[BioC] circlize package: some error message

[Dan Tenenbaum]

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.:)
> 
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> 
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