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Asked: 2026-06-18T18:52:19+00:00

I am having trouble installing the Python package rpy2 . I have already compiled

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I am having trouble installing the Python package rpy2. I have already compiled R as a shared library, but I do not have admin priviledges so I am trying to install rpy2 with:

pip install -user rpy2

However, I am getting the following error:

./rpy/rinterface/_rinterface.c:86:31: fatal error:
readline/readline.h: No such file or directory

compilation terminated.

error: command ‘gcc’ failed with exit status 1

I have downloaded readline to:

/some/path/readline-6.2/

where I can see readline.h (I have also compiled readline just in case)

My question:

How can I make rpy2 (or pip) aware of this location with readline.h to avoid the header compilation error?

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1 Answer

  1. Editorial Team

    You’ll need to actually install readline, not just download it, and then point rpy2 to it with CFLAGS and LDFLAGS.

    Try this approach. It’s almost working for me – I have the same problem, except an additional wrinkle that rpy2 seems to be linking against the system R instead of my homedir install.

    First, I downloaded readline to ~/src/readline-6.2, and installed it with ./configure --prefix=$HOME && make && make install. (You need to install it somewhere, not just download the source.)

    Then I re-compiled R with

    CPPFLAGS="-I/usr/local/include -I$HOME/include/" \
LDFLAGS="-L/usr/local/lib64 -L/usr/local/lib -L$HOME/lib64 -L$HOME/lib" \
./configure --prefix=$HOME --enable-BLAS-shlib --enable-R-shlib
make
make install

    R is definitely now using that readline:

    $ ldd ~/lib64/R/lib/libR.so | grep readline
libreadline.so.6 => /home/dsutherl/lib/libreadline.so.6 (0x00007f8104207000)

    The same for my in-home install of Python (3.2.3, since h5py doesn’t work with 3.3 yet):

    CFLAGS="-I/usr/local/include -I$HOME/include/" \
LDFLAGS="-L/usr/local/lib64 -L/usr/local/lib -L$HOME/lib64 -L$HOME/lib" \
./configure --prefix=$HOME
make
make install

    And again:

    $ ldd ~/lib/python3.2/lib-dynload/readline.cpython-32m.so | grep readline
libreadline.so.6 => /home/dsutherl/lib/libreadline.so.6 (0x00007fbfff5c2000)

    Then I downloaded the rpy2 source and built that:

    CFLAGS="-I/usr/local/include -I$HOME/include/" \
LDFLAGS="-L/usr/local/lib64 -L/usr/local/lib -L$HOME/lib64 -L$HOME/lib" \
python3 setup.py build --r-home $HOME/lib64/R install

    This seemed successful, and ldding the .sos in site-packages/rpy2 links to the right libreadline…but to the system R, instead of mine, despite the explicit --r-home.

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