没有管理员权限安装rpy2 [英] Installing rpy2 without admin privileges

问题描述

我无法安装Python软件包 rpy2 。我已经将R编译为共享库，但我没有管理员权限，所以我试图安装rpy2：

  pip install -user rpy2 
  

但是，我收到以下错误：

./ rpy / rinterface / _rinterface.c：86：31：致命错误：
readline / readline.h：没有这样的文件或目录

编译终止。

错误：命令'gcc'失败，退出状态1

我已经将 readline 下载到：

  /some/path/readline-6.2/ 
  

我可以看到 readline.h （我也编译了 readline 以防万一）

我的问题：

如何使 rpy2 （或pip）知道 readline.h 避免标题编译错误？

解决方

您需要实际安装readline，而不只是下载它，然后用 CFLAGS 来指向 rpy2 code>和 LDFLAGS 。

试试这种方法。它几乎为我工作 - 我有同样的问题，除了一个额外的皱纹，rpy2似乎与系统R，而不是我的homedir安装链接。

首先，我将下载的readline下载到〜/ src / readline-6.2 ，并使用 ./configure --prefix = $ HOME&&&制作&& make install 。 （您需要将它安装在某处，而不只是下载源代码。）

然后我用R

  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现在正在使用readline：

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

家庭安装Python（3.2.3，因为h5py不能与3.3一起工作）：

  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 
  

还有：

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

然后我下载了rpy2源代码并建立了：

  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 
  

这看起来很成功， ldd site-packages / rpy2 中的 .so 链接到右侧 libreadline ...但系统 R ，而不是我的，尽管明确的 - r-家庭。

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?

解决方案

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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