* using log directory ‘/data/gannet/ripley/R/packages/tests-devel/missSBM.Rcheck’
* using R Under development (unstable) (2025-02-15 r87723)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3)
    GNU Fortran (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3)
* running under: Fedora Linux 40 (Workstation Edition)
* using session charset: UTF-8
* using option ‘--no-stop-on-test-error’
* checking for file ‘missSBM/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘missSBM’ version ‘1.0.4’
* 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 ‘missSBM’ can be installed ... [166s/184s] OK
See 'https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-fedora-gcc/missSBM-00install.html' for details.
* used C++ compiler: ‘g++ (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3)’
* 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 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 ... [23s/31s] 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 C/C++/Fortran sources/headers ... 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 ... [31s/39s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [166s/172s] ERROR
  Running ‘spelling.R’
  Running ‘testthat.R’ [165s/171s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(missSBM)
  > 
  > test_check("missSBM")
  
   Adjusting Variational EM for Stochastic Block Model
  
  	Dyads are distributed according to a 'undirected' SBM.
  
  	Imputation assumes a 'covar-dyad' network-sampling process
   iteration #: 2 
  
   Adjusting Variational EM for Stochastic Block Model
  
  	Dyads are distributed according to a 'undirected' SBM.
  
  	Imputation assumes a 'dyad' network-sampling process
   iteration #: 2 
  
   Adjusting Variational EM for Stochastic Block Model
  
  	Dyads are distributed according to a 'undirected' SBM.
  
  	Imputation assumes a 'covar-node' network-sampling process
   iteration #: 2 
  
   Adjusting Variational EM for Stochastic Block Model
  
  	Dyads are distributed according to a 'undirected' SBM.
  
  	Imputation assumes a 'node' network-sampling process
   iteration #: 2 
  Tested sampling:
   - dyad
   - node
   - double-standard
   - block-node
   - block-dyad
  
   Adjusting Variational EM for Stochastic Block Model
  
  	Imputation assumes a 'dyad' network-sampling process
  
   Initialization of 3 model(s). 
  Tested sampling:
   - dyad
   - node
   - double-standard
   - block-node
   - block-dyadTested sampling:
   - dyad
   - node
   - double-standard
   - block-node
   - block-dyad
  sampling: dyad new better on connectivity
  node
  double-standard
  block-node new better on mixture
   new better on mixture
   Adjusting Variational EM for Stochastic Block Model
   iteration #: 2 
   iteration #: 3 
   iteration #: 4 
   iteration #: 5 
   iteration #: 6 
   iteration #: 7 
   iteration #: 8 
   iteration #: 9 
   iteration #: 10 
   iteration #: 11 
   iteration #: 12 
   iteration #: 13 
   iteration #: 14 
   iteration #: 15 
   iteration #: 16 
   iteration #: 17 
   iteration #: 18 
   iteration #: 19 
   iteration #: 20 
   iteration #: 21 
   iteration #: 22 
   iteration #: 23 
   iteration #: 24 
   iteration #: 25 
   iteration #: 26 
   iteration #: 27 
   iteration #: 28 
  
   Adjusting Variational EM for Stochastic Block Model
  
  	Dyads are distributed according to a 'undirected' SBM.
  
  	Imputation assumes a 'node' network-sampling process
   iteration #: 2 
   iteration #: 3 
   iteration #: 4 
   iteration #: 5 
   iteration #: 6 
   iteration #: 7 
   iteration #: 8 
   iteration #: 9 
   iteration #: 10 
   iteration #: 11 
   iteration #: 12 
   iteration #: 13 
   iteration #: 14 
   iteration #: 15 
   iteration #: 16 
   iteration #: 17 
   iteration #: 18 
   iteration #: 19 
   iteration #: 20 
   iteration #: 21 
   iteration #: 22 
   iteration #: 23 
   iteration #: 24 
   iteration #: 25 
   iteration #: 26 
   iteration #: 27 
   iteration #: 28 
  
  
   Adjusting Variational EM for Stochastic Block Model
  
  	Imputation assumes a 'node' network-sampling process
  
   Initialization of 1 model(s). 
   Performing VEM inference
   	Model with 3 blocks.
  
  
  
  
  
  
  
  
  
  
  
  
  
  
   Adjusting Variational EM for Stochastic Block Model
   iteration #: 2 
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  [ FAIL 17 | WARN 1 | SKIP 0 | PASS 372 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-TOP-LEVEL-consistency.R:121:5'): check consistency against Tim's code for dyad sampling with covariates ──
  `ARI_new` is not strictly more than `tol_ARI`. Difference: -0.5
  ── Failure ('test-TOP-LEVEL-consistency.R:123:5'): check consistency against Tim's code for dyad sampling with covariates ──
  `ARI_gap` is not strictly more than `tol_ARI`. Difference: -0.5
  ── Failure ('test-sbm-MAR_bernoulli-with-covariates.R:23:3'): SimpleSBM_fit 'Bernoulli' model, undirected, one covariate, dyad sampling, MAR ──
  rmse(mySBM$connectParam$mean, sampler_undirected_cov$connectParam$mean) is not strictly less than 0.075. Difference: 0.925
  ── Failure ('test-sbm-MAR_bernoulli-with-covariates.R:24:3'): SimpleSBM_fit 'Bernoulli' model, undirected, one covariate, dyad sampling, MAR ──
  ARI(mySBM$memberships, sampler_undirected_cov$memberships) is not strictly more than 0.95. Difference: -0.95
  ── Failure ('test-sbm-MAR_bernoulli-with-covariates.R:41:3'): SimpleSBM_fit 'Bernoulli' model, directed, one covariate, dyad sampling, MAR ──
  rmse(mySBM$connectParam$mean, sampler_directed_cov$connectParam$mean) is not strictly less than 0.075. Difference: 0.925
  ── Failure ('test-sbm-MAR_bernoulli-with-covariates.R:42:3'): SimpleSBM_fit 'Bernoulli' model, directed, one covariate, dyad sampling, MAR ──
  ARI(mySBM$memberships, sampler_directed_cov$memberships) is not strictly more than 0.95. Difference: -0.95
  ── Failure ('test-sbm-bernoulli-with-covariates.R:29:3'): SimpleSBM_fit 'Bernoulli' model, undirected, one covariate ──
  rmse(mySBM_missSBM$connectParam$mean, mySBM_sbm$connectParam$mean) is not strictly less than 0.05. Difference: 0.95
  ── Failure ('test-sbm-bernoulli-with-covariates.R:30:3'): SimpleSBM_fit 'Bernoulli' model, undirected, one covariate ──
  ARI(mySBM_missSBM$memberships, mySBM_sbm$memberships) is not strictly more than 0.8. Difference: -0.8
  ── Failure ('test-sbm-bernoulli-with-covariates.R:31:3'): SimpleSBM_fit 'Bernoulli' model, undirected, one covariate ──
  rmse(mySBM_missSBM$loglik, mySBM_sbm$loglik) is not strictly less than 0.01. Difference: 33.9
  ── Failure ('test-sbm-bernoulli-with-covariates.R:34:3'): SimpleSBM_fit 'Bernoulli' model, undirected, one covariate ──
  rmse(mySBM_missSBM$connectParam$mean, sampler_undirected_cov$connectParam$mean) is not strictly less than 0.1. Difference: 0.9
  ── Failure ('test-sbm-bernoulli-with-covariates.R:35:3'): SimpleSBM_fit 'Bernoulli' model, undirected, one covariate ──
  rmse(mySBM_missSBM$covarParam, sampler_undirected_cov$covarParam) is not strictly less than 0.1. Difference: 0.9
  ── Failure ('test-sbm-bernoulli-with-covariates.R:36:3'): SimpleSBM_fit 'Bernoulli' model, undirected, one covariate ──
  ARI(mySBM_missSBM$memberships, sampler_undirected_cov$memberships) is not strictly more than 0.85. Difference: -0.85
  ── Failure ('test-sbm-bernoulli-with-covariates.R:58:3'): SimpleSBM_fit 'Bernoulli' model, directed, one covariate ──
  rmse(mySBM_missSBM$connectParam$mean, mySBM_sbm$connectParam$mean) is not strictly less than 0.1. Difference: 0.9
  ── Failure ('test-sbm-bernoulli-with-covariates.R:59:3'): SimpleSBM_fit 'Bernoulli' model, directed, one covariate ──
  ARI(mySBM_missSBM$memberships, mySBM_sbm$memberships) is not strictly more than 0.8. Difference: -0.8
  ── Failure ('test-sbm-bernoulli-with-covariates.R:60:3'): SimpleSBM_fit 'Bernoulli' model, directed, one covariate ──
  rmse(mySBM_missSBM$loglik, mySBM_sbm$loglik) is not strictly less than 0.05. Difference: 34
  ── Failure ('test-sbm-bernoulli-with-covariates.R:63:3'): SimpleSBM_fit 'Bernoulli' model, directed, one covariate ──
  rmse(mySBM_missSBM$connectParam$mean, sampler_directed_cov$connectParam$mean) is not strictly less than 0.1. Difference: 0.9
  ── Failure ('test-sbm-bernoulli-with-covariates.R:64:3'): SimpleSBM_fit 'Bernoulli' model, directed, one covariate ──
  ARI(mySBM_missSBM$memberships, sampler_directed_cov$memberships) is not strictly more than 0.85. Difference: -0.85
  
  [ FAIL 17 | WARN 1 | SKIP 0 | PASS 372 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [55s/122s] OK
* checking PDF version of manual ... [12s/16s] 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