[BioC] rhdf5 segfault

Brad Friedman 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).


> 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)

[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

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