This appears to only be an issue for compound types, which I have
previously been able to load as dataframes using h5read(). But using
h5read() to load strings, integers, floats, etc, and groups that contain
datasets of these types, returns the values as expected.
I have installed hdf5r (using R's install.package() command, since there
isn't a Debian package for this library) and with this library I am able to
load compound datasets as dataframes. As an example, the following code
returns a dataframe as expected:
library(hdf5r)
data_file <- 'path_to_data_file.hdf5'
dataset_path <- '/dataset/path'
file.h5 <- H5File$new(data_file, mode = 'r')
dataset <- file.h5[[dataset_path]]
df <- data.frame(dataset$read())
dataset$close()
file.h5$close()
So it seems to me that this must be an issue with the rhdf5 package itself.
I can't see how to obtain further details about the error, with everything
I've tried the only error message I receive is:
Error in H5Dread(h5dataset = h5dataset, h5spaceFile = h5spaceFile,
h5spaceMem = h5spaceMem, :
HDF5. Dataset. Read failed.
Is there anything else I can do to provide further details?
All the best,
Rob
