installing graph tool on Mac OS X 10.8 by MacPorts
Hello. Installing graph tool is quite harsh (at least for me) due to the large dependency on previously installed libs. MacPorts seems useful since it finds and install automatically all dependencies of any lib you`re trying to install. These benefits notwithstanding, I'm having some troubles while concluding my installation. After installing all required libs using MacPorts, I can't configure graph tool (by ./configure). Using ./configure purely, I get this: checking consistency of all components of python development environment... no configure: error: in `/Users/JaquelinyLima/Documents/graphtool': configure: error: Could not link test program to Python. Maybe the main Python library has been installed in some non-standard library path. If so, pass it to configure, via the LDFLAGS environment variable. Example: ./configure LDFLAGS="-L/usr/non-standard-path/python/lib" ============================================================================ ERROR! You probably have to install the development version of the Python package for your distribution. The exact name of this package varies among them. Using ./configure PYTHON=/Apps/MacPorts/Python2.7 (macports location): ================ Detecting python ================ checking whether /Apps/MacPorts/Python2.7 version is >= 2.6... no configure: error: Python interpreter is too old
On 12/26/2013 12:25 AM, Igor Strozzi wrote:
Hello. Installing graph tool is quite harsh (at least for me) due to the large dependency on previously installed libs. MacPorts seems useful since it finds and install automatically all dependencies of any lib you`re trying to install. These benefits notwithstanding, I'm having some troubles while concluding my installation. After installing all required libs using MacPorts, I can't configure graph tool (by ./configure).
Why not simply installing the package itself using macports as well?
Using ./configure purely, I get this:
checking consistency of all components of python development environment... no configure: error: in `/Users/JaquelinyLima/Documents/graphtool': configure: error: Could not link test program to Python. Maybe the main Python library has been installed in some non-standard library path. If so, pass it to configure, via the LDFLAGS environment variable. Example: ./configure LDFLAGS="-L/usr/non-standard-path/python/lib" ============================================================================ ERROR! You probably have to install the development version of the Python package for your distribution. The exact name of this package varies among them.
Using ./configure PYTHON=/Apps/MacPorts/Python2.7 (macports location):
================ Detecting python ================ checking whether /Apps/MacPorts/Python2.7 version is >= 2.6... no configure: error: Python interpreter is too old
As the first error message says, you have to pass the correct compiler directives so that it can find the libraries via LDFLAGS... I think you are better off simply attempting to install it via macports, which takes care of this as well. Cheers, Tiago -- Tiago de Paula Peixoto <tiago@skewed.de>
Well, sometimes the most simple solutions are the hardest to see. I didn't look for graph tool as a macports native package. Silly me :P An offtopic question: I found this group almost at random. Can we ask any graph-tool related doubt? Btw, ---> Extracting py27-graph-tool ---> Configuring py27-graph-tool ---> Building py27-graph-tool it's been almost an hour and it is still building graph tool`s package. Any insights on how normal is this wait? Em quarta-feira, 25 de dezembro de 2013 21h25min57s UTC-2, Igor Strozzi escreveu:
Hello. Installing graph tool is quite harsh (at least for me) due to the large dependency on previously installed libs. MacPorts seems useful since it finds and install automatically all dependencies of any lib you`re trying to install. These benefits notwithstanding, I'm having some troubles while concluding my installation. After installing all required libs using MacPorts, I can't configure graph tool (by ./configure).
Using ./configure purely, I get this:
checking consistency of all components of python development environment... no configure: error: in `/Users/JaquelinyLima/Documents/graphtool': configure: error: Could not link test program to Python. Maybe the main Python library has been installed in some non-standard library path. If so, pass it to configure, via the LDFLAGS environment variable. Example: ./configure LDFLAGS="-L/usr/non-standard-path/python/lib"
============================================================================ ERROR! You probably have to install the development version of the Python package for your distribution. The exact name of this package varies among them.
Using ./configure PYTHON=/Apps/MacPorts/Python2.7 (macports location):
================ Detecting python ================ checking whether /Apps/MacPorts/Python2.7 version is >= 2.6... no configure: error: Python interpreter is too old
I closed the terminal window so I could run the port command again. This happened: MacBook-Air-de-Jaqueliny:~ JaquelinyLima$ sudo port install py27-graph-tool @2.2.27 Password: Waiting for lock on /opt/local/var/macports/registry/.registry.lock I have no idea on what does it mean.
---> Computing dependencies for py27-graph-tool I got this. Then I installed spyder and ran an working algorithm and got this: ---> Building py27-graph-tool ---> Staging py27-graph-tool into destroot ---> Installing py27-graph-tool @2.2.27_0 ---> Activating py27-graph-tool @2.2.27_0 ---> Cleaning py27-graph-tool ---> Updating database of binaries: 100.0% ---> Scanning binaries for linking errors: 9.2% Warning: Error parsing file /Applications/MacPorts/Python 2.7/Python Launcher.app/Contents/MacOS/Python Launcher: Error opening or reading file ---> Scanning binaries for linking errors: 100.0% ---> No broken files found. Then I installed spyder and ran an working algorithm and got this: dyld: lazy symbol binding failed: Symbol not found: __ZN5boost6python7objects23register_dynamic_id_auxENS0_9type_infoEPFNSt3__14pairIPvS2_EES5_E Referenced from: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/graph_tool/libgraph_tool_core.so Expected in: flat namespace dyld: Symbol not found: __ZN5boost6python7objects23register_dynamic_id_auxENS0_9type_infoEPFNSt3__14pairIPvS2_EES5_E Referenced from: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/graph_tool/libgraph_tool_core.so Expected in: flat namespace
I got this. ---> Computing dependencies for py27-graph-tool ---> Building py27-graph-tool ---> Staging py27-graph-tool into destroot ---> Installing py27-graph-tool @2.2.27_0 ---> Activating py27-graph-tool @2.2.27_0 ---> Cleaning py27-graph-tool ---> Updating database of binaries: 100.0% ---> Scanning binaries for linking errors: 9.2% Warning: Error parsing file /Applications/MacPorts/Python 2.7/Python Launcher.app/Contents/MacOS/Python Launcher: Error opening or reading file ---> Scanning binaries for linking errors: 100.0% ---> No broken files found. Then I installed spyder and ran an working algorithm and got this: dyld: lazy symbol binding failed: Symbol not found: __ZN5boost6python7objects23register_dynamic_id_auxENS0_9type_infoEPFNSt3__14pairIPvS2_EES5_E Referenced from: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/graph_tool/libgraph_tool_core.so Expected in: flat namespace dyld: Symbol not found: __ZN5boost6python7objects23register_dynamic_id_auxENS0_9type_infoEPFNSt3__14pairIPvS2_EES5_E Referenced from: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/graph_tool/libgraph_tool_core.so Expected in: flat namespace
Hi, Please report any problems with the macports package to the macports project at: https://trac.macports.org/newticket Also, please be careful with double posting to this list. The google groups interface you are using is just a reflection of the actual mailing list located at: http://lists.skewed.de/mailman/listinfo/graph-tool Whenever you post and delete a message to the google group, it is not deleted in the mailing list. So, currently you have been flooding the list with many repeated messages... Cheers, Tiago On 12/26/2013 09:35 PM, Igor Strozzi wrote:
I got this.
---> Computing dependencies for py27-graph-tool ---> Building py27-graph-tool ---> Staging py27-graph-tool into destroot ---> Installing py27-graph-tool @2.2.27_0 ---> Activating py27-graph-tool @2.2.27_0 ---> Cleaning py27-graph-tool ---> Updating database of binaries: 100.0% ---> Scanning binaries for linking errors: 9.2% Warning: Error parsing file /Applications/MacPorts/Python 2.7/Python Launcher.app/Contents/MacOS/Python Launcher: Error opening or reading file ---> Scanning binaries for linking errors: 100.0% ---> No broken files found.
Then I installed spyder and ran an working algorithm and got this:
dyld: lazy symbol binding failed: Symbol not found: __ZN5boost6python7objects23register_dynamic_id_auxENS0_9type_infoEPFNSt3__14pairIPvS2_EES5_E Referenced from: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/graph_tool/libgraph_tool_core.so Expected in: flat namespace
dyld: Symbol not found: __ZN5boost6python7objects23register_dynamic_id_auxENS0_9type_infoEPFNSt3__14pairIPvS2_EES5_E Referenced from: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/graph_tool/libgraph_tool_core.so Expected in: flat namespace
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-- Tiago de Paula Peixoto <tiago@skewed.de>
Sorry for the flood, and many thanks for the help, Tiago. I'll be more careful in the next times. By the way, don't we have an 'edit' button?
On 12/29/2013 10:33 PM, Igor Strozzi wrote:
Sorry for the flood, and many thanks for the help, Tiago. I'll be more careful in the next times. By the way, don't we have an 'edit' button?
The google group is just an interface to a regular mailing list. Once an email is sent, it can no longer be edited. Cheers, Tiago -- Tiago de Paula Peixoto <tiago@skewed.de>
hello all, I get the same errors as the ones posted above when I install the package through macports. dyld: lazy symbol binding failed: Symbol not found: __ZN5boost6python7objects23register_dynamic_id_auxENS0_9type_infoEPFNSt3__14pairIPvS2_EES5_E Referenced from: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/graph_tool/libgraph_tool_core.so Expected in: flat namespace dyld: Symbol not found: __ZN5boost6python7objects23register_dynamic_id_auxENS0_9type_infoEPFNSt3__14pairIPvS2_EES5_E Referenced from: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/graph_tool/libgraph_tool_core.so Expected in: flat namespace It builds fine, but when I import graph_tool in python, I get this error. I have tried several different things, but I have not been able to fix it. Is there a stable version we can install through macports? I am new here, but just a suggestion. I have found the installation process for this package to be fraught with so many difficulties. For such a useful package, maybe more effort needs to be invested in making it easily accessible to install. This is perhaps the only advantage I really think networkx has at the moment. Anyway, I'd like help with this. Thanks very much. -- View this message in context: http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com/... Sent from the Main discussion list for the graph-tool project mailing list archive at Nabble.com.
On 01/28/2014 01:58 AM, adebayoj wrote:
hello all,
I get the same errors as the ones posted above when I install the package through macports.
dyld: lazy symbol binding failed: Symbol not found: __ZN5boost6python7objects23register_dynamic_id_auxENS0_9type_infoEPFNSt3__14pairIPvS2_EES5_E Referenced from: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/graph_tool/libgraph_tool_core.so Expected in: flat namespace
dyld: Symbol not found: __ZN5boost6python7objects23register_dynamic_id_auxENS0_9type_infoEPFNSt3__14pairIPvS2_EES5_E Referenced from: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/graph_tool/libgraph_tool_core.so Expected in: flat namespace Y It builds fine, but when I import graph_tool in python, I get this error. I have tried several different things, but I have not been able to fix it. Is there a stable version we can install through macports?
This is a stable version. The problem is probably due to boost python being compiled against a different python version, or with a different compiler. Questions related to installations through macports are better handled by the macports project. You can submit a bug report at: https://trac.macports.org/auth/login/?next=/newticket They are usually very responsive.
I am new here, but just a suggestion. I have found the installation process for this package to be fraught with so many difficulties. For such a useful package, maybe more effort needs to be invested in making it easily accessible to install. This is perhaps the only advantage I really think networkx has at the moment.
Networkx is a pure python package, and requires no compilation. Graph-tool requires compilation, since the backbone is in C++, and it depends on other C/C++ libraries. Because of this, there will always be more hurdles with graph-tool than with networkx, since all dependencies need to be in place, and much fewer people understand how to set them up. This is made trivial by operating systems which perform automatic dependency tracking, such as virtually any GNU/Linux distro. MacOS lacks this in the OS, but it is provided by macports (and homebrew, and fink), which is a huge help, but it is not perfect, as you have seen. I try to make this easier by offering pre-compiled packages, but it is unfeasible to do this for every OS/Architecture out there. I would make pre-compiled packages for MacOS, since it would quench about 90% of the compilation problems reported to me, but I don't have access to a modern MacOS machine. But I'm always open to constructive suggestions... Best, Tiago -- Tiago de Paula Peixoto <tiago@skewed.de>
participants (3)
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adebayoj -
Igor Strozzi -
Tiago de Paula Peixoto