* using log directory ‘/data/localhost/ripley/R/packages/tests-MKL/LAGOtrials.Rcheck’ * using R Under development (unstable) (2026-10-28 r90786) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (GCC) 16.2.1 20260819 (Red Hat 16.2.1-2) GNU Fortran (GCC) 16.2.1 20260819 (Red Hat 16.2.1-2) * running under: Fedora Linux 44 (Server Edition) * using session charset: UTF-8 * current time: 2026-10-29 14:02:07 UTC * using option ‘--no-stop-on-test-error’ * checking for file ‘LAGOtrials/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘LAGOtrials’ version ‘1.1.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for executable files ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘LAGOtrials’ can be installed ... [14s/13s] OK * used C++ compiler: ‘g++ (GCC) 16.2.1 20260819 (Red Hat 16.2.1-2)’ * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking whether startup messages can be suppressed ... OK * checking use of S3 registration ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... [14s/15s] OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd line widths ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking pragmas in C/C++ headers and code ... OK * checking compilation flags used ... OK * checking compiled code ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘spelling.R’ Running ‘testthat.R’ [194s/251s] [194s/251s] ERROR Running the tests in ‘tests/testthat.R’ failed. Complete output: > # This file is part of the standard setup for testthat. > # It is recommended that you do not modify it. > # > # Where should you do additional test configuration? > # Learn more about the roles of various files in: > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview > # * https://testthat.r-lib.org/articles/special-files.html > > library(testthat) > library(LAGOtrials) > > test_check("LAGOtrials") Saving _problems/test-center-period-factors-36.R Saving _problems/test-covariate-treatment-contrasts-212.R [1] "When 'cost_list_of_vectors' is provided, 'default_cost_fxn_type' is ignored." Call: glm(formula = pp3_oxytocin_mother ~ coaching_updt + launch_duration + birth_volume_100, family = family_object, data = data, weights = weights) Coefficients: Estimate Std. Error z value Pr(>|z|) (Intercept) -2.299892 0.068371 -33.638 < 2e-16 *** coaching_updt 0.025137 0.006112 4.113 3.91e-05 *** launch_duration 1.024470 0.074135 13.819 < 2e-16 *** birth_volume_100 0.664511 0.029627 22.429 < 2e-16 *** --- Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 (Dispersion parameter for binomial family taken to be 1) Null deviance: 8470.8 on 6123 degrees of freedom Residual deviance: 5161.2 on 6120 degrees of freedom AIC: 5169.2 Number of Fisher Scoring iterations: 6 [1] "When 'cost_list_of_vectors' is provided, 'default_cost_fxn_type' is ignored." Call: glm(formula = pp3_oxytocin_mother ~ coaching_updt + launch_duration + birth_volume_100, family = family_object, data = data, weights = weights) Coefficients: Estimate Std. Error z value Pr(>|z|) (Intercept) -2.299892 0.068371 -33.638 < 2e-16 *** coaching_updt 0.025137 0.006112 4.113 3.91e-05 *** launch_duration 1.024470 0.074135 13.819 < 2e-16 *** birth_volume_100 0.664511 0.029627 22.429 < 2e-16 *** --- Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 (Dispersion parameter for binomial family taken to be 1) Null deviance: 8470.8 on 6123 degrees of freedom Residual deviance: 5161.2 on 6120 degrees of freedom AIC: 5169.2 Number of Fisher Scoring iterations: 6 [1] "When 'cost_list_of_vectors' is provided, 'default_cost_fxn_type' is ignored." Call: glm(formula = pp3_oxytocin_mother ~ coaching_updt + launch_duration + birth_volume_100, family = family_object, data = data, weights = weights) Coefficients: Estimate Std. Error z value Pr(>|z|) (Intercept) -2.299892 0.068371 -33.638 < 2e-16 *** coaching_updt 0.025137 0.006112 4.113 3.91e-05 *** launch_duration 1.024470 0.074135 13.819 < 2e-16 *** birth_volume_100 0.664511 0.029627 22.429 < 2e-16 *** --- Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 (Dispersion parameter for binomial family taken to be 1) Null deviance: 8470.8 on 6123 degrees of freedom Residual deviance: 5161.2 on 6120 degrees of freedom AIC: 5169.2 Number of Fisher Scoring iterations: 6 i Starting LAGO Optimization i Validating inputs... [1] "When 'cost_list_of_vectors' is provided, 'default_cost_fxn_type' is ignored." [1] "When 'cost_list_of_vectors' is provided, 'default_cost_fxn_type' is ignored." Call: glm(formula = y ~ dose + noise, family = family_object, data = data, weights = weights) Coefficients: Estimate Std. Error z value Pr(>|z|) (Intercept) -0.91555 0.40799 -2.244 0.0248 * dose 0.31040 0.06062 5.120 3.05e-07 *** noise 0.03865 0.05358 0.721 0.4707 --- Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 (Dispersion parameter for binomial family taken to be 1) Null deviance: 257.72 on 199 degrees of freedom Residual deviance: 225.72 on 197 degrees of freedom AIC: 231.72 Number of Fisher Scoring iterations: 4 i Starting LAGO Optimization i Validating inputs... [1] "When 'cost_list_of_vectors' is provided, 'default_cost_fxn_type' is ignored." v Done i Assessing the cost function... v Done i Fitting the outcome model... v Done i Calculating the recommended intervention... v Done > <3 LAGO optimization complete <3 i Printing the output... -- LAGO optimization result ---------------------------------------------------- -- Inputs Input data dimensions: 32 rows, 11 columns Outcome name: mpg Outcome type: continuous 2 intervention component(s): gear, qsec Outcome model family: gaussian Outcome model link: identity Fixed center effects: FALSE Fixed time effects: FALSE Outcome goal: 40 Power goal: not specified Intervention component costs: c(0, 4), c(4, 6) Intervention lower bounds: 0, 0 Intervention upper bounds: 10, 350 -- Outcome model fit Call: glm(formula = mpg ~ gear + qsec, family = family_object, data = data, weights = weights) Coefficients: Estimate Std. Error t value Pr(>|t|) (Intercept) -30.7108 9.6702 -3.176 0.003530 ** gear 4.8711 1.0814 4.505 0.000100 *** qsec 1.8399 0.4465 4.121 0.000288 *** --- Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 (Dispersion parameter for gaussian family taken to be 18.84028) Null deviance: 1126.05 on 31 degrees of freedom Residual deviance: 546.37 on 29 degrees of freedom AIC: 189.61 Number of Fisher Scoring iterations: 2 -- Overall intervention-effect test To see the overall test results, include a 'group' column in the data with values 'treatment' or 'control' (binary outcomes only). -- Recommended intervention gear: 10 qsec: 12 Cost: 116 Estimated outcome: 40.0783 95% CI for the estimated outcome: not available (set include_confidence_set = TRUE) Outcome goal: 40 -- Confidence set Not computed (set include_confidence_set = TRUE to compute it). [1] "When 'cost_list_of_vectors' is provided, 'default_cost_fxn_type' is ignored." [1] "When 'cost_list_of_vectors' is provided, 'default_cost_fxn_type' is ignored." [1] "When 'cost_list_of_vectors' is provided, 'default_cost_fxn_type' is ignored." [1] "When 'cost_list_of_vectors' is provided, 'default_cost_fxn_type' is ignored." [1] "When 'cost_list_of_vectors' is provided, 'default_cost_fxn_type' is ignored." [1] "When 'cost_list_of_vectors' is provided, 'default_cost_fxn_type' is ignored." [1] "When 'cost_list_of_vectors' is provided, 'default_cost_fxn_type' is ignored." Call: glm(formula = pp3_oxytocin_mother ~ coaching_updt + launch_duration + birth_volume_100, family = family_object, data = data, weights = weights) Coefficients: Estimate Std. Error z value Pr(>|z|) (Intercept) -2.299892 0.068371 -33.638 < 2e-16 *** coaching_updt 0.025137 0.006112 4.113 3.91e-05 *** launch_duration 1.024470 0.074135 13.819 < 2e-16 *** birth_volume_100 0.664511 0.029627 22.429 < 2e-16 *** --- Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 (Dispersion parameter for binomial family taken to be 1) Null deviance: 8470.8 on 6123 degrees of freedom Residual deviance: 5161.2 on 6120 degrees of freedom AIC: 5169.2 Number of Fisher Scoring iterations: 6 [1] "When 'cost_list_of_vectors' is provided, 'default_cost_fxn_type' is ignored." Call: glm(formula = pp3_oxytocin_mother ~ coaching_updt + launch_duration + birth_volume_100, family = family_object, data = data, weights = weights) Coefficients: Estimate Std. Error z value Pr(>|z|) (Intercept) -2.299892 0.068371 -33.638 < 2e-16 *** coaching_updt 0.025137 0.006112 4.113 3.91e-05 *** launch_duration 1.024470 0.074135 13.819 < 2e-16 *** birth_volume_100 0.664511 0.029627 22.429 < 2e-16 *** --- Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 (Dispersion parameter for binomial family taken to be 1) Null deviance: 8470.8 on 6123 degrees of freedom Residual deviance: 5161.2 on 6120 degrees of freedom AIC: 5169.2 Number of Fisher Scoring iterations: 6 -- LAGO budget-constrained optimization -- Budget: 60 (maximize). Recommended intervention: gear = 10.000000, qsec = 2.572333 Cost: 59.4339969876842 (of 60). Estimated outcome: 22.7326276102087. -- LAGO budget-constrained optimization -- Budget: 60 (maximize). Recommended intervention: gear = 10.000000, qsec = 2.572333 Cost: 59.4339969876842 (of 60). Estimated outcome: 22.7326276102087. -- LAGO budget-constrained optimization -- Budget: 1e-04 (maximize). ! No reachable intervention fits this budget; increase the budget. -- LAGO budget-constrained optimization -- Budget: 1e+07 (maximize). Recommended intervention: gear = 10.000, qsec = 348.665 Cost: 2135.99015275574 (of 1e+07). Estimated outcome: 659.498484798617. i The budget did not bind: the whole reachable outcome range fits it, so this is the maximum reachable outcome. Saving _problems/test-links-and-covariates-506.R Saving _problems/test-links-and-covariates-507.R Saving _problems/test-model-rows-62.R [1] "When 'cost_list_of_vectors' is provided, 'default_cost_fxn_type' is ignored." If the confidence set calculation takes a long time to run, please consider changing the confidence set step size. Call: glm(formula = pp3_oxytocin_mother ~ coaching_updt + launch_duration + birth_volume_100, family = family_object, data = data, weights = weights) Coefficients: Estimate Std. Error z value Pr(>|z|) (Intercept) -2.299892 0.068371 -33.638 < 2e-16 *** coaching_updt 0.025137 0.006112 4.113 3.91e-05 *** launch_duration 1.024470 0.074135 13.819 < 2e-16 *** birth_volume_100 0.664511 0.029627 22.429 < 2e-16 *** --- Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 (Dispersion parameter for binomial family taken to be 1) Null deviance: 8470.8 on 6123 degrees of freedom Residual deviance: 5161.2 on 6120 degrees of freedom AIC: 5169.2 Number of Fisher Scoring iterations: 6 coaching_updt launch_duration birth_volume_100 CI_lower_bound 81 40 1.5 1.75 0.755 108 27 2.0 1.75 0.811 109 28 2.0 1.75 0.814 110 29 2.0 1.75 0.816 111 30 2.0 1.75 0.819 112 31 2.0 1.75 0.822 CI_upper_bound cost 81 0.851 80000 108 0.851 61900 109 0.855 63600 110 0.859 65300 111 0.863 67000 112 0.867 68700 [1] "When 'cost_list_of_vectors' is provided, 'default_cost_fxn_type' is ignored." If the confidence set calculation takes a long time to run, please consider changing the confidence set step size. Call: glm(formula = mpg ~ gear + qsec, family = family_object, data = data, weights = weights) Coefficients: Estimate Std. Error t value Pr(>|t|) (Intercept) -30.7108 9.6702 -3.176 0.003530 ** gear 4.8711 1.0814 4.505 0.000100 *** qsec 1.8399 0.4465 4.121 0.000288 *** --- Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 (Dispersion parameter for gaussian family taken to be 18.84028) Null deviance: 1126.05 on 31 degrees of freedom Residual deviance: 546.37 on 29 degrees of freedom AIC: 189.61 Number of Fisher Scoring iterations: 2 gear qsec CI_lower_bound CI_upper_bound cost 45 10 3 6.902 40.137 62 56 10 4 9.261 41.458 68 67 10 5 11.589 42.810 74 78 10 6 13.881 44.197 80 89 10 7 16.136 45.622 86 99 9 8 15.118 40.577 88 [1] "When 'cost_list_of_vectors' is provided, 'default_cost_fxn_type' is ignored." Call: glm(formula = mpg ~ gear + qsec, family = family_object, data = data, weights = weights) Coefficients: Estimate Std. Error t value Pr(>|t|) (Intercept) -30.7108 9.6702 -3.176 0.003530 ** gear 4.8711 1.0814 4.505 0.000100 *** qsec 1.8399 0.4465 4.121 0.000288 *** --- Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 (Dispersion parameter for gaussian family taken to be 18.84028) Null deviance: 1126.05 on 31 degrees of freedom Residual deviance: 546.37 on 29 degrees of freedom AIC: 189.61 Number of Fisher Scoring iterations: 2 [1] "When 'cost_list_of_vectors' is provided, 'default_cost_fxn_type' is ignored." Call: glm(formula = mpg ~ gear + qsec, family = family_object, data = data, weights = weights) Coefficients: Estimate Std. Error t value Pr(>|t|) (Intercept) -30.7108 9.6702 -3.176 0.003530 ** gear 4.8711 1.0814 4.505 0.000100 *** qsec 1.8399 0.4465 4.121 0.000288 *** --- Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 (Dispersion parameter for gaussian family taken to be 18.84028) Null deviance: 1126.05 on 31 degrees of freedom Residual deviance: 546.37 on 29 degrees of freedom AIC: 189.61 Number of Fisher Scoring iterations: 2 [1] "When 'cost_list_of_vectors' is provided, 'default_cost_fxn_type' is ignored." Call: glm(formula = mpg ~ disp + hp, family = family_object, data = data, weights = weights) Coefficients: Estimate Std. Error t value Pr(>|t|) (Intercept) 30.735904 1.331566 23.083 < 2e-16 *** disp -0.030346 0.007405 -4.098 0.000306 *** hp -0.024840 0.013385 -1.856 0.073679 . --- Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 (Dispersion parameter for gaussian family taken to be 9.775636) Null deviance: 1126.05 on 31 degrees of freedom Residual deviance: 283.49 on 29 degrees of freedom AIC: 168.62 Number of Fisher Scoring iterations: 2 [1] "When 'cost_list_of_vectors' is provided, 'default_cost_fxn_type' is ignored." Call: glm(formula = mpg ~ gear + qsec, family = family_object, data = data, weights = weights) Coefficients: Estimate Std. Error t value Pr(>|t|) (Intercept) -30.7108 9.6702 -3.176 0.003530 ** gear 4.8711 1.0814 4.505 0.000100 *** qsec 1.8399 0.4465 4.121 0.000288 *** --- Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 (Dispersion parameter for gaussian family taken to be 18.84028) Null deviance: 1126.05 on 31 degrees of freedom Residual deviance: 546.37 on 29 degrees of freedom AIC: 189.61 Number of Fisher Scoring iterations: 2 [1] "When 'cost_list_of_vectors' is provided, 'default_cost_fxn_type' is ignored." Call: glm(formula = pp3_oxytocin_mother ~ coaching_updt + launch_duration + birth_volume_100, family = family_object, data = data, weights = weights) Coefficients: Estimate Std. Error z value Pr(>|z|) (Intercept) -2.299892 0.068371 -33.638 < 2e-16 *** coaching_updt 0.025137 0.006112 4.113 3.91e-05 *** launch_duration 1.024470 0.074135 13.819 < 2e-16 *** birth_volume_100 0.664511 0.029627 22.429 < 2e-16 *** --- Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 (Dispersion parameter for binomial family taken to be 1) Null deviance: 8470.8 on 6123 degrees of freedom Residual deviance: 5161.2 on 6120 degrees of freedom AIC: 5169.2 Number of Fisher Scoring iterations: 6 [1] "When 'cost_list_of_vectors' is provided, 'default_cost_fxn_type' is ignored." If the confidence set calculation takes a long time to run, please consider changing the confidence set step size. Call: glm(formula = pp3_oxytocin_mother ~ coaching_updt + launch_duration + birth_volume_100, family = family_object, data = data, weights = weights) Coefficients: Estimate Std. Error z value Pr(>|z|) (Intercept) -2.299892 0.068371 -33.638 < 2e-16 *** coaching_updt 0.025137 0.006112 4.113 3.91e-05 *** launch_duration 1.024470 0.074135 13.819 < 2e-16 *** birth_volume_100 0.664511 0.029627 22.429 < 2e-16 *** --- Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 (Dispersion parameter for binomial family taken to be 1) Null deviance: 8470.8 on 6123 degrees of freedom Residual deviance: 5161.2 on 6120 degrees of freedom AIC: 5169.2 Number of Fisher Scoring iterations: 6 coaching_updt launch_duration birth_volume_100 CI_lower_bound 81 40 1.5 1.75 0.755 108 27 2.0 1.75 0.811 109 28 2.0 1.75 0.814 110 29 2.0 1.75 0.816 111 30 2.0 1.75 0.819 112 31 2.0 1.75 0.822 CI_upper_bound cost 81 0.851 80000 108 0.851 61900 109 0.855 63600 110 0.859 65300 111 0.863 67000 112 0.867 68700 [1] "When 'cost_list_of_vectors' is provided, 'default_cost_fxn_type' is ignored." Call: glm(formula = pp3_oxytocin_mother ~ coaching_updt + launch_duration + birth_volume_100, family = family_object, data = data, weights = weights) Coefficients: Estimate Std. Error z value Pr(>|z|) (Intercept) -2.299892 0.068371 -33.638 < 2e-16 *** coaching_updt 0.025137 0.006112 4.113 3.91e-05 *** launch_duration 1.024470 0.074135 13.819 < 2e-16 *** birth_volume_100 0.664511 0.029627 22.429 < 2e-16 *** --- Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 (Dispersion parameter for binomial family taken to be 1) Null deviance: 8470.8 on 6123 degrees of freedom Residual deviance: 5161.2 on 6120 degrees of freedom AIC: 5169.2 Number of Fisher Scoring iterations: 6 [1] "When 'cost_list_of_vectors' is provided, 'default_cost_fxn_type' is ignored." If the confidence set calculation takes a long time to run, please consider changing the confidence set step size. Call: glm(formula = y ~ dose, family = family_object, data = data, weights = weights) Coefficients: Estimate Std. Error z value Pr(>|z|) (Intercept) -4.120 2.103 -1.959 0.0501 . dose 2.747 1.285 2.137 0.0326 * --- Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 (Dispersion parameter for binomial family taken to be 1) Null deviance: 22.1807 on 15 degrees of freedom Residual deviance: 9.3631 on 14 degrees of freedom AIC: 13.363 Number of Fisher Scoring iterations: 6 dose CI_lower_bound CI_upper_bound cost 4 2 0.464 1 2 [1] "When 'cost_list_of_vectors' is provided, 'default_cost_fxn_type' is ignored." Call: glm(formula = y ~ dose, family = family_object, data = data, weights = weights) Coefficients: Estimate Std. Error z value Pr(>|z|) (Intercept) -4.120 2.103 -1.959 0.0501 . dose 2.747 1.285 2.137 0.0326 * --- Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 (Dispersion parameter for binomial family taken to be 1) Null deviance: 22.1807 on 15 degrees of freedom Residual deviance: 9.3631 on 14 degrees of freedom AIC: 13.363 Number of Fisher Scoring iterations: 6 [1] "When 'cost_list_of_vectors' is provided, 'default_cost_fxn_type' is ignored." If the confidence set calculation takes a long time to run, please consider changing the confidence set step size. Call: glm(formula = y ~ x, family = family_object, data = data, weights = weights) Coefficients: Estimate Std. Error t value Pr(>|t|) (Intercept) 0.25139 0.33293 0.755 0.457 x 1.46621 0.05717 25.644 <2e-16 *** --- Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 (Dispersion parameter for gaussian family taken to be 0.8736047) Null deviance: 598.972 on 29 degrees of freedom Residual deviance: 24.461 on 28 degrees of freedom AIC: 85.013 Number of Fisher Scoring iterations: 2 x CI_lower_bound CI_upper_bound cost 10 8 11.507 12.455 8 [1] "When 'cost_list_of_vectors' is provided, 'default_cost_fxn_type' is ignored." Call: glm(formula = y ~ dose, family = family_object, data = data, weights = weights) Coefficients: Estimate Std. Error z value Pr(>|z|) (Intercept) -4.120 2.103 -1.959 0.0501 . dose 2.747 1.285 2.137 0.0326 * --- Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 (Dispersion parameter for binomial family taken to be 1) Null deviance: 22.1807 on 15 degrees of freedom Residual deviance: 9.3631 on 14 degrees of freedom AIC: 13.363 Number of Fisher Scoring iterations: 6 [1] "When 'cost_list_of_vectors' is provided, 'default_cost_fxn_type' is ignored." [1] "When 'cost_list_of_vectors' is provided, 'default_cost_fxn_type' is ignored." [1] "When 'cost_list_of_vectors' is provided, 'default_cost_fxn_type' is ignored." [1] "When 'cost_list_of_vectors' is provided, 'default_cost_fxn_type' is ignored." value gear qsec rec_int_cost est_outcome_goal status 1 30 10 6.522269 83.13361 30 ok 2 35 10 9.239851 99.43911 35 ok 3 40 10 11.957433 115.74460 40 ok [1] "When 'cost_list_of_vectors' is provided, 'default_cost_fxn_type' is ignored." [1] "When 'cost_list_of_vectors' is provided, 'default_cost_fxn_type' is ignored." [1] "When 'cost_list_of_vectors' is provided, 'default_cost_fxn_type' is ignored." [1] "When 'cost_list_of_vectors' is provided, 'default_cost_fxn_type' is ignored." [1] "When 'cost_list_of_vectors' is provided, 'default_cost_fxn_type' is ignored." [1] "When 'cost_list_of_vectors' is provided, 'default_cost_fxn_type' is ignored." [1] "When 'cost_list_of_vectors' is provided, 'default_cost_fxn_type' is ignored." [1] "When 'cost_list_of_vectors' is provided, 'default_cost_fxn_type' is ignored." [1] "When 'cost_list_of_vectors' is provided, 'default_cost_fxn_type' is ignored." [1] "When 'cost_list_of_vectors' is provided, 'default_cost_fxn_type' is ignored." [1] "When 'cost_list_of_vectors' is provided, 'default_cost_fxn_type' is ignored." [1] "When 'cost_list_of_vectors' is provided, 'default_cost_fxn_type' is ignored." [1] "When 'cost_list_of_vectors' is provided, 'default_cost_fxn_type' is ignored." [1] "When 'cost_list_of_vectors' is provided, 'default_cost_fxn_type' is ignored." [1] "When 'cost_list_of_vectors' is provided, 'default_cost_fxn_type' is ignored." [1] "When 'cost_list_of_vectors' is provided, 'default_cost_fxn_type' is ignored." [1] "When 'cost_list_of_vectors' is provided, 'default_cost_fxn_type' is ignored." [1] "When 'cost_list_of_vectors' is provided, 'default_cost_fxn_type' is ignored." [1] "When 'cost_list_of_vectors' is provided, 'default_cost_fxn_type' is ignored." [1] "When 'cost_list_of_vectors' is provided, 'default_cost_fxn_type' is ignored." [1] "When 'cost_list_of_vectors' is provided, 'default_cost_fxn_type' is ignored." [1] "When 'cost_list_of_vectors' is provided, 'default_cost_fxn_type' is ignored." [1] "When 'cost_list_of_vectors' is provided, 'default_cost_fxn_type' is ignored." [1] "When 'cost_list_of_vectors' is provided, 'default_cost_fxn_type' is ignored." [1] "When 'cost_list_of_vectors' is provided, 'default_cost_fxn_type' is ignored." [1] "When 'cost_list_of_vectors' is provided, 'default_cost_fxn_type' is ignored." [1] "When 'cost_list_of_vectors' is provided, 'default_cost_fxn_type' is ignored." [1] "When 'cost_list_of_vectors' is provided, 'default_cost_fxn_type' is ignored." [1] "When 'cost_list_of_vectors' is provided, 'default_cost_fxn_type' is ignored." [1] "When 'cost_list_of_vectors' is provided, 'default_cost_fxn_type' is ignored." [1] "When 'cost_list_of_vectors' is provided, 'default_cost_fxn_type' is ignored." [1] "When 'cost_list_of_vectors' is provided, 'default_cost_fxn_type' is ignored." [1] "When 'cost_list_of_vectors' is provided, 'default_cost_fxn_type' is ignored." [1] "When 'cost_list_of_vectors' is provided, 'default_cost_fxn_type' is ignored." [1] "When 'cost_list_of_vectors' is provided, 'default_cost_fxn_type' is ignored." [1] "When 'cost_list_of_vectors' is provided, 'default_cost_fxn_type' is ignored." [1] "When 'cost_list_of_vectors' is provided, 'default_cost_fxn_type' is ignored." [1] "When 'cost_list_of_vectors' is provided, 'default_cost_fxn_type' is ignored." [1] "When 'cost_list_of_vectors' is provided, 'default_cost_fxn_type' is ignored." [1] "When 'cost_list_of_vectors' is provided, 'default_cost_fxn_type' is ignored." [1] "When 'cost_list_of_vectors' is provided, 'default_cost_fxn_type' is ignored." [1] "When 'cost_list_of_vectors' is provided, 'default_cost_fxn_type' is ignored." [1] "When 'cost_list_of_vectors' is provided, 'default_cost_fxn_type' is ignored." [1] "When 'cost_list_of_vectors' is provided, 'default_cost_fxn_type' is ignored." [1] "When 'cost_list_of_vectors' is provided, 'default_cost_fxn_type' is ignored." [1] "When 'cost_list_of_vectors' is provided, 'default_cost_fxn_type' is ignored." [1] "When 'cost_list_of_vectors' is provided, 'default_cost_fxn_type' is ignored." [1] "When 'cost_list_of_vectors' is provided, 'default_cost_fxn_type' is ignored." [1] "When 'cost_list_of_vectors' is provided, 'default_cost_fxn_type' is ignored." [1] "When 'cost_list_of_vectors' is provided, 'default_cost_fxn_type' is ignored." [1] "When 'cost_list_of_vectors' is provided, 'default_cost_fxn_type' is ignored." [1] "When 'cost_list_of_vectors' is provided, 'default_cost_fxn_type' is ignored." [1] "When 'cost_list_of_vectors' is provided, 'default_cost_fxn_type' is ignored." Loading required package: shiny Saving _problems/test-weights-column-167.R [ FAIL 6 | WARN 0 | SKIP 12 | PASS 2286 ] ══ Skipped tests (12) ══════════════════════════════════════════════════════════ • On CRAN (12): 'test-presentation.R:57:1', 'test-presentation.R:80:1', 'test-presentation.R:102:1', 'test-presentation.R:125:1', 'test-presentation.R:150:1', 'test-report.R:102:3', 'test-report.R:119:3', 'test-report.R:146:3', 'test-report.R:161:3', 'test-report.R:176:3', 'test-report.R:196:3', 'test-report.R:226:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test-center-period-factors.R:36:3'): an ordered center is fitted with one effect per center ── Expected `factor_key(ordered)` to equal `factor_key(plain)`. Differences: `actual$rec_int`: 1.942477880 3.000000000 `expected$rec_int`: 1.942477817 3.000000000 ── Failure ('test-covariate-treatment-contrasts.R:212:3'): binary confidence output is invariant for ordered additional covariates ── Expected `covariate_contrast_key(result)` to equal `covariate_contrast_key(plain)`. Differences: `actual$rec_int`: 0.000000000 1.854603415 `expected$rec_int`: 0.000000000 1.854602993 `actual$cost`: 1.85460342 `expected$cost`: 1.85460299 `actual$est`: 0.849999999 `expected$est`: 0.849999926 ── Failure ('test-links-and-covariates.R:506:3'): a factor center_characteristic is found by its level-named coefficient (#68) ── Expected `as_dummy$rec_int` to equal `as_factor$rec_int`. Differences: `actual`: 1.000000000 1.747970154 `expected`: 1.000000001 1.747970030 ── Failure ('test-links-and-covariates.R:507:3'): a factor center_characteristic is found by its level-named coefficient (#68) ── Expected `as_dummy$est_outcome_goal` to equal `as_factor$est_outcome_goal`. Differences: `actual`: 0.849999999 `expected`: 0.849999978 ── Failure ('test-model-rows.R:62:3'): a continuous outcome's confidence set uses only the fitted rows ── Expected `rows_key(with_na)` to equal `rows_key(complete)`. Differences: `actual$rec_int`: 1.695747771 3.000000000 `expected$rec_int`: 1.695747740 3.000000000 ── Failure ('test-weights-column.R:167:7'): lago_optimization() gives the same result with or without a weights column ── Expected `weights_column_key(result)` to equal `weights_column_key(expected)`. Differences: `actual$rec_int`: 0.000000000 1.896834941 `expected$rec_int`: 0.000000000 1.896834727 `actual$est`: 0.849999982 `expected$est`: 0.849999945 [ FAIL 6 | WARN 0 | SKIP 12 | PASS 2286 ] Error: ! Test failures. Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [14s/15s] OK * checking PDF version of manual ... OK * checking HTML version of manual ... OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 1 ERROR See ‘/data/localhost/ripley/R/packages/tests-MKL/LAGOtrials.Rcheck/00check.log’ for details. Command exited with non-zero status 1 Time 5:51.91, 274.32 + 10.66