I am trying to run R in a google collab notebook (which worked fine before, however as I now tried to access it and run it it keeps giving me an error).
I have ran the following:
%load_ext rpy2.ipython
%%R
install.packages('rworldmap')
install.packages('classInt')
install.packages('reshape2')
install.packages('dplyr')
install.packages('ggpubr')
NotImplementedError: Conversion 'py2rpy' not defined for objects of type '<class 'str'>'
I have tried re-opening the notebook or creating a new one but I keep having the same issue.
This is a problem with newer versions. You must downgrade rpy: run in a cell:
!pip install rpy2==3.5.1
restart and try again
From this post.
It would be best if you first uninstalled the currently loaded rpy2 package:
!pip uninstall rpy2 -y
Then install an older version of rpy2 (3.0.0, works for me):
!pip install rpy2==3.0.0
Use magic commands and enjoy R&python interactively:
%load_ext rpy2.ipython
Example:
%%R
x<-1:5
x
I did put R on path using the .bashrc file. And yet, I do not have access to R through the command line. I have nevertheless no issues with RStudio. When I check for the R location with which R, I get /home/myself/anaconda3/bin/R. I have Ubuntu 20.04. The error message that I get is /home/myself/anaconda3/lib/R/bin/exec/R: error while loading shared libraries: libreadline.so.6: cannot open shared object file: No such file or directory. I have version R version 4.1.3 which I have installed recently. Working in JupyterLab in anaconda, I installed again R in a conda environement. Unfortunately, I get inside the conda environment the same error message.
When I try to install the missing package, I get the message:libreadline6 : PreDepends: multiarch-support but it is not installable.
I also tried to install libreadline with conda, conda install -c conda-forge m2-libreadline (as suggested on the anaconda site) as well as conda install -n base -c conda-forge libreadline.so.6. The message I get is: `PackagesNotFoundError: The following packages are not available from current channels:
libreadline.so.6
m2-libreadline`
I will highly appreciate your help. Thanks.
I'm facing difficulties downloading the r package rsvg. I created first an environment with conda for the latest R version 4.0.2 following these instructions. I was able to download many other R packages & bioconductor packages without problem, however, this one produces huge pile of lines while configuring it and ends with errors downloadind its dependencies (systemfonts, stringi, stringr, gdtools, magick, svglite, knitr). My exact command is install.packages("rsvg", dependencies =T). Trying to download each of those packages produced also a tree of required dependencies (with configuration fail at the end of each).
Among the lines I noticed this error /user/include/freetype2/freetype/config/ftheader.h:3:12: fatal error x86_64-linux-gnu/freetype2/config/fthreader.h no such file or directory which make me suspect that my R installation is incopmlete or corrupted. I tested it with other R versions (e.g. R 3.6.0) yet the same error appear. Installing it on windows (Rstudio 3.6.2) also didn't work, and now I'm wondering if this package needs to be installed differently or it is system related problem? Any help would be highly appreciated
You need to create a new environment and then you can install R 4.+ in Anaconda. Follow these steps.
conda create --name r4-base
After activating r4-base run these commands
conda install -c conda-forge r-base
conda install -c conda-forge/label/gcc7 r-base
Finally, you will notice r-basa version 4 will be installed.
Thereafter, you can install any supported packages. But with this only, you won't have the ability to use it in the Jupyter notebook. You need to install install.packages('IRkernel') and Jupyter notebook as well if you want to use it. Otherwise you are good to go with R-Studio.
For Jupyter Installation and RKernel.
conda install jupyter
Then open the R console. Write in R console
install.packages('IRkernel')
IRkernel::installspec()
Congrats! You can use Notebook for Python and R.
I am trying to take advantage of the Juypter notebook with the R kernel. R-essentials via conda does not include the forecast package.
However someone has seemed to create one:
https://anaconda.org/r/r-forecast
I have installed the package with conda install -c r r-forecast=7.3 per the directions. Seems to install without issue.
When I launch the R kernel in Jupyter and attach the forecast library, it starts off fine and then errors. However I can't understand what the error means to even begin a fix.
Thoughts?
I am trying to run R code in Jupyter and the R Kernel was added. Most of the time, packages can be installed successfully. However, some of the packages, such as RCurl and ggmap, would got error while installing.
Example:
install.packages("RCurl")
Warning message in install.packages("RCurl"):
“installation of package ‘RCurl’ had non-zero exit status”Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
What should I do?
Try to specify CRAN as repository in your install.packages statement when installing RCurl and ggmap. For example:
install.packages("RCurl", repos='http://cran.us.r-project.org')
This Stack Overflow post on installing R packages through Anaconda/Jupyter beyond those included in R essential provides more detail.
(Side note: I had encountered the same issue when trying to install R packages on computer clusters. This solution worked for me.)
use conda comment:
conda install r-RCurl
I kept getting the non-zero exit status when trying to install packages with Jupyter notebook with R kernel and was failing because of multiple dependencies when wanting to install a package. I am not an expert in any of these so please forgive me if I make an error in explaining or if it is a non-issue for you but please feel free to comment to clear things out. I just want to share my success story so hopefully it can help someone else: I am working on a MacBook Pro. Here are the information I get when I run R.version() on my jupyter notebook with R kernel:
$platform 'x86_64-conda_cos6-linux-gnu'
$arch 'x86_64'
$os 'linux-gnu'
$system 'x86_64, linux-gnu'
$language 'R'
$version.string 'R version 3.6.1 (2019-07-05)'
These are the steps to take to fix the issue:
Go to https://anaconda.org/
Search the package name that you are trying to install
Copy the one line that is given to install the package, it should be something like:
Conda install -c r r-caret #conda install -c r r-package_name
NOTE: sometimes during installing packages, you’re asked whether or not you want to continue, so add --y at the end of the above statement to continue, so something like this
Conda install -c r r-caret --y
(I will always add it just to be on the safe side)
Click on the new launcher (+ icon) to create a new notebook with PySpark (once opened it has .ipynp extension)
On the first cell paste the copied line from step 2 and run
Once done, restart the kernel on the current notebook
Restart the kernel on your other notebook with R kernel
Run library(package_name) on your notebook with R kernel (e.x. library(caret))
install.packages("Hmisc", .libPaths(), repos='http://cran.us.r-project.org')
This command will install the packagae in the conda
"/home/user/anaconda3/lib/R/library" and use the cran r repository as source.
Add path in Anaconda
As per this answer,
one can also add additional paths in anaconda to load libraries from (for eg., the location where R studio saves the user-installed packages) with
.libPaths( c( .libPaths(), "~/userLibrary") )
For example, the following worked for me:
In Anaconda :
.libPaths( c( .libPaths(), "C:\Users\name\Documents\R\win-library\3.5") )
When I tried to add anaconda's library path to RStudio, it resulted in errors (The procedure entry point MARK_NOT_MUTABLE could not be located in the dynamic link library << arose 4 times in succession) after installation of a package, though the package seemed to load.
Replace name with your local user folder name
Add/change path in RStudio
A useful link to make changes in default user-installed library paths :
https://www.accelebrate.com/library/how-to-articles/r-rstudio-library
To find out where a package has been installed:
find.package('package_name')
The directions nobody else supplied worked for me, but I found this guide, and it worked. Spent way too much time trying all these when I just needed a few simple commands. https://developers.refinitiv.com/en/article-catalog/article/setup-jupyter-notebook-r
I already had R and python installed, so I skipped to step 3. The only seems to mention windows, but it worked for me on mac as well. After following them I was able to install the packages using install.packages("dplyr", repos = "http://cran.us.r-project.org") in a cell in jupyter.
You have to create a directory in which your package will be and do for eg:
install.packages('ggplot2',loc='your directory')
First Step: You can install the IRkernel packages by running the following command in an R console:install.packages('IRkernel')
Second Step: You will have to make Jupyter see the newly installed R kernel by installing a kernel spec. To install system-wide, set user to False in the installspec command IRkernel::installspec(user = FALSE)
Setup Jupyter Notebook for R