Knime Python bundle not working

[ricciV1]

Hey @steffen_KNIME,

I added the channels as you requested but nothing changed. (I dont know why they are not there but they were listed all the time before)

My error log looks the same as in @AD1529 post.

[bwilhelm]

Hi @AD1529,

I agree, the error message isn’t very informative. It looks like conda-lock doesn’t handle this situation well. Running micromamba create --dry-run --platform linux-64 -f env.yml with your environment file provides a clearer explanation:

error    libmamba Could not solve for environment specs
    The following package could not be installed
    └─ shap =0.46.0 does not exist (perhaps a typo or a missing channel).
critical libmamba Could not solve for environment specs

The issue is that version 0.46.0 of the shap package isn’t available. I was able to resolve the environment by changing the version to 0.45.1.

Edit: This is the answer for this message by @AD1529 (I mentioned the wrong person).

[ricciV1]

Hey @bwilhelm,
I ran micromamba create --dry-run --platform linux-64 -f env.yml in the anaconda(miniconda) prompt after having to install micromamba in my environment (base).

After running said command I got the message:

error    libmamba Could not solve for environment specs
    The following package could not be installed
    └─ selenium ==4.25.0 is not installable because it requires
       └─ selenium-manager =4.25, which requires
          └─ __glibc >=2.17,<3.0.0a0, which is missing on the system.
critical libmamba Could not solve for environment specs

Furthermore I saw that the commercial channel repo.anaconda.com was used.

I hope we can avoid using this channel.

Kind regards, Ricci

[bwilhelm]

Hi @ricciV1,

Apologies for the confusion in my previous response; I mixed up the issues discussed in this thread.

Furthermore I saw that the commercial channel repo.anaconda.com was used.

I recommend addressing this first. It looks like you’re still using the YAML file from this post. To avoid using the commercial anaconda or main channels, remove “defaults” from your channel list (since “defaults” refers to “default_channels” in your conda config). With the following channel list, your environment resolved successfully on my Linux machine:

channels:
  - conda-forge
  - knime

I’m unsure about the error __glibc >=2.17,<3.0.0a0, which is missing on the system. I can’t investigate this on my system, but I hope it won’t be an issue when using the conda-forge channel.

[ricciV1]

Hi @bwilhelm,

yes it seems I did not save my last change with the channels.

Updated env.yml:

name: knime_python_env
channels:
  - conda-forge
  - knime
dependencies:
  - knime-extension==5.3.0
  - knime-python-base==5.3.0
  - python==3.11.9
  - selenium==4.25.0
  - webdriver-manager
  - pillow
  - beautifulsoup4

I ran micromamba create --dry-run --platform linux-64 -f env.yml but it resultes in the same issue:

I tried running it without --platform linux-64 and the result was:

BUT it proceeded to list more → see attached .txt
micromamba_result_win64.txt (13.5 KB)

[ricciV1]

EDIT

1. I updated my dependencies (including Selenium to 4.26.1 (latest)) but nothing changed.
2. I set my channels in the config specifically to conda-forge and knime and removed defaults. I set the priority to: strict

The error still persists.

[bwilhelm]

Hi @ricciV1,

Did you try running the build_python_extension.py command again? I think the conda-lock call to micromamba may differ slightly from the command I used to debug the issue. A colleague was able to use the build_python_extension.py command on a Windows machine with your environment definition.

[Daniela_Rotelli]

Hi @bwilhelm,

it worked!!!
In my previous attempts I removed the dependency and it did not work.
Changing it to 0.45.1 solved the problem!

I really don’t know how to thank you.
This issue made me mad.

Daniela

[ricciV1]

Hey @bwilhelm @steffen_KNIME,

it works now! …somehow
I do not know what has changed… maybe it was the channels … maybe not - but it seems to work.

Thanks to everyone for addressing this issue so promptly and helping out!

Kind regards Ricci

[MartinDDDD]

Looks two birds were killed with one stone (or in one thread ).

Flagging the post regarding different shap version as solution as I think it relates most to the initial problem raised by Daniela.