[BioC] mzR installation

[Dan Tenenbaum]

----- Original Message -----
> From: "Dan Tenenbaum" <dtenenba at fhcrc.org>
> To: "Dirk Eddelbuettel" <edd at debian.org>
> Cc: "Kevin Ushey" <kevinushey at gmail.com>, bioconductor at r-project.org, gtsiliki at bioacademy.gr
> Sent: Monday, February 10, 2014 6:57:06 PM
> Subject: Re: [BioC] mzR installation
> 
> 
> 
> ----- Original Message -----
> > From: "Dan Tenenbaum" <dtenenba at fhcrc.org>
> > To: "Dirk Eddelbuettel" <edd at debian.org>
> > Cc: "Kevin Ushey" <kevinushey at gmail.com>,
> > bioconductor at r-project.org, gtsiliki at bioacademy.gr
> > Sent: Monday, February 10, 2014 6:50:31 PM
> > Subject: Re: [BioC] mzR installation
> > 
> > 
> > 
> > ----- Original Message -----
> > > From: "Dirk Eddelbuettel" <edd at debian.org>
> > > To: "Dan Tenenbaum" <dtenenba at fhcrc.org>
> > > Cc: gtsiliki at bioacademy.gr, bioconductor at r-project.org, "Dirk
> > > Eddelbuettel" <edd at debian.org>, "Kevin Ushey"
> > > <kevinushey at gmail.com>, "Steffen Neumann" <sneumann at ipb-halle.de>
> > > Sent: Monday, February 10, 2014 6:36:56 PM
> > > Subject: Re: [BioC] mzR installation
> > > 
> > > 
> > > On 10 February 2014 at 10:21, Dan Tenenbaum wrote:
> > > | What the error message is saying is that installing Rcpp 0.11.0
> > > | is
> > > | the way around this.
> > > | Unfortunately, that's not all.
> > > | 
> > > | The latest version of mzR is currently not available for Mac
> > > | because of an issue in Rcpp which needs to be
> > > | fixed. Looks like it has been fixed in Github but not yet
> > > | propagated to CRAN. So as soon as you see a version of Rcpp
> > > | higher
> > > | than 0.11.0 on
> > > | this page:
> > > | 
> > > | http://cran.r-project.org/web/packages/Rcpp/index.html
> > > | 
> > > | ...try again.
> > > 
> > > Or just install Rcpp from it current (and *very stable*) source
> > > repository:
> > > https://github.com/RcppCore/Rcpp
> > > 
> > 
> > You can also do this:
> > 
> > source("http://bioconductor.org/biocLite.R")
> > biocLite("mzR", type="source")
> > 
> > But this (and the github url that Dirk suggests) requires that you
> > have the appropriate compilers installed, which on Mac requires
> > that
> > you install Xcode and its "command line tools" package.
> > 
> 
> And you may also need the clang compiler (since Rcpp won't compile
> with the version of g++ that is available by default on Mac OS X).
> I'm working with Dirk and Kevin to get a patched version out so you
> don't need to do all this.
> 


A new version of mzR (1.8.1.1) is now available via:
source("http://bioconductor.org/biocLite.R")
biocLite("mzR")

This does not require any special tools to be installed. Sorry for the inconvenience. Let me know if you continue to have issues. 

Dan



> Thanks,
> Dan
> 
> 
> > Dan
> > 
> > 
> > > Dirk
> > > 
> > > --
> > > Dirk Eddelbuettel | edd at debian.org | http://dirk.eddelbuettel.com
> > >
> > 
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