[BioC] question about xvfb-run GeneAnswers

[Ou, Jianhong]

Dear list,

I met problem in generate pdf file when use GeneAnswers. When open "test.pdf" after xvfb-run following codes, it alerts  "There was an error opening this document. This file cannot be opened because it has no pages."

How could I figure out this problem? Thanks.

$ xvfb-run R
...
> library(GeneAnswers)
Loading required package: igraph
Loading required package: RCurl
Loading required package: bitops
Loading required package: annotate
Loading required package: AnnotationDbi
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")'.

Loading required package: XML
Loading required package: RSQLite
Loading required package: DBI
Loading required package: MASS
Loading required package: rgl
Loading required package: Heatplus
Loading required package: RColorBrewer
> data('humanGeneInput')
> data('humanExpr')
> x <- geneAnswersBuilder(humanGeneInput, 'org.Hs.eg.db', categoryType='GO.BP', testType='hyperG', pvalueT=0.1, FDR.correction=TRUE, geneExpressionProfile=humanExpr)
[1] "geneInput has built in ..."
Loading required package: org.Hs.eg.db

Loading required package: GO.db

[1] "annLib and categoryType have built in ..."
[1] "genesInCategory has built in ..."
[1] "Enrichment test is only performed based on annotated genes"
[1] "testType, pvalueT and enrichmentInfo have built in ..."
[1] "geneExpressionProfile has been built in ..."
[1] "GeneAnswers instance has been successfully created!"
> xx <- geneAnswersReadable(x)
[1] "Mapping geneInput ..."
[1] "Mapping genesInCategory ..."
[1] "Mapping enrichmentInfo rownames ..."
[1] "Mapping geneExprProfile rownames ..."
> pdf("~/test.pdf")
> geneAnswersChartPlots(xx,chartType="pieChart",newWindow=F)
> dev.off()
pdf 
  2 
> sessionInfo()
R version 2.13.0 (2011-04-13)
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=C              LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       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] GO.db_2.5.0          org.Hs.eg.db_2.5.0   GeneAnswers_1.8.0   
 [4] RColorBrewer_1.0-2   Heatplus_1.22.0      rgl_0.92.798        
 [7] MASS_7.3-13          RSQLite_0.9-4        DBI_0.2-5           
[10] XML_3.4-0            annotate_1.30.1      AnnotationDbi_1.14.1
[13] Biobase_2.12.1       RCurl_1.6-1          bitops_1.0-4.1      
[16] igraph_0.5.5-2      

loaded via a namespace (and not attached):
[1] graph_1.30.0     grid_2.13.0      RBGL_1.28.0      Rgraphviz_1.30.1
[5] tools_2.13.0     xtable_1.5-6 

Yours sincerely,

Jianhong Ou

jianhong.ou at umassmed.edu