Hi everyone,

I am currently trying to read an H5 file in Rstudio using the rhdf5 package (version 2.38.1) The file is organized as shown in this image:

Here's my problem: When I try to 1)load the full TPC_tables group in a variable or 2) read TPC tables which are quite large (99999 x 5), I do not have any issue as shown in this code block:

> TPC_group=h5read(file="/Users/julienballbe/Downloads/New_cell_file_full_test.h5",name='/TPC_tables')
> head(t(TPC_group$'29'))
        [,1]      [,2] [,3]        [,4]        [,5]
[1,] 0.52002 -69.81251    0 -0.04637020 0.007849086
[2,] 0.52004 -69.81251    0 -0.04497140 0.069939827
[3,] 0.52006 -69.81251    0 -0.04270432 0.113353990
[4,] 0.52008 -69.78125    0 -0.03992725 0.138853552
[5,] 0.52010 -69.75000    0 -0.03693670 0.149527574
[6,] 0.52012 -69.75000    0 -0.03394280 0.149694873
> TPC=h5read(file="/Users/julienballbe/Downloads/New_cell_file_full_test.h5",name='/TPC_tables/29')
> head(t(TPC))
        [,1]      [,2] [,3]        [,4]        [,5]
[1,] 0.52002 -69.81251    0 -0.04637020 0.007849086
[2,] 0.52004 -69.81251    0 -0.04497140 0.069939827
[3,] 0.52006 -69.81251    0 -0.04270432 0.113353990
[4,] 0.52008 -69.78125    0 -0.03992725 0.138853552
[5,] 0.52010 -69.75000    0 -0.03693670 0.149527574
[6,] 0.52012 -69.75000    0 -0.03394280 0.149694873

However, when I try to load SF_tables group, or sub groups (like "Sweep_29"), which are only composed of at most 20-elements array into a variable, I get the following error

> SF_group=h5read(file="/Users/julienballbe/Downloads/New_cell_file_full_test.h5",name='/SF_tables')
Error in H5Dread(h5dataset = h5dataset, h5spaceFile = h5spaceFile, h5spaceMem = h5spaceMem,  : 
  Not enough memory to read data! Try to read a subset of data by specifying the index or count parameter.
Error: Error in h5checktype(). H5Identifier not valid.
> SF=h5read(file="/Users/julienballbe/Downloads/New_cell_file_full_test.h5",name='/SF_tables/Sweep_29')
Error in H5Dread(h5dataset = h5dataset, h5spaceFile = h5spaceFile, h5spaceMem = h5spaceMem,  : 
  Not enough memory to read data! Try to read a subset of data by specifying the index or count parameter.

I suppose, but I am not certain, that the Error comes from the fact that some of these array may be empty, because if I delete those empty arrays, the error does not appear, but why does it return 'Not enough memory to read data'?

Thank you for any help you can give me!

Best Julien