genbankr removed - may need to fix URL detection?

[sckott]

after the recent change in the not_transferred.txt file 2d11fdd#diff-ab03bde500c2e24f32f95e7997328b83

the next build of the registry ropensci/roregistry@eab0860 removed genbankr but it's still in https://github.com/ropensci/roregistry/blob/gh-pages/registry_urls.json

the git remote for genbankr is https://git.bioconductor.org/packages/genbankr instead of the typical pattern like https://github.com/CornellLabofOrnithology/auk.git

i'm guessing somewhere in makeregistry R code or in codemeta we don't allow for that url pattern

cc @maelle

[maelle]

I'm sorry for getting back to this issue so late.

@sckott can you confirm the repo has been cloned to the server?

[sckott]

yes, genbankr is cloned on the server

[maelle]

Right i found a problem in codemetar.

Related question, can one guess a dev repo from a Bioconductor git URL? I.e. if the git URL is https://git.bioconductor.org/packages/genbankr what is the dev repo? I think one cannot guess it? (in which case I'd let that link be NULL)

[maelle]

@llrs since we've just discussed another Bioconductor thing, I'm asking you: "Related question, can one guess a dev repo from a Bioconductor git URL? I.e. if the git URL is https://git.bioconductor.org/packages/genbankr what is the dev repo? I think one cannot guess it?" Thanks in advance 🙏

[sckott]

can one guess a dev repo from a Bioconductor git URL?

dont know

[llrs]

No problem @maelle. The devel is the master branch. The releases are named branches of the repo RELEASE_3_X. So the devel of genbankr is on master branch on git.bioconductor.org/packages/genbankr and the version for Bioconductor release is on RELEASE_3_10 which is the one shown on bioconductor.org/packages/release/genbankr

[maelle]

Thank you! And that git repo has no viewable interface like GitHub repos do?

[llrs]

Not yet, they said they would set up something but at the moment there isn't anything browsable.

[maelle]

Good to know! Thanks!

[maelle]

@cboettig does a git URL like above qualify as codeRepository?

[cboettig]

Good question -- I think it would, but probably worth us opening an issue on https://github.com/codemeta/codemeta to discuss?

[maelle]

codemeta/codemeta#234

[maelle]

I haven't got any answer in the codemeta issue yet @cboettig.

[maelle]

👋 @cboettig