This is because "-3" is parsed as an option to the command. You can use
"--" to signify the end of the options and pass "-3" properly like so:
gconftool-2 -t int -s /app/myvalue -- -3
** Package changed: gconf2 (Ubuntu) => gconf (Ubuntu)
** Changed in: gconf (Ubuntu)
Status: New => Invalid
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https://bugs.launchpad.net/bugs/1263671
Title:
gconftool-2 does not accept negative values with --set
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