Hello Fabrice,

I was having the same problem using the Starr package(depends on affxparser) and tried the following:

 To re-install affxparser alone using:

> source("http://bioconductor.org/biocLite.R")
BiocInstaller version 1.2.1, ?biocLite for help
> update.packages("affxparser", repos=biocinstallRepos(), type= "source")

Is this the correct way to install from source (setting type = "source")?

In my case this did not prevent R from crashing.

Thanks for any suggestions.

Best,
Noah


On Nov 17, 2011, at 6:48 AM, Fabrice Berger wrote:

> 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
>> 
> 
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