CRAN Package Check Results for Package SuperLearner

Last updated on 2019-09-19 13:46:23 CEST.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 2.0-25 6.43 463.76 470.19 OK
r-devel-linux-x86_64-debian-gcc 2.0-25 5.90 342.18 348.08 OK
r-devel-linux-x86_64-fedora-clang 2.0-25 540.24 OK
r-devel-linux-x86_64-fedora-gcc 2.0-25 527.14 OK
r-devel-windows-ix86+x86_64 2.0-25 16.00 598.00 614.00 OK
r-patched-linux-x86_64 2.0-25 5.75 450.16 455.91 OK
r-patched-solaris-x86 2.0-25 998.50 OK
r-release-linux-x86_64 2.0-25 5.33 439.75 445.08 OK
r-release-windows-ix86+x86_64 2.0-25 10.00 426.00 436.00 ERROR
r-release-osx-x86_64 2.0-25 NOTE
r-oldrel-windows-ix86+x86_64 2.0-25 7.00 357.00 364.00 OK
r-oldrel-osx-x86_64 2.0-25 OK

Check Details

Version: 2.0-25
Check: examples
Result: ERROR
    Running examples in 'SuperLearner-Ex.R' failed
    The error most likely occurred in:
    
    > ### Name: SL.biglasso
    > ### Title: SL wrapper for biglasso
    > ### Aliases: SL.biglasso
    >
    > ### ** Examples
    >
    >
    > data(Boston, package = "MASS")
    > Y = Boston$medv
    > # Remove outcome from covariate dataframe.
    > X = Boston[, -14]
    >
    > set.seed(1)
    >
    > # Sample rows to speed up example.
    > row_subset = sample(nrow(X), 30)
    >
    > # Subset rows and columns & use only 2 folds to speed up example.
    > sl = SuperLearner(Y[row_subset], X[row_subset, 1:2, drop = FALSE],
    + family = gaussian(), cvControl = list(V = 2),
    + SL.library = "SL.biglasso")
    Loading required namespace: biglasso
    > sl
    
    Call:
    SuperLearner(Y = Y[row_subset], X = X[row_subset, 1:2, drop = FALSE], family = gaussian(),
     SL.library = "SL.biglasso", cvControl = list(V = 2))
    
    
     Risk Coef
    SL.biglasso_All 155.8912 1
    >
    > pred = predict(sl, X)
    Error in big.matrix(nrow = nrow(x), ncol = ncol(x), type = type, init = NULL, :
     Error: memory could not be allocated for instance of type big.matrix
    Calls: predict ... predict.SL.biglasso -> <Anonymous> -> <Anonymous> -> big.matrix
    Execution halted
Flavor: r-release-windows-ix86+x86_64

Version: 2.0-25
Check: tests
Result: ERROR
     Running 'testthat.R' [76s]
    Running the tests in 'tests/testthat.R' failed.
    Complete output:
     > if(require("testthat")) {
     + library("SuperLearner")
     + test_check("SuperLearner")
     + }
     Loading required package: testthat
     Loading required package: nnls
     Super Learner
     Version: 2.0-25
     Package created on 2019-08-05
    
    
     Call:
     SuperLearner(Y = Y_reg, X = X, family = gaussian(), SL.library = c(SL.library,
     xgb_grid$names), cvControl = list(V = 2))
    
    
     Risk Coef
     SL.mean_All 1.100027 0.73787916
     SL.xgboost_All 1.532526 0.01813212
     SL.xgb.1_All 1.290361 0.24398872
     SL.xgb.2_All 1.176793 0.00000000
     SL.xgb.3_All 1.321512 0.00000000
     SL.xgb.4_All 1.223680 0.00000000
     SL.xgb.5_All 1.593716 0.00000000
     SL.xgb.6_All 1.544470 0.00000000
     SL.xgb.7_All 1.600138 0.00000000
     SL.xgb.8_All 1.555782 0.00000000
     SL.xgb.9_All 1.642955 0.00000000
     SL.xgb.10_All 1.637269 0.00000000
     SL.xgb.11_All 1.643616 0.00000000
     SL.xgb.12_All 1.638586 0.00000000
     -- 1. Error: (unknown) (@test-biglasso.R#23) ----------------------------------
     memory could not be allocated for instance of type big.matrix
     1: SuperLearner::SL.biglasso(Y_gaus, X, X, family = gaussian(), obsWeights = rep(1,
     nrow(X))) at testthat/test-biglasso.R:23
     2: bigmemory::as.big.matrix(X)
     3: bigmemory::as.big.matrix(X)
     4: big.matrix(nrow = nrow(x), ncol = ncol(x), type = type, init = NULL, dimnames = dimnames(x),
     separated = separated, backingfile = backingfile, backingpath = backingpath,
     descriptorfile = descriptorfile, binarydescriptor = binarydescriptor, shared = shared)
     5: stop(paste("Error: memory could not be allocated for instance", "of type big.matrix"))
    
     Y
     0 1
     53 47
     $grid
     NULL
    
     $names
     [1] "SL.randomForest_1"
    
     $base_learner
     [1] "SL.randomForest"
    
     $params
     $params$ntree
     [1] 100
    
    
     [1] "SL.randomForest_1" "X" "Y"
     [4] "create_rf" "data"
    
     Call:
     SuperLearner(Y = Y, X = X, family = binomial(), SL.library = create_rf$names,
     cvControl = list(V = 2))
    
    
     Risk Coef
     SL.randomForest_1_All 0.047901 1
     $grid
     mtry
     1 1
     2 4
     3 20
    
     $names
     [1] "SL.randomForest_1" "SL.randomForest_2" "SL.randomForest_3"
    
     $base_learner
     [1] "SL.randomForest"
    
     $params
     list()
    
    
     Call:
     SuperLearner(Y = Y, X = X, family = binomial(), SL.library = create_rf$names,
     cvControl = list(V = 2))
    
    
     Risk Coef
     SL.randomForest_1_All 0.06229353 0.1023683
     SL.randomForest_2_All 0.05076692 0.8976317
     SL.randomForest_3_All 0.05654268 0.0000000
     $grid
     alpha
     1 0.00
     2 0.25
     3 0.50
     4 0.75
     5 1.00
    
     $names
     [1] "SL.glmnet_0" "SL.glmnet_0.25" "SL.glmnet_0.5" "SL.glmnet_0.75"
     [5] "SL.glmnet_1"
    
     $base_learner
     [1] "SL.glmnet"
    
     $params
     list()
    
     [1] "SL.glmnet_0" "SL.glmnet_0.25" "SL.glmnet_0.5" "SL.glmnet_0.75"
     [5] "SL.glmnet_1"
    
     Call:
     SuperLearner(Y = Y, X = X, family = binomial(), SL.library = ls(learners),
     cvControl = list(V = 2), env = learners)
    
    
     Risk Coef
     SL.glmnet_0_All 0.06578497 0
     SL.glmnet_0.25_All 0.06393436 1
     SL.glmnet_0.5_All 0.06552848 0
     SL.glmnet_0.75_All 0.06939863 0
     SL.glmnet_1_All 0.08319900 0
    
     Call:
     SuperLearner(Y = Y, X = X_clean, family = binomial(), SL.library = c("SL.mean",
     svm$names), cvControl = list(V = 3))
    
    
     Risk Coef
     SL.mean_All 0.25993856 0.0000000
     SL.svm_polynomial_All 0.07494856 0.4917546
     SL.svm_radial_All 0.07714246 0.0000000
     SL.svm_sigmoid_All 0.07428697 0.5082454
     ExtraTrees:
     - # of trees: 500
     - node size: 5
     - # of dim: 13
     - # of tries: 4
     - type: numeric (regression)
     - multi-task: no
     ExtraTrees:
     - # of trees: 500
     - node size: 1
     - # of dim: 13
     - # of tries: 3
     - type: factor (classification)
     - multi-task: no
    
     Call:
     SuperLearner(Y = Y_bin, X = X, family = binomial(), SL.library = sl_lib,
     cvControl = list(V = 2))
    
    
     Risk Coef
     SL.extraTrees_All 0.10638648 0
     SL.ranger_All 0.09621615 1
     SL.mean_All 0.25320000 0
     $grid
     NULL
    
     $names
     [1] "SL.extraTrees_1"
    
     $base_learner
     [1] "SL.extraTrees"
    
     $params
     list()
    
    
     Call:
     SuperLearner(Y = Y_bin, X = X, family = binomial(), SL.library = c("SL.mean",
     lib$names), cvControl = list(V = 2))
    
    
     Risk Coef
     SL.mean_All 0.2112000 0
     SL.extraTrees_1_All 0.1011586 1
     SL.extraTrees_1 <- function(...) SL.extraTrees(...)
     $grid
     NULL
    
     $names
     [1] "SL.extraTrees_1"
    
     $base_learner
     [1] "SL.extraTrees"
    
     $params
     list()
    
     [1] "SL.extraTrees_1"
     [1] 1
    
     Call:
     SuperLearner(Y = Y_bin, X = X, family = binomial(), SL.library = c("SL.mean",
     lib$names), cvControl = list(V = 2), env = sl_env)
    
    
     Risk Coef
     SL.mean_All 0.2112000 0
     SL.extraTrees_1_All 0.1171381 1
     $grid
     mtry
     1 1
     2 2
    
     $names
     [1] "SL.extraTrees_1" "SL.extraTrees_2"
    
     $base_learner
     [1] "SL.extraTrees"
    
     $params
     list()
    
     [1] "SL.extraTrees_1" "SL.extraTrees_2"
    
     Call:
     SuperLearner(Y = Y_bin, X = X, family = binomial(), SL.library = c("SL.mean",
     lib$names), cvControl = list(V = 2), env = sl_env)
    
    
     Risk Coef
     SL.mean_All 0.2292000 0
     SL.extraTrees_1_All 0.1384171 0
     SL.extraTrees_2_All 0.1224645 1
     $grid
     mtry
     1 1
     2 2
    
     $names
     [1] "SL.extraTrees_1" "SL.extraTrees_2"
    
     $base_learner
     [1] "SL.extraTrees"
    
     $params
     list()
    
     [1] "SL.extraTrees_1" "SL.extraTrees_2"
    
     Call:
     SuperLearner(Y = Y_bin, X = X, family = binomial(), SL.library = c("SL.mean",
     lib$names), cvControl = list(V = 2), env = sl_env)
    
    
     Risk Coef
     SL.mean_All 0.2292000 0
     SL.extraTrees_1_All 0.1251496 0
     SL.extraTrees_2_All 0.1137550 1
    
     Call: glm(formula = Y ~ ., family = family, data = X, weights = obsWeights,
     model = model)
    
     Coefficients:
     (Intercept) crim zn indus chas nox
     3.646e+01 -1.080e-01 4.642e-02 2.056e-02 2.687e+00 -1.777e+01
     rm age dis rad tax ptratio
     3.810e+00 6.922e-04 -1.476e+00 3.060e-01 -1.233e-02 -9.527e-01
     black lstat
     9.312e-03 -5.248e-01
    
     Degrees of Freedom: 505 Total (i.e. Null); 492 Residual
     Null Deviance: 42720
     Residual Deviance: 11080 AIC: 3028
    
     Call:
     glm(formula = Y ~ ., family = family, data = X, weights = obsWeights,
     model = model)
    
     Deviance Residuals:
     Min 1Q Median 3Q Max
     -15.595 -2.730 -0.518 1.777 26.199
    
     Coefficients:
     Estimate Std. Error t value Pr(>|t|)
     (Intercept) 3.646e+01 5.103e+00 7.144 3.28e-12 ***
     crim -1.080e-01 3.286e-02 -3.287 0.001087 **
     zn 4.642e-02 1.373e-02 3.382 0.000778 ***
     indus 2.056e-02 6.150e-02 0.334 0.738288
     chas 2.687e+00 8.616e-01 3.118 0.001925 **
     nox -1.777e+01 3.820e+00 -4.651 4.25e-06 ***
     rm 3.810e+00 4.179e-01 9.116 < 2e-16 ***
     age 6.922e-04 1.321e-02 0.052 0.958229
     dis -1.476e+00 1.995e-01 -7.398 6.01e-13 ***
     rad 3.060e-01 6.635e-02 4.613 5.07e-06 ***
     tax -1.233e-02 3.760e-03 -3.280 0.001112 **
     ptratio -9.527e-01 1.308e-01 -7.283 1.31e-12 ***
     black 9.312e-03 2.686e-03 3.467 0.000573 ***
     lstat -5.248e-01 5.072e-02 -10.347 < 2e-16 ***
     ---
     Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
    
     (Dispersion parameter for gaussian family taken to be 22.51785)
    
     Null deviance: 42716 on 505 degrees of freedom
     Residual deviance: 11079 on 492 degrees of freedom
     AIC: 3027.6
    
     Number of Fisher Scoring iterations: 2
    
    
     Call:
     glm(formula = Y ~ ., family = family, data = X, weights = obsWeights,
     model = model)
    
     Deviance Residuals:
     Min 1Q Median 3Q Max
     -2.9747 -0.4250 -0.0911 0.2720 3.5929
    
     Coefficients:
     Estimate Std. Error z value Pr(>|z|)
     (Intercept) 10.682635 3.921395 2.724 0.006446 **
     crim -0.040649 0.049796 -0.816 0.414321
     zn 0.012134 0.010678 1.136 0.255786
     indus -0.040715 0.045615 -0.893 0.372078
     chas 0.248209 0.653283 0.380 0.703989
     nox -3.601085 2.924365 -1.231 0.218170
     rm 1.155157 0.374843 3.082 0.002058 **
     age -0.018660 0.009319 -2.002 0.045252 *
     dis -0.518934 0.146286 -3.547 0.000389 ***
     rad 0.255522 0.061391 4.162 3.15e-05 ***
     tax -0.009500 0.003107 -3.057 0.002233 **
     ptratio -0.409317 0.103191 -3.967 7.29e-05 ***
     black -0.001451 0.002558 -0.567 0.570418
     lstat -0.318436 0.054735 -5.818 5.96e-09 ***
     ---
     Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
    
     (Dispersion parameter for binomial family taken to be 1)
    
     Null deviance: 669.76 on 505 degrees of freedom
     Residual deviance: 296.39 on 492 degrees of freedom
     AIC: 324.39
    
     Number of Fisher Scoring iterations: 7
    
     [1] "coefficients" "residuals" "fitted.values"
     [4] "effects" "R" "rank"
     [7] "qr" "family" "linear.predictors"
     [10] "deviance" "aic" "null.deviance"
     [13] "iter" "weights" "prior.weights"
     [16] "df.residual" "df.null" "y"
     [19] "converged" "boundary" "call"
     [22] "formula" "terms" "data"
     [25] "offset" "control" "method"
     [28] "contrasts" "xlevels"
    
     Call:
     glm(formula = Y ~ ., family = family, data = X, weights = obsWeights,
     model = model)
    
     Deviance Residuals:
     Min 1Q Median 3Q Max
     -15.595 -2.730 -0.518 1.777 26.199
    
     Coefficients:
     Estimate Std. Error t value Pr(>|t|)
     (Intercept) 3.646e+01 5.103e+00 7.144 3.28e-12 ***
     crim -1.080e-01 3.286e-02 -3.287 0.001087 **
     zn 4.642e-02 1.373e-02 3.382 0.000778 ***
     indus 2.056e-02 6.150e-02 0.334 0.738288
     chas 2.687e+00 8.616e-01 3.118 0.001925 **
     nox -1.777e+01 3.820e+00 -4.651 4.25e-06 ***
     rm 3.810e+00 4.179e-01 9.116 < 2e-16 ***
     age 6.922e-04 1.321e-02 0.052 0.958229
     dis -1.476e+00 1.995e-01 -7.398 6.01e-13 ***
     rad 3.060e-01 6.635e-02 4.613 5.07e-06 ***
     tax -1.233e-02 3.760e-03 -3.280 0.001112 **
     ptratio -9.527e-01 1.308e-01 -7.283 1.31e-12 ***
     black 9.312e-03 2.686e-03 3.467 0.000573 ***
     lstat -5.248e-01 5.072e-02 -10.347 < 2e-16 ***
     ---
     Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
    
     (Dispersion parameter for gaussian family taken to be 22.51785)
    
     Null deviance: 42716 on 505 degrees of freedom
     Residual deviance: 11079 on 492 degrees of freedom
     AIC: 3027.6
    
     Number of Fisher Scoring iterations: 2
    
    
     Call:
     glm(formula = Y ~ ., family = family, data = X, weights = obsWeights,
     model = model)
    
     Deviance Residuals:
     Min 1Q Median 3Q Max
     -2.9747 -0.4250 -0.0911 0.2720 3.5929
    
     Coefficients:
     Estimate Std. Error z value Pr(>|z|)
     (Intercept) 10.682635 3.921395 2.724 0.006446 **
     crim -0.040649 0.049796 -0.816 0.414321
     zn 0.012134 0.010678 1.136 0.255786
     indus -0.040715 0.045615 -0.893 0.372078
     chas 0.248209 0.653283 0.380 0.703989
     nox -3.601085 2.924365 -1.231 0.218170
     rm 1.155157 0.374843 3.082 0.002058 **
     age -0.018660 0.009319 -2.002 0.045252 *
     dis -0.518934 0.146286 -3.547 0.000389 ***
     rad 0.255522 0.061391 4.162 3.15e-05 ***
     tax -0.009500 0.003107 -3.057 0.002233 **
     ptratio -0.409317 0.103191 -3.967 7.29e-05 ***
     black -0.001451 0.002558 -0.567 0.570418
     lstat -0.318436 0.054735 -5.818 5.96e-09 ***
     ---
     Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
    
     (Dispersion parameter for binomial family taken to be 1)
    
     Null deviance: 669.76 on 505 degrees of freedom
     Residual deviance: 296.39 on 492 degrees of freedom
     AIC: 324.39
    
     Number of Fisher Scoring iterations: 7
    
    
     Call:
     SuperLearner(Y = Y_gaus, X = X, family = gaussian(), SL.library = c("SL.mean",
     "SL.glm"))
    
    
     Risk Coef
     SL.mean_All 84.74142 0.0134192
     SL.glm_All 23.62549 0.9865808
     V1
     Min. :-3.921
     1st Qu.:17.514
     Median :22.124
     Mean :22.533
     3rd Qu.:27.345
     Max. :44.376
    
     Call:
     SuperLearner(Y = Y_bin, X = X, family = binomial(), SL.library = c("SL.mean",
     "SL.glm"))
    
    
     Risk Coef
     SL.mean_All 0.23580362 0.01315872
     SL.glm_All 0.09519266 0.98684128
     V1
     Min. :0.004942
     1st Qu.:0.035424
     Median :0.196222
     Mean :0.375494
     3rd Qu.:0.781687
     Max. :0.991313
     Got an error, as expected.
     <simpleError in cbind2(1, newx) %*% nbeta: Cholmod error 'X and/or Y have wrong dimensions' at file ../MatrixOps/cholmod_sdmult.c, line 90>
     Got an error, as expected.
     <simpleError in cbind2(1, newx) %*% nbeta: Cholmod error 'X and/or Y have wrong dimensions' at file ../MatrixOps/cholmod_sdmult.c, line 90>
     Call:
     lda(X, grouping = Y, prior = prior, method = method, tol = tol,
     CV = CV, nu = nu)
    
     Prior probabilities of groups:
     0 1
     0.6245059 0.3754941
    
     Group means:
     crim zn indus chas nox rm age dis
     0 5.2936824 4.708861 13.622089 0.05379747 0.5912399 5.985693 77.93228 3.349307
     1 0.8191541 22.431579 7.003316 0.09473684 0.4939153 6.781821 53.01211 4.536371
     rad tax ptratio black lstat
     0 11.588608 459.9209 19.19968 340.6392 16.042468
     1 6.157895 322.2789 17.21789 383.3425 7.015947
    
     Coefficients of linear discriminants:
     LD1
     crim 0.0012515925
     zn 0.0095179029
     indus -0.0166376334
     chas 0.1399207112
     nox -2.9934367740
     rm 0.5612713068
     age -0.0128420045
     dis -0.3095403096
     rad 0.0695027989
     tax -0.0027771271
     ptratio -0.2059853828
     black 0.0006058031
     lstat -0.0816668897
     Call:
     lda(X, grouping = Y, prior = prior, method = method, tol = tol,
     CV = CV, nu = nu)
    
     Prior probabilities of groups:
     0 1
     0.6245059 0.3754941
    
     Group means:
     crim zn indus chas nox rm age dis
     0 5.2936824 4.708861 13.622089 0.05379747 0.5912399 5.985693 77.93228 3.349307
     1 0.8191541 22.431579 7.003316 0.09473684 0.4939153 6.781821 53.01211 4.536371
     rad tax ptratio black lstat
     0 11.588608 459.9209 19.19968 340.6392 16.042468
     1 6.157895 322.2789 17.21789 383.3425 7.015947
    
     Coefficients of linear discriminants:
     LD1
     crim 0.0012515925
     zn 0.0095179029
     indus -0.0166376334
     chas 0.1399207112
     nox -2.9934367740
     rm 0.5612713068
     age -0.0128420045
     dis -0.3095403096
     rad 0.0695027989
     tax -0.0027771271
     ptratio -0.2059853828
     black 0.0006058031
     lstat -0.0816668897
    
     Call:
     stats::lm(formula = Y ~ ., data = X, weights = obsWeights, model = model)
    
     Coefficients:
     (Intercept) crim zn indus chas nox
     3.646e+01 -1.080e-01 4.642e-02 2.056e-02 2.687e+00 -1.777e+01
     rm age dis rad tax ptratio
     3.810e+00 6.922e-04 -1.476e+00 3.060e-01 -1.233e-02 -9.527e-01
     black lstat
     9.312e-03 -5.248e-01
    
    
     Call:
     stats::lm(formula = Y ~ ., data = X, weights = obsWeights, model = model)
    
     Residuals:
     Min 1Q Median 3Q Max
     -15.595 -2.730 -0.518 1.777 26.199
    
     Coefficients:
     Estimate Std. Error t value Pr(>|t|)
     (Intercept) 3.646e+01 5.103e+00 7.144 3.28e-12 ***
     crim -1.080e-01 3.286e-02 -3.287 0.001087 **
     zn 4.642e-02 1.373e-02 3.382 0.000778 ***
     indus 2.056e-02 6.150e-02 0.334 0.738288
     chas 2.687e+00 8.616e-01 3.118 0.001925 **
     nox -1.777e+01 3.820e+00 -4.651 4.25e-06 ***
     rm 3.810e+00 4.179e-01 9.116 < 2e-16 ***
     age 6.922e-04 1.321e-02 0.052 0.958229
     dis -1.476e+00 1.995e-01 -7.398 6.01e-13 ***
     rad 3.060e-01 6.635e-02 4.613 5.07e-06 ***
     tax -1.233e-02 3.760e-03 -3.280 0.001112 **
     ptratio -9.527e-01 1.308e-01 -7.283 1.31e-12 ***
     black 9.312e-03 2.686e-03 3.467 0.000573 ***
     lstat -5.248e-01 5.072e-02 -10.347 < 2e-16 ***
     ---
     Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
    
     Residual standard error: 4.745 on 492 degrees of freedom
     Multiple R-squared: 0.7406, Adjusted R-squared: 0.7338
     F-statistic: 108.1 on 13 and 492 DF, p-value: < 2.2e-16
    
    
     Call:
     stats::lm(formula = Y ~ ., data = X, weights = obsWeights, model = model)
    
     Residuals:
     Min 1Q Median 3Q Max
     -0.80469 -0.23612 -0.03105 0.23080 1.05224
    
     Coefficients:
     Estimate Std. Error t value Pr(>|t|)
     (Intercept) 1.6675402 0.3662392 4.553 6.67e-06 ***
     crim 0.0003028 0.0023585 0.128 0.897888
     zn 0.0023028 0.0009851 2.338 0.019808 *
     indus -0.0040254 0.0044131 -0.912 0.362135
     chas 0.0338534 0.0618295 0.548 0.584264
     nox -0.7242540 0.2741160 -2.642 0.008501 **
     rm 0.1357981 0.0299915 4.528 7.48e-06 ***
     age -0.0031071 0.0009480 -3.278 0.001121 **
     dis -0.0748924 0.0143135 -5.232 2.48e-07 ***
     rad 0.0168160 0.0047612 3.532 0.000451 ***
     tax -0.0006719 0.0002699 -2.490 0.013110 *
     ptratio -0.0498376 0.0093885 -5.308 1.68e-07 ***
     black 0.0001466 0.0001928 0.760 0.447370
     lstat -0.0197591 0.0036395 -5.429 8.91e-08 ***
     ---
     Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
    
     Residual standard error: 0.3405 on 492 degrees of freedom
     Multiple R-squared: 0.5192, Adjusted R-squared: 0.5065
     F-statistic: 40.86 on 13 and 492 DF, p-value: < 2.2e-16
    
     [1] "coefficients" "residuals" "fitted.values" "effects"
     [5] "weights" "rank" "assign" "qr"
     [9] "df.residual" "xlevels" "call" "terms"
    
     Call:
     stats::lm(formula = Y ~ ., data = X, weights = obsWeights, model = model)
    
     Residuals:
     Min 1Q Median 3Q Max
     -15.595 -2.730 -0.518 1.777 26.199
    
     Coefficients:
     Estimate Std. Error t value Pr(>|t|)
     (Intercept) 3.646e+01 5.103e+00 7.144 3.28e-12 ***
     crim -1.080e-01 3.286e-02 -3.287 0.001087 **
     zn 4.642e-02 1.373e-02 3.382 0.000778 ***
     indus 2.056e-02 6.150e-02 0.334 0.738288
     chas 2.687e+00 8.616e-01 3.118 0.001925 **
     nox -1.777e+01 3.820e+00 -4.651 4.25e-06 ***
     rm 3.810e+00 4.179e-01 9.116 < 2e-16 ***
     age 6.922e-04 1.321e-02 0.052 0.958229
     dis -1.476e+00 1.995e-01 -7.398 6.01e-13 ***
     rad 3.060e-01 6.635e-02 4.613 5.07e-06 ***
     tax -1.233e-02 3.760e-03 -3.280 0.001112 **
     ptratio -9.527e-01 1.308e-01 -7.283 1.31e-12 ***
     black 9.312e-03 2.686e-03 3.467 0.000573 ***
     lstat -5.248e-01 5.072e-02 -10.347 < 2e-16 ***
     ---
     Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
    
     Residual standard error: 4.745 on 492 degrees of freedom
     Multiple R-squared: 0.7406, Adjusted R-squared: 0.7338
     F-statistic: 108.1 on 13 and 492 DF, p-value: < 2.2e-16
    
    
     Call:
     stats::lm(formula = Y ~ ., data = X, weights = obsWeights, model = model)
    
     Residuals:
     Min 1Q Median 3Q Max
     -0.80469 -0.23612 -0.03105 0.23080 1.05224
    
     Coefficients:
     Estimate Std. Error t value Pr(>|t|)
     (Intercept) 1.6675402 0.3662392 4.553 6.67e-06 ***
     crim 0.0003028 0.0023585 0.128 0.897888
     zn 0.0023028 0.0009851 2.338 0.019808 *
     indus -0.0040254 0.0044131 -0.912 0.362135
     chas 0.0338534 0.0618295 0.548 0.584264
     nox -0.7242540 0.2741160 -2.642 0.008501 **
     rm 0.1357981 0.0299915 4.528 7.48e-06 ***
     age -0.0031071 0.0009480 -3.278 0.001121 **
     dis -0.0748924 0.0143135 -5.232 2.48e-07 ***
     rad 0.0168160 0.0047612 3.532 0.000451 ***
     tax -0.0006719 0.0002699 -2.490 0.013110 *
     ptratio -0.0498376 0.0093885 -5.308 1.68e-07 ***
     black 0.0001466 0.0001928 0.760 0.447370
     lstat -0.0197591 0.0036395 -5.429 8.91e-08 ***
     ---
     Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
    
     Residual standard error: 0.3405 on 492 degrees of freedom
     Multiple R-squared: 0.5192, Adjusted R-squared: 0.5065
     F-statistic: 40.86 on 13 and 492 DF, p-value: < 2.2e-16
    
    
     Call:
     SuperLearner(Y = Y_gaus, X = X, family = gaussian(), SL.library = c("SL.mean",
     "SL.lm"))
    
    
     Risk Coef
     SL.mean_All 84.6696 0.02186479
     SL.lm_All 24.3340 0.97813521
     V1
     Min. :-3.695
     1st Qu.:17.557
     Median :22.128
     Mean :22.533
     3rd Qu.:27.303
     Max. :44.189
    
     Call:
     SuperLearner(Y = Y_bin, X = X, family = binomial(), SL.library = c("SL.mean",
     "SL.lm"))
    
    
     Risk Coef
     SL.mean_All 0.2349366 0
     SL.lm_All 0.1125027 1
     V1
     Min. :0.0000
     1st Qu.:0.1281
     Median :0.3530
     Mean :0.3899
     3rd Qu.:0.6091
     Max. :1.0000
    
     Call:
     SuperLearner(Y = Y, X = X, family = binomial(), SL.library = SL.library,
     method = "method.NNLS", verbose = F, cvControl = list(V = 2))
    
    
     Risk Coef
     SL.rpart_All 0.1986827 0.31226655
     SL.glmnet_All 0.1803963 0.66105261
     SL.mean_All 0.2534500 0.02668084
     Error in (function (Y, X, newX, ...) : bad algorithm
     Error in (function (Y, X, newX, ...) : bad algorithm
     Error in (function (Y, X, newX, ...) : bad algorithm
    
     Call:
     SuperLearner(Y = Y, X = X, family = binomial(), SL.library = c(SL.library,
     "SL.bad_algorithm"), method = "method.NNLS", verbose = T, cvControl = list(V = 2))
    
    
    
     Risk Coef
     SL.rpart_All 0.1921176 0.08939677
     SL.glmnet_All 0.1635548 0.91060323
     SL.mean_All 0.2504500 0.00000000
     SL.bad_algorithm_All NA 0.00000000
    
     Call:
     SuperLearner(Y = Y, X = X, family = binomial(), SL.library = SL.library,
     method = "method.NNLS2", verbose = F, cvControl = list(V = 2))
    
    
     Risk Coef
     SL.rpart_All 0.2279346 0.05397859
     SL.glmnet_All 0.1670620 0.94602141
     SL.mean_All 0.2504500 0.00000000
    
     Call:
     SuperLearner(Y = Y, X = X, family = binomial(), SL.library = SL.library,
     method = "method.NNloglik", verbose = F, cvControl = list(V = 2))
    
    
     Risk Coef
     SL.rpart_All 0.5804469 0.1760951
     SL.glmnet_All 0.5010294 0.8239049
     SL.mean_All 0.6964542 0.0000000
     Error in (function (Y, X, newX, ...) : bad algorithm
     Error in (function (Y, X, newX, ...) : bad algorithm
     Error in (function (Y, X, newX, ...) : bad algorithm
    
     Call:
     SuperLearner(Y = Y, X = X, family = binomial(), SL.library = c(SL.library,
     "SL.bad_algorithm"), method = "method.NNloglik", verbose = T, cvControl = list(V = 2))
    
    
    
     Risk Coef
     SL.rpart_All Inf 0.1338597
     SL.glmnet_All 0.5027498 0.8661403
     SL.mean_All 0.7000679 0.0000000
     SL.bad_algorithm_All NA 0.0000000
    
     Call:
     SuperLearner(Y = Y, X = X, family = binomial(), SL.library = SL.library,
     method = "method.CC_LS", verbose = F, cvControl = list(V = 2))
    
    
     Risk Coef
     SL.rpart_All 0.2033781 0.16438434
     SL.glmnet_All 0.1740498 0.82391928
     SL.mean_All 0.2516500 0.01169638
    
     Call:
     SuperLearner(Y = Y, X = X, family = binomial(), SL.library = SL.library,
     method = "method.CC_nloglik", verbose = F, cvControl = list(V = 2))
    
    
     Risk Coef
     SL.rpart_All 295.8455 0.1014591
     SL.glmnet_All 205.3289 0.7867610
     SL.mean_All 277.1389 0.1117798
     Error in (function (Y, X, newX, ...) : bad algorithm
     Error in (function (Y, X, newX, ...) : bad algorithm
     Error in (function (Y, X, newX, ...) : bad algorithm
    
     Call:
     SuperLearner(Y = Y, X = X, family = binomial(), SL.library = c(SL.library,
     "SL.bad_algorithm"), method = "method.CC_nloglik", verbose = T, cvControl = list(V = 2))
    
    
    
     Risk Coef
     SL.rpart_All 212.5569 0.2707202
     SL.glmnet_All 193.9384 0.7292798
     SL.mean_All 277.1389 0.0000000
     SL.bad_algorithm_All NA 0.0000000
    
     Call:
     SuperLearner(Y = Y, X = X, family = binomial(), SL.library = SL.library,
     method = "method.AUC", verbose = F, cvControl = list(V = 2))
    
    
     Risk Coef
     SL.rpart_All 0.2533780 0.3333333
     SL.glmnet_All 0.1869683 0.3333333
     SL.mean_All 0.5550495 0.3333333
     Error in (function (Y, X, newX, ...) : bad algorithm
     Error in (function (Y, X, newX, ...) : bad algorithm
     Removing failed learners: SL.bad_algorithm_All
     Error in (function (Y, X, newX, ...) : bad algorithm
    
     Call:
     SuperLearner(Y = Y, X = X, family = binomial(), SL.library = c(SL.library,
     "SL.bad_algorithm"), method = "method.AUC", verbose = T, cvControl = list(V = 2))
    
    
    
     Risk Coef
     SL.rpart_All 0.2467721 0.2982123
     SL.glmnet_All 0.1705535 0.3508938
     SL.mean_All 0.5150135 0.3508938
     SL.bad_algorithm_All NA 0.0000000
     Call:
     qda(X, grouping = Y, prior = prior, method = method, tol = tol,
     CV = CV, nu = nu)
    
     Prior probabilities of groups:
     0 1
     0.6245059 0.3754941
    
     Group means:
     crim zn indus chas nox rm age dis
     0 5.2936824 4.708861 13.622089 0.05379747 0.5912399 5.985693 77.93228 3.349307
     1 0.8191541 22.431579 7.003316 0.09473684 0.4939153 6.781821 53.01211 4.536371
     rad tax ptratio black lstat
     0 11.588608 459.9209 19.19968 340.6392 16.042468
     1 6.157895 322.2789 17.21789 383.3425 7.015947
     Call:
     qda(X, grouping = Y, prior = prior, method = method, tol = tol,
     CV = CV, nu = nu)
    
     Prior probabilities of groups:
     0 1
     0.6245059 0.3754941
    
     Group means:
     crim zn indus chas nox rm age dis
     0 5.2936824 4.708861 13.622089 0.05379747 0.5912399 5.985693 77.93228 3.349307
     1 0.8191541 22.431579 7.003316 0.09473684 0.4939153 6.781821 53.01211 4.536371
     rad tax ptratio black lstat
     0 11.588608 459.9209 19.19968 340.6392 16.042468
     1 6.157895 322.2789 17.21789 383.3425 7.015947
     Y
     0 1
     62 38
    
     Call:
     SuperLearner(Y = Y, X = X, family = binomial(), SL.library = sl_lib, cvControl = list(V = 2))
    
    
    
     Risk Coef
     SL.randomForest_All 0.04141665 1
     SL.mean_All 0.23560000 0
     $grid
     NULL
    
     $names
     [1] "SL.randomForest_1"
    
     $base_learner
     [1] "SL.randomForest"
    
     $params
     list()
    
    
     Call:
     SuperLearner(Y = Y, X = X, family = binomial(), SL.library = create_rf$names,
     cvControl = list(V = 2))
    
    
     Risk Coef
     SL.randomForest_1_All 0.06761492 1
     SL.randomForest_1 <- function(...) SL.randomForest(...)
     $grid
     NULL
    
     $names
     [1] "SL.randomForest_1"
    
     $base_learner
     [1] "SL.randomForest"
    
     $params
     list()
    
     [1] "SL.randomForest_1"
     [1] 1
    
     Call:
     SuperLearner(Y = Y, X = X, family = binomial(), SL.library = create_rf$names,
     cvControl = list(V = 2), env = sl_env)
    
    
     Risk Coef
     SL.randomForest_1_All 0.056687 1
     $grid
     mtry
     1 1
     2 2
    
     $names
     [1] "SL.randomForest_1" "SL.randomForest_2"
    
     $base_learner
     [1] "SL.randomForest"
    
     $params
     list()
    
     [1] "SL.randomForest_1" "SL.randomForest_2"
    
     Call:
     SuperLearner(Y = Y, X = X, family = binomial(), SL.library = create_rf$names,
     cvControl = list(V = 2), env = sl_env)
    
    
     Risk Coef
     SL.randomForest_1_All 0.05775282 0.2130143
     SL.randomForest_2_All 0.05021309 0.7869857
     $grid
     mtry
     1 1
     2 2
    
     $names
     [1] "SL.randomForest_1" "SL.randomForest_2"
    
     $base_learner
     [1] "SL.randomForest"
    
     $params
     list()
    
     [1] "SL.randomForest_1" "SL.randomForest_2"
    
     Call:
     SuperLearner(Y = Y, X = X, family = binomial(), SL.library = create_rf$names,
     cvControl = list(V = 2), env = sl_env)
    
    
     Risk Coef
     SL.randomForest_1_All 0.04492449 0.4071852
     SL.randomForest_2_All 0.03961866 0.5928148
     $grid
     mtry nodesize maxnodes
     1 1 NULL NULL
     2 2 NULL NULL
    
     $names
     [1] "SL.randomForest_1_NULL_NULL" "SL.randomForest_2_NULL_NULL"
    
     $base_learner
     [1] "SL.randomForest"
    
     $params
     list()
    
     [1] "SL.randomForest_1_NULL_NULL" "SL.randomForest_2_NULL_NULL"
    
     Call:
     SuperLearner(Y = Y, X = X, family = binomial(), SL.library = create_rf$names,
     cvControl = list(V = 2), env = sl_env)
    
    
     Risk Coef
     SL.randomForest_1_NULL_NULL_All 0.04645335 0.2596168
     SL.randomForest_2_NULL_NULL_All 0.04111806 0.7403832
     $grid
     mtry maxnodes
     1 1 5
     2 2 5
     3 1 10
     4 2 10
     5 1 NULL
     6 2 NULL
    
     $names
     [1] "SL.randomForest_1_5" "SL.randomForest_2_5" "SL.randomForest_1_10"
     [4] "SL.randomForest_2_10" "SL.randomForest_1_NULL" "SL.randomForest_2_NULL"
    
     $base_learner
     [1] "SL.randomForest"
    
     $params
     list()
    
    
     Call:
     SuperLearner(Y = Y, X = X, family = binomial(), SL.library = create_rf$names,
     cvControl = list(V = 2), env = sl_env)
    
    
     Risk Coef
     SL.randomForest_1_5_All 0.05181234 0.0000000
     SL.randomForest_2_5_All 0.04334241 0.0000000
     SL.randomForest_1_10_All 0.04782853 0.3745053
     SL.randomForest_2_10_All 0.04335836 0.6254947
     SL.randomForest_1_NULL_All 0.04870680 0.0000000
     SL.randomForest_2_NULL_All 0.04383429 0.0000000
    
     Call:
     SuperLearner(Y = Y, X = X, family = binomial(), SL.library = create_rf$names,
     cvControl = list(V = 2))
    
    
     Risk Coef
     SL.randomForest_1_5_All 0.05171393 0
     SL.randomForest_2_5_All 0.04183487 0
     SL.randomForest_1_10_All 0.04885838 0
     SL.randomForest_2_10_All 0.03917066 1
     SL.randomForest_1_NULL_All 0.04730564 0
     SL.randomForest_2_NULL_All 0.04117284 0
    
     Call:
     SuperLearner(Y = Y, X = X, family = binomial(), SL.library = create_rf$names,
     cvControl = list(V = 2))
    
    
     Risk Coef
     SL.randomForest_1_5_All 0.05147493 0.00000000
     SL.randomForest_2_5_All 0.04114267 0.00000000
     SL.randomForest_1_10_All 0.04763217 0.00000000
     SL.randomForest_2_10_All 0.03809721 0.07433538
     SL.randomForest_1_NULL_All 0.04806088 0.00000000
     SL.randomForest_2_NULL_All 0.03820266 0.92566462
     Ranger result
    
     Call:
     ranger::ranger(`_Y` ~ ., data = cbind(`_Y` = Y, X), num.trees = num.trees, mtry = mtry, min.node.size = min.node.size, replace = replace, sample.fraction = sample.fraction, case.weights = obsWeights, write.forest = write.forest, probability = probability, num.threads = num.threads, verbose = verbose)
    
     Type: Regression
     Number of trees: 500
     Sample size: 506
     Number of independent variables: 13
     Mtry: 3
     Target node size: 5
     Variable importance mode: none
     Splitrule: variance
     OOB prediction error (MSE): 10.61927
     R squared (OOB): 0.874457
     Ranger result
    
     Call:
     ranger::ranger(`_Y` ~ ., data = cbind(`_Y` = Y, X), num.trees = num.trees, mtry = mtry, min.node.size = min.node.size, replace = replace, sample.fraction = sample.fraction, case.weights = obsWeights, write.forest = write.forest, probability = probability, num.threads = num.threads, verbose = verbose)
    
     Type: Probability estimation
     Number of trees: 500
     Sample size: 506
     Number of independent variables: 13
     Mtry: 3
     Target node size: 1
     Variable importance mode: none
     Splitrule: gini
     OOB prediction error (Brier s.): 0.08262419
     Ranger result
    
     Call:
     ranger::ranger(`_Y` ~ ., data = cbind(`_Y` = Y, X), num.trees = num.trees, mtry = mtry, min.node.size = min.node.size, replace = replace, sample.fraction = sample.fraction, case.weights = obsWeights, write.forest = write.forest, probability = probability, num.threads = num.threads, verbose = verbose)
    
     Type: Regression
     Number of trees: 500
     Sample size: 506
     Number of independent variables: 13
     Mtry: 3
     Target node size: 5
     Variable importance mode: none
     Splitrule: variance
     OOB prediction error (MSE): 10.48759
     R squared (OOB): 0.8760137
     Ranger result
    
     Call:
     ranger::ranger(`_Y` ~ ., data = cbind(`_Y` = Y, X), num.trees = num.trees, mtry = mtry, min.node.size = min.node.size, replace = replace, sample.fraction = sample.fraction, case.weights = obsWeights, write.forest = write.forest, probability = probability, num.threads = num.threads, verbose = verbose)
    
     Type: Probability estimation
     Number of trees: 500
     Sample size: 506
     Number of independent variables: 13
     Mtry: 3
     Target node size: 1
     Variable importance mode: none
     Splitrule: gini
     OOB prediction error (Brier s.): 0.08395011
     Generalized Linear Model of class 'speedglm':
    
     Call: speedglm::speedglm(formula = Y ~ ., data = X, family = family, weights = obsWeights, maxit = maxit, k = k)
    
     Coefficients:
     (Intercept) crim zn indus chas nox
     3.646e+01 -1.080e-01 4.642e-02 2.056e-02 2.687e+00 -1.777e+01
     rm age dis rad tax ptratio
     3.810e+00 6.922e-04 -1.476e+00 3.060e-01 -1.233e-02 -9.527e-01
     black lstat
     9.312e-03 -5.248e-01
    
     Generalized Linear Model of class 'speedglm':
    
     Call: speedglm::speedglm(formula = Y ~ ., data = X, family = family, weights = obsWeights, maxit = maxit, k = k)
    
     Coefficients:
     ------------------------------------------------------------------
     Estimate Std. Error t value Pr(>|t|)
     (Intercept) 3.646e+01 5.103459 7.1441 3.28e-12 ***
     crim -1.080e-01 0.032865 -3.2865 1.09e-03 **
     zn 4.642e-02 0.013728 3.3816 7.78e-04 ***
     indus 2.056e-02 0.061496 0.3343 7.38e-01
     chas 2.687e+00 0.861580 3.1184 1.93e-03 **
     nox -1.777e+01 3.819744 -4.6513 4.25e-06 ***
     rm 3.810e+00 0.417925 9.1161 1.98e-18 ***
     age 6.922e-04 0.013210 0.0524 9.58e-01
     dis -1.476e+00 0.199455 -7.3980 6.01e-13 ***
     rad 3.060e-01 0.066346 4.6129 5.07e-06 ***
     tax -1.233e-02 0.003760 -3.2800 1.11e-03 **
     ptratio -9.527e-01 0.130827 -7.2825 1.31e-12 ***
     black 9.312e-03 0.002686 3.4668 5.73e-04 ***
     lstat -5.248e-01 0.050715 -10.3471 7.78e-23 ***
    
     -------------------------------------------------------------------
     Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
    
     ---
     null df: 505; null deviance: 42716.3;
     residuals df: 492; residuals deviance: 11078.78;
     # obs.: 506; # non-zero weighted obs.: 506;
     AIC: 3027.609; log Likelihood: -1498.804;
     RSS: 11078.8; dispersion: 22.51785; iterations: 1;
     rank: 14; max tolerance: 1e+00; convergence: FALSE.
     Generalized Linear Model of class 'speedglm':
    
     Call: speedglm::speedglm(formula = Y ~ ., data = X, family = family, weights = obsWeights, maxit = maxit, k = k)
    
     Coefficients:
     ------------------------------------------------------------------
     Estimate Std. Error z value Pr(>|z|)
     (Intercept) 10.682635 3.921395 2.7242 6.45e-03 **
     crim -0.040649 0.049796 -0.8163 4.14e-01
     zn 0.012134 0.010678 1.1364 2.56e-01
     indus -0.040715 0.045615 -0.8926 3.72e-01
     chas 0.248209 0.653283 0.3799 7.04e-01
     nox -3.601085 2.924365 -1.2314 2.18e-01
     rm 1.155156 0.374843 3.0817 2.06e-03 **
     age -0.018660 0.009319 -2.0023 4.53e-02 *
     dis -0.518934 0.146286 -3.5474 3.89e-04 ***
     rad 0.255522 0.061391 4.1622 3.15e-05 ***
     tax -0.009500 0.003107 -3.0574 2.23e-03 **
     ptratio -0.409317 0.103191 -3.9666 7.29e-05 ***
     black -0.001452 0.002558 -0.5674 5.70e-01
     lstat -0.318436 0.054735 -5.8178 5.96e-09 ***
    
     -------------------------------------------------------------------
     Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
    
     ---
     null df: 505; null deviance: 669.76;
     residuals df: 492; residuals deviance: 296.39;
     # obs.: 506; # non-zero weighted obs.: 506;
     AIC: 324.3944; log Likelihood: -148.1972;
     RSS: 1107.5; dispersion: 1; iterations: 7;
     rank: 14; max tolerance: 7.55e-12; convergence: TRUE.
     Generalized Linear Model of class 'speedglm':
    
     Call: speedglm::speedglm(formula = Y ~ ., data = X, family = family, weights = obsWeights, maxit = maxit, k = k)
    
     Coefficients:
     ------------------------------------------------------------------
     Estimate Std. Error t value Pr(>|t|)
     (Intercept) 3.646e+01 5.103459 7.1441 3.28e-12 ***
     crim -1.080e-01 0.032865 -3.2865 1.09e-03 **
     zn 4.642e-02 0.013728 3.3816 7.78e-04 ***
     indus 2.056e-02 0.061496 0.3343 7.38e-01
     chas 2.687e+00 0.861580 3.1184 1.93e-03 **
     nox -1.777e+01 3.819744 -4.6513 4.25e-06 ***
     rm 3.810e+00 0.417925 9.1161 1.98e-18 ***
     age 6.922e-04 0.013210 0.0524 9.58e-01
     dis -1.476e+00 0.199455 -7.3980 6.01e-13 ***
     rad 3.060e-01 0.066346 4.6129 5.07e-06 ***
     tax -1.233e-02 0.003760 -3.2800 1.11e-03 **
     ptratio -9.527e-01 0.130827 -7.2825 1.31e-12 ***
     black 9.312e-03 0.002686 3.4668 5.73e-04 ***
     lstat -5.248e-01 0.050715 -10.3471 7.78e-23 ***
    
     -------------------------------------------------------------------
     Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
    
     ---
     null df: 505; null deviance: 42716.3;
     residuals df: 492; residuals deviance: 11078.78;
     # obs.: 506; # non-zero weighted obs.: 506;
     AIC: 3027.609; log Likelihood: -1498.804;
     RSS: 11078.8; dispersion: 22.51785; iterations: 1;
     rank: 14; max tolerance: 1e+00; convergence: FALSE.
     Generalized Linear Model of class 'speedglm':
    
     Call: speedglm::speedglm(formula = Y ~ ., data = X, family = family, weights = obsWeights, maxit = maxit, k = k)
    
     Coefficients:
     ------------------------------------------------------------------
     Estimate Std. Error z value Pr(>|z|)
     (Intercept) 10.682635 3.921395 2.7242 6.45e-03 **
     crim -0.040649 0.049796 -0.8163 4.14e-01
     zn 0.012134 0.010678 1.1364 2.56e-01
     indus -0.040715 0.045615 -0.8926 3.72e-01
     chas 0.248209 0.653283 0.3799 7.04e-01
     nox -3.601085 2.924365 -1.2314 2.18e-01
     rm 1.155156 0.374843 3.0817 2.06e-03 **
     age -0.018660 0.009319 -2.0023 4.53e-02 *
     dis -0.518934 0.146286 -3.5474 3.89e-04 ***
     rad 0.255522 0.061391 4.1622 3.15e-05 ***
     tax -0.009500 0.003107 -3.0574 2.23e-03 **
     ptratio -0.409317 0.103191 -3.9666 7.29e-05 ***
     black -0.001452 0.002558 -0.5674 5.70e-01
     lstat -0.318436 0.054735 -5.8178 5.96e-09 ***
    
     -------------------------------------------------------------------
     Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
    
     ---
     null df: 505; null deviance: 669.76;
     residuals df: 492; residuals deviance: 296.39;
     # obs.: 506; # non-zero weighted obs.: 506;
     AIC: 324.3944; log Likelihood: -148.1972;
     RSS: 1107.5; dispersion: 1; iterations: 7;
     rank: 14; max tolerance: 7.55e-12; convergence: TRUE.
     Linear Regression Model of class 'speedlm':
    
     Call: speedglm::speedlm(formula = Y ~ ., data = X, weights = obsWeights)
    
     Coefficients:
     (Intercept) crim zn indus chas nox
     3.646e+01 -1.080e-01 4.642e-02 2.056e-02 2.687e+00 -1.777e+01
     rm age dis rad tax ptratio
     3.810e+00 6.922e-04 -1.476e+00 3.060e-01 -1.233e-02 -9.527e-01
     black lstat
     9.312e-03 -5.248e-01
    
     Linear Regression Model of class 'speedlm':
    
     Call: speedglm::speedlm(formula = Y ~ ., data = X, weights = obsWeights)
    
     Coefficients:
     ------------------------------------------------------------------
     coef se t p.value
     (Intercept) 36.459488 5.103459 7.144 3.283e-12 ***
     crim -0.108011 0.032865 -3.287 1.087e-03 **
     zn 0.046420 0.013727 3.382 7.781e-04 ***
     indus 0.020559 0.061496 0.334 7.383e-01
     chas 2.686734 0.861580 3.118 1.925e-03 **
     nox -17.766611 3.819744 -4.651 4.246e-06 ***
     rm 3.809865 0.417925 9.116 1.979e-18 ***
     age 0.000692 0.013210 0.052 9.582e-01
     dis -1.475567 0.199455 -7.398 6.013e-13 ***
     rad 0.306049 0.066346 4.613 5.071e-06 ***
     tax -0.012335 0.003761 -3.280 1.112e-03 **
     ptratio -0.952747 0.130827 -7.283 1.309e-12 ***
     black 0.009312 0.002686 3.467 5.729e-04 ***
     lstat -0.524758 0.050715 -10.347 7.777e-23 ***
    
     -------------------------------------------------------------------
     Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
     ---
     Residual standard error: 4.745298 on 492 degrees of freedom;
     observations: 506; R^2: 0.741; adjusted R^2: 0.734;
     F-statistic: 108.1 on 13 and 492 df; p-value: 0.
     Linear Regression Model of class 'speedlm':
    
     Call: speedglm::speedlm(formula = Y ~ ., data = X, weights = obsWeights)
    
     Coefficients:
     ------------------------------------------------------------------
     coef se t p.value
     (Intercept) 1.667540 0.366239 4.553 6.670e-06 ***
     crim 0.000303 0.002358 0.128 8.979e-01
     zn 0.002303 0.000985 2.338 1.981e-02 *
     indus -0.004025 0.004413 -0.912 3.621e-01
     chas 0.033853 0.061829 0.548 5.843e-01
     nox -0.724254 0.274116 -2.642 8.501e-03 **
     rm 0.135798 0.029992 4.528 7.483e-06 ***
     age -0.003107 0.000948 -3.278 1.121e-03 **
     dis -0.074892 0.014313 -5.232 2.482e-07 ***
     rad 0.016816 0.004761 3.532 4.515e-04 ***
     tax -0.000672 0.000270 -2.490 1.311e-02 *
     ptratio -0.049838 0.009389 -5.308 1.677e-07 ***
     black 0.000147 0.000193 0.760 4.474e-01
     lstat -0.019759 0.003639 -5.429 8.912e-08 ***
    
     -------------------------------------------------------------------
     Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
     ---
     Residual standard error: 0.340537 on 492 degrees of freedom;
     observations: 506; R^2: 0.519; adjusted R^2: 0.506;
     F-statistic: 40.86 on 13 and 492 df; p-value: 0.
     Linear Regression Model of class 'speedlm':
    
     Call: speedglm::speedlm(formula = Y ~ ., data = X, weights = obsWeights)
    
     Coefficients:
     ------------------------------------------------------------------
     coef se t p.value
     (Intercept) 36.459488 5.103459 7.144 3.283e-12 ***
     crim -0.108011 0.032865 -3.287 1.087e-03 **
     zn 0.046420 0.013727 3.382 7.781e-04 ***
     indus 0.020559 0.061496 0.334 7.383e-01
     chas 2.686734 0.861580 3.118 1.925e-03 **
     nox -17.766611 3.819744 -4.651 4.246e-06 ***
     rm 3.809865 0.417925 9.116 1.979e-18 ***
     age 0.000692 0.013210 0.052 9.582e-01
     dis -1.475567 0.199455 -7.398 6.013e-13 ***
     rad 0.306049 0.066346 4.613 5.071e-06 ***
     tax -0.012335 0.003761 -3.280 1.112e-03 **
     ptratio -0.952747 0.130827 -7.283 1.309e-12 ***
     black 0.009312 0.002686 3.467 5.729e-04 ***
     lstat -0.524758 0.050715 -10.347 7.777e-23 ***
    
     -------------------------------------------------------------------
     Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
     ---
     Residual standard error: 4.745298 on 492 degrees of freedom;
     observations: 506; R^2: 0.741; adjusted R^2: 0.734;
     F-statistic: 108.1 on 13 and 492 df; p-value: 0.
     Linear Regression Model of class 'speedlm':
    
     Call: speedglm::speedlm(formula = Y ~ ., data = X, weights = obsWeights)
    
     Coefficients:
     ------------------------------------------------------------------
     coef se t p.value
     (Intercept) 1.667540 0.366239 4.553 6.670e-06 ***
     crim 0.000303 0.002358 0.128 8.979e-01
     zn 0.002303 0.000985 2.338 1.981e-02 *
     indus -0.004025 0.004413 -0.912 3.621e-01
     chas 0.033853 0.061829 0.548 5.843e-01
     nox -0.724254 0.274116 -2.642 8.501e-03 **
     rm 0.135798 0.029992 4.528 7.483e-06 ***
     age -0.003107 0.000948 -3.278 1.121e-03 **
     dis -0.074892 0.014313 -5.232 2.482e-07 ***
     rad 0.016816 0.004761 3.532 4.515e-04 ***
     tax -0.000672 0.000270 -2.490 1.311e-02 *
     ptratio -0.049838 0.009389 -5.308 1.677e-07 ***
     black 0.000147 0.000193 0.760 4.474e-01
     lstat -0.019759 0.003639 -5.429 8.912e-08 ***
    
     -------------------------------------------------------------------
     Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
     ---
     Residual standard error: 0.340537 on 492 degrees of freedom;
     observations: 506; R^2: 0.519; adjusted R^2: 0.506;
     F-statistic: 40.86 on 13 and 492 df; p-value: 0.
     == testthat results ===========================================================
     [ OK: 66 | SKIPPED: 0 | WARNINGS: 22 | FAILED: 1 ]
     1. Error: (unknown) (@test-biglasso.R#23)
    
     Error: testthat unit tests failed
     Execution halted
Flavor: r-release-windows-ix86+x86_64

Version: 2.0-25
Check: package dependencies
Result: NOTE
    Packages suggested but not available for checking: 'genefilter', 'sva'
Flavor: r-release-osx-x86_64