Last updated on 2024-12-23 12:49:37 CET.
| Package | ERROR | OK |
|---|---|---|
| CALIBERrfimpute | 13 | |
| Rdiagnosislist | 3 | 10 |
Current CRAN status: OK: 13
Current CRAN status: ERROR: 3, OK: 10
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\2024_12_18_01_50_01_11818\RtmpgxK3eg
Warning in sub(folder, "", thisfile) :
TRE pattern compilation error 'Invalid back reference'
Error in sub(folder, "", thisfile) :
invalid regular expression 'D:\temp\2024_12_18_01_50_01_11818\RtmpgxK3eg', 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%, :, is.double, match, order, rank
> 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\2024_12_18_01_50_01_11818\RtmpE7iSLm', 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\2024_12_18_01_50_01_11818\RtmpE7iSLm/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\2024_12_18_01_50_01_11818\RtmpWEh1bw', 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\2024_12_08_01_50_01_8405\Rtmp0UbezP
Warning in sub(folder, "", thisfile) :
TRE pattern compilation error 'Invalid back reference'
Error in sub(folder, "", thisfile) :
invalid regular expression 'D:\temp\2024_12_08_01_50_01_8405\Rtmp0UbezP', 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' [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%, :, is.double, match, order, rank
> 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\2024_12_08_01_50_01_8405\RtmpIpKNvL', 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\2024_12_08_01_50_01_8405\RtmpIpKNvL/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\2024_12_08_01_50_01_8405\Rtmpk7tHp6', 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\2024_12_20_01_50_00_19051\RtmpInOPeZ
Warning in sub(folder, "", thisfile) :
TRE pattern compilation error 'Invalid back reference'
Error in sub(folder, "", thisfile) :
invalid regular expression 'D:\temp\2024_12_20_01_50_00_19051\RtmpInOPeZ', 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' [29s]
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%, :, is.double, match, order, rank
> 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\2024_12_20_01_50_00_19051\RtmpshAIoE', 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\2024_12_20_01_50_00_19051\RtmpshAIoE/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\2024_12_20_01_50_00_19051\RtmpakVdg1', 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