superclass "Mnumeric" not defined in the environment of the object's class

[emamm1 (Ahmed Dewedar)]

I had a diffrent issue posted before the blackout of the forum I find it relevant to this post so I replay here instead of creating a new post again

colinbrislawn Colin J Brislawn
February 8

Hello Ahmed,

Based on a quick google, folks were getting the

superclass "Mnumeric" not defined in the environment of the object's class

error when there was a problem with their installation.

Did get any errors when installing Qiime2 using conda? Have you had any other issues with R packages when using this environment?

Before we dive into the technical troubleshooting, it might be worth removing this environment and simply installing it again to see if that fixes the problem.

Let me know what you try next!

So I re-installed the qiime again to see if there is any problem as I cant remember from the first install

(base) [email protected]:~$ conda env create -n qiime2 --file qiime2-2021.11-py38-linux-conda.yml
Collecting package metadata (repodata.json): done
Solving environment: done
Preparing transaction: done
Verifying transaction: /
SafetyError: The package for r-base located at /home/ahmdef221/miniconda3/pkgs/r-base-4.0.5-hb93adac_3
appears to be corrupted. The path 'lib/R/doc/html/packages.html'
has an incorrect size.
reported size: 2946 bytes
actual size: 41608 bytes

ClobberError: This transaction has incompatible packages due to a shared path.
packages: bioconda/linux-64::perl-compress-raw-bzip2-2.087-pl526he1b5a44_0, bioconda/linux-64::perl-extutils-makemaker-7.36-pl526_1, bioconda/linux-64::perl-io-zlib-1.10-pl526_2, bioconda/linux-64::perl-archive-tar-2.18-pl526_3, bioconda/linux-64::perl-json-4.02-pl526_0
path: 'lib/5.26.2/x86_64-linux-thread-multi/perllocal.pod'

ClobberError: This transaction has incompatible packages due to a shared path.
packages: conda-forge/linux-64::openjdk-11.0.1-h516909a_1016, conda-forge/linux-64::freetype-2.10.4-h0708190_1
path: 'lib/libfreetype.so'

done
Executing transaction: | Enabling notebook extension jupyter-js-widgets/extension...
- Validating: OK

done

To activate this environment, use

$ conda activate qiime2

To deactivate an active environment, use

$ conda deactivate

Bsides I think I may have the same problems as I have diffrent versions of R on the env

.libPaths()
[1] "/home/ahmdef221/R/x86_64-pc-linux-gnu-library/3.4"
[2] "/opt/local/lib/R/site-library"
[3] "/usr/lib/R/site-library"
[4] "/usr/lib/R/library"

Any advise here

[colinbrislawn (Colin J Brislawn)]

Hello Ahmed,

Welcome back. Thanks for trying that.

I'm still seeing several errors, which is not good.

@emamm1

ClobberError: This transaction has incompatible packages due to a shared path.

@emamm1

SafetyError: The package for r-base located at /home/ahmdef221/miniconda3/pkgs/r-base-4.0.5-hb93adac_3
appears to be corrupted. The path 'lib/R/doc/html/packages.html'
has an incorrect size.

Double check the install instructions. Looks like you are using qiime2 as a conda environment, instead of qiime2-2021.11. While conda does not care about env names, I'm worried you may have other stuff installed into your qiime2 conda environment that may cause problems. Or maybe something else is messing with the install.

Keep in mind that all the qiime2 software should be installed by conda into that single conda env, and any other packages could cause compatibility issues.