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anmartinezs / pyseg_system

De novo analysis for cryo-electron tomography
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An error about graph-tool #5

Open wenzl1337 opened 4 years ago

wenzl1337 commented 4 years ago

When I run pyseg_system/code/tests/tracing_grid.sh, there's an error

./tracing_grid.sh python ../pyseg/scripts/tests/mcf_synthetic_test.py do_short /home/wenzl/programs/pyseg_system-master/sys/soft/miniconda2/lib/python2.7/site-packages/graph_tool/all.py:40: RuntimeWarning: Error importing draw module, proceeding nevertheless: /home/wenzl/programs/pyseg_system-master/sys/soft/miniconda2/lib/python2.7/site-packages/graph_tool/draw/libgraph_tool_draw.so: undefined symbol: _ZN5Cairo7Context9show_textERKNSt7cxx1112basic_stringIcSt11char_traitsIcESaIcEEE warnings.warn(msg, RuntimeWarning) ^CTraceback (most recent call last): File "../pyseg/scripts/tests/mcf_synthetic_test.py", line 12, in from pyseg.scripts import mcf_graph File "/home/wenzl/programs/pyseg_system-master/code/pyseg/init__.py", line 12, in import disperse_io File "/home/wenzl/programs/pyseg_system-master/code/pyseg/disperse_io/init.py", line 11, in from disperse_io import * ......

I find there's something wrong with pyseg_system-master/sys/soft/miniconda2/lib/python2.7/site-packages/graph_tool/all.py., which contains a command: from graph_tool.draw import *. As I type this command in python, the same error as above would happen. How can i solve this issue?

anmartinezs commented 4 years ago

It seems that graph-tool were not installed properly in your computer, did not you get any error during the installation?

Graph-tool is an external python library, more information about this package in https://graph-tool.skewed.de/

wenzl1337 commented 4 years ago

When I installed this software, everything seemed OK. There was no error occur and graph_tool was also installed successfully. I removed the whole directory today and installed pyseg again, the same error happened.

anmartinezs commented 4 years ago

After installation, are you still getting the next followng error?you had before: _I find there's something wrong with pyseg_system-master/sys/soft/miniconda2/lib/python2.7/site-packages/graph_tool/all.py., which contains a command: from graphtool.draw import *. As I type this command in python, the same error as above would happen. How can i solve this issue? If this is the case, graph-tool was not installed properly, which computer and OS are you using?

wenzl1337 commented 4 years ago

ubuntu18.04

anmartinezs commented 4 years ago

Have you tried to install graph-tool externally? see the link in a previous post.

El mié., 15 jul. 2020 7:13, wenzl1337 notifications@github.com escribió:

ubuntu18.04

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