[BioC] rhdf5 segfault

[Wolfgang Huber]

Dear Brad

thank you. When I use the instance of ‘charvec’ loaded from your charvec.rda file, then I can reproduce the error you observe:
"Error: segfault from C stack overflow”  and return to R prompt after running the below code once,
"Segmentation fault: 11” and termination of the R process after the second time.
So this might be related to the content or size of the character vector.

I leave the rest to Bernd (package maintainer). This should be enough information to get going.

Btw, your original post as received in my inbox did not contain an attachment, and it appears that attachments are also stripped from here: 
https://stat.ethz.ch/pipermail/bioconductor/2013-December/056760.html

——
library("rhdf5")
if (TRUE) load("charvec.rda") else charvec = paste(1:16630)

hdf5.file <- tempfile()
h5createFile(hdf5.file)
h5write(charvec, hdf5.file, "foo")
got <- h5read(hdf5.file, "foo")

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

Kind regards
	Wolfgang


On 26 Dec 2013, at 17:49, Brad Friedman <friedman.brad at gene.com> wrote:

> Hi, Wolfgang
> 
> Thanks for your response. I attached a file charvec.rda to the original posting....maybe I did this wrong? I'm attaching it here. Do you mind trying one more time if you can reproduce my error?
> 
> Thanks,
> 
> Brad
> 
> 
> On Wed, Dec 25, 2013 at 11:06 AM, Wolfgang Huber <whuber at embl.de> wrote:
> 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
>         Wolfgang
> 
> --------------------------
> library("rhdf5")
> 
> ## load("charvec.rda")  ## provides "charvec"
> charvec = paste(1:16630)
> 
> str(charvec)
> 
> hdf5.file <- tempfile()
> h5createFile(hdf5.file)
> 
> h5write(charvec, hdf5.file, "foo")
> got <- h5read(hdf5.file, "foo")
> 
> stopifnot(all(got==charvec), length(got)==length(charvec))
> 
> sessionInfo()
> 
> ----------------------------------------------
> > sessionInfo()
> R Under development (unstable) (2013-12-25 r64540)
> Platform: x86_64-apple-darwin13.0.0/x86_64 (64-bit)
> 
> locale:
> [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
> > _______________________________________________
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> > https://stat.ethz.ch/mailman/listinfo/bioconductor
> > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
> 
> 
> <charvec.rda>