Dcm2bids_3.2.0.sif doesn't work

Software Support
1

Summary of what happened:

The new container of dcm2bids still isn’t functioning properly, despite multiple re-pulls.

Command used (and if a helper script was used, a link to the helper script or the command generated):

apptainer run -e --containall dcm2bids_3.2.0.sif --help

Version:

dcm2bids_3.2.0

Environment (Docker, Singularity / Apptainer, custom installation):

apptainer

Data formatted according to a validatable standard? Please provide the output of the validator:

PASTE VALIDATOR OUTPUT HERE

Relevant log outputs (up to 20 lines):

WARNING: DEPRECATED USAGE: Environment variable SINGULARITY_BIND will not be supported in the future, use APPTAINER_BIND instead
Traceback (most recent call last):
  File "/venv/bin/dcm2bids", line 5, in <module>
    from dcm2bids.cli.dcm2bids import main
  File "<frozen importlib._bootstrap>", line 1360, in _find_and_load
  File "<frozen importlib._bootstrap>", line 1322, in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 1262, in _find_spec
  File "/venv/lib/python3.12/site-packages/__editable___dcm2bids_3_2_0_finder.py", line 20, in find_spec
    return cls._find_spec(fullname, Path(pkg_path))
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/venv/lib/python3.12/site-packages/__editable___dcm2bids_3_2_0_finder.py", line 38, in _find_spec
    if candidate.exists():
       ^^^^^^^^^^^^^^^^^^
  File "/venv/lib/python3.12/pathlib.py", line 860, in exists
    self.stat(follow_symlinks=follow_symlinks)
  File "/venv/lib/python3.12/pathlib.py", line 840, in stat
    return os.stat(self, follow_symlinks=follow_symlinks)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
PermissionError: [Errno 13] Permission denied: '/dcm2bids/dcm2bids/__init__.py'```

### Screenshots / relevant information:
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2

Hi @Zhilin,

I cannot replicate your error with my 3.2.0 container. How did you pull the container? What if you add --fakeroot as one of the apptainer arguments?

Best,
Steven

3

Hi @Zhilin,

It might be related to the version of apptainer you use. If you can run apptainer --version and tell us the version, that’d be helpful. Also, you can try other versions if available and see if it outputs the same error.

Interestingly, a GH issue was just opened yesterday with the exact same error.

Running your container in apptainer 1.3.4 is just fine. Running it in 1.2.5 (or older versions of singularity) gives […same output as above…]

Cheers,
Sam

4

This is the version of my apptainer.

apptainer --version
apptainer version 1.1.3+234-g235a7f8f5-dirty

Thank you! I will try other versions of Apptainer to see if that resolves the issue.

5

Thank you very much for your help. In fact, I had already tried your suggestion before raising the issue. The problem has now been resolved; it was indeed due to the version of the container. When I set the Apptainer version to 1.3.5, the program ran normally.