knitr pandoc:“无法使用pdf编写器生成pdf输出" [英] knitr pandoc: "cannot produce pdf output with pdf writer"

问题描述

最前:在knitr中使用 pandoc()，在尝试将.md或.Rmd编译为PDF时会抱怨.

Up front: using pandoc() in knitr, it complains when trying to compile .md or .Rmd into a PDF.

我正在简化可重复性研究的过程，正如许多地方所记录的那样.我正在使用 pandoc 和 knitr 并生成出色的文档.我还试图简化一些不擅长编程的同事，但我们正在尝试使用类似的文件.对于以用户友好"为基础的以降价为中心的编辑器，有几个选项，由于种种原因，我选择RStudio(对我来说，这是emacs/ess，但这是不同的).

I'm streamlining the process for reproducible research, as has been documented in many places. I'm using pandoc and knitr and producing great documents. I'm also trying to streamline for some co-workers who are not as adept with programming, yet we're trying to use similar files. There are several options for "user friendly" markdown-centric editors, and for several reasons I'm leaning on RStudio (for them, emacs/ess for me, but that's different).

我的工作流程:给他们一个markdown(.md或.Rmd)文件，让他们能够进行更改并将其重新呈现为PDF.不幸的是，RStudio不允许(AFAICT)设置模板或其他任意的Pandoc配置参数(例如，章节，数字部分)，因此在R/knitr中使用 pandoc()非常有意义.

My workflow: give them a markdown (.md or .Rmd) file and have them be able to make changes and optionally re-render it into a PDF. Unfortunately, RStudio does not (AFAICT) allow setting templates or other arbitrary pandoc configuration parameters (e.g., chapters, number-sections), so using pandoc() in R/knitr makes a lot of sense here.

使用 whitepaper.Rmd 作为输入文件，我在R中运行 pandoc('whitepaper.Rmd'，'pdf')并立即获得:

Using whitepaper.Rmd as the input file, I run pandoc('whitepaper.Rmd', 'pdf') in R and immediately get:

> pandoc('whitepaper.Rmd', 'pdf')
executing pandoc  -t latex --standalone --smart --number-sections --template=report.tex -f markdown -t pdf -o whitepaper.pdf "whitepaper.Rmd"
pandoc.exe: cannot produce pdf output with pdf writer
Error in (function (input, format, ext, cfg)  : conversion failed

我在特定于knitr的标头中明确包含"t:latex"，尽管没有它， pandoc()仍在系统调用中添加"-t pdf"，这在pandoc.exe 不接受.

I explicitly have "t:latex" in my knitr-specific header, though without it, pandoc() is still adding "-t pdf" to the system call, something that pandoc.exe does not accept.

通过故障排除，如果我删除'-t pdf'，该命令也可以正常工作，因此输入文件本身似乎没有问题:

With troubleshooting, the command works just fine if I remove '-t pdf', so it seems that there is nothing wrong with the input file itself:

> system('pandoc  -t latex --standalone --smart --number-sections --template=report.tex -f markdown -o whitepaper.pdf "whitepaper.Rmd"')

关于此主题还有许多其他对话: 14586177 ， 14508429 ，15258233 ，和受到广泛讨论的 11025123 .他们全都解决了需要命令行工作，额外的中间步骤，外部Makefile或 knit2pdf()(不使用texi2pdf的代码)的解决方案.

There have been numerous other conversations regarding this topic: 14586177, 14508429, 15258233, and the heavily-discussed 11025123. They all resolve to solutions that require command-line work, extra middle-steps, external Makefiles, or knit2pdf() (which uses texi2pdf, not desired).

我所看到的约束:

• 在R环境中轻松操作；
• 利用Yihui的"<！-pandoc ...-> "文件内配置(我继续在模板之间任意切换(例如以下示例之一)；
• 最好用一个标准化"命令(即" pandoc('whitepaper.Rmd'，'pdf')")执行此操作.

• operate easily within the R environment;
• take advantage of Yihui's "<!--pandoc ... -->" in-file configuration (which allows me to continue to switch arbitrarily between my templates, for one of several examples);
• preferably, execute this with a single "standardized" command (i.e., "pandoc('whitepaper.Rmd', 'pdf')").

...因此，一旦在文件中设置了参数，编辑和重新渲染就比较麻烦.

... so that, once the parameters are set in-file, editing and re-rendering is relatively brain-dead.

我可以修补和覆盖Yihui的 knitr ::: pandoc_one()来删除有害的'-t'和格式，但是我想知道其他地方可能会有哪些副作用.这种解决方案既不可持续，也不是正确的方法(tm)".

I can patch and overwrite Yihui's knitr:::pandoc_one() to remove the offending addition of '-t' and format, but I wonder what side-effects that might have elsewhere. This solution isn't sustainable nor "The Right Way (tm)".

有关解决此问题的正确方法(tm)"的建议?我想念一个简单/显而易见的解决方案吗?

Suggestions for "Right Ways (tm)" to solve this problem? Am I missing an easy/obvious solution?

顺便说一句:谢谢谢一辉(Yihui Xie)的针织衫，以及约翰麦克法兰(John MacFarlane)的pandoc.太棒了！(也许我可以向其中一个或两个提交补丁建议，以解决我的用例，尽管如果只是我一个人，那可能就不值得了.)

BTW: thanks, Yihui Xie, for knitr, and John MacFarlane for pandoc. Awesomeness! (Perhaps I could submit patch suggestions to either or both to work around for my use-case, though if it's just me then it might not be worthwhile.)

推荐答案

我认为您需要的所有信息都在?pandoc 中，其中包括运行 system("pandoc-h)查看可能的输出格式.从中您了解到

I think all there information you need is there in ?pandoc, which includes the example of running system("pandoc -h") to see possible output formats. From that you learn that

输出格式:asciidoc，beamer，上下文，docbook，docx，dzslides，epub，epub3，fb2，html，html5，json，latex，man，markdown，markdown_github，markdown_mmd，markdown_phpextra，markdown_strict，mediawiki，本机，odt，opendocument，opml，org，pdf *，纯文本，reallyjs，rst，rtf，s5，slideous，slidy，texinfo，纺织品[*对于pdf输出，请使用乳胶或投影仪，以及-o FILENAME.pdf]

Output formats: asciidoc, beamer, context, docbook, docx, dzslides, epub, epub3, fb2, html, html5, json, latex, man, markdown, markdown_github, markdown_mmd, markdown_phpextra, markdown_strict, mediawiki, native, odt, opendocument, opml, org, pdf*, plain, revealjs, rst, rtf, s5, slideous, slidy, texinfo, textile [*for pdf output, use latex or beamer and -o FILENAME.pdf]

因此，基本上 format ="pdf" 是无效的，您应该使用 pandoc("tmp.Rmd"，format ="latex"，ext ="pdf")(根据?pandoc 的描述，默认为 ext ="pdf" 部分，因此，您真正需要的只是 pandoc("tmp.Rmd"，"latex")).至于为什么 pandoc('whitepaper.Rmd'，'pdf')导致使用 -t pdf 进行调用，那么，您告诉它在第二个参数中执行此操作到您的 pandoc()调用.

So basically format = "pdf" is invalid, you should use pandoc("tmp.Rmd", format = "latex", ext = "pdf") (and acutally the ext="pdf" part is the default, according to ?pandoc, so all you really need is pandoc("tmp.Rmd", "latex")). As for why pandoc('whitepaper.Rmd', 'pdf') resulted in a call with -t pdf, well, you told it to do that in the second argument to your pandoc() call.

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