12:37 Muhammad Moinur Rahman (bofh) 

biology/htslib: Moved man to share/man

Approved by:    portmgr (blanket)

    2eb9c98

21:55 Robert Clausecker (fuz) 

biology/htslib: fix build on armv7

This project includes some SIMD-enhanced functions for ARM NEON.
Unfortunately the code uses a bunch of intrinsics only available on
aarch64.  Disable the use of NEON on armv6 and armv7 to fix the build
on these platforms.

See also:	https://github.com/samtools/htslib/issues/1603
Approved by:	portmgr (build fix blanket)

    bba4910

23:23 Jason W. Bacon (jwb) 

biology/htslib: Update to 1.17

Numerous enhancements and fixes

Changes:    https://github.com/samtools/htslib/releases

Reported by:    portscout

    5ce4151

23:16 Jason W. Bacon (jwb) 

biology/htslib: Update to 1.16

Numerous minor enhancements and bug fixes

Changes: https://github.com/samtools/htslib/releases

    2d9e290

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

14:20 Tobias C. Berner (tcberner) 

biology: remove 'Created by' lines

A big Thank You to the original contributors of these ports:

  *  Aaron Dalton <aaron@FreeBSD.org>
  *  Akinori MUSHA aka knu <knu@idaemons.org>
  *  Andrey Zakhvatov
  *  Bob Zimmermann <rpz@cse.wustl.edu>
  *  Camson Huynh <chuynh@biolateral.com.au>
  *  Dan Siercks <dsiercks@uwm.edu>
  *  Fernan Aguero <fernan@iib.unsam.edu.ar>
  *  Hannes Hauswedell <h2+fbsdports@fsfe.org>
  *  J. Bacon <jwb@FreeBSD.org>
  *  Jason Bacon <jwb@FreeBSD.org>
  *  Jeremy <karlj000@unbc.ca>
  *  Johann Visagie <johann@egenetics.com>
  *  Johann Visagie <wjv@FreeBSD.org>
  *  Mauricio Herrera Cuadra <mauricio@arareko.net>
  *  Motomichi Matsuzaki <mzaki@biol.s.u-tokyo.ac.jp>
  *  Motomichi Matsuzaki <mzaki@e-mail.ne.jp>
  *  Motomichi Matsuzaki <mzaki@m.u-tokyo.ac.jp>
  *  Motomichi Matsuzaki <mzaki@niid.go.jp>
  *  Po-Chuan Hsieh <sunpoet@FreeBSD.org>
  *  Razi Khaja <razi@genet.sickkids.on.ca>
  *  Reed A. Cartwright <cartwright@asu.edu>
  *  Ryo MIYAMOTO
  *  Ryo MIYAMOTO <rmiya@cc.hirosaki-u.ac.jp>
  *  Sangwoo Shim <sangwoos@gmail.com>
  *  Sunpoet Po-Chuan Hsieh <sunpoet@FreeBSD.org>
  *  Tassilo Philipp <tphilipp@potion-studios.com>
  *  Tony Maher
  *  Tony Maher <tonym@biolateral.com.au>
  *  Wen Heping <wen@FreeBSD.org>
  *  Wen Heping <wenheping@gmail.com>
  *  Yonatan <onatan@gmail.com>
  *  Yuri Victorovich <yuri@rawbw.com>
  *  ballen
  *  barnhart@genetics.wustl.edu
  *  camson@bilateral.com.au
  *  chuynh@biolateral.com.au
  *  dbader@eece.unm.edu
  *  frankch@waru.life.nthu.edu.tw
  *  h2
  *  lentferj
  *  maho@FreeBSD.org
  *  mzaki@biol.s.u-tokyo.ac.jp
  *  tonym
  *  wen@FreeBSD.org

With hat:	portmgr

    37526bb

15:04 Jason W. Bacon (jwb) 

biology/htslib: Update to 1.15

A few minor bug fixes and enhancements
No API changes affecting existing dependents

Reported by:    portscout

    b3b13f5

17:56 Jason W. Bacon (jwb) 

biology/htslib: Update to 1.14

Several minor enhancements and fixes

Changes: https://github.com/samtools/htslib/tags

    134a1c9

21:18 Bernhard Froehlich (decke) 

biology/htslib: Add CPE information

Approved by:	portmgr (blanket)

    8522c83

13:16 Jason W. Bacon (jwb) 

htslib: Update to 1.13

Numerous enhancements and bug fixes

Changes:        https://github.com/samtools/htslib/releases/tag/1.13

    5fa0712

14:31 Mathieu Arnold (mat) 

Remove # $FreeBSD$ from Makefiles.

    305f148

17:14 jwb 

biology/htslib: Update to 1.12
biology/samtools: Update to 1.12
biology/bcftools: Update to 1.12

Numerous enhancements, performance improvements, and bug fixes since 1.11

Build-tested all other htslib dependents, no revbumps should be needed

Reported by:    portscout

 

20:30 jwb 

biology/htslib: Upgrade to 1.11.0

Numerous bug fixes, new features and performance improvements since 1.10
https://github.com/samtools/htslib/releases/tag/1.11

Reported by:    portscout

 

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

 

19:27 fernape 

biology/htslib: update to 1.9

PR:	230170
Submitted by:	ndowens.fbsd@yandex.com
Approved by:	tcberner (mentor)
Differential Revision:	https://reviews.freebsd.org/D16568

 

18:11 yuri 

biology/htslib: Update 1.6 -> 1.8

Port changes:
* Use DISTVERSION
* Add USES=localbase instead of CPPFLAGS/LDFLAGS
* Move USES=ssl to CURL_USES=ssl
* Update WWW

PR:		228908
Approved by:	maintainer's timeout (cartwright@asu.edu; 35 days)

 

10:19 pizzamig 

biology/htslib biology/bcftools biology/samtools: Update to 1.6

PR:		223094
Submitted by:	mzaki@niid.go.jp
Approved by:	cartwright@asu.edu (maintainer)
Approved by:	olivier (mentor)
Differential Revision:	https://reviews.freebsd.org/D12768

 

15:21 mat 

Use USES=pathfix where applicable.

PR:		213195
Submitted by:	mat
Exp-run by:	antoine
Sponsored by:	Absolight
Differential Revision:	https://reviews.freebsd.org/D8093

 

20:28 pi 

biology/{htslib|samtools|bcftools}: 1.3 -> 1.3.1

Changes:
  https://sourceforge.net/p/samtools/mailman/message/35033807/

PR:		209653
Submitted by:	cartwright@asu.edu (maintainer)

 

13:29 mat 

Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c.

With hat:	portmgr
Sponsored by:	Absolight

 

01:31 junovitch 

biology/{bcftools,htslib,samtools}: update 1.2.x -> 1.3

- Update ports to 1.3 and set BUILD_DEPENDS of dependent ports to require
  version 1.3 of htslib.
- Add CURL option to htslib
- Add TEST_TARGET with perl and bash dependencies for testing
- Tidy up spacing and pkg-message's

PR:		205524
PR:		205525
PR:		205526
Submitted by:	cartwright@asu.edu (maintainer)

 

15:16 mat 

Update ports in the [bcd]* categories to not use GH_COMMIT.

With minor cleanups to make things simpler.

With hat:	portmgr
Sponsored by:	Absolight

 

12:45 robak 

biology/htslib: update 1.1 -> 1.2.1

PR:		198291
Submitted by:	Reed Cartwright <cartwright@asu.edu>

 

22:35 pawel 

HTSlib is an implementation of a unified C library for accessing common file
formats, such as SAM, CRAM, VCF, and BCF, used for high-throughput sequencing
data. It is the core library used by samtools and bcftools.

WWW: http://www.htslib.org/

PR:		195591
Submitted by:	Reed A. Cartwright <cartwright@asu.edu>