R Under development (unstable) (2025-01-22 r87618 ucrt) -- "Unsuffered Consequences"
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> 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 0 | WARN 2 | SKIP 0 | PASS 141 ]
[ FAIL 0 | WARN 2 | SKIP 0 | PASS 141 ]
>
> proc.time()
user system elapsed
10.71 2.65 13.31