From robin at lindinglab.org  Tue Feb 10 12:10:48 2015
From: robin at lindinglab.org (Xavier Robin)
Date: Tue, 10 Feb 2015 12:10:48 +0100
Subject: [Rd] =?utf-8?q?R_CMD_check=3A_Uses_the_superseded_package=3A_?=
 =?utf-8?b?4oCYZG9TTk9X4oCZ?=
In-Reply-To: <1423561955.27822.73.camel@iarc.fr>
References: <54D92FE9.8010502@bric.ku.dk> <1423561955.27822.73.camel@iarc.fr>
Message-ID: <54D9E738.2060304@bric.ku.dk>

Oh, I completely missed that one.
It's very neat as it seems to work both on Windows and Unix.

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 The CRAN package snow is superseded by the parallel package which is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 Uses the superseded package: ?doSNOW?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 The "superseded" part is more confusing to me, though.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



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