out="${DATASET}.trna.txt"

Close

foo appears unused. Verify it or export it.

Problematic code:

foo=42
echo "$FOO"

Correct code:

foo=42
echo "$foo"

Rationale:

Variables not used for anything are often associated with bugs, so ShellCheck warns about them.

Also note that something like local let foo=42 does not make a let statement local -- it instead declares an additional local variable named let.

Exceptions

ShellCheck may not always realize that the variable is in use (especially with indirection), and may not realize you don't care (with throwaway variables or unimplemented features).

For throwaway variables, consider using _ as a dummy:

read _ last _ zip _ _ <<< "$str"
echo "$last, $zip"

or use a directive to disable the warning:

# shellcheck disable=SC2034
read first last email zip lat lng <<< "$str"
echo "$last, $zip"

For indirection, there's not much you can do without rewriting to use arrays or similar:

bar=42  # will always appear unused
foo=bar
echo "${!foo}"

This is expected behavior, and not a bug. There is no good way to statically analyze indirection in shell scripts, just like static C analyzers have a hard time preventing segfaults.

As always, there are ways to [[ignore]] this and other messages if they frequently get in your way.

Notice

Original content from the ShellCheck https://github.com/koalaman/shellcheck/wiki.

  echo O | tRNAscan-SE $dom_opt -o "${DATASET}.trna.txt" -q "$fa" || true

Close

Double quote to prevent globbing and word splitting.

Problematic code:

echo $1
for i in $*; do :; done # this done and the next one also applies to expanding arrays.
for i in $@; do :; done

Correct code:

echo "$1"
for i in "$@"; do :; done # or, 'for i; do'

Rationale

The first code looks like "print the first argument". It's actually "Split the first argument by IFS (spaces, tabs and line feeds). Expand each of them as if it was a glob. Join all the resulting strings and filenames with spaces. Print the result."

The second one looks like "iterate through all arguments". It's actually "join all the arguments by the first character of IFS (space), split them by IFS and expand each of them as globs, and iterate on the resulting list". The third one skips the joining part.

Quoting variables prevents word splitting and glob expansion, and prevents the script from breaking when input contains spaces, line feeds, glob characters and such.

Strictly speaking, only expansions themselves need to be quoted, but for stylistic reasons, entire arguments with multiple variable and literal parts are often quoted as one:

$HOME/$dir/dist/bin/$file        # Unquoted (bad)
"$HOME"/"$dir"/dist/bin/"$file"  # Minimal quoting (good)
"$HOME/$dir/dist/bin/$file"      # Canonical quoting (good)

When quoting composite arguments, make sure to exclude globs and brace expansions, which lose their special meaning in double quotes: "$HOME/$dir/src/*.c" will not expand, but "$HOME/$dir/src"/*.c will.

Note that $( ) starts a new context, and variables in it have to be quoted independently:

echo "This $variable is quoted $(but this $variable is not)"
echo "This $variable is quoted $(and now this "$variable" is too)"

Exceptions

Sometimes you want to split on spaces, like when building a command line:

options="-j 5 -B"
make $options file

Just quoting this doesn't work. Instead, you should have used an array (bash, ksh, zsh):

options=(-j 5 -B) # ksh: set -A options -- -j 5 -B
make "${options[@]}" file

or a function (POSIX):

make_with_flags() { make -j 5 -B "$@"; }
make_with_flags file

To split on spaces but not perform glob expansion, Posix has a set -f to disable globbing. You can disable word splitting by setting IFS=''.

Similarly, you might want an optional argument:

debug=""
[[ $1 == "--trace-commands" ]] && debug="-x"
bash $debug script

Quoting this doesn't work, since in the default case, "$debug" would expand to one empty argument while $debug would expand into zero arguments. In this case, you can use an array with zero or one elements as outlined above, or you can use an unquoted expansion with an alternate value:

debug=""
[[ $1 == "--trace-commands" ]] && debug="yes"
bash ${debug:+"-x"} script

This is better than an unquoted value because the alternative value can be properly quoted, e.g. wget ${output:+ -o "$output"}.

---

As always, this warning can be [[ignore]]d on a case-by-case basis.

this is especially relevant when BASH many not be available for the array work around. For example, use in eval or in command options where script has total control of the variables...

FLAGS="-av -e 'ssh -x' --delete --delete-excluded"
...
# shellcheck disable=SC2086
eval rsync $FLAGS ~/dir remote_host:dir

Notice

Original content from the ShellCheck https://github.com/koalaman/shellcheck/wiki.