using -knitr- to weave Rnw files in RStudio

Question

This seems to be a recurrent problem for who is willing to write dynamic documents with knitr in RStudio (see also here for instance). Unfortunately I haven't find a solution on Stack Overflow or by googling more in general.

Here is a toy example I am trying to compile in RStudio. It is the minimal-example-002.Rnw (link):

\documentclass{article}
\usepackage[T1]{fontenc}

\begin{document}

Here is a code chunk.

<<foo, fig.height=4>>=
1+1
letters
chartr('xie', 'XIE', c('xie yihui', 'Yihui Xie'))
par(mar=c(4, 4, .2, .2)); plot(rnorm(100))
@

You can also write inline expressions, e.g. $\pi=\Sexpr{pi}$, and \Sexpr{1.598673e8} is a big number.

\end{document}

My problem is that I am not able to compile the pdf in RStudio by using knitr, while by changing the default weaving option to sweave I get the final pdf.

More specifically, I work in Windows 7, latest RStudio version (0.98.1103), I weave the file using the knitr option and I disabled the "always enable Rnw concordance" box.

Did this happen to you? Any help would be highly appreciated, thank you very much.

EDIT

Apparently it is not an RStudio problem, as I tried to compile the document from R with:

library('knitr')
knit('minimal_ex.Rnw')

and I get the same error:

processing file: minimal_ex.Rnw

  |                                                                       
  |                                                                 |   0%
  |                                                                       
  |......................                                           |  33%
  ordinary text without R code


  |                                                                       
  |...........................................                      |  67%
label: foo (with options) 
List of 1
 $ fig.height: num 4

Quitting from lines 8-10 (minimal_ex.Rnw) 
Errore in data.frame(..., check.names = FALSE) : 
  arguments imply differing number of rows: 3, 0
Inoltre: Warning messages:
1: In is.na(res[, 1]) :
  is.na() applied to non-(list or vector) of type 'NULL'
2: In is.na(res) : is.na() applied to non-(list or vector) of type 'NULL'

EDIT 2:

This is my session info:

R version 3.1.1 (2014-07-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)

locale:
[1] LC_COLLATE=Italian_Italy.1252  LC_CTYPE=Italian_Italy.1252    LC_MONETARY=Italian_Italy.1252 LC_NUMERIC=C                  
[5] LC_TIME=Italian_Italy.1252    

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

other attached packages:
[1] knitr_1.10.5

loaded via a namespace (and not attached):
[1] tools_3.1.1

I get final pdf with both knitr and sweave. Is minimal_ex.tex created? — Robert
Not reproducible for me, either. Have you seen knitr FAQ 1? bit.ly/knitr-faq — Yihui Xie
@Robert If I try to weave exactly the same lines with Sweave I get the pdf. I uploaded my session info. Thanks! — Stefano Lombardi
@Yihui thanks for putting me on the right: I checked the version of R, updated it to the latest one and now everything works pretty well! Sorry for bothering you, hope at least this will be helpful for future users. Thanks for the great work you have been doing! :) — Stefano Lombardi

Stefano Lombardi Stefano Lombardi · Accepted Answer · 2015-05-25T22:16:13

After spending hours to try to figure out the problem, I updated R (v 3.2.0) and everything works fine now. It is not clear if the problem was due to some packages conflict, for sure it wasn't an RStudio problem (as I had initially thought).

using -knitr- to weave Rnw files in RStudio

2 Answers