[BioC] question about xvfb-run GeneAnswers

[Ou, Jianhong]

Hi Jim,

I also tried to set newWindow = TRUE. Same problem.

Yours sincerely,

Jianhong Ou

jianhong.ou at umassmed.edu


On Sep 30, 2011, at 11:05 AM, James W. MacDonald wrote:

> Hi Jianhong Ou,
> 
> On 9/30/2011 9:40 AM, Ou, Jianhong wrote:
>> 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()
> 
> Just a shot in the dark here, but don't you want newWindow = TRUE?
> 
> Best,
> 
> Jim
> 
> 
>> 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
>> 
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> 
> -- 
> James W. MacDonald, M.S.
> Biostatistician
> Douglas Lab
> University of Michigan
> Department of Human Genetics
> 5912 Buhl
> 1241 E. Catherine St.
> Ann Arbor MI 48109-5618
> 734-615-7826
> 
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