 2.40.1.
2019-06-29gnu: r-edger: Update to 3.26.5.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-edger): Update to 3.26.5.
2019-06-29gnu: r-systempiper: Update to 1.18.2.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-systempiper): Update to 1.18.2.
2019-06-29gnu: r-rsubread: Update to 1.34.4.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-rsubread): Update to 1.34.4.
2019-06-29gnu: r-genomicscores: Update to 1.8.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-genomicscores): Update to 1.8.1.
2019-06-29gnu: r-dose: Update to 3.10.2.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-dose): Update to 3.10.2.
2019-06-28gnu: python-llvmlite: Build against LLVM 7.Marius Bakke
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.
2019-06-28gnu: Add beets-bandcamp.Jakob L. Kreuze
* gnu/packages/music.scm (beets-bandcamp): New variable. Signed-off-by: Tobias Geerinckx-Rice <me@tobias.gr>
2019-06-28gnu: musescore: Update to 3.2.Nicolas Goaziou
* gnu/packages/music.scm (musescore): Update to 3.2.
2019-06-28gnu: snap: Update to 5.Nicolas Goaziou
* gnu/packages/education.scm (snap): Update to 5.
2019-06-28gnu: atlas: All phases return #t.Efraim Flashner
* gnu/packages/maths.scm (atlas)[arguments]: Ensure all custom phases return #t.
2019-06-28gnu: krita: Update to 4.2.2.Nicolas Goaziou
* 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.
2019-06-28gnu: Add quazip.Nicolas Goaziou
* gnu/packages/compression.scm (quazip): New variable.
2019-06-27gnu: linux-libre@4.14: Update to 4.14.131.Mark H Weaver
* gnu/packages/linux.scm (%linux-libre-4.14-version): Update to 4.14.131. (%linux-libre-4.14-hash): Update hash.
2019-06-27gnu: linux-libre@4.9: Update to 4.9.184.Mark H Weaver
* gnu/packages/linux.scm (linux-libre-4.9): Update to 4.9.184.
2019-06-27gnu: linux-libre@4.4: Update to 4.4.184.Mark H Weaver
* gnu/packages/linux.scm (linux-libre-4.4): Update to 4.4.184.
2019-06-27gnu: pigx-scrnaseq: Update to 0.0.8.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (pigx-scrnaseq): Update to 0.0.8.
2019-06-27gnu: mame: Update to 0.211.Rutger Helling
* gnu/packages/emulators.scm (mame): Update to 0.211.
2019-06-27tests: Avoid TCP port collision between lint.scm and guix-daemon.sh.Ludovic Courtès
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.
2019-06-27ui: 'show-derivation-outputs' accepts <derivation-input> records.Ludovic Courtès
* guix/ui.scm (show-derivation-outputs): Handle <derivation-input> records.
2019-06-27ui: 'show-what-to-build' accepts derivation inputs.Ludovic Courtès
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'.
2019-06-27packages: 'specification->package+output' distinguishes "no output specified".Ludovic Courtès
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.
2019-06-27derivations: 'build-derivations' can be passed derivation inputs.Ludovic Courtès
* guix/derivations.scm (build-derivations): Accept <derivation-input> records among DERIVATIONS. * tests/derivations.scm ("build-derivations with specific output"): Test it.
2019-06-27derivations: 'derivation' preserves pointer equality.Ludovic Courtès
* guix/derivations.scm (derivation): Check if FILE is already in %DERIVATION-CACHE and return it if it is.
2019-06-27derivations: <derivation-input> now aggregates a <derivation>.Ludovic Courtès
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>.
2019-06-27graph: Use 'derivation-input-derivation'.Ludovic Courtès
* guix/scripts/graph.scm (derivation-dependencies): Use 'derivation-input-derivation'.
2019-06-27ui: 'show-what-to-build' uses 'derivation-build-plan'.Ludovic Courtès
* 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.
2019-06-27derivations: Rewrite and replace 'derivations-prerequisites-to-build'.Ludovic Courtès
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.
2019-06-27derivations: Add 'derivation-input'.Ludovic Courtès
* guix/derivations.scm (derivation-input): New procedure. * tests/grafts.scm (make-derivation-input): Remove. ("graft-derivation, unused outputs not depended on"): Use 'derivation-input'.
2019-06-27ui: Add 'display-search-results' and use it.Ludovic Courtès
* 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'.
2019-06-27syscalls: Add 'terminal-rows'.Ludovic Courtès
* 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.
2019-06-27ui: 'relevance' considers regexps connected with a logical and.Ludovic Courtès
* guix/ui.scm (relevance)[score]: Change to return 0 when one of REGEXPS doesn't match. * tests/ui.scm ("package-relevance"): New test.
2019-06-27accounts: Use 'fsync' instead of 'fdatasync'.Ludovic Courtès
* gnu/build/accounts.scm (catch-ENOSYS): Remove. (database-writer): Use 'fsync' instead of 'fdatasync'.
2019-06-27gnu: dosbox: Update to 0.74-3.Rutger Helling
* gnu/packages/emulators.scm (dosbox): Update to 0.74-3.
2019-06-27gnu: rep-gtk: Update to 0.90.8.3.Arun Isaac
* 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.
2019-06-27gnu: sawfish: Update to 1.12.0.Benjamin Slade
* 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>
2019-06-26gnu: electron-cash: Update to 4.0.7.Vagrant Cascadian
* gnu/packages/finance (electron-cash): Update to 4.0.7.
2019-06-27Revert "gnu: openssh: Don't create the PRIVSEP_PATH directory."Tobias Geerinckx-Rice
This reverts commit 46475f72ab6127e7818fdea4a0ea9cc07c60a5f4.
2019-06-27Revert "gnu: openssh: Clean-up custom install phase."Tobias Geerinckx-Rice
This reverts commit 7754136e464e02284624ad05c196d9ec26099143.
2019-06-26gnu: supertux: Fix homepage.Nicolas Goaziou
* gnu/packages/games.scm (supertux)[homepage]: Fix URL.
2019-06-26gnu: Add texmacs.Andreas Enge
* gnu/packages/text-editors.scm (texmacs): New variable.
2019-06-26gnu: python-pathpy: Update to 11.5.0.Ricardo Wurmus
* 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.
2019-06-26gnu: Add python-jaraco-packaging.Ricardo Wurmus
* gnu/packages/python-xyz.scm (python-jaraco-packaging): New variable.
2019-06-26gnu: Add python-pytest-virtualenv.Ricardo Wurmus
* gnu/packages/python-check.scm (python-pytest-virtualenv): New variable.
2019-06-26gnu: Add python-pytest-fixture-config.Ricardo Wurmus
* gnu/packages/python-check.scm (python-pytest-fixture-config): New variable.
2019-06-26gnu: Add python-pytest-shutil.Ricardo Wurmus
* gnu/packages/python-check.scm (python-pytest-shutil): New variable.
2019-06-26gnu: Add python-pytest-flake8.Ricardo Wurmus
* gnu/packages/python-check.scm (python-pytest-flake8): New variable.
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