I keep receiving this prompt when installing R packages. When I hit "Yes", it just repeats itself. It turns off, then reopens with the same prompt. I've exited out of R and it did not work. What is this prompt asking?
I think this means that you already have that package installed. Stop executing that line and you should be fine.
Restart RStudio or run install.packages() in R CLI or R GUI.
As the other answer stated, it might mean that you already have the package installed.
Regardless if that holds or not, install.packages() should install the latest version of the package, i.e. also update it if necessary.
As explained in this answer, an update can fail if the package you are trying to update is already loaded.
In many cases, simply restarting R session is sufficient to unload the package, which can then be updated without any problems.
In your case, this did not help as evidenced by the prompt occurring over and over again.
To solve this problem, you can first try to restart RStudio (and not just your R session).
If that does not help, avoid using RStudio at all (which might load some packages automatically): run R from the command line or R GUI (bundled with R) and update the packages in a completely clean session.
As stated in the answer linked above, also "make sure you are not loading any packages through a start-up file (Rprofile.site or .Rprofile)".
Related
I updated R using installr and asked to copy my library. (Even though I've never had this work, I keep hoping maybe it will someday as the package gets updated.) Opened up RStudio and, as usual, it can't find any of the packages that were in my old library. I next copied all the files from my old library into my new library, and several critical ones still don't work. For example, when I tried to load tidyverse, the message I receive is:
Error: package or namespace load failed for ‘tidyverse’: package ‘lazyeval’ was installed by an R version with different internals; it needs to be reinstalled for use with this R version.
I tried remove.packages("tidyverse") and then install.packages("tidyverse", dependencies = TRUE), and I still get the same message about the package lazyeval. I tried installing lazyeval, but then, when I go through those same steps again to try to use tidyverse, now it's lubridate that was installed by an R version with different internals.
How can I avoid this incredibly irritating and time-sucking iterative process of trying to install a package, seeing that the internals are wrong for some dependent package, installing whatever package was the problem, installing the package I actually care about, and then figuring out what other dependencies are problems?
The tidyverse package hardly contains anything: its main purpose is to get a bunch of other packages loaded. Removing it and updating it won't help update the other packages. You could do what #phago29 suggested in their comment, but an easier way is just to update everything. Run this command in an R session:
update.packages(ask = FALSE, checkBuilt = TRUE)
A few notes:
If you have admin capabilities, run as admin, and it will update your main library. If you don't, it'll install new copies in your user account.
Even though you're saying ask = FALSE, it may ask some questions about whether you can build packages from source. Answer "Yes" if your system is set up to do that, "No" if not. If you're not sure, try "Yes", and if you get install failures, run it again and say "No".)
This is likely to run for a while, so go away and have a coffee or something.
I am trying to embed RInside to my application on win7 64-bit system but when I initialize an RInside:
Rin = new RInside(argc, argv);
the following message appears:
Error in loadNamespace(name) : there is no package called 'Rcpp'
This error only occurs with Windows.
I think you get that issue when your .libPaths() differ--in other words run the .libPaths() function to see the paths stored by R for its use. Then check where RInside is installed, and make sure Rcpp is installed there too. It is a setup issue.
In other words, it should work if you have Rcpp and RInside installed where the basic R libraries are. Otherwise you have to tell the (embedded) R session about the other location (and before it starts).
There are more Windows users on the list, so you could try asking on rcpp-devel.
First get your default library locations by command ".Library" in R.
Get Rcpp package from https://cran.r-project.org/web/packages/Rcpp/index.html.
Unzip and copy folder "Rcpp" to your default library locations obtained from step1.
Now you are ready to install packages which have dependencies on Rcpp.
Dirk is right in this case, BUT if the .libPaths() does not work, then please also check if you have the latest packages.
I am posting this as an ancillary answer backup which I ran into with the shiny package backend switch of their code needing Rcpp!
In this case of getting the "no package" error message, I fixed it by:
Selecting devtools package and then using this line below. (if you don't have devtools then get it with install.packages("devtools")
devtools::install_github("rstudio/shiny")
The development version of the package handled this better, and added the package as a dependency.
Mods - I realize this is an answer to an old question, but I might help others not wasting an hour like I just did.
You might find it easy if the answers are for both R studio users and non R studio users.
R Studio users
First get your default library locations by command ".Library" in R.
Get Rcpp package from https://cran.r-project.org/web/packages/Rcpp/index.html.
Unzip and copy folder "Rcpp" to your default library locations obtained from step 1, you will find another folder named library, paste the unzip folder in it.
Non R studio Users
First get your default library locations by command ".libPath" in R.
Get Rcpp package from https://cran.r-project.org/web/packages/Rcpp/index.html.
Unzip and copy folder "Rcpp" to your default library locations obtained from step 1, you will find another folder named library, paste the unzip folder in it.
I was also getting this error while trying to run the 'ggplot' function from the ggplot2 package. After trying the suggestions posted here and elsewhere (checking file paths, restarting R, clearing out my environment, etc.) and encountering several other cryptic error messages, it turned out that I needed to download the latest version of base R for Windows (v3.4.1) and update my version of R-Studio to the latest version also (v1.0.153).
After doing this my 'ggplot' function was working again and I was able to render my figure from R Studio without any further issues.
I was also getting this message when trying to use ggplot. I first updating both my R for Windows to 3.4.3. Then updating R studio to version 1.1.423; then, updating all of the packages and being sure to access the R version 3.4.3 from R studio, I still got the message. None of these things fixed the error. I was ready to give up until I noticed that I was calling library(ggplot) and had ggplot::ggplot in my code. THIS WAS THE PROBLEM. I changed it to library(ggplot2) and the instance to ggplot2::ggplot(...). THIS FIXEd the problems.
I was facing a similar issue, and I simply installed the said package. It's working perfectly for me.
I initially tried, using RStudio, to install rgl using install.packages("rgl"), which appeared to have worked. It did give me a message that the binary is older than the source, and that it would install from the binary, but I received no other messages. However library(rgl) gets stuck and doesn't do anything.
I removed the package using remove.packages(rgl), and attempted to install from source using R CMD INSTALL rgl_0.95.1409.tar.gz. That gets stuck on "testing if installed package can be loaded." I had X11 installed, but I downloaded XQuartz 2.7.8 and tried again, with the same result.
?rgl::plot3d in RStudio does take me to the documentation for the plot3d function, so I think it installed, just not completely/successfully (rgl::plot3d as an attempt to call the plot3d function also results in endless computation).
However, I finally did manage to load rgl (and use plot3d) by manually launching the Xapp from the Terminal prior to loading the library in my current R session (just X in Terminal, xterm by itself doesn't seem to have the same effect). Can anyone explain why this might be the case, and if there is a workaround to avoid having to manually launch the Xapp? (I do not want to have an application running when I do not need it, but I will also probably sometimes forget to launch the Xapp prior to running this script.)
I'm running OS X Yosemite (10.10.5), RStudio 0.98.1103, R 3.1.3 3.2.2.
The 'rgl' package does not use XQuartz, but rather opens a separate X11 window. Not being able to launch X(11) automatically makes me think that either your system PATH does not have the X11 server in the search path or an environment variable needs to be fixed. I wasn't able to see any differences in the Sys.getenv() results after loading rgl but I see that I have these in my PATH: /usr/X11/bin:/usr/X11R6/bin1
For a while I was rather confused about this as well. The XQuartz.app appeared very similar to the the X11.app , showing up with the very similar icons, (both appearing in the Taskbar as "X".)
I am trying to embed RInside to my application on win7 64-bit system but when I initialize an RInside:
Rin = new RInside(argc, argv);
the following message appears:
Error in loadNamespace(name) : there is no package called 'Rcpp'
This error only occurs with Windows.
I think you get that issue when your .libPaths() differ--in other words run the .libPaths() function to see the paths stored by R for its use. Then check where RInside is installed, and make sure Rcpp is installed there too. It is a setup issue.
In other words, it should work if you have Rcpp and RInside installed where the basic R libraries are. Otherwise you have to tell the (embedded) R session about the other location (and before it starts).
There are more Windows users on the list, so you could try asking on rcpp-devel.
First get your default library locations by command ".Library" in R.
Get Rcpp package from https://cran.r-project.org/web/packages/Rcpp/index.html.
Unzip and copy folder "Rcpp" to your default library locations obtained from step1.
Now you are ready to install packages which have dependencies on Rcpp.
Dirk is right in this case, BUT if the .libPaths() does not work, then please also check if you have the latest packages.
I am posting this as an ancillary answer backup which I ran into with the shiny package backend switch of their code needing Rcpp!
In this case of getting the "no package" error message, I fixed it by:
Selecting devtools package and then using this line below. (if you don't have devtools then get it with install.packages("devtools")
devtools::install_github("rstudio/shiny")
The development version of the package handled this better, and added the package as a dependency.
Mods - I realize this is an answer to an old question, but I might help others not wasting an hour like I just did.
You might find it easy if the answers are for both R studio users and non R studio users.
R Studio users
First get your default library locations by command ".Library" in R.
Get Rcpp package from https://cran.r-project.org/web/packages/Rcpp/index.html.
Unzip and copy folder "Rcpp" to your default library locations obtained from step 1, you will find another folder named library, paste the unzip folder in it.
Non R studio Users
First get your default library locations by command ".libPath" in R.
Get Rcpp package from https://cran.r-project.org/web/packages/Rcpp/index.html.
Unzip and copy folder "Rcpp" to your default library locations obtained from step 1, you will find another folder named library, paste the unzip folder in it.
I was also getting this error while trying to run the 'ggplot' function from the ggplot2 package. After trying the suggestions posted here and elsewhere (checking file paths, restarting R, clearing out my environment, etc.) and encountering several other cryptic error messages, it turned out that I needed to download the latest version of base R for Windows (v3.4.1) and update my version of R-Studio to the latest version also (v1.0.153).
After doing this my 'ggplot' function was working again and I was able to render my figure from R Studio without any further issues.
I was also getting this message when trying to use ggplot. I first updating both my R for Windows to 3.4.3. Then updating R studio to version 1.1.423; then, updating all of the packages and being sure to access the R version 3.4.3 from R studio, I still got the message. None of these things fixed the error. I was ready to give up until I noticed that I was calling library(ggplot) and had ggplot::ggplot in my code. THIS WAS THE PROBLEM. I changed it to library(ggplot2) and the instance to ggplot2::ggplot(...). THIS FIXEd the problems.
I was facing a similar issue, and I simply installed the said package. It's working perfectly for me.
When installing a Rcpp package on Windows, you need to ensure that the package DLL is unloaded or you get a "Permission Denied" error when copying the new DLL. This means restarting R on every recompile, which is pretty annoying. Is there any way to unload the package DLL without killing R?
I've tried the detach("package:my_package", force=TRUE) command, but it doesnt unload the DLL.
Opinions are divided on this. I often prefer to run the builds and test outside of my main R session(s), simply by chaining R CMD INSTALL with Rscript (or, on Linux, r calls from littler) to test the new build. If you use proper options to R CMD INSTALL ... to skip parts that may take extra time you get a quick turnaround AND are assured that you do get a fresh build.
And if you want the same behaviour by clicking a button, RStudio offers it too.
If you want to do this in your main R session (without using RStudio, which makes reinstalling the package and reloading R very easy), you can use devtools:
library(devtools)
load_all("path/to/my/package")
Among other things, load_all will reload all your R code, and re-compile and reattach the DLL.
I guess you need to run library.dynam.unload to unload DLLs.