Package evaluation of FlashWeave on Julia 1.11.4 (a71dd056e0*) started at 2025-04-08T15:29:44.837 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 6.88s ################################################################################ # Installation # Installing FlashWeave... Resolving package versions... Installed HDF5 ─ v0.16.16 Updating `~/.julia/environments/v1.11/Project.toml` [2be3f83a] + FlashWeave v0.19.2 Updating `~/.julia/environments/v1.11/Manifest.toml` [66dad0bd] + AliasTables v1.1.3 [ec485272] + ArnoldiMethod v0.4.0 [861a8166] + Combinatorics v1.0.2 [34da2185] + Compat v4.16.0 [9a962f9c] + DataAPI v1.16.0 [864edb3b] + DataStructures v0.18.22 [8bb1440f] + DelimitedFiles v1.9.1 [31c24e10] + Distributions v0.25.118 [ffbed154] + DocStringExtensions v0.9.4 [5789e2e9] + FileIO v1.17.0 [1a297f60] + FillArrays v1.13.0 [2be3f83a] + FlashWeave v0.19.2 [86223c79] + Graphs v1.12.1 ⌅ [f67ccb44] + HDF5 v0.16.16 [34004b35] + HypergeometricFunctions v0.3.28 [d25df0c9] + Inflate v0.1.5 [92d709cd] + IrrationalConstants v0.2.4 ⌅ [033835bb] + JLD2 v0.4.54 [692b3bcd] + JLLWrappers v1.7.0 [682c06a0] + JSON v0.21.4 [2ab3a3ac] + LogExpFunctions v0.3.29 [3da0fdf6] + MPIPreferences v0.1.11 [1914dd2f] + MacroTools v0.5.15 [e1d29d7a] + Missings v1.2.0 [bac558e1] + OrderedCollections v1.8.0 [90014a1f] + PDMats v0.11.33 [69de0a69] + Parsers v2.8.1 ⌅ [aea7be01] + PrecompileTools v1.2.1 [21216c6a] + Preferences v1.4.3 [43287f4e] + PtrArrays v1.3.0 [1fd47b50] + QuadGK v2.11.2 [189a3867] + Reexport v1.2.2 [ae029012] + Requires v1.3.1 [79098fc4] + Rmath v0.8.0 [699a6c99] + SimpleTraits v0.9.4 [47aef6b3] + SimpleWeightedGraphs v1.5.0 [a2af1166] + SortingAlgorithms v1.2.1 [276daf66] + SpecialFunctions v2.5.0 [90137ffa] + StaticArrays v1.9.13 [1e83bf80] + StaticArraysCore v1.4.3 [10745b16] + Statistics v1.11.1 [82ae8749] + StatsAPI v1.7.0 ⌅ [2913bbd2] + StatsBase v0.33.21 [4c63d2b9] + StatsFuns v1.4.0 [3bb67fe8] + TranscodingStreams v0.11.3 [0234f1f7] + HDF5_jll v1.14.6+0 [e33a78d0] + Hwloc_jll v2.12.0+0 [7cb0a576] + MPICH_jll v4.3.0+1 [f1f71cc9] + MPItrampoline_jll v5.5.3+0 [9237b28f] + MicrosoftMPI_jll v10.1.4+3 [fe0851c0] + OpenMPI_jll v5.0.7+2 [458c3c95] + OpenSSL_jll v3.0.16+0 [efe28fd5] + OpenSpecFun_jll v0.5.6+0 [f50d1b31] + Rmath_jll v0.5.1+0 [477f73a3] + libaec_jll v1.1.3+0 [0dad84c5] + ArgTools v1.1.2 [56f22d72] + Artifacts v1.11.0 [2a0f44e3] + Base64 v1.11.0 [ade2ca70] + Dates v1.11.0 [8ba89e20] + Distributed v1.11.0 [f43a241f] + Downloads v1.6.0 [7b1f6079] + FileWatching v1.11.0 [b77e0a4c] + InteractiveUtils v1.11.0 [4af54fe1] + LazyArtifacts v1.11.0 [b27032c2] + LibCURL v0.6.4 [76f85450] + LibGit2 v1.11.0 [8f399da3] + Libdl v1.11.0 [37e2e46d] + LinearAlgebra v1.11.0 [56ddb016] + Logging v1.11.0 [d6f4376e] + Markdown v1.11.0 [a63ad114] + Mmap v1.11.0 [ca575930] + NetworkOptions v1.2.0 [44cfe95a] + Pkg v1.11.0 [de0858da] + Printf v1.11.0 [9a3f8284] + Random v1.11.0 [ea8e919c] + SHA v0.7.0 [9e88b42a] + Serialization v1.11.0 [1a1011a3] + SharedArrays v1.11.0 [6462fe0b] + Sockets v1.11.0 [2f01184e] + SparseArrays v1.11.0 [4607b0f0] + SuiteSparse [fa267f1f] + TOML v1.0.3 [a4e569a6] + Tar v1.10.0 [cf7118a7] + UUIDs v1.11.0 [4ec0a83e] + Unicode v1.11.0 [e66e0078] + CompilerSupportLibraries_jll v1.1.1+0 [deac9b47] + LibCURL_jll v8.6.0+0 [e37daf67] + LibGit2_jll v1.7.2+0 [29816b5a] + LibSSH2_jll v1.11.0+1 [c8ffd9c3] + MbedTLS_jll v2.28.6+0 [14a3606d] + MozillaCACerts_jll v2023.12.12 [4536629a] + OpenBLAS_jll v0.3.27+1 [05823500] + OpenLibm_jll v0.8.5+0 [bea87d4a] + SuiteSparse_jll v7.7.0+0 [83775a58] + Zlib_jll v1.2.13+1 [8e850b90] + libblastrampoline_jll v5.11.0+0 [8e850ede] + nghttp2_jll v1.59.0+0 [3f19e933] + p7zip_jll v17.4.0+2 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. To see why use `status --outdated -m` Building HDF5 → `~/.julia/scratchspaces/44cfe95a-1eb2-52ea-b672-e2afdf69b78f/114e20044677badbc631ee6fdc80a67920561a29/build.log` Installation completed after 12.23s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompilation completed after 42.32s ################################################################################ # Testing # Testing FlashWeave Status `/tmp/jl_j4All0/Project.toml` [861a8166] Combinatorics v1.0.2 [864edb3b] DataStructures v0.18.22 [8bb1440f] DelimitedFiles v1.9.1 [31c24e10] Distributions v0.25.118 [5789e2e9] FileIO v1.17.0 [2be3f83a] FlashWeave v0.19.2 [86223c79] Graphs v1.12.1 ⌅ [f67ccb44] HDF5 v0.16.16 ⌅ [033835bb] JLD2 v0.4.54 [682c06a0] JSON v0.21.4 [47aef6b3] SimpleWeightedGraphs v1.5.0 [860ef19b] StableRNGs v1.0.2 [10745b16] Statistics v1.11.1 ⌅ [2913bbd2] StatsBase v0.33.21 [ade2ca70] Dates v1.11.0 [8ba89e20] Distributed v1.11.0 [37e2e46d] LinearAlgebra v1.11.0 [56ddb016] Logging v1.11.0 [9a3f8284] Random v1.11.0 [1a1011a3] SharedArrays v1.11.0 [2f01184e] SparseArrays v1.11.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_j4All0/Manifest.toml` [66dad0bd] AliasTables v1.1.3 [ec485272] ArnoldiMethod v0.4.0 [861a8166] Combinatorics v1.0.2 [34da2185] Compat v4.16.0 [9a962f9c] DataAPI v1.16.0 [864edb3b] DataStructures v0.18.22 [8bb1440f] DelimitedFiles v1.9.1 [31c24e10] Distributions v0.25.118 [ffbed154] DocStringExtensions v0.9.4 [5789e2e9] FileIO v1.17.0 [1a297f60] FillArrays v1.13.0 [2be3f83a] FlashWeave v0.19.2 [86223c79] Graphs v1.12.1 ⌅ [f67ccb44] HDF5 v0.16.16 [34004b35] HypergeometricFunctions v0.3.28 [d25df0c9] Inflate v0.1.5 [92d709cd] IrrationalConstants v0.2.4 ⌅ [033835bb] JLD2 v0.4.54 [692b3bcd] JLLWrappers v1.7.0 [682c06a0] JSON v0.21.4 [2ab3a3ac] LogExpFunctions v0.3.29 [3da0fdf6] MPIPreferences v0.1.11 [1914dd2f] MacroTools v0.5.15 [e1d29d7a] Missings v1.2.0 [bac558e1] OrderedCollections v1.8.0 [90014a1f] PDMats v0.11.33 [69de0a69] Parsers v2.8.1 ⌅ [aea7be01] PrecompileTools v1.2.1 [21216c6a] Preferences v1.4.3 [43287f4e] PtrArrays v1.3.0 [1fd47b50] QuadGK v2.11.2 [189a3867] Reexport v1.2.2 [ae029012] Requires v1.3.1 [79098fc4] Rmath v0.8.0 [699a6c99] SimpleTraits v0.9.4 [47aef6b3] SimpleWeightedGraphs v1.5.0 [a2af1166] SortingAlgorithms v1.2.1 [276daf66] SpecialFunctions v2.5.0 [860ef19b] StableRNGs v1.0.2 [90137ffa] StaticArrays v1.9.13 [1e83bf80] StaticArraysCore v1.4.3 [10745b16] Statistics v1.11.1 [82ae8749] StatsAPI v1.7.0 ⌅ [2913bbd2] StatsBase v0.33.21 [4c63d2b9] StatsFuns v1.4.0 [3bb67fe8] TranscodingStreams v0.11.3 [0234f1f7] HDF5_jll v1.14.6+0 [e33a78d0] Hwloc_jll v2.12.0+0 [7cb0a576] MPICH_jll v4.3.0+1 [f1f71cc9] MPItrampoline_jll v5.5.3+0 [9237b28f] MicrosoftMPI_jll v10.1.4+3 [fe0851c0] OpenMPI_jll v5.0.7+2 [458c3c95] OpenSSL_jll v3.0.16+0 [efe28fd5] OpenSpecFun_jll v0.5.6+0 [f50d1b31] Rmath_jll v0.5.1+0 [477f73a3] libaec_jll v1.1.3+0 [0dad84c5] ArgTools v1.1.2 [56f22d72] Artifacts v1.11.0 [2a0f44e3] Base64 v1.11.0 [ade2ca70] Dates v1.11.0 [8ba89e20] Distributed v1.11.0 [f43a241f] Downloads v1.6.0 [7b1f6079] FileWatching v1.11.0 [b77e0a4c] InteractiveUtils v1.11.0 [4af54fe1] LazyArtifacts v1.11.0 [b27032c2] LibCURL v0.6.4 [76f85450] LibGit2 v1.11.0 [8f399da3] Libdl v1.11.0 [37e2e46d] LinearAlgebra v1.11.0 [56ddb016] Logging v1.11.0 [d6f4376e] Markdown v1.11.0 [a63ad114] Mmap v1.11.0 [ca575930] NetworkOptions v1.2.0 [44cfe95a] Pkg v1.11.0 [de0858da] Printf v1.11.0 [9a3f8284] Random v1.11.0 [ea8e919c] SHA v0.7.0 [9e88b42a] Serialization v1.11.0 [1a1011a3] SharedArrays v1.11.0 [6462fe0b] Sockets v1.11.0 [2f01184e] SparseArrays v1.11.0 [4607b0f0] SuiteSparse [fa267f1f] TOML v1.0.3 [a4e569a6] Tar v1.10.0 [8dfed614] Test v1.11.0 [cf7118a7] UUIDs v1.11.0 [4ec0a83e] Unicode v1.11.0 [e66e0078] CompilerSupportLibraries_jll v1.1.1+0 [deac9b47] LibCURL_jll v8.6.0+0 [e37daf67] LibGit2_jll v1.7.2+0 [29816b5a] LibSSH2_jll v1.11.0+1 [c8ffd9c3] MbedTLS_jll v2.28.6+0 [14a3606d] MozillaCACerts_jll v2023.12.12 [4536629a] OpenBLAS_jll v0.3.27+1 [05823500] OpenLibm_jll v0.8.5+0 [bea87d4a] SuiteSparse_jll v7.7.0+0 [83775a58] Zlib_jll v1.2.13+1 [8e850b90] libblastrampoline_jll v5.11.0+0 [8e850ede] nghttp2_jll v1.59.0+0 [3f19e933] p7zip_jll v17.4.0+2 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. Testing Running tests... Precompiling DistributionsTestExt... 2944.2 ms ✓ Distributions → DistributionsTestExt 1 dependency successfully precompiled in 4 seconds. 48 already precompiled. Preparing tests Test Summary: | Pass Total Time all modules in test set | 1 1 0.4s Testing io.jl Test Summary: | Pass Total Time networks | 4 4 5.8s Test Summary: | Pass Total Time table data | 20 20 15.6s Test Summary: | Pass Total Time transposed | 4 4 0.2s Test Summary: | Pass Total Time string factors | 4 4 0.2s Test Summary: | Pass Total Time numeric IDs | 2 2 1.0s Testing preprocessing.jl ┌ Warning: Adaptive CLR is inefficient with sparse data, using dense format for normalization └ @ FlashWeave ~/.julia/packages/FlashWeave/j91Ng/src/preprocessing.jl:542 ┌ Warning: adaptive pseudo-counts for 1 samples were lower than machine precision due to insufficient counts, removing them └ @ FlashWeave ~/.julia/packages/FlashWeave/j91Ng/src/preprocessing.jl:125 Test Summary: | Pass Total Time clr_adapt eps | 2 2 25.8s ┌ Warning: Adaptive CLR is inefficient with sparse data, using dense format for normalization └ @ FlashWeave ~/.julia/packages/FlashWeave/j91Ng/src/preprocessing.jl:542 ┌ Warning: Adaptive CLR is inefficient with sparse data, using dense format for normalization └ @ FlashWeave ~/.julia/packages/FlashWeave/j91Ng/src/preprocessing.jl:542 ┌ Warning: Adaptive CLR is inefficient with sparse data, using dense format for normalization └ @ FlashWeave ~/.julia/packages/FlashWeave/j91Ng/src/preprocessing.jl:542 ┌ Warning: Adaptive CLR is inefficient with sparse data, using dense format for normalization └ @ FlashWeave ~/.julia/packages/FlashWeave/j91Ng/src/preprocessing.jl:542 Test Summary: | Pass Total Time norm per test type | 20 20 37.8s ┌ Warning: Adaptive CLR is inefficient with sparse data, using dense format for normalization └ @ FlashWeave ~/.julia/packages/FlashWeave/j91Ng/src/preprocessing.jl:542 Test Summary: | Pass Total Time filter data | 12 12 1.4s Test Summary: | Pass Total Time mi_nz fits fz_nz | 1 1 11.1s ┌ Warning: Skipping one-hot encoding, only experts should choose this option └ @ FlashWeave ~/.julia/packages/FlashWeave/j91Ng/src/preprocessing.jl:396 ┌ Warning: Skipping one-hot encoding, only experts should choose this option └ @ FlashWeave ~/.julia/packages/FlashWeave/j91Ng/src/preprocessing.jl:396 ┌ Warning: Skipping one-hot encoding, only experts should choose this option └ @ FlashWeave ~/.julia/packages/FlashWeave/j91Ng/src/preprocessing.jl:396 ┌ Warning: Skipping one-hot encoding, only experts should choose this option └ @ FlashWeave ~/.julia/packages/FlashWeave/j91Ng/src/preprocessing.jl:396 Test Summary: | Pass Total Time meta data | 18 18 17.0s Testing contingency.jl Test Summary: | Pass Total Time dense | 4 4 3.2s Test Summary: | Pass Total Time sparse | 4 4 1.9s Test Summary: | Pass Total Time sparse_ctab all-zero Y /w Nz | 1 1 2.6s Testing statfuns.jl Test Summary: | Pass Total Time correlation | 6 6 7.5s Test Summary: | Pass Total Time mutual information | 4 4 2.3s Test Summary: | Pass Total Time FDR correction | 2 2 1.6s Testing tests.jl Test Summary: | Pass Total Time mi | 3 3 3.4s Test Summary: | Pass Total Time mi_nz | 3 3 0.9s Test Summary: | Pass Total Time fz | 3 3 0.8s Test Summary: | Pass Total Time fz_nz | 3 3 9.1s Testing misc.jl Test Summary: | Pass Total Time precision_conversion | 32 32 1.8s Testing learning.jl (this can take a couple of minutes) Test Summary: | Pass Total Time univar nbrs | 5 5 15.6s ┌ Warning: Skipping normalization, only experts should choose this option └ @ FlashWeave ~/.julia/packages/FlashWeave/j91Ng/src/learning.jl:508 ┌ Warning: Skipping normalization, only experts should choose this option └ @ FlashWeave ~/.julia/packages/FlashWeave/j91Ng/src/learning.jl:508 ┌ Warning: Skipping normalization, only experts should choose this option └ @ FlashWeave ~/.julia/packages/FlashWeave/j91Ng/src/learning.jl:508 ┌ Warning: Skipping normalization, only experts should choose this option └ @ FlashWeave ~/.julia/packages/FlashWeave/j91Ng/src/learning.jl:508 Test Summary: | Pass Total Time meta conditioning | 4 4 1m46.4s ┌ Warning: 37 variables have insufficient observations (< 160 ('n_obs_min')) and will not be used for interaction prediction └ @ FlashWeave ~/.julia/packages/FlashWeave/j91Ng/src/learning.jl:77 ┌ Warning: 37 variables have insufficient observations (< 160 ('n_obs_min')) and will not be used for interaction prediction └ @ FlashWeave ~/.julia/packages/FlashWeave/j91Ng/src/learning.jl:77 ┌ Warning: 37 variables have insufficient observations (< 160 ('n_obs_min')) and will not be used for interaction prediction └ @ FlashWeave ~/.julia/packages/FlashWeave/j91Ng/src/learning.jl:77 ┌ Warning: 37 variables have insufficient observations (< 160 ('n_obs_min')) and will not be used for interaction prediction └ @ FlashWeave ~/.julia/packages/FlashWeave/j91Ng/src/learning.jl:77 ┌ Warning: 37 variables have insufficient observations (< 160 ('n_obs_min')) and will not be used for interaction prediction └ @ FlashWeave ~/.julia/packages/FlashWeave/j91Ng/src/learning.jl:77 ┌ Warning: 37 variables have insufficient observations (< 160 ('n_obs_min')) and will not be used for interaction prediction └ @ FlashWeave ~/.julia/packages/FlashWeave/j91Ng/src/learning.jl:77 ┌ Warning: Adaptive CLR is inefficient with sparse data, using dense format for normalization └ @ FlashWeave ~/.julia/packages/FlashWeave/j91Ng/src/preprocessing.jl:542 ┌ Warning: Adaptive CLR is inefficient with sparse data, using dense format for normalization └ @ FlashWeave ~/.julia/packages/FlashWeave/j91Ng/src/preprocessing.jl:542 ┌ Warning: Adaptive CLR is inefficient with sparse data, using dense format for normalization └ @ FlashWeave ~/.julia/packages/FlashWeave/j91Ng/src/preprocessing.jl:542 ┌ Warning: Adaptive CLR is inefficient with sparse data, using dense format for normalization └ @ FlashWeave ~/.julia/packages/FlashWeave/j91Ng/src/preprocessing.jl:542 ┌ Warning: Adaptive CLR is inefficient with sparse data, using dense format for normalization └ @ FlashWeave ~/.julia/packages/FlashWeave/j91Ng/src/preprocessing.jl:542 Test Summary: | Pass Total Time LGL_backend | 80 80 3m09.2s Test Summary: | Pass Total Time pcor_recursive_fits_iterative | 4 4 31.0s ┌ Warning: 37 variables have insufficient observations (< 160 ('n_obs_min')) and will not be used for interaction prediction └ @ FlashWeave ~/.julia/packages/FlashWeave/j91Ng/src/learning.jl:77 ┌ Warning: 37 variables have insufficient observations (< 160 ('n_obs_min')) and will not be used for interaction prediction └ @ FlashWeave ~/.julia/packages/FlashWeave/j91Ng/src/learning.jl:77 ┌ Warning: Adaptive CLR is inefficient with sparse data, using dense format for normalization └ @ FlashWeave ~/.julia/packages/FlashWeave/j91Ng/src/preprocessing.jl:542 Test Summary: | Pass Total Time precision_32 | 4 4 27.4s ┌ Warning: 37 variables have insufficient observations (< 160 ('n_obs_min')) and will not be used for interaction prediction └ @ FlashWeave ~/.julia/packages/FlashWeave/j91Ng/src/learning.jl:77 ┌ Warning: 2 factor variables with more than two categories were detected (ENV4, ENV5), splitting them into separate dummy variables (One Hot) └ @ FlashWeave ~/.julia/packages/FlashWeave/j91Ng/src/preprocessing.jl:63 ┌ Warning: 2 factor variables with more than two categories were detected (ENV4, ENV5), splitting them into separate dummy variables (One Hot) └ @ FlashWeave ~/.julia/packages/FlashWeave/j91Ng/src/preprocessing.jl:63 ┌ Warning: 2 factor variables with more than two categories were detected (ENV4, ENV5), splitting them into separate dummy variables (One Hot) └ @ FlashWeave ~/.julia/packages/FlashWeave/j91Ng/src/preprocessing.jl:63 ┌ Warning: 2 factor variables with more than two categories were detected (ENV4, ENV5), splitting them into separate dummy variables (One Hot) └ @ FlashWeave ~/.julia/packages/FlashWeave/j91Ng/src/preprocessing.jl:63 Test Summary: | Pass Total Time learn_network | 12 12 46.8s Test Summary: | Pass Total Time fast_elim | 1 1 1.6s Test Summary: | Pass Total Time duplicates | 1 1 2.0s ┌ Warning: Adaptive CLR is inefficient with sparse data, using dense format for normalization └ @ FlashWeave ~/.julia/packages/FlashWeave/j91Ng/src/preprocessing.jl:542 Test Summary: | Pass Total Time convergence | 1 1 1.8s Test Summary: | Pass Total Time hiton msg | 1 1 4.7s ┌ Warning: 37 variables have insufficient observations (< 160 ('n_obs_min')) and will not be used for interaction prediction └ @ FlashWeave ~/.julia/packages/FlashWeave/j91Ng/src/learning.jl:77 ┌ Warning: 37 variables have insufficient observations (< 160 ('n_obs_min')) and will not be used for interaction prediction └ @ FlashWeave ~/.julia/packages/FlashWeave/j91Ng/src/learning.jl:77 ┌ Warning: 37 variables have insufficient observations (< 160 ('n_obs_min')) and will not be used for interaction prediction └ @ FlashWeave ~/.julia/packages/FlashWeave/j91Ng/src/learning.jl:77 ┌ Warning: 37 variables have insufficient observations (< 160 ('n_obs_min')) and will not be used for interaction prediction └ @ FlashWeave ~/.julia/packages/FlashWeave/j91Ng/src/learning.jl:77 ┌ Warning: Adaptive CLR is inefficient with sparse data, using dense format for normalization └ @ FlashWeave ~/.julia/packages/FlashWeave/j91Ng/src/preprocessing.jl:542 ┌ Warning: Adaptive CLR is inefficient with sparse data, using dense format for normalization └ @ FlashWeave ~/.julia/packages/FlashWeave/j91Ng/src/preprocessing.jl:542 Test Summary: | Pass Total Time bnb heuristic | 16 16 33.3s Test Summary: | Pass Total Time experimental kwargs | 1 1 4.3s Test Summary: | Pass Total Time non-zero variables | 8 8 12.9s ┌ Warning: 37 variables have insufficient observations (< 160 ('n_obs_min')) and will not be used for interaction prediction └ @ FlashWeave ~/.julia/packages/FlashWeave/j91Ng/src/learning.jl:77 ┌ Warning: 37 variables have insufficient observations (< 160 ('n_obs_min')) and will not be used for interaction prediction └ @ FlashWeave ~/.julia/packages/FlashWeave/j91Ng/src/learning.jl:77 Test Summary: | Pass Total Time shared data | 6 6 9.8s Finished testing (took 728s) Testing FlashWeave tests passed Testing completed after 537.61s PkgEval succeeded after 807.44s