Hi everyone,
I have a student who is having issues installing the newest Qiime2 release in the local environment of his Windows PC. I've determined it's an issue with the .yml file, but I can't seem to get beyond that. (For context, I'm a Mac user.) After running wget to pull the file from the repository, we're having issues running:
conda env create -n qiime2-amplicon-2023.9 --file qiime2-amplicon-2023.9-py38-linux-conda.yml
We tried running with plugins disabled, and got the same error. The error message mentions an issue with the mapping values not being allowed, which could be due to incorrect indentation or other syntax problems, but when I look at the yml file, it looks good to me. Help!
Here's the full error report (I tried running on one of the classroom PCs and got the same error):
>>>>>>>>>>>>>>>>>>>>>> ERROR REPORT <<<<<<<<<<<<<<<<<<<<<<
Traceback (most recent call last): File "C:\Users\macyrick\miniconda3\Lib\site-packages\conda\exception_handler.py", line 17, in __call__ return func(*args, **kwargs) ^^^^^^^^^^^^^^^^^^^^^ File "C:\Users\macyrick\miniconda3\Lib\site-packages\conda_env\cli\main.py", line 56, in do_call exit_code = getattr(module, func_name)(arguments, parser) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Users\macyrick\miniconda3\Lib\site-packages\conda\notices\core.py", line 124, in wrapper return func(*args, **kwargs) ^^^^^^^^^^^^^^^^^^^^^ File "C:\Users\macyrick\miniconda3\Lib\site-packages\conda_env\cli\main_create.py", line 105, in execute spec = specs.detect( ^^^^^^^^^^^^^ File "C:\Users\macyrick\miniconda3\Lib\site-packages\conda_env\specs\__init__.py", line 72, in detect if spec.can_handle(): ^^^^^^^^^^^^^^^^^ File "C:\Users\macyrick\miniconda3\Lib\site-packages\conda_env\specs\yaml_file.py", line 19, in can_handle self._environment = env.from_file(self.filename) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Users\macyrick\miniconda3\Lib\site-packages\conda_env\env.py", line 191, in from_file return from_yaml(yamlstr, filename=filename) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Users\macyrick\miniconda3\Lib\site-packages\conda_env\env.py", line 158, in from_yaml data = yaml_safe_load(yamlstr) ^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Users\macyrick\miniconda3\Lib\site-packages\conda\common\serialize.py", line 53, in yaml_safe_load return _yaml_safe().load(string) ^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Users\macyrick\miniconda3\Lib\site-packages\ruamel\yaml\main.py", line 434, in load return constructor.get_single_data() ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Users\macyrick\miniconda3\Lib\site-packages\ruamel\yaml\constructor.py", line 119, in get_single_data node = self.composer.get_single_node() ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Users\macyrick\miniconda3\Lib\site-packages\ruamel\yaml\composer.py", line 76, in get_single_node document = self.compose_document() ^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Users\macyrick\miniconda3\Lib\site-packages\ruamel\yaml\composer.py", line 102, in compose_document self.parser.get_event() File "C:\Users\macyrick\miniconda3\Lib\site-packages\ruamel\yaml\parser.py", line 168, in get_event self.current_event = self.state() ^^^^^^^^^^^^ File "C:\Users\macyrick\miniconda3\Lib\site-packages\ruamel\yaml\parser.py", line 253, in parse_document_end token = self.scanner.peek_token() ^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Users\macyrick\miniconda3\Lib\site-packages\ruamel\yaml\scanner.py", line 188, in peek_token self.fetch_more_tokens() File "C:\Users\macyrick\miniconda3\Lib\site-packages\ruamel\yaml\scanner.py", line 288, in fetch_more_tokens return self.fetch_value() ^^^^^^^^^^^^^^^^^^ File "C:\Users\macyrick\miniconda3\Lib\site-packages\ruamel\yaml\scanner.py", line 657, in fetch_value raise ScannerError( ruamel.yaml.scanner.ScannerError: mapping values are not allowed here in "<unicode string>", line 5, column 60: ... automatically to the target URL: <a href="https://raw.githubuse ... ^ (line: 5)
$ C:\Users\macyrick\miniconda3\Scripts\conda-env-script.py create -n qiime2-amplicon-2023.9 --file qiime2-amplicon-2023.9-py38-linux-conda.yml
environment variables:
CIO_TEST=
CONDA_AUTO_UPDATE_CONDA=false
CONDA_DEFAULT_ENV=qiime2-amplicon-2023.9
CONDA_EXE=C:\Users\macyrick\miniconda3\condabin..\Scripts\conda.exe
CONDA_EXES="C:\Users\macyrick\miniconda3\condabin..\Scripts\conda.exe"
CONDA_PREFIX=C:\Users\macyrick\miniconda3\envs\qiime2-amplicon-2023.9
CONDA_PREFIX_1=C:\Users\macyrick\miniconda3
CONDA_PROMPT_MODIFIER=(qiime2-amplicon-2023.9)
CONDA_PYTHON_EXE=C:\Users\macyrick\miniconda3\python.exe
CONDA_ROOT=C:\Users\macyrick\miniconda3
CONDA_SHLVL=2
CURL_CA_BUNDLE=
HOMEPATH=\Users\macyrick
LD_PRELOAD=
PATH=C:\Users\macyrick\miniconda3\envs\qiime2-amplicon-
2023.9;C:\Users\macyrick\miniconda3\envs\qiime2-amplicon-
2023.9\Library\mingw-w64\bin;C:\Users\macyrick\miniconda3\envs\qiime2-
amplicon-
2023.9\Library\usr\bin;C:\Users\macyrick\miniconda3\envs\qiime2-
amplicon-2023.9\Library\bin;C:\Users\macyrick\miniconda3\envs\qiime2-
amplicon-2023.9\Scripts;C:\Users\macyrick\miniconda3\envs\qiime2-
amplicon-2023.9\bin;C:\Users\macyrick\miniconda3\condabin;C:\Program
Files (x86)\Common Files\Oracle\Java\javapath;C:\WINDOWS\system32;C:\W
INDOWS;C:\WINDOWS\System32\Wbem;C:\WINDOWS\System32\WindowsPowerShell
v1.0;C:\WINDOWS\System32\OpenSSH;C:\WINDOWS\CCM;C:\Program Files
(x86)\Common Files\Pulse Secure\VC142.CRT\X64;C:\Program
Files\PowerShell\7;C:\Program Files\PuTTY;C:\Users\macyrick\miniconda3
;C:\Users\macyrick\miniconda3\Library\mingw-
w64\bin;C:\Users\macyrick\miniconda3\Library\usr\bin;C:\Users\macyrick
\miniconda3\Library\bin;C:\Users\macyrick\miniconda3\Scripts;C:\Users
macyrick\AppData\Local\Microsoft\WindowsApps
PSMODULEPATH=C:\Program Files\WindowsPowerShell\Modules;C:\WINDOWS\system32\Windows
PowerShell\v1.0\Modules
REQUESTS_CA_BUNDLE=
SSL_CERT_FILE=C:\Users\macyrick\miniconda3\Library\ssl\cacert.pem
VBOX_MSI_INSTALL_PATH=C:\Program Files\Oracle\VirtualBox\active environment : qiime2-amplicon-2023.9 active env location : C:\Users\macyrick\miniconda3\envs\qiime2-amplicon-2023.9 shell level : 2 user config file : C:\Users\macyrick\.condarc
populated config files : C:\Users\macyrick.condarc
conda version : 23.9.0
conda-build version : not installed
python version : 3.11.4.final.0
virtual packages : __archspec=1=x86_64
__win=0=0
base environment : C:\Users\macyrick\miniconda3 (writable)
conda av data dir : C:\Users\macyrick\miniconda3\etc\conda
conda av metadata url : None
channel URLs : bioconda/win-64
bioconda/noarch
main/win-64
main/noarch
r/win-64
r/noarch
msys2/win-64
msys2/noarch
package cache : C:\Users\macyrick\miniconda3\pkgs
C:\Users\macyrick.conda\pkgs
C:\Users\macyrick\AppData\Local\conda\conda\pkgs
envs directories : C:\Users\macyrick\miniconda3\envs
C:\Users\macyrick.conda\envs
C:\Users\macyrick\AppData\Local\conda\conda\envs
platform : win-64
user-agent : conda/23.9.0 requests/2.31.0 CPython/3.11.4 Windows/10 Windows/10.0.19044
administrator : False
netrc file : None
offline mode : FalseAn unexpected error has occurred. Conda has prepared the above report.
If you suspect this error is being caused by a malfunctioning plugin,
consider using the --no-plugins option to turn off plugins.Example: conda --no-plugins install
Alternatively, you can set the CONDA_NO_PLUGINS environment variable on
the command line to run the command without plugins enabled.Example: CONDA_NO_PLUGINS=true conda install
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