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 penni...@sc.tamu.edu Supercomputing Facility Texas A&M University [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel