CRAN Package Check Results for Maintainer ‘Cyril Leven <cyril.leven at chu-brest.fr>’

Last updated on 2025-12-28 03:52:00 CET.

Package	ERROR	OK
posologyr	1	12

Package posologyr

Current CRAN status: ERROR: 1, OK: 12

Version: 1.2.8
Check: examples
Result: ERROR Running examples in 'posologyr-Ex.R' failed The error most likely occurred in: > ### Name: poso_dose_auc > ### Title: Estimate the dose needed to reach a target area under the > ### concentration-time curve (AUC) > ### Aliases: poso_dose_auc > > ### ** Examples > > rxode2::setRxThreads(2L) # limit the number of threads > > # model > mod_run001 <- function() { + ini({ + THETA_Cl <- 4.0 + THETA_Vc <- 70.0 + THETA_Ka <- 1.0 + ETA_Cl ~ 0.2 + ETA_Vc ~ 0.2 + ETA_Ka ~ 0.2 + prop.sd <- sqrt(0.05) + }) + model({ + TVCl <- THETA_Cl + TVVc <- THETA_Vc + TVKa <- THETA_Ka + + Cl <- TVCl*exp(ETA_Cl) + Vc <- TVVc*exp(ETA_Vc) + Ka <- TVKa*exp(ETA_Ka) + + K20 <- Cl/Vc + Cc <- centr/Vc + + d/dt(depot) = -Ka*depot + d/dt(centr) = Ka*depot - K20*centr + Cc ~ prop(prop.sd) + }) + } > # df_patient01: event table for Patient01, following a 30 minutes intravenous > # infusion > df_patient01 <- data.frame(ID=1, + TIME=c(0.0,1.0,14.0), + DV=c(NA,25.0,5.5), + AMT=c(2000,0,0), + EVID=c(1,0,0), + DUR=c(0.5,NA,NA)) > # estimate the optimal dose to reach an AUC(0-12h) of 45 h.mg/l > poso_dose_auc(dat=df_patient01,prior_model=mod_run001, + time_auc=12,target_auc=45) ℹ parameter labels from comments are typically ignored in non-interactive mode ℹ Need to run with the source intact to parse comments Error in `[.data.table`(f_all_endpoints, , `:=`(f, get(as.character(DVID))), : attempt access index 16/16 in VECTOR_ELT Calls: poso_dose_auc ... init_eta -> residual_error_all_endpoints -> [ -> [.data.table Execution halted Flavor: r-devel-windows-x86_64

Version: 1.2.8
Check: tests
Result: ERROR Running 'testthat.R' [49s] Running the tests in 'tests/testthat.R' failed. Complete output: > library(rxode2) rxode2 5.0.1 using 2 threads (see ?getRxThreads) no cache: create with `rxCreateCache()` > library(posologyr) > library(testthat) > setRxThreads(2L) #for CRAN, following the advice of mattfidler > > test_check("posologyr") Saving _problems/test_doseoptim-108.R Saving _problems/test_doseoptim-218.R Saving _problems/test_doseoptim_cmt-60.R Saving _problems/test_doseoptim_tdm-53.R Saving _problems/test_doseoptim_tdm-82.R Saving _problems/test_doseoptim_tdm-112.R Saving _problems/test_issue_10-41.R Saving _problems/test_issue_10-49.R Saving _problems/test_issue_28-60.R Saving _problems/test_issue_29-53.R Saving _problems/test_issue_30-50.R Saving _problems/test_issue_32-60.R Saving _problems/test_issue_52-37.R Saving _problems/test_map_iov-64.R Saving _problems/test_map_mlx-78.R Saving _problems/test_map_nlmixr-42.R Saving _problems/test_map_nm-51.R Saving _problems/test_rxui-39.R [ FAIL 18 | WARN 0 | SKIP 4 | PASS 10 ] ══ Skipped tests (4) ═══════════════════════════════════════════════════════════ • On CRAN (2): 'test_rxui.R:48:3', 'test_rxui.R:128:3' • empty test (2): , ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test_doseoptim.R:97:3'): Same optimal dose with or without providing MAP estimates ── Error in ``[.data.table`(f_all_endpoints, , `:=`(f, get(as.character(DVID))), by = seq_len(nrow(f_all_endpoints)))`: attempt access index 18/18 in VECTOR_ELT Backtrace: ▆ 1. ├─testthat::expect_equal(...) at test_doseoptim.R:97:3 2. │ └─testthat::quasi_label(enquo(expected), expected.label) 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) 4. └─posologyr::poso_dose_conc(...) 5. └─posologyr:::read_optim_distribution_input(...) 6. └─posologyr::poso_estim_map(dat, prior_model, nocb = nocb, return_model = TRUE) 7. └─posologyr:::init_eta(...) 8. └─posologyr:::residual_error_all_endpoints(...) 9. ├─f_all_endpoints[, `:=`(f, get(as.character(DVID))), by = seq_len(nrow(f_all_endpoints))] 10. └─data.table:::`[.data.table`(...) ── Error ('test_doseoptim.R:211:3'): Optimization results do not deviate from known values for multiple dose regimen ── Error in ``[.data.table`(f_all_endpoints, , `:=`(f, get(as.character(DVID))), by = seq_len(nrow(f_all_endpoints)))`: attempt access index 22/22 in VECTOR_ELT Backtrace: ▆ 1. ├─testthat::expect_equal(...) at test_doseoptim.R:211:3 2. │ └─testthat::quasi_label(enquo(object), label) 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) 4. └─posologyr::poso_time_cmin(...) 5. └─posologyr:::read_optim_distribution_input(...) 6. └─posologyr::poso_estim_map(dat, prior_model, nocb = nocb, return_model = TRUE) 7. └─posologyr:::init_eta(...) 8. └─posologyr:::residual_error_all_endpoints(...) 9. ├─f_all_endpoints[, `:=`(f, get(as.character(DVID))), by = seq_len(nrow(f_all_endpoints))] 10. └─data.table:::`[.data.table`(...) ── Error ('test_doseoptim_cmt.R:57:3'): Optimal dose can be estimated for dosing in any compartment ── Error in ``[.data.table`(f_all_endpoints, , `:=`(f, get(as.character(DVID))), by = seq_len(nrow(f_all_endpoints)))`: attempt access index 26/26 in VECTOR_ELT Backtrace: ▆ 1. ├─testthat::expect_equal(...) at test_doseoptim_cmt.R:57:3 2. │ └─testthat::quasi_label(enquo(object), label) 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) 4. └─posologyr::poso_dose_conc(...) 5. └─posologyr::poso_estim_map(...) 6. └─posologyr:::init_eta(...) 7. └─posologyr:::residual_error_all_endpoints(...) 8. ├─f_all_endpoints[, `:=`(f, get(as.character(DVID))), by = seq_len(nrow(f_all_endpoints))] 9. └─data.table:::`[.data.table`(...) ── Error ('test_doseoptim_tdm.R:49:3'): Optimization results do not deviate from known values following TDM events when the last time is a float number ── Error in ``[.data.table`(f_all_endpoints, , `:=`(f, get(as.character(DVID))), by = seq_len(nrow(f_all_endpoints)))`: attempt access index 23/23 in VECTOR_ELT Backtrace: ▆ 1. ├─testthat::expect_equal(...) at test_doseoptim_tdm.R:49:3 2. │ └─testthat::quasi_label(enquo(object), label) 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) 4. └─posologyr::poso_time_cmin(...) 5. └─posologyr::poso_estim_map(...) 6. └─posologyr:::init_eta(...) 7. └─posologyr:::residual_error_all_endpoints(...) 8. ├─f_all_endpoints[, `:=`(f, get(as.character(DVID))), by = seq_len(nrow(f_all_endpoints))] 9. └─data.table:::`[.data.table`(...) ── Error ('test_doseoptim_tdm.R:78:13'): Optimization results do not deviate from known values following TDM events when the last time is an integer ── Error in ``[.data.table`(f_all_endpoints, , `:=`(f, get(as.character(DVID))), by = seq_len(nrow(f_all_endpoints)))`: attempt access index 23/23 in VECTOR_ELT Backtrace: ▆ 1. ├─testthat::expect_equal(...) at test_doseoptim_tdm.R:78:13 2. │ └─testthat::quasi_label(enquo(object), label) 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) 4. └─posologyr::poso_time_cmin(...) 5. └─posologyr::poso_estim_map(...) 6. └─posologyr:::init_eta(...) 7. └─posologyr:::residual_error_all_endpoints(...) 8. ├─f_all_endpoints[, `:=`(f, get(as.character(DVID))), by = seq_len(nrow(f_all_endpoints))] 9. └─data.table:::`[.data.table`(...) ── Error ('test_doseoptim_tdm.R:109:13'): The functions issue a warning when parameters are ignored because TDM=true ── Error in ``[.data.table`(f_all_endpoints, , `:=`(f, get(as.character(DVID))), by = seq_len(nrow(f_all_endpoints)))`: attempt access index 23/23 in VECTOR_ELT Backtrace: ▆ 1. ├─testthat::expect_warning(...) at test_doseoptim_tdm.R:109:13 2. │ └─testthat:::expect_condition_matching_(...) 3. │ └─testthat:::quasi_capture(...) 4. │ ├─testthat (local) .capture(...) 5. │ │ └─base::withCallingHandlers(...) 6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. └─posologyr::poso_time_cmin(...) 8. └─posologyr::poso_estim_map(...) 9. └─posologyr:::init_eta(...) 10. └─posologyr:::residual_error_all_endpoints(...) 11. ├─f_all_endpoints[, `:=`(f, get(as.character(DVID))), by = seq_len(nrow(f_all_endpoints))] 12. └─data.table:::`[.data.table`(...) ── Error ('test_issue_10.R:38:3'): poso_mcmc_pop accepts burn_in == n_iter ───── Error in ``[.data.table`(f_all_endpoints, , `:=`(f, get(as.character(DVID))), by = seq_len(nrow(f_all_endpoints)))`: attempt access index 2/2 in VECTOR_ELT Backtrace: ▆ 1. ├─testthat::expect_equal(...) at test_issue_10.R:38:3 2. │ └─testthat::quasi_label(enquo(object), label) 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) 4. └─posologyr::poso_estim_mcmc(...) 5. └─base::lapply(...) 6. └─posologyr (local) FUN(X[[i]], ...) 7. └─posologyr:::residual_error_all_endpoints(...) 8. ├─f_all_endpoints[, `:=`(f, get(as.character(DVID))), by = seq_len(nrow(f_all_endpoints))] 9. └─data.table:::`[.data.table`(...) ── Error ('test_issue_10.R:45:3'): poso_mcmc_pop accepts burn_in < n_iter ────── Error in ``[.data.table`(f_all_endpoints, , `:=`(f, get(as.character(DVID))), by = seq_len(nrow(f_all_endpoints)))`: attempt access index 2/2 in VECTOR_ELT Backtrace: ▆ 1. ├─testthat::expect_equal(...) at test_issue_10.R:45:3 2. │ └─testthat::quasi_label(enquo(object), label) 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) 4. └─posologyr::poso_estim_mcmc(...) 5. └─base::lapply(...) 6. └─posologyr (local) FUN(X[[i]], ...) 7. └─posologyr:::residual_error_all_endpoints(...) 8. ├─f_all_endpoints[, `:=`(f, get(as.character(DVID))), by = seq_len(nrow(f_all_endpoints))] 9. └─data.table:::`[.data.table`(...) ── Error ('test_issue_28.R:56:3'): poso_estim_map provides estimates even when predicted concentrations are zero ── Error in ``[.data.table`(f_all_endpoints, , `:=`(f, get(as.character(DVID))), by = seq_len(nrow(f_all_endpoints)))`: attempt access index 17/17 in VECTOR_ELT Backtrace: ▆ 1. ├─testthat::expect_equal(...) at test_issue_28.R:56:3 2. │ └─testthat::quasi_label(enquo(object), label) 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) 4. └─posologyr::poso_estim_map(...) 5. └─posologyr:::init_eta(...) 6. └─posologyr:::residual_error_all_endpoints(...) 7. ├─f_all_endpoints[, `:=`(f, get(as.character(DVID))), by = seq_len(nrow(f_all_endpoints))] 8. └─data.table:::`[.data.table`(...) ── Error ('test_issue_29.R:49:3'): poso_estim_map provides estimates even when the IIV is zero ── Error in ``[.data.table`(f_all_endpoints, , `:=`(f, get(as.character(DVID))), by = seq_len(nrow(f_all_endpoints)))`: attempt access index 16/16 in VECTOR_ELT Backtrace: ▆ 1. ├─testthat::expect_equal(...) at test_issue_29.R:49:3 2. │ └─testthat::quasi_label(enquo(object), label) 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) 4. └─posologyr::poso_estim_map(...) 5. └─posologyr:::init_eta(...) 6. └─posologyr:::residual_error_all_endpoints(...) 7. ├─f_all_endpoints[, `:=`(f, get(as.character(DVID))), by = seq_len(nrow(f_all_endpoints))] 8. └─data.table:::`[.data.table`(...) ── Error ('test_issue_30.R:50:1'): (code run outside of `test_that()`) ───────── Error in ``[.data.table`(f_all_endpoints, , `:=`(f, get(as.character(DVID))), by = seq_len(nrow(f_all_endpoints)))`: attempt access index 22/22 in VECTOR_ELT Backtrace: ▆ 1. └─posologyr::poso_estim_map(df_patientA_tdm, mod_MTXHD_joerger2011) at test_issue_30.R:50:1 2. └─posologyr:::init_eta(...) 3. └─posologyr:::residual_error_all_endpoints(...) 4. ├─f_all_endpoints[, `:=`(f, get(as.character(DVID))), by = seq_len(nrow(f_all_endpoints))] 5. └─data.table:::`[.data.table`(...) ── Error ('test_issue_32.R:55:3'): Dosing optim functions can use models with IOV ── Error in ``[.data.table`(f_all_endpoints, , `:=`(f, get(as.character(DVID))), by = seq_len(nrow(f_all_endpoints)))`: attempt access index 26/26 in VECTOR_ELT Backtrace: ▆ 1. ├─testthat::expect_equal(...) at test_issue_32.R:55:3 2. │ └─testthat::quasi_label(enquo(object), label) 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) 4. └─posologyr::poso_time_cmin(...) 5. └─posologyr:::read_optim_distribution_input(...) 6. └─posologyr::poso_estim_map(dat, prior_model, nocb = nocb, return_model = TRUE) 7. └─posologyr:::init_eta(...) 8. └─posologyr:::residual_error_all_endpoints(...) 9. ├─f_all_endpoints[, `:=`(f, get(as.character(DVID))), by = seq_len(nrow(f_all_endpoints))] 10. └─data.table:::`[.data.table`(...) ── Error ('test_issue_52.R:37:3'): single IIV ────────────────────────────────── Error in ``[.data.table`(f_all_endpoints, , `:=`(f, get(as.character(DVID))), by = seq_len(nrow(f_all_endpoints)))`: attempt access index 16/16 in VECTOR_ELT Backtrace: ▆ 1. └─posologyr::poso_estim_map(patient_data, mod_run001) at test_issue_52.R:37:3 2. └─posologyr:::init_eta(...) 3. └─posologyr:::residual_error_all_endpoints(...) 4. ├─f_all_endpoints[, `:=`(f, get(as.character(DVID))), by = seq_len(nrow(f_all_endpoints))] 5. └─data.table:::`[.data.table`(...) ── Error ('test_map_iov.R:62:1'): (code run outside of `test_that()`) ────────── Error in ``[.data.table`(f_all_endpoints, , `:=`(f, get(as.character(DVID))), by = seq_len(nrow(f_all_endpoints)))`: attempt access index 26/26 in VECTOR_ELT Backtrace: ▆ 1. └─posologyr::poso_estim_map(...) at test_map_iov.R:62:1 2. └─posologyr:::init_eta(...) 3. └─posologyr:::residual_error_all_endpoints(...) 4. ├─f_all_endpoints[, `:=`(f, get(as.character(DVID))), by = seq_len(nrow(f_all_endpoints))] 5. └─data.table:::`[.data.table`(...) ── Error ('test_map_mlx.R:76:1'): (code run outside of `test_that()`) ────────── Error in ``[.data.table`(f_all_endpoints, , `:=`(f, get(as.character(DVID))), by = seq_len(nrow(f_all_endpoints)))`: attempt access index 18/18 in VECTOR_ELT Backtrace: ▆ 1. └─posologyr::poso_estim_map(...) at test_map_mlx.R:76:1 2. └─posologyr:::init_eta(...) 3. └─posologyr:::residual_error_all_endpoints(...) 4. ├─f_all_endpoints[, `:=`(f, get(as.character(DVID))), by = seq_len(nrow(f_all_endpoints))] 5. └─data.table:::`[.data.table`(...) ── Error ('test_map_nlmixr.R:40:1'): (code run outside of `test_that()`) ─────── Error in ``[.data.table`(f_all_endpoints, , `:=`(f, get(as.character(DVID))), by = seq_len(nrow(f_all_endpoints)))`: attempt access index 22/22 in VECTOR_ELT Backtrace: ▆ 1. └─posologyr::poso_estim_map(...) at test_map_nlmixr.R:40:1 2. └─posologyr:::init_eta(...) 3. └─posologyr:::residual_error_all_endpoints(...) 4. ├─f_all_endpoints[, `:=`(f, get(as.character(DVID))), by = seq_len(nrow(f_all_endpoints))] 5. └─data.table:::`[.data.table`(...) ── Error ('test_map_nm.R:49:1'): (code run outside of `test_that()`) ─────────── Error in ``[.data.table`(f_all_endpoints, , `:=`(f, get(as.character(DVID))), by = seq_len(nrow(f_all_endpoints)))`: attempt access index 17/17 in VECTOR_ELT Backtrace: ▆ 1. └─posologyr::poso_estim_map(...) at test_map_nm.R:49:1 2. └─posologyr:::init_eta(...) 3. └─posologyr:::residual_error_all_endpoints(...) 4. ├─f_all_endpoints[, `:=`(f, get(as.character(DVID))), by = seq_len(nrow(f_all_endpoints))] 5. └─data.table:::`[.data.table`(...) ── Error ('test_rxui.R:39:3'): readme model equivalent ───────────────────────── Error in ``[.data.table`(f_all_endpoints, , `:=`(f, get(as.character(DVID))), by = seq_len(nrow(f_all_endpoints)))`: attempt access index 16/16 in VECTOR_ELT Backtrace: ▆ 1. └─posologyr::poso_estim_map(patient_data, mod_run001) at test_rxui.R:39:3 2. └─posologyr:::init_eta(...) 3. └─posologyr:::residual_error_all_endpoints(...) 4. ├─f_all_endpoints[, `:=`(f, get(as.character(DVID))), by = seq_len(nrow(f_all_endpoints))] 5. └─data.table:::`[.data.table`(...) [ FAIL 18 | WARN 0 | SKIP 4 | PASS 10 ] Error: ! Test failures. Execution halted Flavor: r-devel-windows-x86_64