First of all, thanks for all the help and suggestions. Little by
little I am undestanding more of the whole building process.
Now for the results :)
Using JF's test, I don't see any errors, ie nm doesn't print any
symbol names. (BTW, could that script be useful in the validation code
of fink?) Using oTool -L on all the libs, I now see, with Dan's patch
that much more libs are linked. But not for libajax and libnucleus:
libajax.5.0.0.dylib:
/sw/lib/EMBOSS/libajax.5.dylib (compatibility version 6.0.0, current
version 6.0.0)
/usr/lib/libgcc_s.1.dylib (compatibility version 1.0.0, current
version 1.0.0)
/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current
version 111.0.0)
libnucleus.5.0.0.dylib:
/sw/lib/EMBOSS/libnucleus.5.dylib (compatibility version 6.0.0,
current version 6.0.0)
/sw/lib/EMBOSS/libajax.5.dylib (compatibility version 6.0.0, current
version 6.0.0)
/usr/lib/libgcc_s.1.dylib (compatibility version 1.0.0, current
version 1.0.0)
/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current
version 111.0.0)
Not sure if that is a problem.
Unfortunately, I still get the same error:
t/1....Can't load '/sw/src/fink.build/bio-emboss-pm588-5.0.0.1-1/Bio-
Emboss-5.0.0.1/blib/arch/auto/Bio/Emboss/Emboss.bundle' for module
Bio::Emboss: dlopen(/sw/src/fink.build/bio-emboss-pm588-5.0.0.1-1/Bio-
Emboss-5.0.0.1/blib/arch/auto/Bio/Emboss/Emboss.bundle, 1): Symbol not
found: _XS_Bio__Emboss_ajStrTokenCount
Referenced from: /sw/src/fink.build/bio-emboss-pm588-5.0.0.1-1/Bio-
Emboss-5.0.0.1/blib/arch/auto/Bio/Emboss/Emboss.bundle
Expected in: dynamic lookup
This is with the line
BEGIN { delete $ENV{PERL_DL_NONLAZY}; };
NOT commented out (the code as is). And based on Peter's comment, that
means that there is still something missing:
> Yes, this makes it pass RTLD_NOW to dlopen() which is similar to
> setting
> DYLD_BIND_AT_LAUNCH. It should work with this set, if it does not it
> means there is a missing lib or symbol when linking the loadable
> bundle.
Actually, if I *do* comment out that line, the error changes to:
t/1....Can't load '/sw/src/fink.build/bio-emboss-pm588-5.0.0.1-1/Bio-
Emboss-5.0.0.1/blib/arch/auto/Bio/Emboss/Emboss.bundle' for module
Bio::Emboss: dlopen(/sw/src/fink.build/bio-emboss-pm588-5.0.0.1-1/Bio-
Emboss-5.0.0.1/blib/arch/auto/Bio/Emboss/Emboss.bundle, 2): Symbol not
found: _XS_Bio__Emboss_ajStrTokenCount
Referenced from: /sw/src/fink.build/bio-emboss-pm588-5.0.0.1-1/Bio-
Emboss-5.0.0.1/blib/arch/auto/Bio/Emboss/Emboss.bundle
Expected in: dynamic lookup
at t/1.t line 11
Note the 2) instead of the 1)
So then I thought, maybe there are symbols or libs missing in
Emboss.bundle? oTool -L on that file shows:
/sw/src/fink.build/bio-emboss-pm588-5.0.0.1-1/Bio-Emboss-5.0.0.1/blib/
arch/auto/Bio/Emboss/Emboss.bundle:
/sw/lib/EMBOSS/libnucleus.5.dylib (compatibility version 6.0.0,
current version 6.0.0)
/sw/lib/EMBOSS/libajax.5.dylib (compatibility version 6.0.0, current
version 6.0.0)
/sw/lib/EMBOSS/libajaxg.5.dylib (compatibility version 6.0.0, current
version 6.0.0)
/usr/lib/libgcc_s.1.dylib (compatibility version 1.0.0, current
version 1.0.0)
/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current
version 111.0.0)
That seems ok to me, since ajStrTokenCount is part of libajax.
Of course, disabling testing solves the building error, but not the
errors above.
cheers,
- Koen (still struggling)
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