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* biology/jalview: Fix build by using gradle-7.6.1 instead of gradle-8.0.1Yuri Victorovich2023-06-181-2/+2
| | | | | | The gradle upgrade seems to have broken jalview. Reported by: fallout
* biology/jalview: Update 2.11.1.4 -> 2.11.2.5Yuri Victorovich2022-10-122-8/+8
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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
* cleanup: drop support for EOL FreeBSD 11.XRene Ladan2021-09-301-2/+0
| | | | | | | | | | | | | | | | | Search criteria used: - 11.4 - OSREL* - OSVER* - *_FreeBSD_11 Input from: - adridg: devel/qca-legacy - jbeich: _WITH_DPRINTF, _WITH_GETLINE, GNU bfd workarounds - sunpoet: security/p5-*OpenSSL* Reviewed by: doceng, kde, multimedia, perl, python, ruby, rust Differential Revision: https://reviews.freebsd.org/D32008 Test Plan: make index
* biology/jalview: Fix buildGuangyuan Yang2021-06-271-2/+2
| | | | | | | | | When switching the build dependency from devel/gradle to devel/gradle6, the build is accidentally broken. This attempts to revert part of the change and fix build. Fixes: 55044a2200a4c42b6b653349f0a65dfca3f96f36 Approved by: lwhsu (mentor, implicit), portmgr (fix build)
* devel/gradle6: New portGuangyuan Yang2021-06-271-2/+2
| | | | | | | | | | | | | devel/gradle needs to be updated to 7.x, while some ports build failed under the newer version, including: - biology/jalview - biology/igv Updated them to use this devel/gradle6 until they officially support 7.x. No functional changes for these ports. Approved by: lwhsu (mentor)
* biology/jalview: Broken on 11Yuri Victorovich2021-06-052-4/+3
| | | | | | Also fix number of lines in pkg-descr, and replace space with tab. Reported by: fallout
* Clean up some thingsTobias Kortkamp2021-05-011-2/+0
| | | | | | | | | | - Fix typos - Remove duplicate variables - Remove nop variables - Clean up commented PORTREVISION - Add missing USES Reported by: portscan
* biology/jalview: Update 2.07 -> 2.11.1.4Yuri Victorovich2021-04-256-80/+62
| | | | Take maintainership.
* all: Remove all other $FreeBSD keywords.Mathieu Arnold2021-04-061-3/+0
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* Remove # $FreeBSD$ from Makefiles.Mathieu Arnold2021-04-061-1/+0
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* Restrict to Java 8, since this doesn't compile with Java 11Greg Lewis2020-12-261-0/+1
| | | | | | | PR: 251774 Notes: svn path=/head/; revision=559318
* Clean up after java/openjdk6 and java/openjdk6-jre removalJung-uk Kim2019-11-262-3/+2
| | | | | | | | | | | | | | | java/openjdk6 support was removed from Mk/bsd.java.mk (r512662) and java/openjdk6 and java/openjdk6-jre were removed from the ports tree (r512663). Now this patch completely removes remaining stuff from the ports tree. PR: 241953 (exp-run) Reviewed by: glewis Approved by: portmgr (antoine) Differential Revision: https://reviews.freebsd.org/D22342 Notes: svn path=/head/; revision=518482
* - Fix trailing whitespace in pkg-descrs, categories [a-f]*Dmitry Marakasov2016-05-191-3/+3
| | | | | | | Approved by: portmgr blanket Notes: svn path=/head/; revision=415498
* Remove $FreeBSD$ from patches files in categories a-j.Mathieu Arnold2015-05-221-2/+0
| | | | | | | | With hat: portmgr Sponsored by: Absolight Notes: svn path=/head/; revision=387021
* Cleanup plistBaptiste Daroussin2014-10-201-1/+0
| | | | Notes: svn path=/head/; revision=371237
* Fix properties on pkg-plistBaptiste Daroussin2014-01-211-1/+0
| | | | Notes: svn path=/head/; revision=340671
* Support stageBaptiste Daroussin2014-01-201-5/+4
| | | | Notes: svn path=/head/; revision=340487
* 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
* Decommissioning java 1.5 (EOLed since October 2009):Baptiste Daroussin2012-12-101-1/+1
| | | | | | | suppress any reference to USE_JAVA= 1.5+ (part1) Notes: svn path=/head/; revision=308600
* - Reassign to the heap at maintainer's requestThomas Abthorpe2012-10-011-6/+2
| | | | Notes: svn path=/head/; revision=305130
* Now that the Java 1.3 and Java 1.4 ports are deprecated and will expire soon,Mark Linimon2011-07-211-1/+1
| | | | | | | | | | | | | | | | | | | remove support for them from bsd.java.mk. As Jikes is not available in Java 1.5 or higher, remove it from bsd.java.mk too (suggested by hq@) and from the ports which used it (only occurences were USE_JIKES=no). Support for the Blackdown VM is also removed, as it is not available in Java 1.5 and higher. Also remove the mapping from Java 1.1-1.4 to Java 1.5+ in bsd.java.mk to detect old, broken ports; therefore bump the minimal value of JAVA_VERSION to 1.5. While here, replace static values of JAVA_VERSION in files/*.in by %%JAVA_VERSION%% . PR: ports/158969 Submitted by: rene Tested on: pointyhat-west -exp Notes: svn path=/head/; revision=278068
* - Get Rid MD5 supportMartin Wilke2011-03-191-1/+0
| | | | Notes: svn path=/head/; revision=271305
* Bump portrevision due to upgrade of devel/gettext.Edwin Groothuis2008-06-061-1/+1
| | | | | | | | | | | | | The affected ports are the ones with gettext as a run-dependency according to ports/INDEX-7 (5007 of them) and the ones with USE_GETTEXT in Makefile (29 of them). PR: ports/124340 Submitted by: edwin@ Approved by: portmgr (pav) Notes: svn path=/head/; revision=214428
* - 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
* Jalview is a multiple alignment editor written in Java. It is used widely in aHerve Quiroz2006-02-136-0/+136
variety of web pages (e.g. the EBI Clustalw server and the Pfam protein domain database) and is also available as a general purpose alignment editor. WWW: http://www.jalview.org PR: 93054 Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar> Notes: svn path=/head/; revision=155905
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