Installing on Apple M3 Max

VLoz · June 25, 2024, 7:44pm

Hi,

I am trying to install qiime2-metagenome-2024.5-py38-osx-conda.yml on a Apple M3 Max.

I downloaded miniconda without problems.
I ran the following code:

conda install wget

wget https://data.qiime2.org/distro/metagenome/qiime2-metagenome-2024.5-py38-osx-conda.yml

CONDA_SUBDIR=osx-64 conda env create -n qiime2-metagenome-2024.5 --file qiime2-metagenome-2024.5-py38-osx-conda.yml

I got the following error:
Error while loading conda entry point: conda-libmamba-solver (dlopen(/opt/miniconda3/lib/python3.12/site-packages/libmambapy/bindings.cpython-312-darwin.so, 0x0002): Library not loaded: @rpath/libcrypto.3.dylib
Referenced from: /opt/miniconda3/lib/libmamba.2.0.0.dylib
Reason: tried: '/opt/miniconda3/lib/libcrypto.3.dylib' (mach-o file, but is an incompatible architecture (have 'x86_64', need 'arm64')), '/opt/miniconda3/lib/python3.12/site-packages/libmambapy/../../../libcrypto.3.dylib' (mach-o file, but is an incompatible architecture (have 'x86_64', need 'arm64')), '/opt/miniconda3/lib/python3.12/site-packages/libmambapy/../../../libcrypto.3.dylib' (mach-o file, but is an incompatible architecture (have 'x86_64', need 'arm64')), '/opt/miniconda3/bin/../lib/libcrypto.3.dylib' (mach-o file, but is an incompatible architecture (have 'x86_64', need 'arm64')), '/opt/miniconda3/bin/../lib/libcrypto.3.dylib' (mach-o file, but is an incompatible architecture (have 'x86_64', need 'arm64')), '/usr/local/lib/libcrypto.3.dylib' (no such file), '/usr/lib/libcrypto.3.dylib' (no such file, not in dyld cache))
Error while loading conda entry point: conda-content-trust (dlopen(/opt/miniconda3/lib/python3.12/site-packages/cryptography/hazmat/bindings/_rust.cpython-312-darwin.so, 0x0002): Library not loaded: @rpath/libssl.3.dylib
Referenced from: /opt/miniconda3/lib/python3.12/site-packages/cryptography/hazmat/bindings/_rust.cpython-312-darwin.so
Reason: tried: '/opt/miniconda3/lib/python3.12/site-packages/cryptography/hazmat/bindings/../../../../../libssl.3.dylib' (mach-o file, but is an incompatible architecture (have 'x86_64', need 'arm64')), '/opt/miniconda3/lib/python3.12/site-packages/cryptography/hazmat/bindings/../../../../../libssl.3.dylib' (mach-o file, but is an incompatible architecture (have 'x86_64', need 'arm64')), '/opt/miniconda3/bin/../lib/libssl.3.dylib' (mach-o file, but is an incompatible architecture (have 'x86_64', need 'arm64')), '/opt/miniconda3/bin/../lib/libssl.3.dylib' (mach-o file, but is an incompatible architecture (have 'x86_64', need 'arm64')), '/usr/local/lib/libssl.3.dylib' (no such file), '/usr/lib/libssl.3.dylib' (no such file, not in dyld cache))
Collecting package metadata (repodata.json): failed

>>>>>>>>>>>>>>>>>>>>>> ERROR REPORT <<<<<<<<<<<<<<<<<<<<<<

Traceback (most recent call last):
  File "/opt/miniconda3/lib/python3.12/site-packages/conda/exception_handler.py", line 18, in __call__
    return func(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^
  File "/opt/miniconda3/lib/python3.12/site-packages/conda/cli/main.py", line 84, in main_subshell
    exit_code = do_call(args, parser)
                ^^^^^^^^^^^^^^^^^^^^^
  File "/opt/miniconda3/lib/python3.12/site-packages/conda/cli/conda_argparse.py", line 200, in do_call
    result = getattr(module, func_name)(args, parser)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/miniconda3/lib/python3.12/site-packages/conda/notices/core.py", line 132, in wrapper
    return func(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^
  File "/opt/miniconda3/lib/python3.12/site-packages/conda/cli/main_env_create.py", line 170, in execute
    result[installer_type] = installer.install(
                             ^^^^^^^^^^^^^^^^^^
  File "/opt/miniconda3/lib/python3.12/site-packages/conda/env/installers/conda.py", line 51, in install
    unlink_link_transaction = solver.solve_for_transaction(
                              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/miniconda3/lib/python3.12/site-packages/conda/core/solve.py", line 153, in solve_for_transaction
    unlink_precs, link_precs = self.solve_for_diff(
                               ^^^^^^^^^^^^^^^^^^^^
  File "/opt/miniconda3/lib/python3.12/site-packages/conda/core/solve.py", line 222, in solve_for_diff
    final_precs = self.solve_final_state(
                  ^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/miniconda3/lib/python3.12/site-packages/conda/core/solve.py", line 367, in solve_final_state
    ssc = self._collect_all_metadata(ssc)
          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/miniconda3/lib/python3.12/site-packages/conda/common/io.py", line 86, in decorated
    return f(*args, **kwds)
           ^^^^^^^^^^^^^^^^
  File "/opt/miniconda3/lib/python3.12/site-packages/conda/core/solve.py", line 583, in _collect_all_metadata
    index, r = self._prepare(prepared_specs)
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/miniconda3/lib/python3.12/site-packages/conda/core/solve.py", line 1304, in _prepare
    reduced_index = get_reduced_index(
                    ^^^^^^^^^^^^^^^^^^
  File "/opt/miniconda3/lib/python3.12/site-packages/conda/core/index.py", line 378, in get_reduced_index
    new_records = SubdirData.query_all(
                  ^^^^^^^^^^^^^^^^^^^^^
  File "/opt/miniconda3/lib/python3.12/site-packages/conda/core/subdir_data.py", line 161, in query_all
    result = tuple(
             ^^^^^^
  File "/opt/miniconda3/lib/python3.12/concurrent/futures/_base.py", line 619, in result_iterator
    yield _result_or_cancel(fs.pop())
          ^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/miniconda3/lib/python3.12/concurrent/futures/_base.py", line 317, in _result_or_cancel
    return fut.result(timeout)
           ^^^^^^^^^^^^^^^^^^^
  File "/opt/miniconda3/lib/python3.12/concurrent/futures/_base.py", line 456, in result
    return self.__get_result()
           ^^^^^^^^^^^^^^^^^^^
  File "/opt/miniconda3/lib/python3.12/concurrent/futures/_base.py", line 401, in __get_result
    raise self._exception
  File "/opt/miniconda3/lib/python3.12/concurrent/futures/thread.py", line 58, in run
    result = self.fn(*self.args, **self.kwargs)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/miniconda3/lib/python3.12/site-packages/conda/core/subdir_data.py", line 146, in subdir_query
    return tuple(
           ^^^^^^
  File "/opt/miniconda3/lib/python3.12/site-packages/conda/core/subdir_data.py", line 168, in query
    self.load()
  File "/opt/miniconda3/lib/python3.12/site-packages/conda/core/subdir_data.py", line 271, in load
    _internal_state = self._load()
                      ^^^^^^^^^^^^
  File "/opt/miniconda3/lib/python3.12/site-packages/conda/core/subdir_data.py", line 317, in _load
    repodata, state = fetcher.fetch_latest_parsed()
                      ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/miniconda3/lib/python3.12/site-packages/conda/gateways/repodata/__init__.py", line 730, in fetch_latest_parsed
    parsed, state = self.fetch_latest()
                    ^^^^^^^^^^^^^^^^^^^
  File "/opt/miniconda3/lib/python3.12/site-packages/conda/gateways/repodata/__init__.py", line 847, in fetch_latest
    raw_repodata = repo.repodata_parsed(cache.state)  # type: ignore
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/miniconda3/lib/python3.12/site-packages/conda/gateways/repodata/jlap/interface.py", line 87, in repodata_parsed
    repodata_json_or_none = fetch.request_url_jlap_state(
                            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/miniconda3/lib/python3.12/site-packages/conda/gateways/repodata/jlap/fetch.py", line 309, in request_url_jlap_state
    response = download_and_hash(
               ^^^^^^^^^^^^^^^^^^
  File "/opt/miniconda3/lib/python3.12/site-packages/conda/gateways/repodata/jlap/fetch.py", line 243, in download_and_hash
    response = session.get(url, stream=True, timeout=timeout, headers=headers)
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/miniconda3/lib/python3.12/site-packages/requests/sessions.py", line 602, in get
    return self.request("GET", url, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/miniconda3/lib/python3.12/site-packages/requests/sessions.py", line 589, in request
    resp = self.send(prep, **send_kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/miniconda3/lib/python3.12/site-packages/requests/sessions.py", line 703, in send
    r = adapter.send(request, **kwargs)
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/miniconda3/lib/python3.12/site-packages/requests/adapters.py", line 486, in send
    resp = conn.urlopen(
           ^^^^^^^^^^^^^
  File "/opt/miniconda3/lib/python3.12/site-packages/urllib3/connectionpool.py", line 769, in urlopen
    conn = self._get_conn(timeout=pool_timeout)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/miniconda3/lib/python3.12/site-packages/urllib3/connectionpool.py", line 295, in _get_conn
    return conn or self._new_conn()
                   ^^^^^^^^^^^^^^^^
  File "/opt/miniconda3/lib/python3.12/site-packages/urllib3/connectionpool.py", line 1060, in _new_conn
    raise ImportError(
ImportError: Can't connect to HTTPS URL because the SSL module is not available.

$ /opt/miniconda3/bin/conda env create -n qiime2-metagenome-2024.5 --file qiime2-metagenome-2024.5-py38-osx-conda.yml

environment variables:
CIO_TEST=
CONDA_DEFAULT_ENV=base
CONDA_EXE=/opt/miniconda3/bin/conda
CONDA_PREFIX=/opt/miniconda3
CONDA_PROMPT_MODIFIER=(base)
CONDA_PYTHON_EXE=/opt/miniconda3/bin/python
CONDA_ROOT=/opt/miniconda3
CONDA_SHLVL=1
CONDA_SUBDIR=osx-64
CURL_CA_BUNDLE=
INFOPATH=/opt/homebrew/share/info:
LD_PRELOAD=
MANPATH=/opt/homebrew/share/man::
PATH=/opt/miniconda3/bin:/opt/miniconda3/condabin:/opt/homebrew/bin:/opt/ho
mebrew/sbin:/Library/Frameworks/Python.framework/Versions/3.12/bin:/us
r/local/bin:/System/Cryptexes/App/usr/bin:/usr/bin:/bin:/usr/sbin:/sbi
n:/miniconda3/bin:/var/run/com.apple.security.cryptexd/codex.system/bo
otstrap/usr/local/bin:/var/run/com.apple.security.cryptexd/codex.syste
m/bootstrap/usr/bin:/var/run/com.apple.security.cryptexd/codex.system/
bootstrap/usr/appleinternal/bin
REQUESTS_CA_BUNDLE=
SSL_CERT_FILE=

 active environment : base
active env location : /opt/miniconda3
        shell level : 1
   user config file : /Users/valerylozada/.condarc

populated config files : /Users/valerylozada/.condarc
conda version : 24.5.0
conda-build version : not installed
python version : 3.12.3.final.0
solver : classic
virtual packages : __archspec=1=x86_64
__conda=24.5.0=0
__osx=14.3.1=0
__unix=0=0
base environment : /opt/miniconda3 (writable)
conda av data dir : /opt/miniconda3/etc/conda
conda av metadata url : None
channel URLs : main/osx-64
main/noarch
r/osx-64
r/noarch
package cache : /opt/miniconda3/pkgs
/Users/valerylozada/.conda/pkgs
envs directories : /opt/miniconda3/envs
/Users/valerylozada/.conda/envs
platform : osx-64
user-agent : conda/24.5.0 requests/2.31.0 CPython/3.12.3 Darwin/23.3.0 OSX/14.3.1 aau/0.4.4 c/. s/. e/.
UID:GID : 502:20
netrc file : None
offline mode : False

An 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.

Any suggestions on how to fix this issue?

Thanks!

lizgehret · June 26, 2024, 4:26pm

Hey @VLoz,

It seems like something may have gone sideways with your miniconda installation. Let's have you try the following:

Fully uninstall miniconda from your machine.
Re-install miniconda3 using these linked instructions.
Skip the wget step, and do a direct install of qiime2 as follows:

CONDA_SUBDIR=osx-64 conda env create -n qiime2-metagenome-2024.5 -f https://github.com/qiime2/distributions/blob/dev/2024.5/metagenome/released/qiime2-metagenome-macos-latest-conda.yml

conda activate qiime2-metagenome-2024.5

conda config --env --set subdir osx-64

Let us know if you're successful, or if you run into any other issues! Cheers

VLoz · June 26, 2024, 8:55pm

Hi @lizgehret

I tried your suggestions and still got an error. See below.

CONDA_SUBDIR=osx-64 conda env create -n qiime2-metagenome-2024.5 -f distributions/2024.5/metagenome/released/qiime2-metagenome-macos-latest-conda.yml at dev · qiime2/distributions · GitHub


# >>>>>>>>>>>>>>>>>>>>>> ERROR REPORT <<<<<<<<<<<<<<<<<<<<<<

    Traceback (most recent call last):
      File "/opt/miniconda3/lib/python3.12/site-packages/conda/exception_handler.py", line 17, in __call__
        return func(*args, **kwargs)
               ^^^^^^^^^^^^^^^^^^^^^
      File "/opt/miniconda3/lib/python3.12/site-packages/conda/cli/main.py", line 83, in main_subshell
        exit_code = do_call(args, parser)
                    ^^^^^^^^^^^^^^^^^^^^^
      File "/opt/miniconda3/lib/python3.12/site-packages/conda/cli/conda_argparse.py", line 199, in do_call
        result = getattr(module, func_name)(args, parser)
                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
      File "/opt/miniconda3/lib/python3.12/site-packages/conda/notices/core.py", line 131, in wrapper
        return func(*args, **kwargs)
               ^^^^^^^^^^^^^^^^^^^^^
      File "/opt/miniconda3/lib/python3.12/site-packages/conda/cli/main_env_create.py", line 112, in execute
        spec = specs.detect(
               ^^^^^^^^^^^^^
      File "/opt/miniconda3/lib/python3.12/site-packages/conda/env/specs/__init__.py", line 71, in detect
        if spec.can_handle():
           ^^^^^^^^^^^^^^^^^
      File "/opt/miniconda3/lib/python3.12/site-packages/conda/env/specs/yaml_file.py", line 18, in can_handle
        self._environment = env.from_file(self.filename)
                            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
      File "/opt/miniconda3/lib/python3.12/site-packages/conda/env/env.py", line 172, in from_file
        return from_yaml(yamlstr, filename=filename)
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
      File "/opt/miniconda3/lib/python3.12/site-packages/conda/env/env.py", line 138, in from_yaml
        data = yaml_safe_load(yamlstr)
               ^^^^^^^^^^^^^^^^^^^^^^^
      File "/opt/miniconda3/lib/python3.12/site-packages/conda/common/serialize.py", line 45, in yaml_safe_load
        return _yaml_safe().load(string)
               ^^^^^^^^^^^^^^^^^^^^^^^^^
      File "/opt/miniconda3/lib/python3.12/site-packages/ruamel/yaml/main.py", line 434, in load
        return constructor.get_single_data()
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
      File "/opt/miniconda3/lib/python3.12/site-packages/ruamel/yaml/constructor.py", line 119, in get_single_data
        node = self.composer.get_single_node()
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
      File "/opt/miniconda3/lib/python3.12/site-packages/ruamel/yaml/composer.py", line 76, in get_single_node
        document = self.compose_document()
                   ^^^^^^^^^^^^^^^^^^^^^^^
      File "/opt/miniconda3/lib/python3.12/site-packages/ruamel/yaml/composer.py", line 102, in compose_document
        self.parser.get_event()
      File "/opt/miniconda3/lib/python3.12/site-packages/ruamel/yaml/parser.py", line 168, in get_event
        self.current_event = self.state()
                             ^^^^^^^^^^^^
      File "/opt/miniconda3/lib/python3.12/site-packages/ruamel/yaml/parser.py", line 253, in parse_document_end
        token = self.scanner.peek_token()
                ^^^^^^^^^^^^^^^^^^^^^^^^^
      File "/opt/miniconda3/lib/python3.12/site-packages/ruamel/yaml/scanner.py", line 188, in peek_token
        self.fetch_more_tokens()
      File "/opt/miniconda3/lib/python3.12/site-packages/ruamel/yaml/scanner.py", line 288, in fetch_more_tokens
        return self.fetch_value()
               ^^^^^^^^^^^^^^^^^^
      File "/opt/miniconda3/lib/python3.12/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 213, column 75:
         ... age-responsive" style="word-wrap: break-word;">
                                             ^ (line: 213)

`$ /opt/miniconda3/bin/conda env create -n qiime2-metagenome-2024.5 -f https://github.com/qiime2/distributions/blob/dev/2024.5/metagenome/released/qiime2-metagenome-macos-latest-conda.yml`

  environment variables:
                 CIO_TEST=<not set>
        CONDA_DEFAULT_ENV=base
                CONDA_EXE=/opt/miniconda3/bin/conda
             CONDA_PREFIX=/opt/miniconda3
    CONDA_PROMPT_MODIFIER=(base)
         CONDA_PYTHON_EXE=/opt/miniconda3/bin/python
               CONDA_ROOT=/opt/miniconda3
              CONDA_SHLVL=1
             CONDA_SUBDIR=osx-64
           CURL_CA_BUNDLE=<not set>
                 INFOPATH=/opt/homebrew/share/info:
               LD_PRELOAD=<not set>
                  MANPATH=/opt/homebrew/share/man::
                     PATH=/opt/miniconda3/bin:/opt/miniconda3/condabin:/opt/homebrew/bin:/opt/ho
                          mebrew/sbin:/Library/Frameworks/Python.framework/Versions/3.12/bin:/us
                          r/local/bin:/System/Cryptexes/App/usr/bin:/usr/bin:/bin:/usr/sbin:/sbi
                          n:/miniconda3/bin:/var/run/com.apple.security.cryptexd/codex.system/bo
                          otstrap/usr/local/bin:/var/run/com.apple.security.cryptexd/codex.syste
                          m/bootstrap/usr/bin:/var/run/com.apple.security.cryptexd/codex.system/
                          bootstrap/usr/appleinternal/bin
       REQUESTS_CA_BUNDLE=<not set>
            SSL_CERT_FILE=<not set>

     active environment : base
    active env location : /opt/miniconda3
            shell level : 1
       user config file : /Users/valerylozada/.condarc
 populated config files : /Users/valerylozada/.condarc
          conda version : 24.4.0
    conda-build version : not installed
         python version : 3.12.3.final.0
                 solver : classic
       virtual packages : __archspec=1=m1
                          __conda=24.4.0=0
                          __osx=10.16=0
                          __unix=0=0
       base environment : /opt/miniconda3  (writable)
      conda av data dir : /opt/miniconda3/etc/conda
  conda av metadata url : None
           channel URLs : https://repo.anaconda.com/pkgs/main/osx-64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/r/osx-64
                          https://repo.anaconda.com/pkgs/r/noarch
          package cache : /opt/miniconda3/pkgs
                          /Users/valerylozada/.conda/pkgs
       envs directories : /opt/miniconda3/envs
                          /Users/valerylozada/.conda/envs
               platform : osx-64
             user-agent : conda/24.4.0 requests/2.31.0 CPython/3.12.3 Darwin/23.3.0 OSX/10.16 aau/0.4.4 c/. s/. e/.
                UID:GID : 502:20
             netrc file : None
           offline mode : False


An 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 <package>

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 <package>

If submitted, this report will be used by core maintainers to improve
future releases of conda.
Would you like conda to send this report to the core maintainers? [y/N]:

lizgehret · June 27, 2024, 4:49pm

Hey @VLoz,

This is very unusual! I had one of my colleagues test out this install (they also have an apple silicon chip) and they didn't run into this issue.

I'm curious if you run into the same thing with other qiime 2 distributions - I kind of suspect not, but we should test that out just to cover our bases. Would you mind doing the same install process for the amplicon distribution, and let me know if you receive the same error? Commands as follows:

CONDA_SUBDIR=osx-64 conda env create -n qiime2-amplicon-2024.5 -f https://github.com/qiime2/distributions/blob/dev/2024.5/amplicon/released/qiime2-amplicon-macos-latest-conda.yml

conda activate qiime2-amplicon-2024.5

conda config --env --set subdir osx-64

Thanks!

lizgehret · June 27, 2024, 8:49pm

An off-topic reply has been split into a new topic: error installing metagenome 2024.5 on apple m3

Please keep replies on-topic in the future.

VLoz · June 27, 2024, 9:08pm

@lizgehret I get an error as well when I ran that line of code.

CONDA_SUBDIR=osx-64 conda env create -n qiime2-amplicon-2024.5 -f distributions/2024.5/amplicon/released/qiime2-amplicon-macos-latest-conda.yml at dev · qiime2/distributions · GitHub

Retrieving notices: ...working... /opt/miniconda3/lib/python3.12/site-packages/urllib3/connectionpool.py:1099: InsecureRequestWarning: Unverified HTTPS request is being made to host 'repo.anaconda.com'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#tls-warnings
  warnings.warn(
/opt/miniconda3/lib/python3.12/site-packages/urllib3/connectionpool.py:1099: InsecureRequestWarning: Unverified HTTPS request is being made to host 'repo.anaconda.com'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#tls-warnings
  warnings.warn(
done

# >>>>>>>>>>>>>>>>>>>>>> ERROR REPORT <<<<<<<<<<<<<<<<<<<<<<

    Traceback (most recent call last):
      File "/opt/miniconda3/lib/python3.12/site-packages/conda/exception_handler.py", line 17, in __call__
        return func(*args, **kwargs)
               ^^^^^^^^^^^^^^^^^^^^^
      File "/opt/miniconda3/lib/python3.12/site-packages/conda/cli/main.py", line 83, in main_subshell
        exit_code = do_call(args, parser)
                    ^^^^^^^^^^^^^^^^^^^^^
      File "/opt/miniconda3/lib/python3.12/site-packages/conda/cli/conda_argparse.py", line 199, in do_call
        result = getattr(module, func_name)(args, parser)
                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
      File "/opt/miniconda3/lib/python3.12/site-packages/conda/notices/core.py", line 126, in wrapper
        return_value = func(*args, **kwargs)
                       ^^^^^^^^^^^^^^^^^^^^^
      File "/opt/miniconda3/lib/python3.12/site-packages/conda/cli/main_env_create.py", line 112, in execute
        spec = specs.detect(
               ^^^^^^^^^^^^^
      File "/opt/miniconda3/lib/python3.12/site-packages/conda/env/specs/__init__.py", line 71, in detect
        if spec.can_handle():
           ^^^^^^^^^^^^^^^^^
      File "/opt/miniconda3/lib/python3.12/site-packages/conda/env/specs/yaml_file.py", line 18, in can_handle
        self._environment = env.from_file(self.filename)
                            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
      File "/opt/miniconda3/lib/python3.12/site-packages/conda/env/env.py", line 172, in from_file
        return from_yaml(yamlstr, filename=filename)
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
      File "/opt/miniconda3/lib/python3.12/site-packages/conda/env/env.py", line 138, in from_yaml
        data = yaml_safe_load(yamlstr)
               ^^^^^^^^^^^^^^^^^^^^^^^
      File "/opt/miniconda3/lib/python3.12/site-packages/conda/common/serialize.py", line 45, in yaml_safe_load
        return _yaml_safe().load(string)
               ^^^^^^^^^^^^^^^^^^^^^^^^^
      File "/opt/miniconda3/lib/python3.12/site-packages/ruamel/yaml/main.py", line 434, in load
        return constructor.get_single_data()
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
      File "/opt/miniconda3/lib/python3.12/site-packages/ruamel/yaml/constructor.py", line 119, in get_single_data
        node = self.composer.get_single_node()
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
      File "/opt/miniconda3/lib/python3.12/site-packages/ruamel/yaml/composer.py", line 76, in get_single_node
        document = self.compose_document()
                   ^^^^^^^^^^^^^^^^^^^^^^^
      File "/opt/miniconda3/lib/python3.12/site-packages/ruamel/yaml/composer.py", line 102, in compose_document
        self.parser.get_event()
      File "/opt/miniconda3/lib/python3.12/site-packages/ruamel/yaml/parser.py", line 168, in get_event
        self.current_event = self.state()
                             ^^^^^^^^^^^^
      File "/opt/miniconda3/lib/python3.12/site-packages/ruamel/yaml/parser.py", line 253, in parse_document_end
        token = self.scanner.peek_token()
                ^^^^^^^^^^^^^^^^^^^^^^^^^
      File "/opt/miniconda3/lib/python3.12/site-packages/ruamel/yaml/scanner.py", line 188, in peek_token
        self.fetch_more_tokens()
      File "/opt/miniconda3/lib/python3.12/site-packages/ruamel/yaml/scanner.py", line 288, in fetch_more_tokens
        return self.fetch_value()
               ^^^^^^^^^^^^^^^^^^
      File "/opt/miniconda3/lib/python3.12/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 213, column 75:
         ... age-responsive" style="word-wrap: break-word;">
                                             ^ (line: 213)

`$ /opt/miniconda3/bin/conda env create -n qiime2-amplicon-2024.5 -f https://github.com/qiime2/distributions/blob/dev/2024.5/amplicon/released/qiime2-amplicon-macos-latest-conda.yml`

  environment variables:
                 CIO_TEST=<not set>
        CONDA_DEFAULT_ENV=base
                CONDA_EXE=/opt/miniconda3/bin/conda
             CONDA_PREFIX=/opt/miniconda3
    CONDA_PROMPT_MODIFIER=(base)
         CONDA_PYTHON_EXE=/opt/miniconda3/bin/python
               CONDA_ROOT=/opt/miniconda3
              CONDA_SHLVL=1
             CONDA_SUBDIR=osx-64
           CURL_CA_BUNDLE=<not set>
                 INFOPATH=/opt/homebrew/share/info:
               LD_PRELOAD=<not set>
                  MANPATH=/opt/homebrew/share/man::
                     PATH=/opt/miniconda3/bin:/opt/miniconda3/condabin:/opt/homebrew/bin:/opt/ho
                          mebrew/sbin:/Library/Frameworks/Python.framework/Versions/3.12/bin:/us
                          r/local/bin:/System/Cryptexes/App/usr/bin:/usr/bin:/bin:/usr/sbin:/sbi
                          n:/miniconda3/bin:/var/run/com.apple.security.cryptexd/codex.system/bo
                          otstrap/usr/local/bin:/var/run/com.apple.security.cryptexd/codex.syste
                          m/bootstrap/usr/bin:/var/run/com.apple.security.cryptexd/codex.system/
                          bootstrap/usr/appleinternal/bin
       REQUESTS_CA_BUNDLE=<not set>
            SSL_CERT_FILE=<not set>

     active environment : base
    active env location : /opt/miniconda3
            shell level : 1
       user config file : /Users/valerylozada/.condarc
 populated config files : /Users/valerylozada/.condarc
          conda version : 24.4.0
    conda-build version : not installed
         python version : 3.12.3.final.0
                 solver : classic
       virtual packages : __archspec=1=m1
                          __conda=24.4.0=0
                          __osx=10.16=0
                          __unix=0=0
       base environment : /opt/miniconda3  (writable)
      conda av data dir : /opt/miniconda3/etc/conda
  conda av metadata url : None
           channel URLs : https://repo.anaconda.com/pkgs/main/osx-64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/r/osx-64
                          https://repo.anaconda.com/pkgs/r/noarch
          package cache : /opt/miniconda3/pkgs
                          /Users/valerylozada/.conda/pkgs
       envs directories : /opt/miniconda3/envs
                          /Users/valerylozada/.conda/envs
               platform : osx-64
             user-agent : conda/24.4.0 requests/2.31.0 CPython/3.12.3 Darwin/23.3.0 OSX/10.16 aau/0.4.4 c/. s/. e/.
                UID:GID : 502:20
             netrc file : None
           offline mode : False


An 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 <package>

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 <package>

If submitted, this report will be used by core maintainers to improve
future releases of conda.
Would you like conda to send this report to the core maintainers? [y/N]:

lizgehret · June 27, 2024, 9:10pm

Hey @VLoz,

Thanks for giving that a try - can you try one more thing for me? I'm curious if the same thing happens with older QIIME 2 release versions. Try again with the following commands and let me know what the outcome is:

CONDA_SUBDIR=osx-64 conda env create -n qiime2-amplicon-2024.2 -f https://github.com/qiime2/distributions/blob/dev/2024.2/amplicon/released/qiime2-amplicon-macos-latest-conda.yml

We'll get to the bottom of this!

VLoz · June 27, 2024, 9:55pm

@lizgehret Yes, same thing happens.

CONDA_SUBDIR=osx-64 conda env create -n qiime2-amplicon-2024.2 -f https://github.com/qiime2/distributions/blob/dev/2024.2/amplicon/released/qiime2-amplicon-macos-latest-conda.yml


# >>>>>>>>>>>>>>>>>>>>>> ERROR REPORT <<<<<<<<<<<<<<<<<<<<<<

    Traceback (most recent call last):
      File "/opt/miniconda3/lib/python3.12/site-packages/conda/exception_handler.py", line 18, in __call__
        return func(*args, **kwargs)
               ^^^^^^^^^^^^^^^^^^^^^
      File "/opt/miniconda3/lib/python3.12/site-packages/conda/cli/main.py", line 84, in main_subshell
        exit_code = do_call(args, parser)
                    ^^^^^^^^^^^^^^^^^^^^^
      File "/opt/miniconda3/lib/python3.12/site-packages/conda/cli/conda_argparse.py", line 200, in do_call
        result = getattr(module, func_name)(args, parser)
                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
      File "/opt/miniconda3/lib/python3.12/site-packages/conda/notices/core.py", line 132, in wrapper
        return func(*args, **kwargs)
               ^^^^^^^^^^^^^^^^^^^^^
      File "/opt/miniconda3/lib/python3.12/site-packages/conda/cli/main_env_create.py", line 113, in execute
        spec = specs.detect(
               ^^^^^^^^^^^^^
      File "/opt/miniconda3/lib/python3.12/site-packages/conda/env/specs/__init__.py", line 71, in detect
        if spec.can_handle():
           ^^^^^^^^^^^^^^^^^
      File "/opt/miniconda3/lib/python3.12/site-packages/conda/env/specs/yaml_file.py", line 19, in can_handle
        self._environment = env.from_file(self.filename)
                            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
      File "/opt/miniconda3/lib/python3.12/site-packages/conda/env/env.py", line 173, in from_file
        return from_yaml(yamlstr, filename=filename)
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
      File "/opt/miniconda3/lib/python3.12/site-packages/conda/env/env.py", line 139, in from_yaml
        data = yaml_safe_load(yamlstr)
               ^^^^^^^^^^^^^^^^^^^^^^^
      File "/opt/miniconda3/lib/python3.12/site-packages/conda/common/serialize.py", line 46, in yaml_safe_load
        return _yaml_safe().load(string)
               ^^^^^^^^^^^^^^^^^^^^^^^^^
      File "/opt/miniconda3/lib/python3.12/site-packages/ruamel/yaml/main.py", line 434, in load
        return constructor.get_single_data()
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
      File "/opt/miniconda3/lib/python3.12/site-packages/ruamel/yaml/constructor.py", line 119, in get_single_data
        node = self.composer.get_single_node()
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
      File "/opt/miniconda3/lib/python3.12/site-packages/ruamel/yaml/composer.py", line 76, in get_single_node
        document = self.compose_document()
                   ^^^^^^^^^^^^^^^^^^^^^^^
      File "/opt/miniconda3/lib/python3.12/site-packages/ruamel/yaml/composer.py", line 102, in compose_document
        self.parser.get_event()
      File "/opt/miniconda3/lib/python3.12/site-packages/ruamel/yaml/parser.py", line 168, in get_event
        self.current_event = self.state()
                             ^^^^^^^^^^^^
      File "/opt/miniconda3/lib/python3.12/site-packages/ruamel/yaml/parser.py", line 253, in parse_document_end
        token = self.scanner.peek_token()
                ^^^^^^^^^^^^^^^^^^^^^^^^^
      File "/opt/miniconda3/lib/python3.12/site-packages/ruamel/yaml/scanner.py", line 188, in peek_token
        self.fetch_more_tokens()
      File "/opt/miniconda3/lib/python3.12/site-packages/ruamel/yaml/scanner.py", line 288, in fetch_more_tokens
        return self.fetch_value()
               ^^^^^^^^^^^^^^^^^^
      File "/opt/miniconda3/lib/python3.12/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 213, column 75:
         ... age-responsive" style="word-wrap: break-word;">
                                             ^ (line: 213)

`$ /opt/miniconda3/bin/conda env create -n qiime2-amplicon-2024.2 -f https://github.com/qiime2/distributions/blob/dev/2024.2/amplicon/released/qiime2-amplicon-macos-latest-conda.yml`

  environment variables:
                 CIO_TEST=<not set>
        CONDA_DEFAULT_ENV=base
                CONDA_EXE=/opt/miniconda3/bin/conda
             CONDA_PREFIX=/opt/miniconda3
    CONDA_PROMPT_MODIFIER=(base)
         CONDA_PYTHON_EXE=/opt/miniconda3/bin/python
               CONDA_ROOT=/opt/miniconda3
              CONDA_SHLVL=1
             CONDA_SUBDIR=osx-64
           CURL_CA_BUNDLE=<not set>
                 INFOPATH=/opt/homebrew/share/info:
               LD_PRELOAD=<not set>
                  MANPATH=/opt/homebrew/share/man::
                     PATH=/opt/miniconda3/bin:/opt/miniconda3/condabin:/opt/homebrew/bin:/opt/ho
                          mebrew/sbin:/Library/Frameworks/Python.framework/Versions/3.12/bin:/us
                          r/local/bin:/System/Cryptexes/App/usr/bin:/usr/bin:/bin:/usr/sbin:/sbi
                          n:/miniconda3/bin:/var/run/com.apple.security.cryptexd/codex.system/bo
                          otstrap/usr/local/bin:/var/run/com.apple.security.cryptexd/codex.syste
                          m/bootstrap/usr/bin:/var/run/com.apple.security.cryptexd/codex.system/
                          bootstrap/usr/appleinternal/bin
       REQUESTS_CA_BUNDLE=<not set>
            SSL_CERT_FILE=<not set>

     active environment : base
    active env location : /opt/miniconda3
            shell level : 1
       user config file : /Users/valerylozada/.condarc
 populated config files : /Users/valerylozada/.condarc
          conda version : 24.5.0
    conda-build version : not installed
         python version : 3.12.4.final.0
                 solver : classic
       virtual packages : __archspec=1=x86_64
                          __conda=24.5.0=0
                          __osx=14.3.1=0
                          __unix=0=0
       base environment : /opt/miniconda3  (writable)
      conda av data dir : /opt/miniconda3/etc/conda
  conda av metadata url : None
           channel URLs : https://repo.anaconda.com/pkgs/main/osx-64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/r/osx-64
                          https://repo.anaconda.com/pkgs/r/noarch
          package cache : /opt/miniconda3/pkgs
                          /Users/valerylozada/.conda/pkgs
       envs directories : /opt/miniconda3/envs
                          /Users/valerylozada/.conda/envs
               platform : osx-64
             user-agent : conda/24.5.0 requests/2.32.2 CPython/3.12.4 Darwin/23.3.0 OSX/14.3.1 aau/0.4.4 c/. s/. e/.
                UID:GID : 502:20
             netrc file : None
           offline mode : False


An 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 <package>

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 <package>

If submitted, this report will be used by core maintainers to improve
future releases of conda.
Would you like conda to send this report to the core maintainers? [y/N]:

lizgehret · July 2, 2024, 5:40pm

Hey @VLoz,

I've searched around for this error, and didn't find much - but it seems possible there's a corrupted file somewhere that's causing problems. Can you try running conda clean --all and then attempting to re-install (any of the qiime2 environments) and see if that fixes the problem?

VLoz · July 2, 2024, 6:27pm

Hi @lizgehret,

I ran conda clean --all and it worked. However, when I tried to download the qiime2 it gave me the same error.

lizgehret · July 9, 2024, 5:42pm

Hey @VLoz,

Apologies for the delay! Let's try one more thing.

(For full disclosure, I don't have a ton of confidence in this working but I think it's worth a shot)

Go ahead and uninstall miniconda one more time, re-install it again and try installing QIIME 2 using the Mac intel chip instructions (i.e. without the CONDA_SUBDIR environment variable). Your silicon chip should need the osx-64 subdir designation, but I think it's worth trying one more install without, just to see what happens.

If this doesn't work, it may be worth installing Docker and running QIIME 2 within a virtual machine (even though that's not the most convenient option).

VLoz · July 11, 2024, 9:42pm

@lizgehret Thanks! it worked!

system · August 12, 2024, 3:42am

This topic was automatically closed 31 days after the last reply. New replies are no longer allowed.