[BioC] Keep getting warning messages of package 'XYZ' was built under R version 2.8.1

[Patrick Aboyoun]

Daren,
The current policy for bioconductor.org is to follow CRAN conventions.  
The Windows and Mac OS X binary packages in CRAN-like repositories  
differentiate between minor releases (x.y and x.(y+1)), but not  
between subminor releases (x.y.z and x.y.(z+1)). Given that subminor  
releases tend to contain mainly bug fixes with a light sprinkling of  
enhancements and (ideally) no major changes, what justification is  
there to stay at R 2.8.0 rather than upgrade to R 2.8.1? Because  
subminor releases shouldn't break existing systems, even IT  
departments tend not to have their blood levels rise when asked to  
upgrade a software from version x.y.z to x.y.(z+1).

As with all things in the Bioconductor project, all decisions are  
subject to review and modification. Keep in mind that there is a cost  
in maintaining subminor binary package repositories so the benefits  
must be judged against that cost.


Patrick


Quoting Daren Tan <daren76 at hotmail.com>:

>
> Please clarify my understanding.
>
> When R version 2.8.0 was released, all packages in Bioconductor   
> version 2.3 was built with it. During this period, any installation   
> of packages in bioconductor 2.3 did not give any warnings. With the   
> minor release R version 2.8.1, Bioconductor version 2.3 was rebuilt   
> with it. Any installation of packages in bioconductor 2.3 will now   
> give warnings that they were built with 2.8.1.
>
> If my understanding is right, would it better for Bioconductor to   
> have minor release like 2.3.X in synchrony with R 2.8.X ?
>
> ________________________________
>> Date: Sun, 22 Feb 2009 05:28:29 -0500
>> Subject: Re: [BioC] Keep getting warning messages of package 'XYZ'   
>> was built under R version 2.8.1
>> From: stvjc at channing.harvard.edu
>> To: daren76 at hotmail.com
>> CC: bioconductor at stat.math.ethz.ch
>>
>> This is a warning. It is telling you that there is a mismatch   
>> between the version of R that you are running (2.8.0,
>> which is not current) and 2.8.1 (the current version, that we use   
>> to build the packages). There is no indication
>>
>> that anything is "broken", but it is not really possible to give   
>> any assurances of the sort you seek. To get rid
>> of the warning, which will only be observed at install time, you   
>> would need to upgrade R to 2.8.1. If you run the
>>
>> examples of the package, or build the vignette, and find that the   
>> computations you generate agree with those
>> of the vignette, that would be some assurance that nothing is   
>> drastically wrong.
>>
>>
>> On Sun, Feb 22, 2009 at 1:18 AM, Daren Tan> wrote:
>>
>>
>>
>>
>>
>> I just installed another bioconductor package "seqinr". I only   
>> noticed the warning message today, and fear that my R or   
>> bioconductor is broken. Please give me some assurance it is working  
>>  fine. I dread to reinstall R and bioconductor again.
>>
>>
>>
>>
>>> library("seqinr")
>>
>> Warning message:
>>
>> package 'seqinr' was built under R version 2.8.1
>>
>>
>>
>>> sessionInfo()
>>
>> R version 2.8.0 (2008-10-20)
>>
>> i386-pc-mingw32
>>
>> locale:
>>
>> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United   
>> States.1252;LC_MONETARY=English_United   
>> States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
>>
>> attached base packages:
>>
>> [1] stats graphics grDevices utils datasets methods base
>>
>> other attached packages:
>>
>> [1] seqinr_2.0-2
>>
>> loaded via a namespace (and not attached):
>>
>> [1] tools_2.8.0
>>
>>
>>
>> _______________________________________________
>>
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>>
>> Bioconductor at stat.math.ethz.ch
>>
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>
>> Search the archives:   
>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>
>>
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