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Port details
jalview Viewer and editor for multiple sequence alignments
2.11.1.4 biology on this many watch lists=0 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout 2.11.1.4Version of this port present on the latest quarterly branch.
Maintainer: yuri@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2006-02-13 09:43:01
Last Update: 2021-09-30 21:23:30
Commit Hash: 620968a
Also Listed In: java
License: GPLv3
Description:
SVNWeb : git : Homepage
pkg-plist: as obtained via: make generate-plist
Expand this list (5 items)
Collapse this list.
  1. bin/jalview
  2. /usr/local/share/java/jalview/jalview.jar
  3. /usr/local/share/licenses/jalview-2.11.1.4/catalog.mk
  4. /usr/local/share/licenses/jalview-2.11.1.4/LICENSE
  5. /usr/local/share/licenses/jalview-2.11.1.4/GPLv3
Collapse this list.
Dependency lines:
  • jalview>0:biology/jalview
To install the port:
cd /usr/ports/biology/jalview/ && make install clean
To add the package, run one of these commands:
  • pkg install biology/jalview
  • pkg install jalview
PKGNAME: jalview
Flavors: there is no flavor information for this port.
distinfo:
Packages (timestamps in pop-ups are UTC):
jalview
ABIlatestquarterly
FreeBSD:11:aarch642.07_22.07_3
FreeBSD:11:amd64--
FreeBSD:11:armv62.07_22.07_3
FreeBSD:11:i386--
FreeBSD:11:mips--
FreeBSD:11:mips64--
FreeBSD:12:aarch642.07_22.11.1.4
FreeBSD:12:amd642.11.1.42.11.1.4
FreeBSD:12:armv62.07_2-
FreeBSD:12:armv72.07_2-
FreeBSD:12:i3862.11.1.42.11.1.4
FreeBSD:12:mips--
FreeBSD:12:mips64--
FreeBSD:12:powerpc64-2.07_3
FreeBSD:13:aarch642.07_32.11.1.4
FreeBSD:13:amd642.11.1.42.11.1.4
FreeBSD:13:armv6--
FreeBSD:13:armv7--
FreeBSD:13:i3862.11.1.42.11.1.4
FreeBSD:13:mips--
FreeBSD:13:mips64--
FreeBSD:13:powerpc64-2.11.1.4
FreeBSD:14:aarch64--
FreeBSD:14:amd64--
FreeBSD:14:armv6--
FreeBSD:14:armv7--
FreeBSD:14:i3862.11.1.4-
FreeBSD:14:mips--
FreeBSD:14:mips64--
FreeBSD:14:powerpc642.07_3-
 

Dependencies
NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
Build dependencies:
  1. gradle : devel/gradle6
  2. java : java/openjdk11
Runtime dependencies:
  1. java : java/openjdk11
There are no ports dependent upon this port

Configuration Options:
Options name:
FreshPorts was unable to extract/find any pkg message
Master Sites:
Expand this list (1 items)
Collapse this list.
  1. https://www.jalview.org/source/
Collapse this list.

Number of commits found: 23

Commit History - (may be incomplete: see SVNWeb link above for full details)
DateByDescription
30 Sep 2021 21:23:30
 files touched by this commit commit hash:620968a43a5f9bb3fa98ab20f257a4c0d864caa7  2.11.1.4
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
27 Jun 2021 09:30:39
 files touched by this commit commit hash:389294d2b118284d007bf6a6df9b2530e4d6348a  2.11.1.4
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)
27 Jun 2021 01:51:07
 files touched by this commit commit hash:55044a2200a4c42b6b653349f0a65dfca3f96f36  2.11.1.4
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)
05 Jun 2021 18:53:07
 files touched by this commit commit hash:8b8c1272ea64f9db05d8b5cfed709881429df479  2.11.1.4
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
01 May 2021 17:55:55
 files touched by this commit commit hash:6707a3c942b51ab3e3cf110383e3119dfe2e49b0  2.11.1.4
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
25 Apr 2021 23:00:36
 files touched by this commit commit hash:af49fbec4f0f6453b4b3dfe522107ed2918ae8f7  2.11.1.4
Yuri Victorovich (yuri) search for other commits by this committer
biology/jalview: Update 2.07 -> 2.11.1.4

Take maintainership.
06 Apr 2021 14:31:13
 files touched by this commit commit hash:135fdeebb99c3569e42d8162b265e15d29bd937d  2.07_3
Mathieu Arnold (mat) search for other commits by this committer
all: Remove all other $FreeBSD keywords.
06 Apr 2021 14:31:07
 files touched by this commit commit hash:305f148f482daf30dcf728039d03d019f88344eb  2.07_3
Mathieu Arnold (mat) search for other commits by this committer
Remove # $FreeBSD$ from Makefiles.
26 Dec 2020 23:01:20
Original commit files touched by this commit Revision:559318  2.07_3
glewis search for other commits by this committer
Restrict to Java 8, since this doesn't compile with Java 11

PR:			251774
26 Nov 2019 21:46:13
Original commit files touched by this commit Revision:518482  2.07_3
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
19 May 2016 10:21:25
Original commit files touched by this commit Revision:415498  2.07_2
amdmi3 search for other commits by this committer
- Fix trailing whitespace in pkg-descrs, categories [a-f]*

Approved by:	portmgr blanket
22 May 2015 13:34:22
Original commit files touched by this commit Revision:387021  2.07_2
mat search for other commits by this committer
Remove $FreeBSD$ from patches files in categories a-j.

With hat:	portmgr
Sponsored by:	Absolight
20 Oct 2014 07:10:48
Original commit files touched by this commit Revision:371237  2.07_2
bapt search for other commits by this committer
Cleanup plist
21 Jan 2014 23:18:05
Original commit files touched by this commit Revision:340671  2.07_2
bapt search for other commits by this committer
Fix properties on pkg-plist
20 Jan 2014 23:10:11
Original commit files touched by this commit Revision:340487  2.07_2
bapt search for other commits by this committer
Support stage
20 Sep 2013 15:55:44
Original commit files touched by this commit Revision:327709  2.07_2
bapt search for other commits by this committer
Add NO_STAGE all over the place in preparation for the staging support (cat:
biology)
10 Dec 2012 11:25:28
Original commit files touched by this commit Revision:308600  2.07_2
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)
01 Oct 2012 14:45:17
Original commit files touched by this commit Revision:305130  2.07_2
tabthorpe search for other commits by this committer
- Reassign to the heap at maintainer's request
21 Jul 2011 05:03:02
Original commit files touched by this commit   2.07_2
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
19 Mar 2011 12:38:54
Original commit files touched by this commit   2.07_2
miwi search for other commits by this committer
- Get Rid MD5 support
06 Jun 2008 13:08:29
Original commit files touched by this commit   2.07_2
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)
19 May 2007 20:32:57
Original commit files touched by this commit   2.07_1
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}.
13 Feb 2006 09:42:13
Original commit files touched by this commit   2.07
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>

Number of commits found: 23