Thanks to another post and a lot of experimenting, I have found the following things out:
Permission Denied tends to be the result of:
>not running the program as Administraor (despite being logged into that account)
>running the program ONCE as a non-administrator
>needing to restart the computer after installing or re-installing drivers
>>>Fixing this:
The easy way: restart the computer
the other way: kill bash.exe and isz.exe
((UPDATE*)) this no longer fixes the Permission denied error. (error posted below for clarification).
However, I have now expanded my testing to two different Galileo gen 2 boards and two different windows server 2012 computers (one is 2012, the other is 2012 R2 with Update.)
At the current time, one computer is attempting to upload, but is "stuck" at this:
----------------------------------------
cygwin warning:
MS-DOS style path detected: C:\Users\Administrator\Desktop\arduino-windows-1.0.4\arduino-1.5.3-Intel.1.0.4/hardware/arduino/x86/tools/izmir/clupload_win.sh
starting download script
Preferred POSIX equivalent is: /cygdrive/c/Users/Administrator/Desktop/arduino-windows-1.0.4/arduino-1.5.3-Intel.1.0.4/hardware/arduino/x86/tools/izmir/clupload_win.sh
Args to shell: C:\Users\Administrator\Desktop\arduino-windows-1.0.4\arduino-1.5.3-Intel.1.0.4/hardware/tools/x86/bin C:\Users\ADMINI~1\AppData\Local\Temp\build4677676268785205264.tmp/sketch_jan11a.cpp.elf COM8
CYGWIN environment variable option "nodosfilewarning" turns off this warning.
COM PORT 8
Consult the user's guide for more details about POSIX paths:
http://cygwin.com/cygwin-ug-net/using.html#using-pathnames
#!/bin/sh
echo "starting download script"
Converted COM Port COM8 to tty port /dev/ttyS7
echo "Args to shell:" $*
Sending Command String to move to download if not already in download mode
# ARG 1: Path to lsz executable.
# ARG 2: Elf File to download
# ARG 3: COM port to use.
#path contains \ need to change all to /
path_to_exe=$1
fixed_path=${path_to_exe//\\/\/}
#COM ports are not always setup to be addressed via COM for redirect.
Deleting existing sketch on target
#/dev/ttySx are present. Howwever, COMy -> /dev/ttySx where x = y - 1
com_port_arg=$3
com_port_id=${com_port_arg/COM/}
echo "COM PORT" $com_port_id
tty_port_id=/dev/ttyS$((com_port_id-1))
echo "Converted COM Port" $com_port_arg "to tty port" $tty_port_id
echo "Sending Command String to move to download if not already in download mode"
echo "~sketch download" > $tty_port_id
#Move the existing sketch on target.
echo "Deleting existing sketch on target"
$fixed_path/lsz.exe --escape -c "mv -f /sketch/sketch.elf /sketch/sketch.elf.old" <> $tty_port_id 1>&0
---------------------------------------------------------------------
The other computer is still getting the no such file or directory error.
((UPDATE*))
------------------------------------PERMISSION DENIED ERROR (while run as Administrator, after manually killing bash.exe and lsz.exe prior to running)------------------
#!/bin/sh
starting download script
Args to shell: C:\Users\Administrator\Desktop\arduino-windows-1.0.4\arduino-1.5.3-Intel.1.0.4/hardware/tools/x86/bin C:\Users\ADMINI~1\AppData\Local\Temp\build2671300318666315755.tmp/sketch_jan11a.cpp.elf COM8
echo "starting download script"
COM PORT 8
echo "Args to shell:" $*
Converted COM Port COM8 to tty port /dev/ttyS7
Sending Command String to move to download if not already in download mode
# ARG 1: Path to lsz executable.
# ARG 2: Elf File to download
# ARG 3: COM port to use.
#path contains \ need to change all to /
path_to_exe=$1
fixed_path=${path_to_exe//\\/\/}
#COM ports are not always setup to be addressed via COM for redirect.
#/dev/ttySx are present. Howwever, COMy -> /dev/ttySx where x = y - 1
Deleting existing sketch on target
com_port_arg=$3
com_port_id=${com_port_arg/COM/}
echo "COM PORT" $com_port_id
tty_port_id=/dev/ttyS$((com_port_id-1))
echo "Converted COM Port" $com_port_arg "to tty port" $tty_port_id
echo "Sending Command String to move to download if not already in download mode"
echo "~sketch download" > $tty_port_id
C:\Users\Administrator\Desktop\arduino-windows-1.0.4\arduino-1.5.3-Intel.1.0.4/hardware/arduino/x86/tools/izmir/clupload_win.sh: line 24: /dev/ttyS7: Permission denied
#Move the existing sketch on target.
echo "Deleting existing sketch on target"
$fixed_path/lsz.exe --escape -c "mv -f /sketch/sketch.elf /sketch/sketch.elf.old" <> $tty_port_id 1>&0
C:\Users\Administrator\Desktop\arduino-windows-1.0.4\arduino-1.5.3-Intel.1.0.4/hardware/arduino/x86/tools/izmir/clupload_win.sh: line 28: /dev/ttyS7: Permission denied
# Execute the target download command
#Download the file.
host_file_name=$2
$fixed_path/lsz.exe --escape --binary --overwrite $host_file_name <> $tty_port_id 1>&0
C:\Users\Administrator\Desktop\arduino-windows-1.0.4\arduino-1.5.3-Intel.1.0.4/hardware/arduino/x86/tools/izmir/clupload_win.sh: line 34: /dev/ttyS7: Permission denied
#mv the downloaded file to /sketch/sketch.elf
Moving downloaded file to /sketch/sketch.elf on target
target_download_name="${host_file_name##*/}"
echo "Moving downloaded file to /sketch/sketch.elf on target"
#$fixed_path/lsz.exe --escape -c "cp sketch /sketch/sketch.elf" <> $tty_port_id 1>&0
$fixed_path/lsz.exe --escape -c "mv $target_download_name /sketch/sketch.elf; chmod +x /sketch/sketch.elf" <> $tty_port_id 1>&0
C:\Users\Administrator\Desktop\arduino-windows-1.0.4\arduino-1.5.3-Intel.1.0.4/hardware/arduino/x86/tools/izmir/clupload_win.sh: line 40: /dev/ttyS7: Permission denied
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