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SCIInstitute / Seg3D

Seg3D is a free volume segmentation and processing tool developed by the NIH Center for Integrative Biomedical Computing at the University of Utah Scientific Computing and Imaging (SCI) Institute.
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Linux build fails on error in ThirdParty/GDCM #417

Open cribe78 opened 1 year ago

cribe78 commented 1 year ago

Description

Attempting to build Seg3D in a containerized Ubuntu 22.04 fails at step "Building CXX object Modules/ThirdParty/GDCM/src/gdcm/Source/MediaStorageAndFileFormat/CMakeFiles/gdcmMSFF.dir/gdcmImageChangePhotometricInterpretation.cxx.o ". While this appears to be due to a bug in an upstream 3rd party project, GDCM, it is unclear how to alter to build system to potentially pull in a different version of GDCM.

Relevant selection from output of "make": seg3d-make.log

Steps to Reproduce

  1. Create an apptainer definition file named Apptainer with the following contents:

Bootstrap: docker From: ubuntu:22.04

%post apt-get -y update export DEBIAN_FRONTEND=noninteractive apt install -y cmake build-essential qtbase5-dev qt5-qmake wget libqt5svg5-dev git subversion \ textlive-latex-extra libboost-python-dev libtirpc-dev wget https://github.com/SCIInstitute/Seg3D/archive/refs/tags/v2.5.1.tar.gz tar xzf v2.5.1.tar.gz cd /Seg3D-2.5.1/bin cmake -DQt5_PATH:PATH=/usr/lib/x86_64-linux-gnu/qt5 ../Superbuild make make install

  1. Run "apptainer build Seg3D.sif Apptainer

Expected behavior: The make step completes successfully and a container image is created.

Actual behavior: The error listed above is encountered during the make step.

Versions

Version 2.5.1. Also tested on Git master branch with same results.

cribe78 commented 1 year ago

Uploaded apptainer definition file: apptainer.txt

The text pasted in bug report is missing a necessary \ at the end of the "apt install -y" line. I can convert the apptainer definition file to a Dockerfile if requested.