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I have encountered this problem on Mac OS X with Mono 3.2.1, and debian with Mono 184.108.40.206 (Debian 220.127.116.11-8) and fsharp built from source from github.
If you run fsharpi as root/via sudo then it creates the directory registry and the file last-btime
$ sudo fsharpi
If you then run fsharpi as non-root then you get a (apparently non-fatal) error on startup:
F# Interactive for F# 3.0 (Open Source Edition)
Freely distributed under the Apache 2.0 Open Source License
For help type #help;;
> While saving registry data at /Library/Frameworks/Mono.framework/Versions/3.2.1/lib/../etc/mono/4.5/../registry/last-btime: System.UnauthorizedAccessException: Access to the path "/Library/Frameworks/Mono.framework/Versions/3.2.1/etc/mono/registry/last-btime" is denied.
at System.IO.FileStream..ctor (System.String path, FileMode mode, FileAccess access, FileShare share, Int32 bufferSize, Boolean anonymous, FileOptions options) [0x00000] in <filename unknown>:0
at System.IO.FileStream..ctor (System.String path, FileMode mode, FileAccess access, FileShare share) [0x00000] in <filename unknown>:0
at (wrapper remoting-invoke-with-check) System.IO.FileStream:.ctor (string,System.IO.FileMode,System.IO.FileAccess,System.IO.FileShare)
at System.IO.StreamWriter..ctor (System.String path, Boolean append, System.Text.Encoding encoding, Int32 bufferSize) [0x00000] in <filename unknown>:0
at System.IO.StreamWriter..ctor (System.String path, Boolean append, System.Text.Encoding encoding) [0x00000] in <filename unknown>:0
at (wrapper remoting-invoke-with-check) System.IO.StreamWriter:.ctor (string,bool,System.Text.Encoding)
at Microsoft.Win32.KeyHandler.SaveRegisteredBootTime (System.String path, Int64 btime) [0x00000] in <filename unknown>:0
removing the registry directory seems to fix the problem.
Fixed in master.