From htl10 at users.sourceforge.net  Tue Feb  8 19:24:35 2011
From: htl10 at users.sourceforge.net (Hin-Tak Leung)
Date: Tue, 8 Feb 2011 18:24:35 +0000 (GMT)
Subject: [Rd] bug in codetools/R CMD check?
In-Reply-To: <alpine.LFD.2.02.1102081730560.12643@gannet.stats.ox.ac.uk>
Message-ID: <133261.3368.qm@web29506.mail.ird.yahoo.com>

--- On Tue, 8/2/11, Prof Brian Ripley <ripley at stats.ox.ac.uk> wrote:

> From: Prof Brian Ripley <ripley at stats.ox.ac.uk>
> Subject: Re: [Rd] bug in codetools/R CMD check?
> To: "Hin-Tak Leung" <htl10 at users.sourceforge.net>
> Cc: luke-tierney at uiowa.edu, david.clayton at cimr.cam.ac.uk, r-devel at r-project.org
> Date: Tuesday, 8 February, 2011, 17:36
> On Tue, 8 Feb 2011, Hin-Tak Leung
> wrote:
> 
> > --- On Tue, 8/2/11, luke-tierney at uiowa.edu
> <luke-tierney at uiowa.edu>
> wrote:
> >
> >> From: luke-tierney at uiowa.edu
> <luke-tierney at uiowa.edu>
> >> Subject: Re: [Rd] bug in codetools/R CMD check?
> >> To: "Hin-Tak Leung" <htl10 at users.sourceforge.net>
> >> Cc: david.clayton at cimr.cam.ac.uk,
> r-devel at r-project.org
> >> Date: Tuesday, 8 February, 2011, 15:34
> >> Thanks -- will try to have a look
> >> sometime soon.
> >>
> >> luke
> >
> >
> > Thanks.
> >
> > Also, regardless of whether that's a bug in codetools
> or snpMatrix 
> > (I am okay if you turn this around to say there is
> some coding style 
> > we shouldn't do in there, for which I'd apologize),
> there seems to 
> > be a small bug or inconsistency, and certainly in R or
> codetools, in 
> > that the codetools message is shown in all 4 platforms
> - linux, mac, 
> > win32, win64 - but the error status, whether it is
> correct or not, 
> > only propagate back up to the "R CMD check" harness in
> the case of 
> > win64 and not for the other 3 platforms. It should
> pass or fail with 
> > a warning consistently on all platforms.
> 
> Are you sure this is the same version of R and
> codetools?? If you mean 
> BioC's check farm, that often has version skew.? I see
> the message 
> consistently on all my platforms ....

That's what I mean - the codetools message are seen consistently on all platforms, but the warning status only propagate back up to R CMD check (and resulted in a "1 warning" status) for win64 only; so R CMD check is behaving inconsistently, regardless of whether the message is genuine or not.

http://bioconductor.org/checkResults/2.7/bioc-LATEST/snpMatrix/gewurz-checksrc.html
* using R version 2.12.1 (2010-12-16)
* using platform: x86_64-pc-mingw32 (64-bit)
codetools message, status 1, 1 warning

http://bioconductor.org/checkResults/2.7/bioc-LATEST/snpMatrix/pelham-checksrc.html
* using R version 2.12.1 Patched (2010-12-17 r53867)
* using platform: i386-apple-darwin9.8.0 (32-bit)
codetools message, no error status, no warning

http://bioconductor.org/checkResults/2.7/bioc-LATEST/snpMatrix/liverpool-checksrc.html
* using R version 2.12.1 (2010-12-16)
* using platform: i386-pc-mingw32 (32-bit)
codetools message, status 1, no warning

http://bioconductor.org/checkResults/2.7/bioc-LATEST/snpMatrix/lamb2-checksrc.html
* using R version 2.12.1 (2010-12-16)
* using platform: x86_64-unknown-linux-gnu (64-bit)
codetools message, no error status, no warning


The mac OS X box has a slightly different version of R, but the other seems to be the same, and yet the error status and also whether the warning status is propate back is different. The codetools message is seen in all cases.

Hin-Tak









[Rd] bug in codetools/R CMD check?
Hin-Tak Leung