conda install error

[lixiang117423]

When I used conda to install, the following error message appeared. I changed several servers and got the same error message.

mamba install bioconda::resistify=0.5.2

Looking for: ['bioconda::resistify=0.5.2']

conda-forge/linux-64                                        Using cache
conda-forge/noarch                                          Using cache
bioconda/linux-64                                           Using cache
bioconda/noarch                                             Using cache
/home/lixiang/miniforge-pypy3/lib/pypy3.9/multiprocessing/resource_tracker.py:216: UserWarning: resource_tracker: There appear to be 2 leaked semaphore objects to clean up at shutdown
  warnings.warn('resource_tracker: There appear to be %d '

[SwiftSeal]

Hi @lixiang117423

This issue appears to be related to conda itself - I can see some other conda users experiencing this conda/conda#9589. Does the install fail or is it just giving a warning? If it is failing, I'd probably advise trying a fresh install of conda/mamba/micromamba and see if that fixes it, or at least updating conda to the latest version if it isn't already. Alternatively if you have access to apptainer/docker, the biocontainers version should be useable.

I'll keep an eye on the issue as I am releasing a new version in the next couple of weeks which will use a slightly different conda recipe!

[lixiang117423]

It seems to be a conda problem. I tried to install it on different cloud servers but it didn't work.
Can I compile it directly to get the executable file?

Looking forward to your next version.

Thanks :)

[SwiftSeal]

As it's a python program, I unfortunately cannot compile it into an executable! Could you run and give me the outputs of the following:
conda info
conda config --show-sources
conda list --show-channel-urls

That should help identify the problem. What I would recommend:

1. Try reinstalling conda, or alternatively use micromamba which will be faster and shouldn't experience that specific error.
2. If you have access to docker, podman, or apptainer, you can use the biocontainers image which should be stable across devices.
3. Try installing from source by downloading the latest release on github and running pip install .. This isn't my favourite approach as PyPi often struggles with the scikit-learn dependency (I believe this is due to an issue with setuptools on their end).

Thanks!

[lixiang117423]

👉👉👉➡️  conda info

     active environment : resistify_0.6.2
    active env location : /home/lixiang/mambaforge/envs/resistify_0.6.2
            shell level : 3
       user config file : /home/lixiang/.condarc
 populated config files : /home/lixiang/mambaforge/.condarc
                          /home/lixiang/.condarc
          conda version : 24.9.2
    conda-build version : not installed
         python version : 3.12.7.final.0
                 solver : libmamba (default)
       virtual packages : __archspec=1=cascadelake
                          __conda=24.9.2=0
                          __glibc=2.35=0
                          __linux=5.15.0=0
                          __unix=0=0
       base environment : /home/lixiang/mambaforge  (writable)
      conda av data dir : /home/lixiang/mambaforge/etc/conda
  conda av metadata url : None
           channel URLs : https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge/linux-64
                          https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge/noarch
                          https://mirrors.ustc.edu.cn/anaconda/pkgs/free/linux-64
                          https://mirrors.ustc.edu.cn/anaconda/pkgs/free/noarch
                          https://mirrors.ustc.edu.cn/anaconda/pkgs/main/linux-64
                          https://mirrors.ustc.edu.cn/anaconda/pkgs/main/noarch
                          https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64
                          https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/noarch
                          https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free/linux-64
                          https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free/noarch
                          https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main/linux-64
                          https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main/noarch
                          https://conda.anaconda.org/conda-forge/linux-64
                          https://conda.anaconda.org/conda-forge/noarch
          package cache : /home/lixiang/mambaforge/pkgs
                          /home/lixiang/.conda/pkgs
       envs directories : /home/lixiang/mambaforge/envs
                          /home/lixiang/.conda/envs
               platform : linux-64
             user-agent : conda/24.9.2 requests/2.32.3 CPython/3.12.7 Linux/5.15.0-92-generic ubuntu/22.04.3 glibc/2.35 solver/libmamba conda-libmamba-solver/24.9.0 libmambapy/1.5.9
                UID:GID : 1000:1000
             netrc file : None
           offline mode : False

👉👉👉➡️  conda config --show-sources
==> /home/lixiang/mambaforge/.condarc <==
channels:
  - conda-forge

==> /home/lixiang/.condarc <==
channels:
  - https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
  - https://mirrors.ustc.edu.cn/anaconda/pkgs/free
  - https://mirrors.ustc.edu.cn/anaconda/pkgs/main
  - https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
  - https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
  - https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main

👉👉👉➡️  conda list --show-channel-urls
# packages in environment at /home/lixiang/mambaforge/envs/resistify_0.6.2:
#
# Name                    Version                   Build  Channel

[SwiftSeal]

Hmmm it looks like you don't have anything installed in that environment, and you also don't have the bioconda channel listed which resistify is available on.

I have released a new version which should be easier to install, try:

conda create -n resistify -c conda-forge -c bioconda resistify

and it should work 👀

[SwiftSeal]

This issue is quite old so will now close - feel free to reopen if still experiencing issues!