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### Running command:
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###   /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data COTAN
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* checking for file ‘COTAN/DESCRIPTION’ ... OK
* preparing ‘COTAN’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘Guided_tutorial_v2.Rmd’ using rmarkdown
Warning: program compiled against libxml 212 using older 211
trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/samples/GSM2861nnn/GSM2861514/suppl//GSM2861514_E175_Only_Cortical_Cells_DGE.txt.gz?tool=geoquery'
Content type 'application/x-gzip' length 1509523 bytes (1.4 MB)
==================================================
downloaded 1.4 MB


 *** caught segfault ***
address 0x7a00000072, cause 'memory not mapped'

Traceback:
 1: parDist(scale(pcaCells), method = "euclidean")
 2: cleanPlots(obj)
 3: multi_assign(substitute(x), value, parent.frame())
 4: doTryCatch(return(expr), name, parentenv, handler)
 5: tryCatchOne(expr, names, parentenv, handlers[[1L]])
 6: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
 7: doTryCatch(return(expr), name, parentenv, handler)
 8: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),     names[nh], parentenv, handlers[[nh]])
 9: tryCatchList(expr, classes, parentenv, handlers)
10: tryCatch(multi_assign(substitute(x), value, parent.frame()),     invalid_lhs = function(e) {        stop("invalid `%<-%` left-hand side, ", e$message, call. = FALSE)    }, invalid_rhs = function(e) {        stop("invalid `%<-%` right-hand side, ", e$message, call. = FALSE)    })
11: c(pcaCellsPlot, pcaCellsData, genesPlot, UDEPlot, nuPlot, zoomedNuPlot) %<-%     cleanPlots(obj)
12: eval(expr, envir)
13: eval(expr, envir)
14: withVisible(eval(expr, envir))
15: withCallingHandlers(code, 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)})
16: eval(call)
17: eval(call)
18: with_handlers({    for (expr in tle$exprs) {        ev <- withVisible(eval(expr, envir))        watcher$capture_plot_and_output()        watcher$print_value(ev$value, ev$visible, envir)    }    TRUE}, handlers)
19: doWithOneRestart(return(expr), restart)
20: withOneRestart(expr, restarts[[1L]])
21: withRestartList(expr, restarts[-nr])
22: doWithOneRestart(return(expr), restart)
23: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
24: withRestartList(expr, restarts)
25: withRestarts(with_handlers({    for (expr in tle$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)
26: evaluate::evaluate(...)
27: 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$render, options))
28: in_dir(input_dir(), expr)
29: in_input_dir(evaluate(code, envir = env, new_device = FALSE,     keep_warning = if (is.numeric(options$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)))
30: eng_r(options)
31: block_exec(params)
32: call_block(x)
33: process_group(group)
34: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),     error = function(e) if (xfun::pkg_available("rlang", "1.0.0")) rlang::entrace(e))
35: xfun:::handle_error(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),     error = function(e) if (xfun::pkg_available("rlang", "1.0.0")) rlang::entrace(e)),     function(loc) {        setwd(wd)        write_utf8(res, output %n% stdout())        paste0("\nQuitting from lines ", loc)    }, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
36: process_file(text, output)
37: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
38: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(),     output_dir = getwd(), ...)
39: vweave_rmarkdown(...)
40: engine$weave(file, quiet = quiet, encoding = enc)
41: doTryCatch(return(expr), name, parentenv, handler)
42: tryCatchOne(expr, names, parentenv, handlers[[1L]])
43: tryCatchList(expr, classes, parentenv, handlers)
44: tryCatch({    engine$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)))})
45: tools::buildVignettes(dir = ".", tangle = TRUE)
An irrecoverable exception occurred. R is aborting now ...