I tried installing R 2.7.0 (devel) on my PPC Mac and ran into several  
errors that are probably not worth trying to work around at this  
stage in R 2.7.0 development. I tried your set of commands with R  
2.6.0 and annaffy 1.10.0 and got the correct output. My best guess is  
that R 2.7.0 is broken right now and causing the problems. I probably  
won't look into trying to resolve problems with annaffy/R 2.7.0 for  
several months, until development stabilizes.

For now, stick with R 2.6.0 and the release version of annaffy. One  
important note: any aafTable objects you have saved from a version of  
annaffy prior to 1.9.2 will have unexpected results when you try to  
use them in R 2.6.0. The new R release adds an additional requirement  
for S4 method dispatch that versions of annaffy prior to 1.9.2 did  
not take care of.

-Colin

On Oct 8, 2007, at 18:21 , Paul Leo wrote:

> Thanks Colin,
>
> That would be great! I tried one other test also after my email. I  
> loaded the old version of annaffy that worked under R2.5 into R2.7.  
> The same “bad” behaviour resulted. I suspected the problems came  
> from the merge commands …. Which is probably less commonly used  
> with annaffy… However my tested included using exactly the same  
> data_table object in both R versions just before using the saveHTML  
> command (saved workspace under R2.5 loaded into R2.7 and just the  
> saveHTML was run : same effect). Hope that info is of some use…
>
>  Attached is the output.

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