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2018-09-05gnu: r-diffusionmap: Update to 1.1-0.1.Ricardo Wurmus
* gnu/packages/graph.scm (r-diffusionmap): Update to 1.1-0.1.
2018-09-05gnu: r-seurat: Update to 2.3.4.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-seurat): Update to 2.3.4. [source]: Remove snippet. [arguments]: Remove. [native-inputs]: Remove. [propagated-inputs]: Remove r-caret, r-diffusionmap, r-fnn, r-gdata, r-ranger, r-stringr, r-tclust, and rvgam; add r-httr.
2018-09-05gnu: r-msnbase: Update to 2.6.3.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-msnbase): Update to 2.6.3.
2018-09-05gnu: r-maldiquant: Update to 1.18.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-maldiquant): Update to 1.18.
2018-09-05gnu: r-seqminer: Update to 6.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-seqminer): Update to 6.1.
2018-09-05gnu: r-genomicfeatures: Update to 1.32.2.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.32.2.
2018-09-05gnu: r-rtracklayer: Update to 1.40.6.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.40.6.
2018-09-05gnu: r-delayedarray: Update to 0.6.5.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-delayedarray): Update to 0.6.5.
2018-09-05gnu: r-rsamtools: Update to 1.32.3.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-rsamtools): Update to 1.32.3.
2018-09-05gnu: r-biocparallel: Update to 1.14.2.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.14.2.
2018-09-05gnu: r-genomicranges: Update to 1.32.6.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.32.6.
2018-09-05gnu: r-limma: Update to 3.36.3.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-limma): Update to 3.36.3.
2018-09-05gnu: r-variantannotation: Update to 1.26.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.26.1.
2018-09-05gnu: r-edger: Update to 3.22.3.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-edger): Update to 3.22.3.
2018-09-05gnu: r-iranges: Update to 2.14.11.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-iranges): Update to 2.14.11.
2018-09-05gnu: r-biocviews: Update to 1.48.3.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-biocviews): Update to 1.48.3.
2018-09-05gnu: r-annotationforge: Update to 1.22.2.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-annotationforge): Update to 1.22.2.
2018-09-05gnu: r-chippeakanno: Update to 3.14.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-chippeakanno): Update to 3.14.1.
2018-09-05gnu: Add r-clipr.Ricardo Wurmus
* gnu/packages/cran.scm (r-clipr): New variable.
2018-09-05gnu: Add r-rdpack.Ricardo Wurmus
* gnu/packages/cran.scm (r-rdpack): New variable.
2018-09-05gnu: Add r-gbrd.Ricardo Wurmus
* gnu/packages/cran.scm (r-gbrd): New variable.
2018-09-05gnu: Add r-polynom.Ricardo Wurmus
* gnu/packages/cran.scm (r-polynom): New variable.
2018-09-05gnu: Add r-fansi.Ricardo Wurmus
* gnu/packages/cran.scm (r-fansi): New variable.
2018-09-05gnu: guix-daemon: Add dependency on Guile-Gcrypt.Ludovic Courtès
This is a followup to 53166aec987957efba917c83f093817d6cf6e943, which made Guile-Gcrypt a hard dependency. * gnu/packages/package-management.scm (guix-daemon)[inputs]: Add GUILE-GCRYPT.
2018-09-05gnu: cuirass: Add dependency on Guile-Gcrypt.Ludovic Courtès
This is a followup to 53166aec987957efba917c83f093817d6cf6e943, which added a hard dependency of Guix on Guile-Gcrypt. * gnu/packages/ci.scm (cuirass)[inputs]: Add GUILE-GCRYPT. [arguments]: In 'wrap-program' phase, use 'string-join' to compute 'mods'. Define 'objs' for use in GUILE_LOAD_COMPILED_PATH, and take objects from lib/guile/X.Y/site-ccache.
2018-09-05gnu: guile-fibers: Install .go files to "…/site-ccache".Ludovic Courtès
* gnu/packages/guile.scm (guile-fibers)[arguments]: New field.
2018-09-05slepc: Upgrade to 3.9.2.Eric Bavier
* gnu/packages/maths.scm (slepc): Upgrade to 3.9.2.
2018-09-05petsc: Upgrade to 3.9.3.Eric Bavier
* gnu/packages/maths.scm (petsc): Upgrade to 3.9.3. [arguments]: Remove unnecessary configure flags.
2018-09-05petsc: Move example code to "examples" output.Eric Bavier
* gnu/packages/maths.scm (petsc)[arguments]: New 'move-examples' phase.
2018-09-05gnu: Add SUNDIALS.Eric Bavier
* gnu/packages/maths.scm (sundials, sundials-openmpi): New variables.
2018-09-05gnu: packages: mp3: Use HTTPS where possible.Alex Vong
* gnu/packages/mp3.scm (libmad)[home-page]: Use HTTPS. (libid3tag)[home-page]: Likewise. (mp3info)[source, home-page]: Likewise. (mpg123)[source]: Likewise. (libmpcdec)[source, home-page]: Likewise. Signed-off-by: 宋文武 <iyzsong@member.fsf.org>
2018-09-05gnu: eyed3: Update home page.Alex Vong
* gnu/packages/mp3.scm (eyed3)[home-page]: Update to redirected HTTPS URL. Signed-off-by: 宋文武 <iyzsong@member.fsf.org>
2018-09-05gnu: guix: Update to 3d43017.Ludovic Courtès
* gnu/packages/package-management.scm (guix): Update to 3d43017.
2018-09-05tests: Adjust 'add-file-tree-to-store' test for lack of /bin/sh.Ludovic Courtès
* tests/store.scm (%shell): New variable. ("add-file-tree-to-store"): Use it instead of "/bin/sh". This fixes builds in the chroot build environment.
2018-09-05gnu: xorg: Fix typo.Ludovic Courtès
* gnu/packages/xorg.scm: Fix typo in Benjamin's email address.
2018-09-05channels: Add 'latest-channel-derivation' convenience procedure.Ludovic Courtès
* guix/channels.scm (latest-channel-derivations): Remove. (latest-channel-instances*, latest-channel-derivation): New procedures.
2018-09-05gnu: python-tables: Update to 3.4.4.Ricardo Wurmus
* gnu/packages/python.scm (python-tables): Update to 3.4.4.
2018-09-05gnu: python-pybigwig: Update to 0.3.12.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-pybigwig): Update to 0.3.12. [propagated-inputs]: Add python-numpy.
2018-09-05gnu: libbigwig: Update to 0.4.2.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (libbigwig): Update to 0.4.2. [source]: Fetch from git. [arguments]: Disable tests; remove build phases "disable-curl-test" and "create-target-dirs". [native-inputs]: Add python-2.
2018-09-05gnu: nss-pam-ldapd: Update to 0.9.10.Ricardo Wurmus
* gnu/packages/openldap.scm (nss-pam-ldapd): Update to 0.9.10.
2018-09-05gnu: dolphin-emu: Update to commit 5f0d825.Rutger Helling
* gnu/packages/emulators.scm (dolphin-emu): Update to commit 5f0d825.
2018-09-04gnu: Zsh: Patch some tests that began failing in 5.6.Leo Famulari
* gnu/packages/shells.scm (zsh)[arguments]: Patch the tests rather than deleting them.
2018-09-04gnu: Zsh: Update to 5.6 [fixes CVE-2018-{0502,13259}].Leo Famulari
* gnu/packages/shells.scm (zsh): Update to 5.6. [arguments]: Skip some tests.
2018-09-04Switch to Guile-Gcrypt.Ludovic Courtès
This removes (guix hash) and (guix pk-crypto), which now live as part of Guile-Gcrypt (version 0.1.0.) * guix/gcrypt.scm, guix/hash.scm, guix/pk-crypto.scm, tests/hash.scm, tests/pk-crypto.scm: Remove. * configure.ac: Test for Guile-Gcrypt. Remove LIBGCRYPT and LIBGCRYPT_LIBDIR assignments. * m4/guix.m4 (GUIX_ASSERT_LIBGCRYPT_USABLE): Remove. * README: Add Guile-Gcrypt to the dependencies; move libgcrypt as "required unless --disable-daemon". * doc/guix.texi (Requirements): Likewise. * gnu/packages/bash.scm, guix/derivations.scm, guix/docker.scm, guix/git.scm, guix/http-client.scm, guix/import/cpan.scm, guix/import/cran.scm, guix/import/crate.scm, guix/import/elpa.scm, guix/import/gnu.scm, guix/import/hackage.scm, guix/import/texlive.scm, guix/import/utils.scm, guix/nar.scm, guix/pki.scm, guix/scripts/archive.scm, guix/scripts/authenticate.scm, guix/scripts/download.scm, guix/scripts/hash.scm, guix/scripts/pack.scm, guix/scripts/publish.scm, guix/scripts/refresh.scm, guix/scripts/substitute.scm, guix/store.scm, guix/store/deduplication.scm, guix/tests.scm, tests/base32.scm, tests/builders.scm, tests/challenge.scm, tests/cpan.scm, tests/crate.scm, tests/derivations.scm, tests/gem.scm, tests/nar.scm, tests/opam.scm, tests/pki.scm, tests/publish.scm, tests/pypi.scm, tests/store-deduplication.scm, tests/store.scm, tests/substitute.scm: Adjust imports. * gnu/system/vm.scm: Likewise. (guile-sqlite3&co): Rename to... (gcrypt-sqlite3&co): ... this. Add GUILE-GCRYPT. (expression->derivation-in-linux-vm)[config]: Remove. (iso9660-image)[config]: Remove. (qemu-image)[config]: Remove. (system-docker-image)[config]: Remove. * guix/scripts/pack.scm: Adjust imports. (guile-sqlite3&co): Rename to... (gcrypt-sqlite3&co): ... this. Add GUILE-GCRYPT. (self-contained-tarball)[build]: Call 'make-config.scm' without #:libgcrypt argument. (squashfs-image)[libgcrypt]: Remove. [build]: Call 'make-config.scm' without #:libgcrypt. (docker-image)[config, json]: Remove. [build]: Add GUILE-GCRYPT to the extensions Remove (guix config) from the imported modules. * guix/self.scm (specification->package): Remove "libgcrypt", add "guile-gcrypt". (compiled-guix): Remove #:libgcrypt. [guile-gcrypt]: New variable. [dependencies]: Add it. [*core-modules*]: Remove #:libgcrypt from 'make-config.scm' call. Add #:extensions. [*config*]: Remove #:libgcrypt from 'make-config.scm' call. (%dependency-variables): Remove %libgcrypt. (make-config.scm): Remove #:libgcrypt. * build-aux/build-self.scm (guile-gcrypt): New variable. (make-config.scm): Remove #:libgcrypt. (build-program)[fake-gcrypt-hash]: New variable. Add (gcrypt hash) to the imported modules. Adjust load path assignments. * gnu/packages/package-management.scm (guix)[propagated-inputs]: Add GUILE-GCRYPT. [arguments]: In 'wrap-program' phase, add GUILE-GCRYPT to the search path.
2018-09-04inferior: Add home-page and location package accessors.Ludovic Courtès
* guix/inferior.scm (inferior-package-home-page) (inferior-package-location): New procedures. * tests/inferior.scm ("inferior-packages"): Test them.
2018-09-04gnu: Add emacs-picpocket.Alex Vong
* gnu/packages/emacs.scm (emacs-picpocket): New public variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2018-09-04gnu: petsc-openmpi: Configure with support for hdf5 data format.Paul Garlick
* gnu/packages/maths.scm (petsc-openmpi)[inputs]: Add hdf5-parallel-openmpi. [arguments]: Add '--with-hdf5-include' and '--with-hdf5-lib' flags. Add 'set-test-environment' phase. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2018-09-04gnu: kicad: Update to 5.0.0.Jonathan Brielmaier
* gnu/packages/engineering.scm (kicad): Update to 5.0.0. [source]: Change from git to url-fetch. [arguments]: Remove now unneeded build version parameter. [inputs]: Add opencascade-oce. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2018-09-04gnu: ghc-zlib: Enable tests.Arun Isaac
* gnu/packages/haskell.scm (ghc-zlib)[arguments]: Enable tests. Allow building with newer tasty. [native-inputs]: Add ghc-quickcheck, ghc-tasty, ghc-tasty-hunit and ghc-tasty-quickcheck.
2018-09-04gnu: ghc-integer-logarithms: Allow building with newer tasty.Arun Isaac
* gnu/packages/haskell.scm (ghc-integer-logarithms)[arguments]: Allow building with newer tasty.
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