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KennthShang / PhaVIP

Phage virion protein classifier
GNU General Public License v3.0
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error in conda env create -f phavip.yml -n phavip #2

Open yyyyyuzj opened 1 year ago

yyyyyuzj commented 1 year ago

image The Python version of my virtual environment is 3.8，the R version is 4.3.1。 When I downloaded the R package separately, an error was reported as follows： image

KennthShang commented 1 year ago

Hi,

First of all, the env is not allowed to be installed seperately. The are the r-script in conda and the version should be consist with other package in the env.

And it seems there is an error when install the yml. Several options for handling the problem.

  1. reinstall a miniconda (99% solve your problen)
  2. deactivate your env frist, then add a channel for mainland china and reinstall again.
  3. create a new env and install the required package listed in yml one by one.

But what you should not do is DO NOT directly install the r package in your deephost r env. lots of bugs may occur.

Best, Jiayu

yyyyyuzj commented 1 year ago

Hi,Jiayu Thank you for your enthusiastic answer. I will try these solutions one by one. Yours， Zhenjing

At 2023-08-09 11:52:24, "Kennth Shang" @.***> wrote:

Hi,

First of all, the env is not allowed to be installed seperately. The are the r-script in conda and the version should be consist with other package in the env.

And it seems there is an error when install the yml. Several options for handling the problem.

reinstall a miniconda (99% solve your problen) deactivate your env frist, then add a channel for mainland china and reinstall again. create a new env and install the required package listed in yml one by one.

But what you should not do is DO NOT directly install the r package in your deephost r env. lots of bugs may occur.

Best, Jiayu

— Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you authored the thread.Message ID: @.***>

yyyyyuzj commented 1 year ago

I want to retrain the model, but it's stuck here. I checked the model and it's fine. I don't know where the problem lies image image

KennthShang commented 1 year ago

Sorry, I do not know that either.

Should be a problem caused by your device (GPU) I suppose. You can try to turn off the GPU setup and try only the CPU first.

Or maybe you can use a small demo dataset for debugging.

Best, Jiayu

yyyyyuzj commented 1 year ago

hh，The problem has been resolved, it's the GPU.

At 2023-08-18 18:53:16, "Kennth Shang" @.***> wrote:

Sorry, I do not know that either.

Should be a problem caused by your device (GPU) I suppose. You can try to turn off the GPU setup and try only the CPU first.

Or maybe you can use a small demo dataset for debugging.

Best, Jiayu

— Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you authored the thread.Message ID: @.***>