[BioC] rtracklayer export fails

Michael Dondrup michael.dondrup at uni.no
Sat Feb 19 21:21:10 CET 2011


Hi,
I am trying to use export in the rtracklayer package on R 2.12.1 on MacOS but already the example fails, see below:

Best
Michael

> example(export)

export>   track <- import(system.file("tests", "v1.gff", package = "rtracklayer"))

export>   ## Not run: export(track, "my.gff", version = "3")
export>   ## equivalently,
export>   ## Not run: export(track, "my.gff3")
export>   ## or
export>   ## Not run: 
export> ##D   con <- file("my.gff3")
export> ##D   export(track, con, "gff3")
export> ##D   close(con)
export> ##D   
export> ## End(Not run)
export>   ## or as a string
export>   export(track, format = "gff3")
Error: evaluation nested too deeply: infinite recursion / options(expressions=)?
> sessionInfo()
R version 2.12.1 (2010-12-16)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)

locale:
[1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] rtracklayer_1.10.6 RCurl_1.4-3        bitops_1.0-4.1     IRanges_1.8.9     

loaded via a namespace (and not attached):
 [1] annotate_1.28.0      AnnotationDbi_1.12.0 Biobase_2.10.0       Biostrings_2.18.2   
 [5] BSgenome_1.18.0      DBI_0.2-5            DESeq_1.2.1          genefilter_1.32.0   
 [9] geneplotter_1.28.0   GenomicRanges_1.2.0  grid_2.12.1          RColorBrewer_1.0-2  
[13] RSQLite_0.9-2        splines_2.12.1       survival_2.36-2      tools_2.12.1        
[17] XML_3.2-0            xtable_1.5-6        
> 



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