[Bioc-devel] S4 accessor conflict (MoleculeExperiement)

[Ramos Perez, Marcel]

Hi Nick,

Git blame says the 'molecules' method and generic have been in SpatialExperiment for at least 2 years.

It looks like the maintainers of MoleculeExperiment should import the molecules generic and export only their method.

The other option is to have a separate package with only SpatialGenerics (à la MatrixGenerics) but this would require
considerable collaboration between multiple parties.

Best regards,

Marcel


On 10/29/23 11:02 PM, Nick Robertson via Bioc-devel wrote:

Dear All,


The new update of SpatialExperiement includes a molecules() method, and this appears to be causing a conflict with the MoleculeExperiement<https://github.com/SydneyBioX/MoleculeExperiment><https://github.com/SydneyBioX/MoleculeExperiment> molecules() accessor.
When calling  molecules(me, assayName = "detected")​, the following error is reported:

unable to find an inherited method for function 'molecules' for signature '"MoleculeExperiment"'

Adding MoleculeExperiement:: to the molecules() call fixes the issue, but this is not ideal, as it really should not be necessary since a molecules() method exists for the MoleculeExperiement class.

Additionally, MoleculeExperiement was explicitly built to be interoperable with SpatialExperiement and imports SpatialExperiement::SpatialExperiement() in order to output spe objects.

Is there any way to overcome this conflict?

Regards,
Nick

        [[alternative HTML version deleted]]

_______________________________________________
Bioc-devel using r-project.org<mailto:Bioc-devel using r-project.org> mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel


---
Marcel Ramos
Bioconductor Core Team
Roswell Park Comprehensive Cancer Center
Dept. of Biostatistics & Bioinformatics
Elm St. & Carlton St.
Buffalo, New York 14263


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]]