[BioC] DEXSeq availability

[Wyatt McMahon]

Thanks so much, Dan!  I did that and now it works!

-----Original Message-----
From: Dan Tenenbaum [mailto:dtenenba at fhcrc.org]
Sent: Monday, December 05, 2011 4:02 PM
To: Wyatt McMahon [guest]
Cc: bioconductor at r-project.org; wmcmahon at vbi.vt.edu
Subject: Re: [BioC] DEXSeq availability

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