Last updated on 2025-12-28 03:51:56 CET.
| Package | ERROR | NOTE | OK |
|---|---|---|---|
| ggPMX | 1 | 3 | 9 |
Current CRAN status: ERROR: 1, NOTE: 3, OK: 9
Version: 1.3.2
Check: tests
Result: ERROR
Running 'testthat.R' [251s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
> library(testthat)
> library(ggPMX)
> library(data.table)
Attaching package: 'data.table'
The following object is masked from 'package:base':
%notin%
> setDTthreads(1)
> test_check("ggPMX")
Attaching package: 'dplyr'
The following objects are masked from 'package:data.table':
between, first, last
The following objects are masked from 'package:stats':
filter, lag
The following objects are masked from 'package:base':
intersect, setdiff, setequal, union
Saving _problems/test-assertions-273.R
Saving _problems/test-assertions-296.R
Saving _problems/test-assertions-434.R
Saving _problems/test-assertions-441.R
Saving _problems/test-assertions-448.R
Saving _problems/test-config-185.R
Saving _problems/test-config-228.R
Saving _problems/test-config-250.R
Saving _problems/test-config-262.R
Saving _problems/test-config-267.R
Saving _problems/test-ggforce-facet-paginate-50.R
Saving _problems/test-gpar-95.R
Saving _problems/test-nonmem_reader-51.R
Saving _problems/test-nonmem_reader-68.R
Saving _problems/test-nonmem_reader-77.R
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Saving _problems/test-nonmem_reader-94.R
Saving _problems/test-nonmem_reader-102.R
Saving _problems/test-param_table-4.R
Saving _problems/test-plot-base-6.R
Saving _problems/test-plot-defaults-3.R
Saving _problems/test-plot-density-116.R
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Saving _problems/test-plot-eta-pairs-5.R
Saving _problems/test-plot-individual-14.R
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Saving _problems/test-pmx-all-compute-4.R
Saving _problems/test-pmx-all-plots-4.R
Saving _problems/test-pmx-plot-eta-cov-4.R
Saving _problems/test-pmx-plot-vpc-6.R
Saving _problems/test-pmx-plots-distribution-4.R
Saving _problems/test-pmx-plots-saem-convergence-3.R
Saving _problems/test-pmx-plots-scatter-4.R
Saving _problems/test-pmx-post_load-7.R
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Saving _problems/test-pmx-vpc-bin-4.R
Saving _problems/test-pmxClass-4.R
Saving _problems/test-pmx_filter-4.R
Saving _problems/test-pmx_list_nm_tables-31.R
Saving _problems/test-pmx_list_nm_tables-43.R
Saving _problems/test-pmx_update-4.R
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convergence of SAEM parameter estimates file does not exist.
Saving _problems/test-utils-427.R
convergence of SAEM parameter estimates file does not exist.
Saving _problems/test-utils-432.R
convergence of SAEM parameter estimates file does not exist.
Saving _problems/test-utils-442.R
[ FAIL 74 | WARN 0 | SKIP 18 | PASS 365 ]
══ Skipped tests (18) ══════════════════════════════════════════════════════════
• On CRAN (6): 'test-nlmixr.R:3:5', 'test-nlmixr.R:43:5',
'test-nlmixr.R:117:5', 'test-nonmem_reader.R:115:13', 'test-utils.R:107:5',
'test-vdiff.R:6:5'
• On Windows (10): 'test-pmx_nlmixr.R:2:3', 'test-reader.R:8:5',
'test-reader.R:17:13', 'test-reader.R:27:13', 'test-reader.R:39:13',
'test-reader.R:57:13', 'test-reader.R:77:13', 'test-reader.R:94:5',
'test-reader.R:116:13', 'test-reader.R:125:13'
• file.exists(test_path("censoring1_project.zip")) is not TRUE (1):
'test-simBlq-npde.R:1:1'
• skipping ChartsData export warning test (1): 'test-utils.R:89:5'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-2023table.R:11:9'): Monolix 2023 tables read in correctly (Issue #369) ──
Error in ``[.data.table`(dat, , `:=`(section.name, gsub("<|>", "", line[1])), section)`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. ├─withr::with_tempdir(...) at test-2023table.R:6:5
2. │ └─withr::with_dir(tmp, code)
3. │ └─base::force(code)
4. ├─utils::capture.output(...) at test-2023table.R:10:7
5. │ └─base::withVisible(...elt(i))
6. └─ggPMX::pmx_mlxtran("warfarin_PD_project.mlxtran") at test-2023table.R:11:9
7. └─ggPMX::parse_mlxtran(file_name)
8. ├─dat[, `:=`(section.name, gsub("<|>", "", line[1])), section]
9. └─data.table:::`[.data.table`(...)
── Error ('test-assertions.R:273:5'): is_pmxclass: pmxclass variable is pmxclass ──
Error in ``[.data.table`(df_cor, , `:=`(corr_exp, corr_eqn(corr)), "EFFECT,variable")`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. └─ggPMX::theophylline() at test-assertions.R:273:5
2. └─ggPMX::pmx_mlx(...)
3. └─ggPMX::pmx(...)
4. └─pmxClass$new(...)
5. └─ggPMX (local) initialize(...)
6. └─ggPMX:::pmx_initialize(...)
7. ├─base::do.call(set_plot, c(ctr = self, x))
8. └─ggPMX (local) `<fn>`(...)
9. └─ctr$add_plot(conf, pname)
10. └─ggPMX:::pmx_add_plot(self, private, x, pname)
11. ├─ggPMX::plot_pmx(x, dx = x$dx)
12. └─ggPMX:::plot_pmx.eta_cov(x, dx = x$dx)
13. ├─df_cor[, `:=`(corr_exp, corr_eqn(corr)), "EFFECT,variable"]
14. └─data.table:::`[.data.table`(...)
── Error ('test-assertions.R:296:5'): is_ggplot: ggplot variable is ggplot ─────
Error in ``[.data.table`(df_cor, , `:=`(corr_exp, corr_eqn(corr)), "EFFECT,variable")`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. └─ggPMX::theophylline() at test-assertions.R:296:5
2. └─ggPMX::pmx_mlx(...)
3. └─ggPMX::pmx(...)
4. └─pmxClass$new(...)
5. └─ggPMX (local) initialize(...)
6. └─ggPMX:::pmx_initialize(...)
7. ├─base::do.call(set_plot, c(ctr = self, x))
8. └─ggPMX (local) `<fn>`(...)
9. └─ctr$add_plot(conf, pname)
10. └─ggPMX:::pmx_add_plot(self, private, x, pname)
11. ├─ggPMX::plot_pmx(x, dx = x$dx)
12. └─ggPMX:::plot_pmx.eta_cov(x, dx = x$dx)
13. ├─df_cor[, `:=`(corr_exp, corr_eqn(corr)), "EFFECT,variable"]
14. └─data.table:::`[.data.table`(...)
── Error ('test-assertions.R:434:5'): is_valid_plot_name: variable is valid plot name ──
Error in ``[.data.table`(df_cor, , `:=`(corr_exp, corr_eqn(corr)), "EFFECT,variable")`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. └─ggPMX::theophylline() at test-assertions.R:434:5
2. └─ggPMX::pmx_mlx(...)
3. └─ggPMX::pmx(...)
4. └─pmxClass$new(...)
5. └─ggPMX (local) initialize(...)
6. └─ggPMX:::pmx_initialize(...)
7. ├─base::do.call(set_plot, c(ctr = self, x))
8. └─ggPMX (local) `<fn>`(...)
9. └─ctr$add_plot(conf, pname)
10. └─ggPMX:::pmx_add_plot(self, private, x, pname)
11. ├─ggPMX::plot_pmx(x, dx = x$dx)
12. └─ggPMX:::plot_pmx.eta_cov(x, dx = x$dx)
13. ├─df_cor[, `:=`(corr_exp, corr_eqn(corr)), "EFFECT,variable"]
14. └─data.table:::`[.data.table`(...)
── Error ('test-assertions.R:441:5'): is_valid_plot_name: variable is not valid plot name ──
Error in ``[.data.table`(df_cor, , `:=`(corr_exp, corr_eqn(corr)), "EFFECT,variable")`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. └─ggPMX::theophylline() at test-assertions.R:441:5
2. └─ggPMX::pmx_mlx(...)
3. └─ggPMX::pmx(...)
4. └─pmxClass$new(...)
5. └─ggPMX (local) initialize(...)
6. └─ggPMX:::pmx_initialize(...)
7. ├─base::do.call(set_plot, c(ctr = self, x))
8. └─ggPMX (local) `<fn>`(...)
9. └─ctr$add_plot(conf, pname)
10. └─ggPMX:::pmx_add_plot(self, private, x, pname)
11. ├─ggPMX::plot_pmx(x, dx = x$dx)
12. └─ggPMX:::plot_pmx.eta_cov(x, dx = x$dx)
13. ├─df_cor[, `:=`(corr_exp, corr_eqn(corr)), "EFFECT,variable"]
14. └─data.table:::`[.data.table`(...)
── Error ('test-assertions.R:448:5'): is_valid_plot_name: NA is not valid plot name ──
Error in ``[.data.table`(df_cor, , `:=`(corr_exp, corr_eqn(corr)), "EFFECT,variable")`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. └─ggPMX::theophylline() at test-assertions.R:448:5
2. └─ggPMX::pmx_mlx(...)
3. └─ggPMX::pmx(...)
4. └─pmxClass$new(...)
5. └─ggPMX (local) initialize(...)
6. └─ggPMX:::pmx_initialize(...)
7. ├─base::do.call(set_plot, c(ctr = self, x))
8. └─ggPMX (local) `<fn>`(...)
9. └─ctr$add_plot(conf, pname)
10. └─ggPMX:::pmx_add_plot(self, private, x, pname)
11. ├─ggPMX::plot_pmx(x, dx = x$dx)
12. └─ggPMX:::plot_pmx.eta_cov(x, dx = x$dx)
13. ├─df_cor[, `:=`(corr_exp, corr_eqn(corr)), "EFFECT,variable"]
14. └─data.table:::`[.data.table`(...)
── Error ('test-config.R:175:13'): pmx_mlx params: my_settings with cats.labels, effects and covariates;
result: identical labels ──
Error in ``[.data.table`(df_cor, , `:=`(corr_exp, corr_eqn(corr)), "EFFECT,variable")`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. └─ggPMX::pmx_mlx(...) at test-config.R:175:13
2. └─ggPMX::pmx(...)
3. └─pmxClass$new(...)
4. └─ggPMX (local) initialize(...)
5. └─ggPMX:::pmx_initialize(...)
6. ├─base::do.call(set_plot, c(ctr = self, x))
7. └─ggPMX (local) `<fn>`(...)
8. └─ctr$add_plot(conf, pname)
9. └─ggPMX:::pmx_add_plot(self, private, x, pname)
10. ├─ggPMX::plot_pmx(x, dx = x$dx)
11. └─ggPMX:::plot_pmx.eta_cov(x, dx = x$dx)
12. ├─df_cor[, `:=`(corr_exp, corr_eqn(corr)), "EFFECT,variable"]
13. └─data.table:::`[.data.table`(...)
── Error ('test-config.R:218:13'): pmx_mlx params: my_settings with cats.labels and without effects and covariates;
result: identical labels ──
Error in ``[.data.table`(df_cor, , `:=`(corr_exp, corr_eqn(corr)), "EFFECT,variable")`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. └─ggPMX::pmx_mlx(...) at test-config.R:218:13
2. └─ggPMX::pmx(...)
3. └─pmxClass$new(...)
4. └─ggPMX (local) initialize(...)
5. └─ggPMX:::pmx_initialize(...)
6. ├─base::do.call(set_plot, c(ctr = self, x))
7. └─ggPMX (local) `<fn>`(...)
8. └─ctr$add_plot(conf, pname)
9. └─ggPMX:::pmx_add_plot(self, private, x, pname)
10. ├─ggPMX::plot_pmx(x, dx = x$dx)
11. └─ggPMX:::plot_pmx.eta_cov(x, dx = x$dx)
12. ├─df_cor[, `:=`(corr_exp, corr_eqn(corr)), "EFFECT,variable"]
13. └─data.table:::`[.data.table`(...)
── Error ('test-config.R:250:5'): pmx_warnings: x, warn; result: identical output ──
Error in ``[.data.table`(df_cor, , `:=`(corr_exp, corr_eqn(corr)), "EFFECT,variable")`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. └─ggPMX::theophylline() at test-config.R:250:5
2. └─ggPMX::pmx_mlx(...)
3. └─ggPMX::pmx(...)
4. └─pmxClass$new(...)
5. └─ggPMX (local) initialize(...)
6. └─ggPMX:::pmx_initialize(...)
7. ├─base::do.call(set_plot, c(ctr = self, x))
8. └─ggPMX (local) `<fn>`(...)
9. └─ctr$add_plot(conf, pname)
10. └─ggPMX:::pmx_add_plot(self, private, x, pname)
11. ├─ggPMX::plot_pmx(x, dx = x$dx)
12. └─ggPMX:::plot_pmx.eta_cov(x, dx = x$dx)
13. ├─df_cor[, `:=`(corr_exp, corr_eqn(corr)), "EFFECT,variable"]
14. └─data.table:::`[.data.table`(...)
── Error ('test-config.R:262:5'): pmx_warnings: x, warn; result: error missing arguments ──
Error in ``[.data.table`(df_cor, , `:=`(corr_exp, corr_eqn(corr)), "EFFECT,variable")`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. └─ggPMX::theophylline() at test-config.R:262:5
2. └─ggPMX::pmx_mlx(...)
3. └─ggPMX::pmx(...)
4. └─pmxClass$new(...)
5. └─ggPMX (local) initialize(...)
6. └─ggPMX:::pmx_initialize(...)
7. ├─base::do.call(set_plot, c(ctr = self, x))
8. └─ggPMX (local) `<fn>`(...)
9. └─ctr$add_plot(conf, pname)
10. └─ggPMX:::pmx_add_plot(self, private, x, pname)
11. ├─ggPMX::plot_pmx(x, dx = x$dx)
12. └─ggPMX:::plot_pmx.eta_cov(x, dx = x$dx)
13. ├─df_cor[, `:=`(corr_exp, corr_eqn(corr)), "EFFECT,variable"]
14. └─data.table:::`[.data.table`(...)
── Error ('test-config.R:267:5'): pmx_warnings: x, warn; result: message ───────
Error in ``[.data.table`(df_cor, , `:=`(corr_exp, corr_eqn(corr)), "EFFECT,variable")`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. └─ggPMX::theophylline() at test-config.R:267:5
2. └─ggPMX::pmx_mlx(...)
3. └─ggPMX::pmx(...)
4. └─pmxClass$new(...)
5. └─ggPMX (local) initialize(...)
6. └─ggPMX:::pmx_initialize(...)
7. ├─base::do.call(set_plot, c(ctr = self, x))
8. └─ggPMX (local) `<fn>`(...)
9. └─ctr$add_plot(conf, pname)
10. └─ggPMX:::pmx_add_plot(self, private, x, pname)
11. ├─ggPMX::plot_pmx(x, dx = x$dx)
12. └─ggPMX:::plot_pmx.eta_cov(x, dx = x$dx)
13. ├─df_cor[, `:=`(corr_exp, corr_eqn(corr)), "EFFECT,variable"]
14. └─data.table:::`[.data.table`(...)
── Error ('test-ggforce-facet-paginate.R:50:5'): n_pages: params: plot without pages result: NULL ──
Error in ``[.data.table`(df_cor, , `:=`(corr_exp, corr_eqn(corr)), "EFFECT,variable")`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. └─ggPMX::theophylline() at test-ggforce-facet-paginate.R:50:5
2. └─ggPMX::pmx_mlx(...)
3. └─ggPMX::pmx(...)
4. └─pmxClass$new(...)
5. └─ggPMX (local) initialize(...)
6. └─ggPMX:::pmx_initialize(...)
7. ├─base::do.call(set_plot, c(ctr = self, x))
8. └─ggPMX (local) `<fn>`(...)
9. └─ctr$add_plot(conf, pname)
10. └─ggPMX:::pmx_add_plot(self, private, x, pname)
11. ├─ggPMX::plot_pmx(x, dx = x$dx)
12. └─ggPMX:::plot_pmx.eta_cov(x, dx = x$dx)
13. ├─df_cor[, `:=`(corr_exp, corr_eqn(corr)), "EFFECT,variable"]
14. └─data.table:::`[.data.table`(...)
── Error ('test-gpar.R:95:5'): pmx_gpar ranges are applied to the plot ─────────
Error in ``[.data.table`(df_cor, , `:=`(corr_exp, corr_eqn(corr)), "EFFECT,variable")`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. └─ggPMX::theophylline() at test-gpar.R:95:5
2. └─ggPMX::pmx_mlx(...)
3. └─ggPMX::pmx(...)
4. └─pmxClass$new(...)
5. └─ggPMX (local) initialize(...)
6. └─ggPMX:::pmx_initialize(...)
7. ├─base::do.call(set_plot, c(ctr = self, x))
8. └─ggPMX (local) `<fn>`(...)
9. └─ctr$add_plot(conf, pname)
10. └─ggPMX:::pmx_add_plot(self, private, x, pname)
11. ├─ggPMX::plot_pmx(x, dx = x$dx)
12. └─ggPMX:::plot_pmx.eta_cov(x, dx = x$dx)
13. ├─df_cor[, `:=`(corr_exp, corr_eqn(corr)), "EFFECT,variable"]
14. └─data.table:::`[.data.table`(...)
── Error ('test-nonmem_reader.R:48:13'): pmx_nm: params: npde, iwres, ipred;
result: can read NONMEM-Output ──
Error in ``[.data.table`(df_cor, , `:=`(corr_exp, corr_eqn(corr)), "EFFECT,variable")`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. └─ggPMX::pmx_nm(...) at test-nonmem_reader.R:48:13
2. └─pmxClass$new(...)
3. └─ggPMX (local) initialize(...)
4. └─ggPMX:::pmx_initialize(...)
5. ├─base::do.call(set_plot, c(ctr = self, x))
6. └─ggPMX (local) `<fn>`(...)
7. └─ctr$add_plot(conf, pname)
8. └─ggPMX:::pmx_add_plot(self, private, x, pname)
9. ├─ggPMX::plot_pmx(x, dx = x$dx)
10. └─ggPMX:::plot_pmx.eta_cov(x, dx = x$dx)
11. ├─df_cor[, `:=`(corr_exp, corr_eqn(corr)), "EFFECT,variable"]
12. └─data.table:::`[.data.table`(...)
── Error ('test-nonmem_reader.R:68:13'): pmx_nm: params: simfile;
result: can read NONMEM-Output ──
Error in ``[.data.table`(df_cor, , `:=`(corr_exp, corr_eqn(corr)), "EFFECT,variable")`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. └─ggPMX::pmx_nm(directory = nonmem_dir, runno = "001", simfile = "custom_sim.lst") at test-nonmem_reader.R:68:13
2. └─pmxClass$new(...)
3. └─ggPMX (local) initialize(...)
4. └─ggPMX:::pmx_initialize(...)
5. ├─base::do.call(set_plot, c(ctr = self, x))
6. └─ggPMX (local) `<fn>`(...)
7. └─ctr$add_plot(conf, pname)
8. └─ggPMX:::pmx_add_plot(self, private, x, pname)
9. ├─ggPMX::plot_pmx(x, dx = x$dx)
10. └─ggPMX:::plot_pmx.eta_cov(x, dx = x$dx)
11. ├─df_cor[, `:=`(corr_exp, corr_eqn(corr)), "EFFECT,variable"]
12. └─data.table:::`[.data.table`(...)
── Error ('test-nonmem_reader.R:77:13'): pmx_nm: params: obs is T;
result: warning ──
Error in ``[.data.table`(df_cor, , `:=`(corr_exp, corr_eqn(corr)), "EFFECT,variable")`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_warning(...) at test-nonmem_reader.R:77:13
2. │ └─testthat:::quasi_capture(...)
3. │ ├─testthat (local) .capture(...)
4. │ │ └─base::withCallingHandlers(...)
5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
6. └─ggPMX::pmx_nm(directory = nonmem_dir, runno = "001", obs = TRUE)
7. └─pmxClass$new(...)
8. └─ggPMX (local) initialize(...)
9. └─ggPMX:::pmx_initialize(...)
10. ├─base::do.call(set_plot, c(ctr = self, x))
11. └─ggPMX (local) `<fn>`(...)
12. └─ctr$add_plot(conf, pname)
13. └─ggPMX:::pmx_add_plot(self, private, x, pname)
14. ├─ggPMX::plot_pmx(x, dx = x$dx)
15. └─ggPMX:::plot_pmx.eta_cov(x, dx = x$dx)
16. ├─df_cor[, `:=`(corr_exp, corr_eqn(corr)), "EFFECT,variable"]
17. └─data.table:::`[.data.table`(...)
── Error ('test-nonmem_reader.R:85:13'): pmx_nm: params: Endpoint value does not correspond to dvid values;
result: warning ──
Error in ``[.data.table`(df_cor, , `:=`(corr_exp, corr_eqn(corr)), "EFFECT,variable")`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_warning(...) at test-nonmem_reader.R:85:13
2. │ └─testthat:::quasi_capture(...)
3. │ ├─testthat (local) .capture(...)
4. │ │ └─base::withCallingHandlers(...)
5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
6. └─ggPMX::pmx_nm(directory = nonmem_dir, runno = "001", endpoint = 12)
7. └─pmxClass$new(...)
8. └─ggPMX (local) initialize(...)
9. └─ggPMX:::pmx_initialize(...)
10. ├─base::do.call(set_plot, c(ctr = self, x))
11. └─ggPMX (local) `<fn>`(...)
12. └─ctr$add_plot(conf, pname)
13. └─ggPMX:::pmx_add_plot(self, private, x, pname)
14. ├─ggPMX::plot_pmx(x, dx = x$dx)
15. └─ggPMX:::plot_pmx.eta_cov(x, dx = x$dx)
16. ├─df_cor[, `:=`(corr_exp, corr_eqn(corr)), "EFFECT,variable"]
17. └─data.table:::`[.data.table`(...)
── Error ('test-nonmem_reader.R:94:13'): pmx_nm: params: Endpoint value corresponds to dvid values;
result: error ──
Error in ``[.data.table`(df_cor, , `:=`(corr_exp, corr_eqn(corr)), "EFFECT,variable")`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat (local) expect_fn(...) at test-nonmem_reader.R:94:13
2. │ └─testthat:::quasi_capture(...)
3. │ ├─testthat (local) .capture(...)
4. │ │ └─base::withCallingHandlers(...)
5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
6. └─ggPMX::pmx_nm(...)
7. └─pmxClass$new(...)
8. └─ggPMX (local) initialize(...)
9. └─ggPMX:::pmx_initialize(...)
10. ├─base::do.call(set_plot, c(ctr = self, x))
11. └─ggPMX (local) `<fn>`(...)
12. └─ctr$add_plot(conf, pname)
13. └─ggPMX:::pmx_add_plot(self, private, x, pname)
14. ├─ggPMX::plot_pmx(x, dx = x$dx)
15. └─ggPMX:::plot_pmx.eta_cov(x, dx = x$dx)
16. ├─df_cor[, `:=`(corr_exp, corr_eqn(corr)), "EFFECT,variable"]
17. └─data.table:::`[.data.table`(...)
── Error ('test-nonmem_reader.R:102:13'): pmx_nm: params: settings is not pmxSettingsClass object;
result: can read NONMEM-Output ──
Error in ``[.data.table`(df_cor, , `:=`(corr_exp, corr_eqn(corr)), "EFFECT,variable")`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. └─ggPMX::pmx_nm(directory = nonmem_dir, runno = "001", settings = list(use.titles = TRUE)) at test-nonmem_reader.R:102:13
2. └─pmxClass$new(...)
3. └─ggPMX (local) initialize(...)
4. └─ggPMX:::pmx_initialize(...)
5. ├─base::do.call(set_plot, c(ctr = self, x))
6. └─ggPMX (local) `<fn>`(...)
7. └─ctr$add_plot(conf, pname)
8. └─ggPMX:::pmx_add_plot(self, private, x, pname)
9. ├─ggPMX::plot_pmx(x, dx = x$dx)
10. └─ggPMX:::plot_pmx.eta_cov(x, dx = x$dx)
11. ├─df_cor[, `:=`(corr_exp, corr_eqn(corr)), "EFFECT,variable"]
12. └─data.table:::`[.data.table`(...)
── Error ('test-param_table.R:4:3'): (code run outside of `test_that()`) ───────
Error in ``[.data.table`(df_cor, , `:=`(corr_exp, corr_eqn(corr)), "EFFECT,variable")`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. └─ggPMX::theophylline() at test-param_table.R:4:3
2. └─ggPMX::pmx_mlx(...)
3. └─ggPMX::pmx(...)
4. └─pmxClass$new(...)
5. └─ggPMX (local) initialize(...)
6. └─ggPMX:::pmx_initialize(...)
7. ├─base::do.call(set_plot, c(ctr = self, x))
8. └─ggPMX (local) `<fn>`(...)
9. └─ctr$add_plot(conf, pname)
10. └─ggPMX:::pmx_add_plot(self, private, x, pname)
11. ├─ggPMX::plot_pmx(x, dx = x$dx)
12. └─ggPMX:::plot_pmx.eta_cov(x, dx = x$dx)
13. ├─df_cor[, `:=`(corr_exp, corr_eqn(corr)), "EFFECT,variable"]
14. └─data.table:::`[.data.table`(...)
── Error ('test-plot-base.R:6:3'): (code run outside of `test_that()`) ─────────
Error in ``[.data.table`(df_cor, , `:=`(corr_exp, corr_eqn(corr)), "EFFECT,variable")`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. └─ggPMX::theophylline() at test-plot-base.R:6:3
2. └─ggPMX::pmx_mlx(...)
3. └─ggPMX::pmx(...)
4. └─pmxClass$new(...)
5. └─ggPMX (local) initialize(...)
6. └─ggPMX:::pmx_initialize(...)
7. ├─base::do.call(set_plot, c(ctr = self, x))
8. └─ggPMX (local) `<fn>`(...)
9. └─ctr$add_plot(conf, pname)
10. └─ggPMX:::pmx_add_plot(self, private, x, pname)
11. ├─ggPMX::plot_pmx(x, dx = x$dx)
12. └─ggPMX:::plot_pmx.eta_cov(x, dx = x$dx)
13. ├─df_cor[, `:=`(corr_exp, corr_eqn(corr)), "EFFECT,variable"]
14. └─data.table:::`[.data.table`(...)
── Error ('test-plot-defaults.R:3:3'): (code run outside of `test_that()`) ─────
Error in ``[.data.table`(df_cor, , `:=`(corr_exp, corr_eqn(corr)), "EFFECT,variable")`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. └─ggPMX:::test_pmxClass_helpers() at test-plot-defaults.R:3:3
2. └─ggPMX::pmx_mlx(...) at ./helper-pmxClass.R:8:3
3. └─ggPMX::pmx(...)
4. └─pmxClass$new(...)
5. └─ggPMX (local) initialize(...)
6. └─ggPMX:::pmx_initialize(...)
7. ├─base::do.call(set_plot, c(ctr = self, x))
8. └─ggPMX (local) `<fn>`(...)
9. └─ctr$add_plot(conf, pname)
10. └─ggPMX:::pmx_add_plot(self, private, x, pname)
11. ├─ggPMX::plot_pmx(x, dx = x$dx)
12. └─ggPMX:::plot_pmx.eta_cov(x, dx = x$dx)
13. ├─df_cor[, `:=`(corr_exp, corr_eqn(corr)), "EFFECT,variable"]
14. └─data.table:::`[.data.table`(...)
── Error ('test-plot-density.R:116:5'): (code run outside of `test_that()`) ────
Error in ``[.data.table`(dat, , `:=`(section.name, gsub("<|>", "", line[1])), section)`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. ├─base::suppressWarnings(...) at test-plot-density.R:115:3
2. │ └─base::withCallingHandlers(...)
3. └─ggPMX::pmx_mlxtran(mlxpath, config = "standing") at test-plot-density.R:116:5
4. └─ggPMX::parse_mlxtran(file_name)
5. ├─dat[, `:=`(section.name, gsub("<|>", "", line[1])), section]
6. └─data.table:::`[.data.table`(...)
── Error ('test-plot-distribution.R:151:5'): distrib.hist: params: labels, type and etc. result: ggplot ──
Error in ``[.data.table`(df_cor, , `:=`(corr_exp, corr_eqn(corr)), "EFFECT,variable")`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. └─ggPMX::theophylline() at test-plot-distribution.R:151:5
2. └─ggPMX::pmx_mlx(...)
3. └─ggPMX::pmx(...)
4. └─pmxClass$new(...)
5. └─ggPMX (local) initialize(...)
6. └─ggPMX:::pmx_initialize(...)
7. ├─base::do.call(set_plot, c(ctr = self, x))
8. └─ggPMX (local) `<fn>`(...)
9. └─ctr$add_plot(conf, pname)
10. └─ggPMX:::pmx_add_plot(self, private, x, pname)
11. ├─ggPMX::plot_pmx(x, dx = x$dx)
12. └─ggPMX:::plot_pmx.eta_cov(x, dx = x$dx)
13. ├─df_cor[, `:=`(corr_exp, corr_eqn(corr)), "EFFECT,variable"]
14. └─data.table:::`[.data.table`(...)
── Error ('test-plot-distribution.R:174:5'): distrib.hist: params: x equals NULL result: error ──
Error in ``[.data.table`(df_cor, , `:=`(corr_exp, corr_eqn(corr)), "EFFECT,variable")`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. └─ggPMX::theophylline() at test-plot-distribution.R:174:5
2. └─ggPMX::pmx_mlx(...)
3. └─ggPMX::pmx(...)
4. └─pmxClass$new(...)
5. └─ggPMX (local) initialize(...)
6. └─ggPMX:::pmx_initialize(...)
7. ├─base::do.call(set_plot, c(ctr = self, x))
8. └─ggPMX (local) `<fn>`(...)
9. └─ctr$add_plot(conf, pname)
10. └─ggPMX:::pmx_add_plot(self, private, x, pname)
11. ├─ggPMX::plot_pmx(x, dx = x$dx)
12. └─ggPMX:::plot_pmx.eta_cov(x, dx = x$dx)
13. ├─df_cor[, `:=`(corr_exp, corr_eqn(corr)), "EFFECT,variable"]
14. └─data.table:::`[.data.table`(...)
── Error ('test-plot-distribution.R:210:5'): distrib.box: params: labels, type, etc. result: ggplot ──
Error in ``[.data.table`(df_cor, , `:=`(corr_exp, corr_eqn(corr)), "EFFECT,variable")`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. └─ggPMX::theophylline() at test-plot-distribution.R:210:5
2. └─ggPMX::pmx_mlx(...)
3. └─ggPMX::pmx(...)
4. └─pmxClass$new(...)
5. └─ggPMX (local) initialize(...)
6. └─ggPMX:::pmx_initialize(...)
7. ├─base::do.call(set_plot, c(ctr = self, x))
8. └─ggPMX (local) `<fn>`(...)
9. └─ctr$add_plot(conf, pname)
10. └─ggPMX:::pmx_add_plot(self, private, x, pname)
11. ├─ggPMX::plot_pmx(x, dx = x$dx)
12. └─ggPMX:::plot_pmx.eta_cov(x, dx = x$dx)
13. ├─df_cor[, `:=`(corr_exp, corr_eqn(corr)), "EFFECT,variable"]
14. └─data.table:::`[.data.table`(...)
── Error ('test-plot-distribution.R:228:5'): distrib.box: params: x equals NULL result: error ──
Error in ``[.data.table`(df_cor, , `:=`(corr_exp, corr_eqn(corr)), "EFFECT,variable")`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. └─ggPMX::theophylline() at test-plot-distribution.R:228:5
2. └─ggPMX::pmx_mlx(...)
3. └─ggPMX::pmx(...)
4. └─pmxClass$new(...)
5. └─ggPMX (local) initialize(...)
6. └─ggPMX:::pmx_initialize(...)
7. ├─base::do.call(set_plot, c(ctr = self, x))
8. └─ggPMX (local) `<fn>`(...)
9. └─ctr$add_plot(conf, pname)
10. └─ggPMX:::pmx_add_plot(self, private, x, pname)
11. ├─ggPMX::plot_pmx(x, dx = x$dx)
12. └─ggPMX:::plot_pmx.eta_cov(x, dx = x$dx)
13. ├─df_cor[, `:=`(corr_exp, corr_eqn(corr)), "EFFECT,variable"]
14. └─data.table:::`[.data.table`(...)
── Error ('test-plot-distribution.R:258:5'): distrib.box: params: strat.facet is not NULL result: gg ──
Error in ``[.data.table`(df_cor, , `:=`(corr_exp, corr_eqn(corr)), "EFFECT,variable")`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. └─ggPMX::theophylline() at test-plot-distribution.R:258:5
2. └─ggPMX::pmx_mlx(...)
3. └─ggPMX::pmx(...)
4. └─pmxClass$new(...)
5. └─ggPMX (local) initialize(...)
6. └─ggPMX:::pmx_initialize(...)
7. ├─base::do.call(set_plot, c(ctr = self, x))
8. └─ggPMX (local) `<fn>`(...)
9. └─ctr$add_plot(conf, pname)
10. └─ggPMX:::pmx_add_plot(self, private, x, pname)
11. ├─ggPMX::plot_pmx(x, dx = x$dx)
12. └─ggPMX:::plot_pmx.eta_cov(x, dx = x$dx)
13. ├─df_cor[, `:=`(corr_exp, corr_eqn(corr)), "EFFECT,variable"]
14. └─data.table:::`[.data.table`(...)
── Error ('test-plot-distribution.R:285:5'): shrinkage_layer: params: hist type result: LayerInstance ──
Error in ``[.data.table`(df_cor, , `:=`(corr_exp, corr_eqn(corr)), "EFFECT,variable")`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. └─ggPMX::theophylline() at test-plot-distribution.R:285:5
2. └─ggPMX::pmx_mlx(...)
3. └─ggPMX::pmx(...)
4. └─pmxClass$new(...)
5. └─ggPMX (local) initialize(...)
6. └─ggPMX:::pmx_initialize(...)
7. ├─base::do.call(set_plot, c(ctr = self, x))
8. └─ggPMX (local) `<fn>`(...)
9. └─ctr$add_plot(conf, pname)
10. └─ggPMX:::pmx_add_plot(self, private, x, pname)
11. ├─ggPMX::plot_pmx(x, dx = x$dx)
12. └─ggPMX:::plot_pmx.eta_cov(x, dx = x$dx)
13. ├─df_cor[, `:=`(corr_exp, corr_eqn(corr)), "EFFECT,variable"]
14. └─data.table:::`[.data.table`(...)
── Error ('test-plot-distribution.R:299:5'): shrinkage_layer: params: dx contain eta data result: warning ──
Error in ``[.data.table`(df_cor, , `:=`(corr_exp, corr_eqn(corr)), "EFFECT,variable")`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. └─ggPMX::theophylline() at test-plot-distribution.R:299:5
2. └─ggPMX::pmx_mlx(...)
3. └─ggPMX::pmx(...)
4. └─pmxClass$new(...)
5. └─ggPMX (local) initialize(...)
6. └─ggPMX:::pmx_initialize(...)
7. ├─base::do.call(set_plot, c(ctr = self, x))
8. └─ggPMX (local) `<fn>`(...)
9. └─ctr$add_plot(conf, pname)
10. └─ggPMX:::pmx_add_plot(self, private, x, pname)
11. ├─ggPMX::plot_pmx(x, dx = x$dx)
12. └─ggPMX:::plot_pmx.eta_cov(x, dx = x$dx)
13. ├─df_cor[, `:=`(corr_exp, corr_eqn(corr)), "EFFECT,variable"]
14. └─data.table:::`[.data.table`(...)
── Error ('test-plot-distribution.R:310:5'): shrinkage_layer: params: box type result: LayerInstance ──
Error in ``[.data.table`(df_cor, , `:=`(corr_exp, corr_eqn(corr)), "EFFECT,variable")`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. └─ggPMX::theophylline() at test-plot-distribution.R:310:5
2. └─ggPMX::pmx_mlx(...)
3. └─ggPMX::pmx(...)
4. └─pmxClass$new(...)
5. └─ggPMX (local) initialize(...)
6. └─ggPMX:::pmx_initialize(...)
7. ├─base::do.call(set_plot, c(ctr = self, x))
8. └─ggPMX (local) `<fn>`(...)
9. └─ctr$add_plot(conf, pname)
10. └─ggPMX:::pmx_add_plot(self, private, x, pname)
11. ├─ggPMX::plot_pmx(x, dx = x$dx)
12. └─ggPMX:::plot_pmx.eta_cov(x, dx = x$dx)
13. ├─df_cor[, `:=`(corr_exp, corr_eqn(corr)), "EFFECT,variable"]
14. └─data.table:::`[.data.table`(...)
── Error ('test-plot-distribution.R:328:13'): plot_distribution: params: dx contain eta data,
x is distrib object result: error ──
Error in ``[.data.table`(df_cor, , `:=`(corr_exp, corr_eqn(corr)), "EFFECT,variable")`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. └─ggPMX::theophylline() at test-plot-distribution.R:328:13
2. └─ggPMX::pmx_mlx(...)
3. └─ggPMX::pmx(...)
4. └─pmxClass$new(...)
5. └─ggPMX (local) initialize(...)
6. └─ggPMX:::pmx_initialize(...)
7. ├─base::do.call(set_plot, c(ctr = self, x))
8. └─ggPMX (local) `<fn>`(...)
9. └─ctr$add_plot(conf, pname)
10. └─ggPMX:::pmx_add_plot(self, private, x, pname)
11. ├─ggPMX::plot_pmx(x, dx = x$dx)
12. └─ggPMX:::plot_pmx.eta_cov(x, dx = x$dx)
13. ├─df_cor[, `:=`(corr_exp, corr_eqn(corr)), "EFFECT,variable"]
14. └─data.table:::`[.data.table`(...)
── Error ('test-plot-distribution.R:346:13'): plot_pmx.distrib: params: dx contain eta data,
x is distrib object result: error ──
Error in ``[.data.table`(df_cor, , `:=`(corr_exp, corr_eqn(corr)), "EFFECT,variable")`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. └─ggPMX::theophylline() at test-plot-distribution.R:346:13
2. └─ggPMX::pmx_mlx(...)
3. └─ggPMX::pmx(...)
4. └─pmxClass$new(...)
5. └─ggPMX (local) initialize(...)
6. └─ggPMX:::pmx_initialize(...)
7. ├─base::do.call(set_plot, c(ctr = self, x))
8. └─ggPMX (local) `<fn>`(...)
9. └─ctr$add_plot(conf, pname)
10. └─ggPMX:::pmx_add_plot(self, private, x, pname)
11. ├─ggPMX::plot_pmx(x, dx = x$dx)
12. └─ggPMX:::plot_pmx.eta_cov(x, dx = x$dx)
13. ├─df_cor[, `:=`(corr_exp, corr_eqn(corr)), "EFFECT,variable"]
14. └─data.table:::`[.data.table`(...)
── Error ('test-plot-eta-pairs.R:5:3'): (code run outside of `test_that()`) ────
Error in ``[.data.table`(df_cor, , `:=`(corr_exp, corr_eqn(corr)), "EFFECT,variable")`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. └─ggPMX::theophylline() at test-plot-eta-pairs.R:5:3
2. └─ggPMX::pmx_mlx(...)
3. └─ggPMX::pmx(...)
4. └─pmxClass$new(...)
5. └─ggPMX (local) initialize(...)
6. └─ggPMX:::pmx_initialize(...)
7. ├─base::do.call(set_plot, c(ctr = self, x))
8. └─ggPMX (local) `<fn>`(...)
9. └─ctr$add_plot(conf, pname)
10. └─ggPMX:::pmx_add_plot(self, private, x, pname)
11. ├─ggPMX::plot_pmx(x, dx = x$dx)
12. └─ggPMX:::plot_pmx.eta_cov(x, dx = x$dx)
13. ├─df_cor[, `:=`(corr_exp, corr_eqn(corr)), "EFFECT,variable"]
14. └─data.table:::`[.data.table`(...)
── Error ('test-plot-individual.R:14:5'): (code run outside of `test_that()`) ──
Error in ``[.data.table`(dat, , `:=`(section.name, gsub("<|>", "", line[1])), section)`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. ├─base::suppressWarnings(...) at test-plot-individual.R:13:3
2. │ └─base::withCallingHandlers(...)
3. └─ggPMX::pmx_mlxtran(mlxpath, config = "standing") at test-plot-individual.R:14:5
4. └─ggPMX::parse_mlxtran(file_name)
5. ├─dat[, `:=`(section.name, gsub("<|>", "", line[1])), section]
6. └─data.table:::`[.data.table`(...)
── Error ('test-plot-residual.R:5:3'): (code run outside of `test_that()`) ─────
Error in ``[.data.table`(df_cor, , `:=`(corr_exp, corr_eqn(corr)), "EFFECT,variable")`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. └─ggPMX::theophylline() at test-plot-residual.R:5:3
2. └─ggPMX::pmx_mlx(...)
3. └─ggPMX::pmx(...)
4. └─pmxClass$new(...)
5. └─ggPMX (local) initialize(...)
6. └─ggPMX:::pmx_initialize(...)
7. ├─base::do.call(set_plot, c(ctr = self, x))
8. └─ggPMX (local) `<fn>`(...)
9. └─ctr$add_plot(conf, pname)
10. └─ggPMX:::pmx_add_plot(self, private, x, pname)
11. ├─ggPMX::plot_pmx(x, dx = x$dx)
12. └─ggPMX:::plot_pmx.eta_cov(x, dx = x$dx)
13. ├─df_cor[, `:=`(corr_exp, corr_eqn(corr)), "EFFECT,variable"]
14. └─data.table:::`[.data.table`(...)
── Error ('test-plot.R:4:3'): (code run outside of `test_that()`) ──────────────
Error in ``[.data.table`(df_cor, , `:=`(corr_exp, corr_eqn(corr)), "EFFECT,variable")`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. └─ggPMX:::test_pmxClass_helpers() at test-plot.R:4:3
2. └─ggPMX::pmx_mlx(...) at ./helper-pmxClass.R:8:3
3. └─ggPMX::pmx(...)
4. └─pmxClass$new(...)
5. └─ggPMX (local) initialize(...)
6. └─ggPMX:::pmx_initialize(...)
7. ├─base::do.call(set_plot, c(ctr = self, x))
8. └─ggPMX (local) `<fn>`(...)
9. └─ctr$add_plot(conf, pname)
10. └─ggPMX:::pmx_add_plot(self, private, x, pname)
11. ├─ggPMX::plot_pmx(x, dx = x$dx)
12. └─ggPMX:::plot_pmx.eta_cov(x, dx = x$dx)
13. ├─df_cor[, `:=`(corr_exp, corr_eqn(corr)), "EFFECT,variable"]
14. └─data.table:::`[.data.table`(...)
── Error ('test-pmx-all-compute.R:4:3'): (code run outside of `test_that()`) ───
Error in ``[.data.table`(df_cor, , `:=`(corr_exp, corr_eqn(corr)), "EFFECT,variable")`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. └─ggPMX::theophylline() at test-pmx-all-compute.R:4:3
2. └─ggPMX::pmx_mlx(...)
3. └─ggPMX::pmx(...)
4. └─pmxClass$new(...)
5. └─ggPMX (local) initialize(...)
6. └─ggPMX:::pmx_initialize(...)
7. ├─base::do.call(set_plot, c(ctr = self, x))
8. └─ggPMX (local) `<fn>`(...)
9. └─ctr$add_plot(conf, pname)
10. └─ggPMX:::pmx_add_plot(self, private, x, pname)
11. ├─ggPMX::plot_pmx(x, dx = x$dx)
12. └─ggPMX:::plot_pmx.eta_cov(x, dx = x$dx)
13. ├─df_cor[, `:=`(corr_exp, corr_eqn(corr)), "EFFECT,variable"]
14. └─data.table:::`[.data.table`(...)
── Error ('test-pmx-all-plots.R:4:3'): (code run outside of `test_that()`) ─────
Error in ``[.data.table`(df_cor, , `:=`(corr_exp, corr_eqn(corr)), "EFFECT,variable")`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. └─ggPMX:::test_pmxClass_helpers() at test-pmx-all-plots.R:4:3
2. └─ggPMX::pmx_mlx(...) at ./helper-pmxClass.R:8:3
3. └─ggPMX::pmx(...)
4. └─pmxClass$new(...)
5. └─ggPMX (local) initialize(...)
6. └─ggPMX:::pmx_initialize(...)
7. ├─base::do.call(set_plot, c(ctr = self, x))
8. └─ggPMX (local) `<fn>`(...)
9. └─ctr$add_plot(conf, pname)
10. └─ggPMX:::pmx_add_plot(self, private, x, pname)
11. ├─ggPMX::plot_pmx(x, dx = x$dx)
12. └─ggPMX:::plot_pmx.eta_cov(x, dx = x$dx)
13. ├─df_cor[, `:=`(corr_exp, corr_eqn(corr)), "EFFECT,variable"]
14. └─data.table:::`[.data.table`(...)
── Error ('test-pmx-plot-eta-cov.R:4:3'): (code run outside of `test_that()`) ──
Error in ``[.data.table`(df_cor, , `:=`(corr_exp, corr_eqn(corr)), "EFFECT,variable")`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. └─ggPMX::theophylline() at test-pmx-plot-eta-cov.R:4:3
2. └─ggPMX::pmx_mlx(...)
3. └─ggPMX::pmx(...)
4. └─pmxClass$new(...)
5. └─ggPMX (local) initialize(...)
6. └─ggPMX:::pmx_initialize(...)
7. ├─base::do.call(set_plot, c(ctr = self, x))
8. └─ggPMX (local) `<fn>`(...)
9. └─ctr$add_plot(conf, pname)
10. └─ggPMX:::pmx_add_plot(self, private, x, pname)
11. ├─ggPMX::plot_pmx(x, dx = x$dx)
12. └─ggPMX:::plot_pmx.eta_cov(x, dx = x$dx)
13. ├─df_cor[, `:=`(corr_exp, corr_eqn(corr)), "EFFECT,variable"]
14. └─data.table:::`[.data.table`(...)
── Error ('test-pmx-plot-vpc.R:6:3'): (code run outside of `test_that()`) ──────
Error in ``[.data.table`(df_cor, , `:=`(corr_exp, corr_eqn(corr)), "EFFECT,variable")`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. └─ggPMX::theophylline() at test-pmx-plot-vpc.R:6:3
2. └─ggPMX::pmx_mlx(...)
3. └─ggPMX::pmx(...)
4. └─pmxClass$new(...)
5. └─ggPMX (local) initialize(...)
6. └─ggPMX:::pmx_initialize(...)
7. ├─base::do.call(set_plot, c(ctr = self, x))
8. └─ggPMX (local) `<fn>`(...)
9. └─ctr$add_plot(conf, pname)
10. └─ggPMX:::pmx_add_plot(self, private, x, pname)
11. ├─ggPMX::plot_pmx(x, dx = x$dx)
12. └─ggPMX:::plot_pmx.eta_cov(x, dx = x$dx)
13. ├─df_cor[, `:=`(corr_exp, corr_eqn(corr)), "EFFECT,variable"]
14. └─data.table:::`[.data.table`(...)
── Error ('test-pmx-plots-distribution.R:4:3'): (code run outside of `test_that()`) ──
Error in ``[.data.table`(df_cor, , `:=`(corr_exp, corr_eqn(corr)), "EFFECT,variable")`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. └─ggPMX::theophylline() at test-pmx-plots-distribution.R:4:3
2. └─ggPMX::pmx_mlx(...)
3. └─ggPMX::pmx(...)
4. └─pmxClass$new(...)
5. └─ggPMX (local) initialize(...)
6. └─ggPMX:::pmx_initialize(...)
7. ├─base::do.call(set_plot, c(ctr = self, x))
8. └─ggPMX (local) `<fn>`(...)
9. └─ctr$add_plot(conf, pname)
10. └─ggPMX:::pmx_add_plot(self, private, x, pname)
11. ├─ggPMX::plot_pmx(x, dx = x$dx)
12. └─ggPMX:::plot_pmx.eta_cov(x, dx = x$dx)
13. ├─df_cor[, `:=`(corr_exp, corr_eqn(corr)), "EFFECT,variable"]
14. └─data.table:::`[.data.table`(...)
── Error ('test-pmx-plots-saem-convergence.R:3:3'): (code run outside of `test_that()`) ──
Error in ``[.data.table`(df_cor, , `:=`(corr_exp, corr_eqn(corr)), "EFFECT,variable")`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. └─ggPMX::theophylline() at test-pmx-plots-saem-convergence.R:3:3
2. └─ggPMX::pmx_mlx(...)
3. └─ggPMX::pmx(...)
4. └─pmxClass$new(...)
5. └─ggPMX (local) initialize(...)
6. └─ggPMX:::pmx_initialize(...)
7. ├─base::do.call(set_plot, c(ctr = self, x))
8. └─ggPMX (local) `<fn>`(...)
9. └─ctr$add_plot(conf, pname)
10. └─ggPMX:::pmx_add_plot(self, private, x, pname)
11. ├─ggPMX::plot_pmx(x, dx = x$dx)
12. └─ggPMX:::plot_pmx.eta_cov(x, dx = x$dx)
13. ├─df_cor[, `:=`(corr_exp, corr_eqn(corr)), "EFFECT,variable"]
14. └─data.table:::`[.data.table`(...)
── Error ('test-pmx-plots-scatter.R:4:3'): (code run outside of `test_that()`) ──
Error in ``[.data.table`(df_cor, , `:=`(corr_exp, corr_eqn(corr)), "EFFECT,variable")`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. └─ggPMX::theophylline() at test-pmx-plots-scatter.R:4:3
2. └─ggPMX::pmx_mlx(...)
3. └─ggPMX::pmx(...)
4. └─pmxClass$new(...)
5. └─ggPMX (local) initialize(...)
6. └─ggPMX:::pmx_initialize(...)
7. ├─base::do.call(set_plot, c(ctr = self, x))
8. └─ggPMX (local) `<fn>`(...)
9. └─ctr$add_plot(conf, pname)
10. └─ggPMX:::pmx_add_plot(self, private, x, pname)
11. ├─ggPMX::plot_pmx(x, dx = x$dx)
12. └─ggPMX:::plot_pmx.eta_cov(x, dx = x$dx)
13. ├─df_cor[, `:=`(corr_exp, corr_eqn(corr)), "EFFECT,variable"]
14. └─data.table:::`[.data.table`(...)
── Error ('test-pmx-post_load.R:7:13'): post_load: params:input, dxs are dataframes, dxs$finegrid is NULL;
result: list ──
Error in ``[.data.table`(df_cor, , `:=`(corr_exp, corr_eqn(corr)), "EFFECT,variable")`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. └─ggPMX::theophylline() at test-pmx-post_load.R:7:13
2. └─ggPMX::pmx_mlx(...)
3. └─ggPMX::pmx(...)
4. └─pmxClass$new(...)
5. └─ggPMX (local) initialize(...)
6. └─ggPMX:::pmx_initialize(...)
7. ├─base::do.call(set_plot, c(ctr = self, x))
8. └─ggPMX (local) `<fn>`(...)
9. └─ctr$add_plot(conf, pname)
10. └─ggPMX:::pmx_add_plot(self, private, x, pname)
11. ├─ggPMX::plot_pmx(x, dx = x$dx)
12. └─ggPMX:::plot_pmx.eta_cov(x, dx = x$dx)
13. ├─df_cor[, `:=`(corr_exp, corr_eqn(corr)), "EFFECT,variable"]
14. └─data.table:::`[.data.table`(...)
── Error ('test-pmx-post_load.R:21:13'): post_load: params:input, dxs are dataframes, dxs$finegrid is NULL;
result: list ──
Error in ``[.data.table`(df_cor, , `:=`(corr_exp, corr_eqn(corr)), "EFFECT,variable")`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. └─ggPMX::theophylline() at test-pmx-post_load.R:21:13
2. └─ggPMX::pmx_mlx(...)
3. └─ggPMX::pmx(...)
4. └─pmxClass$new(...)
5. └─ggPMX (local) initialize(...)
6. └─ggPMX:::pmx_initialize(...)
7. ├─base::do.call(set_plot, c(ctr = self, x))
8. └─ggPMX (local) `<fn>`(...)
9. └─ctr$add_plot(conf, pname)
10. └─ggPMX:::pmx_add_plot(self, private, x, pname)
11. ├─ggPMX::plot_pmx(x, dx = x$dx)
12. └─ggPMX:::plot_pmx.eta_cov(x, dx = x$dx)
13. ├─df_cor[, `:=`(corr_exp, corr_eqn(corr)), "EFFECT,variable"]
14. └─data.table:::`[.data.table`(...)
── Error ('test-pmx-post_load.R:33:13'): input_finegrid: params:input, finegrid;
result: data.frame ──
Error in ``[.data.table`(df_cor, , `:=`(corr_exp, corr_eqn(corr)), "EFFECT,variable")`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. └─ggPMX::theophylline() at test-pmx-post_load.R:33:13
2. └─ggPMX::pmx_mlx(...)
3. └─ggPMX::pmx(...)
4. └─pmxClass$new(...)
5. └─ggPMX (local) initialize(...)
6. └─ggPMX:::pmx_initialize(...)
7. ├─base::do.call(set_plot, c(ctr = self, x))
8. └─ggPMX (local) `<fn>`(...)
9. └─ctr$add_plot(conf, pname)
10. └─ggPMX:::pmx_add_plot(self, private, x, pname)
11. ├─ggPMX::plot_pmx(x, dx = x$dx)
12. └─ggPMX:::plot_pmx.eta_cov(x, dx = x$dx)
13. ├─df_cor[, `:=`(corr_exp, corr_eqn(corr)), "EFFECT,variable"]
14. └─data.table:::`[.data.table`(...)
── Error ('test-pmx-post_load.R:42:13'): input_finegrid: params: input, finegrid is NULL;
result: can read NONMEM-Output ──
Error in ``[.data.table`(df_cor, , `:=`(corr_exp, corr_eqn(corr)), "EFFECT,variable")`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. └─ggPMX::theophylline() at test-pmx-post_load.R:42:13
2. └─ggPMX::pmx_mlx(...)
3. └─ggPMX::pmx(...)
4. └─pmxClass$new(...)
5. └─ggPMX (local) initialize(...)
6. └─ggPMX:::pmx_initialize(...)
7. ├─base::do.call(set_plot, c(ctr = self, x))
8. └─ggPMX (local) `<fn>`(...)
9. └─ctr$add_plot(conf, pname)
10. └─ggPMX:::pmx_add_plot(self, private, x, pname)
11. ├─ggPMX::plot_pmx(x, dx = x$dx)
12. └─ggPMX:::plot_pmx.eta_cov(x, dx = x$dx)
13. ├─df_cor[, `:=`(corr_exp, corr_eqn(corr)), "EFFECT,variable"]
14. └─data.table:::`[.data.table`(...)
── Error ('test-pmx-post_load.R:51:13'): post_load_eta: params:input, ds are dataframes, input$ID is factor, occ;
result: error ──
Error in ``[.data.table`(df_cor, , `:=`(corr_exp, corr_eqn(corr)), "EFFECT,variable")`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. └─ggPMX::theophylline() at test-pmx-post_load.R:51:13
2. └─ggPMX::pmx_mlx(...)
3. └─ggPMX::pmx(...)
4. └─pmxClass$new(...)
5. └─ggPMX (local) initialize(...)
6. └─ggPMX:::pmx_initialize(...)
7. ├─base::do.call(set_plot, c(ctr = self, x))
8. └─ggPMX (local) `<fn>`(...)
9. └─ctr$add_plot(conf, pname)
10. └─ggPMX:::pmx_add_plot(self, private, x, pname)
11. ├─ggPMX::plot_pmx(x, dx = x$dx)
12. └─ggPMX:::plot_pmx.eta_cov(x, dx = x$dx)
13. ├─df_cor[, `:=`(corr_exp, corr_eqn(corr)), "EFFECT,variable"]
14. └─data.table:::`[.data.table`(...)
── Error ('test-pmx-post_load.R:61:13'): post_load_eta: params:input, ds are dataframes, input$ID is factor, occ;
result: error ──
Error in ``[.data.table`(df_cor, , `:=`(corr_exp, corr_eqn(corr)), "EFFECT,variable")`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. └─ggPMX::theophylline() at test-pmx-post_load.R:61:13
2. └─ggPMX::pmx_mlx(...)
3. └─ggPMX::pmx(...)
4. └─pmxClass$new(...)
5. └─ggPMX (local) initialize(...)
6. └─ggPMX:::pmx_initialize(...)
7. ├─base::do.call(set_plot, c(ctr = self, x))
8. └─ggPMX (local) `<fn>`(...)
9. └─ctr$add_plot(conf, pname)
10. └─ggPMX:::pmx_add_plot(self, private, x, pname)
11. ├─ggPMX::plot_pmx(x, dx = x$dx)
12. └─ggPMX:::plot_pmx.eta_cov(x, dx = x$dx)
13. ├─df_cor[, `:=`(corr_exp, corr_eqn(corr)), "EFFECT,variable"]
14. └─data.table:::`[.data.table`(...)
── Error ('test-pmx-post_load.R:72:13'): post_load_eta: params:input, ds are dataframes, input$ID is factor, occ;
result: error ──
Error in ``[.data.table`(df_cor, , `:=`(corr_exp, corr_eqn(corr)), "EFFECT,variable")`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. └─ggPMX::theophylline() at test-pmx-post_load.R:72:13
2. └─ggPMX::pmx_mlx(...)
3. └─ggPMX::pmx(...)
4. └─pmxClass$new(...)
5. └─ggPMX (local) initialize(...)
6. └─ggPMX:::pmx_initialize(...)
7. ├─base::do.call(set_plot, c(ctr = self, x))
8. └─ggPMX (local) `<fn>`(...)
9. └─ctr$add_plot(conf, pname)
10. └─ggPMX:::pmx_add_plot(self, private, x, pname)
11. ├─ggPMX::plot_pmx(x, dx = x$dx)
12. └─ggPMX:::plot_pmx.eta_cov(x, dx = x$dx)
13. ├─df_cor[, `:=`(corr_exp, corr_eqn(corr)), "EFFECT,variable"]
14. └─data.table:::`[.data.table`(...)
── Error ('test-pmx-post_load.R:83:13'): post_load_eta: params:input, ds are dataframes, ds$ID is factor, occ;
result: error ──
Error in ``[.data.table`(df_cor, , `:=`(corr_exp, corr_eqn(corr)), "EFFECT,variable")`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. └─ggPMX::theophylline() at test-pmx-post_load.R:83:13
2. └─ggPMX::pmx_mlx(...)
3. └─ggPMX::pmx(...)
4. └─pmxClass$new(...)
5. └─ggPMX (local) initialize(...)
6. └─ggPMX:::pmx_initialize(...)
7. ├─base::do.call(set_plot, c(ctr = self, x))
8. └─ggPMX (local) `<fn>`(...)
9. └─ctr$add_plot(conf, pname)
10. └─ggPMX:::pmx_add_plot(self, private, x, pname)
11. ├─ggPMX::plot_pmx(x, dx = x$dx)
12. └─ggPMX:::plot_pmx.eta_cov(x, dx = x$dx)
13. ├─df_cor[, `:=`(corr_exp, corr_eqn(corr)), "EFFECT,variable"]
14. └─data.table:::`[.data.table`(...)
── Error ('test-pmx-report.R:8:5'): (code run outside of `test_that()`) ────────
Error in ``[.data.table`(df_cor, , `:=`(corr_exp, corr_eqn(corr)), "EFFECT,variable")`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. ├─withr::with_tempdir(...) at test-pmx-report.R:2:3
2. │ └─withr::with_dir(tmp, code)
3. │ └─base::force(code)
4. └─ggPMX::theophylline() at test-pmx-report.R:8:5
5. └─ggPMX::pmx_mlx(...)
6. └─ggPMX::pmx(...)
7. └─pmxClass$new(...)
8. └─ggPMX (local) initialize(...)
9. └─ggPMX:::pmx_initialize(...)
10. ├─base::do.call(set_plot, c(ctr = self, x))
11. └─ggPMX (local) `<fn>`(...)
12. └─ctr$add_plot(conf, pname)
13. └─ggPMX:::pmx_add_plot(self, private, x, pname)
14. ├─ggPMX::plot_pmx(x, dx = x$dx)
15. └─ggPMX:::plot_pmx.eta_cov(x, dx = x$dx)
16. ├─df_cor[, `:=`(corr_exp, corr_eqn(corr)), "EFFECT,variable"]
17. └─data.table:::`[.data.table`(...)
── Error ('test-pmx-vpc-bin.R:4:3'): (code run outside of `test_that()`) ───────
Error in ``[.data.table`(df_cor, , `:=`(corr_exp, corr_eqn(corr)), "EFFECT,variable")`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. └─ggPMX::theophylline() at test-pmx-vpc-bin.R:4:3
2. └─ggPMX::pmx_mlx(...)
3. └─ggPMX::pmx(...)
4. └─pmxClass$new(...)
5. └─ggPMX (local) initialize(...)
6. └─ggPMX:::pmx_initialize(...)
7. ├─base::do.call(set_plot, c(ctr = self, x))
8. └─ggPMX (local) `<fn>`(...)
9. └─ctr$add_plot(conf, pname)
10. └─ggPMX:::pmx_add_plot(self, private, x, pname)
11. ├─ggPMX::plot_pmx(x, dx = x$dx)
12. └─ggPMX:::plot_pmx.eta_cov(x, dx = x$dx)
13. ├─df_cor[, `:=`(corr_exp, corr_eqn(corr)), "EFFECT,variable"]
14. └─data.table:::`[.data.table`(...)
── Error ('test-pmxClass.R:4:3'): (code run outside of `test_that()`) ──────────
Error in ``[.data.table`(df_cor, , `:=`(corr_exp, corr_eqn(corr)), "EFFECT,variable")`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. └─ggPMX:::test_pmxClass_helpers() at test-pmxClass.R:4:3
2. └─ggPMX::pmx_mlx(...) at ./helper-pmxClass.R:8:3
3. └─ggPMX::pmx(...)
4. └─pmxClass$new(...)
5. └─ggPMX (local) initialize(...)
6. └─ggPMX:::pmx_initialize(...)
7. ├─base::do.call(set_plot, c(ctr = self, x))
8. └─ggPMX (local) `<fn>`(...)
9. └─ctr$add_plot(conf, pname)
10. └─ggPMX:::pmx_add_plot(self, private, x, pname)
11. ├─ggPMX::plot_pmx(x, dx = x$dx)
12. └─ggPMX:::plot_pmx.eta_cov(x, dx = x$dx)
13. ├─df_cor[, `:=`(corr_exp, corr_eqn(corr)), "EFFECT,variable"]
14. └─data.table:::`[.data.table`(...)
── Error ('test-pmx_filter.R:4:3'): (code run outside of `test_that()`) ────────
Error in ``[.data.table`(df_cor, , `:=`(corr_exp, corr_eqn(corr)), "EFFECT,variable")`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. └─ggPMX:::test_pmxClass_helpers() at test-pmx_filter.R:4:3
2. └─ggPMX::pmx_mlx(...) at ./helper-pmxClass.R:8:3
3. └─ggPMX::pmx(...)
4. └─pmxClass$new(...)
5. └─ggPMX (local) initialize(...)
6. └─ggPMX:::pmx_initialize(...)
7. ├─base::do.call(set_plot, c(ctr = self, x))
8. └─ggPMX (local) `<fn>`(...)
9. └─ctr$add_plot(conf, pname)
10. └─ggPMX:::pmx_add_plot(self, private, x, pname)
11. ├─ggPMX::plot_pmx(x, dx = x$dx)
12. └─ggPMX:::plot_pmx.eta_cov(x, dx = x$dx)
13. ├─df_cor[, `:=`(corr_exp, corr_eqn(corr)), "EFFECT,variable"]
14. └─data.table:::`[.data.table`(...)
── Error ('test-pmx_list_nm_tables.R:31:5'): pmx_is.nm.model: params: nm_model object; result: TRUE ──
Error in ``[.data.table`(df_cor, , `:=`(corr_exp, corr_eqn(corr)), "EFFECT,variable")`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. └─ggPMX::theophylline() at test-pmx_list_nm_tables.R:31:5
2. └─ggPMX::pmx_mlx(...)
3. └─ggPMX::pmx(...)
4. └─pmxClass$new(...)
5. └─ggPMX (local) initialize(...)
6. └─ggPMX:::pmx_initialize(...)
7. ├─base::do.call(set_plot, c(ctr = self, x))
8. └─ggPMX (local) `<fn>`(...)
9. └─ctr$add_plot(conf, pname)
10. └─ggPMX:::pmx_add_plot(self, private, x, pname)
11. ├─ggPMX::plot_pmx(x, dx = x$dx)
12. └─ggPMX:::plot_pmx.eta_cov(x, dx = x$dx)
13. ├─df_cor[, `:=`(corr_exp, corr_eqn(corr)), "EFFECT,variable"]
14. └─data.table:::`[.data.table`(...)
── Error ('test-pmx_list_nm_tables.R:43:5'): pmx_as.nm.table.list: params: theophylline; result: TRUE ──
Error in ``[.data.table`(df_cor, , `:=`(corr_exp, corr_eqn(corr)), "EFFECT,variable")`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. └─ggPMX::theophylline() at test-pmx_list_nm_tables.R:43:5
2. └─ggPMX::pmx_mlx(...)
3. └─ggPMX::pmx(...)
4. └─pmxClass$new(...)
5. └─ggPMX (local) initialize(...)
6. └─ggPMX:::pmx_initialize(...)
7. ├─base::do.call(set_plot, c(ctr = self, x))
8. └─ggPMX (local) `<fn>`(...)
9. └─ctr$add_plot(conf, pname)
10. └─ggPMX:::pmx_add_plot(self, private, x, pname)
11. ├─ggPMX::plot_pmx(x, dx = x$dx)
12. └─ggPMX:::plot_pmx.eta_cov(x, dx = x$dx)
13. ├─df_cor[, `:=`(corr_exp, corr_eqn(corr)), "EFFECT,variable"]
14. └─data.table:::`[.data.table`(...)
── Error ('test-pmx_update.R:4:3'): (code run outside of `test_that()`) ────────
Error in ``[.data.table`(df_cor, , `:=`(corr_exp, corr_eqn(corr)), "EFFECT,variable")`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. └─ggPMX:::helper_updateplots() at test-pmx_update.R:4:3
2. └─ggPMX::pmx_mlx(...) at ./helper-update_plots.R:8:3
3. └─ggPMX::pmx(...)
4. └─pmxClass$new(...)
5. └─ggPMX (local) initialize(...)
6. └─ggPMX:::pmx_initialize(...)
7. ├─base::do.call(set_plot, c(ctr = self, x))
8. └─ggPMX (local) `<fn>`(...)
9. └─ctr$add_plot(conf, pname)
10. └─ggPMX:::pmx_add_plot(self, private, x, pname)
11. ├─ggPMX::plot_pmx(x, dx = x$dx)
12. └─ggPMX:::plot_pmx.eta_cov(x, dx = x$dx)
13. ├─df_cor[, `:=`(corr_exp, corr_eqn(corr)), "EFFECT,variable"]
14. └─data.table:::`[.data.table`(...)
── Error ('test-reader.R:324:7'): Same number of rows in predictions and input dataset after creating monolix controller ──
Error in ``[.data.table`(df_cor, , `:=`(corr_exp, corr_eqn(corr)), "EFFECT,variable")`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. ├─withr::with_tempdir(...) at test-reader.R:301:5
2. │ └─withr::with_dir(tmp, code)
3. │ └─base::force(code)
4. └─ggPMX::pmx_mlx(...) at test-reader.R:324:7
5. └─ggPMX::pmx(...)
6. └─pmxClass$new(...)
7. └─ggPMX (local) initialize(...)
8. └─ggPMX:::pmx_initialize(...)
9. ├─base::do.call(set_plot, c(ctr = self, x))
10. └─ggPMX (local) `<fn>`(...)
11. └─ctr$add_plot(conf, pname)
12. └─ggPMX:::pmx_add_plot(self, private, x, pname)
13. ├─ggPMX::plot_pmx(x, dx = x$dx)
14. └─ggPMX:::plot_pmx.eta_cov(x, dx = x$dx)
15. ├─df_cor[, `:=`(corr_exp, corr_eqn(corr)), "EFFECT,variable"]
16. └─data.table:::`[.data.table`(...)
── Error ('test-shrinkage.R:4:3'): (code run outside of `test_that()`) ─────────
Error in ``[.data.table`(df_cor, , `:=`(corr_exp, corr_eqn(corr)), "EFFECT,variable")`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. └─ggPMX:::test_pmxClass_helpers() at test-shrinkage.R:4:3
2. └─ggPMX::pmx_mlx(...) at ./helper-pmxClass.R:8:3
3. └─ggPMX::pmx(...)
4. └─pmxClass$new(...)
5. └─ggPMX (local) initialize(...)
6. └─ggPMX:::pmx_initialize(...)
7. ├─base::do.call(set_plot, c(ctr = self, x))
8. └─ggPMX (local) `<fn>`(...)
9. └─ctr$add_plot(conf, pname)
10. └─ggPMX:::pmx_add_plot(self, private, x, pname)
11. ├─ggPMX::plot_pmx(x, dx = x$dx)
12. └─ggPMX:::plot_pmx.eta_cov(x, dx = x$dx)
13. ├─df_cor[, `:=`(corr_exp, corr_eqn(corr)), "EFFECT,variable"]
14. └─data.table:::`[.data.table`(...)
── Error ('test-utils.R:15:5'): pk_pd is working ───────────────────────────────
Error in ``[.data.table`(df_cor, , `:=`(corr_exp, corr_eqn(corr)), "EFFECT,variable")`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. ├─utils::capture.output(ctr <- pk_pd()) at test-utils.R:15:5
2. │ └─base::withVisible(...elt(i))
3. └─ggPMX::pk_pd()
4. └─ggPMX::pmx_mlx(...)
5. └─ggPMX::pmx(...)
6. └─pmxClass$new(...)
7. └─ggPMX (local) initialize(...)
8. └─ggPMX:::pmx_initialize(...)
9. ├─base::do.call(set_plot, c(ctr = self, x))
10. └─ggPMX (local) `<fn>`(...)
11. └─ctr$add_plot(conf, pname)
12. └─ggPMX:::pmx_add_plot(self, private, x, pname)
13. ├─ggPMX::plot_pmx(x, dx = x$dx)
14. └─ggPMX:::plot_pmx.eta_cov(x, dx = x$dx)
15. ├─df_cor[, `:=`(corr_exp, corr_eqn(corr)), "EFFECT,variable"]
16. └─data.table:::`[.data.table`(...)
── Error ('test-utils.R:21:5'): pk_pd params: code; result: identical structure ──
Error in ``[.data.table`(df_cor, , `:=`(corr_exp, corr_eqn(corr)), "EFFECT,variable")`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. ├─utils::capture.output(ctr <- pk_pd(code = "4")) at test-utils.R:21:5
2. │ └─base::withVisible(...elt(i))
3. └─ggPMX::pk_pd(code = "4")
4. └─ggPMX::pmx_mlx(...)
5. └─ggPMX::pmx(...)
6. └─pmxClass$new(...)
7. └─ggPMX (local) initialize(...)
8. └─ggPMX:::pmx_initialize(...)
9. ├─base::do.call(set_plot, c(ctr = self, x))
10. └─ggPMX (local) `<fn>`(...)
11. └─ctr$add_plot(conf, pname)
12. └─ggPMX:::pmx_add_plot(self, private, x, pname)
13. ├─ggPMX::plot_pmx(x, dx = x$dx)
14. └─ggPMX:::plot_pmx.eta_cov(x, dx = x$dx)
15. ├─df_cor[, `:=`(corr_exp, corr_eqn(corr)), "EFFECT,variable"]
16. └─data.table:::`[.data.table`(...)
── Error ('test-utils.R:97:5'): parse_mlxtran: params: folder name ─────────────
Error in ``[.data.table`(dat, , `:=`(section.name, gsub("<|>", "", line[1])), section)`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. ├─base::suppressWarnings(parse_mlxtran(file_name)) at test-utils.R:97:5
2. │ └─base::withCallingHandlers(...)
3. └─ggPMX::parse_mlxtran(file_name)
4. ├─dat[, `:=`(section.name, gsub("<|>", "", line[1])), section]
5. └─data.table:::`[.data.table`(...)
── Error ('test-utils.R:150:5'): parse_mlxtran: params: no exist file_name ─────
Error in ``[.data.table`(dat, , `:=`(section.name, gsub("<|>", "", line[1])), section)`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. ├─base::suppressWarnings(parse_mlxtran(mlxpath)) at test-utils.R:150:5
2. │ └─base::withCallingHandlers(...)
3. └─ggPMX::parse_mlxtran(mlxpath)
4. ├─dat[, `:=`(section.name, gsub("<|>", "", line[1])), section]
5. └─data.table:::`[.data.table`(...)
── Error ('test-utils.R:213:5'): parse_mlxtran params: file_name result: identical names ──
Error in ``[.data.table`(dat, , `:=`(section.name, gsub("<|>", "", line[1])), section)`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. ├─base::suppressWarnings(parse_mlxtran(file_name = mlxtran_path)) at test-utils.R:213:5
2. │ └─base::withCallingHandlers(...)
3. └─ggPMX::parse_mlxtran(file_name = mlxtran_path)
4. ├─dat[, `:=`(section.name, gsub("<|>", "", line[1])), section]
5. └─data.table:::`[.data.table`(...)
── Error ('test-utils.R:221:5'): parse_mlxtran params: file_name result: identical inherits ──
Error in ``[.data.table`(dat, , `:=`(section.name, gsub("<|>", "", line[1])), section)`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. ├─base::suppressWarnings(parse_mlxtran(file_name = mlxtran_path)) at test-utils.R:221:5
2. │ └─base::withCallingHandlers(...)
3. └─ggPMX::parse_mlxtran(file_name = mlxtran_path)
4. ├─dat[, `:=`(section.name, gsub("<|>", "", line[1])), section]
5. └─data.table:::`[.data.table`(...)
── Error ('test-utils.R:228:5'): parse_mlxtran params: file_name result: identical structure ──
Error in ``[.data.table`(dat, , `:=`(section.name, gsub("<|>", "", line[1])), section)`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. ├─base::suppressWarnings(parse_mlxtran(file_name = mlxtran_path)) at test-utils.R:228:5
2. │ └─base::withCallingHandlers(...)
3. └─ggPMX::parse_mlxtran(file_name = mlxtran_path)
4. ├─dat[, `:=`(section.name, gsub("<|>", "", line[1])), section]
5. └─data.table:::`[.data.table`(...)
── Error ('test-utils.R:383:7'): theophylline: params: NULL result: identical inherits ──
Error in ``[.data.table`(df_cor, , `:=`(corr_exp, corr_eqn(corr)), "EFFECT,variable")`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_true(...) at test-utils.R:383:7
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. ├─base::inherits(theophylline(), c("pmxClass", "R6"))
5. └─ggPMX::theophylline()
6. └─ggPMX::pmx_mlx(...)
7. └─ggPMX::pmx(...)
8. └─pmxClass$new(...)
9. └─ggPMX (local) initialize(...)
10. └─ggPMX:::pmx_initialize(...)
11. ├─base::do.call(set_plot, c(ctr = self, x))
12. └─ggPMX (local) `<fn>`(...)
13. └─ctr$add_plot(conf, pname)
14. └─ggPMX:::pmx_add_plot(self, private, x, pname)
15. ├─ggPMX::plot_pmx(x, dx = x$dx)
16. └─ggPMX:::plot_pmx.eta_cov(x, dx = x$dx)
17. ├─df_cor[, `:=`(corr_exp, corr_eqn(corr)), "EFFECT,variable"]
18. └─data.table:::`[.data.table`(...)
── Error ('test-utils.R:388:7'): theophylline: params: settings, result: identical names ──
Error in ``[.data.table`(df_cor, , `:=`(corr_exp, corr_eqn(corr)), "EFFECT,variable")`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. └─ggPMX::theophylline(...) at test-utils.R:388:7
2. └─ggPMX::pmx_mlx(...)
3. └─ggPMX::pmx(...)
4. └─pmxClass$new(...)
5. └─ggPMX (local) initialize(...)
6. └─ggPMX:::pmx_initialize(...)
7. ├─base::do.call(set_plot, c(ctr = self, x))
8. └─ggPMX (local) `<fn>`(...)
9. └─ctr$add_plot(conf, pname)
10. └─ggPMX:::pmx_add_plot(self, private, x, pname)
11. ├─ggPMX::plot_pmx(x, dx = x$dx)
12. └─ggPMX:::plot_pmx.eta_cov(x, dx = x$dx)
13. ├─df_cor[, `:=`(corr_exp, corr_eqn(corr)), "EFFECT,variable"]
14. └─data.table:::`[.data.table`(...)
── Error ('test-utils.R:410:7'): theophylline: params: settings, result: identical levels and labels ──
Error in ``[.data.table`(df_cor, , `:=`(corr_exp, corr_eqn(corr)), "EFFECT,variable")`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. └─ggPMX::theophylline(...) at test-utils.R:410:7
2. └─ggPMX::pmx_mlx(...)
3. └─ggPMX::pmx(...)
4. └─pmxClass$new(...)
5. └─ggPMX (local) initialize(...)
6. └─ggPMX:::pmx_initialize(...)
7. ├─base::do.call(set_plot, c(ctr = self, x))
8. └─ggPMX (local) `<fn>`(...)
9. └─ctr$add_plot(conf, pname)
10. └─ggPMX:::pmx_add_plot(self, private, x, pname)
11. ├─ggPMX::plot_pmx(x, dx = x$dx)
12. └─ggPMX:::plot_pmx.eta_cov(x, dx = x$dx)
13. ├─df_cor[, `:=`(corr_exp, corr_eqn(corr)), "EFFECT,variable"]
14. └─data.table:::`[.data.table`(...)
── Error ('test-utils.R:427:7'): pk_occ: params: NULL result: identical inherits ──
Error in ``[.data.table`(df_cor, , `:=`(corr_exp, corr_eqn(corr)), "EFFECT,variable")`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_true(inherits(pk_occ(), c("pmxClass", "R6"))) at test-utils.R:427:7
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. ├─base::inherits(pk_occ(), c("pmxClass", "R6"))
5. └─ggPMX::pk_occ()
6. └─ggPMX::pmx_mlx(...)
7. └─ggPMX::pmx(...)
8. └─pmxClass$new(...)
9. └─ggPMX (local) initialize(...)
10. └─ggPMX:::pmx_initialize(...)
11. ├─base::do.call(set_plot, c(ctr = self, x))
12. └─ggPMX (local) `<fn>`(...)
13. └─ctr$add_plot(conf, pname)
14. └─ggPMX:::pmx_add_plot(self, private, x, pname)
15. ├─ggPMX::plot_pmx(x, dx = x$dx)
16. └─ggPMX:::plot_pmx.eta_cov(x, dx = x$dx)
17. ├─df_cor[, `:=`(corr_exp, corr_eqn(corr)), "EFFECT,variable"]
18. └─data.table:::`[.data.table`(...)
── Error ('test-utils.R:432:7'): pk_occ: params: NULL result: identical structure ──
Error in ``[.data.table`(df_cor, , `:=`(corr_exp, corr_eqn(corr)), "EFFECT,variable")`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. └─ggPMX::pk_occ() at test-utils.R:432:7
2. └─ggPMX::pmx_mlx(...)
3. └─ggPMX::pmx(...)
4. └─pmxClass$new(...)
5. └─ggPMX (local) initialize(...)
6. └─ggPMX:::pmx_initialize(...)
7. ├─base::do.call(set_plot, c(ctr = self, x))
8. └─ggPMX (local) `<fn>`(...)
9. └─ctr$add_plot(conf, pname)
10. └─ggPMX:::pmx_add_plot(self, private, x, pname)
11. ├─ggPMX::plot_pmx(x, dx = x$dx)
12. └─ggPMX:::plot_pmx.eta_cov(x, dx = x$dx)
13. ├─df_cor[, `:=`(corr_exp, corr_eqn(corr)), "EFFECT,variable"]
14. └─data.table:::`[.data.table`(...)
── Error ('test-utils.R:442:7'): pk_occ: params: NULL result: identical inherits ──
Error in ``[.data.table`(df_cor, , `:=`(corr_exp, corr_eqn(corr)), "EFFECT,variable")`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. └─ggPMX::pk_occ() at test-utils.R:442:7
2. └─ggPMX::pmx_mlx(...)
3. └─ggPMX::pmx(...)
4. └─pmxClass$new(...)
5. └─ggPMX (local) initialize(...)
6. └─ggPMX:::pmx_initialize(...)
7. ├─base::do.call(set_plot, c(ctr = self, x))
8. └─ggPMX (local) `<fn>`(...)
9. └─ctr$add_plot(conf, pname)
10. └─ggPMX:::pmx_add_plot(self, private, x, pname)
11. ├─ggPMX::plot_pmx(x, dx = x$dx)
12. └─ggPMX:::plot_pmx.eta_cov(x, dx = x$dx)
13. ├─df_cor[, `:=`(corr_exp, corr_eqn(corr)), "EFFECT,variable"]
14. └─data.table:::`[.data.table`(...)
[ FAIL 74 | WARN 0 | SKIP 18 | PASS 365 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-windows-x86_64
Version: 1.3.2
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building 'ggPMX-guide.Rmd' using rmarkdown
Quitting from ggPMX-guide.Rmd:22-35 [load_package]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `[.data.table`:
! attempt access index 3/3 in VECTOR_ELT
---
Backtrace:
x
1. \-ggPMX::theophylline()
2. \-ggPMX::pmx_mlx(...)
3. \-ggPMX::pmx(...)
4. \-pmxClass$new(...)
5. \-ggPMX (local) initialize(...)
6. \-ggPMX:::pmx_initialize(...)
7. +-base::do.call(set_plot, c(ctr = self, x))
8. \-ggPMX (local) `<fn>`(...)
9. \-ctr$add_plot(conf, pname)
10. \-ggPMX:::pmx_add_plot(self, private, x, pname)
11. +-ggPMX::plot_pmx(x, dx = x$dx)
12. \-ggPMX:::plot_pmx.eta_cov(x, dx = x$dx)
13. +-df_cor[, `:=`(corr_exp, corr_eqn(corr)), "EFFECT,variable"]
14. \-data.table:::`[.data.table`(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'ggPMX-guide.Rmd' failed with diagnostics:
attempt access index 3/3 in VECTOR_ELT
--- failed re-building 'ggPMX-guide.Rmd'
SUMMARY: processing the following file failed:
'ggPMX-guide.Rmd'
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-windows-x86_64
Version: 1.3.2
Check: package dependencies
Result: NOTE
Package suggested but not available for checking: ‘lixoftConnectors’
Flavors: r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64
Version: 1.3.2
Check: installed package size
Result: NOTE
installed size is 6.9Mb
sub-directories of 1Mb or more:
help 2.4Mb
testdata 3.0Mb
Flavors: r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64
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They may not be fully stable and should be used with caution. We make no claims about them.
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