[BioC] installing biocLite('edgeR') issues
Marinus Pennings
pennings at sc.tamu.edu
Mon Jun 10 21:34:23 CEST 2013
hi,
thank you for the fast reply. There are real errors, not just warning.
The package is not build
> library(edgeR)
Error in library(edgeR) : there is no package called 'edgeR'
Here is the output of sessionInfo():
===
> sessionsInfo()
Error: could not find function "sessionsInfo"
> sessionInfo()
R version 3.0.1 (2013-05-16)
Platform: x86_64-unknown-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_US LC_NUMERIC=C LC_TIME=en_US
[4] LC_COLLATE=en_US LC_MONETARY=en_US LC_MESSAGES=en_US
[7] LC_PAPER=C LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=en_US LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] BiocInstaller_1.10.2
loaded via a namespace (and not attached):
[1] tools_3.0.1
>
===
Here is the complete output of biocLite('edgeR'):
========
> biocLite('edgeR')
BioC_mirror: http://bioconductor.org
Using Bioconductor version 2.12 (BiocInstaller 1.10.2), R version 3.0.1.
Installing package(s) 'edgeR'
trying URL
'http://bioconductor.org/packages/2.12/bioc/src/contrib/edgeR_3.2.3.tar.gz'
Content type 'application/x-gzip' length 1211896 bytes (1.2 Mb)
opened URL
==================================================
downloaded 1.2 Mb
* installing *source* package 'edgeR' ...
** libs
icpc -I/g/software/R/3.0.1/intelv13-mkl/lib64/R/include -DNDEBUG
-I./core -I. -I/usr/local/include -fpic -xHost -openmp -O3 -g
-fp-model precise -c R_exact_test_by_deviance.cpp -o
R_exact_test_by_deviance.o
icpc -I/g/software/R/3.0.1/intelv13-mkl/lib64/R/include -DNDEBUG
-I./core -I. -I/usr/local/include -fpic -xHost -openmp -O3 -g
-fp-model precise -c R_loess_by_col.cpp -o R_loess_by_col.o
icpc -I/g/software/R/3.0.1/intelv13-mkl/lib64/R/include -DNDEBUG
-I./core -I. -I/usr/local/include -fpic -xHost -openmp -O3 -g
-fp-model precise -c R_cr_adjust.cpp -o R_cr_adjust.o
icpc -I/g/software/R/3.0.1/intelv13-mkl/lib64/R/include -DNDEBUG
-I./core -I. -I/usr/local/include -fpic -xHost -openmp -O3 -g
-fp-model precise -c R_levenberg.cpp -o R_levenberg.o
icpc -I/g/software/R/3.0.1/intelv13-mkl/lib64/R/include -DNDEBUG
-I./core -I. -I/usr/local/include -fpic -xHost -openmp -O3 -g
-fp-model precise -c R_maximize_interpolant.cpp -o R_maximize_interpolant.o
icpc -I/g/software/R/3.0.1/intelv13-mkl/lib64/R/include -DNDEBUG
-I./core -I. -I/usr/local/include -fpic -xHost -openmp -O3 -g
-fp-model precise -c R_one_group.cpp -o R_one_group.o
icpc -I/g/software/R/3.0.1/intelv13-mkl/lib64/R/include -DNDEBUG
-I./core -I. -I/usr/local/include -fpic -xHost -openmp -O3 -g
-fp-model precise -c R_simple_good_turing.cpp -o R_simple_good_turing.o
icpc -I/g/software/R/3.0.1/intelv13-mkl/lib64/R/include -DNDEBUG
-I./core -I. -I/usr/local/include -fpic -xHost -openmp -O3 -g
-fp-model precise -c core/adj_coxreid.cpp -o core/adj_coxreid.o
icpc -I/g/software/R/3.0.1/intelv13-mkl/lib64/R/include -DNDEBUG
-I./core -I. -I/usr/local/include -fpic -xHost -openmp -O3 -g
-fp-model precise -c core/glm_levenberg.cpp -o core/glm_levenberg.o
icpc -I/g/software/R/3.0.1/intelv13-mkl/lib64/R/include -DNDEBUG
-I./core -I. -I/usr/local/include -fpic -xHost -openmp -O3 -g
-fp-model precise -c core/glm_one_group.cpp -o core/glm_one_group.o
icpc -I/g/software/R/3.0.1/intelv13-mkl/lib64/R/include -DNDEBUG
-I./core -I. -I/usr/local/include -fpic -xHost -openmp -O3 -g
-fp-model precise -c core/interpolator.cpp -o core/interpolator.o
icc -std=gnu99 -I/g/software/R/3.0.1/intelv13-mkl/lib64/R/include
-DNDEBUG -I./core -I. -I/usr/local/include -fpic -xHost -openmp -O3
-g -fp-model precise -c core/fmm_spline.c -o core/fmm_spline.o
icpc -L/usr/local/lib64 -o edgeR.so R_exact_test_by_deviance.o
R_loess_by_col.o R_cr_adjust.o R_levenberg.o R_maximize_interpolant.o
R_one_group.o R_simple_good_turing.o core/adj_coxreid.o
core/glm_levenberg.o core/glm_one_group.o core/interpolator.o
core/fmm_spline.o -L/g/software/intelXE/composer_xe_2013/mkl/lib/intel64
-lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -lpthread -lm -lifport
-lifcoremt -limf -lsvml -lm -lipgo -liomp5 -lirc -lpthread -lirc_s -ldl
/g/software/intelXE/composer_xe_2013.4.183/compiler/lib/intel64/libimf.so:
warning: warning: feupdateenv is not implemented and will always fail
/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../lib64/crt1.o: In
function `_start':
(.text+0x20): undefined reference to `main'
R_exact_test_by_deviance.o: In function `R_exact_test_by_deviance':
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_exact_test_by_deviance.cpp:19:
undefined reference to `Rf_isInteger'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_exact_test_by_deviance.cpp:19:
undefined reference to `Rf_isInteger'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_exact_test_by_deviance.cpp:20:
undefined reference to `Rf_isReal'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_exact_test_by_deviance.cpp:22:
undefined reference to `Rf_asInteger'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_exact_test_by_deviance.cpp:22:
undefined reference to `Rf_asInteger'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_exact_test_by_deviance.cpp:23:
undefined reference to `LENGTH'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_exact_test_by_deviance.cpp:24:
undefined reference to `LENGTH'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_exact_test_by_deviance.cpp:24:
undefined reference to `LENGTH'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_exact_test_by_deviance.cpp:29:
undefined reference to `INTEGER'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_exact_test_by_deviance.cpp:29:
undefined reference to `INTEGER'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_exact_test_by_deviance.cpp:30:
undefined reference to `REAL'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_exact_test_by_deviance.cpp:31:
undefined reference to `Rf_asReal'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_exact_test_by_deviance.cpp:32:
undefined reference to `Rf_asReal'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_exact_test_by_deviance.cpp:37:
undefined reference to `Rf_allocVector'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_exact_test_by_deviance.cpp:37:
undefined reference to `Rf_protect'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_exact_test_by_deviance.cpp:38:
undefined reference to `REAL'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_exact_test_by_deviance.cpp:140:
undefined reference to `Rf_mkString'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_exact_test_by_deviance.cpp:138:
undefined reference to `Rf_unprotect'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_exact_test_by_deviance.cpp:134:
undefined reference to `Rf_unprotect'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_exact_test_by_deviance.cpp:97:
undefined reference to `Rf_pbeta'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_exact_test_by_deviance.cpp:98:
undefined reference to `Rf_pbeta'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_exact_test_by_deviance.cpp:109:
undefined reference to `Rf_lbeta'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_exact_test_by_deviance.cpp:118:
undefined reference to `Rf_lbeta'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_exact_test_by_deviance.cpp:123:
undefined reference to `Rf_lbeta'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_exact_test_by_deviance.cpp:130:
undefined reference to `Rf_lbeta'
R_loess_by_col.o: In function `std::_Deque_base<double const*,
std::allocator<double const*> >::~_Deque_base()':
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_loess_by_col.cpp:12:
undefined reference to `Rf_isReal'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_loess_by_col.cpp:13:
undefined reference to `Rf_isReal'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_loess_by_col.cpp:15:
undefined reference to `LENGTH'
R_loess_by_col.o: In function `R_loess_by_col':
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_loess_by_col.cpp:16:
undefined reference to `Rf_asInteger'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_loess_by_col.cpp:22:
undefined reference to `REAL'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_loess_by_col.cpp:23:
undefined reference to `Rf_asInteger'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_loess_by_col.cpp:24:
undefined reference to `LENGTH'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_loess_by_col.cpp:28:
undefined reference to `REAL'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_loess_by_col.cpp:136:
undefined reference to `Rf_mkString'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_loess_by_col.cpp:32:
undefined reference to `Rf_allocVector'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_loess_by_col.cpp:32:
undefined reference to `Rf_protect'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_loess_by_col.cpp:33:
undefined reference to `Rf_allocMatrix'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_loess_by_col.cpp:33:
undefined reference to `SET_VECTOR_ELT'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_loess_by_col.cpp:34:
undefined reference to `Rf_allocVector'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_loess_by_col.cpp:34:
undefined reference to `SET_VECTOR_ELT'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_loess_by_col.cpp:36:
undefined reference to `VECTOR_ELT'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_loess_by_col.cpp:36:
undefined reference to `REAL'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_loess_by_col.cpp:37:
undefined reference to `VECTOR_ELT'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_loess_by_col.cpp:37:
undefined reference to `REAL'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_loess_by_col.cpp:133:
undefined reference to `Rf_unprotect'
R_cr_adjust.o: In function `R_cr_adjust':
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_cr_adjust.cpp:14:
undefined reference to `Rf_isReal'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_cr_adjust.cpp:15:
undefined reference to `Rf_isReal'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_cr_adjust.cpp:17:
undefined reference to `Rf_asInteger'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_cr_adjust.cpp:18:
undefined reference to `LENGTH'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_cr_adjust.cpp:19:
undefined reference to `LENGTH'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_cr_adjust.cpp:22:
undefined reference to `REAL'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_cr_adjust.cpp:23:
undefined reference to `REAL'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_cr_adjust.cpp:25:
undefined reference to `Rf_allocVector'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_cr_adjust.cpp:25:
undefined reference to `Rf_protect'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_cr_adjust.cpp:26:
undefined reference to `REAL'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_cr_adjust.cpp:44:
undefined reference to `Rf_unprotect'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_cr_adjust.cpp:46:
undefined reference to `Rf_mkString'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_cr_adjust.cpp:40:
undefined reference to `Rf_unprotect'
R_levenberg.o: In function `R_levenberg':
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_levenberg.cpp:6:
undefined reference to `Rf_isReal'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_levenberg.cpp:7:
undefined reference to `Rf_isReal'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_levenberg.cpp:8:
undefined reference to `Rf_isReal'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_levenberg.cpp:9:
undefined reference to `Rf_isReal'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_levenberg.cpp:10:
undefined reference to `Rf_isReal'
R_levenberg.o:/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_levenberg.cpp:11:
more undefined references to `Rf_isReal' follow
R_levenberg.o: In function `R_levenberg':
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_levenberg.cpp:14:
undefined reference to `Rf_asInteger'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_levenberg.cpp:15:
undefined reference to `Rf_asInteger'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_levenberg.cpp:16:
undefined reference to `LENGTH'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_levenberg.cpp:17:
undefined reference to `LENGTH'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_levenberg.cpp:22:
undefined reference to `LENGTH'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_levenberg.cpp:24:
undefined reference to `LENGTH'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_levenberg.cpp:26:
undefined reference to `LENGTH'
R_levenberg.o:/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_levenberg.cpp:28:
more undefined references to `LENGTH' follow
R_levenberg.o: In function `R_levenberg':
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_levenberg.cpp:33:
undefined reference to `REAL'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_levenberg.cpp:33:
undefined reference to `REAL'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_levenberg.cpp:33:
undefined reference to `REAL'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_levenberg.cpp:34:
undefined reference to `REAL'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_levenberg.cpp:34:
undefined reference to `REAL'
R_levenberg.o:/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_levenberg.cpp:34:
more undefined references to `REAL' follow
R_levenberg.o: In function `R_levenberg':
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_levenberg.cpp:37:
undefined reference to `Rf_allocVector'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_levenberg.cpp:37:
undefined reference to `Rf_protect'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_levenberg.cpp:38:
undefined reference to `Rf_allocMatrix'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_levenberg.cpp:38:
undefined reference to `SET_VECTOR_ELT'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_levenberg.cpp:39:
undefined reference to `Rf_allocMatrix'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_levenberg.cpp:39:
undefined reference to `SET_VECTOR_ELT'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_levenberg.cpp:40:
undefined reference to `Rf_allocVector'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_levenberg.cpp:40:
undefined reference to `SET_VECTOR_ELT'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_levenberg.cpp:41:
undefined reference to `Rf_allocVector'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_levenberg.cpp:41:
undefined reference to `SET_VECTOR_ELT'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_levenberg.cpp:42:
undefined reference to `Rf_allocVector'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_levenberg.cpp:42:
undefined reference to `SET_VECTOR_ELT'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_levenberg.cpp:43:
undefined reference to `VECTOR_ELT'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_levenberg.cpp:43:
undefined reference to `REAL'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_levenberg.cpp:44:
undefined reference to `VECTOR_ELT'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_levenberg.cpp:44:
undefined reference to `REAL'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_levenberg.cpp:45:
undefined reference to `VECTOR_ELT'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_levenberg.cpp:45:
undefined reference to `REAL'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_levenberg.cpp:46:
undefined reference to `VECTOR_ELT'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_levenberg.cpp:46:
undefined reference to `INTEGER'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_levenberg.cpp:47:
undefined reference to `VECTOR_ELT'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_levenberg.cpp:47:
undefined reference to `LOGICAL'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_levenberg.cpp:50:
undefined reference to `Rf_asInteger'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_levenberg.cpp:50:
undefined reference to `Rf_asReal'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_levenberg.cpp:72:
undefined reference to `Rf_unprotect'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_levenberg.cpp:78:
undefined reference to `Rf_mkString'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_levenberg.cpp:76:
undefined reference to `Rf_unprotect'
R_maximize_interpolant.o: In function `R_maximize_interpolant':
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_maximize_interpolant.cpp:7:
undefined reference to `Rf_isReal'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_maximize_interpolant.cpp:8:
undefined reference to `Rf_isReal'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_maximize_interpolant.cpp:11:
undefined reference to `LENGTH'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_maximize_interpolant.cpp:12:
undefined reference to `REAL'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_maximize_interpolant.cpp:13:
undefined reference to `REAL'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_maximize_interpolant.cpp:14:
undefined reference to `LENGTH'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_maximize_interpolant.cpp:19:
undefined reference to `Rf_allocVector'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_maximize_interpolant.cpp:19:
undefined reference to `Rf_protect'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_maximize_interpolant.cpp:20:
undefined reference to `REAL'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_maximize_interpolant.cpp:31:
undefined reference to `Rf_unprotect'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_maximize_interpolant.cpp:33:
undefined reference to `Rf_mkString'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_maximize_interpolant.cpp:28:
undefined reference to `Rf_unprotect'
R_one_group.o: In function `R_one_group':
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_one_group.cpp:6:
undefined reference to `Rf_asInteger'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_one_group.cpp:7:
undefined reference to `Rf_asInteger'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_one_group.cpp:8:
undefined reference to `LENGTH'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_one_group.cpp:10:
undefined reference to `Rf_asInteger'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_one_group.cpp:11:
undefined reference to `Rf_asReal'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_one_group.cpp:12:
undefined reference to `Rf_isReal'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_one_group.cpp:13:
undefined reference to `Rf_isReal'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_one_group.cpp:15:
undefined reference to `LENGTH'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_one_group.cpp:16:
undefined reference to `LENGTH'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_one_group.cpp:19:
undefined reference to `Rf_isInteger'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_one_group.cpp:23:
undefined reference to `INTEGER'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_one_group.cpp:24:
undefined reference to `R_alloc'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_one_group.cpp:26:
undefined reference to `REAL'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_one_group.cpp:28:
undefined reference to `REAL'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_one_group.cpp:29:
undefined reference to `REAL'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_one_group.cpp:32:
undefined reference to `Rf_allocVector'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_one_group.cpp:32:
undefined reference to `Rf_protect'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_one_group.cpp:33:
undefined reference to `Rf_allocVector'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_one_group.cpp:33:
undefined reference to `SET_VECTOR_ELT'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_one_group.cpp:34:
undefined reference to `Rf_allocVector'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_one_group.cpp:34:
undefined reference to `SET_VECTOR_ELT'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_one_group.cpp:35:
undefined reference to `VECTOR_ELT'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_one_group.cpp:35:
undefined reference to `REAL'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_one_group.cpp:36:
undefined reference to `VECTOR_ELT'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_one_group.cpp:36:
undefined reference to `LOGICAL'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_one_group.cpp:60:
undefined reference to `Rf_unprotect'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_one_group.cpp:63:
undefined reference to `Rf_mkString'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_one_group.cpp:55:
undefined reference to `Rf_unprotect'
R_simple_good_turing.o: In function `R_simple_good_turing':
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_simple_good_turing.cpp:14:
undefined reference to `Rf_asReal'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_simple_good_turing.cpp:15:
undefined reference to `Rf_isInteger'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_simple_good_turing.cpp:16:
undefined reference to `Rf_isInteger'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_simple_good_turing.cpp:17:
undefined reference to `LENGTH'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_simple_good_turing.cpp:18:
undefined reference to `LENGTH'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_simple_good_turing.cpp:19:
undefined reference to `INTEGER'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_simple_good_turing.cpp:20:
undefined reference to `INTEGER'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_simple_good_turing.cpp:25:
undefined reference to `R_alloc'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_simple_good_turing.cpp:54:
undefined reference to `Rf_allocVector'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_simple_good_turing.cpp:54:
undefined reference to `Rf_protect'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_simple_good_turing.cpp:55:
undefined reference to `Rf_ScalarReal'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_simple_good_turing.cpp:55:
undefined reference to `SET_VECTOR_ELT'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_simple_good_turing.cpp:56:
undefined reference to `Rf_allocVector'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_simple_good_turing.cpp:56:
undefined reference to `SET_VECTOR_ELT'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_simple_good_turing.cpp:57:
undefined reference to `VECTOR_ELT'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_simple_good_turing.cpp:57:
undefined reference to `REAL'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_simple_good_turing.cpp:96:
undefined reference to `Rf_unprotect'
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_simple_good_turing.cpp:99:
undefined reference to `Rf_mkString'
core/glm_levenberg.o: In function `glm_levenberg::fit(double const*,
double const*, double const&, double*, double*)':
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/core/glm_levenberg.cpp:83:
undefined reference to `R_NaReal'
core/glm_one_group.o: In function `glm_one_group(int const&, int const&,
double const&, double const*, double const*, double const&)':
/scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/core/glm_one_group.cpp:17:
undefined reference to `R_NegInf'
make: *** [edgeR.so] Error 1
ERROR: compilation failed for package 'edgeR'
* removing '/g/software/R/3.0.1/intelv13-mkl/lib64/R/library/edgeR'
===
Again, thank you so much for the fast reply.
------------------------
Marinus Pennings
pennings at sc.tamu.edu
Supercomputing Facility
Texas A&M University
On 06/10/2013 12:43 PM, Dan Tenenbaum wrote:
> Hi Markus,
>
>
>
> On Mon, Jun 10, 2013 at 10:24 AM, Marinus Pennings <pennings at sc.tamu.edu> wrote:
>> Hi,
>>
>> I'm installing some bioconductor packages for one of our users. Here are
>> the steps:
>>
>> - dource(http://bioconductor.org/biocLite.R")
>> - biocLite()
>> - biocLite('edgeR')
>>
>> The first steps can be executed without any problem but the
>> biocLite('edgeR') command causes a lot of errors (below are the first few
>> error lines):
>>
>> =====
>> icpc -L/usr/local/lib64 -o edgeR.so R_exact_test_by_deviance.o
>> R_loess_by_col.o R_cr_adjust.o R_levenberg.o R_maximize_interpolant.o
>> R_one_group.o R_simple_good_turing.o core/adj_coxreid.o core/glm_levenberg.o
>> core/glm_one_group.o core/interpolator.o core/fmm_spline.o
>> -L/g/software/intelXE/composer_xe_2013/mkl/lib/intel64 -lmkl_intel_lp64
>> -lmkl_intel_thread -lmkl_core -lpthread -lm -lifport -lifcoremt -limf -lsvml
>> -lm -lipgo -liomp5 -lirc -lpthread -lirc_s -ldl
>> /g/software/intelXE/composer_xe_2013.4.183/compiler/lib/intel64/libimf.so:
>> warning: warning: feupdateenv is not implemented and will always fail
>> /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../lib64/crt1.o: In function
>> `_start':
>> (.text+0x20): undefined reference to `main'
>> R_exact_test_by_deviance.o: In function `R_exact_test_by_deviance':
>> /scratch/pennings/tmp/Rtmp5LmotH/R.INSTALL22017e509b8c/edgeR/src/R_exact_test_by_deviance.cpp:19:
>> undefined reference to `Rf_isInteger'
>> /scratch/pennings/tmp/Rtmp5LmotH/R.INSTALL22017e509b8c/edgeR/src/R_exact_test_by_deviance.cpp:19:
>> undefined reference to `Rf_isInteger'
>> =====
>>
>> Seems the problem starts when trying to create lib edgeR.so
>>
>> Here are the sytem specs I use:
>> R version 3.0.1
>> intel compilers v13.1.2
>> mkl v11.0.4
>>
>> When I build R using gcc and without mkl I can install "biocLite('edgeR')"
>> without any problems. Anybody had similar problems with intel compilers?
>>
> These may be just warnings; it's hard to tell with this little bit of output.
> Are you able to
>
> library(edgeR)
>
> After this?
>
> Can you please send the complete output of the
> biocLite("edgeR")
> command as well as the output of sessionInfo()?
> Thanks,
> Dan
>
>
>> Thanks,
>> Marinus
>>
>> --
>> ------------------------
>> Marinus Pennings
>> pennings at sc.tamu.edu
>> Supercomputing Facility
>> Texas A&M University
>>
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor at r-project.org
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> Search the archives:
>> http://news.gmane.org/gmane.science.biology.informatics.conductor
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