I've been working with a script that utilizes metaMS and xcms to look at GCMS CDF files. The script, I'm assuming, is fine, because I literally only changed a database file before it started throwing errors.
I have since changed the database file back to what it was before, tried earlier iterations of the script, reinstalled both R and R studio and subsequently reinstalling BiocManager to reinstall metaMS and xcms, but to no avail.
It's having particular trouble with MSnbase and rtools, saying I need rtools to install packages, but that rtools is not compatible with my version of R (I'm using R 3.6 and R Studio 1.2.1335 - I am open to updating but this often causes issues with certain packages so I'm trying to avoid that).
I even tried to run as administrator to reinstall, and it's still not working.
I'm including images of the various errors I've encountered.
If you have ANY ideas I am open to them. I am at a complete loss.
P.S. I am definitely installing the dependencies. I've tried installing via command line and through the installer.
Related
I'm really stuck and need some help.
After installing R 4.0.2, I'm getting this error message on R visualizations in Power BI Desktop which were previously working
"Error: package or namespace load failed for 'ggplot2':
package 'ggplot2' was installed before R 4.0.0: please re-install it.
Execution halted"
I already tried to:
reinstall R 4.0.2
reinstall RStudio
reinstall ggplot2
reinstall all packages
reinstall Power BI Desktop. My version is August-2020
Still it does not work.
Considerations:
My visualizations were working well before I installed R 4.0.2
My visualizations are working well on other PCs
When I run the code on RStudio I don't get any error
Any thoughts?
You probably need to go here: https://powerbi.microsoft.com/en-us/support/, but some guesses:
When you did the reinstall, you didn't clean up the old one, so you now have a mix of old and new versions of things. If you can run R code, run
system.file(package="ggplot2")
That's where it is finding the bad version of ggplot2. Get rid of it, and reinstall. If that's not enough, run
.libPaths()
in the broken copy of R. Completely eradicate every directory mentioned there, and reinstall R and all of your contributed packages. (I don't use Power BI, so this might also require you to wipe out some part of it: do so, and reinstall it.)
After all of this, run
packageDescription("ggplot2")
In the last line (or close to it) of what gets printed, you should see something like this:
Built: R 4.0.2; ; 2020-07-16 22:49:23 UTC; unix
If you see that it was built before 4.0.2, then either you missed deleting something, or you (or Microsoft) reinstalled some old version. Then it's probably time to contact that URL above.
I've come across a common problem but do not understand the logic of how R works.
So I had R 3.4 and all my libraries were in /usr/local/.../R/3.4 local direction. These libraries were installed using super user admin rights.
I've recently upgraded to R 4.0.0.2, and installed Rstudio, and do not run Rstudio as super user. I've created a new local direction ~/R/x86_ubuntu/4.0 local library.
Now the .libPaths() has the first entry as my local directory, and subsequent paths point to previous library paths.
So if i enter install.packages(foo), the error says,
This package package ‘foo’ was installed before R 4.0.0: please re-install it.Error: package ‘dotCall64’ could not be loaded.'
However I am re-installing the package from source, yet I get the error that I could not re-install it.
I have also tried the install.updates(check=TRUE,ask=FALSE) command and this still gave the same answer.
There are similar posts to this problem, but I just need an explanation as to why this is failing?
Is it because of the library paths conflict? R is trying to load a previous older 3.4 library directory?
This does not make sense because I've downloaded all my 4.0 libraries from source? why is it still pulling from the older versions?
Should I just remove other library paths? Should I delete my old previous library folders?
Currently running R version 3.6.2 and RStudio version 1.2.5033 (both the latest versions as of today).
I have installed the R/Cape package from https://CRAN.R-project.org/package=cape, although when I try to load the package into R studio using:
library(cape)
I get the following from the RStudio console. RStudio then stops responding. I have tried this in just R as well and R also stops responding.
Can anybody please tell me if they've had any similar experiences and how they resolved them? Or if you've managed to install the 'cape' package how you did so?
The 'cape' library depends on other packages like 'htmltools' and many others. This is not an error message, just a warning. It means that some of the functions from 'tools:rstudio' will be replaced by other functions with the same name. See this answer which already addresses this.
As for the non-responsive behaviour, it is probably unrelated to the warnings discussed above. Try reinstalling R and updating all your packages. In Rstudio, you can update all your packages by clicking Tools > Update Packages > Select All > Install Updates.
after updating my R version to 3.6.1 version - the rGrain and rGraphviz packages do not work. First the error was suggesting that the packages are not writable. However after updating some libraries and trying to source it outside from the BiocManager right now the error appears saying that the compilation fails. Does anybody know how to fix it?
I have already tried multiple options like sourcing it outside and directly from BiocManager and other sources however with no results.
I would appreciate any type of help suggesting how to fix or just install packages gRain and Rgraphviz.
Not writable is biocmanager being poorly programmed and somehow wanting to install some secondary packages into the main R folder in program files, rather than the usual R\win-library\ in documents.
You can workaround that by launching the R console or Studio with administrator privileges when installing/updating.
Running happily with R 3.4 and RStudio 1.0.143 under Win10 this problem occured bringing project development to a halt. Downloads each occur and are unzipped and then the a presumably first file in the first item gets:
Error in install.packages : cannot open file 'C:/Users/Admin/Documents/R/
win-library/3.4/file30504386b80/rJava/javadoc/resources/background.gif':
Permission denied
and the prompt returns.
Updating to R version 3.4.1 (2017-06-30), RStudio Version 1.0.153 was to no avail. Using the OS to remolve all R versions and trying again with 3.4.1 did not work. Removing R again and deleting the R directory to refresh the library did not work. My virius software like to tell how helpful it has been and has not, so that issue seems unlikely.
Giving the user full control of the R library did not help.
could package-updates be a tag like install-updates?
It looks there is a problem between Java and rJava.
You should try reinstalling Java using chocolatey package manager (https://chocolatey.org/) and then reinstall rJava package.
I had a similar issue two weeks ago on a windows laptop.
I had this problem for a long time. only in RStudio.
Install the package on R and Library it. Go to RStudio and require the package.
It works!