20:35 Nuno Teixeira (eduardo) 

biology/vcftools: Move man pages to share/man

Approved by:	portmgr (blanket)

    ebba67d

01:29 Jason W. Bacon (jwb) 

biology/vcftools: Unbreak build with clang 16

Add -std=c++14

Reported by:    pkg-fallout

    76d07b4

21:10 Stefan Eßer (se) 

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)

    b7f0544

20:28 Bernhard Froehlich (decke) 

biology/vcftools: Add CPE information

Approved by:	portmgr (blanket)

    311f6fb

08:09 Mathieu Arnold (mat) 

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

    cf118cc

14:31 Mathieu Arnold (mat) 

Remove # $FreeBSD$ from Makefiles.

    305f148

01:29 jwb 

biology/vcftools: Update to 0.1.16, a security release

Approved by:    jrm (mentor)
Differential Revision:  https://reviews.freebsd.org/D16587

 

01:07 jwb 

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

 

23:05 jwb 

biology/vcftools: Upgrade to latest release 0.1.15

Approved by:    jrm (mentor)
Differential Revision:  https://reviews.freebsd.org/D13276

 

17:06 jbeich 

Assume "pkg-config zlib" works after 9.x reached EOL

Many ports passed ZLIB_CFLAGS="-I/usr/include" ZLIB_LIBS="-L/usr/lib -lz"
which is unsafe at least with lang/gcc* that override some system headers
and have newer libgcc_s.so that our old version in base may not be
forward-compatible with.

 

10:09 mat 

Fixup USE_GITHUB usage.

It already sets DISTNAME to a very nice unique name, do not set it
yourself.

Sponsored by:	Absolight

 

17:07 rakuco 

New port: biology/vcftools.

A set of tools written in Perl and C++ for working with VCF files, such as
those generated by the 1000 Genomes Project.

WWW: https://github.com/vcftools/vcftools

PR:		206926
Submitted by:	Jason Bacon <bacon4000@gmail.com>