[BioC] caught segfault in arrayQualityMetrics

[Laurent Gatto]

Dear all,

While running the latest arrayQualityMetrics version I with a recent
R-devel version, I stumbled on the following issue.

> library("arrayQualityMetrics")
> library("ALLMLL")
> sessionInfo()
R version 2.13.0 Under development (unstable) (2010-09-19 r52946)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_GB.utf8       LC_NUMERIC=C
 [3] LC_TIME=en_GB.utf8        LC_COLLATE=en_GB.utf8
 [5] LC_MONETARY=C             LC_MESSAGES=en_GB.utf8
 [7] LC_PAPER=en_GB.utf8       LC_NAME=C
 [9] LC_ADDRESS=C              LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_GB.utf8 LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] ALLMLL_1.2.8               arrayQualityMetrics_3.0.14
[3] vsn_3.17.2                 affyPLM_1.25.1
[5] preprocessCore_1.11.0      gcrma_2.21.1
[7] affy_1.27.3                Biobase_2.9.2

loaded via a namespace (and not attached):
 [1] affyio_1.17.4        annotate_1.27.2      AnnotationDbi_1.11.8
 [4] beadarray_1.17.1     Biostrings_2.17.47   DBI_0.2-5
 [7] genefilter_1.31.2    grid_2.13.0          hwriter_1.2
[10] IRanges_1.7.38       lattice_0.19-12      latticeExtra_0.6-15
[13] limma_3.5.21         marray_1.27.0        RColorBrewer_1.0-2
[16] RSQLite_0.9-2        simpleaffy_2.25.0    splines_2.13.0
[19] stats4_2.13.0        survival_2.36-1      SVGAnnotation_0.6-0
[22] XML_3.1-1            xtable_1.5-6

> data(MLL.A)
> rMLL=rma(MLL.A)
> arrayQualityMetrics(expressionset = rMLL,outdir="AQM",force=TRUE)
The report will be written into directory 'AQM'.
KernSmooth 2.23 loaded
Copyright M. P. Wand 1997-2009
(loaded the KernSmooth namespace)

 *** caught segfault ***
address 0x28, cause 'memory not mapped'

Traceback:
 1: .Call.graphics(fnname, ..., PACKAGE = "grid")
 2: grid.Call.graphics("L_raster", x$raster, x$x, x$y, x$width,
x$height,     resolveHJust(x$just, x$hjust), resolveVJust(x$just,
x$vjust),     x$interpolate)
 3: drawDetails.rastergrob(x, recording = FALSE)
 4: drawDetails(x, recording = FALSE)
 5: drawGrob(x)
 6: recordGraphics(drawGrob(x), list(x = x), getNamespace("grid"))
 7: grid.draw.grob(rg)
 8: grid.draw(rg)
 9: grid.raster(as.raster(zmat), interpolate = interpolate, x = xlow,
   y = ylow, width = xhigh - xlow, height = yhigh - ylow, just =
c("left",         "bottom"), default.units = "native")
10: PFUN(x = rep(xm, length(ym)), y = rep(ym, each = length(xm)),
z = as.numeric(dens), subscripts = TRUE, at = seq(from = 0,         to
= 1.01 * max(dens), length = cuts + 2), col.regions = colramp(cuts +
      1), ...)
11: panel.smoothScatter(x = A[, x], y = M[, y], nbin = 250, raster =
TRUE,     ...)
12: function (x, y, ...) panel.smoothScatter(x = A[, x], y = M[, y],
nbin = 250, raster = TRUE,     ...)(x = 1L, y = 1L)
13: do.call(FUN, args)
14: checkArgsAndCall(panel, pargs)
15: doTryCatch(return(expr), name, parentenv, handler)
16: tryCatchOne(expr, names, parentenv, handlers[[1L]])
17: tryCatchList(expr, classes, parentenv, handlers)
18: tryCatch(checkArgsAndCall(panel, pargs), error = function(e) panel.error(e))
19: printFunction(x, ...)
20: print.trellis(qm$plot[[1]])
21: print(qm$plot[[1]])
22: aqm.report.qm(p, obj[[i]], i, names(obj)[i])
23: aqm.writereport(reporttitle, expressionset, obj)
24: arrayQualityMetrics(expressionset = rMLL, outdir = "AQM", force = TRUE)
25: arrayQualityMetrics(expressionset = rMLL, outdir = "AQM", force = TRUE)

I reproduced this with R 2.12.0 beta (as on the BioC 2.7: Multiple
platform build/check report) and got the same issue, so I suspect it
is specific to my installation. Has any one observed similar problems?
Any hints are welcome.

Thank you very much in advance.

Best wishes,

Laurent