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non port: biology/hmmer/Makefile

Number of commits found: 36

Thursday, 22 Feb 2024
13:23 Muhammad Moinur Rahman (bofh) search for other commits by this committer
biology/hmmer: Moved man to share/man

Approved by:    portmgr (blanket)
commit hash: c0800517ea855594a57280bc776d2185e84bcc20 commit hash: c0800517ea855594a57280bc776d2185e84bcc20 commit hash: c0800517ea855594a57280bc776d2185e84bcc20 commit hash: c0800517ea855594a57280bc776d2185e84bcc20 c080051
Tuesday, 27 Jun 2023
19:34 Rene Ladan (rene) search for other commits by this committer
all: remove explicit versions in USES=python for "3.x+"

The logic in USES=python will automatically convert this to 3.8+ by
itself.

Adjust two ports that only had Python 3.7 mentioned but build fine
on Python 3.8 too.

finance/quickfix: mark BROKEN with PYTHON

libtool: compile:  c++ -DHAVE_CONFIG_H -I. -I../.. -I -I. -I.. -I../.. -I../C++
-DLIBICONV_PLUG -DPYTHON_MAJOR_VERSION=3 -Wno-unused-variable
-Wno-maybe-uninitialized -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong
-fno-strict-aliasing -DLIBICONV_PLUG -Wall -ansi
-Wno-unused-command-line-argument -Wpointer-arith -Wwrite-strings
-Wno-overloaded-virtual -Wno-deprecated-declarations -Wno-deprecated -std=c++0x
-MT _quickfix_la-QuickfixPython.lo -MD -MP -MF
.deps/_quickfix_la-QuickfixPython.Tpo -c QuickfixPython.cpp  -fPIC -DPIC -o
.libs/_quickfix_la-QuickfixPython.o
warning: unknown warning option '-Wno-maybe-uninitialized'; did you mean
'-Wno-uninitialized'? [-Wunknown-warning-option]
QuickfixPython.cpp:175:11: fatal error: 'Python.h' file not found
          ^~~~~~~~~~
1 warning and 1 error generated.

Reviewed by:	portmgr, vishwin, yuri
Differential Revision:	<https://reviews.freebsd.org/D40568>
commit hash: 3d9a815d9c5acbb71f4bb07738bdeab4879feacb commit hash: 3d9a815d9c5acbb71f4bb07738bdeab4879feacb commit hash: 3d9a815d9c5acbb71f4bb07738bdeab4879feacb commit hash: 3d9a815d9c5acbb71f4bb07738bdeab4879feacb 3d9a815
Tuesday, 11 Oct 2022
20:13 Jason W. Bacon (jwb) search for other commits by this committer
biology/hmmer: Update to 3.3.2

No release notes.  See commits for changes:
https://github.com/EddyRivasLab/hmmer

PR:             266968
Reported by:    mzaki@e-mail.ne.jp
commit hash: b532c5dd966eb638a5616fc7819657f007c08848 commit hash: b532c5dd966eb638a5616fc7819657f007c08848 commit hash: b532c5dd966eb638a5616fc7819657f007c08848 commit hash: b532c5dd966eb638a5616fc7819657f007c08848 b532c5d
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
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
Wednesday, 10 Mar 2021
16:09 pkubaj search for other commits by this committer
biology/hmmer: disable on powerpc64le and powerpcspe

Altivec/VSX code in this port works only on big-endian POWER.
powerpcspe has neither SSE2 nor Altivec.
Original commitRevision:568013 
Thursday, 24 Sep 2020
20:29 linimon search for other commits by this committer
Also enable on powerpc64le.

Approved by:	portmgr (tier-2 blanket)
Original commitRevision:549947 
Wednesday, 29 Jan 2020
05:55 fernape search for other commits by this committer
biology/hmmer: update to 3.3

PR:	243244
Submitted by:	mzaki@e-mail.ne.jp (maintainer)
Original commitRevision:524533 
Friday, 26 Jul 2019
20:46 gerald search for other commits by this committer
Bump PORTREVISION for ports depending on the canonical version of GCC
as defined in Mk/bsd.default-versions.mk which has moved from GCC 8.3
to GCC 9.1 under most circumstances now after revision 507371.

This includes ports
 - with USE_GCC=yes or USE_GCC=any,
 - with USES=fortran,
 - using Mk/bsd.octave.mk which in turn features USES=fortran, and
 - with USES=compiler specifying openmp, nestedfct, c11, c++0x, c++11-lang,
   c++11-lib, c++14-lang, c++17-lang, or gcc-c++11-lib
plus, everything INDEX-11 shows with a dependency on lang/gcc9 now.

PR:		238330
Original commitRevision:507372 
Monday, 18 Feb 2019
01:30 linimon search for other commits by this committer
vec_splats function is not supported by base GCC.  Add USES=compiler:c11
to fix build on powerpc platforms.

PR:		235514
Submitted by:	Piotr Kubaj
Approved by:	portmgr (tier-2 blanket)
Original commitRevision:493230 
Wednesday, 11 Jul 2018
15:15 swills search for other commits by this committer
biology/hmmer: update to 3.2.1

PR:		229693
Submitted by:	Motomichi Matsuzaki <mzaki@niid.go.jp> (maintainer)
Original commitRevision:474455 
Monday, 18 Dec 2017
04:28 linimon search for other commits by this committer
Back out previous commits by jbeich demand.
Original commitRevision:456588 
02:41 linimon search for other commits by this committer
Bah.  Remove spare line from cut-and-paste.
Original commitRevision:456579 
02:32 linimon search for other commits by this committer
Attempt to fix build on non-x86 archs.  Untested, but does no harm
on x86.

Approved by:	portmgr (tier-2 blanket)
Original commitRevision:456578 
Saturday, 11 Nov 2017
12:51 wen search for other commits by this committer
- Update to 3.1b2
- Pass maintainership to submitter

PR:		223561
Submitted by:	mzaki@niid.go.jp
Approved by:	bacon4000@gmail.com(previous maintainer)
Original commitRevision:453972 
Friday, 13 Oct 2017
11:14 bapt search for other commits by this committer
Remove dead master sites
Original commitRevision:451981 
Sunday, 25 Jun 2017
00:29 linimon search for other commits by this committer
Begin deorbit burn of ia64.  We have not attempted to build packages for
it for many years.

While here, alphabetize ARCHs, pet portlint, and modernize usages.

Approved by:	portmgr (tier-2 blanket)
Original commitRevision:444251 
Friday, 11 Dec 2015
08:48 miwi search for other commits by this committer
- Update maintainer mail address
- Update/Remove MASTER_SITE

PR:		204755
Submitted by:	 jwbacon@tds.net (maintainer)
Approved by:	mat (mentor)
Differential Revision:	D4493
Original commitRevision:403506 
Thursday, 2 Apr 2015
15:41 amdmi3 search for other commits by this committer
- Remove deprecated option
- Tweak compiler flags
- Add LICENSE
- Pass maintainership to submitter

PR:		199066
Submitted by:	jwbacon@tds.net
Original commitRevision:383013 
Tuesday, 15 Jul 2014
14:54 adamw search for other commits by this committer
Add DOCS to OPTIONS_DEFINE to ports that check for PORT_OPTIONS:MDOCS.

While here, use OPTIONS helpers and re-enable manpage installation.
Original commitRevision:361934 
Monday, 30 Dec 2013
18:08 antoine search for other commits by this committer
Stage support
Original commitRevision:338155 
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, 3 Aug 2013
08:45 az search for other commits by this committer
- Convert to new perl framework
- Trim Makefile header
Original commitRevision:324181 
Saturday, 20 Jul 2013
15:08 wen search for other commits by this committer
- Update to 3.0
- Convert to optionsNG
- Drop maintainership
Original commitRevision:323349 
Monday, 1 Oct 2012
14:55 wen search for other commits by this committer
- Take maintainership
Original commitRevision:305131 
14:45 tabthorpe search for other commits by this committer
- Reassign to the heap at maintainer's request
Original commitRevision:305130 
Sunday, 1 Feb 2009
08:17 pgollucci search for other commits by this committer
- Update download locations, update WWW

Reported by:    -fetch-original pointyhat run
Original commit
Thursday, 25 Nov 2004
22:58 sem search for other commits by this committer
- Remove a junk white space.
Original commit
22:35 sem search for other commits by this committer
- Update to 2.3.2
- Add WITH_PVM knob
- Pass maintainership to submitter

PR:             ports/74331
Submitted by:   Fernan Aguero <fernan(at)iib.unsam.edu.ar>
Original commit
Saturday, 20 Nov 2004
08:09 linimon search for other commits by this committer
With portmgr hat on, reset inactive maintainer.  These ports are now up
for adoption.
Original commit
Friday, 7 Mar 2003
05:56 ade search for other commits by this committer
Clear moonlight beckons.
Requiem mors pacem pkg-comment,
And be calm ports tree.

E Nomini Patri, E Fili, E Spiritu Sancti.
Original commit
Thursday, 11 Jul 2002
10:52 wjv search for other commits by this committer
- Add patch that will, for -CURRENT only, change:  -pthread -> -lc_r
- Bump $PORTREVISION

Prompted by:    Various questions from Rune Linding <linding@EMBL-Heidelberg.DE>
Original commit
Wednesday, 22 Aug 2001
14:18 wjv search for other commits by this committer
- Update port to version 2.2g    
Original commit
Thursday, 5 Jul 2001
09:58 wjv search for other commits by this committer
- General clean-up of port.   - Install PDF and HTML documentation.   - Take
over maintainership.    
Original commit
Wednesday, 4 Jul 2001
13:16 wjv search for other commits by this committer
- Add %%PORTDOCS%% support to pkg-plist.   - $INSTALL_MAN -> $INSTALL_DATA in
Makefile where appropriate.    
Original commit

Number of commits found: 36