* using log directory ‘/Users/ripley/R/packages/tests-devel/iSTATS.Rcheck’
* using R Under development (unstable) (2026-09-18 r90566)
* using platform: aarch64-apple-darwin27.0.0
* R was compiled by
    Apple clang version 21.0.0 (clang-2100.3.34.2)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Golden Gate 27.0.1
* using session charset: UTF-8
* current time: 2026-10-10 15:07:25 UTC
* using option ‘--no-stop-on-test-error’
* checking for file ‘iSTATS/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘iSTATS’ version ‘1.8’
* 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 ‘iSTATS’ can be installed ... OK
* checking installed package size ... INFO
  installed size is  5.4Mb
  sub-directories of 1Mb or more:
    app   4.4Mb
* checking package 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 ... 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘alignment-regions.R’
  Running ‘app-helpers.R’
  Running ‘app-ui-navigation.R’
  Running ‘icoshift-regression.R’
  Running ‘selected-regions.R’
  Running ‘session-isolation.R’
  Running ‘shiny-alignment.R’
  Running ‘shiny-flow.R’
  Running ‘shiny-selected-regions.R’
  Running ‘shiny-stocsy.R’
  Running ‘spectra-plot.R’
 [12s/13s] ERROR
Running the tests in ‘tests/app-helpers.R’ failed.
Complete output:
  > library(iSTATS)
  Loading required package: shinyBS
  Loading required package: shinyWidgets
  > 
  > app_functions <- system.file("app", "functions.R", package = "iSTATS")
  > stopifnot(nzchar(app_functions))
  > helpers <- new.env(parent = globalenv())
  > sys.source(app_functions, envir = helpers)
  > 
  > set.seed(42)
  > x <- matrix(rnorm(120), 12, 10)
  > x[, 2] <- -x[, 1]
  > cases <- list(
  +   random = x,
  +   ties = round(x),
  +   single = x[, 1, drop = FALSE],
  +   one_sample = x[1, , drop = FALSE],
  +   constant = cbind(x, 1),
  +   missing = replace(x, c(1, 20), NA_real_)
  + )
  > 
  > for (m in cases) {
  +   for (method in c("pearson", "spearman")) {
  +     reference <- suppressWarnings(stats::cor(m, method = method))
  +     for (driver in seq_len(ncol(m))) {
  +       actual <- suppressWarnings(helpers$driver_correlations(m, driver)[[method]])
  +       stopifnot(isTRUE(all.equal(actual, unname(reference[driver, ]),
  +                                 tolerance = 1e-14)))
  +     }
  +   }
  + }
  > 
  > # The vectorized Shapiro-Wilk and rank helpers must equal, bit for bit, one
  > # shapiro.test()/rank() call per column: small n branches, ties, constant and
  > # tiny-range columns, missing/infinite values and invalid sample sizes.
  > reference_p <- function(m) vapply(seq_len(ncol(m)), function(h)
  +   tryCatch(stats::shapiro.test(m[, h])$p.value, error = function(e) NA_real_), 0)
  > reference_ranks <- function(m)
  +   if (nrow(m) > 1L) apply(m, 2L, rank, na.last = "keep") else row(m)
  > shapiro_cases <- list(matrix(rnorm(2 * 4), 2), matrix(rnorm(5001 * 2), 5001))
  > for (n in c(3:12, 20, 52)) {
  +   y <- matrix(rexp(n * 40), n)
  +   y[, 2] <- round(y[, 2])
  +   y[, 3] <- 1
  +   y[, 4] <- y[, 4] * 1e-12 + 5
  +   y[, 5] <- c(rep(0, n - 1), 1)
  +   y[, 6] <- -0
  +   shapiro_cases[[length(shapiro_cases) + 1L]] <- y
  + }
  > y <- matrix(rnorm(52 * 8), 52, dimnames = list(NULL, paste0("c", 1:8)))
  > y[1, 1] <- NA; y[2, 2] <- Inf; y[, 3] <- NaN; y[1:50, 4] <- NA
  > shapiro_cases[[length(shapiro_cases) + 1L]] <- y
  > default_blocks <- helpers$.column_blocks
  > for (block_size in c(8192L, 3L)) {     # one block, and many uneven blocks
  +   helpers$.column_blocks <- function(columns, size = block_size)
  +     default_blocks(columns, size)
  +   for (m in c(cases, shapiro_cases)) {
  +     stopifnot(identical(helpers$.shapiro_p_values(m), reference_p(m)),
  +               identical(helpers$.spearman_ranks(m), reference_ranks(m)))
  +   }
  + }
  Error: identical(helpers$.shapiro_p_values(m), reference_p(m)) is not TRUE
  Execution halted
* checking PDF version of manual ... OK
* checking HTML version of manual ... OK
* checking for detritus in the temp directory ... OK
* DONE

Status: 1 ERROR
See
  ‘/Users/ripley/R/packages/tests-devel/iSTATS.Rcheck/00check.log’
for details.

       40.55 real        33.03 user         6.30 sys