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?
Related
I have installed Anaconda 3 for Mac M1 and I am trying to create a new environment for R. However, everytime I try to do this, I am faced with the below error:
Conda Prompt Error Message
I am faced with this error irrespective of whether I try to do this in anaconda navigator or conda prompt. I have already tried removing Anaconda completely and reinstalling it again but to no avail. Is there anything I can do here?
Update: As requested, here is an additional screenshot:
Mamba install r-eesentials
Mamba install r-essentials output
[Disclosure: I am a volunteer on the Conda Forge R team.]
Conda users who want to use R should prioritize Conda Forge. The Anaconda company has not actively maintained R packages since v3.6.
If installing Conda for the first time, I recommend Miniforge variants (specifically, Mambaforge), rather than the Anaconda distributions (which prioritize defaults/anaconda channel).
Also note that osx-arm64 support for R through Conda is currently sparse. We are actively working on migrating, but for simplicity of workflow, I still recommend Conda users to install a osx-64 version of Conda and use that platform when installing R. You can always create native osx-arm64 environments when you actually need them (e.g., native TensorFlow with Metal support).
I used to work in R 3.4.0 version. Hovewer, this version doesn't support such packages as keras and tensorflow.
I was adviced to upgrade my R version to the newest one.
I downloaded the most recent R version 4.0.2 from the official site, then ran the following code:
install.packages("keras")
library(keras)
install_keras()
And got the following error:
Error in install_keras() :
You should call install_keras() only in a fresh R session that has not yet initialized Keras and TensorFlow (this is to avoid DLL in use errors during installation)
After this, when I tried to quit R session by q() , I faced the following error:
Error: option error has NULL value
Error: no more error handlers available (recursive errors?); invoking 'abort' restart
Error: option error has NULL value
I've never faced such an error before. When I used old R version, I typed q() and then had to choose between y and n. No errors appeared.
I'm asking you to help to to solve this problem.
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 activate r4-base
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.
Find the location of R.exe on your computer. In my computer, this executable is at
C:\Program Files\R\R-3.4.3\bin
Open another Anaconda Prompt as Administrator and change directories to wherever R.exe is on your computer with cd file path. On my computer, it’s cd C:\Program Files\R\R-3.4.3\bin, but it might be different for you.
Then run R from within Anaconda Prompt in Admin mode with R.exe
You’ll notice that you’re in an R session. From here, run the following three commands into the terminal.
install.packages("devtools")
devtools::install_github("IRkernel/IRkernel")
IRkernel::installspec()
In order, they (1) install the devtools package which gets you the install_github() function, (2) install the IR Kernel from GitHub, and (3) tell Jupyter where to find the IR Kernel.
Open Jupyter notebook and enjoy your new R kernel!
Get more information here
#Rheatey Bash works perfectly. but i was facing python.exe this program cant start because api-ms-win-core-path-l1-1-0.dll python system error. this is a problem running on windows 7 but i resolved this issue by installing the kernel following https://richpauloo.github.io/2018-05-16-Installing-the-R-kernel-in-Jupyter-Lab/ and it works fine
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 had problems with the anaconda R (especially installing packages lately caused a problem I could not solve where any attempt to install a package led to non-zero exiting status). Installing a separate R distribution and let Rstudio pick that one and not the one given by anaconda solved all problems for the last months.
Now I want to work with Jupyter and also use nteract or hydrogen from Atom. However, Jupyter uses the R from anaconda and so does then nteract/hydrogen. Therefore, I have the problem again being unable to install 75% of the packages for unknown reasons. I could of course try to find the cause of that BUT I also invested hours into that so I think the easiest/fastest way is to let Jupyter pick the same R that Rstudio uses since I have a fully working environment there...
Can anybody please explain to me how I can make jupyter pick the IRkernel that I installed in Rstudio instead of the anaconda IRkernel? Just deleting the anaconda kernel did not work of course. I also tried IRkernel::installspec() as suggested by the docs.
After deleting the Anaconda R, I had to run R in the terminal and run this:
install.packages(c('repr', 'IRdisplay', 'evaluate', 'crayon', 'pbdZMQ', 'devtools', 'uuid', 'digest'))
devtools::install_github('IRkernel/IRkernel', force=T)
IRkernel::installspec()
Then it worked.
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