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### Running command:
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### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data alabaster.spatial
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* checking for file ‘alabaster.spatial/DESCRIPTION’ ... OK
* preparing ‘alabaster.spatial’:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘userguide.Rmd’ using rmarkdown
*** caught segfault ***
address 0x38219380, 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: FUN(path, ...)
9: altReadObject(file.path(path, "assays", y - 1L), ...)
10: readSummarizedExperiment(path, metadata = metadata, ...)
11: readRangedSummarizedExperiment(path, metadata, ...)
12: readSingleCellExperiment(path, metadata, ...)
13: meth(path, metadata = metadata, ...)
14: readObject(tmp)
15: eval(expr, envir)
16: eval(expr, envir)
17: withVisible(eval(expr, envir))
18: 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)})
19: eval(call)
20: eval(call)
21: with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers)
22: doWithOneRestart(return(expr), restart)
23: withOneRestart(expr, restarts[[1L]])
24: withRestartList(expr, restarts[-nr])
25: doWithOneRestart(return(expr), restart)
26: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
27: withRestartList(expr, restarts)
28: withRestarts(with_handlers({ for (expr in tle$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)
29: evaluate::evaluate(...)
30: 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$render, options))
31: in_dir(input_dir(), expr)
32: in_input_dir(evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$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)))
33: eng_r(options)
34: block_exec(params)
35: call_block(x)
36: process_group(group)
37: 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) })
38: 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()))
39: 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)
40: process_file(text, output)
41: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
42: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...)
43: vweave_rmarkdown(...)
44: engine$weave(file, quiet = quiet, encoding = enc)
45: doTryCatch(return(expr), name, parentenv, handler)
46: tryCatchOne(expr, names, parentenv, handlers[[1L]])
47: tryCatchList(expr, classes, parentenv, handlers)
48: tryCatch({ engine$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)))})
49: tools::buildVignettes(dir = ".", tangle = TRUE)
An irrecoverable exception occurred. R is aborting now ...
Segmentation fault (core dumped)