fmriprep: singularity build 1.3.1 fails immediately
Looks like there are some issues with the 1.3.1 build in singularity. I get a TemplateFlow warning and a bunch of DeprecationWarnings as soon as I submit. The standard output shows that BIDS compliance was checked, but there’s nothing else in the log. The error log is below. My system has singularity v. 2.6.1.
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling
back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling
back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling
back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling
back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/site-packages/nilearn/datasets/neurovault.py:16: DeprecationWarning: Using or importing the ABCs from '
collections' instead of from 'collections.abc' is deprecated, and in 3.8 it will stop working
from collections import Container
/usr/local/miniconda/lib/python3.7/site-packages/templateflow/conf/__init__.py:22: ResourceWarning: TemplateFlow: repository not found at
/home/fmriprep/.cache/templateflow. Populating a TemplateFlow stub.
If the path reported above is not the desired location for Templateflow, please set the TEMPLATEFLOW_HOME environment variable.
warn(_msg, ResourceWarning)
/usr/local/miniconda/lib/python3.7/site-packages/datalad/utils.py:75: DeprecationWarning: dist() and linux_distribution() functions are de
precated in Python 3.5
= platform.linux_distribution()[:2]
/usr/local/miniconda/lib/python3.7/site-packages/datalad/utils.py:903: DeprecationWarning: Using or importing the ABCs from 'collections'
instead of from 'collections.abc' is deprecated, and in 3.8 it will stop working
is_decorating = not kwargs and len(args) == 1 and isinstance(args[0], collections.Callable)
/usr/local/miniconda/lib/python3.7/site-packages/datalad/support/param.py:30: DeprecationWarning: inspect.getargspec() is deprecated, use
inspect.signature() or inspect.getfullargspec()
_KNOWN_ARGS = getargspec(argparse.Action.__init__)[0] + ['action']
/usr/local/miniconda/lib/python3.7/site-packages/datalad/interface/base.py:321: DeprecationWarning: inspect.getargspec() is deprecated, us
e inspect.signature() or inspect.getfullargspec()
args, varargs, varkw, defaults = getargspec(func)
About this issue
- Original URL
- State: closed
- Created 5 years ago
- Comments: 20 (10 by maintainers)
Commits related to this issue
- FIX: Require environment variable to use DataLad This PR adds a check on ``TEMPLATEFLOW_USE_DATALAD`` (default unset or false) which needs to evaluate to ``True`` in order to use DataLad. This fix a... — committed to templateflow/python-client by oesteban 5 years ago
- [skip ci] Force templateflow>=0.1.2 for containers Fixes #1534 — committed to nipreps/fmriprep by oesteban 5 years ago
I realized that as soon as you asked about command line. The job is currently running (>4 minutes) without errors and has actually progressed to processing the data.
Thanks!