BioC 2.11: BUILD report for GeneExpressionSignature on lamb1

* checking for file ‘GeneExpressionSignature/DESCRIPTION’ ... OK
* preparing ‘GeneExpressionSignature’:
* checking DESCRIPTION meta-information ... OK
* installing the package to re-build vignettes
* creating vignettes ...sh: line 1:  8500 Segmentation fault      '/home/biocbuild/bbs-2.11-bioc/R/bin/Rscript' --vanilla --default-packages= -e "tools::buildVignettes(dir = '.')" > '/tmp/Rtmp7lr042/xshell20315c6a1fcd' 2>&1
 ERROR
Loading required package: Biobase
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

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    ‘browseVignettes()’. To cite Bioconductor, see
    ‘citation("Biobase")’, and for packages ‘citation("pkgname")’.

Loading required package: PGSEA
Loading required package: GO.db
Loading required package: AnnotationDbi
Loading required package: DBI

Loading required package: KEGG.db

KEGG.db contains mappings based on older data because the original
  resource was removed from the the public domain before the most
  recent update was produced. This package should now be considered
  deprecated and future versions of Bioconductor may not have it
  available.  One possible alternative to consider is to look at the
  reactome.db package

Loading required package: annaffy
Loading required package: GEOquery
Setting options(‘download.file.method.GEOquery’=‘curl’)
Loading required package: apcluster
Loading required package: Rcpp

Attaching package: ‘apcluster’

The following object(s) are masked from ‘package:stats’:

    heatmap


 *** caught segfault ***
address (nil), cause ‘memory not mapped’

Traceback:
 1: .Call("apclusterC", s, as.integer(maxits), as.integer(convits),     as.double(lam), as.logical(details))
 2: .local(s, x, ...)
 3: apcluster(1 - ds)
 4: apcluster(1 - ds)
 5: eval(expr, envir, enclos)
 6: eval(expr, .GlobalEnv)
 7: withVisible(eval(expr, .GlobalEnv))
 8: doTryCatch(return(expr), name, parentenv, handler)
 9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
10: tryCatchList(expr, classes, parentenv, handlers)
11: 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))})
12: try(withVisible(eval(expr, .GlobalEnv)), silent = TRUE)
13: evalFunc(ce, options)
14: driver$runcode(drobj, chunk, chunkopts)
15: utils::Sweave(f, quiet = quiet)
16: doTryCatch(return(expr), name, parentenv, handler)
17: tryCatchOne(expr, names, parentenv, handlers[[1L]])
18: tryCatchList(expr, classes, parentenv, handlers)
19: 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)})
20: tools::buildVignettes(dir = ".")
aborting ...
Summary

Command output
