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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 xcore
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* checking for file ‘xcore/DESCRIPTION’ ... OK
* preparing ‘xcore’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘xcore_vignette.Rmd’ using rmarkdown
*** caught segfault ***
address 0x110, cause 'invalid permissions'
Traceback:
1: ridgePvals(x = x_, y = y_, beta = beta, lambda = lambda, standardizex = FALSE, svdX = svdX[[xnm_]])
2: eval(c.expr, envir = args, enclos = envir)
3: eval(c.expr, envir = args, enclos = envir)
4: doTryCatch(return(expr), name, parentenv, handler)
5: tryCatchOne(expr, names, parentenv, handlers[[1L]])
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatch(eval(c.expr, envir = args, enclos = envir), error = function(e) e)
8: FUN(X[[i]], ...)
9: lapply(X = S, FUN = FUN, ...)
10: doTryCatch(return(expr), name, parentenv, handler)
11: tryCatchOne(expr, names, parentenv, handlers[[1L]])
12: tryCatchList(expr, classes, parentenv, handlers)
13: 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))})
14: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
15: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
16: FUN(X[[i]], ...)
17: lapply(seq_len(cores), inner.do)
18: mclapply(argsList, FUN, mc.preschedule = preschedule, mc.set.seed = set.seed, mc.silent = silent, mc.cores = cores)
19: e$fun(obj, substitute(ex), parent.frame(), e$data)
20: foreach::foreach(x_ = iterators::iter(suppressWarnings(suppressMessages(mae[, , xnames]))), xnm_ = xnames, .inorder = TRUE, .final = function(x) setNames(x, xnames)) %:% foreach::foreach(y_ = iterators::iter(mae[[yname]][, names(groups), drop = FALSE]), id_ = names(groups), .inorder = TRUE, .final = function(x) setNames(x, names(groups)), .export = "ridgePvals") %dopar% { y_ <- y_ - mae[[uname]] lambda <- regression_models[[xnm_]][[id_]]$lambda.min beta <- coef(regression_models[[xnm_]][[id_]], s = lambda) beta <- beta[-1, ] ridgePvals(x = x_, y = y_, beta = beta, lambda = lambda, standardizex = FALSE, svdX = svdX[[xnm_]]) }
21: modelGeneExpression_significance_testing_wraper(mae = mae, yname = yname, uname = uname, xnames = xnames, groups = groups, standardize = standardize, regression_models = regression_models)
22: modelGeneExpression(mae = mae, xnames = "remap", nfolds = 5)
23: eval(expr, envir)
24: eval(expr, envir)
25: withVisible(eval(expr, envir))
26: withCallingHandlers(code, message = function (cnd) { watcher$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$push(cnd) switch(on_error, continue = invokeRestart("eval_continue"), stop = invokeRestart("eval_stop"), error = NULL)})
27: eval(call)
28: eval(call)
29: with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers)
30: doWithOneRestart(return(expr), restart)
31: withOneRestart(expr, restarts[[1L]])
32: withRestartList(expr, restarts[-nr])
33: doWithOneRestart(return(expr), restart)
34: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
35: withRestartList(expr, restarts)
36: withRestarts(with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
37: evaluate::evaluate(...)
38: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$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))
39: in_dir(input_dir(), expr)
40: 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$render, options)))
41: eng_r(options)
42: block_exec(params)
43: call_block(x)
44: process_group(group)
45: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (xfun::pkg_available("rlang", "1.0.0")) { if (is_R_CMD_build() || is_R_CMD_check()) { cnd = tryCatch(rlang::entrace(e), error = identity) error <<- format(cnd) } else { rlang::entrace(e) } } })
46: xfun:::handle_error(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (xfun::pkg_available("rlang", "1.0.0")) { if (is_R_CMD_build() || is_R_CMD_check()) { cnd = tryCatch(rlang::entrace(e), error = identity) error <<- format(cnd) } else { rlang::entrace(e) } } }), function(loc) { setwd(wd) write_utf8(res, output %n% stdout()) paste0("\nQuitting from ", loc, if (!is.null(error)) paste0("\n", rule(), error, "\n", rule()))}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
47: process_file(text, output)
48: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
49: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...)
50: vweave_rmarkdown(...)
51: engine$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: ridgePvals(x = x_, y = y_, beta = beta, lambda = lambda, standardizex = FALSE, svdX = svdX[[xnm_]])
2: eval(c.expr, envir = args, enclos = envir)
3: eval(c.expr, envir = args, enclos = envir)
4: doTryCatch(return(expr), name, parentenv, handler)
5: tryCatchOne(expr, names, parentenv, handlers[[1L]])
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatch(eval(c.expr, envir = args, enclos = envir), error = function(e) e)
8: FUN(X[[i]], ...)
9: lapply(X = S, FUN = FUN, ...)
10: doTryCatch(return(expr), name, parentenv, handler)
11: tryCatchOne(expr, names, parentenv, handlers[[1L]])
12: tryCatchList(expr, classes, parentenv, handlers)
13: 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))})
14: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
15: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
16: FUN(X[[i]], ...)
17: lapply(seq_len(cores), inner.do)
18: mclapply(argsList, FUN, mc.preschedule = preschedule, mc.set.seed = set.seed, mc.silent = silent, mc.cores = cores)
19: e$fun(obj, substitute(ex), parent.frame(), e$data)
20: foreach::foreach(x_ = iterators::iter(suppressWarnings(suppressMessages(mae[, , xnames]))), xnm_ = xnames, .inorder = TRUE, .final = function(x) setNames(x, xnames)) %:% foreach::foreach(y_ = iterators::iter(mae[[yname]][, names(groups), drop = FALSE]), id_ = names(groups), .inorder = TRUE, .final = function(x) setNames(x, names(groups)), .export = "ridgePvals") %dopar% { y_ <- y_ - mae[[uname]] lambda <- regression_models[[xnm_]][[id_]]$lambda.min beta <- coef(regression_models[[xnm_]][[id_]], s = lambda) beta <- beta[-1, ] ridgePvals(x = x_, y = y_, beta = beta, lambda = lambda, standardizex = FALSE, svdX = svdX[[xnm_]]) }
21: modelGeneExpression_significance_testing_wraper(mae = mae, yname = yname, uname = uname, xnames = xnames, groups = groups, standardize = standardize, regression_models = regression_models)
22: modelGeneExpression(mae = mae, xnames = "remap", nfolds = 5)
23: eval(expr, envir)
24: eval(expr, envir)
25: withVisible(eval(expr, envir))
26: 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)})
27: eval(call)
28: eval(call)
29: with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers)
30: doWithOneRestart(return(expr), restart)
31: withOneRestart(expr, restarts[[1L]])
32: withRestartList(expr, restarts[-nr])
33: doWithOneRestart(return(expr), restart)
34: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
35: withRestartList(expr, restarts)
36: withRestarts(with_handlers({ for (expr in tle$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)
37: evaluate::evaluate(...)
38: 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$render, options))
39: in_dir(input_dir(), expr)
40: in_input_dir(evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$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)))
41: eng_r(options)
42: block_exec(params)
43: call_block(x)
44: process_group(group)
45: 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) } } })
46: 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)
47: process_file(text, output)
48: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
49: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...)
50: vweave_rmarkdown(...)
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 ...
Quitting from xcore_vignette.Rmd:226-238 [unnamed-chunk-15]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `FUN()`:
! pvalues elements must be instances of class data.frame
---
Backtrace:
▆
1. └─xcore::modelGeneExpression(mae = mae, xnames = "remap", nfolds = 5)
2. └─base::lapply(pvalues, repVarianceWeightedAvgZscore, groups = groups)
3. └─xcore (local) FUN(X[[i]], ...)
4. └─base::stopifnot(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'xcore_vignette.Rmd' failed with diagnostics:
pvalues elements must be instances of class data.frame
--- failed re-building ‘xcore_vignette.Rmd’
SUMMARY: processing the following file failed:
‘xcore_vignette.Rmd’
Error: Vignette re-building failed.
Execution halted
