Package check result: OK Changes to worse in reverse depends: Package: restez Check: tests New result: ERROR Running ‘test-all.R’ [22s/28s] Running the tests in ‘tests/test-all.R’ failed. Complete output: > library(testthat) > test_check("restez") Loading required package: restez ... Creating 'test_db_fldr/restez' ... Creating 'test_db_fldr/restez/downloads' ... Creating 'test_db_fldr/restez' ... Creating 'test_db_fldr/restez/downloads' ... Creating 'test_db_fldr/restez' ... Creating 'test_db_fldr/restez/downloads' ... Creating 'test_db_fldr/restez' ... Creating 'test_db_fldr/restez/downloads' ... Creating 'test_db_fldr/restez' ... Creating 'test_db_fldr/restez/downloads' ... Creating 'test_db_fldr/restez' ... Creating 'test_db_fldr/restez/downloads' ... Creating 'test_db_fldr/restez' ... Creating 'test_db_fldr/restez/downloads' ... Creating 'test_db_fldr/restez' ... Creating 'test_db_fldr/restez/downloads' ... Creating 'test_db_fldr/restez' ... Creating 'test_db_fldr/restez/downloads' Inspecting 1 file(s) to add to the database ... ... 'test.seq.gz' (1/1) Done. ... Creating 'test_db_fldr/restez' ... Creating 'test_db_fldr/restez/downloads' ... Creating 'test_db_fldr/restez' ... Creating 'test_db_fldr/restez/downloads' Inspecting 1 file(s) to add to the database ... ... 'test.seq.gz' (1/1) Done. ... Creating 'test_db_fldr/restez' ... Creating 'test_db_fldr/restez/downloads' ... Creating 'test_db_fldr/restez' ... Creating 'test_db_fldr/restez/downloads' ──────────────────────────────────────────────────────────────────────────────── Looking up latest GenBank release ... ... release number 1000 ... found 1 sequence files ──────────────────────────────────────────────────────────────────────────────── Which sequence file types would you like to download? Choose from those listed below: • 1 - 'type1' 1 files and 1e-07 GB Provide one or more numbers separated by spaces. e.g. to download all Mammalian sequences, type: "" followed by Enter Which files would you like to download? ──────────────────────────────────────────────────────────────────────────────── You've selected a total of 1 file(s) and 1e-07 GB of uncompressed data. These represent: • 'type1' Based on stated GenBank files sizes, we estimate ... ... 2e-08 GB for compressed, downloaded files ... 1.22e-07 GB for the SQL database Leading to a total of 1.42e-07 GB Please note, the real sizes of the database and its downloads cannot be accurately predicted beforehand. These are just estimates, actual sizes may differ by up to a factor of two. Is this OK? ──────────────────────────────────────────────────────────────────────────────── Downloading ... ... 'file1.seq' (1/1) Done. Enjoy your day. ... Creating 'test_db_fldr/restez' ... Creating 'test_db_fldr/restez/downloads' ... Creating 'test_db_fldr/restez' ... Creating 'test_db_fldr/restez/downloads' ... Creating 'test_db_fldr/restez' ... Creating 'test_db_fldr/restez/downloads' ... Creating 'test_db_fldr/restez' ... Creating 'test_db_fldr/restez/downloads' ... Creating 'test_db_fldr/restez' ... Creating 'test_db_fldr/restez/downloads' ... Creating 'test_db_fldr/restez' ... Creating 'test_db_fldr/restez/downloads' ... Creating 'test_db_fldr/restez' ... Creating 'test_db_fldr/restez/downloads' ... Creating 'test_db_fldr/restez' ... Creating 'test_db_fldr/restez/downloads' ... Creating 'test_db_fldr/restez' ... Creating 'test_db_fldr/restez/downloads' ... '1' (1/10) ... ... Hmmmm... no records found in that file. ... '2' (2/10) ... ... Hmmmm... no records found in that file. ... '3' (3/10) ... ... Hmmmm... no records found in that file. ... '4' (4/10) ... ... Hmmmm... no records found in that file. ... '5' (5/10) ... ... Hmmmm... no records found in that file. ... '6' (6/10) ... ... Hmmmm... no records found in that file. ... '7' (7/10) ... ... Hmmmm... no records found in that file. ... '8' (8/10) ... ... Hmmmm... no records found in that file. ... '9' (9/10) ... ... Hmmmm... no records found in that file. ... '10' (10/10) ... ... Hmmmm... no records found in that file. ... Creating 'test_db_fldr/restez' ... Creating 'test_db_fldr/restez/downloads' ... Creating 'test_db_fldr/restez' ... Creating 'test_db_fldr/restez/downloads' ... Creating 'test_db_fldr/restez' ... Creating 'test_db_fldr/restez/downloads' ... Creating 'test_db_fldr/restez' ... Creating 'test_db_fldr/restez/downloads' ... Creating 'test_db_fldr/restez' ... Creating 'test_db_fldr/restez/downloads' ... ... Your database is out-of-date. Latest release is 256 ... ... Your database is up-to-date example text example text'example text'example text ... Creating 'test_db_fldr/restez' ... Creating 'test_db_fldr/restez/downloads' Checking setup status at ... ... Creating 'test_db_fldr/restez' ... Creating 'test_db_fldr/restez/downloads' Checking setup status at ... ──────────────────────────────────────────────────────────────────────────────── Restez path ... ... Path 'test_db_fldr/restez' ... Does path exist? 'Yes' ──────────────────────────────────────────────────────────────────────────────── Download ... ... Path 'test_db_fldr/restez/downloads' ... Does path exist? 'Yes' ... N. files 0 ... Total size 0 ... GenBank division selections '' ... GenBank Release '0' ... Last updated '' ──────────────────────────────────────────────────────────────────────────────── Database ... ... Path 'test_db_fldr/restez/sql_db' ... Does path exist? 'No' ... Total size NA ... Does the database have data? 'No' ... Number of sequences 0 ... Min. sequence length '0' ... Max. sequence length 'Inf' ... Last_updated '' Checking setup status at ... ──────────────────────────────────────────────────────────────────────────────── Restez path ... ... Path 'test_db_fldr/restez' ... Does path exist? 'Yes' ──────────────────────────────────────────────────────────────────────────────── Download ... ... Path 'test_db_fldr/restez/downloads' ... Does path exist? 'Yes' ... N. files 0 ... Total size 0 ... GenBank division selections '' ... GenBank Release '0' ... Last updated '' ──────────────────────────────────────────────────────────────────────────────── Database ... ... Path 'test_db_fldr/restez/sql_db' ... Does path exist? 'Yes' ... Total size 780K ... Does the database have data? 'Yes' ... Number of sequences 10 ... Min. sequence length '0' ... Max. sequence length 'Inf' ... Last_updated '' ... Creating 'test_db_fldr/restez' ... Creating 'test_db_fldr/restez/downloads' ... Creating 'test_db_fldr/restez' ... Creating 'test_db_fldr/restez/downloads' ──────────────────────────────────────────────────────────────────────────────── Restez path ... ... Path 'test_db_fldr/restez' ... Does path exist? 'Yes' ──────────────────────────────────────────────────────────────────────────────── Download ... ... Path 'test_db_fldr/restez/downloads' ... Does path exist? 'Yes' ... N. files 0 ... Total size 0 ... GenBank division selections '' ... GenBank Release '0' ... Last updated '' ──────────────────────────────────────────────────────────────────────────────── Database ... ... Path 'test_db_fldr/restez/sql_db' ... Does path exist? 'No' ... Total size NA ... Does the database have data? 'No' ... Number of sequences 0 ... Min. sequence length '0' ... Max. sequence length 'Inf' ... Last_updated '' [ FAIL 1 | WARN 1 | SKIP 2 | PASS 138 ] ══ Skipped tests (2) ═══════════════════════════════════════════════════════════ • On CRAN (1): 'test-db-tools.R:138:3' • On Linux (1): 'test-db-tools.R:79:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test-get-tools.R:36:3'): gb_sequence_get() works ────────────────── names(seq_dnabin_2) not equal to `id_2`. 2/2 mismatches x[1]: "KF683087" y[1]: "AC092268" x[2]: "AC092268" y[2]: "KF683087" [ FAIL 1 | WARN 1 | SKIP 2 | PASS 138 ] Error: Test failures Execution halted Package: TrialEmulation Check: tests New result: ERROR Running ‘testthat.R’ [210s/198s] 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