Unable to run 'pdflatex'
Hi everyone,
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'
Also
class(picorna_interest_alignment)
returns
[1] "MsaDNAMultipleAlignment"
attr(,"package")
[1] "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,
Emily
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Unable to run pdflatex
written by jean.charles.cancel •
This might be a stupid question, but do you have a LaTeX distribution installed?
You might consider this alternative approach, without R: C: Is there a command line tool that can take an alignment fasta and input and outp
Yup! I've got a LaTeX distribution installed.
I could find a solution to doing this another way, but I am most interested in understanding why it won't work. After testing examples it seems that it will work on package example, but not my sequence alignment. Not certain why.
Have you got some other minimal data you can try/download?
It would be wise to figure out if this is a problem with your data (which given that their examples run, it sounds like it could be), rather than the program.
Hello, I am currently working on the same package and the same error will show up whatsoever.
You say you managed to do with otherwise. Please could you point this solution at me ? I am new to bioinformatics and I'm loosing some hairs right now ^^'
Many thanks in advance
The doc says:
This applies also to the path including to the path to the current directory where things are written to by default. On which OS are you? And do you have funny characters in your path?