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###
### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data flowCHIC
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* checking for file ‘flowCHIC/DESCRIPTION’ ... OK
* preparing ‘flowCHIC’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ...sh: line 1: 18414 Segmentation fault: 11  '/Library/Frameworks/R.framework/Resources/bin/Rscript' --vanilla --default-packages= -e "tools::buildVignettes(dir = '.', tangle = TRUE)" > '/tmp/RtmpAaGdqS/xshellea63fc59b18' 2>&1
 ERROR
--- re-building ‘flowCHICmanual.Rnw’ using Sweave
Warning in metaMDS(mat.dist, autotransform = FALSE) :
  stress is (nearly) zero: you may have insufficient data
Warning in metaMDS(mat.dist, autotransform = FALSE) :
  stress is (nearly) zero: you may have insufficient data

 *** caught segfault ***
address 0x0, cause 'unknown'

Traceback:
 1: ptest(permat[indx, ], ...)
 2: FUN(X[[i]], ...)
 3: lapply(X = X, FUN = FUN, ...)
 4: sapply(1:permutations, function(indx, ...) ptest(permat[indx,     ], ...))
 5: vectorfit(X, P, permutations, strata, choices, w = w, ...)
 6: envfit.default(mds.out, abiotic, permutation = 999)
 7: envfit(mds.out, abiotic, permutation = 999)
 8: .local(x, y, ...)
 9: plot_nmds(Results_overlaps_incol, Results_xor_incol, abiotic = abiotic_incol[,     -1])
10: plot_nmds(Results_overlaps_incol, Results_xor_incol, abiotic = abiotic_incol[,     -1])
11: eval(expr, .GlobalEnv)
12: eval(expr, .GlobalEnv)
13: withVisible(eval(expr, .GlobalEnv))
14: doTryCatch(return(expr), name, parentenv, handler)
15: tryCatchOne(expr, names, parentenv, handlers[[1L]])
16: tryCatchList(expr, classes, parentenv, handlers)
17: 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, nlines = 1L)        prefix <- paste("Error in", dcall, ": ")        LONG <- 75L        sm <- strsplit(conditionMessage(e), "\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 && isTRUE(getOption("show.error.messages"))) {        cat(msg, file = outFile)        .Internal(printDeferredWarnings())    }    invisible(structure(msg, class = "try-error", condition = e))})
18: try(withVisible(eval(expr, .GlobalEnv)), silent = TRUE)
19: evalFunc(ce, options)
20: tryCatchList(expr, classes, parentenv, handlers)
21: tryCatch(evalFunc(ce, options), finally = {    cat("\n")    sink()})
22: driver$runcode(drobj, chunk, chunkopts)
23: utils::Sweave(...)
24: engine$weave(file, quiet = quiet, encoding = enc)
25: doTryCatch(return(expr), name, parentenv, handler)
26: tryCatchOne(expr, names, parentenv, handlers[[1L]])
27: tryCatchList(expr, classes, parentenv, handlers)
28: 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)))})
29: tools::buildVignettes(dir = ".", tangle = TRUE)
An irrecoverable exception occurred. R is aborting now ...