> Message: 5
> Date: Mon, 29 Mar 2010 19:12:51 -0600
> From: "George N. White III" <[email protected]>
> To: HDF Users Discussion List <[email protected]>
> Subject: Re: [Hdf-forum] R hdf5 package error
> Message-ID:
> <[email protected]>
> Content-Type: text/plain; charset=ISO-8859-1
>
> On 3/29/10, [email protected] <[email protected]> wrote:
> >
> > I was wondering if anyone has experience with the hdf5 package for the R
> > statistical software. Right now we can get the code to compile and while
> > it usually reads existing hdf5 files it doesn't write hdf5 files that can
> > be read by itself or other software.
> >
> > We have tried installing this on various Linux machines (both Red Hat and
> > Ubuntu) by using both the package managers and compiling the code from
> > scratch. We've compiled using both HDF5 1.8 and 1.6 and neither works.
>
> We use R routinely with files converted using h4toh5, but 99% of the time we
> use hdf5load. We try to use the platform's hdf5 library, which in our case
> is
> 1.6 on Ubuntu and 1.8 via macports on MacOSX.
>
> There have been versions of the R hdf5 library for Ubuntu, but some versions
> abort when they encounter elements in the hdf5 that aren't supported. Our
> files have such elements but the information is redundant, so we patch the
> library to omit the unsupported elements.
>
> Have you run "example(hdf5save)" successfully?
Yes, that runs fine. In fact, as long as we don't quit out of R we can
both read and write files, but if we quit and restart R then we can no
longer read the files we just wrote and were able to read a second ago.
> > Specifically, this simple test in R produces the following error
> >
> > Step 1: create file (run from within R)
> >
> > library(hdf5)
> > data = 1:10
> > hdf5save("test.h5","dat")
>
> did you mean: hdf5save("test.h5","data")
That's a typo...just in the email, not in what I've been running -- I
actually meant for both to be "dat"
> >
> > Step 2: exit and then restart R
> >
> > hdf5load("test.h5")
> >
> > HDF5-DIAG: Error detected in HDF5 library version: 1.6.6 thread
> > 47700932800864. Back trace follows.
> > #000: H5F.c line 2049 in H5Fopen(): unable to open file
> > major(04): File interface
> > minor(17): Unable to open file
>
> This looks more like a permission problem. If you change the filename to
> "/tmp/test.h5" do you get the same error?
yes I get the same error
I also checked that I do have read/write permissions for the file. In
addition from outside R I ran
h5dump test.h5
which returned
h5dump error: unable to open file "test.h5"
An additional odd bit of info is that we do have one computer that runs
an older version of Ubuntu where the library has worked for a long time
and we only discovered this error when our sysadmin tried putting this
on our Redhat cluster. Even when we download the same exact version of
hdf5 and the R hdf5 library that is on the machine that does work we
still can't get things to work. We also found that on our newer Ubuntu
machines that the version that comes from the Synaptic package manager
doesn't work either.
We are just storing vectors of floats so the data format is nothing odd
that should be hard to read or write.
Also, for what it's worth, I tried contacting the author of the R hdf5
package about a week ago and got no response.
> > #001: H5F.c line 1829 in H5F_open(): unable to read superblock
> > major(04): File interface
> > minor(24): Read failed
> > #002: H5Fsuper.c line 114 in H5F_read_superblock(): unable to find file
> > signature
> > major(04): File interface
> > minor(19): Not an HDF5 file
> > #003: H5F.c line 1281 in H5F_locate_signature(): unable to find a valid
> > file signature
> > major(05): Low-level I/O layer
> > minor(29): Unable to initialize object
> > Error in hdf5load("test.h5") : unable to open HDF file: test.h5
>
>
> --
> George N. White III <[email protected]>
> Head of St. Margarets Bay, Nova Scotia
>
>
>
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>
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>
> End of Hdf-forum Digest, Vol 9, Issue 55
> ****************************************
--
________________________________________________________________________
Michael Dietze [email protected]
Assistant Professor www.life.uiuc.edu/dietze
Department of Plant Biology (217) 265-8020
University of Illinois 1405 IGB / 183 Morrill
_______________________________________________
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