[BioC] DESeq2

[Dan Tenenbaum]

On Wed, Mar 20, 2013 at 3:56 PM, Mariana Boroni <marianaboroni at gmail.com> wrote:
> Hi,
> I've installed R-devel (R-3.0) and now I'm attempting to install the DESeq2 package with this command:
>
> source("http://bioconductor.org/biocLite.R")
> biocLite("DESeq2")
> But I get the following error:
>
>> biocLite("DESeq2")
> BioC_mirror: http://bioconductor.org
> Using Bioconductor version 2.12 (BiocInstaller 1.9.8), R version 3.0.0.
> Installing package(s) 'DESeq2'
>
>    package ‘DESeq2’ is available as a source package but not as a binary
>
> Mensagens de aviso perdidas:
> package ‘DESeq2’ is not available (for R version 3.0.0 alpha)
>
> But in the DESeq2 viginete they use R 3.0.0
> Session Info
>
> R version 3.0.0 alpha (2013-03-09 r62188), x86_64-unknown-linux-gnu
>
> Locale: LC_CTYPE=en_US.UTF-8, LC_NUMERIC=C, LC_TIME=en_US.UTF-8, LC_COLLATE=C, LC_MONETARY=en_US.UTF-8, LC_MESSAGES=en_US.UTF-8, LC_PAPER=C, LC_NAME=C, LC_ADDRESS=C, LC_TELEPHONE=C, LC_MEASUREMENT=en_US.UTF-8, LC_IDENTIFICATION=C
>
> Base packages: base, datasets, grDevices, graphics, grid, methods, parallel, stats, utils
>
> Other packages: Biobase 2.19.3, BiocGenerics 0.5.6, DESeq2 0.99.16, DEXSeq 1.5.9, GenomicRanges 1.11.35, IRanges 1.17.36, KernSmooth 2.23-9, MASS 7.3-24, RColorBrewer 1.0-5, Rcpp 0.10.2, RcppArmadillo 0.3.800.0, caTools 1.14, gdata 2.12.0, gplots 2.11.0, gtools 2.7.0, lattice 0.20-13,
> locfit 1.5-8, parathyroidSE 0.99.1, vsn 3.27.2
>
> Loaded via a namespace (and not attached): AnnotationDbi 1.21.13, BiocInstaller 1.9.7, Biostrings 2.27.11, DBI 0.2-5, DESeq 1.11.6, RCurl 1.95-4.1, RSQLite 0.11.2, Rsamtools 1.11.21, XML 3.95-0.2, affy 1.37.4, affyio 1.27.1
>
>
> My
>> sessionInfo()
> R version 3.0.0 alpha (2013-03-18 r62312)
> Platform: x86_64-apple-darwin10.8.0 (64-bit)
>
> locale:
> [1] pt_BR.UTF-8/pt_BR.UTF-8/pt_BR.UTF-8/C/pt_BR.UTF-8/pt_BR.UTF-8
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] BiocInstaller_1.9.8
>
> loaded via a namespace (and not attached):
> [1] tools_3.0.0
>
>
> Any help?


For the time being, there are no Mac binary packages available for R
3.0 alpha and beta (but there are for earlier versions of R-3.0).

Because of upcoming changes to Mac support in R-3.0, detailed here:
https://stat.ethz.ch/pipermail/r-sig-mac/2013-March/010003.html

...we are still testing our new Mac builds.

You can work around this by installing the package as follows:

source("http://bioconductor.org/biocLite.R")
biocLite("DESeq2", type="source")

This will require that you have XCode installed (be sure you also
install the "command line tools" download that is optional with
Mountain Lion).

Dan


>
> Thanks
> ______________________________
> Mariana Boroni
> Doutoranda em Bioinformática
> Laboratório de Genética Bioquímica
> Universidade Federal de Minas Gerais
> Tel: +55 31 3409-2628
>         +55 31 9413-4242
>
>
>         [[alternative HTML version deleted]]
>
>
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