[BioC] Biobase 2.8 with R 2.13.0 fails on my Mac

[Vincent Carey]

I reproduced this error with a fresh install of the R for MacOSX
binary.  I do not know the specific solution for the binary
installation of Biobase at this time.  However, I do routinely install
and update Xcode tools for mac osx.  And biocLite("Biobase",
type="source") created a properly loadable installation.  I would
recommend installation of Xcode tools to allow you greater versatility
in such situations.

On Thu, Apr 14, 2011 at 6:29 PM, Janet Young <jayoung at fhcrc.org> wrote:
> Hi,
>
> Thanks for the new version - I'm looking forward to using it.  I've installed it fine on the
> linux machine I use, but not on Mac - I'm not sure if it's a problem with R, or with
> Biobase, or with my setup (do I need to to try harder to get rid of R-2.12?).  I think
> I've given all the relevant information below.
>
> all the best,
>
> Janet
>
>
>
>
>> source("http://www.bioconductor.org/biocLite.R")
> BioC_mirror = http://bioconductor.org
> Change using chooseBioCmirror().
>> biocLite("Biobase")
> Using R version 2.13.0, biocinstall version 2.8.3.
> Installing Bioconductor version 2.8 packages:
> [1] "Biobase"
> Please wait...
>
> trying URL
> 'http://bioconductor.org/packages/2.8/bioc/bin/macosx/leopard/contrib/2.13/Biobase_2.12.0.tgz'
> Content type 'application/x-gzip' length 2427717 bytes (2.3 Mb)
> opened URL
> ==================================================
> downloaded 2.3 Mb
>
>
> The downloaded packages are in
>        /var/folders/z5/z5O6DCxcG60UeeZiA7+v1E+++Tc/-Tmp-//RtmpP6YQAN/downloaded_packages
>> library(Biobase)
> Error in dyn.load(file, DLLpath = DLLpath, ...) :
>  unable to load shared object
> '/Library/Frameworks/R.framework/Versions/2.13/Resources/library/Biobase/libs/i386/Biobase.so':
>
> dlopen(/Library/Frameworks/R.framework/Versions/2.13/Resources/library/Biobase/libs/i386/Biobase.
> so, 6): Library not loaded: /Library/Frameworks/R.framework/Versions/2.12/Resources/lib/libR.dylib
>  Referenced from:
> /Library/Frameworks/R.framework/Versions/2.13/Resources/library/Biobase/libs/i386/Biobase.so
>  Reason: image not found
> Error: package/namespace load failed for 'Biobase'
>
>
>
>> sessionInfo()
> R version 2.13.0 (2011-04-13)
> Platform: i386-apple-darwin9.8.0/i386 (32-bit)
>
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> loaded via a namespace (and not attached):
> [1] tools_2.13.0
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
>