Last updated on 2024-06-11 16:49:50 CEST.
| Package | FAIL | ERROR | NOTE | OK |
|---|---|---|---|---|
| CohortCharacteristics | 1 | 7 | 5 | |
| DrugUtilisation | 1 | 2 | 10 | |
| omopgenerics | 13 | |||
| PatientProfiles | 13 |
Current CRAN status: ERROR: 1, NOTE: 7, OK: 5
Version: 0.2.1
Check: installed package size
Result: NOTE
installed size is 6.2Mb
sub-directories of 1Mb or more:
doc 5.6Mb
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-windows-x86_64, r-release-macos-arm64, r-release-macos-x86_64, r-release-windows-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64
Version: 0.2.1
Check: tests
Result: ERROR
Running 'spelling.R' [0s]
Running 'testthat.R' [170s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
>
> library(testthat)
> library(CohortCharacteristics)
>
> test_check("CohortCharacteristics")
Starting 2 test processes
[ FAIL 4 | WARN 0 | SKIP 11 | PASS 129 ]
══ Skipped tests (11) ══════════════════════════════════════════════════════════
• On CRAN (10): 'test-plotCharacteristics.R:2:3',
'test-plotLargeScaleCharacteristics.R:3:3', 'test-plotSummarised.R:2:3',
'test-plotSummarised.R:94:3', 'test-plotSummarised.R:203:3',
'test-plotSummarised.R:308:3',
'test-summariseLargeScaleCharacteristics.R:2:3',
'test-tableSummarised.R:2:3', 'test-tableSummarised.R:124:3',
'test-summariseCharacteristics.R:1122:3'
• empty test (1): 'test-tableSummarised.R:266:1'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-summariseCharacteristics.R:377:3'): test empty cohort ──────────
Error in `dplyr::collect(removeClass(x, "cdm_table"))`: Failed to collect lazy table.
Caused by error:
! rapi_execute: Failed to run query
Error: Out of Memory Error: Failed to allocate block of 65536 bytes (bad allocation)
Backtrace:
▆
1. ├─PatientProfiles (local) mockCohortCharacteristics(...) at test-summariseCharacteristics.R:377:3
2. │ └─CDMConnector::cdm_from_con(...)
3. │ └─omopgenerics::newCohortTable(...)
4. │ └─omopgenerics:::validateGeneratedCohortSet(cohort, soft = .softValidation)
5. │ └─omopgenerics:::cdi(cohort)
6. │ ├─base::sort(dplyr::pull(dplyr::distinct(dplyr::select(x, "cohort_definition_id"))))
7. │ ├─dplyr::pull(dplyr::distinct(dplyr::select(x, "cohort_definition_id")))
8. │ └─dbplyr:::pull.tbl_sql(dplyr::distinct(dplyr::select(x, "cohort_definition_id")))
9. │ ├─dplyr::collect(.data)
10. │ └─omopgenerics:::collect.cohort_table(.data)
11. │ ├─dplyr::collect(attr(x, "cohort_set"))
12. │ └─omopgenerics:::collect.cdm_table(attr(x, "cohort_set"))
13. │ ├─dplyr::collect(removeClass(x, "cdm_table"))
14. │ └─dbplyr:::collect.tbl_sql(removeClass(x, "cdm_table"))
15. │ ├─base::withCallingHandlers(...)
16. │ ├─dbplyr::db_collect(...)
17. │ └─dbplyr:::db_collect.DBIConnection(...)
18. │ ├─DBI::dbSendQuery(con, sql)
19. │ └─duckdb::dbSendQuery(con, sql)
20. │ └─duckdb (local) .local(conn, statement, ...)
21. │ └─duckdb:::duckdb_result(...)
22. │ └─duckdb:::duckdb_execute(res)
23. │ └─duckdb:::rapi_execute(...)
24. └─base::.handleSimpleError(...)
25. └─dbplyr (local) h(simpleError(msg, call))
26. └─cli::cli_abort("Failed to collect lazy table.", parent = cnd)
27. └─rlang::abort(...)
── Failure ('test-summariseCharacteristics.R:1009:3'): arguments cohortIntersect ──
Expected `... <- NULL` to run without any errors.
i Actually got a <rlang_error> with text:
Can't query parent pid.
── Failure ('test-summariseCharacteristics.R:1020:3'): arguments cohortIntersect ──
"Cohort 1 (flag) anytime before" %in% (results %>% dplyr::pull("variable_name")) is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-summariseCharacteristics.R:1025:3'): arguments cohortIntersect ──
... %>% as.numeric() (`actual`) not identical to 3 (`expected`).
`actual`:
`expected`: 3
[ FAIL 4 | WARN 0 | SKIP 11 | PASS 129 ]
Error: Test failures
Execution halted
Flavor: r-devel-windows-x86_64
Version: 0.2.1
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building 'a05_summariseCohortEntries.Rmd' using rmarkdown
trying URL 'https://example-data.ohdsi.dev/GiBleed.zip'
Content type 'application/zip' length 6754786 bytes (6.4 MB)
==================================================
downloaded 6.4 MB
Warning in dev.off(dv) : processing of the plot ran out of memory
Quitting from lines 74-84 [unnamed-chunk-4] (a05_summariseCohortEntries.Rmd)
Error: processing vignette 'a05_summariseCohortEntries.Rmd' failed with diagnostics:
Failed to collect lazy table.
Caused by error:
! rapi_execute: Failed to run query
Error: Out of Memory Error: Failed to allocate block of 262144 bytes (bad allocation)
--- failed re-building 'a05_summariseCohortEntries.Rmd'
Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
Warning in readLines(tf) :
incomplete final line found on 'D:\temp\Rtmpor4I92\file4cd70c661c2235'
Mingw-w64 runtime failure:
VirtualProtect failed with code 0x5af
SUMMARY: processing the following files failed:
'a05_summariseCohortEntries.Rmd'
'a06_summarisePatientCharacteristics.Rmd'
'a07_summariseLargeScaleCharacteristics.Rmd'
'a08_summariseCohortOverlap.Rmd' 'a09_summariseCohortTiming.Rmd'
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-windows-x86_64
Version: 0.2.1
Check: PDF version of manual
Result: WARN
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Flavor: r-devel-windows-x86_64
Version: 0.2.1
Check: PDF version of manual without index
Result: ERROR
Re-running with no redirection of stdout/stderr.
Flavor: r-devel-windows-x86_64
Current CRAN status: FAIL: 1, ERROR: 2, OK: 10
Version: 0.6.1
Check: dependencies in R code
Result: NOTE
Error: memory exhausted
Execution halted
Flavor: r-devel-windows-x86_64
Version: 0.6.1
Check: replacement functions
Result: WARN
Fatal error: couldn't allocate node stack
The argument of a replacement function which corresponds to the right
hand side must be named 'value'.
Flavor: r-devel-windows-x86_64
Version: 0.6.1
Check: foreign function calls
Result: NOTE
Error: cannot allocate vector of size 2.3 Mb
Call sequence:
12: (function (n)
{
if (existsInFrame(n, envenv))
envenv[[n]]
else {
e <- mkenv()
envenv[[n]] <- e
key <- env[[n]]
ekey <- if (is.list(key))
key$eagerKey
else key
data <- lazyLoadDBfetch(ekey, datafile, compressed, envhook)
parent.env(e) <- data$enclos %||% emptyenv()
list2env(data$bindings, e)
if (!is.null(data$attributes))
attributes(e) <- data$attributes
if (!is.null(data$isS4) && data$isS4)
.Internal(setS4Object(e, TRUE, TRUE))
if (is.list(key)) {
expr <- quote(lazyLoadDBfetch(KEY, datafile, compressed,
envhook))
.Internal(makeLazy(names(key$lazyKeys), key$lazyKeys,
expr, parent.env(environment()), e))
}
if (!is.n
Execution halted
See chapter 'System and foreign language interfaces' in the 'Writing R
Extensions' manual.
Flavor: r-devel-windows-x86_64
Version: 0.6.1
Check: R code for possible problems
Result: NOTE
Error in inDL(x, as.logical(local), as.logical(now), ...) :
unable to load shared object 'D:/RCompile/recent/R/library/tools/libs/x64/tools.dll':
LoadLibrary failure: Die Auslagerungsdatei ist zu klein, um diesen Vorgang durchzuführen.
Calls: loadNamespace -> library.dynam -> dyn.load -> inDL
Execution halted
Flavor: r-devel-windows-x86_64
Version: 0.6.1
Check: for code/documentation mismatches
Result: WARN
Warning in gzfile(file, "rb") :
cannot open compressed file 'D:/RCompile/recent/R/library/tools/R/sysdata.rdx', probable reason 'Not enough space'
Error in gzfile(file, "rb") : cannot open the connection
Calls: loadNamespace -> lazyLoad -> lazyLoadDBexec -> readRDS -> gzfile
Execution halted
Flavor: r-devel-windows-x86_64
Version: 0.6.1
Check: examples
Result: ERROR
Running examples in 'DrugUtilisation-Ex.R' failed
The error occurred in:
Flavor: r-devel-windows-x86_64
Version: 0.6.1
Check: tests
Result: ERROR
Flavor: r-devel-windows-x86_64
Version: 0.6.1
Check: for unstated dependencies in vignettes
Result: FAIL
Flavor: r-devel-windows-x86_64
Version: 0.6.1
Check: running R code from vignettes
Result: ERROR
Errors in running code in vignettes:
when running code in ‘a01_introCreateCohort.Rmd’
...
> cdm <- mockDrugUtilisation(numberIndividual = 200)
> conceptSet_json <- codesFromConceptSet(here::here("inst/Concept"),
+ cdm)
When sourcing ‘a01_introCreateCohort.R’:
Error: Invalid path:
/private/var/folders/k4/0jwzxmln0nb8y6rkzprptb640000gq/T/RtmpaUdmHy/fileb7c05b9ab202/vignettes/inst/Concept
Execution halted
Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
‘a01_introCreateCohort.Rmd’ using ‘UTF-8’... failed
‘a02_scalingOfInstantiateCohorts.Rmd’ using ‘UTF-8’... [0s/0s] OK
‘a03_addIndications-example.Rmd’ using ‘UTF-8’... [23s/26s] OK
‘a04_addDrugInfo.Rmd’ using ‘UTF-8’... [49s/51s] OK
‘a05_treatmentDiscontinuation.Rmd’ using ‘UTF-8’... [0s/0s] OK
‘a06_treatmentSummary.Rmd’ using ‘UTF-8’... [10s/10s] OK
‘a07_characteriseACohort.Rmd’ using ‘UTF-8’... [0s/0s] OK
‘routePatternDose.Rmd’ using ‘UTF-8’... [21s/21s] OK
Flavor: r-oldrel-macos-arm64
Version: 0.6.1
Check: running R code from vignettes
Result: ERROR
Errors in running code in vignettes:
when running code in ‘a01_introCreateCohort.Rmd’
...
> cdm <- mockDrugUtilisation(numberIndividual = 200)
> conceptSet_json <- codesFromConceptSet(here::here("inst/Concept"),
+ cdm)
When sourcing ‘a01_introCreateCohort.R’:
Error: Invalid path:
/private/var/folders/2b/t0kwbtmn3p7brv2mvx39c9cr0000gn/T/RtmpFAlOrE/file15fb13269ba11/vignettes/inst/Concept
Execution halted
Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
‘a01_introCreateCohort.Rmd’ using ‘UTF-8’... failed
‘a02_scalingOfInstantiateCohorts.Rmd’ using ‘UTF-8’... [0s/0s] OK
‘a03_addIndications-example.Rmd’ using ‘UTF-8’... [28s/27s] OK
‘a04_addDrugInfo.Rmd’ using ‘UTF-8’... [68s/67s] OK
‘a05_treatmentDiscontinuation.Rmd’ using ‘UTF-8’... [0s/0s] OK
‘a06_treatmentSummary.Rmd’ using ‘UTF-8’... [11s/11s] OK
‘a07_characteriseACohort.Rmd’ using ‘UTF-8’... [0s/0s] OK
‘routePatternDose.Rmd’ using ‘UTF-8’... [29s/28s] OK
Flavor: r-oldrel-macos-x86_64
Current CRAN status: OK: 13
Current CRAN status: OK: 13