[Bioc-devel] Problem with GRanges

[Martin Morgan]

On 10/15/2013 05:04 AM, Michael Lawrence wrote:
> You need a new version of GenomicRanges, because IRanges changed.
> Unfortunately there is no way to force a package update when a dependency
> changes. Sorry.

BiocInstaller::biocLite() can help (diagnose) these problems. Martin

>
>
> On Tue, Oct 15, 2013 at 1:25 AM, Kristoffer Knudsen <
> kristoffer.knudsen at bric.ku.dk> wrote:
>
>> I seem to have problems with the latest update of GRanges:
>>
>>
>>
>>> library('GenomicRanges')
>>
>>> packageVersion('GenomicRanges')
>>
>>
>> [1] '1.13.54'
>>
>>> GRanges( seqnames='chr1', ranges=IRanges(start=10,end=100),strand='+')
>>
>>
>>
>> GRanges with 1 range and 0 metadata columns:
>>
>>        seqnames    ranges strand
>>
>>           <Rle> <IRanges>  <Rle>
>>
>>    [1]     chr1 [10, 100]      +
>>
>>    ---
>>
>>    seqlengths:
>>
>> Error in get(name, envir = asNamespace(pkg), inherits = FALSE) :
>>
>>    object 'labeledLine' not found
>>
>>
>>
>>
>> And it gives me the same error for the example in the GRanges-class help
>> file.
>>
>>
>>
>> Any ideas?
>>
>>
>>
>>> sessionInfo()
>>
>> R version 3.0.2 (2013-09-25)
>>
>> Platform: x86_64-apple-darwin10.8.0 (64-bit)
>>
>>
>>
>> locale:
>>
>> [1] C
>>
>>
>>
>> attached base packages:
>>
>> [1] grDevices utils     datasets  parallel  stats     graphics  methods
>> base
>>
>>
>>
>> other attached packages:
>>
>> [1] BiocInstaller_1.11.4  GenomicRanges_1.13.54 IRanges_1.19.40
>> fastcluster_1.1.11    reshape2_1.2.2        ggplot2_0.9.3.1
>>
>> [7] RSQLite_0.11.4        DBI_0.2-7             BiocGenerics_0.7.8
>>
>>
>>
>> loaded via a namespace (and not attached):
>>
>>   [1] MASS_7.3-29        RColorBrewer_1.0-5 colorspace_1.2-4
>> dichromat_2.0-0    digest_0.6.3       grid_3.0.2         gtable_0.1.2
>>
>>   [8] labeling_0.2       munsell_0.4.2      plyr_1.8           proto_0.3-10
>>        scales_0.2.3       stats4_3.0.2       stringr_0.6.2
>>
>> [15] tools_3.0.2
>>
>>
>>
>>
>>
>> --
>>
>> Kristoffer Vitting-Seerup, cand.scient. (M.Sc.),
>>
>> Ph.D Fellow
>>
>> Sandelin Group
>>
>>
>>
>> Bioinformatics Centre | Biotech Research & Innovation Centre (BRIC), Dep.
>> Of Biology
>>
>> University of Copenhagen
>>
>> Ole Maaløes Vej 5
>>
>> DK-2200 Copenhagen N
>>
>> http://binf.ku.dk | http://www.bric.ku.dk
>>          [[alternative HTML version deleted]]
>>
>>
>> _______________________________________________
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>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>>
>
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>
>
>
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