[BioC] arrayQualityMetrics does not produce interactive plots

Wolfgang Huber whuber at embl.de
Wed Oct 9 17:46:36 CEST 2013 

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.
> 
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