R and HDF5 Question

I am trying to load an hdf5 file into R and running into some
problems. 

This builds fine. The library seems to load without issue, but no
data is returned when I try to load a file:

    > library(hdf5)
    > hdf5load("test.h5")
    > NULL

Yet,

    osx:data scott$ h5dump test.h5 HDF5 "test.h5" { GROUP
"/" { DATASET "dset" { DATATYPE H5T_STD_I32LE DATASPACE SIMPLE
{ ( 31 ) / ( 31 ) } DATA { (0): 1, 2, 4, 8, 16, 32, 64, 128, 256,
512, 1024, 2048, 4096, 8192, (14): 16384, 32768, 65536, 131072,
262144, 524288, 1048576, 2097152, (22): 4194304, 8388608, 16777216,
33554432, 67108864, 134217728, (28): 268435456, 536870912,
1073741824 } } } }

Any thoughts?

That did it, boy do I feel silly.

Thanks!

On Fri, Nov 13, 2009 at 10:16 PM, Berwin A Turlach
<berwin at maths.uwa.edu.au>wrote:

  

G'day Scott,

On Fri, 13 Nov 2009 09:52:43 -0700
Scott MacDonald <scott.p.macdonald at gmail.com> wrote:

    

I am trying to load an hdf5 file into R and running into some
problems.
      

It's a while that I used hdf5 files and that package in R, but:

    

This builds fine. The library seems to load without issue, but no
data is returned when I try to load a file:

    > library(hdf5)
    > hdf5load("test.h5")
    > NULL

Is NULL the return of the hdf5load command or are you typing it on the
command line?

Anyway, .hdf5 files can contain several objects, just as R's .rda
file.  load() will load an .rda file and put all objects in that file
into the workspace.  Likewise, hdf5load() loads an hdf5 file and puts
all objects in that file into the workspace.

    

Yet,

    osx:data scott$ h5dump test.h5 HDF5 "test.h5" { GROUP
"/" { DATASET "dset" { DATATYPE H5T_STD_I32LE DATASPACE SIMPLE
{ ( 31 ) / ( 31 ) } DATA { (0): 1, 2, 4, 8, 16, 32, 64, 128, 256,
512, 1024, 2048, 4096, 8192, (14): 16384, 32768, 65536, 131072,
262144, 524288, 1048576, 2097152, (22): 4194304, 8388608, 16777216,
33554432, 67108864, 134217728, (28): 268435456, 536870912,
1073741824 } } } }

Any thoughts?
      

Did you try an ls() after the hdf5load() command?  If the hdf5load()
command was successfull, an ls() should show you that an object with
name "dset" is now in your workspace; if I read the output above
correctly.

HTH.

Cheers,

       Berwin



    

	[[alternative HTML version deleted]]