Yes,  Linux beaglebone 4.4.68-ti-r110 #1 SMP Wed Jun 21 04:31:35 UTC 2017 
armv7l GNU/Linux has some unexpected problems with UART's

We have a bunch of pcb's coming in and all of a sudden TTYO4 (hardwired) 
doesn't work. Cannot receive characters. Terminals were checked as active. 
Program worked fine on 3.8 kernels.
lrwxrwxrwx 1 root root          5 Dec 24 12:29 /dev/ttyO0 -> ttyS0
lrwxrwxrwx 1 root root          5 Dec 24 12:29 /dev/ttyO1 -> ttyS1
lrwxrwxrwx 1 root root          5 Dec 24 12:29 /dev/ttyO2 -> ttyS2
lrwxrwxrwx 1 root root          5 Dec 24 12:29 /dev/ttyO4 -> ttyS4
I think capes load OK:

root@beaglebone:~# dmesg | grep bone
[    0.000000] Kernel command line: console=ttyO0,115200n8 
bone_capemgr.disable_partno=BB-BONELT-HDMI,BB-BONELT-HDMIN 
bone_capemgr.enable_partno=cape-universal root=/dev/mmcblk1p1 ro 
rootfstype=ext4 rootwait coherent_pool=1M net.ifnames=0 quiet 
cape_universal=enable
[    2.346745] bone_capemgr bone_capemgr: Baseboard: 
'A335BNLT,AIA0,5016BBBI3094'
[    2.346780] bone_capemgr bone_capemgr: 
compatible-baseboard=ti,beaglebone-black - #slots=4
[    2.385761] bone_capemgr bone_capemgr: slot #0: No cape found
[    2.425756] bone_capemgr bone_capemgr: slot #1: No cape found
[    2.465750] bone_capemgr bone_capemgr: slot #2: No cape found
[    2.505751] bone_capemgr bone_capemgr: slot #3: No cape found
[    2.505785] bone_capemgr bone_capemgr: enabled_partno PARTNO 
'cape-universal' VER 'N/A' PR '0'
[    2.505798] bone_capemgr bone_capemgr: slot #4: override
[    2.505812] bone_capemgr bone_capemgr: Using override eeprom data at 
slot 4
[    2.505827] bone_capemgr bone_capemgr: slot #4: 'Override Board 
Name,00A0,Override Manuf,cape-universal'
[    2.506195] bone_capemgr bone_capemgr: initialized OK.
[    2.746273] bone_capemgr bone_capemgr: slot #4: dtbo 
'cape-universal-00A0.dtbo' loaded; overlay id #0

What can be done?

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