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
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Received on Wed Mar 10 2010 - 19:30:03 PST
