shiny app with downloadable md report, error: "pandoc: Could not find data file" when run by shiny-server

Question

我创建了一个闪亮的应用程序，它提供了一个下载按钮。按下时，将以 html 格式创建降价报告。这是应用程序：

server <- function(input, output) {
  output$report <- downloadHandler(
    filename = "report.html",
    content = function(file){
      tempReport <- file.path(tempdir(), "report.Rmd")
      file.copy("report.Rmd", tempReport, overwrite = TRUE)
      out <- rmarkdown::render(tempReport, output_file = file)
    }
  )
}

ui <- fluidPage(
  downloadButton("report", label=NULL)
)

shinyApp(ui = ui, server = server)

report.Rmd 看起来像这样：

---
output: html_document
---
## Hello
```{r map}
leaflet::leaflet()
```

如果我运行来自 rstudio-server 的应用程序一切正常：创建并下载独立的 html 文件。它包括传单地图。

但是，如果我从 shiny-server 运行它得到的只是以下错误：

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

pandoc: Could not find data file /usr/lib64/R/library/leaflet/htmlwidgets/lib/leaflet/
Warnung: Error in : pandoc document conversion failed with error 97
Stack trace (innermost first):
    53: pandoc_convert
    52: convert
    51: rmarkdown::render
    50: download$func [/srv/shiny-server/biserver/downReport/app.R#7]
     1: runApp
Error : An error has occurred. Check your logs or contact the app author for clarification.

该错误似乎是由rmarkdown、shiny-server 和leaflet 组合触发的。例如，从报告中删除传单可以修复它。

非常感谢任何帮助。

这是 sessionInfo() 的输出：

R version 3.3.3 (2017-03-06)
Platform: x86_64-redhat-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

locale:
 [1] LC_CTYPE=de_DE.UTF-8       LC_NUMERIC=C               
LC_TIME=de_DE.UTF-8        LC_COLLATE=de_DE.UTF-8    
 [5] LC_MONETARY=de_DE.UTF-8    LC_MESSAGES=de_DE.UTF-8    
LC_PAPER=de_DE.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C             
LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] shiny_1.0.3

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.10    digest_0.6.12   rprojroot_1.2   mime_0.5        
R6_2.2.1        xtable_1.8-2    jsonlite_1.4   
 [8] backports_1.0.5 magrittr_1.5    evaluate_0.10   stringi_1.1.5   
leaflet_1.1.0   rmarkdown_1.5   tools_3.3.3    
[15] stringr_1.2.0   htmlwidgets_0.8 crosstalk_1.0.0 yaml_2.1.14     
httpuv_1.3.3    htmltools_0.3.6 knitr_1.15.1

我正在使用 Shiny Server v1.5.3.838 (Node.js v6.10.0)。这是我闪亮的-server.conf:

run_as shiny;
# Define a server that listens of port 3839.
server {
   listen 3839;

  location / {
     site_dir /srv/shiny-server/biserver;
     log_dir /var/log/shiny-server;
  }
}

Answer 1

同样的问题... 已解决。

shiny-server 和 rstudio 服务器在安装目录中嵌入了 pandoc。

只需删除闪亮服务器的坏 pandoc 二进制文件，并在同一位置对新的 pandoc 版本执行逻辑 link，或者在我的情况下，我使用了本地 rstudio 服务器的 pandoc 版本正在工作。

shiny app with downloadable md report, error: "pandoc: Could not find data file" when run by shiny-server

shiny app with downloadable md report, error: "pandoc: Could not find data file" when run by shiny-server

r

leaflet

r-markdown

shiny

shiny-server