biology/cufflinks2.2.1.89_15

*/*: update boost consumers after boost-1.92

*/*: bump consumers after devel/boost update

biology/cufflinks: fix build with Boost-1.89 (+)

Reported by:	fallout

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

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/boost: bump consumers after library update

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

biology/cufflinks: Unbreak

biology/cufflinks: mark as BROKEN after recent boost upgrade

PR:	246106

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)

devel/automake: update to 1.16.5

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

Remove # $FreeBSD$ from Makefiles.

- 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/cufflinks: fix build on recent current

biology/htslib: Upgrade to 1.10.2

Numerous bug fixes and enhancements since 1.9:
https://github.com/samtools/htslib/tags

Bump PORTREVISION on dependents that don't require additional patching

PR:             248089

biology/cufflinks: fix build on GCC architectures

Using Boost requires modern compiler.

MFH:		2020Q3 (fix build blanket)

biology/cufflinks: Update 2.2.1-83 -> 2.2.1-89

Add the pull request that fixes the boost::thread build failures.

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/cufflinks: Fix build on i386 by removing the hard-coded -m64

Reported by:	fallout

New port: biology/cufflinks: Cufflinks assembles transcripts, estimates their abundance, etc