[BioC] Problem installing affy in Debian lenny 64 bits

Martin Morgan mtmorgan at fhcrc.org
Thu Sep 24 15:23:36 CEST 2009

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

Hope that sets you in the right direction.


>> 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
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Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
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