Started up a fresh install on the PBX-BB cape and I am unable to get any of 
my previous configs or the default configs to start. 

Ive loaded the device tree overlay into /lib/firmware and unloaded the HDMI 
Audio Cape. When the config starts it fails at the setup.sh line. Here is 
the output.

machinekit@beaglebone:~$ machinekit
MACHINEKIT - 0.1
Machine configuration directory is 
'/home/machinekit/machinekit/configs/ARM.Beaglebone.PBX'
Machine configuration file is 'Comet_Metric.ini'
Starting Machinekit...
io started
Unrecognized line skipped: POC     FMS     LEN     DIAM    COMMENT
halcmd loadusr io started
Comet.hal:5: execv(./setup.sh): Permission denied
Comet.hal:5: program './setup.sh' failed, returned 1
Shutting down and cleaning up Machinekit...
Cleanup done
Machinekit terminated with an error.  You can find more information in the 
log:
    /home/machinekit/linuxcnc_debug.txt
and
    /home/machinekit/linuxcnc_print.txt
as well as in the output of the shell command 'dmesg' and in the terminal


Output from Cape manager

machinekit@beaglebone:~$ cat /sys/devices/bone_capemgr.*/slots
 0: 54:PF--- 
 1: 55:PF--- 
 2: 56:PF--- 
 3: 57:PF--- 
 4: ff:P-O-L Bone-LT-eMMC-2G,00A0,Texas Instrument,BB-BONE-EMMC-2G
 5: ff:P-O-- Bone-Black-HDMI,00A0,Texas Instrument,BB-BONELT-HDMI
 6: ff:P-O-L Bone-Black-HDMIN,00A0,Texas Instrument,BB-BONELT-HDMIN
machinekit@beaglebone:~$ 


Linuxcnc_debug

4657
  PID TTY      STAT   TIME COMMAND
Stopping realtime threads
Unloading hal components


linuxcnc_print

RUN_IN_PLACE=no
LINUXCNC_DIR=
LINUXCNC_BIN_DIR=/usr/bin
LINUXCNC_TCL_DIR=/usr/lib/tcltk/linuxcnc
LINUXCNC_SCRIPT_DIR=
LINUXCNC_RTLIB_DIR=/usr/lib/linuxcnc
LINUXCNC_CONFIG_DIR=
LINUXCNC_LANG_DIR=/usr/share/linuxcnc/tcl/msgs
INIVAR=/usr/libexec/linuxcnc/inivar
HALCMD=halcmd
LINUXCNC_EMCSH=/usr/bin/wish8.6
INIFILE=/home/machinekit/machinekit/configs/ARM.Beaglebone.PBX/Comet_Metric.ini
PARAMETER_FILE=metric.var
TASK=milltask
HALUI=halui
DISPLAY=axis
Starting Machinekit server program: linuxcncsvr
Loading Real Time OS, RTAPI, and HAL_LIB modules
Starting Machinekit IO program: io
Starting HAL User Interface program: halui
Killing task linuxcncsvr, PID=4657
Removing HAL_LIB, RTAPI, and Real Time OS modules
Removing NML shared memory segments


What else is there to check?
 

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