gnu: Remove duplicate from (gnu packages gnupg).

* gnu/packages/gnupg.scm (perl-gnupg-interface): Remove duplicate.

gnu: Remove duplicate from (gnu packages bioinformatics).

* gnu/packages/bioinformatics.scm (r-annotationfilter): Remove duplicate.

gnu: Remove duplicate from (gnu packages cran).

* gnu/packages/cran.scm (r-bbmle): Remove duplicate.

gnu: Remove duplicates from (gnu packages java).

* gnu/packages/java.scm (java-commons-net, java-asm): Remove duplicates.

gnu: r-org-hs-eg-db: Clarify description.

* gnu/packages/bioinformatics.scm (r-org-hs-eg-db)[description]: Clarify.

gnu: r-org-hs-eg-db: Update to 3.5.0.

* gnu/packages/bioinformatics.scm (r-org-hs-eg-db): Update to 3.5.0.

gnu: r-org-hs-eg-db: Remove duplicate package definition.

* gnu/packages/bioinformatics.scm (r-org-hs-eg-db): Remove duplicate variable.

gnu: linux-libre: Remove Tegra DRM from arm configuration.

The code fails to compile on armhf using our configuration.
See <https://patchwork.kernel.org/patch/9688615/> for details.

* gnu/packages/aux-files/linux-libre/4.14-arm.conf: Remove Tegra DRM support.

gnu: linux-libre: Remove Nouveau from arm configuration.

The Nouveau code fails to compile on armhf with our configuration.

* gnu/packages/aux-files/linux-libre/4.14-arm.conf: Disable Nouveau.

gnu: dino: Update to 0.0-2-2a514d096.

* gnu/packages/messaging.scm (dino): Update to 0.0-2-2a514d096.
[source]: Do not fetch libsignal-protocol-c submodule.
[arguments]: Add phase "unpack-sources" to unpack our sources for
libsignal-protocol-c.
[native-inputs]: Add "libsignal-protocol-c-source".

build-system/go: Don't let Go executables refer to the Go compiler.

* guix/build/go-build-system.scm (remove-store-reference, remove-go-references):
New procedures.
(%standard-phases): Add 'remove-go-references' phase.
* guix/build-system/go.scm (go-build): Add allow-go-reference? key.

gnu: vim: Update to 8.0.1300.

* gnu/packages/vim.scm (vim): Update to 8.0.1300.

gnu: tuxguitar: Build with icedtea-8.

* gnu/packages/music.scm (tuxguitar)[arguments]: Use icedtea-8.

gnu: java-swt: Update to 4.7.1a.

* gnu/packages/java.scm (java-swt): Update to 4.7.1a.
[arguments]: Build with icedtea-8.
[inputs]: Remove "icecat".

gnu: eolie: Update to 0.9.12.

* gnu/packages/gnome.scm (eolie): Update to 0.9.12.
[inputs]: Add python-dateutil.

doc: Write "file system" instead of "partition" as appopriate.

* doc/guix.texi (Preparing for Installation): Write "file system" instead
of "partition" as appopriate.

gnu: Move database packages from python.scm to databases.scm.

* gnu/packages/python.scm (python-ccm, python2-ccm, python2-pysqlite,
python-sqlalchemy, python2-sqlalchemy, python-sqlalchemy-utils,
python2-sqlalchemy-utils, python-alembic, python2-alembic,
python-pickleshare, python2-pickleshare, python-apsw, python2-apsw,
python2-neo4j-driver, python2-py2neo, python-psycopg2, python2-psycopg2,
python-sadisplay, python2-sadisplay, python-mysqlclient,
python2-mysqlclient, python-hiredis, python2-hiredis, python-fakeredis,
python2-fakeredis, python-redis, python2-redis, python-rq, python2-rq,
python-trollius-redis, python2-trollius-redis, python-sqlparse,
python2-sqlparse, python-sql, python2-sql): Move from here...
* gnu/packages/databases.scm: ...to here.
* gnu/packages/tryton.scm,
gnu/packages/python-web.scm,
gnu/packages/nutrition.scm,
gnu/packages/medical.scm: Adjust accordingly.

gnu: python-scikit-learn: Move from python.scm to machine-learning.scm.

* gnu/packages/python.scm (python-scikit-learn, python2-scikit-learn): Move
from here...
* gnu/packages/machine-learning.scm: ...to here.

gnu: Move more web packages from python.scm to python-web.scm.

* gnu/packages/python.scm (python-pastescript, python2-pastescript,
python-paste, python2-paste, python-werkzeug, python2-werkzeug, python-bottle,
python2-bottle, python-wtforms, python2-wtforms): Move from here...
* gnu/packages/python-web.scm: ...to here.

gnu: Move testing packages from python.scm to check.scm.

* gnu/packages/python.scm (python-behave-web-api, python2-behave-web-api,
python-mock, python2-mock, python-mock-2, python-nose, python2-nose,
python-nose2, python2-nose2, python-unittest2, python2-unittest2,
python-pytest, python2-pytest, python-pytest-3.0, python2-pytest-3.0,
python-pytest-cov, python2-pytest-cov, python-pytest-runner,
python2-pytest-runner, python-pytest-mock, python2-pytest-mock,
python-pytest-xdist, python2-pytest-xdist, python-scripttest,
python2-scripttest, python-testtools, python2-testtools, python-testscenarios,
python2-testscenarios, python-testresources, python2-testresources,
python-subunit, python2-subunit, python-fixtures, python2-fixtures,
python-testrepository, python2-testrepository, python-coverage,
python2-coverage, python-cov-core, python2-cov-core, python-testpath,
python2-testpath, python-testlib, python2-testlib, python-pytest-cache,
python2-pytest-cache, python-pytest-localserver, python-pytest-xprocess,
python-pytest-subtesthack, python2-pytest-subtesthack, python-hypothesis,
python2-hypothesis, python-lit, python2-lit, python-pytest-pep8,
python2-pytest-pep8, python-pytest-flakes, python2-pytest-flakes,
python2-coverage-test-runner, python-pylint, python2-pylint,
python-paramunittest, python2-python-paramunittest, python-pytest-warnings,
python2-pytest-warnings, python-pytest-capturelog, python2-pytest-capturelog,
python-pytest-catchlog, python2-pytest-catchlog, python-nosexcover,
python2-nosexcover, python-discover, python2-discover, behave, python-rednose,
python2-rednose, python-nose-randomly, python2-nose-randomly,
python-nose-timer, python2-nose-timer): Move from here...
* gnu/packages/check.scm: ...to here.
* gnu/packages/admin.scm,
gnu/packages/android.scm,
gnu/packages/backup.scm,
gnu/packages/bioinformatics.scm,
gnu/packages/calendar.scm,
gnu/packages/dav.scm,
gnu/packages/django.scm,
gnu/packages/freedesktop.scm,
gnu/packages/haskell.scm,
gnu/packages/image.scm,
gnu/packages/irc.scm,
gnu/packages/jrnl.scm,
gnu/packages/ldc.scm,
gnu/packages/libffi.scm,
gnu/packages/mail.scm,
gnu/packages/mpd.scm,
gnu/packages/openstack.scm,
gnu/packages/package-management.scm,
gnu/packages/password-utils.scm,
gnu/packages/python-crypto.scm,
gnu/packages/python-web.scm,
gnu/packages/rdf.scm,
gnu/packages/statistics.scm,
gnu/packages/storage.scm,
gnu/packages/time.scm,
gnu/packages/tls.scm,
gnu/packages/tor.scm,
gnu/packages/tryton.scm: Adjust accordingly.

gnu: Add qmidiroute.

* gnu/packages/music.scm (qmidiroute): New variable.

gnu: cheese: Update to 3.26.0.

* gnu/packages/gnome.scm (cheese): Update to 3.26.0

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

gnu: Add emacs-transmission.

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

gnu: cool-retro-term: Fix qml path.

* gnu/packages/terminals.scm (cool-retro-term): Fix qml path.

gnu: eog: Update to 3.26.2.

* gnu/packages/gnome.scm (eog): Update to 3.26.2.

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

gnu: gnome-disk-utility: Update to 3.26.2.

* gnu/packages/gnome.scm (gnome-disk-utility): Update to 3.26.2.

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

gnu: nftables: Update to 0.8.

* gnu/packages/linux.scm (nftables): Update to 0.8.

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

gnu: libnftnl: Update to 1.0.8.

* gnu/packages/linux.scm (libnftnl): Update to 1.0.8.

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

workers: Display backtrace in pre-unwind handler.

* guix/workers.scm (worker-thunk): Add (const #f) as the 'catch'
handler, and move previous handler as pre-unwind handler.  Protect
against 'make-stack' returning #f.

workers: Add test with exceptions.

* tests/workers.scm ("exceptions"): New test.

workers: 'pool-idle?' returns true only if the workers are idle.

Fixes <https://bugs.gnu.org/28779>.
Reported by Eric Bavier <bavier@cray.com>.

* guix/workers.scm (<pool>)[busy]: New field.
(worker-thunk): Add #:idle and #:busy and use them.
(make-pool): Pass #:busy and #:idle to 'worker-thunk'.  Pass a 'busy'
value to '%make-pool'.
* guix/workers.scm (pool-idle?): Check whether 'pool-busy' returns zero
and adjust docstring.

gnu: Add qucs-s.

* gnu/packages/engineering.scm (qucs-s): New variable.

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

gnu: syslinux: Add explicit dependency on mtools.

Suggested by Adam Van Ymeren <adam@vany.ca>
at <https://bugs.gnu.org/28974>.

* gnu/packages/bootloaders.scm (syslinux)[inputs]: Add MTOOLS.
[ARGUMENTS]: In 'patch-files' phase, patch references to 'mcopy' and
'mattrib'.

gnu: wget: Add wget2.

* gnu/packages/wget.scm (wget2): New variable.

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

gnu: spectrwm: Update to 3.1.0.

* gnu/packages/wm.scm (spectrwm): Update to 3.1.0.

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

gnu: xpra: Fix paths.

* gnu/packages/xorg.scm (xpra): [arguments]: Add '--without-opengl',
'--without-Xdummy' and '--without-Xdummy-wrapper' to #:configure-flags. Add
substitutions to #phases for proper paths.

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

gnu: messaging: Enable OMEMO for dino.

* gnu/packages/messaging.scm (dino): Update to commit
f6ac5bbd26638412a2289fd1d28ef12de1d7e8b5.
[inputs]: Add libsignal-protocol-c and libgcrypt.
[arguments]: Change #configure-flags to "-DSHARED_SIGNAL_PROTOCOL=yes".

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

gnu: messaging: Add libsignal-protocol-c.

* gnu/packages/messaging.scm (libsignal-protocol-c): New variable.

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

ui: Add source file name to the package search metrics.

* guix/ui.scm (%package-metrics): Include 'package-location'.  Increase
score of the other fields.

gnu: Move more packages from python to python-web.

* gnu/packages/python.scm (python-requests, python2-requests)
(python-requests-2.7, python-oauthlib, python2-oauthlib)
(python-furl, python2-furl, python-wsgi-intercept)
(python-publicsuffix, python2-publicsuffix)
(python-publicsuffix2, python2-publicsuffix2): Move to...
* gnu/packages/python-web.scm: ... here.
* gnu/packages/bioinformatics.scm, gnu/packages/finance.scm:
gnu/packages/maths.scm, gnu/packages/terminals.scm,
gnu/packages/video.scm, gnu/packages/virtualization.scm: Adjust
accordingly.

gnu: Move Python packages from crypto to python-crypto.

* gnu/packages/crypto.scm (python-asn1crypto, python2-asn1crypto)
(python-pynacl, python2-roca-detect): Move to python-crypto.scm.
* gnu/packages/gnupg.scm (python2-pgpdump): Move to python-crypto.scm.
* gnu/packages/python-crypto.scm (python-asn1crypto, python2-asn1crypto)
(python-pynacl, python2-pgpdump, python2-roca-detect): New variables.

gnu: Move crypto packages from python to python-crypto.

* gnu/packages/python.scm (python-passlib, python2-passlib)
(python-py-bcrypt, python2-py-bcrypt)
(python-paramiko, python2-paramiko, python-ecdsa, python2-ecdsa)
(python-pycrypto, python2-pycrypto, python-keyring, python2-keyring)
(python-certifi, python2-certifi)
(python-cryptography-vectors, python2-cryptography-vectors)
(python-cryptography, python2-cryptography)
(python-pyopenssl, python2-pyopenssl)
(python-axolotl-curve25519, python2-axolotl-curve25519)
(python-axolotl, python2-axolotl, python2-slowaes)
(python-pyaes, python2-pyaes): Move to...
* gnu/packages/python-crypto.scm: ... here.  New file.
* gnu/local.mk (GNU_SYSTEM_MODULES): Add it.
* gnu/packages/admin.scm, gnu/packages/backup.scm,
gnu/packages/crypto.scm, gnu/packages/finance.scm,
gnu/packages/irc.scm, gnu/packages/jrnl.scm,
gnu/packages/messaging.scm, gnu/packages/openstack.scm,
gnu/packages/python-web.scm, gnu/packages/tls.scm,
gnu/packages/xorg.scm: Adjust accordingly.

cve: Use 'http-fetch/cached' instead of having custom caching.

That way CVE fetching benefits from 'If-Modified-Since' handling.

* guix/http-client.scm (http-fetch/cached): Add #:write-cache and
 #:cache-miss parameters and honor them.
* guix/cve.scm (%current-year-ttl, %past-year-ttl): Reduce.
(call-with-cve-port): Remove.
(write-cache): New procedure.
(fetch-vulnerabilities): Rewrite in terms of 'http-fetch/cached'.

download: Improve efficiency of 'write-request' over TLS.

This is another instance of <https://bugs.gnu.org/22966>.
The Microsoft-IIS/7.5 server at static.nvd.nist.gov would sometimes hang
when receiving our requests byte by byte.

* guix/build/download.scm (tls-wrap) [!guile-2.0]: Add 'setvbuf' call.

gnu: linux-libre: Update to 4.14.

* gnu/packages/linux.scm (%linux-libre-version): Update to 4.14.
(%linux-libre-hash): Update hash.
* gnu/packages/aux-files/linux-libre/4.13-arm.conf,
gnu/packages/aux-files/linux-libre/4.13-i686.conf,
gnu/packages/aux-files/linux-libre/4.13-x86_64.conf: Delete files.
* gnu/packages/aux-files/linux-libre/4.14-arm.conf,
gnu/packages/aux-files/linux-libre/4.14-i686.conf,
gnu/packages/aux-files/linux-libre/4.14-x86_64.conf: New files.
* Makefile.am (AUX_FILES): Update accordingly.

gnu: linux-libre@4.9: Update to 4.9.62.

* gnu/packages/linux.scm (linux-libre-4.9): Update to 4.9.62.

gnu: linux-libre@4.4: Update to 4.4.98.

* gnu/packages/linux.scm (linux-libre-4.4): Update to 4.4.98.

gnu: icecat: Add more fixes from upstream mozilla-esr52.

Add fixes for CVE-2017-7830, the remaining 1/2 changesets for CVE-2017-7828,
the remaining 1/19 changesets for CVE-2017-7826, and selected other fixes.

* gnu/packages/gnuzilla.scm (icecat)[source]: Add selected fixes from the
upstream mozilla-esr52 repository.
* gnu/packages/patches/icecat-bug-1348660-pt5.patch,
gnu/packages/patches/icecat-bug-1415133.patch: New files.
* gnu/local.mk (dist_patch_DATA): Add them.

gnu: icecat: Label patches to reflect CVE assignments.

Document that we include 18/19 changesets for CVE-2017-7826, and 1/2
changesets for CVE-2017-7828.

* gnu/packages/gnuzilla.scm (icecat)[source]: Rename patches to reflect CVE
assignments.

gnu: iproute2: Update to 4.14.1.

* gnu/packages/linux.scm (iproute): Update to 4.14.1.

gnu: gnucash: Use HTTPS for www.gnucash.org.

* gnu/packages/gnucash.scm (gnucash, gnucash-docs)[home-page]: Use HTTPS.

gnu: gnucash: Update to 2.6.18.

* gnu/packages/gnucash.scm (gnucash): Update to 2.6.18.

gnu: youtube-dl: Update to 2017.11.15.

* gnu/packages/video.scm (youtube-dl): Update to 2017.11.15.

gnu: geoclue: Use HTTPS for home page.

* gnu/packages/gnome.scm (geoclue)[home-page]: Use HTTPS.

gnu: geoclue: Update to 2.4.7.

* gnu/packages/gnome.scm (geoclue): Update to 2.4.7.

gnu: aria2: Update to 1.33.1.

* gnu/packages/bittorrent.scm (aria2): Update 1.33.1.

gnu: smartmontools: Mark up description.

* gnu/packages/admin.scm (smartmontools)[description]: Use @dfn.

gnu: smartmontools: Update to 6.6.

* gnu/packages/admin.scm (smartmontools): Update to 6.6.

gnu: devhelp: Update to 3.26.0.

* gnu/packages/gnome.scm (devhelp): Update to 3.26.0.

gnu: Add guile-wiredtiger.

* gnu/packages/databases.scm (guile-wiredtiger): New variable.

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

download: Pass the timeout to 'ftp-retr'.

This ensures the timeout applies when connecting to the port returned by
PASV.

* guix/ftp-client.scm (ftp-list): Add #:timeout parameter.  Use
'connect*' instead of 'connect' and pass TIMEOUT.
(ftp-retr): Likewise.
* guix/build/download.scm (ftp-fetch): Pass TIMEOUT to 'ftp-retr'.

tests: install: Increase target-size.

1200 MiB are too small for a btrfs-root-os, thus let increase it.

* gnu/tests/install.scm (run-install): Increase target-size to 2200 MiB.
(%btrfs-root-installation-script): Increase my-root partition size to 2G.

grafts: Clarify the status of the workaround for <bugs.gnu.org/24659>.

* guix/build/graft.scm (mkdir-p*): Annotate.

gnu: Update awscli to 1.11.185.

* gnu/packages/python-web.scm (awscli): Update to 1.11.185.

gnu: gnome-calculator: Update to 3.26.0.

* gnu/packages/gnome.scm (gnome-calculator): Update to 3.26.0.

gnu: gnome-system-monitor: Update to 3.26.0.

* gnu/packages/gnome.scm (gnome-system-monitor): Update to 3.26.0.

gnu: exim: Use HTTPS for home page.

* gnu/packages/mail.scm (exim)[home-page]: Use HTTPS.

gnu: iproute2: Update to 4.14.0.

* gnu/packages/linux.scm (iproute): Update to 4.14.0.

gnu: Move web packages from python to python-web.

This is in part to address <https://bugs.gnu.org/27284>.

* gnu/packages/python.scm (python-httplib2, python2-httplib2)
(python-sockjs-tornado, python2-sockjs-tornado)
(python-flask-babel, python2-flask-babel)
(python-html5lib, python2-html5lib)
(python-html5lib-0.9, python2-html5lib-0.9)
(python-html5-parser, python2-html5-parser)
(python-webencodings, python2-webencodings)
(python-openid, python2-openid, python-cssutils, python2-cssutils)
(python-cssselect, python2-cssutils)
(python-openid-cla, python2-openid-cla)
(python-openid-teams, python2-openid-teams)
(python-tornado, python2-tornado)
(python-tornado-http-auth, python-terminado, python2-terminado)
(python-webob, python2-webob, python-zope-event, python2-zope-event)
(python-zope-interface, python2-zope-interface)
(python-zope-exceptions, python2-zope-exceptions)
(python-zope-testing, python2-zope-testing)
(python-zope-testrunner, python2-zope-testrunner)
(python-zope-i18nmessageid, python2-zope-i18nmessageid)
(python-zope-schema, python2-zope-schema)
(python-zope-configuration, python2-zope-configuration)
(python-zope-proxy, python2-zope-proxy)
(python-zope-location, python2-zope-location)
(python-zope-security, python2-zope-security)
(python-zope-component, python2-zope-component)
(python-ndg-httpsclient, python2-ndg-httpsclient)
(python-websocket-client, python2-websocket-client)
(python-requests-toolbelt, python2-requests-toolbelt)
(python-rauth, python2-rauth, python-urllib3, python2-urllib3)
(awscli, python-wsgiproxy2, python2-wsgiproxy2)
(python-pastedeploy, python2-pastedeploy)
(python-webtest, python2-webtest, python-flask, python2-flask)
(python-flast-wtf, python2-flask-wtf)
(python-flask-multistatic, python2-flask-multistatic)
(python-cookies, python2-cookies)
(python-responses, python2-responses)
(python-geventhttpclient, python2-geventhttpclient)
(python-requests-oauthlib, python2-requests-oauthlib)
(python-url, python2-url, python-cachecontrol, python2-cachecontrol)
(python-betamax, python2-betamax)
(python-betamax-matchers, python2-betamax-matchers)
(python-s3transfer, python2-s3transfer)
(python-flask-restful, python-flask-basicauth)
(python-flask-sqlalchemy, python-flask-restplus)
(python-flask-restful-swagger, python-htmlmin, python2-htmlmin)
(python-flask-htmlmin, python2-flask-htmlmin)
(python-flask-login, python2-flask-login)
(python-oauth2client, python-flask-oidc)
(python-webassets, python-cssmin, python2-cssmin)
(python-elasticsearch, python2-elasticsearch)
(python-flask-script, python2-flask-script)
(python-flask-migrate, python2-flask-migrate)
(python-genshi, python2-genshi)
(python-flask-principal, python2-flask-principal)
(python-flask-httpauth, python2-flask-httpauth)
(python-uritemplate, python2-uritemplate): Move to...
* gnu/packages/python-web.scm: ... here.  New file.
* gnu/local.mk (GNU_SYSTEM_MODULES): Add it.
* gnu/packages/admin.scm, gnu/packages/backup.scm,
gnu/packages/dav.scm, gnu/packages/django.scm,
gnu/packages/docker.scm, gnu/packages/ebook.scm,
gnu/packages/logging.scm, gnu/packages/mail.scm,
gnu/packages/music.scm, gnu/packages/openstack.scm,
gnu/packages/package-management.scm, gnu/packages/rdf.scm,
gnu/packages/tls.scm, gnu/packages/tor.scm,
gnu/packages/tryton.scm, gnu/packages/version-control.scm,
gnu/packages/web-browsers.scm,
gnu/packages/web.scm: Adjust accordingly.

gnu: diamond: Update to 0.9.13.

* gnu/packages/bioinformatics.scm (diamond): Update to 0.9.13.

gnu: Move test packages from perl to perl-check.

* gnu/packages/perl.scm (perl-test2-bundle-extended,
perl-test2-plugin-nowarnings, perl-test-base, perl-test-class,
perl-test-class-most, perl-test-cleannamespaces, perl-test-command,
perl-test-cpan-meta, perl-test-cpan-meta-json, perl-test-deep,
perl-test-differences, perl-test-directory, perl-test-eol,
perl-test-exception, perl-test-fatal, perl-test-file-sharedir-dist,
perl-test-files, perl-test-harness, perl-test-leaktrace,
perl-test-longstring, perl-test-manifest, perl-test-memory-cycle,
perl-test-mockobject, perl-test-mocktime, perl-test-most, perl-test-needs,
perl-test-notabs, perl-test-nowarnings, perl-test-number-delta,
perl-test-output, perl-test-pod, perl-test-pod-coverage, perl-test-requires,
perl-test-script, perl-test-sharedfork, perl-test-simple, perl-test-taint,
perl-test-tester, perl-test-trap, perl-test-utf8, perl-test-warn,
perl-test-warnings, perl-test-without-module, perl-test-writevariants,
perl-test-yaml, perl-test-trailingspace): Move variables to ...
* gnu/packages/perl-check.scm: ... this new file.
* gnu/local.mk (GNU_SYSTEM_MODULES): Add it.
* gnu/packages/admin.scm,
gnu/packages/bioinformatics.scm,
gnu/packages/crypto.scm,
gnu/packages/databases.scm,
gnu/packages/glib.scm,
gnu/packages/gnupg.scm,
gnu/packages/image-viewers.scm,
gnu/packages/language.scm,
gnu/packages/networking.scm,
gnu/packages/package-management.scm,
gnu/packages/perl.scm,
gnu/packages/terminals.scm,
gnu/packages/tex.scm,
gnu/packages/version-control.scm,
gnu/packages/web.scm,
gnu/packages/xml.scm,
gnu/packages/xorg.scm: Use perl-check module.

gnu: ghc-tls: Move to (gnu packages tls).

* gnu/packages/haskell.scm (ghc-tls): Move from here...
* gnu/packages/tls.scm (ghc-tls): ...to here.
* gnu/packages/haskell-web.scm: Use (gnu packages tls).

gnu: Move crypto packages from haskell to haskell-crypto.

* gnu/packages/haskell.scm (ghc-asn1-types, ghc-asn1-encoding, ghc-asn1-parse,
ghc-crypto-api, ghc-crypto-api-tests, ghc-cryptohash, ghc-cryptohash-md5,
ghc-cryptohash-sha1, ghc-cryptonite, ghc-digest, ghc-entropy, ghc-pem,
ghc-puremd5, ghc-sha, ghc-x509, ghc-x509-store, ghc-x509-validation,
ghc-x509-system): Move variables to ...
* gnu/packages/haskell-crypto.scm: ... this new file.
* gnu/local.mk (GNU_SYSTEM_MODULES): Add it.
* gnu/packages/haskell.scm,
gnu/packages/haskell-web.scm,
gnu/packages/version-control.scm: Include haskell-crypto module.

gnu: Move web packages from haskell to haskell-web.

* gnu/packages/haskell.scm (ghc-tagsoup, ghc-cookie, ghc-http-types, ghc-http,
ghc-http-client, ghc-http-client-tls, ghc-http-date, ghc-http2,
ghc-http-conduit, ghc-wai, ghc-wai-logger, ghc-wai-extra, ghc-wai-conduit,
ghc-warp, ghc-warp-tls, ghc-xss-sanitize, ghc-css-text, ghc-mime-types,
ghc-html, ghc-xhtml, ghc-blaze-html, ghc-aeson, ghc-aeson-pretty,
ghc-aeson-qq, ghc-multipart): Move variables to ...
* gnu/packages/haskell-web.scm: ... this new file.
* gnu/local.mk (GNU_SYSTEM_MODULES): Add it.
* gnu/packages/haskell.scm,
gnu/packages/idris.scm,
gnu/packages/version-control.scm,
gnu/packages/wm.scm: Include haskell-web module.

gnu: Move testing packages from haskell to haskell-check.

* gnu/packages/haskell.scm (ghc-clock-bootstrap, ghc-tasty-ant-xml,
ghc-tasty-smallcheck, ghc-tasty-quickcheck, ghc-tasty-golden, ghc-tasty,
ghc-tasty-hunit, ghc-tasty-kat, ghc-tasty-th, ghc-tasty-rerun,
ghc-quickcheck-instances, ghc-quickcheck-unicode, ghc-quickcheck-io,
ghc-quickcheck, ghc-test-framework, ghc-test-framework-hunit,
ghc-test-framework-quickcheck2, ghc-test-framework-th, ghc-hunit,
hspec-discover, ghc-hspec-core, ghc-hspec-meta, ghc-hspec, ghc-hspec-contrib,
ghc-hspec-expectations): Move variables to ...
* gnu/packages/haskell-check.scm: ... this new file.
* gnu/local.mk (GNU_SYSTEM_MODULES): Add it.
* gnu/packages/haskell.scm,
gnu/packages/idris.scm,
gnu/packages/version-control.scm,
gnu/packages/wm.scm: Include haskell-check module.

gnu: cd-hit: Update source tarball hash.

* gnu/packages/bioinformatics.scm (cd-hit)[source]: Update hash.

Revert "gnu: totem: Enable parallel build."

This reverts commit e5f748a6c0c774265f52c7246ee7b80bec6d3522.

services: guix: Remove dependency on 'lsof'.

This is a followup to b8f59cdc20e9d83ce63523ef917e95fcee07f134:
'list-runtime-roots' no longer depends on 'lsof'.

* gnu/services/base.scm (<guix-configuration>)[lsof]: Remove.
(guix-shepherd-service): Adjust accordingly.
* doc/guix.texi (Base Services): Adjust accordingly.
* gnu/system.scm (%base-packages): Remove LSOF.

gnu: guix: Update snapshot.

* gnu/packages/package-management.scm (guix): Update to ff23b47.

tests: 'guix-gc.sh' passes even when 'out' or 'drv' are defined as env vars.

This fixes a test failure exhibited by
fb17a89912c2a3738dae716e30481c11e1c6f0ac whereby assignments to 'out' in
guix-gc.sh would go to the 'out' environment variable, when it exists,
which in turn prevents garbage collection of $out.

* tests/guix-gc.sh: Add 'unset' invocations.

gnu: ibus: Update to 1.5.17.

* gnu/packages/ibus.scm (ibus): Update to 1.5.17.

gnu: ibus: Enable wayland support.

* gnu/packages/ibus.scm (ibus)[arguments]: Add configure flag to enable
wayland support.
[inputs]: Add wayland.

gnu: libsoup: Update to 2.60.2.

* gnu/packages/gnome.scm (libsoup): Update to 2.60.2.

list-runtime-roots: Ignore PIDs we cannot access.

This allows running as non-root.
Fixes a regression introduced in b8f59cdc20e9d83ce63523ef917e95fcee07f134.

* nix/scripts/list-runtime-roots.in (referenced-files): Handle EACCES in
addition to ENOENT.

download: Use HTTPS for the first ImageMagick mirror.

* guix/download.scm (%mirrors)[imagemagick]: Use HTTPS for <sunsite.icm.edu.pl>.

download: Try FTP servers last.

* guix/download.scm (%mirrors)[savannah, kernel.org, apache, xorg, imagemagick]:
Re-arrange so that FTP is last.

gnu: imagemagick: Update to 6.9.9-23.

* gnu/packages/imagemagick.scm (imagemagick): Update to 6.9.9-23.

list-runtime-roots: Canonicalize store items.

Looking at 'addAdditionalRoots' in libstore/gc.cc, it looks like it
should always have been this way.  In practice it probably doesn't make
much of a difference.

* nix/scripts/list-runtime-roots.in (canonicalize-store-item): New
procedure.
<top level>: Use it.

list-runtime-roots: Do not use 'lsof'.

This makes things a bit faster (0.8s instead of 1.4s on my laptop).

* nix/scripts/list-runtime-roots.in (lsof-roots): Remove.
(proc-fd-roots): Return the empty list when 'scandir' returns #f.
(referenced-files): New procedure.
Use it at the top level.

doc: Better explain GC roots.

Fixes <https://bugs.gnu.org/24194>.
Reported by J. Eppler <j.eppler@openmailbox.org>.

* doc/guix.texi (Invoking guix-daemon): Add index entries for GC roots.
Add xref to "Invoking guix gc".
(Invoking guix gc): Add the string "GC roots"; mention /var/guix/gcroots.
(Additional Build Options): Add index entries.  Better explain --root.
(Invoking guix environment): Add xref to "Invoking guix gc".

gnu: Remove unrar.

This package is abandoned upstream and contains serious bugs:

http://seclists.org/oss-sec/2017/q3/329
https://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2017-14120
https://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2017-14121
https://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2017-14122

* gnu/packages/compression.scm (unrar): Remove variable.

gnu: linux-libre: Change URL to HTTPS.

* gnu/packages/linux.scm (linux-libre): Change URL to HTTPS.

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

gnu: mupdf: Unbundle mujs.

* gnu/packages/pdf.scm (mupdf)[source]: Remove bundled mujs.
[inputs]: Add mujs.

gnu: Add mujs.

* gnu/packages/javascript.scm (mujs): New variable.

gnu: mupdf: Use https.

* gnu/packages/pdf.scm (mupdf)[source]: Use https.
[home-page]: Same.

gnu: pdf.scm: Arrange modules alphabetically.

* gnu/packages/pdf.scm: Arrange modules alphabetically.

gnu: lash: Don't build static libraries.

* gnu/packages/audio.scm (lash)[arguments]: Add configure-flag to
disable static libraries.

gnu: lash: Don't build lashd.

This fixes bug#28174.

* gnu/packages/audio.scm (lash)[arguments]: Add phase to skip building lashd.

gnu: glib-networking: Update to 2.54.1.

* gnu/packages/gnome.scm (glib-networking): Update to 2.54.1.

gnu: ffmpeg: Reduce the size of the closure.

* gnu/packages/video.scm (ffmpeg)[arguments]: Add new configure flags to
disable the html man pages and the static libraries.