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:
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 $PATH; sencond, comment out RPY_DOWNLOAD_DIR/src/Rpy.h line 77 as #include Rdevices.h. Then,
python setup.py install --prefix=/PATH_TO_WHERE_RPY_WILL_BE_INSTALLED
hope this will help.
Le-Shin
On Jul 14, 2012, at 7:15 PM, Chukhman, Morris wrote:
When I try to install rpy-1.0.3 against R-2.11.1 or R-2.15.1 I get the following error about the version number being unobtainable from R --version.
python setup.py install --prefix=/path/to/shared/python RHOMES= [] DEBUG= True Setting RHOMES to ['/argus/app/rhel60/R_2.11.1/lib64/R'] Traceback (most recent call last): File "setup.py", line 109, in <module> RVERSION = rpy_tools.get_R_VERSION(RHOME, force_exec=True) File "/argus/app/src/rpy-1.0.3/rpy_tools.py", line 103, in get_R_VERSION raise RuntimeError("Couldn't obtain version number from output\n" RuntimeError: Couldn't obtain version number from output of `R --version'.
This is the R --version output:
galaxy[rpy-1.0.3]$ 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:
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:
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:
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:
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:
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:
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" 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" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
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