Trouble installing scikit-bio on Windows

3.4k views Asked by At

When attempting to install the scikit-bio toolkit via pip on Windows XP using Python 2.78 and Visual C++ 2008 Express Edition, the process is interrupted with the following message issued by VC:

cl : Command line error D8021 : invalid numeric argument '/Wno-error=declaration
-after-statement' 

Concerning this error, Microsoft Developer Network website just says:

invalid numeric argument 'number'

A number greater than 65,534 was specified as a numeric argument.

I did not (yet) attempted to install scikit-bio under Linux (Ubuntu 12.04 Precise), but I am under the impression that it will work fine (as everything goes as regards Linux).

Has anyone ever succeeded installing scikit-bio under Windows (XP, 7, 8)? Any hints?

Thanks in advance!

2

There are 2 answers

0
gregcaporaso On

At this time, scikit-bio doesn't officially support windows. We'd definitely be interested in hearing about people's efforts to install, test, and use scikit-bio on Windows, but we don't have developers with expertise in this area.

This is related to biocore/skbio#941.

2
Guillermo Luque On

I've installed Anaconda's Python (3.5) on a Windows 10 machine. As you should know, there is no official version of scikit-bio for this platform, but you can install it with this workaround:

  1. Download the latest source from the Scikit-bio Github repository.
  2. Using a tool like 7-zip, unzip it at your home directory.
  3. Open a command line client and change to the source's directory

    cd %HOMEPATH%\scikit-bio-master
    
  4. Using Notepad++ edit the file setup.py

    "C:\Program Files (x86)\Notepad++\notepad++" setup.py
    
  5. Look for the line where the ssw_extra_compile_args variable is defined and change it. You can comment the previous version and redefine the variable in a new line:

    #ssw_extra_compile_args = ['-Wno-error=declaration-after-statement']
    ssw_extra_compile_args = []
    
  6. Save the changes, close the editor and run the installation with this command:

    python setup.py install
    
  7. Hopefully you won't receive any error messages. Open an Anaconda's Python session (using the command python) and test if Scikit-Bio was installed rightly using print(skbio.art).

Scikit-Bio on Windows 10

By the way, I've previously installed Visual Studio 2015 Community Edition with C++ SDK features enabled, in order to meet the compiler requirements for the package (Scikit-Bio) installation.