TSSi 1.5.0 Julian Gehring
Snapshot Date: 2013-03-24 17:01:43 -0700 (Sun, 24 Mar 2013) | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/TSSi | Last Changed Rev: 70052 / Revision: 74774 | Last Changed Date: 2012-10-01 15:43:56 -0700 (Mon, 01 Oct 2012) |
| george2 | Linux (Ubuntu 12.04.1 LTS) / x86_64 | [ ERROR ] | skipped | |
moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK |
petty | 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 ... ERROR
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: ‘BiocGenerics’
The following objects are masked from ‘package:parallel’:
clusterApply, clusterApplyLB, clusterCall,
clusterEvalQ, clusterExport, clusterMap, parApply,
parCapply, parLapply, parLapplyLB, parRapply,
parSapply, parSapplyLB
The following object is masked from ‘package:stats’:
xtabs
The following objects are masked from ‘package:base’:
Filter, Find, Map, Position, Reduce, anyDuplicated,
as.data.frame, cbind, colnames, duplicated, eval,
get, intersect, lapply, mapply, match, mget, order,
paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
rep.int, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unlist
Attaching package: ‘TSSi’
The following object is 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$runcode(drobj, chunk, chunkopts)
17: utils::Sweave(...)
18: engine$weave(file, quiet = quiet)
19: doTryCatch(return(expr), name, parentenv, handler)
20: tryCatchOne(expr, names, parentenv, handlers[[1L]])
21: tryCatchList(expr, classes, parentenv, handlers)
22: tryCatch({ engine$weave(file, quiet = quiet) find_vignette_product(name, by = "weave", engine = engine)}, error = function(e) { stop(gettextf("processing vignette ‘%s’ failed with diagnostics:\n%s", file, conditionMessage(e)), domain = NA, call. = FALSE)})
23: tools::buildVignettes(dir = ".", tangle = FALSE)
aborting ...
Segmentation fault (core dumped)