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non port: biology/bcftools/Makefile

Number of commits found: 26

Saturday, 2 Mar 2024
18:38 Nuno Teixeira (eduardo) search for other commits by this committer
biology/bcftools: Move man pages to share/man

Approved by:	portmgr (blanket)
commit hash: 29f179ab379bef7741461a9c745ebc6cc935d466 commit hash: 29f179ab379bef7741461a9c745ebc6cc935d466 commit hash: 29f179ab379bef7741461a9c745ebc6cc935d466 commit hash: 29f179ab379bef7741461a9c745ebc6cc935d466 29f179a
Friday, 24 Feb 2023
23:30 Jason W. Bacon (jwb) search for other commits by this committer
biology/bcftools: Update to 1.17

Numerous enhancements and bug fixes

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

Reported by:    portscout
commit hash: 65b8ab93497d27dee8afc5c3451a5303210595d1 commit hash: 65b8ab93497d27dee8afc5c3451a5303210595d1 commit hash: 65b8ab93497d27dee8afc5c3451a5303210595d1 commit hash: 65b8ab93497d27dee8afc5c3451a5303210595d1 65b8ab9
Thursday, 5 Jan 2023
23:19 Jason W. Bacon (jwb) search for other commits by this committer
biology/bcftools: Update to 1.16

New plugin variant-distance to annotate records with distance to the
nearest variant
Numerous minor enhancements and bug fixes

Changes: https://github.com/samtools/bcftools/releases
commit hash: adfc9433b02c9fbd48a51de471dc4f43a22d240f commit hash: adfc9433b02c9fbd48a51de471dc4f43a22d240f commit hash: adfc9433b02c9fbd48a51de471dc4f43a22d240f commit hash: adfc9433b02c9fbd48a51de471dc4f43a22d240f adfc943
Wednesday, 7 Sep 2022
21:10 Stefan E├čer (se) search for other commits by this committer
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)
commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52 commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52 commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52 commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52 b7f0544
Wednesday, 20 Jul 2022
14:20 Tobias C. Berner (tcberner) search for other commits by this committer
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
commit hash: 37526bbd4e50616d87f70e1c788ae4895d88d671 commit hash: 37526bbd4e50616d87f70e1c788ae4895d88d671 commit hash: 37526bbd4e50616d87f70e1c788ae4895d88d671 commit hash: 37526bbd4e50616d87f70e1c788ae4895d88d671 37526bb
Saturday, 26 Feb 2022
15:04 Jason W. Bacon (jwb) search for other commits by this committer
biology/bcftools: Update to 1.15

Several small enhancements
Changes: https://github.com/samtools/bcftools/releases

Reported by:    portscout
commit hash: 734d2c4df0a562d5be9ef181424ebec5ab7b2222 commit hash: 734d2c4df0a562d5be9ef181424ebec5ab7b2222 commit hash: 734d2c4df0a562d5be9ef181424ebec5ab7b2222 commit hash: 734d2c4df0a562d5be9ef181424ebec5ab7b2222 734d2c4
Wednesday, 12 Jan 2022
19:41 Tobias C. Berner (tcberner) search for other commits by this committer
math/gsl: bump portrevision of consumers after update to 2.7.1

PR:		260201
commit hash: 654acd81409d31495f8b1b11db61e1afbf640981 commit hash: 654acd81409d31495f8b1b11db61e1afbf640981 commit hash: 654acd81409d31495f8b1b11db61e1afbf640981 commit hash: 654acd81409d31495f8b1b11db61e1afbf640981 654acd8
Saturday, 18 Dec 2021
17:56 Jason W. Bacon (jwb) search for other commits by this committer
biology/bcftools: Update to 1.14

A few minor enhancements and bug fixes

Changes: https://github.com/samtools/bcftools/tags
commit hash: 9302b3e21ff4b44c0003d01b51c648a40ac30ac2 commit hash: 9302b3e21ff4b44c0003d01b51c648a40ac30ac2 commit hash: 9302b3e21ff4b44c0003d01b51c648a40ac30ac2 commit hash: 9302b3e21ff4b44c0003d01b51c648a40ac30ac2 9302b3e
Monday, 12 Jul 2021
13:30 Jason W. Bacon (jwb) search for other commits by this committer
biology/bcftools: Update to 1.13

Numerous enhancements and bug fixes

Changes:        https://github.com/samtools/bcftools/releases/tag/1.13
Reported by:    portscout
commit hash: 94c639f5ff163d57758c0631c7280c9f0fd2e86e commit hash: 94c639f5ff163d57758c0631c7280c9f0fd2e86e commit hash: 94c639f5ff163d57758c0631c7280c9f0fd2e86e commit hash: 94c639f5ff163d57758c0631c7280c9f0fd2e86e 94c639f
Wednesday, 16 Jun 2021
19:31 Tobias C. Berner (tcberner) search for other commits by this committer
math/gsl: update to 2.7

From [1]

* What is new in gsl-2.7:
	* fixed doc bug for gsl_histogram_min_bin (lhcsky at 163.com)
	* fixed bug #60335 (spmatrix test failure, J. Lamb)
	* fixed bug #36577
	* clarified documentation on interpolation accelerators (V. Krishnan)
	* fixed bug #45521 (erroneous GSL_ERROR_NULL in ode-initval2, thanks to M.
Sitte)
	* fixed doc bug #59758
	* fixed bug #58202 (rstat median for n=5)
	* added support for native C complex number types in gsl_complex
	   when using a C11 compiler
	* upgraded to autoconf 2.71, automake 1.16.3, libtool 2.4.6
	* updated exponential fitting example for nonlinear least squares
	* added banded LU decomposition and solver (gsl_linalg_LU_band)
	* New functions added to the library:
	      - gsl_matrix_norm1
	      - gsl_spmatrix_norm1
	      - gsl_matrix_complex_conjtrans_memcpy
	      - gsl_linalg_QL: decomp, unpack
	      - gsl_linalg_complex_QR_* (thanks to Christian Krueger)
	      - gsl_vector_sum
	      - gsl_matrix_scale_rows
	      - gsl_matrix_scale_columns
	      - gsl_multilarge_linear_matrix_ptr
	      - gsl_multilarge_linear_rhs_ptr
	      - gsl_spmatrix_dense_add (renamed from gsl_spmatrix_add_to_dense)
	      - gsl_spmatrix_dense_sub
	      - gsl_linalg_cholesky_band: solvem, svxm, scale, scale_apply
	      - gsl_linalg_QR_UD: decomp, lssolve
	      - gsl_linalg_QR_UU: decomp, lssolve, QTvec
	      - gsl_linalg_QR_UZ: decomp
	      - gsl_multifit_linear_lcurvature
	      - gsl_spline2d_eval_extrap
	* bug fix in checking vector lengths in gsl_vector_memcpy (dieggsy@pm.me)
	* made gsl_sf_legendre_array_index() inline and documented
	      - gsl_sf_legendre_nlm()

[1] http://git.savannah.gnu.org/cgit/gsl.git/tree/NEWS

PR:		256423
Exp-run by:	antoine
commit hash: 63e653adaa7493aa98f17f9fbc834c0aed7e096e commit hash: 63e653adaa7493aa98f17f9fbc834c0aed7e096e commit hash: 63e653adaa7493aa98f17f9fbc834c0aed7e096e commit hash: 63e653adaa7493aa98f17f9fbc834c0aed7e096e 63e653a
Tuesday, 6 Apr 2021
14:31 Mathieu Arnold (mat) search for other commits by this committer
Remove # $FreeBSD$ from Makefiles.
commit hash: 305f148f482daf30dcf728039d03d019f88344eb commit hash: 305f148f482daf30dcf728039d03d019f88344eb commit hash: 305f148f482daf30dcf728039d03d019f88344eb commit hash: 305f148f482daf30dcf728039d03d019f88344eb 305f148
Saturday, 20 Mar 2021
17:14 jwb search for other commits by this committer
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
Original commitRevision:568874 
Thursday, 5 Nov 2020
20:34 jwb search for other commits by this committer
biology/bcftools: Upgrade to 1.11

Numerous new features, bug fixes and performance enhancements
https://github.com/samtools/bcftools/releases/tag/1.11

Reported by:    portscout
Original commitRevision:554157 
Monday, 3 Aug 2020
18:16 jwb search for other commits by this committer
biology/bcftools: Upgrade to 1.10.2

Numerous bug fixes and enhancements since 1.9:
https://github.com/samtools/bcftools/tags

Take maintainership per ports/248089.

PR:             ports/248089
Original commitRevision:544096 
17:40 jwb search for other commits by this committer
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
Original commitRevision:544090 
Friday, 25 Oct 2019
23:41 tcberner search for other commits by this committer
math/gsl: update to 2.6

- math/p5-Math-GSL does not seem to have any upstream activity to make it work
with this version -> mark it broken
  - this also breaks the two consumers of this port

- biology/gemma: has a conflict with cblas, and is makred broken.

PR:		241363
Exp-run by:	antoine
Original commitRevision:515671 
Thursday, 2 Aug 2018
19:30 fernape search for other commits by this committer
biology/bcftools: update to 1.9

While here:

* Update LICENSE handling
* Move all commands to bin/

PR:	230169
Submitted by:	ndowens.fbsd@yandex.com
Approved by:	tcberner (mentor)
Differential Revision:	https://reviews.freebsd.org/D16543
Original commitRevision:476247 
Saturday, 23 Jun 2018
08:27 tcberner search for other commits by this committer
Update math/gsl to 2.5

PR:		229067
Original commitRevision:473116 
Monday, 4 Dec 2017
15:27 mat search for other commits by this committer
Add a USES=python:env, that will not add a dependency on Python.

It has the same effect than setting PYTHON_NO_DEPENDS, but in a more
compact way.

Sponsored by:	Absolight
Original commitRevision:455518 
Wednesday, 25 Oct 2017
10:19 pizzamig search for other commits by this committer
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
Original commitRevision:452840 
Monday, 3 Jul 2017
20:38 tcberner search for other commits by this committer
Update math/gsl to 2.4

Exp-Run by:	antoine
PR:		220408
Original commitRevision:444988 
Tuesday, 2 May 2017
05:26 tcberner search for other commits by this committer
Update math/gsl to 2.3

This release introduces some new features and fixes several bugs:
	http://savannah.gnu.org/forum/forum.php?forum_id=8751

* update to 2.3 and take maintainership
* update math/py-gsl to 2.2.0 for gsl2 support
* update math/rubygem-rb-gsl to 2.1.0.2 for gsl2 support

PR:		218952
Exp-run by:	antoine
Reviewed by:	mat, rakuco
Approved by:	rakuco (mentor)
Differential Revision:	https://reviews.freebsd.org/D10522
Original commitRevision:439928 
Thursday, 26 May 2016
20:28 pi search for other commits by this committer
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)
Original commitRevision:415914 
Friday, 1 Apr 2016
13:29 mat search for other commits by this committer
Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c.

With hat:	portmgr
Sponsored by:	Absolight
Original commitRevision:412344 
Friday, 25 Dec 2015
01:31 junovitch search for other commits by this committer
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)
Original commitRevision:404398 
Friday, 5 Jun 2015
21:01 pi search for other commits by this committer
New port: biology/bcftools

BCFtools is a set of utilities that manipulate variant calls in the
Variant Call Format (VCF) and its binary counterpart BCF. All
commands work transparently with both VCFs and BCFs, both
uncompressed and BGZF-compressed.

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

PR:		199747
Submitted by:	cartwright@asu.edu
Original commitRevision:388638 

Number of commits found: 26