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
>
>
> 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) :
^^^^^^^^ really?
> not an HDF5 file
> Error in library(rhdf5) : .First.lib failed
this sounds like a workspace left over from old attempts.
rhdf5 saves some information in .hdf5* files in the working
directory in which it was attached.
look for those and get rid of them if they are
causing problems. i regret that i don't know their exact
function.
>
>
> ..but when I start R from somewhere else (say /tmp/),
> everything works...
>
>
> any hint ?
>
>
>
> Laurent
>
>
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor@stat.math.ethz.ch
> http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
>
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.
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
> http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
>
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
> > http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
> >
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor@stat.math.ethz.ch
> http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
On Fri, Jul 19, 2002 at 08:53:54AM -0400, Vincent Carey 525-2265
wrote:
> >
> >
> > 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) :
>
> ^^^^^^^^ really?
Yes your honor, I used the middle mouse button to paste the R
output...
>
> > not an HDF5 file
> > Error in library(rhdf5) : .First.lib failed
>
> this sounds like a workspace left over from old attempts.
> rhdf5 saves some information in .hdf5* files in the working
> directory in which it was attached.
I was suspecting something like that (but could not find them
because I did 'ls -lt | head' rather then 'ls -lta | head'
(looks like I'd have better stayed in bed today)
> look for those and get rid of them if they are
> causing problems. i regret that i don't know their exact
> function.
...I am currently thinking about how to recover things from the
previous session, how could one save R objects using rhdf5, etc...
I hope a documentation is coming...
Thanks for the lightning fast enlightment,
L.
