• using R Under development (unstable) (2024-12-18 r87448)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     Debian clang version 19.1.5 (1)     Debian flang-new version 19.1.5 (1)
• running under: Debian GNU/Linux trixie/sid
• using session charset: UTF-8
• 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
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• checking for sufficient/correct file permissions ... OK
• checking whether package ‘spsurv’ can be installed ... OK See the install log for details.
• used C++ compiler: ‘Debian clang version 19.1.5 (1)’
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• checking examples ... [10s/13s] ERROR Running examples in ‘spsurv-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### 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 ... [28s/33s] ERROR   Running ‘testthat.R’ [28s/33s] 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 9.6e-05 seconds   Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.96 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: 4.007 seconds (Warm-up)   Chain 1: 3.974 seconds (Sampling)   Chain 1: 7.981 seconds (Total)   Chain 1:      SAMPLING FOR MODEL 'spbp' NOW (CHAIN 1).   Chain 1:   Chain 1: Gradient evaluation took 8.9e-05 seconds   Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.89 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: 5.501 seconds (Warm-up)   Chain 1: 4.034 seconds (Sampling)   Chain 1: 9.535 seconds (Total)   Chain 1:   [ FAIL 1 | WARN 5 | 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 5 | SKIP 0 | PASS 0 ]   Error: Test failures   Execution halted
• checking for unstated dependencies in vignettes ... OK
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• checking for non-standard things in the check directory ... OK
• DONE

Status: 2 ERRORs