[BioC] affxparser::readCdfHeader() core dumps

[Kasper Daniel Hansen]

This issue was solved by re-installing R (off-list correspondence).

Kasper

On Jan 5, 2010, at 12:43 PM, Kasper Daniel Hansen wrote:

> 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]]
>> 
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> 
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