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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 developed a solution using R and want to transfer it to the production server (CentOS 7) which has no Internet connection to install packages. To facilitate installation of packages, I used packrat to bundle the packages I used in my R script to the project.
Using packrat::bundle(), I have created a tar file of the project and moved the file to the server and untar the zip file.
According to a post in Blogger, once I open the project, When R is started from that directory, Packrat will do its magic and make sure the software environment is the same as on the source machine.
However, when I open the project in Server (using R-Studio Server 0.99), nothing happens and it throws error of unknown packages.
When manually execute the "packarat/init.R" file below error is thrown
Error in ensurePackageSymlink(source, target) :
Target '/home/R_Projects/prjName/packrat/lib-R/base' already exists and is not a symlink
Well, I found the problem and solve it. The symlink error is related to centOS (it is not related to R). I just simply removed all the folders inside the
/home/R_Projects/prjName/packrat/lib-R
Because these folder exist, the packrat is unable to create symlink with the same name inside the lib-R folder. If I remove them, it will create a link (shortcut) to the actual folder where the r package is located.
Hope it helps future readers.
I am working on a remote server using RStudio. This server has no access to the Internet. I would like to install the package "stringi." I have looked at this stackoverflow article, but whenever I use the command
install.packages("stringi_0.5-5.tar.gz",
configure.vars="ICUDT_DIR=/my/directory/for/icudt.zip")
It simply tries to access the Internet, which it cannot do. Up until now I have been using Tools -> Install Packages -> Install from Packaged Archive File. However, due to this error, I can no longer use this method.
How can I install this package?
If you have no internet access on local machines, you can build a distributable source package that includes all the required
ICU data files (for off-line use) by omitting some relevant lines in
the .Rbuildignore file. The following command sequence should do the trick:
wget https://github.com/gagolews/stringi/archive/master.zip -O stringi.zip
unzip stringi.zip
sed -i '/\/icu..\/data/d' stringi-master/.Rbuildignore
R CMD build stringi-master
Assuming the most recent development version is 1.3.1,
a file named stringi_1.3.1.tar.gz is created in the current working directory.
The package can now be installed (the source bundle may be propagated via
scp etc.) by executing:
R CMD INSTALL stringi_1.3.1.tar.gz
or by calling install.packages("stringi_1.3.1.tar.gz", repos=NULL),
from within an R session.
For a Linux machine the easiest way is from my point of view:
Download the release you need from Rexamine in tar.gz format to your local pc. In opposition to the version on CRAN it already contains the icu55\data\ folder.
Move the archive to your target linux machine without internet access
run R CMD INSTALL stringi-1.0-1.tar.gz (in case of release 1.0-1)
You provided the wrong value of configure.vars.
It indicates that you have to give the directory's name, not a final file name.
Correct your code to the following:
install.packages("stringi_0.5-5.tar.gz",
configure.vars="ICUDT_DIR=/my/directory/for/")
Regards,
Sean
Follow the steps below
Download icudt55l.zip seperately from server where you have internet access with
wget http://www.mini.pw.edu.pl/~gagolews/stringi/icudt55l.zip
Copy the downloaded packages to the server where you want to install stringi
Execute the following command
R CMD INSTALL --configure-vars='ICUDT_DIR=/tmp/ALL' stringi_1.1.6.tar.gz
icudt55l.zip is copied to /tmp/ALL
The suggestion from #gagolews almost worked for me. Here's what actually did the trick with RStudio.
Download the master.zip file that will save as stringi-master.zip.
Unzip the file onto your desktop. The unzipped folder should be stringi-master.
Edit the .Rbuildignore file by removing ^src/icu55/data and ^src/icu61/data or similar lines.
Move the folder from your desktop to the home directory of your server.
Create a New Project in RStudio with ~/stringi-master as the Existing Directory
From RStudio's menu, select Build and Build Source Package. (You may need to first select Configure Build Tools. For Project build tools choose Package then select OK.)
It should create a tar.gz file, in the following format: stringi_x.x.(x+1).tar.gz. For example, if the current version of stringi is 1.5.3, it will create version 1.5.4. (I received a few warnings that didn't seem to affect the outcome.)
Move the newly created package to your local repository. Update the repository index. And install the package.
I am using R 2.13.0 with windows 7, after giving my user full privileges to the R folder (as described here).
This allows me to install new packages just fine.
However, when using update.packages(), to update existing packages, I keep getting the following error (for example, when updating the MASS package):
package 'MASS' successfully unpacked and MD5 sums checked
Warning: unable to move temporary installation
'C:\Program
Files\R\R-2.13.0\library\file6cae3bcf\MASS'
to 'C:\Program
Files\R\R-2.13.0\library\MASS'
Any suggestions on how to fix this?
p.s: Running R as an administrator or shifting the library location out of Program Files is not a solution (it's a hack - but I am looking for a solution)
I found that the problem indeed is the antivirus "real time file system protection". I do the following to fix the problem:
trace(utils:::unpackPkgZip, edit=TRUE)
I edit line 140 (line 142 in R 3.4.4):
Sys.sleep(0.5)
to:
Sys.sleep(2)
I seems like the antivirus stalls the creation of the package tmp dir. After changing it to 2 seconds the error is gone.
EDIT: to do this programmatically execute
trace(utils:::unpackPkgZip, quote(Sys.sleep(2)), at = which(grepl("Sys.sleep", body(utils:::unpackPkgZip), fixed = TRUE)))
(credits #DavidArenburg)
Just to update everyone, I (think that I) found out the source of the problem: antivirus.
The "real time file system protection" was blocking R from copying the files between folders once they were downloaded.
Upon adding the R directory to the exception list (coupled with adding user permission and installing R on D:\R), and the problem went away. With all of this work, I might as well switch to Linux (I should, really...)
(I updated my post with the above information: http://www.r-statistics.com/2011/04/how-to-upgrade-r-on-windows-7/)
I hope it will help someone in the future,
Tal
If you cannot turn off your antivirus, due to corporate policy for example, here is a workaround that I found. Debugging the unzip package function and then stepping through it gives the antivirus enough time to do its job without interfering. Use this command:
debug(utils:::unpackPkgZip)
install.packages("packageName")
and then step through the code (by pressing enter many times) when R starts debugging during the installation.
I found this solution here.
If you can just download the binary straight from CRAN. On windows when downloaded it will be a zip file. Now manually unzip this into the ..library/ folder of your R (.libPaths()). It worked for me on some packages.
I had this problem installing both swirl and dplyr. I am working on Windows 64-bit.
Warning: unable to move temporary installation
What I did is I accessed my temporary files on the C: drive, and opened my file extractor program and I extracted the files from the temp file in the C: drive to my R program files in the C: drive, by manually copying them. THIS WORKED FOR BOTH dpylr and swirl. Stoked!
Cheers,
Peach
Can you not use the lib.loc parameter to only update packages in your personal library (in user)?
There should be no way to enable a normal, non-augmented user to change files in the program files folder, so the only thing you can do (if you don't want to augment the user) is to have R not updating packages there.
A workaround is to avoid installing R in the program files folder (which may be more or less of a hack than just shifting the library location out of it, depending on your point of view).
Finally, if lib.loc doesn't cut it, you can look at the source code for update.packages and create your own customized version that will always avoid the common library location in program files.
I just met the same question, and the solution I found out was that you should install packages using the original R software (plus, you should choose the right mirror site, some of them are blocked). At first I used Rstudio to install packages and I got the same problem as you met. Hope this is helpful.
I have run into this error several times. In my own case, it is because our admins want us to use remote virtual disks (on Windows 7) for our files and everything is locked up tight as a drum. The only way I can use R packages is in a lib directory on that remote virtual disk. This wouldn't be a problem except that the network isn't always smooth and fast. Thus, when I need a package, especially one with several other packages in tow (e.g., MBESS), I either have to go through the get.packages() process multiple times until it finally finishes or make it IT's headache to do quick like the bunny for me. I can't always wait for IT.
I just went to the library folder (Windows XP) and deleted all fileXXXX folders. Reran the install an it is worked.
I had the same problem. Since the issue seems to be the antivirus blocking the transf of a downloaded file, I tried a different download method in the install.packages and it worked.
For example:
install.packages("stringr", method = "curl")
You must go into the properties of the R folder and change the security parameters. You can enable the option to write and modify for all users.
The error : "unable to move temporary installation" is basically arising due to any of the antivirus running on your system.
Try unzipping the downloaded file from the Temp folder into the default library path (you can get it by running .libPaths() in R session).
I'm using a MRAN and I was having so many versioning issues. Trying to work with tidyverse and ggplot2 and by upgrading to the latest version from Microsoft it solved all of my R-Studio versioning issues.
Version info:
Microsoft R Open 3.5.1
The enhanced R distribution from Microsoft
Default CRAN mirror snapshot taken on 2018-08-01.
Download Microsoft R Open 3.5.1
Whenever I try to install a package in R, I get the following error:
Error in readRDS(file) : unknown input format
This just started occurring after I had a system crash. I am running 32 bit R 2.13.0 under windows 7. I tried removing and re-installing R, but continue to get the error. Is there any way I can fix this without deleting everything (i.e. all the packages I've installed) and starting over?
Thanks
These are suggestions I have come across:
Delete your .Rhistory and .RData files in the directory in which you are running R.
Run update.packages()
Try and detect "bad files" in your library directories. You can do this in R
# List the library paths
# The issue is likely to be in the first directory
paths = .libPaths()
## Try and detect bad files
list.files(paths,
pattern = "^00LOCK*|*\\.rds$|*\\.RDS$",
full.names = TRUE)
## List files of size 0
l = list.files(paths, full.names = TRUE)
l[sapply(l, file.size) == 0]
Delete any files/directories highlighted. You could use file.remove() if you really wanted to.
Delete the directory in which you have stored your downloaded packages.
Only solution 3 worked for me.
Ref:
R-sig-Debian mailing list
Option 3 was a combination of answers provided by different people over the last few years, including Chunxiao Xu, Larry Hunsicker and Frank Harrell
Run find /usr/local/lib/R/site-library/ /usr/lib/R/library/ /usr/lib/R/site-library/ ~/.local/lib/ -iname '*rds' -a -size 0 and then delete the files found.
Chunxiao Xu and Rando Hinn's solution above worked for me, with a minor tweak.
First, change directories to your personal R package directory, then run: find -iname '*rds' -a -size 0
Delete the directories containing any 0 length files in the above list. Then reopen R (or RStudio) and reinstall the deleted packages.
You should now be able to list the packages again.
Chunxiao Xu's original suggestion above lists ALL of the R package directories. But the exact locations of these directories will vary from installation to installation, and their addresses will have to be edited for your installation.
Larry Hunsicker
Something simple to try: if it is an .rda file use load instead of readRDS. You can then save the loaded file as an .rds and try readRDS again.
Here is what I had to do to solve this error:
Open your Rstudio, go to install tab under packages
Note your install to library path.(where your package will be saved)
Go to the install library path.And hard delete the recent packages
Refresh you package details in Rstudio
This happened to me after I had to reboot my machine in the middle of installing several R packages. I removed the latest installed packages by physically removing the files in the appropriate library directory, reinstalled them, and all was well. I also had to remove a 00LOCK directory in the library directory.
You might have some problem with R packages .
See if the problem has occurred after you installed some packed or did you copied the packages.
What you can do is Copy all the packages from Library and save it somewhere, then Copy some packages on the Library and restart the R test it and see how it works you have to try with all the packages one by one .
I has the same issue and it was due to package problem.
I also had several problems opening an .RDS file, either "error reading from connection" or "unknown input format". I tried with several R versions, with version 3.4.2. the following worked:
(I accidentally uninstalled rstudio and installed it again, also installed older R version 3.4.2, I don't know if that changes anything)
set up a new working directory
I opened the RDS file directly instead of downloading it (so only saved to temp files), then I was able to open it in R
I moved it from temp files to my new working directory and used the Data_Essay_Account <- readRDS("C:/.../newdirectory/Data_Essay_Account.RDS") command and it worked.
Somehow properly downloading it and then moving it did not work, only after I had it in the temp files. Hard deleting packages did not work for me as I tried that initially.
Unlike the top few answers here, my issue was resolved not by doing anything with my installation of RStudio or cleaning local files, but by re-writing the RDS file.
I could confirm this because the file was stored in the cloud, and reading it from a variety of windows and mac laptops all failed, but similar RDS files from the same S3 bucket worked without a problem.
When I re-wrote the RDS file, the problem went away.
I checked for this issue on several forums and then I tried this and it worked for me:
1) Remove the ggplot2 package first
remove.packages("ggplot2")
2) Then Install the package again
install.packages("ggplot2")
3) restart rstudio and install your package again, hope this helps
Seems that the issue was with the required package (ggplot2 in my case) got corrupt and was hampering the installation of any new dependent package.
I had the same problem as the OP, but in my case the problem .rds files were not 0 bytes but had file size >0 and were full of NULL characters (at least that's what I saw when I opened them in Notepad++)
By using debugonce(loadNamespace) before loading the library that was giving me the error (in my example it was the VIM package) I eventually traced my problem to corrupted .rds files in the META folder of the forcats package, which was installed as a 5th generation import when I installed VIM
(In the rstudio environment pane)
__NamesSpacesLoading__ chr[1:5] "forcats" "haven" "rio" "car" "VIM"
I then fixed by VIM problem simply by removing and reinstalling forcats
Adapting the code in #csgillespie accepted answer, I could have found this by trying to read all the rds files as below
paths = .libPaths()
l <- list.files(paths,
pattern = "*\\.rds$",
ignore.case = T,
recursive = T,
full.names = TRUE)
checkRDS <- function(file) {
tryCatch({
readRDS(file)
"OK"
},
error = function(cond) {
return("Error")
})
}
l[sapply(l,checkRDS)=="Error"]
I was able to fix it by using .libPaths() and finding the 4.1 folder (my version of R was 4.1, so may differ). From there I closed R studio and deleted all the folders for each package.
I reinstalled all packages and found the packages which wouldn't download through the error messages. When I located the packages that didn't download I installed them by using: install.packages("package", type = "binary").
A bit long but solved all my issues.
My mirror was misconfigured. My mirror is Oregon State University because that is what I am closest too. Here is a list of mirrors. Call this code before installing any packages. More information in ?options.
mirror <- "https://ftp.osuosl.org/pub/cran/"
local({
r <- getOption("repos")
r["CRAN"] <- mirror
options(repos = r)
})
The workaround
Execute this command in the R console:
options(pkgType = "source")
You're good to go.