linux-initrd: Add virtio modules to '%base-initrd-modules'.

Fixes a regression in installation tests, whereby 'guix system init'
would report that virtio modules are missing for the target devices.
In practice virtio modules were always available since 'base-initrd' was
always called with #:virtio? #t.  This commit simply moves them to
'%base-initrd-modules' so that 'guix system' knows they're available.

Reported by Danny Milosavljevic <dannym@scratchpost.org> at
<https://debbugs.gnu.org/cgi/bugreport.cgi?bug=30629#112>.

* gnu/system/linux-initrd.scm (default-initrd-modules): Add virtio
modules.
(base-initrd): Remove #:virtio? and 'virtio-modules'.
* gnu/system/vm.scm (expression->derivation-in-linux-vm)
(system-qemu-image, virtualized-operating-system): Remove uses of
 #:virtio?.
* doc/guix.texi (Initial RAM Disk): Update 'base-initrd' doc.

system: beaglebone-black: Use 'initrd-modules'.

* gnu/system/examples/beaglebone-black.tmpl: Use 'initrd-modules'
instead of 'initrd'.

vm: Add missing modules to the 'expression->derivation-in-linux-vm' initrd.

Fixes a regression introduced in
bc499b113a598c0e7863da9887a4133472985713, whereby the default initrd
used by 'expression->derivation-in-linux-vm' would lack all the usual
modules: virtio, nls_iso8859-1, etc.

* gnu/system/vm.scm (expression->derivation-in-linux-vm): Pass
 #:linux-modules to 'base-initrd'.

linux-initrd: 'file-system-modules' returns the right module list.

Fixes a bug whereby, for an "iso9660" file system, it would return
'("iso9660" "isofs"), i.e., both the key and the value.

Reported by Danny Milosavljevic <dannym@scratchpost.org>
at <https://debbugs.gnu.org/cgi/bugreport.cgi?bug=30629#115>.

* gnu/system/linux-initrd.scm (lookup-procedure): 'vhash-assoc' returns
a key/value pair; match it.

gnu: cutadapt: Update to 1.16.

* gnu/packages/bioinformatics.scm (cutadapt): Update to 1.16.
[source]: Fetch via git.
[arguments]: Remove.
[native-inputs]: Replace python-nose with python-pytest.

gnu: python-xopen: Update to 0.3.2.

* gnu/packages/python.scm (python-xopen): Update to 0.3.2.

gnu: Add r-hpar.

* gnu/packages/bioconductor.scm: New file.
* gnu/local.mk (GNU_SYSTEM_MODULES): Add it.

gnu: Add r-powerplus.

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

gnu: Add r-np.

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

gnu: Add r-phontools.

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

gnu: Add r-complexplus.

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

gnu: Add r-expm.

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

gnu: Add r-trend.

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

gnu: Add r-cubature.

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

gnu: Add r-urca.

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

gnu: Add r-fractal.

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

gnu: Add r-extradistr.

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

gnu: Add r-tsa.

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

gnu: Add r-wmtsa.

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

gnu: Add r-tseries.

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