16:42 Jason W. Bacon (jwb) 

biology/freebayes: Drop redundant tabixpp dep

tabixpp is included as a git submodule

    b0cafd4

01:22 Jason W. Bacon (jwb) 

biology/freebayes: Bump PORTREVISION for biology/htslib update

    fea5f77

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

20:23 Jason W. Bacon (jwb) 

biology/freebayes: Update to 1.3.6

Minor dependency updates, but mostly build system improvements
Changes:        https://github.com/freebayes/freebayes/tags

Reported by:    portscout

    09167ae

13:26 Piotr Kubaj (pkubaj) 

biology/freebayes: enable on riscv64

    b473e20

01:14 Piotr Kubaj (pkubaj) 

biology/freebayes: builds fine on armv7

    0e5026a

20:49 Jason W. Bacon (jwb) 

biology/freebayes: Update to 1.3.5

Fixes build on powerpc64 and aarch64, possibly others.

Changes:        https://github.com/freebayes/freebayes/tags

PR:             259627
Reported by:    pkubaj

    dc64b13

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

01:46 linimon 

For ports on riscv64 that fail the same (or similar ways) to aarch64, mark
them BROKEN.

While here, pet portlint (Makevar order).

Approved by:	portmgr (tier-2 blanket)

 

18:14 se 

Fix build with -fno-common

 

20:46 gerald 

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

 

01:35 gerald 

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

 

09:28 linimon 

Upgrade these ports to USES=compiler:c++11-lang to fix build on gcc-based
archs such as powerpc64.

Tested for no effect on amd64.

While here, pet portlint.

Approved by:	portgmr (tier-2 blanket)

 

23:52 linimon 

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

While here, pet portlint.

Approved by:	portmgr (tier-2 blanket)

 

00:07 jwb 

biology/freebayes: Bayesian haplotype-based polymorphism discovery and
genotyping

Approved by:    jrm (mentor)
Differential Revision:  https://reviews.freebsd.org/D15116