CODEWITHSUNDEEP
rbash
Lucas Alanis
Lucas Alanis

Reputation: 1278

Why is the following parameter in a bash script not working properly?

I have the following bash script:

#!/bin/bash

while getopts "1:2:3:4:" arg; do

case "$arg" in

1)
    fileWithSpeeds=$OPTARG
    ;;
2)
    titleOfGraph=$OPTARG
    ;;
3)
    lowestHP=$OPTARG
    ;;
4)
    highestHP=$OPTARG
    ;;

esac

done

./myPlotter.R $fileWithSpeeds $titleOfGraph $lowestHP $highestHP

Basically, myPlotter.R makes one plot from data in a given file (details are not important for this question). When called in the command line in the following way:

./myPlotter.R myFile "My Title" 30 34

The script works fine (don't pay attention to myFile, 30, 34; they are just other parameters but not important for this question. I left them there for this question just in case). However, when called from the bash script like:

./bashPlot.sh -1 myFile -2 "My Title" -3 30 -4 34

I get an error message (Error in args[3]:args[4], "NAs introduced by coercion" if helpful). When running:

echo ./myPlotter.R $fileWithSpeeds $titleOfGraph $lowestHP $highestHP

I noticed that it looks like the following 

 ./myPlotter.R myFile My Title 30 34

which means that the title is counting as two arguments ('My' and 'Title') when it shouldn't. So I decided to modify the line to 

./myPlotter.R $fileWithSpeeds \"$titleOfGraph\" $lowestHP $highestHP

and the echo of the line gave:

./myPlotter.R myFile "My Title" 30 34

But I still end with the same error. My guess is that the title is still two arguments ('"My' and '"Title'). Is there a way to fix this? Here is the R script if helpful:

#!/usr/bin/env Rscript

# the arguments come in this way: 
# args[1] is a file containing the maximum speeds of different cars (one per line) 
# args[2] is the title that the plot will have
# args[3] contains the horsepower of the engine of the first car in args[1] (the lowest)
# args[4] contains the horsepower of the engine of the last car in args[1] (the highest)
# NOTE1: the speeds in args[1] must be listed starting from the car 
# with the lowest horsepower to the car with the highest horsepower 
# NOTE2: in args[1], a car must differ from the next one by 1 horsepower, i.e., if
# there are 5 speeds, and the horsepower of the first car in the file is 30, then the 
# the horsepower of the second one must be 31, the third one 32, .... the fifth one must
# be 34.

args<-commandArgs(TRUE)

# creating the vector with the horsepower of each car

horsepowers = numeric()

for (i in args[3]:args[4]) {

        horsepowers = c(horsepowers,i)

}

# reading file with speeds and getting vector with speeds

speeds <- read.csv(file=args[1],head=FALSE,sep="\n")$V1

# creating plot with speeds in previous vector

outputTitle = gsub(" ","", args[2] , fixed=TRUE)

pdf(paste(outputTitle, ".pdf", sep = ""))

plot(horsepowers, speeds, type="o", col="red", xlab="horsepowers", ylab="speeds")

# giving a title to the plot

title(main=args[2], col.main="Black")

Upvotes: 0

Views: 57

Answers (2)

clt60
clt60

Reputation: 63972

If you debug you script with

bash -x bashplot.sh .... arguments....

you will able to detect what's happened.

use quotes everywhere, so:

fileWithSpeeds="$OPTARG"   #... and such

and

./myPlotter.R "$fileWithSpeeds" "$titleOfGraph" "$lowestHP" "$highestHP"

Upvotes: 2

Lucas Alanis
Lucas Alanis

Reputation: 1278

Changing 

./myPlotter.R $fileWithSpeeds \"$titleOfGraph\" $lowestHP $highestHP

to

./myPlotter.R $fileWithSpeeds "$titleOfGraph" $lowestHP $highestHP

fixed the problem. It was just a minor mistake on my part.

Upvotes: 0

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