Your software needs to be updated.

I tried biocLite() with your version of R

Using R version 2.13.0, biocinstall version 2.8.4.
Installing Bioconductor version 2.8 packages:
[1] "Repitools"
Please wait...

Warning message:
In getDependencies(pkgs, dependencies, available, lib) :
  package 'Repitools' is not available (for R version 2.13.0 Patched)

Please upgrade your R to the current release, 2.14 and install Repitools
using biocLite in that R.
You will then have an Repitools with version >= 1.0 and if problems
persist, please post full details.


On Tue, Nov 8, 2011 at 7:09 AM, gillian [guest] <guest@bioconductor.org>wrote:

>
> I'm following the Repitools_vignette instruction guide (
> http://www.bioconductor.org/packages/devel/bioc/vignettes/Repitools/inst/doc/Repitools_vignette.pdf)
> and I'm stuck with the part where you need to use clusterPlots.
>
> >From the guide it seems like clusterPlots is part of Repitools, but I
> have Repitools installed (featureScores, for example, works fine), and
> clusterPlots doesn't work:
>
> > cpUnscaled=clusterPlots(fsUnscaled,n.clusters=1,plot.type='line')Error:
> could not find function "clusterPlots"
>
> So it looks like I don't have whatever library it's a part of installed,
> but I can't tell what that is.  I've got pretty much everything from the
> session info of the guide installed:
> Their Session Info:
> This vignette was created in:
> sessionInfo()
> R version 2.13.0 (2011-04-13)
> Platform: x86_64-unknown-linux-gnu (64-bit)
> locale:
> [1] LC_CTYPE=en_AU.UTF-8
> [3] LC_TIME=en_AU.UTF-8
> [5] LC_MONETARY=C
> [7] LC_PAPER=en_AU.UTF-8
> [9] LC_ADDRESS=C
> [11] LC_MEASUREMENT=en_AU.UTF-8
> LC_NUMERIC=C
> LC_COLLATE=en_AU.UTF-8
> LC_MESSAGES=en_AU.UTF-8
> LC_NAME=C
> LC_TELEPHONE=C
> LC_IDENTIFICATION=C
> attached base packages:
> [1] grid
> stats
> graphics
> [8] base
> grDevices utils
> other attached packages:
> [1] BSgenome.Hsapiens36bp.UCSC.hg18mappability_1.0
> [2] gplots_2.8.0
> [3] caTools_1.12
> [4] bitops_1.0-4.1
> [5] gdata_2.8.2
> [6] gtools_2.6.2
> [7] Ringo_1.16.0
> [8]
> Matrix_0.999375-50
>
> [9] lattice_0.19-26
> [10] limma_3.8.2
> [11] RColorBrewer_1.0-2
> [12] Biobase_2.12.1
> [13] edgeR_2.2.5
> [14] BSgenome.Hsapiens.UCSC.hg18_1.3.17
> [15] BSgenome_1.20.0
> [16] Biostrings_2.20.1
> [17] Repitools_0.99.1
> [18] GenomicRanges_1.4.6
> [19] IRanges_1.10.4
>
>
>
>
>
>
>
>
> loaded via a namespace (and not attached):
> [1] annotate_1.30.0
>    AnnotationDbi_1.14.1
>    DBI_0.2-5
> [4] genefilter_1.34.0
>    RSQLite_0.9-4
>    splines_2.13.0
> [7] survival_2.36-9
>    xtable_1.5-6
>
>
> but still no luck.  Anyone got any idea where I can find clusterPlots, or
> what I'm missing?
>
> Thanks,
>
> Gillian
>
>
>  -- output of sessionInfo():
>
> > sessionInfo()
> R version 2.13.0 (2011-04-13)
> Platform: x86_64-pc-linux-gnu (64-bit)
>
> locale:
>  [1] LC_CTYPE=en_GB.utf8       LC_NUMERIC=C
>  [3] LC_TIME=en_GB.utf8        LC_COLLATE=en_GB.utf8
>  [5] LC_MONETARY=C             LC_MESSAGES=en_GB.utf8
>  [7] LC_PAPER=en_GB.utf8       LC_NAME=C
>  [9] LC_ADDRESS=C              LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_GB.utf8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] grid      stats     graphics  grDevices utils     datasets  methods
> [8] base
>
> other attached packages:
>  [1] gplots_2.10.1       KernSmooth_2.23-5   caTools_1.12
>  [4] bitops_1.0-4.1      gdata_2.8.2         gtools_2.6.2
>  [7] Ringo_1.16.0        Matrix_1.0-1        lattice_0.19-26
> [10] limma_3.8.1         RColorBrewer_1.0-5  Biobase_2.12.1
> [13] edgeR_2.2.6         Rsamtools_1.4.3     Biostrings_2.20.0
> [16] GenomicRanges_1.4.3 IRanges_1.10.0      Repitools_1.1.0
>
> loaded via a namespace (and not attached):
>  [1] annotate_1.30.1      AnnotationDbi_1.14.1 BSgenome_1.20.0
>  [4] DBI_0.2-5            genefilter_1.34.0    RSQLite_0.9-4
>  [7] splines_2.13.0       survival_2.36-9      tools_2.13.0
> [10] xtable_1.6-0
>
> --
> Sent via the guest posting facility at bioconductor.org.
>
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