• using R version 4.4.3 RC (2025-02-20 r87772)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     gcc-14 (Debian 14.2.0-16) 14.2.0     GNU Fortran (Debian 14.2.0-16) 14.2.0
• running under: Debian GNU/Linux trixie/sid
• using session charset: UTF-8
• checking for file ‘TrialEmulation/DESCRIPTION’ ... OK
• this is package ‘TrialEmulation’ version ‘0.0.4.0’
• 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 ‘TrialEmulation’ can be installed ... OK See the install log for details.
• used C++ compiler: ‘g++-14 (Debian 14.2.0-16) 14.2.0’
• checking package directory ... OK
• checking for future file timestamps ... 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 ... [2s/3s] OK
• checking whether the package can be loaded with stated dependencies ... [2s/3s] OK
• checking whether the package can be unloaded cleanly ... [2s/3s] OK
• checking whether the namespace can be loaded with stated dependencies ... [2s/3s] OK
• checking whether the namespace can be unloaded cleanly ... [2s/3s] OK
• checking loading without being on the library search path ... [3s/4s] 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 ... [19s/23s] OK
• checking Rd files ... [1s/1s] OK
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• checking Rd line widths ... OK
• checking Rd cross-references ... OK
• checking for missing documentation entries ... OK
• checking for code/documentation mismatches ... OK
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• checking for unstated dependencies in examples ... OK
• checking contents of ‘data’ directory ... OK
• checking data for non-ASCII characters ... [5s/8s] 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
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• checking compiled code ... OK
• checking installed files from ‘inst/doc’ ... OK
• checking files in ‘vignettes’ ... OK
• checking examples ... [16s/23s] OK
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [271s/343s] ERROR   Running ‘testthat.R’ [271s/343s] 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 10 | WARN 1 | SKIP 33 | PASS 429 ]      ══ 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:73:3'): sample_controls works with trial_sequence objects containing te_datastore_duckdb objects ──   sort(sc_01@outcome_data@data$id) (`actual`) not equal to c(...) (`expected`).        `actual`: 7 9 14 15 21 21 29 32 and 32 more...   `expected`: 1 10 13 14 15 21 27 29 32 ...   ── Failure ('test-te_datastore_duckdb.R:83:3'): sample_controls works with trial_sequence objects containing te_datastore_duckdb objects ──   sc_02@outcome_data@n_rows (`actual`) not equal to 756 (`expected`).        `actual`: 761.0   `expected`: 756.0   ── Failure ('test-te_datastore_duckdb.R:101:3'): sample_controls works with trial_sequence objects containing te_datastore_duckdb objects ──   sort(sc_01@outcome_data@data$sample_weight) (`actual`) not equal to c(rep(1, 14), rep(100, 17)) (`expected`).        `actual[29:33]`: 100 100 100 100 100   `expected[29:31]`: 100 100 100   ── Failure ('test-te_datastore_duckdb.R:102:3'): sample_controls works with trial_sequence objects containing te_datastore_duckdb objects ──   sort(sc_02@outcome_data@data$sample_weight) (`actual`) not equal to c(rep(1, 14), rep(2, 742)) (`expected`).        `actual[754:761]`: 2 2 2 2 2 2 2 2   `expected[754:756]`: 2 2 2   ── Failure ('test-te_datastore_duckdb.R:112:3'): sample_controls works with trial_sequence objects containing te_datastore_duckdb objects ──   sort(sc_04@outcome_data@data$id) (`actual`) not equal to c(...) (`expected`).        `actual`: 16.0 20.0 44.0 44.0 44.0 44.0 44.0 49.0 53.0 53.0 and 18 more...   `expected`: 2.0 14.0 16.0 33.0 34.0 44.0 44.0 44.0 44.0 44.0 ...   ── Failure ('test-te_datastore_duckdb.R:152:3'): load_expanded_data works with trial_sequence objects containing te_datastore_duckdb objects ──   sort(sc_01@outcome_data@data$id) (`actual`) not equal to c(...) (`expected`).        `actual`: 7 9 14 15 21 21 29 32 and 32 more...   `expected`: 1 10 13 14 15 21 27 29 32 ...   ── Failure ('test-te_datastore_duckdb.R:162:3'): load_expanded_data works with trial_sequence objects containing te_datastore_duckdb objects ──   sc_02@outcome_data@n_rows (`actual`) not equal to 756 (`expected`).        `actual`: 761.0   `expected`: 756.0   ── Failure ('test-te_datastore_duckdb.R:182:3'): load_expanded_data works with trial_sequence objects containing te_datastore_duckdb objects ──   sort(sc_01@outcome_data@data$sample_weight) (`actual`) not equal to c(rep(1, 14), rep(100, 17)) (`expected`).        `actual[29:33]`: 100 100 100 100 100   `expected[29:31]`: 100 100 100   ── Failure ('test-te_datastore_duckdb.R:183:3'): load_expanded_data works with trial_sequence objects containing te_datastore_duckdb objects ──   sort(sc_02@outcome_data@data$sample_weight) (`actual`) not equal to c(rep(1, 14), rep(2, 742)) (`expected`).        `actual[754:761]`: 2 2 2 2 2 2 2 2   `expected[754:756]`: 2 2 2   ── Failure ('test-te_datastore_duckdb.R:193:3'): load_expanded_data works with trial_sequence objects containing te_datastore_duckdb objects ──   sort(sc_04@outcome_data@data$id) (`actual`) not equal to c(...) (`expected`).        `actual`: 16.0 20.0 44.0 44.0 44.0 44.0 44.0 49.0 53.0 53.0 and 18 more...   `expected`: 2.0 14.0 16.0 33.0 34.0 44.0 44.0 44.0 44.0 44.0 ...      [ FAIL 10 | WARN 1 | SKIP 33 | PASS 429 ]   Error: Test failures   Execution halted
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [119s/155s] OK
• checking PDF version of manual ... [8s/10s] OK
• checking HTML version of manual ... [2s/4s] OK
• checking for non-standard things in the check directory ... OK
• DONE

Status: 1 ERROR