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「踩坑实录」一个让我调试4小时的 dolomite-base 安装问题

用户11414625

发布于 2025-02-25 01:00:50

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文章被收录于专栏：生信星球520生信星球520

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代码可运行

这个包是celldex的依赖项，而celldex则是singler的配套参考数据包。所以我们安装celldex就会自动安装他。

省流提示：解决问题最终成功的尝试是2.3，其他步骤不需要操作了。但可以从中学习一下都有啥可以干的，毕竟谁也没有上帝视角，不知道哪个尝试会有效嘛。

希望你看到这些报错和尝试不要害怕，产生畏难情绪，其实难度都在我这里，展示这个过程是为了做记录，学方法。以后有不是我教的内容，才会需要自己配置环境的，如果是我教的，我会负责。

1.构建wheel非常慢，然后报错

Wheel 是 Python 的一种预编译包格式，文件扩展名为 .whl。它是 Python 打包机制的一个重要组成部分，可以看作是一个"ready-to-install"（即开即用）的包格式。

正常情况下pip install 会自动完成编译的工作，但这次遇到了报错。

 error: command '/tmp/pip-build-env-upbakww0/overlay/bin/cmake' failed with exit code 2
      [end of output]
  
  note: This error originates from a subprocess, and is likely not a problem with pip.
  ERROR: Failed building wheel for dolomite_base
Failed to build dolomite_base
ERROR: Failed to build installable wheels for some pyproject.toml based projects (dolomite_base)

估计是ubuntu缺什么零件。pip install -v 可以显示详细日志，便于排查问题，报错如下：

  cmake -S lib -B build/temp.linux-x86_64-cpython-311 -Dpybind11_DIR=/tmp/pip-build-env-asv1jvd9/overlay/lib/python3.11/site-packages/pybind11/share/cmake/pybind11 -DPYTHON_EXECUTABLE=/home/bio02/miniconda3/envs/sc3/bin/python3.11 -DCMAKE_BUILD_TYPE=Release -DCMAKE_LIBRARY_OUTPUT_DIRECTORY=/tmp/pip-install-8pmbmqc6/dolomite-base_ed6d850d5123490f96c1ae0aa089c8fa/build/lib.linux-x86_64-cpython-311/dolomite_base
  -- The CXX compiler identification is GNU 9.4.0
  -- Detecting CXX compiler ABI info
  -- Detecting CXX compiler ABI info - done
  -- Check for working CXX compiler: /usr/bin/c++ - skipped
  -- Detecting CXX compile features
  -- Detecting CXX compile features - done
  -- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.2.11")
  -- Could NOT find HDF5 (missing: HDF5_LIBRARIES HDF5_INCLUDE_DIRS C CXX)
  -- Could NOT find HDF5 (missing: HDF5_LIBRARIES HDF5_INCLUDE_DIRS C CXX)



  [ 11%] Creating directories for 'chihaya-populate'
  [ 22%] Performing download step (git clone) for 'chihaya-populate'
  Cloning into 'chihaya-src'...
  fatal: unable to access 'https://github.com/ArtifactDB/chihaya/': GnuTLS recv error (-110): The TLS connection was non-properly terminated.
  Cloning into 'chihaya-src'...
  error: RPC failed; curl 56 GnuTLS recv error (-110): The TLS connection was non-properly terminated.
  fatal: the remote end hung up unexpectedly
  Cloning into 'chihaya-src'...
  fatal: unable to access 'https://github.com/ArtifactDB/chihaya/': Failed to connect to github.com port 443: Connection timed out
  Had to git clone more than once: 3 times.
  CMake Error at chihaya-subbuild/chihaya-populate-prefix/tmp/chihaya-populate-gitclone.cmake:50 (message):
    Failed to clone repository: 'https://github.com/ArtifactDB/chihaya'


  make[2]: *** [CMakeFiles/chihaya-populate.dir/build.make:102: chihaya-populate-prefix/src/chihaya-populate-stamp/chihaya-populate-download] Error 1
  make[1]: *** [CMakeFiles/Makefile2:87: CMakeFiles/chihaya-populate.dir/all] Error 2
  make: *** [Makefile:91: all] Error 2

  CMake Error at /tmp/pip-build-env-asv1jvd9/overlay/lib/python3.11/site-packages/cmake/data/share/cmake-3.31/Modules/FetchContent.cmake:1918 (message):
    Build step for chihaya failed: 2
  Call Stack (most recent call first):
    /tmp/pip-build-env-asv1jvd9/overlay/lib/python3.11/site-packages/cmake/data/share/cmake-3.31/Modules/FetchContent.cmake:1609 (__FetchContent_populateSubbuild)
    /tmp/pip-build-env-asv1jvd9/overlay/lib/python3.11/site-packages/cmake/data/share/cmake-3.31/Modules/FetchContent.cmake:2145:EVAL:2 (__FetchContent_doPopulation)
    /tmp/pip-build-env-asv1jvd9/overlay/lib/python3.11/site-packages/cmake/data/share/cmake-3.31/Modules/FetchContent.cmake:2145 (cmake_language)
    /tmp/pip-build-env-asv1jvd9/overlay/lib/python3.11/site-packages/cmake/data/share/cmake-3.31/Modules/FetchContent.cmake:2384 (__FetchContent_Populate)
    /tmp/pip-install-8pmbmqc6/dolomite-base_ed6d850d5123490f96c1ae0aa089c8fa/build/temp.linux-x86_64-cpython-311/_deps/takane-src/extern/CMakeLists.txt:23 (FetchContent_MakeAvailable)


  -- Configuring incomplete, errors occurred!


  An error occurred while building the project, please ensure you have the most updated version of setuptools, setuptools_scm and wheel with:
     pip install -U setuptools setuptools_scm wheel


  error: command '/tmp/pip-build-env-asv1jvd9/overlay/bin/cmake' failed with exit code 1
  error: subprocess-exited-with-error

  × Building wheel for dolomite_base (pyproject.toml) did not run successfully.
  │ exit code: 1
  ╰─> See above for output.

  note: This error originates from a subprocess, and is likely not a problem with pip.
  full command: /home/bio02/miniconda3/envs/sc3/bin/python3.11 /home/bio02/miniconda3/envs/sc3/lib/python3.11/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py build_wheel /tmp/tmplhya7b20
  cwd: /tmp/pip-install-8pmbmqc6/dolomite-base_ed6d850d5123490f96c1ae0aa089c8fa
  Building wheel for dolomite_base (pyproject.toml) ... error
  ERROR: Failed building wheel for dolomite_base
Failed to build dolomite_base
ERROR: Failed to build installable wheels for some pyproject.toml based projects (dolomite_base)

其实两大段的关键词都是ERROR: Failed building wheel for dolomite_base，编译失败！

2.最终成功的尝试：下载whl，修改后装它

pip页面会提供预编译版本的whl文件，直接使用即可跳过编译的步骤

文件名中包括了python版本和设备的平台。其中ubuntu适用的是manyliux，适用mac的是macos。

遇到3个问题：

1.报错说whl文件不适用当前平台

 dolomite_base-0.4.2-cp311-cp311-manylinux_1_2_x86_64.whl is not a supported wheel on this platform.ubuntu

解决办法：下载manylinux版本，改文件名，去掉平台名字，加上none-any即可安装!

改名字，真是一个看起来不咋地但有效的行为！

https://blog.csdn.net/yuangan1529/article/details/116696624

改为： dolomite_base-0.4.2-cp311-none-any.whl就可以安装了

2.python3.11对应的最新版本的wheel文件，编译软件与我电脑上的版本不相同

conda list能列出来了，但是import报错！

说编译时使用的glibc版本为2.32，但我的ubuntu最多只能更新到2.31，要求二者一致，因此能安装但import就会报错

/lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.32' not found (required by /home/bio02/miniconda3/envs/sc2/lib/python3.11/site-packages/dolomite_base/lib_dolomite_base.cpython-311-x86_64-linux-gnu.so)

检查glibc版本的办法是：

ldd --version

试图更新glibc,发现最新只能到2.31

sudo apt-get install libc6-dev

eading package lists... Done
Building dependency tree
Reading state information... Done
libc6-dev is already the newest version (2.31-0ubuntu9.17).
libc6-dev set to manually installed.
The following packages were automatically installed and are no longer required:
  libfwupdplugin1 libxmlb1
Use 'sudo apt autoremove' to remove them.
0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.

给我整愣住了。不能升级自己电脑上的glibc，那我使用whl的上一个版本吧。

3.安装python3.10对应的whl文件，报错循环导入

 python -c 'import dolomite_base'
Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "/home/bio02/miniconda3/envs/sc2/lib/python3.11/site-packages/dolomite_base/__init__.py", line 18, in <module>
    from .save_object import save_object, validate_saves
  File "/home/bio02/miniconda3/envs/sc2/lib/python3.11/site-packages/dolomite_base/save_object.py", line 3, in <module>
    from .validate_object import validate_object
  File "/home/bio02/miniconda3/envs/sc2/lib/python3.11/site-packages/dolomite_base/validate_object.py", line 3, in <module>
    from . import lib_dolomite_base as lib
ImportError: cannot import name 'lib_dolomite_base' from partially initialized module 'dolomite_base' (most likely due to a circular import) (/home/bio02/miniconda3/envs/sc2/lib/python3.11/site-packages/dolomite_base/__init__.py)

原本想去改miniconda库里的文件，但报错没有权限修改，如果要改其实也可以，就是先chord设置一下权限再改。

但我选择了更安全的方式--whl本质是zip压缩包，所以用7-zip解压，改完代码然后重新压缩，选择压缩类型为zip，命名时后缀写whl，即可正常安装和使用。

按照ai提示修改了两处源代码，解决了其循环导入的问题。

通过网盘分享的文件：dolomite_base-0.4.2-cp311-none-any.whl
链接: https://pan.baidu.com/s/1Asaveg9mP1xz9IroZTJDSA?pwd=883m 提取码: 883m 
--来自百度网盘超级会员v5的分享

下载此文件放在工作目录下

conda activate sc2
pip install dolomite_base-0.4.2-cp311-none-any.whl

然后再继续装celldex等，就没有问题了。

3.最终石沉大海的其他尝试

还有各种无用尝试，花了三四个小时。真是个难缠的bug

3.1 退一个版本，安装旧版本的dolomite_base和celldex

但发现，即使已经有了dolomite旧版本，celldex安装时还是会更新他，因为celldex没有指定要求什么版本的dolomite_base，就默认安装最新版！

解决办法是把这两个包的版本都指定好再安装。

pip install celldex==0.1.1 dolomite_base==0.4.0

但又有新问题，dolomite_base有好几个同系列的包，全体依赖最新版的dolomite_base！所以要退大家一起退吧！

尝试发现，一起退也不行，指定的太多了，其他的包无法解决环境冲突了！我去，流氓软件全家桶！

冲突的表现是有报错，而且运行jupyternotebook里原本调好了的代码会：

 cannot import name 'TatamiNumericPointer' from 'mattress' (/home/bio02/miniconda3/envs/sc2/lib/python3.11/site-packages/mattress/__init__.py)

3.2 试图解决编译环境的问题

跟着ai的提示去装和更新各种编译工具

企图用源码方式装新版的GLIBC2.32，那一大堆报错，我都不知道该咋问，中途放弃。

cmake版本更新成功，但报错信息无任何变化，说明更新了没有用

sudo apt-get update
sudo apt-get install -y software-properties-common lsb-release wget
sudo apt-get remove --purge cmake
wget -O - https://apt.kitware.com/keys/kitware-archive-latest.asc | sudo apt-key add -
sudo apt-add-repository "deb https://apt.kitware.com/ubuntu/ $(lsb_release -cs) main"
sudo apt-get update
sudo apt-get install cmake

gcc 和g++更新，也没有用

sudo apt-get update
sudo apt-get install -y gcc-11 g++-11
sudo update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-11 100
sudo update-alternatives --install /usr/bin/g++ g++ /usr/bin/g++-11 100

3.3 试图安装github的版本

方法是从github页面上下载zip，然后解压并cd进去，pip .即可，但是遇到新的问题

说是setuptools-scm无法自动检测版本。AI 提示修改源码，越改问题越多，遂放弃。

 pip install .
Looking in indexes: https://pypi.mirrors.ustc.edu.cn/simple/
Processing /mnt/c/Users/win10/Desktop/python250208/day7.8/dolomite-base-master
  Installing build dependencies ... done
  Getting requirements to build wheel ... error
  error: subprocess-exited-with-error

  × Getting requirements to build wheel did not run successfully.
  │ exit code: 1
  ╰─> [46 lines of output]


      An error occurred while building the project, please ensure you have the most updated version of setuptools, setuptools_scm and wheel with:
         pip install -U setuptools setuptools_scm wheel


      Traceback (most recent call last):
        File "/home/bio02/miniconda3/envs/sc2/lib/python3.11/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 389, in <module>
          main()
        File "/home/bio02/miniconda3/envs/sc2/lib/python3.11/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 373, in main
          json_out["return_val"] = hook(**hook_input["kwargs"])
                                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        File "/home/bio02/miniconda3/envs/sc2/lib/python3.11/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 143, in get_requires_for_build_wheel
          return hook(config_settings)
                 ^^^^^^^^^^^^^^^^^^^^^
        File "/tmp/pip-build-env-3tljex4b/overlay/lib/python3.11/site-packages/setuptools/build_meta.py", line 334, in get_requires_for_build_wheel
          return self._get_build_requires(config_settings, requirements=[])
                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        File "/tmp/pip-build-env-3tljex4b/overlay/lib/python3.11/site-packages/setuptools/build_meta.py", line 304, in _get_build_requires
          self.run_setup()
        File "/tmp/pip-build-env-3tljex4b/overlay/lib/python3.11/site-packages/setuptools/build_meta.py", line 320, in run_setup
          exec(code, locals())
        File "<string>", line 62, in <module>
        File "/tmp/pip-build-env-3tljex4b/overlay/lib/python3.11/site-packages/setuptools/__init__.py", line 117, in setup
          return distutils.core.setup(**attrs)
                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        File "/tmp/pip-build-env-3tljex4b/overlay/lib/python3.11/site-packages/setuptools/_distutils/core.py", line 148, in setup
          _setup_distribution = dist = klass(attrs)
                                       ^^^^^^^^^^^^
        File "/tmp/pip-build-env-3tljex4b/overlay/lib/python3.11/site-packages/setuptools/dist.py", line 319, in __init__
          _Distribution.__init__(self, dist_attrs)
        File "/tmp/pip-build-env-3tljex4b/overlay/lib/python3.11/site-packages/setuptools/_distutils/dist.py", line 290, in __init__
          self.finalize_options()
        File "/tmp/pip-build-env-3tljex4b/overlay/lib/python3.11/site-packages/setuptools/dist.py", line 681, in finalize_options
          ep(self)
        File "/tmp/pip-build-env-3tljex4b/overlay/lib/python3.11/site-packages/setuptools_scm/_integration/setuptools.py", line 123, in infer_version
          _assign_version(dist, config)
        File "/tmp/pip-build-env-3tljex4b/overlay/lib/python3.11/site-packages/setuptools_scm/_integration/setuptools.py", line 58, in _assign_version
          _version_missing(config)
        File "/tmp/pip-build-env-3tljex4b/overlay/lib/python3.11/site-packages/setuptools_scm/_get_version_impl.py", line 117, in _version_missing
          raise LookupError(
      LookupError: setuptools-scm was unable to detect version for /mnt/c/Users/win10/Desktop/python250208/day7.8/dolomite-base-master.

      Make sure you're either building from a fully intact git repository or PyPI tarballs. Most other sources (such as GitHub's tarballs, a git checkout without the .git folder) don't contain the necessary metadata and will not work.

      For example, if you're using pip, instead of https://github.com/user/proj/archive/master.zip use git+https://github.com/user/proj.git#egg=proj
      [end of output]

  note: This error originates from a subprocess, and is likely not a problem with pip.
error: subprocess-exited-with-error

× Getting requirements to build wheel did not run successfully.
│ exit code: 1
╰─> See above for output.

note: This error originates from a subprocess, and is likely not a problem with pip.

3.4 h5df 找不到的问题

  -- Could NOT find HDF5 (missing: HDF5_LIBRARIES HDF5_INCLUDE_DIRS C CXX)
  -- Could NOT find HDF5 (missing: HDF5_LIBRARIES HDF5_INCLUDE_DIRS C CXX)

查看电脑上是否有hdf5及其开发头文件

dpkg -l | grep hdf5

如果已经安装了 HDF5 和开发包，应该能看到类似以下输出：

ii  libhdf5-103:amd64        1.10.4+repack-10ubuntu1        amd64        Hierarchical Data Format 5 (HDF5) - runtime files
ii  libhdf5-dev              1.10.4+repack-10ubuntu1        amd64        Hierarchical Data Format 5 (HDF5) - development files

如果未安装，就不会输出任何内容。可以通过以下命令安装：

sudo apt-get install libhdf5-dev

3.5 github克隆失败的问题

[ 11%] Creating directories for 'chihaya-populate'
  [ 22%] Performing download step (git clone) for 'chihaya-populate'
  Cloning into 'chihaya-src'...
  fatal: unable to access 'https://github.com/ArtifactDB/chihaya/': GnuTLS recv error (-110): The TLS connection was non-properly terminated.
  Cloning into 'chihaya-src'...
  error: RPC failed; curl 56 GnuTLS recv error (-110): The TLS connection was non-properly terminated.
  fatal: the remote end hung up unexpectedly
  Cloning into 'chihaya-src'...
  fatal: unable to access 'https://github.com/ArtifactDB/chihaya/': Failed to connect to github.com port 443: Connection timed out
  Had to git clone more than once: 3 times.
  CMake Error at chihaya-subbuild/chihaya-populate-prefix/tmp/chihaya-populate-gitclone.cmake:50 (message):
    Failed to clone repository: 'https://github.com/ArtifactDB/chihaya'