Question: Unable to run 'pdflatex'
2
gravatar for emilyc
14 months ago by
emilyc30
emilyc30 wrote:

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

latex R • 789 views
ADD COMMENTlink written 14 months ago by emilyc30

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

ADD REPLYlink modified 14 months ago • written 14 months ago by Joe18k

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.

ADD REPLYlink written 14 months ago by emilyc30

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.

ADD REPLYlink written 14 months ago by Joe18k

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

ADD REPLYlink written 5 weeks ago by jean.charles.cancel0

The doc says:

It is important to point out that all file names need to be LaTeX-compliant, i.e. no special characters and spaces (!) are allowed.

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?

ADD REPLYlink written 14 months ago by Jean-Karim Heriche23k
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