I have ran into an issue installing QIIME. I previously installed the 2022.11 on my system with no issues. I'm guessing something has changed on my system, though I wanted to post in case someone else runs into this issue, or if it is in fact an issue with QIIME so people are aware
environment:
OSX Ventura 13.1 M1 Pro
Iterm in Rosetta mode
Commands:
wget https://data.qiime2.org/distro/core/qiime2-2022.11-py38-osx-conda.yml
CONDA_SUBDIR=osx-64 conda env create -n qiime2-2022.11 --file qiime2-2022.11-py38-osx-conda.yml
Error:
Collecting package metadata (repodata.json): done
Solving environment: done
Downloading and Extracting Packages
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
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/jhch/miniconda3/envs/qiime2-2022.11/bin/.bioconductor-genomeinfodbdata-post-link.sh
==> script messages <==
<None>
==> script output <==
stdout:
stderr: QIIME is caching your current deployment for improved performance. This may take a few moments and should only happen once per deployment.
++ dirname -- /Users/jhch/miniconda3/envs/qiime2-2022.11/bin/installBiocDataPackage.sh
+ SCRIPT_DIR=/Users/jhch/miniconda3/envs/qiime2-2022.11/bin/../share/bioconductor-data-packages
+ json=/Users/jhch/miniconda3/envs/qiime2-2022.11/bin/../share/bioconductor-data-packages/dataURLs.json
++ yq '."genomeinfodbdata-1.2.9".fn' /Users/jhch/miniconda3/envs/qiime2-2022.11/bin/../share/bioconductor-data-packages/dataURLs.json
+ FN='"GenomeInfoDbData_1.2.9.tar.gz"'
+ IFS=
+ read -r value
++ yq '."genomeinfodbdata-1.2.9".urls[]' /Users/jhch/miniconda3/envs/qiime2-2022.11/bin/../share/bioconductor-data-packages/dataURLs.json
+ URLS+=($value)
+ IFS=
+ read -r value
+ URLS+=($value)
+ IFS=
+ read -r value
+ URLS+=($value)
+ IFS=
+ read -r value
++ yq '."genomeinfodbdata-1.2.9".md5' /Users/jhch/miniconda3/envs/qiime2-2022.11/bin/../share/bioconductor-data-packages/dataURLs.json
+ MD5='"7cc138cfb74665fdfa8d1c244eac4879"'
+ STAGING=/Users/jhch/miniconda3/envs/qiime2-2022.11/share/genomeinfodbdata-1.2.9
+ mkdir -p /Users/jhch/miniconda3/envs/qiime2-2022.11/share/genomeinfodbdata-1.2.9
+ TARBALL='/Users/jhch/miniconda3/envs/qiime2-2022.11/share/genomeinfodbdata-1.2.9/"GenomeInfoDbData_1.2.9.tar.gz"'
+ SUCCESS=0
+ for URL in '${URLS[@]}'
++ echo '"https://bioconductor.org/packages/3.16/data/annotation/src/contrib/GenomeInfoDbData_1.2.9.tar.gz"'
++ tr -d '"'
+ URL=https://bioconductor.org/packages/3.16/data/annotation/src/contrib/GenomeInfoDbData_1.2.9.tar.gz
++ echo '"7cc138cfb74665fdfa8d1c244eac4879"'
++ tr -d '"'
+ MD5=7cc138cfb74665fdfa8d1c244eac4879
+ curl -L https://bioconductor.org/packages/3.16/data/annotation/src/contrib/GenomeInfoDbData_1.2.9.tar.gz
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
100 11.1M 100 11.1M 0 0 31.9M 0 --:--:-- --:--:-- --:--:-- 32.0M
+ [[ 0 == 0 ]]
++ uname -s
+ [[ Darwin == \L\i\n\u\x ]]
++ uname -s
+ [[ Darwin == \D\a\r\w\i\n ]]
++ md5 '/Users/jhch/miniconda3/envs/qiime2-2022.11/share/genomeinfodbdata-1.2.9/"GenomeInfoDbData_1.2.9.tar.gz"'
++ cut -f4 -d ' '
+ [[ 7cc138cfb74665fdfa8d1c244eac4879 == \7\c\c\1\3\8\c\f\b\7\4\6\6\5\f\d\f\a\8\d\1\c\2\4\4\e\a\c\4\8\7\9 ]]
+ SUCCESS=1
+ break
+ [[ 1 != 1 ]]
+ R CMD INSTALL --library=/Users/jhch/miniconda3/envs/qiime2-2022.11/lib/R/library '/Users/jhch/miniconda3/envs/qiime2-2022.11/share/genomeinfodbdata-1.2.9/"GenomeInfoDbData_1.2.9.tar.gz"'
During startup - Warning messages:
1: package ‘utils’ in options("defaultPackages") was not found
2: package ‘stats’ in options("defaultPackages") was not found
Error: .onLoad failed in loadNamespace() for 'utils', details:
call: options(op.utils[toset])
error: invalid value for 'editor'
return code: 1
kwargs:
{}
Traceback (most recent call last):
File "/Users/jhch/miniconda3/lib/python3.10/site-packages/conda/exceptions.py", line 1124, in __call__
return func(*args, **kwargs)
File "/Users/jhch/miniconda3/lib/python3.10/site-packages/conda_env/cli/main.py", line 78, in do_call
exit_code = getattr(module, func_name)(args, parser)
File "/Users/jhch/miniconda3/lib/python3.10/site-packages/conda/notices/core.py", line 109, in wrapper
return func(*args, **kwargs)
File "/Users/jhch/miniconda3/lib/python3.10/site-packages/conda_env/cli/main_create.py", line 154, in execute
result[installer_type] = installer.install(prefix, pkg_specs, args, env)
File "/Users/jhch/miniconda3/lib/python3.10/site-packages/conda_env/installers/conda.py", line 58, in install
unlink_link_transaction.execute()
File "/Users/jhch/miniconda3/lib/python3.10/site-packages/conda/core/link.py", line 286, in execute
self._execute(
File "/Users/jhch/miniconda3/lib/python3.10/site-packages/conda/core/link.py", line 761, in _execute
raise CondaMultiError(
conda.CondaMultiErrorclass: LinkError
message:
post-link script failed for package bioconda::bioconductor-genomeinfodbdata-1.2.9-r42hdfd78af_0
location of failed script: /Users/jhch/miniconda3/envs/qiime2-2022.11/bin/.bioconductor-genomeinfodbdata-post-link.sh
==> script messages <==
<None>
==> script output <==
stdout:
stderr: QIIME is caching your current deployment for improved performance. This may take a few moments and should only happen once per deployment.
++ dirname -- /Users/jhch/miniconda3/envs/qiime2-2022.11/bin/installBiocDataPackage.sh
+ SCRIPT_DIR=/Users/jhch/miniconda3/envs/qiime2-2022.11/bin/../share/bioconductor-data-packages
+ json=/Users/jhch/miniconda3/envs/qiime2-2022.11/bin/../share/bioconductor-data-packages/dataURLs.json
++ yq '."genomeinfodbdata-1.2.9".fn' /Users/jhch/miniconda3/envs/qiime2-2022.11/bin/../share/bioconductor-data-packages/dataURLs.json
+ FN='"GenomeInfoDbData_1.2.9.tar.gz"'
+ IFS=
+ read -r value
++ yq '."genomeinfodbdata-1.2.9".urls[]' /Users/jhch/miniconda3/envs/qiime2-2022.11/bin/../share/bioconductor-data-packages/dataURLs.json
+ URLS+=($value)
+ IFS=
+ read -r value
+ URLS+=($value)
+ IFS=
+ read -r value
+ URLS+=($value)
+ IFS=
+ read -r value
++ yq '."genomeinfodbdata-1.2.9".md5' /Users/jhch/miniconda3/envs/qiime2-2022.11/bin/../share/bioconductor-data-packages/dataURLs.json
+ MD5='"7cc138cfb74665fdfa8d1c244eac4879"'
+ STAGING=/Users/jhch/miniconda3/envs/qiime2-2022.11/share/genomeinfodbdata-1.2.9
+ mkdir -p /Users/jhch/miniconda3/envs/qiime2-2022.11/share/genomeinfodbdata-1.2.9
+ TARBALL='/Users/jhch/miniconda3/envs/qiime2-2022.11/share/genomeinfodbdata-1.2.9/"GenomeInfoDbData_1.2.9.tar.gz"'
+ SUCCESS=0
+ for URL in '${URLS[@]}'
++ echo '"https://bioconductor.org/packages/3.16/data/annotation/src/contrib/GenomeInfoDbData_1.2.9.tar.gz"'
++ tr -d '"'
+ URL=https://bioconductor.org/packages/3.16/data/annotation/src/contrib/GenomeInfoDbData_1.2.9.tar.gz
++ echo '"7cc138cfb74665fdfa8d1c244eac4879"'
++ tr -d '"'
+ MD5=7cc138cfb74665fdfa8d1c244eac4879
+ curl -L https://bioconductor.org/packages/3.16/data/annotation/src/contrib/GenomeInfoDbData_1.2.9.tar.gz
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
100 11.1M 100 11.1M 0 0 31.9M 0 --:--:-- --:--:-- --:--:-- 32.0M
+ [[ 0 == 0 ]]
++ uname -s
+ [[ Darwin == \L\i\n\u\x ]]
++ uname -s
+ [[ Darwin == \D\a\r\w\i\n ]]
++ md5 '/Users/jhch/miniconda3/envs/qiime2-2022.11/share/genomeinfodbdata-1.2.9/"GenomeInfoDbData_1.2.9.tar.gz"'
++ cut -f4 -d ' '
+ [[ 7cc138cfb74665fdfa8d1c244eac4879 == \7\c\c\1\3\8\c\f\b\7\4\6\6\5\f\d\f\a\8\d\1\c\2\4\4\e\a\c\4\8\7\9 ]]
+ SUCCESS=1
+ break
+ [[ 1 != 1 ]]
+ R CMD INSTALL --library=/Users/jhch/miniconda3/envs/qiime2-2022.11/lib/R/library '/Users/jhch/miniconda3/envs/qiime2-2022.11/share/genomeinfodbdata-1.2.9/"GenomeInfoDbData_1.2.9.tar.gz"'
During startup - Warning messages:
1: package ‘utils’ in options("defaultPackages") was not found
2: package ‘stats’ in options("defaultPackages") was not found
Error: .onLoad failed in loadNamespace() for 'utils', details:
call: options(op.utils[toset])
error: invalid value for 'editor'
return code: 1
kwargs:
{}
: <exception str() failed>
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/Users/jhch/miniconda3/bin/conda-env", line 7, in <module>
sys.exit(main())
File "/Users/jhch/miniconda3/lib/python3.10/site-packages/conda_env/cli/main.py", line 89, in main
return conda_exception_handler(do_call, args, parser)
File "/Users/jhch/miniconda3/lib/python3.10/site-packages/conda/exceptions.py", line 1424, in conda_exception_handler
return_value = exception_handler(func, *args, **kwargs)
File "/Users/jhch/miniconda3/lib/python3.10/site-packages/conda/exceptions.py", line 1127, in __call__
return self.handle_exception(exc_val, exc_tb)
File "/Users/jhch/miniconda3/lib/python3.10/site-packages/conda/exceptions.py", line 1156, in handle_exception
return self.handle_application_exception(exc_val, exc_tb)
File "/Users/jhch/miniconda3/lib/python3.10/site-packages/conda/exceptions.py", line 1170, in handle_application_exception
self._print_conda_exception(exc_val, exc_tb)
File "/Users/jhch/miniconda3/lib/python3.10/site-packages/conda/exceptions.py", line 1174, in _print_conda_exception
print_conda_exception(exc_val, exc_tb)
File "/Users/jhch/miniconda3/lib/python3.10/site-packages/conda/exceptions.py", line 1101, in print_conda_exception
stderrlog.error("\n%r\n", exc_val)
File "/Users/jhch/miniconda3/lib/python3.10/logging/__init__.py", line 1506, in error
self._log(ERROR, msg, args, **kwargs)
File "/Users/jhch/miniconda3/lib/python3.10/logging/__init__.py", line 1624, in _log
self.handle(record)
File "/Users/jhch/miniconda3/lib/python3.10/logging/__init__.py", line 1633, in handle
if (not self.disabled) and self.filter(record):
File "/Users/jhch/miniconda3/lib/python3.10/logging/__init__.py", line 821, in filter
result = f.filter(record)
File "/Users/jhch/miniconda3/lib/python3.10/site-packages/conda/gateways/logging.py", line 48, in filter
record.msg = record.msg % new_args
File "/Users/jhch/miniconda3/lib/python3.10/site-packages/conda/__init__.py", line 107, in __repr__
errs.append(e.__repr__())
File "/Users/jhch/miniconda3/lib/python3.10/site-packages/conda/__init__.py", line 62, in __repr__
return f"{self.__class__.__name__}: {self}"
File "/Users/jhch/miniconda3/lib/python3.10/site-packages/conda/__init__.py", line 66, in __str__
return str(self.message % self._kwargs)
ValueError: unsupported format character 'T' (0x54) at index 2094
Related Issues I Could Find
The solution proposed here conda clean --all -y did not fix my issue,I also tried removing conda and reinstalling
My issue doesn't seem to be related to downloading packages
I am going to continue investigating, and will post any information I can find
EDIT 1: I've tried this with x86 and arm64 distributions of Conda with python 3.8 and 3.10 all of which give the same error, so it doesn't appear to be a Conda version issue.
