biology/bolt-lmm2.5_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.

*/*: update boost consumers after boost-1.92

biology/bolt-lmm: Update to 2.5

Numerous fixes and enhancements
Changes: https://storage.googleapis.com/broad-alkesgroup-public/ \
	 BOLT-LMM/BOLT-LMM_manual.html#x1-60002.1

Reported by:    Repology

*/*: bump consumers after devel/boost update

*/*: bump PORTREVISION after the upgrade of OpenBLAS

devel/boost: bump consumers after boost upgrade (+)

Get rid of direct dependency ob libbost_system.so, use libboost_thread.so instead

devel/boost: bump consumers after Boost update

*/*: Bump PORTREVISION after math/nlopt update

devel/boost: bump consumers after Boost-1.87 update

Sponsored by:	Future Crew, LLC

*/*: bump PORTREVISION after OpenBLAS upgrade

Remark: this souldn’t be necessary, because the version of the library is the
same, but due to many changes between these releases, it is safer this way.

PR:		284314

devel/boost: bump consu,ers after update Boost to 1.86 release

Sponsored by:	Future Crew, LLC

*/*: bump consumers after devel/boost* update

With hat:	office
Sponsored by:	Future Crew, LLC

*/*: Bump PORTVERSION of math/nlopt consumers

..due to shlib change

*/*: bump PORTREVISION after the upgrade to OpenBLAS

devel/boost: bump consumers after library update

*/*: bump PORTREVISION after the upgrade of OpenBLAS

PR:		273219

devel/boost*: bump all consumers after 1.83.0

*/*: bump all direct Boost cunsumers

*: Bump PORTREVISIONs for math/mpc update to 1.3.1

*/*:	bump libboost*.so libraries consumert after Boost upgrade

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)

*/*: bump all consumers after recent boost upgrade

devel/boost-all: bump all library consumers after boost upgrade

PR:	246106

biology/bolt-lmm: remove unnecessary CFLAGS_powerpc64

biology/bolt-lmm: remove unnecessary flags for powerpc64le

biology/bolt-lmm: Update to 2.3.6

Changes: https://alkesgroup.broadinstitute.org/BOLT-LMM/\
	 BOLT-LMM_manual.html#x1-60002.1

Also fixed build on aarch64: Replaced non-portable _mm_malloc() with
aligned_alloc()

Reported by:    pkg-fallout

Update CONFLICTS definitions in categories a* to c*

Update the CONFLICTS definitions of ports in the following categories:

- accessibility
- archivers
- audio
- benchmarks
- biology
- cad
- chinese
- comms
- converters

An attempt has been made to use generic conflicts patterns that do not
have to be updated whenever a new version of a conflicting port is
added to the ports system.

There is a misunderstanding that the port being built/installed has to
be omitted from the conflicts pattern. This is not true - the port
being built is implicitly non-conflicting due to logic in bsd.port.mk.

Approved by:	portmgr (implicit)

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

Remove # $FreeBSD$ from Makefiles.

Canonicalize powerpc64le CXXFLAGS to be the same as powerpc64.

Approved by:	portmgr (tier-2 blanket)

Bump 46 ports depending on math/openblas because the after the recent math/openblas update the library name changed in openblas.

Fix math/openblas and bump dependent ports

* Fix build on i386 [1]
* Fix science/code_saturne build with new openblas [2]
* Avoid installing private headers [3]
* Prevent build from optimizing for host by correcting build confg [4]
* Bump portrevision of dependent ports [5]

This is correcting issues from r523749 [1][2][4] and r515970 [3]

PR:		231371
Reported by:	build cluster [1]
Reported by:	Dima Pasechnik <dimpase+freebsd@gmail.com> [2]
Reported by:	many [5]
Reviewed by:	mat, bapt
Approved by:	implicit, since this is a build fix

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/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

biology/bolt-lmm: Upgrade to 2.3.4

Remove previously upstreamed patches
New Makefile patch that preserves default behavior and should be palatable
to upstream

PR:             239613 Submitted by:   pkubaj

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/bolt-lmm: Mixed model association testing and variance component analysis

The BOLT-LMM software package currently consists of two main algorithms, the
BOLT-LMM algorithm for mixed model association testing, and the BOLT-REML
algorithm for variance components analysis (i.e., partitioning of
SNP-heritability and estimation of genetic correlations).