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) ahmdef221@ucs-2:~$ 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 bytesClobberError: 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: OKdone
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