Inconsistent "Unable to extract /usr/bin/ssh-agent.exe" message and disappearing files

[Jan Normann Nielsen <jan at dubbekarl dot dk>]

Hello

After using Cygwin for a couple of years, suddenly today a lot of files 
in my Cygwin folder were missing, most notably cygwin.bat and 
bin/ssh-agent.exe. I have no idea what has happened, the files were 
there yesterday. I don't remember if I did an update after yesterday's 
use, but I certainly don't remember any errors occurring if I did. I 
tried reinstalling the openssh package, but it refused to do so. 
Unfortunately I didn't write down the error message but I suspect it was 
the same as the one occurring below.

Instead, I decided to start from scratch. After assuring that I had the 
latest setup-x64.exe, I renamed my old cygwin64 folder and tried 
installing a default installation + opensssh on my C: drive. At the 
install of the openssh package, the installer stopped with the message:

"Unable to extract /usr/bin/ssh-agent.exe The file is in use or some 
other error occurred. Please stop all Cygwin processes and select 
"Retry", or select "Continue" to go on anyway (the file will be updated 
after a reboot)." I chose "Continue" and rebooted. The installer 
reported no errors but this one. First of all, I don't understand the 
error message, because there doesn't seem to be a /usr/bin folder to 
install this file to, and from what I can see, the installer tries to 
install in /bin because it leaves a file "ssh-agent.exe.new" in that 
folder before rebooting. There is no ssh-agent.exe file in that folder 
which was empty at the start of the installation so I don't understand 
why it's not just created instead of forcing me to do a reboot. I choose 
"Continue", and the file did get renamed after a reboot, but Cygwin.bat, 
Cygwin.ico, Cygwin-Terminal.ico were missing from my installation. They 
didn't seem to be created indicating that the installer actually had 
more problems it didn't tell me about.

Strangely enough, if I choose to install Cygwin from scratch in the same 
way except that I choose to install on my secondary (D:) drive, the 
installer doesn't produce the error. But I really don't want Cygwin on 
my D: drive. So I went back to installing on the C: drive again with the 
same error. Then on D: again without producing the problem. I have gone 
back and fourth at least 5 timers, but the last time I also got the 
error installing on my D: drive. There is no consistency on the (except 
for the drive) identical installation attempts.

So I decided to keep Cygwin on my D: drive for the time being after a 
(seemingly) succesful install. I ran Cygwin.bat which created my 
skeleton files and gave me a bash prompt. Then I edited Cygwin.bat and 
put "ssh-agent.exe " in front of the bash command like I had in my old 
installation to aid in handling my SSH keys. I then ran Cygwin.bat which 
made the window pop up for a split second, then it closed again and made 
Cygwin.bat disappear along with bin/ssh-agent.exe. How did that change 
in Cygwin.bat delete (at least) two files? If I now try to recreate 
Cygwin.bat from a backup or save it from my Windows text editor, I get 
either a repeating message from Explorer telling me that I need 
administrator rights (which I have) to copy the file, or my editor tells 
me "Access denied" when trying to save. So the Cygwin installation is 
now broken and I can't repair it. I can delete it and start from scratch 
again.

I can't explain this behavior in any way except maybe a problem with the 
file system or some strange bug in Cygwin. Both drives use NTFS and I've 
run chkdsk on C: telling me there are no problems.

Can anyone explain to me what's happening? I'm running on Windows 10 
with all available updates (tested yesterday).

Best wishes,
Jan


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