aboutsummaryrefslogtreecommitdiff
path: root/biology/seaview
Commit message (Collapse)AuthorAgeFilesLines
* 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
* biology/seaview: Update version 5.0.4=>5.0.5Muhammad Moinur Rahman2021-12-063-77/+4
| | | | Relnotes: http://doua.prabi.fr/software/seaview_data/CHANGES
* biology/seaview: in preparation to FLTK update, unbreak the portAlexey Dokuchaev2021-08-142-3/+74
| | | | | | Ensure there is only one variable definition per each object, as the C (and C++) standards mandated for years and is now enforced by modern toolchains.
* Remove # $FreeBSD$ from Makefiles.Mathieu Arnold2021-04-061-1/+0
|
* Mark BROKEN in 13/14 (via latest llvm update).Mark Linimon2021-02-171-0/+3
| | | | Notes: svn path=/head/; revision=565807
* biology/seaview: Update version 5.0.3=>5.0.4Muhammad Moinur Rahman2020-06-222-4/+4
| | | | | | | Relnotes: http://doua.prabi.fr/software/seaview_data/CHANGES Notes: svn path=/head/; revision=539893
* biology/seaview: Update version 5.0.2=>5.0.3Muhammad Moinur Rahman2020-06-142-4/+4
| | | | | | | Relnotes: http://doua.prabi.fr/software/seaview_data/CHANGES Notes: svn path=/head/; revision=538720
* biology/seaview: Update version 5.0=>5.0.2Muhammad Moinur Rahman2020-03-222-4/+4
| | | | | | | Relnotes: http://doua.prabi.fr/software/seaview Notes: svn path=/head/; revision=528926
* biology/seaview: Update version 4.7=>5.0Muhammad Moinur Rahman2020-02-055-69/+4
| | | | | | | Relnotes:http://doua.prabi.fr/software/seaview Notes: svn path=/head/; revision=525314
* Add USES=xorg USES=gl, ports categories bNiclas Zeising2019-11-041-1/+1
| | | | | | | | Add USES=xorg, USES=gl and in a few cases USES=gnome to ports in categories starting with 'b'. Notes: svn path=/head/; revision=516742
* biology/seaview: Fix build with Clang 6Tobias Kortkamp2018-09-083-0/+65
| | | | | | | | | | | | | | | seaview.cxx:3352:24: error: invalid suffix on literal; C++11 requires a space between literal and identifier [-Wreserved-user-defined-literal] strcat(suggested, "."PDF_OR_PS_EXT); ^ http://beefy12.nyi.freebsd.org/data/head-amd64-default/p479076_s338486/logs/errors/seaview-4.7,1.log PR: 230881 Submitted by: tobik Approved by: bofh (maintainer timeout, 2 weeks) Notes: svn path=/head/; revision=479235
* biology/seaview: Updatye version 4.6.5=>4.7Muhammad Moinur Rahman2018-07-222-4/+4
| | | | | | | Relnotes: http://doua.prabi.fr/software/seaview_data/CHANGES Notes: svn path=/head/; revision=475082
* biology/seaview: Update version 4.6.3=>4.6.5Muhammad Moinur Rahman2018-04-242-6/+8
| | | | | | | - Pet portlint Notes: svn path=/head/; revision=468198
* biology/seaview: Update version 4.6.2=>4.6.3Muhammad Moinur Rahman2018-01-053-7/+8
| | | | | | | | | - Added pkg-plist to pet portlint Relnotes: http://doua.prabi.fr/software/seaview_data/CHANGES Notes: svn path=/head/; revision=458157
* biology/seaview: Update version 4.6.1=>4.6.2Muhammad Moinur Rahman2017-07-212-4/+4
| | | | Notes: svn path=/head/; revision=446346
* biology/seaview: Update version 4.6=>4.6.1Muhammad Moinur Rahman2017-04-112-4/+5
| | | | | | | - Add PORTSCOUT to ignore non-existent 4.6.1.3 version Notes: svn path=/head/; revision=438306
* biology/seaview: Update version 4.5.4.8=>4.6Muhammad Moinur Rahman2016-06-102-7/+4
| | | | | | | - UNBREAK Notes: svn path=/head/; revision=416671
* Deprecate ports broken for more than 6 monthsAntoine Brodin2016-06-031-0/+2
| | | | Notes: svn path=/head/; revision=416324
* Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c.Mathieu Arnold2016-04-011-2/+2
| | | | | | | | With hat: portmgr Sponsored by: Absolight Notes: svn path=/head/; revision=412344
* biology/seaview: Broken, Does not fetch (checksum mismatch)John Marino2015-11-021-0/+2
| | | | Notes: svn path=/head/; revision=400638
* biology/seaview: Update version 4.5.4.7=>4.5.4.8Muhammad Moinur Rahman2015-10-202-3/+3
| | | | Notes: svn path=/head/; revision=399820
* biology/seaview: Update version 4.5.4.6=>4.5.4.7Muhammad Moinur Rahman2015-10-012-4/+3
| | | | Notes: svn path=/head/; revision=398266
* biology/seaview: Update version 4.5.4.4=>4.5.4.6Muhammad Moinur Rahman2015-09-152-5/+5
| | | | Notes: svn path=/head/; revision=396964
* biology/seaview: Update version 4.5.4=>4.5.4.4Muhammad Moinur Rahman2015-05-222-3/+4
| | | | Notes: svn path=/head/; revision=387019
* biology/seaview: Unbreak -- it fetches fineJohn Marino2015-04-111-4/+1
| | | | | | | | | | | The second MASTER_SITES entry worked fine, so this must have been a transient fetch problem. I removed the first entry which is still failing though. Approved by: blanket Notes: svn path=/head/; revision=383812
* Mark as broken unfetchable portsBaptiste Daroussin2015-04-051-0/+2
| | | | Notes: svn path=/head/; revision=383309
* biology/seaview: Update version 4.5.3.4=>4.5.4Muhammad Moinur Rahman2015-03-243-41/+5
| | | | | | | - Remove dependency for libpdf as removed by upstream Notes: svn path=/head/; revision=382078
* biology/seaview: UNBREAKMuhammad Moinur Rahman2015-03-163-15/+38
| | | | | | | | | | | | | - Update version 4.5.2=>4.5.3.4 - Add LICENSE (GPLv3) - Remove PDFLIBS as OPTIONS as it is no loner an optional requirement PR: 198602 Submitted by: pi Approved by: bapt marino (implicit) Notes: svn path=/head/; revision=381381
* Mark BROKEN: Fails to link, tries to use internal fltk symbolsAntoine Brodin2015-02-211-0/+2
| | | | | | | | | | | | | | c++ -o seaview seaview.o custom.o use_mase_files.o regions.o load_seq.o align.o xfmatpt.o comlines.o resource.o nexus.o viewasprots.o racnuc_fetch.o concatenate.o statistics.o trees.o treedraw.o addbootstrap.o least_squares_brl.o pseudoterminal.o unrooted.o pdf_or_ps.o svg.o threads.o Fl_Native_File_Chooser_FLTK.o raa_acnuc.o parser.o md5.o zsockr.o misc_acnuc.o dnapars.o protpars.o seq.o phylip.o lwl.o bionj.o phyml_util.o \ -L/usr/local/lib -lfltk_images -lfltk \ -lXft -lXext -lfontconfig -ljpeg -lpng -lXinerama -L/usr/local/lib -lpdf \ -lX11 -lm -lz -pthread seaview.o: In function `clipboard_contains_alignment(char const*)': seaview.cxx:(.text+0x1c14): undefined reference to `fl_selection_buffer' Reported by: pkg-fallout Notes: svn path=/head/; revision=379482
* Change my non-FreeBSD MAINTAINER mail to bofh@Muhammad Moinur Rahman2014-12-241-1/+1
| | | | | | | Approved by: bapt Notes: svn path=/head/; revision=375378
* Cleanup plistBaptiste Daroussin2014-12-201-1/+0
| | | | Notes: svn path=/head/; revision=375014
* Update the default version of GCC in the Ports Collection from GCC 4.7.4Gerald Pfeifer2014-09-101-0/+1
| | | | | | | | | | | | | to GCC 4.8.3. Part II, Bump PORTREVISIONs. PR: 192025 Tested by: antoine (-exp runs) Approved by: portmgr (implicit) Notes: svn path=/head/; revision=367888
* - Update to 4.5.2Martin Wilke2014-06-042-5/+5
| | | | | | | | | - Pass maintainership to submitter PR: 190564 Notes: svn path=/head/; revision=356437
* - Update to 4.5.1Martin Wilke2014-05-213-8/+13
| | | | | | | | PR: 187975 Submitted by: Ports Fury Notes: svn path=/head/; revision=354710
* - Stage supportMartin Wilke2014-02-272-21/+18
| | | | | | | | | | - Update to version 4.4.3 PR: 187041 Submitted by: ports fury Notes: svn path=/head/; revision=346262
* In preparation for making libtool generate libraries with a sane name, fix allBaptiste Daroussin2013-12-111-2/+2
| | | | | | | LIB_DEPENDS in biology Notes: svn path=/head/; revision=336171
* 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
* - Remove MAKE_JOBS_SAFE variableAlex Kozlov2013-08-141-1/+0
| | | | | | | Approved by: portmgr (bdrewery) Notes: svn path=/head/; revision=324744
* - Update to 4.4.2Martin Wilke2013-07-152-3/+3
| | | | | | | | PR: 180515 Submitted by: Ports Fury Notes: svn path=/head/; revision=323044
* - Update to 4.4.1Martin Wilke2013-03-262-25/+17
| | | | | | | | PR: 177257 Submitted by: Ports Fury Notes: svn path=/head/; revision=315253
* Bump PORTREVISION after DESKTOP_ENTRIES updateMax Brazhnikov2013-01-231-0/+1
| | | | Notes: svn path=/head/; revision=310871
* - Update DESKTOP_ENTRIES:Max Brazhnikov2013-01-071-2/+2
| | | | | | | | | | | | | * rephrase Comment field or use port ${COMMENT} if appropriate * adjust Icon field according to the Desktop Entry Specification * update Categories field: remove deprecated category Application; set main category, if missing - Remove indefinite article and/or rephrase COMMENT - Trim Makefile header - Other minor changes Notes: svn path=/head/; revision=310020
* - Update to version 4.4.0Pawel Pekala2012-10-305-76/+56
| | | | | | | | | | | | | | | | | - Mark MAKE_JOBS_SAFE - Make dependency on print/pdflib optional - Switch to PLIST_FILES While here: - Add missing deps - Add desktop entry PR: ports/172498 Submitted by: KATO Tsuguru <tkato432@yahoo.com> Feature safe: yes Notes: svn path=/head/; revision=306709
* - Reassign to the heap at maintainer's requestThomas Abthorpe2012-10-011-7/+2
| | | | Notes: svn path=/head/; revision=305130
* - update png to 1.5.10Dirk Meyer2012-06-011-1/+1
| | | | Notes: svn path=/head/; revision=297915
* Chase pdflib.so version and bump PORTREVISION accordingly.Alex Dupre2012-01-101-2/+2
| | | | Notes: svn path=/head/; revision=288888
* - unbreakPietro Cerutti2011-11-172-2/+29
| | | | | | | Feature safe: yes Notes: svn path=/head/; revision=285957
* - Mark BROKEN: does not compile with new fltkPav Lucistnik2011-11-041-0/+2
| | | | | | | Reported by: pointyhat Notes: svn path=/head/; revision=285056
generated by cgit v1.2.3 (git 2.25.1) at 2024-11-19 02:09:48 +0000