[BioC] rhdf5 segfault

[Brad Friedman]

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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