Hi Ista,

it's weird I don't know why this happens. I tried so many different ways but
now finally
I found a solution. I wrote a little shell script:

pdflatex -halt-on-error body.tex
bibtex body.aux
pdflatex -halt-on-error body.tex
pdflatex -halt-on-error body.tex

which does the job. So my "External Tools Configuration" looks like the
following now:

library(tools)
setwd("${container_loc}")
system("./body.sh", intern=TRUE)

I get the output into R and as soon as there is an error in my latex code it
the compilation/processing stops and the output is still put into the R
console. 
This was possible by adding the -halt-on-error parameter.

Thanks for your support anyway.

Best,
Syrvn

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