R CMD SHLIB Fortran 90 file which use NetCDF

Question

I would like compile a fortran 90 file which use NetCDF. I have installed NetCDF-Fortran and as shown here, to compile the file test_nc.f90:

program test_nc
    use netcdf
    implicit none
    integer :: ncid, nc_err

    nc_err = nf90_open('test.nc', nf90_nowrite, ncid)
    nc_err = nf90_close(ncid)
end program test_nc

The compilation with gfortran is

gfortran test_nc.f90 -o test_nc `nf-config --fflags --flibs`

where nf-config --fflags --flibs is:

-I/usr/include
-L/usr/lib -lnetcdff -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -lnetcdf -lnetcdf -ldl -lz -lcurl -lm

Replacing program by subroutine is

subroutine test_nc
    use netcdf
    implicit none
    integer :: ncid, nc_err

    nc_err = nf90_open('test.nc', nf90_nowrite, ncid)
    nc_err = nf90_close(ncid)
end subroutine test_nc

However, When I run

R CMD SHLIB test_nc.f90  `nf-config --fflags --flibs`

results in:

gfortran -fno-optimize-sibling-calls  -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-k1TtL4/r-base-3.6.1=. -fstack-protector-strong  -c  test_nc.f90 -o test_nc.o
test_nc.f90:2:8:

    2 |     use netcdf
      |        1
Fatal Error: Cannot open module file ‘netcdf.mod’ for reading at (1): No such file or directory
compilation terminated.

Also, when I try:

R CMD SHLIB test_nc.f90 -I/usr/include -L/usr/lib -lnetcdff -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -lnetcdf -lnetcdf -ldl -lz -lcurl -lm
gfortran -fno-optimize-sibling-calls  -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-k1TtL4/r-base-3.6.1=. -fstack-protector-strong  -c  test_nc.f90 -o test_nc.o

results in:

test_nc.f90:2:8:

    2 |     use netcdf
      |        1
Fatal Error: Cannot open module file ‘netcdf.mod’ for reading at (1): No such file or directory
compilation terminated.
make: *** [/usr/lib/R/etc/Makeconf:195: test_nc.o] Error 1

How can I tell R CMD SHLIB to use the Netcdf-fortran libraries?

?SHLIB shows

R CMD SHLIB -o mylib.so a.f b.f -L/opt/acml3.5.0/gnu64/lib -lacml

So I guess it is possible to do this

Answer 1

In the call to R CMD SHLIB the options you have provided from nf-config are taken only as linker options. The compilation step is failing because setting the search path for the NetCDF Fortran module is required before the link process.

To add the -I... option from nf-config you can use the environment variable PKG_FCFLAGS:

env PKG_FCFLAGS="`nf-config --fflags`" R CMD SHLIB test_nc.f90 `nf-config --flibs`

Alternatively, you can put PKG_FCFLAGS in your Makevars file.

(Note that, unlike C and C++, the include path option for module files is not for the pre-processing stage.)