I’ve managed to install graph-tool version 2.29 (commit d4154c6c) via aptitude installer on Ubuntu 18.04 in a python3 miniconda venv. The following example gist causes a 127 exit code caused by some sort of fudged up library linking to libgraph_tool_draw.so with:
undefined symbol: _ZN5Cairo7Context16select_font_faceERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEENS_9FontSlantENS_10FontWeightE
from graph_tool.all import * g = Graph() ug = Graph(directed=False) ug = Graph() ug.set_directed(False) assert ug.is_directed() == False v1 = g.add_vertex() v2 = g.add_vertex() graph_tool.draw.graph_draw(g, vertex_text=g.vertex_index, vertex_font_size=18, output_size=(200, 200), output="test.png”)
Incidentally, when try to compile graph-tool from upstream master the make routine fails with a libtools error on reading libsigc-2.0.la in my configuration using --with-python-module-path=…/miniconda3/envs/mne/lib/python3.7/site-packages.
On the verge of losing more hair than I can afford. Magic fix commands appreciated.
-Kam
Am 28.02.20 um 21:55 schrieb Kambiz Tavabi:
I’ve managed to install graph-tool version 2.29 (commit d4154c6c) via aptitude installer on Ubuntu 18.04 in a python3 miniconda venv. The following example gist causes a 127 exit code caused by some sort of fudged up library linking to libgraph_tool_draw.so with:
undefined symbol: _ZN5Cairo7Context16select_font_faceERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEENS_9FontSlantENS_10FontWeightE
If you used the ubuntu package, the library was installed in the system's Python environment. The missing symbol is probably due to your anaconda environment having different library versions. If you want to use anaconda, you should install graph-tool from there, otherwise this kind of mismatch is bound to happen.
Incidentally, when try to compile graph-tool from upstream master the make routine fails with a libtools error on reading libsigc-2.0.la http://libsigc-2.0.la in my configuration using --with-python-module-path=…/miniconda3/envs/mne/lib/python3.7/site-packages.
If you want help with compilation, you need to provide more information, including the entire contents of the config.log file, as well as the entire output of the configure command, together with the entire error messages, not only snippets.
Best, Tiago
Hello Tiago, I’ve aped my way through a few install iterations, didn’t have any luck with compiling, however the conda installation in my working venv no longer crashes the python console with exit 127 code! Now, the same gist yields an AttributeError:
Traceback (most recent call last): File "~/miniconda3/envs/mne/lib/python3.7/site-packages/IPython/core/interactiveshell.py", line 3331, in run_code exec(code_obj, self.user_global_ns, self.user_ns) File "<ipython-input-10-e39c37064277>", line 1, in <module> graph_tool.draw.graph_draw(g, vertex_text=g.vertex_index, vertex_font_size=18, AttributeError: module 'graph_tool.draw' has no attribute 'graph_draw'
Thanks for the help. Kam On March 1, 2020 at 1:06:54 PM, de Paula Peixoto Tiago (tiago@skewed.de) wrote:
Am 28.02.20 um 21:55 schrieb Kambiz Tavabi:
I’ve managed to install graph-tool version 2.29 (commit d4154c6c) via aptitude installer on Ubuntu 18.04 in a python3 miniconda venv. The following example gist causes a 127 exit code caused by some sort of fudged up library linking to libgraph_tool_draw.so with:
undefined symbol: _ZN5Cairo7Context16select_font_faceERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEENS_9FontSlantENS_10FontWeightE
If you used the ubuntu package, the library was installed in the system's Python environment. The missing symbol is probably due to your anaconda environment having different library versions. If you want to use anaconda, you should install graph-tool from there, otherwise this kind of mismatch is bound to happen.
Incidentally, when try to compile graph-tool from upstream master the make routine fails with a libtools error on reading libsigc-2.0.la http://libsigc-2.0.la in my configuration using --with-python-module-path=…/miniconda3/envs/mne/lib/python3.7/site-packages.
If you want help with compilation, you need to provide more information, including the entire contents of the config.log file, as well as the entire output of the configure command, together with the entire error messages, not only snippets.
Best, Tiago
-- Tiago de Paula Peixoto tiago@skewed.de
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Am 02.03.20 um 07:18 schrieb Kambiz Tavabi:
Hello Tiago, I’ve aped my way through a few install iterations, didn’t have any luck with compiling, however the conda installation in my working venv no longer crashes the python console with exit 127 code! Now, the same gist yields an AttributeError:
Traceback (most recent call last): File "~/miniconda3/envs/mne/lib/python3.7/site-packages/IPython/core/interactiveshell.py", line 3331, in run_code exec(code_obj, self.user_global_ns, self.user_ns) File "<ipython-input-10-e39c37064277>", line 1, in <module> graph_tool.draw.graph_draw(g, vertex_text=g.vertex_index, vertex_font_size=18, AttributeError: module 'graph_tool.draw' has no attribute 'graph_draw'
The drawing functionality of graph-tool requires the GTK library to be installed, but this is not packaged by anaconda.
If you want drawing to work, you have to move out of anaconda.
Best, Tiago
-
Kambiz Tavabi -
Tiago de Paula Peixoto