[BioC] missing figure text in arrayQualityMetrics

[Daniel Aaen Hansen]

Hi,

I just noticed that the axis labels, title and legend text have gone missing on some of the plots in the quality report. In fact I am not sure which upgrade caused the problem. More specifically, it is the three interactive plots that are missing text labels. The interactive mouse-over text works fine, it is only the static text that is missing from:

Figure 3: Principal Component Analysis.
Figure 6: Density plots.
Figure 12: RNA digestion plot.

Is anyone else having this problem? Or am I missing some dependencies in my installation (see below)? I am using the most recent development version of arrayQualityMetrics.

Best,
Daniel


> sessionInfo()
R version 2.15.1 (2012-06-22)
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=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=C                 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  methods   base     

other attached packages:
[1] arrayQualityMetrics_3.13.5

loaded via a namespace (and not attached):
 [1] affy_1.34.0           affyio_1.24.0         affyPLM_1.32.0       
 [4] annotate_1.34.0       AnnotationDbi_1.18.1  beadarray_2.6.0      
 [7] BeadDataPackR_1.8.0   Biobase_2.16.0        BiocGenerics_0.2.0   
[10] BiocInstaller_1.4.7   Biostrings_2.24.1     Cairo_1.5-1          
[13] cluster_1.14.2        colorspace_1.1-1      DBI_0.2-5            
[16] genefilter_1.38.0     grid_2.15.1           Hmisc_3.9-3          
[19] hwriter_1.3           IRanges_1.14.3        lattice_0.20-6       
[22] latticeExtra_0.6-19   limma_3.12.1          plyr_1.7.1           
[25] preprocessCore_1.18.0 RColorBrewer_1.0-5    reshape2_1.2.1       
[28] RSQLite_0.11.1        setRNG_2011.11-2      splines_2.15.1       
[31] stats4_2.15.1         stringr_0.6           survival_2.36-14     
[34] SVGAnnotation_0.9-0   vsn_3.24.0            XML_3.9-4            
[37] xtable_1.7-0          zlibbioc_1.2.0