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### Running command:
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###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:transformGamPoi.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings transformGamPoi_1.17.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/transformGamPoi.Rcheck’
* using R Under development (unstable) (2026-03-05 r89546)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-03-07 10:12:27 UTC
* checking for file ‘transformGamPoi/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘transformGamPoi’ version ‘1.17.0’
* 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 ‘transformGamPoi’ can be installed ... OK
* used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0’
* 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 ... 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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... INFO
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
acosh_transform    24.334  2.109  26.938
transformGamPoi    18.570  0.575  19.518
residual_transform  9.838  0.531  10.750
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  52: test_code(code = exprs, env = env, reporter = get_reporter() %||%     StopReporter$new())
  53: source_file(path, env = env(env), desc = desc, shuffle = shuffle,     error_call = error_call)
  54: FUN(X[[i]], ...)
  55: lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle,     error_call = error_call)
  56: doTryCatch(return(expr), name, parentenv, handler)
  57: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  58: tryCatchList(expr, classes, parentenv, handlers)
  59: tryCatch(code, testthat_abort_reporter = function(cnd) {    cat(conditionMessage(cnd), "\n")    NULL})
  60: with_reporter(reporters$multi, lapply(test_paths, test_one_file,     env = env, desc = desc, shuffle = shuffle, error_call = error_call))
  61: 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)
  62: 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)
  63: test_dir("testthat", package = package, reporter = reporter,     ..., load_package = "installed")
  64: test_check("transformGamPoi")
  An irrecoverable exception occurred. R is aborting now ...
  Segmentation fault (core dumped)
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR
See
  ‘/home/biocbuild/bbs-3.23-bioc/meat/transformGamPoi.Rcheck/00check.log’
for details.

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###
### Running command:
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###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL transformGamPoi
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* installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’
* installing *source* package ‘transformGamPoi’ ...
** this is package ‘transformGamPoi’ version ‘1.17.0’
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0’
g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c sparse_divide_out_size_factor.cpp -o sparse_divide_out_size_factor.o
g++ -std=gnu++20 -shared -L/home/biocbuild/bbs-3.23-bioc/R/lib -L/usr/local/lib -o transformGamPoi.so RcppExports.o sparse_divide_out_size_factor.o -L/home/biocbuild/bbs-3.23-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.23-bioc/R/site-library/00LOCK-transformGamPoi/00new/transformGamPoi/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (transformGamPoi)

R Under development (unstable) (2026-03-05 r89546) -- "Unsuffered Consequences"
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: x86_64-pc-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(transformGamPoi)
> 
> test_check("transformGamPoi")
Warning: stack imbalance in '::', 82 then 84
Warning: stack imbalance in '{', 73 then 75

 *** caught segfault ***
address 0xffffffffa94593c0, cause 'memory not mapped'

Traceback:
 1: .Call2("C_h5mread", filepath, name, starts, counts, noreduce,     as.vector, as.integer, as.sparse, method, use.H5Dread_chunk,     PACKAGE = "h5mread")
 2: h5mread(filepath, name, starts = index, as.vector = FALSE, as.integer = as.integer,     as.sparse = as.sparse)
 3: .h5mread2(x@filepath, x@name, index, as.integer = as_int)
 4: extract_array(x@seed, index)
 5: extract_array(x@seed, index)
 6: .nextMethod(x = x, index = index)
 7: callNextMethod()
 8: extract_array(x, Nindex)
 9: extract_array(x, Nindex)
10: read_block_as_dense(x, viewport)
11: read_block_as_dense(x, viewport)
12: .read_block(x, viewport, as.sparse = as.sparse)
13: read_block(x, viewport, as.sparse = as.sparse)
14: FUN(viewport, ...)
15: FUN(X[[i]], ...)
16: lapply(X, FUN, ...)
17: lapply(X, FUN, ...)
18: S4Arrays:::bplapply2(seq_along(grid), FUN_WRAPPER, grid, verbose,     FUN, ..., BPPARAM = BPPARAM)
19: gridApply(grid, FUN_WRAPPER, FUN, x, as.sparse, verbose, verbose_read_block,     ..., BPPARAM = BPPARAM, verbose = FALSE)
20: blockApply(x, FUN = .sparse_handler, FUN, ..., as.sparse = NA,     grid = colAutoGrid(x))
21: colblock_APPLY(x = x, FUN = colSums2, na.rm = na.rm, ..., useNames = useNames)
22: blockfun(x, ..., useNames = useNames)
23: .smart_seed_dispatcher(x, generic = MatrixGenerics::colSums2,     blockfun = .DelayedMatrix_block_colSums2, force_block_processing = force_block_processing,     rows = rows, cols = cols, na.rm = na.rm, ..., useNames = useNames)
24: .local(x, rows, cols, na.rm, ..., useNames = useNames)
25: colSums2(Y)
26: colSums2(Y)
27: estimate_size_factors(Y, method = method, verbose = verbose)
28: .handle_size_factors(size_factors, counts)
29: acosh_transform(Y_hdf5)
30: eval(code, test_env)
31: eval(code, test_env)
32: 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)
33: doTryCatch(return(expr), name, parentenv, handler)
34: tryCatchOne(expr, names, parentenv, handlers[[1L]])
35: tryCatchList(expr, classes, parentenv, handlers)
36: 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)
37: doWithOneRestart(return(expr), restart)
38: withOneRestart(expr, restarts[[1L]])
39: 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() {    })
40: test_code(code, parent.frame())
41: test_that("on_disk works", {    n_genes <- 100    n_cells <- 30    beta0 <- rnorm(n = n_genes, mean = 2, sd = 0.3)    sf <- rchisq(n = n_cells, df = 100)    sf <- sf/mean(sf)    Mu <- exp(beta0 %*% t(log(sf)))    Y <- matrix(rnbinom(n = n_genes * n_cells, mu = Mu, size = 0.1),         nrow = n_genes, ncol = n_cells)    Y_hdf5 <- HDF5Array::writeHDF5Array(Y)    res <- acosh_transform(Y)    res1 <- acosh_transform(Y_hdf5)    res2 <- acosh_transform(Y, on_disk = TRUE)    expect_s4_class(res1, "DelayedMatrix")    expect_s4_class(res2, "DelayedMatrix")    expect_equal(res, as.matrix(res1))    expect_equal(res, as.matrix(res2))    Y_sp <- as(Y, "dgCMatrix")    Y_sp_hdf5 <- HDF5Array::writeHDF5Array(Y_sp)    res3 <- acosh_transform(Y_sp)    res4 <- acosh_transform(Y_sp_hdf5)    res5 <- acosh_transform(Y_sp, on_disk = TRUE)    expect_true(HDF5Array::is_sparse(res3))    expect_true(HDF5Array::is_sparse(res4))    expect_true(HDF5Array::is_sparse(res5))    expect_equal(res3, as(res4, "dgCMatrix"), ignore_attr = TRUE)    expect_equal(res3, as(res5, "dgCMatrix"), ignore_attr = TRUE)})
42: eval(code, test_env)
43: eval(code, test_env)
44: 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)
45: doTryCatch(return(expr), name, parentenv, handler)
46: tryCatchOne(expr, names, parentenv, handlers[[1L]])
47: tryCatchList(expr, classes, parentenv, handlers)
48: 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)
49: doWithOneRestart(return(expr), restart)
50: withOneRestart(expr, restarts[[1L]])
51: 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() {    })
52: test_code(code = exprs, env = env, reporter = get_reporter() %||%     StopReporter$new())
53: source_file(path, env = env(env), desc = desc, shuffle = shuffle,     error_call = error_call)
54: FUN(X[[i]], ...)
55: lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle,     error_call = error_call)
56: doTryCatch(return(expr), name, parentenv, handler)
57: tryCatchOne(expr, names, parentenv, handlers[[1L]])
58: tryCatchList(expr, classes, parentenv, handlers)
59: tryCatch(code, testthat_abort_reporter = function(cnd) {    cat(conditionMessage(cnd), "\n")    NULL})
60: with_reporter(reporters$multi, lapply(test_paths, test_one_file,     env = env, desc = desc, shuffle = shuffle, error_call = error_call))
61: 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)
62: 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)
63: test_dir("testthat", package = package, reporter = reporter,     ..., load_package = "installed")
64: test_check("transformGamPoi")
An irrecoverable exception occurred. R is aborting now ...
Segmentation fault (core dumped)