caught segfault in arrayQualityMetrics
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@laurent-gatto-5645
Last seen 1 day ago
Belgium
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
arrayQualityMetrics arrayQualityMetrics • 1.2k views
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@wolfgang-huber-3550
Last seen 5 months ago
EMBL European Molecular Biology Laborat…
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 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Wolfgang Huber EMBL http://www.embl.de/research/units/genome_biology/huber
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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 >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor > > -- Computational Biology Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: M1-B861 Telephone: 206 667-2793
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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 >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at stat.math.ethz.ch >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: >>> http://news.gmane.org/gmane.science.biology.informatics.conductor >> >> > > > -- > Computational Biology > Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 > > Location: M1-B861 > Telephone: 206 667-2793 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > -- Laurent Gatto slashhome.be
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