Is the use of Rscript in wch1/r-debug discouraged?

[jameslamb]

In a project I maintain, we have been using https://hub.docker.com/layers/wch1/r-debug/ for a while now to run various continuous integration jobs trying to replicate the types of testing CRAN does. Thanks so much for maintaining this project!

Starting about 5 days ago, one of those jobs started failing. As of the most recent wch1/r-debug builds, attempting to install {Matrix} from CRAN with Rscript results in the following error.

/usr/bin/ld: cannot find -lgfortran
collect2: error: ld returned 1 exit status
make: *** [/usr/share/R/share/make/shlib.mk:10: Matrix.so] Error 1

Installing it with RDscript succeeds.

Is the use of Rscript in this image discouraged?

Reproducible Example

This example was run on the latest version of wch1/r-debug:latest, pulled today (May 15, 2021).

output of 'docker inspect' (click me)

Using Rscript, installation of {Matrix} failed.

docker run \
    --rm \
    --entrypoint="" \
    -it wch1/r-debug:latest \
    Rscript -e "install.packages('Matrix', repos = 'https://cran.r-project.org')"

With this error:

/usr/bin/ld: cannot find -lgfortran
collect2: error: ld returned 1 exit status
make: *** [/usr/share/R/share/make/shlib.mk:10: Matrix.so] Error 1
ERROR: compilation failed for package ‘Matrix’
* removing ‘/usr/local/lib/R/site-library/Matrix’

The downloaded source packages are in
	‘/tmp/Rtmps7Wj4h/downloaded_packages’
Warning message:
In install.packages("Matrix", repos = "https://cran.r-project.org") :
  installation of package ‘Matrix’ had non-zero exit statu

full log (click me)

Installing package into ‘/usr/local/lib/R/site-library’
(as ‘lib’ is unspecified)
trying URL 'https://cran.r-project.org/src/contrib/Matrix_1.4-1.tar.gz'
Content type 'application/x-gzip' length 2862737 bytes (2.7 MB)
==================================================
downloaded 2.7 MB

* installing *source* package ‘Matrix’ ...
** package ‘Matrix’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
gcc -I"/usr/share/R/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T     -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c CHMfactor.c -o CHMfactor.o
gcc -I"/usr/share/R/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T     -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c Csparse.c -o Csparse.o
gcc -I"/usr/share/R/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T     -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c TMatrix_as.c -o TMatrix_as.o
gcc -I"/usr/share/R/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T     -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c Tsparse.c -o Tsparse.o
gcc -I"/usr/share/R/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T     -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c init.c -o init.o
gcc -I"/usr/share/R/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T     -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c Mutils.c -o Mutils.o
gcc -I"/usr/share/R/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T     -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c chm_common.c -o chm_common.o
gcc -I"/usr/share/R/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T     -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c cs.c -o cs.o
gcc -I"/usr/share/R/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T     -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c cs_utils.c -o cs_utils.o
gcc -I"/usr/share/R/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T     -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c dense.c -o dense.o
gcc -I"/usr/share/R/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T     -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c dgCMatrix.c -o dgCMatrix.o
gcc -I"/usr/share/R/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T     -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c dgTMatrix.c -o dgTMatrix.o
gcc -I"/usr/share/R/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T     -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c dgeMatrix.c -o dgeMatrix.o
gcc -I"/usr/share/R/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T     -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c dpoMatrix.c -o dpoMatrix.o
gcc -I"/usr/share/R/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T     -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c dppMatrix.c -o dppMatrix.o
gcc -I"/usr/share/R/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T     -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c dsCMatrix.c -o dsCMatrix.o
gcc -I"/usr/share/R/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T     -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c dsyMatrix.c -o dsyMatrix.o
gcc -I"/usr/share/R/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T     -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c dspMatrix.c -o dspMatrix.o
gcc -I"/usr/share/R/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T     -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c dtCMatrix.c -o dtCMatrix.o
gcc -I"/usr/share/R/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T     -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c dtTMatrix.c -o dtTMatrix.o
gcc -I"/usr/share/R/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T     -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c dtrMatrix.c -o dtrMatrix.o
gcc -I"/usr/share/R/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T     -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c dtpMatrix.c -o dtpMatrix.o
gcc -I"/usr/share/R/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T     -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c factorizations.c -o factorizations.o
gcc -I"/usr/share/R/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T     -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c ldense.c -o ldense.o
gcc -I"/usr/share/R/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T     -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c lgCMatrix.c -o lgCMatrix.o
gcc -I"/usr/share/R/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T     -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c sparseQR.c -o sparseQR.o
gcc -I"/usr/share/R/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T     -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c abIndex.c -o abIndex.o
gcc -I"/usr/share/R/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T     -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c packedMatrix.c -o packedMatrix.o
make[1]: Entering directory '/tmp/RtmpxZGw2m/R.INSTALL1d4ca03978/Matrix/src/CHOLMOD'
( cd Lib ; make clean )
make[2]: Entering directory '/tmp/RtmpxZGw2m/R.INSTALL1d4ca03978/Matrix/src/CHOLMOD/Lib'
make[2]: Leaving directory '/tmp/RtmpxZGw2m/R.INSTALL1d4ca03978/Matrix/src/CHOLMOD/Lib'
make[1]: Leaving directory '/tmp/RtmpxZGw2m/R.INSTALL1d4ca03978/Matrix/src/CHOLMOD'
make[1]: Entering directory '/tmp/RtmpxZGw2m/R.INSTALL1d4ca03978/Matrix/src/COLAMD'
( cd Source ; make clean )
make[2]: Entering directory '/tmp/RtmpxZGw2m/R.INSTALL1d4ca03978/Matrix/src/COLAMD/Source'
make[2]: Leaving directory '/tmp/RtmpxZGw2m/R.INSTALL1d4ca03978/Matrix/src/COLAMD/Source'
make[1]: Leaving directory '/tmp/RtmpxZGw2m/R.INSTALL1d4ca03978/Matrix/src/COLAMD'
make[1]: Entering directory '/tmp/RtmpxZGw2m/R.INSTALL1d4ca03978/Matrix/src/AMD'
( cd Source ; make clean )
make[2]: Entering directory '/tmp/RtmpxZGw2m/R.INSTALL1d4ca03978/Matrix/src/AMD/Source'
make[2]: Leaving directory '/tmp/RtmpxZGw2m/R.INSTALL1d4ca03978/Matrix/src/AMD/Source'
make[1]: Leaving directory '/tmp/RtmpxZGw2m/R.INSTALL1d4ca03978/Matrix/src/AMD'
make[1]: Entering directory '/tmp/RtmpxZGw2m/R.INSTALL1d4ca03978/Matrix/src/SuiteSparse_config'
make[1]: Leaving directory '/tmp/RtmpxZGw2m/R.INSTALL1d4ca03978/Matrix/src/SuiteSparse_config'
make[1]: Entering directory '/tmp/RtmpxZGw2m/R.INSTALL1d4ca03978/Matrix/src/CHOLMOD'
( cd Lib ; make -f "/usr/lib/R/etc/Makeconf" -f Makefile )
make[2]: Entering directory '/tmp/RtmpxZGw2m/R.INSTALL1d4ca03978/Matrix/src/CHOLMOD/Lib'
gcc -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 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c ../Core/cholmod_aat.c -o cholmod_aat.o
gcc -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 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c ../Core/cholmod_add.c -o cholmod_add.o
gcc -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 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c ../Core/cholmod_band.c -o cholmod_band.o
gcc -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 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c ../Core/cholmod_change_factor.c -o cholmod_change_factor.o
gcc -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 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c ../Core/cholmod_common.c -o cholmod_common.o
gcc -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 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c ../Core/cholmod_complex.c -o cholmod_complex.o
gcc -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 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c ../Core/cholmod_copy.c -o cholmod_copy.o
gcc -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 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c ../Core/cholmod_dense.c -o cholmod_dense.o
gcc -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 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c ../Core/cholmod_error.c -o cholmod_error.o
gcc -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 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c ../Core/cholmod_factor.c -o cholmod_factor.o
gcc -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 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c ../Core/cholmod_memory.c -o cholmod_memory.o
gcc -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 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c ../Core/cholmod_sparse.c -o cholmod_sparse.o
gcc -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 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c ../Core/cholmod_transpose.c -o cholmod_transpose.o
gcc -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 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c ../Core/cholmod_triplet.c -o cholmod_triplet.o
gcc -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 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c ../Core/cholmod_version.c -o cholmod_version.o
gcc -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 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c ../Check/cholmod_check.c -o cholmod_check.o
gcc -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 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c ../Check/cholmod_read.c -o cholmod_read.o
gcc -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 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c ../Check/cholmod_write.c -o cholmod_write.o
gcc -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 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c ../Cholesky/cholmod_amd.c -o cholmod_amd.o
gcc -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 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c ../Cholesky/cholmod_analyze.c -o cholmod_analyze.o
gcc -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 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c ../Cholesky/cholmod_colamd.c -o cholmod_colamd.o
gcc -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 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c ../Cholesky/cholmod_etree.c -o cholmod_etree.o
gcc -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 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c ../Cholesky/cholmod_factorize.c -o cholmod_factorize.o
gcc -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 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c ../Cholesky/cholmod_postorder.c -o cholmod_postorder.o
gcc -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 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c ../Cholesky/cholmod_rcond.c -o cholmod_rcond.o
gcc -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 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c ../Cholesky/cholmod_resymbol.c -o cholmod_resymbol.o
gcc -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 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c ../Cholesky/cholmod_rowcolcounts.c -o cholmod_rowcolcounts.o
gcc -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 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c ../Cholesky/cholmod_rowfac.c -o cholmod_rowfac.o
gcc -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 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c ../Cholesky/cholmod_solve.c -o cholmod_solve.o
gcc -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 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c ../Cholesky/cholmod_spsolve.c -o cholmod_spsolve.o
gcc -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 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c ../MatrixOps/cholmod_drop.c -o cholmod_drop.o
gcc -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 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c ../MatrixOps/cholmod_horzcat.c -o cholmod_horzcat.o
gcc -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 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c ../MatrixOps/cholmod_norm.c -o cholmod_norm.o
gcc -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 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c ../MatrixOps/cholmod_scale.c -o cholmod_scale.o
gcc -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 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c ../MatrixOps/cholmod_sdmult.c -o cholmod_sdmult.o
gcc -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 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c ../MatrixOps/cholmod_ssmult.c -o cholmod_ssmult.o
gcc -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 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c ../MatrixOps/cholmod_submatrix.c -o cholmod_submatrix.o
gcc -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 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c ../MatrixOps/cholmod_vertcat.c -o cholmod_vertcat.o
gcc -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 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c ../MatrixOps/cholmod_symmetry.c -o cholmod_symmetry.o
gcc -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 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c ../Modify/cholmod_rowadd.c -o cholmod_rowadd.o
gcc -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 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c ../Modify/cholmod_rowdel.c -o cholmod_rowdel.o
gcc -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 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c ../Modify/cholmod_updown.c -o cholmod_updown.o
gcc -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 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c ../Supernodal/cholmod_super_numeric.c -o cholmod_super_numeric.o
gcc -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 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c ../Supernodal/cholmod_super_solve.c -o cholmod_super_solve.o
gcc -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 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c ../Supernodal/cholmod_super_symbolic.c -o cholmod_super_symbolic.o
gcc -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 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -DDLONG -c  ../Core/cholmod_aat.c -o cholmod_l_aat.o
gcc -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 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -DDLONG -c  ../Core/cholmod_add.c -o cholmod_l_add.o
gcc -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 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -DDLONG -c  ../Core/cholmod_band.c -o cholmod_l_band.o
gcc -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 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -DDLONG -c  ../Core/cholmod_change_factor.c -o cholmod_l_change_factor.o
gcc -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 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -DDLONG -c  ../Core/cholmod_common.c -o cholmod_l_common.o
gcc -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 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -DDLONG -c  ../Core/cholmod_complex.c -o cholmod_l_complex.o
gcc -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 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -DDLONG -c  ../Core/cholmod_copy.c -o cholmod_l_copy.o
gcc -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 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -DDLONG -c  ../Core/cholmod_dense.c -o cholmod_l_dense.o
gcc -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 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -DDLONG -c  ../Core/cholmod_error.c -o cholmod_l_error.o
gcc -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 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -DDLONG -c  ../Core/cholmod_factor.c -o cholmod_l_factor.o
gcc -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 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -DDLONG -c  ../Core/cholmod_memory.c -o cholmod_l_memory.o
gcc -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 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -DDLONG -c  ../Core/cholmod_sparse.c -o cholmod_l_sparse.o
gcc -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 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -DDLONG -c  ../Core/cholmod_transpose.c -o cholmod_l_transpose.o
gcc -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 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -DDLONG -c  ../Core/cholmod_triplet.c -o cholmod_l_triplet.o
gcc -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 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -DDLONG -c  ../Core/cholmod_version.c -o cholmod_l_version.o
gcc -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 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -DDLONG -c  ../Check/cholmod_check.c -o cholmod_l_check.o
gcc -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 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -DDLONG -c  ../Check/cholmod_read.c -o cholmod_l_read.o
gcc -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 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -DDLONG -c  ../Check/cholmod_write.c -o cholmod_l_write.o
gcc -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 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -DDLONG -c  ../Cholesky/cholmod_amd.c -o cholmod_l_amd.o
gcc -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 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -DDLONG -c  ../Cholesky/cholmod_analyze.c -o cholmod_l_analyze.o
gcc -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 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -DDLONG -c  ../Cholesky/cholmod_colamd.c -o cholmod_l_colamd.o
gcc -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 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -DDLONG -c  ../Cholesky/cholmod_etree.c -o cholmod_l_etree.o
gcc -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 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -DDLONG -c  ../Cholesky/cholmod_factorize.c -o cholmod_l_factorize.o
gcc -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 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -DDLONG -c  ../Cholesky/cholmod_postorder.c -o cholmod_l_postorder.o
gcc -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 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -DDLONG -c  ../Cholesky/cholmod_rcond.c -o cholmod_l_rcond.o
gcc -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 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -DDLONG -c  ../Cholesky/cholmod_resymbol.c -o cholmod_l_resymbol.o
gcc -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 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -DDLONG -c  ../Cholesky/cholmod_rowcolcounts.c -o cholmod_l_rowcolcounts.o
gcc -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 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -DDLONG -c  ../Cholesky/cholmod_rowfac.c -o cholmod_l_rowfac.o
gcc -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 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -DDLONG -c  ../Cholesky/cholmod_solve.c -o cholmod_l_solve.o
gcc -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 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -DDLONG -c  ../Cholesky/cholmod_spsolve.c -o cholmod_l_spsolve.o
gcc -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 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -DDLONG -c  ../MatrixOps/cholmod_drop.c -o cholmod_l_drop.o
gcc -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 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -DDLONG -c  ../MatrixOps/cholmod_horzcat.c -o cholmod_l_horzcat.o
gcc -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 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -DDLONG -c  ../MatrixOps/cholmod_norm.c -o cholmod_l_norm.o
gcc -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 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -DDLONG -c  ../MatrixOps/cholmod_scale.c -o cholmod_l_scale.o
gcc -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 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -DDLONG -c  ../MatrixOps/cholmod_sdmult.c -o cholmod_l_sdmult.o
gcc -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 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -DDLONG -c  ../MatrixOps/cholmod_ssmult.c -o cholmod_l_ssmult.o
gcc -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 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -DDLONG -c  ../MatrixOps/cholmod_submatrix.c -o cholmod_l_submatrix.o
gcc -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 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -DDLONG -c  ../MatrixOps/cholmod_vertcat.c -o cholmod_l_vertcat.o
gcc -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 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -DDLONG -c  ../MatrixOps/cholmod_symmetry.c -o cholmod_l_symmetry.o
gcc -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 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -DDLONG -c  ../Modify/cholmod_rowadd.c -o cholmod_l_rowadd.o
gcc -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 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -DDLONG -c  ../Modify/cholmod_rowdel.c -o cholmod_l_rowdel.o
gcc -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 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -DDLONG -c  ../Modify/cholmod_updown.c -o cholmod_l_updown.o
gcc -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 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -DDLONG -c  ../Supernodal/cholmod_super_numeric.c -o cholmod_l_super_numeric.o
gcc -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 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -DDLONG -c  ../Supernodal/cholmod_super_solve.c -o cholmod_l_super_solve.o
gcc -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 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -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
ar: `u' modifier ignored since `D' is the default (see `U')
make[2]: Leaving directory '/tmp/RtmpxZGw2m/R.INSTALL1d4ca03978/Matrix/src/CHOLMOD/Lib'
make[1]: Leaving directory '/tmp/RtmpxZGw2m/R.INSTALL1d4ca03978/Matrix/src/CHOLMOD'
make[1]: Entering directory '/tmp/RtmpxZGw2m/R.INSTALL1d4ca03978/Matrix/src/COLAMD'
( cd Source ; make -f "/usr/lib/R/etc/Makeconf" -f Makefile lib )
make[2]: Entering directory '/tmp/RtmpxZGw2m/R.INSTALL1d4ca03978/Matrix/src/COLAMD/Source'
gcc -I"/usr/share/R/include" -DNDEBUG -I../Include -I../../SuiteSparse_config     -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c colamd.c -o colamd.o
gcc -I"/usr/share/R/include" -DNDEBUG -I../Include -I../../SuiteSparse_config     -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -I../Include -DDLONG -c colamd.c -o colamd_l.o
ar -rucs ../../COLAMD.a colamd.o colamd_l.o
ar: `u' modifier ignored since `D' is the default (see `U')
make[2]: Leaving directory '/tmp/RtmpxZGw2m/R.INSTALL1d4ca03978/Matrix/src/COLAMD/Source'
make[1]: Leaving directory '/tmp/RtmpxZGw2m/R.INSTALL1d4ca03978/Matrix/src/COLAMD'
make[1]: Entering directory '/tmp/RtmpxZGw2m/R.INSTALL1d4ca03978/Matrix/src/AMD'
( cd Source ; make -f "/usr/lib/R/etc/Makeconf" -f Makefile lib )
make[2]: Entering directory '/tmp/RtmpxZGw2m/R.INSTALL1d4ca03978/Matrix/src/AMD/Source'
gcc -I"/usr/share/R/include" -DNDEBUG -I../Include -I../../SuiteSparse_config     -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -I../Include -DDINT -c amd_aat.c -o amd_i_aat.o
gcc -I"/usr/share/R/include" -DNDEBUG -I../Include -I../../SuiteSparse_config     -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -I../Include -DDLONG -c amd_aat.c -o amd_l_aat.o
gcc -I"/usr/share/R/include" -DNDEBUG -I../Include -I../../SuiteSparse_config     -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -I../Include -DDINT -c amd_1.c -o amd_i_1.o
gcc -I"/usr/share/R/include" -DNDEBUG -I../Include -I../../SuiteSparse_config     -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -I../Include -DDLONG -c amd_1.c -o amd_l_1.o
gcc -I"/usr/share/R/include" -DNDEBUG -I../Include -I../../SuiteSparse_config     -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -I../Include -DDINT -c amd_2.c -o amd_i_2.o
gcc -I"/usr/share/R/include" -DNDEBUG -I../Include -I../../SuiteSparse_config     -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -I../Include -DDLONG -c amd_2.c -o amd_l_2.o
gcc -I"/usr/share/R/include" -DNDEBUG -I../Include -I../../SuiteSparse_config     -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -I../Include -DDINT -c amd_postorder.c -o amd_i_postorder.o
gcc -I"/usr/share/R/include" -DNDEBUG -I../Include -I../../SuiteSparse_config     -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -I../Include -DDLONG -c amd_postorder.c -o amd_l_postorder.o
gcc -I"/usr/share/R/include" -DNDEBUG -I../Include -I../../SuiteSparse_config     -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -I../Include -DDINT -c amd_post_tree.c -o amd_i_post_tree.o
gcc -I"/usr/share/R/include" -DNDEBUG -I../Include -I../../SuiteSparse_config     -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -I../Include -DDLONG -c amd_post_tree.c -o amd_l_post_tree.o
gcc -I"/usr/share/R/include" -DNDEBUG -I../Include -I../../SuiteSparse_config     -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -I../Include -DDINT -c amd_defaults.c -o amd_i_defaults.o
gcc -I"/usr/share/R/include" -DNDEBUG -I../Include -I../../SuiteSparse_config     -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -I../Include -DDLONG -c amd_defaults.c -o amd_l_defaults.o
gcc -I"/usr/share/R/include" -DNDEBUG -I../Include -I../../SuiteSparse_config     -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -I../Include -DDINT -c amd_order.c -o amd_i_order.o
gcc -I"/usr/share/R/include" -DNDEBUG -I../Include -I../../SuiteSparse_config     -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -I../Include -DDLONG -c amd_order.c -o amd_l_order.o
gcc -I"/usr/share/R/include" -DNDEBUG -I../Include -I../../SuiteSparse_config     -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -I../Include -DDINT -c amd_control.c -o amd_i_control.o
gcc -I"/usr/share/R/include" -DNDEBUG -I../Include -I../../SuiteSparse_config     -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -I../Include -DDLONG -c amd_control.c -o amd_l_control.o
gcc -I"/usr/share/R/include" -DNDEBUG -I../Include -I../../SuiteSparse_config     -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -I../Include -DDINT -c amd_info.c -o amd_i_info.o
gcc -I"/usr/share/R/include" -DNDEBUG -I../Include -I../../SuiteSparse_config     -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -I../Include -DDLONG -c amd_info.c -o amd_l_info.o
gcc -I"/usr/share/R/include" -DNDEBUG -I../Include -I../../SuiteSparse_config     -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -I../Include -DDINT -c amd_valid.c -o amd_i_valid.o
gcc -I"/usr/share/R/include" -DNDEBUG -I../Include -I../../SuiteSparse_config     -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -I../Include -DDLONG -c amd_valid.c -o amd_l_valid.o
gcc -I"/usr/share/R/include" -DNDEBUG -I../Include -I../../SuiteSparse_config     -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -I../Include -DDINT -c amd_preprocess.c -o amd_i_preprocess.o
gcc -I"/usr/share/R/include" -DNDEBUG -I../Include -I../../SuiteSparse_config     -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -I../Include -DDLONG -c amd_preprocess.c -o amd_l_preprocess.o
gcc -I"/usr/share/R/include" -DNDEBUG -I../Include -I../../SuiteSparse_config     -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -I../Include -DDINT -c amd_dump.c -o amd_i_dump.o
gcc -I"/usr/share/R/include" -DNDEBUG -I../Include -I../../SuiteSparse_config     -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -I../Include -DDLONG -c amd_dump.c -o amd_l_dump.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
ar: `u' modifier ignored since `D' is the default (see `U')
make[2]: Leaving directory '/tmp/RtmpxZGw2m/R.INSTALL1d4ca03978/Matrix/src/AMD/Source'
make[1]: Leaving directory '/tmp/RtmpxZGw2m/R.INSTALL1d4ca03978/Matrix/src/AMD'
make[1]: Entering directory '/tmp/RtmpxZGw2m/R.INSTALL1d4ca03978/Matrix/src/SuiteSparse_config'
gcc -I"/usr/share/R/include" -DNDEBUG -DNTIMER     -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c SuiteSparse_config.c -o SuiteSparse_config.o
ar -rucs ../SuiteSparse_config.a SuiteSparse_config.o
ar: `u' modifier ignored since `D' is the default (see `U')
make[1]: Leaving directory '/tmp/RtmpxZGw2m/R.INSTALL1d4ca03978/Matrix/src/SuiteSparse_config'
gcc -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 packedMatrix.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 -lgfortran
collect2: error: ld returned 1 exit status
make: *** [/usr/share/R/share/make/shlib.mk:10: Matrix.so] Error 1
ERROR: compilation failed for package ‘Matrix’
* removing ‘/usr/local/lib/R/site-library/Matrix’

The downloaded source packages are in
	‘/tmp/Rtmps7Wj4h/downloaded_packages’
Warning message:
In install.packages("Matrix", repos = "https://cran.r-project.org") :
  installation of package ‘Matrix’ had non-zero exit status

Attempting the same, but with RDscript, succeeds.

docker run \
    --rm \
    --entrypoint="" \
    -it wch1/r-debug:latest \
    RDscript -e "install.packages('Matrix', repos = 'https://cran.r-project.org')"

* DONE (Matrix)

Notes for Reviewers

According to https://cran.r-project.org/web/packages/Matrix/index.html, {Matrix} was last updated about two months ago (March 23, 2022), so I don't think the root cause of this command starting to fail is "new release of {Matrix}".

I suspect that this issue is related to the way those two executables (R and RD) were built / configured.

docker run \
    --rm \
    --entrypoint="" \
    -it wch1/r-debug \
    R CMD config LDFLAGS

# -Wl,-Bsymbolic-functions -Wl,-z,relro

docker run \
    --rm \
    --entrypoint="" \
    -it wch1/r-debug \
    RD CMD config LDFLAGS

# -L/usr/local/lib

Thanks very much for your time and consideration.

[mlampros]

/usr/bin/ld: cannot find -lgfortran

@jameslamb, I had a similar issue when testing an R package with RcppArmadillo code and it seems the libgfortran.so exists in /usr/lib/x86_64-linux-gnu but as libgfortran.so.5.0.0 so I've used a symlink to solve the issue as mentioned in a SO thread,

sudo ln -s /usr/lib/x86_64-linux-gnu/libgfortran.so.5.0.0 /usr/lib/libgfortran.so

# and then 

RDsan

[krlmlr]

@wch: Confirming that

ln -s /usr/lib/x86_64-linux-gnu/libgfortran.so.5.0.0 /usr/lib/libgfortran.so

helps with the linking issue. Should this be added to the Dockerfile ?

[wch]

@krlmlr Sure, do you want to make a PR?