Last updated on 2024-12-22 10:50:33 CET.
| Package | ERROR | NOTE | OK |
|---|---|---|---|
| LMMELSM | 10 | 3 | |
| MIRES | 1 | 10 | 2 |
Current CRAN status: NOTE: 10, OK: 3
Version: 0.2.0
Check: dependencies in R code
Result: NOTE
Namespaces in Imports field not imported from:
‘RcppParallel’ ‘rstantools’
All declared Imports should be used.
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc
Version: 0.2.0
Check: for GNU extensions in Makefiles
Result: NOTE
GNU make is a SystemRequirements.
Flavors: r-patched-linux-x86_64, r-release-linux-x86_64, r-release-macos-arm64, r-release-macos-x86_64, r-release-windows-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64
Version: 0.2.0
Check: installed package size
Result: NOTE
installed size is 99.4Mb
sub-directories of 1Mb or more:
libs 98.4Mb
Flavors: r-release-macos-arm64, r-release-macos-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64
Current CRAN status: ERROR: 1, NOTE: 10, OK: 2
Version: 0.1.0
Check: tests
Result: 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)
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: 0.056 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)
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: 0.061 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)
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: 0.466 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)
Chain 1: Iteration: 20 / 100 [ 20%] (Warmup)
Chain 1: Iteration: 30 / 100 [ 30%] (Warmup)
Chain 1: Iteration: 40 / 100 [ 40%] (Warmup)
Chain 1: Iteration: 50 / 100 [ 50%] (Warmup)
Chain 1: Iteration: 51 / 100 [ 51%] (Sampling)
Chain 1: Iteration: 60 / 100 [ 60%] (Sampling)
Chain 1: Iteration: 70 / 100 [ 70%] (Sampling)
Chain 1: Iteration: 80 / 100 [ 80%] (Sampling)
Chain 1: Iteration: 90 / 100 [ 90%] (Sampling)
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
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.1.0
Check: dependencies in R code
Result: NOTE
Namespaces in Imports field not imported from:
‘pracma’ ‘rstantools’
All declared Imports should be used.
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc
Version: 0.1.0
Check: for GNU extensions in Makefiles
Result: NOTE
GNU make is a SystemRequirements.
Flavors: r-patched-linux-x86_64, r-release-linux-x86_64, r-release-macos-arm64, r-release-macos-x86_64, r-release-windows-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64
Version: 0.1.0
Check: installed package size
Result: NOTE
installed size is 164.3Mb
sub-directories of 1Mb or more:
libs 163.7Mb
Flavors: r-release-macos-arm64, r-release-macos-x86_64, r-release-windows-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64