trouble installing goseq in R v4.4 Bioconductor v3.2

[D-Metzger]

After updating to the latest version of R v4.4 I have not been unable to install a working copy of goseq which has been my preferred go enrichment tool for some time. Would it be possible to update goseq or could you direct me to who I should contact to enquire about goseq updates?

[nadiadavidson]

Hi @D-Metzger ,

@federicomarini will be taking over maintenance of goseq and may be able to help you get it running in R v 4.4.

All the best,
Nadia.

[federicomarini]

Hi @D-Metzger, as of now the goseq package could not build on the Bioc machines, because one of its dependencies was not building (geneLenDataBase).
I currently provided a fix for that, and now geneLenDataBase is building correctly again. Still, the Bioc builds did not complete the operation of re-building the goseq package.

For now, you should be able to install the devel version from github via

devtools::install_github("federicomarini/geneLenDataBase")
devtools::install_github("federicomarini/goseq")

This should be fixed tomorrow according to the build schedule on the Bioc machines - in the meantime, hope the fix I just posted does the job 😉

[D-Metzger]

Thanks @federicomarini ! No luck with the Bioc build yet but the fix you posted is working great!

[federicomarini]

you can imagine that this fix is likely going to be already included in the soon-to-be-happening build round, so as of friday (saturday if in European time zones, likely 😬 ) the workaround should not be needed any more.
I would tend to leave this issue open for a couple of more days, in case someone passes by with a similar issue.
Afterwards, I would add the link to my forked repo into the codebase of goseq to redirect the traffic about it over there.