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warnings although R CMD check runs without any problem

6 messages · Uwe Ligges, Christian Kohler, Brian Ripley +1 more

Original
Christian Kohler
# 
Dear list members,

as I am new to R, I would kindly like to ask for your help.

I checked a package with the 'R CMD check' command and all worked out
well, (only 'OK' status). Loading its vignette afterwards with
'source("package.Rcheck/inst/doc/vignette.R")' yields a message saying
that several (well, in my case more than 50) warnings still exist and
can be viewed via the 'warnings()' command.

My question now is: why are there still warnings even though the check
has been passed without any problems? Generally speaking, would it be
possible to submit this package e.g. to the Bioconductor project, even
if these warnings still exist?


Thanks in advance,
Christian
Uwe Ligges
# 
Can you give examples?

Uwe
Christian Kohler wrote:
Christian Kohler
#
Uwe Ligges wrote:
Hello Uwe,

as the package is to submit to Bioconductor, I should have posted to the
BioC-Help instead but initially it was rather a 'R'-specific question to me.
My apology for that.

Examples for warning messages are
...
ExpressionSet) instead
multiple of the substitution length.
....

In my opinion, these messages solely indicate some 'hints' which do not
interfere with any functionality within the package. Right?
As there is no reference to a file, which triggers these messages, I
have currently no idea where to take a closer look at.

Regards,
Christian
Brian Ripley
#
On Thu, 20 Sep 2007, Christian Kohler wrote:

            

      
      
      
    

        
Because the check process does not consider R-level warnings in examples 
or vignettes, only errors.  Only someone who understands the code will 
know if the warnings are pedagogical, innocuous or serious.  No one says 
that examples should not give warnings, and it may be helpful to 
illustrate when they might occur.

            

      
      
      
    

        
It is possible to submit it, and very likely that it would be acceptable. 
Distributing a package with warnings you do not understand is not a good 
idea, though.

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Christian Kohler
    

    

      
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Prof Brian Ripley wrote:

            

      
      
      
    

        
Dear Prof Ripley & Mr Ligges,

thanks for your help and the quick responses.

Regards,
Christian

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Robert Gentleman
    

    

      
      #
    

  


  

      
Hi,

        
Christian Kohler wrote:

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        
These tell you that you are using data structures that are no longer 
supported and should not be used. You need to fix them - the appropriate 
replacements are also indicated in the help message.

            

      
      
      
    

        
This is also serious. It suggests that you have an error in your 
code. Typically if one replaces the elements in one vector
s[v == x[1]], with those in another vector, namely r, the two sets 
should be the same length. In most (but not all) cases where this 
happens there is a bug.

            

      
      
      
    

        
No, wrong - the first two tell you that you are badly (at least one 
year) out of date in your use of data structures and the last one tells 
you that you probably have a serious problem with your code.

            

      
      
      
    

        
Well, you did not give the whole output, and in it there really are 
names of files and locations.  You can also use an editor to search for
  1) any instance of the work exprSet or phenoData and replace those 
parts of the code with the new classes

  2) search for s[v == x[1]], and then use some of R's debugging methods 
to determine whether there is a bug or not.

  best wishes
    Robert