non port: biology/jalview/Makefile |
Number of commits found: 21 |
Sunday, 18 Jun 2023
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09:58 Yuri Victorovich (yuri)
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
4301fdb |
Wednesday, 12 Oct 2022
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06:58 Yuri Victorovich (yuri)
biology/jalview: Update 2.11.1.4 -> 2.11.2.5
3a7900f |
Wednesday, 7 Sep 2022
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21:10 Stefan Eßer (se)
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)
b7f0544 |
Wednesday, 20 Jul 2022
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14:20 Tobias C. Berner (tcberner)
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
37526bb |
Thursday, 30 Sep 2021
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21:23 Rene Ladan (rene)
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
620968a |
Sunday, 27 Jun 2021
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09:30 Guangyuan Yang (ygy)
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)
389294d |
01:51 Guangyuan Yang (ygy)
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)
55044a2 |
Saturday, 5 Jun 2021
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18:53 Yuri Victorovich (yuri)
biology/jalview: Broken on 11
Also fix number of lines in pkg-descr, and replace space with tab.
Reported by: fallout
8b8c127 |
Saturday, 1 May 2021
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17:55 Tobias Kortkamp (tobik)
Clean up some things
- Fix typos
- Remove duplicate variables
- Remove nop variables
- Clean up commented PORTREVISION
- Add missing USES
Reported by: portscan
6707a3c |
Sunday, 25 Apr 2021
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23:00 Yuri Victorovich (yuri)
biology/jalview: Update 2.07 -> 2.11.1.4
Take maintainership.
af49fbe |
Tuesday, 6 Apr 2021
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14:31 Mathieu Arnold (mat)
Remove # $FreeBSD$ from Makefiles.
305f148 |
Saturday, 26 Dec 2020
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23:01 glewis
Restrict to Java 8, since this doesn't compile with Java 11
PR: 251774
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Tuesday, 26 Nov 2019
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21:46 jkim
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
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Monday, 20 Jan 2014
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23:10 bapt
Support stage
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Friday, 20 Sep 2013
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15:55 bapt
Add NO_STAGE all over the place in preparation for the staging support (cat:
biology)
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Monday, 10 Dec 2012
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11:25 bapt
Decommissioning java 1.5 (EOLed since October 2009):
suppress any reference to USE_JAVA= 1.5+ (part1)
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Monday, 1 Oct 2012
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14:45 tabthorpe
- Reassign to the heap at maintainer's request
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Thursday, 21 Jul 2011
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05:03 linimon
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
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Friday, 6 Jun 2008
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13:08 edwin
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)
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Saturday, 19 May 2007
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20:32 flz
- Welcome X.org 7.2 \o/.
- Set X11BASE to ${LOCALBASE} for recent ${OSVERSION}.
- Bump PORTREVISION for ports intalling files in ${X11BASE}.
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Monday, 13 Feb 2006
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09:42 hq
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>
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Number of commits found: 21 |