What are the disadvantages of using .Rdata files compared to HDF5 or netCDF?

Question

I have been asked to change a software that currently exports .Rdata files so that it exports in a \'platform independent binary format\' such as HDF5 or netCDF. Two reasons

Answer 1

Point 2 is wrong: binary .RData files are portable across hardware & OS platforms. To quote from the help page for ?save:

All R platforms use the XDR (bigendian) representation of C ints and doubles in binary save-d files, and these are portable across all R platforms.

Point 1 is a function of what the data are, and what other programs might usefully be applied to the data. If your code base uses save() to write specified objects which are dataframes or matrices, you could easily write a small function save2hdf() to write them out as hdf or ncdf binary files, then use sed to change all occurrences of save( to save2hdf( in your codebase. At least ncdf will have a performance hit on the reads, but not too bad of a hit. If your code uses saves objects like lists of heterogeneous objects, you probably can't use ncdf or hdf without a great deal of recoding to write out separate component objects.

Also note that netCDF 4 is still problematic in R.