BioC 3.3: BUILD report for spade on morelia

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data spade
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* checking for file ‘spade/DESCRIPTION’ ... OK
* preparing ‘spade’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* running ‘cleanup’
* installing the package to build vignettes
* creating vignettes ...sh: line 1: 51114 Segmentation fault: 11  '/Library/Frameworks/R.framework/Resources/bin/Rscript' --vanilla --default-packages= -e "tools::buildVignettes(dir = '.', tangle = TRUE)" > '/tmp/RtmphposFg/xshellc2b04e412ec0' 2>&1
 ERROR
Loading required package: igraph

Attaching package: ‘igraph’

The following objects are masked from ‘package:stats’:

    decompose, spectrum

The following object is masked from ‘package:base’:

    union

Loading required package: Rclusterpp
Loading required package: Rcpp
Loading required package: RcppEigen
Warning: Package 'spade' is deprecated and will be removed from Bioconductor
  version 3.3
Loading required package: flowCore

Attaching package: ‘flowCore’

The following objects are masked from ‘package:igraph’:

    normalize, parent, tree

Loading required package: lattice
Downsampling file: /private/tmp/RtmphposFg/Rinstc2b07e2affc1/spade/extdata/SimulatedRawData.fcs
Warning in write.FCS(out_frame, outfilename) :
  'write.FCS' is not fully tested and should be considered as experimental.
Targeting 4925 events for /tmp/RtmpJQEEBv/SimulatedRawData.fcs.density.fcs
Warning in write.FCS(out_frame, outfilename) :
  'write.FCS' is not fully tested and should be considered as experimental.
Clustering files...

 *** caught segfault ***
address 0x0, cause 'memory not mapped'

Traceback:
 1: .Call("hclust_from_data", data = x, link = as.integer(method),     dist = as.integer(distance), p = as.numeric(p), DUP = FALSE,     NAOK = FALSE, PACKAGE = "Rclusterpp")
 2: Rclusterpp.hclust(tbl)
 3: SPADE.cluster(SPADE.transform.matrix(data, transforms), k)
 4: SPADE.FCSToTree(sampled_files, cells_file, graph_file, clust_file,     cols = cluster_cols, transforms = transforms, k = k, desired_samples = clustering_samples,     comp = comp)
 5: SPADE.driver(data_file_path, out_dir = output_dir, transforms = transforms,     cluster_cols = c("marker1", "marker2"))
 6: eval(expr, envir, enclos)
 7: eval(expr, .GlobalEnv)
 8: withVisible(eval(expr, .GlobalEnv))
 9: doTryCatch(return(expr), name, parentenv, handler)
10: tryCatchOne(expr, names, parentenv, handlers[[1L]])
11: tryCatchList(expr, classes, parentenv, handlers)
12: tryCatch(expr, error = function(e) {    call <- conditionCall(e)    if (!is.null(call)) {        if (identical(call[[1L]], quote(doTryCatch)))             call <- sys.call(-4L)        dcall <- deparse(call)[1L]        prefix <- paste("Error in", dcall, ": ")        LONG <- 75L        msg <- conditionMessage(e)        sm <- strsplit(msg, "\n")[[1L]]        w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")        if (is.na(w))             w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L],                 type = "b")        if (w > LONG)             prefix <- paste0(prefix, "\n  ")    }    else prefix <- "Error : "    msg <- paste0(prefix, conditionMessage(e), "\n")    .Internal(seterrmessage(msg[1L]))    if (!silent && identical(getOption("show.error.messages"),         TRUE)) {        cat(msg, file = stderr())        .Internal(printDeferredWarnings())    }    invisible(structure(msg, class = "try-error", condition = e))})
13: try(withVisible(eval(expr, .GlobalEnv)), silent = TRUE)
14: evalFunc(ce, options)
15: tryCatchList(expr, classes, parentenv, handlers)
16: tryCatch(evalFunc(ce, options), finally = {    cat("\n")    sink()})
17: driver$runcode(drobj, chunk, chunkopts)
18: utils::Sweave(...)
19: engine$weave(file, quiet = quiet, encoding = enc)
20: doTryCatch(return(expr), name, parentenv, handler)
21: tryCatchOne(expr, names, parentenv, handlers[[1L]])
22: tryCatchList(expr, classes, parentenv, handlers)
23: tryCatch({    engine$weave(file, quiet = quiet, encoding = enc)    setwd(startdir)    find_vignette_product(name, by = "weave", engine = engine)}, error = function(e) {    stop(gettextf("processing vignette '%s' failed with diagnostics:\n%s",         file, conditionMessage(e)), domain = NA, call. = FALSE)})
24: tools::buildVignettes(dir = ".", tangle = TRUE)
An irrecoverable exception occurred. R is aborting now ...
BioC 3.3: BUILD report for spade on morelia

Summary

Command output
