* using log directory 'd:/RCompile/CRANincoming/R-devel/Rdiagnosislist.Rcheck'
* using R Under development (unstable) (2025-02-03 r87683 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.3.0
    GNU Fortran (GCC) 13.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* checking for file 'Rdiagnosislist/DESCRIPTION' ... OK
* this is package 'Rdiagnosislist' version '1.4.1'
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [15s] NOTE
Maintainer: 'Anoop D. Shah <anoop@doctors.org.uk>'

Days since last update: 6
* 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 hidden files and directories ... NOTE
Found the following hidden files and directories:
  .github
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.

CRAN-pack does not know about
  .github
* checking for portable file names ... OK
* checking whether package 'Rdiagnosislist' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... 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 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 ... [17s] OK
* checking Rd files ... 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ... [25s] ERROR
  Running 'testthat.R' [24s]
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 2 | SKIP 0 | PASS 131 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test_loadSNOMED.R:24:2'): Test exporting and reloading sample SNOMED dictionary ──
  dtcomp(TEST$DESCRIPTION, TEST2$DESCRIPTION) is not TRUE
  
  `actual` is a character vector ('Dataset \'current\' has rows not present in \'target\'')
  `expected` is a logical vector (TRUE)
  ── Failure ('test_loadSNOMED.R:25:2'): Test exporting and reloading sample SNOMED dictionary ──
  dtcomp(TEST$RELATIONSHIP, TEST2$RELATIONSHIP) is not TRUE
  
  `actual` is a character vector ('Dataset \'current\' has rows not present in \'target\'')
  `expected` is a logical vector (TRUE)
  ── Failure ('test_loadSNOMED.R:26:2'): Test exporting and reloading sample SNOMED dictionary ──
  dtcomp(TEST$STATEDRELATIONSHIP, TEST2$STATEDRELATIONSHIP) is not TRUE
  
  `actual` is a character vector ('Dataset \'current\' has rows not present in \'target\'')
  `expected` is a logical vector (TRUE)
  ── Failure ('test_loadSNOMED.R:27:2'): Test exporting and reloading sample SNOMED dictionary ──
  dtcomp(TEST$REFSET, TEST2$REFSET) is not TRUE
  
  `actual` is a character vector ('Dataset \'current\' has rows not present in \'target\'')
  `expected` is a logical vector (TRUE)
  ── Failure ('test_loadSNOMED.R:28:2'): Test exporting and reloading sample SNOMED dictionary ──
  dtcomp(TEST$SIMPLEMAP, TEST2$SIMPLEMAP) is not TRUE
  
  `actual` is a character vector ('Dataset \'current\' has rows not present in \'target\'')
  `expected` is a logical vector (TRUE)
  ── Failure ('test_loadSNOMED.R:67:2'): Test exporting and reloading multiple files ──
  dtcomp(TEST$DESCRIPTION, TEST2$DESCRIPTION) is not TRUE
  
  `actual` is a character vector ('Dataset \'current\' has rows not present in \'target\'')
  `expected` is a logical vector (TRUE)
  ── Failure ('test_loadSNOMED.R:68:2'): Test exporting and reloading multiple files ──
  dtcomp(TEST$RELATIONSHIP, TEST2$RELATIONSHIP) is not TRUE
  
  `actual` is a character vector ('Dataset \'current\' has rows not present in \'target\'')
  `expected` is a logical vector (TRUE)
  ── Failure ('test_loadSNOMED.R:69:2'): Test exporting and reloading multiple files ──
  dtcomp(TEST$STATEDRELATIONSHIP, TEST2$STATEDRELATIONSHIP) is not TRUE
  
  `actual` is a character vector ('Dataset \'current\' has rows not present in \'target\'')
  `expected` is a logical vector (TRUE)
  ── Failure ('test_loadSNOMED.R:70:2'): Test exporting and reloading multiple files ──
  dtcomp(TEST$REFSET, TEST2$REFSET) is not TRUE
  
  `actual` is a character vector ('Dataset \'current\' has rows not present in \'target\'')
  `expected` is a logical vector (TRUE)
  ── Failure ('test_loadSNOMED.R:71:2'): Test exporting and reloading multiple files ──
  dtcomp(TEST$SIMPLEMAP, TEST2$SIMPLEMAP) is not TRUE
  
  `actual` is a character vector ('Dataset \'current\' has rows not present in \'target\'')
  `expected` is a logical vector (TRUE)
  
  [ FAIL 10 | WARN 2 | SKIP 0 | PASS 131 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [11s] OK
* checking PDF version of manual ... [24s] OK
* checking HTML version of manual ... [11s] OK
* DONE
Status: 1 ERROR, 2 NOTEs