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branch core-updates updated (1badc85 -> 55174e6)
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From: |
Marius Bakke |
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Subject: |
branch core-updates updated (1badc85 -> 55174e6) |
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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
connect-to-remote-daemon.
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
platforms.
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
derivation.
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
localstatedir.
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 6.1.3.2.
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:
Makefile.am | 5 +-
doc/guix.texi | 22 +-
etc/completion/bash/guix | 4 +-
.../substitutes/berlin.guixsd.org.pub | 0
.../substitutes/hydra.gnu.org.pub | 0
gnu/build/install.scm | 77 +--
gnu/build/linux-initrd.scm | 8 +-
gnu/build/vm.scm | 19 +-
gnu/local.mk | 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/guix-pack-relocatable.sh | 61 ++
tests/guix-pack.sh | 28 +-
tests/pack.scm | 156 ++++-
48 files changed, 1594 insertions(+), 979 deletions(-)
rename berlin.guixsd.org.pub => etc/substitutes/berlin.guixsd.org.pub (100%)
rename hydra.gnu.org.pub => etc/substitutes/hydra.gnu.org.pub (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/guix-pack-relocatable.sh
- branch core-updates updated (1badc85 -> 55174e6),
Marius Bakke <=