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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, ...)
*** caught segfault ***
20:
Traceback:
Traceback:
address 0x110, cause 'invalid permissions'
marina(exprs(x), pheno = pheno, group1 = group1, group2 = group2, 1: 1: rowVars(x1)
rowVars(x1) mu = mu, regulon = regulon, per = per, cores = cores, verbose = verbose)
2: FUN(X[[i]], ...)
2: FUN(X[[i]], ...)
21: 3: marina(exprs(x), pheno = pheno, group1 = group1, group2 = group2, mu = mu, regulon = regulon, per = per, cores = cores, verbose = verbose) 3: lapply(X = S, FUN = FUN, ...)lapply(X = S, FUN = FUN, ...)
4: doTryCatch(return(expr), name, parentenv, handler)
5: tryCatchOne(expr, names, parentenv, handlers[[1L]])22: .local(x, ...)
23: 4: doTryCatch(return(expr), name, parentenv, handler)
5: tryCatchOne(expr, names, parentenv, handlers[[1L]])
6: tryCatchList(expr, classes, parentenv, handlers)marina(dobj, pheno = "subtype", group1 = "MES", group2 = "PN", 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) cores = cores, verbose = FALSE)
.Internal(printDeferredWarnings()) 7: } 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]], ...)
tryCatch(expr, error = function(e) { call <- conditionCall(e)24: 11: if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L)marina(dobj, pheno = "subtype", group1 = "MES", group2 = "PN", lapply(seq_len(cores), inner.do) dcall <- deparse(call, nlines = 1L)
12: mclapply(1:per, function(i, x, y, repos) { expset <- cbind(x, y) repeat { sorder <- sample(ncol(expset), replace = repos) prefix <- paste("Error in", dcall, ": ") cores = cores, verbose = FALSE) if (length(unique(sorder[1:ncol(x)])) > 1 & length(unique(sorder[-(1:ncol(x))])) > 1) break if (verbose) message("-", appendLF = FALSE) LONG <- 75L
sm <- strsplit(conditionMessage(e), "\n")[[1L]]25: } w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) eval(expr, .GlobalEnv) x1 <- filterColMatrix(expset, sorder[1:ncol(x)])
26: y1 <- filterColMatrix(expset, sorder[-(1:ncol(x))]) largo <- rowSums(!is.na(x1)) largoy <- rowSums(!is.na(y1))eval(expr, .GlobalEnv) 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]))
t <- ((rowMeans(x1, na.rm = TRUE) - rowMeans(y1, na.rm = TRUE))/sqrt(((largo - 27: 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)
if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) .Internal(printDeferredWarnings())withVisible(eval(expr, .GlobalEnv))
13: }.local(x, ...)
14: ttestNull(x, y, repos = FALSE, seed = 0, per = per, cores = cores, verbose = verbose)
Traceback:
invisible(structure(msg, class = "try-error", condition = e)) 1: rowVars(x1)15:
2: ttestNull(x, y, repos = FALSE, seed = 0, per = per, cores = cores, FUN(X[[i]], ...)
3: verbose = verbose)
})28: lapply(X = S, FUN = FUN, ...)16:
.local(x, ...) 4: doTryCatch(return(expr), name, parentenv, handler)doTryCatch(return(expr), name, parentenv, handler)
5: tryCatchOne(expr, names, parentenv, handlers[[1L]])
6:
8: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)tryCatchList(expr, classes, parentenv, handlers)
7: 29:
9: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
10: 17: marina(exprs(x)[, pos1], exprs(x)[, pos2], regulon = regulon, per = per, cores = cores, verbose = verbose)
FUN(X[[i]], ...)18:
11: marina(exprs(x)[, pos1], exprs(x)[, pos2], regulon = regulon, per = per, cores = cores, verbose = verbose)
19: .local(x, ...)tryCatchOne(expr, names, parentenv, handlers[[1L]])
20: tryCatch(expr, error = function(e) {30: tryCatchList(expr, classes, parentenv, handlers)marina(exprs(x), pheno = pheno, group1 = group1, group2 = group2,
31: lapply(seq_len(cores), inner.do)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) mu = mu, regulon = regulon, per = per, cores = cores, verbose = verbose)
call <- conditionCall(e) prefix <- paste("Error in", dcall, ": ") LONG <- 75L12: 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], mclapply(1:per, function(i, x, y, repos) {
type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ")21: }marina(exprs(x), pheno = pheno, group1 = group1, group2 = group2, expset <- cbind(x, y) else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") repeat { if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) sorder <- sample(ncol(expset), replace = repos) if (length(unique(sorder[1:ncol(x)])) > 1 & length(unique(sorder[-(1:ncol(x))])) > 1) break dcall <- deparse(call, nlines = 1L) .Internal(seterrmessage(msg[1L])) if (verbose) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) .Internal(printDeferredWarnings()) } 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], message("-", appendLF = FALSE) invisible(structure(msg, class = "try-error", condition = e)) type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ") }}) } x1 <- filterColMatrix(expset, sorder[1:ncol(x)]) mu = mu, regulon = regulon, per = per, cores = cores, verbose = verbose)
22: .local(x, ...)
23: marina(dobj, pheno = "subtype", group1 = "MES", group2 = "PN", y1 <- filterColMatrix(expset, sorder[-(1:ncol(x))]) largo <- rowSums(!is.na(x1)) cores = cores, verbose = FALSE)
else prefix <- "Error : "24: largoy <- rowSums(!is.na(y1))marina(dobj, pheno = "subtype", group1 = "MES", group2 = "PN", cores = cores, verbose = FALSE)
t <- ((rowMeans(x1, na.rm = TRUE) - rowMeans(y1, na.rm = TRUE))/sqrt(((largo - 25: eval(expr, .GlobalEnv)
26: eval(expr, .GlobalEnv)
27: 1) * rowVars(x1) + (largoy - 1) * rowVars(y1))/(largo + withVisible(eval(expr, .GlobalEnv))
msg <- paste0(prefix, conditionMessage(e), "\n") largoy - 2))/sqrt(1/largo + 1/largoy))[, 1]32: try(withVisible(eval(expr, .GlobalEnv)), silent = TRUE)
33: evalFunc(ce, options)
.Internal(seterrmessage(msg[1L])) t <- qnorm(pt(abs(t), largo + largoy - 2, lower.tail = FALSE), lower.tail = FALSE) * sign(t) names(t) <- rownames(x)34: return(t)tryCatchList(expr, classes, parentenv, handlers) if (!silent && isTRUE(getOption("show.error.messages"))) {
35: }, x = x, y = y, repos = repos, mc.cores = cores) cat(msg, file = outFile) .Internal(printDeferredWarnings())
tryCatch(evalFunc(ce, options), finally = {28: doTryCatch(return(expr), name, parentenv, handler)
} cat("\n") sink()13: .local(x, ...)
29: })14: ttestNull(x, y, repos = FALSE, seed = 0, per = per, cores = cores, verbose = verbose)
15: invisible(structure(msg, class = "try-error", condition = e))})
tryCatchOne(expr, names, parentenv, handlers[[1L]])
36: driver$runcode(drobj, chunk, chunkopts)
30: tryCatchList(expr, classes, parentenv, handlers)
31: ttestNull(x, y, repos = FALSE, seed = 0, per = per, cores = cores, verbose = verbose)
tryCatch(expr, error = function(e) {16: .local(x, ...)
17: marina(exprs(x)[, pos1], exprs(x)[, pos2], regulon = regulon, per = per, cores = cores, verbose = verbose)
18: marina(exprs(x)[, pos1], exprs(x)[, pos2], regulon = regulon, per = per, cores = cores, verbose = verbose)
19: .local(x, ...) call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L)37: 8: utils::Sweave(...)
38: engine$weave(file, quiet = quiet, encoding = enc)
prefix <- paste("Error in", dcall, ": ") LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]]try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
9: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))39: 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) prefix <- paste0(prefix, "\n ") } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n")20: marina(exprs(x), pheno = pheno, group1 = group1, group2 = group2, mu = mu, regulon = regulon, per = per, cores = cores, verbose = verbose)
21:
40: .Internal(seterrmessage(msg[1L]))
marina(exprs(x), pheno = pheno, group1 = group1, group2 = group2, tryCatchOne(expr, names, parentenv, handlers[[1L]]) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile)
10: .Internal(printDeferredWarnings()) }FUN(X[[i]], ...)
11: lapply(seq_len(cores), inner.do)
12: 41: invisible(structure(msg, class = "try-error", condition = e))mclapply(1:per, function(i, x, y, repos) {}) mu = mu, regulon = regulon, per = per, cores = cores, verbose = verbose) expset <- cbind(x, y)
32: repeat {tryCatchList(expr, classes, parentenv, handlers)try(withVisible(eval(expr, .GlobalEnv)), silent = TRUE)
sorder <- sample(ncol(expset), replace = repos) if (length(unique(sorder[1:ncol(x)])) > 1 & length(unique(sorder[-(1:ncol(x))])) > 42: tryCatch({ engine$weave(file, quiet = quiet, encoding = enc)
1) break setwd(startdir) output <- find_vignette_product(name, by = "weave", engine = engine) if (verbose) message("-", appendLF = FALSE) } x1 <- filterColMatrix(expset, sorder[1:ncol(x)])22: 33: .local(x, ...) if (!have.makefile && vignette_is_tex(output)) { y1 <- filterColMatrix(expset, sorder[-(1:ncol(x))])evalFunc(ce, options)
23: marina(dobj, pheno = "subtype", group1 = "MES", group2 = "PN", largo <- rowSums(!is.na(x1))
largoy <- rowSums(!is.na(y1)) t <- ((rowMeans(x1, na.rm = TRUE) - rowMeans(y1, na.rm = TRUE))/sqrt(((largo - 1) * rowVars(x1) + (largoy - 1) * rowVars(y1))/(largo + 34: tryCatchList(expr, classes, parentenv, handlers) largoy - 2))/sqrt(1/largo + 1/largoy))[, 1] t <- qnorm(pt(abs(t), largo + largoy - 2, lower.tail = FALSE), lower.tail = FALSE) * sign(t) names(t) <- rownames(x) return(t)}, x = x, y = y, repos = repos, mc.cores = cores)
13: .local(x, ...) texi2pdf(file = output, clean = FALSE, quiet = quiet) cores = cores, verbose = FALSE)
35: tryCatch(evalFunc(ce, options), finally = { cat("\n")
output <- find_vignette_product(name, by = "texi2pdf", sink()})
24:
marina(dobj, pheno = "subtype", group1 = "MES", group2 = "PN", 14: 36: driver$runcode(drobj, chunk, chunkopts)
37: utils::Sweave(...)
38: engine$weave(file, quiet = quiet, encoding = enc)
39: doTryCatch(return(expr), name, parentenv, handler) engine = engine)
40: tryCatchOne(expr, names, parentenv, handlers[[1L]])ttestNull(x, y, repos = FALSE, seed = 0, per = per, cores = cores, verbose = verbose)
41: tryCatchList(expr, classes, parentenv, handlers)
15: cores = cores, verbose = FALSE)
25: } outputs <- c(outputs, output)}, error = function(e) { thisOK <<- FALSE fails <<- c(fails, file)ttestNull(x, y, repos = FALSE, seed = 0, per = per, cores = cores, verbose = verbose)
eval(expr, .GlobalEnv)42:
26: tryCatch({ engine$weave(file, quiet = quiet, encoding = enc) message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", file, conditionMessage(e))) setwd(startdir) output <- find_vignette_product(name, by = "weave", engine = engine)16: eval(expr, .GlobalEnv)
27: withVisible(eval(expr, .GlobalEnv))
if (!have.makefile && vignette_is_tex(output)) {28: doTryCatch(return(expr), name, parentenv, handler)
29: tryCatchOne(expr, names, parentenv, handlers[[1L]]).local(x, ...)
17:
30: })
43: marina(exprs(x)[, pos1], exprs(x)[, pos2], regulon = regulon, texi2pdf(file = output, clean = FALSE, quiet = quiet) output <- find_vignette_product(name, by = "texi2pdf", engine = engine) } outputs <- c(outputs, output)tools::buildVignettes(dir = ".", tangle = TRUE)tryCatchList(expr, classes, parentenv, handlers)
}, error = function(e) {
thisOK <<- FALSE fails <<- c(fails, file)31: An irrecoverable exception occurred. R is aborting now ...
message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", tryCatch(expr, error = function(e) { file, conditionMessage(e))) per = per, cores = cores, verbose = verbose)
18: call <- conditionCall(e)})
marina(exprs(x)[, pos1], exprs(x)[, pos2], regulon = regulon, 43: tools::buildVignettes(dir = ".", tangle = TRUE)
An irrecoverable exception occurred. R is aborting now ...
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 ") } per = per, cores = cores, verbose = verbose) 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: 19: driver$runcode(drobj, chunk, chunkopts).local(x, ...)
20: marina(exprs(x), pheno = pheno, group1 = group1, group2 = group2, mu = mu, regulon = regulon, per = per, cores = cores, verbose = verbose)
21: marina(exprs(x), pheno = pheno, group1 = group1, group2 = group2, mu = mu, regulon = regulon, per = per, cores = cores, verbose = verbose)
22: .local(x, ...)
23: marina(dobj, pheno = "subtype", group1 = "MES", group2 = "PN", cores = cores, verbose = FALSE)
24: 37: utils::Sweave(...)marina(dobj, pheno = "subtype", group1 = "MES", group2 = "PN", cores = cores, verbose = FALSE)
25: eval(expr, .GlobalEnv)
26: eval(expr, .GlobalEnv)
27: withVisible(eval(expr, .GlobalEnv))
38: engine$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$weave(file, quiet = quiet, encoding = enc) setwd(startdir)28: output <- find_vignette_product(name, by = "weave", engine = engine) if (!have.makefile && vignette_is_tex(output)) {doTryCatch(return(expr), name, parentenv, handler) texi2pdf(file = output, clean = FALSE, quiet = quiet) output <- find_vignette_product(name, by = "texi2pdf", engine = engine) } outputs <- c(outputs, output)}, error = function(e) { thisOK <<- FALSE fails <<- c(fails, file) message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", file, conditionMessage(e)))})
43: tools::buildVignettes(dir = ".", tangle = TRUE)
29: An irrecoverable exception occurred. R is aborting now ...
tryCatchOne(expr, names, parentenv, handlers[[1L]])
30: tryCatchList(expr, classes, parentenv, handlers)
31: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L) prefix <- paste("Error in", dcall, ": ") LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ") } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))})
32: try(withVisible(eval(expr, .GlobalEnv)), silent = TRUE)
33: evalFunc(ce, options)
34: tryCatchList(expr, classes, parentenv, handlers)
35: tryCatch(evalFunc(ce, options), finally = { cat("\n") sink()})
36: driver$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
