* guix/inferior.scm (%inferior-cache-directory): New variable.
(inferior-for-channels): New procedure.

* guix/channels.scm (channel-instances->derivation): New procedure.
(latest-channel-derivation): Use it.
(channel-instance-derivations): Make private.

* guix/profiles.scm (packages->manifest)[inferiors-loaded?]: New
variable.
[inferior->entry]: New procedure.
Accept inferior packages when INFERIORS-LOADED? is true.
* tests/guix-package.sh: Add test using a manifest with an inferior.
* tests/inferior.scm ("packages->manifest"): New test.

* guix/inferior.scm (inferior-package->manifest-entry): New procedure.
* tests/inferior.scm (manifest-entry->list): New procedure.
("inferior-package->manifest-entry"): New test.

* guix/inferior.scm (%inferior-package-search-paths)
(inferior-package-native-search-paths)
(inferior-package-search-paths)
(inferior-package-transitive-native-search-paths): New procedures.
* tests/inferior.scm ("inferior-package-search-paths"): New test.

* guix/inferior.scm (open-inferior): Use (ice-9 match).
(inferior-package-input-field, inferior-package-inputs):
(inferior-package-native-inputs)
(inferior-package-propagated-inputs)
(inferior-package-transitive-propagated-inputs): New procedures.
* tests/inferior.scm ("inferior-package-inputs"): New test.

inputs fixlet

* guix/inferior.scm (<inferior>)[packages, table]: New fields.
(open-inferior): Initialize these new fields.
(inferior-packages): Rename to...
(%inferior-packages): ... this.
(inferior-packages): New procedure; force the promise.
(%inferior-package-table, lookup-inferior-packages): New procedures.
* tests/inferior.scm ("lookup-inferior-packages")
("lookup-inferior-packages and eq?-ness"): New tests.

* guix/inferior.scm (read-inferior-response)
(send-inferior-request): New procedures.
(inferior-eval): Rewrite in terms of these.
(proxy, inferior-package-derivation, inferior-package->derivation)
(package-compiler): New procedures.
* tests/inferior.scm ("inferior-package-derivation"): New test.

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

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

This fix ensures that the H5_HAVE_PARALLEL identifier is correctly set
in the file H5pubconf.h.

* gnu/packages/maths.scm (hdf5-parallel-openmpi)[arguments]: Add
the "--enable-parallel" flag to the list of configure flags.  Remove
the incompatible "--enable-cxx" flag.  Add 'mpi-setup' phase.

Signed-off-by: Ludovic Courtès <ludovic.courtes@inria.fr>

* gnu/packages/maths.scm (hdf5)[arguments]: Add condition to 'split'
phase to check for existence of h5fc script.

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

* gnu/packages/rust.scm (rust-1.20)[arguments]<#:phases>[configure]: Remove
unused "localstatedir" setting.

* gnu/packages/ftp.scm (libfilezilla): Update to 0.13.2.
[source]: Use HTTPS.

* gnu/packages/python.scm (python-pyparsing)[home-page]: Update.

* gnu/packages/emacs.scm (emacs-mu4e-conversation)[description]:
Fix 'correspondant' typo.

* gnu/packages/kodi.scm (kodi)[arguments]: Substitute INVOKE for SYSTEM*.

* gnu/packages/kodi.scm (crossguid)[arguments]: Substitute INVOKE for SYSTEM*.

* gnu/packages/gnuzilla.scm (icecat): Update to 60.2.0-gnu1.
[source]: Download pre-release from alpha.gnu.org.  Remove obsolete patches.
Comment out the code to delete the bundled copies of libevent, cairo,
harfbuzz, and graphite2.
[inputs]: Use the latest ffmpeg.  Comment out libevent, cairo, harfbuzz, and
graphite2.
[native-inputs]: Add rust and cargo.
[arguments]: Remove --enable-gio and --disable-gnomeui.  Add --disable-stylo.
Comment out --with-system-{libevent,harfbuzz,graphite2}, --enable-system-cairo.
Import %cargo-build-system-modules.  Add 'patch-cargo-checksums' phase.
* gnu/packages/patches/icecat-CVE-2018-5157-and-CVE-2018-5158.patch,
gnu/packages/patches/icecat-bug-1413868-pt1.patch: Delete files.
* gnu/local.mk (dist_patch_DATA): Remove them.

* gnu/packages/patches/libvpx-use-after-free-in-postproc.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/video.scm (libvpx)[source]: Add patch.

* gnu/packages/python-crypto.scm (python-paramiko): Update to 2.4.2.

* gnu/packages/python-crypto.scm (python-paramiko)[home-page]: Use HTTPS.

* gnu/packages/python.scm (python-rencode): Update to 1.0.5.
[arguments]: Add a 'delete-bogus-test' phase.

* gnu/packages/python.scm (python-hdf4)[arguments]: Substitute INVOKE
for SYSTEM*.

* gnu/packages/skarnet.scm (s6): Update to 2.7.2.1.

* 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.