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Trying to run a shell script in Git Bash. This particular script requires the Rcpp and RcppArmadillo packages. (creating an R package implemented in C++) Because I am on a Windows system I had to install Rtools40. Upon execution of the sh command I get the error:

fatal error - cygheap base mismatch detected - 0x180316408/0x180317408.
This problem is probably due to using incompatible versions of the cygwin DLL.
Search for cygwin1.dll using the Windows Start->Find/Search facility
and delete all but the most recent version.  The most recent version *should*
reside in x:\cygwin\bin, where 'x' is the drive on which you have
installed the cygwin distribution.  Rebooting is also suggested if you
are unable to find another cygwin DLL.

What I've tried:

  1. Following the instructions in the error message. However, a search for cygwin1.dll comes up empty. Additionally, I have never installed Cygwin on my machine.
  2. Updating R, Rtools40, and Git for Windows to the latest versions. This was much needed (apparently Windows doesn't update these programs automatically sigh) but it did not resolve the error message.
  3. Turning off ASLR protections in Windows Security settings as described in this post and this post.
  4. Deleting duplicate msys-2.0.dll files from my drive. This ultimately worked. I will post the solution in detail as an answer to this question.

Hope this helps anyone who, like me, has been sifting through the many posts that don't fully answer this question.

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So here's how I solved this problem. From what I understand, the error message in Git Bash is outdated and deceptive. It references Cygwin, but Git Bash actually uses MSYS2, not Cygwin. So instead of searching for cygwin1.dll, I needed to search my drive for msys-2.0.dll. This file was present in two locations: Git\usr\bin and rtools40\SOMETHING (I don't remember the exact path, but it was associated with Rtools40). As per the directions in the error message, I deleted the version that was older, which happened to be the one associated with Rtools40. That left only one version of msys-2.0.dll on my drive, and the sh command then executed in Git Bash with no issues.

What I'm still confused about: Why hasn't the error message in Git Bash been updated? What's the difference between Cygwin and MSYS2? I know they both impose the UNIX environment on Windows, but are there advantages or disadvantages to one or the other? In the long run, if I want to execute scripts through the command line, is Git Bash sustainable, or should I just create a Linux partition on my machine?

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I came across a post on GitHub that mentioned that if you are running into this issue after getting a "Resource temporarily unavailable" error, then the issue is likely that you are running 32-bit version of Git. Install Git 64 bit, and your issue should go away

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