I aim to install QIIME2-2022.11 on Mac. I encounter the following error similar to (Error to install qiime2-2022.2 with conda). The recommendation involve a Mac with a M1 chip, but my Mac is working with a Intel Core-i9. May I have any suggestion please?
Here is the code I ran after installing Miniconda3, following the installation guide:
ERROR conda.core.link:_execute(733): An error occurred while installing package 'bioconda::bioconductor-genomeinfodbdata-1.2.9-r42hdfd78af_0'.
Rolling back transaction: done
class: LinkError
message:
post-link script failed for package bioconda::bioconductor-genomeinfodbdata-1.2.9-r42hdfd78af_0
location of failed script: /Users/freshlab/miniforge3/envs/qiime2-2022.11/bin/.bioconductor-genomeinfodbdata-post-link.sh
==> script messages <==
<None>
==> script output <==
stdout: ERROR: post-link.sh was unable to download any of the following URLs with the md5sum 7cc138cfb74665fdfa8d1c244eac4879:
"https://bioconductor.org/packages/3.16/data/annotation/src/contrib/GenomeInfoDbData_1.2.9.tar.gz"
"https://bioarchive.galaxyproject.org/GenomeInfoDbData_1.2.9.tar.gz"
"https://depot.galaxyproject.org/software/bioconductor-genomeinfodbdata/bioconductor-genomeinfodbdata_1.2.9_src_all.tar.gz"
Plus many lines...
After the error, I am able to activate the qiime2-2022.11 environment by: conda activate qiime2-2022.11
but when running: qiime --help
The command was not found. zsh: command not found: qiime
Updates:
I try to install qiime2-2022.11 on another Mac, it works fine. So I am wondering would it be a problem on my device.
I try to manually install bioconductor-genomeinfodbdata, but remains unsuccessful. May I ask am I on the right path of solving the issue?
yes, env will be activated as it is created before packages are installed. So this behavior is expected.
Try to delete the env, run conda clean -a, and run installation again.
Can you please provide the terminal output for the following commands:
conda env list
conda --version
I suspect there's still something going on with your conda configuration - I haven't had any issues installing QIIME 2 2022.11 on my Intel Macbook, and we haven't received any other reports of this since the latest release. Either way, we'll get to the bottom of it!
Your version of conda is up to date, but I am wondering if the multiple miniconda instances are what's causing problems here. Can you delete the miniconda instance that's located at /Users/freshlab/opt/miniconda3? Once that's done, I would delete your 2022.11 environment, run conda clean --all once more, and then try a fresh install. Let's see if that resolves the issue!
Thanks for the suggestion!
I firstly remove extra conda environment (only base is kept). Then re-install qiime2 following the standard approach again.
This time something different display on terminal, but generally the same error.
Here is the a few lines of the error:
ERROR conda.core.link:_execute(745): An error occurred while installing package 'bioconda::bioconductor-genomeinfodbdata-1.2.9-r42hdfd78af_0'.
Rolling back transaction: done
class: LinkError
message:
post-link script failed for package bioconda::bioconductor-genomeinfodbdata-1.2.9-r42hdfd78af_0
location of failed script: /Users/freshlab/anaconda3/envs/qiime2-2022.11/bin/.bioconductor-genomeinfodbdata-post-link.sh
==> script messages <==
<None>
==> script output <==
stdout: ERROR: post-link.sh was unable to download any of the following URLs with the md5sum 7cc138cfb74665fdfa8d1c244eac4879:
"https://bioconductor.org/packages/3.16/data/annotation/src/contrib/GenomeInfoDbData_1.2.9.tar.gz"
"https://bioarchive.galaxyproject.org/GenomeInfoDbData_1.2.9.tar.gz"
"https://depot.galaxyproject.org/software/bioconductor-genomeinfodbdata/bioconductor-genomeinfodbdata_1.2.9_src_all.tar.gz"
This is interesting - I'm curious if our development environment will work for you to install. Can you try a fresh install of QIIME 2 using these instructions: https://dev.qiime2.org/latest/quickstart/
You can rename the environment 2022.11 if that's helpful for you - this environment contains all features from 2022.11 release, along with a few new changes from our current development cycle.
If this doesn't work, please provide your full command list (copy/pasted from terminal) along with the error message you receive (if it's different from the above message). Thanks!
going on with your conda configuration - I haven't had any issues installing QIIME 2 2022.11 on my Intel Macbook, and we haven't received any other reports of this since the latest release. Either way, we'll get to the bottom of it! 
