apk add cmake>3.12-suffix not working on alpine docker - docker

I am trying to install Xgboost on an Alpine docker
I was receiving this message:
CMake Error at CMakeLists.txt:1 (cmake_minimum_required):
CMake 3.12 or higher is required. You are running version 3.9.5
then I added the following line before
RUN apk add cmake>3.12-suffix
# RUN pip install cmake
RUN pip3 install xgboost
and I am still getting the following error message.
What am I doing wrong ?
> Step 16/21 : RUN apk add cmake>3.12-suffix
---> Using cache
---> da84d6ee0868
Step 17/21 : RUN pip3 install xgboost
---> Running in c8e77045ea59
Collecting xgboost
Downloading xgboost-1.0.2.tar.gz (821 kB)
ERROR: Command errored out with exit status 1:
command: /usr/bin/python3.6 -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-9m5q6l5k/xgboost/setup.py'"'"';
__file__='"'"'/tmp/pip-install-9m5q6l5k/xgboost/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' egg_info --egg-base /tmp/pip-install-9m5q6l5k/xgboost/pip-egg-info
cwd: /tmp/pip-install-9m5q6l5k/xgboost/
Complete output (35 lines):
+ pwd
+ oldpath=/tmp/pip-install-9m5q6l5k/xgboost
+ cd ./xgboost/
+ mkdir -p build
+ cd build
+ cmake ..
CMake Error at CMakeLists.txt:1 (cmake_minimum_required):
CMake 3.12 or higher is required. You are running version 3.9.5
-- Configuring incomplete, errors occurred!
+ echo -----------------------------
-----------------------------
+ echo Building multi-thread xgboost failed
Building multi-thread xgboost failed
+ echo Start to build single-thread xgboost
Start to build single-thread xgboost
+ cmake .. -DUSE_OPENMP=0
CMake Error at CMakeLists.txt:1 (cmake_minimum_required):
CMake 3.12 or higher is required. You are running version 3.9.5
-- Configuring incomplete, errors occurred!
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "/tmp/pip-install-9m5q6l5k/xgboost/setup.py", line 42, in <module>
LIB_PATH = libpath['find_lib_path']()
File "/tmp/pip-install-9m5q6l5k/xgboost/xgboost/libpath.py", line 50, in find_lib_path
'List of candidates:\n' + ('\n'.join(dll_path)))
XGBoostLibraryNotFound: Cannot find XGBoost Library in the candidate path, did you install compilers and run build.sh in root path?
List of candidates:
/tmp/pip-install-9m5q6l5k/xgboost/xgboost/libxgboost.so
/tmp/pip-install-9m5q6l5k/xgboost/xgboost/../../lib/libxgboost.so
/tmp/pip-install-9m5q6l5k/xgboost/xgboost/./lib/libxgboost.so
/usr/xgboost/libxgboost.so
----------------------------------------
ERROR: Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.

Related

How to launch Jupyter with custom extension using a docker

I am trying to launch, via docker, a jupyterlab with a custom extension(extensionTest). However, I haven't been successful.
Can someone tell me how can i do it? Or put here an example?
What is the best base docker image to use?
Thank you
Best regards
I tried doing this dockerfile, but is not working :
FROM jupyter/minimal-notebook:lab-3.2.3
RUN pip install --no-cache-dir \
astropy \
ipytree \
ipywidgets \
jupyter \
numpy \
poliastro
RUN jupyter labextension install \
jupyterlab-plotly#4.14.2 \
plotlywidget#4.14.2
RUN pip install jupyterlab_widgets
COPY ./extensions/ ./extensions/
WORKDIR ./extensions/
RUN python -m pip install ./extensionTest
RUN jupyter labextension extensionTest
ENTRYPOINT start.sh jupyter lab
Thanks
Error that I get :
ERROR: Command errored out with exit status 1:
command: /opt/conda/bin/python /opt/conda/lib/python3.9/site-packages/pip/_vendor/pep517/in_process/_in_process.py build_wheel /tmp/tmp2m0biqur
cwd: /home/jovyan/extensions/extensionTest
Complete output (44 lines):
INFO:hatch_jupyter_builder.utils:Running jupyter-builder
INFO:hatch_jupyter_builder.utils:Building with hatch_jupyter_builder.npm_builder
INFO:hatch_jupyter_builder.utils:With kwargs: {'build_cmd': 'build:prod', 'npm': ['jlpm']}
INFO:hatch_jupyter_builder.utils:Installing build dependencies with npm. This may take a while...
INFO:hatch_jupyter_builder.utils:> /tmp/pip-build-env-gj35ixm0/overlay/bin/jlpm install
yarn install v1.21.1
info No lockfile found.
[1/4] Resolving packages...
warning #jupyterlab/application > #jupyterlab/apputils > url > querystring#0.2.0: The querystring API is considered Legacy. new code should use the URLSearchParams API instead.
warning #jupyterlab/application > #jupyterlab/ui-components > #blueprintjs/core > popper.js#1.16.1: You can find the new Popper v2 at #popperjs/core, this package is dedicated to the legacy v1
warning #jupyterlab/application > #jupyterlab/ui-components > #blueprintjs/core > react-popper > popper.js#1.16.1: You can find the new Popper v2 at #popperjs/core, this package is dedicated to the legacy v1
warning #jupyterlab/builder > terser-webpack-plugin > cacache > #npmcli/move-file#1.1.2: This functionality has been moved to #npmcli/fs
warning #jupyterlab/builder > #jupyterlab/buildutils > crypto#1.0.1: This package is no longer supported. It's now a built-in Node module. If you've depended on crypto, you should switch to the one that's built-in.
warning #jupyterlab/builder > #jupyterlab/buildutils > verdaccio > request#2.88.0: request has been deprecated, see https://github.com/request/request/issues/3142
warning #jupyterlab/builder > #jupyterlab/buildutils > verdaccio > request > har-validator#5.1.5: this library is no longer supported
warning #jupyterlab/builder > #jupyterlab/buildutils > verdaccio > request > uuid#3.4.0: Please upgrade to version 7 or higher. Older versions may use Math.random() in certain circumstances, which is known to be problematic. See https://v8.dev/blog/math-random for details.
[2/4] Fetching packages...
warning #blueprintjs/core#3.54.0: Invalid bin entry for "upgrade-blueprint-2.0.0-rename" (in "#blueprintjs/core").
warning #blueprintjs/core#3.54.0: Invalid bin entry for "upgrade-blueprint-3.0.0-rename" (in "#blueprintjs/core").
error lib0#0.2.58: The engine "node" is incompatible with this module. Expected version ">=14". Got "12.4.0"
error Found incompatible module.
info Visit https://yarnpkg.com/en/docs/cli/install for documentation about this command.
Traceback (most recent call last):
File "/opt/conda/lib/python3.9/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 363, in <module>
main()
File "/opt/conda/lib/python3.9/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 345, in main
json_out['return_val'] = hook(**hook_input['kwargs'])
File "/opt/conda/lib/python3.9/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 261, in build_wheel
return _build_backend().build_wheel(wheel_directory, config_settings,
File "/tmp/pip-build-env-gj35ixm0/overlay/lib/python3.9/site-packages/hatchling/build.py", line 41, in build_wheel
return os.path.basename(next(builder.build(wheel_directory, ['standard'])))
File "/tmp/pip-build-env-gj35ixm0/overlay/lib/python3.9/site-packages/hatchling/builders/plugin/interface.py", line 136, in build
build_hook.initialize(version, build_data)
File "/tmp/pip-build-env-gj35ixm0/normal/lib/python3.9/site-packages/hatch_jupyter_builder/plugin.py", line 83, in initialize
raise e
File "/tmp/pip-build-env-gj35ixm0/normal/lib/python3.9/site-packages/hatch_jupyter_builder/plugin.py", line 78, in initialize
build_func(self.target_name, version, **build_kwargs)
File "/tmp/pip-build-env-gj35ixm0/normal/lib/python3.9/site-packages/hatch_jupyter_builder/utils.py", line 114, in npm_builder
run(npm_cmd + ["install"], cwd=str(abs_path))
File "/tmp/pip-build-env-gj35ixm0/normal/lib/python3.9/site-packages/hatch_jupyter_builder/utils.py", line 227, in run
return subprocess.check_call(cmd, **kwargs)
File "/opt/conda/lib/python3.9/subprocess.py", line 373, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['/tmp/pip-build-env-gj35ixm0/overlay/bin/jlpm', 'install']' returned non-zero exit status 1.
So, to anyone interested i was able to create a docker file that builds and run you jupyter extension. My code is this:
FROM node:14 AS build-env
RUN apt-get update && \
apt-get install -y python3-pip && \
pip3 install jupyterlab
COPY Path/to/Extension Path/to/Extension
WORKDIR Path/to/extension
RUN yarn install && yarn build && yarn run build
FROM jupyter/minimal-notebook:lab-3.2.3
RUN pip install --no-cache-dir \
astropy \
ipytree \
ipywidgets \
jupyter \
numpy \
poliastro
RUN jupyter labextension install \
jupyterlab-plotly#4.14.2 \
#jupyter-widgets/jupyterlab-manager \
plotlywidget#4.14.2
COPY --from=build-env Path/to/Extension/on/Nodejs Path/to/Extension
RUN jupyter labextension install Path/to/Extension
If someone knows something that can be simplified, let me know :)

Im having problems while running alphacode on ubuntu

I am using Docker Ubuntu.
I have installed the full dataset(dm-code_contests) to /tmp folder and cloned the git repository on /home folder(the repository is code_contests). When I try to run bazel run -c opt \ :print_names_and_sources /tmp/dm-code_contests/code_contests_valid.riegeli(in /home/code_contests folder), it shows error:
Starting local Bazel server and connecting to it...
INFO: Repository local_config_python instantiated at:
/home/code_contests/WORKSPACE:12:10: in <toplevel>
/root/.cache/bazel/_bazel_root/24a36d3f089e715b642fd688d4461183/external/com_github_grpc_grpc/bazel/grpc_deps.bzl:414:21: in grpc_deps
/root/.cache/bazel/_bazel_root/24a36d3f089e715b642fd688d4461183/external/com_github_grpc_grpc/bazel/grpc_python_deps.bzl:43:21: in grpc_python_deps
Repository rule python_configure defined at:
/root/.cache/bazel/_bazel_root/24a36d3f089e715b642fd688d4461183/external/com_github_grpc_grpc/third_party/py/python_configure.bzl:365:35: in <toplevel>
ERROR: An error occurred during the fetch of repository 'local_config_python':
Traceback (most recent call last):
File "/root/.cache/bazel/_bazel_root/24a36d3f089e715b642fd688d4461183/external/com_github_grpc_grpc/third_party/py/python_configure.bzl", line 355, column 35, in _python_autoconf_impl
_create_single_version_package(
File "/root/.cache/bazel/_bazel_root/24a36d3f089e715b642fd688d4461183/external/com_github_grpc_grpc/third_party/py/python_configure.bzl", line 304, column 45, in _create_single_version_package
python_include = _get_python_include(repository_ctx, python_bin)
File "/root/.cache/bazel/_bazel_root/24a36d3f089e715b642fd688d4461183/external/com_github_grpc_grpc/third_party/py/python_configure.bzl", line 236, column 22, in _get_python_include
result = _execute(
File "/root/.cache/bazel/_bazel_root/24a36d3f089e715b642fd688d4461183/external/com_github_grpc_grpc/third_party/py/python_configure.bzl", line 62, column 14, in _execute
_fail("\n".join([
File "/root/.cache/bazel/_bazel_root/24a36d3f089e715b642fd688d4461183/external/com_github_grpc_grpc/third_party/py/python_configure.bzl", line 35, column 9, in _fail
fail("%sPython Configuration Error:%s %s\n" % (red, no_color, msg))
Error in fail: Python Configuration Error: Problem getting python include path for /usr/bin/python3.
<string>:1: DeprecationWarning: The distutils package is deprecated and slated for removal in Python 3.12. Use setuptools or check PEP 632 for potential alternatives
<string>:1: DeprecationWarning: The distutils.sysconfig module is deprecated, use sysconfig instead
Is the Python binary path set up right? (See ./configure or /usr/bin/python3.) Is distutils installed? Are Python headers installed? Try installing python-dev or python3-dev on Debian-based systems. Try python-devel or python3-devel on Redhat-based systems.
ERROR: /home/code_contests/WORKSPACE:12:10: fetching python_configure rule //external:local_config_python: Traceback (most recent call last):
File "/root/.cache/bazel/_bazel_root/24a36d3f089e715b642fd688d4461183/external/com_github_grpc_grpc/third_party/py/python_configure.bzl", line 355, column 35, in _python_autoconf_impl
_create_single_version_package(
File "/root/.cache/bazel/_bazel_root/24a36d3f089e715b642fd688d4461183/external/com_github_grpc_grpc/third_party/py/python_configure.bzl", line 304, column 45, in _create_single_version_package
python_include = _get_python_include(repository_ctx, python_bin)
File "/root/.cache/bazel/_bazel_root/24a36d3f089e715b642fd688d4461183/external/com_github_grpc_grpc/third_party/py/python_configure.bzl", line 236, column 22, in _get_python_include
result = _execute(
File "/root/.cache/bazel/_bazel_root/24a36d3f089e715b642fd688d4461183/external/com_github_grpc_grpc/third_party/py/python_configure.bzl", line 62, column 14, in _execute
_fail("\n".join([
File "/root/.cache/bazel/_bazel_root/24a36d3f089e715b642fd688d4461183/external/com_github_grpc_grpc/third_party/py/python_configure.bzl", line 35, column 9, in _fail
fail("%sPython Configuration Error:%s %s\n" % (red, no_color, msg))
Error in fail: Python Configuration Error: Problem getting python include path for /usr/bin/python3.
<string>:1: DeprecationWarning: The distutils package is deprecated and slated for removal in Python 3.12. Use setuptools or check PEP 632 for potential alternatives
<string>:1: DeprecationWarning: The distutils.sysconfig module is deprecated, use sysconfig instead
Is the Python binary path set up right? (See ./configure or /usr/bin/python3.) Is distutils installed? Are Python headers installed? Try installing python-dev or python3-dev on Debian-based systems. Try python-devel or python3-devel on Redhat-based systems.
ERROR: /root/.cache/bazel/_bazel_root/24a36d3f089e715b642fd688d4461183/external/com_google_riegeli/python/riegeli/records/BUILD:8:13: #com_google_riegeli//python/riegeli/records:record_writer_cc depends on #local_config_python//:python_headers in repository #local_config_python which failed to fetch. no such package '#local_config_python//': Python Configuration Error: Problem getting python include path for /usr/bin/python3.
<string>:1: DeprecationWarning: The distutils package is deprecated and slated for removal in Python 3.12. Use setuptools or check PEP 632 for potential alternatives
<string>:1: DeprecationWarning: The distutils.sysconfig module is deprecated, use sysconfig instead
Is the Python binary path set up right? (See ./configure or /usr/bin/python3.) Is distutils installed? Are Python headers installed? Try installing python-dev or python3-dev on Debian-based systems. Try python-devel or python3-devel on Redhat-based systems.
ERROR: Analysis of target '//:print_names_and_sources' failed; build aborted:
INFO: Elapsed time: 3.701s
INFO: 0 processes.
FAILED: Build did NOT complete successfully (49 packages loaded, 348 targets configured)
FAILED: Build did NOT complete successfully (49 packages loaded, 348 targets configured)
Fetching #com_google_absl; Cloning tags/20211102.0 of https://github.com/abseil/abseil-cpp.git
root#c89a94de94ce://home/code_contests# bazel run -c opt \ :print_names_and_sources /tmp/dm-code_contests/code_contests
_valid.riegeli
ERROR: Skipping ' :print_names_and_sources': no such package ' ': BUILD file not found in any of the following directories. Add a BUILD file to a directory to mark it as a package.
- /home/code_contests/
WARNING: Target pattern parsing failed.
ERROR: no such package ' ': BUILD file not found in any of the following directories. Add a BUILD file to a directory to mark it as a package.
- /home/code_contests/
INFO: Elapsed time: 0.174s
INFO: 0 processes.
FAILED: Build did NOT complete successfully (0 packages loaded)
FAILED: Build did NOT complete successfully (0 packages loaded)
Im new to Ubuntu(as well as bazel). So how can I fix this error and run the project?
link to the source code: https://github.com/deepmind/code_contests
You should make sure your gcc is the latest version.
For python2 you should install it like this:
#Remove bazel and reinstall
bazel clean --expunge
rm -rf ~/.cache/bazel
To re-install follow this instruction
#Install python2 dependency
sudo apt update && sudo apt install python-dev
For a detailed explanation kindly refer to this document. Thank you!

While running Docker build the pip dependencies installation failed

I was trying to create a docker image for a sentiment analysis application. I have the dependencies as follows:
flask
transformers
optimum[onnxruntime]
gunicorn
I have the dockerfile as below:
#Using the base image with python
FROM python:3.8-alpine3.15
#Set our working directory as app
WORKDIR /app
#Installing python dependencies
RUN pip install --upgrade pip
#COPY requirements.txt /
RUN pip install flask transformers optimum[onnxruntime] gunicorn
# Copy the models directory and app.py files
COPY ["./models", "app.py", "./"]
#Exposing the port 5000 from the container
EXPOSE 5000
#Starting the python application
ENTRYPOINT ["gunicorn", "--bind=127.0.0.1:5000", "app:app"]
But I get some errors while executing the following command:
sudo docker build -t sentiment-analysis:v001 .
The error as follows:
Downloading optimum-0.1.2-py3-none-any.whl (33 kB)
Downloading optimum-0.1.1.tar.gz (17 kB)
Installing build dependencies: started
Installing build dependencies: finished with status 'done'
Getting requirements to build wheel: started
Getting requirements to build wheel: finished with status 'done'
Preparing metadata (pyproject.toml): started
Preparing metadata (pyproject.toml): finished with status 'done'
Downloading optimum-0.1.0.tar.gz (16 kB)
Installing build dependencies: started
Installing build dependencies: finished with status 'done'
Getting requirements to build wheel: started
Getting requirements to build wheel: finished with status 'error'
error: subprocess-exited-with-error
× Getting requirements to build wheel did not run successfully.
│ exit code: 1
╰─> [24 lines of output]
Traceback (most recent call last):
File "<string>", line 7, in <module>
FileNotFoundError: [Errno 2] No such file or directory: 'optimum/version.py'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/local/lib/python3.8/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 363, in <module>
main()
File "/usr/local/lib/python3.8/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 345, in main
json_out['return_val'] = hook(**hook_input['kwargs'])
File "/usr/local/lib/python3.8/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 130, in get_requires_for_build_wheel
return hook(config_settings)
File "/tmp/pip-build-env-z7_0v3f_/overlay/lib/python3.8/site-packages/setuptools/build_meta.py", line 338, in get_requires_for_build_wheel
return self._get_build_requires(config_settings, requirements=['wheel'])
File "/tmp/pip-build-env-z7_0v3f_/overlay/lib/python3.8/site-packages/setuptools/build_meta.py", line 320, in _get_build_requires
self.run_setup()
File "/tmp/pip-build-env-z7_0v3f_/overlay/lib/python3.8/site-packages/setuptools/build_meta.py", line 482, in run_setup
super(_BuildMetaLegacyBackend,
File "/tmp/pip-build-env-z7_0v3f_/overlay/lib/python3.8/site-packages/setuptools/build_meta.py", line 335, in run_setup
exec(code, locals())
File "<string>", line 10, in <module>
AssertionError: Error: Could not open 'optimum/version.py' due [Errno 2] No such file or directory: 'optimum/version.py'
[end of output]
note: This error originates from a subprocess, and is likely not a problem with pip.
error: subprocess-exited-with-error
× Getting requirements to build wheel did not run successfully.
│ exit code: 1
╰─> See above for output.
note: This error originates from a subprocess, and is likely not a problem with pip.
The command '/bin/sh -c pip install flask transformers optimum[onnxruntime] gunicorn' returned a non-zero code: 1
What could be the problem? Thank you in advance.
I have run my application using gunicorn with no error. Then I tried to create a docker image to deploy the application. But while creating the docker image I got the error mentioned in the post. I was expecting a docker image that could be deployed.

Building Drake From Source Fails With "ModuleNotFoundError: No module named 'yaml'"

I am following the instructions here: https://drake.mit.edu/from_source.html. I already ran
./setup/mac/install_prereqs.sh
in my python virtualenv (drake-venv) and it succeeded. I then managed to build and run the inclined plane example with Bazel. But trying to build some of the other examples results in errors involving YAML like this:
(drake-venv) benq:acrobot % bazel build acrobot_input --subcommands --verbose_failures --sandbox_debug
INFO: Analyzed target //examples/acrobot:acrobot_input (0 packages loaded, 0 targets configured).
INFO: Found 1 target...
SUBCOMMAND: # //examples/acrobot:acrobot_input_codegen [action 'Action examples/acrobot/gen/acrobot_input.cc', configuration: f8bba554e4e3784a5a24e83c682b75e9b6104059526c94f74d854527a53436a6, execution platform: #local_config_platform//:host]
(cd /private/var/tmp/_bazel_benq/a35a7fa5c4830c980dbc52ab349cb0bc/execroot/drake && \
exec env - \
bazel-out/host/bin/tools/vector_gen/lcm_vector_gen '--src=examples/acrobot/acrobot_input_named_vector.yaml' '--out=bazel-out/darwin-opt/bin/examples/acrobot/gen/acrobot_input.cc' '--out=bazel-out/darwin-opt/bin/examples/acrobot/gen/acrobot_input.h' '--include_prefix=drake')
# Configuration: f8bba554e4e3784a5a24e83c682b75e9b6104059526c94f74d854527a53436a6
# Execution platform: #local_config_platform//:host
ERROR: /Users/benq/Documents/drake/examples/acrobot/BUILD.bazel:30:28: Action examples/acrobot/gen/acrobot_input.cc failed: (Exit 1): sandbox-exec failed: error executing command
(cd /private/var/tmp/_bazel_benq/a35a7fa5c4830c980dbc52ab349cb0bc/sandbox/darwin-sandbox/176/execroot/drake && \
exec env - \
TMPDIR=/var/folders/s0/tfqtn2s54135x0qzt5kxnzs00000gn/T/ \
/usr/bin/sandbox-exec -f /private/var/tmp/_bazel_benq/a35a7fa5c4830c980dbc52ab349cb0bc/sandbox/darwin-sandbox/176/sandbox.sb /var/tmp/_bazel_benq/install/ebbb2540c6000feeb8873385c487a79c/process-wrapper '--timeout=0' '--kill_delay=15' bazel-out/host/bin/tools/vector_gen/lcm_vector_gen '--src=examples/acrobot/acrobot_input_named_vector.yaml' '--out=bazel-out/darwin-opt/bin/examples/acrobot/gen/acrobot_input.cc' '--out=bazel-out/darwin-opt/bin/examples/acrobot/gen/acrobot_input.h' '--include_prefix=drake')
Traceback (most recent call last):
File "/private/var/tmp/_bazel_benq/a35a7fa5c4830c980dbc52ab349cb0bc/sandbox/darwin-sandbox/176/execroot/drake/bazel-out/host/bin/tools/vector_gen/lcm_vector_gen.runfiles/drake/tools/vector_gen/lcm_vector_gen.py", line 10, in <module>
import yaml
ModuleNotFoundError: No module named 'yaml'
Target //examples/acrobot:acrobot_input failed to build
INFO: Elapsed time: 1.059s, Critical Path: 0.58s
INFO: 5 processes: 5 internal.
FAILED: Build did NOT complete successfully
But I'm not sure why this is happening considering that importing yaml in Terminal works:
(drake-venv) benq:acrobot % which python
/Users/benq/Documents/drake/drake-venv/bin/python
(drake-venv) benq:acrobot % python --version
Python 3.9.10
(drake-venv) benq:acrobot % python -c 'import yaml'
(drake-venv) benq:acrobot %
I've already tried reinstalling PyYaml but that didn't help.
Relevant Info:
Operating System: macOS Monterey (12.3)
Architecture: x86_64
Python: Python 3.9.10
Bazel version:
% which bazel; bazel version
/usr/local/bin/bazel
Build label: 5.0.0-homebrew
Build target: bazel-out/darwin-opt/bin/src/main/java/com/google/devtools/build/lib/bazel/BazelServer_deploy.jar
Build time: Tue Jan 1 00:00:00 1980 (315532800)
Build timestamp: 315532800
Build timestamp as int: 315532800
Bazel C++ compiler: Apple clang version 13.1.6 (clang-1316.0.21.2)
Git revision: 06dd087b40
The lcm_vector_gen in the error message is a code-generation tool that's run as part of the build.
It's probably not obeying your which python, but instead using the hard-coded /usr/local/bin/python3.9 from https://github.com/RobotLocomotion/drake/blob/master/tools/py_toolchain/interpreter_paths.bzl.
We don't run or test our builds within a virtual environment, so you've stumbled into a novel situation.
Possibly editing that bzl file linked above (interpreter_paths.bzl), to point MACOS_I386_INTERPRETER_PATH to your venv python (/Users/benq/Documents/drake/drake-venv/bin/python), would fix the error.

Installing python module in Robomaker ROS workspace with colcon

I'm working on a cloud-based robotic application with AWS RoboMaker. I'm using ROS Kinetic, with the build tool colcon.
My robot application depends on a custom python module, which has to be in my workspace. This python module is built by colcon as a python package, not a ROS package. This page explains how to do that with catkin, but this example shows how to adapt it to colcon. So finally my workspace looks like that :
my_workspace/
|--src/
|--my_module/
| |--setup.py
| |--package.xml
| |--subfolders and python scripts...
|--some_ros_pkg1/
|--some_ros_pkg2/
|...
However the command : colcon build <my_workspace> builds all ROS packages but fails to build my python module as a package.
Here's the error I get :
Starting >>> my-module
[54.297s] WARNING:colcon.colcon_ros.task.ament_python.build:Package 'my-module' doesn't explicitly install a marker in the package index (colcon-ros currently does it implicitly but that fallback will be removed in the future)
[54.298s] WARNING:colcon.colcon_ros.task.ament_python.build:Package 'my-module' doesn't explicitly install the 'package.xml' file (colcon-ros currently does it implicitly but that fallback will be removed in the future)
--- stderr: my-module
usage: setup.py [global_opts] cmd1 [cmd1_opts] [cmd2 [cmd2_opts] ...]
or: setup.py --help [cmd1 cmd2 ...]
or: setup.py --help-commands
or: setup.py cmd --help
error: invalid command 'egg_info'
---
Failed <<< my-module [0.56s, exited with code 1]
I found this issue that seems correlated, and thus tried : pip install --upgrade setuptools
...Which fails with the error message :
Collecting setuptools
Using cached https://files.pythonhosted.org/packages/7c/1b/9b68465658cda69f33c31c4dbd511ac5648835680ea8de87ce05c81f95bf/setuptools-50.3.0.zip
Complete output from command python setup.py egg_info:
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "setuptools/__init__.py", line 16, in <module>
import setuptools.version
File "setuptools/version.py", line 1, in <module>
import pkg_resources
File "pkg_resources/__init__.py", line 1365
raise SyntaxError(e) from e
^
SyntaxError: invalid syntax
----------------------------------------
Command "python setup.py egg_info" failed with error code 1 in /tmp/pip-build-uwFamt/setuptools/
And with pip3 install --upgrade setuptools, I get :
Defaulting to user installation because normal site-packages is not writeable
Requirement already up-to-date: setuptools in /home/ubuntu/.local/lib/python3.5/site-packages (50.3.0)
I have both Python 3.5.2 an Python 2.7, but I don't know which one is used by colcon.
So I don't know what to try next, and what the real problem is. Any help welcome !
I managed to correctly install my package and its dependencies. I develop the method below, in case it may help someone someday !
I have been mainly inspired by this old DeepRacer repository.
The workspace tree in the question is wrong. It should look like this:
my_workspace/
|--src/
|--my_wrapper_package/
| |--setup.py
| |--my_package/
| |--__init__.py
| |--subfolders and python scripts...
|--some_ros_pkg1/
|--some_ros_pkg2/
my_wrapper_package may contain more than one python custom package.
A good setup.py example is this one.
You shouldn't put a package.xml next to setup.py : colcon will only look at the dependencies declared in package.xml, and won't collect pip packages.
It may help sometimes to delete the folders my_wrapper_package generated by colcon in install/ and build/. Doing so you force colcon to rebuild and bundle from scratch.

Resources