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* biology/hmmer: Update to 3.3.2Jason W. Bacon2022-10-113-22/+11
| | | | | | | | No release notes. See commits for changes: https://github.com/EddyRivasLab/hmmer PR: 266968 Reported by: mzaki@e-mail.ne.jp
* Remove WWW entries moved into port MakefilesStefan Eßer2022-09-071-2/+0
| | | | | | | | | | Commit b7f05445c00f has added WWW entries to port Makefiles based on WWW: lines in pkg-descr files. This commit removes the WWW: lines of moved-over URLs from these pkg-descr files. Approved by: portmgr (tcberner)
* Add WWW entries to port MakefilesStefan Eßer2022-09-071-0/+1
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 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)
* biology: remove 'Created by' linesTobias C. Berner2022-07-201-2/+0
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 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
* Remove # $FreeBSD$ from Makefiles.Mathieu Arnold2021-04-061-1/+0
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* biology/hmmer: disable on powerpc64le and powerpcspePiotr Kubaj2021-03-101-1/+1
| | | | | | | | Altivec/VSX code in this port works only on big-endian POWER. powerpcspe has neither SSE2 nor Altivec. Notes: svn path=/head/; revision=568013
* Also enable on powerpc64le.Mark Linimon2020-09-241-1/+1
| | | | | | | Approved by: portmgr (tier-2 blanket) Notes: svn path=/head/; revision=549947
* biology/hmmer: update to 3.3Fernando Apesteguía2020-01-294-9/+26
| | | | | | | | PR: 243244 Submitted by: mzaki@e-mail.ne.jp (maintainer) Notes: svn path=/head/; revision=524533
* Convert to UCL & cleanup pkg-message (categories a-c)Mathieu Arnold2019-08-131-2/+6
| | | | Notes: svn path=/head/; revision=508834
* Bump PORTREVISION for ports depending on the canonical version of GCCGerald Pfeifer2019-07-261-0/+1
| | | | | | | | | | | | | | | | | | 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 Notes: svn path=/head/; revision=507372
* vec_splats function is not supported by base GCC. Add USES=compiler:c11Mark Linimon2019-02-181-2/+2
| | | | | | | | | | | to fix build on powerpc platforms. PR: 235514 Submitted by: Piotr Kubaj Approved by: portmgr (tier-2 blanket) Notes: svn path=/head/; revision=493230
* biology/hmmer: update to 3.2.1Steve Wills2018-07-114-46/+23
| | | | | | | | PR: 229693 Submitted by: Motomichi Matsuzaki <mzaki@niid.go.jp> (maintainer) Notes: svn path=/head/; revision=474455
* Back out previous commits by jbeich demand.Mark Linimon2017-12-182-10/+2
| | | | Notes: svn path=/head/; revision=456588
* Bah. Remove spare line from cut-and-paste.Mark Linimon2017-12-181-1/+0
| | | | Notes: svn path=/head/; revision=456579
* Attempt to fix build on non-x86 archs. Untested, but does no harmMark Linimon2017-12-182-2/+11
| | | | | | | | | on x86. Approved by: portmgr (tier-2 blanket) Notes: svn path=/head/; revision=456578
* - Update to 3.1b2Wen Heping2017-11-115-39/+69
| | | | | | | | | | | - Pass maintainership to submitter PR: 223561 Submitted by: mzaki@niid.go.jp Approved by: bacon4000@gmail.com(previous maintainer) Notes: svn path=/head/; revision=453972
* Remove dead master sitesBaptiste Daroussin2017-10-131-0/+2
| | | | Notes: svn path=/head/; revision=451981
* Begin deorbit burn of ia64. We have not attempted to build packages forMark Linimon2017-06-251-1/+1
| | | | | | | | | | | it for many years. While here, alphabetize ARCHs, pet portlint, and modernize usages. Approved by: portmgr (tier-2 blanket) Notes: svn path=/head/; revision=444251
* - Update maintainer mail addressMartin Wilke2015-12-111-1/+1
| | | | | | | | | | | | - Update/Remove MASTER_SITE PR: 204755 Submitted by: jwbacon@tds.net (maintainer) Approved by: mat (mentor) Differential Revision: D4493 Notes: svn path=/head/; revision=403506
* - Remove deprecated optionDmitry Marakasov2015-04-021-9/+16
| | | | | | | | | | | | - Tweak compiler flags - Add LICENSE - Pass maintainership to submitter PR: 199066 Submitted by: jwbacon@tds.net Notes: svn path=/head/; revision=383013
* Cleanup plistBaptiste Daroussin2014-10-201-2/+0
| | | | Notes: svn path=/head/; revision=371237
* Add DOCS to OPTIONS_DEFINE to ports that check for PORT_OPTIONS:MDOCS.Adam Weinberger2014-07-152-14/+21
| | | | | | | While here, use OPTIONS helpers and re-enable manpage installation. Notes: svn path=/head/; revision=361934
* Stage supportAntoine Brodin2013-12-301-13/+4
| | | | Notes: svn path=/head/; revision=338155
* Add NO_STAGE all over the place in preparation for the staging support (cat: ↵Baptiste Daroussin2013-09-201-0/+1
| | | | | | | biology) Notes: svn path=/head/; revision=327709
* - Convert to new perl frameworkAndrej Zverev2013-08-031-1/+1
| | | | | | | - Trim Makefile header Notes: svn path=/head/; revision=324181
* - Update to 3.0Wen Heping2013-07-203-32/+46
| | | | | | | | - Convert to optionsNG - Drop maintainership Notes: svn path=/head/; revision=323349
* - Take maintainershipWen Heping2012-10-011-1/+1
| | | | Notes: svn path=/head/; revision=305131
* - Reassign to the heap at maintainer's requestThomas Abthorpe2012-10-011-6/+2
| | | | Notes: svn path=/head/; revision=305130
* - Get Rid MD5 supportMartin Wilke2011-03-191-1/+0
| | | | Notes: svn path=/head/; revision=271305
* - Update download locations, update WWWPhilip M. Gollucci2009-02-012-2/+2
| | | | | | | Reported by: -fetch-original pointyhat run Notes: svn path=/head/; revision=227349
* SHA256ifyEdwin Groothuis2006-01-221-0/+1
| | | | | | | Approved by: krion@ Notes: svn path=/head/; revision=154141
* - Remove a junk white space.Sergey Matveychuk2004-11-251-1/+1
| | | | Notes: svn path=/head/; revision=122436
* - Update to 2.3.2Sergey Matveychuk2004-11-255-69/+38
| | | | | | | | | | | - Add WITH_PVM knob - Pass maintainership to submitter PR: ports/74331 Submitted by: Fernan Aguero <fernan(at)iib.unsam.edu.ar> Notes: svn path=/head/; revision=122435
* With portmgr hat on, reset inactive maintainer. These ports are now upMark Linimon2004-11-201-1/+1
| | | | | | | for adoption. Notes: svn path=/head/; revision=121990
* SIZEify (maintainer timeout)Trevor Johnson2004-03-311-0/+1
| | | | Notes: svn path=/head/; revision=105747
* Cosmetic fix: use %%DOCSDIR%% macro.Sergey A. Osokin2003-10-221-5/+5
| | | | | | | | | | No functionally changes. Submitted by: Oleg Karachevtsev <ok@etrust.ru> A part of PR: 57992 Notes: svn path=/head/; revision=91882
* Clear moonlight beckons.Ade Lovett2003-03-072-1/+1
| | | | | | | | | | Requiem mors pacem pkg-comment, And be calm ports tree. E Nomini Patri, E Fili, E Spiritu Sancti. Notes: svn path=/head/; revision=77045
* - Add patch that will, for -CURRENT only, change: -pthread -> -lc_rJohann Visagie2002-07-112-0/+23
| | | | | | | | | - Bump $PORTREVISION Prompted by: Various questions from Rune Linding <linding@EMBL-Heidelberg.DE> Notes: svn path=/head/; revision=62806
* - Update port to version 2.2gJohann Visagie2001-08-224-223/+34
| | | | Notes: svn path=/head/; revision=46641
* - General clean-up of port.Johann Visagie2001-07-055-38/+252
| | | | | | | | | | - Install PDF and HTML documentation. - Take over maintainership. Approved by: Silence from previous maintainer; no objections from -ports Notes: svn path=/head/; revision=44780
* - Add %%PORTDOCS%% support to pkg-plist.Johann Visagie2001-07-042-3/+3
| | | | | | | | | | - $INSTALL_MAN -> $INSTALL_DATA in Makefile where appropriate. PR: 28668 Submitted by: Patrick Li <pat@databits.net> Notes: svn path=/head/; revision=44742
* update with the new PORTNAME/PORTVERSION variablesMichael Haro2000-04-081-2/+2
| | | | Notes: svn path=/head/; revision=27416
* fix some pkg/MESSAGE stuffMichael Haro2000-01-291-1/+1
| | | | Notes: svn path=/head/; revision=25253
* Change Id->FreeBSD.David E. O'Brien1999-08-251-1/+1
| | | | Notes: svn path=/head/; revision=20941
* As threatened, enforce the "Capital, no period" rule. Ellipses areTim Vanderhoek1999-06-261-1/+1
| | | | | | | | permitted. Note that, given current numeric motif of PW, this is done in four equally-sized commits of 393 files each. Notes: svn path=/head/; revision=19799
* Weasal and Wabbits and BIG FOOT.Tim Vanderhoek1999-05-021-2/+1
| | | | Notes: svn path=/head/; revision=18337
* Upgrade to 2.1.1Bill Fenner1999-03-083-8/+16
| | | | | | | | PR: ports/10228 Submitted by: Michael Haro mharo@area51.fremont.ca.us Notes: svn path=/head/; revision=17072
* Change *_DEPENDS on lang/perl5 to USE_PERL5 so we won't have anySatoshi Asami1999-01-021-3/+2
| | | | | | | | | | dependencies to perl5 in -current. This might cause some unwanted perl5 installations on -stable (if it was originally RUN_DEPENDS, perl5 will now be installed during build too, etc.), but its lifetime is limited anyway. Notes: svn path=/head/; revision=15765
* Update MASTER_SITES.Bill Fumerola1998-12-091-2/+2
| | | | | | | Thanks To: Fenner's portsurvey and ftpsearch.lycos.com Notes: svn path=/head/; revision=15237
* Remove empty doc dir on deinstall.Steve Price1998-09-271-0/+1
| | | | Notes: svn path=/head/; revision=13429
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