Rcpp: Errors with Rcpp 1.0.6.3

[iago-pssjd]

Hi!,

After updating from RcppCore to 1.0.6.3 I coudln't install last updates of ggstatsplot (0.6.8), statsExpressions (0.7.0), and tidyBF (0.4.3).
It appeared something like:

* installing *source* package ‘statsExpressions’ ...
** package ‘statsExpressions’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading

 *** caught segfault ***
address 0x6e0000005e, cause 'memory not mapped'

Traceback:
 1: Module(module, mustStart = TRUE, where = env)
 2: doTryCatch(return(expr), name, parentenv, handler)
 3: tryCatchOne(expr, names, parentenv, handlers[[1L]])
 4: tryCatchList(expr, classes, parentenv, handlers)
 5: tryCatch(Module(module, mustStart = TRUE, where = env), error = function(e) e)
 6: Rcpp::loadModule("class_model_base", what = TRUE)
 7: fun(libname, pkgname)
 8: doTryCatch(return(expr), name, parentenv, handler)
 9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
10: tryCatchList(expr, classes, parentenv, handlers)
11: tryCatch(fun(libname, pkgname), error = identity)
12: runHook(".onLoad", env, package.lib, package)
13: loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
14: namespaceImport(ns, loadNamespace(i, c(lib.loc, .libPaths()),     versionCheck = vI[[i]]), from = package)
15: loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
16: asNamespace(ns)
17: namespaceImportFrom(ns, loadNamespace(j <- i[[1L]], c(lib.loc,     .libPaths()), versionCheck = vI[[j]]), i[[2L]], from = package)
18: loadNamespace(package = package, lib.loc = lib.loc, keep.source = keep.source,     keep.parse.data = keep.parse.data, partial = TRUE)
19: withCallingHandlers(expr, packageStartupMessage = function(c) invokeRestart("muffleMessage"))
20: suppressPackageStartupMessages(loadNamespace(package = package,     lib.loc = lib.loc, keep.source = keep.source, keep.parse.data = keep.parse.data,     partial = TRUE))
21: code2LazyLoadDB(package, lib.loc = lib.loc, keep.source = keep.source,     keep.parse.data = keep.parse.data, compress = compress, set.install.dir = set.install.dir)
22: tools:::makeLazyLoading("statsExpressions", "/home/iago/R/x86_64-pc-linux-gnu-library/3.6/00LOCK-statsExpressions/00new",     keep.source = FALSE, keep.parse.data = FALSE, set.install.dir = "/home/iago/R/x86_64-pc-linux-gnu-library/3.6/statsExpressions")
An irrecoverable exception occurred. R is aborting now ...
Segmentation fault

I could update them after reinstall Rcpp from CRAN.
Thank you!

[eddelbuettel]

Please see what I wrote to the rcpp-devel list today:

The Rcpp 1.0.6.2 and 1.0.6.3
versions seem to require a rebuild of packages involving rstan or StanHeaders
and/or maybe a few others. In reverse depedency checking I initially ran
into about 170 or so failures almost all from run-time behaviour of tests and
odd segfaults. But having just re-confirmed in the 1.0.6 release what we C++
programmers "know" that some 'weird' run-time issues do go away sometimes
under rebuilds, I opted to reinstall several hundred packages (which I had
not done in May, thinking my branch was doomed when in fact in wasn't) and
that addressed the concern[s].

The script compiledDeps.r can tell you which dependencies of your packages are compiled; I recommend taking a look and installing those. As I said, I am a little confused as _why_ this happens now but this does happen every now and then with C++ stacks (and yes we did change the API/ABI a little but I still didn't expect this).

So please try Rcpp 1.0.6.3 with rebuild stacks _especially when you see such run-time errors_ as the message above is from the 'can we load it?' phase of the rebuilt package.

[eddelbuettel]

I coudln't install last updates of ggstatsplot (0.6.8), statsExpressions (0.7.0), and tidyBF (0.4.3).

Using compiledDeps.r I see all three depend on rstan. I'd start by rebuilding that.

[eddelbuettel]

I just confirmed that in a clean Docker container (using the r-base image we also maintainer as rocker/r-base). I first installed r-cran-rstan and its dependencies as binaries to quicken this, then install rstan (and RcppParallel and metaBMA) from source after which tidyBF installed cleanly as promised.

[eddelbuettel]

Closing this for lack of follow-up --- if you still have issues please reopen with a new example and sufficient detail to reproduce.

That said, I am still not happy that we need this recompilation of some packages and lack better diagnostics as to when we need it. But a simple recompilation seems to fix it.