thank you Seanof course my brain is fried by now with all these felines. yes
you are right...though even with this rectification my problem persists.
Massimo
On Tue, Apr 21, 2009 at 3:24 PM, Sean Davis <sdav...@mail.nih.gov> wrote:
>
>
> 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
>>
>> [[alternative HTML version deleted]]
>>
>> _______________________________________________
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>> R-SIG-Mac@stat.math.ethz.ch
>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>>
>
>
--
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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