TSSi 1.4.0
Julian Gehring
| Snapshot Date: 2013-03-24 16:21:20 -0700 (Sun, 24 Mar 2013) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_11/madman/Rpacks/TSSi | | Last Changed Rev: 70050 / Revision: 74773 | | Last Changed Date: 2012-10-01 15:16:24 -0700 (Mon, 01 Oct 2012) |
| lamb1 | Linux (openSUSE 12.1) / x86_64 | [ ERROR ] | skipped | |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK |
| perceval | Mac OS X Leopard (10.5.8) / i386 | OK | OK | OK |
* checking for file ‘TSSi/DESCRIPTION’ ... OK
* preparing ‘TSSi’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to re-build vignettes
* creating vignettes ...sh: line 1: 3682 Segmentation fault '/home/biocbuild/bbs-2.11-bioc/R/bin/Rscript' --vanilla --default-packages= -e "tools::buildVignettes(dir = '.')" > '/tmp/RtmpBjAkfW/xshellc18ec9b619' 2>&1
ERROR
Loading required package: BiocGenerics
Attaching package: ‘BiocGenerics’
The following object(s) are masked from ‘package:stats’:
xtabs
The following object(s) are masked from ‘package:base’:
Filter, Find, Map, Position, Reduce, anyDuplicated,
cbind, colnames, duplicated, eval, get, intersect,
lapply, mapply, mget, order, paste, pmax, pmax.int,
pmin, pmin.int, rbind, rep.int, rownames, sapply,
setdiff, table, tapply, union, unique
Attaching package: ‘TSSi’
The following object(s) are masked from ‘package:graphics’:
segments
*** caught segfault ***
address (nil), cause ‘memory not mapped’
Traceback:
1: .Call(bobyqa_cpp, par, lower, upper, ctrl, fn1)
2: bobyqa(fn = assessPoisson, par = ratio, lower = lower, control = list(iprint = 0, maxfun = 10 * n^2), counts = counts, lambda = lambda, basal = basal, nRep = NULL)
3: FUN(X[[1L]], ...)
4: lapply(X = reads, FUN = .normalize, fun = fun, offset = offset, basal = basal, initial = initial, lambda = lambda, fit = fit, optimizer = optimizer)
5: normalizeCounts(x, fit = TRUE)
6: normalizeCounts(x, fit = TRUE)
7: eval(expr, envir, enclos)
8: eval(expr, .GlobalEnv)
9: withVisible(eval(expr, .GlobalEnv))
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)[1L] prefix <- paste("Error in", dcall, ": ") LONG <- 75L msg <- conditionMessage(e) sm <- strsplit(msg, "\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 && identical(getOption("show.error.messages"), TRUE)) { cat(msg, file = stderr()) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))})
14: try(withVisible(eval(expr, .GlobalEnv)), silent = TRUE)
15: evalFunc(ce, options)
16: driver$runcode(drobj, chunk, chunkopts)
17: utils::Sweave(f, quiet = quiet)
18: doTryCatch(return(expr), name, parentenv, handler)
19: tryCatchOne(expr, names, parentenv, handlers[[1L]])
20: tryCatchList(expr, classes, parentenv, handlers)
21: tryCatch(utils::Sweave(f, quiet = quiet), error = function(e) { stop(gettextf("processing vignette ‘%s’ failed with diagnostics:\n%s", f, conditionMessage(e)), domain = NA, call. = FALSE)})
22: tools::buildVignettes(dir = ".")
aborting ...