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###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:XeniumIO.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings XeniumIO_1.3.2.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/XeniumIO.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 10:30:32 UTC
* checking for file ‘XeniumIO/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘XeniumIO’ version ‘1.3.2’
* 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 ‘XeniumIO’ 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 ... 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 ‘tinytest.R’
 ERROR
Running the tests in ‘tests/tinytest.R’ failed.
Last 13 lines of output:
  13: withCallingHandlers(current, warning = function(w) {    warnings <<- append(warnings, list(w))    invokeRestart("muffleWarning")}, message = function(m) {    messages <<- append(messages, list(m))    invokeRestart("muffleMessage")})
  14: doTryCatch(return(expr), name, parentenv, handler)
  15: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  16: tryCatchList(expr, classes, parentenv, handlers)
  17: tryCatch(withCallingHandlers(current, warning = function(w) {    warnings <<- append(warnings, list(w))    invokeRestart("muffleWarning")}, message = function(m) {    messages <<- append(messages, list(m))    invokeRestart("muffleMessage")}), error = function(e) errors <<- append(errors, list(e)))
  18: fun(...)
  19: expect_warning(seh5 <- import(TENxXenium(xeniumOut = outfold,     format = "h5")))
  20: eval(expr, envir = e)
  21: eval(expr, envir = e)
  22: FUN(X[[i]], ...)
  23: lapply(basename(testfiles), run_test_file, at_home = at_home,     verbose = verbose, color = color, remove_side_effects = remove_side_effects,     ...)
  24: run_test_dir(testdir, at_home = at_home, cluster = cluster, ...)
  25: tinytest::test_package("XeniumIO")
  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/XeniumIO.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL XeniumIO
###
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* installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’
* installing *source* package ‘XeniumIO’ ...
** this is package ‘XeniumIO’ version ‘1.3.2’
** 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 (XeniumIO)

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.

> if (requireNamespace("tinytest", quietly = TRUE))
+     tinytest::test_package("XeniumIO")
Loading required package: TENxIO
Loading required package: SingleCellExperiment
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'MatrixGenerics'

The following objects are masked from 'package:matrixStats':

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: generics

Attaching package: 'generics'

The following objects are masked from 'package:base':

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
    unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:utils':

    findMatches

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: Seqinfo
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'Biobase'

The following object is masked from 'package:MatrixGenerics':

    rowMedians

The following objects are masked from 'package:matrixStats':

    anyMissing, rowMedians


test-TENxXenium-class.R.......    0 tests    
test-TENxXenium-class.R.......    0 tests    
test-TENxXenium-class.R.......    0 tests    
test-TENxXenium-class.R.......    0 tests    
test-TENxXenium-class.R.......    0 tests    
test-TENxXenium-class.R.......    0 tests    
test-TENxXenium-class.R.......    1 tests OK 
test-TENxXenium-class.R.......    2 tests OK 
 *** caught segfault ***
address 0xffffffffbb39e950, 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 = start, counts = count, as.vector = TRUE,     as.integer = as.integer)
 3: read_h5sparse_component(filepath, group, "shape")
 4: .read_h5sparse_dim(filepath, group)
 5: .get_sparse_matrix_dim(filepath, group, dim = dim)
 6: H5SparseMatrixSeed(filepath, group)
 7: TENxMatrixSeed(filepath, group)
 8: HDF5Array::TENxMatrix(path(con), con@group)
 9: import(con@resources, ...)
10: import(con@resources, ...)
11: import(TENxXenium(xeniumOut = outfold, format = "h5"))
12: import(TENxXenium(xeniumOut = outfold, format = "h5"))
13: withCallingHandlers(current, warning = function(w) {    warnings <<- append(warnings, list(w))    invokeRestart("muffleWarning")}, message = function(m) {    messages <<- append(messages, list(m))    invokeRestart("muffleMessage")})
14: doTryCatch(return(expr), name, parentenv, handler)
15: tryCatchOne(expr, names, parentenv, handlers[[1L]])
16: tryCatchList(expr, classes, parentenv, handlers)
17: tryCatch(withCallingHandlers(current, warning = function(w) {    warnings <<- append(warnings, list(w))    invokeRestart("muffleWarning")}, message = function(m) {    messages <<- append(messages, list(m))    invokeRestart("muffleMessage")}), error = function(e) errors <<- append(errors, list(e)))
18: fun(...)
19: expect_warning(seh5 <- import(TENxXenium(xeniumOut = outfold,     format = "h5")))
20: eval(expr, envir = e)
21: eval(expr, envir = e)
22: FUN(X[[i]], ...)
23: lapply(basename(testfiles), run_test_file, at_home = at_home,     verbose = verbose, color = color, remove_side_effects = remove_side_effects,     ...)
24: run_test_dir(testdir, at_home = at_home, cluster = cluster, ...)
25: tinytest::test_package("XeniumIO")
An irrecoverable exception occurred. R is aborting now ...
Segmentation fault (core dumped)