[Bioc-devel] Requirment for a Vignette

Dear Aedin,

thanks for pointing this out, it is an important issue. The quality of 
the documentation of a package is a good measure of how much care its 
author spent on it.

An exception may apply to infrastructure packages such as for example
"affxparser" that are not supposed to be directly exposed to users - 
but even for them the programmers that use them might benefit from a 
vignette.

Btw, the vignettes for "cellHTS2" have been checked in two days ago, 
Google just hasn't noticed :)

 Best wishes
    Wolfgang

aedin culhane ha scritto:

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