Nothing about this is specific to R.
If you want to guarantee reproducible results you have to use a container/image with libraries added at build time. Anytime you are relying on floating versions or downloaded libraries you will have issues.
If you want to guarantee reproducible results you have to use a container/image with libraries added at build time. Anytime you are relying on floating versions or downloaded libraries you will have issues.
If you can't even get those numbers, then you can suspect any number of things. Maybe you're not using the right data, maybe there was a typo, maybe someone fraudulently manually tweaked the numbers, maybe you forgot to do a step in the processing chain etc etc. There's no way to know what's going on if you can't even be sure how the original numbers were created.