pip install in Cygwin cannot find file error <p>I am on a Mac OS El Capitan, running a Windows 10 64-bit VM inside Parallels. I have Cygwin installed and Anaconda3. I would like to install two packages (pyrsistent and rpy2) using pip. Both of them throw an error "error: [WinError 2] The system cannot find the file specified" without specifying the file it can't find.</p> <p>Here's the output:</p> <pre><code>$ pip install pyrsistent Collecting pyrsistent Using cached pyrsistent-0.11.9.tar.gz Requirement already satisfied (use --upgrade to upgrade): six in c:\anaconda3\lib\site-packages (from pyrsistent) Building wheels for collected packages: pyrsistent Running setup.py bdist_wheel for pyrsistent Complete output from command C:\Anaconda3\python.exe -c "import setuptools;__file__='C:\\cygwin64\\tmp\\pip-build-sqcinj9m\\pyrsistent\\setup.py';exec(compile(open(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" bdist_wheel -d C:\cygwin64\tmp\tmpn25raothpip-wheel-: running bdist_wheel running build running build_py creating build creating build\lib.win-amd64-3.5 copying _pyrsistent_version.py -&gt; build\lib.win-amd64-3.5 creating build\lib.win-amd64-3.5\pyrsistent copying pyrsistent\_checked_types.py -&gt; build\lib.win-amd64-3.5\pyrsistent copying pyrsistent\_field_common.py -&gt; build\lib.win-amd64-3.5\pyrsistent copying pyrsistent\_helpers.py -&gt; build\lib.win-amd64-3.5\pyrsistent copying pyrsistent\_immutable.py -&gt; build\lib.win-amd64-3.5\pyrsistent copying pyrsistent\_pbag.py -&gt; build\lib.win-amd64-3.5\pyrsistent copying pyrsistent\_pclass.py -&gt; build\lib.win-amd64-3.5\pyrsistent copying pyrsistent\_pdeque.py -&gt; build\lib.win-amd64-3.5\pyrsistent copying pyrsistent\_plist.py -&gt; build\lib.win-amd64-3.5\pyrsistent copying pyrsistent\_pmap.py -&gt; build\lib.win-amd64-3.5\pyrsistent copying pyrsistent\_precord.py -&gt; build\lib.win-amd64-3.5\pyrsistent copying pyrsistent\_pset.py -&gt; build\lib.win-amd64-3.5\pyrsistent copying pyrsistent\_pvector.py -&gt; build\lib.win-amd64-3.5\pyrsistent copying pyrsistent\_transformations.py -&gt; build\lib.win-amd64-3.5\pyrsistent copying pyrsistent\__init__.py -&gt; build\lib.win-amd64-3.5\pyrsistent running build_ext building 'pvectorc' extension error: [WinError 2] The system cannot find the file specified ---------------------------------------- Failed building wheel for pyrsistent Failed to build pyrsistent Installing collected packages: pyrsistent Running setup.py install for pyrsistent Complete output from command C:\Anaconda3\python.exe -c "import setuptools, tokenize;__file__='C:\\cygwin64\\tmp\\pip-build-sqcinj9m\\pyrsistent\\setup.py';exec(compile(getattr(tokenize, 'open', open)(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" install --record C:\cygwin64\tmp\pip-_wbdiief-record\install-record.txt --single-version-externally-managed --compile: running install running build running build_py running build_ext building 'pvectorc' extension error: [WinError 2] The system cannot find the file specified ---------------------------------------- Command "C:\Anaconda3\python.exe -c "import setuptools, tokenize;__file__='C:\\cygwin64\\tmp\\pip-build-sqcinj9m\\pyrsistent\\setup.py';exec(compile(getattr(tokenize, 'open', open)(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" install --record C:\cygwin64\tmp\pip-_wbdiief-record\install-record.txt --single-version-externally-managed --compile" failed with error code 1 in C:\cygwin64\tmp\pip-build-sqcinj9m\pyrsistent </code></pre> <p>Both python3 and pip are in the path:</p> <pre><code>$ which pip /cygdrive/c/Anaconda3/Scripts/pip $ which python /cygdrive/c/Anaconda3/python </code></pre> <p>The error is identical when trying to install rpy2 so it's not something particular to the package I'm trying to install. Does anyone have ideas of the problem or ideas for troubleshooting? I've tried debugging into the install.py but the code throwing the error is in C. I've tried doing the install in verbose mode, but it still doesn't say what file it cannot find in that case. (and if you're wondering why I haven't used conda, it's because it doesn't install pyrsistent, and for the rpy2 install, it insists on linking it to its own install of R, and even when specifying my own install, something doesn't link correctly. I've already been down that road and would like to stick to pip).</p>