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tlvu avatar tlvu commented on September 22, 2024

Mamba was installed in the base conda env while the Jupyter is installed in another conda env. Should mamba be installed in the same conda env as the Jupyter?

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fcollonval avatar fcollonval commented on September 22, 2024

Sorry for the late answer.

Mamba was installed in the base conda env while the Jupyter is installed in another conda env. Should mamba be installed in the same conda env as the Jupyter?

No it should not.

"error" : "RuntimeError('LockFile error. Aborting.')",

Could you try running the following command in a terminal on the machine?

/opt/conda/bin/mamba repoquery search * --json

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tlvu avatar tlvu commented on September 22, 2024

Could you try running the following command in a terminal on the machine?

/opt/conda/bin/mamba repoquery search * --json

@fcollonval Sorry for the late reply, from which dir I should run that command? From / I get this error:

usage: mamba [-h] [-V] command ...
mamba: error: unrecognized arguments: boot dev environment.yml etc home lib lib64 media mnt notebook_dir opt proc root run sbin srv sys tmp usr var

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tlvu avatar tlvu commented on September 22, 2024

Might be related, mamba install pyston_lite_autoload -c pyston -c conda-forge I get this error

    Traceback (most recent call last):
      File "/opt/conda/lib/python3.9/site-packages/conda/exceptions.py", line 1114, in __call__
        return func(*args, **kwargs)
      File "/opt/conda/lib/python3.9/site-packages/mamba/mamba.py", line 935, in exception_converter
        raise e
      File "/opt/conda/lib/python3.9/site-packages/mamba/mamba.py", line 929, in exception_converter
        exit_code = _wrapped_main(*args, **kwargs)
      File "/opt/conda/lib/python3.9/site-packages/mamba/mamba.py", line 887, in _wrapped_main
        result = do_call(args, p)
      File "/opt/conda/lib/python3.9/site-packages/mamba/mamba.py", line 750, in do_call
        exit_code = install(args, parser, "install")
      File "/opt/conda/lib/python3.9/site-packages/mamba/mamba.py", line 497, in install
        index = load_channels(pool, channels, repos)
      File "/opt/conda/lib/python3.9/site-packages/mamba/utils.py", line 129, in load_channels
        index = get_index(
      File "/opt/conda/lib/python3.9/site-packages/mamba/utils.py", line 110, in get_index
        is_downloaded = dlist.download(api.MAMBA_DOWNLOAD_FAILFAST)
    RuntimeError: Operation not permitted: '/opt/conda/pkgs/cache/47929eba.json'

But the same using conda works: conda install pyston_lite_autoload -c pyston -c conda-forge

conda-4.13.0
mamba-0.24.0

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tlvu avatar tlvu commented on September 22, 2024

@fcollonval I think I got what you wanted

$ /opt/conda/bin/mamba repoquery search birdy --json

{
  "command": "/opt/conda/bin/mamba repoquery search birdy --json",
  "conda_info": {
    "GID": 1000,
    "UID": 1000,
    "active_prefix": "/opt/conda/envs/birdy",
    "active_prefix_name": "birdy",
    "av_data_dir": "/opt/conda/etc/conda",
    "av_metadata_url_base": null,
    "channels": [
      "https://repo.anaconda.com/pkgs/main/linux-64",
      "https://repo.anaconda.com/pkgs/main/noarch",
      "https://repo.anaconda.com/pkgs/r/linux-64",
      "https://repo.anaconda.com/pkgs/r/noarch"
    ],
    "conda_build_version": "not installed",
    "conda_env_version": "4.13.0",
    "conda_location": "/opt/conda/lib/python3.9/site-packages/conda",
    "conda_prefix": "/opt/conda",
    "conda_private": false,
    "conda_shlvl": 2,
    "conda_version": "4.13.0",
    "config_files": [],
    "default_prefix": "/opt/conda/envs/birdy",
    "env_vars": {
      "CIO_TEST": "<not set>",
      "CONDA_DEFAULT_ENV": "birdy",
      "CONDA_EXE": "/opt/conda/bin/conda",
      "CONDA_PREFIX": "/opt/conda/envs/birdy",
      "CONDA_PREFIX_1": "/opt/conda",
      "CONDA_PROMPT_MODIFIER": "(birdy) ",
      "CONDA_PYTHON_EXE": "/opt/conda/bin/python",
      "CONDA_ROOT": "/opt/conda",
      "CONDA_SHLVL": "2",
      "CURL_CA_BUNDLE": "<not set>",
      "PATH": "/opt/conda/envs/birdy/bin:/opt/conda/condabin:/opt/conda/envs/birdy/bin:/opt/conda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin",
      "REQUESTS_CA_BUNDLE": "<not set>",
      "SSL_CERT_FILE": "<not set>"
    },
    "envs": [],
    "envs_dirs": [
      "/opt/conda/envs",
      "/notebook_dir/writable-workspace/.home/.conda/envs"
    ],
    "netrc_file": null,
    "offline": false,
    "pkgs_dirs": [
      "/opt/conda/pkgs",
      "/notebook_dir/writable-workspace/.home/.conda/pkgs"
    ],
    "platform": "linux-64",
    "python_version": "3.9.12.final.0",
    "rc_path": "/notebook_dir/writable-workspace/.home/.condarc",
    "requests_version": "2.27.1",
    "root_prefix": "/opt/conda",
    "root_writable": true,
    "site_dirs": [],
    "sys.executable": "/opt/conda/bin/python",
    "sys.prefix": "/opt/conda",
    "sys.version": "3.9.12 (main, Apr  5 2022, 06:56:58) \n[GCC 7.5.0]",
    "sys_rc_path": "/opt/conda/.condarc",
    "user_agent": "conda/4.13.0 requests/2.27.1 CPython/3.9.12 Linux/4.18.0-348.20.1.el8_5.x86_64 debian/11 glibc/2.31",
    "user_rc_path": "/notebook_dir/writable-workspace/.home/.condarc",
    "virtual_pkgs": [
      [
        "__linux",
        "4.18.0",
        "0"
      ],
      [
        "__glibc",
        "2.31",
        "0"
      ],
      [
        "__unix",
        "0",
        "0"
      ],
      [
        "__archspec",
        "1",
        "x86_64"
      ]
    ]
  },
  "error": "RuntimeError(\"Operation not permitted: '/opt/conda/pkgs/cache/3e39a7aa.json'\")",
  "exception_name": "RuntimeError",
  "exception_type": "<class 'RuntimeError'>",
  "traceback": "Traceback (most recent call last):\n  File \"/opt/conda/lib/python3.9/site-packages/conda/exceptions.py\", line 1114, in __call__\n    return func(*args, **kwargs)\n  File \"/opt/conda/lib/python3.9/site-packages/mamba/mamba.py\", line 935, in exception_converter\n    raise e\n  File \"/opt/conda/lib/python3.9/site-packages/mamba/mamba.py\", line 929, in exception_converter\n    exit_code = _wrapped_main(*args, **kwargs)\n  File \"/opt/conda/lib/python3.9/site-packages/mamba/mamba.py\", line 887, in _wrapped_main\n    result = do_call(args, p)\n  File \"/opt/conda/lib/python3.9/site-packages/mamba/mamba.py\", line 760, in do_call\n    exit_code = repoquery(args, parser)\n  File \"/opt/conda/lib/python3.9/site-packages/mamba/mamba.py\", line 702, in repoquery\n    pool = repoquery_api.create_pool(channels, platform, use_installed)\n  File \"/opt/conda/lib/python3.9/site-packages/mamba/repoquery.py\", line 46, in create_pool\n    load_channels(\n  File \"/opt/conda/lib/python3.9/site-packages/mamba/utils.py\", line 129, in load_channels\n    index = get_index(\n  File \"/opt/conda/lib/python3.9/site-packages/mamba/utils.py\", line 110, in get_index\n    is_downloaded = dlist.download(api.MAMBA_DOWNLOAD_FAILFAST)\nRuntimeError: Operation not permitted: '/opt/conda/pkgs/cache/3e39a7aa.json'\n"
}

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tlvu avatar tlvu commented on September 22, 2024

"error": "RuntimeError("Operation not permitted: '/opt/conda/pkgs/cache/3e39a7aa.json'")",

But I do have write access to that file, I tried echo >> /opt/conda/pkgs/cache/3e39a7aa.json and it works fine.

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tlvu avatar tlvu commented on September 22, 2024

@fcollonval I found it, the current user have to be the owner of /opt/conda/pkgs/cache/ folder. Just having write-access is not enough for mamba. I was enough for conda.

Should I still keep this issue open to fix the "current user have to be the owner of /opt/conda/pkgs/cache/ folder" to be equivalent with conda? If this won't be fixed then I can close this issue.

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fcollonval avatar fcollonval commented on September 22, 2024

Thanks a lot @tlvu to dig that one up. Would you mind opening an issue in the mamba repository?

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tlvu avatar tlvu commented on September 22, 2024

Thanks a lot @tlvu to dig that one up. Would you mind opening an issue in the mamba repository?

Sure. Will close this issue once the other one in mamba repo opened.

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fcollonval avatar fcollonval commented on September 22, 2024

Thanks

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pgramme avatar pgramme commented on September 22, 2024

Sure. Will close this issue once the other one in mamba repo opened.

Hi! The issue already existed in the main mamba repo: mamba-org/mamba#488
To me it was fixed in mamba 1.2.0 (cf issue's discussion)

PS: I'm using mamba but not gator, Googling for the error first brought me here...

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tlvu avatar tlvu commented on September 22, 2024

Sure. Will close this issue once the other one in mamba repo opened.

Hi! The issue already existed in the main mamba repo: mamba-org/mamba#488 To me it was fixed in mamba 1.2.0 (cf issue's discussion)

PS: I'm using mamba but not gator, Googling for the error first brought me here...

Closing as per comment above. Thanks @pgramme

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