[Bio-Linux] Package GenomicRanges library

[Tim Booth]

Hi,

I updated GenomicRanges along with all the core Bioconductor packages
when I made the RAPIDR package.  That was last month.  Since then there
is a new Bioconductor release but I'm not planning another round of
updates as it will take me days to sort out all the new packages.

Since I can't see your script I don't know why it is trying to unload
GenomicRanges but it makes sense that you can't do that while RAPIDR is
loaded.

If the script is a standalone script are you running it with the
--vanilla option to R?

Cheers,

TIM

On Tue, 2015-10-27 at 19:23 +0100, Pau Marc Muñoz Torres wrote:
> Hello
> 
> 
>   Has   Package GenomicRanges library from R been updated
> recently ? when i execute a funtion of rapdir
> 
> 
> library("RAPIDR")
> makeBinnedCountsFile(c("nfamele1_sorted.bam","nfamele2_sorted.bam","nMALE1_sorted.bam","nMALE2_sorted.bam","T-SRR611848_1_sorted.bam"),c("nfamele1","nfamele2","nMALE1","nMALE2","T-SRR611848"),"binnedcounts.r",mask=NULL,k=20000)
> 
> 
> 
> 
> I am getting the following error in a script that was working a month
> before
> 
> 
> Error in unloadNamespace(package) : 
>   namespace ‘GenomicRanges’ is imported by ‘RAPIDR’,
> ‘GenomicAlignments’, ‘Rsamtools’ so cannot be unloaded
> Error in library(pkg, character.only = TRUE, logical.return = TRUE,
> lib.loc = lib.loc,  : 
>   Package ‘GenomicRanges’ version 1.20.8 cannot be unloaded
> 
> 
> what can i do?
> 
> 
> Pau Marc Muñoz Torres
> 
> skype: pau_marc
> http://www.linkedin.com/in/paumarc
> http://www.researchgate.net/profile/Pau_Marc_Torres3/info/
> 
> 
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-- 
Tim Booth <tbooth at ceh.ac.uk>

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