I tried to install R packages using RStudio Package Manager using the following code:
install.packages("dplyr", type = "source")
and
install.packages("dplyr")
and it gives the following error:
Error in install.packages : invalid version specification 'r56550'
What should I do? I tried to google the error but nothing comes up. I have tried to delete and reinstall R and RStudio but i still received the error. I tried to download both the existing binary and the source file and neither ways worked. I tried to install different packages and repeated in both R and Rstudio and nothing worked.
Thank you!
Update 1: I'm using R version 4.0.5 and RStudio version 1.4.1106. I have also downloaded Rtools40 according to the instruction in the following website: https://cran.r-project.org/bin/windows/Rtools/. I'm using Windows. By 'R Manager' I meant the package manager console in RStudio.
Update 2: I'm not sure if there is no network issue or proxy. If I download the packages directly through the CRAN mirror, then it works. But we are trying to download packages in an offline environment, that's why I need RStudio Package Manager.
I am trying install the R package 'deSolve' in a Jupyter notebook, but I get the following error:
> install.packages("deSolve")
Warning message in install.packages("deSolve"):
“installation of package ‘deSolve’ had non-zero exit status”Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
I get the exact same error message when I try to install any package (I've tried tidyverse, lubridate, and RCurl). I am totally new to Jupyter notebooks but have used R before. Is there a different way to install packages using a notebook?
I am using Jupyter Labs through Anaconda "out of the box."
I created an R environment and launch Jupyter Labs with that environment activated.
I am using R version 3.6.1
Appreciate any help you can give on this. And please let me know what additional information you need to help diagnose. Thanks!
Found out you can do it through Anaconda Navigator by selecting the environment you are using and then selecting packages to install.
In notebook
load_ext rpy2.ipython
import rpy2.robjects.packages as repackages
utils = repackages.importr(‘utils’)
utils.chooseCRANmirrow(ind=1) #select mirrow
packnames = (‘deSolve’)
from rpy2.robjects.vectors import StrVector
utils.install_packages(StrVector(packages))
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
I have R 3.2.2 setup installed in my system,with RStudio version 0.99.489. When I tried to install rJava package,
install.packages("rJava")
I am getting following Error:
Warning in install.packages :
downloaded length 4878 != reported length 200
Error in install.packages : subscript out of bounds
But if I run the below command before installing any package,it works fine, but I don't want to do this every time I install a package.
options(repos=structure(c(CRAN="http://cran.us.r-project.org")))
You can stick the line you want executed at every startup in your .Rprofile file which should be in your home directory. I have 3.2.3 version of R and that worked; however I do get a warning message about using a non-http version of the site.
Similarly to you, I was finding the original repository the system was using was failing to install the packages--not finding the package or downloading a file with too few bytes, perhaps because of a transient problem. You might want to consider not putting this in your .Rprofile file or commenting the line outin case this is a temporary workaround.
I want to install http://cran.r-project.org/src/contrib/Archive/mecdf/ using RStudio but when I use
> install.packages('C:\\Users\\jandre\\Desktop\\mecdf_0.6.1.tar.gz', repos=NULL, type="source")
I get this error:
Installing package into ‘C:/Users/jandre/Documents/R/win-library/3.1’
(as ‘lib’ is unspecified)
'C:\Program' is not recognized as an internal or external command,
operable program or batch file.
Warning in install.packages :
running command '"C:/Program Files/R/R-3.1.1/bin/x64/R" CMD INSTALL -l "C:\Users\jandre\Documents\R\win-library\3.1" "C:/Users/jandre/Desktop/mecdf_0.6.1.tar.gz"' had status 1
Warning in install.packages :
installation of package ‘C:/Users/jandre/Desktop/mecdf_0.6.1.tar.gz’ had non-zero exit status
This occurs in every package I want to install using the tar.gz file. I'm on Win7 x64. RStudio Version 0.98.1028
Can't think of a way to fix this at the moment -- sorry -- but the R administration manual says explicitly:
Note that installing R into a directory whose path contains spaces is not supported, and at least some aspects (such as installing source packages) will not work.
I don't know why this doesn't bite people much more often, given that C:/Program Files/... seems like a relatively normal place to install things on Windows.
I would also expect that the double quotation marks around your R executable name ("C:/Program Files/R/R-3.1.1/bin/x64/R") in the system call should have protected you from this problem ... ?
I had the same error message with the installation of some packages(under Windows 10 OS with R and Rstudio).
It seems that the R software (not R Studio) is dealing with the library where package are installed.
I uninstalled R and Rstudio and installed it a path without space (ex: C:\Program\R).I tried to load the packages that previously failed and it seemed to fix the problem.