Error in Colab Notebook: `GLIBCXX_3.4.29' not found

[ajasja]

Hi,

The default notebook does not run: (I just used Run all with all default options).

Here is link to a copy of the notebook: https://colab.research.google.com/drive/11bH_aFT2Wm_0r3UQk4JNFTbsa3hJcXEb?usp=sharing

No module named 'pyrosetta'
---------------------------------------------------------------------------
ImportError                               Traceback (most recent call last)
[<ipython-input-3-2d0e067d8df6>](https://localhost:8080/#) in <module>
      4     sys.path.insert(0, f"/usr/local/lib/python{python_version}/site-packages/")
      5 
----> 6 from igfold.utils.visualize import *
      7 from igfold import IgFoldRunner
      8 

12 frames
[/usr/local/lib/python3.8/site-packages/pandas/core/window/ewm.py](https://localhost:8080/#) in <module>
     13 
     14 from pandas._libs.tslibs import Timedelta
---> 15 import pandas._libs.window.aggregations as window_aggregations
     16 from pandas._typing import (
     17     Axis,

ImportError: /lib/x86_64-linux-gnu/libstdc++.so.6: version `GLIBCXX_3.4.29' not found (required by /usr/local/lib/python3.8/site-packages/pandas/_libs/window/aggregations.cpython-38-x86_64-linux-gnu.so)

---------------------------------------------------------------------------
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To view examples of installing some common dependencies, click the
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---------------------------------------------------------------------------

[kimdn]

I experienced the same error today.

[jeffreyruffolo]

Hi, thanks for pointing this out. I’m currently trying to work through some issues adapting IgFold to the updated environment on Colab. Hopefully will have this fixed soon!

[Wei-Lan]

I experienced the same error today. +1

[ramosemi]

same here! has anyone been able to run the default sequence? How to install GLIBCXX?

[JPereira-FJB]

I experienced the same error today. Any fix?

[ramosemi]

I couldn't find a fix for Collab but ended up using Cosmic2 server which hosts IgFold: https://cosmic2.sdsc.edu:8443/gateway/tools.action

I generated models of an scFv and a VHH/nanobody we have been using for pre-clinical CAR T cell development.

Curiously, IgFold and the Antibody Grafting app on the Rosie2 server omits a key amino acid from CDR3 in my antibody (F is deleted entirely), there is a second deletion in the light chain too. Is there a reason for this? Any resources I could read more?

Thank you IgFold team, really incredible work!

Emilio

---

From: JPereira-FJB @.> Sent: Wednesday, May 24, 2023 4:12 AM To: Graylab/IgFold @.> Cc: Ramos, Emilio @.>; Comment @.> Subject: Re: [Graylab/IgFold] Error in Colab Notebook: `GLIBCXX_3.4.29' not found (Issue #27)

I experienced the same error today. Any fix? — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you commented. Message ID: Graylab/IgFold/issues/27/1560927170@ github. com ‍ ‍ ‍ ‍ ‍ ‍ ‍ ‍ ‍ ZjQcmQRYFpfptBannerStart This Message Is From an External Sender This message came from outside your organization.

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I experienced the same error today. Any fix?

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[jeffreyruffolo]

Hello all, sorry for the delays on getting this fixed. Colab has been updating the base environment fairly often over the last several months and it has been difficult to keep the notebook up to date. I hope to have this fixed soon to work on the current version of Colab.

[JPereira-FJB]

I couldn't find a fix for Collab but ended up using Cosmic2 server which hosts IgFold: https://cosmic2.sdsc.edu:8443/gateway/tools.action>

This is a university server, right? Is it open to the public for testing, or something?

[ramosemi]

https://cosmic-cryoem.org/tools/igfold/ You should be able to run from Cosmic

---

From: JPereira-FJB @.> Sent: Thursday, May 25, 2023 12:36 AM To: Graylab/IgFold @.> Cc: Ramos, Emilio @.>; Comment @.> Subject: Re: [Graylab/IgFold] Error in Colab Notebook: `GLIBCXX_3.4.29' not found (Issue #27)

I couldn't find a fix for Collab but ended up using Cosmic2 server which hosts IgFold: https: //cosmic2. sdsc. edu: 8443/gateway/tools. action> This is a university server, right? Is it open to the public for testing, or something? —Reply ZjQcmQRYFpfptBannerStart This Message Is From an External Sender This message came from outside your organization.

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I couldn't find a fix for Collab but ended up using Cosmic2 server which hosts IgFold: https://cosmic2.sdsc.edu:8443/gateway/tools.action>https://urldefense.com/v3/__https://cosmic2.sdsc.edu:8443/gateway/tools.action*3E__;JQ!!LQC6Cpwp!tOLDLxKJnCDZrZfLbm9kSqRgoUF14E0WpBqYGqmkr4-_8G8QWW3kUMv3goD99kPJI2GZPQHwdiAAGjJj_W8-VTcAme8A$

This is a university server, right? Is it open to the public for testing, or something?

— Reply to this email directly, view it on GitHubhttps://urldefense.com/v3/__https://github.com/Graylab/IgFold/issues/27*issuecomment-1562424007__;Iw!!LQC6Cpwp!tOLDLxKJnCDZrZfLbm9kSqRgoUF14E0WpBqYGqmkr4-_8G8QWW3kUMv3goD99kPJI2GZPQHwdiAAGjJj_W8-VSjv7Uel$, or unsubscribehttps://urldefense.com/v3/__https://github.com/notifications/unsubscribe-auth/ATGPS6C4W56VGV76U2WW7R3XH4DYZANCNFSM6AAAAAAVGVBD4I__;!!LQC6Cpwp!tOLDLxKJnCDZrZfLbm9kSqRgoUF14E0WpBqYGqmkr4-_8G8QWW3kUMv3goD99kPJI2GZPQHwdiAAGjJj_W8-VTNb0C_0$. You are receiving this because you commented.Message ID: @.***>

[wwl5600]

the same error today. Any fix?

[jeffreyruffolo]

This should be fixed now!

[ajasja]

Thanks!

[JPereira-FJB]

This should be fixed now!

I now run into a different error (No module named 'igfold', even though IgFold seems to be properly installed with no warnings or errors in the previous step).

---------------------------------------------------------------------------
ModuleNotFoundError                       Traceback (most recent call last)
[<ipython-input-3-2d0e067d8df6>](https://localhost:8080/#) in <cell line: 6>()
      4     sys.path.insert(0, f"/usr/local/lib/python{python_version}/site-packages/")
      5 
----> 6 from igfold.utils.visualize import *
      7 from igfold import IgFoldRunner
      8 

ModuleNotFoundError: No module named 'igfold'

---------------------------------------------------------------------------
NOTE: If your import is failing due to a missing package, you can
manually install dependencies using either !pip or !apt.

To view examples of installing some common dependencies, click the
"Open Examples" button below.
---------------------------------------------------------------------------

[ajasja]

Yes, I get the same. Did not have time to dig in yet, but it's probably worth opening a new issue. @JPereira-FJB @jeffreyruffolo pip install igfold seem to fail for some reason?