8000 Conda packaging nighres v1.5.1 · Issue #208 · nighres/nighres · GitHub
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Dhananjhay opened this issue Nov 25, 2024 · 1 comment
Open

Conda packaging nighres v1.5.1 #208

Dhananjhay opened this issue Nov 25, 2024 · 1 comment

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@Dhananjhay
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Dhananjhay commented Nov 25, 2024 •
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Hi, I've created an unofficial conda package for nighres v1.5.1 (https://anaconda.org/khanlab/nighres), and the conda recipe can be found here (https://github.com/Dhananjhay/staged-recipes/tree/djay/add-nighres). When I try running example_01_tissue_classification.py, I get the following output/error:

File not found:
Invalid file path

 The underlying Java code did not execute cleanly: 
<class 'nighresjava.JavaError'>
Traceback (most recent call last):
  File "/local/scratch/nighres_test/tissue.py", line 52, in <module>
    skullstripping_results = nighres.brain.mp2rage_skullstripping(
  File "/home/ROBARTS/dbansal7/miniconda3/envs/nighres-test/lib/python3.10/site-packages/nighres/brain/mp2rage_skullstripping.py", line 166, in mp2rage_skullstripping
    algo.execute()
#
# A fatal error has been detected by the Java Runtime Environment:
#
#  SIGSEGV (0xb) at pc=0x00007f57e32936f0, pid=11042, tid=0x00007f57e31f84c0
#
# JRE version: OpenJDK Runtime Environment (Zulu 8.78.0.19-CA-linux64) (8.0_412-b08) (build 1.8.0_412-b08)
# Java VM: OpenJDK 64-Bit Server VM (25.412-b08 mixed mode linux-amd64 )
# Problematic frame:
# C  [libc.so.6+0x9a6f0]  cfree+0x20
#
# Core dump written. Default location: /local/scratch/nighres_test/core or core.11042
#
# An error report file with more information is saved as:
# /local/scratch/nighres_test/hs_err_pid11042.log
#
# If you would like to submit a bug report, please visit:
#   http://www.azul.com/support/
# The crash happened outside the Java Virtual Machine in native code.
# See problematic frame for where to report the bug.
#
Aborted (core dumped)
@piloubazin
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something to do with conda not compiling the Java part of the code maybe? Other installation methods run the examples smoothly

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@piloubazin @Dhananjhay
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