bug in codetools/R CMD check?
--- 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