pip install in Cygwin cannot find file error - python-3.x

Question

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.
Here's the output:
$ 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 -> build\lib.win-amd64-3.5
creating build\lib.win-amd64-3.5\pyrsistent
copying pyrsistent\_checked_types.py -> build\lib.win-amd64-3.5\pyrsistent
copying pyrsistent\_field_common.py -> build\lib.win-amd64-3.5\pyrsistent
copying pyrsistent\_helpers.py -> build\lib.win-amd64-3.5\pyrsistent
copying pyrsistent\_immutable.py -> build\lib.win-amd64-3.5\pyrsistent
copying pyrsistent\_pbag.py -> build\lib.win-amd64-3.5\pyrsistent
copying pyrsistent\_pclass.py -> build\lib.win-amd64-3.5\pyrsistent
copying pyrsistent\_pdeque.py -> build\lib.win-amd64-3.5\pyrsistent
copying pyrsistent\_plist.py -> build\lib.win-amd64-3.5\pyrsistent
copying pyrsistent\_pmap.py -> build\lib.win-amd64-3.5\pyrsistent
copying pyrsistent\_precord.py -> build\lib.win-amd64-3.5\pyrsistent
copying pyrsistent\_pset.py -> build\lib.win-amd64-3.5\pyrsistent
copying pyrsistent\_pvector.py -> build\lib.win-amd64-3.5\pyrsistent
copying pyrsistent\_transformations.py -> build\lib.win-amd64-3.5\pyrsistent
copying pyrsistent\__init__.py -> 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
Both python3 and pip are in the path:
$ which pip
/cygdrive/c/Anaconda3/Scripts/pip
$ which python
/cygdrive/c/Anaconda3/python
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).

Answer 1

Here is a workaround for anyone who is stuck installing python packages on Windows. There are several sites that have Windows binaries for python packages. I was able to find a binary for rpy2 here but there are several other sites too, if you just google something like "python Windows binaries". Then I did:
pip install rpy2-2.7.4-cp35-none-win_amd64.whl
pyrsistent was not in that website or any of several other binaries websites I found. But someone else on my dev team sent me the /pyrsistent directory inside his Anaconda3/Lib/site-packages directory and after copying it to the same directory on my machine, I was able to import pyrsistent as well.
It's not pretty, but it worked.