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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 SpaceTrooper
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* checking for file ‘SpaceTrooper/DESCRIPTION’ ... OK
* preparing ‘SpaceTrooper’:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘Protein_tutorial_vignette.Rmd’ using rmarkdown
--- finished re-building ‘Protein_tutorial_vignette.Rmd’
--- re-building ‘RNA_tutorial_vignette.rmd’ using rmarkdown
*** caught segfault ***
address 0xffffffff963dc1e8, 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: TENxMatrix(path, group)
9: .read_from_hdf5(run, genome = genome, version = version)
10: FUN(...)
11: withCallingHandlers({ ERROR_CALL_DEPTH <<- (function() sys.nframe() - 1L)() FUN(...)}, error = function(e) { annotated_condition <- handle_error(e) stop(annotated_condition)}, warning = handle_warning)
12: doTryCatch(return(expr), name, parentenv, handler)
13: tryCatchOne(expr, names, parentenv, handlers[[1L]])
14: tryCatchList(expr, classes, parentenv, handlers)
15: tryCatch({ withCallingHandlers({ ERROR_CALL_DEPTH <<- (function() sys.nframe() - 1L)() FUN(...) }, error = function(e) { annotated_condition <- handle_error(e) stop(annotated_condition) }, warning = handle_warning)}, error = identity)
16: FUN(X[[i]], ...)
17: (function (X, FUN, ...) { FUN <- match.fun(FUN) if (!is.vector(X) || is.object(X)) X <- as.list(X) .Internal(lapply(X, FUN))})(X = "/tmp/RtmpqojGw5/Rinst1bf45043bb9f82/SpaceTrooper/extdata/Xenium_small/cell_feature_matrix.h5", FUN = function (...) { if (!identical(timeout, WORKER_TIMEOUT)) { setTimeLimit(timeout, timeout, TRUE) on.exit(setTimeLimit(Inf, Inf, FALSE)) } if (!is.null(globalOptions)) base::options(globalOptions) if (stop.on.error && ERROR_OCCURRED) { UNEVALUATED } else { .rng_reset_generator("L'Ecuyer-CMRG", SEED) output <- tryCatch({ withCallingHandlers({ ERROR_CALL_DEPTH <<- (function() sys.nframe() - 1L)() FUN(...) }, error = function(e) { annotated_condition <- handle_error(e) stop(annotated_condition) }, warning = handle_warning) }, error = identity) if (force.GC) gc(verbose = FALSE, full = FALSE) SEED <<- .rng_next_substream(SEED) output } }, type = "auto", version = "auto", genome = NULL, compressed = NULL, mtx.two.pass = FALSE, mtx.class = "CsparseMatrix", mtx.threads = 1)
18: do.call(lapply, args)
19: BiocParallel:::.workerLapply_impl(...)
20: (function (...) BiocParallel:::.workerLapply_impl(...))(X = "/tmp/RtmpqojGw5/Rinst1bf45043bb9f82/SpaceTrooper/extdata/Xenium_small/cell_feature_matrix.h5", FUN = function (run, type, version, genome, compressed, mtx.two.pass, mtx.class, mtx.threads) { cur.type <- .type_chooser(run, type) if (cur.type == "mtx") { .read_from_sparse(run, version = version, is.prefix = FALSE, compressed = compressed, mtx.two.pass = mtx.two.pass, mtx.class = mtx.class, mtx.threads = mtx.threads) } else if (cur.type == "prefix") { .read_from_sparse(run, version = version, is.prefix = TRUE, compressed = compressed, mtx.two.pass = mtx.two.pass, mtx.class = mtx.class, mtx.threads = mtx.threads) } else { .read_from_hdf5(run, genome = genome, version = version) } }, ARGS = list(type = "auto", version = "auto", genome = NULL, compressed = NULL, mtx.two.pass = FALSE, mtx.class = "CsparseMatrix", mtx.threads = 1), OPTIONS = list(log = FALSE, threshold = "INFO", stop.on.error = TRUE, as.error = TRUE, timeout = NA_integer_, force.GC = FALSE, globalOptions = NULL), BPRNGSEED = c(10407L, -1845281618L, 1398435159L, -1001522772L, 566930109L, 78860890L, 824280083L), GLOBALS = list(), PACKAGES = character(0))
21: do.call(msg$data$fun, msg$data$args)
22: doTryCatch(return(expr), name, parentenv, handler)
23: tryCatchOne(expr, names, parentenv, handlers[[1L]])
24: tryCatchList(expr, classes, parentenv, handlers)
25: tryCatch({ .autoload_s4_classes(msg$data$args$X) do.call(msg$data$fun, msg$data$args)}, error = function(e) { list(.error_worker_comm(e, "worker evaluation failed"))})
26: .bpworker_EXEC(msg, bplog(backend$BPPARAM))
27: .recv_any(manager$backend)
28: .recv_any(manager$backend)
29: .manager_recv(manager)
30: .manager_recv(manager)
31: .collect_result(manager, reducer, progress, BPPARAM)
32: .bploop_impl(ITER = ITER, FUN = FUN, ARGS = ARGS, BPPARAM = BPPARAM, BPOPTIONS = BPOPTIONS, BPREDO = BPREDO, reducer = reducer, progress.length = length(redo_index))
33: bploop.lapply(manager, BPPARAM = BPPARAM, BPOPTIONS = BPOPTIONS, ...)
34: bploop(manager, BPPARAM = BPPARAM, BPOPTIONS = BPOPTIONS, ...)
35: .bpinit(manager = manager, X = X, FUN = FUN, ARGS = ARGS, BPPARAM = BPPARAM, BPOPTIONS = BPOPTIONS, BPREDO = BPREDO)
36: bplapply(samples, FUN = .tenx_loader, type = type, version = version, genome = genome, compressed = compressed, mtx.two.pass = mtx.two.pass, mtx.class = match.arg(mtx.class), mtx.threads = mtx.threads, BPPARAM = BPPARAM)
37: bplapply(samples, FUN = .tenx_loader, type = type, version = version, genome = genome, compressed = compressed, mtx.two.pass = mtx.two.pass, mtx.class = match.arg(mtx.class), mtx.threads = mtx.threads, BPPARAM = BPPARAM)
38: DropletUtils::read10xCounts(countmat_file, col.names = TRUE)
39: SpatialExperimentIO::readXeniumSXE(dirName = dirName, countMatPattern = cfm, metaDataPattern = metadataFPattern, coordNames = coordNames, returnType = "SPE", addExperimentXenium = FALSE, altExps = NULL, addParquetPaths = FALSE)
40: readXeniumSPE(xeniumFolder, computeMissingMetrics = TRUE, keepPolygons = TRUE)
41: eval(expr, envir)
42: eval(expr, envir)
43: withVisible(eval(expr, envir))
44: 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)})
45: eval(call)
46: eval(call)
47: with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers)
48: doWithOneRestart(return(expr), restart)
49: withOneRestart(expr, restarts[[1L]])
50: withRestartList(expr, restarts[-nr])
51: doWithOneRestart(return(expr), restart)
52: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
53: withRestartList(expr, restarts)
54: withRestarts(with_handlers({ for (expr in tle$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)
55: evaluate::evaluate(...)
56: 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$render, options))
57: in_dir(input_dir(), expr)
58: in_input_dir(evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$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)))
59: eng_r(options)
60: block_exec(params)
61: call_block(x)
62: process_group(group)
63: 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) })
64: 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()))
65: 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)
66: process_file(text, output)
67: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
68: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...)
69: vweave_rmarkdown(...)
70: engine$weave(file, quiet = quiet, encoding = enc)
71: doTryCatch(return(expr), name, parentenv, handler)
72: tryCatchOne(expr, names, parentenv, handlers[[1L]])
73: tryCatchList(expr, classes, parentenv, handlers)
74: tryCatch({ engine$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)))})
75: tools::buildVignettes(dir = ".", tangle = TRUE)
An irrecoverable exception occurred. R is aborting now ...
Segmentation fault (core dumped)