[BioC] trouble with rhdf5 and hdf5.datasets

Laurent Gautier laurent@cbs.dtu.dk
Sun, 21 Jul 2002 15:33:59 +0200


On Sun, Jul 21, 2002 at 10:17:28AM -0400, Byron Ellis wrote:
> The problem, I believe, is that HDF5 makes no guarrantee about the
> ordering of the groups/datasets at any particular time (i.e. mad[[1]]
> today is not neccessarily mad[[1]] tomorrow). At the very least, though, I
> should go through and fix it so it fails gracefully :-)


while you are into the segfault side of things, you may also want to
try the following:

> hdf5.open(file("whatever"))
Segmentation fault

(I know, the user is not suppposed to do that, unless he/she read the
help file in diagonal ;) (hey, did I ?)... but doing that
generates a 
"
> library(rhdf5)
Error in firstlib(which.lib.loc, package) : 
	not an HDF5 file
Error in library(rhdf5) : .First.lib failed
"
at the next try)



L.



> 
> Byron Ellis (bellis@hsph.harvard.edu)
> "Oook" - The Librarian
> 
> Please finger bellis@hsph.harvard.edu for PGP keys
> 
> On Sun, 21 Jul 2002, Vincent Carey 525-2265 wrote:
> 
> > > >
> > > > do.call("$", list("mad", "chip1"))
> > > NULL
> > 
> > here you want to refer to mad, not its name, do not use "mad"
> > 
> > do.call("$", list(mad, "chip1"))
> > 
> > should work
> > 
> > also i have noted that there is a problem in some of the
> > doc -- specifically the man page for
> > hdf5.open -- that refers to hdf5.create.group.
> > the latter has been supplanted, it seems, by hdf5.group.
> > 
> > i did reproduce your segfault, that needs to be looked at.
> > unfortunately the weather here is very nice....
> > 
> > _______________________________________________
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> > Bioconductor@stat.math.ethz.ch
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> > 
> 
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