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

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

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

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

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

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

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

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

* guix/import/cran.scm (cran-fetch): Rename procedure ...
(fetch-description): ... to this.

* guix/import/cran.scm (package->upstream-name): New procedure.

* gnu/packages/xml.scm (xmlstarlet): New variable.

* gnu/packages/audio.scm (zita-convolver)[source]: Add snippet.

* gnu/packages/audio.scm (zita-resampler)[source]: Add snippet.

* gnu/packages/ruby.scm (ruby-ansi): New variable.

* gnu/packages/bioinformatics.scm (edirect): Update to 3.50.
[native-inputs]: Remove "unzip".

Fixes <http://bugs.gnu.org/16791>.

* gnu/packages/patches/w3m-force-ssl_verify_server-on.patch: New file.
* gnu/packages/patches/w3m-disable-sslv2-and-sslv3.patch: New file.
* gnu/packages/patches/w3m-disable-weak-ciphers.patch: New file.
* gnu/packages/w3m.scm (w3m)[source]: Add patches.
* gnu-system.am (dist_patch_DATA): Add the new files.

* gnu/packages/patches/w3m-fix-compile.patch: Rename this file...
* gnu/packages/patches/w3m-libgc.patch: ...to this, and adjust patch
prefix level to '-p1'.
* gnu-system.am (dist_patch_DATA): Update patch name.
* gnu/packages/w3m.scm (w3m)[source]: Update patch name.
[source]: Drop patch flag -p0.

* guix/build-system/gnu.scm (package-with-explicit-inputs): Use
  'ensure-keyword-arguments' instead of appending to ARGS.
* gnu/packages/commencement.scm (static-bash-for-glibc): Add missing
  #:guile argument.

* guix/utils.scm (delkw, ensure-keyword-arguments): New procedures.
* tests/utils.scm ("ensure-keyword-arguments"): New test.

* guix/http-client.scm (read-header-line): New procedure.  Use it.

* gnu/packages/package-management.scm (guix-devel): Update to f888c0b1.

* guix/http-client.scm: Fix Guile version number in comment for Guile
commit 5a10e41.

* gnu/packages/maths.scm (gmsh): Update to 2.11.0.
  [arguments]: Replace 'check phase.

* guix/scripts/lint.scm (package-vulnerabilities): Catch
'getaddrinfo-error'.

* gnu/packages/admin.scm (sudo)[arguments]: Pass
--with-rundir=/var/run/sudo since /var/run is cleaned up at boot time on
GuixSD whereas /run is not.

This makes sure that critical errors such as unbound-variable do not go
undetected.

* gnu/services.scm (cleanup-gexp): Introduce local 'fail-safe' macro and
use it.  Remove uses of 'false-if-exception'.

* gnu/packages/ldc.scm (ldc)[license]: Replace invalid use of
'license:x11-style' by LICENSE:BOOST1.0.

The .gem file stored in GEM_HOME after install is both redundant and an
archive that stores timestamped files which makes builds
non-deterministic, so delete it after 'gem install'.

* guix/build/ruby-build-system.scm (install): Remove cached gem after
  install.

* gnu/packages/java.scm (icedtea7): Rename variable to...
(icedtea-7): ...this.
(icedtea): Refer to "icedtea-7".

* gnu/packages/java.scm (icedtea6): Rename variable to...
(icedtea-6): ...this.

* gnu/packages/java.scm (icedtea6): Change package name to "icedtea".
(icedtea7): Inherit package name.

* gnu/packages/java.scm (icedtea): New variable.
(swt)[native-inputs]: Replace "icedtea6" with "icedtea".
* gnu/packages/bioinformatics.scm (htsjdk)[native-inputs]: Likewise.
(ngs-java)[inputs]: Likewise.
* gnu/packages/kodi.scm (kodi)[native-inputs]: Replace "icedtea7" with
"icedtea".
* gnu/packages/ruby.scm (ruby-rjb)[native-inputs]: Replace "icedtea7"
with "icedtea".

* gnu/packages/java.scm (icedtea6)[arguments]: Unpack OpenJDK sources to
"openjdk.src".
(icedtea7)[arguments]: Inherit "--with-openjdk-src-dir" flag; refer to
"openjdk.src" in build phases; simplify "unpack" phase.
[native-inputs]: Rename "openjdk-drop" to "openjdk-src".

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

* configure.ac: Change version to 0.9.1.

* doc/guix.texi: substitute 'the the' with 'the'.

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

* guix/build/pull.scm (call-with-process, report-build-progress)
(p-for-each): Remove.
(build-guix): Load and compile files in one process.

* gnu/packages/ebook.scm (calibre): Update to 2.48.0.

* gnu/packages/ldc.scm: New file.
* gnu/packages/patches/ldc-disable-tests.patch: New file.
* gnu-system.am (GNU_SYSTEM_MODULES): Add ldc.scm.
  (dist_patch_DATA): Add patch file.

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

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