Building on MacOS Sierra - linker error: library not found -lyaml-cpp about dcm2niix HOT 8 CLOSED

@benjaminirving supports the YAML-based dcm2niibatch, and I do not have OSX Sierra. However, I assume you can still build the generic (non-batching) dcm2niix by using the "make" command which will run
g++ -dead_strip -O3 -I. main_console.cpp nii_dicom.cpp jpg_0XC3.cpp ujpeg.cpp nifti1_io_core.cpp nii_ortho.cpp nii_dicom_batch.cpp -o dcm2niix -DmyDisableOpenJPEG -DmyDisableJasper

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Yes, building dcm2niix works just fine.
The problem only affects linking dcm2niibatch against yaml-cpp.

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@neurolabusc, the generic dcm2niix should also still run using cmake build.

@dangom, thanks for the report. that's strange. I have been holding off upgrading to macOS Sierra for the meanwhile. The upgrade to Sierra might have broken your homebrew links. Have you tried uninstalling and reinstalling yaml-cpp after upgrade? Otherwise, I'll take the plunge and upgrade to Sierra.

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I've tried reinstalling both yaml-cpp and libyaml, and rolling back to an earlier version of cmake. The problem persisted.
I also don't think this has anything to do with homebrew. All paths look correct when I check the cmake generated files.

Unfortunately I can't go back and check the links.txtgenerated on El Capitan, because I don't have it anymore. Do you see if the flag -L/usr/local/lib is set?

If that is the case, then perhaps it's easier to add something to the CMakeLists.txt to always add this extra flag, rather than risking the update?

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-L/usr/local/lib is not set in links.txt on El Capital. Only -lyaml-cpp is set.

It sounds like for some reason /usr/local/lib has been dropped from the default compiler search path in macOS Sierra.

Could you run clang -Xlinker -v in bash. I get

Library search paths:
/usr/lib
/usr/local/lib

I agree with you and I'll add it as an extra flag on the CMakeLists.txt to be safe.

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Could you see if this branch fixes your issue?

https://github.com/rordenlab/dcm2niix/tree/sierra_yaml_fix

Thanks,
Ben

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Hi Ben,

the branch fixes the issue.
Running clang -Xlinker -v gives me the following lib search paths:

Library search paths:
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.12.sdk/usr/lib

And here is the version info:

$ clang -v
Apple LLVM version 8.0.0 (clang-800.0.38)
Target: x86_64-apple-darwin16.0.0
Thread model: posix
InstalledDir: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin

Either a feature of the Sierra upgrade or an issue with my computer.

In any case, thanks for the quick answers.

Cheers,
Daniel

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Thanks Daniel.

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