CRAN Package Check Results for Maintainer ‘Stephen Martin <stephenSRMMartin at gmail.com>’

Last updated on 2024-12-22 13:49:21 CET.

Package	ERROR	NOTE	OK
LMMELSM		10	3
MIRES	1	10	2

Package LMMELSM

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

Package MIRES

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