Hello,
I recently installed julia (Version 0.6.0-dev.1393 (2016-12-09 01:03 UTC)/ Commit e19a8bf (164 days old master)/x86_64-linux-gnu) on my Ubuntu 16.04 machine.
I am getting various errors after installing the packages Mamba and Jags; and module DataArrays.
I need the packages to run Bayesian structural equation modeling, which I currently run in R. I am hoping that I can improve the speed of the computation by switching to Julia.
I already have JAGS 4.1.0 installed on my machine and the binary can be found in /usr/local/bin/jags. Is this okay? in the installation manual I read " This version of the Jags.jl package assumes that Jags is installed and the jags binary is on $PATH. The variable JAGS_HOME is currently initialized either from ~/.juliarc.jl or from an environment variable JAGS_HOME. JAGS_HOME currently only used in runtests.jl to disable attempting to run tests that need the Jags executable on $PATH." However, I am not sure how I can test the $PATH.
I can install the packages (e.g. Pkg.add("Mamba), but there are some underlying errors. For example, while testing with Pkg.test(“Mamba”) I get “extra token “NAtype” after end of expression” and other errors, which I am not sure how to addrees. I include the full message below.
Could you please help me with this? I tried to run a search online but couldn’t find an answer. I might have missed something basic but I am new to the use of Julia.
Thanks in advance for any help,
Michela
This is the full message:
Pkg.init(“Mamba”)
INFO: Initializing package repository /home/michela/.julia/v0.6
INFO: Package directory /home/michela/.julia/v0.6 is already initialized.
Pkg.test(“Mamba”)
INFO: Testing Mamba
Running tests:
Testing …/doc/tutorial/line.jl
ERROR: LoadError: LoadError: syntax: extra token “NAtype” after end of expression
in include_from_node1(::String) at ./loading.jl:532
in include(::String) at ./sysimg.jl:14
in include_from_node1(::String) at ./loading.jl:532
in include(::String) at ./sysimg.jl:14
in anonymous at ./:2
in eval(::Module, ::Any) at ./boot.jl:236
in process_options(::Base.JLOptions) at ./client.jl:248
in _start() at ./client.jl:335
while loading /home/michela/.julia/v0.6/DataArrays/src/natype.jl, in expression starting on line 22
while loading /home/michela/.julia/v0.6/DataArrays/src/DataArrays.jl, in expression starting on line 58
ERROR: LoadError: Failed to precompile DataArrays to /home/michela/.julia/lib/v0.6/DataArrays.ji.
in compilecache(::String) at ./loading.jl:672
in require(::Symbol) at ./loading.jl:424
in include_from_node1(::String) at ./loading.jl:532
in include(::String) at ./sysimg.jl:14
in anonymous at ./:2
in eval(::Module, ::Any) at ./boot.jl:236
in process_options(::Base.JLOptions) at ./client.jl:248
in _start() at ./client.jl:335
while loading /home/michela/.julia/v0.6/Gadfly/src/Gadfly.jl, in expression starting on line 8
ERROR: LoadError: LoadError: LoadError: Failed to precompile Gadfly to /home/michela/.julia/lib/v0.6/Gadfly.ji.
in compilecache(::String) at ./loading.jl:672
in require(::Symbol) at ./loading.jl:453
in include_from_node1(::String) at ./loading.jl:532
in eval(::Module, ::Any) at ./boot.jl:236
in require(::Symbol) at ./loading.jl:446
in include_from_node1(::String) at ./loading.jl:532
in include(::String) at ./sysimg.jl:14
in macro expansion; at /home/michela/.julia/v0.6/Mamba/test/utils.jl:5 [inlined]
in macro expansion; at /home/michela/.julia/v0.6/Mamba/test/runtests.jl:0 [inlined]
in anonymous at ./:?
in include_from_node1(::String) at ./loading.jl:532
in include(::String) at ./sysimg.jl:14
in process_options(::Base.JLOptions) at ./client.jl:271
in _start() at ./client.jl:335
while loading /home/michela/.julia/v0.6/Mamba/src/Mamba.jl, in expression starting on line 38
while loading /home/michela/.julia/v0.6/Mamba/test/…/doc/tutorial/line.jl, in expression starting on line 1
while loading /home/michela/.julia/v0.6/Mamba/test/runtests.jl, in expression starting on line 33
=====================================================[ ERROR: Mamba ]======================================================
failed process: Process(/usr/bin/julia -Cx86-64 -J/usr/lib/x86_64-linux-gnu/julia/sys.so --compile=yes --depwarn=yes --check-bounds=yes --code-coverage=none --color=yes --compilecache=yes /home/michela/.julia/v0.6/Mamba/test/runtests.jl, ProcessExited(1)) [1]
===========================================================================================================================
ERROR: Mamba had test errors
in #test#61(::Bool, ::Function, ::Array{AbstractString,1}) at ./pkg/entry.jl:749
in (::Base.Pkg.Entry.#kw##test)(::Array{Any,1}, ::Base.Pkg.Entry.#test, ::Array{AbstractString,1}) at ./:0
in (::Base.Pkg.Dir.##2#3{Array{Any,1},Base.Pkg.Entry.#test,Tuple{Array{AbstractString,1}}})() at ./pkg/dir.jl:31
in cd(::Base.Pkg.Dir.##2#3{Array{Any,1},Base.Pkg.Entry.#test,Tuple{Array{AbstractString,1}}}, ::String) at ./file.jl:69
in #cd#1(::Array{Any,1}, ::Function, ::Function, ::Array{AbstractString,1}, ::Vararg{Array{AbstractString,1},N}) at ./pkg/dir.jl:31
in (::Base.Pkg.Dir.#kw##cd)(::Array{Any,1}, ::Base.Pkg.Dir.#cd, ::Function, ::Array{AbstractString,1}, ::Vararg{Array{AbstractString,1},N}) at ./:0
in #test#3(::Bool, ::Function, ::String, ::Vararg{String,N}) at ./pkg/pkg.jl:258
in test(::String, ::Vararg{String,N}) at ./pkg/pkg.jl:258