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Bootloader code configures vbus pin with pulldown enabled.
#ifdef INTERFACE_USB
/* enable GPIO9 with a pulldown to sniff VBUS */
rcc_peripheral_enable_clock(&RCC_AHB1ENR, RCC_AHB1ENR_IOPAEN);
gpio_mode_setup(GPIOA, GPIO_MODE_INPUT, GPIO_PUPD_PULLDOWN, GPIO9);
#endif
According to stmf40x manual pullup/pulldowns must not be enabled for 5v pins.
6. To sustain a voltage higher than V DD +0.3, the internal pull-up and pull-down resistors must be disabled.
The documentation mentions 1k1 pulldown for VBUS (which obviously has to handle 5v), but it may be totally separate from normal GPIO pulldown.
In contrast to that, PX4Firmware doesn't enable pulldown. OTGFS vbus sensing configuration is also different. I see OTGFS_GCCFG_NOVBUSSENS bit set in px4firmware. OTG_FS_GCCFG_NOVBUSSENS is not set in libopencm3.
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