[Rd] bug in codetools/R CMD check?

[Hin-Tak Leung]

--- 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.

Hin-Tak 

> On Thu, 3 Feb 2011, Hin-Tak Leung wrote:
> 
> > Hi Mr Tierney,
> >
> > I have noticed an error message from R 1.12.x's CMD
> check for a while (apparently prof Ripley completely rewrote
> CMD check in R 1.12+)
> > e.g.:
> > http://bioconductor.org/checkResults/2.7/bioc-LATEST/snpMatrix/lamb2-checksrc.html
> >
> > ----------------
> > * checking R code for possible problems ... NOTE
> > Warning: non-unique value when setting 'row.names':
> ‘new’
> > Error in `row.names<-.data.frame`(`*tmp*`, value =
> c("1", "new", "new" :
> >  duplicate 'row.names' are not allowed
> > Calls: <Anonymous> ... rownames<- ->
> row.names<- -> row.names<-.data.frame
> > Execution halted
> > -----------------
> >
> > yet everything is okey dokey at http://bioconductor.org/checkResults/2.7/bioc-LATEST/#S
> under the snpMatrix entry.
> >
> > I believe it might be a bug in
> codetools::incLocalSrcInfo (used by "R CMD check") and here
> is what I think the fix(?) - but I am not entirely sure what
> that routine does and why other package writers haven't
> noticed similiar problems before:
> >
> > diff -ur codetools/R/codetools.R
> codetools-fix/R/codetools.R
> > --- codetools/R/codetools.R   
> 2011-01-07 15:52:58.000000000 +0000
> > +++ codetools-fix/R/codetools.R   
> 2011-02-03 10:03:54.000000000 +0000
> > @@ -823,8 +823,9 @@
> >     new <- list(srcfile = if
> (is.null(w$srcfile)) NA_character_ else w$srcfile,
> >             
>    frow = if (is.null(w$frow)) NA_integer_
> else w$frow,
> >             
>    lrow = if (is.null(w$lrow)) NA_integer_
> else w$lrow)
> > +    new <- as.data.frame(new,
> stringsAsFactors = FALSE)
> >     if (is.null(value))
> > -        value <-
> as.data.frame(new, stringsAsFactors = FALSE)
> > +        value <- new
> >     else
> >         value <-
> rbind(value, new)
> >     assign("srcinfo", value,
> entry)
> >
> >
> > Apply this "fix" would result in snpMatrix's "R CMD
> check" churning out:
> >
> > ---------------------
> > .ld.withmany: local variable ‘names.components’
> assigned but may not be used
> > .ld.withmany: local variable ‘nsnps.for.each’
> assigned but may not be used
> > misinherits: local variable ‘nc.snps’ assigned but
> may not be used
> > misinherits: local variable ‘nr.snps’ assigned but
> may not be used
> > qq.chisq: local variable ‘lab’ assigned but may
> not be used
> > read.HapMap.data: local variable ‘base’ assigned
> but may not be used
> > read.HapMap.data: local variable ‘build’ assigned
> but may not be used
> > read.HapMap.data: local variable ‘finish’ assigned
> but may not be used
> > read.HapMap.data: local variable ‘strand’ assigned
> but may not be used
> > tdt.snp: local variable ‘nc.snps’ assigned but may
> not be used
> > tdt.snp: local variable ‘nr.snps’ assigned but may
> not be used
> > ---------------------
> >
> > which is more like expected check warnings.
> >
> > Care to comment?
> >
> > Hin-Tak Leung
> >
> >
> >
> >
> > ______________________________________________
> > R-devel at r-project.org
> mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-devel
> 
> -- 
> Luke Tierney
> Statistics and Actuarial Science
> Ralph E. Wareham Professor of Mathematical Sciences
> University of Iowa           
>       Phone:       
>      319-335-3386
> Department of Statistics and       
> Fax:           
>    319-335-3017
>     Actuarial Science
> 241 Schaeffer Hall           
>       email:      luke at stat.uiowa.edu
> Iowa City, IA 52242         
>        WWW:  http://www.stat.uiowa.edu