Closed CarmenTamayo closed 4 months ago
Please also update the epiparameter version number for renv:
You can find the value to use by running sessioninfo::package_info("epiparameter")
, which will tell you which version is installed on your local computer.
Could you also update epiparameter usage in the EpiNow2 child document? yes, that's on my to-do list, to update the usage also on the rmd chunks
@joshwlambert @Bisaloo hi both, do you think we could merge this PR? the only issue I've not been able to resolve is issue #127 , where I'm unsure how {epiparameter} could be used to update what's now being done by epitrix/distcrete Other than that, this could be merged after being reviewed
@CarmenTamayo I will review this afternoon and get back to you by EOD.
Given the number of commits to number of files changed I think this PR would be a good candidate for a squash merge.
Please also add yourself as a package author (role = "aut"
) in the DESCRIPTION
before we merge this @CarmenTamayo :pray:
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Please also add yourself as a package author (
role = "aut"
) in theDESCRIPTION
before we merge this @CarmenTamayo 🙏
Done here https://github.com/epiverse-trace/episoap/pull/100/commits/013a44d695b58298d97349c0e624076b0be808a6
Not sure why the test-reports
workflow is failing, looking at the setup-r-dependencies@v2
output from sessionInfo()
neither {episoap} or it's dependencies for the templates are being installed, even though they were on previous actions runs when the workflow passed. Could use the setup-renv@2
workflow (https://github.com/r-lib/actions/tree/v2-branch/setup-renv) to ensure the packages required to build the reports are installed with their correct versions. @Bisaloo & @chartgerink let me know if you think this is a suitable fix?
@joshwlambert - are we confident that's the underlying problem, really? If the workflow worked before and has not changed, it feels like something else must be causing this. I just re-ran the workflow and it seems like there is a different problem that requires some debugging to make the action
Quitting from lines 215-230 [unnamed-chunk-2] (skeleton.Rmd)
Error in `value[[3L]]()`:
! Package 'ggplot2' version 3.5.0 cannot be unloaded:
Error in unloadNamespace(package) : namespace 'ggplot2' is imported by 'episoap' so cannot be unloaded
Backtrace:
To fix the workflow, I would see what changed since the last time the workflow succeeded and find the root cause.
@chartgerink I think the misunderstanding is because I was looking at the first test report workflow to fail. It seems the error in recent workflow failures is different.
The packages being installed by setup-r-dependencies
are the most recent versions, or at least newer than specified in the skeleton.Rmd
lock file. The error seems to be that the action cannot unload the newer version. This would presumably be resolved by just installing the versions specified in the lock file in the first place, but I'm unsure how to do this without pulling the lock file into a renv.lock
file and using the setup-renv
workflow mentioned above.
What's the best approach?
Changes in epiparameter usage to update template contents to the latest version of the package:
epidist
uses diseases rather than pathogensepidist()
toepidist_db()
to extract from database (lines 380-385)epidist$params
toas.list(get_parameters(si_epiparameter))
(line 387)<- as.list so it can be used with function on line 406family(epidist)
to extract distribution name (line 388)epiparameter
usage in code chunks to estimate Rt (EpiNow2, R0)