This happens shortly after one of the Installing PackageXXX lines, and crashes the Pkg.instantiate().
Rerunning Pkg.instantiate() seems to ignore the error, but doesn't fix it.
ERROR: MethodError: no method matching getindex(::Nothing, ::String)
Stacktrace:
[1] #build_versions#47(::Bool, ::Function, ::Pkg.Types.Context, ::Array{Base.UUID,1}) at /root/julia-1.0.5/usr/share/julia/stdlib/v1.0/Pkg/src/Operations.jl:1044
[2] build_versions at /root/julia-1.0.5/usr/share/julia/stdlib/v1.0/Pkg/src/Operations.jl:1033 [inlined]
[3] up(::Pkg.Types.Context, ::Array{Pkg.Types.PackageSpec,1}) at /root/julia-1.0.5/usr/share/julia/stdlib/v1.0/Pkg/src/Operations.jl:1247
[4] #up#31(::Pkg.Types.UpgradeLevel, ::Pkg.Types.PackageMode, ::Bool, ::Base.Iterators.Pairs{Union{},Union{},Tuple{},NamedTuple{(),Tuple{}}}, ::Function, ::Pkg.Types.Context, ::Array{Pkg.Types.PackageSpec,1}) at /root/julia-1.0.5/usr/share/julia/stdlib/v1.0/Pkg/src/API.jl:203
[5] #up at ./none:0 [inlined]
[6] #up#26 at /root/julia-1.0.5/usr/share/julia/stdlib/v1.0/Pkg/src/API.jl:168 [inlined]
[7] #up at ./none:0 [inlined]
[8] resolve at /root/julia-1.0.5/usr/share/julia/stdlib/v1.0/Pkg/src/API.jl:208 [inlined]
[9] do_resolve!(::Dict{Symbol,Any}, ::Array{String,1}, ::Dict{Symbol,Any}) at /root/julia-1.0.5/usr/share/julia/stdlib/v1.0/Pkg/src/REPLMode.jl:665
[10] #invokelatest#1(::Base.Iterators.Pairs{Union{},Union{},Tuple{},NamedTuple{(),Tuple{}}}, ::Function, ::Any, ::Any, ::Vararg{Any,N} where N) at ./essentials.jl:697
[11] invokelatest(::Any, ::Any, ::Vararg{Any,N} where N) at ./essentials.jl:696
[12] do_cmd!(::Pkg.REPLMode.PkgCommand, ::REPL.LineEditREPL) at /root/julia-1.0.5/usr/share/julia/stdlib/v1.0/Pkg/src/REPLMode.jl:603
[13] #do_cmd#33(::Bool, ::Function, ::REPL.LineEditREPL, ::String) at /root/julia-1.0.5/usr/share/julia/stdlib/v1.0/Pkg/src/REPLMode.jl:577
[14] do_cmd at /root/julia-1.0.5/usr/share/julia/stdlib/v1.0/Pkg/src/REPLMode.jl:573 [inlined]
[15] (::getfield(Pkg.REPLMode, Symbol("##50#53")){REPL.LineEditREPL,REPL.LineEdit.Prompt})(::REPL.LineEdit.MIState, ::Base.GenericIOBuffer{Array{UInt8,1}}, ::Bool) at /root/julia-1.0.5/usr/share/julia/stdlib/v1.0/Pkg/src/REPLMode.jl:923
[16] #invokelatest#1 at ./essentials.jl:697 [inlined]
[17] invokelatest at ./essentials.jl:696 [inlined]
[18] run_interface(::REPL.Terminals.TextTerminal, ::REPL.LineEdit.ModalInterface, ::REPL.LineEdit.MIState) at /root/julia-1.0.5/usr/share/julia/stdlib/v1.0/REPL/src/LineEdit.jl:2273
[19] run_frontend(::REPL.LineEditREPL, ::REPL.REPLBackendRef) at /root/julia-1.0.5/usr/share/julia/stdlib/v1.0/REPL/src/REPL.jl:1034
[20] run_repl(::REPL.AbstractREPL, ::Any) at /root/julia-1.0.5/usr/share/julia/stdlib/v1.0/REPL/src/REPL.jl:191
[21] (::getfield(Base, Symbol("##720#722")){Bool,Bool,Bool,Bool})(::Module) at ./client.jl:355
[22] #invokelatest#1 at ./essentials.jl:697 [inlined]
[23] invokelatest at ./essentials.jl:696 [inlined]
[24] run_main_repl(::Bool, ::Bool, ::Bool, ::Bool, ::Bool) at ./client.jl:339
[25] exec_options(::Base.JLOptions) at ./client.jl:277
[26] _start() at ./client.jl:425
To fix it, you need to call Pkg.resolve().
This will find the orphans in the manifest file and clear up the issue, or at least highlight the real problem.
Also read the help for Pkg.rm (by typing ]?rm at the julia REPL).
So if you remove a package in the Manifest file but leave behind some orphans,
you will likely have Pkg.instantiate() issues later.