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* 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
* Add BioPerl, a collection of Perl5 mods for bioinformatics/genomicsNeil Blakey-Milner2000-07-286-0/+258
PR: ports/20252 Submitted by: Johann Visagie <johann@egenetics.com> Notes: svn path=/head/; revision=31084