Hello world!

I was trying to use msa package to make several mulitple alignement.

I was enjoying the function msaPrettyPrint() to generate nice pdfs.

I try this

msaPrettyPrint(myFirstAlignment, output="pdf", showNames="none",
               showLogo="none", askForOverwrite=FALSE, verbose=FALSE)

And there was a problem:

Error in texi2dvi(texfile, quiet = !verbose, pdf = identical(output, "pdf"),  : 
  unable to run 'pdflatex' on 'myFirstAlignment.tex'
In addition: Warning message:
running command '"pdflatex" -interaction=nonstopmode "myFirstAlignment.tex"' had status 1 

Then i checked the "myFirstAlignment.tex" file with TexMaker ( i used latex before for writing papers) and then i noticed a mistake in one path :

\begin{document}
​\begin{texshade}{C:/Users/SEBAST~1/AppData/Local/Temp/RtmpMTD00Y/seq21e04fc62d6c.fasta}

So I simply test to correct the path to:

\begin{texshade}{C:/Users/SEBASTIEN/AppData/Local/Temp/RtmpMTD00Y/seq21e04fc62d6c.fasta}

And then run the compilation and the pdf finally comes out!

How can I fix it in R without using texmaker? How I can specify where msaPrettyPrint writes the files?

Thanks you.

See my last answer in A: Using msa msaPrettyPrint(): saving multiple alignement fasta file

PROBLEM SOLVED