Error with sklearn on installing by pip

[wook2014]

I am trying to install altanalyze in a conda environment on linux server. I tried to install directly by pip install AltAnalyze but there comes an error:

ERROR: Command errored out with exit status 1:
     command: /data/bioinf/jyuan/miniconda/altanalyse/bin/python -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-kzJa7S/sklearn/setup.py'"'"'; __file__='"'"'/tmp/pip-install-kzJa7S/sklearn/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' egg_info --egg-base /tmp/pip-pip-egg-info-mMZ7G6
         cwd: /tmp/pip-install-kzJa7S/sklearn/
    Complete output (5 lines):
    Traceback (most recent call last):
      File "<string>", line 1, in <module>
      File "/tmp/pip-install-kzJa7S/sklearn/setup.py", line 9, in <module>
        with open("README.md", encoding='utf-8') as f:
    TypeError: 'encoding' is an invalid keyword argument for this function
    ----------------------------------------
ERROR: Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.

I tried to download the sklearn-0.0.post9.tar.gz , changed the line which occurs the problem according to:
https://stackoverflow.com/questions/12541370/typeerror-encoding-is-an-invalid-keyword-argument-for-this-function
from

with open("README.md", encoding='utf-8') as f:

to

import io
with io.open("README.md", encoding='utf-8') as f:

and install it before altanalyze but it seemed that sklearn is not supported now:

The 'sklearn' PyPI package is deprecated, use 'scikit-learn'
rather than 'sklearn' for pip commands. 

Here is how to fix this error in the main use cases:
- use 'pip install scikit-learn' rather than 'pip install sklearn'
- replace 'sklearn' by 'scikit-learn' in your pip requirements files
  (requirements.txt, setup.py, setup.cfg, Pipfile, etc ...)
- if the 'sklearn' package is used by one of your dependencies,
  it would be great if you take some time to track which package uses
  'sklearn' instead of 'scikit-learn' and report it to their issue tracker
- as a last resort, set the environment variable
  SKLEARN_ALLOW_DEPRECATED_SKLEARN_PACKAGE_INSTALL=True to avoid this error

More information is available at
https://github.com/scikit-learn/sklearn-pypi-package

If the previous advice does not cover your use case, feel free to report it at
https://github.com/scikit-learn/sklearn-pypi-package/issues/new

Is there any update on scikit-learn to fix the problem?

[macoreL]

I came into the same issues. Is it fixed?

[nsalomonis]

Yes, you can use a docker container of AltAnalyze provided here:frankligy/SNAF: Splicing Neo Antigen Finder (SNAF) is an easy-to-use Python package to identify splicing-derived tumor neoantigens from RNA sequencing data, it further leverages both deep learning and hierarchical Bayesian models to prioritize certain candidates for experimental validationgithub.comBest,NathanOn Sep 23, 2024, at 7:46 AM, macoreL ***@***.***> wrote: I came into the same issues. Is it fixed? —Reply to this email directly, view it on GitHub, or unsubscribe.You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[ciel1021]

I am afraid this docker container is also not work as well. I tried to access it with singularity.

[frankligy]

Hi @ciel1021,

Could you elaborate on what issue you encounter when using the container? Some instructions on installation and how to use it are provided here:

install: https://snaf.readthedocs.io/en/latest/installation.html#step-1-altanalyze
run: https://snaf.readthedocs.io/en/latest/tutorial.html#running-altanalyze-to-identify-alternative-splicing-events

Best,
Frank

[ciel1021]

Hi @frankligy
basically I install the singularity by conda install and try to get the docker container. Here is the error message I got:

`singularity exec --bind /mnt/data1/home/jaquino altanalyze_0.7.0.1.sif altanalyze

INFO: Converting SIF file to temporary sandbox...

FATAL: "altanalyze": executable file not found in $PATH

INFO: Cleaning up image...

`
Thank you so much for your help, I appreciate your quick response.

[frankligy]

Hi @ciel1021,

Just to answer the installation and running docker container question.

First, when you pull the image from docker hub, since this is not a read-only image, you should use --sandbox and write it to a folder:

singularity build --sandbox altanalyze/ docker://frankligy123/altanalyze:0.7.0.1

instead of

singularity build altanalyze.sif docker://frankligy123/altanalyze:0.7.0.1

Then when you run the container, you should bind your host system to /mnt folder in virtual container, and use the writable folder instead of read-only sif:

singularity run -B $PWD:/mnt --writable altanalyze/ identify bam 4

There will be other caveats but these are the two I spotted from what I saw so far.

Best,
Frank