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branch core-updates updated (203795a -> 724eaef)
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From: |
Ludovic Courtès |
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Subject: |
branch core-updates updated (203795a -> 724eaef) |
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Date: |
Wed, 13 Jan 2016 17:19:49 +0000 |
civodul pushed a change to branch core-updates
in repository guix.
from 203795a gnu: perl: Add fix for CVE-2015-8607.
adds 2097787 gnu: Add Asymptote.
adds f6cddbe gnu: ldb: Update to 1.1.24.
adds 77553df gnu: samba: Update to 4.3.3.
adds f1e3a8a gnu: utf8proc: Update to 1.3.1.
adds 50b40d0 gnu: Add libuv-julia.
adds c2e87ca gnu: julia: Update to 0.4.2.
adds 2a6afac gnu: gtk+-2: Add patch to support GUIX_GTK2_PATH.
adds 4828ff9 gnu: gtk+: Add patch to support GUIX_GTK3_PATH.
adds 35a6dab git-download: Correctly implement recursive checkouts.
adds d28ef43 ui: Update copyright year in '--version' output.
adds db5a944 guix package: Allow multiple '--search' flags.
adds 94af9da services: boot: Reinstate /tmp and /var/run deletion.
adds be7be9e services: Move /tmp cleanup to a separate service.
adds fb74174 linux-boot: Remove verbose output for module loads.
adds fe542b9 gnu: emacs: Remove 'info.info'.
adds 1075b43 gnu: Add emacs-undo-tree.
adds a7ec569 gnu: Add LDC.
adds 7d1f8d4 gnu: calibre: Update to 2.48.0.
adds f07041f build: pull: Compile .scm files in one process.
adds f9b9a03 doc: Remove double occurrence of words.
adds 03cea32 build: Bump version number.
adds 43c565d gnu: Add Jellyfish.
adds d914889 gnu: icedtea6, icedtea7: Unpack to "openjdk.src".
adds d2540f8 gnu: Add and use default IcedTea.
adds 5452588 gnu: icedtea6, icedtea7: Rename package to "icedtea".
adds d028740 gnu: icedtea6: Rename to icedtea-6.
adds a243e12 gnu: icedtea7: Rename to icedtea-7.
adds 7266848 build: ruby: Remove cached gem after install.
adds 341ae58 gnu: ldc: Fix license.
adds 3c4c8c3 services: cleanup-service: Catch 'system-error' instead
of everything.
adds 7b78f35 gnu: sudo: Use /var/run/sudo instead of /run/sudo.
adds f888c0b lint: cve: Catch host name lookup errors.
adds c7b0841 gnu: gmsh: Update to 2.11.0.
adds 1c63daf http-client: Fix erroneous comment.
adds dff9141 gnu: guix: Update development snapshot to f888c0b.
adds 793a43f http-client: Work around <http://bugs.gnu.org/22273>.
adds 6071122 utils: Add 'ensure-keyword-arguments'.
adds d4aaf95 build-system/gnu: Make 'package-with-explicit-inputs'
idempotent.
adds e635200 gnu: w3m: Update patch to use '-p1'.
adds 62339e2 gnu: w3m: Enable SSL, disable broken protocols and
ciphers.
adds 5dfd276 gnu: edirect: Update to 3.50.
adds 7d3a1a2 gnu: Add ruby-ansi.
adds 6dff495 gnu: zita-resampler: Drop the '-march=native'
optimization.
adds 29e255c gnu: zita-convolver: Drop the '-march=native'
optimization.
adds fe9451c gnu: Add xmlstarlet.
adds d1c1160 import: Add package->upstream-name procedure.
adds 34a75d3 import: Rename "cran-fetch" to "fetch-description".
adds 21e4d6a gnu: Add RSQLite.
adds cefaa79 gnu: Add RCurl.
adds 543ded3 gnu: Add r-xml.
adds ca65d38 gnu: Add lambda.r.
adds b9ff33b gnu: Add futile.options.
adds 6b82f56 gnu: Add futile.logger.
adds bc89912 gnu: Add snow.
adds 555e339 gnu: Add Biobase.
adds 8b7bce7 gnu: Add AnnotationDbi.
adds c465fa7 gnu: Add biomaRt.
adds e91d362 gnu: Add BiocParallel.
adds bf15935 gnu: Add Biostrings.
adds f8d74f7 gnu: Add Rsamtools.
adds 6e76dda gnu: Add SummarizedExperiment.
adds d8a828a gnu: Add GenomicAlignments.
adds 317755f gnu: Add rtracklayer.
adds 2fd7c04 gnu: Add GenomicFeatures.
adds fb25d88 gnu: Add GO.db.
adds d706257 gnu: Add SparseM.
adds a8227e4 gnu: Add DT.
adds a69a593 gnu: Add base64enc.
adds 8bfe007 gnu: Add R.methodsS3.
adds c8c75a8 gnu: Add R.oo.
adds 9c94b53 gnu: Add R.utils.
adds a63efbb gnu: Add R.cache.
adds 3703ffb gnu: Add R.rsp.
adds e05c37d gnu: Add matrixStats.
adds d547ce5 gnu: Add topGO.
adds a28d646 gnu: Add viridis.
adds fbf6045 gnu: Add plotly.
adds c63cef6 gnu: Add BSgenome.
adds c43a011 gnu: Add impute.
adds 03ea5a3 gnu: Add seqPattern.
adds cb933df gnu: Add genomation.
adds 0a5ec70 emacs: Display supported systems in "Package Info".
adds fbbaa4d gnu: mpv: Remove 'samba' input.
adds c8d969b gnu: Add Pfff.
adds b110869 doc: Add elaborate package search example.
adds c0a9589 doc: Document network-manager-service.
adds 19e5258 gnu: webkitgtk: Update to 2.10.4.
adds a65e26f gnu: epiphany: Update to 3.18.2.
adds 9ef824c gnu: xterm: Update to 322.
adds 2409f37 gnu: Add missing (gnu packages gcc) import.
adds 17ad0a2 build-system/python: 'pypi-uri' takes an optional file
name extension.
adds bea25ae gnu: nss: Update to 3.21 [fixes CVE-2015-7575].
adds 3a04d5d gnu: lm-sensors: Update source and home-page URLs.
adds f32274a gnu: i2c-tools: Update source and home-page URLs.
adds 4c40fa0 gnu: ruby-2.1: Update to 2.1.8.
adds 13035f5 gnu: icecat: Update to 38.5.2-gnu1.
adds 695bea9 gnu: r: Update to 3.2.3.
adds 6573ac8 gnu: bedtools: Use modify-phases.
adds 9b9b7ff gnu: bedtools: Update to 2.25.0.
adds ce9a304 build: Fix out-of-tree building of documentation.
adds a916c82 gnu: man-pages: Update to 4.04.
adds 4a6635f gnu: texlive: Use modify-phases syntax.
adds 4879d2f gnu: gp2c: Update to 0.0.9pl5.
adds ec70fec gnu: youtube-dl: Update to 2016.01.09.
adds 81f3e0c gnu: Add fxtract.
adds 6b0d24b gnu: linux-libre: Update to 4.4.
adds 9f40b11 gnu: icedtea-6: Fix directory name in "unpack" phase.
adds 94c3a6f gnu: global: Update to 6.5.2.
adds 9d9951d gnu: global: Use modify-phases syntax.
adds 16aa649 gnu: sudo: Add fix for CVE-2015-5602.
adds d33fa0c doc: Show bootstrapping at the package level.
adds 27ab3ce build: Warn against long hash bang lines for tests.
adds bb25130 build: 'make check' errors out if file name limits would
be hit.
adds 3abe813 gnu: boost: Use modify-phases.
adds c91d3fb gnu: boost: Update to 1.60.0.
adds 0917e80 doc: Fix typo in "Build Systems".
adds 98f2339 gnu: skribilo: Update to 0.9.3.
adds 93ce8a8 build: Use 127 as the Linux hash-bang limit.
adds c447341 gnu: samtools: Update to 1.3.
adds 75418ae gnu: isc-dhcp: Update to 4.3.3-P1 [fixes CVE-2015-8605].
adds 883fc5e emacs: Add missing shell completions.
adds 0820733 emacs: Complete --file in 'guix build' popup.
adds e4e2154 emacs: Make "guix-emacs.el" independent.
adds 6d268e5 emacs: Move loading packages to "guix-emacs.el".
adds e5a19fe gnu: julia: Update to 0.4.3.
adds 8c9ef2c monad-repl: Close connection when leaving the monad REPL.
adds b8a3530 build-system/gnu: 'dist-package' can be passed the phases.
adds 7a2eed3 hydra: Add missing phase and inputs for 'make dist' job.
new 8c986ab Merge branch 'master' into core-updates
new 724eaef tests: Use sed instead of grep as a package with no
dependencies.
The 2 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:
.gitignore | 3 +
Makefile.am | 45 +-
build-aux/hydra/guix.scm | 28 +-
configure.ac | 5 +-
daemon.am | 6 +-
doc.am | 16 +-
doc/guix.texi | 91 +++-
doc/images/bootstrap-packages.dot | 105 +++
emacs/guix-command.el | 1 +
emacs/guix-emacs.el | 21 +-
emacs/guix-init.el | 13 -
emacs/guix-main.scm | 1 +
emacs/guix-pcomplete.el | 7 +-
emacs/guix-ui-package.el | 19 +-
gnu-system.am | 17 +-
gnu/build/linux-boot.scm | 3 +-
gnu/build/linux-modules.scm | 2 +-
gnu/packages/admin.scm | 13 +-
gnu/packages/algebra.scm | 6 +-
gnu/packages/audio.scm | 24 +-
gnu/packages/bdw-gc.scm | 2 +-
gnu/packages/bioinformatics.scm | 692 ++++++++++++++++++--
gnu/packages/boost.scm | 56 +-
gnu/packages/code.scm | 28 +-
gnu/packages/commencement.scm | 5 +-
gnu/packages/ebook.scm | 6 +-
gnu/packages/emacs.scm | 45 +-
gnu/packages/gnome.scm | 4 +-
gnu/packages/gnuzilla.scm | 9 +-
gnu/packages/graphics.scm | 3 +-
gnu/packages/gtk.scm | 18 +-
gnu/packages/java.scm | 127 ++--
gnu/packages/julia.scm | 129 +++-
gnu/packages/kodi.scm | 2 +-
gnu/packages/ldc.scm | 118 ++++
gnu/packages/libreoffice.scm | 15 +-
gnu/packages/linux-libre-i686.conf | 220 +++++--
gnu/packages/linux-libre-x86_64.conf | 252 +++++---
gnu/packages/linux.scm | 12 +-
gnu/packages/man.scm | 15 +-
gnu/packages/maths.scm | 14 +-
gnu/packages/package-management.scm | 6 +-
gnu/packages/patches/asymptote-gsl2.patch | 33 +
.../patches/bedtools-32bit-compilation.patch | 171 -----
gnu/packages/patches/boost-mips-avoid-m32.patch | 15 -
gnu/packages/patches/csound-header-ordering.patch | 20 +
.../patches/gtk2-respect-GUIX_GTK2_PATH.patch | 46 ++
.../patches/gtk3-respect-GUIX_GTK3_PATH.patch | 38 ++
.../patches/julia-0.3.10-fix-empty-array.patch | 13 -
gnu/packages/patches/ldc-disable-tests.patch | 90 +++
.../patches/libcmis-fix-test-onedrive.patch | 35 +
gnu/packages/patches/nss-pkgconfig.patch | 27 +-
gnu/packages/patches/openimageio-boost-1.60.patch | 47 ++
gnu/packages/patches/sudo-CVE-2015-5602.patch | 372 +++++++++++
.../patches/w3m-disable-sslv2-and-sslv3.patch | 24 +
.../patches/w3m-disable-weak-ciphers.patch | 24 +
gnu/packages/patches/w3m-fix-compile.patch | 15 -
.../patches/w3m-force-ssl_verify_server-on.patch | 24 +
gnu/packages/patches/w3m-libgc.patch | 28 +
gnu/packages/plotutils.scm | 71 ++-
gnu/packages/ruby.scm | 42 ++-
gnu/packages/samba.scm | 8 +-
gnu/packages/skribilo.scm | 9 +-
gnu/packages/statistics.scm | 450 +++++++++++++-
gnu/packages/texlive.scm | 119 ++--
gnu/packages/textutils.scm | 46 +-
gnu/packages/video.scm | 6 +-
gnu/packages/w3m.scm | 7 +-
gnu/packages/webkit.scm | 6 +-
gnu/packages/xml.scm | 25 +
gnu/packages/xorg.scm | 5 +-
gnu/services.scm | 69 ++-
gnu/system.scm | 8 +-
guix/build-system/gnu.scm | 16 +-
guix/build-system/python.scm | 9 +-
guix/build/git.scm | 43 +-
guix/build/pull.scm | 149 ++---
guix/build/ruby-build-system.scm | 19 +-
guix/http-client.scm | 26 +-
guix/import/cran.scm | 46 +-
guix/monad-repl.scm | 22 +-
guix/scripts/lint.scm | 13 +-
guix/scripts/package.scm | 33 +-
guix/ui.scm | 4 +-
guix/utils.scm | 42 ++-
m4/guix.m4 | 27 +-
tests/graph.scm | 2 +-
tests/guix-package.sh | 20 +-
tests/utils.scm | 10 +-
89 files changed, 3583 insertions(+), 995 deletions(-)
create mode 100644 doc/images/bootstrap-packages.dot
create mode 100644 gnu/packages/ldc.scm
create mode 100644 gnu/packages/patches/asymptote-gsl2.patch
delete mode 100644 gnu/packages/patches/bedtools-32bit-compilation.patch
delete mode 100644 gnu/packages/patches/boost-mips-avoid-m32.patch
create mode 100644 gnu/packages/patches/csound-header-ordering.patch
create mode 100644 gnu/packages/patches/gtk2-respect-GUIX_GTK2_PATH.patch
create mode 100644 gnu/packages/patches/gtk3-respect-GUIX_GTK3_PATH.patch
delete mode 100644 gnu/packages/patches/julia-0.3.10-fix-empty-array.patch
create mode 100644 gnu/packages/patches/ldc-disable-tests.patch
create mode 100644 gnu/packages/patches/libcmis-fix-test-onedrive.patch
create mode 100644 gnu/packages/patches/openimageio-boost-1.60.patch
create mode 100644 gnu/packages/patches/sudo-CVE-2015-5602.patch
create mode 100644 gnu/packages/patches/w3m-disable-sslv2-and-sslv3.patch
create mode 100644 gnu/packages/patches/w3m-disable-weak-ciphers.patch
delete mode 100644 gnu/packages/patches/w3m-fix-compile.patch
create mode 100644 gnu/packages/patches/w3m-force-ssl_verify_server-on.patch
create mode 100644 gnu/packages/patches/w3m-libgc.patch
- branch core-updates updated (203795a -> 724eaef),
Ludovic Courtès <=