Question: Using msa msaPrettyPrint(): issues with latex
gravatar for Olorin
13 months ago by
Olorin50 wrote:

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 :


So I simply test to correct the path to:


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.


ADD COMMENTlink modified 13 months ago • written 13 months ago by Olorin50
gravatar for Olorin
13 months ago by
Olorin50 wrote:

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


ADD COMMENTlink written 13 months ago by Olorin50
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