Installing R package from source fails

[GabrielHoffman]

I am having an installation issue.

On R 4.1.0 and 4.2.0 on CentOS 7.6.1810 installing PRIMME 3.2-3 fails with the following error:

* installing *source* package ‘PRIMME’ ...
** package ‘PRIMME’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
g++ -std=gnu++14 -I"/hpc/packages/minerva-centos7/R/4.2.0/lib64/R/include" -DNDEBUG  -I'/hpc/packages/minerva-centos7/rpackages/4.2.0/site-library/Rcpp/include' -I'/hpc/packages/minerva-centos7/R/4.2.0/lib64/R/library/Matrix/include' -I/usr/local/include  -I../inst/include  -DPRIMME_INT_SIZE=0 -DF77UNDERSCORE -DUSE_XHEEV -DUSE_ZGESV -DUSE_XHEGV -DPRIMME_INT_SIZE=0 -DPRIMME_WITHOUT_FLOAT -DPRIMME_BLAS_RCOMPLEX -fpic  -O3 -fopenmp  -c RcppExports.cpp -o RcppExports.o
gcc -I"/hpc/packages/minerva-centos7/R/4.2.0/lib64/R/include" -DNDEBUG  -I'/hpc/packages/minerva-centos7/rpackages/4.2.0/site-library/Rcpp/include' -I'/hpc/packages/minerva-centos7/R/4.2.0/lib64/R/library/Matrix/include' -I/usr/local/include   -fpic  -I/hpc/packages/minerva-centos7/pcre2/10.35/include -O3 -fopenmp  -c init.c -o init.o
g++ -std=gnu++14 -I"/hpc/packages/minerva-centos7/R/4.2.0/lib64/R/include" -DNDEBUG  -I'/hpc/packages/minerva-centos7/rpackages/4.2.0/site-library/Rcpp/include' -I'/hpc/packages/minerva-centos7/R/4.2.0/lib64/R/library/Matrix/include' -I/usr/local/include  -I../inst/include  -DPRIMME_INT_SIZE=0 -DF77UNDERSCORE -DUSE_XHEEV -DUSE_ZGESV -DUSE_XHEGV -DPRIMME_INT_SIZE=0 -DPRIMME_WITHOUT_FLOAT -DPRIMME_BLAS_RCOMPLEX -fpic  -O3 -fopenmp  -c primmeR.cpp -o primmeR.o
make[1]: Entering directory `/tmp/RtmpMyo4pV/R.INSTALL3165311191421/PRIMME/src/primme'
g++ -std=gnu++14 -I/hpc/packages/minerva-centos7/R/4.2.0/lib64/R/include -DNDEBUG -O3 -fopenmp  -fpic -I../inst/include  -DPRIMME_INT_SIZE=0 -DF77UNDERSCORE -DUSE_XHEEV -DUSE_ZGESV -DUSE_XHEGV -DPRIMME_INT_SIZE=0 -DPRIMME_WITHOUT_FLOAT -DPRIMME_BLAS_RCOMPLEX  /hpc/packages/minerva-centos7/proj/8.1.0/include:/hpc/packages/minerva-centos7/gdal/3.3.1/include -I../../inst/include -Iinclude -c eigs/auxiliary_eigs.cpp -o eigs/auxiliary_eigs.o
g++: error: /hpc/packages/minerva-centos7/proj/8.1.0/include:/hpc/packages/minerva-centos7/gdal/3.3.1/include: No such file or directory
make[1]: *** [eigs/auxiliary_eigs.o] Error 1
make[1]: Leaving directory `/tmp/RtmpMyo4pV/R.INSTALL3165311191421/PRIMME/src/primme'
make: *** [primme/libprimme.a] Error 2
ERROR: compilation failed for package ‘PRIMME’
* removing ‘/hpc/users/hoffmg01/.Rlib/R_420/PRIMME’
* restoring previous ‘/hpc/users/hoffmg01/.Rlib/R_420/PRIMME’

The downloaded source packages are in
	‘/tmp/Rtmp9xHZoS/downloaded_packages’
Warning message:
In install.packages("PRIMME") :
  installation of package ‘PRIMME’ had non-zero exit status

I can fix this manually in bash by running g++ replacing

/hpc/packages/minerva-centos7/proj/8.1.0/include:/hpc/packages/minerva-centos7/gdal/3.3.1/include 

with

-I/hpc/packages/minerva-centos7/proj/8.1.0/include:/hpc/packages/minerva-centos7/gdal/3.3.1/include 

Just adding -I fixed it. But then I had to write a bash script to run g++ outside R.

Can you fix this directly in a makefile? I couldn't figure out how

Thanks,
Gabriel