Error installing Jags Mamba and DataArrays: extra token "NAtype" after end of expression


#1

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


#2

The first thing you should try is upgrading to the latest release candidate. See this topic. FWIW, using this version DataArrays.jl loads on my machine using the latest RC and released packages, and tests run correctly.


#3

Wherever you installed a 6 month old nightly master build from should not be used. Install a stable release from the generic linux binaries.