Last updated on 2025-02-07 08:51:53 CET.
| Package | ERROR | OK |
|---|---|---|
| CALIBERrfimpute | 13 | |
| Rdiagnosislist | 1 | 12 |
Current CRAN status: OK: 13
Current CRAN status: ERROR: 1, OK: 12
Version: 1.4.0
Check: tests
Result: ERROR
Running 'testthat.R' [22s]
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]$table, envir = SNOMED, :
object 'REFSET' not found
[ FAIL 10 | WARN 2 | SKIP 0 | PASS 131 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test_loadSNOMED.R:17:2'): Test exporting and reloading sample SNOMED dictionary ──
TEST$DESCRIPTION not equal to TEST2$DESCRIPTION.
Attributes: < Component "index": Attributes: < Component "__conceptId__typeId__term__active": Mean relative difference: 0.1006897 > >
Attributes: < Component "index": Attributes: < Component "__term__active": Attributes: < Component "starts": Numeric: lengths (1571, 1590) differ > > >
Attributes: < Component "index": Attributes: < Component "__term__active": Mean relative difference: 0.6429508 > >
Attributes: < Component "index": Attributes: < Component "__typeId__active": Attributes: < Component "maxgrpn": Mean relative difference: 0.6378132 > > >
Attributes: < Component "index": Attributes: < Component "__typeId__active": Attributes: < Component "starts": Numeric: lengths (4, 598) differ > > >
Attributes: < Component "index": Attributes: < Component "__typeId__active": Mean relative difference: 0.5417598 > >
── Failure ('test_loadSNOMED.R:18:2'): Test exporting and reloading sample SNOMED dictionary ──
TEST$RELATIONSHIP not equal to TEST2$RELATIONSHIP.
Attributes: < Component "index": Attributes: < Component "__destinationId__sourceId__typeId__active": Attributes: < Component "maxgrpn": Mean relative difference: 0.5 > > >
Attributes: < Component "index": Attributes: < Component "__destinationId__sourceId__typeId__active": Attributes: < Component "starts": Numeric: lengths (1730, 1773) differ > > >
Attributes: < Component "index": Attributes: < Component "__destinationId__sourceId__typeId__active": Mean relative difference: 0.001739979 > >
Attributes: < Component "index": Attributes: < Component "__destinationId__typeId__active": Attributes: < Component "maxgrpn": Mean relative difference: 0.5352113 > > >
Attributes: < Component "index": Attributes: < Component "__destinationId__typeId__active": Attributes: < Component "starts": Numeric: lengths (474, 827) differ > > >
Attributes: < Component "index": Attributes: < Component "__destinationId__typeId__active": Mean relative difference: 0.4650144 > >
Attributes: < Component "index": Attributes: < Component "__sourceId__destinationId__typeId__active": Attributes: < Component "maxgrpn": Mean relative difference: 0.5 > > >
Attributes: < Component "index": Attributes: < Component "__sourceId__destinationId__typeId__active": Attributes: < Component "starts": Numeric: lengths (1730, 1773) differ > > >
Attributes: < Component "index": Attributes: < Component "__sourceId__destinationId__typeId__active": Mean relative difference: 0.001739979 > >
── Failure ('test_loadSNOMED.R:19:2'): Test exporting and reloading sample SNOMED dictionary ──
TEST$STATEDRELATIONSHIP not equal to TEST2$STATEDRELATIONSHIP.
Attributes: < Component "index": Attributes: < Component "__destinationId__sourceId__typeId__active": Mean relative difference: 0.005240747 > >
Attributes: < Component "index": Attributes: < Component "__destinationId__typeId__active": Attributes: < Component "maxgrpn": Mean relative difference: 0.1 > > >
Attributes: < Component "index": Attributes: < Component "__destinationId__typeId__active": Attributes: < Component "starts": Numeric: lengths (132, 169) differ > > >
Attributes: < Component "index": Attributes: < Component "__destinationId__typeId__active": Mean relative difference: 0.2120774 > >
Attributes: < Component "index": Attributes: < Component "__sourceId__destinationId__typeId__active": Mean relative difference: 0.005240747 > >
── Failure ('test_loadSNOMED.R:20:2'): Test exporting and reloading sample SNOMED dictionary ──
TEST$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$DESCRIPTION.
Attributes: < Component "index": Attributes: < Component "__conceptId__typeId__term__active": Attributes: < Component "maxgrpn": Mean relative difference: 1 > > >
Attributes: < Component "index": Attributes: < Component "__conceptId__typeId__term__active": Attributes: < Component "starts": Numeric: lengths (1596, 1595) differ > > >
Attributes: < Component "index": Attributes: < Component "__conceptId__typeId__term__active": Mean relative difference: 0.1006897 > >
Attributes: < Component "index": Attributes: < Component "__term__active": Attributes: < Component "starts": Numeric: lengths (1571, 1580) differ > > >
Attributes: < Component "index": Attributes: < Component "__term__active": Mean relative difference: 0.8291013 > >
Attributes: < Component "index": Attributes: < Component "__typeId__active": Attributes: < Component "maxgrpn": Mean relative difference: 0.4134396 > > >
Attributes: < Component "index": Attributes: < Component "__typeId__active": Attributes: < Component "starts": Numeric: lengths (4, 24) differ > > >
Attributes: < Component "index": Attributes: < Component "__typeId__active": Mean relative difference: 0.760869 > >
── Failure ('test_loadSNOMED.R:57:2'): Test exporting and reloading multiple files ──
TEST$RELATIONSHIP not equal to TEST2$RELATIONSHIP.
Attributes: < Component "index": Attributes: < Component "__destinationId__sourceId__typeId__active": Attributes: < Component "maxgrpn": Mean relative difference: 0.5 > > >
Attributes: < Component "index": Attributes: < Component "__destinationId__sourceId__typeId__active": Attributes: < Component "starts": Numeric: lengths (1730, 1773) differ > > >
Attributes: < Component "index": Attributes: < Component "__destinationId__sourceId__typeId__active": Mean relative difference: 0.001739979 > >
Attributes: < Component "index": Attributes: < Component "__destinationId__typeId__active": Attributes: < Component "maxgrpn": Mean relative difference: 0.5352113 > > >
Attributes: < Component "index": Attributes: < Component "__destinationId__typeId__active": Attributes: < Component "starts": Numeric: lengths (474, 827) differ > > >
Attributes: < Component "index": Attributes: < Component "__destinationId__typeId__active": Mean relative difference: 0.4650144 > >
Attributes: < Component "index": Attributes: < Component "__sourceId__destinationId__typeId__active": Attributes: < Component "maxgrpn": Mean relative difference: 0.5 > > >
Attributes: < Component "index": Attributes: < Component "__sourceId__destinationId__typeId__active": Attributes: < Component "starts": Numeric: lengths (1730, 1773) differ > > >
Attributes: < Component "index": Attributes: < Component "__sourceId__destinationId__typeId__active": Mean relative difference: 0.001739979 > >
── Failure ('test_loadSNOMED.R:58:2'): Test exporting and reloading multiple files ──
TEST$STATEDRELATIONSHIP not equal to TEST2$STATEDRELATIONSHIP.
Attributes: < Component "index": Attributes: < Component "__destinationId__sourceId__typeId__active": Mean relative difference: 0.005240747 > >
Attributes: < Component "index": Attributes: < Component "__destinationId__typeId__active": Attributes: < Component "maxgrpn": Mean relative difference: 0.1 > > >
Attributes: < Component "index": Attributes: < Component "__destinationId__typeId__active": Attributes: < Component "starts": Numeric: lengths (132, 169) differ > > >
Attributes: < Component "index": Attributes: < Component "__destinationId__typeId__active": Mean relative difference: 0.2120774 > >
Attributes: < Component "index": Attributes: < Component "__sourceId__destinationId__typeId__active": Mean relative difference: 0.005240747 > >
── Failure ('test_loadSNOMED.R:59:2'): Test exporting and reloading multiple files ──
TEST$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': 112 element mismatches
[ FAIL 10 | WARN 2 | SKIP 0 | PASS 131 ]
Error: Test failures
Execution halted
Flavor: r-devel-windows-x86_64