为什么rpy2包在码头建造阶段出现错误？

Question

我正在尝试构建一个Docker容器，它应该是bookworm并运行python 3.9。默认情况下，bookworm默认安装python 3.10。我必须使用bookworm，因为它是生产的要求。

问题是NumPy与它不兼容。所以我不得不使用python 3.9。现在，我得到了一个错误，无法从rpy2安装requirements.txt包。

我的码头档案

FROM debian:bookworm-20210816-slim


COPY ./requirements.txt /mmm/requirements.txt

WORKDIR /mmm
RUN apt-get -y update
RUN apt-get -y upgrade
RUN apt-get install curl -y


RUN apt-get install -y libgit2-dev
RUN apt install -y r-cran-remotes
RUN apt-get -y install r-base

RUN apt-get install python3.9 -y
RUN apt-get install python3.9-distutils -y
RUN apt-get install python3.9-apt -y
RUN apt-get install wget -y

RUN update-alternatives --install /usr/bin/python3 python3 /usr/bin/python3.9 1
RUN curl https://bootstrap.pypa.io/get-pip.py -o get-pip.py
RUN python3.9 get-pip.py
RUN pip --version
RUN pip3 --version

RUN apt-get install -y libnlopt-dev
RUN apt-get -y install gcc
RUN python3.9 -c 'print("Hi")'

RUN pip3 install --no-cache-dir flask pipupgrade
RUN pip3 install --upgrade pip setuptools
RUN apt-get install gfortran
RUN apt-get -y update
RUN apt-get install --no-install-recommends software-properties-common dirmngr -y
RUN wget -qO- https://cloud.r-project.org/bin/linux/ubuntu/marutter_pubkey.asc | tee -a /etc/apt/trusted.gpg.d/cran_ubuntu_key.asc
RUN add-apt-repository "deb https://cloud.r-project.org/bin/linux/ubuntu $(lsb_release -cs)-cran40/"
RUN apt-get install --no-install-recommends r-base

RUN R -e "update.packages(repos='http://cran.rstudio.com/', ask=FALSE, checkBuilt=TRUE)"
RUN R -e "install.packages('remotes',dependencies=TRUE)"
RUN R -e "require(remotes)"
RUN R -e "remotes::install_version('minqa')"
RUN R -e "remotes::install_version('RcppEigen')"
RUN R -e "remotes::install_version('nloptr')"
RUN R -e "remotes::install_version('lme4')"
RUN R -e "remotes::install_version('pbkrtest')"
RUN R -e "remotes::install_version('lmerTest')"
RUN R -e "install.packages('lmerTest',dependencies=TRUE)"
RUN pip3 install pandas
RUN pip3 install scipy
RUN pip3 install ray
RUN pip3 install --no-cache-dir -r requirements.txt
ENV SSO "ENABLE"


COPY . /mmm

EXPOSE 8086

CMD ["python3.9", "manage.py", "run"]

我的Requirements.txt文件

rpy2
Werkzeug
nltk
Flask_Script
pytest
numba
pymongo
statsmodels
Flask_MonitoringDashboard
pingouin
flasgger
cryptography
Flask_RESTful
Flask_Cors
marshmallow
config_with_yaml
Flask
boto3
requests
fastapi
PyJWT
scikit_learn
pytz
markupsafe
itsdangerous
pysftp
protobuf

我的错误

  Found existing installation: numpy 1.23.1
    Uninstalling numpy-1.23.1:
      Successfully uninstalled numpy-1.23.1
  Running setup.py install for rpy2: started
  Running setup.py install for rpy2: finished with status 'error'
  error: subprocess-exited-with-error
  
  × Running setup.py install for rpy2 did not run successfully.
  │ exit code: 1
  ╰─> [172 lines of output]
      cffi mode is CFFI_MODE.ANY
      Looking for R home with: R RHOME
      R home found: /usr/lib/R
      R exec path: /usr/lib/R/bin/R
      Looking for R CONFIG with: /usr/lib/R/bin/R CMD config --ldflags
      ['-Wl,--export-dynamic -fopenmp -Wl,-z,relro -L/usr/lib/R/lib -lR -lpcre2-8 -llzma -lbz2 -lz -ltirpc -lrt -ldl -lm -licuuc -licui18n', '']
      R exec path: /usr/lib/R/bin/R
      Looking for R CONFIG with: /usr/lib/R/bin/R CMD config --cppflags
      ['-I/usr/share/R/include', '']
      cffi mode is CFFI_MODE.ANY
      Looking for R home with: R RHOME
      R home found: /usr/lib/R
      R exec path: /usr/lib/R/bin/R
      Looking for R CONFIG with: /usr/lib/R/bin/R CMD config --ldflags
      ['-Wl,--export-dynamic -fopenmp -Wl,-z,relro -L/usr/lib/R/lib -lR -lpcre2-8 -llzma -lbz2 -lz -ltirpc -lrt -ldl -lm -licuuc -licui18n', '']
      R exec path: /usr/lib/R/bin/R
      Looking for R CONFIG with: /usr/lib/R/bin/R CMD config --cppflags
      ['-I/usr/share/R/include', '']
      running install
      /usr/local/lib/python3.9/dist-packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools.
        warnings.warn(
      running build
      cffi mode: CFFI_MODE.ANY
      running build_py
      file _rinterface_cffi_abi.py (for module _rinterface_cffi_abi) not found
      creating build
      creating build/lib.linux-x86_64-cpython-39
      creating build/lib.linux-x86_64-cpython-39/rpy2
      copying ./rpy2/__init__.py -> build/lib.linux-x86_64-cpython-39/rpy2
      copying ./rpy2/situation.py -> build/lib.linux-x86_64-cpython-39/rpy2
      copying ./rpy2/_rinterface_cffi_build.py -> build/lib.linux-x86_64-cpython-39/rpy2
      copying ./rpy2/rinterface.py -> build/lib.linux-x86_64-cpython-39/rpy2
      creating build/lib.linux-x86_64-cpython-39/rpy2/rlike
      copying ./rpy2/rlike/container.py -> build/lib.linux-x86_64-cpython-39/rpy2/rlike
      ## Some more copying added by the stackoverflow user ##
      copying ./rpy2/rinterface_lib/R_API_eventloop.c -> build/lib.linux-x86_64-cpython-39/rpy2/rinterface_lib
      copying ./rpy2/rinterface_lib/RPY2.h -> build/lib.linux-x86_64-cpython-39/rpy2/rinterface_lib
      copying ./rpy2/rinterface_lib/_bufferprotocol.c -> build/lib.linux-x86_64-cpython-39/rpy2/rinterface_lib
      file _rinterface_cffi_abi.py (for module _rinterface_cffi_abi) not found
      generating cffi module 'build/lib.linux-x86_64-cpython-39/_rinterface_cffi_abi.py'
      running build_ext
      generating cffi module 'build/temp.linux-x86_64-cpython-39/_rinterface_cffi_api.c'
      creating build/temp.linux-x86_64-cpython-39
      building 'rpy2.rinterface_lib._bufferprotocol' extension
      creating build/temp.linux-x86_64-cpython-39/rpy2
      creating build/temp.linux-x86_64-cpython-39/rpy2/rinterface_lib
      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 -fPIC -I/usr/include/python3.9 -c rpy2/rinterface_lib/_bufferprotocol.c -o build/temp.linux-x86_64-cpython-39/rpy2/rinterface_lib/_bufferprotocol.o
      rpy2/rinterface_lib/_bufferprotocol.c:2:10: fatal error: Python.h: No such file or directory
          2 | #include <Python.h>
            |          ^~~~~~~~~~
      compilation terminated.
      error: command '/usr/bin/x86_64-linux-gnu-gcc' failed with exit code 1
      [end of output]
  
  note: This error originates from a subprocess, and is likely not a problem with pip.
error: legacy-install-failure

× Encountered error while trying to install package.
╰─> rpy2

note: This is an issue with the package mentioned above, not pip.
hint: See above for output from the failure.
The command '/bin/sh -c pip3 install --no-cache-dir -r requirements.txt' returned a non-zero code: 1

如何使用bookworm，python 3.9创建一个能够正确安装numpy、pandas、ray和rpy2库而不发生冲突的对接者映像。

Answer 1

尝试一下；您仍然需要在python文件中进行复制。

FROM debian:bookworm-20210816-slim
RUN apt-get update
RUN apt-get update && apt-get install -y software-properties-common dirmngr wget
RUN add-apt-repository -y ppa:deadsnakes/ppa && apt-get install -y python3.9 python3.9-distutils
RUN wget https://bootstrap.pypa.io/get-pip.py && python3.9 get-pip.py && python3.9 -m pip install --upgrade pip
RUN wget -qO- https://cloud.r-project.org/bin/linux/ubuntu/marutter_pubkey.asc |  tee -a /etc/apt/trusted.gpg.d/cran_ubuntu_key.asc
RUN add-apt-repository "deb https://cloud.r-project.org/bin/linux/ubuntu $(lsb_release -cs)-cran40/"
RUN apt-get install -y --no-install-recommends r-base
RUN pip install pandas scipy ray rpy2 Werkzeug nltk Flask_Script pytest numba pymongo statsmodels \
    Flask_MonitoringDashboard pingouin flasgger cryptography Flask_RESTful Flask_Cors marshmallow \
    config_with_yaml Flask boto3 requests fastapi PyJWT scikit_learn pytz markupsafe itsdangerous pysftp protobuf
CMD ["python3.9", "manage.py", "run"]