Build fails during cmake due to Hausdorff binary

CBICA / CaPTk

Cancer Imaging Phenomics Toolkit (CaPTk) is a software platform to perform image analysis and predictive modeling tasks. Documentation: https://cbica.github.io/CaPTk

https://www.cbica.upenn.edu/captk

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Build fails during cmake due to Hausdorff binary #1144

Open MarkBergman-cbica opened 4 years ago

MarkBergman-cbica commented 4 years ago

Describe the bug Building from source, following instructions in 5_


-- Trying to find DCMTK expecting DCMTKConfig.cmake - ok
-- Downloading pre-compiled hausdorff
-- [download 0% complete]
...
-- [download 100% complete]
-- Extracting pre-compiled hausdorff
CMake Error at src/applications/CMakeLists.txt:247 (CONFIGURE_FILE):
  Syntax error in cmake code at

    /cbica/home/bergman/comp_space/CaPTk/CaPTk/src/applications/CMakeLists.txt:247

  when parsing string

The "strings" that follow in the errors from cmake are binary data.

It looks like the content of the binary file is being used in CMakeLists.txt, not the filename:

    243   IF( NOT EXISTS "${FILE_TO_EXTRACT}" )
    244 
    245     # copy from LFS folder
    246     IF( EXISTS ${LFS_FILE_TO_CHECK} )
    247       CONFIGURE_FILE( ${LFS_FILE_TO_CHECK} ${FILE_TO_EXTRACT} )
    248     ENDIF()

sarthakpati commented 4 years ago

Just did a clean CMake config and it succeeded without issue:

(base) patis@/cbica/home/patis/projects/captk_myFork/bin>$ cmake ..
[SNIP!]
-- Trying to find DCMTK expecting DCMTKConfig.cmake
-- Trying to find DCMTK expecting DCMTKConfig.cmake - ok
-- Downloading pre-compiled hausdorff
-- [download 0% complete]
[SNIP!]
-- [download 100% complete]
-- Extracting pre-compiled hausdorff
-- Configuring done
-- Generating done
-- Build files have been written to: ~patis/projects/captk_myFork/bin

Paging @CBICA/devteam to see if anyone can replicate this.

AlexanderGetka-cbica commented 4 years ago

I can replicate the issue Mark is experiencing from a completely clean build. CONFIGURE_FILE is attempting to parse over the binary data. To prevent this you can add COPYONLY to the call on line 247: CONFIGURE_FILE( ${LFS_FILE_TO_CHECK} ${FILE_TO_EXTRACT} COPYONLY )

Putting this here just in case anyone else wants to attempt this while I figure out the other errors I'm getting with the build on the cluster.

AlexanderGetka-cbica commented 4 years ago

BTW, the latest errors are along the lines of the below repeated for a bunch of different targets. All can't find Eigen.

CMake Error at cmake_modules/CaPTk_macros.cmake:19 (ADD_EXECUTABLE): Target "BreastTexturePipeline" links to target "Eigen3::Eigen" but the target was not found. Perhaps a find_package() call is missing for an IMPORTED target, or an ALIAS target is missing? Call Stack (most recent call first): src/applications/BreastTexturePipeline/CMakeLists.txt:21 (CAPTK_ADD_EXECUTABLE)

EDIT: Configure succeeds, this happens during generation step.

ashishsingh18 commented 4 years ago

Even I can replicate the error. Here's a screenshot of configure step.

Clicking on 'Configure' again without changing anything, the errors go away and the 'configure' step succeeds.

Clicking 'Generate' then gives Eigen errors as for @AlexanderGetka-cbica

AlexanderGetka-cbica commented 4 years ago

Maybe this is relevant? Seems like a weird conflict between how Eigen's CMake configuration works and the particular eigen package installed.

ashishsingh18 commented 4 years ago

Seems very relevant - same error. Looking deeper into the superbuild, specifically at OpenCV, it looks like it is picking up Eigen3_DIR from '/usr/share/eigen3'

PhucNgo1711 commented 4 years ago

This issue with Eigen not being picked up properly was there when I tried to build with older superbuilds on the cluster too.

ashishsingh18 commented 4 years ago

This issue with Eigen not being picked up properly was there when I tried to build with older superbuilds on the cluster too.

Yes, I remember.

MarkBergman-cbica commented 4 years ago

In the message dated: Tue, 28 Jul 2020 12:45:14 -0700, The pithy ruminations from PhucNgo1711 on [[External] Re: [CBICA/CaPTk] Build fails during cmake due to Hausdorff binary (#1144)] were: => This issue with Eigen not being picked up properly was there when I tried to build with older superbuilds on the cluster too.

Yes, and I wasn't able to find the cause.

Mark

=> => -- => You are receiving this because you authored the thread. => Reply to this email directly or view it on GitHub: => https://github.com/CBICA/CaPTk/issues/1144#issuecomment-665240090

-- Mark Bergman voice: 215-746-4061
mark.bergman@pennmedicine.upenn.edu fax: 215-614-0266 http://www.med.upenn.edu/cbica/ IT Technical Director, Center for Biomedical Image Computing and Analytics Department of Radiology University of Pennsylvania