summaryrefslogtreecommitdiff
path: root/biology/molden (follow)
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/molden: Update 6.7 -> 7.1Yuri Victorovich2022-07-233-11/+18
| | | | | PR: 265245 Approved by: jmd@ (maintainer)
* 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/molden: Unbreak build; Correct WWWYuri Victorovich2022-07-155-1/+86
| | | | | | | | | | For unbreak: - pass FFLAGS to the build - fix several errors in C - remove the failing 'ex' command from makefile Reported by: fallout Approved by: portmgr (unbreak)
* *: Clean up some thingsTobias Kortkamp2022-01-171-1/+1
| | | | | | | - Fix typos - Fix overwritten variables Reported by: portscan
* biology/molden: update to 6.7Johannes M Dieterich2022-01-056-890/+48
| | | | | PR: 238858 Reported by: yuri@
* graphics/mesa-libs: Bump reverse deps for libglvndKevin Bowling2021-06-221-1/+1
| | | | | | | | | | Per discussion with bapt on helping pkg handle the changing of these deps and avoiding impossible upgrade senarios. PR: 246767 Reviewed by: manu, bapt Approved by: x11 Differential Revision: https://reviews.freebsd.org/D30824
* Deorbit RESTRICTED && NO_CDROM, part one.Mathieu Arnold2021-05-061-2/+1
| | | | | | | | For ports that already use the licenses framwork, merge the content of RESTRICTED/NO_CDROM/LEGAL* entries into LICENSEs. Approved by: rene Differential Revision: https://reviews.freebsd.org/D30010
* Remove # $FreeBSD$ from Makefiles.Mathieu Arnold2021-04-061-1/+0
|
* biology/molden: Fix build with gfortran10Yuri Victorovich2021-03-291-1/+9
| | | | Notes: svn path=/head/; revision=569522
* 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
* Bump PORTREVISION for ports depending on the canonical version of GCCGerald Pfeifer2019-07-261-1/+1
| | | | | | | | | | | | | | | | | | as defined in Mk/bsd.default-versions.mk which has moved from GCC 8.3 to GCC 9.1 under most circumstances now after revision 507371. This includes ports - with USE_GCC=yes or USE_GCC=any, - with USES=fortran, - using Mk/bsd.octave.mk which in turn features USES=fortran, and - with USES=compiler specifying openmp, nestedfct, c11, c++0x, c++11-lang, c++11-lib, c++14-lang, c++17-lang, or gcc-c++11-lib plus, everything INDEX-11 shows with a dependency on lang/gcc9 now. PR: 238330 Notes: svn path=/head/; revision=507372
* Related to revision 499061 bump ports with USES=fortran to have themGerald Pfeifer2019-04-221-1/+1
| | | | | | | | | | benefit from the improved situation where libgcc_s is only used when absolutely necessary. Suggested by: tijl Notes: svn path=/head/; revision=499638
* Bump PORTREVISION for ports depending on the canonical version of GCCGerald Pfeifer2018-12-121-0/+1
| | | | | | | | | | | | | | | | | | defined via Mk/bsd.default-versions.mk which has moved from GCC 7.4 t GCC 8.2 under most circumstances. This includes ports - with USE_GCC=yes or USE_GCC=any, - with USES=fortran, - using Mk/bsd.octave.mk which in turn features USES=fortran, and - with USES=compiler specifying openmp, nestedfct, c11, c++0x, c++11-lang, c++11-lib, c++14-lang, c++17-lang, or gcc-c++11-lib plus, as a double check, everything INDEX-11 showed depending on lang/gcc7. PR: 231590 Notes: svn path=/head/; revision=487272
* biology/molden: update to 5.8.2Johannes M Dieterich2018-11-133-10/+45
| | | | | | | | | | Also add do-install-{option}-on targets and shadow ${MKDIR} commands. PR: 233060 Submitted by: yuri Notes: svn path=/head/; revision=484858
* biology/molden: Unbreak: fix the problem that it can't find libgcc_s.so from gccYuri Victorovich2018-11-071-1/+2
| | | | | | | | | | Add $(LDFLAGS) to makefile. While here, add USES=gl. Approved by: portmgr Notes: svn path=/head/; revision=484371
* Bump PORTREVISION for ports depending on the canonical version of GCCGerald Pfeifer2018-07-291-1/+1
| | | | | | | | | | | | | | | | | in the ports tree (via Mk/bsd.default-versions.mk and lang/gcc) which has now moved from GCC 6 to GCC 7 by default. This includes ports - featuring USE_GCC=yes or USE_GCC=any, - featuring USES=fortran, - using Mk/bsd.octave.mk which in turn features USES=fortran, and those - with USES=compiler specifying one of openmp, nestedfct, c11, c++0x, c++11-lib, c++11-lang, c++14-lang, c++17-lang, or gcc-c++11-lib. PR: 222542 Notes: svn path=/head/; revision=475857
* biology/molden: Unbreak by updating the MASTER_SITES URLYuri Victorovich2018-07-201-2/+1
| | | | | | | The upstream keeps changing the URL. Notes: svn path=/head/; revision=475001
* Mark BROKEN: unfetchaableAntoine Brodin2018-07-201-0/+1
| | | | | | | Reported by: pkg-fallout Notes: svn path=/head/; revision=474994
* biology/molden: Unbreak by updating the MASTER_SITES URLYuri Victorovich2018-07-131-2/+1
| | | | Notes: svn path=/head/; revision=474570
* Mark BROKEN: unfetchableAntoine Brodin2018-07-131-0/+1
| | | | | | | | Reported by: pkg-fallout MFH: 2018Q3 Notes: svn path=/head/; revision=474562
* biolog/molden: unbreak after at least two intransparent distfile updatesJohannes M Dieterich2018-05-202-6/+4
| | | | | | | | | Reviewed by: zeising (mentor) Approved by: zeising (mentor) Differential Revision: https://reviews.freebsd.org/D15333 Notes: svn path=/head/; revision=470488
* Mark BROKEN: checksum and size mismatchAntoine Brodin2018-05-071-0/+2
| | | | | | | | Reported by: pkg-fallout MFH: 2018Q2 Notes: svn path=/head/; revision=469265
* Bump PORTREVISIONs of all users of math/mpc that we just updated toGerald Pfeifer2018-03-101-1/+1
| | | | | | | version 1.1.0 (via revision 464079). Notes: svn path=/head/; revision=464084
* biology/molden: chase another intransparent upstream distfile upgrade.Johannes M Dieterich2017-11-012-4/+4
| | | | | | | | | Reviewed by: swills (mentor), mat Approved by: swills (mentor) Differential Revision: https://reviews.freebsd.org/D12829 Notes: svn path=/head/; revision=453261
* biology/molden: unbreak by chasing latest intransparent distfile update.Johannes M Dieterich2017-09-282-4/+4
| | | | | | | | | Reviewed by: swills (mentor) Approved by: swills (mentor) Differential Revision: https://reviews.freebsd.org/D12521 Notes: svn path=/head/; revision=450799
* Bump PORTREVISION for ports depending on the canonical version of GCCGerald Pfeifer2017-09-101-1/+1
| | | | | | | | | | | | | | | | | (via Mk/bsd.default-versions.mk and lang/gcc) which has moved from GCC 5.4 to GCC 6.4 under most circumstances. This includes ports - with USE_GCC=yes or USE_GCC=any, - with USES=fortran, - using Mk/bsd.octave.mk which in turn features USES=fortran, and - with USES=compiler specifying openmp, nestedfct, c++11-lib, c++11-lang, c++14-lang, c++0x, c11, or gcc-c++11-lib. PR: 219275 Notes: svn path=/head/; revision=449591
* Chase next distfile update. Upstream contacted whether we would be allowed ↵Johannes M Dieterich2017-07-132-4/+4
| | | | | | | | | | | to host a distfile copy. Reviewed by: swills (mentor) Approved by: swills (mentor) Differential Revision: https://reviews.freebsd.org/D11586 Notes: svn path=/head/; revision=445717
* biology/molden: Unbreak by chasing their latest opaque update to the ↵Johannes M Dieterich2017-07-122-7/+5
| | | | | | | | | | | distribution. Reviewed by: swills (mentor) Approved by: swills (mentor) Differential Revision: https://reviews.freebsd.org/D11338 Notes: svn path=/head/; revision=445570
* Mark BROKEN.Mathieu Arnold2017-06-221-0/+2
| | | | | | | | | | | => Attempting to fetch ftp://ftp.cmbi.ru.nl/pub/molgraph/molden/molden5.7.tar.gz fetch: ftp://ftp.cmbi.ru.nl/pub/molgraph/molden/molden5.7.tar.gz: size mismatch: expected 5339411, actual 5339467 => Couldn't fetch it - please try to retrieve this Sponsored by: Absolight Notes: svn path=/head/; revision=444104
* Previous commit unbroke the port.Mark Linimon2017-06-031-2/+0
| | | | | | | Reported by: xmj Notes: svn path=/head/; revision=442480
* biology/molden: Chase recent upstream change of molden distfile.Johannes M Dieterich2017-05-242-4/+4
| | | | | | | | | Reviewed by: swills (mentor) Approved by: swills (mentor) Differential Revision: https://reviews.freebsd.org/D10864 Notes: svn path=/head/; revision=441560
* 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
* Mark BROKEN: checksum and size mismatchAntoine Brodin2017-05-191-0/+2
| | | | | | | Reported by: pkg-fallout Notes: svn path=/head/; revision=441258
* Bump PORTREVISIONs for ports depending on the canonical version of GCC andGerald Pfeifer2017-04-011-1/+1
| | | | | | | | | | | | | | | | | lang/gcc which have moved from GCC 4.9.4 to GCC 5.4 (at least under some circumstances such as versions of FreeBSD or platforms). This includes ports - with USE_GCC=yes or USE_GCC=any, - with USES=fortran, - using using Mk/bsd.octave.mk which in turn has USES=fortran, and - with USES=compiler specifying openmp, nestedfct, c++11-lib, c++14-lang, c++11-lang, c++0x, c11, or gcc-c++11-lib. PR: 216707 Notes: svn path=/head/; revision=437439
* biology/molden: Unbreak port, regenerate checksums, increment PORTREVISION.Johannes M Dieterich2017-02-112-7/+5
| | | | | | | | | Reviewed by: swills (mentor), pi (former maintainer) Approved by: swills (mentor), pi (former maintainer) Differential Revision: https://reviews.freebsd.org/D9501 Notes: svn path=/head/; revision=433832
* - Mark BROKEN: does not fetch, size/checksum mismatchDmitry Marakasov2017-02-071-0/+2
| | | | | | | Approved by: portmgr blanket Notes: svn path=/head/; revision=433554
* Bump PORTREVISIONS for ports depending on the canonical version of GCC andGerald Pfeifer2016-12-071-1/+1
| | | | | | | | | | | | | | | | | | lang/gcc which have moved from GCC 4.8.5 to GCC 4.9.4 (at least under some circumstances such as versions of FreeBSD or platforms), part II. The first part covered ports with USE_GCC=yes, USE_GCC=any, or one of gcc-c++11-lib, openmp, nestedfct, c++11-lib as well as c++14-lang, c++11-lang, c++0x, c11 requested via USES=compiler. This adds ports with USES=fortran and ports using Mk/bsd.octave.mk which in turn has USES=fortran. PR: 214965 Reported by: thierry Notes: svn path=/head/; revision=428057
* biology/molden: distfile was updated in xwin.cKurt Jaeger2016-12-032-4/+4
| | | | Notes: svn path=/head/; revision=427627
* biology/molden: add missing LICENSE_NAMEKurt Jaeger2016-11-101-1/+2
| | | | | | | Reported by: pkg-fallout Notes: svn path=/head/; revision=425830
* biology/molden: fix distinfo, set LICENSEKurt Jaeger2016-11-092-7/+11
| | | | | | | | | Submitted by: marino Reported by: Eduardo Lemos de Sa <eduardo.lemosdesa@gmail.com> MFH: 2016Q4 Notes: svn path=/head/; revision=425806
* Mark BROKEN: unfetchable, size mismatchAntoine Brodin2016-10-011-0/+1
| | | | | | | Reported by: pkg-fallout Notes: svn path=/head/; revision=423039
* biology/molden: 5.4 -> 5.7Kurt Jaeger2016-08-262-6/+4
| | | | | | | | | | | | | - Adds editable text fields that are longer than the visible string and introduces a new way of selecting a range of amino acids. - introduces interfaces to the open source packages openbabel and pharmer. Openbabel is used to create 2D images of the molecules in a .sdf file. It is also used to do 2D fingerprint searching. Pharmer is used to pharmacophore (3D) searching against indexed databases of .sdf files. Notes: svn path=/head/; revision=420890
* - Mark BROKEN: does not fetch (distfile was removed from ftp)Dmitry Marakasov2016-08-221-0/+2
| | | | | | | Approved by: portmgr blanket Notes: svn path=/head/; revision=420601
* - Fix trailing whitespace in pkg-descrs, categories [a-f]*Dmitry Marakasov2016-05-191-1/+1
| | | | | | | Approved by: portmgr blanket Notes: svn path=/head/; revision=415498
* biology/molden: updated distfile, take maintainerKurt Jaeger2016-01-202-4/+4
| | | | | | | | | - upstream distfile is moving target with same version number Submitted by: antoine Notes: svn path=/head/; revision=406795
* Mark BROKEN: checksum and size mismatchAntoine Brodin2016-01-201-0/+1
| | | | | | | Reported by: pkg-fallout Notes: svn path=/head/; revision=406791
* biology/molden: 5.0.7 -> 5.4Kurt Jaeger2016-01-185-192/+799
| | | | | | | | | | | | | | | | | Changes: - Missing hydrogens atoms of HETATM molecules (pdb files) are stored locally. - Pdb files can now be clipped. - Fixes missing residues. Introduces an alternative way of generating rotamers, without using z-matrices. This potentially a faster algorithm. - Supports Movie making through avconv/ffmpeg. - calculates the Electron Localization Function (ELF). - Updated code of ambfor/ambmd to speed up optimisations/MD of proteins solvated in water (Jan, 2014). PR: 204341 Notes: svn path=/head/; revision=406605
* 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
generated by cgit v1.2.3 (git 2.25.1) at 2024-08-18 16:59:37 +0000