Error in install.packages :
path[1]="\Users\name\Documents\R\win-library\4.1": Access is denied
I am trying to install basic r packages, and keep getting this error even though I have full permissions for this folder. I have tried different packages so it is something going on with my permissions.
Hey I figured it out using this guide I was confused because I had permissions to the document folder but because it was being backed up to the network I was getting an error. I also had to manually set permissions to the r-library files to make sure they weren't 'read only'
I have had this problem in the past. The way I fixed it was to close R, navigate to C:\Users\name\Documents in Windows Explorer, delete a file called '.Rhistory' located in that directory.
I then reopened R and then used the install.packages function as normal, and it ran with no problems.
I am new to Version control and this is my first attempt. I am also a novice in R. just did an online course. I have installed Git and was trying to add the Version control through Rstudio Global options. The Git executable file path shows "user/bin/git" But when I go to create a Project>version control>Git- I get an error "Git was not detected on the path" I dug deeper and ran cmd in the mac terminal- which git and got the location as "/usr/local/bin/git", I also did a $ git --exec-path and got the location as "/usr/local/Cellar/git/2.30.0/libexec/git-core" I understand the executable path is somewhere else. I understand that I need to change the path but Rstudio is not allowing the changing of the path, and I am unable to edit the path to "/usr/local/Cellar/git/2.30.0/libexec/git-core" from "user/bin/git". I tried manually entering but that doesnt work, I browsed through the file s and sub folders and selected the executable file location , but it still doesnt change. Please help.
Welcome to stackoverflow: You can find a step by step support on the official support site of rstudio. Here you get detailed instructions on how to use version control with RStudio: https://support.rstudio.com/hc/en-us/articles/200532077-Version-Control-with-Git-and-SVN
I'm working in RStudio and am attempting to install the dplyr package. I have installed various other packages without problem but have hit a problem with this.
It seems there are various parts to the install, some of these worked but the problem happens when I get 'the dependency BH'. This is the error:
>Installing package into ‘\\xxxxxxxx.local/Desktops/jagnew/My Documents/R/win-library/3.3’
(as ‘lib’ is unspecified)
also installing the dependency ‘BH’
>trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.3/BH_1.62.0-1.zip'
Content type 'application/zip' length 16150075 bytes (15.4 MB)
downloaded 15.4 MB
>trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.3/dplyr_0.5.0.zip'
Content type 'application/zip' length 2556205 bytes (2.4 MB)
downloaded 2.4 MB
>Error in install.packages : cannot open file '\\xxxxxxx.local/Desktops/jagnew/My Documents/R/win-library/3.3/file142032c9327b/BH/include/boost/function/detail/gen_maybe_include.pl': Permission denied
I have changed the directory/libpath as it did not appear that the file was downloading to the correct folder. file142032c9327b is now in the correct path, but path specified in the error is only correct up to /boost, there is no function folder here..?
I'm not sure if this missing folder is the issue, as the error says 'Permission denied', but it seems odd.
I had the same issue. Tried doing the following and worked for me:
Run the RStudio as administrator
Under the Packages tab, click Install and change Install to Library option to C:/Program...../R/../library and select the desired package to install.
Hope it works.
I had the same problem. R gave me an error message whenever I tried to install a new, or update an existing package. I don't remember what the message said exactly, but it was saying "Cannot open file (...) access denied". I tried all the following. Not sure what exactly fixed the problem, but now I can update and/or install new packages:
Open R/RStudio as administrator;
Change the R library folder (where packages are installed) security settings, and grant full access to my computer user account. Link1, link2;
(I think this was what fixed the problem) Follow instructions on this link. It prompted me to install another package, "devtools". Then it worked.
Well, I think my problem was a special case, but it might benefit someone. I had the Windows Defender Ransomware Protection set to ON. That was blocking rsession.exe by default. Allowing rsession.exe solved the problem.
TL;DR
The "Documents" (or "My Documents") directory is a special location in Windows. I don't know if the system itself processes its permissions differently or if antiviruses target operations inside this directory more strictly, but many R users have issues installing packages in the personal library inside this folder (even if running R as administrator). Other answers haven't worked.
For me, what solved the problem was to put the personal library directly under X:\\Users\username\ instead of under Documents, which is the R default on Windows. To make it permanent, I set a user environment variable R_USER to %USERPROFILE%. Here is a nice guide of how to set environment variables in Windows.
Note: after this change, you may need to move your .Rprofile, .Renviron, etc. files from Documents to the user profile directory.
Details
The default location for R's user "home" directory on Windows is X:\\Users\username\Documents. This is because there is no concept of HOME in Windows, just of a "personal" directory (Documents): https://cran.r-project.org/bin/windows/base/rw-FAQ.html#What-are-HOME-and-working-directories_003f
Therefore, by default, the personal library location is under X:\\Users\username\Documents\R\win-library\X.Y\. You can get the exact location on your machine with this command in the R console:
Sys.getenv('R_LIBS_USER')
I was getting this same cannot open file error when trying to install or update packages, even when running as administrator. I suspected of directory permissions, checked it within the directories' "properties" without luck. Removed the whole R\win-library tree and recreated it and nothing... Finally, I tried to move the personal library location to my users' directory:
.libPaths('X://Users/username/R/win-library/X.Y/')
And it worked!
Warning in install.packages :
cannot create file '/usr/local/Cellar/r/3.6.2/lib/R/doc/html/packages.html', reason 'Permission denied'
Warning in install.packages :
cannot update HTML package index
I had the same permission issue when trying to download a pkg--ISLR. Fixed it after following the above answers.
In case, some are new to R studio like me. These were my steps to install a pkg.
Click Terminal next to Console in R studio
Type sudo r, to run r as an administrator
install.packages("ISLR") to install your package
--- Please select a CRAN mirror for use in this session ---
https://cran.rstudio.com/src/contrib/ISLR_1.2.tar.gz
Secure CRAN mirrors
1: 0-Cloud [https] 2: Australia (Canberra) [https]
3: Australia (Melbourne 1) [https] 4: Australia (Melbourne 2) [https]
Pick a number -- a mirror site, then click enter.
Voilà! Package installed.
I had faced also this issue. The one and only solution that helped me was to turn off my firewall. Then I was able to download all packages.
The problem solved for me after running R in admin mode and disabling Antivirus.
Translating #Shubham Yadav's answer to code mode would be something like this: install.packages("your_package", lib = "C:/Program Files/R/R-4.0.3/library")
It's working for me (running RStudio as admin, course).
This procedure worked for me.
Removed existing package with remove.packages()
ran RStudio as an admin
Installed by specifying the libpath: devtools::install_github('https://github.com/Rdatatable/data.table/tree/frollmax', lib=.libPaths()[2])
For me what worked was manually deleting within the library directory the folder that I had problem with updating. And then install.package() again.
I had faced the same issue.
I tried below steps to resolve this issue:
Launch RGui application.
Go to Packages section and select Install Packages.
Select the Package that you want to install from the Packages pop up window.
And click OK, that's it package will get successfully installed.
After following above steps, you can run use your package from RStudio.
I ran into this issue today where rlang couldn't install the newest version and so tidyverse wouldn't work. I tried running as admin, changing install location, running as admin, permitting rstudio through Windows Defender Randsomware Protection, and installing DevTools. The only thing that worked was to uninstall RStudio, reboot, reinstall.
I have a computer behind a very restrictive proxy server it only allows me to surf the web and download programs it does not allow programs like the Atom text editor to download it's packages.
My question is how do I install them using only browser based downloads?
It is certainly possible:
Find the package you want to install, for example the activate-power-mode package.
Click on the Repo button to go to the GitHub repository.
Click Releases towards the top of the UI, then click on the most recent release, 0.4.1 in this case.
Download the source code release in either Zip or GZip depending on your platform.
Extract the content of the archive to a known permanent location, I have chosen:
C:\Source\Atom
Run the following command from your terminal / command prompt (make sure to include quotes around the path):
apm link "C:\Source\Atom\activate-power-mode-0.4.1"
Restart or Reload Ctrl-Alt-R Atom and the package will now be installed.
You can alternatively extract the package directly to your ~/.atom/packages folder however you will have to rename the folder to exactly match the name of the package, additionally uninstalling the package from Atom will delete the files which could be annoying if it is an accidental deletion.
Because of package dependencies a safest bet is this:
Install package normally on connected computer
Copy contents from your ~/.atom/packages
Paste contents to ~/.atom/packages on offline computer
Restart Atom
At least this worked for me like a charm.
The answer of Richard Slater is informative and the answer of Andriy Buday could look less professional. But, in my case, the answer of Andriy Buday was also very important.
I tried to install two packages atom-beautify and prettier-atom by following the answer of Richard Slater and had some problems of not being able to find some modules. It was not only me who had these problems. Consider checking the following links.
The issue of "cannot find module event-kit"
https://github.com/Glavin001/atom-beautify/issues/1734
https://github.com/Glavin001/atom-beautify/issues/1366#issuecomment-269716306
When I decompressed a file (atom-beautify-0.30.3.tar.gz) I received from GitHub respository, I could find out directories like appveyor, docs, and examples. But I could not find out a directory named node_modules which was present when I installed this package atom-beautify using Atom Editor online.
To check if the absence of directory node_modules is the only problem, I went through the following steps.
Start Atom Editor.
Install atom-beautify using Atom Editor online like the answer of Andriy Buday suggests.
Close Atom Editor.
Move atom-beautify directory from ~/.atom/packages (that was %HOMEDIRECTORY%%HOMEPATH%.atom\packages in my case because I used cmd on Windows 10) to somewhere else.
Decompress atom-beautify-0.30.3.tar.gz and move or copy atom-beautify-0.30.3 directory from this decompressed result into %HOMEDIRECTORY%%HOMEPATH%.atom\packages as the answer of Andriy Buday suggests.
Rename directory %HOMEDIRECTORY%%HOMEPATH%.atom\packages\atom-beautify-0.30.3 to %HOMEDIRECTORY%%HOMEPATH%.atom\packages\atom-beautify as the answer of Richard Slater suggests.
Move or copy node_modules directory from the directory moved at step 4 into %HOMEDIRECTORY%%HOMEPATH%.atom\packages\atom-beautify.
Start Atom Editor.
I found that no error message appeared and that package atom-beautify worked properly, thus I am thinking that absence of node_modules directory was the only problem of the file atom-beautify-0.30.3.tar.gz I received from GitHub repository.
I am afraid if it is normal that directory node_modules is not contained in the file atom-beautify-0.30.3.tar.gz downloaded from GitHub repository because of any rules I do not know yet, like placing directories like node_modules somewhere else. If there really are such rules and somebody tells me about such rules by adding an answer or a comment here, I will appreciate it a lot.
I am not sure if it is same with all other packages, but I found that it was same at least with package prettier-atom.
I wish it helps somebody.
+++++++++++++++++++++++++++
I found why the directory node_modules was not contained in atom-beautify-0.30.3.tar.gz.
I checked answers of the following link.
How can I manually download packages for atom editor and install them (manually)?
Answer by D3181 included a link to a page of http://discuss.atom.io/ (I could get a helpful answer by Alchiadus from the link) and suggested running apm install in the package's directory. If it is necessary to use a file downloaded from GitHub repository like atom-beautify-0.30.3.tar.gz, it is necessary to run apm install in the package's directory before copying or moving into %HOMEDIRECTORY%%HOMEPATH%\.atom\package (~/.atom/package in case of *nix) of the offline computer.
Decompress the file downloaded from GitHub repository like atom-beautify-0.30.3.tar.gz.
Go into the directory like atom-beautify-0.30.3 of the decompressed result.
Run apm install on an online computer. (If the directory of apm.cmd is not in PATH, run {directory of apm.cmd}\apm.cmd install.)
Rename directory like atom-beautify-0.30.3 to the correct name of the package like atom-beautify.
Move directory with the correct name of the package like atom-beautify into %HOMEDIRECTORY%%HOMEPATH%\.atom\packages of the offline computer.
Run Atom Editor on the offline computer and check if the package works properly.
It seems normal that the directory node_modules is not included the the compressed file downloaded from GitHub repository.
I try install eclim using Graphical Installer by http://eclim.org/install.html tutorial. Installation process complited without errors, but eclim not working. Not found $ $ECLIPSE_HOME/eclimd file on my eclipse root directory, but $HOME/.vim was created succesful.
Where I should look for eclimd?
I just found this thread with no solution trying to figure out the same thing.
I was able to find the launcher under:
"~/.eclipse/org.eclipse.platform_4.7.0_155965261_linux_gtk_x86_64/"
I was just looking for a solution as I was facing the same problem to choose eclipse installation directory otherwise I was unable to proceed eclim installation. However I tried to choose different directories and finally I found the right installation directory
"/Applications/Eclipse.app/Contents/Eclipse"
That worked for me I hope this will help you as well.