search

stan-dev / rstan

RStan, the R interface to Stan
https://mc-stan.org
1.04k stars 269 forks source link

RStan & StanHeaders Downstream Patching Status #1053

Open andrjohns opened 1 year ago

andrjohns commented 1 year ago

I'm consolidating the tables/issues from #1034 and #1046, since they're spread across multiple comments and somewhat buried.

Note that these tables/failures should be considered cumulative - any patches needed for the 2.21 & 2.26 combination are also needed for the 2.26 & 2.26 combination, and beyond.

Needed for RStan 2.21 & StanHeaders 2.26 Combination:

Package Version Action Resolved On CRAN
beanz 2.4 PR Opened
CARME 0.1 PR Merged ✓ ✓
conStruct 1.0.4 PR Opened ✓ ✓
densEstBayes 1.0-2.1 No public repo, emailed maintainer ✓ ✓
dfpk 3.5.1 PR Opened
glmmfields 0.1.4 PR Opened ✓ ✓
glmmPen 1.5.2.11 PR Opened ✓ ✓
idem 5.1 PR Opened
nlmixr2est 2.1.3 PR Opened ✓ ✓
OpenMx 2.21.1 PR Merged ✓ ✓
ProbReco 0.1.0.1 PR Opened ✓ ✓
publipha 0.1.1 PR Opened ✓ ✓
rPBK 0.2.0 No public repo, emailed maintainer ✓ ✓
rstanemax 0.1.3 PR Opened ✓ ✓
rxode2ll 2.0.9 PR Merged ✓ ✓
ssMousetrack 1.1.5 PR Opened ✓ ✓
survHE 1.1.2 PR Merged ✓ ✓
trialr 0.1.5 PR Opened ✓ ✓
visit 2.1 PR Opened
PosteriorBootstrap 0.1.1 PR Opened ✓ ✓
rxode2parse 2.0.13 PR Opened ✓ ✓
oncomsm 0.1.3 PR Opened ✓ ✓

Needed for RStan 2.26 & StanHeaders 2.26 Combination:

Package Version Action Resolved On CRAN
baggr 0.7.4 PR Opened ✓ ✓
bakR 0.2.4 PR Opened ✓ ✓
BeeGUTS 1.0.0 PR Opened ✓ ✓
bmstdr 0.3.0 PR Opened ✓ ✓
cbq 0.2.0.2 PR Opened ✓ ✓
expertsurv 1.0.0 PR Merged ✓ ✓
hwep 2.0.0 PR Opened ✓ ✓
isotracer 1.1.3 PR Opened ✓ ✓
lgpr 1.1.5 PR Opened ✓ ✓
MADPop 1.1.4 PR Opened ✓ ✓
oncomsm 0.1.2 PR Opened ✓ ✓
rmdcev 1.2.4 PR Opened ✓ ✓
RoBTT 1.0.0 PR Opened ✓ ✓
rstanarm 2.21.3 PR Opened ✓ ✓
rts2 0.4 PR Opened ✓ ✓

Needed for RStan 2.26 & StanHeaders 2.31 Combination:

Package Version Action Resolved On CRAN
EcoEnsemble 1.0.1 No public repo, emailed maintainer ✓ ✓
prophet 1.0 expose_stan_functions failure Resolved N/A
ctsem 3.7.2 PR Opened ✓ ✓
RoBTT 1.0.1 PR Opened ✓ ✓
tmbstan 1.0.4 PR Opened ✓ ✓
TriDimRegression 1.0.1 Stanc3 Issue Resolved N/A
andrjohns commented 1 year ago

I've now also checked the packages which will fail once deprecated syntax has expired (2.32+). The majority cannot be updated until 2.26 is on CRAN (and the new array syntax supported), but I've submitted PRs for the packages that can be updated now:

Upcoming Failures from Expired Syntax

Package Version Cause Action Resolved On CRAN
AovBay 0.1.0 Array syntax      
baggr 0.7.6 Array syntax      
bakR 0.4.0 Array syntax      
BANOVA 1.2.1 Array syntax
BASiCStan 1.0.0 Array syntax      
bayes4psy 1.2.11 Array syntax      
bayesdfa 1.2.0 Array syntax      
bayesGAM 0.0.2 Array syntax, Reserved word - 'offset'    
BayesianPlatformDesignTimeTrend 1.0.0 Array syntax      
bayesZIB 0.0.4 Array syntax      
beanz 2.4 Array syntax      
BeeGUTS 1.0.0 Array syntax      
bellreg 0.0.1 Array syntax      
BINtools 0.2.0 Array syntax      
bistablehistory 1.1.1 Array syntax      
blavaan 0.4-7 Array syntax      
bmgarch 1.1.0 Array syntax      
bmggum 0.1.0 Array syntax      
bmlm 1.3.12 Array syntax      
bmscstan 1.2.1.0 Array syntax      
bmstdr 0.3.0 Array syntax      
breathteststan 0.8.4 Array syntax      
bws 0.1.0 Array syntax      
CARME 0.1.1 Array syntax      
CausalQueries 0.1.0 Array syntax      
cbq 0.2.0.2 Array syntax, Reserved word - 'offset'    
CNVRG 1.0.0 Array syntax      
conStruct 1.0.5 Array syntax      
ctsem 3.7.6 Array syntax      
DCPO 0.5.3 Array syntax      
densEstBayes 1.0-2.2 Array syntax      
dfpk 3.5.1 Array syntax      
disbayes 1.0.0 Array syntax      
dynamite 1.1.1 Array syntax      
EcoEnsemble 1.0.3 Array syntax      
eggCounts 2.3-2 Array syntax      
EloSteepness 0.4.7 Array syntax      
expertsurv 1.1.0 Array syntax      
fcirt 0.1.0 Array syntax      
FlexReg 1.2 Array syntax    
footBayes 0.1.0 Array syntax       
gastempt 0.5.5 Array syntax      
geostan 0.4.1 Array syntax, Reserved word - 'offset'    
glmmfields 0.1.7 Array syntax, Reserved word - 'offset'    
GPP 0.1 Array syntax      
gppm 0.2.0 Array syntax      
GPRMortality 0.1.0 Array syntax      
greencrab.toolkit 0.1 Array syntax      
hbamr 1.0.5 Array syntax      
hBayesDM 1.2.1 Array syntax      
HCT 0.1.3 Array syntax, # comments      
historicalborrowlong 0.0.5 Array syntax      
hsstan 0.8.1 Array syntax      
idem 5.1 Array syntax      
IgGeneUsage 1.12.0 Array syntax      
isotracer 1.1.4 Array syntax      
jfa 0.6.5 Array syntax      
lgpr 1.1.5 Array syntax      
LMMELSM 0.2.0 Array syntax      
MADPop 1.1.4 Array syntax      
MapeBay 0.1.0 Array syntax      
metaBMA 0.6.7 Array syntax      
MetaStan 1.0.0 Array syntax      
MIRES 0.1.0 Array syntax      
multinma 0.5.0 Array syntax      
networkscaleup 0.1-1 Array syntax      
OncoBayes2 0.8-8 Array syntax      
oncomsm 0.1.3 Array syntax, Reserved word - 'lower'    
pcFactorStan 1.5.3 Array syntax      
pema 0.1.3 Array syntax      
phacking 0.1.0 Array syntax      
PoolTestR 0.1.3 Array syntax      
PosteriorBootstrap 0.1.2 Array syntax      
ppcseq 1.6.0 Array syntax      
prome 1.5.6.70 Array syntax      
psrwe 3.1 Array syntax      
publipha 0.1.1 Array syntax, Reserved word - 'lower'    
rater 1.3.0 Array syntax      
RBesT 1.6-6 Array syntax      
rbioacc 1.1-0 Array syntax      
rbmi 1.2.3 Array syntax      
rcbayes 0.2.0 Array syntax      
rmBayes 0.1.15 Array syntax      
rmdcev 1.2.5 Array syntax      
rmsb 0.1.0 Array syntax      
RoBTT 1.0.3 Array syntax      
rPBK 0.2.1 Array syntax      
rstan 2.26.21 Array syntax PR Opened      
rstanarm 2.21.3 Array syntax      
rstanemax 0.1.4 Array syntax      
rts2 0.4 Array syntax      
sccomp 1.2.1 Array syntax      
scMET 1.0.0 Array syntax      
spsurv 1.0.0 Array syntax      
ssMousetrack 1.1.5 Array syntax      
StanMoMo 1.1.0 Array syntax, Reserved word - 'offset'    
surveil 0.2.1 Array syntax      
thurstonianIRT 0.12.1 Array syntax      
tidybayes 3.0.4 Array syntax      
tipsae 0.0.12 Array syntax      
tmbstan 1.0.9 Reserved word - 'upper' PR Opened   ✓
trialr 0.1.6 Array syntax      
TriDimRegression 1.0.1 Array syntax      
truncnormbayes 0.0.2 Array syntax      
ubms 1.2.2 Array syntax      
visit 2.1 Array syntax      
walker 1.0.6-1 Array syntax      
YPPE 1.0.1 Array syntax      
zoid 1.1.0 Array syntax      
wds15 commented 1 year ago

just to note... R 4.3.0 is out - wouldn't it be a good time-point to get rstan and StanHeaders updates pushed to CRAN right now? This would ensure that the entire rstan based package universe get a fresh rebuild, which likely would be a good thing given the big changes with 2.26.