Error in re-building vignettes:
  ...
wavelengths found in column 1
wavelengths found in column 1
wavelengths found in column 1

 *** caught segfault ***
address 0x7ffa0000001a, cause 'memory not mapped'

Traceback:
 1: tryInline(call, cb, cntxt)
 2: cmpCall(e, cb, cntxt)
 3: cmp(subexp, cb, ncntxt, setloc = FALSE)
 4: h(e, cb, cntxt)
 5: tryInline(call, cb, cntxt)
 6: cmpCall(e, cb, cntxt)
 7: cmp(then.expr, cb, cntxt)
 8: h(e, cb, cntxt)
 9: tryInline(call, cb, cntxt)
10: cmpCall(e, cb, cntxt)
11: cmp(subexp, cb, cntxt, setloc = FALSE)
12: h(e, cb, cntxt)
13: tryInline(call, cb, cntxt)
14: cmpCall(e, cb, cntxt)
15: cmp(then.expr, cb, cntxt)
16: h(e, cb, cntxt)
17: tryInline(call, cb, cntxt)
18: cmpCall(e, cb, cntxt)
19: cmp(subexp, cb, ncntxt, setloc = FALSE)
20: h(e, cb, cntxt)
21: tryInline(call, cb, cntxt)
22: cmpCall(e, cb, cntxt)
23: cmp(e, cb, cntxt, setloc = FALSE)
24: genCode(body(f), ncntxt, loc = loc)
25: cmpfun(f)
26: doTryCatch(return(expr), name, parentenv, handler)
27: tryCatchOne(expr, names, parentenv, handlers[[1L]])
28: tryCatchList(expr, classes, parentenv, handlers)
29: tryCatch(cmpfun(f), error = function(e) {    notifyCompilerError(paste(e$message, "at", deparse(e$call)))    f})
30: compiler:::tryCmpfun(function (tcsres1, tcsres2, plot = FALSE,     interactive = FALSE, col = c("blue", "red", "darkgrey"),     new = TRUE, montecarlo = FALSE, nsamp = 1000, psize = 0.001,     lwd = 1, view = 70, scale.y = 1) {    dat1 <- tcsres1[, c("x", "y", "z")]    dat2 <- tcsres2[, c("x", "y", "z")]    vol1 <- convhulln(dat1, "FA")$vol    vol2 <- convhulln(dat2, "FA")$vol    if (!montecarlo) {        rat1 <- d2q(cbind(0, cbind(1, as.matrix(dat1))))        rat2 <- d2q(cbind(0, cbind(1, as.matrix(dat2))))        vert1 <- redundant(rat1, representation = "V")$output        vert2 <- redundant(rat2, representation = "V")$output        Hvert1 <- scdd(vert1, representation = "V")$output        Hvert2 <- scdd(vert2, representation = "V")$output        Hinter <- rbind(Hvert1, Hvert2)        Vinter <- scdd(Hinter, representation = "H")$output        Voverlap <- data.frame(q2d(Vinter[, -c(1, 2)]))        names(Voverlap) = c("x", "y", "z")        if (dim(Voverlap)[1] > 3) {            overlapVol <- convhulln(Voverlap, "FA")$vol        }        else {            overlapVol <- 0        }        vsmallest <- overlapVol/min(c(vol1, vol2))        vboth <- overlapVol/(sum(c(vol1, vol2)) - overlapVol)        res <- data.frame(vol1, vol2, overlapvol = overlapVol,             vsmallest, vboth)    }    if (montecarlo) {        pmin <- apply(rbind(dat1, dat2), 2, min)        pmax <- apply(rbind(dat1, dat2), 2, max)        samples <- apply(rbind(pmin, pmax), 2, function(x) runif(nsamp,             x[1], x[2]))        sindex <- 1:dim(samples)[1]        newvol1 <- sapply(sindex, function(x) convhulln(rbind(dat1,             samples[x, ]), "FA")$vol)        newvol2 <- sapply(sindex, function(x) convhulln(rbind(dat2,             samples[x, ]), "FA")$vol)        invol1 <- sapply(newvol1, function(x) isTRUE(x <= vol1))        invol2 <- sapply(newvol2, function(x) isTRUE(x <= vol2))        s_in1 <- length(which(invol1))        s_in2 <- length(which(invol2))        s_inboth <- length(which(invol1 & invol2))        s_ineither <- length(which(invol1 | invol2))        psmallest <- s_inboth/c(s_in1, s_in2)[which.min(c(vol1,             vol2))]        pboth <- s_inboth/s_ineither        res <- data.frame(vol1, vol2, s_in1, s_in2, s_inboth,             s_ineither, psmallest, pboth)    }    if (plot) {        if (length(col) < 3)             col <- c(rep(col, 2)[1:2], "darkgrey")        if (interactive) {            if (!requireNamespace("rgl", quietly = TRUE))                 stop(dQuote("rgl"), " package needed for interactive plots. Please install it, or use interactive=FALSE.",                   call. = FALSE)            if (!isNamespaceLoaded("rgl"))                 requireNamespace("rgl")            if (new)                 rgl::open3d(FOV = 1, mouseMode = c("zAxis", "xAxis",                   "zoom"))            tcsvol(tcsres1, col = col[1], fill = F)            tcsvol(tcsres2, col = col[2], fill = F)            if (!montecarlo) {                if (dim(Voverlap)[1] > 3) {                  attr(Voverlap, "clrsp") <- "tcs"                  tcsvol(Voverlap, col = col[3])                }            }            if (montecarlo == TRUE) {                rgl::spheres3d(samples[which(invol1 & !invol2),                   ], type = "s", lit = F, radius = psize, col = col[1])                rgl::spheres3d(samples[which(invol2 & !invol1),                   ], type = "s", lit = F, radius = psize, col = col[2])                if (s_inboth > 0) {                  rgl::spheres3d(samples[which(invol1 & invol2),                     ], type = "s", lit = F, radius = psize, col = col[3])                }            }        }        if (!interactive) {            plotrange <- apply(rbind(tcsres1, tcsres2), 2, range)            if (dim(Voverlap)[1] > 3) {                attr(Voverlap, "clrsp") <- "tcs"                vol(Voverlap, col = col[3], new = new, xlim = plotrange[,                   "x"], ylim = plotrange[, "y"], zlim = plotrange[,                   "z"], view = view)                vol(tcsres1, col = col[1], fill = FALSE, lwd = lwd,                   new = FALSE)                vol(tcsres2, col = col[2], fill = FALSE, lwd = lwd,                   new = FALSE)            }            else {                vol(tcsres1, col = col[1], fill = FALSE, lwd = lwd,                   new = new, xlim = plotrange[, "x"], ylim = plotrange[,                     "y"], zlim = plotrange[, "z"], view = view)                vol(tcsres2, col = col[2], fill = FALSE, lwd = lwd,                   new = FALSE)            }        }    }    res})
31: voloverlap(tcs.sicalis.T, tcs.sicalis.C)
32: eval(expr, envir, enclos)
33: eval(expr, envir, enclos)
34: withVisible(eval(expr, envir, enclos))
35: withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler,     error = eHandler, message = mHandler)
36: handle(ev <- withCallingHandlers(withVisible(eval(expr, envir,     enclos)), warning = wHandler, error = eHandler, message = mHandler))
37: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval(expr,     envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)))
38: evaluate_call(expr, parsed$src[[i]], envir = envir, enclos = enclos,     debug = debug, last = i == length(out), use_try = stop_on_error !=         2L, keep_warning = keep_warning, keep_message = keep_message,     output_handler = output_handler, include_timing = include_timing)
39: evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$warning),     keep_message = !isFALSE(options$message), stop_on_error = if (options$error &&         options$include) 0L else 2L, output_handler = knit_handlers(options$render,         options))
40: in_dir(input_dir(), evaluate(code, envir = env, new_device = FALSE,     keep_warning = !isFALSE(options$warning), keep_message = !isFALSE(options$message),     stop_on_error = if (options$error && options$include) 0L else 2L,     output_handler = knit_handlers(options$render, options)))
41: block_exec(params)
42: call_block(x)
43: process_group.block(group)
44: process_group(group)
45: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),     error = function(e) {        setwd(wd)        cat(res, sep = "\n", file = output %n% "")        message("Quitting from lines ", paste(current_lines(i),             collapse = "-"), " (", knit_concord$get("infile"),             ") ")    })
46: process_file(text, output)
47: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet,     encoding = encoding)
48: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv())
49: vweave_rmarkdown(...)
50: engine$weave(file, quiet = quiet, encoding = enc)
51: doTryCatch(return(expr), name, parentenv, handler)
52: tryCatchOne(expr, names, parentenv, handlers[[1L]])
53: tryCatchList(expr, classes, parentenv, handlers)
54: tryCatch({    engine$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)})
55: buildVignettes(dir = "/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/pavo.Rcheck/vign_test/pavo")
An irrecoverable exception occurred. R is aborting now ...
Segmentation fault