graph-tool 1.1.2 on macbook with mac os 10.4.11

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graph-tool 1.1.2 on macbook with mac os 10.4.11

Spiros Spirou
Hi all,

I'm trying to compile graph-tool on a macbook with mac os x v10.4.11,  
but compilation fails as follows:

  /opt/local/bin/i386-apple-darwin8.11.1-gcc-4.2.2 -DHAVE_CONFIG_H -
I. -I../.. -I. -I.. -I../boost-workaround -DHAVE_CONFIG_H -Wall -I/
opt/local/include/python2.5 -pthread -I/opt/local/include/
boost-1_34_1 -ftemplate-depth-150 -O99 -Wno-unknown-pragmas -MT  
graph.lo -MD -MP -MF .deps/graph.Tpo -c graph.cc  -fno-common -DPIC -
o .libs/graph.o
graph.cc: In function 'void catch_sig_stop(int)':
graph.cc:560: error: 'SIGPWR' was not declared in this scope
graph.cc: In member function 'void  
graph_tool::GraphInterface::InitSignalHandling()':
graph.cc:593: error: 'SIGPWR' was not declared in this scope
make[3]: *** [graph.lo] Error 1
make[2]: *** [all-recursive] Error 1
make[1]: *** [all-recursive] Error 1
make: *** [all] Error 2

My system is:
python v2.5.1
gcc v4.2.2
boost v1.34.1

I'm using the following configure command:
sudo ./configure --prefix=/opt/local --with-boost=/opt/local --
disable-visibility CC=/opt/local/bin/i386-apple-darwin8.11.1-
gcc-4.2.2 CXX=/opt/local/bin/i386-apple-darwin8.11.1-gcc-4.2.2  
PYTHON_VERSION=2.5 LDFLAGS=-L/opt/local/lib/

Any ideas?

Thanks,

Spiros


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Re: graph-tool 1.1.2 on macbook with mac os 10.4.11

Tiago de Paula Peixoto
On 01/20/2008 03:27 PM, Spiros Spirou wrote:
> Hi all,
>
> I'm trying to compile graph-tool on a macbook with mac os x v10.4.11,
> but compilation fails as follows:

[...]

> graph.cc:560: error: 'SIGPWR' was not declared in this scope

[...]

> Any ideas?

Oops. Looks like SIGPWR is not defined in MacOS X. I've committed a fix
for this in the git repository. Please get the newest git version, and
see if you have any trouble now.

Thanks for the bug report.

Tiago

--
Tiago de Paula Peixoto <[hidden email]>


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Re: graph-tool 1.1.2 on macbook with mac os 10.4.11

Spiros Spirou

On 22 Ιαν 2008, at 2:47 ΜΜ, Tiago de Paula Peixoto wrote:

> On 01/20/2008 03:27 PM, Spiros Spirou wrote:
>> Hi all,
>> I'm trying to compile graph-tool on a macbook with mac os x v10.4.11,
>> but compilation fails as follows:
>
> [...]
>
>> graph.cc:560: error: 'SIGPWR' was not declared in this scope
>
> [...]
>
>> Any ideas?
>
> Oops. Looks like SIGPWR is not defined in MacOS X. I've committed a  
> fix
> for this in the git repository. Please get the newest git version, and
> see if you have any trouble now.
>

Thanks! This is fixed now, but there's another problem later on. It  
seems that the linker on mac os x v10.4.11 does not support the '-E'  
option. Here's the error I get:

/usr/bin/ld: unknown flag: -E

I'm not sure what I need to change to eliminate this option, if  
possible. Could you please help?

Thanks,

Spiros
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Re: graph-tool 1.1.2 on macbook with mac os 10.4.11

Tiago de Paula Peixoto
On 01/23/2008 01:37 PM, Spiros Spirou wrote:
> Thanks! This is fixed now, but there's another problem later on. It  
> seems that the linker on mac os x v10.4.11 does not support the '-E'  
> option. Here's the error I get:
>
> /usr/bin/ld: unknown flag: -E
>
> I'm not sure what I need to change to eliminate this option, if  
> possible. Could you please help?

Do you know what linker is used in MacOS X? Could you please send me the
output of ld --version (or the equivalent for this linker)?

Cheers,
Tiago

--
Tiago de Paula Peixoto <[hidden email]>

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Re: graph-tool 1.1.2 on macbook with mac os 10.4.11

Spiros Spirou

On 23 Ιαν 2008, at 10:18 ΜΜ, Tiago de Paula Peixoto wrote:

> On 01/23/2008 01:37 PM, Spiros Spirou wrote:
>> Thanks! This is fixed now, but there's another problem later on. It
>> seems that the linker on mac os x v10.4.11 does not support the '-E'
>> option. Here's the error I get:
>>
>> /usr/bin/ld: unknown flag: -E
>>
>> I'm not sure what I need to change to eliminate this option, if
>> possible. Could you please help?
>
> Do you know what linker is used in MacOS X? Could you please send  
> me the
> output of ld --version (or the equivalent for this linker)?
>
>

Sorry for not sending this earlier. I'm not sure that it helps, but  
here it is:

spirosspirou$ /usr/bin/ld -v
Apple Computer, Inc. version cctools-622.5.obj~13

Is the '-E' option really necessary? Could we just remove it from the  
LDFLAGS for darwin? (Problem is, I don't know how to do this :) ).

Thanks,

Spiros


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Re: graph-tool 1.1.2 on macbook with mac os 10.4.11

Tiago de Paula Peixoto
On 01/24/2008 09:18 AM, Spiros Spirou wrote:

> On 23 Ιαν 2008, at 10:18 ΜΜ, Tiago de Paula Peixoto wrote:
>
>> On 01/23/2008 01:37 PM, Spiros Spirou wrote:
>>> Thanks! This is fixed now, but there's another problem later on. It
>>> seems that the linker on mac os x v10.4.11 does not support the '-E'
>>> option. Here's the error I get:
>>>
>>> /usr/bin/ld: unknown flag: -E
>>>
>>> I'm not sure what I need to change to eliminate this option, if
>>> possible. Could you please help?
>>
>> Do you know what linker is used in MacOS X? Could you please send  
>> me the
>> output of ld --version (or the equivalent for this linker)?
>>
>>
>
> Sorry for not sending this earlier. I'm not sure that it helps, but  
> here it is:
>
> spirosspirou$ /usr/bin/ld -v
> Apple Computer, Inc. version cctools-622.5.obj~13
>
> Is the '-E' option really necessary? Could we just remove it from the
> LDFLAGS for darwin? (Problem is, I don't know how to do this :) ).
The behaviour of the '-E' flag in GNU ld is necessary to export all
dynamic symbols, which is not done by default. So indeed we need this,
since the run_action() functionality, which compiles and loads C++ code
from python at run time, needs all symbols to be exported properly. I
looked at apple's (darwin) ld manpage, http://www.hmug.org/man/1/ld.php,
and at first glance, found no equivalent option. So I'm just going to
drop this for any liker that doesn't support the option, and hope it
will do what we want by default. The git version already contains this
fix. Please tell me if it compiles for you now...

Cheers,
Tiago

--
Tiago de Paula Peixoto <[hidden email]>


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Re: graph-tool 1.1.2 on macbook with mac os 10.4.11

Spiros Spirou
Hi Tiago,

On 24 Ιαν 2008, at 4:10 ΜΜ, Tiago de Paula Peixoto wrote:

> On 01/24/2008 09:18 AM, Spiros Spirou wrote:
>> On 23 Ιαν 2008, at 10:18 ΜΜ, Tiago de Paula Peixoto wrote:
>>> On 01/23/2008 01:37 PM, Spiros Spirou wrote:
>>>> Thanks! This is fixed now, but there's another problem later on. It
>>>> seems that the linker on mac os x v10.4.11 does not support the  
>>>> '-E'
>>>> option. Here's the error I get:
>>>>
>>>> /usr/bin/ld: unknown flag: -E
>>>>
>>>> I'm not sure what I need to change to eliminate this option, if
>>>> possible. Could you please help?
>>>
>>> Do you know what linker is used in MacOS X? Could you please  
>>> send  me the
>>> output of ld --version (or the equivalent for this linker)?
>>>
>>>
>> Sorry for not sending this earlier. I'm not sure that it helps,  
>> but  here it is:
>> spirosspirou$ /usr/bin/ld -v
>> Apple Computer, Inc. version cctools-622.5.obj~13
>> Is the '-E' option really necessary? Could we just remove it from the
>> LDFLAGS for darwin? (Problem is, I don't know how to do this :) ).
>
> The behaviour of the '-E' flag in GNU ld is necessary to export all
> dynamic symbols, which is not done by default. So indeed we need this,
> since the run_action() functionality, which compiles and loads C++  
> code
> from python at run time, needs all symbols to be exported properly. I
> looked at apple's (darwin) ld manpage, http://www.hmug.org/man/1/ 
> ld.php,
> and at first glance, found no equivalent option. So I'm just going to
> drop this for any liker that doesn't support the option, and hope it
> will do what we want by default. The git version already contains this
> fix. Please tell me if it compiles for you now...
>
>

Thank you for the prompt response! This release got me further, but  
I've hit another wall that looks scary. Here it is:

vtable for __cxxabiv1::__function_type_info
std::range_error::range_error(std::basic_string<char,  
std::char_traits<char>, std::allocator<char> > const&)
collect2: ld returned 1 exit status
make[3]: *** [libgraph_tool.la] Error 1

Is it that some prototypes do not match? I'm really clueless...

Cheers,

Spiros
 
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Re: graph-tool 1.1.2 on macbook with mac os 10.4.11

Tiago de Paula Peixoto
On 01/24/2008 04:46 PM, Spiros Spirou wrote:

> Hi Tiago,
>
> On 24 Ιαν 2008, at 4:10 ΜΜ, Tiago de Paula Peixoto wrote:
>
>> On 01/24/2008 09:18 AM, Spiros Spirou wrote:
>>> On 23 Ιαν 2008, at 10:18 ΜΜ, Tiago de Paula Peixoto wrote:
>>>> On 01/23/2008 01:37 PM, Spiros Spirou wrote:
>>>>> Thanks! This is fixed now, but there's another problem later on. It
>>>>> seems that the linker on mac os x v10.4.11 does not support the  
>>>>> '-E'
>>>>> option. Here's the error I get:
>>>>>
>>>>> /usr/bin/ld: unknown flag: -E
>>>>>
>>>>> I'm not sure what I need to change to eliminate this option, if
>>>>> possible. Could you please help?
>>>> Do you know what linker is used in MacOS X? Could you please  
>>>> send  me the
>>>> output of ld --version (or the equivalent for this linker)?
>>>>
>>>>
>>> Sorry for not sending this earlier. I'm not sure that it helps,  
>>> but  here it is:
>>> spirosspirou$ /usr/bin/ld -v
>>> Apple Computer, Inc. version cctools-622.5.obj~13
>>> Is the '-E' option really necessary? Could we just remove it from the
>>> LDFLAGS for darwin? (Problem is, I don't know how to do this :) ).
>> The behaviour of the '-E' flag in GNU ld is necessary to export all
>> dynamic symbols, which is not done by default. So indeed we need this,
>> since the run_action() functionality, which compiles and loads C++  
>> code
>> from python at run time, needs all symbols to be exported properly. I
>> looked at apple's (darwin) ld manpage, http://www.hmug.org/man/1/ 
>> ld.php,
>> and at first glance, found no equivalent option. So I'm just going to
>> drop this for any liker that doesn't support the option, and hope it
>> will do what we want by default. The git version already contains this
>> fix. Please tell me if it compiles for you now...
>>
>>
>
> Thank you for the prompt response! This release got me further, but  
> I've hit another wall that looks scary. Here it is:
>
> vtable for __cxxabiv1::__function_type_info
> std::range_error::range_error(std::basic_string<char,  
> std::char_traits<char>, std::allocator<char> > const&)
> collect2: ld returned 1 exit status
> make[3]: *** [libgraph_tool.la] Error 1
>
> Is it that some prototypes do not match? I'm really clueless...
Strange... Could you please send me the full compilation output
attached? Also, what version of GCC are you using?

Cheers,
Tiago

--
Tiago de Paula Peixoto <[hidden email]>


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Re: graph-tool 1.1.2 on macbook with mac os 10.4.11

Spiros Spirou
Hi Tiago,

On 24 Ιαν 2008, at 7:48 ΜΜ, Tiago de Paula Peixoto wrote:

> On 01/24/2008 04:46 PM, Spiros Spirou wrote:

>> Thank you for the prompt response! This release got me further,  
>> but  I've hit another wall that looks scary. Here it is:
>> vtable for __cxxabiv1::__function_type_info
>> std::range_error::range_error(std::basic_string<char,  
>> std::char_traits<char>, std::allocator<char> > const&)
>> collect2: ld returned 1 exit status
>> make[3]: *** [libgraph_tool.la] Error 1
>> Is it that some prototypes do not match? I'm really clueless...
>
> Strange... Could you please send me the full compilation output
> attached?
Attached.
It seems that the linker has unresolved symbols. I tried configuring  
the path to libstdc++ ('-L/opt/local/lib/gcc42') in LDFLAG, but I get  
the same error.

> Also, what version of GCC are you using?

4.2.2

Cheers,

Spiros

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Re: graph-tool 1.1.2 on macbook with mac os 10.4.11

Tiago de Paula Peixoto
On 01/25/2008 08:56 AM, Spiros Spirou wrote:

> Hi Tiago,
>
> On 24 Ιαν 2008, at 7:48 ΜΜ, Tiago de Paula Peixoto wrote:
>
>> On 01/24/2008 04:46 PM, Spiros Spirou wrote:
>
>>> Thank you for the prompt response! This release got me further, but
>>> I've hit another wall that looks scary. Here it is:
>>> vtable for __cxxabiv1::__function_type_info
>>> std::range_error::range_error(std::basic_string<char,  
>>> std::char_traits<char>, std::allocator<char> > const&)
>>> collect2: ld returned 1 exit status
>>> make[3]: *** [libgraph_tool.la] Error 1
>>> Is it that some prototypes do not match? I'm really clueless...
>>
>> Strange... Could you please send me the full compilation output
>> attached?
>
> Attached.
>
> ---------------------------------------------------------------------
>
> It seems that the linker has unresolved symbols. I tried configuring
> the path to libstdc++ ('-L/opt/local/lib/gcc42') in LDFLAG, but I get
> the same error.
>
The compiler is not linking to the standard C++ library and to the zlib
and bzip2 libraries, and all the dynamic symbols are turning up
unresolved. libtool was supposed to handle all this... Please try the
following link command in the src/graph/ directory, and tell me the
result:

/bin/sh ../../libtool --tag=CXX   --mode=link /opt/local/bin/i386-apple-darwin8.11.1-gcc-4.2.2 -Wall -I/opt/local/include/python2.5 -pthread -I/opt/local/include/boost-1_34_1 -ftemplate-depth-150  -O99  -Wno-unknown-pragmas -module -avoid-version -export-dynamic -no-undefined  -L/opt/local/lib/ -o libgraph_tool.la -rpath /opt/local/lib/python2.5/site-packages/graph_tool graph.lo graph_python_interface.lo graph_properties.lo graph_correlations.lo graph_edge_correlations.lo graph_correlations_combined.lo graph_correlations_neighbours.lo graph_assortativity.lo graph_clustering.lo graph_extended_clustering.lo graph_generation.lo graph_distance.lo graph_distance_sampled.lo graph_reciprocity.lo graph_minimum_spanning_tree.lo graph_community.lo graph_community_network.lo graph_line_graph.lo graph_betweenness.lo graph_rewiring.lo graph_layout.lo graph_io.lo graph_bind.lo graphml.lo read_graphviz_spirit.lo -L/opt/local/lib/python2.5 -lpython2.5 -L/opt/local/lib  -lboost_python -lboost
_iostreams -lexpat -lz -lbzip2 -lstdc++

Cheers,
Tiago

--
Tiago de Paula Peixoto <[hidden email]>


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Re: graph-tool 1.1.2 on macbook with mac os 10.4.11

Spiros Spirou
Hi Tiago,

Thanks for the support so far!

On 25 Ιαν 2008, at 5:23 ΜΜ, Tiago de Paula Peixoto wrote:

> On 01/25/2008 08:56 AM, Spiros Spirou wrote:
>> Hi Tiago,
>> On 24 Ιαν 2008, at 7:48 ΜΜ, Tiago de Paula Peixoto wrote:
>>> On 01/24/2008 04:46 PM, Spiros Spirou wrote:
>>>> Thank you for the prompt response! This release got me further,  
>>>> but I've hit another wall that looks scary. Here it is:
>>>> vtable for __cxxabiv1::__function_type_info
>>>> std::range_error::range_error(std::basic_string<char,  
>>>> std::char_traits<char>, std::allocator<char> > const&)
>>>> collect2: ld returned 1 exit status
>>>> make[3]: *** [libgraph_tool.la] Error 1
>>>> Is it that some prototypes do not match? I'm really clueless...
>>>
>>> Strange... Could you please send me the full compilation output
>>> attached?
>> Attached.
>> ---------------------------------------------------------------------
>> It seems that the linker has unresolved symbols. I tried configuring
>> the path to libstdc++ ('-L/opt/local/lib/gcc42') in LDFLAG, but I get
>> the same error.
>
> The compiler is not linking to the standard C++ library and to the  
> zlib
> and bzip2 libraries, and all the dynamic symbols are turning up
> unresolved. libtool was supposed to handle all this... Please try the
> following link command in the src/graph/ directory, and tell me the
> result:
>
> /bin/sh ../../libtool --tag=CXX   --mode=link /opt/local/bin/i386-
> apple-darwin8.11.1-gcc-4.2.2 -Wall -I/opt/local/include/python2.5 -
> pthread -I/opt/local/include/boost-1_34_1 -ftemplate-depth-150  -
> O99  -Wno-unknown-pragmas -module -avoid-version -export-dynamic -
> no-undefined  -L/opt/local/lib/ -o libgraph_tool.la -rpath /opt/
> local/lib/python2.5/site-packages/graph_tool graph.lo  
> graph_python_interface.lo graph_properties.lo graph_correlations.lo  
> graph_edge_correlations.lo graph_correlations_combined.lo  
> graph_correlations_neighbours.lo graph_assortativity.lo  
> graph_clustering.lo graph_extended_clustering.lo  
> graph_generation.lo graph_distance.lo graph_distance_sampled.lo  
> graph_reciprocity.lo graph_minimum_spanning_tree.lo  
> graph_community.lo graph_community_network.lo graph_line_graph.lo  
> graph_betweenness.lo graph_rewiring.lo graph_layout.lo graph_io.lo  
> graph_bind.lo graphml.lo read_graphviz_spirit.lo -L/opt/local/lib/
> python2.5 -lpython2.5 -L/opt/local/lib  -lboost_python -lboost
> _iostreams -lexpat -lz -lbzip2 -lstdc++
>

Here it is:


/opt/local/bin/i386-apple-darwin8.11.1-gcc-4.2.2  -o .libs/
libgraph_tool.so -bundle  .libs/graph.o .libs/
graph_python_interface.o .libs/graph_properties.o .libs/
graph_correlations.o .libs/graph_edge_correlations.o .libs/
graph_correlations_combined.o .libs/
graph_correlations_neighbours.o .libs/graph_assortativity.o .libs/
graph_clustering.o .libs/graph_extended_clustering.o .libs/
graph_generation.o .libs/graph_distance.o .libs/
graph_distance_sampled.o .libs/graph_reciprocity.o .libs/
graph_minimum_spanning_tree.o .libs/graph_community.o .libs/
graph_community_network.o .libs/graph_line_graph.o .libs/
graph_betweenness.o .libs/graph_rewiring.o .libs/graph_layout.o .libs/
graph_io.o .libs/graph_bind.o .libs/graphml.o .libs/
read_graphviz_spirit.o  -L/opt/local/lib/ -L/opt/local/lib/python2.5 -
lpython2.5 -L/opt/local/lib -lboost_python -lboost /opt/local/lib/
libexpat.dylib -lz -lbzip2 /opt/local/lib/gcc42/libstdc++.dylib -L/
opt/local/var/macports/build/
_opt_local_var_macports_sources_rsync.macports.org_release_ports_lang_gc
c42/work/build/i386-apple-darwin8.11.1/libstdc++-v3/src -L/opt/local/
var/macports/build/
_opt_local_var_macports_sources_rsync.macports.org_release_ports_lang_gc
c42/work/build/i386-apple-darwin8.11.1/libstdc++-v3/src/.libs -pthread
/usr/bin/ld: warning -L: directory name (/opt/local/var/macports/
build/
_opt_local_var_macports_sources_rsync.macports.org_release_ports_lang_gc
c42/work/build/i386-apple-darwin8.11.1/libstdc++-v3/src) does not exist
/usr/bin/ld: warning -L: directory name (/opt/local/var/macports/
build/
_opt_local_var_macports_sources_rsync.macports.org_release_ports_lang_gc
c42/work/build/i386-apple-darwin8.11.1/libstdc++-v3/src/.libs) does  
not exist
/usr/bin/ld: can't locate file for: -lboost
collect2: ld returned 1 exit status

Cheers,

Spiros


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Re: graph-tool 1.1.2 on macbook with mac os 10.4.11

Tiago de Paula Peixoto
On 01/25/2008 03:44 PM, Spiros Spirou wrote:
> Hi Tiago,
>
> Thanks for the support so far!

It's quite alright. :-)

> /usr/bin/ld: can't locate file for: -lboost
> collect2: ld returned 1 exit status

I think -lboost_iostreams got broken with a line break in the command
line. Could you please try again?

Cheers,
Tiago

--
Tiago de Paula Peixoto <[hidden email]>


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Re: graph-tool 1.1.2 on macbook with mac os 10.4.11

Spiros Spirou

On 25 Ιαν 2008, at 5:48 ΜΜ, Tiago de Paula Peixoto wrote:
>
> I think -lboost_iostreams got broken with a line break in the command
> line. Could you please try again?
>
>

My mistake. Here's the correct output:

/opt/local/bin/i386-apple-darwin8.11.1-gcc-4.2.2  -o .libs/
libgraph_tool.so -bundle  .libs/graph.o .libs/
graph_python_interface.o .libs/graph_properties.o .libs/
graph_correlations.o .libs/graph_edge_correlations.o .libs/
graph_correlations_combined.o .libs/
graph_correlations_neighbours.o .libs/graph_assortativity.o .libs/
graph_clustering.o .libs/graph_extended_clustering.o .libs/
graph_generation.o .libs/graph_distance.o .libs/
graph_distance_sampled.o .libs/graph_reciprocity.o .libs/
graph_minimum_spanning_tree.o .libs/graph_community.o .libs/
graph_community_network.o .libs/graph_line_graph.o .libs/
graph_betweenness.o .libs/graph_rewiring.o .libs/graph_layout.o .libs/
graph_io.o .libs/graph_bind.o .libs/graphml.o .libs/
read_graphviz_spirit.o  -L/opt/local/lib/ -L/opt/local/lib/python2.5 -
lpython2.5 -L/opt/local/lib -lboost_python -lboost_iostreams /opt/
local/lib/libexpat.dylib -lz -lbzip2 /opt/local/lib/gcc42/libstdc+
+.dylib -L/opt/local/var/macports/build/
_opt_local_var_macports_sources_rsync.macports.org_release_ports_lang_gc
c42/work/build/i386-apple-darwin8.11.1/libstdc++-v3/src -L/opt/local/
var/macports/build/
_opt_local_var_macports_sources_rsync.macports.org_release_ports_lang_gc
c42/work/build/i386-apple-darwin8.11.1/libstdc++-v3/src/.libs -pthread
/usr/bin/ld: warning -L: directory name (/opt/local/var/macports/
build/
_opt_local_var_macports_sources_rsync.macports.org_release_ports_lang_gc
c42/work/build/i386-apple-darwin8.11.1/libstdc++-v3/src) does not exist
/usr/bin/ld: warning -L: directory name (/opt/local/var/macports/
build/
_opt_local_var_macports_sources_rsync.macports.org_release_ports_lang_gc
c42/work/build/i386-apple-darwin8.11.1/libstdc++-v3/src/.libs) does  
not exist
/usr/bin/ld: can't locate file for: -lbzip2
collect2: ld returned 1 exit status

I have something called libbz2 in /opt/local/lib. Is this the bzip2  
library?

Cheers,

Spiros


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Re: graph-tool 1.1.2 on macbook with mac os 10.4.11

Tiago de Paula Peixoto
On 01/25/2008 06:48 PM, Spiros Spirou wrote:
> I have something called libbz2 in /opt/local/lib. Is this the bzip2  
> library?

Yes, this is it. Please change -lbzip2 to -lbz2 and try again.
Cheers.

--
Tiago de Paula Peixoto <[hidden email]>


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Re: graph-tool 1.1.2 on macbook with mac os 10.4.11

Spiros Spirou

On 25 Ιαν 2008, at 10:51 ΜΜ, Tiago de Paula Peixoto wrote:

> On 01/25/2008 06:48 PM, Spiros Spirou wrote:
>> I have something called libbz2 in /opt/local/lib. Is this the  
>> bzip2  library?
>
> Yes, this is it. Please change -lbzip2 to -lbz2 and try again.
> Cheers.
>

OK, here's what I got:

/opt/local/bin/i386-apple-darwin8.11.1-gcc-4.2.2  -o .libs/
libgraph_tool.so -bundle  .libs/graph.o .libs/
graph_python_interface.o .libs/graph_properties.o .libs/
graph_correlations.o .libs/graph_edge_correlations.o .libs/
graph_correlations_combined.o .libs/
graph_correlations_neighbours.o .libs/graph_assortativity.o .libs/
graph_clustering.o .libs/graph_extended_clustering.o .libs/
graph_generation.o .libs/graph_distance.o .libs/
graph_distance_sampled.o .libs/graph_reciprocity.o .libs/
graph_minimum_spanning_tree.o .libs/graph_community.o .libs/
graph_community_network.o .libs/graph_line_graph.o .libs/
graph_betweenness.o .libs/graph_rewiring.o .libs/graph_layout.o .libs/
graph_io.o .libs/graph_bind.o .libs/graphml.o .libs/
read_graphviz_spirit.o  -L/opt/local/lib/ -L/opt/local/lib/python2.5 -
lpython2.5 -L/opt/local/lib -lboost_python -lboost_iostreams /opt/
local/lib/libexpat.dylib -lz -lbz2 /opt/local/lib/gcc42/libstdc+
+.dylib -L/opt/local/var/macports/build/
_opt_local_var_macports_sources_rsync.macports.org_release_ports_lang_gc
c42/work/build/i386-apple-darwin8.11.1/libstdc++-v3/src -L/opt/local/
var/macports/build/
_opt_local_var_macports_sources_rsync.macports.org_release_ports_lang_gc
c42/work/build/i386-apple-darwin8.11.1/libstdc++-v3/src/.libs -pthread
/usr/bin/ld: warning -L: directory name (/opt/local/var/macports/
build/
_opt_local_var_macports_sources_rsync.macports.org_release_ports_lang_gc
c42/work/build/i386-apple-darwin8.11.1/libstdc++-v3/src) does not exist
/usr/bin/ld: warning -L: directory name (/opt/local/var/macports/
build/
_opt_local_var_macports_sources_rsync.macports.org_release_ports_lang_gc
c42/work/build/i386-apple-darwin8.11.1/libstdc++-v3/src/.libs) does  
not exist
/usr/bin/ld: Undefined symbols:
__Unwind_Resume
collect2: ld returned 1 exit status

S.
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Re: graph-tool 1.1.2 on macbook with mac os 10.4.11

Tiago de Paula Peixoto
On 01/27/2008 08:28 AM, Spiros Spirou wrote:
> OK, here's what I got:
>
> /opt/local/bin/i386-apple-darwin8.11.1-gcc-4.2.2  -o .libs/

(...)

> /usr/bin/ld: Undefined symbols:
> __Unwind_Resume
> collect2: ld returned 1 exit status

It just occurred to me that the gcc binary is being used to link the
library, not g++! That's probably the reason of all these undefined
references... In your first message, I saw you ran configure with
CXX=/opt/local/bin/i386-apple-darwin8.11.1-gcc-4.2.2. This is
incorrect. You needed to do something like
CXX=/opt/local/bin/i386-apple-darwin8.11.1-g++-4.2.2, assuming that's
what g++ is called on your system. Please try a whole build from
scratch, using g++ this time, and see if you still encounter any
problems.

Cheers,
Tiago

--
Tiago de Paula Peixoto <[hidden email]>


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Re: graph-tool 1.1.2 on macbook with mac os 10.4.11

Spiros Spirou
Hi Tiago,

On 27 Ιαν 2008, at 7:41 ΜΜ, Tiago de Paula Peixoto wrote:

>
> It just occurred to me that the gcc binary is being used to link the
> library, not g++! That's probably the reason of all these undefined
> references... In your first message, I saw you ran configure with
> CXX=/opt/local/bin/i386-apple-darwin8.11.1-gcc-4.2.2. This is
> incorrect. You needed to do something like
> CXX=/opt/local/bin/i386-apple-darwin8.11.1-g++-4.2.2, assuming that's
> what g++ is called on your system. Please try a whole build from
> scratch, using g++ this time, and see if you still encounter any
> problems.
>
>

I thought that gcc is just the front-end to the compilers underneath.  
Thanks for your patience so far...

I did what you suggested, but I still get undefined symbols, although  
different ones. Strangely, these seem to be related to libbz2, which  
is in /opt/local/lib. Here's the output:

/bin/sh ../../libtool --tag=CXX   --mode=compile /opt/local/bin/i386-
apple-darwin8.11.1-g++-mp-4.2 -DHAVE_CONFIG_H -I. -I../..  -I. -I.. -
I../boost-workaround -DHAVE_CONFIG_H  -Wall -I/opt/local/include/
python2.5 -pthread -I/opt/local/include/boost-1_34_1 -ftemplate-
depth-150  -O99  -Wno-unknown-pragmas -MT read_graphviz_spirit.lo -MD  
-MP -MF .deps/read_graphviz_spirit.Tpo -c -o read_graphviz_spirit.lo  
read_graphviz_spirit.cpp
  /opt/local/bin/i386-apple-darwin8.11.1-g++-mp-4.2 -DHAVE_CONFIG_H -
I. -I../.. -I. -I.. -I../boost-workaround -DHAVE_CONFIG_H -Wall -I/
opt/local/include/python2.5 -pthread -I/opt/local/include/
boost-1_34_1 -ftemplate-depth-150 -O99 -Wno-unknown-pragmas -MT  
read_graphviz_spirit.lo -MD -MP -MF .deps/read_graphviz_spirit.Tpo -c  
read_graphviz_spirit.cpp  -fno-common -DPIC -o .libs/
read_graphviz_spirit.o
mv -f .deps/read_graphviz_spirit.Tpo .deps/read_graphviz_spirit.Plo
/bin/sh ../../libtool --tag=CXX   --mode=link /opt/local/bin/i386-
apple-darwin8.11.1-g++-mp-4.2 -Wall -I/opt/local/include/python2.5 -
pthread -I/opt/local/include/boost-1_34_1 -ftemplate-depth-150  -O99  
-Wno-unknown-pragmas -module -avoid-version -export-dynamic -no-
undefined  -L/opt/local/lib/ -L/opt/local/lib/gcc42 -o  
libgraph_tool.la -rpath /opt/local/lib/python2.5/site-packages/
graph_tool graph.lo graph_python_interface.lo graph_properties.lo  
graph_correlations.lo graph_edge_correlations.lo  
graph_correlations_combined.lo graph_correlations_neighbours.lo  
graph_assortativity.lo graph_clustering.lo  
graph_extended_clustering.lo graph_generation.lo graph_distance.lo  
graph_distance_sampled.lo graph_reciprocity.lo  
graph_minimum_spanning_tree.lo graph_community.lo  
graph_community_network.lo graph_line_graph.lo graph_betweenness.lo  
graph_rewiring.lo graph_layout.lo graph_io.lo graph_bind.lo  
graphml.lo read_graphviz_spirit.lo -L/opt/local/lib/python2.5 -
lpython2.5 -L/opt/local/lib  -lboost_python -lboost_iostreams -lexpat
/opt/local/bin/i386-apple-darwin8.11.1-g++-mp-4.2  -o .libs/
libgraph_tool.so -bundle  .libs/graph.o .libs/
graph_python_interface.o .libs/graph_properties.o .libs/
graph_correlations.o .libs/graph_edge_correlations.o .libs/
graph_correlations_combined.o .libs/
graph_correlations_neighbours.o .libs/graph_assortativity.o .libs/
graph_clustering.o .libs/graph_extended_clustering.o .libs/
graph_generation.o .libs/graph_distance.o .libs/
graph_distance_sampled.o .libs/graph_reciprocity.o .libs/
graph_minimum_spanning_tree.o .libs/graph_community.o .libs/
graph_community_network.o .libs/graph_line_graph.o .libs/
graph_betweenness.o .libs/graph_rewiring.o .libs/graph_layout.o .libs/
graph_io.o .libs/graph_bind.o .libs/graphml.o .libs/
read_graphviz_spirit.o  -L/opt/local/lib/ -L/opt/local/lib/gcc42 -L/
opt/local/lib/python2.5 -lpython2.5 -L/opt/local/lib -lboost_python -
lboost_iostreams /opt/local/lib/libexpat.dylib -pthread
/usr/bin/ld: Undefined symbols:
_crc32
_deflate
_deflateEnd
_deflateInit2_
_deflateReset
_inflate
_inflateEnd
_inflateInit2_
_inflateReset
_BZ2_bzCompress
_BZ2_bzCompressEnd
_BZ2_bzCompressInit
_BZ2_bzDecompress
_BZ2_bzDecompressEnd
_BZ2_bzDecompressInit
collect2: ld returned 1 exit status
make[3]: *** [libgraph_tool.la] Error 1
make[2]: *** [all-recursive] Error 1
make[1]: *** [all-recursive] Error 1
make: *** [all] Error 2

Thanks,

Spiros
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Re: graph-tool 1.1.2 on macbook with mac os 10.4.11

Tiago de Paula Peixoto
On 01/28/2008 01:30 PM, Spiros Spirou wrote:

> Hi Tiago,
>
> On 27 Ιαν 2008, at 7:41 ΜΜ, Tiago de Paula Peixoto wrote:
>> It just occurred to me that the gcc binary is being used to link the
>> library, not g++! That's probably the reason of all these undefined
>> references... In your first message, I saw you ran configure with
>> CXX=/opt/local/bin/i386-apple-darwin8.11.1-gcc-4.2.2. This is
>> incorrect. You needed to do something like
>> CXX=/opt/local/bin/i386-apple-darwin8.11.1-g++-4.2.2, assuming that's
>> what g++ is called on your system. Please try a whole build from
>> scratch, using g++ this time, and see if you still encounter any
>> problems.
>>
>>
>
> I thought that gcc is just the front-end to the compilers underneath.
> Thanks for your patience so far...
>
> I did what you suggested, but I still get undefined symbols, although
> different ones. Strangely, these seem to be related to libbz2, which
> is in /opt/local/lib. Here's the output:
Try the link with -lbz2 and -lz. You can set LDFLAGS to "-lbz2 -lz" when
issuing configure. I don't know why it is trying to link to those
libraries directly, since graph_tool uses them only through
boost_iostreams, and we're making a dynamic library. I suspect this must
be related either to the way things are linked in MacOS X, or maybe how
things are installed on your system, I'm not sure. If this works, I'll
add "-lbz2 -lz" to graph_tool build by default, since it doesn't really
hurt.

Cheers,
Tiago

--
Tiago de Paula Peixoto <[hidden email]>


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Re: graph-tool 1.1.2 on macbook with mac os 10.4.11

Spiros Spirou
Hi Tiago,

On 28 Ιαν 2008, at 9:11 ΜΜ, Tiago de Paula Peixoto wrote:

>
> Try the link with -lbz2 and -lz. You can set LDFLAGS to "-lbz2 -lz"  
> when
> issuing configure. I don't know why it is trying to link to those
> libraries directly, since graph_tool uses them only through
> boost_iostreams, and we're making a dynamic library. I suspect this  
> must
> be related either to the way things are linked in MacOS X, or maybe  
> how
> things are installed on your system, I'm not sure. If this works, I'll
> add "-lbz2 -lz" to graph_tool build by default, since it doesn't  
> really
> hurt.

This looked better:

(cd .libs && rm -f libgraph_tool.la && ln -s ../libgraph_tool.la  
libgraph_tool.la)
Making all in graph_tool
make[3]: Nothing to be done for `all'.
Making all in .
make[3]: Nothing to be done for `all-am'.
make[2]: Nothing to be done for `all-am'.

But, when I did 'graph-tool --help', here's what I got:

   File "/opt/local/bin/graph-tool", line 128
     return "|".join(metavars) if len(metavars) > 0 else None
                                ^
SyntaxError: invalid syntax

Cheers,

S.
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Re: graph-tool 1.1.2 on macbook with mac os 10.4.11

Tiago de Paula Peixoto
On 01/29/2008 02:02 PM, Spiros Spirou wrote:

> Hi Tiago,
>
> On 28 Ιαν 2008, at 9:11 ΜΜ, Tiago de Paula Peixoto wrote:
>> Try the link with -lbz2 and -lz. You can set LDFLAGS to "-lbz2 -lz"
>> when issuing configure. I don't know why it is trying to link to
>> those libraries directly, since graph_tool uses them only through
>> boost_iostreams, and we're making a dynamic library. I suspect this
>> must be related either to the way things are linked in MacOS X, or
>> maybe how things are installed on your system, I'm not sure. If this
>> works, I'll add "-lbz2 -lz" to graph_tool build by default, since it
>> doesn't really hurt.
>
> This looked better:
>
> (cd .libs && rm -f libgraph_tool.la && ln -s ../libgraph_tool.la  
> libgraph_tool.la)
> Making all in graph_tool
> make[3]: Nothing to be done for `all'.
> Making all in .
> make[3]: Nothing to be done for `all-am'.
> make[2]: Nothing to be done for `all-am'.
>
> But, when I did 'graph-tool --help', here's what I got:
>
>    File "/opt/local/bin/graph-tool", line 128
>      return "|".join(metavars) if len(metavars) > 0 else None
>                                 ^
> SyntaxError: invalid syntax
Are you sure you are using python 2.5? What is the result of 'python
--version'?

Cheers,
Tiago

--
Tiago de Paula Peixoto <[hidden email]>


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