Precompilation Error : GSAMethod not defined

Hey there!

First of all, thanks for Pumas! I am still a newcomer to the pk/pd domain, but it is a smooth journey so far ;).

I have a problem during the precompilation of pumas 1.1.0 on a remote machine running Julia pro 1.5.3 :

(ALL_Pumas) pkg> precompile
Precompiling project...
[ Info: Precompiling Pumas [4f2c3c20-a4ac-11e9-067b-e5872d3484cf]
ERROR: LoadError: LoadError: UndefVarError: GSAMethod not defined
 [1] getproperty(::Module, ::Symbol) at ./Base.jl:26
 [2] top-level scope at /home/martensen/.julia/packages/Pumas/iIBBr/src/estimation/gsa.jl:1
 [3] include(::Function, ::Module, ::String) at ./Base.jl:380
 [4] include at ./Base.jl:368 [inlined]
 [5] include(::String) at /home/martensen/.julia/packages/Pumas/iIBBr/src/Pumas.jl:1
 [6] top-level scope at /home/martensen/.julia/packages/Pumas/iIBBr/src/Pumas.jl:51
 [7] include(::Function, ::Module, ::String) at ./Base.jl:380
 [8] include(::Module, ::String) at ./Base.jl:368
 [9] top-level scope at none:2
 [10] eval at ./boot.jl:331 [inlined]
 [11] eval(::Expr) at ./client.jl:467
 [12] top-level scope at ./none:3
in expression starting at /home/martensen/.julia/packages/Pumas/iIBBr/src/estimation/gsa.jl:1
in expression starting at /home/martensen/.julia/packages/Pumas/iIBBr/src/Pumas.jl:51

My current environment contains:

(ALL_Pumas) pkg> st
Project ALL_Pumas v0.1.0
Status `~/code/ALL_Pumas/Project.toml`
  [336ed68f] CSV v0.7.10
  [a93c6f00] DataFrames v0.21.8
  [2b5f629d] DiffEqBase v6.57.8
  [41bf760c] DiffEqSensitivity v6.43.0
  [5789e2e9] FileIO v1.6.4
  [1dea7af3] OrdinaryDiffEq v5.52.0
  [4f2c3c20] Pumas v1.1.0
  [9e88b42a] Serialization

julia> versioninfo()
Julia Version 1.5.3
Commit 788b2c77c1 (2020-11-09 13:37 UTC)
Platform Info:
  OS: Linux (x86_64-pc-linux-gnu)
  CPU: Intel(R) Xeon(R) Gold 6138 CPU @ 2.00GHz
  LIBM: libopenlibm
  LLVM: libLLVM-9.0.1 (ORCJIT, skylake-avx512)
  JULIA_DEPOT_PATH = /home/martensen/.julia
  JULIA_LOAD_PATH = /home/martensen/.julia/environments/JuliaPro_v1.5.3-1:@:@v#.#:@stdlib

Locally I am able to use the latest release, but on the remote machine, it fails.
Am I missing something important here? :slight_smile:


Can you try ]rm DiffEqSensitivity and then start a new Julia session and ]instantiate, it looks like you have pulled in a newer version of DiffEqSensitivity whereas Pumas v1.1 requires DiffEqSensitivity <6.36.0

I also completely removed .julia and tried to precompile just pumas. The outcome seems to be the same.

When I add pumas, it show

(@JuliaPro_v1.5.3-1) pkg> add Pumas
  Resolving package versions...
  Installed ArrayLayouts ─ v0.1.5
  Installed Zygote ─────── v0.4.12
Updating `~/.julia/environments/JuliaPro_v1.5.3-1/Project.toml`
  [4f2c3c20] + Pumas v1.1.0
Updating `~/.julia/environments/JuliaPro_v1.5.3-1/Manifest.toml`
  [c3fe647b] + AbstractAlgebra v0.11.2
  [621f4979] + AbstractFFTs v1.0.1
  [80f14c24] + AbstractMCMC v2.2.1
  [79e6a3ab] + Adapt v3.2.0
  [0bf59076] + AdvancedHMC v0.2.27
  [dce04be8] + ArgCheck v1.1.0
  [ec485272] + ArnoldiMethod v0.1.0
  [7d9fca2a] + Arpack v0.4.0
  [68821587] + Arpack_jll v3.5.0+3
  [4fba245c] + ArrayInterface v2.14.17
  [4c555306] + ArrayLayouts v0.1.5
  [13072b0f] + AxisAlgorithms v1.0.0
  [39de3d68] + AxisArrays v0.4.3
  [198e06fe] + BangBang v0.3.30
  [336ed68f] + CSV v0.7.10
  [49dc2e85] + Calculus v0.5.1
  [a603d957] + CanonicalTraits v0.2.4
  [324d7699] + CategoricalArrays v0.8.3
  [d360d2e6] + ChainRulesCore v0.9.29
  [861a8166] + Combinatorics v1.0.2
  [38540f10] + CommonSolve v0.2.0
  [bbf7d656] + CommonSubexpressions v0.3.0
  [e66e0078] + CompilerSupportLibraries_jll v0.3.4+0
  [a33af91c] + CompositionsBase v0.1.0
  [88cd18e8] + ConsoleProgressMonitor v0.1.2
  [187b0558] + ConstructionBase v1.1.0
  [a93c6f00] + DataFrames v0.21.8
  [82cc6244] + DataInterpolations v3.3.1
  [244e2a9f] + DefineSingletons v0.1.1
  [2b5f629d] + DiffEqBase v6.57.8
  [459566f4] + DiffEqCallbacks v2.16.0
  [01453d9d] + DiffEqDiffTools v1.7.0
  [c894b116] + DiffEqJump v6.13.0
  [77a26b50] + DiffEqNoiseProcess v5.5.2
  [41bf760c] + DiffEqSensitivity v6.43.0
  [163ba53b] + DiffResults v1.0.3
  [b552c78f] + DiffRules v1.0.2
  [31c24e10] + Distributions v0.23.2
  [da5c29d0] + EllipsisNotation v1.0.0
  [d4d017d3] + ExponentialUtilities v1.8.0
  [7a1cc6ca] + FFTW v1.3.2
  [f5851436] + FFTW_jll v3.3.9+7
  [9aa1b823] + FastClosures v0.3.2
  [1a297f60] + FillArrays v0.8.14
  [6a86dc24] + FiniteDiff v2.8.0
  [59287772] + Formatting v0.4.2
  [f6369f11] + ForwardDiff v0.10.17
  [069b7b12] + FunctionWrappers v1.1.2
  [6b9d7cbe] + GeneralizedGenerated v0.2.8
  [af5da776] + GlobalSensitivity v1.0.0
  [19dc6840] + HCubature v1.5.0
  [0e44f5e4] + Hwloc v1.3.0
  [e33a78d0] + Hwloc_jll v2.4.1+0
  [7869d1d1] + IRTools v0.3.3
  [615f187c] + IfElse v0.1.0
  [d25df0c9] + Inflate v0.1.2
  [22cec73e] + InitialValues v0.2.10
  [505f98c9] + InplaceOps v0.3.0
  [1d5cc7b8] + IntelOpenMP_jll v2018.0.3+2
  [a98d9a8b] + Interpolations v0.13.1
  [8197267c] + IntervalSets v0.5.2
  [41ab1584] + InvertedIndices v1.0.0
  [c8e1da08] + IterTools v1.3.0
  [42fd0dbc] + IterativeSolvers v0.9.0
  [b14d175d] + JuliaVariables v0.2.4
  [5ab0869b] + KernelDensity v0.6.2
  [b964fa9f] + LaTeXStrings v1.2.1
  [2ee39098] + LabelledArrays v1.5.0
  [23fbe1c1] + Latexify v0.14.11
  [a5e1c1ea] + LatinHypercubeSampling v1.7.3
  [73f95e8e] + LatticeRules v0.0.1
  [4af54fe1] + LazyArtifacts v1.3.0
  [093fc24a] + LightGraphs v1.3.5
  [d3d80556] + LineSearches v7.1.1
  [e6f89c97] + LoggingExtras v0.4.5
  [bdcacae8] + LoopVectorization v0.10.0
  [c7f686f2] + MCMCChains v4.7.1
  [856f044c] + MKL_jll v2021.1.1+1
  [e80e1ace] + MLJModelInterface v0.4.1
  [d8e11817] + MLStyle v0.4.9
  [128add7d] + MicroCollections v0.1.0
  [e1d29d7a] + Missings v0.4.5
  [961ee093] + ModelingToolkit v3.21.0
  [4886b29c] + MonteCarloIntegration v0.0.1
  [46d2c3a1] + MuladdMacro v0.2.2
  [29142fd5] + NCA v1.0.3
  [d41bc354] + NLSolversBase v7.5.0
  [2774e3e8] + NLsolve v4.5.1
  [872c559c] + NNlib v0.6.6
  [77ba4419] + NaNMath v0.3.5
  [71a1bf82] + NameResolution v0.1.5
  [c020b1a1] + NaturalSort v1.0.0
  [8913a72c] + NonlinearSolve v0.3.8
  [6fe1bfb0] + OffsetArrays v1.6.2
  [4536629a] + OpenBLAS_jll v0.3.9+5
  [efe28fd5] + OpenSpecFun_jll v0.5.3+4
  [429524aa] + Optim v0.22.0
  [1dea7af3] + OrdinaryDiffEq v5.52.0
  [90014a1f] + PDMats v0.9.12
  [d96e819e] + Parameters v0.12.2
  [e409e4f3] + PoissonRandom v0.4.0
  [2dfb63ee] + PooledArrays v0.5.3
  [85a6dd25] + PositiveFactorizations v0.2.4
  [8162dcfd] + PrettyPrint v0.2.0
  [08abe8d2] + PrettyTables v0.11.1
  [33c8b6b6] + ProgressLogging v0.1.4
  [92933f4c] + ProgressMeter v1.5.0
  [4f2c3c20] + Pumas v1.1.0
  [1fd47b50] + QuadGK v2.4.1
  [67601950] + Quadrature v1.1.0
  [c6596682] + QuantileRegressions v0.1.6
  [8a4e6c94] + QuasiMonteCarlo v0.2.2
  [74087812] + Random123 v1.3.1
  [fb686558] + RandomExtensions v0.4.3
  [e6cf234a] + RandomNumbers v1.4.0
  [b3c3ace0] + RangeArrays v0.3.2
  [c84ed2f1] + Ratios v0.4.0
  [3cdcf5f2] + RecipesBase v1.1.1
  [731186ca] + RecursiveArrayTools v2.11.0
  [f2c3362d] + RecursiveFactorization v0.1.11
  [42d2dcc6] + Referenceables v0.1.2
  [ae5879a3] + ResettableStacks v1.1.0
  [37e2e3b7] + ReverseDiff v1.7.0
  [79098fc4] + Rmath v0.6.1
  [f50d1b31] + Rmath_jll v0.2.2+2
  [f2b01f46] + Roots v1.0.8
  [476501e8] + SLEEFPirates v0.6.8
  [1bc83da4] + SafeTestsets v0.0.1
  [0bca4576] + SciMLBase v1.8.3
  [321657f4] + ScientificTypes v1.1.1
  [91c51154] + SentinelArrays v1.2.16
  [efcf1570] + Setfield v0.7.0
  [1277b4bf] + ShiftedArrays v1.0.0
  [699a6c99] + SimpleTraits v0.9.3
  [ed01d8cd] + Sobol v1.4.0
  [a2af1166] + SortingAlgorithms v0.3.1
  [47a9eef4] + SparseDiffTools v1.13.0
  [276daf66] + SpecialFunctions v0.10.3
  [171d559e] + SplittablesBase v0.1.13
  [860ef19b] + StableRNGs v1.0.0
  [90137ffa] + StaticArrays v0.12.5
  [64bff920] + StatisticalTraits v0.1.1
  [2913bbd2] + StatsBase v0.33.3
  [4c63d2b9] + StatsFuns v0.9.6
  [3eaba693] + StatsModels v0.6.21
  [789caeaf] + StochasticDiffEq v6.33.0
  [09ab397b] + StructArrays v0.4.2
  [856f2bd8] + StructTypes v1.4.0
  [d1185830] + SymbolicUtils v0.5.2
  [5d786b92] + TerminalLoggers v0.1.3
  [8290d209] + ThreadingUtilities v0.2.3
  [ac1d9e8a] + ThreadsX v0.1.7
  [a759f4b9] + TimerOutputs v0.5.8
  [9f7883ad] + Tracker v0.2.16
  [28d57a85] + Transducers v0.4.60
  [84d833dd] + TransformVariables v0.3.4
  [592b5752] + Trapz v2.0.2
  [3a884ed6] + UnPack v1.0.2
  [1986cc42] + Unitful v1.6.0
  [3d5dd08c] + VectorizationBase v0.16.2
  [19fa3120] + VertexSafeGraphs v0.1.2
  [efce3f68] + WoodburyMatrices v0.5.3
  [e88e6eb3] + Zygote v0.4.12
  [700de1a5] + ZygoteRules v0.2.1
  [9fa8497b] + Future
  [4607b0f0] + SuiteSparse

So it adds DiffEqSensitivity v6.43.0 as default, even though it is specified as v6.14in the Project.toml in .julia/packages/Pumas/.... This seems strange.

Edit After adding DiffEqSensitity@6.14.0 it works! Thank you!

1 Like

Good to hear that you got it working. However, be aware that the installation of Pumas through JuliaPro will go away relatively soon. In the future, it will be possible to access Pumas over JuliaHub or as a stand-alone download from

Thanks for letting me know.

Since we are working on an Ubuntu machine, will the download for Linux also be available? Or do we ( as a University using Pumas for research) need to get in contact with the sales team? To be honest, I have no prior experience with JuliaHub, so if I am missing something please forgive my ignorance.