[BioC] DEXSeq availability

[Dan Tenenbaum]

Hi Wyatt,


On Mon, Dec 5, 2011 at 12:58 PM, Wyatt McMahon [guest]
<guest at bioconductor.org> wrote:
>
> I'm trying to install DEXSeq using the code that I have copied from many places:
> source("http://bioconductor.org/biocLite.R")
> biocLite("DEXSeq")
>
> The message I always receive following the second command is:
> Using R version 2.13.0, biocinstall version 2.8.4.
> Installing Bioconductor version 2.8 packages:
> [1] "DEXSeq"
> Please wait...
>
> Warning message:
> In getDependencies(pkgs, dependencies, available, lib) :
>  package ‘DEXSeq’ is not available (for R version 2.13.0)
>
> I have also tried installing it using a zip file and get the following:
> Error: package 'Biobase' required by 'DEXSeq' could not be found
> In addition: Warning message:
> package 'DEXSeq' was built under R version 2.15.0
>
>  -- output of sessionInfo():
>
>> sessionInfo()
> R version 2.13.0 (2011-04-13)
> Platform: i386-pc-mingw32/i386 (32-bit)
>
> locale:
> [1] LC_COLLATE=English_United States.1252
> [2] LC_CTYPE=English_United States.1252
> [3] LC_MONETARY=English_United States.1252
> [4] LC_NUMERIC=C
> [5] LC_TIME=English_United States.1252
>
> attached base packages:
> [1] grid      stats     graphics  grDevices utils     datasets  methods
> [8] base
>
> other attached packages:
>  [1] DEGseq_1.6.2        samr_2.0            matrixStats_0.2.2
>  [4] R.methodsS3_1.2.1   impute_1.26.0       ShortRead_1.10.4
>  [7] Rsamtools_1.4.2     lattice_0.19-23     Biostrings_2.20.1
> [10] GenomicRanges_1.4.6 IRanges_1.10.4      gplots_2.8.0
> [13] caTools_1.12        bitops_1.0-4.1      gdata_2.8.2
> [16] gtools_2.6.2        qvalue_1.26.0
>
> --
> Sent via the guest posting facility at bioconductor.org.
>
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The package DEXSeq did not exist in R 2.13.
If you want to use it, you need to upgrade to R 2.14. Then the
commands you tried above will work.

Dan