[Bioc-devel] problem installing biocLite package
Dan Tenenbaum
dtenenba at fhcrc.org
Tue Jun 25 19:57:01 CEST 2013
On Tue, Jun 25, 2013 at 9:12 AM, Marinus Pennings <pennings at 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
> pennings at sc.tamu.edu
> Supercomputing Facility
> Texas A&M University
>
>
> [[alternative HTML version deleted]]
>
> _______________________________________________
> Bioc-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
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