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
To build R, you need readline, readline_devel, and gfortran have been installed
already. Then,
./configure --enable-R-shlib --prefix=/YOUR_PATH_TO_WHERE_R_WILL_BE_INSTALLED/R
make
make install
To build rpy, you need to first, add R/lib to $LD_LIBRARY_PATH and R/bin to
$PATH; sencond, comment
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
Hi Ryan,
it seems like your compiler can't find the R header files. I don't know on
which linux distro your're running Galaxy and if you installed with a
package manager it or compiled it, but you should try to install R headers
(the development packages). For example in Ubuntu an apt-get install
Hi Ryan
Our sysadmin spent quite some time on this problem...in the end, he gave
up and installed R 2.9.0 on our new server.
So, we ended up with two versions of R: one is used for rpy (we define:
R_HOME=/***/***/galaxy/helpers/R/R-2.9.0 in the 'run.sh' script), and
an up-to-date version of
Subject: Re: [galaxy-dev] rpy and R
Hi Ryan,
it seems like your compiler can't find the R header files. I don't know on
which linux distro your're running Galaxy and if you installed with a
package manager it or compiled it, but you should try to install R headers
(the development packages
Sarah Diehl wrote:
Hi all,
I'm currently working on setting up a fresh Galaxy server at our
institute. I'm going through the tool dependencies list and install
everything on it. I installed the latest R version (2.12.2) and now
I'm trying to install rpy. With some workarounds I managed to
Hi Nate,
thank you very much for your help! I managed to figure out the problem.
There seemed to be an old version of R and somehow (I still don't know
how) the rpy installation did only find the old one. I hard-coded the
directory of the new R in the setup.py (everything else failed) and
