biology/salmon1.10.3_2

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/salmon: Fix Boost detection with CMake 4

Approved by:	portmgr (fixit blanket)

biology/salmon: fix build on powerpc64le

Test amd64 path first and only if that fails use the arm path.
arm path works just fine on powerpc64le.

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/salmon: Unbreak: Relax libgff version requirement

Also drop unnecessary libboost dep

Reported by:    pkg-fallout

*: WITH_DEBUG is a user feature not a port one

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

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

biology/salmon: Update to tag 1.10.3

Fix build under clang19:
    Patch out deprecated atomic template copy
    Unbundle eigen and libdivide
    https://github.com/COMBINE-lab/salmon/issues/988
Upstream updates to improve ARM support
Changes: https://github.com/COMBINE-lab/salmon/commits/master/

Reported by:    pkg-fallout

devel/boost: bump consumers after Boost update

devel/boost: bump consumers after Boost-1.87 update

Sponsored by:	Future Crew, LLC

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

devel/onetbb: Update to 2021.13.0

and bump dependent ports' revisions.

Release notes:	https://github.com/oneapi-src/oneTBB/blob/v2021.13.0/RELEASE_NOTES.md

devel/onetbb: Update to 2021.12.0

and bump dependent ports' revisions.

Release notes: https://github.com/oneapi-src/oneTBB/releases/tag/v2021.12.0

cleanup: remove occurrences of WITH_DEBUG

DEBUG like all ports features, must not ever be set in a port, they are
user facing features, that the user needs to enable in their
environment/make.conf, either by defining WITH_DEBUG globally, or by
setting WITH_DEBUG_PORTS with origin of ports they want DEBUG enabled
in.

devel/onetbb: Update to 2021.11.0

and bump dependent ports' revisions.

Release notes: https://github.com/oneapi-src/oneTBB/releases/tag/v2021.11.0

devel/onetbb: Update to 2021.10.0

and bump dependent ports' revisions.

Release notes: https://github.com/oneapi-src/oneTBB/releases/tag/v2021.10.0

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

biology/salmon: Transcript-level quantification of RNA-seq

Salmon is a wicked-fast program to produce a highly-accurate,
transcript-level quantification estimates from RNA-seq data. Salmon
achieves is accuracy and speed via a number of different innovations,
including the use of quasi-mapping (accurate but fast-to-compute
proxies for traditional read alignments), and massively-parallel
stochastic collapsed variational inference. The result is a versatile
tool that fits nicely into many differnt pipelines.