RStan & StanHeaders Downstream Patching Status

[andrjohns]

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]

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]

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.