I reinstalled Julia0.6.2. When I run Pkg.init() in the new installed Julia, I got the similar error as follows.
julia> Pkg.init()
INFO: Initializing package repository E:\package\v0.6
INFO: Cloning METADATA from https://github.com/JuliaLang/METADATA.jl
ERROR: GitError(Code:ECERTIFICATE, Class:OS, user cancelled certificate check: )
Stacktrace:
[1] macro expansion at .\libgit2\error.jl:99 [inlined]
[2] clone(::String, ::String, ::Base.LibGit2.CloneOptions) at .\libgit2\reposit
ory.jl:276
[3] #clone#100(::String, ::Bool, ::Ptr{Void}, ::Nullable{Base.LibGit2.AbstractC
redentials}, ::Function, ::String, ::String) at .\libgit2\libgit2.jl:562
[4] (::Base.LibGit2.#kw##clone)(::Array{Any,1}, ::Base.LibGit2.#clone, ::String
, ::String) at .\<missing>:0
[5] (::Base.Pkg.Dir.##8#10{String,String})() at .\pkg\dir.jl:55
[6] cd(::Base.Pkg.Dir.##8#10{String,String}, ::String) at .\file.jl:59
[7] init(::String, ::String) at .\pkg\dir.jl:53
[8] init() at .\pkg\pkg.jl:85