messages option is usually the way to hide messages in the resulting document but it works if the underlying code in indeed using messages for that.
I believe you are using bigrquery package for that.
I understand from the code that it should be quiet in non interactive session. Does it show in the output document when you render() or in notebook mode in IDE under the chunk ?
I think the progressbar is done using progress package, and it should not show in R Markdown document. I tried this
---
title: "test"
output:
html_document: default
---
```{r}
library(progress)
pb <- progress_bar$new(total = 100, clear = FALSE)
for (i in 1:100) {
pb$tick()
Sys.sleep(1 / 100)
}
```
This may come from somewhere else and without more information, I don't really know.
Hope it helps