我从我的应用程序闪亮生成pdf报告时遇到问题,该报告托管在服务器上.
该应用程序工作正常,但当我按下按钮下载报告时,我收到此错误:
pandoc version 1.12.3 or higher is required and was not found.
问题是,如果我输入pandoc -v
我得到:
pandoc 1.12.3.3
Compiled with texmath 0.6.6, highlighting-kate 0.5.6.1.
Syntax highlighting is supported for the following languages:
actionscript, ada, apache, asn1, asp, awk, bash, bibtex, boo, c, changelog,
clojure, cmake, coffee, coldfusion, commonlisp, cpp, cs, css, curry, d,
diff, djangotemplate, doxygen, doxygenlua, dtd, eiffel, email, erlang,
fortran, fsharp, gnuassembler, go, haskell, haxe, html, ini, java, javadoc,
Javascript, json, jsp, julia, latex, lex, literatecurry, literatehaskell,
lua, makefile, mandoc, markdown, matlab, maxima, metafont, mips, modelines,
modula2, modula3, monobasic, nasm, noweb, objectivec, objectivecpp, ocaml,
octave, pascal, perl, php, pike, postscript, prolog, python, r,
relaxngcompact, restructuredtext, rhtml, roff, ruby, rust, scala, scheme,
sci, sed, sgml, sql, sqlmysql, sqlpostgresql, tcl, texinfo, verilog, vhdl,
xml, xorg, xslt, xul, yacc, yaml
Default user data directory: /home/daniele/.pandoc
Copyright (C) 2006-2013 John MacFarlane
Web: http://johnmacfarlane.net/pandoc
This is free software; see the source for copying conditions. There is no
warranty, not even for merchantability or fitness for a particular purpose.
所以我想我有正确的版本.还安装了TexLive并且路径在$PATH
.
Server.R
library(shiny)
library(drsmooth)
library(shinyBS)
library(knitr)
library(xtable)
library(rmarkdown)
shinyServer(function(input, output,session) {
output$downloadReport <- downloadHandler(
filename = function() {
paste('report', sep = '.','pdf')
},
cOntent= function(file) {
src <- normalizePath('report.Rmd')
# temporarily switch to the temp dir, in case you do not have write
# permission to the current working directory
owd <- setwd(tempdir())
on.exit(setwd(owd))
file.copy(src, 'report.Rmd')
library(rmarkdown)
out <- render('report.Rmd')
file.rename(out, file)
})
output$tb <- renderUI({
p(h4("Report")),
"Dowload a the report of your analysis in a pdf format",
tags$br(),downloadButton('downloadReport',label="Download report"),
tags$em("This option will be available soon")
})
})
*report.Rmd*不包含任何类型的计算,它只是文本.pdf生成在我的本地版本(MacOS)上运行正常,但在服务器上运行不正常.
在此先感谢,如果需要,我在这里提供其他信息.
丹尼尔
1> 小智..:
进入RStudio并找到系统环境变量 RSTUDIO_PANDOC
Sys.getenv("RSTUDIO_PANDOC")
然后在调用render命令之前将其放入R脚本中.
Sys.setenv(RSTUDIO_PANDOC="--- insert directory here ---")
在我努力寻找rmarkdown如何找到pandoc后,这对我有用.我必须检查github来查看源代码.
另一个选择是将它添加到项目本地的`.Renviron`文件中`RSTUDIO_PANDOC =/usr/lib/rstudio/bin/pandoc`参考:https://csgillespie.github.io/efficientR/3-3- R-startup.html#renviron
这对我有用,而在bash中使用`export`命令却没有(我尝试将`pandoc`目录附加到`$ PATH`并设置`$ RSTUDIO_PANDOC`).
2> John Blischa..:
另一个选项是这个适用于所有R脚本的选项是全局定义此变量.
在Debian/Ubuntu上,将以下行添加到.bashrc文件中:
export RSTUDIO_PANDOC=/usr/lib/rstudio/bin/pandoc
在macOS上,将以下内容添加到.bash_profile文件中:
export RSTUDIO_PANDOC=/Applications/RStudio.app/Contents/MacOS/pandoc
在Windows上(使用Git Bash),将以下内容添加到.bashrc文件中:
export RSTUDIO_PANDOC="/c/Program Files/RStudio/bin/pandoc/"
3> 小智..:
解决此问题的最简单方法是在调用RMarkdown :: render之前在crontab命令中传递Sys.setenv(..)命令。您需要用分号分隔两个命令:
R -e "Sys.setenv(RSTUDIO_PANDOC='/usr/lib/rstudio-server/bin/pandoc'); rmarkdown::render('File.Rmd', output_file='output.html')"
(请记住,rstudio-server路径与非服务器版本不同)