[BioC] rhdf5 segfault
friedman.brad at gene.com
Tue Dec 24 01:11:41 CET 2013
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).
> load("charvec.rda") ## provides "charvec"
chr [1:16630] "lincRNA:chr8:119735533-119736887 forward strand" ...
> hdf5.file <- tempfile()
> h5write(charvec, hdf5.file, "foo")
> got <- h5read(hdf5.file, "foo")
Error: segfault from C stack overflow
R version 3.0.1 (2013-05-16)
Platform: x86_64-apple-darwin10.8.0 (64-bit)
attached base packages:
 stats graphics grDevices utils datasets methods base
other attached packages:
loaded via a namespace (and not attached):
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