Update Question

[thompj27]

If I want to update annotables for a build more recent than your git hub, is it simply a matter of cloning and building the annotables package? In other words, does building the package automatically go to the latest ensembl build? If yes, where do I change the code to reflect the current version so ensembl_version returns the correct value.

I did clone and build the package successfully, but ensembl_version still reports ensembl 91 and it would be work to compare to a known older version. I'm not so familiar with these data packages and I'm having trouble dissecting the package to find the source code that's hitting ensembl to answer the versioning question myself.

Thanks,
John Thompson

[stephenturner]

It does. I think you'll have to use an archived version, e.g., https://bioconductor.org/packages/release/bioc/vignettes/biomaRt/inst/doc/biomaRt.html#using-archived-versions-of-ensembl

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On Thu, Aug 30, 2018 at 4:12 PM John Thompson ***@***.***> wrote: If I want to update annotables for a build more recent than your git hub, is it simply a matter of cloning and building the annotables package? In other words, does building the package automatically go to the latest ensembl build? If yes, where do I change the code to reflect the current version so ensembl_version returns the correct value. I did clone and build the package successfully, but ensembl_version still reports ensembl 91 and it would be work to compare to a known older version. I'm not so familiar with these data packages and I'm having trouble dissecting the package to find the source code that's hitting ensembl to answer the versioning question myself. Thanks, John Thompson — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#14>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAcFLEZf8q1Al5XIFb2j-pWPdEXLFrLbks5uWEdDgaJpZM4WUJDa> .

[thompj27]

Thanks for the quick response! So if I build it today without specifying an archived version I should be getting R92 which is current as of today.

It looks like you encode the Ensembl release number as the last bit of the package version. I can set that in the DESCRIPTION file. But where to I update the version so that the ensembl_version flag reports the correct updated version?

[stephenturner]

So I'm looking at the code and it's the ensembl_version object that's created during the build process that's recording the actual version.

ensembl_version <- listMarts() %>%
    filter(biomart == "ENSEMBL_MART_ENSEMBL") %>%
    pull(version)
save_data(ensembl_version, name = "ensembl_version")

The version in the DESCRIPTION is just something I put in manually.