SBC (rebuild) #494
build.yml
on: workflow_dispatch
Build and deploy
/
Determine package to build
2s
Build and deploy
/
Build source pkg and vignettes
46m 49s
Build and deploy
/
Build pkgdown site (ropensci only)
0s
Matrix: Build and deploy / linux
Matrix: Build and deploy / macos
Matrix: Build and deploy / wasm
Matrix: Build and deploy / windows
Build and deploy
/
Deploy to docs server
0s
Build and deploy
/
Set Github Status
5s
Annotations
1 error and 8 warnings
|
Build and deploy / Build source pkg and vignettes:
SBC#L1
* creating vignettes ... ERROR
Setting r-universe rmarkdown theme...
--- re-building ‘SBC.Rmd’ using rmarkdown
Loading required package: rmarkdown
Setting r-universe rmarkdown theme...
Setting r-universe rmarkdown theme...
Setting r-universe rmarkdown theme...
Setting r-universe rmarkdown theme...
Setting r-universe rmarkdown theme...
--- finished re-building ‘SBC.Rmd’
--- re-building ‘bad_parametrization.Rmd’ using rmarkdown
--- finished re-building ‘bad_parametrization.Rmd’
--- re-building ‘brms.Rmd’ using rmarkdown
Setting r-universe rmarkdown theme...
Setting r-universe rmarkdown theme...
Setting r-universe rmarkdown theme...
Setting r-universe rmarkdown theme...
--- finished re-building ‘brms.Rmd’
--- re-building ‘computational_algorithm1.Rmd’ using rmarkdown
Setting r-universe rmarkdown theme...
Setting r-universe rmarkdown theme...
Setting r-universe rmarkdown theme...
Setting r-universe rmarkdown theme...
Setting r-universe rmarkdown theme...
Setting r-universe rmarkdown theme...
Setting r-universe rmarkdown theme...
--- finished re-building ‘computational_algorithm1.Rmd’
--- re-building ‘discrete_vars.Rmd’ using rmarkdown
Setting r-universe rmarkdown theme...
Setting r-universe rmarkdown theme...
Setting r-universe rmarkdown theme...
Setting r-universe rmarkdown theme...
Quitting from lines 256-257 [unnamed-chunk-12] (discrete_vars.Rmd)
Error: processing vignette 'discrete_vars.Rmd' failed with diagnostics:
there is no package called 'rjags'
--- failed re-building ‘discrete_vars.Rmd’
--- re-building ‘implementing_backends.Rmd’ using rmarkdown
Quitting from lines 169-171 [poisson_ranks] (implementing_backends.Rmd)
Error: processing vignette 'implementing_backends.Rmd' failed with diagnostics:
The data.frame needs a 'variable' and 'rank' columns
--- failed re-building ‘implementing_backends.Rmd’
--- re-building ‘indexing.Rmd’ using rmarkdown
--- finished re-building ‘indexing.Rmd’
--- re-building ‘limits_of_SBC.Rmd’ using rmarkdown
Setting r-universe rmarkdown theme...
Setting r-universe rmarkdown theme...
Setting r-universe rmarkdown theme...
Setting r-universe rmarkdown theme...
[WARNING] Could not convert TeX math
\mathbf{\mu} \sim MVN(0, \mathbf{\Sigma})\\
y \sim MVN(\mathbf{\mu}, \mathbf{\Sigma})\\
\mathbf{\Sigma} = \left(\begin{matrix}
1 & 0.8 \\
0.8 & 1 \\
\end{matrix}\right)
, rendering as TeX:
\mathbf{\mu} \sim MVN(0, \mathbf{\Sigma}
^
unexpected control sequence \\
expecting "%", "\\label", "\\tag", "\\nonumber", whitespace or "\\allowbreak"
--- finished re-building ‘limits_of_SBC.Rmd’
--- re-building ‘rank_visualizations.Rmd’ using rmarkdown
--- finished re-building ‘rank_visualizations.Rmd’
--- re-building ‘rejection_sampling.Rmd’ using rmarkdown
Setting r-universe rmarkdown theme...
Setting r-universe rmarkdown theme...
Setting r-universe rmarkdown theme...
Setting r-universe rmarkdown theme...
[WARNING] Could not convert TeX math
\begin{equation}
\pi(\theta | y, a = 1) = \frac{\pi(a = 1 | y) \pi(y | \theta)\pi(\theta)}{\int_\Theta \mathrm{d}\tilde\theta \: \pi(a = 1 | y) \pi(y | \tilde\theta)\pi(\tilde\theta)} =
\frac{\pi(y | \theta)\pi(\theta)}{\int_\Theta \mathrm{d}\tilde\theta \: \pi(y | \tilde\theta)\pi(\tilde\theta)} = \pi(\theta | y)
\end{equation}
, rendering as TeX
--- finished re-building ‘rejection_sampling.Rmd’
--- re-building ‘small_model_workflow.Rmd’ using rmarkdown
Setting r-universe rmarkdown theme...
Setting r-universe rmarkdown theme...
Setting r-universe rmarkdown theme...
Setting r-universe rmarkdown theme...
--- finished re-building ‘small_model_workflow.Rmd’
SUMMARY: processing the following files failed:
‘discrete_vars.Rmd’ ‘implementing_backends.Rmd’
Error: Vignette re-building failed.
Execution halted
If this is expected, consider precomputing your vignettes: https://ropensci.org/blog/2019/12/08/precompute-vignettes/
|
|
Build and deploy / Build R-release for MacOS:
SBC#L1
Check: dependencies in R code, Result: WARNING
'::' or ':::' imports not declared from:
‘cachem’ ‘future’ ‘HistogramTools’ ‘rjags’ ‘rlang’ ‘scales’
‘spatstat.geom’
Namespaces in Imports field not imported from:
‘abind’ ‘R6’ ‘stringi’
All declared Imports should be used.
There are ::: calls to the package's namespace in its code. A package
almost never needs to use ::: for its own objects:
‘capture_all_outputs’ ‘compute_SBC_single’
Check: S3 generic/method consistency, Result: WARNING
plot_coverage_diff:
function(x, variables, prob, interval_type, parameters, max_points)
plot_coverage_diff.SBC_results:
function(x, variables, prob, interval_type, max_points)
plot_rank_hist:
function(x, variables, bins, prob, ..., parameters)
plot_rank_hist.SBC_results:
function(x, variables, bins, prob, parameters)
plot_rank_hist:
function(x, variables, bins, prob, ..., parameters)
plot_rank_hist.data.frame:
function(x, variables, bins, prob, max_rank, parameters)
print:
function(x, ...)
print.SBC_nuts_diagnostics_summary:
function(x)
print:
function(x, ...)
print.SBC_results_summary:
function(x)
print:
function(x, ...)
print.SBC_diagnostic_messages:
function(x, include_ok, print_func)
summary:
function(object, ...)
summary.SBC_results:
function(x)
summary:
function(object, ...)
summary.SBC_nuts_diagnostics:
function(diagnostics)
summary:
function(object, ...)
summary.SBC_RStanOptimizing_diagnostics:
function(x)
summary:
function(object, ...)
summary.SBC_ADVI_diagnostics:
function(x)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Check: Rd cross-references, Result: WARNING
Package unavailable to check Rd xrefs: ‘rjags’
Missing link or links in Rd file 'combine-functions.Rd':
‘ECDF-plots’
Missing link or links in Rd file 'ECDF-plots.Rd':
‘combine-functions’
See section 'Cross-references' in the 'Writing R Extensions' manual.
Check: for missing documentation entries, Result: WARNING
Undocumented code objects:
‘calculate_sds_draws_matrix’ ‘draws_rvars_to_standata’
‘draws_rvars_to_standata_single’ ‘SBC_backend_mock_rng’
‘SBC_diagnostic_messages’ ‘validate_SBC_datasets’
‘validate_SBC_results’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Check: Rd \usage sections, Result: WARNING
Undocumented arguments in Rd file 'SBC_backend_brms_from_generator.Rd'
‘generator’ ‘...’
Undocumented arguments in Rd file 'SBC_backend_default_thin_ranks.Rd'
‘backend’
Undocumented arguments in Rd file 'SBC_backend_hash_for_cache.Rd'
‘backend’
Undocumented arguments in Rd file 'SBC_backend_mock.Rd'
‘output’ ‘message’ ‘warning’ ‘error’
Undocumented arguments in Rd file 'SBC_fit.Rd'
‘backend’ ‘generated’ ‘cores’
Undocumented arguments in Rd file 'SBC_fit_to_draws_matrix.Rd'
‘fit’
Undocumented arguments in Rd file 'SBC_print_example_model.Rd'
‘interface’
Undocumented arguments in Rd file 'SBC_results.Rd'
‘stats’ ‘fits’ ‘backend_diagnostics’ ‘default_diagnostics’ ‘outputs’
‘messages’ ‘warnings’ ‘errors’
Undocumented arguments in Rd file 'SBC_statistics_from_single_fit.Rd'
‘fit’ ‘variables’ ‘generated’
Undocumented arguments in Rd file 'bind_derived_quantities.Rd'
‘dq1’ ‘dq2’
Undocumented arguments in Rd file 'bind_globals.Rd'
‘globals1’ ‘globals2’
Undocumented arguments in Rd file 'calculate_prior_sd.Rd'
‘datasets’
Undocumented arguments in Rd file 'check_all_SBC_diagnostics.Rd'
‘x’
Undocumented arguments in Rd file 'combine_args.Rd'
‘args1’ ‘args2’
Undocumented arguments in Rd file 'compute_dquants.Rd'
‘draws’ ‘generated’ ‘dquants’
Undocumented arguments in Rd file 'data_for_ecdf_plots.Rd'
‘x’ ‘...’ ‘prob’ ‘gamma’ ‘K’
Undocumented arguments in Rd file 'defau
|
|
Build and deploy / Build R-devel for MacOS :
SBC#L1
Check: dependencies in R code, Result: WARNING
'::' or ':::' imports not declared from:
‘cachem’ ‘future’ ‘HistogramTools’ ‘rjags’ ‘rlang’ ‘scales’
‘spatstat.geom’
Namespaces in Imports field not imported from:
‘abind’ ‘R6’ ‘stringi’
All declared Imports should be used.
There are ::: calls to the package's namespace in its code. A package
almost never needs to use ::: for its own objects:
‘capture_all_outputs’ ‘compute_SBC_single’
Check: S3 generic/method consistency, Result: WARNING
plot_coverage_diff:
function(x, variables, prob, interval_type, parameters, max_points)
plot_coverage_diff.SBC_results:
function(x, variables, prob, interval_type, max_points)
plot_rank_hist:
function(x, variables, bins, prob, ..., parameters)
plot_rank_hist.SBC_results:
function(x, variables, bins, prob, parameters)
plot_rank_hist:
function(x, variables, bins, prob, ..., parameters)
plot_rank_hist.data.frame:
function(x, variables, bins, prob, max_rank, parameters)
print:
function(x, ...)
print.SBC_nuts_diagnostics_summary:
function(x)
print:
function(x, ...)
print.SBC_results_summary:
function(x)
print:
function(x, ...)
print.SBC_diagnostic_messages:
function(x, include_ok, print_func)
summary:
function(object, ...)
summary.SBC_results:
function(x)
summary:
function(object, ...)
summary.SBC_nuts_diagnostics:
function(diagnostics)
summary:
function(object, ...)
summary.SBC_RStanOptimizing_diagnostics:
function(x)
summary:
function(object, ...)
summary.SBC_ADVI_diagnostics:
function(x)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Check: Rd cross-references, Result: WARNING
Package unavailable to check Rd xrefs: ‘rjags’
Missing link(s) in Rd file 'combine-functions.Rd':
‘ECDF-plots’
Missing link(s) in Rd file 'ECDF-plots.Rd':
‘combine-functions’
See section 'Cross-references' in the 'Writing R Extensions' manual.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
combine-functions.Rd: ECDF-plots
ECDF-plots.Rd: combine-functions
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Check: for missing documentation entries, Result: WARNING
Undocumented code objects:
‘calculate_sds_draws_matrix’ ‘draws_rvars_to_standata’
‘draws_rvars_to_standata_single’ ‘SBC_backend_mock_rng’
‘SBC_diagnostic_messages’ ‘validate_SBC_datasets’
‘validate_SBC_results’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Check: Rd \usage sections, Result: WARNING
Undocumented arguments in Rd file 'SBC_backend_brms_from_generator.Rd'
‘generator’ ‘...’
Undocumented arguments in Rd file 'SBC_backend_default_thin_ranks.Rd'
‘backend’
Undocumented arguments in Rd file 'SBC_backend_hash_for_cache.Rd'
‘backend’
Undocumented arguments in Rd file 'SBC_backend_mock.Rd'
‘output’ ‘message’ ‘warning’ ‘error’
Undocumented arguments in Rd file 'SBC_fit.Rd'
‘backend’ ‘generated’ ‘cores’
Undocumented arguments in Rd file 'SBC_fit_to_draws_matrix.Rd'
‘fit’
Undocumented arguments in Rd file 'SBC_print_example_model.Rd'
‘interface’
Undocumented arguments in Rd file 'SBC_results.Rd'
‘stats’ ‘fits’ ‘backend_diagnostics’ ‘default_diagnostics’ ‘outputs’
‘messages’ ‘warnings’ ‘errors’
Undocumented arguments in Rd file 'SBC_statistics_from_single_fit.Rd'
‘fit’ ‘variables’ ‘generated’
Undocumented arguments in Rd file 'bind_derived_quantities.Rd'
‘dq1’ ‘dq2’
Undocumented arguments in Rd file 'bind_globals.Rd'
‘globals1’ ‘globals2’
Undocumented arguments in Rd file 'calculate_prior_sd.Rd'
‘datasets’
Undocumented arguments in Rd file 'check_all_SBC_diagnostics.Rd'
‘x’
Undocumented arguments in Rd file 'combine_args.
|
|
Build and deploy / Build R-oldrel for MacOS:
SBC#L1
Check: dependencies in R code, Result: WARNING
'::' or ':::' imports not declared from:
‘cachem’ ‘future’ ‘HistogramTools’ ‘rjags’ ‘rlang’ ‘scales’
‘spatstat.geom’
Namespaces in Imports field not imported from:
‘abind’ ‘R6’ ‘stringi’
All declared Imports should be used.
There are ::: calls to the package's namespace in its code. A package
almost never needs to use ::: for its own objects:
‘capture_all_outputs’ ‘compute_SBC_single’
Check: S3 generic/method consistency, Result: WARNING
plot_coverage_diff:
function(x, variables, prob, interval_type, parameters, max_points)
plot_coverage_diff.SBC_results:
function(x, variables, prob, interval_type, max_points)
plot_rank_hist:
function(x, variables, bins, prob, ..., parameters)
plot_rank_hist.SBC_results:
function(x, variables, bins, prob, parameters)
plot_rank_hist:
function(x, variables, bins, prob, ..., parameters)
plot_rank_hist.data.frame:
function(x, variables, bins, prob, max_rank, parameters)
print:
function(x, ...)
print.SBC_nuts_diagnostics_summary:
function(x)
print:
function(x, ...)
print.SBC_results_summary:
function(x)
print:
function(x, ...)
print.SBC_diagnostic_messages:
function(x, include_ok, print_func)
summary:
function(object, ...)
summary.SBC_results:
function(x)
summary:
function(object, ...)
summary.SBC_nuts_diagnostics:
function(diagnostics)
summary:
function(object, ...)
summary.SBC_RStanOptimizing_diagnostics:
function(x)
summary:
function(object, ...)
summary.SBC_ADVI_diagnostics:
function(x)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Check: Rd cross-references, Result: WARNING
Package unavailable to check Rd xrefs: ‘rjags’
Missing link or links in documentation object 'combine-functions.Rd':
‘ECDF-plots’
Missing link or links in documentation object 'ECDF-plots.Rd':
‘combine-functions’
See section 'Cross-references' in the 'Writing R Extensions' manual.
Check: for missing documentation entries, Result: WARNING
Undocumented code objects:
‘calculate_sds_draws_matrix’ ‘draws_rvars_to_standata’
‘draws_rvars_to_standata_single’ ‘SBC_backend_mock_rng’
‘SBC_diagnostic_messages’ ‘validate_SBC_datasets’
‘validate_SBC_results’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Check: Rd \usage sections, Result: WARNING
Undocumented arguments in documentation object 'SBC_backend_brms_from_generator'
‘generator’ ‘...’
Undocumented arguments in documentation object 'SBC_backend_default_thin_ranks'
‘backend’
Undocumented arguments in documentation object 'SBC_backend_hash_for_cache'
‘backend’
Undocumented arguments in documentation object 'SBC_backend_mock'
‘output’ ‘message’ ‘warning’ ‘error’
Undocumented arguments in documentation object 'SBC_fit'
‘backend’ ‘generated’ ‘cores’
Undocumented arguments in documentation object 'SBC_fit_to_draws_matrix'
‘fit’
Undocumented arguments in documentation object 'SBC_print_example_model'
‘interface’
Undocumented arguments in documentation object 'SBC_results'
‘stats’ ‘fits’ ‘backend_diagnostics’ ‘default_diagnostics’ ‘outputs’
‘messages’ ‘warnings’ ‘errors’
Undocumented arguments in documentation object 'SBC_statistics_from_single_fit'
‘fit’ ‘variables’ ‘generated’
Undocumented arguments in documentation object 'bind_derived_quantities'
‘dq1’ ‘dq2’
Undocumented arguments in documentation object 'bind_globals'
‘globals1’ ‘globals2’
Undocumented arguments in documentation object 'calculate_prior_sd'
‘datasets’
Undocumented arguments in documentation object 'check_all_SBC_diagnostics'
‘x’
Undocumented arguments in documentation object 'combine_args'
‘args1’ ‘args2’
Undocumented arguments in documentation object 'compute_dquants'
|
|
Build and deploy / Build R-release for Linux:
SBC#L1
Check: dependencies in R code, Result: WARNING
'::' or ':::' imports not declared from:
‘HistogramTools’ ‘cachem’ ‘future’ ‘rjags’ ‘rlang’ ‘scales’
‘spatstat.geom’
Namespaces in Imports field not imported from:
‘R6’ ‘abind’ ‘stringi’
All declared Imports should be used.
There are ::: calls to the package's namespace in its code. A package
almost never needs to use ::: for its own objects:
‘capture_all_outputs’ ‘compute_SBC_single’
Check: S3 generic/method consistency, Result: WARNING
plot_coverage_diff:
function(x, variables, prob, interval_type, parameters, max_points)
plot_coverage_diff.SBC_results:
function(x, variables, prob, interval_type, max_points)
plot_rank_hist:
function(x, variables, bins, prob, ..., parameters)
plot_rank_hist.SBC_results:
function(x, variables, bins, prob, parameters)
plot_rank_hist:
function(x, variables, bins, prob, ..., parameters)
plot_rank_hist.data.frame:
function(x, variables, bins, prob, max_rank, parameters)
print:
function(x, ...)
print.SBC_nuts_diagnostics_summary:
function(x)
print:
function(x, ...)
print.SBC_results_summary:
function(x)
print:
function(x, ...)
print.SBC_diagnostic_messages:
function(x, include_ok, print_func)
summary:
function(object, ...)
summary.SBC_results:
function(x)
summary:
function(object, ...)
summary.SBC_nuts_diagnostics:
function(diagnostics)
summary:
function(object, ...)
summary.SBC_RStanOptimizing_diagnostics:
function(x)
summary:
function(object, ...)
summary.SBC_ADVI_diagnostics:
function(x)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Check: Rd cross-references, Result: WARNING
Package unavailable to check Rd xrefs: ‘rjags’
Missing link or links in Rd file 'ECDF-plots.Rd':
‘combine-functions’
Missing link or links in Rd file 'combine-functions.Rd':
‘ECDF-plots’
See section 'Cross-references' in the 'Writing R Extensions' manual.
Check: for missing documentation entries, Result: WARNING
Undocumented code objects:
‘SBC_backend_mock_rng’ ‘SBC_diagnostic_messages’
‘calculate_sds_draws_matrix’ ‘draws_rvars_to_standata’
‘draws_rvars_to_standata_single’ ‘validate_SBC_datasets’
‘validate_SBC_results’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Check: Rd \usage sections, Result: WARNING
Undocumented arguments in Rd file 'SBC_backend_brms_from_generator.Rd'
‘generator’ ‘...’
Undocumented arguments in Rd file 'SBC_backend_default_thin_ranks.Rd'
‘backend’
Undocumented arguments in Rd file 'SBC_backend_hash_for_cache.Rd'
‘backend’
Undocumented arguments in Rd file 'SBC_backend_mock.Rd'
‘output’ ‘message’ ‘warning’ ‘error’
Undocumented arguments in Rd file 'SBC_fit.Rd'
‘backend’ ‘generated’ ‘cores’
Undocumented arguments in Rd file 'SBC_fit_to_draws_matrix.Rd'
‘fit’
Undocumented arguments in Rd file 'SBC_print_example_model.Rd'
‘interface’
Undocumented arguments in Rd file 'SBC_results.Rd'
‘stats’ ‘fits’ ‘backend_diagnostics’ ‘default_diagnostics’ ‘outputs’
‘messages’ ‘warnings’ ‘errors’
Undocumented arguments in Rd file 'SBC_statistics_from_single_fit.Rd'
‘fit’ ‘variables’ ‘generated’
Undocumented arguments in Rd file 'bind_derived_quantities.Rd'
‘dq1’ ‘dq2’
Undocumented arguments in Rd file 'bind_globals.Rd'
‘globals1’ ‘globals2’
Undocumented arguments in Rd file 'calculate_prior_sd.Rd'
‘datasets’
Undocumented arguments in Rd file 'check_all_SBC_diagnostics.Rd'
‘x’
Undocumented arguments in Rd file 'combine_args.Rd'
‘args1’ ‘args2’
Undocumented arguments in Rd file 'compute_dquants.Rd'
‘draws’ ‘generated’ ‘dquants’
Undocumented arguments in Rd file 'data_for_ecdf_plots.Rd'
‘x’ ‘...’ ‘prob’ ‘gamma’ ‘K’
Undocumented arguments in Rd file 'defau
|
|
Build and deploy / Build R-release for Windows:
SBC#L1
Check: dependencies in R code, Result: WARNING
'::' or ':::' imports not declared from:
'HistogramTools' 'cachem' 'future' 'rjags' 'rlang' 'scales'
'spatstat.geom'
Namespaces in Imports field not imported from:
'R6' 'abind' 'stringi'
All declared Imports should be used.
There are ::: calls to the package's namespace in its code. A package
almost never needs to use ::: for its own objects:
'capture_all_outputs' 'compute_SBC_single'
Check: S3 generic/method consistency, Result: WARNING
plot_coverage_diff:
function(x, variables, prob, interval_type, parameters, max_points)
plot_coverage_diff.SBC_results:
function(x, variables, prob, interval_type, max_points)
plot_rank_hist:
function(x, variables, bins, prob, ..., parameters)
plot_rank_hist.SBC_results:
function(x, variables, bins, prob, parameters)
plot_rank_hist:
function(x, variables, bins, prob, ..., parameters)
plot_rank_hist.data.frame:
function(x, variables, bins, prob, max_rank, parameters)
print:
function(x, ...)
print.SBC_nuts_diagnostics_summary:
function(x)
print:
function(x, ...)
print.SBC_results_summary:
function(x)
print:
function(x, ...)
print.SBC_diagnostic_messages:
function(x, include_ok, print_func)
summary:
function(object, ...)
summary.SBC_results:
function(x)
summary:
function(object, ...)
summary.SBC_nuts_diagnostics:
function(diagnostics)
summary:
function(object, ...)
summary.SBC_RStanOptimizing_diagnostics:
function(x)
summary:
function(object, ...)
summary.SBC_ADVI_diagnostics:
function(x)
See section 'Generic functions and methods' in the 'Writing R
Extensions' manual.
Check: Rd cross-references, Result: WARNING
Package unavailable to check Rd xrefs: 'rjags'
Missing link or links in Rd file 'ECDF-plots.Rd':
'combine-functions'
Missing link or links in Rd file 'combine-functions.Rd':
'ECDF-plots'
See section 'Cross-references' in the 'Writing R Extensions' manual.
Check: for missing documentation entries, Result: WARNING
Undocumented code objects:
'SBC_backend_mock_rng' 'SBC_diagnostic_messages'
'calculate_sds_draws_matrix' 'draws_rvars_to_standata'
'draws_rvars_to_standata_single' 'validate_SBC_datasets'
'validate_SBC_results'
All user-level objects in a package should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Check: Rd \usage sections, Result: WARNING
Undocumented arguments in Rd file 'SBC_backend_brms_from_generator.Rd'
'generator' '...'
Undocumented arguments in Rd file 'SBC_backend_default_thin_ranks.Rd'
'backend'
Undocumented arguments in Rd file 'SBC_backend_hash_for_cache.Rd'
'backend'
Undocumented arguments in Rd file 'SBC_backend_mock.Rd'
'output' 'message' 'warning' 'error'
Undocumented arguments in Rd file 'SBC_fit.Rd'
'backend' 'generated' 'cores'
Undocumented arguments in Rd file 'SBC_fit_to_draws_matrix.Rd'
'fit'
Undocumented arguments in Rd file 'SBC_print_example_model.Rd'
'interface'
Undocumented arguments in Rd file 'SBC_results.Rd'
'stats' 'fits' 'backend_diagnostics' 'default_diagnostics' 'outputs'
'messages' 'warnings' 'errors'
Undocumented arguments in Rd file 'SBC_statistics_from_single_fit.Rd'
'fit' 'variables' 'generated'
Undocumented arguments in Rd file 'bind_derived_quantities.Rd'
'dq1' 'dq2'
Undocumented arguments in Rd file 'bind_globals.Rd'
'globals1' 'globals2'
Undocumented arguments in Rd file 'calculate_prior_sd.Rd'
'datasets'
Undocumented arguments in Rd file 'check_all_SBC_diagnostics.Rd'
'x'
Undocumented arguments in Rd file 'combine_args.Rd'
'args1' 'args2'
Undocumented arguments in Rd file 'compute_dquants.Rd'
'draws' 'generated' 'dquants'
Undocumented arguments in Rd file 'data_for_ecdf_plots.Rd'
'x' '...' 'prob' 'gamma' 'K'
Undocumented arguments in Rd file 'defau
|
|
Build and deploy / Build R-oldrel for Windows:
SBC#L1
Check: dependencies in R code, Result: WARNING
'::' or ':::' imports not declared from:
'HistogramTools' 'cachem' 'future' 'rjags' 'rlang' 'scales'
'spatstat.geom'
Namespaces in Imports field not imported from:
'R6' 'abind' 'stringi'
All declared Imports should be used.
There are ::: calls to the package's namespace in its code. A package
almost never needs to use ::: for its own objects:
'capture_all_outputs' 'compute_SBC_single'
Check: S3 generic/method consistency, Result: WARNING
plot_coverage_diff:
function(x, variables, prob, interval_type, parameters, max_points)
plot_coverage_diff.SBC_results:
function(x, variables, prob, interval_type, max_points)
plot_rank_hist:
function(x, variables, bins, prob, ..., parameters)
plot_rank_hist.SBC_results:
function(x, variables, bins, prob, parameters)
plot_rank_hist:
function(x, variables, bins, prob, ..., parameters)
plot_rank_hist.data.frame:
function(x, variables, bins, prob, max_rank, parameters)
print:
function(x, ...)
print.SBC_nuts_diagnostics_summary:
function(x)
print:
function(x, ...)
print.SBC_results_summary:
function(x)
print:
function(x, ...)
print.SBC_diagnostic_messages:
function(x, include_ok, print_func)
summary:
function(object, ...)
summary.SBC_results:
function(x)
summary:
function(object, ...)
summary.SBC_nuts_diagnostics:
function(diagnostics)
summary:
function(object, ...)
summary.SBC_RStanOptimizing_diagnostics:
function(x)
summary:
function(object, ...)
summary.SBC_ADVI_diagnostics:
function(x)
See section 'Generic functions and methods' in the 'Writing R
Extensions' manual.
Check: Rd cross-references, Result: WARNING
Package unavailable to check Rd xrefs: 'rjags'
Missing link or links in documentation object 'ECDF-plots.Rd':
'combine-functions'
Missing link or links in documentation object 'combine-functions.Rd':
'ECDF-plots'
See section 'Cross-references' in the 'Writing R Extensions' manual.
Check: for missing documentation entries, Result: WARNING
Undocumented code objects:
'SBC_backend_mock_rng' 'SBC_diagnostic_messages'
'calculate_sds_draws_matrix' 'draws_rvars_to_standata'
'draws_rvars_to_standata_single' 'validate_SBC_datasets'
'validate_SBC_results'
All user-level objects in a package should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Check: Rd \usage sections, Result: WARNING
Undocumented arguments in documentation object 'SBC_backend_brms_from_generator'
'generator' '...'
Undocumented arguments in documentation object 'SBC_backend_default_thin_ranks'
'backend'
Undocumented arguments in documentation object 'SBC_backend_hash_for_cache'
'backend'
Undocumented arguments in documentation object 'SBC_backend_mock'
'output' 'message' 'warning' 'error'
Undocumented arguments in documentation object 'SBC_fit'
'backend' 'generated' 'cores'
Undocumented arguments in documentation object 'SBC_fit_to_draws_matrix'
'fit'
Undocumented arguments in documentation object 'SBC_print_example_model'
'interface'
Undocumented arguments in documentation object 'SBC_results'
'stats' 'fits' 'backend_diagnostics' 'default_diagnostics' 'outputs'
'messages' 'warnings' 'errors'
Undocumented arguments in documentation object 'SBC_statistics_from_single_fit'
'fit' 'variables' 'generated'
Undocumented arguments in documentation object 'bind_derived_quantities'
'dq1' 'dq2'
Undocumented arguments in documentation object 'bind_globals'
'globals1' 'globals2'
Undocumented arguments in documentation object 'calculate_prior_sd'
'datasets'
Undocumented arguments in documentation object 'check_all_SBC_diagnostics'
'x'
Undocumented arguments in documentation object 'combine_args'
'args1' 'args2'
Undocumented arguments in documentation object 'compute_dquants'
|
|
Build and deploy / Build R-devel for Windows:
SBC#L1
Check: dependencies in R code, Result: WARNING
'::' or ':::' imports not declared from:
'HistogramTools' 'cachem' 'future' 'rjags' 'rlang' 'scales'
'spatstat.geom'
Namespaces in Imports field not imported from:
'R6' 'abind' 'stringi'
All declared Imports should be used.
There are ::: calls to the package's namespace in its code. A package
almost never needs to use ::: for its own objects:
'capture_all_outputs' 'compute_SBC_single'
Check: S3 generic/method consistency, Result: WARNING
plot_coverage_diff:
function(x, variables, prob, interval_type, parameters, max_points)
plot_coverage_diff.SBC_results:
function(x, variables, prob, interval_type, max_points)
plot_rank_hist:
function(x, variables, bins, prob, ..., parameters)
plot_rank_hist.SBC_results:
function(x, variables, bins, prob, parameters)
plot_rank_hist:
function(x, variables, bins, prob, ..., parameters)
plot_rank_hist.data.frame:
function(x, variables, bins, prob, max_rank, parameters)
print:
function(x, ...)
print.SBC_nuts_diagnostics_summary:
function(x)
print:
function(x, ...)
print.SBC_results_summary:
function(x)
print:
function(x, ...)
print.SBC_diagnostic_messages:
function(x, include_ok, print_func)
summary:
function(object, ...)
summary.SBC_results:
function(x)
summary:
function(object, ...)
summary.SBC_nuts_diagnostics:
function(diagnostics)
summary:
function(object, ...)
summary.SBC_RStanOptimizing_diagnostics:
function(x)
summary:
function(object, ...)
summary.SBC_ADVI_diagnostics:
function(x)
See section 'Generic functions and methods' in the 'Writing R
Extensions' manual.
Check: Rd cross-references, Result: WARNING
Package unavailable to check Rd xrefs: 'rjags'
Missing link(s) in Rd file 'ECDF-plots.Rd':
'combine-functions'
Missing link(s) in Rd file 'combine-functions.Rd':
'ECDF-plots'
See section 'Cross-references' in the 'Writing R Extensions' manual.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
ECDF-plots.Rd: combine-functions
combine-functions.Rd: ECDF-plots
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Check: for missing documentation entries, Result: WARNING
Undocumented code objects:
'SBC_backend_mock_rng' 'SBC_diagnostic_messages'
'calculate_sds_draws_matrix' 'draws_rvars_to_standata'
'draws_rvars_to_standata_single' 'validate_SBC_datasets'
'validate_SBC_results'
All user-level objects in a package should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Check: Rd \usage sections, Result: WARNING
Undocumented arguments in Rd file 'SBC_backend_brms_from_generator.Rd'
'generator' '...'
Undocumented arguments in Rd file 'SBC_backend_default_thin_ranks.Rd'
'backend'
Undocumented arguments in Rd file 'SBC_backend_hash_for_cache.Rd'
'backend'
Undocumented arguments in Rd file 'SBC_backend_mock.Rd'
'output' 'message' 'warning' 'error'
Undocumented arguments in Rd file 'SBC_fit.Rd'
'backend' 'generated' 'cores'
Undocumented arguments in Rd file 'SBC_fit_to_draws_matrix.Rd'
'fit'
Undocumented arguments in Rd file 'SBC_print_example_model.Rd'
'interface'
Undocumented arguments in Rd file 'SBC_results.Rd'
'stats' 'fits' 'backend_diagnostics' 'default_diagnostics' 'outputs'
'messages' 'warnings' 'errors'
Undocumented arguments in Rd file 'SBC_statistics_from_single_fit.Rd'
'fit' 'variables' 'generated'
Undocumented arguments in Rd file 'bind_derived_quantities.Rd'
'dq1' 'dq2'
Undocumented arguments in Rd file 'bind_globals.Rd'
'globals1' 'globals2'
Undocumented arguments in Rd file 'calculate_prior_sd.Rd'
'datasets'
Undocumented arguments in Rd file 'check_all_SBC_diagnostics.Rd'
'x'
Undocumented arguments in Rd file 'combine_args.
|
|
Build and deploy / Build R-devel for Linux:
SBC#L1
Check: dependencies in R code, Result: WARNING
'::' or ':::' imports not declared from:
‘HistogramTools’ ‘cachem’ ‘future’ ‘rjags’ ‘rlang’ ‘scales’
‘spatstat.geom’
Namespaces in Imports field not imported from:
‘R6’ ‘abind’ ‘stringi’
All declared Imports should be used.
There are ::: calls to the package's namespace in its code. A package
almost never needs to use ::: for its own objects:
‘capture_all_outputs’ ‘compute_SBC_single’
Check: S3 generic/method consistency, Result: WARNING
plot_coverage_diff:
function(x, variables, prob, interval_type, parameters, max_points)
plot_coverage_diff.SBC_results:
function(x, variables, prob, interval_type, max_points)
plot_rank_hist:
function(x, variables, bins, prob, ..., parameters)
plot_rank_hist.SBC_results:
function(x, variables, bins, prob, parameters)
plot_rank_hist:
function(x, variables, bins, prob, ..., parameters)
plot_rank_hist.data.frame:
function(x, variables, bins, prob, max_rank, parameters)
print:
function(x, ...)
print.SBC_nuts_diagnostics_summary:
function(x)
print:
function(x, ...)
print.SBC_results_summary:
function(x)
print:
function(x, ...)
print.SBC_diagnostic_messages:
function(x, include_ok, print_func)
summary:
function(object, ...)
summary.SBC_results:
function(x)
summary:
function(object, ...)
summary.SBC_nuts_diagnostics:
function(diagnostics)
summary:
function(object, ...)
summary.SBC_RStanOptimizing_diagnostics:
function(x)
summary:
function(object, ...)
summary.SBC_ADVI_diagnostics:
function(x)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Check: Rd cross-references, Result: WARNING
Package unavailable to check Rd xrefs: ‘rjags’
Missing link(s) in Rd file 'ECDF-plots.Rd':
‘combine-functions’
Missing link(s) in Rd file 'combine-functions.Rd':
‘ECDF-plots’
See section 'Cross-references' in the 'Writing R Extensions' manual.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
ECDF-plots.Rd: combine-functions
combine-functions.Rd: ECDF-plots
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Check: for missing documentation entries, Result: WARNING
Undocumented code objects:
‘SBC_backend_mock_rng’ ‘SBC_diagnostic_messages’
‘calculate_sds_draws_matrix’ ‘draws_rvars_to_standata’
‘draws_rvars_to_standata_single’ ‘validate_SBC_datasets’
‘validate_SBC_results’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Check: Rd \usage sections, Result: WARNING
Undocumented arguments in Rd file 'SBC_backend_brms_from_generator.Rd'
‘generator’ ‘...’
Undocumented arguments in Rd file 'SBC_backend_default_thin_ranks.Rd'
‘backend’
Undocumented arguments in Rd file 'SBC_backend_hash_for_cache.Rd'
‘backend’
Undocumented arguments in Rd file 'SBC_backend_mock.Rd'
‘output’ ‘message’ ‘warning’ ‘error’
Undocumented arguments in Rd file 'SBC_fit.Rd'
‘backend’ ‘generated’ ‘cores’
Undocumented arguments in Rd file 'SBC_fit_to_draws_matrix.Rd'
‘fit’
Undocumented arguments in Rd file 'SBC_print_example_model.Rd'
‘interface’
Undocumented arguments in Rd file 'SBC_results.Rd'
‘stats’ ‘fits’ ‘backend_diagnostics’ ‘default_diagnostics’ ‘outputs’
‘messages’ ‘warnings’ ‘errors’
Undocumented arguments in Rd file 'SBC_statistics_from_single_fit.Rd'
‘fit’ ‘variables’ ‘generated’
Undocumented arguments in Rd file 'bind_derived_quantities.Rd'
‘dq1’ ‘dq2’
Undocumented arguments in Rd file 'bind_globals.Rd'
‘globals1’ ‘globals2’
Undocumented arguments in Rd file 'calculate_prior_sd.Rd'
‘datasets’
Undocumented arguments in Rd file 'check_all_SBC_diagnostics.Rd'
‘x’
Undocumented arguments in Rd file 'combine_args.
|
Artifacts
Produced during runtime
| Name | Size | |
|---|---|---|
|
package-linux-devel
|
314 KB |
|
|
package-linux-release
|
315 KB |
|
|
package-macos-devel-arm64
|
315 KB |
|
|
package-macos-oldrel-arm64
|
311 KB |
|
|
package-macos-release-arm64
|
316 KB |
|
|
package-source
|
200 KB |
|
|
package-wasm-oldrel
|
195 KB |
|
|
package-wasm-release
|
201 KB |
|
|
package-windows-devel
|
314 KB |
|
|
package-windows-oldrel
|
309 KB |
|
|
package-windows-release
|
315 KB |
|