[BioC] SScore Compatibility Problems?

[Wolfgang Huber]

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
> 
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