Downstream Deprecated / Expired Syntax

[andrjohns]

Opening this issue to track the status of downstream packages. All dependencies have now had PRs submitted or the maintainers notified.

Status

• Patches not yet merged: 23
• Patches merged, not yet on CRAN: 15

Patches not yet merged

Package	Status	Merged	On CRAN
AovBay	Maintainer emailed
bbmix	PR Opened
BINtools	Maintainer emailed
bmggum	PR Opened
bws	PR Opened
cbq	PR Opened
densEstBayes	Orphaned
fcirt	PR Opened
glmmPen	PR Opened
hBayesDM	PR Opened
idem	PR Opened
imt	PR Opened
MetaStan	PR Opened
multipleDL	PR Opened
oncomsm	PR Opened
morseTKTD
phacking	PR Opened
psBayesborrow	PR Opened
rts2	PR Opened
spsurv	Github Stan code broken issue opened
survstan	PR Opened
truncnormbayes	PR Opened
YPPE	PR Opened

Patches merged, not yet on CRAN

Package	Status	Merged	On CRAN
bayesforecast	PR Opened	☑️
beanz	PR Opened	☑️
bmstdr	PR Opened	☑️
bsynth	PR Opened	☑️
CARME	PR Opened	☑️
cloneRate	PR Opened	☑️
CNVRG	PR Opened	☑️
DCPO	PR Opened	☑️
jfa	PR Opened	☑️
mlts	PR Opened	☑️
publipha	PR Opened	☑️
rcbayes	PR Opened	☑️
trialr	PR Opened	☑️
WhiteLabRt	PR Opened	☑️
zoid	PR Opened	☑️

EDIT: Will now remove rows once packages updated on CRAN

[jgabry]

Wow, thank you @andrjohns! If we need to do another round of notifying maintainers I'm happy to help.

[cdriveraus]

ctsem is fixed and on cran

[andrjohns]

ctsem is fixed and on cran

@cdriveraus Unfortunately there is still deprecated array syntax (as well as integer division without %/%) in your package: https://github.com/cdriveraus/ctsem/compare/master...andrjohns:ctsem:deprecated-syntax?expand=1

[cdriveraus]

Ugh. Is there an easy test I can call for this to avoid such silly mistakes?

[andrjohns]

The warnings aren't properly displayed in rstan 2.26 (@bgoodri is submitting 2.32 soon which should fix this). In the interim, you can test using either the experimental branch:

remotes::install_github("stan-dev/rstan@experimental", subdir="StanHeaders")
remotes::install_github("stan-dev/rstan@experimental", subdir="rstan/rstan")

Or by using the parser in cmdstanr:

mod <- cmdstanr::cmdstan_model(path_to_stanfile, compile = FALSE)
mod$check_syntax()

[sbfnk]

EpiNow2 is fixed and on CRAN

[cdriveraus]

ctsem is too, properly this time, I think ;)

[zhengxiaoUVic]

Thank you, @andrjohns Andrew, for providing the information. I have updated the deprecated syntax for array declarations just in time before the release of Stan 2.33. The 'rmBayes' R package is now available on CRAN.