Arch Linux User Repository

Errors

Traceback (most recent call last):
  File "/usr/bin/conda-build", line 33, in <module>
    sys.exit(load_entry_point('conda-build==3.20.5', 'console_scripts', 'conda-build')())
  File "/usr/bin/conda-build", line 25, in importlib_load_entry_point
    return next(matches).load()
  File "/usr/lib/python3.9/importlib/metadata.py", line 77, in load
    module = import_module(match.group('module'))
  File "/usr/lib/python3.9/importlib/__init__.py", line 127, in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
  File "<frozen importlib._bootstrap>", line 1030, in _gcd_import
  File "<frozen importlib._bootstrap>", line 1007, in _find_and_load
  File "<frozen importlib._bootstrap>", line 986, in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 680, in _load_unlocked
  File "<frozen importlib._bootstrap_external>", line 790, in exec_module
  File "<frozen importlib._bootstrap>", line 228, in _call_with_frames_removed
  File "/usr/lib/python3.9/site-packages/conda_build/cli/main_build.py", line 12, in <module>
    from glob2 import glob
ModuleNotFoundError: No module named 'glob2'

If you see something like this, the "error" is that AUR packages are not rebuilt when the system Python version is upgraded, which just happened again with 3.9. You need to manually upgrade each and every Python package from AUR, unfortunately. That is quite a caveat, because not everyone notices that something specific like Python is upgraded when they run pacman -Syu and see a list of 200 or more packages. This also happens with Node.js and what not.

Solution

So I have just bumped the package here as well as python-conda-build, which triggers updates with e.g. yay -Su. However, some dependencies may not have a new version now. What we could do for this case is to increase pkgrel for those other packages. It feels hacky, but at least it works.

Addendum

I am sorry for the inconvenience. Now the remaining problem is: Because of the bunch of dependencies and dependencies of dependencies, it is easy to miss one of them. =) Secondly, I do not own all the dependencies, so some will need manual maintenance either way, unfortunately. For example, you will need to reinstall python-glob2-git. Please let us know here if anyone of you runs into issues and we will try to help.

Notes

To rebuild, you need to pass the --rebuild option.

Example: yay -S python-glob2-git --rebuild

conda is not installed in your environment test01, but in the "base environment". If you installed conda with this package, there's no need for conda update conda though. You should update it with whatever AUR helper you're using.

Hi,

I just installed python-conda (fresh installation). When I run 'conda update conda', here is what I get. Thanks for your help!

$ conda update conda

PackageNotInstalledError: Package is not installed in prefix.
prefix: /home/$USER/.conda/envs/test01
package name: conda


(test01)

See the ouput of 'conda info -a':

$ conda info -a

    active environment : None
            shell level : 0
    user config file : /home/$USER/.condarc
populated config files : /home/$USER/.condarc
      conda version : 4.5.4
conda-build version : 3.10.5
     python version : 3.6.5.final.0
   base environment : /usr  (read only)
       channel URLs : <https://repo.anaconda.com/pkgs/main/linux-64>
                      <https://repo.anaconda.com/pkgs/main/noarch>
                      <https://repo.anaconda.com/pkgs/free/linux-64>
                      <https://repo.anaconda.com/pkgs/free/noarch>
                      <https://repo.anaconda.com/pkgs/r/linux-64>
                      <https://repo.anaconda.com/pkgs/r/noarch>
                      <https://repo.anaconda.com/pkgs/pro/linux-64>
                      <https://repo.anaconda.com/pkgs/pro/noarch>
                      <https://conda.anaconda.org/conda-forge/linux-64>
                      <https://conda.anaconda.org/conda-forge/noarch>
      package cache : /home/$USER/.conda/pkgs
   envs directories : /home/$USER/.conda/envs
                      /usr/envs
           platform : linux-64
         user-agent : conda/4.5.4 requests/2.18.4 CPython/3.6.5 Linux/4.16.13-1-ARCH arch/ glibc/2.27
            UID:GID : 1000:1000
         netrc file : None
       offline mode : False

# conda environments:
#
test01                *  /home/$USER/.conda/envs/test01
base                     /usr

sys.version: 3.6.5 (default, May 11 2018, 04:00:52) 
...
sys.prefix: /usr
sys.executable: /usr/bin/python3
conda location: /usr/lib/python3.6/site-packages/conda
conda-build: /usr/bin/conda-build
conda-convert: /usr/bin/conda-convert
conda-develop: /usr/bin/conda-develop
conda-env: /usr/bin/conda-env
conda-index: /usr/bin/conda-index
conda-inspect: /usr/bin/conda-inspect
conda-metapackage: /usr/bin/conda-metapackage
conda-render: /usr/bin/conda-render
conda-skeleton: /usr/bin/conda-skeleton
conda-verify: /usr/bin/conda-verify
user site dirs:

CIO_TEST: <not set>
CONDA_ROOT: /usr
CONDA_SHLVL: 0
MOZ_PLUGIN_PATH: /usr/lib/mozilla/plugins
PATH: /home/$USER/.local/bin:/usr/local/sbin:/usr/local/bin:/usr/bin:/usr/bin/site_perl:/usr/bin/vendor_perl:/usr/bin/core_perl:/usr/bin/site_perl:/usr/bin/vendor_perl:/usr/bin/core_perl
REQUESTS_CA_BUNDLE: <not set>
SSL_CERT_FILE: <not set>
WINDOWPATH: 1


WARNING: could not import _license.show_info
# try:
# $ conda install -n root _license

Add

pkgs_dirs:
  - ~/.conda/pkgs
envs_dirs:
  - ~/.conda/envs

to your ~/.condarc.

It should probably be reported upstream that the default paths should be relative to the user home, not relative to the base directory.

I'm having this issue when creating conda environment:

Solving environment: failed

NotWritableError: The current user does not have write permissions to a required path. path: /usr/pkgs/urls.txt uid: 1000 gid: 1000

If you feel that permissions on this path are set incorrectly, you can manually change them by executing

$ sudo chown 1000:1000 /usr/pkgs/urls.txt

In general, it's not advisable to use 'sudo conda'.

Sorry for the format :)

Great! Thanks for your work cyrevolt :)

For completeness, here's the content of the conda script as generated by the miniconda installer on one of my machines:

#!/home/user/miniconda3/bin/python

# -*- coding: utf-8 -*-
import re
import sys

from conda.cli import main

if __name__ == '__main__':
    sys.argv[0] = re.sub(r'(-script\.pyw?|\.exe)?$', '', sys.argv[0])
    sys.exit(main())

conda-env is the same, except that from conda.cli import main becomes from conda_env.cli.main import main (as you are doing in the PKGBUILD).

BTW completion is working perfectly for me on the fish shell. I don't think there's completion for any other shell though.

I have figured out how to get conda-env to work and it is now included. Enjoy! :)

Thank you for your suggestions mdeff!

1. I've looked into conda-env, and it is part of the main conda repo, and it is even being installed. I cannot find a conda-env executable file though. The README says even that it should be installed into the "base environment" by running: conda install -c conda conda-env I am not sure how this can be simply added to the package yet.

2. I a m not a csh user; I know setenv from fish, which appears to be just a compatibility thing and should actually be set -x, according to https://github.com/fish-shell/fish-shell/issues/2704 - it is the counterpart to bash's export, if I understand correctly. I am using it in the -git version of this package. I need to read more about this.

3. Well if we don't use setenv / set -x for zsh and fish, it makes sense to remove the export for bash also. It should be the same for all shells. I'll investigate.

4. Yup, I'm adding it. I am not sure yet though what the completion actually provides. I tried it out, but conda bu for example does not complete in neither shell. I opened a new terminal and even sourced the respective file again.

5. Awesome! I should also reach out to upstream to clarify packaging issues. The seemed to prefer the curl pipe sudo bash pattern to avoid/circumvent distro packaging so far. I hope they will be cooperative. :)

I've spotted some issues with that package:

1. /usr/bin/conda-env is not installed. I guess this file (along with /usr/bin/conda) is generated by the installer. Without conda-env users cannot access the conda env commands, e.g. conda env export.
2. Does the csh shell needs setenv instead of set? (installer uses setenv)
3. The bash shell does not need export (the variable can stay private, as done by the installer)
4. Similarly to _CONDA_EXE, _CONDA_ROOT should be set to /. For fish, set _CONDA_ROOT / (it is used for auto-completion).
5. I've submitted a PR to auto-complete conda env in fish (https://github.com/conda/conda/pull/7101).

The issues are now fixed and it works again. :) I tested with bash, fish, and zsh.

You may need to set pkgs_dirs in your condarc. To do so, you can use the CLI: https://github.com/conda/conda/blob/caedbbfe37860f3b61466408cc9ae199b3ffe910/CHANGELOG.md#4315-2017-03-20

Thanks everyone for helping and enjoy conda! :)