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branch staging updated (69e0aac -> 6969c4d)
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From: |
Marius Bakke |
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Subject: |
branch staging updated (69e0aac -> 6969c4d) |
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Date: |
Mon, 18 Jun 2018 09:41:59 -0400 (EDT) |
mbakke pushed a change to branch staging
in repository guix.
from 69e0aac gnu: zathura-pdf-mupdf: Link to JPEG libraries.
new 73d1891 gnu: OpenBLAS: Update to 0.3.0.
adds 9b25e1d gnu: erlang: Delete the bootstrap phase.
adds b5453aa gnu: erlang: Patch occurrences of /bin/sh in the source.
adds e7a25d2 gnu: elixir: Enable more tests and remove patch.
adds 2c5f8aa gnu: Add emacs-puppet-mode.
adds f3ad05e gnu: address@hidden: Update to 4.14.49.
adds 95d9d95 gnu: linux-libre: Update to 4.17.1.
adds 3287245 gnu: wine-staging-patchset-data: Update to 3.10.
adds 14cb796 gnu: wine-staging: Update to 3.10.
adds 5b47ea9 gnu: font-gnu-unifont: Update to 11.0.01.
adds b374047 gnu: speedtest-cli: Update to 2.0.2.
adds 35a7e57 gnu: vim-airline: Update to 0.9.
adds 261348e gnu: vim-fugitive: Update to 2.3.
adds c71cc13 gnu: vim-syntastic: Update to 3.9.0.
adds 3d39130 gnu: Add libostree.
adds efdaf8d gnu: Add umoci.
adds 7714a06 gnu: Add skopeo.
adds e68e4a9 gnu: fabric: Disable problematic tests.
adds 66266d3 gnu: borg: Update to 1.1.6.
adds feed519 gnu: python-urwid, python2-urwid: Update to 2.0.1.
adds b5edc47 gnu: flann: Fix builds with CMake >= 3.11.
adds 4c97a36 substitute: Erase the current line when reporting
progress.
adds 2bf9351 substitute: Make progress message shorter.
adds 90977eb gnu: guile-bytestructures: Update to 1.0.3.
adds 8d09bfe system: Move ~/.config/guix/current first in PATH and
INFOPATH.
adds 5909bdc .gitignore: Add doc/stamp-[0-9].
adds a9e7d65 gnu: multipath-tools: Fix build.
adds 6921e95 gnu: mame: Fix renaming executable.
adds 38212ff import: utils: Import more dependencies.
adds 67cb662 gnu: mes: Update to 0.15.
adds bea07c7 gnu: python-llfuse: Update to 1.3.3.
adds 25e071e services: nginx: Support extra content in the http block.
adds 359e30c gnu: Add qtwebview.
adds b5792b9 gnu: Add qtwebglplugin.
adds 502a822 gnu: tor: Update to 0.3.3.7.
adds 3a30ae0 gnu: openimageio: Update to 1.7.19.
adds 4b3480d gnu: cheese: Update to 3.28.0.
adds 14618a1 gnu: vkquake: Update to 1.00.0.
adds c24b154 tests: Honor the return value of 'start-service'.
adds 0c6ade0 gnu: openrct2: Update to 0.2.0.
adds 85df1a8 gnu: Add r-ggsci.
adds 5219c5c gnu: Add r-ggsignif.
adds 5cbaaee gnu: Add r-ggpubr.
adds 141e43b gnu: Add r-ellipse.
adds cbf6017 gnu: Add r-flashclust.
adds e83841a gnu: Add r-factominer.
adds f22bfee gnu: Add r-factoextra.
adds 0c9868a gnu: Add r-nbclust.
adds 546fc4a gnu: Add r-hdf5r.
adds 846325a gnu: Add r-writexl.
adds 693b4d0 gnu: r-globaloptions: Update to 0.1.0.
adds 7b60ab3 gnu: r-circlize: Update to 0.4.4.
adds 5fa9be1 gnu: r-getoptlong: Update to 0.1.7.
adds d87130c gnu: r-sp: Update to 1.3-1.
adds a151f1e gnu: r-extremes: Update to 2.0-9.
adds d0396c8 gnu: r-rcpproll: Update to 0.3.0.
adds 2bce779 gnu: r-stringdist: Update to 0.9.5.1.
adds 1268a99 gnu: r-statnet-common: Update to 4.1.2.
adds 8d2f8ae gnu: r-extradistr: Update to 1.8.9.
adds 014818b gnu: r-cubature: Update to 1.3-13.
adds 36dc359 gnu: r-radiant-data: Update to 0.9.5.
adds fa7236f gnu: r-later: Update to 0.7.3.
adds 1df9a0c gnu: r-reticulate: Update to 1.8.
adds 0357db5 gnu: r-rgooglemaps: Update to 1.4.2.
adds 3399dc9 gnu: r-munsell: Update to 0.5.0.
adds 26a53dd gnu: r-stringi: Update to 1.2.3.
adds d086829 gnu: r-highr: Update to 0.7.
adds 6221de1 gnu: r-rmarkdown: Update to 1.10.
adds 242ffd6 gnu: r-zoo: Update to 1.8-2.
adds c812f468 gnu: r-rjson: Update to 0.2.20.
adds 5b730eb gnu: r-biocviews: Update to 1.48.1.
adds 5b2a339 gnu: r-s4vectors: Update to 0.18.3.
adds 13b8dcf gnu: r-seurat: Update to 2.3.2.
adds 6ccd88e gnu: r-factoextra: Fix syntax error.
adds 8c655f3 nls: Update 'fr' translation.
adds 935cb93 gnu: emacspeak: Update to 48.0.
adds 4bf474b gnu: emacs-orgalist: Update to 1.8.
adds 844cc1c gnu: pigx-scrnaseq: Update to 0.0.5.
adds e2f8be0 pull: Add '--list-generations'.
adds 2b78360 gnu: sssd: Update to 1.16.2.
adds ff76a1e gnu: python-gnupg: Update to 0.4.3.
adds b262aba gnu: python-gnupg: Return #t from phase.
adds 0b5c16c Fix typo in (gnu packages gtk) header.
adds 0975ca3 services: tor: Mark end of auto-generated configuration
block.
adds 40c1b61 gnu: Add tmate.
adds 0dc5723 gnu: Add python-requests-file.
adds f4adbe7 gnu: Add python-tldextract.
adds b863b50 gnu: Add python-pynamecheap.
adds 85d79a7 gnu: Add python-dns-lexicon.
adds 03439df gnu: libgcrypt: Fix CVE-2018-0495.
adds 3931c76 database: 'with-database' can now initialize new
databases.
adds f8f9f7c database: Fail registration when encountering
unregistered references.
adds 6892f0a store-copy: 'read-reference-graph' returns a list of
records.
adds c5a2e1f build: Require Guile-SQLite3.
adds 33fddb7 database: Provide a way to specify the schema location.
adds 866ee8c database: 'register-path' creates the database directory
if needed.
adds 0d0438e deduplicate: Fix a couple of thinkos.
adds b85e2ff database: Remove extra SQL parameter in
'update-or-insert'.
adds 4bd86f0 database: Add #:reset-timestamps? to 'register-path'.
adds 122a6ca database: Replace existing entries in Refs.
adds 49c393c database: 'reset-timestamps' sets file permissions as
well.
adds be43c08 vm: 'expression->derivation-in-linux-vm' code can now use
dlopen.
adds c45477d install: Use (guix store database) instead of
'guix-register'.
adds ef1297e database: 'sqlite-register' takes a database, not a file
name.
adds 31a63be database: Add 'register-items'.
adds 078c232 install: Use 'reset-timestamps' from (guix store
database).
adds eb9fe97 database: Allow for deterministic database construction.
adds df2f640 store: Remove 'register-path'.
adds ea0a06c Remove 'guix-register' and its traces.
adds ce573b1 gnu: pigx-bsseq: Update to 0.0.9.
adds 53131ea gnu: Add minimap2.
adds f715f10 gnu: fio: Update to 3.7.
adds ab6f400 gnu: password-store: Update to 1.7.2.
adds 43fa239 gnu: emacs-password-store: Update to 1.7.2.
adds ecbac51 gnu: openrct2: Downgrade to 0.1.1.
adds 1ba7a62 gnu: python-nose-timer: Update to 0.7.2.
adds f716196 gnu: perl-dbi: Update to 1.641.
adds 6dd5f2e gnu: qrencode: Update to 4.0.2.
adds d518261 gnu: cppcheck: Update to 1.84.
adds 19611b7 gnu: python-freezegun: Return #t from phase.
adds ef0d765 gnu: python-freezegun: Update to 0.3.10.
adds b6c675c gnu: GnuPG 1.4: Update to 1.4.23.
adds 44d1b95 gnu: python-click-log: Update to 0.3.2.
adds a4bae9a gnu: vdirsyncer: Update to 0.6.6.
adds af09bed guix: ui: Allow translation of dates.
adds e3173fe gnu: botan: Update to 2.6.0 [fixes CVE-2018-{9127,9860}].
adds 0effadc gnu: libressl: Update to 2.7.4 [fixes
CVE-2018-{0495,0732}].
adds baed923 self: Add 'guix-daemon' to the result.
adds 112c2c0 gnu: Add lightgbm.
adds a8fb82a gnu: Add vowpal-wabbit.
adds 565af91 gnu: emacs-racket-mode: Update and bug fix.
adds a9a685c offload: Gracefully handle invalid results from
'machines.scm'.
adds 411959b linux-initrd: Module check correctly handles hyphen vs.
underscore.
adds 96fd9a0 gnu: Go 1.9: Update to 1.9.7.
adds 9297fc6 gnu: Go 1.10: Update to 1.10.3.
adds b494bbe gnu: certbot, python-acme: Update to 0.25.1.
adds bb15b58 gnu: Add r-bayseq.
adds dfac7eb gnu: Add r-bsgenome-dmelanogaster-ucsc-dm3-masked.
adds 6fbd759 gnu: Add r-bsgenome-hsapiens-ucsc-hg19-masked.
adds 2bece69 gnu: Add r-bsgenome-mmusculus-ucsc-mm9-masked.
adds 609f4ad gnu: Add r-chipcomp.
adds 0490f9d gnu: Add r-riboprofiling.
adds 6ffdfe6 gnu: Add r-riboseqr.
adds 0564022 gnu: innoextract: Update to 1.7.
adds a32279f gnu: Add r-interactionset.
adds cf9a29b gnu: Add r-genomicinteractions.
adds abde01f gnu: neofetch: Update to 4.0.2.
adds 752ff6e gnu: r-cubature: Update to 1.4.
adds beb2d4b gnu: nickle: Update to 2.81.
adds 50632f0 gnu: perl-xml-atom: Propagate inputs.
adds 9332d70 gnu: perl-xml-xpath: Propagate inputs.
adds 26d66a5 gnu: perl-xml-xpath: Update to 1.42.
adds 657bed3 gnu: fcitx: Use HTTPS home page.
adds 50ca5fb gnu: fcitx: Update to 4.2.9.6.
adds 914c6f6 gnu: fcitx-configtool: Update to 0.4.10.
adds d21fb90 gnu: perl-xml-libxml-simple: Update to 0.99.
adds 5bc4188 gnu: gource: Update to 0.49.
adds 0ce92d7 gnu: python-pyrfc3339: Update to 1.1.
adds 52d5b73 gnu: spice-protocol: Update to 0.12.14.
adds 14b0c49 gnu: f2fs-tools: Update to 1.10.0.
adds a756fa5 gnu: light: Update to 1.1.
adds d41a5f8 gnu: light: Return #t from phase.
adds ad21323 gnu: cpuid: Update to 20180519.
adds 265048c offload: Fix error message in 'guix offload test'.
adds 7b04497 hydra: Make sure we add an absolute file name to the load
path.
adds 0017e55 gnu: Add shadowsocks.
adds 4ce4fc5 system: Add os-with-u-boot.
adds a7c8716 gnu: grub: Fix build on i686.
adds 12e530b gnu: BIND: Fix CVE-2018-5738.
adds 901bcb7 gnu: pigx-chipseq: Update to 0.0.16.
adds c099f6a gnu: java-eclipse-jetty-security-9.2: Ignore test error.
adds f69a1d0 gnu: Add java-eclipse-jetty-xml.
adds 38b5757 gnu. Add java-eclipse-jetty-xml-9.2.
adds d736511 gnu: Add java-eclipse-jetty-webapp.
adds 087583a gnu: Add java-eclipse-jetty-webapp-9.2.
adds 7d65489 gnu: Add java-plexus-cli.
adds ab621bf gnu: Add java-qdox.
adds 8f5caf9 gnu: Add maven-plugin-api.
adds 7a42f05 gnu: Add maven-core-bootstrap.
adds a59d5f3 gnu: Add maven-plugin-annotations.
adds 9f25cba gnu: Add java-plexus-component-metadata.
adds b822544 gnu: Add maven-core.
adds e2c7d32 gnu: Add maven-embedder.
adds ff7a0fc gnu: Add maven-wagon-provider-api.
adds f216a9f gnu: Add maven-wagon-provider-test.
adds 0d1b3b3 gnu: Add maven-wagon-file.
adds 53360e4 gnu: Add maven-wagon-tck-http.
adds c3f5ec6 gnu: Add maven-wagon-http-shared.
adds aa06dd0 gnu: Add maven-wagon-http.
adds 19126bb gnu: Add maven-resolver-transport-wagon.
adds 0c1e98e gnu: Add maven-compat.
adds 8c2c105 gnu: Add maven.
adds 697a9d0 gnu: groovy: Add groovy-xml to the closure.
adds 806f599 gnu: wesnoth: Update to 1.14.3.
adds bba0fa2 Add guix-daemon Bash completion file.
adds e8b3a15 gnu: Add dehydrated.
adds f77886c gnu: Add restic.
adds 38ab778 doc: Clarify when branches are "frozen".
adds cdbcfc1 gnu: linux-libre: Fix build on AArch64.
adds 7727f91 gnu: openal: Update to 0.18.2.
adds 57b1dba gnu: libedit: Update to 20180525-3.1.
adds 406c83f gnu: perl: Fix CVE-2018-12015.
adds 259341c gnu: ldb: Fix build on 32-bit systems.
adds 30e26b6 gnu: ffmpeg: Update to 4.0.1.
adds ec8cdd0 gnu: maim: Update to 5.5.2.
adds 4c0df1a gnu: offlineimap: Update to 7.2.1.
adds ed2ae0d gnu: strace: Update to 4.23.
adds a14de83 gnu: upx: Fix CVE-2017-15056.
adds 3348e9f gnu: emacs-fish-completion: Don't propagate inputs.
adds 6710206 gnu: magit: Update to 2.13.0.
adds 554eaae gnu: diffoscope: Update to 96.
adds f3a34b9 gnu: gsl: Update to 2.5.
adds a89faa3 self: Install .go files to 'lib/guile/X.Y/site-ccache'.
adds f82fe68 gnu: Add perl-x11-protocol-other.
adds b2d5b00 gnu: Add perl-cpan-changes.
adds 048657c gnu: Add perl-module-manifest.
adds 52b1551 gnu: Add perl-test-distmanifest.
adds 32315df gnu: Add perl-file-finder.
adds 0943b0b gnu: Add perl-test-perltidy.
adds 469e827 gnu: perltidy: Update to 20180220.
adds c582917 gnu: clusterssh: Update to 4.13.2.
adds 33f61dc gnu: Remove Mr. Rescue.
adds b4eae99 gnu: texlive-bin: Use absolute path to ghostscript
executable "gs".
adds 47de00a gnu: encfs: Update to 1.9.5.
adds 021d629 gnu: address@hidden: Update to 4.4.138.
adds d5ce359 gnu: address@hidden: Update to 4.9.109.
adds 3b682b2 gnu: address@hidden: Update to 4.14.50.
adds d06352d gnu: linux-libre: Update to 4.17.2.
adds 32eb442 build-system/r: Accept #:r argument.
new 6969c4d Merge branch 'master' into staging
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 | 2 +-
Makefile.am | 28 +-
README | 3 +-
build-aux/hydra/gnu-system.scm | 3 +-
build-aux/pre-inst-env.in | 6 +-
configure.ac | 5 +-
doc/contributing.texi | 11 +-
doc/guix.texi | 69 +-
etc/completion/bash/guix-daemon | 30 +
gnu/build/install.scm | 59 +-
gnu/build/linux-modules.scm | 1 +
gnu/build/vm.scm | 6 +-
gnu/local.mk | 10 +-
gnu/packages/admin.scm | 80 +-
gnu/packages/aidc.scm | 5 +-
gnu/packages/audio.scm | 4 +-
gnu/packages/backup.scm | 127 +-
gnu/packages/base.scm | 11 +
gnu/packages/benchmark.scm | 10 +-
gnu/packages/bioconductor.scm | 308 +-
gnu/packages/bioinformatics.scm | 85 +-
gnu/packages/bootloaders.scm | 23 +-
gnu/packages/check.scm | 19 +-
gnu/packages/compression.scm | 12 +-
gnu/packages/cran.scm | 327 +-
gnu/packages/crypto.scm | 27 +-
gnu/packages/databases.scm | 4 +-
gnu/packages/dav.scm | 5 +-
gnu/packages/dns.scm | 2 +
gnu/packages/elixir.scm | 36 +-
gnu/packages/emacs.scm | 139 +-
gnu/packages/emulators.scm | 3 +-
gnu/packages/erlang.scm | 24 +
gnu/packages/fcitx.scm | 18 +-
gnu/packages/fonts.scm | 16 +-
gnu/packages/games.scm | 165 +-
gnu/packages/geo.scm | 4 +-
gnu/packages/gnome.scm | 4 +-
gnu/packages/gnupg.scm | 29 +-
gnu/packages/golang.scm | 8 +-
gnu/packages/graphics.scm | 4 +-
gnu/packages/groovy.scm | 3 +-
gnu/packages/gtk.scm | 2 +-
gnu/packages/guile.scm | 18 +-
gnu/packages/java.scm | 62 +
gnu/packages/libedit.scm | 4 +-
gnu/packages/linux.scm | 59 +-
gnu/packages/machine-learning.scm | 76 +
gnu/packages/mail.scm | 4 +-
gnu/packages/maths.scm | 11 +-
gnu/packages/maven.scm | 948 +-
gnu/packages/mes.scm | 8 +-
gnu/packages/networking.scm | 46 +-
gnu/packages/nickle.scm | 5 +-
gnu/packages/package-management.scm | 98 +-
gnu/packages/password-utils.scm | 5 +-
gnu/packages/patches/bind-CVE-2018-5738.patch | 100 +
.../binutils-aarch64-symbol-relocation.patch | 36 +
.../patches/elixir-disable-failing-tests.patch | 284 -
gnu/packages/patches/flann-cmake-3.11.patch | 84 +
.../patches/gnupg-1.4-CVE-2018-12020.patch | 50 -
.../patches/password-store-gnupg-compat.patch | 28 -
.../patches/perl-archive-tar-CVE-2018-12015.patch | 36 +
.../python-nose-timer-drop-ordereddict.patch | 44 -
gnu/packages/patches/strace-kernel-4.16.patch | 92 -
gnu/packages/patches/upx-fix-CVE-2017-15056.patch | 96 +
gnu/packages/perl-check.scm | 51 +
gnu/packages/perl.scm | 90 +-
gnu/packages/python.scm | 158 +-
gnu/packages/qt.scm | 50 +
gnu/packages/samba.scm | 9 +-
gnu/packages/spice.scm | 4 +-
gnu/packages/sssd.scm | 5 +-
gnu/packages/statistics.scm | 21 +-
gnu/packages/terminals.scm | 34 +
gnu/packages/tex.scm | 7 +-
gnu/packages/time.scm | 4 +-
gnu/packages/tls.scm | 83 +-
gnu/packages/tor.scm | 4 +-
gnu/packages/version-control.scm | 4 +-
gnu/packages/video.scm | 4 +-
gnu/packages/vim.scm | 95 +-
gnu/packages/virtualization.scm | 110 +
gnu/packages/web.scm | 110 +-
gnu/packages/wine.scm | 6 +-
gnu/packages/xdisorg.scm | 4 +-
gnu/packages/xml.scm | 20 +-
gnu/packages/xorg.scm | 29 +
gnu/services/base.scm | 5 +-
gnu/services/networking.scm | 6 +-
gnu/services/web.scm | 9 +-
gnu/system.scm | 8 +-
gnu/system/file-systems.scm | 11 +-
gnu/system/install.scm | 16 +-
gnu/system/mapped-devices.scm | 16 +-
gnu/system/vm.scm | 436 +-
gnu/tests/admin.scm | 7 +-
gnu/tests/base.scm | 62 +-
gnu/tests/dict.scm | 7 +-
gnu/tests/mail.scm | 13 +-
gnu/tests/messaging.scm | 14 +-
gnu/tests/nfs.scm | 7 +-
gnu/tests/rsync.scm | 7 +-
gnu/tests/ssh.scm | 8 +-
gnu/tests/version-control.scm | 20 +-
gnu/tests/web.scm | 8 +-
guix/build-system/r.scm | 4 +-
guix/build/store-copy.scm | 121 +-
guix/config.scm.in | 12 +-
guix/import/utils.scm | 2 +-
guix/nar.scm | 3 +-
guix/scripts/offload.scm | 14 +-
guix/scripts/pack.scm | 243 +-
guix/scripts/pull.scm | 149 +-
guix/scripts/substitute.scm | 4 +-
guix/scripts/system.scm | 3 +-
guix/self.scm | 88 +-
guix/store.scm | 29 -
guix/store/database.scm | 235 +-
guix/store/deduplication.scm | 13 +-
{nix/libstore => guix/store}/schema.sql | 0
guix/ui.scm | 7 +-
guix/utils.scm | 6 +
nix/guix-register/guix-register.cc | 254 -
nix/libstore/store-api.cc | 26 -
nix/libstore/store-api.hh | 4 -
nix/local.mk | 18 +-
po/doc/guix-manual.fr.po | 18381 ++++---------------
tests/gexp.scm | 17 +-
tests/guix-register.sh | 191 -
tests/store-database.scm | 45 +-
tests/store-deduplication.scm | 9 +-
tests/store.scm | 22 +-
133 files changed, 8299 insertions(+), 17094 deletions(-)
create mode 100644 etc/completion/bash/guix-daemon
create mode 100644 gnu/packages/patches/bind-CVE-2018-5738.patch
create mode 100644
gnu/packages/patches/binutils-aarch64-symbol-relocation.patch
delete mode 100644 gnu/packages/patches/elixir-disable-failing-tests.patch
create mode 100644 gnu/packages/patches/flann-cmake-3.11.patch
delete mode 100644 gnu/packages/patches/gnupg-1.4-CVE-2018-12020.patch
delete mode 100644 gnu/packages/patches/password-store-gnupg-compat.patch
create mode 100644 gnu/packages/patches/perl-archive-tar-CVE-2018-12015.patch
delete mode 100644
gnu/packages/patches/python-nose-timer-drop-ordereddict.patch
delete mode 100644 gnu/packages/patches/strace-kernel-4.16.patch
create mode 100644 gnu/packages/patches/upx-fix-CVE-2017-15056.patch
rename {nix/libstore => guix/store}/schema.sql (100%)
delete mode 100644 nix/guix-register/guix-register.cc
delete mode 100644 tests/guix-register.sh
- branch staging updated (69e0aac -> 6969c4d),
Marius Bakke <=