Last updated on 2025-01-30 01:49:45 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.3 | 7.66 | 137.91 | 145.57 | OK | |
| r-devel-linux-x86_64-debian-gcc | 1.4.0 | 5.67 | 57.32 | 62.99 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 1.4.0 | 152.88 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 1.4.0 | 155.77 | OK | |||
| r-devel-windows-x86_64 | 1.3 | 8.00 | 121.00 | 129.00 | ERROR | |
| r-patched-linux-x86_64 | 1.3 | 5.87 | 120.19 | 126.06 | OK | |
| r-release-linux-x86_64 | 1.3 | 6.76 | 118.96 | 125.72 | OK | |
| r-release-macos-arm64 | 1.4.0 | 60.00 | OK | |||
| r-release-macos-x86_64 | 1.3 | 154.00 | OK | |||
| r-release-windows-x86_64 | 1.3 | 9.00 | 118.00 | 127.00 | ERROR | |
| r-oldrel-macos-arm64 | 1.3 | 65.00 | OK | |||
| r-oldrel-macos-x86_64 | 1.3 | 150.00 | OK | |||
| r-oldrel-windows-x86_64 | 1.3 | 10.00 | 132.00 | 142.00 | ERROR |
Version: 1.4.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [11s/13s]
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$DESCRIPTION.
Attributes: < Component "index": Attributes: < Component "__conceptId__typeId__term__active": Attributes: < Component "maxgrpn": Mean relative difference: 1 > > >
Attributes: < Component "index": Attributes: < Component "__conceptId__typeId__term__active": Attributes: < Component "starts": Numeric: lengths (1596, 1595) differ > > >
Attributes: < Component "index": Attributes: < Component "__conceptId__typeId__term__active": Mean relative difference: 0.1006897 > >
Attributes: < Component "index": Attributes: < Component "__term__active": Attributes: < Component "starts": Numeric: lengths (1571, 1583) differ > > >
Attributes: < Component "index": Attributes: < Component "__term__active": Mean relative difference: 0.677056 > >
Attributes: < Component "index": Attributes: < Component "__typeId__active": Attributes: < Component "maxgrpn": Mean relative difference: 0.6207289 > > >
Attributes: < Component "index": Attributes: < Component "__typeId__active": Attributes: < Component "starts": Numeric: lengths (4, 19) differ > > >
Attributes: < Component "index": Attributes: < Component "__typeId__active": Mean relative difference: 0.4855221 > >
── Failure ('test_loadSNOMED.R:18:2'): Test exporting and reloading sample SNOMED dictionary ──
TEST$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$STATEDRELATIONSHIP.
Attributes: < Component "index": Attributes: < Component "__destinationId__sourceId__typeId__active": Mean relative difference: 0.006129247 > >
Attributes: < Component "index": Attributes: < Component "__destinationId__typeId__active": Attributes: < Component "maxgrpn": Mean relative difference: 0.4 > > >
Attributes: < Component "index": Attributes: < Component "__destinationId__typeId__active": Attributes: < Component "starts": Numeric: lengths (132, 228) differ > > >
Attributes: < Component "index": Attributes: < Component "__destinationId__typeId__active": Mean relative difference: 0.3173756 > >
Attributes: < Component "index": Attributes: < Component "__sourceId__destinationId__typeId__active": Mean relative difference: 0.006129247 > >
── Failure ('test_loadSNOMED.R:20:2'): Test exporting and reloading sample SNOMED dictionary ──
TEST$REFSET not equal to TEST2$REFSET.
Column 'active': 394 element mismatches
── Failure ('test_loadSNOMED.R:21:2'): Test exporting and reloading sample SNOMED dictionary ──
TEST$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$DESCRIPTION.
Attributes: < Component "index": Attributes: < Component "__conceptId__typeId__term__active": Attributes: < Component "maxgrpn": Mean relative difference: 1 > > >
Attributes: < Component "index": Attributes: < Component "__conceptId__typeId__term__active": Attributes: < Component "starts": Numeric: lengths (1596, 1595) differ > > >
Attributes: < Component "index": Attributes: < Component "__conceptId__typeId__term__active": Mean relative difference: 0.1006897 > >
Attributes: < Component "index": Attributes: < Component "__term__active": Attributes: < Component "starts": Numeric: lengths (1571, 1583) differ > > >
Attributes: < Component "index": Attributes: < Component "__term__active": Mean relative difference: 0.677056 > >
Attributes: < Component "index": Attributes: < Component "__typeId__active": Attributes: < Component "maxgrpn": Mean relative difference: 0.6207289 > > >
Attributes: < Component "index": Attributes: < Component "__typeId__active": Attributes: < Component "starts": Numeric: lengths (4, 19) differ > > >
Attributes: < Component "index": Attributes: < Component "__typeId__active": Mean relative difference: 0.4855221 > >
── Failure ('test_loadSNOMED.R:57:2'): Test exporting and reloading multiple files ──
TEST$RELATIONSHIP not equal to TEST2$RELATIONSHIP.
Attributes: < Component "index": Attributes: < Component "__destinationId__sourceId__typeId__active": Attributes: < Component "maxgrpn": Mean relative difference: 0.5 > > >
Attributes: < Component "index": Attributes: < Component "__destinationId__sourceId__typeId__active": Attributes: < Component "starts": Numeric: lengths (1730, 1764) differ > > >
Attributes: < Component "index": Attributes: < Component "__destinationId__sourceId__typeId__active": Mean relative difference: 0.002060094 > >
Attributes: < Component "index": Attributes: < Component "__destinationId__typeId__active": Attributes: < Component "maxgrpn": Mean relative difference: 0.5774648 > > >
Attributes: < Component "index": Attributes: < Component "__destinationId__typeId__active": Attributes: < Component "starts": Numeric: lengths (474, 873) differ > > >
Attributes: < Component "index": Attributes: < Component "__destinationId__typeId__active": Mean relative difference: 0.5773458 > >
Attributes: < Component "index": Attributes: < Component "__sourceId__destinationId__typeId__active": Attributes: < Component "maxgrpn": Mean relative difference: 0.5 > > >
Attributes: < Component "index": Attributes: < Component "__sourceId__destinationId__typeId__active": Attributes: < Component "starts": Numeric: lengths (1730, 1764) differ > > >
Attributes: < Component "index": Attributes: < Component "__sourceId__destinationId__typeId__active": Mean relative difference: 0.002060094 > >
── Failure ('test_loadSNOMED.R:58:2'): Test exporting and reloading multiple files ──
TEST$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$REFSET.
Column 'active': 406 element mismatches
── Failure ('test_loadSNOMED.R:60:2'): Test exporting and reloading multiple files ──
TEST$SIMPLEMAP not equal to TEST2$SIMPLEMAP.
Column 'active': 124 element mismatches
[ FAIL 10 | WARN 0 | SKIP 0 | PASS 131 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.3
Check: examples
Result: ERROR
Running examples in 'Rdiagnosislist-Ex.R' failed
The error most likely occurred in:
> ### Name: loadSNOMED
> ### Title: Load SNOMED CT files from a folder(s) into R data.table objects
> ### Aliases: loadSNOMED
>
> ### ** Examples
>
> # Create a TEST environment and load the sample dictionaries
> TEST <- sampleSNOMED()
>
> # Export to temporary directory
> exportSNOMEDenvir(TEST, tempdir())
NULL
>
> # Try to import using the loadSNOMED function
> TEST2 <- loadSNOMED(tempdir(), active_only = FALSE)
Attempting to load from D:\temp\2025_01_27_01_50_00_25464\RtmpA74vXq
Warning in sub(folder, "", thisfile) :
TRE pattern compilation error 'Invalid back reference'
Error in sub(folder, "", thisfile) :
invalid regular expression 'D:\temp\2025_01_27_01_50_00_25464\RtmpA74vXq', reason 'Invalid back reference'
Calls: loadSNOMED -> message -> .makeMessage -> lapply -> sub
Execution halted
Flavor: r-devel-windows-x86_64
Version: 1.3
Check: tests
Result: ERROR
Running 'testthat.R' [25s]
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 159 3 0 conceptId,term,laterality
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 24 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 685 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: [NULL]
13: descendantId
Total: 0MB using type_size
[ FAIL 2 | WARN 2 | SKIP 0 | PASS 124 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_loadSNOMED.R:14:2'): Test exporting and reloading sample SNOMED dictionary ──
Error in `sub(folder, "", thisfile)`: invalid regular expression 'D:\temp\2025_01_27_01_50_00_25464\Rtmp40372n', reason 'Invalid back reference'
Backtrace:
▆
1. └─Rdiagnosislist::loadSNOMED(tempdir(), active_only = FALSE) at test_loadSNOMED.R:14:9
2. ├─base::message("Attempting to load ", sub(folder, "", thisfile))
3. │ └─base::.makeMessage(..., domain = domain, appendLF = appendLF)
4. │ └─base::lapply(list(...), as.character)
5. └─base::sub(folder, "", thisfile)
── Error ('test_loadSNOMED.R:51:2'): Test exporting and reloading multiple files ──
Error in `sub(folder, "", thisfile)`: invalid regular expression 'D:\temp\2025_01_27_01_50_00_25464\Rtmp40372n/1', reason 'Invalid back reference'
Backtrace:
▆
1. └─Rdiagnosislist::loadSNOMED(...) at test_loadSNOMED.R:51:9
2. ├─base::message("Attempting to load ", sub(folder, "", thisfile))
3. │ └─base::.makeMessage(..., domain = domain, appendLF = appendLF)
4. │ └─base::lapply(list(...), as.character)
5. └─base::sub(folder, "", thisfile)
[ FAIL 2 | WARN 2 | SKIP 0 | PASS 124 ]
Error: Test failures
Execution halted
Flavor: r-devel-windows-x86_64
Version: 1.3
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building 'SNOMEDcodelists.Rmd' using rmarkdown
Quitting from lines 79-98 [unnamed-chunk-1] (SNOMEDcodelists.Rmd)
Error: processing vignette 'SNOMEDcodelists.Rmd' failed with diagnostics:
invalid regular expression 'D:\temp\2025_01_27_01_50_00_25464\RtmpkLMNOd', reason 'Invalid back reference'
--- failed re-building 'SNOMEDcodelists.Rmd'
--- re-building 'convertingAndCreatingCodelists.Rmd' using rmarkdown
--- finished re-building 'convertingAndCreatingCodelists.Rmd'
--- re-building 'creatingConceptDatabaseForNLP.Rmd' using rmarkdown
--- finished re-building 'creatingConceptDatabaseForNLP.Rmd'
--- re-building 'customHierarchy.Rmd' using rmarkdown
--- finished re-building 'customHierarchy.Rmd'
SUMMARY: processing the following file failed:
'SNOMEDcodelists.Rmd'
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-windows-x86_64
Version: 1.3
Check: examples
Result: ERROR
Running examples in 'Rdiagnosislist-Ex.R' failed
The error most likely occurred in:
> ### Name: loadSNOMED
> ### Title: Load SNOMED CT files from a folder(s) into R data.table objects
> ### Aliases: loadSNOMED
>
> ### ** Examples
>
> # Create a TEST environment and load the sample dictionaries
> TEST <- sampleSNOMED()
>
> # Export to temporary directory
> exportSNOMEDenvir(TEST, tempdir())
NULL
>
> # Try to import using the loadSNOMED function
> TEST2 <- loadSNOMED(tempdir(), active_only = FALSE)
Attempting to load from D:\temp\2025_01_25_01_50_00_18228\Rtmpu0Gjuk
Warning in sub(folder, "", thisfile) :
TRE pattern compilation error 'Invalid back reference'
Error in sub(folder, "", thisfile) :
invalid regular expression 'D:\temp\2025_01_25_01_50_00_18228\Rtmpu0Gjuk', reason 'Invalid back reference'
Calls: loadSNOMED -> message -> .makeMessage -> lapply -> sub
Execution halted
Flavor: r-release-windows-x86_64
Version: 1.3
Check: tests
Result: ERROR
Running 'testthat.R' [25s]
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 159 3 0 conceptId,term,laterality
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 24 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 685 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: [NULL]
13: descendantId
Total: 0MB using type_size
[ FAIL 2 | WARN 2 | SKIP 0 | PASS 124 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_loadSNOMED.R:14:2'): Test exporting and reloading sample SNOMED dictionary ──
Error in `sub(folder, "", thisfile)`: invalid regular expression 'D:\temp\2025_01_25_01_50_00_18228\RtmpOaV6d1', reason 'Invalid back reference'
Backtrace:
▆
1. └─Rdiagnosislist::loadSNOMED(tempdir(), active_only = FALSE) at test_loadSNOMED.R:14:9
2. ├─base::message("Attempting to load ", sub(folder, "", thisfile))
3. │ └─base::.makeMessage(..., domain = domain, appendLF = appendLF)
4. │ └─base::lapply(list(...), as.character)
5. └─base::sub(folder, "", thisfile)
── Error ('test_loadSNOMED.R:51:2'): Test exporting and reloading multiple files ──
Error in `sub(folder, "", thisfile)`: invalid regular expression 'D:\temp\2025_01_25_01_50_00_18228\RtmpOaV6d1/1', reason 'Invalid back reference'
Backtrace:
▆
1. └─Rdiagnosislist::loadSNOMED(...) at test_loadSNOMED.R:51:9
2. ├─base::message("Attempting to load ", sub(folder, "", thisfile))
3. │ └─base::.makeMessage(..., domain = domain, appendLF = appendLF)
4. │ └─base::lapply(list(...), as.character)
5. └─base::sub(folder, "", thisfile)
[ FAIL 2 | WARN 2 | SKIP 0 | PASS 124 ]
Error: Test failures
Execution halted
Flavor: r-release-windows-x86_64
Version: 1.3
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building 'SNOMEDcodelists.Rmd' using rmarkdown
Quitting from lines 79-98 [unnamed-chunk-1] (SNOMEDcodelists.Rmd)
Error: processing vignette 'SNOMEDcodelists.Rmd' failed with diagnostics:
invalid regular expression 'D:\temp\2025_01_25_01_50_00_18228\RtmpoFXyVR', reason 'Invalid back reference'
--- failed re-building 'SNOMEDcodelists.Rmd'
--- re-building 'convertingAndCreatingCodelists.Rmd' using rmarkdown
--- finished re-building 'convertingAndCreatingCodelists.Rmd'
--- re-building 'creatingConceptDatabaseForNLP.Rmd' using rmarkdown
--- finished re-building 'creatingConceptDatabaseForNLP.Rmd'
--- re-building 'customHierarchy.Rmd' using rmarkdown
--- finished re-building 'customHierarchy.Rmd'
SUMMARY: processing the following file failed:
'SNOMEDcodelists.Rmd'
Error: Vignette re-building failed.
Execution halted
Flavor: r-release-windows-x86_64
Version: 1.3
Check: examples
Result: ERROR
Running examples in 'Rdiagnosislist-Ex.R' failed
The error most likely occurred in:
> ### Name: loadSNOMED
> ### Title: Load SNOMED CT files from a folder(s) into R data.table objects
> ### Aliases: loadSNOMED
>
> ### ** Examples
>
> # Create a TEST environment and load the sample dictionaries
> TEST <- sampleSNOMED()
>
> # Export to temporary directory
> exportSNOMEDenvir(TEST, tempdir())
NULL
>
> # Try to import using the loadSNOMED function
> TEST2 <- loadSNOMED(tempdir(), active_only = FALSE)
Attempting to load from D:\temp\2025_01_29_01_50_00_32701\RtmpSgljvV
Warning in sub(folder, "", thisfile) :
TRE pattern compilation error 'Invalid back reference'
Error in sub(folder, "", thisfile) :
invalid regular expression 'D:\temp\2025_01_29_01_50_00_32701\RtmpSgljvV', reason 'Invalid back reference'
Calls: loadSNOMED -> message -> .makeMessage -> lapply -> sub
Execution halted
Flavor: r-oldrel-windows-x86_64
Version: 1.3
Check: tests
Result: ERROR
Running 'testthat.R' [30s]
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 159 3 0 conceptId,term,laterality
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 24 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 685 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: [NULL]
13: descendantId
Total: 0MB using type_size
[ FAIL 2 | WARN 2 | SKIP 0 | PASS 124 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_loadSNOMED.R:14:2'): Test exporting and reloading sample SNOMED dictionary ──
Error in `sub(folder, "", thisfile)`: invalid regular expression 'D:\temp\2025_01_29_01_50_00_32701\RtmpAt5Wlm', reason 'Invalid back reference'
Backtrace:
▆
1. └─Rdiagnosislist::loadSNOMED(tempdir(), active_only = FALSE) at test_loadSNOMED.R:14:9
2. ├─base::message("Attempting to load ", sub(folder, "", thisfile))
3. │ └─base::.makeMessage(..., domain = domain, appendLF = appendLF)
4. │ └─base::lapply(list(...), as.character)
5. └─base::sub(folder, "", thisfile)
── Error ('test_loadSNOMED.R:51:2'): Test exporting and reloading multiple files ──
Error in `sub(folder, "", thisfile)`: invalid regular expression 'D:\temp\2025_01_29_01_50_00_32701\RtmpAt5Wlm/1', reason 'Invalid back reference'
Backtrace:
▆
1. └─Rdiagnosislist::loadSNOMED(...) at test_loadSNOMED.R:51:9
2. ├─base::message("Attempting to load ", sub(folder, "", thisfile))
3. │ └─base::.makeMessage(..., domain = domain, appendLF = appendLF)
4. │ └─base::lapply(list(...), as.character)
5. └─base::sub(folder, "", thisfile)
[ FAIL 2 | WARN 2 | SKIP 0 | PASS 124 ]
Error: Test failures
Execution halted
Flavor: r-oldrel-windows-x86_64
Version: 1.3
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building 'SNOMEDcodelists.Rmd' using rmarkdown
Quitting from lines 79-98 [unnamed-chunk-1] (SNOMEDcodelists.Rmd)
Error: processing vignette 'SNOMEDcodelists.Rmd' failed with diagnostics:
invalid regular expression 'D:\temp\2025_01_29_01_50_00_32701\Rtmpuyp55l', reason 'Invalid back reference'
--- failed re-building 'SNOMEDcodelists.Rmd'
--- re-building 'convertingAndCreatingCodelists.Rmd' using rmarkdown
--- finished re-building 'convertingAndCreatingCodelists.Rmd'
--- re-building 'creatingConceptDatabaseForNLP.Rmd' using rmarkdown
--- finished re-building 'creatingConceptDatabaseForNLP.Rmd'
--- re-building 'customHierarchy.Rmd' using rmarkdown
--- finished re-building 'customHierarchy.Rmd'
SUMMARY: processing the following file failed:
'SNOMEDcodelists.Rmd'
Error: Vignette re-building failed.
Execution halted
Flavor: r-oldrel-windows-x86_64