deprecated package in BioC 3.11 - PAPi

[tnaake]

Hi,

PAPi was identified as being non-maintained/unresponsive and will be deprecated in the next BioC release. PAPi is described in the section 2.7.4 Pathway analysis. I am wondering if we should keep it for historical reasons or remove it from the metaRbolomics book.

[stanstrup]

If it can still be found and installed I would keep it.

[jorainer]

But I would definitely note somewhere that it is deprecated - non-maintained software can be dangerous and I, as a user, would not like to use that.

[stanstrup]

I am just afraid of it getting very inconsistent and difficult to keep up to date.
We cannot keep track of all the packages.

[jorainer]

Good point

[tnaake]

Was it not the initial idea to have an up-to date resource with relevant software packages for metabolomics packages? Is it possible to have a subsection where we list deprecated packages and describe their function? Or to mark those packages in the tables that are deprecated? Of course this will require some effort of maintenance, but I think if we receive input at least from users we could mark those packages somehow. I also think that we should not actively check for all of the packages if they are still functional, just in the case of reporting certain packages.

[sneumann]

I'd be hesitant to commit manual work to that. We're in parallel lobbying to get
also FAIRer software, where ideally we'd have automatic access to "last changed" information,
which would be great to have in our resource. Findability and Accessibility rulez :-)
Yours, Steffen