Please remove this file manually (you may need to reboot to free file handles)

[orena1]

Checklist

• I added a descriptive title
• I searched open reports and couldn't find a duplicate

What happened?

I am trying to install anaconda on a a mounted network drive which I think is a bit slow, I am running this command:
./conda.exe constructor --prefix /mnt/nasquatch/data/colabs/anaconda3/ --extract-conda-pkgs
(I am using this command and not the ./Anaconda3-2022.05-Linux-x86_64.sh -u -b -p /mnt/nasquatch/data/colabs/anaconda3 to avoid extracting the packages each time)
and get this error:

./conda.exe constructor --prefix /mnt/nasquatch/data/colabs/anaconda3/ --extract-conda-pkgs
Extracting : regex-2022.3.15-py39h7f8727e_0.conda:   0%|▎                                                                                                                             1/431 [00:04<34:57,  4.88s/it]
Could not remove or rename /mnt/nasquatch/data/colabs/anaconda3/pkgs/libspatialindex-1.9.3-h2531618_0u9jnfyfi/pkg-libspatialindex-1.9.3-h2531618_0.tar.zst.  Please remove this file manually (you may need to reboot to free file handles)

concurrent.futures.process._RemoteTraceback:
'''
Traceback (most recent call last):
  File "concurrent/futures/process.py", line 384, in wait_result_broken_or_wakeup
  File "multiprocessing/connection.py", line 256, in recv
TypeError: __init__() missing 1 required positional argument: 'msg'
'''

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "entry_point.py", line 69, in <module>
  File "concurrent/futures/process.py", line 559, in _chain_from_iterable_of_lists
  File "concurrent/futures/_base.py", line 608, in result_iterator
  File "concurrent/futures/_base.py", line 445, in result
  File "concurrent/futures/_base.py", line 390, in __get_result
concurrent.futures.process.BrokenProcessPool: A process in the process pool was terminated abruptly while the future was running or pending.
[69850] Failed to execute script entry_point
'''

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "entry_point.py", line 69, in <module>
  File "concurrent/futures/process.py", line 559, in _chain_from_iterable_of_lists
  File "concurrent/futures/_base.py", line 608, in result_iterator
  File "concurrent/futures/_base.py", line 445, in result
  File "concurrent/futures/_base.py", line 390, in __get_result
concurrent.futures.process.BrokenProcessPool: A process in the process pool was terminated abruptly while the future was running or pending.
[69655] Failed to execute script entry_point

I have permission for the folder, I think it just a bit slow in updating it, from what I see here:
https://github.com/conda/conda/blob/fc92ea3353cce71df24fac31ce333ec9f8cf7ba7/conda/gateways/disk/delete.py#L153
there is a max_retries variable, but I do not see that it is used at all. I assume if I would have managed to increase its value it will work, but as I am working with a conda.exe I am not sure how to modify/debug the code.

Conda Info

./conda.exe info

     active environment : None
            shell level : 0
       user config file : /home/andermannlab/.condarc
 populated config files :
          conda version : 4.10.3
    conda-build version : not installed
         python version : 3.9.7.final.0
       virtual packages : __cuda=11.4=0
                          __linux=5.15.0=0
                          __glibc=2.31=0
                          __unix=0=0
                          __archspec=1=x86_64
       base environment : /tmp/_MEIfxUMNt  (read only)
      conda av data dir : /tmp/_MEIfxUMNt/etc/conda
  conda av metadata url : None
           channel URLs : 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
          package cache : /tmp/_MEIfxUMNt/pkgs
                          /home/andermannlab/.conda/pkgs
       envs directories : /home/andermannlab/.conda/envs
                          /tmp/_MEIfxUMNt/envs
               platform : linux-64
             user-agent : conda/4.10.3 requests/2.26.0 CPython/3.9.7 Linux/5.15.0-48-generic ubuntu/20.04.5 glibc/2.31
                UID:GID : 1000:1000
             netrc file : None
           offline mode : False

Conda Config

NA

Conda list

./conda.exe list --show-channel-urls

EnvironmentLocationNotFound: Not a conda environment: /tmp/_MEIHthzwn

Additional Context

No response

[orena1]

The problem was that I was missing mfsymlinks option for the CIFS mount options in /etc/fstab
I've found the problem (when trying to move an already installed version [on the same path] to the NAS], when I did this I got this error:
ln: failed to create symbolic link 'test': Operation not supported
Which is much more informative, maybe it could be added, I'll have a look [I'm keeping the ticket open until I'll try to implement better error message]

[travishathaway]

@orena1, thank you for reporting this. I have moved this issue to the "constructor" repository because this issue is more relevant here.

Please update us with the status as you learn more about it.

If at anytime you feel that nothing else needs to be done, I encourage you to close this issue.

[github-actions]

Hi there, thank you for your contribution!

This issue has been automatically marked as stale because it has not had recent activity. It will be closed automatically if no further activity occurs.

If you would like this issue to remain open please:

1. Verify that you can still reproduce the issue at hand
2. Comment that the issue is still reproducible and include:
   - What OS and version you reproduced the issue on
   - What steps you followed to reproduce the issue

NOTE: If this issue was closed prematurely, please leave a comment.

Thanks!

[jaimergp]

not stale

[orena1]

Thanks, I think my report include the exact problem.
I assume it would be good to have a better error log, instead of
[69655] Failed to execute script entry_point
something about the symlink, right?

[jaimergp]

This was fixed in conda-standalone earlier this year. The exceptions should be more informative now. Thanks!