Open MarkBergman-cbica opened 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.
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.
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.
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
Maybe this is relevant? Seems like a weird conflict between how Eigen's CMake configuration works and the particular eigen package installed.
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'
This issue with Eigen not being picked up properly was there when I tried to build with older superbuilds on the cluster too.
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.
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
Describe the bug Building from source, following instructions in 5_
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: