[BioC] trouble with 'library(rhdf5)'

Peter Dimitrov dimitrov@gnf.org
19 Jul 2002 18:23:57 -0700


On Fri, 2002-07-19 at 06:06, Byron Ellis wrote:
> I think rhdf5 might make a temporary hdf5 file (.something) when its
> loaded---if that gets corrupted and bound on library load you would see
> that error.
> 

Yep, that is the case, look at line 38 in hdf5.c in the src directory,
users should have write permissions to create files in R's working
directory:

SEXP HDF_init(void) 
{
...
    /* setup a work area for temp and intermediate files */
    file = HDF_fileopen(".hdf5.Rwork", H5P_DEFAULT);
    PROTECT(HDF_workfile = H5Fsexp(file));
    setVar(install(".hdf5.Rwork"), HDF_workfile, R_GlobalEnv);
...
}

Peter Dimitrov

> Byron Ellis (bellis@hsph.harvard.edu)
> "Oook" - The Librarian
> 
> Please finger bellis@hsph.harvard.edu for PGP keys
> 
> On Fri, 19 Jul 2002, Laurent Gautier wrote:
> 
> > Dear all,
> > 
> > 
> > I came across unexplainable (for me) things with
> > the package rhdf5.
> > 
> > When starting R from my home directory, I get the following:
> > 
> > 
> > > library(rhdf5)
> > Error in firstlib(which.lib.loc, package) : 
> > 	not an HDF5 file
> > Error in library(rhdf5) : .First.lib failed
> > 
> > 
> > ..but when I start R from somewhere else (say /tmp/),
> > everything works...
> > 
> > 
> > any hint ?
> > 
> > 
> > 
> > Laurent
> > 
> > 
> > 
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor@stat.math.ethz.ch
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> > 
> 
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