gnu: bash: Update to patch level 42.

* gnu/packages/bash.scm (%patch-series-4.3): Add patches 40 to 42.

gnu: commencement: Initial Texinfo uses initial Perl.

* gnu/packages/commencement.scm (texinfo-boot0)[inputs]: Use
PERL-BOOT0.

gnu: perl: Build deterministically, and make byproducts deterministic.

With this, a --rounds=2 build passes, and timestamps in POD files can be
controlled with 'SOURCE_DATE_EPOCH'.

* gnu/packages/patches/perl-deterministic-ordering.patch,
gnu/packages/patches/perl-no-build-time.patch,
gnu/packages/patches/perl-source-date-epoch.patch: New files.
* gnu/packages/perl.scm (perl)[source]: Use them.
* gnu-system.am (dist_patch_DATA): Add them.

gnu: perl: Update to 5.22.0.

* gnu/packages/perl.scm (perl)[source]: Update to 5.22.0.  Remove
"perl-module-pluggable-search.patch" since Module::Pluggable appears to
be gone.
[arguments] <configure-phase>: Adjust Cwd.pm file name.  Replace
-std=c89 with -std=gnu89.
* gnu/packages/commencement.scm (perl-boot0): Add 'disable-pthreads'
phase.
* gnu/packages/patches/perl-no-sys-dirs.patch: Update.
* gnu/packages/patches/perl-module-pluggable-search.patch: Remove.
* gnu-system.am (dist_patch_DATA): Adjust accordingly.

gnu: gmp: Disable parallel tests.

* gnu/packages/multiprecision.scm (gmp)[arguments]: Disable parallel tests.

build: Add missing patches to the distribution.

* gnu-system.am (dist_patch_DATA): Add glibc-hurd-extern-inline.patch
and plink-1.07-unclobber-i.patch.

Merge branch 'master' into core-updates

gnu: numactl: Update to 2.0.11.

* gnu/packages/linux.scm (numactl)[source]: Update to 2.0.11.
  [native-inputs]: Drop autotools.
  [arguments]: Drop phase calling autogen.sh.

gnu: wget: Update to 1.17.1.

* gnu/packages/wget.scm (wget): Update to 1.17.1.

gnu: gcc: Use the system zlib.

* gnu/packages/gcc.scm (gcc-4.7) <configure-flags>: Pass
'--with-system-zlib'.
* gnu/packages/commencement.scm (gcc-boot0)[arguments]: Remove
'--with-system-zlib' from the configure flags.
* gnu/packages/commencement.scm (zlib-final): New variable.
(gcc-final)[arguments]: Add ZLIB-FINAL to #:allowed-references.
Pass -L and -Wl,-rpath for zlib in LDFLAGS, as a configure flag.
[inputs]: Add LD-WRAPPER-BOOT3 and ZLIB-FINAL.

gnu: gcc-final: Remove unnecessary CPPFLAGS.

* gnu/packages/commencement.scm (gcc-final)[arguments]: Remove
unnecessary CPPFLAGS from #:make-flags.

gnu: Move sparsehash to datastructures module.

* gnu/packages/crypto.scm (sparsehash): Move variable to...
* gnu/packages/datastructures.scm: ...new file.
* gnu-system.am (GNU_SYSTEM_MODULES): Add it.

gnu: Add r-lattice.

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

gnu: Add r-gridbase.

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

gnu: Add r-plotrix.

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

gnu: Add r-readr.

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

gnu: Rename r-data.table to r-data-table.

* gnu/packages/statistics.scm (r-data.table): Rename variable ...
(r-data-table): ... to this.
[description]: Clarify relation to data.frame.
[license]: Use correct license.

import: cran: Parse DESCRIPTION instead of HTML.

* guix/import/cran.scm (description->alist, listify,
  beautify-description, description->package): New procedures.
(table-datum, downloads->url, nodes->text, cran-sxml->sexp): Remove
proceduces.
(latest-release): Use parsed DESCRIPTION instead of SXML.
* tests/cran.scm: Rewrite to match importer.

import: cran: Match more license strings.

* guix/import/cran.scm (string->license): Match more license strings to
  license symbols.

gnu: Add snap-aligner.

* gnu/packages/bioinformatics.scm (snap-aligner): New variable.