srnas
Installation problem
Hi Sandro,
I'm having a problem installing barnaba in python3.9: Installation initially seems fine:
pip install barnaba Requirement already satisfied: barnaba in /home/sabine/.local/lib/python3.9/site-packages (0.1.7) Requirement already satisfied: numpy in /home/sabine/anaconda3/envs/barnaba/lib/python3.9/site-packages (from barnaba) (1.22.3) Requirement already satisfied: mdtraj in /home/sabine/.local/lib/python3.9/site-packages (from barnaba) (1.9.7) Requirement already satisfied: future in /home/sabine/anaconda3/envs/barnaba/lib/python3.9/site-packages (from barnaba) (0.18.2) Requirement already satisfied: scipy in /home/sabine/.local/lib/python3.9/site-packages (from barnaba) (1.8.0) Requirement already satisfied: astunparse in /home/sabine/.local/lib/python3.9/site-packages (from mdtraj->barnaba) (1.6.3) Requirement already satisfied: pyparsing in /home/sabine/.local/lib/python3.9/site-packages (from mdtraj->barnaba) (3.0.8) Requirement already satisfied: wheel<1.0,>=0.23.0 in /home/sabine/anaconda3/envs/barnaba/lib/python3.9/site-packages (from astunparse->mdtraj->barnaba) (0.37.1) Requirement already satisfied: six<2.0,>=1.6.1 in /home/sabine/anaconda3/envs/barnaba/lib/python3.9/site-packages (from astunparse->mdtraj->barnaba) (1.16.0)
But when I try to run it, I get an error:
(barnaba) sabine@sabine-Swift-SF314-511:~/bin$ barnaba
Traceback (most recent call last):
File "/home/sabine/.local/bin/barnaba", line 16, in
from barnaba import commandline
File "/home/sabine/.local/lib/python3.9/site-packages/barnaba/init.py", line 3, in
from .functions import *
File "/home/sabine/.local/lib/python3.9/site-packages/barnaba/functions.py", line 19, in
import mdtraj as md
File "/home/sabine/.local/lib/python3.9/site-packages/mdtraj/init.py", line 55, in
from ._lprmsd import lprmsd
ImportError: /home/sabine/.local/lib/python3.9/site-packages/mdtraj/_lprmsd.cpython-39-x86_64-linux-gnu.so: undefined symbol: _ZSt28__throw_bad_array_new_lengthv
Do you have any idea how to fix this?
Cheers Sabine
Hi Sabine,
Have you tried to import mdtraj alone? maybe the problem is related to lprmsd?
From: sreisser @.***> Sent: 14 April 2022 10:25:42 To: srnas/barnaba Cc: Subscribed Subject: [srnas/barnaba] Installation problem (Issue #47)
Hi Sandro,
I'm having a problem installing barnaba in python3.9: Installation initially seems fine:
pip install barnaba Requirement already satisfied: barnaba in /home/sabine/.local/lib/python3.9/site-packages (0.1.7) Requirement already satisfied: numpy in /home/sabine/anaconda3/envs/barnaba/lib/python3.9/site-packages (from barnaba) (1.22.3) Requirement already satisfied: mdtraj in /home/sabine/.local/lib/python3.9/site-packages (from barnaba) (1.9.7) Requirement already satisfied: future in /home/sabine/anaconda3/envs/barnaba/lib/python3.9/site-packages (from barnaba) (0.18.2) Requirement already satisfied: scipy in /home/sabine/.local/lib/python3.9/site-packages (from barnaba) (1.8.0) Requirement already satisfied: astunparse in /home/sabine/.local/lib/python3.9/site-packages (from mdtraj->barnaba) (1.6.3) Requirement already satisfied: pyparsing in /home/sabine/.local/lib/python3.9/site-packages (from mdtraj->barnaba) (3.0.8) Requirement already satisfied: wheel<1.0,>=0.23.0 in /home/sabine/anaconda3/envs/barnaba/lib/python3.9/site-packages (from astunparse->mdtraj->barnaba) (0.37.1) Requirement already satisfied: six<2.0,>=1.6.1 in /home/sabine/anaconda3/envs/barnaba/lib/python3.9/site-packages (from astunparse->mdtraj->barnaba) (1.16.0)
But when I try to run it, I get an error:
(barnaba) @.***:~/bin$ barnaba Traceback (most recent call last): File "/home/sabine/.local/bin/barnaba", line 16, in from barnaba import commandline File "/home/sabine/.local/lib/python3.9/site-packages/barnaba/init.py", line 3, in from .functions import * File "/home/sabine/.local/lib/python3.9/site-packages/barnaba/functions.py", line 19, in import mdtraj as md File "/home/sabine/.local/lib/python3.9/site-packages/mdtraj/init.py", line 55, in from ._lprmsd import lprmsd ImportError: /home/sabine/.local/lib/python3.9/site-packages/mdtraj/_lprmsd.cpython-39-x86_64-linux-gnu.so: undefined symbol: _ZSt28__throw_bad_array_new_lengthv
Do you have any idea how to fix this?
Cheers Sabine
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