Convert *.md to *.pdf using RStudio

Question

I think I have a MikTeX problem. In RStudio I clicked on the Knit PDF button and received this error message.

This is pdfTeX, Version 3.1415926-2.3-1.40.12 (MiKTeX 2.9 64-bit)
pdflatex: The memory dump file could not be found.
pdflatex: Data: pdflatex.fmt

I then followed the first instruction at http://docs.miktex.org/manual/formats.html Then I rebooted my computer.

At this point I do not know if I need to add a memory dump file and if so, the details of how to do so.

I then tried Knit Word and that worked beautifully, producing a Word 2007 document.

I am using RStudio. I have an R markup document Ira.Rmd. It produced files Ira.md and Ira.html. I would like to save as Ira.pdf. I downloaded and ran pandoc on the command line with

pandoc  Ira.md –o Ira.pdf. 

I received the following error message.

Pandoc: Error producing PDF from TeX source. This is pdfTeX, Version 3.1415926-2.3.1.40.12 Pdflatex: The memory dump file could not be found. Pdflatex: Data: pdflatex.fmt

Can someone explain in simple terms how I can perform this file conversion? I am using the following.

Windows 7. R Version: 3.0.2 RStudio Version: 0.98.684

I did read https://github.com/rstudio/rmarkdown but I still do not understand how to convert my file.

UPDATE I am editing my question.

I am trying to convert an R markdown file to PDF. I created the RMD file in R Studio. With a click of a button I successfully produced the HTML file which is filled with R code.

I am using R version 3.0.2

I am using RStudio version 0.98.684

I do not know if the following is relevant.

My .Rprofile file contains the following line.

setwd("C:/Users/Ira/Documents/Statistics")

I ran the following

> getwd()
[1] "C:/Users/Ira/Documents/Statistics"

I have attempted all of the suggestions. Thank you. However, I continue to receive error messages when trying to convert to PDF. My most recent posts attempted to post the error messages.

The real Rmarkup file is: IraAppliedStats.Rmd

Clicking on Knit produces the desired HTML file.

I successfully ran the commands:

install.packages("devtools"); devtools::install_github("rstudio/rmarkdown")

library(rmarkdown)

From the console I ran the following command, but I received an error.

render(input = "toPDF2.rmd", output_format = "pdf_document", output_file = "toPDF2.pdf")

I observed the monitor. After a few chunks were produced I started to see multiple messages such as the following after a few chunks were completed.

*Warning in (if (out_format(c("latex", "sweave", "listings", "markdown"))) sanitize_fn else str_c)(path, : dots in figure paths replaced with _ ("IraAppliedStats_Rmd_files/figure-latex/unnamed-chunk-10")*

Also each chunk had the following message.

ordinary text without R code

Much of the document is R code. The same line appears when I am producing the HTML file.

The essence of the error message seems to be.

pandoc.exe: Error producing PDF from TeX source. This is pdfTeX, Version 3.1415926-2.3-1.40.12 (MiKTeX 2.9 64-bit) pdflatex: The memory dump file could not be found.

Using Notepad, I then added the following two lines to the top of the IraAppliedStats.md file.

*title: IraAppliedStats.md output: pdf_document*

I closed Notepad.

I again ran the command.

render(input = "IraAppliedStats.Rmd", output_format = "pdf_document", output_file =    "IraAppliedStats.Rmd.pdf")

This did not appear to help as I again received an error message and there was no PDF file produced.

End of addition/edit

Answer 1

You have to install RStudio after installing MikTek.

Answer 2

Using the rmarkdown package (included with RStudio Version 0.98.682, the current preview release) it's very simple to convert Rmd to PDF, there is a single function that will do the conversion: render.

Here's my markdown file (the example one that is created when you start a new Rmd in RStudio), Assume it's called Untitled.Rmd and saved in the working directory (and assuming your LaTeX distribution is fully up-to-date, and you have the latest version of Pandoc):

---
title: "Untitled"    # you must have lines similar to these in your Rmd file
output: pdf_document # this is how R knows to convert this file to a PDF
---

This is an R Markdown document. Markdown is a simple formatting syntax for authoring HTML, PDF, and MS Word documents. Click the **Help** toolbar button for more details on using R Markdown.

When you click the **Knit** button a document will be generated that includes both content as well as the output of any embedded R code chunks within the document. You can embed an R code chunk like this:

```{r}
summary(cars)
```

You can also embed plots, for example:

```{r, echo=FALSE}
plot(cars)
```

Note that the `echo = FALSE` parameter was added to the code chunk to prevent printing of the R code that generated the plot.

Then I run in the console:

library(rmarkdown)
render("Untitled.Rmd") # you could also use "Untitled.md"

And then I get Untitled.pdf in my working directory, which looks like this:

Alternatively, here is the long-hand way to do this, if you can't use that version of RStudio, or don't want to include those title: and output: lines in your markdown code:

  # Load packages.  
  require(knitr)
  require(markdown)

  # Process your .Rmd and generate a .pdf file 
  # (including smart punctuation and grey background of code blocks)
  # For this step you'll need to have two other programs installed on your computer
  # 1. Pandoc: http://johnmacfarlane.net/pandoc/installing.html
  # 2. LaTeX: follow the instructions on the Pandoc download page

  filen <- my_rmd_filename # name of the markdown file without .Rmd suffix
  knit(paste0(filen,".Rmd"))
  system(paste0("pandoc -s ", paste0(filen,".md"), " -t latex -o ", paste0(filen,".pdf"), " --highlight-style=tango  -S"))

  # Now find the location on your computer where the PDF file was created:
  getwd()

More details about the packages & versions I'm using for this:

> sessionInfo()
R version 3.0.2 (2013-09-25)
Platform: x86_64-w64-mingw32/x64 (64-bit)

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

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

other attached packages:
[1] rmarkdown_0.1.4

loaded via a namespace (and not attached):
[1] evaluate_0.5.1 formatR_0.10   knitr_1.5      stringr_0.6.2  tools_3.0.2    yaml_2.1.10