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

[Marc Carlson]

Hi Daren,

You should always be using the very latest version of R (2.8.1 in this
case) since the minor revisions are supposed to indicate bug fixes  and
not additional functionality (added functionality is supposed to go into
the development branch).  For Bioconductor releases we do not use a
minor version number because Bioconductor is not a a single thing the
way that R is, but is instead a collection of packages. 

We synchronize our release 2.3 to go with R 2.8.1 by building all the
software packages in Bioconductor nightly.  If for some reason a bug fix
in R were to cause a problem in one of our packages, then we will update
the affected package and bump the minor version number of that package
to indicate that there had been a bug fix in it.  You can then use
sessionInfo() to see if the version numbers on your packages are the
latest ones that are available for your particular release of
bioconductor, or you can just use biocLite() and update.packages() to
automatically update your packages to the very latest available as
described here:

http://www.bioconductor.org/docs/install/


  Marc






Daren Tan wrote:
> 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
>>
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>>
>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
>>
>>
>>     
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