conda install error with qiime2-2023.2

Technical Support
1

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

2
3

Hello @elaine.xu, the primary cause of this error appears to be:

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

This looks like a transient issue that was most likely caused by their server being down at the time your install attempted to access it. I was able to run that curl command in my terminal right now. Can you run the installation of QIIME 2 from the beginning again and let us know if it still doesn't work? Thank you.

4

Thanks for your reply, Oddant1. I tried to re-install Qiime2 but still met the same error message. I tried to get the package independently by curl command. Also saw the same error message. Any suggestion to solve this problem?

Elaine

5

Are you installing QIIME 2 on a laptop you own or is this an institutional cluster or what? Additionally, if it is a laptop you own, is it on an institution's wifi? It is possible that the host the curl command is targeting is blocked on your internet.

6

Hi Oddant, Thanks for your quick reply. I installed QIIME2 on my own laptop by a private wifi. I successfully downloaded this package with the same link by wget instead of curl. I have no idea on how to modify this command during the installation of QIIME2. Any suggestion? Thanks.

7

@elaine.xu, unfortunately there is no good way to replace curl with wget in the command. That install script is not written by us it is a part of the dependency. It is very strange that you can wget the file but not curl it. Just about the only thing I can think of at this point is disabling the firewall on your laptop and trying again just make sure to turn the firewall back on afterwards. Usually when we see an issue like this, it is just a transient issue to do with their server being down when the curl runs.