I am a starter in R and new to StackOverflow and this is the first time I raise a question, I hope i'm following all the rules...
Anyway. I got R (3.5.0 version) and R-Studio on my laptop with Win 10 Home installed (under the same parent folder 'D:\') and reset the temporary file directory to a folder in D:\ so that the Chinese in C:\Users\中文\documents (which is the default place for tempo files) doesn't affect the connection btw R-studio and R (I was told any relevant directory has to be in English to make R-Studio work).
The problem is, I cannot install the 'graphics' package when I run
install.packages('graphics')
The resulting error says something like this:
>Error in install.packages : Updating loaded packages
>Restarting R session...
>Error in gzfile(file, "wb") : cannot open the connection
>Error saving session (options): R code execution error
>WARNING: Forcing suspend of process in spite of all session data not being fully saved.
It's quite weird since the 'graphics' package is pretty basic and as a matter of fact I haven't found anyone reporting such errors on the internet.
It also bothers me that other packages like 'forecast' and 'XML' can be successfully installed without any error report.
I've looked at some similar questions on StackOverflow, having error reports with "Error in gzfile(file, "wb") : cannot open the connection", but they all seem to have something else to complete the sentence. In my case it just stops the error description with "cannot open the connection". Also I couldn't find people having similar problems with "Error saving session (options): R code execution error".
I do realize that this is quite unusual. I can't even find the proper tags other than r for this question. Although it seems that no one has trouble with the 'graphics', this problem is really bothering me and I hope someone can give possible solutions. Thanks a lot.
Related
I am a relatively new R user. I've been knitting documents in the past using RStudio to create HTML and PDF outputs of my R files.
I have no idea what changed, but approximately 1 month ago I tried to knit a document and got the error portrayed in the picture. I am borderline-competent at R on my best days but otherwise have virtually no knowledge of anything "computer" or "coding" outside of what I've learned from DataCamp regarding R. I have been trying to figure out what happened so that I can continue knitting files, but legitimately do not understand.
I would be more than happy to provide any additional information/context that you need to help me solve this problem but, unfortunately, I just don't know where to start or what's required.
I know this is a bit of a bullshit question and I've tried to avoid asking about it for a while b/c I know I don't know enough to ask it correctly, but I'm at a point where I just want to start knitting again and I'll do whatever it takes to get back to that!
The things I've tried so far are:
Downloading and installing the newest version of R
Downloading and installing RStudio again
Downloading and installing MacTeX again
Trying random solutions from Stack Overflow that involve writing things in my "Terminal" (which I subsequently erase when they don't work).
I am using a MacBook Pro running macOS Catalina 10.15.7 for what it's worth.
I've copied and pasted the text of the error message below:
Error in file(filename, "r", encoding = encoding) :
cannot open the connection
Calls: source -> file
In addition: Warning message:
In file(filename, "r", encoding = encoding) :
cannot open file 'renv/activate.R': No such file or directory
Execution halted
I had the same error and didn't want to run my Rmd files from the console, so there is the solution for using the button again (which I found here):
> usethis::edit_r_profile()
* Modify 'C:/Users/User/Documents/.Rprofile'
* Restart R for changes to take effect
The output then shows you the path to your file. Just copy that path to the address bar in your explorer and choose the program you want to open it with. I chose the normal text editor. Delete "source('renv/activate.R.')" from this file, restart R, and everything should work fine again.
I tried to load data to my R working directory and receive this error:
Error: bad restore file magic number (file may be corrupted) -- no data loaded
In addition: Warning message:
file ‘classize.RData’ has magic number 'RDX3'
Use of save versions prior to 2 is deprecated
I googled it and tried many options, unsuccessfully.
My Rstudio version is: 1.2.5033 (The error was happening before updating as well)
I create a new project, in the new directory, I put the data file
The data file is "classize.RData"
I have another alternative which is "classize.RDS" with the sugesstion to use readRDS(file = "classize.RDS"). When using this command, I receive that error:
cannot read workspace version 3 written by R 3.6.1; need R 3.5.0 or newer
This is in the context of a statistical course at university and my teacher assistant is unable to help me out, and whitout resolving this issue, I cannot move forward in the resolution of the needed exrecices. So please, couly you help me resolve that problem.
ps: all the students have access to the same data, It's just for me that it's not working, therefore the file should not be corrupted.
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 want to launch R help, I type ?dir.create. It is giving me this strange error:
Error in file(out, "wt") : cannot open the connection
In addition: Warning message:
In file(out, "wt") :
cannot open file
'C:\Users\XYZ~1\AppData\Local\Temp\Rtmp86bEoJ\Rtxt32dcef24de2': No
such file or directory
Please help me. What do I do to overcome this problem? Even googling this problem didn't give me much info.
This happens when the temporary directory used by R is deleted. This usually happens when user or the system cleans up the tmp directory while the R session is running. Typically happens if the R session is open for a long time.
Remedy is very simple. You don't actually need to restart R. Just re-create the temporary directory by:
tempdir()
# [1] "C:\Users\XYZ~1\AppData\Local\Temp\Rtmp86bEoJ\Rtxt32dcef24de2"
dir.create(tempdir())
NOTE: this happens to me more and more often in Windows 10... even within like 8 hour session only! Not sure why this happens. See this question: https://superuser.com/questions/1502272/windows-10-cleaning-up-my-temp-dir-too-often
Ok.Thank you all.I was able to resolve this by changing the directory and exiting R and re-logging into swirl.
Upon startup in RStudio. Before doing anything I get the following error display on the console window:
Error: STRING_ELT() can only be applied to a 'character vector', not a 'raw'
I'm working on a Windows 10 OS R version 3.2.2
How can I get rid of the message? How can I identify where the source of where this error is coming from? I'm thinking it may have something to do with a previous session but I'm having trouble identifying the pattern for why this error occurs.
In RStudio I went to Session - Clear Workspace
Then I went to Session - Terminate R
Then I went to Session - Restart R
Then I closed the program and restarted it. Some how that fixed the issue.
I had a similar error. In my case, the default Computer\HKEY_LOCAL_MACHINE\SOFTWARE\R-core\R64\Current Version regkey was pointing to some ancient 2015 version of a Microsoft Revolution Analytics version of R. Not sure how that happened, but I updated it to point to the latest version of R in C:\Program Files\R\R-4.1.2 and all was well.
YMMV