Failing to build for ros2 humble?

[TSoli]

I am having trouble installing the package as per the ros2 installation instructions. I have now tried on two separate laptops running Linux Mint 21.3 (which is based on Ubuntu 22.04) and I am getting the same result. First I installed by following these instructions from the docs for linux and choosing pangolin viewer. The only differences really are that

• I installed from the opencv 4.x branch since 4.5.5 suggested in the docs was having issues with compiling
• I also used opencv_contrib to attempt to install all of the extra modules (it seemed xfeatures2d and cvv were required later on anyway for this package). This meant compiling with the -DWITH_QT=5 option.

After that I followed the instructions in the docs to install for ROS2 again choosing pangolin. In the final step to colcon build --symlink-install I get the following errors

CMake Deprecation Warning at CMakeLists.txt:11 (cmake_policy):
  The OLD behavior for policy CMP0074 will be removed from a future version
  of CMake.

  The cmake-policies(7) manual explains that the OLD behaviors of all
  policies are deprecated and that a policy should be set to OLD only under
  specific short-term circumstances.  Projects should be ported to the NEW
  behavior and not rely on setting a policy to OLD.


CMake Warning at CMakeLists.txt:195 (add_library):
  Cannot generate a safe runtime search path for target
  stella_vslam_ros_system because files in some directories may conflict with
  libraries in implicit directories:

    runtime library [libgomp.so.1] in /usr/lib/gcc/x86_64-linux-gnu/11 may be hidden by files in:
      /home/tariq/miniconda3/lib
    runtime library [libsqlite3.so.0] in /usr/lib/x86_64-linux-gnu may be hidden by files in:
      /home/tariq/miniconda3/lib

  Some of these libraries may not be found correctly.


CMake Warning at src/CMakeLists.txt:11 (add_executable):
  Cannot generate a safe runtime search path for target run_slam because
  files in some directories may conflict with libraries in implicit
  directories:

    runtime library [libgomp.so.1] in /usr/lib/gcc/x86_64-linux-gnu/11 may be hidden by files in:
      /home/tariq/miniconda3/lib
    runtime library [libsqlite3.so.0] in /usr/lib/x86_64-linux-gnu may be hidden by files in:
      /home/tariq/miniconda3/lib

  Some of these libraries may not be found correctly.


CMake Warning at src/CMakeLists.txt:12 (add_executable):
  Cannot generate a safe runtime search path for target run_slam_offline
  because files in some directories may conflict with libraries in implicit
  directories:

    runtime library [libgomp.so.1] in /usr/lib/gcc/x86_64-linux-gnu/11 may be hidden by files in:
      /home/tariq/miniconda3/lib
    runtime library [libsqlite3.so.0] in /usr/lib/x86_64-linux-gnu may be hidden by files in:
      /home/tariq/miniconda3/lib

  Some of these libraries may not be found correctly.


In file included from /home/tariq/ros2_ws/src/stella_vslam_ros/src/stella_vslam_ros.cc:7:
/opt/ros/humble/include/tf2_eigen/tf2_eigen/tf2_eigen.h:32:2: warning: #warning This header is obsolete, please include tf2_eigen/tf2_eigen.hpp instead [-Wcpp]
   32 | #warning This header is obsolete, please include tf2_eigen/tf2_eigen.hpp instead
      |  ^~~~~~~
In file included from /home/tariq/ros2_ws/src/stella_vslam_ros/src/stella_vslam_ros.cc:7:
/opt/ros/humble/include/tf2_eigen/tf2_eigen/tf2_eigen.h:32:2: warning: #warning This header is obsolete, please include tf2_eigen/tf2_eigen.hpp instead [-Wcpp]
   32 | #warning This header is obsolete, please include tf2_eigen/tf2_eigen.hpp instead
      |  ^~~~~~~
In file included from /home/tariq/ros2_ws/src/stella_vslam_ros/src/stella_vslam_ros.cc:7:
/opt/ros/humble/include/tf2_eigen/tf2_eigen/tf2_eigen.h:32:2: warning: #warning This header is obsolete, please include tf2_eigen/tf2_eigen.hpp instead [-Wcpp]
   32 | #warning This header is obsolete, please include tf2_eigen/tf2_eigen.hpp instead
      |  ^~~~~~~
In file included from /home/tariq/ros2_ws/src/stella_vslam_ros/src/stella_vslam_ros.cc:8:
/opt/ros/humble/include/tf2_geometry_msgs/tf2_geometry_msgs/tf2_geometry_msgs.h:35:2: warning: #warning This header is obsolete, please include tf2_geometry_msgs/tf2_geometr
y_msgs.hpp instead [-Wcpp]
   35 | #warning This header is obsolete, please include tf2_geometry_msgs/tf2_geometry_msgs.hpp instead
      |  ^~~~~~~
In file included from /home/tariq/ros2_ws/src/stella_vslam_ros/src/stella_vslam_ros.cc:8:
/opt/ros/humble/include/tf2_geometry_msgs/tf2_geometry_msgs/tf2_geometry_msgs.h:35:2: warning: #warning This header is obsolete, please include tf2_geometry_msgs/tf2_geometr
y_msgs.hpp instead [-Wcpp]
   35 | #warning This header is obsolete, please include tf2_geometry_msgs/tf2_geometry_msgs.hpp instead
      |  ^~~~~~~
In file included from /home/tariq/ros2_ws/src/stella_vslam_ros/src/stella_vslam_ros.cc:8:
/opt/ros/humble/include/tf2_geometry_msgs/tf2_geometry_msgs/tf2_geometry_msgs.h:35:2: warning: #warning This header is obsolete, please include tf2_geometry_msgs/tf2_geometr
y_msgs.hpp instead [-Wcpp]
   35 | #warning This header is obsolete, please include tf2_geometry_msgs/tf2_geometry_msgs.hpp instead
      |  ^~~~~~~
/usr/bin/ld: warning: libopencv_imgcodecs.so.4.5d, needed by /opt/ros/humble/lib/libcv_bridge.so, may conflict with libopencv_imgcodecs.so.409
/usr/bin/ld: warning: libopencv_core.so.4.5d, needed by /opt/ros/humble/lib/libcv_bridge.so, may conflict with libopencv_core.so.409
/usr/bin/ld: warning: libopencv_imgcodecs.so.4.5d, needed by /opt/ros/humble/lib/libcv_bridge.so, may conflict with libopencv_imgcodecs.so.409
/usr/bin/ld: warning: libopencv_core.so.4.5d, needed by /opt/ros/humble/lib/libcv_bridge.so, may conflict with libopencv_core.so.409
/usr/bin/ld: /lib/libgdal.so.30: undefined reference to `curl_easy_getinfo@CURL_OPENSSL_4'
/usr/bin/ld: /lib/libgdal.so.30: undefined reference to `curl_multi_perform@CURL_OPENSSL_4'
/usr/bin/ld: /lib/libgdal.so.30: undefined reference to `curl_multi_cleanup@CURL_OPENSSL_4'
/usr/bin/ld: /lib/x86_64-linux-gnu/libnetcdf.so.19: undefined reference to `curl_global_init@CURL_OPENSSL_4'
/usr/bin/ld: /lib/libgdal.so.30: undefined reference to `curl_mime_init@CURL_OPENSSL_4'
/usr/bin/ld: /usr/local/lib/libstella_vslam.so: undefined reference to `g2o::csparse::CSparse::solve(double*, double*) const'
/usr/bin/ld: /usr/local/lib/libstella_vslam.so: undefined reference to `g2o::csparse::CSparse::factor()'
/usr/bin/ld: /usr/local/lib/libstella_vslam.so: undefined reference to `g2o::csparse::CSparse::CSparse()'
/usr/bin/ld: /usr/local/lib/libstella_vslam.so: undefined reference to `spdlog::details::log_msg::log_msg(spdlog::source_loc, fmt::v9::basic_string_view<char>, spdlog::level
::level_enum, fmt::v9::basic_string_view<char>)'
/usr/bin/ld: /lib/libgdal.so.30: undefined reference to `curl_multi_remove_handle@CURL_OPENSSL_4'
/usr/bin/ld: /usr/local/lib/libstella_vslam.so: undefined reference to `g2o::csparse::CSparse::freeSymbolic()'
/usr/bin/ld: /usr/local/lib/libstella_vslam.so: undefined reference to `g2o::csparse::CSparse::hasSymbolic() const'
/usr/bin/ld: /lib/libgdal.so.30: undefined reference to `curl_mime_addpart@CURL_OPENSSL_4'
/usr/bin/ld: /lib/libgdal.so.30: undefined reference to `curl_version_info@CURL_OPENSSL_4'
/usr/bin/ld: /usr/local/lib/libstella_vslam.so: undefined reference to `g2o::csparse::CSparse::sparseView()'
/usr/bin/ld: /lib/libgdal.so.30: undefined reference to `curl_mime_name@CURL_OPENSSL_4'
/usr/bin/ld: /lib/libgdal.so.30: undefined reference to `curl_mime_filename@CURL_OPENSSL_4'
/usr/bin/ld: /lib/libgdal.so.30: undefined reference to `curl_multi_info_read@CURL_OPENSSL_4'
/usr/bin/ld: /lib/libgdal.so.30: undefined reference to `curl_easy_setopt@CURL_OPENSSL_4'
/usr/bin/ld: /usr/local/lib/libstella_vslam.so: undefined reference to `g2o::csparse::CSparse::factorize()'
/usr/bin/ld: /lib/libgdal.so.30: undefined reference to `curl_mime_free@CURL_OPENSSL_4'
/usr/bin/ld: /lib/libgdal.so.30: undefined reference to `curl_easy_cleanup@CURL_OPENSSL_4'
/usr/bin/ld: /lib/libgdal.so.30: undefined reference to `curl_mime_data_cb@CURL_OPENSSL_4'
/usr/bin/ld: /lib/libgdal.so.30: undefined reference to `curl_easy_perform@CURL_OPENSSL_4'
/usr/bin/ld: /lib/libgdal.so.30: undefined reference to `curl_easy_init@CURL_OPENSSL_4'
/usr/bin/ld: /lib/libgdal.so.30: undefined reference to `curl_multi_add_handle@CURL_OPENSSL_4'
/usr/bin/ld: /usr/local/lib/libstella_vslam.so: undefined reference to `g2o::csparse::CSparse::amd(g2o::csparse::CSparse::SparseView const&, Eigen::Matrix<int, -1, 1, 0, -1,
 1>&)'
/usr/bin/ld: /usr/local/lib/libstella_vslam.so: undefined reference to `g2o::csparse::CSparse::analyze_p(int*)'
/usr/bin/ld: /usr/local/lib/libstella_vslam.so: undefined reference to `g2o::csparse::CSparse::writeSparse(std::__cxx11::basic_string<char, std::char_traits<char>, std::allo
cator<char> > const&) const'
/usr/bin/ld: /lib/libgdal.so.30: undefined reference to `curl_slist_free_all@CURL_OPENSSL_4'
/usr/bin/ld: /lib/x86_64-linux-gnu/libnetcdf.so.19: undefined reference to `curl_easy_strerror@CURL_OPENSSL_4'
/usr/bin/ld: /usr/local/lib/libstella_vslam.so: undefined reference to `g2o::csparse::CSparse::freeFactor()'
/usr/bin/ld: /usr/local/lib/libstella_vslam.so: undefined reference to `g2o::csparse::CSparse::analyze()'
/usr/bin/ld: /lib/libgdal.so.30: undefined reference to `curl_slist_append@CURL_OPENSSL_4'
/usr/bin/ld: /lib/libgdal.so.30: undefined reference to `curl_multi_poll@CURL_OPENSSL_4'
/usr/bin/ld: /lib/libgdal.so.30: undefined reference to `curl_version@CURL_OPENSSL_4'
/usr/bin/ld: /usr/local/lib/libstella_vslam.so: undefined reference to `g2o::csparse::CSparse::choleskyNz() const'
/usr/bin/ld: /lib/libgdal.so.30: undefined reference to `curl_multi_setopt@CURL_OPENSSL_4'
/usr/bin/ld: /lib/libgdal.so.30: undefined reference to `curl_mime_data@CURL_OPENSSL_4'
/usr/bin/ld: /lib/libgdal.so.30: undefined reference to `curl_multi_init@CURL_OPENSSL_4'
/usr/bin/ld: /usr/local/lib/libstella_vslam.so: undefined reference to `g2o::csparse::CSparse::~CSparse()'
/usr/bin/ld: /lib/libgdal.so.30: undefined reference to `curl_multi_wait@CURL_OPENSSL_4'
/usr/bin/ld: /lib/x86_64-linux-gnu/libnetcdf.so.19: undefined reference to `curl_global_cleanup@CURL_OPENSSL_4'
/usr/bin/ld: /lib/libgdal.so.30: undefined reference to `curl_easy_getinfo@CURL_OPENSSL_4'
/usr/bin/ld: /lib/libgdal.so.30: undefined reference to `curl_multi_perform@CURL_OPENSSL_4'
/usr/bin/ld: /lib/libgdal.so.30: undefined reference to `curl_multi_cleanup@CURL_OPENSSL_4'
/usr/bin/ld: /lib/x86_64-linux-gnu/libnetcdf.so.19: undefined reference to `curl_global_init@CURL_OPENSSL_4'
/usr/bin/ld: /lib/libgdal.so.30: undefined reference to `curl_mime_init@CURL_OPENSSL_4'
/usr/bin/ld: /usr/local/lib/libstella_vslam.so: undefined reference to `g2o::csparse::CSparse::solve(double*, double*) const'
/usr/bin/ld: /usr/local/lib/libstella_vslam.so: undefined reference to `g2o::csparse::CSparse::factor()'
/usr/bin/ld: /usr/local/lib/libstella_vslam.so: undefined reference to `g2o::csparse::CSparse::CSparse()'
/usr/bin/ld: /usr/local/lib/libstella_vslam.so: undefined reference to `spdlog::details::log_msg::log_msg(spdlog::source_loc, fmt::v9::basic_string_view<char>, spdlog::level
::level_enum, fmt::v9::basic_string_view<char>)'
/usr/bin/ld: /lib/libgdal.so.30: undefined reference to `curl_multi_remove_handle@CURL_OPENSSL_4'
/usr/bin/ld: /usr/local/lib/libstella_vslam.so: undefined reference to `g2o::csparse::CSparse::freeSymbolic()'
/usr/bin/ld: /usr/local/lib/libstella_vslam.so: undefined reference to `g2o::csparse::CSparse::hasSymbolic() const'
/usr/bin/ld: /lib/libgdal.so.30: undefined reference to `curl_mime_addpart@CURL_OPENSSL_4'
/usr/bin/ld: /lib/libgdal.so.30: undefined reference to `curl_version_info@CURL_OPENSSL_4'
/usr/bin/ld: /usr/local/lib/libstella_vslam.so: undefined reference to `g2o::csparse::CSparse::sparseView()'
/usr/bin/ld: /lib/libgdal.so.30: undefined reference to `curl_mime_name@CURL_OPENSSL_4'
/usr/bin/ld: /lib/libgdal.so.30: undefined reference to `curl_mime_filename@CURL_OPENSSL_4'
/usr/bin/ld: /lib/libgdal.so.30: undefined reference to `curl_multi_info_read@CURL_OPENSSL_4'
/usr/bin/ld: /lib/libgdal.so.30: undefined reference to `curl_easy_setopt@CURL_OPENSSL_4'
/usr/bin/ld: /usr/local/lib/libstella_vslam.so: undefined reference to `g2o::csparse::CSparse::factorize()'
collect2: error: ld returned 1 exit status
/usr/bin/ld: /lib/libgdal.so.30: undefined reference to `curl_mime_free@CURL_OPENSSL_4'
gmake[2]: *** [src/CMakeFiles/run_slam.dir/build.make:689: src/run_slam] Error 1
gmake[1]: *** [CMakeFiles/Makefile2:210: src/CMakeFiles/run_slam.dir/all] Error 2
gmake[1]: *** Waiting for unfinished jobs....
/usr/bin/ld: /lib/libgdal.so.30: undefined reference to `curl_easy_cleanup@CURL_OPENSSL_4'
/usr/bin/ld: /lib/libgdal.so.30: undefined reference to `curl_mime_data_cb@CURL_OPENSSL_4'
/usr/bin/ld: /lib/libgdal.so.30: undefined reference to `curl_easy_perform@CURL_OPENSSL_4'
/usr/bin/ld: /lib/libgdal.so.30: undefined reference to `curl_easy_init@CURL_OPENSSL_4'
/usr/bin/ld: /lib/libgdal.so.30: undefined reference to `curl_multi_add_handle@CURL_OPENSSL_4'
/usr/bin/ld: /usr/local/lib/libstella_vslam.so: undefined reference to `g2o::csparse::CSparse::amd(g2o::csparse::CSparse::SparseView const&, Eigen::Matrix<int, -1, 1, 0, -1,
 1>&)'
/usr/bin/ld: /usr/local/lib/libstella_vslam.so: undefined reference to `g2o::csparse::CSparse::analyze_p(int*)'
/usr/bin/ld: /usr/local/lib/libstella_vslam.so: undefined reference to `g2o::csparse::CSparse::writeSparse(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const'
/usr/bin/ld: /lib/libgdal.so.30: undefined reference to `curl_slist_free_all@CURL_OPENSSL_4'
/usr/bin/ld: /lib/x86_64-linux-gnu/libnetcdf.so.19: undefined reference to `curl_easy_strerror@CURL_OPENSSL_4'
/usr/bin/ld: /usr/local/lib/libstella_vslam.so: undefined reference to `g2o::csparse::CSparse::freeFactor()'
/usr/bin/ld: /usr/local/lib/libstella_vslam.so: undefined reference to `g2o::csparse::CSparse::analyze()'
/usr/bin/ld: /lib/libgdal.so.30: undefined reference to `curl_slist_append@CURL_OPENSSL_4'
/usr/bin/ld: /lib/libgdal.so.30: undefined reference to `curl_multi_poll@CURL_OPENSSL_4'
/usr/bin/ld: /lib/libgdal.so.30: undefined reference to `curl_version@CURL_OPENSSL_4'
/usr/bin/ld: /usr/local/lib/libstella_vslam.so: undefined reference to `g2o::csparse::CSparse::choleskyNz() const'
/usr/bin/ld: /lib/libgdal.so.30: undefined reference to `curl_multi_setopt@CURL_OPENSSL_4'
/usr/bin/ld: /lib/libgdal.so.30: undefined reference to `curl_mime_data@CURL_OPENSSL_4'
/usr/bin/ld: /lib/libgdal.so.30: undefined reference to `curl_multi_init@CURL_OPENSSL_4'
/usr/bin/ld: /usr/local/lib/libstella_vslam.so: undefined reference to `g2o::csparse::CSparse::~CSparse()'
/usr/bin/ld: /lib/libgdal.so.30: undefined reference to `curl_multi_wait@CURL_OPENSSL_4'
/usr/bin/ld: /lib/x86_64-linux-gnu/libnetcdf.so.19: undefined reference to `curl_global_cleanup@CURL_OPENSSL_4'
collect2: error: ld returned 1 exit status
gmake[2]: *** [src/CMakeFiles/run_slam_offline.dir/build.make:689: src/run_slam_offline] Error 1
gmake[1]: *** [CMakeFiles/Makefile2:236: src/CMakeFiles/run_slam_offline.dir/all] Error 2
gmake: *** [Makefile:146: all] Error 2
---
Failed   <<< stella_vslam_ros [33.7s, exited with code 2]

Summary: 0 packages finished [34.5s]
  1 package failed: stella_vslam_ros
  1 package had stderr output: stella_vslam_ros

I also tried building the example repo from the source installation and that was failing but I do not think it should be related?

I don't know if the errors on the two separate machines were exactly the same but they were definitely similar.

[TSoli]

I basically uninstalled conda (actually just renamed the miniconda3 dir and removed lines from .bashrc) and then re did all the installation steps with opencv 4.5.5 and it seems it built. I think somehow cmake was using the libraries in my conda environment rather than the system ones. This seems like a shitty workaround. If anyone knows how I can force cmake to ignore these conda env files then that would be much appreciated.