[R] warnings although R CMD check runs without any problem

[Christian Kohler]

Uwe Ligges wrote:
> Can you give examples?
>
> Uwe
>
>
> Christian Kohler wrote:
>   
>> 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
>>
>>
>>
>>     
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>   
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

>warnings()
>1:The exprSet class is deprecated, use ExpressionSet instead
...
>6: The phenoData class is deprecated, use AnnotatedDataFrame (with
ExpressionSet) instead
>13: In s[v == x[1]] <- r : Number of elements to be replaced is not a
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

-- 

Christian Kohler
Institute of Functional Genomics
Computational Diagnostics
University of Regensburg
D-93147 Regensburg (Germany)