• using R version 3.6.2 (2019-12-12)
• using platform: x86_64-apple-darwin15.6.0 (64-bit)
• using session charset: UTF-8
• checking for file ‘rstanarm/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘rstanarm’ version ‘2.21.1’
• package encoding: UTF-8
• checking package namespace information ... OK
• checking package dependencies ... OK
• checking if this is a source package ... OK
• checking if there is a namespace ... OK
• checking for executable files ... OK
• checking for hidden files and directories ... OK
• checking for portable file names ... OK
• checking for sufficient/correct file permissions ... OK
• checking whether package ‘rstanarm’ can be installed ... [27m/27m] OK
• checking installed package size ... NOTE
    installed size is 177.2Mb
    sub-directories of 1Mb or more:
      R 1.5Mb
      doc 4.5Mb
      libs 170.6Mb
• checking package directory ... OK
• checking ‘build’ directory ... OK
• checking DESCRIPTION meta-information ... OK
• checking top-level files ... OK
• checking for left-over files ... OK
• checking index information ... OK
• checking package subdirectories ... OK
• checking R files for non-ASCII characters ... OK
• checking R files for syntax errors ... OK
• checking whether the package can be loaded ... OK
• checking whether the package can be loaded with stated dependencies ... OK
• checking whether the package can be unloaded cleanly ... OK
• checking whether the namespace can be loaded with stated dependencies ... OK
• checking whether the namespace can be unloaded cleanly ... OK
• checking loading without being on the library search path ... OK
• checking dependencies in R code ... NOTE
  Namespace in Imports field not imported from: ‘RcppParallel’
    All declared Imports should be used.
• checking S3 generic/method consistency ... OK
• checking replacement functions ... OK
• checking foreign function calls ... OK
• checking R code for possible problems ... [39s/39s] OK
• checking Rd files ... OK
• checking Rd metadata ... OK
• checking Rd cross-references ... OK
• checking for missing documentation entries ... OK
• checking for code/documentation mismatches ... OK
• checking Rd \usage sections ... OK
• checking Rd contents ... OK
• checking for unstated dependencies in examples ... OK
• checking contents of ‘data’ directory ... OK
• checking data for non-ASCII characters ... OK
• checking data for ASCII and uncompressed saves ... OK
• checking line endings in shell scripts ... OK
• checking line endings in C/C++/Fortran sources/headers ... OK
• checking line endings in Makefiles ... OK
• checking compilation flags in Makevars ... OK
• checking for GNU extensions in Makefiles ... NOTE
  GNU make is a SystemRequirements.
• checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
• checking compiled code ... OK
• checking installed files from ‘inst/doc’ ... OK
• checking files in ‘vignettes’ ... OK
• checking examples ... ERROR
  Running examples in ‘rstanarm-Ex.R’ failed
  The error most likely occurred in:
  
  > ### Name: example_jm
  > ### Title: Example joint longitudinal and time-to-event model
  > ### Aliases: example_jm
  >
  > ### ** Examples
  >
  > # set.seed(123)
  > if (.Platform$OS.type != "windows" || .Platform$r_arch !="i386")
  + example_jm <-
  + stan_jm(formulaLong = logBili ~ year + (1 | id),
  + dataLong = pbcLong[1:101,],
  + formulaEvent = survival::Surv(futimeYears, death) ~ sex + trt,
  + dataEvent = pbcSurv[1:15,],
  + time_var = "year",
  + # this next line is only to keep the example small in size!
  + chains = 1, seed = 12345, iter = 100, refresh = 0)
  Loading required namespace: data.table
  Fitting a univariate joint model.
  
  Please note the warmup may be much slower than later iterations!
  [1] "Error in sampler$call_sampler(args_list[[i]]) : "
  [2] " empty_nested() must be true before calling recover_memory()"
  error occurred during calling the sampler; sampling not done
  Error in check_stanfit(stanfit) :
    Invalid stanfit object produced please report bug
  Calls: stan_jm -> stan_jm.fit -> check_stanfit
  Execution halted
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [13s/40s] ERROR
    Running ‘testthat.R’ [12s/40s]
  Running the tests in ‘tests/testthat.R’ failed.
  Last 13 lines of output:
              ^
    /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/StanHeaders/include/stan/math/rev/mat/fun/squared_distance.hpp:64:11: warning: unused type alias 'idx_t' [-Wunused-local-typedef]
        using idx_t = typename index_type<matrix_d>::type;
              ^
    make: *** [file470c5064b71c.o] Interrupt: 2
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Error (test_stan_functions.R:70:1): (code run outside of `test_that()`) ─────
    Error: $ operator is invalid for atomic vectors
    Backtrace:
        █
     1. └─rstan::expose_stan_functions(stanc_ret, rebuild = TRUE, verbose = TRUE) test_stan_functions.R:70:0
    
    [ FAIL 1 | WARN 0 | SKIP 0 | PASS 1 ]
    Error: Test failures
    Execution halted
• checking for unstated dependencies in vignettes ...