HDF5 Error

question
juno
hdf5

#1

Hi, I just installed Julia via Atom and had a lot of issues but finally worked it out after reading a lot of suggestions here http://discuss.junolab.org/t/not-able-to-install-juno-via-atom/562/26. Now when I try to run my code, I’m getting this error in the code:


Failed to precompile HDF5 to /Users/ashley/.julia/lib/v0.5/HDF5.ji.
 in compilecache(::String) at loading.jl:593
 in require(::Symbol) at loading.jl:422
 in require(::Symbol) at sys.dylib:?
 in include_string(::String, ::String) at loading.jl:441
 in include_string(::String, ::String, ::Int64) at eval.jl:28
 in include_string(::Module, ::String, ::String, ::Int64, ::Vararg{Int64,N}) at eval.jl:32
 in (::Atom.##53#56{String,Int64,String})() at eval.jl:40
 in withpath(::Atom.##53#56{String,Int64,String}, ::String) at utils.jl:30
 in withpath(::Function, ::String) at eval.jl:46
 in macro expansion at eval.jl:57 [inlined]
 in (::Atom.##52#55{Dict{String,Any}})() at task.jl:60

And then the error that was output into the Console is this:

ERROR: LoadError: LoadError: HDF5 not properly installed. Please run Pkg.build("HDF5")
 in error(::String) at ./error.jl:21
 in error(::String) at /Applications/Julia-0.5.app/Contents/Resources/julia/lib/julia/sys.dylib:?
 in include_from_node1(::String) at ./loading.jl:488
 in include_from_node1(::String) at /Applications/Julia-0.5.app/Contents/Resources/julia/lib/julia/sys.dylib:?
 in include_from_node1(::String) at ./loading.jl:488
 in include_from_node1(::String) at /Applications/Julia-0.5.app/Contents/Resources/julia/lib/julia/sys.dylib:?
 in macro expansion; at ./none:2 [inlined]
 in anonymous at ./<missing>:?
 in eval(::Module, ::Any) at ./boot.jl:234
 in eval(::Module, ::Any) at /Applications/Julia-0.5.app/Contents/Resources/julia/lib/julia/sys.dylib:?
 in process_options(::Base.JLOptions) at ./client.jl:239
 in _start() at ./client.jl:318
 in _start() at /Applications/Julia-0.5.app/Contents/Resources/julia/lib/julia/sys.dylib:?
while loading /Users/ashley/.julia/v0.5/HDF5/src/plain.jl, in expression starting on line 23
while loading /Users/ashley/.julia/v0.5/HDF5/src/HDF5.jl, in expression starting on line 3

So as suggested, I ran this: Pkg.build(“HDF5”)
And this is what I’m now encountering:

INFO: Building HDF5
================================[ ERROR: HDF5 ]=================================

LoadError: SystemError: unable to read directory /Users/ashley/.julia/v0.5/Homebrew/deps/usr/Library/Taps/staticfloat/homebrew-juliatranslated: No such file or directory
while loading /Users/ashley/.julia/v0.5/HDF5/deps/build.jl, in expression starting on line 27

================================================================================

================================[ BUILD ERRORS ]================================

WARNING: HDF5 had build errors.

 - packages with build errors remain installed in /Users/ashley/.julia/v0.5
 - build the package(s) and all dependencies with `Pkg.build("HDF5")`
 - build a single package by running its `deps/build.jl` script

================================================================================

Any suggestions? I have no idea what to do.


#2

Guessing here but can you try Pkg.build("Homebrew")?
(It looks like the Homebrew package may not have been properly installed?)