Hi

I am trying to run arrayQualityMetrics on a number of pd.hugene.2.0.st samples (CEL files) and encountering the same error on two different machines with fresh installs of Bioconductor and arrayQualityMetrics, one with R 3.1.1 and another with 3.1.2 on Macs. The sessionInfo() of the 3.1.1 machine is as follow 

R version 3.1.1 (2014-07-10)
Platform: x86_64-apple-darwin13.1.0 (64-bit)

locale:
[1] en_CA.UTF-8/en_CA.UTF-8/en_CA.UTF-8/C/en_CA.UTF-8/en_CA.UTF-8

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils    
[7] datasets  methods   base     

other attached packages:
 [1] pd.hugene.2.0.st_3.10.0    RSQLite_1.0.0             
 [3] DBI_0.3.1                  oligo_1.30.0              
 [5] Biostrings_2.34.1          XVector_0.6.0             
 [7] IRanges_2.0.1              S4Vectors_0.4.0           
 [9] Biobase_2.26.0             oligoClasses_1.28.0       
[11] BiocGenerics_0.12.1        arrayQualityMetrics_3.22.0
[13] BiocInstaller_1.16.1      

loaded via a namespace (and not attached):
 [1] acepack_1.3-3.3       affxparser_1.38.0     affy_1.44.0          
 [4] affyio_1.34.0         affyPLM_1.42.0        annotate_1.44.0      
 [7] AnnotationDbi_1.28.1  base64_1.1            beadarray_2.16.0     
[10] BeadDataPackR_1.18.0  bit_1.1-12            Cairo_1.5-6          
[13] cluster_1.15.3        codetools_0.2-9       colorspace_1.2-4     
[16] ff_2.2-13             foreach_1.4.2         foreign_0.8-61       
[19] Formula_1.1-2         gcrma_2.38.0          genefilter_1.48.1    
[22] GenomeInfoDb_1.2.4    GenomicRanges_1.18.3  grid_3.1.1           
[25] gridSVG_1.4-2         Hmisc_3.14-6          hwriter_1.3.2        
[28] illuminaio_0.8.0      iterators_1.0.7       lattice_0.20-29      
[31] latticeExtra_0.6-26   limma_3.22.1          nnet_7.3-8           
[34] plyr_1.8.1            preprocessCore_1.28.0 RColorBrewer_1.1-2   
[37] Rcpp_0.11.3           reshape2_1.4.1        RJSONIO_1.3-0        
[40] rpart_4.1-8           setRNG_2013.9-1       splines_3.1.1        
[43] stringr_0.6.2         survival_2.37-7       SVGAnnotation_0.93-1 
[46] tools_3.1.1           vsn_3.34.0            XML_3.98-1.1         
[49] xtable_1.7-4          zlibbioc_1.12.0      

Basically I am running oligo to read the files and calling arrayQualityMetrics just after

library(oligo)

library(arrayQualityMetrics)

mydata <- read.celfiles(filenames = list.celfiles())

arrayQualityMetrics(expressionset = mydata, force = T, do.logtransform = T)

The error when running arrayQualityMetrics the first time gives

The directory 'arrayQualityMetrics report for mydata' has been created. Error in svgStyleAttributes(style) : All SVG style attribute values must have length 1​

and when running a second time

Error in gridsvg(name = "arrayQualityMetrics report for mydata/pca.svg",  :
  Only one 'gridsvg' device may be used at a time
In addition: Warning message:
closing unused connection 3 (arrayQualityMetrics report for mydata/index.html) 

Traceback is as follows:

7: stop("Only one 'gridsvg' device may be used at a time")
6: gridsvg(name = "arrayQualityMetrics report for mydata/pca.svg",
       width = 4.44721359549996, height = 4.44721359549996, res = 72,
       prefix = paste("Fig", "pca", sep = ":"), usePaths = "none")
5: eval(expr, envir, enclos)
4: eval(substitute(gridsvg(name = path, width = w, height = h, res = dpi,
       prefix = paste("Fig", name, sep = ":"), usePaths = "none")))
3: reportModule(p = p, module = modules[[i]], currentIndex = currentIndex,
       arrayTable = arrayTableCompact, outdir = outdir)
2: aqm.writereport(modules = m, arrayTable = x$pData, reporttitle = reporttitle,
       outdir = outdir)
1: arrayQualityMetrics(expressionset = mydata, do.logtransform = T,
       force = T)​

Any help appreciated.

Dear Paulo

the problem is fixed by using gridSVG >= 1.4-3 (thanks to Paul Murrell for his quick response!). Currently this can be obtained from R-Forge, eventually also from CRAN. Let me know whether this works for you.

Wolfgang

I recently got the same error and use dev.off(which(unlist(.Devices) == "gridsvg")) to make it work  

Dear Paulo

thank you for your report! In fact the same problem occurs now on the build servers, both in release (http://bioconductor.org/checkResults/release/bioc-LATEST/arrayQualityMetrics/zin1-buildsrc.html ) and devel (http://bioconductor.org/checkResults/devel/bioc-LATEST/arrayQualityMetrics/zin2-buildsrc.html ). I'll explore and get back with, hopefully, a solution.

The problem seems to be an interaction of the gridSVG and lattice packages, I reproduced it with the following small example:

library("lattice")
library("gridSVG")

options(error=recover)

df = data.frame(x=1:10, y=1:10, which=factor(rep(1:2, each=5)))
p1 = xyplot(y~x, groups=which, data=df, type = "l")

gridsvg(name = "test1.svg")
print(p1)
gridSVG::dev.off()

# Error in svgStyleAttributes(style) :
#  All SVG style attribute values must have length 1

I contacted the maintainer of gridSVG as well as the author of gridSVG::gridsvg.

Best wishes

Wolfgang