Hello,

    I initially sent this email to the regular bioconductor mailing list 
but they told me I probably should sent it here.

I'm installing some bioclite packages for one of our users. Config 
params are

R version: 3.0.1
build with: intel composerxe version 13 using mkl

I installed using the info on the website. The first two steps are 
executed without error
|
source("http://bioconductor.org/biocLite.R")
biocLite()|

However, when I try to execute the  command

biocLite('edgeR')


I get the error messages below.

NOTE, when I used a gnu non-mkl version of R 3.0.1 I was able to install 
everything without any problem:

output of "biocLite('edgeR')":

 >  biocLite('edgeR')
BioC_mirror: http://bioconductor.org
Using Bioconductor version 2.12 (BiocInstaller 1.10.2), R version 3.0.1.
Installing package(s) 'edgeR'


trying URL 
'http://bioconductor.org/packages/2.12/bioc/src/contrib/edgeR_3.2.3.tar.gz'
Content type 'application/x-gzip' length 1211896 bytes (1.2 Mb)
opened URL

==================================================
downloaded 1.2 Mb

* installing *source* package 'edgeR' ...
** libs
icpc -I/g/software/R/3.0.1/intelv13-mkl/lib64/R/include -DNDEBUG 
-I./core -I.  -I/usr/local/include    -fpic  -xHost -openmp -O3 -g 
-fp-model precise  -c R_exact_test_by_deviance.cpp -o 
R_exact_test_by_deviance.o
icpc -I/g/software/R/3.0.1/intelv13-mkl/lib64/R/include -DNDEBUG 
-I./core -I.  -I/usr/local/include    -fpic  -xHost -openmp -O3 -g 
-fp-model precise  -c R_loess_by_col.cpp -o R_loess_by_col.o
icpc -I/g/software/R/3.0.1/intelv13-mkl/lib64/R/include -DNDEBUG 
-I./core -I.  -I/usr/local/include    -fpic  -xHost -openmp -O3 -g 
-fp-model precise  -c R_cr_adjust.cpp -o R_cr_adjust.o
icpc -I/g/software/R/3.0.1/intelv13-mkl/lib64/R/include -DNDEBUG 
-I./core -I.  -I/usr/local/include    -fpic  -xHost -openmp -O3 -g 
-fp-model precise  -c R_levenberg.cpp -o R_levenberg.o
icpc -I/g/software/R/3.0.1/intelv13-mkl/lib64/R/include -DNDEBUG 
-I./core -I.  -I/usr/local/include    -fpic  -xHost -openmp -O3 -g 
-fp-model precise  -c R_maximize_interpolant.cpp -o R_maximize_interpolant.o
icpc -I/g/software/R/3.0.1/intelv13-mkl/lib64/R/include -DNDEBUG 
-I./core -I.  -I/usr/local/include    -fpic  -xHost -openmp -O3 -g 
-fp-model precise  -c R_one_group.cpp -o R_one_group.o
icpc -I/g/software/R/3.0.1/intelv13-mkl/lib64/R/include -DNDEBUG 
-I./core -I.  -I/usr/local/include    -fpic  -xHost -openmp -O3 -g 
-fp-model precise  -c R_simple_good_turing.cpp -o R_simple_good_turing.o
icpc -I/g/software/R/3.0.1/intelv13-mkl/lib64/R/include -DNDEBUG 
-I./core -I.  -I/usr/local/include    -fpic  -xHost -openmp -O3 -g 
-fp-model precise  -c core/adj_coxreid.cpp -o core/adj_coxreid.o
icpc -I/g/software/R/3.0.1/intelv13-mkl/lib64/R/include -DNDEBUG 
-I./core -I.  -I/usr/local/include    -fpic  -xHost -openmp -O3 -g 
-fp-model precise  -c core/glm_levenberg.cpp -o core/glm_levenberg.o
icpc -I/g/software/R/3.0.1/intelv13-mkl/lib64/R/include -DNDEBUG 
-I./core -I.  -I/usr/local/include    -fpic  -xHost -openmp -O3 -g 
-fp-model precise  -c core/glm_one_group.cpp -o core/glm_one_group.o
icpc -I/g/software/R/3.0.1/intelv13-mkl/lib64/R/include -DNDEBUG 
-I./core -I.  -I/usr/local/include    -fpic  -xHost -openmp -O3 -g 
-fp-model precise  -c core/interpolator.cpp -o core/interpolator.o
icc -std=gnu99 -I/g/software/R/3.0.1/intelv13-mkl/lib64/R/include 
-DNDEBUG -I./core -I.  -I/usr/local/include    -fpic  -xHost -openmp -O3 
-g -fp-model precise  -c core/fmm_spline.c -o core/fmm_spline.o
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/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_exact_test_by_deviance.cpp:19: 
undefined reference to `Rf_isInteger'
/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_exact_test_by_deviance.cpp:19: 
undefined reference to `Rf_isInteger'
/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_exact_test_by_deviance.cpp:20: 
undefined reference to `Rf_isReal'
/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_exact_test_by_deviance.cpp:22: 
undefined reference to `Rf_asInteger'
/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_exact_test_by_deviance.cpp:22: 
undefined reference to `Rf_asInteger'
/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_exact_test_by_deviance.cpp:23: 
undefined reference to `LENGTH'
/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_exact_test_by_deviance.cpp:24: 
undefined reference to `LENGTH'
/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_exact_test_by_deviance.cpp:24: 
undefined reference to `LENGTH'
/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_exact_test_by_deviance.cpp:29: 
undefined reference to `INTEGER'
/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_exact_test_by_deviance.cpp:29: 
undefined reference to `INTEGER'
/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_exact_test_by_deviance.cpp:30: 
undefined reference to `REAL'
/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_exact_test_by_deviance.cpp:31: 
undefined reference to `Rf_asReal'
/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_exact_test_by_deviance.cpp:32: 
undefined reference to `Rf_asReal'
/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_exact_test_by_deviance.cpp:37: 
undefined reference to `Rf_allocVector'
/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_exact_test_by_deviance.cpp:37: 
undefined reference to `Rf_protect'
/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_exact_test_by_deviance.cpp:38: 
undefined reference to `REAL'
/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_exact_test_by_deviance.cpp:140: 
undefined reference to `Rf_mkString'
/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_exact_test_by_deviance.cpp:138: 
undefined reference to `Rf_unprotect'
/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_exact_test_by_deviance.cpp:134: 
undefined reference to `Rf_unprotect'
/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_exact_test_by_deviance.cpp:97: 
undefined reference to `Rf_pbeta'
/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_exact_test_by_deviance.cpp:98: 
undefined reference to `Rf_pbeta'
/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_exact_test_by_deviance.cpp:109: 
undefined reference to `Rf_lbeta'
/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_exact_test_by_deviance.cpp:118: 
undefined reference to `Rf_lbeta'
/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_exact_test_by_deviance.cpp:123: 
undefined reference to `Rf_lbeta'
/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_exact_test_by_deviance.cpp:130: 
undefined reference to `Rf_lbeta'
R_loess_by_col.o: In function `std::_Deque_base<double const*, 
std::allocator<double const*> >::~_Deque_base()':
/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_loess_by_col.cpp:12: 
undefined reference to `Rf_isReal'
/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_loess_by_col.cpp:13: 
undefined reference to `Rf_isReal'
/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_loess_by_col.cpp:15: 
undefined reference to `LENGTH'
R_loess_by_col.o: In function `R_loess_by_col':
/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_loess_by_col.cpp:16: 
undefined reference to `Rf_asInteger'
/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_loess_by_col.cpp:22: 
undefined reference to `REAL'
/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_loess_by_col.cpp:23: 
undefined reference to `Rf_asInteger'
/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_loess_by_col.cpp:24: 
undefined reference to `LENGTH'
/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_loess_by_col.cpp:28: 
undefined reference to `REAL'
/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_loess_by_col.cpp:136: 
undefined reference to `Rf_mkString'
/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_loess_by_col.cpp:32: 
undefined reference to `Rf_allocVector'
/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_loess_by_col.cpp:32: 
undefined reference to `Rf_protect'
/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_loess_by_col.cpp:33: 
undefined reference to `Rf_allocMatrix'
/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_loess_by_col.cpp:33: 
undefined reference to `SET_VECTOR_ELT'
/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_loess_by_col.cpp:34: 
undefined reference to `Rf_allocVector'
/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_loess_by_col.cpp:34: 
undefined reference to `SET_VECTOR_ELT'
/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_loess_by_col.cpp:36: 
undefined reference to `VECTOR_ELT'
/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_loess_by_col.cpp:36: 
undefined reference to `REAL'
/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_loess_by_col.cpp:37: 
undefined reference to `VECTOR_ELT'
/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_loess_by_col.cpp:37: 
undefined reference to `REAL'
/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_loess_by_col.cpp:133: 
undefined reference to `Rf_unprotect'
R_cr_adjust.o: In function `R_cr_adjust':
/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_cr_adjust.cpp:14: 
undefined reference to `Rf_isReal'
/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_cr_adjust.cpp:15: 
undefined reference to `Rf_isReal'
/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_cr_adjust.cpp:17: 
undefined reference to `Rf_asInteger'
/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_cr_adjust.cpp:18: 
undefined reference to `LENGTH'
/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_cr_adjust.cpp:19: 
undefined reference to `LENGTH'
/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_cr_adjust.cpp:22: 
undefined reference to `REAL'
/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_cr_adjust.cpp:23: 
undefined reference to `REAL'
/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_cr_adjust.cpp:25: 
undefined reference to `Rf_allocVector'
/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_cr_adjust.cpp:25: 
undefined reference to `Rf_protect'
/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_cr_adjust.cpp:26: 
undefined reference to `REAL'
/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_cr_adjust.cpp:44: 
undefined reference to `Rf_unprotect'
/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_cr_adjust.cpp:46: 
undefined reference to `Rf_mkString'
/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_cr_adjust.cpp:40: 
undefined reference to `Rf_unprotect'
R_levenberg.o: In function `R_levenberg':
/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_levenberg.cpp:6: 
undefined reference to `Rf_isReal'
/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_levenberg.cpp:7: 
undefined reference to `Rf_isReal'
/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_levenberg.cpp:8: 
undefined reference to `Rf_isReal'
/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_levenberg.cpp:9: 
undefined reference to `Rf_isReal'
/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_levenberg.cpp:10: 
undefined reference to `Rf_isReal'
R_levenberg.o:/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_levenberg.cpp:11: 
more undefined references to `Rf_isReal' follow
R_levenberg.o: In function `R_levenberg':
/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_levenberg.cpp:14: 
undefined reference to `Rf_asInteger'
/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_levenberg.cpp:15: 
undefined reference to `Rf_asInteger'
/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_levenberg.cpp:16: 
undefined reference to `LENGTH'
/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_levenberg.cpp:17: 
undefined reference to `LENGTH'
/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_levenberg.cpp:22: 
undefined reference to `LENGTH'
/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_levenberg.cpp:24: 
undefined reference to `LENGTH'
/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_levenberg.cpp:26: 
undefined reference to `LENGTH'
R_levenberg.o:/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_levenberg.cpp:28: 
more undefined references to `LENGTH' follow
R_levenberg.o: In function `R_levenberg':
/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_levenberg.cpp:33: 
undefined reference to `REAL'
/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_levenberg.cpp:33: 
undefined reference to `REAL'
/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_levenberg.cpp:33: 
undefined reference to `REAL'
/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_levenberg.cpp:34: 
undefined reference to `REAL'
/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_levenberg.cpp:34: 
undefined reference to `REAL'
R_levenberg.o:/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_levenberg.cpp:34: 
more undefined references to `REAL' follow
R_levenberg.o: In function `R_levenberg':
/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_levenberg.cpp:37: 
undefined reference to `Rf_allocVector'
/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_levenberg.cpp:37: 
undefined reference to `Rf_protect'
/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_levenberg.cpp:38: 
undefined reference to `Rf_allocMatrix'
/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_levenberg.cpp:38: 
undefined reference to `SET_VECTOR_ELT'
/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_levenberg.cpp:39: 
undefined reference to `Rf_allocMatrix'
/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_levenberg.cpp:39: 
undefined reference to `SET_VECTOR_ELT'
/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_levenberg.cpp:40: 
undefined reference to `Rf_allocVector'
/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_levenberg.cpp:40: 
undefined reference to `SET_VECTOR_ELT'
/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_levenberg.cpp:41: 
undefined reference to `Rf_allocVector'
/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_levenberg.cpp:41: 
undefined reference to `SET_VECTOR_ELT'
/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_levenberg.cpp:42: 
undefined reference to `Rf_allocVector'
/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_levenberg.cpp:42: 
undefined reference to `SET_VECTOR_ELT'
/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_levenberg.cpp:43: 
undefined reference to `VECTOR_ELT'
/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_levenberg.cpp:43: 
undefined reference to `REAL'
/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_levenberg.cpp:44: 
undefined reference to `VECTOR_ELT'
/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_levenberg.cpp:44: 
undefined reference to `REAL'
/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_levenberg.cpp:45: 
undefined reference to `VECTOR_ELT'
/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_levenberg.cpp:45: 
undefined reference to `REAL'
/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_levenberg.cpp:46: 
undefined reference to `VECTOR_ELT'
/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_levenberg.cpp:46: 
undefined reference to `INTEGER'
/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_levenberg.cpp:47: 
undefined reference to `VECTOR_ELT'
/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_levenberg.cpp:47: 
undefined reference to `LOGICAL'
/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_levenberg.cpp:50: 
undefined reference to `Rf_asInteger'
/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_levenberg.cpp:50: 
undefined reference to `Rf_asReal'
/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_levenberg.cpp:72: 
undefined reference to `Rf_unprotect'
/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_levenberg.cpp:78: 
undefined reference to `Rf_mkString'
/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_levenberg.cpp:76: 
undefined reference to `Rf_unprotect'
R_maximize_interpolant.o: In function `R_maximize_interpolant':
/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_maximize_interpolant.cpp:7: 
undefined reference to `Rf_isReal'
/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_maximize_interpolant.cpp:8: 
undefined reference to `Rf_isReal'
/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_maximize_interpolant.cpp:11: 
undefined reference to `LENGTH'
/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_maximize_interpolant.cpp:12: 
undefined reference to `REAL'
/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_maximize_interpolant.cpp:13: 
undefined reference to `REAL'
/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_maximize_interpolant.cpp:14: 
undefined reference to `LENGTH'
/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_maximize_interpolant.cpp:19: 
undefined reference to `Rf_allocVector'
/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_maximize_interpolant.cpp:19: 
undefined reference to `Rf_protect'
/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_maximize_interpolant.cpp:20: 
undefined reference to `REAL'
/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_maximize_interpolant.cpp:31: 
undefined reference to `Rf_unprotect'
/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_maximize_interpolant.cpp:33: 
undefined reference to `Rf_mkString'
/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_maximize_interpolant.cpp:28: 
undefined reference to `Rf_unprotect'
R_one_group.o: In function `R_one_group':
/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_one_group.cpp:6: 
undefined reference to `Rf_asInteger'
/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_one_group.cpp:7: 
undefined reference to `Rf_asInteger'
/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_one_group.cpp:8: 
undefined reference to `LENGTH'
/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_one_group.cpp:10: 
undefined reference to `Rf_asInteger'
/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_one_group.cpp:11: 
undefined reference to `Rf_asReal'
/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_one_group.cpp:12: 
undefined reference to `Rf_isReal'
/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_one_group.cpp:13: 
undefined reference to `Rf_isReal'
/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_one_group.cpp:15: 
undefined reference to `LENGTH'
/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_one_group.cpp:16: 
undefined reference to `LENGTH'
/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_one_group.cpp:19: 
undefined reference to `Rf_isInteger'
/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_one_group.cpp:23: 
undefined reference to `INTEGER'
/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_one_group.cpp:24: 
undefined reference to `R_alloc'
/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_one_group.cpp:26: 
undefined reference to `REAL'
/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_one_group.cpp:28: 
undefined reference to `REAL'
/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_one_group.cpp:29: 
undefined reference to `REAL'
/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_one_group.cpp:32: 
undefined reference to `Rf_allocVector'
/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_one_group.cpp:32: 
undefined reference to `Rf_protect'
/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_one_group.cpp:33: 
undefined reference to `Rf_allocVector'
/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_one_group.cpp:33: 
undefined reference to `SET_VECTOR_ELT'
/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_one_group.cpp:34: 
undefined reference to `Rf_allocVector'
/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_one_group.cpp:34: 
undefined reference to `SET_VECTOR_ELT'
/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_one_group.cpp:35: 
undefined reference to `VECTOR_ELT'
/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_one_group.cpp:35: 
undefined reference to `REAL'
/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_one_group.cpp:36: 
undefined reference to `VECTOR_ELT'
/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_one_group.cpp:36: 
undefined reference to `LOGICAL'
/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_one_group.cpp:60: 
undefined reference to `Rf_unprotect'
/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_one_group.cpp:63: 
undefined reference to `Rf_mkString'
/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_one_group.cpp:55: 
undefined reference to `Rf_unprotect'
R_simple_good_turing.o: In function `R_simple_good_turing':
/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_simple_good_turing.cpp:14: 
undefined reference to `Rf_asReal'
/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_simple_good_turing.cpp:15: 
undefined reference to `Rf_isInteger'
/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_simple_good_turing.cpp:16: 
undefined reference to `Rf_isInteger'
/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_simple_good_turing.cpp:17: 
undefined reference to `LENGTH'
/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_simple_good_turing.cpp:18: 
undefined reference to `LENGTH'
/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_simple_good_turing.cpp:19: 
undefined reference to `INTEGER'
/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_simple_good_turing.cpp:20: 
undefined reference to `INTEGER'
/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_simple_good_turing.cpp:25: 
undefined reference to `R_alloc'
/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_simple_good_turing.cpp:54: 
undefined reference to `Rf_allocVector'
/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_simple_good_turing.cpp:54: 
undefined reference to `Rf_protect'
/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_simple_good_turing.cpp:55: 
undefined reference to `Rf_ScalarReal'
/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_simple_good_turing.cpp:55: 
undefined reference to `SET_VECTOR_ELT'
/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_simple_good_turing.cpp:56: 
undefined reference to `Rf_allocVector'
/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_simple_good_turing.cpp:56: 
undefined reference to `SET_VECTOR_ELT'
/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_simple_good_turing.cpp:57: 
undefined reference to `VECTOR_ELT'
/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_simple_good_turing.cpp:57: 
undefined reference to `REAL'
/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_simple_good_turing.cpp:96: 
undefined reference to `Rf_unprotect'
/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_simple_good_turing.cpp:99: 
undefined reference to `Rf_mkString'
core/glm_levenberg.o: In function `glm_levenberg::fit(double const*, 
double const*, double const&, double*, double*)':
/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/core/glm_levenberg.cpp:83: 
undefined reference to `R_NaReal'
core/glm_one_group.o: In function `glm_one_group(int const&, int const&, 
double const&, double const*, double const*, double const&)':
/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/core/glm_one_group.cpp:17: 
undefined reference to `R_NegInf'
make: *** [edgeR.so] Error 1
ERROR: compilation failed for package 'edgeR'
* removing '/g/software/R/3.0.1/intelv13-mkl/lib64/R/library/edgeR'

The downloaded source packages are in
         '/scratch/pennings/tmp/Rtmpgds5sk/downloaded_packages'
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Warning message:
In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
   installation of package 'edgeR' had non-zero exit status
 >
 >




Thanks,
    Marinus


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


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