一、软件安装问题

（1）ERROR: Failed building wheel for XXX

1）问题描述：2020.09.09，安装BBKNN时，出现了ERROR: Failed building wheel for annoy

Building wheels for collected packages: annoy
  Building wheel for annoy (setup.py) ... error
  ERROR: Command errored out with exit status 1:
   command: 'D:\Anaconda3\python.exe' -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'C:\\Users\\WangYue\\AppData\\Local\\Temp\\pip-install-l6dexm5d\
\annoy\\setup.py'"'"'; __file__='"'"'C:\\Users\\WangYue\\AppData\\Local\\Temp\\pip-install-l6dexm5d\\annoy\\setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', ope
n)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' bdist_wheel -d 'C:\Users\WangYue\AppDat
a\Local\Temp\pip-wheel-3kv114q5'
       cwd: C:\Users\WangYue\AppData\Local\Temp\pip-install-l6dexm5d\annoy\
  Complete output (10 lines):
  running bdist_wheel
  running build
  running build_py
  creating build
  creating build\lib.win-amd64-3.8
  creating build\lib.win-amd64-3.8\annoy
  copying annoy\__init__.py -> build\lib.win-amd64-3.8\annoy
  running build_ext
  building 'annoy.annoylib' extension
  error: Microsoft Visual C++ 14.0 is required. Get it with "Build Tools for Visual Studio": https://visualstudio.microsoft.com/downloads/
  ----------------------------------------
  ERROR: Failed building wheel for annoy
  Running setup.py clean for annoy
Failed to build annoy
Installing collected packages: annoy, bbknn
    Running setup.py install for annoy ... error
    ERROR: Command errored out with exit status 1:
     command: 'D:\Anaconda3\python.exe' -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'C:\\Users\\WangYue\\AppData\\Local\\Temp\\pip-install-l6dexm5
d\\annoy\\setup.py'"'"'; __file__='"'"'C:\\Users\\WangYue\\AppData\\Local\\Temp\\pip-install-l6dexm5d\\annoy\\setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', o
pen)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record 'C:\Users\WangYue\Ap
pData\Local\Temp\pip-record-ytf4d7dj\install-record.txt' --single-version-externally-managed --compile --install-headers 'D:\Anaconda3\Include\annoy'
         cwd: C:\Users\WangYue\AppData\Local\Temp\pip-install-l6dexm5d\annoy\
    Complete output (10 lines):
    running install
    running build
    running build_py
    creating build
    creating build\lib.win-amd64-3.8
    creating build\lib.win-amd64-3.8\annoy
    copying annoy\__init__.py -> build\lib.win-amd64-3.8\annoy
    running build_ext
    building 'annoy.annoylib' extension
    error: Microsoft Visual C++ 14.0 is required. Get it with "Build Tools for Visual Studio": https://visualstudio.microsoft.com/downloads/
    ----------------------------------------
ERROR: Command errored out with exit status 1: 'D:\Anaconda3\python.exe' -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'C:\\Users\\WangYue\\AppData\
\Local\\Temp\\pip-install-l6dexm5d\\annoy\\setup.py'"'"'; __file__='"'"'C:\\Users\\WangYue\\AppData\\Local\\Temp\\pip-install-l6dexm5d\\annoy\\setup.py'"'"';f=ge
tattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' inst
all --record 'C:\Users\WangYue\AppData\Local\Temp\pip-record-ytf4d7dj\install-record.txt' --single-version-externally-managed --compile --install-headers 'D:\Ana
conda3\Include\annoy' Check the logs for full command output.

2）问题归类：ERROR: Failed building wheel for XXX
3）解决方案：在Pythonlibs网站上下载对应的python包的wheel(.whl)文件，然后pip install .whl文件的绝对路径，或者cd到,whl文件的路径，然后pip install .whl文件。

D:\PythonProject\scRNA_basic>pip install annoy-1.16.3-cp38-cp38-win_amd64.whl
Processing d:\pythonproject\scrna_basic\annoy-1.16.3-cp38-cp38-win_amd64.whl
Installing collected packages: annoy
Successfully installed annoy-1.16.3

再安装BBKNN，安装成功。

D:\PythonProject\scRNA_basic>pip install bbknn
Collecting bbknn
  Using cached bbknn-1.3.12-py3-none-any.whl (8.1 kB)
Requirement already satisfied: scikit-learn in d:\anaconda3\lib\site-packages (from bbknn) (0.23.2)
Requirement already satisfied: scipy in d:\anaconda3\lib\site-packages (from bbknn) (1.5.0)
Requirement already satisfied: packaging in d:\anaconda3\lib\site-packages (from bbknn) (20.4)
Requirement already satisfied: numpy in d:\anaconda3\lib\site-packages (from bbknn) (1.18.5)
Requirement already satisfied: umap-learn in d:\anaconda3\lib\site-packages (from bbknn) (0.4.6)
Requirement already satisfied: annoy in d:\anaconda3\lib\site-packages (from bbknn) (1.16.3)
Requirement already satisfied: Cython in d:\anaconda3\lib\site-packages (from bbknn) (0.29.21)
Requirement already satisfied: threadpoolctl>=2.0.0 in d:\anaconda3\lib\site-packages (from scikit-learn->bbknn) (2.1.0)
Requirement already satisfied: joblib>=0.11 in d:\anaconda3\lib\site-packages (from scikit-learn->bbknn) (0.16.0)
Requirement already satisfied: six in d:\anaconda3\lib\site-packages (from packaging->bbknn) (1.15.0)
Requirement already satisfied: pyparsing>=2.0.2 in d:\anaconda3\lib\site-packages (from packaging->bbknn) (2.4.7)
Requirement already satisfied: numba!=0.47,>=0.46 in d:\anaconda3\lib\site-packages (from umap-learn->bbknn) (0.50.1)
Requirement already satisfied: llvmlite<0.34,>=0.33.0.dev0 in d:\anaconda3\lib\site-packages (from numba!=0.47,>=0.46->umap-learn->bbknn) (0.33.0+1.g022ab0f)
Requirement already satisfied: setuptools in d:\anaconda3\lib\site-packages (from numba!=0.47,>=0.46->umap-learn->bbknn) (49.2.0.post20200714)
Installing collected packages: bbknn
Successfully installed bbknn-1.3.12

（2）Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.

1）问题描述：2020.09.10，安装Stream时，出现了Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.

(py-stream) wangyue@LAPTOP-FMOR2BIN:/mnt/d/tmp$ conda install numpy
Collecting package metadata (current_repodata.json): done
Solving environment: /
The environment is inconsistent, please check the package plan carefully
The following packages are causing the inconsistency:

  - <unknown>/linux-64::stream==0.4.1=py36r36hc99cbb1_0
failed with initial frozen solve. Retrying with flexible solve.
Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): failed

# >>>>>>>>>>>>>>>>>>>>>> ERROR REPORT <<<<<<<<<<<<<<<<<<<<<<

    Traceback (most recent call last):
      File "/mnt/d/Linux/software/anaconda/lib/python3.7/site-packages/conda/exceptions.py", line 1079, in __call__
        return func(*args, **kwargs)
      File "/mnt/d/Linux/software/anaconda/lib/python3.7/site-packages/conda/cli/main.py", line 84, in _main
        exit_code = do_call(args, p)
      File "/mnt/d/Linux/software/anaconda/lib/python3.7/site-packages/conda/cli/conda_argparse.py", line 83, in do_call        return getattr(module, func_name)(args, parser)
      File "/mnt/d/Linux/software/anaconda/lib/python3.7/site-packages/conda/cli/main_install.py", line 20, in execute
        install(args, parser, 'install')
      File "/mnt/d/Linux/software/anaconda/lib/python3.7/site-packages/conda/cli/install.py", line 265, in install
        should_retry_solve=(_should_retry_unfrozen or repodata_fn != repodata_fns[-1]),
      File "/mnt/d/Linux/software/anaconda/lib/python3.7/site-packages/conda/core/solve.py", line 117, in solve_for_transaction
        should_retry_solve)
      File "/mnt/d/Linux/software/anaconda/lib/python3.7/site-packages/conda/core/solve.py", line 158, in solve_for_diff        force_remove, should_retry_solve)
      File "/mnt/d/Linux/software/anaconda/lib/python3.7/site-packages/conda/core/solve.py", line 262, in solve_final_state
        ssc = self._collect_all_metadata(ssc)
      File "/mnt/d/Linux/software/anaconda/lib/python3.7/site-packages/conda/common/io.py", line 88, in decorated
        return f(*args, **kwds)
      File "/mnt/d/Linux/software/anaconda/lib/python3.7/site-packages/conda/core/solve.py", line 425, in _collect_all_metadata
        index, r = self._prepare(prepared_specs)
      File "/mnt/d/Linux/software/anaconda/lib/python3.7/site-packages/conda/core/solve.py", line 1021, in _prepare
        self.subdirs, prepared_specs, self._repodata_fn)
      File "/mnt/d/Linux/software/anaconda/lib/python3.7/site-packages/conda/core/index.py", line 228, in get_reduced_index
        repodata_fn=repodata_fn)
      File "/mnt/d/Linux/software/anaconda/lib/python3.7/site-packages/conda/core/subdir_data.py", line 105, in query_all
        result = tuple(concat(executor.map(subdir_query, channel_urls)))
      File "/mnt/d/Linux/software/anaconda/lib/python3.7/concurrent/futures/_base.py", line 598, in result_iterator
        yield fs.pop().result()
      File "/mnt/d/Linux/software/anaconda/lib/python3.7/concurrent/futures/_base.py", line 435, in result
        return self.__get_result()
      File "/mnt/d/Linux/software/anaconda/lib/python3.7/concurrent/futures/_base.py", line 384, in __get_result
        raise self._exception
      File "/mnt/d/Linux/software/anaconda/lib/python3.7/concurrent/futures/thread.py", line 57, in run
        result = self.fn(*self.args, **self.kwargs)
      File "/mnt/d/Linux/software/anaconda/lib/python3.7/site-packages/conda/core/subdir_data.py", line 98, in <lambda>
        package_ref_or_match_spec))
      File "/mnt/d/Linux/software/anaconda/lib/python3.7/site-packages/conda/core/subdir_data.py", line 110, in query
        self.load()
      File "/mnt/d/Linux/software/anaconda/lib/python3.7/site-packages/conda/core/subdir_data.py", line 174, in load
        _internal_state = self._load()
      File "/mnt/d/Linux/software/anaconda/lib/python3.7/site-packages/conda/core/subdir_data.py", line 276, in _load
        _internal_state = self._process_raw_repodata_str(raw_repodata_str)
      File "/mnt/d/Linux/software/anaconda/lib/python3.7/site-packages/conda/core/subdir_data.py", line 349, in _process_raw_repodata_str
        json_obj = json.loads(raw_repodata_str or '{}')
      File "/mnt/d/Linux/software/anaconda/lib/python3.7/json/__init__.py", line 348, in loads
        return _default_decoder.decode(s)
      File "/mnt/d/Linux/software/anaconda/lib/python3.7/json/decoder.py", line 337, in decode
        obj, end = self.raw_decode(s, idx=_w(s, 0).end())
      File "/mnt/d/Linux/software/anaconda/lib/python3.7/json/decoder.py", line 355, in raw_decode
        raise JSONDecodeError("Expecting value", s, err.value) from None
    json.decoder.JSONDecodeError: Expecting value: line 1645278 column 32 (char 47595349)

`$ /mnt/d/Linux/software/anaconda/bin/conda install numpy`

  environment variables:
                 CIO_TEST=<not set>
        CMAKE_PREFIX_PATH=/mnt/d/Linux/software/anaconda/envs/py-
                          stream:/mnt/d/Linux/software/anaconda/envs/py-
                          stream/x86_64-conda_cos6-linux-gnu/sysroot/usr
         CONDA_BACKUP_F90=/mnt/d/Linux/software/anaconda/envs/py-
                          stream/bin/x86_64-conda_cos6-linux-gnu-gfortran
        CONDA_BACKUP_HOST=x86_64-conda_cos6-linux-gnu
     CONDA_BACKUP_LDFLAGS=-Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,
                          --disable-new-dtags -Wl,--gc-sections
                          -Wl,-rpath,/mnt/d/Linux/software/anaconda/envs/py-stream/lib
                          -L/mnt/d/Linux/software/anaconda/envs/py-stream/lib
      CONDA_BUILD_SYSROOT=/mnt/d/Linux/software/anaconda/envs/py-stream/x86_64-conda_cos6-linux-
                          gnu/sysroot
        CONDA_DEFAULT_ENV=py-stream
                CONDA_EXE=/mnt/d/Linux/software/anaconda/bin/conda
             CONDA_PREFIX=/mnt/d/Linux/software/anaconda/envs/py-stream
           CONDA_PREFIX_1=/mnt/d/Linux/software/anaconda
    CONDA_PROMPT_MODIFIER=(py-stream)
         CONDA_PYTHON_EXE=/mnt/d/Linux/software/anaconda/bin/python
               CONDA_ROOT=/mnt/d/Linux/software/anaconda
              CONDA_SHLVL=2
           CURL_CA_BUNDLE=<not set>
                     PATH=/mnt/d/Linux/software/anaconda/bin:/mnt/d/Linux/software/anaconda/envs
                          /py-stream/bin:/mnt/d/Linux/software/anaconda/condabin:/usr/local/sbin
                          :/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/ga
                          mes:/mnt/c/Program Files/WindowsApps/CanonicalGroupLimited.Ubuntu18.04
                          onWindows_1804.2020.824.0_x64__79rhkp1fndgsc:/mnt/c/Windows/system32:/
                          mnt/c/Windows:/mnt/c/Windows/System32/Wbem:/mnt/c/Windows/System32/Win
                          dowsPowerShell/v1.0:/mnt/c/Windows/System32/OpenSSH:/mnt/c/Program
                          Files (x86)/NVIDIA Corporation/PhysX/Common:/mnt/c/Program
                          Files/NVIDIA Corporation/NVIDIA NvDLISR:/mnt/d/计算机软件/putty:/mnt/d/Anac
                          onda3:/mnt/d/Anaconda3/Library/mingw-w64/bin:/mnt/d/Anaconda3/Library/
                          usr/bin:/mnt/d/Anaconda3/Library/bin:/mnt/d/Anaconda3/Scripts:/mnt/c/U
                          sers/WangYue/AppData/Local/Microsoft/WindowsApps:/snap/bin
       REQUESTS_CA_BUNDLE=<not set>
            SSL_CERT_FILE=<not set>

     active environment : py-stream
    active env location : /mnt/d/Linux/software/anaconda/envs/py-stream
            shell level : 2
       user config file : /home/wangyue/.condarc
 populated config files : /home/wangyue/.condarc
          conda version : 4.8.4
    conda-build version : 3.18.11
         python version : 3.7.6.final.0
       virtual packages : __glibc=2.27
       base environment : /mnt/d/Linux/software/anaconda  (writable)
           channel URLs : https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda/linux-64
                          https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda/noarch
                          https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/msys2/linux-64
                          https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/msys2/noarch
                          https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64
                          https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/noarch
                          https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free/linux-64
                          https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free/noarch
                          https://conda.anaconda.org/bioconda/linux-64
                          https://conda.anaconda.org/bioconda/noarch
                          https://conda.anaconda.org/r/linux-64
                          https://conda.anaconda.org/r/noarch
                          https://repo.anaconda.com/pkgs/main/linux-64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/r/linux-64
                          https://repo.anaconda.com/pkgs/r/noarch
                          https://conda.anaconda.org/conda-forge/linux-64
                          https://conda.anaconda.org/conda-forge/noarch
                          https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/pytorch/linux-64
                          https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/pytorch/noarch
          package cache : /mnt/d/Linux/software/anaconda/pkgs
                          /home/wangyue/.conda/pkgs
       envs directories : /mnt/d/Linux/software/anaconda/envs
                          /home/wangyue/.conda/envs
               platform : linux-64
             user-agent : conda/4.8.4 requests/2.22.0 CPython/3.7.6 Linux/4.4.0-18362-Microsoft ubuntu/18.04.5 glibc/2.27
                UID:GID : 1000:1000
             netrc file : None
           offline mode : False


An unexpected error has occurred. Conda has prepared the above report.

If submitted, this report will be used by core maintainers to improve
future releases of conda.
Would you like conda to send this report to the core maintainers?

[y/N]:

2）比较特征的点是：1、在报错开头会提示，failed with repodata from current_repodata.json, will retry with next repodata source 2、报错的最后会询问是否上报，Would you like conda to send this report to the core maintainers? [y/N]。
3）解决方案：

conda clean -i