* gnu/packages/xml.scm (perl-xml-compile): Update to 1.60.
[propagated-inputs]: Add perl-carp, perl-scalar-list-utils, and
perl-types-serialiser.

* gnu/packages/emacs.scm (emacs-orgalist): Update to 1.9.

* gnu/packages/graphics.scm (openscenegraph): Update to 3.6.3.
[source]: Use GIT-FILE-NAME.
[inputs]: Remove unused pth and qtbase.

* gnu/packages/graphviz.scm (python-pydot): Update to 1.2.4.
[arguments]: Run the test suite.
[native-inputs]: Add python-chardet.

* gnu/packages/debian.scm, gnu/packages/syndication.scm: Add comments.

* gnu/packages/debian.scm (ubuntu-keyring): Update to 2018.09.18.1.

* gnu/packages/databases.scm (perl-dbd-mysql): Update to 4.048.

* gnu/packages/rust.scm (rust-1.20)[arguments]<#:phases>[fix-mtime-bug]:
Delete.
[reset-timestamps-after-changes]: Modify.
(rust-1.24): Don't delete "fix-mtime-bug" since now it doesn't ever
get created.

* gnu/packages/rust.scm (rust-1.23)[arguments]<#:phases>
[patch-cargo-tests, ignore-glibc-2.27-incompatible-test,fix-mtime-bug]: Move
to...
(rust-1.20): ... here.

* gnu/packages/linux.scm (%linux-libre-version): Update to 4.18.9.
(%linux-libre-hash): Update hash.

* gnu/packages/linux.scm (%linux-libre-4.14-version): Update to 4.14.71.
(%linux-libre-4.14-hash): Update hash.

* gnu/packages/linux.scm (linux-libre-4.9): Update to 4.9.128.

* gnu/packages/linux.scm (linux-libre-4.4): Update to 4.4.157.

* gnu/packages/bittorrent.scm (qbittorrent): Update to 4.1.3.
[inputs]: Use python-wrapper instead of python.

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

* gnu/packages/gprolog.scm (gprolog): Update to 1.4.5.
[source]: Add an alternate source URL.

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

* gnu/packages/bioinformatics.scm (rsem): Update to 1.3.1.
[source]: Fetch from git; remove patch; delete bundled samtools.
[arguments]: Pass make flags; adjust phases.
[inputs]: Remove ncurses and samtools-0.1; add htslib-1.3.
* gnu/packages/patches/rsem-makefile.patch: Remove patch.
* gnu/local.mk (dist_patch_DATA): Remove it.

* gnu/packages/haskell.scm (ghc-pandoc-citeproc): Update to 0.14.3.1.

* gnu/packages/haskell.scm (ghc-xml-conduit): Update to 1.8.0.1.
[inputs]: Add ghc-doctest.

* gnu/packages/machine-learning.scm (python2-scikit-learn)[arguments]:
Override check phase to disable broken tests and pass environment variables.

* gnu/packages/cran.scm (r-parmigene): New variable.

* gnu/packages/emacs.scm (emacs-dired-sidebar): New public variable.

* gnu/packages/gnome.scm (eolie)[home-page]: Set to wiki.gnome.org/Apps/Eolie.

* gnu/services/networking.scm (<iptables-configuration>): New record type.
(iptables-service-type): New variable.
* gnu/tests/networking.scm (run-iptables-test): New procedure.
(%test-iptables): New variable.
* doc/guix.texi (Networking Services): Document it.

* gnu/packages/bootloaders.scm (u-boot)[home-page]: Use HTTPS.

* gnu/packages/security-token.scm (ccid): Update to 1.4.30.

* gnu/packages/xiph.scm (opusfile): Update to 0.11.

* gnu/packages/xdisorg.scm (scrot, unclutter, xautolock, nxbelld)
[arguments]: Use INVOKE.

* gnu/packages/shells.scm (mksh)[arguments]: Use INVOKE...
(scsh)[arguments]: ...and also return #t from all phases.

* gnu/packages/maths.scm (ruby-asciimath)[arguments]: Return #t from
all phases.
* gnu/packages/rails.scm (ruby-debug-inspector)[arguments]: Substitute
INVOKE for SYSTEM*.
* gnu/packages/ruby.scm (ruby-permutation, ruby-blankslate)
(ruby-minitest-pretty-diff, ruby-guard, ruby-rb-inotify, ruby-tins)
(ruby-gem-hadar, ruby-term-ansicolor, ruby-json-pure)
(ruby-activesupport, ruby-redcloth, ruby-netrc, ruby-unf-ext, ruby-yard)
(ruby-turn, ruby-sqlite3, ruby-shoulda-context, ruby-shoulda-matchers)
(ruby-shoulda, ruby-httpclient, ruby-ansi, ruby-bio-commandeer)
(ruby-rubytest, ruby-brass, ruby-qed, ruby-ae, ruby-lemon, ruby-hashery)
(ruby-rc4, ruby-concurrent)[arguments]: Likewise.

* gnu/packages/ruby.scm (ruby-heredoc-unindent)[description]: Fix typo.

* gnu/packages/telephony.scm (libiax2, mumble)[arguments]: Use INVOKE.

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

* gnu/packages/scsi.scm (sg3-utils): Update to 1.44.

* gnu/packages/gnome.scm (shotwell): Update to 0.28.4.

Fixes CVE-2018-{16391,16392,16393,16418,16419,16420,16421,16422,16423,16424,
16425,16426,16427}.

* gnu/packages/security-token.scm (opensc): Update to 0.19.0.

* gnu/packages/lisp.scm (sbcl-slynk-boot0): Update to commit
cbf84c36c4eca8b032e3fd16177a7bc02df3ec4c.
[origin]<snippet>: Replace slynk/util references with the built system name
slynk-util. Remove compile-time invocations of slynk-require.
(sbcl-slynk-util): Inherit from sbcl-slynk-boot0.
[inputs]: Add sbcl-slynk-boot0.
[arguments]: Set an appropriate asd-file and asd-system-name.
(sbcl-slynk-arglists)[arguments]: Set an appropriate asdf-system-name.
(sbcl-slynk-fancy-inspector)[arguments]: Likewise.
(sbcl-slynk-package-fu)[arguments]: Likewise.
(sbcl-slynk-mrepl)[arguments]: Likewise.
(sbcl-slynk-trace-dialog)[arguments]: Likewise.
(sbcl-slynk-profiler)[arguments]: Likewise.
(sbcl-slynk-indentation)[arguments]: Likewise.
(sbcl-slynk-retro)[arguments]: Likewise.

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

The asdf documentation specifies that asdf:load-asd should be preferred to
calling load on a system definition file.

* guix/build/lisp-utils.scm (compile-system): Replace load with asdf:load-asd.
(system-dependencies): Likewise.
(test-system): Likewise.

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

* guix/build/lisp-utils.scm (lisp-eval-program): Replace system* and error
handling with invoke.

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

* guix/build/lisp-system.scm: (lisp-eval-program): Log the arguments to
system*.

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

Add support for dependencies of the form (:version <name> <version>),
(:feature <feature> <dependency-specification>) and (:require <module-name>),
as defined by
<https://common-lisp.net/project/asdf/asdf.html#The-defsystem-grammar

>.

* guix/build/lisp-utils.scm (normalize-dependency): New variable.
(make-asd-file)[dependencies]: Use it to generate dependencies with normalized
names.
[dependency-name]: New variable.
[registry]: Use it to flatten the normalized dependencies.

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