Issue with pip install

[willowsblade]

Hi,

I'm trying to get the Jupyter Notebook set up on a windows10 computer. I start in Git Bash, and am able to download the repository using git clone https://github.com/caporaso-lab/tax-credit and enter into the directory. All files appear to be present and correct.

However, when I run pip install . I run into an error message that ends with:
error: Microsoft Visual C++ 14.0 is required. Get it with "Microsoft Visual C++ Build Tools": https://visualstudio.microsoft.com/downloads/

----------------------------------------

Command "c:\users\dhtaft\appdata\local\programs\python\python37\python.exe -u -c "import setuptools, tokenize;file='C:\Users\dhtaft\AppData\Local\Temp\pip-install-ju6h6plq\biom-format\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\dhtaft\AppData\Local\Temp\pip-record-1fv6ujlf\install-record.txt --single-version-externally-managed --compile" failed with error code 1 in C:\Users\dhtaft\AppData\Local\Temp\pip-install-ju6h6plq\biom-format\

and the compiling fails. I do have Visual Studio 2019 installed, along with the python development tools. Are there additional modules in Visual Studio that should be installed? I get a similar error message when trying to run the setup.py file with python setup.py install --user, but the total message is much shorter:

$ python setup.py install --user
running install
running bdist_egg
running egg_info
creating tax_credit.egg-info
writing tax_credit.egg-info\PKG-INFO
writing dependency_links to tax_credit.egg-info\dependency_links.txt
writing requirements to tax_credit.egg-info\requires.txt
writing top-level names to tax_credit.egg-info\top_level.txt
writing manifest file 'tax_credit.egg-info\SOURCES.txt'
reading manifest file 'tax_credit.egg-info\SOURCES.txt'
writing manifest file 'tax_credit.egg-info\SOURCES.txt'
installing library code to build\bdist.win-amd64\egg
running install_lib
C:\Users\dhtaft\AppData\Local\Programs\Python\Python37\lib\site-packages\setuptools\dist.py:472: UserWarning: Normalizing '0.0.0-dev' to '0.0.0.dev0'
normalized_version,
warning: install_lib: 'build\lib' does not exist -- no Python modules to install

creating build
creating build\bdist.win-amd64
creating build\bdist.win-amd64\egg
creating build\bdist.win-amd64\egg\EGG-INFO
copying tax_credit.egg-info\PKG-INFO -> build\bdist.win-amd64\egg\EGG-INFO
copying tax_credit.egg-info\SOURCES.txt -> build\bdist.win-amd64\egg\EGG-INFO
copying tax_credit.egg-info\dependency_links.txt -> build\bdist.win-amd64\egg\EGG-INFO
copying tax_credit.egg-info\requires.txt -> build\bdist.win-amd64\egg\EGG-INFO
copying tax_credit.egg-info\top_level.txt -> build\bdist.win-amd64\egg\EGG-INFO
zip_safe flag not set; analyzing archive contents...
creating dist
creating 'dist\tax_credit-0.0.0.dev0-py3.7.egg' and adding 'build\bdist.win-amd64\egg' to it
removing 'build\bdist.win-amd64\egg' (and everything under it)
Processing tax_credit-0.0.0.dev0-py3.7.egg
Copying tax_credit-0.0.0.dev0-py3.7.egg to c:\users\dhtaft\appdata\roaming\python\python37\site-packages
Adding tax-credit 0.0.0.dev0 to easy-install.pth file

Installed c:\users\dhtaft\appdata\roaming\python\python37\site-packages\tax_credit-0.0.0.dev0-py3.7.egg
Processing dependencies for tax-credit==0.0.0.dev0
Searching for joblib
Reading https://pypi.org/simple/joblib/
Downloading https://files.pythonhosted.org/packages/cd/c1/50a758e8247561e58cb87305b1e90b171b8c767b15b12a1734001f41d356/joblib-0.13.2-py2.py3-none-any.whl#sha256=21e0c34a69ad7fde4f2b1f3402290e9ec46f545f15f1541c582edfe05d87b63a
Best match: joblib 0.13.2
Processing joblib-0.13.2-py2.py3-none-any.whl
Installing joblib-0.13.2-py2.py3-none-any.whl to c:\users\dhtaft\appdata\roaming\python\python37\site-packages
Adding joblib 0.13.2 to easy-install.pth file

Installed c:\users\dhtaft\appdata\roaming\python\python37\site-packages\joblib-0.13.2-py3.7.egg
Searching for scikit-learn
Reading https://pypi.org/simple/scikit-learn/
Downloading https://files.pythonhosted.org/packages/47/a6/5cfab2684c3da61dece651796aefb2542a1970a8ba9b9efee4f730ccd90b/scikit_learn-0.20.3-cp37-cp37m-win_amd64.whl#sha256=0ae00d570331b8a5c552f721167818b4739a5c855fbc76b11231ccdea2dd26ab
Best match: scikit-learn 0.20.3
Processing scikit_learn-0.20.3-cp37-cp37m-win_amd64.whl
Installing scikit_learn-0.20.3-cp37-cp37m-win_amd64.whl to c:\users\dhtaft\appdata\roaming\python\python37\site-packages
writing requirements to c:\users\dhtaft\appdata\roaming\python\python37\site-packages\scikit_learn-0.20.3-py3.7-win-amd64.egg\EGG-INFO\requires.txt
Adding scikit-learn 0.20.3 to easy-install.pth file

Installed c:\users\dhtaft\appdata\roaming\python\python37\site-packages\scikit_learn-0.20.3-py3.7-win-amd64.egg
Searching for seaborn
Reading https://pypi.org/simple/seaborn/
Downloading https://files.pythonhosted.org/packages/a8/76/220ba4420459d9c4c9c9587c6ce607bf56c25b3d3d2de62056efe482dadc/seaborn-0.9.0-py3-none-any.whl#sha256=42e627b24e849c2d3bbfd059e00005f6afbc4a76e4895baf44ae23fe8a4b09a5
Best match: seaborn 0.9.0
Processing seaborn-0.9.0-py3-none-any.whl
Installing seaborn-0.9.0-py3-none-any.whl to c:\users\dhtaft\appdata\roaming\python\python37\site-packages
writing requirements to c:\users\dhtaft\appdata\roaming\python\python37\site-packages\seaborn-0.9.0-py3.7.egg\EGG-INFO\requires.txt
Adding seaborn 0.9.0 to easy-install.pth file

Installed c:\users\dhtaft\appdata\roaming\python\python37\site-packages\seaborn-0.9.0-py3.7.egg
Searching for scikit-bio
Reading https://pypi.org/simple/scikit-bio/
Downloading https://files.pythonhosted.org/packages/2d/ff/3a909ae8c212305846f7e87f86f3902408b55b958eccedf5d4349e76c671/scikit-bio-0.5.5.tar.gz#sha256=9fa813be66e88a994f7b7a68b8ba2216e205c525caa8585386ebdeebed6428df
Best match: scikit-bio 0.5.5
Processing scikit-bio-0.5.5.tar.gz
Writing C:\Users\dhtaft\AppData\Local\Temp\easy_install-7rsetfye\scikit-bio-0.5.5\setup.cfg
Running scikit-bio-0.5.5\setup.py -q bdist_egg --dist-dir C:\Users\dhtaft\AppData\Local\Temp\easy_install-7rsetfye\scikit-bio-0.5.5\egg-dist-tmp-eepyj_p3
no previously-included directories found matching 'doc\build'
no previously-included directories found matching 'doc\source\generated'
warning: no previously-included files matching '.pyc' found anywhere in distribution
warning: no previously-included files matching '.pyo' found anywhere in distribution
warning: no previously-included files matching '.so' found anywhere in distribution
warning: no previously-included files matching '..swp' found anywhere in distribution
warning: no previously-included files matching '.coverage' found anywhere in distribution
error: Setup script exited with error: Microsoft Visual C++ 14.0 is required. Get it with "Microsoft Visual C++ Build Tools": https://visualstudio.microsoft.com/downloads/

Is there an additional dependency I'm missing?

Thanks

[nbokulich]

Hi @willowsblade ,

and the compiling fails. I do have Visual Studio 2019 installed, along with the python development tools

Do you have the correct version installed? Looks like v. 14.0 is required.

Ultimately, it looks like this is an issue with installing scikit-bio and/or biom-format — tax-credit installed without issue. I recommend trying to install those packages independently and check out their github and/or support sites for more information.

Also: this repo is a bit outdated... we replaced it with tax-credit-code and tax-credit-data to keep those resources separate, and some minor updates have been made to the code and data. Please clone and work from those repositories.