* using log directory ‘/data/gannet/ripley/R/packages/tests-clang/missSBM.Rcheck’
* using R Under development (unstable) (2025-02-28 r87848)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
clang version 20.1.0-rc3
flang version 20.1.0-rc3
* 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 ... [169s/199s] OK
See 'https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-fedora-clang/missSBM-00install.html' for details.
* used C++ compiler: ‘clang version 20.1.0-rc3’
* checking installed package size ... OK
* 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 ... [26s/34s] 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 ... [33s/42s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [150s/144s] ERROR
Running ‘spelling.R’
Running ‘testthat.R’ [149s/143s]
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 ]
â•â• Failed tests â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•
── 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 ... [45s/108s] OK
* checking PDF version of manual ... [13s/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