[Bioc-devel] Large vignettes

Lluís Revilla ||u|@@rev|||@ @end|ng |rom gm@||@com
Thu Jan 12 11:29:10 CET 2023

Hi all,

Perhaps instead of long vignettes, it would be better to use a book hosted
and in sync with the packages at Bioconductor.
There are already a few: https://www.bioconductor.org/books/release/
But I was not able to find how to submit such bookdowns to Bioconductor (I
briefly searched the website and the dev book at
I think the limits are less restrictive and there is no minimum size of
chapters or documentation, but I am not sure.

Some authors already have books outside bioconductor to have extensive
examples of their packages.
They will also benefit from having them with the Bioconductor framework and
in sync with the packages released to the users.



On Wed, 4 Jan 2023 at 21:39, Vincent Carey <stvjc using channing.harvard.edu>

> I am glad you brought this up here, and I welcome further discussion on
> this mailing list.  It is important to understand the constraints on
> development
> that arise from Bioconductor's package guidelines.
> I don't think we want to change the limits on package payload size without
> understanding the consequences for users and our build system.  The split
> approach mentioned by Lambda seems sensible to me, and I hope it is
> not too burdensome.  Additional commentary and details from the community
> are welcome.
> On Wed, Jan 4, 2023 at 3:21 PM Lambda Moses <dlu2 using caltech.edu> wrote:
> > Hi Adam,
> >
> > I also got this problem, and I would like some input from Bioc Core
> > Team. I worked around it by writing a minimal vignette in the main
> > branch. Then I made a documentation branch, where I have the same code
> > as in main branch, but with more elaborate vignettes used to build a
> > pkgdown website. I made a rule for myself that I can only merge from the
> > main or devel branch to the documentation branch but not the other way
> > round. I would switch branch when I find a bug or want a new feature
> > while writing the vignettes. You can see the main branch here:
> > https://github.com/pachterlab/voyager/tree/main The documentation branch
> > here: https://github.com/pachterlab/voyager/tree/documentation
> >
> > I kind of wonder if the 5 MB rule is outdated in the age of increasing
> > computer power and internet speed. A jpeg photo can easily exceed 5 MB.
> > I also wonder if this rule is deliberately kept for good reasons, like
> > to make R more inclusive to disadvantaged people with limited internet
> > services.
> >
> > Regards,
> >
> > Lambda
> >
> > _______________________________________________
> > Bioc-devel using r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >
> --
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