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Problems with installation R packages
(3 answers)
Closed 5 years ago.
From today, every time I try to install a new package on R (3.4.1) with Rstudio 1.0.143 I receive this error message:
Warning: unable to access index for repository https://www.stats.ox.ac.uk/pub/RWin/src/contrib:
cannot open URL 'https://www.stats.ox.ac.uk/pub/RWin/src/contrib/PACKAGES'
I change the CRAN mirror in Global options>packages but it still shows this error. The packages have started downloading from a different server than stats.ox.ac.uk but there is huge delay while R tries to connect to stats.ox.ac.uk. Is this a global problem, or just happening to me? If global, is there a workaround to stop this serror message from showing?
Thanks.
Deep
(Dwaipayan Adhya)
I'm guessing this is a temporary issue (but an annoying one nonetheless and one that I dealt with this morning). That repository is most likely an additional one set alongside the "CRAN" repository as "CRANextra". The solution is to redefine the repos option to not include CRANextra. You can use the setRepositories() command and unselect "CRANextra". Alternatively you could just run the following code which will remove all repositories except the "CRAN" selection.
options(repos = getOption("repos")["CRAN"])
Related
I have an R package, created by someone else that I have been made a collaborator on, that I want to work on and develop. I've already cloned the repository to my local computer through the Create Project > Clone from GitHub route in RStudio, and since then I've been editing the scripts, but not working with it as a package. As in, I had been adding functions and working on a Shiny interface, but not following any R package development rules (loading packages directly into the .R files, not updating the NAMESPACE, using roxygen2 conventions, etc.).
Everything I've read mentions devtools::install_github, but I don't want to install and use it, I want to edit it like I've been doing. I also want it to still be connected to Git (so I can continue to commit and pull from the remote server, once my collaborators make edits). I've tried devtools::load_all() and devtools::document(), but it gives me this warning:
Error in FUN(X[[i]], ...) :
bad restore file magic number (file may be corrupted) -- no data loaded
In addition: Warning messages:
1: In readChar(con, 5L, useBytes = TRUE) :
truncating string with embedded nuls
2: file ‘file_example.rda’ has magic number 'X'
Use of save versions prior to 2 is deprecated
Do I need to delete my local copy and do something different to work with it as a package so that the functionality of roxygen2 and the NAMESPACE documentation will work correctly? Or is there an obvious reason for this error/something I'm missing about how to work with it as a package, how it is currently?
Thanks!
It looks like file_example.rda is corrupt
Can you just load it in R and check what it contains?
You could try:
tools::resaveRdaFiles( 'file_example.rda', compress='xz' )
And see if that saves it in a way that is acceptable?
I've spent the last 4 hours trying to find out why I wasn't able to install any packages in R (it started with me trying to install a package I was developing). It would just stall for +5 minutes without doing anything or outputting anything to the terminal. I tracked the issue down to the following call:
repos <- structure("https://cran.rstudio.com/", .Names = "CRAN")
type <- "both"
utils::available.packages(utils::contrib.url(repos, type), type = type)
I realized after a while that it was just the RStudio CRAN mirror, and when I changed the repo to "https://cran.case.edu/", it started working. However, there was literally no indication of this on the surface--and it took forever for me to find out what the problem was.
My question is this: Is there a way of using multiple CRAN repos so when one fails, others are used? Or at least a way that will prevent this from happening again?
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 keep hitting this error today and I already download the plyr from github but it still doesn't work. I restarted R-studio even my PC after installing plyr..
It appears the problem may be due to a change made to the way R resolves references to external DLLs, as mentioned halfway through the thread here.
Adding the parameter PACKAGE="plyr" to the .Call function call on line 12 of R/loop_apply.R in the source (clone from github), and then installing the package from that source (install.packages("<path to plyr source>", type="source", repos=NULL)) seems to fix it.
I don't know what is going on, everything was working great but suddenly I started to have this error message on the documentation:
Error in fetch(key) : lazy-load database '......descopl.rdb' is
corrupt
I removed almost all my code and build again then publish to Github, but when I use the other laptop to download the package, the package is being downloaded and loaded but I can't call any of the functions, and the documentation states that error.
I don't know what caused the problem, I am using roxygen to generate the documentation.
https://github.com/WilliamKinaan/descopl
It seems that the error arises when the package cannot be decompressed by R (as #rawr established, it is corrupt). This solutions have worked for me:
1) Check for possible errors in the creation of the .Rdb files
2) Try restarting your R session (e.g. .rs.restartR() if in RStudio)
3) The package might have been installed in your computer (even though it does not work). Remove it using ?remove.packages()
I have had this problem with roxygen2 as well. Couldn't see any problem with any of my functions. In the end deleting the .rdb file and then getting roxygen2 to rebuild it seemed to solve the problem.
I think the explanation for what is causing this is here.
It's related to devtools.
Per #Zfunk
cd ~/Rlibs/descopl/help
rm *.rdb
Restart R. Look at the help for the package again. Fixed!
I received this error after re-installing a library whilst another R session was running.
Simply restarting the existing R session(s) solved for me (i.e. running .rs.restartR() to restart the sessions)
If you are using R-studio:
1) ctrl+shift+f10 to restart r session
2) tools -> Check for package updates -> update all packages
3) library(ggmap)
Problem is solved.
Basically all answers require restarting R to resolve the issue, but I found myself in an environment where I really didn't want to restart R.
I am posting here a somewhat hack-ish solution suggested by Jim Hester in a bug report about the lazy-load corruption issue.
The gist of it is that the package may have some vestigial S3 methods listed in session's .__S3MethodsTable__. environment. I don't have a very systematic way of identifying which S3 methods in that environment come from where, but I think a good place to start is the print methods, and looking for S3method registrations in the package's NAMESPACE.
You can then remove those S3 methods from the .__S3MethodsTable__. environment and try again, e.g.
rm(list="print.object", envir = get(".__S3MethodsTable__.", envir = baseenv()))
You may also need to unload some DLLs if some new messages come up like
no such symbol glue_ in package /usr/local/lib/R/site-library/glue/libs/glue.so
You can check getLoadedDLLs() to see which such files are loaded in your session. In the case of glue here, the following resolved the issue:
library.dynam.unload('glue', '/usr/local/lib/R/site-library/glue')
I got this error on RStudio on mac OS - updating all the packages and restarting r session did the trick.