[BioC] problem using affxparser on MacOSX

[Fabrice Berger]

Dear BioC users,

I could solve the problem.

If some of you have the same troubles, I solved it by re-installing 
affxparser from the sources instead of using the binary package 
installed by default.

Fabrice Berger

------------------------------------

On 17/11/11 12:26, Fabrice Berger 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.
>
> Thanks,
>
> Fabrice Berger
>