[BioC] caught segfault in arrayQualityMetrics
Laurent Gatto
laurent.gatto at gmail.com
Mon Oct 4 18:14:23 CEST 2010
On 4 October 2010 14:37, Martin Morgan <mtmorgan at fhcrc.org> wrote:
> 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)?
I'm afraid not. I still have the error with today's 2.13.0 (2010-10-03
r53155) on Ubuntu 10.04.
Laurent
> sessionInfo()
R version 2.13.0 Under development (unstable) (2010-10-03 r53155)
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] arrayQualityMetrics_3.0.14 vsn_3.17.2
[3] affyPLM_1.25.1 preprocessCore_1.11.0
[5] gcrma_2.21.1 affy_1.27.3
[7] 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_0.19-11 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_2.35-8 SVGAnnotation_0.6-0
[22] XML_3.1-1 xtable_1.5-6
> 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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>>
>>
>
>
> --
> Computational Biology
> Fred Hutchinson Cancer Research Center
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>
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--
Laurent Gatto
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