Do you own the package on GitHub? If so, I would change the name, if not, I would suggest to the author/maintainer to change the name given that there is a conflict with the main archive for R packages.
Otherwise, I don't think there is a great way to get udpdate.packages() to ignore packages in the pane. But something simple like this should probably work in a script or if you run it interactively to do batch updates:
dont_update <- function(pkgs) {
need_updating <- data.frame(old.packages())
to_update <- need_updating[!need_updating$Package %in% pkgs, ]
install.packages(to_update$Package)
}
dont_update("pkg")
This function will accept a vector of package names to be excluded from updating. All others will be updated. When you run dont_update("pkg"), pkg won't be updated, but other packages will. Can modify the function as you see fit.