* using log directory ‘/data/gannet/ripley/R/packages/tests-ATLAS/aphylo.Rcheck’
* using R Under development (unstable) (2023-03-01 r83924)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (GCC) 12.2.1 20221121 (Red Hat 12.2.1-4)
    GNU Fortran (GCC) 12.2.1 20221121 (Red Hat 12.2.1-4)
* running under: Fedora Linux 36 (Workstation Edition)
* using session charset: UTF-8
* using option ‘--no-stop-on-test-error’
* checking for file ‘aphylo/DESCRIPTION’ ... OK
* this is package ‘aphylo’ version ‘0.3-2’
* 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 ‘aphylo’ can be installed ... [106s/103s] OK
* used C++ compiler: ‘g++ (GCC) 12.2.1 20221121 (Red Hat 12.2.1-4)’
* checking C++ specification ... NOTE
  Specified C++11: please drop specification unless essential
* 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 ... 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 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 ... [29s/43s] 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 ... [51s/67s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘tinytest.R’ [60s/92s]
 [61s/93s] ERROR
Running the tests in ‘tests/tinytest.R’ failed.
Complete output:
  > library(aphylo)
  Loading required package: ape
  > 
  > # Just for testing
  > if ( requireNamespace("tinytest", quietly=TRUE) ){
  +   
  +   expect_output <- function(x, pattern) {
  +     
  +     ans  <- paste(capture.output(eval(x)), collapse = "\n")
  +     test <- grepl(pattern, ans)
  +     
  +     tinytest::tinytest(
  +       result = test,
  +       call   = sys.call(sys.parent(1)),
  +       diff   = paste("Expected:", pattern, ". Returned:", ans)
  +     )
  +   }
  +   
  +   expect_lt <- function(a,b) {
  +     
  +     tinytest::tinytest(
  +       result = a < b,
  +       call   = sys.call(sys.parent(1)),
  +       diff   = paste("b - a = ", b - a)
  +     )
  +     
  +   }
  +   
  +   expect_length <- function(x,n) {
  +     
  +     tinytest::tinytest(
  +       result = length(x) == n,
  +       call   = sys.call(sys.parent(1)),
  +       diff   = paste("length(x) = ", length(x), " but expected ", n)
  +     )
  +     
  +   }
  +   
  +   
  +   tinytest::test_package("aphylo")
  + }
  
  test-aphylo-ape-info.r........    0 tests    
  test-aphylo-ape-info.r........    0 tests    
  test-aphylo-ape-info.r........    0 tests    
  test-aphylo-ape-info.r........    0 tests    
  test-aphylo-ape-info.r........    0 tests    
  test-aphylo-ape-info.r........    1 tests OK 
  test-aphylo-ape-info.r........    2 tests OK 
  test-aphylo-ape-info.r........    3 tests OK 
  test-aphylo-ape-info.r........    4 tests OK 
  test-aphylo-ape-info.r........    5 tests OK 
  test-aphylo-ape-info.r........    6 tests OK 
  test-aphylo-ape-info.r........    7 tests OK 
  test-aphylo-ape-info.r........    8 tests OK 
  test-aphylo-ape-info.r........    9 tests OK 
  test-aphylo-ape-info.r........   10 tests OK 
  test-aphylo-ape-info.r........   11 tests OK 
  test-aphylo-ape-info.r........   12 tests OK 
  test-aphylo-ape-info.r........   13 tests OK 
  test-aphylo-ape-info.r........   14 tests OK 
  test-aphylo-ape-info.r........   15 tests OK 
  test-aphylo-ape-info.r........   16 tests OK 
  test-aphylo-ape-info.r........   17 tests OK 
  test-aphylo-ape-info.r........   18 tests OK 0.4s
  
  test-aphylo_from_data_frame.R.    0 tests    
  test-aphylo_from_data_frame.R.    0 tests    
  test-aphylo_from_data_frame.R.    0 tests    
  test-aphylo_from_data_frame.R.    0 tests    
  test-aphylo_from_data_frame.R.    0 tests    
  test-aphylo_from_data_frame.R.    0 tests    
  test-aphylo_from_data_frame.R.    0 tests    
  test-aphylo_from_data_frame.R.    0 tests    
  test-aphylo_from_data_frame.R.    0 tests    
  test-aphylo_from_data_frame.R.    0 tests    
  test-aphylo_from_data_frame.R.    1 tests OK 
  test-aphylo_from_data_frame.R.    1 tests OK 
  test-aphylo_from_data_frame.R.    1 tests OK 
  test-aphylo_from_data_frame.R.    2 tests OK 
  test-aphylo_from_data_frame.R.    3 tests OK 
  test-aphylo_from_data_frame.R.    4 tests OK 
  test-aphylo_from_data_frame.R.    4 tests OK 
  test-aphylo_from_data_frame.R.    5 tests OK 
  test-aphylo_from_data_frame.R.    5 tests OK 
  test-aphylo_from_data_frame.R.    5 tests OK 
  test-aphylo_from_data_frame.R.    5 tests OK 
  test-aphylo_from_data_frame.R.    5 tests OK 
  test-aphylo_from_data_frame.R.    6 tests OK 99ms
  
  test-auc.r....................    0 tests    
  test-auc.r....................    0 tests    
  test-auc.r....................    0 tests    
  test-auc.r....................    0 tests    
  test-auc.r....................    0 tests    
  test-auc.r....................    0 tests    
  test-auc.r....................    1 tests OK 65ms
  
  test-balance.r................    0 tests    
  test-balance.r................    0 tests    
  test-balance.r................    0 tests    
  test-balance.r................    1 tests OK 
  test-balance.r................    1 tests OK 
  test-balance.r................    2 tests OK 
  test-balance.r................    2 tests OK 
  test-balance.r................    3 tests OK 
  test-balance.r................    4 tests OK 14ms
  
  test-cv.R.....................    0 tests    
  test-cv.R.....................    0 tests    Convergence has been reached with 500 steps. avg Geweke's Z: -1.6070. (50 final count of samples).
  --------------------------------------------------------------------------------
  Leave-one-out cross validation of aphylo model with 20 cases
    1 done...  2 done...  3 done...  4 done...  5 done...  6 done...  7 done...  8 done...  9 done... 10 done... 11 done... 12 done... 13 done... 14 done... 15 done... 16 done... 17 done... 18 done... 19 done... 20 done...
  test-cv.R.....................    0 tests    Convergence has been reached with 500 steps. avg Geweke's Z: -1.8159. (50 final count of samples).
  
  test-cv.R.....................    0 tests    
  test-cv.R.....................    1 tests OK 
  test-cv.R.....................    1 tests OK 
  test-cv.R.....................    2 tests OK 
  test-cv.R.....................    2 tests OK 
  test-cv.R.....................    2 tests OK Convergence has been reached with 500 steps. avg Geweke's Z: 0.4760. (50 final count of samples).
  --------------------------------------------------------------------------------
  Leave-one-out cross validation of aphylo model with 2 cases
    1 done...  2 done...
  test-cv.R.....................    2 tests OK Convergence has been reached with 500 steps. avg Geweke's Z: 0.9530. (50 final count of samples).
  
  test-cv.R.....................    2 tests OK 10.3s
  
  test-data-management.r........    0 tests    
  test-data-management.r........    0 tests    
  test-data-management.r........    0 tests    
  test-data-management.r........    0 tests    
  test-data-management.r........    1 tests OK 
  test-data-management.r........    2 tests OK 
  test-data-management.r........    3 tests OK 
  test-data-management.r........    4 tests OK 
  test-data-management.r........    5 tests OK 
  test-data-management.r........    5 tests OK 
  test-data-management.r........    5 tests OK 
  test-data-management.r........    5 tests OK 
  test-data-management.r........    5 tests OK 
  test-data-management.r........    6 tests OK 0.1s
  
  test-formula.r................    0 tests    
  test-formula.r................    0 tests    
  test-formula.r................    0 tests    
  test-formula.r................    0 tests    
  test-formula.r................    0 tests    
  test-formula.r................    0 tests    
  test-formula.r................    1 tests OK 
  test-formula.r................    2 tests OK 
  test-formula.r................    2 tests OK 
  test-formula.r................    2 tests OK 
  test-formula.r................    3 tests OK 
  test-formula.r................    3 tests OK 
  test-formula.r................    4 tests OK 
  test-formula.r................    5 tests OK 
  test-formula.r................    6 tests OK 
  test-formula.r................    7 tests OK 
  test-formula.r................    8 tests OK 
  test-formula.r................    8 tests OK 
  test-formula.r................    8 tests OK 
  test-formula.r................    8 tests OK 
  test-formula.r................    8 tests OK 
  test-formula.r................    9 tests OK 
  test-formula.r................   10 tests OK 0.8s
  
  test-impute_duplications.R....    0 tests    
  test-impute_duplications.R....    0 tests    
  test-impute_duplications.R....    0 tests    
  test-impute_duplications.R....    0 tests    
  test-impute_duplications.R....    0 tests    
  test-impute_duplications.R....    0 tests    
  test-impute_duplications.R....    0 tests    
  test-impute_duplications.R....    1 tests OK 0.1s
  
  test-indexing.R...............    0 tests    
  test-indexing.R...............    0 tests    
  test-indexing.R...............    1 tests OK 
  test-indexing.R...............    2 tests OK 
  test-indexing.R...............    3 tests OK 
  test-indexing.R...............    4 tests OK 
  test-indexing.R...............    5 tests OK 
  test-indexing.R...............    6 tests OK 
  test-indexing.R...............    7 tests OK 
  test-indexing.R...............    8 tests OK 
  test-indexing.R...............    8 tests OK 34ms
  
  test-loglikelihood.r..........    0 tests    
  test-loglikelihood.r..........    0 tests    
  test-loglikelihood.r..........    0 tests    
  test-loglikelihood.r..........    0 tests    
  test-loglikelihood.r..........    0 tests    
  test-loglikelihood.r..........    0 tests    
  test-loglikelihood.r..........    0 tests    
  test-loglikelihood.r..........    0 tests    
  test-loglikelihood.r..........    0 tests    
  test-loglikelihood.r..........    0 tests    
  test-loglikelihood.r..........    0 tests    
  test-loglikelihood.r..........    0 tests    
  test-loglikelihood.r..........    0 tests    
  test-loglikelihood.r..........    0 tests    
  test-loglikelihood.r..........    0 tests    
  test-loglikelihood.r..........    0 tests    
  test-loglikelihood.r..........    0 tests    
  test-loglikelihood.r..........    0 tests    
  test-loglikelihood.r..........    0 tests    
  test-loglikelihood.r..........    0 tests    
  test-loglikelihood.r..........    0 tests    
  test-loglikelihood.r..........    0 tests    
  test-loglikelihood.r..........    0 tests    
  test-loglikelihood.r..........    0 tests    
  test-loglikelihood.r..........    0 tests    
  test-loglikelihood.r..........    0 tests    
  test-loglikelihood.r..........    0 tests    
  test-loglikelihood.r..........    0 tests    
  test-loglikelihood.r..........    1 tests OK 
  test-loglikelihood.r..........    1 tests OK 
  test-loglikelihood.r..........    1 tests OK 
  test-loglikelihood.r..........    1 tests OK 
  test-loglikelihood.r..........    1 tests OK 
  test-loglikelihood.r..........    1 tests OK 
  test-loglikelihood.r..........    1 tests OK 
  test-loglikelihood.r..........    1 tests OK 
  test-loglikelihood.r..........    1 tests OK 
  test-loglikelihood.r..........    1 tests OK 
  test-loglikelihood.r..........    1 tests OK 
  test-loglikelihood.r..........    1 tests OK 
  test-loglikelihood.r..........    1 tests OK 
  test-loglikelihood.r..........    1 tests OK 
  test-loglikelihood.r..........    1 tests OK 
  test-loglikelihood.r..........    1 tests OK 
  test-loglikelihood.r..........    1 tests OK 
  test-loglikelihood.r..........    1 tests OK 
  test-loglikelihood.r..........    1 tests OK 
  test-loglikelihood.r..........    1 tests OK 
  test-loglikelihood.r..........    1 tests OK 
  test-loglikelihood.r..........    1 tests OK 
  test-loglikelihood.r..........    1 tests OK 
  test-loglikelihood.r..........    1 tests OK 
  test-loglikelihood.r..........    1 tests OK 
  test-loglikelihood.r..........    1 tests OK 
  test-loglikelihood.r..........    1 tests OK 
  test-loglikelihood.r..........    1 tests OK 
  test-loglikelihood.r..........    2 tests OK 
  test-loglikelihood.r..........    2 tests OK 
  test-loglikelihood.r..........    2 tests OK 
  test-loglikelihood.r..........    2 tests OK 
  test-loglikelihood.r..........    2 tests OK 
  test-loglikelihood.r..........    3 tests OK 
  test-loglikelihood.r..........    3 tests OK 
  test-loglikelihood.r..........    3 tests OK 
  test-loglikelihood.r..........    3 tests OK 
  test-loglikelihood.r..........    3 tests OK 
  test-loglikelihood.r..........    3 tests OK 
  test-loglikelihood.r..........    3 tests OK 
  test-loglikelihood.r..........    3 tests OK 
  test-loglikelihood.r..........    3 tests OK 
  test-loglikelihood.r..........    3 tests OK 
  test-loglikelihood.r..........    3 tests OK 
  test-loglikelihood.r..........    3 tests OK 
  test-loglikelihood.r..........    3 tests OK 
  test-loglikelihood.r..........    3 tests OK 
  test-loglikelihood.r..........    3 tests OK 
  test-loglikelihood.r..........    3 tests OK 
  test-loglikelihood.r..........    3 tests OK 
  test-loglikelihood.r..........    3 tests OK 
  test-loglikelihood.r..........    3 tests OK 
  test-loglikelihood.r..........    3 tests OK 
  test-loglikelihood.r..........    3 tests OK 
  test-loglikelihood.r..........    3 tests OK 
  test-loglikelihood.r..........    3 tests OK 
  test-loglikelihood.r..........    3 tests OK 
  test-loglikelihood.r..........    3 tests OK 
  test-loglikelihood.r..........    3 tests OK 
  test-loglikelihood.r..........    3 tests OK 
  test-loglikelihood.r..........    3 tests OK 
  test-loglikelihood.r..........    3 tests OK 
  test-loglikelihood.r..........    3 tests OK 
  test-loglikelihood.r..........    3 tests OK 
  test-loglikelihood.r..........    3 tests OK 
  test-loglikelihood.r..........    3 tests OK 
  test-loglikelihood.r..........    3 tests OK 
  test-loglikelihood.r..........    3 tests OK 
  test-loglikelihood.r..........    3 tests OK 
  test-loglikelihood.r..........    3 tests OK 
  test-loglikelihood.r..........    3 tests OK 
  test-loglikelihood.r..........    3 tests OK 
  test-loglikelihood.r..........    3 tests OK 
  test-loglikelihood.r..........    3 tests OK 
  test-loglikelihood.r..........    3 tests OK 
  test-loglikelihood.r..........    3 tests OK 
  test-loglikelihood.r..........    3 tests OK 
  test-loglikelihood.r..........    3 tests OK 
  test-loglikelihood.r..........    3 tests OK 
  test-loglikelihood.r..........    3 tests OK 
  test-loglikelihood.r..........    3 tests OK 
  test-loglikelihood.r..........    3 tests OK 
  test-loglikelihood.r..........    4 tests OK 
  test-loglikelihood.r..........    4 tests OK 
  test-loglikelihood.r..........    4 tests OK 
  test-loglikelihood.r..........    4 tests OK 
  test-loglikelihood.r..........    4 tests OK 
  test-loglikelihood.r..........    4 tests OK 
  test-loglikelihood.r..........    4 tests OK 
  test-loglikelihood.r..........    4 tests OK 
  test-loglikelihood.r..........    4 tests OK 
  test-loglikelihood.r..........    4 tests OK 
  test-loglikelihood.r..........    4 tests OK 
  test-loglikelihood.r..........    5 tests OK 
  test-loglikelihood.r..........    5 tests OK 
  test-loglikelihood.r..........    5 tests OK 
  test-loglikelihood.r..........    6 tests OK 0.1s
  
  test-panther.r................    0 tests    
  test-panther.r................    0 tests    
  test-panther.r................    1 tests OK 
  test-panther.r................    2 tests OK 70ms
  
  test-parameter-estimates-and-formulas.r    0 tests    
  test-parameter-estimates-and-formulas.r    0 tests    
  test-parameter-estimates-and-formulas.r    0 tests    
  test-parameter-estimates-and-formulas.r    0 tests    
  test-parameter-estimates-and-formulas.r    0 tests    
  test-parameter-estimates-and-formulas.r    0 tests    
  test-parameter-estimates-and-formulas.r    0 tests    
  test-parameter-estimates-and-formulas.r    0 tests    
  test-parameter-estimates-and-formulas.r    0 tests    
  test-parameter-estimates-and-formulas.r    0 tests    
  test-parameter-estimates-and-formulas.r    0 tests    
  test-parameter-estimates-and-formulas.r    0 tests    
  test-parameter-estimates-and-formulas.r    0 tests    
  test-parameter-estimates-and-formulas.r    0 tests    
  test-parameter-estimates-and-formulas.r    0 tests    
  test-parameter-estimates-and-formulas.r    0 tests    
  test-parameter-estimates-and-formulas.r    0 tests    
  test-parameter-estimates-and-formulas.r    0 tests    
  test-parameter-estimates-and-formulas.r    0 tests    
  test-parameter-estimates-and-formulas.r    1 tests OK 
  test-parameter-estimates-and-formulas.r    1 tests OK 
  test-parameter-estimates-and-formulas.r    1 tests OK 
  test-parameter-estimates-and-formulas.r    1 tests OK 
  test-parameter-estimates-and-formulas.r    1 tests OK 
  test-parameter-estimates-and-formulas.r    1 tests OK 
  test-parameter-estimates-and-formulas.r    1 tests OK 
  test-parameter-estimates-and-formulas.r    1 tests OK 
  test-parameter-estimates-and-formulas.r    1 tests OK 
  test-parameter-estimates-and-formulas.r    1 tests OK 
  test-parameter-estimates-and-formulas.r    1 tests OK 
  test-parameter-estimates-and-formulas.r    1 tests OK 
  test-parameter-estimates-and-formulas.r    1 tests OK 
  test-parameter-estimates-and-formulas.r    1 tests OK 
  test-parameter-estimates-and-formulas.r    1 tests OK 
  test-parameter-estimates-and-formulas.r    1 tests OK 
  test-parameter-estimates-and-formulas.r    1 tests OK 
  test-parameter-estimates-and-formulas.r    1 tests OK 
  test-parameter-estimates-and-formulas.r    1 tests OK 
  test-parameter-estimates-and-formulas.r    1 tests OK 
  test-parameter-estimates-and-formulas.r    1 tests OK 
  test-parameter-estimates-and-formulas.r    1 tests OK 
  test-parameter-estimates-and-formulas.r    1 tests OK 
  test-parameter-estimates-and-formulas.r    1 tests OK 
  test-parameter-estimates-and-formulas.r    1 tests OK 
  test-parameter-estimates-and-formulas.r    1 tests OK 
  test-parameter-estimates-and-formulas.r    1 tests OK 
  test-parameter-estimates-and-formulas.r    2 tests 1 fails 13.7s
  
  test-parameter-estimates.r....    0 tests    
  test-parameter-estimates.r....    0 tests    
  test-parameter-estimates.r....    0 tests    
  test-parameter-estimates.r....    0 tests    
  test-parameter-estimates.r....    0 tests    
  test-parameter-estimates.r....    0 tests    
  test-parameter-estimates.r....    0 tests    
  test-parameter-estimates.r....    0 tests    
  test-parameter-estimates.r....    0 tests    
  test-parameter-estimates.r....    1 tests OK 
  test-parameter-estimates.r....    2 tests OK 
  test-parameter-estimates.r....    3 tests OK 
  test-parameter-estimates.r....    4 tests OK 
  test-parameter-estimates.r....    5 tests OK 
  test-parameter-estimates.r....    5 tests OK 
  test-parameter-estimates.r....    6 tests OK 
  test-parameter-estimates.r....    7 tests OK 
  test-parameter-estimates.r....    8 tests OK 
  test-parameter-estimates.r....    9 tests OK 
  test-parameter-estimates.r....   10 tests OK 
  test-parameter-estimates.r....   11 tests OK 
  test-parameter-estimates.r....   11 tests OK 
  test-parameter-estimates.r....   11 tests OK 
  test-parameter-estimates.r....   11 tests OK 
  test-parameter-estimates.r....   11 tests OK 
  test-parameter-estimates.r....   11 tests OK 
  test-parameter-estimates.r....   12 tests OK 
  test-parameter-estimates.r....   13 tests OK 
  test-parameter-estimates.r....   13 tests OK 
  test-parameter-estimates.r....   13 tests OK 
  test-parameter-estimates.r....   13 tests OK 
  test-parameter-estimates.r....   13 tests OK 
  test-parameter-estimates.r....   13 tests OK 
  test-parameter-estimates.r....   13 tests OK Convergence has been reached with 5000 steps. avg Geweke's Z: 0.2638. (400 final count of samples).
  
  test-parameter-estimates.r....   13 tests OK Convergence has been reached with 5000 steps. Gelman-Rubin's R: 1.0514. (400 final count of samples).
  
  test-parameter-estimates.r....   13 tests OK 
  test-parameter-estimates.r....   13 tests OK 
  test-parameter-estimates.r....   14 tests OK 33.4s
  
  test-plot_loglike.r...........    0 tests    
  test-plot_loglike.r...........    0 tests    
  test-plot_loglike.r...........    1 tests OK 
  test-plot_loglike.r...........    1 tests OK 
  test-plot_loglike.r...........    2 tests OK 0.4s
  
  test-predict.r................    0 tests    
  test-predict.r................    0 tests    
  test-predict.r................    0 tests    
  test-predict.r................    0 tests    
  test-predict.r................    0 tests    
  test-predict.r................    0 tests    
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  test-predict.r................    0 tests    
  test-predict.r................    0 tests    
  test-predict.r................    0 tests    
  test-predict.r................    0 tests    
  test-predict.r................    1 tests OK 
  test-predict.r................    2 tests OK 
  test-predict.r................    2 tests OK 
  test-predict.r................    2 tests OK 
  test-predict.r................    2 tests OK 
  test-predict.r................    2 tests OK 
  test-predict.r................    3 tests OK 
  test-predict.r................    3 tests OK 
  test-predict.r................    3 tests OK 
  test-predict.r................    3 tests OK No convergence yet (steps count: 2000). Gelman-Rubin's R: 1.3084. Trying with the next bulk.
  No convergence reached after 2000 steps (200 final count of samples).
  
  test-predict.r................    3 tests OK 
  test-predict.r................    3 tests OK 
  test-predict.r................    3 tests OK 
  test-predict.r................    4 tests OK 
  test-predict.r................    5 tests OK 
  test-predict.r................    5 tests OK 
  test-predict.r................    5 tests OK 
  test-predict.r................    5 tests OK 
  test-predict.r................    5 tests OK 
  test-predict.r................    5 tests OK 
  test-predict.r................    5 tests OK 
  test-predict.r................    5 tests OK 
  test-predict.r................    6 tests OK 
  test-predict.r................    7 tests OK 
  test-predict.r................    8 tests OK 
  test-predict.r................    8 tests OK 
  test-predict.r................    8 tests OK 
  test-predict.r................    8 tests OK 
  test-predict.r................    9 tests OK 
  test-predict.r................    9 tests OK 
  test-predict.r................   10 tests OK 
  test-predict.r................   10 tests OK 
  test-predict.r................   10 tests OK 
  test-predict.r................   10 tests OK 
  test-predict.r................   10 tests OK 
  test-predict.r................   10 tests OK 
  test-predict.r................   11 tests OK 
  test-predict.r................   11 tests OK 
  test-predict.r................   11 tests OK Convergence has been reached with 2000 steps. Gelman-Rubin's R: 1.0711. (200 final count of samples).
  
  test-predict.r................   11 tests OK 
  test-predict.r................   11 tests OK 
  test-predict.r................   11 tests OK 
  test-predict.r................   11 tests OK 
  test-predict.r................   11 tests OK 
  test-predict.r................   11 tests OK 
  test-predict.r................   11 tests OK 
  test-predict.r................   12 tests OK 
  test-predict.r................   12 tests OK 
  test-predict.r................   12 tests OK 
  test-predict.r................   13 tests OK 
  test-predict.r................   14 tests OK 
  test-predict.r................   15 tests OK 9.4s
  
  test-pseq-reduce.r............    0 tests    
  test-pseq-reduce.r............    0 tests    
  test-pseq-reduce.r............    0 tests    
  test-pseq-reduce.r............    0 tests    
  test-pseq-reduce.r............    0 tests    Convergence has been reached with 1000 steps. avg Geweke's Z: 7.6524. (100 final count of samples).
  
  test-pseq-reduce.r............    0 tests    
  test-pseq-reduce.r............    0 tests    Convergence has been reached with 1000 steps. avg Geweke's Z: 7.6524. (100 final count of samples).
  
  test-pseq-reduce.r............    0 tests    
  test-pseq-reduce.r............    1 tests OK 
  test-pseq-reduce.r............    1 tests OK Convergence has been reached with 1000 steps. avg Geweke's Z: 5.0372. (100 final count of samples).
  
  test-pseq-reduce.r............    1 tests OK 
  test-pseq-reduce.r............    1 tests OK Convergence has been reached with 1000 steps. avg Geweke's Z: 5.0372. (100 final count of samples).
  
  test-pseq-reduce.r............    1 tests OK 
  test-pseq-reduce.r............    2 tests OK 3.8s
  
  test-sim_phylo.r..............    0 tests    
  test-sim_phylo.r..............    0 tests    
  test-sim_phylo.r..............    0 tests    
  test-sim_phylo.r..............    0 tests    
  test-sim_phylo.r..............    0 tests    
  test-sim_phylo.r..............    1 tests OK 
  test-sim_phylo.r..............    1 tests OK 
  test-sim_phylo.r..............    1 tests OK 
  test-sim_phylo.r..............    1 tests OK 
  test-sim_phylo.r..............    1 tests OK 
  test-sim_phylo.r..............    2 tests OK 
  test-sim_phylo.r..............    3 tests OK 
  test-sim_phylo.r..............    3 tests OK 
  test-sim_phylo.r..............    3 tests OK 
  test-sim_phylo.r..............    3 tests OK 
  test-sim_phylo.r..............    3 tests OK 
  test-sim_phylo.r..............    3 tests OK 
  test-sim_phylo.r..............    3 tests OK 
  test-sim_phylo.r..............    4 tests OK 
  test-sim_phylo.r..............    4 tests OK 
  test-sim_phylo.r..............    4 tests OK 
  test-sim_phylo.r..............    5 tests OK 
  test-sim_phylo.r..............    5 tests OK 
  test-sim_phylo.r..............    5 tests OK 
  test-sim_phylo.r..............    5 tests OK 
  test-sim_phylo.r..............    6 tests OK 
  test-sim_phylo.r..............    6 tests OK 
  test-sim_phylo.r..............    6 tests OK 
  test-sim_phylo.r..............    6 tests OK 
  test-sim_phylo.r..............    6 tests OK 
  test-sim_phylo.r..............    7 tests OK 
  test-sim_phylo.r..............    8 tests OK 
  test-sim_phylo.r..............    8 tests OK 
  test-sim_phylo.r..............    9 tests OK 
  test-sim_phylo.r..............    9 tests OK 
  test-sim_phylo.r..............    9 tests OK 
  test-sim_phylo.r..............    9 tests OK 
  test-sim_phylo.r..............   10 tests OK 
  test-sim_phylo.r..............   11 tests OK 
  test-sim_phylo.r..............   12 tests OK 
  test-sim_phylo.r..............   13 tests OK 
  test-sim_phylo.r..............   13 tests OK 
  test-sim_phylo.r..............   14 tests OK 
  test-sim_phylo.r..............   14 tests OK 
  test-sim_phylo.r..............   14 tests OK 
  test-sim_phylo.r..............   14 tests OK 
  test-sim_phylo.r..............   14 tests OK 
  test-sim_phylo.r..............   14 tests OK 
  test-sim_phylo.r..............   14 tests OK 
  test-sim_phylo.r..............   15 tests OK 
  test-sim_phylo.r..............   16 tests OK 
  test-sim_phylo.r..............   17 tests OK 
  test-sim_phylo.r..............   17 tests OK 
  test-sim_phylo.r..............   17 tests OK 
  test-sim_phylo.r..............   17 tests OK 
  test-sim_phylo.r..............   18 tests OK 
  test-sim_phylo.r..............   18 tests OK 
  test-sim_phylo.r..............   18 tests OK 
  test-sim_phylo.r..............   18 tests OK 
  test-sim_phylo.r..............   19 tests OK 13.9s
  ----- FAILED[data]: test-parameter-estimates-and-formulas.r<128--128>
   call| expect_equal(summary(ans1)$statistics[, "Mean"], ans0$par)
   diff| Mean relative difference: 0.04623728
  Error: 1 out of 118 tests failed
  In addition: Warning message:
  While using multiple chains, a single initial point has been passed via `initial`: c(0.9, 0.5, 0.1, 0.05, 0.5). The values will be recycled. Ideally you would want to start each chain from different locations. 
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking re-building of vignette outputs ... [34s/42s] OK
* checking PDF version of manual ... [9s/14s] 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, 1 NOTE
See
  ‘/data/gannet/ripley/R/packages/tests-ATLAS/aphylo.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 7:54.63, 346.42 + 25.35