[R-SIG-Mac] R code chunks

[John Magnotti]

The failure to find pdflatex may have to do with how R GUI tries to
discover the system path (or pdflatex is actually not on your system). A
while back, Ian Gow suggested adding the location of the pdflatex binary to
the path to fix this issue.

The top of that thread is here:
https://stat.ethz.ch/pipermail/r-sig-mac/2015-March/011335.html

The solution suggested by Ian Gow is in the first reply.

hope that helps,

John

On Tue, Apr 12, 2016 at 8:05 AM, Mollie Brooks <mollieebrooks at gmail.com>
wrote:

> Hi Ivan,
>
> Using the R GUI and the built-in editor, you should be able to format your
> document in the standard Rmarkdown or knitr way and save it with the
> appropriate extension (Rmd or Rnw), but only run lines within chunks in the
> console (using command + enter in the normal way). You can make sure all
> the chunks are working in that way. Then to format the whole document you
> can use a command in the Terminal as described in the links Tom sent or
> reopen the document in Rstudio.
>
> Somehow my R GUI can’t find the right pieces to make the pdf, so I have to
> use the Terminal. render("EstObsErr.Rmd") produces the error
> /usr/local/bin/pandoc EstObsErr.utf8.md --to latex --from
> markdown+autolink_bare_uris+ascii_identifiers+tex_math_single_backslash-implicit_figures
> --output EstObsErr.pdf --template
> /Library/Frameworks/R.framework/Versions/3.2/Resources/library/rmarkdown/rmd/latex/default-1.14.tex
> --highlight-style tango --latex-engine pdflatex --variable
> 'geometry:margin=1in'
> pandoc: pdflatex not found. pdflatex is needed for pdf output.
> Error: pandoc document conversion failed with error 41
>
> cheers,
> Mollie
>
> ------------------------
> Mollie Brooks, PhD
> Postdoctoral Researcher, Population Ecology Research Group
> Department of Evolutionary Biology & Environmental Studies, University of
> Zürich
> http://www.popecol.org/team/mollie-brooks/
>
> > On 12Apr 2016, at 12:57, Ivan Calandra <ivan.calandra at univ-reims.fr>
> wrote:
> >
> > Thank you for your answer.
> >
> > I don't usually use the Terminal, so I'm not sure how to do it.
> > But do you mean to start it from the Terminal and then use the R GUI or
> do everything in the Terminal? In the latter case, I would prefer using
> RStudio... My question was about using the R GUI Editor rather than RStudio.
> >
> > Ivan
> >
> > --
> > Ivan Calandra, PhD
> > University of Reims Champagne-Ardenne
> > GEGENAA - EA 3795
> > CREA - 2 esplanade Roland Garros
> > 51100 Reims, France
> > +33(0)3 26 77 36 89
> > ivan.calandra at univ-reims.fr
> > --
> > https://www.researchgate.net/profile/Ivan_Calandra
> > https://publons.com/author/705639/
> >
> > Le 12/04/2016 11:41, Tom Hopper a écrit :
> >> Ivan,
> >>
> >> You need to run knitr manually from the terminal (RStudio automates
> this with the “knit” button). See
> >>
> >> http://joshldavis.com/2014/04/12/beginners-tutorial-for-knitr/
> >> http://kbroman.org/knitr_knutshell/pages/Rmarkdown.html
> >>
> >> for short tutorials on using knitr from the terminal.
> >>
> >> Regards,
> >>
> >> Tom
> >>
> >>> On 201604 12, at 05:15, Ivan Calandra <ivan.calandra at univ-reims.fr
> <mailto:ivan.calandra at univ-reims.fr>> wrote:
> >>>
> >>> Dear Mac useRs,
> >>>
> >>> A colleague of mine have introduced me to rmarkdown and knitr to
> produce nice reports. The other interesting thing here is to have so-called
> chunks of code, which I find very practical to organize scripts.
> >>>
> >>> I have found that it works well within RStudio. But is there a way to
> enable chunks within the R GUI (and its great editor)?
> >>> What I don't like with RStudio (except that I need to install still
> another software, and place is limited on the 256GB SSD of my MacBook Air)
> is that it is not able to work on multiple screens.
> >>>
> >>> Thank you in advance for your help.
> >>> Ivan
> >>>
> >>> --
> >>> Ivan Calandra, PhD
> >>> University of Reims Champagne-Ardenne
> >>> GEGENAA - EA 3795
> >>> CREA - 2 esplanade Roland Garros
> >>> 51100 Reims, France
> >>> +33(0)3 26 77 36 89
> >>> ivan.calandra at univ-reims.fr <mailto:ivan.calandra at univ-reims.fr>
> >>> --
> >>> https://www.researchgate.net/profile/Ivan_Calandra
> >>> https://publons.com/author/705639/
> >>>
> >>> _______________________________________________
> >>> R-SIG-Mac mailing list
> >>> R-SIG-Mac at r-project.org
> >>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
> >>
> >
> > _______________________________________________
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>
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