Cant install bio_embeddings in colab

[IliasGewr]

I am trying to use SeqVec in colab but the following installation commands probably dont work anymore (maybe is a dependencies version think).

i use these commands to install:

!pip3 install -U pip > /dev/null
!pip3 install -U bio_embeddings[all] > /dev/null

and i get this

**WARNING: bio-embeddings 0.1.3 does not provide the extra 'all'
error: subprocess-exited-with-error

× pip subprocess to install build dependencies did not run successfully.
│ exit code: 1
╰─> See above for output.

note: This error originates from a subprocess, and is likely not a problem with pip.
error: subprocess-exited-with-error

× pip subprocess to install build dependencies did not run successfully.
│ exit code: 1
╰─> See above for output.

note: This error originates from a subprocess, and is likely not a problem with pip.**

Is there a colab example that works these days?

[J-JEMINA]

I am trying to use PhageRBP detect and facing the same issue!
Please help @sacdallago

[AlvaroLopezMalizia]

Hi! I got the same error trying to use the SeqVec in colab

(https://colab.research.google.com/github/sacdallago/bio_embeddings/blob/develop/notebooks/extract_supervised_from_seqvec.ipynb).

!pip3 install -U pip > /dev/null
!pip3 install -U bio_embeddings[all] > /dev/null

error: subprocess-exited-with-error

× pip subprocess to install build dependencies did not run successfully.
│ exit code: 1
╰─> See above for output.

note: This error originates from a subprocess, and is likely not a problem with pip.
error: subprocess-exited-with-error

× pip subprocess to install build dependencies did not run successfully.
│ exit code: 1
╰─> See above for output.

note: This error originates from a subprocess, and is likely not a problem with pip.

Any suggestion on how I can fix it?

Thanks

[dimicorn]

Hi, I have got the same error

How can I fix it?

Thanks in advance

[AlvaroLopezMalizia]

Hi, I have got the same error

How can I fix it?

Thanks in advance

Hi,

I encountered the same error, but I found a solution that worked for me. As a Windows user, I used a Ubuntu environment via WSL. I installed Python version 3.8 and then ran pip install bio-embedding[all]. I couldn't get it to work from Colab, so I ended up using Jupyter Notebook instead. This setup allowed everything to work properly.

Hope this helps!

Best,
Álvaro