biology/star2.7.11.a_1

Release numerous ports to ports@

I've been retired for a few years, and it is unlikely I will be doing
any more scientific computing support in the future.  I have continued
to maintain ~160 ports to the best of my ability, mainly as a favor to
the community, but I can no longer justify the time and effort
required.  I am therefore releasing most of my scientific ports, along
with a few others, to ports@.  I will continue to maintain ports I am
actively using and those for which I am upstream.

all: drop support for FreeBSD 13, mips and risc64sf

Reviewed by:            many (*)
Differential Revision:  https://reviews.freebsd.org/D55624
Differential Revision:  https://reviews.freebsd.org/D55642 (merged in from bofh)

many (*)
  acm arrowd brooks cmt dch decke dinoex eduardo fluffy fuz gahr garga
  jbeich joerg jrm kai kenrap martymac matthew mfechner michaelo mizhka
  nobutaka pkubaj se tagattie thj

  Anton Saietskii
  GenericRikka
  Gert Doering
  Jan Bramkamp
  Oleh Hushchenkov
  Oleksandr Kryvulia
  Ralf van der Enden
  Yamagi

  desktop kde python tcltk office

biology/star: Use EXTRACT_AFTER_ARGS to omit unused htslib dir

Reduces I/O during builds

PR:             278751
Reported by:    diizzy

biology/star: Fix SIMD issue on non-amd64

Also remove some extraneous build flags from upstream Makefile

PR:             273240
Reported by:    dizzy

biology/star: fix build on !amd64

The port tries to force AVX2, but it's only available on amd64.

biology/star: Update to 2.7.11a

A few bug fixes and new features
Add USE_GCC as a temporary hack for input read issue
This was also an issue in 2.7.10b

Changes: https://github.com/alexdobin/STAR/releases

biology/star: Set NOT_FOR_ARCHS to all 32-bit processors

biology/star: Update to 2.7.10b

Numerous fixes and enhancements
Changes: https://github.com/alexdobin/STAR/releases

biology/star: Bump PORTREVISION for biology/htslib update

Remove WWW entries moved into port Makefiles

Commit b7f05445c00f has added WWW entries to port Makefiles based on
WWW: lines in pkg-descr files.

This commit removes the WWW: lines of moved-over URLs from these
pkg-descr files.

Approved by:		portmgr (tcberner)

Add WWW entries to port Makefiles

It has been common practice to have one or more URLs at the end of the
ports' pkg-descr files, one per line and prefixed with "WWW:". These
URLs should point at a project website or other relevant resources.

Access to these URLs required processing of the pkg-descr files, and
they have often become stale over time. If more than one such URL was
present in a pkg-descr file, only the first one was tarnsfered into
the port INDEX, but for many ports only the last line did contain the
port specific URL to further information.

There have been several proposals to make a project URL available as
a macro in the ports' Makefiles, over time.

This commit implements such a proposal and moves one of the WWW: entries
of each pkg-descr file into the respective port's Makefile. A heuristic
attempts to identify the most relevant URL in case there is more than
one WWW: entry in some pkg-descr file. URLs that are not moved into the
Makefile are prefixed with "See also:" instead of "WWW:" in the pkg-descr
files in order to preserve them.

There are 1256 ports that had no WWW: entries in pkg-descr files. These
ports will not be touched in this commit.

The portlint port has been adjusted to expect a WWW entry in each port
Makefile, and to flag any remaining "WWW:" lines in pkg-descr files as
deprecated.

Approved by:		portmgr (tcberner)

biology/star: Broken on systems where OpenMP isn't enabled

Reported by:	fallout
Approved by:	portmgr (blanket)

biology/star: Update to 2.7.9a

Also unbundle htslib

Changes:        https://github.com/alexdobin/STAR/releases/tag/2.7.9a

One more small cleanup, forgotten yesterday. Reported by:	lwhsu

Remove # $FreeBSD$ from Makefiles.

biology/star: Drop dependency on gcc

Replace compiler:openmp with compiler:c++11-lang and localbase

PR:             port/247753, ports/252379

biology/star: Upgrade to 2.7.3a

Several compatibility and feature enhancements

biology/star: Upgrade to 2.7.2d

Fix chimeric output bug.

Numerous other minor fixes and enhancements since 2.7.0.

Reported by:    portscout

Bump PORTREVISION for ports depending on the canonical version of GCC as defined in Mk/bsd.default-versions.mk which has moved from GCC 8.3 to GCC 9.1 under most circumstances now after revision 507371.

This includes ports
 - with USE_GCC=yes or USE_GCC=any,
 - with USES=fortran,
 - using Mk/bsd.octave.mk which in turn features USES=fortran, and
 - with USES=compiler specifying openmp, nestedfct, c11, c++0x, c++11-lang,
   c++11-lib, c++14-lang, c++17-lang, or gcc-c++11-lib
plus, everything INDEX-11 shows with a dependency on lang/gcc9 now.

PR:		238330

biology/star: Force newer GCC on platforms with GCC 4.2 base

PR:             237700
Submitted by:   pkubaj

biology/star: Modify PKGBASE to avoid conflict with archivers/star

biology/star: Spliced Transcripts Alignment to a Reference

STAR is an extremely fast RNA-seq aligner, an alternative to tophat2,
hisat2, bowtie, subread, etc.