[BioC] ReadAffy crashes R-devel on mac

[Helen Zhou]

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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> 
> 



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