在 Shiny 应用程序中下载报告失败

问题描述 投票：0回答：1

在我的 Shiny 应用程序中，用户可以构建可自定义的报告 - 好吧，这就是要实现的目的......

现在用户必须选择所有元素（摘要、直方图、附加注释）以保持简单。然后，输入小部件中的所有内容都会转移到报告创建中（请参阅 app.R 中的 

downloadhandler()
）。

报告可以是 html 或 pdf。两种变体都在不同阶段失败。

但是现在让我们看一下代码并进行澄清：您可以复制代码并运行它。唯一需要更改的是两个文件中的 html 或 pdf（app.R 和 report.Rmd，请参阅注释）。

app.R

# the packages I'm using (hopefully a complete list)
#library(pandoc)
#library(tinytex)
#library(bookdown)
#library(markdown)
#library(rmarkdown)
#library(knitr)
#pandoc_activate()

ui <- fluidPage(
    fluidRow(
        # Inputarea
        # Choose which elements should be added to the Report
        column(5,
            br(),
            checkboxGroupInput(
                inputId = "show_elements",
                label = "Choose elements to be in report",
                choices = c("Abstract","Histogram","Additional Comments"),
                selected = c("Abstract","Histogram","Additional Comments")
                #inline = FALSE,
                #width = NULL,
                #choiceNames = NULL,
                #choiceValues = NULL
            ),
            br(),
            br(),
            hr(),
            br(),
            # if Abstract is checked, then it is shown in the UI
            conditionalPanel(
                condition = "input.show_elements.includes('Abstract')",
                textAreaInput(inputId="caption", label=NULL, value ="Abstract data", width = "1000px", height="100px")
            ),
            br(),
            # if Histogram is checked, then it is shown in the UI
            conditionalPanel(
                condition = "input.show_elements.includes('Histogram')",
            sliderInput(inputId = "bins",
                    label = "Number of bins:",
                    min = 1,
                    max = 50,
                    value = 30)
            ),
            # if Additional Comments is checked, then it is shown in the UI
            conditionalPanel(
                condition = "input.show_elements.includes('Additional Comments')",
                textAreaInput(inputId="caption_1", label=NULL, value ="further notes for the report", width = "1000px", height="100px")
            )
        ),
        # Outputarea
        column(7,
            br(),
            # if Abstract is checked, then it is shown in the UI
            conditionalPanel(
                condition = "input.show_elements.includes('Abstract')",
                verbatimTextOutput("abstract")
            ),
            br(),
            # if Histogram is checked, then it is shown in the UI
            conditionalPanel(
                condition = "input.show_elements.includes('Histogram')",
                plotOutput(outputId = "distPlot")
            ),
            br(),
            # if Additional Comments is checked, then it is shown in the UI
            conditionalPanel(
                condition = "input.show_elements.includes('Additional Comments')",
                verbatimTextOutput("add_com")
            ),
            br(),
            # The download button 
            downloadButton("reportGeneration", "Download Report")
        )
    )
)

server <- function(input, output) {
    # Output corresponding to "Abstract"
    output$abstract <- renderText({ input$caption })

    # Output corresponding to "Histogram"
    output$distPlot <- renderPlot({

        x    <- faithful$waiting
        bins <- seq(min(x), max(x), length.out = input$bins + 1)

        hist(x, breaks = bins, col = "#007bc2", border = "white",
           xlab = "Waiting time to next eruption (in mins)",
           main = "Histogram of waiting times")

    })

    # Output corresponding to "Additional Comments"
    output$add_com <- renderText({ input$caption_1 })



    # Download the document (html or pdf)
    output$reportGeneration <- downloadHandler(
        filename = "report.html",  # if necessary change to report.pdf (app.R and report.Rmd must have either html or pdf)
        content = function(file) {
            tempReport<-file.path("C:/Users/tueftla/R","report.Rmd")
            file.copy('report.Rmd', tempReport, overwrite = TRUE)
            params = list(text1=input$caption, value1=input$bins, text2=input$caption_1)
            rmarkdown::render(
                input =tempReport,
                output_file = file,
                params = params,
                envir = new.env(parent = globalenv())
            )
        
        }
    )

}

shinyApp(ui, server)

报告。Rmd

<!-- YAML header with the three parameters -->
---
title: "My R Markdown Document"
author: "tueftla"
date: "`r format(Sys.time(), '%d.%m.%Y')`"
output: html_document <!-- Depending on the app.R it could be also pdf_document -->
params:
  text1: NA
  text2: NA
  value1: NA
---

```{r include=FALSE}
library(knitr)
```
 
## Abstract <!-- Here the first parameter text1 should be used -->
 
```{r, results='asis',echo=FALSE,warning=FALSE}
print(params[["text1"]])
```
 

## Histogram <!-- Here the third parameter value1 should be used -->
 
```{r results='asis',echo=FALSE,warning=FALSE}
x <- faithful$waiting
bins <- seq(min(x), max(x), length.out = params[["value1"]] + 1)

hist(x, breaks = bins, col = "#007bc2", border = "white",
     xlab = "Waiting time to next eruption (in mins)",
     main = "Histogram of waiting times")
```

## Additional Comments <!-- Here the second parameter text2 should be used -->

```{r, results='asis',echo=FALSE,warning=FALSE}
print(params[["text2"]])
```

当我使用 

runApp()
和 html 输出（在两个文件中）启动 Shiny 应用程序时，控制台输出以下行：

Listening on http://127.0.0.1:3347
processing file: report.Rmd
output file: report.knit.md
"C:/Users/tueftla/AppData/Local/r-pandoc/r-pandoc/3.1.12.2/pandoc" +RTS -K512m -RTS report.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output pandoc50a034b324e1.html --lua-filter "C:\Users\tueftla\AppData\Local\R\win-library\4.3\rmarkdown\rmarkdown\lua\pagebreak.lua" --lua-filter "C:\Users\tueftla\AppData\Local\R\win-library\4.3\rmarkdown\rmarkdown\lua\latex-div.lua" --embed-resources --standalone --variable bs3=TRUE --section-divs --template "C:\Users\tueftla\AppData\Local\R\win-library\4.3\rmarkdown\rmd\h\default.html" --no-highlight --variable highlightjs=1 --variable theme=bootstrap --mathjax --variable "mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML" --include-in-header "C:\Users\tueftla\AppData\Local\Temp\Rtmp04VMVZ\rmarkdown-str50a01a17b14.html"
Output created: C:\Users\tueftla\AppData\Local\Temp\Rtmp04VMVZ\file50a062984a73.html

它似乎以某种方式工作，因为它说它已创建... 但是 html 文件不存在。文件夹Rtmp04VMVZ存在并且有一些文件...

问题1：我根据控制台创建的html文件在哪里？！是否可以直接下载它，或者甚至更好地指定保存 html 的文件夹？

现在让我们使用 

pdf 输出
（在两个文件中）执行 runApp() 并查看控制台输出：

Listening on http://127.0.0.1:3347
processing file: report.Rmd
output file: report.knit.md
"C:/Users/tueftla/AppData/Local/r-pandoc/r-pandoc/3.1.12.2/pandoc" +RTS -K512m -RTS report.knit.md --to latex --from markdown+autolink_bare_uris+tex_math_single_backslash --output pandoc50a0326f48e.tex --lua-filter "C:\Users\tueftla\AppData\Local\R\win-library\4.3\rmarkdown\rmarkdown\lua\pagebreak.lua" --lua-filter "C:\Users\tueftla\AppData\Local\R\win-library\4.3\rmarkdown\rmarkdown\lua\latex-div.lua" --embed-resources --standalone --highlight-style tango --pdf-engine pdflatex --variable graphics --variable "geometry:margin=1in"
Warning in system2(..., stdout = if (use_file_stdout()) f1 else FALSE, stderr = f2)
'"pdflatex"' not found
Warning: Error in : LaTeX failed to compile C:\Users\tueftla\AppData\Local\Temp\Rtmp04VMVZ\file50a026d52af1.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips.
    1: runApp

对我来说，它似乎因为缺少 pdflatex 而失败？！调试提示没有改变任何东西（从我的角度来看）...

问题2：这里有什么问题以及如何解决？就像我在第一个问题中提到的那样，是否可以只下载 pdf，或者甚至更好地指定应保存 pdf 的文件夹？

非常感谢您的帮助！

EDIT_1：我稍微更改了

report.Rmd
文件。在代码块中，我仅使用 
params
...

的值 
<!-- YAML header with the three parameters -->
    ---
    title: "My R Markdown Document"
    author: "tueftla"
    date: "`r format(Sys.time(), '%d.%m.%Y')`"
    output: html_document <!-- Depending on the app.R it could be also pdf_document -->
    params:
      text1: NA
      text2: NA
      value1: NA
    ---
    
    ```{r include=FALSE}
    library(knitr)
    ```
     
    ## Abstract <!-- Here the first parameter text1 should be used -->
     
    ```{r, results='asis',echo=FALSE,warning=FALSE}
    print("Abstract") #print(params[["text1"]])
    ```
     
    
    ## Histogram <!-- Here the third parameter value1 should be used -->
     
    ```{r results='asis',echo=FALSE,warning=FALSE}
    x <- faithful$waiting
    bins <- seq(min(x), max(x), length.out = 5 + 1) #bins <- seq(min(x), max(x), length.out = params[["value1"]] + 1)
    
    hist(x, breaks = bins, col = "#007bc2", border = "white",
         xlab = "Waiting time to next eruption (in mins)",
         main = "Histogram of waiting times")
    ```
    
    ## Additional Comments <!-- Here the second parameter text2 should be used -->
    
    ```{r, results='asis',echo=FALSE,warning=FALSE}
    print("Addidtional comments"]) #print(params[["text2"]])
    ```

...运行时

runApp()
渲染也失败，我收到这些错误消息

Listening on http://127.0.0.1:4084

processing file: report.Rmd
                                                                                                                                                                                                     
output file: report.knit.md

"C:/Users/tueftla/AppData/Local/r-pandoc/r-pandoc/3.1.12.2/pandoc" +RTS -K512m -RTS report.knit.md --to latex --from markdown+autolink_bare_uris+tex_math_single_backslash --output pandoc7fcc19ef2230.tex --lua-filter "C:\Users\tueftla\AppData\Local\R\win-library\4.3\rmarkdown\rmarkdown\lua\pagebreak.lua" --lua-filter "C:\Users\tueftla\AppData\Local\R\win-library\4.3\rmarkdown\rmarkdown\lua\latex-div.lua" --embed-resources --standalone --highlight-style tango --pdf-engine pdflatex --variable graphics --variable "geometry:margin=1in" 
! Sorry, but C:\Users\tueftla\AppData\Local\Programs\MiKTeX\miktex\bin\x64\pdflatex.exe failed.

! The log file contains hopefully all information, to make MiKTeX run again

!   C:\Users\tueftla\AppData\Local\MiKTeX\miktex\log\pdflatex.log

Warning: Error in : LaTeX failed to compile C:\Users\tueftla\AppData\Local\Temp\Rtmp2rsGxa\file7fcc51044777.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See file7fcc51044777.log for more info.
  1: runApp

日志文件(

C:\Users\tueftla\AppData\Local\MiKTeX\miktex\log\pdflatex.log
)

2024-03-11 16:51:35,134+0100 INFO  pdflatex - this process (24692) started by Rgui in directory C:\Users\tueftla\R with command line: C:\Users\tueftla\AppData\Local\Programs\MiKTeX\miktex\bin\x64\pdflatex.exe -halt-on-error -interaction=batchmode C:\Users\tueftla\AppData\Local\Temp\Rtmp2rsGxa\file7fcc51044777.tex
2024-03-11 16:51:35,134+0100 INFO  pdflatex - running on Windows 10.0.19045
2024-03-11 16:51:35,139+0100 INFO  pdflatex - this is MiKTeX-PDFTEX 4.19.0 (1.40.26) (MiKTeX 24.3)
2024-03-11 16:51:35,170+0100 INFO  pdflatex - allowing known shell commands
2024-03-11 16:51:35,229+0100 INFO  pdflatex - going to create file: pdflatex.fmt
2024-03-11 16:51:35,229+0100 INFO  pdflatex.core - start process: miktex formats build pdflatex --engine pdftex
2024-03-11 16:51:51,269+0100 FATAL pdflatex.core - GUI framework cannot be initialized.
2024-03-11 16:51:51,269+0100 FATAL pdflatex.core - Data: 
2024-03-11 16:51:51,269+0100 FATAL pdflatex.core - Source: Libraries\MiKTeX\UI\Qt\mikuiqt.cpp:126
2024-03-11 16:51:51,273+0100 FATAL pdflatex - GUI framework cannot be initialized.
2024-03-11 16:51:51,273+0100 FATAL pdflatex - Info: 
2024-03-11 16:51:51,273+0100 FATAL pdflatex - Source: Libraries\MiKTeX\UI\Qt\mikuiqt.cpp
2024-03-11 16:51:51,273+0100 FATAL pdflatex - Line: 126
2024-03-11 16:51:51,276+0100 INFO  pdflatex - this process (24692) finishes with exit code 1
2024-03-11 16:51:51,283+0100 WARN  pdflatex.core - still open: C:/Users/tueftla/AppData/Local/Temp/Rtmp2rsGxa/file7fcc51044777.tex
2024-03-11 16:51:51,283+0100 WARN  pdflatex.core - still open: file7fcc51044777.log
r shiny r-markdown
1个回答
0
投票

使用 

<!-- ... -->
作为注释仅适用于一个地方：R Markdown 文档的 content 中。在您的 R markdown 文档中，您在 YAML 标头之前、YAML 标头内部以及 R 代码块内部都有类似的注释，但这些注释都无法正确解析或运行。

使用上述更改来调整您的代码。 （

app.R
不变。）

报告。Rmd

---
title: "My R Markdown Document"
author: "tueftla"
date: "`r format(Sys.time(), '%d.%m.%Y')`"
output: html_document
params:
  text1: NA
  text2: NA
  value1: NA
---

```{r include=FALSE}
library(knitr)
```
 
## Abstract <!-- Here the first parameter text1 should be used -->
 
```{r, results='asis',echo=FALSE,warning=FALSE}
print(params[["text1"]])
```
 

## Histogram <!-- Here the third parameter value1 should be used -->
 
```{r results='asis',echo=FALSE,warning=FALSE}
x <- faithful$waiting
bins <- seq(min(x), max(x), length.out = params[["value1"]] + 1)

hist(x, breaks = bins, col = "#007bc2", border = "white",
     xlab = "Waiting time to next eruption (in mins)",
     main = "Histogram of waiting times")
```

## Additional Comments <!-- Here the second parameter text2 should be used -->

```{r, results='asis',echo=FALSE,warning=FALSE}
print(params[["text2"]])
```

这样，我可以渲染 HTML，并在更改 

output_format=
和文件扩展名后渲染 PDF，两者都没有错误。

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