gnu: chez-scheme: Remove use of 'ghostscript-gs' wrapper.

This is a followup to commit d2478b4cdd6f1db44f4725b39489aca89d3d9180.

* gnu/packages/chez.scm (chez-scheme)[native-inputs]: Replace
'ghostscript-gs' with 'ghostscript'.

Merge branch 'master' into core-updates

gnu: Add opensmtpd-extras.

* gnu/packages/mail.scm (opensmtpd-extras): New variable.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>

gnu: Add opensmtpd.

* gnu/packages/mail.scm (opensmtpd): New variable.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>

gnu: Add libasr.

* gnu/packages/dns.scm (libasr): New variable.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>

gnu: zile: Use 'modify-phases' syntax.

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

gnu: zile: Update to 2.4.13.

* gnu/packages/zile.scm (zile): Update to 2.4.13.
[home-page]: Use https.

tests: Make sure child process of 'pivot-root' test exits.

* tests/syscalls.scm ("pivot-root"): Use 'test-equal'.  Wrap child body
in 'dynamic-wind'.

tests: Fix typo in 'with-graft' transformation test.

This is a followup to 645b9df858683dc05ffa04c9eb2fdc45ccef4a65.

* tests/scripts-build.scm ("options->transformation, with-graft"): Use
'with-graft', not 'with-input'.

Use (ice-9 binary-ports) instead of (rnrs io ports).

This reduces the closure of (guix ui) from 123 to 106 modules.

* guix/derivations.scm: Use (ice-9 binary-ports) instead of (rnrs io
ports).
(map-derivation)[substitute-file]: Use 'read-string' instead of
'get-string-all'.
* guix/ftp-client.scm: Likewise.
* guix/hash.scm: Likewise.
* guix/http-client.scm: Likewise.
* guix/pki.scm (ensure-acl, current-acl): Likewise.
* guix/scripts/archive.scm (authorize-key)[read-key]: Likewise.
* guix/scripts/authenticate.scm (read-canonical-sexp)
(read-hash-data): Likewise.
* guix/scripts/download.scm: Likewise.
* guix/scripts/offload.scm (register-gc-root, remove-gc-roots)
(send-files): Likewise.
* guix/scripts/publish.scm (lazy-read-file-sexp): Likewise.
* guix/scripts/refresh.scm: Likewise.
* guix/scripts/substitute.scm (check-acl-initialized): Likewise.
* guix/serialization.scm (read-maybe-utf8-string): Likewise.
* guix/scripts/hash.scm (guix-hash): Use 'force-output' instead of
'flush-output-port'.
* guix/store.scm (process-stderr): Likewise.
* guix/tests.scm: Likewise.
* guix/utils.scm: Use (ice-9 binary-ports) and autoload (rnrs io ports)
for 'make-custom-binary-input-port'.

lint: Suggest @code instead of quotes.

* guix/scripts/lint.scm (%quoted-identifier-rx): New variable.
(check-description-style)[check-quotes]: New procedure.
Use it.
* tests/lint.scm ("description: suggest ornament instead of quotes"):
New test.

gnu: Add Ao.

* gnu/packages/engineering.scm (ao): New variable.

gnu: glfw: Propagate the relevant inputs.

* gnu/packages/gl.scm (glfw)[inputs]: Rename to...
[propagated-inputs]: ... this.  Add LIBXXF86VM.

container: Allow 'container-excursion' to the same namespaces.

Before that, 'container-excursion' would call 'setns' even when the
target namespace is the one the caller is already in, which would fail.

* gnu/build/linux-container.scm (container-excursion): Introduce
'source' and 'target'.  Compare the result of 'readlink' on these
instead of comparing file descriptors to decide whether to call
'setns'.
* tests/containers.scm ("container-excursion, same namespace"): New test.

gnu: Add r-biocstyle.

* gnu/packages/bioinformatics.scm (r-biocstyle): New variable.

gnu: Add r-biocviews.

* gnu/packages/bioinformatics.scm (r-biocviews): New variable.

gnu: Add iperf.

* gnu/packages/networking.scm (iperf): New variable.

Signed-off-by: Marius Bakke <mbakke@fastmail.com>

gnu: python-dateutil, python-dateutil-2: Update to new home-page.

* gnu/packages/python.scm (python-dateutil, python2-dateutil,
  python-dateutil-2, python2-dateutil-2)[home-page]: Update URL.

gnu: Add r-optparse.

* gnu/packages/bioinformatics.scm (r-optparse): New variable.

gnu: Add r-getopt.

* gnu/packages/bioinformatics.scm (r-getopt): New variable.

gnu: Add GHC 8.0.1.

* gnu/packages/haskell.scm (ghc-8): New variable.

gnu: Add ghc-hashtables.

* gnu/packages/haskell.scm (ghc-hashtables): New variable.

gnu: Add ghc-easyplot.

* gnu/packages/haskell.scm (ghc-easyplot): New variable.

gnu: Add ghc-hmatrix-gsl-stats.

* gnu/packages/haskell.scm (ghc-hmatrix-gsl-stats): New variable.

gnu: Add ghc-hmatrix-special.

* gnu/packages/haskell.scm (ghc-hmatrix-special): New variable.

gnu: Add ghc-hmatrix-gsl.

* gnu/packages/haskell.scm (ghc-hmatrix-gsl): New variable.

gnu: Add ghc-hmatrix.

* gnu/packages/haskell.scm (ghc-hmatrix): New variable.

gnu: Add ghc-storable-complex.

* gnu/packages/haskell.scm (ghc-storable-complex): New variable.

gnu: Add chez-fmt.

* gnu/packages/chez.scm (chez-fmt): New variable.

gnu: Add chez-irregex.

* gnu/packages/chez.scm (chez-irregex): New variable.

gnu: Add chez-matchable

* gnu/packages/chez.scm (chez-matchable): New variable.

gnu: Add chez-sockets

* gnu/packages/chez.scm (chez-sockets): New variable.

gnu: Add chez-web

* gnu/packages/chez.scm (chez-web): New variable.

gnu: Add chez-srfi.

* gnu/packages/chez.scm (chez-srfi): New variable.

gnu: chez-scheme: Move to new module.

* gnu/packages/scheme.scm (chez-scheme, nanopass, stex): Move variables ...
* gnu/packages/chez.scm (chez-scheme, nanopass, stex): ... here. New module.
* gnu/local.mk (GNU_SYSTEM_MODULES): Add new file.

gnu: chez-scheme: Fix i686 build.

* gnu/packages/scheme.scm (chez-scheme): Add 'configure-flags', generalize
  'configure' phase and simplify 'install-doc' phase.

gnu: chez-scheme: Add search-path.

* gnu/packages/scheme.scm (chez-scheme)[native-search-paths]: New field.

build: Remove reference to nonexistant patch file.

* gnu/local.mk: Remove reference to kobodeluxe-spelling.patch,
  which was removed during a revision to the submitted kobodeluxe package.

gnu: kobodeluxe: Indicate origin of kobodeluxe-paths.patch.

* gnu/packages/patches/kobodeluxe-paths.patch: Update header, pointing
  to Debian tarball for provenance.

gnu: mariadb: Update to 10.1.18.

* gnu/packages/databases.scm (mariadb): Update to 10.1.18.

gnu: mysql: Update to 5.7.16.

* gnu/packages/databases.scm (mysql): Update to 5.7.16.

gnu: Add kobodeluxe.

* gnu/packages/games.scm (kobodeluxe): New variable.
* gnu/packages/patches/kobodeluxe-paths.patch: New file.
* gnu/packages/patches/kobodeluxe-enemies-pipe-decl.patch: New file.
* gnu/packages/patches/kobodeluxe-const-charp-conversion.patch: New file.
* gnu/packages/patches/kobodeluxe-manpage-minus-not-hyphen.patch: New file.
* gnu/packages/patches/kobodeluxe-midicon-segmentation-fault.patch: New file.
* gnu/packages/patches/kobodeluxe-graphics-window-signed-char.patch: New file.
* gnu/local.mk (dist_patch_DATA): Register it.

gnu: torsocks: Update to 2.2.0.

* gnu/packages/patches/torsocks-dns-test.patch: Delete file.
* gnu/local.mk: Remove it.
* gnu/packages/tor.scm (torsocks): Update to 2.2.0.
[source]: Remove patch. Change method from 'git-fetch' to 'url-fetch'.
Remove 'file-name'.
[arguments]: Remove 'bootstrap' phase.
[native-inputs]: Remove autoconf, automake and libtool. Also remove
obsoleted perl-test-harness.
[home-page]: Use https URL.
(define-module): Don't import perl.

Signed-off-by: Marius Bakke <mbakke@fastmail.com>

gnu: hdf4: Really fix non-x86 architectures.

This is a follow-up to commit 60da9fb1100787c49ed4910eacf50e83c6462dcc.

* gnu/local.mk (dist_patch_DATA): Register patch.
* gnu/packages/maths.scm (hdf4)[source]: Add patch.

gnu: enlightenment: Update to 0.21.3.

* gnu/packages/enlightenment.scm (enlightenment): Update to 0.21.3.

gnu: dbus: Fix bad 'origin' form in dbus-1.10.12.

This is a followup to commit dcaf70897a0bad38a4638a2905aaa3c46b1f1402.

* gnu/packages/glib.scm (dbus-1.10.12)[source]: Remove unneeded 'method'
field, so that 'inherit' comes first.

grafts: Remove unnecessary 'umask' call.

This is a followup to d72267863382041b84a9712eea354882be72ef55.

* guix/build/graft.scm (rewrite-directory): Remove 'umask' call.

grafts: Apply the right grafts in the presence of multiple outputs.

Fixes <http://bugs.gnu.org/24712>.

* guix/grafts.scm (cumulative-grafts): Add grafts for all the outputs of
DRV.
* tests/grafts.scm ("graft-derivation, replaced derivation has multiple
outputs"): New test.

guix build: Add '--with-graft'.

* guix/scripts/build.scm (transform-package-inputs/graft): New procedure.
(%transformations): Add 'with-graft'.
(%transformation-options): Likewise.
(show-transformation-options-help): Document it.
* tests/scripts-build.scm ("options->transformation, with-graft"): New
test.
* doc/guix.texi (Package Transformation Options): Document it.

guix build: Factorize transformation option parsing.

* guix/scripts/build.scm (%transformation-options): Introduce 'parser'
procedure and use it.

guix build: Extract '--with-input' replacement spec parsing.

* guix/scripts/build.scm (evaluate-replacement-specs): New procedure.
(transform-package-inputs)[not-equal]: Remove.
[replacements]: Define in terms of 'evaluate-replacement-specs'.

gnu: tor: Update to 0.2.8.9.

* gnu/packages/tor.scm (tor): Update to 0.2.8.9.

gnu: vapoursynth: Update to 34.

* gnu/packages/video.scm (vapoursynth): Update to 34.

gnu: zimg: Update to 2.3.

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

gnu: jasper: Update to 1.900.5.

* gnu/packages/image.scm (jasper): Update to 1.900.5.
[source]: Remove patches.
[native-inputs]: Remove unzip.
* gnu/packages/patches/jasper-CVE-2007-2721.patch,
gnu/packages/patches/jasper-CVE-2008-3520.patch,
gnu/packages/patches/jasper-CVE-2008-3522.patch,
gnu/packages/patches/jasper-CVE-2011-4516-and-CVE-2011-4517.patch,
gnu/packages/patches/jasper-CVE-2014-8137.patch,
gnu/packages/patches/jasper-CVE-2014-8138.patch,
gnu/packages/patches/jasper-CVE-2014-8157.patch,
gnu/packages/patches/jasper-CVE-2014-8158.patch,
gnu/packages/patches/jasper-CVE-2014-9029.patch,
gnu/packages/patches/jasper-CVE-2016-1577.patch,
gnu/packages/patches/jasper-CVE-2016-1867.patch,
gnu/packages/patches/jasper-CVE-2016-2089.patch,
gnu/packages/patches/jasper-CVE-2016-2116.patch: Delete files.
* gnu/local.mk (dist_patch_DATA): Remove them.

Merge branch 'master' into core-updates

gnu: diffoscope: Update to 61.

* gnu/packages/package-management.scm (diffoscope): Update to 61.

gnu: guile-lib: Update to 0.2.3.

* gnu/packages/guile.scm (guile-lib): Update to 0.2.3.
[arguments]: Adjust 'patch-module-dir' to change both 'moddir' and
'godir'; use '@GUILE_EFFECTIVE_VERSION@' instead of a hard-coded
"2.0".  Add 'check' phase.
[native-inputs]: New field.

gnu: guile-lib: Use 'modify-phases'.

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

gnu: recutils: Adjust to Bash 4.4.

* gnu/packages/databases.scm (recutils)[arguments]: Add
'set-bash4.4-header-location' phase.

gnu: openssh: Enable kerberos features.

* gnu/packages/ssh.scm (openssh) [arguments]: Add flag --with-kerberos5.
[inputs]: Add mit-krb5.

gnu: linux-libre: Update to 4.8.2.

* gnu/packages/linux.scm (%linux-libre-version, %linux-libre-hash)
(linux-libre): Update to 4.8.2.

gnu: linux-libre@4.4: Update to 4.4.25.

* gnu/packages/linux.scm (linux-libre-4.4): Update to 4.4.25.

gnu: Add xpad.

* gnu/packages/gnome.scm (xpad): New variable.

Signed-off-by: Kei Kebreau <kei@openmailbox.org>

gnu: python-requests-toolbelt: Fix build failure by adding missing dependencies.

* gnu/packages/python.scm (python-requests-toolbelt)[native-inputs]: Add
python-betamax, python-mock and python-pytest.

gnu: Add python-betamax.

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

gnu: python-vobject: Disable the test suite.

The tests were silently skipped with Python 3.4. With Python 3.5, this caused
the python-vobject build to fail.

* gnu/packages/python.scm (python-vobject, python2-vobject)[arguments]: Disable
the tests.

gnu: python-wsgi-intercept: Fix build failure with Python 3.5.

* gnu/packages/python.scm (python-wsgi-intercept)[native-inputs]:
Add python-urllib3.

gnu: Add rcas-web.

* gnu/packages/bioinformatics.scm (rcas-web): New variable.

gnu: Add r-rcas.

* gnu/packages/bioinformatics.scm (r-rcas): New variable.

gnu: irrlicht: Update to 1.8.4.

* gnu/packages/games.scm (irrlicht): Update to 1.8.4.
[arguments]: Delete phase "apply-patch/mesa-10-fix".
[native-inputs]: Remove "patch/mesa-10-fix".
* gnu/packages/patches/irrlicht-mesa-10.patch: Delete file.
* gnu/local.mk (dist_path_DATA): Remove irrlicht patch.

gnu: extremetuxracer: Update to 0.7.3.

* gnu/packages/games.scm (extremetuxracer): Update to 0.7.3.
[inputs]: Remove freetype, mesa, libice, libpng, sdl, sdl-mixer,
sdl-image, libsm, libunwind, libx11, libext, libxi, libxmu, libxt, tcl,
zlib; add sfml.
[arguments]: Remove field.

gnu: sfml: Install pkgconfig files.

* gnu/packages/game-development.scm (sfml)[arguments]: Add configure
flag to install pkgconfig files.

gnu: artanis: Remove implied $(DESTDIR) usage.

* gnu/packages/patches/artanis-fix-Makefile.in.patch: New file.
* gnu/local.mk (dist_patch_DATA): Register patch.
* gnu/packages/guile.scm (artanis)[source]: Use patch.
[arguments]: Remove DESTDIR from #:make-flags.

Signed-off-by: Marius Bakke <mbakke@fastmail.com>

gnu: wrap-python3:  Use a bash wrapper for 'python3-config'.

See <http://lists.gnu.org/archive/html/guix-devel/2016-07/msg00008.html>
for details.

* gnu/packages/python.scm (wrap-python3)[arguments]: Use a bash wrapper
instead of a symlink for python3-config.

gnu: node: Update to 6.8.0.

Remove <https://debbugs.gnu.org/23744> and
<https://debbugs.gnu.org/23723> workaround.

* gnu/packages/node.scm (node): Update to 6.8.0.
  (node)[arguments]: Disabled more tests. Remove custom 'patch-shebangs'
  phase. Manually patch npm script shebang in new 'patch-npm-shebang'
  phase.
* gnu/packages/patches/node-9077.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add patches.

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

gnu: ruby-json-pure: Fix tests.

* gnu/packages/ruby.scm (ruby-json-pure)[arguments]: Remove unneeded
reference to 'json-java.gemspec' in 'Gemfile'.

gnu: bundler: Update to 1.13.5.

* gnu/packages/ruby.scm (bundler): Update to 1.13.5.

gnu: Add geierlein.

* gnu/packages/finance.scm (geierlein): New variable.

gnu: Add sslh.

* gnu/packages/networking.scm (sslh): New variable.

gnu: httping: Update to 2.5.

* gnu/packages/networking.scm (httping): Update to 2.5.

gnu: Add fbida.

* gnu/packages/pdf.scm (fbida): New variable.

import: utils: Remove dependency on (json) module.

This fixes a regression introduced by commit
fbe9c1012820ab72f022a6ec958c35b431ae7a74.

* guix/import/utils.scm: Remove unused (json) module.

gnu: python-requests-mock: Fix build failure with Python 3.5.

* gnu/packages/openstack.scm (python-requests-mock,
python2-requests-mock)[native-inputs]: Add python-docutils.

gnu: xonsh: Disable the test suite.

The tests were silently skipped with Python 3.4. With Python 3.5, this caused
the xonsh build to fail.

* gnu/packages/shells.scm (xonsh)[arguments]: Disable the tests.

gnu: hdf4: Fix non-x86 architectures.

* gnu/packages/patches/hdf4-architectures.patch: New file.
* gnu/local.mk (dist_patch_DATA): Register patch.
* gnu/packages/maths.scm (hdf4)[source]: Add patch.

gnu: certbot, python-acme: Update to 0.9.3.

These packages should be updated together.

* gnu/packages/tls.scm (certbot): Update to 0.9.3.
[source]: Use pypi-uri.
(python-acme, python2-acme): Update to 0.9.3.
[source]: Use pypi-uri.

gnu: python-dnspython: Update to 0.15.0.

* gnu/packages/python.scm (python-dnspython, python2-dnspython): Update
to 0.15.0.

gnu: python-werkzeug: Update to 0.11.11.

* gnu/packages/python.scm (python-werkzeug, python2-werkzeug):
Update to 0.11.11.

gnu: python-pyopenssl: Update to 16.1.0.

* gnu/packages/python.scm (python-pyopenssl, python2-pyopenssl): Update
to 16.1.0
[source]: Use pypi-uri.

gnu: python-pyasn1: Update to 0.1.9.

* gnu/packages/python.scm (python-pyasn1, python2-pyasn1): Update to 0.1.9.
[source]: Use pypi-uri.

gnu: Add python-whoosh.

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

gnu: Add arm-none-eabi-toolchain variants.

* gnu/packages/embedded.scm (arm-none-eabi-toolchain): New procedure.
(arm-none-eabi-toolchain-4.9, arm-none-eabi-nano-toolchain-4.9,
arm-none-eabi-toolchain-6, arm-none-eabi-nano-toolchain-6): New
variables.

Co-authored-by: Ricardo Wurmus <rekado@elephly.net>

gnu: Add arm-none-eabi-gcc-6.

* gnu/packages/embedded.scm (gcc-arm-none-eabi-6): New variable.
* gnu/packages/patches/gcc-6-arm-none-eabi-multilib.patch: New file.
* gnu/packages/patches/gcc-6-cross-environment-variables.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add the patches.

gnu: python-ndg-httpsclient: Disable tests.

The tests were silently skipped with Python 3.4. With Python 3.5, this caused
the python-ndg-httpsclient build to fail.

* gnu/packages/python.scm (python-ndg-httpsclient)[arguments]: Disable tests.

gnu: python-execnet: Disable tests.

The tests were silently skipped with Python 3.4. With Python 3.5, this
caused the python-execnet build to fail.

* gnu/packages/python.scm (python-execnet, python2-execnet)[arguments]: Disable
tests.

gnu: youtube-dl: Disable the tests.

The tests were silently skipped with Python 3.4. With Python 3.5, this
caused the youtube-dl build to fail.

* gnu/packages/video.scm (youtube-dl)[arguments]: Disable tests.

gnu: youtube-dl: Update to 2016-10-16.

* gnu/packages/video.scm (youtube-dl): Update to 2016-10-16.

gnu: youtube-dl: Update to 2016-10-16.

* gnu/packages/video.scm (youtube-dl): Update to 2016-10-16.

gnu: radicale: Run the test suite with py.test.

* gnu/packages/dav.scm (radicale)[native-inputs]: Add python-pytest.
[arguments]: Replace the 'check' phase and run the tests with python-pytest.