* using log directory ‘/data/gannet/ripley/R/packages/tests-ATLAS/abn.Rcheck’
* using R Under development (unstable) (2024-03-25 r86192)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc-13 (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Fedora Linux 36 (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 ‘3.0.6’
* 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 ... [359s/524s] OK
* used C compiler: ‘gcc-13 (GCC) 13.2.0’
* used C++ compiler: ‘g++-13 (GCC) 13.2.0’
* 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 ... [5s/18s] OK
* checking whether the package can be unloaded cleanly ... [5s/11s] 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 ... [5s/15s] 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/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 ... [29s/129s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’/data/gannet/ripley/R/ATLAS/bin/BATCH: line 60: 516404 CPU time limit exceeded (core dumped) ${R_HOME}/bin/R -f ${in} ${opts} ${R_BATCH_OPTIONS} > ${out} 2>&1
 [30m/38m]
 [30m/38m] 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 3.0.6 (2024-03-21) 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.
  Loading required package: sp
  This is INLA_24.02.09 built 2024-02-09 03:35:28 UTC.
   - See www.r-inla.org/contact-us for how to get help.
   - List available models/likelihoods/etc with inla.list.models()
   - Use inla.doc(<NAME>) to access documentation
  
  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')
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [62s/87s] OK
* checking PDF version of manual ... [17s/27s] OK
* checking HTML version of manual ... [7s/13s] 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-ATLAS/abn.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 59:19.37, 2385.44 + 74.58