Anaconda installation failing on Linux

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1
  • operating system: Pop!_OS 21.04 LTS (an Ubuntu distro)

  1. First I installed Anaconda successfully
    sh Anaconda3-2021.05-Linux-x86_64.sh

  2. Tried to install dependencies:
    conda install scipy matplotlib scikit-learn mayavi ipython-notebook

Collecting package metadata (current_repodata.json): failed
WARNING conda.exceptions:print_unexpected_error_report(1213): KeyError('pkgs_dirs')
Traceback (most recent call last):
  File "/home/jdien/anaconda3/lib/python3.8/site-packages/conda/exceptions.py", line 1079, in __call__
    return func(*args, **kwargs)
  File "/home/jdien/anaconda3/lib/python3.8/site-packages/conda/cli/main.py", line 84, in _main
    exit_code = do_call(args, p)
  File "/home/jdien/anaconda3/lib/python3.8/site-packages/conda/cli/conda_argparse.py", line 83, in do_call
    return getattr(module, func_name)(args, parser)
  File "/home/jdien/anaconda3/lib/python3.8/site-packages/conda/cli/main_install.py", line 20, in execute
    install(args, parser, 'install')
  File "/home/jdien/anaconda3/lib/python3.8/site-packages/conda/cli/install.py", line 261, in install
    unlink_link_transaction = solver.solve_for_transaction(
  File "/home/jdien/anaconda3/lib/python3.8/site-packages/conda/core/solve.py", line 114, in solve_for_transaction
    unlink_precs, link_precs = self.solve_for_diff(update_modifier, deps_modifier,
  File "/home/jdien/anaconda3/lib/python3.8/site-packages/conda/core/solve.py", line 157, in solve_for_diff
    final_precs = self.solve_final_state(update_modifier, deps_modifier, prune, ignore_pinned,
  File "/home/jdien/anaconda3/lib/python3.8/site-packages/conda/core/solve.py", line 262, in solve_final_state
    ssc = self._collect_all_metadata(ssc)
  File "/home/jdien/anaconda3/lib/python3.8/site-packages/conda/common/io.py", line 88, in decorated
    return f(*args, **kwds)
  File "/home/jdien/anaconda3/lib/python3.8/site-packages/conda/core/solve.py", line 397, in _collect_all_metadata
    _supplement_index_with_system(virtual_pkg_index)
  File "/home/jdien/anaconda3/lib/python3.8/site-packages/conda/core/index.py", line 164, in _supplement_index_with_system
    dist_name, dist_version = context.os_distribution_name_version
  File "/home/jdien/anaconda3/lib/python3.8/site-packages/conda/_vendor/auxlib/decorators.py", line 268, in new_fget
    cache[inner_attname] = func(self)
  File "/home/jdien/anaconda3/lib/python3.8/site-packages/conda/base/context.py", line 806, in os_distribution_name_version
    from conda._vendor.distro import id, version
  File "/home/jdien/anaconda3/lib/python3.8/site-packages/conda/_vendor/distro.py", line 1084, in <module>
    _distro = LinuxDistribution()
  File "/home/jdien/anaconda3/lib/python3.8/site-packages/conda/_vendor/distro.py", line 599, in __init__
    self._lsb_release_info = self._get_lsb_release_info() \
  File "/home/jdien/anaconda3/lib/python3.8/site-packages/conda/_vendor/distro.py", line 943, in _get_lsb_release_info
    raise subprocess.CalledProcessError(code, cmd, stdout, stderr)
subprocess.CalledProcessError: Command 'lsb_release -a' returned non-zero exit status 1.

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/jdien/anaconda3/lib/python3.8/site-packages/conda/exceptions.py", line 1211, in print_unexpected_error_report
    message_builder.append(get_main_info_str(error_report['conda_info']))
  File "/home/jdien/anaconda3/lib/python3.8/site-packages/conda/cli/main_info.py", line 240, in get_main_info_str
    info_dict['_' + key] = ('\n' + 26 * ' ').join(info_dict[key])
KeyError: 'pkgs_dirs'

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

    Traceback (most recent call last):
      File "/home/jdien/anaconda3/lib/python3.8/site-packages/conda/exceptions.py", line 1079, in __call__
        return func(*args, **kwargs)
      File "/home/jdien/anaconda3/lib/python3.8/site-packages/conda/cli/main.py", line 84, in _main
        exit_code = do_call(args, p)
      File "/home/jdien/anaconda3/lib/python3.8/site-packages/conda/cli/conda_argparse.py", line 83, in do_call
        return getattr(module, func_name)(args, parser)
      File "/home/jdien/anaconda3/lib/python3.8/site-packages/conda/cli/main_install.py", line 20, in execute
        install(args, parser, 'install')
      File "/home/jdien/anaconda3/lib/python3.8/site-packages/conda/cli/install.py", line 261, in install
        unlink_link_transaction = solver.solve_for_transaction(
      File "/home/jdien/anaconda3/lib/python3.8/site-packages/conda/core/solve.py", line 114, in solve_for_transaction
        unlink_precs, link_precs = self.solve_for_diff(update_modifier, deps_modifier,
      File "/home/jdien/anaconda3/lib/python3.8/site-packages/conda/core/solve.py", line 157, in solve_for_diff
        final_precs = self.solve_final_state(update_modifier, deps_modifier, prune, ignore_pinned,
      File "/home/jdien/anaconda3/lib/python3.8/site-packages/conda/core/solve.py", line 262, in solve_final_state
        ssc = self._collect_all_metadata(ssc)
      File "/home/jdien/anaconda3/lib/python3.8/site-packages/conda/common/io.py", line 88, in decorated
        return f(*args, **kwds)
      File "/home/jdien/anaconda3/lib/python3.8/site-packages/conda/core/solve.py", line 397, in _collect_all_metadata
        _supplement_index_with_system(virtual_pkg_index)
      File "/home/jdien/anaconda3/lib/python3.8/site-packages/conda/core/index.py", line 164, in _supplement_index_with_system
        dist_name, dist_version = context.os_distribution_name_version
      File "/home/jdien/anaconda3/lib/python3.8/site-packages/conda/_vendor/auxlib/decorators.py", line 268, in new_fget
        cache[inner_attname] = func(self)
      File "/home/jdien/anaconda3/lib/python3.8/site-packages/conda/base/context.py", line 806, in os_distribution_name_version
        from conda._vendor.distro import id, version
      File "/home/jdien/anaconda3/lib/python3.8/site-packages/conda/_vendor/distro.py", line 1084, in <module>
        _distro = LinuxDistribution()
      File "/home/jdien/anaconda3/lib/python3.8/site-packages/conda/_vendor/distro.py", line 599, in __init__
        self._lsb_release_info = self._get_lsb_release_info() \
      File "/home/jdien/anaconda3/lib/python3.8/site-packages/conda/_vendor/distro.py", line 943, in _get_lsb_release_info
        raise subprocess.CalledProcessError(code, cmd, stdout, stderr)
    subprocess.CalledProcessError: Command 'lsb_release -a' returned non-zero exit status 1.

`$ /home/jdien/anaconda3/bin/conda install scipy matplotlib scikit-learn mayavi ipython-notebook`

  environment variables:
conda info could not be constructed.
KeyError('pkgs_dirs')

also tried pip:
pip install mne

ERROR: Exception:
Traceback (most recent call last):
  File "/home/jdien/anaconda3/lib/python3.8/site-packages/pip/_internal/cli/base_command.py", line 189, in _main
    status = self.run(options, args)
  File "/home/jdien/anaconda3/lib/python3.8/site-packages/pip/_internal/cli/req_command.py", line 178, in wrapper
    return func(self, options, args)
  File "/home/jdien/anaconda3/lib/python3.8/site-packages/pip/_internal/commands/install.py", line 267, in run
    session = self.get_default_session(options)
  File "/home/jdien/anaconda3/lib/python3.8/site-packages/pip/_internal/cli/req_command.py", line 76, in get_default_session
    self._session = self.enter_context(self._build_session(options))
  File "/home/jdien/anaconda3/lib/python3.8/site-packages/pip/_internal/cli/req_command.py", line 86, in _build_session
    session = PipSession(
  File "/home/jdien/anaconda3/lib/python3.8/site-packages/pip/_internal/network/session.py", line 245, in __init__
    self.headers["User-Agent"] = user_agent()
  File "/home/jdien/anaconda3/lib/python3.8/site-packages/pip/_internal/network/session.py", line 132, in user_agent
    zip(["name", "version", "id"], distro.linux_distribution()),
  File "/home/jdien/anaconda3/lib/python3.8/site-packages/pip/_vendor/distro.py", line 125, in linux_distribution
    return _distro.linux_distribution(full_distribution_name)
  File "/home/jdien/anaconda3/lib/python3.8/site-packages/pip/_vendor/distro.py", line 681, in linux_distribution
    self.version(),
  File "/home/jdien/anaconda3/lib/python3.8/site-packages/pip/_vendor/distro.py", line 741, in version
    self.lsb_release_attr('release'),
  File "/home/jdien/anaconda3/lib/python3.8/site-packages/pip/_vendor/distro.py", line 903, in lsb_release_attr
    return self._lsb_release_info.get(attribute, '')
  File "/home/jdien/anaconda3/lib/python3.8/site-packages/pip/_vendor/distro.py", line 556, in __get__
    ret = obj.__dict__[self._fname] = self._f(obj)
  File "/home/jdien/anaconda3/lib/python3.8/site-packages/pip/_vendor/distro.py", line 1014, in _lsb_release_info
    stdout = subprocess.check_output(cmd, stderr=devnull)
  File "/home/jdien/anaconda3/lib/python3.8/subprocess.py", line 415, in check_output
    return run(*popenargs, stdout=PIPE, timeout=timeout, check=True,
  File "/home/jdien/anaconda3/lib/python3.8/subprocess.py", line 516, in run
    raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command '('lsb_release', '-a')' returned non-zero exit status 1.
Traceback (most recent call last):
  File "/home/jdien/anaconda3/bin/pip", line 11, in <module>
    sys.exit(main())
  File "/home/jdien/anaconda3/lib/python3.8/site-packages/pip/_internal/cli/main.py", line 73, in main
    return command.main(cmd_args)
  File "/home/jdien/anaconda3/lib/python3.8/site-packages/pip/_internal/cli/base_command.py", line 111, in main
    return self._main(args)
  File "/home/jdien/anaconda3/lib/python3.8/site-packages/pip/_internal/cli/base_command.py", line 226, in _main
    self.handle_pip_version_check(options)
  File "/home/jdien/anaconda3/lib/python3.8/site-packages/pip/_internal/cli/req_command.py", line 145, in handle_pip_version_check
    session = self._build_session(
  File "/home/jdien/anaconda3/lib/python3.8/site-packages/pip/_internal/cli/req_command.py", line 86, in _build_session
    session = PipSession(
  File "/home/jdien/anaconda3/lib/python3.8/site-packages/pip/_internal/network/session.py", line 245, in __init__
    self.headers["User-Agent"] = user_agent()
  File "/home/jdien/anaconda3/lib/python3.8/site-packages/pip/_internal/network/session.py", line 132, in user_agent
    zip(["name", "version", "id"], distro.linux_distribution()),
  File "/home/jdien/anaconda3/lib/python3.8/site-packages/pip/_vendor/distro.py", line 125, in linux_distribution
    return _distro.linux_distribution(full_distribution_name)
  File "/home/jdien/anaconda3/lib/python3.8/site-packages/pip/_vendor/distro.py", line 681, in linux_distribution
    self.version(),
  File "/home/jdien/anaconda3/lib/python3.8/site-packages/pip/_vendor/distro.py", line 741, in version
    self.lsb_release_attr('release'),
  File "/home/jdien/anaconda3/lib/python3.8/site-packages/pip/_vendor/distro.py", line 903, in lsb_release_attr
    return self._lsb_release_info.get(attribute, '')
  File "/home/jdien/anaconda3/lib/python3.8/site-packages/pip/_vendor/distro.py", line 556, in __get__
    ret = obj.__dict__[self._fname] = self._f(obj)
  File "/home/jdien/anaconda3/lib/python3.8/site-packages/pip/_vendor/distro.py", line 1014, in _lsb_release_info
    stdout = subprocess.check_output(cmd, stderr=devnull)
  File "/home/jdien/anaconda3/lib/python3.8/subprocess.py", line 415, in check_output
    return run(*popenargs, stdout=PIPE, timeout=timeout, check=True,
  File "/home/jdien/anaconda3/lib/python3.8/subprocess.py", line 516, in run
    raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command '('lsb_release', '-a')' returned non-zero exit status 1.

and with conda:


conda create --name=mne --channel=conda-forge mne

Collecting package metadata (current_repodata.json): failed
WARNING conda.exceptions:print_unexpected_error_report(1213): KeyError('pkgs_dirs')
Traceback (most recent call last):
  File "/home/jdien/anaconda3/lib/python3.8/site-packages/conda/exceptions.py", line 1079, in __call__
    return func(*args, **kwargs)
  File "/home/jdien/anaconda3/lib/python3.8/site-packages/conda/cli/main.py", line 84, in _main
    exit_code = do_call(args, p)
  File "/home/jdien/anaconda3/lib/python3.8/site-packages/conda/cli/conda_argparse.py", line 83, in do_call
    return getattr(module, func_name)(args, parser)
  File "/home/jdien/anaconda3/lib/python3.8/site-packages/conda/cli/main_create.py", line 41, in execute
    install(args, parser, 'create')
  File "/home/jdien/anaconda3/lib/python3.8/site-packages/conda/cli/install.py", line 261, in install
    unlink_link_transaction = solver.solve_for_transaction(
  File "/home/jdien/anaconda3/lib/python3.8/site-packages/conda/core/solve.py", line 114, in solve_for_transaction
    unlink_precs, link_precs = self.solve_for_diff(update_modifier, deps_modifier,
  File "/home/jdien/anaconda3/lib/python3.8/site-packages/conda/core/solve.py", line 157, in solve_for_diff
    final_precs = self.solve_final_state(update_modifier, deps_modifier, prune, ignore_pinned,
  File "/home/jdien/anaconda3/lib/python3.8/site-packages/conda/core/solve.py", line 262, in solve_final_state
    ssc = self._collect_all_metadata(ssc)
  File "/home/jdien/anaconda3/lib/python3.8/site-packages/conda/common/io.py", line 88, in decorated
    return f(*args, **kwds)
  File "/home/jdien/anaconda3/lib/python3.8/site-packages/conda/core/solve.py", line 397, in _collect_all_metadata
    _supplement_index_with_system(virtual_pkg_index)
  File "/home/jdien/anaconda3/lib/python3.8/site-packages/conda/core/index.py", line 164, in _supplement_index_with_system
    dist_name, dist_version = context.os_distribution_name_version
  File "/home/jdien/anaconda3/lib/python3.8/site-packages/conda/_vendor/auxlib/decorators.py", line 268, in new_fget
    cache[inner_attname] = func(self)
  File "/home/jdien/anaconda3/lib/python3.8/site-packages/conda/base/context.py", line 806, in os_distribution_name_version
    from conda._vendor.distro import id, version
  File "/home/jdien/anaconda3/lib/python3.8/site-packages/conda/_vendor/distro.py", line 1084, in <module>
    _distro = LinuxDistribution()
  File "/home/jdien/anaconda3/lib/python3.8/site-packages/conda/_vendor/distro.py", line 599, in __init__
    self._lsb_release_info = self._get_lsb_release_info() \
  File "/home/jdien/anaconda3/lib/python3.8/site-packages/conda/_vendor/distro.py", line 943, in _get_lsb_release_info
    raise subprocess.CalledProcessError(code, cmd, stdout, stderr)
subprocess.CalledProcessError: Command 'lsb_release -a' returned non-zero exit status 1.

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/jdien/anaconda3/lib/python3.8/site-packages/conda/exceptions.py", line 1211, in print_unexpected_error_report
    message_builder.append(get_main_info_str(error_report['conda_info']))
  File "/home/jdien/anaconda3/lib/python3.8/site-packages/conda/cli/main_info.py", line 240, in get_main_info_str
    info_dict['_' + key] = ('\n' + 26 * ' ').join(info_dict[key])
KeyError: 'pkgs_dirs'

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

    Traceback (most recent call last):
      File "/home/jdien/anaconda3/lib/python3.8/site-packages/conda/exceptions.py", line 1079, in __call__
        return func(*args, **kwargs)
      File "/home/jdien/anaconda3/lib/python3.8/site-packages/conda/cli/main.py", line 84, in _main
        exit_code = do_call(args, p)
      File "/home/jdien/anaconda3/lib/python3.8/site-packages/conda/cli/conda_argparse.py", line 83, in do_call
        return getattr(module, func_name)(args, parser)
      File "/home/jdien/anaconda3/lib/python3.8/site-packages/conda/cli/main_create.py", line 41, in execute
        install(args, parser, 'create')
      File "/home/jdien/anaconda3/lib/python3.8/site-packages/conda/cli/install.py", line 261, in install
        unlink_link_transaction = solver.solve_for_transaction(
      File "/home/jdien/anaconda3/lib/python3.8/site-packages/conda/core/solve.py", line 114, in solve_for_transaction
        unlink_precs, link_precs = self.solve_for_diff(update_modifier, deps_modifier,
      File "/home/jdien/anaconda3/lib/python3.8/site-packages/conda/core/solve.py", line 157, in solve_for_diff
        final_precs = self.solve_final_state(update_modifier, deps_modifier, prune, ignore_pinned,
      File "/home/jdien/anaconda3/lib/python3.8/site-packages/conda/core/solve.py", line 262, in solve_final_state
        ssc = self._collect_all_metadata(ssc)
      File "/home/jdien/anaconda3/lib/python3.8/site-packages/conda/common/io.py", line 88, in decorated
        return f(*args, **kwds)
      File "/home/jdien/anaconda3/lib/python3.8/site-packages/conda/core/solve.py", line 397, in _collect_all_metadata
        _supplement_index_with_system(virtual_pkg_index)
      File "/home/jdien/anaconda3/lib/python3.8/site-packages/conda/core/index.py", line 164, in _supplement_index_with_system
        dist_name, dist_version = context.os_distribution_name_version
      File "/home/jdien/anaconda3/lib/python3.8/site-packages/conda/_vendor/auxlib/decorators.py", line 268, in new_fget
        cache[inner_attname] = func(self)
      File "/home/jdien/anaconda3/lib/python3.8/site-packages/conda/base/context.py", line 806, in os_distribution_name_version
        from conda._vendor.distro import id, version
      File "/home/jdien/anaconda3/lib/python3.8/site-packages/conda/_vendor/distro.py", line 1084, in <module>
        _distro = LinuxDistribution()
      File "/home/jdien/anaconda3/lib/python3.8/site-packages/conda/_vendor/distro.py", line 599, in __init__
        self._lsb_release_info = self._get_lsb_release_info() \
      File "/home/jdien/anaconda3/lib/python3.8/site-packages/conda/_vendor/distro.py", line 943, in _get_lsb_release_info
        raise subprocess.CalledProcessError(code, cmd, stdout, stderr)
    subprocess.CalledProcessError: Command 'lsb_release -a' returned non-zero exit status 1.

`$ /home/jdien/anaconda3/bin/conda create --name=mne --channel=conda-forge mne`

  environment variables:
conda info could not be constructed.
KeyError('pkgs_dirs')
2

Hello @jdien07 and welcome to the forum!

It appears that the following command is failing:

lsb_release -a

Can you try running this in the terminal and see what output it produces?

Best,
Richard

3

(base) jdien@joelux:~$ lsb_release -a
Traceback (most recent call last):
File “/usr/bin/lsb_release”, line 25, in
import lsb_release
ModuleNotFoundError: No module named ‘lsb_release’

4

Ah, your feedback gave me an important clue, thank you! The problem is that I was trying to figure out how to execute .py python files via the system command in Matlab, but its shell was pointed towards the wrong python installation, not the anaconda one with the mne module. Following some instructions I found on a website, I used a command called update-alternatives to point it at the anaconda one. However, it seems that this command changed the symbolic link for the entire OS, not just Matlab’s shell, and so it messed up various things including lsb_release. I’ve put the symbolic link back the way it was, so this problem is fixed, but now I need to find the correct way to get Matlab’s shell to use anaconda.