Unable to install QIIME2 on Mac OS 10

Giuseppe_Troiano · August 12, 2022, 4:42pm

Dears,
I'm not able to install QIIME 2 on my MAC. I was able to install Miniconda but when I run the following command:

conda env create -n qiime2-2022.2 --file qiime2-2022.2-py38-osx-conda.yml

I get some errors and QIIME 2 doesn't work.

Collecting package metadata (repodata.json): done
Solving environment: done

stderr: QIIME is caching your current deployment for improved performance. This may take a few moments and should only happen once per deployment.
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
100 416 100 416 0 0 1752 0 --:--:-- --:--:-- --:--:-- 1755
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
100 153 100 153 0 0 181 0 --:--:-- --:--:-- --:--:-- 181
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
100 153 100 153 0 0 167 0 --:--:-- --:--:-- --:--:-- 167

return code: 1

kwargs:
{}

Traceback (most recent call last):
File "/Users/imac/opt/miniconda3/lib/python3.9/site-packages/conda/exceptions.py", line 1114, in call
return func(*args, **kwargs)
File "/Users/imac/opt/miniconda3/lib/python3.9/site-packages/conda_env/cli/main.py", line 80, in do_call
exit_code = getattr(module, func_name)(args, parser)
File "/Users/imac/opt/miniconda3/lib/python3.9/site-packages/conda_env/cli/main_create.py", line 143, in execute
result[installer_type] = installer.install(prefix, pkg_specs, args, env)
File "/Users/imac/opt/miniconda3/lib/python3.9/site-packages/conda_env/installers/conda.py", line 59, in install
unlink_link_transaction.execute()
File "/Users/imac/opt/miniconda3/lib/python3.9/site-packages/conda/core/link.py", line 281, in execute
self._execute(tuple(concat(interleave(self.prefix_action_groups.values()))))
File "/Users/imac/opt/miniconda3/lib/python3.9/site-packages/conda/core/link.py", line 744, in _execute
raise CondaMultiError(tuple(concatv(
conda.CondaMultiErrorclass: LinkError
message:
post-link script failed for package bioconda::bioconductor-genomeinfodbdata-1.2.7-r41hdfd78af_1
location of failed script: /Users/imac/opt/miniconda3/envs/qiime2-2022.2/bin/.bioconductor-genomeinfodbdata-post-link.sh
==> script messages <==

==> script output <==
stdout: ERROR: post-link.sh was unable to download any of the following URLs with the md5sum 74c82f26111062a9ceb3c5331088cd56:
https://bioconductor.org/packages/3.14/data/annotation/src/contrib/GenomeInfoDbData_1.2.7.tar.gz
https://bioarchive.galaxyproject.org/GenomeInfoDbData_1.2.7.tar.gz
https://depot.galaxyproject.org/software/bioconductor-genomeinfodbdata/bioconductor-genomeinfodbdata_1.2.7_src_all.tar.gz

stderr: QIIME is caching your current deployment for improved performance. This may take a few moments and should only happen once per deployment.
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
100 416 100 416 0 0 1752 0 --:--:-- --:--:-- --:--:-- 1755
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
100 153 100 153 0 0 181 0 --:--:-- --:--:-- --:--:-- 181
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
100 153 100 153 0 0 167 0 --:--:-- --:--:-- --:--:-- 167

return code: 1

kwargs:
{}

: <exception str() failed>

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "/Users/imac/opt/miniconda3/bin/conda-env", line 7, in
sys.exit(main())
File "/Users/imac/opt/miniconda3/lib/python3.9/site-packages/conda_env/cli/main.py", line 91, in main
return conda_exception_handler(do_call, args, parser)
File "/Users/imac/opt/miniconda3/lib/python3.9/site-packages/conda/exceptions.py", line 1404, in conda_exception_handler
return_value = exception_handler(func, *args, **kwargs)
File "/Users/imac/opt/miniconda3/lib/python3.9/site-packages/conda/exceptions.py", line 1117, in call
return self.handle_exception(exc_val, exc_tb)
File "/Users/imac/opt/miniconda3/lib/python3.9/site-packages/conda/exceptions.py", line 1148, in handle_exception
return self.handle_application_exception(exc_val, exc_tb)
File "/Users/imac/opt/miniconda3/lib/python3.9/site-packages/conda/exceptions.py", line 1162, in handle_application_exception
self._print_conda_exception(exc_val, exc_tb)
File "/Users/imac/opt/miniconda3/lib/python3.9/site-packages/conda/exceptions.py", line 1166, in _print_conda_exception
print_conda_exception(exc_val, exc_tb)
File "/Users/imac/opt/miniconda3/lib/python3.9/site-packages/conda/exceptions.py", line 1091, in print_conda_exception
stderrlog.error("\n%r\n", exc_val)
File "/Users/imac/opt/miniconda3/lib/python3.9/logging/init.py", line 1475, in error
self._log(ERROR, msg, args, **kwargs)
File "/Users/imac/opt/miniconda3/lib/python3.9/logging/init.py", line 1589, in _log
self.handle(record)
File "/Users/imac/opt/miniconda3/lib/python3.9/logging/init.py", line 1598, in handle
if (not self.disabled) and self.filter(record):
File "/Users/imac/opt/miniconda3/lib/python3.9/logging/init.py", line 806, in filter
result = f.filter(record)
File "/Users/imac/opt/miniconda3/lib/python3.9/site-packages/conda/gateways/logging.py", line 51, in filter
record.msg = record.msg % new_args
File "/Users/imac/opt/miniconda3/lib/python3.9/site-packages/conda/init.py", line 101, in repr
errs.append(e.repr())
File "/Users/imac/opt/miniconda3/lib/python3.9/site-packages/conda/init.py", line 58, in repr
return '%s: %s' % (self.class.name, str(self))
File "/Users/imac/opt/miniconda3/lib/python3.9/site-packages/conda/init.py", line 62, in str
return str(self.message % self._kwargs)
ValueError: unsupported format character 'T' (0x54) at index 835
(base) imac@MacBook-Pro-4 ~ % conda activate qiime2-2022.2
(qiime2-2022.2) imac@MacBook-Pro-4 ~ % qiime --help
zsh: command not found: qiime

Sorry if I have disturbed you.

Regards

Giuseppe Troiano

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colinbrislawn · August 14, 2022, 11:45am

This seems to be an issue with the bioconductor-genomeinfodbdata package.

You are not the only one having this issue. GitHub bioconda issue #13846, also #36436

Thanks for letting us know. Hang tight while we sort this out...

Oddant1 · August 16, 2022, 9:03pm

Hello @Giuseppe_Troiano, you should be able to able to install QIIME 2 now if you try again. Thank you.

Giuseppe_Troiano · August 17, 2022, 11:20am

It works!!!! Thank you very much!!!

system · September 17, 2022, 5:21pm

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