[BioC] installing biocLite('edgeR') issues

Martin Morgan mtmorgan at fhcrc.org
Tue Jun 11 03:03:07 CEST 2013


On 06/10/2013 12:34 PM, Marinus Pennings wrote:
> hi,
>
> thank you for the fast reply. There are real errors, not just warning. The
> package is not build
>  > library(edgeR)
> Error in library(edgeR) : there is no package called 'edgeR'
>
> Here is the output of sessionInfo():
>
> ===
>  > sessionsInfo()
> Error: could not find function "sessionsInfo"
>  > sessionInfo()
> R version 3.0.1 (2013-05-16)
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
> locale:
>   [1] LC_CTYPE=en_US       LC_NUMERIC=C         LC_TIME=en_US
>   [4] LC_COLLATE=en_US     LC_MONETARY=en_US    LC_MESSAGES=en_US
>   [7] LC_PAPER=C           LC_NAME=C            LC_ADDRESS=C
> [10] LC_TELEPHONE=C       LC_MEASUREMENT=en_US LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods base
>
> other attached packages:
> [1] BiocInstaller_1.10.2
>
> loaded via a namespace (and not attached):
> [1] tools_3.0.1
>  >
> ===
>
>
> Here is the complete output of biocLite('edgeR'):
>
> ========
>  > biocLite('edgeR')
> BioC_mirror: http://bioconductor.org
> Using Bioconductor version 2.12 (BiocInstaller 1.10.2), R version 3.0.1.
> Installing package(s) 'edgeR'
> trying URL
> 'http://bioconductor.org/packages/2.12/bioc/src/contrib/edgeR_3.2.3.tar.gz'
> Content type 'application/x-gzip' length 1211896 bytes (1.2 Mb)
> opened URL
> ==================================================
> downloaded 1.2 Mb
>
> * installing *source* package 'edgeR' ...
> ** libs
> icpc -I/g/software/R/3.0.1/intelv13-mkl/lib64/R/include -DNDEBUG -I./core -I.
> -I/usr/local/include    -fpic  -xHost -openmp -O3 -g -fp-model precise  -c
> R_exact_test_by_deviance.cpp -o R_exact_test_by_deviance.o
> icpc -I/g/software/R/3.0.1/intelv13-mkl/lib64/R/include -DNDEBUG -I./core -I.
> -I/usr/local/include    -fpic  -xHost -openmp -O3 -g -fp-model precise  -c
> R_loess_by_col.cpp -o R_loess_by_col.o
> icpc -I/g/software/R/3.0.1/intelv13-mkl/lib64/R/include -DNDEBUG -I./core -I.
> -I/usr/local/include    -fpic  -xHost -openmp -O3 -g -fp-model precise  -c
> R_cr_adjust.cpp -o R_cr_adjust.o
> icpc -I/g/software/R/3.0.1/intelv13-mkl/lib64/R/include -DNDEBUG -I./core -I.
> -I/usr/local/include    -fpic  -xHost -openmp -O3 -g -fp-model precise  -c
> R_levenberg.cpp -o R_levenberg.o
> icpc -I/g/software/R/3.0.1/intelv13-mkl/lib64/R/include -DNDEBUG -I./core -I.
> -I/usr/local/include    -fpic  -xHost -openmp -O3 -g -fp-model precise  -c
> R_maximize_interpolant.cpp -o R_maximize_interpolant.o
> icpc -I/g/software/R/3.0.1/intelv13-mkl/lib64/R/include -DNDEBUG -I./core -I.
> -I/usr/local/include    -fpic  -xHost -openmp -O3 -g -fp-model precise  -c
> R_one_group.cpp -o R_one_group.o
> icpc -I/g/software/R/3.0.1/intelv13-mkl/lib64/R/include -DNDEBUG -I./core -I.
> -I/usr/local/include    -fpic  -xHost -openmp -O3 -g -fp-model precise  -c
> R_simple_good_turing.cpp -o R_simple_good_turing.o
> icpc -I/g/software/R/3.0.1/intelv13-mkl/lib64/R/include -DNDEBUG -I./core -I.
> -I/usr/local/include    -fpic  -xHost -openmp -O3 -g -fp-model precise  -c
> core/adj_coxreid.cpp -o core/adj_coxreid.o
> icpc -I/g/software/R/3.0.1/intelv13-mkl/lib64/R/include -DNDEBUG -I./core -I.
> -I/usr/local/include    -fpic  -xHost -openmp -O3 -g -fp-model precise  -c
> core/glm_levenberg.cpp -o core/glm_levenberg.o
> icpc -I/g/software/R/3.0.1/intelv13-mkl/lib64/R/include -DNDEBUG -I./core -I.
> -I/usr/local/include    -fpic  -xHost -openmp -O3 -g -fp-model precise  -c
> core/glm_one_group.cpp -o core/glm_one_group.o
> icpc -I/g/software/R/3.0.1/intelv13-mkl/lib64/R/include -DNDEBUG -I./core -I.
> -I/usr/local/include    -fpic  -xHost -openmp -O3 -g -fp-model precise  -c
> core/interpolator.cpp -o core/interpolator.o
> icc -std=gnu99 -I/g/software/R/3.0.1/intelv13-mkl/lib64/R/include -DNDEBUG
> -I./core -I.  -I/usr/local/include    -fpic  -xHost -openmp -O3 -g -fp-model
> precise  -c core/fmm_spline.c -o core/fmm_spline.o
> icpc -L/usr/local/lib64 -o edgeR.so R_exact_test_by_deviance.o R_loess_by_col.o
> R_cr_adjust.o R_levenberg.o R_maximize_interpolant.o R_one_group.o
> R_simple_good_turing.o core/adj_coxreid.o core/glm_levenberg.o
> core/glm_one_group.o core/interpolator.o core/fmm_spline.o
> -L/g/software/intelXE/composer_xe_2013/mkl/lib/intel64 -lmkl_intel_lp64
> -lmkl_intel_thread -lmkl_core -lpthread -lm -lifport -lifcoremt -limf -lsvml -lm
> -lipgo -liomp5 -lirc -lpthread -lirc_s -ldl
> /g/software/intelXE/composer_xe_2013.4.183/compiler/lib/intel64/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'


I guess that

$ cat > tmp.c
#include <Rinternals.h>
void foo(SEXP x) { Rf_asInteger(x); }
^D
$ R CMD SHLIB tmp.c

results in the same error? Rf_asInteger etc. are defined in the R library; on my 
system R has decided that the compiler (clang++) is happy when the -shared flag 
is added; this is discovered during configuration and reflected in variables in 
the RHOME/etc/Makeconf file. I'm not sure what is going wrong with your icpc / R 
configuration

Maybe that points in a helpful direction? If no one else with icpc experience 
steps forward the next best bet (with the minimal example of tmp.c above) is 
probably the R-devel mailing list.

Martin

> /scratch/pennings/tmp/RtmpLskxk6/R.INSTALL266d5e500303/edgeR/src/R_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
>
> _______________________________________________
> 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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