Issue in 2.24 with boost library using apt package
Hello,
As posted in issue #360 (closed) I have a problem when running all_shortest_paths()
. It seems that part of the boost library can not be found / is not linked. I tried installing it through apt
as well as manually compiling. I was not able to resolve the issue.
To my system - uname -a
:
- Kubuntu 4.10.0-37-generic 41-Ubuntu SMP Fri Oct 6 20:20:37 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
Installed packages (libboost-all) - apt list --installed | grep boost
:
- libboost-all-dev/zesty,now 1.62.0.1 amd64 [installed]
- libboost-atomic-dev/zesty,now 1.62.0.1 amd64 [installed,automatic]
- libboost-atomic1.62-dev/zesty,now 1.62.0+dfsg-4 amd64 [installed,automatic]
- libboost-atomic1.62.0/zesty,now 1.62.0+dfsg-4 amd64 [installed,automatic]
- libboost-chrono-dev/zesty,now 1.62.0.1 amd64 [installed,automatic]
- libboost-chrono1.62-dev/zesty,now 1.62.0+dfsg-4 amd64 [installed,automatic]
- libboost-chrono1.62.0/zesty,now 1.62.0+dfsg-4 amd64 [installed,automatic]
- libboost-context-dev/zesty,now 1.62.0.1 amd64 [installed,automatic]
- libboost-context1.62-dev/zesty,now 1.62.0+dfsg-4 amd64 [installed,automatic]
- libboost-context1.62.0/zesty,now 1.62.0+dfsg-4 amd64 [installed]
- libboost-coroutine-dev/zesty,now 1.62.0.1 amd64 [installed,automatic]
- libboost-coroutine1.62-dev/zesty,now 1.62.0+dfsg-4 amd64 [installed,automatic]
- libboost-coroutine1.62.0/zesty,now 1.62.0+dfsg-4 amd64 [installed,automatic]
- libboost-date-time-dev/zesty,now 1.62.0.1 amd64 [installed,automatic]
- libboost-date-time1.62-dev/zesty,now 1.62.0+dfsg-4 amd64 [installed,automatic]
- libboost-date-time1.62.0/zesty,now 1.62.0+dfsg-4 amd64 [installed,automatic]
- libboost-dev/zesty,now 1.62.0.1 amd64 [installed,automatic]
- libboost-exception-dev/zesty,now 1.62.0.1 amd64 [installed,automatic]
- libboost-exception1.62-dev/zesty,now 1.62.0+dfsg-4 amd64 [installed,automatic]
- libboost-fiber-dev/zesty,now 1.62.0.1 amd64 [installed,automatic]
- libboost-fiber1.62-dev/zesty,now 1.62.0+dfsg-4 amd64 [installed,automatic]
- libboost-fiber1.62.0/zesty,now 1.62.0+dfsg-4 amd64 [installed,automatic]
- libboost-filesystem-dev/zesty,now 1.62.0.1 amd64 [installed,automatic]
- libboost-filesystem1.62-dev/zesty,now 1.62.0+dfsg-4 amd64 [installed,automatic]
- libboost-filesystem1.62.0/zesty,now 1.62.0+dfsg-4 amd64 [installed]
- libboost-graph-dev/zesty,now 1.62.0.1 amd64 [installed,automatic]
- libboost-graph-parallel-dev/zesty,now 1.62.0.1 amd64 [installed,automatic]
- libboost-graph-parallel1.62-dev/zesty,now 1.62.0+dfsg-4 amd64 [installed,automatic]
- libboost-graph-parallel1.62.0/zesty,now 1.62.0+dfsg-4 amd64 [installed,automatic]
- libboost-graph1.62-dev/zesty,now 1.62.0+dfsg-4 amd64 [installed,automatic]
- libboost-graph1.62.0/zesty,now 1.62.0+dfsg-4 amd64 [installed,automatic]
- libboost-iostreams-dev/zesty,now 1.62.0.1 amd64 [installed,automatic]
- libboost-iostreams1.62-dev/zesty,now 1.62.0+dfsg-4 amd64 [installed,automatic]
- libboost-iostreams1.62.0/zesty,now 1.62.0+dfsg-4 amd64 [installed]
- libboost-locale-dev/zesty,now 1.62.0.1 amd64 [installed,automatic]
- libboost-locale1.62-dev/zesty,now 1.62.0+dfsg-4 amd64 [installed,automatic]
- libboost-locale1.62.0/zesty,now 1.62.0+dfsg-4 amd64 [installed,automatic]
- libboost-log-dev/zesty,now 1.62.0.1 amd64 [installed,automatic]
- libboost-log1.62-dev/zesty,now 1.62.0+dfsg-4 amd64 [installed,automatic]
- libboost-log1.62.0/zesty,now 1.62.0+dfsg-4 amd64 [installed,automatic]
- libboost-math-dev/zesty,now 1.62.0.1 amd64 [installed,automatic]
- libboost-math1.62-dev/zesty,now 1.62.0+dfsg-4 amd64 [installed,automatic]
- libboost-math1.62.0/zesty,now 1.62.0+dfsg-4 amd64 [installed,automatic]
- libboost-mpi-dev/zesty,now 1.62.0.1 amd64 [installed,automatic]
- libboost-mpi-python-dev/zesty,now 1.62.0.1 amd64 [installed,automatic]
- libboost-mpi-python1.62-dev/zesty,now 1.62.0+dfsg-4 amd64 [installed,automatic]
- libboost-mpi-python1.62.0/zesty,now 1.62.0+dfsg-4 amd64 [installed,automatic]
- libboost-mpi1.62-dev/zesty,now 1.62.0+dfsg-4 amd64 [installed,automatic]
- libboost-mpi1.62.0/zesty,now 1.62.0+dfsg-4 amd64 [installed,automatic]
- libboost-program-options-dev/zesty,now 1.62.0.1 amd64 [installed,automatic]
- libboost-program-options1.62-dev/zesty,now 1.62.0+dfsg-4 amd64 [installed,automatic]
- libboost-program-options1.62.0/zesty,now 1.62.0+dfsg-4 amd64 [installed,automatic]
- libboost-python-dev/zesty,now 1.62.0.1 amd64 [installed,automatic]
- libboost-python1.62-dev/zesty,now 1.62.0+dfsg-4 amd64 [installed,automatic]
- libboost-python1.62.0/zesty,now 1.62.0+dfsg-4 amd64 [installed,automatic]
- libboost-random-dev/zesty,now 1.62.0.1 amd64 [installed,automatic]
- libboost-random1.62-dev/zesty,now 1.62.0+dfsg-4 amd64 [installed,automatic]
- libboost-random1.62.0/zesty,now 1.62.0+dfsg-4 amd64 [installed,automatic]
- libboost-regex-dev/zesty,now 1.62.0.1 amd64 [installed,automatic]
- libboost-regex1.62-dev/zesty,now 1.62.0+dfsg-4 amd64 [installed,automatic]
- libboost-regex1.62.0/zesty,now 1.62.0+dfsg-4 amd64 [installed,automatic]
- libboost-serialization-dev/zesty,now 1.62.0.1 amd64 [installed,automatic]
- libboost-serialization1.62-dev/zesty,now 1.62.0+dfsg-4 amd64 [installed,automatic]
- libboost-serialization1.62.0/zesty,now 1.62.0+dfsg-4 amd64 [installed,automatic]
- libboost-signals-dev/zesty,now 1.62.0.1 amd64 [installed,automatic]
- libboost-signals1.62-dev/zesty,now 1.62.0+dfsg-4 amd64 [installed,automatic]
- libboost-signals1.62.0/zesty,now 1.62.0+dfsg-4 amd64 [installed,automatic]
- libboost-system-dev/zesty,now 1.62.0.1 amd64 [installed,automatic]
- libboost-system1.62-dev/zesty,now 1.62.0+dfsg-4 amd64 [installed,automatic]
- libboost-system1.62.0/zesty,now 1.62.0+dfsg-4 amd64 [installed]
- libboost-test-dev/zesty,now 1.62.0.1 amd64 [installed,automatic]
- libboost-test1.62-dev/zesty,now 1.62.0+dfsg-4 amd64 [installed,automatic]
- libboost-test1.62.0/zesty,now 1.62.0+dfsg-4 amd64 [installed,automatic]
- libboost-thread-dev/zesty,now 1.62.0.1 amd64 [installed,automatic]
- libboost-thread1.62-dev/zesty,now 1.62.0+dfsg-4 amd64 [installed,automatic]
- libboost-thread1.62.0/zesty,now 1.62.0+dfsg-4 amd64 [installed]
- libboost-timer-dev/zesty,now 1.62.0.1 amd64 [installed,automatic]
- libboost-timer1.62-dev/zesty,now 1.62.0+dfsg-4 amd64 [installed,automatic]
- libboost-timer1.62.0/zesty,now 1.62.0+dfsg-4 amd64 [installed,automatic]
- libboost-tools-dev/zesty,now 1.62.0.1 amd64 [installed,automatic]
- libboost-type-erasure-dev/zesty,now 1.62.0.1 amd64 [installed,automatic]
- libboost-type-erasure1.62-dev/zesty,now 1.62.0+dfsg-4 amd64 [installed,automatic]
- libboost-type-erasure1.62.0/zesty,now 1.62.0+dfsg-4 amd64 [installed,automatic]
- libboost-wave-dev/zesty,now 1.62.0.1 amd64 [installed,automatic]
- libboost-wave1.62-dev/zesty,now 1.62.0+dfsg-4 amd64 [installed,automatic]
- libboost-wave1.62.0/zesty,now 1.62.0+dfsg-4 amd64 [installed,automatic]
- libboost1.62-dev/zesty,now 1.62.0+dfsg-4 amd64 [installed,automatic]
- libboost1.62-tools-dev/zesty,now 1.62.0+dfsg-4 amd64 [installed,automatic]
Installed graph-tools:
- python3-graph-tool/unstable,now 2.24-1 amd64 [installed]
Apt sources:
- deb http://downloads.skewed.de/apt/zesty zesty universe
- deb-src http://downloads.skewed.de/apt/zesty zesty universe
The complete error message
from PyCharm is as follows:
- /usr/bin/python3.5: symbol lookup error: /usr/lib/python3/dist-packages/graph_tool/topology/libgraph_tool_topology.so: undefined symbol: _ZN5boost7context12stack_traits12default_sizeEv
When using ldd
to show the dependencies of the libgraph_tool_topology.so I get the following output:
- linux-vdso.so.1 => (0x00007fff9ef82000)
- libpython3.5m.so.1.0 => /usr/lib/x86_64-linux-gnu/libpython3.5m.so.1.0 (0x00007fc37b2f4000)
- libboost_python-py35.so.1.62.0 => /usr/lib/x86_64-linux-gnu/libboost_python-py35.so.1.62.0 (0x00007fc37b0ac000)
- libstdc++.so.6 => /usr/lib/x86_64-linux-gnu/libstdc++.so.6 (0x00007fc37ad24000)
- libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007fc37aa1b000)
- libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007fc37a654000)
- libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1 (0x00007fc37a43b000)
- libgomp.so.1 => /usr/lib/x86_64-linux-gnu/libgomp.so.1 (0x00007fc37a20d000)
- libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00007fc379fef000)
- libexpat.so.1 => /lib/x86_64-linux-gnu/libexpat.so.1 (0x00007fc379dc5000)
- libz.so.1 => /lib/x86_64-linux-gnu/libz.so.1 (0x00007fc379ba9000)
- libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007fc3799a5000)
- libutil.so.1 => /lib/x86_64-linux-gnu/libutil.so.1 (0x00007fc3797a0000)
- /lib64/ld-linux-x86-64.so.2 (0x000055a7deee4000)
I hope this is not a mistake on my part. The issue persisted when I installed it through apt like this:
sudo apt-get install python3-graph-tool
I can provide more information if necessary. I don't know what else could be helpful though.