> > Dear all, > > I'm running Debian lenny 64 bits. I tried to install affy package, > from > Bioconductor using the following commands: > >> source("http://bioconductor.org/biocLite.R") >> biocLite('affy') > > I had to install some packages in the system to fulfill dependency > requirements, > including the package liblapack-dev. Afetr this, I manage to compile > and install > without errors. However, when I try to load the library I get the > following > error: > >> library(affy) > Error in dyn.load(file, DLLpath = DLLpath, ...) : > unable to load shared library > '/home/mlrodrigues/R/x86_64-pc-linux-gnu-library/2.9/preprocessCore/ > libs/preprocessCore.so': > /usr/lib/atlas/liblapack.so.3gf: undefined symbol: ATL_chemv > Error: package/namespace load failed for 'affy' > > Does anyone know how to workaround this problem? > > Many thanks, > > Sofia Braga, MD Computational Genomics Laboratory Instituto Gulbenkian Ciencia sbraga at igc.gulbenkian.pt

Hi Sofia -- Sofia Braga wrote: > > > >> >> Dear all, >> >> I'm running Debian lenny 64 bits. I tried to install affy package, from >> Bioconductor using the following commands: >> >>> source("http://bioconductor.org/biocLite.R") >>> biocLite('affy') >> >> I had to install some packages in the system to fulfill dependency >> requirements, >> including the package liblapack-dev. Afetr this, I manage to compile >> and install >> without errors. However, when I try to load the library I get the >> following >> error: >> >>> library(affy) >> Error in dyn.load(file, DLLpath = DLLpath, ...) : >> unable to load shared library >> '/home/mlrodrigues/R/x86_64-pc-linux-gnu- library/2.9/preprocessCore/libs/preprocessCore.so': >> >> /usr/lib/atlas/liblapack.so.3gf: undefined symbol: ATL_chemv A little bit of a guess, but the error is coming from /usr/lib/atlas/liblapack, which suggests that your system is configured to find this lapack library. On the other hand, you had to install liblapack-dev, which if I'm reading the lenny page is installing /usr/lib/liblapack.so. It also seems that atlas/liblapack.so.3gf is somehow installed incorrectly, e.g., with a missing dependency on the corresponding blas library. So I think you need to clean up your system installation. Also, if R was installed with, say, the atlas/liblapack (look at R_HOME/etc/Makeconf, for instance), then you'll need to reinstall R to match the cleaned up configuration. Hope that sets you in the right direction. Martin >> Error: package/namespace load failed for 'affy' >> >> Does anyone know how to workaround this problem? >> >> Many thanks, >> >> > > Sofia Braga, MD > Computational Genomics Laboratory > Instituto Gulbenkian Ciencia > sbraga at igc.gulbenkian.pt > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor -- Martin Morgan Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793