On Dec 2, 2007, at 10:55 AM, Koen van der Drift wrote:
>
> On Dec 2, 2007, at 1:07 AM, Peter O'Gorman wrote:
>
>>
>> I suggest that you find out what plsc is (rebuild the package that
>> makes
>> libajaxg.5.dylib, and grep for it) and why it is not available (what
>> provides it? grep -rl plsc /sw/lib
>
> Thanks Peter,
>
> The grep command revealed two broken aliases. One of them was from
> the emboss package, which I fixed, and I don't get the error
> anymore. The other one was lebecpg.4.dylib, which seems to belong to
> postgresql. I think I once installed it, but right now I don't have
> that installed anymore. Not sure why it is still on my system and
> why it would contain plsc, maybe just a coincidence.
>
> But, I now get another similar 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
> at t/1.t line 11
OK, I solved that by commenting out the following line in the test file:
BEGIN { delete $ENV{PERL_DL_NONLAZY}; };
This does the following (see http://www.perl.com/lpt/a/520):
[quote]... it passes a flag to dlopen which attempts to ensure that
all functions are relocated as soon as the shared object is loaded.
Sounds complicated? In the normal, "lazy" operation of the dynamic
loader, the loader doesn't actually load all the functions from the
library file into memory at one go - instead, it merely notices that
it has a bunch more functions available; when a function is called, it
loads up the appropriate part of the object into memory, and jumps to
it. (Not entirely unlike the behaviour of use autouse or AutoSplit.)
Setting [PERL_DL_NONLAZY] forces the loader to load up all functions
at once, so that it can ensure that it really does have code for all
the functions it claims to have code for; this is usually what you
want to do when testing.[/quote]
However, now I get the following, again similar 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, 2): Symbol not
found: _XAllocColor
Referenced from: /sw/lib/EMBOSS/libeplplot.3.dylib
Expected in: dynamic lookup
at t/1.t line 11
Compilation failed in require at t/1.t line 11.
As I understand, _XAllocColor is part of libX1, and I have X11 and the
X11SDK installed from the Leopard DVD. I re-installed both, rebuild
emboss, and then tried bio-emboss-pm588 again, but still the same error.
Any clues?
thanks,
- Koen.
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