Dear Jeremy! I have written a package rhdf5 that can handle compound data types as well. The H5T_UNIX_TIME type is not yet supported, but it should be possible to read the floats into a data.frame.
I put the H5T_UNIX_TIME type on my list and will add it in the next weeks. Currently, you can download the package from http://www-huber.embl.de/users/befische/rhdf5/ It will appear on bioconductor in the next couple of days. Best, Bernd > From: Jeremy Reeve <jeremy.ree...@gmail.com> > Date: Wed, Nov 30, 2011 at 10:22 PM > Subject: [Rd] HDF5 compound data types and h5r/hdf5 R packages > To: r-devel@r-project.org > > > Hi there, > > > I have a Java process that writes HDF5 files with the following > approximate structure: > > group "xxx" { > > group "yyy" { > > dataset {} > dataset {} > > } > > group "zzz" { > > dataset {} > dataset {} > > } > > } > > where dataset is a rank one dataspace having a compound datatype defined as: > > H5T_UNIX_TIME, float, float, float, float > > I have tried R packages h5r and hdf5 in an attempt to read the file > but examining the source of h5r and reading documentation for hdf5 > here: http://xweb.geos.ed.ac.uk/~hcp/Rhdf5.html leads me to believe > that compound datatypes are not supported by these packages. My guess > is that mapping arbitrary type definitions in HDF5 to available types > in R might be somewhat tricky. Incidentally, h5dump has trouble > displaying the data in the dataset but I think this is to do with the > time 'field': > > DATASPACE SIMPLE { ( 33 ) / ( H5S_UNLIMITED ) } > DATA { > h5dump error: unable to print data > } > > Since I am new to both HDF5 and R I wonder if there are better > approaches to storing the information I have that will allow me to use > either h5r or hdf5 packages unmodified. I expect I can contribute > changes to either of the packages that will allow me to do what I > describe but fall short of general compound datatype support. > > Any comments or advice gratefully received. > > Regards...Jeremy > > [[alternative HTML version deleted]] > > ______________________________________________ > R-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel -- Bernd Fischer EMBL Heidelberg Meyerhofstraße 1 69117 Heidelberg Tel: +49 [0] 6221 387-8131 E-Mail: bernd.fisc...@embl.de Homepage: http://www.ebi.ac.uk/~bfischer ______________________________________________ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
