Hello,
I am trying to natively install qiime2-2019.7 on my Mac OS High Sierra. I ran the command below:
conda env create -n qiime2-2019.7 --file qiime2-2019.7-py36-osx-conda.yml
The error message I keep getting is as follows
conda env create -n qiime2-2019.7 --file qiime2-2019.7-py36-osx-conda.yml
Collecting package metadata (repodata.json): done
Solving environment: done
Preparing transaction: done
Verifying transaction: done
Executing transaction: / b'Enabling notebook extension jupyter-js-widgets/extension...\n - Validating: \x1b[32mOK\x1b[0m\n'
done
ERROR conda.core.link:_execute(700): An error occurred while installing package 'bioconda::bioconductor-genomeinfodbdata-1.2.1-r351_0'.
Rolling back transaction: done
class: LinkError
message:
post-link script failed for package bioconda::bioconductor-genomeinfodbdata-1.2.1-r351_0
location of failed script: /Users/ylor/miniconda3/envs/qiime2-2019.7/bin/.bioconductor-genomeinfodbdata-post-link.sh
==> script messages <==
==> script output <==
stdout: 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.gzstderr: % Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
curl: (60) SSL certificate problem: unable to get local issuer certificate
More details here: curl - SSL CA Certificatescurl failed to verify the legitimacy of the server and therefore could not
establish a secure connection to it. To learn more about this situation and
how to fix it, please visit the web page mentioned above.
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
curl: (60) SSL certificate problem: unable to get local issuer certificate
More details here: curl - SSL CA Certificatescurl failed to verify the legitimacy of the server and therefore could not
establish a secure connection to it. To learn more about this situation and
how to fix it, please visit the web page mentioned above.
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
curl: (60) SSL certificate problem: unable to get local issuer certificate
More details here: curl - SSL CA Certificatescurl failed to verify the legitimacy of the server and therefore could not
establish a secure connection to it. To learn more about this situation and
how to fix it, please visit the web page mentioned above.return code: 1
kwargs:
{}Traceback (most recent call last):
File "/Users/ylor/miniconda3/lib/python3.7/site-packages/conda/exceptions.py", line 1074, in call
return func(*args, **kwargs)
File "/Users/ylor/miniconda3/lib/python3.7/site-packages/conda_env/cli/main.py", line 78, in do_call
exit_code = getattr(module, func_name)(args, parser)
File "/Users/ylor/miniconda3/lib/python3.7/site-packages/conda_env/cli/main_create.py", line 102, in execute
result[installer_type] = installer.install(prefix, pkg_specs, args, env)
File "/Users/ylor/miniconda3/lib/python3.7/site-packages/conda_env/installers/conda.py", line 32, in install
unlink_link_transaction.execute()
File "/Users/ylor/miniconda3/lib/python3.7/site-packages/conda/core/link.py", line 249, in execute
self._execute(tuple(concat(interleave(itervalues(self.prefix_action_groups)))))
File "/Users/ylor/miniconda3/lib/python3.7/site-packages/conda/core/link.py", line 716, in _execute
rollback_excs,
conda.CondaMultiErrorclass: LinkError
message:
post-link script failed for package bioconda::bioconductor-genomeinfodbdata-1.2.1-r351_0
location of failed script: /Users/ylor/miniconda3/envs/qiime2-2019.7/bin/.bioconductor-genomeinfodbdata-post-link.sh
==> script messages <==
==> script output <==
stdout: 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.gzstderr: % Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
curl: (60) SSL certificate problem: unable to get local issuer certificate
More details here: curl - SSL CA Certificatescurl failed to verify the legitimacy of the server and therefore could not
establish a secure connection to it. To learn more about this situation and
how to fix it, please visit the web page mentioned above.
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
curl: (60) SSL certificate problem: unable to get local issuer certificate
More details here: curl - SSL CA Certificatescurl failed to verify the legitimacy of the server and therefore could not
establish a secure connection to it. To learn more about this situation and
how to fix it, please visit the web page mentioned above.
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
curl: (60) SSL certificate problem: unable to get local issuer certificate
More details here: curl - SSL CA Certificatescurl failed to verify the legitimacy of the server and therefore could not
establish a secure connection to it. To learn more about this situation and
how to fix it, please visit the web page mentioned above.return code: 1
kwargs:
{}: <exception str() failed>
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/Users/ylor/miniconda3/bin/conda-env", line 7, in
sys.exit(main())
File "/Users/ylor/miniconda3/lib/python3.7/site-packages/conda_env/cli/main.py", line 89, in main
return conda_exception_handler(do_call, args, parser)
File "/Users/ylor/miniconda3/lib/python3.7/site-packages/conda/exceptions.py", line 1366, in conda_exception_handler
return_value = exception_handler(func, *args, **kwargs)
File "/Users/ylor/miniconda3/lib/python3.7/site-packages/conda/exceptions.py", line 1077, in call
return self.handle_exception(exc_val, exc_tb)
File "/Users/ylor/miniconda3/lib/python3.7/site-packages/conda/exceptions.py", line 1108, in handle_exception
return self.handle_application_exception(exc_val, exc_tb)
File "/Users/ylor/miniconda3/lib/python3.7/site-packages/conda/exceptions.py", line 1124, in handle_application_exception
self._print_conda_exception(exc_val, exc_tb)
File "/Users/ylor/miniconda3/lib/python3.7/site-packages/conda/exceptions.py", line 1128, in _print_conda_exception
print_conda_exception(exc_val, exc_tb)
File "/Users/ylor/miniconda3/lib/python3.7/site-packages/conda/exceptions.py", line 1051, in print_conda_exception
stderrlog.error("\n%r\n", exc_val)
File "/Users/ylor/miniconda3/lib/python3.7/logging/init.py", line 1407, in error
self._log(ERROR, msg, args, **kwargs)
File "/Users/ylor/miniconda3/lib/python3.7/logging/init.py", line 1514, in _log
self.handle(record)
File "/Users/ylor/miniconda3/lib/python3.7/logging/init.py", line 1523, in handle
if (not self.disabled) and self.filter(record):
File "/Users/ylor/miniconda3/lib/python3.7/logging/init.py", line 751, in filter
result = f.filter(record)
File "/Users/ylor/miniconda3/lib/python3.7/site-packages/conda/gateways/logging.py", line 60, in filter
record.msg = record.msg % new_args
File "/Users/ylor/miniconda3/lib/python3.7/site-packages/conda/init.py", line 123, in repr
errs.append(e.repr())
File "/Users/ylor/miniconda3/lib/python3.7/site-packages/conda/init.py", line 62, in repr
return '%s: %s' % (self.class.name, text_type(self))
File "/Users/ylor/miniconda3/lib/python3.7/site-packages/conda/init.py", line 81, in str
return text_type(self.message % self._kwargs)
ValueError: unsupported format character 'T' (0x54) at index 684
I have tried deleting and installing miniconda multiple times as well as deleting and downloading the qiime2-2019.7-py36-osx-conda.yml file multiple times to no avail. I have also tried downloading the file not being downloaded and unpacking that by hand, but that does not work either.
Any suggestions would be greatly appreciated!
Thank you.