I might have identified the function, @jonah
And it might be third party fault
Does this function name ring any bell? (from https://rdrr.io/github/Bioconductor-mirror/AnnotationDbi/src/R/AnnDbPkg-templates-common.R)
warnIfDef <- function(){
if(grepl("PFAM",x)){
bimapName <- paste0(prefix,"PFAM")
}else{
bimapName <- paste0(prefix,"PROSITE")
}
x <- dc[[bimapName]]
msg = wmsg(paste0(bimapName,
" is defunct. ",
"Please use select() if you need access to PFAM or PROSITE accessions. \n"))
if(interactive()){
.Defunct(msg=msg)
}
}
error traceback:
> traceback()
9: stop(paste(msg, collapse = ""), call. = FALSE, domain = NA)
8: .Defunct(msg = msg)
7: (function ()
{
if (grepl("PFAM", x)) {
bimapName <- paste0(prefix, "PFAM")
}
else {
bimapName <- paste0(prefix, "PROSITE")
}
x <- dc[[bimapName]]
msg = wmsg(paste0(bimapName, " is defunct. ", "Please use select() if you need access to PFAM or PROSITE accessions. \n"))
if (interactive()) {
.Defunct(msg = msg)
}
})()
6: FUN(X[[i]], ...)
5: lapply(X = X, FUN = FUN, ...)
4: sapply(li, exists, where = i, mode = mode, inherits = FALSE)
3: apropos(model_re, mode = "S4", ignore.case = FALSE)
2: stan_model(file, model_name = model_name, model_code = model_code,
stanc_ret = NULL, boost_lib = boost_lib, eigen_lib = eigen_lib,
save_dso = save_dso, verbose = verbose)
1: rstan::stan(file = "norm_hkg.stan", data = list(y = t(d.epithelial$counts[d.epithelial$genes$symbol %in%
hk_600, ]), S = ncol(d.epithelial[d.epithelial$genes$symbol %in%
hk_600, ]), G = nrow(d.epithelial[d.epithelial$genes$symbol %in%
hk_600, ])))