Last updated on 2025-05-07 19:51:33 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 6.4.1 | 17.58 | 242.47 | 260.05 | OK | |
| r-devel-linux-x86_64-debian-gcc | 6.4.1 | 12.38 | 168.63 | 181.01 | OK | |
| r-devel-linux-x86_64-fedora-clang | 6.4.1 | 300.67 | ERROR | |||
| r-devel-linux-x86_64-fedora-gcc | 6.4.1 | 312.34 | ERROR | |||
| r-devel-windows-x86_64 | 6.4.1 | 19.00 | 275.00 | 294.00 | OK | |
| r-patched-linux-x86_64 | 6.4.1 | 18.77 | 232.30 | 251.07 | OK | |
| r-release-linux-x86_64 | 6.4.1 | 16.95 | 231.37 | 248.32 | OK | |
| r-release-macos-arm64 | 6.4.1 | 73.00 | OK | |||
| r-release-macos-x86_64 | 6.4.1 | 143.00 | OK | |||
| r-release-windows-x86_64 | 6.4.1 | 19.00 | 278.00 | 297.00 | OK | |
| r-oldrel-macos-arm64 | 6.4.1 | 96.00 | OK | |||
| r-oldrel-macos-x86_64 | 6.4.1 | 149.00 | OK | |||
| r-oldrel-windows-x86_64 | 6.4.1 | 28.00 | 355.00 | 383.00 | OK |
Version: 6.4.1
Check: examples
Result: ERROR
Running examples in ‘PatientLevelPrediction-Ex.R’ failed
The error most likely occurred in:
> ### Name: covariateSummary
> ### Title: covariateSummary
> ### Aliases: covariateSummary
>
> ### ** Examples
>
> data("simulationProfile")
> plpData <- simulatePlpData(simulationProfile, n = 100)
Generating covariates
Loading required namespace: FeatureExtraction
Error in connection_valid(dbObj@ptr) :
no slot of name "ptr" for this object of class "CovariateData"
Calls: simulatePlpData ... isValidAndromeda -> <Anonymous> -> <Anonymous> -> connection_valid
Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc
Version: 6.4.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [36s/131s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(PatientLevelPrediction)
> test_check("PatientLevelPrediction")
Internet: TRUE
attempting to download GiBleed
trying URL 'https://raw.githubusercontent.com/OHDSI/EunomiaDatasets/main/datasets/GiBleed/GiBleed_5.3.zip'
Content type 'application/zip' length 6861852 bytes (6.5 MB)
==================================================
downloaded 6.5 MB
attempting to extract and load: /tmp/Rtmp0evfAU/working_dir/RtmphKWvrN/GiBleed_5.3.zip to: /tmp/Rtmp0evfAU/working_dir/RtmphKWvrN/GiBleed_5.3.sqlite
Cohorts created in table main.cohort
No cdm database id entered so using cdmDatabaseSchema - if cdmDatabaseSchema is the same for multiple different databases, please use cdmDatabaseId to specify a unique identifier for the database and version
Connecting using SQLite driver
Constructing the at risk cohort
Executing SQL took 0.38 secs
Fetching cohorts from server
Loading cohorts took 4.06 secs
Constructing features on server
Executing SQL took 0.273 secs
Fetching data from server
Fetching data took 8.94 secs
Fetching outcomes from server
Loading outcomes took 0.265 secs
Error in `FUN()`:
! In path: "/data/gannet/ripley/R/packages/tests-clang/PatientLevelPrediction.Rcheck/tests/testthat/setup.R"
Caused by error in `connection_valid()`:
! no slot of name "ptr" for this object of class "CovariateData"
Backtrace:
▆
1. ├─testthat::test_check("PatientLevelPrediction")
2. │ └─testthat::test_dir(...)
3. │ └─testthat:::test_files(...)
4. │ └─testthat:::test_files_serial(...)
5. │ └─testthat:::test_files_setup_state(...)
6. │ └─testthat::source_test_setup(".", env)
7. │ └─testthat::source_dir(path, "^setup.*\\.[rR]$", env = env, wrap = FALSE)
8. │ └─base::lapply(...)
9. │ └─testthat (local) FUN(X[[i]], ...)
10. │ └─testthat::source_file(path, env = env, chdir = chdir, wrap = wrap)
11. │ ├─base::withCallingHandlers(...)
12. │ └─base::eval(exprs, env)
13. │ └─base::eval(exprs, env)
14. │ └─PatientLevelPrediction::getPlpData(...) at tests/testthat/setup.R:50:3
15. │ ├─covariateData$metaData
16. │ └─covariateData$metaData
17. │ ├─x[[name]]
18. │ └─x[[name]]
19. │ └─Andromeda (local) .local(x, i, ...)
20. │ └─Andromeda:::checkIfValid(x)
21. │ └─Andromeda::isValidAndromeda(x)
22. │ ├─duckdb::dbIsValid(x)
23. │ └─duckdb::dbIsValid(x)
24. │ └─RSQLite:::connection_valid(dbObj@ptr)
25. └─base::.handleSimpleError(...)
26. └─testthat (local) h(simpleError(msg, call))
27. └─rlang::abort(...)
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 6.4.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [54s/64s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(PatientLevelPrediction)
> test_check("PatientLevelPrediction")
Internet: TRUE
attempting to download GiBleed
trying URL 'https://raw.githubusercontent.com/OHDSI/EunomiaDatasets/main/datasets/GiBleed/GiBleed_5.3.zip'
Content type 'application/zip' length 6861852 bytes (6.5 MB)
==================================================
downloaded 6.5 MB
attempting to extract and load: /tmp/RtmpHrIvPd/working_dir/Rtmp75WGph/GiBleed_5.3.zip to: /tmp/RtmpHrIvPd/working_dir/Rtmp75WGph/GiBleed_5.3.sqlite
Cohorts created in table main.cohort
No cdm database id entered so using cdmDatabaseSchema - if cdmDatabaseSchema is the same for multiple different databases, please use cdmDatabaseId to specify a unique identifier for the database and version
Connecting using SQLite driver
Constructing the at risk cohort
Executing SQL took 0.0721 secs
Fetching cohorts from server
Loading cohorts took 0.0856 secs
Constructing features on server
Executing SQL took 0.264 secs
Fetching data from server
Fetching data took 1.8 secs
Fetching outcomes from server
Loading outcomes took 0.0918 secs
Error in `FUN()`:
! In path: "/data/gannet/ripley/R/packages/tests-devel/PatientLevelPrediction.Rcheck/tests/testthat/setup.R"
Caused by error in `connection_valid()`:
! no slot of name "ptr" for this object of class "CovariateData"
Backtrace:
▆
1. ├─testthat::test_check("PatientLevelPrediction")
2. │ └─testthat::test_dir(...)
3. │ └─testthat:::test_files(...)
4. │ └─testthat:::test_files_serial(...)
5. │ └─testthat:::test_files_setup_state(...)
6. │ └─testthat::source_test_setup(".", env)
7. │ └─testthat::source_dir(path, "^setup.*\\.[rR]$", env = env, wrap = FALSE)
8. │ └─base::lapply(...)
9. │ └─testthat (local) FUN(X[[i]], ...)
10. │ └─testthat::source_file(path, env = env, chdir = chdir, wrap = wrap)
11. │ ├─base::withCallingHandlers(...)
12. │ └─base::eval(exprs, env)
13. │ └─base::eval(exprs, env)
14. │ └─PatientLevelPrediction::getPlpData(...) at tests/testthat/setup.R:50:3
15. │ ├─covariateData$metaData
16. │ └─covariateData$metaData
17. │ ├─x[[name]]
18. │ └─x[[name]]
19. │ └─Andromeda (local) .local(x, i, ...)
20. │ └─Andromeda:::checkIfValid(x)
21. │ └─Andromeda::isValidAndromeda(x)
22. │ ├─duckdb::dbIsValid(x)
23. │ └─duckdb::dbIsValid(x)
24. │ └─RSQLite:::connection_valid(dbObj@ptr)
25. └─base::.handleSimpleError(...)
26. └─testthat (local) h(simpleError(msg, call))
27. └─rlang::abort(...)
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc