Stable release channel for TLG catalog

[walkowif]

In order to successfully build the TLG Catalog for stable package versions, I had to temporarily remove some contents of files in book/tables/pharmacokinetic.

Before merging we'll have to figure out what to do about it.

Two TLG Catalog versions (development and stable) deployed concurrently can be viewed here (unless they were overwritten by a scheduled job).

This PR also adds ideas from https://github.com/insightsengineering/idr-tasks/issues/581.

[github-actions]

Unit Tests Summary

    1 files  2 suites   1m 1s ⏱️
  26 tests 0 ✔️   26 💤 0 ❌
281 runs  0 ✔️ 281 💤 0 ❌

Results for commit 716223a.

♻️ This comment has been updated with latest results.

[cicdguy]

In order to successfully build the TLG Catalog for stable package versions, I had to temporarily remove some contents of files in book/tables/pharmacokinetic.
Before merging we'll have to figure out what to do about it.

What was the issue with these?

[walkowif]

In order to successfully build the TLG Catalog for stable package versions, I had to temporarily remove some contents of files in book/tables/pharmacokinetic.
Before merging we'll have to figure out what to do about it.

What was the issue with these?

There were various errors, for example:

https://github.com/insightsengineering/tlg-catalog/actions/runs/6297102070/job/17093397369

Error in `format_sigfig()`:
! could not find function "format_sigfig"
Backtrace:
 1. ... %>% ...
 2. tern::analyze_vars_in_cols(...)

https://github.com/insightsengineering/tlg-catalog/actions/runs/6296594726/job/17091890939

! error in evaluating the argument 'obj' in selecting a method for function 'next_rpos': error in evaluating the argument 'obj' in selecting a method for function 'next_rpos': unused argument (alt_counts = TRUE)
Backtrace:
 1. ... %>% ...
 8. base::.handleSimpleError(...)
 9. base (local) h(simpleError(msg, call))

I think they might be related to some NEST package features used by TLG Catalog being unavailable in package versions released to https://insightsengineering.r-universe.dev/.

[cicdguy]

I think they might be related to some NEST package features used by TLG Catalog being unavailable in package versions released to https://insightsengineering.r-universe.dev/.

Yeah that makes sense. @insightsengineering/nest-sme - can we get some insight into these errors when you guys get a chance? We can provide more details if needed.

[edelarua]

@cicdguy @walkowif,

Both errors are caused by updates made in tern 0.9.0.9002 (this PR). Would this be fixed after the upcoming tern 0.9.1 release?

[cicdguy]

Would this be fixed after the upcoming tern 0.9.1 release?

Very likely that it'll be fixed following the release, yes. We'll just wait till the next release before pushing this out. Thanks, @edelarua!

[walkowif]

Now we have this error when generating the TLG Catalog for stable package versions:

Quitting from lines 81-107 [variant2] (mmrmt01.qmd)
Error:
! 'free_cores' is not an exported object from 'namespace:mmrm'
Backtrace:
 1. tern.mmrm::fit_mmrm(...)
 7. base::ifelse(parallel, mmrm::free_cores(), 1L)
Execution halted

[edelarua]

Now we have this error when generating the TLG Catalog for stable package versions:

Quitting from lines 81-107 [variant2] (mmrmt01.qmd)
Error:
! 'free_cores' is not an exported object from 'namespace:mmrm'
Backtrace:
 1. tern.mmrm::fit_mmrm(...)
 7. base::ifelse(parallel, mmrm::free_cores(), 1L)
Execution halted

@walkowif it seems like the Statistical Engineering team has replaced this function in mmrm v0.3.3 but has not yet released tern.mmrm v0.2.3 (latest is v0.2.2.9006) which accounts for this change in mmrm. I'm not sure when the next planned release for tern.mmrm is (it was an uncommitted item on Kendis).

[cicdguy]

Let's leave this qmd out for now (just rename it to .qmd.refactor-pending or something).

[walkowif]

Eventually, these two files had to be renamed:

• book/graphs/efficacy/mmrmg02.qmd.refactor-pending
• book/tables/efficacy/mmrmt01.qmd.refactor-pending

[cicdguy]

Okay we'll revisit these 2 later. Let's get this merged for now

[danielinteractive]

So now that mmrm is released on CRAN and tern.mmrm is fixed, this should be resolvable

[imazubi]

FYI, the MMRM module from the teal.gallery is showing some errors as well. I tried out with different user input values.