Colcon fails to find 'sh' environment variables on Python 3.11.1
notalltim opened this issue · 13 comments
notalltim commented
after following the instructions on docs.ros.org to install from source I am getting the following error when running. I have tried with both bash and fish. Any help would be appreciated.
VERBOSE=1 colcon build --symlink-install --packages-skip-by-dep python_qt_binding --cmake-args -DTHIRDPARTY_Asio=ON -- no-warn-unused-cli
Starting >>> ament_package
Starting >>> ament_lint
Starting >>> gtest_vendor
Starting >>> fastcdr
Starting >>> ament_cppcheck
Starting >>> iceoryx_hoofs
Starting >>> osrf_pycommon
[1.406s] colcon.colcon_core.shell ERROR Exception in shell extension 'sh': The environment shouldn't be empty
Traceback (most recent call last):
File "/usr/lib/python3.11/site-packages/colcon_core/shell/__init__.py", line 298, in get_command_environment
return await extension.generate_command_environment(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/python3.11/site-packages/colcon_core/shell/sh.py", line 147, in generate_command_environment
env = await get_environment_variables(cmd, cwd=str(build_base))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/python3.11/site-packages/colcon_core/shell/__init__.py", line 364, in get_environment_variables
assert len(env) > 0, "The environment shouldn't be empty"
AssertionError: The environment shouldn't be empty
Starting >>> osrf_testing_tools_cpp
Starting >>> google_benchmark_vendor
[1.406s] colcon.colcon_ros.task.ament_python.build ERROR Could not find a shell extension for the command environment
Starting >>> urdfdom_headers
[1.407s] colcon.colcon_core.shell ERROR Exception in shell extension 'sh': The environment shouldn't be empty
Traceback (most recent call last):
File "/usr/lib/python3.11/site-packages/colcon_core/shell/__init__.py", line 298, in get_command_environment
return await extension.generate_command_environment(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/python3.11/site-packages/colcon_core/shell/sh.py", line 147, in generate_command_environment
env = await get_environment_variables(cmd, cwd=str(build_base))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/python3.11/site-packages/colcon_core/shell/__init__.py", line 364, in get_environment_variables
assert len(env) > 0, "The environment shouldn't be empty"
AssertionError: The environment shouldn't be empty
Starting >>> ament_pycodestyle
[1.407s] colcon.colcon_ros.task.ament_python.build ERROR Could not find a shell extension for the command environment
[1.407s] colcon.colcon_core.shell ERROR Exception in shell extension 'sh': The environment shouldn't be empty
Traceback (most recent call last):
File "/usr/lib/python3.11/site-packages/colcon_core/shell/__init__.py", line 298, in get_command_environment
return await extension.generate_command_environment(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/python3.11/site-packages/colcon_core/shell/sh.py", line 147, in generate_command_environment
env = await get_environment_variables(cmd, cwd=str(build_base))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/python3.11/site-packages/colcon_core/shell/__init__.py", line 364, in get_environment_variables
assert len(env) > 0, "The environment shouldn't be empty"
AssertionError: The environment shouldn't be empty
Failed <<< ament_package [0.00s, exited with code 1]
[1.407s] colcon.colcon_cmake.task.cmake.build ERROR Could not find a shell extension for the command environment
Failed <<< ament_lint [0.00s, exited with code 1]
[1.412s] colcon.colcon_core.shell ERROR Exception in shell extension 'sh': The environment shouldn't be empty
Traceback (most recent call last):
File "/usr/lib/python3.11/site-packages/colcon_core/shell/__init__.py", line 298, in get_command_environment
return await extension.generate_command_environment(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/python3.11/site-packages/colcon_core/shell/sh.py", line 147, in generate_command_environment
env = await get_environment_variables(cmd, cwd=str(build_base))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/python3.11/site-packages/colcon_core/shell/__init__.py", line 364, in get_environment_variables
assert len(env) > 0, "The environment shouldn't be empty"
AssertionError: The environment shouldn't be empty
Failed <<< gtest_vendor [0.01s, exited with code 1]
[1.412s] colcon.colcon_cmake.task.cmake.build ERROR Could not find a shell extension for the command environment
[1.412s] colcon.colcon_core.shell ERROR Exception in shell extension 'sh': The environment shouldn't be empty
Traceback (most recent call last):
File "/usr/lib/python3.11/site-packages/colcon_core/shell/__init__.py", line 298, in get_command_environment
return await extension.generate_command_environment(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/python3.11/site-packages/colcon_core/shell/sh.py", line 147, in generate_command_environment
env = await get_environment_variables(cmd, cwd=str(build_base))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/python3.11/site-packages/colcon_core/shell/__init__.py", line 364, in get_environment_variables
assert len(env) > 0, "The environment shouldn't be empty"
AssertionError: The environment shouldn't be empty
[1.412s] colcon.colcon_ros.task.ament_python.build ERROR Could not find a shell extension for the command environment
[1.412s] colcon.colcon_core.shell ERROR Exception in shell extension 'sh': The environment shouldn't be empty
Traceback (most recent call last):
File "/usr/lib/python3.11/site-packages/colcon_core/shell/__init__.py", line 298, in get_command_environment
return await extension.generate_command_environment(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/python3.11/site-packages/colcon_core/shell/sh.py", line 147, in generate_command_environment
env = await get_environment_variables(cmd, cwd=str(build_base))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/python3.11/site-packages/colcon_core/shell/__init__.py", line 364, in get_environment_variables
assert len(env) > 0, "The environment shouldn't be empty"
AssertionError: The environment shouldn't be empty
Failed <<< fastcdr [0.01s, exited with code 1]
[1.412s] colcon.colcon_cmake.task.cmake.build ERROR Could not find a shell extension for the command environment
Failed <<< ament_cppcheck [0.01s, exited with code 1]
[1.415s] colcon.colcon_core.shell ERROR Exception in shell extension 'sh': The environment shouldn't be empty
Traceback (most recent call last):
File "/usr/lib/python3.11/site-packages/colcon_core/shell/__init__.py", line 298, in get_command_environment
return await extension.generate_command_environment(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/python3.11/site-packages/colcon_core/shell/sh.py", line 147, in generate_command_environment
env = await get_environment_variables(cmd, cwd=str(build_base))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/python3.11/site-packages/colcon_core/shell/__init__.py", line 364, in get_environment_variables
assert len(env) > 0, "The environment shouldn't be empty"
AssertionError: The environment shouldn't be empty
Failed <<< iceoryx_hoofs [0.01s, exited with code 1]
[1.415s] colcon.colcon_ros.task.ament_python.build ERROR Could not find a shell extension for the command environment
[1.415s] colcon.colcon_core.shell ERROR Exception in shell extension 'sh': The environment shouldn't be empty
Traceback (most recent call last):
File "/usr/lib/python3.11/site-packages/colcon_core/shell/__init__.py", line 298, in get_command_environment
return await extension.generate_command_environment(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/python3.11/site-packages/colcon_core/shell/sh.py", line 147, in generate_command_environment
env = await get_environment_variables(cmd, cwd=str(build_base))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/python3.11/site-packages/colcon_core/shell/__init__.py", line 364, in get_environment_variables
assert len(env) > 0, "The environment shouldn't be empty"
AssertionError: The environment shouldn't be empty
[1.415s] colcon.colcon_cmake.task.cmake.build ERROR Could not find a shell extension for the command environment
Failed <<< osrf_pycommon [0.01s, exited with code 1]
[1.418s] colcon.colcon_core.shell ERROR Exception in shell extension 'sh': The environment shouldn't be empty
Traceback (most recent call last):
File "/usr/lib/python3.11/site-packages/colcon_core/shell/__init__.py", line 298, in get_command_environment
return await extension.generate_command_environment(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/python3.11/site-packages/colcon_core/shell/sh.py", line 147, in generate_command_environment
env = await get_environment_variables(cmd, cwd=str(build_base))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/python3.11/site-packages/colcon_core/shell/__init__.py", line 364, in get_environment_variables
assert len(env) > 0, "The environment shouldn't be empty"
AssertionError: The environment shouldn't be empty
Failed <<< osrf_testing_tools_cpp [0.01s, exited with code 1]
[1.418s] colcon.colcon_cmake.task.cmake.build ERROR Could not find a shell extension for the command environment
[1.420s] colcon.colcon_core.shell ERROR Exception in shell extension 'sh': The environment shouldn't be empty
Traceback (most recent call last):
File "/usr/lib/python3.11/site-packages/colcon_core/shell/__init__.py", line 298, in get_command_environment
return await extension.generate_command_environment(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/python3.11/site-packages/colcon_core/shell/sh.py", line 147, in generate_command_environment
env = await get_environment_variables(cmd, cwd=str(build_base))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/python3.11/site-packages/colcon_core/shell/__init__.py", line 364, in get_environment_variables
assert len(env) > 0, "The environment shouldn't be empty"
AssertionError: The environment shouldn't be empty
Failed <<< google_benchmark_vendor [0.01s, exited with code 1]
[1.420s] colcon.colcon_cmake.task.cmake.build ERROR Could not find a shell extension for the command environment
Failed <<< urdfdom_headers [0.01s, exited with code 1]
Aborted <<< ament_pycodestyle [0.29
This command worked before the most recent update including package list in case it is helpful
Packages Altered:
Install abseil-cpp-20220623.1-2.fc37.x86_64 @fedora
Install libmd-1.0.4-2.fc37.x86_64 @fedora
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cottsay commented
I recall having similar issues a few years ago, and the problem was related to parsing elaborate environment variables. Could you please dump your environment (using env) and either post it here or send it to me? Be sure to sanitize any sensitive information before sharing it.
notalltim commented
env.txt
env_kitty.txt
Here you go
cottsay commented
Shoot, I'm not seeing any problems. I've updated my Fedora 37 machine as well, and I still can't reproduce this behavior.
Can you try posting your command environment script files from build/ament_package/colcon_command_prefix_*?
notalltim commented
# generated from colcon_core/shell/template/command_prefix.sh.em
does not generate anything but the comment
notalltim commented
weirdly ament_pycodestlye did generate a colcon_command_prefix_setup_py.sh.env here it is
CHROME_DESKTOP=code-url-handler.desktop
COLCON=1
COLORTERM=truecolor
DBUS_SESSION_BUS_ADDRESS=unix:path=/run/user/1000/bus
DESKTOP_SESSION=gnome
DISPLAY=:0
EDITOR=/usr/bin/nano
GDK_BACKEND=x11
GDMSESSION=gnome
GDM_LANG=en_US.UTF-8
GIO_LAUNCHED_DESKTOP_FILE=/usr/share/applications/code.desktop
GIO_LAUNCHED_DESKTOP_FILE_PID=5768
GIT_ASKPASS=/usr/share/code/resources/app/extensions/git/dist/askpass.sh
GJS_DEBUG_OUTPUT=stderr
GJS_DEBUG_TOPICS=JS ERROR;JS LOG
GNOME_SETUP_DISPLAY=:1
HOME=/home/tgallion
INVOCATION_ID=c5c9ac6e0ea74d0bb4ebacda0e005884
JOURNAL_STREAM=8:29595
LANG=en_US.UTF-8
LOGNAME=tgallion
MANAGERPID=2250
NO_AT_BRIDGE=1
ORIGINAL_XDG_CURRENT_DESKTOP=GNOME
PATH=/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/var/lib/snapd/snap/bin
POSH_THEME=/home/tgallion/.poshthemes/star.omp.json
PWD=/home/tgallion/ros2_humble/build/ament_pycodestyle
QT_IM_MODULE=ibus
SESSION_MANAGER=local/unix:@/tmp/.ICE-unix/2343,unix/unix:/tmp/.ICE-unix/2343
SHELL=/usr/bin/fish
SHLVL=2
SSH_AUTH_SOCK=/run/user/1000/keyring/ssh
SYSTEMD_EXEC_PID=2394
TERM=xterm-256color
TERM_PROGRAM=vscode
TERM_PROGRAM_VERSION=1.74.2
USER=tgallion
USERNAME=tgallion
VSCODE_GIT_ASKPASS_EXTRA_ARGS=--ms-enable-electron-run-as-node
VSCODE_GIT_ASKPASS_MAIN=/usr/share/code/resources/app/extensions/git/dist/askpass-main.js
VSCODE_GIT_ASKPASS_NODE=/usr/share/code/code
VSCODE_GIT_IPC_HANDLE=/run/user/1000/vscode-git-61af660bed.sock
WAYLAND_DISPLAY=wayland-0
XAUTHORITY=/run/user/1000/.mutter-Xwaylandauth.WXOHX1
XDG_CURRENT_DESKTOP=GNOME
XDG_DATA_DIRS=/home/tgallion/.local/share/flatpak/exports/share:/var/lib/flatpak/exports/share:/home/tgallion/.local/share/flatpak/exports/share:/var/lib/flatpak/exports/share:/home/tgallion/.local/share/flatpak/exports/share:/var/lib/flatpak/exports/share:/home/tgallion/.local/share/flatpak/exports/share:/var/lib/flatpak/exports/share:/usr/local/share/:/usr/share/:/var/lib/snapd/desktop
XDG_MENU_PREFIX=gnome-
XDG_RUNTIME_DIR=/run/user/1000
XDG_SESSION_CLASS=user
XDG_SESSION_DESKTOP=gnome
XDG_SESSION_TYPE=wayland
XMODIFIERS=@im=ibus
_=/usr/bin/env
omp_last_status_generation=3
omp_lastcommand=rm -rf build/ install/ log/
notalltim commented
don't know why I did not think to try this earlier but the following works for individual packages and builds fine it just fails when building a set of packages
colcon build --symlink-install --packages-up-to ament_lint --cmake-args -DTHIRDPARTY_Asio=ON --no-warn-unused-cli
notalltim commented
using the sequential executor seems to fix it so it seems to be related to parallel builds. Also parallel builds with --parallel-workers 1 seem to work
cottsay commented
I was finally able to reproduce this. The regression is caused by python3.11-3.11.1-1.fc37. You can dnf downgrade python3.11 for now as a workaround.
cottsay commented
I'm now moderately confident that this is python/cpython#100133. It really doesn't look like there is a trivial workaround, so my advice is to avoid Python 3.11.1. The ticket says that we should expect the fix to be part of 3.11.2.
yashi commented
Just adding a confirmation that Debian version of python3 3.11.1-3 is also affected. Using 3.10.9-1 works fine.
cottsay commented
It looks like Python v3.11.2 was released this week.
cottsay commented
This Python regression was fixed a while back and I've heard nothing of re-occurrence, so I'm going to close this. Feel free to reopen if you encounter this again.