[BioC] problem using affxparser on MacOSX

[Sean Davis]

On Thu, Nov 17, 2011 at 6:26 AM, Fabrice Berger
<fabrice.berger at gmail.com> wrote:
> Dear BioC users,
>
> I encounter some troubles using affxparser, that causes R segfault. I was
> originally using affyILM, which makes use of affxparser function to read cel
> files. As I got errors relating to affxparser, I then tested affxparser with
> the following commands :
>
> setwd("Datasets/ls133/HG-U133A_tag_Latin_Square")
> library(affy)
> cel<-list.celfiles()
> library(affxparser)
> readCelHeader(cel[1])
>
> and get the following error :
>
>  *** caught segfault ***
> address 0xfffffffc, cause 'memory not mapped'
>
> Traceback:
>  1: .Call("R_affx_get_cel_file_header", filename, PACKAGE = "affxparser")
>  2: readCelHeader(cel[1])
>
> Possible actions:
> 1: abort (with core dump, if enabled)
> 2: normal R exit
> 3: exit R without saving workspace
> 4: exit R saving workspace
> Selection:
>
> Can you point me to some possible explanations for this R crash or give me
> instructions to solve the problem? I'm using the last release of R and BioC
> on MacOSX. Never had troubles with previous releases.

Hi, Fabrice.

This has been reported on bioc-devel.  The fix appears to be to
reinstall R using the most recent binary from CRAN and then reinstall
packages (perhaps not all need to be reinstalled, but it isn't clear
to me which are affected).

Sean