[BioC] Affy crashes if cdf environment missing

Laurent Gautier laurent at cbs.dtu.dk
Wed Apr 30 18:21:49 MEST 2003

On Wed, Apr 30, 2003 at 10:42:12AM -0400, James MacDonald wrote:
> Hi,
> I just wanted to let the affy developers know that the devel version of affy completely bombs out if you don't have the requisite cdf environment installed.
> Details:
> OS: Win XP
> R: 1.7.0
> Affy: 1.2.10
> Biobase: 1.3.17
> tkWidgets: 1.2.13 <- I think these are the only two version-level dependencies

I believe there is also a dependency towards 'reposTools'
 (although no version number is specified).
Which version do you use ?
> If I read in some e.g., RG-U34A chips without the rgu34acdf environment installed, and then try to do anything with the AffyBatch, I get the following error:
> Error in how[[i]] : subscript out of bounds
> Error in inherits(cdf.env, "try-error") : Object "cdf.env" not found

It looks like a silly bug in the 'autodownload' mecanism (one more). I'll look at that.

> If you are willing to wait about 10 minutes, you can then use the computer. Otherwise it requires a reboot to recover.

This is annoying, but fairly out of the control of developpers of the affy pack.

> And yeah, I know, whaddaya expect if you don't have things set up correctly? Just doing my part to make Bioconductor fool proof ;-D

The mecanism involved is an attempt to free people from the trouble of taking
care of (some of) the logistics. It should be fool proof (especially with
Win XP ? ;) ). Thanks for the report.


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