Check results for 'abn'

using R version 4.3.3 (2024-02-29)
using platform: x86_64-apple-darwin20 (64-bit)
R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0
running under: macOS Ventura 13.3.1
using session charset: UTF-8
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 ... 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 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 ... [81s/63s] OK See the install log for details.
used C compiler: ‘Apple clang version 14.0.3 (clang-1403.0.22.14.1)’
used C++ compiler: ‘Apple clang version 14.0.3 (clang-1403.0.22.14.1)’
used SDK: ‘MacOSX11.3.sdk’
checking installed package size ... NOTE installed size is 13.8Mb sub-directories of 1Mb or more: data 1.0Mb extdata 2.9Mb libs 8.8Mb
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 R files for non-ASCII characters ... OK
checking R files for syntax errors ... OK
checking whether the package can be loaded ... [2s/3s] OK
checking whether the package can be loaded with stated dependencies ... [2s/3s] OK
checking whether the package can be unloaded cleanly ... [2s/4s] OK
checking whether the namespace can be loaded with stated dependencies ... [2s/3s] OK
checking whether the namespace can be unloaded cleanly ... [2s/3s] OK
checking loading without being on the library search path ... [2s/4s] OK
checking startup messages can be suppressed ... [2s/3s] 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 ... [14s/20s] OK
checking Rd files ... [1s/1s] OK
checking Rd metadata ... 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 ... [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 compiled code ... OK
checking installed files from ‘inst/doc’ ... OK
checking files in ‘vignettes’ ... OK
checking examples ... [7s/9s] OK
checking for unstated dependencies in ‘tests’ ... OK
checking tests ... [11m/13m] ERROR Running ‘testthat.R’ [11m/13m] 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 58 | PASS 376 ] ══ Skipped tests (58) ══════════════════════════════════════════════════════════ • 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 (53): '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', 'test-tographviz.R:171:3' • Plot classic view is deprecated. (1): 'test-plot-abn.R:117:3' • empty test (2): 'test-abn-methods.R:7:1', 'test-abn-methods.R:15:1' ══ 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 58 | PASS 376 ] 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 in ‘inst/doc’ ... OK
checking re-building of vignette outputs ... [26s/26s] OK
checking PDF version of manual ... [7s/7s] OK
DONE Status: 1 ERROR, 2 NOTEs
using check arguments '--no-clean-on-error '