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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:CyTOFpower.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings CyTOFpower_1.9.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/CyTOFpower.Rcheck’
* using R Under development (unstable) (2024-03-18 r86148)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CyTOFpower/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CyTOFpower’ version ‘1.9.0’
* 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 hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘CyTOFpower’ 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 ... NOTE
Problems with news in ‘NEWS’:
  Cannot process chunk/lines:
    Changes in version 0.99.0 (2021-09-15)
* 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 ... OK
* 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 ... 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 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: 26318 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:
  39: tryCatch(withCallingHandlers({    eval(code, test_env)    if (!handled && !is.null(test)) {        skip_empty()    }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,     message = handle_message, error = handle_error), error = handle_fatal,     skip = function(e) {    })
  40: test_code(test = NULL, code = exprs, env = env, default_reporter = StopReporter$new())
  41: source_file(path, env = env(env), desc = desc, error_call = error_call)
  42: FUN(X[[i]], ...)
  43: lapply(test_paths, test_one_file, env = env, desc = desc, error_call = error_call)
  44: doTryCatch(return(expr), name, parentenv, handler)
  45: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  46: tryCatchList(expr, classes, parentenv, handlers)
  47: tryCatch(code, testthat_abort_reporter = function(cnd) {    cat(conditionMessage(cnd), "\n")    NULL})
  48: with_reporter(reporters$multi, lapply(test_paths, test_one_file,     env = env, desc = desc, error_call = error_call))
  49: 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, error_call = error_call)
  50: 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)
  51: test_dir("testthat", package = package, reporter = reporter,     ..., load_package = "installed")
  52: test_check("CyTOFpower")
  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, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.19-bioc/meat/CyTOFpower.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL CyTOFpower
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘CyTOFpower’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (CyTOFpower)

R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-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(CyTOFpower)
> 
> test_check("CyTOFpower")
[[1]]
  marker_name nb_donor rho subject_effect mu0 dispersion nb_cell_per_sample
1          m1        3   1            0.1  10          3                  1

[[2]]
  marker_name nb_donor rho subject_effect mu0 dispersion nb_cell_per_sample
1          m2        3 1.1            0.1  10          3                  1

  marker_name nb_donor rho subject_effect mu0 dispersion nb_cell_per_sample
1          m1        3 1.0            0.1  10          3                  3
2          m2        3 1.1            0.1  10          3                  3
3          m3        3 1.0            0.1  10          3                  3
  marker_name nb_donor rho subject_effect mu0 dispersion nb_cell_per_sample
1          m1        3 1.0            0.1  10          3                  3
2          m2        3 1.1            0.1  10          3                  3
3          m3        3 1.0            0.1  10          3                  3
  marker_name nb_donor rho subject_effect mu0 dispersion nb_cell_per_sample
1          m1        3 1.0            0.1  10          3                  3
2          m2        3 1.1            0.1  10          3                  3
3          m3        3 1.0            0.1  10          3                  3
[[1]]
  marker_name nb_donor rho subject_effect mu0 dispersion nb_cell_per_sample
1          m1        3   1            0.1  10          3                  3

[[2]]
  marker_name nb_donor rho subject_effect mu0 dispersion nb_cell_per_sample
1          m2        3 1.1            0.1  10          3                  3

[[3]]
  marker_name nb_donor rho subject_effect mu0 dispersion nb_cell_per_sample
1          m3        3   1            0.1  10          3                  3

[[1]]
  marker_name nb_donor rho subject_effect mu0 dispersion nb_cell_per_sample
1          m1        3   1            0.1  10          3                  3

[[2]]
  marker_name nb_donor rho subject_effect mu0 dispersion nb_cell_per_sample
1          m2        3 1.1            0.1  10          3                  3

[[3]]
  marker_name nb_donor rho subject_effect mu0 dispersion nb_cell_per_sample
1          m3        3   1            0.1  10          3                  3

[[1]]
  marker_name nb_donor rho subject_effect mu0 dispersion nb_cell_per_sample
1          m1        3   1            0.1  10          3                  3

[[2]]
  marker_name nb_donor rho subject_effect mu0 dispersion nb_cell_per_sample
1          m2        3 1.1            0.1  10          3                  3

[[3]]
  marker_name nb_donor rho subject_effect mu0 dispersion nb_cell_per_sample
1          m3        3   1            0.1  10          3                  3

Joining with `by = join_by(markers)`
Joining with `by = join_by(markers)`

 *** caught segfault ***
address 0x0, cause 'unknown'

Traceback:
 1: .Call(merPredDCreate, as(X, "matrix"), Lambdat, LamtUt, Lind,     RZX, Ut, Utr, V, VtV, Vtr, Xwts, Zt, beta0, delb, delu, theta,     u0)
 2: initializePtr()
 3: .Object$initialize(...)
 4: initialize(value, ...)
 5: initialize(value, ...)
 6: methods::new(def, ...)
 7: (new("refMethodDef", .Data = function (...) {    methods::new(def, ...)}, mayCall = c("methods", "new"), name = "new", refClassName = "refGeneratorSlot",     superClassMethod = ""))(Zt = new("dgCMatrix", i = c(0L, 0L, 1L, 1L, 2L, 2L), p = 0:6, Dim = c(3L, 6L), Dimnames = list(c("donor_1", "donor_2", "donor_3"), c("sample_1", "sample_4", "sample_2", "sample_5", "sample_3", "sample_6")), x = c(1, 1, 1, 1, 1, 1),     factors = list()), theta = 1, Lambdat = new("dgCMatrix",     i = 0:2, p = 0:3, Dim = c(3L, 3L), Dimnames = list(NULL,         NULL), x = c(1, 1, 1), factors = list()), Lind = c(1L, 1L, 1L), n = 6L, X = c(1, 1, 1, 1, 1, 1, 0, 1, 0, 1, 0, 1))
 8: do.call(merPredD$new, c(reTrms[c("Zt", "theta", "Lambdat", "Lind")],     n = nrow(X), list(X = X)))
 9: (function (fr, X, reTrms, REML = TRUE, start = NULL, verbose = 0,     control = lmerControl(), ...) {    p <- ncol(X)    rho <- new.env(parent = parent.env(environment()))    rho$pp <- do.call(merPredD$new, c(reTrms[c("Zt", "theta",         "Lambdat", "Lind")], n = nrow(X), list(X = X)))    REMLpass <- if (REML)         p    else 0L    rho$resp <- if (missing(fr))         mkRespMod(REML = REMLpass, ...)    else mkRespMod(fr, REML = REMLpass)    pp <- resp <- NULL    rho$lmer_Deviance <- lmer_Deviance    devfun <- function(theta) .Call(lmer_Deviance, pp$ptr(),         resp$ptr(), as.double(theta))    environment(devfun) <- rho    if (is.null(start) && all(reTrms$cnms == "(Intercept)") &&         length(reTrms$flist) == length(reTrms$lower) && !is.null(y <- model.response(fr))) {        v <- sapply(reTrms$flist, function(f) var(ave(y, f)))        v.e <- var(y) - sum(v)        if (!is.na(v.e) && v.e > 0) {            v.rel <- v/v.e            if (all(v.rel >= reTrms$lower^2))                 rho$pp$setTheta(sqrt(v.rel))        }    }    if (length(rho$resp$y) > 0)         devfun(rho$pp$theta)    rho$lower <- reTrms$lower    devfun})(fr = list(y = c(1.5296604950904, 0.732668256045411, 1.35044074027497, 1.35044074027497, 1.75322890111027, 1.35044074027497), group_id = c(1L, 2L, 1L, 2L, 1L, 2L), donor_id = c(1L, 1L, 2L, 2L, 3L, 3L), `(weights)` = c(3, 3, 3, 3, 3, 3)), X = c(1, 1, 1, 1, 1, 1, 0, 1, 0, 1, 0, 1), reTrms = list(    Zt = new("dgCMatrix", i = c(0L, 0L, 1L, 1L, 2L, 2L), p = 0:6,         Dim = c(3L, 6L), Dimnames = list(c("donor_1", "donor_2",         "donor_3"), c("sample_1", "sample_4", "sample_2", "sample_5",         "sample_3", "sample_6")), x = c(1, 1, 1, 1, 1, 1), factors = list()),     theta = 1, Lind = c(1L, 1L, 1L), Gp = c(0L, 3L), lower = 0,     Lambdat = new("dgCMatrix", i = 0:2, p = 0:3, Dim = c(3L,     3L), Dimnames = list(NULL, NULL), x = c(1, 1, 1), factors = list()),     flist = list(donor_id = c(1L, 1L, 2L, 2L, 3L, 3L)), cnms = list(        donor_id = "(Intercept)"), Ztlist = list(`1 | donor_id` = new("dgCMatrix",         i = c(0L, 0L, 1L, 1L, 2L, 2L), p = 0:6, Dim = c(3L, 6L        ), Dimnames = list(c("donor_1", "donor_2", "donor_3"),             c("sample_1", "sample_4", "sample_2", "sample_5",             "sample_3", "sample_6")), x = c(1, 1, 1, 1, 1, 1),         factors = list())), nl = c(donor_id = 3L)), REML = TRUE,     wmsgs = character(0), start = NULL, verbose = 0L, control = list(        optimizer = "nloptwrap", restart_edge = TRUE, boundary.tol = 1e-05,         calc.derivs = TRUE, use.last.params = FALSE, checkControl = list(            check.nobs.vs.rankZ = "ignore", check.nobs.vs.nlev = "stop",             check.nlev.gtreq.5 = "ignore", check.nlev.gtr.1 = "stop",             check.nobs.vs.nRE = "stop", check.rankX = "message+drop.cols",             check.scaleX = "warning", check.formula.LHS = "stop"),         checkConv = list(check.conv.grad = list(action = "warning",             tol = 0.002, relTol = NULL), check.conv.singular = list(            action = "message", tol = 1e-04), check.conv.hess = list(            action = "warning", tol = 1e-06)), optCtrl = list()))
10: do.call(mkLmerDevfun, c(lmod, list(start = start, verbose = verbose,     control = control)))
11: lmer(formula$formula, data = data_i, weights = weights)
12: doTryCatch(return(expr), name, parentenv, handler)
13: tryCatchOne(expr, names, parentenv, handlers[[1L]])
14: tryCatchList(expr, classes, parentenv, handlers)
15: tryCatch({    y <- meds[i, ]    data_i <- cbind(cbind(y, weights), formula$data)    if (formula$random_terms) {        fit <- lmer(formula$formula, data = data_i, weights = weights)    }    else {        fit <- lm(formula$formula, data = data_i, weights = weights)    }    test <- glht(fit, contrast)    summary(test)$test$pvalues}, error = function(e) NA)
16: diffcyt::testDS_LMM(d_counts = ls_features$counts, d_medians = ls_features$medians,     formula = ls_form_contrast$formula, contrast = ls_form_contrast$contrast)
17: function_run_diffcytDSLMM(ls_form_contrast = ls_contrast_LMM,     df_experiment_info = df_exp_info, ls_features = ls_features)
18: eval(code, test_env)
19: eval(code, test_env)
20: withCallingHandlers({    eval(code, test_env)    if (!handled && !is.null(test)) {        skip_empty()    }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,     message = handle_message, error = handle_error)
21: doTryCatch(return(expr), name, parentenv, handler)
22: tryCatchOne(expr, names, parentenv, handlers[[1L]])
23: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
24: doTryCatch(return(expr), name, parentenv, handler)
25: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),     names[nh], parentenv, handlers[[nh]])
26: tryCatchList(expr, classes, parentenv, handlers)
27: tryCatch(withCallingHandlers({    eval(code, test_env)    if (!handled && !is.null(test)) {        skip_empty()    }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,     message = handle_message, error = handle_error), error = handle_fatal,     skip = function(e) {    })
28: test_code(desc, code, env = parent.frame(), default_reporter = local_interactive_reporter())
29: test_that("Run diffcyt-DS-LMM model", {    set.seed(123)    ls_contrast_LMM <- function_formula_contrast_diffcytDSLMM_randomeffect(df_experiment_info = df_exp_info)    ls_features <- function_compute_diffcyt_features(d_sumexp)    ls_res_model_lmm <- function_run_diffcytDSLMM(ls_form_contrast = ls_contrast_LMM,         df_experiment_info = df_exp_info, ls_features = ls_features)    expect_type(ls_res_model_lmm, "list")    expect_identical(names(ls_res_model_lmm), c("model_fit",         "result_summary"))    expect_equal(ls_res_model_lmm$result_summary$p_adj, c(0.1,         0, 0.5), tolerance = 1)})
30: eval(code, test_env)
31: eval(code, test_env)
32: withCallingHandlers({    eval(code, test_env)    if (!handled && !is.null(test)) {        skip_empty()    }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,     message = handle_message, error = handle_error)
33: doTryCatch(return(expr), name, parentenv, handler)
34: tryCatchOne(expr, names, parentenv, handlers[[1L]])
35: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
36: doTryCatch(return(expr), name, parentenv, handler)
37: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),     names[nh], parentenv, handlers[[nh]])
38: tryCatchList(expr, classes, parentenv, handlers)
39: tryCatch(withCallingHandlers({    eval(code, test_env)    if (!handled && !is.null(test)) {        skip_empty()    }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,     message = handle_message, error = handle_error), error = handle_fatal,     skip = function(e) {    })
40: test_code(test = NULL, code = exprs, env = env, default_reporter = StopReporter$new())
41: source_file(path, env = env(env), desc = desc, error_call = error_call)
42: FUN(X[[i]], ...)
43: lapply(test_paths, test_one_file, env = env, desc = desc, error_call = error_call)
44: doTryCatch(return(expr), name, parentenv, handler)
45: tryCatchOne(expr, names, parentenv, handlers[[1L]])
46: tryCatchList(expr, classes, parentenv, handlers)
47: tryCatch(code, testthat_abort_reporter = function(cnd) {    cat(conditionMessage(cnd), "\n")    NULL})
48: with_reporter(reporters$multi, lapply(test_paths, test_one_file,     env = env, desc = desc, error_call = error_call))
49: 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, error_call = error_call)
50: 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)
51: test_dir("testthat", package = package, reporter = reporter,     ..., load_package = "installed")
52: test_check("CyTOFpower")
An irrecoverable exception occurred. R is aborting now ...