[BioC] trouble with rhdf5 and hdf5.datasets

[Byron Ellis]

You should be able to use the standard "[[" semantics when accessing
groups or datasets under rhdf5. this elimnates the need for the "do.call"

Byron Ellis (bellis@hsph.harvard.edu)
"Oook" - The Librarian

Please finger bellis@hsph.harvard.edu for PGP keys

On Sun, 21 Jul 2002, Laurent Gautier wrote:

> Dear all,
> 
> I observed unexplainable things with rhdf5. I do not
> know if they could be avoided. 
> 
> I am trying to access datasets in a group using the
> function 'do.call' with "$" (since the name of the
> dataset will only be known at run-time)... and I have
> a hard time with that (example below). Does anybody
> have experience with that ?
> 
> 
> ## example from the help file
> > mad <- hdf5.open("microarray.h5")
> >        # Create a new group inside the file
> >        hdf5.group(mad,"chip1")
> >        hdf5.dataset(mad$chip1,"raw", dim=c(534,534))
> > 
> >        raw <- mad$chip1$raw
> >        for(i in 1:534) 
> +            { raw[i,1:534] <- runif(534) }
> 
> > 
> > do.call("$", list("mad", "chip1"))
> NULL
> 
> # uh, uh....
> 
> 
> > mad$chip1
>   	Name	Type	Date		Comment
> [1]	raw	Dataset	21/07/2002 16:26
> 
> # let's try again...
> 
> > do.call("$", list("mad", "chip1"))
> NULL
> > mad
>   	Name	Type	Date		Comment
> [1]	chip1	Group	
> 
> # show stopper
> 
> > mad[[1]]
> Segmentation fault
> 
> 
> 
> 
> 
> Thanks,
> 
> 
> 
> 
> Laurent
> 
> 
> 
> 
> 
> 
> -- 
> --------------------------------------------------------------
> Laurent Gautier			CBS, Building 208, DTU
> PhD. Student			DK-2800 Lyngby,Denmark	
> tel: +45 45 25 24 85		http://www.cbs.dtu.dk/laurent
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