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Added missing Ubuntu prerequisite to installation instructions #1547

Merged
merged 2 commits into from
Oct 12, 2023
Merged

Added missing Ubuntu prerequisite to installation instructions #1547

merged 2 commits into from
Oct 12, 2023

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andreped
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@andreped andreped commented Sep 14, 2023 •
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Summary

I have added a missing installation instruction necessary to install monailabel on Ubuntu.

Issue

If you attempt to install monailabel through pip on Ubuntu, you need python3-dev. This is due to the openslide-python dependency that needs to be compiled during installation (see here for more information about this issue).

If not, installation will fail resulting in the error log:

Logs 
Building wheels for collected packages: openslide-python
  Building wheel for openslide-python (setup.py) ... error
  ERROR: Command errored out with exit status 1:
   command: /home/UserName/Documents/Code/Public/MONAILabel/venv/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-gokcgsel/openslide-python/setup.py'"'"'; __file__='"'"'/tmp/pip-install-gokcgsel/openslide-python/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' bdist_wheel -d /tmp/pip-wheel-18fput0p
       cwd: /tmp/pip-install-gokcgsel/openslide-python/
  Complete output (24 lines):
  /tmp/pip-install-gokcgsel/openslide-python/setup.py:19: DistDeprecationWarning: Features are deprecated and will be removed in a future version. See https://github.com/pypa/setuptools/issues/65.
    'performance': Feature(
  /usr/lib/python3.8/distutils/core.py:108: DistDeprecationWarning: Features are deprecated and will be removed in a future version. See https://github.com/pypa/setuptools/issues/65.
    _setup_distribution = dist = klass(attrs)
  running bdist_wheel
  running build
  running build_py
  creating build
  creating build/lib.linux-x86_64-3.8
  creating build/lib.linux-x86_64-3.8/openslide
  copying openslide/deepzoom.py -> build/lib.linux-x86_64-3.8/openslide
  copying openslide/_version.py -> build/lib.linux-x86_64-3.8/openslide
  copying openslide/__init__.py -> build/lib.linux-x86_64-3.8/openslide
  copying openslide/lowlevel.py -> build/lib.linux-x86_64-3.8/openslide
  running build_ext
  building 'openslide._convert' extension
  creating build/temp.linux-x86_64-3.8
  creating build/temp.linux-x86_64-3.8/openslide
  x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/home/UserName/Documents/Code/Public/MONAILabel/venv/include -I/usr/include/python3.8 -c openslide/_convert.c -o build/temp.linux-x86_64-3.8/openslide/_convert.o
  openslide/_convert.c:20:10: fatal error: Python.h: No such file or directory
     20 | #include <Python.h>
        |          ^~~~~~~~~~
  compilation terminated.
  error: command 'x86_64-linux-gnu-gcc' failed with exit status 1
  ----------------------------------------
  ERROR: Failed building wheel for openslide-python
  Running setup.py clean for openslide-python
Failed to build openslide-python
Installing collected packages: openslide-python
    Running setup.py install for openslide-python ... error
    ERROR: Command errored out with exit status 1:
     command: /home/UserName/Documents/Code/Public/MONAILabel/venv/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-gokcgsel/openslide-python/setup.py'"'"'; __file__='"'"'/tmp/pip-install-gokcgsel/openslide-python/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /tmp/pip-record-vje_xlb7/install-record.txt --single-version-externally-managed --compile --install-headers /home/UserName/Documents/Code/Public/MONAILabel/venv/include/site/python3.8/openslide-python
         cwd: /tmp/pip-install-gokcgsel/openslide-python/
    Complete output (24 lines):
    /tmp/pip-install-gokcgsel/openslide-python/setup.py:19: DistDeprecationWarning: Features are deprecated and will be removed in a future version. See https://github.com/pypa/setuptools/issues/65.
      'performance': Feature(
    /usr/lib/python3.8/distutils/core.py:108: DistDeprecationWarning: Features are deprecated and will be removed in a future version. See https://github.com/pypa/setuptools/issues/65.
      _setup_distribution = dist = klass(attrs)
    running install
    running build
    running build_py
    creating build
    creating build/lib.linux-x86_64-3.8
    creating build/lib.linux-x86_64-3.8/openslide
    copying openslide/deepzoom.py -> build/lib.linux-x86_64-3.8/openslide
    copying openslide/_version.py -> build/lib.linux-x86_64-3.8/openslide
    copying openslide/__init__.py -> build/lib.linux-x86_64-3.8/openslide
    copying openslide/lowlevel.py -> build/lib.linux-x86_64-3.8/openslide
    running build_ext
    building 'openslide._convert' extension
    creating build/temp.linux-x86_64-3.8
    creating build/temp.linux-x86_64-3.8/openslide
    x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/home/UserName/Documents/Code/Public/MONAILabel/venv/include -I/usr/include/python3.8 -c openslide/_convert.c -o build/temp.linux-x86_64-3.8/openslide/_convert.o
    openslide/_convert.c:20:10: fatal error: Python.h: No such file or directory
       20 | #include <Python.h>
          |          ^~~~~~~~~~
    compilation terminated.
    error: command 'x86_64-linux-gnu-gcc' failed with exit status 1
    ----------------------------------------
ERROR: Command errored out with exit status 1: /home/UserName/Documents/Code/Public/MONAILabel/venv/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-gokcgsel/openslide-python/setup.py'"'"'; __file__='"'"'/tmp/pip-install-gokcgsel/openslide-python/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /tmp/pip-record-vje_xlb7/install-record.txt --single-version-externally-managed --compile --install-headers /home/UserName/Documents/Code/Public/MONAILabel/venv/include/site/python3.8/openslide-python Check the logs for full command output.

This error was observed on Ubuntu 20.04 with Python 3.8 attempting to install latest release of monailabel from PyPI.

Note that a PR to build precompiled binaries of openslide-python has been made, so this might not be an issue in the future, but the PR has yet to be merged or included in the latest release (see openslide/openslide-python#188)

@andreped
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Forgot to sign off commit, so I fixed it in a new commit.

@SachidanandAlle SachidanandAlle merged commit 1f00c6b into Project-MONAI:main Oct 12, 2023
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@SachidanandAlle SachidanandAlle SachidanandAlle approved these changes

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@andreped @SachidanandAlle