gnu: Add r-bitops.

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

gnu: Add AdaptiveSparsity.

* gnu/packages/machine-learning.scm (r-adaptivesparsity): New variable.

gnu: Add r-rcpparmadillo.

* gnu/packages/maths.scm (armadillo-for-rcpparmadillo): New variable.
* gnu/packages/statistics.scm (r-rcpparmadillo): New variable.

gnu: Add armadillo.

* gnu/packages/maths.scm (armadillo): New variable.

gnu: Add libgit2.

* gnu/packages/version-control.scm (libgit2): New variable.

gnu: mafft: Update to 7.267.

* gnu/packages/bioinformatics.scm (mafft): Update to 7.267.
[arguments]: Don't include mafft-homologs manpage.
[inputs]: Add gawk and grep.
[propagated-inputs]: Add coreutils.

gnu: rxvt-unicode: Install the terminal capability data.

This provides the necessary terminal capability data, which are required
by ncurses-based applications.

* gnu/packages/xdisorg.scm (rxvt-unicode)[native-inputs]: Add ncurses.
[arguments]: Set the destination of the terminfo files.
[native-search-path]: New field.  Make them automatically available to
the user.

gnu: msmtp: Update to 1.6.3.

* gnu/packages/mail.scm (msmtp): Update to 1.6.3.
[inputs]: Add libsecret.

gnu: claws-mail: Update to 3.13.1.

* gnu/packages/mail.scm (claws-mail): Update to 3.13.1.

gnu: python-cython: Update to 0.23.4.

* gnu/packages/python.scm (python-cython): Update to 0.23.4.

gnu: ruby: Update to 2.2.4.

This version fixes CVE-2015-7551.

* gnu/packages/ruby.scm (ruby): Update to 2.2.4.

packages: Remove now redundant graph procedures.

These procedures are now redundant with those in (guix graph) and are no
longer used since commit a51cbecb.

* gnu/packages.scm (vhash-refq, package-dependencies)
(package-direct-dependents, package-transitive-dependents)
(package-covering-dependents): Remove.

gnu: offlineimap: Update to 6.6.0.

* gnu/packages/mail.scm (offlineimap): Update to 6.6.0.

gnu: gnupg: Update to 1.4.20.

* gnu/packages/gnupg.scm (gnupg-1): Update to 1.4.20.

gnu: Add gnome-shell.

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

gnu: Add gnome-control-center.

* gnu/packages/gnome.scm (gnome-control-center): New variable.

gnu: Add gnome-bluetooth.

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

gnu: Add libgtop.

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

gnu: Add colord-gtk.

* gnu/packages/freedesktop.scm (colord-gtk): New variable.

gnu: Add telepathy-logger.

* gnu/packages/freedesktop.scm (telepathy-logger): New variable.