Sorry, that's all I have. Le-Shin
On Jul 15, 2012, at 4:41 AM, Morris Chukhman wrote:
> Yes! That seems to have worked! Thank you very much, Le-Shin!
>
> Are there any more of these dependencies that require these little "patches"
> to build and install properly?
>
> Morris
>
> On 7/14/2012 8:16 PM, Le-Shin Wu wrote:
>> 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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>>>>
>>>> http://lists.bx.psu.edu/
>>>
>>> ___________________________________________________________
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>
>
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