[BioC] SScore Compatibility Problems?

[Kasper Daniel Hansen]

This is indeed a problem with affxparser on the Mac Intel platform  
using R-2.4.x, which I maintain. It really has to do with the fact  
that R-2.4.x on Mac used a custom GCC build that had some really low  
level problems with the system libraries.

The short version of the story is that if you are using an Intel Mac  
you need R-2.5.x and you need to compile affxparser with the Apple  
version of GCC 4 to get it to work. This last thing with the compiler  
is luckily the default, so if you just update R it should work.

If you update R you can also delete /usr/local/gcc4.0 which had the  
custom compiler which is obsolete.

Kasper

On Jul 20, 2007, at 10:06 AM, Richard Kennedy 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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