Re: [AMBER] Installation - NetCDF C compile failed

From: Jiří Dluhoš <>
Date: Sat, 20 Jan 2018 23:15:12 +0100 (CET)

"which flex" reports "/usr/bin/flex".
I installed flex using "sudo apt-get install flex" and if I re-run that, it
returns "flex is already the newest version (2.6.0-11)."

"gcc --version" returns "gcc (Ubuntu 5.4.0-6ubuntu1~16.04.5) 5.4.0 20160609"

Thank you for your help.

---------- Původní e-mail ----------
Od: David A Case <>
Komu: AMBER Mailing List <>
Datum: 20. 1. 2018 16:31:29
Předmět: Re: [AMBER] Installation - NetCDF C compile failed
"On Fri, Jan 19, 2018, Dan Roe wrote:

> Unfortunately I don't have access to the Windows 10 linux environment
> so I'm limited in how much I can help.

Errors referring to "yyunput" are always related to flex.

What does "which flex" report? How it you install it?

I don't think it can hurt to (re-)run "sudo apt-get flex". Beyond that, I'm
not sure how to debug this. I have Windows 10, and everything works for me.
But it's certainly possible that my Windows installation is older than
What do you get when typing "gcc --version"?

We're hoping to offer a windows binary package (doesn't rely on the Linux
subsystem) for AmberTools18. Also, you could try to "non-conda" binary
download for AmberTools17, and see if it will run in the Windows Linux
subsystem. But I'd certainly understand if you didn't want to try this,
since there is little guarantee that it will work.


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