biology/canu2.3

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/canu: Update to 2.3

Several bug fixes and enhancements
Changes: https://github.com/marbl/canu/releases
Should fix package build on arm64
Change WWW to something portscout can use

Reported by:    pkg-fallout

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

*/*: bump portrevision after java_default=25 update

Included all ports that have USES=java.

PR:	293559

*/*: bump portrevision after java_default=21 update

PR:	272855

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

devel/boost: bump consumers after Boost-1.87 update

Sponsored by:	Future Crew, LLC

Mk/**java.mk: Convert bsd.java.mk to USES

The following features have been added or changed:
- Instead of USE_JAVA use USES=java. This defaults to
  USES=java:build,run if NO_BUILD is undefined. Else it defaults to
  USES=java:run
- Instead of USE_ANT=yes use USES=java:ant which also implies
  USES=java:build
- Instead of JAVA_BUILD=yes use USES=java:build. Does not imply run or
  extract
- Instead of JAVA_EXTRACT=yes use USES=java:extract does not imply
  build or run
- Instead of JAVA_RUN=yes use USES=java:run does not imply extract or
  build
- Instead of USE_JAVA=<version> use USES=java and JAVA_VERSION=<version>

Approved by: mat (portmgr), glewis
Differential Revision:  https://reviews.freebsd.org/D48201

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

biology/canu: Fix build with llvm16

- Pet portclippy

Approved by:	portmgr (blanket)
Sponsored by:	The FreeBSD Foundation

biology/canu: Fix build under clang 16

Also add cpu_any.c to theoretically support any 64-bit CPU
Drop unused simde patches

Reported by:    pkg-fallout

*/*: Refactor java/openjdk7 removal

- java/openjdk7* has been removed from the tree since 2022-09-03 however
  the relevant codebases in bsd.java.mk has not been removed and the
  consumers has also not been updated to use the next jdk version. This
  commit updates all relevant consumers to use JAVA_VERSION=8 instead of
  JAVA_VERSION=1.7
- Since the introduction of jdk version 18 it looks like similar with
  jdk version 8(java version string 1.8). This is prone to error as it
  looks similar and is only seperated by a '.'. Remove using
  JAVA_VERSION with dotted fomat of java version string and update all
  consumers to utilize version 8 instead of 1.8.

Approved by:	portmgr (blanket)

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/canu: fix CATEGORIES

biology/canu: Update to 2.2

FreeBSD port: Add support for aarch64 and powerpc64 using simde
Not yet supported upstream

Several upstream bug fixes and minor enhancements since 2.1

Changes: https://github.com/marbl/canu/tags

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

Remove # $FreeBSD$ from Makefiles.

biology/canu: Drop dependency on gcc

Replace compiler:openmp with compiler:c++11-lang and localbase

PR:             port/247753, ports/252379

biology/canu: Upgrade to 2.1

Numerous functional improvements for ease of use and output quality
A few bug fixes

Reported by:    portscout

Mark as BROKEN on powerpc64:

utgcns/libboost/boost/smart_ptr/detail/sp_counted_impl.hpp:81:5: error: 'get_deleter' declared as a 'virtual' field

This may have something to do with compiler:openmp in USES.  However,
it has broken for more than 6 months at this point.

Approved by:	portmgr (tier-2 blanket)

biology/canu: Upgrade to 2.0

Several routine enhancements and bug fixes

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

biology/canu: Upgrade to 1.9

Numerous bug fixes and enhancements

Reported by:    portscout

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

- Update WWW

Approved by:	portmgr blanket

biology/canu: Fix build on powerpc64 and aarch64

Should also work on powerpc and arm*, but unable to test

PR:             237105
Reported by:    pkubaj

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

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

devel/boost-*: update to 1.69.0

Changes:	http://www.boost.org/users/history/version_1_69_0.html
PR:		232525
Exp-run by:	antoine
Differential Revision:	https://reviews.freebsd.org/D17645

biology/canu: Upgrade to 1.8, add experimental SLURM integration

Solves build issue with gcc8.

PR:             232930
Reported by:    gerald
Approved by:    jrm (mentor, implicit)

devel/boost-*: update to 1.68.0

- Switch to C++14 for libboost_system to support C++14 consumers

Changes:	http://www.boost.org/users/history/version_1_68_0.html
PR:		229569
Exp-run by:	antoine
Differential Revision:	https://reviews.freebsd.org/D16165

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

Mark as broken on aarch64, and, where appropriate, armvX.

While here, pet portlint.

Approved by:	portmgr (tier-2 blanket)

biology/canu: Upgrade to 1.7 release

Approved by:    jrm (mentor)
Differential Revision:  https://reviews.freebsd.org/D15201

devel/boost-*: update to 1.67.0

Changes:	http://www.boost.org/users/history/version_1_67_0.html
PR:		227427
Exp-run by:	antoine
Differential Revision:	https://reviews.freebsd.org/D15030

Bump PORTREVISIONs of all users of math/mpc that we just updated to version 1.1.0 (via revision 464079).

devel/boost-*: update to 1.66.0

Changes:	http://www.boost.org/users/history/version_1_66_0.html
PR:		223922
Exp-run by:	antoine
Differential Revision:	https://reviews.freebsd.org/D13279

biology/canu: Replace += with = for depends

Approved by:    jrm
Differential Revision:  https://reviews.freebsd.org/D13574

[new port] biology/canu: Single molecule sequence assembler

Approved by: jrm (mentor) or wen (mentor)
Differential Revision:  https://reviews.freebsd.org/D13574