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sanderlab / CellBox

CellBox: Interpretable Machine Learning for Perturbation Biology
MIT License
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Problem while setting up Cellbox locally #13

Closed Debanitrkl closed 3 years ago

Debanitrkl commented 3 years ago

Capture I'm getting this error when I'm trying to run python3.6 setup.py install in the cellbox folder

DesmondYuan commented 3 years ago

Thanks for the question. Can you please specify your system environment also the virtualenv/conda information? PS: using GIST or quote feature of GitHub for script blocks might be a better practice, instead of screenshots.

e.g. Some codes or outputs
Debanitrkl commented 3 years ago

My Environment information:

(env) C:\Users\LENOVO\Desktop\deepASL-master\CellBox>pip list Package Version

absl-py 0.11.0 astor 0.8.1 astunparse 1.6.3 cachetools 4.2.1 cellbox 0.3.1 certifi 2020.12.5 chardet 4.0.0 flatbuffers 1.12 gast 0.2.2 google-auth 1.25.0 google-auth-oauthlib 0.4.2 google-pasta 0.2.0 grpcio 1.32.0 h5py 2.10.0 idna 2.10 importlib-metadata 1.7.0 Keras-Applications 1.0.8 Keras-Preprocessing 1.1.2 Markdown 3.2.2 numpy 1.19.0 oauthlib 3.1.0 opt-einsum 3.2.1 pip 20.1.1 protobuf 3.12.2 pyasn1 0.4.8 pyasn1-modules 0.2.8 python-dateutil 2.8.1 pytz 2021.1 requests 2.25.1 requests-oauthlib 1.3.0 rsa 4.7 setuptools 47.1.0 six 1.15.0 tensorboard 1.15.0 tensorboard-plugin-wit 1.8.0 tensorflow 2.4.1 tensorflow-estimator 2.4.0 termcolor 1.1.0 typing-extensions 3.7.4.3 urllib3 1.26.3 Werkzeug 1.0.1 wheel 0.36.2 wrapt 1.12.1 zipp 3.1.0

The error I'm getting while running the python setup.py install

(env) C:\Users\LENOVO\Desktop\deepASL-master\CellBox\cellbox>python setup.py install
running install
running bdist_egg
running egg_info
writing cellbox.egg-info\PKG-INFO
writing dependency_links to cellbox.egg-info\dependency_links.txt
writing requirements to cellbox.egg-info\requires.txt
writing top-level names to cellbox.egg-info\top_level.txt
reading manifest file 'cellbox.egg-info\SOURCES.txt'
writing manifest file 'cellbox.egg-info\SOURCES.txt'
installing library code to build\bdist.win-amd64\egg
running install_lib
running build_py
creating build\bdist.win-amd64\egg
creating build\bdist.win-amd64\egg\cellbox
copying build\lib\cellbox\config.py -> build\bdist.win-amd64\egg\cellbox
copying build\lib\cellbox\dataset.py -> build\bdist.win-amd64\egg\cellbox
copying build\lib\cellbox\kernel.py -> build\bdist.win-amd64\egg\cellbox
copying build\lib\cellbox\model.py -> build\bdist.win-amd64\egg\cellbox
copying build\lib\cellbox\train.py -> build\bdist.win-amd64\egg\cellbox
copying build\lib\cellbox\utils.py -> build\bdist.win-amd64\egg\cellbox
copying build\lib\cellbox\version.py -> build\bdist.win-amd64\egg\cellbox
copying build\lib\cellbox\__init__.py -> build\bdist.win-amd64\egg\cellbox
byte-compiling build\bdist.win-amd64\egg\cellbox\config.py to config.cpython-38.pyc
byte-compiling build\bdist.win-amd64\egg\cellbox\dataset.py to dataset.cpython-38.pyc
byte-compiling build\bdist.win-amd64\egg\cellbox\kernel.py to kernel.cpython-38.pyc
byte-compiling build\bdist.win-amd64\egg\cellbox\model.py to model.cpython-38.pyc
byte-compiling build\bdist.win-amd64\egg\cellbox\train.py to train.cpython-38.pyc
byte-compiling build\bdist.win-amd64\egg\cellbox\utils.py to utils.cpython-38.pyc
byte-compiling build\bdist.win-amd64\egg\cellbox\version.py to version.cpython-38.pyc
byte-compiling build\bdist.win-amd64\egg\cellbox\__init__.py to __init__.cpython-38.pyc
creating build\bdist.win-amd64\egg\EGG-INFO
copying cellbox.egg-info\PKG-INFO -> build\bdist.win-amd64\egg\EGG-INFO
copying cellbox.egg-info\SOURCES.txt -> build\bdist.win-amd64\egg\EGG-INFO
copying cellbox.egg-info\dependency_links.txt -> build\bdist.win-amd64\egg\EGG-INFO
copying cellbox.egg-info\requires.txt -> build\bdist.win-amd64\egg\EGG-INFO
copying cellbox.egg-info\top_level.txt -> build\bdist.win-amd64\egg\EGG-INFO
copying cellbox.egg-info\zip-safe -> build\bdist.win-amd64\egg\EGG-INFO
creating 'dist\cellbox-0.3.1-py3.8.egg' and adding 'build\bdist.win-amd64\egg' to it
removing 'build\bdist.win-amd64\egg' (and everything under it)
Processing cellbox-0.3.1-py3.8.egg
Removing c:\users\lenovo\desktop\deepasl-master\cellbox\env\lib\site-packages\cellbox-0.3.1-py3.8.egg
Copying cellbox-0.3.1-py3.8.egg to c:\users\lenovo\desktop\deepasl-master\cellbox\env\lib\site-packages
cellbox 0.3.1 is already the active version in easy-install.pth

Installed c:\users\lenovo\desktop\deepasl-master\cellbox\env\lib\site-packages\cellbox-0.3.1-py3.8.egg
Processing dependencies for cellbox==0.3.1
Searching for scipy==1.3.0
Reading https://pypi.org/simple/scipy/
Downloading https://files.pythonhosted.org/packages/cb/97/361c8c6ceb3eb765371a702ea873ff2fe112fa40073e7d2b8199db8eb56e/scipy-1.3.0.tar.gz#sha256=c3bb4bd2aca82fb498247deeac12265921fe231502a6bc6edea3ee7fe6c40a7a
Best match: scipy 1.3.0
Processing scipy-1.3.0.tar.gz
Writing C:\Users\LENOVO\AppData\Local\Temp\easy_install-jlmou2fo\scipy-1.3.0\setup.cfg
Running scipy-1.3.0\setup.py -q bdist_egg --dist-dir C:\Users\LENOVO\AppData\Local\Temp\easy_install-jlmou2fo\scipy-1.3.0\egg-dist-tmp-7lc6gnll
C:\Users\LENOVO\AppData\Local\Temp\easy_install-jlmou2fo\scipy-1.3.0\setup.py:111: DeprecationWarning: the imp module is deprecated in favour of importlib; see the module's documentation for alternative uses
  import imp
C:\Users\LENOVO\AppData\Local\Temp\easy_install-jlmou2fo\scipy-1.3.0\setup.py:386: UserWarning: Unrecognized setuptools command ('-q bdist_egg --dist-dir C:\Users\LENOVO\AppData\Local\Temp\easy_install-jlmou2fo\scipy-1.3.0\egg-dist-tmp-7lc6gnll'), proceeding with g
enerating Cython sources and expanding templates
  warnings.warn("Unrecognized setuptools command ('{}'), proceeding with "
Running from scipy source directory.
Could not locate executable g77
Could not locate executable f77
Could not locate executable ifort
Could not locate executable ifl
Could not locate executable f90
Could not locate executable DF
Could not locate executable efl
Could not locate executable gfortran
Could not locate executable f95
Could not locate executable g95
Could not locate executable efort
Could not locate executable efc
Could not locate executable flang
don't know how to compile Fortran code on platform 'nt'
C:\Users\LENOVO\Desktop\deepASL-master\CellBox\env\lib\site-packages\numpy\distutils\system_info.py:1748: UserWarning:
    Lapack (http://www.netlib.org/lapack/) libraries not found.
    Directories to search for the libraries can be specified in the
    numpy/distutils/site.cfg file (section [lapack]) or by setting
    the LAPACK environment variable.
  return getattr(self, '_calc_info_{}'.format(name))()
C:\Users\LENOVO\Desktop\deepASL-master\CellBox\env\lib\site-packages\numpy\distutils\system_info.py:1748: UserWarning:
    Lapack (http://www.netlib.org/lapack/) sources not found.
    Directories to search for the sources can be specified in the
    numpy/distutils/site.cfg file (section [lapack_src]) or by setting
    the LAPACK_SRC environment variable.
  return getattr(self, '_calc_info_{}'.format(name))()
error: No lapack/blas resources found.
DesmondYuan commented 3 years ago

Thanks! @cannin and I think the problem is likely related to Windows system, which is not something we are actively maintaining at present. You might want to try i) pipenv installation or ii) a UNIX environment.

@judyueshen has more experience with pipenv, could you please help @Debanitrkl out?

Debanitrkl commented 3 years ago

@DesmondYuan , yes I'm dual booting my system and will shift to UNIX and try it out

judyueshen commented 3 years ago

@Debanitrkl Thanks for reporting the issue! For the pipenv option, give this a try, and it should work.

Pipfile.txt

Debanitrkl commented 3 years ago

@judyueshen I'm getting this error while trying to install pipenv


(env) C:\Users\LENOVO\Desktop\deepASL-master\CellBox>pipenv --python 3.6 install
Courtesy Notice: Pipenv found itself running within a virtual environment, so it will automatically use that environment, instead of creating its own for any project. You can set PIPENV_IGNORE_VIRTUALENVS=1 to force pipenv to ignore that environment and create its
own instead. You can set PIPENV_VERBOSITY=-1 to suppress this warning.
Pipfile.lock not found, creating...
Locking [dev-packages] dependencies...
 Locking...Building requirements...
Resolving dependencies...
Success!
Locking [packages] dependencies...
 Locking...Building requirements...
Resolving dependencies...
Locking Failed!
CRITICAL:pipenv.patched.notpip._internal.index.package_finder:Could not find a version that satisfies the requirement tensorflow==1.15.0 (from -r C:\Users\LENOVO\AppData\Local\Temp\pipenvfqhhlkt9requirements\pipenv-cvlsxc6u-constraints.txt (line 3)) (from versions:
 2.2.0rc1, 2.2.0rc2, 2.2.0rc3, 2.2.0rc4, 2.2.0, 2.2.1, 2.2.2, 2.3.0rc0, 2.3.0rc1, 2.3.0rc2, 2.3.0, 2.3.1, 2.3.2, 2.4.0rc0, 2.4.0rc1, 2.4.0rc2, 2.4.0rc3, 2.4.0rc4, 2.4.0, 2.4.1)
[ResolutionFailure]:   File "c:/users/lenovo/desktop/deepasl-master/cellbox/env/lib/site-packages/pipenv/resolver.py", line 741, in _main
[ResolutionFailure]:       resolve_packages(pre, clear, verbose, system, write, requirements_dir, packages, dev)
[ResolutionFailure]:   File "c:/users/lenovo/desktop/deepasl-master/cellbox/env/lib/site-packages/pipenv/resolver.py", line 702, in resolve_packages
[ResolutionFailure]:       results, resolver = resolve(
[ResolutionFailure]:   File "c:/users/lenovo/desktop/deepasl-master/cellbox/env/lib/site-packages/pipenv/resolver.py", line 684, in resolve
[ResolutionFailure]:       return resolve_deps(
[ResolutionFailure]:   File "c:\users\lenovo\desktop\deepasl-master\cellbox\env\lib\site-packages\pipenv\utils.py", line 1395, in resolve_deps
[ResolutionFailure]:       results, hashes, markers_lookup, resolver, skipped = actually_resolve_deps(
[ResolutionFailure]:   File "c:\users\lenovo\desktop\deepasl-master\cellbox\env\lib\site-packages\pipenv\utils.py", line 1108, in actually_resolve_deps
[ResolutionFailure]:       resolver.resolve()
[ResolutionFailure]:   File "c:\users\lenovo\desktop\deepasl-master\cellbox\env\lib\site-packages\pipenv\utils.py", line 833, in resolve
[ResolutionFailure]:       raise ResolutionFailure(message=str(e))
[pipenv.exceptions.ResolutionFailure]: Warning: Your dependencies could not be resolved. You likely have a mismatch in your sub-dependencies.
  First try clearing your dependency cache with $ pipenv lock --clear, then try the original command again.
 Alternatively, you can use $ pipenv install --skip-lock to bypass this mechanism, then run $ pipenv graph to inspect the situation.
  Hint: try $ pipenv lock --pre if it is a pre-release dependency.
ERROR: No matching distribution found for tensorflow==1.15.0 (from -r C:\Users\LENOVO\AppData\Local\Temp\pipenvfqhhlkt9requirements\pipenv-cvlsxc6u-constraints.txt (line 3))
Debanitrkl commented 3 years ago

And when I'm trying to clear the env, this error shows up

(env) C:\Users\LENOVO\Desktop\deepASL-master\CellBox>pipenv lock --clear
Courtesy Notice: Pipenv found itself running within a virtual environment, so it will automatically use that environment, instead of creating its own for any project. You can set PIPENV_IGNORE_VIRTUALENVS=1 to force pipenv to ignore that environment and create its
own instead. You can set PIPENV_VERBOSITY=-1 to suppress this warning.
Locking [dev-packages] dependencies...
 Locking...Building requirements...
Resolving dependencies...
Success!
Locking [packages] dependencies...
 Locking...Building requirements...
Resolving dependencies...
Locking Failed!
ERROR:pip.subprocessor:Command errored out with exit status 1:
 command: 'C:\Users\LENOVO\Desktop\deepASL-master\CellBox\env\Scripts\python.exe' 'C:\Users\LENOVO\Desktop\deepASL-master\CellBox\env\lib\site-packages\pipenv\patched\notpip' install --ignore-installed --no-user --prefix 'C:\Users\LENOVO\AppData\Local\Temp\pip-buil
d-env-l5nngsp0\overlay' --no-warn-script-location --no-binary :none: --only-binary :none: -i https://pypi.org/simple -- wheel setuptools 'Cython>=0.29.2' 'numpy==1.13.3; python_version=='"'"'3.5'"'"'' 'numpy==1.13.3; python_version=='"'"'3.6'"'"'' 'numpy==1.14.5; p
ython_version>='"'"'3.7'"'"''
     cwd: None
Complete output (269 lines):
Ignoring numpy: markers 'python_version == "3.5"' don't match your environment
Ignoring numpy: markers 'python_version == "3.6"' don't match your environment
Collecting wheel
  Using cached wheel-0.36.2-py2.py3-none-any.whl (35 kB)
Collecting setuptools
  Using cached setuptools-53.0.0-py3-none-any.whl (784 kB)
Collecting Cython>=0.29.2
  Using cached Cython-0.29.21-cp38-cp38-win_amd64.whl (1.7 MB)
Collecting numpy==1.14.5
  Using cached numpy-1.14.5.zip (4.9 MB)
Installing collected packages: wheel, setuptools, Cython, numpy
  Creating C:\Users\LENOVO\AppData\Local\Temp\pip-build-env-l5nngsp0\overlay\Scripts
    Running setup.py install for numpy: started
    Running setup.py install for numpy: finished with status 'error'
    ERROR: Command errored out with exit status 1:
     command: 'C:\Users\LENOVO\Desktop\deepASL-master\CellBox\env\Scripts\python.exe' -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'C:\\Users\\LENOVO\\AppData\\Local\\Temp\\pip-install-st35bpk9\\numpy\\setup.py'"'"'; __file__='"'"'C:\\Users\\LENOVO\\A
ppData\\Local\\Temp\\pip-install-st35bpk9\\numpy\\setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record 'C:\Users\LENOVO\AppDat
a\Local\Temp\pip-record-hxsm4o8r\install-record.txt' --single-version-externally-managed --prefix 'C:\Users\LENOVO\AppData\Local\Temp\pip-build-env-l5nngsp0\overlay' --compile --install-headers 'C:\Users\LENOVO\Desktop\deepASL-master\CellBox\env\include\site\python
3.8\numpy'
         cwd: C:\Users\LENOVO\AppData\Local\Temp\pip-install-st35bpk9\numpy\
    Complete output (249 lines):
    Running from numpy source directory.

    Note: if you need reliable uninstall behavior, then install
    with pip instead of using `setup.py install`:

      - `pip install .`       (from a git repo or downloaded source
                               release)
      - `pip install numpy`   (last NumPy release on PyPi)

    C:\Users\LENOVO\AppData\Local\Temp\pip-install-st35bpk9\numpy\numpy\distutils\misc_util.py:464: SyntaxWarning: "is" with a literal. Did you mean "=="?
      return is_string(s) and ('*' in s or '?' is s)
    blas_opt_info:
    blas_mkl_info:
    No module named 'numpy.distutils._msvccompiler' in numpy.distutils; trying from distutils
    customize MSVCCompiler
      libraries mkl_rt not found in ['C:\\Users\\LENOVO\\Desktop\\deepASL-master\\CellBox\\env\\lib', 'C:\\']
      NOT AVAILABLE

    blis_info:
    No module named 'numpy.distutils._msvccompiler' in numpy.distutils; trying from distutils
    customize MSVCCompiler
      libraries blis not found in ['C:\\Users\\LENOVO\\Desktop\\deepASL-master\\CellBox\\env\\lib', 'C:\\']
      NOT AVAILABLE

    openblas_info:
    No module named 'numpy.distutils._msvccompiler' in numpy.distutils; trying from distutils
    customize MSVCCompiler
    No module named 'numpy.distutils._msvccompiler' in numpy.distutils; trying from distutils
    customize MSVCCompiler
      libraries openblas not found in ['C:\\Users\\LENOVO\\Desktop\\deepASL-master\\CellBox\\env\\lib', 'C:\\']
    get_default_fcompiler: matching types: '['gnu', 'intelv', 'absoft', 'compaqv', 'intelev', 'gnu95', 'g95', 'intelvem', 'intelem', 'flang']'
    customize GnuFCompiler
    Could not locate executable g77
    Could not locate executable f77
    customize IntelVisualFCompiler
    Could not locate executable ifort
    Could not locate executable ifl
    customize AbsoftFCompiler
    Could not locate executable f90
    customize CompaqVisualFCompiler
    Could not locate executable DF
    customize IntelItaniumVisualFCompiler
    Could not locate executable efl
    customize Gnu95FCompiler
    Could not locate executable gfortran
    Could not locate executable f95
    customize G95FCompiler
    Could not locate executable g95
    customize IntelEM64VisualFCompiler
    customize IntelEM64TFCompiler
    Could not locate executable efort
    Could not locate executable efc
    customize PGroupFlangCompiler
    Could not locate executable flang
    don't know how to compile Fortran code on platform 'nt'
      NOT AVAILABLE

    atlas_3_10_blas_threads_info:
    Setting PTATLAS=ATLAS
    No module named 'numpy.distutils._msvccompiler' in numpy.distutils; trying from distutils
    customize MSVCCompiler
      libraries tatlas not found in ['C:\\Users\\LENOVO\\Desktop\\deepASL-master\\CellBox\\env\\lib', 'C:\\']
      NOT AVAILABLE

    atlas_3_10_blas_info:
    No module named 'numpy.distutils._msvccompiler' in numpy.distutils; trying from distutils
    customize MSVCCompiler
      libraries satlas not found in ['C:\\Users\\LENOVO\\Desktop\\deepASL-master\\CellBox\\env\\lib', 'C:\\']
      NOT AVAILABLE

    atlas_blas_threads_info:
    Setting PTATLAS=ATLAS
    No module named 'numpy.distutils._msvccompiler' in numpy.distutils; trying from distutils
    customize MSVCCompiler
      libraries ptf77blas,ptcblas,atlas not found in ['C:\\Users\\LENOVO\\Desktop\\deepASL-master\\CellBox\\env\\lib', 'C:\\']
      NOT AVAILABLE

    atlas_blas_info:
    No module named 'numpy.distutils._msvccompiler' in numpy.distutils; trying from distutils
    customize MSVCCompiler
      libraries f77blas,cblas,atlas not found in ['C:\\Users\\LENOVO\\Desktop\\deepASL-master\\CellBox\\env\\lib', 'C:\\']
      NOT AVAILABLE

    C:\Users\LENOVO\AppData\Local\Temp\pip-install-st35bpk9\numpy\numpy\distutils\system_info.py:624: UserWarning:
        Atlas (http://math-atlas.sourceforge.net/) libraries not found.
        Directories to search for the libraries can be specified in the
        numpy/distutils/site.cfg file (section [atlas]) or by setting
        the ATLAS environment variable.
      self.calc_info()
    blas_info:
    No module named 'numpy.distutils._msvccompiler' in numpy.distutils; trying from distutils
    customize MSVCCompiler
      libraries blas not found in ['C:\\Users\\LENOVO\\Desktop\\deepASL-master\\CellBox\\env\\lib', 'C:\\']
      NOT AVAILABLE

    C:\Users\LENOVO\AppData\Local\Temp\pip-install-st35bpk9\numpy\numpy\distutils\system_info.py:624: UserWarning:
        Blas (http://www.netlib.org/blas/) libraries not found.
        Directories to search for the libraries can be specified in the
        numpy/distutils/site.cfg file (section [blas]) or by setting
        the BLAS environment variable.
      self.calc_info()
    blas_src_info:
      NOT AVAILABLE

    C:\Users\LENOVO\AppData\Local\Temp\pip-install-st35bpk9\numpy\numpy\distutils\system_info.py:624: UserWarning:
        Blas (http://www.netlib.org/blas/) sources not found.
        Directories to search for the sources can be specified in the
        numpy/distutils/site.cfg file (section [blas_src]) or by setting
        the BLAS_SRC environment variable.
      self.calc_info()
      NOT AVAILABLE

    'svnversion' is not recognized as an internal or external command,
    operable program or batch file.
    non-existing path in 'numpy\\distutils': 'site.cfg'
    'svnversion' is not recognized as an internal or external command,
    operable program or batch file.
    F2PY Version 2
    lapack_opt_info:
    lapack_mkl_info:
    No module named 'numpy.distutils._msvccompiler' in numpy.distutils; trying from distutils
    customize MSVCCompiler
      libraries mkl_rt not found in ['C:\\Users\\LENOVO\\Desktop\\deepASL-master\\CellBox\\env\\lib', 'C:\\']
      NOT AVAILABLE

    openblas_lapack_info:
    No module named 'numpy.distutils._msvccompiler' in numpy.distutils; trying from distutils
    customize MSVCCompiler
    No module named 'numpy.distutils._msvccompiler' in numpy.distutils; trying from distutils
    customize MSVCCompiler
      libraries openblas not found in ['C:\\Users\\LENOVO\\Desktop\\deepASL-master\\CellBox\\env\\lib', 'C:\\']
      NOT AVAILABLE

    openblas_clapack_info:
    No module named 'numpy.distutils._msvccompiler' in numpy.distutils; trying from distutils
    customize MSVCCompiler
    No module named 'numpy.distutils._msvccompiler' in numpy.distutils; trying from distutils
    customize MSVCCompiler
      libraries openblas,lapack not found in ['C:\\Users\\LENOVO\\Desktop\\deepASL-master\\CellBox\\env\\lib', 'C:\\']
      NOT AVAILABLE

    atlas_3_10_threads_info:
    Setting PTATLAS=ATLAS
    No module named 'numpy.distutils._msvccompiler' in numpy.distutils; trying from distutils
    customize MSVCCompiler
      libraries tatlas,tatlas not found in C:\Users\LENOVO\Desktop\deepASL-master\CellBox\env\lib
    No module named 'numpy.distutils._msvccompiler' in numpy.distutils; trying from distutils
    customize MSVCCompiler
      libraries lapack_atlas not found in C:\Users\LENOVO\Desktop\deepASL-master\CellBox\env\lib
    No module named 'numpy.distutils._msvccompiler' in numpy.distutils; trying from distutils
    customize MSVCCompiler
      libraries tatlas,tatlas not found in C:\
    No module named 'numpy.distutils._msvccompiler' in numpy.distutils; trying from distutils
    customize MSVCCompiler
      libraries lapack_atlas not found in C:\
    <class 'numpy.distutils.system_info.atlas_3_10_threads_info'>
      NOT AVAILABLE

    atlas_3_10_info:
    No module named 'numpy.distutils._msvccompiler' in numpy.distutils; trying from distutils
    customize MSVCCompiler
      libraries satlas,satlas not found in C:\Users\LENOVO\Desktop\deepASL-master\CellBox\env\lib
    No module named 'numpy.distutils._msvccompiler' in numpy.distutils; trying from distutils
    customize MSVCCompiler
      libraries lapack_atlas not found in C:\Users\LENOVO\Desktop\deepASL-master\CellBox\env\lib
    No module named 'numpy.distutils._msvccompiler' in numpy.distutils; trying from distutils
    customize MSVCCompiler
      libraries satlas,satlas not found in C:\
    No module named 'numpy.distutils._msvccompiler' in numpy.distutils; trying from distutils
    customize MSVCCompiler
      libraries lapack_atlas not found in C:\
    <class 'numpy.distutils.system_info.atlas_3_10_info'>
      NOT AVAILABLE

    atlas_threads_info:
    Setting PTATLAS=ATLAS
    No module named 'numpy.distutils._msvccompiler' in numpy.distutils; trying from distutils
    customize MSVCCompiler
      libraries ptf77blas,ptcblas,atlas not found in C:\Users\LENOVO\Desktop\deepASL-master\CellBox\env\lib
    No module named 'numpy.distutils._msvccompiler' in numpy.distutils; trying from distutils
    customize MSVCCompiler
      libraries lapack_atlas not found in C:\Users\LENOVO\Desktop\deepASL-master\CellBox\env\lib
    No module named 'numpy.distutils._msvccompiler' in numpy.distutils; trying from distutils
    customize MSVCCompiler
      libraries ptf77blas,ptcblas,atlas not found in C:\
    No module named 'numpy.distutils._msvccompiler' in numpy.distutils; trying from distutils
    customize MSVCCompiler
      libraries lapack_atlas not found in C:\
    <class 'numpy.distutils.system_info.atlas_threads_info'>
      NOT AVAILABLE

    atlas_info:
    No module named 'numpy.distutils._msvccompiler' in numpy.distutils; trying from distutils
    customize MSVCCompiler
      libraries f77blas,cblas,atlas not found in C:\Users\LENOVO\Desktop\deepASL-master\CellBox\env\lib
    No module named 'numpy.distutils._msvccompiler' in numpy.distutils; trying from distutils
    customize MSVCCompiler
      libraries lapack_atlas not found in C:\Users\LENOVO\Desktop\deepASL-master\CellBox\env\lib
    No module named 'numpy.distutils._msvccompiler' in numpy.distutils; trying from distutils
    customize MSVCCompiler
      libraries f77blas,cblas,atlas not found in C:\
    No module named 'numpy.distutils._msvccompiler' in numpy.distutils; trying from distutils
    customize MSVCCompiler
      libraries lapack_atlas not found in C:\
    <class 'numpy.distutils.system_info.atlas_info'>
      NOT AVAILABLE

    lapack_info:
    No module named 'numpy.distutils._msvccompiler' in numpy.distutils; trying from distutils
    customize MSVCCompiler
      libraries lapack not found in ['C:\\Users\\LENOVO\\Desktop\\deepASL-master\\CellBox\\env\\lib', 'C:\\']
      NOT AVAILABLE

    C:\Users\LENOVO\AppData\Local\Temp\pip-install-st35bpk9\numpy\numpy\distutils\system_info.py:624: UserWarning:
        Lapack (http://www.netlib.org/lapack/) libraries not found.
        Directories to search for the libraries can be specified in the
        numpy/distutils/site.cfg file (section [lapack]) or by setting
        the LAPACK environment variable.
      self.calc_info()
    lapack_src_info:
      NOT AVAILABLE

    C:\Users\LENOVO\AppData\Local\Temp\pip-install-st35bpk9\numpy\numpy\distutils\system_info.py:624: UserWarning:
        Lapack (http://www.netlib.org/lapack/) sources not found.
        Directories to search for the sources can be specified in the
        numpy/distutils/site.cfg file (section [lapack_src]) or by setting
        the LAPACK_SRC environment variable.
      self.calc_info()
      NOT AVAILABLE

    C:\Python38\lib\distutils\dist.py:274: UserWarning: Unknown distribution option: 'define_macros'
      warnings.warn(msg)
    running install
    running build
    running config_cc
    unifing config_cc, config, build_clib, build_ext, build commands --compiler options
    running config_fc
    unifing config_fc, config, build_clib, build_ext, build commands --fcompiler options
    running build_src
    build_src
    building py_modules sources
    creating build
    creating build\src.win-amd64-3.8
    creating build\src.win-amd64-3.8\numpy
    creating build\src.win-amd64-3.8\numpy\distutils
    building library "npymath" sources
    No module named 'numpy.distutils._msvccompiler' in numpy.distutils; trying from distutils
    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: 'C:\Users\LENOVO\Desktop\deepASL-master\CellBox\env\Scripts\python.exe' -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'C:\\Users\\LENOVO\\AppData\\Local\\Temp\\pip-install-st35bpk9\\numpy\\setup.py'"'"'; _
_file__='"'"'C:\\Users\\LENOVO\\AppData\\Local\\Temp\\pip-install-st35bpk9\\numpy\\setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install
 --record 'C:\Users\LENOVO\AppData\Local\Temp\pip-record-hxsm4o8r\install-record.txt' --single-version-externally-managed --prefix 'C:\Users\LENOVO\AppData\Local\Temp\pip-build-env-l5nngsp0\overlay' --compile --install-headers 'C:\Users\LENOVO\Desktop\deepASL-maste
r\CellBox\env\include\site\python3.8\numpy' Check the logs for full command output.
----------------------------------------
Traceback (most recent call last):
  File "c:/users/lenovo/desktop/deepasl-master/cellbox/env/lib/site-packages/pipenv/resolver.py", line 764, in <module>
    main()
  File "c:/users/lenovo/desktop/deepasl-master/cellbox/env/lib/site-packages/pipenv/resolver.py", line 758, in main
    _main(parsed.pre, parsed.clear, parsed.verbose, parsed.system, parsed.write,
  File "c:/users/lenovo/desktop/deepasl-master/cellbox/env/lib/site-packages/pipenv/resolver.py", line 741, in _main
    resolve_packages(pre, clear, verbose, system, write, requirements_dir, packages, dev)
  File "c:/users/lenovo/desktop/deepasl-master/cellbox/env/lib/site-packages/pipenv/resolver.py", line 702, in resolve_packages
    results, resolver = resolve(
  File "c:/users/lenovo/desktop/deepasl-master/cellbox/env/lib/site-packages/pipenv/resolver.py", line 684, in resolve
    return resolve_deps(
  File "C:\Users\LENOVO\Desktop\deepASL-master\CellBox\env\lib\site-packages\pipenv\utils.py", line 1395, in resolve_deps
    results, hashes, markers_lookup, resolver, skipped = actually_resolve_deps(
  File "C:\Users\LENOVO\Desktop\deepASL-master\CellBox\env\lib\site-packages\pipenv\utils.py", line 1108, in actually_resolve_deps
    resolver.resolve()
  File "C:\Users\LENOVO\Desktop\deepASL-master\CellBox\env\lib\site-packages\pipenv\utils.py", line 823, in resolve
    results = self.resolver.resolve(max_rounds=environments.PIPENV_MAX_ROUNDS)
  File "C:\Users\LENOVO\Desktop\deepASL-master\CellBox\env\lib\site-packages\pipenv\patched\piptools\resolver.py", line 180, in resolve
    has_changed, best_matches = self._resolve_one_round()
  File "C:\Users\LENOVO\Desktop\deepASL-master\CellBox\env\lib\site-packages\pipenv\patched\piptools\resolver.py", line 268, in _resolve_one_round
    their_constraints.extend(self._iter_dependencies(best_match))
  File "C:\Users\LENOVO\Desktop\deepASL-master\CellBox\env\lib\site-packages\pipenv\patched\piptools\resolver.py", line 383, in _iter_dependencies
    dependencies = self.repository.get_dependencies(ireq)
  File "C:\Users\LENOVO\Desktop\deepASL-master\CellBox\env\lib\site-packages\pipenv\patched\piptools\repositories\pypi.py", line 229, in get_dependencies
    legacy_results = self.get_legacy_dependencies(ireq)
  File "C:\Users\LENOVO\Desktop\deepASL-master\CellBox\env\lib\site-packages\pipenv\patched\piptools\repositories\pypi.py", line 350, in get_legacy_dependencies
    results, ireq = self.resolve_reqs(
  File "C:\Users\LENOVO\Desktop\deepASL-master\CellBox\env\lib\site-packages\pipenv\patched\piptools\repositories\pypi.py", line 306, in resolve_reqs
    results = resolver._resolve_one(reqset, ireq)
  File "C:\Users\LENOVO\Desktop\deepASL-master\CellBox\env\lib\site-packages\pipenv\patched\notpip\_internal\legacy_resolve.py", line 339, in _resolve_one
    abstract_dist = self._get_abstract_dist_for(req_to_install)
  File "C:\Users\LENOVO\Desktop\deepASL-master\CellBox\env\lib\site-packages\pipenv\patched\notpip\_internal\legacy_resolve.py", line 287, in _get_abstract_dist_for
    abstract_dist = self.preparer.prepare_linked_requirement(req)
  File "C:\Users\LENOVO\Desktop\deepASL-master\CellBox\env\lib\site-packages\pipenv\patched\notpip\_internal\operations\prepare.py", line 508, in prepare_linked_requirement
    abstract_dist = _get_prepared_distribution(
  File "C:\Users\LENOVO\Desktop\deepASL-master\CellBox\env\lib\site-packages\pipenv\patched\notpip\_internal\operations\prepare.py", line 95, in _get_prepared_distribution
    abstract_dist.prepare_distribution_metadata(finder, build_isolation)
  File "C:\Users\LENOVO\Desktop\deepASL-master\CellBox\env\lib\site-packages\pipenv\patched\notpip\_internal\distributions\sdist.py", line 38, in prepare_distribution_metadata
    self._setup_isolation(finder)
  File "C:\Users\LENOVO\Desktop\deepASL-master\CellBox\env\lib\site-packages\pipenv\patched\notpip\_internal\distributions\sdist.py", line 66, in _setup_isolation
    self.req.build_env.install_requirements(
  File "C:\Users\LENOVO\Desktop\deepASL-master\CellBox\env\lib\site-packages\pipenv\patched\notpip\_internal\build_env.py", line 202, in install_requirements
    call_subprocess(args, spinner=spinner)
  File "C:\Users\LENOVO\Desktop\deepASL-master\CellBox\env\lib\site-packages\pipenv\patched\notpip\_internal\utils\subprocess.py", line 242, in call_subprocess
    raise InstallationError(exc_msg)
pipenv.patched.notpip._internal.exceptions.InstallationError: Command errored out with exit status 1: 'C:\Users\LENOVO\Desktop\deepASL-master\CellBox\env\Scripts\python.exe' 'C:\Users\LENOVO\Desktop\deepASL-master\CellBox\env\lib\site-packages\pipenv\patched\notpip
' install --ignore-installed --no-user --prefix 'C:\Users\LENOVO\AppData\Local\Temp\pip-build-env-l5nngsp0\overlay' --no-warn-script-location --no-binary :none: --only-binary :none: -i https://pypi.org/simple -- wheel setuptools 'Cython>=0.29.2' 'numpy==1.13.3; pyt
hon_version=='"'"'3.5'"'"'' 'numpy==1.13.3; python_version=='"'"'3.6'"'"'' 'numpy==1.14.5; python_version>='"'"'3.7'"'"'' Check the logs for full command output.
judyueshen commented 3 years ago

It seems like you're using pyenv at the same time. Can you maybe try the pipenv process without the env virtual environment? Alternatively, go to this webpage, https://towardsdatascience.com/python-environment-101-1d68bda3094d, try following the instruction under the section "pipenv and pyenv virtual conflict".

If you still get errors, could you please let me know the output when you give the following commands? Thanks! where python if you have multiple version of python, where python3.6 where pip where pipenv

Debanitrkl commented 3 years ago

@judyueshen thanks! It worked. I think we can close this issue now