Hello!
I tried to install qiime2-2023.2 with miniconda3 under Windows Subsystem for Linux but met error message.
The error message was below.
ERROR conda.core.link:_execute(740): 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: /home/elaine/miniconda3/envs/qiime2-2023.2/bin/.bioconductor-genomeinfodbdata-post-link.sh
==> script messages <==
==> 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 -- /home/elaine/miniconda3/envs/qiime2-2023.2/bin/installBiocDataPackage.sh
- SCRIPT_DIR=/home/elaine/miniconda3/envs/qiime2-2023.2/bin/../share/bioconductor-data-packages
- json=/home/elaine/miniconda3/envs/qiime2-2023.2/bin/../share/bioconductor-data-packages/dataURLs.json
++ yq '."genomeinfodbdata-1.2.9".fn' /home/elaine/miniconda3/envs/qiime2-2023.2/bin/../share/bioconductor-data-packages/dataURLs.json - FN='"GenomeInfoDbData_1.2.9.tar.gz"'
++ yq '."genomeinfodbdata-1.2.9".urls' /home/elaine/miniconda3/envs/qiime2-2023.2/bin/../share/bioconductor-data-packages/dataURLs.json - IFS=
- read -r value
- URLS+=($value)
- IFS=
- read -r value
- URLS+=($value)
- IFS=
- read -r value
- URLS+=($value)
- IFS=
- read -r value
++ yq '."genomeinfodbdata-1.2.9".md5' /home/elaine/miniconda3/envs/qiime2-2023.2/bin/../share/bioconductor-data-packages/dataURLs.json - MD5='"7cc138cfb74665fdfa8d1c244eac4879"'
- STAGING=/home/elaine/miniconda3/envs/qiime2-2023.2/share/genomeinfodbdata-1.2.9
- mkdir -p /home/elaine/miniconda3/envs/qiime2-2023.2/share/genomeinfodbdata-1.2.9
- TARBALL='/home/elaine/miniconda3/envs/qiime2-2023.2/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
0 0 0 0 0 0 0 0 --:--:-- 0:00:19 --:--:-- 0curl: (6) Could not resolve host: bioconductor.org
return code: 6
kwargs:
{}
Traceback (most recent call last):
File "/home/elaine/miniconda3/lib/python3.10/site-packages/conda/exceptions.py", line 1132, in call
return func(*args, **kwargs)
File "/home/elaine/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 "/home/elaine/miniconda3/lib/python3.10/site-packages/conda/notices/core.py", line 121, in wrapper
return func(*args, **kwargs)
File "/home/elaine/miniconda3/lib/python3.10/site-packages/conda_env/cli/main_create.py", line 152, in execute
result[installer_type] = installer.install(prefix, pkg_specs, args, env)
File "/home/elaine/miniconda3/lib/python3.10/site-packages/conda_env/installers/conda.py", line 62, in install
unlink_link_transaction.execute()
File "/home/elaine/miniconda3/lib/python3.10/site-packages/conda/core/link.py", line 283, in execute
self._execute(tuple(chain(*chain(*zip(*self.prefix_action_groups.values())))))
File "/home/elaine/miniconda3/lib/python3.10/site-packages/conda/core/link.py", line 756, 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: /home/elaine/miniconda3/envs/qiime2-2023.2/bin/.bioconductor-genomeinfodbdata-post-link.sh
==> script messages <==
==> 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 -- /home/elaine/miniconda3/envs/qiime2-2023.2/bin/installBiocDataPackage.sh
- SCRIPT_DIR=/home/elaine/miniconda3/envs/qiime2-2023.2/bin/../share/bioconductor-data-packages
- json=/home/elaine/miniconda3/envs/qiime2-2023.2/bin/../share/bioconductor-data-packages/dataURLs.json
++ yq '."genomeinfodbdata-1.2.9".fn' /home/elaine/miniconda3/envs/qiime2-2023.2/bin/../share/bioconductor-data-packages/dataURLs.json - FN='"GenomeInfoDbData_1.2.9.tar.gz"'
++ yq '."genomeinfodbdata-1.2.9".urls' /home/elaine/miniconda3/envs/qiime2-2023.2/bin/../share/bioconductor-data-packages/dataURLs.json - IFS=
- read -r value
- URLS+=($value)
- IFS=
- read -r value
- URLS+=($value)
- IFS=
- read -r value
- URLS+=($value)
- IFS=
- read -r value
++ yq '."genomeinfodbdata-1.2.9".md5' /home/elaine/miniconda3/envs/qiime2-2023.2/bin/../share/bioconductor-data-packages/dataURLs.json - MD5='"7cc138cfb74665fdfa8d1c244eac4879"'
- STAGING=/home/elaine/miniconda3/envs/qiime2-2023.2/share/genomeinfodbdata-1.2.9
- mkdir -p /home/elaine/miniconda3/envs/qiime2-2023.2/share/genomeinfodbdata-1.2.9
- TARBALL='/home/elaine/miniconda3/envs/qiime2-2023.2/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
0 0 0 0 0 0 0 0 --:--:-- 0:00:19 --:--:-- 0curl: (6) Could not resolve host: bioconductor.org
return code: 6
kwargs:
{}
: <exception str() failed>
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/elaine/miniconda3/bin/conda-env", line 7, in
sys.exit(main())
File "/home/elaine/miniconda3/lib/python3.10/site-packages/conda_env/cli/main.py", line 89, in main
return conda_exception_handler(do_call, args, parser)
File "/home/elaine/miniconda3/lib/python3.10/site-packages/conda/exceptions.py", line 1432, in conda_exception_handler return_value = exception_handler(func, *args, **kwargs)
File "/home/elaine/miniconda3/lib/python3.10/site-packages/conda/exceptions.py", line 1135, in call
return self.handle_exception(exc_val, exc_tb)
File "/home/elaine/miniconda3/lib/python3.10/site-packages/conda/exceptions.py", line 1164, in handle_exception
return self.handle_application_exception(exc_val, exc_tb)
File "/home/elaine/miniconda3/lib/python3.10/site-packages/conda/exceptions.py", line 1178, in handle_application_exception
self._print_conda_exception(exc_val, exc_tb)
File "/home/elaine/miniconda3/lib/python3.10/site-packages/conda/exceptions.py", line 1182, in _print_conda_exception
print_conda_exception(exc_val, exc_tb)
File "/home/elaine/miniconda3/lib/python3.10/site-packages/conda/exceptions.py", line 1109, in print_conda_exception
stderrlog.error("\n%r\n", exc_val)
File "/home/elaine/miniconda3/lib/python3.10/logging/init.py", line 1506, in error
self._log(ERROR, msg, args, **kwargs)
File "/home/elaine/miniconda3/lib/python3.10/logging/init.py", line 1624, in _log
self.handle(record)
File "/home/elaine/miniconda3/lib/python3.10/logging/init.py", line 1633, in handle
if (not self.disabled) and self.filter(record):
File "/home/elaine/miniconda3/lib/python3.10/logging/init.py", line 821, in filter
result = f.filter(record)
File "/home/elaine/miniconda3/lib/python3.10/site-packages/conda/gateways/logging.py", line 48, in filter
record.msg = record.msg % new_args
File "/home/elaine/miniconda3/lib/python3.10/site-packages/conda/init.py", line 99, in repr
errs.append(e.repr())
File "/home/elaine/miniconda3/lib/python3.10/site-packages/conda/init.py", line 54, in repr
return f"{self.class.name}: {self}"
File "/home/elaine/miniconda3/lib/python3.10/site-packages/conda/init.py", line 58, in str
return str(self.message % self._kwargs)
ValueError: unsupported format character 'T' (0x54) at index 2092
It seemed to have some problem to install genomeinfodbdata-1.2.9. I tried to install genomeinfodbdata independently but still saw the similar message. Any idea on how to solve it? Many thanks.
Elaine