Levi Waldron comments

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                                            Levi Waldron

Error in h5checktype(). The provided H5Identifier is not a dataset identifier.

Thanks for looking into this @vjcitn! Helpful for me too.

incorporate MetaPhlAn 4

Sorry for the delay @mhmism - yes we are planning for a bioBakery 4 update. We are currently waiting for the release of HUMAnN 4 so that we can re-process...

specifying chromosome does not map aliases if gene is correct on another chromosome

@Aggarwal-Ayush just checking if this is still on your radar?

specifying chromosome does not map aliases if gene is correct on another chromosome

I mean the error it introduced in R CMD CHECK... -- Levi Waldron Associate Professor Department of Epidemiology and Biostatistics CUNY Graduate School of Public Health and Health Policy Institute...

specifying chromosome does not map aliases if gene is correct on another chromosome

Hi @Aggarwal-Ayush I just did some other minor updates and am getting ready to update CRAN in advance of posting the response to reviewers. Any luck?

What is the recommended way to run R CMD check with these containers?

I think Vince has funding specifically to fully containerize the official build system, and to make it straightforward for anyone to test packages on the same container. Not sure of...

data dictionary

Should be done along with #26 . @ftzohra22

This could be added to the ontology maps, so that the original terms are included as aliases. https://github.com/waldronlab/curatedMetagenomicDataCuration/commit/422dfd9535e809739949f88790c0eb5b81a1a78c

Map template to formal ontologies

@ftzohra22 would you do this? It would just be a two-column spreadsheet of mappings different grammar.