question about xvfb-run GeneAnswers
1
0
Entering edit mode
Ou, Jianhong ★ 1.3k
@ou-jianhong-4539
Last seen 3 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
ADD COMMENT
0
Entering edit mode
@james-w-macdonald-5106
Last seen 1 day 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
ADD COMMENT
0
Entering edit mode
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 >
ADD REPLY

Login before adding your answer.

Traffic: 810 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6