- using R Under development (unstable) (2024-12-20 r87452)
- using platform: x86_64-pc-linux-gnu
- R was compiled by
gcc-14 (Debian 14.2.0-8) 14.2.0
GNU Fortran (Debian 14.2.0-8) 14.2.0
- running under: Debian GNU/Linux trixie/sid
- using session charset: UTF-8
- checking for file ‘MIRES/DESCRIPTION’ ... OK
- this is package ‘MIRES’ version ‘0.1.0’
- 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 ‘MIRES’ can be installed ... OK
See the install log for details.
- used C++ compiler: ‘g++-14 (Debian 14.2.0-8) 14.2.0’
- checking C++ specification ... OK
- checking package directory ... OK
- checking for future file timestamps ... 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 ... [3s/4s] OK
- checking whether the package can be loaded with stated dependencies ... [3s/3s] OK
- checking whether the package can be unloaded cleanly ... [3s/3s] OK
- checking whether the namespace can be loaded with stated dependencies ... [3s/4s] OK
- checking whether the namespace can be unloaded cleanly ... [3s/4s] OK
- checking loading without being on the library search path ... [7s/7s] OK
- checking use of S3 registration ... OK
- checking dependencies in R code ... OK
- checking S3 generic/method consistency ... OK
- checking replacement functions ... OK
- checking foreign function calls ... OK
- checking R code for possible problems ... [17s/19s] OK
- checking Rd files ... [0s/0s] 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 contents of ‘data’ directory ... OK
- checking data for non-ASCII characters ... [0s/0s] OK
- checking LazyData ... 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 ... INFO
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 examples ... [7s/8s] OK
- checking for unstated dependencies in ‘tests’ ... OK
- checking tests ... [40s/48s] ERROR
Running ‘testthat.R’ [40s/47s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(MIRES)
>
> test_check("MIRES")
[1] "no object returned"
[1] "no object returned"
Chain 1: ------------------------------------------------------------
Chain 1: EXPERIMENTAL ALGORITHM:
Chain 1: This procedure has not been thoroughly tested and may be unstable
Chain 1: or buggy. The interface is subject to change.
Chain 1: ------------------------------------------------------------
Chain 1:
Chain 1:
Chain 1:
Chain 1: Gradient evaluation took 0.025269 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 252.69 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: Begin eta adaptation.
Chain 1: Iteration: 1 / 250 [ 0%] (Adaptation)
Chain 1: Iteration: 50 / 250 [ 20%] (Adaptation)
Chain 1: Iteration: 100 / 250 [ 40%] (Adaptation)
Chain 1: Iteration: 150 / 250 [ 60%] (Adaptation)
Chain 1: Iteration: 200 / 250 [ 80%] (Adaptation)
Chain 1: Success! Found best value [eta = 1] earlier than expected.
Chain 1:
Chain 1: Begin stochastic gradient ascent.
Chain 1: iter ELBO delta_ELBO_mean delta_ELBO_med notes
Chain 1: 100 -1499.252 1.000 1.000
Chain 1: 200 -1221.577 0.614 1.000 MEAN ELBO CONVERGED
Chain 1:
Chain 1: Drawing a sample of size 1000 from the approximate posterior...
Chain 1: COMPLETED.
SAMPLING FOR MODEL 'redifhm_all' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 0.0009 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 9 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 1: Iteration: 2 / 10 [ 20%] (Warmup)
Chain 1: Iteration: 3 / 10 [ 30%] (Warmup)
Chain 1: Iteration: 4 / 10 [ 40%] (Warmup)
Chain 1: Iteration: 5 / 10 [ 50%] (Warmup)
Chain 1: Iteration: 6 / 10 [ 60%] (Sampling)
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Chain 1: Iteration: 8 / 10 [ 80%] (Sampling)
Chain 1: Iteration: 9 / 10 [ 90%] (Sampling)
Chain 1: Iteration: 10 / 10 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.056 seconds (Warm-up)
Chain 1: 0.231 seconds (Sampling)
Chain 1: 0.287 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'redifhm_all' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 0.000527 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 5.27 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 1: Iteration: 2 / 10 [ 20%] (Warmup)
Chain 1: Iteration: 3 / 10 [ 30%] (Warmup)
Chain 1: Iteration: 4 / 10 [ 40%] (Warmup)
Chain 1: Iteration: 5 / 10 [ 50%] (Warmup)
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Chain 1: Iteration: 8 / 10 [ 80%] (Sampling)
Chain 1: Iteration: 9 / 10 [ 90%] (Sampling)
Chain 1: Iteration: 10 / 10 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.061 seconds (Warm-up)
Chain 1: 0.011 seconds (Sampling)
Chain 1: 0.072 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'redifhm_all' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 0.00053 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 5.3 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 1: Iteration: 2 / 10 [ 20%] (Warmup)
Chain 1: Iteration: 3 / 10 [ 30%] (Warmup)
Chain 1: Iteration: 4 / 10 [ 40%] (Warmup)
Chain 1: Iteration: 5 / 10 [ 50%] (Warmup)
Chain 1: Iteration: 6 / 10 [ 60%] (Sampling)
Chain 1: Iteration: 7 / 10 [ 70%] (Sampling)
Chain 1: Iteration: 8 / 10 [ 80%] (Sampling)
Chain 1: Iteration: 9 / 10 [ 90%] (Sampling)
Chain 1: Iteration: 10 / 10 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.06 seconds (Warm-up)
Chain 1: 0.084 seconds (Sampling)
Chain 1: 0.144 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'redifhm_all' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 0.000483 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 4.83 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 1: Iteration: 2 / 10 [ 20%] (Warmup)
Chain 1: Iteration: 3 / 10 [ 30%] (Warmup)
Chain 1: Iteration: 4 / 10 [ 40%] (Warmup)
Chain 1: Iteration: 5 / 10 [ 50%] (Warmup)
Chain 1: Iteration: 6 / 10 [ 60%] (Sampling)
Chain 1: Iteration: 7 / 10 [ 70%] (Sampling)
Chain 1: Iteration: 8 / 10 [ 80%] (Sampling)
Chain 1: Iteration: 9 / 10 [ 90%] (Sampling)
Chain 1: Iteration: 10 / 10 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.087 seconds (Warm-up)
Chain 1: 0.25 seconds (Sampling)
Chain 1: 0.337 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'redifhm_all' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 0.000422 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 4.22 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 1: Iteration: 2 / 10 [ 20%] (Warmup)
Chain 1: Iteration: 3 / 10 [ 30%] (Warmup)
Chain 1: Iteration: 4 / 10 [ 40%] (Warmup)
Chain 1: Iteration: 5 / 10 [ 50%] (Warmup)
Chain 1: Iteration: 6 / 10 [ 60%] (Sampling)
Chain 1: Iteration: 7 / 10 [ 70%] (Sampling)
Chain 1: Iteration: 8 / 10 [ 80%] (Sampling)
Chain 1: Iteration: 9 / 10 [ 90%] (Sampling)
Chain 1: Iteration: 10 / 10 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.28 seconds (Warm-up)
Chain 1: 0.443 seconds (Sampling)
Chain 1: 0.723 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'redifhm_all' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 0.000432 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 4.32 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 1: Iteration: 2 / 10 [ 20%] (Warmup)
Chain 1: Iteration: 3 / 10 [ 30%] (Warmup)
Chain 1: Iteration: 4 / 10 [ 40%] (Warmup)
Chain 1: Iteration: 5 / 10 [ 50%] (Warmup)
Chain 1: Iteration: 6 / 10 [ 60%] (Sampling)
Chain 1: Iteration: 7 / 10 [ 70%] (Sampling)
Chain 1: Iteration: 8 / 10 [ 80%] (Sampling)
Chain 1: Iteration: 9 / 10 [ 90%] (Sampling)
Chain 1: Iteration: 10 / 10 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.215 seconds (Warm-up)
Chain 1: 0.518 seconds (Sampling)
Chain 1: 0.733 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'redifhm_all' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 0.000395 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 3.95 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 1: Iteration: 2 / 10 [ 20%] (Warmup)
Chain 1: Iteration: 3 / 10 [ 30%] (Warmup)
Chain 1: Iteration: 4 / 10 [ 40%] (Warmup)
Chain 1: Iteration: 5 / 10 [ 50%] (Warmup)
Chain 1: Iteration: 6 / 10 [ 60%] (Sampling)
Chain 1: Iteration: 7 / 10 [ 70%] (Sampling)
Chain 1: Iteration: 8 / 10 [ 80%] (Sampling)
Chain 1: Iteration: 9 / 10 [ 90%] (Sampling)
Chain 1: Iteration: 10 / 10 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.487 seconds (Warm-up)
Chain 1: 0.258 seconds (Sampling)
Chain 1: 0.745 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'redifhm_all' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 0.000405 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 4.05 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 1: Iteration: 2 / 10 [ 20%] (Warmup)
Chain 1: Iteration: 3 / 10 [ 30%] (Warmup)
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Chain 1: Iteration: 9 / 10 [ 90%] (Sampling)
Chain 1: Iteration: 10 / 10 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.466 seconds (Warm-up)
Chain 1: 0.41 seconds (Sampling)
Chain 1: 0.876 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'redifhm_all' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 0.000371 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 3.71 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: There aren't enough warmup iterations to fit the
Chain 1: three stages of adaptation as currently configured.
Chain 1: Reducing each adaptation stage to 15%/75%/10% of
Chain 1: the given number of warmup iterations:
Chain 1: init_buffer = 7
Chain 1: adapt_window = 38
Chain 1: term_buffer = 5
Chain 1:
Chain 1: Iteration: 1 / 100 [ 1%] (Warmup)
Chain 1: Iteration: 10 / 100 [ 10%] (Warmup)
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Chain 1: Iteration: 100 / 100 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 8.218 seconds (Warm-up)
Chain 1: 7.269 seconds (Sampling)
Chain 1: 15.487 seconds (Total)
Chain 1:
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 93 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_density_funs.R:20:5'): posterior_density_funs_sigmas calls DP when needed. ──
Error in `validate_ll(log_ratios)`: All input values must be finite or -Inf.
Backtrace:
▆
1. ├─base::suppressWarnings(...) at test_density_funs.R:20:5
2. │ └─base::withCallingHandlers(...)
3. └─MIRES:::posterior_density_funs_sigmas(test_obj, tol_rel_obj = 1)
4. └─base::sapply(...)
5. └─base::lapply(X = X, FUN = FUN, ...)
6. └─MIRES (local) FUN(X[[i]], ...)
7. ├─rstan::vb(...)
8. └─rstan::vb(...)
9. └─rstan (local) .local(object, ...)
10. ├─base::suppressWarnings(loo::psis(lr, r_eff = 1))
11. │ └─base::withCallingHandlers(...)
12. ├─loo::psis(lr, r_eff = 1)
13. └─loo:::psis.default(lr, r_eff = 1)
14. └─loo:::importance_sampling.default(...)
15. └─loo:::importance_sampling.matrix(...)
16. └─loo:::validate_ll(log_ratios)
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 93 ]
Error: Test failures
Execution halted
- checking PDF version of manual ... [5s/7s] OK
- checking HTML version of manual ... [1s/2s] OK
- checking for non-standard things in the check directory ... OK
- DONE
Status: 1 ERROR