aboutsummaryrefslogtreecommitdiff
path: root/biology/p5-bioperl
Commit message (Collapse)AuthorAgeFilesLines
* Make it so that the default Perl is always called perl5.Mathieu Arnold2015-09-141-63/+63
| | | | | | | | | | | | | | | | | | | - 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
* - Fix shebangsDmitry Marakasov2015-05-301-3/+9
| | | | | | | | | | | - Add NO_ARCH - Add missing EXAMPLES option Approved by: portmgr blanket MFH: 2015Q2 Notes: svn path=/head/; revision=387940
* Reassign biology/ perl modules to perl@.Adam Weinberger2015-05-081-2/+1
| | | | | | | | | | | While here: Regenerate p5-AcePerl's patches using makepatch. Make p5-Bio-ASN1-EntrezGene depend on p5-bioperl, instead of the other way around. Bump PORTREVISION on those two ports. Notes: svn path=/head/; revision=385811
* Some OCD cleanups on some of the perl@ ports.Adam Weinberger2015-03-122-849/+841
| | | | | | | | | | | | | | | | - Remove dependencies in core - Put testing depends in TEST_DEPENDS - Remove unnecessary bsd.port.options.mk inclusions - Remove checks for Perl versions that no longer exist in the ports tree - Sort plists, some of which were so jumbled that I have to assume the plist was randomized before committing A lot of the plist changes in this commit are moving PERL5_MAN3 after SITE_PERL. It's repo churn now, but it makes updating the ports later far easier. Notes: svn path=/head/; revision=381151
* Change the way Perl modules are installed, update the default Perl to 5.18.Mathieu Arnold2014-11-261-0/+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 Daroussin2014-10-201-156/+0
| | | | Notes: svn path=/head/; revision=371237
* biology/p5-bioperl: fix pkg-descr sidenote linkKurt Jaeger2014-08-041-1/+1
| | | | Notes: svn path=/head/; revision=363961
* - Update to 1.6.924 [1]Wen Heping2014-07-273-10/+11
| | | | | | | | | | - Reset maintainer to perl@ PR: 192088 [1] Submitted by: Kurt Jaeger<pi@FreeBSD.org> [1] Notes: svn path=/head/; revision=363015
* - Update to 1.6.923Wen Heping2014-05-305-1532/+1440
| | | | | | | | | | - Add STAGE support PR: 190342 Submitted by: Muhammad Moinur Rahman <5u623l20@gmail.com> Notes: svn path=/head/; revision=355863
* Mark as broken unstaged perl portsBaptiste Daroussin2014-04-091-0/+1
| | | | | | | With hat: portmgr Notes: svn path=/head/; revision=350675
* 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 Daroussin2013-09-201-0/+1
| | | | | | | biology) Notes: svn path=/head/; revision=327709
* - Convert to new perl frameworkAndrej Zverev2013-08-061-1/+2
| | | | | | | | | - Trim Makefile header Approved by: wen@ (maintainer) Notes: svn path=/head/; revision=324306
* - Avoid of using SITE_PERLAndrej Zverev2013-06-071-2/+1
| | | | | | | | | | | - Remove depend on DB_File.pm since it part of perl distribution PR: ports/178877 Submitted by: az Approved by: matainer (timeout) Notes: svn path=/head/; revision=320153
* - 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
* - Remove SITE_PERL from *_DEPENDSAndrej Zverev2012-06-301-39/+39
| | | | | | | Approved by: portmgr@ (bapt@) Notes: svn path=/head/; revision=300240
* - update png to 1.5.10Dirk Meyer2012-06-011-1/+1
| | | | Notes: svn path=/head/; revision=297915
* 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
* - remove maintainer tags from pkg-descrEitan Adler2011-10-221-2/+0
| | | | | | | | Approved by: portmgr Approved by: bapt (mentor) Notes: svn path=/head/; revision=284139
* - Get Rid MD5 supportMartin Wilke2011-03-191-1/+0
| | | | Notes: svn path=/head/; revision=271305
* - update to 1.4.1Dirk Meyer2010-03-281-1/+1
| | | | | | | | Reviewed by: exp8 run on pointyhat Supported by: miwi Notes: svn path=/head/; revision=251605
* - update to jpeg-8Dirk Meyer2010-02-051-1/+1
| | | | Notes: svn path=/head/; revision=249285
* - Remove unneeded dependencies which is in perl-5.8.9 distJun Kuriyama2010-01-291-3/+1
| | | | | | | | | (part 19; last!). Approved by: portmgr (itetcu) Notes: svn path=/head/; revision=248805
* - Update to 1.6.1Wen Heping2009-12-045-912/+939
| | | | | | | Approved by: maintainer (via Email) Notes: svn path=/head/; revision=245194
* - bump all port that indirectly depends on libjpeg and have not yet been ↵Dirk Meyer2009-07-311-0/+1
| | | | | | | | | bumped or updated Requested by: edwin Notes: svn path=/head/; revision=238701
* - lang/perl5.6 is dead, remove PERL_LEVEL/PERL_VERSION < 500801 checksPhilip M. Gollucci2009-07-221-10/+1
| | | | | | | | | PR: ports/135398 Tested by: 2 -exp runs by pav Approved by: portmgr (pav) Notes: svn path=/head/; revision=238202
* Remove variable PERL_VER from the ports tree at all - becauseSergey Skvortsov2009-03-051-2/+2
| | | | | | | it is obsolete since Perl 5.6.0. Notes: svn path=/head/; revision=229523
* - Update to 1.6.0Renato Botelho2009-02-236-1082/+1559
| | | | | | | | PR: ports/131989 Submitted by: maintainer Notes: svn path=/head/; revision=228936
* Fix plist with perl 5.8.9.Anton Berezin2009-01-141-1/+2
| | | | | | | Approved by: portmgr (pav, implicit) Notes: svn path=/head/; revision=226081
* - Take advantage of CPAN macro from bsd.sites.mk, change ↵Marcelo Araujo2008-04-171-2/+1
| | | | | | | | | | | | ${MASTER_SITE_PERL_CPAN} to CPAN. PR: ports/122674 Submitted by: Philip M. Gollucci <pgollucci@p6m7g8.com> Reworked by: araujo (myself) Approved by: portmgr (pav) Notes: svn path=/head/; revision=211450
* Welcome bsd.perl.mk. Add support for constructs such as USE_PERL5=5.8.0+.Mark Linimon2007-09-081-3/+0
| | | | | | | | | | | Drop support for antique perl. Work done by: gabor Sponsored by: Google Summer of Code 2007 Hat: portmgr Notes: svn path=/head/; revision=199069
* - Welcome X.org 7.2 \o/.Florent Thoumie2007-05-191-0/+1
| | | | | | | | - Set X11BASE to ${LOCALBASE} for recent ${OSVERSION}. - Bump PORTREVISION for ports intalling files in ${X11BASE}. Notes: svn path=/head/; revision=191544
* SHA256ifyEdwin Groothuis2006-01-221-0/+1
| | | | | | | Approved by: krion@ Notes: svn path=/head/; revision=154141
* Add conflicst:Edwin Groothuis2005-12-041-0/+2
| | | | | | | | | CONFLICTS= p5-bioperl-1.[13579]* Submitted by: Mauricio Herrera Cuadra <arareko@yahoo.com>,Fernan Aguero <fernan@iib.unsam.edu.ar> Notes: svn path=/head/; revision=150421
* - add missing MAN1 and MAN3Yen-Ming Lee2004-09-032-357/+537
| | | | | | | | | | | | - apply DATADIR, EXAMPLESDIR, and DOCSDIR in PLIST - update the usage of NOPORTDOCS PR: 71322 Submitted by: leeym Approved by: Fernan Aguero <fernan@iib.unsam.edu.ar> Notes: svn path=/head/; revision=118056
* After devel/p5-File-Temp has gained an IGNORE for PERL_LEVEL > 500800, allMathieu Arnold2004-08-121-1/+3
| | | | | | | | these ports were broken because they always depended on it. I've rearranged all the dependencies to fit the new scheme. Notes: svn path=/head/; revision=116026
* Add size data, approved by maintainers.Trevor Johnson2004-03-181-0/+1
| | | | Notes: svn path=/head/; revision=104520
* Unmark as broken for 4.x; instead, mark as ignore for perl < 5.6.Mark Linimon2004-03-081-2/+2
| | | | Notes: svn path=/head/; revision=103263
* BROKEN on 4.x: Configure failsKris Kennaway2004-02-221-1/+7
| | | | Notes: svn path=/head/; revision=101631
* Major update from 0.7.2 to 1.4 by new maintainer. This is almost a completeMark Linimon2004-01-216-405/+1689
| | | | | | | | | | | | | | | | | | | | | | | rework of the port. See the page http://news.open-bio.org/archives/cat_bioperl.html for the changes between 1.2 and 1.4. The older changes are in the CVS tree. From the new maintainer: Note that this new port just handles the installation of bioperl and not of additional extra stuff (bioperl-gui, bioperl-corba-server, bioperl-corba-client). This is unlike the behaviour of the current port. The extra stuff, though still functional, had very little adoption among users, and does not appear to be currently supported/maintained. PR: ports/47303 (and subsequent) Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar> (new maintainer) Notes: svn path=/head/; revision=98688
* utilize SITE_PERLYing-Chieh Liao2003-10-242-265/+264
| | | | | | | | PR: 58166 Submitted by: Cheng-Lung Sung <clsung@dragon2.net> Notes: svn path=/head/; revision=92059
* 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
* - Update to version 0.7.2, somewhat overdue. :-)Johann Visagie2002-01-252-27/+53
| | | | Notes: svn path=/head/; revision=53709
* - Properly list run-time dependencies in RUN_DEPENDS in Makefile.Johann Visagie2001-08-133-40/+46
| | | | | | | | | | - Deploy %%PERL_VER%% and %%PERL_ARCH%% pragmas consistently throughout pkg-plist. (Ouch, that was embarrassing.) - Bump PORTREVISION due to the above. - Update my email address and the project's URL in pkg-descr. Notes: svn path=/head/; revision=46170
* - Update to version 0.7.1Johann Visagie2001-07-044-3/+24
| | | | | | | - Add a build-time message to inform the user of available options. Notes: svn path=/head/; revision=44743
* Embarrassingly long overdue update to 0.7.0, including optional support forJohann Visagie2001-06-263-66/+300
| | | | | | | GUI (Tk) and CORBA extensions. Notes: svn path=/head/; revision=44463
* Update to version 0.6.2James E. Housley2000-10-133-174/+132
| | | | | | | | PR: 21954 Submitted by: Johann Visagie <johann@egenetics.com> MAINTAINER Notes: svn path=/head/; revision=33772