From simon.urbanek at r-project.org  Fri Apr 18 03:43:03 2014
From: simon.urbanek at r-project.org (Simon Urbanek)
Date: Thu, 17 Apr 2014 21:43:03 -0400
Subject: [Rd] R-3.1.0 OSX Snow Leopard installs old binary
In-Reply-To: <CABtg=Kmy_g9WieTot8i261rVEX2+Fmd-rpPBVG4devfybXrhFg@mail.gmail.com>
References: <CABtg=KmwERwaJ+JwEG6G6NeZLmHoPc+PJNk+0CjMqWs=BwXD0g@mail.gmail.com>
	<C2E40931-DA04-496B-82EF-58179FCDD8C7@r-project.org>
	<CABtg=K=m2+jvc+8nJgANeXFMZnbK=nrZY73=9N+cATzdC6HfQQ@mail.gmail.com>
	<15EDAF28-8C7F-49D9-8E36-BF705E6EE1C3@r-project.org>
	<CABtg=Kmy_g9WieTot8i261rVEX2+Fmd-rpPBVG4devfybXrhFg@mail.gmail.com>
Message-ID: <EC946039-7029-431B-88D8-B8DF0A512E0C@r-project.org>

On Apr 17, 2014, at 9:24 PM, G?bor Cs?rdi <csardi.gabor at gmail.com> wrote:

> On Thu, Apr 17, 2014 at 9:07 PM, Simon Urbanek <simon.urbanek at r-project.org> wrote:
> [...]
> 
> No, the issue is that igraph suggests graph yet fails when it's not present. It should guard against failure is case it's not available. I didn't look at this particular case, but sometimes that is necessary to break infinite dependency loops.
> 
> So if I make 'graph' a dependency via Imports, then everything will be OK? 
> 
> We can rely on Imports and Depends from BioC being available, but not on Suggests?
> 

The Suggests failure has nothing to do with BioC. Only packages listed in Depends/Imports are required for a package to work so there is no guarantee for any packages in Suggests to be available - hence the package should not break if they are not available - that's the whole point of Suggests. If you list it in Depends/Imports then it won't even get to the check if those packages are not available - it won't build at all. I didn't look at the dependencies in this particular case, but one reason to use Suggests is to break dependency loops: if A depends on B and B on A, then there is no way to install them, so typically A suggests B and B depends on A so that A can be installed and checked first without B and then B checked with A and finally A with B. If A breaks without B then it makes such bootstrapping impossible - we found some packages with this issue, that's why mentioned this - I don't know if that's the case with igraph or not.

As for BioC, the builds for BioC are independent of CRAN, so CRAN doesn't build BioC packages and thus their availability is subject to manual intervention - on the OS X build machine there is currently no automated way to track BioC packages, but we're working on it.

Cheers,
Simon



[Rd] R-3.1.0 OSX Snow Leopard installs old binary
Simon Urbanek