Trouble building Drake with Bazel

Question

I have been attempting to build Drake from source with Bazel on Ubuntu 18.04 but the following error occurs when I run

bazel build ...

from the Drake root directory:

ERROR: /home/username/dir/drake/bindings/pydrake/BUILD.bazel:56:37: Action bindings/pydrake/documentation_pybind.h failed (Exit 1) mkdoc failed: error executing command bazel-out/host/bin/tools/workspace/pybind11/mkdoc -DDRAKE_COMMON_SYMBOLIC_DETAIL_HEADER -DEIGEN_MPL2_ONLY -DHAVE_CSTDDEF '-DFMT_HEADER_ONLY=1' '-DFMT_NO_FMT_STRING_ALIAS=1' -DHAVE_SPDLOG ... (remaining 1096 argument(s) skipped)

Use --sandbox_debug to see verbose messages from the sandbox
external/eigen/include/_usr_include_eigen3/Eigen/Core:66:12: fatal error: 'new' file not found
Traceback (most recent call last):
  File "/home/username/.cache/bazel/_bazel_username/6e98757561df7a931d098ab985a3e673/sandbox/linux-sandbox/1371/execroot/drake/bazel-out/host/bin/tools/workspace/pybind11/mkdoc.runfiles/drake/tools/workspace/pybind11/mkdoc.py", line 841, in <module>
    main()
  File "/home/username/.cache/bazel/_bazel_username/6e98757561df7a931d098ab985a3e673/sandbox/linux-sandbox/1371/execroot/drake/bazel-out/host/bin/tools/workspace/pybind11/mkdoc.runfiles/drake/tools/workspace/pybind11/mkdoc.py", line 805, in main
    severities.count(cindex.Diagnostic.Fatal)))
RuntimeError: Parsing headers using the clang library failed with 0 error(s) and 1 fatal error(s)
----------------
Note: The failure of target //tools/workspace/pybind11:mkdoc (with exit code 1) may have been caused by the fact that it is running under Python 3 instead of Python 2. Examine the error to determine if that appears to be the problem. Since this target is built in the host configuration, the only way to change its version is to set --host_force_python=PY2, which affects the entire build.

If this error started occurring in Bazel 0.27 and later, it may be because the Python toolchain now enforces that targets analyzed as PY2 and PY3 run under a Python 2 and Python 3 interpreter, respectively. See https://github.com/bazelbuild/bazel/issues/7899 for more information.
----------------
INFO: Elapsed time: 2345.311s, Critical Path: 321.76s
INFO: 1378 processes: 1378 linux-sandbox.
FAILED: Build did NOT complete successfully

Prior to building, I ran:

sudo ./setup/ubuntu/install_prereqs.sh

as mentioned in the installation instructions.

I had also set the environment variables for the c and c++ compilers to $CC=/usr/bin/gcc and $CXX=/usr/bin/gcc because I was suspicious of compiler issues being the problem. To compare against this, I also tried to build with $CC=/usr/bin/clang-9 and $CXX=/usr/bin/clang++-9, with a different resulting error:

ERROR: /home/username/dir/drake/systems/framework/BUILD.bazel:213:17: C++ compilation of rule '//systems/framework:cache_and_dependency_tracker' failed (Exit 1) clang-9 failed: error executing command /usr/bin/clang-9 -U_FORTIFY_SOURCE -fstack-protector -Wall -Wthread-safety -Wself-assign -fcolor-diagnostics -fno-omit-frame-pointer -g0 -O2 '-D_FORTIFY_SOURCE=1' -DNDEBUG -ffunction-sections ... (remaining 77 argument(s) skipped)
Use --sandbox_debug to see verbose messages from the sandbox
In file included from systems/framework/cache.cc:1:
bazel-out/k8-opt/bin/systems/framework/_virtual_includes/cache_and_dependency_tracker/drake/systems/framework/cache.h:7:10: fatal error: 'cstdint' file not found
#include <cstdint>
         ^~~~~~~~~

I suspect that there is some issue with the include paths that are being used during build since both compilers were unable to find standard files, however I am unsure of what to try next or how to fix this. Any suggestions or advice would be greatly appreciated!

Answer 1

This seems to be the same problem that I encountered. My Question is here Encounter "RuntimeError: The operating system's C++ standard library is not installed correctly" when build drake from source using bazel and I solve my problem following @jwnimmer-tri's answer.

It turns out that Clang is looking for GCC's standard library and it seems that it looks for GCC with higher version (not sure). I guess the problem is that you have gcc-8 installed but not g++-8, so after you install g++-8 you can fix the issue. Another possible way to solve your problem is to follow @jwnimmer-tri's answer in my question to remove gcc-8 completely.