question about xvfb-run GeneAnswers
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Ou, Jianhong ★ 1.3k
@ou-jianhong-4539
Last seen 4 days ago
United States
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
GO GeneAnswers GO GeneAnswers • 1.4k views
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@james-w-macdonald-5106
Last seen 13 hours ago
United States
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
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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 >
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