ERROR conda.core.link:_execute(730)

[xuanxuan-Jin]

Describe the bug ERROR conda.core.link:_execute(730): An error occurred while installing package 'bioconda::bioconductor-genomeinfodbdata-1.2.1-r351_0'.

To Reproduce Could not create conda environment from /lustre/grp/bitcap/jinxx/source/varCA/rules/../envs/prepare.yml: Expected behavior A clear and concise description of what you expected to happen.

here is my log file : Building DAG of jobs... Creating conda environment envs/prepare.yml... Downloading and installing remote packages. CreateCondaEnvironmentException: Could not create conda environment from /lustre/grp/bitcap/jinxx/source/varCA/rules/../envs/prepare.yml: Collecting package metadata (repodata.json): ...working... done Solving environment: ...working... done Preparing transaction: ...working... done Verifying transaction: ...working... done Executing transaction: ...working... done ERROR conda.core.link:_execute(730): An error occurred while installing package 'bioconda::bioconductor-genomeinfodbdata-1.2.1-r351_0'. Rolling back transaction: ...working... done class: LinkError message: post-link script failed for package bioconda::bioconductor-genomeinfodbdata-1.2.1-r351_0 location of failed script: /lustre/grp/bitcap/jinxx/source/varCA/.snakemake/conda/942e2afa/bin/.bioconductor-genomeinfodbdata-post-link.sh ==> script messages <== <None> ==> script output <== stdout: /lustre/grp/bitcap/jinxx/source/varCA/.snakemake/conda/942e2afa/share/bioconductor-genomeinfodbdata-1.2.1-0/GenomeInfoDbData_1.2.1.tar.gz: FAILED ERROR: post-link.sh was unable to download any of the following URLs with the md5sum 2fd536521151e2ff37217b5cfee8cec4: https://bioconductor.org/packages/3.9/data/annotation/src/contrib/GenomeInfoDbData_1.2.1.tar.gz https://bioarchive.galaxyproject.org/GenomeInfoDbData_1.2.1.tar.gz https://depot.galaxyproject.org/software/bioconductor-genomeinfodbdata/bioconductor-genomeinfodbdata_1.2.1_src_all.tar.gz

stderr: % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 100 415 100 415 0 0 374 0 0:00:01 0:00:01 --:--:-- 374 md5sum: WARNING: 1 computed checksum did NOT match % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- 0:00:03 --:--:-- 0 curl: (7) Failed to connect to bioarchive.galaxyproject.org port 443: No route to host % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- 0:00:03 --:--:-- 0 curl: (7) Failed to connect to depot.galaxyproject.org port 443: No route to host

return code: 1

kwargs: {}

Traceback (most recent call last): File "/lustre/grp/bitcap/jinxx/miniconda3/lib/python3.9/site-packages/conda/exceptions.py", line 1082, in call return func(*args, **kwargs) File "/lustre/grp/bitcap/jinxx/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 "/lustre/grp/bitcap/jinxx/miniconda3/lib/python3.9/site-packages/conda_env/cli/main_create.py", line 142, in execute result[installer_type] = installer.install(prefix, pkg_specs, args, env) File "/lustre/grp/bitcap/jinxx/miniconda3/lib/python3.9/site-packages/conda_env/installers/conda.py", line 59, in install unlink_link_transaction.execute() File "/lustre/grp/bitcap/jinxx/miniconda3/lib/python3.9/site-packages/conda/core/link.py", line 281, in execute self._execute(tuple(concat(interleave(itervalues(self.prefix_action_groups))))) File "/lustre/grp/bitcap/jinxx/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-1.2.1-r351_0 location of failed script: /lustre/grp/bitcap/jinxx/source/varCA/.snakemake/conda/942e2afa/bin/.bioconductor-genomeinfodbdata-post-link.sh ==> script messages <== <None> ==> script output <== stdout: /lustre/grp/bitcap/jinxx/source/varCA/.snakemake/conda/942e2afa/share/bioconductor-genomeinfodbdata-1.2.1-0/GenomeInfoDbData_1.2.1.tar.gz: FAILED ERROR: post-link.sh was unable to download any of the following URLs with the md5sum 2fd536521151e2ff37217b5cfee8cec4: https://bioconductor.org/packages/3.9/data/annotation/src/contrib/GenomeInfoDbData_1.2.1.tar.gz https://bioarchive.galaxyproject.org/GenomeInfoDbData_1.2.1.tar.gz https://depot.galaxyproject.org/software/bioconductor-genomeinfodbdata/bioconductor-genomeinfodbdata_1.2.1_src_all.tar.gz

stderr: % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 100 415 100 415 0 0 374 0 0:00:01 0:00:01 --:--:-- 374 md5sum: WARNING: 1 computed checksum did NOT match % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- 0:00:03 --:--:-- 0 curl: (7) Failed to connect to bioarchive.galaxyproject.org port 443: No route to host % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- 0:00:03 --:--:-- 0 curl: (7) Failed to connect to depot.galaxyproject.org port 443: No route to host

return code: 1

kwargs: {}

: <exception str() failed>

During handling of the above exception, another exception occurred:

Traceback (most recent call last): File "/lustre/grp/bitcap/jinxx/miniconda3/bin/conda-env", line 7, in sys.exit(main()) File "/lustre/grp/bitcap/jinxx/miniconda3/lib/python3.9/site-packages/conda_env/cli/main.py", line 91, in main return conda_exception_handler(do_call, args, parser) File "/lustre/grp/bitcap/jinxx/miniconda3/lib/python3.9/site-packages/conda/exceptions.py", line 1374, in conda_exception_handler return_value = exception_handler(func, *args, **kwargs) File "/lustre/grp/bitcap/jinxx/miniconda3/lib/python3.9/site-packages/conda/exceptions.py", line 1085, in call return self.handle_exception(exc_val, exc_tb) File "/lustre/grp/bitcap/jinxx/miniconda3/lib/python3.9/site-packages/conda/exceptions.py", line 1116, in handle_exception return self.handle_application_exception(exc_val, exc_tb) File "/lustre/grp/bitcap/jinxx/miniconda3/lib/python3.9/site-packages/conda/exceptions.py", line 1132, in handle_application_exception self._print_conda_exception(exc_val, exc_tb) File "/lustre/grp/bitcap/jinxx/miniconda3/lib/python3.9/site-packages/conda/exceptions.py", line 1136, in _print_conda_exception print_conda_exception(exc_val, exc_tb) File "/lustre/grp/bitcap/jinxx/miniconda3/lib/python3.9/site-packages/conda/exceptions.py", line 1059, in print_conda_exception stderrlog.error("\n%r\n", exc_val) File "/lustre/grp/bitcap/jinxx/miniconda3/lib/python3.9/logging/init.py", line 1475, in error self._log(ERROR, msg, args, **kwargs) File "/lustre/grp/bitcap/jinxx/miniconda3/lib/python3.9/logging/init.py", line 1589, in _log self.handle(record) File "/lustre/grp/bitcap/jinxx/miniconda3/lib/python3.9/logging/init.py", line 1598, in handle if (not self.disabled) and self.filter(record): File "/lustre/grp/bitcap/jinxx/miniconda3/lib/python3.9/logging/init.py", line 806, in filter result = f.filter(record) File "/lustre/grp/bitcap/jinxx/miniconda3/lib/python3.9/site-packages/conda/gateways/logging.py", line 61, in filter record.msg = record.msg % new_args File "/lustre/grp/bitcap/jinxx/miniconda3/lib/python3.9/site-packages/conda/init.py", line 132, in repr errs.append(e.repr()) File "/lustre/grp/bitcap/jinxx/miniconda3/lib/python3.9/site-packages/conda/init.py", line 71, in repr return '%s: %s' % (self.class.name, text_type(self)) File "/lustre/grp/bitcap/jinxx/miniconda3/lib/python3.9/site-packages/conda/init.py", line 90, in str return text_type(self.message % self._kwargs) ValueError: unsupported format character 'T' (0x54) at index 852

File "/lustre/grp/bitcap/jinxx/miniconda3/envs/snakemake/lib/python3.10/site-packages/snakemake/deployment/conda.py", line 333, in create