Related
I am having an issue starting RStudio (desktop) that I did not have before.
When I fire-up RStudio, within seconds, the grey screen freezes with the following error message:
RStudio Initialization Error
Unable to establish connection with R session
Once I click 'OK', I get the following two error messages:
RStudio
Unexpected exception: The complexity of the regular expression exceeded predefined bounds...
and...
R encountered a fatal error. The session was terminated.
Any help in resolving these errors is much appreciated.
The "unexpected exception" error reads as though something's going wrong with RStudio trying to run something it's loading automatically as it is starting up. So, the related question is: how can I start RStudio fresh without opening any of the previous files/code/data?
I have tried uninstalling and reinstalling both R and RStudio, and R is installed fine (I can open and work on the R console).
I am working with:
Mac OSX 10.10.5
R 3.3.3
RStudio 1.1.423
Thank you!
Just received word from the RStudio team and their solution worked for me.
Indeed, RStudio is crashing while attempting to open a file you had
opened from a previous session. You should be able to work around this
by resetting your RStudio state.
The instructions to reset RStudio are here. Relevant excerpts:
RStudio Desktop stores your custom settings and options in a hidden
directory called RStudio-Desktop. If this directory does not exist,
RStudio will create it on start up. This directory includes user
settings, log files, and other state information. Removing (or
renaming) this directory will reset RStudio's state analogous to a
fresh installation.
We recommend renaming this directory to create a backup version
instead of completely deleting it. This allows you to save your
settings, in case you want to revert back to them. Additionally, if
you experienced a crash or RStudio failed to start, this directory may
contain vital information for determining the source of the error. In
this case, we recommend renaming this directory to
backup-rstudio-desktop and sending it along if asked by RStudio
Support.
So, simply removing the ~/.rstudio-desktop file (actually, renaming it to ~/backup-rstudio-desktop so that I have a backup) just solved the start-up issue!
As a FYI to anybody who tried the solution above without success, I ended up updating/reinstalling the xfun package (install.packages("xfun")), which resolved this issue for me when resetting my RStudio state did not.
I've found a number of questions related to this warning when installing or updating packages in R/RStudio, but none seem to completely match my situation:
Corporate Windows 7 system, so no access to admin privileges
No way to make changes to McAfee Anti-Virus exceptions lists
R is fully installed in the user space C:\Users\[myname]\R
RStudio fully installed in userspace C\Users\[myname]\RStudio
no permission issues in either of the directories... I have full access control over them
Problem only started after installing R 3.4, but RStudio has randomly failing at start or hanging for a few months now
R_LIBS_USER added as user environment variable, pointing to right directory
.libPaths() show correct directories, both system and user
R version 3.4.2, RStudio version 1.0.153
Uninstalled both R and Rstudio and did a clean re-install of both
Tried trace(utils:::unpackPkgZip,edit = T) and edited Line 140 Sys.sleep(0.5) to Sys.sleep(2), which sometimes works temporarily but the edit won't stay put... resets to Sys.sleep(0.5) on every session restart
Happens in both RStudio and RGui
Any package larger than a few Kb gives the message:
package ‘packagename’ successfully unpacked and MD5 sums checked
Warning in install.packages :
unable to move temporary installation ‘C:\Users\[myname]\R\win-library\3.4\file2b884fc37c13\packagename’ to ‘C:\Users\[myname]\R\win-library\3.4\packagename’
The packages are failing to install or update. So, my questions are:
is there a way to avoid the problem altogether that doesn't require admin privileges or changes to the antivirus policies?
is there a way to get the edit to unpackPkgZip to save permanently?
At this point, I'm stumped. I suspect it has something to do with the antivirus temporarily locking the file/directory after download, but I can't do anything about it from that end. The Sys.sleep(2) seems to do the trick, but I can't keep doing that before every package install or update and can't seem to get the edit to stay put.
This was the only thing that worked for me on this issue (the uninstalling antivirus software didn't get me anywhere, unfortunately), so hopeful it works for you.
On Windows systems, sometimes installation of libraries may be running too fast, creating the error "unable to move temporary installation". Then the package is not found in the user library, because it hasn't been moved over...
To fix, try: trace(utils:::unpackPkgZip, edit=TRUE)
Then go to Line 140 in the code and change Sys.sleep(0.5) to Sys.sleep(2.5)
This is a nice longer term solution that does not require manual package moving, uninstalling software, replacing admin responsibilities, or individually routing packages to certain locations.
My original reply is below, but I've subsequently found a better solution.
Execute the following line:
Trace(utils:::unpackPkgZip, edit=TRUE)
Note that there three colons in there, not two.
Then edit line 142, from Sys.sleep(0.5) to: Sys.sleep(2.0), and click to save the edit (the line number may vary slightly). Unfortunately this does not hold across R sessions, but it only takes 10 seconds to do this, and then you can install packages for the current session to your heart's content.
Original answer:
I ran into the same problem at work. I was able to use Sheldon's suggested approach, but as noted that can get tedious quickly. As an alternative, I found I could go to the location of the downloaded zip file(s) in my temp directory (as reported by install.packages), unzip the file or files (there will be multiple zip files if there are dependent packages), and then move or copy all the unzipped directories straight into my R\win-library\3.4 directory. This isn't a whole lot of fun either, but I find it to be less painful than stepping through the debugger, per Sheldon's method, especially when multiple dependencies are involved and also have to be installed.
If you cannot turn off your antivirus here is a workaround that I found that doesn't involve editing the unpackPkgZip file. 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 want to make this change more permanent you can add the debug code into your Rprofile file, see here, but you'll still need to use step through the unzip function each time a package is installed.
Got the same error - seems to be a company gp / access security problem.
It might also be worthwhile checking whether the folder it fails to write to has a Read Only structure (Right Click - Properties). This folder's address can be found by running: .libPaths()[1] in R.
An ad hoc solution to this problem is to unzip and store the downloaded (but not moved) packages using a piece of R code below. You will get an error stating where the binary packages are located (something like: C:/Users/....AppData/...)
Now you can simply unzip the files from here to your .libPaths() location
zipF <- list.files("C:/Users/<YOURNAMEHERE>/AppData/Local/Temp/Rtmp4Apz6Z/downloaded_packages", full.names = TRUE)
outDir <- .libPaths()[1]
for(i in 1: length(zipF)) {
unzip(zipF[i],exdir=outDir)
}
A more general solution will still be extremely worthwhile, as this is unfortunately a common problem when updating R on Windows.
We've had the same problem at my workplace, and one of my coworkers discovered a great workaround. Unfortunately it's a temporary thing you'll need to do each time you install packages, rather than a permanent fix. We're running corporate Windows 8 (no admin privileges) with McAfee, and I've tested this in R 3.4.0-3.4.3.
Temporarily turning off McAfee's "On-Access Scan" feature (in Threat Prevention) solved this for us -- R packages now all install on the first try the way they're intended to. Here's detailed steps to turn that off:
Right-click the McAfee icon in the notification area at the right of
your taskbar, and select McAfee Endpoint Security.
Click on Threat Prevention. This opens up a screen where you should see categories such as "Access Protection", "Exploit Prevention", and "On-Access Scan".
Un-check "Enable On-Access Scan", and then click Apply. (NB: it's
easy to forget to click Apply, but it's essential)
Once you've installed your packages, it's best to repeat the process to turn On-Access Scan back on.
I fixed my instance of this problem (Windows 7) by removing the 'Read-Only' attribute of the folder R was trying to move stuff to.
I went to the Run command from the Start menu in Windows (7) and typed
attrib -r +s drive:\\
Note that just right clicking the folder and trying to change properties didn't take, as per this link from Microsoft: https://support.microsoft.com/en-us/help/326549/you-cannot-view-or-change-the-read-only-or-the-system-attributes-of-fo
Hope that helps someone.
I hope this change doesn't screw me in other ways.
This was the error message that was spit out for me:
package ‘mlogit’ successfully unpacked and MD5 sums checked
Warning in install.packages :
unable to move temporary installation ‘C:\Users\E\Documents\R\win-
library\3.4\file9ec6cfb5e40\mlogit’ to ‘C:\Users\E\Documents\R\win-
library\3.4\mlogit’
The downloaded binary packages are in
C:\Users\E\AppData\Local\Temp\RtmpS0uNDm\downloaded_packages
What I did was went to where the package was downloaded (C:\Users\E\AppData\Local\Temp\RtmpS0uNDm\downloaded_packages) and then copied that zipped file to the desktop then used Winzip to unzip to my file directory where all the packages for R are stored (C:\Users\E\Documents\R\win-library\3.4). It now will load in R.
library("mlogit")
Loading required package: Formula
Loading required package: maxLik
Loading required package: miscTools
....
It worked well for me as it was the only package that was not downloading for some reason. Might not be helpful if you have to do this for every package.
I also found one solution if above solutions wouldn't work in corporate antivirus.
First change the path of package installation use this command and execute in R:
install.packages('caTools','D:\\ML\\Tools\\Installed\\RPackages')
Now it will show a console's error that unable to move and the package is placed on to some location. just remember this location, we need this zip file for further operations.
Now use this command:
install.packages("D:/ML/Tools/Installed/RPackages/caTools_1.17.1.zip", repos = NULL, type = "win.binary", lib="D:/ML/Tools/Installed/R-3.4.3/library")
I struggled with the same issue. For me (on Windows 10), the issue was using MalwareBytes (Premium trial). I uninstalled it and went back to using Windows Defender, and the issue was resolved. Perhaps if more time, I can find out how to create an exception and/or file checking delay for MalwareBytes (i.e., which is a pretty good program), but the user-guide (https://www.malwarebytes.com/pdf/guides/Malwarebytes-User-Guide.pdf) is unclear on this.
Extending the Sys.sleep value to 3.5 on line 142 in the unpackPkgZip function works manually via
trace(utils:::unpackPkgZip, edit=TRUE)
However, it can also be done programmatically by running the following before install.packages:
localUnpackPkgZip <- utils:::unpackPkgZip
body(localUnpackPkgZip)[[14]][[4]][[4]][[4]][[3]][[3]][[2]][[2]] <- substitute(3.5)
assignInNamespace("unpackPkgZip", localUnpackPkgZip, "utils")
This must be run every time you have a new session. You can run it multiple times in the same session without issue.
If you run the below statement right before the install.packages expression then it should install the package:
trace("unpackPkgZip", where=asNamespace("utils"), quote(Sys.sleep(2.5)), at=14L, print=FALSE)
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
I just downloaded R3.0.0 in Windows 7, 64 bit.
When I click on the R icon, R launches but with the following error and warning
Error in loadNamespace(name) : there is no package called ‘modeltools’
During startup - Warning message:
unable to restore saved data in .RData
and when I try to start RStudio, it does not launch but says
The R session had a fatal error
Below is a screenshot of the current home page for RStudio support:
A simple reinstall should solve your problem. Do be sure to verify the downloaded file's integrity by checking its MD5 hash. I'm not a Windows user so I can't recommend any particular software in particular to do this. I guess a good starting point would be Microsoft's FCIV (read about it here and here). But, I'm sure there are lots of GUI alternatives too.
At the RStudio download page you'll notice that the correct MD5 hashes are listed, along with the correct file sizes.
As for your error about the .RData file, that sounds like a corrupt .RData file that should be deleted. Most likely, somewhere along the line, you clicked on "yes" when R asked you if you wanted to save the current session (rather than you explicitly deciding to save the session, and thus, giving the file a proper name). Since the file has a dot before it, you'll probably need to enable "show hidden files and folders" to find it.
Also, remember that after reinstalling R, you'll have to also reinstall all of your installed packages before you can use them! After you have R and RStudio back up running, try something like:
update.packages(checkBuilt = TRUE)
to reinstall all of the packages you installed from CRAN. If you've installed packages from GitHub and other places, you would need to reinstall those manually.
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