1. There is a typo:
> -LICENSE_NAME_VMD= Visaul Molecular Dynamics Software License Agreement
> +LICENSE_NAME_VMD= Visual Molecular Dynamics Software License Agreement
2. Dependencies are missing:
Arch package mentions these 2 dependencies (https://aur.archlinux.org/cgit/aur.git/tree/PKGBUILD?h=vmd):
* 'openbabel: additional file formats support'
* 'sqlite: dmsplugin'
They should be made direct dependencies of vmd.
3. USES=shebangfix is missing:
> Error: '/usr/bin/tclsh' is an invalid shebang you need USES=shebangfix for 'lib/vmd/plugins/noarch/tcl/topotools1.7/topoatoms.tcl'
> Error: '/usr/bin/tclsh' is an invalid shebang you need USES=shebangfix for 'lib/vmd/plugins/noarch/tcl/topotools1.7/topoangles.tcl'
> Error: '/usr/bin/tclsh' is an invalid shebang you need USES=shebangfix for 'lib/vmd/plugins/noarch/tcl/topotools1.7/topodihedrals.tcl'
> Error: '/usr/bin/tclsh' is an invalid shebang you need USES=shebangfix for 'lib/vmd/plugins/noarch/tcl/topotools1.7/topolammps.tcl'
> Error: '/usr/bin/tclsh' is an invalid shebang you need USES=shebangfix for 'lib/vmd/plugins/noarch/tcl/topotools1.7/topoutils.tcl'
> Error: '/usr/bin/tclsh' is an invalid shebang you need USES=shebangfix for 'lib/vmd/plugins/noarch/tcl/topotools1.7/topohelpers.tcl'
4. LICENSE doesn't mention that direct source download and package caching is not allowed. There is in fact the direct download link. I suggest to apply these patches that will allow the packages to be built automatically:
> -MASTER_SITES= http://jedi.ks.uiuc.edu/~johns/raytracer/files/0.99b6/:tachyon \
> +MASTER_SITES= http://www.ks.uiuc.edu/Research/vmd/vmd-1.9.3/files/final/ \
> + http://jedi.ks.uiuc.edu/~johns/raytracer/files/0.99b6/:tachyon \
> -LICENSE_PERMS_VMD= auto-accept
> +LICENSE_PERMS_VMD= dist-mirror pkg-mirror auto-accept
Created attachment 183544 [details]
Fixed for vmd
The attached patch fixes most of your comments, except for:
2) openbabel: I cannot find any reference in the source code that actually uses openbabel, thus I am skipping it as a dependency.
4) The license (in clause 2) explicitly requires that people get directed to their website to obtain a copy of the program (and thus implicitly that we cannot mirror nor distribute the program)
I need to compile test this patch on multiple versions of FreeBSD, then I'll commit it.
A commit references this bug:
Date: Sun Jun 18 06:03:30 UTC 2017
New revision: 443820
science/vmd: various fixes
- fix spelling of VMD license 
- use USES=tcl,tk instead of direct dependency
- patch vmd to support (tcl|tk)86
- fix shebang for tcl 
- fix detection of netcdf
- add sqlite as a dependency (for dmsplugin) 
- 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
Reported by: Yuri Victorovich <firstname.lastname@example.org>
Committed, thanks for reporting.
tachyon-0.99b6.tar.gz doesn't fetch any more. I tried several times over 3 days.
I can confirm it works for me (now):
===> License VMD BSD3CLAUSE STRIDE accepted by the user
===> vmd-1.9.3_3 depends on file: /usr/local/sbin/pkg - found
=> tachyon-0.99b6.tar.gz doesn't seem to exist in /usr/ports/distfiles/.
=> Attempting to fetch http://jedi.ks.uiuc.edu/~johns/raytracer/files/0.99b6/tachyon-0.99b6.tar.gz
tachyon-0.99b6.tar.gz 100% of 2911 kB 49 kBps 00m59s
===> Fetching all distfiles required by vmd-1.9.3_3 for building
=> SHA256 Checksum OK for vmd-1.9.3.src.tar.gz.
=> SHA256 Checksum OK for tachyon-0.99b6.tar.gz.
=> SHA256 Checksum OK for stride.tar.gz.
Can you visit the website http://jedi.ks.uiuc.edu/~johns/raytracer/files/0.99b6/?
(In reply to David Naylor from comment #5)
Yes, it fetches.
> 2) openbabel: I cannot find any reference in the source code that actually
uses openbabel, thus I am skipping it as a dependency.
> molfile_plugin/src/babelplugin.c:711: babelbin = getenv("VMDBABELBIN");
actually uses the openbabel executable.
But since this is only a runtime dependency from one of the plugins and through the environment variable, I think RUN_DEPENDS can be omitted in this case.