Running ‘testthat.R’ [36s/40s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  > library(HealthMarkers)
  > 
  > test_check("HealthMarkers")
  charlson_index(): reading input 'df' — 1 rows × 19 variables
  charlson_index(): reading input 'df' — 1 rows × 19 variables
  charlson_index(): reading input 'data' — 1 rows × 1 variables
  frailty_index(): preparing inputs (1 rows, 2 deficits)
  frailty_index(): col_map: a, b
  frailty_index(): results: di range [0.500, 0.500] (1 rows, 2 deficits)
  Saving _problems/test-frailty_index-19.R
  kidney_failure_risk(): reading input 'df' — 1 rows × 4 variables
  kidney_failure_risk(): col_map: age -> 'age', sex -> 'sex', eGFR -> 'eGFR', UACR -> 'UACR'
  kidney_failure_risk(): computing markers:
    KFRE_2yr  [age, sex, eGFR, UACR -- 2-year kidney failure risk]
    KFRE_5yr  [age, sex, eGFR, UACR -- 5-year kidney failure risk]
  kidney_failure_risk(): results: KFRE_2yr 1/1, KFRE_5yr 1/1
  obesity_indices(): reading input 'base_df' — 2 rows × 5 variables
  obesity_indices(): col_map: weight -> 'wt', height -> 'ht', waist -> 'waist', hip -> 'hip'
  obesity_indices(): computing markers:
    BMI, BMI_cat, WHR, WHtR, AVI, BAI, ABSI, BRI, CI
  obesity_indices(): results: weight_kg 2/2, height_m 2/2, BMI 2/2, BMI_cat 2/2, WHR 2/2, waist_to_height_ratio 2/2, waist_to_BMI_ratio 2/2, weight_to_height_ratio 2/2, AVI 2/2, BAI 2/2, ABSI 2/2, BRI 2/2, CI 2/2
  psych_markers(): preparing inputs
  phq9_score(): preparing inputs
  psych_markers(): results: 1 rows, 31 new columns
  [ FAIL 1 | WARN 1 | SKIP 574 | PASS 55 ]
  
  ══ Skipped tests (574) ═════════════════════════════════════════════════════════
  • On CRAN (574): 'test-adipo_is.R:36:3', 'test-adipo_is.R:43:3',
    'test-adipo_is.R:57:3', 'test-adipo_is.R:64:3', 'test-adipo_is.R:76:3',
    'test-adipo_is.R:88:3', 'test-adipo_is.R:101:3', 'test-adipo_is.R:111:3',
    'test-adipo_is.R:129:3', 'test-adipo_is.R:151:3', 'test-adipo_is.R:161:3',
    'test-adipo_is.R:176:3', 'test-adipo_is.R:183:3', 'test-adipo_is.R:190:3',
    'test-adipo_is.R:202:3', 'test-adipo_is.R:213:3', 'test-adipo_is.R:221:3',
    'test-adiposity_sds.R:13:3', 'test-adiposity_sds.R:22:3',
    'test-adiposity_sds.R:30:3', 'test-adiposity_sds.R:39:3',
    'test-adiposity_sds.R:47:3', 'test-adiposity_sds.R:60:3',
    'test-adiposity_sds.R:68:3', 'test-adiposity_sds.R:76:3',
    'test-adiposity_sds.R:85:3', 'test-adiposity_sds.R:92:3',
    'test-adiposity_sds.R:100:3', 'test-adiposity_sds.R:109:3',
    'test-adiposity_sds_strat.R:21:3', 'test-adiposity_sds_strat.R:38:3',
    'test-adiposity_sds_strat.R:51:3', 'test-adiposity_sds_strat.R:64:3',
    'test-adiposity_sds_strat.R:77:3', 'test-adiposity_sds_strat.R:90:3',
    'test-adiposity_sds_strat.R:103:3', 'test-adiposity_sds_strat.R:119:3',
    'test-adiposity_sds_strat.R:130:3', 'test-adiposity_sds_strat.R:143:3',
    'test-adiposity_sds_strat.R:155:3', 'test-adiposity_sds_strat.R:165:3',
    'test-adiposity_sds_strat.R:180:3', 'test-adiposity_sds_strat.R:191:3',
    'test-adiposity_sds_strat.R:201:3', 'test-adiposity_sds_strat.R:210:3',
    'test-allostatic_load.R:7:3', 'test-allostatic_load.R:21:3',
    'test-allostatic_load.R:29:3', 'test-allostatic_load.R:42:3',
    'test-allostatic_load.R:52:3', 'test-allostatic_load.R:60:3',
    'test-allostatic_load.R:69:3', 'test-allostatic_load.R:77:3',
    'test-allostatic_load.R:85:3', 'test-allostatic_load.R:95:3',
    'test-allostatic_load.R:107:3', 'test-alm_bmi_index.R:6:3',
    'test-alm_bmi_index.R:27:3', 'test-alm_bmi_index.R:36:3',
    'test-alm_bmi_index.R:45:3', 'test-alm_bmi_index.R:59:3',
    'test-alm_bmi_index.R:85:3', 'test-alm_bmi_index.R:133:3',
    'test-alm_bmi_index.R:147:3', 'test-alm_bmi_index.R:168:3',
    'test-alm_bmi_index.R:182:3', 'test-atherogenic_indices.R:8:3',
    'test-atherogenic_indices.R:22:3', 'test-atherogenic_indices.R:30:3',
    'test-atherogenic_indices.R:37:3', 'test-atherogenic_indices.R:44:3',
    'test-atherogenic_indices.R:53:3', 'test-atherogenic_indices.R:60:3',
    'test-atherogenic_indices.R:71:3', 'test-atherogenic_indices.R:81:3',
    'test-bode_index.R:6:3', 'test-bode_index.R:11:3', 'test-bode_index.R:18:3',
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    'test-bode_index.R:62:3', 'test-bode_index.R:82:3', 'test-bode_index.R:94:3',
    'test-bode_index.R:113:3', 'test-bode_index.R:135:3',
    'test-bode_index.R:150:3', 'test-bode_index.R:163:3',
    'test-bode_index.R:171:3', 'test-bone_markers.R:32:3',
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    'test-bone_markers.R:122:3', 'test-bone_markers.R:130:3',
    'test-calc_sds.R:40:3', 'test-calc_sds.R:68:3', 'test-calc_sds.R:107:3',
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    'test-charlson_index.R:155:3', 'test-ckd_stage.R:2:3',
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    'test-ckd_stage.R:42:3', 'test-ckd_stage.R:52:3', 'test-ckd_stage.R:61:3',
    'test-ckd_stage.R:71:3', 'test-ckd_stage.R:81:3',
    'test-corrected_calcium.R:6:3', 'test-corrected_calcium.R:36:3',
    'test-corrected_calcium.R:47:3', 'test-corrected_calcium.R:76:3',
    'test-corrected_calcium.R:86:3', 'test-corrected_calcium.R:101:3',
    'test-corrected_calcium.R:124:3', 'test-corrected_calcium.R:137:3',
    'test-corrected_calcium.R:149:3', 'test-corrected_calcium.R:163:3',
    'test-corrected_calcium.R:172:3', 'test-corrected_calcium.R:181:3',
    'test-corrected_calcium.R:190:3', 'test-cvd_risk.R:22:3',
    'test-cvd_risk.R:28:3', 'test-cvd_risk.R:37:3', 'test-cvd_risk.R:47:3',
    'test-cvd_risk.R:59:3', 'test-cvd_risk.R:71:3', 'test-cvd_risk.R:88:3',
    'test-cvd_risk.R:97:3', 'test-cvd_risk.R:103:3', 'test-cvd_risk.R:116:3',
    'test-cvd_risk.R:125:3', 'test-cvd_risk.R:131:3', 'test-cvd_risk.R:138:3',
    'test-cvd_risk.R:148:3', 'test-cvd_risk.R:159:3', 'test-cvd_risk.R:168:3',
    'test-cvd_risk.R:176:3', 'test-cvd_risk.R:182:3', 'test-cvd_risk.R:192:3',
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    'test-cvd_risk.R:226:3', 'test-cvd_risk.R:236:3', 'test-cvd_risk.R:243:3',
    'test-cvd_risk.R:251:3', 'test-cvd_risk.R:258:3', 'test-cvd_risk.R:265:3',
    'test-fasting_is.R:4:3', 'test-fasting_is.R:12:3', 'test-fasting_is.R:35:3',
    'test-fasting_is.R:45:3', 'test-fasting_is.R:78:3', 'test-fasting_is.R:85:3',
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    'test-frailty_index.R:131:3', 'test-frax_score.R:11:3',
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    'test-pulmo_markers.R:127:3', 'test-pulmo_markers.R:141:3',
    'test-pulmo_markers.R:152:3', 'test-pulmo_markers.R:163:3',
    'test-pulmo_markers.R:173:3', 'test-pulmo_markers.R:184:3',
    'test-pulmo_markers.R:199:3', 'test-renal_markers.R:18:3',
    'test-renal_markers.R:28:3', 'test-renal_markers.R:38:3',
    'test-renal_markers.R:47:3', 'test-renal_markers.R:59:3',
    'test-renal_markers.R:76:3', 'test-renal_markers.R:87:3',
    'test-renal_markers.R:99:3', 'test-renal_markers.R:119:3',
    'test-saliva_markers.R:7:3', 'test-saliva_markers.R:32:3',
    'test-saliva_markers.R:61:3', 'test-saliva_markers.R:77:3',
    'test-saliva_markers.R:92:3', 'test-saliva_markers.R:107:3',
    'test-saliva_markers.R:122:3', 'test-saliva_markers.R:137:3',
    'test-sarc_f_score.R:6:3', 'test-sarc_f_score.R:21:3',
    'test-sarc_f_score.R:30:3', 'test-sarc_f_score.R:39:3',
    'test-sarc_f_score.R:51:3', 'test-sarc_f_score.R:79:3',
    'test-sarc_f_score.R:94:3', 'test-sarc_f_score.R:111:3',
    'test-sarc_f_score.R:132:3', 'test-spirometry_markers.R:15:3',
    'test-spirometry_markers.R:41:3', 'test-spirometry_markers.R:50:3',
    'test-spirometry_markers.R:59:3', 'test-spirometry_markers.R:87:3',
    'test-spirometry_markers.R:99:3', 'test-spirometry_markers.R:123:3',
    'test-spirometry_markers.R:135:3', 'test-spirometry_markers.R:150:3',
    'test-spirometry_markers.R:161:3', 'test-spirometry_markers.R:174:3',
    'test-sweat_markers.R:6:3', 'test-sweat_markers.R:38:3',
    'test-sweat_markers.R:62:3', 'test-sweat_markers.R:80:3',
    'test-sweat_markers.R:98:3', 'test-sweat_markers.R:116:3',
    'test-sweat_markers.R:136:3', 'test-sweat_markers.R:152:3',
    'test-tracer_dxa_is.R:7:3', 'test-tracer_dxa_is.R:38:3',
    'test-tracer_dxa_is.R:57:3', 'test-tracer_dxa_is.R:110:3',
    'test-tracer_dxa_is.R:141:3', 'test-tracer_dxa_is.R:165:3',
    'test-tracer_dxa_is.R:189:3', 'test-tracer_dxa_is.R:212:3',
    'test-tracer_dxa_is.R:235:3', 'test-urine_markers.R:6:3',
    'test-urine_markers.R:27:3', 'test-urine_markers.R:73:3',
    'test-urine_markers.R:96:3', 'test-urine_markers.R:108:3',
    'test-urine_markers.R:121:3', 'test-urine_markers.R:137:3',
    'test-urine_markers.R:149:3', 'test-urine_markers.R:168:3',
    'test-urine_markers.R:180:3', 'test-utils_helpers.R:5:3',
    'test-utils_helpers.R:20:3', 'test-utils_helpers.R:36:3',
    'test-utils_helpers.R:49:3', 'test-utils_helpers.R:61:3',
    'test-utils_helpers.R:71:3', 'test-utils_helpers.R:80:3',
    'test-utils_helpers.R:90:3', 'test-utils_helpers.R:99:3',
    'test-utils_helpers.R:108:3', 'test-utils_helpers.R:117:3',
    'test-utils_helpers.R:126:3', 'test-utils_helpers.R:136:3',
    'test-utils_helpers.R:145:3', 'test-utils_helpers.R:154:3',
    'test-utils_helpers.R:162:3', 'test-utils_helpers.R:170:3',
    'test-utils_infer_cols.R:23:3', 'test-utils_infer_cols.R:33:3',
    'test-utils_infer_cols.R:40:3', 'test-utils_infer_cols.R:60:3',
    'test-utils_infer_cols.R:67:3', 'test-validate_inputs.R:9:3',
    'test-validate_inputs.R:17:3', 'test-validate_inputs.R:26:3',
    'test-vitamin_d_status.R:6:3', 'test-vitamin_d_status.R:16:3',
    'test-vitamin_d_status.R:25:3', 'test-vitamin_d_status.R:34:3',
    'test-vitamin_d_status.R:40:3', 'test-vitamin_d_status.R:58:3',
    'test-vitamin_d_status.R:70:3', 'test-vitamin_d_status.R:78:3',
    'test-vitamin_d_status.R:92:3', 'test-vitamin_markers.R:25:3',
    'test-vitamin_markers.R:33:3', 'test-vitamin_markers.R:42:3',
    'test-vitamin_markers.R:58:3', 'test-vitamin_markers.R:72:3',
    'test-vitamin_markers.R:87:3', 'test-vitamin_markers.R:97:3',
    'test-vitamin_markers.R:107:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-frailty_index.R:16:5'): frailty_index errors without di installed ──
  Expected `frailty_index(tibble::tibble(a = 1, b = 0))` to throw a error.
  Backtrace:
      ▆
   1. ├─withr::with_libpaths(...) at test-frailty_index.R:15:3
   2. │ └─base::force(code)
   3. └─testthat::expect_error(...) at test-frailty_index.R:16:5
  
  [ FAIL 1 | WARN 1 | SKIP 574 | PASS 55 ]
  Error:
  ! Test failures.
  Execution halted