[Bioc-devel] Requirment for a Vignette

aedin culhane aedin at jimmy.harvard.edu
Mon Sep 24 20:17:10 CEST 2007

Thanks Robert,
This is great.

A google search of  "No vignettes available" 
site:http://bioconductor.org/packages/2.1/bioc/  returns 8 hits.

A google search of  "No vignettes available" 
site:http://bioconductor.org/packages/2.0/bioc/  returns 15 hits

I looked in the code of 1 package (plier) and did not see any .rnw file. 
     I also tried to open the vignette using the command 
vignette("plier")  and this returns

Warning message:
vignette 'plier' *not* found


Robert Gentleman wrote:
> Aedin Culhane wrote:
>> Dear All,
>> May I ask a little query?
>> Increasingly, there are Bioconductor packages (many core) without a 
>> vignette. 
>   I hope not. It is a requirement, and no less of one for core packages 
> than for anyone else.  But it is a requirement only for release, not 
> devel.  Operationally, we do not take submissions that are not for 
> release, so all submissions must have vignettes. But many of the core 
> related packages in devel may not have one, and most new ones are 
> unlikely to have one until very close to release, when we finalize the 
> API we are going to support for the next release.
>   We (the core developers) do use the bioc-devel repository as a way to 
> share ideas so that things there are often very intermediate, and we 
> expect anyone working off of that to be aware of the risks involved in 
> using software under active development.
>  In just a few days you will see the manifest for the 2.1 release 
> change, and all packages that are not scheduled for release will be 
> dropped. Once that happens, we will look for missing vignettes, but you 
> could send me (either on or off list) a set of the packages that you 
> have found without them, and I will start pushing on people to produce 
> something.
>   But as I am sure you are aware someone can easily circumvent any 
> technical requirement we impose, so the only really reliable way to push 
> on a developer to provide good documentation, is for their users to ask 
> for more.  That also provides some feedback to the developer that their 
> code is being used, so that more development effort is of benefit.
>  best wishes
>    Robert
>> In my own work, I have found several BioC package tutorials/vignettes 
>> invaluable.  They assisted me learn Bioconductor, but additional they 
>> provide one with a understanding of the objective of a package and a 
>> grasp of the order and procedures required to execute its many functions.
>> Has the requirement for a package vignette in Bioconductor packages 
>> slackened?
>> Thanks a million
>> Aedin
>> _______________________________________________
>> Bioc-devel at stat.math.ethz.ch mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel

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