[BioC] installing biocLite('edgeR') issues

Marinus Pennings pennings at sc.tamu.edu
Mon Jun 10 21:34:23 CEST 2013


hi,

thank you for the fast reply. There are real errors, not just warning. 
The package is not build
 > library(edgeR)
Error in library(edgeR) : there is no package called 'edgeR'

Here is the output of sessionInfo():

===
 > sessionsInfo()
Error: could not find function "sessionsInfo"
 > sessionInfo()
R version 3.0.1 (2013-05-16)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
  [1] LC_CTYPE=en_US       LC_NUMERIC=C         LC_TIME=en_US
  [4] LC_COLLATE=en_US     LC_MONETARY=en_US    LC_MESSAGES=en_US
  [7] LC_PAPER=C           LC_NAME=C            LC_ADDRESS=C
[10] LC_TELEPHONE=C       LC_MEASUREMENT=en_US LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods base

other attached packages:
[1] BiocInstaller_1.10.2

loaded via a namespace (and not attached):
[1] tools_3.0.1
 >
===


Here is the complete 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/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_exact_test_by_deviance.cpp:19: 
undefined reference to `Rf_isInteger'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_exact_test_by_deviance.cpp:19: 
undefined reference to `Rf_isInteger'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_exact_test_by_deviance.cpp:20: 
undefined reference to `Rf_isReal'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_exact_test_by_deviance.cpp:22: 
undefined reference to `Rf_asInteger'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_exact_test_by_deviance.cpp:22: 
undefined reference to `Rf_asInteger'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_exact_test_by_deviance.cpp:23: 
undefined reference to `LENGTH'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_exact_test_by_deviance.cpp:24: 
undefined reference to `LENGTH'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_exact_test_by_deviance.cpp:24: 
undefined reference to `LENGTH'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_exact_test_by_deviance.cpp:29: 
undefined reference to `INTEGER'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_exact_test_by_deviance.cpp:29: 
undefined reference to `INTEGER'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_exact_test_by_deviance.cpp:30: 
undefined reference to `REAL'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_exact_test_by_deviance.cpp:31: 
undefined reference to `Rf_asReal'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_exact_test_by_deviance.cpp:32: 
undefined reference to `Rf_asReal'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_exact_test_by_deviance.cpp:37: 
undefined reference to `Rf_allocVector'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_exact_test_by_deviance.cpp:37: 
undefined reference to `Rf_protect'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_exact_test_by_deviance.cpp:38: 
undefined reference to `REAL'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_exact_test_by_deviance.cpp:140: 
undefined reference to `Rf_mkString'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_exact_test_by_deviance.cpp:138: 
undefined reference to `Rf_unprotect'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_exact_test_by_deviance.cpp:134: 
undefined reference to `Rf_unprotect'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_exact_test_by_deviance.cpp:97: 
undefined reference to `Rf_pbeta'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_exact_test_by_deviance.cpp:98: 
undefined reference to `Rf_pbeta'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_exact_test_by_deviance.cpp:109: 
undefined reference to `Rf_lbeta'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_exact_test_by_deviance.cpp:118: 
undefined reference to `Rf_lbeta'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_exact_test_by_deviance.cpp:123: 
undefined reference to `Rf_lbeta'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/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/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_loess_by_col.cpp:12: 
undefined reference to `Rf_isReal'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_loess_by_col.cpp:13: 
undefined reference to `Rf_isReal'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/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/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_loess_by_col.cpp:16: 
undefined reference to `Rf_asInteger'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_loess_by_col.cpp:22: 
undefined reference to `REAL'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_loess_by_col.cpp:23: 
undefined reference to `Rf_asInteger'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_loess_by_col.cpp:24: 
undefined reference to `LENGTH'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_loess_by_col.cpp:28: 
undefined reference to `REAL'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_loess_by_col.cpp:136: 
undefined reference to `Rf_mkString'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_loess_by_col.cpp:32: 
undefined reference to `Rf_allocVector'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_loess_by_col.cpp:32: 
undefined reference to `Rf_protect'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_loess_by_col.cpp:33: 
undefined reference to `Rf_allocMatrix'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_loess_by_col.cpp:33: 
undefined reference to `SET_VECTOR_ELT'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_loess_by_col.cpp:34: 
undefined reference to `Rf_allocVector'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_loess_by_col.cpp:34: 
undefined reference to `SET_VECTOR_ELT'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_loess_by_col.cpp:36: 
undefined reference to `VECTOR_ELT'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_loess_by_col.cpp:36: 
undefined reference to `REAL'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_loess_by_col.cpp:37: 
undefined reference to `VECTOR_ELT'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_loess_by_col.cpp:37: 
undefined reference to `REAL'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/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/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_cr_adjust.cpp:14: 
undefined reference to `Rf_isReal'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_cr_adjust.cpp:15: 
undefined reference to `Rf_isReal'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_cr_adjust.cpp:17: 
undefined reference to `Rf_asInteger'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_cr_adjust.cpp:18: 
undefined reference to `LENGTH'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_cr_adjust.cpp:19: 
undefined reference to `LENGTH'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_cr_adjust.cpp:22: 
undefined reference to `REAL'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_cr_adjust.cpp:23: 
undefined reference to `REAL'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_cr_adjust.cpp:25: 
undefined reference to `Rf_allocVector'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_cr_adjust.cpp:25: 
undefined reference to `Rf_protect'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_cr_adjust.cpp:26: 
undefined reference to `REAL'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_cr_adjust.cpp:44: 
undefined reference to `Rf_unprotect'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_cr_adjust.cpp:46: 
undefined reference to `Rf_mkString'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_cr_adjust.cpp:40: 
undefined reference to `Rf_unprotect'
R_levenberg.o: In function `R_levenberg':
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_levenberg.cpp:6: 
undefined reference to `Rf_isReal'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_levenberg.cpp:7: 
undefined reference to `Rf_isReal'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_levenberg.cpp:8: 
undefined reference to `Rf_isReal'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_levenberg.cpp:9: 
undefined reference to `Rf_isReal'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_levenberg.cpp:10: 
undefined reference to `Rf_isReal'
R_levenberg.o:/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_levenberg.cpp:11: 
more undefined references to `Rf_isReal' follow
R_levenberg.o: In function `R_levenberg':
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_levenberg.cpp:14: 
undefined reference to `Rf_asInteger'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_levenberg.cpp:15: 
undefined reference to `Rf_asInteger'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_levenberg.cpp:16: 
undefined reference to `LENGTH'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_levenberg.cpp:17: 
undefined reference to `LENGTH'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_levenberg.cpp:22: 
undefined reference to `LENGTH'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_levenberg.cpp:24: 
undefined reference to `LENGTH'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_levenberg.cpp:26: 
undefined reference to `LENGTH'
R_levenberg.o:/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_levenberg.cpp:28: 
more undefined references to `LENGTH' follow
R_levenberg.o: In function `R_levenberg':
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_levenberg.cpp:33: 
undefined reference to `REAL'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_levenberg.cpp:33: 
undefined reference to `REAL'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_levenberg.cpp:33: 
undefined reference to `REAL'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_levenberg.cpp:34: 
undefined reference to `REAL'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_levenberg.cpp:34: 
undefined reference to `REAL'
R_levenberg.o:/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_levenberg.cpp:34: 
more undefined references to `REAL' follow
R_levenberg.o: In function `R_levenberg':
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_levenberg.cpp:37: 
undefined reference to `Rf_allocVector'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_levenberg.cpp:37: 
undefined reference to `Rf_protect'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_levenberg.cpp:38: 
undefined reference to `Rf_allocMatrix'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_levenberg.cpp:38: 
undefined reference to `SET_VECTOR_ELT'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_levenberg.cpp:39: 
undefined reference to `Rf_allocMatrix'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_levenberg.cpp:39: 
undefined reference to `SET_VECTOR_ELT'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_levenberg.cpp:40: 
undefined reference to `Rf_allocVector'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_levenberg.cpp:40: 
undefined reference to `SET_VECTOR_ELT'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_levenberg.cpp:41: 
undefined reference to `Rf_allocVector'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_levenberg.cpp:41: 
undefined reference to `SET_VECTOR_ELT'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_levenberg.cpp:42: 
undefined reference to `Rf_allocVector'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_levenberg.cpp:42: 
undefined reference to `SET_VECTOR_ELT'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_levenberg.cpp:43: 
undefined reference to `VECTOR_ELT'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_levenberg.cpp:43: 
undefined reference to `REAL'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_levenberg.cpp:44: 
undefined reference to `VECTOR_ELT'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_levenberg.cpp:44: 
undefined reference to `REAL'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_levenberg.cpp:45: 
undefined reference to `VECTOR_ELT'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_levenberg.cpp:45: 
undefined reference to `REAL'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_levenberg.cpp:46: 
undefined reference to `VECTOR_ELT'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_levenberg.cpp:46: 
undefined reference to `INTEGER'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_levenberg.cpp:47: 
undefined reference to `VECTOR_ELT'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_levenberg.cpp:47: 
undefined reference to `LOGICAL'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_levenberg.cpp:50: 
undefined reference to `Rf_asInteger'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_levenberg.cpp:50: 
undefined reference to `Rf_asReal'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_levenberg.cpp:72: 
undefined reference to `Rf_unprotect'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_levenberg.cpp:78: 
undefined reference to `Rf_mkString'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_levenberg.cpp:76: 
undefined reference to `Rf_unprotect'
R_maximize_interpolant.o: In function `R_maximize_interpolant':
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_maximize_interpolant.cpp:7: 
undefined reference to `Rf_isReal'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_maximize_interpolant.cpp:8: 
undefined reference to `Rf_isReal'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_maximize_interpolant.cpp:11: 
undefined reference to `LENGTH'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_maximize_interpolant.cpp:12: 
undefined reference to `REAL'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_maximize_interpolant.cpp:13: 
undefined reference to `REAL'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_maximize_interpolant.cpp:14: 
undefined reference to `LENGTH'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_maximize_interpolant.cpp:19: 
undefined reference to `Rf_allocVector'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_maximize_interpolant.cpp:19: 
undefined reference to `Rf_protect'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_maximize_interpolant.cpp:20: 
undefined reference to `REAL'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_maximize_interpolant.cpp:31: 
undefined reference to `Rf_unprotect'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_maximize_interpolant.cpp:33: 
undefined reference to `Rf_mkString'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_maximize_interpolant.cpp:28: 
undefined reference to `Rf_unprotect'
R_one_group.o: In function `R_one_group':
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_one_group.cpp:6: 
undefined reference to `Rf_asInteger'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_one_group.cpp:7: 
undefined reference to `Rf_asInteger'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_one_group.cpp:8: 
undefined reference to `LENGTH'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_one_group.cpp:10: 
undefined reference to `Rf_asInteger'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_one_group.cpp:11: 
undefined reference to `Rf_asReal'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_one_group.cpp:12: 
undefined reference to `Rf_isReal'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_one_group.cpp:13: 
undefined reference to `Rf_isReal'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_one_group.cpp:15: 
undefined reference to `LENGTH'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_one_group.cpp:16: 
undefined reference to `LENGTH'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_one_group.cpp:19: 
undefined reference to `Rf_isInteger'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_one_group.cpp:23: 
undefined reference to `INTEGER'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_one_group.cpp:24: 
undefined reference to `R_alloc'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_one_group.cpp:26: 
undefined reference to `REAL'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_one_group.cpp:28: 
undefined reference to `REAL'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_one_group.cpp:29: 
undefined reference to `REAL'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_one_group.cpp:32: 
undefined reference to `Rf_allocVector'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_one_group.cpp:32: 
undefined reference to `Rf_protect'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_one_group.cpp:33: 
undefined reference to `Rf_allocVector'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_one_group.cpp:33: 
undefined reference to `SET_VECTOR_ELT'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_one_group.cpp:34: 
undefined reference to `Rf_allocVector'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_one_group.cpp:34: 
undefined reference to `SET_VECTOR_ELT'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_one_group.cpp:35: 
undefined reference to `VECTOR_ELT'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_one_group.cpp:35: 
undefined reference to `REAL'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_one_group.cpp:36: 
undefined reference to `VECTOR_ELT'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_one_group.cpp:36: 
undefined reference to `LOGICAL'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_one_group.cpp:60: 
undefined reference to `Rf_unprotect'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_one_group.cpp:63: 
undefined reference to `Rf_mkString'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/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/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_simple_good_turing.cpp:14: 
undefined reference to `Rf_asReal'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_simple_good_turing.cpp:15: 
undefined reference to `Rf_isInteger'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_simple_good_turing.cpp:16: 
undefined reference to `Rf_isInteger'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_simple_good_turing.cpp:17: 
undefined reference to `LENGTH'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_simple_good_turing.cpp:18: 
undefined reference to `LENGTH'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_simple_good_turing.cpp:19: 
undefined reference to `INTEGER'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_simple_good_turing.cpp:20: 
undefined reference to `INTEGER'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_simple_good_turing.cpp:25: 
undefined reference to `R_alloc'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_simple_good_turing.cpp:54: 
undefined reference to `Rf_allocVector'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_simple_good_turing.cpp:54: 
undefined reference to `Rf_protect'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_simple_good_turing.cpp:55: 
undefined reference to `Rf_ScalarReal'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_simple_good_turing.cpp:55: 
undefined reference to `SET_VECTOR_ELT'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_simple_good_turing.cpp:56: 
undefined reference to `Rf_allocVector'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_simple_good_turing.cpp:56: 
undefined reference to `SET_VECTOR_ELT'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_simple_good_turing.cpp:57: 
undefined reference to `VECTOR_ELT'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_simple_good_turing.cpp:57: 
undefined reference to `REAL'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_simple_good_turing.cpp:96: 
undefined reference to `Rf_unprotect'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/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/RtmpLskxk6/R.INSTALL266d5e500303/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/RtmpLskxk6/R.INSTALL266d5e500303/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'
===

Again, thank you so much for the fast reply.

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

On 06/10/2013 12:43 PM, Dan Tenenbaum wrote:
> Hi Markus,
>
>
>
> On Mon, Jun 10, 2013 at 10:24 AM, Marinus Pennings <pennings at sc.tamu.edu> wrote:
>> 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?
>>
> These may be just warnings; it's hard to tell with this little bit of output.
> Are you able to
>
> library(edgeR)
>
> After this?
>
> Can you please send the complete output of the
> biocLite("edgeR")
> command as well as the output of sessionInfo()?
> Thanks,
> Dan
>
>
>> Thanks,
>>    Marinus
>>
>> --
>> ------------------------
>> Marinus Pennings
>> pennings at sc.tamu.edu
>> Supercomputing Facility
>> Texas A&M University
>>
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor at r-project.org
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> Search the archives:
>> http://news.gmane.org/gmane.science.biology.informatics.conductor



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