From dtenenba at fredhutch.org  Mon Oct 27 20:33:50 2014
From: dtenenba at fredhutch.org (Dan Tenenbaum)
Date: Mon, 27 Oct 2014 12:33:50 -0700 (PDT)
Subject: [Rd] OSX Yosemite (10.10): Are package binaries the same as for
 OSX Mavericks (10.9)?
In-Reply-To: <CAFDcVCT_=9EfVW=ZZy_Q7Nw7YZxJgmpveK1BUci7iDRtVdKsGQ@mail.gmail.com>
Message-ID: <417165047.270497.1414438430656.JavaMail.root@fredhutch.org>



----- Original Message -----
> From: "Henrik Bengtsson" <hb at biostat.ucsf.edu>
> To: "Dan Tenenbaum" <dtenenba at fredhutch.org>
> Cc: "R-devel" <r-devel at r-project.org>
> Sent: Monday, October 27, 2014 12:21:49 PM
> Subject: Re: [Rd] OSX Yosemite (10.10): Are package binaries the same as for OSX Mavericks (10.9)?
> 
> On Mon, Oct 27, 2014 at 11:23 AM, Dan Tenenbaum
> <dtenenba at fredhutch.org> wrote:
> >
> >
> > ----- Original Message -----
> >> From: "Dan Tenenbaum" <dtenenba at fredhutch.org>
> >> To: "Henrik Bengtsson" <hb at biostat.ucsf.edu>
> >> Cc: "R-devel" <r-devel at r-project.org>
> >> Sent: Monday, October 27, 2014 11:21:59 AM
> >> Subject: Re: [Rd] OSX Yosemite (10.10): Are package binaries the
> >> same as for OSX Mavericks (10.9)?
> >>
> >>
> >>
> >> ----- Original Message -----
> >> > From: "Henrik Bengtsson" <hb at biostat.ucsf.edu>
> >> > To: "R-devel" <r-devel at r-project.org>
> >> > Sent: Monday, October 27, 2014 11:16:10 AM
> >> > Subject: [Rd] OSX Yosemite (10.10): Are package binaries the
> >> > same
> >> > as for OSX Mavericks (10.9)?
> >> >
> >> > I'm trying to help someone to troubleshoot possible OSX Yosemite
> >> > issues, but I've only got access to OSX (< 10.9) so I cannot
> >> > check
> >> > myself.
> >> >
> >> > When building/installing binary R packages, there are different
> >> > binaries depending on OSX version.  For instance, CRAN provides
> >> > different binaries for 'OS X Snow Leopard' and 'OS X Mavericks',
> >> > e.g.
> >> > http://cran.r-project.org/web/packages/matrixStats/index.html.
> >> >
> >> > What about the new OSX Yosemite?  From
> >> > http://cran.r-project.org/doc/manuals/r-devel/R-admin.html#Yosemite
> >> > it
> >> > looks like its binaries are the same/compatible with those of
> >> > 'OS X
> >> > Mavericks' - can someone please confirm this?  Another way to
> >> > put
> >> > it,
> >> > if a repository provides OSX Mavericks binaries will an OSX
> >> > Yosemite
> >> > user install these or we s/he fall back to installing from
> >> > source?
> >> >
> >>
> >> Yes, a Yosemite user will by default be installing packages built
> >> on
> >> Mavericks using the Mavericks build of R, and they should work.
> >>
> >
> > Provided of course that that Yosemite user is using the Mavericks
> > build of R. They could also be using the Snow Leopard build of R
> > which should also work, and would be installing by default
> > packages build on Snow Leopard using the Snow Leopard build of R.
> 
> Thanks for this Dan.
> 
> As far as I understand, for an OSX user to install binary packages
> option 'pkgType' has to be set to either "mac.binary" or
> "mac.binary.mavericks".  A few questions for clarification:
> 
> Q. Is it the default that 'pkgType' be set to "mac.binary" on OSX (<
> 10.9) and to "mac.binary.mavericks" on OSX (>= 10.9)?
> 

> Q. Are you saying that if an OSX (>= 10.9) user uses
> options(pkgType="mac.binary"), then install.packages() will install
> the OSX 10.6 (Snow Leopard) binaries *and* that these binaries are
> backward compatible and should work equally well?
> 
> Q. In other words, if a user have problems with a particular OSX 10.9
> (Mavericks) binary, would a first step of troubleshooting be to ask
> that user to try the OSX 10.6 (Snow Leopard) build?
> 
> Q. If a user has options(pkgType="mac.binary.mavericks"), but the
> repository does not provide such binaries, will install.packages()
> fall back to "mac.binary", or will it go directly to "source"?
> 


First of all, this should be on R-SIG-Mac. 

It all depends on what build of R you are using. You can be on Snow Leopard or later (including Mavericks and Yosemite)  and use the Snow Leopard build. The default package type will be mac.binary.

You can be on Mavericks or later and using the Mavericks build of R and your package type will by default be mac.binary.mavericks.

The two types of binary packages are NOT binary compatible! You should not mix and match them. (Technically, if a given package does not have native code in it, it should work, but you don't really want to go there.)

If you're using the Mavericks build of R and the repository does not provide mac.binary.mavericks packages, don't (see above) install mac.binary packages, install from source.

Dan



> /Henrik
> 
> PS. <rant>From a non-active OSX user, using names instead of numbers
> to refer to versions is cute but insane. You need a very good memory
> to keep track of the ordering of Snow Leopard, Leopard, Mavericks
> etc.
> and it's not getting easier.</rant>  It would be great if R/BioC and
> everyone else would always present the version number when talking
> about OSX version and only use the name for redundancy.
> 
> >
> > Dan
> >
> >
> >> Dan
> >>
> >>
> >> > Thanks
> >> >
> >> > Henrik
> >> >
> >> > ______________________________________________
> >> > R-devel at r-project.org mailing list
> >> > https://stat.ethz.ch/mailman/listinfo/r-devel
> >> >
> >>
> >> ______________________________________________
> >> R-devel at r-project.org mailing list
> >> https://stat.ethz.ch/mailman/listinfo/r-devel
> >>
>



[Rd] OSX Yosemite (10.10): Are package binaries the same as for OSX Mavericks (10.9)?
Dan Tenenbaum