[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
Thanks
Aedin
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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