I am running GLMMs in R but have run into the issue of package version inconsistencies between TMB, Matrix (both pre-installed) and glmmTMB (the GLMM package).
I have attempted to (1) follow the instructions in the warning message, (2) reinstall all three versions from source on github, and (3) clean reinstall RStudio and repeat, but cannot seem to get the versions to match up.
I'm not sure if this is even an issue (beyond a warning) considering the versions are so close to one another, but would like to resolve this just in case. Any rec's/instructions to fix this is greatly appreciated.
Warning message in R when loading glmmTMB
Related
for my Statistical analyses, I need to use the Packages ggplot2 and lmerTest.
While installing lmerTest I updated R and was able to use the function. But after this update, I was not able to use ggplot2 anymore. So I downgraded it.
If I want to install lmerTest now it shows the Error:
install.packages("lmerTest")
Warning in install.packages :
installation of package ‘lmerTest’ had non-zero exit status
---- there is no package called ‘lmerTest’
When I Google that problem I just find the answer to update R, but then ggplot2 won't work. I cant use lme4 instead because here is missing the p-value.
Is there no way to use both, ggplot2 and lmerTest, with Ubuntu??
I'm definitely no expert. Thanks for any help, sincerely
Maria
I was developing a package when I found a new error when building the package.The error makes reference to a line that previously didn't have any problem and I didn't modify. However it run smoothly in a fresh R session when I ran the code or knit the vignette alone.
Long story short: I found that this error happens when a suggested package (by my package's DESCRIPTION) is loaded before my package.
How can I control this?
The reason of the error is that my package (A) has a function is named exactly the same as the other package (B) because it does the same kind of process, but I use a different name for the same arguments (and in my version I provide other arguments as well). A solution I found is to use A::function, but that would be uglier to the reader. Is there any other solution?
This didn't happened in previous cycles of development. I have observed it on the latest R version R version 3.4.3 (2017-11-30) -- "Kite-Eating Tree" and in the devel version of R. The packages are build using both R CMD build package and devtools::check()
The conflicting package is in Suggests: part of the DESCRIPTION file of the package
This question might be related to this other one.
Title says the core of it. I've been wanting to learn R and I thought that swirl sounded nice. I can't get swirl to install, so just as an experiment I tried another package. I get the same error message. I'm getting this in both R and R Studio.
My input and error message are here:
install.packages("swirl")
## package ‘swirl’ is available as a source package but not as a binary
## Warning message:
## package ‘swirl’ is not available (for R Under development)
The first time I tried it I did get to chose a CRAN mirror, but otherwise I've been just spinning my gears.
I'm on a Mac and running OS X Yosemite, I tried looking for any issues similar to this and I am stuck. Any help is appreciated.
It looks like you're using a bleeding edge version of R ("R Under development").
Downgrade to the latest stable version and you should be fine.
Using Julia Studio (Win XP) and trying to add package DataFrames - how can the following error be resolved?
Unknown dependency for GARCH: NLopt
(How can I verify that a package was installed) Running dv = DataArray([1,2,3]) says DataArray not defined. So it seems stuck.
You're using a rather old version of julia (0.1.x) and the GARCH package doesn't support it. Try installing a development version from source (it takes a bit the first time, but should be quite automatic) or try a development binary.
Edit: Also, this issue may now be taken care of if you want to do Pkg.update() and try again.
I'm building R packages in R 3.0.1 on a Windows machine, using Rtools30 and the 'Build' tools associated with RStudio, which I assume is tied in with devtools (which is up-to-date). My typical process to build a package is:
Load All
Reoxygenize
Build & Reload
Check
Build Source Package
If everything goes without errors or warnings, I then:
install.packages("foo.tar.gz", repos=NULL, type="source")
Since upgrading to R 3.0.1, I now get this warning:
Warning in install.packages :
foo.tar.gz is not available (for R version 3.0.1)
I also tried before installing, and it did not get rid of the warning:
options(install.packages.check.source = FALSE)
Also, I notice this warning when I open the devtools library:
WARNING: Rtools 3.0 found on the path at c:/Rtools is not compatible with R 3.0.1.
Which is weird, Rtools 3.0 is suppose to be good from R >2.15.1 to R 3.0.x
Any ideas what is going on?
This is RStudio specific, as they wrap and/or changed a lot of functions from the utils for better integration. The problem lies with a call to getDependencies() to check for dependencies. But that function will also check whether the original package exists on CRAN and throws the given warning when it doesn't. A package you just built on your own computer is obviously not on CRAN, hence the warning.
In the source of the native install.packages(), getDependencies() isn't called in case you build from source or install from a different repository respectively. RStudio on the other hand calls getDependencies() before it passes everything on to the native install.packages() function.
This has to my knowledge no further effects, apart from confusing people. I didn't find a way to conveniently get rid of this in RStudio, as suppressWarnings() doesn't work in this context due to the complex way RStudio deals with this.
In a basic R console, you shouldn't have any problem.
So for the time being, I'd just ignore this and hope the RStudio team finds time to take care of this minor glitch.