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When running renee v2.6.1 using ccbrpipeliner 7, we encounter the following numpy errors in multiple rules (inner_distance and rseqc):
Activating singularity image /data/CCBR_Pipeliner/SIFS/ccbr_rseqc_4.0.0_v2.sif
Traceback (most recent call last):
File "/data/CCBR_Pipeliner/Tools/ccbr_tools/v0.1/numpy/_core/__init__.py", line 23, in <module>
from . import multiarray
File "/data/CCBR_Pipeliner/Tools/ccbr_tools/v0.1/numpy/_core/multiarray.py", line 10, in <module>
from . import overrides
File "/data/CCBR_Pipeliner/Tools/ccbr_tools/v0.1/numpy/_core/overrides.py", line 8, in <module>
from numpy._core._multiarray_umath import (
ModuleNotFoundError: No module named 'numpy._core._multiarray_umath'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/data/CCBR_Pipeliner/Tools/ccbr_tools/v0.1/numpy/__init__.py", line 114, in <module>
from numpy.__config__ import show as show_config
File "/data/CCBR_Pipeliner/Tools/ccbr_tools/v0.1/numpy/__config__.py", line 4, in <module>
from numpy._core._multiarray_umath import (
File "/data/CCBR_Pipeliner/Tools/ccbr_tools/v0.1/numpy/_core/__init__.py", line 49, in <module>
raise ImportError(msg)
ImportError:
IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE!
Importing the numpy C-extensions failed. This error can happen for
many reasons, often due to issues with your setup or how NumPy was
installed.
...
...
Traceback (most recent call last):
File "/usr/local/bin/infer_experiment.py", line 53, in <module>
from qcmodule import SAM
File "/usr/local/lib/python3.8/dist-packages/qcmodule/SAM.py", line 19, in <module>
from bx.binned_array import BinnedArray
File "/usr/local/lib/python3.8/dist-packages/bx/binned_array.py", line 19, in <module>
from numpy import (
File "/data/CCBR_Pipeliner/Tools/ccbr_tools/v0.1/numpy/__init__.py", line 119, in <module>
raise ImportError(msg) from e
ImportError: Error importing numpy: you should not try to import numpy from
its source directory; please exit the numpy source tree, and relaunch
your python interpreter from there.
This error seems to be similar to the one encountered in XAVIER. see CCBR/XAVIER#122
When running
renee v2.6.1
using ccbrpipeliner 7, we encounter the following numpy errors in multiple rules (inner_distance
andrseqc
):This error seems to be similar to the one encountered in XAVIER. see CCBR/XAVIER#122
Possible solution maybe similar to CCBR/XAVIER#123
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