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branch core-updates updated (12b6f65 -> 2cf0221)
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From: |
Ludovic Courtès |
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Subject: |
branch core-updates updated (12b6f65 -> 2cf0221) |
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Date: |
Mon, 23 May 2016 13:04:39 +0000 (UTC) |
civodul pushed a change to branch core-updates
in repository guix.
from 12b6f65 gnu: openssl: Remove workaround for GCC 4.9.3 (no longer
used).
adds 9495cf9 gnu: Rename letsencrypt to certbot. Upgrade certbot and
python-acme to 0.6.0.
adds 2477836 gnu: certbot: Update home page URL.
adds 6d461b2 gnu: git: Fix search path specification for
'GIT_SSL_CAINFO'.
adds 52e1def gnu: guix: Update development snapshot.
adds 6e94a57 guix build: Do not show what to build when '-d' is used.
adds c22a475 guix build: Catch 'getaddrinfo-error' for '--log-file'.
adds cd436bf download: Support content-addressed mirrors.
adds 8a7680a gnu: cross-base: Add srfi-26 for glibc.
adds e6a9050 gnu: wxmaxima: Update to 16.04.2.
adds e91fd7f gnu: love: Update to 0.10.1.
adds 277a7d8 gnu: libnotify: Add dependency on gobject-introspection.
adds 9365ee1 gnu: Add gnome-tweak-tool.
adds d8f3795 gnu: minetest: Update to 0.4.14.
adds b7ab191 gnu: Add libbsd.
adds 74dd0e4 gnu: libidn: Update license.
adds 90cd0e1 gnu: owncloud-client: Update to 2.2.0.
adds 3f61f92 gnu: libinput: Update to 1.3.0.
adds 5c6fdaa gnu: exempi: Update to 2.3.0.
adds 9c0c77f gnu: Add gtkspell3.
adds 6605612 gnu: libmbim: Update to 1.12.4.
adds 1fb8e07 gnu: libqmi: Update to 1.14.2.
adds a2ccaa0 gnu: qemu: Update to 2.6.0.
adds 2b19338 gnu: libical: Update to 2.0.0.
adds e9eb24b gnu: bluez: Update to 5.39.
adds 30897c6 gnu: mdadm: Update to 3.4.
adds 2f9e312 gnu: iw: Update to 4.3.
adds 9a12ca7 gnu: wireless-regdb: Update to 2016.05.02.
adds ec37403 gnu: postgresql: Update to 9.5.3.
adds 6747a85 gnu: tdb: Update to 1.3.9.
adds 3fef0a2 gnu: unixodbc: Update to 2.3.4.
adds b4370be gnu: python-cryptography, python-cryptography-vectors:
Update to 1.3.2.
adds 66395a6 gnu: gmsh: Add missing inputs.
adds 6b287c5 download: Update debian mirrors.
adds fd02719 gnu: fvwm: Update to 2.6.6.
adds 284539c gnu: geeqie: Update source location.
adds bf512da gnu: giblib: Add mirror for source.
adds 3a66217 gnu: gkrellm: Update urls.
adds d03f944 gnu: guile-irregex: Update to 0.9.4.
adds a83e604 gnu: hmmer: Update urls.
adds 44877dc gnu: hugs: Update urls.
adds 002528b gnu: rapicorn: Fix tests.
adds 81b9875 gnu: Add SBC.
adds 8226c27 gnu:: java-swt: Use ant-build-system.
adds 7d0c3c8 gnu: python-pandas: Update to 0.18.1.
adds 99404ff gnu: mu: Use 'modify-phases'.
adds 789bda8 gnu: mu: Install emacs files in a proper place.
adds 704f219 gnu: mu: Install emacs autoloads.
adds 47c96a5 gnu: mu: Update to 0.9.16.
adds 80ed14d gnu: asymptote: Install Emacs data.
adds f17a544 gnu: Add utfcpp.
adds d3699b3 gnu: Add ledger.
adds 8bfd602 build: Accept dates with space-padded hour field.
adds 8a0ac5b gnu: tmux: Update to 2.2.
adds b6c2f7d gnu: libgit2: Update to 0.24.1.
adds af3ac1f gnu: imagemagick: Update to 6.9.4-1.
adds 9583e07 import cran: Use URL for Bioconductor 3.3.
adds dbfeba5 gnu: r-biocgenerics: Update to 0.18.0.
adds a936bf5 gnu: r-dnacopy: Update to 1.46.0.
adds 3654a61 gnu: r-s4vectors: Update to 0.10.0.
adds 952ff8c gnu: r-iranges: Update to 2.6.0.
adds d1ab3d8 gnu: r-genomeinfodb: Update to 1.8.0.
adds 052ee32 gnu: r-variantannotation: Update to 1.18.0.
adds e782ca3 gnu: r-xvector: Update to 0.12.0.
adds 828980c gnu: r-genomicranges: Update to 1.24.0.
adds 4466a02 gnu: r-biobase: Update to 2.32.0.
adds c4a4e17 gnu: r-annotationdbi: Update to 1.34.0.
adds 63cea37 gnu: r-biomart: Update to 2.28.0.
adds 6a2a0de gnu: r-biocparallel: Update to 1.6.0.
adds 2477d97 gnu: r-biostrings: Update to 2.40.0.
adds b4c5a0d gnu: r-rsamtools: Update to 1.24.0.
adds d848ed7 gnu: r-summarizedexperiment: Update to 1.2.0.
adds 3cd551e gnu: r-genomicalignments: Update to 1.8.0.
adds d23fbf1 gnu: r-rtracklayer: Update to 1.32.0.
adds c12b0a5 gnu: r-genomicfeatures: Update to 1.24.0.
adds 0c56023 gnu: r-graph: Update to 1.50.0.
adds e48e88c gnu: r-topgo: Update to 2.24.0.
adds 5190ed1 gnu: r-bsgenome: Update to 1.40.0.
adds d1bff89 gnu: r-impute: Update to 1.46.0.
adds 7555817 gnu: r-seqpattern: Update to 1.4.0.
adds 8adc3b6 gnu: r-genomation: Update to 1.4.0.
adds 1f5786a gnu: r-seqlogo: Update to 1.38.0.
adds a0fe3ae gnu: r-motifrg: Update to 1.16.0.
adds 96101b6 gnu: r-zlibbioc: Update to 1.18.0.
adds 9916ae1 import cran: latest-bioconductor-release: Wrap
Bioconductor URL in list.
adds 11e4c1f gnu: Add geiser-next.
adds cb307c0 gnu: cflow: Update to 1.5.
adds 4f04243 gnu: 'uncompressed-file-fetch' no longer depends on gzip.
adds a9e41d2 gnu: emacs-constants: Factorize home-page in source URL.
adds 122395f gnu: diamond: Update to 0.8.1.
adds daaeed7 gnu: vsearch: Update to 1.11.1.
adds 849485f gnu: sortmerna: Update to 2.1b.
adds f99f3f2 gnu: emacs-constants: Update to 2.6.
adds 787afdd import: Exit with non-zero when an unknown importer is
asked.
adds 1495903 import: Gracefully report import failures.
adds aa8fff0 store: Clarify 'query-path-hash' docstring.
adds 1c29f3e gnu: emacs-constants: Remove old patch.
adds 99effc8 lint: Honor 'cpe-name' and 'cpe-version' package
properties.
adds bbb5d8a gnu: gd: Specify 'cpe-name'.
adds fb2b0f5 gnu: gd: Fix-CVE-2016-3074.
adds 9576cc7 gnu: Add emacs-zenburn-theme.
adds ad42be8 gnu: libndp: Update to 1.6 [fixes CVE-2016-3698].
adds f1876bf gnu: Add signify.
adds dbd40ac gnu: python2-pandas: Fix native-inputs.
adds e62ffce gnu: Add Piranha.
adds 7c54499 gnu: diamond: Do not specify target architecture.
adds 614f392 gnu: gnumach-headers: Update to 1.7.
adds eb3be3a gnu: mig: Update to 1.7.
adds 0affdfb gnu: hurd-headers: Update to 0.8.
adds bd9fe0f gnu: Add krona-tools.
adds 65e46ca gnu: qtkeychain: Update to 0.6.2.
adds 64851f4 gnu: wmbattery: Fix UPower-related memory leak.
adds 9123115 gnu: Add ntfs-3g.
adds b7b27a8 gnu: octave: Update to 4.0.2.
adds 21f0513 Update name for Kei Kebreau.
adds 5c447e2 gnu: Add emacs-smartparens.
adds 3fdb2a8 gnu: giflib: Update to 5.1.4 [fixes CVE-2015-7555,
CVE-2016-3977].
adds 44c5f02 gnu: giflib: Use 'modify-phases'.
adds 0947698 gnu: Add r-biased-urn.
adds 39b3033 gnu: flann: Strip .mex file.
adds 4584802 gnu: python: Add 'python' variables for different
major/minor versions.
adds 9684e30 gnu: flann: Do not install .a files.
adds 119b839 gnu: expat: Fix CVE-2016-0718. Improve fix for
CVE-2015-1283.
adds 0e40755 gnu: jemalloc: Update to 4.2.0.
adds 0fc4a8a gnu: btrfs-progs: Update to 4.5.3.
adds 186ed87 gnu: r-genomeinfodb: Update to 1.8.1.
adds 679e670 gnu: r-variantannotation: Update to 1.18.1.
adds 73af676 gnu: r-annotationdbi: Update to 1.34.2.
adds d742056 gnu: r-biocparallel: Update to 1.6.2.
adds 192e1ea gnu: r-summarizedexperiment: Update to 1.2.2.
adds 8ede249 gnu: r-genomicfeatures: Update to 1.24.2.
adds eb1a5b6 gnu: r-rcpp: Update to 0.12.5.
adds a76b3f6 gnu: r-dbi: Update to 0.4-1.
adds 9a0ccf4 gnu: r-bh: Update to 1.60.0-2.
adds 84e5368 gnu: r-evaluate: Update to 0.9.
adds df25b00 gnu: r-formatr: Update to 1.4.
adds d5130e6 gnu: r-highr: Update to 0.6.
adds 1b206ae gnu: r-knitr: Update to 1.13.
adds 383f633 gnu: r-testthat: Update to 1.0.2.
adds c1e2c9d gnu: r-openssl: Update to 0.9.3.
adds 3624ad7 gnu: r-git2r: Update to 0.15.0.
adds 133f27b gnu: r-devtools: Update to 1.11.1.
adds 2f7ac06 gnu: r-plotrix: Update to 3.6-2.
adds f0c56a2 gnu: r-rmarkdown: Update to 0.9.6.
adds b8f6a97 gnu: r-r-rsp: Update to 0.30.0.
adds 95513f2 gnu: r-matrixstats: Update to 0.50.2.
adds c969453 gnu: r-plotly: Update to 3.6.0.
adds f6225d1 gnu: r-jsonlite: Update to 0.9.20.
adds 7740f58 gnu: r-genomation: Update to 1.4.2.
adds 945eef8 gnu: armadillo: Update to 6.700.7.
adds 813efdd gnu: r-rcpparmadillo: Update to 0.6.700.6.0.
adds 2d69c16 gnu: Add gcc-objc-4.9.
adds 8b196ad gnu: Add default gcc-objc.
adds a5948c0 gnu: Add gcc-objc++-4.9.
adds 987a118 gnu: Add default gcc-objc++.
adds 932f2b7 ant-build-system: Add unpack phase.
adds 4483a11 gnu: linux-libre-4.4: Update to 4.4.11.
adds 3c9a718 gnu: linux-libre: Update to 4.5.5.
adds 3cabdea graph: Use absolute file name canonicalization.
adds 97507eb derivations: 'derivation' sorts items in the resulting
object.
adds a773c31 graph: Allow store file names for 'derivation' and
'references' graphs.
adds 30d4bc0 substitute: Gracefully handle invalid store file names.
adds cf8b312 grafts: Preserve empty directories when grafting.
adds ece6864 grafts: Rename files whose name matches a graft.
adds 28dee3d build: Fix 'AM_V_at' typo.
adds a56be43 gnu: Add dia.
adds b9b447b gnu: Add sicp.
adds 5489941 gnu: Add envstore.
adds 3c47489 gnu: Add gnome-calendar.
adds 88bb419 gnu: Add python2-rope.
adds 13913c5 gnu: imagemagick: Update to 6.9.4-4.
adds 624d4e2 gnu: gnu-pw-mgr: Update to 2.0.
new bc73a84 Merge branch 'master' into core-updates
new 2cf0221 gnu: pcre: Remove now-unneeded replacement.
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:
.mailmap | 1 +
Makefile.am | 2 +-
doc/guix.texi | 27 +
gnu/local.mk | 9 +-
gnu/packages/bioinformatics.scm | 220 +++---
gnu/packages/calendar.scm | 11 +-
gnu/packages/code.scm | 4 +-
gnu/packages/crypto.scm | 42 ++
gnu/packages/databases.scm | 15 +-
gnu/packages/dillo.scm | 2 +-
gnu/packages/emacs.scm | 96 ++-
gnu/packages/finance.scm | 106 +++
gnu/packages/fltk.scm | 2 +-
gnu/packages/freedesktop.scm | 18 +-
gnu/packages/fvwm.scm | 10 +-
gnu/packages/game-development.scm | 6 +-
gnu/packages/games.scm | 12 +-
gnu/packages/gcc.scm | 22 +
gnu/packages/gd.scm | 9 +-
gnu/packages/geeqie.scm | 8 +-
gnu/packages/gkrellm.scm | 5 +-
gnu/packages/gnome.scm | 128 +++-
gnu/packages/gnu-pw-mgr.scm | 5 +-
gnu/packages/gnustep.scm | 12 +-
gnu/packages/gnuzilla.scm | 6 +-
gnu/packages/graphics.scm | 31 +-
gnu/packages/grub.scm | 5 +-
gnu/packages/gtk.scm | 29 +
gnu/packages/guile.scm | 7 +-
gnu/packages/hugs.scm | 5 +-
gnu/packages/hurd.scm | 12 +-
gnu/packages/image.scm | 54 +-
gnu/packages/imagemagick.scm | 4 +-
gnu/packages/java.scm | 74 +-
gnu/packages/jemalloc.scm | 4 +-
gnu/packages/libbsd.scm | 47 ++
gnu/packages/libidn.scm | 5 +-
gnu/packages/linux.scm | 96 ++-
gnu/packages/mail.scm | 60 +-
gnu/packages/maths.scm | 50 +-
gnu/packages/music.scm | 2 +-
gnu/packages/networking.scm | 4 +-
gnu/packages/owncloud.scm | 4 +-
gnu/packages/package-management.scm | 8 +-
.../patches/emacs-constants-lisp-like.patch | 81 ---
.../patches/expat-CVE-2015-1283-refix.patch | 42 ++
gnu/packages/patches/expat-CVE-2016-0718.patch | 761 ++++++++++++++++++++
gnu/packages/patches/gd-CVE-2016-3074.patch | 36 +
.../patches/gnome-tweak-tool-search-paths.patch | 52 ++
gnu/packages/patches/mdadm-gcc-4.9-fix.patch | 38 -
.../python-pandas-fix-tslib-test-failure.patch | 141 ----
gnu/packages/pcre.scm | 8 -
gnu/packages/plotutils.scm | 27 +-
gnu/packages/python.scm | 91 ++-
gnu/packages/qemu.scm | 9 +-
gnu/packages/qt.scm | 6 +-
gnu/packages/scheme.scm | 59 +-
gnu/packages/{marst.scm => shellutils.scm} | 39 +-
gnu/packages/statistics.scm | 91 ++-
gnu/packages/textutils.scm | 44 +-
gnu/packages/tls.scm | 42 +-
gnu/packages/tmux.scm | 5 +-
gnu/packages/version-control.scm | 5 +-
gnu/packages/web.scm | 100 ++-
gnu/packages/xfce.scm | 2 +-
gnu/packages/xml.scm | 1 +
guix/build/ant-build-system.scm | 12 +
guix/build/download.scm | 105 ++-
guix/build/graft.scm | 28 +-
guix/derivations.scm | 133 ++--
guix/download.scm | 45 +-
guix/graph.scm | 2 +-
guix/import/cran.scm | 8 +-
guix/import/gnu.scm | 48 +-
guix/scripts/build.scm | 13 +-
guix/scripts/graph.scm | 82 ++-
guix/scripts/import.scm | 11 +-
guix/scripts/lint.scm | 21 +-
guix/scripts/substitute.scm | 12 +-
guix/store.scm | 2 +-
guix/upstream.scm | 5 +-
tests/derivations.scm | 27 +
tests/grafts.scm | 41 ++
tests/guix-graph.sh | 18 +-
84 files changed, 2737 insertions(+), 835 deletions(-)
create mode 100644 gnu/packages/libbsd.scm
delete mode 100644 gnu/packages/patches/emacs-constants-lisp-like.patch
create mode 100644 gnu/packages/patches/expat-CVE-2015-1283-refix.patch
create mode 100644 gnu/packages/patches/expat-CVE-2016-0718.patch
create mode 100644 gnu/packages/patches/gd-CVE-2016-3074.patch
create mode 100644 gnu/packages/patches/gnome-tweak-tool-search-paths.patch
delete mode 100644 gnu/packages/patches/mdadm-gcc-4.9-fix.patch
delete mode 100644
gnu/packages/patches/python-pandas-fix-tslib-test-failure.patch
copy gnu/packages/{marst.scm => shellutils.scm} (50%)
- branch core-updates updated (12b6f65 -> 2cf0221),
Ludovic Courtès <=