CRAN Package Check Results for Maintainer ‘Tiago F.V. Maié <tiagomaie at hotmail.com>’

Last updated on 2025-12-04 07:52:00 CET.

Package	ERROR
CimpleG	6

Package CimpleG

Current CRAN status:

Additional issues

M1mac

Version: 1.0.0
Check: dependencies in R code
Result: NOTE Namespace in Imports field not imported from: ‘devtools’ All declared Imports should be used. Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc

Version: 1.0.0
Check: tests
Result: ERROR Running ‘spelling.R’ Running ‘testthat.R’ [426s/219s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(CimpleG) --------------------- CimpleG version 1.0.0 --------------------- > > test_check("CimpleG") Starting 2 test processes. > test-CimpleG.R: Warning: stack imbalance in '::', 115 then 117 > test-CimpleG.R: Warning: stack imbalance in '<-', 113 then 115 > test-CimpleG.R: Setting options('download.file.method.GEOquery'='auto') > test-CimpleG.R: Setting options('GEOquery.inmemory.gpl'=FALSE) > test-CimpleG.R: OMP: Warning #96: Cannot form a team with 24 threads, using 2 instead. > test-CimpleG.R: OMP: Hint Consider unsetting KMP_DEVICE_THREAD_LIMIT (KMP > test-CimpleG.R: _ALL_THREADS), KMP_TEAMS_THREAD_LIMIT, and OMP_THREAD_LIMIT (if any are set). > test-CimpleG.R: Warning: stack imbalance in '{', 109 then 111 Saving _problems/test3-CimpleG-xgboost-13.R [ FAIL 1 | WARN 0 | SKIP 4 | PASS 62 ] ══ Skipped tests (4) ═══════════════════════════════════════════════════════════ • On CRAN (3): 'test1-CimpleG-decisiontree.R:3:3', 'test1-CimpleG-nnet.R:3:3', 'test1-CimpleG-rf.R:3:3' • parallel not working properly locally (1): 'test8-CimpleG-parallel.R:4:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test3-CimpleG-xgboost.R:5:3'): signatures are generated w/ xgboost ── <purrr_error_indexed/rlang_error/error/condition> Error in `purrr::map(.x = target_columns, .f = work_helper)`: i In index: 1. Caused by error in `x$callbacks <- purrr::map(x$callbacks, function(x) as.function(c(formals(x), body(x)), env = rlang::base_env()))`: ! ALTLIST classes must provide a Set_elt method [class: XGBAltrepPointerClass, pkg: xgboost] Backtrace: ▆ 1. ├─base::suppressWarnings(...) at test3-CimpleG-xgboost.R:5:3 2. │ └─base::withCallingHandlers(...) 3. ├─base::suppressMessages(...) 4. │ └─base::withCallingHandlers(...) 5. ├─CimpleG::CimpleG(...) 6. ├─CimpleG:::CimpleG.matrix(...) 7. │ └─CimpleG:::CimpleG_main(...) 8. │ ├─purrr::map(.x = target_columns, .f = work_helper) %>% ... 9. │ └─purrr::map(.x = target_columns, .f = work_helper) 10. │ └─purrr:::map_("list", .x, .f, ..., .progress = .progress) 11. │ ├─purrr:::with_indexed_errors(...) 12. │ │ └─base::withCallingHandlers(...) 13. │ ├─purrr:::call_with_cleanup(...) 14. │ └─CimpleG (local) .f(.x[[i]], ...) 15. │ └─CimpleG:::train_general_model(...) 16. │ └─cimpleg_final_model %>% butcher::axe_call() %>% butcher::axe_env() 17. ├─butcher::axe_env(.) 18. ├─workflows:::axe_env.workflow(.) 19. │ ├─butcher::axe_env(fit, verbose = verbose, ...) 20. │ └─butcher:::axe_env.model_fit(fit, verbose = verbose, ...) 21. │ ├─butcher::axe_env(x$fit, verbose = verbose, ...) 22. │ └─butcher:::axe_env.xgb.Booster(x$fit, verbose = verbose, ...) 23. └─base::.handleSimpleError(...) 24. └─purrr (local) h(simpleError(msg, call)) 25. └─cli::cli_abort(...) 26. └─rlang::abort(...) [ FAIL 1 | WARN 0 | SKIP 4 | PASS 62 ] Error: ! Test failures. Execution halted Flavor: r-devel-linux-x86_64-fedora-clang

Version: 1.0.0
Check: tests
Result: ERROR Running ‘spelling.R’ Running ‘testthat.R’ [408s/212s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(CimpleG) --------------------- CimpleG version 1.0.0 --------------------- > > test_check("CimpleG") Starting 2 test processes. > test-CimpleG.R: Warning: stack imbalance in '::', 115 then 117 > test-CimpleG.R: Warning: stack imbalance in '<-', 113 then 115 > test-CimpleG.R: Setting options('download.file.method.GEOquery'='auto') > test-CimpleG.R: Setting options('GEOquery.inmemory.gpl'=FALSE) > test-CimpleG.R: Warning: stack imbalance in '{', 109 then 111 Saving _problems/test3-CimpleG-xgboost-13.R [ FAIL 1 | WARN 0 | SKIP 4 | PASS 62 ] ══ Skipped tests (4) ═══════════════════════════════════════════════════════════ • On CRAN (3): 'test1-CimpleG-decisiontree.R:3:3', 'test1-CimpleG-nnet.R:3:3', 'test1-CimpleG-rf.R:3:3' • parallel not working properly locally (1): 'test8-CimpleG-parallel.R:4:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test3-CimpleG-xgboost.R:5:3'): signatures are generated w/ xgboost ── <purrr_error_indexed/rlang_error/error/condition> Error in `purrr::map(.x = target_columns, .f = work_helper)`: i In index: 1. Caused by error in `x$callbacks <- purrr::map(x$callbacks, function(x) as.function(c(formals(x), body(x)), env = rlang::base_env()))`: ! ALTLIST classes must provide a Set_elt method [class: XGBAltrepPointerClass, pkg: xgboost] Backtrace: ▆ 1. ├─base::suppressWarnings(...) at test3-CimpleG-xgboost.R:5:3 2. │ └─base::withCallingHandlers(...) 3. ├─base::suppressMessages(...) 4. │ └─base::withCallingHandlers(...) 5. ├─CimpleG::CimpleG(...) 6. ├─CimpleG:::CimpleG.matrix(...) 7. │ └─CimpleG:::CimpleG_main(...) 8. │ ├─purrr::map(.x = target_columns, .f = work_helper) %>% ... 9. │ └─purrr::map(.x = target_columns, .f = work_helper) 10. │ └─purrr:::map_("list", .x, .f, ..., .progress = .progress) 11. │ ├─purrr:::with_indexed_errors(...) 12. │ │ └─base::withCallingHandlers(...) 13. │ ├─purrr:::call_with_cleanup(...) 14. │ └─CimpleG (local) .f(.x[[i]], ...) 15. │ └─CimpleG:::train_general_model(...) 16. │ └─cimpleg_final_model %>% butcher::axe_call() %>% butcher::axe_env() 17. ├─butcher::axe_env(.) 18. ├─workflows:::axe_env.workflow(.) 19. │ ├─butcher::axe_env(fit, verbose = verbose, ...) 20. │ └─butcher:::axe_env.model_fit(fit, verbose = verbose, ...) 21. │ ├─butcher::axe_env(x$fit, verbose = verbose, ...) 22. │ └─butcher:::axe_env.xgb.Booster(x$fit, verbose = verbose, ...) 23. └─base::.handleSimpleError(...) 24. └─purrr (local) h(simpleError(msg, call)) 25. └─cli::cli_abort(...) 26. └─rlang::abort(...) [ FAIL 1 | WARN 0 | SKIP 4 | PASS 62 ] Error: ! Test failures. Execution halted Flavor: r-devel-linux-x86_64-fedora-gcc

Version: 1.0.0
Check: tests
Result: ERROR Running ‘spelling.R’ [0s/0s] Running ‘testthat.R’ [48s/25s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(CimpleG) --------------------- CimpleG version 1.0.0 --------------------- > > test_check("CimpleG") Starting 2 test processes. > test-CimpleG.R: Setting options('download.file.method.GEOquery'='auto') > test-CimpleG.R: Setting options('GEOquery.inmemory.gpl'=FALSE) Saving _problems/test3-CimpleG-xgboost-13.R [ FAIL 1 | WARN 0 | SKIP 4 | PASS 62 ] ══ Skipped tests (4) ═══════════════════════════════════════════════════════════ • On CRAN (3): 'test1-CimpleG-decisiontree.R:3:3', 'test1-CimpleG-nnet.R:3:3', 'test1-CimpleG-rf.R:3:3' • parallel not working properly locally (1): 'test8-CimpleG-parallel.R:4:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test3-CimpleG-xgboost.R:5:3'): signatures are generated w/ xgboost ── <purrr_error_indexed/rlang_error/error/condition> Error in `purrr::map(.x = target_columns, .f = work_helper)`: i In index: 1. Caused by error in `x$callbacks <- purrr::map(x$callbacks, function(x) as.function(c(formals(x), body(x)), env = rlang::base_env()))`: ! ALTLIST classes must provide a Set_elt method [class: XGBAltrepPointerClass, pkg: xgboost] Backtrace: ▆ 1. ├─base::suppressWarnings(...) at test3-CimpleG-xgboost.R:5:3 2. │ └─base::withCallingHandlers(...) 3. ├─base::suppressMessages(...) 4. │ └─base::withCallingHandlers(...) 5. ├─CimpleG::CimpleG(...) 6. ├─CimpleG:::CimpleG.matrix(...) 7. │ └─CimpleG:::CimpleG_main(...) 8. │ ├─purrr::map(.x = target_columns, .f = work_helper) %>% ... 9. │ └─purrr::map(.x = target_columns, .f = work_helper) 10. │ └─purrr:::map_("list", .x, .f, ..., .progress = .progress) 11. │ ├─purrr:::with_indexed_errors(...) 12. │ │ └─base::withCallingHandlers(...) 13. │ ├─purrr:::call_with_cleanup(...) 14. │ └─CimpleG (local) .f(.x[[i]], ...) 15. │ └─CimpleG:::train_general_model(...) 16. │ └─cimpleg_final_model %>% butcher::axe_call() %>% butcher::axe_env() 17. ├─butcher::axe_env(.) 18. ├─workflows:::axe_env.workflow(.) 19. │ ├─butcher::axe_env(fit, verbose = verbose, ...) 20. │ └─butcher:::axe_env.model_fit(fit, verbose = verbose, ...) 21. │ ├─butcher::axe_env(x$fit, verbose = verbose, ...) 22. │ └─butcher:::axe_env.xgb.Booster(x$fit, verbose = verbose, ...) 23. └─base::.handleSimpleError(...) 24. └─purrr (local) h(simpleError(msg, call)) 25. └─cli::cli_abort(...) 26. └─rlang::abort(...) [ FAIL 1 | WARN 0 | SKIP 4 | PASS 62 ] Error: ! Test failures. Execution halted Flavor: r-release-macos-arm64

Version: 1.0.0
Check: tests
Result: ERROR Running ‘spelling.R’ [0s/0s] Running ‘testthat.R’ [150s/86s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(CimpleG) --------------------- CimpleG version 1.0.0 --------------------- > > test_check("CimpleG") Starting 2 test processes. Saving _problems/test3-CimpleG-xgboost-13.R [ FAIL 1 | WARN 0 | SKIP 4 | PASS 62 ] ══ Skipped tests (4) ═══════════════════════════════════════════════════════════ • On CRAN (3): 'test1-CimpleG-decisiontree.R:3:3', 'test1-CimpleG-nnet.R:3:3', 'test1-CimpleG-rf.R:3:3' • parallel not working properly locally (1): 'test8-CimpleG-parallel.R:4:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test3-CimpleG-xgboost.R:5:3'): signatures are generated w/ xgboost ── <purrr_error_indexed/rlang_error/error/condition> Error in `purrr::map(.x = target_columns, .f = work_helper)`: i In index: 1. Caused by error in `x$callbacks <- purrr::map(x$callbacks, function(x) as.function(c(formals(x), body(x)), env = rlang::base_env()))`: ! ALTLIST classes must provide a Set_elt method [class: XGBAltrepPointerClass, pkg: xgboost] Backtrace: ▆ 1. ├─base::suppressWarnings(...) at test3-CimpleG-xgboost.R:5:3 2. │ └─base::withCallingHandlers(...) 3. ├─base::suppressMessages(...) 4. │ └─base::withCallingHandlers(...) 5. ├─CimpleG::CimpleG(...) 6. ├─CimpleG:::CimpleG.matrix(...) 7. │ └─CimpleG:::CimpleG_main(...) 8. │ ├─purrr::map(.x = target_columns, .f = work_helper) %>% ... 9. │ └─purrr::map(.x = target_columns, .f = work_helper) 10. │ └─purrr:::map_("list", .x, .f, ..., .progress = .progress) 11. │ ├─purrr:::with_indexed_errors(...) 12. │ │ └─base::withCallingHandlers(...) 13. │ ├─purrr:::call_with_cleanup(...) 14. │ └─CimpleG (local) .f(.x[[i]], ...) 15. │ └─CimpleG:::train_general_model(...) 16. │ └─cimpleg_final_model %>% butcher::axe_call() %>% butcher::axe_env() 17. ├─butcher::axe_env(.) 18. ├─workflows:::axe_env.workflow(.) 19. │ ├─butcher::axe_env(fit, verbose = verbose, ...) 20. │ └─butcher:::axe_env.model_fit(fit, verbose = verbose, ...) 21. │ ├─butcher::axe_env(x$fit, verbose = verbose, ...) 22. │ └─butcher:::axe_env.xgb.Booster(x$fit, verbose = verbose, ...) 23. └─base::.handleSimpleError(...) 24. └─purrr (local) h(simpleError(msg, call)) 25. └─cli::cli_abort(...) 26. └─rlang::abort(...) [ FAIL 1 | WARN 0 | SKIP 4 | PASS 62 ] Error: ! Test failures. Execution halted Flavor: r-release-macos-x86_64

Version: 1.0.0
Check: package dependencies
Result: NOTE Package suggested but not available for checking: ‘EpiDISH’ 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’ [44s/23s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(CimpleG) --------------------- CimpleG version 1.0.0 --------------------- > > test_check("CimpleG") Starting 2 test processes. > test-CimpleG.R: Setting options('download.file.method.GEOquery'='auto') > test-CimpleG.R: Setting options('GEOquery.inmemory.gpl'=FALSE) Saving _problems/test3-CimpleG-xgboost-13.R [ FAIL 1 | WARN 0 | SKIP 4 | PASS 62 ] ══ Skipped tests (4) ═══════════════════════════════════════════════════════════ • On CRAN (3): 'test1-CimpleG-decisiontree.R:3:3', 'test1-CimpleG-nnet.R:3:3', 'test1-CimpleG-rf.R:3:3' • parallel not working properly locally (1): 'test8-CimpleG-parallel.R:4:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test3-CimpleG-xgboost.R:5:3'): signatures are generated w/ xgboost ── <purrr_error_indexed/rlang_error/error/condition> Error in `purrr::map(.x = target_columns, .f = work_helper)`: i In index: 1. Caused by error in `x$callbacks <- purrr::map(x$callbacks, function(x) as.function(c(formals(x), body(x)), env = rlang::base_env()))`: ! ALTLIST classes must provide a Set_elt method [class: XGBAltrepPointerClass, pkg: xgboost] Backtrace: ▆ 1. ├─base::suppressWarnings(...) at test3-CimpleG-xgboost.R:5:3 2. │ └─base::withCallingHandlers(...) 3. ├─base::suppressMessages(...) 4. │ └─base::withCallingHandlers(...) 5. ├─CimpleG::CimpleG(...) 6. ├─CimpleG:::CimpleG.matrix(...) 7. │ └─CimpleG:::CimpleG_main(...) 8. │ ├─purrr::map(.x = target_columns, .f = work_helper) %>% ... 9. │ └─purrr::map(.x = target_columns, .f = work_helper) 10. │ └─purrr:::map_("list", .x, .f, ..., .progress = .progress) 11. │ ├─purrr:::with_indexed_errors(...) 12. │ │ └─base::withCallingHandlers(...) 13. │ ├─purrr:::call_with_cleanup(...) 14. │ └─CimpleG (local) .f(.x[[i]], ...) 15. │ └─CimpleG:::train_general_model(...) 16. │ └─cimpleg_final_model %>% butcher::axe_call() %>% butcher::axe_env() 17. ├─butcher::axe_env(.) 18. ├─workflows:::axe_env.workflow(.) 19. │ ├─butcher::axe_env(fit, verbose = verbose, ...) 20. │ └─butcher:::axe_env.model_fit(fit, verbose = verbose, ...) 21. │ ├─butcher::axe_env(x$fit, verbose = verbose, ...) 22. │ └─butcher:::axe_env.xgb.Booster(x$fit, verbose = verbose, ...) 23. └─base::.handleSimpleError(...) 24. └─purrr (local) h(simpleError(msg, call)) 25. └─cli::cli_abort(...) 26. └─rlang::abort(...) [ FAIL 1 | WARN 0 | SKIP 4 | PASS 62 ] Error: ! Test failures. Execution halted Flavor: r-oldrel-macos-arm64

Version: 1.0.0
Check: tests
Result: ERROR Running ‘spelling.R’ [0s/0s] Running ‘testthat.R’ [160s/90s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(CimpleG) --------------------- CimpleG version 1.0.0 --------------------- > > test_check("CimpleG") Starting 2 test processes. > test-CimpleG.R: Setting options('download.file.method.GEOquery'='auto') > test-CimpleG.R: Setting options('GEOquery.inmemory.gpl'=FALSE) Saving _problems/test3-CimpleG-xgboost-13.R [ FAIL 1 | WARN 0 | SKIP 4 | PASS 62 ] ══ Skipped tests (4) ═══════════════════════════════════════════════════════════ • On CRAN (3): 'test1-CimpleG-decisiontree.R:3:3', 'test1-CimpleG-nnet.R:3:3', 'test1-CimpleG-rf.R:3:3' • parallel not working properly locally (1): 'test8-CimpleG-parallel.R:4:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test3-CimpleG-xgboost.R:5:3'): signatures are generated w/ xgboost ── <purrr_error_indexed/rlang_error/error/condition> Error in `purrr::map(.x = target_columns, .f = work_helper)`: i In index: 1. Caused by error in `x$callbacks <- purrr::map(x$callbacks, function(x) as.function(c(formals(x), body(x)), env = rlang::base_env()))`: ! ALTLIST classes must provide a Set_elt method [class: XGBAltrepPointerClass, pkg: xgboost] Backtrace: ▆ 1. ├─base::suppressWarnings(...) at test3-CimpleG-xgboost.R:5:3 2. │ └─base::withCallingHandlers(...) 3. ├─base::suppressMessages(...) 4. │ └─base::withCallingHandlers(...) 5. ├─CimpleG::CimpleG(...) 6. ├─CimpleG:::CimpleG.matrix(...) 7. │ └─CimpleG:::CimpleG_main(...) 8. │ ├─purrr::map(.x = target_columns, .f = work_helper) %>% ... 9. │ └─purrr::map(.x = target_columns, .f = work_helper) 10. │ └─purrr:::map_("list", .x, .f, ..., .progress = .progress) 11. │ ├─purrr:::with_indexed_errors(...) 12. │ │ └─base::withCallingHandlers(...) 13. │ ├─purrr:::call_with_cleanup(...) 14. │ └─CimpleG (local) .f(.x[[i]], ...) 15. │ └─CimpleG:::train_general_model(...) 16. │ └─cimpleg_final_model %>% butcher::axe_call() %>% butcher::axe_env() 17. ├─butcher::axe_env(.) 18. ├─workflows:::axe_env.workflow(.) 19. │ ├─butcher::axe_env(fit, verbose = verbose, ...) 20. │ └─butcher:::axe_env.model_fit(fit, verbose = verbose, ...) 21. │ ├─butcher::axe_env(x$fit, verbose = verbose, ...) 22. │ └─butcher:::axe_env.xgb.Booster(x$fit, verbose = verbose, ...) 23. └─base::.handleSimpleError(...) 24. └─purrr (local) h(simpleError(msg, call)) 25. └─cli::cli_abort(...) 26. └─rlang::abort(...) [ FAIL 1 | WARN 0 | SKIP 4 | PASS 62 ] Error: ! Test failures. Execution halted Flavor: r-oldrel-macos-x86_64