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"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:

  http://lists.bx.psu.edu/

___________________________________________________________
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:

  http://lists.bx.psu.edu/


___________________________________________________________
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:

 http://lists.bx.psu.edu/

Reply via email to