Short of a solution there are two posts with similar problems online:
https://git.skewed.de/count0/graph-tool/issues/277
The issue seems to normally revolve around using different versions of Python or packages when compiling. Maybe ask your network admin to recompile paying particular attention to that and see if it fixes it?
Best wishes,
Philipp
From: Alexandre Hannud Abdo [mailto:abdo@member.fsf.org]
Sent: 31 January 2017 21:04
To: Main discussion list for the graph-tool project <graph-tool@skewed.de>
Subject: [graph-tool] general "did not match C++ signature" error
Ni !
The import working means that Python can find the Python component of graph tool.
The error you get has to do with boost Python not finding, for a call internal to the Python component, a corresponding function in the C++ component that matches it's argument types.
Thus, this happens if any of the pieces involved do not match. A common cause is version mismatch.
Ldd is useful to check some of those: the versions of libraries linked to the C++ component.
In your led output I see
libpython2.6.so.1.0 => /usr/lib64/libpython2.6.so.1.0 (0x00007ffff38ce000)
Thus it seems to be the case that the package got compiled against Python 2.6, yet got installed for Python 2.7 .
Cheers
ale
On Sunday, January 29, 2017, bloodymeli <bloodymeli@gmail.com> wrote:
Hi,
Graph-tool was manually compiled on a local cluster (based on RedHat) by a
network admin. The python command
import graph_tool
works fine, but almost every other command results in an error related to
"did not match C++ signature":
For example,
gtGraph=graph_tool.load_graph("yeast.graphml")
(attached) results in:
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/usr/local/epd/lib/python2.7/site-packages/graph_tool/__init__.py",
line 2702, in load_graph
g.load(file_name, fmt, ignore_vp, ignore_ep, ignore_gp)
File "/usr/local/epd/lib/python2.7/site-packages/graph_tool/__init__.py",
line 2320, in load
ignore_ep, ignore_gp)
Boost.Python.ArgumentError: Python argument types in
GraphInterface.read_from_file(GraphInterface, str, NoneType, str, list,
list, list)
did not match C++ signature:
read_from_file(graph_tool::GraphInterface {lvalue},
std::__cxx11::basic_string<char, std::char_traits<char>,
std::allocator<char> >, boost::python::api::object,
std::__cxx11::basic_string<char, std::char_traits<char>,
std::allocator<char> >, boost::python::list, boost::python::list,
boost::python::list)
Following some other posts in the mailing list, I've applied the ldd command
and:
ldd
/usr/local/epd/lib/python2.7/site-packages/graph_tool/libgraph_tool_core.so
linux-vdso.so.1 => (0x00007ffff7ffe000)
libboost_iostreams.so.1.59.0 => /usr/lib64/libboost_iostreams.so.1.59.0
(0x00007ffff5c46000)
libboost_python.so.5 => /usr/lib64/libboost_python.so.5
(0x00007ffff59f5000)
libboost_regex.so.1.59.0 => /usr/lib64/libboost_regex.so.1.59.0
(0x00007ffff56df000)
libboost_coroutine.so.1.59.0 => /usr/lib64/libboost_coroutine.so.1.59.0
(0x00007ffff54d4000)
libCGAL.so.12 =>
/usr/local/cgal-releases-CGAL-4.9/build/release/lib/libCGAL.so.12
(0x00007ffff52af000)
libexpat.so.1 => /lib64/libexpat.so.1 (0x00007ffff5087000)
libstdc++.so.6 =>
/usr/local/gcc5.3/bin/../lib/gcc/x86_64-unknown-linux-gnu/5.3.0/../../../../lib64/libstdc++.so.6
(0x00007ffff4cf8000)
libm.so.6 => /lib64/libm.so.6 (0x00007ffff4a74000)
libc.so.6 => /lib64/libc.so.6 (0x00007ffff46e0000)
libgcc_s.so.1 =>
/usr/local/gcc5.3/bin/../lib/gcc/x86_64-unknown-linux-gnu/5.3.0/../../../../lib64/libgcc_s.so.1
(0x00007ffff44c9000)
libbz2.so.1 => /lib64/libbz2.so.1 (0x00007ffff42b8000)
libz.so.1 => /usr/local/epd/lib/libz.so.1 (0x00007ffff409a000)
librt.so.1 => /lib64/librt.so.1 (0x00007ffff3e91000)
libpthread.so.0 => /lib64/libpthread.so.0 (0x00007ffff3c74000)
libpython2.6.so.1.0 => /usr/lib64/libpython2.6.so.1.0 (0x00007ffff38ce000)
libicudata.so.42 => /usr/lib64/libicudata.so.42 (0x00007ffff2788000)
libicui18n.so.42 => /usr/lib64/libicui18n.so.42 (0x00007ffff23f2000)
libicuuc.so.42 => /usr/lib64/libicuuc.so.42 (0x00007ffff20a0000)
libboost_context.so.1.59.0 => /usr/lib64/libboost_context.so.1.59.0
(0x00007ffff1e96000)
libboost_thread.so.1.59.0 => /usr/lib64/libboost_thread.so.1.59.0
(0x00007ffff1c74000)
libboost_chrono.so.1.59.0 => /usr/lib64/libboost_chrono.so.1.59.0
(0x00007ffff1a6d000)
libboost_system.so.1.59.0 => /usr/lib64/libboost_system.so.1.59.0
(0x00007ffff1869000)
libmpfr.so.1 => /usr/lib64/libmpfr.so.1 (0x00007ffff161c000)
libgmp.so.3 => /usr/lib64/libgmp.so.3 (0x00007ffff13c1000)
/lib64/ld-linux-x86-64.so.2 (0x0000003f14800000)
libdl.so.2 => /lib64/libdl.so.2 (0x00007ffff11bc000)
libutil.so.1 => /lib64/libutil.so.1 (0x00007ffff0fb9000)
yeast.graphml
<http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com/file/n4026983/yeast.graphml>
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