• using R Under development (unstable) (2025-02-26 r87829)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     gcc (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3)     GNU Fortran (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3)
• running under: Fedora Linux 40 (Workstation Edition)
• using session charset: UTF-8
• using option ‘--no-stop-on-test-error’
• checking for file ‘abn/DESCRIPTION’ ... OK
• this is package ‘abn’ version ‘3.1.1’
• package encoding: UTF-8
• checking package namespace information ... OK
• checking package dependencies ... OK
• checking if this is a source package ... OK
• checking if there is a namespace ... OK
• checking for executable files ... OK
• checking for hidden files and directories ... OK
• checking for portable file names ... OK
• checking for sufficient/correct file permissions ... OK
• checking whether package ‘abn’ can be installed ... [5m/11m] OK See the install log for details.
• used C compiler: ‘gcc (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3)’
• used C++ compiler: ‘g++ (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3)’
• checking package directory ... OK
• checking ‘build’ directory ... OK
• checking DESCRIPTION meta-information ... OK
• checking top-level files ... OK
• checking for left-over files ... OK
• checking index information ... OK
• checking package subdirectories ... OK
• checking code files for non-ASCII characters ... OK
• checking R files for syntax errors ... OK
• checking whether the package can be loaded ... [6s/17s] OK
• checking whether the package can be loaded with stated dependencies ... [5s/16s] OK
• checking whether the package can be unloaded cleanly ... [5s/14s] OK
• checking whether the namespace can be loaded with stated dependencies ... [5s/15s] OK
• checking whether the namespace can be unloaded cleanly ... [5s/14s] OK
• checking loading without being on the library search path ... [5s/15s] OK
• checking whether startup messages can be suppressed ... [6s/20s] OK
• checking use of S3 registration ... OK
• checking dependencies in R code ... OK
• checking S3 generic/method consistency ... OK
• checking replacement functions ... OK
• checking foreign function calls ... OK
• checking R code for possible problems ... [61s/162s] OK
• checking Rd files ... OK
• checking Rd metadata ... OK
• checking Rd line widths ... OK
• checking Rd cross-references ... OK
• checking for missing documentation entries ... OK
• checking for code/documentation mismatches ... OK
• checking Rd \usage sections ... OK
• checking Rd contents ... OK
• checking for unstated dependencies in examples ... OK
• checking contents of ‘data’ directory ... OK
• checking data for non-ASCII characters ... OK
• checking LazyData ... OK
• checking data for ASCII and uncompressed saves ... OK
• checking line endings in shell scripts ... OK
• checking line endings in C/C++/Fortran sources/headers ... OK
• checking line endings in Makefiles ... OK
• checking compilation flags in Makevars ... OK
• checking for GNU extensions in Makefiles ... OK
• checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
• checking use of PKG_*FLAGS in Makefiles ... OK
• checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK
• checking pragmas in C/C++ headers and code ... OK
• checking compilation flags used ... OK
• checking compiled code ... OK
• checking installed files from ‘inst/doc’ ... OK
• checking files in ‘vignettes’ ... OK
• checking examples ... [35s/120s] OK
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [7m/34m] ERROR   Running ‘testthat.R’ [7m/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.   [ FAIL 9 | WARN 0 | SKIP 55 | PASS 448 ]      ══ Skipped tests (55) ══════════════════════════════════════════════════════════   • 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 (52): '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-fitabn_mle.R:562:11', 'test-fitabn_mle.R:674:11',     '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'   • Plot classic view is deprecated. (1): 'test-plot-abn.R:117:3'      ══ Failed tests ════════════════════════════════════════════════════════════════   ── Failure ('test-simulateabn.R:780:13'): simulateAbn() simulation works with method 'mle' ──   Expected `{ ... }` to run without any errors.   i Actually got a <simpleError> with text:     DAG matrix contains trivial cycles (nonzero values on diagonal)   Backtrace:       ▆    1. ├─base::suppressWarnings(...) at test-simulateabn.R:761:5    2. │ └─base::withCallingHandlers(...)    3. ├─base::suppressMessages(...) at test-simulateabn.R:762:7    4. │ └─base::withCallingHandlers(...)    5. ├─utils::capture.output(...) at test-simulateabn.R:763:9    6. │ └─base::withVisible(...elt(i))    7. └─testthat::expect_no_error(...) at test-simulateabn.R:779:11   ── Failure ('test-simulateabn.R:783:13'): simulateAbn() simulation works with method 'mle' ──   Expected `{ ... }` to run without any errors.   i Actually got a <simpleError> with text:     object 'myres.mle.grp' not found   Backtrace:       ▆    1. ├─base::suppressWarnings(...) at test-simulateabn.R:761:5    2. │ └─base::withCallingHandlers(...)    3. ├─base::suppressMessages(...) at test-simulateabn.R:762:7    4. │ └─base::withCallingHandlers(...)    5. ├─utils::capture.output(...) at test-simulateabn.R:763:9    6. │ └─base::withVisible(...elt(i))    7. └─testthat::expect_no_error(...) at test-simulateabn.R:782:11   ── Error ('test-simulateabn.R:794:5'): simulateAbn() simulation works with method 'mle' ──   Error in `eval(code, test_env)`: object 'mysim.grp' not found   Backtrace:       ▆    1. ├─base::prop.table(table(mysim.grp$Outdoor)) at test-simulateabn.R:794:5    2. └─base::table(mysim.grp$Outdoor)   ── Error ('test-simulateabn.R:953:13'): simulateAbn() works with grouping in real data. ──   Error in `validate_abnDag(dag, data.df = data.df, returnDag = TRUE)`: DAG matrix contains trivial cycles (nonzero values on diagonal)   Backtrace:        ▆     1. ├─base::suppressMessages(...) at test-simulateabn.R:914:3     2. │ └─base::withCallingHandlers(...)     3. ├─base::suppressWarnings(...) at test-simulateabn.R:915:5     4. │ └─base::withCallingHandlers(...)     5. ├─utils::capture.output(...) at test-simulateabn.R:917:9     6. │ └─base::withVisible(...elt(i))     7. └─abn::fitAbn(object = mydag, method = "mle") at test-simulateabn.R:953:13     8. └─abn::fitAbn.mle(...)     9. └─abn::createAbnDag(dag, data.df = data.df, data.dists = data.dists)    10. └─abn::validate_abnDag(dag, data.df = data.df, returnDag = TRUE)   ── Failure ('test-tographviz.R:80:11'): toGraphviz() works with all distributions. ──   Expected `{ ... }` to run without any errors.   i Actually got a <simpleError> with text:     DAG matrix contains trivial cycles (nonzero values on diagonal)   Backtrace:       ▆    1. ├─utils::capture.output(...) at test-tographviz.R:53:3    2. │ └─base::withVisible(...elt(i))    3. ├─base::suppressMessages(...) at test-tographviz.R:54:5    4. │ └─base::withCallingHandlers(...)    5. └─testthat::expect_no_error(...) at test-tographviz.R:78:7   ── Failure ('test-tographviz.R:89:5'): toGraphviz() works with all distributions. ──   Expected `{ ... }` to run without any errors.   i Actually got a <simpleError> with text:     object 'myres.mle' not found   ── Failure ('test-tographviz.R:97:5'): toGraphviz() works with all distributions. ──   Expected `{ ... }` to run without any errors.   i Actually got a <simpleError> with text:     object 'myres.mle' not found   ── Failure ('test-tographviz.R:105:5'): toGraphviz() works with all distributions. ──   Expected `{ ... }` to run without any errors.   i Actually got a <simpleError> with text:     'dag' must comprise only 1's or 0's   ── Error ('test-tographviz.R:134:5'): toGraphviz() works with all distributions. ──   Error in `eval(code, test_env)`: object 'myres.mle' not found   Backtrace:       ▆    1. ├─testthat::expect_warning(...) at test-tographviz.R:133:3    2. │ └─testthat:::expect_condition_matching(...)    3. │ └─testthat:::quasi_capture(...)    4. │ ├─testthat (local) .capture(...)    5. │ │ └─base::withCallingHandlers(...)    6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))    7. └─abn::toGraphviz(...) at test-tographviz.R:134:5      [ FAIL 9 | WARN 0 | SKIP 55 | PASS 448 ]   Deleting unused snapshots:   • tographviz/graph.dot   • tographviz/graph1.dot   • tographviz/graph_group.dot   Error: Test failures   Execution halted
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [67s/253s] ERROR Error(s) in re-building vignettes: --- re-building ‘data_simulation.Rmd’ using rmarkdown --- finished re-building ‘data_simulation.Rmd’ --- re-building ‘mixed_effect_BN_model.Rmd’ using rmarkdown ** Processing: /data/gannet/ripley/R/packages/tests-devel/abn.Rcheck/vign_test/abn/vignettes/mixed_effect_BN_model_files/figure-html/unnamed-chunk-3-1.png 288x288 pixels, 3x8 bits/pixel, RGB Input IDAT size = 10733 bytes Input file size = 10823 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 8278   zc = 9 zm = 8 zs = 1 f = 0   zc = 1 zm = 8 zs = 2 f = 0   zc = 9 zm = 8 zs = 3 f = 0   zc = 9 zm = 8 zs = 0 f = 5   zc = 9 zm = 8 zs = 1 f = 5   zc = 1 zm = 8 zs = 2 f = 5   zc = 9 zm = 8 zs = 3 f = 5                                 Selecting parameters:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 8278 Output IDAT size = 8278 bytes (2455 bytes decrease) Output file size = 8356 bytes (2467 bytes = 22.79% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-devel/abn.Rcheck/vign_test/abn/vignettes/mixed_effect_BN_model_files/figure-html/unnamed-chunk-4-1.png 288x288 pixels, 3x8 bits/pixel, RGB Input IDAT size = 13423 bytes Input file size = 13513 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 9984   zc = 9 zm = 8 zs = 1 f = 0   zc = 1 zm = 8 zs = 2 f = 0   zc = 9 zm = 8 zs = 3 f = 0   zc = 9 zm = 8 zs = 0 f = 5   zc = 9 zm = 8 zs = 1 f = 5   zc = 1 zm = 8 zs = 2 f = 5   zc = 9 zm = 8 zs = 3 f = 5                                 Selecting parameters:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 9984 Output IDAT size = 9984 bytes (3439 bytes decrease) Output file size = 10062 bytes (3451 bytes = 25.54% decrease) Quitting from lines 153-159 [unnamed-chunk-5] (mixed_effect_BN_model.Rmd) Error: processing vignette 'mixed_effect_BN_model.Rmd' failed with diagnostics: DAG matrix contains trivial cycles (nonzero values on diagonal) --- failed re-building ‘mixed_effect_BN_model.Rmd’ --- re-building ‘model_specification.Rmd’ using rmarkdown --- finished re-building ‘model_specification.Rmd’ --- re-building ‘multiprocessing.Rmd’ using rmarkdown --- finished re-building ‘multiprocessing.Rmd’ --- re-building ‘parameter_learning.Rmd’ using rmarkdown --- finished re-building ‘parameter_learning.Rmd’ --- re-building ‘quick_start_example.Rmd’ using rmarkdown --- finished re-building ‘quick_start_example.Rmd’ --- re-building ‘structure_learning.Rmd’ using rmarkdown --- finished re-building ‘structure_learning.Rmd’ SUMMARY: processing the following file failed:   ‘mixed_effect_BN_model.Rmd’ Error: Vignette re-building failed. Execution halted
• checking PDF version of manual ... [18s/54s] OK
• checking HTML version of manual ... [9s/32s] OK
• checking for non-standard things in the check directory ... OK
• checking for detritus in the temp directory ... OK
• DONE

Status: 2 ERRORs