This sounds like it may have been a download issue or a corrupt repo, 
and/or a bug in any fallback code that Pkg might contain to attempt to deal 
with problems in cloning. If you can reproduce it reliably, would be 
valuable to report the sequence of steps you used to get into the error 

On Sunday, September 18, 2016 at 6:38:52 AM UTC-7, Michael Borregaard wrote:
> Thanks a lot, Jeffrey! Incredibly, this worked.
> Best,
> Michael
> On Fri, Sep 16, 2016 at 6:48 PM, Jeffrey Sarnoff < 
> <javascript:>> wrote:
>> 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 
>> julia-0.5.0-rc4-osx10.7+.dmg 
>> <>
>> install
>> Then start julia and quit().  Then start Julia and do Pkg.update() then 
>> quit().
>> 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
>>> 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/
>>>  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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