Hi everyone!
Today I downloaded a new version of R (4.0.0) because I thought it would help the packages that I am using run better. However, with me being a super noob apparently, I did not make sure that all my packages would be transferred to this new version of R. Now, when I am trying to download packages (like tidyverse), I get all sorts of errors and the package is not downloaded. Does anyone know what to do? I get a whole list of these errors you can see below:
Can you copy and paste those all error messages here. Screen shots are not easy to read or work with.
However it looks like a lot of one or more prerequisite packages are not loading automatically as they are supposed to and you will need to install them manually. It will be a lot easier to diagnose the problem with a readable set of error message.
Hi! Thanks for replying. In this part are the errors, I hope it helps.
The downloaded source packages are in
‘C:\Users\asoph\AppData\Local\Temp\Rtmpe2ftCJ\downloaded_packages’
I already solved it! I just needed a different verison of Rtools in the end.
Whilst R4.0.0 may certainly be new to you, it is itself already more than 3 years old. If you are taking time to go through some pain to modernise your R experience, would it not be wise to adopt the most recent version of R ?
Yes that is probably better. I just wanted to make sure that I could install the package that I need (Platypus). But I am also having some trouble with that now. I just need to figure out if I can install the newer version of R without losing all those packages that I already installed now.
I used installr now to get the newer version, let's hope it works.
Okay I did it but it does not open that newer version in Rstudio for some reason
Any error messages?
Is R opening okay on its own?
Yes, I got the new version now (4.3.1). However, I still cannot install the package that I need. I now that it should work for this version, because my colleague is also using it. I am getting this error:
BiocManager::install("Platypus")
'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories", package =
"BiocManager")' for details.
Replacement repositories:
CRAN: https://cran.rstudio.com/
Bioconductor version 3.17 (BiocManager 1.30.21), R 4.3.1 (2023-06-16 ucrt)
Installing package(s) 'Platypus'
Warning message:
package ‘Platypus’ is not available for Bioconductor version '3.17'
A version of this package for your version of R might be available elsewhere,
see the ideas at
I am not likely to be of much help as I have not used Windows in 10 or 15 years and I am not a Bioconductor user but I'd suggest having a look at the author's Git page and seeing if there may be a way to install from there.
I solved it in the end, thanks for all the help!
Could you tell us what you did for other R users who may have a similar problem? Thanks.
Yes ofcourse, I am not exactly sure what solved it in the end though. My guess is that the packages were only saved in the system library, and if there comes a lock on it somewhere you can not alter that then. I found somewhere that you can prevent the locks by adding this: BiocManager::install("jsonlite", force = TRUE, INSTALL_opts = '--no-lock'). But I already had the lock on there so that did not really help for me. So what I did is make sure that the packages were downloaded in the user library instead of the system library, by first making a directory and then doing this: .libPaths(c("C:/Users/asoph/OneDrive/Documenten/R/win-library/4.3.1")). And after that it seemed to work much better. And then for installing Platypus I downloaded the tar.gz file from the github and then using this command: install.packages("Platypus", lib = "C:/Users/asoph/OneDrive/Documenten/R/win-library/4.3.1", dependencies = TRUE), but honestly I am not sure if the lib parameter works because it seemed to also put it in the user library without that parameter. I hope this helps if anyone has the same struggle. I think that in most cases if you download the newer R version is makes this user library itself, because my colleague did not seem to have this problem.
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