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)
> 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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