[genoPlotR-help] could not find function \"read_comparison_from_file

[Lionel Guy]

Hi Wing,

Have you loaded the library? 

> library(genoPlotR)

Can you mail the result of

> sessionInfo()

so that I can see which version of genoPlotR you are using?
It's strange that it can perform the two first commands but breaks on the third one...

Cheers,

Lionel

On 12 Sep 2013, at 9:51 , wing sze ho <howingsze86 at hotmail.com> wrote:

> Dear Dr. Lionel,
> 
> Was trying to work on the examples in section 7.2.3 (Getting started with genoPlotR) and encountered some problem.
> 
> Below are the commands that i followed exactly according to the manual. However, it seems that "read_comparison_from_blast" couldn't be found. Please advice.
> 
> 
> Loading Tcl/Tk interface ... done
> Loading required package: stats
> Loading required package: graphics
> Loading required package: MASS
> Loading required package: nnet
> Loading required package: survival
> Loading required package: splines
> > BH <- try(read_dna_seg_from_file("NC_005956.gbk"))
> > BQ <- try(read_dna_seg_from_file("NC_005955.gbk"))
> > BH_vs_BQ <- try(read_comparison_from_blast("NC_005956_vs_NC_005955.blast"))
> > xlims <- list(c(1,50000), c(1,50000))
> > plot_gene_map(dna_segs=list(BH, BQ),
> + comparisons=list(BH_vs_BQ),
> + xlims=xlims,
> + main="BH vs BQ, comparison of the first 50 kb",
> + gene_type="side_blocks",
> + dna_seg_scale=TRUE, scale=FALSE)
> > BH_vs_BQ
> [1] "Error in try(read_comparison_from_blast(\"NC_005956_vs_NC_005955.blast\")) : \n  could not find function \"read_comparison_from_blast\"\n"
> attr(,"class")
> [1] "try-error"
> attr(,"condition")
> <simpleError in doTryCatch(return(expr), name, parentenv, handler): could not find function "read_comparison_from_blast">
> 
> 
> many thanks.
> 
> best wishes,
> wing sze
> 

--
Lionel Guy
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email: guy.lionel at gmail.com, mobile: +46 (0)73 9760618, phone: +46 (0)18 410 7398