Issues with glibc compatibility when install QIIME 2 2021.4

[sunkilmoon (Ben)]

Hi Keegan,

Good point. However, when trying

wget https://data.qiime2.org/distro/core/qiime2-2021.4-py38-linux-conda.yml
conda env create -n qiime2-2021.4 --file qiime2-2021.4-py38-linux-conda.yml

I find

Collecting package metadata: done

Solving environment: failed

ResolvePackageNotFound:

q2-feature-classifier=2021.4.0 -> q2-quality-control=2021.4 -> q2-taxa=2021.4 -> nodejs[version='>=15.14.0,<16.0a0'] -> __glibc[version='>=2.17,<3.0.a0']
q2-taxa=2021.4.0 -> nodejs[version='>=15.14.0,<16.0a0'] -> __glibc[version='>=2.17,<3.0.a0']
nodejs=15.14.0 -> __glibc[version='>=2.17,<3.0.a0']
q2-quality-control=2021.4.0 -> q2-taxa=2021.4 -> nodejs[version='>=15.14.0,<16.0a0'] -> __glibc[version='>=2.17,<3.0.a0']
q2-diversity=2021.4.0 -> nodejs[version='>=15.14.0,<16.0a0'] -> __glibc[version='>=2.17,<3.0.a0']
q2-demux=2021.4.0 -> nodejs[version='>=15.14.0,<16.0a0'] -> __glibc[version='>=2.17,<3.0.a0'] 

Would you have any pointers?

This post seems similar: https://forum.qiime2.org/t/qiime2-2018-11-installation-resolvepackagenotfound-error/7205/3

However, in their case the issue magically disappeared and it seems magic is not in my favour right now.

[thermokarst]

Hi @sunkilmoon - I moved this post into a new category, that way others can find it more easily.

Please run the following, and copy-and-paste the results here:

conda info

This will help us assess what is going on. Thanks!

[sunkilmoon (Ben)]

Wonderful, thanks Matt!

     active environment : None
            shell level : 0
       user config file : [redacted]/.condarc
 populated config files : [redacted]/.condarc
          conda version : 4.6.7
    conda-build version : 3.10.5
         python version : 3.6.5.final.0
       base environment : /opt/gridware/depots/8e896c5a/el7/pkg/apps/anaconda3/5.2.0/bin  (read only)
           channel URLs : [new users can only put 2 links I see]
          package cache : [redacted]/.conda/pkgs
                          /opt/apps/apps/binapps/anaconda3/2020.07/pkgs
       envs directories : [redacted]/.conda/envs
                          /opt/gridware/depots/8e896c5a/el7/pkg/apps/anaconda3/5.2.0/bin/envs
               platform : linux-64
             user-agent : conda/4.6.7 requests/2.18.4 CPython/3.6.5 Linux/3.10.0-1127.19.1.el7.x86_64 centos/7.9.2009 glibc/2.17
                UID:GID : 473363:10000
             netrc file : None
           offline mode : False

I tried conda clean --all

• it did not help.

Many thanks.

[thermokarst]

Thanks! That's just what I needed. Please note I edited your post to format as a code block.

There are two issues here, first, it looks like you might've skipped the first step in the install instructions. I say that because of this:

@sunkilmoon

conda version : 4.6.7

which means your conda is almost 2.5 years old - you'll need to update to a newer version of conda.

Besides the conda issue, you also appear to have a very old version of glibc

@sunkilmoon

glibc/2.17

This version of glibc is over 8 years old, which will be a problem when installing many packages via conda, including those on bioconda and conda-forge, which are all built with more recent versions of glibc. You'll have to chat with your sysadmin to reconcile that issue. This glibc version is why you saw the ResolvePackageNotFound errors above - this is a system-level package, not one that can installed or updated via conda.

I wish I had better news for you - keep us posted.

:qiime2: