Thank you very much Michael and Martin,
it worked.

Ugo




From: Michael Lawrence <lawrence.michael@gene.com>
Date: Wed, 16 Jul 2014 05:35:19 -0700
To: Ugo Borello <ugo.borello@inserm.fr>
Cc: "bioconductor@r-project.org" <bioconductor@r-project.org>
Subject: Re: [BioC] NCBI gff3 annotation file and read.gff()

Takes a couple of minutes but seems to work with:

gff <- rtracklayer::import("ref_Macaca_fascicularis_5.0_top_level.gff3.gz")

And it's not necessary to ungzip it.


On Wed, Jul 16, 2014 at 5:05 AM, Ugo Borello <ugo.borello@inserm.fr> wrote:
> Hi,
> 
> I am trying to read without success, a gff file downloaded from the NCBI
> genomes ftp directory.
> 
> library("genomes")
>> > annot <-
> read.gff('~/Desktop/NCBI_Anno/ref_Macaca_fascicularis_5.0_top_level.gff3')
> Error in `$<-.data.frame`(`*tmp*`, "description", value = "") :
>   replacement has 1 row, data has 0
> 
> Any hint/help?
> 
> Thank you
> 
> Ugo
> 
> 
> 
> 
>> > sessionInfo()
> R version 3.1.1 (2014-07-10)
> Platform: x86_64-apple-darwin10.8.0 (64-bit)
> 
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
> 
> attached base packages:
> [1] parallel  stats     graphics  grDevices utils     datasets  methods
> base
> 
> other attached packages:
>  [1] genomes_2.10.0       Biostrings_2.32.1    XVector_0.4.0
> GenomicRanges_1.16.3 GenomeInfoDb_1.0.2
>  [6] IRanges_1.22.9       BiocGenerics_0.10.0  RCurl_1.95-4.1
> bitops_1.0-6         XML_3.98-1.1
> 
> loaded via a namespace (and not attached):
> [1] stats4_3.1.1    tools_3.1.1     zlibbioc_1.10.0
> 
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