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I had a r markdown file copied from Roger Peng's tutorial. And I was able to knit to html and Word but had problems knitting to pdf. The test.Rmd code: 

My First Knitr Document
===============================

This is some text (i.e. a text chunk).

here is a code chunk
```{r}
set.seed(1)
x <- rnorm(100)
mean(x)
```

After clicking 'knit to pdf', error: 

Output created: test.pdf
Error in tools::file_path_as_absolute(output_file) : 
file 'test.pdf' does not exist
Calls: <Anonymous> -> <Anonymous>
In addition: Warning messages:
1: running command '"pdflatex" -halt-on-error -interaction=batchmode 
"test.tex"' had status 1 
2: In readLines(logfile) : incomplete final line found on 'test.log'
Execution halted

When I run 'latexmk -version' in cmd (windows), I got: 

latexmk: warning: running with administrator privileges
latexmk: The script engine  could not be found
latexmk: Data: scriptEngine="perl.exe"

My session info: 

R version 3.4.4 (2018-03-15)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

Matrix products: default

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] tinytex_0.4 sp_1.2-7   

loaded via a namespace (and not attached):
[1] Rcpp_0.12.16    lattice_0.20-35 withr_2.1.2     digest_0.6.15   
rprojroot_1.3-2 grid_3.4.4     
[7] R6_2.2.2        backports_1.1.2 magrittr_1.5    evaluate_0.10.1 
httr_1.3.1      stringi_1.1.7  
[13] rmarkdown_1.9   devtools_1.13.5 tools_3.4.4     stringr_1.3.0   
yaml_2.1.18     compiler_3.4.4 
[19] memoise_1.1.0   htmltools_0.3.6 knitr_1.20

My MikTex version: basic-miktex-2.9.6.

Updated, to be more precise, the same code worked well on mac (R version 3.4.0 though).
More information: I installed RStudio on E disk while MikTex on C disk.
Also, I am able to use R Sweave compile pdf.

I appreciate if anyone could help.

HW-Scientist
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1 Answers1

2

If you click on the little arrow besides "knit" you should be able to "knit to pdf". R markdown will then add the correct YAML header to your document:

---
output:
  pdf_document: default
---
My First Knitr Document
===============================

This is some text (i.e. a text chunk).

here is a code chunk
```{r}
set.seed(1)
x <- rnorm(100)
mean(x)
```

This works for me. Just insert the Header and click on knit.

Next time: please take a quick look at the Documentation

Hope this helps :)

BerriJ
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  • Thanks Kaktus. I do have the header, just forgot to post. Also I can run the Rmd file successfully on mac, even without the header. – HW-Scientist Mar 27 '18 at 16:23