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2018-06-02gnu: r-shortread: Update to 1.38.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-shortread): Update to 1.38.0.
2018-06-02gnu: r-gostats: Update to 2.46.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-gostats): Update to 2.46.0.
2018-06-02gnu: r-category: Update to 2.46.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-category): Update to 2.46.0.
2018-06-02gnu: r-gseabase: Update to 1.42.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-gseabase): Update to 1.42.0.
2018-06-02gnu: r-rbgl: Update to 1.56.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-rbgl): Update to 1.56.0.
2018-06-02gnu: r-annotationforge: Update to 1.22.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-annotationforge): Update to 1.22.0.
2018-06-02gnu: r-dexseq: Update to 1.26.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-dexseq): Update to 1.26.0.
2018-06-02gnu: r-deseq2: Update to 1.20.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-deseq2): Update to 1.20.0.
2018-06-02gnu: r-genefilter: Update to 1.62.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-genefilter): Update to 1.62.0.
2018-06-02gnu: r-geneplotter: Update to 1.58.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-geneplotter): Update to 1.58.0.
2018-06-02gnu: r-copynumber: Update to 1.20.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-copynumber): Update to 1.20.0.
2018-06-02gnu: r-annotate: Update to 1.58.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-annotate): Update to 1.58.0.
2018-06-02gnu: r-qdnaseq: Update to 1.16.0.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-qdnaseq): Update to 1.16.0. [propagated-inputs]: Add r-biocparallel.
2018-06-02gnu: r-cghcall: Update to 2.42.0.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-cghcall): Update to 2.42.0.
2018-06-02gnu: r-cghbase: Update to 1.40.0.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-cghbase): Update to 1.40.0.
2018-06-02gnu: r-marray: Update to 1.58.0.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-marray): Update to 1.58.0. [propagated-inputs]: Remove r-biobase.
2018-06-02gnu: r-chippeakanno: Update to 3.14.0.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-chippeakanno): Update to 3.14.0. [propagated-inputs]: Add r-biostrings, r-delayedarray, r-genomicranges, r-iranges, and r-s4vectors.
2018-06-02gnu: r-ripseeker: Update to 1.20.0.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-ripseeker): Update to 1.20.0.
2018-06-02gnu: r-diffbind: Update to 2.8.0.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-diffbind): Update to 2.8.0. [propagated-inputs]: Add r-genomicranges, r-ggplot2, and r-summarizedexperiment.
2018-06-02gnu: r-regioner: Update to 1.12.0.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-regioner): Update to 1.12.0. [propagated-inputs]: Add r-s4vectors.
2018-06-02gnu: r-hpar: Update to 1.22.2.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-hpar): Update to 1.22.2.
2018-06-02gnu: r-minimal: Update to 3.5.0.Ricardo Wurmus
* gnu/packages/statistics.scm (r-with-tests): New variable derived from r-minimal; update to 3.5.0. [arguments]: Build recommended packages. (r-minimal): Inherit from r-with-tests. [arguments]: Disable recommended packages and tests.
2018-06-02gnu: emacs-elfeed: Update to 3.0.0.Clément Lassieur
* gnu/packages/emacs.scm (emacs-elfeed): Update to 3.0.0.
2018-06-02self: Include gnu/build/* in the result.Ludovic Courtès
Previously, modules like gnu/build/cross-toolchain.scm or gnu/build/svg.scm were missing from the result. * guix/self.scm (compiled-guix)[*system-modules*]: Add gnu/build/* to #:extra-files. (imported-files)[same-target?]: New procedure. [build]: Call 'delete-duplicates' on FILES.
2018-06-02self: 'compiled-files' builds the given list of files.Ludovic Courtès
* guix/self.scm (compiled-files): Add 'module-files' parameter. [build]: 'process-directory' now honors MODULE-FILES instead of building any '.scm' file it sees. (scheme-node): Adjust accordingly.
2018-06-02self: Improve backtraces for 'imported-files'.Ludovic Courtès
* guix/self.scm (imported-files): Pass #:env-vars.
2018-06-01gnu: icecat: Add more fixes from upstream esr52.Mark H Weaver
* gnu/packages/gnuzilla.scm (icecat)[source]: Add selected fixes from the upstream mozilla-esr52 repository.
2018-06-01self: Show backtraces on more columns.Ludovic Courtès
* guix/self.scm (compiled-modules): Add "COLUMNS" to #:env-vars.
2018-06-01self: Add dependency on guile-gdbm-ffi.Ludovic Courtès
Fixes a regression introduced in 331ac4cc239727992329207ba428b3f26cae91d9 whereby "guile-gdbm-ffi" would now be mandatory. * guix/self.scm (specification->package): Add "guile-gdbm-ffi" and "guile2.0-gdbm-ffi". (compiled-guix)[guile-gdbm-ffi]: New variables. [dependencies]: Add it.
2018-06-01gnu: qtbase: Fix build on older kernels.Ricardo Wurmus
* gnu/packages/qt.scm (qtbase)[arguments]: Add configure flags "-no-feature-getentropy" and "-no-feature-renameat2".
2018-06-01Add (guix store deduplication).Caleb Ristvedt
* guix/store/database.scm (register-path): Add #:deduplicate? and call 'deduplicate' when it's true. (counting-wrapper-port, nar-sha256): Move to... * guix/store/deduplication.scm: ... here. New file. * tests/store-deduplication.scm: New file. * Makefile.am (STORE_MODULES): Add deduplication.scm. (SCM_TESTS) [HAVE_GUILE_SQLITE3]: Add store-deduplication.scm. Co-authored-by: Ludovic Courtès <ludo@gnu.org>
2018-06-01database: 'register-path' resets timestamps.Ludovic Courtès
* guix/store/database.scm (reset-timestamps): New procedure. (register-path): Use it.
2018-06-01Add (gnu store database).Caleb Ristvedt
* guix/config.scm.in (%store-database-directory): New variable. * guix/store/database.scm: New file. * tests/store-database.scm: New file. * Makefile.am (STORE_MODULES): New variable. (MODULES, MODULES_NOT_COMPILED): Adjust accordingly. (SCM_TESTS) [HAVE_GUILE_SQLITE3]: Add tests/store-database.scm. Co-authored-by: Ludovic Courtès <ludo@gnu.org>
2018-06-01build: Check for Guile-SQLite3.Ludovic Courtès
* m4/guix.m4 (GUIX_CHECK_GUILE_SQLITE3): New macro. * configure.ac: Use it and define 'HAVE_GUILE_SQLITE3'. * guix/self.scm (specification->package): Add "guile-sqlite3". (compiled-guix)[guile-sqlite3]: New variable. [dependencies]: Add it.
2018-06-01vm: Use 'with-extensions'.Ludovic Courtès
* gnu/system/vm.scm (system-docker-image)[build]: Use 'with-extensions'. Remove 'add-to-load-path' calls.
2018-06-01profiles: Use 'with-extensions'.Ludovic Courtès
* guix/profiles.scm (manual-database)[build]: Use 'with-extensions'. Remove 'add-to-load-path' call. * guix/man-db.scm: Use (gdbm) the normal way; remove 'module-autoload!' call.
2018-06-01bootloader: grub: Use 'with-extensions'.Ludovic Courtès
* gnu/bootloader/grub.scm (svg->png): Use 'with-extensions'. Remove 'add-to-load-path' calls. * gnu/build/svg.scm: Use (rsvg) and (cairo) the normal way. Remove 'module-autoload!' calls.
2018-06-01bootloader: grub: Simplify 'svg->png'.Ludovic Courtès
* gnu/bootloader/grub.scm (svg->png): Remove now unneeded #:guile-for-build argument.
2018-06-01tests: ssh: Use 'with-extensions'.Ludovic Courtès
* gnu/tests/ssh.scm (run-ssh-test)[test]: Wrap body in 'with-extensions'. Remove %load-path manipulation code.
2018-06-01pack: Use 'with-extensions' when referring to (guix docker).Ludovic Courtès
* guix/docker.scm: Use module (json) the normal way. * guix/scripts/pack.scm (docker-image)[build]: Wrap in 'with-extensions'.
2018-06-01gexp: Add 'with-extensions'.Ludovic Courtès
* guix/gexp.scm (<gexp>)[extensions]: New field. (gexp-attribute): New procedure. (gexp-modules): Write in terms of 'gexp-attribute'. (gexp-extensions): New procedure. (gexp->derivation): Add #:effective-version. [extension-flags]: New procedure. Honor extensions of EXP. (current-imported-extensions): New syntax parameter. (with-extensions): New macro. (gexp): Honor CURRENT-IMPORTED-EXTENSIONS. (compiled-modules): Add #:extensions and honor it. (load-path-expression): Likewise. (gexp->script, gexp->file): Honor extensions. * tests/gexp.scm (%extension-package): New variable. ("gexp-extensions & ungexp") ("gexp-extensions & ungexp-splicing") ("gexp-extensions and literal Scheme object") ("gexp->derivation & with-extensions") ("program-file & with-extensions"): New tests. * doc/guix.texi (G-Expressions): Document 'with-extensions'.
2018-06-01pack: Adjust test to expect relative symlinks.Ludovic Courtès
Reported by Chris Marusich <cmmarusich@gmail.com>. Fixes <https://bugs.gnu.org/31560>. * tests/pack.scm ("self-contained-tarball"): Rename 'guile' to 'bin'. Expect 'bin/Guile' to be a relative symlink.
2018-06-01tests: Fix arguments in pack test.Ricardo Wurmus
This is a follow-up to commit 5ffac538aa604b71814ac74579626f0d3110b96e. * tests/pack.scm (self-contained-tarball): Adjust arguments to "self-contained-tarball".
2018-06-01gexp: 'compiled-modules' no longer overrides (guix build utils).Ludovic Courtès
Until now 'compiled-modules' would override (guix build utils) with its own. Thus, when asked to build a different (guix build utils), via #:module-path, it would fail badly because a (guix build utils) module was already loaded and possibly incompatible with the new one. This happened when running 'guix pull --branch=core-updates' from current master: in 'core-updates', (guix build utils) exports 'ignore-error?' but in 'master' it does not. Thus, 'guix pull' would fail with: no binding `invoke-error?' in module (guix build utils) builder for `/gnu/store/…-module-import-compiled.drv' failed with exit code 1 cannot build derivation `/gnu/store/…-compute-guix-derivation.drv': 1 dependencies couldn't be built This patch fixes it. * guix/gexp.scm (compiled-modules)[build-utils-hack?]: New variable. [build]: Load MODULES/build/utils.scm when it exists.
2018-06-01gnu: rust: Add support for building 32-bit packages on 64-bit hosts.Robin Templeton
* gnu/packages/rust.scm (rust-bootstrap, rust-1.23): Use nix-system->gnu-triplet to determine the system type. (rust-1.19): Use readelf instead of nm in the atomic-lock-free test. (rust-1.23): Disable the cargo_test_env test. Disable parallel execution of tests. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2018-06-01gnu: Add git-annex.Timothy Sample
* gnu/packages/version-control.scm (git-annex): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2018-06-01gnu: Add ghc-disk-free-space.Timothy Sample
* gnu/packages/haskell.scm (ghc-disk-free-space): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2018-06-01gnu: ghc-psqueues: Allow building with newer versions of QuickCheck.Timothy Sample
* gnu/packages/haskell.scm (ghc-psqueues)[arguments]: Add configure flag to allow newer versions of QuickCheck. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2018-06-01gnu: Add ghc-safesemaphore.Timothy Sample
* gnu/packages/haskell.scm (ghc-safesemaphore): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2018-06-01gnu: Add ghc-esqueleto.Timothy Sample
* gnu/packages/haskell.scm (ghc-esqueleto): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
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