aboutsummaryrefslogtreecommitdiff
path: root/biology/p5-Bio-NEXUS
Commit message (Collapse)AuthorAgeFilesLines
* 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
|
* Fix every instance of RUN_DEPENDS:=${BUILD_DEPENDS} in p5 ports, exceptDag-Erling Smørgrav2018-10-061-2/+2
| | | | | | | | | | for where it resulted in a change in output from build-depends-list or run-depends-list. Approved by: portmgr (adamw) Notes: svn path=/head/; revision=481365
* Update WWWSunpoet Po-Chuan Hsieh2018-05-271-1/+1
| | | | | | | | | | search.cpan.org is shutting down. It will redirect to metacpan.org after June 25, 2018. With hat: perl Notes: svn path=/head/; revision=470993
* - Fix trailing whitespace in pkg-descrs, categories [a-f]*Dmitry Marakasov2016-05-191-1/+1
| | | | | | | Approved by: portmgr blanket Notes: svn path=/head/; revision=415498
* Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c.Mathieu Arnold2016-04-011-4/+4
| | | | | | | | With hat: portmgr Sponsored by: Absolight Notes: svn path=/head/; revision=412344
* Make it so that the default Perl is always called perl5.Mathieu Arnold2015-09-141-3/+3
| | | | | | | | | | | | | | | | | | | - Move Perl's man1 files along with its man3 files. - Move where Perl installs its modules man1 pages. - Convert the ports installing man1 pages. - Make different Perl versions installable at the same time. Though you should note that only the default version can be used to install Perl modules, and the non default Perl versions cannot use the modules installed via ports if they contain .so as they are installed in a version specific directory. Reviewed by: bapt (the Mk bits) Exp-run by: antoine Sponsored by: Absolight Differential Revision: https://reviews.freebsd.org/D3542 Notes: svn path=/head/; revision=396892
* - Add NO_ARCHDmitry Marakasov2015-05-311-0/+1
| | | | | | | Approved by: portmgr blanket Notes: svn path=/head/; revision=388088
* Change the way Perl modules are installed, update the default Perl to 5.18.Mathieu Arnold2014-11-262-1/+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
* Cleanup plistBaptiste Daroussin2014-10-201-6/+0
| | | | Notes: svn path=/head/; revision=371237
* - Stage supportMartin Wilke2014-01-312-33/+31
| | | | Notes: svn path=/head/; revision=341989
* 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 frameworkMathieu Arnold2013-08-021-1/+2
| | | | | | | | - Trim Makefile header - Remove MAKE_JOBS_SAFE=yes, it's the default. Notes: svn path=/head/; revision=324174
* For perl@ owned ports:Eitan Adler2013-03-291-6/+2
| | | | | | | | - Fix COMMENT - Trim header Notes: svn path=/head/; revision=315509
* - Update to 0.78Sunpoet Po-Chuan Hsieh2012-02-113-44/+58
| | | | | | | | | - Sort TEST_DEPENDS, MAN1, MAN3 and PLIST Changes: http://search.cpan.org/dist/Bio-NEXUS/doc/changes.txt Notes: svn path=/head/; revision=290895
* - Update to 0.77Wen Heping2012-02-093-5/+8
| | | | Notes: svn path=/head/; revision=290756
* At the moment 1385 ports use BUILD_DEPENDS= ${RUN_DEPENDS} and 450Eitan Adler2012-01-211-1/+1
| | | | | | | | | | | | | ports use BUILD_DEPENDS:= ${RUN_DEPENDS}. This patch fixes ports that are currently broken. This is a temporary measure until we organically stop using := or someone(s) spend a lot of time changing all the ports over. Explicit duplication > := > = and this just moves ports one step to the left Approved by: portmgr Notes: svn path=/head/; revision=289563
* - Use canonical format for FreeBSD.org MAINTAINER addressesSunpoet Po-Chuan Hsieh2010-12-252-2/+1
| | | | | | | | | | | - Remove obsolete MD5 checksum while I'm here PR: ports/152844 Submitted by: sunpoet (myself) Approved by: miwi (with portmgr hat) Notes: svn path=/head/; revision=266895
* - Update to 0.76Wen Heping2010-09-252-4/+4
| | | | Notes: svn path=/head/; revision=261818
* - Update to 0.75Wen Heping2010-09-073-6/+12
| | | | | | | - Reset maintainer to perl@ Notes: svn path=/head/; revision=260679
* Bio::NEXUS package provides an object-oriented, Perl-basedMartin Wilke2009-08-224-0/+90
applications programming interface (API) to the NEXUS file format of Maddison, et al., 1997 (Syst. Biol. 46:590-621). NEXUS is a powerful and extensible format designed for use in evolutionary analysis, including the analysis of molecular sequence data as well as classical morphological and life-history data. NEXUS is the input or output format for software such as PAUP*, MacClade, Mesquite, SIMMAP, MrBayes, Nexplorer, and so on. This package also contains the demonstration applications nexplot.pl (plot character data with a tree) and nextool.pl (allowing programmatic editing, e.g., selecting particular clades or subsets of data). WWW: http://search.cpan.org/dist/Bio-NEXUS/ PR: ports/137983 Submitted by: Wen Heping <wenheping at gmail.com> Notes: svn path=/head/; revision=240135
generated by cgit v1.2.3 (git 2.25.1) at 2024-11-16 08:17:30 +0000