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2018-09-05gnu: r-httpuv: Update to 1.4.5.Ricardo Wurmus
* gnu/packages/web.scm (r-httpuv): Update to 1.4.5. [native-inputs]: Add pkg-config.
2018-09-05gnu: r-scran: Update to 1.8.4.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-scran): Update to 1.8.4.
2018-09-05gnu: r-scater: Update to 1.8.4.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-scater): Update to 1.8.4.
2018-09-05gnu: r-hdf5array: Update to 1.8.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-hdf5array): Update to 1.8.1.
2018-09-05gnu: r-ggbio: Update to 1.28.5.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-ggbio): Update to 1.28.5. [propagated-inputs]: Add r-rlang.
2018-09-05gnu: r-biovizbase: Update to 1.28.2.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-biovizbase): Update to 1.28.2. [propagated-inputs]: Add r-rlang.
2018-09-05gnu: r-keggrest: Update to 1.20.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-keggrest): Update to 1.20.1.
2018-09-05gnu: r-edaseq: Update to 2.14.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-edaseq): Update to 2.14.1.
2018-09-05gnu: r-igraph: Update to 1.2.2.Ricardo Wurmus
* gnu/packages/graph.scm (r-igraph): Update to 1.2.2.
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.
2018-09-05gnu: xorg: Fix typo.Ludovic Courtès
* gnu/packages/xorg.scm: Fix typo in Benjamin's email address.
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.
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