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 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