[BioC] affxparser::readCdfHeader() core dumps

[Kasper Daniel Hansen]

Hi Neelan

I could not reproduce this, using R-2.10 patched on OS X Snow Leopard, using Apple's gcc 4.2.

This might be something specific to your platform, so please give us the following information
* The full output of sessionInfo (you are missing the package versions in the output below)
* Details on how you installed affxparser (I assume using biocLite, but please tell me)
* The output (from R) of options("pkgType")
* What OS X platform are you on (Tiger, Leopard, Snow Leopard) and how did you install R (using the CRAN binary I assume, but please confirm)
* What is the output of the following command run in the Terminal (assuming that R starts the R version you are using)

`R CMD config CXX` --version

(these are "backticks" on a US keyboard they are typically the upper left hand key (shared with ~))

Kasper

On Jan 5, 2010, at 8:44 AM, Neelanjan Mukherjee wrote:

> Sorry, I forgot to include the sessinInfo:
> 
>> sessionInfo()
> R version 2.10.1 (2009-12-14) 
> i386-apple-darwin8.11.1 
> 
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
> 
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base 
>> library("AffymetrixDataTestFiles")
>> pathname <- "annotationData/chipTypes/Test3/1.XDA/Test3.CDF"
>> pathname <- system.file(pathname, package="AffymetrixDataTestFiles")
>> stopifnot(file.exists(pathname))
>> print(pathname)
> [1] "/Users/Neel/Library/R/2.10/library/AffymetrixDataTestFiles/annotationData/chipTypes/Test3/1.XDA/Test3.CDF"
>> library("affxparser")
>> hdr <- readCdfHeader(pathname)
> 
> *** caught segfault ***
> address 0xfffffffc, cause 'memory not mapped'
> 
> Traceback:
> 1: .Call("R_affx_get_cdf_file_header", filename, PACKAGE = "affxparser")
> 2: readCdfHeader(pathname)
> 
> 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: 
> 
> 
> 	[[alternative HTML version deleted]]
> 
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor