Re: [Rd] bug in codetools/R CMD check?

[Prof Brian Ripley]

On Tue, 8 Feb 2011, Hin-Tak Leung wrote:

--- On Tue, 8/2/11, luke-tier...@uiowa.edu <luke-tier...@uiowa.edu> wrote:
From: luke-tier...@uiowa.edu <luke-tier...@uiowa.edu>
Subject: Re: [Rd] bug in codetools/R CMD check?
To: "Hin-Tak Leung" <ht...@users.sourceforge.net>
Cc: david.clay...@cimr.cam.ac.uk, r-devel@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 ....


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@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:      l...@stat.uiowa.edu
Iowa City, IA 52242         
       WWW:  http://www.stat.uiowa.edu




______________________________________________
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel


--
Brian D. Ripley,                  rip...@stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595______________________________________________
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel