From josh.m.ulrich at gmail.com  Wed Feb 11 17:26:25 2015
From: josh.m.ulrich at gmail.com (Joshua Ulrich)
Date: Wed, 11 Feb 2015 10:26:25 -0600
Subject: [Rd] =?utf-8?q?R_CMD_check=3A_Uses_the_superseded_package=3A_?=
	=?utf-8?b?4oCYZG9TTk9X4oCZ?=
In-Reply-To: <54D9E738.2060304@bric.ku.dk>
References: <54D92FE9.8010502@bric.ku.dk> <1423561955.27822.73.camel@iarc.fr>
	<54D9E738.2060304@bric.ku.dk>
Message-ID: <CAPPM_gQdkEO6-suh8Y9Tp6OHVV4VjnTmebwPkdnQARzk700-0g@mail.gmail.com>

On Tue, Feb 10, 2015 at 5:10 AM, Xavier Robin <robin at lindinglab.org> wrote:
> Oh, I completely missed that one.
> It's very neat as it seems to work both on Windows and Unix.
>
It works on both Windows and *nix because it combines functionality
from snow (Windows) and multicore (*nix).

> Thanks!
> Xavier
>
>
> On 10/02/15 10:52, Martyn Plummer wrote:
>> The CRAN package snow is superseded by the parallel package which is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 Uses the superseded package: ?doSNOW?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
>>>
>
>
> --
> Xavier Robin, PhD
> Cellular Signal Integration Group (C-SIG)  - Linding Lab
> Biotech Research and Innovation Center (BRIC) - University of Copenhagen
> Anker Engelundsvej, DTU Campus, Building 301, DK-2800 Lyngby, DENMARK
> Mobile: +45 42 799 833
> www.lindinglab.org - www.bric.ku.dk
>
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel



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