@am221 this is an absolute mess to debug. But based on what the error message says what is possible is that deep in the code deprecated functions from a (?) Bioconductor package are being used that might have to be fixed.
The last two options seem to have been deprecated from the package and might no longer be supported - and possibly create the error message.
I have no idea what will happen if you just delete them or you might have to replace them with new settings depending on what you want to do.
As an additional remark: the workflow in its current state cannot be run by anyone without the data and even then there are several loose ends and so on. So there is absolutely no guarantee that this point will fix the whole things since the workflow has lots of R scripts and dependencies so something else might be lurking. If you are the creator of this workflow and know what you are doing: fine. Otherwise proceed with extra caution.
@am221 non other than what the error message says. You will have to check the number of rows and items that go into the function.
Maybe you extract the data from the R node before and check the values. But as I said. The whole workflow seems complicated and you should make sure you understand what these functions and packages do.