12:42 Jason W. Bacon (jwb) 

biology/vcflib: Update to 1.0.10

A few bug fixes and code cleanup
Changes: https://github.com/vcflib/vcflib/releases

Reported by:    portscout

    86c8816

20:35 Nuno Teixeira (eduardo) 

biology/vcflib: Move man pages to share/man

Approved by:	portmgr (blanket)

    44f5f66

05:37 Jan Beich (jbeich)  Author: Nathan Fisher

lang/zig: update to 0.11.0

Changes:	https://ziglang.org/download/0.11.0/release-notes.html
PR:		273124
Approved by:	dch (maintainer)

    8c1e3e6

22:59 Robert Clausecker (fuz) 

biology/vcflib: not for armv6/7

Requires OpenMP which is not supported on armv6/armv7.

Approved by:	portmgr (build fix blanket)
MFH:		2023Q3

    931dd7a

15:35 Jason W. Bacon (jwb) 

biology/vcflib: Update to 1.0.7

Fixes regression in 1.0.6

Made Zig language support a default off option
Zig is experimental and problematic

Reported by:    portscout

    5fee60f

16:25 Jason W. Bacon (jwb) 

biology/vcflib: Unbreak build on aarch64, probably others

Patch out hard-coded -march=native, not supported by clang aarch64

    0d9ff1b

22:05 Jason W. Bacon (jwb) 

biology/vcflib: Update to 1.0.6

A few minor upstream fixes
Unbundle WFA2-lib, which may be useful outside vcflib
Update some submodules to latest commit (no recent releases available)

    4512fe6

14:14 Jason W. Bacon (jwb) 

biology/vcflib: Patch in time.h for struct timespec

Forgot to add patch file to repo during upgrade
Needed on 12.3-RELEASE

    62e0649

23:51 Jan Beich (jbeich) 

lang/zig: rebuild consumers after 91552559ae79

Propagate standard library and miscompilation fixes into binary packages.

    ded326a

17:13 Jason W. Bacon (jwb) 

biology/vcflib: Update to 1.0.5

Numerous new features and enhancements

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

Reported by:    portscout

    459cb89

01:29 Jason W. Bacon (jwb) 

biology/vcflib: Bump PORTREVISION for biology/htslib update

    edf777d

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

14:53 Stefan Eßer (se) 

Fix CONFLICTS_INSTALL in benchmarks and biology

Approved by:	portmgr (implicit)

    b521142

18:36 Stefan Eßer (se) 

Update CONFLICTS definitions in categories a* to c*

Update the CONFLICTS definitions of ports in the following categories:

- accessibility
- archivers
- audio
- benchmarks
- biology
- cad
- chinese
- comms
- converters

An attempt has been made to use generic conflicts patterns that do not
have to be updated whenever a new version of a conflicting port is
added to the ports system.

There is a misunderstanding that the port being built/installed has to
be omitted from the conflicts pattern. This is not true - the port
being built is implicitly non-conflicting due to logic in bsd.port.mk.

Approved by:	portmgr (implicit)

    bdd2d4a

00:09 Jason W. Bacon (jwb) 

biology/vcflib: Update to 1.0.3

Several new commands
A few bug fixes and enhancements

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

Reported by:    portscout

    8859320

21:49 Piotr Kubaj (pkubaj) 

biology/vcflib: unbreak on riscv64

    ed59e0d

14:23 Jason W. Bacon (jwb) 

biology/vcflib: Update to 1.0.2

Switch to github submodules for most deps rather than patch build system
Fixes build on powerpc64 and aarch64, possibly others

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

PR:             259622
Reported by:    pkubaj

    e02229c

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

16:39 pkubaj 

biology/vcflib: fix build on powerpc64le

Use GCC for its SSE -> AltiVec translation:
In file included from src/ssw.cpp:38:
In file included from /usr/lib/clang/11.0.1/include/emmintrin.h:13:
In file included from /usr/lib/clang/11.0.1/include/xmmintrin.h:13:
/usr/lib/clang/11.0.1/include/mmintrin.h:33:5: error: use of undeclared
identifier '__builtin_ia32_emms'; did you mean '__builtin_isless'?
    __builtin_ia32_emms();

 

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)

 

17:40 jwb 

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

 

00:03 linimon 

Mark these ports as broken on aarch64.

Approved by:	portmgr (tier-2 blanket)

 

03:11 jwb 

biology/vcflib: C++ library and CLI tools for parsing and manipulating VCF files

Approved by:    jrm (mentor)
Differential Revision:  https://reviews.freebsd.org/D15109