On 03 Dec 2007, at 07:02, Peter O'Gorman wrote:
> Jean-François Mertens wrote:
>>>
>> On 03 Dec 2007, at 05:35, Peter O'Gorman wrote:
>>
>>>
>>> Did you check with otool -L that libeplplot loads libX11?
>>
>> But I see that Peter will give you a quicker fix - at least for
>> this specific problem - the principle is the same, and if
>> you want to be thorough you go through the check I
>> suggested _ it doesn't take that long .. :)
>
> Hehe, I thought I was doing a reasonable job of giving him the
> tools so
> that he could learn to figure stuff out by himself :-)
hoping I helped a bit too _
just thought that when the same type of problem was re-occurring with
the same pkg, it was better to give some more systematic tools..
JF
>
> Sorry, I did not see your email to Koen about this (was it off-list?).
Right _ it was _though I tried to use "Reply-to-all" throughout..
Here is what I can reconstruct
(and I see it is in my first reply that I forgot the "reply-all":
>
> On 03 Dec 2007, at 02:52, Koen van der Drift wrote:
>
>
>> 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.
>>
>
> Try to build your pkg (adding libs if necessary to the link
> commands) such
> that all undefined symbols of all Mach-O files have a " (from ..."
> in the output
> of "nm -m"
>
> Jean-Francois
>
________
On Dec 2, 2007, at 9:17 PM, Jean-François Mertens wrote:
> Try to build your pkg (adding libs if necessary to the link
> commands) such
> that all undefined symbols of all Mach-O files have a " (from ..."
> in the output
> of "nm -m"
>
Could you explain how to do that, I have no idea what you mean :-(
thanks,
- Koen.
________
On 03 Dec 2007, at 03:30, Koen van der Drift wrote:
>
> On Dec 2, 2007, at 9:17 PM, Jean-François Mertens wrote:
>
>
>> Try to build your pkg (adding libs if necessary to the link
>> commands) such
>> that all undefined symbols of all Mach-O files have a " (from ..."
>> in the output
>> of "nm -m"
>>
>
> Could you explain how to do that, I have no idea what you mean :-(
>
dpkg -S emboss | xargs file | fgrep 'Mach-O' | cut -f1 -d:
will give you the list of all binaries in your pkg
Then, for each of those in turn, say $f, run
nm -mgu $f | fgrep -v ' (from '
and you'll see all symbols for which it may be better to tell the
linker where
to find them...
(to understand what this is doing, run first on some example just
nm -mgu $f
to see what you eliminate, and why the others are the culprits for
your problems)
Best,
Jean-Francois
__________________
On Dec 2, 2007, at 11:49 PM, Jean-François Mertens wrote:
> But I see that Peter will give you a quicker fix - at least for
> this specific problem - the principle is the same, and if
> you want to be thorough you go through the check I
> suggested _ it doesn't take that long .. :)
>
Actually there are dozes of binaries in emboss (it's a suite of
programs). Only three of them have the word 'emboss' in them. If I
change the test to:
dpkg -L emboss | grep bin | xargs file | fgrep 'Mach-O' | cut -f1 -d:
I still get a long list, assuming that I didn't make an error. So it
would take some more time to go through all of them one by one :)
thanks for all the help,
- Koen.
_______________
On 03 Dec 2007, at 05:37, Koen van der Drift wrote:
>
> On Dec 2, 2007, at 10:05 PM, Jean-François Mertens wrote:
>
>
>> Then, for each of those in turn, say $f, run
>>
>> nm -mgu $f | fgrep -v ' (from '
>>
>
> This line doesn't return anything. Is it complete, it looks like
> there is something missing at the end?
>
It shouldn't return anything ! Did you try it for all binaries in the
pkg ?
JF
_________________
On 03 Dec 2007, at 05:59, Koen van der Drift wrote:
>
> On Dec 2, 2007, at 11:49 PM, Jean-François Mertens wrote:
>
>
>> But I see that Peter will give you a quicker fix - at least for
>> this specific problem - the principle is the same, and if
>> you want to be thorough you go through the check I
>> suggested _ it doesn't take that long .. :)
>>
>
> Actually there are dozes of binaries in emboss (it's a suite of
> programs). Only three of them have the word 'emboss' in them. If I
> change the test to:
>
> dpkg -L emboss | grep bin | xargs file | fgrep 'Mach-O' | cut -f1 -d:
>
> I still get a long list, assuming that I didn't make an error. So
> it would take some more time to go through all of them one by one :)
>
No .. That's why the file in question was labeled "$f" in :
> dpkg -S emboss | xargs file | fgrep 'Mach-O' | cut -f1 -d:
> will give you the list of all binaries in your pkg
>
> Then, for each of those in turn, say $f, run
>
> nm -mgu $f | fgrep -v ' (from '
>
to do in fact :
for f in `dpkg -S emboss | xargs file | fgrep 'Mach-O' | cut -f1 -d:` \
do echo $f;
nm -mgu $f | fgrep -v ' (from '
done
Cheers,
JF
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