Closed jwscook closed 4 years ago
I'm surprised you had to do that:
bleaberry[~] mkdir trial
bleaberry[~] cd trial
bleaberry[~/trial] JULIA_MPI_PATH=/usr/local julia
_
_ _ _(_)_ | Documentation: https://docs.julialang.org
(_) | (_) (_) |
_ _ _| |_ __ _ | Type "?" for help, "]?" for Pkg help.
| | | | | | |/ _` | |
| | |_| | | | (_| | | Version 1.4.0 (2020-03-21)
_/ |\__'_|_|_|\__'_| | Official https://julialang.org/ release
|__/ |
(@v1.4) pkg> activate .
Activating new environment at `~/trial/Project.toml`
(trial) pkg> add https://github.com/ScottishCovidResponse/Simulation.jl.git
...
(trial) pkg> build Simulation
...
julia> using Simulation
[ Info: Precompiling Simulation [ed2dc23b-ada4-5fdb-a26f-56368a14ad8f]
WARNING: Method definition abbr(Unitful.Unit{:Year, Unitful.Dimensions{(Unitful.Dimension{:Time}(power=Base.Rational{Int64}(num=1, den=1)),)}()}) in module Unitful at /Users/richardr/.julia/packages/Unitful/PZjMS/src/user.jl:178 overwritten in module Units at /Users/richardr/.julia/packages/Unitful/PZjMS/src/user.jl:178.
** incremental compilation may be fatally broken for this module **
WARNING: Method definition dot(Any, Any, Any) in module LinearAlgebra at /Users/julia/buildbot/worker/package_macos64/build/usr/share/julia/stdlib/v1.4/LinearAlgebra/src/generic.jl:924 overwritten in module Optim at /Users/richardr/.julia/packages/Optim/Agd3B/src/multivariate/precon.jl:23.
** incremental compilation may be fatally broken for this module **
Creating Diversity to Phylo interface...
julia>
I do have R and MPI libraries already installed, but this installed all of the other Julia packages locally as far as I can tell.
There were some broken precompilation things, and I'm sure I didn't use to have to set the JULIA_MPI_PATH, but otherwise it seems to have worked? Maybe it's something to do with the way you installed it?
(trial) pkg> add git@github.com:ScottishCovidResponse/Simulation.jl.git
I've just spun up a blank Docker container from ubuntu:latest
to try the install. I've gotten as far as you, but fail at pkg> test Simulation
(@v1.5) pkg> activate .
Activating environment at `/simulation_env/Project.toml`
(simulation_env) pkg> add https://github.com/ScottishCovidResponse/Simulation.jl.git
Updating git-repo `https://github.com/ScottishCovidResponse/Simulation.jl.git`
Updating registry at `~/.julia/registries/General`
Resolving package versions...
No Changes to `/simulation_env/Project.toml`
No Changes to `/simulation_env/Manifest.toml`
(simulation_env) pkg> build Simulation
Building CodecZlib → `~/.julia/packages/CodecZlib/5t9zO/deps/build.log`
Building TimeZones → `~/.julia/packages/TimeZones/X323b/deps/build.log`
Building MPI ──────→ `~/.julia/packages/MPI/ZfFyE/deps/build.log`
Building CMake ────→ `~/.julia/packages/CMake/ULbyn/deps/build.log`
Building Blosc ────→ `~/.julia/packages/Blosc/ZgcAM/deps/build.log`
Building HDF5 ─────→ `~/.julia/packages/HDF5/ECBXn/deps/build.log`
Building GR ───────→ `~/.julia/packages/GR/yMV3y/deps/build.log`
Building Plots ────→ `~/.julia/packages/Plots/kgqnU/deps/build.log`
Building Conda ────→ `~/.julia/packages/Conda/3rPhK/deps/build.log`
Building RCall ────→ `~/.julia/packages/RCall/g7dhB/deps/build.log`
Building NetCDF ───→ `~/.julia/packages/NetCDF/RrTZz/deps/build.log`
(simulation_env) pkg> test Simulation
Testing Simulation
Status `/tmp/jl_PHv4TD/Project.toml`
[c9ce4bd3] ArchGDAL v0.3.2
[39de3d68] AxisArrays v0.4.3
[49dc2e85] Calculus v0.5.1
[34da2185] Compat v3.8.0
[a93c6f00] DataFrames v0.20.2
[31c24e10] Distributions v0.23.2
[d3d5718d] Diversity v0.5.1
[a58aae7d] EcoBase v0.1.3
[becb17da] Feather v0.5.5
[19dc6840] HCubature v1.4.0
[6deec6e2] IndexedTables v0.12.6
[a98d9a8b] Interpolations v0.12.9
[4138dd39] JLD v0.10.0
[a93385a2] JuliaDB v0.13.0
[da04e1cc] MPI v0.13.1
[e1d29d7a] Missings v0.4.3
[30363a11] NetCDF v0.10.2
[429524aa] Optim v0.20.6
[aea672f4] Phylo v0.4.2
[91a5bcdd] Plots v1.1.2
[6f49c342] RCall v0.13.4
[3cdcf5f2] RecipesBase v1.0.1
[ae029012] Requires v1.0.1
[ed2dc23b] Simulation v0.0.0 `https://github.com/ScottishCovidResponse/Simulation.jl.git#epi`
[348f2d5d] SpatialEcology v0.9.4
[2913bbd2] StatsBase v0.33.0
[1986cc42] Unitful v1.1.0
[ade2ca70] Dates
[76f85450] LibGit2
[8f399da3] Libdl
[37e2e46d] LinearAlgebra
[56ddb016] Logging
[d6f4376e] Markdown
[de0858da] Printf
[3fa0cd96] REPL
[9a3f8284] Random
[ea8e919c] SHA
[10745b16] Statistics
[8dfed614] Test
[cf7118a7] UUIDs
Status `/tmp/jl_PHv4TD/Manifest.toml`
[1520ce14] AbstractTrees v0.3.3
[79e6a3ab] Adapt v1.0.1
[c9ce4bd3] ArchGDAL v0.3.2
[ec485272] ArnoldiMethod v0.0.4
[7d9fca2a] Arpack v0.4.0
[68821587] Arpack_jll v3.5.0+3
[4fba245c] ArrayInterface v2.8.5
[69666777] Arrow v0.2.4
[13072b0f] AxisAlgorithms v1.0.0
[39de3d68] AxisArrays v0.4.3
[9e28174c] BinDeps v1.0.1
[b99e7846] BinaryProvider v0.5.8
[a74b3585] Blosc v0.6.0
[6e34b625] Bzip2_jll v1.0.6+2
[fa961155] CEnum v0.2.0
[631607c0] CMake v1.2.0
[d5fb7624] CMakeWrapper v0.2.3
[49dc2e85] Calculus v0.5.1
[324d7699] CategoricalArrays v0.7.7
[944b1d66] CodecZlib v0.6.0
[35d6a980] ColorSchemes v3.8.0
[3da002f7] ColorTypes v0.10.2
[5ae59095] Colors v0.12.0
[861a8166] Combinatorics v1.0.1
[bbf7d656] CommonSubexpressions v0.2.0
[34da2185] Compat v3.8.0
[e66e0078] CompilerSupportLibraries_jll v0.3.3+0
[8f4d0f93] Conda v1.4.1
[a9693cdc] CondaBinDeps v0.2.0
[187b0558] ConstructionBase v1.0.0
[d38c429a] Contour v0.5.2
[d58978e5] Dagger v0.8.0
[9a962f9c] DataAPI v1.2.0
[a93c6f00] DataFrames v0.20.2
[1313f7d8] DataFramesMeta v0.5.0
[9a8bc11e] DataStreams v0.4.2
[864edb3b] DataStructures v0.17.13
[e2d170a0] DataValueInterfaces v1.0.0
[e7dc6d0d] DataValues v0.4.13
[163ba53b] DiffResults v1.0.2
[b552c78f] DiffRules v1.0.1
[3c3547ce] DiskArrays v0.2.3
[b4f34e82] Distances v0.8.2
[31c24e10] Distributions v0.23.2
[d3d5718d] Diversity v0.5.1
[ffbed154] DocStringExtensions v0.8.1
[497a8b3b] DoubleFloats v1.1.8
[a58aae7d] EcoBase v0.1.3
[da5c29d0] EllipsisNotation v0.4.0
[e2ba6199] ExprTools v0.1.1
[8f5d6c58] EzXML v1.1.0
[c87230d0] FFMPEG v0.3.0
[b22a6f82] FFMPEG_jll v4.1.0+2
[becb17da] Feather v0.5.5
[5789e2e9] FileIO v1.2.4
[1a297f60] FillArrays v0.8.7
[6a86dc24] FiniteDiff v2.3.0
[53c48c17] FixedPointNumbers v0.8.0
[53afe959] FlatBuffers v0.5.4
[59287772] Formatting v0.4.1
[f6369f11] ForwardDiff v0.10.10
[d7e528f0] FreeType2_jll v2.10.1+2
[559328eb] FriBidi_jll v1.0.5+2
[add2ef01] GDAL v1.1.0
[a7073274] GDAL_jll v3.0.4+0
[d604d12d] GEOS_jll v3.8.1+0
[28b8d3ca] GR v0.48.0
[01680d73] GenericSVD v0.3.0
[c145ed77] GenericSchur v0.4.0
[68eda718] GeoFormatTypes v0.3.0
[cf35fbd7] GeoInterface v0.5.4
[4d00f742] GeometryTypes v0.8.2
[c27321d9] Glob v1.3.0
[19dc6840] HCubature v1.4.0
[f67ccb44] HDF5 v0.13.1
[0234f1f7] HDF5_jll v1.10.5+5
[6deec6e2] IndexedTables v0.12.6
[d25df0c9] Inflate v0.1.2
[a98d9a8b] Interpolations v0.12.9
[8197267c] IntervalSets v0.5.0
[d8418881] Intervals v1.1.0
[41ab1584] InvertedIndices v1.0.0
[c8e1da08] IterTools v1.3.0
[1c8ee90f] IterableTables v1.0.0
[82899510] IteratorInterfaceExtensions v1.0.0
[4138dd39] JLD v0.10.0
[682c06a0] JSON v0.21.0
[a93385a2] JuliaDB v0.13.0
[c1c5ebd0] LAME_jll v3.100.0+0
[7f8f8fb0] LearnBase v0.3.0
[deac9b47] LibCURL_jll v7.68.0+0
[29816b5a] LibSSH2_jll v1.9.0+1
[dd192d2f] LibVPX_jll v1.8.1+1
[94ce4f54] Libiconv_jll v1.16.0+2
[093fc24a] LightGraphs v1.3.2
[d3d80556] LineSearches v7.0.1
[30fc2ffe] LossFunctions v0.6.0
[da04e1cc] MPI v0.13.1
[1914dd2f] MacroTools v0.5.5
[c8ffd9c3] MbedTLS_jll v2.16.0+2
[442fdcdd] Measures v0.3.1
[f9f48841] MemPool v0.2.0
[e1d29d7a] Missings v0.4.3
[78c3b35d] Mocking v0.7.1
[d41bc354] NLSolversBase v7.6.1
[77ba4419] NaNMath v0.3.3
[30363a11] NetCDF v0.10.2
[4d1e1d77] Nullables v1.0.0
[6fe1bfb0] OffsetArrays v1.0.4
[e7412a2a] Ogg_jll v1.3.3+0
[a15396b6] OnlineStats v1.0.2
[925886fa] OnlineStatsBase v1.2.8
[4536629a] OpenBLAS_jll v0.3.9+2
[458c3c95] OpenSSL_jll v1.1.1+2
[efe28fd5] OpenSpecFun_jll v0.5.3+3
[429524aa] Optim v0.20.6
[91d4177d] Opus_jll v1.3.1+0
[bac558e1] OrderedCollections v1.1.0
[90014a1f] PDMats v0.9.12
[58948b4f] PROJ_jll v6.3.0+0
[d96e819e] Parameters v0.12.0
[69de0a69] Parsers v1.0.2
[06bb1623] PenaltyFunctions v0.2.1
[aea672f4] Phylo v0.4.2
[ccf2f8ad] PlotThemes v2.0.0
[995b91a9] PlotUtils v1.0.0
[91a5bcdd] Plots v1.1.2
[f27b6e38] Polynomials v0.8.0
[2dfb63ee] PooledArrays v0.5.3
[85a6dd25] PositiveFactorizations v0.2.3
[1fd47b50] QuadGK v2.3.1
[be4d8f0f] Quadmath v0.5.4
[6f49c342] RCall v0.13.4
[9ae346a0] RandomBooleanMatrices v0.1.1
[e6cf234a] RandomNumbers v1.4.0
[b3c3ace0] RangeArrays v0.3.2
[c84ed2f1] Ratios v0.4.0
[3cdcf5f2] RecipesBase v1.0.1
[01d81517] RecipesPipeline v0.1.6
[189a3867] Reexport v0.2.0
[ae029012] Requires v1.0.1
[79098fc4] Rmath v0.6.1
[f50d1b31] Rmath_jll v0.2.2+0
[76ed43ae] SQLite_jll v3.31.1+0
[1277b4bf] ShiftedArrays v1.0.0
[992d4aef] Showoff v0.3.1
[699a6c99] SimpleTraits v0.9.2
[ed2dc23b] Simulation v0.0.0 `https://github.com/ScottishCovidResponse/Simulation.jl.git#epi`
[a2af1166] SortingAlgorithms v0.3.1
[348f2d5d] SpatialEcology v0.9.4
[276daf66] SpecialFunctions v0.10.0
[90137ffa] StaticArrays v0.12.2
[2913bbd2] StatsBase v0.33.0
[4c63d2b9] StatsFuns v0.9.4
[3eaba693] StatsModels v0.6.11
[09ab397b] StructArrays v0.4.3
[7522ee7d] SweepOperator v0.3.0
[3783bdb8] TableTraits v1.0.0
[382cd787] TableTraitsUtils v1.0.1
[bd369af6] Tables v1.0.4
[e0df1984] TextParse v1.0.0
[f269a46b] TimeZones v1.1.1
[0796e94c] Tokenize v0.5.8
[3bb67fe8] TranscodingStreams v0.9.5
[30578b45] URIParser v0.4.1
[1986cc42] Unitful v1.1.0
[81def892] VersionParsing v1.2.0
[ea10d353] WeakRefStrings v0.6.2
[1b915085] WinReg v0.3.1
[efce3f68] WoodburyMatrices v0.5.2
[02c8fc9c] XML2_jll v2.9.9+4
[83775a58] Zlib_jll v1.2.11+9
[0ac62f75] libass_jll v0.14.0+1
[f638f0a6] libfdk_aac_jll v0.1.6+1
[f27f6e37] libvorbis_jll v1.3.6+2
[1270edf5] x264_jll v2019.5.25+1
[dfaa095f] x265_jll v3.0.0+0
[2a0f44e3] Base64
[ade2ca70] Dates
[8bb1440f] DelimitedFiles
[8ba89e20] Distributed
[9fa8497b] Future
[b77e0a4c] InteractiveUtils
[76f85450] LibGit2
[8f399da3] Libdl
[37e2e46d] LinearAlgebra
[56ddb016] Logging
[d6f4376e] Markdown
[a63ad114] Mmap
[44cfe95a] Pkg
[de0858da] Printf
[9abbd945] Profile
[3fa0cd96] REPL
[9a3f8284] Random
[ea8e919c] SHA
[9e88b42a] Serialization
[1a1011a3] SharedArrays
[6462fe0b] Sockets
[2f01184e] SparseArrays
[10745b16] Statistics
[4607b0f0] SuiteSparse
[8dfed614] Test
[cf7118a7] UUIDs
[4ec0a83e] Unicode
[ Info: Running tests for files:
= AbioticEnv.jl
= AdditionalDiversity.jl
= Demographics.jl
= Ecosystem.jl
= Energy.jl
= EpiEnv.jl
= EpiGenerate.jl
= EpiHelper.jl
= EpiLandscape.jl
= EpiList.jl
= EpiParams.jl
= EpiSystem.jl
= EpiTraits.jl
= Generate.jl
= HabitatUpdate.jl
= Helper.jl
= Movement.jl
= SpeciesList.jl
= TraitRelationship.jl
= Traits.jl
[ Info: Running tests...
* Testing AbioticEnv.jl ...
WARNING: Method definition abbr(Unitful.Unit{:Year, Unitful.Dimensions{(Unitful.Dimension{:Time}(power=Base.Rational{Int64}(num=1, den=1)),)}()}) in module Unitful at /root/.julia/packages/Unitful/PZjMS/src/user.jl:178 overwritten in module Units at /root/.julia/packages/Unitful/PZjMS/src/user.jl:178.
** incremental compilation may be fatally broken for this module **
┌ Warning: Use of `Poly` from v1.0 forward will require `using Polynomials.PolyCompat`
│ caller = Polynomials.PolyCompat.Poly(::Array{Double64,1}) at Poly.jl:26
└ @ Polynomials.PolyCompat ~/.julia/packages/Polynomials/ghqdF/src/polynomials/Poly.jl:26
┌ Warning: `@get!(dict, key, default)` at /root/.julia/packages/Dagger/sdZXi/src/compute.jl:74 is deprecated, use `get!(()->default, dict, key)` instead.
│ caller = #macroexpand#38 at expr.jl:108 [inlined]
└ @ Core ./expr.jl:108
ERROR: LoadError: LoadError: UndefVarError: Weight not defined
Stacktrace:
[1] top-level scope at /root/.julia/packages/OnlineStats/iY7aT/src/viz/recipes.jl:2
[2] include(::Function, ::Module, ::String) at ./Base.jl:382
[3] include at ./Base.jl:370 [inlined]
[4] include(::String) at /root/.julia/packages/OnlineStats/iY7aT/src/OnlineStats.jl:1
[5] top-level scope at /root/.julia/packages/OnlineStats/iY7aT/src/OnlineStats.jl:65
[6] include(::Function, ::Module, ::String) at ./Base.jl:382
[7] include(::Module, ::String) at ./Base.jl:370
[8] top-level scope at none:2
[9] eval at ./boot.jl:331 [inlined]
[10] eval(::Expr) at ./client.jl:467
[11] top-level scope at ./none:3
in expression starting at /root/.julia/packages/OnlineStats/iY7aT/src/viz/recipes.jl:2
in expression starting at /root/.julia/packages/OnlineStats/iY7aT/src/OnlineStats.jl:65
ERROR: LoadError: Failed to precompile OnlineStats [a15396b6-48d5-5d58-9928-6d29437db91e] to /root/.julia/compiled/v1.5/OnlineStats/G3mU6_DKDXO.ji.
Stacktrace:
[1] error(::String) at ./error.jl:33
[2] compilecache(::Base.PkgId, ::String) at ./loading.jl:1289
[3] _require(::Base.PkgId) at ./loading.jl:1029
[4] require(::Base.PkgId) at ./loading.jl:927
[5] require(::Module, ::Symbol) at ./loading.jl:922
[6] include(::Function, ::Module, ::String) at ./Base.jl:382
[7] include(::Module, ::String) at ./Base.jl:370
[8] top-level scope at none:2
[9] eval at ./boot.jl:331 [inlined]
[10] eval(::Expr) at ./client.jl:467
[11] top-level scope at ./none:3
in expression starting at /root/.julia/packages/JuliaDB/7cG1k/src/JuliaDB.jl:21
ERROR: LoadError: LoadError: LoadError: Failed to precompile JuliaDB [a93385a2-3734-596a-9a66-3cfbb77141e6] to /root/.julia/compiled/v1.5/JuliaDB/4FA8g_DKDXO.ji.
Stacktrace:
[1] error(::String) at ./error.jl:33
[2] compilecache(::Base.PkgId, ::String) at ./loading.jl:1289
[3] _require(::Base.PkgId) at ./loading.jl:1029
[4] require(::Base.PkgId) at ./loading.jl:927
[5] require(::Module, ::Symbol) at ./loading.jl:922
[6] include(::Function, ::Module, ::String) at ./Base.jl:382
[7] include at ./Base.jl:370 [inlined]
[8] include(::String) at /root/.julia/packages/Simulation/mPQIb/src/Simulation.jl:41
[9] top-level scope at /root/.julia/packages/Simulation/mPQIb/src/ClimatePref/ClimatePref.jl:18
[10] include(::Function, ::Module, ::String) at ./Base.jl:382
[11] include at ./Base.jl:370 [inlined]
[12] include(::String) at /root/.julia/packages/Simulation/mPQIb/src/Simulation.jl:41
[13] top-level scope at /root/.julia/packages/Simulation/mPQIb/src/Simulation.jl:43
[14] include(::Function, ::Module, ::String) at ./Base.jl:382
[15] include(::Module, ::String) at ./Base.jl:370
[16] top-level scope at none:2
[17] eval at ./boot.jl:331 [inlined]
[18] eval(::Expr) at ./client.jl:467
[19] top-level scope at ./none:3
in expression starting at /root/.julia/packages/Simulation/mPQIb/src/ClimatePref/ReadGBIF.jl:1
in expression starting at /root/.julia/packages/Simulation/mPQIb/src/ClimatePref/ClimatePref.jl:18
in expression starting at /root/.julia/packages/Simulation/mPQIb/src/Simulation.jl:43
ERROR: LoadError: LoadError: Failed to precompile Simulation [ed2dc23b-ada4-5fdb-a26f-56368a14ad8f] to /root/.julia/compiled/v1.5/Simulation/zj4lo_DKDXO.ji.
Stacktrace:
[1] error(::String) at ./error.jl:33
[2] compilecache(::Base.PkgId, ::String) at ./loading.jl:1289
[3] _require(::Base.PkgId) at ./loading.jl:1029
[4] require(::Base.PkgId) at ./loading.jl:927
[5] require(::Module, ::Symbol) at ./loading.jl:922
[6] include(::String) at ./client.jl:457
[7] top-level scope at /root/.julia/packages/Simulation/mPQIb/test/runtests.jl:20
[8] include(::String) at ./client.jl:457
[9] top-level scope at none:6
in expression starting at /root/.julia/packages/Simulation/mPQIb/test/test_AbioticEnv.jl:1
in expression starting at /root/.julia/packages/Simulation/mPQIb/test/runtests.jl:17
ERROR: Package Simulation errored during testing
I'll see what I need to do to get the tests running.
I installed R from these instructions https://linuxize.com/post/how-to-install-r-on-ubuntu-18-04/, and installed MPI from apt install mpich
. I didn't have to specify a JULIA_MPI_PATH
for julia to find it.
Unnecessary
I should have pkg> test Simulation#epi
, then no need to downgrade.
############# Original below #############
Having downgraded a couple of packages:
pkg> add IndexedTables@0.12.5
pkg> add OnlineStats@1.01
(simulation_env) pkg> test Simulation
Testing Simulation
Status `/tmp/jl_vG0BlH/Project.toml`
[c9ce4bd3] ArchGDAL v0.3.2
[39de3d68] AxisArrays v0.4.3
[49dc2e85] Calculus v0.5.1
[34da2185] Compat v3.8.0
[a93c6f00] DataFrames v0.20.0
[31c24e10] Distributions v0.23.2
[d3d5718d] Diversity v0.5.1
[a58aae7d] EcoBase v0.1.3
[becb17da] Feather v0.5.4
[19dc6840] HCubature v1.4.0
[6deec6e2] IndexedTables v0.12.5
[a98d9a8b] Interpolations v0.12.9
[4138dd39] JLD v0.10.0
[a93385a2] JuliaDB v0.13.0
[da04e1cc] MPI v0.13.1
[e1d29d7a] Missings v0.4.3
[30363a11] NetCDF v0.10.2
[429524aa] Optim v0.20.6
[aea672f4] Phylo v0.4.2
[91a5bcdd] Plots v0.27.1
[6f49c342] RCall v0.13.4
[3cdcf5f2] RecipesBase v0.8.0
[ae029012] Requires v1.0.1
[ed2dc23b] Simulation v0.0.0 `https://github.com/ScottishCovidResponse/Simulation.jl.git#epi`
[348f2d5d] SpatialEcology v0.9.4
[2913bbd2] StatsBase v0.32.2
[1986cc42] Unitful v1.1.0
[ade2ca70] Dates
[76f85450] LibGit2
[8f399da3] Libdl
[37e2e46d] LinearAlgebra
[56ddb016] Logging
[d6f4376e] Markdown
[de0858da] Printf
[3fa0cd96] REPL
[9a3f8284] Random
[ea8e919c] SHA
[10745b16] Statistics
[8dfed614] Test
[cf7118a7] UUIDs
Status `/tmp/jl_vG0BlH/Manifest.toml`
[c9ce4bd3] ArchGDAL v0.3.2
[ec485272] ArnoldiMethod v0.0.4
[7d9fca2a] Arpack v0.4.0
[68821587] Arpack_jll v3.5.0+3
[4fba245c] ArrayInterface v2.8.5
[69666777] Arrow v0.2.4
[13072b0f] AxisAlgorithms v1.0.0
[39de3d68] AxisArrays v0.4.3
[9e28174c] BinDeps v1.0.1
[b99e7846] BinaryProvider v0.5.8
[a74b3585] Blosc v0.6.0
[6e34b625] Bzip2_jll v1.0.6+2
[fa961155] CEnum v0.2.0
[631607c0] CMake v1.2.0
[d5fb7624] CMakeWrapper v0.2.3
[49dc2e85] Calculus v0.5.1
[324d7699] CategoricalArrays v0.7.7
[944b1d66] CodecZlib v0.6.0
[35d6a980] ColorSchemes v3.8.0
[3da002f7] ColorTypes v0.10.2
[5ae59095] Colors v0.12.0
[861a8166] Combinatorics v1.0.1
[bbf7d656] CommonSubexpressions v0.2.0
[34da2185] Compat v3.8.0
[e66e0078] CompilerSupportLibraries_jll v0.3.3+0
[8f4d0f93] Conda v1.4.1
[a9693cdc] CondaBinDeps v0.2.0
[187b0558] ConstructionBase v1.0.0
[d38c429a] Contour v0.5.2
[d58978e5] Dagger v0.8.0
[9a962f9c] DataAPI v1.2.0
[a93c6f00] DataFrames v0.20.0
[1313f7d8] DataFramesMeta v0.5.0
[9a8bc11e] DataStreams v0.4.2
[864edb3b] DataStructures v0.17.13
[e2d170a0] DataValueInterfaces v1.0.0
[e7dc6d0d] DataValues v0.4.13
[163ba53b] DiffResults v1.0.2
[b552c78f] DiffRules v1.0.1
[3c3547ce] DiskArrays v0.2.3
[b4f34e82] Distances v0.8.2
[31c24e10] Distributions v0.23.2
[d3d5718d] Diversity v0.5.1
[ffbed154] DocStringExtensions v0.8.1
[497a8b3b] DoubleFloats v1.1.8
[a58aae7d] EcoBase v0.1.3
[da5c29d0] EllipsisNotation v0.4.0
[e2ba6199] ExprTools v0.1.1
[8f5d6c58] EzXML v1.1.0
[c87230d0] FFMPEG v0.3.0
[b22a6f82] FFMPEG_jll v4.1.0+2
[becb17da] Feather v0.5.4
[5789e2e9] FileIO v1.2.4
[1a297f60] FillArrays v0.8.7
[6a86dc24] FiniteDiff v2.3.0
[53c48c17] FixedPointNumbers v0.8.0
[53afe959] FlatBuffers v0.5.4
[59287772] Formatting v0.4.1
[f6369f11] ForwardDiff v0.10.10
[d7e528f0] FreeType2_jll v2.10.1+2
[559328eb] FriBidi_jll v1.0.5+2
[add2ef01] GDAL v1.1.0
[a7073274] GDAL_jll v3.0.4+0
[d604d12d] GEOS_jll v3.8.1+0
[28b8d3ca] GR v0.48.0
[01680d73] GenericSVD v0.3.0
[c145ed77] GenericSchur v0.4.0
[68eda718] GeoFormatTypes v0.3.0
[cf35fbd7] GeoInterface v0.5.4
[4d00f742] GeometryTypes v0.8.2
[c27321d9] Glob v1.3.0
[19dc6840] HCubature v1.4.0
[f67ccb44] HDF5 v0.13.1
[0234f1f7] HDF5_jll v1.10.5+5
[6deec6e2] IndexedTables v0.12.5
[d25df0c9] Inflate v0.1.2
[a98d9a8b] Interpolations v0.12.9
[8197267c] IntervalSets v0.5.0
[d8418881] Intervals v1.1.0
[41ab1584] InvertedIndices v1.0.0
[c8e1da08] IterTools v1.3.0
[1c8ee90f] IterableTables v1.0.0
[82899510] IteratorInterfaceExtensions v1.0.0
[4138dd39] JLD v0.10.0
[682c06a0] JSON v0.21.0
[a93385a2] JuliaDB v0.13.0
[c1c5ebd0] LAME_jll v3.100.0+0
[7f8f8fb0] LearnBase v0.2.2
[deac9b47] LibCURL_jll v7.68.0+0
[29816b5a] LibSSH2_jll v1.9.0+1
[dd192d2f] LibVPX_jll v1.8.1+1
[94ce4f54] Libiconv_jll v1.16.0+2
[093fc24a] LightGraphs v1.3.2
[d3d80556] LineSearches v7.0.1
[30fc2ffe] LossFunctions v0.5.1
[da04e1cc] MPI v0.13.1
[1914dd2f] MacroTools v0.5.5
[c8ffd9c3] MbedTLS_jll v2.16.0+2
[442fdcdd] Measures v0.3.1
[f9f48841] MemPool v0.2.0
[e1d29d7a] Missings v0.4.3
[78c3b35d] Mocking v0.7.1
[d41bc354] NLSolversBase v7.6.1
[77ba4419] NaNMath v0.3.3
[30363a11] NetCDF v0.10.2
[4d1e1d77] Nullables v1.0.0
[6fe1bfb0] OffsetArrays v1.0.4
[e7412a2a] Ogg_jll v1.3.3+0
[a15396b6] OnlineStats v1.1.0
[925886fa] OnlineStatsBase v1.1.0
[4536629a] OpenBLAS_jll v0.3.9+2
[458c3c95] OpenSSL_jll v1.1.1+2
[efe28fd5] OpenSpecFun_jll v0.5.3+3
[429524aa] Optim v0.20.6
[91d4177d] Opus_jll v1.3.1+0
[bac558e1] OrderedCollections v1.1.0
[90014a1f] PDMats v0.9.12
[58948b4f] PROJ_jll v6.3.0+0
[d96e819e] Parameters v0.12.0
[69de0a69] Parsers v1.0.2
[06bb1623] PenaltyFunctions v0.1.2
[aea672f4] Phylo v0.4.2
[ccf2f8ad] PlotThemes v2.0.0
[995b91a9] PlotUtils v1.0.0
[91a5bcdd] Plots v0.27.1
[f27b6e38] Polynomials v0.8.0
[2dfb63ee] PooledArrays v0.5.3
[85a6dd25] PositiveFactorizations v0.2.3
[1fd47b50] QuadGK v2.3.1
[be4d8f0f] Quadmath v0.5.4
[6f49c342] RCall v0.13.4
[9ae346a0] RandomBooleanMatrices v0.1.1
[e6cf234a] RandomNumbers v1.4.0
[b3c3ace0] RangeArrays v0.3.2
[c84ed2f1] Ratios v0.4.0
[3cdcf5f2] RecipesBase v0.8.0
[189a3867] Reexport v0.2.0
[ae029012] Requires v1.0.1
[79098fc4] Rmath v0.6.1
[f50d1b31] Rmath_jll v0.2.2+0
[76ed43ae] SQLite_jll v3.31.1+0
[1277b4bf] ShiftedArrays v1.0.0
[992d4aef] Showoff v0.3.1
[699a6c99] SimpleTraits v0.9.2
[ed2dc23b] Simulation v0.0.0 `https://github.com/ScottishCovidResponse/Simulation.jl.git#epi`
[a2af1166] SortingAlgorithms v0.3.1
[348f2d5d] SpatialEcology v0.9.4
[276daf66] SpecialFunctions v0.10.0
[90137ffa] StaticArrays v0.12.2
[2913bbd2] StatsBase v0.32.2
[4c63d2b9] StatsFuns v0.9.4
[3eaba693] StatsModels v0.6.11
[09ab397b] StructArrays v0.4.1
[7522ee7d] SweepOperator v0.3.0
[3783bdb8] TableTraits v1.0.0
[382cd787] TableTraitsUtils v1.0.1
[bd369af6] Tables v0.2.11
[e0df1984] TextParse v1.0.0
[f269a46b] TimeZones v1.1.1
[0796e94c] Tokenize v0.5.8
[3bb67fe8] TranscodingStreams v0.9.5
[30578b45] URIParser v0.4.1
[1986cc42] Unitful v1.1.0
[81def892] VersionParsing v1.2.0
[ea10d353] WeakRefStrings v0.6.2
[1b915085] WinReg v0.3.1
[efce3f68] WoodburyMatrices v0.5.2
[02c8fc9c] XML2_jll v2.9.9+4
[83775a58] Zlib_jll v1.2.11+9
[0ac62f75] libass_jll v0.14.0+1
[f638f0a6] libfdk_aac_jll v0.1.6+1
[f27f6e37] libvorbis_jll v1.3.6+2
[1270edf5] x264_jll v2019.5.25+1
[dfaa095f] x265_jll v3.0.0+0
[2a0f44e3] Base64
[ade2ca70] Dates
[8bb1440f] DelimitedFiles
[8ba89e20] Distributed
[9fa8497b] Future
[b77e0a4c] InteractiveUtils
[76f85450] LibGit2
[8f399da3] Libdl
[37e2e46d] LinearAlgebra
[56ddb016] Logging
[d6f4376e] Markdown
[a63ad114] Mmap
[44cfe95a] Pkg
[de0858da] Printf
[9abbd945] Profile
[3fa0cd96] REPL
[9a3f8284] Random
[ea8e919c] SHA
[9e88b42a] Serialization
[1a1011a3] SharedArrays
[6462fe0b] Sockets
[2f01184e] SparseArrays
[10745b16] Statistics
[4607b0f0] SuiteSparse
[8dfed614] Test
[cf7118a7] UUIDs
[4ec0a83e] Unicode
[ Info: Running tests for files:
= AbioticEnv.jl
= AdditionalDiversity.jl
= Demographics.jl
= Ecosystem.jl
= Energy.jl
= EpiEnv.jl
= EpiGenerate.jl
= EpiHelper.jl
= EpiLandscape.jl
= EpiList.jl
= EpiParams.jl
= EpiSystem.jl
= EpiTraits.jl
= Generate.jl
= HabitatUpdate.jl
= Helper.jl
= Movement.jl
= SpeciesList.jl
= TraitRelationship.jl
= Traits.jl
[ Info: Running tests...
* Testing AbioticEnv.jl ...
WARNING: Method definition abbr(Unitful.Unit{:Year, Unitful.Dimensions{(Unitful.Dimension{:Time}(power=Base.Rational{Int64}(num=1, den=1)),)}()}) in module Unitful at /root/.julia/packages/Unitful/PZjMS/src/user.jl:178 overwritten in module Units at /root/.julia/packages/Unitful/PZjMS/src/user.jl:178.
** incremental compilation may be fatally broken for this module **
┌ Warning: Use of `Poly` from v1.0 forward will require `using Polynomials.PolyCompat`
│ caller = Polynomials.PolyCompat.Poly(::Array{Double64,1}) at Poly.jl:26
└ @ Polynomials.PolyCompat ~/.julia/packages/Polynomials/ghqdF/src/polynomials/Poly.jl:26
┌ Warning: `@get!(dict, key, default)` at /root/.julia/packages/Dagger/sdZXi/src/compute.jl:74 is deprecated, use `get!(()->default, dict, key)` instead.
│ caller = #macroexpand#38 at expr.jl:108 [inlined]
└ @ Core ./expr.jl:108
WARNING: Compat.Random is deprecated, use Random instead.
likely near /root/.julia/packages/Simulation/mPQIb/src/Biodiversity/Landscape.jl:3
WARNING: Compat.Random is deprecated, use Random instead.
likely near /root/.julia/packages/Simulation/mPQIb/src/Biodiversity/Cache.jl:4
Creating Diversity to Phylo interface...
WARNING: Compat.Test is deprecated, use Test instead.
likely near /root/.julia/packages/Simulation/mPQIb/test/test_AbioticEnv.jl:3
* Testing AdditionalDiversity.jl ...
Creating Phylo RCall interface...
ERROR: LoadError: LoadError: TypeError: in BinaryTree, in RT, expected RT<:Phylo.Rooted, got Type{DataFrames.DataFrame}
Stacktrace:
[1] SpeciesList(::Int64, ::Int64, ::Array{Int64,1}, ::SolarRequirement, ::BirthOnlyMovement{GaussianKernel,NoBoundary}, ::EqualPop{Unitful.FreeUnits{(month^-1,),𝐓^-1,nothing}}, ::Array{Bool,1}, ::Array{Float64,1}) at /root/.julia/packages/Simulation/mPQIb/src/Biodiversity/SpeciesList.jl:76
[2] SpeciesList at /root/.julia/packages/Simulation/mPQIb/src/Biodiversity/SpeciesList.jl:101 [inlined]
[3] TestEcosystem() at /root/.julia/packages/Simulation/mPQIb/test/TestCases.jl:34
[4] top-level scope at /root/.julia/packages/Simulation/mPQIb/test/test_AdditionalDiversity.jl:9
[5] include(::String) at ./client.jl:457
[6] top-level scope at /root/.julia/packages/Simulation/mPQIb/test/runtests.jl:20
[7] include(::String) at ./client.jl:457
[8] top-level scope at none:6
in expression starting at /root/.julia/packages/Simulation/mPQIb/test/test_AdditionalDiversity.jl:9
in expression starting at /root/.julia/packages/Simulation/mPQIb/test/runtests.jl:17
ERROR: Package Simulation errored during testing
(simulation_env) pkg> test Simulation#epi
Testing Simulation
Status `/tmp/jl_7HXZUM/Project.toml`
[c9ce4bd3] ArchGDAL v0.3.2
[39de3d68] AxisArrays v0.4.3
[49dc2e85] Calculus v0.5.1
[34da2185] Compat v3.8.0
[a93c6f00] DataFrames v0.20.0
[31c24e10] Distributions v0.23.2
[d3d5718d] Diversity v0.5.1
[a58aae7d] EcoBase v0.1.3
[becb17da] Feather v0.5.4
[19dc6840] HCubature v1.4.0
[6deec6e2] IndexedTables v0.12.6
[a98d9a8b] Interpolations v0.12.9
[4138dd39] JLD v0.10.0
[a93385a2] JuliaDB v0.13.0
[da04e1cc] MPI v0.13.1
[e1d29d7a] Missings v0.4.3
[30363a11] NetCDF v0.10.2
[429524aa] Optim v0.20.6
[aea672f4] Phylo v0.4.2
[91a5bcdd] Plots v0.27.1
[6f49c342] RCall v0.13.4
[3cdcf5f2] RecipesBase v0.8.0
[ae029012] Requires v1.0.1
[ed2dc23b] Simulation v0.0.0 `https://github.com/ScottishCovidResponse/Simulation.jl.git#epi`
[348f2d5d] SpatialEcology v0.9.4
[2913bbd2] StatsBase v0.32.2
[1986cc42] Unitful v1.1.0
[ade2ca70] Dates
[76f85450] LibGit2
[8f399da3] Libdl
[37e2e46d] LinearAlgebra
[56ddb016] Logging
[d6f4376e] Markdown
[de0858da] Printf
[3fa0cd96] REPL
[9a3f8284] Random
[ea8e919c] SHA
[10745b16] Statistics
[8dfed614] Test
[cf7118a7] UUIDs
Status `/tmp/jl_7HXZUM/Manifest.toml`
[1520ce14] AbstractTrees v0.3.3
[c9ce4bd3] ArchGDAL v0.3.2
[ec485272] ArnoldiMethod v0.0.4
[7d9fca2a] Arpack v0.4.0
[68821587] Arpack_jll v3.5.0+3
[4fba245c] ArrayInterface v2.8.5
[69666777] Arrow v0.2.4
[13072b0f] AxisAlgorithms v1.0.0
[39de3d68] AxisArrays v0.4.3
[9e28174c] BinDeps v1.0.1
[b99e7846] BinaryProvider v0.5.8
[a74b3585] Blosc v0.6.0
[6e34b625] Bzip2_jll v1.0.6+2
[fa961155] CEnum v0.2.0
[631607c0] CMake v1.2.0
[d5fb7624] CMakeWrapper v0.2.3
[49dc2e85] Calculus v0.5.1
[324d7699] CategoricalArrays v0.7.7
[944b1d66] CodecZlib v0.6.0
[35d6a980] ColorSchemes v3.8.0
[3da002f7] ColorTypes v0.10.2
[5ae59095] Colors v0.12.0
[861a8166] Combinatorics v1.0.1
[bbf7d656] CommonSubexpressions v0.2.0
[34da2185] Compat v3.8.0
[e66e0078] CompilerSupportLibraries_jll v0.3.3+0
[8f4d0f93] Conda v1.4.1
[a9693cdc] CondaBinDeps v0.2.0
[187b0558] ConstructionBase v1.0.0
[d38c429a] Contour v0.5.2
[d58978e5] Dagger v0.8.0
[9a962f9c] DataAPI v1.2.0
[a93c6f00] DataFrames v0.20.0
[1313f7d8] DataFramesMeta v0.5.0
[9a8bc11e] DataStreams v0.4.2
[864edb3b] DataStructures v0.17.13
[e2d170a0] DataValueInterfaces v1.0.0
[e7dc6d0d] DataValues v0.4.13
[163ba53b] DiffResults v1.0.2
[b552c78f] DiffRules v1.0.1
[3c3547ce] DiskArrays v0.2.3
[b4f34e82] Distances v0.8.2
[31c24e10] Distributions v0.23.2
[d3d5718d] Diversity v0.5.1
[ffbed154] DocStringExtensions v0.8.1
[497a8b3b] DoubleFloats v1.1.8
[a58aae7d] EcoBase v0.1.3
[da5c29d0] EllipsisNotation v0.4.0
[e2ba6199] ExprTools v0.1.1
[8f5d6c58] EzXML v1.1.0
[c87230d0] FFMPEG v0.3.0
[b22a6f82] FFMPEG_jll v4.1.0+2
[becb17da] Feather v0.5.4
[5789e2e9] FileIO v1.2.4
[1a297f60] FillArrays v0.8.7
[6a86dc24] FiniteDiff v2.3.0
[53c48c17] FixedPointNumbers v0.8.0
[53afe959] FlatBuffers v0.5.4
[59287772] Formatting v0.4.1
[f6369f11] ForwardDiff v0.10.10
[d7e528f0] FreeType2_jll v2.10.1+2
[559328eb] FriBidi_jll v1.0.5+2
[add2ef01] GDAL v1.1.0
[a7073274] GDAL_jll v3.0.4+0
[d604d12d] GEOS_jll v3.8.1+0
[28b8d3ca] GR v0.48.0
[01680d73] GenericSVD v0.3.0
[c145ed77] GenericSchur v0.4.0
[68eda718] GeoFormatTypes v0.3.0
[cf35fbd7] GeoInterface v0.5.4
[4d00f742] GeometryTypes v0.8.2
[c27321d9] Glob v1.3.0
[19dc6840] HCubature v1.4.0
[f67ccb44] HDF5 v0.13.1
[0234f1f7] HDF5_jll v1.10.5+5
[6deec6e2] IndexedTables v0.12.6
[d25df0c9] Inflate v0.1.2
[a98d9a8b] Interpolations v0.12.9
[8197267c] IntervalSets v0.5.0
[d8418881] Intervals v1.1.0
[41ab1584] InvertedIndices v1.0.0
[c8e1da08] IterTools v1.3.0
[1c8ee90f] IterableTables v1.0.0
[82899510] IteratorInterfaceExtensions v1.0.0
[4138dd39] JLD v0.10.0
[682c06a0] JSON v0.21.0
[a93385a2] JuliaDB v0.13.0
[c1c5ebd0] LAME_jll v3.100.0+0
[7f8f8fb0] LearnBase v0.2.2
[deac9b47] LibCURL_jll v7.68.0+0
[29816b5a] LibSSH2_jll v1.9.0+1
[dd192d2f] LibVPX_jll v1.8.1+1
[94ce4f54] Libiconv_jll v1.16.0+2
[093fc24a] LightGraphs v1.3.2
[d3d80556] LineSearches v7.0.1
[30fc2ffe] LossFunctions v0.5.1
[da04e1cc] MPI v0.13.1
[1914dd2f] MacroTools v0.5.5
[c8ffd9c3] MbedTLS_jll v2.16.0+2
[442fdcdd] Measures v0.3.1
[f9f48841] MemPool v0.2.0
[e1d29d7a] Missings v0.4.3
[78c3b35d] Mocking v0.7.1
[d41bc354] NLSolversBase v7.6.1
[77ba4419] NaNMath v0.3.3
[30363a11] NetCDF v0.10.2
[4d1e1d77] Nullables v1.0.0
[6fe1bfb0] OffsetArrays v1.0.4
[e7412a2a] Ogg_jll v1.3.3+0
[a15396b6] OnlineStats v1.2.0
[925886fa] OnlineStatsBase v1.2.8
[4536629a] OpenBLAS_jll v0.3.9+2
[458c3c95] OpenSSL_jll v1.1.1+2
[efe28fd5] OpenSpecFun_jll v0.5.3+3
[429524aa] Optim v0.20.6
[91d4177d] Opus_jll v1.3.1+0
[bac558e1] OrderedCollections v1.1.0
[90014a1f] PDMats v0.9.12
[58948b4f] PROJ_jll v6.3.0+0
[d96e819e] Parameters v0.12.0
[69de0a69] Parsers v1.0.2
[06bb1623] PenaltyFunctions v0.1.2
[aea672f4] Phylo v0.4.2
[ccf2f8ad] PlotThemes v2.0.0
[995b91a9] PlotUtils v1.0.0
[91a5bcdd] Plots v0.27.1
[f27b6e38] Polynomials v0.8.0
[2dfb63ee] PooledArrays v0.5.3
[85a6dd25] PositiveFactorizations v0.2.3
[1fd47b50] QuadGK v2.3.1
[be4d8f0f] Quadmath v0.5.4
[6f49c342] RCall v0.13.4
[9ae346a0] RandomBooleanMatrices v0.1.1
[e6cf234a] RandomNumbers v1.4.0
[b3c3ace0] RangeArrays v0.3.2
[c84ed2f1] Ratios v0.4.0
[3cdcf5f2] RecipesBase v0.8.0
[189a3867] Reexport v0.2.0
[ae029012] Requires v1.0.1
[79098fc4] Rmath v0.6.1
[f50d1b31] Rmath_jll v0.2.2+0
[76ed43ae] SQLite_jll v3.31.1+0
[1277b4bf] ShiftedArrays v1.0.0
[992d4aef] Showoff v0.3.1
[699a6c99] SimpleTraits v0.9.2
[ed2dc23b] Simulation v0.0.0 `https://github.com/ScottishCovidResponse/Simulation.jl.git#epi`
[a2af1166] SortingAlgorithms v0.3.1
[348f2d5d] SpatialEcology v0.9.4
[276daf66] SpecialFunctions v0.10.0
[90137ffa] StaticArrays v0.12.2
[2913bbd2] StatsBase v0.32.2
[4c63d2b9] StatsFuns v0.9.4
[3eaba693] StatsModels v0.6.11
[09ab397b] StructArrays v0.4.1
[7522ee7d] SweepOperator v0.3.0
[3783bdb8] TableTraits v1.0.0
[382cd787] TableTraitsUtils v1.0.1
[bd369af6] Tables v0.2.11
[e0df1984] TextParse v1.0.0
[f269a46b] TimeZones v1.1.1
[0796e94c] Tokenize v0.5.8
[3bb67fe8] TranscodingStreams v0.9.5
[30578b45] URIParser v0.4.1
[1986cc42] Unitful v1.1.0
[81def892] VersionParsing v1.2.0
[ea10d353] WeakRefStrings v0.6.2
[1b915085] WinReg v0.3.1
[efce3f68] WoodburyMatrices v0.5.2
[02c8fc9c] XML2_jll v2.9.9+4
[83775a58] Zlib_jll v1.2.11+9
[0ac62f75] libass_jll v0.14.0+1
[f638f0a6] libfdk_aac_jll v0.1.6+1
[f27f6e37] libvorbis_jll v1.3.6+2
[1270edf5] x264_jll v2019.5.25+1
[dfaa095f] x265_jll v3.0.0+0
[2a0f44e3] Base64
[ade2ca70] Dates
[8bb1440f] DelimitedFiles
[8ba89e20] Distributed
[9fa8497b] Future
[b77e0a4c] InteractiveUtils
[76f85450] LibGit2
[8f399da3] Libdl
[37e2e46d] LinearAlgebra
[56ddb016] Logging
[d6f4376e] Markdown
[a63ad114] Mmap
[44cfe95a] Pkg
[de0858da] Printf
[9abbd945] Profile
[3fa0cd96] REPL
[9a3f8284] Random
[ea8e919c] SHA
[9e88b42a] Serialization
[1a1011a3] SharedArrays
[6462fe0b] Sockets
[2f01184e] SparseArrays
[10745b16] Statistics
[4607b0f0] SuiteSparse
[8dfed614] Test
[cf7118a7] UUIDs
[4ec0a83e] Unicode
[ Info: Running tests for files:
= AbioticEnv.jl
= AdditionalDiversity.jl
= Demographics.jl
= Ecosystem.jl
= Energy.jl
= EpiEnv.jl
= EpiGenerate.jl
= EpiHelper.jl
= EpiLandscape.jl
= EpiList.jl
= EpiParams.jl
= EpiSystem.jl
= EpiTraits.jl
= Generate.jl
= HabitatUpdate.jl
= Helper.jl
= Movement.jl
= SpeciesList.jl
= TraitRelationship.jl
= Traits.jl
[ Info: Running tests...
* Testing AbioticEnv.jl ...
Creating Diversity to Phylo interface...
WARNING: Compat.Test is deprecated, use Test instead.
likely near /root/.julia/packages/Simulation/mPQIb/test/test_AbioticEnv.jl:3
* Testing AdditionalDiversity.jl ...
Creating Phylo RCall interface...
ERROR: LoadError: LoadError: TypeError: in BinaryTree, in RT, expected RT<:Phylo.Rooted, got Type{DataFrames.DataFrame}
Stacktrace:
[1] SpeciesList(::Int64, ::Int64, ::Array{Int64,1}, ::SolarRequirement, ::BirthOnlyMovement{GaussianKernel,NoBoundary}, ::EqualPop{Unitful.FreeUnits{(month^-1,),𝐓^-1,nothing}}, ::Array{Bool,1}, ::Array{Float64,1}) at /root/.julia/packages/Simulation/mPQIb/src/Biodiversity/SpeciesList.jl:76
[2] SpeciesList at /root/.julia/packages/Simulation/mPQIb/src/Biodiversity/SpeciesList.jl:101 [inlined]
[3] TestEcosystem() at /root/.julia/packages/Simulation/mPQIb/test/TestCases.jl:34
[4] top-level scope at /root/.julia/packages/Simulation/mPQIb/test/test_AdditionalDiversity.jl:9
[5] include(::String) at ./client.jl:457
[6] top-level scope at /root/.julia/packages/Simulation/mPQIb/test/runtests.jl:20
[7] include(::String) at ./client.jl:457
[8] top-level scope at none:6
in expression starting at /root/.julia/packages/Simulation/mPQIb/test/test_AdditionalDiversity.jl:9
in expression starting at /root/.julia/packages/Simulation/mPQIb/test/runtests.jl:17
ERROR: Package Simulation errored during testing
Also need to install picante in R.
install.packages("picante", repos="http://R-Forge.R-project.org", dependencies=TRUE)
Downgrade notes:
OnlineStatsBase@1.0.2
Phylo@0.3.3
edit - didn't make the testspass
From a clean docker container:
sudo docker run -it ubuntu:latest
apt update
apt install -y curl
apt install -y vim
apt install -y git
apt install -y gcc
apt install -y g++
apt install -y gfortran
apt install -y mpich
apt install -y apt-transport-https software-properties-common
apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9
add-apt-repository 'deb https://cloud.r-project.org/bin/linux/ubuntu bionic-cran35/'
apt update
apt install -y r-base
R -e 'install.packages("picante", dependencies=TRUE)'
git clone https://github.com/JuliaLang/julia.git
cd julia
git checkout release-1.4
make -j
echo "alias julia=\"$(pwd)/julia\"" >> ~/.bashrc
. ~/.bashrc
cd ..
mkdir env
cd env
julia
using Pkg
Pkg.activate(".")
Pkg.add(PackageSpec(url="https://github.com/ScottishCovidResponse/Simulation.jl.git"))
Pkg.build("Simulation")
Pkg.test("Simulation")
The bits excluding the julia commands could become a Dockerfile
See also https://github.com/ScottishCovidResponse/Simulation.jl/pull/2 for more notes. The missing ingredient was DataAPI
so in summary:
pkg> add Phylo@0.3.3
pkg> add OnlineStats@1.2.0
pkg> add DataAPI@1.2.0
I'm embarrassed to say that Phylo
is my package, and I had enormous difficulties updating that to be compatible with Project.toml
a few weeks ago, but it seemed like we had finally fixed all of the problems. It would be great to work out how that's damaging things so I can fix it.
Simulation.jl builds and tests pass after https://github.com/ScottishCovidResponse/Simulation.jl/pull/3
Using the current master I am still getting errors due to not having the picante
R package. The solution was to manually install it from R. Shouldn't we have this as an automatic step during build
?
We could do - should we also install R itself because I for one had to install it specifically for this project. The same thing could be asked about installing MPI...
Yeah, I also had to install both R and MPI. I am not sure if it's advised against to have something outside of the Julia environment installed when we run build. Is there any option to have an internal R and MPI installation, similar to how Conda.jl has its own internal Python installation?
According the the RCall.jl docs, "RCall.jl will automatically install R for you using Conda if it doesn't detect that you have R 3.4.0 or later installed already."
Conversely, according to the MPI.jl docs, "MPI.jl requires a shared library MPI installation for C (supporting MPI standard 3.0), and a C compiler available via the mpicc command: this is required as part of the build process to determine the necessary type definitions and constants."
So it should be possible to do away with the R installation, but not the MPI.
If you do away with the R installation, then you can't install picante earlier though, and you have to do it in the code. I do this in testing here, with something like:
using RCall
# Create a temporary directory to work in
libdir = mktempdir();
if !rcopy(R"require(picante)")
rcall(Symbol(".libPaths"), libdir);
reval("install.packages(\"picante\", lib=\"$libdir\", repos=\"http://cran.r-project.org\")");
!rcopy(R"require(picante, lib.loc=c(\"$libdir\", .libPaths()))") &&
@warn "ape R package not installed and would not install, skipping R crossvalidation"
end
The reason I installed to a temporary folder was so that it wouldn't interfere with someone's default R installation if RCall is picking that up... picante will only need to be installed for the testing, so it'll slow that down a bit because it'll need to be installed every time, but it should only need to happen then.
However, it looks like this is a test that we could survive without on people's laptops, so we could speed things up by doing the full R and picante installation on travis, but just wrap lines 62-69 in:
if rcopy(R"require(picante)")
...
end
so they will be ignored if you don't have picante installed. Then you might be able to drop the R and picante installation on people's laptops completely...
I can't test any of this because I have (and need) R installed on my laptop, but maybe someone else can?
So it should be possible to do away with the R installation, but not the MPI.
Note that the latest MPI.jl now installs MPI automatically using BinaryBuilder (https://discourse.julialang.org/t/ann-mpi-jl-0-14-changes/39126). But it still takes time.
I made a complete pigs ear of it, but I managed to get caching of the MPI installation working on travis in https://github.com/ScottishCovidResponse/Simulation.jl/pull/21
Close this down. Create a new issue for binary builder as and when.
I needed to
install.packages("picante", repos="http://R-Forge.R-project.org", dependencies=TRUE)
add git@github.com:JuliaBinaryWrappers/PROJ_jll.jl.git
add git@github.com:JuliaBinaryWrappers/GDAL_jll.jl.git
add git@github.com:yeesian/ArchGDAL.jl.git#v0.2.2
add git@github.com:ScottishCovidResponse/Simulation.jl.git
need to create a new env to make sure this is reproducible