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Old 06-20-2017, 06:43 AM   #1
balaena
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Location: Germany

Join Date: Jan 2015
Posts: 29
Default problems installing cummeRbund

Hi

I am having a hard time installing cummeRbund on Ubuntu 14.04. I have upgraded to the latest R version 3.4.0 and tried to install it like so:

source("https://bioconductor.org/biocLite.R")
biocLite("cummeRbund")

However, I always get error messages about unresolved dependencies and the cummeRbund is not installed afterwards. After download of the files, the output looks like so:

Code:
* installing *source* package ‘Matrix’ ...
** Paket ‘Matrix’ erfolgreich entpackt und MD5 Summen überprüft
** libs
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DNTIMER -I./SuiteSparse_config     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c CHMfactor.c -o CHMfactor.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DNTIMER -I./SuiteSparse_config     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c Csparse.c -o Csparse.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DNTIMER -I./SuiteSparse_config     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c TMatrix_as.c -o TMatrix_as.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DNTIMER -I./SuiteSparse_config     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c Tsparse.c -o Tsparse.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DNTIMER -I./SuiteSparse_config     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c init.c -o init.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DNTIMER -I./SuiteSparse_config     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c Mutils.c -o Mutils.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DNTIMER -I./SuiteSparse_config     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c chm_common.c -o chm_common.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DNTIMER -I./SuiteSparse_config     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c cs.c -o cs.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DNTIMER -I./SuiteSparse_config     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c cs_utils.c -o cs_utils.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DNTIMER -I./SuiteSparse_config     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c dense.c -o dense.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DNTIMER -I./SuiteSparse_config     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c dgCMatrix.c -o dgCMatrix.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DNTIMER -I./SuiteSparse_config     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c dgTMatrix.c -o dgTMatrix.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DNTIMER -I./SuiteSparse_config     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c dgeMatrix.c -o dgeMatrix.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DNTIMER -I./SuiteSparse_config     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c dpoMatrix.c -o dpoMatrix.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DNTIMER -I./SuiteSparse_config     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c dppMatrix.c -o dppMatrix.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DNTIMER -I./SuiteSparse_config     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c dsCMatrix.c -o dsCMatrix.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DNTIMER -I./SuiteSparse_config     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c dsyMatrix.c -o dsyMatrix.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DNTIMER -I./SuiteSparse_config     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c dspMatrix.c -o dspMatrix.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DNTIMER -I./SuiteSparse_config     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c dtCMatrix.c -o dtCMatrix.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DNTIMER -I./SuiteSparse_config     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c dtTMatrix.c -o dtTMatrix.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DNTIMER -I./SuiteSparse_config     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c dtrMatrix.c -o dtrMatrix.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DNTIMER -I./SuiteSparse_config     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c dtpMatrix.c -o dtpMatrix.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DNTIMER -I./SuiteSparse_config     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c factorizations.c -o factorizations.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DNTIMER -I./SuiteSparse_config     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c ldense.c -o ldense.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DNTIMER -I./SuiteSparse_config     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c lgCMatrix.c -o lgCMatrix.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DNTIMER -I./SuiteSparse_config     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c sparseQR.c -o sparseQR.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DNTIMER -I./SuiteSparse_config     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c abIndex.c -o abIndex.o
make[1]: Verzeichnis »/tmp/RtmpospOic/R.INSTALL6c601d9bae94/Matrix/src/CHOLMOD« wird betreten
( cd Lib ; make clean )
make[2]: Verzeichnis »/tmp/RtmpospOic/R.INSTALL6c601d9bae94/Matrix/src/CHOLMOD/Lib« wird betreten
make[2]: Verzeichnis »/tmp/RtmpospOic/R.INSTALL6c601d9bae94/Matrix/src/CHOLMOD/Lib« wird verlassen
make[1]: Verzeichnis »/tmp/RtmpospOic/R.INSTALL6c601d9bae94/Matrix/src/CHOLMOD« wird verlassen
make[1]: Verzeichnis »/tmp/RtmpospOic/R.INSTALL6c601d9bae94/Matrix/src/COLAMD« wird betreten
( cd Source ; make clean )
make[2]: Verzeichnis »/tmp/RtmpospOic/R.INSTALL6c601d9bae94/Matrix/src/COLAMD/Source« wird betreten
make[2]: Verzeichnis »/tmp/RtmpospOic/R.INSTALL6c601d9bae94/Matrix/src/COLAMD/Source« wird verlassen
make[1]: Verzeichnis »/tmp/RtmpospOic/R.INSTALL6c601d9bae94/Matrix/src/COLAMD« wird verlassen
make[1]: Verzeichnis »/tmp/RtmpospOic/R.INSTALL6c601d9bae94/Matrix/src/AMD« wird betreten
( cd Source ; make clean )
make[2]: Verzeichnis »/tmp/RtmpospOic/R.INSTALL6c601d9bae94/Matrix/src/AMD/Source« wird betreten
make[2]: Verzeichnis »/tmp/RtmpospOic/R.INSTALL6c601d9bae94/Matrix/src/AMD/Source« wird verlassen
make[1]: Verzeichnis »/tmp/RtmpospOic/R.INSTALL6c601d9bae94/Matrix/src/AMD« wird verlassen
make[1]: Verzeichnis »/tmp/RtmpospOic/R.INSTALL6c601d9bae94/Matrix/src/SuiteSparse_config« wird betreten
make[1]: Verzeichnis »/tmp/RtmpospOic/R.INSTALL6c601d9bae94/Matrix/src/SuiteSparse_config« wird verlassen
make[1]: Verzeichnis »/tmp/RtmpospOic/R.INSTALL6c601d9bae94/Matrix/src/CHOLMOD« wird betreten
( cd Lib ; make )
make[2]: Verzeichnis »/tmp/RtmpospOic/R.INSTALL6c601d9bae94/Matrix/src/CHOLMOD/Lib« wird betreten
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c ../Core/cholmod_aat.c -o cholmod_aat.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c ../Core/cholmod_add.c -o cholmod_add.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c ../Core/cholmod_band.c -o cholmod_band.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c ../Core/cholmod_change_factor.c -o cholmod_change_factor.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c ../Core/cholmod_common.c -o cholmod_common.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c ../Core/cholmod_complex.c -o cholmod_complex.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c ../Core/cholmod_copy.c -o cholmod_copy.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c ../Core/cholmod_dense.c -o cholmod_dense.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c ../Core/cholmod_error.c -o cholmod_error.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c ../Core/cholmod_factor.c -o cholmod_factor.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c ../Core/cholmod_memory.c -o cholmod_memory.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c ../Core/cholmod_sparse.c -o cholmod_sparse.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c ../Core/cholmod_transpose.c -o cholmod_transpose.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c ../Core/cholmod_triplet.c -o cholmod_triplet.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c ../Core/cholmod_version.c -o cholmod_version.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c ../Check/cholmod_check.c -o cholmod_check.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c ../Check/cholmod_read.c -o cholmod_read.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c ../Check/cholmod_write.c -o cholmod_write.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c ../Cholesky/cholmod_amd.c -o cholmod_amd.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c ../Cholesky/cholmod_analyze.c -o cholmod_analyze.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c ../Cholesky/cholmod_colamd.c -o cholmod_colamd.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c ../Cholesky/cholmod_etree.c -o cholmod_etree.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c ../Cholesky/cholmod_factorize.c -o cholmod_factorize.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c ../Cholesky/cholmod_postorder.c -o cholmod_postorder.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c ../Cholesky/cholmod_rcond.c -o cholmod_rcond.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c ../Cholesky/cholmod_resymbol.c -o cholmod_resymbol.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c ../Cholesky/cholmod_rowcolcounts.c -o cholmod_rowcolcounts.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c ../Cholesky/cholmod_rowfac.c -o cholmod_rowfac.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c ../Cholesky/cholmod_solve.c -o cholmod_solve.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c ../Cholesky/cholmod_spsolve.c -o cholmod_spsolve.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c ../MatrixOps/cholmod_drop.c -o cholmod_drop.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c ../MatrixOps/cholmod_horzcat.c -o cholmod_horzcat.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c ../MatrixOps/cholmod_norm.c -o cholmod_norm.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c ../MatrixOps/cholmod_scale.c -o cholmod_scale.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c ../MatrixOps/cholmod_sdmult.c -o cholmod_sdmult.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c ../MatrixOps/cholmod_ssmult.c -o cholmod_ssmult.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c ../MatrixOps/cholmod_submatrix.c -o cholmod_submatrix.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c ../MatrixOps/cholmod_vertcat.c -o cholmod_vertcat.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c ../MatrixOps/cholmod_symmetry.c -o cholmod_symmetry.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c ../Modify/cholmod_rowadd.c -o cholmod_rowadd.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c ../Modify/cholmod_rowdel.c -o cholmod_rowdel.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c ../Modify/cholmod_updown.c -o cholmod_updown.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c ../Supernodal/cholmod_super_numeric.c -o cholmod_super_numeric.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c ../Supernodal/cholmod_super_solve.c -o cholmod_super_solve.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c ../Supernodal/cholmod_super_symbolic.c -o cholmod_super_symbolic.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -DDLONG -c  ../Core/cholmod_aat.c -o cholmod_l_aat.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -DDLONG -c  ../Core/cholmod_add.c -o cholmod_l_add.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -DDLONG -c  ../Core/cholmod_band.c -o cholmod_l_band.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -DDLONG -c  ../Core/cholmod_change_factor.c -o cholmod_l_change_factor.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -DDLONG -c  ../Core/cholmod_common.c -o cholmod_l_common.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -DDLONG -c  ../Core/cholmod_complex.c -o cholmod_l_complex.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -DDLONG -c  ../Core/cholmod_copy.c -o cholmod_l_copy.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -DDLONG -c  ../Core/cholmod_dense.c -o cholmod_l_dense.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -DDLONG -c  ../Core/cholmod_error.c -o cholmod_l_error.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -DDLONG -c  ../Core/cholmod_factor.c -o cholmod_l_factor.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -DDLONG -c  ../Core/cholmod_memory.c -o cholmod_l_memory.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -DDLONG -c  ../Core/cholmod_sparse.c -o cholmod_l_sparse.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -DDLONG -c  ../Core/cholmod_transpose.c -o cholmod_l_transpose.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -DDLONG -c  ../Core/cholmod_triplet.c -o cholmod_l_triplet.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -DDLONG -c  ../Core/cholmod_version.c -o cholmod_l_version.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -DDLONG -c  ../Check/cholmod_check.c -o cholmod_l_check.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -DDLONG -c  ../Check/cholmod_read.c -o cholmod_l_read.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -DDLONG -c  ../Check/cholmod_write.c -o cholmod_l_write.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -DDLONG -c  ../Cholesky/cholmod_amd.c -o cholmod_l_amd.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -DDLONG -c  ../Cholesky/cholmod_analyze.c -o cholmod_l_analyze.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -DDLONG -c  ../Cholesky/cholmod_colamd.c -o cholmod_l_colamd.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -DDLONG -c  ../Cholesky/cholmod_etree.c -o cholmod_l_etree.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -DDLONG -c  ../Cholesky/cholmod_factorize.c -o cholmod_l_factorize.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -DDLONG -c  ../Cholesky/cholmod_postorder.c -o cholmod_l_postorder.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -DDLONG -c  ../Cholesky/cholmod_rcond.c -o cholmod_l_rcond.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -DDLONG -c  ../Cholesky/cholmod_resymbol.c -o cholmod_l_resymbol.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -DDLONG -c  ../Cholesky/cholmod_rowcolcounts.c -o cholmod_l_rowcolcounts.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -DDLONG -c  ../Cholesky/cholmod_rowfac.c -o cholmod_l_rowfac.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -DDLONG -c  ../Cholesky/cholmod_solve.c -o cholmod_l_solve.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -DDLONG -c  ../Cholesky/cholmod_spsolve.c -o cholmod_l_spsolve.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -DDLONG -c  ../MatrixOps/cholmod_drop.c -o cholmod_l_drop.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -DDLONG -c  ../MatrixOps/cholmod_horzcat.c -o cholmod_l_horzcat.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -DDLONG -c  ../MatrixOps/cholmod_norm.c -o cholmod_l_norm.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -DDLONG -c  ../MatrixOps/cholmod_scale.c -o cholmod_l_scale.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -DDLONG -c  ../MatrixOps/cholmod_sdmult.c -o cholmod_l_sdmult.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -DDLONG -c  ../MatrixOps/cholmod_ssmult.c -o cholmod_l_ssmult.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -DDLONG -c  ../MatrixOps/cholmod_submatrix.c -o cholmod_l_submatrix.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -DDLONG -c  ../MatrixOps/cholmod_vertcat.c -o cholmod_l_vertcat.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -DDLONG -c  ../MatrixOps/cholmod_symmetry.c -o cholmod_l_symmetry.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -DDLONG -c  ../Modify/cholmod_rowadd.c -o cholmod_l_rowadd.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -DDLONG -c  ../Modify/cholmod_rowdel.c -o cholmod_l_rowdel.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -DDLONG -c  ../Modify/cholmod_updown.c -o cholmod_l_updown.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -DDLONG -c  ../Supernodal/cholmod_super_numeric.c -o cholmod_l_super_numeric.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -DDLONG -c  ../Supernodal/cholmod_super_solve.c -o cholmod_l_super_solve.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -DDLONG -c  ../Supernodal/cholmod_super_symbolic.c -o cholmod_l_super_symbolic.o
ar -rucs ../../CHOLMOD.a cholmod_aat.o cholmod_add.o cholmod_band.o cholmod_change_factor.o cholmod_common.o cholmod_complex.o cholmod_copy.o cholmod_dense.o cholmod_error.o cholmod_factor.o cholmod_memory.o cholmod_sparse.o cholmod_transpose.o cholmod_triplet.o cholmod_version.o cholmod_check.o cholmod_read.o cholmod_write.o cholmod_amd.o cholmod_analyze.o cholmod_colamd.o cholmod_etree.o cholmod_factorize.o cholmod_postorder.o cholmod_rcond.o cholmod_resymbol.o cholmod_rowcolcounts.o cholmod_rowfac.o cholmod_solve.o cholmod_spsolve.o cholmod_drop.o cholmod_horzcat.o cholmod_norm.o cholmod_scale.o cholmod_sdmult.o cholmod_ssmult.o cholmod_submatrix.o cholmod_vertcat.o cholmod_symmetry.o cholmod_rowadd.o cholmod_rowdel.o cholmod_updown.o cholmod_super_numeric.o cholmod_super_solve.o cholmod_super_symbolic.o  cholmod_l_aat.o cholmod_l_add.o cholmod_l_band.o cholmod_l_change_factor.o cholmod_l_common.o cholmod_l_complex.o cholmod_l_copy.o cholmod_l_dense.o cholmod_l_error.o cholmod_l_factor.o cholmod_l_memory.o cholmod_l_sparse.o cholmod_l_transpose.o cholmod_l_triplet.o cholmod_l_version.o cholmod_l_check.o cholmod_l_read.o cholmod_l_write.o cholmod_l_amd.o cholmod_l_analyze.o cholmod_l_colamd.o cholmod_l_etree.o cholmod_l_factorize.o cholmod_l_postorder.o cholmod_l_rcond.o cholmod_l_resymbol.o cholmod_l_rowcolcounts.o cholmod_l_rowfac.o cholmod_l_solve.o cholmod_l_spsolve.o cholmod_l_drop.o cholmod_l_horzcat.o cholmod_l_norm.o cholmod_l_scale.o cholmod_l_sdmult.o cholmod_l_ssmult.o cholmod_l_submatrix.o cholmod_l_vertcat.o cholmod_l_symmetry.o cholmod_l_rowadd.o cholmod_l_rowdel.o cholmod_l_updown.o cholmod_l_super_numeric.o cholmod_l_super_solve.o cholmod_l_super_symbolic.o 
make[2]: Verzeichnis »/tmp/RtmpospOic/R.INSTALL6c601d9bae94/Matrix/src/CHOLMOD/Lib« wird verlassen
make[1]: Verzeichnis »/tmp/RtmpospOic/R.INSTALL6c601d9bae94/Matrix/src/CHOLMOD« wird verlassen
make[1]: Verzeichnis »/tmp/RtmpospOic/R.INSTALL6c601d9bae94/Matrix/src/COLAMD« wird betreten
( cd Source ; make lib )
make[2]: Verzeichnis »/tmp/RtmpospOic/R.INSTALL6c601d9bae94/Matrix/src/COLAMD/Source« wird betreten
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../Include -I../../SuiteSparse_config     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c colamd_global.c -o colamd_global.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../Include -I../../SuiteSparse_config     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c colamd.c -o colamd.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../Include -I../../SuiteSparse_config     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -I../Include -DDLONG -c colamd.c -o colamd_l.o
ar -rucs ../../COLAMD.a colamd_global.o colamd.o colamd_l.o
make[2]: Verzeichnis »/tmp/RtmpospOic/R.INSTALL6c601d9bae94/Matrix/src/COLAMD/Source« wird verlassen
make[1]: Verzeichnis »/tmp/RtmpospOic/R.INSTALL6c601d9bae94/Matrix/src/COLAMD« wird verlassen
make[1]: Verzeichnis »/tmp/RtmpospOic/R.INSTALL6c601d9bae94/Matrix/src/AMD« wird betreten
( cd Source ; make lib )
make[2]: Verzeichnis »/tmp/RtmpospOic/R.INSTALL6c601d9bae94/Matrix/src/AMD/Source« wird betreten
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../Include -I../../SuiteSparse_config     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -I../Include -DDINT -c amd_aat.c -o amd_i_aat.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../Include -I../../SuiteSparse_config     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -I../Include -DDLONG -c amd_aat.c -o amd_l_aat.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../Include -I../../SuiteSparse_config     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -I../Include -DDINT -c amd_1.c -o amd_i_1.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../Include -I../../SuiteSparse_config     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -I../Include -DDLONG -c amd_1.c -o amd_l_1.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../Include -I../../SuiteSparse_config     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -I../Include -DDINT -c amd_2.c -o amd_i_2.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../Include -I../../SuiteSparse_config     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -I../Include -DDLONG -c amd_2.c -o amd_l_2.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../Include -I../../SuiteSparse_config     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -I../Include -DDINT -c amd_postorder.c -o amd_i_postorder.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../Include -I../../SuiteSparse_config     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -I../Include -DDLONG -c amd_postorder.c -o amd_l_postorder.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../Include -I../../SuiteSparse_config     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -I../Include -DDINT -c amd_post_tree.c -o amd_i_post_tree.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../Include -I../../SuiteSparse_config     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -I../Include -DDLONG -c amd_post_tree.c -o amd_l_post_tree.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../Include -I../../SuiteSparse_config     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -I../Include -DDINT -c amd_defaults.c -o amd_i_defaults.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../Include -I../../SuiteSparse_config     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -I../Include -DDLONG -c amd_defaults.c -o amd_l_defaults.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../Include -I../../SuiteSparse_config     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -I../Include -DDINT -c amd_order.c -o amd_i_order.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../Include -I../../SuiteSparse_config     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -I../Include -DDLONG -c amd_order.c -o amd_l_order.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../Include -I../../SuiteSparse_config     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -I../Include -DDINT -c amd_control.c -o amd_i_control.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../Include -I../../SuiteSparse_config     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -I../Include -DDLONG -c amd_control.c -o amd_l_control.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../Include -I../../SuiteSparse_config     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -I../Include -DDINT -c amd_info.c -o amd_i_info.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../Include -I../../SuiteSparse_config     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -I../Include -DDLONG -c amd_info.c -o amd_l_info.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../Include -I../../SuiteSparse_config     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -I../Include -DDINT -c amd_valid.c -o amd_i_valid.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../Include -I../../SuiteSparse_config     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -I../Include -DDLONG -c amd_valid.c -o amd_l_valid.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../Include -I../../SuiteSparse_config     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -I../Include -DDINT -c amd_preprocess.c -o amd_i_preprocess.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../Include -I../../SuiteSparse_config     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -I../Include -DDLONG -c amd_preprocess.c -o amd_l_preprocess.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../Include -I../../SuiteSparse_config     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -I../Include -DDINT -c amd_dump.c -o amd_i_dump.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../Include -I../../SuiteSparse_config     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -I../Include -DDLONG -c amd_dump.c -o amd_l_dump.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../Include -I../../SuiteSparse_config     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -I../Include -DDINT -c amd_global.c -o amd_i_global.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../Include -I../../SuiteSparse_config     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -I../Include -DDLONG -c amd_global.c -o amd_l_global.o
ar -rucs ../../AMD.a amd_i_aat.o amd_l_aat.o amd_i_1.o amd_l_1.o amd_i_2.o amd_l_2.o amd_i_postorder.o amd_l_postorder.o amd_i_post_tree.o amd_l_post_tree.o amd_i_defaults.o amd_l_defaults.o amd_i_order.o amd_l_order.o amd_i_control.o amd_l_control.o amd_i_info.o amd_l_info.o amd_i_valid.o amd_l_valid.o amd_i_preprocess.o amd_l_preprocess.o amd_i_dump.o amd_l_dump.o amd_i_global.o amd_l_global.o 
make[2]: Verzeichnis »/tmp/RtmpospOic/R.INSTALL6c601d9bae94/Matrix/src/AMD/Source« wird verlassen
make[1]: Verzeichnis »/tmp/RtmpospOic/R.INSTALL6c601d9bae94/Matrix/src/AMD« wird verlassen
make[1]: Verzeichnis »/tmp/RtmpospOic/R.INSTALL6c601d9bae94/Matrix/src/SuiteSparse_config« wird betreten
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DNTIMER     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c SuiteSparse_config.c -o SuiteSparse_config.o
ar -rucs ../SuiteSparse_config.a SuiteSparse_config.o
make[1]: Verzeichnis »/tmp/RtmpospOic/R.INSTALL6c601d9bae94/Matrix/src/SuiteSparse_config« wird verlassen
gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o Matrix.so CHMfactor.o Csparse.o TMatrix_as.o Tsparse.o init.o Mutils.o chm_common.o cs.o cs_utils.o dense.o dgCMatrix.o dgTMatrix.o dgeMatrix.o dpoMatrix.o dppMatrix.o dsCMatrix.o dsyMatrix.o dspMatrix.o dtCMatrix.o dtTMatrix.o dtrMatrix.o dtpMatrix.o factorizations.o ldense.o lgCMatrix.o sparseQR.o abIndex.o CHOLMOD.a COLAMD.a AMD.a SuiteSparse_config.a -llapack -lblas -lgfortran -lm -lquadmath -L/usr/lib/R/lib -lR
/usr/bin/ld: cannot find -llapack
/usr/bin/ld: cannot find -lblas
collect2: error: ld returned 1 exit status
make: *** [Matrix.so] Fehler 1
ERROR: compilation failed for package ‘Matrix’
* removing ‘/home/kai/R/x86_64-pc-linux-gnu-library/3.4/Matrix’
ERROR: dependency ‘Matrix’ is not available for package ‘survival’
* removing ‘/home/kai/R/x86_64-pc-linux-gnu-library/3.4/survival’
ERROR: dependency ‘Matrix’ is not available for package ‘SummarizedExperiment’
* removing ‘/home/kai/R/x86_64-pc-linux-gnu-library/3.4/SummarizedExperiment’
ERROR: dependency ‘survival’ is not available for package ‘Hmisc’
* removing ‘/home/kai/R/x86_64-pc-linux-gnu-library/3.4/Hmisc’
ERROR: dependency ‘SummarizedExperiment’ is not available for package ‘GenomicAlignments’
* removing ‘/home/kai/R/x86_64-pc-linux-gnu-library/3.4/GenomicAlignments’
ERROR: dependency ‘GenomicAlignments’ is not available for package ‘rtracklayer’
* removing ‘/home/kai/R/x86_64-pc-linux-gnu-library/3.4/rtracklayer’
ERROR: dependency ‘rtracklayer’ is not available for package ‘GenomicFeatures’
* removing ‘/home/kai/R/x86_64-pc-linux-gnu-library/3.4/GenomicFeatures’
ERROR: dependency ‘rtracklayer’ is not available for package ‘BSgenome’
* removing ‘/home/kai/R/x86_64-pc-linux-gnu-library/3.4/BSgenome’
ERROR: dependencies ‘SummarizedExperiment’, ‘BSgenome’, ‘rtracklayer’, ‘GenomicFeatures’ are not available for package ‘VariantAnnotation’
* removing ‘/home/kai/R/x86_64-pc-linux-gnu-library/3.4/VariantAnnotation’
ERROR: dependencies ‘GenomicFeatures’, ‘rtracklayer’ are not available for package ‘ensembldb’
* removing ‘/home/kai/R/x86_64-pc-linux-gnu-library/3.4/ensembldb’
ERROR: dependencies ‘Hmisc’, ‘SummarizedExperiment’, ‘GenomicAlignments’, ‘GenomicFeatures’, ‘VariantAnnotation’, ‘ensembldb’ are not available for package ‘biovizBase’
* removing ‘/home/kai/R/x86_64-pc-linux-gnu-library/3.4/biovizBase’
ERROR: dependencies ‘rtracklayer’, ‘GenomicFeatures’, ‘BSgenome’, ‘biovizBase’, ‘GenomicAlignments’ are not available for package ‘Gviz’
* removing ‘/home/kai/R/x86_64-pc-linux-gnu-library/3.4/Gviz’
ERROR: dependencies ‘rtracklayer’, ‘Gviz’ are not available for package ‘cummeRbund’
* removing ‘/home/kai/R/x86_64-pc-linux-gnu-library/3.4/cummeRbund’

The downloaded source packages are in
	‘/tmp/RtmpFtq5Gl/downloaded_packages’
Es gab 13 Warnungen (Anzeige mit warnings())
And these are the 13 warnings:

Code:
> warnings()
Warnmeldungen:
1: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘Matrix’ had non-zero exit status
2: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘survival’ had non-zero exit status
3: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘SummarizedExperiment’ had non-zero exit status
4: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘Hmisc’ had non-zero exit status
5: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘GenomicAlignments’ had non-zero exit status
6: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘rtracklayer’ had non-zero exit status
7: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘GenomicFeatures’ had non-zero exit status
8: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘BSgenome’ had non-zero exit status
9: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘VariantAnnotation’ had non-zero exit status
10: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘ensembldb’ had non-zero exit status
11: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘biovizBase’ had non-zero exit status
12: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘Gviz’ had non-zero exit status
13: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘cummeRbund’ had non-zero exit status
I have came across the recommendation to install libcurl4-openssl-dev libxml2-dev via apt-get, but to no avail.

Any idea?

Thank you very much!
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Old 06-20-2017, 06:53 AM   #2
GenoMax
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Location: East Coast USA

Join Date: Feb 2008
Posts: 6,975
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For lpack libraries see this thread. As for blas see this thread for libraries needed.

Last edited by GenoMax; 06-20-2017 at 08:33 AM.
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Old 06-20-2017, 08:31 AM   #3
balaena
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Location: Germany

Join Date: Jan 2015
Posts: 29
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this seems to have made it

thank you!

now it complains about the cuffdiff output. But I need to have a closer look on that and probably open a different thread if I can't resolve that.
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