R Sweave does not compile automatically the .bbl file necessary to detect citations in the text. I found a solution with compiling in another program (https://community.rstudio.com/t/impossible-to-cite-with-biblatex-in-r-sweave/35008/2) but it would much more convenient not to compile three times the same file (on two different softwares).
One of the comments here (RStudio will not write a .bbl file when compiling .Rnw file with citations in natbib) mentioned the fact that maybe R Sweave does not run bibtex. Is there something to do to fix this problem ?
(Question also asked here : https://community.rstudio.com/t/r-sweave-does-not-create-a-bbl-file-on-linux-ubuntu/35110)
I finally got the solution, here's what I did :
based on the comments of user1329307, I uninstalled MikTeX and the complete TeX distributions on my computer. Since I use Ubuntu, I used purge to remove MikTeX, TeXLive, tex-commons, etc.
then, I installed (or re-installed) TinyTeX (details here)
I installed manually the packages I needed with tlmgr_install(). Normally, it can be done automatically but that's what I did.
finally, I replaced biber by bibtex in \usepackage[backend = biber]{biblatex} (this person explains why it is important)
This last step made it work, but I don't know if the previous ones are important or not. Since user1329307 succeeded in compiling the bibliography too, I suppose it is necessary but there's no way for me to prove it.
Anyway, now, when I compile the Sweave document, the bibliography is directly created. Thanks a lot to user1329307 for his/her ideas.
Edit : I re-installed MikTeX after all of this and it works too.
Related
I am new to the R/exams package and I try to produce a pdf document from one of the templates provided by the developers. (http://www.R-exams.org/templates/confint3/)
I am able to compile a Rnw file into a HTML document using the commands
library("exams")
exams2html("confint3.Rnw")
When calling the function
exams2pdf("confint3.Rnw")
it gives the error message
! LaTeX Error: File `Sweave.sty' not found.
I have Latex installed and there are no problems using it in general. I do not understand:
Do I need to tell exams2pdf() the location of the latex installation?
Do I need to define a template (as plain.tex) first? How should it look like?
What is it that I do not understand?
I looked at the documentation of the exams package, I also tried exams2pdf() after installing and calling library("tinytex").
Any help where to look at or what to do is highly appreciated. Thank you!
Minimal example:
install.packages("exams")
install.packages("tth")
library("exams")
set.seed(1090)
exams2html("confint3.Rnw")
set.seed(1090)
exams2pdf("confint3.Rnw")
It is hard to diagnose what exactly goes wrong with the information provided. In any case, when running pdfLaTeX either through utils::texi2dvi() (the default when the R package tinytex is not installed) or through tinytex::latexmk() (the default when the R package tinytex is installed) does not find the Sweave.sty file provided by the R base system. What is not clear to me which LaTeX engine is running in the background: MikTeX on Windows?
There are several strategies that could resolve this issue:
Tell your LaTeX installation about the texmf directory provided by the R base system so that it is found no matter where on your system you call pdfLaTeX.
Use a different LaTeX installation, e.g., by installing TinyTeX (the LaTeX distribution) through tinytex (the R package): tinytex::install_tinytex(). This might be particularly attractive if you are not actually a LaTeX user and just need it to compile PDF exams.
Avoid using the Sweave.sty file in a custom template file, say myplain.tex. A suggestion for such a file is included at the end of this post.
Further details are discussed in this thread: https://tex.stackexchange.com/questions/153193/latex-error-sweave-sty-not-found
As for your three questions:
As already explained above: exams2pdf() leverages either utils::texi2dvi() or tinytex::latexmk(). So these need to know about the LaTeX installation - but this seems to be the case. They just don't find the texmf provided by base R.
You should not have to do this but it is certainly an option that you can use. As a starting point, run exams_skeleton(markup = "latex", writer = "exams2pdf"). Among other things this creates a templates folder where you could put the myplain.tex template below.
As I said above, it's hard to answer that with the information provided. Hopefully, one of the clues provided here gets you a couple of steps forward.
Content of myplain.tex:
\documentclass[a4paper]{article}
\usepackage[utf8]{inputenc}
\usepackage{a4wide,graphicx,color,verbatim,url,fancyvrb,ae,amsmath,amssymb,booktabs,longtable,eurosym}
\newenvironment{question}{\item \textbf{Problem}\newline}{}
\newenvironment{solution}{\textbf{Solution}\newline}{}
\newenvironment{answerlist}{\renewcommand{\labelenumi}{(\alph{enumi})}\begin{enumerate}}{\end{enumerate}}
\providecommand{\tightlist}{\setlength{\itemsep}{0pt}\setlength{\parskip}{0pt}}
\setkeys{Gin}{keepaspectratio}
\DefineVerbatimEnvironment{Sinput}{Verbatim}{fontshape=sl}
\DefineVerbatimEnvironment{Soutput}{Verbatim}{}
\DefineVerbatimEnvironment{Scode}{Verbatim}{fontshape=sl}
\newenvironment{Schunk}{}{}
\begin{document}
\begin{enumerate}
%% \exinput{exercises}
\end{enumerate}
\end{document}
i have been trying to implement a tikz chunk in bookdown first by myself, then by following this thread.
unfornutately, i keep running into various errors and incompatibilities, such as this one:
Error in tools::texi2dvi(texf, pdf = !to_svg, clean = TRUE) :
unable to run 'pdflatex' on '.\tikzf702b605920.tex'
(even though by itself tinytex::pdflatex('test.tex') works fine)
on his blog and github Yihui Xie mentioned that it's definitely possible, but i wasn't able to find any working example, so i was hoping if perhaps anyone here could share one, please (or point out what am i doing wrong)
#PaulLemmens, i found what was the problem for me. disclaimer here, i use windows and none of my colleagues who use r on linux/macos have this problem.
issue was arising with knitr when engine=tikz is used in one of the chunks. For it to work installation of imagemagick (https://www.imagemagick.org/script/index.php) and GhostScript (https://www.ghostscript.com/) is needed. as well as that, i had to rewrite knitr (https://github.com/darthaline/knitr) slightly. it's a quick and dirty solution, but it worked for me. on line 281 of R/engine.R the path to imagemagick's convert is hardcoded cause otherwise it seems that windows interprets it as 'convert.exe' from System32 directory (ImageMagick PATH not being recognized with engine = "tikz" in knitr)
I haven't been able to use the neater knitter package with the code chunks.
Basically there's only a few number of occasions in which it interprets them well, but for the most of it the chunks are not recognized as such. That is:
Running a markdown from RStudio only renders chunks before the file is saved. If the file has been saved, then it will show the code as is: no R output.
I also tried using knitr from within LyX, and this presented other problems. The simplest example knitr.lyx was rendered correctly as a pdf, but not html. Using more complicated documents, like the RJournal template showed other errors.
Rscript --verbose --no-save --no-restore
At first I thought it had to do with my Rstudio installation, but now I'm not so sure anymore.
By the way, I'm on Ubuntu 15.04 and the files that I'm using are examples from the documentation:
Rstudio > New File > Rmarkdown... renders R output only before it's saved.
knitr's manual in LyX from Github repo.
I found the answer for this.
It's very obvious and yet easy to overlook if you don't know it.
The problem was in saving the file with the wrong extension.
If you're using R code chunks you need .Rmd extension in Rstudio.
As I was starting with markdown I was using .md. Pfff.
I would like to use knitr to create presentations that embed R objects and code.
For IT reasons I am restricted to vim, so i have found the available Rstudio+knitr examples fairly unhelpful. The vim section of the knitr documents is also very skinny, and therefore unhelpful.
Is someone able to provide some guidance on how to compile a *.Rnw or *.Rmd file using knitr (or alternately point me to a decent online tutorial?) using some combination of vim, R, and the command line?
thanks in advance
Instead of going through Rstudio, you can use the functions in the knitr package directly. There are some options you can tweak, but to get started, all you have to do is call the knit() function on your .Rnw file:
library(knitr)
knit('my_input.Rnw')
If you're missing some of Rstudio's features, it's worth remembering that most of them are just making use of things that are already available in various R packages, so you can usually find a way to use them when you don't have Rstudio available.
I've been struggling for a week now trying to figure out how to generate reports in R using either Sweave or Brew. I should say right at the beginning that I have never used Tex before but I understand the logic of it.
I have read this document several times. However, I cannot even get a simple example to parse. Brew successfully converts a simple markup file (just a title and some text) to a .tex file (no error). But it never ever converts tex to a pdf.
> library(tools)
> library(brew)
> brew("population.brew", "population.tex")
> texi2dvi("population.tex", pdf = TRUE)
The last step always fails with:
Error in texi2dvi("population.tex", pdf = TRUE) :
Running 'texi2dvi' on 'population.tex' failed.
What am I doing wrong?
The report I am trying to build is fairly simple. I have 157 different analysis to summarize. Each one has 4 plots, 1 table and a summary. I just want
output plot 1,2,3,4
output table
\pagebreak
...
that's it. Can anyone help me get further? I use osx, don't have Tex installed.
thanks
You cannot run this without texi2dvi or TeX installed.
An alternative may be html output -- the hwriter package is useful for that.
That said, if you want to produce pdf out, Sweave is the way to go. Frank Harrell's site has a lot of useful info but all this requires a bit of familiarity with LaTeX so you may need to install and learn that first.
If you are on OSX, might as well install the full tex live
http://mirror.ctan.org/systems/mac/mactex/MacTeX.mpkg.zip
It is a big download, but it will be nice to never have to install additional packages.
Another solution: the ascii package in conjonction to your favorite markup language (asciidoc, txt2tags, restructuredtext, org or textile).
http://eusebe.github.com/ascii/
It may be worthwhile spending a week or so just using LaTeX without R and going through a bunch of introductory LaTeX tutorials.
Thus, when you start producing Sweave or Brew documents and you get errors, you will be better able to identify whether the error is arising from LaTeX or Sweave / Brew.
A couple of Windows tools that make it easy to get started with LaTeX include MikTeX + TeXnicCenter or MikTeX + WinEdt.
Another solution is to try a solution of connecting R to microsoft.
It is much weaker then Sweave, but for basic reporting might be what you need.
You might want to go through the example sessions given here: Exporting R output to MS-Word with R2wd (an example session)
I've also been hearing a lot of good things about the knitr package. It seems to resemble Sweave a lot, but add some more to it. I would definitely take a look at it.