* using log directory 'd:/RCompile/CRANincoming/R-devel/abn.Rcheck' * using R Under development (unstable) (2024-01-17 r85813 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 12.3.0 GNU Fortran (GCC) 12.3.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * checking for file 'abn/DESCRIPTION' ... OK * this is package 'abn' version '3.0.5' * package encoding: UTF-8 * checking CRAN incoming feasibility ... [11s] NOTE Maintainer: 'Matteo Delucchi ' New submission Package was archived on CRAN Possibly misspelled words in DESCRIPTION: GLM (55:119, 55:288) INLA (58:272) acyclic (54:129) iid (56:316) multivariable (55:262) CRAN repository db overrides: X-CRAN-Comment: Archived on 2023-12-21 as issues were not corrected even on re-submission. 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/ * checking package namespace information ... OK * checking package dependencies ... NOTE Package suggested but not available for checking: 'INLA' * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking whether package 'abn' can be installed ... OK * used C compiler: 'gcc.exe (GCC) 12.3.0' * used C++ compiler: 'g++.exe (GCC) 12.3.0' * checking installed package size ... OK * 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 ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking whether startup messages can be suppressed ... 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 ... [26s] 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 sizes of PDF files under 'inst/doc' ... OK * checking installed files from 'inst/doc' ... OK * checking files in 'vignettes' ... OK * checking examples ... ERROR Running examples in 'abn-Ex.R' failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: fitAbn > ### Title: Fit an additive Bayesian network model > ### Aliases: fitAbn fitAbn.bayes fitAbn.mle regressionLoop > ### Keywords: models > > ### ** Examples > > ## Built-in dataset with a subset of cols > mydat <- ex0.dag.data[,c("b1","b2","b3","g1","b4","p2","p4")] > > ## setup distribution list for each node > mydists <- list(b1="binomial", b2="binomial", b3="binomial", g1="gaussian", + b4="binomial", p2="poisson", p4="poisson") > > ## Null model - all independent variables > mydag.empty <- matrix(0, nrow=7, ncol=7) > colnames(mydag.empty) <- rownames(mydag.empty) <- names(mydat) > > ## Now fit the model to calculate its goodness-of-fit > myres <- fitAbn(dag=mydag.empty, + data.df=mydat, + data.dists=mydists) Error in library(p, character.only = TRUE) : there is no package called 'INLA' Calls: fitAbn -> fitAbn.bayes -> %do% -> -> library Execution halted * checking for unstated dependencies in 'tests' ... OK * checking tests ... [383s] ERROR Running 'testthat.R' [383s] 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 3.0.5 (2024-01-18) 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") 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 30 | WARN 0 | SKIP 38 | PASS 389 ] ══ Skipped tests (38) ══════════════════════════════════════════════════════════ • BuildScoreCache(method=mle) crashes with Poisson nodes (1): 'test-fitabn_mle.R:132:3' • 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 (7): 'test-build_score_cache.R:380:3', 'test-build_score_cache.R:428:3', 'test-fitabn.R:106:3', 'test-plot-abn.R:34:3', 'test-simulateabn.R:490:3', 'test-tographviz.R:27:3', 'test-tographviz.R:171:3' • Plot classic view is deprecated. (1): 'test-plot-abn.R:117:3' • empty test (25): 'test-abn-methods.R:15:1', 'test-abn-methods.R:71:1', 'test-abn-methods.R:186:1', 'test-build_score_cache.R:326:1', 'test-build_score_cache_mle.R:1:1', 'test-build_score_cache_mle.R:34:1', 'test-build_score_cache_mle.R:84:1', 'test-build_score_cache_mle.R:119:1', 'test-build_score_cache_mle.R:155:1', 'test-build_score_cache_mle.R:214:1', 'test-build_score_cache_mle.R:252:1', 'test-fitabn_mle.R:1:1', 'test-fitabn_mle.R:35:1', 'test-fitabn_mle.R:84:1', 'test-fitabn_mle.R:195:1', 'test-fitabn_mle.R:283:1', 'test-fitabn_mle.R:379:1', 'test-fitabn_mle.R:475:1', 'test-fitabn_mle.R:585:1', 'test-mostprobable.R:163:1', 'test-search_hillclimber.R:48:1', 'test-simulateabn.R:559:1', 'test-simulateabn.R:630:1', 'test-simulateabn.R:729:1', 'test-simulateabn.R:829:1' • 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:117:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-abn-methods.R:228:3'): print.abnFit() works. ─────────────────── Error in `library(p, character.only = TRUE)`: there is no package called 'INLA' Backtrace: ▆ 1. └─abn::fitAbn(object = mp.dag, create.graph = TRUE, verbose = FALSE) at test-abn-methods.R:228:3 2. └─abn::fitAbn.bayes(...) 3. └─... %do% ... 4. └─e$fun(obj, substitute(ex), parent.frame(), e$data) 5. └─base::library(p, character.only = TRUE) ── Error ('test-abn-methods.R:251:3'): summary.abnFit() works. ───────────────── Error in `library(p, character.only = TRUE)`: there is no package called 'INLA' Backtrace: ▆ 1. └─abn::fitAbn(object = mp.dag, create.graph = TRUE, verbose = FALSE) at test-abn-methods.R:251:3 2. └─abn::fitAbn.bayes(...) 3. └─... %do% ... 4. └─e$fun(obj, substitute(ex), parent.frame(), e$data) 5. └─base::library(p, character.only = TRUE) ── Error ('test-abn-methods.R:274:3'): coef.abnFit() works. ──────────────────── Error in `library(p, character.only = TRUE)`: there is no package called 'INLA' Backtrace: ▆ 1. └─abn::fitAbn(object = mp.dag, create.graph = TRUE, verbose = FALSE) at test-abn-methods.R:274:3 2. └─abn::fitAbn.bayes(...) 3. └─... %do% ... 4. └─e$fun(obj, substitute(ex), parent.frame(), e$data) 5. └─base::library(p, character.only = TRUE) ── Error ('test-abn-methods.R:297:3'): AIC.abnFit() works. ───────────────────── Error in `library(p, character.only = TRUE)`: there is no package called 'INLA' Backtrace: ▆ 1. └─abn::fitAbn(object = mp.dag, create.graph = TRUE, verbose = FALSE) at test-abn-methods.R:297:3 2. └─abn::fitAbn.bayes(...) 3. └─... %do% ... 4. └─e$fun(obj, substitute(ex), parent.frame(), e$data) 5. └─base::library(p, character.only = TRUE) ── Error ('test-abn-methods.R:320:3'): BIC.abnFit() works. ───────────────────── Error in `library(p, character.only = TRUE)`: there is no package called 'INLA' Backtrace: ▆ 1. └─abn::fitAbn(object = mp.dag, create.graph = TRUE, verbose = FALSE) at test-abn-methods.R:320:3 2. └─abn::fitAbn.bayes(...) 3. └─... %do% ... 4. └─e$fun(obj, substitute(ex), parent.frame(), e$data) 5. └─base::library(p, character.only = TRUE) ── Error ('test-abn-methods.R:343:3'): logLik.abnFit() works. ────────────────── Error in `library(p, character.only = TRUE)`: there is no package called 'INLA' Backtrace: ▆ 1. └─abn::fitAbn(object = mp.dag, create.graph = TRUE, verbose = FALSE) at test-abn-methods.R:343:3 2. └─abn::fitAbn.bayes(...) 3. └─... %do% ... 4. └─e$fun(obj, substitute(ex), parent.frame(), e$data) 5. └─base::library(p, character.only = TRUE) ── Error ('test-abn-methods.R:366:3'): family.abnFit() works. ────────────────── Error in `library(p, character.only = TRUE)`: there is no package called 'INLA' Backtrace: ▆ 1. └─abn::fitAbn(object = mp.dag, create.graph = TRUE, verbose = FALSE) at test-abn-methods.R:366:3 2. └─abn::fitAbn.bayes(...) 3. └─... %do% ... 4. └─e$fun(obj, substitute(ex), parent.frame(), e$data) 5. └─base::library(p, character.only = TRUE) ── Error ('test-abn-methods.R:389:3'): nobs.abnFit() works. ──────────────────── Error in `library(p, character.only = TRUE)`: there is no package called 'INLA' Backtrace: ▆ 1. └─abn::fitAbn(object = mp.dag, create.graph = TRUE, verbose = FALSE) at test-abn-methods.R:389:3 2. └─abn::fitAbn.bayes(...) 3. └─... %do% ... 4. └─e$fun(obj, substitute(ex), parent.frame(), e$data) 5. └─base::library(p, character.only = TRUE) ── Error ('test-abn-methods.R:412:3'): plot.abnFit() works. ──────────────────── Error in `library(p, character.only = TRUE)`: there is no package called 'INLA' Backtrace: ▆ 1. └─abn::fitAbn(object = mp.dag, create.graph = TRUE, verbose = FALSE) at test-abn-methods.R:412:3 2. └─abn::fitAbn.bayes(...) 3. └─... %do% ... 4. └─e$fun(obj, substitute(ex), parent.frame(), e$data) 5. └─base::library(p, character.only = TRUE) ── Failure ('test-calc_node_inla_glm.R:6:5'): calc.node.inla.glm() works ─────── Expected `{ ... }` to run without any errors. i Actually got a with text: there is no package called 'INLA' ── Failure ('test-calc_node_inla_glm.R:28:5'): calc.node.inla.glm() works ────── Expected `{ ... }` to run without any errors. i Actually got a with text: there is no package called 'INLA' ── Failure ('test-calc_node_inla_glmm.R:7:5'): calc.node.inla.glmm() works ───── Expected `{ ... }` to run without any errors. i Actually got a with text: there is no package called 'INLA' ── Failure ('test-calc_node_inla_glmm.R:29:5'): calc.node.inla.glmm() works ──── Expected `{ ... }` to run without any errors. i Actually got a with text: there is no package called 'INLA' ── Failure ('test-fitabn.R:48:5'): fitAbn() wrapper of 'mle' and 'bayes' works ── Expected `{ ... }` to run without any errors. i Actually got a with text: there is no package called 'INLA' ── Error ('test-fitabn.R:50:3'): fitAbn() wrapper of 'mle' and 'bayes' works ─── Error in `eval(code, test_env)`: object 'm.0.bayes.1' not found Backtrace: ▆ 1. └─testthat::expect_s3_class(m.0.bayes.1, class = "abnFit") at test-fitabn.R:50:3 2. └─testthat::quasi_label(enquo(object), arg = "object") 3. └─rlang::eval_bare(expr, quo_get_env(quo)) ── Error ('test-fitabn.R:58:3'): fitAbn() works with DAG as formula statement ── Error in `library(p, character.only = TRUE)`: there is no package called 'INLA' Backtrace: ▆ 1. ├─testthat::expect_silent(...) at test-fitabn.R:58:3 2. │ └─testthat:::quasi_capture(enquo(object), NULL, evaluate_promise) 3. │ ├─testthat (local) .capture(...) 4. │ │ ├─withr::with_output_sink(...) 5. │ │ │ └─base::force(code) 6. │ │ ├─base::withCallingHandlers(...) 7. │ │ └─base::withVisible(code) 8. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 9. └─abn::fitAbn(...) 10. └─abn::fitAbn.bayes(...) 11. └─... %do% ... 12. └─e$fun(obj, substitute(ex), parent.frame(), e$data) 13. └─base::library(p, character.only = TRUE) ── Failure ('test-fitabn.R:75:3'): fitAbn() catches wrong arguments. ─────────── Expected `fitAbn(...)` to run without any errors. i Actually got a with text: there is no package called 'INLA' ── Failure ('test-fitabn.R:77:3'): fitAbn() catches wrong arguments. ─────────── Expected `fitAbn(...)` to run without any errors. i Actually got a with text: there is no package called 'INLA' ── Failure ('test-fitabn.R:98:5'): fitAbn() runs in parallel ─────────────────── Expected `{ ... }` to run without any errors. i Actually got a with text: there is no package called 'INLA' ── Failure ('test-fitabn.R:101:5'): fitAbn() runs in parallel ────────────────── Expected `{ ... }` to run without any errors. i Actually got a with text: there is no package called 'INLA' ── Failure ('test-fitabn.R:131:3'): fitAbn() works with control arguments ────── Expected `fitAbn(...)` to run without any errors. i Actually got a with text: there is no package called 'INLA' ── Failure ('test-fitabn.R:132:3'): fitAbn() works with control arguments ────── Expected `fitAbn(...)` to run without any errors. i Actually got a with text: there is no package called 'INLA' ── Failure ('test-fitabn.R:168:3'): fitAbn() works with control arguments ────── Expected `fitAbn(...)` to run without any errors. i Actually got a with text: there is no package called 'INLA' ── Failure ('test-fitabn.R:169:3'): fitAbn() works with control arguments ────── Expected `fitAbn(...)` to run without any errors. i Actually got a with text: there is no package called 'INLA' ── Error ('test-fitabn.R:203:5'): fitAbn() is backward compatible ────────────── Error in `library(p, character.only = TRUE)`: there is no package called 'INLA' Backtrace: ▆ 1. ├─testthat::expect_silent(...) at test-fitabn.R:202:3 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:203:5 10. └─abn::fitAbn.bayes(...) 11. └─... %do% ... 12. └─e$fun(obj, substitute(ex), parent.frame(), e$data) 13. └─base::library(p, character.only = TRUE) ── Error ('test-fitabn_bayes.R:6:3'): Test fitAbn.bayes() ────────────────────── Error in `library(p, character.only = TRUE)`: there is no package called 'INLA' Backtrace: ▆ 1. └─abn::fitAbn(...) at test-fitabn_bayes.R:6:3 2. └─abn::fitAbn.bayes(...) 3. └─... %do% ... 4. └─e$fun(obj, substitute(ex), parent.frame(), e$data) 5. └─base::library(p, character.only = TRUE) ── Error ('test-mostprobable.R:64:5'): mostProbable() is backward compatible with `ex0.dag.data` ── Error in `library(p, character.only = TRUE)`: there is no package called 'INLA' Backtrace: ▆ 1. ├─testthat::expect_message(...) at test-mostprobable.R:63:3 2. │ └─testthat:::expect_condition_matching(...) 3. │ └─testthat:::quasi_capture(...) 4. │ ├─testthat (local) .capture(...) 5. │ │ └─base::withCallingHandlers(...) 6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. └─abn::fitAbn(dag = mp.dag, data.df = mydat, data.dists = mydists) at test-mostprobable.R:64:5 8. └─abn::fitAbn.bayes(...) 9. └─... %do% ... 10. └─e$fun(obj, substitute(ex), parent.frame(), e$data) 11. └─base::library(p, character.only = TRUE) ── Failure ('test-mostprobable.R:138:7'): mostProbable() is backward compatible with `ex1.dag.data` ── Expected `{ ... }` to run without any errors. i Actually got a with text: there is no package called 'INLA' ── Error ('test-mostprobable.R:148:5'): mostProbable() is backward compatible with `ex1.dag.data` ── Error in `library(p, character.only = TRUE)`: there is no package called 'INLA' Backtrace: ▆ 1. ├─testthat::expect_no_message(...) at test-mostprobable.R:147:3 2. │ └─testthat:::expect_no_(...) 3. │ └─testthat:::quasi_capture(enquo(object), NULL, capture) 4. │ ├─testthat (local) .capture(...) 5. │ │ └─rlang::try_fetch(...) 6. │ │ └─base::withCallingHandlers(...) 7. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 8. └─abn::fitAbn(object = mp.dag) at test-mostprobable.R:148:5 9. └─abn::fitAbn.bayes(...) 10. └─... %do% ... 11. └─e$fun(obj, substitute(ex), parent.frame(), e$data) 12. └─base::library(p, character.only = TRUE) ── Error ('test-plot-abn.R:131:3'): Plot from fitAbn() works ─────────────────── Error in `library(p, character.only = TRUE)`: there is no package called 'INLA' Backtrace: ▆ 1. └─abn::fitAbn(...) at test-plot-abn.R:131:3 2. └─abn::fitAbn.bayes(...) 3. └─... %do% ... 4. └─e$fun(obj, substitute(ex), parent.frame(), e$data) 5. └─base::library(p, character.only = TRUE) [ FAIL 30 | WARN 0 | SKIP 38 | PASS 389 ] 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 ... OK * checking PDF version of manual ... [25s] OK * checking HTML version of manual ... [19s] OK * DONE Status: 2 ERRORs, 2 NOTEs