[BioC] installing biocLite('edgeR') issues
Marinus Pennings
pennings at sc.tamu.edu
Mon Jun 10 19:24:23 CEST 2013
Hi,
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
/g/software/intelXE/composer_xe_2013.4.183/compiler/lib/intel64/libimf.so:
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':
/scratch/pennings/tmp/Rtmp5LmotH/R.INSTALL22017e509b8c/edgeR/src/R_exact_test_by_deviance.cpp:19:
undefined reference to `Rf_isInteger'
/scratch/pennings/tmp/Rtmp5LmotH/R.INSTALL22017e509b8c/edgeR/src/R_exact_test_by_deviance.cpp:19:
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?
Thanks,
Marinus
--
------------------------
Marinus Pennings
pennings at sc.tamu.edu
Supercomputing Facility
Texas A&M University
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