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* 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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* - Convert to option helper install target (add OPTIONS_DEFINE=DOCSAlexey Dokuchaev2018-01-111-2/+4
| | | | | | | | | when it was missing) - Invoke INSTALL_DATA where appropriate instead of INSTALL_MAN - Fix some whitespace and formatting bugs along the way Notes: svn path=/head/; revision=458761
* Designatate 4 ports as unsafe for parallel buildingJohn Marino2015-01-191-0/+1
| | | | | | | | | All had similar errors that it couldn't find something during the build, yet built on a subsequent pass with no adjustments. Most I've seen before on previous bulk runs. Notes: svn path=/head/; revision=377443
* Change the way Perl modules are installed, update the default Perl to 5.18.Mathieu Arnold2014-11-261-1/+1
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Before, we had: site_perl : lib/perl5/site_perl/5.18 site_perl/perl_arch : lib/perl5/site_perl/5.18/mach perl_man3 : lib/perl5/5.18/man/man3 Now we have: site_perl : lib/perl5/site_perl site_arch : lib/perl5/site_perl/mach/5.18 perl_man3 : lib/perl5/site_perl/man/man3 Modules without any .so will be installed at the same place regardless of the Perl version, minimizing the upgrade when the major Perl version is changed. It uses a version dependent directory for modules with compiled bits. As PERL_ARCH is no longer needed in plists, it has been removed from PLIST_SUB. The USE_PERL5=fixpacklist keyword is removed, the .packlist file is now always removed, as is perllocal.pod. The old site_perl and site_perl/arch directories have been kept in the default Perl @INC for all Perl ports, and will be phased out as these old Perl versions expire. PR: 194969 Differential Revision: https://reviews.freebsd.org/D1019 Exp-run by: antoine Reviewed by: perl@ Approved by: portmgr Notes: svn path=/head/; revision=373448
* - Convert ports from benchmarks/ and biology/ to new USES=pythonMarcus von Appen2014-10-191-1/+1
| | | | | | | Approved by: portmgr (implicit) Notes: svn path=/head/; revision=371171
* Convert a bunch of EXTRACT_SUFX=... into USES=tar:...Adam Weinberger2014-07-291-2/+1
| | | | | | | Approved by: portmgr (not really, but touches unstaged ports) Notes: svn path=/head/; revision=363374
* Fix shebang line in Perl and Python scripts.Raphael Kubo da Costa2014-06-201-13/+6
| | | | | | | | PR: 191146 Submitted by: mzaki@m.u-tokyo.ac.jp (maintainer) Notes: svn path=/head/; revision=358567
* Update to 1.2.10.Raphael Kubo da Costa2014-06-173-35/+23
| | | | | | | | PR: 191129 Submitted by: mzaki@m.u-tokyo.ac.jp (maintainer) Notes: svn path=/head/; revision=358183
* - add stage supportOlli Hauer2014-06-011-12/+6
| | | | Notes: svn path=/head/; revision=356099
* - Convert USE_GMAKE to USESMartin Wilke2014-03-131-2/+1
| | | | Notes: svn path=/head/; revision=348042
* Remove trailing whitespaces from category biologyEmanuel Haupt2014-02-211-1/+1
| | | | Notes: svn path=/head/; revision=345397
* According to the Porter's Handbook (5.12.2.3.) default options must be added toEmanuel Haupt2014-02-101-0/+2
| | | | | | | | | | | | | | OPTIONS_DEFINE. This policy has been implemented only recently that's why we have many ports violating this policy. This patch adds the default options specified in the Porter's Handbook to OPTIONS_DEFINE where they are being used. Ports maintained by gnome@FreeBSD.org, kde@FreeBSD.org and x11@FreeBSD.org have been excluded. Approved by: portmgr (bapt) Notes: svn path=/head/; revision=343634
* Convert biology to MDOCS and MEXAMPLESAdam Weinberger2014-01-031-1/+4
| | | | Notes: svn path=/head/; revision=338550
* Add NO_STAGE all over the place in preparation for the staging support (cat: ↵Baptiste Daroussin2013-09-201-5/+2
| | | | | | | biology) Notes: svn path=/head/; revision=327709
* - convert to the new perl5 frameworkAndrej Zverev2013-09-071-1/+2
| | | | | | | Approved by: portmgr (bapt@, blanket) Notes: svn path=/head/; revision=326575
* Update to 1.1.04Julien Laffaye2011-06-095-126/+35
| | | | | | | | | PR: ports/157527 Submitted by: Motomichi Matsuzaki <mzaki@m.u-tokyo.ac.jp> Approved by: bapt (mentor) Notes: svn path=/head/; revision=275282
* - Get Rid MD5 supportMartin Wilke2011-03-191-1/+0
| | | | Notes: svn path=/head/; revision=271305
* Velvet is a de novo genomic assembler specially designed for short readDmitry Marakasov2009-11-076-0/+243
sequencing technologies, such as Solexa or 454, developed by Daniel Zerbino and Ewan Birney at the European Bioinformatics Institute (EMBL-EBI). Citation: Velvet: algorithms for de novo short read assembly using de Bruijn graphs. D.R. Zerbino and E. Birney. Genome Research 18: 821-829 (2008) WWW: http://www.ebi.ac.uk/~zerbino/velvet/ PR: 140147 Submitted by: Motomichi Matsuzaki <mzaki@m.u-tokyo.ac.jp> Notes: svn path=/head/; revision=243919
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