[BioC] segfault ReadAffy cause 'memory not mapped'

[Brian D. Peyser PhD]

Below is some previous info on this issue; Dr Bolstad, did you issue a
patch to affyio?

I had just pulled the latest source from SVN with the hope that I could
manage to hack it and noticed this at the top of read_abatch.c:

** Sept 18, 2013 -  improve 64bit support for read_abatch

I haven't tried running these big calcs since then. Should I give a try
now?

-Brian

On Wed, 2013-08-21 at 16:21 -0700, Ben Bolstad wrote:
> Well, internally  read_abatch is using allocMatrix() to actually allocate
> the main block of memory that will be used to store the probe intensities.
>  However, there are a lot of places where "int" is used as the indexing
> variable. Probably if I had had better foresight when I wrote this code 10
> years ago, I'd have used something a bit more specific (eg int64_t). I'm
> guessing it is one of these sorts of things that is causing the crash.
> I'll try to get around to refactoring the code at some point.
> 
> If you'd like you could send me the gdb backtrace at the point of the
> segfault and I could investigate further.
> 
> Best,
> 
> Ben
> 
> 
> > On 8/1/13 5:33 PM, Loraine, Ann wrote:
> >> Hello,
> >>
> >> I am trying to process several thousand CEL files using the ReadAffy
> >> command.
> >>
> >> The machine has 96 Gb RAM.
> >>
> >> However I get this error:
> >>
> >> > expr=ReadAffy(filenames=d.uniq$cel,celfile.path='CEL',sampleNames=d.uniq$gsm,compress=T)
> >>
> >>  *** caught segfault ***
> >> address 0x7fc79b4b1048, cause 'memory not mapped'
> >>
> >
> > I also have a problem loading many (3750) Affy hgu133plus2 arrays into
> > an AffyBatch. I was able to run this with ~2900 arrays, but not since
> > adding ~800 more. At right around 16 GiB allocated, I get a segfault
> > like:
> >
> >  *** caught segfault ***
> > address 0x2aa6b6067048, cause 'memory not mapped'
> >
> > Traceback:
> >  1: .Call("read_abatch", filenames, rm.mask, rm.outliers, rm.extra,
> > ref.cdfName, dim.intensity[c(1, 2)], verbose, PACKAGE = "affyio")
> >  2: read.affybatch(filenames = as.character(pdata$Filename))
> >
<snip>

-- 
Brian D. Peyser PhD
Special Assistant to the Associate Director
Office of the Associate Director
Developmental Therapeutics Program
Division of Cancer Treatment and Diagnosis
National Cancer Institute
National Institutes of Health
301-524-5587 (mobile)