carlobaldassi / gaussdca.jl Goto Github PK

WARNING: isreadable is deprecated as it implied that the file would actually be readable by the user; consider using `isfile` instead. see also the system man page for `access`
 in depwarn(::String, ::Symbol) at ./deprecated.jl:64
 in isreadable at ./deprecated.jl:166 [inlined]
 in isreadable at ./deprecated.jl:162 [inlined]
 in check_arguments(::String, ::Float64, ::Symbol, ::Float64, ::Symbol, ::Int64) at /home/dzea/.julia/v0.5/GaussDCA/src/GaussDCA.jl:78
 in #gDCA#1(::Float64, ::Symbol, ::Float64, ::Symbol, ::Int64, ::Bool, ::Function, ::String) at /home/dzea/.julia/v0.5/GaussDCA/src/GaussDCA.jl:30
 in gDCA(::String) at /home/dzea/.julia/v0.5/GaussDCA/src/GaussDCA.jl:30

ERROR: PosDefException: matrix is not positive definite; Cholesky factorization failed.

(v1.1) pkg> test GaussDCA

   Testing GaussDCA
 Resolving package versions...
    Status `/tmp/tmpAji1Kz/Manifest.toml`
  [34da2185] Compat v2.1.0
  [a0c94c4b] FastaIO v0.5.0
  [92fee26a] GZip v0.5.0
  [92cae0f8] GaussDCA v0.0.0 [`~/.julia/dev/GaussDCA`]
  [2a0f44e3] Base64  [`@stdlib/Base64`]
  [ade2ca70] Dates  [`@stdlib/Dates`]
  [8bb1440f] DelimitedFiles  [`@stdlib/DelimitedFiles`]
  [8ba89e20] Distributed  [`@stdlib/Distributed`]
  [b77e0a4c] InteractiveUtils  [`@stdlib/InteractiveUtils`]
  [76f85450] LibGit2  [`@stdlib/LibGit2`]
  [8f399da3] Libdl  [`@stdlib/Libdl`]
  [37e2e46d] LinearAlgebra  [`@stdlib/LinearAlgebra`]
  [56ddb016] Logging  [`@stdlib/Logging`]
  [d6f4376e] Markdown  [`@stdlib/Markdown`]
  [a63ad114] Mmap  [`@stdlib/Mmap`]
  [44cfe95a] Pkg  [`@stdlib/Pkg`]
  [de0858da] Printf  [`@stdlib/Printf`]
  [3fa0cd96] REPL  [`@stdlib/REPL`]
  [9a3f8284] Random  [`@stdlib/Random`]
  [ea8e919c] SHA  [`@stdlib/SHA`]
  [9e88b42a] Serialization  [`@stdlib/Serialization`]
  [1a1011a3] SharedArrays  [`@stdlib/SharedArrays`]
  [6462fe0b] Sockets  [`@stdlib/Sockets`]
  [2f01184e] SparseArrays  [`@stdlib/SparseArrays`]
  [10745b16] Statistics  [`@stdlib/Statistics`]
  [8dfed614] Test  [`@stdlib/Test`]
  [cf7118a7] UUIDs  [`@stdlib/UUIDs`]
  [4ec0a83e] Unicode  [`@stdlib/Unicode`]
[ Info: Running Main.GaussDCATests.test1
theta = 0.3633365278439081 threshold = 19.0
M = 106 N = 53 Meff = 91.99999999999997
Test Failed at ~/.julia/dev/GaussDCA/test/runtests.jl:51
  Expression: d1[k] ≈ d2[k]
   Evaluated: 0.8330339 ≈ 0.3001522
ERROR: LoadError: There was an error during testing
in expression starting at ~/.julia/dev/GaussDCA/test/runtests.jl:93
ERROR: Package GaussDCA errored during testing

julia> test2()
removing duplicate sequences... done: 97 -> 94
theta = 0.3681218129968263 threshold = 147.0
M = 94 N = 400 Meff = 25.8138802992673
ERROR: PosDefException: matrix is not positive definite; Cholesky factorization failed.
Stacktrace:
 [1] checkpositivedefinite at /build/julia/src/julia-1.1.1/usr/share/julia/stdlib/v1.1/LinearAlgebra/src/factorization.jl:11 [inlined]
 [2] #cholesky!#96(::Bool, ::Function, ::LinearAlgebra.Hermitian{Float64,Array{Float64,2}}, ::Val{false}) at /build/julia/src/julia-1.1.1/usr/share/julia/stdlib/v1.1/LinearAlgebra/src/cholesky.jl:153
 [3] #cholesky! at ./none:0 [inlined]
 [4] #cholesky!#97(::Bool, ::Function, ::Array{Float64,2}, ::Val{false}) at /build/julia/src/julia-1.1.1/usr/share/julia/stdlib/v1.1/LinearAlgebra/src/cholesky.jl:185
 [5] #cholesky! at ./none:0 [inlined] (repeats 2 times)
 [6] #cholesky#101 at /build/julia/src/julia-1.1.1/usr/share/julia/stdlib/v1.1/LinearAlgebra/src/cholesky.jl:275 [inlined]
 [7] cholesky at /build/julia/src/julia-1.1.1/usr/share/julia/stdlib/v1.1/LinearAlgebra/src/cholesky.jl:275 [inlined] (repeats 2 times)
 [8] #gDCA#1(::Float64, ::Symbol, ::Float64, ::Symbol, ::Int64, ::Bool, ::Function, ::String) at ~/.julia/dev/GaussDCA/src/GaussDCA.jl:48
 [9] (::getfield(GaussDCA, Symbol("#kw##gDCA")))(::NamedTuple{(:pseudocount, :score, :remove_dups),Tuple{Float64,Symbol,Bool}}, ::typeof(gDCA), ::String) at ./none:0
 [10] test2() at ./REPL[57]:2
 [11] top-level scope at none:0

julia> test3()
removing duplicate sequences... done: 106 -> 98
GaussDCA: using slower fallbacks
theta = 0.3626005800258088 threshold = 19.0
M = 98 N = 53 Meff = 92.0
ERROR: PosDefException: matrix is not positive definite; Cholesky factorization failed.
Stacktrace:
 [1] checkpositivedefinite at /build/julia/src/julia-1.1.1/usr/share/julia/stdlib/v1.1/LinearAlgebra/src/factorization.jl:11 [inlined]
 [2] #cholesky!#96(::Bool, ::Function, ::LinearAlgebra.Hermitian{Float64,Array{Float64,2}}, ::Val{false}) at /build/julia/src/julia-1.1.1/usr/share/julia/stdlib/v1.1/LinearAlgebra/src/cholesky.jl:153
 [3] #cholesky! at ./none:0 [inlined]
 [4] #cholesky!#97(::Bool, ::Function, ::Array{Float64,2}, ::Val{false}) at /build/julia/src/julia-1.1.1/usr/share/julia/stdlib/v1.1/LinearAlgebra/src/cholesky.jl:185
 [5] #cholesky! at ./none:0 [inlined] (repeats 2 times)
 [6] #cholesky#101 at /build/julia/src/julia-1.1.1/usr/share/julia/stdlib/v1.1/LinearAlgebra/src/cholesky.jl:275 [inlined]
 [7] cholesky at /build/julia/src/julia-1.1.1/usr/share/julia/stdlib/v1.1/LinearAlgebra/src/cholesky.jl:275 [inlined] (repeats 2 times)
 [8] #gDCA#1(::Float64, ::Symbol, ::Float64, ::Symbol, ::Int64, ::Bool, ::Function, ::String) at /home/macpasz/.julia/dev/GaussDCA/src/GaussDCA.jl:48
 [9] #gDCA at ./none:0 [inlined]
 [10] test3() at ./REPL[59]:3
 [11] top-level scope at none:0