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non port: biology/jalview/Makefile

Number of commits found: 21

Sunday, 18 Jun 2023
09:58 Yuri Victorovich (yuri) search for other commits by this committer
biology/jalview: Fix build by using gradle-7.6.1 instead of gradle-8.0.1

The gradle upgrade seems to have broken jalview.

Reported by:	fallout
commit hash: 4301fdb6560833e91ec4fd4b50cccee532fddb01 commit hash: 4301fdb6560833e91ec4fd4b50cccee532fddb01 commit hash: 4301fdb6560833e91ec4fd4b50cccee532fddb01 commit hash: 4301fdb6560833e91ec4fd4b50cccee532fddb01 4301fdb
Wednesday, 12 Oct 2022
06:58 Yuri Victorovich (yuri) search for other commits by this committer
biology/jalview: Update 2.11.1.4 -> 2.11.2.5
commit hash: 3a7900f35ad1dd7d0b4d152e66e9e357c7b2c158 commit hash: 3a7900f35ad1dd7d0b4d152e66e9e357c7b2c158 commit hash: 3a7900f35ad1dd7d0b4d152e66e9e357c7b2c158 commit hash: 3a7900f35ad1dd7d0b4d152e66e9e357c7b2c158 3a7900f
Wednesday, 7 Sep 2022
21:10 Stefan E├čer (se) search for other commits by this committer
Add WWW entries to port Makefiles

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)
commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52 commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52 commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52 commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52 b7f0544
Wednesday, 20 Jul 2022
14:20 Tobias C. Berner (tcberner) search for other commits by this committer
biology: remove 'Created by' lines

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
commit hash: 37526bbd4e50616d87f70e1c788ae4895d88d671 commit hash: 37526bbd4e50616d87f70e1c788ae4895d88d671 commit hash: 37526bbd4e50616d87f70e1c788ae4895d88d671 commit hash: 37526bbd4e50616d87f70e1c788ae4895d88d671 37526bb
Thursday, 30 Sep 2021
21:23 Rene Ladan (rene) search for other commits by this committer
cleanup: drop support for EOL FreeBSD 11.X

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
commit hash: 620968a43a5f9bb3fa98ab20f257a4c0d864caa7 commit hash: 620968a43a5f9bb3fa98ab20f257a4c0d864caa7 commit hash: 620968a43a5f9bb3fa98ab20f257a4c0d864caa7 commit hash: 620968a43a5f9bb3fa98ab20f257a4c0d864caa7 620968a
Sunday, 27 Jun 2021
09:30 Guangyuan Yang (ygy) search for other commits by this committer
biology/jalview: Fix build

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)
commit hash: 389294d2b118284d007bf6a6df9b2530e4d6348a commit hash: 389294d2b118284d007bf6a6df9b2530e4d6348a commit hash: 389294d2b118284d007bf6a6df9b2530e4d6348a commit hash: 389294d2b118284d007bf6a6df9b2530e4d6348a 389294d
01:51 Guangyuan Yang (ygy) search for other commits by this committer
devel/gradle6: New port

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)
commit hash: 55044a2200a4c42b6b653349f0a65dfca3f96f36 commit hash: 55044a2200a4c42b6b653349f0a65dfca3f96f36 commit hash: 55044a2200a4c42b6b653349f0a65dfca3f96f36 commit hash: 55044a2200a4c42b6b653349f0a65dfca3f96f36 55044a2
Saturday, 5 Jun 2021
18:53 Yuri Victorovich (yuri) search for other commits by this committer
biology/jalview: Broken on 11

Also fix number of lines in pkg-descr, and replace space with tab.

Reported by:	fallout
commit hash: 8b8c1272ea64f9db05d8b5cfed709881429df479 commit hash: 8b8c1272ea64f9db05d8b5cfed709881429df479 commit hash: 8b8c1272ea64f9db05d8b5cfed709881429df479 commit hash: 8b8c1272ea64f9db05d8b5cfed709881429df479 8b8c127
Saturday, 1 May 2021
17:55 Tobias Kortkamp (tobik) search for other commits by this committer
Clean up some things

- Fix typos
- Remove duplicate variables
- Remove nop variables
- Clean up commented PORTREVISION
- Add missing USES

Reported by:	portscan
commit hash: 6707a3c942b51ab3e3cf110383e3119dfe2e49b0 commit hash: 6707a3c942b51ab3e3cf110383e3119dfe2e49b0 commit hash: 6707a3c942b51ab3e3cf110383e3119dfe2e49b0 commit hash: 6707a3c942b51ab3e3cf110383e3119dfe2e49b0 6707a3c
Sunday, 25 Apr 2021
23:00 Yuri Victorovich (yuri) search for other commits by this committer
biology/jalview: Update 2.07 -> 2.11.1.4

Take maintainership.
commit hash: af49fbec4f0f6453b4b3dfe522107ed2918ae8f7 commit hash: af49fbec4f0f6453b4b3dfe522107ed2918ae8f7 commit hash: af49fbec4f0f6453b4b3dfe522107ed2918ae8f7 commit hash: af49fbec4f0f6453b4b3dfe522107ed2918ae8f7 af49fbe
Tuesday, 6 Apr 2021
14:31 Mathieu Arnold (mat) search for other commits by this committer
Remove # $FreeBSD$ from Makefiles.
commit hash: 305f148f482daf30dcf728039d03d019f88344eb commit hash: 305f148f482daf30dcf728039d03d019f88344eb commit hash: 305f148f482daf30dcf728039d03d019f88344eb commit hash: 305f148f482daf30dcf728039d03d019f88344eb 305f148
Saturday, 26 Dec 2020
23:01 glewis search for other commits by this committer
Restrict to Java 8, since this doesn't compile with Java 11

PR:			251774
Original commitRevision:559318 
Tuesday, 26 Nov 2019
21:46 jkim search for other commits by this committer
Clean up after java/openjdk6 and java/openjdk6-jre removal

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
Original commitRevision:518482 
Monday, 20 Jan 2014
23:10 bapt search for other commits by this committer
Support stage
Original commitRevision:340487 
Friday, 20 Sep 2013
15:55 bapt search for other commits by this committer
Add NO_STAGE all over the place in preparation for the staging support (cat:
biology)
Original commitRevision:327709 
Monday, 10 Dec 2012
11:25 bapt search for other commits by this committer
Decommissioning java 1.5 (EOLed since October 2009):
suppress any reference to USE_JAVA=	1.5+ (part1)
Original commitRevision:308600 
Monday, 1 Oct 2012
14:45 tabthorpe search for other commits by this committer
- Reassign to the heap at maintainer's request
Original commitRevision:305130 
Thursday, 21 Jul 2011
05:03 linimon search for other commits by this committer
Now that the Java 1.3 and Java 1.4 ports are deprecated and will expire soon,
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
Original commit
Friday, 6 Jun 2008
13:08 edwin search for other commits by this committer
Bump portrevision due to upgrade of devel/gettext.

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)
Original commit
Saturday, 19 May 2007
20:32 flz search for other commits by this committer
- Welcome X.org 7.2 \o/.
- Set X11BASE to ${LOCALBASE} for recent ${OSVERSION}.
- Bump PORTREVISION for ports intalling files in ${X11BASE}.
Original commit
Monday, 13 Feb 2006
09:42 hq search for other commits by this committer
Jalview is a multiple alignment editor written in Java. It is used widely in a
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>
Original commit

Number of commits found: 21