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Finite State Machine Labs (FSMLabs) - whose version of Linux is called RTLinux - used the licence to "impose restricted terms on distribution of a GPL-covered program," the FSF said in a statement.
The FSF opposes the use of software patents, believing their use to be a "harmful government policy of creating monopolies that restrict computer users".
The Foundation also believes that the patent licence violates the GPL of the Linux kernel. The GNU GPL states that any software incorporating the Linux source code is already licensed under the GPL, and is itself subject to the terms of the licence. The GNU GPL also states that all improved versions of GPL software must be released as free software.
FSMLabs' patent covers "real-time interrupt handling using a software emulation layer for interrupt masking, so that interrupts can be prioritised," the FSF said. But, the Foundation argued, the idea could not be patented because it has been used before.
The patent has been used to impose restrictive terms on software covered by the GPL, and imposing them is a violation of the licence, the FSF said. The FSF is not a copyright holder of Linux, however, and so cannot enforce the GPL.
Neither party could be reached for comment on the issue.