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 >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > > -- > 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 > > ********************************************************** > Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues >