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"CXXABI_1.3.9' not found" error

See original GitHub issue

Summary:

Hi, I installed pyani through conda and I am getting a “CXXABI_1.3.9’ not found” error. No errors in installation

Reproducible Steps:

conda install pyani average_nucleotide_identity.py

Current Output:

Traceback (most recent call last): File “/home/odin/.conda/envs/py36/bin/average_nucleotide_identity.py”, line 4, in <module> import(‘pkg_resources’).run_script(‘pyani==0.2.3’, ‘average_nucleotide_identity.py’) File “/home/odin/.conda/envs/py36/lib/python3.6/site-packages/pkg_resources/init.py”, line 742, in run_script self.require(requires)[0].run_script(script_name, ns) File “/home/odin/.conda/envs/py36/lib/python3.6/site-packages/pkg_resources/init.py”, line 1510, in run_script exec(script_code, namespace, namespace) File “/home/odin/.conda/envs/py36/lib/python3.6/site-packages/pyani-0.2.3-py3.6.egg/EGG-INFO/scripts/average_nucleotide_identity.py”, line 169, in <module> File “/home/odin/.conda/envs/py36/lib/python3.6/site-packages/pyani-0.2.3-py3.6.egg/pyani/pyani_graphics.py”, line 29, in <module> File “/home/odin/.conda/envs/py36/lib/python3.6/site-packages/scipy/cluster/init.py”, line 27, in <module> from . import vq, hierarchy File “/home/odin/.conda/envs/py36/lib/python3.6/site-packages/scipy/cluster/hierarchy.py”, line 179, in <module> import scipy.spatial.distance as distance File “/home/odin/.conda/envs/py36/lib/python3.6/site-packages/scipy/spatial/init.py”, line 93, in <module> from .kdtree import * File “/home/odin/.conda/envs/py36/lib/python3.6/site-packages/scipy/spatial/kdtree.py”, line 8, in <module> import scipy.sparse File “/home/odin/.conda/envs/py36/lib/python3.6/site-packages/scipy/sparse/init.py”, line 229, in <module> from .csr import * File “/home/odin/.conda/envs/py36/lib/python3.6/site-packages/scipy/sparse/csr.py”, line 15, in <module> from ._sparsetools import csr_tocsc, csr_tobsr, csr_count_blocks,
ImportError: /home/odin/.conda/envs/py36/lib/python3.6/site-packages/matplotlib/…/…/…/libstdc++.so.6: version `CXXABI_1.3.9’ not found (required by /home/odin/.conda/envs/py36/lib/python3.6/site-packages/scipy/sparse/_sparsetools.cpython-36m-x86_64-linux-gnu.so)

pyani Version:

0.2.3

Python Version:

3.6

Operating System:

Ubuntu 17.04

Issue Analytics

State:
Created 6 years ago
Reactions:5
Comments:6 (2 by maintainers)

Top GitHub Comments

17reactions

jmartin18commented, Feb 20, 2018

I was able to solve by pip uninstalling/reinstalling scipy

0reactions

IsabelMeranercommented, Jan 30, 2019

I was able to solve by pip uninstalling/reinstalling scipy

The same worked for me.

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