1

Getting this Error Message:

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 

When running this series of commands in rStudio:

library(msa)
mySequenceFile <- system.file("examples", "exampleAA.fasta", package="msa")
mySequences <- readAAStringSet(mySequenceFile)
mySequences

myFirstAlignment <- msa(mySequences)
msaPrettyPrint(myFirstAlignment)

This was after a fresh install of the msa package in rStudio and MikTex.

Any suggestions?

1

Please see https://support.bioconductor.org/p/91525/#91537 for answer.

See my last answer on this page.

Tex doesnt handle weird char in path.

You have to specify "safe" path and file name in file, Alfile arguments in msaPrettyPrint() Use tex output for msaPrettyPrint() and compile it with texi2pdf(tex_file, clean=TRUE)

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