From plummerm at iarc.fr  Tue Feb 10 10:52:36 2015
From: plummerm at iarc.fr (Martyn Plummer)
Date: Tue, 10 Feb 2015 09:52:36 +0000
Subject: [Rd] =?utf-8?q?R_CMD_check=3A_Uses_the_superseded_package=3A_?=
 =?utf-8?b?4oCYZG9TTk9X4oCZ?=
In-Reply-To: <54D92FE9.8010502@bric.ku.dk>
References: <54D92FE9.8010502@bric.ku.dk>
Message-ID: <1423561955.27822.73.camel@iarc.fr>

The CRAN package snow is superseded by the parallel package which is
distributed with R since version 2.14.0. Here are the release notes

 \item There is a new package \pkg{parallel}.

 It incorporates (slightly revised) copies of packages
 \CRANpkg{multicore} and \CRANpkg{snow} (excluding MPI, PVM and NWS
 clusters).  Code written to use the higher-level API functions in
 those packages should work unchanged (apart from changing any
 references to their namespaces to a reference to \pkg{parallel},
 and links explicitly to \CRANpkg{multicore} or \CRANpkg{snow} on help
 pages).

So you should replace your dependency on doSNOW with doParallel, which
is the equivalent foreach adapter for the parallel package.

Martyn

On Mon, 2015-02-09 at 23:08 +0100, Xavier Robin wrote:
> Dear list,
> 
> When I run an R CMD check --as-cran on my package (pROC) I get the
> following note:
> > Uses the superseded package: ?doSNOW?
> The fact that it uses the doSNOW package is correct as I have the
> following example in an .Rd file:
> > #ifdef windows
> > if (require(doSNOW)) {
> >     registerDoSNOW(cl <- makeCluster(2, type = "SOCK"))
> >     ci(roc2, method="bootstrap", parallel=TRUE)
> >     \dontrun{ci(roc2, method="bootstrap", parallel=TRUE)}
> >     \dontshow{ci(roc2, method="bootstrap", parallel=TRUE, boot.n=20)}
> >     stopCluster(cl)
> > }
> > #endif
> > #ifdef unix
> > if (require(doMC)) {
> >     registerDoMC(2)
> >     \dontrun{ci(roc2, method="bootstrap", parallel=TRUE)}
> >     \dontshow{ci(roc2, method="bootstrap", parallel=TRUE, boot.n=20)}
> > }
> > #endif
> 
> The "superseded" part is more confusing to me, though. The doSNOW
> package seems to be still available on CRAN with no special notice,
> listed in the HighPerformanceComputing view likewise, and under active
> development (last change a couple of days ago on R-Forge). I could find
> no mention of what it has been superseded with. Surprisingly, Google was
> no help on this.
> 
> I could see the note is triggered in QC.R file of the tools package.
> However this finding is not much help and leaves me just as confused as
> before.
> 
> I recall spending quite some time to setup this example to run both
> under Windows and Unix. doSNOW was the only way I could get it to work
> there. doMC is apparently still available for Unix only. I couldn't get
> doRNG to work on either platforms.
> 
> So what is R CMD check noticing me about?
> Should I ignore the notice, or take an action? If so, which one?
> 
> Best wishes,
> Xavier
> 



[Rd] =?utf-8?q?R_CMD_check=3A_Uses_the_superseded_package=3A_?= =?utf-8?b?4oCYZG9TTk9X4oCZ?=
Martyn Plummer