Closed martinaxgloria closed 4 months ago
traversaro
commented
4 months ago No, sudo should never be necessary when operating inside conda environments (and pixi under the hood creates a conda environment). I guess you had some previous version of urdf_parser_py / urdfdom_py installed in the system via sudo? That however is strange, in theory it should not be visible by conda.
Can you please report the output of pip list --verbose outside the pixi environment, and the out of env ?
traversaro
commented
4 months ago As the error complains that urdfdom-py 1.2.1 is already installed, I guess I know what is happening: you have urdfdom-py installed via ROS2, and probably the PYTHONPATH env variable is leaking python packages that are not related to the conda environment.
traversaro
commented
4 months ago As the error complains that
urdfdom-py 1.2.1is already installed, I guess I know what is happening: you have urdfdom-py installed via ROS2, and probably the PYTHONPATH env variable is leaking python packages that are not related to the conda environment.
Indeed, I just replicated the failure with:
sudo curl -sSL https://raw.githubusercontent.com/ros/rosdistro/master/ros.key -o /usr/share/keyrings/ros-archive-keyring.gpg
echo "deb [arch=$(dpkg --print-architecture) signed-by=/usr/share/keyrings/ros-archive-keyring.gpg] http://packages.ros.org/ros2/ubuntu $(. /etc/os-release && echo $UBUNTU_CODENAME) main" | sudo tee /etc/apt/sources.list.d/ros2.list > /dev/null
sudo apt install ros-humble-urdfdom-py
source /opt/ros/humble/setup.shand then
traversaro@IITBMP014LW012:~/test3/icub-models-generator$ pixi run test_generated_models
✨ Pixi task (default): echo Automatic build of models via icub-models-generator. > ./deploy_commit_message
✨ Pixi task (default): echo ### Dependencies information of dependencies installed manually: >> ./deploy_commit_message
✨ Pixi task (default): export URDF_PARSER_PY_COMMIT=31474b9baaf7c3845b40e5a9aa87d5900a2282c3 && pip install git+https://github.com/ros/urdf_parser_py.git@$URDF_PARSER_PY_COMMIT --no-deps && echo urdf_parser_py commit: ros/urdf_parser_py@$URDF_PARSER_PY_COMMIT >> ./deploy_commit_message
Collecting git+https://github.com/ros/urdf_parser_py.git@31474b9baaf7c3845b40e5a9aa87d5900a2282c3
Cloning https://github.com/ros/urdf_parser_py.git (to revision 31474b9baaf7c3845b40e5a9aa87d5900a2282c3) to /tmp/pip-req-build-3d7g5llz
Running command git clone --filter=blob:none --quiet https://github.com/ros/urdf_parser_py.git /tmp/pip-req-build-3d7g5llz
Running command git rev-parse -q --verify 'sha^31474b9baaf7c3845b40e5a9aa87d5900a2282c3'
Running command git fetch -q https://github.com/ros/urdf_parser_py.git 31474b9baaf7c3845b40e5a9aa87d5900a2282c3
Running command git checkout -q 31474b9baaf7c3845b40e5a9aa87d5900a2282c3
Resolved https://github.com/ros/urdf_parser_py.git to commit 31474b9baaf7c3845b40e5a9aa87d5900a2282c3
Preparing metadata (setup.py) ... done
Building wheels for collected packages: urdfdom_py
Building wheel for urdfdom_py (setup.py) ... done
Created wheel for urdfdom_py: filename=urdfdom_py-0.3.3-py3-none-any.whl size=13006 sha256=6dde5dd835c7790a9d32a6fe0f731737e6805642bf62289b60552774a4996ca6
Stored in directory: /home/traversaro/.cache/pip/wheels/53/6d/23/a9c5a6b60dcfe19b179860b42187516458e778fce6e4e36e09
Successfully built urdfdom_py
Installing collected packages: urdfdom_py
Attempting uninstall: urdfdom_py
Found existing installation: urdfdom-py 1.2.1
Uninstalling urdfdom-py-1.2.1:
ERROR: Could not install packages due to an OSError: [Errno 13] Permission denied: 'urdf.py'
Consider using the `--user` option or check the permissions.@martinaxgloria fyi executing the pip install with sudo probably you corrupted your ROS apt installation, you probably can reinstall the ros-humble-urdfdom-py to fix this.
traversaro
commented
4 months ago Anyhow, this is indeed quite confusing, I reported the issue to pixi devs at https://github.com/prefix-dev/pixi/issues/826 .
martinaxgloria
commented
4 months ago Can you please report the output of
pip list --verboseoutside the pixi environment, and the out ofenv?
ruben-arts
commented
4 months ago Could you try to add the following:
Put the following in the file: clean_env.sh:
export PYTHONPATH=
export PYTHONUSERBASE=disabled_by_wrong_valueand add it to the pixi.toml via:
[activation]
scripts = ["clean_env.sh"]And then restart you pixi shell or pixi run
martinaxgloria
commented
4 months ago Hi @ruben-arts, thanks for the reply. I created a new file clean_env.sh in the same path as the pixi.toml and I did what you suggested. Running pixi run worked with no errors
@traversaro do you think that this workaround is let's say less cumbersome than https://github.com/robotology/icub-models-generator/pull/263?
ruben-arts
commented
4 months ago Awesome :100:
We'll have something like:
[activation]
env = { PYTHONPATH = "" }Which would make it even easier and clearer to the user but for now this is the easiest workaround as it also adds it to the pixi shell.
Full isolation is something we still have to find a solution for. Stay posted :smile:
traversaro
commented
4 months ago @ruben-arts thanks for chiming in!
@traversaro do you think that this workaround is let's say less cumbersome than #263?
For sure, feel free to update the PR or open a new one (you should have access now).
traversaro
commented
4 months ago Thanks @ruben-arts and @martinaxgloria, fixed in https://github.com/robotology/icub-models-generator/pull/263 .
After https://github.com/robotology/icub-models-generator/pull/261, I tried to use new
pixifeatures to generate the model to debug https://github.com/robotology/icub-models-generator/pull/260. Following the instructions in the README.md, when running:I obtained:
Probably it's due to a missing
sudoinurdfdom_pyinstallation I guess. In fact, adding a sudo in here:https://github.com/robotology/icub-models-generator/blob/f0f2099dc85885b816ceb2209471c67578eaeaab/pixi.toml#L16
no errors where retrieved in the generation of the models.
cc @traversaro @Nicogene