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###
### Running command:
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### /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data EGSEA
###
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* checking for file ‘EGSEA/DESCRIPTION’ ... OK
* preparing ‘EGSEA’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘EGSEA.Rnw’ using knitr
*** caught segfault ***
address 0x110, cause 'invalid permissions'
Traceback:
1: local.stat(data = X.mat)
2: safe(X.mat = args$logCPM, y.vec = group, C.mat = args$C.mat, print.it = FALSE, Pi.mat = 100)
3: withVisible(...elt(i))
4: capture.output(temp <- safe(X.mat = args$logCPM, y.vec = group, C.mat = args$C.mat, print.it = FALSE, Pi.mat = 100))
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(args.all, runsafe.contrast, mc.cores = num.workers)
16: runsafe(voom.results = voom.results, contrast = contrast, gs.annot = gs.annot, num.workers = num.threads, verbose = verbose)
17: runbaseGSEA(method = args$baseGSEA, args$voom.results, args$contrast, args$gs.annot, num.threads = args$num.threads, verbose = args$verbose)
18: doTryCatch(return(expr), name, parentenv, handler)
19: tryCatchOne(expr, names, parentenv, handlers[[1L]])
20: tryCatchList(expr, classes, parentenv, handlers)
21: tryCatch({ temp.result <- runbaseGSEA(method = args$baseGSEA, args$voom.results, args$contrast, args$gs.annot, num.threads = args$num.threads, verbose = args$verbose) if (args$verbose) message(paste0("Running ", toupper(args$baseGSEA), " on all ", "contrasts ... COMPLETED")) else { message(args$baseGSEA, "*", appendLF = FALSE) } return(temp.result)}, error = function(e) { message(toupper(args$baseGSEA), " encountered an error -> ", e)})
22: FUN(X[[i]], ...)
23: lapply(X = S, FUN = FUN, ...)
24: doTryCatch(return(expr), name, parentenv, handler)
25: tryCatchOne(expr, names, parentenv, handlers[[1L]])
26: tryCatchList(expr, classes, parentenv, handlers)
27: 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))})
28: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
29: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
30: FUN(X[[i]], ...)
31: lapply(seq_len(cores), inner.do)
32: mclapply(args.all, runbaseGSEAParallelWorker, mc.cores = num.workers)
33: runegsea(voom.results = voom.results, contrast = contrast, limma.tops = limma.tops, baseGSEAs = baseGSEAs, combineMethod = combineMethod, combineWeights = NULL, gs.annot = gs.annot, logFC = logFC, logFC.cutoff = logFC.cutoff, fdr.cutoff = fdr.cutoff, vote.bin.width = vote.bin.width, keep.base = keep.base, num.workers = num.threads, verbose = verbose)
34: egsea.main(voom.results, contrasts, gs.annots, baseGSEAs, combineMethod, combineWeights, sort.by, report.dir, kegg.dir, logFC, symbolsMap, minSize, display.top, logFC.cutoff, fdr.cutoff, sum.plot.cutoff, sum.plot.axis, vote.bin.width, keep.base, verbose, num.threads, report, keep.limma, keep.set.scores, interactive)
35: withCallingHandlers(expr, warning = function(w) if (inherits(w, classes)) tryInvokeRestart("muffleWarning"))
36: suppressWarnings(return(egsea.main(voom.results, contrasts, gs.annots, baseGSEAs, combineMethod, combineWeights, sort.by, report.dir, kegg.dir, logFC, symbolsMap, minSize, display.top, logFC.cutoff, fdr.cutoff, sum.plot.cutoff, sum.plot.axis, vote.bin.width, keep.base, verbose, num.threads, report, keep.limma, keep.set.scores, interactive)))
37: egsea(voom.results = v, contrasts = contrasts, gs.annots = gs.annots, symbolsMap = v$genes, baseGSEAs = baseMethods, report.dir = "./il13-egsea-report", sort.by = "avg.rank", num.threads = 4, report = FALSE)
38: eval(expr, envir)
39: eval(expr, envir)
40: withVisible(eval(expr, envir))
41: withCallingHandlers(code, message = function (cnd) { watcher$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$push(cnd) switch(on_error, continue = invokeRestart("eval_continue"), stop = invokeRestart("eval_stop"), error = NULL)})
42: eval(call)
43: eval(call)
44: with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers)
45: doWithOneRestart(return(expr), restart)
46: withOneRestart(expr, restarts[[1L]])
47: withRestartList(expr, restarts[-nr])
48: doWithOneRestart(return(expr), restart)
49: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
50: withRestartList(expr, restarts)
51: withRestarts(with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
52: evaluate::evaluate(...)
53: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$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))
54: in_dir(input_dir(), expr)
55: 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$render, options)))
56: eng_r(options)
57: block_exec(params)
58: call_block(x)
59: process_group(group)
60: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (xfun::pkg_available("rlang", "1.0.0")) { if (is_R_CMD_build() || is_R_CMD_check()) { cnd = tryCatch(rlang::entrace(e), error = identity) error <<- format(cnd) } else { rlang::entrace(e) } } })
61: xfun:::handle_error(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (xfun::pkg_available("rlang", "1.0.0")) { if (is_R_CMD_build() || is_R_CMD_check()) { cnd = tryCatch(rlang::entrace(e), error = identity) error <<- format(cnd) } else { rlang::entrace(e) } } }), function(loc) { setwd(wd) write_utf8(res, output %n% stdout()) paste0("\nQuitting from ", loc, if (!is.null(error)) paste0("\n", rule(), error, "\n", rule()))}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
62: process_file(text, output)
63: (if (grepl("\\.[Rr]md$", file)) knit2html else if (grepl("\\.[Rr]rst$", file)) knit2pandoc else knit)(file, encoding = encoding, quiet = quiet, envir = globalenv(), ...)
64: engine$weave(file, quiet = quiet, encoding = enc)
65: doTryCatch(return(expr), name, parentenv, handler)
66: tryCatchOne(expr, names, parentenv, handlers[[1L]])
67: tryCatchList(expr, classes, parentenv, handlers)
68: tryCatch({ engine$weave(file, quiet = quiet, encoding = enc) setwd(startdir) output <- find_vignette_product(name, by = "weave", engine = engine) if (!have.makefile && vignette_is_tex(output)) { texi2pdf(file = output, clean = FALSE, quiet = quiet) output <- find_vignette_product(name, by = "texi2pdf", engine = engine) } outputs <- c(outputs, output)}, error = function(e) { thisOK <<- FALSE fails <<- c(fails, file) message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", file, conditionMessage(e)))})
69: tools::buildVignettes(dir = ".", tangle = TRUE)
An irrecoverable exception occurred. R is aborting now ...
*** caught segfault ***
address 0x110, cause 'invalid permissions'
Traceback:
1: local.stat(data = X.mat)
2: safe(X.mat = args$logCPM, y.vec = group, C.mat = args$C.mat, print.it = FALSE, Pi.mat = 100)
3: withVisible(...elt(i))
4: capture.output(temp <- safe(X.mat = args$logCPM, y.vec = group, C.mat = args$C.mat, print.it = FALSE, Pi.mat = 100))
5: FUN(X[[i]], ...)
6: lapply(X = S, FUN = FUN, ...)
7: doTryCatch(return(expr), name, parentenv, handler)
8: tryCatchOne(expr, names, parentenv, handlers[[1L]])
9: tryCatchList(expr, classes, parentenv, handlers)
10: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L) prefix <- paste("Error in", dcall, ": ") LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ") } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))})
11: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
12: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
13: FUN(X[[i]], ...)
14: lapply(seq_len(cores), inner.do)
15: mclapply(args.all, runsafe.contrast, mc.cores = num.workers)
16: runsafe(voom.results = voom.results, contrast = contrast, gs.annot = gs.annot, num.workers = num.threads, verbose = verbose)
17: runbaseGSEA(method = args$baseGSEA, args$voom.results, args$contrast, args$gs.annot, num.threads = args$num.threads, verbose = args$verbose)
18: doTryCatch(return(expr), name, parentenv, handler)
19: tryCatchOne(expr, names, parentenv, handlers[[1L]])
20: tryCatchList(expr, classes, parentenv, handlers)
21: tryCatch({ temp.result <- runbaseGSEA(method = args$baseGSEA, args$voom.results, args$contrast, args$gs.annot, num.threads = args$num.threads, verbose = args$verbose) if (args$verbose) message(paste0("Running ", toupper(args$baseGSEA), " on all ", "contrasts ... COMPLETED")) else { message(args$baseGSEA, "*", appendLF = FALSE) } return(temp.result)}, error = function(e) { message(toupper(args$baseGSEA), " encountered an error -> ", e)})
22: FUN(X[[i]], ...)
23: lapply(X = S, FUN = FUN, ...)
24: doTryCatch(return(expr), name, parentenv, handler)
25: tryCatchOne(expr, names, parentenv, handlers[[1L]])
26: tryCatchList(expr, classes, parentenv, handlers)
27: 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))})
28: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
29: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
30: FUN(X[[i]], ...)
31: lapply(seq_len(cores), inner.do)
32: mclapply(args.all, runbaseGSEAParallelWorker, mc.cores = num.workers)
33: runegsea(voom.results = voom.results, contrast = contrast, limma.tops = limma.tops, baseGSEAs = baseGSEAs, combineMethod = combineMethod, combineWeights = NULL, gs.annot = gs.annot, logFC = logFC, logFC.cutoff = logFC.cutoff, fdr.cutoff = fdr.cutoff, vote.bin.width = vote.bin.width, keep.base = keep.base, num.workers = num.threads, verbose = verbose)
34: egsea.main(voom.results, contrasts, gs.annots, baseGSEAs, combineMethod, combineWeights, sort.by, report.dir, kegg.dir, logFC, symbolsMap, minSize, display.top, logFC.cutoff, fdr.cutoff, sum.plot.cutoff, sum.plot.axis, vote.bin.width, keep.base, verbose, num.threads, report, keep.limma, keep.set.scores, interactive)
35: withCallingHandlers(expr, warning = function(w) if (inherits(w, classes)) tryInvokeRestart("muffleWarning"))
36: suppressWarnings(return(egsea.main(voom.results, contrasts, gs.annots, baseGSEAs, combineMethod, combineWeights, sort.by, report.dir, kegg.dir, logFC, symbolsMap, minSize, display.top, logFC.cutoff, fdr.cutoff, sum.plot.cutoff, sum.plot.axis, vote.bin.width, keep.base, verbose, num.threads, report, keep.limma, keep.set.scores, interactive)))
37: egsea(voom.results = v, contrasts = contrasts, gs.annots = gs.annots, symbolsMap = v$genes, baseGSEAs = baseMethods, report.dir = "./il13-egsea-report", sort.by = "avg.rank", num.threads = 4, report = FALSE)
38: eval(expr, envir)
39: eval(expr, envir)
40: withVisible(eval(expr, envir))
41: withCallingHandlers(code, 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)})
42: eval(call)
43: eval(call)
44: with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers)
45: doWithOneRestart(return(expr), restart)
46: withOneRestart(expr, restarts[[1L]])
47: withRestartList(expr, restarts[-nr])
48: doWithOneRestart(return(expr), restart)
49: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
50: withRestartList(expr, restarts)
51: withRestarts(with_handlers({ for (expr in tle$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)
52: evaluate::evaluate(...)
53: 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$render, options))
54: in_dir(input_dir(), expr)
55: in_input_dir(evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$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)))
56: eng_r(options)
57: block_exec(params)
58: call_block(x)
59: process_group(group)
60: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (xfun::pkg_available("rlang", "1.0.0")) { if (is_R_CMD_build() || is_R_CMD_check()) { cnd = tryCatch(rlang::entrace(e), error = identity) error <<- format(cnd) } else { rlang::entrace(e) } } })
61: xfun:::handle_error(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (xfun::pkg_available("rlang", "1.0.0")) { if (is_R_CMD_build() || is_R_CMD_check()) { cnd = tryCatch(rlang::entrace(e), error = identity) error <<- format(cnd) } else { rlang::entrace(e) } } }), 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)
62: process_file(text, output)
63: (if (grepl("\\.[Rr]md$", file)) knit2html else if (grepl("\\.[Rr]rst$", file)) knit2pandoc else knit)(file, encoding = encoding, quiet = quiet, envir = globalenv(), ...)
64: engine$weave(file, quiet = quiet, encoding = enc)
65: doTryCatch(return(expr), name, parentenv, handler)
66: tryCatchOne(expr, names, parentenv, handlers[[1L]])
67: tryCatchList(expr, classes, parentenv, handlers)
68: tryCatch({ engine$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)))})
69: tools::buildVignettes(dir = ".", tangle = TRUE)
An irrecoverable exception occurred. R is aborting now ...
*** caught segfault ***
address 0x110, cause 'invalid permissions'
Traceback:
1: solve.default(crossprod(Z), crossprod(Z, X))
2: solve(crossprod(Z), crossprod(Z, X))
3: .lineartest(Y, Z, X, offset, dir, perms, fromGLM = TRUE)
4: .glmtest(response, Z = null, X = alternative, offset = offset, family = "binomial", dir = directional, perms = permutations)
5: gt(factor(group), data.log.sel, subsets = args$gs.annot@idx, permutations = 10000)
6: FUN(X[[i]], ...)
7: lapply(X = S, FUN = FUN, ...)
8: doTryCatch(return(expr), name, parentenv, handler)
9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
10: tryCatchList(expr, classes, parentenv, handlers)
11: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L) prefix <- paste("Error in", dcall, ": ") LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ") } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))})
12: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
13: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
14: FUN(X[[i]], ...)
15: lapply(seq_len(cores), inner.do)
16: mclapply(args.all, runglobaltest.contrast, mc.cores = num.workers)
17: runglobaltest(voom.results = voom.results, contrast = contrast, gs.annot = gs.annot, num.workers = num.threads, verbose = verbose)
18: runbaseGSEA(method = args$baseGSEA, args$voom.results, args$contrast, args$gs.annot, num.threads = args$num.threads, verbose = args$verbose)
19: doTryCatch(return(expr), name, parentenv, handler)
20: tryCatchOne(expr, names, parentenv, handlers[[1L]])
21: tryCatchList(expr, classes, parentenv, handlers)
22: tryCatch({ temp.result <- runbaseGSEA(method = args$baseGSEA, args$voom.results, args$contrast, args$gs.annot, num.threads = args$num.threads, verbose = args$verbose) if (args$verbose) message(paste0("Running ", toupper(args$baseGSEA), " on all ", "contrasts ... COMPLETED")) else { message(args$baseGSEA, "*", appendLF = FALSE) } return(temp.result)}, error = function(e) { message(toupper(args$baseGSEA), " encountered an error -> ", e)})
23: FUN(X[[i]], ...)
24: lapply(X = S, FUN = FUN, ...)
25: doTryCatch(return(expr), name, parentenv, handler)
26: tryCatchOne(expr, names, parentenv, handlers[[1L]])
27: tryCatchList(expr, classes, parentenv, handlers)
28: 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))})
29: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
30: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
31: FUN(X[[i]], ...)
32: lapply(seq_len(cores), inner.do)
33: mclapply(args.all, runbaseGSEAParallelWorker, mc.cores = num.workers)
34: runegsea(voom.results = voom.results, contrast = contrast, limma.tops = limma.tops, baseGSEAs = baseGSEAs, combineMethod = combineMethod, combineWeights = NULL, gs.annot = gs.annot, logFC = logFC, logFC.cutoff = logFC.cutoff, fdr.cutoff = fdr.cutoff, vote.bin.width = vote.bin.width, keep.base = keep.base, num.workers = num.threads, verbose = verbose)
35: egsea.main(voom.results, contrasts, gs.annots, baseGSEAs, combineMethod, combineWeights, sort.by, report.dir, kegg.dir, logFC, symbolsMap, minSize, display.top, logFC.cutoff, fdr.cutoff, sum.plot.cutoff, sum.plot.axis, vote.bin.width, keep.base, verbose, num.threads, report, keep.limma, keep.set.scores, interactive)
36: withCallingHandlers(expr, warning = function(w) if (inherits(w, classes)) tryInvokeRestart("muffleWarning"))
37: suppressWarnings(return(egsea.main(voom.results, contrasts, gs.annots, baseGSEAs, combineMethod, combineWeights, sort.by, report.dir, kegg.dir, logFC, symbolsMap, minSize, display.top, logFC.cutoff, fdr.cutoff, sum.plot.cutoff, sum.plot.axis, vote.bin.width, keep.base, verbose, num.threads, report, keep.limma, keep.set.scores, interactive)))
38: egsea(voom.results = v, contrasts = contrasts, gs.annots = gs.annots, symbolsMap = v$genes, baseGSEAs = baseMethods, report.dir = "./il13-egsea-report", sort.by = "avg.rank", num.threads = 4, report = FALSE)
39: eval(expr, envir)
40: eval(expr, envir)
41: withVisible(eval(expr, envir))
42: withCallingHandlers(code, 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)})
43: eval(call)
44: eval(call)
45: with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers)
46: doWithOneRestart(return(expr), restart)
47: withOneRestart(expr, restarts[[1L]])
48: withRestartList(expr, restarts[-nr])
49: doWithOneRestart(return(expr), restart)
50: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
51: withRestartList(expr, restarts)
52: withRestarts(with_handlers({ for (expr in tle$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)
53: evaluate::evaluate(...)
54: 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$render, options))
55: in_dir(input_dir(), expr)
56: in_input_dir(evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$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)))
57: eng_r(options)
58: block_exec(params)
59: call_block(x)
60: process_group(group)
61: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (xfun::pkg_available("rlang", "1.0.0")) { if (is_R_CMD_build() || is_R_CMD_check()) { cnd = tryCatch(rlang::entrace(e), error = identity) error <<- format(cnd) } else { rlang::entrace(e) } } })
62: xfun:::handle_error(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (xfun::pkg_available("rlang", "1.0.0")) { if (is_R_CMD_build() || is_R_CMD_check()) { cnd = tryCatch(rlang::entrace(e), error = identity) error <<- format(cnd) } else { rlang::entrace(e) } } }), 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)
63: process_file(text, output)
64: (if (grepl("\\.[Rr]md$", file)) knit2html else if (grepl("\\.[Rr]rst$", file)) knit2pandoc else knit)(file, encoding = encoding, quiet = quiet, envir = globalenv(), ...)
65: engine$weave(file, quiet = quiet, encoding = enc)
66: doTryCatch(return(expr), name, parentenv, handler)
67: tryCatchOne(expr, names, parentenv, handlers[[1L]])
68: tryCatchList(expr, classes, parentenv, handlers)
69: tryCatch({ engine$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)))})
70: tools::buildVignettes(dir = ".", tangle = TRUE)
An irrecoverable exception occurred. R is aborting now ...
*** caught segfault ***
address 0x110, cause 'invalid permissions'
Traceback:
1: solve.default(crossprod(Z), crossprod(Z, X))
2: solve(crossprod(Z), crossprod(Z, X))
3: .lineartest(Y, Z, X, offset, dir, perms, fromGLM = TRUE)
4: .glmtest(response, Z = null, X = alternative, offset = offset, family = "binomial", dir = directional, perms = permutations)
5: gt(factor(group), data.log.sel, subsets = args$gs.annot@idx, permutations = 10000)
6: FUN(X[[i]], ...)
7: lapply(X = S, FUN = FUN, ...)
8: doTryCatch(return(expr), name, parentenv, handler)
9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
10: tryCatchList(expr, classes, parentenv, handlers)
11: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L) prefix <- paste("Error in", dcall, ": ") LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ") } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))})
12: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
13: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
14: FUN(X[[i]], ...)
15: lapply(seq_len(cores), inner.do)
16: mclapply(args.all, runglobaltest.contrast, mc.cores = num.workers)
17: runglobaltest(voom.results = voom.results, contrast = contrast, gs.annot = gs.annot, num.workers = num.threads, verbose = verbose)
18: runbaseGSEA(method = args$baseGSEA, args$voom.results, args$contrast, args$gs.annot, num.threads = args$num.threads, verbose = args$verbose)
19: doTryCatch(return(expr), name, parentenv, handler)
20: tryCatchOne(expr, names, parentenv, handlers[[1L]])
21: tryCatchList(expr, classes, parentenv, handlers)
22: tryCatch({ temp.result <- runbaseGSEA(method = args$baseGSEA, args$voom.results, args$contrast, args$gs.annot, num.threads = args$num.threads, verbose = args$verbose) if (args$verbose) message(paste0("Running ", toupper(args$baseGSEA), " on all ", "contrasts ... COMPLETED")) else { message(args$baseGSEA, "*", appendLF = FALSE) } return(temp.result)}, error = function(e) { message(toupper(args$baseGSEA), " encountered an error -> ", e)})
23: FUN(X[[i]], ...)
24: lapply(X = S, FUN = FUN, ...)
25: doTryCatch(return(expr), name, parentenv, handler)
26: tryCatchOne(expr, names, parentenv, handlers[[1L]])
27: tryCatchList(expr, classes, parentenv, handlers)
28: 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))})
29: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
30: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
31: FUN(X[[i]], ...)
32: lapply(seq_len(cores), inner.do)
33: mclapply(args.all, runbaseGSEAParallelWorker, mc.cores = num.workers)
34: runegsea(voom.results = voom.results, contrast = contrast, limma.tops = limma.tops, baseGSEAs = baseGSEAs, combineMethod = combineMethod, combineWeights = NULL, gs.annot = gs.annot, logFC = logFC, logFC.cutoff = logFC.cutoff, fdr.cutoff = fdr.cutoff, vote.bin.width = vote.bin.width, keep.base = keep.base, num.workers = num.threads, verbose = verbose)
35: egsea.main(voom.results, contrasts, gs.annots, baseGSEAs, combineMethod, combineWeights, sort.by, report.dir, kegg.dir, logFC, symbolsMap, minSize, display.top, logFC.cutoff, fdr.cutoff, sum.plot.cutoff, sum.plot.axis, vote.bin.width, keep.base, verbose, num.threads, report, keep.limma, keep.set.scores, interactive)
36: withCallingHandlers(expr, warning = function(w) if (inherits(w, classes)) tryInvokeRestart("muffleWarning"))
37: suppressWarnings(return(egsea.main(voom.results, contrasts, gs.annots, baseGSEAs, combineMethod, combineWeights, sort.by, report.dir, kegg.dir, logFC, symbolsMap, minSize, display.top, logFC.cutoff, fdr.cutoff, sum.plot.cutoff, sum.plot.axis, vote.bin.width, keep.base, verbose, num.threads, report, keep.limma, keep.set.scores, interactive)))
38: egsea(voom.results = v, contrasts = contrasts, gs.annots = gs.annots, symbolsMap = v$genes, baseGSEAs = baseMethods, report.dir = "./il13-egsea-report", sort.by = "avg.rank", num.threads = 4, report = FALSE)
39: eval(expr, envir)
40: eval(expr, envir)
41: withVisible(eval(expr, envir))
42: withCallingHandlers(code, 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)})
43: eval(call)
44: eval(call)
45: with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers)
46: doWithOneRestart(return(expr), restart)
47: withOneRestart(expr, restarts[[1L]])
48: withRestartList(expr, restarts[-nr])
49: doWithOneRestart(return(expr), restart)
50: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
51: withRestartList(expr, restarts)
52: withRestarts(with_handlers({ for (expr in tle$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)
53: evaluate::evaluate(...)
54: 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$render, options))
55: in_dir(input_dir(), expr)
56: in_input_dir(evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$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)))
57: eng_r(options)
58: block_exec(params)
59: call_block(x)
60: process_group(group)
61: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (xfun::pkg_available("rlang", "1.0.0")) { if (is_R_CMD_build() || is_R_CMD_check()) { cnd = tryCatch(rlang::entrace(e), error = identity) error <<- format(cnd) } else { rlang::entrace(e) } } })
62: xfun:::handle_error(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (xfun::pkg_available("rlang", "1.0.0")) { if (is_R_CMD_build() || is_R_CMD_check()) { cnd = tryCatch(rlang::entrace(e), error = identity) error <<- format(cnd) } else { rlang::entrace(e) } } }), 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)
63: process_file(text, output)
64: (if (grepl("\\.[Rr]md$", file)) knit2html else if (grepl("\\.[Rr]rst$", file)) knit2pandoc else knit)(file, encoding = encoding, quiet = quiet, envir = globalenv(), ...)
65: engine$weave(file, quiet = quiet, encoding = enc)
66: doTryCatch(return(expr), name, parentenv, handler)
67: tryCatchOne(expr, names, parentenv, handlers[[1L]])
68: tryCatchList(expr, classes, parentenv, handlers)
69: tryCatch({ engine$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)))})
70: tools::buildVignettes(dir = ".", tangle = TRUE)
An irrecoverable exception occurred. R is aborting now ...
*** caught segfault ***
address 0x110, cause 'invalid permissions'
Traceback:
1: classifyTestsF(fit, fstat.only = TRUE)
2: eBayes(vfit)
3: runora(voom.results = voom.results, contrast = contrast, gs.annot = gs.annot, num.workers = num.threads, verbose = verbose)
4: runbaseGSEA(method = args$baseGSEA, args$voom.results, args$contrast, args$gs.annot, num.threads = args$num.threads, verbose = args$verbose)
5: doTryCatch(return(expr), name, parentenv, handler)
6: tryCatchOne(expr, names, parentenv, handlers[[1L]])
7: tryCatchList(expr, classes, parentenv, handlers)
8: tryCatch({ temp.result <- runbaseGSEA(method = args$baseGSEA, args$voom.results, args$contrast, args$gs.annot, num.threads = args$num.threads, verbose = args$verbose) if (args$verbose) message(paste0("Running ", toupper(args$baseGSEA), " on all ", "contrasts ... COMPLETED")) else { message(args$baseGSEA, "*", appendLF = FALSE) } return(temp.result)}, error = function(e) { message(toupper(args$baseGSEA), " encountered an error -> ", e)})
9: FUN(X[[i]], ...)
10: lapply(X = S, FUN = FUN, ...)
11: doTryCatch(return(expr), name, parentenv, handler)
12: tryCatchOne(expr, names, parentenv, handlers[[1L]])
13: tryCatchList(expr, classes, parentenv, handlers)
14: 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))})
15: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
16: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
17: FUN(X[[i]], ...)
18: lapply(seq_len(cores), inner.do)
19: mclapply(args.all, runbaseGSEAParallelWorker, mc.cores = num.workers)
20: runegsea(voom.results = voom.results, contrast = contrast, limma.tops = limma.tops, baseGSEAs = baseGSEAs, combineMethod = combineMethod, combineWeights = NULL, gs.annot = gs.annot, logFC = logFC, logFC.cutoff = logFC.cutoff, fdr.cutoff = fdr.cutoff, vote.bin.width = vote.bin.width, keep.base = keep.base, num.workers = num.threads, verbose = verbose)
21: egsea.main(voom.results, contrasts, gs.annots, baseGSEAs, combineMethod, combineWeights, sort.by, report.dir, kegg.dir, logFC, symbolsMap, minSize, display.top, logFC.cutoff, fdr.cutoff, sum.plot.cutoff, sum.plot.axis, vote.bin.width, keep.base, verbose, num.threads, report, keep.limma, keep.set.scores, interactive)
22: withCallingHandlers(expr, warning = function(w) if (inherits(w, classes)) tryInvokeRestart("muffleWarning"))
23: suppressWarnings(return(egsea.main(voom.results, contrasts, gs.annots, baseGSEAs, combineMethod, combineWeights, sort.by, report.dir, kegg.dir, logFC, symbolsMap, minSize, display.top, logFC.cutoff, fdr.cutoff, sum.plot.cutoff, sum.plot.axis, vote.bin.width, keep.base, verbose, num.threads, report, keep.limma, keep.set.scores, interactive)))
24: egsea(voom.results = v, contrasts = contrasts, gs.annots = gs.annots, symbolsMap = v$genes, baseGSEAs = baseMethods, report.dir = "./il13-egsea-report", sort.by = "avg.rank", num.threads = 4, report = FALSE)
25: eval(expr, envir)
26: eval(expr, envir)
27: withVisible(eval(expr, envir))
28: withCallingHandlers(code, message = function (cnd) { watcher$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$push(cnd) switch(on_error, continue = invokeRestart("eval_continue"), stop = invokeRestart("eval_stop"), error = NULL)})
29: eval(call)
30: eval(call)
31: with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers)
32: doWithOneRestart(return(expr), restart)
33: withOneRestart(expr, restarts[[1L]])
34: withRestartList(expr, restarts[-nr])
35: doWithOneRestart(return(expr), restart)
36: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
37: withRestartList(expr, restarts)
38: withRestarts(with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
39: evaluate::evaluate(...)
40: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$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))
41: in_dir(input_dir(), expr)
42: 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$render, options)))
43: eng_r(options)
44: block_exec(params)
45: call_block(x)
46: process_group(group)
47: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (xfun::pkg_available("rlang", "1.0.0")) { if (is_R_CMD_build() || is_R_CMD_check()) { cnd = tryCatch(rlang::entrace(e), error = identity) error <<- format(cnd) } else { rlang::entrace(e) } } })
48: xfun:::handle_error(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (xfun::pkg_available("rlang", "1.0.0")) { if (is_R_CMD_build() || is_R_CMD_check()) { cnd = tryCatch(rlang::entrace(e), error = identity) error <<- format(cnd) } else { rlang::entrace(e) } } }), function(loc) { setwd(wd) write_utf8(res, output %n% stdout()) paste0("\nQuitting from ", loc, if (!is.null(error)) paste0("\n", rule(), error, "\n", rule()))}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
49: process_file(text, output)
50: (if (grepl("\\.[Rr]md$", file)) knit2html else if (grepl("\\.[Rr]rst$", file)) knit2pandoc else knit)(file, encoding = encoding, quiet = quiet, envir = globalenv(), ...)
51: engine$weave(file, quiet = quiet, encoding = enc)
52: doTryCatch(return(expr), name, parentenv, handler)
53: tryCatchOne(expr, names, parentenv, handlers[[1L]])
54: tryCatchList(expr, classes, parentenv, handlers)
55: tryCatch({ engine$weave(file, quiet = quiet, encoding = enc) setwd(startdir) output <- find_vignette_product(name, by = "weave", engine = engine) if (!have.makefile && vignette_is_tex(output)) { texi2pdf(file = output, clean = FALSE, quiet = quiet) output <- find_vignette_product(name, by = "texi2pdf", engine = engine) } outputs <- c(outputs, output)}, error = function(e) { thisOK <<- FALSE fails <<- c(fails, file) message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", file, conditionMessage(e)))})
56: tools::buildVignettes(dir = ".", tangle = TRUE)
An irrecoverable exception occurred. R is aborting now ...
*** caught segfault ***
address 0x110, cause 'invalid permissions'
Traceback:
1: contrasts.fit(fit, cont.matrix)
2: gsScoreFun(G, block)
3: padog(esetm = args$logCPM, group = group, paired = FALSE, gslist = args$gsets, NI = 100, verbose = FALSE)
4: FUN(X[[i]], ...)
5: lapply(X = S, FUN = FUN, ...)
6: doTryCatch(return(expr), name, parentenv, handler)
7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
8: tryCatchList(expr, classes, parentenv, handlers)
9: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L) prefix <- paste("Error in", dcall, ": ") LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ") } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))})
10: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
11: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
12: FUN(X[[i]], ...)
13: lapply(seq_len(cores), inner.do)
14: mclapply(args.all, runpadog.contrast, mc.cores = num.workers)
15: runpadog(voom.results = voom.results, contrast = contrast, gs.annot = gs.annot, num.workers = num.threads, verbose = verbose)
16: runbaseGSEA(method = args$baseGSEA, args$voom.results, args$contrast, args$gs.annot, num.threads = args$num.threads, verbose = args$verbose)
17: doTryCatch(return(expr), name, parentenv, handler)
18: tryCatchOne(expr, names, parentenv, handlers[[1L]])
19: tryCatchList(expr, classes, parentenv, handlers)
20: tryCatch({ temp.result <- runbaseGSEA(method = args$baseGSEA, args$voom.results, args$contrast, args$gs.annot, num.threads = args$num.threads, verbose = args$verbose) if (args$verbose) message(paste0("Running ", toupper(args$baseGSEA), " on all ", "contrasts ... COMPLETED")) else { message(args$baseGSEA, "*", appendLF = FALSE) } return(temp.result)}, error = function(e) { message(toupper(args$baseGSEA), " encountered an error -> ", e)})
21: FUN(X[[i]], ...)
22: lapply(X = S, FUN = FUN, ...)
23: doTryCatch(return(expr), name, parentenv, handler)
24: tryCatchOne(expr, names, parentenv, handlers[[1L]])
25: tryCatchList(expr, classes, parentenv, handlers)
26: 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))})
27: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
28: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
29: FUN(X[[i]], ...)
30: lapply(seq_len(cores), inner.do)
31: mclapply(args.all, runbaseGSEAParallelWorker, mc.cores = num.workers)
32: runegsea(voom.results = voom.results, contrast = contrast, limma.tops = limma.tops, baseGSEAs = baseGSEAs, combineMethod = combineMethod, combineWeights = NULL, gs.annot = gs.annot, logFC = logFC, logFC.cutoff = logFC.cutoff, fdr.cutoff = fdr.cutoff, vote.bin.width = vote.bin.width, keep.base = keep.base, num.workers = num.threads, verbose = verbose)
33: egsea.main(voom.results, contrasts, gs.annots, baseGSEAs, combineMethod, combineWeights, sort.by, report.dir, kegg.dir, logFC, symbolsMap, minSize, display.top, logFC.cutoff, fdr.cutoff, sum.plot.cutoff, sum.plot.axis, vote.bin.width, keep.base, verbose, num.threads, report, keep.limma, keep.set.scores, interactive)
34: withCallingHandlers(expr, warning = function(w) if (inherits(w, classes)) tryInvokeRestart("muffleWarning"))
35: suppressWarnings(return(egsea.main(voom.results, contrasts, gs.annots, baseGSEAs, combineMethod, combineWeights, sort.by, report.dir, kegg.dir, logFC, symbolsMap, minSize, display.top, logFC.cutoff, fdr.cutoff, sum.plot.cutoff, sum.plot.axis, vote.bin.width, keep.base, verbose, num.threads, report, keep.limma, keep.set.scores, interactive)))
36: egsea(voom.results = v, contrasts = contrasts, gs.annots = gs.annots, symbolsMap = v$genes, baseGSEAs = baseMethods, report.dir = "./il13-egsea-report", sort.by = "avg.rank", num.threads = 4, report = FALSE)
37: eval(expr, envir)
38: eval(expr, envir)
39: withVisible(eval(expr, envir))
40: withCallingHandlers(code, 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)})
41: eval(call)
42: eval(call)
43: with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers)
44: doWithOneRestart(return(expr), restart)
45: withOneRestart(expr, restarts[[1L]])
46: withRestartList(expr, restarts[-nr])
47: doWithOneRestart(return(expr), restart)
48: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
49: withRestartList(expr, restarts)
50: withRestarts(with_handlers({ for (expr in tle$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)
51: evaluate::evaluate(...)
52: 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$render, options))
53: in_dir(input_dir(), expr)
54: in_input_dir(evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$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)))
55: eng_r(options)
56: block_exec(params)
57: call_block(x)
58: process_group(group)
59: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (xfun::pkg_available("rlang", "1.0.0")) { if (is_R_CMD_build() || is_R_CMD_check()) { cnd = tryCatch(rlang::entrace(e), error = identity) error <<- format(cnd) } else { rlang::entrace(e) } } })
60: xfun:::handle_error(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (xfun::pkg_available("rlang", "1.0.0")) { if (is_R_CMD_build() || is_R_CMD_check()) { cnd = tryCatch(rlang::entrace(e), error = identity) error <<- format(cnd) } else { rlang::entrace(e) } } }), 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)
61: process_file(text, output)
62: (if (grepl("\\.[Rr]md$", file)) knit2html else if (grepl("\\.[Rr]rst$", file)) knit2pandoc else knit)(file, encoding = encoding, quiet = quiet, envir = globalenv(), ...)
63: engine$weave(file, quiet = quiet, encoding = enc)
64: doTryCatch(return(expr), name, parentenv, handler)
65: tryCatchOne(expr, names, parentenv, handlers[[1L]])
66: tryCatchList(expr, classes, parentenv, handlers)
67: tryCatch({ engine$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)))})
68: tools::buildVignettes(dir = ".", tangle = TRUE)
An irrecoverable exception occurred. R is aborting now ...
*** caught segfault ***
address 0x110, cause 'invalid permissions'
Traceback:
1: contrasts.fit(fit, cont.matrix)
2: gsScoreFun(G, block)
3: padog(esetm = args$logCPM, group = group, paired = FALSE, gslist = args$gsets, NI = 100, verbose = FALSE)
4: FUN(X[[i]], ...)
5: lapply(X = S, FUN = FUN, ...)
6: doTryCatch(return(expr), name, parentenv, handler)
7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
8: tryCatchList(expr, classes, parentenv, handlers)
9: 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))})
10: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
11: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
12: FUN(X[[i]], ...)
13: lapply(seq_len(cores), inner.do)
14: mclapply(args.all, runpadog.contrast, mc.cores = num.workers)
15: runpadog(voom.results = voom.results, contrast = contrast, gs.annot = gs.annot, num.workers = num.threads, verbose = verbose)
16: runbaseGSEA(method = args$baseGSEA, args$voom.results, args$contrast, args$gs.annot, num.threads = args$num.threads, verbose = args$verbose)
17: doTryCatch(return(expr), name, parentenv, handler)
18: tryCatchOne(expr, names, parentenv, handlers[[1L]])
19: tryCatchList(expr, classes, parentenv, handlers)
20: tryCatch({ temp.result <- runbaseGSEA(method = args$baseGSEA, args$voom.results, args$contrast, args$gs.annot, num.threads = args$num.threads, verbose = args$verbose) if (args$verbose) message(paste0("Running ", toupper(args$baseGSEA), " on all ", "contrasts ... COMPLETED")) else { message(args$baseGSEA, "*", appendLF = FALSE) } return(temp.result)}, error = function(e) { message(toupper(args$baseGSEA), " encountered an error -> ", e)})
21: FUN(X[[i]], ...)
22: lapply(X = S, FUN = FUN, ...)
23: doTryCatch(return(expr), name, parentenv, handler)
24: tryCatchOne(expr, names, parentenv, handlers[[1L]])
25: tryCatchList(expr, classes, parentenv, handlers)
26: 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))})
27: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
28: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
29: FUN(X[[i]], ...)
30: lapply(seq_len(cores), inner.do)
31: mclapply(args.all, runbaseGSEAParallelWorker, mc.cores = num.workers)
32: runegsea(voom.results = voom.results, contrast = contrast, limma.tops = limma.tops, baseGSEAs = baseGSEAs, combineMethod = combineMethod, combineWeights = NULL, gs.annot = gs.annot, logFC = logFC, logFC.cutoff = logFC.cutoff, fdr.cutoff = fdr.cutoff, vote.bin.width = vote.bin.width, keep.base = keep.base, num.workers = num.threads, verbose = verbose)
33: egsea.main(voom.results, contrasts, gs.annots, baseGSEAs, combineMethod, combineWeights, sort.by, report.dir, kegg.dir, logFC, symbolsMap, minSize, display.top, logFC.cutoff, fdr.cutoff, sum.plot.cutoff, sum.plot.axis, vote.bin.width, keep.base, verbose, num.threads, report, keep.limma, keep.set.scores, interactive)
34: withCallingHandlers(expr, warning = function(w) if (inherits(w, classes)) tryInvokeRestart("muffleWarning"))
35: suppressWarnings(return(egsea.main(voom.results, contrasts, gs.annots, baseGSEAs, combineMethod, combineWeights, sort.by, report.dir, kegg.dir, logFC, symbolsMap, minSize, display.top, logFC.cutoff, fdr.cutoff, sum.plot.cutoff, sum.plot.axis, vote.bin.width, keep.base, verbose, num.threads, report, keep.limma, keep.set.scores, interactive)))
36: egsea(voom.results = v, contrasts = contrasts, gs.annots = gs.annots, symbolsMap = v$genes, baseGSEAs = baseMethods, report.dir = "./il13-egsea-report", sort.by = "avg.rank", num.threads = 4, report = FALSE)
37: eval(expr, envir)
38: eval(expr, envir)
39: withVisible(eval(expr, envir))
40: withCallingHandlers(code, message = function (cnd) { watcher$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$push(cnd) switch(on_error, continue = invokeRestart("eval_continue"), stop = invokeRestart("eval_stop"), error = NULL)})
41: eval(call)
42: eval(call)
43: with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers)
44: doWithOneRestart(return(expr), restart)
45: withOneRestart(expr, restarts[[1L]])
46: withRestartList(expr, restarts[-nr])
47: doWithOneRestart(return(expr), restart)
48: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
49: withRestartList(expr, restarts)
50: withRestarts(with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
51: evaluate::evaluate(...)
52: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$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))
53: in_dir(input_dir(), expr)
54: 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$render, options)))
55: eng_r(options)
56: block_exec(params)
57: call_block(x)
58: process_group(group)
59: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (xfun::pkg_available("rlang", "1.0.0")) { if (is_R_CMD_build() || is_R_CMD_check()) { cnd = tryCatch(rlang::entrace(e), error = identity) error <<- format(cnd) } else { rlang::entrace(e) } } })
60: xfun:::handle_error(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (xfun::pkg_available("rlang", "1.0.0")) { if (is_R_CMD_build() || is_R_CMD_check()) { cnd = tryCatch(rlang::entrace(e), error = identity) error <<- format(cnd) } else { rlang::entrace(e) } } }), function(loc) { setwd(wd) write_utf8(res, output %n% stdout()) paste0("\nQuitting from ", loc, if (!is.null(error)) paste0("\n", rule(), error, "\n", rule()))}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
61: process_file(text, output)
62: (if (grepl("\\.[Rr]md$", file)) knit2html else if (grepl("\\.[Rr]rst$", file)) knit2pandoc else knit)(file, encoding = encoding, quiet = quiet, envir = globalenv(), ...)
63: engine$weave(file, quiet = quiet, encoding = enc)
64: doTryCatch(return(expr), name, parentenv, handler)
65: tryCatchOne(expr, names, parentenv, handlers[[1L]])
66: tryCatchList(expr, classes, parentenv, handlers)
67: 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)))})
68: tools::buildVignettes(dir = ".", tangle = TRUE)
An irrecoverable exception occurred. R is aborting now ...
Quitting from EGSEA.Rnw:363-371 [unnamed-chunk-13]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `runegsea()`:
! ERROR: One of the base methods failed on this dataset (safe).
Remove it and try again.
See error messages for more information.
---
Backtrace:
x
1. \-EGSEA::egsea(...)
2. +-base::suppressWarnings(...)
3. | \-base::withCallingHandlers(...)
4. \-EGSEA:::egsea.main(...)
5. \-EGSEA:::runegsea(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'EGSEA.Rnw' failed with diagnostics:
ERROR: One of the base methods failed on this dataset (safe).
Remove it and try again.
See error messages for more information.
--- failed re-building ‘EGSEA.Rnw’
SUMMARY: processing the following file failed:
‘EGSEA.Rnw’
Error: Vignette re-building failed.
Execution halted
