I am using Rstudio for this at the moment. It appears that pdflatex won't function with msaPrettyPrint
picorna = readDNAStringSet("/home/emily/pipe/RNA_merge/SPAdes/RNA_merge_picorna_of_interest.fasta") picorna_seq = paste(picorna) picorna_name = names(picorna) picorna_df <- data.frame(picorna_name, picorna_seq) picorna_df picorna_interest_alignment <- msaClustalW(picorna) print(picorna_interest_alignment, show = "complete") #shows full thing msaPrettyPrint(picorna_interest_alignment, output = "asis", y=c(7085,7245), showLogo = "none", askForOverwrite = FALSE, verbose = FALSE)
Error is as follows:
Error in texi2dvi(texfile, quiet = !verbose, pdf = identical(output, "pdf"), : unable to run 'pdflatex' on 'picorna_interest_alignment.tex'
 "MsaDNAMultipleAlignment" attr(,"package")  "msa"
Let me know what other information is needed. I have tried many many things. The alignment is relatively long, I have tried to subsection it with the same error resulting. Thanks in advance,