Error when import figtree module in Python [Mac OS X Yosemite]

[DSamuylov]

Hello,

I had been using your library mostly through Python wrapper without any problem on Ubuntu 12.04 and Ubuntu 14.10. Now I migrated to Mac (OS X Yosemite). I am doing exactly the same steps I did with Ubuntu, but there is an error when I import figtree module:

Python 2.7.9 |Anaconda 2.2.0 (x86_64)| (default, Dec 15 2014, 10:37:34) 
>>> import figtree
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
ImportError: dlopen(/Users/denis/Documents/code/figtree/python/figtree.so, 2): Library not loaded: ../lib/libfigtree.so
  Referenced from: /Users/denis/Documents/code/figtree/python/figtree.so
  Reason: image not found

The most weird thing for me is that it seems libfigtree.so exists at that location:

denis@DeSaMac:lib$ pwd
/Users/denis/Documents/code/figtree/lib
denis@DeSaMac:lib$ ls
libann_figtree_version.so   libfigtree.so 

I asked my colleague to install figtree on his laptop (also Mac, OS X Yosemite) without telling him how I did it, and he got the same error. So I might guess there is a problem with installation on OS X or Mac in general. Do you have an idea what can be a reason? I tried to check Makefiles, but I don't have enough experience to spot if there is a problem there...

All the best,
Denis

[gadomski]

Hi Denis,

figtree at this point is set up only to build out on Unix style systems, as it only builds libraries with a *.so extension.

I've put together one solution to the problem in my own fork of figree, on the cmakeify branch: https://github.com/gadomski/figtree/tree/cmakeify. It uses CMake instead of plain makefiles for many-platform building.

To get set up:

git remote add gadomski https://github.com/gadomski/figtree
git fetch gadomski
git checkout gadomski/cmakify
mkdir build && cd build
cmake ..
make

You of course have to have cmake installed on your system — if you don't, I recommend using homebrew to get it.

HTH.

[vmorariu]

Hi Denis,

I agree with Pete--most likely, your problems are due to the fact that when I initially wrote the code, I was not yet using CMake, and Mac was not one of my target platforms. I plan to replace the Visual Studio projects and Unix/Linux makefiles with CMake files, but for now see if Pete's gadomski/cmakify branch fixes your problem.

Vlad

[DSamuylov]

Dear Pete and Vlad,

Thank you a lot for your prompt reply! I managed to make the python wrapper work.

Just to let you know, before I call

python setup.py build_ext --inplace

I had to copy the compiled libraries into lib folder manually

figtree/lib/libann_figtree_version.dylib
figtree/lib/libfigtree.dylib

Otherwise it cannot find them and gives an error during the python module compilation.

Also if I follow Pete's steps on the third one I have a problem:

$ git checkout gadomski/cmakify
error: pathspec 'gadomski/cmakify' did not match any file(s) known to git.

I found that I could call

$ git show-ref

And then use reference to checkout. But I guess I miss an easier correct way...

[gadomski]

Sorry @DSamuylov typo in my instructions, should be gadomski/cmakeify.

@vmorariu let me know if you'd like me to clean up my cmake branch and open a pull request — could be an easy way to offer support for more platforms out of the box.