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

With hat:	office
Sponsored by:	Future Crew, LLC

biology/iqtree: Update to 2.3.6

PR:		280839
Sponsored by:	The FreeBSD Foundation

biology/iqtree: Update to 2.3.5

Release Notes:	https://github.com/iqtree/iqtree2/releases/tag/v2.3.5
Sponsored by:	The FreeBSD Foundation

biology/iqtree: Update to 2.3.4

Release notes:	https://github.com/iqtree/iqtree2/releases/tag/v.2.3.4
Sponsored by:	The FreeBSD Foundation

biology/iqtree: Update to 2.3.2

Changes:	https://github.com/iqtree/iqtree2/releases/tag/v2.3.2
                https://github.com/iqtree/iqtree2/releases/tag/v2.3.1
Sponsored by:	The FreeBSD Foundation

biology/iqtree: Update to 2.2.2.7

Changes:	https://github.com/iqtree/iqtree2/releases/tag/v2.2.2.7
Sponsored by:	The FreeBSD Foundation

*: 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

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

PR:	246106

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

Remove # $FreeBSD$ from Makefiles.

biology/iqtree: Remove USES=compiler:openmp, fix amd64 clang++ build

- USES=compiler:openmp still forces building with GCC.  This is no longer
  necessary on tier 1 platforms, which have openmp in base.

- Mark broken on i386, because base clang doesn't have 64 bit atomic
  functions for i386 (see bug 230888).

PR:		247753, 252379
Submitted by:	cmt (based on)

- Upgrade math/eigen3 to 3.3.8;

- Add some dependencies which might be detected by Find_Package but not
registered;

- Bump PORTREVISION of consumers.

PR:		250833
Submitted by:	/me
Approved by:	tcberner@ (KDE / maintainer) + exp-run

biology/iqtree: Update to version 2.0.6

Upstream changes: https://github.com/Cibiv/IQ-TREE/releases/tag/v2.0.6

biology/iqtree: Update to version 2.0.5

Upstream changes: https://github.com/Cibiv/IQ-TREE/releases/tag/v2.0.5

While here, incorporate portfmt suggestions.

biology/iqtree: Update to version 2.0.4

biology/iqtree: Update to version 1.6.12

Upstream changes: https://github.com/Cibiv/IQ-TREE/releases/tag/v1.6.12

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/iqtree: Update to version 1.6.11

Upstream changes: https://github.com/Cibiv/IQ-TREE/releases/tag/v1.6.11

biology/iqtree: Update to version 1.6.10

Upstream changes: https://github.com/Cibiv/IQ-TREE/releases/tag/v1.6.10

biology/iqtree: switch to outsource cmake build

Update math/eigen3 to 3.3.7

- http://eigen.tuxfamily.org/index.php?title=ChangeLog#Eigen_3.3.6
- http://eigen.tuxfamily.org/index.php?title=ChangeLog#Eigen_3.3.7

Change cmake default behaviour to outsource.

Ports that build out of source now simply can use "USES=cmake"
instead of "USES=cmake:outsource". Ports that fail to build
out of source now need to specify "USES=cmake:insource".

I tried to only set insource where explictely needed.

PR:		232038
Exp-run by:	antoine

biology/iqtree: Update to version 1.6.9

Upstream changes: https://github.com/Cibiv/IQ-TREE/releases/tag/v1.6.9

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

biology/iqtree: Update to version 1.6.8

Upstream release notes:
https://github.com/Cibiv/IQ-TREE/releases/tag/v1.6.8

biology/iqtree: Update to version 1.6.7.1

Upstream changes: https://github.com/Cibiv/IQ-TREE/releases/tag/v1.6.7.1

biology/iqtree: Update to version 1.6.7

Upstream changes: https://github.com/Cibiv/IQ-TREE/releases/tag/v1.6.7

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

biology/iqtree: Update to version 1.6.6

Upstream changes: https://github.com/Cibiv/IQ-TREE/releases/tag/v1.6.6

Mark ports broken on powerpc64, categories a-c.

While here, pet portlint and do some other cleanup.

Approved by:	portmgr (tier-2 blanket)

biology/iqtree: Update to version 1.6.5

Upstream changes: https://github.com/Cibiv/IQ-TREE/releases/tag/v1.6.5

biology/iqtree: Update to version 1.6.4

Upstream changes: https://github.com/Cibiv/IQ-TREE/releases/tag/v1.6.4

biology/iqtree: Update to version 1.6.3

Upstream changes: https://github.com/Cibiv/IQ-TREE/releases/tag/v1.6.3

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

biology/iqtree: Update to version 1.6.2

Upstream changes: http://www.iqtree.org/release/v1.6.2

New USES=eigen

  Usage:
    USES=eigen:<version>[,<type>]

    version: 2 or 3 (required)
    type:    build (default), run

  For example:
    USES=eigen:2,build,run
  will add a BUILD- and RUN_DEPENDS on math/eigen2, and
    USES=eigen:3
  will add a BUILD_DEPENDS on math/eigen3.

* Convert the existing ports to use it
  - biology/iqtree: remove run time dependency (seemed not to be needed)
  - graphics/movit: remove run time dependency (seemed not to be needed)
  - science/avogadro: add run time dependeny (installed cmake file requires it
to be present)

Reviewed by:	rakuco, mat
Differential Revision:	https://reviews.freebsd.org/D13702

biology/iqtree: Fix distinfo after upstream re-released v1.6.1

biology/iqtree: Update to version 1.6.1

Upstream changes: https://github.com/Cibiv/IQ-TREE/releases

Mark several ports newly broken on arm.

While here, pet portlint.

Approved by:	portmgr (tier-2 blanket)

Fix USE_GITHUB usage.

Sponsored by:	Absolight

biology/iqtree: Add EXAMPLES option and fix mess with installation of
example files in first commit

New port, biology/iqtree: Efficient phylogenomic software

WWW: http://www.iqtree.org/