On 06/10/2013 12:34 PM, Marinus Pennings wrote: > 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/libi mf.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_e xact_test_by_deviance.cpp:19: > undefined reference to `Rf_isInteger' I guess that $ cat > tmp.c #include <rinternals.h> void foo(SEXP x) { Rf_asInteger(x); } ^D $ R CMD SHLIB tmp.c results in the same error? Rf_asInteger etc. are defined in the R library; on my system R has decided that the compiler (clang++) is happy when the -shared flag is added; this is discovered during configuration and reflected in variables in the RHOME/etc/Makeconf file. I'm not sure what is going wrong with your icpc / R configuration Maybe that points in a helpful direction? If no one else with icpc experience steps forward the next best bet (with the minimal example of tmp.c above) is probably the R-devel mailing list. Martin > /scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_e xact_test_by_deviance.cpp:19: > undefined reference to `Rf_isInteger' > /scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_e xact_test_by_deviance.cpp:20: > undefined reference to `Rf_isReal' > /scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_e xact_test_by_deviance.cpp:22: > undefined reference to `Rf_asInteger' > /scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_e xact_test_by_deviance.cpp:22: > undefined reference to `Rf_asInteger' > /scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_e xact_test_by_deviance.cpp:23: > undefined reference to `LENGTH' > /scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_e xact_test_by_deviance.cpp:24: > undefined reference to `LENGTH' > /scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_e xact_test_by_deviance.cpp:24: > undefined reference to `LENGTH' > /scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_e xact_test_by_deviance.cpp:29: > undefined reference to `INTEGER' > /scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_e xact_test_by_deviance.cpp:29: > undefined reference to `INTEGER' > /scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_e xact_test_by_deviance.cpp:30: > undefined reference to `REAL' > /scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_e xact_test_by_deviance.cpp:31: > undefined reference to `Rf_asReal' > /scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_e xact_test_by_deviance.cpp:32: > undefined reference to `Rf_asReal' > /scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_e xact_test_by_deviance.cpp:37: > undefined reference to `Rf_allocVector' > /scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_e xact_test_by_deviance.cpp:37: > undefined reference to `Rf_protect' > /scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_e xact_test_by_deviance.cpp:38: > undefined reference to `REAL' > /scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_e xact_test_by_deviance.cpp:140: > undefined reference to `Rf_mkString' > /scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_e xact_test_by_deviance.cpp:138: > undefined reference to `Rf_unprotect' > /scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_e xact_test_by_deviance.cpp:134: > undefined reference to `Rf_unprotect' > /scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_e xact_test_by_deviance.cpp:97: > undefined reference to `Rf_pbeta' > /scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_e xact_test_by_deviance.cpp:98: > undefined reference to `Rf_pbeta' > /scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_e xact_test_by_deviance.cpp:109: > undefined reference to `Rf_lbeta' > /scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_e xact_test_by_deviance.cpp:118: > undefined reference to `Rf_lbeta' > /scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_e xact_test_by_deviance.cpp:123: > undefined reference to `Rf_lbeta' > /scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_e xact_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_l oess_by_col.cpp:12: > undefined reference to `Rf_isReal' > /scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_l oess_by_col.cpp:13: > undefined reference to `Rf_isReal' > /scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_l oess_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_l oess_by_col.cpp:16: > undefined reference to `Rf_asInteger' > /scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_l oess_by_col.cpp:22: > undefined reference to `REAL' > /scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_l oess_by_col.cpp:23: > undefined reference to `Rf_asInteger' > /scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_l oess_by_col.cpp:24: > undefined reference to `LENGTH' > /scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_l oess_by_col.cpp:28: > undefined reference to `REAL' > /scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_l oess_by_col.cpp:136: > undefined reference to `Rf_mkString' > /scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_l oess_by_col.cpp:32: > undefined reference to `Rf_allocVector' > /scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_l oess_by_col.cpp:32: > undefined reference to `Rf_protect' > /scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_l oess_by_col.cpp:33: > undefined reference to `Rf_allocMatrix' > /scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_l oess_by_col.cpp:33: > undefined reference to `SET_VECTOR_ELT' > /scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_l oess_by_col.cpp:34: > undefined reference to `Rf_allocVector' > /scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_l oess_by_col.cpp:34: > undefined reference to `SET_VECTOR_ELT' > /scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_l oess_by_col.cpp:36: > undefined reference to `VECTOR_ELT' > /scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_l oess_by_col.cpp:36: > undefined reference to `REAL' > /scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_l oess_by_col.cpp:37: > undefined reference to `VECTOR_ELT' > /scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_l oess_by_col.cpp:37: > undefined reference to `REAL' > /scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_l oess_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_c r_adjust.cpp:14: > undefined reference to `Rf_isReal' > /scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_c r_adjust.cpp:15: > undefined reference to `Rf_isReal' > /scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_c r_adjust.cpp:17: > undefined reference to `Rf_asInteger' > /scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_c r_adjust.cpp:18: > undefined reference to `LENGTH' > /scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_c r_adjust.cpp:19: > undefined reference to `LENGTH' > /scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_c r_adjust.cpp:22: > undefined reference to `REAL' > /scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_c r_adjust.cpp:23: > undefined reference to `REAL' > /scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_c r_adjust.cpp:25: > undefined reference to `Rf_allocVector' > /scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_c r_adjust.cpp:25: > undefined reference to `Rf_protect' > /scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_c r_adjust.cpp:26: > undefined reference to `REAL' > /scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_c r_adjust.cpp:44: > undefined reference to `Rf_unprotect' > /scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_c r_adjust.cpp:46: > undefined reference to `Rf_mkString' > /scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_c r_adjust.cpp:40: > undefined reference to `Rf_unprotect' > R_levenberg.o: In function `R_levenberg': > /scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_l evenberg.cpp:6: > undefined reference to `Rf_isReal' > /scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_l evenberg.cpp:7: > undefined reference to `Rf_isReal' > /scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_l evenberg.cpp:8: > undefined reference to `Rf_isReal' > /scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_l evenberg.cpp:9: > undefined reference to `Rf_isReal' > /scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_l evenberg.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_l evenberg.cpp:14: > undefined reference to `Rf_asInteger' > /scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_l evenberg.cpp:15: > undefined reference to `Rf_asInteger' > /scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_l evenberg.cpp:16: > undefined reference to `LENGTH' > /scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_l evenberg.cpp:17: > undefined reference to `LENGTH' > /scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_l evenberg.cpp:22: > undefined reference to `LENGTH' > /scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_l evenberg.cpp:24: > undefined reference to `LENGTH' > /scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_l evenberg.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_l evenberg.cpp:33: > undefined reference to `REAL' > /scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_l evenberg.cpp:33: > undefined reference to `REAL' > /scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_l evenberg.cpp:33: > undefined reference to `REAL' > /scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_l evenberg.cpp:34: > undefined reference to `REAL' > /scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_l evenberg.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_l evenberg.cpp:37: > undefined reference to `Rf_allocVector' > /scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_l evenberg.cpp:37: > undefined reference to `Rf_protect' > /scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_l evenberg.cpp:38: > undefined reference to `Rf_allocMatrix' > /scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_l evenberg.cpp:38: > undefined reference to `SET_VECTOR_ELT' > /scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_l evenberg.cpp:39: > undefined reference to `Rf_allocMatrix' > /scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_l evenberg.cpp:39: > undefined reference to `SET_VECTOR_ELT' > /scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_l evenberg.cpp:40: > undefined reference to `Rf_allocVector' > /scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_l evenberg.cpp:40: > undefined reference to `SET_VECTOR_ELT' > /scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_l evenberg.cpp:41: > undefined reference to `Rf_allocVector' > /scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_l evenberg.cpp:41: > undefined reference to `SET_VECTOR_ELT' > /scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_l evenberg.cpp:42: > undefined reference to `Rf_allocVector' > /scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_l evenberg.cpp:42: > undefined reference to `SET_VECTOR_ELT' > /scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_l evenberg.cpp:43: > undefined reference to `VECTOR_ELT' > /scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_l evenberg.cpp:43: > undefined reference to `REAL' > /scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_l evenberg.cpp:44: > undefined reference to `VECTOR_ELT' > /scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_l evenberg.cpp:44: > undefined reference to `REAL' > /scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_l evenberg.cpp:45: > undefined reference to `VECTOR_ELT' > /scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_l evenberg.cpp:45: > undefined reference to `REAL' > /scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_l evenberg.cpp:46: > undefined reference to `VECTOR_ELT' > /scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_l evenberg.cpp:46: > undefined reference to `INTEGER' > /scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_l evenberg.cpp:47: > undefined reference to `VECTOR_ELT' > /scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_l evenberg.cpp:47: > undefined reference to `LOGICAL' > /scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_l evenberg.cpp:50: > undefined reference to `Rf_asInteger' > /scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_l evenberg.cpp:50: > undefined reference to `Rf_asReal' > /scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_l evenberg.cpp:72: > undefined reference to `Rf_unprotect' > /scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_l evenberg.cpp:78: > undefined reference to `Rf_mkString' > /scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_l evenberg.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_m aximize_interpolant.cpp:7: > undefined reference to `Rf_isReal' > /scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_m aximize_interpolant.cpp:8: > undefined reference to `Rf_isReal' > /scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_m aximize_interpolant.cpp:11: > undefined reference to `LENGTH' > /scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_m aximize_interpolant.cpp:12: > undefined reference to `REAL' > /scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_m aximize_interpolant.cpp:13: > undefined reference to `REAL' > /scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_m aximize_interpolant.cpp:14: > undefined reference to `LENGTH' > /scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_m aximize_interpolant.cpp:19: > undefined reference to `Rf_allocVector' > /scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_m aximize_interpolant.cpp:19: > undefined reference to `Rf_protect' > /scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_m aximize_interpolant.cpp:20: > undefined reference to `REAL' > /scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_m aximize_interpolant.cpp:31: > undefined reference to `Rf_unprotect' > /scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_m aximize_interpolant.cpp:33: > undefined reference to `Rf_mkString' > /scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_m aximize_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_o ne_group.cpp:6: > undefined reference to `Rf_asInteger' > /scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_o ne_group.cpp:7: > undefined reference to `Rf_asInteger' > /scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_o ne_group.cpp:8: > undefined reference to `LENGTH' > /scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_o ne_group.cpp:10: > undefined reference to `Rf_asInteger' > /scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_o ne_group.cpp:11: > undefined reference to `Rf_asReal' > /scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_o ne_group.cpp:12: > undefined reference to `Rf_isReal' > /scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_o ne_group.cpp:13: > undefined reference to `Rf_isReal' > /scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_o ne_group.cpp:15: > undefined reference to `LENGTH' > /scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_o ne_group.cpp:16: > undefined reference to `LENGTH' > /scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_o ne_group.cpp:19: > undefined reference to `Rf_isInteger' > /scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_o ne_group.cpp:23: > undefined reference to `INTEGER' > /scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_o ne_group.cpp:24: > undefined reference to `R_alloc' > /scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_o ne_group.cpp:26: > undefined reference to `REAL' > /scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_o ne_group.cpp:28: > undefined reference to `REAL' > /scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_o ne_group.cpp:29: > undefined reference to `REAL' > /scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_o ne_group.cpp:32: > undefined reference to `Rf_allocVector' > /scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_o ne_group.cpp:32: > undefined reference to `Rf_protect' > /scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_o ne_group.cpp:33: > undefined reference to `Rf_allocVector' > /scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_o ne_group.cpp:33: > undefined reference to `SET_VECTOR_ELT' > /scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_o ne_group.cpp:34: > undefined reference to `Rf_allocVector' > /scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_o ne_group.cpp:34: > undefined reference to `SET_VECTOR_ELT' > /scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_o ne_group.cpp:35: > undefined reference to `VECTOR_ELT' > /scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_o ne_group.cpp:35: > undefined reference to `REAL' > /scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_o ne_group.cpp:36: > undefined reference to `VECTOR_ELT' > /scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_o ne_group.cpp:36: > undefined reference to `LOGICAL' > /scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_o ne_group.cpp:60: > undefined reference to `Rf_unprotect' > /scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_o ne_group.cpp:63: > undefined reference to `Rf_mkString' > /scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_o ne_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_s imple_good_turing.cpp:14: > undefined reference to `Rf_asReal' > /scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_s imple_good_turing.cpp:15: > undefined reference to `Rf_isInteger' > /scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_s imple_good_turing.cpp:16: > undefined reference to `Rf_isInteger' > /scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_s imple_good_turing.cpp:17: > undefined reference to `LENGTH' > /scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_s imple_good_turing.cpp:18: > undefined reference to `LENGTH' > /scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_s imple_good_turing.cpp:19: > undefined reference to `INTEGER' > /scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_s imple_good_turing.cpp:20: > undefined reference to `INTEGER' > /scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_s imple_good_turing.cpp:25: > undefined reference to `R_alloc' > /scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_s imple_good_turing.cpp:54: > undefined reference to `Rf_allocVector' > /scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_s imple_good_turing.cpp:54: > undefined reference to `Rf_protect' > /scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_s imple_good_turing.cpp:55: > undefined reference to `Rf_ScalarReal' > /scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_s imple_good_turing.cpp:55: > undefined reference to `SET_VECTOR_ELT' > /scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_s imple_good_turing.cpp:56: > undefined reference to `Rf_allocVector' > /scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_s imple_good_turing.cpp:56: > undefined reference to `SET_VECTOR_ELT' > /scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_s imple_good_turing.cpp:57: > undefined reference to `VECTOR_ELT' > /scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_s imple_good_turing.cpp:57: > undefined reference to `REAL' > /scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_s imple_good_turing.cpp:96: > undefined reference to `Rf_unprotect' > /scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_s imple_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/cor e/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/cor e/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/li bimf.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 > > _______________________________________________ > 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 -- Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. 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