Package: DrugUtilisation Check: tests New result: ERROR Running ‘testthat.R’ [349s/177s] 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/tests.html > # * https://testthat.r-lib.org/reference/test_package.html#special-files > > library(testthat) > library(DrugUtilisation) > > test_check("DrugUtilisation") Starting 2 test processes [ FAIL 6 | WARN 0 | SKIP 43 | PASS 110 ] ══ Skipped tests (43) ══════════════════════════════════════════════════════════ • On CRAN (43): 'test-benchmarkDrugUtilisation.R:2:3', 'test-dailyDose.R:2:3', 'test-addDrugUtilisation.R:3:3', 'test-addDrugUtilisation.R:162:3', 'test-addDrugUtilisation.R:202:3', 'test-generatedAtcCohortSet.R:2:3', 'test-generatedIngredientCohortSet.R:2:3', 'test-generatedIngredientCohortSet.R:32:3', 'test-generatedIngredientCohortSet.R:49:3', 'test-generatedIngredientCohortSet.R:64:3', 'test-generatedIngredientCohortSet.R:93:3', 'test-generateDrugUtilisationCohortSet.R:2:3', 'test-generateDrugUtilisationCohortSet.R:23:3', 'test-generateDrugUtilisationCohortSet.R:209:3', 'test-patterns.R:2:3', 'test-plotProportionOfPatientsCovered.R:2:3', 'test-plotProportionOfPatientsCovered.R:53:3', 'test-plotProportionOfPatientsCovered.R:95:3', 'test-plotTreatment.R:2:3', 'test-plots.R:2:3', 'test-plots.R:93:3', 'test-plots.R:157:3', 'test-require.R:2:3', 'test-require.R:108:3', 'test-require.R:313:3', 'test-require.R:419:3', 'test-require.R:513:3', 'test-require.R:584:3', 'test-indication.R:2:3', 'test-indication.R:201:3', 'test-indication.R:366:3', 'test-indication.R:483:3', 'test-summariseProportionOfPatientsCovered.R:94:3', 'test-summariseProportionOfPatientsCovered.R:170:3', 'test-summariseProportionOfPatientsCovered.R:277:3', 'test-summariseProportionOfPatientsCovered.R:499:3', 'test-summariseProportionOfPatientsCovered.R:552:3', 'test-tables.R:2:3', 'test-tables.R:97:3', 'test-tables.R:222:3', 'test-tables.R:306:3', 'test-tables.R:398:3', 'test-tables.R:457:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test-generateDrugUtilisationCohortSet.R:142:3'): cohort attrition ── any(...) is not TRUE `actual`: FALSE `expected`: TRUE ── Failure ('test-generateDrugUtilisationCohortSet.R:166:3'): cohort attrition ── colnames(cdm$cohort2) (`actual`) not identical to c(omopgenerics::cohortColumns("cohort"), "number_exposures") (`expected`). actual | expected [3] "cohort_start_date" | "cohort_start_date" [3] [4] "cohort_end_date" | "cohort_end_date" [4] [5] "number_exposures" | "number_exposures" [5] [6] "days_prescribed" - ── Failure ('test-generateDrugUtilisationCohortSet.R:177:3'): cohort attrition ── colnames(cdm$cohort3) (`actual`) not identical to c(omopgenerics::cohortColumns("cohort"), "days_prescribed") (`expected`). actual | expected [2] "subject_id" | "subject_id" [2] [3] "cohort_start_date" | "cohort_start_date" [3] [4] "cohort_end_date" | "cohort_end_date" [4] [5] "number_exposures" - [6] "days_prescribed" | "days_prescribed" [5] ── Failure ('test-generateDrugUtilisationCohortSet.R:188:3'): cohort attrition ── colnames(cdm$cohort4) (`actual`) not identical to omopgenerics::cohortColumns("cohort") (`expected`). actual | expected [2] "subject_id" | "subject_id" [2] [3] "cohort_start_date" | "cohort_start_date" [3] [4] "cohort_end_date" | "cohort_end_date" [4] [5] "number_exposures" - [6] "days_prescribed" - ── Failure ('test-generateDrugUtilisationCohortSet.R:202:3'): cohort attrition ── cohort1$number_exposures (`actual`) not identical to c(4L, 1L, 1L) (`expected`). `actual`: `expected`: 4 1 1 ── Failure ('test-generateDrugUtilisationCohortSet.R:203:3'): cohort attrition ── cohort1$days_prescribed (`actual`) not identical to c(134L, 46L, 24L) (`expected`). `actual`: `expected`: 134 46 24 [ FAIL 6 | WARN 0 | SKIP 43 | PASS 110 ] Error: Test failures Execution halted Package: TrialEmulation Check: tests New result: ERROR Running ‘testthat.R’ [214s/205s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(TrialEmulation) > > data.table::setDTthreads(2) > test_check("TrialEmulation") Starting data manipulation Starting data extension Summary of extended data: Number of observations: 1939053 ------------------------------------------------------------ Starting data manipulation P(treatment = 1 | previous treatment = 0) for denominator Call: glm(formula = treatment ~ 1, family = binomial(link = "logit"), data = data) Coefficients: Estimate Std. Error z value Pr(>|z|) (Intercept) -3.84325 0.04785 -80.31 <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: 4329.7 on 21263 degrees of freedom Residual deviance: 4329.7 on 21263 degrees of freedom AIC: 4331.7 Number of Fisher Scoring iterations: 6 P(treatment = 1 | previous treatment = 0) for numerator Call: glm(formula = treatment ~ 1, family = binomial(link = "logit"), data = data) Coefficients: Estimate Std. Error z value Pr(>|z|) (Intercept) -3.84325 0.04785 -80.31 <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: 4329.7 on 21263 degrees of freedom Residual deviance: 4329.7 on 21263 degrees of freedom AIC: 4331.7 Number of Fisher Scoring iterations: 6 P(treatment = 1 | previous treatment = 1) for denominator Call: glm(formula = treatment ~ 1, family = binomial(link = "logit"), data = data) Coefficients: Estimate Std. Error z value Pr(>|z|) (Intercept) 4.37616 0.06815 64.21 <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: 2346.7 on 17555 degrees of freedom Residual deviance: 2346.7 on 17555 degrees of freedom AIC: 2348.7 Number of Fisher Scoring iterations: 7 P(treatment = 1 | previous treatment = 1) for numerator Call: glm(formula = treatment ~ 1, family = binomial(link = "logit"), data = data) Coefficients: Estimate Std. Error z value Pr(>|z|) (Intercept) 4.37616 0.06815 64.21 <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: 2346.7 on 17555 degrees of freedom Residual deviance: 2346.7 on 17555 degrees of freedom AIC: 2348.7 Number of Fisher Scoring iterations: 7 Starting data extension Summary of extended data: Number of observations: 963883 ------------------------------------------------------------ Starting data manipulation P(treatment = 1 | previous treatment = 0) for denominator Call: glm(formula = treatment ~ 1, family = binomial(link = "logit"), data = data) Coefficients: Estimate Std. Error z value Pr(>|z|) (Intercept) -3.32517 0.03599 -92.4 <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: 6948.7 on 23042 degrees of freedom Residual deviance: 6948.7 on 23042 degrees of freedom AIC: 6950.7 Number of Fisher Scoring iterations: 6 P(treatment = 1 | previous treatment = 0) for numerator Call: glm(formula = treatment ~ 1, family = binomial(link = "logit"), data = data) Coefficients: Estimate Std. Error z value Pr(>|z|) (Intercept) -3.32517 0.03599 -92.4 <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: 6948.7 on 23042 degrees of freedom Residual deviance: 6948.7 on 23042 degrees of freedom AIC: 6950.7 Number of Fisher Scoring iterations: 6 P(treatment = 1 | previous treatment = 1) for denominator Call: glm(formula = treatment ~ 1, family = binomial(link = "logit"), data = data) Coefficients: Estimate Std. Error z value Pr(>|z|) (Intercept) 3.9124 0.0453 86.37 <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: 4892.8 on 25356 degrees of freedom Residual deviance: 4892.8 on 25356 degrees of freedom AIC: 4894.8 Number of Fisher Scoring iterations: 6 P(treatment = 1 | previous treatment = 1) for numerator Call: glm(formula = treatment ~ 1, family = binomial(link = "logit"), data = data) Coefficients: Estimate Std. Error z value Pr(>|z|) (Intercept) 3.9124 0.0453 86.37 <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: 4892.8 on 25356 degrees of freedom Residual deviance: 4892.8 on 25356 degrees of freedom AIC: 4894.8 Number of Fisher Scoring iterations: 6 Starting data extension Summary of extended data: Number of observations: 1939053 ------------------------------------------------------------ Starting data manipulation P(treatment = 1 | previous treatment = 0) for denominator Call: glm(formula = treatment ~ age_s + x4 + x2 + x1, family = binomial(link = "logit"), data = data) Coefficients: Estimate Std. Error z value Pr(>|z|) (Intercept) -0.13699 0.25792 -0.531 0.5953 age_s -0.04014 0.19890 -0.202 0.8401 x4 1.09583 0.21355 5.131 2.88e-07 *** x2 0.09687 0.19430 0.499 0.6181 x1 0.61385 0.36325 1.690 0.0911 . --- Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 (Dispersion parameter for binomial family taken to be 1) Null deviance: 232.27 on 169 degrees of freedom Residual deviance: 185.41 on 165 degrees of freedom AIC: 195.41 Number of Fisher Scoring iterations: 4 P(treatment = 1 | previous treatment = 0) for numerator Call: glm(formula = treatment ~ age_s + x4, family = binomial(link = "logit"), data = data) Coefficients: Estimate Std. Error z value Pr(>|z|) (Intercept) 0.12031 0.20308 0.592 0.554 age_s 0.01215 0.19512 0.062 0.950 x4 1.10863 0.21415 5.177 2.26e-07 *** --- Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 (Dispersion parameter for binomial family taken to be 1) Null deviance: 232.27 on 169 degrees of freedom Residual deviance: 188.62 on 167 degrees of freedom AIC: 194.62 Number of Fisher Scoring iterations: 4 P(treatment = 1 | previous treatment = 1) for denominator Call: glm(formula = treatment ~ age_s + x4 + x2 + x1, family = binomial(link = "logit"), data = data) Coefficients: Estimate Std. Error z value Pr(>|z|) (Intercept) 0.6783 0.2797 2.425 0.015318 * age_s -0.1924 0.2115 -0.910 0.362887 x4 0.8536 0.2218 3.849 0.000119 *** x2 0.3246 0.1963 1.653 0.098252 . x1 0.7923 0.4914 1.612 0.106867 --- Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 (Dispersion parameter for binomial family taken to be 1) Null deviance: 188.83 on 150 degrees of freedom Residual deviance: 164.85 on 146 degrees of freedom AIC: 174.85 Number of Fisher Scoring iterations: 4 P(treatment = 1 | previous treatment = 1) for numerator Call: glm(formula = treatment ~ age_s + x4, family = binomial(link = "logit"), data = data) Coefficients: Estimate Std. Error z value Pr(>|z|) (Intercept) 0.7476 0.2520 2.967 0.003011 ** age_s -0.1686 0.2081 -0.810 0.417888 x4 0.7935 0.2163 3.669 0.000244 *** --- Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 (Dispersion parameter for binomial family taken to be 1) Null deviance: 188.83 on 150 degrees of freedom Residual deviance: 170.78 on 148 degrees of freedom AIC: 176.78 Number of Fisher Scoring iterations: 4 Starting data extension Summary of extended data: Number of observations: 500 ------------------------------------------------------------ [ FAIL 2 | WARN 1 | SKIP 33 | PASS 437 ] ══ Skipped tests (33) ══════════════════════════════════════════════════════════ • On CRAN (33): 'test-data_utils.R:6:3', 'test-data_utils.R:111:3', 'test-data_utils.R:131:3', 'test-generics.R:25:3', 'test-generics.R:66:3', 'test-generics.R:95:3', 'test-modelling.R:99:3', 'test-modelling.R:154:3', 'test-modelling.R:175:3', 'test-modelling.R:205:3', 'test-modelling.R:229:3', 'test-modelling.R:266:3', 'test-modelling.R:290:3', 'test-modelling.R:314:3', 'test-modelling.R:357:3', 'test-modelling.R:431:3', 'test-predict.R:26:3', 'test-predict.R:51:3', 'test-predict.R:108:3', 'test-predict.R:171:3', 'test-sampling.R:5:3', 'test-sampling.R:15:3', 'test-sampling.R:34:3', 'test-sampling.R:54:3', 'test-sampling.R:86:3', 'test-sampling.R:103:3', 'test-sampling.R:180:3', 'test-te_weights.R:20:3', 'test-te_weights.R:62:3', 'test-trial_sequence.R:41:3', 'test-trial_sequence.R:45:3', 'test-trial_sequence.R:49:3', 'test-trial_sequence.R:56:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test-te_datastore_duckdb.R:115:3'): sample_controls works with trial_sequence objects containing te_datastore_duckdb objects ── sort(sc_04@outcome_data@data$id) (`actual`) not equal to c(...) (`expected`). `actual[1:14]`: 2 16 20 21 44 44 44 44 44 47 and 4 more... `expected[1:11]`: 16 20 44 44 44 44 44 49 ... `actual[18:28]`: 59 59 59 65 70 70 74 74 and 4 more... `expected[15:28]`: 59 59 59 59 59 60 60 60 74 74 ... ── Failure ('test-te_datastore_duckdb.R:201:3'): load_expanded_data works with trial_sequence objects containing te_datastore_duckdb objects ── sort(sc_04@outcome_data@data$id) (`actual`) not equal to c(...) (`expected`). `actual[1:14]`: 2 16 20 21 44 44 44 44 44 47 and 4 more... `expected[1:11]`: 16 20 44 44 44 44 44 49 ... `actual[18:28]`: 59 59 59 65 70 70 74 74 and 4 more... `expected[15:28]`: 59 59 59 59 59 60 60 60 74 74 ... [ FAIL 2 | WARN 1 | SKIP 33 | PASS 437 ] Error: Test failures Execution halted