[BioC] caught segfault in arrayQualityMetrics

[Wolfgang Huber]

Hi Laurent,

this has nothing directly to do with 'arrayQualityMetrics', but with 
'grid', see the thread starting from 
https://stat.ethz.ch/pipermail/r-devel/2010-October/058680.html

Btw, I also have that problem on a (Lenovo) laptop running Ubunto 10.04, 
but not on a (Asus) desktop running the same OS, nor on a MacBook. In 
the above R-devel thread, people report the problem on Mac. It seems to 
be a rather idiosyncratic OS- and perhaps driver dependent problem. I 
had previously reported my observation to Paul, but I think only in the 
last few days it has turned out that many people (including you) are 
running into this problem, making it more worthwhile to chase up.

As a short-term workaround, you could try on a different machine.

I suppose that any efforts from people with a valgrind and understanding 
of C would be welcome.

	Best wishes
	Wolfgang


Laurent Gatto scripsit 04/10/10 10:10:
> 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
>
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-- 


Wolfgang Huber
EMBL
http://www.embl.de/research/units/genome_biology/huber