[Bioc-devel] Packages removing documentation

Lluís Revilla ||u|@@rev|||@ @end|ng |rom gm@||@com
Mon Aug 1 23:36:06 CEST 2022

Dear Bioconductor community,

One of the oldest requirements of Bioconductor is a vignette with some
executed code.

Recently I found some packages that do not have examples for some
functions and vignettes with executed code in the current release
while they did some versions ago. The vignette was replaced with a
link to resources outside the Bioconductor repository.
These resources might not be in sync with the released code of the
package or might not work. Users, as I did, might get confused if code
linked from the vignette does not work or is not found in the package.

This is possible because submitted packages need to pass all checks
specified by R CMD check and by BioCheck() in the BiocCheck package.
However, once accepted, checks are no longer done with BiocCheck() and
just with R CMD check.

I think it would be desirable to keep the initial high quality of the
packages after the peer review and with the BiocCheck. If authors need
to move their code to a book they can use the book infrastructure set
up by Bioconductor too.
Perhaps Bioconductor checks on existing packages could use the same
version of BiocCheck that was initially used or some specific tests to
ensure that documentation is not dismissed.

I would appreciate your thoughts on this.



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