Instead of implementing a new function writeHaplopainterFile as suggested by @jorainer, I opted to interfere as little as possible with the source code. Everything else looked like code or at least interface duplication, something I am not very happy with. There is simply an option in switchPlotFun that allows to skip the HaploPainter installation check. It still defaults to the previous behavior and will not break existing code.
Instead of implementing a new function
writeHaplopainterFileas suggested by @jorainer, I opted to interfere as little as possible with the source code. Everything else looked like code or at least interface duplication, something I am not very happy with. There is simply an option inswitchPlotFunthat allows to skip theHaploPainterinstallation check. It still defaults to the previous behavior and will not break existing code.R CMD checksuccessful for R-4.1.0 BioC 3.13.Fixes issue #23.