[Bioc-devel] GenomicRanges 1.7.40

[Martin Morgan]

On 03/26/2012 10:07 AM, Hahne, Florian wrote:
> I can't seem to be able to update to the latest GenomicRanges version
> 1.7.40:
> Warning: dependency ŒGenomicRanges (>= 1.7.40)¹ is not available
> This leads to the ShortRead package failing to build:
> Error : package ŒGenomicRanges¹ 1.7.38 was found, but>= 1.7.40 is
> required by ŒShortRead¹
>
>
> I also see all red flags for my Gviz package although I did not submit any
> changes, and the culprit is in GenomicRanges in the 'sort' method:
> example(GRanges)
>
> sort(gr)
> Error in .Call2("Integer_order4", a, b, c, d, decreasing, PACKAGE =
> "IRanges") :
>    'a', 'b', 'c' and 'd' must be integer vectors
>
>
> This is with my currently installed version 1.7.38. As mentioned above I
> can't get the latest version through biocLite, and in order to build from
> the svn I need to install some fairly large dependencies which takes
> forever in the slow network I am in right now. So I am not sure whether
> this issue was already fixed. Would be odd if the package would build
> without such a bug causing an errorŠ
>
> Any idea what's happening?

GenomicRanges isn't passing R CMD build, so isn't available via 
biocLite. You could

svn co 
https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GenomicRanges

and install with R CMD INSTALL

I don't really have insight on sort(gr).

Martin

> Florian
>
>
>> sessionInfo()
> R Under development (unstable) (2012-02-29 r58532)
> Platform: i386-apple-darwin10.8.0/i386 (32-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] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] GenomicRanges_1.7.38 IRanges_1.13.33      BiocGenerics_0.1.14
> [4] BiocInstaller_1.3.9
>
> loaded via a namespace (and not attached):
> [1] stats4_2.15.0 tools_2.15.0
>
>
>
> Florian Hahne
> Novartis Institute For Biomedical Research
> Translational Sciences / Preclinical Safety / PCS Informatics
> Expert Data Integration and Modeling Bioinformatics
> CHBS, WKL-135.2.26
> Novartis Institute For Biomedical Research, Werk Klybeck
> Klybeckstrasse 141
> CH-4057 Basel
> Switzerland
> Phone: +41 61 6967127
> Email : florian.hahne at novartis.com
>
> _______________________________________________
> Bioc-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel


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