[Bioc-devel] Packages removing documentation

Lluís Revilla ||u|@@rev|||@ @end|ng |rom gm@||@com
Tue Aug 2 15:08:26 CEST 2022

Hi Lori,

Many thanks for your quick response.

I think the requirements for new packages are great but I'm not sure
all these standards can be applied to older packages:
The new requirements in BiocCheck might result in warnings and errors
to many packages.
For instance, new submitted packages are required to remove files such
as .Rproj or the .github folder [1, 2], which some older packages have
(including mine).
There was a discussion about these files a couple of years ago in the
community-bioc slack and more recently to allow the inclusion of these
files [3, 4, 5]
Older packages might not have vignettes with executed code, which
might be difficult for maintainers to now rewrite the vignettes.

I don't know enough about the resources of Bioconductor to propose a
good solution.
But I think lower BiocChecks frequency than current checks, such as
once every 3 months or at similar frequencies, would allow
Bioconductor to detect those issues while not imposing too much burden
on the Bioconductor resources.
However, a faster and lighter approach might be using static analysis
on the packages: grep or specific tools such as



[1]: https://bioconductor.org/packages/release/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html#bad-file-check
[2]: https://github.com/Bioconductor/Contributions/issues/2658#issuecomment-1121182390
[3]: https://community-bioc.slack.com/archives/C6MVC96AZ/p1604600559030500
[4]: https://community-bioc.slack.com/archives/C6MVC96AZ/p1649041312699229
[5]: https://community-bioc.slack.com/archives/C6MVC96AZ/p1621466394001900
and subsequent messages

On Tue, 2 Aug 2022 at 13:22, Kern, Lori <Lori.Shepherd using roswellpark.org> wrote:
> Thank you.
> I agree packages should maintain the high integrity that they were accepted with.  For now if you find these packages please let us know their name by sending an email to maintainer using bioconductor.org and we will reach out to notify them they are not in Bioconductor standards and will get a warning to fix or  we will consider deprecating.
> We would like to run BiocCheck but our current resources do not allow for that.  We will look into some other options for trying to run BiocCheck on the current Bioconductor packages for at least status checks.  Hopefully we can find a way to identify these types of packages without increasing the build resource load.
> Cheers,
> Lori Shepherd - Kern
> Bioconductor Core Team
> Roswell Park Comprehensive Cancer Center
> Department of Biostatistics & Bioinformatics
> Elm & Carlton Streets
> Buffalo, New York 14263
> ________________________________
> From: Bioc-devel <bioc-devel-bounces using r-project.org> on behalf of Lluís Revilla <lluis.revilla using gmail.com>
> Sent: Monday, August 1, 2022 5:36 PM
> To: bioc-devel <bioc-devel using r-project.org>
> Subject: [Bioc-devel] Packages removing documentation
> 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.
> Best,
> Lluís
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