CODEWITHSUNDEEP
amazon-sagemakerrdkit
Bill Tatsis
Bill Tatsis

Reputation: 11

amazon-sagemaker-lab:: libXrender.so.1 package

I am trying to use the amazon sagemaker lab environment and the package libXrender is not installed.

sudo privileges are removed and it's not possible to install it with:

apt-get install libxrender1

Is there an easy fix or do I have to contact their support to install the package in their docker container?

Thanks in advance!

Error results from this piece of code:

from rdkit.Chem.Draw import rdMolDraw2D
from rdkit.Chem.Draw.rdMolDraw2D import *

ImportError: libXrender.so.1: cannot open shared object file: No such file or directory

Upvotes: 0

Views: 914

Answers (4)

Matteo Ferla
Matteo Ferla

Reputation: 2378

For anyone stumbling upon this Q because they have a libXrender.so.1 but with root or fakeroot powers, yum install libxrender still causes an error —in Fedora it's libXrender, libXrender1 in Debian, so the apt-get will likely be unhelpful.

In a bulletin board answer Greg Landrum posits it's an X11 issue, and suggests:

conda install -c rdkit nox
conda install -c rdkit cairo

In my case, a Rocky9 Singularity build (library/default/rockylinux:9) installing the following did the job of fixing X11 —which I assume might cause drama elsewhere:

dnf config-manager --enable crb
# CRB is powertools
    yum install xterm xorg-x11-server-Xorg xorg-x11-server-utils xorg-x11-xauth -y
#the xorg-x11-apps is deprecated

Upvotes: 0

Bill Tatsis
Bill Tatsis

Reputation: 11

No problem in installing rdkit. The problem crops up when trying to call one of its visualisation functions rdkit.Chem.Draw.rdMolDraw2D - MolDraw2D requires the help of a rendering library to display the molecules in 2D.

Upvotes: 1

icoxfog417
icoxfog417

Reputation: 187

If you want to use rdkit, we can install it by conda install -c conda-forge rdkit in Studio Lab.

Upvotes: 0

Kirit Thadaka
Kirit Thadaka

Reputation: 507

Yes, sudo privileges are not available in Studio Lab. Your best bet is to find a different library that you can install without sudo privileges.

You can also try - conda install -c conda-forge rdki

Upvotes: 0

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