[BioC] installing biocLite('edgeR') issues

Marinus Pennings pennings at sc.tamu.edu
Mon Jun 10 19:24:23 CEST 2013


    I'm installing some bioconductor packages for one of our users. Here 
are the steps:

- dource(http://bioconductor.org/biocLite.R")
- biocLite()
- biocLite('edgeR')

The first steps can be executed without any problem but the 
biocLite('edgeR') command causes a lot of errors (below are the first 
few error lines):

icpc -L/usr/local/lib64 -o edgeR.so R_exact_test_by_deviance.o 
R_loess_by_col.o R_cr_adjust.o R_levenberg.o R_maximize_interpolant.o 
R_one_group.o R_simple_good_turing.o core/adj_coxreid.o 
core/glm_levenberg.o core/glm_one_group.o core/interpolator.o 
core/fmm_spline.o -L/g/software/intelXE/composer_xe_2013/mkl/lib/intel64 
-lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -lpthread -lm -lifport 
-lifcoremt -limf -lsvml -lm -lipgo -liomp5 -lirc -lpthread -lirc_s -ldl
warning: warning: feupdateenv is not implemented and will always fail
/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../lib64/crt1.o: In 
function `_start':
(.text+0x20): undefined reference to `main'
R_exact_test_by_deviance.o: In function `R_exact_test_by_deviance':
undefined reference to `Rf_isInteger'
undefined reference to `Rf_isInteger'

Seems the problem starts when trying to create lib edgeR.so

Here are the sytem specs  I use:
R version 3.0.1
intel compilers v13.1.2
mkl v11.0.4

When I build R using gcc and without mkl I can install 
"biocLite('edgeR')" without any problems. Anybody had similar problems 
with intel compilers?


Marinus Pennings
pennings at sc.tamu.edu
Supercomputing Facility
Texas A&M University

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