On Tue, Jun 25, 2013 at 9:12 AM, Marinus Pennings <penni...@sc.tamu.edu> wrote: > Hello, > > I initially sent this email to the regular bioconductor mailing list > but they told me I probably should sent it here. >
Actually, what was suggested was to come up with a minimal test case and email the R-devel list (http://stat.ethz.ch/mailman/listinfo/r-devel), not the bioc-devel list. Please see this email: https://stat.ethz.ch/pipermail/bioconductor/2013-June/053192.html But be sure you come up with the minimal test case first. If you just email R-devel asking about an edgeR install problem, they will not help you. Thanks, Dan > 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 _______________________________________________ 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