I forgot to mention the most important part. You have to modify line 100 in
rpy_tools.py that is under the rpy package as
version = re.search(" +([0-9]+\.[0-9][0-9]+\.[0-9]+)", output)
Le-Shin
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
> --version.
>
>
> 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
> http://www.gnu.org/licenses/.
>
> 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:
>>
>> Hi,
>>
>> 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.
>> MD-B143-06
>> Research Triangle Park, NC 27711
>> hester.susan@epa.gov___________________________________________________________
>> Please keep all replies on the list by using "reply all"
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>
>
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