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?
> 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")
>
> 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?
> #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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