[BioC] Mac binaries

[stefano iacus]

Well, let me shed some light on this.
There is one "official" binary version of R for Mac OS X which is 
available only on CRAN under /bin/macos
This comes with an installer that only install R itself,  
base+recommended packages and a GUI front end to R. Call this version 
1.
There is also Jan de Leeuw build of R for Mac OS X which (which is 
prefectly ok) that installs R+almost all CRAN packages and all BioC 
packages (I'm not sure about all BioC). Call this version 2.

On CRAN there is also a set of prebuilt CRAN packages for Mac OS X. 
These are guarantee to work with 1., and they are all packages which 
pass all the checks previewed by R tools to assess the quality of a 
binary build (this is platform dependent)

Most of the BioC 1.5 packages are also distributed in binary form on 
the BioC web site (http://www.bioconductor.org/bin/macosx/2.0/ ).

Both kind of binary packages are accessible for download and install 
via the GUI front-end distributed with 1. Specifically to BioC: with 1. 
also comes the installer of the X11/TclTk libraries. You need to 
install this to use tcltk widgets, which are widly used in BioC.

There is NO NEED to install developer tools to use 1. + the prebuilt 
packages. Developer tools, which means C compiler and other things, ARE 
NEEDED only if one wants to build packages from source (this could 
happen for some packages that can be built on Mac OS X but are not 
distributed as binary by us, as they don't pass all the test)

The installation of 1. needs admin priviledges, but after that packages 
can be installed locally on a per user basis.

BTW: please always use the latest R official release.

There is also a "R for Mac OS X FAQ" available that explains several of 
these aspects.
stefano

On Jan 20, 2005, at 3:13 AM, James Wettenhall wrote:

> Hi Byron and others,
>
>> If they're using the R GUI the Bioconductor Binary packages should be
>> available directly from the "Package Installer..." sheet since AFAIK
>> Stefano builds them along with the other CRAN packages. I'd check, but
>> unfortunately my R GUI crashes (its a -devel branch version) when I 
>> try
>> to get the list of packages.
>
> That sounds perfect.  Can anyone confirm this?  The reason I questioned
> whether Mac binaries existed is that if you click on "Release 1.5
> Packages" link from the main Bioconductor website, you only get Win32 
> and
> Source.
>
>> In any case, you shouldn't need to get admin rights to install 
>> packages
>> on OS X once the Developer Tools are installed.
>
> My users are probably not interested in the Developer Tools unless they
> are absolutely necessary.  I've heard they take a while to install.
>
> The reason I mentioned admin privileges is because I seem to remember 
> that
> at one stage, there was a massive R installer for Mac which installed 
> lots
> of CRAN and Bioconductor packages.  As my biologist client already has 
> R
> installed, I would prefer not to have to ask their I.T. adminstrator to
> reinstall R (in order to get a few missing packages).  I can easily
> install R packages for them (in a suitable directory) without admin
> privileges, as long as binaries are available somewhere.
>
> Thanks,
> James
>
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