On Tue, Apr 21, 2009 at 9:10 AM, Massimo Pinto <pintare...@gmail.com> wrote:
> Greetings all
> last week I attempted to install the genefilter package using
> BiocLite(genefilter) from the R prompt. Despite having a Mac OS X 10.5.6.
> (Tiger), for some reason which I don't understand in full, BioC 2.3
> believes
> I am running on Mac OS X 10.4 (Leopard)
Hi, Massimo.
Os 10.4 is Tiger and 10.5 is Leopard.
Sean
>
>
> > sessionInfo()
> R version 2.8.1 (2008-12-22)
> i386-apple-darwin8.11.1
>
> therefore, when I run biocLite, general Mac binaries are installed and this
> results in execution errors.
>
> Much thanks to the help found on this list, I have downloaded the tarball
> for OSX 10.5 binaries and installed manually. It worked just fine.
>
> Today I have encountered a similar problem with the package affy.
> Accordingly, I have downloaded the OS X 10.5 binaries and installed
> manually:
>
> > install.packages("/Users/massimopinto/Desktop/affy_1.20.2.tgz",
> repos=NULL, dependencies=TRUE)
>
> however, when I load the library:
>
> > 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)'.
>
> Error in dyn.load(file, DLLpath = DLLpath, ...) :
> unable to load shared library
>
> '/Library/Frameworks/R.framework/Resources/library/preprocessCore/libs/i386/preprocessCore.so':
>
>
> dlopen(/Library/Frameworks/R.framework/Resources/library/preprocessCore/libs/i386/preprocessCore.so,
> 6): Library not loaded: /usr/local/lib/libgfortran.2.dylib
> Referenced from:
>
> /Library/Frameworks/R.framework/Resources/library/preprocessCore/libs/i386/preprocessCore.so
> Reason: image not found
> Error: package/namespace load failed for 'affy'
>
> ===the package does not get loaded as a library cannot be found. Similarly,
> I run into problems if I install as follows:
>
> > install.packages("affy", repos="
>
> http://www.bioconductor.org/packages/2.3/bioc/bin/macosx/leopard/contrib/2.8/
> ",
> contriburl="
>
> http://www.bioconductor.org/packages/2.3/bioc/bin/macosx/leopard/contrib/2.8/
> ",
> dependencies=TRUE)
> trying URL '
>
> http://www.bioconductor.org/packages/2.3/bioc/bin/macosx/leopard/contrib/2.8//affy_1.20.2.tgz
> '
> Content type 'application/x-gzip' length 1452708 bytes (1.4 Mb)
> [...]
>
> Could it be that the binaries at
>
> http://www.bioconductor.org/packages/2.3/bioc/bin/macosx/leopard/contrib/2.8/are
> in fact compiled for Tiger?
>
> Massimo
> --
>
> Massimo Pinto
> Post Doctoral Research Fellow
> Enrico Fermi Centre and Italian Public Health Research Institute (ISS),
> Rome
> http://claimid.com/massimopinto
>
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>
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