[BioC] caught segfault in arrayQualityMetrics

Mon Oct 4 15:37:55 CEST 2010

On 10/04/2010 02:50 AM, Wolfgang Huber wrote:
> 
> 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.

does

https://stat.ethz.ch/pipermail/r-devel/2010-October/058710.html

say that the problem is perhaps fixed (r53056 and later)?

Martin

> 
>     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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> 
> 

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