Re: [Fink-devel] dlopen symbol not found
On Dec 4, 2007, at 1:07 AM, Daniel Macks wrote: In particular, it's supplied by the deprecated_Emboss_str.o file in the bio-emboss-pm586 build dir (nm on that file reports it as T). Ahaaa - because I earlier got many warnings for deprecacted files (eg deprecated_Emboss_str.c:3878: warning: 'ajStrTokenCount' is deprecated), I set a flag in the Makefile to not use them. Turns out that the test file still needs them, hence the error :) Not sure if that would have caused my original error - at least this whole discussion revealed that there also was an upstream error. I have committed the updated files for emboss and bio-emboss-pm. thanks again for all the help, - Koen. - SF.Net email is sponsored by: The Future of Linux Business White Paper from Novell. From the desktop to the data center, Linux is going mainstream. Let it simplify your IT future. http://altfarm.mediaplex.com/ad/ck/8857-50307-18918-4 ___ Fink-devel mailing list Fink-devel@lists.sourceforge.net http://news.gmane.org/gmane.os.apple.fink.devel
Re: [Fink-devel] dlopen symbol not found
Koen van der Drift wrote: 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 :) Unfortunately, I still get the same error: t/1Can'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 Actually, if I *do* comment out that line, the error changes to: 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 Note the 2) instead of the 1) That's fine, commenting out that line changed the call to dlopen(). With it there perl does dlopen(/path/to/bundle,RTLD_LAZY); with it commented out it does dlopen(/path/to/bundle,RTLD_NOW); You can see the #defines for these in /usr/include/dlfcn.h. So, it looks like I had it backwards before, I misread the perl and figured it was setting PERL_DL_NONLAZY, but of course it is unsetting it :( Which probably means that the upstream author is aware of the linking issues and is trying to cover them up :( That seems ok to me, since ajStrTokenCount is part of libajax. Yes, but the loader is not looking for ajStrTokenCount, it is looking for XS_Bio__Emboss_ajStrTokenCount. And that is undefined. Did you do jfm's magic on Emboss.bundle? Peter -- Peter O'Gorman http://pogma.com - SF.Net email is sponsored by: The Future of Linux Business White Paper from Novell. From the desktop to the data center, Linux is going mainstream. Let it simplify your IT future. http://altfarm.mediaplex.com/ad/ck/8857-50307-18918-4 ___ Fink-devel mailing list Fink-devel@lists.sourceforge.net http://news.gmane.org/gmane.os.apple.fink.devel
Re: [Fink-devel] dlopen symbol not found
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/1Can'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/1Can'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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Re: [Fink-devel] dlopen symbol not found
On Dec 3, 2007, at 10:01 PM, Peter O'Gorman wrote: Yes, but the loader is not looking for ajStrTokenCount, it is looking for XS_Bio__Emboss_ajStrTokenCount. And that is undefined. Did you do jfm's magic on Emboss.bundle? that gives: Macintosh:Emboss koen$ nm -mgu Emboss.bundle | fgrep -v ' (from ' | grep ajStrTokenCount (undefined) external _XS_Bio__Emboss_ajStrTokenCount (dynamically looked up) (undefined) external _XS_Bio__Emboss_ajStrTokenCountR (dynamically looked up) - Koen. - SF.Net email is sponsored by: The Future of Linux Business White Paper from Novell. From the desktop to the data center, Linux is going mainstream. Let it simplify your IT future. http://altfarm.mediaplex.com/ad/ck/8857-50307-18918-4 ___ Fink-devel mailing list Fink-devel@lists.sourceforge.net http://news.gmane.org/gmane.os.apple.fink.devel
Re: [Fink-devel] dlopen symbol not found
On Mon, Dec 03, 2007 at 09:43:51PM -0500, Koen van der Drift wrote:
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.
[...]
Unfortunately, I still get the same error:
t/1Can'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
[...]
Actually, if I *do* comment out that line, the error changes to:
t/1Can'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.
Careful...the missing symbol is _XS_Bio__Emboss_ajStrTokenCount not
just ajStrTokenCount. XS are symbols from compiled perl modules
themselves, not the libs they link.
On my 10.3 machine (to which I back-ported the 10.4/5 emboss packages
and added my emboss.patch hacks but did not change the PERL_DL_NONLAZY
line), bio-emboss-pm586 passes all its tests. That symbol is defined
within the Emboss.bundle (one of the results of 'nm Emboss.bundle |
grep _XS_Bio__Emboss_ajStrTokenCount' lists it as T). In particular,
it's supplied by the deprecated_Emboss_str.o file in the
bio-emboss-pm586 build dir (nm on that file reports it as T). Do
you have that .o file at all? In the actual compiler command that
creates the Emboss.bundle file (a few lines before the tests are run),
is that .o included in the list of .o files?
Bug that doesn't affect anything: in the bio-emboss-pm.patch,
$EMB_EXT_LIBS should be [EMAIL PROTECTED]@/lib (need to pass the actual
linker flag, not just the pathname where the libs are).
dan
--
Daniel Macks
[EMAIL PROTECTED]
http://www.netspace.org/~dmacks
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Re: [Fink-devel] dlopen symbol not found
On Tue, Dec 04, 2007 at 01:07:42AM -0500, Daniel Macks wrote: Bug that doesn't affect anything: in the bio-emboss-pm.patch, $EMB_EXT_LIBS should be [EMAIL PROTECTED]@/lib (need to pass the actual linker flag, not just the pathname where the libs are). Or actually, don't need to pass anything there at all? Seems like this variable is used *in addition to* the default LDFLAGS, which already has fink's normal lib dir. dan -- Daniel Macks [EMAIL PROTECTED] http://www.netspace.org/~dmacks - SF.Net email is sponsored by: The Future of Linux Business White Paper from Novell. From the desktop to the data center, Linux is going mainstream. Let it simplify your IT future. http://altfarm.mediaplex.com/ad/ck/8857-50307-18918-4 ___ Fink-devel mailing list Fink-devel@lists.sourceforge.net http://news.gmane.org/gmane.os.apple.fink.devel
Re: [Fink-devel] dlopen symbol not found
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/1Can'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 Using the grep command, ajStrTokenCount is in /sw/lib/libajax*, which is installed. I'll have another look at it later today. cheers, - Koen. - SF.Net email is sponsored by: The Future of Linux Business White Paper from Novell. From the desktop to the data center, Linux is going mainstream. Let it simplify your IT future. http://altfarm.mediaplex.com/ad/ck/8857-50307-18918-4 ___ Fink-devel mailing list Fink-devel@lists.sourceforge.net http://news.gmane.org/gmane.os.apple.fink.devel
Re: [Fink-devel] dlopen symbol not found
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/1Can'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/1Can'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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Re: [Fink-devel] dlopen symbol not found
Koen van der Drift wrote:
On Dec 2, 2007, at 10:55 AM, Koen van der Drift wrote:
But, I now get another similar error:
t/1Can'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}; };
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.
However, now I get the following, again similar error:
t/1Can'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.
Did you check with otool -L that libeplplot loads libX11?
Peter
--
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Re: [Fink-devel] dlopen symbol not found
On Dec 2, 2007, at 11:35 PM, Peter O'Gorman wrote: However, now I get the following, again similar error: t/1Can'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. Did you check with otool -L that libeplplot Any suggestions on how I can make it load libX11loads libX11? Hmm, no it doesn't: $ oTool -L libeplplot.* libeplplot.3.2.7.dylib: /sw/lib/EMBOSS/libeplplot.3.dylib (compatibility version 6.0.0, current version 6.7.0) /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) libeplplot.3.dylib: /sw/lib/EMBOSS/libeplplot.3.dylib (compatibility version 6.0.0, current version 6.7.0) /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) libeplplot.dylib: /sw/lib/EMBOSS/libeplplot.3.dylib (compatibility version 6.0.0, current version 6.7.0) /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) Any suggestions on how I can make it load libX11? thanks, - Koen. - SF.Net email is sponsored by: The Future of Linux Business White Paper from Novell. From the desktop to the data center, Linux is going mainstream. Let it simplify your IT future. http://altfarm.mediaplex.com/ad/ck/8857-50307-18918-4 ___ Fink-devel mailing list Fink-devel@lists.sourceforge.net http://news.gmane.org/gmane.os.apple.fink.devel
Re: [Fink-devel] dlopen symbol not found
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 .. :) JF - SF.Net email is sponsored by: The Future of Linux Business White Paper from Novell. From the desktop to the data center, Linux is going mainstream. Let it simplify your IT future. http://altfarm.mediaplex.com/ad/ck/8857-50307-18918-4 ___ Fink-devel mailing list Fink-devel@lists.sourceforge.net http://news.gmane.org/gmane.os.apple.fink.devel
Re: [Fink-devel] dlopen symbol not found
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 - SF.Net email is sponsored by: The Future of Linux Business White Paper from Novell. From the desktop to the data center, Linux is going mainstream. Let it simplify your IT future. http://altfarm.mediaplex.com/ad/ck/8857-50307-18918-4 ___ Fink-devel mailing list Fink-devel@lists.sourceforge.net http://news.gmane.org/gmane.os.apple.fink.devel
Re: [Fink-devel] dlopen symbol not found
Hooray for upstream bugs! All of the shared libraried in emboss-5.0.0-3 are deficient in their linkages. They don't link any other libraries, yet they all use symbols from other libraries. See attached file for output from the fink-dyld-link-test thing in my experimental/ directory on cvs.sf to see what symbols are unresolved. The makefiles all appear to know the libs that would be needed, but intentionally avoid dynamically linking them on darwin (and don't even pass the flags correctly on most other platforms because they didn't read the automake or libtool manual). dan -- Daniel Macks [EMAIL PROTECTED] http://www.netspace.org/~dmacks Preparing... g++ -all_load -multiply_defined suppress -bind_at_load /tmp/vSdsgacKlN.c -o /tmp/z82JuI69tD.o Testing package emboss-ajax5-dev... Examining /sw/lib/libajaxg.dylib... g++ -all_load -multiply_defined suppress -bind_at_load /tmp/vSdsgacKlN.c -o /tmp/z82JuI69tD.o /sw/lib/libajaxg.a /sw/lib/EMBOSS/libajaxg.5.dylib /usr/lib/libSystem.B.dylib ld: Undefined symbols: _ajAcdGetProgram _ajAcdInit _ajAcdInitP _ajCallRegister _ajCharMatchC _ajCharMatchCaseC _ajCharPrefixCaseS _ajDebug _ajDegToRad _ajErr _ajFileClose _ajFileNewOut _ajFmtPrint _ajFmtPrintAppS _ajFmtPrintF _ajFmtPrintS _ajFmtStr _ajFmtString _ajListstrFree _ajListstrGetLength _ajListstrNew _ajListstrPop _ajListstrPushAppend _ajMemAlloc _ajMemCalloc _ajMemCalloc0 _ajMemFree _ajNamInit _ajSeqGetLen _ajSeqGetNameS _ajStrAppendC _ajStrAssignC _ajStrAssignEmptyC _ajStrAssignEmptyS _ajStrAssignS _ajStrDel _ajStrGetCharLast _ajStrGetLen _ajStrGetPtr _ajStrInsertC _ajStrInsertS _ajStrKeepRange _ajStrMatchCaseC _ajStrNewC _ajTimeDel _ajTimeNewToday _ajTimeNewTodayFmt _ajUser _c_pladv _c_plbox _c_plcol0 _c_plend _c_plerrx _c_plerry _c_plfill _c_plgchr _c_plgpage _c_plinit _c_pljoin _c_plline _c_pllsty _c_plmtex _c_plpoin _c_plpsty _c_plptex _c_plschr _c_plscol0 _c_plsdev _c_plsori _c_plspage _c_plssub _c_plvpor _c_plvsta _c_plwid _c_plwind _c_plxsfnam _plsc _plstrl Examining /sw/lib/libajax.dylib... g++ -all_load -multiply_defined suppress -bind_at_load /tmp/vSdsgacKlN.c -o /tmp/z82JuI69tD.o /sw/lib/libajax.a /sw/lib/EMBOSS/libajax.5.dylib /usr/lib/libSystem.B.dylib Testing package emboss-eplplot3-dev... Examining /sw/lib/libeplplot.dylib... g++ -all_load -multiply_defined suppress -bind_at_load /tmp/vSdsgacKlN.c -o /tmp/z82JuI69tD.o /sw/lib/libeplplot.a /sw/lib/EMBOSS/libeplplot.3.dylib /usr/lib/libSystem.B.dylib ld: Undefined symbols: _XAllocColor _XAllocColorCells _XAllocNamedColor _XCheckWindowEvent _XClearWindow _XCloseDisplay _XCopyArea _XCreateColormap _XCreateFontCursor _XCreateGC _XCreatePixmap _XCreateWindow _XDefineCursor _XDestroyWindow _XDrawLine _XDrawLines _XFillPolygon _XFillRectangle _XFlush _XFree _XFreeColors _XFreeGC _XFreePixmap _XGetErrorText _XGetGeometry _XGetImage _XGetVisualInfo _XLookupString _XMapRaised _XOpenDisplay _XPending _XPutImage _XQueryColors _XQueryPointer _XSelectInput _XSetBackground _XSetErrorHandler _XSetForeground _XSetFunction _XSetLineAttributes _XSetStandardProperties _XSetWindowBackground _XSetWindowColormap _XStoreColor _XSync _XSynchronize _XUndefineCursor _XWarpPointer _XWindowEvent _gdFree _gdImageColorAllocate _gdImageColorDeallocate _gdImageCreate _gdImageCreateTrueColor _gdImageDestroy _gdImageFilledPolygon _gdImageFilledRectangle _gdImageGifPtr _gdImageLine _gdImagePngPtrEx _gdImageSetAntiAliased _gdImageSetThickness Testing package emboss-nucleus5-dev... Examining /sw/lib/libnucleus.dylib... g++ -all_load -multiply_defined suppress -bind_at_load /tmp/vSdsgacKlN.c -o /tmp/z82JuI69tD.o /sw/lib/libnucleus.a /sw/lib/EMBOSS/libnucleus.5.dylib /usr/lib/libSystem.B.dylib ld: Undefined symbols: _ajAZToInt _ajAlignDefineSS _ajAlignSetGapR _ajAlignSetMatrixFloat _ajAlignSetRange _ajAlignSetScoreR _ajDebug _ajFmtPrintAppS _ajFmtPrintF _ajMemAlloc _ajMemFree _ajMessCrashFL _ajMessSetErr _ajSeqAssignAccS _ajSeqAssignDescS _ajSeqAssignNameS _ajSeqAssignUsaS _ajSeqDel _ajSeqGapStandard _ajSeqGetAccS _ajSeqGetDescS _ajSeqGetLen _ajSeqGetNameS _ajSeqGetOffend _ajSeqGetOffset _ajSeqGetSeqC _ajSeqGetUsaS _ajSeqIsReversed _ajSeqNewNameS _ajSeqNewRangeC _ajSeqcvtGetCodeK _ajSeqstrCountGaps _ajStrAppendC _ajStrAppendK _ajStrAppendS _ajStrAssignC _ajStrAssignK _ajStrAssignS _ajStrAssignSubC _ajStrCalcCountK _ajStrDel _ajStrDelStatic _ajStrFmtUpper _ajStrGetLen _ajStrGetPtr _ajStrInsertK _ajStrNewC _ajStrReverse _ajStrSetRes _ajMemCalloc _ajMemCalloc0 _ajStrCmpS _ajStrVcmp
Re: [Fink-devel] dlopen symbol not found
On Mon, Dec 03, 2007 at 12:58:18AM -0500, Daniel Macks wrote: Hooray for upstream bugs! All of the shared libraried in emboss-5.0.0-3 are deficient in their linkages. They don't link any other libraries, yet they all use symbols from other libraries. See attached file for output from the fink-dyld-link-test thing in my experimental/ directory on cvs.sf to see what symbols are unresolved. The makefiles all appear to know the libs that would be needed, but intentionally avoid dynamically linking them on darwin (and don't even pass the flags correctly on most other platforms because they didn't read the automake or libtool manual). Attached is a patchset that fixes all these linker messes. May need to redo the Depends/BuildDepends for the emboss.info package set after adding this to the existing emboss.patch file. dan -- Daniel Macks [EMAIL PROTECTED] http://www.netspace.org/~dmacks diff -Nurd -x'*~' EMBOSS-5.0.0.orig/ajax/Makefile.in EMBOSS-5.0.0/ajax/Makefile.in --- EMBOSS-5.0.0.orig/ajax/Makefile.in 2007-07-12 06:53:32.0 -0400 +++ EMBOSS-5.0.0/ajax/Makefile.in 2007-12-03 01:28:50.0 -0500 @@ -85,7 +85,8 @@ $(libajax_la_LDFLAGS) $(LDFLAGS) -o $@ @[EMAIL PROTECTED] = -rpath $(libdir) @[EMAIL PROTECTED] = -rpath $(libdir) -libajaxg_la_LIBADD = +libajaxg_la_LIBADD = libajax.la ../plplot/libeplplot.la +libajaxg_la_DEPENDENCIES = libajax.la ../plplot/libeplplot.la am__libajaxg_la_SOURCES_DIST = ajgraph.c ajhist.c @[EMAIL PROTECTED] = $(am__objects_2) libajaxg_la_OBJECTS = $(am_libajaxg_la_OBJECTS) diff -Nurd -x'*~' EMBOSS-5.0.0.orig/nucleus/Makefile.in EMBOSS-5.0.0/nucleus/Makefile.in --- EMBOSS-5.0.0.orig/nucleus/Makefile.in 2007-07-12 06:53:36.0 -0400 +++ EMBOSS-5.0.0/nucleus/Makefile.in2007-12-03 01:25:23.0 -0500 @@ -55,7 +55,8 @@ am__installdirs = $(DESTDIR)$(libdir) $(DESTDIR)$(includedir) libLTLIBRARIES_INSTALL = $(INSTALL) LTLIBRARIES = $(lib_LTLIBRARIES) -libnucleus_la_LIBADD = +libnucleus_la_LIBADD = ../ajax/libajax.la +libajaxg_la_DEPENDENCIES = ../ajax/libajax.la am__objects_1 = embaln.lo embcom.lo embcons.lo embdata.lo embdbi.lo \ embdmx.lo embdomain.lo embest.lo embexit.lo embgroup.lo \ embiep.lo embindex.lo embinit.lo embmat.lo embmisc.lo \ diff -Nurd -x'*~' EMBOSS-5.0.0.orig/plplot/Makefile.in EMBOSS-5.0.0/plplot/Makefile.in --- EMBOSS-5.0.0.orig/plplot/Makefile.in2007-07-12 06:53:36.0 -0400 +++ EMBOSS-5.0.0/plplot/Makefile.in 2007-12-03 01:15:17.0 -0500 @@ -54,7 +54,7 @@ am__installdirs = $(DESTDIR)$(libdir) $(DESTDIR)$(pkgincludedir) libLTLIBRARIES_INSTALL = $(INSTALL) LTLIBRARIES = $(lib_LTLIBRARIES) -libeplplot_la_LIBADD = +libeplplot_la_LIBADD = $(X_LIBS) -lX11 -lgd am__objects_1 = pdfutils.lo plargs.lo plbox.lo plcont.lo plcore.lo \ plctrl.lo plcvt.lo pldtik.lo plfill.lo plhist.lo plline.lo \ plmap.lo plot3d.lo plpage.lo plsdef.lo plshade.lo plsym.lo \ - SF.Net email is sponsored by: The Future of Linux Business White Paper from Novell. From the desktop to the data center, Linux is going mainstream. Let it simplify your IT future. http://altfarm.mediaplex.com/ad/ck/8857-50307-18918-4___ Fink-devel mailing list Fink-devel@lists.sourceforge.net http://news.gmane.org/gmane.os.apple.fink.devel
Re: [Fink-devel] dlopen symbol not found
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/1Can'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
Re: [Fink-devel] dlopen symbol not found
Koen van der Drift wrote: Hi, I am getting the following error during the test phase of a perl- module package on 10.5: t/1Can'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: _plsc Referenced from: /sw/lib/EMBOSS/libajaxg.5.dylib Expected in: dynamic lookup at t/1.t line 11 Well, the symbol plsc is required by libajaxg.5.dylib, but is not available. This is a danger in allowing undefined symbols in shared libraries. 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). Then you should have enough information available to solve the problem. Sorry I can't give you an answer to the puzzle. Peter -- Peter O'Gorman http://pogma.com - SF.Net email is sponsored by: The Future of Linux Business White Paper from Novell. From the desktop to the data center, Linux is going mainstream. Let it simplify your IT future. http://altfarm.mediaplex.com/ad/ck/8857-50307-18918-4 ___ Fink-devel mailing list Fink-devel@lists.sourceforge.net http://news.gmane.org/gmane.os.apple.fink.devel
