Running ‘testthat.R’ [11s/12s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > require(testthat)
  Loading required package: testthat
  > require(Rdiagnosislist)
  Loading required package: Rdiagnosislist
  Loading required package: readxl
  
  Attaching package: 'Rdiagnosislist'
  
  The following object is masked from 'package:stats':
  
      decompose
  
  The following objects are masked from 'package:base':
  
      intersect, setdiff, union
  
  > require(bit64)
  Loading required package: bit64
  Loading required package: bit
  
  Attaching package: 'bit'
  
  The following object is masked from 'package:base':
  
      xor
  
  Attaching package bit64
  package:bit64 (c) 2011-2017 Jens Oehlschlaegel
  creators: integer64 runif64 seq :
  coercion: as.integer64 as.vector as.logical as.integer as.double as.character as.bitstring
  logical operator: ! & | xor != == < <= >= >
  arithmetic operator: + - * / %/% %% ^
  math: sign abs sqrt log log2 log10
  math: floor ceiling trunc round
  querying: is.integer64 is.vector [is.atomic} [length] format print str
  values: is.na is.nan is.finite is.infinite
  aggregation: any all min max range sum prod
  cumulation: diff cummin cummax cumsum cumprod
  access: length<- [ [<- [[ [[<-
  combine: c rep cbind rbind as.data.frame
  WARNING don't use as subscripts
  WARNING semantics differ from integer
  for more help type ?bit64
  
  Attaching package: 'bit64'
  
  The following object is masked from 'package:utils':
  
      hashtab
  
  The following objects are masked from 'package:base':
  
      %in%, :, colSums, is.double, match, order, rank, rowSums
  
  > require(data.table)
  Loading required package: data.table
  
  Attaching package: 'data.table'
  
  The following object is masked from 'package:bit':
  
      setattr
  
  > 
  > test_check("Rdiagnosislist")
                 NAME NROW NCOL MB                                 COLS
   1:            BODY  160    4  0  conceptId,term,laterality,multipart
   2: BODY_LATERALITY    0    3  0 conceptId,laterality,nonlat_parentId
   3:          CAUSES   84    2  0                       conceptId,term
   4:        FINDINGS  464    2  0                       conceptId,term
   5:      LATERALITY   25    2  0                       conceptId,term
   6:           MORPH    0    2  0                       conceptId,term
   7:      OTHERCAUSE   36    3  0               conceptId,term,semType
   8:         OVERLAP    0    2  0                    findingId,otherId
   9:            QUAL    2    2  0                       conceptId,term
  10:         SEMTYPE  236    2  0                    conceptId,semType
  11:        SEVERITY    0    2  0                       conceptId,term
  12:           STAGE    0    2  0                       conceptId,term
  13:      TRANSITIVE 5094    2  0              ancestorId,descendantId
               KEY
   1:         term
   2:    conceptId
   3:         term
   4:         term
   5:         term
   6:         term
   7:         term
   8:      otherId
   9:         term
  10:    conceptId
  11:         term
  12:         term
  13: descendantId
  Total: 0MB using type_size
  
  SNOMED CT tables loaded into environment:
                   NAME NROW NCOL MB
  1:            CONCEPT  509    5  0
  2:        DESCRIPTION 1596    9  0
  3:        EXTENDEDMAP  915   12  0
  4:            HISTORY  199   14  0
  5:              QUERY 1767    3  0
  6:             REFSET  428    5  0
  7:       RELATIONSHIP 1915   10  0
  8:          SIMPLEMAP  124    6  0
  9: STATEDRELATIONSHIP  329   10  0
                                                                                 COLS
  1:                              id,effectiveTime,active,moduleId,definitionStatusId
  2:                      id,effectiveTime,active,moduleId,conceptId,languageCode,...
  3:        effectiveTime,active,moduleId,refsetId,referencedComponentId,mapGroup,...
  4: OLDCONCEPTID,OLDCONCEPTSTATUS,NEWCONCEPTID,NEWCONCEPTSTATUS,PATH,ISAMBIGUOUS,...
  5:                                                 supertypeId,subtypeId,provenance
  6:                     effectiveTime,active,moduleId,refsetId,referencedComponentId
  7:                      id,effectiveTime,active,moduleId,sourceId,destinationId,...
  8:           effectiveTime,active,moduleId,refsetId,referencedComponentId,mapTarget
  9:                      id,effectiveTime,active,moduleId,sourceId,destinationId,...
                                                          KEY
  1:                                                       id
  2:                                                       id
  3: mapPriority,mapCategoryId,refsetId,referencedComponentId
  4:                                NEWCONCEPTID,OLDCONCEPTID
  5:                                    supertypeId,subtypeId
  6:                           refsetId,referencedComponentId
  7:                                   sourceId,typeId,active
  8:                 refsetId,mapTarget,referencedComponentId
  9:                                   sourceId,typeId,active
  Total: 0MB using type_size
  Error in get(FILENAMES[thispattern == pattern]$table, envir = SNOMED,  : 
    object 'CONCEPT' not found
  Error in get(FILENAMES[thispattern == pattern]$table, envir = SNOMED,  : 
    object 'RELATIONSHIP' not found
  Error in get(FILENAMES[thispattern == pattern]$table, envir = SNOMED,  : 
    object 'SIMPLEMAP' not found
  Error in get(FILENAMES[thispattern == pattern]$table, envir = SNOMED,  : 
    object 'REFSET' not found
  
  SNOMED CT tables loaded into environment:
                   NAME NROW NCOL MB
  1:            CONCEPT  509    5  0
  2:        DESCRIPTION 1596    9  0
  3:        EXTENDEDMAP  915   12  0
  4:            HISTORY  199   14  0
  5:              QUERY 1767    3  0
  6:             REFSET  428    5  0
  7:       RELATIONSHIP 1915   10  0
  8:          SIMPLEMAP  124    6  0
  9: STATEDRELATIONSHIP  329   10  0
                                                                                 COLS
  1:                              id,effectiveTime,active,moduleId,definitionStatusId
  2:                      id,effectiveTime,active,moduleId,conceptId,languageCode,...
  3:        effectiveTime,active,moduleId,refsetId,referencedComponentId,mapGroup,...
  4: OLDCONCEPTID,OLDCONCEPTSTATUS,NEWCONCEPTID,NEWCONCEPTSTATUS,PATH,ISAMBIGUOUS,...
  5:                                                 supertypeId,subtypeId,provenance
  6:                     effectiveTime,active,moduleId,refsetId,referencedComponentId
  7:                      id,effectiveTime,active,moduleId,sourceId,destinationId,...
  8:           effectiveTime,active,moduleId,refsetId,referencedComponentId,mapTarget
  9:                      id,effectiveTime,active,moduleId,sourceId,destinationId,...
                                                          KEY
  1:                                                       id
  2:                                                       id
  3: mapPriority,mapCategoryId,refsetId,referencedComponentId
  4:                                NEWCONCEPTID,OLDCONCEPTID
  5:                                    supertypeId,subtypeId
  6:                           refsetId,referencedComponentId
  7:                                   sourceId,typeId,active
  8:                 refsetId,mapTarget,referencedComponentId
  9:                                   sourceId,typeId,active
  Total: 0MB using type_size
  Error in get(FILENAMES[thispattern == pattern]$table, envir = SNOMED,  : 
    object 'CONCEPT' not found
  Error in get(FILENAMES[thispattern == pattern]$table, envir = SNOMED,  : 
    object 'SIMPLEMAP' not found
  Error in get(FILENAMES[thispattern == pattern]$table, envir = SNOMED,  : 
    object 'REFSET' not found
  [ FAIL 10 | WARN 0 | SKIP 0 | PASS 131 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test_loadSNOMED.R:17:2'): Test exporting and reloading sample SNOMED dictionary ──
  TEST$DESCRIPTION not equal to TEST2$DESCRIPTION.
  Attributes: < Component "index": Attributes: < Component "__conceptId__typeId__term__active": Attributes: < Component "maxgrpn": Mean relative difference: 1 > > >
  Attributes: < Component "index": Attributes: < Component "__conceptId__typeId__term__active": Attributes: < Component "starts": Numeric: lengths (1596, 1595) differ > > >
  Attributes: < Component "index": Attributes: < Component "__conceptId__typeId__term__active": Mean relative difference: 0.1006897 > >
  Attributes: < Component "index": Attributes: < Component "__term__active": Attributes: < Component "starts": Numeric: lengths (1571, 1583) differ > > >
  Attributes: < Component "index": Attributes: < Component "__term__active": Mean relative difference: 0.6121131 > >
  Attributes: < Component "index": Attributes: < Component "__typeId__active": Attributes: < Component "maxgrpn": Mean relative difference: 0.6207289 > > >
  Attributes: < Component "index": Attributes: < Component "__typeId__active": Attributes: < Component "starts": Numeric: lengths (4, 19) differ > > >
  Attributes: < Component "index": Attributes: < Component "__typeId__active": Mean relative difference: 0.7451808 > >
  ── Failure ('test_loadSNOMED.R:18:2'): Test exporting and reloading sample SNOMED dictionary ──
  TEST$RELATIONSHIP not equal to TEST2$RELATIONSHIP.
  Attributes: < Component "index": Attributes: < Component "__destinationId__sourceId__typeId__active": Attributes: < Component "maxgrpn": Mean relative difference: 0.5 > > >
  Attributes: < Component "index": Attributes: < Component "__destinationId__sourceId__typeId__active": Attributes: < Component "starts": Numeric: lengths (1730, 1773) differ > > >
  Attributes: < Component "index": Attributes: < Component "__destinationId__sourceId__typeId__active": Mean relative difference: 0.001708698 > >
  Attributes: < Component "index": Attributes: < Component "__destinationId__typeId__active": Attributes: < Component "maxgrpn": Mean relative difference: 0.5352113 > > >
  Attributes: < Component "index": Attributes: < Component "__destinationId__typeId__active": Attributes: < Component "starts": Numeric: lengths (474, 827) differ > > >
  Attributes: < Component "index": Attributes: < Component "__destinationId__typeId__active": Mean relative difference: 0.5704542 > >
  Attributes: < Component "index": Attributes: < Component "__sourceId__destinationId__typeId__active": Attributes: < Component "maxgrpn": Mean relative difference: 0.5 > > >
  Attributes: < Component "index": Attributes: < Component "__sourceId__destinationId__typeId__active": Attributes: < Component "starts": Numeric: lengths (1730, 1773) differ > > >
  Attributes: < Component "index": Attributes: < Component "__sourceId__destinationId__typeId__active": Mean relative difference: 0.001708698 > >
  ── Failure ('test_loadSNOMED.R:19:2'): Test exporting and reloading sample SNOMED dictionary ──
  TEST$STATEDRELATIONSHIP not equal to TEST2$STATEDRELATIONSHIP.
  Attributes: < Component "index": Attributes: < Component "__destinationId__sourceId__typeId__active": Mean relative difference: 0.004654771 > >
  Attributes: < Component "index": Attributes: < Component "__destinationId__typeId__active": Attributes: < Component "maxgrpn": Mean relative difference: 0.4666667 > > >
  Attributes: < Component "index": Attributes: < Component "__destinationId__typeId__active": Attributes: < Component "starts": Numeric: lengths (132, 177) differ > > >
  Attributes: < Component "index": Attributes: < Component "__destinationId__typeId__active": Mean relative difference: 0.3882823 > >
  Attributes: < Component "index": Attributes: < Component "__sourceId__destinationId__typeId__active": Mean relative difference: 0.004654771 > >
  ── Failure ('test_loadSNOMED.R:20:2'): Test exporting and reloading sample SNOMED dictionary ──
  TEST$REFSET not equal to TEST2$REFSET.
  Column 'active': 427 element mismatches
  ── Failure ('test_loadSNOMED.R:21:2'): Test exporting and reloading sample SNOMED dictionary ──
  TEST$SIMPLEMAP not equal to TEST2$SIMPLEMAP.
  Column 'active': 124 element mismatches
  ── Failure ('test_loadSNOMED.R:56:2'): Test exporting and reloading multiple files ──
  TEST$DESCRIPTION not equal to TEST2$DESCRIPTION.
  Attributes: < Component "index": Attributes: < Component "__conceptId__typeId__term__active": Attributes: < Component "maxgrpn": Mean relative difference: 1 > > >
  Attributes: < Component "index": Attributes: < Component "__conceptId__typeId__term__active": Attributes: < Component "starts": Numeric: lengths (1596, 1595) differ > > >
  Attributes: < Component "index": Attributes: < Component "__conceptId__typeId__term__active": Mean relative difference: 0.1006897 > >
  Attributes: < Component "index": Attributes: < Component "__term__active": Attributes: < Component "starts": Numeric: lengths (1571, 1583) differ > > >
  Attributes: < Component "index": Attributes: < Component "__term__active": Mean relative difference: 0.6121131 > >
  Attributes: < Component "index": Attributes: < Component "__typeId__active": Attributes: < Component "maxgrpn": Mean relative difference: 0.6207289 > > >
  Attributes: < Component "index": Attributes: < Component "__typeId__active": Attributes: < Component "starts": Numeric: lengths (4, 19) differ > > >
  Attributes: < Component "index": Attributes: < Component "__typeId__active": Mean relative difference: 0.7451808 > >
  ── Failure ('test_loadSNOMED.R:57:2'): Test exporting and reloading multiple files ──
  TEST$RELATIONSHIP not equal to TEST2$RELATIONSHIP.
  Attributes: < Component "index": Attributes: < Component "__destinationId__sourceId__typeId__active": Attributes: < Component "maxgrpn": Mean relative difference: 0.6428571 > > >
  Attributes: < Component "index": Attributes: < Component "__destinationId__sourceId__typeId__active": Attributes: < Component "starts": Numeric: lengths (1730, 1859) differ > > >
  Attributes: < Component "index": Attributes: < Component "__destinationId__sourceId__typeId__active": Mean relative difference: 0.001962479 > >
  Attributes: < Component "index": Attributes: < Component "__destinationId__typeId__active": Attributes: < Component "maxgrpn": Mean relative difference: 0.8450704 > > >
  Attributes: < Component "index": Attributes: < Component "__destinationId__typeId__active": Attributes: < Component "starts": Numeric: lengths (474, 1499) differ > > >
  Attributes: < Component "index": Attributes: < Component "__destinationId__typeId__active": Mean relative difference: 0.5451718 > >
  Attributes: < Component "index": Attributes: < Component "__sourceId__destinationId__typeId__active": Attributes: < Component "maxgrpn": Mean relative difference: 0.6428571 > > >
  Attributes: < Component "index": Attributes: < Component "__sourceId__destinationId__typeId__active": Attributes: < Component "starts": Numeric: lengths (1730, 1859) differ > > >
  Attributes: < Component "index": Attributes: < Component "__sourceId__destinationId__typeId__active": Mean relative difference: 0.001962479 > >
  ── Failure ('test_loadSNOMED.R:58:2'): Test exporting and reloading multiple files ──
  TEST$STATEDRELATIONSHIP not equal to TEST2$STATEDRELATIONSHIP.
  Attributes: < Component "index": Attributes: < Component "__destinationId__typeId__active": Attributes: < Component "maxgrpn": Mean relative difference: 0.6666667 > > >
  Attributes: < Component "index": Attributes: < Component "__destinationId__typeId__active": Attributes: < Component "starts": Numeric: lengths (132, 294) differ > > >
  ── Failure ('test_loadSNOMED.R:59:2'): Test exporting and reloading multiple files ──
  TEST$REFSET not equal to TEST2$REFSET.
  Column 'active': 427 element mismatches
  ── Failure ('test_loadSNOMED.R:60:2'): Test exporting and reloading multiple files ──
  TEST$SIMPLEMAP not equal to TEST2$SIMPLEMAP.
  Column 'active': 124 element mismatches
  
  [ FAIL 10 | WARN 0 | SKIP 0 | PASS 131 ]
  Error: Test failures
  Execution halted