Issue with compiling FAST with tests

[shayandoust]

Hello there,

I am having some troubles compiling FAST with FAST_BUILD_TESTS set to on. I am currently packaging this software1 within debian and at this stage this is incomplete. I have tested this on two systems within chroot / clean environments.

The output is as follows during the linking process:

...
[100%] Linking CXX executable bin/testFAST
/usr/bin/ld: CMakeFiles/testFAST.dir/source/FAST/Algorithms/NeuralNetwork/VolumeTests.cpp.o: in function `____C_A_T_C_H____T_E_S_T____32()':
VolumeTests.cpp:(.text+0x2e4): undefined reference to `fast::PatchGenerator::PatchGenerator()'
/usr/bin/ld: VolumeTests.cpp:(.text+0x3bc): undefined reference to `fast::PatchGenerator::setPatchSize(int, int, int)'
/usr/bin/ld: VolumeTests.cpp:(.text+0x766): undefined reference to `fast::PatchStitcher::PatchStitcher()'
/usr/bin/ld: CMakeFiles/testFAST.dir/source/FAST/Algorithms/NeuralNetwork/VolumeTests.cpp.o: in function `fast::PatchStitcher::~PatchStitcher()':
VolumeTests.cpp:(.text._ZN4fast13PatchStitcherD2Ev[_ZN4fast13PatchStitcherD5Ev]+0x3): undefined reference to `vtable for fast::PatchStitcher'
/usr/bin/ld: CMakeFiles/testFAST.dir/source/FAST/Algorithms/NeuralNetwork/VolumeTests.cpp.o: in function `fast::PatchStitcher::~PatchStitcher()':
VolumeTests.cpp:(.text._ZN4fast13PatchStitcherD0Ev[_ZN4fast13PatchStitcherD5Ev]+0x3): undefined reference to `vtable for fast::PatchStitcher'
/usr/bin/ld: CMakeFiles/testFAST.dir/source/FAST/Algorithms/NeuralNetwork/VolumeTests.cpp.o: in function `____C_A_T_C_H____T_E_S_T____32() [clone .cold.249]':
VolumeTests.cpp:(.text.unlikely+0x99): undefined reference to `fast::PatchGenerator::~PatchGenerator()'
collect2: error: ld returned 1 exit status
make[2]: *** [CMakeFiles/testFAST.dir/build.make:977: bin/testFAST] Error 1
make[1]: *** [CMakeFiles/Makefile2:73: CMakeFiles/testFAST.dir/all] Error 2
make: *** [Makefile:130: all] Error 2

Hence, I am unsure what I am doing wrong as I have all of the dependencies installed and recommendation to the right path would be much appreciated!

Many thanks, Shayan

[smistad]

Hi Shayan

I believe this error was introduced when I recently added the WholeSlideImaging module which is set to OFF by default atm.

You can try and test if this is the issue by setting the cmake flag FAST_MODULE_WholeSlideImaging to ON and then try and compile the tests again. Note that you then also need the openslide library installed on your system:

sudo apt install libopenslide0 libopenslide-dev

I will commit a fix for this error asap

[shayandoust]

Hello Smistad,

Thanks for your reply. Setting that cmake option as true does in fact build the tests successfully. This is useful for autopkgtest for package quality assurance.

[smistad]

Great!