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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 MAST
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* checking for file ‘MAST/DESCRIPTION’ ... OK
* preparing ‘MAST’:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘MAITAnalysis.Rmd’ using rmarkdown
Warning: code chunks must not depend on the uncached chunk "data"
Warning: code chunks must not depend on the uncached chunk "zlm"
Warning: code chunks must not depend on the uncached chunk "boots"
--- finished re-building ‘MAITAnalysis.Rmd’
--- re-building ‘MAST-Intro.Rmd’ using rmarkdown
--- finished re-building ‘MAST-Intro.Rmd’
--- re-building ‘MAST-interoperability.Rmd’ using rmarkdown
*** caught segfault ***
address 0xffffffffb9771a40, 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: FUN(X[[i]], ...)
7: FUN(X[[i]], ...)
8: lapply(x@seeds, extract_array, index)
9: lapply(x@seeds, extract_array, index)
10: extract_array(x@seed, index)
11: extract_array(x@seed, index)
12: .nextMethod(x = x, index = index)
13: callNextMethod()
14: extract_array(x, Nindex)
15: extract_array(x, Nindex)
16: read_block_as_dense(x, viewport)
17: read_block_as_dense(x, viewport)
18: .read_block(x, viewport, as.sparse = as.sparse)
19: read_block(x, viewport, as.sparse = as.sparse)
20: FUN(viewport, init, ...)
21: gridReduce(FUN_WRAPPER, grid, init, FUN, x, as.sparse, verbose, verbose_read_block, ..., BREAKIF = BREAKIF_WRAPPER, verbose = FALSE)
22: blockReduce(FUN, x, init, BREAKIF = BREAKIF, grid = grid, as.sparse = as.sparse)
23: .BLOCK_Summary(.Generic, x, ..., na.rm = na.rm)
24: all(new("DelayedMatrix", seed = new("DelayedNaryIsoOp", OP = .Primitive("=="), Rargs = list(), seeds = list(new("DelayedUnaryIsoOpStack", OPS = list(function (a) match.fun(.Generic)(a)), seed = new("HDF5ArraySeed", filepath = "/tmp/RtmpdL2RQ0/HDF5Array_dump/auto139c735a2f6cea.h5", name = "/HDF5ArrayAUTO00001", as_sparse = FALSE, type = NA_character_, dim = c(16302L, 96L), chunkdim = c(13031L, 76L), first_val = 0)), new("HDF5ArraySeed", filepath = "/tmp/RtmpdL2RQ0/HDF5Array_dump/auto139c735a2f6cea.h5", name = "/HDF5ArrayAUTO00001", as_sparse = FALSE, type = NA_character_, dim = c(16302L, 96L), chunkdim = c(13031L, 76L), first_val = 0)))), na.rm = TRUE)
25: all(new("DelayedMatrix", seed = new("DelayedNaryIsoOp", OP = .Primitive("=="), Rargs = list(), seeds = list(new("DelayedUnaryIsoOpStack", OPS = list(function (a) match.fun(.Generic)(a)), seed = new("HDF5ArraySeed", filepath = "/tmp/RtmpdL2RQ0/HDF5Array_dump/auto139c735a2f6cea.h5", name = "/HDF5ArrayAUTO00001", as_sparse = FALSE, type = NA_character_, dim = c(16302L, 96L), chunkdim = c(13031L, 76L), first_val = 0)), new("HDF5ArraySeed", filepath = "/tmp/RtmpdL2RQ0/HDF5Array_dump/auto139c735a2f6cea.h5", name = "/HDF5ArrayAUTO00001", as_sparse = FALSE, type = NA_character_, dim = c(16302L, 96L), chunkdim = c(13031L, 76L), first_val = 0)))), na.rm = TRUE)
26: sanity_check_sca(obj)
27: FromMatrix(exprsArray = list(et = hd5_dat), cData = maits$cdat, fData = maits$fdat)
28: eval(expr, envir)
29: eval(expr, envir)
30: withVisible(eval(expr, envir))
31: 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)})
32: eval(call)
33: eval(call)
34: with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers)
35: doWithOneRestart(return(expr), restart)
36: withOneRestart(expr, restarts[[1L]])
37: withRestartList(expr, restarts[-nr])
38: doWithOneRestart(return(expr), restart)
39: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
40: withRestartList(expr, restarts)
41: withRestarts(with_handlers({ for (expr in tle$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)
42: evaluate::evaluate(...)
43: 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$render, options))
44: in_dir(input_dir(), expr)
45: in_input_dir(evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$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)))
46: eng_r(options)
47: block_exec(params)
48: call_block(x)
49: process_group(group)
50: 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) })
51: 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()))
52: 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)
53: process_file(text, output)
54: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
55: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...)
56: vweave_rmarkdown(...)
57: engine$weave(file, quiet = quiet, encoding = enc)
58: doTryCatch(return(expr), name, parentenv, handler)
59: tryCatchOne(expr, names, parentenv, handlers[[1L]])
60: tryCatchList(expr, classes, parentenv, handlers)
61: tryCatch({ engine$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)))})
62: tools::buildVignettes(dir = ".", tangle = TRUE)
An irrecoverable exception occurred. R is aborting now ...
Segmentation fault (core dumped)