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I have seen a number of different people post this problem (example: Tried to guess R's HOME but no R command in the PATH. OsX 10.6 and Installing rpy2 on Mac OSX 10.8.5), but I have yet to find a viable solution.

I have ensured that I have Python-2.7 installed in my terminal, and since I had recently upgraded by RStudio, I thought that my R was also updated. But everytime I tried to run either:

pip install rpy2

or

easy_install rpy2

I kept getting the same error of Error: Tried to guess R's HOME but no command 'R' in the PATH.

After some googling, I decided to try to download the latest version of R (v 3.4.1), even though I'm very certain it was already updated to begin with. But now I get the following behemoth of an error (I should note that I have condensed it):

In file included from ./rpy/rinterface/_rinterface.c:122:
    ./rpy/rinterface/sequence.c:2173:1: warning: unused function 'ComplexVectorSexp_AsSexp' [-Wunused-function]
    ComplexVectorSexp_AsSexp(PyObject *pyfloat) {
    ^
    11 warnings generated.
    cc -bundle -undefined dynamic_lookup -arch x86_64 -arch i386 -Wl,-F. build/temp.macosx-10.12-intel-2.7/./rpy/rinterface/_rinterface.o -L/usr/local/lib -Lbuild/temp.macosx-10.12-intel-2.7 -L/usr/local/lib -lpcre -llzma -lbz2 -lz -licucore -lm -liconv -lr_utils -o build/lib.macosx-10.12-intel-2.7/rpy2/rinterface/_rinterface.so -fopenmp -F/Library/Frameworks/R.framework/.. -framework R
    clang: error: unsupported option '-fopenmp'
    clang: error: unsupported option '-fopenmp'
    error: command 'cc' failed with exit status 1

    ----------------------------------------
Command "/usr/bin/python -u -c "import setuptools, tokenize;__file__='/private/tmp/pip-build-zT8DaX/rpy2/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /tmp/pip-bDnbE5-record/install-record.txt --single-version-externally-managed --compile" failed with error code 1 in /private/tmp/pip-build-zT8DaX/rpy2/

So now I have a completely different error occurring. I thought that upgrading my R would automatically add it to my environmental variable PATH, but now I'm really at a loss at how to deal with this. I have tried to google this new error but I can't seem to find any solutions that are geared towards installing Rpy2 on a Mac OSX with Python-2.7 and R-3.4. Can anybody offer any kind of advice?

ADDENDUM

I have now tried a variety of other approaches, including downloading XCODE, and updating my GCC compiler, (one such approach is delineated in http://cs.millersville.edu/~gzoppetti/InstallingGccMac.html), and I have also tried to reinstall GCC with the command brew reinstall gcc --without-multilib. I have also edited my PATH environmental variables to include R, CC, and have still had no luck.

Bob McBobson
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3 Answers3

3

I have now figured out that rpy2 installation is contingent upon the right kind of compiler being used. The default compiler for Apple is clang, which does not support rpy2's set up process. So, after acquiring the gcc compiler via homebrew, you can then run brew ls gcc to see the file paths of what gcc compilers are present on your computer. I then ran the following commands in the terminal to change the default compiler from clang to the file path gcc-7, then set the proper flags (which I deduced from reading the error messages yielded by the compiler before), and then install rpy2. 

export CC=/usr/local/Cellar/gcc/7.2.0/bin/x86_64-apple-darwin16.7.0-gcc-7
export CFLAGS="-W"
pip install rpy2==2.8.6

I should note that I installed rpy2 version 2.8.6 since my scripts are in Python 2.7, and rpy2 2.9.0 is only compatible with Python 3.x. Furthermore, I am aware that this answer might not adequately describe the problem for everyone, so I encourage other users to expand and/or correct this solution.

Bob McBobson
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1

The error about "no R in the PATH" is exactly about what it says. To reproduce, open a terminal and enter "R": there should not be any such command found. The solution is to have R findable in the PATH.

Now starting with R-3.4 the tools needed to compile R and and R extensions in C have changed, and the requirements are less standard than one might hope for. This can be debated to be an issue with R and OS X, and there is an open issue in the rpy2 tracker about it.

edit: Note that the issue was resolved and a precompiled binary wheel for rpy2-2.9.3 is now available on pypi.

lgautier
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0

It's possible to do the GCC switch with a single env command:

env CC=/usr/local/Cellar/gcc/7.2.0/bin/gcc-7 pip install rpy2

The reason clang doesn't work with RPy2 is because clang 4.0.0 doesn't include the -fopenmp flag, which is used by R. There's an ongoing open problem thread on the RPy2 Bitbucket about it.

Brandon Lewis
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