From xavier.robin at bric.ku.dk  Mon Feb  9 23:08:41 2015
From: xavier.robin at bric.ku.dk (Xavier Robin)
Date: Mon, 09 Feb 2015 23:08:41 +0100
Subject: [Rd] =?utf-8?q?R_CMD_check=3A_Uses_the_superseded_package=3A_?=
 =?utf-8?b?4oCYZG9TTk9X4oCZ?=
Message-ID: <54D92FE9.8010502@bric.ku.dk>

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 Uses the superseded package: ?doSNOW?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The "superseded" part is more confusing to me, though.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no mention of what it has been superseded with.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