[BioC] Installing rMAT

[Vincent Carey]

On Tue, Jun 23, 2009 at 1:24 PM, Rodrigo Drummond<rddrummond at gmail.com> wrote:
> Greetings,
>
> I am trying to install the rMAT package in a 64bits Intel(R) Core(TM)2 Quad
> 2.50GHz running R version 2.7.2. First I installed gsl and Atlas (with

1) you should always include the result of sessionInfo() when posting a problem
2) 2.7.2 is way out of date and it is unlikely anyone developing will
be able to reproduce
3) the error mentioned concerns availability of BLAS symbols, not the
existence of the
,so file you checked
4) the --library setting you made has a colon in it which seems wrong
-- what OS are you using

> parameters set to build dynamics libraries).
> Before installing rMAT, I also set the variable:
>
> export LD_LIBRARY_PATH=/usr/local/lib:/usr/local/atlas/lib:$LD_LIBRARY_PATH
>
> (gsl dynamic libraries are in /usr/local/lib/ and atlas dynamic libraries
> are in /usr/local/atlas/lib/)
>
> Then I tried to install the package, according to instructions in its
> documentation:
>
> R CMD INSTALL R CMD INSTALL rMAT_1.1.2.tar.gz
> --configure-args="--with-blas='-L/usr/local/atlas/lib/
> --library=:libcblas.so'"
>
> (I also tried R CMD INSTALL rMAT_1.1.2.tar.gz
> --configure-args="--with-blas='-L/usr/local/atlas/lib/
> --library=:libatlas.so'" and to include all atlas libraries in the command
> line: R CMD INSTALL rMAT_1.1.2.tar.gz
> --configure-args="--with-blas='-L/usr/local/atlas/lib/
> --library=:libatlas.so --library=:libcblas.so
> --library=:libf77blas.so--library=:liblapack.so --library=:libptcblas.so
> --library=:libptf77blas.so'", always with similar results).
>
> Apparently, the installation succeeds and only a few warnings were
> generated. However, when I start R and call the package I get the following
> error:
>
>> library(rMAT)
> Creating a new generic function for "summary" in "rMAT"
> Error in dyn.load(file, DLLpath = DLLpath, ...) :
>  unable to load shared library '/usr/lib64/R/library/rMAT/libs/rMAT.so':
>  /usr/lib64/libgsl.so.0: undefined symbol: cblas_ctrmv
> Error: package/namespace load failed for 'rMAT'
>>
>
> I checked and there is indeed a file rMAT.so at
> /usr/lib64/R/library/rMAT/libs/. I don't know what to try now. Does anyone
> know what is the problem, please?
>
> Thanks!
>
> Rodrigo Drummond
>
>        [[alternative HTML version deleted]]
>
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-- 
Vincent Carey, PhD
Biostatistics, Channing Lab
617 525 2265