Richard & Wolfgang,

Thanks so much for your input.  I installed the most recent versions of R
and BioConductor and things are working smoothly again.

Have a great weekend,

Chris

On 7/20/07, Richard Kennedy <rkennedy@vcu.edu> wrote:
>
> 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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