[Bioc-devel] Problem with GRanges

[Martin Morgan]

On 10/15/2013 05:06 AM, Martin Morgan wrote:
> 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

aargh (that pirate sound) I meant to point to BiocInstaller::biocValid() 
(although biocLite() would says that packages are out of date). 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]]
>>>
>>>
>>> _______________________________________________
>>> Bioc-devel at r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>
>>>
>>
>>     [[alternative HTML version deleted]]
>>
>>
>>
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>>
>
>


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