BioC 2.12: BUILD report for clipper on george2

* checking for file ‘clipper/DESCRIPTION’ ... OK
* preparing ‘clipper’:
* 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: org.Hs.eg.db

Loading required package: Matrix
Loading required package: lattice

 *** 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(graph)
 5: .class1(object)
 6: as(moralize.graphNEL(graph), "matrix")
 7: runPathwayVar(expr, classes, graph, nperm, permute)
 8: pathQ(exp, classes, graph, nperm = 100, alphaV = 0.05, b = 100)
 9: eval(expr, envir, enclos)
10: eval(expr, .GlobalEnv)
11: withVisible(eval(expr, .GlobalEnv))
12: doTryCatch(return(expr), name, parentenv, handler)
13: tryCatchOne(expr, names, parentenv, handlers[[1L]])
14: tryCatchList(expr, classes, parentenv, handlers)
15: 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))})
16: try(withVisible(eval(expr, .GlobalEnv)), silent = TRUE)
17: evalFunc(ce, options)
18: driver$runcode(drobj, chunk, chunkopts)
19: utils::Sweave(...)
20: engine$weave(file, quiet = quiet)
21: doTryCatch(return(expr), name, parentenv, handler)
22: tryCatchOne(expr, names, parentenv, handlers[[1L]])
23: tryCatchList(expr, classes, parentenv, handlers)
24: 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)})
25: tools::buildVignettes(dir = ".", tangle = FALSE)
aborting ...
Segmentation fault (core dumped)
Summary

Command output
