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RStan, the R interface to Stan
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Downstream Deprecated / Expired Syntax #1092

Open andrjohns opened 9 months ago

andrjohns commented 9 months ago

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 commented 9 months ago

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

cdriveraus commented 9 months ago

ctsem is fixed and on cran

andrjohns commented 9 months ago

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 commented 9 months ago

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

andrjohns commented 9 months ago

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 commented 9 months ago

EpiNow2 is fixed and on CRAN

cdriveraus commented 8 months ago

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

zhengxiaoUVic commented 4 months ago

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.