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branch staging updated (98bb983 -> e4cddbb)

From: Marius Bakke
Subject: branch staging updated (98bb983 -> e4cddbb)
Date: Mon, 22 May 2017 08:57:53 -0400 (EDT)

mbakke pushed a change to branch staging
in repository guix.

      from  98bb983   gnu: ruby: Update to 2.4.0.
      adds  4100698   doc: Suggest a network test command that will definitely 
be available.
      adds  e0b2e93   system: grub: Expose GRUB's interactive interface 
      adds  6344e95   maint: Really build GuixSD for different systems.
      adds  73c791b   maint: 'release' now depends on 'dist', not 'distcheck'.
      adds  5898968   gnu: Add thermald.
      adds  d7fa39c   services: Add 'thermald-service-type'.
      adds  1edbdb0   gnu: par2cmdline: Update to 0.7.0
      adds  d0abaf8   gnu: Add catdoc.
      adds  9eb0f43   gnu: Update kde frameworks to 5.34.0.
      adds  9b22c4d   gnu: ffmpeg: Update to 3.3.1.
      adds  6365733   doc: Document certificate environment variable needed for 
      adds  9fdda0b   gnu: librecad: Use modular Qt.
      adds  504c285   gnu: Add dcmtk.
      adds  751f858   gnu: Add http-parser.
      adds  dbe874d   gnu: Add ding-libs.
      adds  7fe4e55   gnu: Add sssd.
      adds  cdb2a21   gnu: Add mia.
      adds  90e65ab   gnu: Add java-mockito-1.
      adds  4f4d2e4   gnu: Add java-httpcomponents-httpcore.
      adds  3a068b4   gnu: Add java-httpcomponents-httpcore-nio.
      adds  e1dd78f   gnu: Add java-httpcomponents-httpcore-ab.
      adds  14a671d   gnu: Add java-httpcomponents-httpclient.
      adds  cbce5de   gnu: Add java-httpcomponents-httpmime.
      adds  4b34c21   gnu: Add java-commons-net.
      adds  808cb58   gnu: Add java-jsch.
      adds  a624469   gnu: Add java-commons-compress.
      adds  c48a145   system: grub: Actually default to 'gfxterm' for 
displaying the GRUB menu.
      adds  d44bcd7   gnu: Add java-asm.
      adds  b13a7cf   gnu: Add java-commons-net.
      adds  18fe5ef   gnu: Add libusb4java.
      adds  423b684   gnu: Add java-usb4java.
      adds  ff3f676   gnu: Add java-rsyntaxtextarea.
      adds  77d7b57   gnu: Add java-simple-xml.
      adds  6ee6d0b   gnu: Add java-osgi-annotation.
      adds  37e2e5d   gnu: Add java-osgi-core.
      adds  674e93a   gnu: Add java-eclipse-osgi.
      adds  81b55b1   gnu: Add java-eclipse-equinox-common.
      adds  8af92c8   gnu: Add java-osgi-service-event.
      adds  90368ad   gnu: Add java-eclipse-core-jobs.
      adds  fbaf09e   gnu: Add java-eclipse-equinox-registry.
      adds  65214c8   gnu: Add java-eclipse-equinox-app.
      adds  3f97021   gnu: Add java-eclipse-equinox-preferences.
      adds  4ad3d4f   gnu: Add java-eclipse-core-contenttype.
      adds  6a7f7e4   gnu: Add java-eclipse-core-runtime.
      adds  b3806a1   gnu: Add java-eclipse-core-filesystem.
      adds  e96060d   gnu: Add java-eclipse-core-expressions.
      adds  e8d0f7c   gnu: Add java-eclipse-core-variables.
      adds  7c3d479   gnu: Add java-eclipse-ant-core.
      adds  6636f63   gnu: Add java-eclipse-core-resources.
      adds  1d4234d   gnu: Add java-icu4j.
      adds  afb5858   gnu: Add java-eclipse-compare-core.
      adds  1bb191f   gnu: Add java-eclipse-team-core.
      adds  3134252   gnu: Add java-eclipse-core-commands.
      adds  bf96acf   gnu: Add java-eclipse-text.
      adds  c24d11b   gnu: Add java-eclipse-jdt-core.
      adds  0e660c4   gnu: Add java-log4j-api.
      adds  095494e   licenses: Add EDL 1.0.
      adds  a5cdcf6   gnu: Add java-javax-mail.
      adds  46bb58b   gnu: Add non-mixer.
      adds  4511e0d   gnu: Add non-timeline.
      adds  3ad9039   gnu: antlr2: Simplify build phases.
      adds  6d225e8   gnu: antlr2: Minor stylistic changes.
      adds  f411124   utils: 'compressed-file?' matches ".lzma" files.
      adds  b7ebcfe   doc: Mention 'GUIX_PACKAGE_PATH' in "Defining Packages".
      adds  c22c9fa   services: guix: Authorize the key for
      adds  0e2bfa3   doc: Mention 'sync' after 'dd'.
      adds  a068300   gnu: bind: Rename variable to 'isc-bind'.
      adds  4a3495d   gnu: khard: Update to 0.11.4.
      adds  d116695   hydra: Cross-build Guile 2.2.
      adds  5a3429b   gnu: guile-ssh: Fix bug in 'node-guile-version'.
      adds  ce92d26   ui: Disable Guile deprecation warnings by default.
      adds  b09a8da   bootloader: Add extlinux support.
      adds  9121ce5   bootloader: Adapt vm to new bootloader API.
      adds  bcaf67c   bootloader: Add bootloader name to boot-parameters record.
      adds  3042c5d   scripts: system: Adapt "reconfigure" to new bootloader 
      adds  1229d32   scripts: system: Adapt "init" to new bootloader API.
      adds  3241f7f   scripts: system: Adapt "switch-generation" to new 
bootloader API.
      adds  5641dff   scripts: system: Display bootloader name in 
      adds  7ee7ee1   gnu: guix: Update snapshot.
      adds  14afc7b   gnu: cl-slynk: Clarify the description.
      adds  75e8b3a   gnu: cl-slynk: Explain some naming choices.
      adds  bc389c2   build-system/asdf: Rename %install-prefix to 
      adds  6c76ce3   build-system/asdf: Make it possible to use "lib" as the 
build output.
      adds  290bf61   gnu: cl-stumpwm: Build the library in "lib" and the 
program in "bin".
      adds  3518972   build-system/asdf: Use asdf to determine dependencies.
      adds  0e1371b   build-system/asdf: Don't rename inputs.
      adds  26a16d3   build-system/asdf: Keep ecl's generated archive files.
      adds  6de91ba   build-system/asdf: Make #:lisp a package argument.
      adds  b4c9f0c   build-system/asdf: Parameterize the lisp type and 
implementation globally.
      adds  457702b   build-system/asdf: Pass the system name as an argument to 
the builder.
      adds  0186a46   build-system/asdf: Always pre-load the system's 
definition file.
      adds  40f5617   build-system/asdf: Handle unusually-named systems.
      adds  ac25925   gnu: Add cl-unicode.
      adds  b9afcb9   build-system/asdf: Simplify the use of lisp-eval-program.
      adds  4209c31   build-system/asdf: Retain references to source files for 
binary outputs.
      adds  f56da60   gnu: sbcl-slynk-boot0: Give the package an appropriate 
      adds  0383afa   build-system/asdf: Handle tests defined in external 
      adds  8a3814c   doc: Update the documentation for the asdf build systems.
      adds  e44112e   gnu: Rename stringtemplate3 to java-stringtemplate-3.
      adds  129d926   gnu: java-stringtemplate-3: Do not hardcode version 
      adds  2fcda6d   gnu: java-stringtemplate-3: Enable tests.
      adds  b101b4e   gnu: java-stringtemplate-3: Use return value in build 
      adds  407df78   gnu: stringtemplate4: Inherit from java-stringtemplate-3.
      adds  f4aa4cf   gnu: stringtemplate4: Prettify "generate-grammar" phase.
      adds  64b7efc   gnu: Rename stringtemplate4 to java-stringtemplate.
      adds  1345eeb   gnu: Rename stringtemplate4-4.0.6 to 
      adds  6db77c7   gnu: java-stringtemplate: Get closer to fixing tests.
      adds  ca05bc0   gnu: tor: Update to
      adds  7c9fcb0   import cran: Fetch DESCRIPTION files from Github mirror.
      adds  c9ffa91   import cran: Exclude experiment packages in predicate 
      adds  daaa270   import cran: Add predicate for Bioconductor experiment 
      adds  ff8c179   import cran: Export package predicates.
      adds  a0f4320   import cran: Refactor "needs-zlib?".
      adds  17a69cf   import cran: Check if pkg-config is needed.
      adds  231e48d   gnu: emacspeak: Update to 46.0.
      adds  711a0dc   gnu: glibc/hurd: Use modify-phases syntax.
      adds  441e99d   gnu: glibc/hurd: Do not apply i686 patch.
      adds  16dcac5   gnu: php: Update to 7.1.5.
      adds  516bfed   profiles: Add elapsed time to manual-database hook to 
output message.
      adds  e0bb0a8   gnu: mes: Update to 0.6.
      adds  473f34c   gnu: bundler: Update to 1.14.6.
      adds  21aecec   gnu: ruby-concurrent: Update to 1.0.5.
      adds  44a0591   gnu: certbot, python-acme: Update to 0.14.1.
      adds  8d17147   gnu: ruby-rack: Update to 2.0.3.
      adds  e7620b6   gnu: qemu: Fix CVE-2017-7493.
      adds  5afc737   gnu: mes: Don't fail when (%current-target-system) is #f.
      adds  102a0e8   gnu: emacs-org: Update to 20170515.
      adds  be62e22   build: Compile stackage only if 'guile-json' is available.
      adds  6d35b1c   gnu: aspell: 'dict-dir' set to ~/.guix-profile/lib/aspell 
      adds  411ba51   gnu: Add gspell.
      adds  872a6fd   gnu: tailon: Use absolute paths for commands.
      adds  4b236c8   maint: The 'release' target builds a VM image.
      adds  42ba7b6   gnu: address@hidden: Update to 4.4.68.
      adds  d6a0218   gnu: address@hidden: Update to 4.9.28.
      adds  05bf7f5   gnu: linux-libre: Update to 4.11.1.
      adds  ec84c78   gnu: gnubg: Update to 1.05.
      adds  32199e9   gnu: fizmo: Update to 0.8.4.
      adds  07bf68e   services: openssh: Don't depend on networking.
      adds  c80cd4d   install: Enable SSH in installation image.
      adds  45433bb   gnu: mc: Add unzip to inputs.
      adds  e28cb7a   gnu: gamine: Update to 1.5.
      adds  6aa095f   gnu: manaplus: Update to
      adds  b193fb2   gnu: shadow: Update to 4.5.
      adds  89c83e8   gnu: npth: Update to 1.4.
      adds  0be20a8   gnu: gnupg: Update to 2.1.21.
      adds  b81b894   gnu: openttd: Update to 1.7.0.
      adds  7c5cf7a   gnu: qtscript: Fix building on aarch64.
      adds  45f5bc0   gnu: qtconnectivity: Fix building on armhf and aarch64.
      adds  04f8dec   gnu: qtbase: Don't use bundled double-conversion.
      adds  4e825e2   gnu: qtbase: Update configure flags.
      adds  a20e00d   gnu: qt: Update to 5.8.0.
      adds  41f76ae   services: user-homes: Do not create home directories 
marked as no-create.
      adds  22ef06b   union: Gracefully handle dangling symlinks in the input.
      adds  8ad37ad   bootloader: extlinux: Remove undefined symbols from 
export list.
      adds  7fb6a9d   bootloader: extlinux: Remove syslinux-bootloader.
      adds  51ef4af   gnu: emacs-async: Update to 1.9.2.
      adds  12e72d2   gnu: emacs-helm: Update to 2.7.0.
      adds  03cc1cf   gnu: Add emacs-helm-swoop.
      adds  f69c29f   gnu: Add emacs-helm-projectile.
      adds  2b18ad0   gnu: Add gemma.
      adds  27c81fc   lint: inputs-should-be-native: Add "cmake".
      adds  8cf6a63   gnu: nano: Update to 2.8.3.
      adds  4d2e1d1   gnu: mcelog: Update to 150.
      adds  acf82a1   gnu: btrfs-progs: Update to 4.11.
      adds  ffa5e0a   publish: Fix narinfo rendering for already-compressed 
      adds  7afc2aa   modules: Add more source-less modules.
      adds  e7fbd49   gnu: guile-ssh: Fix potential double-free/use-after-free 
      adds  01cc84d   vm: Support arbitrary partition flags.
      adds  4d415f0   vm: Support creating FAT partitions.
      adds  ecf5d53   vm: Add UEFI loader to disk images.
      adds  8ea98ee   doc: Update for UEFI systems.
      adds  f6da41b   gnu: python-sip: Update to 4.19.2.
      adds  5ac3a67   gnu: python-pyqt: Update to 5.8.2.
      adds  41fa164   gnu: address@hidden: Update to 4.12.
      adds  b55dd31   system: Use Guile 2.2 rather than 2.0 in %BASE-PACKAGES.
      adds  cd6171c   gnu: calibre: Update to 2.85.1.
      adds  7010d23   gnu: calibre: Import dont-load-icons patch from debian.
      adds  d94a99e   gnu: calibre: Import unbundle feedparser patch from 
      adds  29ec085   gnu: calibre: Unbundle python2-markdown.
      adds  b3399a0   gnu: calibre: Unbundle liberation fonts.
      adds  eeba7d3   gnu: calibre: Unbundle chardet.
      adds  9b7dcc2   gnu: calibre: Add missing dependencies.
      adds  affaf98   gnu: calibre: Add exhaustive license list.
      adds  1326166   gnu: calibre: Don't create uninstaller.
      adds  70f8242   gnu: dropbear: Update to 2017.75 [fixes 
      adds  cc5a76a   gnu: Add loksh.
      adds  d30ce4a   gnu: address@hidden: Update to 2.6.10 [security fixes].
      adds  d6bf931   pack: Use 'guile2.0-json' when building with Guile 2.0.
      adds  74460d1   gnu: libssh, guile-ssh: Add a "debug" output.
      adds  82ce81b   gnu: guix: Add 'guile2.0-guix'.
      adds  40fd560   download: Prune the ImageMagick mirror list.
      adds  b17bd26   gnu: imagemagick: Update to 6.9.8-6.
      adds  db531f7   gnu: address@hidden: Update to 3.4.0 [security fixes].
      adds  12eecbf   gnu: address@hidden: Add aarch32-drop.
      adds  fefd4c1   gnu: pcsc-lite: Update to 1.8.21.
      adds  10cb88f   gnu: jbig2dec: Fix CVE-2017-{7885,7975,7976}.
      adds  fda33e4   gnu: ghostscript: Add TODO comment about bundled jbig2dec.
      adds  9a1bfe7   vm: Increase default disk size to account for ESP 
      adds  9f8d6eb   gnu: unionfs-fuse-static: Remove 'unionfsctl' executable.
      adds  ec8d69e   gnu: address@hidden: Update to 4.4.69.
      adds  519fd6c   gnu: address@hidden: Update to 4.9.29.
      adds  a08691d   gnu: linux-libre: Remove CONFIG_SMC from x86 kernel 
      adds  718448e   gnu: linux-libre: Update to 4.11.2.
      adds  8b1ff6f   gnu: vim-full: Disable failing test.
      adds  18f61e0   gnu: vim: Update to 8.0.0600.
      adds  31044e6   gnu: nano: Update to 2.8.4.
      adds  20d2e1f   gnu: fio: Update to 2.20.
      adds  1d0aa4d   gnu: ccid: Update to 1.4.27.
      adds  c522f57   gnu: python-future: Update to 0.16.0.
      adds  abc08cb   gnu: python-biom-format: Update to 2.1.6.
      adds  88682c9   gnu: fasttree: Update to 2.1.10.
      adds  ef81341   gnu: diamond: Update to 0.9.0.
      adds  ba58886   gnu: libaacs: Update to 0.9.0.
      adds  3bc45ad   gnu: vlc: Update to
      adds  cfa7473   gnu: x265: Update to 2.4.
      adds  f1d1ef7   gnu: v4l-utils: Update to 1.12.5.
      adds  65efb3c   bootloader: extlinux: Add a warning message on top of 
generated conf file.
      adds  b458413   gnu: r-mutationalpatterns: Update to 1.2.1.
      adds  3cbfc14   gnu: taxtastic: Update to 0.6.4.
      adds  7569613   gnu: roary: Update to 3.8.2.
      adds  7429723   gnu: fraggenescan: Update to 1.30.
       new  e4cddbb   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:
 .dir-locals.el                                     |    1 +                                        |   37 +-
 build-aux/hydra/gnu-system.scm                     |    2 +-
 doc/guix.texi                                      |  177 ++-
 gnu.scm                                            |    4 +-
 gnu/bootloader.scm                                 |  127 ++
 gnu/bootloader/extlinux.scm                        |  120 ++
 gnu/{system => bootloader}/grub.scm                |  184 ++-
 gnu/build/activation.scm                           |    9 +-
 gnu/build/install.scm                              |   36 +-
 gnu/build/vm.scm                                   |  127 +-
 gnu/                                       |   21 +-
 gnu/packages/admin.scm                             |   60 +-
 gnu/packages/aspell.scm                            |   18 +-
 gnu/packages/aux-files/linux-libre/4.11-i686.conf  |    3 +-
 .../aux-files/linux-libre/4.11-x86_64.conf         |    3 +-
 gnu/packages/backup.scm                            |   15 +-
 gnu/packages/base.scm                              |  121 +-
 gnu/packages/benchmark.scm                         |    8 +-
 gnu/packages/bioinformatics.scm                    |  102 +-
 gnu/packages/dns.scm                               |    4 +-
 gnu/packages/ebook.scm                             |   72 +-
 gnu/packages/emacs.scm                             |  113 +-
 gnu/packages/engineering.scm                       |    3 +-
 gnu/packages/games.scm                             |   26 +-
 gnu/packages/ghostscript.scm                       |    1 +
 gnu/packages/gnome.scm                             |   54 +
 gnu/packages/gnupg.scm                             |   12 +-
 gnu/packages/icu4c.scm                             |   29 +
 gnu/packages/image-processing.scm                  |  130 ++
 gnu/packages/image.scm                             |    5 +-
 gnu/packages/imagemagick.scm                       |    4 +-
 gnu/packages/java.scm                              | 1250 ++++++++++++++++++--
 gnu/packages/kde-frameworks.scm                    |  302 ++---
 gnu/packages/libusb.scm                            |  100 +-
 gnu/packages/linux.scm                             |   27 +-
 gnu/packages/lisp.scm                              |  159 ++-
 gnu/packages/logging.scm                           |   15 +
 gnu/packages/mail.scm                              |    4 +-
 gnu/packages/mc.scm                                |    8 +-
 gnu/packages/mes.scm                               |   27 +-
 gnu/packages/music.scm                             |   51 +
 gnu/packages/nano.scm                              |    4 +-
 gnu/packages/package-management.scm                |   19 +-
 gnu/packages/patches/aspell-default-dict-dir.patch |   20 +
 .../patches/calibre-dont-load-remote-icons.patch   |   45 +
 gnu/packages/patches/calibre-drop-unrar.patch      |   48 +-
 .../patches/calibre-use-packaged-feedparser.patch  |   51 +
 gnu/packages/patches/gspell-dash-test.patch        |   16 +
 gnu/packages/patches/guile-ssh-double-free.patch   |   37 +
 gnu/packages/patches/guile-ssh-rexec-bug.patch     |   16 +
 gnu/packages/patches/jbig2dec-CVE-2017-7885.patch  |   38 +
 gnu/packages/patches/jbig2dec-CVE-2017-7975.patch  |   40 +
 gnu/packages/patches/jbig2dec-CVE-2017-7976.patch  |  122 ++
 ...networkmanager-qt-activeconnection-test-1.patch |   60 -
 ...networkmanager-qt-activeconnection-test-2.patch |   57 -
 gnu/packages/patches/qemu-CVE-2017-7493.patch      |  182 +++
 gnu/packages/patches/qtscript-disable-tests.patch  |   64 +
 .../patches/ruby-concurrent-test-arm.patch         |   26 +-
 .../patches/shadow-4.4-su-snprintf-fix.patch       |   31 -
 gnu/packages/patches/shadow-CVE-2017-2616.patch    |   72 --
 gnu/packages/php.scm                               |   10 +-
 gnu/packages/python.scm                            |    4 +-
 gnu/packages/qemu.scm                              |    1 +
 gnu/packages/qt.scm                                |  162 +--
 gnu/packages/ruby.scm                              |   12 +-
 gnu/packages/security-token.scm                    |   12 +-
 gnu/packages/shells.scm                            |   37 +
 gnu/packages/ssh.scm                               |    8 +-
 gnu/packages/sssd.scm                              |  173 +++
 gnu/packages/textutils.scm                         |   76 +-
 gnu/packages/tls.scm                               |    7 +-
 gnu/packages/tor.scm                               |    6 +-
 gnu/packages/video.scm                             |   27 +-
 gnu/packages/vim.scm                               |    8 +-
 gnu/packages/web.scm                               |   32 +
 gnu/packages/xml.scm                               |   31 +
 gnu/services/base.scm                              |    3 +-
 gnu/services/pm.scm                                |   41 +-
 gnu/services/ssh.scm                               |    2 +-
 gnu/system.scm                                     |   28 +-
 gnu/system/examples/lightweight-desktop.tmpl       |   30 +-
 gnu/system/examples/vm-image.tmpl                  |   53 +
 gnu/system/install.scm                             |   12 +
 gnu/system/linux-initrd.scm                        |    4 +-
 gnu/system/vm.scm                                  |   60 +-
 gnu/tests.scm                                      |    3 +-
 gnu/tests/base.scm                                 |   22 +
 gnu/tests/nfs.scm                                  |    3 +-
 guix/build-system/asdf.scm                         |  109 +-
 guix/build/asdf-build-system.scm                   |  182 ++-
 guix/build/lisp-utils.scm                          |  384 +++---
 guix/build/union.scm                               |   43 +-
 guix/download.scm                                  |    3 -
 guix/import/cran.scm                               |  101 +-
 guix/licenses.scm                                  |    6 +
 guix/modules.scm                                   |   11 +-
 guix/profiles.scm                                  |   18 +-
 guix/scripts/lint.scm                              |    3 +-
 guix/scripts/pack.scm                              |   11 +-
 guix/scripts/publish.scm                           |    3 +-
 guix/scripts/system.scm                            |  236 ++--
 guix/ui.scm                                        |    7 +
 guix/utils.scm                                     |    2 +-
 tests/profiles.scm                                 |   29 +
 tests/publish.scm                                  |   71 +-
 106 files changed, 5098 insertions(+), 1507 deletions(-)
 create mode 100644 gnu/bootloader.scm
 create mode 100644 gnu/bootloader/extlinux.scm
 rename gnu/{system => bootloader}/grub.scm (67%)
 create mode 100644 gnu/packages/image-processing.scm
 create mode 100644 gnu/packages/patches/aspell-default-dict-dir.patch
 create mode 100644 gnu/packages/patches/calibre-dont-load-remote-icons.patch
 create mode 100644 gnu/packages/patches/calibre-use-packaged-feedparser.patch
 create mode 100644 gnu/packages/patches/gspell-dash-test.patch
 create mode 100644 gnu/packages/patches/guile-ssh-double-free.patch
 create mode 100644 gnu/packages/patches/guile-ssh-rexec-bug.patch
 create mode 100644 gnu/packages/patches/jbig2dec-CVE-2017-7885.patch
 create mode 100644 gnu/packages/patches/jbig2dec-CVE-2017-7975.patch
 create mode 100644 gnu/packages/patches/jbig2dec-CVE-2017-7976.patch
 delete mode 100644 
 delete mode 100644 
 create mode 100644 gnu/packages/patches/qemu-CVE-2017-7493.patch
 create mode 100644 gnu/packages/patches/qtscript-disable-tests.patch
 delete mode 100644 gnu/packages/patches/shadow-4.4-su-snprintf-fix.patch
 delete mode 100644 gnu/packages/patches/shadow-CVE-2017-2616.patch
 create mode 100644 gnu/packages/sssd.scm
 create mode 100644 gnu/system/examples/vm-image.tmpl

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