* using log directory ‘/data/gannet/ripley/R/packages/tests-Intel/spsurv.Rcheck’
* using R Under development (unstable) (2024-08-21 r87038)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Intel(R) oneAPI DPC++/C++ Compiler 2024.2.1 (2024.2.1.20240711)
    ifx (IFX) 2024.2.1 20240711
* running under: Fedora Linux 36 (Workstation Edition)
* using session charset: UTF-8
* using option ‘--no-stop-on-test-error’
* checking for file ‘spsurv/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘spsurv’ version ‘1.0.0’
* 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 ‘spsurv’ can be installed ... [445s/553s] OK
* used C++ compiler: ‘Intel(R) oneAPI DPC++/C++ Compiler 2024.2.1 (2024.2.1.20240711)’
* checking C++ specification ... OK
* 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 code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [9s/12s] OK
* checking whether the package can be loaded with stated dependencies ... [8s/19s] OK
* checking whether the package can be unloaded cleanly ... [9s/15s] OK
* checking whether the namespace can be loaded with stated dependencies ... [8s/12s] OK
* checking whether the namespace can be unloaded cleanly ... [9s/13s] OK
* checking loading without being on the library search path ... [16s/23s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘rstantools’
  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 ... [40s/56s] OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... 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 LazyData ... NOTE
  'LazyData' is specified without a 'data' directory
* 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 use of PKG_*FLAGS in Makefiles ... OK
* checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [11s/30s] ERROR
Running examples in ‘spsurv-Ex.R’ failed
The error most likely occurred in:

> ### Name: bppo
> ### Title: Bernstein Polynomial Based Proportional Odds Model
> ### Aliases: bppo
> 
> ### ** Examples
> 
> 
> library("spsurv")
> data("veteran")
Warning in data("veteran") : data set ‘veteran’ not found
> 
> fit <- bppo(Surv(time, status) ~ karno + celltype,
+ data = veteran)
Error in optimHess(theta, fn, gr, control = list(fnscale = -1)) : 
  non-finite value supplied by optim
Calls: bppo ... spbp.mle -> <Anonymous> -> <Anonymous> -> .local -> optimHess
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [54s/135s]
 [54s/136s] ERROR
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(spsurv)
  Loading required package: survival
  Loading required package: loo
  This is loo version 2.8.0
  - Online documentation and vignettes at mc-stan.org/loo
  - As of v2.0.0 loo defaults to 1 core but we recommend using as many as possible. Use the 'cores' argument or set options(mc.cores = NUM_CORES) for an entire session. 
  
  Attaching package: 'loo'
  
  The following object is masked from 'package:testthat':
  
      compare
  
  Loading required package: coda
  Loading required package: MASS
  
  Attaching package: 'spsurv'
  
  The following object is masked from 'package:coda':
  
      traceplot
  
  The following objects are masked from 'package:stats':
  
      coef, confint, vcov
  
  The following object is masked from 'package:base':
  
      mode
  
  > 
  > test_check("spsurv")
  
  SAMPLING FOR MODEL 'spbp' NOW (CHAIN 1).
  Chain 1: 
  Chain 1: Gradient evaluation took 0.000197 seconds
  Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 1.97 seconds.
  Chain 1: Adjust your expectations accordingly!
  Chain 1: 
  Chain 1: 
  Chain 1: Iteration:   1 / 1000 [  0%]  (Warmup)
  Chain 1: Iteration: 100 / 1000 [ 10%]  (Warmup)
  Chain 1: Iteration: 200 / 1000 [ 20%]  (Warmup)
  Chain 1: Iteration: 300 / 1000 [ 30%]  (Warmup)
  Chain 1: Iteration: 400 / 1000 [ 40%]  (Warmup)
  Chain 1: Iteration: 500 / 1000 [ 50%]  (Warmup)
  Chain 1: Iteration: 501 / 1000 [ 50%]  (Sampling)
  Chain 1: Iteration: 600 / 1000 [ 60%]  (Sampling)
  Chain 1: Iteration: 700 / 1000 [ 70%]  (Sampling)
  Chain 1: Iteration: 800 / 1000 [ 80%]  (Sampling)
  Chain 1: Iteration: 900 / 1000 [ 90%]  (Sampling)
  Chain 1: Iteration: 1000 / 1000 [100%]  (Sampling)
  Chain 1: 
  Chain 1:  Elapsed Time: 29.732 seconds (Warm-up)
  Chain 1:                17.295 seconds (Sampling)
  Chain 1:                47.027 seconds (Total)
  Chain 1: 
  
  SAMPLING FOR MODEL 'spbp' NOW (CHAIN 1).
  Chain 1: 
  Chain 1: Gradient evaluation took 0.000205 seconds
  Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 2.05 seconds.
  Chain 1: Adjust your expectations accordingly!
  Chain 1: 
  Chain 1: 
  Chain 1: Iteration:   1 / 1000 [  0%]  (Warmup)
  Chain 1: Iteration: 100 / 1000 [ 10%]  (Warmup)
  Chain 1: Iteration: 200 / 1000 [ 20%]  (Warmup)
  Chain 1: Iteration: 300 / 1000 [ 30%]  (Warmup)
  Chain 1: Iteration: 400 / 1000 [ 40%]  (Warmup)
  Chain 1: Iteration: 500 / 1000 [ 50%]  (Warmup)
  Chain 1: Iteration: 501 / 1000 [ 50%]  (Sampling)
  Chain 1: Iteration: 600 / 1000 [ 60%]  (Sampling)
  Chain 1: Iteration: 700 / 1000 [ 70%]  (Sampling)
  Chain 1: Iteration: 800 / 1000 [ 80%]  (Sampling)
  Chain 1: Iteration: 900 / 1000 [ 90%]  (Sampling)
  Chain 1: Iteration: 1000 / 1000 [100%]  (Sampling)
  Chain 1: 
  Chain 1:  Elapsed Time: 25.438 seconds (Warm-up)
  Chain 1:                18.674 seconds (Sampling)
  Chain 1:                44.112 seconds (Total)
  Chain 1: 
  [ FAIL 1 | WARN 7 | SKIP 0 | PASS 0 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test.R:33:1'): (code run outside of `test_that()`) ──────────────────
  Error in `optimHess(theta, fn, gr, control = list(fnscale = -1))`: non-finite value supplied by optim
  Backtrace:
      ▆
   1. └─spsurv::bppo(Surv(time, status) ~ karno + factor(celltype), data = veteran) at test.R:33:1
   2.   └─spsurv:::spbp.default(...)
   3.     └─spsurv:::spbp.mle(standata = standata, ...)
   4.       ├─rstan::optimizing(...)
   5.       └─rstan::optimizing(...)
   6.         └─rstan (local) .local(object, ...)
   7.           └─stats::optimHess(theta, fn, gr, control = list(fnscale = -1))
  
  [ FAIL 1 | WARN 7 | SKIP 0 | PASS 0 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [76s/181s] OK
* checking PDF version of manual ... [8s/24s] OK
* checking HTML version of manual ... OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE

Status: 2 ERRORs, 3 NOTEs
See
  ‘/data/gannet/ripley/R/packages/tests-Intel/spsurv.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 20:35.37, 760.98 + 47.09