biology/stacks2.68

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.

biology/stacks: fix build without libomp

src/process_radtags.cc:1578:6: error: unknown type name 'omp_lock_t'
 1578 |             omp_lock_t      &thread_outbuf_lock   = outbuf_lock[thread_index];
      |             ^
25 warnings and 10 errors generated.

biology/stacks: Update to 2.68

Numerous fixes and improvements since 2.4
Changes: http://catchenlab.life.illinois.edu/stacks/changelog.php

PR:             283257
Reported by:    alster@vinterdalen.se

biology/stacks: Unbreak build on aarch64

ARM clang is intolerant of implicit demotions in initializers

Reported by:    pkg-fallout

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)

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

Remove # $FreeBSD$ from Makefiles.

biology/stacks: Drop dependency on gcc

Replace compiler:openmp with compiler:c++11-lang and localbase
Set USE_GCC for i386 to work around limitations in clang atomic (PR 230888)

PR:             port/247753, ports/252379

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/stacks: Remove obsolete pkg-message regarding web interface

PHP code no longer included in dist as of v2.4

biology/stacks: Upgrade to 2.4

Improve check to avoid outdated GCC on 2nd tier platforms

Reported by:    portscout

biology/stacks: Upgrade to 2.3

Approved by:    jrm (mentor, implicit)

Bump PORTREVISION for ports depending on the canonical version of GCC defined via Mk/bsd.default-versions.mk which has moved from GCC 7.4 t GCC 8.2 under most circumstances.

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, as a double check, everything INDEX-11 showed depending on lang/gcc7.

PR:		231590

Fix build with tier-2 arches.

PR:		231448
Submitted by:	Piotr Kubaj
Approved by:	maintainer

biology/stacks: Enable OpenMP (oversight in previous commit)

Upgrade to latest release will follow, after testing

Approved by:    jrm (mentor)
Differential Revision:  https://reviews.freebsd.org/D16973

Bump PORTREVISION for ports depending on the canonical version of GCC in the ports tree (via Mk/bsd.default-versions.mk and lang/gcc) which has now moved from GCC 6 to GCC 7 by default.

This includes ports
 - featuring USE_GCC=yes or USE_GCC=any,
 - featuring USES=fortran,
 - using Mk/bsd.octave.mk which in turn features USES=fortran, and those
 - with USES=compiler specifying one of openmp, nestedfct, c11, c++0x,
   c++11-lib, c++11-lang, c++14-lang, c++17-lang, or gcc-c++11-lib.

PR:		222542

Adjust USES to fix builds on gcc-based architectures.

While here, pet portlint.

Tested for no regression on amd64.

Approved by:	portmgr (tier-2 blanket)

biology/stacks: Software pipeline for building loci from short-read sequences

Reviewed by:    mat
Approved by:    jrm (mentor)
Differential Revision:  https://reviews.freebsd.org/D14885