[Bioc-devel] Problem with GRanges

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 Maal?es Vej 5

DK-2200 Copenhagen N

http://binf.ku.dk | http://www.bric.ku.dk
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