[Bioc-devel] GenomicRanges 1.7.40

[Hervé Pagès]

Hi guys,

This is related to the issue Tim reported on the Bioconductor mailing
list. A regression was introduced in IRanges 1.13.33 (which is now
fixed in IRanges 1.13.34) that broke the order/sort/rank methods
for GRanges objects and prevented GenomicRanges 1.7.40 from propagating.
Sorry for that. Hopefully everything should be fine again after the
next build run.

For the impatient, yes you can grab the latest IRanges and GenomicRanges
from svn.

Cheers,
H.

On 03/26/2012 11:13 AM, Martin Morgan wrote:
> 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
>
>


-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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