I have a very similar problem, but the described solution is not working for me. I just updated to RStudio 2024.12.0 and I similarly am observing that plotting commands do not create plots when running the R script, but copy/pasting the plot objects into the console does result in plots appearing in the Plots tab. I already changed my R Markdown settings to deselect "Show output inline for all R Markdown documents" but the issue persists. I will also mention that this same script did not have this issue back in November, before I took a break, but the issue appeared when I returned to the script today. Maybe I accidentally changed a setting? Any ideas out there? Thank you!