Last updated on 2025-05-21 18:50:27 CEST.
| Package | ERROR | WARN | NOTE | OK |
|---|---|---|---|---|
| CohortCharacteristics | 1 | 2 | 10 | |
| DrugUtilisation | 13 | |||
| omopgenerics | 1 | 12 | ||
| OmopViewer | 13 | |||
| PatientProfiles | 13 |
Current CRAN status: ERROR: 1, NOTE: 2, OK: 10
Version: 1.0.0
Check: installed package size
Result: NOTE
installed size is 6.0Mb
sub-directories of 1Mb or more:
doc 4.0Mb
help 1.8Mb
Flavors: r-oldrel-macos-arm64, r-oldrel-macos-x86_64
Version: 1.0.0
Check: DESCRIPTION meta-information
Result: NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
‘reactable’ ‘DT’
A package should be listed in only one of these fields.
Flavors: r-oldrel-macos-arm64, r-oldrel-macos-x86_64
Version: 1.0.0
Check: tests
Result: ERROR
Running ‘spelling.R’ [0s/0s]
Running ‘testthat.R’ [2s/3s]
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
Error in `private$handle_error()`:
! testthat subprocess failed to start, stderr:
ℹ `EUNOMIA_DATA_FOLDER` set to:
'/var/folders/k4/0jwzxmln0nb8y6rkzprptb640000gq/T//RtmpBm1JVj'.
trying URL 'https://example-data.ohdsi.dev/GiBleed.zip'
Content type 'application/zip' length 6754786 bytes (6.4 MB)
==========================
downloaded 3.5 MB
Error in `FUN()`:
! In path: "/Volumes/Builds/packages/big-sur-arm64/results/4.4/CohortCharacteristics.Rcheck/tests/testthat/setup.R"
Caused by error in `utils::download.file()`:
! download from 'https://example-data.ohdsi.dev/GiBleed.zip' failed
Backtrace:
▆
1. ├─global callr_startup_hook()
2. │ └─asNamespace("testthat")$queue_process_setup(...)
3. │ └─asNamespace("testthat")$test_files_setup_state(...)
4. │ └─testthat::source_test_setup(".", env)
5. │ └─testthat::source_dir(path, "^setup.*\\.[rR]$", env = env, wrap = FALSE)
6. │ └─base::lapply(...)
7. │ └─testthat (local) FUN(X[[i]], ...)
8. │ └─testthat::source_file(path, env = env, chdir = chdir, wrap = wrap)
9. │ ├─base::withCallingHandlers(...)
10. │ └─base::eval(exprs, env)
11. │ └─base::eval(exprs, env)
12. │ └─CDMConnector::requireEunomia() at tests/testthat/setup.R:1:1
13. │ └─CDMConnector::downloadEunomiaData(...)
14. │ ├─withr::with_options(...)
15. │ │ └─base::force(code)
16. │ └─utils::download.file(...)
17. └─base::.handleSimpleError(...)
18. └─testthat (local) h(simpleError(msg, call))
19. └─rlang::abort(...)
Warning messages:
1: In utils::download.file(url = url, destfile = file.path(pathToData, :
downloaded length 3635387 != reported length 6754786
2: In utils::download.file(url = url, destfile = file.path(pathToData, :
URL 'https://example-data.ohdsi.dev/GiBleed.zip': status was 'Failed writing received data to disk/application'
Ran 4/4 deferred expressions
Error in deferred_run(env) : could not find function "deferred_run"
Calls: <Anonymous>
Caused by error:
! R session crashed with exit code 1
Backtrace:
▆
1. └─testthat::test_check("CohortCharacteristics")
2. └─testthat::test_dir(...)
3. └─testthat:::test_files(...)
4. └─testthat:::test_files_parallel(...)
5. ├─withr::with_dir(...)
6. │ └─base::force(code)
7. ├─testthat::with_reporter(...)
8. │ └─base::tryCatch(...)
9. │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
10. │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
11. │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
12. └─testthat:::parallel_event_loop_chunky(queue, reporters, ".")
13. └─queue$poll(Inf)
14. └─base::lapply(...)
15. └─testthat (local) FUN(X[[i]], ...)
16. └─private$handle_error(msg, i)
17. └─rlang::abort(...)
Execution halted
Flavor: r-oldrel-macos-arm64
Version: 1.0.0
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘summarise_characteristics.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
Quitting from summarise_characteristics.Rmd:26-54 [unnamed-chunk-2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `h()`:
! error in evaluating the argument 'drv' in selecting a method for function 'dbConnect': cannot open the connection
---
Backtrace:
▆
1. ├─DBI::dbConnect(duckdb(), dbdir = eunomiaDir())
2. ├─duckdb::dbConnect(duckdb(), dbdir = eunomiaDir())
3. │ └─duckdb (local) .local(drv, ...)
4. │ └─duckdb:::path_normalize(dbdir)
5. ├─CDMConnector::eunomiaDir()
6. │ ├─DBI::dbConnect(duckdb::duckdb(datasetLocation))
7. │ └─duckdb::duckdb(datasetLocation)
8. │ └─duckdb:::path_normalize(dbdir)
9. │ └─base::writeLines(character(), out)
10. │ └─base::file(con, "w")
11. └─base::.handleSimpleError(...)
12. └─base (local) h(simpleError(msg, call))
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'summarise_characteristics.Rmd' failed with diagnostics:
error in evaluating the argument 'drv' in selecting a method for function 'dbConnect': cannot open the connection
--- failed re-building ‘summarise_characteristics.Rmd’
--- re-building ‘summarise_cohort_overlap.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
Quitting from summarise_cohort_overlap.Rmd:29-62 [unnamed-chunk-2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `h()`:
! error in evaluating the argument 'drv' in selecting a method for function 'dbConnect': cannot open the connection
---
Backtrace:
▆
1. ├─DBI::dbConnect(duckdb(), dbdir = eunomiaDir())
2. ├─duckdb::dbConnect(duckdb(), dbdir = eunomiaDir())
3. │ └─duckdb (local) .local(drv, ...)
4. │ └─duckdb:::path_normalize(dbdir)
5. ├─CDMConnector::eunomiaDir()
6. │ ├─DBI::dbConnect(duckdb::duckdb(datasetLocation))
7. │ └─duckdb::duckdb(datasetLocation)
8. │ └─duckdb:::path_normalize(dbdir)
9. │ └─base::writeLines(character(), out)
10. │ └─base::file(con, "w")
11. └─base::.handleSimpleError(...)
12. └─base (local) h(simpleError(msg, call))
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'summarise_cohort_overlap.Rmd' failed with diagnostics:
error in evaluating the argument 'drv' in selecting a method for function 'dbConnect': cannot open the connection
--- failed re-building ‘summarise_cohort_overlap.Rmd’
--- re-building ‘summarise_cohort_timing.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
Quitting from summarise_cohort_timing.Rmd:27-60 [unnamed-chunk-2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
NULL
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'summarise_cohort_timing.Rmd' failed with diagnostics:
rapi_execute: Failed to run query
Error: FATAL Error: Failed to create checkpoint because of error: Could not write file "/private/var/folders/k4/0jwzxmln0nb8y6rkzprptb640000gq/T/RtmpKC5V2b/GiBleed_5.3_1.2.duckdb": No space left on device
--- failed re-building ‘summarise_cohort_timing.Rmd’
--- re-building ‘summarise_large_scale_characteristics.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
Quitting from summarise_large_scale_characteristics.Rmd:33-53 [unnamed-chunk-2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
NULL
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'summarise_large_scale_characteristics.Rmd' failed with diagnostics:
rapi_execute: Failed to run query
Error: FATAL Error: Failed to create checkpoint because of error: Could not write file "/private/var/folders/k4/0jwzxmln0nb8y6rkzprptb640000gq/T/Rtmpu5ZjyE/GiBleed_5.3_1.2.duckdb": No space left on device
--- failed re-building ‘summarise_large_scale_characteristics.Rmd’
SUMMARY: processing the following files failed:
‘summarise_characteristics.Rmd’ ‘summarise_cohort_overlap.Rmd’
‘summarise_cohort_timing.Rmd’
‘summarise_large_scale_characteristics.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-oldrel-macos-arm64
Version: 0.5.1
Check: installed package size
Result: NOTE
installed size is 5.6Mb
sub-directories of 1Mb or more:
doc 3.5Mb
help 1.9Mb
Flavor: r-oldrel-windows-x86_64
Current CRAN status: OK: 13
Current CRAN status: WARN: 1, OK: 12
Version: 1.2.0
Check: Rd files
Result: WARN
cannot open the connection
cannot open the connection
cannot open the connection
cannot open the connection
cannot open the connection
cannot open the connection
emptyCohortTable.Rd: Sections \title, and \name must exist and be unique in Rd files
cannot open the connection
emptySummarisedResult.Rd: Sections \title, and \name must exist and be unique in Rd files
cannot open the connection
cannot open the connection
cannot open the connection
cannot open the connection
cannot open the connection
filterSettings.Rd: Sections \title, and \name must exist and be unique in Rd files
problems found in ‘cdmName.Rd’, ‘cdmReference.Rd’, ‘cdmSelect.Rd’, ‘emptyCdmReference.Rd’, ‘emptyCodelist.Rd’, ‘emptyCodelistWithDetails.Rd’, ‘emptyCohortTable.Rd’, ‘emptyOmopTable.Rd’, ‘emptySummarisedResult.Rd’, ‘estimateTypeChoices.Rd’, ‘exportCodelist.Rd’, ‘exportSummarisedResult.Rd’, ‘filterAdditional.Rd’, ‘filterGroup.Rd’, ‘filterSettings.Rd’
Flavor: r-oldrel-macos-arm64
Current CRAN status: OK: 13
Current CRAN status: OK: 13