YAML-cpp linker issue while installing using catkin_make

[luxonis]

YAML-cpp linker issue while installing using catkin_make

[botmayank]

@themarpe nice catch! Thanks a ton that was it 🥳
@saching13 Since I installed ROS using sudo apt install ros-noetic-desktop-full, if I try to remove ros-noetic-perception using apt, it'll uninstall ROS desktop too which I want to avoid. I also think that won't fix it.

For me, the issue is resolved by building and installing yaml-cpp-0.6.3.

TL;DR fix:

1. Remove libyaml-cpp from your system. For me that meant:

sudo rm /usr/local/lib/libyaml-cpp*
sudo rm /lib/x86_64-linux-gnu/libyaml-cpp*

2. Clone release 0.6.3 for libyaml-cpp:
   git clone https://github.com/jbeder/yaml-cpp.git --branch yaml-cpp-0.6.3

3. Build and install libyaml-cpp as per https://github.com/jbeder/yaml-cpp/blob/master/install.txt

mkdir build && cd build
cmake ..
make -j12
sudo make install

4. Build depthai_ros_examples:
   catkin_make --only-pkg-with-deps depthai_examples --cmake-args -D depthai_DIR=<depthai_path>/depthai-core/build/install/lib/cmake/depthai -DPYTHON_EXECUTABLE=/usr/bin/python3

[themarpe]

@botmayank @saching13
Seems like the signature of that function changed.

Required:

YAML::detail::node_data::convert_to_map(std::shared_ptr<YAML::detail::memory_holder>)

Installed:

YAML::detail::node_data::convert_to_map(std::shared_ptr<YAML::detail::memory_holder> const&) 

This is the commit that changed the signature: jbeder/yaml-cpp@0b0bf35#diff-2f31b22281fe05e5b3bc2d4106bac98b28cf93d96c10695b857824672f67f23f [Jun 16, 2020]

I think that the latest release (not latest master branch) https://github.com/jbeder/yaml-cpp/releases/tag/yaml-cpp-0.6.3
should not have this yet applied. [Sep 25, 2019]

TLDR: Remove all yaml-cpp related files in /usr/local (includes, libraries, ...) and rebuild and install the above release (yaml-cpp-0.6.3).

[saching13]

Thanks. I will try to recreate it and see if I can fix on our side.
And cc: @themarpe in case if you have any suggestions on this.

[saching13]

/usr/bin/ld: warning: libopencv_imgcodecs.so.4.2, needed by /opt/ros/noetic/lib/libcv_bridge.so, may conflict with libopencv_imgcodecs.so.4.5

You seem to be having two versions of OpenCV (4.2 and 4.5) which is conflicting while linking.

[botmayank]

That's a warning which I can fix by giving an explicit path to my opencv install. The main ld error IMO is coming from the undefined symbols for YAML methods.

[saching13]

/usr/bin/ld: /opt/ros/noetic/lib/libcamera_calibration_parsers.so: undefined reference to YAML::detail::node_data::convert_to_map(std::shared_ptrYAML::detail::memory_holder)'`

Our packages don't use yaml anywhere. the error is coming from the openCV. and from your setup you are getting only linking error it means that you are able to find the include files but fails to find the build lib file of YAMPCPP.

Can you confirm if using openCV 4 in other packages also creates this issue ? or is it specific to depthai packages ?
And can you share your setup info too so that I can try to recreate it.

[saching13]

I made opencv to import only specific componenets which are needed and might avoid this issue.
can you checkout noetic-opencv-fix from both depthai-ros and depthai-ros-examples and see if it works.
I will try to test it in my other systems in the maintime.

[saching13]

@botmayank I updated the OpenCV dependency. Can you try it and let me know if the new update fixes the issue.
Thanks.

[botmayank]

Hi @saching13 I'm able to successfully build depthai_bridge and depthai_ros_msgs, vision_msgs. Depthai_examples still fails (even noetic devel with the merged noetic-opencv-fix)

I had Opencv 4.2 and 4.5 both installed. I've removed 4.5 since ROS seemed to be dependent on 4.2. I'm still getting the linker errors for linking:

[ 87%] Built target nodelet_stereo
[ 89%] Linking CXX executable /media/mayank/Data/999_Misc/6_OAKD/depthai_ros_ws/devel/lib/depthai_examples/stereo_mimic_node
[ 91%] Linking CXX executable /media/mayank/Data/999_Misc/6_OAKD/depthai_ros_ws/devel/lib/depthai_examples/mobilenet_node
[ 91%] Linking CXX executable /media/mayank/Data/999_Misc/6_OAKD/depthai_ros_ws/devel/lib/depthai_examples/rgb_node
[ 92%] Built target rgb_subscriber_node
[ 93%] Linking CXX executable /media/mayank/Data/999_Misc/6_OAKD/depthai_ros_ws/devel/lib/depthai_examples/rgb_stereo_node
[ 94%] Linking CXX executable /media/mayank/Data/999_Misc/6_OAKD/depthai_ros_ws/devel/lib/depthai_examples/stereo_node
/usr/bin/ld: /opt/ros/noetic/lib/libcamera_calibration_parsers.so: undefined reference to `YAML::detail::node_data::convert_to_map(std::shared_ptr<YAML::detail::memory_holder>)'
collect2: error: ld returned 1 exit status
make[2]: *** [depthai-ros-examples/depthai_examples/CMakeFiles/stereo_node.dir/build.make:241: /media/mayank/Data/999_Misc/6_OAKD/depthai_ros_ws/devel/lib/depthai_examples/stereo_node] Error 1
make[1]: *** [CMakeFiles/Makefile2:2850: depthai-ros-examples/depthai_examples/CMakeFiles/stereo_node.dir/all] Error 2
make[1]: *** Waiting for unfinished jobs....
/usr/bin/ld: /opt/ros/noetic/lib/libcamera_calibration_parsers.so: undefined reference to `YAML::detail::/node_data:usr:convert_to_map/(binstd/:ld::shared_ptr </YAMLopt:/:rosdetail/:noetic:/memory_holderlib>/)libcamera_calibration_parsers.so':
 undefined reference to `YAML::detail::node_data::convert_to_map(std::shared_ptr<YAML::detail::memory_holder>)'collect2: error: ld returned 1 exit status

collect2: error: ld returned 1 exit status
/usr/bin/ld: /opt/ros/noetic/lib/libcamera_calibration_parsers.so: undefined reference to `YAML::detail::node_data::convert_to_map(std::shared_ptr<YAML::detail::memory_holder>)'
collect2: error: ld returned 1 exit status
make[2]: *** [depthai-ros-examples/depthai_examples/CMakeFiles/rgb_node.dir/build.make:241: /media/mayank/Data/999_Misc/6_OAKD/depthai_ros_ws/devel/lib/depthai_examples/rgb_node] Error 1
make[1]: *** [CMakeFiles/Makefile2:3102: depthai-ros-examples/depthai_examples/CMakeFiles/rgb_node.dir/all] Error 2
make[2]: *** [depthai-ros-examples/depthai_examples/CMakeFiles/mobilenet_node.dir/build.make:241: /media/mayank/Data/999_Misc/6_OAKD/depthai_ros_ws/devel/lib/depthai_examples/mobilenet_node] Error 1
make[2]: *** [depthai-ros-examples/depthai_examples/CMakeFiles/rgb_stereo_node.dir/build.make:241: /media/mayank/Data/999_Misc/6_OAKD/depthai_ros_ws/devel/lib/depthai_examples/rgb_stereo_node] Error 1
make[1]: *** [CMakeFiles/Makefile2:2976: depthai-ros-examples/depthai_examples/CMakeFiles/rgb_stereo_node.dir/all] Error 2
make[1]: *** [CMakeFiles/Makefile2:2913: depthai-ros-examples/depthai_examples/CMakeFiles/mobilenet_node.dir/all] Error 2
/usr/bin/ld: /opt/ros/noetic/lib/libcamera_calibration_parsers.so: undefined reference to `YAML::detail::node_data::convert_to_map(std::shared_ptr<YAML::detail::memory_holder>)'
collect2: error: ld returned 1 exit status
make[2]: *** [depthai-ros-examples/depthai_examples/CMakeFiles/stereo_mimic_node.dir/build.make:241: /media/mayank/Data/999_Misc/6_OAKD/depthai_ros_ws/devel/lib/depthai_examples/stereo_mimic_node] Error 1
make[1]: *** [CMakeFiles/Makefile2:3039: depthai-ros-examples/depthai_examples/CMakeFiles/stereo_mimic_node.dir/all] Error 2
make: *** [Makefile:141: all] Error 2
Invoking "make -j12 -l12" failed

[saching13]

Thanks for checking.

Did you try recreating build and development directories ?

And
Can you share your system information and your steps so that I can try to recreate this ?

[botmayank]

Yes I deleted build and devel to retry.

The command I'm using to build (since other packages built successfully...):
catkin_make --only-pkg-with-deps depthai_examples --cmake-args -D depthai_DIR=<depthai_path>/depthai-core/build/install/lib/cmake/depthai -DPYTHON_EXECUTABLE=/usr/bin/python3

Things I've tried:

1. Adding the snippet in the prev comment for CMake to find libyaml
2. Ensuring LD_LIBRARY_PATH env var has /usr/local/lib where libyaml-cpp.so is present
3. Manually adding cpp compiler flags with paths in CMakeLists.txt:
   add_compile_options(-std=c++14 -lyaml-cpp -L/usr/local/lib -I/usr/local/include)
4. Rebuilding libyaml from source from source and installing both .so and .a versions from:
   https://github.com/jbeder/yaml-cpp

What all system info do you want?

1. ROS version: Noetic
2. OS Version: Ubuntu 20.04.2 LTS
3. Arch: x86_64 (output of uname -a: 5.4.0-58-generic #64-Ubuntu SMP Wed Dec 9 08:16:25 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux)

Additional sanity checks:

So the complaining library is libcamera_calibration_parsers.so and the offending symbol is YAML::detail::node_data::convert_to_map(std::shared_ptrYAML::detail::memory_holder)

When I check:
readelf --dynamic /opt/ros/noetic/lib/libcamera_calibration_parsers.so | grep yaml it correctly shows:
0x0000000000000001 (NEEDED) Shared library: [libyaml-cpp.so.0.6]

nm --print-file-name --dynamic /usr/local/lib/libyaml-cpp.so.0.6 | grep convert_to_map also shows:
/usr/local/lib/libyaml-cpp.so.0.6:00000000000bcd3a T _ZN4YAML6detail9node_data14convert_to_mapERKSt10shared_ptrINS0_13memory_holderEE
If I check ldconfig:

sudo ldconfig -p | grep yaml
Output:
sudo ldconfig -p | grep yaml libyaml-0.so.2 (libc6,x86-64) => /lib/x86_64-linux-gnu/libyaml-0.so.2 libyaml-cpp.so.0.6 (libc6,x86-64) => /usr/local/lib/libyaml-cpp.so.0.6 libyaml-cpp.so.0.6 (libc6,x86-64) => /lib/x86_64-linux-gnu/libyaml-cpp.so.0.6 libyaml-cpp.so (libc6,x86-64) => /usr/local/lib/libyaml-cpp.so libyaml-cpp.so (libc6,x86-64) => /lib/x86_64-linux-gnu/libyaml-cpp.so
As far as I can tell, I seem to have the library on my system which even has this symbol (unless there's a minor difference in definition I'm missing). The issue seems to be that ld still doesn't see it although I've tried every which way to tell it where the library is.

[botmayank]

Additionally,

sudo ldconfig -p | grep opencv
[sudo] password for mayank: 
	libopencv_xphoto.so.4.2 (libc6,x86-64) => /lib/x86_64-linux-gnu/libopencv_xphoto.so.4.2
	libopencv_xphoto.so (libc6,x86-64) => /lib/x86_64-linux-gnu/libopencv_xphoto.so
	libopencv_xobjdetect.so.4.2 (libc6,x86-64) => /lib/x86_64-linux-gnu/libopencv_xobjdetect.so.4.2
	libopencv_xobjdetect.so (libc6,x86-64) => /lib/x86_64-linux-gnu/libopencv_xobjdetect.so
	libopencv_ximgproc.so.4.2 (libc6,x86-64) => /lib/x86_64-linux-gnu/libopencv_ximgproc.so.4.2
	libopencv_ximgproc.so (libc6,x86-64) => /lib/x86_64-linux-gnu/libopencv_ximgproc.so
	libopencv_viz.so.4.2 (libc6,x86-64) => /lib/x86_64-linux-gnu/libopencv_viz.so.4.2
	libopencv_viz.so (libc6,x86-64) => /lib/x86_64-linux-gnu/libopencv_viz.so
	libopencv_videostab.so.4.2 (libc6,x86-64) => /lib/x86_64-linux-gnu/libopencv_videostab.so.4.2
	libopencv_videostab.so (libc6,x86-64) => /lib/x86_64-linux-gnu/libopencv_videostab.so
	libopencv_videoio.so.4.2 (libc6,x86-64) => /lib/x86_64-linux-gnu/libopencv_videoio.so.4.2
	libopencv_videoio.so (libc6,x86-64) => /lib/x86_64-linux-gnu/libopencv_videoio.so
	libopencv_video.so.4.2 (libc6,x86-64) => /lib/x86_64-linux-gnu/libopencv_video.so.4.2
	libopencv_video.so (libc6,x86-64) => /lib/x86_64-linux-gnu/libopencv_video.so
	libopencv_tracking.so.4.2 (libc6,x86-64) => /lib/x86_64-linux-gnu/libopencv_tracking.so.4.2
	libopencv_tracking.so (libc6,x86-64) => /lib/x86_64-linux-gnu/libopencv_tracking.so
	libopencv_text.so.4.2 (libc6,x86-64) => /lib/x86_64-linux-gnu/libopencv_text.so.4.2
	libopencv_text.so (libc6,x86-64) => /lib/x86_64-linux-gnu/libopencv_text.so
	libopencv_surface_matching.so.4.2 (libc6,x86-64) => /lib/x86_64-linux-gnu/libopencv_surface_matching.so.4.2
	libopencv_surface_matching.so (libc6,x86-64) => /lib/x86_64-linux-gnu/libopencv_surface_matching.so
	libopencv_superres.so.4.2 (libc6,x86-64) => /lib/x86_64-linux-gnu/libopencv_superres.so.4.2
	libopencv_superres.so (libc6,x86-64) => /lib/x86_64-linux-gnu/libopencv_superres.so
	libopencv_structured_light.so.4.2 (libc6,x86-64) => /lib/x86_64-linux-gnu/libopencv_structured_light.so.4.2
	libopencv_structured_light.so (libc6,x86-64) => /lib/x86_64-linux-gnu/libopencv_structured_light.so
	libopencv_stitching.so.4.2 (libc6,x86-64) => /lib/x86_64-linux-gnu/libopencv_stitching.so.4.2
	libopencv_stitching.so (libc6,x86-64) => /lib/x86_64-linux-gnu/libopencv_stitching.so
	libopencv_stereo.so.4.2 (libc6,x86-64) => /lib/x86_64-linux-gnu/libopencv_stereo.so.4.2
	libopencv_stereo.so (libc6,x86-64) => /lib/x86_64-linux-gnu/libopencv_stereo.so
	libopencv_shape.so.4.2 (libc6,x86-64) => /lib/x86_64-linux-gnu/libopencv_shape.so.4.2
	libopencv_shape.so (libc6,x86-64) => /lib/x86_64-linux-gnu/libopencv_shape.so
	libopencv_saliency.so.4.2 (libc6,x86-64) => /lib/x86_64-linux-gnu/libopencv_saliency.so.4.2
	libopencv_saliency.so (libc6,x86-64) => /lib/x86_64-linux-gnu/libopencv_saliency.so
	libopencv_rgbd.so.4.2 (libc6,x86-64) => /lib/x86_64-linux-gnu/libopencv_rgbd.so.4.2
	libopencv_rgbd.so (libc6,x86-64) => /lib/x86_64-linux-gnu/libopencv_rgbd.so
	libopencv_reg.so.4.2 (libc6,x86-64) => /lib/x86_64-linux-gnu/libopencv_reg.so.4.2
	libopencv_reg.so (libc6,x86-64) => /lib/x86_64-linux-gnu/libopencv_reg.so
	libopencv_quality.so.4.2 (libc6,x86-64) => /lib/x86_64-linux-gnu/libopencv_quality.so.4.2
	libopencv_quality.so (libc6,x86-64) => /lib/x86_64-linux-gnu/libopencv_quality.so
	libopencv_plot.so.4.2 (libc6,x86-64) => /lib/x86_64-linux-gnu/libopencv_plot.so.4.2
	libopencv_plot.so (libc6,x86-64) => /lib/x86_64-linux-gnu/libopencv_plot.so
	libopencv_photo.so.4.2 (libc6,x86-64) => /lib/x86_64-linux-gnu/libopencv_photo.so.4.2
	libopencv_photo.so (libc6,x86-64) => /lib/x86_64-linux-gnu/libopencv_photo.so
	libopencv_phase_unwrapping.so.4.2 (libc6,x86-64) => /lib/x86_64-linux-gnu/libopencv_phase_unwrapping.so.4.2
	libopencv_phase_unwrapping.so (libc6,x86-64) => /lib/x86_64-linux-gnu/libopencv_phase_unwrapping.so
	libopencv_optflow.so.4.2 (libc6,x86-64) => /lib/x86_64-linux-gnu/libopencv_optflow.so.4.2
	libopencv_optflow.so (libc6,x86-64) => /lib/x86_64-linux-gnu/libopencv_optflow.so
	libopencv_objdetect.so.4.2 (libc6,x86-64) => /lib/x86_64-linux-gnu/libopencv_objdetect.so.4.2
	libopencv_objdetect.so (libc6,x86-64) => /lib/x86_64-linux-gnu/libopencv_objdetect.so
	libopencv_ml.so.4.2 (libc6,x86-64) => /lib/x86_64-linux-gnu/libopencv_ml.so.4.2
	libopencv_ml.so (libc6,x86-64) => /lib/x86_64-linux-gnu/libopencv_ml.so
	libopencv_line_descriptor.so.4.2 (libc6,x86-64) => /lib/x86_64-linux-gnu/libopencv_line_descriptor.so.4.2
	libopencv_line_descriptor.so (libc6,x86-64) => /lib/x86_64-linux-gnu/libopencv_line_descriptor.so
	libopencv_imgproc.so.4.2 (libc6,x86-64) => /lib/x86_64-linux-gnu/libopencv_imgproc.so.4.2
	libopencv_imgproc.so (libc6,x86-64) => /lib/x86_64-linux-gnu/libopencv_imgproc.so
	libopencv_imgcodecs.so.4.2 (libc6,x86-64) => /lib/x86_64-linux-gnu/libopencv_imgcodecs.so.4.2
	libopencv_imgcodecs.so (libc6,x86-64) => /lib/x86_64-linux-gnu/libopencv_imgcodecs.so
	libopencv_img_hash.so.4.2 (libc6,x86-64) => /lib/x86_64-linux-gnu/libopencv_img_hash.so.4.2
	libopencv_img_hash.so (libc6,x86-64) => /lib/x86_64-linux-gnu/libopencv_img_hash.so
	libopencv_highgui.so.4.2 (libc6,x86-64) => /lib/x86_64-linux-gnu/libopencv_highgui.so.4.2
	libopencv_highgui.so (libc6,x86-64) => /lib/x86_64-linux-gnu/libopencv_highgui.so
	libopencv_hfs.so.4.2 (libc6,x86-64) => /lib/x86_64-linux-gnu/libopencv_hfs.so.4.2
	libopencv_hfs.so (libc6,x86-64) => /lib/x86_64-linux-gnu/libopencv_hfs.so
	libopencv_hdf.so.4.2 (libc6,x86-64) => /lib/x86_64-linux-gnu/libopencv_hdf.so.4.2
	libopencv_hdf.so (libc6,x86-64) => /lib/x86_64-linux-gnu/libopencv_hdf.so
	libopencv_fuzzy.so.4.2 (libc6,x86-64) => /lib/x86_64-linux-gnu/libopencv_fuzzy.so.4.2
	libopencv_fuzzy.so (libc6,x86-64) => /lib/x86_64-linux-gnu/libopencv_fuzzy.so
	libopencv_freetype.so.4.2 (libc6,x86-64) => /lib/x86_64-linux-gnu/libopencv_freetype.so.4.2
	libopencv_freetype.so (libc6,x86-64) => /lib/x86_64-linux-gnu/libopencv_freetype.so
	libopencv_flann.so.4.2 (libc6,x86-64) => /lib/x86_64-linux-gnu/libopencv_flann.so.4.2
	libopencv_flann.so (libc6,x86-64) => /lib/x86_64-linux-gnu/libopencv_flann.so
	libopencv_features2d.so.4.2 (libc6,x86-64) => /lib/x86_64-linux-gnu/libopencv_features2d.so.4.2
	libopencv_features2d.so (libc6,x86-64) => /lib/x86_64-linux-gnu/libopencv_features2d.so
	libopencv_face.so.4.2 (libc6,x86-64) => /lib/x86_64-linux-gnu/libopencv_face.so.4.2
	libopencv_face.so (libc6,x86-64) => /lib/x86_64-linux-gnu/libopencv_face.so
	libopencv_dpm.so.4.2 (libc6,x86-64) => /lib/x86_64-linux-gnu/libopencv_dpm.so.4.2
	libopencv_dpm.so (libc6,x86-64) => /lib/x86_64-linux-gnu/libopencv_dpm.so
	libopencv_dnn_superres.so.4.2 (libc6,x86-64) => /lib/x86_64-linux-gnu/libopencv_dnn_superres.so.4.2
	libopencv_dnn_superres.so (libc6,x86-64) => /lib/x86_64-linux-gnu/libopencv_dnn_superres.so
	libopencv_dnn_objdetect.so.4.2 (libc6,x86-64) => /lib/x86_64-linux-gnu/libopencv_dnn_objdetect.so.4.2
	libopencv_dnn_objdetect.so (libc6,x86-64) => /lib/x86_64-linux-gnu/libopencv_dnn_objdetect.so
	libopencv_dnn.so.4.2 (libc6,x86-64) => /lib/x86_64-linux-gnu/libopencv_dnn.so.4.2
	libopencv_dnn.so (libc6,x86-64) => /lib/x86_64-linux-gnu/libopencv_dnn.so
	libopencv_datasets.so.4.2 (libc6,x86-64) => /lib/x86_64-linux-gnu/libopencv_datasets.so.4.2
	libopencv_datasets.so (libc6,x86-64) => /lib/x86_64-linux-gnu/libopencv_datasets.so
	libopencv_core.so.4.2 (libc6,x86-64) => /lib/x86_64-linux-gnu/libopencv_core.so.4.2
	libopencv_core.so (libc6,x86-64) => /lib/x86_64-linux-gnu/libopencv_core.so
	libopencv_ccalib.so.4.2 (libc6,x86-64) => /lib/x86_64-linux-gnu/libopencv_ccalib.so.4.2
	libopencv_ccalib.so (libc6,x86-64) => /lib/x86_64-linux-gnu/libopencv_ccalib.so
	libopencv_calib3d.so.4.2 (libc6,x86-64) => /lib/x86_64-linux-gnu/libopencv_calib3d.so.4.2
	libopencv_calib3d.so (libc6,x86-64) => /lib/x86_64-linux-gnu/libopencv_calib3d.so
	libopencv_bioinspired.so.4.2 (libc6,x86-64) => /lib/x86_64-linux-gnu/libopencv_bioinspired.so.4.2
	libopencv_bioinspired.so (libc6,x86-64) => /lib/x86_64-linux-gnu/libopencv_bioinspired.so
	libopencv_bgsegm.so.4.2 (libc6,x86-64) => /lib/x86_64-linux-gnu/libopencv_bgsegm.so.4.2
	libopencv_bgsegm.so (libc6,x86-64) => /lib/x86_64-linux-gnu/libopencv_bgsegm.so
	libopencv_aruco.so.4.2 (libc6,x86-64) => /lib/x86_64-linux-gnu/libopencv_aruco.so.4.2
	libopencv_aruco.so (libc6,x86-64) => /lib/x86_64-linux-gnu/libopencv_aruco.so

[saching13]

@botmayank Looks like your issue is coming from camera_info_manager where it is trying to use camera_calibration_parser link here

Looks like your ros-perception packages are somehow messed up internal linking. Can you try reinstalling those packages properly. That should fix your issue without any extra work.