Install and use RPy2 (using conda) so that it uses default R installation in /usr/lib/R R
I want to call functions from my R packages in Python using RPy2. I installed RPy2 using conda and realized it installed a fresh copy of R inside conda... I don't want that. I just want to have and use one R, the default one in /usr/lib/R.
How to do that? How to force conda and Python and RPy2 to use default R installed in /usr/lib/R?
python r conda rpy2
asked Jul 23 '18 at 19:35
SamoSamo
9001132
add a comment |
I want to call functions from my R packages in Python using RPy2. I installed RPy2 using conda and realized it installed a fresh copy of R inside conda... I don't want that. I just want to have and use one R, the default one in /usr/lib/R.
How to do that? How to force conda and Python and RPy2 to use default R installed in /usr/lib/R?
python r conda rpy2
asked Jul 23 '18 at 19:35
SamoSamo
9001132
Simply point library paths to the non-conda R's library or set needed environment variables to point to needed library.
– Parfait
Jul 23 '18 at 19:51
@Parfait Tried to do that but do not know how obviously, since it still does not work. Is there maybe an article or blog post detailing this? It seems this is all very well document and easy if you are primary using Python and would want to add some R stuff. If you are a pure R user with a lot of custom packages and default R installation there seems to be no details on how to set things up...
– Samo
Jul 25 '18 at 20:34
Did you try specifying R packages inimportrcall:importr("my_package", lib_loc="/path/to/non-conda/R/lib")? You can find this path by opening non-conda R session and call.libPaths().
– Parfait
Jul 26 '18 at 16:41
What's the downside of using the r conda package?
– Nehal J Wani
Aug 1 '18 at 19:04
If I install RPy2 with conda it also installs R (another version) changes R home folder and all sorts of stuff. I am an R user(meaning I have a working R installation with specific version that needs to be maintained on a system wide basis since I have many many many R jobs running and many proprietary R packages written and used. Now, I need to use Python and call functions from my proprietary R packages from Python. The issue I have is that it looks like people using RPy2 mostly use Python and just need to call some R functions and they do not care where and which version of R they have...
– Samo
Aug 2 '18 at 18:00
add a comment |
I want to call functions from my R packages in Python using RPy2. I installed RPy2 using conda and realized it installed a fresh copy of R inside conda... I don't want that. I just want to have and use one R, the default one in /usr/lib/R.
How to do that? How to force conda and Python and RPy2 to use default R installed in /usr/lib/R?
python r conda rpy2
asked Jul 23 '18 at 19:35
SamoSamo
9001132
I want to call functions from my R packages in Python using RPy2. I installed RPy2 using conda and realized it installed a fresh copy of R inside conda... I don't want that. I just want to have and use one R, the default one in /usr/lib/R.
How to do that? How to force conda and Python and RPy2 to use default R installed in /usr/lib/R?
python r conda rpy2
python r conda rpy2
asked Jul 23 '18 at 19:35
SamoSamo
9001132
asked Jul 23 '18 at 19:35
SamoSamo
9001132
asked Jul 23 '18 at 19:35
SamoSamo
9001132
asked Jul 23 '18 at 19:35
SamoSamo
9001132
asked Jul 23 '18 at 19:35
SamoSamo
9001132
9001132
Simply point library paths to the non-conda R's library or set needed environment variables to point to needed library.
– Parfait
Jul 23 '18 at 19:51
@Parfait Tried to do that but do not know how obviously, since it still does not work. Is there maybe an article or blog post detailing this? It seems this is all very well document and easy if you are primary using Python and would want to add some R stuff. If you are a pure R user with a lot of custom packages and default R installation there seems to be no details on how to set things up...
– Samo
Jul 25 '18 at 20:34
Did you try specifying R packages inimportrcall:importr("my_package", lib_loc="/path/to/non-conda/R/lib")? You can find this path by opening non-conda R session and call.libPaths().
– Parfait
Jul 26 '18 at 16:41
What's the downside of using the r conda package?
– Nehal J Wani
Aug 1 '18 at 19:04
If I install RPy2 with conda it also installs R (another version) changes R home folder and all sorts of stuff. I am an R user(meaning I have a working R installation with specific version that needs to be maintained on a system wide basis since I have many many many R jobs running and many proprietary R packages written and used. Now, I need to use Python and call functions from my proprietary R packages from Python. The issue I have is that it looks like people using RPy2 mostly use Python and just need to call some R functions and they do not care where and which version of R they have...
– Samo
Aug 2 '18 at 18:00
add a comment |
Simply point library paths to the non-conda R's library or set needed environment variables to point to needed library.
– Parfait
Jul 23 '18 at 19:51
@Parfait Tried to do that but do not know how obviously, since it still does not work. Is there maybe an article or blog post detailing this? It seems this is all very well document and easy if you are primary using Python and would want to add some R stuff. If you are a pure R user with a lot of custom packages and default R installation there seems to be no details on how to set things up...
– Samo
Jul 25 '18 at 20:34
Did you try specifying R packages inimportrcall:importr("my_package", lib_loc="/path/to/non-conda/R/lib")? You can find this path by opening non-conda R session and call.libPaths().
– Parfait
Jul 26 '18 at 16:41
What's the downside of using the r conda package?
– Nehal J Wani
Aug 1 '18 at 19:04
If I install RPy2 with conda it also installs R (another version) changes R home folder and all sorts of stuff. I am an R user(meaning I have a working R installation with specific version that needs to be maintained on a system wide basis since I have many many many R jobs running and many proprietary R packages written and used. Now, I need to use Python and call functions from my proprietary R packages from Python. The issue I have is that it looks like people using RPy2 mostly use Python and just need to call some R functions and they do not care where and which version of R they have...
– Samo
Aug 2 '18 at 18:00
Simply point library paths to the non-conda R's library or set needed environment variables to point to needed library.
– Parfait
Jul 23 '18 at 19:51
Simply point library paths to the non-conda R's library or set needed environment variables to point to needed library.
– Parfait
Jul 23 '18 at 19:51
@Parfait Tried to do that but do not know how obviously, since it still does not work. Is there maybe an article or blog post detailing this? It seems this is all very well document and easy if you are primary using Python and would want to add some R stuff. If you are a pure R user with a lot of custom packages and default R installation there seems to be no details on how to set things up...
– Samo
Jul 25 '18 at 20:34
@Parfait Tried to do that but do not know how obviously, since it still does not work. Is there maybe an article or blog post detailing this? It seems this is all very well document and easy if you are primary using Python and would want to add some R stuff. If you are a pure R user with a lot of custom packages and default R installation there seems to be no details on how to set things up...
– Samo
Jul 25 '18 at 20:34
Did you try specifying R packages in
importr call: importr("my_package", lib_loc="/path/to/non-conda/R/lib")? You can find this path by opening non-conda R session and call .libPaths().– Parfait
Jul 26 '18 at 16:41
Did you try specifying R packages in
importr call: importr("my_package", lib_loc="/path/to/non-conda/R/lib")? You can find this path by opening non-conda R session and call .libPaths().– Parfait
Jul 26 '18 at 16:41
What's the downside of using the r conda package?
– Nehal J Wani
Aug 1 '18 at 19:04
What's the downside of using the r conda package?
– Nehal J Wani
Aug 1 '18 at 19:04
If I install RPy2 with conda it also installs R (another version) changes R home folder and all sorts of stuff. I am an R user(meaning I have a working R installation with specific version that needs to be maintained on a system wide basis since I have many many many R jobs running and many proprietary R packages written and used. Now, I need to use Python and call functions from my proprietary R packages from Python. The issue I have is that it looks like people using RPy2 mostly use Python and just need to call some R functions and they do not care where and which version of R they have...
– Samo
Aug 2 '18 at 18:00
If I install RPy2 with conda it also installs R (another version) changes R home folder and all sorts of stuff. I am an R user(meaning I have a working R installation with specific version that needs to be maintained on a system wide basis since I have many many many R jobs running and many proprietary R packages written and used. Now, I need to use Python and call functions from my proprietary R packages from Python. The issue I have is that it looks like people using RPy2 mostly use Python and just need to call some R functions and they do not care where and which version of R they have...
– Samo
Aug 2 '18 at 18:00
add a comment |
1 Answer
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Do not use the conda instal to install the rpy2, just use the pip install rpy2. Here are some additional packages you may need to install before the rpy2:
conda install -y PyHamcrest
sudo apt-get install -y libreadline6-dev
pip install rpy2
Some notes:
- The
which pipshould refer to anaconda's path - The environment variable for R (R_HOME and PATH) should be properly set up before you install the
rpy2
After the installation, you may encounter an error when calling
import rpy2.robjects as robjects:
RRuntimeWarning: Error: package or namespace load failed for ‘stats’ in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/usr/local/lib/R/library/stats/libs/stats.so':
libRlapack.so: cannot open shared object file: No such file or directory
To solve this, I found a solution in How I solved the error - libRlapack.so: cannot open shared object file: No such file or directory
You need to locate your libRlapack.so file (in my case this file is in /usr/local/lib/R/lib/), or the following command should show the path to this file:
R CMD ldd /usr/local/lib/R/library/stats/libs/stats.so
and then write this path to the /etc/ld.so.conf.d/libR.conf and then run ldconfig:
echo "/usr/local/lib/R/lib/" >> /etc/ld.so.conf.d/libR.conf && ldconfig
That should fix the problem.
answered Nov 19 '18 at 13:11
qjgodsqjgods
73056
add a comment |
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1 Answer
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1 Answer
1
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oldest
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oldest
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Do not use the conda instal to install the rpy2, just use the pip install rpy2. Here are some additional packages you may need to install before the rpy2:
conda install -y PyHamcrest
sudo apt-get install -y libreadline6-dev
pip install rpy2
Some notes:
- The
which pipshould refer to anaconda's path - The environment variable for R (R_HOME and PATH) should be properly set up before you install the
rpy2
After the installation, you may encounter an error when calling
import rpy2.robjects as robjects:
RRuntimeWarning: Error: package or namespace load failed for ‘stats’ in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/usr/local/lib/R/library/stats/libs/stats.so':
libRlapack.so: cannot open shared object file: No such file or directory
To solve this, I found a solution in How I solved the error - libRlapack.so: cannot open shared object file: No such file or directory
You need to locate your libRlapack.so file (in my case this file is in /usr/local/lib/R/lib/), or the following command should show the path to this file:
R CMD ldd /usr/local/lib/R/library/stats/libs/stats.so
and then write this path to the /etc/ld.so.conf.d/libR.conf and then run ldconfig:
echo "/usr/local/lib/R/lib/" >> /etc/ld.so.conf.d/libR.conf && ldconfig
That should fix the problem.
answered Nov 19 '18 at 13:11
qjgodsqjgods
73056
add a comment |
Do not use the conda instal to install the rpy2, just use the pip install rpy2. Here are some additional packages you may need to install before the rpy2:
conda install -y PyHamcrest
sudo apt-get install -y libreadline6-dev
pip install rpy2
Some notes:
- The
which pipshould refer to anaconda's path - The environment variable for R (R_HOME and PATH) should be properly set up before you install the
rpy2
After the installation, you may encounter an error when calling
import rpy2.robjects as robjects:
RRuntimeWarning: Error: package or namespace load failed for ‘stats’ in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/usr/local/lib/R/library/stats/libs/stats.so':
libRlapack.so: cannot open shared object file: No such file or directory
To solve this, I found a solution in How I solved the error - libRlapack.so: cannot open shared object file: No such file or directory
You need to locate your libRlapack.so file (in my case this file is in /usr/local/lib/R/lib/), or the following command should show the path to this file:
R CMD ldd /usr/local/lib/R/library/stats/libs/stats.so
and then write this path to the /etc/ld.so.conf.d/libR.conf and then run ldconfig:
echo "/usr/local/lib/R/lib/" >> /etc/ld.so.conf.d/libR.conf && ldconfig
That should fix the problem.
answered Nov 19 '18 at 13:11
qjgodsqjgods
73056
add a comment |
Do not use the conda instal to install the rpy2, just use the pip install rpy2. Here are some additional packages you may need to install before the rpy2:
conda install -y PyHamcrest
sudo apt-get install -y libreadline6-dev
pip install rpy2
Some notes:
- The
which pipshould refer to anaconda's path - The environment variable for R (R_HOME and PATH) should be properly set up before you install the
rpy2
After the installation, you may encounter an error when calling
import rpy2.robjects as robjects:
RRuntimeWarning: Error: package or namespace load failed for ‘stats’ in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/usr/local/lib/R/library/stats/libs/stats.so':
libRlapack.so: cannot open shared object file: No such file or directory
To solve this, I found a solution in How I solved the error - libRlapack.so: cannot open shared object file: No such file or directory
You need to locate your libRlapack.so file (in my case this file is in /usr/local/lib/R/lib/), or the following command should show the path to this file:
R CMD ldd /usr/local/lib/R/library/stats/libs/stats.so
and then write this path to the /etc/ld.so.conf.d/libR.conf and then run ldconfig:
echo "/usr/local/lib/R/lib/" >> /etc/ld.so.conf.d/libR.conf && ldconfig
That should fix the problem.
answered Nov 19 '18 at 13:11
qjgodsqjgods
73056
Do not use the conda instal to install the rpy2, just use the pip install rpy2. Here are some additional packages you may need to install before the rpy2:
conda install -y PyHamcrest
sudo apt-get install -y libreadline6-dev
pip install rpy2
Some notes:
- The
which pipshould refer to anaconda's path - The environment variable for R (R_HOME and PATH) should be properly set up before you install the
rpy2
After the installation, you may encounter an error when calling
import rpy2.robjects as robjects:
RRuntimeWarning: Error: package or namespace load failed for ‘stats’ in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/usr/local/lib/R/library/stats/libs/stats.so':
libRlapack.so: cannot open shared object file: No such file or directory
To solve this, I found a solution in How I solved the error - libRlapack.so: cannot open shared object file: No such file or directory
You need to locate your libRlapack.so file (in my case this file is in /usr/local/lib/R/lib/), or the following command should show the path to this file:
R CMD ldd /usr/local/lib/R/library/stats/libs/stats.so
and then write this path to the /etc/ld.so.conf.d/libR.conf and then run ldconfig:
echo "/usr/local/lib/R/lib/" >> /etc/ld.so.conf.d/libR.conf && ldconfig
That should fix the problem.
answered Nov 19 '18 at 13:11
qjgodsqjgods
73056
edited Nov 20 '18 at 1:53
answered Nov 19 '18 at 13:11
qjgodsqjgods
73056
answered Nov 19 '18 at 13:11
qjgodsqjgods
73056
answered Nov 19 '18 at 13:11
qjgodsqjgods
73056
73056
add a comment |
add a comment |
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Simply point library paths to the non-conda R's library or set needed environment variables to point to needed library.
– Parfait
Jul 23 '18 at 19:51
@Parfait Tried to do that but do not know how obviously, since it still does not work. Is there maybe an article or blog post detailing this? It seems this is all very well document and easy if you are primary using Python and would want to add some R stuff. If you are a pure R user with a lot of custom packages and default R installation there seems to be no details on how to set things up...
– Samo
Jul 25 '18 at 20:34
Did you try specifying R packages in
importrcall:importr("my_package", lib_loc="/path/to/non-conda/R/lib")? You can find this path by opening non-conda R session and call.libPaths().– Parfait
Jul 26 '18 at 16:41
What's the downside of using the r conda package?
– Nehal J Wani
Aug 1 '18 at 19:04
If I install RPy2 with conda it also installs R (another version) changes R home folder and all sorts of stuff. I am an R user(meaning I have a working R installation with specific version that needs to be maintained on a system wide basis since I have many many many R jobs running and many proprietary R packages written and used. Now, I need to use Python and call functions from my proprietary R packages from Python. The issue I have is that it looks like people using RPy2 mostly use Python and just need to call some R functions and they do not care where and which version of R they have...
– Samo
Aug 2 '18 at 18:00