library(shiny)
ui <- fluidPage(
  numericInput("num", "num", 5),
  DT::DTOutput("table")
)

makecb <- function(ids) {
  unlist(lapply(ids, function(x) {
    as.character(checkboxInput(paste0("cb_", x), label = paste0("cb_", x)))
  }))
}

server <- function(input, output, session) {
  output$table <- DT::renderDataTable({
    DT::datatable(
      data.frame(x = character(), y = character()),
      escape = FALSE,
      options = list(
        preDrawCallback = htmlwidgets::JS('function() { Shiny.unbindAll(this.api().table().node()); }'),
        drawCallback = htmlwidgets::JS('function() { Shiny.bindAll(this.api().table().node()); } ')
      )
    )
  })

  proxy <- DT::dataTableProxy('table', deferUntilFlush = FALSE)

  observe({
    data <- data.frame(
      x = seq(input$num),
      y = makecb(seq(input$num))
    )
    DT::replaceData(proxy, data, resetPaging = FALSE)
  })

  observe({
    ids <- grep("^cb", names(input), value = TRUE)
    values <- sapply(ids, function(id) {
      input[[id]]
    })
    print(t(values))
  })
}
shinyApp(ui, server)