[BioC] arrayQualityMetrics produces non-interactive PCA plot (Figure 3)

[Vladimir Zhurov]

> This is the first post, so I am not top-posting.

Hello all,

I am having a problem with the arrayQualityMetrics interactive SVG graphics.
The system is Ubuntu 10.04.3 LTS. Viewing was done in Firefox 8 and Chrome 15.

I would greatly appreciate any help with this issue.

Below is the information about system, libraries version and sample R session.

$ uname -a
Linux 2.6.32-36-generic #79-Ubuntu SMP Tue Nov 8 22:29:53 UTC 2011
x86_64 GNU/Linux

$ pkg-config --modversion cairo libxml-2.0
1.10.2
2.7.8

$ R --vanilla

R version 2.14.0 (2011-10-31)
Copyright (C) 2011 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
Platform: x86_64-pc-linux-gnu (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("ALLMLL")
Loading required package: affy
Loading required package: Biobase

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'browseVignettes()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation("pkgname")'.

> data("MLL.A")
> library("arrayQualityMetrics")
> arrayQualityMetrics(MLL.A,
+ outdir="MLL.A_Report",
+ force=TRUE,
+ do.logtransform=TRUE)
The directory 'MLL.A_Report' has been created.
Loading required package: AnnotationDbi

KernSmooth 2.23 loaded
Copyright M. P. Wand 1997-2009
> traceback()
No traceback available 
> warnings()
NULL
> sessionInfo()
R version 2.14.0 (2011-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_CA.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_CA.UTF-8        LC_COLLATE=en_CA.UTF-8    
 [5] LC_MONETARY=en_CA.UTF-8    LC_MESSAGES=en_CA.UTF-8   
 [7] LC_PAPER=C                 LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_CA.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] hgu133acdf_2.9.1           AnnotationDbi_1.16.8      
[3] arrayQualityMetrics_3.10.0 ALLMLL_1.2.11             
[5] affy_1.32.0                Biobase_2.14.0            

loaded via a namespace (and not attached):
 [1] affyio_1.22.0         affyPLM_1.30.0        annotate_1.32.0      
 [4] beadarray_2.4.1       BiocInstaller_1.2.1   Biostrings_2.22.0    
 [7] Cairo_1.5-0           cluster_1.14.1        DBI_0.2-5            
[10] genefilter_1.36.0     grid_2.14.0           Hmisc_3.9-0          
[13] hwriter_1.3           IRanges_1.12.4        KernSmooth_2.23-7    
[16] lattice_0.20-0        latticeExtra_0.6-19   limma_3.10.0         
[19] preprocessCore_1.16.0 RColorBrewer_1.0-5    RSQLite_0.11.0       
[22] setRNG_2009.11-1      splines_2.14.0        survival_2.36-10     
[25] SVGAnnotation_0.9-0   tools_2.14.0          vsn_3.22.0           
[28] XML_3.6-1             xtable_1.6-0          zlibbioc_1.0.0

More details that I had to move down here due to "top-posting" error from the
web form interface.
I apologize for the inconvenience. How is one supposed to post a R session?

Only figure 3 is broken, figures 6 and 12 are interactive. I have attempted
previously discussed fixes such as updating cairo and libxml.