Using msa msaPrettyPrint(): issues with latex
1
0
Entering edit mode
Olorin ▴ 50
@olorin-12230
Last seen 5.0 years ago

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() • 3.0k views
ADD COMMENT
1
Entering edit mode
Olorin ▴ 50
@olorin-12230
Last seen 5.0 years ago

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

PROBLEM SOLVED

ADD COMMENT

Login before adding your answer.

Traffic: 285 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6