configure was actually rerun after installing flex so 'flex' check passed.
Now I tried to uninstall flex and then it gives a warning. I maybe ignored
the message before.
If the script is in bash, why can't it be '/bin/bash' or '/usr/bin/env bash'
?
On Wed, Mar 10, 2010 at 10:02 PM, Jason Swails <jason.swails.gmail.com>wrote:
> On Wed, Mar 10, 2010 at 9:11 PM, InSuk Joung <i.joung.gmail.com> wrote:
> > I had weird errors(?) when running configure.
> > I guess they are probably related.
> >
> > Regarding 'm4', I found that netcdf uses it.
> >
> > Setting AMBERHOME to /home/isjoung/AMBER/amber11
> >
> > ./configure: 363: [[: not found
> > ./configure: 363: no: not found
> > ./configure: 363: no: not found
> >
> > Obtaining the gnu suite version:
> > gcc -v
> > The version is 4.4.1
> > ./configure: 697: [[: not found
> > ./configure: 697: no: not found
> > ./configure: 697: no: not found
> > [: 697: no: unexpected operator
> > [: 697: no: unexpected operator
> >
> > Testing the gcc compiler:
> > gcc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o testp testp.c
> > OK
> >
> > Validating the C++ compiler version:
> > g++ -v
> > The version is 4.4.1
> > OK
> >
> > Testing the gfortran compiler:
> > gfortran -O0 -o testp testp.f
> > OK
> >
> > Testing mixed C/Fortran compilation:
> > gcc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -c -o testp.c.o
> testp.c
> > gfortran -O0 -c -o testp.f.o testp.f
> > gcc -o testp testp.c.o testp.f.o -lgfortran
> > OK
> >
> > Testing flex:
> > OK
> >
> > Configuring NetCDF; (may be time-consuming)
> >
> > NetCDF configure succeeded.
> >
> > Configuring fftw-2.1.5; (may be time-consuming)
> >
> > fftw-2.1.5 configure succeeded.
> >
> > The configuration file, config.h, was successfully created.
> >
> > ./configure: 1311: [[: not found
> > ./configure: 1311: no: not found
> > ./configure: 1311: no: not found
> > The next step is to type 'make -f Makefile_at'
> >
>
> These errors are a result of non-sh-compliance of the configure
> script. configure invokes /bin/sh as the interpreter shell which is
> almost always bash for most systems. Ubuntu, however, uses dash as
> its default sh, a topic that has been discussed here a bit. These
> errors were brought up in a fairly recent post
> http://dev-archive.ambermd.org/201003/0166.html . What's surprising
> to me is that "testing flex" returned OK when your system didn't have
> it...
>
> >
> >
> > On Wed, Mar 10, 2010 at 4:17 PM, case <case.biomaps.rutgers.edu> wrote:
> >
> >> On Wed, Mar 10, 2010, InSuk Joung wrote:
> >>
> >> > I found that 'flex' was not installed in my system. I installed
> 'flex'
> >> and
> >> > re-compiled AT. Then, everything was fine.
> >> > However, I think it would be a better way to give a warning in the
> >> > configuration step.
> >>
> >> It's is *supposed* to do exactly that. Can you move flex out of the way
> >> (so that it is not found) and try to debug why the section in configure
> "
> >> Test
> >> if lex/flex is available and works" (starting about line 933 of
> configure)
> >> is not failing.
> >>
> >> > Same to 'm4' although this gave me a obvious error message during
> >> > compilation.
> >>
> >> What step needs m4? Should we put in a configure test for that as well
> as
> >> for
> >> flex?
> >>
> >> ...thx...dac
> >>
> >>
> >> _______________________________________________
> >> AMBER-Developers mailing list
> >> AMBER-Developers.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber-developers
> >>
> >
> >
> >
> > --
> > Best,
> > InSuk Joung
> > _______________________________________________
> > AMBER-Developers mailing list
> > AMBER-Developers.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber-developers
> >
>
>
>
> --
> ---------------------------------------
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-4032
>
> _______________________________________________
> AMBER-Developers mailing list
> AMBER-Developers.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber-developers
>
--
Best,
InSuk Joung
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Received on Wed Mar 10 2010 - 20:00:02 PST
