Re: rosdep install fails with ament_pep8: No definition of [python3-pep8] for OS version [32] on Fedora 32, deprecated

Robert Kudyba <rkudyba@xxxxxxxxxxx> · Sat, 15 Aug 2020 21:44:55 -0400

I posted on answers.ros.org but these latest errors seem Fedora-specific. I'm getting all of these undefined reference errors
stderr: rviz_rendering
/usr/bin/ld: /usr/lib64/libssh.so.4: undefined reference to `EVP_KDF_ctrl@OPENSSL_1_1_1b'
/usr/bin/ld: /usr/lib64/libssh.so.4: undefined reference to `EVP_KDF_CTX_free@OPENSSL_1_1_1b'
/usr/bin/ld: /usr/lib64/libssh.so.4: undefined reference to `EVP_KDF_CTX_new_id@OPENSSL_1_1_1b'
/usr/bin/ld: /usr/lib64/libSM.so: undefined reference to `uuid_generate@UUID_1.0'
/usr/bin/ld: /usr/lib64/libssh.so.4: undefined reference to `EVP_KDF_ctrl@OPENSSL_1_1_1b'
/usr/bin/ld: /usr/lib64/libssh.so.4: undefined reference to `EVP_KDF_ctrl@OPENSSL_1_1_1b'
/usr/bin/ld: /usr/lib64/libssh.so.4: undefined reference to `EVP_KDF_derive@OPENSSL_1_1_1b'
/usr/bin/ld: /usr/lib64/libssh.so.4: undefined reference to `EVP_KDF_CTX_free@OPENSSL_1_1_1b'
/usr/bin/ld: /usr/lib64/libssh.so.4: undefined reference to `EVP_KDF_CTX_free@OPENSSL_1_1_1b'
/usr/bin/ld: /usr/lib64/libssh.so.4: undefined reference to `EVP_KDF_ctrl@OPENSSL_1_1_1b'
/usr/bin/ld: /usr/lib64/libSM.so: undefined reference to `uuid_unparse_lower@UUID_1.0'
/usr/bin/ld: /usr/lib64/libcurl.so: undefined reference to `SSLv3_client_method@OPENSSL_1_1_0'
/usr/bin/ld: /usr/lib64/libssh.so.4: undefined reference to `EVP_KDF_CTX_new_id@OPENSSL_1_1_1b'
/usr/bin/ld: /usr/lib64/libssh.so.4: undefined reference to `EVP_KDF_CTX_free@OPENSSL_1_1_1b'
/usr/bin/ld: /usr/lib64/libssh.so.4: undefined reference to `EVP_KDF_CTX_new_id@OPENSSL_1_1_1b'
/usr/bin/ld: /usr/lib64/libSM.so: undefined reference to `uuid_generate@UUID_1.0'
/usr/bin/ld: /usr/lib64/libSM.so: undefined reference to `uuid_generate@UUID_1.0'
/usr/bin/ld: /usr/lib64/libssh.so.4: undefined reference to `EVP_KDF_ctrl@OPENSSL_1_1_1b'
/usr/bin/ld: /usr/lib64/libssh.so.4: undefined reference to `EVP_KDF_CTX_new_id@OPENSSL_1_1_1b'
collect2: error: ld returned 1 exit status

I did find a bug report mentioning Matlab/Scilab having conflicting or out of date libraries, https://bugzilla.redhat.com/show_bug.cgi?id=1829790 but we don't have Matlab installed on this server.

Is this worth reporting as a bug?

On Fri, Aug 14, 2020 at 8:29 PM Robert Kudyba <rkudyba@xxxxxxxxxxx> wrote:

First we should clarify that you're now switching to ROS 1 stuff. Catkin is the buildsystem and build tool for ROS 1, you'd use ament and colcon in ROS 2.
ROS 1 and ROS 2 packages are generally not interchangeable. Many packages have branches for supporting both ROS 1 and ROS 2, but you can't generally drop a ROS 1 package into a ROS 2 build environment and expect it to work.

Assuming you're now building a separate ROS 1 distribution from the ROS 2 build you were discussing earlier:
The gl_dependency package only appears to be used in ROS 1, and it's really only a dummy CMake package to make sure some depenencies are installed. You're probably seeing a generic compiler verification check fail in CMake.
We could try skipping the compiler check since the gl_dependency package doesn't really need it, but this really indicates that theres something wrong with your build environment. I'm skeptical that you'll get any of the C/C++ packages to compile correctly, not just gl_dependency.
To be honest, the error doesn't even really seem related to ROS at all.

Just a hunch, but you might try ensuring that glibc-devel and boost-devel are installed, and CMake is up-to-date. Then remove your build and install directories and start again.
 Oh my bad I was testing ROS 1 from this older tutorial: https://kyrofa.com/posts/ros-melodic-on-fedora-27

The ROS 2 error is from running colcon build --symlink-install

/usr/local/bin/anaconda3/bin/python: can't find '__main__' module in '/usr/local/bin/anaconda3/lib/python3.7/site-packages/em'
CMake Error at cmake/safe_execute_process.cmake:11 (message):

  execute_process(/root/ros_catkin_ws/build/catkin/catkin_generated/env_cached.sh
  "/usr/local/bin/anaconda3/bin/python"
  "/usr/local/bin/anaconda3/lib/python3.7/site-packages/em" "--raw-errors"
  "-F"
  "/root/ros_catkin_ws/build/catkin/catkin_generated/pkg.develspace.context.pc.py"
  "-o" "/root/ros_catkin_ws/build/catkin/devel/lib/pkgconfig/catkin.pc"
  "/root/ros_catkin_ws/src/catkin/cmake/em/pkg.pc.em") returned error code 1
Call Stack (most recent call first):
  cmake/em_expand.cmake:25 (safe_execute_process)
  cmake/catkin_package.cmake:327 (em_expand)
  cmake/catkin_package.cmake:102 (_catkin_package)
  CMakeLists.txt:11 (catkin_package)

-- Configuring incomplete, errors occurred!
See also "/root/ros_catkin_ws/build/catkin/CMakeFiles/CMakeOutput.log".
See also "/root/ros_catkin_ws/build/catkin/CMakeFiles/CMakeError.log".
Failed   <<< catkin [0.82s, exited with code 1]

From the error log:
/usr/local/bin/anaconda3/bin/python: can't find '__main__' module in '/usr/local/bin/anaconda3/lib/python3.7/site-packages/em'
CMake Error at cmake/safe_execute_process.cmake:11 (message):

  execute_process(/root/ros_catkin_ws/build/catkin/catkin_generated/env_cached.sh
  "/usr/local/bin/anaconda3/bin/python"
  "/usr/local/bin/anaconda3/lib/python3.7/site-packages/em" "--raw-errors"
  "-F"
  "/root/ros_catkin_ws/build/catkin/catkin_generated/pkg.develspace.context.pc.py"
  "-o" "/root/ros_catkin_ws/build/catkin/devel/lib/pkgconfig/catkin.pc"
  "/root/ros_catkin_ws/src/catkin/cmake/em/pkg.pc.em") returned error code 1
Call Stack (most recent call first):
  cmake/em_expand.cmake:25 (safe_execute_process)
  cmake/catkin_package.cmake:327 (em_expand)
  cmake/catkin_package.cmake:102 (_catkin_package)
  CMakeLists.txt:11 (catkin_package)

-- Configuring incomplete, errors occurred!
See also "/root/ros_catkin_ws/build/catkin/CMakeFiles/CMakeOutput.log".
See also "/root/ros_catkin_ws/build/catkin/CMakeFiles/CMakeError.log".
Failed   <<< catkin [2.08s, exited with code 1]

 /ros_catkin_ws/build/catkin/CMakeFiles/CMakeError.log

  pthread_t thread;
  pthread_create(&thread, NULL, test_func, NULL);
  pthread_detach(thread);
  pthread_cancel(thread);
  pthread_join(thread, NULL);
  pthread_atfork(NULL, NULL, NULL);
  pthread_exit(NULL);

  return 0;
}

Determining if the function pthread_create exists in the pthreads failed with the following output:
Change Dir: /root/ros_catkin_ws/build/catkin/CMakeFiles/CMakeTmp

Run Build Command(s):/usr/bin/gmake cmTC_d2cba/fast && /usr/bin/gmake  -f CMakeFiles/cmTC_d2cba.dir/build.make CMakeFiles/cmTC_d2cba.dir/build
gmake[1]: Entering directory '/root/ros_catkin_ws/build/catkin/CMakeFiles/CMakeTmp'
Building C object CMakeFiles/cmTC_d2cba.dir/CheckFunctionExists.c.o
/usr/bin/cc   -DCHECK_FUNCTION_EXISTS=pthread_create   -o CMakeFiles/cmTC_d2cba.dir/CheckFunctionExists.c.o   -c /usr/share/cmake/Modules/CheckFunctionExists.c
Linking C executable cmTC_d2cba
/usr/bin/cmake -E cmake_link_script CMakeFiles/cmTC_d2cba.dir/link.txt --verbose=1
/usr/bin/cc  -DCHECK_FUNCTION_EXISTS=pthread_create    -rdynamic CMakeFiles/cmTC_d2cba.dir/CheckFunctionExists.c.o  -o cmTC_d2cba  -lpthreads
/usr/bin/ld: cannot find -lpthreads
collect2: error: ld returned 1 exit status
gmake[1]: *** [CMakeFiles/cmTC_d2cba.dir/build.make:107: cmTC_d2cba] Error 1
gmake[1]: Leaving directory '/root/ros_catkin_ws/build/catkin/CMakeFiles/CMakeTmp'
gmake: *** [Makefile:141: cmTC_d2cba/fast] Error 2

Again, this is the type of thing that is typcally handled on answers.ros.org...

Noted; I'll head there after this. 

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