Question: Using msa msaPrettyPrint(): issues with latex
0
gravatar for Olorin
2.3 years ago by
Olorin50
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 :

\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.

 

 
msa latex msaprettyprint() • 1.5k views
ADD COMMENTlink modified 2.3 years ago • written 2.3 years ago by Olorin50
Answer: Using msa msaPrettyPrint(): issues with latex
1
gravatar for Olorin
2.3 years ago by
Olorin50
Olorin50 wrote:

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

PROBLEM SOLVED

ADD COMMENTlink written 2.3 years ago by Olorin50
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 108 users visited in the last hour