[BioC] rhdf5 segfault

Wolfgang Huber whuber at embl.de
Wed Dec 25 20:06:40 CET 2013

Dear Brad

thank you for the feedback, much appreciated. I could not run your code since the file “charvec.rda” is presumably only on your harddrive, but a  similar piece of code (below) worked fine for me. This is on Mac OS 10.9.1, I built R and rhdf5 from source using system libraries from Mac Ports.

Since this seems to be a problem specific for certain installations, we’ll need a reproducible example, exact system description, and more detailed debugging information at the C level (afaIu there are  people locally at your workplace who can help with that).

Kind regards


## load("charvec.rda")  ## provides "charvec"
charvec = paste(1:16630)


hdf5.file <- tempfile()

h5write(charvec, hdf5.file, "foo")
got <- h5read(hdf5.file, "foo")

stopifnot(all(got==charvec), length(got)==length(charvec))


> sessionInfo()
R Under development (unstable) (2013-12-25 r64540)
Platform: x86_64-apple-darwin13.0.0/x86_64 (64-bit)

[1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] rhdf5_2.7.4    fortunes_1.5-2

loaded via a namespace (and not attached):
[1] zlibbioc_1.8.0

On 24 Dec 2013, at 01:11, Brad Friedman <friedman.brad at 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 at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor

More information about the Bioconductor mailing list