You might try changing your stack size limits in your shell, before launching R. e.g.

ulimit -s unlimited

I know I encountered a similar issue with rhdf5 not to long ago reading from a file with a fairly large number of strings, and that was a suitable work around.  Note within R Cstack_info() will also tell you stack size.

At the time I looked into it, at least in my case I tracked it down to a segfault occuring in the H5Dread_helper_STRING function of file H5D.C at line 244, but it looked like the issue might be with the allocation:

char bufSTR[n][size]
 
in the previous line and I can only assume that n*size is too large for the C stack (in my instance, and perhaps yours) at the default settings in your shell.
 

Best,

Ben



On Dec 23, 2013, at 4:11 PM, Brad Friedman <friedman.brad@gene.com> wrote:

> Dear Bernd and List Members:
> 
> I'm getting a segmentation fault reading in a character vector (attached)
> written by rhdf5. If anyone can make a suggestion how to get rhdf5 to read
> this without throwing the error I would appreciate it. The file appears to
> be written correctly since h5dump can read it.
> 
> I got the same error with the same vector on both my mac laptop and our
> linux server, in both cases using the latest version of rhdf5 (2.7.4).
> 
> Brad
> 
>> library(rhdf5)
>> load("charvec.rda")  ## provides "charvec"
> 
> 
>> str(charvec)
> chr [1:16630] "lincRNA:chr8:119735533-119736887 forward strand" ...
>> hdf5.file <- tempfile()
>> h5createFile(hdf5.file)
> [1] TRUE
>> h5write(charvec, hdf5.file, "foo")
>> got <- h5read(hdf5.file, "foo")
> Error: segfault from C stack overflow
>> sessionInfo()
> R version 3.0.1 (2013-05-16)
> Platform: x86_64-apple-darwin10.8.0 (64-bit)
> 
> locale:
> [1] en_CA.UTF-8/en_CA.UTF-8/en_CA.UTF-8/C/en_CA.UTF-8/en_CA.UTF-8
> 
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
> 
> other attached packages:
> [1] rhdf5_2.7.4
> 
> loaded via a namespace (and not attached):
> [1] zlibbioc_1.6.0
> _______________________________________________
> Bioconductor mailing list
> Bioconductor@r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor


	[[alternative HTML version deleted]]

