Unexpected token 'done' error in for loop shell scripting

Question

I get this unexpected 'done' token error

echo -e "Enter the file stem name"
read filestem
for i in {1..22}
do
    `java -cp /export/home/alun/jpsgcs/ CMorgansToTheta $filestem_$i.INPUT.par $filestem_$i.THETA.par`
done

Have you tried adding the #!/bin/bash header to the top of the script? — Cory Klein
– Cory Klein, Commented Jun 18, 2013 at 17:17
Why do you have java -cp .. in backticks? Doesn't make sense, unless you're getting output of the java command to some variable. — user80168
– user80168, Commented Jun 18, 2013 at 17:21
or removing the backticks? Does that java program really return executable bash statements? — Brian Cain
– Brian Cain, Commented Jun 18, 2013 at 17:23
I just tried it on my system, and didn't get that error. Is that the entire script? If not, please update your question to show us all of it (copy-and-paste, don't re-type). As @depesz says, the backticks don't make sense, but they shouldn't cause the symptom you're seeing,. — Keith Thompson
– Keith Thompson, Commented Jun 18, 2013 at 17:24
the -cp is the class path and without those i get classdefnotfound error in java. And that is all the code is and i added #! /bin/bash too. I get the same error. — Vignesh
– Vignesh, Commented Jun 18, 2013 at 19:16

chepner · Accepted Answer · 2013-06-18 20:42:43Z

5

If the Java program writes nothing to output, your for loop is equivalent (because of the backquotes) to

for i in {1..22}
do
done

which produces the error you see. It's likely you simply want to remove the backquotes to run the program 22 time:

echo -e "Enter the file stem name"
read filestem
for i in {1..22}
do
    java -cp /export/home/alun/jpsgcs/ CMorgansToTheta "${filestem}_$i.INPUT.par" "${filestem}_$i.THETA.par"
done

edited Jun 18, 2013 at 20:42

answered Jun 18, 2013 at 17:37

chepner

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2 Comments

chepner Over a year ago

From the shell script or from the Java program? I fixed a small bug in the shell script that would pass the wrong filenames to the Java program.

Vignesh Over a year ago

the unexpected end of file error is from the script. not java program

anubhava · Accepted Answer · 2013-06-18 20:20:49Z

1

In your Java command line:

java -cp /export/home/alun/jpsgcs/ CMorgansToTheta $filestem_$i.INPUT.par $filestem_$i.THETA.par

You are using:

$filestem_$i

Which will be equivalent to:

${filestem_}${i}

because underscore _ is not considered a word boundary in shell and whole filestem_ will be considered variable name. Most likely you should be using:

${filestem}_${i}

Can you show me output of this script?

#!/bin/bash
set -x
echo -e "Enter the file stem name"
read filestem
for i in {1..3}
do
    echo "java -cp /export/home/alun/jpsgcs/ CMorgansToTheta ${filestem}_${i}.INPUT.par ${filestem}_${i}.THETA.par"
done

edited Jun 18, 2013 at 20:20

answered Jun 18, 2013 at 17:47

anubhava

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12 Comments

anubhava Over a year ago

Ok can you post your latest suggested script in your question.

Vignesh Over a year ago

echo -e "Enter the file stem name" read filestem for i in {1..22} do java -cp /export/home/alun/jpsgcs/ cMorgansToTheta ${filestem}_${i}.INPUT.par ${filestem}_${i}.THETA.par done

anubhava Over a year ago

ok looks like you accepted other answer, probably got your problem solved.

Vignesh Over a year ago

That was a misclick. Am sorry about that.

Vignesh Over a year ago

I still get that undefined token done error. There is another weird thing that my "for" is not highlighted in the vi editor. @anubhava

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