services: openssh-service-type: Expose 'openssh-configuration'.

* gnu/services/ssh.scm (<openssh-configuration>): Add default values.
[pubkey-authentication?]: Rename to...
[public-key-authentication?]: ... this.
(openssh-service): Remove.
* doc/guix.texi (Networking Services): Adjust accordingly.

services: Add rottlog.

* gnu/services/admin.scm: New file.
* gnu/local.mk (GNU_SYSTEM_MODULES): Add it.
* doc/guix.texi (Log Rotation): New node.

Co-authored-by: Ludovic Courtès <ludo@gnu.org>

gnu: ghc-process: Replace reference to /bin/sh.

* gnu/packages/haskell.scm (ghc-process)[arguments]: Add phases
"patch-reference-to-/bin/sh" to replace reference to /bin/sh.

gnu: Do not propagate inputs in haskell.scm.

* gnu/packages/haskell.scm
(ghc-streaming-commons)[propagated-inputs]: Move ghc-random...
[inputs]: ...to here; remove ghc-async, add ghc-directory, add
ghc-transformers; move ghc-quickcheck, ghc-hspec...
[native-inputs]: ...to here; add hspec-discover.

(ghc-test-framework)[propagated-inputs]: Move all from here...
[inputs]: ...to here; move ghc-hunit and ghc-quickcheck...
[native-inputs]: ...to here.

(ghc-attoparsec)[propagated-inputs]: Move ghc-scientific...
[inputs]: ...to here; move ghc-quickcheck, ghc-quickcheck-unicode,
ghc-test-framework, ghc-test-framework-quickcheck2, ghc-vector...
[native-inputs]: ...to here.

(ghc-zip-archive)[propagated-inputs]: Move all inputs from here...
[inputs]: ...to here; move ghc-hunit from here...
[native-inputs]: ...to here.

(ghc-network-uri)[inputs]: Add ghc-parsec; move ghc-hunit from here...
[native-inputs]: ...to here.
[propagated-inputs]: Remove.

(ghc-wai)[propagated-inputs]: Move all inputs from here...
[inputs]: ...to here; move ghc-quickcheck, ghc-hunit, and ghc-hspec from
here...
[native-inputs]: ...to here.  Add hspec-discover.

(ghc-wai-extra)[propagated-inputs]: Remove ghc-hspec and ghc-hunit; move
all other inputs from here...
[inputs]: ...to here.
[native-inputs]: Add hspec-discover, ghc-hspec, and ghc-hunit.

(ghc-resourcet, ghc-xss-sanitize, ghc-parsec, ghc-vector, ghc-http,
ghc-base-compat, ghc-base-orphans, ghc-word8)[inputs]: Move all inputs
from here...
[native-inputs]: ...to here.

(ghc-haddock-library, ghc-hspec-contrib, ghc-base-compat,
ghc-base-orphans, ghc-fast-logger, ghc-word8, ghc-aeson-qq,
ghc-logging-facade, ghc-mockery, ghc-yaml, ghc-hslua)[native-inputs]:
Add hspec-discover.

(ghc-fast-logger)[inputs]: Move ghc-hspec from here...
[native-inputs]: ...to here.

(ghc-data-default,
ghc-data-default-instances-base,
ghc-data-default-instances-containers,
ghc-data-default-instances-dlist,
ghc-haddock-api,
ghc-happy,
ghc-haskell-src-exts,
ghc-resourcet,
ghc-xss-sanitize,
ghc-sdl-mixer,
ghc-sdl-image,
ghc-glut,
ghc-gluraw,
ghc-opengl,
cpphs,
ghc-old-time,
ghc-data-default-instances-old-locale,
cabal-install,
ghc-x11,
ghc-x11-xft,
ghc-hashable,
ghc-test-framework-hunit,
ghc-test-framework,
ghc-tf-random,
ghc-transformers-base,
ghc-unix-time,
ghc-http-types,
ghc-iproute,
ghc-regex-base,
ghc-regex-posix,
ghc-regex-tdfa-rc,
ghc-parsers,
ghc-trifecta,
ghc-distributive,
ghc-comonad,
ghc-polyparse,
ghc-profunctors,
ghc-reducers,
ghc-xml,
ghc-exceptions,
ghc-temporary,
ghc-temporary-rc,
ghc-smallcheck,
ghc-tasty-ant-xml,
ghc-quickcheck-instances,
ghc-quickcheck,
ghc-case-insensitive,
ghc-chasingbottoms,
ghc-unordererd-containers,
ghc-uniplate,
ghc-ansi-wl-pprint,
ghc-parsec,
ghc-vector,
ghc-vector-binary-instances,
ghc-http,
ghc-hspec,
ghc-hspec-contrib,
ghc-hspec-core,
ghc-hspec-meta,
ghc-vault,
ghc-monad-control,
ghc-blaze-builder,
ghc-blaze-markup,
ghc-blaze-html,
ghc-async,
ghc-optparse-applicative,
ghc-charset,
ghc-void,
ghc-kan-extensions,
ghc-statevar,
ghc-lens,
ghc-cheapskate,
ghc-semigroupoids,
ghc-contrvariant,
ghc-semigroups,
ghc-free,
ghc-adjunctions,
ghc-fast-logger,
ghc-doctest,
ghc-lifted-base,
ghc-tasty-quickcheck,
ghc-tasty-golden,
ghc-tasty,
ghc-cookie,
ghc-scientific,
ghc-aeson,
ghc-wai-logger,
ghc-pandoc-types,
ghc-texmath,
ghc-regex-pcre-builtin,
ghc-highlighting-kate,
ghc-cmark,
ghc-enclosed-exceptions,
ghc-th-lift,
ghc-th-expand-syns,
ghc-th-reify-many,
ghc-th-orphans,
ghc-haskell-src-meta,
ghc-aeson-qq,
ghc-conduit,
ghc-mockery,
ghc-yaml,
ghc-filemanip,
ghc-juicypixels,
ghc-hslua,
ghc-mime-types,
ghc-http-client,
ghc-hourglass,
ghc-pem,
ghc-asn1-types,
ghc-asn1-encoding,
ghc-asn1-parse,
ghc-tasty-kat,
ghc-cryptonite,
ghc-x509,
ghc-x509-store,
ghc-x509-validation,
ghc-x509-system,
ghc-tls,
ghc-socks,
ghc-connection,
ghc-http-client-tls,
ghc-pandoc)[propagated-inputs]: Move inputs from here...
[inputs]: ...to here.

gnu: r-plotly: Update to 4.5.2.

* gnu/packages/statistics.scm (r-plotly): Update to 4.5.2.
[propagated-inputs]: Remove r-plyr; remove r-viridis; add r-dplyr; add
r-lazyeval; add r-purrr; add r-tibble; add r-viridislite.

gnu: Add r-purrr.

* gnu/packages/statistics.scm (r-purrr): New variable.

gnu: Add r-viridislite.

* gnu/packages/statistics.scm (r-viridislite): New variable.

gnu: libotf: Fix source URI.

* gnu/packages/fontutils.scm (libotf)[source]: Fix suorce URI.

gnu: vsearch: Update to 2.1.2.

* gnu/packages/bioinformatics.scm (vsearch): Update to 2.1.2.

gnu: ffmpeg: Update to 3.1.4.

* gnu/packages/video.scm (ffmpeg): Update to 3.1.4.

gnu: linux-libre: Update to 4.7.6.

* gnu/packages/linux.scm (linux-libre): Update to 4.7.6.

gnu: linux-libre@4.4: Update to 4.4.23.

* gnu/packages/linux.scm (linux-libre-4.4): Update to 4.4.23.

gnu: guitarix: Update to 0.35.1.

* gnu/packages/audio.scm (guitarix): Update to 0.35.1.

gnu: eigen: Update to 3.2.9.

* gnu/packages/algebra.scm (eigen): Update to 3.2.9.

gnu: julia: Update to 0.5.0.

* gnu/packages/julia.scm (libuv-julia): Update to commit
8d5131b6c1595920dd30644cd1435b4f344b46c8.
(libunwind-for-julia): New variable.
(julia): Update to 0.5.0.
[arguments]: Disable stripping of binaries; modify "prepare-deps" phase;
add "fix-llvm-flag" phase; add "set-home" phase; adjust
"hardcode-soname-map" phase; remove fix for "double-conversion" from
"fix-include-and-link-paths" phase; enable "repl" and "replcompletions"
tests; disable "backtrace", "compile", "replutil", and "cmdlineargs"
tests; remove USE_SYSTEM_RMATH flag; remove USE_SYSTEM_GRISU flag.
[inputs]: Replace "llvm-3.5" with "llvm"; replace "libunwind" with
"libunwind-for-julia"; remove "double-conversion"; remove "rmath-julia";
update "suitesparse" origin; replace "virtualenv" origin with
"python2-virtualenv".
[native-inputs]: Add "openssl".

gnu: utf8proc: Update to 2.0.2.

* gnu/packages/textutils.scm (utf8proc): Update to 2.0.2.

gnu: gd: Fix CVE-2016-7568.

* gnu/packages/patches/gd-CVE-2016-7568.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/gd.scm (gd)[source]: Use it.

gnu: rpcbind-configuration: Rename pkg to nfs-utils

* gnu/services/nfs.scm (<rpcbind-configuration>): "pkg" --> "nfs-utils"

gnu: Add quickswitch-i3.

* gnu/packages/wm.scm (quickswitch-i3): New variable.
* gnu/packages/patches/quickswitch-fix-dmenu-check.patch: New file.
* gnu/local.mk (dist_patch_DATA): Register it.

Signed-off-by: 宋文武 <iyzsong@gmail.com>

gnu: Add python-i3-py.

* gnu/packages/wm.scm (python-i3-py, python2-i3-py): New variables.

Signed-off-by: 宋文武 <iyzsong@gmail.com>

gnu: Add emacs-rudel.

* gnu/packages/emacs.scm (emacs-rudel): New variable.

Signed-off-by: 宋文武 <iyzsong@gmail.com>

gnu: shroud: Wrap 'shroud' with 'GUILE_LOAD_COMPILED_PATH'.

* gnu/packages/password-utils.scm (shroud)[arguments]: New field.

gnu: tmux: Update to 2.3.

* gnu/packages/tmux.scm (tmux): Update to 2.3.

gnu: libreoffice: Update to 5.1.5.2.

* gnu/packages/libreoffice.scm (libreoffice): Update to 5.1.5.2.

build: Improve Guile 2.2 compatibility.

* build-aux/compile-all.scm (compile-file*): Ensure loading of
  compilation related modules before going parallel.
* guix/build/pull.scm (build-guix): Ditto.

gnu: xonsh: Remove bundled PLY.

* gnu/packages/shells.scm (xonsh)[source]: Add snippet to remove bundled
python-ply.
[inputs]: Add python-ply.

Signed-off-by: Leo Famulari <leo@famulari.name>

services: Add 'openssh-service'.

* gnu/packages/ssh.scm (openssh)[arguments]: Set sysconfdir to /etc/ssh.
* gnu/services/ssh.scm (<openssh-configuration>): New record type.
(%openssh-accounts): New variable.
(openssh-activation, openssh-config-file, openssh-shepherd-service)
(openssh-service): New procedures.
(openssh-service-type): New variable.
* doc/guix.texi (Networking Services): Document 'openssh-services'.

Co-authored-by: Ludovic Courtès <ludo@gnu.org>

gnu: emacs: Build with m17n support.

* gnu/packages/emacs.scm (emacs): Build with m17n support.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>

gnu: Add m17n-lib.

* gnu/packages/emacs.scm (m17n-lib): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>

gnu: Add m17n-db.

* gnu/packages/emacs.scm (m17n-db): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>

gnu: c-ares: Update to 1.12.0 [fixes CVE-2016-5180].

* gnu/packages/adns.scm (c-ares): Update to 1.12.0.
[source]: Use HTTPS URL.
[home-page]: Use HTTPS URL.

Revert "gnu: %default-extra-linux-options: Remove redundant options."

Options aren't redundant and are required for building the initrd.

This reverts commit 50dbc03647170fded9e0bca0cc4b7e1614aa38db.

gnu: dbus-c++: License has "or later" clause.

* gnu/packages/glib.scm (dbus-c++)[license]: Change to LGPL2.1+.

doc: Give the full key fingerprint instead of the long key ID.

* doc/guix.texi (OPENPGP-SIGNING-KEY-ID): Use fingerprint instead of
long key ID.

gnu: sra-tools: Fix build on i686.

* gnu/packages/bioinformatics.scm (sra-tools)[arguments]: Pass
"VDB_LIBDIR" in make-flags; dynamically link libmagic.

gnu: tilda: Update to 1.3.3.

* gnu/packages/terminals.scm (tilda): Update to 1.3.3.

gnu: Add xonsh.

* gnu/packages/shells.scm (xonsh): New variable.

Signed-off-by: Leo Famulari <leo@famulari.name>

gnu: attic: Superseded by borg.

* gnu/packages/backup.scm (attic)[properties]: New field.

gnu: nestopia-ue: Update to version 1.47.

gnu: higan: Update to version 101.

* gnu/packages/games.scm (higan): Update to version 101.

gnu: git: Add input perl-term-readkey for 'git-svn'.

* gnu/packages/version-control.scm (git)[inputs]: Add perl-term-readkeys.
[arguments]: Add perl-term-readkeys to the PERL5LIB of `git-svn'.

Signed-off-by: 宋文武 <iyzsong@gmail.com>

import: utils: Refactor license->symbol.

* guix/import/utils.scm (license->symbol): Work for all licenses.
* tests/import-utils.scm (license->symbol): Add test.

import: utils: Add spdx-string->license.

* guix/import/utils.scm (spdx-string->license): New variable.
* guix/licenses.scm (agpl1, fdl1.2+): New variables.

import: Move string->license to importers.

* guix/import/gem.scm (string->license): Move from (guix import utils).
* guix/import/pypi.scm (string->license): Move from (guix import utils).

import: Reorder imports in (guix import utils).

* guix/import/utils.scm (define-module): Reorder imports alphabetically.

gnu: linux-libre-beagle-bone-black: Remove kernel variant.

linux-libre-beagle-bone-black is misslabeled. This kernel variant is
for the original beagle board.

* gnu/packages/linux.scm (linux-libre-beagle-bone-black): Remove.

gnu: make-linux-libre: Install device tree files.

* gnu/packages/linux.scm (make-linux-libre): Install device tree files.

gnu: %default-extra-linux-options: Remove redundant options.

* gnu/packages/linux.scm (%default-extra-linux-options): Remove
  redundant options.

gnu: Add sdcc.

* gnu/packages/sdcc.scm (sdcc): New file.
* gnu/local.mk (GNU_SYSTEM_MODULES): Add it.

gnu: Add picocom.

* gnu/packages/terminals.scm (picocom): New variable.

gnu: opendht: Propagate msgpack.

* gnu/packages/crypto.scm (opendht)[inputs]: Remove msgpack.
[propagated-inputs]: Add it.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>

gnu: telephony: Add 'license:' prefix.

* gnu/packages/telephony.scm (commoncpp) [license]: Add prefix.
(ucommon) [license]: Add prefix.
(ccrtp) [license]: Add prefix.
(osip) [license]: Add prefix.
(exosip) [license]: Add prefix.
(sipwitch) [license]: Add prefix.
(libsrtp) [license]: Add prefix.
(libiax2) [license]: Add prefix.
(seren) [license]: Add prefix.
(pjproject-sfl) [license]: Add prefix.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>

gnu: Add gsm.

* gnu/packages/audio.scm (gsm): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>

gnu: Add dbus-c++.

* gnu/packages/glib.scm (dbus-c++): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>

gnu: libressl: Update to 2.5.0.

* gnu/packages/tls.scm (libressl): Update to 2.5.0.

gnu: encfs: Update to 1.9.1.

* gnu/packages/crypto.scm (encfs): Update to 1.9.1.

gnu: btrfs-progs: Update to 4.7.3.

* gnu/packages/linux.scm (btrfs-progs): Update to 4.7.3.

gnu: zip: Use 'modify-phases'.

* gnu/packages/zip.scm (zip)[arguments]: Use 'modify-phases'.

gnu: isc-dhcp: Update bundled bind to 9.9.9-P3 [fixes CVE-2016-2776].

* gnu/packages/admin.scm (isc-dhcp)[inputs]: Update bundled bind to 9.9.9-P3.

gnu: bind: Update to 9.10.4-P3 [fixes CVE-2016-2776].

* gnu/packages/dns.scm (bind): Update to 9.10.4-P3.

gnu: Add python-q.

* gnu/packages/python.scm (python-q, python2-q): New variables.

Signed-off-by: Leo Famulari <leo@famulari.name>

gnu: expat: Fix regression caused by fix for CVE-2016-0718.

* gnu/packages/xml.scm (expat)[replacement]: New field.
(expat/fixed): New variable.
* gnu/packages/patches/expat-CVE-2016-0718-fix-regression.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.

Signed-off-by: Leo Famulari <leo@famulari.name>

gnu: Add gctp.

* gnu/packages/maths.scm (gctp): New variable.

Signed-off-by: Leo Famulari <leo@famulari.name>

gnu: Add gloox.

* gnu/packages/messaging.scm (gloox): New variable.

Signed-off-by: Leo Famulari <leo@famulari.name>

gnu: femtolisp: Don't build on mips64el or armhf.

* gnu/packages/lisp.scm (femtolisp)[supported-systems]: New field,
remove support for mips64el and armhf.

Signed-off-by: Leo Famulari <leo@famulari.name>

gnu: Add gobby.

* gnu/packages/gobby.scm (gobby): New variable.

gnu: Add obby.

* gnu/packages/gobby.scm (obby): New variable.

gnu: Add libnet6.

* gnu/packages/gobby.scm: New file.
* gnu/local.mk (GNU_SYSTEM_MODULES): Add new file.

gnu: Add libxml++-2.

* gnu/packages/gnome.scm (libxml++-2): New variable.

gnu: New default Dovecot service postmaster_address

* gnu/services/mail.scm (dovecot-configuration): Change default for
  postmaster-address, as dovecot is now requiring a non-empty value and
  will fail to start up otherwise.
* doc/guix.texi (Mail Services): Update.

gnu: aria2: Update to 1.27.1.

* gnu/packages/bittorrent.scm (aria2): Update to 1.27.1.

gnu: python-plastid: Update to 1.4.6.

* gnu/packages/bioinformatics.scm (python-plastid, python2-plastid): Update to
1.4.6.
[propagated-inputs]: Add python-termcolor.

gnu: Add python-termcolor.

* gnu/packages/python.scm (python-termcolor, python2-termcolor): New
variables.

gnu: python-pysam: Enable tests.

* gnu/packages/bioinformatics.scm (python-pysam)[source]: Change from
PyPi to source archive due to missing test data.
[arguments]: Add check phase after install.
[native-inputs]: Add python-nose, samtools and bcftools.

gnu: python-pysam: Delete bundled htslib.

* gnu/packages/bioinformatics.scm (python-pysam)[source]: Add snippet
to delete htslib.
[arguments]: Add htslib flags in 'set-flags phase.
[propagated-inputs]: New field. Add htslib.

gnu: python-pysam: Use 'modify-phases'.

* gnu/packages/bioinformatics.scm (python-pysam)[arguments]: Use
'modify-phases'.

gnu: Add bcftools.

* gnu/packages/bioinformatics.scm (bcftools): New variable.

gnu: python2-pbcore: Update to 1.2.10.

* gnu/packages/bioinformatics.scm (python2-pbcore): Update to 1.2.10.
[propagated-inputs]: New field. Add python2-pyxb.

gnu: Add python-pyxb.

* gnu/packages/xml.scm (python-pyxb, python2-pyxb): New variables.

gnu: python-pysam: Update to 0.9.1.4.

* gnu/packages/bioinformatics.scm (python-pysam, python2-pysam): Update
to 0.9.1.4.

guix build: Gracefully handle packages without source for '-S'.

Fixes <http://bugs.gnu.org/22836>.
Reported by Ricardo Wurmus <rekado@elephly.net>.

* guix/scripts/build.scm (options->derivations): Gracefully
handle (package-source p) = #f.

Add missing exports.

Reported by Taylan Ulrich Bayırlı/Kammer <taylanbayirli@gmail.com>
at <https://lists.gnu.org/archive/html/guix-devel/2016-09/msg01686.html>.

* gnu/system/file-systems.scm (%tty-gid): Export.
* guix/build-system/python.scm (default-python, default-python2):
Export.

gnu: openssl-next: Update to 1.1.0b [fixes CVE-2016-6309].

* gnu/packages/tls.scm (openssl-next): Update to 1.1.0b.

gnu: openssl: Update replacement to 1.0.2j [fixes CVE-2016-7052].

* gnu/packages/tls.scm (openssl): Update replacement to 1.0.2j.
(openssl-1.0.2i): Replace with...
(openssl-1.0.2j): ... new variable.

gnu: libftdi: Propagate the libusb input.

* gnu/packages/libftdi.scm (libftdi): Change libusb from an input to a
propagated-input.

Signed-off-by: Leo Famulari <leo@famulari.name>

gnu: ncbi-vdb: Only build on i686 and x86_64.

* gnu/packages/bioinformatics.scm (ncbi-vdb)[supported-systems]: Only
build on i686 and x86_64.
[arguments]: Add mandatory "-msse2" flag to CFLAGS.

gnu: ghc-pandoc: Update to 1.17.2.

* gnu/packages/haskell.scm (ghc-pandoc): Update to 1.17.2.

gnu: ghc-texmath: Update to 0.8.6.5.

* gnu/packages/haskell.scm (ghc-texmath): Update to 0.8.6.5.

gnu: ghc-cmark: Update to 0.5.3.1.

* gnu/packages/haskell.scm (ghc-cmark): Update to 0.5.3.1.

gnu: ghc-highlighting-kate: Update to 0.6.3.

* gnu/packages/haskell.scm (ghc-highlighting-kate): Update to 0.6.3.

gnu: ghc-pandoc-types: Update to 1.16.1.1.

* gnu/packages/haskell.scm (ghc-pandoc-types): Update to 1.16.1.1.

gnu: ghc-tagsoup: Update to 0.14.

* gnu/packages/haskell.scm (ghc-tagsoup): Update to 0.14.

gnu: tbb: Fail on test errors.

* gnu/packages/tbb.scm (tbb)[arguments]: Add phase
"fail-on-test-errors".

gnu: ghc-tls: Update to 1.3.8.

* gnu/packages/haskell.scm (ghc-tls): Update to 1.3.8.

gnu: tbb: Use modify-phases syntax.

* gnu/packages/tbb.scm (tbb)[arguments]: Use "modify-phases" syntax.

gnu: vsearch: Update to 2.1.1.

* gnu/packages/bioinformatics.scm (vsearch): Update to 2.1.1.

gnu: azr3: Fix libsigc++ build errors.

* gnu/packages/audio.scm (azr3)[arguments]: Add "-std=gnu++11" flag.
[source]: Add patch.
* gnu/packages/patches/azr3.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.

gnu: qtractor: Update to 0.7.9.

* gnu/packages/music.scm (qtractor): Update to 0.7.9.

profiles: Build GTK+ input module cache.

* guix/profiles.scm (gtk-im-modules): New procedure.
(%default-profile-hooks): Add it.

profiles: manifest-lookup-package: Optionally match version prefix.

* guix/profiles.scm (manifest-lookup-package): Optionally filter store
item matches by version prefix.