[Bioc-devel] Binary file (flash SWF) in source package?

Martin Morgan mtmorgan at fhcrc.org
Tue Oct 6 16:05:49 CEST 2009

Hi Gabor --

Gábor Csárdi wrote:
> Dear BioC developers,
> what is your current position regarding binary files in BioConductor
> source packages? I have a package that visualizes overlapping
> biclusters, and the interactive visualization part in written in Adobe
> Flex. Flex creates a simple platform-independent SWF binary file that
> can be used with most web browsers.
> Putting this file into the source package has the advantage that one
> does not have to have Adobe Flex installed to install the R package.
> In addition to the binary, the Flex source code would be also included
> in the package, of course, and the package license would be GPL.
> Adobe Flex is free, as free beer, but it is not free or open source
> software.

Thinking out loud a little...

Some of the issues are licensing (ok in this case), added security
responsibilities associated with binary file redistribution,
cross-platform compatibility of redistributed binaries, and potentially
substantially increased package size.

On the other hand having unusual system dependencies has proven to be a
significant challenge for us, and for our users -- even 'simple'
installations can be complicated when there are multiple build machines,
there can be challenging version-matching problems, it can be difficult
to convey the system dependencies to the end users, etc.

In this particular case I think we can proceed, but this isn't meant to
be a general endorsement.


> Thank you, Best Regards,
> Gabor

Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109

Location: Arnold Building M1 B861
Phone: (206) 667-2793

More information about the Bioc-devel mailing list