- using R Under development (unstable) (2026-06-29 r90199 ucrt)
- using platform: x86_64-w64-mingw32
- R was compiled by
gcc.exe (GCC) 14.3.0
GNU Fortran (GCC) 14.3.0
- running under: Windows Server 2022 x64 (build 20348)
- using session charset: UTF-8
* current time: 2026-07-01 16:35:56 UTC
- checking for file 'miniLNM/DESCRIPTION' ... OK
- this is package 'miniLNM' 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 hidden files and directories ... OK
- checking for portable file names ... OK
- checking whether package 'miniLNM' can be installed ... OK
See the install log for details.
- used C++ compiler: 'g++.exe (GCC) 14.3.0'
- checking C++ specification ... INFO
specified C++17
- checking installed package size ... OK
- checking package directory ... OK
- checking 'build' directory ... OK
- checking DESCRIPTION meta-information ... NOTE
Missing dependency on R >= 4.1.0 because package code uses the pipe
|> or function shorthand \(...) syntax added in R 4.1.0.
File(s) using such syntax:
'estimate.R' 'formula.R' 'toy_data.R'
- 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] OK
- checking whether the package can be loaded with stated dependencies ... [3s] OK
- checking whether the package can be unloaded cleanly ... [3s] OK
- checking whether the namespace can be loaded with stated dependencies ... [3s] OK
- checking whether the namespace can be unloaded cleanly ... [3s] OK
- checking loading without being on the library search path ... [6s] 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 ... [8s] OK
- checking Rd files ... [0s] OK
- checking Rd metadata ... 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 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 $(LAPACK_LIBS) ... OK
- checking use of PKG_*FLAGS in Makefiles ... OK
- checking pragmas in C/C++ headers and code ... OK
- checking compiled code ... OK
- checking installed files from 'inst/doc' ... OK
- checking files in 'vignettes' ... OK
- checking examples ... [8s] ERROR
Running examples in 'miniLNM-Ex.R' failed
The error most likely occurred in:
> ### Name: beta_mean
> ### Title: LNM Posterior Mean
> ### Aliases: beta_mean
>
> ### ** Examples
>
> example_data <- lnm_data(N = 50, K = 10)
> xy <- dplyr::bind_cols(example_data[c("X", "y")])
> fit <- lnm(
+ starts_with("y") ~ starts_with("x"), xy,
+ iter = 25, output_samples = 25
+ )
Chain 1: ------------------------------------------------------------
Chain 1: EXPERIMENTAL ALGORITHM:
Chain 1: This procedure has not been thoroughly tested and may be unstable
Chain 1: or buggy. The interface is subject to change.
Chain 1: ------------------------------------------------------------
Chain 1:
Chain 1:
Chain 1:
Chain 1: Gradient evaluation took 0.000687 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 6.87 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: Begin eta adaptation.
Chain 1: Iteration: 1 / 250 [ 0%] (Adaptation)
Chain 1: Iteration: 50 / 250 [ 20%] (Adaptation)
Chain 1: Iteration: 100 / 250 [ 40%] (Adaptation)
Chain 1: Iteration: 150 / 250 [ 60%] (Adaptation)
Chain 1: Iteration: 200 / 250 [ 80%] (Adaptation)
Chain 1: Success! Found best value [eta = 1] earlier than expected.
Chain 1:
Chain 1: Begin stochastic gradient ascent.
Chain 1: iter ELBO delta_ELBO_mean delta_ELBO_med notes
Chain 1: Informational Message: The maximum number of iterations is reached! The algorithm may not have converged.
Chain 1: This variational approximation is not guaranteed to be meaningful.
Chain 1:
Chain 1: Drawing a sample of size 25 from the approximate posterior...
Chain 1: COMPLETED.
Error in if (p$diagnostics$pareto_k > 1) { :
missing value where TRUE/FALSE needed
Calls: lnm ... new -> initialize -> initialize -> vb -> vb -> .local
Execution halted
- checking for unstated dependencies in 'tests' ... OK
- checking tests ... [10s] ERROR
Running 'testthat.R' [10s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
>
> library(testthat)
> library(miniLNM)
>
> test_check("miniLNM")
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 0.000427 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 4.27 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: Informational Message: The maximum number of iterations is reached! The algorithm may not have converged.
Chain 1: This variational approximation is not guaranteed to be meaningful.
Chain 1:
Chain 1: Drawing a sample of size 25 from the approximate posterior...
Chain 1: COMPLETED.
Saving _problems/test-estimate-7.R
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 0.000393 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 3.93 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: Informational Message: The maximum number of iterations is reached! The algorithm may not have converged.
Chain 1: This variational approximation is not guaranteed to be meaningful.
Chain 1:
Chain 1: Drawing a sample of size 25 from the approximate posterior...
Chain 1: COMPLETED.
Saving _problems/test-predict-7.R
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 0.00035 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 3.5 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: Informational Message: The maximum number of iterations is reached! The algorithm may not have converged.
Chain 1: This variational approximation is not guaranteed to be meaningful.
Chain 1:
Chain 1: Drawing a sample of size 25 from the approximate posterior...
Chain 1: COMPLETED.
Saving _problems/test-sample-7.R
[ FAIL 3 | WARN 0 | SKIP 0 | PASS 0 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-estimate.R:4:1'): (code run outside of `test_that()`) ──────────
Error in `if (p$diagnostics$pareto_k > 1) { warning("Pareto k diagnostic value is ", round(p$diagnostics$pareto_k, 2), ". Resampling is disabled.", " Decreasing tol_rel_obj may help if variational algorithm has terminated prematurely.", " Otherwise consider using sampling instead.", call. = FALSE, immediate. = TRUE) } else if (p$diagnostics$pareto_k > 0.7) { warning("Pareto k diagnostic value is ", round(p$diagnostics$pareto_k, 2), ". Resampling is unreliable.", " Increasing the number of draws or decreasing tol_rel_obj may help.", call. = FALSE, immediate. = TRUE) }`: missing value where TRUE/FALSE needed
Backtrace:
▆
1. └─miniLNM::lnm(...) at test-estimate.R:4:1
2. ├─methods::new(...)
3. │ ├─methods::initialize(value, ...)
4. │ └─methods::initialize(value, ...)
5. ├─rstan::vb(stanmodels$lnm, data_list, ...)
6. └─rstan::vb(stanmodels$lnm, data_list, ...)
7. └─rstan (local) .local(object, ...)
── Error ('test-predict.R:4:1'): (code run outside of `test_that()`) ───────────
Error in `if (p$diagnostics$pareto_k > 1) { warning("Pareto k diagnostic value is ", round(p$diagnostics$pareto_k, 2), ". Resampling is disabled.", " Decreasing tol_rel_obj may help if variational algorithm has terminated prematurely.", " Otherwise consider using sampling instead.", call. = FALSE, immediate. = TRUE) } else if (p$diagnostics$pareto_k > 0.7) { warning("Pareto k diagnostic value is ", round(p$diagnostics$pareto_k, 2), ". Resampling is unreliable.", " Increasing the number of draws or decreasing tol_rel_obj may help.", call. = FALSE, immediate. = TRUE) }`: missing value where TRUE/FALSE needed
Backtrace:
▆
1. └─miniLNM::lnm(...) at test-predict.R:4:1
2. ├─methods::new(...)
3. │ ├─methods::initialize(value, ...)
4. │ └─methods::initialize(value, ...)
5. ├─rstan::vb(stanmodels$lnm, data_list, ...)
6. └─rstan::vb(stanmodels$lnm, data_list, ...)
7. └─rstan (local) .local(object, ...)
── Error ('test-sample.R:4:1'): (code run outside of `test_that()`) ────────────
Error in `if (p$diagnostics$pareto_k > 1) { warning("Pareto k diagnostic value is ", round(p$diagnostics$pareto_k, 2), ". Resampling is disabled.", " Decreasing tol_rel_obj may help if variational algorithm has terminated prematurely.", " Otherwise consider using sampling instead.", call. = FALSE, immediate. = TRUE) } else if (p$diagnostics$pareto_k > 0.7) { warning("Pareto k diagnostic value is ", round(p$diagnostics$pareto_k, 2), ". Resampling is unreliable.", " Increasing the number of draws or decreasing tol_rel_obj may help.", call. = FALSE, immediate. = TRUE) }`: missing value where TRUE/FALSE needed
Backtrace:
▆
1. └─miniLNM::lnm(...) at test-sample.R:4:1
2. ├─methods::new(...)
3. │ ├─methods::initialize(value, ...)
4. │ └─methods::initialize(value, ...)
5. ├─rstan::vb(stanmodels$lnm, data_list, ...)
6. └─rstan::vb(stanmodels$lnm, data_list, ...)
7. └─rstan (local) .local(object, ...)
[ FAIL 3 | WARN 0 | 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 ... [37s] OK
- checking PDF version of manual ... [19s] OK
- checking HTML version of manual ... [3s] OK
- DONE
Status: 2 ERRORs, 1 NOTE