[Bioc-devel] Packages removing documentation

Kern, Lori Lor|@Shepherd @end|ng |rom Ro@we||P@rk@org
Tue Aug 2 13:22:14 CEST 2022

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.


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 Llu�s 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.



Bioc-devel using r-project.org mailing list

This email message may contain legally privileged and/or confidential information.  If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited.  If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you.
	[[alternative HTML version deleted]]

More information about the Bioc-devel mailing list