Package: GeneExpressionSignature

Version: 1.5.1

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data GeneExpressionSignature

StartedAt: 2013-03-24 22:40:12 -0700 (Sun, 24 Mar 2013)

EndedAt: 2013-03-24 22:41:59 -0700 (Sun, 24 Mar 2013)

EllapsedTime: 107.1 seconds

RetCode: 1

Status:  ERROR

PackageFile: None

PackageFileSize: NA

* checking for file ‘GeneExpressionSignature/DESCRIPTION’ ... OK
* preparing ‘GeneExpressionSignature’:
* checking DESCRIPTION meta-information ... OK
* installing the package to re-build vignettes
* creating vignettes ... ERROR
Loading required package: Biobase
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

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 is 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$runcode(drobj, chunk, chunkopts)
15: utils::Sweave(...)
16: engine$weave(file, quiet = quiet)
17: doTryCatch(return(expr), name, parentenv, handler)
18: tryCatchOne(expr, names, parentenv, handlers[[1L]])
19: tryCatchList(expr, classes, parentenv, handlers)
20: 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)})
21: tools::buildVignettes(dir = ".", tangle = FALSE)
aborting ...
Segmentation fault (core dumped)