search

caporaso-lab / tax-credit

A repository for storing code and data related to a systematic comparison of short read taxonomy assignment tools
BSD 3-Clause "New" or "Revised" License
16 stars 8 forks source link

Issue with pip install #151

Open willowsblade opened 5 years ago

willowsblade commented 5 years ago

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 commented 5 years ago

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.