Error(s) in re-building vignettes:
--- re-building ‘UserManualSOHPIE.Rmd’ using rmarkdown

 *** caught segfault ***
address 0x110, cause 'invalid permissions'

 *** caught segfault ***
address 0x110, cause 'invalid permissions'

Traceback:
 1: solve.default(Lmat[cp, cp], rowSums(T02[cp, cp]))
 2: solve(Lmat[cp, cp], rowSums(T02[cp, cp]))
 3: SparCC.frac(x = y, kmax = kmax, alpha = alpha, Vmin = Vmin)
 4: sparcc(OTUtab[-j, ])
 5: FUN(X[[i]], ...)
 6: lapply(X = S, FUN = FUN, ...)
 7: doTryCatch(return(expr), name, parentenv, handler)
 8: tryCatchOne(expr, names, parentenv, handlers[[1L]])
 9: tryCatchList(expr, classes, parentenv, handlers)
10: 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))})
11: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
12: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
13: FUN(X[[i]], ...)
14: lapply(seq_len(cores), inner.do)
15: mclapply(group, function(j) sparcc(OTUtab[-j, ])$cor.w)
16: asso_mat(OTUdat = OTUtab, group = newindex_A1)
17: eval(expr, envir)
18: eval(expr, envir)
19: withVisible(eval(expr, envir))
20: withCallingHandlers(code, error = function (e) rlang::entrace(e), message = function (cnd) {    watcher$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)
Traceback:
 1: solve.default(Lmat[cp, cp], rowSums(T02[cp, cp]))
 2: solve(Lmat[cp, cp], rowSums(T02[cp, cp]))    watcher$push(cnd)    switch(on_error, continue = invokeRestart("eval_continue"),         stop = invokeRestart("eval_stop"), error = NULL)})
21: 
 3: SparCC.frac(x = y, kmax = kmax, alpha = alpha, Vmin = Vmin)eval(call)
22: eval(call)
 4: sparcc(OTUtab[-j, ])
 5: FUN(X[[i]], ...)
 6: lapply(X = S, FUN = FUN, ...)
 7: doTryCatch(return(expr), name, parentenv, handler)
 8: 
23: tryCatchOne(expr, names, parentenv, handlers[[1L]])
 9: tryCatchList(expr, classes, parentenv, handlers)
10: tryCatch(expr, error = function(e) {    call <- conditionCall(e)    if (!is.null(call)) {with_handlers({    for (expr in tle$exprs) {        ev <- withVisible(eval(expr, envir))        watcher$capture_plot_and_output()        watcher$print_value(ev$value, ev$visible, envir)    }    TRUE}, handlers)
24: doWithOneRestart(return(expr), restart)
25: withOneRestart(expr, restarts[[1L]])
26: withRestartList(expr, restarts[-nr])
27: doWithOneRestart(return(expr), restart)
28: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
29: withRestartList(expr, restarts)
30: withRestarts(with_handlers({        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  ")    for (expr in tle$exprs) {        ev <- withVisible(eval(expr, envir))        watcher$capture_plot_and_output()        watcher$print_value(ev$value, ev$visible, envir)    }    TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
31: evaluate::evaluate(...)
32: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$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$include)     }    else prefix <- "Error : "    msg <- paste0(prefix, conditionMessage(e), "\n")    .Internal(seterrmessage(msg[1L]))    if (!silent && isTRUE(getOption("show.error.messages"))) {        cat(msg, file = outFile)        .Internal(printDeferredWarnings())    }    invisible(structure(msg, class = "try-error", condition = e))})            0L        else 2L    }, output_handler = knit_handlers(options$render, options))
33: in_dir(input_dir(), expr)
34: 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
11: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
12:         else 2L    }, output_handler = knit_handlers(options$render, options)))
35: eng_r(options)
36: block_exec(params)
37: call_block(x)
38: process_group(group)
39: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),     error = function(e) {        if (progress && is.function(pb$interrupt))             pb$interrupt()        if (is_R_CMD_build() || is_R_CMD_check())             error <<- format(e)    })
40: with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),     error = function(e) {        if (progress && is.function(pb$interrupt))             pb$interrupt()        if (is_R_CMD_build() || is_R_CMD_check())             error <<- format(e)    }), list(rlang_trace_top_env = knit_global()))sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
13: FUN(X[[i]], ...)
14: lapply(seq_len(cores), inner.do)
15: mclapply(group, function(j) sparcc(OTUtab[-j, ])$cor.w)
41: 
16: asso_mat(OTUdat = OTUtab, group = newindex_A1)
17: eval(expr, envir)
18: eval(expr, envir)
19: withVisible(eval(expr, envir))
20: withCallingHandlers(code, error = function (e) xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),     error = function(e) {        if (progress && is.function(pb$interrupt)) rlang::entrace(e), message = function (cnd) {    watcher$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$push(cnd)    switch(on_error, continue = invokeRestart("eval_continue"),         stop = invokeRestart("eval_stop"), error = NULL)})
21: eval(call)
22:             pb$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)) eval(call)
23: 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)
24: doWithOneRestart(return(expr), restart)
25: withOneRestart(expr, restarts[[1L]])
26: withRestartList(expr, restarts[-nr])
27:         paste0("\n", rule(), error, "\n", rule()))}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
42: process_file(text, output)
43: doWithOneRestart(return(expr), restart)
28: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)

29: withRestartList(expr, restarts)
30: withRestarts(with_handlers({    for (expr in tle$exprs) {        ev <- withVisible(eval(expr, envir))        watcher$capture_plot_and_output()        watcher$print_value(ev$value, ev$visible, envir)    }    TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
31: evaluate::evaluate(...)
32: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning,     keep_message = if (is.numeric(options$message)) TRUE else options$message, 44: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(),     output_dir = getwd(), ...)
45: vweave_rmarkdown(...)
46: engine$weave(file, quiet = quiet, encoding = enc)
47: doTryCatch(return(expr), name, parentenv, handler)    stop_on_error = if (is.numeric(options$error)) options$error else {        if (options$error && options$include)             0L        else 2L    }, output_handler = knit_handlers(options$render, options))
33: in_dir(input_dir(), expr)
34: in_input_dir(evaluate(code, envir = env, new_device = FALSE,     keep_warning = if (is.numeric(options$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)))
35: eng_r(options)
36: block_exec(params)
37: call_block(x)
38: process_group(group)
39: 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)    })

48: tryCatchOne(expr, names, parentenv, handlers[[1L]])
49: tryCatchList(expr, classes, parentenv, handlers)
50: tryCatch({    engine$weave(file, quiet = quiet, encoding = enc)    setwd(startdir)    output <- find_vignette_product(name, by = "weave", engine = engine)    if (!have.makefile && vignette_is_tex(output)) {        texi2pdf(file = output, clean = FALSE, quiet = quiet)        output <- find_vignette_product(name, by = "texi2pdf",             engine = engine)    }    outputs <- c(outputs, output)}, error = function(e) {    thisOK <<- FALSE    fails <<- c(fails, file)    message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s",         file, conditionMessage(e)))})
51: tools::buildVignettes(dir = "/Volumes/Builds/packages/sonoma-arm64/results/4.6/SOHPIE.Rcheck/vign_test/SOHPIE",     skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/Rtmps0yuX7/filee6653e9c39f3.rds")
An irrecoverable exception occurred. R is aborting now ...
40: with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),     error = function(e) {        if (progress && is.function(pb$interrupt))             pb$interrupt()        if (is_R_CMD_build() || is_R_CMD_check())             error <<- format(e)    }), list(rlang_trace_top_env = knit_global()))
41: xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),     error = function(e) {        if (progress && is.function(pb$interrupt))             pb$interrupt()        if (is_R_CMD_build() || is_R_CMD_check())             error <<- format(e)    }), list(rlang_trace_top_env = knit_global())), function(loc) {    setwd(wd)    write_utf8(res, output %n% stdout())    paste0("\nQuitting from ", loc, if (!is.null(error))         paste0("\n", rule(), error, "\n", rule()))}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
42: process_file(text, output)
43: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
44: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(),     output_dir = getwd(), ...)
45: vweave_rmarkdown(...)
46: engine$weave(file, quiet = quiet, encoding = enc)
47: doTryCatch(return(expr), name, parentenv, handler)
48: tryCatchOne(expr, names, parentenv, handlers[[1L]])
49: tryCatchList(expr, classes, parentenv, handlers)
50: 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)))})
51: tools::buildVignettes(dir = "/Volumes/Builds/packages/sonoma-arm64/results/4.6/SOHPIE.Rcheck/vign_test/SOHPIE",     skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/Rtmps0yuX7/filee6653e9c39f3.rds")
An irrecoverable exception occurred. R is aborting now ...

 *** caught segfault ***
address 0x110, cause 'invalid permissions'

 *** caught segfault ***
address 0x110, cause 'invalid permissions'

Traceback:
 1: solve.default(Lmat[cp, cp], rowSums(T02[cp, cp]))
 2: solve(Lmat[cp, cp], rowSums(T02[cp, cp]))
 3: SparCC.frac(x = y, kmax = kmax, alpha = alpha, Vmin = Vmin)
 4: sparcc(OTUtab[-j, ])
 5: FUN(X[[i]], ...)
 6: lapply(X = S, FUN = FUN, ...)
 7: doTryCatch(return(expr), name, parentenv, handler)
 8: tryCatchOne(expr, names, parentenv, handlers[[1L]])
 9: tryCatchList(expr, classes, parentenv, handlers)
10: 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))})
11: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
12: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
13: FUN(X[[i]], ...)
14: lapply(seq_len(cores), inner.do)
15: mclapply(group, function(j) sparcc(OTUtab[-j, ])$cor.w)
16: asso_mat(OTUdat = OTUtab, group = newindex_A6)
17: eval(expr, envir)
18: eval(expr, envir)
19: withVisible(eval(expr, envir))
20: withCallingHandlers(code, error = function (e) rlang::entrace(e), message = function (cnd) {    watcher$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$push(cnd)    switch(on_error, continue = invokeRestart("eval_continue"),         stop = invokeRestart("eval_stop"), error = NULL)})
21: eval(call)
22: eval(call)
23: with_handlers({    for (expr in tle$exprs) {        ev <- withVisible(eval(expr, envir))        watcher$capture_plot_and_output()        watcher$print_value(ev$value, ev$visible, envir)    }    TRUE}, handlers)
24: doWithOneRestart(return(expr), restart)
25: withOneRestart(expr, restarts[[1L]])
26: withRestartList(expr, restarts[-nr])
27: doWithOneRestart(return(expr), restart)
28: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
29: withRestartList(expr, restarts)
30: withRestarts(with_handlers({    for (expr in tle$exprs) {        ev <- withVisible(eval(expr, envir))        watcher$capture_plot_and_output()        watcher$print_value(ev$value, ev$visible, envir)    }    TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
31: evaluate::evaluate(...)
32: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$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))
33: in_dir(input_dir(), expr)
34: 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$render, options)))
35: eng_r(options)
36: block_exec(params)
37: call_block(x)
38: process_group(group)
39: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),     error = function(e) {        if (progress && is.function(pb$interrupt))             pb$interrupt()        if (is_R_CMD_build() || is_R_CMD_check())             error <<- format(e)    })
40: with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),     error = function(e) {        if (progress && is.function(pb$interrupt))             pb$interrupt()
Traceback:
 1: solve.default(Lmat[cp, cp], rowSums(T02[cp, cp]))
 2: solve(Lmat[cp, cp], rowSums(T02[cp, cp]))
 3: SparCC.frac(x = y, kmax = kmax, alpha = alpha, Vmin = Vmin)
 4: sparcc(OTUtab[-j, ])
 5: FUN(X[[i]], ...)
 6: lapply(X = S, FUN = FUN, ...)
 7: doTryCatch(return(expr), name, parentenv, handler)        if (is_R_CMD_build() || is_R_CMD_check())             error <<- format(e)    }), list(rlang_trace_top_env = knit_global()))
41: xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),     error = function(e) {
 8: tryCatchOne(expr, names, parentenv, handlers[[1L]])
 9: tryCatchList(expr, classes, parentenv, handlers)
10: tryCatch(expr, error = function(e) {    call <- conditionCall(e)    if (!is.null(call)) {        if (identical(call[[1L]], quote(doTryCatch)))             call <- sys.call(-4L)        dcall <- deparse(call, nlines = 1L)        prefix <- paste("Error in", dcall, ": ")        LONG <- 75L        sm <- strsplit(conditionMessage(e), "\n")[[1L]]        w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")        if (is.na(w))         if (progress && is.function(pb$interrupt))             pb$interrupt()        if (is_R_CMD_build() || is_R_CMD_check())             error <<- format(e)    }), list(rlang_trace_top_env = knit_global())), function(loc) {    setwd(wd)    write_utf8(res, output %n% stdout())    paste0("\nQuitting from ", loc, if (!is.null(error))         paste0("\n", rule(), error, "\n", rule()))}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
42: process_file(text, output)
43: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
44: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(),     output_dir = getwd(), ...)
45: vweave_rmarkdown(...)            w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L],                 type = "b")        if (w > LONG)             prefix <- paste0(prefix, "\n  ")    }    else prefix <- "Error : "    msg <- paste0(prefix, conditionMessage(e), "\n")    .Internal(seterrmessage(msg[1L]))    if (!silent && isTRUE(getOption("show.error.messages"))) {        cat(msg, file = outFile)        .Internal(printDeferredWarnings())    }    invisible(structure(msg, class = "try-error", condition = e))})
11: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
12: 
46: engine$weave(file, quiet = quiet, encoding = enc)
47: doTryCatch(return(expr), name, parentenv, handler)
48: tryCatchOne(expr, names, parentenv, handlers[[1L]])
sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
13: FUN(X[[i]], ...)
14: lapply(seq_len(cores), inner.do)
15: mclapply(group, function(j) sparcc(OTUtab[-j, ])$cor.w)
16: 49: tryCatchList(expr, classes, parentenv, handlers)
50: tryCatch({    engine$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)asso_mat(OTUdat = OTUtab, group = newindex_A6)
17: eval(expr, envir)
18: eval(expr, envir)
19: withVisible(eval(expr, envir))
        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)))})
51: tools::buildVignettes(dir = "/Volumes/Builds/packages/sonoma-arm64/results/4.6/SOHPIE.Rcheck/vign_test/SOHPIE", 20: 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")    skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/Rtmps0yuX7/filee6653e9c39f3.rds")
An irrecoverable exception occurred. R is aborting now ...
    }}, 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)})
21: eval(call)
22: eval(call)
23: with_handlers({    for (expr in tle$exprs) {        ev <- withVisible(eval(expr, envir))        watcher$capture_plot_and_output()        watcher$print_value(ev$value, ev$visible, envir)    }    TRUE}, handlers)
24: doWithOneRestart(return(expr), restart)
25: withOneRestart(expr, restarts[[1L]])
26: withRestartList(expr, restarts[-nr])
27: doWithOneRestart(return(expr), restart)
28: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
29: withRestartList(expr, restarts)
30: withRestarts(with_handlers({    for (expr in tle$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)
31: evaluate::evaluate(...)
32: 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$render, options))
33: in_dir(input_dir(), expr)
34: in_input_dir(evaluate(code, envir = env, new_device = FALSE,     keep_warning = if (is.numeric(options$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)))
35: eng_r(options)
36: block_exec(params)
37: call_block(x)
38: process_group(group)
39: 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)    })
40: 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()))
41: 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)
42: process_file(text, output)
43: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
44: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(),     output_dir = getwd(), ...)
45: vweave_rmarkdown(...)
46: engine$weave(file, quiet = quiet, encoding = enc)
47: doTryCatch(return(expr), name, parentenv, handler)
48: tryCatchOne(expr, names, parentenv, handlers[[1L]])
49: tryCatchList(expr, classes, parentenv, handlers)
50: tryCatch({    engine$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)))})
51: tools::buildVignettes(dir = "/Volumes/Builds/packages/sonoma-arm64/results/4.6/SOHPIE.Rcheck/vign_test/SOHPIE",     skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/Rtmps0yuX7/filee6653e9c39f3.rds")
An irrecoverable exception occurred. R is aborting now ...

 *** caught segfault ***
address 0x110, cause 'invalid permissions'

 *** caught segfault ***
address 0x110, cause 'invalid permissions'

Traceback:

Traceback:
 1: solve.default(Lmat[cp, cp], rowSums(T02[cp, cp]))
 2: solve(Lmat[cp, cp], rowSums(T02[cp, cp]))
 3: SparCC.frac(x = y, kmax = kmax, alpha = alpha, Vmin = Vmin) 1: solve.default(Lmat[cp, cp], rowSums(T02[cp, cp]))
 2: solve(Lmat[cp, cp], rowSums(T02[cp, cp]))

 4: sparcc(OTUtab[-j, ])
 5: FUN(X[[i]], ...)
 6: lapply(X = S, FUN = FUN, ...)
 7: doTryCatch(return(expr), name, parentenv, handler)
 8: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 3: SparCC.frac(x = y, kmax = kmax, alpha = alpha, Vmin = Vmin)
 9: tryCatchList(expr, classes, parentenv, handlers)
10: 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))})
11: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)

 4: sparcc(OTUtab[-j, ])
 5: FUN(X[[i]], ...)12: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
13: FUN(X[[i]], ...)
14: 
 6: lapply(X = S, FUN = FUN, ...)
 7: lapply(seq_len(cores), inner.do)
15: mclapply(group, function(j) sparcc(OTUtab[-j, ])$cor.w)
doTryCatch(return(expr), name, parentenv, handler)
 8: tryCatchOne(expr, names, parentenv, handlers[[1L]])
 9: tryCatchList(expr, classes, parentenv, handlers)
16: asso_mat(OTUdat = OTUtab, group = newindex_B1)
17: eval(expr, envir)
10: tryCatch(expr, error = function(e) {    call <- conditionCall(e)18: eval(expr, envir)
    if (!is.null(call)) {        if (identical(call[[1L]], quote(doTryCatch)))             call <- sys.call(-4L)        dcall <- deparse(call, nlines = 1L)        prefix <- paste("Error in", dcall, ": ")        LONG <- 75L19: withVisible(eval(expr, envir))
        sm <- strsplit(conditionMessage(e), "\n")[[1L]]        w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")        if (is.na(w))             w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L],                 type = "b")        if (w > LONG)             prefix <- paste0(prefix, "\n  ")    }    else prefix <- "Error : "    msg <- paste0(prefix, conditionMessage(e), "\n")    .Internal(seterrmessage(msg[1L]))    if (!silent && isTRUE(getOption("show.error.messages"))) {20: withCallingHandlers(code, error = function (e) rlang::entrace(e), message = function (cnd)         cat(msg, file = outFile)        .Internal(printDeferredWarnings())    }{    watcher$capture_plot_and_output()    if (on_message$capture) {        watcher$push(cnd)    }    if (on_message$silence) {    invisible(structure(msg, class = "try-error", condition = e))})
11: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
12: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
        invokeRestart("muffleMessage")    }}, warning = function (cnd) 13: FUN(X[[i]], ...)
{    if (getOption("warn") >= 2 || getOption("warn") < 0) {        return()14: lapply(seq_len(cores), inner.do)
    }    watcher$capture_plot_and_output()    if (on_warning$capture) {15: mclapply(group, function(j) sparcc(OTUtab[-j, ])$cor.w)
        cnd <- sanitize_call(cnd)        watcher$push(cnd)    }16: asso_mat(OTUdat = OTUtab, group = newindex_B1)
    if (on_warning$silence) {        invokeRestart("muffleWarning")    }17: eval(expr, envir)
}, error = function (cnd) {    watcher$capture_plot_and_output()18: eval(expr, envir)
    cnd <- sanitize_call(cnd)    watcher$push(cnd)    switch(on_error, continue = invokeRestart("eval_continue"),         stop = invokeRestart("eval_stop"), error = NULL)})
19: withVisible(eval(expr, envir))
21: eval(call)
20: withCallingHandlers(code, error = function (e) rlang::entrace(e), message = function (cnd) 22: eval(call)
{    watcher$capture_plot_and_output()    if (on_message$capture) {23: with_handlers({    for (expr in tle$exprs) {        watcher$push(cnd)    }    if (on_message$silence) {        ev <- withVisible(eval(expr, envir))        watcher$capture_plot_and_output()        watcher$print_value(ev$value, ev$visible, envir)        invokeRestart("muffleMessage")    }}, warning = function (cnd)     }    TRUE}, handlers){    if (getOption("warn") >= 2 || getOption("warn") < 0) {        return()
24: doWithOneRestart(return(expr), restart)
25: withOneRestart(expr, restarts[[1L]])
26: withRestartList(expr, restarts[-nr])
27: doWithOneRestart(return(expr), restart)
28: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
29: withRestartList(expr, restarts)
30: withRestarts(with_handlers({    }    watcher$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$push(cnd)    switch(on_error, continue = invokeRestart("eval_continue"),         stop = invokeRestart("eval_stop"), error = NULL)})
21: eval(call)
22: eval(call)
    for (expr in tle$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)
31: 23: with_handlers({    for (expr in tle$exprs) {evaluate::evaluate(...)
32:         ev <- withVisible(eval(expr, envir))        watcher$capture_plot_and_output()        watcher$print_value(ev$value, ev$visible, envir)evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$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$error else {    }    TRUE}, handlers)        if (options$error && options$include)             0L        else 2L
24: doWithOneRestart(return(expr), restart)
25: withOneRestart(expr, restarts[[1L]])    }, output_handler = knit_handlers(options$render, options))
33: 
26: withRestartList(expr, restarts[-nr])in_dir(input_dir(), expr)
34: 
27: doWithOneRestart(return(expr), restart)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
28: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])        else 2L    }, output_handler = knit_handlers(options$render, options)))

29: withRestartList(expr, restarts)
30: withRestarts(with_handlers({35: eng_r(options)
    for (expr in tle$exprs) {        ev <- withVisible(eval(expr, envir))        watcher$capture_plot_and_output()36: block_exec(params)
        watcher$print_value(ev$value, ev$visible, envir)    }    TRUE37: call_block(x)
}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
31: 38: process_group(group)
evaluate::evaluate(...)
32: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$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$include)             0L        else 2L39: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),     error = function(e) {    }, output_handler = knit_handlers(options$render, options))
33:         if (progress && is.function(pb$interrupt))             pb$interrupt()        if (is_R_CMD_build() || is_R_CMD_check())             error <<- format(e)    })
in_dir(input_dir(), expr)
34: 40: with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),     error = function(e) {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,         if (progress && is.function(pb$interrupt))             pb$interrupt()        if (is_R_CMD_build() || is_R_CMD_check())     stop_on_error = if (is.numeric(options$error)) options$error else {        if (options$error && options$include)             0L        else 2L    }, output_handler = knit_handlers(options$render, options)))
35: eng_r(options)
36: block_exec(params)
37:             error <<- format(e)    }), list(rlang_trace_top_env = knit_global()))
41: xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),     error = function(e) {        if (progress && is.function(pb$interrupt))             pb$interrupt()        if (is_R_CMD_build() || is_R_CMD_check()) call_block(x)
38:             error <<- format(e)    }), list(rlang_trace_top_env = knit_global())), function(loc) {    setwd(wd)    write_utf8(res, output %n% stdout())    paste0("\nQuitting from ", loc, if (!is.null(error))         paste0("\n", rule(), error, "\n", rule()))process_group(group)
39: }, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
42: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),     error = function(e) {        if (progress && is.function(pb$interrupt)) process_file(text, output)
43:             pb$interrupt()        if (is_R_CMD_build() || is_R_CMD_check())             error <<- format(e)knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
44:     })
40: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(),     output_dir = getwd(), ...)
with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),     error = function(e) {        if (progress && is.function(pb$interrupt)) 45: vweave_rmarkdown(...)
            pb$interrupt()        if (is_R_CMD_build() || is_R_CMD_check())             error <<- format(e)    }), list(rlang_trace_top_env = knit_global()))
41: 46: engine$weave(file, quiet = quiet, encoding = enc)
xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),     error = function(e) {        if (progress && is.function(pb$interrupt)) 47: doTryCatch(return(expr), name, parentenv, handler)
            pb$interrupt()        if (is_R_CMD_build() || is_R_CMD_check())             error <<- format(e)48: tryCatchOne(expr, names, parentenv, handlers[[1L]])
    }), list(rlang_trace_top_env = knit_global())), function(loc) {    setwd(wd)    write_utf8(res, output %n% stdout())49: tryCatchList(expr, classes, parentenv, handlers)
    paste0("\nQuitting from ", loc, if (!is.null(error))         paste0("\n", rule(), error, "\n", rule()))}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)50: tryCatch({    engine$weave(file, quiet = quiet, encoding = enc)
42: process_file(text, output)    setwd(startdir)    output <- find_vignette_product(name, by = "weave", engine = engine)    if (!have.makefile && vignette_is_tex(output)) {
43: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)        texi2pdf(file = output, clean = FALSE, quiet = quiet)        output <- find_vignette_product(name, by = "texi2pdf",             engine = engine)    }    outputs <- c(outputs, output)}, error = function(e) {    thisOK <<- FALSE    fails <<- c(fails, file)    message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", 
44: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(),         file, conditionMessage(e)))})
    output_dir = getwd(), ...)
45: 51: tools::buildVignettes(dir = "/Volumes/Builds/packages/sonoma-arm64/results/4.6/SOHPIE.Rcheck/vign_test/SOHPIE",     skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/Rtmps0yuX7/filee6653e9c39f3.rds")vweave_rmarkdown(...)
46: engine$weave(file, quiet = quiet, encoding = enc)
47: 
An irrecoverable exception occurred. R is aborting now ...
doTryCatch(return(expr), name, parentenv, handler)
48: tryCatchOne(expr, names, parentenv, handlers[[1L]])
49: tryCatchList(expr, classes, parentenv, handlers)
50: 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)))})
51: tools::buildVignettes(dir = "/Volumes/Builds/packages/sonoma-arm64/results/4.6/SOHPIE.Rcheck/vign_test/SOHPIE",     skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/Rtmps0yuX7/filee6653e9c39f3.rds")
An irrecoverable exception occurred. R is aborting now ...

 *** caught segfault ***
address 0x110, cause 'invalid permissions'

 *** caught segfault ***
address 0x110, cause 'invalid permissions'

Traceback:
 1: solve.default(Lmat[cp, cp], rowSums(T02[cp, cp]))
 2: solve(Lmat[cp, cp], rowSums(T02[cp, cp]))
 3: SparCC.frac(x = y, kmax = kmax, alpha = alpha, Vmin = Vmin)
 4: 
Traceback:
 1: solve.default(Lmat[cp, cp], rowSums(T02[cp, cp]))
 2: solve(Lmat[cp, cp], rowSums(T02[cp, cp]))
 3: SparCC.frac(x = y, kmax = kmax, alpha = alpha, Vmin = Vmin)
 4: sparcc(OTUtab[-j, ])
sparcc(OTUtab[-j, ])
 5: FUN(X[[i]], ...)
 6: lapply(X = S, FUN = FUN, ...)
 7: doTryCatch(return(expr), name, parentenv, handler)
 8:  5: FUN(X[[i]], ...)
tryCatchOne(expr, names, parentenv, handlers[[1L]])
 9:  6: lapply(X = S, FUN = FUN, ...)
 7: doTryCatch(return(expr), name, parentenv, handler)
 8: tryCatchOne(expr, names, parentenv, handlers[[1L]])
 9: tryCatchList(expr, classes, parentenv, handlers)
tryCatchList(expr, classes, parentenv, handlers)
10: 10: tryCatch(expr, error = function(e) {    call <- conditionCall(e)tryCatch(expr, error = function(e) {    call <- conditionCall(e)    if (!is.null(call)) {    if (!is.null(call)) {        if (identical(call[[1L]], quote(doTryCatch)))             call <- sys.call(-4L)        if (identical(call[[1L]], quote(doTryCatch)))             call <- sys.call(-4L)        dcall <- deparse(call, nlines = 1L)        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 <- paste("Error in", dcall, ": ")        LONG <- 75L        sm <- strsplit(conditionMessage(e), "\n")[[1L]]            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))})
        w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")        if (is.na(w))             w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], 11: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
12: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
                type = "b")        if (w > LONG)             prefix <- paste0(prefix, "\n  ")13: FUN(X[[i]], ...)
14: lapply(seq_len(cores), inner.do)
    }    else prefix <- "Error : "    msg <- paste0(prefix, conditionMessage(e), "\n")15: mclapply(group, function(j) sparcc(OTUtab[-j, ])$cor.w)
16: asso_mat(OTUdat = OTUtab, group = newindex_B6)
    .Internal(seterrmessage(msg[1L]))    if (!silent && isTRUE(getOption("show.error.messages"))) {        cat(msg, file = outFile)17: eval(expr, envir)
        .Internal(printDeferredWarnings())    }    invisible(structure(msg, class = "try-error", condition = e))18: eval(expr, envir)
19: withVisible(eval(expr, envir))
})
11: 20: withCallingHandlers(code, error = function (e) rlang::entrace(e), message = function (cnd) {    watcher$capture_plot_and_output()    if (on_message$capture) {try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
12:         watcher$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$silence) {sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
13: FUN(X[[i]], ...)
14: lapply(seq_len(cores), inner.do)
15: mclapply(group, function(j) sparcc(OTUtab[-j, ])$cor.w)        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)})
21: 
16: asso_mat(OTUdat = OTUtab, group = newindex_B6)eval(call)
22: 
17: eval(expr, envir)eval(call)
23: 
18: eval(expr, envir)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)    }
19: withVisible(eval(expr, envir))    TRUE}, handlers)

20: withCallingHandlers(code, error = function (e) 24: doWithOneRestart(return(expr), restart)
rlang::entrace(e), message = function (cnd) {    watcher$capture_plot_and_output()25: withOneRestart(expr, restarts[[1L]])
    if (on_message$capture) {        watcher$push(cnd)    }26: withRestartList(expr, restarts[-nr])
    if (on_message$silence) {        invokeRestart("muffleMessage")    }27: doWithOneRestart(return(expr), restart)
}, warning = function (cnd) {    if (getOption("warn") >= 2 || getOption("warn") < 0) {        return()    }    watcher$capture_plot_and_output()28: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
29: withRestartList(expr, restarts)
    if (on_warning$capture) {        cnd <- sanitize_call(cnd)        watcher$push(cnd)30: withRestarts(with_handlers({    for (expr in tle$exprs) {    }    if (on_warning$silence) {        invokeRestart("muffleWarning")    }}, error = function (cnd) {        ev <- withVisible(eval(expr, envir))        watcher$capture_plot_and_output()        watcher$print_value(ev$value, ev$visible, envir)    }    TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)    watcher$capture_plot_and_output()    cnd <- sanitize_call(cnd)    watcher$push(cnd)
31: evaluate::evaluate(...)    switch(on_error, continue = invokeRestart("eval_continue"),         stop = invokeRestart("eval_stop"), error = NULL)})
21: eval(call)
22: eval(call)

32: 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$render, options))23: with_handlers({    for (expr in tle$exprs) {
33: in_dir(input_dir(), expr)        ev <- withVisible(eval(expr, envir))        watcher$capture_plot_and_output()        watcher$print_value(ev$value, ev$visible, envir)
34: in_input_dir(evaluate(code, envir = env, new_device = FALSE,     }    TRUE}, handlers)    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$render, options)))
35: 
24: doWithOneRestart(return(expr), restart)eng_r(options)
36: 
25: withOneRestart(expr, restarts[[1L]])block_exec(params)
37: 
26: withRestartList(expr, restarts[-nr])call_block(x)
38: 
27: doWithOneRestart(return(expr), restart)process_group(group)
39: 
28: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),     error = function(e) {        if (progress && is.function(pb$interrupt))             pb$interrupt()        if (is_R_CMD_build() || is_R_CMD_check())             error <<- format(e)    })
40: with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),     error = function(e) {        if (progress && is.function(pb$interrupt))             pb$interrupt()        if (is_R_CMD_build() || is_R_CMD_check())             error <<- format(e)    }), list(rlang_trace_top_env = knit_global()))
41: 
29: withRestartList(expr, restarts)
30: withRestarts(with_handlers({    for (expr in tle$exprs) {        ev <- withVisible(eval(expr, envir))        watcher$capture_plot_and_output()xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),     error = function(e) {        if (progress && is.function(pb$interrupt))             pb$interrupt()        if (is_R_CMD_build() || is_R_CMD_check())             error <<- format(e)    }), list(rlang_trace_top_env = knit_global())), function(loc) {    setwd(wd)    write_utf8(res, output %n% stdout())        watcher$print_value(ev$value, ev$visible, envir)    }    TRUE    paste0("\nQuitting from ", loc, if (!is.null(error))         paste0("\n", rule(), error, "\n", rule()))}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
31: 
42: process_file(text, output)
43: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
44: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), evaluate::evaluate(...)
32:     output_dir = getwd(), ...)
45: 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$render, options))
33: vweave_rmarkdown(...)
46: in_dir(input_dir(), expr)
34: engine$weave(file, quiet = quiet, encoding = enc)
47: 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, doTryCatch(return(expr), name, parentenv, handler)
48:     stop_on_error = if (is.numeric(options$error)) options$error else {        if (options$error && options$include)             0LtryCatchOne(expr, names, parentenv, handlers[[1L]])
49:         else 2L    }, output_handler = knit_handlers(options$render, options)))
tryCatchList(expr, classes, parentenv, handlers)
50: 35: eng_r(options)
tryCatch({    engine$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)36: block_exec(params)
        output <- find_vignette_product(name, by = "texi2pdf",             engine = engine)    }    outputs <- c(outputs, output)}, error = function(e) {    thisOK <<- FALSE37: call_block(x)
    fails <<- c(fails, file)    message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s",         file, conditionMessage(e)))})
51: 38: process_group(group)
tools::buildVignettes(dir = "/Volumes/Builds/packages/sonoma-arm64/results/4.6/SOHPIE.Rcheck/vign_test/SOHPIE",     skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/Rtmps0yuX7/filee6653e9c39f3.rds")
39: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),     error = function(e) {An irrecoverable exception occurred. R is aborting now ...
        if (progress && is.function(pb$interrupt))             pb$interrupt()        if (is_R_CMD_build() || is_R_CMD_check())             error <<- format(e)    })
40: 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()))
41: 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)
42: process_file(text, output)
43: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
44: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(),     output_dir = getwd(), ...)
45: vweave_rmarkdown(...)
46: engine$weave(file, quiet = quiet, encoding = enc)
47: doTryCatch(return(expr), name, parentenv, handler)
48: tryCatchOne(expr, names, parentenv, handlers[[1L]])
49: tryCatchList(expr, classes, parentenv, handlers)
50: tryCatch({    engine$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)))})
51: tools::buildVignettes(dir = "/Volumes/Builds/packages/sonoma-arm64/results/4.6/SOHPIE.Rcheck/vign_test/SOHPIE",     skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/Rtmps0yuX7/filee6653e9c39f3.rds")
An irrecoverable exception occurred. R is aborting now ...
Warning in file("", "w+b") :
  cannot open file '/Volumes/Temp/tmp/Rtmp01nZDa/Rf11f672f434d5d': No such file or directory

Quitting from UserManualSOHPIE.Rmd:150-158 [unnamed-chunk-13]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cannot open the connection
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~


Quitting from UserManualSOHPIE.Rmd:150-158 [unnamed-chunk-13]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
file("", "w+b")
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'UserManualSOHPIE.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘UserManualSOHPIE.Rmd’

SUMMARY: processing the following file failed:
  ‘UserManualSOHPIE.Rmd’

Error: Vignette re-building failed.
Execution halted