[BioC] ReadAffy crashes R-devel on mac

Wed Feb 13 20:13:40 CET 2008

I would suggest installing from scratch, making sure that you install  
from source and that your toolchain is set properly to compile from  
scratch on the Mac. Most likely there is some mismatch between  
compiler versions. If you want more information, tell us
   1) Are you using Leopard?
   2) Exactly what compiler you are using (include the build number  
please) and how did you install it.
The answer to 2) might be simple like "I never installed a compiler"  
or "I installed Xcode 3 from the leopard disc" or ...

A good idea would be to read
http://r.research.att.com/tools/
carefully

Kasper

On Feb 13, 2008, at 7:42 AM, Diego Diez wrote:

> Hi Helen,
>
> (sorry for the double message I forgot to cc bioc)
>
> I found the same problem when installing BioC development packages
> with R-devel in a PPC Mac. The reason might be that the binary
> packages are not compiled for PPC in the devel branch although I am
> not sure about it. Anyway, to solve it you should use source packages,
> i.e. either:
>
> source('http://bioconductor.org/bioLite.R')
> biocLite(type="source")
>
> or if you want to update your installation:
>
> library(Biobase)
> update.packages(repos=biocReposList(), type="source")
>
> unfortunately, after realizing my problem I was unable to fix the
> installation and I had to reinstall R-devel and BioC again. Maybe I
> didn't too hard.
>
> Hope this helps.
>
> Diego.
>
> On Feb 13, 2008 8:06 PM, Helen Zhou <zhou.helen at yahoo.com> wrote:
>> Dear Ben,
>>
>> thanks your for your fast reply. I actually thought I
>> installed everything with biocLite() when I changed to
>> R-devel a couple of weeks ago, but I guess I must have
>> messed up somewhere.
>>
>> Unfortunately, I suspect that I have some issues with
>> my installation. I updated the packages by running
>>
>>> repos <- biocReposList()
>>> update.packages(repos=repos, ask=FALSE)
>>
>> but now, what ever I try I run into a problem with
>> Biobase. My previous version was 1.17.8, but after the
>> update it's 1.17.12, but I can't actually load it. In
>> a new R-session with nothing else loaded:
>>
>>> library(Biobase)
>> Loading required package: tools
>> Error in dyn.load(file, ...) :
>>   unable to load shared library
>> '/Library/Frameworks/R.framework/Versions/2.7/Resources/library/ 
>> Biobase/libs/i386/Biobase.so':
>>
>> dlopen(/Library/Frameworks/R.framework/Versions/2.7/Resources/ 
>> library/Biobase/libs/i386/Biobase.so,
>> 6): Library not loaded: /usr/lib/libiconv.2.dylib
>>   Referenced from:
>> /Library/Frameworks/R.framework/Versions/2.7/Resources/library/ 
>> Biobase/libs/i386/Biobase.so
>>   Reason: Incompatible library version: Biobase.so
>> requires version 7.0.0 or later, but libiconv.2.dylib
>> provides version 5.0.0
>> Error: package/namespace load failed for 'Biobase'
>>
>> Regards
>> - Helen
>>
>>
>> --- Ben Bolstad <bmb at bmbolstad.com> wrote:
>>
>>> Looking at your sessionInfo() almost certainly your
>>> affyio is out of
>>> date (both for R-2.6.1 and R-2.7.0),
>>>
>>> Current Release version: 1.6.1
>>> Current Devel version: 1.7.11
>>>
>>> Your error is likely due to mismatched versions of
>>> the packages.
>>>
>>> Best,
>>>
>>> Ben
>>>
>>>
>>>
>>>
>>>
>>> On Wed, 2008-02-13 at 02:07 -0800, Helen Zhou wrote:
>>>> Dear list,
>>>>
>>>> oddly enough, whenever I try to read in affymetrix
>>>> files my R-session crashes. This includes when I
>>> try
>>>> to re-run old scripts. I've never had this issue
>>>> before, but updated from 2.6.1 to 2.7.0 recently.
>>>>
>>>> Any help/comments would be much appreciated! The
>>> full
>>>> list of commands + sessionInfo is shown below.
>>> I've
>>>> tried with other cel files as well (affy mouse
>>>> arrays), but the result is always the same.
>>>>
>>>>> setwd("~/Desktop")
>>>>> library(affy)
>>>> Loading required package: Biobase
>>>> Loading required package: tools
>>>>
>>>> Welcome to Bioconductor
>>>>
>>>>   Vignettes contain introductory material. To
>>> view,
>>>> type
>>>>   'openVignette()'. To cite Bioconductor, see
>>>>   'citation("Biobase")' and for packages
>>>> 'citation(pkgname)'.
>>>>
>>>> Loading required package: affyio
>>>> Loading required package: preprocessCore
>>>>> sessionInfo()
>>>> R version 2.7.0 Under development (unstable)
>>>> (2007-12-22 r43762)
>>>> i386-apple-darwin8.10.1
>>>>
>>>> locale:
>>>>
>>>
>> en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8
>>>>
>>>> attached base packages:
>>>> [1] tools     stats     graphics  grDevices utils
>>>
>>>> datasets  methods   base
>>>>
>>>> other attached packages:
>>>> [1] affy_1.17.3          preprocessCore_1.1.5
>>>> affyio_1.5.11        Biobase_1.17.8
>>>>> raw <- ReadAffy("GSM172068.CEL")
>>>>
>>>>  *** caught bus error ***
>>>> address 0xc, cause 'non-existent physical address'
>>>>
>>>> Traceback:
>>>>  1: .Call("ReadHeader",
>>> as.character(filenames[[1]]),
>>>> PACKAGE = "affyio")
>>>>  2: read.affybatch(filenames = l$filenames,
>>> phenoData
>>>> = l$phenoData,     description = l$description,
>>> notes
>>>> = notes, compress = compress,     rm.mask =
>>> rm.mask,
>>>> rm.outliers = rm.outliers, rm.extra = rm.extra,
>>>
>>>> verbose = verbose, sd = sd, cdfname = cdfname)
>>>>  3: ReadAffy("GSM172068.CEL")
>>>>
>>>> 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:
>>>>
>>>> Regards
>>>> - Helen
>>>>
>>>>
>>>>
>>>
>> _____________________________________________________________________ 
>> _______________
>>>> Be a better friend, newshound, and
>>>>
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>>>
>>>
>>
>>
>>
>>        
>> _____________________________________________________________________ 
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>
>
>
> -- 
> Dr. Diego Diez
> Bioinformatics center,
> Institute for Chemical Research,
> Kyoto University.
> Gokasho, Uji, Kyoto 611-0011 JAPAN
> diez at kuicr.kyoto-u.ac.jp
>
> _______________________________________________
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> gmane.science.biology.informatics.conductor