I have installed R at following location C:\E_Drive\ProgramFiles\R-3.4.3, so I think R environment installed at C:\E_Drive\ProgramFiles\R-3.4.3 will be used when I run the R console, right? Please correct me if I am wrong.
Now, I install a package using the R console.
Now, I download and install RStudio and from the R console of RStudio if I check whether that package is available or not then I see that it is available. I am wondering, how RStudio's R console reported that package is available, I didn't expect that since C:\E_Drive\ProgramFiles\R-3.4.3 is not on my PATH and in no way is linked RStudio with C:\E_Drive\ProgramFiles\R-3.4.3, so I thought RStudio would be referring its own R environment.
Can you please help me understand how my RStudio is referencing the C:\E_Drive\ProgramFiles\R-3.4.3 R environment.
R normally installs packages in the same directory tree as its own binary, but it can also install them elsewhere. On Windows, this generally happens because regular users often don't have write permission in the Program Files directory. The standard Windows installer also records R's location in the registry, so that it doesn't need to be on the PATH to be found by RStudio.
You can find out where Windows or RStudio found R by running R.home() within R. You can find out where R is finding packages in a particular session by running .libPaths().
Related
First time question asker.
I created an Excel/R tool that uses:
Excel VBA to create a CSV file with data for R,
Launch R using a Windows Shell,
Detects when R is finished running and then
Imports the results in a CSV file created by the R script.
Unfortunately, the R code does not work as programed with some package versions created after 3/1/2020, which creates problems for new users because they cannot just install the current package versions or users who want to use conflicting versions for other projects.
I have a solution for users who do not require newer versions of R for their other work; writing a script that installs all the packages and their dependents using the “versions” package. However, I think this approach will constrain users who want to use newer versions of R. **Is this a correct assumption? **
I thought the {checkpoint} package might offer a good solution. I can get it to run in well in RStudio by creating a RStudio project (where I ran the {checkpoint} package to install the 3/1/2020 versions of my packages). However, I have not found a way to run the R script from the Windows Shell. The R script does not seem to be able to access the packages installed in the RStudio project using {checkpoint}. Does anyone have ideas of how I can have Excel VBA launch the start of the R script in a way that it can assess the packages installed in the RStudio project by {checkpoint}? Perhaps there is a Windows Shell call for RStudio similar to the one I use now for R?
Here is the Windows Shell code I currently use for R in case it helps. It works with the versions approach but not the {checkpoint} approach.
rExeCall = "C:\Program Files\R\R-3.6.2\bin\Rscript.exe"
rExeOptns = " --no-environ --no-init-file --no-restore --verbose "
rscrpt=”Tool.R”
Shell (rExeCall & rExeOptns & rscrpt)
Thank you in advance for your help!
I had hoped that my current R shell code would work when I used {checkpoint} to install the correct versions of the packages in an RStudio project.
I tried specifying the .libPaths to the file location for the RStudio projection (per Running R script from PHP in VSCode not recognizing R packages) without success.
I am trying to embed RInside to my application on win7 64-bit system but when I initialize an RInside:
Rin = new RInside(argc, argv);
the following message appears:
Error in loadNamespace(name) : there is no package called 'Rcpp'
This error only occurs with Windows.
I think you get that issue when your .libPaths() differ--in other words run the .libPaths() function to see the paths stored by R for its use. Then check where RInside is installed, and make sure Rcpp is installed there too. It is a setup issue.
In other words, it should work if you have Rcpp and RInside installed where the basic R libraries are. Otherwise you have to tell the (embedded) R session about the other location (and before it starts).
There are more Windows users on the list, so you could try asking on rcpp-devel.
First get your default library locations by command ".Library" in R.
Get Rcpp package from https://cran.r-project.org/web/packages/Rcpp/index.html.
Unzip and copy folder "Rcpp" to your default library locations obtained from step1.
Now you are ready to install packages which have dependencies on Rcpp.
Dirk is right in this case, BUT if the .libPaths() does not work, then please also check if you have the latest packages.
I am posting this as an ancillary answer backup which I ran into with the shiny package backend switch of their code needing Rcpp!
In this case of getting the "no package" error message, I fixed it by:
Selecting devtools package and then using this line below. (if you don't have devtools then get it with install.packages("devtools")
devtools::install_github("rstudio/shiny")
The development version of the package handled this better, and added the package as a dependency.
Mods - I realize this is an answer to an old question, but I might help others not wasting an hour like I just did.
You might find it easy if the answers are for both R studio users and non R studio users.
R Studio users
First get your default library locations by command ".Library" in R.
Get Rcpp package from https://cran.r-project.org/web/packages/Rcpp/index.html.
Unzip and copy folder "Rcpp" to your default library locations obtained from step 1, you will find another folder named library, paste the unzip folder in it.
Non R studio Users
First get your default library locations by command ".libPath" in R.
Get Rcpp package from https://cran.r-project.org/web/packages/Rcpp/index.html.
Unzip and copy folder "Rcpp" to your default library locations obtained from step 1, you will find another folder named library, paste the unzip folder in it.
I was also getting this error while trying to run the 'ggplot' function from the ggplot2 package. After trying the suggestions posted here and elsewhere (checking file paths, restarting R, clearing out my environment, etc.) and encountering several other cryptic error messages, it turned out that I needed to download the latest version of base R for Windows (v3.4.1) and update my version of R-Studio to the latest version also (v1.0.153).
After doing this my 'ggplot' function was working again and I was able to render my figure from R Studio without any further issues.
I was also getting this message when trying to use ggplot. I first updating both my R for Windows to 3.4.3. Then updating R studio to version 1.1.423; then, updating all of the packages and being sure to access the R version 3.4.3 from R studio, I still got the message. None of these things fixed the error. I was ready to give up until I noticed that I was calling library(ggplot) and had ggplot::ggplot in my code. THIS WAS THE PROBLEM. I changed it to library(ggplot2) and the instance to ggplot2::ggplot(...). THIS FIXEd the problems.
I was facing a similar issue, and I simply installed the said package. It's working perfectly for me.
First let me preface this with the disclaimer that I'm new to R, but a longtime Python power user. Given that I love the conda ecosystem and the Jupyter notebook, I'm trying to set them up as my R development environment as well.
So using the instructions at: https://www.continuum.io/blog/developer/jupyter-and-conda-r I've set up a Jupyter Notbook that using an RKernel that should be hitting the installation of R installed in my Anaconda folder (I would think anyway).
Getting it setup was easy peasy and everything is working great for standard R stuff but my analysis requires some R libraries that are not available in r-essentials channel. No problem, I think I know how to install an R library. I go to "C:\Anaconda\R\bin\x64\Rgui.exe" and install rgdal, dismo, and some other packages. To check my work I looked in C:\Anaconda\R\library and there they are.
But when I run a jupyter notebook from the Anaconda command prompt. And start a new R notebook I get a "Error in library(dismo): there is no package called 'dismo'" Wait a sec, I run a ".libPaths()" from the notebook and it looks like its pointing
You can add .libPaths('path_where_your_packages_are') in a code cell at the beginning of your notebook to tell jupyter where your packages are. For me that was .libPaths('~/R/win-library/3.2') (work-around from discnerd who filed this issue on github).
To find out the path to your packages, just install a random package in R and wait for the location to be printed to the console.
More details (likely specific to my system/installations): When running .libPaths() in R, I got 2 locations: one for which admin rights were required for writing, and one for which admin rights were not required for writing. While packages installed through R land in the location where admin rights are not required, jupyter looks at the location where admin rights are required.
You can find out the path to your library with installed.packages()
I am trying to embed RInside to my application on win7 64-bit system but when I initialize an RInside:
Rin = new RInside(argc, argv);
the following message appears:
Error in loadNamespace(name) : there is no package called 'Rcpp'
This error only occurs with Windows.
I think you get that issue when your .libPaths() differ--in other words run the .libPaths() function to see the paths stored by R for its use. Then check where RInside is installed, and make sure Rcpp is installed there too. It is a setup issue.
In other words, it should work if you have Rcpp and RInside installed where the basic R libraries are. Otherwise you have to tell the (embedded) R session about the other location (and before it starts).
There are more Windows users on the list, so you could try asking on rcpp-devel.
First get your default library locations by command ".Library" in R.
Get Rcpp package from https://cran.r-project.org/web/packages/Rcpp/index.html.
Unzip and copy folder "Rcpp" to your default library locations obtained from step1.
Now you are ready to install packages which have dependencies on Rcpp.
Dirk is right in this case, BUT if the .libPaths() does not work, then please also check if you have the latest packages.
I am posting this as an ancillary answer backup which I ran into with the shiny package backend switch of their code needing Rcpp!
In this case of getting the "no package" error message, I fixed it by:
Selecting devtools package and then using this line below. (if you don't have devtools then get it with install.packages("devtools")
devtools::install_github("rstudio/shiny")
The development version of the package handled this better, and added the package as a dependency.
Mods - I realize this is an answer to an old question, but I might help others not wasting an hour like I just did.
You might find it easy if the answers are for both R studio users and non R studio users.
R Studio users
First get your default library locations by command ".Library" in R.
Get Rcpp package from https://cran.r-project.org/web/packages/Rcpp/index.html.
Unzip and copy folder "Rcpp" to your default library locations obtained from step 1, you will find another folder named library, paste the unzip folder in it.
Non R studio Users
First get your default library locations by command ".libPath" in R.
Get Rcpp package from https://cran.r-project.org/web/packages/Rcpp/index.html.
Unzip and copy folder "Rcpp" to your default library locations obtained from step 1, you will find another folder named library, paste the unzip folder in it.
I was also getting this error while trying to run the 'ggplot' function from the ggplot2 package. After trying the suggestions posted here and elsewhere (checking file paths, restarting R, clearing out my environment, etc.) and encountering several other cryptic error messages, it turned out that I needed to download the latest version of base R for Windows (v3.4.1) and update my version of R-Studio to the latest version also (v1.0.153).
After doing this my 'ggplot' function was working again and I was able to render my figure from R Studio without any further issues.
I was also getting this message when trying to use ggplot. I first updating both my R for Windows to 3.4.3. Then updating R studio to version 1.1.423; then, updating all of the packages and being sure to access the R version 3.4.3 from R studio, I still got the message. None of these things fixed the error. I was ready to give up until I noticed that I was calling library(ggplot) and had ggplot::ggplot in my code. THIS WAS THE PROBLEM. I changed it to library(ggplot2) and the instance to ggplot2::ggplot(...). THIS FIXEd the problems.
I was facing a similar issue, and I simply installed the said package. It's working perfectly for me.
On Windows 7 x64, I've got version 3.0.0 of R installed. Further, I've also set the environment variable R_LIBS_USER to point to a network drive. In rgui.exe, executing:
Sys.getenv("R_LIBS_USER")
outputs the same value that I previously set above. Also from R, installing packages into the personal library pointed to by R_LIBS_USER works fine. So far, so good.
With version 0.97.551 of RStudio installed, executing the same code above through RStudio also outputs the same value (as expected). However, from RStudio, my attempts at installing packages into the personal library fails. The error message effectively states that RStudio is unable to write to the personal library defined by R_LIBS_USER.
Before posting to stackoverflow, I checked the support forum for RStudio (http://support.rstudio.org/help/discussions/problems/4608-change-personal-library-for-installing-packages) where an admin states that the problem has to do with R and not RStudio. The admin goes on to reference the RStudio document generated by code
?.libPaths
in the RStudio IDE. The admin also provides additional guidance through link http://support.rstudio.org/help/kb/troubleshooting/getting-help-with-r.
After reviewing the IDE-generated document and forum link, I've determined that my environment is set up correctly. And yet, RStudio still fails.
Has anyone been able to get RStudio personal library working with a filesystem location other than the defaults?
I should clarify my needs a bit more. The environment to which this application will eventually be deployed prohibits normal users from running RStudio as administrators, hence the focus on R_LIBS_USER personal library. So although I know this would work, it is not a realistic option for me.
What I need is for RStudio to exclusively write to R_LIBS_USER and not attempt to also write to R_HOME (my assumption of what I think it is actually attempting to do.)
Add a line .libPaths("~/your-lib-path-here") to your .Rprofile and restart R. .libPaths() lets you write as well as read the the set of default libraries.
Alternately, if you can control the installation commands (i.e. you need your library to be available but it doesn't have to be the default), most R commands such as install.packages have a lib parameter that lets you manually specify the library to install to.
You might consider using an R package management system such as Packrat, which automates the job of installing your application's dependencies to a private library without you having to set it up manually. (Full disclosure, I'm a contributor to this package.) It works under RStudio.