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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 diggit
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* checking for file ‘diggit/DESCRIPTION’ ... OK
* preparing ‘diggit’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘diggit.Rnw’ using Sweave
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: generics
Attaching package: ‘generics’
The following objects are masked from ‘package:base’:
as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
setequal, union
Attaching package: ‘BiocGenerics’
The following objects are masked from ‘package:stats’:
IQR, mad, sd, var, xtabs
The following objects are masked from ‘package:base’:
Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
unsplit, which.max, which.min
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
*** caught segfault ***
address 0x110, cause 'invalid permissions'
*** caught segfault ***
address 0x110, cause 'invalid permissions'
*** caught segfault ***
address 0x110, cause 'invalid permissions'
Traceback:
1: rowVars(x1)
2: FUN(X[[i]], ...)
3: lapply(X = S, FUN = FUN, ...)
4: doTryCatch(return(expr), name, parentenv, handler)
5: tryCatchOne(expr, names, parentenv, handlers[[1L]])
6: tryCatchList(expr, classes, parentenv, handlers)
7: 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))})
8: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
9: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
10: FUN(X[[i]], ...)
11: lapply(seq_len(cores), inner.do)
12: mclapply(1:per, function(i, x, y, repos) { expset <- cbind(x, y) repeat { sorder <- sample(ncol(expset), replace = repos) if (length(unique(sorder[1:ncol(x)])) > 1 & length(unique(sorder[-(1:ncol(x))])) > 1) break if (verbose) message("-", appendLF = FALSE) } x1 <- filterColMatrix(expset, sorder[1:ncol(x)]) y1 <- filterColMatrix(expset, sorder[-(1:ncol(x))]) largo <- rowSums(!is.na(x1)) largoy <- rowSums(!is.na(y1)) t <- ((rowMeans(x1, na.rm = TRUE) - rowMeans(y1, na.rm = TRUE))/sqrt(((largo - 1) * rowVars(x1) + (largoy - 1) * rowVars(y1))/(largo + largoy - 2))/sqrt(1/largo + 1/largoy))[, 1] t <- qnorm(pt(abs(t), largo + largoy - 2, lower.tail = FALSE), lower.tail = FALSE) * sign(t) names(t) <- rownames(x) return(t)}, x = x, y = y, repos = repos, mc.cores = cores)
13: .local(x, ...)
14: ttestNull(x, y, repos = FALSE, seed = 0, per = per, cores = cores, verbose = verbose)
15: ttestNull(x, y, repos = FALSE, seed = 0, per = per, cores = cores, verbose = verbose)
16: .local(x, ...)
17: marina(exprs(x)[, pos1], exprs(x)[, pos2], regulon = regulon, per = per, cores = cores, verbose = verbose)
18: marina(exprs(x)[, pos1], exprs(x)[, pos2], regulon = regulon, per = per, cores = cores, verbose = verbose)
19: .local(x, ...)
20: marina(exprs(x), pheno = pheno, group1 = group1, group2 = group2, mu = mu, regulon = regulon, per = per, cores = cores, verbose = verbose)
Traceback:
21: marina(exprs(x), pheno = pheno, group1 = group1, group2 = group2, mu = mu, regulon = regulon, per = per, cores = cores, verbose = verbose)
22: .local(x, ...)
23: marina(dobj, pheno = "subtype", group1 = "MES", group2 = "PN", cores = cores, verbose = FALSE)
24: marina(dobj, pheno = "subtype", group1 = "MES", group2 = "PN", cores = cores, verbose = FALSE)
25: eval(expr, .GlobalEnv)
26: eval(expr, .GlobalEnv)
27: withVisible(eval(expr, .GlobalEnv))
28: doTryCatch(return(expr), name, parentenv, handler) 1:
rowVars(x1)
2: 29: FUN(X[[i]], ...)
tryCatchOne(expr, names, parentenv, handlers[[1L]])
30: tryCatchList(expr, classes, parentenv, handlers) 3: lapply(X = S, FUN = FUN, ...)
4:
Traceback:
31: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { 1: rowVars(x1) if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L)
2: dcall <- deparse(call, nlines = 1L) prefix <- paste("Error in", dcall, ": ")FUN(X[[i]], ...)
3: doTryCatch(return(expr), name, parentenv, handler)
lapply(X = S, FUN = FUN, ...)
5: tryCatchOne(expr, names, parentenv, handlers[[1L]])
6: LONG <- 75L 4: sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")doTryCatch(return(expr), name, parentenv, handler)
if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) 5: tryCatchOne(expr, names, parentenv, handlers[[1L]])
6: prefix <- paste0(prefix, "\n ") } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L]))tryCatchList(expr, classes, parentenv, handlers)
7: if (!silent && isTRUE(getOption("show.error.messages"))) {tryCatchList(expr, classes, parentenv, handlers) cat(msg, file = outFile)tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) {
.Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e)) 7: tryCatch(expr, error = function(e) { if (identical(call[[1L]], quote(doTryCatch))) }) call <- conditionCall(e)
32: 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)) try(withVisible(eval(expr, .GlobalEnv)), silent = TRUE)
33: call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L) prefix <- paste("Error in", dcall, ": ") LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]]evalFunc(ce, options)
34: tryCatchList(expr, classes, parentenv, handlers) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], prefix <- paste0(prefix, "\n ")
} type = "b") if (w > LONG) else prefix <- "Error : "35: tryCatch(evalFunc(ce, options), finally = { msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) cat("\n") prefix <- paste0(prefix, "\n ") sink()}) } else prefix <- "Error : "
36: driver$runcode(drobj, chunk, chunkopts)
37: utils::Sweave(...) msg <- paste0(prefix, conditionMessage(e), "\n")
38: .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) {engine$weave(file, quiet = quiet, encoding = enc)
39: .Internal(printDeferredWarnings())doTryCatch(return(expr), name, parentenv, handler)
} invisible(structure(msg, class = "try-error", condition = e))})
40: tryCatchOne(expr, names, parentenv, handlers[[1L]])
41: 8: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
9: tryCatchList(expr, classes, parentenv, handlers)sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
42: cat(msg, file = outFile)tryCatch({10: FUN(X[[i]], ...)
.Internal(printDeferredWarnings()) engine$weave(file, quiet = quiet, encoding = enc) setwd(startdir) output <- find_vignette_product(name, by = "weave", engine = engine)11: lapply(seq_len(cores), inner.do)
12: if (!have.makefile && vignette_is_tex(output)) { texi2pdf(file = output, clean = FALSE, quiet = quiet)mclapply(1:per, function(i, x, y, repos) { } output <- find_vignette_product(name, by = "texi2pdf", engine = engine) invisible(structure(msg, class = "try-error", condition = e))})
8: try(lapply(X = S, FUN = FUN, ...), silent = TRUE) } outputs <- c(outputs, output) expset <- cbind(x, y)}, error = function(e) {
9: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) repeat { thisOK <<- FALSE
fails <<- c(fails, file) sorder <- sample(ncol(expset), replace = repos) message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", 10: FUN(X[[i]], ...)
11: lapply(seq_len(cores), inner.do)
12: if (length(unique(sorder[1:ncol(x)])) > 1 & length(unique(sorder[-(1:ncol(x))])) > file, conditionMessage(e))) 1) mclapply(1:per, function(i, x, y, repos) { expset <- cbind(x, y) repeat {}) break
43: if (verbose) message("-", appendLF = FALSE) sorder <- sample(ncol(expset), replace = repos)tools::buildVignettes(dir = ".", tangle = TRUE) }
An irrecoverable exception occurred. R is aborting now ...
if (length(unique(sorder[1:ncol(x)])) > 1 & length(unique(sorder[-(1:ncol(x))])) > 1) break x1 <- filterColMatrix(expset, sorder[1:ncol(x)]) y1 <- filterColMatrix(expset, sorder[-(1:ncol(x))]) largo <- rowSums(!is.na(x1)) largoy <- rowSums(!is.na(y1)) t <- ((rowMeans(x1, na.rm = TRUE) - rowMeans(y1, na.rm = TRUE))/sqrt(((largo - 1) * rowVars(x1) + (largoy - 1) * rowVars(y1))/(largo + if (verbose) largoy - 2))/sqrt(1/largo + 1/largoy))[, 1] message("-", appendLF = FALSE) } x1 <- filterColMatrix(expset, sorder[1:ncol(x)]) y1 <- filterColMatrix(expset, sorder[-(1:ncol(x))]) t <- qnorm(pt(abs(t), largo + largoy - 2, lower.tail = FALSE), largo <- rowSums(!is.na(x1)) lower.tail = FALSE) * sign(t) names(t) <- rownames(x) return(t)}, x = x, y = y, repos = repos, mc.cores = cores) largoy <- rowSums(!is.na(y1))
t <- ((rowMeans(x1, na.rm = TRUE) - rowMeans(y1, na.rm = TRUE))/sqrt(((largo - 13: 1) * rowVars(x1) + (largoy - 1) * rowVars(y1))/(largo + .local(x, ...)
14: largoy - 2))/sqrt(1/largo + 1/largoy))[, 1]ttestNull(x, y, repos = FALSE, seed = 0, per = per, cores = cores, t <- qnorm(pt(abs(t), largo + largoy - 2, lower.tail = FALSE), lower.tail = FALSE) * sign(t) names(t) <- rownames(x) verbose = verbose) return(t)}, x = x, y = y, repos = repos, mc.cores = cores)
13: .local(x, ...)15:
14: ttestNull(x, y, repos = FALSE, seed = 0, per = per, cores = cores, verbose = verbose)
15: ttestNull(x, y, repos = FALSE, seed = 0, per = per, cores = cores, verbose = verbose)
16: .local(x, ...)
17: marina(exprs(x)[, pos1], exprs(x)[, pos2], regulon = regulon, per = per, cores = cores, verbose = verbose)
18: marina(exprs(x)[, pos1], exprs(x)[, pos2], regulon = regulon, per = per, cores = cores, verbose = verbose)
19: .local(x, ...)
20: marina(exprs(x), pheno = pheno, group1 = group1, group2 = group2, mu = mu, regulon = regulon, per = per, cores = cores, verbose = verbose)
21: marina(exprs(x), pheno = pheno, group1 = group1, group2 = group2, ttestNull(x, y, repos = FALSE, seed = 0, per = per, cores = cores, verbose = verbose)
mu = mu, regulon = regulon, per = per, cores = cores, verbose = verbose)
22: 16: .local(x, ...)
.local(x, ...)
23: 17: marina(exprs(x)[, pos1], exprs(x)[, pos2], regulon = regulon, per = per, cores = cores, verbose = verbose)marina(dobj, pheno = "subtype", group1 = "MES", group2 = "PN", cores = cores, verbose = FALSE)
18: marina(exprs(x)[, pos1], exprs(x)[, pos2], regulon = regulon, 24: marina(dobj, pheno = "subtype", group1 = "MES", group2 = "PN", cores = cores, verbose = FALSE) per = per, cores = cores, verbose = verbose)
19:
25: eval(expr, .GlobalEnv).local(x, ...)
20:
26: eval(expr, .GlobalEnv)marina(exprs(x), pheno = pheno, group1 = group1, group2 = group2, mu = mu, regulon = regulon, per = per, cores = cores, verbose = verbose)
27: withVisible(eval(expr, .GlobalEnv))21: marina(exprs(x), pheno = pheno, group1 = group1, group2 = group2, mu = mu, regulon = regulon, per = per, cores = cores, verbose = verbose)
28: doTryCatch(return(expr), name, parentenv, handler)
22: .local(x, ...)
29: tryCatchOne(expr, names, parentenv, handlers[[1L]])
23: marina(dobj, pheno = "subtype", group1 = "MES", group2 = "PN",
30: tryCatchList(expr, classes, parentenv, handlers) cores = cores, verbose = FALSE)
24:
31: tryCatch(expr, error = function(e) {marina(dobj, pheno = "subtype", group1 = "MES", group2 = "PN", cores = cores, verbose = FALSE)
25: eval(expr, .GlobalEnv)
call <- conditionCall(e)26: if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L)eval(expr, .GlobalEnv) dcall <- deparse(call, nlines = 1L)
27: withVisible(eval(expr, .GlobalEnv))
28: doTryCatch(return(expr), name, parentenv, handler)
29: prefix <- paste("Error in", dcall, ": ")tryCatchOne(expr, names, parentenv, handlers[[1L]])
30: tryCatchList(expr, classes, parentenv, handlers) 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"))) {31: cat(msg, file = outFile) .Internal(printDeferredWarnings()) }tryCatch(expr, error = function(e) { invisible(structure(msg, class = "try-error", condition = e))}) call <- conditionCall(e)
32: try(withVisible(eval(expr, .GlobalEnv)), silent = TRUE) if (!is.null(call)) {
if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L)33: prefix <- paste("Error in", dcall, ": ") LONG <- 75LevalFunc(ce, options)
34: tryCatchList(expr, classes, parentenv, handlers)
35: sm <- strsplit(conditionMessage(e), "\n")[[1L]]tryCatch(evalFunc(ce, options), finally = { 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))})
32: try(withVisible(eval(expr, .GlobalEnv)), silent = TRUE)
33: evalFunc(ce, options)
34: tryCatchList(expr, classes, parentenv, handlers)
35: tryCatch(evalFunc(ce, options), finally = { cat("\n") sink() cat("\n") sink()})
36: driver$runcode(drobj, chunk, chunkopts)
37: utils::Sweave(...)
38: engine$weave(file, quiet = quiet, encoding = enc)
39: doTryCatch(return(expr), name, parentenv, handler)
40: tryCatchOne(expr, names, parentenv, handlers[[1L]])
})41: tryCatchList(expr, classes, parentenv, handlers)
42:
36: driver$runcode(drobj, chunk, chunkopts)
37: utils::Sweave(...)tryCatch({
38: engine$weave(file, quiet = quiet, encoding = enc)engine$weave(file, quiet = quiet, encoding = enc)
39: doTryCatch(return(expr), name, parentenv, handler)
40: tryCatchOne(expr, names, parentenv, handlers[[1L]])
41:
*** caught segfault ***
address 0x110, cause 'invalid permissions'
tryCatchList(expr, classes, parentenv, handlers)
42: 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)))})
43: tools::buildVignettes(dir = ".", tangle = TRUE)
An irrecoverable exception occurred. R is aborting now ...
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)))})
43: tools::buildVignettes(dir = ".", tangle = TRUE)
An irrecoverable exception occurred. R is aborting now ...
Traceback:
1: rowVars(x1)
2: FUN(X[[i]], ...)
3: lapply(X = S, FUN = FUN, ...)
4: doTryCatch(return(expr), name, parentenv, handler)
5: tryCatchOne(expr, names, parentenv, handlers[[1L]])
6: tryCatchList(expr, classes, parentenv, handlers)
7: 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))})
8: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
9: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
10: FUN(X[[i]], ...)
11: lapply(seq_len(cores), inner.do)
12: mclapply(1:per, function(i, x, y, repos) { expset <- cbind(x, y) repeat { sorder <- sample(ncol(expset), replace = repos) if (length(unique(sorder[1:ncol(x)])) > 1 & length(unique(sorder[-(1:ncol(x))])) > 1) break if (verbose) message("-", appendLF = FALSE) } x1 <- filterColMatrix(expset, sorder[1:ncol(x)]) y1 <- filterColMatrix(expset, sorder[-(1:ncol(x))]) largo <- rowSums(!is.na(x1)) largoy <- rowSums(!is.na(y1)) t <- ((rowMeans(x1, na.rm = TRUE) - rowMeans(y1, na.rm = TRUE))/sqrt(((largo - 1) * rowVars(x1) + (largoy - 1) * rowVars(y1))/(largo + largoy - 2))/sqrt(1/largo + 1/largoy))[, 1] t <- qnorm(pt(abs(t), largo + largoy - 2, lower.tail = FALSE), lower.tail = FALSE) * sign(t) names(t) <- rownames(x) return(t)}, x = x, y = y, repos = repos, mc.cores = cores)
13: .local(x, ...)
14: ttestNull(x, y, repos = FALSE, seed = 0, per = per, cores = cores, verbose = verbose)
15: ttestNull(x, y, repos = FALSE, seed = 0, per = per, cores = cores, verbose = verbose)
16: .local(x, ...)
17: marina(exprs(x)[, pos1], exprs(x)[, pos2], regulon = regulon, per = per, cores = cores, verbose = verbose)
18: marina(exprs(x)[, pos1], exprs(x)[, pos2], regulon = regulon, per = per, cores = cores, verbose = verbose)
19: .local(x, ...)
20: marina(exprs(x), pheno = pheno, group1 = group1, group2 = group2, mu = mu, regulon = regulon, per = per, cores = cores, verbose = verbose)
21: marina(exprs(x), pheno = pheno, group1 = group1, group2 = group2, mu = mu, regulon = regulon, per = per, cores = cores, verbose = verbose)
22: .local(x, ...)
23: marina(dobj, pheno = "subtype", group1 = "MES", group2 = "PN", cores = cores, verbose = FALSE)
24: marina(dobj, pheno = "subtype", group1 = "MES", group2 = "PN", cores = cores, verbose = FALSE)
25: eval(expr, .GlobalEnv)
26: eval(expr, .GlobalEnv)
27: withVisible(eval(expr, .GlobalEnv))
28: doTryCatch(return(expr), name, parentenv, handler)
29: tryCatchOne(expr, names, parentenv, handlers[[1L]])
30: tryCatchList(expr, classes, parentenv, handlers)
31: 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))})
32: try(withVisible(eval(expr, .GlobalEnv)), silent = TRUE)
33: evalFunc(ce, options)
34: tryCatchList(expr, classes, parentenv, handlers)
35: tryCatch(evalFunc(ce, options), finally = { cat("\n") sink()})
36: driver$runcode(drobj, chunk, chunkopts)
37: utils::Sweave(...)
38: engine$weave(file, quiet = quiet, encoding = enc)
39: doTryCatch(return(expr), name, parentenv, handler)
40: tryCatchOne(expr, names, parentenv, handlers[[1L]])
41: tryCatchList(expr, classes, parentenv, handlers)
42: tryCatch({ engine$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)))})
43: tools::buildVignettes(dir = ".", tangle = TRUE)
An irrecoverable exception occurred. R is aborting now ...
Warning in mclapply(1:per, function(i, x, y, repos) { :
scheduled cores 1, 2, 3, 4 did not deliver results, all values of the jobs will be affected
Error: processing vignette 'diggit.Rnw' failed with diagnostics:
chunk 10
Error in `colnames<-`(`*tmp*`, value = 1:1000) :
attempt to set 'colnames' on an object with less than two dimensions
--- failed re-building ‘diggit.Rnw’
SUMMARY: processing the following file failed:
‘diggit.Rnw’
Error: Vignette re-building failed.
Execution halted
