在 pip 上创建 miniconda docker 映像失败

Question

上下文：

从 miniconda3 创建一个 docker 镜像，并通过 dockerfile 使用 conda create env 安装额外的 conda 和 pip 包。

以下是我得到的错误：

Pip subprocess error: ERROR: Complete output from command /opt/conda/envs/newenv/bin/python -u -c 'import setuptools, tokenize;__file__='"'"'/tmp/pip-install-ouoxn_g_/psutil/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-gj0mtsb8 --python-tag cp36: ERROR: running bdist_wheel

environment.yml 包含 conda 包，然后是 pip 依赖项。所有 conda 包都正常，但第一次 Pip 安装失败，如上。

Dockerfile如下：

FROM continuumio/miniconda3

WORKDIR /.

COPY ./environment.yml ./

RUN conda env create -f ./environment.yml

RUN echo "source activate processenv" > ~/.bashrc
ENV PATH /opt/conda/envs/newenv/bin:$PATH

完整错误如下：

Pip subprocess error:
  ERROR: Complete output from command /opt/conda/envs/newenv/bin/python -u -c 'import setuptools, tokenize;__file__='"'"'/tmp/pip-install-ouoxn_g_/psutil/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-gj0mtsb8 --python-tag cp36:
  ERROR: running bdist_wheel
  running build
  running build_py
  creating build
  creating build/lib.linux-x86_64-3.6
  creating build/lib.linux-x86_64-3.6/psutil
  copying psutil/_psbsd.py -> build/lib.linux-x86_64-3.6/psutil
  copying psutil/_psposix.py -> build/lib.linux-x86_64-3.6/psutil
  copying psutil/_psaix.py -> build/lib.linux-x86_64-3.6/psutil
  copying psutil/__init__.py -> build/lib.linux-x86_64-3.6/psutil
  copying psutil/_pssunos.py -> build/lib.linux-x86_64-3.6/psutil
  copying psutil/_compat.py -> build/lib.linux-x86_64-3.6/psutil
  copying psutil/_pslinux.py -> build/lib.linux-x86_64-3.6/psutil
  copying psutil/_psosx.py -> build/lib.linux-x86_64-3.6/psutil
  copying psutil/_pswindows.py -> build/lib.linux-x86_64-3.6/psutil
  copying psutil/_common.py -> build/lib.linux-x86_64-3.6/psutil
  creating build/lib.linux-x86_64-3.6/psutil/tests
  copying psutil/tests/test_windows.py -> build/lib.linux-x86_64-3.6/psutil/tests
  copying psutil/tests/test_process.py -> build/lib.linux-x86_64-3.6/psutil/tests
  copying psutil/tests/__init__.py -> build/lib.linux-x86_64-3.6/psutil/tests
  copying psutil/tests/test_connections.py -> build/lib.linux-x86_64-3.6/psutil/tests
  copying psutil/tests/test_unicode.py -> build/lib.linux-x86_64-3.6/psutil/tests
  copying psutil/tests/runner.py -> build/lib.linux-x86_64-3.6/psutil/tests
  copying psutil/tests/test_aix.py -> build/lib.linux-x86_64-3.6/psutil/tests
  copying psutil/tests/test_posix.py -> build/lib.linux-x86_64-3.6/psutil/tests
  copying psutil/tests/test_memory_leaks.py -> build/lib.linux-x86_64-3.6/psutil/tests
  copying psutil/tests/test_linux.py -> build/lib.linux-x86_64-3.6/psutil/tests
  copying psutil/tests/test_bsd.py -> build/lib.linux-x86_64-3.6/psutil/tests
  copying psutil/tests/test_system.py -> build/lib.linux-x86_64-3.6/psutil/tests
  copying psutil/tests/__main__.py -> build/lib.linux-x86_64-3.6/psutil/tests
  copying psutil/tests/test_contracts.py -> build/lib.linux-x86_64-3.6/psutil/tests
  copying psutil/tests/test_osx.py -> build/lib.linux-x86_64-3.6/psutil/tests
  copying psutil/tests/test_sunos.py -> build/lib.linux-x86_64-3.6/psutil/tests
  copying psutil/tests/test_misc.py -> build/lib.linux-x86_64-3.6/psutil/tests
  running build_ext
  building 'psutil._psutil_linux' extension
  creating build/temp.linux-x86_64-3.6
  creating build/temp.linux-x86_64-3.6/psutil
  gcc -pthread -B /opt/conda/envs/newenv/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -DPSUTIL_POSIX=1 -DPSUTIL_VERSION=563 -DPSUTIL_LINUX=1 -DPSUTIL_ETHTOOL_MISSING_TYPES=1 -I/opt/conda/envs/processenv/include/python3.6m -c psutil/_psutil_common.c -o build/temp.linux-x86_64-3.6/psutil/_psutil_common.o
  unable to execute 'gcc': No such file or directory
  error: command 'gcc' failed with exit status 1
  ----------------------------------------
  ERROR: Failed building wheel for psutil
ERROR: flair 0.4.4 has requirement urllib3<1.25,>=1.20, but you'll have urllib3 1.25.3 which is incompatible.
    ERROR: Complete output from command /opt/conda/envs/newenv/bin/python -u -c 'import setuptools, tokenize;__file__='"'"'/tmp/pip-install-ouoxn_g_/psutil/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-f2xrpwn0/install-record.txt --single-version-externally-managed --compile:
    ERROR: running install
    running build
    running build_py
    creating build
    creating build/lib.linux-x86_64-3.6
    creating build/lib.linux-x86_64-3.6/psutil
    copying psutil/_psbsd.py -> build/lib.linux-x86_64-3.6/psutil
    copying psutil/_psposix.py -> build/lib.linux-x86_64-3.6/psutil
    copying psutil/_psaix.py -> build/lib.linux-x86_64-3.6/psutil
    copying psutil/__init__.py -> build/lib.linux-x86_64-3.6/psutil
    copying psutil/_pssunos.py -> build/lib.linux-x86_64-3.6/psutil
    copying psutil/_compat.py -> build/lib.linux-x86_64-3.6/psutil
    copying psutil/_pslinux.py -> build/lib.linux-x86_64-3.6/psutil
    copying psutil/_psosx.py -> build/lib.linux-x86_64-3.6/psutil
    copying psutil/_pswindows.py -> build/lib.linux-x86_64-3.6/psutil
    copying psutil/_common.py -> build/lib.linux-x86_64-3.6/psutil
    creating build/lib.linux-x86_64-3.6/psutil/tests
    copying psutil/tests/test_windows.py -> build/lib.linux-x86_64-3.6/psutil/tests
    copying psutil/tests/test_process.py -> build/lib.linux-x86_64-3.6/psutil/tests
    copying psutil/tests/__init__.py -> build/lib.linux-x86_64-3.6/psutil/tests
    copying psutil/tests/test_connections.py -> build/lib.linux-x86_64-3.6/psutil/tests
    copying psutil/tests/test_unicode.py -> build/lib.linux-x86_64-3.6/psutil/tests
    copying psutil/tests/runner.py -> build/lib.linux-x86_64-3.6/psutil/tests
    copying psutil/tests/test_aix.py -> build/lib.linux-x86_64-3.6/psutil/tests
    copying psutil/tests/test_posix.py -> build/lib.linux-x86_64-3.6/psutil/tests
    copying psutil/tests/test_memory_leaks.py -> build/lib.linux-x86_64-3.6/psutil/tests
    copying psutil/tests/test_linux.py -> build/lib.linux-x86_64-3.6/psutil/tests
    copying psutil/tests/test_bsd.py -> build/lib.linux-x86_64-3.6/psutil/tests
    copying psutil/tests/test_system.py -> build/lib.linux-x86_64-3.6/psutil/tests
    copying psutil/tests/__main__.py -> build/lib.linux-x86_64-3.6/psutil/tests
    copying psutil/tests/test_contracts.py -> build/lib.linux-x86_64-3.6/psutil/tests
    copying psutil/tests/test_osx.py -> build/lib.linux-x86_64-3.6/psutil/tests
    copying psutil/tests/test_sunos.py -> build/lib.linux-x86_64-3.6/psutil/tests
    copying psutil/tests/test_misc.py -> build/lib.linux-x86_64-3.6/psutil/tests
    running build_ext
    building 'psutil._psutil_linux' extension
    creating build/temp.linux-x86_64-3.6
    creating build/temp.linux-x86_64-3.6/psutil
    gcc -pthread -B /opt/conda/envs/newenv/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -DPSUTIL_POSIX=1 -DPSUTIL_VERSION=563 -DPSUTIL_LINUX=1 -DPSUTIL_ETHTOOL_MISSING_TYPES=1 -I/opt/conda/envs/processenv/include/python3.6m -c psutil/_psutil_common.c -o build/temp.linux-x86_64-3.6/psutil/_psutil_common.o
    unable to execute 'gcc': No such file or directory
    error: command 'gcc' failed with exit status 1
    ----------------------------------------
ERROR: Command "/opt/conda/envs/newenv/bin/python -u -c 'import setuptools, tokenize;__file__='"'"'/tmp/pip-install-ouoxn_g_/psutil/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-f2xrpwn0/install-record.txt --single-version-externally-managed --compile" failed with error code 1 in /tmp/pip-install-ouoxn_g_/psutil/


CondaEnvException: Pip failed

Answer 1

您的错误中所述存在依赖性问题：

ERROR: flair 0.4.4 has requirement urllib3<1.25,>=1.20, but you'll have urllib3 1.25.3 which is incompatible.

您可以尝试添加pip install "urllib3==1.24"

Answer 2

我想我也必须安装 gcc，因为 miniconda3 没有附带它，我猜。所以在 dockerfile 中为 gcc 提供了一个 apt get 并且它起作用了！