caught segfault in arrayQualityMetrics
1
0
Entering edit mode
@laurent-gatto-5645
Last seen 7 days 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 • 1.0k views
ADD COMMENT •
0
Entering edit mode
@wolfgang-huber-3550
Last seen 23 days 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
ADD COMMENT •
0
Entering edit mode
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
ADD REPLY •
0
Entering edit mode
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
ADD REPLY •

Login before adding your answer.

Similar Posts
Loading Similar Posts
Traffic: 582 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6