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
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