Last updated on 2025-12-20 17:50:37 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.2.8 | 7.38 | 111.28 | 118.66 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 1.2.8 | 4.30 | 75.73 | 80.03 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 1.2.8 | 12.00 | 163.60 | 175.60 | ERROR | |
| r-devel-linux-x86_64-fedora-gcc | 1.2.8 | 11.00 | 155.43 | 166.43 | ERROR | |
| r-devel-windows-x86_64 | 1.2.8 | 11.00 | 528.00 | 539.00 | OK | |
| r-patched-linux-x86_64 | 1.2.8 | 6.85 | 553.98 | 560.83 | OK | |
| r-release-linux-x86_64 | 1.2.8 | 6.30 | 541.76 | 548.06 | OK | |
| r-release-macos-arm64 | 1.2.8 | OK | ||||
| r-release-macos-x86_64 | 1.2.8 | 4.00 | 473.00 | 477.00 | OK | |
| r-release-windows-x86_64 | 1.2.8 | 9.00 | 502.00 | 511.00 | OK | |
| r-oldrel-macos-arm64 | 1.2.8 | OK | ||||
| r-oldrel-macos-x86_64 | 1.2.8 | 5.00 | 552.00 | 557.00 | OK | |
| r-oldrel-windows-x86_64 | 1.2.8 | 12.00 | 597.00 | 609.00 | OK |
Version: 1.2.8
Check: examples
Result: ERROR
Running examples in ‘posologyr-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### 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
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc
Version: 1.2.8
Check: tests
Result: ERROR
Running ‘testthat.R’ [30s/35s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(rxode2)
rxode2 5.0.1 using 3 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-linux-x86_64-debian-clang
Version: 1.2.8
Check: tests
Result: ERROR
Running ‘testthat.R’ [20s/26s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(rxode2)
rxode2 5.0.1 using 3 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-linux-x86_64-debian-gcc
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
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc
Version: 1.2.8
Check: tests
Result: ERROR
Running ‘testthat.R’ [43s/67s]
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-linux-x86_64-fedora-clang
Version: 1.2.8
Check: tests
Result: ERROR
Running ‘testthat.R’ [42s/63s]
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-linux-x86_64-fedora-gcc