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* graphics/tiff: Update to 4.6.0Tijl Coosemans2024-04-271-1/+1
| | | | | PR: 278577 Exp-run by: antoine
* */*: Update WWW to use HTTPS for sourceforge.net projectsRodrigo Osorio2023-11-011-1/+1
| | | | Homepage link is permanent redirected to its HTTPS counterpart
* */*: Bump jpeg-turbo users treewideDaniel Engberg2023-07-281-1/+1
| | | | New major version 3.0.0
* 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
* Remove # $FreeBSD$ from Makefiles.Mathieu Arnold2021-04-061-1/+0
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* Add USES=xorg USES=gl, ports categories bNiclas Zeising2019-11-041-1/+2
| | | | | | | | 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/protomol: Fix doubled USES overwriting the old valueTobias Kortkamp2018-08-251-3/+2
| | | | | | | - Make sure shebangfix is actually used Notes: svn path=/head/; revision=477997
* biology/protomol: Fix build with Clang 6Tobias Kortkamp2018-08-251-0/+1
| | | | | | | | | | | | | | | Report.cpp:208:12: error: invalid operands to binary expression ('std::ostream' (aka 'basic_ostream<char>') and 'const std::__1::ostream' (aka 'const basic_ostream<char>')) *myStream << a; ~~~~~~~~~ ^ ~ /usr/include/c++/v1/ostream:218:20: note: candidate function not viable: no known conversion from 'const std::__1::ostream' (aka 'const basic_ostream<char>') to 'const void *' for 1st argument; take the address of the argument with & basic_ostream& operator<<(const void* __p); ^ ... and so on ... http://beefy11.nyi.freebsd.org/data/head-i386-default/p477696_s338122/logs/errors/protomol-2.0.3_13.log Notes: svn path=/head/; revision=477996
* Revision bump of all ports with USE_GL after consolidation of mesa-libsMatthew Rezny2017-05-231-1/+1
| | | | | | | | Approved by: swills (mentor) Differential Revision: https://reviews.freebsd.org/D10845 Notes: svn path=/head/; revision=441503
* biology/protomol: Support build with C++11 (taken from dports)John Marino2016-12-185-0/+48
| | | | Notes: svn path=/head/; revision=428835
* 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
* Convert ports to use the options helpers in categories [abc]*, and minor fixes.Mathieu Arnold2015-08-191-6/+2
| | | | | | | | Sponsored by: Absolight Differential Revision: https://reviews.freebsd.org/D3412? Notes: svn path=/head/; revision=394778
* - Add LICENSEDmitry Marakasov2015-06-251-1/+12
| | | | | | | | | - Fix shebangs Approved by: porgmgr (bapt) Notes: svn path=/head/; revision=390543
* Convert to COPYTREE_SHAREBaptiste Daroussin2015-06-231-9/+6
| | | | | | | Use options helpers Notes: svn path=/head/; revision=390356
* Convert to USES=jpegAntoine Brodin2015-06-221-1/+1
| | | | Notes: svn path=/head/; revision=390310
* Cleanup DIST* variables.Mathieu Arnold2015-05-111-2/+1
| | | | | | | | | | | | | | When appropriate: - Try to use DISTVERSION{SUF,PRE}FIX - Replace PORTNAME-PORTVERSION by DISTNAME - Convert MASTER_SITES to use macros - Other light cleanup With hat: portmgr Sponsored by: Absolight Notes: svn path=/head/; revision=386097
* Bump portrevision after png updateBaptiste Daroussin2014-12-251-1/+1
| | | | Notes: svn path=/head/; revision=375598
* Change libpng15.so to libpng.so in LIB_DEPENDS to prepare the upgradeAntoine Brodin2014-12-251-1/+1
| | | | Notes: svn path=/head/; revision=375594
* Cleanup plistBaptiste Daroussin2014-10-201-14/+0
| | | | Notes: svn path=/head/; revision=371237
* Update the default version of GCC in the Ports Collection from GCC 4.7.4Gerald Pfeifer2014-09-101-1/+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
* - StagifyDmitry Marakasov2014-08-258-3/+124
| | | | | | | - Fix build Notes: svn path=/head/; revision=366104
* Reset maintainership for ports not staged with no pending PRBaptiste Daroussin2014-07-231-1/+1
| | | | | | | With hat: portmgr Notes: svn path=/head/; revision=362705
* The FreeBSD x11@ and graphics team proudly presentsNiclas Zeising2014-04-161-1/+1
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | a zeising, kwm production, with help from dumbbell, bdrewery: NEW XORG ON FREEBSD 9-STABLE AND 10-STABLE This update switches over to use the new xorg stack by default on FreeBSD 9 and 10 stable, on osversions where vt(9) is available. It is still possible to use the old stack by specifying WITHOUT_NEW_XORG in /etc/make.conf . FreeBSD 8-STABLE and released versions of FreeBSD still use the old version. A package repository with binary packages for new xorg will be available soon. This patch also contains updates of libxcb and related ports, pixman, as well as some drivers and utilities. Bump portrevisions for xf86-* ports, as well as virtualbox-ose-additions due to xserver version change. Apart from these updates, the way shared libraries are handled has been changed for all xorg ports, as well as libxml2 and freetype, which means ltverhack is gone and as a consequence shared libraries have been bumped. The plan is that this change will make library bumps less likely in the future. All affected ports have had their portrevisions bumped as a consequence of this. Fix some issues where WITH_NEW_XORG weren't detected properly on CURRENT. Update instructions, hardware support, and more notes can be found on https://wiki.freebsd.org/Graphics Thanks to: all testers, bdrewery and the FreeBSD x11@ team exp-run by: bdrewery [1] PR: ports/187602 [1] Approved by: portmgr (bdrewery), core (jhb) Notes: svn path=/head/; revision=351411
* Reduce over inclusion of bsd.port.mkBaptiste Daroussin2014-01-151-2/+1
| | | | Notes: svn path=/head/; revision=339845
* In preparation for making libtool generate libraries with a sane name, fix allBaptiste Daroussin2013-12-111-3/+3
| | | | | | | 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
* - adoption of optionsNGJason Helfman2013-03-182-130/+129
| | | | | | | | | | | - trim historical header - fix mixture of DOCS/EXAMPLES -> EXAMPLES - add shared description for GLUT to bodm Approved by: portmgr (miwi) Notes: svn path=/head/; revision=314531
* Switch from libglut to freeglut and retire libglut. Libglut hasn't beenKoop Mast2012-08-041-1/+2
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | developed in years and has been dropped from the MESA 8.0 distribution. Freeglut is a rewrite of glut and is actively developed and is used by many linux distributions instead of libglut. Bump all ports that directly depend on libglut because of the shlib version change. There are some extra items in this patch. *) Because freeglut doesn't have the same dependancies as libglut, some ports need extra dependencies added to USE_XORG to make them build. *) Mark graphics/f90gl broken, f90gl depends on a header that is only shipped with libglut. *) Remove option for libglut/freeglut selection in games/cake, only freeglut remains now. *) While here fix a png related build issue games/vegastrike. Thanks to miwi for running the exp-run. Approved by: portmgr (miwi) Collaboration with: zeising@ Obtained from: xorg-dev staging area. Notes: svn path=/head/; revision=302037
* - update png to 1.5.10Dirk Meyer2012-06-011-2/+2
| | | | Notes: svn path=/head/; revision=297915
* - Add LDFLAGS to CONFIGURE_ENV and MAKE_ENV (as it was done with LDFLAGS)Dmitry Marakasov2011-09-231-2/+0
| | | | | | | | | | | | - Fix all ports that add {CPP,LD}FLAGS to *_ENV to modify flags instead PR: 157936 Submitted by: myself Exp-runs by: pav Approved by: pav Notes: svn path=/head/; revision=282282
* - Get Rid MD5 supportMartin Wilke2011-03-191-1/+0
| | | | Notes: svn path=/head/; revision=271305
* - update to 1.4.1Dirk Meyer2010-03-281-2/+2
| | | | | | | | Reviewed by: exp8 run on pointyhat Supported by: miwi Notes: svn path=/head/; revision=251605
* - update to jpeg-8Dirk Meyer2010-02-051-2/+2
| | | | Notes: svn path=/head/; revision=249285
* - Switch SourceForge ports to the new File Release System: categories ↵Dmitry Marakasov2009-08-221-2/+1
| | | | | | | starting with B,C Notes: svn path=/head/; revision=240067
* - update to jpeg7Dirk Meyer2009-07-181-2/+2
| | | | | | | Tested by: pav on pointyhat Notes: svn path=/head/; revision=238018
* - Update X.org ports to 7.4+ (few ports are more recent than the katamari).Florent Thoumie2009-01-231-1/+1
| | | | | | | | | | | - Bump PORTREVISION for all ports depending on libglut since the shlib version number went from 4 to 3. - Bump PORTREVISION for all ports depending on libXaw as libXaw.so.8 isn't installed anymore. - Couple of ports fixes (mostly missing xorg components added to USE_XORG). Notes: svn path=/head/; revision=226727
* - Remove USE_GCC where it can be satisfied with base compiler on followingPav Lucistnik2008-07-251-1/+0
| | | | | | | FreeBSD versions: 5.3 and up, 6.x, 7.x, 8-CURRENT Notes: svn path=/head/; revision=217485
* - Remove unneeded dependency from gtk12/gtk20 [1]Martin Wilke2008-04-191-2/+2
| | | | | | | | | | | | | | | | | | - Remove USE_XLIB/USE_X_PREFIX/USE_XPM in favor of USE_XORG - Remove X11BASE support in favor of LOCALBASE or PREFIX - Use USE_LDCONFIG instead of INSTALLS_SHLIB - Remove unneeded USE_GCC 3.4+ Thanks to all Helpers: Dmitry Marakasov, Chess Griffin, beech@, dinoex, rafan, gahr, ehaupt, nox, itetcu, flz, pav PR: 116263 Tested on: pointyhat Approved by: portmgr (pav) Notes: svn path=/head/; revision=211584
* - Fix build with GCC 4.2Pietro Cerutti2008-03-282-5/+18
| | | | | | | Approved by: miwi (mentor) Notes: svn path=/head/; revision=210034
* - Remove USE_XLIB/USE_X_PREFIX/USE_XPM in favor of USE_XORGMartin Wilke2008-03-251-2/+1
| | | | | | | | | - Bump PORTREVISION Approved by: portmgr (xorg cleanup) Notes: svn path=/head/; revision=209811
* Mark as broken with gcc4.2.Mark Linimon2007-10-021-0/+4
| | | | Notes: svn path=/head/; revision=200622
* - 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
* Add protomol 2.0.3, OO, component based, framework for molecularEmanuel Haupt2006-05-054-0/+200
dynamics (MD) simulations. PR: 95123 Submitted by: Sangwoo Shim <sangwoos@gmail.com> Notes: svn path=/head/; revision=161442