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August 23, 2022 09:35
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Bioconductor package installation error
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ERROR conda.core.link:_execute(730): An error occurred while installing package 'bioconda::bioconductor-org.dm.eg.db-3.14.0-r41hdfd78af_0'. | |
Rolling back transaction: ...working... done | |
class: LinkError | |
message: | |
post-link script failed for package bioconda::bioconductor-org.dm.eg.db-3.14.0-r41hdfd78af_0 | |
location of failed script: /home/laptop/miniconda3/envs/__bioconductor-org.dm.eg.db@_uv_/bin/.bioconductor-org.dm.eg.db-post-link.sh | |
==> script messages <== | |
<None> | |
==> script output <== | |
stdout: /home/laptop/miniconda3/envs/__bioconductor-org.dm.eg.db@_uv_/share/bioconductor-org.dm.eg.db-3.14.0-0/org.Dm.eg.db_3.14.0.tar.gz: FAILED | |
/home/laptop/miniconda3/envs/__bioconductor-org.dm.eg.db@_uv_/share/bioconductor-org.dm.eg.db-3.14.0-0/org.Dm.eg.db_3.14.0.tar.gz: FAILED | |
/home/laptop/miniconda3/envs/__bioconductor-org.dm.eg.db@_uv_/share/bioconductor-org.dm.eg.db-3.14.0-0/org.Dm.eg.db_3.14.0.tar.gz: FAILED | |
ERROR: post-link.sh was unable to download any of the following URLs with the md5sum 1ae0c515970576d9b369116586cefbe6: | |
https://bioconductor.org/packages/3.14/data/annotation/src/contrib/org.Dm.eg.db_3.14.0.tar.gz | |
https://bioarchive.galaxyproject.org/org.Dm.eg.db_3.14.0.tar.gz | |
https://depot.galaxyproject.org/software/bioconductor-org.dm.eg.db/bioconductor-org.dm.eg.db_3.14.0_src_all.tar.gz | |
stderr: % Total % Received % Xferd Average Speed Time Time Time Current | |
Dload Upload Total Spent Left Speed | |
100 413 100 413 0 0 7076 0 --:--:-- --:--:-- --:--:-- 7120 | |
md5sum: WARNING: 1 computed checksum did NOT match | |
% Total % Received % Xferd Average Speed Time Time Time Current | |
Dload Upload Total Spent Left Speed | |
100 153 100 153 0 0 245 0 --:--:-- --:--:-- --:--:-- 245 | |
md5sum: WARNING: 1 computed checksum did NOT match | |
% Total % Received % Xferd Average Speed Time Time Time Current | |
Dload Upload Total Spent Left Speed | |
100 153 100 153 0 0 233 0 --:--:-- --:--:-- --:--:-- 233 | |
md5sum: WARNING: 1 computed checksum did NOT match | |
return code: 1 | |
kwargs: | |
{} | |
Traceback (most recent call last): | |
File "/home/laptop/miniconda3/lib/python3.9/site-packages/conda/exceptions.py", line 1114, in __call__ | |
return func(*args, **kwargs) | |
File "/home/laptop/miniconda3/lib/python3.9/site-packages/conda/cli/main.py", line 86, in main_subshell | |
exit_code = do_call(args, p) | |
File "/home/laptop/miniconda3/lib/python3.9/site-packages/conda/cli/conda_argparse.py", line 90, in do_call | |
return getattr(module, func_name)(args, parser) | |
File "/home/laptop/miniconda3/lib/python3.9/site-packages/conda/cli/main_create.py", line 41, in execute | |
install(args, parser, 'create') | |
File "/home/laptop/miniconda3/lib/python3.9/site-packages/conda/cli/install.py", line 327, in install | |
handle_txn(unlink_link_transaction, prefix, args, newenv) | |
File "/home/laptop/miniconda3/lib/python3.9/site-packages/conda/cli/install.py", line 356, in handle_txn | |
unlink_link_transaction.execute() | |
File "/home/laptop/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 "/home/laptop/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-org.dm.eg.db-3.14.0-r41hdfd78af_0 | |
location of failed script: /home/laptop/miniconda3/envs/__bioconductor-org.dm.eg.db@_uv_/bin/.bioconductor-org.dm.eg.db-post-link.sh | |
==> script messages <== | |
<None> | |
==> script output <== | |
stdout: /home/laptop/miniconda3/envs/__bioconductor-org.dm.eg.db@_uv_/share/bioconductor-org.dm.eg.db-3.14.0-0/org.Dm.eg.db_3.14.0.tar.gz: FAILED | |
/home/laptop/miniconda3/envs/__bioconductor-org.dm.eg.db@_uv_/share/bioconductor-org.dm.eg.db-3.14.0-0/org.Dm.eg.db_3.14.0.tar.gz: FAILED | |
/home/laptop/miniconda3/envs/__bioconductor-org.dm.eg.db@_uv_/share/bioconductor-org.dm.eg.db-3.14.0-0/org.Dm.eg.db_3.14.0.tar.gz: FAILED | |
ERROR: post-link.sh was unable to download any of the following URLs with the md5sum 1ae0c515970576d9b369116586cefbe6: | |
https://bioconductor.org/packages/3.14/data/annotation/src/contrib/org.Dm.eg.db_3.14.0.tar.gz | |
https://bioarchive.galaxyproject.org/org.Dm.eg.db_3.14.0.tar.gz | |
https://depot.galaxyproject.org/software/bioconductor-org.dm.eg.db/bioconductor-org.dm.eg.db_3.14.0_src_all.tar.gz | |
stderr: % Total % Received % Xferd Average Speed Time Time Time Current | |
Dload Upload Total Spent Left Speed | |
100 413 100 413 0 0 7076 0 --:--:-- --:--:-- --:--:-- 7120 | |
md5sum: WARNING: 1 computed checksum did NOT match | |
% Total % Received % Xferd Average Speed Time Time Time Current | |
Dload Upload Total Spent Left Speed | |
100 153 100 153 0 0 245 0 --:--:-- --:--:-- --:--:-- 245 | |
md5sum: WARNING: 1 computed checksum did NOT match | |
% Total % Received % Xferd Average Speed Time Time Time Current | |
Dload Upload Total Spent Left Speed | |
100 153 100 153 0 0 233 0 --:--:-- --:--:-- --:--:-- 233 | |
md5sum: WARNING: 1 computed checksum did NOT match | |
return code: 1 | |
kwargs: | |
{} | |
: <exception str() failed> | |
During handling of the above exception, another exception occurred: | |
Traceback (most recent call last): | |
File "/home/laptop/miniconda3/bin/conda", line 13, in <module> | |
sys.exit(main()) | |
File "/home/laptop/miniconda3/lib/python3.9/site-packages/conda/cli/main.py", line 128, in main | |
return conda_exception_handler(main, *args, **kwargs) | |
File "/home/laptop/miniconda3/lib/python3.9/site-packages/conda/exceptions.py", line 1404, in conda_exception_handler | |
return_value = exception_handler(func, *args, **kwargs) | |
File "/home/laptop/miniconda3/lib/python3.9/site-packages/conda/exceptions.py", line 1117, in __call__ | |
return self.handle_exception(exc_val, exc_tb) | |
File "/home/laptop/miniconda3/lib/python3.9/site-packages/conda/exceptions.py", line 1148, in handle_exception | |
return self.handle_application_exception(exc_val, exc_tb) | |
File "/home/laptop/miniconda3/lib/python3.9/site-packages/conda/exceptions.py", line 1162, in handle_application_exception | |
self._print_conda_exception(exc_val, exc_tb) | |
File "/home/laptop/miniconda3/lib/python3.9/site-packages/conda/exceptions.py", line 1166, in _print_conda_exception | |
print_conda_exception(exc_val, exc_tb) | |
File "/home/laptop/miniconda3/lib/python3.9/site-packages/conda/exceptions.py", line 1091, in print_conda_exception | |
stderrlog.error("\n%r\n", exc_val) | |
File "/home/laptop/miniconda3/lib/python3.9/logging/__init__.py", line 1475, in error | |
self._log(ERROR, msg, args, **kwargs) | |
File "/home/laptop/miniconda3/lib/python3.9/logging/__init__.py", line 1589, in _log | |
self.handle(record) | |
File "/home/laptop/miniconda3/lib/python3.9/logging/__init__.py", line 1598, in handle | |
if (not self.disabled) and self.filter(record): | |
File "/home/laptop/miniconda3/lib/python3.9/logging/__init__.py", line 806, in filter | |
result = f.filter(record) | |
File "/home/laptop/miniconda3/lib/python3.9/site-packages/conda/gateways/logging.py", line 51, in filter | |
record.msg = record.msg % new_args | |
File "/home/laptop/miniconda3/lib/python3.9/site-packages/conda/__init__.py", line 101, in __repr__ | |
errs.append(e.__repr__()) | |
File "/home/laptop/miniconda3/lib/python3.9/site-packages/conda/__init__.py", line 58, in __repr__ | |
return '%s: %s' % (self.__class__.__name__, str(self)) | |
File "/home/laptop/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 1106 | |
Remove all packages in environment /home/laptop/miniconda3/envs/__bioconductor-org.dm.eg.db@_uv_: | |
Collecting package metadata (current_repodata.json): ...working... done | |
Solving environment: ...working... ^Cfailed with repodata from current_repodata.json, will retry with next repodata source. | |
[2022-08-23 11:14:00 +0200] [163102] [INFO] Handling signal: int | |
CondaError: KeyboardInterrupt | |
^C[2022-08-23 11:14:01 +0200] [163102] [WARNING] Worker with pid 163119 was terminated due to signal 3 | |
[2022-08-23 11:14:01 +0200] [163102] [INFO] Shutting down: Master |
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