arrayQualityMetrics not producing all diagnostic plots
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James F. Reid ▴ 610
@james-f-reid-3148
Last seen 10.3 years ago
Dear all, Since upgrading to the latest version of Bioconductor, I am having problems using the package arrayQualityMetrics because it does not produce a full report (both for single and double channels arrays). Thanks. James. Here is the first example from the arrayQualityMetrics vignette (inst/scripts/arrayQualityMetrics.Rnw) library("ALLMLL") data("MLL.A") library("arrayQualityMetrics") arrayQualityMetrics(expressionset = MLL.A, outdir = "MLL", force = TRUE, do.logtransform = TRUE) produces: Error in UseMethod("xmlAttrs", node) : no applicable method for 'xmlAttrs' applied to an object of class "NULL" without producing all the plots (stops after section 3: Between array comparison), the html report is truncated. > sessionInfo() R version 2.12.0 (2010-10-15) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets tools methods [8] base other attached packages: [1] ALLMLL_1.2.8 arrayQualityMetrics_3.2.0 [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_1.27.3 AnnotationDbi_1.11.10 [4] beadarray_2.0.1 Biostrings_2.17.48 DBI_0.2-5 [7] genefilter_1.31.2 grid_2.12.0 hwriter_1.2 [10] IRanges_1.7.40 lattice_0.19-13 latticeExtra_0.6-14 [13] limma_3.5.21 marray_1.27.0 RColorBrewer_1.0-2 [16] RSQLite_0.9-2 simpleaffy_2.25.0 splines_2.12.0 [19] stats4_2.12.0 survival_2.35-8 SVGAnnotation_0.6-0 [22] XML_3.2-0 xtable_1.5-6 >
arrayQualityMetrics arrayQualityMetrics • 2.0k views
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@martin-morgan-1513
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On 10/27/2010 02:26 AM, James F. Reid wrote: > Dear all, > > Since upgrading to the latest version of Bioconductor, I am having > problems using the package arrayQualityMetrics because it does not > produce a full report (both for single and double channels arrays). HI James -- have you tried updating your installed packages? I notice below that you are using the 'release' version of R (2.12.0) but that many of your packages are from a previous 'devel' version of Bioconductor (odd-numbered second version field, e.g., Biobase 2.9.2). See http://bioconductor.org/install/index.html#update-bioconductor- packages Martin > > Thanks. > James. > > Here is the first example from the arrayQualityMetrics vignette > (inst/scripts/arrayQualityMetrics.Rnw) > > library("ALLMLL") > data("MLL.A") > > library("arrayQualityMetrics") > arrayQualityMetrics(expressionset = MLL.A, > outdir = "MLL", > force = TRUE, > do.logtransform = TRUE) > > produces: > Error in UseMethod("xmlAttrs", node) : no applicable method for > 'xmlAttrs' applied to an object of class "NULL" > > without producing all the plots (stops after section 3: Between array > comparison), the html report is truncated. > >> sessionInfo() > R version 2.12.0 (2010-10-15) > Platform: x86_64-unknown-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=en_US.UTF-8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets tools methods > [8] base > > other attached packages: > [1] ALLMLL_1.2.8 arrayQualityMetrics_3.2.0 > [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_1.27.3 AnnotationDbi_1.11.10 > [4] beadarray_2.0.1 Biostrings_2.17.48 DBI_0.2-5 > [7] genefilter_1.31.2 grid_2.12.0 hwriter_1.2 > [10] IRanges_1.7.40 lattice_0.19-13 latticeExtra_0.6-14 > [13] limma_3.5.21 marray_1.27.0 RColorBrewer_1.0-2 > [16] RSQLite_0.9-2 simpleaffy_2.25.0 splines_2.12.0 > [19] stats4_2.12.0 survival_2.35-8 SVGAnnotation_0.6-0 > [22] XML_3.2-0 xtable_1.5-6 >> > > _______________________________________________ > 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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Dear Martin, On 27/10/2010 14:17, Martin Morgan wrote: > On 10/27/2010 02:26 AM, James F. Reid wrote: >> Dear all, >> >> Since upgrading to the latest version of Bioconductor, I am having >> problems using the package arrayQualityMetrics because it does not >> produce a full report (both for single and double channels arrays). > > HI James -- have you tried updating your installed packages? I notice > below that you are using the 'release' version of R (2.12.0) but that > many of your packages are from a previous 'devel' version of > Bioconductor (odd-numbered second version field, e.g., Biobase 2.9.2). > > See > > http://bioconductor.org/install/index.html#update-bioconductor- packages > > Martin > you're right and I should have updated my packages before sending a mail to the list. However even after updating the problem remains. The error message points to a problem using the library XML. When installing XML I noticed the following: Creating a new generic function for "source" in "XML" Warning in .NonstandardGenericTest(body(fdef), name, stdGenericBody) : the supplied generic function definition for xmlClone does not seem to call 'standardGeneric'; no methods will be dispatched! Any ideas? James. My updated session: > sessionInfo() R version 2.12.0 (2010-10-15) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets tools methods [8] base other attached packages: [1] arrayQualityMetrics_3.2.0 vsn_3.18.0 [3] affyPLM_1.26.0 preprocessCore_1.12.0 [5] gcrma_2.22.0 affy_1.28.0 [7] Biobase_2.10.0 loaded via a namespace (and not attached): [1] affyio_1.18.0 annotate_1.28.0 AnnotationDbi_1.12.0 [4] beadarray_2.0.1 Biostrings_2.18.0 DBI_0.2-5 [7] genefilter_1.32.0 grid_2.12.0 hwriter_1.2 [10] IRanges_1.8.1 lattice_0.19-13 latticeExtra_0.6-14 [13] limma_3.6.4 marray_1.28.0 RColorBrewer_1.0-2 [16] RSQLite_0.9-2 simpleaffy_2.26.0 splines_2.12.0 [19] stats4_2.12.0 survival_2.35-8 SVGAnnotation_0.6-0 [22] XML_3.2-0 xtable_1.5-6 >> >> Thanks. >> James. >> >> Here is the first example from the arrayQualityMetrics vignette >> (inst/scripts/arrayQualityMetrics.Rnw) >> >> library("ALLMLL") >> data("MLL.A") >> >> library("arrayQualityMetrics") >> arrayQualityMetrics(expressionset = MLL.A, >> outdir = "MLL", >> force = TRUE, >> do.logtransform = TRUE) >> >> produces: >> Error in UseMethod("xmlAttrs", node) : no applicable method for >> 'xmlAttrs' applied to an object of class "NULL" >> >> without producing all the plots (stops after section 3: Between array >> comparison), the html report is truncated. >> >>> sessionInfo() >> R version 2.12.0 (2010-10-15) >> Platform: x86_64-unknown-linux-gnu (64-bit) >> >> locale: >> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C >> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 >> [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 >> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C >> [9] LC_ADDRESS=C LC_TELEPHONE=C >> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C >> >> attached base packages: >> [1] stats graphics grDevices utils datasets tools methods >> [8] base >> >> other attached packages: >> [1] ALLMLL_1.2.8 arrayQualityMetrics_3.2.0 >> [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_1.27.3 AnnotationDbi_1.11.10 >> [4] beadarray_2.0.1 Biostrings_2.17.48 DBI_0.2-5 >> [7] genefilter_1.31.2 grid_2.12.0 hwriter_1.2 >> [10] IRanges_1.7.40 lattice_0.19-13 latticeExtra_0.6-14 >> [13] limma_3.5.21 marray_1.27.0 RColorBrewer_1.0-2 >> [16] RSQLite_0.9-2 simpleaffy_2.25.0 splines_2.12.0 >> [19] stats4_2.12.0 survival_2.35-8 SVGAnnotation_0.6-0 >> [22] XML_3.2-0 xtable_1.5-6 >>> >> >> _______________________________________________ >> 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 > >
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On 10/27/2010 06:16 AM, James F. Reid wrote: > Dear Martin, > > On 27/10/2010 14:17, Martin Morgan wrote: >> On 10/27/2010 02:26 AM, James F. Reid wrote: >>> Dear all, >>> >>> Since upgrading to the latest version of Bioconductor, I am having >>> problems using the package arrayQualityMetrics because it does not >>> produce a full report (both for single and double channels arrays). >> >> HI James -- have you tried updating your installed packages? I notice >> below that you are using the 'release' version of R (2.12.0) but that >> many of your packages are from a previous 'devel' version of >> Bioconductor (odd-numbered second version field, e.g., Biobase 2.9.2). >> >> See >> >> http://bioconductor.org/install/index.html#update-bioconductor- packages >> >> Martin >> > > you're right and I should have updated my packages before sending a mail > to the list. However even after updating the problem remains. The error > message points to a problem using the library XML. When installing XML I > noticed the following: > Creating a new generic function for "source" in "XML" > Warning in .NonstandardGenericTest(body(fdef), name, stdGenericBody) : > the supplied generic function definition for xmlClone does not seem to > call 'standardGeneric'; no methods will be dispatched! Hi James -- Hmm. For what it's worth, I don't have problems with a similar set of packages. I have > capabilities() jpeg png tiff tcltk X11 aqua http/ftp sockets TRUE TRUE TRUE TRUE TRUE FALSE TRUE TRUE libxml fifo cledit iconv NLS profmem cairo TRUE TRUE TRUE TRUE TRUE FALSE TRUE What does traceback() say after the error? Do you have the cdf for this package (hgu133acdf_2.7.0; library('hgu133acdf') already installed? The installation warning for XML is not likely the problem. Martin > > Any ideas? > James. > > My updated session: >> sessionInfo() > R version 2.12.0 (2010-10-15) > Platform: x86_64-unknown-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=en_US.UTF-8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets tools methods > [8] base > > other attached packages: > [1] arrayQualityMetrics_3.2.0 vsn_3.18.0 > [3] affyPLM_1.26.0 preprocessCore_1.12.0 > [5] gcrma_2.22.0 affy_1.28.0 > [7] Biobase_2.10.0 > > loaded via a namespace (and not attached): > [1] affyio_1.18.0 annotate_1.28.0 AnnotationDbi_1.12.0 > [4] beadarray_2.0.1 Biostrings_2.18.0 DBI_0.2-5 > [7] genefilter_1.32.0 grid_2.12.0 hwriter_1.2 > [10] IRanges_1.8.1 lattice_0.19-13 latticeExtra_0.6-14 > [13] limma_3.6.4 marray_1.28.0 RColorBrewer_1.0-2 > [16] RSQLite_0.9-2 simpleaffy_2.26.0 splines_2.12.0 > [19] stats4_2.12.0 survival_2.35-8 SVGAnnotation_0.6-0 > [22] XML_3.2-0 xtable_1.5-6 > > >>> >>> Thanks. >>> James. >>> >>> Here is the first example from the arrayQualityMetrics vignette >>> (inst/scripts/arrayQualityMetrics.Rnw) >>> >>> library("ALLMLL") >>> data("MLL.A") >>> >>> library("arrayQualityMetrics") >>> arrayQualityMetrics(expressionset = MLL.A, >>> outdir = "MLL", >>> force = TRUE, >>> do.logtransform = TRUE) >>> >>> produces: >>> Error in UseMethod("xmlAttrs", node) : no applicable method for >>> 'xmlAttrs' applied to an object of class "NULL" >>> >>> without producing all the plots (stops after section 3: Between array >>> comparison), the html report is truncated. >>> >>>> sessionInfo() >>> R version 2.12.0 (2010-10-15) >>> Platform: x86_64-unknown-linux-gnu (64-bit) >>> >>> locale: >>> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C >>> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 >>> [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 >>> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C >>> [9] LC_ADDRESS=C LC_TELEPHONE=C >>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C >>> >>> attached base packages: >>> [1] stats graphics grDevices utils datasets tools methods >>> [8] base >>> >>> other attached packages: >>> [1] ALLMLL_1.2.8 arrayQualityMetrics_3.2.0 >>> [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_1.27.3 AnnotationDbi_1.11.10 >>> [4] beadarray_2.0.1 Biostrings_2.17.48 DBI_0.2-5 >>> [7] genefilter_1.31.2 grid_2.12.0 hwriter_1.2 >>> [10] IRanges_1.7.40 lattice_0.19-13 latticeExtra_0.6-14 >>> [13] limma_3.5.21 marray_1.27.0 RColorBrewer_1.0-2 >>> [16] RSQLite_0.9-2 simpleaffy_2.25.0 splines_2.12.0 >>> [19] stats4_2.12.0 survival_2.35-8 SVGAnnotation_0.6-0 >>> [22] XML_3.2-0 xtable_1.5-6 >>>> >>> >>> _______________________________________________ >>> 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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Hi Martin, On 10/27/2010 04:41 PM, Martin Morgan wrote: > On 10/27/2010 06:16 AM, James F. Reid wrote: >> Dear Martin, >> >> On 27/10/2010 14:17, Martin Morgan wrote: >>> On 10/27/2010 02:26 AM, James F. Reid wrote: >>>> Dear all, >>>> >>>> Since upgrading to the latest version of Bioconductor, I am having >>>> problems using the package arrayQualityMetrics because it does not >>>> produce a full report (both for single and double channels arrays). >>> >>> HI James -- have you tried updating your installed packages? I notice >>> below that you are using the 'release' version of R (2.12.0) but that >>> many of your packages are from a previous 'devel' version of >>> Bioconductor (odd-numbered second version field, e.g., Biobase 2.9.2). >>> >>> See >>> >>> http://bioconductor.org/install/index.html#update-bioconductor- packages >>> >>> Martin >>> >> >> you're right and I should have updated my packages before sending a mail >> to the list. However even after updating the problem remains. The error >> message points to a problem using the library XML. When installing XML I >> noticed the following: >> Creating a new generic function for "source" in "XML" >> Warning in .NonstandardGenericTest(body(fdef), name, stdGenericBody) : >> the supplied generic function definition for xmlClone does not seem to >> call 'standardGeneric'; no methods will be dispatched! > > Hi James -- > > Hmm. For what it's worth, I don't have problems with a similar set of > packages. I have > >> capabilities() > jpeg png tiff tcltk X11 aqua http/ftp sockets > TRUE TRUE TRUE TRUE TRUE FALSE TRUE TRUE > libxml fifo cledit iconv NLS profmem cairo > TRUE TRUE TRUE TRUE TRUE FALSE TRUE > > What does traceback() say after the error? Do you have the cdf for this > package (hgu133acdf_2.7.0; library('hgu133acdf') already installed? The > installation warning for XML is not likely the problem. I have the same capabilities() on my platform. Here is the output of traceback() together with my sessionInfo. Error in UseMethod("xmlAttrs", node) : no applicable method for 'xmlAttrs' applied to an object of class "NULL" > traceback() 18: xmlAttrs(node, addNamespace) 17: xmlGetAttr(clipPath[["path"]], "d") 16: getRect(xmlGetAttr(clipPath[["path"]], "d")) 15: getPlotRegion(n) 14: FUN(X[[1L]], ...) 13: lapply(X, FUN, ...) 12: sapply(tmp, function(n) all(getPlotRegion(n) == vb)) 11: getPlotRegionNodes(doc) 10: is.vector(X) 9: lapply(getPlotRegionNodes(doc), getPlotPoints) 8: getPlotPoints.XMLInternalDocument(doc) 7: annotationInfo$getfun(doc) 6: aqm.highlight(doc, annotationInfo = annotationInfo) 5: annotateSvgMatplot(svgtemp, nameimg, annotationInfo = qm$svg) 4: aqm.report.qm(p, obj[[i]], i, names(obj)[i]) 3: aqm.writereport(reporttitle, expressionset, obj) 2: arrayQualityMetrics(expressionset = MLL.A, outdir = "MLL", force = TRUE, do.logtransform = TRUE) 1: arrayQualityMetrics(expressionset = MLL.A, outdir = "MLL", force = TRUE, do.logtransform = TRUE) > sessionInfo() R version 2.12.0 (2010-10-15) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets tools methods [8] base other attached packages: [1] hgu133acdf_2.7.0 ALLMLL_1.2.8 [3] arrayQualityMetrics_3.2.0 vsn_3.18.0 [5] affyPLM_1.26.0 preprocessCore_1.12.0 [7] gcrma_2.22.0 affy_1.28.0 [9] Biobase_2.10.0 loaded via a namespace (and not attached): [1] affyio_1.18.0 annotate_1.28.0 AnnotationDbi_1.12.0 [4] beadarray_2.0.1 Biostrings_2.18.0 DBI_0.2-5 [7] genefilter_1.32.0 grid_2.12.0 hwriter_1.2 [10] IRanges_1.8.2 KernSmooth_2.23-4 lattice_0.19-13 [13] latticeExtra_0.6-14 limma_3.6.5 marray_1.28.0 [16] RColorBrewer_1.0-2 RSQLite_0.9-2 simpleaffy_2.26.0 [19] splines_2.12.0 stats4_2.12.0 survival_2.35-8 [22] SVGAnnotation_0.6-0 XML_3.2-0 xtable_1.5-6 On another machine with the same sessionInfo I get another error: Error in aqm.highlight(doc, annotationInfo = annotationInfo) : 'length(annotationInfo$annotation)' must be equal to 'length(series)', the #number of objects in the plot. > traceback() 7: stop("'length(annotationInfo$annotation)' must be equal to 'length(series)', the number of objects in the plot.") 6: aqm.highlight(doc, annotationInfo = annotationInfo) 5: annotateSvgMatplot(svgtemp, nameimg, annotationInfo = qm$svg) 4: aqm.report.qm(p, obj[[i]], i, names(obj)[i]) 3: aqm.writereport(reporttitle, expressionset, obj) 2: arrayQualityMetrics(expressionset = MLL.A, outdir = "MLL", force = TRUE, do.logtransform = TRUE) 1: arrayQualityMetrics(expressionset = MLL.A, outdir = "MLL", force = TRUE, do.logtransform = TRUE) Can someone help? Thanks. James. > > Martin > >> >> Any ideas? >> James. >> >> My updated session: >>> sessionInfo() >> R version 2.12.0 (2010-10-15) >> Platform: x86_64-unknown-linux-gnu (64-bit) >> >> locale: >> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C >> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 >> [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 >> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C >> [9] LC_ADDRESS=C LC_TELEPHONE=C >> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C >> >> attached base packages: >> [1] stats graphics grDevices utils datasets tools methods >> [8] base >> >> other attached packages: >> [1] arrayQualityMetrics_3.2.0 vsn_3.18.0 >> [3] affyPLM_1.26.0 preprocessCore_1.12.0 >> [5] gcrma_2.22.0 affy_1.28.0 >> [7] Biobase_2.10.0 >> >> loaded via a namespace (and not attached): >> [1] affyio_1.18.0 annotate_1.28.0 AnnotationDbi_1.12.0 >> [4] beadarray_2.0.1 Biostrings_2.18.0 DBI_0.2-5 >> [7] genefilter_1.32.0 grid_2.12.0 hwriter_1.2 >> [10] IRanges_1.8.1 lattice_0.19-13 latticeExtra_0.6-14 >> [13] limma_3.6.4 marray_1.28.0 RColorBrewer_1.0-2 >> [16] RSQLite_0.9-2 simpleaffy_2.26.0 splines_2.12.0 >> [19] stats4_2.12.0 survival_2.35-8 SVGAnnotation_0.6-0 >> [22] XML_3.2-0 xtable_1.5-6 >> >> >>>> >>>> Thanks. >>>> James. >>>> >>>> Here is the first example from the arrayQualityMetrics vignette >>>> (inst/scripts/arrayQualityMetrics.Rnw) >>>> >>>> library("ALLMLL") >>>> data("MLL.A") >>>> >>>> library("arrayQualityMetrics") >>>> arrayQualityMetrics(expressionset = MLL.A, >>>> outdir = "MLL", >>>> force = TRUE, >>>> do.logtransform = TRUE) >>>> >>>> produces: >>>> Error in UseMethod("xmlAttrs", node) : no applicable method for >>>> 'xmlAttrs' applied to an object of class "NULL" >>>> >>>> without producing all the plots (stops after section 3: Between array >>>> comparison), the html report is truncated. >>>> >>>>> sessionInfo() >>>> R version 2.12.0 (2010-10-15) >>>> Platform: x86_64-unknown-linux-gnu (64-bit) >>>> >>>> locale: >>>> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C >>>> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 >>>> [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 >>>> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C >>>> [9] LC_ADDRESS=C LC_TELEPHONE=C >>>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C >>>> >>>> attached base packages: >>>> [1] stats graphics grDevices utils datasets tools methods >>>> [8] base >>>> >>>> other attached packages: >>>> [1] ALLMLL_1.2.8 arrayQualityMetrics_3.2.0 >>>> [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_1.27.3 AnnotationDbi_1.11.10 >>>> [4] beadarray_2.0.1 Biostrings_2.17.48 DBI_0.2-5 >>>> [7] genefilter_1.31.2 grid_2.12.0 hwriter_1.2 >>>> [10] IRanges_1.7.40 lattice_0.19-13 latticeExtra_0.6-14 >>>> [13] limma_3.5.21 marray_1.27.0 RColorBrewer_1.0-2 >>>> [16] RSQLite_0.9-2 simpleaffy_2.25.0 splines_2.12.0 >>>> [19] stats4_2.12.0 survival_2.35-8 SVGAnnotation_0.6-0 >>>> [22] XML_3.2-0 xtable_1.5-6 >>>>> >>>> >>>> _______________________________________________ >>>> 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 >>> >>> > >
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what do you get for xml2-config --version ? On 28 October 2010 13:36, James F. Reid <james.reid at="" ifom-ieo-="" campus.it=""> wrote: > Hi Martin, > > On 10/27/2010 04:41 PM, Martin Morgan wrote: >> >> On 10/27/2010 06:16 AM, James F. Reid wrote: >>> >>> Dear Martin, >>> >>> On 27/10/2010 14:17, Martin Morgan wrote: >>>> >>>> On 10/27/2010 02:26 AM, James F. Reid wrote: >>>>> >>>>> Dear all, >>>>> >>>>> Since upgrading to the latest version of Bioconductor, I am having >>>>> problems using the package arrayQualityMetrics because it does not >>>>> produce a full report (both for single and double channels arrays). >>>> >>>> HI James -- have you tried updating your installed packages? I notice >>>> below that you are using the 'release' version of R (2.12.0) but that >>>> many of your packages are from a previous 'devel' version of >>>> Bioconductor (odd-numbered second version field, e.g., Biobase 2.9.2). >>>> >>>> See >>>> >>>> http://bioconductor.org/install/index.html#update-bioconductor- packages >>>> >>>> Martin >>>> >>> >>> you're right and I should have updated my packages before sending a mail >>> to the list. However even after updating the problem remains. The error >>> message points to a problem using the library XML. When installing XML I >>> noticed the following: >>> Creating a new generic function for "source" in "XML" >>> Warning in .NonstandardGenericTest(body(fdef), name, stdGenericBody) : >>> ? the supplied generic function definition for xmlClone does not seem to >>> call 'standardGeneric'; no methods will be dispatched! >> >> Hi James -- >> >> Hmm. For what it's worth, I don't have problems with a similar set of >> packages. I have >> >>> capabilities() >> >> ? ? jpeg ? ? ?png ? ? tiff ? ?tcltk ? ? ?X11 ? ? aqua http/ftp ?sockets >> ? ? TRUE ? ? TRUE ? ? TRUE ? ? TRUE ? ? TRUE ? ?FALSE ? ? TRUE ? ? TRUE >> ? libxml ? ? fifo ? cledit ? ?iconv ? ? ?NLS ?profmem ? ?cairo >> ? ? TRUE ? ? TRUE ? ? TRUE ? ? TRUE ? ? TRUE ? ?FALSE ? ? TRUE >> >> What does traceback() say after the error? Do you have the cdf for this >> package (hgu133acdf_2.7.0; library('hgu133acdf') already installed? The >> installation warning for XML is not likely the problem. > > I have the same capabilities() on my platform. > Here is the output of traceback() together with my sessionInfo. > > Error in UseMethod("xmlAttrs", node) : > ?no applicable method for 'xmlAttrs' applied to an object of class "NULL" > >> traceback() > 18: xmlAttrs(node, addNamespace) > 17: xmlGetAttr(clipPath[["path"]], "d") > 16: getRect(xmlGetAttr(clipPath[["path"]], "d")) > 15: getPlotRegion(n) > 14: FUN(X[[1L]], ...) > 13: lapply(X, FUN, ...) > 12: sapply(tmp, function(n) all(getPlotRegion(n) == vb)) > 11: getPlotRegionNodes(doc) > 10: is.vector(X) > 9: lapply(getPlotRegionNodes(doc), getPlotPoints) > 8: getPlotPoints.XMLInternalDocument(doc) > 7: annotationInfo$getfun(doc) > 6: aqm.highlight(doc, annotationInfo = annotationInfo) > 5: annotateSvgMatplot(svgtemp, nameimg, annotationInfo = qm$svg) > 4: aqm.report.qm(p, obj[[i]], i, names(obj)[i]) > 3: aqm.writereport(reporttitle, expressionset, obj) > 2: arrayQualityMetrics(expressionset = MLL.A, outdir = "MLL", force = TRUE, > ? ? ? do.logtransform = TRUE) > 1: arrayQualityMetrics(expressionset = MLL.A, outdir = "MLL", force = TRUE, > ? ? ? do.logtransform = TRUE) > >> sessionInfo() > R version 2.12.0 (2010-10-15) > Platform: x86_64-unknown-linux-gnu (64-bit) > > locale: > ?[1] LC_CTYPE=en_US.UTF-8 ? ? ? LC_NUMERIC=C > ?[3] LC_TIME=en_US.UTF-8 ? ? ? ?LC_COLLATE=en_US.UTF-8 > ?[5] LC_MONETARY=C ? ? ? ? ? ? ?LC_MESSAGES=en_US.UTF-8 > ?[7] LC_PAPER=en_US.UTF-8 ? ? ? LC_NAME=C > ?[9] LC_ADDRESS=C ? ? ? ? ? ? ? LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats ? ? graphics ?grDevices utils ? ? datasets ?tools ? ? methods > [8] base > > other attached packages: > [1] hgu133acdf_2.7.0 ? ? ? ? ?ALLMLL_1.2.8 > [3] arrayQualityMetrics_3.2.0 vsn_3.18.0 > [5] affyPLM_1.26.0 ? ? ? ? ? ?preprocessCore_1.12.0 > [7] gcrma_2.22.0 ? ? ? ? ? ? ?affy_1.28.0 > [9] Biobase_2.10.0 > > loaded via a namespace (and not attached): > ?[1] affyio_1.18.0 ? ? ? ?annotate_1.28.0 ? ? ?AnnotationDbi_1.12.0 > ?[4] beadarray_2.0.1 ? ? ?Biostrings_2.18.0 ? ?DBI_0.2-5 > ?[7] genefilter_1.32.0 ? ?grid_2.12.0 ? ? ? ? ?hwriter_1.2 > [10] IRanges_1.8.2 ? ? ? ?KernSmooth_2.23-4 ? ?lattice_0.19-13 > [13] latticeExtra_0.6-14 ?limma_3.6.5 ? ? ? ? ?marray_1.28.0 > [16] RColorBrewer_1.0-2 ? RSQLite_0.9-2 ? ? ? ?simpleaffy_2.26.0 > [19] splines_2.12.0 ? ? ? stats4_2.12.0 ? ? ? ?survival_2.35-8 > [22] SVGAnnotation_0.6-0 ?XML_3.2-0 ? ? ? ? ? ?xtable_1.5-6 > > On another machine with the same sessionInfo I get another error: > Error in aqm.highlight(doc, annotationInfo = annotationInfo) : > ?'length(annotationInfo$annotation)' must be equal to 'length(series)', the > #number of objects in the plot. > >> traceback() > 7: stop("'length(annotationInfo$annotation)' must be equal to > 'length(series)', the number of objects in the plot.") > 6: aqm.highlight(doc, annotationInfo = annotationInfo) > 5: annotateSvgMatplot(svgtemp, nameimg, annotationInfo = qm$svg) > 4: aqm.report.qm(p, obj[[i]], i, names(obj)[i]) > 3: aqm.writereport(reporttitle, expressionset, obj) > 2: arrayQualityMetrics(expressionset = MLL.A, outdir = "MLL", force = TRUE, > ? ? ? do.logtransform = TRUE) > 1: arrayQualityMetrics(expressionset = MLL.A, outdir = "MLL", force = TRUE, > ? ? ? do.logtransform = TRUE) > > Can someone help? > > Thanks. > James. > >> >> Martin >> >>> >>> Any ideas? >>> James. >>> >>> My updated session: >>>> >>>> sessionInfo() >>> >>> R version 2.12.0 (2010-10-15) >>> Platform: x86_64-unknown-linux-gnu (64-bit) >>> >>> locale: >>> ?[1] LC_CTYPE=en_US.UTF-8 ? ? ? LC_NUMERIC=C >>> ?[3] LC_TIME=en_US.UTF-8 ? ? ? ?LC_COLLATE=en_US.UTF-8 >>> ?[5] LC_MONETARY=C ? ? ? ? ? ? ?LC_MESSAGES=en_US.UTF-8 >>> ?[7] LC_PAPER=en_US.UTF-8 ? ? ? LC_NAME=C >>> ?[9] LC_ADDRESS=C ? ? ? ? ? ? ? LC_TELEPHONE=C >>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C >>> >>> attached base packages: >>> [1] stats ? ? graphics ?grDevices utils ? ? datasets ?tools ? ? methods >>> [8] base >>> >>> other attached packages: >>> [1] arrayQualityMetrics_3.2.0 vsn_3.18.0 >>> [3] affyPLM_1.26.0 ? ? ? ? ? ?preprocessCore_1.12.0 >>> [5] gcrma_2.22.0 ? ? ? ? ? ? ?affy_1.28.0 >>> [7] Biobase_2.10.0 >>> >>> loaded via a namespace (and not attached): >>> ?[1] affyio_1.18.0 ? ? ? ?annotate_1.28.0 ? ? ?AnnotationDbi_1.12.0 >>> ?[4] beadarray_2.0.1 ? ? ?Biostrings_2.18.0 ? ?DBI_0.2-5 >>> ?[7] genefilter_1.32.0 ? ?grid_2.12.0 ? ? ? ? ?hwriter_1.2 >>> [10] IRanges_1.8.1 ? ? ? ?lattice_0.19-13 ? ? ?latticeExtra_0.6-14 >>> [13] limma_3.6.4 ? ? ? ? ?marray_1.28.0 ? ? ? ?RColorBrewer_1.0-2 >>> [16] RSQLite_0.9-2 ? ? ? ?simpleaffy_2.26.0 ? ?splines_2.12.0 >>> [19] stats4_2.12.0 ? ? ? ?survival_2.35-8 ? ? ?SVGAnnotation_0.6-0 >>> [22] XML_3.2-0 ? ? ? ? ? ?xtable_1.5-6 >>> >>> >>>>> >>>>> Thanks. >>>>> James. >>>>> >>>>> Here is the first example from the arrayQualityMetrics vignette >>>>> (inst/scripts/arrayQualityMetrics.Rnw) >>>>> >>>>> library("ALLMLL") >>>>> data("MLL.A") >>>>> >>>>> library("arrayQualityMetrics") >>>>> arrayQualityMetrics(expressionset = MLL.A, >>>>> ? ? ? ? ? ? ? ? ? ? ?outdir = "MLL", >>>>> ? ? ? ? ? ? ? ? ? ? ?force = TRUE, >>>>> ? ? ? ? ? ? ? ? ? ? ?do.logtransform = TRUE) >>>>> >>>>> produces: >>>>> Error in UseMethod("xmlAttrs", node) : no applicable method for >>>>> 'xmlAttrs' applied to an object of class "NULL" >>>>> >>>>> without producing all the plots (stops after section 3: Between array >>>>> comparison), the html report is truncated. >>>>> >>>>>> sessionInfo() >>>>> >>>>> R version 2.12.0 (2010-10-15) >>>>> Platform: x86_64-unknown-linux-gnu (64-bit) >>>>> >>>>> locale: >>>>> ? [1] LC_CTYPE=en_US.UTF-8 ? ? ? LC_NUMERIC=C >>>>> ? [3] LC_TIME=en_US.UTF-8 ? ? ? ?LC_COLLATE=en_US.UTF-8 >>>>> ? [5] LC_MONETARY=C ? ? ? ? ? ? ?LC_MESSAGES=en_US.UTF-8 >>>>> ? [7] LC_PAPER=en_US.UTF-8 ? ? ? LC_NAME=C >>>>> ? [9] LC_ADDRESS=C ? ? ? ? ? ? ? LC_TELEPHONE=C >>>>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C >>>>> >>>>> attached base packages: >>>>> [1] stats ? ? graphics ?grDevices utils ? ? datasets ?tools ? ? methods >>>>> [8] base >>>>> >>>>> other attached packages: >>>>> [1] ALLMLL_1.2.8 ? ? ? ? ? ? ?arrayQualityMetrics_3.2.0 >>>>> [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_1.27.3 ? ? ? AnnotationDbi_1.11.10 >>>>> ? [4] beadarray_2.0.1 ? ? ? Biostrings_2.17.48 ? ?DBI_0.2-5 >>>>> ? [7] genefilter_1.31.2 ? ? grid_2.12.0 ? ? ? ? ? hwriter_1.2 >>>>> [10] IRanges_1.7.40 ? ? ? ?lattice_0.19-13 ? ? ? latticeExtra_0.6-14 >>>>> [13] limma_3.5.21 ? ? ? ? ?marray_1.27.0 ? ? ? ? RColorBrewer_1.0-2 >>>>> [16] RSQLite_0.9-2 ? ? ? ? simpleaffy_2.25.0 ? ? splines_2.12.0 >>>>> [19] stats4_2.12.0 ? ? ? ? survival_2.35-8 ? ? ? SVGAnnotation_0.6-0 >>>>> [22] XML_3.2-0 ? ? ? ? ? ? xtable_1.5-6 >>>>>> >>>>> >>>>> _______________________________________________ >>>>> 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 >>>> >>>> >> >> > > _______________________________________________ > 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 >
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Hi, On 10/28/2010 03:06 PM, Benilton Carvalho wrote: > what do you get for > > xml2-config --version > > ? on the machine that produces the xml based error xml2-config --version 2.6.26 whereas on the machine that complains about length(annotationInfo$annotation) I have a newer version: 2.7.7 James. > > On 28 October 2010 13:36, James F. Reid<james.reid at="" ifom-ieo-="" campus.it=""> wrote: >> Hi Martin, >> >> On 10/27/2010 04:41 PM, Martin Morgan wrote: >>> >>> On 10/27/2010 06:16 AM, James F. Reid wrote: >>>> >>>> Dear Martin, >>>> >>>> On 27/10/2010 14:17, Martin Morgan wrote: >>>>> >>>>> On 10/27/2010 02:26 AM, James F. Reid wrote: >>>>>> >>>>>> Dear all, >>>>>> >>>>>> Since upgrading to the latest version of Bioconductor, I am having >>>>>> problems using the package arrayQualityMetrics because it does not >>>>>> produce a full report (both for single and double channels arrays). >>>>> >>>>> HI James -- have you tried updating your installed packages? I notice >>>>> below that you are using the 'release' version of R (2.12.0) but that >>>>> many of your packages are from a previous 'devel' version of >>>>> Bioconductor (odd-numbered second version field, e.g., Biobase 2.9.2). >>>>> >>>>> See >>>>> >>>>> http://bioconductor.org/install/index.html#update-bioconductor- packages >>>>> >>>>> Martin >>>>> >>>> >>>> you're right and I should have updated my packages before sending a mail >>>> to the list. However even after updating the problem remains. The error >>>> message points to a problem using the library XML. When installing XML I >>>> noticed the following: >>>> Creating a new generic function for "source" in "XML" >>>> Warning in .NonstandardGenericTest(body(fdef), name, stdGenericBody) : >>>> the supplied generic function definition for xmlClone does not seem to >>>> call 'standardGeneric'; no methods will be dispatched! >>> >>> Hi James -- >>> >>> Hmm. For what it's worth, I don't have problems with a similar set of >>> packages. I have >>> >>>> capabilities() >>> >>> jpeg png tiff tcltk X11 aqua http/ftp sockets >>> TRUE TRUE TRUE TRUE TRUE FALSE TRUE TRUE >>> libxml fifo cledit iconv NLS profmem cairo >>> TRUE TRUE TRUE TRUE TRUE FALSE TRUE >>> >>> What does traceback() say after the error? Do you have the cdf for this >>> package (hgu133acdf_2.7.0; library('hgu133acdf') already installed? The >>> installation warning for XML is not likely the problem. >> >> I have the same capabilities() on my platform. >> Here is the output of traceback() together with my sessionInfo. >> >> Error in UseMethod("xmlAttrs", node) : >> no applicable method for 'xmlAttrs' applied to an object of class "NULL" >> >>> traceback() >> 18: xmlAttrs(node, addNamespace) >> 17: xmlGetAttr(clipPath[["path"]], "d") >> 16: getRect(xmlGetAttr(clipPath[["path"]], "d")) >> 15: getPlotRegion(n) >> 14: FUN(X[[1L]], ...) >> 13: lapply(X, FUN, ...) >> 12: sapply(tmp, function(n) all(getPlotRegion(n) == vb)) >> 11: getPlotRegionNodes(doc) >> 10: is.vector(X) >> 9: lapply(getPlotRegionNodes(doc), getPlotPoints) >> 8: getPlotPoints.XMLInternalDocument(doc) >> 7: annotationInfo$getfun(doc) >> 6: aqm.highlight(doc, annotationInfo = annotationInfo) >> 5: annotateSvgMatplot(svgtemp, nameimg, annotationInfo = qm$svg) >> 4: aqm.report.qm(p, obj[[i]], i, names(obj)[i]) >> 3: aqm.writereport(reporttitle, expressionset, obj) >> 2: arrayQualityMetrics(expressionset = MLL.A, outdir = "MLL", force = TRUE, >> do.logtransform = TRUE) >> 1: arrayQualityMetrics(expressionset = MLL.A, outdir = "MLL", force = TRUE, >> do.logtransform = TRUE) >> >>> sessionInfo() >> R version 2.12.0 (2010-10-15) >> Platform: x86_64-unknown-linux-gnu (64-bit) >> >> locale: >> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C >> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 >> [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 >> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C >> [9] LC_ADDRESS=C LC_TELEPHONE=C >> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C >> >> attached base packages: >> [1] stats graphics grDevices utils datasets tools methods >> [8] base >> >> other attached packages: >> [1] hgu133acdf_2.7.0 ALLMLL_1.2.8 >> [3] arrayQualityMetrics_3.2.0 vsn_3.18.0 >> [5] affyPLM_1.26.0 preprocessCore_1.12.0 >> [7] gcrma_2.22.0 affy_1.28.0 >> [9] Biobase_2.10.0 >> >> loaded via a namespace (and not attached): >> [1] affyio_1.18.0 annotate_1.28.0 AnnotationDbi_1.12.0 >> [4] beadarray_2.0.1 Biostrings_2.18.0 DBI_0.2-5 >> [7] genefilter_1.32.0 grid_2.12.0 hwriter_1.2 >> [10] IRanges_1.8.2 KernSmooth_2.23-4 lattice_0.19-13 >> [13] latticeExtra_0.6-14 limma_3.6.5 marray_1.28.0 >> [16] RColorBrewer_1.0-2 RSQLite_0.9-2 simpleaffy_2.26.0 >> [19] splines_2.12.0 stats4_2.12.0 survival_2.35-8 >> [22] SVGAnnotation_0.6-0 XML_3.2-0 xtable_1.5-6 >> >> On another machine with the same sessionInfo I get another error: >> Error in aqm.highlight(doc, annotationInfo = annotationInfo) : >> 'length(annotationInfo$annotation)' must be equal to 'length(series)', the >> #number of objects in the plot. >> >>> traceback() >> 7: stop("'length(annotationInfo$annotation)' must be equal to >> 'length(series)', the number of objects in the plot.") >> 6: aqm.highlight(doc, annotationInfo = annotationInfo) >> 5: annotateSvgMatplot(svgtemp, nameimg, annotationInfo = qm$svg) >> 4: aqm.report.qm(p, obj[[i]], i, names(obj)[i]) >> 3: aqm.writereport(reporttitle, expressionset, obj) >> 2: arrayQualityMetrics(expressionset = MLL.A, outdir = "MLL", force = TRUE, >> do.logtransform = TRUE) >> 1: arrayQualityMetrics(expressionset = MLL.A, outdir = "MLL", force = TRUE, >> do.logtransform = TRUE) >> >> Can someone help? >> >> Thanks. >> James. >> >>> >>> Martin >>> >>>> >>>> Any ideas? >>>> James. >>>> >>>> My updated session: >>>>> >>>>> sessionInfo() >>>> >>>> R version 2.12.0 (2010-10-15) >>>> Platform: x86_64-unknown-linux-gnu (64-bit) >>>> >>>> locale: >>>> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C >>>> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 >>>> [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 >>>> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C >>>> [9] LC_ADDRESS=C LC_TELEPHONE=C >>>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C >>>> >>>> attached base packages: >>>> [1] stats graphics grDevices utils datasets tools methods >>>> [8] base >>>> >>>> other attached packages: >>>> [1] arrayQualityMetrics_3.2.0 vsn_3.18.0 >>>> [3] affyPLM_1.26.0 preprocessCore_1.12.0 >>>> [5] gcrma_2.22.0 affy_1.28.0 >>>> [7] Biobase_2.10.0 >>>> >>>> loaded via a namespace (and not attached): >>>> [1] affyio_1.18.0 annotate_1.28.0 AnnotationDbi_1.12.0 >>>> [4] beadarray_2.0.1 Biostrings_2.18.0 DBI_0.2-5 >>>> [7] genefilter_1.32.0 grid_2.12.0 hwriter_1.2 >>>> [10] IRanges_1.8.1 lattice_0.19-13 latticeExtra_0.6-14 >>>> [13] limma_3.6.4 marray_1.28.0 RColorBrewer_1.0-2 >>>> [16] RSQLite_0.9-2 simpleaffy_2.26.0 splines_2.12.0 >>>> [19] stats4_2.12.0 survival_2.35-8 SVGAnnotation_0.6-0 >>>> [22] XML_3.2-0 xtable_1.5-6 >>>> >>>> >>>>>> >>>>>> Thanks. >>>>>> James. >>>>>> >>>>>> Here is the first example from the arrayQualityMetrics vignette >>>>>> (inst/scripts/arrayQualityMetrics.Rnw) >>>>>> >>>>>> library("ALLMLL") >>>>>> data("MLL.A") >>>>>> >>>>>> library("arrayQualityMetrics") >>>>>> arrayQualityMetrics(expressionset = MLL.A, >>>>>> outdir = "MLL", >>>>>> force = TRUE, >>>>>> do.logtransform = TRUE) >>>>>> >>>>>> produces: >>>>>> Error in UseMethod("xmlAttrs", node) : no applicable method for >>>>>> 'xmlAttrs' applied to an object of class "NULL" >>>>>> >>>>>> without producing all the plots (stops after section 3: Between array >>>>>> comparison), the html report is truncated. >>>>>> >>>>>>> sessionInfo() >>>>>> >>>>>> R version 2.12.0 (2010-10-15) >>>>>> Platform: x86_64-unknown-linux-gnu (64-bit) >>>>>> >>>>>> locale: >>>>>> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C >>>>>> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 >>>>>> [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 >>>>>> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C >>>>>> [9] LC_ADDRESS=C LC_TELEPHONE=C >>>>>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C >>>>>> >>>>>> attached base packages: >>>>>> [1] stats graphics grDevices utils datasets tools methods >>>>>> [8] base >>>>>> >>>>>> other attached packages: >>>>>> [1] ALLMLL_1.2.8 arrayQualityMetrics_3.2.0 >>>>>> [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_1.27.3 AnnotationDbi_1.11.10 >>>>>> [4] beadarray_2.0.1 Biostrings_2.17.48 DBI_0.2-5 >>>>>> [7] genefilter_1.31.2 grid_2.12.0 hwriter_1.2 >>>>>> [10] IRanges_1.7.40 lattice_0.19-13 latticeExtra_0.6-14 >>>>>> [13] limma_3.5.21 marray_1.27.0 RColorBrewer_1.0-2 >>>>>> [16] RSQLite_0.9-2 simpleaffy_2.25.0 splines_2.12.0 >>>>>> [19] stats4_2.12.0 survival_2.35-8 SVGAnnotation_0.6-0 >>>>>> [22] XML_3.2-0 xtable_1.5-6 >>>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> 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 >>>>> >>>>> >>> >>> >> >> _______________________________________________ >> 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 >>
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For the record, I can't reproduce the issue, but my libxml2 is 2.7.3 sessionInfo() is shown below: R version 2.12.0 Patched (2010-10-21 r53386) Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) locale: [1] en_GB.UTF-8/en_GB.UTF-8/C/C/en_GB.UTF-8/en_GB.UTF-8 attached base packages: [1] stats graphics grDevices datasets utils methods base other attached packages: [1] hgu133acdf_2.7.0 arrayQualityMetrics_3.2.0 [3] vsn_3.18.0 affyPLM_1.26.0 [5] preprocessCore_1.12.0 gcrma_2.22.0 [7] ALLMLL_1.2.8 affy_1.28.0 [9] Biobase_2.10.0 loaded via a namespace (and not attached): [1] affyio_1.19.1 annotate_1.28.0 AnnotationDbi_1.12.0 [4] beadarray_2.0.1 Biostrings_2.18.0 DBI_0.2-5 [7] genefilter_1.32.0 grid_2.12.0 hwriter_1.2 [10] IRanges_1.8.0 KernSmooth_2.23-4 lattice_0.19-13 [13] latticeExtra_0.6-14 limma_3.6.5 marray_1.28.0 [16] RColorBrewer_1.0-2 RSQLite_0.9-2 simpleaffy_2.26.0 [19] splines_2.12.0 stats4_2.12.0 survival_2.35-8 [22] SVGAnnotation_0.6-0 tools_2.12.0 XML_3.2-0 [25] xtable_1.5-6 On 28 October 2010 14:16, James F. Reid <james.reid at="" ifom-ieo-="" campus.it=""> wrote: > Hi, > > > On 10/28/2010 03:06 PM, Benilton Carvalho wrote: >> >> what do you get for >> >> xml2-config --version >> >> ? > > on the machine that produces the xml based error > xml2-config --version > 2.6.26 > > whereas on the machine that complains about > length(annotationInfo$annotation) I have a newer version: > 2.7.7 > > James. > >> >> On 28 October 2010 13:36, James F. Reid<james.reid at="" ifom-ieo-="" campus.it=""> >> ?wrote: >>> >>> Hi Martin, >>> >>> On 10/27/2010 04:41 PM, Martin Morgan wrote: >>>> >>>> On 10/27/2010 06:16 AM, James F. Reid wrote: >>>>> >>>>> Dear Martin, >>>>> >>>>> On 27/10/2010 14:17, Martin Morgan wrote: >>>>>> >>>>>> On 10/27/2010 02:26 AM, James F. Reid wrote: >>>>>>> >>>>>>> Dear all, >>>>>>> >>>>>>> Since upgrading to the latest version of Bioconductor, I am having >>>>>>> problems using the package arrayQualityMetrics because it does not >>>>>>> produce a full report (both for single and double channels arrays). >>>>>> >>>>>> HI James -- have you tried updating your installed packages? I notice >>>>>> below that you are using the 'release' version of R (2.12.0) but that >>>>>> many of your packages are from a previous 'devel' version of >>>>>> Bioconductor (odd-numbered second version field, e.g., Biobase 2.9.2). >>>>>> >>>>>> See >>>>>> >>>>>> >>>>>> http://bioconductor.org/install/index.html#update-bioconductor- packages >>>>>> >>>>>> Martin >>>>>> >>>>> >>>>> you're right and I should have updated my packages before sending a >>>>> mail >>>>> to the list. However even after updating the problem remains. The error >>>>> message points to a problem using the library XML. When installing XML >>>>> I >>>>> noticed the following: >>>>> Creating a new generic function for "source" in "XML" >>>>> Warning in .NonstandardGenericTest(body(fdef), name, stdGenericBody) : >>>>> ? the supplied generic function definition for xmlClone does not seem >>>>> to >>>>> call 'standardGeneric'; no methods will be dispatched! >>>> >>>> Hi James -- >>>> >>>> Hmm. For what it's worth, I don't have problems with a similar set of >>>> packages. I have >>>> >>>>> capabilities() >>>> >>>> ? ? jpeg ? ? ?png ? ? tiff ? ?tcltk ? ? ?X11 ? ? aqua http/ftp ?sockets >>>> ? ? TRUE ? ? TRUE ? ? TRUE ? ? TRUE ? ? TRUE ? ?FALSE ? ? TRUE ? ? TRUE >>>> ? libxml ? ? fifo ? cledit ? ?iconv ? ? ?NLS ?profmem ? ?cairo >>>> ? ? TRUE ? ? TRUE ? ? TRUE ? ? TRUE ? ? TRUE ? ?FALSE ? ? TRUE >>>> >>>> What does traceback() say after the error? Do you have the cdf for this >>>> package (hgu133acdf_2.7.0; library('hgu133acdf') already installed? The >>>> installation warning for XML is not likely the problem. >>> >>> I have the same capabilities() on my platform. >>> Here is the output of traceback() together with my sessionInfo. >>> >>> Error in UseMethod("xmlAttrs", node) : >>> ?no applicable method for 'xmlAttrs' applied to an object of class "NULL" >>> >>>> traceback() >>> >>> 18: xmlAttrs(node, addNamespace) >>> 17: xmlGetAttr(clipPath[["path"]], "d") >>> 16: getRect(xmlGetAttr(clipPath[["path"]], "d")) >>> 15: getPlotRegion(n) >>> 14: FUN(X[[1L]], ...) >>> 13: lapply(X, FUN, ...) >>> 12: sapply(tmp, function(n) all(getPlotRegion(n) == vb)) >>> 11: getPlotRegionNodes(doc) >>> 10: is.vector(X) >>> 9: lapply(getPlotRegionNodes(doc), getPlotPoints) >>> 8: getPlotPoints.XMLInternalDocument(doc) >>> 7: annotationInfo$getfun(doc) >>> 6: aqm.highlight(doc, annotationInfo = annotationInfo) >>> 5: annotateSvgMatplot(svgtemp, nameimg, annotationInfo = qm$svg) >>> 4: aqm.report.qm(p, obj[[i]], i, names(obj)[i]) >>> 3: aqm.writereport(reporttitle, expressionset, obj) >>> 2: arrayQualityMetrics(expressionset = MLL.A, outdir = "MLL", force = >>> TRUE, >>> ? ? ? do.logtransform = TRUE) >>> 1: arrayQualityMetrics(expressionset = MLL.A, outdir = "MLL", force = >>> TRUE, >>> ? ? ? do.logtransform = TRUE) >>> >>>> sessionInfo() >>> >>> R version 2.12.0 (2010-10-15) >>> Platform: x86_64-unknown-linux-gnu (64-bit) >>> >>> locale: >>> ?[1] LC_CTYPE=en_US.UTF-8 ? ? ? LC_NUMERIC=C >>> ?[3] LC_TIME=en_US.UTF-8 ? ? ? ?LC_COLLATE=en_US.UTF-8 >>> ?[5] LC_MONETARY=C ? ? ? ? ? ? ?LC_MESSAGES=en_US.UTF-8 >>> ?[7] LC_PAPER=en_US.UTF-8 ? ? ? LC_NAME=C >>> ?[9] LC_ADDRESS=C ? ? ? ? ? ? ? LC_TELEPHONE=C >>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C >>> >>> attached base packages: >>> [1] stats ? ? graphics ?grDevices utils ? ? datasets ?tools ? ? methods >>> [8] base >>> >>> other attached packages: >>> [1] hgu133acdf_2.7.0 ? ? ? ? ?ALLMLL_1.2.8 >>> [3] arrayQualityMetrics_3.2.0 vsn_3.18.0 >>> [5] affyPLM_1.26.0 ? ? ? ? ? ?preprocessCore_1.12.0 >>> [7] gcrma_2.22.0 ? ? ? ? ? ? ?affy_1.28.0 >>> [9] Biobase_2.10.0 >>> >>> loaded via a namespace (and not attached): >>> ?[1] affyio_1.18.0 ? ? ? ?annotate_1.28.0 ? ? ?AnnotationDbi_1.12.0 >>> ?[4] beadarray_2.0.1 ? ? ?Biostrings_2.18.0 ? ?DBI_0.2-5 >>> ?[7] genefilter_1.32.0 ? ?grid_2.12.0 ? ? ? ? ?hwriter_1.2 >>> [10] IRanges_1.8.2 ? ? ? ?KernSmooth_2.23-4 ? ?lattice_0.19-13 >>> [13] latticeExtra_0.6-14 ?limma_3.6.5 ? ? ? ? ?marray_1.28.0 >>> [16] RColorBrewer_1.0-2 ? RSQLite_0.9-2 ? ? ? ?simpleaffy_2.26.0 >>> [19] splines_2.12.0 ? ? ? stats4_2.12.0 ? ? ? ?survival_2.35-8 >>> [22] SVGAnnotation_0.6-0 ?XML_3.2-0 ? ? ? ? ? ?xtable_1.5-6 >>> >>> On another machine with the same sessionInfo I get another error: >>> Error in aqm.highlight(doc, annotationInfo = annotationInfo) : >>> ?'length(annotationInfo$annotation)' must be equal to 'length(series)', >>> the >>> #number of objects in the plot. >>> >>>> traceback() >>> >>> 7: stop("'length(annotationInfo$annotation)' must be equal to >>> 'length(series)', the number of objects in the plot.") >>> 6: aqm.highlight(doc, annotationInfo = annotationInfo) >>> 5: annotateSvgMatplot(svgtemp, nameimg, annotationInfo = qm$svg) >>> 4: aqm.report.qm(p, obj[[i]], i, names(obj)[i]) >>> 3: aqm.writereport(reporttitle, expressionset, obj) >>> 2: arrayQualityMetrics(expressionset = MLL.A, outdir = "MLL", force = >>> TRUE, >>> ? ? ? do.logtransform = TRUE) >>> 1: arrayQualityMetrics(expressionset = MLL.A, outdir = "MLL", force = >>> TRUE, >>> ? ? ? do.logtransform = TRUE) >>> >>> Can someone help? >>> >>> Thanks. >>> James. >>> >>>> >>>> Martin >>>> >>>>> >>>>> Any ideas? >>>>> James. >>>>> >>>>> My updated session: >>>>>> >>>>>> sessionInfo() >>>>> >>>>> R version 2.12.0 (2010-10-15) >>>>> Platform: x86_64-unknown-linux-gnu (64-bit) >>>>> >>>>> locale: >>>>> ?[1] LC_CTYPE=en_US.UTF-8 ? ? ? LC_NUMERIC=C >>>>> ?[3] LC_TIME=en_US.UTF-8 ? ? ? ?LC_COLLATE=en_US.UTF-8 >>>>> ?[5] LC_MONETARY=C ? ? ? ? ? ? ?LC_MESSAGES=en_US.UTF-8 >>>>> ?[7] LC_PAPER=en_US.UTF-8 ? ? ? LC_NAME=C >>>>> ?[9] LC_ADDRESS=C ? ? ? ? ? ? ? LC_TELEPHONE=C >>>>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C >>>>> >>>>> attached base packages: >>>>> [1] stats ? ? graphics ?grDevices utils ? ? datasets ?tools ? ? methods >>>>> [8] base >>>>> >>>>> other attached packages: >>>>> [1] arrayQualityMetrics_3.2.0 vsn_3.18.0 >>>>> [3] affyPLM_1.26.0 ? ? ? ? ? ?preprocessCore_1.12.0 >>>>> [5] gcrma_2.22.0 ? ? ? ? ? ? ?affy_1.28.0 >>>>> [7] Biobase_2.10.0 >>>>> >>>>> loaded via a namespace (and not attached): >>>>> ?[1] affyio_1.18.0 ? ? ? ?annotate_1.28.0 ? ? ?AnnotationDbi_1.12.0 >>>>> ?[4] beadarray_2.0.1 ? ? ?Biostrings_2.18.0 ? ?DBI_0.2-5 >>>>> ?[7] genefilter_1.32.0 ? ?grid_2.12.0 ? ? ? ? ?hwriter_1.2 >>>>> [10] IRanges_1.8.1 ? ? ? ?lattice_0.19-13 ? ? ?latticeExtra_0.6-14 >>>>> [13] limma_3.6.4 ? ? ? ? ?marray_1.28.0 ? ? ? ?RColorBrewer_1.0-2 >>>>> [16] RSQLite_0.9-2 ? ? ? ?simpleaffy_2.26.0 ? ?splines_2.12.0 >>>>> [19] stats4_2.12.0 ? ? ? ?survival_2.35-8 ? ? ?SVGAnnotation_0.6-0 >>>>> [22] XML_3.2-0 ? ? ? ? ? ?xtable_1.5-6 >>>>> >>>>> >>>>>>> >>>>>>> Thanks. >>>>>>> James. >>>>>>> >>>>>>> Here is the first example from the arrayQualityMetrics vignette >>>>>>> (inst/scripts/arrayQualityMetrics.Rnw) >>>>>>> >>>>>>> library("ALLMLL") >>>>>>> data("MLL.A") >>>>>>> >>>>>>> library("arrayQualityMetrics") >>>>>>> arrayQualityMetrics(expressionset = MLL.A, >>>>>>> ? ? ? ? ? ? ? ? ? ? ?outdir = "MLL", >>>>>>> ? ? ? ? ? ? ? ? ? ? ?force = TRUE, >>>>>>> ? ? ? ? ? ? ? ? ? ? ?do.logtransform = TRUE) >>>>>>> >>>>>>> produces: >>>>>>> Error in UseMethod("xmlAttrs", node) : no applicable method for >>>>>>> 'xmlAttrs' applied to an object of class "NULL" >>>>>>> >>>>>>> without producing all the plots (stops after section 3: Between array >>>>>>> comparison), the html report is truncated. >>>>>>> >>>>>>>> sessionInfo() >>>>>>> >>>>>>> R version 2.12.0 (2010-10-15) >>>>>>> Platform: x86_64-unknown-linux-gnu (64-bit) >>>>>>> >>>>>>> locale: >>>>>>> ? [1] LC_CTYPE=en_US.UTF-8 ? ? ? LC_NUMERIC=C >>>>>>> ? [3] LC_TIME=en_US.UTF-8 ? ? ? ?LC_COLLATE=en_US.UTF-8 >>>>>>> ? [5] LC_MONETARY=C ? ? ? ? ? ? ?LC_MESSAGES=en_US.UTF-8 >>>>>>> ? [7] LC_PAPER=en_US.UTF-8 ? ? ? LC_NAME=C >>>>>>> ? [9] LC_ADDRESS=C ? ? ? ? ? ? ? LC_TELEPHONE=C >>>>>>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C >>>>>>> >>>>>>> attached base packages: >>>>>>> [1] stats ? ? graphics ?grDevices utils ? ? datasets ?tools >>>>>>> methods >>>>>>> [8] base >>>>>>> >>>>>>> other attached packages: >>>>>>> [1] ALLMLL_1.2.8 ? ? ? ? ? ? ?arrayQualityMetrics_3.2.0 >>>>>>> [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_1.27.3 >>>>>>> AnnotationDbi_1.11.10 >>>>>>> ? [4] beadarray_2.0.1 ? ? ? Biostrings_2.17.48 ? ?DBI_0.2-5 >>>>>>> ? [7] genefilter_1.31.2 ? ? grid_2.12.0 ? ? ? ? ? hwriter_1.2 >>>>>>> [10] IRanges_1.7.40 ? ? ? ?lattice_0.19-13 ? ? ? latticeExtra_0.6-14 >>>>>>> [13] limma_3.5.21 ? ? ? ? ?marray_1.27.0 ? ? ? ? RColorBrewer_1.0-2 >>>>>>> [16] RSQLite_0.9-2 ? ? ? ? simpleaffy_2.25.0 ? ? splines_2.12.0 >>>>>>> [19] stats4_2.12.0 ? ? ? ? survival_2.35-8 ? ? ? SVGAnnotation_0.6-0 >>>>>>> [22] XML_3.2-0 ? ? ? ? ? ? xtable_1.5-6 >>>>>>>> >>>>>>> >>>>>>> _______________________________________________ >>>>>>> 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 >>>>>> >>>>>> >>>> >>>> >>> >>> _______________________________________________ >>> 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 >>> >
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btw, don't worry about my affyio version... i know i'm doing something i shouldn't. b On 28 October 2010 14:23, Benilton Carvalho <beniltoncarvalho at="" gmail.com=""> wrote: > For the record, I can't reproduce the issue, but my libxml2 is 2.7.3 > > sessionInfo() is shown below: > > R version 2.12.0 Patched (2010-10-21 r53386) > Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) > > locale: > [1] en_GB.UTF-8/en_GB.UTF-8/C/C/en_GB.UTF-8/en_GB.UTF-8 > > attached base packages: > [1] stats ? ? graphics ?grDevices datasets ?utils ? ? methods ? base > > other attached packages: > [1] hgu133acdf_2.7.0 ? ? ? ? ?arrayQualityMetrics_3.2.0 > [3] vsn_3.18.0 ? ? ? ? ? ? ? ?affyPLM_1.26.0 > [5] preprocessCore_1.12.0 ? ? gcrma_2.22.0 > [7] ALLMLL_1.2.8 ? ? ? ? ? ? ?affy_1.28.0 > [9] Biobase_2.10.0 > > loaded via a namespace (and not attached): > ?[1] affyio_1.19.1 ? ? ? ?annotate_1.28.0 ? ? ?AnnotationDbi_1.12.0 > ?[4] beadarray_2.0.1 ? ? ?Biostrings_2.18.0 ? ?DBI_0.2-5 > ?[7] genefilter_1.32.0 ? ?grid_2.12.0 ? ? ? ? ?hwriter_1.2 > [10] IRanges_1.8.0 ? ? ? ?KernSmooth_2.23-4 ? ?lattice_0.19-13 > [13] latticeExtra_0.6-14 ?limma_3.6.5 ? ? ? ? ?marray_1.28.0 > [16] RColorBrewer_1.0-2 ? RSQLite_0.9-2 ? ? ? ?simpleaffy_2.26.0 > [19] splines_2.12.0 ? ? ? stats4_2.12.0 ? ? ? ?survival_2.35-8 > [22] SVGAnnotation_0.6-0 ?tools_2.12.0 ? ? ? ? XML_3.2-0 > [25] xtable_1.5-6 > > > On 28 October 2010 14:16, James F. Reid <james.reid at="" ifom-ieo-="" campus.it=""> wrote: >> Hi, >> >> >> On 10/28/2010 03:06 PM, Benilton Carvalho wrote: >>> >>> what do you get for >>> >>> xml2-config --version >>> >>> ? >> >> on the machine that produces the xml based error >> xml2-config --version >> 2.6.26 >> >> whereas on the machine that complains about >> length(annotationInfo$annotation) I have a newer version: >> 2.7.7 >> >> James. >> >>> >>> On 28 October 2010 13:36, James F. Reid<james.reid at="" ifom-ieo-="" campus.it=""> >>> ?wrote: >>>> >>>> Hi Martin, >>>> >>>> On 10/27/2010 04:41 PM, Martin Morgan wrote: >>>>> >>>>> On 10/27/2010 06:16 AM, James F. Reid wrote: >>>>>> >>>>>> Dear Martin, >>>>>> >>>>>> On 27/10/2010 14:17, Martin Morgan wrote: >>>>>>> >>>>>>> On 10/27/2010 02:26 AM, James F. Reid wrote: >>>>>>>> >>>>>>>> Dear all, >>>>>>>> >>>>>>>> Since upgrading to the latest version of Bioconductor, I am having >>>>>>>> problems using the package arrayQualityMetrics because it does not >>>>>>>> produce a full report (both for single and double channels arrays). >>>>>>> >>>>>>> HI James -- have you tried updating your installed packages? I notice >>>>>>> below that you are using the 'release' version of R (2.12.0) but that >>>>>>> many of your packages are from a previous 'devel' version of >>>>>>> Bioconductor (odd-numbered second version field, e.g., Biobase 2.9.2). >>>>>>> >>>>>>> See >>>>>>> >>>>>>> >>>>>>> http://bioconductor.org/install/index.html#update- bioconductor-packages >>>>>>> >>>>>>> Martin >>>>>>> >>>>>> >>>>>> you're right and I should have updated my packages before sending a >>>>>> mail >>>>>> to the list. However even after updating the problem remains. The error >>>>>> message points to a problem using the library XML. When installing XML >>>>>> I >>>>>> noticed the following: >>>>>> Creating a new generic function for "source" in "XML" >>>>>> Warning in .NonstandardGenericTest(body(fdef), name, stdGenericBody) : >>>>>> ? the supplied generic function definition for xmlClone does not seem >>>>>> to >>>>>> call 'standardGeneric'; no methods will be dispatched! >>>>> >>>>> Hi James -- >>>>> >>>>> Hmm. For what it's worth, I don't have problems with a similar set of >>>>> packages. I have >>>>> >>>>>> capabilities() >>>>> >>>>> ? ? jpeg ? ? ?png ? ? tiff ? ?tcltk ? ? ?X11 ? ? aqua http/ftp ?sockets >>>>> ? ? TRUE ? ? TRUE ? ? TRUE ? ? TRUE ? ? TRUE ? ?FALSE ? ? TRUE ? ? TRUE >>>>> ? libxml ? ? fifo ? cledit ? ?iconv ? ? ?NLS ?profmem ? ?cairo >>>>> ? ? TRUE ? ? TRUE ? ? TRUE ? ? TRUE ? ? TRUE ? ?FALSE ? ? TRUE >>>>> >>>>> What does traceback() say after the error? Do you have the cdf for this >>>>> package (hgu133acdf_2.7.0; library('hgu133acdf') already installed? The >>>>> installation warning for XML is not likely the problem. >>>> >>>> I have the same capabilities() on my platform. >>>> Here is the output of traceback() together with my sessionInfo. >>>> >>>> Error in UseMethod("xmlAttrs", node) : >>>> ?no applicable method for 'xmlAttrs' applied to an object of class "NULL" >>>> >>>>> traceback() >>>> >>>> 18: xmlAttrs(node, addNamespace) >>>> 17: xmlGetAttr(clipPath[["path"]], "d") >>>> 16: getRect(xmlGetAttr(clipPath[["path"]], "d")) >>>> 15: getPlotRegion(n) >>>> 14: FUN(X[[1L]], ...) >>>> 13: lapply(X, FUN, ...) >>>> 12: sapply(tmp, function(n) all(getPlotRegion(n) == vb)) >>>> 11: getPlotRegionNodes(doc) >>>> 10: is.vector(X) >>>> 9: lapply(getPlotRegionNodes(doc), getPlotPoints) >>>> 8: getPlotPoints.XMLInternalDocument(doc) >>>> 7: annotationInfo$getfun(doc) >>>> 6: aqm.highlight(doc, annotationInfo = annotationInfo) >>>> 5: annotateSvgMatplot(svgtemp, nameimg, annotationInfo = qm$svg) >>>> 4: aqm.report.qm(p, obj[[i]], i, names(obj)[i]) >>>> 3: aqm.writereport(reporttitle, expressionset, obj) >>>> 2: arrayQualityMetrics(expressionset = MLL.A, outdir = "MLL", force = >>>> TRUE, >>>> ? ? ? do.logtransform = TRUE) >>>> 1: arrayQualityMetrics(expressionset = MLL.A, outdir = "MLL", force = >>>> TRUE, >>>> ? ? ? do.logtransform = TRUE) >>>> >>>>> sessionInfo() >>>> >>>> R version 2.12.0 (2010-10-15) >>>> Platform: x86_64-unknown-linux-gnu (64-bit) >>>> >>>> locale: >>>> ?[1] LC_CTYPE=en_US.UTF-8 ? ? ? LC_NUMERIC=C >>>> ?[3] LC_TIME=en_US.UTF-8 ? ? ? ?LC_COLLATE=en_US.UTF-8 >>>> ?[5] LC_MONETARY=C ? ? ? ? ? ? ?LC_MESSAGES=en_US.UTF-8 >>>> ?[7] LC_PAPER=en_US.UTF-8 ? ? ? LC_NAME=C >>>> ?[9] LC_ADDRESS=C ? ? ? ? ? ? ? LC_TELEPHONE=C >>>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C >>>> >>>> attached base packages: >>>> [1] stats ? ? graphics ?grDevices utils ? ? datasets ?tools ? ? methods >>>> [8] base >>>> >>>> other attached packages: >>>> [1] hgu133acdf_2.7.0 ? ? ? ? ?ALLMLL_1.2.8 >>>> [3] arrayQualityMetrics_3.2.0 vsn_3.18.0 >>>> [5] affyPLM_1.26.0 ? ? ? ? ? ?preprocessCore_1.12.0 >>>> [7] gcrma_2.22.0 ? ? ? ? ? ? ?affy_1.28.0 >>>> [9] Biobase_2.10.0 >>>> >>>> loaded via a namespace (and not attached): >>>> ?[1] affyio_1.18.0 ? ? ? ?annotate_1.28.0 ? ? ?AnnotationDbi_1.12.0 >>>> ?[4] beadarray_2.0.1 ? ? ?Biostrings_2.18.0 ? ?DBI_0.2-5 >>>> ?[7] genefilter_1.32.0 ? ?grid_2.12.0 ? ? ? ? ?hwriter_1.2 >>>> [10] IRanges_1.8.2 ? ? ? ?KernSmooth_2.23-4 ? ?lattice_0.19-13 >>>> [13] latticeExtra_0.6-14 ?limma_3.6.5 ? ? ? ? ?marray_1.28.0 >>>> [16] RColorBrewer_1.0-2 ? RSQLite_0.9-2 ? ? ? ?simpleaffy_2.26.0 >>>> [19] splines_2.12.0 ? ? ? stats4_2.12.0 ? ? ? ?survival_2.35-8 >>>> [22] SVGAnnotation_0.6-0 ?XML_3.2-0 ? ? ? ? ? ?xtable_1.5-6 >>>> >>>> On another machine with the same sessionInfo I get another error: >>>> Error in aqm.highlight(doc, annotationInfo = annotationInfo) : >>>> ?'length(annotationInfo$annotation)' must be equal to 'length(series)', >>>> the >>>> #number of objects in the plot. >>>> >>>>> traceback() >>>> >>>> 7: stop("'length(annotationInfo$annotation)' must be equal to >>>> 'length(series)', the number of objects in the plot.") >>>> 6: aqm.highlight(doc, annotationInfo = annotationInfo) >>>> 5: annotateSvgMatplot(svgtemp, nameimg, annotationInfo = qm$svg) >>>> 4: aqm.report.qm(p, obj[[i]], i, names(obj)[i]) >>>> 3: aqm.writereport(reporttitle, expressionset, obj) >>>> 2: arrayQualityMetrics(expressionset = MLL.A, outdir = "MLL", force = >>>> TRUE, >>>> ? ? ? do.logtransform = TRUE) >>>> 1: arrayQualityMetrics(expressionset = MLL.A, outdir = "MLL", force = >>>> TRUE, >>>> ? ? ? do.logtransform = TRUE) >>>> >>>> Can someone help? >>>> >>>> Thanks. >>>> James. >>>> >>>>> >>>>> Martin >>>>> >>>>>> >>>>>> Any ideas? >>>>>> James. >>>>>> >>>>>> My updated session: >>>>>>> >>>>>>> sessionInfo() >>>>>> >>>>>> R version 2.12.0 (2010-10-15) >>>>>> Platform: x86_64-unknown-linux-gnu (64-bit) >>>>>> >>>>>> locale: >>>>>> ?[1] LC_CTYPE=en_US.UTF-8 ? ? ? LC_NUMERIC=C >>>>>> ?[3] LC_TIME=en_US.UTF-8 ? ? ? ?LC_COLLATE=en_US.UTF-8 >>>>>> ?[5] LC_MONETARY=C ? ? ? ? ? ? ?LC_MESSAGES=en_US.UTF-8 >>>>>> ?[7] LC_PAPER=en_US.UTF-8 ? ? ? LC_NAME=C >>>>>> ?[9] LC_ADDRESS=C ? ? ? ? ? ? ? LC_TELEPHONE=C >>>>>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C >>>>>> >>>>>> attached base packages: >>>>>> [1] stats ? ? graphics ?grDevices utils ? ? datasets ?tools ? ? methods >>>>>> [8] base >>>>>> >>>>>> other attached packages: >>>>>> [1] arrayQualityMetrics_3.2.0 vsn_3.18.0 >>>>>> [3] affyPLM_1.26.0 ? ? ? ? ? ?preprocessCore_1.12.0 >>>>>> [5] gcrma_2.22.0 ? ? ? ? ? ? ?affy_1.28.0 >>>>>> [7] Biobase_2.10.0 >>>>>> >>>>>> loaded via a namespace (and not attached): >>>>>> ?[1] affyio_1.18.0 ? ? ? ?annotate_1.28.0 ? ? ?AnnotationDbi_1.12.0 >>>>>> ?[4] beadarray_2.0.1 ? ? ?Biostrings_2.18.0 ? ?DBI_0.2-5 >>>>>> ?[7] genefilter_1.32.0 ? ?grid_2.12.0 ? ? ? ? ?hwriter_1.2 >>>>>> [10] IRanges_1.8.1 ? ? ? ?lattice_0.19-13 ? ? ?latticeExtra_0.6-14 >>>>>> [13] limma_3.6.4 ? ? ? ? ?marray_1.28.0 ? ? ? ?RColorBrewer_1.0-2 >>>>>> [16] RSQLite_0.9-2 ? ? ? ?simpleaffy_2.26.0 ? ?splines_2.12.0 >>>>>> [19] stats4_2.12.0 ? ? ? ?survival_2.35-8 ? ? ?SVGAnnotation_0.6-0 >>>>>> [22] XML_3.2-0 ? ? ? ? ? ?xtable_1.5-6 >>>>>> >>>>>> >>>>>>>> >>>>>>>> Thanks. >>>>>>>> James. >>>>>>>> >>>>>>>> Here is the first example from the arrayQualityMetrics vignette >>>>>>>> (inst/scripts/arrayQualityMetrics.Rnw) >>>>>>>> >>>>>>>> library("ALLMLL") >>>>>>>> data("MLL.A") >>>>>>>> >>>>>>>> library("arrayQualityMetrics") >>>>>>>> arrayQualityMetrics(expressionset = MLL.A, >>>>>>>> ? ? ? ? ? ? ? ? ? ? ?outdir = "MLL", >>>>>>>> ? ? ? ? ? ? ? ? ? ? ?force = TRUE, >>>>>>>> ? ? ? ? ? ? ? ? ? ? ?do.logtransform = TRUE) >>>>>>>> >>>>>>>> produces: >>>>>>>> Error in UseMethod("xmlAttrs", node) : no applicable method for >>>>>>>> 'xmlAttrs' applied to an object of class "NULL" >>>>>>>> >>>>>>>> without producing all the plots (stops after section 3: Between array >>>>>>>> comparison), the html report is truncated. >>>>>>>> >>>>>>>>> sessionInfo() >>>>>>>> >>>>>>>> R version 2.12.0 (2010-10-15) >>>>>>>> Platform: x86_64-unknown-linux-gnu (64-bit) >>>>>>>> >>>>>>>> locale: >>>>>>>> ? [1] LC_CTYPE=en_US.UTF-8 ? ? ? LC_NUMERIC=C >>>>>>>> ? [3] LC_TIME=en_US.UTF-8 ? ? ? ?LC_COLLATE=en_US.UTF-8 >>>>>>>> ? [5] LC_MONETARY=C ? ? ? ? ? ? ?LC_MESSAGES=en_US.UTF-8 >>>>>>>> ? [7] LC_PAPER=en_US.UTF-8 ? ? ? LC_NAME=C >>>>>>>> ? [9] LC_ADDRESS=C ? ? ? ? ? ? ? LC_TELEPHONE=C >>>>>>>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C >>>>>>>> >>>>>>>> attached base packages: >>>>>>>> [1] stats ? ? graphics ?grDevices utils ? ? datasets ?tools >>>>>>>> methods >>>>>>>> [8] base >>>>>>>> >>>>>>>> other attached packages: >>>>>>>> [1] ALLMLL_1.2.8 ? ? ? ? ? ? ?arrayQualityMetrics_3.2.0 >>>>>>>> [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_1.27.3 >>>>>>>> AnnotationDbi_1.11.10 >>>>>>>> ? [4] beadarray_2.0.1 ? ? ? Biostrings_2.17.48 ? ?DBI_0.2-5 >>>>>>>> ? [7] genefilter_1.31.2 ? ? grid_2.12.0 ? ? ? ? ? hwriter_1.2 >>>>>>>> [10] IRanges_1.7.40 ? ? ? ?lattice_0.19-13 ? ? ? latticeExtra_0.6-14 >>>>>>>> [13] limma_3.5.21 ? ? ? ? ?marray_1.27.0 ? ? ? ? RColorBrewer_1.0-2 >>>>>>>> [16] RSQLite_0.9-2 ? ? ? ? simpleaffy_2.25.0 ? ? splines_2.12.0 >>>>>>>> [19] stats4_2.12.0 ? ? ? ? survival_2.35-8 ? ? ? SVGAnnotation_0.6-0 >>>>>>>> [22] XML_3.2-0 ? ? ? ? ? ? xtable_1.5-6 >>>>>>>>> >>>>>>>> >>>>>>>> _______________________________________________ >>>>>>>> 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 >>>>>>> >>>>>>> >>>>> >>>>> >>>> >>>> _______________________________________________ >>>> 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 >>>> >> >
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Hi James, 1.) the "length(annotationInfo$annotation)" complaint is (as far as I currently understand it) related to a version incompatibility between newer versions of libcairo on your computer and the SVGAnnotation package. I am working with Duncan to sort this out. (See also https://stat.ethz.ch/pipermail/bioconductor/2010-October/035958.html) What is the output of: pkg-config --modversion cairo on both of your machines? 2.) I have never seen the other error you report (about something being NULL that should be an XML-node), but it smells like it could be a consequence of the same underlying problem: format or content of an SVGH graphics file (which is an XML document) that is not expected by SVGAnnotation. I am sorry that this functionality is so brittle. When it works, it is great, see e.g. http://www-huber.embl.de/users/whuber/arrayQualityMetrics- Reports/CCl4-RIN/QMreport.html Figures 4, 6 and http://www-huber.embl.de/users/whuber/arrayQualityMetrics- Reports/MLL/QMreport.html Figs. 4, 6, 8. I am working right now on making it more robust! For now, all I can offer is the workaround already suggested in the 21 Oct post. Sorry for that, this seems to be the cost of being 'cutting- edge'. Best wishes Wolfgang Il Oct/28/10 3:16 PM, James F. Reid ha scritto: > Hi, > > > On 10/28/2010 03:06 PM, Benilton Carvalho wrote: >> what do you get for >> >> xml2-config --version >> >> ? > > on the machine that produces the xml based error > xml2-config --version > 2.6.26 > > whereas on the machine that complains about > length(annotationInfo$annotation) I have a newer version: > 2.7.7 > > James. > >> >> On 28 October 2010 13:36, James F. Reid<james.reid at="" ifom-ieo-="" campus.it=""> >> wrote: >>> Hi Martin, >>> >>> On 10/27/2010 04:41 PM, Martin Morgan wrote: >>>> >>>> On 10/27/2010 06:16 AM, James F. Reid wrote: >>>>> >>>>> Dear Martin, >>>>> >>>>> On 27/10/2010 14:17, Martin Morgan wrote: >>>>>> >>>>>> On 10/27/2010 02:26 AM, James F. Reid wrote: >>>>>>> >>>>>>> Dear all, >>>>>>> >>>>>>> Since upgrading to the latest version of Bioconductor, I am having >>>>>>> problems using the package arrayQualityMetrics because it does not >>>>>>> produce a full report (both for single and double channels arrays). >>>>>> >>>>>> HI James -- have you tried updating your installed packages? I notice >>>>>> below that you are using the 'release' version of R (2.12.0) but that >>>>>> many of your packages are from a previous 'devel' version of >>>>>> Bioconductor (odd-numbered second version field, e.g., Biobase >>>>>> 2.9.2). >>>>>> >>>>>> See >>>>>> >>>>>> http://bioconductor.org/install/index.html#update-bioconductor- packages >>>>>> >>>>>> >>>>>> Martin >>>>>> >>>>> >>>>> you're right and I should have updated my packages before sending a >>>>> mail >>>>> to the list. However even after updating the problem remains. The >>>>> error >>>>> message points to a problem using the library XML. When installing >>>>> XML I >>>>> noticed the following: >>>>> Creating a new generic function for "source" in "XML" >>>>> Warning in .NonstandardGenericTest(body(fdef), name, stdGenericBody) : >>>>> the supplied generic function definition for xmlClone does not seem to >>>>> call 'standardGeneric'; no methods will be dispatched! >>>> >>>> Hi James -- >>>> >>>> Hmm. For what it's worth, I don't have problems with a similar set of >>>> packages. I have >>>> >>>>> capabilities() >>>> >>>> jpeg png tiff tcltk X11 aqua http/ftp sockets >>>> TRUE TRUE TRUE TRUE TRUE FALSE TRUE TRUE >>>> libxml fifo cledit iconv NLS profmem cairo >>>> TRUE TRUE TRUE TRUE TRUE FALSE TRUE >>>> >>>> What does traceback() say after the error? Do you have the cdf for this >>>> package (hgu133acdf_2.7.0; library('hgu133acdf') already installed? The >>>> installation warning for XML is not likely the problem. >>> >>> I have the same capabilities() on my platform. >>> Here is the output of traceback() together with my sessionInfo. >>> >>> Error in UseMethod("xmlAttrs", node) : >>> no applicable method for 'xmlAttrs' applied to an object of class "NULL" >>> >>>> traceback() >>> 18: xmlAttrs(node, addNamespace) >>> 17: xmlGetAttr(clipPath[["path"]], "d") >>> 16: getRect(xmlGetAttr(clipPath[["path"]], "d")) >>> 15: getPlotRegion(n) >>> 14: FUN(X[[1L]], ...) >>> 13: lapply(X, FUN, ...) >>> 12: sapply(tmp, function(n) all(getPlotRegion(n) == vb)) >>> 11: getPlotRegionNodes(doc) >>> 10: is.vector(X) >>> 9: lapply(getPlotRegionNodes(doc), getPlotPoints) >>> 8: getPlotPoints.XMLInternalDocument(doc) >>> 7: annotationInfo$getfun(doc) >>> 6: aqm.highlight(doc, annotationInfo = annotationInfo) >>> 5: annotateSvgMatplot(svgtemp, nameimg, annotationInfo = qm$svg) >>> 4: aqm.report.qm(p, obj[[i]], i, names(obj)[i]) >>> 3: aqm.writereport(reporttitle, expressionset, obj) >>> 2: arrayQualityMetrics(expressionset = MLL.A, outdir = "MLL", force = >>> TRUE, >>> do.logtransform = TRUE) >>> 1: arrayQualityMetrics(expressionset = MLL.A, outdir = "MLL", force = >>> TRUE, >>> do.logtransform = TRUE) >>> >>>> sessionInfo() >>> R version 2.12.0 (2010-10-15) >>> Platform: x86_64-unknown-linux-gnu (64-bit) >>> >>> locale: >>> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C >>> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 >>> [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 >>> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C >>> [9] LC_ADDRESS=C LC_TELEPHONE=C >>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C >>> >>> attached base packages: >>> [1] stats graphics grDevices utils datasets tools methods >>> [8] base >>> >>> other attached packages: >>> [1] hgu133acdf_2.7.0 ALLMLL_1.2.8 >>> [3] arrayQualityMetrics_3.2.0 vsn_3.18.0 >>> [5] affyPLM_1.26.0 preprocessCore_1.12.0 >>> [7] gcrma_2.22.0 affy_1.28.0 >>> [9] Biobase_2.10.0 >>> >>> loaded via a namespace (and not attached): >>> [1] affyio_1.18.0 annotate_1.28.0 AnnotationDbi_1.12.0 >>> [4] beadarray_2.0.1 Biostrings_2.18.0 DBI_0.2-5 >>> [7] genefilter_1.32.0 grid_2.12.0 hwriter_1.2 >>> [10] IRanges_1.8.2 KernSmooth_2.23-4 lattice_0.19-13 >>> [13] latticeExtra_0.6-14 limma_3.6.5 marray_1.28.0 >>> [16] RColorBrewer_1.0-2 RSQLite_0.9-2 simpleaffy_2.26.0 >>> [19] splines_2.12.0 stats4_2.12.0 survival_2.35-8 >>> [22] SVGAnnotation_0.6-0 XML_3.2-0 xtable_1.5-6 >>> >>> On another machine with the same sessionInfo I get another error: >>> Error in aqm.highlight(doc, annotationInfo = annotationInfo) : >>> 'length(annotationInfo$annotation)' must be equal to >>> 'length(series)', the >>> #number of objects in the plot. >>> >>>> traceback() >>> 7: stop("'length(annotationInfo$annotation)' must be equal to >>> 'length(series)', the number of objects in the plot.") >>> 6: aqm.highlight(doc, annotationInfo = annotationInfo) >>> 5: annotateSvgMatplot(svgtemp, nameimg, annotationInfo = qm$svg) >>> 4: aqm.report.qm(p, obj[[i]], i, names(obj)[i]) >>> 3: aqm.writereport(reporttitle, expressionset, obj) >>> 2: arrayQualityMetrics(expressionset = MLL.A, outdir = "MLL", force = >>> TRUE, >>> do.logtransform = TRUE) >>> 1: arrayQualityMetrics(expressionset = MLL.A, outdir = "MLL", force = >>> TRUE, >>> do.logtransform = TRUE) >>> >>> Can someone help? >>> >>> Thanks. >>> James. >>> >>>> >>>> Martin >>>> >>>>> >>>>> Any ideas? >>>>> James. >>>>> >>>>> My updated session: >>>>>> >>>>>> sessionInfo() >>>>> >>>>> R version 2.12.0 (2010-10-15) >>>>> Platform: x86_64-unknown-linux-gnu (64-bit) >>>>> >>>>> locale: >>>>> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C >>>>> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 >>>>> [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 >>>>> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C >>>>> [9] LC_ADDRESS=C LC_TELEPHONE=C >>>>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C >>>>> >>>>> attached base packages: >>>>> [1] stats graphics grDevices utils datasets tools methods >>>>> [8] base >>>>> >>>>> other attached packages: >>>>> [1] arrayQualityMetrics_3.2.0 vsn_3.18.0 >>>>> [3] affyPLM_1.26.0 preprocessCore_1.12.0 >>>>> [5] gcrma_2.22.0 affy_1.28.0 >>>>> [7] Biobase_2.10.0 >>>>> >>>>> loaded via a namespace (and not attached): >>>>> [1] affyio_1.18.0 annotate_1.28.0 AnnotationDbi_1.12.0 >>>>> [4] beadarray_2.0.1 Biostrings_2.18.0 DBI_0.2-5 >>>>> [7] genefilter_1.32.0 grid_2.12.0 hwriter_1.2 >>>>> [10] IRanges_1.8.1 lattice_0.19-13 latticeExtra_0.6-14 >>>>> [13] limma_3.6.4 marray_1.28.0 RColorBrewer_1.0-2 >>>>> [16] RSQLite_0.9-2 simpleaffy_2.26.0 splines_2.12.0 >>>>> [19] stats4_2.12.0 survival_2.35-8 SVGAnnotation_0.6-0 >>>>> [22] XML_3.2-0 xtable_1.5-6 >>>>> >>>>> >>>>>>> >>>>>>> Thanks. >>>>>>> James. >>>>>>> >>>>>>> Here is the first example from the arrayQualityMetrics vignette >>>>>>> (inst/scripts/arrayQualityMetrics.Rnw) >>>>>>> >>>>>>> library("ALLMLL") >>>>>>> data("MLL.A") >>>>>>> >>>>>>> library("arrayQualityMetrics") >>>>>>> arrayQualityMetrics(expressionset = MLL.A, >>>>>>> outdir = "MLL", >>>>>>> force = TRUE, >>>>>>> do.logtransform = TRUE) >>>>>>> >>>>>>> produces: >>>>>>> Error in UseMethod("xmlAttrs", node) : no applicable method for >>>>>>> 'xmlAttrs' applied to an object of class "NULL" >>>>>>> >>>>>>> without producing all the plots (stops after section 3: Between >>>>>>> array >>>>>>> comparison), the html report is truncated. >>>>>>> >>>>>>>> sessionInfo() >>>>>>> >>>>>>> R version 2.12.0 (2010-10-15) >>>>>>> Platform: x86_64-unknown-linux-gnu (64-bit) >>>>>>> >>>>>>> locale: >>>>>>> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C >>>>>>> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 >>>>>>> [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 >>>>>>> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C >>>>>>> [9] LC_ADDRESS=C LC_TELEPHONE=C >>>>>>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C >>>>>>> >>>>>>> attached base packages: >>>>>>> [1] stats graphics grDevices utils datasets tools methods >>>>>>> [8] base >>>>>>> >>>>>>> other attached packages: >>>>>>> [1] ALLMLL_1.2.8 arrayQualityMetrics_3.2.0 >>>>>>> [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_1.27.3 AnnotationDbi_1.11.10 >>>>>>> [4] beadarray_2.0.1 Biostrings_2.17.48 DBI_0.2-5 >>>>>>> [7] genefilter_1.31.2 grid_2.12.0 hwriter_1.2 >>>>>>> [10] IRanges_1.7.40 lattice_0.19-13 latticeExtra_0.6-14 >>>>>>> [13] limma_3.5.21 marray_1.27.0 RColorBrewer_1.0-2 >>>>>>> [16] RSQLite_0.9-2 simpleaffy_2.25.0 splines_2.12.0 >>>>>>> [19] stats4_2.12.0 survival_2.35-8 SVGAnnotation_0.6-0 >>>>>>> [22] XML_3.2-0 xtable_1.5-6 >>>>>>>> >>>>>>> >>>>>>> _______________________________________________ >>>>>>> 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 >>>>>> >>>>>> >>>> >>>> >>> >>> _______________________________________________ >>> 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 >>> > > _______________________________________________ > 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
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James F. Reid ▴ 610
@james-f-reid-3148
Last seen 10.3 years ago
Wolfgang Huber <whuber at="" ...=""> writes: > > Hi James, > > 1.) the "length(annotationInfo$annotation)" complaint is (as far as I > currently understand it) related to a version incompatibility between > newer versions of libcairo on your computer and the SVGAnnotation > package. I am working with Duncan to sort this out. (See also > https://stat.ethz.ch/pipermail/bioconductor/2010-October/035958.html) > > What is the output of: > pkg-config --modversion cairo > on both of your machines? Hi Wolfgang, on the machine with the length complaint I have 1.10.0 and on the machine with the XML-node complaint I have 1.2.4. Thanks. James. > > 2.) I have never seen the other error you report (about something being > NULL that should be an XML-node), but it smells like it could be a > consequence of the same underlying problem: format or content of an SVGH > graphics file (which is an XML document) that is not expected by > SVGAnnotation. > > I am sorry that this functionality is so brittle. When it works, it is > great, see e.g. > http://www-huber.embl.de/users/whuber/arrayQualityMetrics- Reports/CCl4-RIN/QMreport.html > Figures 4, 6 and > http://www-huber.embl.de/users/whuber/arrayQualityMetrics- Reports/MLL/QMreport.html > Figs. 4, 6, 8. I am working right now on making it more robust! > > For now, all I can offer is the workaround already suggested in the 21 > Oct post. Sorry for that, this seems to be the cost of being 'cutting-edge'. > > Best wishes > Wolfgang >
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