* using log directory ‘/srv/hornik/tmp/CRAN/abn.Rcheck’ * using R Under development (unstable) (2023-08-31 r85038) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 16.0.6 (10) GNU Fortran (Debian 13.2.0-1) 13.2.0 * running under: Debian GNU/Linux trixie/sid * using session charset: UTF-8 * checking for file ‘abn/DESCRIPTION’ ... OK * this is package ‘abn’ version ‘3.0.0’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... [5s/6s] NOTE Maintainer: ‘Matteo Delucchi ’ CRAN repository db overrides: Additional_repositories: https://inla.r-inla-download.org/R/stable/ Suggests or Enhances not in mainstream repositories: INLA Availability using Additional_repositories specification: INLA yes https://inla.r-inla-download.org/R/stable/ The Date field is over a month old. * checking package namespace information ... OK * checking package dependencies ... NOTE Package suggested but not available for checking: ‘INLA’ Package in Depends/Imports which should probably only be in LinkingTo: ‘RcppArmadillo’ * 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 ... [71s/71s] OK * used C compiler: ‘Debian clang version 16.0.6 (11)’ * used C++ compiler: ‘Debian clang version 16.0.6 (11)’ * checking package directory ... OK * checking for future file timestamps ... 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 R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... [1s/1s] OK * checking whether the package can be loaded with stated dependencies ... [1s/1s] OK * checking whether the package can be unloaded cleanly ... [1s/1s] OK * checking whether the namespace can be loaded with stated dependencies ... [1s/1s] OK * checking whether the namespace can be unloaded cleanly ... [1s/1s] OK * checking loading without being on the library search path ... [1s/1s] OK * checking whether startup messages can be suppressed ... [1s/1s] 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 ... [11s/11s] OK * checking Rd files ... [0s/0s] 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 ... NOTE Documented arguments not in \usage in documentation object ‘categorical_bugs’: ‘nodesintercept’ Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to syntactically valid R code. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... [0s/0s] 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 sizes of PDF files under ‘inst/doc’ ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... [6s/4s] NOTE Examples with CPU time > 2.5 times elapsed time user system elapsed ratio scoreContribution 1.593 0.036 0.223 7.305 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... [10m/10m] ERROR Running ‘testthat.R’ [10m/10m] 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 3.0.0 (2022-09-01) is loaded. To cite the package 'abn' in publications call: citation('abn'). Attaching package: 'abn' The following object is masked from 'package:base': factorial > > test_check("abn") dev.new(): using pdf(file="Rplots1.pdf") Iteration 1 - deviance = 801.89 - criterion = 2.014199 Iteration 2 - deviance = 800.5341 - criterion = 0.04426251 Iteration 3 - deviance = 800.5339 - criterion = 5.210016e-06 Iteration 4 - deviance = 800.5339 - criterion = 5.363507e-13 converged Iteration 1 - deviance = 798.6166 - criterion = 1.874215 Iteration 2 - deviance = 797.3505 - criterion = 0.03945357 Iteration 3 - deviance = 797.3503 - criterion = 8.411144e-06 Iteration 4 - deviance = 797.3503 - criterion = 6.416675e-13 converged Iteration 1 - deviance = 800.841 - criterion = 1.953695 Iteration 2 - deviance = 799.4241 - criterion = 0.04384531 Iteration 3 - deviance = 799.424 - criterion = 5.262527e-06 Iteration 4 - deviance = 799.424 - criterion = 7.763524e-13 converged Iteration 1 - deviance = 733.9755 - criterion = 1.056032 Iteration 2 - deviance = 730.6673 - criterion = 0.04998392 Iteration 3 - deviance = 730.577 - criterion = 0.002808114 Iteration 4 - deviance = 730.5768 - criterion = 7.365004e-06 Iteration 5 - deviance = 730.5768 - criterion = 3.999521e-11 converged boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') Iteration 1 - deviance = 733.9755 - criterion = 1.056032 Iteration 2 - deviance = 730.6673 - criterion = 0.04998392 Iteration 3 - deviance = 730.577 - criterion = 0.002808114 Iteration 4 - deviance = 730.5768 - criterion = 7.365004e-06 Iteration 5 - deviance = 730.5768 - criterion = 3.999521e-11 converged boundary (singular) fit: see help('isSingular') Iteration 1 - deviance = 801.89 - criterion = 2.014199 Iteration 2 - deviance = 800.5341 - criterion = 0.04426251 Iteration 3 - deviance = 800.5339 - criterion = 5.210016e-06 Iteration 4 - deviance = 800.5339 - criterion = 5.363507e-13 converged Iteration 1 - deviance = 798.6166 - criterion = 1.874215 Iteration 2 - deviance = 797.3505 - criterion = 0.03945357 Iteration 3 - deviance = 797.3503 - criterion = 8.411144e-06 Iteration 4 - deviance = 797.3503 - criterion = 6.416675e-13 converged Iteration 1 - deviance = 800.841 - criterion = 1.953695 Iteration 2 - deviance = 799.4241 - criterion = 0.04384531 Iteration 3 - deviance = 799.424 - criterion = 5.262527e-06 Iteration 4 - deviance = 799.424 - criterion = 7.763524e-13 converged Iteration 1 - deviance = 733.9755 - criterion = 1.056032 Iteration 2 - deviance = 730.6673 - criterion = 0.04998392 Iteration 3 - deviance = 730.577 - criterion = 0.002808114 Iteration 4 - deviance = 730.5768 - criterion = 7.365004e-06 Iteration 5 - deviance = 730.5768 - criterion = 3.999521e-11 converged boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') Iteration 1 - deviance = 801.89 - criterion = 2.014199 Iteration 2 - deviance = 800.5341 - criterion = 0.04426251 Iteration 3 - deviance = 800.5339 - criterion = 5.210016e-06 Iteration 4 - deviance = 800.5339 - criterion = 5.363507e-13 converged boundary (singular) fit: see help('isSingular') [ FAIL 9 | WARN 0 | SKIP 11 | PASS 595 ] ══ Skipped tests (11) ══════════════════════════════════════════════════════════ • BuildScoreCache(method=mle) crashes with Poisson nodes (1): 'test-fitabn_mle.R:126:3' • Numerical results are not tested for method='bayes' (2): 'test-build_score_cache_bayes.R:51:3', 'test-build_score_cache_bayes.R:104:3' • On CRAN (3): 'test-plot-abn.R:34:3', 'test-tographviz.R:27:3', 'test-tographviz.R:171:3' • Plot classic view is deprecated. (1): 'test-plot-abn.R:117:3' • calc.node.inla.glm() test not yet implemented. (1): 'test-calc_node_inla_glm.R:2:3' • calc.node.inla.glmm() test not yet implemented. (1): 'test-calc_node_inla_glmm.R:2:3' • getmarginals() tests not yet implemented. (1): 'test-getmarginals.R:2:3' • plotting for abnHillClimber is not up to date with searchHillClimber()'s output. (1): 'test-abn-methods.R:113:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test-build_score_cache.R:33:3'): buildScoreCache() checks work fine ── Expected `buildScoreCache(...)` to run without any errors. i Actually got a with text: library INLA is not available! INLA is available from https://www.r-inla.org/download-install. Backtrace: ▆ 1. ├─base::suppressWarnings(...) at test-build_score_cache.R:33:2 2. │ └─base::withCallingHandlers(...) 3. ├─base::suppressMessages(...) at test-build_score_cache.R:34:4 4. │ └─base::withCallingHandlers(...) 5. └─testthat::expect_no_error(...) at test-build_score_cache.R:89:6 ── Failure ('test-build_score_cache.R:33:3'): buildScoreCache() checks work fine ── Expected `buildScoreCache(...)` to run without any errors. i Actually got a with text: library INLA is not available! INLA is available from https://www.r-inla.org/download-install. Backtrace: ▆ 1. ├─base::suppressWarnings(...) at test-build_score_cache.R:33:2 2. │ └─base::withCallingHandlers(...) 3. ├─base::suppressMessages(...) at test-build_score_cache.R:34:4 4. │ └─base::withCallingHandlers(...) 5. └─testthat::expect_no_error(...) at test-build_score_cache.R:98:6 ── Failure ('test-build_score_cache.R:33:3'): buildScoreCache() checks work fine ── Expected `buildScoreCache(...)` to run without any errors. i Actually got a with text: library INLA is not available! INLA is available from https://www.r-inla.org/download-install. Backtrace: ▆ 1. ├─base::suppressWarnings(...) at test-build_score_cache.R:33:2 2. │ └─base::withCallingHandlers(...) 3. ├─base::suppressMessages(...) at test-build_score_cache.R:34:4 4. │ └─base::withCallingHandlers(...) 5. └─testthat::expect_no_error(...) at test-build_score_cache.R:101:6 ── Failure ('test-build_score_cache.R:167:3'): buildScoreCache() is backward compatible ── Expected `{ ... }` to run without any errors. i Actually got a with text: library INLA is not available! INLA is available from https://www.r-inla.org/download-install. Backtrace: ▆ 1. ├─base::suppressMessages(...) at test-build_score_cache.R:167:2 2. │ └─base::withCallingHandlers(...) 3. └─testthat::expect_no_error(...) at test-build_score_cache.R:248:4 ── Error ('test-fitabn.R:62:3'): fitAbn() works with DAG as formula statement ── Error in `fitAbn.bayes(dag, data.df = data.df, data.dists = data.dists, group.var = group.var, cor.vars = cor.vars, compute.fixed = compute.fixed, control = ctrl, mylist = mylist, grouped.vars = grouped.vars, group.ids = group.ids, force.method = force.method)`: library INLA is not available! R-INLA is available from https://www.r-inla.org/download-install. Backtrace: ▆ 1. ├─testthat::expect_silent(...) at test-fitabn.R:62:2 2. │ └─testthat:::quasi_capture(enquo(object), NULL, evaluate_promise) 3. │ ├─testthat (local) .capture(...) 4. │ │ ├─withr::with_output_sink(...) 5. │ │ │ └─base::force(code) 6. │ │ ├─base::withCallingHandlers(...) 7. │ │ └─base::withVisible(code) 8. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 9. └─abn::fitAbn(...) 10. └─abn:::fitAbn.bayes(...) ── Error ('test-fitabn.R:229:3'): fitAbn() is backward compatible ────────────── Error in `fitAbn.bayes(dag, data.df = data.df, data.dists = data.dists, group.var = group.var, cor.vars = cor.vars, compute.fixed = compute.fixed, control = ctrl, mylist = mylist, grouped.vars = grouped.vars, group.ids = group.ids, force.method = force.method)`: library INLA is not available! R-INLA is available from https://www.r-inla.org/download-install. Backtrace: ▆ 1. ├─testthat::expect_silent(...) at test-fitabn.R:229:2 2. │ └─testthat:::quasi_capture(enquo(object), NULL, evaluate_promise) 3. │ ├─testthat (local) .capture(...) 4. │ │ ├─withr::with_output_sink(...) 5. │ │ │ └─base::force(code) 6. │ │ ├─base::withCallingHandlers(...) 7. │ │ └─base::withVisible(code) 8. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 9. └─abn::fitAbn(...) at test-fitabn.R:230:4 10. └─abn:::fitAbn.bayes(...) ── Error ('test-mostprobable.R:178:3'): mostProbable() is backward compatible with `ex3.dag.data` ── Error in `buildScoreCache.bayes(data.df = data.df, data.dists = data.dists, group.var = group.var, cor.vars = cor.vars, dag.banned = dag.banned, dag.retained = dag.retained, max.parents = max.parents, which.nodes = which.nodes, defn.res = defn.res, dry.run = dry.run, verbose = verbose, centre = centre, force.method = force.method, mylist = mylist, grouped.vars = grouped.vars, group.ids = group.ids, control = ctrl)`: library INLA is not available! INLA is available from https://www.r-inla.org/download-install. Backtrace: ▆ 1. └─abn::buildScoreCache(...) at test-mostprobable.R:178:2 2. └─abn:::buildScoreCache.bayes(...) ── Failure ('test-plot-abn.R:30:3'): plotAbn() works ─────────────────────────── plt_dag@adjMat (`actual`) not equal to `data.param.adjMat` (`expected`). actual vs expected [,1] [,2] - actual[1, ] 0 0 + expected[1, ] 0 1 - actual[2, ] 1 0 + expected[2, ] 0 0 ── Error ('test-search_hillclimber.R:62:5'): searchHillClimber() is backward compatible with `ex3.dag.data` ── Error in `buildScoreCache.bayes(data.df = data.df, data.dists = data.dists, group.var = group.var, cor.vars = cor.vars, dag.banned = dag.banned, dag.retained = dag.retained, max.parents = max.parents, which.nodes = which.nodes, defn.res = defn.res, dry.run = dry.run, verbose = verbose, centre = centre, force.method = force.method, mylist = mylist, grouped.vars = grouped.vars, group.ids = group.ids, control = ctrl)`: library INLA is not available! INLA is available from https://www.r-inla.org/download-install. Backtrace: ▆ 1. └─abn::buildScoreCache(...) at test-search_hillclimber.R:62:4 2. └─abn:::buildScoreCache.bayes(...) [ FAIL 9 | WARN 0 | SKIP 11 | PASS 595 ] Deleting unused snapshots: • tographviz/graph.dot • tographviz/graph1.dot • tographviz/graph_group.dot Error: Test failures In addition: Warning messages: 1: In .Internal(gc(verbose, reset, full)) : closing unused connection 9 (<-localhost:11221) 2: In .Internal(gc(verbose, reset, full)) : closing unused connection 8 (<-localhost:11221) 3: In .Internal(gc(verbose, reset, full)) : closing unused connection 6 (<-localhost:11221) 4: In .Internal(gc(verbose, reset, full)) : closing unused connection 5 (<-localhost:11221) Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking re-building of vignette outputs ... [0s/0s] OK * checking PDF version of manual ... [4s/4s] OK * checking HTML version of manual ... [2s/2s] OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 1 ERROR, 4 NOTEs