[BioC] ReadAffy crashes R-devel on mac

[Diego Diez]

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
> > >
> > >
> > >
> >
> ____________________________________________________________________________________
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> > >
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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