[R] make install libgfortran.so.5: cannot open shared object file: No such file or directory; conftest.c:1:10: fatal error: jni.h: No such file or directory

[Ivan Krylov]

On Fri, 18 Nov 2022 16:45:14 -0500
Rob Kudyba <rk3199 using columbia.edu> wrote:

> Here is where the error occurs in make install:
> [...]
> installing packages ...
>   building HTML index ...
> /path/to/R-4.2.2/bin/exec/R: error while loading shared libraries:
> libgfortran.so.5: cannot open shared object file: No such file or
> directory make[2]: *** [install] Error 127
> make[2]: Leaving directory `/path/to/R-4.2.2/src/library'
> make[1]: *** [install] Error 1
> make[1]: Leaving directory `/path/to/rk3199/R-4.2.2/src'
> make: *** [install] Error 1

It should be possible to run R without installing it, as
/path/to/R-4.2.2/bin/R (strictly speaking, as bin/R under the build
directory, if you're building R separately from the source tree). Does
it work?

Does /path/to/R-4.2.2/bin/R -d ldd give you any useful information? Can
you use strace -f -e openat /path/to/R-4.2.2/bin/R to confirm that the
dynamic library loader is looking in /path/to/gcc-11.2/lib64 for the
shared objects?

If /path/to/gcc-11.2/lib64 is missing from both /etc/ld.so.conf and the
environment variable LD_LIBRARY_PATH and you don't want to set it
manually every time, you can either edit /path/to/R-4.2.2/etc/ldpaths
or pass the -Wl,-rpath=/path/to/gcc-11.2/lib64 flag to the linker.

> During make I see this error with Java:

This error is not fatal. rJava won't work, but the rest of R should be
fine.

-- 
Best regards,
Ivan