Package evaluation to test MendelIHT on Julia 1.14.0-DEV.2311 (d99fded7bf*) started at 2026-06-10T01:27:33.773 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.14` Set-up completed after 15.85s ################################################################################ # 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 v4.6.0 [66dad0bd] + AliasTables v1.1.3 [4fba245c] + ArrayInterface v7.25.0 [67c07d97] + Automa v1.1.0 ⌅ [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 v0.2.7 [f70d9fcc] + CommonWorldInvalidations v1.0.0 [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 To see why use `status --outdated -m` Installation completed after 6.05s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompiling project... 5.7 s ✓ BGEN 9.4 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`. 28.6 s ✓ MendelIHT 3 dependencies successfully precompiled in 46 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 74.63s ################################################################################ # Testing # Testing MendelIHT Status `/tmp/jl_PxbaaR/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 v0.25.126 [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 v0.34.11 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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/nfRUl/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 21.2s Test Summary: | Pass Total Time deviance | 1 1 0.5s Test Summary: | Pass Total Time update_μ! | 4 4 1.7s Test Summary: | Pass Total Time _choose! | 7 7 10.0s Test Summary: | Pass Total Time _iht_backtrack | 7 7 0.0s Test Summary: | Pass Total Time standardize! | 12 12 1.5s Test Summary: | Pass Total Time project_k! | 2 2 1.2s Test Summary: | Pass Total Time project_group_sparse! | 5 5 1.2s Test Summary: | Pass Total Time maf_weights | 6 6 2.3s **** 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 **** 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 = -1565.79401195372, backtracks = 0, tol = 0.9396574318407026 Iteration 2: loglikelihood = -1473.2421516839743, backtracks = 0, tol = 0.12051463293956821 Iteration 3: loglikelihood = -1467.6080140741253, backtracks = 0, tol = 0.07642437810742957 Iteration 4: loglikelihood = -1462.7588626458817, backtracks = 0, tol = 0.06720593418022153 Iteration 5: loglikelihood = -1462.4504457279568, backtracks = 1, tol = 0.004651985190301196 Iteration 6: loglikelihood = -1462.3695962870606, backtracks = 1, tol = 0.0024973595378271307 Iteration 7: loglikelihood = -1462.3484541651594, backtracks = 1, tol = 0.0013104837894822078 Iteration 8: loglikelihood = -1462.3429530015408, backtracks = 1, tol = 0.0006719428363255373 Iteration 9: loglikelihood = -1462.341530163198, backtracks = 1, tol = 0.00033740322223991653 Iteration 10: loglikelihood = -1462.341164227843, backtracks = 1, tol = 0.00016658727165511238 Iteration 11: loglikelihood = -1462.3410705611254, backtracks = 1, tol = 8.122426816844843e-5 IHT estimated 10 nonzero SNP predictors and 1 non-genetic predictors. Compute time (sec): 0.10440778732299805 Final loglikelihood: -1462.3410705611254 SNP PVE: 0.7344130124177509 Iterations: 11 Selected genetic predictors: 10×2 DataFrame Row │ Position Estimated_β │ Int64 Float64 ─────┼─────────────────────── 1 │ 60 -0.34246 2 │ 394 0.276533 3 │ 661 -0.751474 4 │ 905 0.244886 5 │ 938 1.02526 6 │ 4538 -1.02778 7 │ 5694 0.111375 8 │ 6892 -0.251338 9 │ 7062 -0.123256 10 │ 7373 -0.121135 Selected nongenetic predictors: 1×2 DataFrame Row │ Position Estimated_β │ Int64 Float64 ─────┼─────────────────────── 1 │ 1 0.00793812Test Summary: | Pass Total Time fit normal SnpLinAlg | 4 4 25.1s **** 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 4.0s **** 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 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 = -1296.5354596427103, backtracks = 0, tol = 0.2329569225920474 Iteration 2: loglikelihood = -1281.5778474643735, backtracks = 0, tol = 0.06806952171541569 Iteration 3: loglikelihood = -1275.172892138202, backtracks = 1, tol = 0.06797356964409644 Iteration 4: loglikelihood = -1273.3596722886134, backtracks = 1, tol = 0.017538527855427852 Iteration 5: loglikelihood = -1272.7181287146086, backtracks = 1, tol = 0.014018965138606334 Iteration 6: loglikelihood = -1271.3288126501056, backtracks = 1, tol = 0.07293200262579941 Iteration 7: loglikelihood = -1271.1215674503342, backtracks = 1, tol = 0.004717133333734951 Iteration 8: loglikelihood = -1271.044814244115, backtracks = 1, tol = 0.002971915632945654 Iteration 9: loglikelihood = -1271.018982301366, backtracks = 1, tol = 0.0024908662798521206 Iteration 10: loglikelihood = -1268.2885380899584, backtracks = 1, tol = 0.07708227687396593 Iteration 11: loglikelihood = -1267.7969797697926, backtracks = 0, tol = 0.01361109561038617 Iteration 12: loglikelihood = -1267.7323289633607, backtracks = 0, tol = 0.005895200624174202 Iteration 13: loglikelihood = -1267.7188901373945, backtracks = 0, tol = 0.0021642848834830253 Iteration 14: loglikelihood = -1267.7154737229453, backtracks = 0, tol = 0.0016532685889079051 Iteration 15: loglikelihood = -1267.7145137147922, backtracks = 0, tol = 0.0005185447440573519 Iteration 16: loglikelihood = -1267.7142327866961, backtracks = 0, tol = 0.00048440230743058223 Iteration 17: loglikelihood = -1267.714149065241, backtracks = 0, tol = 0.00014417092263406867 Iteration 18: loglikelihood = -1267.7141239776206, backtracks = 0, tol = 0.00014444848494766477 Iteration 19: loglikelihood = -1267.714116439829, backtracks = 0, tol = 4.573949489094134e-5 Test Summary: | Pass Total Time fit Poisson SnpLinAlg | 4 4 3.3s **** 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 **** 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 = -1410.4576582693278, backtracks = 0, tol = 0.22991384337448678 Iteration 2: loglikelihood = -1398.4525028727892, backtracks = 0, tol = 0.09891318850824579 Iteration 3: loglikelihood = -1397.1021882684786, backtracks = 1, tol = 0.018729986709601954 Iteration 4: loglikelihood = -1396.643796337857, backtracks = 1, tol = 0.013333279137628438 Iteration 5: loglikelihood = -1396.5109099495137, backtracks = 1, tol = 0.007830496939356488 Iteration 6: loglikelihood = -1395.3264067473353, backtracks = 1, tol = 0.06680680865873721 Iteration 7: loglikelihood = -1395.0260503410984, backtracks = 0, tol = 0.08726076868253645 Iteration 8: loglikelihood = -1392.3334445624962, backtracks = 0, tol = 0.08316837420420799 Iteration 9: loglikelihood = -1392.1420473045002, backtracks = 1, tol = 0.008788568466527863 Iteration 10: loglikelihood = -1392.0919037902481, backtracks = 1, tol = 0.004623297852799724 Iteration 11: loglikelihood = -1392.078460471034, backtracks = 1, tol = 0.002369466576314377 Iteration 12: loglikelihood = -1392.0747837144495, backtracks = 1, tol = 0.0011625243860299568 Iteration 13: loglikelihood = -1392.0737703514092, backtracks = 1, tol = 0.0005355956536678366 Iteration 14: loglikelihood = -1392.073494006896, backtracks = 1, tol = 0.00030687768122845125 Iteration 15: loglikelihood = -1392.0734203405698, backtracks = 1, tol = 0.00016920001952391535 Iteration 16: loglikelihood = -1392.073401107947, backtracks = 1, tol = 8.87918959000384e-5 Test Summary: | Pass Total Time fit NegativeBinomial SnpLinAlg | 4 4 1.3s **** 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 **** 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 = -1791.3078103338864, backtracks = 0, tol = 0.7747303421116436 Iteration 2: loglikelihood = -1499.5944574902671, backtracks = 0, tol = 0.11368089087124908 Iteration 3: loglikelihood = -1444.4907499817277, backtracks = 0, tol = 0.040913732013797076 Iteration 4: loglikelihood = -1437.0169028180842, backtracks = 0, tol = 0.02796936956350395 Iteration 5: loglikelihood = -1436.7186253284083, backtracks = 0, tol = 0.026462913651961222 Iteration 6: loglikelihood = -1433.42793685195, backtracks = 0, tol = 0.0249760868751411 Iteration 7: loglikelihood = -1433.2013445144974, backtracks = 0, tol = 0.002586821220335813 Iteration 8: loglikelihood = -1433.1985028417207, backtracks = 1, tol = 0.00014038220052766697 Iteration 9: loglikelihood = -1433.1066071683786, backtracks = 0, tol = 0.02548679734297348 Iteration 10: loglikelihood = -1432.971208644023, backtracks = 1, tol = 0.0012140213218551088 Iteration 11: loglikelihood = -1432.9349555044566, backtracks = 1, tol = 0.0006647398188287945 Iteration 12: loglikelihood = -1432.9252960563688, backtracks = 1, tol = 0.0003502470922792176 Iteration 13: loglikelihood = -1432.9227551935942, backtracks = 1, tol = 0.00017793195394261467 Iteration 14: loglikelihood = -1432.922097366704, backtracks = 1, tol = 9.071630014303222e-5 Test Summary: | Pass Total Time fit with >1 non-genetic covariates SnpLinAlg | 5 5 1.7s **** 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 **** 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 = -1559.9453906201752, backtracks = 0, tol = 0.32744631566664045 Iteration 2: loglikelihood = -1462.169287254493, backtracks = 0, tol = 0.05803696585827952 Iteration 3: loglikelihood = -1436.648434633705, backtracks = 0, tol = 0.03821780905305451 Iteration 4: loglikelihood = -1433.6587201024759, backtracks = 0, tol = 0.027101020139861594 Iteration 5: loglikelihood = -1433.5722388067452, backtracks = 1, tol = 0.0010669259523509906 Iteration 6: loglikelihood = -1433.5347478510942, backtracks = 0, tol = 0.027930996199662647 Iteration 7: loglikelihood = -1433.4555411760111, backtracks = 1, tol = 0.001036400916040688 Iteration 8: loglikelihood = -1433.4352275554816, backtracks = 1, tol = 0.0005326859720007848 Iteration 9: loglikelihood = -1433.4300198374804, backtracks = 1, tol = 0.00027195450380880406 Iteration 10: loglikelihood = -1433.428686731534, backtracks = 1, tol = 0.00013782510662096407 Iteration 11: loglikelihood = -1433.4283462706444, backtracks = 1, tol = 6.934800076186617e-5 Test Summary: | Pass Total Time model selection on non-genetic covariates | 5 5 0.9s **** 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 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 12.6s **** 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 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 = -1482.6092920782366, backtracks = 0, tol = 0.23268484932999925 Iteration 2: loglikelihood = -1428.4440402572802, backtracks = 0, tol = 0.10084016493463019 Iteration 3: loglikelihood = -1403.2103011083504, backtracks = 0, tol = 0.14419569326016535 Iteration 4: loglikelihood = -1376.3350826454368, backtracks = 0, tol = 0.10974244200662067 Iteration 5: loglikelihood = -1361.0434131136235, backtracks = 0, tol = 0.060987111331758666 Iteration 6: loglikelihood = -1358.447142018099, backtracks = 0, tol = 0.02546954813642346 Iteration 7: loglikelihood = -1357.8648899999025, backtracks = 0, tol = 0.012324495908578209 Iteration 8: loglikelihood = -1357.678117458449, backtracks = 0, tol = 0.0091763589763683 Iteration 9: loglikelihood = -1355.5059211399664, backtracks = 0, tol = 0.061216540738797086 Iteration 10: loglikelihood = -1355.3042296755252, backtracks = 1, tol = 0.0038014894473114304 Iteration 11: loglikelihood = -1355.2314402708307, backtracks = 1, tol = 0.002446205054437304 Iteration 12: loglikelihood = -1355.2094826796508, backtracks = 1, tol = 0.0014504439472231587 Iteration 13: loglikelihood = -1355.2023184426057, backtracks = 1, tol = 0.0011211032803038294 Iteration 14: loglikelihood = -1354.4486858572277, backtracks = 1, tol = 0.0675974355826666 Iteration 15: loglikelihood = -1354.1987038884427, backtracks = 0, tol = 0.008197626383738388 Iteration 16: loglikelihood = -1354.167833181652, backtracks = 0, tol = 0.002593574273593744 Iteration 17: loglikelihood = -1354.1613186119175, backtracks = 0, tol = 0.001199180891069784 Iteration 18: loglikelihood = -1354.1596917696365, backtracks = 0, tol = 0.0007872429541761682 Iteration 19: loglikelihood = -1354.1592884918966, backtracks = 1, tol = 0.00018268479415679928 Iteration 20: loglikelihood = -1354.1591100165406, backtracks = 2, tol = 0.00015764198365559334 Iteration 21: loglikelihood = -1354.1590081542595, backtracks = 2, tol = 0.00011778719655173832 Iteration 22: loglikelihood = -1354.1589505075735, backtracks = 2, tol = 8.941669224449638e-5 1.157538 seconds (3.58 M allocations: 67.868 MiB, 60.46% 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 = -1526.267223368313, backtracks = 0, tol = 0.23268484932999925 Iteration 2: loglikelihood = -1485.250375346527, backtracks = 0, tol = 0.1293025203515781 Iteration 3: loglikelihood = -1449.268931383687, backtracks = 0, tol = 0.10797823473365183 Iteration 4: loglikelihood = -1430.2812524378487, backtracks = 0, tol = 0.08697279855930892 Iteration 5: loglikelihood = -1418.6138803054985, backtracks = 0, tol = 0.08146342056658147 Iteration 6: loglikelihood = -1409.703734370537, backtracks = 0, tol = 0.01471264046499701 Iteration 7: loglikelihood = -1403.3791775720624, backtracks = 0, tol = 0.08425771366333513 Iteration 8: loglikelihood = -1397.3987221709551, backtracks = 0, tol = 0.008725610553182063 Iteration 9: loglikelihood = -1392.8509499073086, backtracks = 0, tol = 0.07765198933861081 Iteration 10: loglikelihood = -1388.7770260247378, backtracks = 0, tol = 0.007427097174787349 Iteration 11: loglikelihood = -1385.6562130474017, backtracks = 0, tol = 0.07833129836575382 Iteration 12: loglikelihood = -1382.8074832434352, backtracks = 0, tol = 0.07836073436255084 Iteration 13: loglikelihood = -1380.2074811934895, backtracks = 0, tol = 0.007286844469657476 Iteration 14: loglikelihood = -1378.215568016606, backtracks = 0, tol = 0.08047984863191218 Iteration 15: loglikelihood = -1376.0655004970931, backtracks = 0, tol = 0.007960202033518403 Iteration 16: loglikelihood = -1374.769870345051, backtracks = 0, tol = 0.07523515990142207 Iteration 17: loglikelihood = -1373.1061664238123, backtracks = 0, tol = 0.07519105355882723 Iteration 18: loglikelihood = -1372.0066382656005, backtracks = 0, tol = 0.07365318978538798 Iteration 19: loglikelihood = -1370.6566019503073, backtracks = 0, tol = 0.007584782836700953 Iteration 20: loglikelihood = -1369.619722444554, backtracks = 0, tol = 0.08011546698292223 Iteration 21: loglikelihood = -1368.3803099541788, backtracks = 0, tol = 0.008009895435155892 Iteration 22: loglikelihood = -1367.4962542970422, backtracks = 0, tol = 0.0012481361129822004 Iteration 23: loglikelihood = -1366.6862612696882, backtracks = 0, tol = 0.00030333001071846093 Iteration 24: loglikelihood = -1366.6392626226545, backtracks = 0, tol = 0.07966994566565291 Iteration 25: loglikelihood = -1365.6606757853867, backtracks = 0, tol = 0.009131043234891738 Iteration 26: loglikelihood = -1364.9167156209546, backtracks = 0, tol = 0.07426538419651106 Iteration 27: loglikelihood = -1364.7419155712162, backtracks = 0, tol = 0.07429097539684025 Iteration 28: loglikelihood = -1364.0175469959242, backtracks = 0, tol = 0.007880402373930234 Iteration 29: loglikelihood = -1363.4013067416906, backtracks = 0, tol = 0.0789290764669777 Iteration 30: loglikelihood = -1362.6803350793539, backtracks = 0, tol = 0.008076415937219777 Iteration 31: loglikelihood = -1362.257865996922, backtracks = 0, tol = 0.0013287592782594002 Iteration 32: loglikelihood = -1361.8622290282508, backtracks = 0, tol = 0.0002779617146708613 Iteration 33: loglikelihood = -1361.1660755440055, backtracks = 1, tol = 8.06053611280072e-5 0.359482 seconds (1.21 M allocations: 22.117 MiB, 10.54% 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 = -3818.0984, backtracks = 0, tol = 0.09193108976334215 Iteration 2: loglikelihood = -3760.2632, backtracks = 0, tol = 0.04445161377793883 Iteration 3: loglikelihood = -3755.7102, backtracks = 1, tol = 0.01408277962213813 Iteration 4: loglikelihood = -3730.0679, backtracks = 1, tol = 0.06745251452744681 Iteration 5: loglikelihood = -3702.0015, backtracks = 0, tol = 0.08770621083387797 Iteration 6: loglikelihood = -3696.5862, backtracks = 1, tol = 0.008660501020277166 Iteration 7: loglikelihood = -3694.7773, backtracks = 1, tol = 0.006170103361317508 Iteration 8: loglikelihood = -3694.1685, backtracks = 1, tol = 0.003792958959716751 Iteration 9: loglikelihood = -3693.9807, backtracks = 1, tol = 0.0026716580206254097 Iteration 10: loglikelihood = -3693.93, backtracks = 1, tol = 0.0015277117527530335 Iteration 11: loglikelihood = -3693.9185, backtracks = 1, tol = 0.0008030459217772707 Iteration 12: loglikelihood = -3693.9163, backtracks = 1, tol = 0.0004091417418527756 Iteration 13: loglikelihood = -3693.9163, backtracks = 1, tol = 0.00020712505704501436 Iteration 14: loglikelihood = -3693.9194, backtracks = 3, tol = 2.605745095120085e-5 30.370149 seconds (20.51 M allocations: 885.589 MiB, 1.16% gc time, 97.95% 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 = -3683.133, backtracks = 0, tol = 0.09193108976334215 Iteration 2: loglikelihood = -3534.91, backtracks = 0, tol = 0.045817587504899386 Iteration 3: loglikelihood = -3296.788, backtracks = 1, tol = 0.012894522572841976 Iteration 4: loglikelihood = -3032.6033, backtracks = 1, tol = 0.006151603568487319 Iteration 5: loglikelihood = -2877.0693, backtracks = 0, tol = 0.09402843403635486 Iteration 6: loglikelihood = -2744.363, backtracks = 0, tol = 0.0945557323831355 Iteration 7: loglikelihood = -2607.9902, backtracks = 0, tol = 0.09490409090021251 Iteration 8: loglikelihood = -2486.8538, backtracks = 0, tol = 0.09038041857636184 Iteration 9: loglikelihood = -2383.4548, backtracks = 0, tol = 0.08595678109060365 Iteration 10: loglikelihood = -2309.5322, backtracks = 0, tol = 0.08650789952387158 Iteration 11: loglikelihood = -2255.4976, backtracks = 0, tol = 0.0896311581950883 Iteration 12: loglikelihood = -2224.674, backtracks = 0, tol = 0.08346683836199778 Iteration 13: loglikelihood = -2205.684, backtracks = 0, tol = 0.08962896938620458 Iteration 14: loglikelihood = -2193.462, backtracks = 0, tol = 0.09185116748409128 Iteration 15: loglikelihood = -2186.7126, backtracks = 0, tol = 0.09146439380302337 Iteration 16: loglikelihood = -2183.596, backtracks = 0, tol = 0.09054319058911157 Iteration 17: loglikelihood = -2181.4038, backtracks = 0, tol = 0.09011589106279554 Iteration 18: loglikelihood = -2180.9966, backtracks = 0, tol = 0.08968316310761441 Iteration 19: loglikelihood = -2180.0435, backtracks = 0, tol = 0.08929024582210668 Iteration 20: loglikelihood = -2178.842, backtracks = 1, tol = 0.008626745740049735 Iteration 21: loglikelihood = -2178.5698, backtracks = 1, tol = 0.0041803338294683886 Iteration 22: loglikelihood = -2178.502, backtracks = 1, tol = 0.0024615627097272783 Iteration 23: loglikelihood = -2178.4817, backtracks = 1, tol = 0.0014139921960719267 Iteration 24: loglikelihood = -2178.4756, backtracks = 1, tol = 0.0007645396964717049 Iteration 25: loglikelihood = -2178.4739, backtracks = 1, tol = 0.0004048841980855145 Iteration 26: loglikelihood = -2178.4736, backtracks = 1, tol = 0.00022658393207423733 Iteration 27: loglikelihood = -2178.4724, backtracks = 2, tol = 6.348467733375219e-5 0.730441 seconds (1.52 M allocations: 25.235 MiB, 67.98% gc time) Test Summary: | Pass Total Time Negative binomial nuisance parameter Float32 matrix | 12 12 36.2s **** 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 **** ┌ 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 5.365359 seconds (1.52 M allocations: 153.063 MiB, 0.80% gc time, 91.64% compilation time) Test Summary: | Pass Total Time initialze beta | 1 1 5.8s 11.153626 seconds (4.01 M allocations: 82.764 MiB, 0.22% gc time, 0.68% compilation time) 5.186815 seconds (3.98 M allocations: 91.678 MiB, 0.95% gc time) 10.620619 seconds (20.47 M allocations: 442.342 MiB, 1.01% gc time, 18.71% compilation time: 77% of which was recompilation) 8.431476 seconds (20.18 M allocations: 434.189 MiB, 0.91% gc time) 38.269217 seconds (5.17 M allocations: 4.298 GiB, 6.51% gc time, 31.76% compilation time) 55.123041 seconds (72.50 k allocations: 183.666 MiB) Test Summary: | Pass Total Time memory_efficient keyword | 7 7 2m29.0s Test Summary: | Pass Total Time update_support! | 10 10 0.8s 14.618 ms (78 allocations: 4.56 KiB) 4.360 μs (0 allocations: 0 bytes) 120.709 μs (4 allocations: 288 bytes) 7.575 μs (0 allocations: 0 bytes) 50.839 μs (2 allocations: 64 bytes) 30.379 μs (0 allocations: 0 bytes) 22.959 μs (0 allocations: 0 bytes) 28.039 μs (0 allocations: 0 bytes) 92.829 μs (0 allocations: 0 bytes) 39.523 ms (78 allocations: 4.56 KiB) 18.640 μs (0 allocations: 0 bytes) 147.198 μs (4 allocations: 288 bytes) 35.839 μs (0 allocations: 0 bytes) 204.838 μs (2 allocations: 64 bytes) 87.160 μs (0 allocations: 0 bytes) 128.899 μs (0 allocations: 0 bytes) 124.719 μs (0 allocations: 0 bytes) 184.328 μs (0 allocations: 0 bytes) Test Summary: | Total Time benchmarks for multivariate function | 0 2m11.5s **** 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 **** **** 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 0.476200 seconds (65.41 k allocations: 6.182 MiB, 66.42% compilation time) Test Summary: | Pass Total Time multivariate fit_iht SnpLinAlg | 7 7 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 **** 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 1.989044 seconds (355.69 k allocations: 171.404 MiB, 61.41% compilation time) Test Summary: | Pass Total Time initialze beta | 5 5 2.6s **** 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, 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: 0:03:53 Cross validating... 13%|████▏ | ETA: 0:00:57 Cross validating... 19%|██████▏ | ETA: 0:00:36 Cross validating... 22%|███████▏ | ETA: 0:00:31 Cross validating... 25%|████████▏ | ETA: 0:00:26 Cross validating... 29%|█████████▏ | ETA: 0:00:23 Cross validating... 32%|██████████▏ | ETA: 0:00:20 Cross validating... 35%|███████████▏ | ETA: 0:00:18 Cross validating... 38%|████████████▎ | ETA: 0:00:15 Cross validating... 41%|█████████████▎ | ETA: 0:00:14 Cross validating... 44%|██████████████▎ | ETA: 0:00:12 Cross validating... 48%|███████████████▎ | ETA: 0:00:11 Cross validating... 51%|████████████████▎ | ETA: 0:00:10 Cross validating... 54%|█████████████████▎ | ETA: 0:00:09 Cross 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Results: k MSE 0 1374.8057679322856 1 1037.2338478194808 2 665.4522648314028 3 468.8593792633759 4 450.02435999499846 5 423.55229187557455 6 401.6806512364139 7 378.68907325727855 8 383.95465242126943 9 391.4881709257694 10 392.8102515080616 11 394.44900751711776 12 400.38879701088786 13 414.5453485689676 14 401.88596443186594 15 419.68903639552013 16 434.5484187930667 17 436.91289454257657 18 424.9480396870773 19 465.03772106164513 20 401.6869675676269 Best k = 7 12.700292 seconds (11.98 M allocations: 319.499 MiB, 1.23% gc time, 62.18% 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... 17%|█████▋ | ETA: 0:00:04 Cross validating... 21%|██████▋ | ETA: 0:00:04 Cross validating... 24%|███████▋ | ETA: 0:00:04 Cross validating... 27%|████████▋ | ETA: 0:00:04 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: 0:00:03 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... 62%|███████████████████▊ | ETA: 0:00:02 Cross validating... 65%|████████████████████▉ | ETA: 0:00:02 Cross validating... 68%|█████████████████████▉ | ETA: 0:00:02 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:01 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:01 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:01 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:01 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:01 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:01 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:00 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:04 Crossvalidation Results: k MSE 0 1374.8057679322856 1 1045.277051351164 2 669.2674482906918 3 470.6404578746021 4 453.9383926826602 5 427.84137900851715 6 407.2084895187974 7 384.9958792751287 8 399.4102008731668 9 410.3112792075955 10 419.9867113642682 11 424.45721413648255 12 427.61457488107624 13 440.2680048283046 14 447.63207730404235 15 446.81453717846216 16 449.4172669388102 17 461.3923071150361 18 465.4667005878815 19 473.6642561800364 20 454.8203647223429 Best k = 7 5.041758 seconds (10.99 M allocations: 232.683 MiB, 0.99% gc time, 1.14% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, normal model | 3 3 18.6s **** 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 **** Cross validating... 3%|█ | ETA: 0:06:49 Cross validating... 8%|██▌ | ETA: 0:02:37 Cross validating... 13%|████▏ | ETA: 0:01:34 Cross validating... 17%|█████▋ | ETA: 0:01:05 Cross validating... 22%|███████▏ | ETA: 0:00:49 Cross validating... 27%|████████▋ | ETA: 0:00:38 Cross validating... 32%|██████████▏ | ETA: 0:00:31 Cross validating... 37%|███████████▋ | ETA: 0:00:25 Cross validating... 41%|█████████████▎ | ETA: 0:00:21 Cross validating... 46%|██████████████▊ | ETA: 0:00:17 Cross validating... 52%|████████████████▊ | ETA: 0:00:13 Cross validating... 57%|██████████████████▎ | ETA: 0:00:11 Cross validating... 62%|███████████████████▊ | ETA: 0:00:09 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:08 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:06 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:04 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:03 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:02 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:01 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:01 Cross validating... 100%|████████████████████████████████| Time: 0:00:15 Crossvalidation Results: k MSE 0 1729.528176879883 1 1325.5143647460936 2 997.3013657226563 3 791.490546081543 4 646.0626335449219 5 531.9808499145508 6 442.06674969482424 7 386.5355822143555 8 354.1033227844239 9 340.7006368713379 10 345.30316854858404 11 347.76408059692386 12 351.73802120971686 13 349.6063938598633 14 352.1646329650879 15 349.9099938964844 16 352.5361734619141 17 355.1070798950195 18 368.4685217895508 19 383.80979385375974 20 386.46325247192385 Best k = 9 17.387721 seconds (13.00 M allocations: 337.054 MiB, 0.60% gc time, 84.88% 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... 11%|███▌ | 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... 29%|█████████▏ | ETA: 0:00:02 Cross validating... 33%|██████████▋ | ETA: 0:00:02 Cross validating... 40%|████████████▊ | ETA: 0:00:02 Cross validating... 44%|██████████████▎ | ETA: 0:00:01 Cross validating... 49%|███████████████▊ | ETA: 0:00:01 Cross validating... 54%|█████████████████▎ | ETA: 0:00:01 Cross validating... 59%|██████████████████▊ | ETA: 0:00:01 Cross validating... 62%|███████████████████▊ | ETA: 0:00:01 Cross validating... 65%|████████████████████▉ | ETA: 0:00:01 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:01 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:01 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:00 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:00 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:02 Crossvalidation Results: k MSE 0 1729.528176879883 1 1325.5143647460936 2 999.1551822509766 3 793.7456620483399 4 646.9407227783204 5 532.0082271728515 6 448.7882953796387 7 389.47058737182624 8 361.7058901977539 9 347.32882653808593 10 359.5835049133301 11 366.39160650634767 12 376.1804705200195 13 373.2962377319336 14 381.92999362182627 15 391.35286383056643 16 387.01034274291993 17 389.62999530029305 18 393.4316708984375 19 411.342888671875 20 403.71597140502934 Best k = 9 2.706052 seconds (10.77 M allocations: 198.491 MiB, 1.76% gc time, 1.91% compilation time) Test Summary: | Pass Total Time Cross validation on Float32 matrix, normal model | 2 2 21.7s **** 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... 3%|█ | ETA: 0:01:08 Cross validating... 6%|██ | ETA: 0:00:35 Cross validating... 8%|██▌ | ETA: 0:00:29 Cross validating... 11%|███▌ | ETA: 0:00:22 Cross validating... 14%|████▋ | ETA: 0:00:17 Cross validating... 17%|█████▋ | ETA: 0:00:14 Cross validating... 21%|██████▋ | ETA: 0:00:12 Cross 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ETA: 0:00:02 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:02 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:01 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:01 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:01 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:01 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 0 462.31813236299973 1 414.4635442368139 2 369.54581545573535 3 335.19084479088036 4 340.09180717185524 5 342.6270124237871 6 346.2098610755826 7 347.35907736545374 8 346.71450926050113 9 349.5894622506955 10 365.74172687370145 11 354.88814903855865 12 353.39302202609207 13 353.7322823457172 14 361.61810779504907 15 367.68870825301667 16 363.83997102982227 17 360.53715155009814 18 411.40294474985194 19 364.3748356127358 20 387.0318080052757 Best k = 3 8.620934 seconds (17.53 M allocations: 421.343 MiB, 1.40% gc time, 34.47% 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... 11%|███▌ | ETA: 0:00:05 Cross validating... 13%|████▏ | ETA: 0:00:05 Cross validating... 16%|█████▏ | ETA: 0:00:05 Cross validating... 19%|██████▏ | ETA: 0:00:05 Cross validating... 22%|███████▏ | ETA: 0:00:05 Cross validating... 25%|████████▏ | ETA: 0:00:04 Cross validating... 29%|█████████▏ | ETA: 0:00:04 Cross validating... 30%|█████████▋ | ETA: 0:00:04 Cross validating... 33%|██████████▋ | ETA: 0:00:04 Cross validating... 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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 0 462.31813236299973 1 414.60316845794296 2 369.6518416858488 3 335.44431558217883 4 348.8626585782746 5 357.9506634447931 6 366.05394984532154 7 366.25637492361625 8 376.170823030353 9 381.7680618163605 10 393.98506353326394 11 396.02974360744605 12 402.5657147241859 13 406.0920344704333 14 420.8697783412281 15 454.1818003081181 16 442.1895486197646 17 445.25105811540004 18 450.0592155361712 19 459.0778831900435 20 458.8311926286973 Best k = 3 5.857899 seconds (17.34 M allocations: 356.640 MiB, 1.51% gc time, 1.19% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, logistic model | 2 2 14.9s **** 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: 0:00:47 Cross validating... 6%|██ | ETA: 0:00:25 Cross validating... 11%|███▌ | ETA: 0:00:15 Cross validating... 14%|████▋ | ETA: 0:00:12 Cross validating... 16%|█████▏ | ETA: 0:00:11 Cross validating... 19%|██████▏ | ETA: 0:00:10 Cross validating... 22%|███████▏ | ETA: 0:00:08 Cross validating... 25%|████████▏ | ETA: 0:00:07 Cross validating... 29%|█████████▏ | ETA: 0:00:07 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: 0:00:05 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... 56%|█████████████████▊ | ETA: 0:00:03 Cross validating... 59%|██████████████████▊ | ETA: 0:00:03 Cross validating... 62%|███████████████████▊ | ETA: 0:00:03 Cross validating... 65%|████████████████████▉ | ETA: 0:00:02 Cross validating... 68%|█████████████████████▉ | ETA: 0:00:02 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:02 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:02 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:01 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:01 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:01 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:01 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:00 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:06 Crossvalidation Results: k MSE 0 463.17037730725224 1 428.4709327529568 2 410.48543374155247 3 385.37619076199746 4 343.6723512702341 5 338.83402078122356 6 320.5050578658385 7 315.29684785439724 8 317.6045845307753 9 317.8834493837195 10 330.68462099122445 11 326.3433586010379 12 326.7438271654895 13 323.1757282135527 14 341.30211008375454 15 352.76267928356117 16 336.25879059410147 17 334.2724761149041 18 337.72198416067397 19 358.4698768324732 20 337.61468730737255 Best k = 7 7.474798 seconds (16.83 M allocations: 400.995 MiB, 7.63% gc time, 38.22% 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... 17%|█████▋ | ETA: 0:00:03 Cross validating... 21%|██████▋ | ETA: 0:00:03 Cross validating... 24%|███████▋ | ETA: 0:00:03 Cross validating... 27%|████████▋ | ETA: 0:00:03 Cross validating... 30%|█████████▋ | ETA: 0:00:03 Cross validating... 33%|██████████▋ | ETA: 0:00:03 Cross validating... 38%|████████████▎ | ETA: 0:00:02 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 0 463.17037730725224 1 428.50908649804217 2 408.23401225587304 3 387.54116388878646 4 347.9825632713288 5 345.1674574862413 6 327.80221487888343 7 322.78980926023934 8 329.40004312652985 9 337.22323741878364 10 342.4201643031744 11 349.331403635407 12 364.4305897351109 13 361.1774694414803 14 367.9252728344833 15 387.6381080670258 16 393.6986609978808 17 420.0111654851088 18 411.24146744708526 19 419.6124567284885 20 414.96044633963027 Best k = 7 4.268911 seconds (17.31 M allocations: 355.462 MiB, 1.28% gc time, 1.21% compilation time) Test Summary: | Pass Total Time Cross validation on Float64 matrix, logistic model | 2 2 12.8s **** 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: 0:01:05 Cross validating... 6%|██ | ETA: 0:00:34 Cross validating... 8%|██▌ | ETA: 0:00:28 Cross validating... 11%|███▌ | ETA: 0:00:21 Cross validating... 14%|████▋ | ETA: 0:00:17 Cross validating... 17%|█████▋ | ETA: 0:00:14 Cross validating... 21%|██████▋ | ETA: 0:00:12 Cross validating... 22%|███████▏ | ETA: 0:00:12 Cross validating... 25%|████████▏ | ETA: 0:00:10 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81%|█████████████████████████▉ | ETA: 0:00:02 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: 0:00:01 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:07 Crossvalidation Results: k MSE 0 490.354412241357 1 459.3468345036037 2 423.312162801313 3 399.1429781829603 4 403.6621142241734 5 405.304119689455 6 414.0961251330924 7 408.41310381072464 8 410.2517555165217 9 413.011852109759 10 416.1541603308961 11 417.1700950044012 12 426.61157831987015 13 419.23277861624695 14 412.4027049222193 15 415.5542909242705 16 412.29140037639274 17 417.08083046055253 18 417.14252266585197 19 415.30892117677786 20 419.47249270072433 Best k = 3 8.591759 seconds (17.00 M allocations: 428.142 MiB, 0.91% gc time, 33.05% 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 **** Cross validating... 3%|█ | ETA: 0:00:04 Cross validating... 6%|██ | ETA: 0:00:04 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: 0:00:03 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: 0:00:03 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... 65%|████████████████████▉ | ETA: 0:00:02 Cross validating... 68%|█████████████████████▉ | 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 0 490.354412241357 1 459.31042775237313 2 423.65666733955163 3 401.16805385735336 4 412.9059085344452 5 417.70915304370783 6 427.1952178070394 7 431.6005329819166 8 435.4892621304873 9 439.36707432661734 10 446.7410289783799 11 449.2345160555893 12 454.6341980341981 13 456.0386679218354 14 451.18468551463206 15 446.02298903869115 16 452.3254438593806 17 462.462982603712 18 467.7918896805029 19 471.1325563385327 20 485.6987043648138 Best k = 3 5.051387 seconds (15.68 M allocations: 326.163 MiB, 1.12% gc time, 1.26% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, Poisson model | 2 2 14.1s **** 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 **** Cross validating... 3%|█ | ETA: 0:01:05 Cross validating... 6%|██ | ETA: 0:00:33 Cross validating... 10%|███ | ETA: 0:00:24 Cross validating... 11%|███▌ | ETA: 0:00:29 Cross validating... 13%|████▏ | ETA: 0:00:32 Cross validating... 14%|████▋ | ETA: 0:00:34 Cross validating... 16%|█████▏ | ETA: 0:00:31 Cross validating... 17%|█████▋ | ETA: 0:00:33 Cross validating... 19%|██████▏ | ETA: 0:00:34 Cross validating... 21%|██████▋ | ETA: 0:00:35 Cross validating... 22%|███████▏ | ETA: 0:00:36 Cross validating... 24%|███████▋ | ETA: 0:00:36 Cross validating... 25%|████████▏ | ETA: 0:00:36 Cross validating... 27%|████████▋ | ETA: 0:00:35 Cross validating... 29%|█████████▏ | ETA: 0:00:35 Cross validating... 30%|█████████▋ | ETA: 0:00:35 Cross validating... 32%|██████████▏ | ETA: 0:00:35 Cross validating... 33%|██████████▋ | ETA: 0:00:34 Cross validating... 37%|███████████▋ | ETA: 0:00:30 Cross validating... 40%|████████████▊ | ETA: 0:00:28 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ETA: 0:00:01 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:01 Cross validating... 100%|████████████████████████████████| Time: 0:00:40 Crossvalidation Results: k MSE 0 282.64086942787833 1 272.04660310262716 2 253.7192793650334 3 233.37142241882236 4 235.0521095221158 5 237.54961553335994 6 240.16197984788477 7 239.28260939401378 8 239.61603974000263 9 243.75972922914184 10 244.2550343484908 11 244.28753059741342 12 242.92155192406432 13 246.2626077747432 14 246.60520698180386 15 248.04267660402172 16 249.44218815928048 17 251.7856945580063 18 251.69227980531406 19 255.43235551634484 20 254.3727240017266 Best k = 3 41.307749 seconds (124.86 M allocations: 3.152 GiB, 1.19% gc time, 6.03% 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 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95%|██████████████████████████████▌ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:10 Crossvalidation Results: k MSE 0 282.64086942787833 1 272.33023154099095 2 254.9010447108347 3 235.70757002510442 4 239.80092457597215 5 246.34953094417673 6 254.1302125694363 7 258.35436182901867 8 255.55896771395618 9 259.78039862064793 10 264.0677344784316 11 266.31057355003736 12 269.26681665717086 13 269.85203340783283 14 280.6066814172248 15 287.7499429424631 16 287.1352280066609 17 292.73216421100295 18 288.9175121848307 19 305.79062183725034 20 301.837494190791 Best k = 3 10.406131 seconds (30.87 M allocations: 635.782 MiB, 1.38% gc time, 0.68% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, NegativeBinomial model | 2 2 52.2s **** 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 **** Cross validating... 3%|█ | ETA: 0:01:11 Cross validating... 6%|██ | ETA: 0:00:36 Cross validating... 10%|███ | ETA: 0:00:24 Cross validating... 14%|████▋ | ETA: 0:00:16 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: 0:00:09 Cross validating... 30%|█████████▋ | ETA: 0:00:08 Cross validating... 33%|██████████▋ | ETA: 0:00:07 Cross validating... 38%|████████████▎ | ETA: 0:00:06 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: 0:00:04 Cross validating... 56%|█████████████████▊ | ETA: 0:00:03 Cross validating... 60%|███████████████████▎ | ETA: 0:00:03 Cross validating... 63%|████████████████████▍ | ETA: 0:00:03 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... 97%|███████████████████████████████ | 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 6.336335 seconds (17.17 M allocations: 344.617 MiB, 1.82% gc time, 47.03% 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... 13%|████▏ | ETA: 0:00:03 Cross validating... 17%|█████▋ | ETA: 0:00:03 Cross validating... 21%|██████▋ | 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... 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100%|████████████████████████████████| Time: 0:00:03 Crossvalidation Results: k MSE 0 709.7238911132813 1 580.5206424560547 2 462.45179821777344 3 375.725685546875 4 311.8335130615235 5 265.69685809326177 6 235.52074707031255 7 221.8731430358887 8 209.48005477905275 9 202.0256286010742 10 206.40357376098632 11 209.8904744873047 12 212.83695938110353 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 3.225454 seconds (16.18 M allocations: 286.940 MiB, 1.39% gc time, 2.06% compilation time) Test Summary: | Pass Total Time Cross validation on floating point matrices, NegativeBinomial model | 2 2 10.1s **** 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 **** 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1274.6921999564472 17 1295.7705918261918 18 1309.813560773017 19 1310.9365971922248 20 1323.3244632515389 Best k = 7 16.970352 seconds (373.20 k allocations: 205.225 MiB, 0.36% gc time, 9.45% compilation time) Test Summary: | Pass Total Time multivariate cross validation SnpLinAlg | 3 3 22.0s Test Summary: | Pass Total Time wrapper univariate | 20 20 2m28.5s **** 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... 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: 0:00:13 Cross validating... 8%|██▌ | ETA: 0:00:13 Cross validating... 9%|██▉ | ETA: 0:00:14 Cross validating... 10%|███▎ | ETA: 0:00:14 Cross 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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 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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 1m29.4s 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:327 [11] top-level scope @ ~/.julia/packages/MendelIHT/ZcxZT/test/runtests.jl:20 [12] include(mapexpr::Function, mod::Module, _path::String) @ Base Base.jl:327 [13] top-level scope @ none:6 [14] eval(m::Module, e::Any) @ Core boot.jl:521 [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 3.1s RNG of the outermost testset: Xoshiro(0xb628cc38fdff0b3d, 0xe9f7209a0c21f48c, 0x730fc4b6f3995548, 0x1a3a207884223030, 0x6af3e8e58152e499) 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 1162.28s 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:326 [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 1280.73s: package tests unexpectedly errored