biology/gmap2025.07.31_1

biology/gmap: enable on remaining architectures

Seems to work fine.
While at it, hook up test suite.

Approved by:	portmgr (build fix blanket)
MFH:		2026Q4

biology/gmap: enable on aarch64 and powerpc64

The aarch64 failure noted in the FIXME was the same broken __builtin_clz
probe that compiled x86 asm("bsr") on powerpc64le, so the configure
cache seeds from the previous commit fix it. powerpc64 builds as well;
the source has explicit big-endian support.

biology/gmap: fix build on powerpc64le

configure probes __builtin_clz and friends with AC_CHECK_DECL, which
always fails with clang, and its asm("bsr") probe is dead code at -O2,
so HAVE_ASM_BSR is defined on every architecture and x86 inline asm is
compiled on powerpc64le. Seed the declaration cache so the builtins are
detected and used.

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/gmap: Update to 2025.07.31

Numerous fixes and enhancements since 2020.09.12
Changes: http://research-pub.gene.com/gmap/

Reported by:    Repology

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: remove 'Created by' lines

A big Thank You to the original contributors of these ports:

  *  Aaron Dalton <aaron@FreeBSD.org>
  *  Akinori MUSHA aka knu <knu@idaemons.org>
  *  Andrey Zakhvatov
  *  Bob Zimmermann <rpz@cse.wustl.edu>
  *  Camson Huynh <chuynh@biolateral.com.au>
  *  Dan Siercks <dsiercks@uwm.edu>
  *  Fernan Aguero <fernan@iib.unsam.edu.ar>
  *  Hannes Hauswedell <h2+fbsdports@fsfe.org>
  *  J. Bacon <jwb@FreeBSD.org>
  *  Jason Bacon <jwb@FreeBSD.org>
  *  Jeremy <karlj000@unbc.ca>
  *  Johann Visagie <johann@egenetics.com>
  *  Johann Visagie <wjv@FreeBSD.org>
  *  Mauricio Herrera Cuadra <mauricio@arareko.net>
  *  Motomichi Matsuzaki <mzaki@biol.s.u-tokyo.ac.jp>
  *  Motomichi Matsuzaki <mzaki@e-mail.ne.jp>
  *  Motomichi Matsuzaki <mzaki@m.u-tokyo.ac.jp>
  *  Motomichi Matsuzaki <mzaki@niid.go.jp>
  *  Po-Chuan Hsieh <sunpoet@FreeBSD.org>
  *  Razi Khaja <razi@genet.sickkids.on.ca>
  *  Reed A. Cartwright <cartwright@asu.edu>
  *  Ryo MIYAMOTO
  *  Ryo MIYAMOTO <rmiya@cc.hirosaki-u.ac.jp>
  *  Sangwoo Shim <sangwoos@gmail.com>
  *  Sunpoet Po-Chuan Hsieh <sunpoet@FreeBSD.org>
  *  Tassilo Philipp <tphilipp@potion-studios.com>
  *  Tony Maher
  *  Tony Maher <tonym@biolateral.com.au>
  *  Wen Heping <wen@FreeBSD.org>
  *  Wen Heping <wenheping@gmail.com>
  *  Yonatan <onatan@gmail.com>
  *  Yuri Victorovich <yuri@rawbw.com>
  *  ballen
  *  barnhart@genetics.wustl.edu
  *  camson@bilateral.com.au
  *  chuynh@biolateral.com.au
  *  dbader@eece.unm.edu
  *  frankch@waru.life.nthu.edu.tw
  *  h2
  *  lentferj
  *  maho@FreeBSD.org
  *  mzaki@biol.s.u-tokyo.ac.jp
  *  tonym
  *  wen@FreeBSD.org

With hat:	portmgr

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)

Fix CONFLICTS entries of multiple ports

There have been lots of missing CONFLICTS_INSTALL entries, either
because conflicting ports were added without updating existing ports,
due to name changes of generated packages, due to mis-understanding
the format and semantics of the conflicts entries, or just due to
typoes in package names.

This patch is the result of a comparison of all files contained in
the official packages with each other. This comparison was based on
packages built with default options and may therefore have missed
further conflicts with optionally installed files.

Where possible, version numbers in conflicts entries have been
generalized, some times taking advantage of the fact that a port
cannot conflict with itself (due to logic in bsd.port.mk that
supresses the pattern match result in that case).

A few ports that set the conflicts variables depending on complex
conditions (e.g. port options), have been left unmodified, despite
probably containing outdated package names.

These changes should only affect the installation of locally built
ports, not the package building with poudriere. They should give an
early indication of the install conflict in cases where currently
the pkg command aborts an installation when it detects that an
existing file would be overwritten,

Approved by:	portmgr (implicit)

Style: improve ONLY_FOR_ARCHS_REASON (grammar, markup, etc.)

ONLY_FOR_ARCHS_REASON is used as part of the sentence and thus should
start with lower-case letter and not end with a period which is added
by the framework, similar to other knobs like BROKEN, IGNORE, et al.

While here, remove needless quoting, add missing Oxford comma, expand
contractions and jargonisms, use correct spelling for proper names.

Remove # $FreeBSD$ from Makefiles.

biology/gmap: enable on powerpc64le

Doesn't build on powerpc64 due to missing big-endian code variants, but builds on powerpc64le.

biology/gmap: Upgrade to 2020.09.12

First upgrade in 5 years, so numerous improvements
Unsure if powerpc is still supported upstream
Code mentions power8, but does not build on my Mac G5

Convert to UCL & cleanup pkg-message (categories a-c)

Enable workaround for building on powerpc64.

Autoconf reports that HAVE_ASM_BSR is true (1).  However, it's a false
positive.

I do not have enough knowledge of autoconf to fix this problem correctly,
so fix src/config.h in post-configure.  Patches welcome.

A proper fix will most likely also fix the build on other tier-2 archs,
but I have not taken the time to test that yet.

Approved by:	portmgr (tier-2 blanket)

Multiple ports: Change maintainer email bacon4000@gmail.com to jwb@FreeBSD.org Remove Created by comments for same user

Approved by: jrm (mentor)
Differential Revision:  https://reviews.freebsd.org/D14128

Try to bring some consistency to ports that have x86-specific pieces.

- in general, if we think that the code is not architecture-specific,
   and instead just enables x86 assembler by default, those should
   use BROKEN rather than IGNORE.  This will allow them to be attempted
   with TRYBROKEN.
 - spell i386 as x86.
 - spell asm as assembler.
 - pet portlint.

These changes should have no effect on tier-1 builds.

Approved by:	portmgr (tier-2 blanket)

For ports that are marked BROKEN on armv6, and also fail to build on armv7, mark them so.

This is part two of a multipart commit to bring armv7 ports to parity
with armv6.

Approved by:	portmgr (tier-2 blanket)
Obtained from:	lonesome.com -exp run

Mark some ports failing on power64.  In cases where the error message was a stub, provide a real one.

While here, pet portlint.

Approved by:	portmgr (tier-2 blanket)

Mark various ports as broken on armv6: invokes x86 asm.

Approved by:	portmgr (tier-2 blanket)

The 64-bit arm arch is actually spelled 'aarch64', not 'arm64'.

Mark broken on all tier-2 archs.

Approved by:	portmgr (tier-2 blanket)

mark some of the ports that don't build on powerpc64 for me

- Update maintainer mail address - Update/Remove MASTER_SITE

PR:		204755
Submitted by:	 jwbacon@tds.net (maintainer)
Approved by:	mat (mentor)
Differential Revision:	D4493

- Update to 2015.09.21 - Add License - Add SIMD option disabled by default to avoid creating official   packags with CPU specific optimizations - Add pkg-message explaining how to get an optimized binary - Assign maintainership to submitter

PR:		203334
Submitted by:	jwbacon at tds.net
Approved by:	Maintainer timeout

Fix MASTER_SITES

Submitted by:	tijl@

Support stage Convert USE_GMAKE to USES=gmake Add dependency on perl which the port need and was getting by chance bump portrevision, dependencies has changed

Add NO_STAGE all over the place in preparation for the staging support (cat: biology)

- fix fetch: wget is not required for fetching

Reported by:    QAT

Update CONFIGURE_ARGS for how we pass CONFIGURE_TARGET to configure script. Specifically, newer autoconf (> 2.13) has different semantic of the configure target. In short, one should use --build=CONFIGURE_TARGET instead of CONFIGURE_TARGET directly. Otherwise, you will get a warning and the old semantic may be removed in later autoconf releases.

To workaround this issue, many ports hack the CONFIGURE_TARGET variable
so that it contains the ``--build='' prefix.

To solve this issue, under the fact that some ports still have
configure script generated by the old autoconf, we use runtime detection
in the do-configure target so that the proper argument can be used.

Changes to Mk/*:
 - Add runtime detection magic in bsd.port.mk
 - Remove CONFIGURE_TARGET hack in various bsd.*.mk
 - USE_GNOME=gnometarget is now an no-op

Changes to individual ports, other than removing the CONFIGURE_TARGET hack:

= pkg-plist changed (due to the ugly CONFIGURE_TARGET prefix in * executables)
  - comms/gnuradio
  - science/abinit
  - science/elmer-fem
  - science/elmer-matc
  - science/elmer-meshgen2d
  - science/elmerfront
  - science/elmerpost

= use x86_64 as ARCH
  - devel/g-wrap

= other changes
  - print/magicfilter
    GNU_CONFIGURE -> HAS_CONFIGURE since it's not generated by autoconf

Total # of ports modified:  1,027
Total # of ports affected: ~7,000 (set GNU_CONFIGURE to yes)

PR:		126524 (obsoletes 52917)
Submitted by:	rafan
Tested on:	two pointyhat 7-amd64 exp runs (by pav)
Approved by:	portmgr (pav)

[patch] cleanup non-supported FreeBSD versions

PR:		ports/111727
Submitted by:	Edwin Groothuis <edwin@mavetju.org>
Approved by:	Bob Zimmermann <rpz@cse.wustl.edu>

Add gmap 2006.04.21, a Genomic Mapping and Alignment Program for mRNA and EST Sequences.

PR:		ports/103651
Submitted by:	Bob Zimmermann <rpz at cse.wustl.edu>