Unable to knit R markdown

Question

The following error is shown when I try to knit my r markdown baring in mind all code runs successfully otherwise.

Error in as.ts(x) : object 'Trainingdatar2000_m' not found
Calls: <Anonymous> ... withVisible -> eval -> eval -> acf -> na.action -> as.ts
In addition: Warning messages:
1: In has_crop_tools() : 
Tool(s) not installed or not in PATH: pdfcrop, ghostcript
-> As a result, figure cropping will be disabled.
2: In has_crop_tools() : 
Tool(s) not installed or not in PATH: pdfcrop, ghostcript
-> As a result, figure cropping will be disabled.
Execution halted```

Answer 1

R Markdown evaluates in its own clean session. Your notebook needs to generate all datasets needed, and will not share objects in the parent session.