[Bioc-devel] Bioconductor packages for R-3.1.0 beta on OSX 10.9

[Dan Tenenbaum]

Hi Diego,

----- Original Message -----
> From: "Diego Diez" <diego10ruiz at gmail.com>
> To: "bioc-devel" <bioc-devel at stat.math.ethz.ch>
> Sent: Friday, April 4, 2014 12:44:20 AM
> Subject: [Bioc-devel] Bioconductor packages for R-3.1.0 beta on OSX 10.9
> 
> Dear all,
> 
> sorry if double posting this. I sent it two days ago using a
> different
> email not registered at bioc-devel and it seems (as for the archives)
> it has not reached destination.
> 
> FYI, it seems the OSX build R 3.1.0 beta has split into snowleopard
> and mavericks builds:
> 
> http://r.research.att.com
> 
> When installing the later and trying to install Bioconductor I get
> the
> following:
> 
> > source("http://bioconductor.org/biocLite.R")
> Warning: unable to access index for repository
> http://www.bioconductor.org/packages/2.14/bioc/bin/macosx/mavericks/contrib/3.1
> 
>    package 'BiocInstaller' is available as a source package but not
>    as a binary
> 
> 'biocLite.R' failed to install 'BiocInstaller', use
>   'install.packages("BiocInstaller",
>   repos="http://www.bioconductor.org/packages/2.14/bioc")'
> Warning message:
> package 'BiocInstaller' is not available (for R version 3.1.0 beta)
> 
> 
> then did the following:
> 
> 
> > install.packages("BiocInstaller",
> +
>   repos="http://www.bioconductor.org/packages/2.14/bioc",type="source")
> trying URL
> 'http://www.bioconductor.org/packages/2.14/bioc/src/contrib/BiocInstaller_1.13.3.tar.gz'
> Content type 'application/x-gzip' length 14183 bytes (13 Kb)
> opened URL
> ==================================================
> downloaded 13 Kb
> 
> * installing *source* package 'BiocInstaller' ...
> ** R
> ** inst
> ** preparing package for lazy loading
> ** help
> *** installing help indices
> ** building package indices
> ** testing if installed package can be loaded
> Bioconductor version 2.14 (BiocInstaller 1.13.3), ?biocLite for help
> * DONE (BiocInstaller)
> 
> The downloaded source packages are in
> '/private/var/folders/dm/96krztk175d19vx9rcsgd2qc0000gn/T/RtmpMt3iRo/downloaded_packages'
> 
> 
> and after that did:
> 
> > biocLite()
> Error: 'no packages in repository (no internet connection?)' while
> trying
>   http://bioconductor.org/packages/2.14/bioc
> 
> which failed, presumably  because the new repository structure is not
> yet supported?


Yes, it's not yet supported. We just ordered some Mavericks machines yesterday which we'll use to build BioC against the new R binary for Mavericks. We'll announce on the Bioconductor and Bioc-devel mailing lists when these builds are ready. 

Until then, you can run the R binary built on Snow Leopard. It will work fine on Mavericks and you'll be able to download binary BioC packages. 

> 
> this did not work either:
> 
> > biocLite(type="source")
> 

That's puzzling. What about installing an individual package from source with biocLite()?
Dan


> Best,
> Diego
> 
> > sessionInfo()
> R version 3.1.0 beta (2014-03-31 r65343)
> Platform: x86_64-apple-darwin13.1.0 (64-bit)
> 
> locale:
> [1] C/UTF-8/C/C/C/C
> 
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
> 
> other attached packages:
> [1] BiocInstaller_1.13.3
> 
> loaded via a namespace (and not attached):
> [1] tools_3.1.0
> 
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