Dear all, This is my first posting and I apologise for any errors or missing information. I am having trouble with arrayQualityMetrics interactive plots, which produce the following error message (within the index.html report): "Note: the figure is static - enhancement with interactive effects failed. This is either due to a version incompatibility of the 'SVGAnnotation' R package and your version of 'Cairo' or 'libcairo', or due to plot misformating. Please consult the Bioconductor mailing list, or contact the maintainer of 'arrayQualityMetrics' with a reproducible example in order to fix this problem." After reading the previous posting about this problem (https://stat.et hz.ch/pipermail/bioconductor/2011-December/042454.html) I updated Cairo and libxml2 using Macports (I am using a MacBook Pro with OSX 10.8.4 and Safari as my web browser) but the problem persists. All my installed packages are up-to-date. I have tried give a replicable example of my problem using "golubEsets" as the expression data and have attached a print-out of the session below. I would be very grateful for any help or advice anyone can provide, Best wishes, Steven R version 3.0.1 (2013-05-16) -- "Good Sport" Copyright (C) 2013 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin10.8.0 (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. Natural language support but running in an English locale R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library("arrayQualityMetrics") Creating a generic function for ???boxplot??? from package ???graphics??? in package ???affyPLM??? Creating a generic function for ???hist??? from package ???graphics??? in package ???affyPLM??? > library("golubEsets") Loading required package: Biobase Loading required package: BiocGenerics Loading required package: parallel Attaching package: ???BiocGenerics??? The following objects are masked from ???package:parallel???: clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB The following object is masked from ???package:stats???: xtabs The following objects are masked from ???package:base???: anyDuplicated, as.data.frame, cbind, colnames, duplicated, eval, Filter, Find, get, intersect, lapply, Map, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rep.int, rownames, sapply, setdiff, sort, table, tapply, union, unique, unlist Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. > data(Golub_Train) > Outputdir <- "/Users/mydirectory/array Quality Metrics/" > arrayQualityMetrics(Golub_Train, outdir=Outputdir) The directory '/Users/mydirectory/array Quality Metrics/' has been created. Error in tmp[i] : invalid subscript type 'list' KernSmooth 2.23 loaded Copyright M. P. Wand 1997-2009 Warning messages: 1: In KernSmooth::bkde2D(x, gridsize = nbin, bandwidth = bandwidth) : Binning grid too coarse for current (small) bandwidth: consider increasing 'gridsize' 2: In KernSmooth::bkde2D(x, gridsize = nbin, bandwidth = bandwidth) : Binning grid too coarse for current (small) bandwidth: consider increasing 'gridsize' 3: In KernSmooth::bkde2D(x, gridsize = nbin, bandwidth = bandwidth) : Binning grid too coarse for current (small) bandwidth: consider increasing 'gridsize' 4: In KernSmooth::bkde2D(x, gridsize = nbin, bandwidth = bandwidth) : Binning grid too coarse for current (small) bandwidth: consider increasing 'gridsize' 5: In KernSmooth::bkde2D(x, gridsize = nbin, bandwidth = bandwidth) : Binning grid too coarse for current (small) bandwidth: consider increasing 'gridsize' 6: In KernSmooth::bkde2D(x, gridsize = nbin, bandwidth = bandwidth) : Binning grid too coarse for current (small) bandwidth: consider increasing 'gridsize' -- output of sessionInfo(): > sessionInfo() R version 3.0.1 (2013-05-16) Platform: x86_64-apple-darwin10.8.0 (64-bit) locale: [1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8 attached base packages: [1] parallel stats graphics grDevices utils datasets methods base other attached packages: [1] golubEsets_1.4.13 Biobase_2.20.1 BiocGenerics_0.6.0 [4] arrayQualityMetrics_3.16.0 loaded via a namespace (and not attached): [1] affy_1.38.1 affyio_1.28.0 affyPLM_1.36.0 annotate_1.38.0 [5] AnnotationDbi_1.22.6 beadarray_2.10.0 BeadDataPackR_1.12.0 BiocInstaller_1.10.3 [9] Biostrings_2.28.0 Cairo_1.5-2 cluster_1.14.4 colorspace_1.2-3 [13] DBI_0.2-7 gcrma_2.32.0 genefilter_1.42.0 grid_3.0.1 [17] Hmisc_3.12-2 hwriter_1.3 IRanges_1.18.4 KernSmooth_2.23-10 [21] lattice_0.20-23 latticeExtra_0.6-26 limma_3.16.8 plyr_1.8 [25] preprocessCore_1.22.0 RColorBrewer_1.0-5 reshape2_1.2.2 rpart_4.1-3 [29] RSQLite_0.11.4 setRNG_2011.11-2 splines_3.0.1 stats4_3.0.1 [33] stringr_0.6.2 survival_2.37-4 SVGAnnotation_0.93-1 tools_3.0.1 [37] vsn_3.28.0 XML_3.95-0.2 xtable_1.7-1 zlibbioc_1.6.0 -- Sent via the guest posting facility at bioconductor.org.

Dear Steven Thank you for reporting this. What do you get from pkg-config --modversion cairo libxml-2.0 libxslt (in the OS terminal) The core of the problem is that arrayQualityMetrics uses the R-package SVGAnnotation to enhance the graphics files produced by R via the system library cairo. Since 'cairo' and 'SVGAnnotation' are maintained by different people, and the SVG-scraping done here relies -as far as I understand- on reverse engineering rather than on a formal API, this occasionally breaks. We'll try to come up with a fix for the short term, and/or a more sustainable solution for the long term. Kind regards Wolfgang On 8 Oct 2013, at 14:21, Steven Cowman [guest] <guest at="" bioconductor.org=""> wrote: > > Dear all, > > This is my first posting and I apologise for any errors or missing information. > > I am having trouble with arrayQualityMetrics interactive plots, which produce the following error message (within the index.html report): > > "Note: the figure is static - enhancement with interactive effects failed. This is either due to a version incompatibility of the 'SVGAnnotation' R package and your version of 'Cairo' or 'libcairo', or due to plot misformating. Please consult the Bioconductor mailing list, or contact the maintainer of 'arrayQualityMetrics' with a reproducible example in order to fix this problem." > > After reading the previous posting about this problem (https://stat. ethz.ch/pipermail/bioconductor/2011-December/042454.html) I updated Cairo and libxml2 using Macports (I am using a MacBook Pro with OSX 10.8.4 and Safari as my web browser) but the problem persists. All my installed packages are up-to-date. > > I have tried give a replicable example of my problem using "golubEsets" as the expression data and have attached a print-out of the session below. > > I would be very grateful for any help or advice anyone can provide, > > Best wishes, > > Steven > > > R version 3.0.1 (2013-05-16) -- "Good Sport" > Copyright (C) 2013 The R Foundation for Statistical Computing > Platform: x86_64-apple-darwin10.8.0 (64-bit) > > R is free software and comes with ABSOLUTELY NO WARRANTY. > You are welcome to redistribute it under certain conditions. > Type 'license()' or 'licence()' for distribution details. > > Natural language support but running in an English locale > > R is a collaborative project with many contributors. > Type 'contributors()' for more information and > 'citation()' on how to cite R or R packages in publications. > > Type 'demo()' for some demos, 'help()' for on-line help, or > 'help.start()' for an HTML browser interface to help. > Type 'q()' to quit R. > >> library("arrayQualityMetrics") > Creating a generic function for ???boxplot??? from package ???graphics??? in package ???affyPLM??? > Creating a generic function for ???hist??? from package ???graphics??? in package ???affyPLM??? >> library("golubEsets") > Loading required package: Biobase > Loading required package: BiocGenerics > Loading required package: parallel > > Attaching package: ???BiocGenerics??? > > The following objects are masked from ???package:parallel???: > > clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, > parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB > > The following object is masked from ???package:stats???: > > xtabs > > The following objects are masked from ???package:base???: > > anyDuplicated, as.data.frame, cbind, colnames, duplicated, eval, Filter, Find, get, > intersect, lapply, Map, mapply, match, mget, order, paste, pmax, pmax.int, pmin, > pmin.int, Position, rank, rbind, Reduce, rep.int, rownames, sapply, setdiff, sort, > table, tapply, union, unique, unlist > > Welcome to Bioconductor > > Vignettes contain introductory material; view with 'browseVignettes()'. To cite > Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. > >> data(Golub_Train) >> Outputdir <- "/Users/mydirectory/array Quality Metrics/" >> arrayQualityMetrics(Golub_Train, outdir=Outputdir) > The directory '/Users/mydirectory/array Quality Metrics/' has been created. > Error in tmp[i] : invalid subscript type 'list' > KernSmooth 2.23 loaded > Copyright M. P. Wand 1997-2009 > Warning messages: > 1: In KernSmooth::bkde2D(x, gridsize = nbin, bandwidth = bandwidth) : > Binning grid too coarse for current (small) bandwidth: consider increasing 'gridsize' > 2: In KernSmooth::bkde2D(x, gridsize = nbin, bandwidth = bandwidth) : > Binning grid too coarse for current (small) bandwidth: consider increasing 'gridsize' > 3: In KernSmooth::bkde2D(x, gridsize = nbin, bandwidth = bandwidth) : > Binning grid too coarse for current (small) bandwidth: consider increasing 'gridsize' > 4: In KernSmooth::bkde2D(x, gridsize = nbin, bandwidth = bandwidth) : > Binning grid too coarse for current (small) bandwidth: consider increasing 'gridsize' > 5: In KernSmooth::bkde2D(x, gridsize = nbin, bandwidth = bandwidth) : > Binning grid too coarse for current (small) bandwidth: consider increasing 'gridsize' > 6: In KernSmooth::bkde2D(x, gridsize = nbin, bandwidth = bandwidth) : > Binning grid too coarse for current (small) bandwidth: consider increasing 'gridsize' > > -- output of sessionInfo(): > >> sessionInfo() > R version 3.0.1 (2013-05-16) > Platform: x86_64-apple-darwin10.8.0 (64-bit) > > locale: > [1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8 > > attached base packages: > [1] parallel stats graphics grDevices utils datasets methods base > > other attached packages: > [1] golubEsets_1.4.13 Biobase_2.20.1 BiocGenerics_0.6.0 > [4] arrayQualityMetrics_3.16.0 > > loaded via a namespace (and not attached): > [1] affy_1.38.1 affyio_1.28.0 affyPLM_1.36.0 annotate_1.38.0 > [5] AnnotationDbi_1.22.6 beadarray_2.10.0 BeadDataPackR_1.12.0 BiocInstaller_1.10.3 > [9] Biostrings_2.28.0 Cairo_1.5-2 cluster_1.14.4 colorspace_1.2-3 > [13] DBI_0.2-7 gcrma_2.32.0 genefilter_1.42.0 grid_3.0.1 > [17] Hmisc_3.12-2 hwriter_1.3 IRanges_1.18.4 KernSmooth_2.23-10 > [21] lattice_0.20-23 latticeExtra_0.6-26 limma_3.16.8 plyr_1.8 > [25] preprocessCore_1.22.0 RColorBrewer_1.0-5 reshape2_1.2.2 rpart_4.1-3 > [29] RSQLite_0.11.4 setRNG_2011.11-2 splines_3.0.1 stats4_3.0.1 > [33] stringr_0.6.2 survival_2.37-4 SVGAnnotation_0.93-1 tools_3.0.1 > [37] vsn_3.28.0 XML_3.95-0.2 xtable_1.7-1 zlibbioc_1.6.0 > > -- > Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor

Dear Wolfgang, Thanks for your reply and explanation. Typing "pkg-config --modversion cairo libxml-2.0 libxslt" into the terminal give the message "command not found". I used Macports to install these libraries, so using the command "port installed" I found these version numbers: libxml2 @2.9.1_0 (active) libxslt @1.1.28_0 (active) cairo @1.12.16_0+x11 (active) I don't know whether or not this give the information you were looking for. Thanks and best wishes, Steve