Question

我正在docker容器中运行Shiny应用程序。该应用程序从Google Analytics（分析）中提取/处理数据，然后将这些数据传递到.Rmd文件中，然后将该文件编织到投影仪演示文稿中，然后提供该文件供下载。 docker映像正在R v3.4.4.上运行rmarkdown v1.10。该应用程序可以正常工作，除了最后一步，在此过程中，我使用render()将.Rmd编织为.pdf。

pdflatex已安装并可以在我的容器中访问：

root@de4bd1ee457a:/# pdflatex
This is pdfTeX, Version 3.14159265-2.6-1.40.18 (TeX Live 2017) (preloaded format=pdflatex)
 restricted \write18 enabled.

我的sessionInfo()

> sessionInfo()
R version 3.4.4 (2018-03-15)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux 9 (stretch)

Matrix products: default
BLAS: /usr/lib/openblas-base/libblas.so.3
LAPACK: /usr/lib/libopenblasp-r0.2.19.so

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

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

loaded via a namespace (and not attached):
[1] compiler_3.4.4

发光的服务器日志：

Listening on http://127.0.0.1:45211
2018-08-07 13:49:19> No scopes have been set, set them via 
options(googleAuthR.scopes.selected) - 
  no authentication attempted.

Attaching package: ‘dplyr’

The following objects are masked from ‘package:stats’:

  filter, lag

The following objects are masked from ‘package:base’:

  intersect, setdiff, setequal, union

2018-08-07 13:49:20> Default Google Project for googleAnalyticsR is now set.  
This is shared with all googleAnalyticsR users. 
If making a lot of API calls, please: 
  1) create your own Google Project at https://console.developers.google.com 
2) Activate the Google Analytics Reporting API 
3) set options(googleAuthR.client_id) and options(googleAuthR.client_secret) 
4) Reload the package.
2018-08-07 13:49:20> Set API cache
2018-08-07 13:49:20> No environment argument found, looked in GA_AUTH_FILE

Attaching package: ‘jsonlite’

The following object is masked from ‘package:shiny’:

  validate

2018-08-07 13:49:36> Downloaded [5045] rows from a total of [5045].


processing file: GA_report.Rmd
`geom_smooth()` using method = 'loess' and formula 'y ~ x'
`geom_smooth()` using method = 'loess' and formula 'y ~ x'
`geom_smooth()` using method = 'loess' and formula 'y ~ x'
`geom_smooth()` using method = 'loess' and formula 'y ~ x'
output file: GA_report.knit.md

我已验证GA_report.knit.md已成功创建（以及.Rmd文件中的所有图形）。在R会话的容器中，我可以在render()文件上运行...knit.md并创建最终的投影仪演示文稿.pdf，而不会出现问题。只是将*.knit.md转换为.pdf并提供下载的最后一步失败了。

当我查看包含我的dir文件的.Rmd时，没有.tex文件，只有GA_report.knit.md和GA_report.utf8.md。

我的.Rmd

的标题

---
output: 
  beamer_presentation:
    theme: "SwCustom"
title: "`r paste0('Draft report: ', params$client)`"
date: "`r Sys.Date()`"
toc: FALSE
classoption: aspectratio=169
editor_options: 
  chunk_output_type: console
params:
  data: NA
  client: NA
---

render()语句

render("report/GA_report.Rmd", 
       output_format = "all",
       output_file = file, 
       params = params, 
       envir = new.env(parent = globalenv()), 
       clean = FALSE, 
       quiet = FALSE)

可以在容器中访问我的自定义投影仪主题

root@de4bd1ee457a:/# kpsewhich beamerthemeSwCustom.sty
/opt/TinyTeX/texmf-dist/tex/latex/beamer/beamerthemeSwCustom.sty

这可能是怎么回事？在完成文件过程中，似乎所有迹象都应指向是，但是我对可能的问题感到困惑。

Answer 1

我相信这与Shiny Server中的最大超时错误有关。我的docker容器正在运行Shiny Server，this issue on the Shiny Server github建议在Shiny Server的downloadHandler()中存在硬编码的超时。由于我的.Rmd文件很大，因此转换为.pdf所需的时间比自动超时要长得多。由于downloadHandler()从未提供我期望下载的内容，因此我将取消该过程，并且最终也不会创建最终的.pdf。

将我的应用程序重构为包括两个按钮，一个用于生成报告，一个用于下载报告。通过允许在downloadedHandler()之外进行.Rmd的编织，从而避免了downloadHandler()的硬编码超时。

render（）无法在容器化的Shiny应用中将.Rmd转换为.pdf

1 个答案: