Rmarkdown in loop, "knit html" button different output than rmarkdown::render - html

Question

edit
This issue is not (necessarily) only related to {htmlTable}. The same happens when rendering a html table which has been styled with the {kableExtra} package (see also this thread).
original question
I'm working in RMarkdown, trying to render a document with htmltables from the htmlTable package in a loop. When I push the "Knit" button in RStudio, everything works great. But when I use the render() function, the htmltables in the loop don't get printed, but the table just before the loop does.
I read that "knit" button and the render function does the same, so I don't understand whats wrong?
This is a working example of a .Rmd file with a hmtlTables:
---
output: html_document
---
## htmlTables
```{r, results='asis'}
library(data.table)
library(htmlTable)
library(ggplot2)
a <- data.table(matrix(seq(1, 100, 5), ncol = 2))
htmlTable(a)
for (i in 10:11) {
cat( paste('## title no.', i, '\n' ) )
print(ggplot(a*i, aes(x = V1, y = V2)) + geom_point())
print(htmlTable(a*i))
cat('\n')
}
```
I need to generate many reports automatically with different parameters, so I need to get this working with render().

Answer 1

htmlTable has defined a print method, which appears to print the table in a new window, change print() to writeLines() will do the trick:
---
output: html_document
---
## htmlTables
```{r, results='asis'}
library(data.table)
library(htmlTable)
library(ggplot2)
a <- data.table(matrix(seq(1, 100, 5), ncol = 2))
htmlTable(a)
for (i in 10:11) {
cat( paste('## title no.', i, '\n' ) )
print(ggplot(a*i, aes(x = V1, y = V2)) + geom_point())
writeLines(htmlTable(a*i))
cat('\n')
}
```
However it still seems a bit strange to me because I believe that the knit button uses rmarkdown::render() under the hood but they have different behaviors in this case.

Answer 2

This depends on how the viewer is detected.
To check this :
---
title: "Check viewer"
output: html_document
---
```{r viewer, echo=FALSE}
getOption("viewer")
```
With knit button:
Check viewer
## NULL
With rmarkdown::render:
Check viewer
## function (url, height = NULL)
## {
## if (!is.character(url) || (length(url) != 1))
## stop("url must be a single element character vector.",
## call. = FALSE)
## if (identical(height, "maximize"))
## height <- -1
## if (!is.null(height) && (!is.numeric(height) || (length(height) !=
## 1)))
## stop("height must be a single element numeric vector or 'maximize'.",
## call. = FALSE)
## invisible(.Call("rs_viewer", url, height, PACKAGE = "(embedding)"))
## }
## <environment: 0x0000020ccb7f26d8>
knit button executes rendering in an environment without defined viewer, whereas rmardown::render in RStudio console uses interactive viewer.
htmlTable allows to set options(htmlTable.cat = TRUE), so that print works, ie doesn't use interactive viewer, see ?htmlTable::htmlTable.
The print-function relies on the [base::interactive()] function
for determining if the output should be sent to a browser or to the terminal.
In vignettes and other directly knitted documents you may need to either set
useViewer = FALSE alternatively set options(htmlTable.cat = TRUE).
---
output: html_document
---
## htmlTables
```{r, results='asis'}
options(htmlTable.cat = TRUE)
library(data.table)
library(htmlTable)
library(ggplot2)
a <- data.table(matrix(seq(1, 100, 5), ncol = 2))
htmlTable(a)
for (i in 10:11) {
cat( paste('## title no.', i, '\n' ) )
print(ggplot(a*i, aes(x = V1, y = V2)) + geom_point())
print(htmlTable(a*i))
cat('\n')
}
```