I'm updating the renv folder from a project in order to adjust the libraries, but it seems I'm having a permission problem. After running renv::init() and trying to installing manually the remaining libraries using install.packages() I always get the message
Error: failed to retrieve 'https://cran.rstudio.com/bin/windows/contrib/4.2/ipeadatar_0.1.6.zip' [error code 23]
1: curl: (23) Failure writing output to destination
2: curl: (23) Failure writing output to destination
Using .libPath() I can see that the renv was created in the "AppData" hidden folder
1] "C:/Users/André Ferreira/AppData/Local/R/cache/R/renv/library/MacroBRA_Wrld-09789847/R-4.2/x86_64-w64-mingw32"
So checking my permissions, I couldn't see anything wrong. Any thoughts about this problem? The thing it's that when I open my .Rmd file and try to knit, I receive the same message "1: curl: (23) Failure writing output to destination", now from rmarkdown retrieve installation, so it may be a configuration/permission problem.
Adding "C:\rtools42\usr\bin" and "C:\Program Files\R\R-4.2.1\bin" in the environment variable didn't help.
As I could see, opening an empty file from rstudio, I could use install.packages() without problem.
Although this doesn't solve the problem directly, you can also instruct renv to use a different library path with something like:
# use a project-local library path
RENV_PATHS_LIBRARY = renv/library
in your project's .Renviron file. Depending on your environment, you might also consider placing the library path in an alternate location.
See https://rstudio.github.io/renv/articles/packages.html#r-cmd-build-and-the-project-library for more details.
installed.packages() command in R lists your installed packages. Mine was working for almost a year and then this command randomly started throwing an error. As this is a built-in command, I am not even sure how to "reinstall" it or address this. Any ideas how to fix the error and get the command working again?
> installed.packages()
Error in gzfile(file, mode) : cannot open the connection
In addition: Warning message:
In gzfile(file, mode) :
cannot open compressed file `'C:\Users\Mitch\AppData\Local\Temp\Rtmp6Dawpa/libloc_190_4464fd2b.rds', probable reason 'No such file or directory'`
One suggestion on here involved this in combination:
.libPaths()
installed.packages(lib.loc = 'my path')
The results of this produced yet another error as shown here. Looks like an issue with the installed file still but how to address is the question:
> installed.packages(lib.loc = 'C:/ProgramFilesCoders/R/R-3.3.2/library')
Error in gzfile(file, mode) : cannot open the connection
In addition: Warning message:
In gzfile(file, mode) :
cannot open compressed file 'C:\Users\Mitch\AppData\Local\Temp\Rtmp6Dawpa/libloc_190_4464fd2b.rds', probable reason 'No such file or directory'
>
That is odd.
What version of R are you running, standard R or Microsoft R? And did you recently update?
If you did recently update, perhaps your packages did not get copied over, hence the 'No such file or directory' statement.
If you haven't updated, I would install a newer version and see if it fixes the issue.
If your uncertain, you can always use the updateR function to check if you have the latest version and choose to install it or not.
library(installr)
updateR()
Good luck,
I think the issue lies in terms of the where the function is looking for the package information. installed.packages() needs an argument lib.loc.
From official documentation
lib.loc character vector describing the location of R library trees to search through
Looks like the function for some reason is looking in AppData\Local\Temp which is the download location and not the installed location.
Without looking at your R_Home and .libPaths() is difficult to nail down where the problem is, however running .libPaths() should give you one or more paths as shown in the below example. None of these should be temp locations.
>.libPaths()
[1] "C:/Users/UserName/Documents/R/win-library/3.4"
[2] "C:/Program Files/R/R-3.4.0/library"
If not, you can set the path within the .libPaths("your path") or pass the path of the library as part of installed.packages(lib.loc = 'your path') and try again.
Sometimes the most simple obvious solution is what works:
I closed my RStudio environment saving it to .RData
I re-opened RStudio and tried the command again
it worked
For the future, some good ideas got posted on here before I thought to try the above. Here are the suggestions that others included in case the above does not work if this problem is encountered by anyone in the future:
Use .libPaths() to find out proper path where this is installed, and then re-run the command with the path included in it like so: installed.packages(lib.loc = 'your path')
Try debugging it with: debug(installed.packages); Expectation is that we will likely find something wrong with .readPkgDesc(lib, fields) while stepping through debug. This was not tried yet so you may encounter things not written up here when you do try it.
Try Updating R in case it is out of date with these commands: library(installr) and updateR().
I am using RSelenium and want to set a Firefox profile. So I tried to reproduce the example of the answer to this question. However, no matter what I change I always get the following error. What am I doing wrong?
I already read in the RSelenium manual that for windows systems RTools should be installed when one wants to make a Firefox profile. I did but nothing changed.
The error is the following:
Error in file(tmpfile, "rb") : cannot open the connection
In addition: Warning messages:
1: running command '"zip" -r9Xjq "C:\Users\mariu\AppData\Local\Temp\RtmpQfl3bl\file15c41fc2411d.zip" "C:\Users\mariu\AppData\Local\Temp\RtmpQfl3bl/firefoxprofile/prefs.js" ' had status 127
2: In file(tmpfile, "rb") :
cannot open file 'C:\Users\mariu\AppData\Local\Temp\RtmpQfl3bl\file15c41fc2411d.zip': No such file or directory
the problem is that Rselenium cannot create a zip file of your Firefox Profile (error status 127), therefore cannot read it in the next command line.
I resolved following this answer:
Create zip file: error running command " " had status 127 .
Do as the link says , shut down R, restart your pc and it should work.
Thanks,
Rob
Sometimes, for some reasons, it is not enough to add Rtools file location to Environmental Variables as was mentioned here. To solve the problem you need to add path within R using folowing code:
writeLines('PATH="${RTOOLS40_HOME}\\usr\\bin;${PATH}"', con = "~/.Renviron")
Then PC needs to be reseted. After that you can check whether path was setted correctly.
Sys.which("make")
## "C:\\rtools40\\usr\\bin\\make.exe
If output of sys.which is "" then something went wrong. By the way the entire procedure has been described here: https://cran.r-project.org/bin/windows/Rtools/.
I'm trying to run two things: first, I'm creating a PDF with 4x5, ending with dev.off(), and then trying to create a new graph. However, after starting the second plot, I get:
Error in gzfile(file, "wb") : cannot open the connection
In addition: Warning message:
In gzfile(file, "wb") :
cannot open compressed file '/var/folders/n9/pw_dz8d13j3gb2xgqb6rfnz00000gn/T/RtmpTfm1Ur/rs-graphics-822a1c83-b3fd-46c3-8028-4e0778f91d0c/4db4b438-ac35-403b-b791-e781baba152c.snapshot', probable reason 'No such file or directory'
Graphics error: Error in gzfile(file, "wb") : cannot open the connection
What is this error? The working directory is one I have read/write access to, and my hard drive isn't full.
Also, I'm using RStudio.
This is a bit late but for anyone coming here for help, I got this error when I was trying to write a file from RStudio and my destination file path was very long. I realized this could be a problem because when I wrote the file to another location with a shorter name and tried to copy it into my original destination, Windows gave me an error saying "File path too long". You might need to save the original file into another location with a shorter absolute path.
Maybe you should look here. At the end it says
Note:
The most common reason for failure is lack of write permission in the current directory. For save.image and for saving at the end of a session this will shown by messages like
Error in gzfile(file, "wb") : unable to open connection
In addition: Warning message:
In gzfile(file, "wb") :
cannot open compressed file '.RDataTmp',
probable reason 'Permission denied'
So rapidly, if you try getwd(), look at where is your working directory set. If you're trying to save your document in a place where it's not in your current working directory, it will throw you this error.
At the end of your error message, it says probable reason 'No such file or directory'
Graphics error: Error in gzfile(file, "wb") : cannot open the connection
My diagnosis would be simply that it's trying to save your item in the wrong place and RStudio is not able to find the right place.
This burned me so hopefully saves someone else some toil. The issue was that the classifiers loaded just fine on OS X but on the Linux deployment system they would fail with the error listed in the question. The issue was the the files on the disk had extension abc.RData but the code modelAbc <- readRDS(file="abc.Rdata"). The difference in the upper and lowercase D in the .RData vs .Rdata extension would fail on Linux. It was not very noticeable but check your extensions for case.
You may have no permission to save file in the directory.
On RStudio, get your working directory by getwd().
Then, go to the directory in linux and observe its owner by ls -l.
Now you can change the owner of the directory by chown -R username directoryname.
But you must be root.
Problem resolved by specifying full file path:
saveRDS(df,'C:\\users\\matt\\desktop\\code\\df.Rdata')
I faced this issue lately. Try turning off your anti-virus and build the package, it might help. It worked for me. Usually anti-virus blocks the permissions and you could avoid it by disabling for sometime just before building a package.
I was trying to save an RDS file to my local Dropbox folder so it syncs with my Dropbox.
I figured out I got the same error because I was trying to create a new folder and looks like saveRDS cannot create a new folder, but it can add files to existing folders. So I changed the path to add the file into an existing folder and it worked!
In my case it was Windows Defender which was preventing Rstudio to write any file on hard drive. Either you need to turn Controlled Folder Access off or add Rstudio in the exclusion list.
I also had this problem when working with RStudio and R Markdown. I was getting this error message and had an annoying number of fatal errors which closed RStudio. My issue was that I was working off a network drive and either the name was too long, as in #AHedge above or my network firewalls were giving me trouble. For the moment, I have moved my working files to my desktop and things seem to be working fine. Not sure what this means for my file management over time.
Just want to add more clarity(scenarios in my experience) to what M Beausoleil mentioned.
When you are using a shared-working-directory and trying to rewrite the RDS files which are already existing in a working-directory written by some other user, you get this error.
As some people have already quoted that deleting the existing RDS files or changing the working directory works. It's not a magic. It just works because you are writing a new RDS file and not trying to re-write the old ones.
I came into the same problem after I re-install a new version of RStudio.
The Rmarkdown file I created using old version of RStudio shows the same problem.
When I use ggplot() to draw a picture the error code are as follow:
Warning in gzfile(file, "wb") :
cannot open compressed file 'I:/Rlearning/.Rproj.user/shared/notebooks/58A1385C-PCA作图/1/2C15461A183AC56C/cco192gb0pow1_t\_rs_rdf_32004888ecb.rdf', probable reason 'No such file or directory'
Error in gzfile(file, "wb") : cannot open the connection
Solution:
Create a new Rmarkdown file
Delete all codes
Copy your old Rmarkdown code into it.
I had the same problem.For me, it was caused due to not having enough disk space on the drive where R studio was installed.Freeing up space works.
The reason for the error is that your username is Chinese.Please create new user folder with English in the user directory.For example, you could name the folder for "DavidSmith".Then, you need create three folders("AppData","Local","Temp").File directory C:\Users\DavidSmith\AppData\Local\Temp.
In the Advanced system settings which will modify the environment variables TMP and TEMP C:\Users\DavidSmith\AppData\Local\Temp.Save them.
After modification, open RStudio and try again.
Notice:TMP and TEMP are modified in the USER VARIABLE.
I just ran into this problem after changing my system locale.
Check your locale using Sys.getlocale().
Change it to appropriate one using Sys.setLocale("LC_ALL","ENG") (replace "ENG" with appropriate one)
I can't say with certainty which locale would be appropriate, but it seems to be coherent with default OS one.
Hope this helps!
I had this error because of an invalid character in the filename to be used to save the file, in my case "/" (there are many such characters that cannot be used in a filename). I removed the character and it was solved.
In my case, I received the error "Error in gzfile(file, "wb") : cannot open the connection" when trying to exit R in the Anaconda Prompt and saving workspace image. I am using Windows 10 and R-3.5.2. To fix it, I had to go to the Program Files folder, right click and the R folder, then selected Properties. Selected the Security tab, then, in the Group or user names box, selected Users, then clicked Edit. In the Permissions for Users, I checked Full control and Modify and saved the changes. Then I was able to save the workspace image.
I have another instance of this error which seems to be new (or at least not listed here or here: apparently it's not OK to save a file with the name aux.RData. I guess it's a reserved filename.
x <- rnorm(9000)
save(x, file = "aux.RData")
Error in gzfile(file, "wb") : no se puede abrir la conexión
Also: Warning message:
In gzfile(file, "wb") :
cannot open compressed file 'aux.RData', probable reason 'No such file or directory'
But when I change the filename saves with no problem:
save(x, file = "aux_file.RData")
Haven't seen this case in the other answers:
if this seems to happen all the time, and to be very persistent when it does happen, check the default directory in your file handling software connection.
In my case FileZilla was logging on to my DigitalOcean droplet as "root" and whenever I used FileZilla to create a directory it was setting write permissions to "root", whereas my RStudio on the same droplet read/wrote as "My_Name". Anytime I set something up in FZ (e.g. large imported files, renamed or copied) the permissions would switch and I'd get this error.
If this is what is causing frequent error messages it can be solved instantly with chown -R My_Name directoryname but in the longer run, if you are going to be using your file handler to define and create a lot of directories, it will pay to create a connection whose default name is the same name you use for RStudio.
In my case, when it happened first, months ago, the solution here worked.
But recently, it came back, constantly... What solved this time was to change the anti-virus. I have not just the Windows defender, but also a 2nd anti-virus, the same in both times. I ended up deinstalling it and installing another antivirus... After this, the problem did not happen again...
After several days trying to solve this same ERROR or problem in my case (Windows 10 and R), I tried to save my file(file.RData) in D disk instead of C disk (where I always was working and I have installed R) and it was fine, without problems,my file was saved in D:/Users.When I tried many times to save it in C disk, always gave me Permission denied.
save(Myfile, file="D:/Users/Myfile.RData")
I encountered this same issue when trying to save an Rds file from an Markdown file. Changing my relative file path to an absolute file path worked for me.
In my case, this error was because the file that I wanted to re-write, was read-only (for whatever reason, I didn't do it myself). I just right-click on the file's name in the folder and unchecked the read-only property. After that it worked.
I'm trying to get R (running on Windows) to download some packages from the Internet, but the download fails because I can't get it to correctly use the necessary proxy server. The output text when I try the Windows menu option Packages > Install package(s)... and select a CRAN mirror is:
> utils:::menuInstallPkgs()
--- Please select a CRAN mirror for use in this session ---
Warning: unable to access index for repository http://cran.opensourceresources.org/bin/windows/contrib/2.12
Warning: unable to access index for repository http://www.stats.ox.ac.uk/pub/RWin/bin/windows/contrib/2.12
Error in install.packages(NULL, .libPaths()[1L], dependencies = NA, type = type) :
no packages were specified
In addition: Warning message:
In open.connection(con, "r") :
cannot open: HTTP status was '407 Proxy Authentication Required'
I know the address and port of the proxy, and I also know the address of the automatic configuration script. I don't know what the authentication is called, but when using the proxy (in a browser and some other applications), I enter a username and password in a dialog window that pops up.
To set the proxy, I tried each of the following:
Sys.setenv(http_proxy="http://proxy.example.com:8080")
Sys.setenv("http_proxy"="http://proxy.example.com:8080")
Sys.setenv(HTTP_PROXY="http://proxy.example.com:8080")
Sys.setenv("HTTP_PROXY"="http://proxy.example.com:8080")
For authentication, I similarly tried setting the http_proxy_user environment variable to:
ask
user:passwd
Leaving it untouched
Am I using the right commands in the right way?
You have two options:
Use --internet2 or setInternet2(TRUE) and set the proxy details in the control panel, in Internet Options
Do not use either --internet2 or setInternet2(FALSE), but specify the environment variables
EDIT: One trick is, you cannot change your mind between 1 and 2, after you have tried it in a session, i.e. if you run the command setInternet2(TRUE) and try to use it e.g. install.packages('reshape2'), should this fail, you cannot then call setInternet2(FALSE). You have to restart the R session.
As of R version 3.2.0, the setInternet2 function can set internet connection settings and change them within the same R session. No need to restart.
When using option 2, one way (which is nice and compact) to specify the username and password is http_proxy="http://user:password#proxy.example.com:8080/"
In the past, I have had most luck with option 2
If you want internet2 to be used everytime you use R you could add the following line to the Rprofile.site file which is located in R.x.x\etc\Rprofile.site
utils::setInternet2(TRUE)
I've solved my trouble editing the file .Renviron as documented in Proxy setting for R.
EDITED
The solutions based on the setInternet2 statement do not work with the recent R versions because setInternet2 is declared defunct.
I'm using the 4.2.1 (on Win 11Pro) while I never had any problems in previous versions .
So to solve the problem need to modify some config files in order to fix the proxy issue not only for packages installation but, in general, also to acced to a remote resource (ie. boundary maps in my case).
The question "Proxy setting for R" collect a lot of solutions. I've found that this one has solved both my problems (packages installation and remote resources) explaining step-by-step how to edit the file .Renviron
Other solutions based on the customization of the file Renviron.site for me doesn't work
install.packages("RCurl")
that will solve your problem.