Installation problem

[sreisser]

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

[sbottaro]

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 — Reply to this email directly, view it on GitHub<https://eur02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fsrnas%2Fbarnaba%2Fissues%2F47&data=04%7C01%7Csandro.bottaro%40bio.ku.dk%7C6977982017d04e46c61a08da1df05e4d%7Ca3927f91cda14696af898c9f1ceffa91%7C0%7C0%7C637855215462635344%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=PJavPc5uR0oHjmlddV6W3hpHfxfp8K%2Fm%2BeeNTJ%2B6QbE%3D&reserved=0>, or unsubscribe<https://eur02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FABYTX7AVT4TO7FYRCQSHMK3VE7JANANCNFSM5TNBBN2A&data=04%7C01%7Csandro.bottaro%40bio.ku.dk%7C6977982017d04e46c61a08da1df05e4d%7Ca3927f91cda14696af898c9f1ceffa91%7C0%7C0%7C637855215462635344%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=8%2FxckvBZNFkMmhLWtWBPVjk8esLxJXSrED10TTNeIFw%3D&reserved=0>. You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[sreisser]

yes seems to be with _lprmsd.cpython-39-x86_64-linux-gnu.so