##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data iSEEhex
###
##############################################################################
##############################################################################


* checking for file ‘iSEEhex/DESCRIPTION’ ... OK
* preparing ‘iSEEhex’:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘iSEEhex.Rmd’ using rmarkdown

 *** caught segfault ***
address 0xffffffffa254a360, 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, "indptr")
 4: .read_h5sparse_indptr(filepath, group)
 5: H5SparseMatrixSeed(filepath = fpath, group = name, dim = details$shape,     sparse.layout = tolower(details$layout))
 6: DelayedArray(H5SparseMatrixSeed(filepath = fpath, group = name,     dim = details$shape, sparse.layout = tolower(details$layout)))
 7: meth(path, metadata = metadata, ...)
 8: readObject(path, metadata = metadata, scRNAseq.realize.assays = scRNAseq.realize.assays,     scRNAseq.realize.reduced.dims = scRNAseq.realize.reduced.dims,     ...)
 9: FUN(path, ...)
10: altReadObject(file.path(path, "assays", y - 1L), ...)
11: readSummarizedExperiment(path, metadata = metadata, ...)
12: readRangedSummarizedExperiment(path, metadata, ...)
13: meth(path, metadata = metadata, ...)
14: readObject(path, metadata = metadata, scRNAseq.realize.assays = scRNAseq.realize.assays,     scRNAseq.realize.reduced.dims = scRNAseq.realize.reduced.dims,     ...)
15: FUN(path, ...)
16: altReadObject(file.path(aedir, y - 1L), ...)
17: meth(path, metadata = metadata, ...)
18: readObject(path, metadata = metadata, scRNAseq.realize.assays = scRNAseq.realize.assays,     scRNAseq.realize.reduced.dims = scRNAseq.realize.reduced.dims,     ...)
19: FUN(path, ...)
20: altReadObject(obj_path, scRNAseq.realize.assays = realize.assays,     scRNAseq.realize.reduced.dims = realize.reduced.dims, ...)
21: fetchDataset("legacy", "2023-12-18", "allen", realize.assays = TRUE)
22: ReprocessedAllenData(assays = "tophat_counts")
23: eval(expr, envir)
24: eval(expr, envir)
25: withVisible(eval(expr, envir))
26: withCallingHandlers(code, error = function (e) rlang::entrace(e), message = function (cnd) {    watcher$capture_plot_and_output()    if (on_message$capture) {        watcher$push(cnd)    }    if (on_message$silence) {        invokeRestart("muffleMessage")    }}, warning = function (cnd) {    if (getOption("warn") >= 2 || getOption("warn") < 0) {        return()    }    watcher$capture_plot_and_output()    if (on_warning$capture) {        cnd <- sanitize_call(cnd)        watcher$push(cnd)    }    if (on_warning$silence) {        invokeRestart("muffleWarning")    }}, error = function (cnd) {    watcher$capture_plot_and_output()    cnd <- sanitize_call(cnd)    watcher$push(cnd)    switch(on_error, continue = invokeRestart("eval_continue"),         stop = invokeRestart("eval_stop"), error = NULL)})
27: eval(call)
28: eval(call)
29: with_handlers({    for (expr in tle$exprs) {        ev <- withVisible(eval(expr, envir))        watcher$capture_plot_and_output()        watcher$print_value(ev$value, ev$visible, envir)    }    TRUE}, handlers)
30: doWithOneRestart(return(expr), restart)
31: withOneRestart(expr, restarts[[1L]])
32: withRestartList(expr, restarts[-nr])
33: doWithOneRestart(return(expr), restart)
34: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
35: withRestartList(expr, restarts)
36: withRestarts(with_handlers({    for (expr in tle$exprs) {        ev <- withVisible(eval(expr, envir))        watcher$capture_plot_and_output()        watcher$print_value(ev$value, ev$visible, envir)    }    TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
37: evaluate::evaluate(...)
38: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning,     keep_message = if (is.numeric(options$message)) TRUE else options$message,     stop_on_error = if (is.numeric(options$error)) options$error else {        if (options$error && options$include)             0L        else 2L    }, output_handler = knit_handlers(options$render, options))
39: in_dir(input_dir(), expr)
40: in_input_dir(evaluate(code, envir = env, new_device = FALSE,     keep_warning = if (is.numeric(options$warning)) TRUE else options$warning,     keep_message = if (is.numeric(options$message)) TRUE else options$message,     stop_on_error = if (is.numeric(options$error)) options$error else {        if (options$error && options$include)             0L        else 2L    }, output_handler = knit_handlers(options$render, options)))
41: eng_r(options)
42: block_exec(params)
43: call_block(x)
44: process_group(group)
45: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),     error = function(e) {        if (progress && is.function(pb$interrupt))             pb$interrupt()        if (is_R_CMD_build() || is_R_CMD_check())             error <<- format(e)    })
46: with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),     error = function(e) {        if (progress && is.function(pb$interrupt))             pb$interrupt()        if (is_R_CMD_build() || is_R_CMD_check())             error <<- format(e)    }), list(rlang_trace_top_env = knit_global()))
47: xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),     error = function(e) {        if (progress && is.function(pb$interrupt))             pb$interrupt()        if (is_R_CMD_build() || is_R_CMD_check())             error <<- format(e)    }), list(rlang_trace_top_env = knit_global())), function(loc) {    setwd(wd)    write_utf8(res, output %n% stdout())    paste0("\nQuitting from ", loc, if (!is.null(error))         paste0("\n", rule(), error, "\n", rule()))}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
48: process_file(text, output)
49: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
50: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(),     output_dir = getwd(), ...)
51: vweave_rmarkdown(...)
52: engine$weave(file, quiet = quiet, encoding = enc)
53: doTryCatch(return(expr), name, parentenv, handler)
54: tryCatchOne(expr, names, parentenv, handlers[[1L]])
55: tryCatchList(expr, classes, parentenv, handlers)
56: tryCatch({    engine$weave(file, quiet = quiet, encoding = enc)    setwd(startdir)    output <- find_vignette_product(name, by = "weave", engine = engine)    if (!have.makefile && vignette_is_tex(output)) {        texi2pdf(file = output, clean = FALSE, quiet = quiet)        output <- find_vignette_product(name, by = "texi2pdf",             engine = engine)    }    outputs <- c(outputs, output)}, error = function(e) {    thisOK <<- FALSE    fails <<- c(fails, file)    message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s",         file, conditionMessage(e)))})
57: tools::buildVignettes(dir = ".", tangle = TRUE)
An irrecoverable exception occurred. R is aborting now ...
Segmentation fault (core dumped)