Mk/bsd.commands.mk: Use absolute path to define GMAKE

Same as BSDMAKE variable.  It is needed by some ports.

Some ports needed fixes:
- devel/rcs57: Regenerate configure with newer autoconf so it can deal
  with MAKE set to an absolute path.  While here fix issues with
  (un)escaping double quotes.  The warnings about this were in
  WRKSRC/src/conf.err.
- lang/gnu-cobol: Patch configure.ac so the MAKE environment variable
  can contain an absolute path, and define MAKE before it is used in
  AM_INIT_AUTOMAKE.  Remove post-patch patching of configure.  It appears
  to have been fixed upstream.
- math/unuran: Remove post-patch, fixed upstream.
- net-mgmt/kismet: Fix post-patch.

PR:		283534
Exp-run by:	antoine

biology/abyss: update 2.3.9 → 2.3.10

PR:	282540

all: drop support for expired FreeBSD 14.0

Simplify expressions for FreeBSD 13.X

Reviewed by:	many

Differential Revision:	https://reviews.freebsd.org/D46601

biology/abyss: update 2.3.8 → 2.3.9

Reported by:	portscout

biology/abyss: update 2.3.7 → 2.3.8

Reported by:	portscout

biology/abyss: Move man pages to share/man

Approved by:	portmgr (blanket)

*/*: bump PORTREVISION after the upgrade of MPICH to 4.1.2

biology/abyss: Update 2.3.5 → 2.3.7

Reported by:	portscout

biology/abyss: Fix build with llvm15

Approved by:	portmgr (blanket)

*: Bump PORTREVISIONs for math/mpc update to 1.3.1

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.

*/*: bump all consumers after recent boost upgrade

biology/abyss: Add test target

biology/abyss: Update 2.3.1 -> 2.3.5

devel/libffi: Bump deps PORTREVISION for shlib change

PR:		263764
Reported by:	VVD <vvd@unislabs.com>

cleanup: drop support for EOL FreeBSD 11.X

Search criteria used:
- 11.4
- OSREL*
- OSVER*
- *_FreeBSD_11

Input from:
- adridg: devel/qca-legacy
- jbeich: _WITH_DPRINTF, _WITH_GETLINE, GNU bfd workarounds
- sunpoet: security/p5-*OpenSSL*

Reviewed by:	doceng, kde, multimedia, perl, python, ruby, rust
Differential Revision: https://reviews.freebsd.org/D32008
Test Plan: make index

biology/abyss: Broken on 11

Reported by:	fallout

biology/abyss: Update 2.3.0-3 -> 2.3.1

Reported by:	portscout

biology/abyss: Update 2.2.5 -> 2.3.0-3

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

Remove # $FreeBSD$ from Makefiles.

biology/abyss: Add PORTSCOUT line

biology/abyss: Update 2.2.4 -> 2.2.5

Reported by:	portscout

Chanse update of devel/libffi

Chase the devel/libffi update
Bump portrevision of all dependent ports to chace shard library version bump
in libffi.
Update LIB_DEPENDS lines where needed to not require a specific version of
libffi.so.

PR:		247028 (for tracking)

biology/abyss: Update 2.2.3 -> 2.2.4

Drop dependency on devel/openmp

- Drop if devel/llvm* was used as a substitute

Approved by:	yuri, rene (earlier version)
Differential Revision:	https://reviews.freebsd.org/D23020

biology/abyss: Broken on i386

Reported by:	fallout

biology/abyss: Update 2.1.5 -> 2.2.3

Reported by:	portscout

devel/boost-*: update to 1.72.0

Changes:	http://www.boost.org/users/history/version_1_72_0.html
PR:		241449
Exp-run by:	antoine
Differential Revision:	https://reviews.freebsd.org/D22136

devel/openmp: update to 9.0.0

- Connect tests to the framework to help QA remaining patches
- Force rebuild all consumers after https://reviews.llvm.org/D59783

Changes:	http://llvm.org/viewvc/llvm-project/openmp/tags/RELEASE_900/final/?view=log
ABI:		https://abi-laboratory.pro/tracker/timeline/llvm_openmp/

devel/boost-*: update to 1.71.0

Changes:	http://www.boost.org/users/history/version_1_71_0.html
PR:		238827
Exp-run by:	antoine
Differential Revision:	https://reviews.freebsd.org/D20774

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/abyss: fix build on big-endian architectures

Use new GCC from ports on GCC architectures.

Merge 25eb9d2a914fb211fdfe04fcda5593f29fd23ff5, fixes build on GCC
architectures.

Also include sys/endian.h and use bswap32 and bswap64 for byte-swapping (PR at
https://github.com/bcgsc/abyss/pull/287 ).

PR:		238737
Approved by:	yuri (maintainer), mat (mentor)
Differential Revision:	https://reviews.freebsd.org/D20717

devel/openmp: phase out

- Expire after the last version without /usr/lib/libomp.so
- Drop SOVERSION for seamless transition (i.e., avoid conditionals)

PR:		236907
Approved by:	bapt (maintainer)
Differential Revision:	https://reviews.freebsd.org/D19767

devel/boost-*: update to 1.70.0

Changes:	http://www.boost.org/users/history/version_1_70_0.html
PR:		235956
Exp-run by:	antoine
Differential Revision:	https://reviews.freebsd.org/D19303

New port: biology/abyss: Assembly By Short Sequences: parallel, paired-end
sequence assembler