[Bioc-devel] installation errors with selected Bioconductor packages on Linux

[Seth Falcon]

Hi Richard,

On 21 Sep 2005, rwang at immunetolerance.org wrote:
> but 11 packages have failed to install repeatedly.  I've appended an
> example of the error message I'm getting, in this case for the affy
> package.  Any advice or insights would be greatly appreciated.
>
> gcc -shared -L/usr/local/lib -o affy.so chipbackground.o
> getall_locations.o mas5calls.o qnorm.o read_abatch.o rma2.o
> rma_background2.o rma_common.o -lz   -L/usr/lib/R/lib -lR
>
> gcc -shared -L/usr/local/lib -o affy.so chipbackground.o
> getall_locations.o mas5calls.o qnorm.o read_abatch.o rma2.o
> rma_background2.o rma_common.o -lz   -L/usr/lib/R/lib -lR
>
> /usr/bin/ld: skipping incompatible /usr/lib/R/lib/libR.so when
> searching for -lR/usr/bin/ld: cannot find -lR
>
> collect2: ld returned 1 exit status

The error message suggests an R installation/system configuration
issue.  How did you install R? 

The problem seems to be that the build is trying to link to libR.so,
but no such library is available.  When you build R from source, you
have a choice of building libR.so or not.  The default is not to build
it.  

When I install the affy package on one of our Linux systems, here's
the call to the linker that I see:

gcc -shared -L/usr/local/lib64 -o affy.so chipbackground.o
getall_locations.o mas5calls.o qnorm.o read_abatch.o rma2.o
rma_background2.o rma_common.o -lz

Notice that there is no -lR.  So I don't have an answer for you, but
perhaps the above gives you some hints of where to look (R site config
stuff --- see the admin manual).  You could also try building R from
source and seeing if that changes anything.

+ seth