system("ssh root\@\remoteIP /usr/bin/ls");

The double quotes interpolate so that \r is going to become a carriage return. That's one source of problems.

Some other tips:

• Don't test as root. Use an unprivileged user so you don't destroy the remote host
• Pre-construct your command so you can view it. eg:

    my $cmd = "ssh $user\@$host /usr/bin/ls";
    warn "Executing '$cmd'";
    system ($cmd);
  [download]

• Consider passing a list to system to avoid some shell processing complications
• Don't roll your own but instead use a module such as Rex

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