[BioC] arrayQualityMetrics bug

[Lavinia Gordon]

Hi,
I think there is a problem with the 2.7 version of arrayQualityMetrics.
Following the example (in the script 
\R\R-2.12.0\library\arrayQualityMetrics\scripts\arrayQualityMetrics.R)

 > library("arrayQualityMetrics")
Loading required package: affyPLM
Loading required package: gcrma
Loading required package: preprocessCore

Attaching package: 'affyPLM'

The following object(s) are masked from 'package:stats':

     resid, residuals, weights

Loading required package: vsn
 > arrayQualityMetrics(expressionset = MLL.A,
+                     outdir = "MLL",
+                     force = TRUE,
+                     do.logtransform = TRUE)
The directory 'MLL' has been created.
Error : cannot allocate vector of size 77.4 Mb
KernSmooth 2.23 loaded
Copyright M. P. Wand 1997-2009
(loaded the KernSmooth namespace)
[[1]]

[[2]]

[[3]]

Error in aqm.report.qm(p, obj[[i]], i, names(obj)[i]) :
   could not find function "svg"
In addition: Warning message:
In arrayQualityMetrics(expressionset = MLL.A, outdir = "MLL", force = 
TRUE,  :
   Could not draw spatial distribution of intensities

 > traceback()
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: i386-pc-mingw32/i386 (32-bit)

locale:
[1] LC_COLLATE=English_Australia.1252  
LC_CTYPE=English_Australia.1252    LC_MONETARY=English_Australia.1252
[4] LC_NUMERIC=C                       LC_TIME=English_Australia.1252

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

other attached packages:
[1] hgu133acdf_2.7.0          arrayQualityMetrics_3.2.0 
vsn_3.18.0                affyPLM_1.26.0
[5] preprocessCore_1.12.0     gcrma_2.22.0              
ALLMLL_1.2.8              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 
beadarray_2.0.1      Biostrings_2.18.0
  [6] DBI_0.2-5            genefilter_1.32.0    grid_2.12.0          
hwriter_1.2          IRanges_1.8.2
[11] KernSmooth_2.23-4    lattice_0.19-13      latticeExtra_0.6-14  
limma_3.6.4          marray_1.28.0
[16] RColorBrewer_1.0-2   RSQLite_0.9-3        simpleaffy_2.26.0    
splines_2.12.0       stats4_2.12.0
[21] survival_2.36-1      SVGAnnotation_0.6-0  tools_2.12.0         
XML_3.2-0.1          xtable_1.5-6

with regards

Lavinia Gordon

-- 
Senior Bioinformatics Officer
Murdoch Childrens Research Institute
Royal Children's Hospital
Flemington Road
Parkville
Victoria 3052
Australia
www.mcri.edu.au