I am writing a report in org mode and would like to show some code blocks as seen in so many tutorials. Here is some official documentation, however it was written for org-mode 6.xx back in 2011.
I have tried all variations that I have found on my search so far:
#+BEGIN_SRC R
for(i in 1:19){
print(i)
}
#+END_SRC
#+BEGIN_SRC R :exports code
for(i in 1:19){
print(i)
}
#+END_SRC
#+BEGIN_SRC R :exports both
for(i in 1:19){
print(i)
}
#+END_SRC
#+begin_src R
for(i in 1:19){
print(i)
}
#+end_src
#+begin_src R :exports code
for(i in 1:19){
print(i)
}
#+end_src
The output looks like this:
I feel this must therefore be an issue with my setup. Here are (as far as I know) the relevant parts of my .emacs:
(setq org-src-fontify-natively t)
(org-babel-do-load-languages
'org-babel-load-languages
'((R . t)
(latex . t)))
I have org-version 8.2.10 and all my LaTeX packages are up to date. I also have things setup for python, which also doesn't work, further pointing to a faulty setup.
The most promising help I could find was this great tutorial, which creates an environment for using org with Latex/HTML exports and my language of choice R. It is all written in an org file, however I still can't find my problem. The code blocks there, if I generate the .tex and pdf files still do not show up correctly.
Edit 1: TeX buffer output
% Created 2016-03-08 Tue 08:18
\documentclass{article}
\usepackage[utf8]{inputenc}
\usepackage[T1]{fontenc}
\usepackage{fixltx2e}
\usepackage{graphicx}
\usepackage{longtable}
\usepackage{float}
\usepackage{wrapfig}
\usepackage{rotating}
\usepackage[normalem]{ulem}
\usepackage{amsmath}
\usepackage{textcomp}
\usepackage{marvosym}
\usepackage{wasysym}
\usepackage{amssymb}
\usepackage{hyperref}
\tolerance=1000
\usepackage{minted}
\author{user name}
\date{\today}
\title{Org-mode and R: An Introduction}
\hypersetup{ pdfkeywords={}, pdfsubject={}, pdfcreator={Emacs 24.5.1 (Org mode 8.2.10)}}
\begin{document}
\maketitle
\setcounter{tocdepth}{2}
\tableofcontents
\lstset{language=R,label= ,caption= ,numbers=none}
\begin{lstlisting}
for(i in 1:19){
print(i) }
\end{lstlisting}
\lstset{language=R,label= ,caption= ,numbers=none}
\begin{lstlisting}
for(i in 1:19){
print(i) }
\end{lstlisting}
\lstset{language=R,label= ,caption= ,numbers=none}
\begin{lstlisting}
for(i in 1:19){
print(i) }
\end{lstlisting}
\lstset{language=R,label= ,caption= ,numbers=none}
\begin{lstlisting}
for(i in 1:19){
print(i) }
\end{lstlisting}
\lstset{language=R,label= ,caption= ,numbers=none}
\begin{lstlisting}
for(i in 1:19){
print(i) }
\end{lstlisting} % Emacs 24.5.1 (Org mode 8.2.10)
\end{document}
Edit 2: Output from the *Org PDF LaTeX Output* buffer
This is pdfTeX, Version 3.14159265-2.6-1.40.16 (TeX Live 2015) (preloaded format=pdflatex)
restricted \write18 enabled.
entering extended mode
(/path/to/this/file.tex
LaTeX2e <2016/02/01>
Babel <3.9q> and hyphenation patterns for 81 language(s) loaded.
(/usr/local/texlive/2015/texmf-dist/tex/latex/base/article.cls
Document Class: article 2014/09/29 v1.4h Standard LaTeX document class
(/usr/local/texlive/2015/texmf-dist/tex/latex/base/size10.clo))
(/usr/local/texlive/2015/texmf-dist/tex/latex/base/inputenc.sty
(/usr/local/texlive/2015/texmf-dist/tex/latex/base/utf8.def
(/usr/local/texlive/2015/texmf-dist/tex/latex/base/t1enc.dfu)
(/usr/local/texlive/2015/texmf-dist/tex/latex/base/ot1enc.dfu)
(/usr/local/texlive/2015/texmf-dist/tex/latex/base/omsenc.dfu)))
(/usr/local/texlive/2015/texmf-dist/tex/latex/base/fontenc.sty
(/usr/local/texlive/2015/texmf-dist/tex/latex/base/t1enc.def))
(/usr/local/texlive/2015/texmf-dist/tex/latex/base/fixltx2e.sty
Package fixltx2e Warning: fixltx2e is not required with releases after 2015
(fixltx2e) All fixes are now in the LaTeX kernel.
(fixltx2e) See the latexrelease package for details.
) (/usr/local/texlive/2015/texmf-dist/tex/latex/graphics/graphicx.sty
(/usr/local/texlive/2015/texmf-dist/tex/latex/graphics/keyval.sty)
(/usr/local/texlive/2015/texmf-dist/tex/latex/graphics/graphics.sty
(/usr/local/texlive/2015/texmf-dist/tex/latex/graphics/trig.sty)
(/usr/local/texlive/2015/texmf-dist/tex/latex/latexconfig/graphics.cfg)
(/usr/local/texlive/2015/texmf-dist/tex/latex/pdftex-def/pdftex.def
(/usr/local/texlive/2015/texmf-dist/tex/generic/oberdiek/infwarerr.sty)
(/usr/local/texlive/2015/texmf-dist/tex/generic/oberdiek/ltxcmds.sty))))
(/usr/local/texlive/2015/texmf-dist/tex/latex/tools/longtable.sty)
(/usr/local/texlive/2015/texmf-dist/tex/latex/float/float.sty)
(/usr/local/texlive/2015/texmf-dist/tex/latex/wrapfig/wrapfig.sty)
(/usr/local/texlive/2015/texmf-dist/tex/latex/rotating/rotating.sty
(/usr/local/texlive/2015/texmf-dist/tex/latex/base/ifthen.sty))
(/usr/local/texlive/2015/texmf-dist/tex/generic/ulem/ulem.sty)
(/usr/local/texlive/2015/texmf-dist/tex/latex/amsmath/amsmath.sty
For additional information on amsmath, use the `?' option.
(/usr/local/texlive/2015/texmf-dist/tex/latex/amsmath/amstext.sty
(/usr/local/texlive/2015/texmf-dist/tex/latex/amsmath/amsgen.sty))
(/usr/local/texlive/2015/texmf-dist/tex/latex/amsmath/amsbsy.sty)
(/usr/local/texlive/2015/texmf-dist/tex/latex/amsmath/amsopn.sty))
(/usr/local/texlive/2015/texmf-dist/tex/latex/base/textcomp.sty
(/usr/local/texlive/2015/texmf-dist/tex/latex/base/ts1enc.def
(/usr/local/texlive/2015/texmf-dist/tex/latex/base/ts1enc.dfu)))
(/usr/local/texlive/2015/texmf-dist/tex/latex/marvosym/marvosym.sty)
(/usr/local/texlive/2015/texmf-dist/tex/latex/wasysym/wasysym.sty)
(/usr/local/texlive/2015/texmf-dist/tex/latex/amsfonts/amssymb.sty
(/usr/local/texlive/2015/texmf-dist/tex/latex/amsfonts/amsfonts.sty))
(/usr/local/texlive/2015/texmf-dist/tex/latex/hyperref/hyperref.sty
(/usr/local/texlive/2015/texmf-dist/tex/generic/oberdiek/hobsub-hyperref.sty
(/usr/local/texlive/2015/texmf-dist/tex/generic/oberdiek/hobsub-generic.sty))
(/usr/local/texlive/2015/texmf-dist/tex/generic/ifxetex/ifxetex.sty)
(/usr/local/texlive/2015/texmf-dist/tex/latex/oberdiek/auxhook.sty)
(/usr/local/texlive/2015/texmf-dist/tex/latex/oberdiek/kvoptions.sty)
(/usr/local/texlive/2015/texmf-dist/tex/latex/hyperref/pd1enc.def)
(/usr/local/texlive/2015/texmf-dist/tex/latex/latexconfig/hyperref.cfg)
(/usr/local/texlive/2015/texmf-dist/tex/latex/url/url.sty))
Package hyperref Message: Driver (autodetected): hpdftex.
(/usr/local/texlive/2015/texmf-dist/tex/latex/hyperref/hpdftex.def
(/usr/local/texlive/2015/texmf-dist/tex/latex/oberdiek/rerunfilecheck.sty))
(/usr/local/texlive/2015/texmf-dist/tex/latex/minted/minted.sty
(/usr/local/texlive/2015/texmf-dist/tex/latex/fancyvrb/fancyvrb.sty
Style option: `fancyvrb' v2.7a, with DG/SPQR fixes, and firstline=lastline fix
<2008/02/07> (tvz))
(/usr/local/texlive/2015/texmf-dist/tex/latex/tools/calc.sty)
(/usr/local/texlive/2015/texmf-dist/tex/latex/ifplatform/ifplatform.sty
(/usr/local/texlive/2015/texmf-dist/tex/generic/oberdiek/catchfile.sty)
Package ifplatform Warning:
shell escape is disabled, so I can only detect \ifwindows.
) (/usr/local/texlive/2015/texmf-dist/tex/latex/etoolbox/etoolbox.sty)
(/usr/local/texlive/2015/texmf-dist/tex/generic/xstring/xstring.sty
(/usr/local/texlive/2015/texmf-dist/tex/generic/xstring/xstring.tex))
(/usr/local/texlive/2015/texmf-dist/tex/latex/lineno/lineno.sty)
(/usr/local/texlive/2015/texmf-dist/tex/latex/base/t1cmtt.fd))
! Package minted Error: You must invoke LaTeX with the -shell-escape flag.
See the minted package documentation for explanation.
Type H <return> for immediate help.
...
l.20 \author
{user name}
! Package minted Error: Missing Pygments output; \inputminted was
probably given a file that does not exist--otherwise, you may need
the outputdir package option, or may be using an incompatible build tool.
See the minted package documentation for explanation.
Type H <return> for immediate help.
...
l.20 \author
{user name}^^M
! Package minted Error: You must have `pygmentize' installed to use this packag
e.
See the minted package documentation for explanation.
Type H <return> for immediate help.
...
l.27 \begin{document}
(.//delete_this.aux)
(/usr/local/texlive/2015/texmf-dist/tex/latex/base/ts1cmr.fd)
(/usr/local/texlive/2015/texmf-dist/tex/context/base/supp-pdf.mkii
[Loading MPS to PDF converter (version 2006.09.02).]
) (/usr/local/texlive/2015/texmf-dist/tex/latex/oberdiek/epstopdf-base.sty
(/usr/local/texlive/2015/texmf-dist/tex/latex/oberdiek/grfext.sty)
(/usr/local/texlive/2015/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg))
(/usr/local/texlive/2015/texmf-dist/tex/latex/hyperref/nameref.sty
(/usr/local/texlive/2015/texmf-dist/tex/generic/oberdiek/gettitlestring.sty))
(.//delete_this.out) (.//delete_this.out)
(/usr/local/texlive/2015/texmf-dist/tex/latex/xcolor/xcolor.sty
(/usr/local/texlive/2015/texmf-dist/tex/latex/latexconfig/color.cfg))
! Package minted Error: Missing Pygments output; \inputminted was
probably given a file that does not exist--otherwise, you may need
the outputdir package option, or may be using an incompatible build tool.
See the minted package documentation for explanation.
Type H <return> for immediate help.
...
l.27 \begin{document}
^^M
(/usr/local/texlive/2015/texmf-dist/tex/latex/wasysym/uwasy.fd)
(/usr/local/texlive/2015/texmf-dist/tex/latex/amsfonts/umsa.fd)
(/usr/local/texlive/2015/texmf-dist/tex/latex/amsfonts/umsb.fd)
(.//delete_this.toc)
! Undefined control sequence.
l.33 \lstset
{language=R,label= ,caption= ,numbers=none}
! LaTeX Error: Environment lstlisting undefined.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
...
l.34 \begin{lstlisting}
! LaTeX Error: \begin{document} ended by \end{lstlisting}.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
...
l.38 \end{lstlisting}
! Undefined control sequence.
l.40 \lstset
{language=R,label= ,caption= ,numbers=none}
! LaTeX Error: Environment lstlisting undefined.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
...
l.41 \begin{lstlisting}
! LaTeX Error: \begin{document} ended by \end{lstlisting}.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
...
l.45 \end{lstlisting}
! Undefined control sequence.
l.48 \lstset
{language=R,label= ,caption= ,numbers=none}
! LaTeX Error: Environment lstlisting undefined.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
...
l.49 \begin{lstlisting}
! LaTeX Error: \begin{document} ended by \end{lstlisting}.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
...
l.53 \end{lstlisting}
! Undefined control sequence.
l.55 \lstset
{language=R,label= ,caption= ,numbers=none}
! LaTeX Error: Environment lstlisting undefined.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
...
l.56 \begin{lstlisting}
! LaTeX Error: \begin{document} ended by \end{lstlisting}.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
...
l.60 \end{lstlisting}
! Undefined control sequence.
l.62 \lstset
{language=R,label= ,caption= ,numbers=none}
! LaTeX Error: Environment lstlisting undefined.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
...
l.63 \begin{lstlisting}
! LaTeX Error: \begin{document} ended by \end{lstlisting}.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
...
l.67 \end{lstlisting}
[1{/usr/local/texlive/2015/texmf-var/fonts/map/pdftex/updmap/pdftex.map}]
(.//delete_this.aux) )
(see the transcript file for additional information){/usr/local/texlive/2015/te
xmf-dist/fonts/enc/dvips/cm-super/cm-super-t1.enc}</usr/local/texlive/2015/texm
f-dist/fonts/type1/public/cm-super/sfbx1440.pfb></usr/local/texlive/2015/texmf-
dist/fonts/type1/public/cm-super/sfrm1000.pfb></usr/local/texlive/2015/texmf-di
st/fonts/type1/public/cm-super/sfrm1200.pfb></usr/local/texlive/2015/texmf-dist
/fonts/type1/public/cm-super/sfrm1728.pfb>
Output written on .//delete_this.pdf (1 page, 50965 bytes).
Transcript written on .//delete_this.log.
