[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

Rob Kudyba rk3199 @end|ng |rom co|umb|@@edu
Mon Nov 21 19:19:22 CET 2022

> В Mon, 21 Nov 2022 10:19:36 -0500
> Rob Kudyba <rk3199 using columbia.edu> пишет:
> > I edited the last line to be:
> > export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/path/to/gcc-11.2/lib64 then
> > make install errored with:
> > /path/to/R-4.2.2/bin/exec/R: error while loading shared libraries:
> > libpcre2-8.so.0: cannot open shared object file: No such file or
> > directory
> >
> > So it appears that the same issue happens for PCRE! I then edited the
> > line to be:
> > export
> >
> LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/path/to/gcc-11.2/lib64:/path/to/pcre2-10.35/lib
> >
> > Then make install finished with:
> > Successfully remade target file `install'.
> Does the installed copy of R work?


Are you running make install as root? Programs starting as root are wary
> of environment variables such as LD_LIBRARY_PATH and may ignore or
> unset them while starting up (otherwise it would be trivial to load user
> code into setuid root binaries and take over the system). You may have
> to load the module again after you obtain the superuser privileges.

Ah I should've mentioned this. I did use sudo to install as the program
modules are shared and installed by root. That has to be the reason.

> "R Installation and Administration" [1] says that the R build process
> remembers the library paths to put into LD_LIBRARY_PATH, but only if
> they are specified in the LDFLAGS parameter, so if there's a set of
> library paths that's not expected to be normally present in
> LD_LIBRARY_PATH, perhaps it's best to mention them explicitly in the
> ./configure call.
> --
> Best regards,
> Ivan
> [1] https://cran.r-project.org/doc/manuals/R-admin.html

What would the ./configure options look like?

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