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branch staging updated (86990ee -> 613ef76)
|
From: |
Leo Famulari |
|
Subject: |
branch staging updated (86990ee -> 613ef76) |
|
Date: |
Tue, 6 Mar 2018 13:59:28 -0500 (EST) |
lfam pushed a change to branch staging
in repository guix.
from 86990ee Merge branch 'master' into staging
adds 04e7b1e gnu: golly: Fix source url.
adds 1debc5b gnu: ghc-uuid: Fix build.
adds 643817e gnu: Add patchmatrix.
adds 40a7997 gnu: efl: Update to 1.20.7.
adds 360ea2b gnu: efl: Use separate "include" output.
adds b180893 gnu: r-dexseq: Update to 1.24.3.
adds 99e4b11 gnu: r-shortread: Update to 1.36.1.
adds 22d9692 gnu: r-edger: Update to 3.20.9.
adds eb8971b gnu: r-limma: Update to 3.34.9.
adds 535014c gnu: r-genomicranges: Update to 1.30.3.
adds 61cbd49 gnu: r-topgo: Update to 2.30.1.
adds 6a0e139 gnu: r-wgcna: Update to 1.63.
adds 9aaf281 gnu: r-scran: Update to 1.6.8.
adds 9d6f392 gnu: r-truncnorm: Update to 1.0-8.
adds 5e38673 gnu: r-pillar: Update to 1.2.1.
adds 29c9c9c gnu: r-rmysql: Update to 0.10.14.
adds 744e06e gnu: r-mass: Update to 7.3-49.
adds e24ccf4 gnu: r-rpart: Update to 4.1-13.
adds e3ddb56 gnu: r-gdtools: Update to 0.1.7.
adds 36e1202 gnu: r-yaml: Update to 2.1.17.
adds dafd13d gnu: r-rcpparmadillo: Update to 0.8.400.0.0.
adds 35d12b0 gnu: r-rmarkdown: Update to 1.9.
adds eaf0905 gnu: r-tidyselect: Update to 0.2.4.
adds bfae3f7 gnu: r-lubridate: Update to 1.7.3.
adds b79e1fb gnu: r-httpuv: Update to 1.3.6.1.
adds b672a81 gnu: Graft glibc to allow execution on Linux 2.6.32.
adds db317b3 gnu: dbacl: Update phase style.
adds 7314a54 gnu: dbacl: Use HTTPS home page.
adds 4f5452a gnu: libftdi: Use HTTPS home page.
adds 4972f9c gnu: nagios: Update to 4.3.4.
adds 57c734a gnu: liblo: Update to 0.29.
adds 66b89ee gnu: python-stem: Update phase style.
adds fbb0164 gnu: privoxy: Update phase style.
adds 68e7632 gnu: onionshare: Update phase style.
adds a9c0a13 gnu: python-stem: Update to 1.6.0.
adds bb47da4 gnu: php: Update to 7.2.3.
adds 1ff14bf gnu: sdcc: Update to 3.7.0.
adds 738aa0c gnu: sdcc: Fix typo in description.
adds 8147d7c gnu: php: Fix test failure.
adds 5026696 gnu: address@hidden: Update to 4.4.119.
adds 8b1f76c gnu: address@hidden: Update to 4.9.85.
adds 433765e gnu: address@hidden: Update to 4.14.23.
adds da525e7 gnu: linux-libre: Update to 4.15.7.
adds e980231 gnu: memcached: Update to 1.5.6.
adds bb17b2b gnu: postgresql: Update to 10.3 [fixes CVE-2018-1058].
adds 703a8b7 gnu: address@hidden: Update to 9.6.8 [fixes
CVE-2018-1058].
adds 8863f2f gnu: icecat: Update to 52.6.0-gnu1.
adds 99654a1 gnu: icecat: Add more fixes from upstream mozilla-esr52.
adds 07ec349 environment: Add --link-profile.
adds e37944d environment: Add --user.
adds f14c933 Add (guix glob).
adds 8661ad2 linux-modules: Add 'device-module-aliases' and related
procedures.
adds 615a89e linux-initrd: Separate file system module logic.
adds bc499b1 system: Add 'initrd-modules' field.
adds 424cea8 guix system: Check for the lack of modules in the initrd.
adds 1a6fb8d gnu: python-flask-babel: Update to 0.11.2.
adds 3c5658c gnu: python-cssutils: Update to 1.0.2.
adds 6f21aca gnu: python-ndg-httpsclient: Update to 0.4.4.
adds e46dd02 gnu: python-webtest: Update to 2.0.29.
adds bda82ef gnu: python-s3transfer: Update to 0.1.13.
adds 0507543 gnu: python-htmlmin: Update to 0.1.12.
adds 6a19218 gnu: python-flask-script: Update to 2.0.6.
adds 12adfdf gnu: Update (gnu packages python-web) phase styles.
adds bb5c358 gnu: b43-tools: Update to 0.0.0-1.27892ef.
adds 315c89f gnu: b43-tools: Update phase style.
adds 3ebf12e gnu: b43-tools: Use HTTPS home page.
adds 0dae492 gnu: ovmf: Use HTTPS home page.
adds f563d19 gnu: ovmf: Update phase style.
adds 65a3c34 gnu: ath9k-htc-firmware: Use INSTALL-FILE.
adds f136c8f gnu: gnome-mpv: Update to 0.14.
adds 5c0f68e gnu: fossil: Update phase style.
adds 2c1cc27 gnu: fortify-headers: Update to 0.9.
adds d338321 gnu: qscintilla: Use HTTPS home page.
adds 467834d gnu: ghc-abstract-deque: Fix typos in description.
adds 3a5c027 gnu: highlight: Update to 3.42.
adds 6e48fbb gnu: highlight: Don't hard-code Lua version.
adds dc8584d gnu: perl-test-harness: Update to 3.41.
adds defe028 gnu: perl-mozilla-ca: Update to 20180117.
adds 139ecde gnu: delta: Remove redundant code.
adds a40f732 gnu: python-webencodings: Fix typo in description.
adds 5658b4c gnu: zerofree: Update to 1.1.1.
adds 6fda93e gnu: libpsl: Update to 0.20.1.
adds b01a1b3 gnu: nghttp2: Update to 1.31.0.
adds 5f4565b gnu: Add r-network.
adds 07a2f34 gnu: Add r-statnet-common.
adds 1088744 gnu: Add r-sna.
adds 4e35c42 gnu: Add r-rbiofabric.
adds 93c21dd gnu: Add r-ttr.
adds 0b64332 gnu: Add r-leaps.
adds d3cb62e gnu: Add r-splus2r.
adds 034ac9d gnu: Add r-ifultools.
adds 0be7eff gnu: Add r-sapa.
adds dceb159 gnu: Add r-quantmod.
adds b6dc325 gnu: Add r-tseries.
adds a2c079a gnu: Add r-wmtsa.
adds 4993a02 gnu: Add r-tsa.
adds 19da7fe gnu: Add r-extradistr.
adds 5b25bc5 gnu: Add r-fractal.
adds 6615a36 gnu: Add r-urca.
adds d32e572 gnu: Add r-cubature.
adds 7531ee8 gnu: Add r-trend.
adds f96eda9 gnu: Add r-expm.
adds 68b6a67 gnu: Add r-complexplus.
adds 7b81a7e gnu: Add r-phontools.
adds d976454 gnu: Add r-np.
adds 2a112be gnu: Add r-powerplus.
adds fa59659 gnu: Add r-hpar.
adds 62a4b95 gnu: python-xopen: Update to 0.3.2.
adds 3ede155 gnu: cutadapt: Update to 1.16.
adds 3cb3a4e linux-initrd: 'file-system-modules' returns the right
module list.
adds 5a3716a vm: Add missing modules to the
'expression->derivation-in-linux-vm' initrd.
adds f850e0d system: beaglebone-black: Use 'initrd-modules'.
adds eac026e linux-initrd: Add virtio modules to
'%base-initrd-modules'.
adds 081d143 gnu: r-performanceanalytics: Update to 1.5.2.
adds fac40f3 gnu: r-dbi: Update to 0.8.
adds ec8b3d4 gnu: r-httpuv: Update to 1.3.6.2.
adds f4009ad gnu: sdl2: Update to 2.0.8.
adds 74a2f8f gnu: hdparm: Update to 9.54.
adds 83a9003 gnu: libseccomp: Update to 2.3.3.
adds dbefd3f gnu: wv: Edit description.
adds 9d13f82 gnu: sslh: Update to 1.19c.
adds e6d30cf gnu: conky: Remove redundant MKDIR-P.
adds 75377c6 gnu: quagga: Update to 1.2.4.
adds add928d gnu: ghc-refact: Fix typo in description.
adds 433dc74 gnu: networking: Add czmq.
adds cf646ac gnu: Add ruby-mocha-on-bacon.
adds a8d2bf3 gnu: Add ruby-bacon-bits.
adds afdb437 gnu: Add ruby-bond.
adds fe5dd5f gnu: Add ruby-czmq-ffi-gen.
adds d0afff2 gnu: Add ruby-cztop.
adds b03eb6a gnu: Add ruby-data_uri.
adds 8279b1d gnu: Add ruby-mimemagic.
adds 62b138c gnu: Add ruby-iruby.
adds 0645da3 gnu: grammalecte: Update to 0.6.2.
adds 5e332c5 gnu: wireshark: Update to 2.4.5.
adds fb547c3 gnu: dictionaries: Add copyright line.
adds bdcf0e6 services: messaging: Prosody config supports file-like
objects.
adds f9e0fcb gnu: Add texlive-fonts-iwona.
adds 30d5547 gnu: Add java-cisd-base.
adds 04ddca2 gnu: Add java-cisd-args4j.
adds 2f0d041 gnu: Add java-cisd-jhdf5.
adds bd97583 gnu: Add fastqc.
adds c8d9960 gnu: Add java-la4j.
adds 24074b0 gnu: Add java-jlargearrays.
adds 4e92911 gnu: Add java-jtransforms.
adds dbb3581 gnu: Add java-jdistlib.
adds 5fef15e gnu: Add java-biojava-core.
adds 93abc97 gnu: Add java-openchart2.
adds f09d16e gnu: Add java-forester.
adds 10645b9 gnu: Add java-forester-1.005.
adds b28c803 gnu: Add java-biojava-phylo.
adds 22c09c3 gnu: Add java-biojava-alignment.
adds e44da58 gnu: Add java-biojava-core-4.0.
adds 5528f9e gnu: Add java-biojava-phylo-4.0.
adds 9ac7db1 gnu: Add java-biojava-alignment-4.0.
adds 9a599c1 gnu: Add java-htsjdk-latest.
adds 719fa95 gnu: Add java-htsjdk-2.10.1.
adds 72299db gnu: Add java-picard-2.10.3.
adds 1adeef3 gnu: Add dropseq-tools.
adds c94752a gnu: tor: Update to 0.3.2.10 [security fixes].
adds 8b2219d linux-modules: Add module-aliases.
adds 1e6b9c6 services: postgresql: Add a default-value to the
postgresql-service-type.
adds e903738 services: mysql: Add a default-value to the
mysql-service-type.
adds bc037c1 services: redis: Add a default-value to the
redis-service-type.
adds 7fc9442 gnu: masscan: Declare a source file-name.
adds a18ee79 gnu: papagayo: Declare a source file-name.
adds 35a01e6 gnu: lv2-mda-piano: Declare a source file-name.
adds 6677c99 gnu: lv2-devel: Declare a source file-name.
adds 70aa07d gnu: qjackrcd: Declare a source file-name.
adds fdf359f gnu: rubberband: Declare a source file-name.
adds a1eb506 gnu: address@hidden: Declare a source file-name.
adds b1d4026 gnu: r-dropbead: Declare a source file-name.
adds 5110672 gnu: seek: Declare a source file-name.
adds d9a069c gnu: libdivsufsort: Declare a source file-name.
adds da49d13 gnu: piranha: Declare a source file-name.
adds eafe96e gnu: sfarkxtc: Declare a source file-name.
adds 277be74 gnu: unshield: Declare a source file-name.
adds c2c04cd gnu: kurly: Declare a source file-name.
adds f5c847e gnu: python-apsw: Declare a source file-name.
adds c553b08 gnu: python-apsw: Use invoke.
adds 5a6f7a6 gnu: emacs-epl: Declare a source file-name.
adds aeb95f1 gnu: emacs-sly: Declare a source file-name.
adds a1dc853 gnu: disorderfs: Declare a source file-name.
adds 661ad6f gnu: freegish: Declare a source file-name.
adds fdbece7 gnu: go-github-com-alsm-ioprogress: Declare a source
file-name.
adds 6de107b gnu: go-github-com-davidjpeacock-cli: Declare a source
file-name.
adds 82f09c0 gnu: go-github-com-aki237-nscjar: Declare a source
file-name.
adds 4c763b4 gnu: antlr3-3.1: Fix java8 issue.
adds 48c8622 gnu: antlr3-3.3: Fix java8 issue.
adds 329dabe git-download: Fetch only the required commit, if possible.
adds 64cdd73 gnu: python-funcy: Fix tests.
adds 692f6e4 gnu: abiword: Disable duplicate icon cache generation.
adds 81ed306 gnu: inkscape: Disable duplicate icon cache generation.
adds 7fa9cca gnu: rocksdb: Update to 5.10.4.
adds 5a43735 gnu: snappy: Update to 1.1.7.
adds 8293d21 gnu: java-snappy: Update to 1.1.7.
adds bbce53c gnu: Add address@hidden
adds 1568cc1 gnu: Add address@hidden
adds 5b0b520 gnu: ceph: Update to 12.2.4.
adds 5275f69 gnu: freexl: Update to 1.0.5 [security fixes].
adds 3e57b7d gnu: multipath-tools: Update to 0.7.4.
adds 03b7195 gnu: liblo: Mark up description.
adds 95943ed gnu: cloc: Update to 1.76.
adds 53244d1 gnu: cloc: Update phase style.
adds e0dbead gnu: ii: Update to 1.8.
adds d035eaa gnu: ii, sic: Use HTTPS home pages.
adds 7730b71 gnu: gitolite: Update to 3.6.7.
adds 92793c7 gnu: gitolite: Update phase style.
adds bd128d5 gnu: footswitch: Remove redundant MKDIR-P.
adds ed36949 gnu: footswitch: Update to 0.1-2.deedd87.
adds 9539016 gnu: tomb: Use HTTPS home page.
adds 635dd0c gnu: tomb: Update phase style.
adds ac1a9ce gnu: papi: Update phase style.
adds 16718b6 services: Add openntpd service.
adds dc97f7e gnu: Add emacs-hcl-mode.
adds 68d70f6 gnu: Add emacs-terraform-mode.
adds 88b1a38 gnu: address@hidden: Update to 4.4.120.
adds ee483a5 gnu: address@hidden: Update to 4.9.86.
adds 6a4eaaf gnu: address@hidden: Update to 4.14.24.
adds ca041ec doc: Adjust 'xset -fp' command to avoid symlinks.
adds 234d7ef build: Always use https substitute URLs.
adds bdbece9 build: Default to berlin.guixsd.org substitutes on
aarch64.
adds f285b17 nls: Add Simplified Chinese translation.
adds f44c7aa ui: Better workaround for lack of '%fresh-auto-compile'
on 2.2.3.
adds 0ebc1b9 gnu: xpra: Update to 2.2.5.
adds f7c870f gnu: papi: Fix documentation location.
adds 211748d gnu: papi: Use HTTPS home page.
adds 0d34993 gnu: openvpn: Update to 2.4.5.
adds 9599339 gnu: openvpn: Mark up description.
adds 530df31 gnu: perl-www-mechanize: Update to 1.87.
adds 55b7cd1 gnu: perl-io-socket-ip: Update to 0.39.
adds cc7a4bb gnu: tocc, libtocc: Use HTTPS home page.
adds 437e5fa gnu: editres: Update to 1.0.7.
adds b5de208 gnu: perl-xml-rss: Update to 1.60.
adds 503a005 gnu: perl-xml-compile-cache: Update to 1.06.
adds 1c3de94 gnu: perl-sub-quote: Update to 2.005000.
adds c8213ff gnu: perl-email-address: Update to 1.909.
adds 0f27780 gnu: java-ops4j-pax-tinybundles: Use distribution bndlib
version.
adds cee03b2 gnu: ovmf: Fix build and add FIXME.
adds 69611d3 gnu: haskell-mode: Fix find emacs-stream elisp directory.
adds 5ad13e6 gnu: emacs-transmission: Update to 0.12.1.
adds 7949c14 ui: 'load*' no longer fails on Guile 2.2.3 upon EACCES or
similar.
adds 08ddb98 gnu: r-gtools: Make output deterministic.
adds fe58ab0 gnu: r-lambda-r: Run unit tests.
adds e325c89 gnu: r-rhdf5: Make build reproducible.
adds 727d847 gnu: htslib: Update to 1.7.
adds c072cf5 gnu: samtools: Update to 1.7.
adds 6f1f8d1 gnu: python-django: Update to 1.11.11 [fixes
CVE-2018-7536 and CVE-2018-7537].
adds 6836c22 gnu: iceauth: Update to 1.0.8.
adds 3720475 gnu: feh: Update to 2.25.
adds 77412c4 gnu: re2: Update to 2018-03-01.
adds 78f19a4 gnu: Remove go-github-com-xtaci-smux.
adds bb0a84f gnu: Remove go-github-com-xtaci-kcp-go.
adds eaca421 gnu: Remove go-github-com-ccding-go-stun.
adds abb8973 gnu: Remove go-github-com-klauspost-cpuid.
adds 7915ef0 gnu: Remove go-github-com-klauspost-reedsolomon.
adds 7d02ae4 gnu: Remove go-github-com-tjfoc-gmsm-sm4.
adds 6482d30 gnu: Remove go-github-com-templexxx-cpufeat.
adds 01794ff gnu: Remove go-github-com-templexxx-xor.
adds 3b52628 gnu: syncthing: Update to 0.14.45.
adds 8a32574 gnu: isc-dhcp: Update to 4.3.6-P1 [fixes
CVE-2018-{5732,5733}].
new 613ef76 Merge branch 'master' into staging
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 | 4 +-
config-daemon.ac | 20 +-
doc/guix.texi | 183 ++++-
gnu/build/linux-modules.scm | 169 +++-
gnu/local.mk | 13 +-
gnu/packages/abiword.scm | 2 +-
gnu/packages/accessibility.scm | 9 +-
gnu/packages/admin.scm | 5 +-
gnu/packages/algebra.scm | 103 ++-
gnu/packages/animation.scm | 1 +
gnu/packages/audio.scm | 11 +-
gnu/packages/base.scm | 11 +
gnu/packages/{figlet.scm => bioconductor.scm} | 36 +-
gnu/packages/bioinformatics.scm | 866 ++++++++++++++++++--
gnu/packages/boost.scm | 14 +
gnu/packages/cmake.scm | 59 +-
gnu/packages/code.scm | 25 +-
gnu/packages/compression.scm | 45 +-
gnu/packages/conky.scm | 4 +-
gnu/packages/cran.scm | 529 ++++++++++++-
gnu/packages/crypto.scm | 11 +-
gnu/packages/curl.scm | 1 +
gnu/packages/databases.scm | 78 +-
gnu/packages/debug.scm | 4 +-
gnu/packages/dictionaries.scm | 17 +-
gnu/packages/django.scm | 4 +-
gnu/packages/emacs.scm | 56 +-
gnu/packages/enlightenment.scm | 8 +-
gnu/packages/file-systems.scm | 1 +
gnu/packages/firmware.scm | 52 +-
gnu/packages/games.scm | 3 +-
gnu/packages/gnuzilla.scm | 133 +---
gnu/packages/golang.scm | 3 +
gnu/packages/graph.scm | 29 +-
gnu/packages/haskell.scm | 10 +-
gnu/packages/image-viewers.scm | 4 +-
gnu/packages/inkscape.scm | 5 +-
gnu/packages/irc.scm | 14 +-
gnu/packages/java.scm | 491 +++++++++++-
gnu/packages/libftdi.scm | 2 +-
gnu/packages/linux.scm | 34 +-
gnu/packages/mail.scm | 4 +-
gnu/packages/monitoring.scm | 5 +-
gnu/packages/music.scm | 28 +
gnu/packages/networking.scm | 50 +-
gnu/packages/ntp.scm | 13 +-
.../patches/antlr3-3_1-fix-java8-compilation.patch | 35 +
.../patches/antlr3-3_3-fix-java8-compilation.patch | 35 +
.../patches/ceph-disable-cpu-optimizations.patch | 64 +-
.../patches/ceph-disable-unittest-throttle.patch | 52 --
gnu/packages/patches/ceph-rocksdb-compat.patch | 63 ++
gnu/packages/patches/gd-CVE-2018-5711.patch | 61 ++
.../patches/glibc-allow-kernel-2.6.32.patch | 39 +
gnu/packages/patches/icecat-bug-1348660-pt5.patch | 727 -----------------
gnu/packages/patches/icecat-bug-1414945.patch | 73 --
gnu/packages/patches/icecat-bug-1415133.patch | 40 -
gnu/packages/patches/icecat-bug-1424373-pt2.patch | 183 -----
gnu/packages/perl-check.scm | 4 +-
gnu/packages/perl.scm | 8 +-
gnu/packages/php.scm | 22 +-
gnu/packages/pretty-print.scm | 14 +-
gnu/packages/profiling.scm | 34 +-
gnu/packages/python-web.scm | 60 +-
gnu/packages/python.scm | 21 +-
gnu/packages/qt.scm | 2 +-
gnu/packages/regex.scm | 4 +-
gnu/packages/ruby.scm | 258 ++++++
gnu/packages/sdcc.scm | 11 +-
gnu/packages/sdl.scm | 4 +-
gnu/packages/search.scm | 4 +-
gnu/packages/statistics.scm | 99 ++-
gnu/packages/storage.scm | 42 +-
gnu/packages/suckless.scm | 4 +-
gnu/packages/syncthing.scm | 226 +-----
gnu/packages/tex.scm | 41 +
gnu/packages/textutils.scm | 8 +-
gnu/packages/tor.scm | 11 +-
gnu/packages/version-control.scm | 22 +-
gnu/packages/video.scm | 4 +-
gnu/packages/vpn.scm | 9 +-
gnu/packages/web.scm | 20 +-
gnu/packages/wv.scm | 12 +-
gnu/packages/xml.scm | 12 +-
gnu/packages/xorg.scm | 12 +-
gnu/services/configuration.scm | 17 +-
gnu/services/databases.scm | 15 +-
gnu/services/messaging.scm | 106 +--
gnu/services/networking.scm | 102 ++-
gnu/system.scm | 7 +
gnu/system/examples/beaglebone-black.tmpl | 9 +-
gnu/system/install.scm | 7 +-
gnu/system/linux-initrd.scm | 118 +--
gnu/system/mapped-devices.scm | 53 +-
gnu/system/vm.scm | 10 +-
gnu/tests/install.scm | 11 +-
guix/build/git.scm | 43 +-
guix/gexp.scm | 7 +
guix/glob.scm | 97 +++
guix/scripts/environment.scm | 159 +++-
guix/scripts/system.scm | 67 +-
guix/ui.scm | 18 +-
po/packages/LINGUAS | 1 +
po/packages/{hu.po => zh_CN.po} | 879 +++++----------------
tests/glob.scm | 58 ++
tests/guix-environment-container.sh | 25 +
105 files changed, 4485 insertions(+), 2833 deletions(-)
copy gnu/packages/{figlet.scm => bioconductor.scm} (52%)
create mode 100644 gnu/packages/patches/antlr3-3_1-fix-java8-compilation.patch
create mode 100644 gnu/packages/patches/antlr3-3_3-fix-java8-compilation.patch
delete mode 100644 gnu/packages/patches/ceph-disable-unittest-throttle.patch
create mode 100644 gnu/packages/patches/ceph-rocksdb-compat.patch
create mode 100644 gnu/packages/patches/gd-CVE-2018-5711.patch
create mode 100644 gnu/packages/patches/glibc-allow-kernel-2.6.32.patch
delete mode 100644 gnu/packages/patches/icecat-bug-1348660-pt5.patch
delete mode 100644 gnu/packages/patches/icecat-bug-1414945.patch
delete mode 100644 gnu/packages/patches/icecat-bug-1415133.patch
delete mode 100644 gnu/packages/patches/icecat-bug-1424373-pt2.patch
create mode 100644 guix/glob.scm
copy po/packages/{hu.po => zh_CN.po} (93%)
create mode 100644 tests/glob.scm
- branch staging updated (86990ee -> 613ef76),
Leo Famulari <=