[BioC] SScore Compatibility Problems?

[Richard Kennedy]

Chris,
 From the traceback, it appears the problem crops up in the affxparser 
routine, which SScore calls to get additional information about the 
*.CEL files.  Something like this had popped up in the pre-release 
Bioconductor 2.0 versions of affxparser on the Mac (which, I had 
thought, disappeared in the final release), and the latest version of 
the sscore package uses routines from the affy package rather than the 
affxparser package to get the additional information.  (I had seen the 
problem appear with the pre-release versions of affxparser, not with 
prior or later versions, which explains why your colleague running R 
2.3.1 does not have this happen).

In short, though, Wolfgang's advice is quite sound.  Updating to the 
latest version should correct the problem.

Best,
Richard Kennedy
Department of Biostatistics
Virginia Commonwealth University


Wolfgang Huber wrote:
> Hi Chris,
>
> could you try with the latest released version of R (2.5.1) and
> Bioconductor packages? And if the error should persist, in the current
> devel versions? And then report the result?
>
> I could imagine that developers have not that much enthusiasm for
> hunting potential bugs in older versions of the software when it indeed
> may be none, or may already have been fixed, and their time could be
> spent improving the current versions.
>
> Best wishes
>  Wolfgang
>
> ------------------------------------------------------------------
> Wolfgang Huber  EBI/EMBL  Cambridge UK  http://www.ebi.ac.uk/huber
>
>
> Chris Parkin ha scritto:
>   
>> Hello,
>>
>> I am trying to use SScore for a microarray analysis, but I keep getting a
>> fatal error:
>> *******************************************************************
>> *** caught bus error ***
>> address 0x8, cause 'non-existent physical address'
>>
>> Traceback:
>>  1: .Call("R_affx_get_cel_file_header", filename, PACKAGE = "affxparser")
>>  2: readCelHeader(filename)
>>  3: readCel(fname[i], readHeader = FALSE, readIntensities = FALSE,
>> readStdvs = TRUE, readPixels = TRUE)
>>  4: SScore(data)
>>
>> Possible actions:
>> 1: abort (with core dump)
>> 2: normal R exit
>> 3: exit R without saving workspace
>> 4: exit R saving workspace
>> Selection:
>> ******************************************************************
>> A co-worker has older versions of R and BioConductor installed and it works
>> fine.  This was his sessionInfo...
>>
>> ***************************************************************>
>> sessionInfo()
>> Version 2.3.1 (2006-06-01)
>> i386-apple-darwin8.6.1
>>
>> attached base packages:
>> [1] "tools"     "methods"   "stats"     "graphics"  "grDevices" "utils"
>> "datasets"  "base"
>>
>> other attached packages:
>> mouse4302cdf    mouse4302      annaffy         KEGG           GO
>> sscore         affy       affyio      Biobase
>>     "1.12.0"     "1.12.0"      "1.4.0"     "1.12.0"     "1.12.0"      "1.4.2"
>>    "1.10.0"      "1.0.0"     "1.10.1"
>> ****************************************************************
>>
>> And this is my session info...
>>
>>     
>>> sessionInfo()
>>>       
>> R version 2.4.1 (2006-12-18)
>> i386-apple-darwin8.8.1
>>
>> locale:
>> en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>>
>> attached base packages:
>> [1] "tools"     "stats"     "graphics"  "grDevices" "utils"     "datasets"
>> [7] "methods"   "base"
>>
>> other attached packages:
>>     sscore affxparser       affy     affyio    Biobase
>>    "1.6.0"    "1.6.2"   "1.12.2"    "1.2.0"   "1.12.2"
>>
>> ***************************************************************
>>
>> Is this just an incompatibility issue?  Does anyone have any ideas?
>>
>> Thanks,
>>
>> Chris
>>
>> Chris Parkin
>> Tufts University Medical School
>> Center for Neuroscience Research
>>
>> 	[[alternative HTML version deleted]]
>>
>>     
>
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