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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:benchdamic.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings benchdamic_1.17.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/benchdamic.Rcheck’
* using R Under development (unstable) (2025-11-04 r88984)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.8
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘benchdamic/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘benchdamic’ version ‘1.17.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 32 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘benchdamic’ can be installed ... OK
* 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 dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘microbiome’
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Non-topic package-anchored link(s) in Rd file 'norm_DESeq2.Rd':
  ‘[DESeq2]{estimateSizeFactors}’

See section 'Cross-references' in the 'Writing R Extensions' manual.
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’/Library/Frameworks/R.framework/Resources/bin/BATCH: line 60: 95734 Segmentation fault: 11  ${R_HOME}/bin/R -f ${in} ${opts} ${R_BATCH_OPTIONS} > ${out} 2>&1

 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  35: withRestarts(tryCatch(withCallingHandlers({    eval(code, test_env)    new_expectations <- the$test_expectations > starting_expectations    if (snapshot_skipped) {        skip("On CRAN")    }    else if (!new_expectations && skip_on_empty) {        skip_empty()    }}, expectation = handle_expectation, packageNotFoundError = function(e) {    if (on_cran()) {        skip(paste0("{", e$package, "} is not installed."))    }}, snapshot_on_cran = function(cnd) {    snapshot_skipped <<- TRUE    invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message,     error = handle_error, interrupt = handle_interrupt), error = handle_fatal),     end_test = function() {    })
  36: test_code(code = exprs, env = env, reporter = get_reporter() %||%     StopReporter$new())
  37: source_file(path, env = env(env), desc = desc, shuffle = shuffle,     error_call = error_call)
  38: FUN(X[[i]], ...)
  39: lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle,     error_call = error_call)
  40: doTryCatch(return(expr), name, parentenv, handler)
  41: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  42: tryCatchList(expr, classes, parentenv, handlers)
  43: tryCatch(code, testthat_abort_reporter = function(cnd) {    cat(conditionMessage(cnd), "\n")    NULL})
  44: with_reporter(reporters$multi, lapply(test_paths, test_one_file,     env = env, desc = desc, shuffle = shuffle, error_call = error_call))
  45: test_files_serial(test_dir = test_dir, test_package = test_package,     test_paths = test_paths, load_helpers = load_helpers, reporter = reporter,     env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,     desc = desc, load_package = load_package, shuffle = shuffle,     error_call = error_call)
  46: test_files(test_dir = path, test_paths = test_paths, test_package = package,     reporter = reporter, load_helpers = load_helpers, env = env,     stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,     load_package = load_package, parallel = parallel, shuffle = shuffle)
  47: test_dir("testthat", package = package, reporter = reporter,     ..., load_package = "installed")
  48: test_check("benchdamic")
  An irrecoverable exception occurred. R is aborting now ...
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.23-bioc/meat/benchdamic.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL benchdamic
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library’
* installing *source* package ‘benchdamic’ ...
** this is package ‘benchdamic’ version ‘1.17.0’
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
Found more than one class "dist" in cache; using the first, from namespace 'BiocGenerics'
Also defined by ‘spam’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Found more than one class "dist" in cache; using the first, from namespace 'BiocGenerics'
Also defined by ‘spam’
** testing if installed package can be loaded from final location
Found more than one class "dist" in cache; using the first, from namespace 'BiocGenerics'
Also defined by ‘spam’
** testing if installed package keeps a record of temporary installation path
* DONE (benchdamic)

R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(benchdamic)
Found more than one class "dist" in cache; using the first, from namespace 'BiocGenerics'
Also defined by 'spam'
> 
> test_check("benchdamic")

 *** caught segfault ***
address 0x33df00000, cause 'invalid permissions'

Traceback:
 1: FUN(X[[i]], ...)
 2: lapply(X, FUN, ...)
 3: pblapply(X = X, FUN = FUN, ..., cl = cl)
 4: pbapply::pbsapply(perm_list, compute_genewise_scores, indiv_mat = indiv_mat,     avg_xtx_inv_tx = avg_xtx_inv_tx, cl = par_clust)
 5: vc_score_2use(y = y, x = x, indiv = indiv_fact, phi = phi, w = w,     Sigma_xi = Sigma_xi, na_rm = na.rm, n_perm = n_perm, progressbar = progressbar,     parallel_comp = parallel_comp, nb_cores = nb_cores)
 6: vc_test_perm(y = y_lcpm_res, x = x_res, indiv = sample_group,     phi = phi, w = w, Sigma_xi = cov_variables2test_eff, n_perm = n_perm,     progressbar = progressbar, parallel_comp = parallel_comp,     nb_cores = nb_cores, genewise_pvals = TRUE, adaptive = adaptive,     max_adaptive = max_adaptive, homogen_traj = homogen_traj,     na.rm = na.rm_gsaseq)
 7: dgsa_seq(exprmat = exprmat, object = object, covariates = covariates,     variables2test = variables2test, weights_var2test_condi = weights_var2test_condi,     genesets = NULL, sample_group = sample_group, cov_variables2test_eff = cov_variables2test_eff,     which_test = which_test, which_weights = which_weights, n_perm = n_perm,     progressbar = progressbar, parallel_comp = parallel_comp,     nb_cores = nb_cores, preprocessed = preprocessed, gene_based_weights = gene_based_weights,     bw = bw, kernel = kernel, transform = transform, padjust_methods = padjust_methods,     lowess_span = lowess_span, R = R, adaptive = adaptive, max_adaptive = max_adaptive,     homogen_traj = homogen_traj, na.rm_gsaseq = na.rm_dearseq,     verbose = FALSE)
 8: dearseq::dear_seq(object = input, covariates = covariates, variables2test = variables2test,     sample_group = sample_group, which_test = test, parallel_comp = FALSE,     n_perm = n_perm, progressbar = FALSE, preprocessed = preprocessed)
 9: withCallingHandlers(expr, message = function(c) if (inherits(c,     classes)) tryInvokeRestart("muffleMessage"))
10: suppressMessages(dearseq::dear_seq(object = input, covariates = covariates,     variables2test = variables2test, sample_group = sample_group,     which_test = test, parallel_comp = FALSE, n_perm = n_perm,     progressbar = FALSE, preprocessed = preprocessed))
11: withCallingHandlers(expr, warning = function(w) if (inherits(w,     classes)) tryInvokeRestart("muffleWarning"))
12: suppressWarnings(suppressMessages(dearseq::dear_seq(object = input,     covariates = covariates, variables2test = variables2test,     sample_group = sample_group, which_test = test, parallel_comp = FALSE,     n_perm = n_perm, progressbar = FALSE, preprocessed = preprocessed)))
13: DA_dearseq(object = ps, variables2test = "group", test = "permutation",     preprocessed = FALSE, verbose = FALSE)
14: eval(code, test_env)
15: eval(code, test_env)
16: withCallingHandlers({    eval(code, test_env)    new_expectations <- the$test_expectations > starting_expectations    if (snapshot_skipped) {        skip("On CRAN")    }    else if (!new_expectations && skip_on_empty) {        skip_empty()    }}, expectation = handle_expectation, packageNotFoundError = function(e) {    if (on_cran()) {        skip(paste0("{", e$package, "} is not installed."))    }}, snapshot_on_cran = function(cnd) {    snapshot_skipped <<- TRUE    invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message,     error = handle_error, interrupt = handle_interrupt)
17: doTryCatch(return(expr), name, parentenv, handler)
18: tryCatchOne(expr, names, parentenv, handlers[[1L]])
19: tryCatchList(expr, classes, parentenv, handlers)
20: tryCatch(withCallingHandlers({    eval(code, test_env)    new_expectations <- the$test_expectations > starting_expectations    if (snapshot_skipped) {        skip("On CRAN")    }    else if (!new_expectations && skip_on_empty) {        skip_empty()    }}, expectation = handle_expectation, packageNotFoundError = function(e) {    if (on_cran()) {        skip(paste0("{", e$package, "} is not installed."))    }}, snapshot_on_cran = function(cnd) {    snapshot_skipped <<- TRUE    invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message,     error = handle_error, interrupt = handle_interrupt), error = handle_fatal)
21: doWithOneRestart(return(expr), restart)
22: withOneRestart(expr, restarts[[1L]])
23: withRestarts(tryCatch(withCallingHandlers({    eval(code, test_env)    new_expectations <- the$test_expectations > starting_expectations    if (snapshot_skipped) {        skip("On CRAN")    }    else if (!new_expectations && skip_on_empty) {        skip_empty()    }}, expectation = handle_expectation, packageNotFoundError = function(e) {    if (on_cran()) {        skip(paste0("{", e$package, "} is not installed."))    }}, snapshot_on_cran = function(cnd) {    snapshot_skipped <<- TRUE    invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message,     error = handle_error, interrupt = handle_interrupt), error = handle_fatal),     end_test = function() {    })
24: test_code(code, parent.frame())
25: test_that("DA methods produce pValMat and statInfo", code = {    data("ps_plaque_16S")    ps <- ps_plaque_16S    ps <- norm_edgeR(ps, method = "TMM")    ps <- norm_DESeq2(ps, method = "poscounts")    ps <- norm_CSS(ps, method = "CSS")    ps <- norm_edgeR(ps, method = "none")    ps <- phyloseq::filter_taxa(physeq = ps, flist = function(x) sum(x >         0) >= 3, prune = TRUE)    set.seed(123)    group <- sample(x = c("grp1", "grp2"), size = phyloseq::nsamples(ps),         replace = TRUE)    phyloseq::sample_data(ps)[, "group"] <- as.factor(group)    expectations <- function(da, name) {        expect_true(grepl("pValMat", names(da)[1]))        expect_equal(nrow(da[["pValMat"]]), phyloseq::ntaxa(ps))        expect_equal(rownames(da[["pValMat"]]), phyloseq::taxa_names(ps))        expect_true(grepl("statInfo", names(da)[2]))        expect_true(grepl("name", names(da)[length(names(da))]))        expect_equal(name, da[["name"]])    }    da <- DA_edgeR(ps, group_name = "group", design = ~1 + group,         coef = 2, norm = "TMM")    expectations(da, name = "edgeR.TMM")    da <- DA_DESeq2(ps, design = ~1 + group, norm = "poscounts",         contrast = c("group", "grp2", "grp1"))    expectations(da, name = "DESeq2.poscounts")    da <- DA_limma(ps, design = ~1 + group, coef = 2, norm = "TMM")    expectations(da, name = "limma.TMM")    da <- DA_metagenomeSeq(object = ps, design = ~1 + group,         coef = "groupgrp2", norm = "CSS", model = "fitFeatureModel",         verbose = FALSE)    expectations(da, name = "metagenomeSeq.CSS.fitFeatureModel")    da <- DA_metagenomeSeq(object = ps, design = ~1 + group,         coef = "groupgrp2", norm = "CSS", model = "fitZig", verbose = FALSE)    expectations(da, name = "metagenomeSeq.CSS.fitZig")    da <- DA_corncob(ps, formula = ~1 + group, formula_null = ~1,         phi.formula = ~1 + group, phi.formula_null = ~1 + group,         test = "Wald", coefficient = "groupgrp2")    expectations(da, name = "corncob.Wald")    da <- DA_ALDEx2(ps, design = "group", mc.samples = 128, test = "t",         paired.test = FALSE, denom = "iqlr", contrast = c("group",             "grp2", "grp1"), verbose = FALSE)    expectations(da, name = "ALDEx2.iqlr.t.unpaired")    da <- DA_MAST(ps, rescale = "median", design = ~1 + group,         coefficient = "groupgrp2", verbose = FALSE)    expectations(da, name = "MAST.median")    da <- DA_Seurat(ps, norm = "LogNormalize", scale.factor = 10000,         test = "wilcox", contrast = c("group", "grp2", "grp1"),         verbose = FALSE)    expectations(da, name = "Seurat.LogNormalize.SF10000.wilcox")    da <- DA_ANCOM(object = ps, fix_formula = "group", contrast = c("group",         "grp2", "grp1"), BC = TRUE, verbose = FALSE)    expectations(da, name = "ANCOM.BC")    da <- DA_NOISeq(object = ps, contrast = c("group", "grp2",         "grp1"), norm = "tmm", verbose = FALSE)    expectations(da, name = "NOISeq.tmm")    da <- DA_dearseq(object = ps, variables2test = "group", test = "permutation",         preprocessed = FALSE, verbose = FALSE)    expectations(da, name = "dearseq.permutation.1000")    da <- DA_linda(object = ps, formula = "~ group", contrast = c("group",         "grp2", "grp1"), zero.handling = "pseudo-count", verbose = FALSE)    expectations(da, name = "linda.win0.03.pc0.5")    da <- DA_Maaslin2(object = ps, normalization = "TSS", transform = "LOG",         analysis_method = "LM", fixed_effects = "group", contrast = c("group",             "grp2", "grp1"), verbose = FALSE)    expectations(da, name = "Maaslin2.TSSnorm.LOGtrans.LM")    da <- DA_maaslin3(object = ps, normalization = "TSS", transform = "LOG",         median_comparison_abundance = TRUE, formula = ~group,         stat_type = "abundance", pvalue_type = "joint", contrast = c("group",             "grp2", "grp1"), verbose = FALSE)    expectations(da, name = "maaslin3.TSSnorm.LOGtrans.med.abS.jointP")    da <- DA_mixMC(object = ps, contrast = c("group", "grp2",         "grp1"), verbose = FALSE)    expectations(da, name = "mixMC.pc1")    da <- DA_ZicoSeq(object = ps, contrast = c("group", "grp2",         "grp1"), feature.dat.type = "count", is.winsor = TRUE,         outlier.pct = 0.03, winsor.end = "top", verbose = FALSE)    expectations(da, name = "ZicoSeq.winsor0.03top.post25.ref0.5.excl0.2")})
26: eval(code, test_env)
27: eval(code, test_env)
28: withCallingHandlers({    eval(code, test_env)    new_expectations <- the$test_expectations > starting_expectations    if (snapshot_skipped) {        skip("On CRAN")    }    else if (!new_expectations && skip_on_empty) {        skip_empty()    }}, expectation = handle_expectation, packageNotFoundError = function(e) {    if (on_cran()) {        skip(paste0("{", e$package, "} is not installed."))    }}, snapshot_on_cran = function(cnd) {    snapshot_skipped <<- TRUE    invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message,     error = handle_error, interrupt = handle_interrupt)
29: doTryCatch(return(expr), name, parentenv, handler)
30: tryCatchOne(expr, names, parentenv, handlers[[1L]])
31: tryCatchList(expr, classes, parentenv, handlers)
32: tryCatch(withCallingHandlers({    eval(code, test_env)    new_expectations <- the$test_expectations > starting_expectations    if (snapshot_skipped) {        skip("On CRAN")    }    else if (!new_expectations && skip_on_empty) {        skip_empty()    }}, expectation = handle_expectation, packageNotFoundError = function(e) {    if (on_cran()) {        skip(paste0("{", e$package, "} is not installed."))    }}, snapshot_on_cran = function(cnd) {    snapshot_skipped <<- TRUE    invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message,     error = handle_error, interrupt = handle_interrupt), error = handle_fatal)
33: doWithOneRestart(return(expr), restart)
34: withOneRestart(expr, restarts[[1L]])
35: withRestarts(tryCatch(withCallingHandlers({    eval(code, test_env)    new_expectations <- the$test_expectations > starting_expectations    if (snapshot_skipped) {        skip("On CRAN")    }    else if (!new_expectations && skip_on_empty) {        skip_empty()    }}, expectation = handle_expectation, packageNotFoundError = function(e) {    if (on_cran()) {        skip(paste0("{", e$package, "} is not installed."))    }}, snapshot_on_cran = function(cnd) {    snapshot_skipped <<- TRUE    invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message,     error = handle_error, interrupt = handle_interrupt), error = handle_fatal),     end_test = function() {    })
36: test_code(code = exprs, env = env, reporter = get_reporter() %||%     StopReporter$new())
37: source_file(path, env = env(env), desc = desc, shuffle = shuffle,     error_call = error_call)
38: FUN(X[[i]], ...)
39: lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle,     error_call = error_call)
40: doTryCatch(return(expr), name, parentenv, handler)
41: tryCatchOne(expr, names, parentenv, handlers[[1L]])
42: tryCatchList(expr, classes, parentenv, handlers)
43: tryCatch(code, testthat_abort_reporter = function(cnd) {    cat(conditionMessage(cnd), "\n")    NULL})
44: with_reporter(reporters$multi, lapply(test_paths, test_one_file,     env = env, desc = desc, shuffle = shuffle, error_call = error_call))
45: test_files_serial(test_dir = test_dir, test_package = test_package,     test_paths = test_paths, load_helpers = load_helpers, reporter = reporter,     env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,     desc = desc, load_package = load_package, shuffle = shuffle,     error_call = error_call)
46: test_files(test_dir = path, test_paths = test_paths, test_package = package,     reporter = reporter, load_helpers = load_helpers, env = env,     stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,     load_package = load_package, parallel = parallel, shuffle = shuffle)
47: test_dir("testthat", package = package, reporter = reporter,     ..., load_package = "installed")
48: test_check("benchdamic")
An irrecoverable exception occurred. R is aborting now ...