07:34 Fernando Apesteguía (fernape)  Author: Älven

biology/bwa: update 0.7.18 => 0.7.19

ChangeLog:
https://github.com/lh3/bwa/blob/master/NEWS.md#release-0719-22-march-2025

Notable changes:

 * Bugfix: internal @HD lines. The bug was introduced in 0.7.18.
 * Merged #414, #391, #346, #312, #311, #308, #291, #288, #286 and #212

PR:		285620
Reported by:	alster@vinterdalen.se (maintainer)

    b66379c

16:29 Zsolt Udvari (uzsolt)  Author: Älven

biology/bwa: small improvements

Add supplementary WWWs.
Remove unneeded USES=tar:bzip2. Upstream uses common tar.gz archives.

PR:		283873
Approved by:	submitter is maintainer

    b4d1145

13:36 Jason W. Bacon (jwb) 

bwa: New maintainer

    4822295

13:31 Jason W. Bacon (jwb) 

biology/bwa: Update to 0.7.18

Official support for aarch64 (we already had this patched in)
A few minor enhancements and fixes
Changes: https://github.com/lh3/bwa/releases

PR:             282923
Reported by:    alster@vinterdalen.se

    f488a27

08:16 Baptiste Daroussin (bapt) 

MAN?PREFIX: eleminate its usage  and move man to share/man

    1b819e4

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

17:34 Piotr Kubaj (pkubaj) 

biology/bwa: don't use GCC on powerpc64le

Now that the port uses simde, it builds fine without gcc's translation.

    f75ac0c

14:56 Jason W. Bacon (jwb) 

biology/bwa: Unbreak on most non-x86 platforms using simde

    c74d976

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

15:01 pkubaj 

biology/bwa: fix build on powerpc64le

Use GCC's SSE->Altivec translation:
In file included from ksw.c:29:
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:50:12: error: invalid conversion
between vector type '__m64' (vector of 1 'long long' value) and integer type
'int' of different size
    return (__m64)__builtin_ia32_vec_init_v2si(__i, 0);

 

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)

 

11:17 tcberner 

biology/bwa: fix build on recent current

Obtained
from:	https://github.com/lh3/bwa/commit/2a1ae7b6f34a96ea25be007ac9d91e57e9d32284

 

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

 

06:13 linimon 

For ports that are marked BROKEN on armv6, and also fail to build on
armv7, mark them so.

This is part two of a multipart commit to bring armv7 ports to parity
with armv6.

Approved by:	portmgr (tier-2 blanket)
Obtained from:	lonesome.com -exp run

 

15:21 jwb 

biology/bwa: Upgrade to 0.7.17

Approved by:    jrm (mentor)
Differential Revision:  https://reviews.freebsd.org/D13283

 

20:02 linimon 

Mark some ports failing on armv6, for errors classified as "???".

While here, pet portlint.

Approved by:	portmgr (tier-2 blanket)

 

03:35 linimon 

Mark some ports failing on power64.  In cases where the error message
was a stub, provide a real one.

While here, pet portlint.

Approved by:	portmgr (tier-2 blanket)

 

03:40 linimon 

Mark various ports broken on aarch64 and armv6.

Approved by:	portmgr (tier-2 blanket)

 

09:07 linimon 

Attempt to fix build on non-x86 archs.

Approved by:	portmgr (tier-2 blanket)

 

16:07 swills 

mark some of the ports that don't build on powerpc64 for me

 

08:48 miwi 

- Update maintainer mail address
- Update/Remove MASTER_SITE

PR:		204755
Submitted by:	 jwbacon@tds.net (maintainer)
Approved by:	mat (mentor)
Differential Revision:	D4493

 

18:39 rm 

BWA is a program for aligning sequencing reads against a large reference
genome (e.g. human genome). It has two major components, one for read shorter
than 150bp and the other for longer reads.

WWW: http://sourceforge.net/projects/bio-bwa/

PR:		203158
Submitted by:	Jason Bacon <jwbacon@tds.net>