Question: import.gff3 bug in rtracklayer v1.6
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gravatar for Hubert Rehrauer
10.0 years ago by
Hubert Rehrauer100 wrote:
Dear all I used rtracklayer under R v 2.8.2 and everything worked fine. Now I upgraded to R 2.10 and rtracklayer 1.6 When importing a gff3 file I get the following error: > gff <- import.gff3(system.file("tests", "v3.gff", package = > "rtracklayer")) > Error in DataFrame(xd, attrList) : > different row counts implied by arguments This error occurs for any gff3 file I try to import. Here is my complete configuration: > sessionInfo() > R version 2.10.0 (2009-10-26) > x86_64-apple-darwin9.8.0 > > locale: > [1] de_CH.UTF-8/de_CH.UTF-8/C/C/de_CH.UTF-8/de_CH.UTF-8 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > other attached packages: > [1] rtracklayer_1.6.0 RCurl_1.2-1 bitops_1.0-4.1 > loaded via a namespace (and not attached): > [1] Biobase_2.6.0 Biostrings_2.14.7 BSgenome_1.14.2 > IRanges_1.4.4 tools_2.10.0 XML_2.6-0 Can anyone help me? best regards, hubert [[alternative HTML version deleted]]
rtracklayer • 416 views
ADD COMMENTlink modified 10.0 years ago by Michael Lawrence620 • written 10.0 years ago by Hubert Rehrauer100
Answer: import.gff3 bug in rtracklayer v1.6
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gravatar for Michael Lawrence
10.0 years ago by
Michael Lawrence620 wrote:
On Thu, Nov 26, 2009 at 12:35 AM, Hubert Rehrauer < Hubert.Rehrauer@fgcz.ethz.ch> wrote: > Dear all > > I used rtracklayer under R v 2.8.2 and everything worked fine. Now I > upgraded to R 2.10 and rtracklayer 1.6 > > When importing a gff3 file I get the following error: > > > gff <- import.gff3(system.file("tests", "v3.gff", package = > > "rtracklayer")) > > Error in DataFrame(xd, attrList) : > > different row counts implied by arguments > > This error occurs for any gff3 file I try to import. > > Here is my complete configuration: > > sessionInfo() > > R version 2.10.0 (2009-10-26) > > x86_64-apple-darwin9.8.0 > > > > locale: > > [1] de_CH.UTF-8/de_CH.UTF-8/C/C/de_CH.UTF-8/de_CH.UTF-8 > > > > attached base packages: > > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > > [1] rtracklayer_1.6.0 RCurl_1.2-1 bitops_1.0-4.1 > > loaded via a namespace (and not attached): > > [1] Biobase_2.6.0 Biostrings_2.14.7 BSgenome_1.14.2 > > IRanges_1.4.4 tools_2.10.0 XML_2.6-0 > > Can anyone help me? > > This is due to a change in the way IRanges converts lists to DataFrames. I restored it to the way it was before, so that it is consistent with data.frame. Ported to stable branch, upcoming version 1.4.9. best regards, > hubert > > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]
ADD COMMENTlink written 10.0 years ago by Michael Lawrence620
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