[Top][All Lists]

[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]

branch core-updates updated (1badc85 -> 55174e6)

From: Marius Bakke
Subject: branch core-updates updated (1badc85 -> 55174e6)
Date: Wed, 7 Nov 2018 15:13:09 -0500 (EST)

mbakke pushed a change to branch core-updates
in repository guix.

      from  1badc85   gnu: ceph: Update to 13.2.2.
      adds  7082873   bash completion: Restore completion of available packages 
for 'guix build'.
      adds  5f7dd09   pull: Make '--dry-run' behave as expected.
      adds  cbe7387   self: Remove extra paren in manual version string.
      adds  aa919fb   maint: Move substitute public keys to etc/substitutes.
      adds  8d3beb3   self: Install substitute keys.
      adds  2e4d833   ssh: Honor the SOCKET-NAME argument of 
      adds  7f860a8   gnu: services: dns: Fix 'ddclient-activation'.
      adds  b588adc   gnu: c-ares: Update to 1.15.0.
      adds  730e5fb   Revert "gnu: c-ares: Update to 1.15.0."
      adds  c58f3eb   gnu: ffmpeg: Update to 4.1.
      adds  418dd6a   gnu: jq: Update to 1.6.
      adds  c3b8300   gnu: jq: Don't use NAME in source URI.
      adds  b1eeeb8   gnu: terraform-docs: Update to 0.5.0.
      adds  fe4fb27   gnu: youtube-dl: Update to 2018.11.03.
      adds  cddc030   gnu: Add r-weights.
      adds  3527f60   gnu: guile-sqlite3: Update home page.
      adds  6cf502d   self: Rename 'sub-directory' to 'file-append*'.
      adds  a2f9920   nls: Update 'de' translation.
      adds  e374477   self: Install shell completion files.
      adds  158c02d   gnu: Add xcb-util-errors.
      adds  4cceb14   gnu: libgit2: Work around test failures on 32-bit 
      adds  f256142   gnu: Syncthing: Update to 0.14.52.
      adds  9da4848   guix: Update to Bioconductor 3.8.
      adds  c6b05ba   gnu: nginx: Update to 1.14.1 [security fixes].
      adds  ec4c81f   pack: Move store database creation to a separate 
      adds  b27ef1d   pack: Import (guix store database) only when 
'--localstatedir' is passed.
      adds  c5ce2db   install: Add 'install-database-and-gc-roots'.
      adds  f5a2fb1   pack: Docker backend now honors '--localstatedir'.
      adds  598a6b8   pack: Squashfs backend now honors '--localstatedir'.
      adds  1ff5378   pack: Add test for 'self-contained-tarball' with 
      adds  72dc64f   store-copy: Canonicalize the mtime and permissions of the 
store copy.
      adds  b07014f   pack: Add test for '--relocatable'.
      adds  b20aef9   gnu: GnuPG: Update to 2.2.11.
      adds  02e2133   gnu: LibreOffice: Update to
      adds  cbb5d2e   gnu: kodi: Fix typo.
      adds  581720b   gnu: Add guile-newt.
      adds  f4e8bc5   services: kmscon: Do not switch to vt at start.
      adds  2d9dace   services: kmscon: Add an auto-login option.
      adds  a7903ca   gnu: terminals: Change libtsm and kmscon repositories.
      adds  8243f4e   gnu: slang: Use a correct location for terminfo dirs.
      adds  bfa5662   gnu: Add r-rcppannoy.
      adds  b58940c   gnu: Add r-ncdf4.
      adds  1e605c0   gnu: Add r-biocmanager.
      adds  61686921  gnu: r-hpar: Update to 1.24.0.
      adds  9865256   gnu: r-diffbind: Update to 2.10.0.
      adds  f1c606c   gnu: r-marray: Update to 1.60.0.
      adds  46cdcee   gnu: r-cghbase: Update to 1.42.0.
      adds  9add093   gnu: r-cghcall: Update to 2.44.0.
      adds  a92f523   gnu: r-qdnaseq: Update to 1.18.0.
      adds  95ee4a4   gnu: r-multtest: Update to 2.38.0.
      adds  14520b6   gnu: r-graph: Update to 1.60.0.
      adds  57d2fcd   gnu: r-chippeakanno: Update to 3.16.0.
      adds  4728e27   gnu: r-bayseq: Update to 2.16.0.
      adds  aa802ea   gnu: r-chipcomp: Update to 1.12.0.
      adds  e9427b2   gnu: r-ripseeker: Update to 1.22.0.
      adds  e22e462   gnu: r-riboprofiling: Update to 1.12.0.
      adds  c4fed65   gnu: r-riboseqr: Update to 1.16.0.
      adds  bbc4787   gnu: r-interactionset: Update to 1.10.0.
      adds  5f2d0e6   gnu: r-genomicinteractions: Update to 1.16.0.
      adds  b858338   gnu: r-ctc: Update to 1.56.0.
      adds  6ea9ae9   gnu: r-goseq: Update to 1.34.0.
      adds  016afac   gnu: r-glimma: Update to 1.10.0.
      adds  c348cfe   gnu: r-rots: Update to 1.10.0.
      adds  6f1e1d0   gnu: r-inspect: Update to 1.12.0.
      adds  318bcbc   gnu: r-dnabarcodes: Update to 1.12.0.
      adds  286157d   gnu: Add r-biocneighbors.
      adds  ed35d7c   gnu: r-ruvseq: Update to 1.16.0.
      adds  d639d88   gnu: r-regioner: Update to 1.14.0.
      adds  bb47aca   gnu: Add hdf5-1.10.
      adds  269182b   gnu: r-rgraphviz: Update to 2.26.0.
      adds  0dd84df   gnu: r-ps: Update to 1.2.1.
      adds  65dd0e6   gnu: r-pkgload: Update to 1.0.2.
      adds  ec0ee08   gnu: r-ffbase: Update to 0.12.7.
      adds  56af171   gnu: r-ipred: Update to 0.9-8.
      adds  5d986a3   gnu: r-psych: Update to 1.8.10.
      adds  cea8a60   gnu: r-xts: Update to 0.11-2.
      adds  84d0d86   gnu: r-sjmisc: Update to 2.7.6.
      adds  244a5c4   gnu: r-flextable: Update to 0.4.6.
      adds  3d6fa1a   gnu: r-sessioninfo: Update to 1.1.1.
      adds  fc532b4   gnu: r-remotes: Update to 2.0.2.
      adds  7466c3b   gnu: r-rcmdcheck: Update to 1.3.1.
      adds  a44f8b0   gnu: r-pander: Update to 0.6.3.
      adds  600a25e   gnu: r-mass: Update to 7.3-51.1.
      adds  1966d8f   gnu: r-lattice: Update to 0.20-38.
      adds  83ca17d   gnu: r-matrix: Update to 1.2-15.
      adds  0de3ebb   gnu: r-survival: Update to 2.43-1.
      adds  9094eb8   gnu: r-roxygen2: Update to 6.1.1.
      adds  466397c   gnu: r-dt: Update to 0.5.
      adds  1b35523   gnu: r-tidyr: Update to 0.8.2.
      adds  9bd7848   gnu: r-preprocesscore: Update to 1.44.0.
      adds  00281ea   gnu: r-modelmetrics: Update to 1.2.2.
      adds  090d4c0   gnu: r-annotate: Update to 1.60.0.
      adds  dadd682   gnu: r-copynumber: Update to 1.22.0.
      adds  f4a95a0   gnu: r-geneplotter: Update to 1.60.0.
      adds  85fb33a   gnu: r-genefilter: Update to 1.64.0.
      adds  b5c552e   gnu: r-deseq2: Update to 1.22.1.
      adds  856444a   gnu: r-dexseq: Update to 1.28.0.
      adds  2ff6604   gnu: r-annotationforge: Update to 1.24.0.
      adds  19a6149   gnu: r-rbgl: Update to 1.58.0.
      adds  6dfb0b2   gnu: r-gseabase: Update to 1.44.0.
      adds  95ae5ac   gnu: r-category: Update to 2.48.0.
      adds  4a4b5b8   gnu: r-gostats: Update to 2.48.0.
      adds  9adf78c   gnu: r-shortread: Update to 1.40.0.
      adds  bf25930   gnu: r-systempiper: Update to 1.16.0.
      adds  5c996ca   gnu: r-grohmm: Update to 1.16.0.
      adds  2f28ffd   gnu: r-biocgenerics: Update to 0.28.0.
      adds  36d7d82   gnu: r-biocinstaller: Update to 1.32.1.
      adds  c8dbb5f   gnu: r-biocviews: Update to 1.50.1.
      adds  6087f5c   gnu: r-biocstyle: Update to 2.10.0.
      adds  a127d35   gnu: r-bioccheck: Update to 1.18.0.
      adds  70f2758   gnu: r-dnacopy: Update to 1.56.0.
      adds  a037453   gnu: r-s4vectors: Update to 0.20.0.
      adds  9a8dd51   gnu: r-iranges: Update to 2.16.0.
      adds  1287169   gnu: r-genomeinfodb: Update to 1.18.0.
      adds  08cd2d5   gnu: r-edger: Update to 3.24.0.
      adds  ca2945c   gnu: r-variantannotation: Update to 1.28.1.
      adds  78d2ffd   gnu: r-limma: Update to 3.38.2.
      adds  fb10fb7   gnu: r-xvector: Update to 0.22.0.
      adds  8d3906a   gnu: r-genomicranges: Update to 1.34.0.
      adds  5b82e12   gnu: r-biobase: Update to 2.42.0.
      adds  3986e0d   gnu: r-annotationdbi: Update to 1.44.0.
      adds  3359d44   gnu: r-biomart: Update to 2.38.0.
      adds  cd88289   gnu: r-biocparallel: Update to 1.16.0.
      adds  4804c59   gnu: r-biostrings: Update to 2.50.0.
      adds  7f3778e   gnu: r-rsamtools: Update to 1.34.0.
      adds  de4c38f   gnu: r-delayedarray: Update to 0.8.0.
      adds  9fd4350   gnu: r-summarizedexperiment: Update to 1.12.0.
      adds  52b9533   gnu: r-genomicalignments: Update to 1.18.0.
      adds  c5f1d1c   gnu: r-rtracklayer: Update to 1.42.0.
      adds  8a0d57d   gnu: r-genomicfeatures: Update to 1.34.1.
      adds  44fa14d   gnu: r-topgo: Update to 2.34.0.
      adds  78ecdbc   gnu: r-bsgenome: Update to 1.50.0.
      adds  d11bc25   gnu: r-impute: Update to 1.56.0.
      adds  45ba2ca   gnu: r-seqpattern: Update to 1.14.0.
      adds  c5b0815   gnu: r-genomation: Update to 1.14.0.
      adds  34f1c60   gnu: r-seqlogo: Update to 1.48.0.
      adds  2919fef   gnu: r-motifrg: Update to 1.26.0.
      adds  7d7c702   gnu: r-zlibbioc: Update to 1.28.0.
      adds  4819689   gnu: r-rhtslib: Update to 1.14.0.
      adds  338f860   gnu: r-bamsignals: Update to 1.14.0.
      adds  ad90921   gnu: r-mutationalpatterns: Update to 1.8.0.
      adds  d2b60be   gnu: r-tximport: Update to 1.10.0.
      adds  cec8f09   gnu: r-annotationfilter: Update to 1.6.0.
      adds  2e9d811   gnu: r-chipseq: Update to 1.32.0.
      adds  739a856   gnu: r-copywriter: Update to 2.14.0.
      adds  18604a7   gnu: r-methylkit: Update to 1.8.0.
      adds  8af8688   gnu: r-sva: Update to 3.30.0.
      adds  691ce09   gnu: r-protgenerics: Update to 1.14.0.
      adds  511abd7   gnu: r-affyio: Update to 1.52.0.
      adds  2b08548   gnu: r-affy: Update to 1.60.0.
      adds  0e16fc4   gnu: r-vsn: Update to 3.50.0.
      adds  2c4311d   gnu: r-mzid: Update to 1.20.0.
      adds  73d7475   gnu: r-pcamethods: Update to 1.74.0.
      adds  762aca7   gnu: r-msnbase: Update to 2.8.0.
      adds  675d91a   gnu: r-msnid: Update to 1.16.0.
      adds  800954e   gnu: r-aroma-light: Update to 3.12.0.
      adds  7812e6b   gnu: r-deseq: Update to 1.34.0.
      adds  b03951f   gnu: r-edaseq: Update to 2.16.0.
      adds  d7ea34b   gnu: r-interactivedisplaybase: Update to 1.20.0.
      adds  147633d   gnu: r-annotationhub: Update to 2.14.1.
      adds  95df764   gnu: r-fastseg: Update to 1.28.0.
      adds  4984212   gnu: r-keggrest: Update to 1.22.0.
      adds  122e099   gnu: r-gage: Update to 2.32.0.
      adds  d78c6ac   gnu: r-genomicfiles: Update to 1.18.0.
      adds  5ae5a8e   gnu: r-complexheatmap: Update to 1.20.0.
      adds  0c96e4b   gnu: r-dirichletmultinomial: Update to 1.24.0.
      adds  e8e78c4   gnu: r-ensembldb: Update to 2.6.0.
      adds  cdab2dc   gnu: r-organismdbi: Update to 1.24.0.
      adds  e7a0bc1   gnu: r-biovizbase: Update to 1.30.0.
      adds  f20c766   gnu: r-ggbio: Update to 1.30.0.
      adds  181a843   gnu: r-gqtlbase: Update to 1.14.0.
      adds  220ac15   gnu: r-snpstats: Update to 1.32.0.
      adds  4b91335   gnu: r-erma: Update to 0.14.0.
      adds  da679b5   gnu: r-ldblock: Update to 1.12.0.
      adds  ea55326   gnu: r-gqtlstats: Update to 1.14.0.
      adds  d57445c   gnu: r-gviz: Update to 1.26.0.
      adds  85b16c0   gnu: r-gwascat: Update to 2.14.0.
      adds  7468a76   gnu: r-sushi: Update to 1.20.0.
      adds  8023912   gnu: r-fithic: Update to 1.8.0.
      adds  d055f19   gnu: r-hitc: Update to 1.26.0.
      adds  edb9124   gnu: r-qvalue: Update to 2.14.0.
      adds  3c83360   gnu: r-beachmat: Update to 1.4.0.
      adds  f93ec63   gnu: r-singlecellexperiment: Update to 1.4.0.
      adds  48f2791   gnu: r-scater: Update to 1.10.0.
      adds  70a3a76   gnu: r-scran: Update to 1.10.1.
      adds  900ce2b   gnu: r-delayedmatrixstats: Update to 1.4.0.
      adds  a1c2bf8   gnu: r-rcas: Update to 1.8.0.
      adds  611a255   gnu: r-rhdf5: Update to 2.26.0.
      adds  8e48d36   gnu: r-hdf5array: Update to 1.10.0.
      adds  37200db   gnu: r-rhdf5lib: Update to 1.4.0.
      adds  9255198   gnu: r-mzr: Update to 2.16.0.
      adds  970c999   linux-initrd: Make sure 'build-initrd' can delete files.
      adds  0875982   gnu: cuirass: Update to 0b40dca.
      adds  dcb4512   services: cuirass: Add 'ttl' configuration field.
      adds  fff67cc   gnu: prodigal: Fetch sources from git.
      adds  21335fd   gnu: ngless: Install links to required tools.
      adds  8e58319   gnu: bamtools: Fetch sources from git.
      adds  20ee3e8   gnu: bedtools-2.18: Fetch sources from stable URL.
      adds  383cb7b   gnu: bioawk: Fetch sources from git.
      adds  007a81d   gnu: python-biom-format: Fetch source from git.
      adds  239716f   gnu: python-biom-format: Update to 2.1.7.
      adds  7ca49ab   gnu: ribodiff: Fetch sources from git.
      adds  91b71cf   gnu: fxtract: Fetch sources from git.
      adds  f09e8ab   gnu: clementine: Build with sqlite-with-column-metadata.
      adds  b113f39   gnu: gemma: Fetch sources from git.
      adds  152bebd   gnu: gemma: Update to 0.98.
      adds  8d75adb   gnu: grit: Fetch sources from git.
      adds  c8f02c1   gnu: grit: Update to 2.0.5.
      adds  57be690   gnu: hisat2: Use versioned source URL.
      adds  b8a6230   gnu: java-htsjdk: Fetch sources from git.
      adds  f073159   gnu: idr: Fetch sources from git.
      adds  6fe323b   gnu: kaiju: Fetch sources from git.
      adds  2dc2839   gnu: kaiju: Update to 1.6.3.
      adds  b31e156   gnu: fio: Update to 3.11.
       new  55174e6   Merge branch 'master' into core-updates

The 1 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.

Summary of changes:                                        |   5 +-
 doc/guix.texi                                      |  22 +-
 etc/completion/bash/guix                           |   4 +-
 .../substitutes/              |   0
 .../substitutes/                  |   0
 gnu/build/install.scm                              |  77 +--
 gnu/build/linux-initrd.scm                         |   8 +-
 gnu/build/vm.scm                                   |  19 +-
 gnu/                                       |   3 +-
 gnu/packages/benchmark.scm                         |   6 +-
 gnu/packages/bioconductor.scm                      | 134 ++--
 gnu/packages/bioinformatics.scm                    | 761 +++++++++++----------
 gnu/packages/ci.scm                                |   6 +-
 gnu/packages/cran.scm                              | 156 ++++-
 gnu/packages/gnupg.scm                             |   4 +-
 gnu/packages/graph.scm                             |   4 +-
 gnu/packages/guile.scm                             |  40 +-
 gnu/packages/kodi.scm                              |   4 +-
 gnu/packages/libreoffice.scm                       |   4 +-
 gnu/packages/maths.scm                             |  19 +
 gnu/packages/music.scm                             |   2 +-
 gnu/packages/patches/gemma-intel-compat.patch      |  44 --
 gnu/packages/patches/jq-CVE-2015-8863.patch        |  45 --
 gnu/packages/patches/libgit2-oom-test.patch        |  62 ++
 gnu/packages/slang.scm                             |  14 +-
 gnu/packages/statistics.scm                        |  39 +-
 gnu/packages/syncthing.scm                         |   4 +-
 gnu/packages/terminals.scm                         | 178 ++---
 gnu/packages/terraform.scm                         |  11 +-
 gnu/packages/version-control.scm                   |   3 +-
 gnu/packages/video.scm                             |   8 +-
 gnu/packages/web.scm                               |  18 +-
 gnu/packages/xorg.scm                              |  52 ++
 gnu/services/base.scm                              |  11 +-
 gnu/services/cuirass.scm                           |   6 +-
 gnu/services/dns.scm                               |   4 +-
 guix/build-system/r.scm                            |   2 +-
 guix/build/store-copy.scm                          |  28 +
 guix/docker.scm                                    |  16 +-
 guix/import/cran.scm                               |   4 +-
 guix/scripts/pack.scm                              | 415 ++++++-----
 guix/scripts/pull.scm                              |  17 +-
 guix/self.scm                                      |  47 +-
 guix/ssh.scm                                       |   2 +-
 po/guix/de.po                                      |  20 +-
 tests/                     |  61 ++
 tests/                                 |  28 +-
 tests/pack.scm                                     | 156 ++++-
 48 files changed, 1594 insertions(+), 979 deletions(-)
 rename => etc/substitutes/ (100%)
 rename => etc/substitutes/ (100%)
 delete mode 100644 gnu/packages/patches/gemma-intel-compat.patch
 delete mode 100644 gnu/packages/patches/jq-CVE-2015-8863.patch
 create mode 100644 gnu/packages/patches/libgit2-oom-test.patch
 create mode 100644 tests/

reply via email to

[Prev in Thread] Current Thread [Next in Thread]