[BioC] ReadAffy crashes R-devel on mac

[Martin Morgan]

Hi Helen -- this might be an inscrutable Mac problem for which someone
else will have to chime in, but just in case, you say

>> repos <- biocReposList()
>> update.packages(repos=repos, ask=FALSE)

'biocReposList' implies that Biobase is loaded. On some platforms
trying to update Biobase will then fail. The correct sequence is

% R --vanilla
> source('http://bioconductor.org/bioLite.R')
> update.packages(repos=biocinstallRepos(), ask=FALSE)

Hope that helps,

Martin

Helen Zhou <zhou.helen at yahoo.com> writes:

> 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
>> > 
>> > 
>> >      
>>
> ____________________________________________________________________________________
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>> > 
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>> 
>
>
>
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-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
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