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.

Package	Status	Merged	On CRAN
AovBay	Maintainer emailed
BASICStan	PR Opened	☑️
bayesforecast	PR Opened
bayesGAM	PR Opened
bbmix	PR Opened
beanz	PR Opened
BINtools	Maintainer emailed
bmggum	PR Opened
bmstdr	PR Opened
bws	PR Opened
CARME	PR Opened
cbq	PR Opened
cloneRate	PR Opened
CNVRG	PR Opened
DCPO	PR Opened	☑️
decontX	PR Opened
densEstBayes	Orphaned
fcirt	PR Opened
gastempt	PR Opened
glmmPen	PR Opened
hBayesDM	PR Opened
idem	PR Opened
IgGeneUsage	PR Opened
LMMELSM	PR Opened
MetaStan	PR Opened
MIRES	PR Opened
multipleDL	PR Opened
OncoBayes2	Maintainer emailed
oncomsm	PR Opened
pema	PR Opened	☑️
phacking	PR Opened
PoolTestR	PR Opened
ppcseq	PR Opened
publipha	PR Opened
rcbayes	PR Opened
rmdcev	PR Opened
rts2	PR Opened
sccomp	PR Opened
scMET	PR Opened
spsurv	Github Stan code broken issue opened
ssMousetrack	PR Opened
trialr	PR Opened	☑️
truncnormbayes	PR Opened
visit	PR Opened
YPPE	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.