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().
Related
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.
I updated my Mac to OS10 and attempting to run RStudio Knit, and get the error:
"evaluate 0.7.2 is required but 0.7 is available".
I tried this and did not fixed the issue:
remove.packages("evaluate")
install.packages("evaluate")
Any help would be appreciated.
Try setting up the below option and by rerunning the code.
getOption("repos")
options(repos = c(CRAN = "https://cran.rstudio.org"))
It also happened to me. I downloaded evaluate zip file from here https://cran.rstudio.com/web/packages/evaluate/index.html
and then manually installed it in R Studio (Tools-InstallPackages-zip file).
Good luck !
install.packages('evaluate')
Warning in install.packages :
unable to access index for repository HTTP://cran.rstudio.com/bin/windows/contrib/3.4:
cannot open URL 'HTTP://cran.rstudio.com/bin/windows/contrib/3.4/PACKAGES'
When you compile the update or remove sentences, if the output like this, you could make some settings, since maybe the problem is your internet. Follow the steps:
Open Rstudio.
Click tools.
Choose global options->packages.
Modify CRAN to the country you living. like, China or Japan. Cause your browser maybe work only you do this.
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 having trouble roxygenizing a package. It was last working several months ago and I haven't checked since, so not sure if a snippet of code I added broke it, if my system's configuration changed, or if roxygen2 changed.
I've tried calling it through devtools::document, in a --vanilla R sesssion with roxygen2::roxygenize('taRifx') from the directory above it, roxygenize('.') from the project base directory, tried running as root in case it was a permissions thing, etc.
Here's the RStudio version:
==> roxygenize('.', roclets=c('rd'))
* checking for changes ... ERROR
Error in file(con, "r") : cannot open the connection
Package code is here:
https://github.com/gsk3/taRifx
How do I fix this?
You'll need to change line 1242 of the Rfunctions.R file to #examples instead of #example. For proper formatting you'll also need to change the # in email addresses to ##.
For some reason I am suddenly not able to install packages in R (I have subsequently updated to the latest version of R and am running Windows 7). For example, if I type:
install.packages('beeswarm')
Installing package into ‘D:/Rlibs’ (as ‘lib’ is unspecified)
--- Please select a CRAN mirror for use in this session --- trying URL 'http://www.stats.bris.ac.uk/R/bin/windows/contrib/3.0/beeswarm_0.1.5.zip'
Content type 'text/html' length unknown opened URL downloaded 1859
bytes
Error in read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package",
"Type")) : cannot open the connection In addition: Warning
messages: 1: In unzip(zipname, exdir = dest) : error 1 in extracting
from zip file 2: In read.dcf(file.path(pkgname, "DESCRIPTION"),
c("Package", "Type")) : cannot open compressed file
'beeswarm/DESCRIPTION', probable reason 'No such file or directory'
I have read that in Windows 7 there can be important restrictions on rights to writing to certain folders etc. so I've gone to some lengths to install R and library folders in non-default areas of my computer, and to allow myself rights to certain folders, but to no avail. Possibly also of importance is when I type:
.libPaths()
# [1] "D:/Rlibs"
# [2] "C:/Users/L.Halsey/Documents/R/win-library/3.0"
# [3] "C:/Users/L.Halsey/Documents/Documents/R-3.0.1/library"
I have created several folders in an attempt to create one that I could successfully install libraries into and set them up to be recognised by R using 'environment variables' from the start button. I don't know how to delete any of them though - not sure if this is relevant to my overall problem of not now being able to install/update packages for some reason.
The error being reported is inability to open a connection. In Windows that is often a firewall problem and is in the Windows R FAQ. The usual first attempt should be to run internet2.dll. From a console session you can use:
setInternet2(TRUE)
(You are correct in thinking this is not due to your library setup. The error says nothing about permissions.) I don't think just typing .libPaths should return that character vector since on my machine I would need to type .libPaths() to see something like that. If you wanted to reduce the number of places for libraries you can use the .libPaths function for setting the values. This would pick the second and third of the existing paths
.libPaths( .libPaths()[2:3] )
The inner call retrieves the path vector and the outer call sets it to a reduced vector.
Running RStudio as administrator fixed it for me!
I will probably duplicate a lot of other answers on the stackoverflow, but I got exactly the same error as OP, namely:
Warning messages: 1: In unzip(zipname, exdir = dest) : error 1 in extracting from zip file 2: In read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package", "Type")) : cannot open compressed file 'zoo/DESCRIPTION', probable reason 'No such file or directory'
Turned out, while I as a user had permissions to write in a certain directory, R did not. In order to be sure you don't have something similar, do following:
get a usb drive, let's name it E
download package source as a .zip file and store it onto usb-drive in some directory, let's name it E:/source
Create directory for libraries on the usb drive, let's name it E:/libs
Install packages calling R command install.package from the R console and setting all relevant directories to point to your usb drive:
(here I use package zoo as an example)
install.packages("E:/source/zoo_1.7-12.zip",
destdir = 'E:/source', # no "/" after the path
lib = 'E:/libs',
repos = NULL)
Load the package from the directory, where you installed it:
library('zoo', lib.loc = 'E:/libs')
After you are sure, it works this way on your usb drive, you can start resolving directories permissions, and try out by changing the paths in the code above.
update:
In some windows environments even your usb-stick might be protected from read-write by the R. Make sure you check the permissions using the machine you are working from.
The following worked for me (based on the answer above)
install.packages("clustvarsel", lib = "C:/Users/dnentchev/My Programs/R-3.2.2/library")
I had the same problem. I turned the windows firewall off, and Run RStudio as administrator. so, that error fixed.