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###
### Running command:
###
###   /home/biocbuild/R/R-4.4-devel-2024.03.20/bin/R CMD check --install=check:randRotation.install-out.txt --library=/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library --no-vignettes --timings randRotation_1.15.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/randRotation.Rcheck’
* using R Under development (unstable) (2024-03-19 r86153)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘randRotation/DESCRIPTION’ ... OK
* this is package ‘randRotation’ version ‘1.15.0’
* 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 ‘randRotation’ 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 loading without being on the library search path ... 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 ... NOTE
checkRd: (-1) qqunif.Rd:35: Lost braces; missing escapes or markup?
    35 | A list of \code{x} and {y} coordinates, as in \code{\link[stats:qqnorm]{qqplot}}.
       |                        ^
* 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
Examples with CPU (user + system) or elapsed time > 5s
      user system elapsed
pFdr 9.652   0.26   9.932
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’/home/biocbuild/R/R-4.4-devel-2024.03.20/bin/BATCH: line 60: 2426578 Segmentation fault      (core dumped) ${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:
  33: 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) {    })
  34: test_code(test = NULL, code = exprs, env = env, default_reporter = StopReporter$new())
  35: source_file(path, env = env(env), desc = desc, error_call = error_call)
  36: FUN(X[[i]], ...)
  37: lapply(test_paths, test_one_file, env = env, desc = desc, error_call = error_call)
  38: doTryCatch(return(expr), name, parentenv, handler)
  39: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  40: tryCatchList(expr, classes, parentenv, handlers)
  41: tryCatch(code, testthat_abort_reporter = function(cnd) {    cat(conditionMessage(cnd), "\n")    NULL})
  42: with_reporter(reporters$multi, lapply(test_paths, test_one_file,     env = env, desc = desc, error_call = error_call))
  43: 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)
  44: 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)
  45: test_dir("testthat", package = package, reporter = reporter,     ..., load_package = "installed")
  46: test_check("randRotation")
  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
  ‘/home/biocbuild/bbs-3.19-bioc/meat/randRotation.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/R/R-4.4-devel-2024.03.20/bin/R CMD INSTALL randRotation
###
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* installing to library ‘/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library’
* installing *source* package ‘randRotation’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
Loading required namespace: randRotation
*** 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 (randRotation)

R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu

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(randRotation)
> 
> test_check("randRotation")

 *** caught segfault ***
address 0x40ff4000000000c4, cause 'memory not mapped'

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$initialize(...)
 4: initialize(value, ...)
 5: initialize(value, ...)
 6: methods::new(def, ...)
 7: (new("refMethodDef", .Data = function (...) {    methods::new(def, ...)}, mayCall = c("methods", "new"), name = "new", refClassName = "refGeneratorSlot",     superClassMethod = ""))(Zt = new("dgCMatrix", i = c(1L, 1L, 1L, 1L, 1L, 0L, 0L, 0L, 0L, 0L), p = 0:10, Dim = c(2L, 10L),     Dimnames = list(c("1", "2"), c("1", "2", "3", "4", "5", "6",     "7", "8", "9", "10")), x = c(1, 1, 1, 1, 1, 1, 1, 1, 1, 1    ), factors = list()), theta = 1, Lambdat = new("dgCMatrix",     i = 0:1, p = 0:2, Dim = c(2L, 2L), Dimnames = list(NULL,         NULL), x = c(1, 1), factors = list()), Lind = c(1L, 1L), n = 10L, X = c(1, 1, 1, 1, 1, 1, 1, 1, 1, 1))
 8: do.call(merPredD$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(feature1 = c(4.26295428488079, 4.76359346114046, 2.77573211472169, 3.7642934435605, 4.75790308981071, 3.2661373616721, 2.35872889597135, 3.01915639166027, 1.20291047492804, 4.29931230256343), individual = c(2L, 2L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 1L), `(weights)` = c(0.982182115828618, 0.356714132521302, 0.371800082316622, 0.282239230861887, 0.902778743347153, 1.06480755032971, 1.03167171501555, 0.511772374436259, 0.981017540255561, 0.508052448788658)), X = c(1, 1, 1, 1, 1, 1, 1, 1, 1, 1), reTrms = list(    Zt = new("dgCMatrix", i = c(1L, 1L, 1L, 1L, 1L, 0L, 0L, 0L,     0L, 0L), p = 0:10, Dim = c(2L, 10L), Dimnames = list(c("1",     "2"), c("1", "2", "3", "4", "5", "6", "7", "8", "9", "10"    )), x = c(1, 1, 1, 1, 1, 1, 1, 1, 1, 1), factors = list()),     theta = 1, Lind = c(1L, 1L), Gp = c(0L, 2L), lower = 0, Lambdat = new("dgCMatrix",         i = 0:1, p = 0:2, Dim = c(2L, 2L), Dimnames = list(NULL,             NULL), x = c(1, 1), factors = list()), flist = list(        individual = c(2L, 2L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 1L        )), cnms = list(individual = "(Intercept)"), Ztlist = list(        `1 | individual` = new("dgCMatrix", i = c(1L, 1L, 1L,         1L, 1L, 0L, 0L, 0L, 0L, 0L), p = 0:10, Dim = c(2L, 10L        ), Dimnames = list(c("1", "2"), c("1", "2", "3", "4",         "5", "6", "7", "8", "9", "10")), x = c(1, 1, 1, 1, 1,         1, 1, 1, 1, 1), factors = list())), nl = c(individual = 2L)),     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(feature1 ~ 1 + (1 | individual), data = df1, weights = w)
12: eval(code, test_env)
13: eval(code, test_env)
14: 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)
15: doTryCatch(return(expr), name, parentenv, handler)
16: tryCatchOne(expr, names, parentenv, handlers[[1L]])
17: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
18: doTryCatch(return(expr), name, parentenv, handler)
19: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),     names[nh], parentenv, handlers[[nh]])
20: tryCatchList(expr, classes, parentenv, handlers)
21: 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) {    })
22: test_code(desc, code, env = parent.frame(), default_reporter = local_interactive_reporter())
23: test_that("Random rotation gives same coefficients if all coefs are set as coef.d ?",     {        set.seed(0)        pdata = data.frame(phenotype = rep(c("Control", "Cancer"),             c(5, 5)))        features = 10        edata = matrix(rnorm(features * nrow(pdata)), nrow = features)        rownames(edata) = paste0("feature", 1:nrow(edata))        mod1 = model.matrix(~phenotype, pdata)        rr1 = initRandrot(Y = edata, X = mod1, coef.h = -1)        fit1 = lm.fit(x = mod1, y = t(edata))        edata.rotated = randrot(rr1)        fit.rotated = lm.fit(x = mod1, y = t(edata.rotated))        expect_equal(coef(fit1), coef(fit.rotated))        weights = matrix(runif(length(edata)) + 0.2, nrow = nrow(edata))        rr1 = suppressWarnings(initRandrot(Y = edata, X = mod1,             coef.h = -1, weights = weights))        coefs <- vapply(seq_len(features), function(i) coef(lm.wfit(x = mod1,             y = edata[i, ], w = weights[i, ])), numeric(ncol(mod1)))        edata.rot = randrot(rr1)        coefs.rot <- vapply(seq_len(features), function(i) coef(lm.wfit(x = mod1,             y = edata.rot[i, ], w = weights[i, ])), numeric(ncol(mod1)))        expect_equal(coefs, coefs.rot)        library(lme4)        colnames(pdata) <- "individual"        pdata$individual <- as.factor(rep(c("2", "1"), c(5, 5)))        df1 <- cbind(pdata, t(edata[1, , drop = FALSE]), w = weights[1,             ], phenotype = as.factor(c("Cancer.tissue", "Control.tissue")))        df1$feature1 = df1$feature1 + as.numeric(df1$individual)        df1$feature1 = df1$feature1 + as.numeric(df1$phenotype)        me0 <- lmer(feature1 ~ 1 + (1 | individual), data = df1,             weights = w)        me1 <- lmer(feature1 ~ 1 + phenotype + (1 | individual),             data = df1, weights = w)        mod1 <- as.matrix(cbind(getME(me1, "X"), getME(me1, "Z")))        mod1 <- mod1[, c(1, 3, 4, 2)]        mod1 <- mod1[, c(1, 2, 4)]        rr1 <- suppressWarnings(initRandrot(Y = t(df1$feature1),             X = mod1, coef.h = ncol(mod1), weights = t(df1$w)))        edata.rot <- randrot(rr1)        df2 <- df1        df2$feature1 <- edata.rot[1, ]        me0.rot <- lmer(feature1 ~ 1 + (1 | individual), data = df2,             weights = w)        expect_equal(ranef(me0), ranef(me0.rot), tolerance = 1e-05)        expect_equal(fixef(me0), fixef(me0.rot), tolerance = 1e-05)    })
24: eval(code, test_env)
25: eval(code, test_env)
26: withCallingHandlers({    eval(code, test_env)    if (!handled && !is.null(test)) {        skip_empty()    }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,     message = handle_message, error = handle_error)
27: doTryCatch(return(expr), name, parentenv, handler)
28: tryCatchOne(expr, names, parentenv, handlers[[1L]])
29: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
30: doTryCatch(return(expr), name, parentenv, handler)
31: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),     names[nh], parentenv, handlers[[nh]])
32: tryCatchList(expr, classes, parentenv, handlers)
33: tryCatch(withCallingHandlers({    eval(code, test_env)    if (!handled && !is.null(test)) {        skip_empty()    }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,     message = handle_message, error = handle_error), error = handle_fatal,     skip = function(e) {    })
34: test_code(test = NULL, code = exprs, env = env, default_reporter = StopReporter$new())
35: source_file(path, env = env(env), desc = desc, error_call = error_call)
36: FUN(X[[i]], ...)
37: lapply(test_paths, test_one_file, env = env, desc = desc, error_call = error_call)
38: doTryCatch(return(expr), name, parentenv, handler)
39: tryCatchOne(expr, names, parentenv, handlers[[1L]])
40: tryCatchList(expr, classes, parentenv, handlers)
41: tryCatch(code, testthat_abort_reporter = function(cnd) {    cat(conditionMessage(cnd), "\n")    NULL})
42: with_reporter(reporters$multi, lapply(test_paths, test_one_file,     env = env, desc = desc, error_call = error_call))
43: 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)
44: 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)
45: test_dir("testthat", package = package, reporter = reporter,     ..., load_package = "installed")
46: test_check("randRotation")
An irrecoverable exception occurred. R is aborting now ...