[BioC] problem using affxparser on MacOSX

Fabrice Berger fabrice.berger at gmail.com
Thu Nov 17 12:26:31 CET 2011


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



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