CRAN Package Check Results for Package abn

Last updated on 2024-06-19 12:27:01 CEST.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 3.1.1 226.73 226.38 453.11 NOTE --no-tests
r-devel-linux-x86_64-debian-gcc 3.1.1 150.32 161.50 311.82 NOTE --no-tests
r-devel-linux-x86_64-fedora-clang 3.1.1 2431.75 ERROR
r-devel-linux-x86_64-fedora-gcc 3.1.1 2441.50 ERROR
r-devel-windows-x86_64 3.1.1 175.00 304.00 479.00 NOTE
r-patched-linux-x86_64 3.1.1 166.07 213.91 379.98 NOTE --no-tests
r-release-linux-x86_64 3.1.1 168.29 217.21 385.50 NOTE --no-tests
r-release-macos-arm64 3.1.1 385.00 ERROR
r-release-macos-x86_64 3.1.1 738.00 ERROR
r-release-windows-x86_64 3.1.1 174.00 310.00 484.00 NOTE
r-oldrel-macos-arm64 3.1.1 440.00 ERROR
r-oldrel-macos-x86_64 3.1.1 805.00 ERROR
r-oldrel-windows-x86_64 3.1.1 216.00 401.00 617.00 ERROR

Additional issues

ATLAS MKL noLD OpenBLAS

Check Details

Version: 3.1.1
Flags: --no-tests
Check: package dependencies
Result: NOTE Package suggested but not available for checking: ‘INLA’ Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-patched-linux-x86_64, r-release-linux-x86_64

Version: 3.1.1
Check: installed package size
Result: NOTE installed size is 5.6Mb sub-directories of 1Mb or more: extdata 3.0Mb 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: 3.1.1
Check: tests
Result: ERROR Running ‘testthat.R’ [30m/35m] 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(abn) abn version 3.1.1 (2024-05-22) is loaded. To cite the package 'abn' in publications call: citation('abn'). Attaching package: 'abn' The following object is masked from 'package:base': factorial > > require(RhpcBLASctl) Loading required package: RhpcBLASctl > omp_set_num_threads(2) > > test_check("abn") Loading required package: Matrix Running in single core mode. 'cluster.type' is ignored. Running in single core mode. 'cluster.type' is ignored. Running in single core mode. 'cluster.type' is ignored. Running in single core mode. 'cluster.type' is ignored. Flavor: r-devel-linux-x86_64-fedora-clang

Version: 3.1.1
Check: tests
Result: ERROR Running ‘testthat.R’ [30m/34m] 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(abn) abn version 3.1.1 (2024-05-22) is loaded. To cite the package 'abn' in publications call: citation('abn'). Attaching package: 'abn' The following object is masked from 'package:base': factorial > > require(RhpcBLASctl) Loading required package: RhpcBLASctl > omp_set_num_threads(2) > > test_check("abn") Loading required package: Matrix Running in single core mode. 'cluster.type' is ignored. Running in single core mode. 'cluster.type' is ignored. Running in single core mode. 'cluster.type' is ignored. Running in single core mode. 'cluster.type' is ignored. Flavor: r-devel-linux-x86_64-fedora-gcc

Version: 3.1.1
Check: package dependencies
Result: NOTE Package suggested but not available for checking: ‘INLA’ Flavors: r-release-macos-arm64, r-release-macos-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64

Version: 3.1.1
Check: tests
Result: ERROR Running ‘testthat.R’ [255s/256s] Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: 9. │ │ └─base::withCallingHandlers(...) 10. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 11. └─abn::buildScoreCache(...) 12. └─abn::buildScoreCache.bayes(...) 13. └─... %do% ... 14. └─e$fun(obj, substitute(ex), parent.frame(), e$data) 15. └─base::library(p, character.only = TRUE) [ FAIL 7 | WARN 0 | SKIP 56 | PASS 444 ] Deleting unused snapshots: • tographviz/graph.dot • tographviz/graph1.dot • tographviz/graph_group.dot Error: Test failures Execution halted Flavor: r-release-macos-arm64

Version: 3.1.1
Check: tests
Result: ERROR Running ‘testthat.R’ [492s/492s] Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: 9. │ │ └─base::withCallingHandlers(...) 10. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 11. └─abn::buildScoreCache(...) 12. └─abn::buildScoreCache.bayes(...) 13. └─... %do% ... 14. └─e$fun(obj, substitute(ex), parent.frame(), e$data) 15. └─base::library(p, character.only = TRUE) [ FAIL 7 | WARN 0 | SKIP 56 | PASS 444 ] Deleting unused snapshots: • tographviz/graph.dot • tographviz/graph1.dot • tographviz/graph_group.dot Error: Test failures Execution halted Flavor: r-release-macos-x86_64

Version: 3.1.1
Check: tests
Result: ERROR Running ‘testthat.R’ [295s/301s] Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: 9. │ │ └─base::withCallingHandlers(...) 10. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 11. └─abn::buildScoreCache(...) 12. └─abn::buildScoreCache.bayes(...) 13. └─... %do% ... 14. └─e$fun(obj, substitute(ex), parent.frame(), e$data) 15. └─base::library(p, character.only = TRUE) [ FAIL 7 | WARN 0 | SKIP 56 | PASS 444 ] Deleting unused snapshots: • tographviz/graph.dot • tographviz/graph1.dot • tographviz/graph_group.dot Error: Test failures Execution halted Flavor: r-oldrel-macos-arm64

Version: 3.1.1
Check: running R code from vignettes
Result: WARN Errors in running code in vignettes: when running code in ‘model_specification.Rmd’ ... + length(max.pars))) > for (i in max.pars) { + mycache <- buildScoreCache(data.df = mydat, data.dists = mydists, + method = "bayes", max.parents = i) + mp .... [TRUNCATED] When sourcing ‘model_specification.R’: Error: there is no package called ‘INLA’ Execution halted when running code in ‘quick_start_example.Rmd’ ... + b .... [TRUNCATED] > max.par <- 4 > mycache <- buildScoreCache(data.df = mydat, data.dists = mydists, + method = "bayes", max.parents = max.par) When sourcing ‘quick_start_example.R’: Error: there is no package called ‘INLA’ Execution halted ‘data_simulation.Rmd’ using ‘UTF-8’... [0s/0s] OK ‘mixed_effect_BN_model.Rmd’ using ‘UTF-8’... [5s/5s] OK ‘model_specification.Rmd’ using ‘UTF-8’... failed ‘multiprocessing.Rmd’ using ‘UTF-8’... [0s/0s] OK ‘parameter_learning.Rmd’ using ‘UTF-8’... [0s/0s] OK ‘quick_start_example.Rmd’ using ‘UTF-8’... failed ‘structure_learning.Rmd’ using ‘UTF-8’... [1s/1s] OK Flavor: r-oldrel-macos-arm64

Version: 3.1.1
Check: tests
Result: ERROR Running ‘testthat.R’ [535s/574s] Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: 9. │ │ └─base::withCallingHandlers(...) 10. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 11. └─abn::buildScoreCache(...) 12. └─abn::buildScoreCache.bayes(...) 13. └─... %do% ... 14. └─e$fun(obj, substitute(ex), parent.frame(), e$data) 15. └─base::library(p, character.only = TRUE) [ FAIL 7 | WARN 0 | SKIP 56 | PASS 444 ] Deleting unused snapshots: • tographviz/graph.dot • tographviz/graph1.dot • tographviz/graph_group.dot Error: Test failures Execution halted Flavor: r-oldrel-macos-x86_64

Version: 3.1.1
Check: running R code from vignettes
Result: WARN Errors in running code in vignettes: when running code in ‘model_specification.Rmd’ ... + length(max.pars))) > for (i in max.pars) { + mycache <- buildScoreCache(data.df = mydat, data.dists = mydists, + method = "bayes", max.parents = i) + mp .... [TRUNCATED] When sourcing ‘model_specification.R’: Error: there is no package called ‘INLA’ Execution halted when running code in ‘quick_start_example.Rmd’ ... + b .... [TRUNCATED] > max.par <- 4 > mycache <- buildScoreCache(data.df = mydat, data.dists = mydists, + method = "bayes", max.parents = max.par) When sourcing ‘quick_start_example.R’: Error: there is no package called ‘INLA’ Execution halted ‘data_simulation.Rmd’ using ‘UTF-8’... [0s/0s] OK ‘mixed_effect_BN_model.Rmd’ using ‘UTF-8’... [9s/9s] OK ‘model_specification.Rmd’ using ‘UTF-8’... failed ‘multiprocessing.Rmd’ using ‘UTF-8’... [0s/0s] OK ‘parameter_learning.Rmd’ using ‘UTF-8’... [0s/0s] OK ‘quick_start_example.Rmd’ using ‘UTF-8’... failed ‘structure_learning.Rmd’ using ‘UTF-8’... [2s/2s] OK Flavor: r-oldrel-macos-x86_64

Version: 3.1.1
Check: tests
Result: ERROR Running 'testthat.R' [125s] 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(abn) abn version 3.1.1 (2024-05-22) is loaded. To cite the package 'abn' in publications call: citation('abn'). Attaching package: 'abn' The following object is masked from 'package:base': factorial > > require(RhpcBLASctl) Loading required package: RhpcBLASctl > omp_set_num_threads(2) > > test_check("abn") Loading required package: Matrix Running in single core mode. 'cluster.type' is ignored. Running in single core mode. 'cluster.type' is ignored. Running in single core mode. 'cluster.type' is ignored. Running in single core mode. 'cluster.type' is ignored. [ FAIL 7 | WARN 0 | SKIP 82 | PASS 301 ] ══ Skipped tests (82) ══════════════════════════════════════════════════════════ • BuildScoreCache(method=mle) crashes with Poisson nodes (1): 'test-fitabn_mle.R:138:3' • INLA is not tested on CRAN (1): 'test-search_hillclimber.R:79:7' • On CRAN (51): 'test-Coutput.R:1:1', 'test-abn-methods.R:29:3', 'test-abn-methods.R:55:3', 'test-abn-methods.R:76:3', 'test-abn-methods.R:102:3', 'test-abn-methods.R:125:3', 'test-abn-methods.R:154:3', 'test-abn-methods.R:177:3', 'test-abn-methods.R:200:3', 'test-abn-methods.R:228:3', 'test-abn-methods.R:253:3', 'test-abn-methods.R:278:3', 'test-abn-methods.R:303:3', 'test-abn-methods.R:328:3', 'test-abn-methods.R:353:3', 'test-abn-methods.R:378:3', 'test-abn-methods.R:403:3', 'test-abn-methods.R:428:3', 'test-build_score_cache.R:122:3', 'test-build_score_cache.R:181:3', 'test-build_score_cache.R:331:3', 'test-build_score_cache.R:386:3', 'test-build_score_cache.R:434:3', 'test-build_score_cache_bayes.R:2:3', 'test-build_score_cache_bayes.R:33:3', 'test-build_score_cache_bayes.R:91:3', 'test-build_score_cache_bayes.R:127:3', 'test-calc_node_inla_glm.R:2:3', 'test-calc_node_inla_glmm.R:2:3', 'test-fitabn.R:26:3', 'test-fitabn.R:56:3', 'test-fitabn.R:75:3', 'test-fitabn.R:94:3', 'test-fitabn.R:136:3', 'test-fitabn.R:190:3', 'test-fitabn.R:379:3', 'test-fitabn_bayes.R:2:3', 'test-mostprobable.R:2:3', 'test-mostprobable.R:12:3', 'test-mostprobable.R:79:3', 'test-mostprobable.R:169:3', 'test-mostprobable.R:211:3', 'test-plot-abn.R:34:3', 'test-plot-abn.R:125:3', 'test-search_heuristic.R:2:3', 'test-search_hillclimber.R:16:3', 'test-search_hillclimber.R:84:3', 'test-simulateabn.R:508:3', 'test-simulateabn.R:810:3', 'test-tographviz.R:27:3', 'test-tographviz.R:171:3' • Plot classic view is deprecated. (1): 'test-plot-abn.R:117:3' • `buildScoreCache.mle()` is tested mainly on Unix-like systems. (6): 'test-build_score_cache_mle.R:32:5', 'test-build_score_cache_mle.R:84:5', 'test-build_score_cache_mle.R:121:5', 'test-build_score_cache_mle.R:159:5', 'test-build_score_cache_mle.R:220:5', 'test-build_score_cache_mle.R:260:5' • empty test (2): 'test-abn-methods.R:15:1', 'test-build_score_cache_mle.R:264:1' • fitAbn.mle() is tested mainly on Unix-like systems (8): 'test-fitabn_mle.R:32:7', 'test-fitabn_mle.R:83:7', 'test-fitabn_mle.R:132:7', 'test-fitabn_mle.R:286:7', 'test-fitabn_mle.R:384:7', 'test-fitabn_mle.R:482:7', 'test-fitabn_mle.R:592:9', 'test-fitabn_mle.R:704:9' • simulateAbn() is tested mainly on Unix-like systems (12): 'test-simulateabn.R:35:5', 'test-simulateabn.R:90:5', 'test-simulateabn.R:139:5', 'test-simulateabn.R:188:5', 'test-simulateabn.R:236:5', 'test-simulateabn.R:304:5', 'test-simulateabn.R:373:5', 'test-simulateabn.R:422:5', 'test-simulateabn.R:471:5', 'test-simulateabn.R:704:5', 'test-simulateabn.R:805:5', 'test-simulateabn.R:994:9' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test-build_score_cache.R:41:7'): buildScoreCache() checks work fine ── Expected `buildScoreCache(data.df = df, data.dists = dists)` to run without any errors. i Actually got a <packageNotFoundError> with text: there is no package called 'INLA' Backtrace: ▆ 1. ├─base::suppressWarnings(...) at test-build_score_cache.R:33:3 2. │ └─base::withCallingHandlers(...) 3. ├─base::suppressMessages(...) at test-build_score_cache.R:34:5 4. │ └─base::withCallingHandlers(...) 5. └─testthat::expect_no_error(buildScoreCache(data.df = df, data.dists = dists)) at test-build_score_cache.R:41:7 ── Failure ('test-build_score_cache.R:42:7'): buildScoreCache() checks work fine ── Expected `buildScoreCache(data.df = df, data.dists = dists, method = "Bayes")` to run without any errors. i Actually got a <packageNotFoundError> with text: there is no package called 'INLA' Backtrace: ▆ 1. ├─base::suppressWarnings(...) at test-build_score_cache.R:33:3 2. │ └─base::withCallingHandlers(...) 3. ├─base::suppressMessages(...) at test-build_score_cache.R:34:5 4. │ └─base::withCallingHandlers(...) 5. └─testthat::expect_no_error(...) at test-build_score_cache.R:42:7 ── Failure ('test-build_score_cache.R:43:7'): buildScoreCache() checks work fine ── Expected `buildScoreCache(data.df = df, data.dists = dists, method = "bayes")` to run without any errors. i Actually got a <packageNotFoundError> with text: there is no package called 'INLA' Backtrace: ▆ 1. ├─base::suppressWarnings(...) at test-build_score_cache.R:33:3 2. │ └─base::withCallingHandlers(...) 3. ├─base::suppressMessages(...) at test-build_score_cache.R:34:5 4. │ └─base::withCallingHandlers(...) 5. └─testthat::expect_no_error(...) at test-build_score_cache.R:43:7 ── Failure ('test-build_score_cache.R:49:7'): buildScoreCache() checks work fine ── Expected `buildScoreCache(...)` to run without any errors. i Actually got a <packageNotFoundError> with text: there is no package called 'INLA' Backtrace: ▆ 1. ├─base::suppressWarnings(...) at test-build_score_cache.R:33:3 2. │ └─base::withCallingHandlers(...) 3. ├─base::suppressMessages(...) at test-build_score_cache.R:34:5 4. │ └─base::withCallingHandlers(...) 5. └─testthat::expect_no_error(...) at test-build_score_cache.R:49:7 ── Failure ('test-build_score_cache.R:53:7'): buildScoreCache() checks work fine ── Expected `buildScoreCache(...)` to run without any errors. i Actually got a <packageNotFoundError> with text: there is no package called 'INLA' Backtrace: ▆ 1. ├─base::suppressWarnings(...) at test-build_score_cache.R:33:3 2. │ └─base::withCallingHandlers(...) 3. ├─base::suppressMessages(...) at test-build_score_cache.R:34:5 4. │ └─base::withCallingHandlers(...) 5. └─testthat::expect_no_error(...) at test-build_score_cache.R:53:7 ── Failure ('test-build_score_cache.R:62:7'): buildScoreCache() checks work fine ── Expected `buildScoreCache(...)` to run without any errors. i Actually got a <packageNotFoundError> with text: there is no package called 'INLA' Backtrace: ▆ 1. ├─base::suppressWarnings(...) at test-build_score_cache.R:33:3 2. │ └─base::withCallingHandlers(...) 3. ├─base::suppressMessages(...) at test-build_score_cache.R:34:5 4. │ └─base::withCallingHandlers(...) 5. └─testthat::expect_no_error(...) at test-build_score_cache.R:62:7 ── Error ('test-build_score_cache.R:66:7'): buildScoreCache() checks work fine ── <packageNotFoundError/error/condition> Error in `library(p, character.only = TRUE)`: there is no package called 'INLA' Backtrace: ▆ 1. ├─base::suppressWarnings(...) at test-build_score_cache.R:33:3 2. │ └─base::withCallingHandlers(...) 3. ├─base::suppressMessages(...) at test-build_score_cache.R:34:5 4. │ └─base::withCallingHandlers(...) 5. ├─testthat::expect_warning(...) at test-build_score_cache.R:66:7 6. │ └─testthat:::expect_condition_matching(...) 7. │ └─testthat:::quasi_capture(...) 8. │ ├─testthat (local) .capture(...) 9. │ │ └─base::withCallingHandlers(...) 10. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 11. └─abn::buildScoreCache(...) 12. └─abn::buildScoreCache.bayes(...) 13. └─... %do% ... 14. └─e$fun(obj, substitute(ex), parent.frame(), e$data) 15. └─base::library(p, character.only = TRUE) [ FAIL 7 | WARN 0 | SKIP 82 | PASS 301 ] Deleting unused snapshots: • tographviz/graph.dot • tographviz/graph1.dot • tographviz/graph_group.dot Error: Test failures Execution halted Flavor: r-oldrel-windows-x86_64