I recently tried to run some sample code from R package: circlize, and got an error message (please see below) ===== > library(circlize) > circos.genomicInitialize(df) > df = data.frame(name = c("TP53", "TP63", "TP73"), + start = c(7565097, 189349205, 3569084), + end = c(7590856, 189615068, 3652765), + stringsAsFactors = FALSE) > df name start end 1 TP53 7565097 7590856 2 TP63 189349205 189615068 3 TP73 3569084 3652765 > circos.genomicInitialize(df) > circos.clear() > circos.genomicInitialize(df, major.by = 10000) Error in seq.default(xlim[1], 10^nchar(round(max(x2 - x1 + 1))), by = major.by) : wrong sign in 'by' argument === And my session information: > sessionInfo() R version 3.1.1 (2014-07-10) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.utf8 LC_NUMERIC=C [3] LC_TIME=en_US.utf8 LC_COLLATE=C [5] LC_MONETARY=en_US.utf8 LC_MESSAGES=en_US.utf8 [7] LC_PAPER=en_US.utf8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] circlize_0.1.0 loaded via a namespace (and not attached): [1] AnnotationDbi_1.26.0 Biobase_2.24.0 BiocGenerics_0.10.0 [4] DBI_0.2-7 DESeq2_1.4.5 GenomeInfoDb_1.0.2 [7] GenomicRanges_1.16.3 IRanges_1.22.9 RColorBrewer_1.0-5 [10] RSQLite_0.11.4 Rcpp_0.11.2 RcppArmadillo_0.4.320.0 [13] XML_3.98-1.1 XVector_0.4.0 annotate_1.42.1 [16] genefilter_1.46.1 geneplotter_1.42.0 grid_3.1.1 [19] lattice_0.20-29 locfit_1.5-9.1 parallel_3.1.1 [22] splines_3.1.1 stats4_3.1.1 survival_2.37-7 [25] xtable_1.7-3 > === Wonder anyone could please help me out with this? Thank you very much for your time.:) [[alternative HTML version deleted]]

Since circlize is not a Bioconductor package, you might have better luck asking on R-help (http://stat.ethz.ch/mailman/listinfo/r-help) or contacting the maintainer (listed at http://cran.r-project.org/web/packages/circlize/index.html). Dan ----- Original Message ----- > From: "Fix Ace" <acefix at="" rocketmail.com=""> > To: bioconductor at r-project.org > Sent: Thursday, August 7, 2014 6:21:18 PM > Subject: [BioC] circlize package: some error message > > I recently tried to run some sample code from R package: circlize, > and got an error message (please see below) ===== > library(circlize) > > circos.genomicInitialize(df) > df = data.frame(name = c("TP53", > "TP63", "TP73"), + start = c(7565097, 189349205, 3569084), > + end = c(7590856, 189615068, 3652765), > + stringsAsFactors = FALSE) > df name start end > 1 TP53 7565097 7590856 > 2 TP63 189349205 189615068 > 3 TP73 3569084 3652765 > circos.genomicInitialize(df) > > circos.clear() > circos.genomicInitialize(df, major.by = 10000) > Error in seq.default(xlim[1], 10^nchar(round(max(x2 - x1 + 1))), by > = > major.by) : wrong sign in 'by' argument === And my session > information: > sessionInfo() R version 3.1.1 (2014-07-10) > Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] > LC_CTYPE=en_US.utf8 LC_NUMERIC=C [3] LC_TIME=en_US.utf8 > LC_COLLATE=C [5] LC_MONETARY=en_US.utf8 > LC_MESSAGES=en_US.utf8 [7] LC_PAPER=en_US.utf8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C attached base > packages: > [1] stats graphics grDevices utils datasets methods base > other attached packages: > [1] circlize_0.1.0 loaded via a namespace (and not attached): [1] > AnnotationDbi_1.26.0 Biobase_2.24.0 BiocGenerics_0.10.0 > [4] DBI_0.2-7 DESeq2_1.4.5 > GenomeInfoDb_1.0.2 [7] GenomicRanges_1.16.3 > IRanges_1.22.9 RColorBrewer_1.0-5 > [10] RSQLite_0.11.4 Rcpp_0.11.2 > RcppArmadillo_0.4.320.0 > [13] XML_3.98-1.1 XVector_0.4.0 annotate_1.42.1 > [16] genefilter_1.46.1 geneplotter_1.42.0 grid_3.1.1 > [19] lattice_0.20-29 locfit_1.5-9.1 parallel_3.1.1 > [22] splines_3.1.1 stats4_3.1.1 survival_2.37-7 > [25] xtable_1.7-3 > === > > Wonder anyone could please help me out with this? > > Thank you very much for your time.:) > > [[alternative HTML version deleted]] > > _______________________________________________ > 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 >