Package evaluation to test MendelIHT on Julia 1.14.0-DEV.2435 (e1b2c72e96*) started at 2026-06-26T00:36:46.481 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.14` Set-up completed after 14.45s ################################################################################ # Installation # Installing MendelIHT... Resolving package versions... Updating `~/.julia/environments/v1.14/Project.toml` [921c7187] + MendelIHT v1.4.11 Updating `~/.julia/environments/v1.14/Manifest.toml` [7d9f7c33] + Accessors v0.1.44 [79e6a3ab] + Adapt v4.7.0 [66dad0bd] + AliasTables v1.1.3 [4fba245c] + ArrayInterface v7.25.0 [67c07d97] + Automa v1.2.0 ⌅ [6db4b851] + BGEN v0.1.17 [28d598bf] + BGZFStreams v0.3.2 [47718e42] + BioGenerics v0.1.5 [62783981] + BitTwiddlingConvenienceFunctions v0.1.6 [e1450e63] + BufferedStreams v1.2.2 [2a0fbf3d] + CPUSummary v0.2.7 [336ed68f] + CSV v0.10.16 [fb6a15b2] + CloseOpenIntervals v0.1.13 [523fee87] + CodecBzip2 v0.8.5 [ba30903b] + CodecXz v0.7.4 [944b1d66] + CodecZlib v0.7.8 [6b39b394] + CodecZstd v0.8.7 [861a8166] + Combinatorics v1.1.0 [38540f10] + CommonSolve v0.2.8 [f70d9fcc] + CommonWorldInvalidations v1.1.0 [34da2185] + Compat v4.18.1 [a33af91c] + CompositionsBase v0.1.2 [187b0558] + ConstructionBase v1.6.0 [adafc99b] + CpuId v0.3.1 [a8cc5b0e] + Crayons v4.1.1 [a10d1c49] + DBInterface v2.6.1 [9a962f9c] + 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[bea87d4a] + SuiteSparse_jll v7.10.1+0 [83775a58] + Zlib_jll v1.3.2+0 [3161d3a3] + Zstd_jll v1.5.7+1 [8e850b90] + libblastrampoline_jll v5.15.0+0 [8e850ede] + nghttp2_jll v1.69.0+0 [3f19e933] + p7zip_jll v17.8.0+0 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. To see why use `status --outdated -m` Installation completed after 5.45s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompiling project... 4.2 s ✓ BGEN 7.2 s ✓ VCFTools WARNING: Constructor for type "MvNormal" was extended in `MendelIHT` without explicit qualification or import.  NOTE: Assumed "MvNormal" refers to `Distributions.MvNormal`. This behavior is deprecated and may differ in future versions.  NOTE: This behavior may have differed in Julia versions prior to 1.12.  Hint: If you intended to create a new generic function of the same name, use `function MvNormal end`.  Hint: To silence the warning, qualify `MvNormal` as `Distributions.MvNormal` in the method signature or explicitly `import Distributions: MvNormal`. 22.0 s ✓ MendelIHT 3 dependencies successfully precompiled in 35 seconds. 171 already precompiled. 1 dependency had output during precompilation: ┌ MendelIHT │ WARNING: Constructor for type "MvNormal" was extended in `MendelIHT` without explicit qualification or import. │ NOTE: Assumed "MvNormal" refers to `Distributions.MvNormal`. This behavior is deprecated and may differ in future versions. │ NOTE: This behavior may have differed in Julia versions prior to 1.12. │ Hint: If you intended to create a new generic function of the same name, use `function MvNormal end`. │ Hint: To silence the warning, qualify `MvNormal` as `Distributions.MvNormal` in the method signature or explicitly `import Distributions: MvNormal`. └ Precompilation completed after 61.88s ################################################################################ # Testing # Testing MendelIHT Status `/tmp/jl_hNJU0a/Project.toml` ⌅ [6db4b851] BGEN v0.1.17 [6e4b80f9] BenchmarkTools v1.8.0 [336ed68f] CSV v0.10.16 [a93c6f00] DataFrames v1.8.2 [8bb1440f] DelimitedFiles v1.9.1 [b4f34e82] Distances v0.10.12 [31c24e10] Distributions v0.25.127 [38e38edf] GLM v1.9.5 [921c7187] MendelIHT v1.4.11 [92933f4c] ProgressMeter v1.11.0 [189a3867] Reexport v1.2.2 [4e780e97] SnpArrays v0.3.23 [276daf66] SpecialFunctions v2.8.0 [2913bbd2] StatsBase v0.34.12 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nghttp2_jll v1.69.0+0 [3f19e933] p7zip_jll v17.8.0+0 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. Testing Running tests... ┌ Warning: accessing `Type.name` is deprecated without replacement. If for detection, use `Base.isType(x)`. │ caller = Distributions.MvNormal(σ::Vector{Float64}) at mvnormal.jl:219 └ @ Distributions ~/.julia/packages/Distributions/Oj6YW/src/multivariate/mvnormal.jl:219 ┌ Warning: `MvNormal(σ::AbstractVector{<:Real})` is deprecated, use `MvNormal(LinearAlgebra.Diagonal(map(abs2, σ)))` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `cholesky!(A::RealHermSymComplexHerm{<:Real}, ::Val{true}; kwargs...)` is deprecated, use `cholesky!(A, RowMaximum(); kwargs...)` instead. │ caller = iht_stepsize!(v::MendelIHT.mIHTVariable{Float64, LinearAlgebra.Transpose{Float64, SnpArrays.SnpLinAlg{Float64}}}) at multivariate.jl:241 └ @ MendelIHT ~/.julia/packages/MendelIHT/ZcxZT/src/multivariate.jl:241 Test Summary: | Pass Total Time loglikelihood | 4 4 14.8s Test Summary: | Pass Total Time deviance | 1 1 0.4s Test Summary: | Pass Total Time update_μ! | 4 4 1.4s Test Summary: | Pass Total Time _choose! | 7 7 9.5s Test Summary: | Pass Total Time _iht_backtrack | 7 7 0.0s Test Summary: | Pass Total Time standardize! | 12 12 1.3s Test Summary: | Pass Total Time project_k! | 2 2 0.9s Test Summary: | Pass Total Time project_group_sparse! | 5 5 1.2s Test Summary: | Pass Total Time maf_weights | 6 6 2.0s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse linear regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1656.689294332362, backtracks = 0, tol = 2.2363880096280964 Iteration 2: loglikelihood = -1466.8627517943046, backtracks = 0, tol = 0.12298647643330679 Iteration 3: loglikelihood = -1443.4900015479432, backtracks = 0, tol = 0.04692298729827573 Iteration 4: loglikelihood = -1442.523455855152, backtracks = 0, tol = 0.007735013387434267 Iteration 5: loglikelihood = -1442.5112240491221, backtracks = 1, tol = 0.0005620537558620376 Iteration 6: loglikelihood = -1442.5079174421585, backtracks = 1, tol = 0.0002923215748842439 Iteration 7: loglikelihood = -1442.5070297625607, backtracks = 1, tol = 0.00014789665330505573 Iteration 8: loglikelihood = -1442.506795946492, backtracks = 1, tol = 7.282318687348562e-5 IHT estimated 10 nonzero SNP predictors and 1 non-genetic predictors. Compute time (sec): 0.07470321655273438 Final loglikelihood: -1442.506795946492 SNP PVE: 0.8951873608313258 Iterations: 8 Selected genetic predictors: 10×2 DataFrame Row │ Position Estimated_β │ Int64 Float64 ─────┼─────────────────────── 1 │ 1918 0.831542 2 │ 3623 -0.118687 3 │ 3877 1.09136 4 │ 3884 -2.39461 5 │ 4198 0.799242 6 │ 4933 0.381979 7 │ 5062 -0.129833 8 │ 5534 0.206162 9 │ 6331 -0.360702 10 │ 7381 -0.862136 Selected nongenetic predictors: 1×2 DataFrame Row │ Position Estimated_β │ Int64 Float64 ─────┼─────────────────────── 1 │ 1 0.000392709Test Summary: | Pass Total Time fit normal SnpLinAlg | 4 4 22.1s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse logistic regression Number of threads = 1 Link functin = LogitLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -379.72375963518977, backtracks = 0, tol = 0.6062552017348442 Iteration 2: loglikelihood = -294.14222098196217, backtracks = 0, tol = 0.39035964909167 Iteration 3: loglikelihood = -258.44215825745147, backtracks = 0, tol = 0.18072720194601524 Iteration 4: loglikelihood = -248.39092317275637, backtracks = 1, tol = 0.0581811999889429 Iteration 5: loglikelihood = -241.2861695402178, backtracks = 2, tol = 0.10199490430383734 Iteration 6: loglikelihood = -236.0344401262056, backtracks = 2, tol = 0.10444957184614982 Iteration 7: loglikelihood = -232.75639772007577, backtracks = 2, tol = 0.03618239958756675 Iteration 8: loglikelihood = -230.9028935826695, backtracks = 3, tol = 0.022566251649321353 Iteration 9: loglikelihood = -229.2332883500926, backtracks = 3, tol = 0.02394599965909332 Iteration 10: loglikelihood = -227.8109863155336, backtracks = 3, tol = 0.02260237147851236 Iteration 11: loglikelihood = -226.61429831284372, backtracks = 3, tol = 0.02153016573221634 Iteration 12: loglikelihood = -225.614543213995, backtracks = 3, tol = 0.020073248773013197 Iteration 13: loglikelihood = -225.15228734295533, backtracks = 3, tol = 0.10266272165892033 Iteration 14: loglikelihood = -224.5524858306654, backtracks = 2, tol = 0.010910053499902256 Iteration 15: loglikelihood = -223.90430308527087, backtracks = 3, tol = 0.10669566586572145 Iteration 16: loglikelihood = -223.43342440058004, backtracks = 1, tol = 0.009912340440473734 Iteration 17: loglikelihood = -223.19474883510568, backtracks = 3, tol = 0.10429355504005154 Iteration 18: loglikelihood = -222.7530868660152, backtracks = 1, tol = 0.010133510239484585 Iteration 19: loglikelihood = -222.4546375562022, backtracks = 3, tol = 0.009382230171462355 Iteration 20: loglikelihood = -225.04961416047087, backtracks = 3, tol = 0.13141028198780508 Iteration 21: loglikelihood = -221.57583298738808, backtracks = 0, tol = 0.12983606150115481 Iteration 22: loglikelihood = -220.9953587123894, backtracks = 0, tol = 0.018278220962270587 Iteration 23: loglikelihood = -220.46528702030645, backtracks = 0, tol = 0.10912949798131547 Iteration 24: loglikelihood = -220.22939682199817, backtracks = 1, tol = 0.006133557493960293 Iteration 25: loglikelihood = -220.1149031779291, backtracks = 3, tol = 0.005637364497494655 Iteration 26: loglikelihood = -237.91408320706802, backtracks = 3, tol = 0.1311916630585333 Iteration 27: loglikelihood = -222.6667401701631, backtracks = 0, tol = 0.13008576394077564 Iteration 28: loglikelihood = -220.0179912284672, backtracks = 0, tol = 0.10981267805412102 Iteration 29: loglikelihood = -219.80873468505163, backtracks = 1, tol = 0.006242686572879014 Iteration 30: loglikelihood = -219.71412932030552, backtracks = 1, tol = 0.0052581541847830735 Iteration 31: loglikelihood = -219.67346582214395, backtracks = 3, tol = 0.002736072071808146 Iteration 32: loglikelihood = -236.63118723570068, backtracks = 3, tol = 0.12536959025201838 Iteration 33: loglikelihood = -222.42522446507616, backtracks = 0, tol = 0.12480632457239557 Iteration 34: loglikelihood = -219.76952387571325, backtracks = 0, tol = 0.10782393864869841 Iteration 35: loglikelihood = -219.54239052596037, backtracks = 0, tol = 0.010969385336776636 Iteration 36: loglikelihood = -219.51051719556185, backtracks = 0, tol = 0.0038143069815270263 Iteration 37: loglikelihood = -219.49562270628724, backtracks = 1, tol = 0.0015360028505860806 Iteration 38: loglikelihood = -222.2776344615594, backtracks = 3, tol = 0.10706948875570901 Iteration 39: loglikelihood = -219.86344247649652, backtracks = 0, tol = 0.10682440099239575 Iteration 40: loglikelihood = -219.50637292175287, backtracks = 0, tol = 0.010145149683589566 Iteration 41: loglikelihood = -219.45601478260392, backtracks = 0, tol = 0.004786594360325445 Iteration 42: loglikelihood = -219.44279315931445, backtracks = 0, tol = 0.0023300326568676676 Iteration 43: loglikelihood = -219.434262597912, backtracks = 0, tol = 0.002159682320412748 Iteration 44: loglikelihood = -219.42706752504972, backtracks = 0, tol = 0.0019986878272562235 Iteration 45: loglikelihood = -219.4208881668612, backtracks = 0, tol = 0.001781315196828412 Iteration 46: loglikelihood = -219.41556755717227, backtracks = 0, tol = 0.0017266268818688624 Iteration 47: loglikelihood = -219.41098445944962, backtracks = 0, tol = 0.001504993867218278 Iteration 48: loglikelihood = -219.4070309112888, backtracks = 0, tol = 0.001495426527055874 Iteration 49: loglikelihood = -219.40362030781677, backtracks = 0, tol = 0.001286324051089446 Iteration 50: loglikelihood = -219.4006747755802, backtracks = 0, tol = 0.001295957349435961 Iteration 51: loglikelihood = -219.39813103252988, backtracks = 0, tol = 0.0011058748112207813 Iteration 52: loglikelihood = -219.3959322024177, backtracks = 0, tol = 0.0011233728145861855 Iteration 53: loglikelihood = -219.39403166729804, backtracks = 0, tol = 0.0009536994758608786 Iteration 54: loglikelihood = -219.39238763268273, backtracks = 0, tol = 0.0009739180646352119 Iteration 55: loglikelihood = -219.39096560226784, backtracks = 0, tol = 0.0008239389039648708 Iteration 56: loglikelihood = -219.38973473800374, backtracks = 0, tol = 0.0008444580901064712 Iteration 57: loglikelihood = -219.3886694316569, backtracks = 0, tol = 0.0007126409505425607 Iteration 58: loglikelihood = -219.38774685610232, backtracks = 0, tol = 0.0007323063866727435 Iteration 59: loglikelihood = -219.3869479529937, backtracks = 0, tol = 0.00061686194275372 Iteration 60: loglikelihood = -219.3862557798823, backtracks = 0, tol = 0.0006351404346176769 Iteration 61: loglikelihood = -219.3856561234815, backtracks = 0, tol = 0.000534269842115572 Iteration 62: loglikelihood = -219.38513638040487, backtracks = 0, tol = 0.0005509480422217535 Iteration 63: loglikelihood = -219.38468593224545, backtracks = 0, tol = 0.0004629512780606966 Iteration 64: loglikelihood = -219.38429538513583, backtracks = 0, tol = 0.0004779860767529819 Iteration 65: loglikelihood = -219.38395679466737, backtracks = 0, tol = 0.0004013057505476397 Iteration 66: loglikelihood = -219.38366314739872, backtracks = 0, tol = 0.0004147454994836376 Iteration 67: loglikelihood = -219.38340849212824, backtracks = 0, tol = 0.00034797985178746597 Iteration 68: loglikelihood = -219.38318758502183, backtracks = 0, tol = 0.0003599207374415984 Iteration 69: loglikelihood = -219.38299596326374, backtracks = 0, tol = 0.0003018217223394219 Iteration 70: loglikelihood = -219.3828297011887, backtracks = 0, tol = 0.00031238270039476616 Iteration 71: loglikelihood = -219.38268544908368, backtracks = 0, tol = 0.00026184698528793125 Iteration 72: loglikelihood = -219.3825602648841, backtracks = 0, tol = 0.0002711550905775348 Iteration 73: loglikelihood = -219.38245163239276, backtracks = 0, tol = 0.00022721198022395564 Iteration 74: loglikelihood = -219.38235734460943, backtracks = 0, tol = 0.00023539371282360467 Iteration 75: loglikelihood = -219.38227551018164, backtracks = 0, tol = 0.0001971920991460162 Iteration 76: loglikelihood = -219.382204472153, backtracks = 0, tol = 0.00020436848993624394 Iteration 77: loglikelihood = -219.3821428080304, backtracks = 0, tol = 0.00017116393516432852 Iteration 78: loglikelihood = -219.38208927292968, backtracks = 0, tol = 0.00017744788492952903 Iteration 79: loglikelihood = -219.38204279645043, backtracks = 0, tol = 0.00014859040670150365 Iteration 80: loglikelihood = -219.38200244272016, backtracks = 0, tol = 0.00015408544066832546 Iteration 81: loglikelihood = -219.38196740593906, backtracks = 0, tol = 0.00012900826739905896 Iteration 82: loglikelihood = -219.38193698216227, backtracks = 0, tol = 0.00013380816660865064 Iteration 83: loglikelihood = -219.38191056455443, backtracks = 0, tol = 0.00011201756190578927 Iteration 84: loglikelihood = -219.3818876233726, backtracks = 0, tol = 0.000116206527337935 Iteration 85: loglikelihood = -219.38186770147453, backtracks = 0, tol = 9.727268703830643e-5 Test Summary: | Pass Total Time fit Bernoulli SnpLinAlg | 4 4 3.9s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse Poisson regression Number of threads = 1 Link functin = LogLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1464.509096143566, backtracks = 0, tol = 0.376512198930164 Iteration 2: loglikelihood = -1320.9187438060453, backtracks = 0, tol = 0.07539682516806469 Iteration 3: loglikelihood = -1296.8275585149086, backtracks = 0, tol = 0.05527790706592373 Iteration 4: loglikelihood = -1281.3834994870906, backtracks = 0, tol = 0.05913199800016367 Iteration 5: loglikelihood = -1275.8280342154821, backtracks = 0, tol = 0.028316597699195326 Iteration 6: loglikelihood = -1273.327775834038, backtracks = 1, tol = 0.015576798431509373 Iteration 7: loglikelihood = -1270.838613966484, backtracks = 1, tol = 0.052609642328142164 Iteration 8: loglikelihood = -1264.4919157714608, backtracks = 0, tol = 0.0515785764373397 Iteration 9: loglikelihood = -1263.209821461347, backtracks = 0, tol = 0.06018956292448178 Iteration 10: loglikelihood = -1261.954830495145, backtracks = 0, tol = 0.015117594720095518 Iteration 11: loglikelihood = -1261.6323529385754, backtracks = 1, tol = 0.006231246002339729 Iteration 12: loglikelihood = -1261.3979097463978, backtracks = 2, tol = 0.004208449280973203 Iteration 13: loglikelihood = -1261.2382435885784, backtracks = 2, tol = 0.004240267648907084 Iteration 14: loglikelihood = -1261.140974538947, backtracks = 2, tol = 0.002873330021503564 Iteration 15: loglikelihood = -1261.0828835206232, backtracks = 2, tol = 0.0025184864820425572 Iteration 16: loglikelihood = -1261.0482701110266, backtracks = 2, tol = 0.001651815521240226 Iteration 17: loglikelihood = -1261.0276373561462, backtracks = 2, tol = 0.0014722533733943456 Iteration 18: loglikelihood = -1261.0152626520064, backtracks = 2, tol = 0.0009351388264176549 Iteration 19: loglikelihood = -1261.0077885617222, backtracks = 2, tol = 0.0008635900662791727 Iteration 20: loglikelihood = -1261.0032291671127, backtracks = 2, tol = 0.0005930936807599523 Iteration 21: loglikelihood = -1261.000425231443, backtracks = 2, tol = 0.0005137319153970036 Iteration 22: loglikelihood = -1260.9986868501312, backtracks = 2, tol = 0.00039359063480475404 Iteration 23: loglikelihood = -1260.997603167851, backtracks = 2, tol = 0.0003098909959782519 Iteration 24: loglikelihood = -1260.9969240382395, backtracks = 2, tol = 0.00026077270946769877 Iteration 25: loglikelihood = -1260.9964969121331, backtracks = 2, tol = 0.00020334978539370688 Iteration 26: loglikelihood = -1260.9962273029992, backtracks = 2, tol = 0.00017217592581766323 Iteration 27: loglikelihood = -1260.996056690047, backtracks = 2, tol = 0.0001341202073507711 Iteration 28: loglikelihood = -1260.9959484431702, backtracks = 2, tol = 0.00011325810224716819 Iteration 29: loglikelihood = -1260.995879638768, backtracks = 2, tol = 8.813506784987112e-5 Test Summary: | Pass Total Time fit Poisson SnpLinAlg | 4 4 3.2s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse NegativeBinomial regression Number of threads = 1 Link functin = LogLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1504.9909535374893, backtracks = 0, tol = 0.36712317753532187 Iteration 2: loglikelihood = -1461.5167384478718, backtracks = 0, tol = 0.13129961893757724 Iteration 3: loglikelihood = -1452.2378786381478, backtracks = 0, tol = 0.09569620036052881 Iteration 4: loglikelihood = -1444.056214679881, backtracks = 0, tol = 0.08888720604407072 Iteration 5: loglikelihood = -1443.7067655147837, backtracks = 1, tol = 0.008570959446920365 Iteration 6: loglikelihood = -1443.57895534185, backtracks = 1, tol = 0.005937174654756905 Iteration 7: loglikelihood = -1443.1243951695496, backtracks = 1, tol = 0.05586602888540725 Iteration 8: loglikelihood = -1443.0721507702297, backtracks = 1, tol = 0.003442928074117585 Iteration 9: loglikelihood = -1443.0553045408856, backtracks = 1, tol = 0.0018570475173254695 Iteration 10: loglikelihood = -1443.049628050003, backtracks = 1, tol = 0.0012355324037216526 Iteration 11: loglikelihood = -1443.0477378184821, backtracks = 1, tol = 0.0008910706841990299 Iteration 12: loglikelihood = -1443.047165013013, backtracks = 1, tol = 0.000540322519731539 Iteration 13: loglikelihood = -1443.0470059215934, backtracks = 1, tol = 0.00028943830061006737 Iteration 14: loglikelihood = -1443.0469630533462, backtracks = 1, tol = 0.00014924827689146735 Iteration 15: loglikelihood = -1443.0469516013268, backtracks = 1, tol = 7.632394276749185e-5 Test Summary: | Pass Total Time fit NegativeBinomial SnpLinAlg | 4 4 1.2s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse linear regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1762.8916584807541, backtracks = 0, tol = 0.837482296930505 Iteration 2: loglikelihood = -1516.2049943783552, backtracks = 0, tol = 0.10470576393586899 Iteration 3: loglikelihood = -1457.607641454393, backtracks = 0, tol = 0.049907078973743885 Iteration 4: loglikelihood = -1437.3606141812456, backtracks = 0, tol = 0.029343527323011716 Iteration 5: loglikelihood = -1435.9358693980896, backtracks = 0, tol = 0.02511962261443016 Iteration 6: loglikelihood = -1435.1607017916397, backtracks = 0, tol = 0.025962565022880586 Iteration 7: loglikelihood = -1434.9380381619048, backtracks = 0, tol = 0.0035913536929302855 Iteration 8: loglikelihood = -1434.9335216774796, backtracks = 0, tol = 0.00045446614603609386 Iteration 9: loglikelihood = -1434.9334011805342, backtracks = 0, tol = 8.168128766175044e-5 Test Summary: | Pass Total Time fit with >1 non-genetic covariates SnpLinAlg | 5 5 1.6s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse linear regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1536.985161890279, backtracks = 0, tol = 0.30544644816507227 Iteration 2: loglikelihood = -1455.4672091606049, backtracks = 0, tol = 0.053086756705882074 Iteration 3: loglikelihood = -1441.2574795139917, backtracks = 0, tol = 0.035150773363714305 Iteration 4: loglikelihood = -1437.884436527266, backtracks = 0, tol = 0.029168811912956675 Iteration 5: loglikelihood = -1437.5108462301514, backtracks = 0, tol = 0.03056309014211801 Iteration 6: loglikelihood = -1437.3922580646145, backtracks = 0, tol = 0.03196027317886166 Iteration 7: loglikelihood = -1437.2187713418928, backtracks = 0, tol = 0.0028707614594008805 Iteration 8: loglikelihood = -1437.2182263413672, backtracks = 1, tol = 0.00010266095066984249 Iteration 9: loglikelihood = -1437.2180852856575, backtracks = 1, tol = 4.88362304974966e-5 Test Summary: | Pass Total Time model selection on non-genetic covariates | 5 5 0.8s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse linear regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 15 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1473.12410014528, backtracks = 0, tol = 0.11162633196865429 Iteration 2: loglikelihood = -1448.37403799896, backtracks = 0, tol = 0.07736217654955346 Iteration 3: loglikelihood = -1429.8981769610311, backtracks = 1, tol = 0.056531823476744666 Iteration 4: loglikelihood = -1404.7133956159753, backtracks = 0, tol = 0.10125409614175711 Iteration 5: loglikelihood = -1397.466171579031, backtracks = 0, tol = 0.05343369325195712 Iteration 6: loglikelihood = -1395.7490747391416, backtracks = 0, tol = 0.08843871418165569 Iteration 7: loglikelihood = -1395.4877576477586, backtracks = 0, tol = 0.0089247040684952 Iteration 8: loglikelihood = -1395.442237061722, backtracks = 0, tol = 0.005277867116132827 Iteration 9: loglikelihood = -1395.4302205892106, backtracks = 0, tol = 0.0027680467744013336 Iteration 10: loglikelihood = -1395.1973617039414, backtracks = 0, tol = 0.0905690065560604 Iteration 11: loglikelihood = -1395.0048067729406, backtracks = 0, tol = 0.007650485819168939 Iteration 12: loglikelihood = -1394.9835209063683, backtracks = 0, tol = 0.0035232591741737973 Iteration 13: loglikelihood = -1394.9793628241396, backtracks = 0, tol = 0.001852195878065177 Iteration 14: loglikelihood = -1394.9779889816232, backtracks = 0, tol = 0.0012530451800711444 Iteration 15: loglikelihood = -1394.977503420045, backtracks = 0, tol = 0.0006829444661300923 Iteration 16: loglikelihood = -1394.9773714862843, backtracks = 1, tol = 0.00022881022816864142 Iteration 17: loglikelihood = -1394.977310220191, backtracks = 2, tol = 0.0001217788197399568 Iteration 18: loglikelihood = -1394.977273607278, backtracks = 2, tol = 8.822469907087602e-5 **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse linear regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 3 Prior weight scaling = off Doubly sparse projection = on Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1535.4672180567934, backtracks = 0, tol = 0.17016419679985048 Iteration 2: loglikelihood = -1508.04343741211, backtracks = 0, tol = 0.21718489399873087 Iteration 3: loglikelihood = -1448.2717322168082, backtracks = 0, tol = 0.15334504607402907 Iteration 4: loglikelihood = -1437.5669418734744, backtracks = 0, tol = 0.08425396177776269 Iteration 5: loglikelihood = -1434.3602241747528, backtracks = 0, tol = 0.03199716666887782 Iteration 6: loglikelihood = -1434.239273652971, backtracks = 2, tol = 0.003498168340088273 Iteration 7: loglikelihood = -1434.1475478538455, backtracks = 2, tol = 0.0030522911015526556 Iteration 8: loglikelihood = -1434.0913475157126, backtracks = 2, tol = 0.0021931576818355514 Iteration 9: loglikelihood = -1434.0584761985995, backtracks = 2, tol = 0.0016688209654910561 Iteration 10: loglikelihood = -1434.0393127719108, backtracks = 2, tol = 0.001317554485128468 Iteration 11: loglikelihood = -1434.0281644425422, backtracks = 2, tol = 0.0010393713220469248 Iteration 12: loglikelihood = -1434.0216963632631, backtracks = 2, tol = 0.0008158673348111212 Iteration 13: loglikelihood = -1434.0179556115852, backtracks = 2, tol = 0.0006363671566384319 Iteration 14: loglikelihood = -1433.8972844529703, backtracks = 2, tol = 0.02105646084267335 Iteration 15: loglikelihood = -1433.6170929347984, backtracks = 1, tol = 0.011448126839540936 Iteration 16: loglikelihood = -1433.5408744767515, backtracks = 2, tol = 0.0040324300639331045 Iteration 17: loglikelihood = -1433.4945867179188, backtracks = 2, tol = 0.003005268578298657 Iteration 18: loglikelihood = -1433.467626121943, backtracks = 2, tol = 0.002187229771831438 Iteration 19: loglikelihood = -1433.4521439235273, backtracks = 2, tol = 0.0016467936133078437 Iteration 20: loglikelihood = -1433.4432822302874, backtracks = 2, tol = 0.0012631945762950846 Iteration 21: loglikelihood = -1433.4382075829426, backtracks = 2, tol = 0.0009580287583338291 Iteration 22: loglikelihood = -1433.4352962137846, backtracks = 2, tol = 0.0007222437442123496 Iteration 23: loglikelihood = -1433.4336216439426, backtracks = 2, tol = 0.0005424739396431532 Iteration 24: loglikelihood = -1433.43265547142, backtracks = 2, tol = 0.00040628145880685523 Iteration 25: loglikelihood = -1433.4320960523787, backtracks = 2, tol = 0.0003034179918772475 Iteration 26: loglikelihood = -1433.4317709097872, backtracks = 2, tol = 0.00022583740291084404 Iteration 27: loglikelihood = -1433.4315812027676, backtracks = 2, tol = 0.0001673653861249394 Iteration 28: loglikelihood = -1432.5898379532837, backtracks = 2, tol = 0.025080215054031605 Iteration 29: loglikelihood = -1431.7678006470733, backtracks = 1, tol = 0.017181190475547538 Iteration 30: loglikelihood = -1430.3157393955933, backtracks = 1, tol = 0.07333968264200234 Iteration 31: loglikelihood = -1429.706868513855, backtracks = 0, tol = 0.020015111727945754 Iteration 32: loglikelihood = -1429.5802551945537, backtracks = 1, tol = 0.00756937670420323 Iteration 33: loglikelihood = -1429.5139450553559, backtracks = 2, tol = 0.003906515984506227 Iteration 34: loglikelihood = -1429.4691972325213, backtracks = 2, tol = 0.003683664863256486 Iteration 35: loglikelihood = -1428.8607526222902, backtracks = 2, tol = 0.08711763846658777 Iteration 36: loglikelihood = -1428.6178427111051, backtracks = 1, tol = 0.006558345246943271 Iteration 37: loglikelihood = -1428.5424083746184, backtracks = 2, tol = 0.0033912200662443866 Iteration 38: loglikelihood = -1428.4933608487952, backtracks = 2, tol = 0.0030098214824111793 Iteration 39: loglikelihood = -1428.4620745885088, backtracks = 2, tol = 0.0025951371119133128 Iteration 40: loglikelihood = -1428.4427329028306, backtracks = 2, tol = 0.002148184701148465 Iteration 41: loglikelihood = -1428.4311433050725, backtracks = 2, tol = 0.0017160493175770867 Iteration 42: loglikelihood = -1428.4243474878394, backtracks = 2, tol = 0.0013407892924840973 Iteration 43: loglikelihood = -1428.420413936832, backtracks = 2, tol = 0.0010343694042998534 Iteration 44: loglikelihood = -1428.4181556141762, backtracks = 2, tol = 0.0007948565534422845 Iteration 45: loglikelihood = -1428.4168664091337, backtracks = 2, tol = 0.000608309643427293 Iteration 46: loglikelihood = -1428.4161334920516, backtracks = 2, tol = 0.0004622621654004415 Iteration 47: loglikelihood = -1428.4157180925672, backtracks = 2, tol = 0.00034956951660978575 Iteration 48: loglikelihood = -1428.4154831711999, backtracks = 2, tol = 0.00026348047442121094 Iteration 49: loglikelihood = -1428.4153505233908, backtracks = 2, tol = 0.00019816133989405092 Iteration 50: loglikelihood = -1428.4152757065372, backtracks = 2, tol = 0.00014882628973647444 Iteration 51: loglikelihood = -1428.4152335404317, backtracks = 2, tol = 0.00011167501044822909 Iteration 52: loglikelihood = -1428.4152097888611, backtracks = 2, tol = 8.375238803842589e-5 Test Summary: | Pass Total Time Correlated predictors and double sparsity Float64 matrix | 2 2 10.0s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse NegativeBinomial regression Number of threads = 1 Link functin = LogLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1600.521765501404, backtracks = 0, tol = 0.21538414139964365 Iteration 2: loglikelihood = -1504.7727540478193, backtracks = 0, tol = 0.11845983597303475 Iteration 3: loglikelihood = -1438.3140699813532, backtracks = 0, tol = 0.09953737387018254 Iteration 4: loglikelihood = -1400.4471161028898, backtracks = 0, tol = 0.08160245189432863 Iteration 5: loglikelihood = -1381.781450202779, backtracks = 0, tol = 0.09173543387566391 Iteration 6: loglikelihood = -1374.1587411446728, backtracks = 0, tol = 0.040946145681038736 Iteration 7: loglikelihood = -1361.8039812495822, backtracks = 0, tol = 0.08596126100273906 Iteration 8: loglikelihood = -1359.1263061729992, backtracks = 0, tol = 0.02137519271974427 Iteration 9: loglikelihood = -1358.2238582924545, backtracks = 0, tol = 0.013463485278736418 Iteration 10: loglikelihood = -1357.79618944452, backtracks = 0, tol = 0.011404474064797967 Iteration 11: loglikelihood = -1357.564027061992, backtracks = 0, tol = 0.005409000179880063 Iteration 12: loglikelihood = -1357.438698933848, backtracks = 0, tol = 0.006082975575287267 Iteration 13: loglikelihood = -1357.3699054016565, backtracks = 0, tol = 0.0028156547721231166 Iteration 14: loglikelihood = -1357.3324320979953, backtracks = 0, tol = 0.0032760150406863377 Iteration 15: loglikelihood = -1357.3119133834607, backtracks = 0, tol = 0.001534135591228059 Iteration 16: loglikelihood = -1357.300715845679, backtracks = 0, tol = 0.0017747083396179762 Iteration 17: loglikelihood = -1357.294600068992, backtracks = 0, tol = 0.0008394671627795885 Iteration 18: loglikelihood = -1357.291261704458, backtracks = 0, tol = 0.0009637976515815271 Iteration 19: loglikelihood = -1357.2894418572764, backtracks = 0, tol = 0.0004588829372767344 Iteration 20: loglikelihood = -1357.2884487250913, backtracks = 0, tol = 0.0005238719393764721 Iteration 21: loglikelihood = -1357.2879080892308, backtracks = 0, tol = 0.0002505134268177035 Iteration 22: loglikelihood = -1357.287613180836, backtracks = 0, tol = 0.0002847907405854243 Iteration 23: loglikelihood = -1357.287452809869, backtracks = 0, tol = 0.00013661414579260644 Iteration 24: loglikelihood = -1357.2873653733072, backtracks = 0, tol = 0.00015478822397838645 Iteration 25: loglikelihood = -1357.287317865936, backtracks = 0, tol = 7.443697923402991e-5 0.966486 seconds (2.27 M allocations: 45.143 MiB, 61.05% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse NegativeBinomial regression Number of threads = 1 Link functin = LogLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1625.566020619094, backtracks = 0, tol = 0.21538414139964365 Iteration 2: loglikelihood = -1574.9476372281554, backtracks = 0, tol = 0.13616802026722105 Iteration 3: loglikelihood = -1545.7769491470974, backtracks = 0, tol = 0.11088470159921823 Iteration 4: loglikelihood = -1514.5047728173288, backtracks = 0, tol = 0.06612386023711703 Iteration 5: loglikelihood = -1487.7046443060738, backtracks = 0, tol = 0.07979653030346935 Iteration 6: loglikelihood = -1465.0787565670064, backtracks = 0, tol = 0.10105804360268415 Iteration 7: loglikelihood = -1450.9066705488651, backtracks = 0, tol = 0.0843482846794713 Iteration 8: loglikelihood = -1442.8711238899361, backtracks = 0, tol = 0.08340003207451235 Iteration 9: loglikelihood = -1432.8742319520197, backtracks = 0, tol = 0.07913879483854286 Iteration 10: loglikelihood = -1426.1485003994144, backtracks = 0, tol = 0.005933808161309358 Iteration 11: loglikelihood = -1420.3752275250336, backtracks = 0, tol = 0.002224539341838281 Iteration 12: loglikelihood = -1413.9102253980532, backtracks = 0, tol = 0.08199398494904823 Iteration 13: loglikelihood = -1408.9620515388763, backtracks = 0, tol = 0.007336274758378361 Iteration 14: loglikelihood = -1405.0792781690407, backtracks = 0, tol = 0.0020640439314186442 Iteration 15: loglikelihood = -1401.6362101033817, backtracks = 0, tol = 0.0006624945921886718 Iteration 16: loglikelihood = -1398.6435949352572, backtracks = 0, tol = 0.0006288713325398364 Iteration 17: loglikelihood = -1395.9743306832738, backtracks = 0, tol = 0.000499885782934986 Iteration 18: loglikelihood = -1393.609110006768, backtracks = 0, tol = 0.0003789669660342644 Iteration 19: loglikelihood = -1392.3743476078478, backtracks = 0, tol = 0.07088492533853158 Iteration 20: loglikelihood = -1389.926605976835, backtracks = 0, tol = 0.07089236900240335 Iteration 21: loglikelihood = -1387.9047140192479, backtracks = 0, tol = 0.0055453121676067975 Iteration 22: loglikelihood = -1386.3378734380653, backtracks = 0, tol = 0.0016881023701678765 Iteration 23: loglikelihood = -1384.8696444898349, backtracks = 0, tol = 0.0005934190668640364 Iteration 24: loglikelihood = -1383.5532339350686, backtracks = 0, tol = 0.0004880804277398208 Iteration 25: loglikelihood = -1382.3336324678953, backtracks = 0, tol = 0.0003050057025025407 Iteration 26: loglikelihood = -1381.2199676778548, backtracks = 0, tol = 0.00024236510447718843 Iteration 27: loglikelihood = -1381.1699368726354, backtracks = 0, tol = 0.06751540609661026 Iteration 28: loglikelihood = -1379.5623425744802, backtracks = 0, tol = 0.06752044745867841 Iteration 29: loglikelihood = -1378.4196783529835, backtracks = 0, tol = 0.0049983392110343194 Iteration 30: loglikelihood = -1377.599290653246, backtracks = 0, tol = 0.0017064316352814557 Iteration 31: loglikelihood = -1376.8062345082164, backtracks = 0, tol = 0.0005914492791833598 Iteration 32: loglikelihood = -1376.088281228783, backtracks = 0, tol = 0.00041701751494316845 Iteration 33: loglikelihood = -1375.4085525285343, backtracks = 0, tol = 0.00022540223074067576 Iteration 34: loglikelihood = -1374.7783283870056, backtracks = 0, tol = 0.00017907641075744338 Iteration 35: loglikelihood = -1374.2370695735713, backtracks = 0, tol = 0.06654454244423295 Iteration 36: loglikelihood = -1373.4290355771204, backtracks = 0, tol = 0.009301090790496402 Iteration 37: loglikelihood = -1372.7974439720456, backtracks = 0, tol = 0.0028168521500290034 Iteration 38: loglikelihood = -1372.2752225029935, backtracks = 0, tol = 0.0012961505219169119 Iteration 39: loglikelihood = -1371.735182501872, backtracks = 0, tol = 0.00125687746232998 Iteration 40: loglikelihood = -1371.247559724251, backtracks = 0, tol = 0.00047529188394560413 Iteration 41: loglikelihood = -1370.7602827086846, backtracks = 0, tol = 0.0007341981446268879 Iteration 42: loglikelihood = -1370.3116876131237, backtracks = 0, tol = 0.00024304074320115354 Iteration 43: loglikelihood = -1369.5024104888498, backtracks = 1, tol = 0.0002646529049052633 Iteration 44: loglikelihood = -1368.7293997238053, backtracks = 1, tol = 0.00017805936967456 Iteration 45: loglikelihood = -1368.0962037692798, backtracks = 1, tol = 0.00023724294110069868 Iteration 46: loglikelihood = -1367.544504161432, backtracks = 1, tol = 0.00023324203221543712 Iteration 47: loglikelihood = -1367.075241285644, backtracks = 1, tol = 0.00020958123842466946 Iteration 48: loglikelihood = -1366.6848058396126, backtracks = 1, tol = 0.00018460882903536524 Iteration 49: loglikelihood = -1366.361824910022, backtracks = 1, tol = 0.00015836042648776573 Iteration 50: loglikelihood = -1366.0953647252834, backtracks = 1, tol = 0.00014367880140335183 Iteration 51: loglikelihood = -1365.8710415218093, backtracks = 1, tol = 0.00012574349893692947 Iteration 52: loglikelihood = -1365.6667156298058, backtracks = 1, tol = 0.00010615941698052618 Iteration 53: loglikelihood = -1365.437697522596, backtracks = 1, tol = 8.512229241034289e-5 0.576783 seconds (2.20 M allocations: 39.791 MiB, 3.84% gc time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse NegativeBinomial regression Number of threads = 1 Link functin = LogLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -3722.6045, backtracks = 0, tol = 0.09162480357771732 Iteration 2: loglikelihood = -3664.928, backtracks = 0, tol = 0.04889751236198953 Iteration 3: loglikelihood = -3659.42, backtracks = 1, tol = 0.01571603029351751 Iteration 4: loglikelihood = -3657.85, backtracks = 1, tol = 0.008067081085442289 Iteration 5: loglikelihood = -3657.4292, backtracks = 1, tol = 0.004535828705391197 Iteration 6: loglikelihood = -3657.325, backtracks = 1, tol = 0.002259561376182492 Iteration 7: loglikelihood = -3657.2952, backtracks = 1, tol = 0.0011867679311289413 Iteration 8: loglikelihood = -3657.287, backtracks = 1, tol = 0.0005890309130845457 Iteration 9: loglikelihood = -3657.2861, backtracks = 1, tol = 0.00030265814041626453 Iteration 10: loglikelihood = -3657.2905, backtracks = 3, tol = 3.7647929651962515e-5 24.243167 seconds (13.25 M allocations: 640.202 MiB, 1.55% gc time, 97.46% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse NegativeBinomial regression Number of threads = 1 Link functin = LogLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -3600.1414, backtracks = 0, tol = 0.09162480357771732 Iteration 2: loglikelihood = -3465.6108, backtracks = 0, tol = 0.05062901468610535 Iteration 3: loglikelihood = -3256.9092, backtracks = 1, tol = 0.014854194898113526 Iteration 4: loglikelihood = -3014.9578, backtracks = 1, tol = 0.007560829350489504 Iteration 5: loglikelihood = -2764.1765, backtracks = 1, tol = 0.003377994025801955 Iteration 6: loglikelihood = -2677.0398, backtracks = 0, tol = 0.08658079404747414 Iteration 7: loglikelihood = -2536.1077, backtracks = 0, tol = 0.10431221370073442 Iteration 8: loglikelihood = -2424.978, backtracks = 0, tol = 0.10345188878806483 Iteration 9: loglikelihood = -2347.8538, backtracks = 0, tol = 0.09088820058171743 Iteration 10: loglikelihood = -2283.4846, backtracks = 0, tol = 0.09089549543031795 Iteration 11: loglikelihood = -2245.8477, backtracks = 0, tol = 0.09044574751556575 Iteration 12: loglikelihood = -2211.7324, backtracks = 0, tol = 0.09062289223047586 Iteration 13: loglikelihood = -2199.6707, backtracks = 0, tol = 0.09053077793044 Iteration 14: loglikelihood = -2192.444, backtracks = 0, tol = 0.09317239276411791 Iteration 15: loglikelihood = -2188.2786, backtracks = 0, tol = 0.10556404234833473 Iteration 16: loglikelihood = -2185.514, backtracks = 0, tol = 0.10551566122829246 Iteration 17: loglikelihood = -2184.7737, backtracks = 0, tol = 0.10577728796446566 Iteration 18: loglikelihood = -2183.706, backtracks = 0, tol = 0.10588150684981065 Iteration 19: loglikelihood = -2181.8687, backtracks = 1, tol = 0.01510360960802245 Iteration 20: loglikelihood = -2181.4988, backtracks = 1, tol = 0.007284119197091984 Iteration 21: loglikelihood = -2181.4155, backtracks = 1, tol = 0.003595576957503812 Iteration 22: loglikelihood = -2181.396, backtracks = 1, tol = 0.001791026023138515 Iteration 23: loglikelihood = -2181.3906, backtracks = 1, tol = 0.0008966110530553863 Iteration 24: loglikelihood = -2181.3884, backtracks = 1, tol = 0.0004497052945247565 Iteration 25: loglikelihood = -2181.3867, backtracks = 1, tol = 0.00022525424958020227 Iteration 26: loglikelihood = -2181.3857, backtracks = 3, tol = 2.9360762227146462e-5 0.214918 seconds (1.53 M allocations: 25.378 MiB) Test Summary: | Pass Total Time Negative binomial nuisance parameter Float32 matrix | 12 12 28.6s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** ┌ Warning: accessing `Type.name` is deprecated without replacement. If for detection, use `Base.isType(x)`. │ caller = ProgressMeter.Progress(n::Int64, dt::Int64, desc::String, barlen::Nothing, color::Symbol, output::Base.PipeEndpoint; offset::Int64) at deprecated.jl:1 └ @ ProgressMeter ~/.julia/packages/ProgressMeter/N660J/src/deprecated.jl:1 Running sparse linear regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -2896.6116813943763, backtracks = 0, tol = 1.0257704354307222 Iteration 2: loglikelihood = -1753.4720992614753, backtracks = 0, tol = 0.28706825512903816 Iteration 3: loglikelihood = -1460.3823326395225, backtracks = 0, tol = 0.1059822007319242 Iteration 4: loglikelihood = -1438.5292259047123, backtracks = 0, tol = 0.028655431669451118 Iteration 5: loglikelihood = -1438.0856032112097, backtracks = 0, tol = 0.0034955373515602557 Iteration 6: loglikelihood = -1438.0744350329464, backtracks = 0, tol = 0.0005882060650840543 Iteration 7: loglikelihood = -1438.0741395461057, backtracks = 0, tol = 8.427264473927088e-5 5.000983 seconds (1.02 M allocations: 132.822 MiB, 7.31% gc time, 85.49% compilation time) Test Summary: | Pass Total Time initialze beta | 1 1 5.4s 9.753714 seconds (4.00 M allocations: 82.389 MiB, 0.26% gc time, 0.63% compilation time) 5.348256 seconds (3.98 M allocations: 91.678 MiB, 0.43% gc time) 10.599438 seconds (20.38 M allocations: 438.630 MiB, 0.97% gc time, 16.90% compilation time: 78% of which was recompilation) 8.370305 seconds (20.18 M allocations: 434.189 MiB, 1.09% gc time) 36.185673 seconds (3.36 M allocations: 4.228 GiB, 6.18% gc time, 30.04% compilation time) 53.857339 seconds (72.50 k allocations: 183.670 MiB, 0.13% gc time) Test Summary: | Pass Total Time memory_efficient keyword | 7 7 2m20.5s Test Summary: | Pass Total Time update_support! | 10 10 0.6s 14.740 ms (78 allocations: 4.56 KiB) 4.337 μs (0 allocations: 0 bytes) 146.899 μs (4 allocations: 288 bytes) 7.196 μs (0 allocations: 0 bytes) 47.180 μs (2 allocations: 64 bytes) 30.339 μs (0 allocations: 0 bytes) 25.899 μs (0 allocations: 0 bytes) 30.990 μs (0 allocations: 0 bytes) 93.479 μs (0 allocations: 0 bytes) 38.864 ms (78 allocations: 4.56 KiB) 18.320 μs (0 allocations: 0 bytes) 159.239 μs (4 allocations: 288 bytes) 34.020 μs (0 allocations: 0 bytes) 255.107 μs (2 allocations: 64 bytes) 84.889 μs (0 allocations: 0 bytes) 132.399 μs (0 allocations: 0 bytes) 145.068 μs (0 allocations: 0 bytes) 213.638 μs (0 allocations: 0 bytes) Test Summary: | Total Time benchmarks for multivariate function | 0 2m09.9s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse Multivariate Gaussian regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 12 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -2900.9186300194497, backtracks = 0, tol = 0.1480224208200413 Iteration 2: loglikelihood = -2869.406464695619, backtracks = 0, tol = 0.035126790460779864 Iteration 3: loglikelihood = -2868.084702693443, backtracks = 0, tol = 0.0055693496163324524 Iteration 4: loglikelihood = -2868.034423817725, backtracks = 0, tol = 0.001118951762895177 Iteration 5: loglikelihood = -2868.030857635375, backtracks = 0, tol = 0.00031182601179138955 Iteration 6: loglikelihood = -2868.0305288614227, backtracks = 0, tol = 0.00010393305949947338 Iteration 7: loglikelihood = -2868.0304966516946, backtracks = 0, tol = 3.100862049859014e-5 0.404450 seconds (43.84 k allocations: 5.329 MiB, 62.51% compilation time) Test Summary: | Pass Total Time multivariate fit_iht SnpLinAlg | 7 7 11.8s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse Multivariate Gaussian regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 12 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -2878.028812628852, backtracks = 0, tol = 2.5661768673084553 Iteration 2: loglikelihood = -2868.563037890196, backtracks = 0, tol = 0.024335274263285057 Iteration 3: loglikelihood = -2868.0815051475474, backtracks = 0, tol = 0.004072558228741048 Iteration 4: loglikelihood = -2868.0352100240902, backtracks = 0, tol = 0.0013135682973484317 Iteration 5: loglikelihood = -2868.0309297231934, backtracks = 0, tol = 0.000386434110747091 Iteration 6: loglikelihood = -2868.0305335492912, backtracks = 0, tol = 0.00011924564415557833 Iteration 7: loglikelihood = -2868.0304968517494, backtracks = 0, tol = 3.603726989721193e-5 1.881720 seconds (256.79 k allocations: 167.477 MiB, 54.33% compilation time) Test Summary: | Pass Total Time initialze beta | 5 5 2.5s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** ┌ Warning: accessing `Type.name` is deprecated without replacement. If for detection, use `Base.isType(x)`. │ caller = ProgressMeter.Progress(n::Int64, desc::String, offset::Int64; kwargs::Base.Pairs{Symbol, Union{}, Nothing, @NamedTuple{}}) at deprecated.jl:5 └ @ ProgressMeter ~/.julia/packages/ProgressMeter/N660J/src/deprecated.jl:5 Cross validating... 3%|█ | ETA: 0:03:23 Cross validating... 11%|███▌ | ETA: 0:00:57 Cross validating... 14%|████▋ | ETA: 0:00:44 Cross validating... 17%|█████▋ | ETA: 0:00:35 Cross validating... 21%|██████▋ | ETA: 0:00:29 Cross validating... 24%|███████▋ | ETA: 0:00:25 Cross validating... 27%|████████▋ | ETA: 0:00:22 Cross validating... 30%|█████████▋ | ETA: 0:00:19 Cross validating... 33%|██████████▋ | ETA: 0:00:17 Cross validating... 37%|███████████▋ | ETA: 0:00:15 Cross validating... 40%|████████████▊ | ETA: 0:00:13 Cross validating... 43%|█████████████▊ | ETA: 0:00:12 Cross validating... 46%|██████████████▊ | ETA: 0:00:10 Cross validating... 49%|███████████████▊ | ETA: 0:00:09 Cross validating... 52%|████████████████▊ 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validating... 100%|████████████████████████████████| Time: 0:00:11 Crossvalidation Results: k MSE 0 3340.1915119908804 1 1524.7670653630646 2 1151.2205104018058 3 976.685182908203 4 740.0046175633415 5 468.3957443295121 6 432.364989285948 7 376.5314706066106 8 362.6832125138314 9 361.7514972304219 10 370.59803433430034 11 377.5327889668545 12 370.29403476360426 13 373.36497162731234 14 385.28472481826896 15 376.25657444343585 16 381.6094699452229 17 409.3869321868427 18 381.812944904904 19 437.48936903655846 20 399.23554952430936 Best k = 9 11.539070 seconds (11.70 M allocations: 308.011 MiB, 0.80% gc time, 59.52% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 5%|█▌ | ETA: 0:00:04 Cross validating... 8%|██▌ | ETA: 0:00:04 Cross validating... 11%|███▌ | ETA: 0:00:04 Cross validating... 14%|████▋ | ETA: 0:00:04 Cross validating... 17%|█████▋ | ETA: 0:00:04 Cross validating... 21%|██████▋ | ETA: 0:00:04 Cross validating... 24%|███████▋ | ETA: 0:00:04 Cross validating... 27%|████████▋ | ETA: 0:00:03 Cross validating... 30%|█████████▋ | ETA: 0:00:03 Cross validating... 33%|██████████▋ | ETA: 0:00:03 Cross validating... 37%|███████████▋ | ETA: 0:00:03 Cross validating... 40%|████████████▊ | ETA: 0:00:03 Cross validating... 43%|█████████████▊ | ETA: 0:00:03 Cross validating... 46%|██████████████▊ | ETA: 0:00:02 Cross validating... 49%|███████████████▊ | ETA: 0:00:02 Cross validating... 52%|████████████████▊ | ETA: 0:00:02 Cross validating... 56%|█████████████████▊ | ETA: 0:00:02 Cross validating... 59%|██████████████████▊ | ETA: 0:00:02 Cross validating... 60%|███████████████████▎ | ETA: 0:00:02 Cross validating... 63%|████████████████████▍ | ETA: 0:00:02 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:02 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:01 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:01 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:01 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:01 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:01 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:01 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:00 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:04 Crossvalidation Results: k MSE 0 3340.1915119908804 1 1525.8559126883617 2 1154.7325465222866 3 978.6082036308137 4 741.9056030679409 5 471.42174183023104 6 436.62497326171206 7 388.8308883801334 8 375.8635613924329 9 377.86686884553217 10 388.83726786505576 11 398.0131572527955 12 398.6070183653128 13 404.3940256473146 14 416.03671609111694 15 418.1239070498537 16 426.9345602681216 17 430.11042242934786 18 435.199335271196 19 456.41806118143995 20 440.85256079096393 Best k = 8 4.958047 seconds (11.03 M allocations: 232.695 MiB, 0.99% gc time, 1.39% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, normal model | 3 3 17.3s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:05:44 Cross validating... 10%|███ | ETA: 0:01:48 Cross validating... 16%|█████▏ | ETA: 0:01:01 Cross validating... 19%|██████▏ | ETA: 0:00:49 Cross validating... 24%|███████▋ | ETA: 0:00:38 Cross validating... 29%|█████████▏ | ETA: 0:00:30 Cross validating... 33%|██████████▋ | ETA: 0:00:24 Cross validating... 40%|████████████▊ | ETA: 0:00:19 Cross validating... 46%|██████████████▊ | ETA: 0:00:14 Cross validating... 52%|████████████████▊ | ETA: 0:00:11 Cross validating... 57%|██████████████████▎ | ETA: 0:00:09 Cross validating... 62%|███████████████████▊ | ETA: 0:00:08 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:06 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:05 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:03 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:02 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:01 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:01 Cross validating... 100%|████████████████████████████████| Time: 0:00:13 Crossvalidation Results: k MSE 0 1704.0600762939455 1 1417.45146875 2 1130.8825018920897 3 852.196940612793 4 665.6110124511719 5 540.9377231445313 6 457.04047042846685 7 403.79274972534176 8 363.35701882934575 9 368.5260715942383 10 368.87391690063475 11 371.2265381469727 12 373.1671583862305 13 376.4113221130371 14 378.9314528808594 15 384.0013336486817 16 385.2211520996094 17 388.80986712646484 18 390.3811181640625 19 393.14724011230464 20 428.76918542480473 Best k = 8 14.502541 seconds (12.31 M allocations: 306.878 MiB, 0.45% gc time, 83.36% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 6%|██ | ETA: 0:00:02 Cross validating... 13%|████▏ | ETA: 0:00:02 Cross validating... 17%|█████▋ | ETA: 0:00:02 Cross validating... 22%|███████▏ | ETA: 0:00:02 Cross validating... 25%|████████▏ | ETA: 0:00:02 Cross validating... 30%|█████████▋ | ETA: 0:00:02 Cross validating... 35%|███████████▏ | ETA: 0:00:02 Cross validating... 41%|█████████████▎ | ETA: 0:00:02 Cross validating... 48%|███████████████▎ | ETA: 0:00:01 Cross validating... 54%|█████████████████▎ | ETA: 0:00:01 Cross validating... 59%|██████████████████▊ | ETA: 0:00:01 Cross validating... 63%|████████████████████▍ | ETA: 0:00:01 Cross validating... 68%|█████████████████████▉ | ETA: 0:00:01 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:01 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:00 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:00 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:00 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:02 Crossvalidation Results: k MSE 0 1704.0600762939455 1 1420.5762518310548 2 1131.5849588623046 3 855.0420641479493 4 674.8908276977539 5 545.9770030517578 6 459.1417315979005 7 406.09286169433597 8 367.2887281188965 9 381.6224089660645 10 384.0946915588379 11 389.609864440918 12 394.59947103881836 13 395.5088812561035 14 397.5371060791016 15 411.7367098388672 16 408.11374301147464 17 423.46475250244146 18 421.09763107299807 19 429.0834950866699 20 434.3221114807129 Best k = 8 2.700798 seconds (10.62 M allocations: 195.240 MiB, 1.67% gc time, 1.74% compilation time) Test Summary: | Pass Total Time Cross validation on Float32 matrix, normal model | 2 2 18.4s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:01:01 Cross validating... 6%|██ | ETA: 0:00:32 Cross validating... 10%|███ | ETA: 0:00:22 Cross validating... 13%|████▏ | ETA: 0:00:18 Cross validating... 16%|█████▏ | ETA: 0:00:15 Cross validating... 19%|██████▏ | ETA: 0:00:12 Cross validating... 22%|███████▏ | ETA: 0:00:11 Cross validating... 25%|████████▏ | ETA: 0:00:10 Cross validating... 29%|█████████▏ | ETA: 0:00:09 Cross validating... 32%|██████████▏ | ETA: 0:00:08 Cross 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ETA: 0:00:01 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:01 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:01 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:00 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:07 Crossvalidation Results: k MSE 0 463.11367197357436 1 317.11828101406763 2 290.9202621027711 3 280.3735954491305 4 259.53569562275146 5 231.75243634863045 6 232.54334936020462 7 239.15896448923155 8 237.2472859823302 9 243.10658343202795 10 242.11443205021885 11 241.35756040235395 12 260.26739697315173 13 245.97726411707038 14 244.07541998147843 15 276.47365178405937 16 264.8256802277093 17 267.387087635467 18 281.59251261690866 19 258.9663433938632 20 284.75236498943445 Best k = 5 8.292883 seconds (17.58 M allocations: 413.345 MiB, 0.91% gc time, 31.94% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:04 Cross validating... 6%|██ | ETA: 0:00:04 Cross validating... 10%|███ | ETA: 0:00:05 Cross validating... 13%|████▏ | ETA: 0:00:05 Cross validating... 16%|█████▏ | ETA: 0:00:05 Cross validating... 19%|██████▏ | ETA: 0:00:04 Cross validating... 21%|██████▋ | ETA: 0:00:04 Cross validating... 24%|███████▋ | ETA: 0:00:04 Cross validating... 27%|████████▋ | ETA: 0:00:04 Cross validating... 30%|█████████▋ | ETA: 0:00:04 Cross validating... 33%|██████████▋ | ETA: 0:00:04 Cross validating... 37%|███████████▋ | ETA: 0:00:04 Cross validating... 40%|████████████▊ | ETA: 0:00:03 Cross validating... 43%|█████████████▊ | ETA: 0:00:03 Cross validating... 46%|██████████████▊ | ETA: 0:00:03 Cross 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0:00:00 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:05 Crossvalidation Results: k MSE 0 463.11367197357436 1 317.97778846776566 2 291.39466730820186 3 278.5523590689537 4 261.7746604828763 5 236.62610983588672 6 240.7186075553056 7 249.67441844796326 8 254.70582643370685 9 257.1135108321365 10 272.1321304139037 11 269.151531838649 12 277.83788916477215 13 284.50052988404434 14 287.5788363889711 15 287.39192224628437 16 296.61634330688366 17 293.9070665133761 18 310.14892371457574 19 307.86858159821236 20 320.533487149308 Best k = 5 5.835811 seconds (17.94 M allocations: 375.202 MiB, 1.15% gc time, 1.00% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, logistic model | 2 2 14.5s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:45 Cross validating... 8%|██▌ | ETA: 0:00:19 Cross validating... 13%|████▏ | ETA: 0:00:12 Cross validating... 16%|█████▏ | ETA: 0:00:10 Cross validating... 19%|██████▏ | ETA: 0:00:09 Cross validating... 22%|███████▏ | ETA: 0:00:08 Cross validating... 25%|████████▏ | ETA: 0:00:07 Cross validating... 29%|█████████▏ | ETA: 0:00:06 Cross validating... 32%|██████████▏ | ETA: 0:00:06 Cross validating... 35%|███████████▏ | ETA: 0:00:05 Cross validating... 38%|████████████▎ | ETA: 0:00:05 Cross validating... 41%|█████████████▎ | ETA: 0:00:04 Cross validating... 44%|██████████████▎ | ETA: 0:00:04 Cross validating... 48%|███████████████▎ | ETA: 0:00:04 Cross validating... 51%|████████████████▎ | ETA: 0:00:04 Cross validating... 54%|█████████████████▎ | ETA: 0:00:03 Cross validating... 57%|██████████████████▎ | ETA: 0:00:03 Cross validating... 60%|███████████████████▎ | ETA: 0:00:03 Cross validating... 63%|████████████████████▍ | ETA: 0:00:02 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:02 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:02 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:02 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:01 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:01 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:01 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:01 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:01 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:05 Crossvalidation Results: k MSE 0 463.57241775345835 1 434.1787267458682 2 407.36633817947217 3 391.02863733899983 4 369.87986278635026 5 346.38927207840266 6 345.1834951549797 7 348.2854334792403 8 352.29840913868804 9 351.5634176161704 10 357.88842761059317 11 357.02956235615227 12 367.6452903992916 13 362.04640967660396 14 384.6001000161815 15 402.60909570697083 16 386.6585808822842 17 388.24728535954216 18 393.90631817987577 19 370.0883500223362 20 356.52315112920803 Best k = 6 6.722834 seconds (16.57 M allocations: 390.300 MiB, 5.58% gc time, 36.61% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:03 Cross validating... 6%|██ | ETA: 0:00:04 Cross validating... 10%|███ | ETA: 0:00:03 Cross validating... 13%|████▏ | ETA: 0:00:03 Cross validating... 16%|█████▏ | ETA: 0:00:03 Cross validating... 19%|██████▏ | ETA: 0:00:03 Cross validating... 22%|███████▏ | ETA: 0:00:03 Cross validating... 25%|████████▏ | ETA: 0:00:03 Cross validating... 29%|█████████▏ | ETA: 0:00:03 Cross validating... 32%|██████████▏ | ETA: 0:00:03 Cross validating... 35%|███████████▏ | ETA: 0:00:03 Cross validating... 38%|████████████▎ | ETA: 0:00:03 Cross validating... 41%|█████████████▎ | ETA: 0:00:02 Cross validating... 44%|██████████████▎ | ETA: 0:00:02 Cross validating... 48%|███████████████▎ | ETA: 0:00:02 Cross validating... 51%|████████████████▎ | ETA: 0:00:02 Cross validating... 54%|█████████████████▎ | ETA: 0:00:02 Cross validating... 57%|██████████████████▎ | ETA: 0:00:02 Cross validating... 60%|███████████████████▎ | ETA: 0:00:02 Cross validating... 63%|████████████████████▍ | ETA: 0:00:02 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:01 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:01 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:01 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:01 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:01 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:01 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:01 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:00 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:04 Crossvalidation Results: k MSE 0 463.57241775345835 1 434.5138320293306 2 408.12652691635316 3 392.41868165304163 4 372.3297008378915 5 349.1631018281411 6 351.7162693591246 7 358.21165317553215 8 370.8470374132426 9 375.9064733719839 10 384.4617860479276 11 389.0335749287412 12 405.4918390046657 13 409.0327426303147 14 424.346822354035 15 432.19332837273106 16 435.62903243102534 17 433.39572529651616 18 446.77617210429116 19 451.0657427916706 20 445.59050823074153 Best k = 5 4.193746 seconds (17.31 M allocations: 356.390 MiB, 1.27% gc time, 1.70% compilation time) Test Summary: | Pass Total Time Cross validation on Float64 matrix, logistic model | 2 2 11.8s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:55 Cross validating... 6%|██ | ETA: 0:00:29 Cross validating... 10%|███ | ETA: 0:00:20 Cross validating... 13%|████▏ | ETA: 0:00:16 Cross validating... 16%|█████▏ | ETA: 0:00:13 Cross validating... 19%|██████▏ | ETA: 0:00:11 Cross validating... 22%|███████▏ | ETA: 0:00:10 Cross validating... 25%|████████▏ | ETA: 0:00:09 Cross validating... 29%|█████████▏ | ETA: 0:00:08 Cross validating... 32%|██████████▏ | ETA: 0:00:07 Cross validating... 33%|██████████▋ | ETA: 0:00:07 Cross validating... 37%|███████████▋ | ETA: 0:00:06 Cross validating... 40%|████████████▊ | ETA: 0:00:06 Cross validating... 43%|█████████████▊ | ETA: 0:00:05 Cross validating... 46%|██████████████▊ | ETA: 0:00:05 Cross validating... 49%|███████████████▊ | ETA: 0:00:04 Cross validating... 52%|████████████████▊ | ETA: 0:00:04 Cross validating... 56%|█████████████████▊ | ETA: 0:00:04 Cross validating... 59%|██████████████████▊ | ETA: 0:00:03 Cross validating... 62%|███████████████████▊ | ETA: 0:00:03 Cross validating... 65%|████████████████████▉ | ETA: 0:00:03 Cross validating... 68%|█████████████████████▉ | ETA: 0:00:02 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:02 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:02 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:02 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:01 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:01 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:01 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:01 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:07 Crossvalidation Results: k MSE 0 644.0873763083249 1 504.9472343876795 2 412.18182626245175 3 386.8075321457156 4 353.4526378039352 5 349.0762736407891 6 339.76813385538156 7 346.5519930400282 8 343.74327381297064 9 346.52387097169856 10 346.0371011894028 11 345.89893173554947 12 348.20199765498944 13 362.30324038262523 14 359.0291752561279 15 369.1310739140299 16 351.1828952294395 17 353.27503487181116 18 354.1214955285378 19 361.3995357220829 20 357.7928314997296 Best k = 6 7.731519 seconds (15.71 M allocations: 380.327 MiB, 0.94% gc time, 30.71% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:04 Cross validating... 6%|██ | ETA: 0:00:05 Cross validating... 10%|███ | ETA: 0:00:04 Cross validating... 13%|████▏ | ETA: 0:00:04 Cross validating... 16%|█████▏ | ETA: 0:00:04 Cross validating... 19%|██████▏ | ETA: 0:00:04 Cross validating... 22%|███████▏ | ETA: 0:00:04 Cross validating... 25%|████████▏ | ETA: 0:00:04 Cross validating... 29%|█████████▏ | ETA: 0:00:04 Cross validating... 32%|██████████▏ | ETA: 0:00:04 Cross validating... 33%|██████████▋ | ETA: 0:00:04 Cross validating... 37%|███████████▋ | ETA: 0:00:04 Cross validating... 40%|████████████▊ | ETA: 0:00:03 Cross validating... 43%|█████████████▊ | ETA: 0:00:03 Cross validating... 46%|██████████████▊ | ETA: 0:00:03 Cross validating... 49%|███████████████▊ | ETA: 0:00:03 Cross validating... 52%|████████████████▊ | ETA: 0:00:03 Cross validating... 56%|█████████████████▊ | ETA: 0:00:02 Cross validating... 59%|██████████████████▊ | ETA: 0:00:02 Cross validating... 62%|███████████████████▊ | ETA: 0:00:02 Cross validating... 65%|████████████████████▉ | ETA: 0:00:02 Cross validating... 68%|█████████████████████▉ | ETA: 0:00:02 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:02 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:01 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:01 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:01 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:01 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:01 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:01 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:05 Crossvalidation Results: k MSE 0 644.0873763083249 1 501.16561644901924 2 414.2395393005737 3 388.3239853272688 4 356.91422556113446 5 353.3502074549491 6 346.21596394277304 7 366.10393038504435 8 351.5088321348966 9 368.98759912218355 10 369.162280446103 11 369.3685253027517 12 378.064877128762 13 376.5063229920808 14 390.143928708134 15 386.63599717107604 16 378.5601580717569 17 394.1686571726453 18 396.56621964379883 19 405.6689322199905 20 410.722867301501 Best k = 6 5.692216 seconds (14.82 M allocations: 301.822 MiB, 0.96% gc time, 1.07% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, Poisson model | 2 2 13.9s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:01:31 Cross validating... 6%|██ | ETA: 0:00:46 Cross validating... 10%|███ | ETA: 0:00:40 Cross validating... 11%|███▌ | ETA: 0:00:42 Cross validating... 14%|████▋ | ETA: 0:00:38 Cross validating... 16%|█████▏ | ETA: 0:00:40 Cross validating... 17%|█████▋ | ETA: 0:00:40 Cross validating... 19%|██████▏ | ETA: 0:00:37 Cross validating... 21%|██████▋ | ETA: 0:00:37 Cross validating... 22%|███████▏ | ETA: 0:00:38 Cross validating... 24%|███████▋ | ETA: 0:00:39 Cross validating... 25%|████████▏ | ETA: 0:00:39 Cross validating... 27%|████████▋ | ETA: 0:00:39 Cross validating... 29%|█████████▏ | ETA: 0:00:39 Cross validating... 30%|█████████▋ | ETA: 0:00:38 Cross validating... 32%|██████████▏ | ETA: 0:00:38 Cross validating... 33%|██████████▋ | ETA: 0:00:37 Cross validating... 37%|███████████▋ | ETA: 0:00:34 Cross validating... 40%|████████████▊ | ETA: 0:00:30 Cross validating... 43%|█████████████▊ | ETA: 0:00:27 Cross validating... 44%|██████████████▎ | ETA: 0:00:26 Cross validating... 48%|███████████████▎ | ETA: 0:00:23 Cross validating... 49%|███████████████▊ | ETA: 0:00:22 Cross validating... 51%|████████████████▎ | ETA: 0:00:21 Cross validating... 52%|████████████████▊ | ETA: 0:00:21 Cross validating... 54%|█████████████████▎ | ETA: 0:00:20 Cross validating... 56%|█████████████████▊ | ETA: 0:00:20 Cross validating... 57%|██████████████████▎ | ETA: 0:00:19 Cross validating... 59%|██████████████████▊ | ETA: 0:00:18 Cross validating... 60%|███████████████████▎ | ETA: 0:00:18 Cross validating... 62%|███████████████████▊ | ETA: 0:00:17 Cross validating... 63%|████████████████████▍ | ETA: 0:00:17 Cross validating... 65%|████████████████████▉ | ETA: 0:00:16 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:16 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:14 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:13 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:13 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:12 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:11 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:09 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:08 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:07 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:06 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:06 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:05 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:04 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:03 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:03 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:02 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:01 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:01 Cross validating... 100%|████████████████████████████████| Time: 0:00:42 Crossvalidation Results: k MSE 0 334.99523471007603 1 259.9926103207415 2 231.12660333574905 3 222.15762589285043 4 218.93320337254826 5 216.1000369221365 6 216.94425129301524 7 219.62748686216221 8 219.97346479546638 9 220.9719469696372 10 222.7202833987563 11 223.41495730463694 12 223.3570830940438 13 223.8570962939953 14 228.6396350714997 15 225.1783192770746 16 228.60830917299143 17 230.00359690031098 18 229.07205557378177 19 225.21830278238446 20 228.2470151029911 Best k = 5 42.495901 seconds (133.45 M allocations: 3.428 GiB, 1.15% gc time, 5.46% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:04 Cross validating... 6%|██ | ETA: 0:00:05 Cross validating... 8%|██▌ | ETA: 0:00:05 Cross validating... 10%|███ | ETA: 0:00:06 Cross validating... 11%|███▌ | ETA: 0:00:07 Cross validating... 13%|████▏ | ETA: 0:00:07 Cross validating... 14%|████▋ 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0:00:02 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:02 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:02 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:02 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:02 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:02 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:01 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:01 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:01 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:01 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:01 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:01 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:11 Crossvalidation Results: k MSE 0 334.99523471007603 1 260.25076970636053 2 232.15315205061205 3 223.51200855935275 4 220.81629476401727 5 218.99107009476907 6 221.5195107637721 7 227.0733385729264 8 228.86237012055284 9 231.416091169303 10 231.87886136345628 11 235.73429690780108 12 240.85341577906914 13 242.82995924349714 14 256.58034489085645 15 252.63879355590947 16 262.99064486553624 17 265.8226868020538 18 269.859166799132 19 270.43071079713405 20 279.0373449748681 Best k = 5 11.947108 seconds (36.88 M allocations: 768.379 MiB, 1.13% gc time, 0.57% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, NegativeBinomial model | 2 2 54.9s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:01:03 Cross validating... 6%|██ | ETA: 0:00:32 Cross validating... 10%|███ | ETA: 0:00:22 Cross validating... 14%|████▋ | ETA: 0:00:15 Cross validating... 16%|█████▏ | ETA: 0:00:14 Cross validating... 19%|██████▏ | ETA: 0:00:11 Cross validating... 22%|███████▏ | ETA: 0:00:10 Cross validating... 27%|████████▋ | ETA: 0:00:08 Cross validating... 30%|█████████▋ | ETA: 0:00:07 Cross validating... 33%|██████████▋ | ETA: 0:00:06 Cross validating... 38%|████████████▎ | ETA: 0:00:05 Cross validating... 41%|█████████████▎ | ETA: 0:00:05 Cross validating... 46%|██████████████▊ | ETA: 0:00:04 Cross validating... 49%|███████████████▊ | ETA: 0:00:04 Cross validating... 52%|████████████████▊ | ETA: 0:00:03 Cross validating... 57%|██████████████████▎ | ETA: 0:00:03 Cross validating... 60%|███████████████████▎ | ETA: 0:00:03 Cross validating... 63%|████████████████████▍ | ETA: 0:00:02 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:02 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:02 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:02 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:01 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:01 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:01 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:00 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:05 Crossvalidation Results: k MSE 0 709.7238911132813 1 600.8470166015625 2 478.37098138427734 3 399.75837347412113 4 316.3170971069336 5 274.59901690673826 6 232.61785809326173 7 221.00282696533208 8 205.62119918823245 9 198.3431817626953 10 200.94596459960937 11 201.86666357421876 12 202.35683154296873 13 208.02664166259768 14 206.9071481628418 15 209.87240182495117 16 216.0480528869629 17 212.0296098022461 18 217.49209603881837 19 225.60646734619144 20 213.36869631958012 Best k = 9 5.938643 seconds (16.96 M allocations: 336.354 MiB, 2.21% gc time, 44.37% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 5%|█▌ | ETA: 0:00:03 Cross validating... 8%|██▌ | ETA: 0:00:03 Cross validating... 11%|███▌ | ETA: 0:00:03 Cross validating... 14%|████▋ | ETA: 0:00:03 Cross validating... 19%|██████▏ | ETA: 0:00:03 Cross validating... 24%|███████▋ | ETA: 0:00:02 Cross validating... 27%|████████▋ | ETA: 0:00:02 Cross validating... 30%|█████████▋ | ETA: 0:00:02 Cross validating... 33%|██████████▋ | ETA: 0:00:02 Cross validating... 38%|████████████▎ | ETA: 0:00:02 Cross validating... 43%|█████████████▊ | ETA: 0:00:02 Cross validating... 48%|███████████████▎ | ETA: 0:00:02 Cross validating... 52%|████████████████▊ | ETA: 0:00:02 Cross validating... 56%|█████████████████▊ | ETA: 0:00:01 Cross 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212.83695938110353 13 217.36745034790042 14 219.17275009155276 15 218.94907879638671 16 225.10276358032226 17 228.24513723754882 18 225.50167910766604 19 235.0626920776367 20 227.98946899414062 Best k = 9 3.237060 seconds (16.17 M allocations: 286.682 MiB, 1.47% gc time, 1.80% compilation time) Test Summary: | Pass Total Time Cross validation on floating point matrices, NegativeBinomial model | 2 2 9.7s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 2%|▋ | ETA: 0:01:20 Cross validating... 3%|█ | ETA: 0:01:00 Cross validating... 4%|█▎ | ETA: 0:00:48 Cross validating... 5%|█▋ | ETA: 0:00:42 Cross validating... 6%|█▉ | ETA: 0:00:37 Cross validating... 7%|██▎ | ETA: 0:00:33 Cross validating... 8%|██▌ | ETA: 0:00:31 Cross validating... 9%|██▉ | ETA: 0:00:29 Cross 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| ETA: 0:00:01 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:01 Cross validating... 98%|███████████████████████████████▍| ETA: 0:00:00 Cross validating... 99%|███████████████████████████████▋| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:19 Crossvalidation Results: k MSE 1 3696.0497786717997 2 3355.8459149408204 3 2855.1490685664035 4 2668.7623246012517 5 2481.107581036007 6 2298.2563645588143 7 2071.7243823571857 8 1994.3790592135224 9 1991.4375295465272 10 1989.1156338691428 11 1997.8630774850467 12 2015.4950480696452 13 2022.9618643267634 14 2023.0349718751074 15 2063.8007318021364 16 2049.3911035547894 17 2066.526978575171 18 2074.4772956983375 19 2082.6320080433043 20 2084.999761195549 Best k = 10 19.291497 seconds (330.69 k allocations: 226.533 MiB, 0.49% gc time, 8.38% compilation time) Test Summary: | Pass Total Time multivariate cross validation SnpLinAlg | 3 3 24.0s Test Summary: | Pass Total Time wrapper univariate | 20 20 2m00.8s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 2%|▋ | ETA: 0:00:10 Cross validating... 3%|█ | ETA: 0:00:10 Cross validating... 4%|█▎ | ETA: 0:00:11 Cross validating... 5%|█▋ | ETA: 0:00:11 Cross validating... 6%|█▉ | ETA: 0:00:12 Cross validating... 7%|██▎ | ETA: 0:00:12 Cross validating... 8%|██▌ | ETA: 0:00:12 Cross validating... 9%|██▉ | ETA: 0:00:13 Cross validating... 10%|███▎ | ETA: 0:00:14 Cross validating... 11%|███▌ | ETA: 0:00:15 Cross validating... 12%|███▉ | ETA: 0:00:15 Cross validating... 13%|████▏ | ETA: 0:00:16 Cross validating... 14%|████▌ | ETA: 0:00:16 Cross validating... 15%|████▊ | ETA: 0:00:16 Cross validating... 16%|█████▏ | ETA: 0:00:18 Cross validating... 17%|█████▌ | ETA: 0:00:18 Cross validating... 18%|█████▊ | ETA: 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Cross validating... 39%|████████████▌ | ETA: 0:00:14 Cross validating... 40%|████████████▊ | ETA: 0:00:14 Cross validating... 41%|█████████████▏ | ETA: 0:00:14 Cross validating... 42%|█████████████▌ | ETA: 0:00:13 Cross validating... 43%|█████████████▊ | ETA: 0:00:13 Cross validating... 44%|██████████████▏ | ETA: 0:00:13 Cross validating... 45%|██████████████▍ | ETA: 0:00:12 Cross validating... 46%|██████████████▊ | ETA: 0:00:12 Cross validating... 47%|███████████████ | ETA: 0:00:12 Cross validating... 48%|███████████████▍ | ETA: 0:00:12 Cross validating... 49%|███████████████▋ | ETA: 0:00:11 Cross validating... 50%|████████████████ | ETA: 0:00:11 Cross validating... 51%|████████████████▍ | ETA: 0:00:11 Cross validating... 52%|████████████████▋ | ETA: 0:00:11 Cross validating... 53%|█████████████████ | ETA: 0:00:11 Cross validating... 54%|█████████████████▎ | ETA: 0:00:10 Cross validating... 55%|█████████████████▋ | ETA: 0:00:10 Cross validating... 56%|█████████████████▉ | ETA: 0:00:10 Cross validating... 57%|██████████████████▎ | ETA: 0:00:10 Cross validating... 58%|██████████████████▌ | ETA: 0:00:10 Cross validating... 59%|██████████████████▉ | ETA: 0:00:10 Cross validating... 60%|███████████████████▎ | ETA: 0:00:09 Cross validating... 61%|███████████████████▌ | ETA: 0:00:09 Cross validating... 62%|███████████████████▉ | ETA: 0:00:09 Cross validating... 63%|████████████████████▏ | ETA: 0:00:09 Cross validating... 64%|████████████████████▌ | ETA: 0:00:08 Cross validating... 65%|████████████████████▊ | ETA: 0:00:08 Cross validating... 66%|█████████████████████▏ | ETA: 0:00:08 Cross validating... 67%|█████████████████████▌ | ETA: 0:00:07 Cross validating... 68%|█████████████████████▊ | ETA: 0:00:07 Cross validating... 69%|██████████████████████▏ | ETA: 0:00:07 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:07 Cross validating... 71%|██████████████████████▊ | ETA: 0:00:07 Cross validating... 72%|███████████████████████ | ETA: 0:00:06 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:06 Cross validating... 74%|███████████████████████▋ | ETA: 0:00:06 Cross validating... 75%|████████████████████████ | ETA: 0:00:06 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:05 Cross validating... 77%|████████████████████████▋ | ETA: 0:00:05 Cross validating... 78%|█████████████████████████ | ETA: 0:00:05 Cross validating... 79%|█████████████████████████▎ | ETA: 0:00:05 Cross validating... 80%|█████████████████████████▋ | ETA: 0:00:05 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:04 Cross validating... 82%|██████████████████████████▎ | ETA: 0:00:04 Cross validating... 83%|██████████████████████████▌ | ETA: 0:00:04 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:04 Cross validating... 85%|███████████████████████████▎ | ETA: 0:00:03 Cross validating... 86%|███████████████████████████▌ | ETA: 0:00:03 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:03 Cross validating... 88%|████████████████████████████▏ | ETA: 0:00:03 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:02 Cross validating... 90%|████████████████████████████▊ | ETA: 0:00:02 Cross validating... 91%|█████████████████████████████▏ | ETA: 0:00:02 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:02 Cross validating... 93%|█████████████████████████████▊ | ETA: 0:00:02 Cross validating... 94%|██████████████████████████████▏ | ETA: 0:00:01 Cross validating... 95%|██████████████████████████████▍ | ETA: 0:00:01 Cross validating... 96%|██████████████████████████████▊ | ETA: 0:00:01 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:01 Cross validating... 98%|███████████████████████████████▍| ETA: 0:00:00 Cross validating... 99%|███████████████████████████████▋| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:23 Crossvalidation Results: k MSE 1 2838.788679198002 2 2514.3973428708136 3 2305.6176519676274 4 2222.025304867614 5 2075.1670384588365 6 2067.7948989723845 7 2053.427506114907 8 2086.405384830965 9 2080.984460901671 10 2105.131199502364 11 2132.407165368786 12 2138.267187460652 13 2166.002210829576 14 2194.9918295115804 15 2189.890403738045 16 2191.181293229578 17 2209.4669750564362 18 2221.2595493644303 19 2238.7425945763257 20 2253.9559571797727 Best k = 7 **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 2%|▋ | ETA: 0:00:10 Cross validating... 3%|█ | ETA: 0:00:10 Cross validating... 4%|█▎ | ETA: 0:00:11 Cross validating... 5%|█▋ | ETA: 0:00:11 Cross validating... 6%|█▉ | ETA: 0:00:12 Cross validating... 7%|██▎ | ETA: 0:00:12 Cross validating... 8%|██▌ | ETA: 0:00:12 Cross validating... 9%|██▉ | ETA: 0:00:13 Cross validating... 10%|███▎ | ETA: 0:00:14 Cross validating... 11%|███▌ | ETA: 0:00:15 Cross validating... 12%|███▉ | ETA: 0:00:15 Cross validating... 13%|████▏ | ETA: 0:00:16 Cross validating... 14%|████▌ | ETA: 0:00:16 Cross validating... 15%|████▊ | ETA: 0:00:16 Cross validating... 16%|█████▏ | ETA: 0:00:18 Cross validating... 17%|█████▌ | ETA: 0:00:18 Cross validating... 18%|█████▊ | ETA: 0:00:18 Cross validating... 19%|██████▏ | ETA: 0:00:18 Cross validating... 20%|██████▍ | ETA: 0:00:18 Cross validating... 21%|██████▊ | ETA: 0:00:18 Cross validating... 22%|███████ | ETA: 0:00:17 Cross validating... 23%|███████▍ | ETA: 0:00:16 Cross validating... 24%|███████▋ | ETA: 0:00:16 Cross validating... 25%|████████ | ETA: 0:00:16 Cross validating... 26%|████████▍ | ETA: 0:00:15 Cross validating... 27%|████████▋ | ETA: 0:00:15 Cross validating... 28%|█████████ | ETA: 0:00:15 Cross validating... 29%|█████████▎ | ETA: 0:00:15 Cross validating... 30%|█████████▋ | ETA: 0:00:15 Cross validating... 31%|█████████▉ | ETA: 0:00:15 Cross 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ETA: 0:00:11 Cross validating... 51%|████████████████▍ | ETA: 0:00:11 Cross validating... 52%|████████████████▋ | ETA: 0:00:11 Cross validating... 53%|█████████████████ | ETA: 0:00:10 Cross validating... 54%|█████████████████▎ | ETA: 0:00:10 Cross validating... 55%|█████████████████▋ | ETA: 0:00:10 Cross validating... 56%|█████████████████▉ | ETA: 0:00:10 Cross validating... 57%|██████████████████▎ | ETA: 0:00:10 Cross validating... 58%|██████████████████▌ | ETA: 0:00:10 Cross validating... 59%|██████████████████▉ | ETA: 0:00:09 Cross validating... 60%|███████████████████▎ | ETA: 0:00:09 Cross validating... 61%|███████████████████▌ | ETA: 0:00:09 Cross validating... 62%|███████████████████▉ | ETA: 0:00:09 Cross validating... 63%|████████████████████▏ | ETA: 0:00:08 Cross validating... 64%|████████████████████▌ | ETA: 0:00:08 Cross validating... 65%|████████████████████▊ | ETA: 0:00:08 Cross validating... 66%|█████████████████████▏ | ETA: 0:00:08 Cross validating... 67%|█████████████████████▌ | ETA: 0:00:07 Cross validating... 68%|█████████████████████▊ | ETA: 0:00:07 Cross validating... 69%|██████████████████████▏ | ETA: 0:00:07 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:07 Cross validating... 71%|██████████████████████▊ | ETA: 0:00:07 Cross validating... 72%|███████████████████████ | ETA: 0:00:06 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:06 Cross validating... 74%|███████████████████████▋ | ETA: 0:00:06 Cross validating... 75%|████████████████████████ | ETA: 0:00:06 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:05 Cross validating... 77%|████████████████████████▋ | ETA: 0:00:05 Cross validating... 78%|█████████████████████████ | ETA: 0:00:05 Cross validating... 79%|█████████████████████████▎ | ETA: 0:00:05 Cross validating... 80%|█████████████████████████▋ | ETA: 0:00:05 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:04 Cross validating... 82%|██████████████████████████▎ | ETA: 0:00:04 Cross validating... 83%|██████████████████████████▌ | ETA: 0:00:04 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:04 Cross validating... 85%|███████████████████████████▎ | ETA: 0:00:03 Cross validating... 86%|███████████████████████████▌ | ETA: 0:00:03 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:03 Cross validating... 88%|████████████████████████████▏ | ETA: 0:00:03 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:02 Cross validating... 90%|████████████████████████████▊ | ETA: 0:00:02 Cross validating... 91%|█████████████████████████████▏ | ETA: 0:00:02 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:02 Cross validating... 93%|█████████████████████████████▊ | ETA: 0:00:02 Cross validating... 94%|██████████████████████████████▏ | ETA: 0:00:01 Cross validating... 95%|██████████████████████████████▍ | ETA: 0:00:01 Cross validating... 96%|██████████████████████████████▊ | ETA: 0:00:01 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:01 Cross validating... 98%|███████████████████████████████▍| ETA: 0:00:00 Cross validating... 99%|███████████████████████████████▋| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:23 Crossvalidation Results: k MSE 1 2838.788679198002 2 2514.3973428708136 3 2305.6176519676274 4 2222.025304867614 5 2075.1670384588365 6 2067.7948989723845 7 2053.427506114907 8 2086.405384830965 9 2080.984460901671 10 2105.131199502364 11 2132.407165368786 12 2138.267187460652 13 2166.002210829576 14 2194.9918295115804 15 2189.890403738045 16 2191.181293229578 17 2209.4669750564362 18 2221.2595493644303 19 2238.7425945763257 20 2253.9559571797727 Best k = 7 **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 2%|▋ | ETA: 0:00:10 Cross validating... 3%|█ | ETA: 0:00:10 Cross validating... 4%|█▎ | ETA: 0:00:11 Cross validating... 5%|█▋ | ETA: 0:00:11 Cross validating... 6%|█▉ | ETA: 0:00:12 Cross validating... 7%|██▎ | ETA: 0:00:12 Cross validating... 8%|██▌ | ETA: 0:00:12 Cross validating... 9%|██▉ | ETA: 0:00:13 Cross validating... 10%|███▎ | ETA: 0:00:14 Cross validating... 11%|███▌ | ETA: 0:00:15 Cross validating... 12%|███▉ | ETA: 0:00:16 Cross validating... 13%|████▏ | ETA: 0:00:16 Cross validating... 14%|████▌ | ETA: 0:00:16 Cross validating... 15%|████▊ | ETA: 0:00:17 Cross validating... 16%|█████▏ | ETA: 0:00:18 Cross validating... 17%|█████▌ | ETA: 0:00:18 Cross validating... 18%|█████▊ | ETA: 0:00:18 Cross validating... 19%|██████▏ | ETA: 0:00:19 Cross validating... 20%|██████▍ | ETA: 0:00:19 Cross validating... 21%|██████▊ | ETA: 0:00:18 Cross validating... 22%|███████ | ETA: 0:00:17 Cross validating... 23%|███████▍ | ETA: 0:00:17 Cross validating... 24%|███████▋ | 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validating... 44%|██████████████▏ | ETA: 0:00:13 Cross validating... 45%|██████████████▍ | ETA: 0:00:12 Cross validating... 46%|██████████████▊ | ETA: 0:00:12 Cross validating... 47%|███████████████ | ETA: 0:00:12 Cross validating... 48%|███████████████▍ | ETA: 0:00:12 Cross validating... 49%|███████████████▋ | ETA: 0:00:11 Cross validating... 50%|████████████████ | ETA: 0:00:11 Cross validating... 51%|████████████████▍ | ETA: 0:00:11 Cross validating... 52%|████████████████▋ | ETA: 0:00:11 Cross validating... 53%|█████████████████ | ETA: 0:00:11 Cross validating... 54%|█████████████████▎ | ETA: 0:00:10 Cross validating... 55%|█████████████████▋ | ETA: 0:00:10 Cross validating... 56%|█████████████████▉ | ETA: 0:00:10 Cross validating... 57%|██████████████████▎ | ETA: 0:00:10 Cross validating... 58%|██████████████████▌ | ETA: 0:00:10 Cross validating... 59%|██████████████████▉ | ETA: 0:00:10 Cross validating... 60%|███████████████████▎ | ETA: 0:00:09 Cross validating... 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77%|████████████████████████▋ | ETA: 0:00:05 Cross validating... 78%|█████████████████████████ | ETA: 0:00:05 Cross validating... 79%|█████████████████████████▎ | ETA: 0:00:05 Cross validating... 80%|█████████████████████████▋ | ETA: 0:00:05 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:04 Cross validating... 82%|██████████████████████████▎ | ETA: 0:00:04 Cross validating... 83%|██████████████████████████▌ | ETA: 0:00:04 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:04 Cross validating... 85%|███████████████████████████▎ | ETA: 0:00:03 Cross validating... 86%|███████████████████████████▌ | ETA: 0:00:03 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:03 Cross validating... 88%|████████████████████████████▏ | ETA: 0:00:03 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:02 Cross validating... 90%|████████████████████████████▊ | ETA: 0:00:02 Cross validating... 91%|█████████████████████████████▏ | ETA: 0:00:02 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:02 Cross validating... 93%|█████████████████████████████▊ | ETA: 0:00:02 Cross validating... 94%|██████████████████████████████▏ | ETA: 0:00:01 Cross validating... 95%|██████████████████████████████▍ | ETA: 0:00:01 Cross validating... 96%|██████████████████████████████▊ | ETA: 0:00:01 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:01 Cross validating... 98%|███████████████████████████████▍| ETA: 0:00:00 Cross validating... 99%|███████████████████████████████▋| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:23 Crossvalidation Results: k MSE 1 2838.788679198002 2 2514.3973428708136 3 2305.6176519676274 4 2222.025304867614 5 2075.1670384588365 6 2067.7948989723845 7 2053.427506114907 8 2086.405384830965 9 2080.984460901671 10 2105.131199502364 11 2132.407165368786 12 2138.267187460652 13 2166.002210829576 14 2194.9918295115804 15 2189.890403738045 16 2191.181293229578 17 2209.4669750564362 18 2221.2595493644303 19 2238.7425945763257 20 2253.9559571797727 Best k = 7 Test Summary: | Pass Total Time wrapper multivariate | 8 8 1m25.4s read BGEN and VCF: Error During Test at /home/pkgeval/.julia/packages/MendelIHT/ZcxZT/test/wrapper_test.jl:184 Got exception outside of a @test startproc must be called before process Stacktrace: [1] error(s::String) @ Base error.jl:56 [2] process(codec::CodecZlib.ZlibDecompressor, input::TranscodingStreams.Memory, output::TranscodingStreams.Memory, error_ref::TranscodingStreams.Error) @ CodecZlib ~/.julia/packages/CodecZlib/lEc2s/src/decompression.jl:186 [3] decompress(io::IOStream, v::Variant, h::BGEN.Header; decompressed::Nothing) @ BGEN ~/.julia/packages/BGEN/dfgRU/src/genotypes.jl:72 [4] first_allele_dosage!(b::Bgen, v::Variant; T::Type, mean_impute::Bool, clear_decompressed::Bool, data::Nothing, decompressed::Nothing, is_decompressed::Bool) @ BGEN ~/.julia/packages/BGEN/dfgRU/src/genotypes.jl:571 [5] convert_bgen_gt(t::Type{Float64}, b::Bgen) @ MendelIHT ~/.julia/packages/MendelIHT/ZcxZT/src/wrapper.jl:380 [6] macro expansion @ ./timing.jl:741 [inlined] [7] macro expansion @ ~/.julia/packages/MendelIHT/ZcxZT/test/wrapper_test.jl:187 [inlined] [8] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:2246 [inlined] [9] top-level scope @ ~/.julia/packages/MendelIHT/ZcxZT/test/wrapper_test.jl:185 [10] include(mapexpr::Function, mod::Module, _path::String) @ Base Base.jl:326 [11] top-level scope @ ~/.julia/packages/MendelIHT/ZcxZT/test/runtests.jl:20 [12] include(mapexpr::Function, mod::Module, _path::String) @ Base Base.jl:326 [13] top-level scope @ none:6 [14] eval(m::Module, e::Any) @ Core boot.jl:522 [15] exec_options(opts::Base.JLOptions) @ Base client.jl:321 [16] _start() @ Base client.jl:596 Test Summary: | Error Total Time read BGEN and VCF | 1 1 2.8s RNG of the outermost testset: Xoshiro(0xbea2888e58be1b67, 0x0ccf92c655bbdb22, 0x4d355f899b0bd944, 0x032e3e65b9e4db28, 0x7d5fd359766ee939) ERROR: LoadError: Some tests did not pass: 0 passed, 0 failed, 1 errored, 0 broken. in expression starting at /home/pkgeval/.julia/packages/MendelIHT/ZcxZT/test/wrapper_test.jl:184 in expression starting at /home/pkgeval/.julia/packages/MendelIHT/ZcxZT/test/runtests.jl:20 Testing failed after 1063.61s ERROR: LoadError: Package MendelIHT errored during testing Stacktrace: [1] pkgerror(msg::String) @ Pkg.Types /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Types.jl:68 [2] test(ctx::Pkg.Types.Context, pkgs::Vector{PackageSpec}; coverage::Bool, julia_args::Cmd, test_args::Cmd, test_fn::Nothing, force_latest_compatible_version::Bool, allow_earlier_backwards_compatible_versions::Bool, allow_reresolve::Bool) @ Pkg.Operations /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Operations.jl:3247 [3] test(ctx::Pkg.Types.Context, pkgs::Vector{PackageSpec}; coverage::Bool, test_fn::Nothing, julia_args::Cmd, test_args::Cmd, force_latest_compatible_version::Bool, allow_earlier_backwards_compatible_versions::Bool, allow_reresolve::Bool, kwargs::@Kwargs{io::IOContext{IO}}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:587 [4] test(pkgs::Vector{PackageSpec}; io::IOContext{IO}, kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:172 [5] test(pkgs::Vector{String}; kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:160 [6] test(pkg::String; kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:159 [inlined] [7] top-level scope @ /PkgEval.jl/scripts/evaluate.jl:223 [8] include(mod::Module, _path::String) @ Base Base.jl:325 [9] exec_options(opts::Base.JLOptions) @ Base client.jl:355 [10] _start() @ Base client.jl:596 in expression starting at /PkgEval.jl/scripts/evaluate.jl:214 PkgEval failed after 1165.45s: package tests unexpectedly errored