BioC 2.12: BUILD report for graphite on george2

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

Loading required package: Biobase
Welcome to Bioconductor

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


Loading required package: KEGGgraph
Loading required package: XML

Attaching package: ‘XML’

The following object is masked from ‘package:graph’:

    addNode

Loading required package: org.Hs.eg.db

Loading required package: R.utils
Loading required package: R.oo
Loading required package: R.methodsS3
R.methodsS3 v1.4.2 (2012-06-22) successfully loaded. See ?R.methodsS3 for help.
R.oo v1.13.0 (2013-03-08) successfully loaded. See ?R.oo for help.

Attaching package: ‘R.oo’

The following object is masked from ‘package:KEGGgraph’:

    getName, getTitle

The following object is masked from ‘package:methods’:

    getClasses, getMethods

The following object is masked from ‘package:base’:

    attach, detach, gc, load, save

R.utils v1.19.5 (2013-01-11) successfully loaded. See ?R.utils for help.

Attaching package: ‘R.utils’

The following object is masked from ‘package:utils’:

    timestamp

The following object is masked from ‘package:base’:

    cat, commandArgs, getOption, inherits, isOpen, parse, warnings

Warning in .simpleDuplicateClass(def, prev) :
  the specification for S3 class “AsIs” in package ‘XMLRPC’ seems equivalent to one from package ‘BiocGenerics’ and is not turning on duplicate class definitions for this class
Scalable Robust Estimators with High Breakdown Point (version 1.3-02)

Loading required package: gRbase
Loading required package: MASS

Attaching package: ‘MASS’

The following object is masked from ‘package:AnnotationDbi’:

    select

Loading required package: Rcpp
Loading required package: RcppEigen
Loading required package: Matrix
Loading required package: lattice
Loading required package: RcppArmadillo

Attaching package: ‘RcppArmadillo’

The following object is masked from ‘package:RcppEigen’:

    fastLm, fastLmPure

Loading required package: igraph

Attaching package: ‘igraph’

The following object is masked from ‘package:R.oo’:

    hierarchy

The following object is masked from ‘package:KEGGgraph’:

    edges, neighborhood

The following object is masked from ‘package:graphite’:

    edges

The following object is masked from ‘package:graph’:

    degree, edges

Loading required package: RBGL

Attaching package: ‘RBGL’

The following object is masked from ‘package:igraph’:

    transitivity


Attaching package: ‘gRbase’

The following object is masked from ‘package:R.oo’:

    compile

The following object is masked from ‘package:Biobase’:

    description<-

Loading required package: qpgraph
Loading required package: fields
Loading required package: spam
Spam version 0.29-2 (2012-08-17) is loaded.
Type ‘help( Spam)’ or ‘demo( spam)’ for a short introduction 
and overview of this package.
Help for individual functions is also obtained by adding the
suffix ‘.spam’ to the function name, e.g. ‘help( chol.spam)’.

Attaching package: ‘spam’

The following object is masked from ‘package:RBGL’:

    bandwidth

The following object is masked from ‘package:R.utils’:

    cleanup

The following object is masked from ‘package:base’:

    backsolve, forwardsolve


 *** caught segfault ***
address 0x4, cause ‘memory not mapped’

Traceback:
 1: sp_moralize(amat)
 2: moralizeMAT_spC(amat)
 3: moralizeMAT(graphNEL2dgCMatrix(object), result = result)
 4: moralize.graphNEL(dag)
 5: moralize(dag)
 6: .processGraph(dag)
 7: .procParams(exp1, exp2, dag)
 8: test(exp1, exp2, g, alpha, ...)
 9: runTopologyGSASingle(pathway, switchTest(test), exp1, exp2, alpha,     ...)
10: runTopologyGSA(p, "var", exp1, exp2, 0.05)
11: eval(expr, envir, enclos)
12: eval(expr, .GlobalEnv)
13: withVisible(eval(expr, .GlobalEnv))
14: doTryCatch(return(expr), name, parentenv, handler)
15: tryCatchOne(expr, names, parentenv, handlers[[1L]])
16: tryCatchList(expr, classes, parentenv, handlers)
17: 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))})
18: try(withVisible(eval(expr, .GlobalEnv)), silent = TRUE)
19: evalFunc(ce, options)
20: driver$runcode(drobj, chunk, chunkopts)
21: utils::Sweave(...)
22: engine$weave(file, quiet = quiet)
23: doTryCatch(return(expr), name, parentenv, handler)
24: tryCatchOne(expr, names, parentenv, handlers[[1L]])
25: tryCatchList(expr, classes, parentenv, handlers)
26: 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)})
27: tools::buildVignettes(dir = ".", tangle = FALSE)
aborting ...
Segmentation fault (core dumped)
Summary

Command output
