Fix configure script to correctly retrieve cc path and flags.

[cinquin]

R CMD apparently outputs warnings such as "WARNING: ignoring environment value of R_HOME" to stdout, which ends up messing up configuration of the CC, CFLAGS, and CPPFLAGS environment variables.

This change allowed me to build the package under FreeBSD after setting R_HOME (I have another change in a different branch that bypasses R_HOME altogether, but that might not be desirable if there are multiple local R installs).

[codecov-io]

Codecov Report

Merging #46 into master will not change coverage. The diff coverage is n/a.

@@           Coverage Diff           @@
##           master      #46   +/-   ##
=======================================
  Coverage   77.77%   77.77%           
=======================================
  Files          48       48           
  Lines        2034     2034           
=======================================
  Hits         1582     1582           
  Misses        452      452

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[jeroen]

I have never encountered this warning. This would have to be fixed where that warning originates...

[jeroen]

Why is FreeBSD ignoring the R_HOME environment variable in the shell script? It shouldn't?

Are you aware this configure script should only be invoked by R itself when installing the package, never manually?

[cinquin]

Installing the CRAN package from R failed for me. I just followed the path of least resistance to get a working install, and I figured I would share this so others encountering the same problem can benefit.

I agree that the optimal fix might lie somewhere else, but at least this provides immediate relief.

[jeroen]

Can you show the full install log? I feel this is another problem.