(SOLVED) hal_gpio: Operation not permitted fault cannot be solved

Print file information:
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/modules
LINUXCNC_CONFIG_DIR=
LINUXCNC_LANG_DIR=/usr/lib/tcltk/linuxcnc/msgs
INIVAR=inivar
HALCMD=halcmd
LINUXCNC_EMCSH=/usr/bin/wish8.6
LINUXCNC - 2.9.4
Machine configuration directory is '/home/cnc/linuxcnc/configs/my-mill'
Machine configuration file is 'my-mill.ini'
INIFILE=/home/cnc/linuxcnc/configs/my-mill/my-mill.ini
VERSION=1.1
PARAMETER_FILE=linuxcnc.var
TPMOD=
HOMEMOD=
TASK=milltask
HALUI=
DISPLAY=axis
COORDINATES=X Y Z A
KINEMATICS=trivkins coordinates=XYZA
Starting LinuxCNC...
Starting LinuxCNC server program: linuxcncsvr
Loading Real Time OS, RTAPI, and HAL_LIB modules
Starting LinuxCNC IO program: io
linuxcnc TPMOD=tpmod HOMEMOD=homemod EMCMOT=motmod
Found file(REL): ./my-mill.hal
Shutting down and cleaning up LinuxCNC...
Removing HAL_LIB, RTAPI, and Real Time OS modules
Removing NML shared memory segments

Debug file information:
Note: Using POSIX realtime
Failed to register output pin collection
hal_gpio: rtapi_app_main: Operation not permitted (-1)
./my-mill.hal:4: waitpid failed /usr/bin/rtapi_app hal_gpio
./my-mill.hal:4: /usr/bin/rtapi_app exited without becoming ready
./my-mill.hal:4: insmod for hal_gpio failed, returned -1
2307
Stopping realtime threads
Unloading hal components
Note: Using POSIX realtime

cnc@raspberrypi:~$ groups
cnc tty disk dialout sudo audio video plugdev users input render netdev i2c bluetooth gpio spi

Failed to register output pin collection

This has nothing to do with permissions. It has to do with the pins you have chosen. The error message did not mention permissions. A lot of issues are able to be resolved by users reading the errors messages and not jumping to conclusions.
The thread also includes information regarding choosing pins that are allocated to SPI. Either you missed this or chose to ignore it.
The example hal & ini files do work with a fresh install, I have tested these myself.