I have had this happen, too.  My suggestion is  grounded in persistence 
rather than deep mastery of Julia's structural and file relationships.
So someone else may have a more studied approach with some explaining. 
 Until then,

quit() Julia.
To have an new install be really clean, first cd  to <whereitis>/.julia/ 
and delete the directory `v0.5` -- if that is overkill because you do not 
want to redo many Pkg.add()s then cd v0.5 and delete the METADATA directory 
the REQUIRE file and the META_BRANCH file and the entry for whatever 
packages you had added just before this difficulty (including those that 
have hiccuped on precompile).   
now delete and then reget the most current binary for your system 
Then start julia and quit().  Then start Julia and do Pkg.update() then 
Then start julia and do Pkg.add() for 1 package you want then quit(). then 
start julia and do using <thatpackage> (so it precompiles) and quit().
now try using that package.

On Friday, September 16, 2016 at 4:43:06 AM UTC-4, Michael Borregaard wrote:
> Hi, Is this the right forum for troubleshooting / issues with my julia 
> install?
> I have kept having problems with packages giving error on precompile, 
> rendering julia unusable. I then reinstalled julia-0.5-rc4, and removed my 
> .julia folder from my home dir to do a fresh install. Now, Julia fails with 
> an error message when I do Pkg.update():
> julia> Pkg.update()
> INFO: Initializing package repository /Users/michael/.julia/v0.5
> INFO: Cloning METADATA from https://github.com/JuliaLang/METADATA.jl
> ERROR: SystemError (with /Users/michael/.julia/v0.5/METADATA): rmdir: 
> Directory not empty
>  in #systemerror#51 at ./error.jl:34 [inlined]
>  in (::Base.#kw##systemerror)(::Array{Any,1}, ::Base.#systemerror, 
> ::Symbol, ::Bool) at ./<missing>:0
>  in #rm#7(::Bool, ::Bool, ::Function, ::String) at ./file.jl:125
>  in #rm#7(::Bool, ::Bool, ::Function, ::String) at 
> /Applications/Julia-0.5.app/Contents/Resources/julia/lib/julia/sys.dylib:?
>  in (::Base.Filesystem.#kw##rm)(::Array{Any,1}, ::Base.Filesystem.#rm, 
> ::String) at ./<missing>:0
>  in init(::String, ::String) at ./pkg/dir.jl:62
>  in #cd#1(::Array{Any,1}, ::Function, ::Function, ::String, 
> ::Vararg{Any,N}) at ./pkg/dir.jl:28
>  in update() at ./pkg/pkg.jl:210
> I assums that a completely clean install should work. Are there keys to 
> delete etc that will give me a properly clean install? I am on Mac OS X 
> (newest version).
> Thanks!

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