Re: [R] hdf5 package segfault when processing large data

2009-08-25 Thread Marcus Daniels
Hi Budi and Bill, As a workaround, you could try setting your stack limit to a larger limit (ulimit -s). I'll change that to a heap allocation. Thanks, Marcus William Dunlap wrote: This is probably due to the code in hdf5.c allocating a huge matrix, buf, on the stack with 883

Re: [R] hdf5 package segfault when processing large data

2009-08-24 Thread William Dunlap
> -Original Message- > From: r-help-boun...@r-project.org > [mailto:r-help-boun...@r-project.org] On Behalf Of Budi Mulyono > Sent: Monday, August 24, 2009 3:38 AM > To: r-help@r-project.org > Subject: [R] hdf5 package segfault when processing large data > > Hi th

[R] hdf5 package segfault when processing large data

2009-08-24 Thread Budi Mulyono
Hi there, I am currently working on something that uses hdf5 library. I think hdf5 is a great data format, I've used it somewhat extensively in python via PyTables. I was looking for something similar to that in R. The closest I can get is this library: hdf5. While it does not work the same way as