Hello!

I just started using DESeq2 for myy RNAseq data analysis and whenever I re-open the project I created to work and I try to call the package DESeq2 with library, I get an error like the one below but for different packages evertime I open the project:

*> library("DESeq2")
Error: package or namespace load failed for 'DESeq2' in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
 no package named 'nnet' is found
In addition: Warning message:
the 'DESeq2' package has been compiled with version R 3.5.2.*

So far, I have had to separately install the following packages (in the order, R has been asking be to do): BiocManager::install("annotate") BiocManager::install("GenomeInfoDb") BiocManager::install("GenomicRanges") BiocManager::install("DelayedArray") BiocManager::install("vsn") BiocManager::install("farver") BiocManager::install("hexbin") BiocManager::install("pheatmap") BiocManager::install("yaml") BiocManager::install("vctrs")

And today, when I re-openned I got a new one to install again... It is "nnet". It is quite annoying that everytime I want to work again on my project, I have to install a completely new package...

Does anyone have any idea of why it does that ? Any tips to make it stop so DESeq2 can be called without any incident ?

I would be really grateful for your help,

Diana

This sounds like maybe you've ended up with a whole bunch of packages installed with one version of R, but then you're trying to use them in a different version of R, and this is causing some confilcts.

I'd suggest looking at the the BiocManager::valid() function, which should report back whether you're using the appropriate version of Bioconductor for the R you're running, and what you need to do to make sure all your package versions are in sync.

You should just be able to install DESeq2 with BiocManager::install("DESeq2") one time, and then all the dependencies should be installed by the software. If you stick with BiocManager, it should handle all the dependencies and you shouldn't have to deal with any missing packages (unless you manually have removed them, in which case you could just start from square 1 and re-install DESeq2 with BiocManager).

Thank you both for your answers. I did use BiocManager::install("DESeq2") to download the package but Mike was right the valid() function showed me that I was using an older version of R so I updated it as well as all the packages that needed to be updated and now I don't have anymore that error.