1.9.4_3scienceΣ=1 1.9.4_2Version of this port present on the latest quarterly branch.
IGNORE: license restrictions require manual fetching of the distribution source. Please visit http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD with a browser. You will be required to register, log in, and accept the University of Illinois agreement before you can download the vmd-1.9.4a57.src.tar.gz source. Place this distfile in /usr/ports/distfiles and try again.
There is no maintainer for this port.
Any concerns regarding this port should be directed to the FreeBSD Ports mailing list via ports@FreeBSD.org
VMD (Visual Molecular Dynamics) is a molecular visualization program for
displaying, animating, and analyzing large biomolecular systems. It
utilizes 3D graphics and built-in scripting (Tcl and Python) for
interactive exploration.
Key features include:
- Visualization of molecular dynamics simulations.
- Support for over 60 molecular file formats and data types.
- Various rendering styles (licorice, ribbons, van der Waals spheres).
- High-quality rendering, animation, and stereo display.
- Integrated analysis tools and custom scripting for advanced analysis.
- GPU acceleration and no inherent limits on molecular size.
- Cross-platform availability (Windows, macOS, and Linux).
Remove WWW entries moved into port Makefiles
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 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.
(Only the first 15 lines of the commit message are shown above )
graphics/mesa-libs: Bump reverse deps for libglvnd
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
Add USES=xorg USES=gl, ports categories s
Add USES=xorg and USES=gl to ports in categories starting with 's'
While here, try to sprinkle other USES (mostly gnome and sdl) as needed.
Bump PORTREVISION for ports depending on the canonical version of GCC
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
Bump PORTREVISION for ports depending on the canonical version of GCC
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
science/vmd: License auto-accept -> no-auto-accept
VMD license requires specific acknowledgement if VMD is used for published
results, therefore no auto-accept.
science/vmd: Add RESTRICTED clause.
This software comes from the University of Illinois, same as science/namd,
and is for non-commercial use only.
Also add it to ports/LEGAL.
Approved by: portmgr blanket
science/vmd: various fixes
- fix spelling of VMD license [1]
- use USES=tcl,tk instead of direct dependency
- patch vmd to support (tcl|tk)86
- fix shebang for tcl [1]
- fix detection of netcdf
- add sqlite as a dependency (for dmsplugin) [1]
- add expact as a dependency (for hoomdplugin)
- rework configuration:
- explicitly list required components (CONFIGURE_ARGS)
- call configure directly (instead of via gmake(1))
- patch configure to accept TCLLDFLAGS and TKLDFLAGS
- pass PREFIX as an environment variable instead of using sed(1)
- patch Make-arch to accept environment TCLLDFLAGS and NETCDFLDFLAGS
- add support for parallel building (except for building plugins)
- bump PORTREVISION
PR: 219642
Reported by: Yuri Victorovich <yuri@rawbw.com>
Revision bump of all ports with USE_GL after consolidation of mesa-libs
Approved by: swills (mentor)
Differential Revision: https://reviews.freebsd.org/D10845
science/vmd: update to 1.9.3
- update MASTER_SITES to use upstream stride (the old - repackages - sources
were no longer working).
- take maintainership: although I don't use the software I am happy to respond
to PR's and check for updates periodically,
- add license information for each source:
- vmd: custom license that requires the user to explicitly download (and
accept the license before downloading). Mark the license as
auto-accept here as the present of the DISTFILE will indicate that
the license has been accepted
- tachyon: standard 3-clause BSD license :-)
- stride: almost BSD license, except only for academic use (i.e.
non-commersial) and a requirement to report bugs to the author.
Add a plain text copy of the license file to the port.
- add missing dependencies: gl, x11
- fix detection of python.
- simplify configure patch.
- update pkg-plist for changes in plugin versions.
Bump PORTREVISIONS for ports depending on the canonical version of GCC and
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).
In particular that is 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.
science/vmd: Unbreak on F10+
This patch removes the hardcoded "gcc" so that it works with USE_GCC
variable. There is a slightly newer version of vmd available, so a
version upgrade may soon follow.
PR: 197103
Submitted by: Sakaue Mamoru
Update the default version of GCC in the Ports Collection from GCC 4.7.4
to GCC 4.8.3.
Part II, Bump PORTREVISIONs.
PR: 192025
Tested by: antoine (-exp runs)
Approved by: portmgr (implicit)
Stage science/vmd
I clobbered the Makefile diff (sorry danfe@). The entire makefile was
tabbed over 3 times. There was also no respect for 80 columns so a good
part of the clobber came from line wrapping. I also made $TAR use
real switches (e.g. -xzf) rather than undocumented by supported (zxf)
This is another manual package / obtain restricted data files/ only port
so I can't test much of it.
PR: 193090
Submitted by: turutani (Kyoto)
Remove indefinite articles and trailing periods from COMMENT, plus
minor COMMENT typos and surrounding whitespace fixes. A few Makefiles
where not included as they contain Latin-1 characters that break
the Phabricator workflow. Categories P-S.
CR: D422
Approved by: portmgr (bapt)
Convert GMAKE to MAKE_CMD
Please note that lots of invocation of MAKE_CMD here are wrong as they do not
properly respect MAKE_ENV and friends
With hat: portmgr
- Remove bogus conditional IGNORE for PACKAGE_BUILDING; these should
be IGNOREd regardless of PACKAGE_BUILDING. Soem have no MASTER_SITES
and require manual fetching, others are already marked RESTRICTED.
- Trim headers
- Convert some pre-fetch errors into IGNORE
- Remove needless quoting in java/jdk7-doc IGNORE
With hat: portmgr
Fix minor nit: use the canconical FreeBSD.org form for email addresses.
This was causing me issues when attempting to gather certain statistics.
While here trim header
Approved by: miwi, adrian, tj
No objection from: db, bjk, cperciva, scheidell, osa
- Add files/patch-bin_vmd.csh, files/patch-bin_vmd.sh
to fix a runtime error (the "ARCH" value is not set)
- Bump PORTREVISION
- Remove MD5 checksum from distinfo
- Set ONLY_FOR_ARCHS (i386 and amd64)
PR: ports/152955
Submitted by: Benjamin Kaduk <kaduk-fbsd at mit.edu> (maintainer)
Add vmd, a molecular visualization program for displaying, animating, and
analyzing large biomolecular systems using 3-D graphics and built-in scripting.
PR: ports/70509
Submitted by: Stephen Montgomery-Smith <stephen@math.missouri.edu>
