Today I received this message, while working with my Bela with a CTAG Cape. I was working in SuperCollider, but the same message appears when running C++ examples.
I did nothing out of the ordinary prior to the message appearing.
I see that this post concerns a similar problem: [https://forum.bela.io/d/1314-bela-mini-pru-interrupt-timeout]

Running project ...
PRU interrupt timeout, -1 110 Connection timed out
PRU interrupt timeout, -1 110 Connection timed out
Underrun detected: 551 blocks dropped
PRU interrupt timeout, -1 110 Connection timed out
Underrun detected: 552 blocks dropped
PRU interrupt timeout, -1 110 Connection timed out
Underrun detected: 551 blocks dropped
McASP error, abort
PRU interrupt timeout, -1 110 Connection timed out
Makefile:595: recipe for target 'runide' failed
make: *** [runide] Error 1
Bela stopped

Here is the dmesg

[    0.846325] davinci_mdio: dt: updated phy_id[0] from phy_mask[fffffffe]
[    0.847745] libphy: 4a101000.mdio: probed
[    0.847779] davinci_mdio 4a101000.mdio: phy[0]: device 4a101000.mdio:00, driver SMSC LAN8710/LAN8720
[    0.848676] cpsw 4a100000.ethernet: Detected MACID = 34:03:de:62:2b:80
[    0.848856] cpsw 4a100000.ethernet: cpts: overflow check period 2125
[    0.851296] ehci_hcd: USB 2.0 'Enhanced' Host Controller (EHCI) Driver
[    0.851373] ehci-platform: EHCI generic platform driver
[    0.851666] ehci-omap: OMAP-EHCI Host Controller driver
[    0.852295] usbcore: registered new interface driver usb-storage
[    0.855256] 47401300.usb-phy supply vcc not found, using dummy regulator
[    0.858445] musb-hdrc: ConfigData=0xde (UTMI-8, dyn FIFOs, bulk combine, bulk split, HB-ISO Rx, HB-ISO Tx, SoftConn)
[    0.858472] musb-hdrc: MHDRC RTL version 2.0 
[    0.858484] musb-hdrc: setup fifo_mode 4
[    0.858513] musb-hdrc: 28/31 max ep, 16384/16384 memory
[    0.860567] 47401b00.usb-phy supply vcc not found, using dummy regulator
[    0.863516] musb-hdrc: ConfigData=0xde (UTMI-8, dyn FIFOs, bulk combine, bulk split, HB-ISO Rx, HB-ISO Tx, SoftConn)
[    0.863544] musb-hdrc: MHDRC RTL version 2.0 
[    0.863555] musb-hdrc: setup fifo_mode 4
[    0.863581] musb-hdrc: 28/31 max ep, 16384/16384 memory
[    0.863748] musb-hdrc musb-hdrc.1.auto: MUSB HDRC host driver
[    0.863790] musb-hdrc musb-hdrc.1.auto: new USB bus registered, assigned bus number 1
[    0.864148] usb usb1: New USB device found, idVendor=1d6b, idProduct=0002
[    0.864166] usb usb1: New USB device strings: Mfr=3, Product=2, SerialNumber=1
[    0.864178] usb usb1: Product: MUSB HDRC host driver
[    0.864190] usb usb1: Manufacturer: Linux 4.4.113-ti-xenomai-r149 musb-hcd
[    0.864202] usb usb1: SerialNumber: musb-hdrc.1.auto
[    0.865364] hub 1-0:1.0: USB hub found
[    0.865440] hub 1-0:1.0: 1 port detected
[    0.877894] mousedev: PS/2 mouse device common for all mice
[    0.881048] omap_rtc 44e3e000.rtc: rtc core: registered 44e3e000.rtc as rtc0
[    0.882455] i2c /dev entries driver
[    0.884727] omap_wdt: OMAP Watchdog Timer Rev 0x01: initial timeout 60 sec
[    0.885858] omap_hsmmc 48060000.mmc: Got CD GPIO
[    0.949540] mmc0: host does not support reading read-only switch, assuming write-enable
[    0.951994] hidraw: raw HID events driver (C) Jiri Kosina
[    0.952858] usbcore: registered new interface driver usbhid
[    0.952872] usbhid: USB HID core driver
[    0.953371] ashmem: initialized
[    0.954456]  remoteproc0: wkup_m3 is available
[    0.954477]  remoteproc0: Note: remoteproc is still under development and considered experimental.
[    0.954488]  remoteproc0: THE BINARY FORMAT IS NOT YET FINALIZED, and backward compatibility isn't yet guaranteed.
[    0.954720] mmc0: new high speed SDHC card at address 1234
[    0.960916] NET: Registered protocol family 10
[    0.961857] mmcblk0: mmc0:1234 SA16G 14.4 GiB 
[    0.964014] mip6: Mobile IPv6
[    0.964052] NET: Registered protocol family 17
[    0.964319]  mmcblk0: p1 p2
[    0.966426] Key type dns_resolver registered
[    0.966459] mpls_gso: MPLS GSO support
[    0.966878] omap_voltage_late_init: Voltage driver support not added
[    0.977730] PM: Cannot get wkup_m3_ipc handle
[    0.982313] ThumbEE CPU extension supported.
[    0.983930] registered taskstats version 1
[    0.984233] zswap: loaded using pool lzo/zbud
[    0.992395] Btrfs loaded
[    0.994814] Key type encrypted registered
[    0.998482] input: tps65217_pwr_but as /devices/platform/ocp/44e0b000.i2c/i2c-0/0-0024/input/input0
[    1.019769] mmc1: MAN_BKOPS_EN bit is not set
[    1.023564] mmc1: new high speed MMC card at address 0001
[    1.025190] mmcblk1: mmc1:0001 M62704 3.56 GiB 
[    1.027267] mmcblk1boot0: mmc1:0001 M62704 partition 1 2.00 MiB
[    1.027761] tps65217 0-0024: TPS65217 ID 0xe version 1.2
[    1.028496] at24 0-0050: 32768 byte 24c256 EEPROM, writable, 1 bytes/write
[    1.028562] omap_i2c 44e0b000.i2c: bus 0 rev0.11 at 400 kHz
[    1.030447] omap_i2c 4802a000.i2c: bus 1 rev0.11 at 100 kHz
[    1.031300] mmcblk1boot1: mmc1:0001 M62704 partition 2 2.00 MiB
[    1.033299]  mmcblk1: p1 p2
[    1.036954]  remoteproc0: powering up wkup_m3
[    1.036987]  remoteproc0: Booting fw image am335x-pm-firmware.elf, size 217148
[    1.037307]  remoteproc0: remote processor wkup_m3 is now up
[    1.037332] wkup_m3_ipc 44e11324.wkup_m3_ipc: CM3 Firmware Version = 0x192
[    1.041398] bone_capemgr bone_capemgr: Baseboard: 'A335BNLT,00C0,3818BBBK13C8'
[    1.041438] bone_capemgr bone_capemgr: compatible-baseboard=ti,beaglebone-black - #slots=4
[    1.077698] bone_capemgr bone_capemgr: slot #0: No cape found
[    1.117683] bone_capemgr bone_capemgr: slot #1: No cape found
[    1.157684] bone_capemgr bone_capemgr: slot #2: No cape found
[    1.197680] bone_capemgr bone_capemgr: slot #3: No cape found
[    1.197810] bone_capemgr bone_capemgr: initialized OK.
[    1.198274] PM: bootloader does not support rtc-only!
[    1.199397] omap_rtc 44e3e000.rtc: setting system clock to 2000-01-01 00:00:00 UTC (946684800)
[    1.199434] of_cfs_init
[    1.199592] of_cfs_init: OK
[    1.207640] PM: Hibernation image not present or could not be loaded.
[    1.224166] EXT4-fs (mmcblk0p2): mounted filesystem with ordered data mode. Opts: (null)
[    1.224277] VFS: Mounted root (ext4 filesystem) readonly on device 179:2.
[    1.226284] devtmpfs: mounted
[    1.226883] Freeing unused kernel memory: 456K
[    1.633332] systemd[1]: System time before build time, advancing clock.
[    1.733563] ip_tables: (C) 2000-2006 Netfilter Core Team
[    1.766143] random: systemd: uninitialized urandom read (16 bytes read, 24 bits of entropy available)
[    1.770026] random: systemd: uninitialized urandom read (16 bytes read, 24 bits of entropy available)
[    1.783530] systemd[1]: systemd 232 running in system mode. (+PAM +AUDIT +SELINUX +IMA +APPARMOR +SMACK +SYSVINIT +UTMP +LIBCRYPTSETUP +GCRYPT +GNUTLS +ACL +XZ +LZ4 +SECCOMP +BLKID +ELFUTILS +KMOD +IDN)
[    1.784388] systemd[1]: Detected architecture arm.
[    1.786414] systemd[1]: Set hostname to .
[    1.991224] random: systemd-sysv-ge: uninitialized urandom read (16 bytes read, 26 bits of entropy available)
[    2.027348] random: systemd-gpt-aut: uninitialized urandom read (16 bytes read, 27 bits of entropy available)
[    2.027895] random: systemd-gpt-aut: uninitialized urandom read (16 bytes r
Your code is printing to the console too quickly. Check your audio thread for print messages.

Best, Adam