- using R Under development (unstable) (2026-02-12 r89409)
- using platform: aarch64-apple-darwin23
- R was compiled by
Apple clang version 17.0.0 (clang-1700.3.19.1)
GNU Fortran (GCC) 14.2.0
- running under: macOS Sequoia 15.7.1
- using session charset: UTF-8
* current time: 2026-02-13 02:18:56 UTC
- checking for file ‘SOHPIE/DESCRIPTION’ ... OK
- checking extension type ... Package
- this is package ‘SOHPIE’ version ‘1.0.6’
- package encoding: UTF-8
- checking package namespace information ... OK
- checking package dependencies ... OK
- checking if this is a source package ... OK
- checking if there is a namespace ... OK
- checking for executable files ... OK
- checking for hidden files and directories ... OK
- checking for portable file names ... OK
- checking for sufficient/correct file permissions ... OK
- checking whether package ‘SOHPIE’ can be installed ... [1s/1s] OK
See the install log for details.
- checking installed package size ... OK
- checking package directory ... OK
- checking ‘build’ directory ... OK
- checking DESCRIPTION meta-information ... OK
- checking top-level files ... OK
- checking for left-over files ... OK
- checking index information ... OK
- checking package subdirectories ... OK
- checking code files for non-ASCII characters ... OK
- checking R files for syntax errors ... OK
- checking whether the package can be loaded ... [0s/0s] OK
- checking whether the package can be loaded with stated dependencies ... [0s/0s] OK
- checking whether the package can be unloaded cleanly ... [0s/0s] OK
- checking whether the namespace can be loaded with stated dependencies ... [0s/0s] OK
- checking whether the namespace can be unloaded cleanly ... [0s/0s] OK
- checking loading without being on the library search path ... [0s/0s] OK
- checking dependencies in R code ... OK
- checking S3 generic/method consistency ... OK
- checking replacement functions ... OK
- checking foreign function calls ... OK
- checking R code for possible problems ... [1s/1s] OK
- checking Rd files ... [0s/0s] OK
- checking Rd metadata ... OK
- checking Rd cross-references ... OK
- checking for missing documentation entries ... OK
- checking for code/documentation mismatches ... OK
- checking Rd \usage sections ... OK
- checking Rd contents ... OK
- checking for unstated dependencies in examples ... OK
- checking contents of ‘data’ directory ... OK
- checking data for non-ASCII characters ... [0s/0s] OK
- checking LazyData ... OK
- checking data for ASCII and uncompressed saves ... OK
- checking installed files from ‘inst/doc’ ... OK
- checking files in ‘vignettes’ ... OK
- checking examples ... [0s/0s] OK
- checking for unstated dependencies in ‘tests’ ... OK
- checking tests ... [14s/7s] OK
Running ‘testthat.R’ [13s/7s]
- checking for unstated dependencies in vignettes ... OK
- checking package vignettes ... OK
- checking re-building of vignette outputs ... [19s/12s] ERROR
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]], ...)
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)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) watcher$push(cnd) switch(on_error, continue = invokeRestart("eval_continue"),
4: sparcc(OTUtab[-j, ])
5: FUN(X[[i]], ...)
6: lapply(X = S, FUN = FUN, ...)
7: doTryCatch(return(expr), name, parentenv, handler)
8: tryCatchOne(expr, names, parentenv, handlers[[1L]])
9: tryCatchList(expr, classes, parentenv, handlers)
10: stop = invokeRestart("eval_stop"), error = NULL)})
21: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L) prefix <- paste("Error in", dcall, ": ") LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ") } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))eval(call)
22: eval(call)})
11: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
12: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
23: with_handlers({ for (expr in tle$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: 13: FUN(X[[i]], ...)
withOneRestart(expr, restarts[[1L]])
26: 14: lapply(seq_len(cores), inner.do)
withRestartList(expr, restarts[-nr])
27: 15: mclapply(group, function(j) sparcc(OTUtab[-j, ])$cor.w)
doWithOneRestart(return(expr), restart)
28: 16: asso_mat(OTUdat = OTUtab, group = newindex_A1)
withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
29: 17: eval(expr, envir)
withRestartList(expr, restarts)
30: 18: eval(expr, envir)
withRestarts(with_handlers({ for (expr in tle$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(...)
19: withVisible(eval(expr, envir))
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$render, options))
20: withCallingHandlers(code, error = function (e) rlang::entrace(e), message = function (cnd) 33: in_dir(input_dir(), expr)
{ watcher$capture_plot_and_output() if (on_message$capture) { watcher$push(cnd) } if (on_message$silence) { invokeRestart("muffleMessage") }}, warning = function (cnd) 34: in_input_dir(evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, { if (getOption("warn") >= 2 || getOption("warn") < 0) { return() keep_message = if (is.numeric(options$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))) } watcher$capture_plot_and_output() if (on_warning$capture) {
35: eng_r(options)
36: block_exec(params) cnd <- sanitize_call(cnd) watcher$push(cnd) } if (on_warning$silence) { invokeRestart("muffleWarning") }
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 (cnd) { watcher$capture_plot_and_output() error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() cnd <- sanitize_call(cnd) watcher$push(cnd) switch(on_error, continue = invokeRestart("eval_continue"), if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) }), list(rlang_trace_top_env = knit_global())) stop = invokeRestart("eval_stop"), error = NULL)})
41: xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), 21: eval(call)
error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt()22: eval(call)
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)) 23: with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers)
24: doWithOneRestart(return(expr), restart) paste0("\n", rule(), error, "\n", rule()))}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
42: process_file(text, output)
25: withOneRestart(expr, restarts[[1L]])43: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
26: withRestartList(expr, restarts[-nr])44: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...)
27: doWithOneRestart(return(expr), restart)
45: vweave_rmarkdown(...)
28: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
46: engine$weave(file, quiet = quiet, encoding = enc)
47: doTryCatch(return(expr), name, parentenv, handler)
48: tryCatchOne(expr, names, parentenv, handlers[[1L]])
29: withRestartList(expr, restarts)
49: tryCatchList(expr, classes, parentenv, handlers)
30: withRestarts(with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output()
50: tryCatch({ watcher$print_value(ev$value, ev$visible, envir) } TRUE engine$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)}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
31: }, error = function(e) { thisOK <<- FALSE fails <<- c(fails, file)evaluate::evaluate(...)
32: message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", file, conditionMessage(e)))})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 {
51: tools::buildVignettes(dir = "/Volumes/Builds/packages/sonoma-arm64/results/4.6/SOHPIE.Rcheck/vign_test/SOHPIE", if (options$error && options$include) 0L else 2L skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmpDNNoM1/file101e15acc12ee.rds")
An irrecoverable exception occurred. R is aborting now ...
}, 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/RtmpDNNoM1/file101e15acc12ee.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$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) }), list(rlang_trace_top_env = knit_global()))
41: xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check())
Traceback:
1: solve.default(Lmat[cp, cp], rowSums(T02[cp, cp]))
2: solve(Lmat[cp, cp], rowSums(T02[cp, cp]))
3: SparCC.frac(x = y, kmax = kmax, alpha = alpha, Vmin = Vmin)
4: sparcc(OTUtab[-j, ])
error <<- format(e) }), list(rlang_trace_top_env = knit_global())), function(loc) { setwd(wd) write_utf8(res, output %n% stdout()) paste0("\nQuitting from ", loc, if (!is.null(error)) paste0("\n", rule(), error, "\n", rule()))}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
42: process_file(text, output)
43: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
44: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...)
45: vweave_rmarkdown(...)
5: FUN(X[[i]], ...)
6: lapply(X = S, FUN = FUN, ...)
7: 46: engine$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$weave(file, quiet = quiet, encoding = enc) setwd(startdir) output <- find_vignette_product(name, by = "weave", engine = engine)doTryCatch(return(expr), name, parentenv, handler)
8: tryCatchOne(expr, names, parentenv, handlers[[1L]])
9: tryCatchList(expr, classes, parentenv, handlers) if (!have.makefile && vignette_is_tex(output)) { texi2pdf(file = output, clean = FALSE, quiet = quiet) output <- find_vignette_product(name, by = "texi2pdf", engine = engine) } outputs <- c(outputs, output)}, error = function(e) { thisOK <<- FALSE
10: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L) prefix <- paste("Error in", dcall, ": ") LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], fails <<- c(fails, file) message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", file, conditionMessage(e)))})
51: tools::buildVignettes(dir = "/Volumes/Builds/packages/sonoma-arm64/results/4.6/SOHPIE.Rcheck/vign_test/SOHPIE", skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmpDNNoM1/file101e15acc12ee.rds")
An irrecoverable exception occurred. R is aborting now ...
type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ") } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))})
11: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
12: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
13: FUN(X[[i]], ...)
14: lapply(seq_len(cores), inner.do)
15: mclapply(group, function(j) sparcc(OTUtab[-j, ])$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() 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/RtmpDNNoM1/file101e15acc12ee.rds")
An irrecoverable exception occurred. R is aborting now ...
*** 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, ])$cor.w)
16: asso_mat(OTUdat = OTUtab, group = newindex_B1)
17: eval(expr, envir)
18: eval(expr, envir)
19: withVisible(eval(expr, envir))
20: withCallingHandlers(code, error = function (e) rlang::entrace(e), message = function (cnd) { watcher$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$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) }), list(rlang_trace_top_env = knit_global()))
41: xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$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/RtmpDNNoM1/file101e15acc12ee.rds")
*** caught segfault ***
address 0x110, cause 'invalid permissions'
An irrecoverable exception occurred. R is aborting now ...
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_B1)
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() 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/RtmpDNNoM1/file101e15acc12ee.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, ])$cor.w)
16: asso_mat(OTUdat = OTUtab, group = newindex_B6)
17: eval(expr, envir)
18: eval(expr, envir)
19: withVisible(eval(expr, envir))
Traceback:
1: solve.default(Lmat[cp, cp], rowSums(T02[cp, cp]))
2: solve(Lmat[cp, cp], rowSums(T02[cp, cp]))
3: SparCC.frac(x = y, kmax = kmax, alpha = alpha, Vmin = Vmin)
4: sparcc(OTUtab[-j, ])
5: FUN(X[[i]], ...)
6: lapply(X = S, FUN = FUN, ...)
20: withCallingHandlers(code, error = function (e) rlang::entrace(e), message = function (cnd) { watcher$capture_plot_and_output() if (on_message$capture) { watcher$push(cnd) } if (on_message$silence) { invokeRestart("muffleMessage") }}, warning = function (cnd)
7: doTryCatch(return(expr), name, parentenv, handler)
8: tryCatchOne(expr, names, parentenv, handlers[[1L]])
9: tryCatchList(expr, classes, parentenv, handlers)
10: tryCatch(expr, error = function(e) {{ if (getOption("warn") >= 2 || getOption("warn") < 0) { return() } watcher$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$push(cnd) switch(on_error, continue = invokeRestart("eval_continue"), stop = invokeRestart("eval_stop"), error = NULL)})
21: eval(call)
22: eval(call)
23: with_handlers({ call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L) prefix <- paste("Error in", dcall, ": ") LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ") } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) for (expr in tle$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({ .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: 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, lapply(seq_len(cores), inner.do)
15: mclapply(group, function(j) sparcc(OTUtab[-j, ])$cor.w)
16: asso_mat(OTUdat = OTUtab, group = newindex_B6)
17: eval(expr, envir)
18: eval(expr, envir)
19: withVisible(eval(expr, envir))
20: withCallingHandlers(code, error = function (e) rlang::entrace(e), message = function (cnd) { watcher$capture_plot_and_output() 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$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) if (on_message$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$capture_plot_and_output() }), list(rlang_trace_top_env = knit_global()))
41: xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) }), list(rlang_trace_top_env = knit_global())), function(loc) { setwd(wd) write_utf8(res, output %n% stdout()) paste0("\nQuitting from ", loc, if (!is.null(error)) paste0("\n", rule(), error, "\n", rule()))}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
42: process_file(text, output)
43: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet) cnd <- sanitize_call(cnd) watcher$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$visible, envir) }
44: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...)
45: vweave_rmarkdown(...)
46: engine$weave(file, quiet = quiet, encoding = enc)
47: doTryCatch(return(expr), name, parentenv, handler)
48: tryCatchOne(expr, names, parentenv, handlers[[1L]])
49: TRUE}, handlers)
24: doWithOneRestart(return(expr), restart)
25: withOneRestart(expr, restarts[[1L]])
26: withRestartList(expr, restarts[-nr])tryCatchList(expr, classes, parentenv, handlers)
50: tryCatch({ engine$weave(file, quiet = quiet, encoding = enc) setwd(startdir) output <- find_vignette_product(name, by = "weave", engine = engine) if (!have.makefile && vignette_is_tex(output)) { texi2pdf(file = output, clean = FALSE, quiet = quiet) output <- find_vignette_product(name, by = "texi2pdf", engine = engine) } outputs <- c(outputs, output)
27: doWithOneRestart(return(expr), restart)
28: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
29: withRestartList(expr, restarts)
30: withRestarts(with_handlers({ for (expr in tle$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: }, 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/RtmpDNNoM1/file101e15acc12ee.rds")
An irrecoverable exception occurred. R is aborting now ...
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/RtmpDNNoM1/file101e15acc12ee.rds")
An irrecoverable exception occurred. R is aborting now ...
Warning in file("", "w+b") :
cannot open file '/Volumes/Temp/tmp/Rtmp4D6gRl/Rf105c06a524e05': 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
- checking PDF version of manual ... [3s/3s] OK
- DONE
Status: 1 ERROR
- using check arguments '--no-clean-on-error '