CRAN Package Check Results for Maintainer ‘Egill Fridgeirsson <e.fridgeirsson at erasmusmc.nl>’

Last updated on 2025-05-08 04:52:33 CEST.

Package	ERROR	OK
PatientLevelPrediction	2	11

Package PatientLevelPrediction

Current CRAN status: ERROR: 2, OK: 11

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’ [34s/37s] 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/RtmpXgpVSg/working_dir/RtmpvilzdN/GiBleed_5.3.zip to: /tmp/RtmpXgpVSg/working_dir/RtmpvilzdN/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 0.0589 secs Fetching cohorts from server Loading cohorts took 0.379 secs Constructing features on server Executing SQL took 0.237 secs Fetching data from server Fetching data took 1.66 secs Fetching outcomes from server Loading outcomes took 0.15 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