To build R, you need readline, readline_devel, and gfortran have been installed
./configure --enable-R-shlib --prefix=/YOUR_PATH_TO_WHERE_R_WILL_BE_INSTALLED/R
To build rpy, you need to first, add R/lib to $LD_LIBRARY_PATH and R/bin to
$PATH; sencond, comment out RPY_DOWNLOAD_DIR/src/Rpy.h line 77 as #include
python setup.py install --prefix=/PATH_TO_WHERE_RPY_WILL_BE_INSTALLED
hope this will help.
On Jul 14, 2012, at 7:15 PM, Chukhman, Morris wrote:
> When I try to install rpy-1.0.3 against R-2.11.1 or R-2.15.1 I get the
> following error about the version number being unobtainable from R
> python setup.py install --prefix=/path/to/shared/python
> RHOMES= 
> DEBUG= True
> Setting RHOMES to ['/argus/app/rhel60/R_2.11.1/lib64/R']
> Traceback (most recent call last):
> File "setup.py", line 109, in <module>
> RVERSION = rpy_tools.get_R_VERSION(RHOME, force_exec=True)
> File "/argus/app/src/rpy-1.0.3/rpy_tools.py", line 103, in get_R_VERSION
> raise RuntimeError("Couldn't obtain version number from output\n"
> RuntimeError: Couldn't obtain version number from output
> of `R --version'.
> This is the R --version output:
> galaxy[rpy-1.0.3]$ R --version
> R version 2.11.1 (2010-05-31)
> Copyright (C) 2010 The R Foundation for Statistical Computing
> ISBN 3-900051-07-0
> R is free software and comes with ABSOLUTELY NO WARRANTY.
> You are welcome to redistribute it under the terms of the
> GNU General Public License version 2.
> For more information about these matters see
> Although rpy2 builds and installs successfully the linear_regression.py
> module can't seem to use it. It is looking for the rpy module not the rpy2
> module. If I ln -s rpy2 rpy, it appears to run but gives an name not
> defined error in a line like dat= r.list(...
> What is the proper procedure for installing the R and rpy dependencies?
> What versions are recommended with the current galaxy on mercurial?
> On Thu, June 28, 2012 3:51 pm, Susan Hester wrote:
>> I'm trying to register in Galaxy on the public server and under the
>> "user" tab "register" is greyed out? How do I register?
>> Susan Hester, Ph.D.
>> Research Biologist
>> Systems Biology Branch
>> Integrated Systems Toxicology Division (ISTD)
>> National Health and Environmental Effects Research Lab
>> US Environmental Protection Agency
>> 109 T.W. Alexander Dr.
>> Research Triangle Park, NC 27711
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> Please keep all replies on the list by using "reply all"
> in your mail client. To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
Please keep all replies on the list by using "reply all"
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and other Galaxy lists, please use the interface at: