Hello, 

I just upgraded R 3.5.1 via CRAN and I am trying to use "windows()" function after loading "Biostrings" library like this:

> source("http://www.bioconductor.org/biocLite.R")
> biocLite("Biostrings")
> library(Biostrings)
> windows()

I get the following error messages:

Error in (function (classes, fdef, mtable)  : 
unable to find an inherited method for function ‘windows’ for signature ‘"missing"’

In R 3.4.4, that "windows()" function works well. Do you know how to fix it?

My environment is as follows:

Microsoft Windows [Version 10.0.17134.345]

> R.version
platform       x86_64-w64-mingw32          
arch           x86_64                      
os             mingw32                     
system         x86_64, mingw32             
status                                     
major          3                           
minor          5.1                         
year           2018                        
month          07                          
day            02                          
svn rev        74947                       
language       R                           
version.string R version 3.5.1 (2018-07-02)
nickname       Feather Spray

Cheers,

Hiro

This issue is being caused by a property called masking.  There are two methods called windows(), one is available in base R (via a package called grDevices) and the other in Biostrings.  In a fresh new R session only the method that opens a graphical windows is available & so it works.  However, once you load Biostrings the method in that package (which does something completely different) take precedence.  

If you want to ensure you use the other version you can use the package name and :: nomenclature to call the windows function e.g.

grDevices::windows()