Last updated on 2026-05-02 23:51:01 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.8.0 | 24.89 | 496.70 | 521.59 | OK | |
| r-devel-linux-x86_64-debian-gcc | 0.8.0 | 18.28 | 368.11 | 386.39 | OK | |
| r-devel-linux-x86_64-fedora-clang | 0.8.0 | 42.00 | 712.46 | 754.46 | OK | |
| r-devel-linux-x86_64-fedora-gcc | 0.8.0 | 41.00 | 770.44 | 811.44 | OK | |
| r-devel-windows-x86_64 | 0.8.0 | 29.00 | 445.00 | 474.00 | ERROR | |
| r-patched-linux-x86_64 | 0.8.0 | 25.27 | 467.66 | 492.93 | OK | |
| r-release-linux-x86_64 | 0.8.0 | 24.41 | 464.73 | 489.14 | OK | |
| r-release-macos-arm64 | 0.8.0 | 8.00 | 136.00 | 144.00 | OK | |
| r-release-macos-x86_64 | 0.8.0 | 21.00 | 512.00 | 533.00 | OK | |
| r-release-windows-x86_64 | 0.8.0 | 26.00 | 468.00 | 494.00 | OK | |
| r-oldrel-macos-arm64 | 0.8.0 | 9.00 | 144.00 | 153.00 | OK | |
| r-oldrel-macos-x86_64 | 0.8.0 | 23.00 | 1155.00 | 1178.00 | OK | |
| r-oldrel-windows-x86_64 | 0.8.0 | 29.00 | 629.00 | 658.00 | OK |
Version: 0.8.0
Check: examples
Result: ERROR
Running examples in 'medicalcoder-Ex.R' failed
The error most likely occurred in:
> ### Name: comorbidities
> ### Title: Comorbidities
> ### Aliases: comorbidities
>
> ### ** Examples
>
> pccc_v3.1_results <-
+ comorbidities(data = mdcr,
+ icd.codes = "code",
+ id.vars = "patid",
+ dx.var = "dx",
+ method = "pccc_v3.1",
+ flag.method = 'current',
+ poa = 1)
> summary(pccc_v3.1_results)
condition label dxpr_or_tech_count
1 congeni_genetic Other Congenital or Genetic Defect 3225
2 cvd Cardiovascular 5147
3 gi Gastrointestinal 5652
4 hemato_immu Hematologic or Immunologic 2832
5 malignancy Malignancy 3784
6 metabolic Metabolic 3407
7 misc Miscellaneous, Not Elsewhere Classified 764
8 neonatal Premature & Neonatal 1516
9 neuromusc Neurologic or Neuromuscular 5828
10 renal Renal Urologic 2787
11 respiratory Respiratory 3260
12 any_tech_dep Any Technology Dependence 7012
13 any_transplant Any Transplantation 1585
14 cmrb_flag Any Condition 20871
15 num_cmrb >= 2 conditions 10657
16 num_cmrb >= 3 conditions 4582
17 num_cmrb >= 4 conditions 1571
18 num_cmrb >= 5 conditions 418
19 num_cmrb >= 6 conditions 88
20 num_cmrb >= 7 conditions 13
21 num_cmrb >= 8 conditions 2
22 num_cmrb >= 9 conditions 0
23 num_cmrb >= 10 conditions 0
24 num_cmrb >= 11 conditions 0
dxpr_or_tech_percent dxpr_only_count dxpr_only_percent tech_only_count
1 8.428728242 3225 8.4287282 0
2 13.451988919 4560 11.9178297 283
3 14.771836287 1420 3.7112540 3855
4 7.401599498 2832 7.4015995 0
5 9.889707804 3784 9.8897078 0
6 8.904396006 3356 8.7711045 40
7 1.996759187 121 0.3162407 643
8 3.962155664 1516 3.9621557 0
9 15.231822696 4564 11.9282839 316
10 7.283989337 1876 4.9030370 555
11 8.520202812 1848 4.8298573 755
12 18.326276724 NA NA NA
13 4.142491245 NA NA NA
14 54.547592912 NA NA NA
15 27.852699807 NA NA NA
16 11.975328002 NA NA NA
17 4.105901417 NA NA NA
18 1.092467723 NA NA NA
19 0.229993205 NA NA NA
20 0.033976269 NA NA NA
21 0.005227118 NA NA NA
22 0.000000000 NA NA NA
23 0.000000000 NA NA NA
24 0.000000000 NA NA NA
tech_only_percent dxpr_and_tech_count dxpr_and_tech_percent
1 0.0000000 0 0.00000000
2 0.7396372 304 0.79452198
3 10.0752705 377 0.98531180
4 0.0000000 0 0.00000000
5 0.0000000 0 0.00000000
6 0.1045424 11 0.02874915
7 1.6805185 0 0.00000000
8 0.0000000 0 0.00000000
9 0.8258847 948 2.47765407
10 1.4505253 356 0.93042706
11 1.9732372 657 1.71710836
12 NA NA NA
13 NA NA NA
14 NA NA NA
15 NA NA NA
16 NA NA NA
17 NA NA NA
18 NA NA NA
19 NA NA NA
20 NA NA NA
21 NA NA NA
22 NA NA NA
23 NA NA NA
24 NA NA NA
>
> pccc_v3.1_subcondition_results <-
+ comorbidities(data = mdcr,
+ icd.codes = "code",
+ id.vars = "patid",
+ dx.var = "dx",
+ method = "pccc_v3.1",
+ flag.method = 'current',
+ poa = 1,
+ subconditions = TRUE)
> summary(pccc_v3.1_subcondition_results)
condition subcondition count
1 congeni_genetic <NA> 3225
2 congeni_genetic bone_and_joint_anomalies 825
3 congeni_genetic chromosomal_anomalies 1544
4 congeni_genetic diaphragm_and_abdominal_wall_anomalies 300
5 congeni_genetic other_congenital_anomalies 754
6 cvd <NA> 5147
7 cvd cardiomyopathies 240
8 cvd conduction_disorder 653
9 cvd device_and_technology_use 587
10 cvd dysrhythmias 1130
11 cvd endocardium_diseases 278
12 cvd heart_and_great_vessel_malformations 2320
13 cvd other 1247
14 cvd transplantation 271
15 gi <NA> 5652
16 gi chronic_liver_disease_and_cirrhosis 290
17 gi congenital_anomalies 709
18 gi device_and_technology_use 4232
19 gi inflammatory_bowel_disease 264
20 gi other 295
21 gi transplantation 343
22 hemato_immu <NA> 2832
23 hemato_immu acquired_immunodeficiency 11
24 hemato_immu aplastic_anemias 823
25 hemato_immu coagulation_hemorrhagic 100
26 hemato_immu diffuse_diseases_of_connective_tissue 125
27 hemato_immu hemophagocytic_syndromes 59
28 hemato_immu hereditary_anemias 771
29 hemato_immu hereditary_immunodeficiency 909
30 hemato_immu leukopenia 28
31 hemato_immu other 12
32 hemato_immu polyarteritis_nodosa_and_related_conditions 46
33 hemato_immu sarcoidosis 3
34 hemato_immu transplantation 181
35 malignancy <NA> 3784
36 malignancy neoplasms 3525
37 malignancy transplantation 452
38 metabolic <NA> 3407
39 metabolic amino_acid_metabolism 194
40 metabolic carbohydrate_metabolism 130
41 metabolic device_and_technology_use 51
42 metabolic endocrine_disorders 884
43 metabolic lipid_metabolism 354
44 metabolic other_metabolic_disorders 1870
45 metabolic storage_disorders 82
46 misc <NA> 764
47 misc device_and_technology_use 643
48 misc transplantation 121
49 neonatal <NA> 1516
50 neonatal birth_asphyxia 11
51 neonatal cerebral_hemorrhage_at_birth 84
52 neonatal extreme_immaturity 349
53 neonatal fetal_malnutrition 45
54 neonatal hypoxic_ischemic_encephalopathy 130
55 neonatal other 247
56 neonatal respiratory_diseases 950
57 neonatal spinal_cord_injury_at_birth 0
58 neuromusc <NA> 5828
59 neuromusc brain_and_spinal_cord_malformations 1767
60 neuromusc cns_degeneration_and_diseases 1474
61 neuromusc device_and_technology_use 1264
62 neuromusc epilepsy 833
63 neuromusc infantile_cerebral_palsy 1322
64 neuromusc intellectual_disabilities 161
65 neuromusc movement_diseases 146
66 neuromusc muscular_dystrophies_and_myopathies 147
67 neuromusc occlusion_of_cerebral_arteries 92
68 neuromusc other_neurologic_disorders 848
69 renal <NA> 2787
70 renal chronic_bladder_diseases 519
71 renal chronic_renal_failure 627
72 renal congenital_anomalies 915
73 renal device_and_technology_use 911
74 renal other 217
75 renal transplantation 322
76 respiratory <NA> 3260
77 respiratory chronic_respiratory_diseases 1092
78 respiratory cystic_fibrosis 400
79 respiratory device_and_technology_use 1412
80 respiratory other 22
81 respiratory respiratory_malformations 1091
82 respiratory transplantation 39
percent_of_cohort percent_of_those_with_condition
1 8.428728242 NA
2 2.156186294 25.5813953
3 4.035335320 47.8759690
4 0.784067743 9.3023256
5 1.970623595 23.3798450
6 13.451988919 NA
7 0.627254195 4.6629104
8 1.706654122 12.6870021
9 1.534159218 11.4047018
10 2.953321834 21.9545366
11 0.726569442 5.4012046
12 6.063457216 45.0748009
13 3.259108254 24.2277055
14 0.708274528 5.2652030
15 14.771836287 NA
16 0.757932152 5.1309271
17 1.853013434 12.5442321
18 11.060582301 74.8761500
19 0.689979614 4.6709130
20 0.770999948 5.2193914
21 0.896450787 6.0686483
22 7.401599498 NA
23 0.028749151 0.3884181
24 2.150959176 29.0607345
25 0.261355914 3.5310734
26 0.326694893 4.4138418
27 0.154199990 2.0833333
28 2.015054101 27.2245763
29 2.375725263 32.0974576
30 0.073179656 0.9887006
31 0.031362710 0.4237288
32 0.120223721 1.6242938
33 0.007840677 0.1059322
34 0.473054205 6.3912429
35 9.889707804 NA
36 9.212795986 93.1553911
37 1.181328733 11.9450317
38 8.904396006 NA
39 0.507030474 5.6941591
40 0.339762689 3.8156736
41 0.133291516 1.4969181
42 2.310386284 25.9465806
43 0.925199937 10.3903728
44 4.887355601 54.8869974
45 0.214311850 2.4068095
46 1.996759187 NA
47 1.680518530 84.1623037
48 0.316240657 15.8376963
49 3.962155664 NA
50 0.028749151 0.7255937
51 0.219538968 5.5408971
52 0.912132142 23.0211082
53 0.117610162 2.9683377
54 0.339762689 8.5751979
55 0.645549109 16.2928760
56 2.482881188 62.6649077
57 0.000000000 NA
58 15.231822696 NA
59 4.618159009 30.3191489
60 3.852386179 25.2916953
61 3.303538759 21.6884008
62 2.177094768 14.2930679
63 3.455125189 22.6835964
64 0.420783022 2.7625257
65 0.381579635 2.5051476
66 0.384193194 2.5223061
67 0.240447441 1.5785861
68 2.216298155 14.5504461
69 7.283989337 NA
70 1.356437196 18.6221744
71 1.638701584 22.4973089
72 2.391406618 32.8310011
73 2.380952381 32.6874776
74 0.567142334 7.7861500
75 0.841566045 11.5536419
76 8.520202812 NA
77 2.854006586 33.4969325
78 1.045423658 12.2699387
79 3.690345513 43.3128834
80 0.057498301 0.6748466
81 2.851393027 33.4662577
82 0.101928807 1.1963190
>
> charlson_results <-
+ comorbidities(data = mdcr,
+ icd.codes = "code",
+ id.vars = "patid",
+ dx.var = "dx",
+ method = "charlson_quan2011",
+ flag.method = 'current',
+ poa = 1)
Warning: Assuming all codes provided are secondary diagnostic codes. Define `primarydx.var` or `primarydx` if this assumption is incorrect.
> summary(charlson_results)
Error in as.data.frame.integer(x[[i]], optional = TRUE) :
row names contain missing values
Calls: summary ... data.frame -> as.data.frame -> as.data.frame.integer
Execution halted
Flavor: r-devel-windows-x86_64
Version: 0.8.0
Check: tests
Result: ERROR
Running 'test-asserts.R' [16s]
Running 'test-charlson.R' [26s]
Running 'test-comorbidities.R' [5s]
Running 'test-data-frame-tools.R' [5s]
Running 'test-elixhauser-example.R' [5s]
Running 'test-elixhauser-poa-na.R' [6s]
Running 'test-elixhauser.R' [4s]
Running 'test-icd_compact_to_full.R' [4s]
Running 'test-internal-data.R' [18s]
Running 'test-is_icd.R' [19s]
Running 'test-locked-bindings.R' [7s]
Running 'test-longitudinal-comorbidities.R' [11s]
Running 'test-longitudinal-pccc-v3.1.R' [5s]
Running 'test-lookup_icd_codes.R' [6s]
Running 'test-pccc-deltas.R' [15s]
Running 'test-pccc.R' [17s]
Running 'test-poa-in-cumulative.R' [4s]
Running 'test-primarydx.R' [5s]
Running 'test-summary-charlson.R' [6s]
Running 'test-summary-elixhauser.R' [6s]
Running 'test-summary-pccc-subconditions.R' [7s]
Running 'test-summary-pccc.R' [9s]
Running 'test-tibble-datatable.R' [11s]
Running 'test-vs-ahrq.R' [6s]
Running 'test-vs-pccc_1.0.7.R' [8s]
Running 'test-zero-row-inputs.R' [5s]
Running 'utilities.R' [0s]
Running the tests in 'tests/test-summary-charlson.R' failed.
Complete output:
> source('utilities.R')
> ################################################################################
> # Tests for summarizing Charlson comorbidities
> library(medicalcoder)
>
> ################################################################################
> # Prepare input with an age variable to exercise age scoring logic
> mdcr$age <- as.integer(substr(as.character(mdcr$patid), 1, 2))
>
> charlson <- comorbidities(
+ data = mdcr,
+ id.vars = "patid",
+ icdv.var = "icdv",
+ icd.codes = "code",
+ dx.var = "dx",
+ method = "charlson_quan2011",
+ flag.method = "current",
+ poa = 1L,
+ primarydx = 0L,
+ age.var = "age"
+ )
>
> summary_current <- summary(charlson)
Error in as.data.frame.integer(x[[i]], optional = TRUE) :
row names contain missing values
Calls: summary ... data.frame -> as.data.frame -> as.data.frame.integer
Execution halted
Flavor: r-devel-windows-x86_64
Version: 0.8.0
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building 'charlson.Rmd' using rmarkdown
Quitting from charlson.Rmd:87-89 [unnamed-chunk-4]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `as.data.frame.integer()`:
! row names contain missing values
---
Backtrace:
▆
1. ├─utils::str(summary(mdcr_results))
2. ├─base::summary(mdcr_results)
3. └─medicalcoder:::summary.medicalcoder_comorbidities(mdcr_results)
4. └─medicalcoder:::.charlson_summary(object)
5. ├─base::merge(...)
6. ├─stats::setNames(...)
7. ├─base::as.data.frame(...)
8. └─base::as.data.frame.table(...)
9. ├─base::eval(ex)
10. │ └─base::eval(ex)
11. └─base::data.frame(...)
12. ├─base::as.data.frame(x[[i]], optional = TRUE)
13. └─base::as.data.frame.integer(x[[i]], optional = TRUE)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'charlson.Rmd' failed with diagnostics:
row names contain missing values
--- failed re-building 'charlson.Rmd'
--- re-building 'comorbidities.Rmd' using rmarkdown
--- finished re-building 'comorbidities.Rmd'
--- re-building 'elixhauser.Rmd' using rmarkdown
--- finished re-building 'elixhauser.Rmd'
--- re-building 'icd.Rmd' using rmarkdown
--- finished re-building 'icd.Rmd'
--- re-building 'pccc.Rmd' using rmarkdown
--- finished re-building 'pccc.Rmd'
SUMMARY: processing the following file failed:
'charlson.Rmd'
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-windows-x86_64