* using log directory ‘/data/gannet/ripley/R/packages/tests-ATLAS/soilKey.Rcheck’
* using R Under development (unstable) (2026-05-19 r90065)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (GCC) 15.2.1 20260123 (Red Hat 15.2.1-7)
    GNU Fortran (GCC) 15.2.1 20260123 (Red Hat 15.2.1-7)
* running under: Fedora Linux 42 (Workstation Edition)
* using session charset: UTF-8
* current time: 2026-05-22 09:53:36 UTC
* using option ‘--no-stop-on-test-error’
* checking for file ‘soilKey/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘soilKey’ version ‘0.9.97’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘soilKey’ can be installed ... [69s/152s] OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [134s/307s] OK
* checking Rd files ... [9s/20s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [8m/23m]
 [8m/23m] ERROR
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(soilKey)
  
  Attaching package: 'soilKey'
  
  The following object is masked from 'package:base':
  
      %||%
  
  > 
  > test_check("soilKey")
  
  -- ClassificationResult (WRB 2022) --
  
  Name: Geric Ferric Rhodic Chromic Ferralsol (Clayic, Humic, Dystric, Ochric,
  Rubic)
  RSG/Order: Ferralsols
  Qualifiers: Geric, Ferric, Rhodic, Chromic, Clayic, Humic, Dystric, Ochric,
  Rubic, FALSE, FALSE, FALSE, FALSE, TRUE, FALSE, FALSE, FALSE, FALSE, FALSE,
  al_ox_pct, fe_ox_pct, phosphate_retention_pct, volcanic_glass_pct, FALSE,
  volcanic_glass_pct, FALSE, FALSE, plinthite_pct, FALSE, plinthite_pct, FALSE,
  plinthite_pct, FALSE, top_cm, bottom_cm, FALSE, TRUE, TRUE, TRUE, FALSE, FALSE,
  redoximorphic_features_pct, FALSE, redoximorphic_features_pct, FALSE, FALSE,
  p_mehlich3_mg_kg, FALSE, p_mehlich3_mg_kg, FALSE, FALSE, FALSE, FALSE, FALSE,
  FALSE, TRUE, FALSE, FALSE, TRUE, TRUE, FALSE, FALSE, FALSE, FALSE, TRUE, FALSE,
  TRUE, FALSE
  Evidence grade: A
  
  -- Ambiguities 
  - TC: Indeterminate -- missing 3 attribute(s): artefacts_pct,
  geomembrane_present, technic_hardmaterial_pct
  - CR: Indeterminate -- missing 1 attribute(s): permafrost_temp_C
  - VR: Indeterminate -- missing 1 attribute(s): slickensides
  - SC: Indeterminate -- missing 1 attribute(s): ec_dS_m
  - PZ: Indeterminate -- missing 2 attribute(s): al_ox_pct, fe_ox_pct
  - PT: Indeterminate -- missing 1 attribute(s): plinthite_pct
  - ST: Indeterminate -- missing 1 attribute(s): redoximorphic_features_pct
  
  -- Missing data that would refine result 
  artefacts_pct, geomembrane_present, technic_hardmaterial_pct,
  permafrost_temp_C, slickensides, ec_dS_m, redoximorphic_features_pct,
  al_ox_pct, fe_ox_pct, phosphate_retention_pct, volcanic_glass_pct,
  plinthite_pct
  
  -- Warnings 
  ! 12 distinct attribute(s) missing across the key trace -- see $missing_data
  
  -- Key trace 
  (16 RSGs tested before assignment)
  1. HS Histosols -- failed
  2. AT Anthrosols -- failed
  3. TC Technosols -- NA (3 attrs missing)
  4. CR Cryosols -- NA (1 attrs missing)
  5. LP Leptosols -- failed
  6. SN Solonetz -- failed
  7. VR Vertisols -- NA (1 attrs missing)
  8. SC Solonchaks -- NA (1 attrs missing)
  9. GL Gleysols -- failed (1 attrs missing)
  10. AN Andosols -- failed (4 attrs missing)
  11. PZ Podzols -- NA (2 attrs missing)
  12. PT Plinthosols -- NA (1 attrs missing)
  13. PL Planosols -- failed
  14. ST Stagnosols -- NA (1 attrs missing)
  15. NT Nitisols -- failed
  16. FR Ferralsols -- PASSED
  
  -- ClassificationResult (WRB 2022) --
  
  Name: Geric Ferric Rhodic Chromic Ferralsol (Clayic, Humic, Dystric, Ochric,
  Rubic)
  RSG/Order: Ferralsols
  Qualifiers: Geric, Ferric, Rhodic, Chromic, Clayic, Humic, Dystric, Ochric,
  Rubic, FALSE, FALSE, FALSE, FALSE, TRUE, FALSE, FALSE, FALSE, FALSE, FALSE,
  al_ox_pct, fe_ox_pct, phosphate_retention_pct, volcanic_glass_pct, FALSE,
  volcanic_glass_pct, FALSE, FALSE, plinthite_pct, FALSE, plinthite_pct, FALSE,
  plinthite_pct, FALSE, top_cm, bottom_cm, FALSE, TRUE, TRUE, TRUE, FALSE, FALSE,
  redoximorphic_features_pct, FALSE, redoximorphic_features_pct, FALSE, FALSE,
  p_mehlich3_mg_kg, FALSE, p_mehlich3_mg_kg, FALSE, FALSE, FALSE, FALSE, FALSE,
  FALSE, TRUE, FALSE, FALSE, TRUE, TRUE, FALSE, FALSE, FALSE, FALSE, TRUE, FALSE,
  TRUE, FALSE
  Evidence grade: A
  
  -- Ambiguities 
  - TC: Indeterminate -- missing 3 attribute(s): artefacts_pct,
  geomembrane_present, technic_hardmaterial_pct
  - CR: Indeterminate -- missing 1 attribute(s): permafrost_temp_C
  - VR: Indeterminate -- missing 1 attribute(s): slickensides
  - SC: Indeterminate -- missing 1 attribute(s): ec_dS_m
  - PZ: Indeterminate -- missing 2 attribute(s): al_ox_pct, fe_ox_pct
  - PT: Indeterminate -- missing 1 attribute(s): plinthite_pct
  - ST: Indeterminate -- missing 1 attribute(s): redoximorphic_features_pct
  
  -- Missing data that would refine result 
  artefacts_pct, geomembrane_present, technic_hardmaterial_pct,
  permafrost_temp_C, slickensides, ec_dS_m, redoximorphic_features_pct,
  al_ox_pct, fe_ox_pct, phosphate_retention_pct, volcanic_glass_pct,
  plinthite_pct
  
  -- Warnings 
  ! 12 distinct attribute(s) missing across the key trace -- see $missing_data
  
  -- Key trace 
  (16 RSGs tested before assignment)
  1. HS Histosols -- failed
  2. AT Anthrosols -- failed
  3. TC Technosols -- NA (3 attrs missing)
  4. CR Cryosols -- NA (1 attrs missing)
  5. LP Leptosols -- failed
  6. SN Solonetz -- failed
  7. VR Vertisols -- NA (1 attrs missing)
  8. SC Solonchaks -- NA (1 attrs missing)
  9. GL Gleysols -- failed (1 attrs missing)
  10. AN Andosols -- failed (4 attrs missing)
  11. PZ Podzols -- NA (2 attrs missing)
  12. PT Plinthosols -- NA (1 attrs missing)
  13. PL Planosols -- failed
  14. ST Stagnosols -- NA (1 attrs missing)
  15. NT Nitisols -- failed
  16. FR Ferralsols -- PASSED
  
  warning: solve(): system is singular; attempting approx solution
  ! No OSSL profiles within 50 km of (lat=60, lon=100). Falling back to the global library.
  Saving _problems/test-v0953-performance-60.R
  
  -- inspect_bdsolos_csv: bdsolos_synth.csv --
  
  i Header line: 1   separator: ,
  i Total columns: 24
  i Mapped to soilKey: 20
  i Unmapped: 3
  
  -- Mapped columns 
  horizonte -> `designation`
  limite_sup -> `top_cm`
  limite_inf -> `bottom_cm`
  matiz_umido -> `munsell_hue_moist`
  valor_umido -> `munsell_value_moist`
  croma_umido -> `munsell_chroma_moist`
  matiz_seco -> `munsell_hue_dry`
  valor_seco -> `munsell_value_dry`
  croma_seco -> `munsell_chroma_dry`
  argila -> `clay_pct`
  silte -> `silt_pct`
  areia -> `sand_pct`
  ph_em_agua -> `ph_h2o`
  ph_em_kcl -> `ph_kcl`
  c_org -> `oc_pct`
  ca_troc -> `ca_cmol`
  mg_troc -> `mg_cmol`
  k_troc -> `k_cmol`
  al_troc -> `al_cmol`
  p_assim -> `p_mehlich3_mg_kg`
  
  -- Unmapped columns (will be ignored) 
  id_perfil
  latitude
  longitude
  
  -- Munsell coverage 
  matiz_umido: FOUND
  valor_umido: FOUND
  croma_umido: FOUND
  
  -- Taxon column (surveyor's SiBCS reference) 
  classificacao
  i fread failed on this file; falling back to utils::read.csv2 (slower).
  [ FAIL 1 | WARN 12 | SKIP 73 | PASS 4211 ]
  
  ══ Skipped tests (73) ══════════════════════════════════════════════════════════
  • BDsolos RJ.csv not available (5): 'test-v0983-argic-films-audit.R:163:3',
    'test-v0983-argic-films-audit.R:183:3',
    'test-v0986-ferralic-engine-aqp-fallback.R:91:3',
    'test-v0989-texture-engine-fallback.R:83:3',
    'test-v0990-argic-designation-inference.R:144:3'
  • B_incipiente nao passou para esta fixture; carater_cambissolico depende disso
    (1): 'test-sibcs-pendentes-v072.R:494:5'
  • Bundled AfSP sample not present (4):
    'test-v0977-afsp-and-vertisol-routing.R:77:3',
    'test-v0977-afsp-and-vertisol-routing.R:94:3',
    'test-v0977-afsp-and-vertisol-routing.R:119:3',
    'test-v0977-afsp-and-vertisol-routing.R:136:3'
  • Bundled KSSL sample not present (3): 'test-v0974-usda-wrb-crosswalk.R:108:3',
    'test-v0974-usda-wrb-crosswalk.R:127:3',
    'test-v0974-usda-wrb-crosswalk.R:151:3'
  • Bundled KSSL+NASIS sample not present (5): 'test-v0975-kssl-nasis.R:7:3',
    'test-v0975-kssl-nasis.R:25:3', 'test-v0975-kssl-nasis.R:46:3',
    'test-v0975-kssl-nasis.R:65:3', 'test-v0975-kssl-nasis.R:82:3'
  • Bundled stratified WoSIS sample not present (4):
    'test-v0973-wosis-stratified.R:7:3', 'test-v0973-wosis-stratified.R:26:3',
    'test-v0973-wosis-stratified.R:46:3', 'test-v0973-wosis-stratified.R:68:3'
  • DT is installed or shiny is missing -- skip this branch (1):
    'test-v0939-shiny-app.R:13:5'
  • ESDB raster root not found. Set SOILKEY_ESDB_RASTER_ROOT to test. (8):
    'test-v0944-esdb-raster.R:33:3', 'test-v0944-esdb-raster.R:44:3',
    'test-v0944-esdb-raster.R:54:3', 'test-v0944-esdb-raster.R:61:3',
    'test-v0944-esdb-raster.R:71:3', 'test-v0944-esdb-raster.R:78:3',
    'test-v0944-esdb-raster.R:84:3', 'test-v0944-esdb-raster.R:94:3'
  • Live BDsolos test gated by SOILKEY_NETWORK_TESTS env var (1):
    'test-v0955-bdsolos.R:434:5'
  • Live test gated by AGROAPI_TOKEN + SOILKEY_NETWORK_TESTS env vars (1):
    'test-v0954-smartsolos-api.R:269:5'
  • Network tests disabled. Set SOILKEY_NETWORK_TESTS=1 to enable. (1):
    'test-v0948-spatial-lookups.R:151:3'
  • On CRAN (1): 'test-report.R:176:3'
  • Repo root not found (8): 'test-v0951-docker-ci.R:34:3',
    'test-v0951-docker-ci.R:45:3', 'test-v0951-docker-ci.R:56:3',
    'test-v0951-docker-ci.R:67:3', 'test-v0951-docker-ci.R:79:3',
    'test-v0951-docker-ci.R:93:3', 'test-v0952-vignette-pt.R:23:3',
    'test-v0952-vignette-pt.R:43:3'
  • Repo root not found from test working directory (1):
    'test-v0951-docker-ci.R:27:3'
  • afsp_sample not bundled (1): 'test-v0985-andisol-buried-extend.R:225:3'
  • afsp_sample not present locally; run download_extdata_cache() (1):
    'test-v0994-lazy-fetch.R:37:7'
  • argic helper does not match this fixture; depth bound check passed (1):
    'test-usda-spodosols-v085.R:142:5'
  • chromote installed -- cannot exercise the missing-pkg path (1):
    'test-v0955-bdsolos.R:220:5'
  • ellmer is installed; cannot exercise the missing-package error path (1):
    'test-vlm-providers.R:22:3'
  • file.exists(file.path("inst", "extdata", "canonical", "WRB_4th_2022.rda")) is
    not TRUE (1): 'test-v0964-qualifiers.R:258:3'
  • horizonte_A_humico nao casa (1): 'test-sibcs-argissolos-sg-pbac-v074.R:149:5'
  • horizonte_A_humico nao casa com fixture; skip downstream check (1):
    'test-sibcs-argissolos-sg-pbac-v074.R:68:5'
  • jsonlite is installed; cannot exercise the missing-pkg path (1):
    'test-v0971-redape.R:156:3'
  • kssl_nasis_sample not bundled (1): 'test-v0984-spodic-engine-aware.R:172:3'
  • kssl_nasis_sample.rds not bundled (3):
    'test-v0991-kssl-reference-alias.R:27:3',
    'test-v0991-kssl-reference-alias.R:40:3',
    'test-v0991-kssl-reference-alias.R:69:3'
  • kssl_sample.rds not bundled (1): 'test-v0991-kssl-reference-alias.R:14:3'
  • load_afsp_sample cache not present locally (1):
    'test-v0994-lazy-fetch.R:64:7'
  • munsellinterpol installed -- can't exercise the missing-pkg path (1):
    'test-v0947-munsell-prediction.R:137:5'
  • nem concrecionario nem litoplintico passam para esta fixture (1):
    'test-sibcs-argissolos-sg-pva-v074.R:46:5'
  • pls is installed -- cannot exercise the missing-package path (1):
    'test-v0946-pls-training.R:32:5'
  • redape_geotab dataset not available (3): 'test-v0981-sibcs-subordem.R:93:3',
    'test-v0981-sibcs-subordem.R:114:3', 'test-v0981-sibcs-subordem.R:131:3'
  • rmarkdown is installed; cannot exercise the missing-package path (1):
    'test-report.R:164:3'
  • shiny is installed -- can't exercise the missing-package path (1):
    'test-v0939-shiny-app.R:5:5'
  • wosis_stratified_sample.rds not bundled (5):
    'test-v0988-wosis-reference-alias.R:12:3',
    'test-v0988-wosis-reference-alias.R:23:3',
    'test-v0988-wosis-reference-alias.R:34:3',
    'test-v0988-wosis-reference-alias.R:64:3',
    'test-v0991-kssl-reference-alias.R:52:3'
  • {febr} is not installed (1): 'test-v0957-febr.R:149:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-v0953-performance.R:60:5'): median classification time is sane (<= 5s/pedon on dev hardware) ──
  Expected `row$median_seconds` < 5.
  Actual comparison: 9.3 >= 5.0
  Difference: 4.3 >= 0
  
  [ FAIL 1 | WARN 12 | SKIP 73 | PASS 4211 ]
  Error:
  ! Test failures.
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [101s/228s] OK
* checking PDF version of manual ... [78s/205s] OK
* checking HTML version of manual ... [88s/204s] OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE

Status: 1 ERROR
See
  ‘/data/gannet/ripley/R/packages/tests-ATLAS/soilKey.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 46:21.80, 1020.46 + 38.50