* using log directory ‘/data/gannet/ripley/R/packages/tests-Suggests/abn.Rcheck’
* using R Under development (unstable) (2025-06-24 r88351)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (GCC) 15.1.1 20250521 (Red Hat 15.1.1-2)
    GNU Fortran (GCC) 15.1.1 20250521 (Red Hat 15.1.1-2)
* running under: Fedora Linux 42 (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 ‘3.1.8’
* 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 ... [243s/61s] OK
* used C compiler: ‘gcc (GCC) 15.1.1 20250521 (Red Hat 15.1.1-2)’
* used C++ compiler: ‘g++ (GCC) 15.1.1 20250521 (Red Hat 15.1.1-2)’
* 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 ... 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 ... [58s/59s] 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 ... [17s/17s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [33m/33m]
 [33m/33m] ERROR
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 3.1.8 (2025-06-24) is loaded.
  To cite the package 'abn' in publications call: citation('abn').
  
  Attaching package: 'abn'
  
  The following object is masked from 'package:base':
  
      factorial
  
  > 
  > # Set the number of threads for BLAS and OpenMP if possible
  > if (requireNamespace("RhpcBLASctl", quietly = TRUE)) {
  +   RhpcBLASctl::blas_set_num_threads(2)
  + } else {
  +   # E.g., on CRAN noSuggests environment, RhpcBLASctl is not available
  +   message("RhpcBLASctl is not available, BLAS thread control will not be set.")
  + }
  RhpcBLASctl is not available, BLAS thread control will not be set.
  > 
  > 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.
  Package brglm not available, number of passed tests might be different[ FAIL 4 | WARN 0 | SKIP 59 | PASS 374 ]
  
  ══ Skipped tests (59) ══════════════════════════════════════════════════════════
  • BuildScoreCache(method=mle) crashes with Poisson nodes (1):
    'test-fitabn_mle.R:138:3'
  • INLA is not tested on CRAN (2): 'test-build_score_cache.R:124:5',
    'test-search_hillclimber.R:79:7'
  • On CRAN (54): 'test-Coutput.R:1:1', 'test-abn-internal.R:138:3',
    '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:129:3',
    'test-build_score_cache.R:188:3', 'test-build_score_cache.R:338:3',
    'test-build_score_cache.R:393:3', 'test-build_score_cache.R:441:3',
    '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:126:3',
    '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:118:3'
  • empty test (1): 'test-build_score_cache_mle.R:224:1'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-abn-infotheo.R:18:3'): discretization() works ──────────────────
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'entropy'
  Backtrace:
      ▆
   1. └─base::loadNamespace(x) at test-abn-infotheo.R:18:3
   2.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   3.     └─base (local) withOneRestart(expr, restarts[[1L]])
   4.       └─base (local) doWithOneRestart(return(expr), restart)
  ── Error ('test-abn-infotheo.R:62:3'): miData() works ──────────────────────────
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'entropy'
  Backtrace:
      ▆
   1. ├─testthat::expect_equal(...) at test-abn-infotheo.R:62:3
   2. │ └─testthat::quasi_label(enquo(expected), expected.label, arg = "expected")
   3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
   4. └─base::loadNamespace(x)
   5.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   6.     └─base (local) withOneRestart(expr, restarts[[1L]])
   7.       └─base (local) doWithOneRestart(return(expr), restart)
  ── Error ('test-abn-infotheo.R:84:3'): entropyData() works ─────────────────────
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'entropy'
  Backtrace:
      ▆
   1. └─base::loadNamespace(x) at test-abn-infotheo.R:84:3
   2.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   3.     └─base (local) withOneRestart(expr, restarts[[1L]])
   4.       └─base (local) doWithOneRestart(return(expr), restart)
  ── Error ('test-abn-toolbox.R:149:3'): skewness() works ────────────────────────
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'moments'
  Backtrace:
      ▆
   1. ├─testthat::expect_equal(abn:::skewness(x = data), moments::skewness(x = data)) at test-abn-toolbox.R:149:3
   2. │ └─testthat::quasi_label(enquo(expected), expected.label, arg = "expected")
   3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
   4. └─base::loadNamespace(x)
   5.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   6.     └─base (local) withOneRestart(expr, restarts[[1L]])
   7.       └─base (local) doWithOneRestart(return(expr), restart)
  
  [ FAIL 4 | WARN 0 | SKIP 59 | PASS 374 ]
  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 ... [13s/13s] OK
* checking HTML version of manual ... OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE

Status: 1 ERROR
See
  ‘/data/gannet/ripley/R/packages/tests-Suggests/abn.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 38:18.20, 2418.22 + 36.74