Build fails on FreeBSD due to handling of fileno()

[BarrySmith]

Machine platform:
uname_result(system='FreeBSD', node='petsc-fbsd02', release='12.1-RELEASE-p1', version='FreeBSD 12.1-RELEASE-p1 GENERIC', machine='amd64', processor='amd64')
Python version:
3.6.9 (default, Dec 10 2019, 01:10:29)
[GCC 4.2.1 Compatible FreeBSD Clang 6.0.1 (tags/RELEASE_601/final 335540)]

Error while building

             from ../config.h:612,
             from ncgen.y:13:

ncgen.y:22:12: error: expected identifier or '(' before '!' token
22 | extern int fileno(FILE*);
| ^~~~~~
ncgen.l:28:12: error: expected identifier or '(' before '!' token
28 | extern int fileno(FILE*);

The problem comes from netcdf include files prototyping fileno() while the Freebsd includes provide fileno() as a macro under some conditions.

Attached is the entire configure and build process.
netcdf.log

[DennisHeimbigner]

Try removing it from ncgen3/ncgeny.c (the actual parser).
Tell me if it works.

[BarrySmith]

Sorry I missed this message earlier.

If I remove the fileno declarations from the four files ncgen3/ncgen.l ncgen.y and ncgen/ncgen.l ncgen.y and run make makeparse in those two directories then the code can be compiled.

But I don't know how to modify the netcdf build systems to do this.

[DennisHeimbigner]

Ok, try changing the files ncgen3/ncgen
try surrounding the fileno def in ncgen.l and ncgen.y
with

#ifndef fileno
...
#endif
and see if that fixes the problem.

[BarrySmith]

Protecting just the fileno in ncgen.l and ncgen.y does not work because the build with configure; make does not actually regenerate the .c files (which for some unclear reason are in the repository even though they seem to be generated files). If I remove all the fileno() extern from all the files including the .c then netcdf builds fine.

I don't understand enough about the configure; make system to figure out why the .c files are not generated with the new values at configure; make time. BTW: I am building from a git clone but I don't think that should matter.

[DennisHeimbigner]

They are not regenerated so that users without bison/flex installed and still use the library.
The files that need fixing are, as you note, ncgen.y and ncgen.l.
However whenever we modify those we invoke the rebuild procedure
defined in Makefile.am
The question is if removing the externs altogether will build with OSX, Windows, etc.

[BarrySmith]

Will this issue be fixed in the next point release of netcdf? This is preventing us from upgrading PETSc to use the latest NetCDF release and we don't want to be several releases behind.

[DennisHeimbigner]

I thought I put it in one of the PR, but let me check and create a separate PR for it.