Dev 221 djlabhub chain breaker #34

yambottle · 2024-02-23T17:00:51Z

Status of this PR: Tested the chain-breaker update, this new base image works fine. Still need to:

re-organize this repo: update doc. CI will be temporarily disabled for now, until we have a clear roadmap of if we are going to continue with Jupyterhub or not, if not, then this repo will be archived.
archive djlab-docker, image dependency reference

ethho

singleuser build (docker compose -f singleuser/docker-compose.yaml up --build singleuser) is breaking.

.github/workflows/singleuser-release.yaml

README.md

singleuser/docker-compose.yaml

ethho · 2024-03-13T15:01:32Z

singleuser/Dockerfile

+    # Install dependencies: pip and conda
+    && conda install -y -n base python=${PYTHON_VERSION} \
+    && pip install -r /tmp/config/pip_requirements.txt \
+    && conda install --yes --file /tmp/config/conda_requirements.txt \


This build fails with

❯ dkc up --build singleuser [+] Building 33.8s (8/8) FINISHED docker:default => [singleuser internal] load build definition from Dockerfile 0.0s => => transferring dockerfile: 881B 0.0s => [singleuser internal] load metadata for quay.io/jupyter/minimal-notebook:hub-4.0.2 0.4s => [singleuser internal] load .dockerignore 0.0s => => transferring context: 2B 0.0s => [singleuser internal] load build context 0.0s => => transferring context: 388B 0.0s => CACHED [singleuser 1/4] FROM quay.io/jupyter/minimal-notebook:hub-4.0.2@sha256:628aee34f9cb673f9a90489 0.0s => [singleuser 2/4] COPY ./config /tmp/config 0.1s => [singleuser 3/4] RUN bash /tmp/config/apt_install.sh && cp /tmp/config/before_start_hook.sh / 11.6s => ERROR [singleuser 4/4] RUN [ -d "/home/jovyan/work" ] && rm -r /home/jovyan/work && conda ins 21.4s ------ > [singleuser 4/4] RUN [ -d "/home/jovyan/work" ] && rm -r /home/jovyan/work && conda install -y -n base python=3.10 && pip install -r /tmp/config/pip_requirements.txt && conda install --yes --file /tmp/config/conda_requirements.txt && conda clean --all -f -y: 2.104 Channels: 2.104 - conda-forge 2.104 Platform: linux-64 2.104 Collecting package metadata (repodata.json): ...working... done 20.91 Solving environment: ...working... failed 20.97 20.97 SpecsConfigurationConflictError: Requested specs conflict with configured specs. 20.97 requested specs: 20.97 - python=3.10 20.97 pinned specs: 20.97 - python=3.11 20.97 Use 'conda config --show-sources' to look for 'pinned_specs' and 'track_features' 20.97 configuration parameters. Pinned specs may also be defined in the file 20.97 /opt/conda/conda-meta/pinned. 20.97 20.97 ------ failed to solve: process "/bin/bash -o pipefail -c [ -d \"/home/jovyan/work\" ] && rm -r /home/jovyan/work && conda install -y -n base python=${PYTHON_VERSION} && pip install -r /tmp/config/pip_requirements.txt && conda install --yes --file /tmp/config/conda_requirements.txt && conda clean --all -f -y" did not complete successfully: exit code: 1

Seems like the authors of quay.io/jupyter/minimal-notebook:hub-${JUPYTERHUB_VERSION} have a specific Python version pinned, and the recommendation is to not override it (conda/conda#9016 (comment)).

IMO we should remove conda install -y -n base python=${PYTHON_VERSION} and just use whatever Python version is pinned in the base image.

When I remove the conda install, build succeeds but we get the error:

❯ dkc -f singleuser/docker-compose.yaml up --build singleuser [+] Building 0.4s (9/9) FINISHED docker:default => [singleuser internal] load build definition from Dockerfile 0.0s => => transferring dockerfile: 882B 0.0s => [singleuser internal] load metadata for quay.io/jupyter/minimal-notebook:hub-4.0.2 0.2s => [singleuser internal] load .dockerignore 0.0s => => transferring context: 2B 0.0s => [singleuser internal] load build context 0.0s => => transferring context: 388B 0.0s => [singleuser 1/4] FROM quay.io/jupyter/minimal-notebook:hub-4.0.2@sha256:628aee34f9cb673f9a90489788d0052a9f2e311ed72fc23b8f5918db 0.0s => CACHED [singleuser 2/4] COPY ./config /tmp/config 0.0s => CACHED [singleuser 3/4] RUN bash /tmp/config/apt_install.sh && cp /tmp/config/before_start_hook.sh /usr/local/bin/before 0.0s => CACHED [singleuser 4/4] RUN [ -d "/home/jovyan/work" ] && rm -r /home/jovyan/work && pip install -r /tmp/config/pip_requ 0.0s => [singleuser] exporting to image 0.0s => => exporting layers 0.0s => => writing image sha256:ae5090756d458ccaeaa1d7f4a2b42c661aa91b035bdeafefea94f52f280914e4 0.0s => => naming to docker.io/datajoint/djlabhub:singleuser-4.0.2-py3.10 0.0s [+] Running 1/0 ✔ Container djlabhub-singleuser Created 0.0s Attaching to djlabhub-singleuser djlabhub-singleuser | Entered start.sh with args: start-notebook.py djlabhub-singleuser | Running hooks in: /usr/local/bin/start-notebook.d as uid: 0 gid: 0 djlabhub-singleuser | Done running hooks in: /usr/local/bin/start-notebook.d djlabhub-singleuser | Running hooks in: /usr/local/bin/before-notebook.d as uid: 0 gid: 0 djlabhub-singleuser | Sourcing shell script: /usr/local/bin/before-notebook.d/10activate-conda-env.sh djlabhub-singleuser | Sourcing shell script: /usr/local/bin/before-notebook.d/before_start_hook.sh djlabhub-singleuser | INFO::Datajoint Startup Hook djlabhub-singleuser | INFO::Changing Markdown Preview to preview as default djlabhub-singleuser | INFO::Cloning repo https://github.com/datajoint/datajoint-tutorials.git djlabhub-singleuser | fatal: destination path '/home/jovyan/datajoint-tutorials' already exists and is not an empty directory. djlabhub-singleuser exited with code 128

I added there because previously we had some wired dependencies that can only be installed by conda, but I don't think we need it anymore. I'll take the conda install out

@ethho Updated, please take a look

@yambottle Still failing, the conda lines are still in the Dockerfile:

❯ JUPYTERHUB_VERSION=4.0.2 PYTHON_VERSION=3.10 docker compose -f singleuser/docker-compose.yaml up --build singleuser [+] Building 28.6s (8/8) FINISHED docker:default => [singleuser internal] load build definition from Dockerfile 0.0s => => transferring dockerfile: 881B 0.0s => [singleuser internal] load metadata for quay.io/jupyter/minimal-notebook:hub-4.0.2 0.7s => [singleuser internal] load .dockerignore 0.0s => => transferring context: 2B 0.0s => [singleuser 1/4] FROM quay.io/jupyter/minimal-notebook:hub-4.0.2@sha256:c31664d79087a351962a8d411576a52b0ded36869d3ca2dc7be75e65 0.0s => [singleuser internal] load build context 0.0s => => transferring context: 388B 0.0s => CACHED [singleuser 2/4] COPY ./config /tmp/config 0.0s => CACHED [singleuser 3/4] RUN bash /tmp/config/apt_install.sh && cp /tmp/config/before_start_hook.sh /usr/local/bin/before 0.0s => ERROR [singleuser 4/4] RUN [ -d "/home/jovyan/work" ] && rm -r /home/jovyan/work && conda install -y -n base python=3.1 27.7s ------ > [singleuser 4/4] RUN [ -d "/home/jovyan/work" ] && rm -r /home/jovyan/work && conda install -y -n base python=3.10 && pip install -r /tmp/config/pip_requirements.txt && conda install --yes --file /tmp/config/conda_requirements.txt && conda clean --all -f -y: 1.918 Channels: 1.918 - conda-forge 1.918 Platform: linux-64 1.918 Collecting package metadata (repodata.json): ...working... done 26.86 Solving environment: ...working... failed 26.94 26.94 SpecsConfigurationConflictError: Requested specs conflict with configured specs. 26.94 requested specs: 26.94 - python=3.10 26.94 pinned specs: 26.94 - python=3.11 26.94 Use 'conda config --show-sources' to look for 'pinned_specs' and 'track_features' 26.94 configuration parameters. Pinned specs may also be defined in the file 26.94 /opt/conda/conda-meta/pinned. 26.94 26.94 ------ failed to solve: process "/bin/bash -o pipefail -c [ -d \"/home/jovyan/work\" ] && rm -r /home/jovyan/work && conda install -y -n base python=${PYTHON_VERSION} && pip install -r /tmp/config/pip_requirements.txt && conda install --yes --file /tmp/config/conda_requirements.txt && conda clean --all -f -y" did not complete successfully: exit code: 1

@ethho Sorry, I forgot to push my changes...

@yambottle Build is failing with a different error:

Console Log

$ JUPYTERHUB_VERSION=4.0.2 PYTHON_VERSION=3.10 docker compose -f singleuser/docker-compose.yaml up --build singleuser bhub-singleuser | error: subprocess-exited-with-error djlabhub-singleuser | djlabhub-singleuser | × Building wheel for scikit-image (pyproject.toml) did not run successfully. djlabhub-singleuser | │ exit code: 1 djlabhub-singleuser | ╰─> [863 lines of output] djlabhub-singleuser | setup.py:9: DeprecationWarning: djlabhub-singleuser | djlabhub-singleuser | `numpy.distutils` is deprecated since NumPy 1.23.0, as a result djlabhub-singleuser | of the deprecation of `distutils` itself. It will be removed for djlabhub-singleuser | Python >= 3.12. For older Python versions it will remain present. djlabhub-singleuser | It is recommended to use `setuptools < 60.0` for those Python versions. djlabhub-singleuser | For more details, see: djlabhub-singleuser | https://numpy.org/devdocs/reference/distutils_status_migration.html djlabhub-singleuser | djlabhub-singleuser | djlabhub-singleuser | from numpy.distutils.command.build_ext import build_ext as npy_build_ext djlabhub-singleuser | Partial import of skimage during the build process. djlabhub-singleuser | Compiling /tmp/pip-install-10mv3j2k/scikit-image_bb7651ef5b5542cf9a96f0a046530a7f/skimage/morphology/_skeletonize_3d_cy.pyx because it changed. djlabhub-singleuser | [1/1] Cythonizing /tmp/pip-install-10mv3j2k/scikit-image_bb7651ef5b5542cf9a96f0a046530a7f/skimage/morphology/_skeletonize_3d_cy.pyx djlabhub-singleuser | running bdist_wheel djlabhub-singleuser | running build djlabhub-singleuser | running config_cc djlabhub-singleuser | INFO: unifing config_cc, config, build_clib, build_ext, build commands --compiler options djlabhub-singleuser | running config_fc djlabhub-singleuser | INFO: unifing config_fc, config, build_clib, build_ext, build commands --fcompiler options djlabhub-singleuser | running build_src djlabhub-singleuser | INFO: build_src djlabhub-singleuser | INFO: building extension "skimage._shared.geometry" sources djlabhub-singleuser | INFO: building extension "skimage._shared.transform" sources # ... djlabhub-singleuser | copying skimage/feature/_texture.pxd -> build/lib.linux-x86_64-3.11/skimage/feature djlabhub-singleuser | copying skimage/feature/safe_openmp.pxd -> build/lib.linux-x86_64-3.11/skimage/feature djlabhub-singleuser | copying skimage/feature/_haar.pxd -> build/lib.linux-x86_64-3.11/skimage/feature djlabhub-singleuser | copying skimage/segmentation/_slic.pyx -> build/lib.linux-x86_64-3.11/skimage/segmentation djlabhub-singleuser | copying skimage/segmentation/_watershed_cy.pyx -> build/lib.linux-x86_64-3.11/skimage/segmentation djlabhub-singleuser | copying skimage/segmentation/_felzenszwalb_cy.pyx -> build/lib.linux-x86_64-3.11/skimage/segmentation djlabhub-singleuser | copying skimage/segmentation/_quickshift_cy.pyx -> build/lib.linux-x86_64-3.11/skimage/segmentation djlabhub-singleuser | copying skimage/segmentation/heap_general.pxi -> build/lib.linux-x86_64-3.11/skimage/segmentation djlabhub-singleuser | copying skimage/segmentation/heap_watershed.pxi -> build/lib.linux-x86_64-3.11/skimage/segmentation djlabhub-singleuser | copying skimage/util/_remap.pyx -> build/lib.linux-x86_64-3.11/skimage/util djlabhub-singleuser | copying skimage/measure/_marching_cubes_classic_cy.pyx -> build/lib.linux-x86_64-3.11/skimage/measure djlabhub-singleuser | copying skimage/measure/_moments_cy.pyx -> build/lib.linux-x86_64-3.11/skimage/measure djlabhub-singleuser | copying skimage/measure/_marching_cubes_lewiner_cy.pyx -> build/lib.linux-x86_64-3.11/skimage/measure djlabhub-singleuser | copying skimage/measure/_find_contours_cy.pyx -> build/lib.linux-x86_64-3.11/skimage/measure djlabhub-singleuser | copying skimage/measure/_ccomp.pyx -> build/lib.linux-x86_64-3.11/skimage/measure djlabhub-singleuser | copying skimage/measure/_pnpoly.pyx -> build/lib.linux-x86_64-3.11/skimage/measure djlabhub-singleuser | copying skimage/measure/_ccomp.pxd -> build/lib.linux-x86_64-3.11/skimage/measure djlabhub-singleuser | copying skimage/filters/_multiotsu.pyx -> build/lib.linux-x86_64-3.11/skimage/filters djlabhub-singleuser | copying skimage/draw/_draw.pyx -> build/lib.linux-x86_64-3.11/skimage/draw djlabhub-singleuser | copying skimage/io/_plugins/_colormixer.pyx -> build/lib.linux-x86_64-3.11/skimage/io/_plugins djlabhub-singleuser | copying skimage/io/_plugins/_histograms.pyx -> build/lib.linux-x86_64-3.11/skimage/io/_plugins djlabhub-singleuser | copying skimage/future/graph/_ncut_cy.pyx -> build/lib.linux-x86_64-3.11/skimage/future/graph djlabhub-singleuser | copying skimage/filters/rank/bilateral_cy.pyx -> build/lib.linux-x86_64-3.11/skimage/filters/rank djlabhub-singleuser | copying skimage/filters/rank/percentile_cy.pyx -> build/lib.linux-x86_64-3.11/skimage/filters/rank djlabhub-singleuser | copying skimage/filters/rank/core_cy.pyx -> build/lib.linux-x86_64-3.11/skimage/filters/rank djlabhub-singleuser | copying skimage/filters/rank/core_cy_3d.pyx -> build/lib.linux-x86_64-3.11/skimage/filters/rank djlabhub-singleuser | copying skimage/filters/rank/generic_cy.pyx -> build/lib.linux-x86_64-3.11/skimage/filters/rank djlabhub-singleuser | copying skimage/filters/rank/core_cy.pxd -> build/lib.linux-x86_64-3.11/skimage/filters/rank djlabhub-singleuser | copying skimage/filters/rank/core_cy_3d.pxd -> build/lib.linux-x86_64-3.11/skimage/filters/rank djlabhub-singleuser | running build_ext djlabhub-singleuser | INFO: customize UnixCCompiler djlabhub-singleuser | INFO: customize UnixCCompiler using ConditionalOpenMP djlabhub-singleuser | INFO: CCompilerOpt.cc_test_flags[1086] : testing flags (-march=native) djlabhub-singleuser | INFO: C compiler: gcc -pthread -B /opt/conda/compiler_compat -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/conda/include -fPIC -O2 -isystem /opt/conda/include -fPIC djlabhub-singleuser | djlabhub-singleuser | creating /tmp/tmpsgj0w8s1/tmp djlabhub-singleuser | creating /tmp/tmpsgj0w8s1/tmp/pip-build-env-ggt2lzqz djlabhub-singleuser | creating /tmp/tmpsgj0w8s1/tmp/pip-build-env-ggt2lzqz/overlay djlabhub-singleuser | creating /tmp/tmpsgj0w8s1/tmp/pip-build-env-ggt2lzqz/overlay/lib djlabhub-singleuser | creating /tmp/tmpsgj0w8s1/tmp/pip-build-env-ggt2lzqz/overlay/lib/python3.11 djlabhub-singleuser | creating /tmp/tmpsgj0w8s1/tmp/pip-build-env-ggt2lzqz/overlay/lib/python3.11/site-packages djlabhub-singleuser | creating /tmp/tmpsgj0w8s1/tmp/pip-build-env-ggt2lzqz/overlay/lib/python3.11/site-packages/numpy djlabhub-singleuser | creating /tmp/tmpsgj0w8s1/tmp/pip-build-env-ggt2lzqz/overlay/lib/python3.11/site-packages/numpy/distutils djlabhub-singleuser | creating /tmp/tmpsgj0w8s1/tmp/pip-build-env-ggt2lzqz/overlay/lib/python3.11/site-packages/numpy/distutils/checks djlabhub-singleuser | INFO: compile options: '-I/opt/conda/include/python3.11 -c' djlabhub-singleuser | extra options: '-march=native' djlabhub-singleuser | WARN: CCompilerOpt.dist_test[637] : CCompilerOpt._dist_test_spawn[771] : Command (gcc -pthread -B /opt/conda/compiler_compat -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/conda/include -fPIC -O2 -isystem /opt/conda/include -fPIC -I/opt/conda/include/python3.11 -c /tmp/pip-build-env-ggt2lzqz/overlay/lib/python3.11/site-packages/numpy/distutils/checks/test_flags.c -o /tmp/tmpsgj0w8s1/tmp/pip-build-env-ggt2lzqz/overlay/lib/python3.11/site-packages/numpy/distutils/checks/test_flags.o -MMD -MF /tmp/tmpsgj0w8s1/tmp/pip-build-env-ggt2lzqz/overlay/lib/python3.11/site-packages/numpy/distutils/checks/test_flags.o.d -march=native) failed with exit status 127 output -> djlabhub-singleuser | [Errno 2] No such file or directory: 'gcc' djlabhub-singleuser | WARN: CCompilerOpt.cc_test_flags[1090] : testing failed djlabhub-singleuser | INFO: CCompilerOpt.cc_test_flags[1086] : testing flags (-O3) djlabhub-singleuser | INFO: C compiler: gcc -pthread -B /opt/conda/compiler_compat -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/conda/include -fPIC -O2 -isystem /opt/conda/include -fPIC djlabhub-singleuser | djlabhub-singleuser | INFO: compile options: '-I/opt/conda/include/python3.11 -c' djlabhub-singleuser | extra options: '-O3' djlabhub-singleuser | WARN: CCompilerOpt.dist_test[637] : CCompilerOpt._dist_test_spawn[771] : Command (gcc -pthread -B /opt/conda/compiler_compat -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/conda/include -fPIC -O2 -isystem /opt/conda/include -fPIC -I/opt/conda/include/python3.11 -c /tmp/pip-build-env-ggt2lzqz/overlay/lib/python3.11/site-packages/numpy/distutils/checks/test_flags.c -o /tmp/tmpsgj0w8s1/tmp/pip-build-env-ggt2lzqz/overlay/lib/python3.11/site-packages/numpy/distutils/checks/test_flags.o -MMD -MF /tmp/tmpsgj0w8s1/tmp/pip-build-env-ggt2lzqz/overlay/lib/python3.11/site-packages/numpy/distutils/checks/test_flags.o.d -O3) failed with exit status 127 output -> djlabhub-singleuser | [Errno 2] No such file or directory: 'gcc' djlabhub-singleuser | WARN: CCompilerOpt.cc_test_flags[1090] : testing failed djlabhub-singleuser | INFO: CCompilerOpt.cc_test_flags[1086] : testing flags (-Werror) djlabhub-singleuser | INFO: C compiler: gcc -pthread -B /opt/conda/compiler_compat -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/conda/include -fPIC -O2 -isystem /opt/conda/include -fPIC djlabhub-singleuser | djlabhub-singleuser | INFO: compile options: '-I/opt/conda/include/python3.11 -c' djlabhub-singleuser | extra options: '-Werror' djlabhub-singleuser | WARN: CCompilerOpt.dist_test[637] : CCompilerOpt._dist_test_spawn[771] : Command (gcc -pthread -B /opt/conda/compiler_compat -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/conda/include -fPIC -O2 -isystem /opt/conda/include -fPIC -I/opt/conda/include/python3.11 -c /tmp/pip-build-env-ggt2lzqz/overlay/lib/python3.11/site-packages/numpy/distutils/checks/test_flags.c -o /tmp/tmpsgj0w8s1/tmp/pip-build-env-ggt2lzqz/overlay/lib/python3.11/site-packages/numpy/distutils/checks/test_flags.o -MMD -MF /tmp/tmpsgj0w8s1/tmp/pip-build-env-ggt2lzqz/overlay/lib/python3.11/site-packages/numpy/distutils/checks/test_flags.o.d -Werror) failed with exit status 127 output -> djlabhub-singleuser | [Errno 2] No such file or directory: 'gcc' djlabhub-singleuser | WARN: CCompilerOpt.cc_test_flags[1090] : testing failed djlabhub-singleuser | INFO: CCompilerOpt.__init__[1795] : check requested baseline djlabhub-singleuser | INFO: CCompilerOpt.cc_test_flags[1086] : testing flags (-msse) djlabhub-singleuser | INFO: C compiler: gcc -pthread -B /opt/conda/compiler_compat -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/conda/include -fPIC -O2 -isystem /opt/conda/include -fPIC djlabhub-singleuser | djlabhub-singleuser | INFO: compile options: '-I/opt/conda/include/python3.11 -c' djlabhub-singleuser | extra options: '-msse' djlabhub-singleuser | WARN: CCompilerOpt.dist_test[637] : CCompilerOpt._dist_test_spawn[771] : Command (gcc -pthread -B /opt/conda/compiler_compat -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/conda/include -fPIC -O2 -isystem /opt/conda/include -fPIC -I/opt/conda/include/python3.11 -c /tmp/pip-build-env-ggt2lzqz/overlay/lib/python3.11/site-packages/numpy/distutils/checks/test_flags.c -o /tmp/tmpsgj0w8s1/tmp/pip-build-env-ggt2lzqz/overlay/lib/python3.11/site-packages/numpy/distutils/checks/test_flags.o -MMD -MF /tmp/tmpsgj0w8s1/tmp/pip-build-env-ggt2lzqz/overlay/lib/python3.11/site-packages/numpy/distutils/checks/test_flags.o.d -msse) failed with exit status 127 output -> djlabhub-singleuser | [Errno 2] No such file or directory: 'gcc' djlabhub-singleuser | WARN: CCompilerOpt.cc_test_flags[1090] : testing failed djlabhub-singleuser | INFO: CCompilerOpt.cc_test_flags[1086] : testing flags (-msse2) djlabhub-singleuser | INFO: C compiler: gcc -pthread -B /opt/conda/compiler_compat -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/conda/include -fPIC -O2 -isystem /opt/conda/include -fPIC djlabhub-singleuser | djlabhub-singleuser | INFO: compile options: '-I/opt/conda/include/python3.11 -c' djlabhub-singleuser | extra options: '-msse2' djlabhub-singleuser | WARN: CCompilerOpt.dist_test[637] : CCompilerOpt._dist_test_spawn[771] : Command (gcc -pthread -B /opt/conda/compiler_compat -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/conda/include -fPIC -O2 -isystem /opt/conda/include -fPIC -I/opt/conda/include/python3.11 -c /tmp/pip-build-env-ggt2lzqz/overlay/lib/python3.11/site-packages/numpy/distutils/checks/test_flags.c -o /tmp/tmpsgj0w8s1/tmp/pip-build-env-ggt2lzqz/overlay/lib/python3.11/site-packages/numpy/distutils/checks/test_flags.o -MMD -MF /tmp/tmpsgj0w8s1/tmp/pip-build-env-ggt2lzqz/overlay/lib/python3.11/site-packages/numpy/distutils/checks/test_flags.o.d -msse2) failed with exit status 127 output -> djlabhub-singleuser | [Errno 2] No such file or directory: 'gcc' djlabhub-singleuser | WARN: CCompilerOpt.cc_test_flags[1090] : testing failed djlabhub-singleuser | INFO: CCompilerOpt.feature_test[1560] : testing feature 'SSE' with flags () djlabhub-singleuser | INFO: C compiler: gcc -pthread -B /opt/conda/compiler_compat -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/conda/include -fPIC -O2 -isystem /opt/conda/include -fPIC djlabhub-singleuser | djlabhub-singleuser | INFO: compile options: '-I/opt/conda/include/python3.11 -c' djlabhub-singleuser | WARN: CCompilerOpt.dist_test[637] : CCompilerOpt._dist_test_spawn[771] : Command (gcc -pthread -B /opt/conda/compiler_compat -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/conda/include -fPIC -O2 -isystem /opt/conda/include -fPIC -I/opt/conda/include/python3.11 -c /tmp/pip-build-env-ggt2lzqz/overlay/lib/python3.11/site-packages/numpy/distutils/checks/cpu_sse.c -o /tmp/tmpsgj0w8s1/tmp/pip-build-env-ggt2lzqz/overlay/lib/python3.11/site-packages/numpy/distutils/checks/cpu_sse.o -MMD -MF /tmp/tmpsgj0w8s1/tmp/pip-build-env-ggt2lzqz/overlay/lib/python3.11/site-packages/numpy/distutils/checks/cpu_sse.o.d) failed with exit status 127 output -> djlabhub-singleuser | [Errno 2] No such file or directory: 'gcc' djlabhub-singleuser | WARN: CCompilerOpt.feature_test[1576] : testing failed djlabhub-singleuser | INFO: CCompilerOpt.feature_test[1560] : testing feature 'SSE2' with flags () djlabhub-singleuser | INFO: C compiler: gcc -pthread -B /opt/conda/compiler_compat -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/conda/include -fPIC -O2 -isystem /opt/conda/include -fPIC djlabhub-singleuser | djlabhub-singleuser | INFO: compile options: '-I/opt/conda/include/python3.11 -c' djlabhub-singleuser | WARN: CCompilerOpt.dist_test[637] : CCompilerOpt._dist_test_spawn[771] : Command (gcc -pthread -B /opt/conda/compiler_compat -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/conda/include -fPIC -O2 -isystem /opt/conda/include -fPIC -I/opt/conda/include/python3.11 -c /tmp/pip-build-env-ggt2lzqz/overlay/lib/python3.11/site-packages/numpy/distutils/checks/cpu_sse2.c -o /tmp/tmpsgj0w8s1/tmp/pip-build-env-ggt2lzqz/overlay/lib/python3.11/site-packages/numpy/distutils/checks/cpu_sse2.o -MMD -MF /tmp/tmpsgj0w8s1/tmp/pip-build-env-ggt2lzqz/overlay/lib/python3.11/site-packages/numpy/distutils/checks/cpu_sse2.o.d) failed with exit status 127 output -> djlabhub-singleuser | [Errno 2] No such file or directory: 'gcc' djlabhub-singleuser | WARN: CCompilerOpt.feature_test[1576] : testing failed djlabhub-singleuser | INFO: CCompilerOpt.__init__[1804] : check requested dispatch-able features djlabhub-singleuser | INFO: CCompilerOpt.cc_test_flags[1086] : testing flags (-msse3) djlabhub-singleuser | INFO: C compiler: gcc -pthread -B /opt/conda/compiler_compat -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/conda/include -fPIC -O2 -isystem /opt/conda/include -fPIC djlabhub-singleuser | djlabhub-singleuser | INFO: compile options: '-I/opt/conda/include/python3.11 -c' djlabhub-singleuser | extra options: '-msse3' djlabhub-singleuser | WARN: CCompilerOpt.dist_test[637] : CCompilerOpt._dist_test_spawn[771] : Command (gcc -pthread -B /opt/conda/compiler_compat -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/conda/include -fPIC -O2 -isystem /opt/conda/include -fPIC -I/opt/conda/include/python3.11 -c /tmp/pip-build-env-ggt2lzqz/overlay/lib/python3.11/site-packages/numpy/distutils/checks/test_flags.c -o /tmp/tmpsgj0w8s1/tmp/pip-build-env-ggt2lzqz/overlay/lib/python3.11/site-packages/numpy/distutils/checks/test_flags.o -MMD -MF /tmp/tmpsgj0w8s1/tmp/pip-build-env-ggt2lzqz/overlay/lib/python3.11/site-packages/numpy/distutils/checks/test_flags.o.d -msse3) failed with exit status 127 output -> djlabhub-singleuser | [Errno 2] No such file or directory: 'gcc' djlabhub-singleuser | WARN: CCompilerOpt.cc_test_flags[1090] : testing failed djlabhub-singleuser | INFO: CCompilerOpt.feature_test[1560] : testing feature 'SSE3' with flags () djlabhub-singleuser | INFO: C compiler: gcc -pthread -B /opt/conda/compiler_compat -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/conda/include -fPIC -O2 -isystem /opt/conda/include -fPIC djlabhub-singleuser | djlabhub-singleuser | INFO: compile options: '-I/opt/conda/include/python3.11 -c' djlabhub-singleuser | WARN: CCompilerOpt.dist_test[637] : CCompilerOpt._dist_test_spawn[771] : Command (gcc -pthread -B /opt/conda/compiler_compat -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/conda/include -fPIC -O2 -isystem /opt/conda/include -fPIC -I/opt/conda/include/python3.11 -c /tmp/pip-build-env-ggt2lzqz/overlay/lib/python3.11/site-packages/numpy/distutils/checks/cpu_sse3.c -o /tmp/tmpsgj0w8s1/tmp/pip-build-env-ggt2lzqz/overlay/lib/python3.11/site-packages/numpy/distutils/checks/cpu_sse3.o -MMD -MF /tmp/tmpsgj0w8s1/tmp/pip-build-env-ggt2lzqz/overlay/lib/python3.11/site-packages/numpy/distutils/checks/cpu_sse3.o.d) failed with exit status 127 output -> djlabhub-singleuser | [Errno 2] No such file or directory: 'gcc' djlabhub-singleuser | WARN: CCompilerOpt.feature_test[1576] : testing failed djlabhub-singleuser | INFO: CCompilerOpt.cc_test_flags[1086] : testing flags (-mssse3) djlabhub-singleuser | INFO: C compiler: gcc -pthread -B /opt/conda/compiler_compat -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/conda/include -fPIC -O2 -isystem /opt/conda/include -fPIC djlabhub-singleuser | djlabhub-singleuser | INFO: compile options: '-I/opt/conda/include/python3.11 -c' djlabhub-singleuser | extra options: '-mssse3' djlabhub-singleuser | WARN: CCompilerOpt.dist_test[637] : CCompilerOpt._dist_test_spawn[771] : Command (gcc -pthread -B /opt/conda/compiler_compat -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/conda/include -fPIC -O2 -isystem /opt/conda/include -fPIC -I/opt/conda/include/python3.11 -c /tmp/pip-build-env-ggt2lzqz/overlay/lib/python3.11/site-packages/numpy/distutils/checks/test_flags.c -o /tmp/tmpsgj0w8s1/tmp/pip-build-env-ggt2lzqz/overlay/lib/python3.11/site-packages/numpy/distutils/checks/test_flags.o -MMD -MF /tmp/tmpsgj0w8s1/tmp/pip-build-env-ggt2lzqz/overlay/lib/python3.11/site-packages/numpy/distutils/checks/test_flags.o.d -mssse3) failed with exit status 127 output -> djlabhub-singleuser | [Errno 2] No such file or directory: 'gcc' djlabhub-singleuser | WARN: CCompilerOpt.cc_test_flags[1090] : testing failed djlabhub-singleuser | INFO: CCompilerOpt.cc_test_flags[1086] : testing flags (-msse4.1) djlabhub-singleuser | INFO: C compiler: gcc -pthread -B /opt/conda/compiler_compat -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/conda/include -fPIC -O2 -isystem /opt/conda/include -fPIC djlabhub-singleuser | djlabhub-singleuser | INFO: compile options: '-I/opt/conda/include/python3.11 -c' djlabhub-singleuser | extra options: '-msse4.1' djlabhub-singleuser | WARN: CCompilerOpt.dist_test[637] : CCompilerOpt._dist_test_spawn[771] : Command (gcc -pthread -B /opt/conda/compiler_compat -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/conda/include -fPIC -O2 -isystem /opt/conda/include -fPIC -I/opt/conda/include/python3.11 -c /tmp/pip-build-env-ggt2lzqz/overlay/lib/python3.11/site-packages/numpy/distutils/checks/test_flags.c -o /tmp/tmpsgj0w8s1/tmp/pip-build-env-ggt2lzqz/overlay/lib/python3.11/site-packages/numpy/distutils/checks/test_flags.o -MMD -MF /tmp/tmpsgj0w8s1/tmp/pip-build-env-ggt2lzqz/overlay/lib/python3.11/site-packages/numpy/distutils/checks/test_flags.o.d -msse4.1) failed with exit status 127 output -> djlabhub-singleuser | [Errno 2] No such file or directory: 'gcc' djlabhub-singleuser | WARN: CCompilerOpt.cc_test_flags[1090] : testing failed djlabhub-singleuser | INFO: CCompilerOpt.cc_test_flags[1086] : testing flags (-mpopcnt) djlabhub-singleuser | INFO: C compiler: gcc -pthread -B /opt/conda/compiler_compat -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/conda/include -fPIC -O2 -isystem /opt/conda/include -fPIC djlabhub-singleuser | djlabhub-singleuser | INFO: compile options: '-I/opt/conda/include/python3.11 -c' djlabhub-singleuser | extra options: '-mpopcnt' djlabhub-singleuser | WARN: CCompilerOpt.dist_test[637] : CCompilerOpt._dist_test_spawn[771] : Command (gcc -pthread -B /opt/conda/compiler_compat -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/conda/include -fPIC -O2 -isystem /opt/conda/include -fPIC -I/opt/conda/include/python3.11 -c /tmp/pip-build-env-ggt2lzqz/overlay/lib/python3.11/site-packages/numpy/distutils/checks/test_flags.c -o /tmp/tmpsgj0w8s1/tmp/pip-build-env-ggt2lzqz/overlay/lib/python3.11/site-packages/numpy/distutils/checks/test_flags.o -MMD -MF /tmp/tmpsgj0w8s1/tmp/pip-build-env-ggt2lzqz/overlay/lib/python3.11/site-packages/numpy/distutils/checks/test_flags.o.d -mpopcnt) failed with exit status 127 output -> djlabhub-singleuser | [Errno 2] No such file or directory: 'gcc' djlabhub-singleuser | WARN: CCompilerOpt.cc_test_flags[1090] : testing failed djlabhub-singleuser | INFO: CCompilerOpt.cc_test_flags[1086] : testing flags (-msse4.2) djlabhub-singleuser | INFO: C compiler: gcc -pthread -B /opt/conda/compiler_compat -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/conda/include -fPIC -O2 -isystem /opt/conda/include -fPIC djlabhub-singleuser | djlabhub-singleuser | INFO: compile options: '-I/opt/conda/include/python3.11 -c' djlabhub-singleuser | extra options: '-msse4.2' djlabhub-singleuser | WARN: CCompilerOpt.dist_test[637] : CCompilerOpt._dist_test_spawn[771] : Command (gcc -pthread -B /opt/conda/compiler_compat -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/conda/include -fPIC -O2 -isystem /opt/conda/include -fPIC -I/opt/conda/include/python3.11 -c /tmp/pip-build-env-ggt2lzqz/overlay/lib/python3.11/site-packages/numpy/distutils/checks/test_flags.c -o /tmp/tmpsgj0w8s1/tmp/pip-build-env-ggt2lzqz/overlay/lib/python3.11/site-packages/numpy/distutils/checks/test_flags.o -MMD -MF /tmp/tmpsgj0w8s1/tmp/pip-build-env-ggt2lzqz/overlay/lib/python3.11/site-packages/numpy/distutils/checks/test_flags.o.d -msse4.2) failed with exit status 127 output -> djlabhub-singleuser | [Errno 2] No such file or directory: 'gcc' djlabhub-singleuser | WARN: CCompilerOpt.cc_test_flags[1090] : testing failed djlabhub-singleuser | INFO: CCompilerOpt.cc_test_flags[1086] : testing flags (-mavx) djlabhub-singleuser | INFO: C compiler: gcc -pthread -B /opt/conda/compiler_compat -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/conda/include -fPIC -O2 -isystem /opt/conda/include -fPIC djlabhub-singleuser | djlabhub-singleuser | INFO: compile options: '-I/opt/conda/include/python3.11 -c' djlabhub-singleuser | extra options: '-mavx' djlabhub-singleuser | WARN: CCompilerOpt.dist_test[637] : CCompilerOpt._dist_test_spawn[771] : Command (gcc -pthread -B /opt/conda/compiler_compat -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/conda/include -fPIC -O2 -isystem /opt/conda/include -fPIC -I/opt/conda/include/python3.11 -c /tmp/pip-build-env-ggt2lzqz/overlay/lib/python3.11/site-packages/numpy/distutils/checks/test_flags.c -o /tmp/tmpsgj0w8s1/tmp/pip-build-env-ggt2lzqz/overlay/lib/python3.11/site-packages/numpy/distutils/checks/test_flags.o -MMD -MF /tmp/tmpsgj0w8s1/tmp/pip-build-env-ggt2lzqz/overlay/lib/python3.11/site-packages/numpy/distutils/checks/test_flags.o.d -mavx) failed with exit status 127 output -> djlabhub-singleuser | [Errno 2] No such file or directory: 'gcc' djlabhub-singleuser | WARN: CCompilerOpt.cc_test_flags[1090] : testing failed djlabhub-singleuser | INFO: CCompilerOpt.cc_test_flags[1086] : testing flags (-mf16c) djlabhub-singleuser | INFO: C compiler: gcc -pthread -B /opt/conda/compiler_compat -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/conda/include -fPIC -O2 -isystem /opt/conda/include -fPIC djlabhub-singleuser | djlabhub-singleuser | INFO: compile options: '-I/opt/conda/include/python3.11 -c' djlabhub-singleuser | extra options: '-mf16c' djlabhub-singleuser | WARN: CCompilerOpt.dist_test[637] : CCompilerOpt._dist_test_spawn[771] : Command (gcc -pthread -B /opt/conda/compiler_compat -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/conda/include -fPIC -O2 -isystem /opt/conda/include -fPIC -I/opt/conda/include/python3.11 -c /tmp/pip-build-env-ggt2lzqz/overlay/lib/python3.11/site-packages/numpy/distutils/checks/test_flags.c -o /tmp/tmpsgj0w8s1/tmp/pip-build-env-ggt2lzqz/overlay/lib/python3.11/site-packages/numpy/distutils/checks/test_flags.o -MMD -MF /tmp/tmpsgj0w8s1/tmp/pip-build-env-ggt2lzqz/overlay/lib/python3.11/site-packages/numpy/distutils/checks/test_flags.o.d -mf16c) failed with exit status 127 output -> djlabhub-singleuser | [Errno 2] No such file or directory: 'gcc' djlabhub-singleuser | WARN: CCompilerOpt.cc_test_flags[1090] : testing failed djlabhub-singleuser | INFO: CCompilerOpt.cc_test_flags[1086] : testing flags (-mfma) djlabhub-singleuser | INFO: C compiler: gcc -pthread -B /opt/conda/compiler_compat -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/conda/include -fPIC -O2 -isystem /opt/conda/include -fPIC djlabhub-singleuser | djlabhub-singleuser | INFO: compile options: '-I/opt/conda/include/python3.11 -c' djlabhub-singleuser | extra options: '-mfma' djlabhub-singleuser | WARN: CCompilerOpt.dist_test[637] : CCompilerOpt._dist_test_spawn[771] : Command (gcc -pthread -B /opt/conda/compiler_compat -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/conda/include -fPIC -O2 -isystem /opt/conda/include -fPIC -I/opt/conda/include/python3.11 -c /tmp/pip-build-env-ggt2lzqz/overlay/lib/python3.11/site-packages/numpy/distutils/checks/test_flags.c -o /tmp/tmpsgj0w8s1/tmp/pip-build-env-ggt2lzqz/overlay/lib/python3.11/site-packages/numpy/distutils/checks/test_flags.o -MMD -MF /tmp/tmpsgj0w8s1/tmp/pip-build-env-ggt2lzqz/overlay/lib/python3.11/site-packages/numpy/distutils/checks/test_flags.o.d -mfma) failed with exit status 127 output -> djlabhub-singleuser | [Errno 2] No such file or directory: 'gcc' djlabhub-singleuser | WARN: CCompilerOpt.cc_test_flags[1090] : testing failed djlabhub-singleuser | INFO: CCompilerOpt.cc_test_flags[1086] : testing flags (-mavx2) djlabhub-singleuser | INFO: C compiler: gcc -pthread -B /opt/conda/compiler_compat -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/conda/include -fPIC -O2 -isystem /opt/conda/include -fPIC djlabhub-singleuser | djlabhub-singleuser | INFO: compile options: '-I/opt/conda/include/python3.11 -c' djlabhub-singleuser | extra options: '-mavx2' djlabhub-singleuser | WARN: CCompilerOpt.dist_test[637] : CCompilerOpt._dist_test_spawn[771] : Command (gcc -pthread -B /opt/conda/compiler_compat -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/conda/include -fPIC -O2 -isystem /opt/conda/include -fPIC -I/opt/conda/include/python3.11 -c /tmp/pip-build-env-ggt2lzqz/overlay/lib/python3.11/site-packages/numpy/distutils/checks/test_flags.c -o /tmp/tmpsgj0w8s1/tmp/pip-build-env-ggt2lzqz/overlay/lib/python3.11/site-packages/numpy/distutils/checks/test_flags.o -MMD -MF /tmp/tmpsgj0w8s1/tmp/pip-build-env-ggt2lzqz/overlay/lib/python3.11/site-packages/numpy/distutils/checks/test_flags.o.d -mavx2) failed with exit status 127 output -> djlabhub-singleuser | [Errno 2] No such file or directory: 'gcc' djlabhub-singleuser | WARN: CCompilerOpt.cc_test_flags[1090] : testing failed djlabhub-singleuser | INFO: CCompilerOpt.cc_test_flags[1086] : testing flags (-mavx512f -mno-mmx) djlabhub-singleuser | INFO: C compiler: gcc -pthread -B /opt/conda/compiler_compat -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/conda/include -fPIC -O2 -isystem /opt/conda/include -fPIC djlabhub-singleuser | djlabhub-singleuser | INFO: compile options: '-I/opt/conda/include/python3.11 -c' djlabhub-singleuser | extra options: '-mavx512f -mno-mmx' djlabhub-singleuser | WARN: CCompilerOpt.dist_test[637] : CCompilerOpt._dist_test_spawn[771] : Command (gcc -pthread -B /opt/conda/compiler_compat -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/conda/include -fPIC -O2 -isystem /opt/conda/include -fPIC -I/opt/conda/include/python3.11 -c /tmp/pip-build-env-ggt2lzqz/overlay/lib/python3.11/site-packages/numpy/distutils/checks/test_flags.c -o /tmp/tmpsgj0w8s1/tmp/pip-build-env-ggt2lzqz/overlay/lib/python3.11/site-packages/numpy/distutils/checks/test_flags.o -MMD -MF /tmp/tmpsgj0w8s1/tmp/pip-build-env-ggt2lzqz/overlay/lib/python3.11/site-packages/numpy/distutils/checks/test_flags.o.d -mavx512f -mno-mmx) failed with exit status 127 output -> djlabhub-singleuser | [Errno 2] No such file or directory: 'gcc' djlabhub-singleuser | WARN: CCompilerOpt.cc_test_flags[1090] : testing failed djlabhub-singleuser | INFO: CCompilerOpt.cc_test_flags[1086] : testing flags (-mavx512cd) djlabhub-singleuser | INFO: C compiler: gcc -pthread -B /opt/conda/compiler_compat -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/conda/include -fPIC -O2 -isystem /opt/conda/include -fPIC djlabhub-singleuser | djlabhub-singleuser | INFO: compile options: '-I/opt/conda/include/python3.11 -c' djlabhub-singleuser | extra options: '-mavx512cd' djlabhub-singleuser | WARN: CCompilerOpt.dist_test[637] : CCompilerOpt._dist_test_spawn[771] : Command (gcc -pthread -B /opt/conda/compiler_compat -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/conda/include -fPIC -O2 -isystem /opt/conda/include -fPIC -I/opt/conda/include/python3.11 -c /tmp/pip-build-env-ggt2lzqz/overlay/lib/python3.11/site-packages/numpy/distutils/checks/test_flags.c -o /tmp/tmpsgj0w8s1/tmp/pip-build-env-ggt2lzqz/overlay/lib/python3.11/site-packages/numpy/distutils/checks/test_flags.o -MMD -MF /tmp/tmpsgj0w8s1/tmp/pip-build-env-ggt2lzqz/overlay/lib/python3.11/site-packages/numpy/distutils/checks/test_flags.o.d -mavx512cd) failed with exit status 127 output -> djlabhub-singleuser | [Errno 2] No such file or directory: 'gcc' djlabhub-singleuser | WARN: CCompilerOpt.cc_test_flags[1090] : testing failed djlabhub-singleuser | INFO: CCompilerOpt.feature_test[1560] : testing feature 'AVX512CD' with flags () djlabhub-singleuser | INFO: C compiler: gcc -pthread -B /opt/conda/compiler_compat -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/conda/include -fPIC -O2 -isystem /opt/conda/include -fPIC djlabhub-singleuser | djlabhub-singleuser | INFO: compile options: '-I/opt/conda/include/python3.11 -c' djlabhub-singleuser | WARN: CCompilerOpt.dist_test[637] : CCompilerOpt._dist_test_spawn[771] : Command (gcc -pthread -B /opt/conda/compiler_compat -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/conda/include -fPIC -O2 -isystem /opt/conda/include -fPIC -I/opt/conda/include/python3.11 -c /tmp/pip-build-env-ggt2lzqz/overlay/lib/python3.11/site-packages/numpy/distutils/checks/cpu_avx512cd.c -o /tmp/tmpsgj0w8s1/tmp/pip-build-env-ggt2lzqz/overlay/lib/python3.11/site-packages/numpy/distutils/checks/cpu_avx512cd.o -MMD -MF /tmp/tmpsgj0w8s1/tmp/pip-build-env-ggt2lzqz/overlay/lib/python3.11/site-packages/numpy/distutils/checks/cpu_avx512cd.o.d) failed with exit status 127 output -> djlabhub-singleuser | [Errno 2] No such file or directory: 'gcc' djlabhub-singleuser | WARN: CCompilerOpt.feature_test[1576] : testing failed djlabhub-singleuser | INFO: CCompilerOpt.cc_test_flags[1086] : testing flags (-mavx512vl -mavx512bw -mavx512dq) djlabhub-singleuser | INFO: C compiler: gcc -pthread -B /opt/conda/compiler_compat -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/conda/include -fPIC -O2 -isystem /opt/conda/include -fPIC djlabhub-singleuser | djlabhub-singleuser | INFO: compile options: '-I/opt/conda/include/python3.11 -c' djlabhub-singleuser | extra options: '-mavx512vl -mavx512bw -mavx512dq' djlabhub-singleuser | WARN: CCompilerOpt.dist_test[637] : CCompilerOpt._dist_test_spawn[771] : Command (gcc -pthread -B /opt/conda/compiler_compat -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/conda/include -fPIC -O2 -isystem /opt/conda/include -fPIC -I/opt/conda/include/python3.11 -c /tmp/pip-build-env-ggt2lzqz/overlay/lib/python3.11/site-packages/numpy/distutils/checks/test_flags.c -o /tmp/tmpsgj0w8s1/tmp/pip-build-env-ggt2lzqz/overlay/lib/python3.11/site-packages/numpy/distutils/checks/test_flags.o -MMD -MF /tmp/tmpsgj0w8s1/tmp/pip-build-env-ggt2lzqz/overlay/lib/python3.11/site-packages/numpy/distutils/checks/test_flags.o.d -mavx512vl -mavx512bw -mavx512dq) failed with exit status 127 output -> djlabhub-singleuser | [Errno 2] No such file or directory: 'gcc' djlabhub-singleuser | WARN: CCompilerOpt.cc_test_flags[1090] : testing failed djlabhub-singleuser | INFO: CCompilerOpt.feature_test[1560] : testing feature 'AVX512_SKX' with flags () djlabhub-singleuser | INFO: C compiler: gcc -pthread -B /opt/conda/compiler_compat -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/conda/include -fPIC -O2 -isystem /opt/conda/include -fPIC djlabhub-singleuser | djlabhub-singleuser | INFO: compile options: '-I/opt/conda/include/python3.11 -c' djlabhub-singleuser | WARN: CCompilerOpt.dist_test[637] : CCompilerOpt._dist_test_spawn[771] : Command (gcc -pthread -B /opt/conda/compiler_compat -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/conda/include -fPIC -O2 -isystem /opt/conda/include -fPIC -I/opt/conda/include/python3.11 -c /tmp/pip-build-env-ggt2lzqz/overlay/lib/python3.11/site-packages/numpy/distutils/checks/cpu_avx512_skx.c -o /tmp/tmpsgj0w8s1/tmp/pip-build-env-ggt2lzqz/overlay/lib/python3.11/site-packages/numpy/distutils/checks/cpu_avx512_skx.o -MMD -MF /tmp/tmpsgj0w8s1/tmp/pip-build-env-ggt2lzqz/overlay/lib/python3.11/site-packages/numpy/distutils/checks/cpu_avx512_skx.o.d) failed with exit status 127 output -> djlabhub-singleuser | [Errno 2] No such file or directory: 'gcc' djlabhub-singleuser | WARN: CCompilerOpt.feature_test[1576] : testing failed djlabhub-singleuser | INFO: CCompilerOpt.feature_test[1560] : testing feature 'SSSE3' with flags () djlabhub-singleuser | INFO: C compiler: gcc -pthread -B /opt/conda/compiler_compat -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/conda/include -fPIC -O2 -isystem /opt/conda/include -fPIC djlabhub-singleuser | djlabhub-singleuser | INFO: compile options: '-I/opt/conda/include/python3.11 -c' djlabhub-singleuser | WARN: CCompilerOpt.dist_test[637] : CCompilerOpt._dist_test_spawn[771] : Command (gcc -pthread -B /opt/conda/compiler_compat -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/conda/include -fPIC -O2 -isystem /opt/conda/include -fPIC -I/opt/conda/include/python3.11 -c /tmp/pip-build-env-ggt2lzqz/overlay/lib/python3.11/site-packages/numpy/distutils/checks/cpu_ssse3.c -o /tmp/tmpsgj0w8s1/tmp/pip-build-env-ggt2lzqz/overlay/lib/python3.11/site-packages/numpy/distutils/checks/cpu_ssse3.o -MMD -MF /tmp/tmpsgj0w8s1/tmp/pip-build-env-ggt2lzqz/overlay/lib/python3.11/site-packages/numpy/distutils/checks/cpu_ssse3.o.d) failed with exit status 127 output -> djlabhub-singleuser | [Errno 2] No such file or directory: 'gcc' djlabhub-singleuser | WARN: CCompilerOpt.feature_test[1576] : testing failed djlabhub-singleuser | INFO: CCompilerOpt.__init__[1820] : initialize targets groups djlabhub-singleuser | INFO: CCompilerOpt.__init__[1822] : parse target group simd_test djlabhub-singleuser | INFO: CCompilerOpt._parse_target_tokens[2033] : skip targets (AVX512_SKX VSX2 SSE42 VXE ASIMD FMA4 VSX4 VX (AVX2 FMA3) AVX512F XOP VSX3 NEON VXE2 SSE2 VSX) not part of baseline or dispatch-able features djlabhub-singleuser | INFO: CCompilerOpt.generate_dispatch_header[2366] : generate CPU dispatch header: (build/src.linux-x86_64-3.11/numpy/distutils/include/npy_cpu_dispatch_config.h) djlabhub-singleuser | WARN: CCompilerOpt.generate_dispatch_header[2375] : dispatch header dir build/src.linux-x86_64-3.11/numpy/distutils/include does not exist, creating it djlabhub-singleuser | INFO: customize UnixCCompiler djlabhub-singleuser | INFO: customize UnixCCompiler using ConditionalOpenMP djlabhub-singleuser | INFO: C compiler: gcc -pthread -B /opt/conda/compiler_compat -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/conda/include -fPIC -O2 -isystem /opt/conda/include -fPIC djlabhub-singleuser | djlabhub-singleuser | INFO: compile options: '-I/opt/conda/include/python3.11 -c' djlabhub-singleuser | extra options: '-fopenmp' djlabhub-singleuser | INFO: gcc: test.c djlabhub-singleuser | djlabhub-singleuser | djlabhub-singleuser | [Errno 2] No such file or directory: 'gcc' djlabhub-singleuser | djlabhub-singleuser | djlabhub-singleuser | INFO: building 'skimage._shared.geometry' extension djlabhub-singleuser | INFO: compiling C sources djlabhub-singleuser | INFO: C compiler: gcc -pthread -B /opt/conda/compiler_compat -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/conda/include -fPIC -O2 -isystem /opt/conda/include -fPIC djlabhub-singleuser | djlabhub-singleuser | creating build/temp.linux-x86_64-3.11/skimage djlabhub-singleuser | creating build/temp.linux-x86_64-3.11/skimage/_shared djlabhub-singleuser | INFO: compile options: '-I/tmp/pip-build-env-ggt2lzqz/overlay/lib/python3.11/site-packages/numpy/core/include -Ibuild/src.linux-x86_64-3.11/numpy/distutils/include -I/opt/conda/include/python3.11 -c' djlabhub-singleuser | INFO: gcc: skimage/_shared/geometry.c djlabhub-singleuser | djlabhub-singleuser | djlabhub-singleuser | [Errno 2] No such file or directory: 'gcc' djlabhub-singleuser | djlabhub-singleuser | djlabhub-singleuser | error: Command "gcc -pthread -B /opt/conda/compiler_compat -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/conda/include -fPIC -O2 -isystem /opt/conda/include -fPIC -I/tmp/pip-build-env-ggt2lzqz/overlay/lib/python3.11/site-packages/numpy/core/include -Ibuild/src.linux-x86_64-3.11/numpy/distutils/include -I/opt/conda/include/python3.11 -c skimage/_shared/geometry.c -o build/temp.linux-x86_64-3.11/skimage/_shared/geometry.o -MMD -MF build/temp.linux-x86_64-3.11/skimage/_shared/geometry.o.d" failed with exit status 127 djlabhub-singleuser | INFO: djlabhub-singleuser | ########### EXT COMPILER OPTIMIZATION ########### djlabhub-singleuser | INFO: Platform : djlabhub-singleuser | Architecture: x64 djlabhub-singleuser | Compiler : gcc djlabhub-singleuser | djlabhub-singleuser | CPU baseline : djlabhub-singleuser | Requested : 'min' djlabhub-singleuser | Enabled : none djlabhub-singleuser | Flags : none djlabhub-singleuser | Extra checks: none djlabhub-singleuser | djlabhub-singleuser | CPU dispatch : djlabhub-singleuser | Requested : 'max -xop -fma4' djlabhub-singleuser | Enabled : none djlabhub-singleuser | Generated : none djlabhub-singleuser | INFO: CCompilerOpt.cache_flush[864] : write cache to path -> /tmp/pip-install-10mv3j2k/scikit-image_bb7651ef5b5542cf9a96f0a046530a7f/build/temp.linux-x86_64-3.11/ccompiler_opt_cache_ext.py djlabhub-singleuser | [end of output] djlabhub-singleuser | djlabhub-singleuser | note: This error originates from a subprocess, and is likely not a problem with pip. djlabhub-singleuser | ERROR: Failed building wheel for scikit-image djlabhub-singleuser | Failed to build scikit-image djlabhub-singleuser | ERROR: Could not build wheels for scikit-image, which is required to install pyproject.toml-based projects djlabhub-singleuser exited with code 1

@ethho I'm not sure why I can't reproduce this error, but I might found the cause. I've added gcc in the apt_install.sh

@yambottle This build is still failing on my machine (x86, though in theory arch shouldn't matter with Docker?). Since you can presumably build and push the image on your machine, I'll approve this PR to unblock. Installing scikit-image using conda or apt instead of pip might work better, since these distributions typically ship the built library instead of compiling as part of setup.py

Error Log

# ... djlabhub-singleuser | INFO: compile options: '-I/opt/conda/include/python3.11 -c' djlabhub-singleuser | extra options: '-msse -msse2 -Werror' djlabhub-singleuser | WARN: CCompilerOpt.dist_test[637] : CCompilerOpt._dist_test_spawn[771] : Command (gcc -pthread -B /opt/conda/compiler_compat -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/conda/include -fPIC -O2 -isystem /opt/conda/include -fPIC -I/opt/conda/include/python3.11 -c /tmp/pip-build-env-g3vfvlx7/overlay/lib/python3.11/site-packages/numpy/distutils/checks/cpu_sse.c -o /tmp/tmpzpuol27x/tmp/pip-build-env-g3vfvlx7/overlay/lib/python3.11/site-packages/numpy/distutils/checks/cpu_sse.o -MMD -MF /tmp/tmpzpuol27x/tmp/pip-build-env-g3vfvlx7/overlay/lib/python3.11/site-packages/numpy/distutils/checks/cpu_sse.o.d -msse -msse2 -Werror) failed with exit status 1 output -> djlabhub-singleuser | In file included from /usr/lib/gcc/x86_64-linux-gnu/11/include/xmmintrin.h:34, djlabhub-singleuser | from /tmp/pip-build-env-g3vfvlx7/overlay/lib/python3.11/site-packages/numpy/distutils/checks/cpu_sse.c:14: djlabhub-singleuser | /usr/lib/gcc/x86_64-linux-gnu/11/include/mm_malloc.h:27:10: fatal error: stdlib.h: No such file or directory djlabhub-singleuser | 27 | #include <stdlib.h> djlabhub-singleuser | | ^~~~~~~~~~ djlabhub-singleuser | compilation terminated. djlabhub-singleuser | djlabhub-singleuser | WARN: CCompilerOpt.feature_test[1576] : testing failed djlabhub-singleuser | INFO: CCompilerOpt.feature_test[1560] : testing feature 'SSE2' with flags (-msse -msse2) djlabhub-singleuser | INFO: C compiler: gcc -pthread -B /opt/conda/compiler_compat -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/conda/include -fPIC -O2 -isystem /opt/conda/include -fPIC djlabhub-singleuser | djlabhub-singleuser | INFO: compile options: '-I/opt/conda/include/python3.11 -c' djlabhub-singleuser | extra options: '-msse -msse2 -Werror' djlabhub-singleuser | WARN: CCompilerOpt.dist_test[637] : CCompilerOpt._dist_test_spawn[771] : Command (gcc -pthread -B /opt/conda/compiler_compat -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/conda/include -fPIC -O2 -isystem /opt/conda/include -fPIC -I/opt/conda/include/python3.11 -c /tmp/pip-build-env-g3vfvlx7/overlay/lib/python3.11/site-packages/numpy/distutils/checks/cpu_sse2.c -o /tmp/tmpzpuol27x/tmp/pip-build-env-g3vfvlx7/overlay/lib/python3.11/site-packages/numpy/distutils/checks/cpu_sse2.o -MMD -MF /tmp/tmpzpuol27x/tmp/pip-build-env-g3vfvlx7/overlay/lib/python3.11/site-packages/numpy/distutils/checks/cpu_sse2.o.d -msse -msse2 -Werror) failed with exit status 1 output -> djlabhub-singleuser | In file included from /usr/lib/gcc/x86_64-linux-gnu/11/include/xmmintrin.h:34, djlabhub-singleuser | from /usr/lib/gcc/x86_64-linux-gnu/11/include/emmintrin.h:31, djlabhub-singleuser | from /tmp/pip-build-env-g3vfvlx7/overlay/lib/python3.11/site-packages/numpy/distutils/checks/cpu_sse2.c:14: djlabhub-singleuser | /usr/lib/gcc/x86_64-linux-gnu/11/include/mm_malloc.h:27:10: fatal error: stdlib.h: No such file or directory djlabhub-singleuser | 27 | #include <stdlib.h> djlabhub-singleuser | | ^~~~~~~~~~ djlabhub-singleuser | compilation terminated. djlabhub-singleuser | djlabhub-singleuser | WARN: CCompilerOpt.feature_test[1576] : testing failed djlabhub-singleuser | INFO: CCompilerOpt.__init__[1804] : check requested dispatch-able features djlabhub-singleuser | INFO: CCompilerOpt.cc_test_flags[1086] : testing flags (-msse3) djlabhub-singleuser | INFO: C compiler: gcc -pthread -B /opt/conda/compiler_compat -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/conda/include -fPIC -O2 -isystem /opt/conda/include -fPIC djlabhub-singleuser | djlabhub-singleuser | INFO: compile options: '-I/opt/conda/include/python3.11 -c' djlabhub-singleuser | extra options: '-msse3' djlabhub-singleuser | INFO: CCompilerOpt.cc_test_flags[1086] : testing flags (-mssse3) djlabhub-singleuser | INFO: C compiler: gcc -pthread -B /opt/conda/compiler_compat -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/conda/include -fPIC -O2 -isystem /opt/conda/include -fPIC djlabhub-singleuser | djlabhub-singleuser | INFO: compile options: '-I/opt/conda/include/python3.11 -c' djlabhub-singleuser | extra options: '-mssse3' djlabhub-singleuser | INFO: CCompilerOpt.cc_test_flags[1086] : testing flags (-msse4.1) djlabhub-singleuser | INFO: C compiler: gcc -pthread -B /opt/conda/compiler_compat -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/conda/include -fPIC -O2 -isystem /opt/conda/include -fPIC djlabhub-singleuser | djlabhub-singleuser | INFO: compile options: '-I/opt/conda/include/python3.11 -c' djlabhub-singleuser | extra options: '-msse4.1' djlabhub-singleuser | INFO: CCompilerOpt.feature_test[1560] : testing feature 'SSE41' with flags (-msse -msse2 -msse3 -mssse3 -msse4.1) djlabhub-singleuser | INFO: C compiler: gcc -pthread -B /opt/conda/compiler_compat -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/conda/include -fPIC -O2 -isystem /opt/conda/include -fPIC djlabhub-singleuser | djlabhub-singleuser | INFO: compile options: '-I/opt/conda/include/python3.11 -c' djlabhub-singleuser | extra options: '-msse -msse2 -msse3 -mssse3 -msse4.1 -Werror' djlabhub-singleuser | WARN: CCompilerOpt.dist_test[637] : CCompilerOpt._dist_test_spawn[771] : Command (gcc -pthread -B /opt/conda/compiler_compat -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/conda/include -fPIC -O2 -isystem /opt/conda/include -fPIC -I/opt/conda/include/python3.11 -c /tmp/pip-build-env-g3vfvlx7/overlay/lib/python3.11/site-packages/numpy/distutils/checks/cpu_sse41.c -o /tmp/tmpzpuol27x/tmp/pip-build-env-g3vfvlx7/overlay/lib/python3.11/site-packages/numpy/distutils/checks/cpu_sse41.o -MMD -MF /tmp/tmpzpuol27x/tmp/pip-build-env-g3vfvlx7/overlay/lib/python3.11/site-packages/numpy/distutils/checks/cpu_sse41.o.d -msse -msse2 -msse3 -mssse3 -msse4.1 -Werror) failed with exit status 1 output -> djlabhub-singleuser | In file included from /usr/lib/gcc/x86_64-linux-gnu/11/include/xmmintrin.h:34, djlabhub-singleuser | from /usr/lib/gcc/x86_64-linux-gnu/11/include/emmintrin.h:31, djlabhub-singleuser | from /usr/lib/gcc/x86_64-linux-gnu/11/include/pmmintrin.h:31, djlabhub-singleuser | from /usr/lib/gcc/x86_64-linux-gnu/11/include/tmmintrin.h:31, djlabhub-singleuser | from /usr/lib/gcc/x86_64-linux-gnu/11/include/smmintrin.h:32, djlabhub-singleuser | from /tmp/pip-build-env-g3vfvlx7/overlay/lib/python3.11/site-packages/numpy/distutils/checks/cpu_sse41.c:14: djlabhub-singleuser | /usr/lib/gcc/x86_64-linux-gnu/11/include/mm_malloc.h:27:10: fatal error: stdlib.h: No such file or directory djlabhub-singleuser | 27 | #include <stdlib.h> djlabhub-singleuser | | ^~~~~~~~~~ djlabhub-singleuser | compilation terminated. djlabhub-singleuser | djlabhub-singleuser | WARN: CCompilerOpt.feature_test[1576] : testing failed djlabhub-singleuser | INFO: CCompilerOpt.feature_test[1560] : testing feature 'SSE3' with flags (-msse -msse2 -msse3) djlabhub-singleuser | INFO: C compiler: gcc -pthread -B /opt/conda/compiler_compat -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/conda/include -fPIC -O2 -isystem /opt/conda/include -fPIC djlabhub-singleuser | djlabhub-singleuser | INFO: compile options: '-I/opt/conda/include/python3.11 -c' djlabhub-singleuser | extra options: '-msse -msse2 -msse3 -Werror' djlabhub-singleuser | WARN: CCompilerOpt.dist_test[637] : CCompilerOpt._dist_test_spawn[771] : Command (gcc -pthread -B /opt/conda/compiler_compat -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/conda/include -fPIC -O2 -isystem /opt/conda/include -fPIC -I/opt/conda/include/python3.11 -c /tmp/pip-build-env-g3vfvlx7/overlay/lib/python3.11/site-packages/numpy/distutils/checks/cpu_sse3.c -o /tmp/tmpzpuol27x/tmp/pip-build-env-g3vfvlx7/overlay/lib/python3.11/site-packages/numpy/distutils/checks/cpu_sse3.o -MMD -MF /tmp/tmpzpuol27x/tmp/pip-build-env-g3vfvlx7/overlay/lib/python3.11/site-packages/numpy/distutils/checks/cpu_sse3.o.d -msse -msse2 -msse3 -Werror) failed with exit status 1 output -> djlabhub-singleuser | In file included from /usr/lib/gcc/x86_64-linux-gnu/11/include/xmmintrin.h:34, djlabhub-singleuser | from /usr/lib/gcc/x86_64-linux-gnu/11/include/emmintrin.h:31, djlabhub-singleuser | from /usr/lib/gcc/x86_64-linux-gnu/11/include/pmmintrin.h:31, djlabhub-singleuser | from /tmp/pip-build-env-g3vfvlx7/overlay/lib/python3.11/site-packages/numpy/distutils/checks/cpu_sse3.c:14: djlabhub-singleuser | /usr/lib/gcc/x86_64-linux-gnu/11/include/mm_malloc.h:27:10: fatal error: stdlib.h: No such file or directory djlabhub-singleuser | 27 | #include <stdlib.h> djlabhub-singleuser | | ^~~~~~~~~~ djlabhub-singleuser | compilation terminated. djlabhub-singleuser | djlabhub-singleuser | WARN: CCompilerOpt.feature_test[1576] : testing failed djlabhub-singleuser | INFO: CCompilerOpt.cc_test_flags[1086] : testing flags (-mpopcnt) djlabhub-singleuser | INFO: C compiler: gcc -pthread -B /opt/conda/compiler_compat -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/conda/include -fPIC -O2 -isystem /opt/conda/include -fPIC djlabhub-singleuser | djlabhub-singleuser | INFO: compile options: '-I/opt/conda/include/python3.11 -c' djlabhub-singleuser | extra options: '-mpopcnt' djlabhub-singleuser | INFO: CCompilerOpt.cc_test_flags[1086] : testing flags (-msse4.2) djlabhub-singleuser | INFO: C compiler: gcc -pthread -B /opt/conda/compiler_compat -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/conda/include -fPIC -O2 -isystem /opt/conda/include -fPIC djlabhub-singleuser | djlabhub-singleuser | INFO: compile options: '-I/opt/conda/include/python3.11 -c' djlabhub-singleuser | extra options: '-msse4.2' djlabhub-singleuser | INFO: CCompilerOpt.cc_test_flags[1086] : testing flags (-mavx) djlabhub-singleuser | INFO: C compiler: gcc -pthread -B /opt/conda/compiler_compat -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/conda/include -fPIC -O2 -isystem /opt/conda/include -fPIC djlabhub-singleuser | djlabhub-singleuser | INFO: compile options: '-I/opt/conda/include/python3.11 -c' djlabhub-singleuser | extra options: '-mavx' djlabhub-singleuser | INFO: CCompilerOpt.cc_test_flags[1086] : testing flags (-mf16c) djlabhub-singleuser | INFO: C compiler: gcc -pthread -B /opt/conda/compiler_compat -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/conda/include -fPIC -O2 -isystem /opt/conda/include -fPIC djlabhub-singleuser | djlabhub-singleuser | INFO: compile options: '-I/opt/conda/include/python3.11 -c' djlabhub-singleuser | extra options: '-mf16c' djlabhub-singleuser | INFO: CCompilerOpt.cc_test_flags[1086] : testing flags (-mfma) djlabhub-singleuser | INFO: C compiler: gcc -pthread -B /opt/conda/compiler_compat -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/conda/include -fPIC -O2 -isystem /opt/conda/include -fPIC djlabhub-singleuser | djlabhub-singleuser | INFO: compile options: '-I/opt/conda/include/python3.11 -c' djlabhub-singleuser | extra options: '-mfma' djlabhub-singleuser | INFO: CCompilerOpt.feature_test[1560] : testing feature 'FMA3' with flags (-msse -msse2 -msse3 -mssse3 -msse4.1 -mpopcnt -msse4.2 -mavx -mf16c -mfma) djlabhub-singleuser | INFO: C compiler: gcc -pthread -B /opt/conda/compiler_compat -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/conda/include -fPIC -O2 -isystem /opt/conda/include -fPIC djlabhub-singleuser | djlabhub-singleuser | INFO: compile options: '-I/opt/conda/include/python3.11 -c' djlabhub-singleuser | extra options: '-msse -msse2 -msse3 -mssse3 -msse4.1 -mpopcnt -msse4.2 -mavx -mf16c -mfma -Werror' djlabhub-singleuser | WARN: CCompilerOpt.dist_test[637] : CCompilerOpt._dist_test_spawn[771] : Command (gcc -pthread -B /opt/conda/compiler_compat -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/conda/include -fPIC -O2 -isystem /opt/conda/include -fPIC -I/opt/conda/include/python3.11 -c /tmp/pip-build-env-g3vfvlx7/overlay/lib/python3.11/site-packages/numpy/distutils/checks/cpu_fma3.c -o /tmp/tmpzpuol27x/tmp/pip-build-env-g3vfvlx7/overlay/lib/python3.11/site-packages/numpy/distutils/checks/cpu_fma3.o -MMD -MF /tmp/tmpzpuol27x/tmp/pip-build-env-g3vfvlx7/overlay/lib/python3.11/site-packages/numpy/distutils/checks/cpu_fma3.o.d -msse -msse2 -msse3 -mssse3 -msse4.1 -mpopcnt -msse4.2 -mavx -mf16c -mfma -Werror) failed with exit status 1 output -> djlabhub-singleuser | In file included from /usr/lib/gcc/x86_64-linux-gnu/11/include/xmmintrin.h:34, djlabhub-singleuser | from /tmp/pip-build-env-g3vfvlx7/overlay/lib/python3.11/site-packages/numpy/distutils/checks/cpu_fma3.c:14: djlabhub-singleuser | /usr/lib/gcc/x86_64-linux-gnu/11/include/mm_malloc.h:27:10: fatal error: stdlib.h: No such file or directory djlabhub-singleuser | 27 | #include <stdlib.h> djlabhub-singleuser | | ^~~~~~~~~~ djlabhub-singleuser | compilation terminated. djlabhub-singleuser | djlabhub-singleuser | WARN: CCompilerOpt.feature_test[1576] : testing failed djlabhub-singleuser | INFO: CCompilerOpt.feature_test[1560] : testing feature 'AVX' with flags (-msse -msse2 -msse3 -mssse3 -msse4.1 -mpopcnt -msse4.2 -mavx) djlabhub-singleuser | INFO: C compiler: gcc -pthread -B /opt/conda/compiler_compat -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/conda/include -fPIC -O2 -isystem /opt/conda/include -fPIC djlabhub-singleuser | djlabhub-singleuser | INFO: compile options: '-I/opt/conda/include/python3.11 -c' djlabhub-singleuser | extra options: '-msse -msse2 -msse3 -mssse3 -msse4.1 -mpopcnt -msse4.2 -mavx -Werror' djlabhub-singleuser | WARN: CCompilerOpt.dist_test[637] : CCompilerOpt._dist_test_spawn[771] : Command (gcc -pthread -B /opt/conda/compiler_compat -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/conda/include -fPIC -O2 -isystem /opt/conda/include -fPIC -I/opt/conda/include/python3.11 -c /tmp/pip-build-env-g3vfvlx7/overlay/lib/python3.11/site-packages/numpy/distutils/checks/cpu_avx.c -o /tmp/tmpzpuol27x/tmp/pip-build-env-g3vfvlx7/overlay/lib/python3.11/site-packages/numpy/distutils/checks/cpu_avx.o -MMD -MF /tmp/tmpzpuol27x/tmp/pip-build-env-g3vfvlx7/overlay/lib/python3.11/site-packages/numpy/distutils/checks/cpu_avx.o.d -msse -msse2 -msse3 -mssse3 -msse4.1 -mpopcnt -msse4.2 -mavx -Werror) failed with exit status 1 output -> djlabhub-singleuser | In file included from /usr/lib/gcc/x86_64-linux-gnu/11/include/xmmintrin.h:34, djlabhub-singleuser | from /usr/lib/gcc/x86_64-linux-gnu/11/include/immintrin.h:31, djlabhub-singleuser | from /tmp/pip-build-env-g3vfvlx7/overlay/lib/python3.11/site-packages/numpy/distutils/checks/cpu_avx.c:14: djlabhub-singleuser | /usr/lib/gcc/x86_64-linux-gnu/11/include/mm_malloc.h:27:10: fatal error: stdlib.h: No such file or directory djlabhub-singleuser | 27 | #include <stdlib.h> djlabhub-singleuser | | ^~~~~~~~~~ djlabhub-singleuser | compilation terminated. djlabhub-singleuser | djlabhub-singleuser | WARN: CCompilerOpt.feature_test[1576] : testing failed djlabhub-singleuser | INFO: CCompilerOpt.__init__[1820] : initialize targets groups djlabhub-singleuser | INFO: CCompilerOpt.__init__[1822] : parse target group simd_test djlabhub-singleuser | INFO: CCompilerOpt._parse_target_tokens[2033] : skip targets ((FMA3 AVX2) FMA4 VSX3 SSE2 XOP VX AVX512_SKX SSE42 VSX2 NEON AVX512F VXE2 VXE ASIMD VSX4 VSX) not part of baseline or dispatch-able features djlabhub-singleuser | INFO: CCompilerOpt.generate_dispatch_header[2366] : generate CPU dispatch header: (build/src.linux-x86_64-3.11/numpy/distutils/include/npy_cpu_dispatch_config.h) djlabhub-singleuser | WARN: CCompilerOpt.generate_dispatch_header[2375] : dispatch header dir build/src.linux-x86_64-3.11/numpy/distutils/include does not exist, creating it djlabhub-singleuser | INFO: customize UnixCCompiler djlabhub-singleuser | INFO: customize UnixCCompiler using ConditionalOpenMP djlabhub-singleuser | INFO: C compiler: gcc -pthread -B /opt/conda/compiler_compat -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/conda/include -fPIC -O2 -isystem /opt/conda/include -fPIC djlabhub-singleuser | djlabhub-singleuser | INFO: compile options: '-I/opt/conda/include/python3.11 -c' djlabhub-singleuser | extra options: '-fopenmp' djlabhub-singleuser | INFO: gcc: test.c djlabhub-singleuser | test.c:1:17: warning: extra tokens at end of #include directive djlabhub-singleuser | 1 | #include <omp.h>int main(int argc, char** argv) { return(0); } djlabhub-singleuser | | ^~~ djlabhub-singleuser | INFO: gcc -pthread -B /opt/conda/compiler_compat -shared -Wl,--allow-shlib-undefined -Wl,-rpath,/opt/conda/lib -Wl,-rpath-link,/opt/conda/lib -L/opt/conda/lib -Wl,--allow-shlib-undefined -Wl,-rpath,/opt/conda/lib -Wl,-rpath-link,/opt/conda/lib -L/opt/conda/lib test.o -o libtestlib.so -fopenmp djlabhub-singleuser | /opt/conda/compiler_compat/ld: cannot find crti.o: No such file or directory djlabhub-singleuser | collect2: error: ld returned 1 exit status djlabhub-singleuser | INFO: building 'skimage._shared.geometry' extension djlabhub-singleuser | INFO: compiling C sources djlabhub-singleuser | INFO: C compiler: gcc -pthread -B /opt/conda/compiler_compat -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/conda/include -fPIC -O2 -isystem /opt/conda/include -fPIC djlabhub-singleuser | djlabhub-singleuser | creating build/temp.linux-x86_64-3.11/skimage djlabhub-singleuser | creating build/temp.linux-x86_64-3.11/skimage/_shared djlabhub-singleuser | INFO: compile options: '-I/tmp/pip-build-env-g3vfvlx7/overlay/lib/python3.11/site-packages/numpy/core/include -Ibuild/src.linux-x86_64-3.11/numpy/distutils/include -I/opt/conda/include/python3.11 -c' djlabhub-singleuser | INFO: gcc: skimage/_shared/geometry.c djlabhub-singleuser | In file included from skimage/_shared/geometry.c:19: djlabhub-singleuser | /opt/conda/include/python3.11/Python.h:23:12: fatal error: stdlib.h: No such file or directory djlabhub-singleuser | 23 | # include <stdlib.h> djlabhub-singleuser | | ^~~~~~~~~~ djlabhub-singleuser | compilation terminated. djlabhub-singleuser | error: Command "gcc -pthread -B /opt/conda/compiler_compat -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/conda/include -fPIC -O2 -isystem /opt/conda/include -fPIC -I/tmp/pip-build-env-g3vfvlx7/overlay/lib/python3.11/site-packages/numpy/core/include -Ibuild/src.linux-x86_64-3.11/numpy/distutils/include -I/opt/conda/include/python3.11 -c skimage/_shared/geometry.c -o build/temp.linux-x86_64-3.11/skimage/_shared/geometry.o -MMD -MF build/temp.linux-x86_64-3.11/skimage/_shared/geometry.o.d" failed with exit status 1 djlabhub-singleuser | INFO: djlabhub-singleuser | ########### EXT COMPILER OPTIMIZATION ########### djlabhub-singleuser | INFO: Platform : djlabhub-singleuser | Architecture: x64 djlabhub-singleuser | Compiler : gcc djlabhub-singleuser | djlabhub-singleuser | CPU baseline : djlabhub-singleuser | Requested : 'min' djlabhub-singleuser | Enabled : none djlabhub-singleuser | Flags : none djlabhub-singleuser | Extra checks: none djlabhub-singleuser | djlabhub-singleuser | CPU dispatch : djlabhub-singleuser | Requested : 'max -xop -fma4' djlabhub-singleuser | Enabled : none djlabhub-singleuser | Generated : none djlabhub-singleuser | INFO: CCompilerOpt.cache_flush[864] : write cache to path -> /tmp/pip-install-x6ioq4v_/scikit-image_6f43e31248b94ec38fb134e74e35de3e/build/temp.linux-x86_64-3.11/ccompiler_opt_cache_ext.py djlabhub-singleuser | [end of output] djlabhub-singleuser | djlabhub-singleuser | note: This error originates from a subprocess, and is likely not a problem with pip. djlabhub-singleuser | Failed to build scikit-image djlabhub-singleuser | ERROR: Failed building wheel for scikit-image djlabhub-singleuser | ERROR: Could not build wheels for scikit-image, which is required to install pyproject.toml-based projects djlabhub-singleuser exited with code 1

hub/config/jupyterhub_config.py

Co-authored-by: Ethan Ho <53266718+ethho@users.noreply.github.com>

… requires gcc to build

ethho

I was unable to successfully build single-user image on my machine, though @yambottle is able to. See conversation history for details. Rest of the PR LGTM

yambottle · 2024-03-15T16:13:19Z

I was unable to successfully build single-user image on my machine, though @yambottle is able to. See conversation history for details. Rest of the PR LGTM

Going to merge it now

yambottle and others added 9 commits September 14, 2023 16:37

refactor: ⬆️ upgrade djlabhub

b846922

Merge branch 'datajoint:master' into master

5382b72

feat: 🚧 chain breaker

3b71b09

fix: 🐛 remove example password

66c12a2

feat: 🚧 enable local docker jhub

b0278b4

feat: 🚧 add djlab tag

b40f0ce

fix: 🐛 add hub config in the image

499f717

chore: 🚧 try oauth on local but it doesn't work because of SSL

6517250

feat: ✨ adding more env config and comment on config reference doc

36d5f49

yambottle closed this Feb 23, 2024

yambottle reopened this Feb 23, 2024

yambottle marked this pull request as draft February 23, 2024 17:07

yambottle added 2 commits February 23, 2024 11:09

build: 🚚 requires legacy files to pass the test

05f4296

fix: disable cicd before refactor

de9e55e

yambottle marked this pull request as ready for review February 23, 2024 17:16

yambottle marked this pull request as draft February 23, 2024 17:19

yambottle added 2 commits March 8, 2024 01:25

fix: 🐛 add djlab container name

3084ecf

refactor: ♻️ put previous image in the legacy

fd5218f

yambottle requested a review from ttngu207 March 12, 2024 15:08

yambottle marked this pull request as ready for review March 12, 2024 15:08

yambottle requested a review from ethho March 12, 2024 22:03

ethho requested changes Mar 13, 2024

View reviewed changes

ethho reviewed Mar 13, 2024

View reviewed changes

hub/config/jupyterhub_config.py Outdated Show resolved Hide resolved

Update hub/config/jupyterhub_config.py

30ddaed

Co-authored-by: Ethan Ho <53266718+ethho@users.noreply.github.com>

yambottle requested a review from ethho March 13, 2024 22:47

fix: 🐛 remove conda

66f68a8

yambottle mentioned this pull request Mar 14, 2024

DEV-221 feat(codebook_docker_template): ✨ codebook profile image template datajoint/.github#22

Merged

fix: 🐛 unreleased python dependency for the base image python version…

684f913

… requires gcc to build

ethho approved these changes Mar 15, 2024

View reviewed changes

ethho mentioned this pull request Mar 15, 2024

DEV-527: test fetching auth_state from notebook #35

Merged

yambottle merged commit c775e69 into datajoint:master Mar 15, 2024
1 check passed

yambottle deleted the DEV-221-djlabhub-chain-breaker branch March 15, 2024 16:13

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Dev 221 djlabhub chain breaker #34

Dev 221 djlabhub chain breaker #34

yambottle commented Feb 23, 2024 •

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ethho Mar 14, 2024 •

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yambottle commented Mar 15, 2024

Dev 221 djlabhub chain breaker #34

Dev 221 djlabhub chain breaker #34

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yambottle commented Mar 15, 2024

yambottle commented Feb 23, 2024 •

edited

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ethho Mar 14, 2024 •

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