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:
- /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
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=
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=
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=
SSL_CERT_FILE=
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