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non port: biology/seqan/Makefile

Number of commits found: 22

Wednesday, 7 Sep 2022
21:10 Stefan Eßer (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
Friday, 29 Oct 2021
09:50 Stefan Eßer (se) search for other commits by this committer
*/*: Remove redundant '-[0-9]*' from CONFLICTS

The conflict checks compare the patterns first against the package
names without version (as reported by "pkg query "%n"), then - if
there was no match - agsinst the full package names including the
version (as reported by "pkg query "%n-%v").

Many CONFLICTS definitions used patterns like "bash-[0-9]*" to filter
for the bash package in any version. But that pattern is functionally
identical with just "bash".

Approved by:	portmgr (blanket)
commit hash: 819f25b36d45b8ac5593ec8e6f470d9ad454b08a commit hash: 819f25b36d45b8ac5593ec8e6f470d9ad454b08a commit hash: 819f25b36d45b8ac5593ec8e6f470d9ad454b08a commit hash: 819f25b36d45b8ac5593ec8e6f470d9ad454b08a 819f25b
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, 10 Mar 2018
06:21 yuri search for other commits by this committer
biology/seqan-apps, biology/seqan: Update to 2.4.0

Port changes for biology/seqan-apps:
* Changed to DISTVERSION
* Updated COMMENT
* Added USES=compiler:openmp
* Removed BROKEN_xx (upstream now claims support for these architectures)
* Removed USE_GCC
* Added SSE4/AVX2/NATIVE SIMD options

Port changes for biology/seqan:
* Changed to DISTVERSION
* Added NO_ARCH
* Added PORTDOCS=*
* Updated do-install

PR:		225682
Submitted by:	Hannes Hauswedell <h2+fbsdports@fsfe.org> (maintainer)
Approved by:	tcberner (mentor, implicit)
Original commitRevision:464043 
Wednesday, 14 Sep 2016
19:38 pawel search for other commits by this committer
- Update biology/seqan and bilogy/seqan-apps to version 2.2.0 [1]
- Fix spelling in pkg-descr

PR:		212682 [1]
Submitted by:	Hannes Hauswedell (maintainer) [1]
Original commitRevision:422156 
Friday, 27 May 2016
16:10 amdmi3 search for other commits by this committer
- Do install cmake and pkgconfig modules
- While here, switch to options helpers

PR:		209710
Submitted by:	h2+fbsdports@fsfe.org (maintainer)
Original commitRevision:415945 
Tuesday, 10 May 2016
01:05 junovitch search for other commits by this committer
biology/seqan: update 1.3.1 -> 2.1.1
biology/seqan1: create port from current SeqAn 1.3.1 for legacy usage
UPDATING: document SeqAn updates and seqan1 port for legacy usage

PR:		204127
Submitted by:	Hannes Hauswedell <h2+fbsdports@fsfe.org>
Original commitRevision:414898 
Saturday, 21 Mar 2015
11:53 marino search for other commits by this committer
biology/segan: Limit GCC to 4.8 while waiting for update

Due to questionable c++, GCC 4.9 and newer cannot build seqan.  An update
has been in the works that will enable clang compilers and all versions
of GCC to build seqan, but it is not quite ready yet.  While waiting for
it, limit the version of GCC used to 4.8.

PR:	196851
Original commitRevision:381791 
Sunday, 19 Oct 2014
07:38 mva search for other commits by this committer
- Convert ports from benchmarks/ and biology/ to new USES=python

Approved by:	portmgr (implicit)
Original commitRevision:371171 
Wednesday, 10 Sep 2014
20:50 gerald search for other commits by this committer
Update the default version of GCC in the Ports Collection from GCC 4.7.4
to GCC 4.8.3.

Part II, Bump PORTREVISIONs.

PR:		192025
Tested by:	antoine (-exp runs)
Approved by:	portmgr (implicit)
Original commitRevision:367888 
Thursday, 10 Jul 2014
22:29 adamw search for other commits by this committer
Use gcc on all platforms.

PR:		191692
Submitted by:	maintainer
Original commitRevision:361497 
Sunday, 1 Jun 2014
11:42 ohauer search for other commits by this committer
- add stage support
- adjust BSDn license
Original commitRevision:356100 
Monday, 10 Mar 2014
20:55 gerald search for other commits by this committer
Update the default version of GCC used in the Ports Collection from
GCC 4.6.4 to GCC 4.7.3.  This entails updating the lang/gcc port as
well as changing the default in Mk/bsd.default-versions.mk.

Part II, Bump PORTREVISIONs.

PR:		182136
Supported by:	Christoph Moench-Tegeder <cmt@burggraben.net> (fixing many ports)
Tested by:	bdrewery (two -exp runs)
Original commitRevision:347809 
Friday, 7 Mar 2014
15:52 bapt search for other commits by this committer
Convert b* to USES=zip
Original commitRevision:347402 
Saturday, 26 Oct 2013
00:52 gerald search for other commits by this committer
Update to libmpc version 1.0.1 which brings the following fixes:

 - Switched to automake 1.11.6, see CVE-2012-3386.
 - #14669: Fixed extraction of CC from gmp.h.
 - Fixed case of intermediate zero real or imaginary part in mpc_fma,
   found by hydra with GMP_CHECK_RANDOMIZE=1346362345.

This is on top of the following changes from version 1.0

 - Licence change towards LGPLv3+ for the code and GFDLv1.3+ (with no
   invariant sections) for the documentation.
 - 100% of all lines are covered by tests
 - Renamed functions
   . mpc_mul_2exp to mpc_mul_2ui
   . mpc_div_2exp to mpc_div_2ui
 - 0^0, which returned (NaN,NaN) previously, now returns (1,+0).
 - Removed compatibility with K&R compilers, which was untestable due
   to lack of such compilers.
 - New functions
   . mpc_log10
   . mpc_mul_2si, mpc_div_2si
 - Speed-ups
   . mpc_fma
 - Bug fixes
   . mpc_div and mpc_norm now return a value indicating the effective
     rounding direction, as the other functions.
   . mpc_mul, mpc_sqr and mpc_norm now return correct results even if
     there are over- or underflows during the computation.
   . mpc_asin, mpc_proj, mpc_sqr: Wrong result when input variable has
     infinite part and equals output variable is corrected.
   . mpc_fr_sub: Wrong return value for imaginary part is corrected.

Convert to the new LIB_DEPENDS standard and remove hard-coded
.so versions from a couple of dependent ports.

Bump PORTREVISIONS of all dependent ports.

PR:		183141
Approved by:	portmgr (bdrewery)
Original commitRevision:331644 
Friday, 20 Sep 2013
15:55 bapt search for other commits by this committer
Add NO_STAGE all over the place in preparation for the staging support (cat:
biology)
Original commitRevision:327709 
Saturday, 17 Aug 2013
16:27 gerald search for other commits by this committer
Replace USE_GCC=4.6+ and USE_GCC=4.4+ by USE_GCC=yes.

Right now this is a noop in the former case and a noop in the latter
case unless lang/gcc44 has been installed explicitly.

This puts a bit more emphasis on standardizing on a canonical version
"current" GCC and makes it easier to update that canonical version
by changing the default in Mk/bsd.gcc.mk and updating the lang/gcc port.

That is, USE_GCC=yes means "use a decent/modern version of GCC" without
having to worry about details.

Approved by:	portmgr (bdrewery)
Original commitRevision:324851 
Friday, 22 Mar 2013
20:06 makc search for other commits by this committer
- convert USE_CMAKE to USES
- while here clean up some ports from CMAKE_VERBOSE, which is intended
  for users

Approved by:	portmgr (miwi)
Original commitRevision:314960 
Saturday, 21 Jul 2012
22:20 gerald search for other commits by this committer
Replace USE_GCC=4.4+ by USE_GCC=4.6+ since GCC 4.4 is on its way out.

Approved by:	maintainer
Original commit
Thursday, 7 Jun 2012
13:04 amdmi3 search for other commits by this committer
- Fix maintainer email

Submitted by:   maintainer via private email
Original commit
Wednesday, 6 Jun 2012
17:51 amdmi3 search for other commits by this committer
SeqAn is an open source C++ library of efficient algorithms
and data structures for the analysis of sequences with the
focus on biological data. The library is licensed under the
3-clause BSD license except the applications which are GPL.

WWW: http://www.seqan.de/

PR:             167571
Submitted by:   Hannes <h2+fbsdports@fsfe.org>
Original commit

Number of commits found: 22