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:
    'continue_sequence.R' 'get_exchange_rates.R'
Running examples in 'shinyscholar-Ex.R' failed
The error most likely occurred in:

> ### Name: create_template
> ### Title: Create a skeleton application containing empty modules
> ### Aliases: create_template
> 
> ### ** Examples
> 
> td <- tempfile()
> dir.create(td, recursive = TRUE)
> 
> modules <- data.frame(
+ "component" = c("data", "data", "plot", "plot"),
+ "long_component" = c("Load data", "Load data", "Plot data", "Plot data"),
+ "module" = c("user", "database", "histogram", "scatter"),
+ "long_module" = c("Upload your own data", "Query a database to obtain data",
+ "Plot the data as a histogram", "Plot the data as a scatterplot"),
+ "map" = c(TRUE, TRUE, FALSE, FALSE),
+ "result" = c(FALSE, FALSE, TRUE, TRUE),
+ "rmd" = c(TRUE, TRUE, TRUE, TRUE),
+ "save" = c(TRUE, TRUE, TRUE, TRUE),
+ "async" = c(TRUE, FALSE, FALSE, FALSE))
> 
> common_objects = c("raster", "histogram", "scatter")
> 
> create_template(path = td, name = "demo",
+ common_objects = common_objects, modules = modules,
+ author = "Simon E. H. Smart", include_map = TRUE, include_table = TRUE,
+ include_code = TRUE, install = FALSE)
Warning in readRDS(con) :
  URL 'https://CRAN.R-project.org/web/packages/packages.rds': Timeout of 60 seconds was reached
Error in readRDS(con) : cannot read from connection
Calls: create_template ... <Anonymous> -> as.data.frame -> read_CRAN_object -> readRDS
Execution halted
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:
    'app_server.R' 'function.R'
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:
    'show_group_enrichment.R'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.5/SIGN.Rcheck/00install.out' for details.
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:
    'p_sie.R' 'prp.R' 'siie.R'
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:
    'resilp.R'
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:
    'formula_interface.r' 'node_time_to_event.r'
File 'Sim.DiffProc/libs/x64/Sim.DiffProc.dll':
  Found non-API call to R: 'SET_TYPEOF'

Compiled code should not call non-API entry points in R.

See 'Writing portable packages' in the 'Writing R Extensions' manual,
and section 'Moving into C API compliance' for issues with the use of
non-API entry points.
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:
    'call_api.R' 'sfa_load__shares_outstanding.R' 'sfa_load_companies.R'
    'sfa_load_shareprices.R' 'sfa_load_statement.R'
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:
    'bootstrap-projection.R' 'bundle_sim.R' 'calc_coverage.R'
    'calc_rejection.R' 'utilities.R'
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:
    'anon.R'
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    simpleCache [0.0.1]
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:
    'markdown_block.R'
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:
    'imgocr.R'
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Version (Date)
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:
    'calculate-effect-sizes.R'
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:
    'debug.R'
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:
    'predict.sitar.R'
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:
    'SiZer.R'
Running examples in 'skellam-Ex.R' failed
The error most likely occurred in:

> ### Name: skellam.reg
> ### Title: Regression assuming a Skellam distribution
> ### Aliases: skellam.reg
> ### Keywords: Skellam regression
> 
> ### ** Examples
> 
> require('skellam')
> 
> set.seed(0)
> 
> x <- rnorm(1000)
> y1 <- rpois(1000, exp(1 + 1 * x) )
> y2 <- rpois(1000 , exp(-1 + 1 * x) )
> y <- y2 - y1
> skellam.reg(y, x)
Error in stats::optim(mod$estimate, skelreg, hessian = TRUE, control = list(maxit = 5000)) : 
  function cannot be evaluated at initial parameters
Calls: skellam.reg -> <Anonymous>
Execution halted
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:
    'ext-annotate_expr.R'
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:
    'add_ci_bounds_mc_power.R' 'calculate_gefficiency.R'
    'eval_design_custom_mc.R' 'eval_design_survival_mc.R' 'skprGUI.R'
Running 'abind.R' [0s]
  Comparing 'abind.Rout' to 'abind.Rout.save' ... OK
  Running 'apply.R' [0s]
  Comparing 'apply.Rout' to 'apply.Rout.save' ... OK
  Running 'crossprod.R' [0s]
  Comparing 'crossprod.Rout' to 'crossprod.Rout.save' ... OK
  Running 'dimgets.R' [0s]
  Running 'extract.R' [0s]
  Comparing 'extract.Rout' to 'extract.Rout.save' ... OK
  Running 'matrix.R' [0s]
  Comparing 'matrix.Rout' to 'matrix.Rout.save' ... OK
  Running 'matrix_dimnames.R' [0s]
  Comparing 'matrix_dimnames.Rout' to 'matrix_dimnames.Rout.save' ... OK
  Running 'rollup.R' [0s]
  Comparing 'rollup.Rout' to 'rollup.Rout.save' ... OK
  Running 'split.R' [0s]
  Comparing 'split.Rout' to 'split.Rout.save' ... OK
  Running 'ssa_valid.R' [0s]
  Comparing 'ssa_valid.Rout' to 'ssa_valid.Rout.save' ... OK
  Running 'stm.R' [0s]
  Comparing 'stm.Rout' to 'stm.Rout.save' ... OK
  Running 'stm_apply.R' [0s]
  Comparing 'stm_apply.Rout' to 'stm_apply.Rout.save' ... OK
  Running 'stm_rollup.R' [0s]
  Comparing 'stm_rollup.Rout' to 'stm_rollup.Rout.save' ...113a114,115
> _row_tsums: reduced 1 (3) zeros
> _row_tsums: 0.000s [0.000s/0.000s]
  Running 'stm_subassign.R' [0s]
  Comparing 'stm_subassign.Rout' to 'stm_subassign.Rout.save' ... OK
  Running 'stm_ttcrossprod.R' [0s]
  Comparing 'stm_ttcrossprod.Rout' to 'stm_ttcrossprod.Rout.save' ... OK
  Running 'stm_valid.R' [0s]
  Comparing 'stm_valid.Rout' to 'stm_valid.Rout.save' ... OK
  Running 'stm_zeros.R' [0s]
  Comparing 'stm_zeros.Rout' to 'stm_zeros.Rout.save' ... OK
  Running 'subassign.R' [0s]
  Comparing 'subassign.Rout' to 'subassign.Rout.save' ... OK
  Running 'util.R' [0s]
  Comparing 'util.Rout' to 'util.Rout.save' ... OK
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  'lseq'
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:
    'sk.R' 'sk_export.R' 'sk_index.R' 'sk_pars.R' 'sk_plot.R'
Check process probably crashed or hung up for 20 minutes ... killed
Most likely this happened in the example checks (?),
if not, ignore the following last lines of example output:
> cleanEx()
> nameEx("snvec")
> ### * snvec
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: snvec
> ### Title: Calculate Earth’s Obliquity and Precession in the Past
> ### Aliases: snvec
> 
> ### ** Examples
> 
> 
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()
> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
Time elapsed:  0.44 0.01 0.46 NA NA 
> grDevices::dev.off()
null device 
          1 
> ###
> ### Local variables: ***
> ### mode: outline-minor ***
> ### outline-regexp: "\\(> \\)?### [*]+" ***
> ### End: ***
> quit('no')
======== End of example output (where/before crash/hang up occured ?) ========
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:
    'PowerRelation.R' 'SocialRanking.R' 'copeland.R' 'generator.R'
    'makePowerRelationMonotonic.R'
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:
    'meteoReaders.R'
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:
    'objects.R'
File 'spaMM/libs/x64/spaMM.dll':
  Found non-API call to R: 'PRVALUE'

Compiled code should not call non-API entry points in R.

See 'Writing portable packages' in the 'Writing R Extensions' manual,
and section 'Moving into C API compliance' for issues with the use of
non-API entry points.
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:
    'available-data.R' 'convert.R' 'duckdb-helpers.R' 'get-zones.R'
    'internal-utils.R' 'quick-get.R'
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:
    'sim_functional_process.R'
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:
    'dnnModel.R' 'interGradientsDL.R' 'loadData.R' 'spatialClustering.R'
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:
    'kinetic_ising_ensemble.R'
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:
    'highest_concentration.R' 'plot_points.R'
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:
    'federov.R'
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Roadmap of specklestar package
Running 'testthat.R' [3s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(spectralGraphTopology)
  
  Attaching package: 'spectralGraphTopology'
  
  The following object is masked from 'package:stats':
  
      D
  
  > 
  > test_check("spectralGraphTopology")
  [ FAIL 3 | WARN 0 | SKIP 0 | PASS 43 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-learnGraphTopology.R:21:1'): (code run outside of `test_that()`) ──
  <purrr_error_indexed/rlang_error/error/condition>
  Error in `purrr::pmap(all_pars, build_and_run_test, desc = desc_stub, code = captured, 
      .interpret_glue = .interpret_glue)`: ℹ In index: 1.
  Caused by error:
  ! Failed to parse glue component
  Caused by error in `parse()`:
  ! <text>:1:1: unexpected ','
  1: ,
      ^
  ── Error ('test-learnSmoothSignalGraph.R:9:1'): (code run outside of `test_that()`) ──
  <purrr_error_indexed/rlang_error/error/condition>
  Error in `purrr::pmap(all_pars, build_and_run_test, desc = desc_stub, code = captured, 
      .interpret_glue = .interpret_glue)`: ℹ In index: 1.
  Caused by error:
  ! Failed to parse glue component
  Caused by error in `parse()`:
  ! <text>:1:1: unexpected ','
  1: ,
      ^
  ── Error ('test-operators.R:122:1'): (code run outside of `test_that()`) ───────
  <purrr_error_indexed/rlang_error/error/condition>
  Error in `purrr::pmap(all_pars, build_and_run_test, desc = desc_stub, code = captured, 
      .interpret_glue = .interpret_glue)`: ℹ In index: 1.
  Caused by error:
  ! Failed to parse glue component
  Caused by error in `parse()`:
  ! <text>:1:1: unexpected ','
  1: ,
      ^
  
  [ FAIL 3 | WARN 0 | SKIP 0 | PASS 43 ]
  Error: Test failures
  Execution halted
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:
    'analysis_age.R' 'analysis_alpha.R' 'analysis_helpers.R'
    'analysis_helpers_table.R' 'analysis_photo.R' 'analysis_radio.R'
    'analysis_setup.R' 'export_Output_Settings.R' 'export_download.R'
    'export_helpers.R' 'export_helpers_plot.R' 'export_helpers_table.R'
    'import_examples.R' 'import_examples_box.R'
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:
    'innprod.R' 'utils.R'
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:
    'import_qiime2_tax_table.R' 'import_sintax_tax_table.R'
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Feature Changes
Missing dependency on R >= 4.2.0 because package code uses the pipe
  placeholder syntax added in R 4.2.0.
  File(s) using such syntax:
    'addlearn_local.R'
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:
    'summary.spjctest.R' 'summary.spqtest.R'
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    updates of 10th May 2021
Missing dependency on R >= 4.2.0 because package code uses the pipe
  placeholder syntax added in R 4.2.0.
  File(s) using such syntax:
    'qts-prcomp.R'
Running examples in 'squat-Ex.R' failed
The error most likely occurred in:

> ### Name: autoplot.qtsclust
> ### Title: Plot for 'qtsclust' objects
> ### Aliases: autoplot.qtsclust
> 
> ### ** Examples
> 
> ## Don't show: 
> if (requireNamespace("ggplot2", quietly = TRUE)) (if (getRversion() >= "3.4") withAutoprint else force)({ # examplesIf
+ ## End(Don't show)
+ out <- kmeans(vespa64$igp[1:10], n_clusters = 2)
+ ggplot2::autoplot(out)
+ ## Don't show: 
+ }) # examplesIf
> out <- kmeans(vespa64$igp[1:10], n_clusters = 2)
Error in `check_option_compatibility()`:
! The L2 metric is neither dilation-invariant nor affine-invariant.
Backtrace:
     ▆
  1. ├─(if (getRversion() >= "3.4") withAutoprint else force)(...)
  2. │ └─base::source(...)
  3. │   ├─base::withVisible(eval(ei, envir))
  4. │   └─base::eval(ei, envir)
  5. │     └─base::eval(ei, envir)
  6. ├─squat::kmeans(vespa64$igp[1:10], n_clusters = 2)
  7. └─squat:::kmeans.qts_sample(vespa64$igp[1:10], n_clusters = 2)
  8.   └─fdacluster::fdakmeans(...)
  9.     └─fdacluster:::check_option_compatibility(...)
 10.       └─cli::cli_abort("The L2 metric is neither dilation-invariant nor affine-invariant.")
 11.         └─rlang::abort(...)
Execution halted
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:
    'classification.R' 'regression.R' 'staccuracy.R' 'unpackaged_utils.R'
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:
    'stamp.direction.r'
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:
    'stat_frequency.R'
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:
    'od_list.R' 'od_resource.R' 'od_utils.R' 'other_endpoints.R'
    'sc_data.R' 'schema.R' 'schema_uri.R' 'sdmx_table.R' 'table.R'
    'table_as_data_frame.R' 'table_json.R' 'table_meta.R' 'table_saved.R'
Found the following possibly unsafe calls:
File 'statnet.common/R/control.utilities.R':
  unlockBinding("snctrl", environment(snctrl))
  unlockBinding("snctrl", environment(update_my_snctrl))
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:
    'tables.R'
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:
    'coxph_methods.R' 'glm_methods.R' 'standardize_custom.R' 'utils.R'
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:
    'do_bma.R' 'evaluate_models.R' 'gam_model_probs.R'
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:
    'stm_diag.R' 'stm_effects.R' 'stm_network.R'
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:
    'Functions.R'
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:
    'sepstlppm.R' 'sepstppm.R'
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:
    'defStormsList.R'
Error(s) in re-building vignettes:
--- re-building 'stratifyR-vignette.Rmd' using rmarkdown

Quitting from lines 636-641 [unnamed-chunk-9] (stratifyR-vignette.Rmd)
Error: processing vignette 'stratifyR-vignette.Rmd' failed with diagnostics:
subscript out of bounds
--- failed re-building 'stratifyR-vignette.Rmd'

SUMMARY: processing the following file failed:
  'stratifyR-vignette.Rmd'

Error: Vignette re-building failed.
Execution halted
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:
    'apportion_inverse.R' 'apportion_polygon.R' 'apportion_web.R'
    'prep_reach_dist.R'
File 'stringfish/libs/x64/stringfish.dll':
  Found non-API calls to R: 'LEVELS', 'STDVEC_DATAPTR'

Compiled code should not call non-API entry points in R.

See 'Writing portable packages' in the 'Writing R Extensions' manual,
and section 'Moving into C API compliance' for issues with the use of
non-API entry points.
File 'stringi/libs/x64/stringi.dll':
  Found non-API calls to R: 'LEVELS', 'NAMED'

Compiled code should not call non-API entry points in R.

See 'Writing portable packages' in the 'Writing R Extensions' manual,
and section 'Moving into C API compliance' for issues with the use of
non-API entry points.
File 'stringmagic/libs/x64/stringmagic.dll':
  Found non-API call to R: 'STRING_PTR'

Compiled code should not call non-API entry points in R.

See 'Writing portable packages' in the 'Writing R Extensions' manual,
and section 'Moving into C API compliance' for issues with the use of
non-API entry points.
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:
    'generic_stroke.R' 'index_plot.R' 'mfi_calc.R' 'pase_calc.R'
efpFunctional: multiple local function definitions for 'plotProcess'
  with different formal arguments
mefp.efp: multiple local function definitions for 'computeEmpProc' with
  different formal arguments
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:
    'geom_glyph_ribbon.R'
File 'sumR/libs/x64/sumR.dll':
  Found non-API call to R: 'STRING_PTR'

Compiled code should not call non-API entry points in R.

See 'Writing portable packages' in the 'Writing R Extensions' manual,
and section 'Moving into C API compliance' for issues with the use of
non-API entry points.
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:
    'make.surv.R' 'plot_tranformed_km.R' 'utils_make_surv.R'
    'utils_plot_survHE.R'
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:
    'add.R' 'filters.R' 'get.R' 'helpers.R'
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:
    'scoreFull.R' 'scoreHalf.R' 'scoreLVCF.R' 'scoreNVCF.R'
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:
    'survival_class.R'
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:
    'suso_gql_helpers.R' 'suso_gql_uploadMap.R'
Check process probably crashed or hung up for 20 minutes ... killed
Most likely this happened in the example checks (?),
if not, ignore the following last lines of example output:
> 
> ### Name: wlasso.plot
> ### Title: Plot weighted LASSO object
> ### Aliases: wlasso.plot
> 
> ### ** Examples
> 
> data(simdata_lasso_binomial)
> mcv <- wlasso(data = simdata_lasso_binomial, col.y = "y", col.x = 1:50,
+               family = "binomial", cluster = "cluster", strata = "strata",
+               weights = "weights", method = "dCV", k=10, R=1)
> wlasso.plot(mcv)
> 
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()
> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
Time elapsed:  8.47 0.89 9.37 NA NA 
> grDevices::dev.off()
null device 
          1 
> ###
> ### Local variables: ***
> ### mode: outline-minor ***
> ### outline-regexp: "\\(> \\)?### [*]+" ***
> ### End: ***
> quit('no')
======== End of example output (where/before crash/hang up occured ?) ========
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Additional functions and data sets
    Amendments to functions
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    pre-release switchboard (2020 - 2021)
Error(s) in re-building vignettes:
--- re-building 'odesystem.Rmd' using rmarkdown

Quitting from lines 77-83 [unnamed-chunk-5] (odesystem.Rmd)
Error: processing vignette 'odesystem.Rmd' failed with diagnostics:
Error 1 occurred building shared library.
--- failed re-building 'odesystem.Rmd'

--- re-building 'quick_start.Rmd' using rmarkdown
--- finished re-building 'quick_start.Rmd'

SUMMARY: processing the following file failed:
  'odesystem.Rmd'

Error: Vignette re-building failed.
Execution halted
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:
    'class_methods.R' 'convert.R' 'freq.R' 'lilypond.R' 'lp_render.R'
    'midi.R' 'modes.R' 'notes.R' 'plot.R' 'scales.R' 'sf.R' 'snippet.R'
    'strings.R' 'transpose.R'
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:
    'fmt_class.R' 'jmvtab.b.R' 'tab.R' 'tab_classes.R' 'tab_xl.R'
    'utils.R'
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:
    'plott.R' 'read_cats_csv.R'
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:
    'add_lines.R' 'init.R' 'plots.R' 'report.R' 'tokenize.R'
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:
    'auth0.R' 'config.R' 'entra_id.R' 'google.R' 'utils.R'
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:
    'depreciation_interest.R' 'friction_period.R' 'nl_med_prices.R'
    'nl_pat_fam_prices.R' 'nl_ppp.R' 'nl_price_index.R'
    'nl_prod_oth_prices.R'
Running 'counting.R' [0s]
  Comparing 'counting.Rout' to 'counting.Rout.save' ...26a27,28
> counting ... 9 string(s) using 19 nodes [0.00s]
> writing  ... 16 strings [0.00s]
47a50
> counting ... 9 string(s) using 19 nodes [0.00s]
49a53,54
> counting ... 9 string(s) using 19 nodes [0.00s]
> writing  ... 16 strings [0.00s]
70a76,77
> counting ... 2 string(s) using 5 nodes [0.00s]
> writing  ... 2 strings [0.00s]
77a85,86
> counting ... 2 string(s) using 5 nodes [0.00s]
> writing  ... 4 strings [0.00s]
86a96,97
> counting ... 2 string(s) using 6 nodes [0.00s]
> writing  ... 5 strings [0.00s]
96a108,109
> counting ... 2 string(s) using 6 nodes [0.00s]
> writing  ... 5 strings [0.00s]
106a120
> counting ... 2 string(s) using 5 nodes [0.00s]
108a123,124
> counting ... 2 string(s) using 5 nodes [0.00s]
> writing  ... 2 strings [0.00s]
  Running 'counting_useBytes.R' [0s]
  Comparing 'counting_useBytes.Rout' to 'counting_useBytes.Rout.save' ...32a33,34
> counting ... 10 string(s) using 19 nodes [0.00s]
> writing  ... 19 strings [0.00s]
56a59
> counting ... 10 string(s) using 19 nodes [0.00s]
58a62,63
> counting ... 10 string(s) using 19 nodes [0.00s]
> writing  ... 19 strings [0.00s]
82a88,89
> counting ... 2 string(s) using 5 nodes [0.00s]
> writing  ... 2 strings [0.00s]
89a97,98
> counting ... 2 string(s) using 5 nodes [0.00s]
> writing  ... 5 strings [0.00s]
99a109,110
> counting ... 2 string(s) using 6 nodes [0.00s]
> writing  ... 6 strings [0.00s]
110a122,123
> counting ... 2 string(s) using 6 nodes [0.00s]
> writing  ... 6 strings [0.00s]
121a135
> counting ... 2 string(s) using 5 nodes [0.00s]
123a138,139
> counting ... 2 string(s) using 5 nodes [0.00s]
> writing  ... 2 strings [0.00s]
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:
    'parse_schema.R'
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:
    'format_code.R'
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:
    'tcplCytoPt.R' 'tcplFit2.R' 'tcplQueryAPI.R' 'tcplVarMat.R'
Running examples in 'teal.modules.clinical-Ex.R' failed
The error most likely occurred in:

> ### Name: tm_a_gee
> ### Title: teal Module: Generalized Estimating Equations (GEE) analysis
> ### Aliases: tm_a_gee
> 
> ### ** Examples
> 
> library(dplyr)

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

> data <- teal_data()
> data <- within(data, {
+   ADSL <- tmc_ex_adsl
+   ADQS <- tmc_ex_adqs %>%
+     filter(ABLFL != "Y" & ABLFL2 != "Y") %>%
+     mutate(
+       AVISIT = as.factor(AVISIT),
+       AVISITN = rank(AVISITN) %>%
+         as.factor() %>%
+         as.numeric() %>%
+         as.factor(),
+       AVALBIN = AVAL < 50 # Just as an example to get a binary endpoint.
+     ) %>%
+     droplevels()
+ })
> datanames <- c("ADSL", "ADQS")
> datanames(data) <- datanames
Warning: `datanames<-()` was deprecated in teal.data 0.7.0.
ℹ invalid to use `datanames()<-` or `names()<-` on an object of class
  `teal_data`. See ?names.teal_data
> join_keys(data) <- default_cdisc_join_keys[datanames]
> 
> app <- init(
+   data = data,
+   modules = modules(
+     tm_a_gee(
+       label = "GEE",
+       dataname = "ADQS",
+       aval_var = choices_selected("AVALBIN", fixed = TRUE),
+       id_var = choices_selected(c("USUBJID", "SUBJID"), "USUBJID"),
+       arm_var = choices_selected(c("ARM", "ARMCD"), "ARM"),
+       visit_var = choices_selected(c("AVISIT", "AVISITN"), "AVISIT"),
+       paramcd = choices_selected(
+         choices = value_choices(data[["ADQS"]], "PARAMCD", "PARAM"),
+         selected = "FKSI-FWB"
+       ),
+       cov_var = choices_selected(c("BASE", "AGE", "SEX", "BASE:AVISIT"), NULL)
+     )
+   )
+ )
Initializing tm_a_gee (prototype)
Error in as.list(data@env) : 
  no slot of name "env" for this object of class "teal_data"
Calls: init -> create_app_id -> as.list
Execution halted
Running examples in 'teal.modules.general-Ex.R' failed
The error most likely occurred in:

> ### Name: tm_a_pca
> ### Title: 'teal' module: Principal component analysis
> ### Aliases: tm_a_pca
> 
> ### ** Examples
> 
> library(teal.widgets)
> 
> # general data example
> data <- teal_data()
> data <- within(data, {
+   require(nestcolor)
+   USArrests <- USArrests
+ })
> 
> datanames(data) <- "USArrests"
Warning: `datanames<-()` was deprecated in teal.data 0.7.0.
ℹ invalid to use `datanames()<-` or `names()<-` on an object of class
  `teal_data`. See ?names.teal_data
> 
> app <- init(
+   data = data,
+   modules = modules(
+     tm_a_pca(
+       "PCA",
+       dat = data_extract_spec(
+         dataname = "USArrests",
+         select = select_spec(
+           choices = variable_choices(
+             data = data[["USArrests"]], c("Murder", "Assault", "UrbanPop", "Rape")
+           ),
+           selected = c("Murder", "Assault"),
+           multiple = TRUE
+         ),
+         filter = NULL
+       ),
+       ggplot2_args = ggplot2_args(
+         labs = list(subtitle = "Plot generated by PCA Module")
+       )
+     )
+   )
+ )
[INFO] 2025-02-15 05:43:18.6720 pid:37568 token:[] teal.modules.general Initializing tm_a_pca
Error in as.list(data@env) : 
  no slot of name "env" for this object of class "teal_data"
Calls: init -> create_app_id -> as.list
Execution halted
Running examples in 'teal-Ex.R' failed
The error most likely occurred in:

> ### Name: example_module
> ### Title: An example 'teal' module
> ### Aliases: example_module
> 
> ### ** Examples
> 
> app <- init(
+   data = teal_data(IRIS = iris, MTCARS = mtcars),
+   modules = example_module()
+ )
Error in as.list(data@env) : 
  no slot of name "env" for this object of class "teal_data"
Calls: init -> create_app_id -> as.list
Execution halted
Error(s) in re-building vignettes:
--- re-building 'adding-support-for-reporting.Rmd' using rmarkdown

Quitting from lines 106-112 [unnamed-chunk-4] (adding-support-for-reporting.Rmd)
Error: processing vignette 'adding-support-for-reporting.Rmd' failed with diagnostics:
no slot of name "env" for this object of class "teal_data"
--- failed re-building 'adding-support-for-reporting.Rmd'

--- re-building 'bootstrap-themes-in-teal.Rmd' using rmarkdown
--- finished re-building 'bootstrap-themes-in-teal.Rmd'

--- re-building 'creating-custom-modules.Rmd' using rmarkdown

Quitting from lines 174-183 [unnamed-chunk-4] (creating-custom-modules.Rmd)
Error: processing vignette 'creating-custom-modules.Rmd' failed with diagnostics:
no slot of name "env" for this object of class "teal_data"
--- failed re-building 'creating-custom-modules.Rmd'

--- re-building 'data-as-shiny-module.Rmd' using rmarkdown
--- finished re-building 'data-as-shiny-module.Rmd'

--- re-building 'filter-panel.Rmd' using rmarkdown
--- finished re-building 'filter-panel.Rmd'

--- re-building 'getting-started-with-teal.Rmd' using rmarkdown

Quitting from lines 33-52 [unnamed-chunk-1] (getting-started-with-teal.Rmd)
Error: processing vignette 'getting-started-with-teal.Rmd' failed with diagnostics:
no slot of name "env" for this object of class "teal_data"
--- failed re-building 'getting-started-with-teal.Rmd'

--- re-building 'including-data-in-teal-applications.Rmd' using rmarkdown
--- finished re-building 'including-data-in-teal-applications.Rmd'

--- re-building 'teal-options.Rmd' using rmarkdown
--- finished re-building 'teal-options.Rmd'

SUMMARY: processing the following files failed:
  'adding-support-for-reporting.Rmd' 'creating-custom-modules.Rmd'
  'getting-started-with-teal.Rmd'

Error: Vignette re-building failed.
Execution halted
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:
    'incidence_rate.R'
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:
    'georeference_overlay.R'
File 'testthat/libs/x64/testthat.dll':
  Found non-API calls to R: 'SET_BODY', 'SET_CLOENV', 'SET_FORMALS'

Compiled code should not call non-API entry points in R.

See 'Writing portable packages' in the 'Writing R Extensions' manual,
and section 'Moving into C API compliance' for issues with the use of
non-API entry points.
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:
    'utils-perm.R'
Error(s) in re-building vignettes:
--- re-building 'textplot-examples.Rnw' using knitr

Attaching package: 'igraph'

The following objects are masked from 'package:stats':

    decompose, spectrum

The following object is masked from 'package:base':

    union

trying URL 'https://raw.githubusercontent.com/jwijffels/udpipe.models.ud.2.5/master/inst/udpipe-ud-2.5-191206/english-ewt-ud-2.5-191206.udpipe'
Content type 'application/octet-stream' length 16309608 bytes (15.6 MB)
==================================================
downloaded 15.6 MB

trying URL 'https://raw.githubusercontent.com/jwijffels/udpipe.models.ud.2.5/master/inst/udpipe-ud-2.5-191206/dutch-alpino-ud-2.5-191206.udpipe'
Content type 'application/octet-stream' length 17047727 bytes (16.3 MB)
============================================
downloaded 14.6 MB


Quitting from lines 103-116 [unnamed-chunk-5] (textplot-examples.Rnw)
Error: processing vignette 'textplot-examples.Rnw' failed with diagnostics:
external pointer is not valid
--- failed re-building 'textplot-examples.Rnw'

SUMMARY: processing the following file failed:
  'textplot-examples.Rnw'

Error: Vignette re-building failed.
Execution halted
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:
    'nlp_build_chunks.R' 'sem_search_corpus.R'
Missing dependency on R >= 4.2.0 because package code uses the pipe
  placeholder syntax added in R 4.2.0.
  File(s) using such syntax:
    'textra.R'
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:
    'mock_tbl.R'
File 'tibble/libs/x64/tibble.dll':
  Found non-API call to R: 'SET_S4_OBJECT'

Compiled code should not call non-API entry points in R.

See 'Writing portable packages' in the 'Writing R Extensions' manual,
and section 'Moving into C API compliance' for issues with the use of
non-API entry points.
File 'tibblify/libs/x64/tibblify.dll':
  Found non-API calls to R: 'FRAME', 'HASHTAB', 'PRENV', 'PRVALUE',
    'R_PromiseExpr', 'Rf_findVarInFrame3', 'SETLENGTH', 'SET_BODY',
    'SET_CLOENV', 'SET_FORMALS', 'SET_GROWABLE_BIT', 'SET_TRUELENGTH',
    'STRING_PTR'

Compiled code should not call non-API entry points in R.

See 'Writing portable packages' in the 'Writing R Extensions' manual,
and section 'Moving into C API compliance' for issues with the use of
non-API entry points.
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:
    'explain_methods.R' 'fit.gets.R' 'fit.group_lasso.R' 'm.R'
    'post_process.R'
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:
    'import_fst_chunked.R' 'pkg_load.R' 'round0.R'
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:
    'functions_chr_int.R' 'gate_app.R' 'methods.R'
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Initial Release (v0.1.0)
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:
    'checks.R' 'compute-indexes.R' 'dimension-reduction.R'
    'distribution-fit.R' 'drought-indexes.R' 'init.R' 'normalise.R'
    'rescaling.R' 'swap-values.R' 'temporal-aggregation.R'
    'variable-transformation.R'
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Minor changes:
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:
    'tidymodl.R'
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:
    'tidy_plate.R'
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:
    'answer_as_key_value.R' 'answer_as_named_list.R' 'answer_as_text.R'
    'answer_using_sql.R' 'answer_using_tools.R' 'chat_history.R'
    'internal_extraction.R' 'internal_request_llm_provider.R'
    'internal_test_helpers.R' 'llm_providers.R' 'misc_llm_verify.R'
    'persistent_chat.R' 'send_prompt.R' 'tidyprompt.R'
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:
    'import_instruments.R' 'make_choose_all_table.R'
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:
    'describe_data.r' 'helper_functions.r' 'tidy_stats.R'
    'tidy_stats.afex.r' 'tidy_stats.brmsfit.r' 'tidy_stats.emmeans.R'
    'tidy_stats.irr.r' 'tidy_stats.lavaan.r' 'tidy_stats.lmerMod.r'
    'tidy_stats.nlme.r' 'tidy_stats.psych.r' 'tidy_stats.tidystats.r'
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:
    'tw_search.R'
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:
    'geom_weekly_timeslots.R'
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:
    'base-lenses.R'
Found the following significant warnings:
  tcltkimg.c:93:1: warning: function declaration isn't a prototype [-Wstrict-prototypes]
  tcltkimg.c:94:1: warning: function declaration isn't a prototype [-Wstrict-prototypes]
  tcltkimg.c:317:29: warning: format '%d' expects argument of type 'int', but argument 2 has type 'DWORD' {aka 'long unsigned int'} [-Wformat=]
See 'd:/Rcompile/CRANpkg/local/4.5/tkrplot.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 13.3.0'
Missing dependency on R >= 4.2.0 because package code uses the pipe
  placeholder syntax added in R 4.2.0.
  File(s) using such syntax:
    'position_diverge.R'
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:
    'Get_time_entries.R'
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:
    'dat_checks.R' 'setters_and_getters.R'
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:
    'response_builder.R'
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:
    'replace_leading_whitespace.R'
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:
    'predict.R' 'train.R' 'variables.R'
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:
    'tree_mesh.R' 'zzz.R'
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:
    'TreeMineR.R'
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:
    'get_troopdata.R'
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:
    'get_item_metadata.R' 'get_subscribed_metadata.R'
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  'log2console'
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:
    'calc_distance.R' 'reason_dataleaks.R' 'viz_dataleaks.R'
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:
    'benchmark.R' 'print.R'
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:
    'centrality.R' 'compare_gvar.R' 'posterior_plot.R'
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:
    'ts_maintune.R'
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:
    'berkowitz.R' 'dac.R' 'gmm.R' 'hongli.R' 'minzar.R' 'nyblom.R'
    'shortfall_de.R' 'signbias.R' 'var.R' 'var_cp.R'
Running examples in 'TukeyC-Ex.R' failed
The error most likely occurred in:

> ### Name: TukeyC
> ### Title: The TukeyC Test for Single Experiments
> ### Aliases: TukeyC TukeyC.default TukeyC.lm TukeyC.formula TukeyC.aovlist
> ###   TukeyC.lmerMod
> ### Keywords: package
> 
> ### ** Examples
> 
> ##
> ## Examples:Randomized Complete Block Design (RCBD)
> ## More details: demo(package='TukeyC')
> ##
> 
> ## The parameters can be: formula, aov, lm, aovlist and lmerMod
> 
> data(RCBD)
> 
> ## From: formula
> tk1 <- with(RCBD,
+             TukeyC(y ~ blk + tra,
+                    data=dfm,
+                    which='tra'))
Error in data.frame(means = aux_mt1, reps = reps) : 
  arguments imply differing number of rows: 0, 5
Calls: with ... TukeyC.formula -> TukeyC -> TukeyC.lm -> data.frame
Execution halted
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:
    'show_parliament.R' 'show_province_and_party.R'
File 'typetracer/libs/x64/typetracer.dll':
  Found non-API call to R: 'SET_BODY'

Compiled code should not call non-API entry points in R.

See 'Writing portable packages' in the 'Writing R Extensions' manual,
and section 'Moving into C API compliance' for issues with the use of
non-API entry points.
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    uktrans_get is fixed when start_date is used (#2)
    Extra layer of of NULL returns to fail gracefully with an informative message.
    Removed travis & appveyor and using gh_actions instead.
    Using gh-pages to create the pkgdown website.
    Create an app as vignette page to search with the help of uklr.
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:
    'readtextgrid.R'
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:
    'annotate_mf.R' 'annotate_mf_all.R'
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:
    'unm_summary.R'
Missing dependency on R >= 4.2.0 because package code uses the pipe
  placeholder syntax added in R 4.2.0.
  File(s) using such syntax:
    'available_version.R'
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:
    'intersection_powerset.R' 'pr.R'
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:
    'paste.R'
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_accuracy.R'
Found the following significant warnings:
  randutils.c:60:12: warning: function declaration isn't a prototype [-Wstrict-prototypes]
See 'd:/Rcompile/CRANpkg/local/4.5/uuid.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 13.3.0'
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:
    'benchmark_event.R' 'benchmark_score.R' 'benchmark_time.R'
    'compare_means_between_groups.R' 'compare_means_within_groups.R'
    'compare_rates_between_groups.R' 'compare_rates_within_groups.R'
    'get_concordant_discordant_pairs.R'
    'get_confidence_intervals_within_groups.R'
    'table_observed_expected.R' 'test_chisq_one.R' 'test_mcnemar.R'
    'test_n_1_prop.R' 'test_t.R' 'test_t_paired.R'
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:
    'datasets.R'
Check process probably crashed or hung up for 20 minutes ... killed
Most likely this happened in the example checks (?),
if not, ignore the following last lines of example output:

======== End of example output (where/before crash/hang up occured ?) ========
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:
    'vineCopulas.R'
File 'vctrs/libs/x64/vctrs.dll':
  Found non-API calls to R: 'FRAME', 'HASHTAB', 'LEVELS', 'PRENV',
    'PRVALUE', 'R_PromiseExpr', 'Rf_findVarInFrame3', 'SETLENGTH',
    'SET_BODY', 'SET_CLOENV', 'SET_ENCLOS', 'SET_FORMALS',
    'SET_GROWABLE_BIT', 'SET_S4_OBJECT', 'SET_TRUELENGTH',
    'STDVEC_DATAPTR', 'STRING_PTR', 'TRUELENGTH', 'UNSET_S4_OBJECT'

Compiled code should not call non-API entry points in R.

See 'Writing portable packages' in the 'Writing R Extensions' manual,
and section 'Moving into C API compliance' for issues with the use of
non-API entry points.
File 'versus/libs/x64/versus.dll':
  Found non-API call to R: 'STRING_PTR'

Compiled code should not call non-API entry points in R.

See 'Writing portable packages' in the 'Writing R Extensions' manual,
and section 'Moving into C API compliance' for issues with the use of
non-API entry points.
File 'vetr/libs/x64/vetr.dll':
  Found non-API call to R: 'SET_TYPEOF'

Compiled code should not call non-API entry points in R.

See 'Writing portable packages' in the 'Writing R Extensions' manual,
and section 'Moving into C API compliance' for issues with the use of
non-API entry points.
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:
    'functions_upload.R' 'mod_hidecan.R'
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:
    'knn_domain_score.R' 'mars_domain_score.R' 'nn_domain_score.R'
    'normalized_domain_plot.R' 'rf_domain_score.R' 'simple_domain_plot.R'
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:
    'viralmodel.R' 'viralpreds.R' 'viraltab.R' 'viralvis.R'
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:
    'glob_cub_vis.R' 'glob_knn_vis.R' 'glob_nn_vis.R' 'viralx_knn.R'
    'viralx_knn_glob.R' 'viralx_knn_shap.R' 'viralx_knn_vis.R'
    'viralx_mars.R' 'viralx_mars_shap.R' 'viralx_mars_vis.R'
    'viralx_nn.R' 'viralx_nn_glob.R' 'viralx_nn_shap.R' 'viralx_nn_vis.R'
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:
    'customiseText.R' 'datatableInternal.R' 'formatEstimateName.R'
    'formatEstimateValue.R' 'formatHeader.R' 'formatTable.R' 'fxTable.R'
    'gtTable.R' 'helperFunctions.R' 'mockResults.R' 'plot.R' 'tidy.R'
    'utilities.R' 'visOmopTable.R' 'visTable.R'
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    vortexRdata pre-1.0.3
File 'vroom/libs/x64/vroom.dll':
  Found non-API calls to R: 'SETLENGTH', 'SET_TRUELENGTH',
    'STDVEC_DATAPTR'

Compiled code should not call non-API entry points in R.

See 'Writing portable packages' in the 'Writing R Extensions' manual,
and section 'Moving into C API compliance' for issues with the use of
non-API entry points.
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:
    'walkscore.R'
File 'warp/libs/x64/warp.dll':
  Found non-API calls to R: 'Rf_findVarInFrame3', 'STRING_PTR'

Compiled code should not call non-API entry points in R.

See 'Writing portable packages' in the 'Writing R Extensions' manual,
and section 'Moving into C API compliance' for issues with the use of
non-API entry points.
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:
    'flextable.R'
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:
    'multi_scale.R'
Error(s) in re-building vignettes:
--- re-building 'WeightIt.Rmd' using rmarkdown_notangle
--- finished re-building 'WeightIt.Rmd'

--- re-building 'estimating-effects.Rmd' using rmarkdown_notangle

Quitting from lines 398-410 [unnamed-chunk-16] (estimating-effects.Rmd)
Error: processing vignette 'estimating-effects.Rmd' failed with diagnostics:
Assertion failed. One of the following must apply:
 * checkmate::check_character(hypothesis): Must comply to pattern '='
 * checkmate::check_numeric(hypothesis): Must be of type 'numeric', not 'character'
 * checkmate::check_formula(hypothesis): Must be a formula, not character
 * checkmate::check_matrix(hypothesis): Must be of type 'matrix', not 'character'
 * checkmate::check_function(hypothesis): Must be a function, not 'character'
 * checkmate::check_null(hypothesis): Must be NULL
--- failed re-building 'estimating-effects.Rmd'

--- re-building 'installing-packages.Rmd' using rmarkdown_notangle
--- finished re-building 'installing-packages.Rmd'

SUMMARY: processing the following file failed:
  'estimating-effects.Rmd'

Error: Vignette re-building failed.
Execution halted
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Major changes
    Minor changes
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:
    'plot_network.R'
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:
    'coords_from_words.R' 'get_available_languages.R'
    'words_from_coords.R'
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:
    'export.R' 'week.R'
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:
    'Cs.r' 'DI.R' 'GetTO.r' 'HAI.R' 'Lixn.R' 'conProcess.R'
    'ltraj_move2.R' 'move2_ltraj.R'
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:
    'general_gd.R' 'plot_gd.R' 'window_gd.R'
Running 'spelling.R' [0s]
  Running 'testthat.R' [24s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > require(testthat)
  Loading required package: testthat
  > test_check("wordmap")
  Loading required package: wordmap
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 115 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-textplot.R:14:5'): textplot_terms works with dictionary ──────
  `print(textplot_terms(wmp1, data_dictionary_LSD2015, max_highlighted = 10))` produced warnings.
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 115 ]
  Error: Test failures
  Execution halted
Found the following significant warnings:
  RSDTD.c:134:7: warning: 'xmlSkipBlankChars' is deprecated [-Wdeprecated-declarations]
  RSDTD.c:135:7: warning: 'xmlParseMarkupDecl' is deprecated [-Wdeprecated-declarations]
  RUtils.c:142:5: warning: 'xmlSubstituteEntitiesDefault' is deprecated [-Wdeprecated-declarations]
See 'd:/Rcompile/CRANpkg/local/4.5/XML.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 13.3.0'
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:
    'add_frag.R' 'data_frag.R' 'list_as_xml_document.R' 'read_fragment.R'
    'tag.R' 'write_xml.R' 'xml_fragment.R' 'xmlbuilder.R'
File 'yyjsonr/libs/x64/yyjsonr.dll':
  Found non-API calls to R: 'SETLENGTH', 'SET_GROWABLE_BIT',
    'SET_TRUELENGTH'

Compiled code should not call non-API entry points in R.

See 'Writing portable packages' in the 'Writing R Extensions' manual,
and section 'Moving into C API compliance' for issues with the use of
non-API entry points.
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:
    'zcta.R'
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:
    'cache_report.R' 'list_deposit.R'
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:
    'deposit_stats.R' 'scrap_stats.R'
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:
    'convert-jyear-legacy.R'
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:
    'notate.R'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
Package suggested but not available for checking: ‘pct’
Package which this enhances but not available for checking: ‘asreml’
Package suggested but not available for checking: ‘sharpshootR’
Package suggested but not available for checking: ‘arcgisbinding’
Package suggested but not available for checking: ‘ArchaeoData’
Packages suggested but not available for checking:
  'sfit', 'expectile', 'HaarSeg', 'mpcbs'
Package suggested but not available for checking: ‘asteRiskData’
File ‘audio/libs/audio.so’:
  Found non-API call to R: ‘R_checkActivity’

Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package suggested but not available for checking: ‘lixoftConnectors’
Depends: includes the non-default packages:
  'dplyr', 'glue', 'janitor', 'lubridate', 'readr', 'snakecase',
  'stringr'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Package suggested but not available for checking: ‘fdpbandsdata’
Package suggested but not available for checking: ‘ffbase’
Package suggested but not available for checking: ‘rrelaxiv’
Packages suggested but not available for checking: 'cmdstanr', 'blavsam'
Package suggested but not available for checking: ‘cmdstanr’
Packages suggested but not available for checking:
  'adiposerefdata', 'musclerefdata'
Running ‘testthat.R’ [7s/8s]
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/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  > library(box.lsp)
  > 
  > test_check("box.lsp")
  [ FAIL 1 | WARN 0 | SKIP 5 | PASS 2 ]
  
  ══ Skipped tests (5) ═══════════════════════════════════════════════════════════
  • On CRAN (5): 'test-lsp_aaa_regression.R:2:3',
    'test-lsp_completion_package_attach_list.R:2:3',
    'test-lsp_completion_package_three_dots.R:2:3',
    'test-lsp_completion_whole_package.R:2:3', 'test-signature.R:2:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-lsp_completion_package_attach_list.R:64:1'): completion of package attach list does not return non-attached functions ──
  <no_such_process/ps_error/error/condition>
  Error: Failed to send signal to some processes: 2655718 (???)
  Backtrace:
      ▆
   1. ├─withr (local) `<fn>`()
   2. └─client$process$kill_tree() at tests/testthat/helper-utils.R:84:7
   3.   └─processx:::process_kill_tree(self, private, grace, close_connections)
   4.     └─get("ps_kill_tree", asNamespace("ps"))(private$tree_id)
   5.       └─ps::ps_send_signal(procs, sig)
   6.         └─ps:::process_signal_result(p, res, "Failed to send signal to")
  
  [ FAIL 1 | WARN 0 | SKIP 5 | PASS 2 ]
  Error: Test failures
  Execution halted
Package suggested but not available for checking: ‘glmmADMB’
Package suggested but not available for checking: ‘orcutt’
Running ‘testthat.R’ [36s/48s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library("testthat")
  > 
  > test_check("btergm")
  Loading required package: btergm
  Registered S3 methods overwritten by 'btergm':
    method    from
    plot.gof  ergm
    print.gof ergm
  Package:  btergm
  Version:  1.10.12
  Date:     2024-03-31
  Authors:  Philip Leifeld (University of Manchester)
            Skyler J. Cranmer (The Ohio State University)
            Bruce A. Desmarais (Pennsylvania State University)
  
  [ FAIL 1 | WARN 2 | SKIP 8 | PASS 51 ]
  
  ══ Skipped tests (8) ═══════════════════════════════════════════════════════════
  • On CRAN (8): 'test-btergm.R:82:3', 'test-btergm.R:180:3',
    'test-btergm.R:197:3', 'test-data.R:4:3', 'test-interpret.R:4:3',
    'test-interpret.R:32:3', 'test-interpret.R:59:3', 'test-interpret.R:87:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-btergm.R:73:3'): offset argument in btergm works without composition change ──
  Error in `ergm::ergm.pl(nw, Clist.miss, model, theta.offset = c(rep(FALSE, 
      length(l$rhs.terms) - 1), TRUE), verbose = FALSE, control = control.ergm)`: VECTOR_ELT() can only be applied to a 'list', not a 'NULL'
  Backtrace:
      ▆
   1. ├─base::suppressWarnings(...) at test-btergm.R:73:3
   2. │ └─base::withCallingHandlers(...)
   3. └─btergm::btergm(...)
   4.   └─ergm::ergm.pl(...)
  
  [ FAIL 1 | WARN 2 | SKIP 8 | PASS 51 ]
  Error: Test failures
  Execution halted
Package suggested but not available for checking: ‘dimRed’
Package suggested but not available for checking: ‘ReGenesees’
Package suggested but not available for checking: ‘rnaturalearthhires’
Package suggested but not available for checking: ‘rkeops’
Package suggested but not available for checking: ‘darts’
Package suggested but not available for checking: ‘countreg’
Package unavailable to check Rd xrefs: ‘cmdstanr’
Package suggested but not available for checking: ‘entab’
Package suggested but not available for checking: ‘userfriendlyscience’
Package suggested but not available for checking: ‘monocle3’
Package suggested but not available for checking: ‘tobit1’
Package suggested but not available for checking: ‘HiCseg’
Package suggested but not available for checking: ‘PopGenome’
Package suggested but not available for checking: ‘disttree’
Package which this enhances but not available for checking: ‘rkward’
Package suggested but not available for checking: ‘bvpSolve’
Package suggested but not available for checking: ‘CAM’
Packages suggested but not available for checking: 'conosPanel', 'p2data'
File ‘curl/libs/curl.so’:
  Found non-API call to R: ‘R_new_custom_connection’

Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Running ‘spelling.R’ [0s/0s]
  Running ‘testthat.R’ [10s/74s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(curl)
  Using libcurl 8.12.1-DEV with GnuTLS/3.8.9
  > 
  > # Comply with CRAN policy: skip tests if no internet
  > if(curl::has_internet()){
  +   test_check("curl")
  + }
  This is libcurl version 8.12.1-DEV with GnuTLS/3.8.9 
  Using test server: https://hb.r-universe.dev 
  [ FAIL 2 | WARN 0 | SKIP 4 | PASS 252 ]
  
  ══ Skipped tests (4) ═══════════════════════════════════════════════════════════
  • On CRAN (4): 'test-idn.R:4:3', 'test-multi-download.R:14:3',
    'test-seek.R:2:3', 'test-winssl.R:2:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-multi.R:147:5'): total_con and multi_fdset ───────────────────
  length(c(fdset$reads, fdset$writes)) is not less than min(total_con, res$pending). Difference: 1
  ── Failure ('test-multi.R:164:5'): host_con and multi_fdset ────────────────────
  length(c(fdset$reads, fdset$writes)) is not less than min(host_con, res$pending). Difference: 1
  
  [ FAIL 2 | WARN 0 | SKIP 4 | PASS 252 ]
  Error: Test failures
  Execution halted
Package which this enhances but not available for checking: ‘RGtk2’
Packages which this enhances but not available for checking:
  'gurobi', 'rcbc'
Package suggested but not available for checking: ‘dartR.captive’
Package suggested but not available for checking: ‘choroplethr’
Package suggested but not available for checking: ‘SASxport’
Package suggested but not available for checking: ‘Rdonlp2’
Package suggested but not available for checking: ‘RDCOMClient’
Package which this enhances but not available for checking: ‘gurobi’
Package suggested but not available for checking: ‘gurobi’
Package which this enhances but not available for checking: ‘INLA’
Package suggested but not available for checking: ‘BOLTSSIRR’
Package suggested but not available for checking: ‘pkgmaker’
Package suggested but not available for checking: ‘dsBaseClient’
Packages suggested but not available for checking: 'dsBase', 'dsBaseClient'
Packages suggested but not available for checking: 'dsBaseClient', 'dsBase'
Package suggested but not available for checking: ‘lle’
Package suggested but not available for checking: ‘readxlsb’
The following files should probably not be installed:
  ‘econet.tex’

Consider the use of a .Rinstignore file: see ‘Writing R Extensions’,
or move the vignette sources from ‘inst/doc’ to ‘vignettes’.
Package suggested but not available for checking: ‘eggCountsExtra’
Package suggested but not available for checking: ‘epidict’
Package suggested but not available for checking: ‘taskscheduleR’
Found the following significant warnings:
  Rd warning: no hsearch.rds meta data for package ergm
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/ergm.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-14 (Debian 14.2.0-16) 14.2.0’
Package suggested but not available for checking: ‘ExactData’
Package suggested but not available for checking: ‘cec2013’
Package suggested but not available for checking: ‘exuberdata’
Missing link or links in Rd file 'fast.Rd':
  ‘[rgrass:readRAST]{rgrass::read_RAST()}’
  ‘[rgrass:readVECT]{rgrass::read_VECT()}’

See section 'Cross-references' in the 'Writing R Extensions' manual.
Package suggested but not available for checking: ‘coxKM’
Package suggested but not available for checking: ‘hasseDiagram’
Package suggested but not available for checking: ‘gridlayout’
Packages suggested but not available for checking:
  'nCDunnett', 'reliaR', 'STAR'
Package suggested but not available for checking: ‘fivethirtyeightdata’
Package unavailable to check Rd xrefs: ‘fivethirtyeightdata’
Package suggested but not available for checking: ‘bcp’
Package suggested but not available for checking: ‘RandomFields’
Package suggested but not available for checking: ‘dggrids’
Packages suggested but not available for checking:
  'extraTrees', 'foba', 'nodeHarvest', 'obliqueRF', 'penalizedLDA',
  'relaxo', 'rrlda'
Package suggested but not available for checking: ‘gputools’
Package suggested but not available for checking: ‘paleofire’
Package suggested but not available for checking: ‘gdxrrw’
Package suggested but not available for checking: ‘genderdata’
Package suggested but not available for checking: ‘geomarocdata’
Package suggested but not available for checking: ‘RandomFields’

Package which this enhances but not available for checking: ‘INLA’
Package suggested but not available for checking: ‘RGtk2’
Package suggested but not available for checking: ‘edmcr’
Package suggested but not available for checking: ‘colorfulVennPlot’
Package which this enhances but not available for checking: ‘HadoopStreaming’
Package suggested but not available for checking: ‘microViz’
Packages suggested but not available for checking: 'hubExamples', 'hubVis'
Package suggested but not available for checking: ‘hurricaneexposuredata’
Package suggested but not available for checking: ‘SparkR’
Package suggested but not available for checking: ‘icd’
Package suggested but not available for checking: ‘rggobi’
Package suggested but not available for checking: ‘IFCdata’
Package suggested but not available for checking: ‘accdata’
Package unavailable to check Rd xrefs: ‘INLA’
Package suggested but not available for checking: ‘surveyspec’
File ‘iotools/libs/iotools.so’:
  Found non-API calls to R: ‘R_GetConnection’, ‘R_ReadConnection’,
    ‘R_WriteConnection’, ‘Rf_StringFalse’, ‘Rf_StringTrue’,
    ‘Rf_isBlankString’

Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package suggested but not available for checking: ‘iucnrdata’
Package suggested but not available for checking: ‘locClass’
Packages suggested but not available for checking: 'gurobi', 'cplexAPI'
File ‘JavaGD/libs/JavaGD.so’:
  Found ‘__sprintf_chk’, possibly from ‘sprintf’ (C)
    Object: ‘jGDtalk.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package suggested but not available for checking: ‘clonevol’
Package suggested but not available for checking: ‘remMap’
Package suggested but not available for checking: ‘kanjistat.data’
Package suggested but not available for checking: ‘RGeostats’
Package suggested but not available for checking: ‘kadmin’
Packages suggested but not available for checking:
  'koRpus.lang.de', 'koRpus.lang.es', 'koRpus.lang.fr',
  'koRpus.lang.it', 'koRpus.lang.nl', 'koRpus.lang.pt',
  'koRpus.lang.ru'

Package which this enhances but not available for checking: ‘rkward’
Package suggested but not available for checking: ‘optpart’
Packages suggested but not available for checking:
  'gWidgets', 'gWidgetsRGtk2', 'RGtk2'
Package suggested but not available for checking: ‘scio’
Package suggested but not available for checking: ‘kerdiest’
Package suggested but not available for checking: ‘depth’
Packages suggested but not available for checking: 'lpjmlkit', 'quitte'
Package suggested but not available for checking: ‘marssTMB’
Package suggested but not available for checking: ‘traits’
Package suggested but not available for checking: ‘metaumbrella’
Package suggested but not available for checking: ‘mvPot’
Package suggested but not available for checking: ‘structSSI’
Package suggested but not available for checking: ‘microcontax.data’
Package unavailable to check Rd xrefs: ‘microcontax.data’
Package suggested but not available for checking: ‘midfielddata’
Package suggested but not available for checking: ‘wqs’
Package suggested but not available for checking: ‘mixRasch’
Packages suggested but not available for checking:
  'ueadata1', 'ueadata2', 'ueadata3', 'ueadata4', 'ueadata5',
  'ueadata6', 'ueadata7', 'ueadata8'
Package suggested but not available for checking: ‘mlr3proba’
Package suggested but not available for checking: ‘alstructure’

Packages which this enhances but not available for checking:
  'miraculix', 'RandomFieldsUtils', 'MoBPSmaps'
Package suggested but not available for checking: ‘ArchR’
Package suggested but not available for checking: ‘rglwidget’
Package suggested but not available for checking: ‘rTubeDB’
Package unavailable to check Rd xrefs: ‘rTubeDB’
Package suggested but not available for checking: ‘spatialClust’
Package suggested but not available for checking: ‘fastshp’
Packages which this enhances but not available for checking:
  'NGCHMDemoData', 'NGCHMSupportFiles'
Package which this enhances but not available for checking: ‘jpndistrict’
Packages suggested but not available for checking: 'Rvmmin', 'Rcgmin'
Package suggested but not available for checking: ‘simpar’
Package suggested but not available for checking: ‘openNLPmodels.en’
Found the following significant warnings:
  Rd warning: pkg_deps.Rd:40: missing link ‘parse_pkg_refs’
  Rd warning: pkg_download.Rd:53: missing link ‘parse_pkg_refs’
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/pak.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-14 (Debian 14.2.0-16) 14.2.0’
Package suggested but not available for checking: ‘CorShrink’
Package suggested but not available for checking: ‘PythonInR’
Package suggested but not available for checking: ‘DMwR’
Package suggested but not available for checking: ‘pinnacle.API’
Package suggested but not available for checking: ‘pmartRdata’
Package suggested but not available for checking: ‘pollimetrydata’
Packages suggested but not available for checking: 'gurobi', 'rcbc'
Packages suggested but not available for checking:
  'gurobi', 'rcbc', 'cplexAPI'
Packages suggested but not available for checking: 'cmdstanr', 'iwmm'
Package suggested but not available for checking: ‘cin’
Running examples in ‘ProtE-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: dianno
> ### Title: DIA NN proteomics data analysis
> ### Aliases: dianno
> 
> ### ** Examples
> 
> #Example of running the function with paths for two groups.
> # The file path is a placeholder, replace it with an actual file.
> 
> jittered.pg_matrix.tsv <- system.file("extdata", "report.pg_matrix.tsv", package = "ProtE")
> dianno(file = jittered.pg_matrix.tsv,
+        group_names = c("Healthy","Control"),
+        samples_per_group = c(5,5), filtering_value = 80)
The ProtE process starts now!
Error in grid.newpage() : 
  could not open file '/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/ProtE/extdata/ProtE_Analysis/Plots/meanSdPlot.bmp'
Calls: dianno
Execution halted
Package suggested but not available for checking: ‘rdt’
Package suggested but not available for checking: ‘spDataLarge’
Package suggested but not available for checking: ‘bootmlm’
Packages suggested but not available for checking: 'cairoDevice', 'RGtk2'
Depends: includes the non-default packages:
  'biclust', 'fabia', 'iBBiG', 'superbiclust', 'BcDiag', 'BicARE',
  's4vd', 'BiBitR'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Package suggested but not available for checking: ‘ROpenOffice’
Depends: includes the non-default packages:
  'IQCC', 'qcc', 'qicharts2', 'randtests', 'rmarkdown',
  'TeachingDemos', 'tseries'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Package suggested but not available for checking: ‘conics’
Package suggested but not available for checking: ‘dataui’
File ‘readxl/libs/readxl.so’:
  Found non-API calls to R: ‘Rf_StringFalse’, ‘Rf_StringTrue’

Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package suggested but not available for checking: ‘resourcecodedata’
Packages suggested but not available for checking:
  'mimic.demo', 'eicu.demo'
File ‘RInside/libs/RInside.so’:
  Found ‘srand’, possibly from ‘srand’ (C)
    Object: ‘RInside.o’
File ‘RInside/libs/RInside.so’:
  Found non-API calls to R: ‘R_CStackLimit’, ‘R_CleanTempDir’,
    ‘R_DefParams’, ‘R_ReplDLLinit’, ‘R_RunExitFinalizers’,
    ‘R_SetParams’, ‘R_SignalHandlers’, ‘R_TempDir’, ‘Rf_endEmbeddedR’,
    ‘Rf_initEmbeddedR’, ‘run_Rmainloop’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf.
Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Note: information on .o files is not available
File ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rJava/libs/rJava.so’:
  Found ‘_exit’, possibly from ‘_exit’ (C)
  Found ‘stderr’, possibly from ‘stderr’ (C)
  Found ‘stdout’, possibly from ‘stdout’ (C)
File ‘rJava/libs/rJava.so’:
  Found non-API calls to R: ‘R_CStackLimit’, ‘R_CStackStart’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.
Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Packages suggested but not available for checking:
  'DoubletFinder', 'RcppPlanc'
Package suggested but not available for checking: ‘bridgestan’
Note: information on .o files is not available
File ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rserve/libs/Rserve.so’:
  Found ‘exit’, possibly from ‘exit’ (C)
  Found ‘rand’, possibly from ‘rand’ (C)
  Found ‘random’, possibly from ‘random’ (C)
  Found ‘srandom’, possibly from ‘srandom’ (C)
  Found ‘stderr’, possibly from ‘stderr’ (C)
File ‘Rserve/libs/Rserve.so’:
  Found non-API calls to R: ‘R_Consolefile’, ‘R_Outputfile’,
    ‘R_TempDir’, ‘R_Visible’, ‘getInputHandler’, ‘ptr_R_Busy’,
    ‘ptr_R_ClearerrConsole’, ‘ptr_R_FlushConsole’, ‘ptr_R_ReadConsole’,
    ‘ptr_R_ResetConsole’, ‘ptr_R_ShowMessage’, ‘ptr_R_WriteConsole’,
    ‘ptr_R_WriteConsoleEx’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.
Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package suggested but not available for checking: ‘Vdgraph’
Package suggested but not available for checking: ‘nimbleAPT’
Running examples in ‘rusquant-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: getIPO
> ### Title: Get IPO calendar data from Investing.com
> ### Aliases: getIPO
> 
> ### ** Examples
> 
> getIPO(from=Sys.Date(),to=Sys.Date()+3)
Error in getIPO(from = Sys.Date(), to = Sys.Date() + 3) : 
  object 'Records' not found
Execution halted
Package which this enhances but not available for checking: ‘glmmADMB’
Package suggested but not available for checking: ‘rWCVPdata’
Package suggested but not available for checking: ‘networkTomography’
Packages which this enhances but not available for checking:
  'gurobi', 'pogs'
Packages suggested but not available for checking: 'MuSiC', 'seAMLessData'
Package suggested but not available for checking: ‘BPCells’
Packages suggested but not available for checking: 'BPCells', 'presto'
Package suggested but not available for checking: ‘rCOSA’
Package unavailable to check Rd xrefs: ‘rCOSA’
Running ‘testthat.R’ [2s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(shiny.info)
  > 
  > test_check("shiny.info")
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 24 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-lintr.R:1:1'): (code run outside of `test_that()`) ─────────────
  Error: Function with_defaults was deprecated in lintr version 3.0.0. Use linters_with_defaults or modify_defaults instead.
  Backtrace:
      ▆
   1. └─lintr::with_defaults(...) at test-lintr.R:1:1
   2.   └─lintr:::lintr_deprecated(...)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 24 ]
  Error: Test failures
  Execution halted
Package suggested but not available for checking: ‘uchardet’
Package which this enhances but not available for checking: ‘kmndirs’
Package suggested but not available for checking: ‘captioner’
Package suggested but not available for checking: ‘SciencesPo’
Package suggested but not available for checking: ‘NLMR’
Depends: includes the non-default packages:
  'spatstat.data', 'spatstat.univar', 'spatstat.geom',
  'spatstat.random', 'spatstat.explore', 'spatstat.model',
  'spatstat.linnet', 'spatstat', 'rpanel', 'tcltk'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Depends: includes the non-default packages:
  'spatstat.data', 'spatstat.sparse', 'spatstat.univar',
  'spatstat.geom', 'spatstat.random', 'spatstat.explore',
  'spatstat.model', 'spatstat.linnet', 'spatstat'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Depends: includes the non-default packages:
  'spatstat.data', 'spatstat.univar', 'spatstat.geom',
  'spatstat.random', 'spatstat.explore', 'spatstat.model'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Depends: includes the non-default packages:
  'spatstat.data', 'spatstat.univar', 'spatstat.sparse',
  'spatstat.geom', 'spatstat.random', 'spatstat.explore',
  'spatstat.model', 'spatstat'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Depends: includes the non-default packages:
  'spatstat.data', 'spatstat.univar', 'spatstat.geom',
  'spatstat.random', 'spatstat.explore', 'nlme', 'rpart'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Depends: includes the non-default packages:
  'spatstat.data', 'spatstat.univar', 'spatstat.geom',
  'spatstat.random', 'spatstat.explore', 'spatstat.model',
  'spatstat.linnet'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Running ‘testthat.R’ [4s/5s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(spectralGraphTopology)
  
  Attaching package: 'spectralGraphTopology'
  
  The following object is masked from 'package:stats':
  
      D
  
  > 
  > test_check("spectralGraphTopology")
  [ FAIL 3 | WARN 0 | SKIP 0 | PASS 43 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-learnGraphTopology.R:21:1'): (code run outside of `test_that()`) ──
  <purrr_error_indexed/rlang_error/error/condition>
  Error in `purrr::pmap(all_pars, build_and_run_test, desc = desc_stub, code = captured, 
      .interpret_glue = .interpret_glue)`: ℹ In index: 1.
  Caused by error:
  ! Failed to parse glue component
  Caused by error in `parse()`:
  ! <text>:1:1: unexpected ','
  1: ,
      ^
  ── Error ('test-learnSmoothSignalGraph.R:9:1'): (code run outside of `test_that()`) ──
  <purrr_error_indexed/rlang_error/error/condition>
  Error in `purrr::pmap(all_pars, build_and_run_test, desc = desc_stub, code = captured, 
      .interpret_glue = .interpret_glue)`: ℹ In index: 1.
  Caused by error:
  ! Failed to parse glue component
  Caused by error in `parse()`:
  ! <text>:1:1: unexpected ','
  1: ,
      ^
  ── Error ('test-operators.R:122:1'): (code run outside of `test_that()`) ───────
  <purrr_error_indexed/rlang_error/error/condition>
  Error in `purrr::pmap(all_pars, build_and_run_test, desc = desc_stub, code = captured, 
      .interpret_glue = .interpret_glue)`: ℹ In index: 1.
  Caused by error:
  ! Failed to parse glue component
  Caused by error in `parse()`:
  ! <text>:1:1: unexpected ','
  1: ,
      ^
  
  [ FAIL 3 | WARN 0 | SKIP 0 | PASS 43 ]
  Error: Test failures
  Execution halted
Running examples in ‘squat-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: autoplot.qtsclust
> ### Title: Plot for 'qtsclust' objects
> ### Aliases: autoplot.qtsclust
> 
> ### ** Examples
> 
> ## Don't show: 
> if (requireNamespace("ggplot2", quietly = TRUE)) (if (getRversion() >= "3.4") withAutoprint else force)({ # examplesIf
+ ## End(Don't show)
+ out <- kmeans(vespa64$igp[1:10], n_clusters = 2)
+ ggplot2::autoplot(out)
+ ## Don't show: 
+ }) # examplesIf
> out <- kmeans(vespa64$igp[1:10], n_clusters = 2)
Error in `check_option_compatibility()`:
! The L2 metric is neither dilation-invariant nor affine-invariant.
Backtrace:
     ▆
  1. ├─(if (getRversion() >= "3.4") withAutoprint else force)(...)
  2. │ └─base::source(...)
  3. │   ├─base::withVisible(eval(ei, envir))
  4. │   └─base::eval(ei, envir)
  5. │     └─base::eval(ei, envir)
  6. ├─squat::kmeans(vespa64$igp[1:10], n_clusters = 2)
  7. └─squat:::kmeans.qts_sample(vespa64$igp[1:10], n_clusters = 2)
  8.   └─fdacluster::fdakmeans(...)
  9.     └─fdacluster:::check_option_compatibility(...)
 10.       └─cli::cli_abort("The L2 metric is neither dilation-invariant nor affine-invariant.")
 11.         └─rlang::abort(...)
Execution halted
Package suggested but not available for checking: ‘starsdata’
Package suggested but not available for checking: ‘asreml’
Package suggested but not available for checking: ‘networksis’
Packages suggested but not available for checking: 'pct', 'rsgeo'
Package suggested but not available for checking: ‘StrathE2E2examples’
Package suggested but not available for checking: ‘STRaitRazoR’
Package suggested but not available for checking: ‘velocyto.R’
Package suggested but not available for checking: ‘extraTrees’
Packages suggested but not available for checking:
  'survHEinla', 'survHEhmc', 'INLA'
Package suggested but not available for checking: ‘swephRdata’
Packages suggested but not available for checking: 'sylly.de', 'sylly.es'
Package suggested but not available for checking: ‘odeintr’
Package suggested but not available for checking: ‘tashudata’
Dependence on R version ‘4.2.3’ not with patchlevel 0
Package which this enhances but not available for checking: ‘R2wd’
Running examples in ‘teal.modules.general-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: tm_a_pca
> ### Title: 'teal' module: Principal component analysis
> ### Aliases: tm_a_pca
> 
> ### ** Examples
> 
> library(teal.widgets)
> 
> # general data example
> data <- teal_data()
> data <- within(data, {
+   require(nestcolor)
+   USArrests <- USArrests
+ })
> 
> datanames(data) <- "USArrests"
Warning: `datanames<-()` was deprecated in teal.data 0.7.0.
ℹ invalid to use `datanames()<-` or `names()<-` on an object of class
  `teal_data`. See ?names.teal_data
> 
> app <- init(
+   data = data,
+   modules = modules(
+     tm_a_pca(
+       "PCA",
+       dat = data_extract_spec(
+         dataname = "USArrests",
+         select = select_spec(
+           choices = variable_choices(
+             data = data[["USArrests"]], c("Murder", "Assault", "UrbanPop", "Rape")
+           ),
+           selected = c("Murder", "Assault"),
+           multiple = TRUE
+         ),
+         filter = NULL
+       ),
+       ggplot2_args = ggplot2_args(
+         labs = list(subtitle = "Plot generated by PCA Module")
+       )
+     )
+   )
+ )
[INFO] 2025-02-15 06:11:13.0418 pid:1614518 token:[] teal.modules.general Initializing tm_a_pca
Error in as.list(data@env) : 
  no slot of name "env" for this object of class "teal_data"
Calls: init -> create_app_id -> as.list
Execution halted
Package suggested but not available for checking: ‘NetSwan’
Package suggested but not available for checking: ‘RClickhouse’
Packages suggested but not available for checking:
  'Rcampdf', 'tm.lexicon.GeneralInquirer'
Packages suggested but not available for checking:
  'RGtk2', 'gWidgets2RGtk2'
Package suggested but not available for checking: ‘toscaData’
Package suggested but not available for checking: ‘taxidata’
Error(s) in re-building vignettes:
  ...
--- re-building ‘mtram.Rnw’ using knitr
** Processing: figure/mtram-toenail_OR_2-1.png
1800x1200 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 260592 bytes
Input file size = 261042 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0
  zc = 9  zm = 8  zs = 1  f = 0
  zc = 1  zm = 8  zs = 2  f = 0
  zc = 9  zm = 8  zs = 3  f = 0
  zc = 9  zm = 8  zs = 0  f = 5		IDAT size = 234718
  zc = 9  zm = 8  zs = 1  f = 5
  zc = 1  zm = 8  zs = 2  f = 5
  zc = 9  zm = 8  zs = 3  f = 5
                               
Selecting parameters:
  zc = 9  zm = 8  zs = 0  f = 5		IDAT size = 234718

Output IDAT size = 234718 bytes (25874 bytes decrease)
Output file size = 234796 bytes (26246 bytes = 10.05% decrease)


Quitting from lines 1329-1334 [mtram-toenail_glmer_RS] (mtram.Rnw)
Error: processing vignette 'mtram.Rnw' failed with diagnostics:
PIRLS loop resulted in NaN value
--- failed re-building ‘mtram.Rnw’

--- re-building ‘tram.Rnw’ using knitr
--- finished re-building ‘tram.Rnw’

SUMMARY: processing the following file failed:
  ‘mtram.Rnw’

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘fwelnet’
Package suggested but not available for checking: ‘TreeDistData’
Packages suggested but not available for checking: 'rrelaxiv', 'gurobi'
Package which this enhances but not available for checking: ‘sl3’
Package suggested but not available for checking: ‘USA.state.boundaries.data’
Packages suggested but not available for checking: 'vaers', 'vaersND'
Package suggested but not available for checking: ‘prepr’
Packages suggested but not available for checking: 'iptools', 'rgeolocate'
Package suggested but not available for checking: ‘wordnetDicts’
Package suggested but not available for checking: ‘wmtsa’
Packages suggested but not available for checking:
  'RNRCS', 'metScanR', 'rnoaa'
Running ‘testthat.R’ [36s/46s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library("testthat")
  > 
  > test_check("btergm")
  Loading required package: btergm
  Registered S3 methods overwritten by 'btergm':
    method    from
    plot.gof  ergm
    print.gof ergm
  Package:  btergm
  Version:  1.10.12
  Date:     2024-03-31
  Authors:  Philip Leifeld (University of Manchester)
            Skyler J. Cranmer (The Ohio State University)
            Bruce A. Desmarais (Pennsylvania State University)
  
  [ FAIL 1 | WARN 2 | SKIP 8 | PASS 51 ]
  
  ══ Skipped tests (8) ═══════════════════════════════════════════════════════════
  • On CRAN (8): 'test-btergm.R:82:3', 'test-btergm.R:180:3',
    'test-btergm.R:197:3', 'test-data.R:4:3', 'test-interpret.R:4:3',
    'test-interpret.R:32:3', 'test-interpret.R:59:3', 'test-interpret.R:87:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-btergm.R:73:3'): offset argument in btergm works without composition change ──
  Error in `ergm::ergm.pl(nw, Clist.miss, model, theta.offset = c(rep(FALSE, 
      length(l$rhs.terms) - 1), TRUE), verbose = FALSE, control = control.ergm)`: VECTOR_ELT() can only be applied to a 'list', not a 'NULL'
  Backtrace:
      ▆
   1. ├─base::suppressWarnings(...) at test-btergm.R:73:3
   2. │ └─base::withCallingHandlers(...)
   3. └─btergm::btergm(...)
   4.   └─ergm::ergm.pl(...)
  
  [ FAIL 1 | WARN 2 | SKIP 8 | PASS 51 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘citmre.Rmd’ using rmarkdown

Quitting from lines 42-45 [plot_1] (citmre.Rmd)
Error: processing vignette 'citmre.Rmd' failed with diagnostics:
need finite 'xlim' values
--- failed re-building ‘citmre.Rmd’

SUMMARY: processing the following file failed:
  ‘citmre.Rmd’

Error: Vignette re-building failed.
Execution halted
Running ‘spelling.R’ [0s/0s]
  Running ‘testthat.R’ [11s/75s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(curl)
  Using libcurl 8.12.1-DEV with GnuTLS/3.8.9
  > 
  > # Comply with CRAN policy: skip tests if no internet
  > if(curl::has_internet()){
  +   test_check("curl")
  + }
  This is libcurl version 8.12.1-DEV with GnuTLS/3.8.9 
  Using test server: https://hb.r-universe.dev 
  [ FAIL 2 | WARN 0 | SKIP 4 | PASS 252 ]
  
  ══ Skipped tests (4) ═══════════════════════════════════════════════════════════
  • On CRAN (4): 'test-idn.R:4:3', 'test-multi-download.R:14:3',
    'test-seek.R:2:3', 'test-winssl.R:2:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-multi.R:147:5'): total_con and multi_fdset ───────────────────
  length(c(fdset$reads, fdset$writes)) is not less than min(total_con, res$pending). Difference: 1
  ── Failure ('test-multi.R:164:5'): host_con and multi_fdset ────────────────────
  length(c(fdset$reads, fdset$writes)) is not less than min(host_con, res$pending). Difference: 1
  
  [ FAIL 2 | WARN 0 | SKIP 4 | PASS 252 ]
  Error: Test failures
  Execution halted
Running ‘testthat.R’ [155s/193s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(GauPro)
  Loading required package: mixopt
  Loading required package: dplyr
  
  Attaching package: 'dplyr'
  
  The following object is masked from 'package:testthat':
  
      matches
  
  The following objects are masked from 'package:stats':
  
      filter, lag
  
  The following objects are masked from 'package:base':
  
      intersect, setdiff, setequal, union
  
  Loading required package: ggplot2
  Loading required package: splitfngr
  Loading required package: numDeriv
  Loading required package: rmarkdown
  Loading required package: tidyr
  
  Attaching package: 'tidyr'
  
  The following object is masked from 'package:testthat':
  
      matches
  
  > 
  > test_check("GauPro")
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 3087 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test_kernel_model_and_kernels.R:215:7'): Cts kernels 1D ───────────
  11 Product gpvmatches 9 / 39 seed = 318757 is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 3087 ]
  Error: Test failures
  Execution halted
Running examples in ‘ProtE-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: dianno
> ### Title: DIA NN proteomics data analysis
> ### Aliases: dianno
> 
> ### ** Examples
> 
> #Example of running the function with paths for two groups.
> # The file path is a placeholder, replace it with an actual file.
> 
> jittered.pg_matrix.tsv <- system.file("extdata", "report.pg_matrix.tsv", package = "ProtE")
> dianno(file = jittered.pg_matrix.tsv,
+        group_names = c("Healthy","Control"),
+        samples_per_group = c(5,5), filtering_value = 80)
The ProtE process starts now!
Error in grid.newpage() : 
  could not open file '/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/ProtE/extdata/ProtE_Analysis/Plots/meanSdPlot.bmp'
Calls: dianno
Execution halted
Running ‘testthat.R’ [4s/5s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(rjaf)
  > 
  > test_check("rjaf")
  Error: sample_fraction too small, no observations sampled. Ranger will EXIT now.
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 1 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-rjaf.R:7:3'): rjaf function computes correctly ─────────────────
  Error in `predict.ranger.forest(forest, data, predict.all, num.trees, type, 
      se.method, seed, num.threads, verbose, object$inbag.counts, 
      ...)`: User interrupt or internal error.
  Backtrace:
       ▆
    1. ├─rjaf::rjaf(...) at test-rjaf.R:7:3
    2. │ └─rjaf::residualize(data.trainest, y, vars, nfold)
    3. │   ├─... %>% dplyr::select(-fold)
    4. │   └─base::lapply(...)
    5. │     └─rjaf (local) FUN(X[[i]], ...)
    6. │       ├─stats::predict(...)
    7. │       └─ranger:::predict.ranger(...)
    8. │         ├─stats::predict(...)
    9. │         └─ranger:::predict.ranger.forest(...)
   10. ├─dplyr::select(., -fold)
   11. └─dplyr::bind_rows(.)
   12.   └─rlang::list2(...)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 1 ]
  Error: Test failures
  Execution halted
Note: information on .o files is not available
File ‘/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/rJava/libs/rJava.so’:
  Found ‘_exit’, possibly from ‘_exit’ (C)
  Found ‘stderr’, possibly from ‘stderr’ (C)
  Found ‘stdout’, possibly from ‘stdout’ (C)
File ‘rJava/libs/rJava.so’:
  Found non-API calls to R: ‘R_CStackLimit’, ‘R_CStackStart’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.
Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Note: information on .o files is not available
File ‘/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/Rserve/libs/Rserve.so’:
  Found ‘exit’, possibly from ‘exit’ (C)
  Found ‘rand’, possibly from ‘rand’ (C)
  Found ‘random’, possibly from ‘random’ (C)
  Found ‘srandom’, possibly from ‘srandom’ (C)
  Found ‘stderr’, possibly from ‘stderr’ (C)
File ‘Rserve/libs/Rserve.so’:
  Found non-API calls to R: ‘R_Consolefile’, ‘R_Outputfile’,
    ‘R_TempDir’, ‘R_Visible’, ‘getInputHandler’, ‘ptr_R_Busy’,
    ‘ptr_R_ClearerrConsole’, ‘ptr_R_FlushConsole’, ‘ptr_R_ReadConsole’,
    ‘ptr_R_ResetConsole’, ‘ptr_R_ShowMessage’, ‘ptr_R_WriteConsole’,
    ‘ptr_R_WriteConsoleEx’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.
Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Running ‘testthat.R’ [2s/4s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(shiny.info)
  > 
  > test_check("shiny.info")
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 24 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-lintr.R:1:1'): (code run outside of `test_that()`) ─────────────
  Error: Function with_defaults was deprecated in lintr version 3.0.0. Use linters_with_defaults or modify_defaults instead.
  Backtrace:
      ▆
   1. └─lintr::with_defaults(...) at test-lintr.R:1:1
   2.   └─lintr:::lintr_deprecated(...)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 24 ]
  Error: Test failures
  Execution halted
Running examples in ‘teal.modules.general-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: tm_a_pca
> ### Title: 'teal' module: Principal component analysis
> ### Aliases: tm_a_pca
> 
> ### ** Examples
> 
> library(teal.widgets)
> 
> # general data example
> data <- teal_data()
> data <- within(data, {
+   require(nestcolor)
+   USArrests <- USArrests
+ })
> 
> datanames(data) <- "USArrests"
Warning: `datanames<-()` was deprecated in teal.data 0.7.0.
ℹ invalid to use `datanames()<-` or `names()<-` on an object of class
  `teal_data`. See ?names.teal_data
> 
> app <- init(
+   data = data,
+   modules = modules(
+     tm_a_pca(
+       "PCA",
+       dat = data_extract_spec(
+         dataname = "USArrests",
+         select = select_spec(
+           choices = variable_choices(
+             data = data[["USArrests"]], c("Murder", "Assault", "UrbanPop", "Rape")
+           ),
+           selected = c("Murder", "Assault"),
+           multiple = TRUE
+         ),
+         filter = NULL
+       ),
+       ggplot2_args = ggplot2_args(
+         labs = list(subtitle = "Plot generated by PCA Module")
+       )
+     )
+   )
+ )
[INFO] 2025-02-16 05:57:23.2100 pid:1469022 token:[] teal.modules.general Initializing tm_a_pca
Error in as.list(data@env) : 
  no slot of name "env" for this object of class "teal_data"
Calls: init -> create_app_id -> as.list
Execution halted
Running examples in ‘webdav-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: webdav_download_file
> ### Title: Download a file from the WebDAV server
> ### Aliases: webdav_download_file
> 
> ### ** Examples
> 
> # Example usage with a public WebDAV server.
> library(magrittr)
> library(httr2)
> test_server <- "https://www.webdavserver.com/" %>%
+   request() %>%
+   req_retry(max_tries = 1, max_seconds = 2, backoff =  ~ 1) %>%
+   req_perform()
Error in `req_perform()`:
! Failed to perform HTTP request.
Caused by error in `curl::curl_fetch_memory()`:
! Timeout was reached [www.webdavserver.com]: Connection timed out after 10002 milliseconds
Backtrace:
    ▆
 1. ├─... %>% req_perform()
 2. └─httr2::req_perform(.)
 3.   └─base::tryCatch(...)
 4.     └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 5.       └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 6.         └─value[[3L]](cond)
Execution halted
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Package suggested but not available for checking: ‘metaboliteIDmapping’
installed size is  5.6Mb
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Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.4/AMISforInfectiousDiseases.Rcheck/00install.out’ for details.
installed size is 27.2Mb
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installed size is 22.1Mb
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Package suggested but not available for checking: ‘AffymetrixDataTestFiles’
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Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.4/BayesChange.Rcheck/00install.out’ for details.
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Error(s) in re-building vignettes:
--- re-building ‘article.Rnw’ using Sweave
Setting levels: control = No, case = Yes
Loading required package: glmnet
Loading required package: Matrix
Loaded glmnet 4.1-8
Setting levels: control = No, case = Yes
Setting levels: control = No, case = Yes
Loading required package: Biostrings
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm,
    append, as.data.frame, basename, cbind, colnames, dirname,
    do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rownames, sapply, setdiff, table, tapply, union, unique,
    unsplit, which.max, which.min

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following objects are masked from 'package:Matrix':

    expand, unname

The following object is masked from 'package:utils':

    findMatches

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: XVector
Loading required package: GenomeInfoDb

Attaching package: 'Biostrings'

The following object is masked from 'package:base':

    strsplit

Error: processing vignette 'article.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'article.tex' failed.
LaTeX errors:
!pdfTeX error: pdflatex (file bbm10): Font bbm10 at 657 not found
 ==> Fatal error occurred, no output PDF file produced!
--- failed re-building 'article.Rnw'

SUMMARY: processing the following file failed:
  'article.Rnw'

Error: Vignette re-building failed.
Execution halted
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Package suggested but not available for checking: ‘BRugs’
installed size is 118.5Mb
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installed size is 10.8Mb
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installed size is 166.1Mb
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installed size is  9.6Mb
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installed size is  5.6Mb
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installed size is  5.3Mb
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installed size is  6.2Mb
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installed size is  7.3Mb
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installed size is  9.0Mb
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installed size is  9.7Mb
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installed size is 13.6Mb
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installed size is  5.6Mb
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installed size is 19.2Mb
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installed size is  5.7Mb
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installed size is  5.5Mb
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installed size is 96.6Mb
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installed size is  6.7Mb
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installed size is  5.9Mb
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installed size is 19.0Mb
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installed size is  5.3Mb
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installed size is  5.6Mb
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installed size is  6.0Mb
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installed size is  8.2Mb
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installed size is  7.6Mb
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installed size is 48.1Mb
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installed size is  7.7Mb
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installed size is 54.9Mb
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installed size is 10.1Mb
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installed size is  6.6Mb
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installed size is 159.1Mb
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installed size is  7.5Mb
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installed size is  7.7Mb
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installed size is 33.9Mb
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installed size is  7.0Mb
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installed size is 13.6Mb
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installed size is  5.4Mb
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installed size is 189.6Mb
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installed size is 125.3Mb
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installed size is 65.1Mb
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installed size is 106.2Mb
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installed size is  6.8Mb
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installed size is 15.4Mb
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installed size is  5.2Mb
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installed size is  7.4Mb
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installed size is 10.3Mb
  sub-directories of 1Mb or more:
    data   8.4Mb
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Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.4/boodist.Rcheck/00install.out’ for details.
installed size is 396.6Mb
  sub-directories of 1Mb or more:
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installed size is 93.4Mb
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installed size is  5.1Mb
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installed size is  5.5Mb
  sub-directories of 1Mb or more:
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installed size is 52.7Mb
  sub-directories of 1Mb or more:
    libs  52.3Mb
installed size is  9.8Mb
  sub-directories of 1Mb or more:
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installed size is 45.3Mb
  sub-directories of 1Mb or more:
    libs  45.0Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
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installed size is  9.0Mb
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installed size is  5.4Mb
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Warning in file(open = "w+") :
  cannot open file '/var/folders/k4/0jwzxmln0nb8y6rkzprptb640000gq/T//RtmpC6o3yj/Rf95733f83f62c': No space left on device
Error in file(open = "w+") : cannot open the connection
Calls: <Anonymous> -> .load_package_quietly -> .try_quietly -> file
Execution halted
* using check arguments '--no-clean-on-error '
installed size is  8.4Mb
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installed size is 12.5Mb
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    lib          5.3Mb
installed size is 31.9Mb
  sub-directories of 1Mb or more:
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installed size is 110.8Mb
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    libs  109.9Mb
installed size is  9.1Mb
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installed size is 15.6Mb
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installed size is 173.7Mb
  sub-directories of 1Mb or more:
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installed size is  5.3Mb
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Package suggested but not available for checking: ‘org.Mm.eg.db’
installed size is  6.2Mb
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Error(s) in re-building vignettes:
--- re-building ‘bunching_examples.Rmd’ using rmarkdown
! kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 bbm10

! mkdir: ././opt/tex/texmf-var/fonts/pk/ljfour/public: Permission denied

! mktexpk: /opt/tex/texmf-dist/web2c/mktexdir /opt/tex/texmf-var/fonts/pk/ljfour/public/bbm failed.

! kpathsea: Appending font creation commands to missfont.log.

Error: processing vignette 'bunching_examples.Rmd' failed with diagnostics:
LaTeX failed to compile /Volumes/Builds/packages/big-sur-arm64/results/4.4/bunching.Rcheck/vign_test/bunching/vignettes/bunching_examples.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See bunching_examples.log for more info.
--- failed re-building ‘bunching_examples.Rmd’

--- re-building ‘bunching_theory.Rmd’ using rmarkdown
! kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 bbm10

! mkdir: ././opt/tex/texmf-var/fonts/pk/ljfour/public: Permission denied

! mktexpk: /opt/tex/texmf-dist/web2c/mktexdir /opt/tex/texmf-var/fonts/pk/ljfour/public/bbm failed.

! kpathsea: Appending font creation commands to missfont.log.

Error: processing vignette 'bunching_theory.Rmd' failed with diagnostics:
LaTeX failed to compile /Volumes/Builds/packages/big-sur-arm64/results/4.4/bunching.Rcheck/vign_test/bunching/vignettes/bunching_theory.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See bunching_theory.log for more info.
--- failed re-building ‘bunching_theory.Rmd’

SUMMARY: processing the following files failed:
  ‘bunching_examples.Rmd’ ‘bunching_theory.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  8.3Mb
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installed size is 22.4Mb
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installed size is 133.6Mb
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installed size is 20.2Mb
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installed size is 129.4Mb
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installed size is 56.6Mb
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installed size is 11.9Mb
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installed size is 63.7Mb
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installed size is  9.9Mb
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installed size is  7.4Mb
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Package suggested but not available for checking: ‘batchelor’
installed size is  6.2Mb
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installed size is  5.1Mb
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installed size is 10.6Mb
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installed size is  8.1Mb
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installed size is 49.1Mb
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installed size is 12.2Mb
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installed size is  5.6Mb
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installed size is 22.3Mb
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installed size is  5.4Mb
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installed size is 20.2Mb
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installed size is  6.6Mb
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installed size is  7.1Mb
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installed size is  7.5Mb
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installed size is 53.8Mb
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installed size is  5.1Mb
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installed size is  6.3Mb
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installed size is 167.8Mb
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installed size is  5.2Mb
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installed size is 18.1Mb
  sub-directories of 1Mb or more:
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installed size is 22.1Mb
  sub-directories of 1Mb or more:
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installed size is 24.5Mb
  sub-directories of 1Mb or more:
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installed size is  6.1Mb
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installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   5.5Mb
installed size is 15.1Mb
  sub-directories of 1Mb or more:
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installed size is 17.5Mb
  sub-directories of 1Mb or more:
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installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
Package suggested but not available for checking: ‘pbdMPI’
installed size is  9.2Mb
  sub-directories of 1Mb or more:
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Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.4/chartreview.Rcheck/00install.out’ for details.
Running examples in ‘checkmate-Ex.R’ failed
The error most likely occurred in:

> ### Name: checkDataTable
> ### Title: Check if an argument is a data table
> ### Aliases: checkDataTable check_data_table assertDataTable
> ###   assert_data_table testDataTable test_data_table expect_data_table
> 
> ### ** Examples
> 
> library(data.table)
Error in library(data.table) : there is no package called ‘data.table’
Execution halted
installed size is  5.5Mb
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installed size is 18.0Mb
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installed size is  8.0Mb
  sub-directories of 1Mb or more:
    doc       5.7Mb
    extdata   2.1Mb
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    R         2.8Mb
    extdata   4.3Mb
Packages required but not available:
  'TxDb.Hsapiens.UCSC.hg38.knownGene',
  'TxDb.Hsapiens.UCSC.hg19.knownGene',
  'TxDb.Mmusculus.UCSC.mm10.knownGene'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.8Mb
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installed size is  7.1Mb
  sub-directories of 1Mb or more:
    data   1.8Mb
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installed size is  7.5Mb
  sub-directories of 1Mb or more:
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installed size is 21.2Mb
  sub-directories of 1Mb or more:
    libs  20.9Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    doc    3.5Mb
    libs   1.2Mb
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    libs   9.3Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    extdata   5.3Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   3.4Mb
    doc    1.8Mb
installed size is 48.6Mb
  sub-directories of 1Mb or more:
    extdata  48.5Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc   4.3Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
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installed size is 18.4Mb
  sub-directories of 1Mb or more:
    libs  16.5Mb
installed size is 38.1Mb
  sub-directories of 1Mb or more:
    libs  36.0Mb
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    libs  11.3Mb
Packages suggested but not available for checking:
  'monocle3', 'SharedObject'
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.4/clusterMI.Rcheck/00install.out’ for details.
installed size is 18.0Mb
  sub-directories of 1Mb or more:
    libs  17.3Mb
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    libs   8.0Mb
installed size is 84.4Mb
  sub-directories of 1Mb or more:
    libs  83.9Mb
installed size is 19.5Mb
  sub-directories of 1Mb or more:
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Package suggested but not available for checking: ‘moe430a.db’
installed size is 17.3Mb
  sub-directories of 1Mb or more:
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installed size is  6.2Mb
  sub-directories of 1Mb or more:
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installed size is 10.1Mb
  sub-directories of 1Mb or more:
    libs   9.2Mb
installed size is 41.1Mb
  sub-directories of 1Mb or more:
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Package suggested but not available for checking: ‘BSgenome.Hsapiens.UCSC.hg19’
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc       3.2Mb
    extdata   1.7Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
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installed size is  5.6Mb
  sub-directories of 1Mb or more:
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    help   1.9Mb
installed size is 10.1Mb
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installed size is 22.3Mb
  sub-directories of 1Mb or more:
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    libs  19.2Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc       2.6Mb
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installed size is 66.7Mb
  sub-directories of 1Mb or more:
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installed size is  7.0Mb
  sub-directories of 1Mb or more:
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installed size is 16.2Mb
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installed size is  7.0Mb
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installed size is  5.1Mb
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installed size is 35.0Mb
  sub-directories of 1Mb or more:
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Packages suggested but not available for checking:
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installed size is 11.2Mb
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installed size is 19.7Mb
  sub-directories of 1Mb or more:
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installed size is  6.5Mb
  sub-directories of 1Mb or more:
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installed size is 101.0Mb
  sub-directories of 1Mb or more:
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installed size is  7.2Mb
  sub-directories of 1Mb or more:
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installed size is  6.1Mb
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installed size is  5.7Mb
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installed size is  7.8Mb
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installed size is  5.6Mb
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installed size is  5.0Mb
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Package suggested but not available for checking: ‘ProData’
installed size is 18.0Mb
  sub-directories of 1Mb or more:
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installed size is  7.2Mb
  sub-directories of 1Mb or more:
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installed size is  7.4Mb
  sub-directories of 1Mb or more:
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installed size is  8.3Mb
  sub-directories of 1Mb or more:
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installed size is 13.5Mb
  sub-directories of 1Mb or more:
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installed size is  5.1Mb
  sub-directories of 1Mb or more:
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installed size is  5.9Mb
  sub-directories of 1Mb or more:
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Package suggested but not available for checking: ‘testthat’
installed size is  5.5Mb
  sub-directories of 1Mb or more:
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installed size is  6.9Mb
  sub-directories of 1Mb or more:
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installed size is  8.2Mb
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installed size is 15.9Mb
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installed size is  7.1Mb
  sub-directories of 1Mb or more:
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installed size is  5.3Mb
  sub-directories of 1Mb or more:
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installed size is 10.4Mb
  sub-directories of 1Mb or more:
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    libs   6.9Mb
installed size is  5.4Mb
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installed size is  6.0Mb
  sub-directories of 1Mb or more:
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installed size is 50.2Mb
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Package suggested but not available for checking: ‘BSgenome.Scerevisiae.UCSC.sacCer3’
installed size is  6.5Mb
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Package suggested but not available for checking: ‘EnsDb.Hsapiens.v86’
installed size is 29.3Mb
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installed size is  6.8Mb
  sub-directories of 1Mb or more:
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installed size is 13.1Mb
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installed size is  5.8Mb
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installed size is  8.1Mb
  sub-directories of 1Mb or more:
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installed size is  8.6Mb
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installed size is 201.7Mb
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Package which this enhances but not available for checking: ‘pbdMPI’
installed size is  8.1Mb
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Error(s) in re-building vignettes:
--- re-building ‘intro.Rmd’ using rmarkdown



Quitting from lines 48-52 [unnamed-chunk-2] (intro.Rmd)
Execution halted
--- re-building ‘windows.Rmd’ using rmarkdown
--- finished re-building ‘windows.Rmd’

SUMMARY: processing the following file failed:
  ‘intro.Rmd’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ...* using check arguments '--no-clean-on-error '
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installed size is  5.0Mb
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Packages which this enhances but not available for checking:
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installed size is 10.5Mb
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installed size is 27.8Mb
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installed size is  5.8Mb
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installed size is  6.3Mb
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installed size is 36.3Mb
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installed size is  5.1Mb
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installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   4.5Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    java   7.5Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    doc    2.7Mb
    libs   4.6Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   7.2Mb
LazyData DB of 5.1 MB without LazyDataCompression set
  See §1.1.6 of 'Writing R Extensions'
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   1.8Mb
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    doc    3.0Mb
    libs   7.3Mb
installed size is 84.0Mb
  sub-directories of 1Mb or more:
    libs  83.6Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    data   1.9Mb
    libs   5.2Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    libs   7.3Mb
installed size is 29.0Mb
  sub-directories of 1Mb or more:
    libs  28.9Mb
installed size is 15.2Mb
  sub-directories of 1Mb or more:
    libs  14.5Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   3.9Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    doc    3.1Mb
    help   1.3Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc   5.8Mb
installed size is 17.7Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    help   2.2Mb
    libs  13.0Mb
installed size is 44.6Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs  42.4Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    doc       4.8Mb
    extdata   2.1Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
prepare_Rd: package version mismatch: 
glmmTMB was built with TMB package version 1.9.15
Current TMB package version is 1.9.16
Please re-install glmmTMB from source or restore original ‘TMB’ package (see '?reinstalling' for more information)
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    doc    1.8Mb
    help   1.6Mb
    libs   3.6Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
Package suggested but not available for checking: ‘OSAT’
Packages which this enhances but not available for checking:
  'gurobi', 'Rcplex'
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    extdata   2.1Mb
    libs      2.3Mb
installed size is 17.9Mb
  sub-directories of 1Mb or more:
    libs  17.8Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data          1.8Mb
    htmlwidgets   3.7Mb
installed size is 19.5Mb
  sub-directories of 1Mb or more:
    libs  18.7Mb
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs   7.5Mb
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.4/DFD.Rcheck/00install.out’ for details.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs   3.7Mb
Package suggested but not available for checking: ‘zFPKM’
installed size is 16.9Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs  15.0Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   4.2Mb
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    doc  10.8Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
installed size is 48.1Mb
  sub-directories of 1Mb or more:
    libs  47.5Mb
installed size is 97.2Mb
  sub-directories of 1Mb or more:
    libs  96.4Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc       1.5Mb
    extdata   4.2Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   3.4Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    libs   6.9Mb
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    libs  10.1Mb
installed size is 16.2Mb
  sub-directories of 1Mb or more:
    include  15.8Mb
installed size is 47.9Mb
  sub-directories of 1Mb or more:
    libs  47.2Mb
installed size is 51.2Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    libs  47.6Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   4.7Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
    libs   2.3Mb
installed size is 20.9Mb
  sub-directories of 1Mb or more:
    doc    6.7Mb
    libs  13.5Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    R         3.0Mb
    data      2.0Mb
    extdata   2.3Mb
Package unavailable to check Rd xrefs: ‘doMPI’
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    assets   2.9Mb
    doc      2.2Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    libs   7.2Mb
installed size is 12.4Mb
  sub-directories of 1Mb or more:
    libs  12.2Mb
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    libs   9.2Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc   2.5Mb
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    data   1.6Mb
    libs   7.7Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc   4.9Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   5.4Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    appinformation   4.1Mb
installed size is 85.0Mb
  sub-directories of 1Mb or more:
    libs  84.3Mb
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    libs   5.1Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    htmlwidgets   5.5Mb
installed size is 13.2Mb
  sub-directories of 1Mb or more:
    libs  13.1Mb
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs   5.6Mb
installed size is 49.4Mb
  sub-directories of 1Mb or more:
    libs  48.6Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    extdata   5.6Mb
installed size is 13.1Mb
  sub-directories of 1Mb or more:
    R      3.6Mb
    data   8.0Mb
    doc    1.1Mb
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    data   2.5Mb
    doc    1.4Mb
    libs   2.9Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   3.9Mb
    libs   1.1Mb
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    libs   7.9Mb
installed size is 12.7Mb
  sub-directories of 1Mb or more:
    libs       11.3Mb
    shiny_app   1.1Mb
installed size is 18.3Mb
  sub-directories of 1Mb or more:
    R      2.5Mb
    libs  15.5Mb
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.4/eatRep.Rcheck/00install.out’ for details.
installed size is 13.5Mb
  sub-directories of 1Mb or more:
    doc    1.3Mb
    libs  11.7Mb
installed size is 224.4Mb
  sub-directories of 1Mb or more:
    doc     3.5Mb
    libs  219.9Mb
installed size is 13.4Mb
  sub-directories of 1Mb or more:
    libs  13.3Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   1.7Mb
    doc    1.7Mb
    libs   2.0Mb
installed size is 92.2Mb
  sub-directories of 1Mb or more:
    help   2.7Mb
    libs  89.1Mb
installed size is 41.6Mb
  sub-directories of 1Mb or more:
    libs  41.4Mb
installed size is 106.4Mb
  sub-directories of 1Mb or more:
    libs  105.7Mb
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    doc       5.1Mb
    extdata   5.1Mb
installed size is 162.9Mb
  sub-directories of 1Mb or more:
    libs  162.8Mb
installed size is 50.5Mb
  sub-directories of 1Mb or more:
    libs  49.5Mb
installed size is 39.2Mb
  sub-directories of 1Mb or more:
    libs  39.1Mb
installed size is 85.7Mb
  sub-directories of 1Mb or more:
    libs  84.5Mb
Packages required but not available:
  'IlluminaHumanMethylationEPICanno.ilm10b4.hg19',
  'IlluminaHumanMethylation450kanno.ilmn12.hg19'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    libs   2.2Mb
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    libs   8.5Mb
installed size is 18.1Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs  15.9Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   3.9Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    emoji_fonts   6.4Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   7.2Mb
Package suggested but not available for checking: ‘Rmpi’
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    R      3.0Mb
    help   4.1Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc    2.9Mb
    help   2.5Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   3.2Mb
    libs   2.8Mb
installed size is 147.3Mb
  sub-directories of 1Mb or more:
    doc     1.5Mb
    libs  143.3Mb
installed size is 17.2Mb
  sub-directories of 1Mb or more:
    libs  14.7Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs   4.1Mb
Package suggested but not available for checking: ‘gcspikelite’
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   4.2Mb
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    doc    1.3Mb
    libs   3.2Mb
installed size is 14.1Mb
  sub-directories of 1Mb or more:
    doc  13.3Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    libs   2.3Mb
installed size is 40.0Mb
  sub-directories of 1Mb or more:
    libs  39.6Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc    1.3Mb
    libs   3.6Mb
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.4/evesim.Rcheck/00install.out’ for details.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    R     2.0Mb
    doc   2.9Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data      2.5Mb
    doc       1.6Mb
    extdata   2.4Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
installed size is 14.1Mb
  sub-directories of 1Mb or more:
    exiftool  14.0Mb
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    libs   9.2Mb
installed size is 13.6Mb
  sub-directories of 1Mb or more:
    libs  13.0Mb
installed size is 31.4Mb
  sub-directories of 1Mb or more:
    libs  30.7Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    doc    2.5Mb
    libs   4.7Mb
installed size is 11.8Mb
  sub-directories of 1Mb or more:
    libs  11.5Mb
Error(s) in re-building vignettes:
--- re-building ‘jss.Rmd’ using rmarkdown
This is pdfTeX, Version 3.141592653-2.6-1.40.24 (TeX Live 2022) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode

kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+57/600 --dpi 657 bbm10
mkdir: ././opt/tex/texmf-var/fonts/pk/ljfour/public: Permission denied
mktexpk: /opt/tex/texmf-dist/web2c/mktexdir /opt/tex/texmf-var/fonts/pk/ljfour/public/bbm failed.
kpathsea: Appending font creation commands to missfont.log.
This is pdfTeX, Version 3.141592653-2.6-1.40.24 (TeX Live 2022) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode

kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+57/600 --dpi 657 bbm10
mkdir: ././opt/tex/texmf-var/fonts/pk/ljfour/public: Permission denied
mktexpk: /opt/tex/texmf-dist/web2c/mktexdir /opt/tex/texmf-var/fonts/pk/ljfour/public/bbm failed.
kpathsea: Appending font creation commands to missfont.log.
This is pdfTeX, Version 3.141592653-2.6-1.40.24 (TeX Live 2022) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode

kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+57/600 --dpi 657 bbm10
mkdir: ././opt/tex/texmf-var/fonts/pk/ljfour/public: Permission denied
mktexpk: /opt/tex/texmf-dist/web2c/mktexdir /opt/tex/texmf-var/fonts/pk/ljfour/public/bbm failed.
kpathsea: Appending font creation commands to missfont.log.
Error: processing vignette 'jss.Rmd' failed with diagnostics:
LaTeX failed to compile /Volumes/Builds/packages/big-sur-arm64/results/4.4/fairadapt.Rcheck/vign_test/fairadapt/vignettes/jss.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips.
--- failed re-building ‘jss.Rmd’

SUMMARY: processing the following file failed:
  ‘jss.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  6.3Mb
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    help   1.2Mb
installed size is 11.8Mb
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installed size is  5.2Mb
  sub-directories of 1Mb or more:
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    help   1.3Mb
installed size is 18.2Mb
  sub-directories of 1Mb or more:
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    help   1.8Mb
    libs  12.6Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
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    libs   2.5Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
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    help   1.7Mb
installed size is 45.4Mb
  sub-directories of 1Mb or more:
    libs  44.8Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    images   3.1Mb
    libs     2.9Mb
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    data   4.5Mb
    doc    1.1Mb
    libs   2.8Mb
installed size is 50.4Mb
  sub-directories of 1Mb or more:
    libs  50.2Mb
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    libs   7.5Mb
installed size is 50.2Mb
  sub-directories of 1Mb or more:
    libs  49.8Mb
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    data   5.6Mb
    libs   2.6Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    libs   7.6Mb
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    libs  11.1Mb
installed size is 35.2Mb
  sub-directories of 1Mb or more:
    libs  35.1Mb
installed size is 14.5Mb
  sub-directories of 1Mb or more:
    libs  14.4Mb
installed size is 15.8Mb
  sub-directories of 1Mb or more:
    data  15.7Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   3.9Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs   5.7Mb
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    data   4.7Mb
    libs   5.1Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    libs   2.2Mb
installed size is 48.2Mb
  sub-directories of 1Mb or more:
    libs  47.8Mb
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    libs   7.8Mb
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    libs   9.8Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    doc    3.9Mb
installed size is 14.9Mb
  sub-directories of 1Mb or more:
    R      1.9Mb
    doc    1.5Mb
    help   2.1Mb
    libs   8.9Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    libs   7.5Mb
installed size is 40.2Mb
  sub-directories of 1Mb or more:
    libs  38.5Mb
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    libs  11.0Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc   2.7Mb
installed size is 17.0Mb
  sub-directories of 1Mb or more:
    libs  16.9Mb
installed size is 25.5Mb
  sub-directories of 1Mb or more:
    libs  25.1Mb
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   4.8Mb
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs   9.5Mb
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    libs   7.2Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   5.8Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    libs   1.2Mb
installed size is 61.9Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    libs  57.5Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    doc    1.8Mb
    help   1.1Mb
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    R         5.6Mb
    doc       2.1Mb
    extdata   2.1Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc   4.9Mb
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   7.1Mb
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    libs  11.2Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   2.6Mb
    libs   2.5Mb
installed size is 48.5Mb
  sub-directories of 1Mb or more:
    libs  47.1Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data      1.4Mb
    extdata   3.8Mb
installed size is 29.9Mb
  sub-directories of 1Mb or more:
    lib   10.6Mb
    libs  18.9Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc   4.0Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   6.1Mb
installed size is 12.5Mb
  sub-directories of 1Mb or more:
    libs  11.5Mb
installed size is 11.8Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    doc    3.6Mb
    libs   5.0Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    help   2.3Mb
    libs   3.2Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    libs   7.5Mb
installed size is 315.7Mb
  sub-directories of 1Mb or more:
    libs  314.5Mb
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    doc   9.1Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    R   7.9Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    R      3.1Mb
    help   1.3Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    htmlwidgets   3.9Mb
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    libs   7.4Mb
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    libs   7.3Mb
installed size is 32.1Mb
  sub-directories of 1Mb or more:
    libs  31.4Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    fonts   6.6Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    fonts   6.1Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   3.4Mb
installed size is 23.3Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    doc    1.1Mb
    help   1.0Mb
    libs  18.1Mb
installed size is 12.3Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    help   2.6Mb
    libs   6.1Mb
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   6.2Mb
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    libs   8.6Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    R   6.6Mb
installed size is 105.4Mb
  sub-directories of 1Mb or more:
    data   5.0Mb
    doc    1.8Mb
    libs  97.5Mb
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.4/fRLR.Rcheck/00install.out’ for details.
installed size is 55.2Mb
  sub-directories of 1Mb or more:
    libs  54.4Mb
Packages suggested but not available for checking:
  'extraTrees', 'foba', 'nodeHarvest', 'obliqueRF', 'relaxo', 'rrlda'
Package suggested but not available for checking: ‘RTCGA.rnaseq’
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    libs   9.7Mb
Running ‘spelling.R’ [0s/0s]
  Running ‘testthat.R’ [8s/9s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(fs)
  > 
  > test_check("fs")
  [ FAIL 1 | WARN 0 | SKIP 3 | PASS 3482 ]
  
  ══ Skipped tests (3) ═══════════════════════════════════════════════════════════
  Error in base::nchar(wide_chars$test, type = "width") : 
    cannot open file '/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/cli/R/sysdata.rdb': No such file or directory
  Calls: test_check ... unicode_pre -> setup_unicode_width_fix -> <Anonymous>
  Execution halted
Error(s) in re-building vignettes:
--- re-building ‘function-comparisons.Rmd’ using rmarkdown
Error: processing vignette 'function-comparisons.Rmd' failed with diagnostics:
there is no package called ‘rlang’
--- failed re-building ‘function-comparisons.Rmd’

SUMMARY: processing the following file failed:
  ‘function-comparisons.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 20.4Mb
  sub-directories of 1Mb or more:
    libs  19.7Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   7.1Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    help   4.6Mb
installed size is 55.0Mb
  sub-directories of 1Mb or more:
    libs  54.8Mb
installed size is 25.8Mb
  sub-directories of 1Mb or more:
    doc    2.0Mb
    libs  22.2Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
Package which this enhances but not available for checking: ‘doMPI’
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    doc   7.4Mb
installed size is 36.2Mb
  sub-directories of 1Mb or more:
    doc   31.8Mb
    libs   3.8Mb
installed size is 11.8Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs   9.7Mb
installed size is 112.1Mb
  sub-directories of 1Mb or more:
    libs  111.6Mb
installed size is 96.4Mb
  sub-directories of 1Mb or more:
    extdata   1.6Mb
    libs     92.8Mb
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    libs   6.5Mb
installed size is 16.8Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs  15.5Mb
installed size is 278.2Mb
  sub-directories of 1Mb or more:
    L8NY18    2.2Mb
    libs    274.7Mb
installed size is 256.6Mb
  sub-directories of 1Mb or more:
    extdata    1.3Mb
    libs     253.7Mb
installed size is 12.9Mb
  sub-directories of 1Mb or more:
    libs  11.9Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    extdata   3.8Mb
installed size is 18.0Mb
  sub-directories of 1Mb or more:
    libs  17.5Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    doc       1.5Mb
    extdata   3.4Mb
    libs      1.4Mb
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs   9.3Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc    2.0Mb
    libs   4.3Mb
installed size is 46.8Mb
  sub-directories of 1Mb or more:
    libs  46.1Mb
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    extdata   3.0Mb
    libs      4.0Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
installed size is 105.4Mb
  sub-directories of 1Mb or more:
    R       2.1Mb
    libs  103.0Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc       2.1Mb
    extdata   3.5Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc    1.3Mb
    libs   4.9Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    help   1.3Mb
    libs   4.4Mb
installed size is 22.3Mb
  sub-directories of 1Mb or more:
    R        12.0Mb
    extdata   6.3Mb
    help      3.8Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   1.9Mb
    libs   2.0Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
installed size is 111.8Mb
  sub-directories of 1Mb or more:
    doc     1.2Mb
    libs  109.4Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc   5.7Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
installed size is 33.2Mb
  sub-directories of 1Mb or more:
    libs  32.9Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    extdata   4.9Mb
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    doc       3.0Mb
    extdata   1.6Mb
    libs      3.0Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    libs   7.3Mb
installed size is 22.3Mb
  sub-directories of 1Mb or more:
    help   1.2Mb
    libs  20.4Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   4.2Mb
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    R     1.1Mb
    doc   7.3Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    doc    2.3Mb
    help   1.1Mb
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    doc        1.1Mb
    help       2.4Mb
    testdata   4.8Mb
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    doc    3.9Mb
    libs   2.2Mb
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    extdata   9.1Mb
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    doc    9.5Mb
    help   1.1Mb
installed size is 18.0Mb
  sub-directories of 1Mb or more:
    Giac  17.9Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    libs   7.1Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   4.9Mb
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    libs   8.4Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc    3.1Mb
    help   3.0Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   3.4Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   6.7Mb
Packages suggested but not available for checking:
  'BSgenome.Hsapiens.UCSC.hg18.masked',
  'BSgenome.Hsapiens.UCSC.hg19.masked'
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    libs   7.4Mb
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    libs   9.8Mb
installed size is 207.6Mb
  sub-directories of 1Mb or more:
    doc     1.9Mb
    libs  204.4Mb
installed size is 25.1Mb
  sub-directories of 1Mb or more:
    libs  24.3Mb
installed size is 93.0Mb
  sub-directories of 1Mb or more:
    libs  92.3Mb
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    libs  10.0Mb
installed size is 67.4Mb
  sub-directories of 1Mb or more:
    libs  66.2Mb
installed size is 160.0Mb
  sub-directories of 1Mb or more:
    libs  158.6Mb
installed size is 45.7Mb
  sub-directories of 1Mb or more:
    libs  45.5Mb
installed size is 98.1Mb
  sub-directories of 1Mb or more:
    doc             1.3Mb
    libs           91.6Mb
    test_data       2.3Mb
    vignette_data   2.1Mb
installed size is 33.6Mb
  sub-directories of 1Mb or more:
    libs  31.7Mb
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    doc    1.3Mb
    libs   9.9Mb
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    libs  10.9Mb
Packages suggested but not available for checking:
  'SeqArray', 'SeqVarTools'
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc   5.0Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    libs   6.9Mb
Packages suggested but not available for checking:
  'org.Pt.eg.db', 'org.Mmu.eg.db', 'org.Mm.eg.db', 'org.Rn.eg.db',
  'org.Dr.eg.db', 'org.Dm.eg.db', 'org.Ce.eg.db'
installed size is  5.6Mb
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    data   4.2Mb
    libs   1.0Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
installed size is 47.0Mb
  sub-directories of 1Mb or more:
    i     43.6Mb
    libs   2.6Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    R   7.0Mb
installed size is 35.8Mb
  sub-directories of 1Mb or more:
    libs  35.4Mb
installed size is 197.5Mb
  sub-directories of 1Mb or more:
    libs  196.5Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs   6.3Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    doc    3.5Mb
installed size is 56.3Mb
  sub-directories of 1Mb or more:
    libs  53.8Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    help   5.2Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
installed size is 15.9Mb
  sub-directories of 1Mb or more:
    libs  15.8Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    help   2.2Mb
    libs   3.9Mb
installed size is 15.7Mb
  sub-directories of 1Mb or more:
    data   3.9Mb
    libs  10.5Mb
installed size is 18.5Mb
  sub-directories of 1Mb or more:
    libs  16.1Mb
installed size is 59.8Mb
  sub-directories of 1Mb or more:
    libs  59.6Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R     2.0Mb
    doc   2.8Mb
installed size is 39.0Mb
  sub-directories of 1Mb or more:
    libs  38.5Mb
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    libs                     5.6Mb
    supplementary_material   3.1Mb
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    libs   9.3Mb
installed size is 13.3Mb
  sub-directories of 1Mb or more:
    libs  12.8Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    extdata   5.0Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs   2.4Mb
installed size is 12.3Mb
  sub-directories of 1Mb or more:
    libs  11.9Mb
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    doc    4.1Mb
    libs   3.4Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    R      2.8Mb
    data   1.1Mb
    help   2.8Mb
installed size is 68.1Mb
  sub-directories of 1Mb or more:
    libs  67.2Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   4.9Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    extdata   2.5Mb
    libs      2.3Mb
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    htmlwidgets   8.2Mb
installed size is 27.9Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    libs  25.6Mb
installed size is 275.7Mb
  sub-directories of 1Mb or more:
    R       2.1Mb
    help    1.0Mb
    java  272.1Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs    1.5Mb
    shiny   4.3Mb
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    HaDeX   4.0Mb
    doc     4.0Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   3.0Mb
    libs   2.5Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   3.2Mb
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    data   2.9Mb
    doc    2.4Mb
    libs   6.2Mb
installed size is 11.9Mb
  sub-directories of 1Mb or more:
    libs  11.4Mb
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    libs   9.2Mb
installed size is 85.4Mb
  sub-directories of 1Mb or more:
    libs  84.0Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    R         3.1Mb
    extdata   1.3Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc   5.2Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc           2.7Mb
    htmlwidgets   2.8Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   4.7Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    data   7.3Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    data   5.8Mb
    libs   4.8Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    libs   6.7Mb
installed size is 36.2Mb
  sub-directories of 1Mb or more:
    libs  35.2Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   4.9Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    doc    3.7Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc   5.3Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc   5.1Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   5.2Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    R      1.6Mb
    doc    1.9Mb
    libs   1.8Mb
installed size is 23.8Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs  19.7Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    extdata   2.6Mb
    libs      3.3Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    libs   7.1Mb
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    libs  10.4Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   3.8Mb
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    highlight   1.0Mb
    libs        7.5Mb
Found the following significant warnings:
  clang: warning: argument unused during compilation: '-mpopcnt' [-Wunused-command-line-argument]
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.4/highs.Rcheck/00install.out’ for details.
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
installed size is 56.2Mb
  sub-directories of 1Mb or more:
    libs  56.1Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data   1.0Mb
    libs   4.9Mb
installed size is 83.3Mb
  sub-directories of 1Mb or more:
    libs  82.8Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    help   2.3Mb
    libs   2.6Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    libs   4.0Mb
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    libs  10.6Mb
installed size is 95.3Mb
  sub-directories of 1Mb or more:
    libs  93.8Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    doc    4.0Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    app   1.7Mb
    doc   3.3Mb
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    libs   9.6Mb
installed size is 16.9Mb
  sub-directories of 1Mb or more:
    libs  16.6Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    data   7.8Mb
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    libs   7.4Mb
installed size is 90.0Mb
  sub-directories of 1Mb or more:
    libs  89.5Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   3.5Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    doc    2.3Mb
    help   1.1Mb
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    libs   8.6Mb
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    libs   8.5Mb
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    dict   1.5Mb
    libs   5.4Mb
installed size is 50.5Mb
  sub-directories of 1Mb or more:
    libs  49.9Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    extdata   5.5Mb
    libs      1.7Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    extdata   4.8Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    extdata   5.7Mb
installed size is 23.5Mb
  sub-directories of 1Mb or more:
    libs  23.3Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    doc   6.3Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc    2.8Mb
    libs   1.8Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   6.7Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    doc    1.7Mb
    libs   1.0Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   5.6Mb
Packages suggested but not available for checking:
  'BSgenome.Hsapiens.1000genomes.hs37d5',
  'BSgenome.Hsapiens.UCSC.hg38', 'BSgenome.Mmusculus.UCSC.mm10'
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    libs   7.6Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   5.6Mb
installed size is 19.3Mb
  sub-directories of 1Mb or more:
    libs  17.8Mb
Package suggested but not available for checking: ‘mixAK’
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    data   3.0Mb
    libs   5.5Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc    2.5Mb
    libs   2.6Mb
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.4/idem.Rcheck/00install.out’ for details.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   5.0Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    libs   4.6Mb
installed size is 23.8Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    doc    1.2Mb
    help   2.9Mb
    libs  17.1Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
installed size is 33.0Mb
  sub-directories of 1Mb or more:
    data      1.4Mb
    doc       3.7Mb
    extdata   1.0Mb
    include   3.3Mb
    libs     22.9Mb
installed size is 21.7Mb
  sub-directories of 1Mb or more:
    libs   10.5Mb
    share  10.2Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   5.5Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    data   3.4Mb
    doc    1.6Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R   5.1Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    java   4.2Mb
installed size is 93.2Mb
  sub-directories of 1Mb or more:
    libs  92.5Mb
installed size is 18.3Mb
  sub-directories of 1Mb or more:
    doc    4.1Mb
    libs  12.1Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
installed size is 12.3Mb
  sub-directories of 1Mb or more:
    libs  11.0Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   5.8Mb
installed size is 39.5Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs  38.1Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   7.1Mb
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    doc   9.7Mb
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    libs  10.7Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data           1.4Mb
    libs           1.8Mb
    shiny-server   1.0Mb
File ‘iotools/libs/iotools.so’:
  Found non-API calls to R: ‘R_GetConnection’, ‘R_ReadConnection’,
    ‘R_WriteConnection’

Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
installed size is 13.5Mb
  sub-directories of 1Mb or more:
    libs  12.2Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc   5.2Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    libs   8.1Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc       2.0Mb
    extdata   3.3Mb
Warning in file(outFile, "wt") :
  cannot open file 'IsoplotR-Ex.R': No space left on device
Error in file(outFile, "wt") : cannot open the connection
Execution halted
installed size is 93.5Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    doc    2.3Mb
    libs  88.2Mb
installed size is 15.5Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs  13.6Mb
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.4/IVPP.Rcheck/00install.out’ for details.
installed size is 19.7Mb
  sub-directories of 1Mb or more:
    art_profiles   1.5Mb
    libs          17.3Mb
installed size is 35.7Mb
  sub-directories of 1Mb or more:
    libs  35.2Mb
Packages suggested but not available for checking: 'lfa', 'gcatest'
File ‘JavaGD/libs/JavaGD.so’:
  Found ‘_sprintf’, possibly from ‘sprintf’ (C)
    Object: ‘jGDtalk.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    htmlwidgets   5.7Mb
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    doc       2.3Mb
    extdata   4.0Mb
    help      2.0Mb
installed size is 102.5Mb
  sub-directories of 1Mb or more:
    libs  101.1Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    extdata   5.5Mb
    libs      1.7Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
installed size is 12.8Mb
  sub-directories of 1Mb or more:
    libs  12.5Mb
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    libs   9.6Mb
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    libs   7.2Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
installed size is 40.0Mb
  sub-directories of 1Mb or more:
    libs  39.5Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    libs   5.4Mb
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    R      4.0Mb
    i18n   6.7Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    libs   3.9Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   3.6Mb
installed size is 34.2Mb
  sub-directories of 1Mb or more:
    libs  32.8Mb
installed size is 22.5Mb
  sub-directories of 1Mb or more:
    libs  22.0Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs   3.9Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    examples      2.8Mb
    htmlwidgets   1.1Mb
    www           2.7Mb
installed size is 17.0Mb
  sub-directories of 1Mb or more:
    libs  16.8Mb
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    doc    3.3Mb
    help   8.0Mb
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    libs  11.1Mb
installed size is 18.3Mb
  sub-directories of 1Mb or more:
    libs  17.9Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc       3.2Mb
    extdata   1.2Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   3.8Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    data   1.6Mb
    libs   4.1Mb
installed size is 13.0Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    libs  10.4Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    R   5.2Mb
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    data   8.2Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    data   5.9Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc    3.1Mb
    libs   3.3Mb
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    libs   8.2Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   3.8Mb
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs   5.8Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    doc    1.7Mb
    help   1.1Mb
Package unavailable to check Rd xrefs: ‘mixAK’
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
installed size is 26.2Mb
  sub-directories of 1Mb or more:
    libs  24.8Mb
Package suggested but not available for checking: ‘V8’
installed size is 72.9Mb
  sub-directories of 1Mb or more:
    doc    2.5Mb
    libs  68.5Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
installed size is 16.1Mb
  sub-directories of 1Mb or more:
    libs  15.7Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc   5.3Mb
installed size is 48.5Mb
  sub-directories of 1Mb or more:
    help   1.1Mb
    libs  45.6Mb
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    data   1.8Mb
    libs   9.1Mb
installed size is 115.7Mb
  sub-directories of 1Mb or more:
    libs  114.4Mb
installed size is 43.5Mb
  sub-directories of 1Mb or more:
    libs  43.3Mb
installed size is 12.8Mb
  sub-directories of 1Mb or more:
    R         2.0Mb
    doc       1.0Mb
    extdata   1.2Mb
    libs      8.0Mb
installed size is 68.5Mb
  sub-directories of 1Mb or more:
    libs  67.8Mb
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    libs  10.3Mb
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.4/lmap.Rcheck/00install.out’ for details.
installed size is 27.4Mb
  sub-directories of 1Mb or more:
    R          1.5Mb
    doc        1.6Mb
    libs      22.2Mb
    testdata   1.3Mb
installed size is 99.6Mb
  sub-directories of 1Mb or more:
    libs  98.6Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    R              2.1Mb
    doc-overview   2.2Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    libs   7.6Mb
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    doc    4.0Mb
    libs   5.2Mb
installed size is 65.4Mb
  sub-directories of 1Mb or more:
    libs  65.0Mb
installed size is 33.7Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs  31.7Mb
installed size is 27.9Mb
  sub-directories of 1Mb or more:
    libs  27.8Mb
Package suggested but not available for checking: ‘EnsDb.Hsapiens.v75’
installed size is 19.6Mb
  sub-directories of 1Mb or more:
    libs  18.0Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data   4.0Mb
    libs   1.8Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    extdata   4.5Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   3.6Mb
installed size is 91.2Mb
  sub-directories of 1Mb or more:
    libs  88.9Mb
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    libs   9.8Mb
installed size is 108.9Mb
  sub-directories of 1Mb or more:
    doc     1.6Mb
    libs  106.6Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    libs   3.7Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    libs   2.0Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    R   5.0Mb
installed size is 24.4Mb
  sub-directories of 1Mb or more:
    libs  24.2Mb
installed size is 38.1Mb
  sub-directories of 1Mb or more:
    libs  37.7Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
installed size is 55.9Mb
  sub-directories of 1Mb or more:
    doc    6.3Mb
    libs  48.9Mb
installed size is 24.2Mb
  sub-directories of 1Mb or more:
    libs  22.8Mb
Package suggested but not available for checking: ‘dittoSeq’
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error: package or namespace load failed for 'testthat' in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
   there is no package called 'R6'
  Execution halted
Packages suggested but not available for checking: 'lumi', 'beadarray'
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    data   2.3Mb
    libs   4.8Mb
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    libs   9.5Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data      3.3Mb
    extdata   1.3Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    doc   6.9Mb
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    libs   9.8Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    doc    3.5Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
installed size is 33.5Mb
  sub-directories of 1Mb or more:
    mapdata  33.4Mb
installed size is 22.2Mb
  sub-directories of 1Mb or more:
    data          1.3Mb
    doc           1.6Mb
    htmlwidgets   3.5Mb
    libs         15.3Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    R   8.4Mb
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.4/mappoly.Rcheck/00install.out’ for details.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   2.0Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc   6.4Mb
installed size is 18.2Mb
  sub-directories of 1Mb or more:
    examples   2.7Mb
    libs      14.2Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   3.5Mb
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    libs   9.3Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    libs   2.8Mb
Packages suggested but not available for checking:
  'BSgenome.Hsapiens.NCBI.GRCh38', 'org.Mm.eg.db', 'wiggleplotr'
installed size is 18.9Mb
  sub-directories of 1Mb or more:
    libs  18.6Mb
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    libs   7.4Mb
installed size is 13.2Mb
  sub-directories of 1Mb or more:
    java   3.3Mb
    libs   8.9Mb
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    doc    1.3Mb
    libs   6.6Mb
installed size is 14.1Mb
  sub-directories of 1Mb or more:
    libs  13.2Mb
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    libs   9.0Mb
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    libs   8.8Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    data   3.9Mb
installed size is 16.3Mb
  sub-directories of 1Mb or more:
    doc    3.8Mb
    libs  12.3Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc   2.9Mb
installed size is 34.3Mb
  sub-directories of 1Mb or more:
    libs  33.2Mb
installed size is 19.6Mb
  sub-directories of 1Mb or more:
    libs  19.1Mb
installed size is 21.3Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    libs  18.8Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    doc   6.8Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    libs  10.3Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc       1.9Mb
    extdata   5.3Mb
installed size is 85.7Mb
  sub-directories of 1Mb or more:
    libs  84.2Mb
installed size is 52.7Mb
  sub-directories of 1Mb or more:
    libs  51.4Mb
installed size is 19.0Mb
  sub-directories of 1Mb or more:
    libs  18.0Mb
Package suggested but not available for checking: ‘TxDb.Hsapiens.UCSC.hg19.knownGene’
installed size is 155.5Mb
  sub-directories of 1Mb or more:
    libs  154.0Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   3.6Mb
installed size is 20.2Mb
  sub-directories of 1Mb or more:
    libs  19.1Mb
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    libs   5.4Mb
installed size is 129.7Mb
  sub-directories of 1Mb or more:
    libs  129.0Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    R      3.1Mb
    help   2.3Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   4.2Mb
installed size is 14.4Mb
  sub-directories of 1Mb or more:
    data       3.0Mb
    examples  10.3Mb
Packages suggested but not available for checking:
  'hgu133plus2.db', 'hgu133a.db', 'hgu95av2.db'
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R   4.9Mb
installed size is 20.4Mb
  sub-directories of 1Mb or more:
    libs  20.0Mb
installed size is 91.3Mb
  sub-directories of 1Mb or more:
    libs  90.8Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    help   2.0Mb
    libs   2.6Mb
installed size is 13.7Mb
  sub-directories of 1Mb or more:
    libs  12.1Mb
installed size is 29.0Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    doc    3.6Mb
    libs  21.4Mb
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    libs   6.5Mb
installed size is 23.3Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs  20.6Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
Packages suggested but not available for checking:
  'BSgenome.Hsapiens.UCSC.hg38', 'BSgenome.Hsapiens.UCSC.hg19',
  'BSgenome.Mmusculus.UCSC.mm10'
installed size is 20.5Mb
  sub-directories of 1Mb or more:
    doc    6.1Mb
    lib    9.1Mb
    libs   4.6Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
installed size is 14.9Mb
  sub-directories of 1Mb or more:
    libs  14.2Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   5.5Mb
installed size is 27.6Mb
  sub-directories of 1Mb or more:
    libs  27.5Mb
installed size is 22.5Mb
  sub-directories of 1Mb or more:
    libs  22.4Mb
installed size is 42.4Mb
  sub-directories of 1Mb or more:
    libs  41.9Mb
installed size is 41.2Mb
  sub-directories of 1Mb or more:
    libs        1.4Mb
    redengine  39.6Mb
installed size is 164.3Mb
  sub-directories of 1Mb or more:
    libs  163.7Mb
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    libs   7.5Mb
Packages suggested but not available for checking: 'mixAK', 'BRugs'
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc       2.4Mb
    extdata   1.2Mb
    libs      1.6Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
installed size is 26.6Mb
  sub-directories of 1Mb or more:
    libs  24.1Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
installed size is 41.3Mb
  sub-directories of 1Mb or more:
    libs  41.0Mb
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.4/MixtureMissing.Rcheck/00install.out’ for details.
installed size is 11.9Mb
  sub-directories of 1Mb or more:
    libs  11.6Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   4.4Mb
Package suggested but not available for checking: ‘IlluminaHumanMethylation450kmanifest’
installed size is 243.0Mb
  sub-directories of 1Mb or more:
    include   10.0Mb
    libs     232.6Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    data   2.3Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
installed size is 134.8Mb
  sub-directories of 1Mb or more:
    doc     1.2Mb
    libs  132.7Mb
installed size is 50.2Mb
  sub-directories of 1Mb or more:
    libs  49.7Mb
installed size is 28.6Mb
  sub-directories of 1Mb or more:
    libs  27.9Mb
installed size is 15.6Mb
  sub-directories of 1Mb or more:
    images   1.1Mb
    shiny   14.5Mb
installed size is 16.8Mb
  sub-directories of 1Mb or more:
    doc    1.3Mb
    libs  15.0Mb
installed size is 29.9Mb
  sub-directories of 1Mb or more:
    libs  29.8Mb
installed size is 121.1Mb
  sub-directories of 1Mb or more:
    libs  119.3Mb
installed size is 19.6Mb
  sub-directories of 1Mb or more:
    libs  19.4Mb
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    libs  10.4Mb
Packages suggested but not available for checking:
  'doMPI', 'optiSel', 'alstructure'

Packages which this enhances but not available for checking:
  'miraculix', 'RandomFieldsUtils', 'MoBPSmaps'
Packages suggested but not available for checking:
  'ArchR', 'TxDb.Hsapiens.UCSC.hg38.refGene',
  'TxDb.Hsapiens.UCSC.hg19.knownGene', 'BSgenome.Hsapiens.UCSC.hg19'
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   5.3Mb
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    libs   8.2Mb
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    doc    1.7Mb
    libs   4.4Mb
installed size is 14.8Mb
  sub-directories of 1Mb or more:
    htmlwidgets  14.7Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   3.7Mb
    theo   1.1Mb
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   7.1Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs     3.0Mb
    raster   2.2Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   3.0Mb
    libs   2.6Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    R   2.0Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
installed size is 13.3Mb
  sub-directories of 1Mb or more:
    libs  12.3Mb
installed size is 92.1Mb
  sub-directories of 1Mb or more:
    libs  91.8Mb
installed size is 14.1Mb
  sub-directories of 1Mb or more:
    data   1.6Mb
    libs  12.1Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    extdata   1.7Mb
    libs      2.3Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc    3.3Mb
    libs   1.7Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    data   4.5Mb
    libs   3.9Mb
installed size is 45.4Mb
  sub-directories of 1Mb or more:
    libs  45.0Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    R   6.0Mb
installed size is 18.1Mb
  sub-directories of 1Mb or more:
    libs  17.0Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   4.3Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   5.5Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs   7.2Mb
Package suggested but not available for checking: ‘leukemiasEset’
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    doc   6.4Mb
installed size is 16.4Mb
  sub-directories of 1Mb or more:
    libs  15.4Mb
installed size is 98.0Mb
  sub-directories of 1Mb or more:
    libs  97.7Mb
installed size is 271.0Mb
  sub-directories of 1Mb or more:
    R       2.0Mb
    doc     4.2Mb
    libs  264.0Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
installed size is 42.6Mb
  sub-directories of 1Mb or more:
    libs  42.3Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    help   2.0Mb
    libs   2.3Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc   4.3Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    R      1.9Mb
    doc    2.0Mb
    libs   1.8Mb
installed size is 13.3Mb
  sub-directories of 1Mb or more:
    libs  12.0Mb
Package suggested but not available for checking: ‘DLBCL’
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    java   2.5Mb
    libs   6.6Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   5.7Mb
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    libs   8.9Mb
installed size is 16.3Mb
  sub-directories of 1Mb or more:
    extdata  16.2Mb
installed size is 25.7Mb
  sub-directories of 1Mb or more:
    data     1.9Mb
    libs    22.5Mb
    models   1.1Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   4.3Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   4.2Mb
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    libs  10.5Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    data   4.0Mb
    doc    3.5Mb
installed size is 13.9Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    doc    6.5Mb
    libs   4.8Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
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Package suggested but not available for checking: ‘MicrobiotaProcess’
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Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.4/pbdMPI.Rcheck/00install.out’ for details.
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installed size is 154.6Mb
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installed size is  5.0Mb
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Error(s) in re-building vignettes:
--- re-building ‘tutorial.Rmd’ using rmarkdown
! kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 bbm10

! mkdir: ././opt/tex/texmf-var/fonts/pk/ljfour/public: Permission denied

! mktexpk: /opt/tex/texmf-dist/web2c/mktexdir /opt/tex/texmf-var/fonts/pk/ljfour/public/bbm failed.

! kpathsea: Appending font creation commands to missfont.log.

Error: processing vignette 'tutorial.Rmd' failed with diagnostics:
LaTeX failed to compile /Volumes/Builds/packages/big-sur-arm64/results/4.4/pcSteiner.Rcheck/vign_test/pcSteiner/vignettes/tutorial.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See tutorial.log for more info.
--- failed re-building ‘tutorial.Rmd’

SUMMARY: processing the following file failed:
  ‘tutorial.Rmd’

Error: Vignette re-building failed.
Execution halted
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Packages suggested but not available for checking:
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installed size is 10.7Mb
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installed size is 20.0Mb
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installed size is 227.0Mb
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installed size is 20.8Mb
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installed size is 11.5Mb
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installed size is 15.3Mb
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installed size is 16.2Mb
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installed size is 17.8Mb
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installed size is 140.5Mb
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Package required but not available: ‘UniProt.ws’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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Package unavailable to check Rd xrefs: ‘BRugs’
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installed size is 16.3Mb
  sub-directories of 1Mb or more:
    doc       1.7Mb
    extdata   4.1Mb
    libs      9.6Mb
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    libs   8.7Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   4.5Mb
installed size is 13.0Mb
  sub-directories of 1Mb or more:
    R      4.1Mb
    libs   7.8Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
installed size is 93.6Mb
  sub-directories of 1Mb or more:
    libs  92.8Mb
installed size is 14.7Mb
  sub-directories of 1Mb or more:
    libs  14.6Mb
installed size is 24.3Mb
  sub-directories of 1Mb or more:
    libs  23.6Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc       2.6Mb
    rstudio   1.6Mb
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    data   5.6Mb
    etc    1.9Mb
    po     1.2Mb
installed size is 21.7Mb
  sub-directories of 1Mb or more:
    data   4.5Mb
    libs  16.2Mb
installed size is 15.8Mb
  sub-directories of 1Mb or more:
    libs  15.0Mb
installed size is 14.7Mb
  sub-directories of 1Mb or more:
    libs  14.4Mb
installed size is 32.7Mb
  sub-directories of 1Mb or more:
    libs  31.8Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    data   2.9Mb
    libs   3.3Mb
installed size is 13.8Mb
  sub-directories of 1Mb or more:
    libs  13.0Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    extdata   1.1Mb
    libs      3.8Mb
installed size is 65.8Mb
  sub-directories of 1Mb or more:
    libs  63.9Mb
installed size is 66.1Mb
  sub-directories of 1Mb or more:
    libs  65.5Mb
installed size is 27.2Mb
  sub-directories of 1Mb or more:
    blp   20.1Mb
    libs   5.9Mb
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.4/rbm25.Rcheck/00install.out’ for details.
installed size is 14.3Mb
  sub-directories of 1Mb or more:
    libs  14.0Mb
installed size is 91.9Mb
  sub-directories of 1Mb or more:
    libs  91.2Mb
installed size is 20.2Mb
  sub-directories of 1Mb or more:
    cont  20.1Mb
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    R     2.0Mb
    doc   4.5Mb
    po    2.4Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    corpora   7.5Mb
Packages suggested but not available for checking:
  'hgu133plus2.db', 'pd.hg.u133.plus.2'
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.4/Rcplex.Rcheck/00install.out’ for details.
installed size is 21.1Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs  18.8Mb
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    include   6.6Mb
    libs      2.2Mb
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    libs   9.4Mb
installed size is 39.7Mb
  sub-directories of 1Mb or more:
    include  37.8Mb
    libs      1.8Mb
installed size is 46.6Mb
  sub-directories of 1Mb or more:
    include  46.5Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
installed size is 34.0Mb
  sub-directories of 1Mb or more:
    include   9.5Mb
    libs     24.1Mb
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    libs   8.1Mb
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.4/RcppMeCab.Rcheck/00install.out’ for details.
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    libs   9.1Mb
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    include   6.7Mb
    libs      2.7Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    libs   8.3Mb
installed size is 14.5Mb
  sub-directories of 1Mb or more:
    doc       1.1Mb
    include   6.3Mb
    libs      5.2Mb
installed size is 23.0Mb
  sub-directories of 1Mb or more:
    include        7.2Mb
    jsonexamples   3.8Mb
    libs          11.8Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    include   1.2Mb
    libs      5.4Mb
installed size is 19.4Mb
  sub-directories of 1Mb or more:
    data   1.9Mb
    libs  15.7Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    R      4.6Mb
    data   1.5Mb
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    libs   8.9Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.4/realTimeloads.Rcheck/00install.out’ for details.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    data   1.7Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    2.5Mb
    libs   2.5Mb
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    htmlwidgets   9.8Mb
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    data   9.0Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc    3.3Mb
    libs   2.9Mb
installed size is 30.0Mb
  sub-directories of 1Mb or more:
    libs        1.5Mb
    redengine  28.4Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   4.3Mb
installed size is 18.3Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    libs  14.5Mb
installed size is 11.9Mb
  sub-directories of 1Mb or more:
    libs  11.1Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    libs   4.9Mb
Package which this enhances but not available for checking: ‘Rcplex’
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    doc    3.5Mb
    libs   4.0Mb
installed size is 25.2Mb
  sub-directories of 1Mb or more:
    libs  23.8Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   6.7Mb
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    doc    3.9Mb
    libs   5.1Mb
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    libs   9.3Mb
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   6.8Mb
installed size is 17.3Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    doc    1.2Mb
    libs  13.8Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    extdata   1.3Mb
    java      2.9Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs      3.4Mb
    swagger   1.4Mb
installed size is 42.1Mb
  sub-directories of 1Mb or more:
    libs  42.0Mb
installed size is 28.3Mb
  sub-directories of 1Mb or more:
    include   2.4Mb
    libs     24.1Mb
    models    1.6Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   3.7Mb
Package suggested but not available for checking: ‘ccdata’
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc        1.1Mb
    examples   1.9Mb
installed size is 22.6Mb
  sub-directories of 1Mb or more:
    libs  21.8Mb
installed size is 46.4Mb
  sub-directories of 1Mb or more:
    libs  45.0Mb
installed size is 13.4Mb
  sub-directories of 1Mb or more:
    data  13.3Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data      1.9Mb
    doc       1.2Mb
    extdata   1.9Mb
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    doc   6.9Mb
installed size is 28.6Mb
  sub-directories of 1Mb or more:
    libs  27.3Mb
installed size is 36.4Mb
  sub-directories of 1Mb or more:
    doc     7.1Mb
    fonts   1.5Mb
    libs   24.5Mb
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    doc          10.3Mb
    htmlwidgets   1.2Mb
installed size is 17.8Mb
  sub-directories of 1Mb or more:
    data   1.6Mb
    libs  15.4Mb
File ‘RInside/libs/RInside.so’:
  Found ‘_srand’, possibly from ‘srand’ (C)
    Object: ‘RInside.o’
File ‘RInside/libs/RInside.so’:
  Found non-API calls to R: ‘R_CStackLimit’, ‘R_CleanTempDir’,
    ‘R_DefParams’, ‘R_ReplDLLinit’, ‘R_RunExitFinalizers’,
    ‘R_SetParams’, ‘R_SignalHandlers’, ‘R_TempDir’, ‘Rf_endEmbeddedR’,
    ‘Rf_initEmbeddedR’, ‘run_Rmainloop’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf.
Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 13.1Mb
  sub-directories of 1Mb or more:
    libs  13.0Mb
installed size is 25.2Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs  23.7Mb
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    libs   8.7Mb
Note: information on .o files is not available
File ‘/Volumes/Builds/packages/big-sur-arm64/results/4.4/rJava.Rcheck/rJava/libs/rJava.so’:
  Found ‘___stderrp’, possibly from ‘stderr’ (C)
  Found ‘___stdoutp’, possibly from ‘stdout’ (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    java   4.2Mb
installed size is 55.9Mb
  sub-directories of 1Mb or more:
    include   3.4Mb
    libs     51.6Mb
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    java  12.0Mb
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    java  10.8Mb
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    datasets  10.2Mb
installed size is 28.3Mb
  sub-directories of 1Mb or more:
    R     4.0Mb
    exe  23.8Mb
installed size is 27.8Mb
  sub-directories of 1Mb or more:
    libs  27.7Mb
installed size is 24.7Mb
  sub-directories of 1Mb or more:
    extdata  24.0Mb
installed size is 44.8Mb
  sub-directories of 1Mb or more:
    libs  44.2Mb
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    libs   8.6Mb
installed size is 19.2Mb
  sub-directories of 1Mb or more:
    lemon   2.8Mb
    libs   16.1Mb
installed size is 161.2Mb
  sub-directories of 1Mb or more:
    libs  160.2Mb
installed size is 71.3Mb
  sub-directories of 1Mb or more:
    include   7.3Mb
    lib      37.3Mb
    libs     26.2Mb
Packages suggested but not available for checking:
  'DoubletFinder', 'RcppPlanc', 'reactome.db'
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    libs   6.4Mb
installed size is 12.5Mb
  sub-directories of 1Mb or more:
    libs  12.3Mb
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    libs   8.4Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    rmd   6.0Mb
Found the following significant warnings:
  Warning: Software mark not found in path.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.4/RMark.Rcheck/00install.out’ for details.
installed size is 143.2Mb
  sub-directories of 1Mb or more:
    libs  142.8Mb
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.4/RmecabKo.Rcheck/00install.out’ for details.
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    R      3.0Mb
    libs   5.7Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    R          1.0Mb
    libs       1.1Mb
    minizinc   3.3Mb
installed size is 44.3Mb
  sub-directories of 1Mb or more:
    libs  43.3Mb
installed size is 30.5Mb
  sub-directories of 1Mb or more:
    libs  30.3Mb
installed size is 84.5Mb
  sub-directories of 1Mb or more:
    libs  83.9Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    libs  11.9Mb
installed size is 31.3Mb
  sub-directories of 1Mb or more:
    libs  30.1Mb
installed size is 19.7Mb
  sub-directories of 1Mb or more:
    libs  19.5Mb
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    java  12.1Mb
installed size is 18.7Mb
  sub-directories of 1Mb or more:
    libs  18.5Mb
Packages which this enhances but not available for checking:
  'pbdMPI', 'Rmpi'
Packages unavailable to check Rd xrefs: ‘pbdMPI’, ‘Rmpi’
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.0Mb
installed size is 119.5Mb
  sub-directories of 1Mb or more:
    extdata    2.0Mb
    libs     117.3Mb
installed size is 13.5Mb
  sub-directories of 1Mb or more:
    libs  12.4Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   2.9Mb
    doc    1.7Mb
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    R  11.4Mb
installed size is 20.9Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs  18.3Mb
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    libs   8.2Mb
installed size is 40.5Mb
  sub-directories of 1Mb or more:
    libs  40.3Mb
Packages suggested but not available for checking:
  'affydata', 'hgu95av2cdf', 'beadarrayExampleData',
  'illuminaHumanv3.db'
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   1.7Mb
installed size is 95.9Mb
  sub-directories of 1Mb or more:
    libs  95.1Mb
installed size is 22.6Mb
  sub-directories of 1Mb or more:
    libs  22.0Mb
installed size is 38.9Mb
  sub-directories of 1Mb or more:
    libs  38.3Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    libs   4.9Mb
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    doc               1.7Mb
    libs              5.2Mb
    simulationStudy   1.5Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
installed size is 17.4Mb
  sub-directories of 1Mb or more:
    doc  15.2Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    R         3.7Mb
    extdata   2.7Mb
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    data   2.7Mb
    libs   5.4Mb
installed size is 15.8Mb
  sub-directories of 1Mb or more:
    R      5.0Mb
    libs   9.6Mb
installed size is 88.8Mb
  sub-directories of 1Mb or more:
    libs  87.7Mb
installed size is 26.6Mb
  sub-directories of 1Mb or more:
    libs  25.7Mb
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   6.0Mb
installed size is 49.3Mb
  sub-directories of 1Mb or more:
    libs  49.2Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    extdata   4.5Mb
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs   5.7Mb
installed size is 33.6Mb
  sub-directories of 1Mb or more:
    libs  32.2Mb
installed size is 99.2Mb
  sub-directories of 1Mb or more:
    libs  98.6Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   3.3Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc   4.2Mb
installed size is 20.0Mb
  sub-directories of 1Mb or more:
    libs  19.8Mb
Note: information on .o files is not available
File ‘/Volumes/Builds/packages/big-sur-arm64/results/4.4/Rserve.Rcheck/Rserve/libs/Rserve.so’:
  Found ‘___stderrp’, possibly from ‘stderr’ (C)
  Found ‘_abort’, possibly from ‘abort’ (C)
  Found ‘_exit’, possibly from ‘exit’ (C)
  Found ‘_rand’, possibly from ‘rand’ (C)
  Found ‘_random’, possibly from ‘random’ (C)
  Found ‘_sprintf’, possibly from ‘sprintf’ (C)
  Found ‘_srandom’, possibly from ‘srandom’ (C)
File ‘Rserve/libs/Rserve.so’:
  Found non-API calls to R: ‘R_Consolefile’, ‘R_Outputfile’,
    ‘R_TempDir’, ‘R_Visible’, ‘getInputHandler’, ‘ptr_R_Busy’,
    ‘ptr_R_ClearerrConsole’, ‘ptr_R_FlushConsole’, ‘ptr_R_ReadConsole’,
    ‘ptr_R_ResetConsole’, ‘ptr_R_ShowMessage’, ‘ptr_R_WriteConsole’,
    ‘ptr_R_WriteConsoleEx’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.
Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 23.8Mb
  sub-directories of 1Mb or more:
    libs  23.6Mb
installed size is 26.4Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    libs  24.9Mb
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    libs   8.9Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    R      4.4Mb
    help   1.5Mb
installed size is 46.6Mb
  sub-directories of 1Mb or more:
    libs  46.0Mb
installed size is 12.5Mb
  sub-directories of 1Mb or more:
    libs  11.7Mb
installed size is 311.3Mb
  sub-directories of 1Mb or more:
    R       2.0Mb
    doc     4.7Mb
    libs  303.8Mb
installed size is 94.7Mb
  sub-directories of 1Mb or more:
    libs  94.4Mb
installed size is 57.3Mb
  sub-directories of 1Mb or more:
    libs  56.6Mb
installed size is 49.4Mb
  sub-directories of 1Mb or more:
    exec   1.7Mb
    lib   34.2Mb
    libs  11.7Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    external   1.6Mb
    libs       4.3Mb
installed size is 37.2Mb
  sub-directories of 1Mb or more:
    libs  21.3Mb
installed size is 29.1Mb
  sub-directories of 1Mb or more:
    libs  28.6Mb
installed size is 26.5Mb
  sub-directories of 1Mb or more:
    swipl  26.1Mb
Package unavailable to check Rd xrefs: ‘Rglpk’
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    rmarkdown  11.1Mb
installed size is 18.3Mb
  sub-directories of 1Mb or more:
    libs  18.2Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs       2.4Mb
    projects   2.9Mb
installed size is 122.6Mb
  sub-directories of 1Mb or more:
    R       1.0Mb
    libs  120.8Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    R   6.0Mb
installed size is 29.4Mb
  sub-directories of 1Mb or more:
    doc    7.8Mb
    libs  20.7Mb
installed size is 219.9Mb
  sub-directories of 1Mb or more:
    data    1.5Mb
    libs  217.5Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    extdata   1.0Mb
    libs      4.5Mb
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    R      3.1Mb
    libs   2.4Mb
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
    libs   6.5Mb
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.4/RulesTools.Rcheck/00install.out’ for details.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc   4.7Mb
installed size is 48.4Mb
  sub-directories of 1Mb or more:
    libs  47.2Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    include   5.1Mb
installed size is 64.9Mb
  sub-directories of 1Mb or more:
    include   5.1Mb
    libs     59.5Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data      3.2Mb
    extdata   2.4Mb
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    java  10.7Mb
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    libs   9.3Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    doc    3.9Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   5.0Mb
installed size is 13.9Mb
  sub-directories of 1Mb or more:
    libs  13.8Mb
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    R         2.0Mb
    include   1.1Mb
    libs      5.8Mb
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    libs    7.6Mb
    yacas   1.3Mb
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    libs    8.3Mb
    yacas   1.3Mb
installed size is 15.5Mb
  sub-directories of 1Mb or more:
    libs  15.4Mb
installed size is 36.5Mb
  sub-directories of 1Mb or more:
    libs  35.4Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    libs   7.3Mb
installed size is 16.6Mb
  sub-directories of 1Mb or more:
    libs  15.5Mb
installed size is 14.9Mb
  sub-directories of 1Mb or more:
    libs  13.8Mb
installed size is 22.4Mb
  sub-directories of 1Mb or more:
    libs  22.2Mb
installed size is 55.6Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    libs  53.0Mb
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    help   3.4Mb
    libs   3.8Mb
Packages suggested but not available for checking:
  'networkTomography', 'org.Sc.sgd.db'
installed size is 53.6Mb
  sub-directories of 1Mb or more:
    libs  53.5Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    bin   4.5Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   3.3Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc       5.1Mb
    extdata   1.1Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    doc    3.9Mb
    libs   3.2Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   3.9Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   3.0Mb
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    libs   8.5Mb
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    data   4.9Mb
    libs   3.5Mb
Packages which this enhances but not available for checking:
  'gurobi', 'Rcplex', 'pogs'
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    doc    2.3Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   3.2Mb
    libs   2.9Mb
Package suggested but not available for checking: ‘SingleCellSignalR’
installed size is 18.8Mb
  sub-directories of 1Mb or more:
    libs  18.2Mb
installed size is 31.7Mb
  sub-directories of 1Mb or more:
    cppad     9.4Mb
    include   4.6Mb
    libs     17.1Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   3.9Mb
Packages suggested but not available for checking:
  'AUCell', 'infercnv', 'Nebulosa'
Package unavailable to check Rd xrefs: ‘infercnv’
installed size is 20.9Mb
  sub-directories of 1Mb or more:
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Package which this enhances but not available for checking: ‘glmGamPoi’
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   3.9Mb
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    libs   5.3Mb
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    libs   8.8Mb
installed size is 87.8Mb
  sub-directories of 1Mb or more:
    libs  85.9Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    R   8.6Mb
installed size is 19.3Mb
  sub-directories of 1Mb or more:
    extdata  18.0Mb
installed size is 20.0Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    libs  16.2Mb
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   8.2Mb
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    data   2.9Mb
    libs   7.9Mb
Package suggested but not available for checking: ‘org.Rn.eg.db’
Package suggested but not available for checking: ‘rsbml’
installed size is 34.5Mb
  sub-directories of 1Mb or more:
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installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    R      2.3Mb
    libs   2.6Mb
installed size is 21.5Mb
  sub-directories of 1Mb or more:
    libs    19.7Mb
    models   1.6Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   4.1Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    libs   4.4Mb
installed size is 17.5Mb
  sub-directories of 1Mb or more:
    doc    6.4Mb
    libs  10.2Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data        1.4Mb
    sequences   1.9Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    data   5.7Mb
    libs   1.1Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    libs   4.3Mb
installed size is 55.5Mb
  sub-directories of 1Mb or more:
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    libs  53.3Mb
installed size is 19.6Mb
  sub-directories of 1Mb or more:
    libs  18.3Mb
installed size is 11.3Mb
  sub-directories of 1Mb or more:
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    libs   8.3Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
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    doc   5.2Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    libs   7.4Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc   5.1Mb
installed size is 265.4Mb
  sub-directories of 1Mb or more:
    doc       1.8Mb
    libs    258.9Mb
    sqlite    1.5Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
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installed size is  9.5Mb
  sub-directories of 1Mb or more:
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    libs   4.1Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
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    extdata   4.2Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
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installed size is  9.5Mb
  sub-directories of 1Mb or more:
    www   9.4Mb
installed size is 20.5Mb
  sub-directories of 1Mb or more:
    www  19.7Mb
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    www   7.6Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
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installed size is 21.1Mb
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installed size is 14.2Mb
  sub-directories of 1Mb or more:
    R     2.1Mb
    www  10.3Mb
installed size is 12.1Mb
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installed size is  6.0Mb
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    help      1.7Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    libs   1.9Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    doc   6.5Mb
installed size is 18.9Mb
  sub-directories of 1Mb or more:
    extdata  13.0Mb
    libs      5.2Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    doc    1.0Mb
    libs   2.7Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
installed size is 14.9Mb
  sub-directories of 1Mb or more:
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Package suggested but not available for checking: ‘BSgenome.Hsapiens.UCSC.hg38’
installed size is  9.9Mb
  sub-directories of 1Mb or more:
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installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   2.5Mb
installed size is 22.4Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs  20.0Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   2.7Mb
installed size is 11.9Mb
  sub-directories of 1Mb or more:
    R      3.0Mb
    libs   6.8Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
installed size is 11.8Mb
  sub-directories of 1Mb or more:
    R         2.1Mb
    extdata   1.3Mb
    libs      7.8Mb
installed size is 15.5Mb
  sub-directories of 1Mb or more:
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installed size is  7.1Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   5.0Mb
installed size is 38.2Mb
  sub-directories of 1Mb or more:
    libs  37.6Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   5.1Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
    libs   2.2Mb
installed size is 31.7Mb
  sub-directories of 1Mb or more:
    libs  31.3Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc   4.5Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
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installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.4/smer.Rcheck/00install.out’ for details.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data   3.3Mb
    libs   2.2Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.2Mb
installed size is 16.4Mb
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    libs  10.6Mb
Package which this enhances but not available for checking: ‘Rmpi’
installed size is  6.1Mb
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    extdata   3.1Mb
    libs      2.7Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc   4.2Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    R     4.0Mb
    doc   1.1Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data      3.8Mb
    extdata   1.1Mb
installed size is 13.6Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    doc    1.3Mb
    libs   9.8Mb
Package suggested but not available for checking: ‘DropletUtils’
installed size is  6.7Mb
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    data   4.9Mb
    doc    1.0Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
installed size is 19.1Mb
  sub-directories of 1Mb or more:
    data   4.7Mb
    libs  14.3Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    libs   2.4Mb
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    extdata   5.9Mb
    libs      2.0Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    include   2.1Mb
    libs      3.0Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    libs   2.6Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    R   5.9Mb
installed size is 39.1Mb
  sub-directories of 1Mb or more:
    R      3.1Mb
    libs  34.7Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    java   1.8Mb
installed size is 13.7Mb
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S3 methods shown with full name in Rd file 'SparseM.ontology.Rd':
  ‘as.matrix.csr’ ‘is.matrix.csr’ ‘is.matrix.csc’ ‘is.matrix.ssr’
  ‘is.matrix.ssc’ ‘is.matrix.coo’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
installed size is 47.7Mb
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Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.4/spaths.Rcheck/00install.out’ for details.
installed size is 95.1Mb
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    libs  94.2Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   2.6Mb
    help   1.7Mb
    libs   1.2Mb
installed size is 13.0Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs  11.5Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs   4.1Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    help   2.6Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc   4.5Mb
installed size is 22.5Mb
  sub-directories of 1Mb or more:
    libs  21.6Mb
installed size is 13.4Mb
  sub-directories of 1Mb or more:
    data   3.3Mb
    libs   9.5Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    libs   8.1Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    data     2.6Mb
    shapes   3.2Mb
installed size is  5.9Mb
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    data   4.3Mb
    help   1.5Mb
installed size is  9.7Mb
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    doc   6.0Mb
    etc   2.1Mb
installed size is  6.1Mb
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    doc   4.6Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    doc    3.1Mb
    libs   3.5Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
installed size is 12.4Mb
  sub-directories of 1Mb or more:
    extdata   1.2Mb
    libs     10.9Mb
installed size is 27.5Mb
  sub-directories of 1Mb or more:
    libs  27.2Mb
installed size is 17.3Mb
  sub-directories of 1Mb or more:
    libs  16.2Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs   3.4Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    data   1.8Mb
    doc    1.5Mb
installed size is 17.6Mb
  sub-directories of 1Mb or more:
    doc       1.1Mb
    extdata   2.6Mb
    libs     12.5Mb
installed size is  6.6Mb
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installed size is  9.2Mb
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installed size is  7.1Mb
  sub-directories of 1Mb or more:
    doc   5.5Mb
installed size is 90.4Mb
  sub-directories of 1Mb or more:
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Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.4/SQLFormatteR.Rcheck/00install.out’ for details.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   5.4Mb
installed size is 13.4Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    help   1.1Mb
    libs  10.9Mb
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    doc   8.2Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    shiny-squid   5.4Mb
installed size is 41.3Mb
  sub-directories of 1Mb or more:
    libs  40.2Mb
installed size is 125.3Mb
  sub-directories of 1Mb or more:
    libs  124.8Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   3.4Mb
installed size is 35.7Mb
  sub-directories of 1Mb or more:
    libs  35.1Mb
installed size is 49.9Mb
  sub-directories of 1Mb or more:
    libs  49.6Mb
installed size is 17.0Mb
  sub-directories of 1Mb or more:
    include  11.7Mb
    lib       3.3Mb
installed size is 100.9Mb
  sub-directories of 1Mb or more:
    libs  100.1Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc   2.9Mb
    nc    1.7Mb
installed size is  8.9Mb
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    libs   5.1Mb
installed size is  5.0Mb
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    data   3.5Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    extdata   2.4Mb
    libs      4.2Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
Package suggested but not available for checking: ‘imputeMissings’
installed size is  6.2Mb
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installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   4.3Mb
installed size is 94.3Mb
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    libs  93.2Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   1.7Mb
    libs   2.4Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    data   7.3Mb
installed size is 34.5Mb
  sub-directories of 1Mb or more:
    libs  33.5Mb
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   6.9Mb
installed size is 47.5Mb
  sub-directories of 1Mb or more:
    joss_paper   1.2Mb
    libs        45.5Mb
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    libs   6.7Mb
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    libs  10.2Mb
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    libs   8.8Mb
installed size is  5.7Mb
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    doc   5.0Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
installed size is 12.9Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   9.9Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    libs   7.9Mb
installed size is 34.7Mb
  sub-directories of 1Mb or more:
    libs  33.8Mb
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    doc    7.1Mb
    libs   1.8Mb
installed size is  5.3Mb
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    libs   4.2Mb
installed size is  6.7Mb
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    data   2.0Mb
    doc    3.1Mb
    help   1.0Mb
installed size is 14.9Mb
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    libs   3.9Mb
installed size is  7.9Mb
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    libs   7.2Mb
installed size is  7.0Mb
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    doc   2.3Mb
installed size is 63.5Mb
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installed size is  5.9Mb
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    doc    2.5Mb
installed size is  6.8Mb
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installed size is 10.1Mb
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    libs   9.0Mb
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    data   2.3Mb
    doc    5.3Mb
installed size is 31.0Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs  28.9Mb
installed size is 63.6Mb
  sub-directories of 1Mb or more:
    libs  63.1Mb
installed size is  8.6Mb
  sub-directories of 1Mb or more:
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installed size is 45.9Mb
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    libs  45.4Mb
installed size is  6.2Mb
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    dist5   2.1Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
installed size is 25.0Mb
  sub-directories of 1Mb or more:
    libs  24.3Mb
installed size is 45.8Mb
  sub-directories of 1Mb or more:
    libs  44.9Mb
Error(s) in re-building vignettes:
--- re-building ‘odesystem.Rmd’ using rmarkdown

Quitting from lines 77-83 [unnamed-chunk-5] (odesystem.Rmd)
Error: processing vignette 'odesystem.Rmd' failed with diagnostics:
Error 1 occurred building shared library.
--- failed re-building ‘odesystem.Rmd’

--- re-building ‘quick_start.Rmd’ using rmarkdown
--- finished re-building ‘quick_start.Rmd’

SUMMARY: processing the following file failed:
  ‘odesystem.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.0Mb
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    doc    1.8Mb
installed size is 21.3Mb
  sub-directories of 1Mb or more:
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    libs   19.4Mb
Error: inferior call failed
Execution halted
Please remove or rename the files.
See section ‘Package subdirectories’ in the ‘Writing R Extensions’
manual.
Problems with news in ‘inst/NEWS.Rd’:
  cannot open the connection
Fatal error: cannot create 'R_TempDir'
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Fatal error: cannot create 'R_TempDir'
* checking Rd \usage sections ...* using check arguments '--no-clean-on-error '
installed size is 24.9Mb
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installed size is  6.2Mb
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    R         2.3Mb
    extdata   3.1Mb
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    libs  11.0Mb
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    data   4.3Mb
    libs   4.5Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc   5.9Mb
installed size is 13.7Mb
  sub-directories of 1Mb or more:
    java  12.7Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    libs   4.5Mb
installed size is 15.0Mb
  sub-directories of 1Mb or more:
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    libs  13.3Mb
Found the following possibly unsafe calls:
Fatal error: cannot create 'R_TempDir'

Fatal error: cannot create 'R_TempDir'
installed size is 13.5Mb
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installed size is  5.1Mb
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installed size is 10.5Mb
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    libs   1.8Mb
installed size is 37.2Mb
  sub-directories of 1Mb or more:
    doc    1.3Mb
    libs  35.5Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
installed size is 19.2Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    libs  16.5Mb
installed size is  5.8Mb
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See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.4/tergo.Rcheck/00install.out’ for details.
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Packages suggested but not available for checking:
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Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.4/triptych.Rcheck/00install.out’ for details.
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Packages suggested but not available for checking: 'RNRCS', 'metScanR'
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Package required but not available: ‘pwalign’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
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Error(s) in re-building vignettes:
--- re-building ‘benchmarks.Rmd’ using rmarkdown
fatal: not a git repository (or any parent up to mount point /Volumes)
Stopping at filesystem boundary (GIT_DISCOVERY_ACROSS_FILESYSTEM not set).
--- finished re-building ‘benchmarks.Rmd’

--- re-building ‘diseasystore-ecdc-respiratory-viruses.Rmd’ using rmarkdown
--- finished re-building ‘diseasystore-ecdc-respiratory-viruses.Rmd’

--- re-building ‘diseasystore-google-covid-19.Rmd’ using rmarkdown
--- finished re-building ‘diseasystore-google-covid-19.Rmd’

--- re-building ‘diseasystore.Rmd’ using rmarkdown
--- finished re-building ‘diseasystore.Rmd’

--- re-building ‘extending-diseasystore-example.Rmd’ using rmarkdown

Quitting from lines 537-540 [stratifications_positive_sex_age_plot] (extending-diseasystore-example.Rmd)
Error: processing vignette 'extending-diseasystore-example.Rmd' failed with diagnostics:
Faceting variables must have at least one value.
--- failed re-building ‘extending-diseasystore-example.Rmd’

--- re-building ‘extending-diseasystore.Rmd’ using rmarkdown
--- finished re-building ‘extending-diseasystore.Rmd’

SUMMARY: processing the following file failed:
  ‘extending-diseasystore-example.Rmd’

Error: Vignette re-building failed.
Execution halted
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Package suggested but not available for checking: ‘pwalign’
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installed size is 46.0Mb
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installed size is 99.4Mb
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installed size is  7.9Mb
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Packages suggested but not available for checking:
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Running ‘testthat.R’ [6s/14s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(GPfit)
  > 
  > test_check("GPfit", reporter = "summary")
  GP_deviance: 
  GP_deviance: ...
  GPfit: 
  GP_fit creates GP model: ..............
  corr_matrix: 
  corr_matrix: ......
  predict.GP: 
  GP model for predictions: ......1..2......
  
  ══ Failed ══════════════════════════════════════════════════════════════════════
  ── 1. Failure ('test_predict.GP.R:64:9'): check predict.GP ─────────────────────
  smse2 >= 0 & smse2 < 30 is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  
  ── 2. Failure ('test_predict.GP.R:81:9'): check predict.GP ─────────────────────
  sum(gpp2$complete_data[, 5] - ms2 < 1e-05) >= 10 is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  
  ══ DONE ════════════════════════════════════════════════════════════════════════
  Error: Test failures
  Execution halted
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Package required but not available: ‘QSutils’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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Packages suggested but not available for checking:
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installed size is 19.2Mb
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Packages suggested but not available for checking: 'ANCOMBC', 'mia'
Package unavailable to check Rd xrefs: ‘ANCOMBC’
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Packages suggested but not available for checking: 'BioNet', 'DLBCL'
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Packages suggested but not available for checking:
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Package required but not available: ‘ggkegg’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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Installation failed.
See ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.4/pbdMPI.Rcheck/00install.out’ for details.
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Package suggested but not available for checking: ‘ggtreeExtra’
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installed size is  8.5Mb
  sub-directories of 1Mb or more:
    libs   8.3Mb
installed size is 12.3Mb
  sub-directories of 1Mb or more:
    R      4.0Mb
    libs   7.2Mb
installed size is 21.7Mb
  sub-directories of 1Mb or more:
    libs  21.0Mb
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    data   5.6Mb
    etc    1.9Mb
    po     1.2Mb
installed size is 21.5Mb
  sub-directories of 1Mb or more:
    data   4.5Mb
    libs  15.9Mb
installed size is 16.2Mb
  sub-directories of 1Mb or more:
    libs  15.4Mb
installed size is 14.9Mb
  sub-directories of 1Mb or more:
    libs  14.6Mb
installed size is 30.9Mb
  sub-directories of 1Mb or more:
    libs  30.1Mb
installed size is 13.4Mb
  sub-directories of 1Mb or more:
    libs  12.6Mb
installed size is 67.4Mb
  sub-directories of 1Mb or more:
    libs  65.4Mb
installed size is 67.2Mb
  sub-directories of 1Mb or more:
    libs  66.7Mb
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.4/Rblpapi.Rcheck/00install.out’ for details.
installed size is 14.2Mb
  sub-directories of 1Mb or more:
    libs  14.0Mb
installed size is 82.1Mb
  sub-directories of 1Mb or more:
    libs  81.4Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
Package suggested but not available for checking: ‘pd.hg.u133.plus.2’
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.4/Rcplex.Rcheck/00install.out’ for details.
installed size is 22.0Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs  19.7Mb
installed size is 40.3Mb
  sub-directories of 1Mb or more:
    include  37.8Mb
    libs      2.3Mb
installed size is 50.3Mb
  sub-directories of 1Mb or more:
    include  50.2Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
installed size is 34.7Mb
  sub-directories of 1Mb or more:
    include   9.5Mb
    libs     24.7Mb
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    libs   8.2Mb
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.4/RcppMeCab.Rcheck/00install.out’ for details.
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    include   6.7Mb
    libs      2.6Mb
installed size is 14.3Mb
  sub-directories of 1Mb or more:
    doc       1.1Mb
    include   6.3Mb
    libs      5.0Mb
installed size is 23.9Mb
  sub-directories of 1Mb or more:
    include        7.2Mb
    jsonexamples   3.8Mb
    libs          12.6Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    include   1.2Mb
    libs      5.7Mb
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
installed size is 19.9Mb
  sub-directories of 1Mb or more:
    data   1.9Mb
    libs  16.2Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    data   1.7Mb
    libs   1.1Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    2.5Mb
    libs   2.4Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    doc    3.3Mb
    libs   3.0Mb
installed size is 31.5Mb
  sub-directories of 1Mb or more:
    libs        1.5Mb
    redengine  29.9Mb
installed size is 18.3Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    libs  14.4Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    libs   4.9Mb
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    doc    3.5Mb
    libs   3.9Mb
installed size is 26.6Mb
  sub-directories of 1Mb or more:
    libs  25.1Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    libs   6.7Mb
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    doc    3.9Mb
    libs   5.2Mb
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    libs   9.6Mb
Packages suggested but not available for checking: 'PADOG', 'safe'
Packages unavailable to check Rd xrefs: ‘PADOG’, ‘safe’
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   7.1Mb
installed size is 17.2Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    doc    1.2Mb
    libs  13.6Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs      3.4Mb
    swagger   1.4Mb
installed size is 33.5Mb
  sub-directories of 1Mb or more:
    libs  33.3Mb
installed size is 28.5Mb
  sub-directories of 1Mb or more:
    include   2.4Mb
    libs     24.4Mb
    models    1.6Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   3.6Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc        1.1Mb
    examples   1.9Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   4.0Mb
installed size is 24.5Mb
  sub-directories of 1Mb or more:
    libs  23.7Mb
installed size is 46.3Mb
  sub-directories of 1Mb or more:
    libs  44.9Mb
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    libs   7.4Mb
Running ‘testthat.R’ [68s/58s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(Rforestry)
  ## 
  ##  Rforestry (Version 0.10.0, Build Date: R 4.4.1; x86_64-apple-darwin20; 2025-01-31 00:47:56 UTC; unix)
  ##  See https://github.com/forestry-labs for additional documentation.
  ##  Please cite software as:
  ##    Soren R. Kunzel, Theo F. Saarinen, Edward W. Liu, Jasjeet S. Sekhon. 2019.
  ##    ''Linear Aggregation in Tree-based Estimators.'' arXiv preprint 
  ##    arXiv:1906.06463. https://arxiv.org/abs/1906.06463 
  ##
  > 
  > test_check("Rforestry")
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 1422 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-forestry.R:48:3'): Tests that random forest is working correctly ──
  `rf <- forestry(x = iris[, -1], y = iris[, 1], seed = seed_i)` threw an error with unexpected message.
  Expected match: "A parameter passed is not assigned: object 'seed_i' not found\n"
  Actual message: "A parameter passed is not assigned: Error in eval(code, test_env): object 'seed_i' not found\n"
  Backtrace:
       ▆
    1. ├─testthat::expect_error(...) at test-forestry.R:48:3
    2. │ └─testthat:::quasi_capture(...)
    3. │   ├─testthat (local) .capture(...)
    4. │   │ └─base::withCallingHandlers(...)
    5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
    6. └─Rforestry::forestry(x = iris[, -1], y = iris[, 1], seed = seed_i)
    7.   └─base::tryCatch(...)
    8.     └─base (local) tryCatchList(expr, classes, parentenv, handlers)
    9.       └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
   10.         └─value[[3L]](cond)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 1422 ]
  Error: Test failures
  Execution halted
installed size is  7.7Mb
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    libs   6.9Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data      1.9Mb
    doc       1.2Mb
    extdata   1.9Mb
installed size is 28.8Mb
  sub-directories of 1Mb or more:
    libs  27.6Mb
installed size is 37.5Mb
  sub-directories of 1Mb or more:
    doc     7.1Mb
    fonts   1.5Mb
    libs   25.6Mb
installed size is 18.3Mb
  sub-directories of 1Mb or more:
    data   1.6Mb
    libs  15.9Mb
installed size is 13.3Mb
  sub-directories of 1Mb or more:
    libs  13.2Mb
installed size is 25.4Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs  23.8Mb
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    libs   8.7Mb
Note: information on .o files is not available
File ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.4/rJava.Rcheck/rJava/libs/rJava.so’:
  Found ‘___stderrp’, possibly from ‘stderr’ (C)
  Found ‘___stdoutp’, possibly from ‘stdout’ (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 55.9Mb
  sub-directories of 1Mb or more:
    include   3.4Mb
    libs     51.7Mb
installed size is 28.1Mb
  sub-directories of 1Mb or more:
    libs  27.9Mb
installed size is 44.9Mb
  sub-directories of 1Mb or more:
    libs  44.3Mb
installed size is 158.7Mb
  sub-directories of 1Mb or more:
    libs  157.7Mb
installed size is 72.0Mb
  sub-directories of 1Mb or more:
    include   7.3Mb
    lib      37.8Mb
    libs     26.4Mb
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    libs   6.2Mb
installed size is 12.9Mb
  sub-directories of 1Mb or more:
    libs  12.7Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
Found the following significant warnings:
  Warning: Software mark not found in path.
See ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.4/RMark.Rcheck/00install.out’ for details.
installed size is 138.3Mb
  sub-directories of 1Mb or more:
    libs  137.9Mb
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.4/RmecabKo.Rcheck/00install.out’ for details.
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    R      3.0Mb
    libs   6.0Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    R          1.0Mb
    libs       1.1Mb
    minizinc   3.3Mb
installed size is 44.9Mb
  sub-directories of 1Mb or more:
    libs  43.9Mb
installed size is 30.8Mb
  sub-directories of 1Mb or more:
    libs  30.6Mb
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.4/Rmpi.Rcheck/00install.out’ for details.
installed size is 72.2Mb
  sub-directories of 1Mb or more:
    libs  71.6Mb
installed size is 13.2Mb
  sub-directories of 1Mb or more:
    libs  12.9Mb
installed size is 31.8Mb
  sub-directories of 1Mb or more:
    libs  30.5Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   3.0Mb
    doc    2.3Mb
installed size is 19.0Mb
  sub-directories of 1Mb or more:
    libs  18.8Mb
installed size is 120.9Mb
  sub-directories of 1Mb or more:
    extdata    2.0Mb
    libs     118.7Mb
installed size is 13.6Mb
  sub-directories of 1Mb or more:
    libs  12.5Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
    doc    1.7Mb
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    R  12.1Mb
installed size is 21.2Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs  18.6Mb
installed size is 40.7Mb
  sub-directories of 1Mb or more:
    libs  40.6Mb
Package suggested but not available for checking: ‘illuminaHumanv3.db’
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   1.7Mb
installed size is 85.6Mb
  sub-directories of 1Mb or more:
    libs  84.8Mb
installed size is 22.9Mb
  sub-directories of 1Mb or more:
    libs  22.3Mb
installed size is 39.5Mb
  sub-directories of 1Mb or more:
    libs  38.9Mb
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    doc               1.7Mb
    libs              5.1Mb
    simulationStudy   1.5Mb
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.4/ROracle.Rcheck/00install.out’ for details.
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    data   2.7Mb
    libs   5.5Mb
installed size is 14.6Mb
  sub-directories of 1Mb or more:
    R      5.0Mb
    libs   8.3Mb
installed size is 77.7Mb
  sub-directories of 1Mb or more:
    libs  76.5Mb
installed size is 28.0Mb
  sub-directories of 1Mb or more:
    libs  27.0Mb
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   5.9Mb
installed size is 53.1Mb
  sub-directories of 1Mb or more:
    libs  53.0Mb
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    libs   7.9Mb
installed size is 34.0Mb
  sub-directories of 1Mb or more:
    libs  32.6Mb
installed size is 100.2Mb
  sub-directories of 1Mb or more:
    libs  99.6Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc   5.3Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc   3.3Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc   4.2Mb
installed size is 22.8Mb
  sub-directories of 1Mb or more:
    libs  22.6Mb
Note: information on .o files is not available
File ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.4/Rserve.Rcheck/Rserve/libs/Rserve.so’:
  Found ‘___stderrp’, possibly from ‘stderr’ (C)
  Found ‘_abort’, possibly from ‘abort’ (C)
  Found ‘_exit’, possibly from ‘exit’ (C)
  Found ‘_rand’, possibly from ‘rand’ (C)
  Found ‘_random’, possibly from ‘random’ (C)
  Found ‘_sprintf’, possibly from ‘sprintf’ (C)
  Found ‘_srandom’, possibly from ‘srandom’ (C)
File ‘Rserve/libs/Rserve.so’:
  Found non-API calls to R: ‘R_Consolefile’, ‘R_Outputfile’,
    ‘R_TempDir’, ‘R_Visible’, ‘getInputHandler’, ‘ptr_R_Busy’,
    ‘ptr_R_ClearerrConsole’, ‘ptr_R_FlushConsole’, ‘ptr_R_ReadConsole’,
    ‘ptr_R_ResetConsole’, ‘ptr_R_ShowMessage’, ‘ptr_R_WriteConsole’,
    ‘ptr_R_WriteConsoleEx’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.
Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 25.2Mb
  sub-directories of 1Mb or more:
    libs  24.9Mb
installed size is 27.5Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    libs  24.9Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    libs  10.1Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    R      4.2Mb
    help   1.5Mb
installed size is 47.6Mb
  sub-directories of 1Mb or more:
    libs  47.0Mb
installed size is 12.3Mb
  sub-directories of 1Mb or more:
    libs  11.5Mb
installed size is 311.9Mb
  sub-directories of 1Mb or more:
    R       1.9Mb
    doc     4.7Mb
    libs  304.6Mb
installed size is 84.1Mb
  sub-directories of 1Mb or more:
    libs  83.8Mb
installed size is 57.9Mb
  sub-directories of 1Mb or more:
    libs  57.3Mb
installed size is 50.0Mb
  sub-directories of 1Mb or more:
    exec   1.7Mb
    lib   34.7Mb
    libs  11.7Mb
installed size is 38.0Mb
  sub-directories of 1Mb or more:
    libs  22.1Mb
installed size is 28.0Mb
  sub-directories of 1Mb or more:
    libs  27.6Mb
installed size is 27.9Mb
  sub-directories of 1Mb or more:
    swipl  27.5Mb
installed size is 18.0Mb
  sub-directories of 1Mb or more:
    libs  17.9Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs       2.0Mb
    projects   2.9Mb
installed size is 123.1Mb
  sub-directories of 1Mb or more:
    R       1.0Mb
    libs  121.2Mb
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    libs   7.5Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    R   6.1Mb
installed size is 28.9Mb
  sub-directories of 1Mb or more:
    doc    7.8Mb
    libs  20.2Mb
installed size is 221.0Mb
  sub-directories of 1Mb or more:
    data    1.5Mb
    libs  218.5Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    extdata   1.0Mb
    libs      4.0Mb
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    R      3.0Mb
    libs   2.5Mb
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
    libs   6.6Mb
installed size is 48.7Mb
  sub-directories of 1Mb or more:
    libs  47.4Mb
installed size is 65.4Mb
  sub-directories of 1Mb or more:
    include   5.1Mb
    libs     59.9Mb
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    libs   9.3Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    doc    3.9Mb
installed size is 14.4Mb
  sub-directories of 1Mb or more:
    libs  14.3Mb
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    R         2.0Mb
    include   1.1Mb
    libs      6.3Mb
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    libs    7.7Mb
    yacas   1.3Mb
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    libs    8.4Mb
    yacas   1.3Mb
installed size is 12.3Mb
  sub-directories of 1Mb or more:
    libs  12.2Mb
installed size is 37.9Mb
  sub-directories of 1Mb or more:
    libs  36.8Mb
installed size is 16.8Mb
  sub-directories of 1Mb or more:
    libs  15.6Mb
installed size is 14.4Mb
  sub-directories of 1Mb or more:
    libs  13.3Mb
installed size is 23.0Mb
  sub-directories of 1Mb or more:
    libs  22.8Mb
installed size is 54.3Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    libs  51.8Mb
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    help   3.4Mb
    libs   3.9Mb
installed size is 54.8Mb
  sub-directories of 1Mb or more:
    libs  54.7Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   3.1Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc    3.9Mb
    libs   3.1Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    libs   3.9Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   3.1Mb
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    libs   7.9Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    data   3.9Mb
    libs   3.6Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
Package suggested but not available for checking: ‘Linnorm’
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   3.2Mb
    libs   2.8Mb
installed size is 18.0Mb
  sub-directories of 1Mb or more:
    libs  17.4Mb
installed size is 32.1Mb
  sub-directories of 1Mb or more:
    cppad     9.4Mb
    include   4.6Mb
    libs     17.4Mb
installed size is 21.3Mb
  sub-directories of 1Mb or more:
    libs  20.5Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   4.0Mb
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    libs   5.5Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R          3.0Mb
    external   1.2Mb
installed size is 89.4Mb
  sub-directories of 1Mb or more:
    libs  87.4Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
installed size is 18.9Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    libs  15.0Mb
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   8.5Mb
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    data   2.9Mb
    libs   7.8Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
Package suggested but not available for checking: ‘ctsemOMX’
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    R      3.0Mb
    libs   2.5Mb
installed size is 22.8Mb
  sub-directories of 1Mb or more:
    libs    21.1Mb
    models   1.6Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   4.0Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    libs   4.5Mb
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    libs   8.1Mb
installed size is 18.3Mb
  sub-directories of 1Mb or more:
    doc    6.4Mb
    libs  11.0Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data        1.4Mb
    sequences   1.9Mb
Found the following significant warnings:
  SingleChromosomeVCFIndex.cpp:109:51: warning: format specifies type 'long' but the argument has type 'int64_t' (aka 'long long') [-Wformat]
See ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.4/seqminer.Rcheck/00install.out’ for details.
* used C compiler: ‘Apple clang version 14.0.3 (clang-1403.0.22.14.1)’
* used C++ compiler: ‘Apple clang version 14.0.3 (clang-1403.0.22.14.1)’
* used SDK: ‘MacOSX11.3.sdk’
installed size is 19.4Mb
  sub-directories of 1Mb or more:
    libs  17.9Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   5.7Mb
    libs   1.1Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    libs   4.2Mb
installed size is 56.5Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs  54.3Mb
installed size is 19.9Mb
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Packages suggested but not available for checking:
  'BPCells', 'monocle', 'presto'
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    R      1.7Mb
    libs   8.3Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    R     2.0Mb
    doc   5.2Mb
installed size is 272.6Mb
  sub-directories of 1Mb or more:
    doc       1.8Mb
    libs    266.1Mb
    sqlite    1.5Mb
installed size is 11.2Mb
  sub-directories of 1Mb or more:
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installed size is 14.1Mb
  sub-directories of 1Mb or more:
    R     2.0Mb
    www  10.3Mb
installed size is 18.6Mb
  sub-directories of 1Mb or more:
    extdata  13.0Mb
    libs      4.9Mb
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    doc    1.0Mb
    libs   3.2Mb
installed size is 14.5Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs  12.4Mb
installed size is 22.8Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs  20.3Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   2.8Mb
installed size is 11.1Mb
  sub-directories of 1Mb or more:
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    extdata   1.3Mb
    libs      7.6Mb
installed size is 15.7Mb
  sub-directories of 1Mb or more:
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installed size is 39.2Mb
  sub-directories of 1Mb or more:
    libs  38.5Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
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    libs   1.9Mb
installed size is 33.1Mb
  sub-directories of 1Mb or more:
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installed size is  9.2Mb
  sub-directories of 1Mb or more:
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installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.4/smer.Rcheck/00install.out’ for details.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
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    libs   2.2Mb
installed size is 15.9Mb
  sub-directories of 1Mb or more:
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    doc    3.4Mb
    libs  10.8Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    extdata   3.1Mb
    libs      2.8Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
installed size is 13.8Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    doc    1.3Mb
    libs  10.0Mb
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    libs   7.2Mb
installed size is 19.3Mb
  sub-directories of 1Mb or more:
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    libs  14.5Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    libs   2.9Mb
installed size is  8.4Mb
  sub-directories of 1Mb or more:
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    libs      2.0Mb
installed size is  5.6Mb
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    libs      3.3Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
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    libs   2.5Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
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installed size is  6.8Mb
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installed size is 39.9Mb
  sub-directories of 1Mb or more:
    R      3.1Mb
    libs  35.5Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    doc    1.3Mb
    libs   1.5Mb
installed size is 13.9Mb
  sub-directories of 1Mb or more:
    libs  13.9Mb
installed size is 47.0Mb
  sub-directories of 1Mb or more:
    libs  46.3Mb
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.4/spaths.Rcheck/00install.out’ for details.
installed size is 95.0Mb
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installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
installed size is  5.5Mb
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installed size is 13.2Mb
  sub-directories of 1Mb or more:
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installed size is  6.1Mb
  sub-directories of 1Mb or more:
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installed size is  5.1Mb
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installed size is  5.4Mb
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installed size is 23.1Mb
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installed size is 14.0Mb
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installed size is  6.3Mb
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installed size is  8.7Mb
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installed size is  7.1Mb
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installed size is 12.0Mb
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installed size is  7.2Mb
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installed size is 28.2Mb
  sub-directories of 1Mb or more:
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installed size is 18.2Mb
  sub-directories of 1Mb or more:
    libs  17.0Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
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installed size is  5.1Mb
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installed size is  5.2Mb
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installed size is 17.3Mb
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installed size is  7.2Mb
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installed size is  9.3Mb
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installed size is 92.2Mb
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installed size is 13.3Mb
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installed size is 41.9Mb
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installed size is 117.0Mb
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installed size is  5.4Mb
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installed size is 36.4Mb
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installed size is 51.0Mb
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installed size is 17.4Mb
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installed size is 92.1Mb
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installed size is  9.9Mb
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installed size is  7.5Mb
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installed size is 25.4Mb
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installed size is 94.9Mb
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installed size is 46.7Mb
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installed size is 10.5Mb
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installed size is  8.2Mb
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installed size is 34.6Mb
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installed size is  9.7Mb
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installed size is  5.1Mb
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installed size is  5.7Mb
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installed size is 15.5Mb
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installed size is  8.1Mb
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installed size is 64.8Mb
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installed size is  6.9Mb
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installed size is 10.4Mb
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installed size is 11.3Mb
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installed size is 31.1Mb
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installed size is 65.0Mb
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installed size is  8.6Mb
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installed size is 46.9Mb
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installed size is 22.2Mb
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installed size is 44.8Mb
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installed size is 25.5Mb
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installed size is 11.9Mb
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installed size is  9.4Mb
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installed size is 15.2Mb
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installed size is  7.5Mb
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installed size is 10.5Mb
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installed size is 38.1Mb
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installed size is  6.7Mb
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installed size is  9.6Mb
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installed size is 47.9Mb
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installed size is 203.0Mb
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installed size is 68.9Mb
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installed size is  9.0Mb
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Package required but not available: ‘ggtreeExtra’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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installed size is 53.4Mb
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Installation failed.
See ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.4/triptych.Rcheck/00install.out’ for details.
installed size is 20.8Mb
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installed size is 133.9Mb
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installed size is 15.0Mb
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installed size is  8.5Mb
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installed size is 100.0Mb
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installed size is 19.8Mb
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installed size is 120.1Mb
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installed size is 23.6Mb
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installed size is 26.5Mb
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installed size is  6.0Mb
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installed size is 65.0Mb
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installed size is  5.6Mb
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installed size is 24.5Mb
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installed size is  6.1Mb
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Package which this enhances but not available for checking: 'asreml'
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Package suggested but not available for checking: 'metaboliteIDmapping'
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installed size is  5.4Mb
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installed size is  5.2Mb
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Package suggested but not available for checking: 'arcgisbinding'
Package suggested but not available for checking: 'ArchaeoData'
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installed size is 14.4Mb
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Running 'testthat.R' [46s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(ARUtools)
  > 
  > test_check("ARUtools")
  ERROR: Unknown command "TMPDIR=D:/temp/2025_02_16_01_50_00_32289/RtmpSOUrGL/file2262ca063c48". Did you mean command "preview"?
  ERROR: Unknown command "TMPDIR=D:/temp/2025_02_16_01_50_00_32289/RtmpSOUrGL/file2262c4ff77032". Did you mean command "preview"?
  Extracting Dates and Times...
  ! Omitted 1 extra, non-json/GPS files
  ! Detected 2 log files
  [ FAIL 2 | WARN 0 | SKIP 6 | PASS 566 ]
  
  ══ Skipped tests (6) ═══════════════════════════════════════════════════════════
  • On CRAN (5): 'test-08_selections.R:27:3', 'test-08_selections.R:91:3',
    'test-08_selections.R:198:3', 'test-10_clean_logs.R:29:3',
    'test-10_clean_logs.R:61:3'
  • SoX not available (1): 'test-07_wave_files.R:193:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-09_create_dirs.R:35:3'): create_dirs() ───────────────────────
  `... <- NULL` produced warnings.
  ── Failure ('test-09_create_dirs.R:78:3'): create_dirs() ───────────────────────
  `... <- NULL` produced warnings.
  
  [ FAIL 2 | WARN 0 | SKIP 6 | PASS 566 ]
  Deleting unused snapshots:
  • 08_selections/sim-selection-weights2.svg
  • 08_selections/sim-selection-weights3.svg
  Error: Test failures
  Execution halted
Check process probably crashed or hung up for 20 minutes ... killed
Most likely this happened in the example checks (?),
if not, ignore the following last lines of example output:
+ GTATGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTC
+ CTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATTACAGGCGAACATACTTACTAAAGTGTGTTA
+ ATTAATTAATGCTTGTAGGACATAATAATAACAATTGAATGTCTGCACAGCCACTTTCCACACAGACATC'
> my_seqblock<-genbank_seqblock(my_sequence)
> cat(my_seqblock)
    1    6     11   16    21   26    31   36    41   46    51   56   
    |    |     |    |     |    |     |    |     |    |     |    |    
    |||||||||| |||||||||| |||||||||| |||||||||| |||||||||| ||||||||||
  1 GATCACAGGT CTATCACCCT ATTAACCACT CACGGGAGCT CTCCATGCAT TTGGTATTTT
 61 CGTCTGGGGG GTATGCACGC GATAGCATTG CGAGACGCTG GAGCCGGAGC ACCCTATGTC
121 GCAGTATCTG TCTTTGATTC CTGCCTCATC CTATTATTTA TCGCACCTAC GTTCAATATT
181 ACAGGCGAAC ATACTTACTA AAGTGTGTTA ATTAATTAAT GCTTGTAGGA CATAATAATA
241 ACAATTGAAT GTCTGCACAG CCACTTTCCA CACAGACATC> 
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()
> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
Time elapsed:  0.57 0.07 0.63 NA NA 
> grDevices::dev.off()
null device 
          1 
> ###
> ### Local variables: ***
> ### mode: outline-minor ***
> ### outline-regexp: "\\(> \\)?### [*]+" ***
> ### End: ***
> quit('no')
======== End of example output (where/before crash/hang up occured ?) ========
installed size is  6.6Mb
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    include   6.5Mb
Package suggested but not available for checking: 'asteRiskData'
installed size is  5.1Mb
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    doc    2.6Mb
    libs   1.0Mb
installed size is 40.5Mb
  sub-directories of 1Mb or more:
    libs  39.7Mb
Package suggested but not available for checking: 'lixoftConnectors'
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   5.3Mb
Package required and available but unsuitable version: 'methods'

Depends: includes the non-default packages:
  'dplyr', 'glue', 'janitor', 'lubridate', 'readr', 'snakecase',
  'stringr'
Adding so many packages to the search path is excessive and importing
selectively is preferable.

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    doc    4.9Mb
    libs   3.4Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    libs   3.5Mb
Package suggested but not available for checking: 'fdpbandsdata'
installed size is  5.9Mb
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    data   3.1Mb
    libs   1.3Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    doc    4.4Mb
    help   2.2Mb
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   5.1Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs   5.4Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    extdata   4.1Mb
    libs      1.2Mb
Package suggested but not available for checking: 'doMC'
installed size is 13.3Mb
  sub-directories of 1Mb or more:
    doc   10.8Mb
    libs   1.5Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
installed size is 13.8Mb
  sub-directories of 1Mb or more:
    libs  12.7Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    help   1.9Mb
    libs   3.3Mb
installed size is 17.2Mb
  sub-directories of 1Mb or more:
    libs  16.5Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    2.7Mb
    libs   1.7Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    doc    2.8Mb
    libs   2.2Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   3.7Mb
    doc    1.0Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    R     1.9Mb
    doc   3.8Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    doc    1.4Mb
    libs   2.2Mb
installed size is 12.8Mb
  sub-directories of 1Mb or more:
    libs  12.7Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   3.3Mb
    doc    1.2Mb
    libs   1.4Mb
Package suggested but not available for checking: 'BRugs'
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   1.7Mb
    libs   3.6Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    doc    3.3Mb
    help   1.1Mb
    libs   1.5Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc    2.9Mb
    libs   1.3Mb
installed size is 150.3Mb
  sub-directories of 1Mb or more:
    include  149.3Mb
Package suggested but not available for checking: 'ffbase'
Package suggested but not available for checking: 'rrelaxiv'
installed size is 17.5Mb
  sub-directories of 1Mb or more:
    libs  17.2Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data      1.6Mb
    extdata   2.0Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   1.6Mb
    help   2.4Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    extdata   4.8Mb
    libs      1.2Mb
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    R          1.2Mb
    libs       5.3Mb
    testdata   1.4Mb
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    libs   8.5Mb
Package suggested but not available for checking: 'cmdstanr'
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    data   7.0Mb
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    data   7.7Mb
    libs   1.1Mb
installed size is 40.5Mb
  sub-directories of 1Mb or more:
    include  10.5Mb
    lib      29.5Mb
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    R     3.8Mb
    doc   3.6Mb
Package suggested but not available for checking: 'glmmADMB'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/BRugs.Rcheck/00install.out' for details.
installed size is 12.3Mb
  sub-directories of 1Mb or more:
    components   1.0Mb
    fonts        2.4Mb
    lib          5.0Mb
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    doc    2.8Mb
    libs   3.2Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/btb.Rcheck/00install.out' for details.
Running 'testthat.R' [36s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library("testthat")
  > 
  > test_check("btergm")
  Loading required package: btergm
  Registered S3 methods overwritten by 'btergm':
    method    from
    plot.gof  ergm
    print.gof ergm
  Package:  btergm
  Version:  1.10.12
  Date:     2024-03-31
  Authors:  Philip Leifeld (University of Manchester)
            Skyler J. Cranmer (The Ohio State University)
            Bruce A. Desmarais (Pennsylvania State University)
  
  [ FAIL 1 | WARN 2 | SKIP 8 | PASS 51 ]
  
  ══ Skipped tests (8) ═══════════════════════════════════════════════════════════
  • On CRAN (8): 'test-btergm.R:82:3', 'test-btergm.R:180:3',
    'test-btergm.R:197:3', 'test-data.R:4:3', 'test-interpret.R:4:3',
    'test-interpret.R:32:3', 'test-interpret.R:59:3', 'test-interpret.R:87:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-btergm.R:73:3'): offset argument in btergm works without composition change ──
  Error in `ergm::ergm.pl(nw, Clist.miss, model, theta.offset = c(rep(FALSE, 
      length(l$rhs.terms) - 1), TRUE), verbose = FALSE, control = control.ergm)`: VECTOR_ELT() can only be applied to a 'list', not a 'NULL'
  Backtrace:
      ▆
   1. ├─base::suppressWarnings(...) at test-btergm.R:73:3
   2. │ └─base::withCallingHandlers(...)
   3. └─btergm::btergm(...)
   4.   └─ergm::ergm.pl(...)
  
  [ FAIL 1 | WARN 2 | SKIP 8 | PASS 51 ]
  Error: Test failures
  Execution halted
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc   4.9Mb
installed size is 11.8Mb
  sub-directories of 1Mb or more:
    data   9.9Mb
Package suggested but not available for checking: 'ReGenesees'
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc   4.8Mb
Package suggested but not available for checking: 'rnaturalearthhires'
Check process probably crashed or hung up for 20 minutes ... killed
Most likely this happened in the example checks (?),
if not, ignore the following last lines of example output:
> ##D #...or calculate the DI and LPD of the trained model:
> ##D # DI = trainDI(model=model, LPD = TRUE)
> ##D 
> ##D # the DI can now be used to compute the AOA (here with LPD):
> ##D studyArea = rast(system.file("extdata/predictors_chile.tif", package = "CAST"))
> ##D AOA = aoa(studyArea, model = model, trainDI = DI, LPD = TRUE, maxLPD = 1)
> ##D print(AOA)
> ##D plot(AOA)
> ##D plot(AOA$AOA)
> ##D plot(AOA$LPD)
> ## End(Not run)
> 
> 
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()
> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
Time elapsed:  10.23 0.78 11.03 NA NA 
> grDevices::dev.off()
null device 
          1 
> ###
> ### Local variables: ***
> ### mode: outline-minor ***
> ### outline-regexp: "\\(> \\)?### [*]+" ***
> ### End: ***
> quit('no')
======== End of example output (where/before crash/hang up occured ?) ========
Package suggested but not available for checking: 'rkeops'
installed size is 17.5Mb
  sub-directories of 1Mb or more:
    doc   16.4Mb
    libs   1.0Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   3.2Mb
    doc    2.0Mb
    libs   1.7Mb
installed size is 38.7Mb
  sub-directories of 1Mb or more:
    include  38.4Mb
Package suggested but not available for checking: 'darts'
Package suggested but not available for checking: 'countreg'
Package unavailable to check Rd xrefs: 'cmdstanr'
Package suggested but not available for checking: 'entab'
Package suggested but not available for checking: 'userfriendlyscience'
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    doc   7.2Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    doc    3.6Mb
    help   1.0Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    extdata   5.3Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   3.4Mb
    doc    1.9Mb
Package suggested but not available for checking: 'monocle3'
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   5.2Mb
Package suggested but not available for checking: 'tobit1'
Package suggested but not available for checking: 'PopGenome'
Package suggested but not available for checking: 'disttree'
Package which this enhances but not available for checking: 'rkward'
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc    3.6Mb
    help   1.9Mb
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    doc   9.4Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    libs   2.8Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs   2.8Mb
Package suggested but not available for checking: 'CAM'
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc   5.4Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   4.1Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    libs   1.2Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    R     2.1Mb
    doc   3.2Mb
Running examples in 'correlation-Ex.R' failed
The error most likely occurred in:

> ### Name: cormatrix_to_excel
> ### Title: Easy export of correlation matrix to Excel
> ### Aliases: cormatrix_to_excel
> ### Keywords: Excel correlation matrix
> 
> ### ** Examples
> 
> ## Don't show: 
> if (requireNamespace("openxlsx2", quietly = TRUE)) (if (getRversion() >= "3.4") withAutoprint else force)({ # examplesIf
+ ## End(Don't show)
+ ## Don't show: 
+ .old_wd <- setwd(tempdir())
+ ## End(Don't show)
+ # Basic example
+ suppressWarnings(cormatrix_to_excel(mtcars,
+   select = c("mpg", "cyl", "disp", "hp", "carb"), filename = "cormatrix1"
+ ))
+ suppressWarnings(cormatrix_to_excel(iris,
+   p_adjust = "none",
+   filename = "cormatrix2"
+ ))
+ suppressWarnings(cormatrix_to_excel(airquality,
+   method = "spearman",
+   filename = "cormatrix3"
+ ))
+ ## Don't show: 
+ setwd(.old_wd)
+ ## End(Don't show)
+ ## Don't show: 
+ }) # examplesIf
> .old_wd <- setwd(tempdir())
> suppressWarnings(cormatrix_to_excel(mtcars, select = c("mpg", "cyl", "disp", 
+     "hp", "carb"), filename = "cormatrix1"))
# Correlation Matrix (pearson-method)

Parameter |      mpg |      cyl |     disp |       hp |    carb
---------------------------------------------------------------
mpg       |          | -0.85*** | -0.85*** | -0.78*** | -0.55**
cyl       | -0.85*** |          |  0.90*** |  0.83*** |  0.53**
disp      | -0.85*** |  0.90*** |          |  0.79*** |   0.39*
hp        | -0.78*** |  0.83*** |  0.79*** |          | 0.75***
carb      |  -0.55** |   0.53** |    0.39* |  0.75*** |        

p-value adjustment method: Holm (1979)
Error: x must be class wbColour
Execution halted
Running 'testthat.R' [26s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(correlation)
  > 
  > test_check("correlation")
  
  For i = 2 j = 1  A cell entry of 0 was replaced with correct =  0.5.  Check your data!
  For i = 2 j = 1  A cell entry of 0 was replaced with correct =  0.5.  Check your data!
  [ FAIL 2 | WARN 1 | SKIP 11 | PASS 124 ]
  
  ══ Skipped tests (11) ══════════════════════════════════════════════════════════
  • On CRAN (11): 'test-as.list.R:7:3', 'test-correlation.R:172:3',
    'test-correlation.R:195:3', 'test-display_print_dataframe.R:2:3',
    'test-display_print_dataframe.R:14:3', 'test-display_print_matrix.R:4:3',
    'test-display_print_matrix.R:13:3', 'test-display_print_matrix.R:31:3',
    'test-methods.R:9:3', 'test-renaming.R:9:3',
    'test-selecting_variables.R:28:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-cormatrix_to_excel.R:3:3'): cormatrix_to_excel select ──────────
  Error: x must be class wbColour
  Backtrace:
      ▆
   1. └─testthat::expect_snapshot(...) at test-cormatrix_to_excel.R:3:3
   2.   └─rlang::cnd_signal(state$error)
  ── Error ('test-cormatrix_to_excel.R:16:3'): cormatrix_to_excel p_adjust ───────
  Error: x must be class wbColour
  Backtrace:
      ▆
   1. └─testthat::expect_snapshot(...) at test-cormatrix_to_excel.R:16:3
   2.   └─rlang::cnd_signal(state$error)
  
  [ FAIL 2 | WARN 1 | SKIP 11 | PASS 124 ]
  Error: Test failures
  Execution halted
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    data   4.5Mb
    doc    1.6Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    doc    2.8Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    include   6.6Mb
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    include   7.8Mb
Error(s) in re-building vignettes:
--- re-building 'cran.Rmd' using rmarkdown
--- finished re-building 'cran.Rmd'

--- re-building 'degree.Rmd' using rmarkdown

Quitting from lines 46-52 [unnamed-chunk-2] (degree.Rmd)
Error: processing vignette 'degree.Rmd' failed with diagnostics:
no applicable method for 'inner_join' applied to an object of class "NULL"
--- failed re-building 'degree.Rmd'

--- re-building 'introduction.Rmd' using rmarkdown
--- finished re-building 'introduction.Rmd'

SUMMARY: processing the following file failed:
  'degree.Rmd'

Error: Vignette re-building failed.
Execution halted
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   5.7Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
    doc    1.5Mb
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    data   1.7Mb
    libs   7.5Mb
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs   6.5Mb
File 'curl/libs/x64/curl.dll':
  Found non-API call to R: 'R_new_custom_connection'

Compiled code should not call non-API entry points in R.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
Package which this enhances but not available for checking: 'RGtk2'
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    R      2.6Mb
    doc    1.2Mb
    help   1.1Mb
    libs   1.2Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    extdata       1.3Mb
    htmlwidgets   1.4Mb
Package which this enhances but not available for checking: 'doMC'
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   4.4Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   5.0Mb
Package suggested but not available for checking: 'SASxport'
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    3.0Mb
    libs   1.4Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   4.2Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    help   2.2Mb
    libs   1.9Mb
Package suggested but not available for checking: 'Rdonlp2'
Package suggested but not available for checking: 'RDCOMClient'
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    R      1.7Mb
    doc    1.8Mb
    help   1.7Mb
    libs   1.2Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data          1.8Mb
    htmlwidgets   3.6Mb
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    doc  10.8Mb
Package suggested but not available for checking: 'gurobi'
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc       1.5Mb
    extdata   4.2Mb
Package suggested but not available for checking: 'BOLTSSIRR'
installed size is 16.9Mb
  sub-directories of 1Mb or more:
    include  15.8Mb
installed size is 14.2Mb
  sub-directories of 1Mb or more:
    libs  13.5Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    libs   2.5Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
    libs   1.1Mb
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    doc    6.7Mb
    libs   1.7Mb
Package which this enhances but not available for checking: 'gurobi'
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    R         1.9Mb
    data      1.9Mb
    extdata   2.3Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    assets   2.9Mb
    doc      2.2Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data      1.6Mb
    extdata   3.2Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc   2.5Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/DRviaSPCN.Rcheck/00install.out' for details.
Package suggested but not available for checking: 'dsBaseClient'
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    htmlwidgets   5.4Mb
installed size is 31.1Mb
  sub-directories of 1Mb or more:
    libs  30.3Mb
Error(s) in re-building vignettes:
--- re-building 'editing.Rmd' using rmarkdown
--- finished re-building 'editing.Rmd'

--- re-building 'real-data.Rmd' using rmarkdown
trying URL 'https://data.canadensys.net/ipt/archive.do?r=vascan&v=37.12'
downloaded 1.4 MB


Quitting from lines 71-79 [download-unzip] (real-data.Rmd)
Error: processing vignette 'real-data.Rmd' failed with diagnostics:
download from 'https://data.canadensys.net/ipt/archive.do?r=vascan&v=37.12' failed
--- failed re-building 'real-data.Rmd'

--- re-building 'validation.Rmd' using rmarkdown
--- finished re-building 'validation.Rmd'

--- re-building 'what-is-dwc.Rmd' using rmarkdown
--- finished re-building 'what-is-dwc.Rmd'

SUMMARY: processing the following file failed:
  'real-data.Rmd'

Error: Vignette re-building failed.
Execution halted
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    extdata   5.1Mb
installed size is 12.4Mb
  sub-directories of 1Mb or more:
    R      3.5Mb
    data   7.3Mb
    doc    1.1Mb
Package suggested but not available for checking: 'lle'
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   2.5Mb
    doc    1.4Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   3.9Mb
installed size is  5.3Mb
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    data   3.0Mb
    libs   1.7Mb
installed size is 15.6Mb
  sub-directories of 1Mb or more:
    doc    3.5Mb
    libs  11.1Mb
The following files should probably not be installed:
  'econet.tex'

Consider the use of a .Rinstignore file: see 'Writing R Extensions',
or move the vignette sources from 'inst/doc' to 'vignettes'.
installed size is  7.4Mb
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    help   2.7Mb
    libs   4.3Mb
Package suggested but not available for checking: 'eggCountsExtra'
installed size is  7.1Mb
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    libs   6.4Mb
Error(s) in re-building vignettes:
--- re-building 'EHRtemporalVariability.Rmd' using rmarkdown

Quitting from lines 139-146 [readCSV] (EHRtemporalVariability.Rmd)
Error: processing vignette 'EHRtemporalVariability.Rmd' failed with diagnostics:
cannot read from connection
--- failed re-building 'EHRtemporalVariability.Rmd'

SUMMARY: processing the following file failed:
  'EHRtemporalVariability.Rmd'

Error: Vignette re-building failed.
Execution halted
installed size is  5.4Mb
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    libs   4.1Mb
installed size is  6.6Mb
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    R      2.3Mb
    help   3.6Mb
Package suggested but not available for checking: 'epidict'
installed size is  5.1Mb
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    doc   2.8Mb
installed size is 10.7Mb
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    libs   6.8Mb
installed size is  5.1Mb
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Package suggested but not available for checking: 'ExactData'
installed size is 14.2Mb
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    exiftool  14.1Mb
Package suggested but not available for checking: 'cec2013'
Package suggested but not available for checking: 'exuberdata'
installed size is  5.8Mb
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    help   1.2Mb
installed size is  5.2Mb
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    doc    3.0Mb
    help   1.3Mb
installed size is  7.4Mb
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    doc    2.5Mb
    help   1.8Mb
    libs   2.0Mb
installed size is  5.7Mb
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    R      2.8Mb
    help   1.8Mb
Missing link or links in Rd file 'fast.Rd':
  '[rgrass:readRAST]{rgrass::read_RAST()}'
  '[rgrass:readVECT]{rgrass::read_VECT()}'

See section 'Cross-references' in the 'Writing R Extensions' manual.
installed size is  5.6Mb
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    images   3.1Mb
    libs     1.3Mb
installed size is  5.7Mb
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    doc    1.1Mb
    libs   1.1Mb
Package suggested but not available for checking: 'coxKM'
installed size is  6.3Mb
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    libs   1.2Mb
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installed size is  5.7Mb
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    data   3.7Mb
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Running 'spelling.R' [0s]
  Running 'testthat.R' [201s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > suppressMessages(library(testthat))
  > 
  > test_check("fbar")
  Loading required package: fbar
  [ FAIL 2 | WARN 13 | SKIP 2 | PASS 44 ]
  
  ══ Skipped tests (2) ═══════════════════════════════════════════════════════════
  • known theoretical issue (2): 'test-full-size.R:36:3', 'test-full-size.R:46:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-utilities.R:27:5'): Works correctly with http://bigg.ucsd.edu/static/models/iJO1366.json ──
  Error in `readBin(structure(4L, class = c("url", "connection"), conn_id = <pointer: 0x00000000000001e5>), 
      raw(0), 32768L)`: cannot read from connection
  Backtrace:
      ▆
   1. ├─fbar::get_BiGG(address) at test-utilities.R:27:5
   2. │ └─jsonlite::fromJSON(address)
   3. │   └─jsonlite:::parse_and_simplify(...)
   4. │     └─jsonlite:::parseJSON(txt, bigint_as_char)
   5. │       └─jsonlite:::parse_con(txt, bigint_as_char)
   6. └─base::readBin(`<url>`, `<raw>`, 32768L)
  ── Error ('test-utilities.R:27:5'): Works correctly with http://bigg.ucsd.edu/static/models/iAF1260.json ──
  Error in `readBin(structure(4L, class = c("url", "connection"), conn_id = <pointer: 0x00000000000001f2>), 
      raw(0), 32768L)`: cannot read from connection
  Backtrace:
      ▆
   1. ├─fbar::get_BiGG(address) at test-utilities.R:27:5
   2. │ └─jsonlite::fromJSON(address)
   3. │   └─jsonlite:::parse_and_simplify(...)
   4. │     └─jsonlite:::parseJSON(txt, bigint_as_char)
   5. │       └─jsonlite:::parse_con(txt, bigint_as_char)
   6. └─base::readBin(`<url>`, `<raw>`, 32768L)
  
  [ FAIL 2 | WARN 13 | SKIP 2 | PASS 44 ]
  Error: Test failures
  Execution halted
installed size is  6.9Mb
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installed size is  7.5Mb
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    R      1.8Mb
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    help   2.1Mb
    libs   1.6Mb
installed size is  5.1Mb
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    data   2.3Mb
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Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/fdrDiscreteNull.Rcheck/00install.out' for details.
installed size is  5.2Mb
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    data   1.8Mb
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installed size is  5.7Mb
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    data   1.8Mb
    libs   2.2Mb
installed size is 10.4Mb
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    R         4.6Mb
    doc       2.1Mb
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Running 'testthat.R' [61s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(findPackage)
  > 
  > test_check("findPackage")
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 5 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-findPackage.R:27:3'): errors ───────────────────────────────────
  Error in `readRDS(con)`: cannot read from connection
  Backtrace:
      ▆
   1. ├─testthat::expect_equal(...) at test-findPackage.R:27:3
   2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
   3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
   4. ├─base::nrow(findPackage("MCDA", sortOrder = "D"))
   5. └─findPackage::findPackage("MCDA", sortOrder = "D")
   6.   └─tools::CRAN_package_db()
   7.     ├─base::as.data.frame(...)
   8.     └─tools:::read_CRAN_object(CRAN_baseurl_for_web_area(), "web/packages/packages.rds")
   9.       └─base::readRDS(con)
  
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 5 ]
  Error: Test failures
  Execution halted
installed size is 14.0Mb
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Package suggested but not available for checking: 'gridlayout'
Packages suggested but not available for checking: 'reliaR', 'STAR'
Package suggested but not available for checking: 'fivethirtyeightdata'
Package unavailable to check Rd xrefs: 'fivethirtyeightdata'
installed size is  7.7Mb
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installed size is  5.8Mb
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installed size is 22.9Mb
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installed size is 10.7Mb
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installed size is  7.1Mb
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installed size is  5.2Mb
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installed size is  6.1Mb
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installed size is  6.4Mb
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Package suggested but not available for checking: 'RandomFields'
installed size is  9.1Mb
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installed size is  5.1Mb
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installed size is  8.6Mb
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installed size is 33.5Mb
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Package suggested but not available for checking: 'paleofire'
installed size is 110.8Mb
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installed size is 108.9Mb
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Package suggested but not available for checking: 'gdxrrw'
installed size is  6.1Mb
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Package suggested but not available for checking: 'genderdata'
installed size is 13.5Mb
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installed size is  6.7Mb
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installed size is  5.8Mb
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installed size is  6.7Mb
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Package suggested but not available for checking: 'geomarocdata'
installed size is 22.0Mb
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installed size is  5.8Mb
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installed size is  6.0Mb
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installed size is  5.0Mb
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Package suggested but not available for checking: 'RGtk2'
installed size is  6.2Mb
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installed size is 10.0Mb
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installed size is  6.0Mb
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installed size is  5.9Mb
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installed size is 18.2Mb
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installed size is  5.8Mb
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installed size is 10.8Mb
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installed size is  5.9Mb
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Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/GSEMA.Rcheck/00install.out' for details.
installed size is  5.9Mb
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installed size is  6.3Mb
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installed size is 267.8Mb
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Package required and available but unsuitable version: 'h3lib'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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Package suggested but not available for checking: 'colorfulVennPlot'
Package which this enhances but not available for checking: 'HadoopStreaming'
installed size is  5.0Mb
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Package suggested but not available for checking: 'microViz'
installed size is  7.6Mb
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Error(s) in re-building vignettes:
--- re-building 'htrSPRanalysis-vignette.Rmd' using knitr
trying URL 'https://gitlab.oit.duke.edu/janice/htrspranalysis/-/raw/master/inst/extdata/titration_data.xlsx?ref_type=heads'
Content type 'application/octet-stream' length 4816423 bytes (4.6 MB)
=========================
downloaded 2.3 MB


Quitting from lines 93-121 [unnamed-chunk-3] (htrSPRanalysis-vignette.Rmd)
Error: processing vignette 'htrSPRanalysis-vignette.Rmd' failed with diagnostics:
download from 'https://gitlab.oit.duke.edu/janice/htrspranalysis/-/raw/master/inst/extdata/titration_data.xlsx?ref_type=heads' failed
--- failed re-building 'htrSPRanalysis-vignette.Rmd'

SUMMARY: processing the following file failed:
  'htrSPRanalysis-vignette.Rmd'

Error: Vignette re-building failed.
Execution halted
installed size is  6.3Mb
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Package suggested but not available for checking: 'hurricaneexposuredata'
installed size is  7.3Mb
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installed size is  7.4Mb
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installed size is  6.4Mb
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installed size is  5.6Mb
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installed size is 10.7Mb
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installed size is  5.0Mb
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installed size is 21.6Mb
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installed size is 21.6Mb
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installed size is  5.5Mb
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Package suggested but not available for checking: 'surveyspec'
File 'iotools/libs/x64/iotools.dll':
  Found non-API calls to R: 'R_GetConnection', 'R_ReadConnection',
    'R_WriteConnection'

Compiled code should not call non-API entry points in R.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
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installed size is 14.6Mb
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Package suggested but not available for checking: 'kanjistat.data'
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Package which this enhances but not available for checking: 'rkward'
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installed size is 10.0Mb
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installed size is  6.9Mb
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installed size is  5.7Mb
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Package suggested but not available for checking: 'rsyslog'
installed size is  5.4Mb
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Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/magick.Rcheck/00install.out' for details.
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installed size is  6.0Mb
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Depends: includes the non-default packages:
  'MASS', 'boot', 'RColorBrewer', 'scatterplot3d', 'tcltk', 'tcltk2',
  'tkrplot', 'rpanel', 'rgl'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
installed size is  5.5Mb
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    libs   4.1Mb
installed size is  5.6Mb
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    libs   4.4Mb
installed size is  5.4Mb
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    R      2.2Mb
    help   2.3Mb
installed size is  5.2Mb
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    data   4.1Mb
installed size is  5.9Mb
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    doc    2.3Mb
    help   2.0Mb
    libs   1.2Mb
installed size is  9.8Mb
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    R      1.8Mb
    doc    3.6Mb
    libs   2.3Mb
Package suggested but not available for checking: 'structSSI'
Package suggested but not available for checking: 'microcontax.data'
Package unavailable to check Rd xrefs: 'microcontax.data'
installed size is  8.6Mb
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    doc    5.5Mb
    lib    1.2Mb
    libs   1.2Mb
Package suggested but not available for checking: 'midfielddata'
installed size is 25.4Mb
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    libs        1.1Mb
    redengine  24.2Mb
installed size is  7.8Mb
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    libs   7.2Mb
Package suggested but not available for checking: 'mixRasch'
installed size is 27.6Mb
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    libs     17.0Mb
Package suggested but not available for checking: 'mlr3proba'
installed size is  8.3Mb
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    doc    1.2Mb
    libs   6.3Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
Package suggested but not available for checking: 'alstructure'

Packages which this enhances but not available for checking:
  'miraculix', 'RandomFieldsUtils', 'MoBPSmaps'
Packages suggested but not available for checking:
  'ArchR', 'TxDb.Hsapiens.UCSC.hg38.refGene'
installed size is  5.0Mb
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    data   4.8Mb
installed size is 14.7Mb
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    htmlwidgets  14.7Mb
installed size is  5.2Mb
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    data   2.0Mb
    libs   1.5Mb
installed size is  5.6Mb
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    doc    3.3Mb
    libs   1.0Mb
installed size is  8.6Mb
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    R      2.0Mb
    data   4.5Mb
    libs   1.2Mb
installed size is  6.0Mb
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    R   5.9Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    data   1.0Mb
    doc    6.4Mb
installed size is 17.5Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    doc    4.2Mb
    libs  11.3Mb
installed size is  6.3Mb
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    doc    2.3Mb
    help   2.0Mb
    libs   1.0Mb
installed size is  5.8Mb
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    R     1.9Mb
    doc   2.0Mb
Package suggested but not available for checking: 'rTubeDB'
Package unavailable to check Rd xrefs: 'rTubeDB'
installed size is 16.2Mb
  sub-directories of 1Mb or more:
    extdata  16.2Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data     1.9Mb
    libs     2.4Mb
    models   1.1Mb
Package suggested but not available for checking: 'spatialClust'
installed size is  6.9Mb
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    data   3.3Mb
    doc    3.5Mb
installed size is  9.7Mb
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    data   1.5Mb
    doc    6.5Mb
    libs   1.2Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/nbfar.Rcheck/00install.out' for details.
installed size is 16.3Mb
  sub-directories of 1Mb or more:
    libs  16.0Mb
installed size is  5.8Mb
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    doc    2.5Mb
    libs   1.5Mb
Package suggested but not available for checking: 'fastshp'
installed size is 14.8Mb
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    libs  14.0Mb
installed size is  7.3Mb
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    data   1.5Mb
    doc    5.1Mb
installed size is  5.1Mb
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    doc   4.0Mb
installed size is 27.8Mb
  sub-directories of 1Mb or more:
    CppCode   4.8Mb
    R         8.5Mb
    include  11.7Mb
    libs      1.2Mb
Package which this enhances but not available for checking: 'jpndistrict'
installed size is  6.1Mb
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    doc       1.2Mb
    extdata   3.7Mb
Package suggested but not available for checking: 'simpar'
installed size is  6.6Mb
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    libs   2.6Mb
    mods   3.3Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   4.1Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc    5.3Mb
    libs   1.6Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   5.5Mb
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    R         1.5Mb
    doc       5.7Mb
    extdata   1.5Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    R            1.5Mb
    test_files   4.2Mb
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    R      2.7Mb
    data   1.0Mb
    doc    1.7Mb
    help   3.3Mb
    libs   1.4Mb
Check process probably crashed or hung up for 20 minutes ... killed
Most likely this happened in the example checks (?),
if not, ignore the following last lines of example output:
> ### * read_input
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: read_input
> ### Title: Read input file
> ### Aliases: read_input
> 
> ### ** Examples
> 
>   input_file <- system.file('extdata', 'sample-data-ecap2.csv', package = 'oncmap')
>   input <- read_input("tests/testthat/ecap1.csv")
> 
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()
> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
Time elapsed:  1.59 0.18 1.78 NA NA 
> grDevices::dev.off()
null device 
          1 
> ###
> ### Local variables: ***
> ### mode: outline-minor ***
> ### outline-regexp: "\\(> \\)?### [*]+" ***
> ### End: ***
> quit('no')
======== End of example output (where/before crash/hang up occured ?) ========
Package suggested but not available for checking: 'unix'
installed size is 30.3Mb
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    libs   19.9Mb
    share  10.2Mb
installed size is  5.1Mb
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    doc    2.4Mb
    libs   1.6Mb
installed size is  5.6Mb
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    data   4.6Mb
installed size is 16.4Mb
  sub-directories of 1Mb or more:
    R        2.6Mb
    data     1.4Mb
    libs     5.1Mb
    models   4.8Mb
Package suggested but not available for checking: 'openNLPmodels.en'
installed size is  5.6Mb
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    doc   4.1Mb
installed size is  8.4Mb
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    doc    2.6Mb
    libs   5.3Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    libs   1.7Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    extdata   2.1Mb
    libs      1.4Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc    5.0Mb
    libs   1.3Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    help   1.1Mb
Package suggested but not available for checking: 'Rcplex'
Loading this package had a fatal error status code 1
Loading log:
Loading required package: tools
You are working with 
packagefinder version 0.3.5

Error: package or namespace load failed for 'packagefinder':
 .onAttach failed in attachNamespace() for 'packagefinder', details:
  call: pf$Package
  error: object of type 'closure' is not subsettable
Execution halted
Error(s) in re-building vignettes:
--- re-building 'An_Introduction_to_packager.Rasciidoc' using rasciidoc
Warning in run_knit(file_name, knit = knit, envir = envir, write_to_disk = write_to_disk) :
  Setting option knit to TRUE based on the file contents!


processing file: D:\RCompile\CRANpkg\local\4.4\packager.Rcheck\vign_test\packager\vignettes\An_Introduction_to_packager.Rasciidoc
installed size is  7.0Mb
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    doc       1.9Mb
    extdata   4.7Mb
installed size is 15.1Mb
  sub-directories of 1Mb or more:
    library  14.3Mb
Package suggested but not available for checking: 'CorShrink'
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc    3.1Mb
    libs   2.8Mb
Check process probably crashed or hung up for 20 minutes ... killed
Most likely this happened in the example checks (?),
if not, ignore the following last lines of example output:
> ### Aliases: ybp2date date2ybp
> 
> ### ** Examples
> 
> ybp2date(-10000)
[1] "-8050-01-01 UTC"
> ybp2date(0)
[1] "1950-01-01 UTC"
> # back and forth
> date2ybp(ybp2date(-10000))
[1] -10000
> 
> 
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()
> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
Time elapsed:  6.45 0.34 6.83 NA NA 
> grDevices::dev.off()
null device 
          1 
> ###
> ### Local variables: ***
> ### mode: outline-minor ***
> ### outline-regexp: "\\(> \\)?### [*]+" ***
> ### End: ***
> quit('no')
======== End of example output (where/before crash/hang up occured ?) ========
installed size is  5.1Mb
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    R      3.5Mb
    data   1.5Mb
installed size is 11.1Mb
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    R      8.0Mb
    help   3.0Mb
installed size is  7.1Mb
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    R      3.3Mb
    help   3.6Mb
installed size is  6.5Mb
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    R      3.2Mb
    help   3.2Mb
installed size is  6.8Mb
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    R      2.8Mb
    help   3.8Mb
installed size is  7.1Mb
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    R      3.1Mb
    help   3.8Mb
installed size is  5.6Mb
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    lib    2.9Mb
    libs   2.4Mb
installed size is  6.3Mb
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    data   2.7Mb
    doc    1.2Mb
installed size is  5.1Mb
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    doc        1.4Mb
    examples   1.7Mb
installed size is  6.2Mb
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    data   2.1Mb
    libs   1.4Mb
installed size is 12.1Mb
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    libs   8.5Mb
Package suggested but not available for checking: 'PythonInR'
installed size is 20.3Mb
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    share  12.8Mb
installed size is 10.1Mb
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    libs   9.1Mb
Package suggested but not available for checking: 'DMwR'
installed size is 13.2Mb
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    include  11.2Mb
    libs      1.8Mb
installed size is  5.2Mb
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    doc    1.4Mb
    libs   1.2Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc       1.5Mb
    extdata   3.1Mb
installed size is  5.4Mb
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    data   1.6Mb
    doc    2.1Mb
installed size is  6.7Mb
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    data   1.4Mb
    doc    2.1Mb
    libs   1.5Mb
installed size is  6.8Mb
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    htmlwidgets   3.9Mb
Package suggested but not available for checking: 'pmartRdata'
Package suggested but not available for checking: 'pollimetrydata'
installed size is 11.8Mb
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    R      6.3Mb
    data   4.3Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   2.6Mb
    doc    1.8Mb
installed size is  5.5Mb
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    extdata   2.8Mb
    libs      1.2Mb
installed size is  6.6Mb
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    doc   6.2Mb
installed size is  6.1Mb
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    doc    3.6Mb
    libs   1.3Mb
installed size is  9.6Mb
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    R      1.3Mb
    doc    4.7Mb
    help   1.0Mb
    libs   1.6Mb
installed size is 15.4Mb
  sub-directories of 1Mb or more:
    libs  14.3Mb
Running 'test-all.R' [2s]
Running the tests in 'tests/test-all.R' failed.
Complete output:
  > library(testthat)
  > library(profvis)
  > 
  > test_check("profvis")
  [ FAIL 1 | WARN 0 | SKIP 7 | PASS 14 ]
  
  ══ Skipped tests (7) ═══════════════════════════════════════════════════════════
  • On CRAN (7): 'test-pause.R:16:3', 'test-profvis.R:2:3',
    'test-profvis.R:16:3', 'test-profvis.R:27:3', 'test-profvis.R:41:3',
    'test-profvis.R:52:3', 'test-profvis.R:56:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-pause.R:4:3'): pause takes expected time ─────────────────────
  abs(time - 0.2)/0.2 is not strictly less than 0.1. Difference: 3.61e-16
  
  [ FAIL 1 | WARN 0 | SKIP 7 | PASS 14 ]
  Error: Test failures
  Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/proj4.Rcheck/00install.out' for details.
Packages suggested but not available for checking: 'unix', 'cmdstanr'
installed size is 26.4Mb
  sub-directories of 1Mb or more:
    libs  17.1Mb
    proj   9.0Mb
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    libs   7.8Mb
Running examples in 'promor-Ex.R' failed
The error most likely occurred in:

> ### Name: heatmap_na
> ### Title: Visualize missing data
> ### Aliases: heatmap_na
> 
> ### ** Examples
> 
> ## Generate a raw_df object with default settings. No technical replicates.
> raw_df <- create_df(
+   prot_groups = "https://raw.githubusercontent.com/caranathunge/promor_example_data/main/pg1.txt",
+   exp_design = "https://raw.githubusercontent.com/caranathunge/promor_example_data/main/ed1.txt"
+ )
Warning in scan(file = file, what = what, sep = sep, quote = quote, dec = dec,  :
  URL 'https://raw.githubusercontent.com/caranathunge/promor_example_data/main/pg1.txt': Timeout of 60 seconds was reached
Error in scan(file = file, what = what, sep = sep, quote = quote, dec = dec,  : 
  cannot read from connection
Calls: create_df -> read.csv -> read.table -> scan
Execution halted
Package suggested but not available for checking: 'cin'
Package suggested but not available for checking: 'rdt'
installed size is 16.0Mb
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    libs  15.8Mb
installed size is  6.3Mb
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    doc   5.6Mb
installed size is  9.2Mb
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    libs   8.8Mb
installed size is  5.6Mb
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    gui          1.6Mb
    staticdocs   3.3Mb
installed size is 26.3Mb
  sub-directories of 1Mb or more:
    libs  25.6Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc   5.2Mb
Package suggested but not available for checking: 'spDataLarge'
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    data  10.8Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc   4.4Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    extdata   3.3Mb
    libs      2.8Mb
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    R         1.7Mb
    contrib   3.7Mb
    doc       2.9Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
    libs   1.2Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc         2.0Mb
    shiny_app   1.2Mb
Package suggested but not available for checking: 'bootmlm'
Packages suggested but not available for checking: 'rcom', 'RDCOMClient'
installed size is 10.4Mb
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    data   2.0Mb
    doc    6.6Mb
    libs   1.0Mb
installed size is 11.3Mb
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    doc           5.3Mb
    htmlwidgets   1.8Mb
    libs          2.1Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc   5.5Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data      2.2Mb
    extdata   1.4Mb
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    htmlwidgets  10.0Mb
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    api           3.2Mb
    htmlwidgets   6.8Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   4.6Mb
Auto-generated content requiring editing in Rd file 'RApiDatetime-package.Rd':
  \references: 'This optional section can contain literature or other refere...'
  \seealso: 'Optional links to other man pages'
  \examples: '# Optional simple examples of the most important functions'
installed size is  8.0Mb
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    doc       1.7Mb
    extdata   4.1Mb
    libs      1.3Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    R      3.1Mb
    libs   1.4Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc       2.6Mb
    rstudio   1.5Mb
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    data   4.5Mb
    etc    1.9Mb
    po     1.2Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   3.9Mb
    libs   1.5Mb
installed size is 12.5Mb
  sub-directories of 1Mb or more:
    libs  11.3Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   4.2Mb
Package suggested but not available for checking: 'ROpenOffice'
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    R     1.2Mb
    doc   4.5Mb
    po    2.4Mb
Package suggested but not available for checking: 'conics'
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    corpora   7.4Mb
Package suggested but not available for checking: 'pd.hg.u133.plus.2'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/Rcplex.Rcheck/00install.out' for details.
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    include   6.7Mb
    libs      1.2Mb
installed size is 39.7Mb
  sub-directories of 1Mb or more:
    include  38.1Mb
    libs      1.4Mb
installed size is 47.6Mb
  sub-directories of 1Mb or more:
    include  47.2Mb
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    include   9.6Mb
    libs      1.2Mb
installed size is  8.0Mb
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    include   6.4Mb
    libs      1.1Mb
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    doc       1.1Mb
    include   6.4Mb
    libs      1.3Mb
installed size is 13.2Mb
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    include        7.2Mb
    jsonexamples   3.8Mb
    libs           2.0Mb
installed size is 11.4Mb
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    libs   9.4Mb
installed size is  5.7Mb
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    data   1.7Mb
    libs   2.1Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    R      3.8Mb
    data   1.5Mb
Package suggested but not available for checking: 'dataui'
File 'readxl/libs/x64/readxl.dll':
  Found non-API calls to R: 'Rf_StringFalse', 'Rf_StringTrue'

Compiled code should not call non-API entry points in R.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
installed size is 16.9Mb
  sub-directories of 1Mb or more:
    redengine  16.6Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    libs   2.1Mb
Package which this enhances but not available for checking: 'Rcplex'
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc    3.5Mb
    libs   1.3Mb
Running examples in 'rempsyc-Ex.R' failed
The error most likely occurred in:

> ### Name: cormatrix_excel
> ### Title: Easy export of correlation matrix to Excel
> ### Aliases: cormatrix_excel
> ### Keywords: Excel correlation matrix
> 
> ### ** Examples
> 
> ## Don't show: 
> if (requireNamespace("correlation", quietly = TRUE) && requireNamespace("openxlsx2", quietly = TRUE)) (if (getRversion() >= "3.4") withAutoprint else force)({ # examplesIf
+ ## End(Don't show)
+ ## Don't show: 
+ .old_wd <- setwd(tempdir())
+ ## End(Don't show)
+ # Basic example
+ cormatrix_excel(mtcars, select = c("mpg", "cyl", "disp", "hp", "carb"), filename = "cormatrix1")
+ cormatrix_excel(iris, p_adjust = "none", filename = "cormatrix2")
+ cormatrix_excel(airquality, method = "spearman", filename = "cormatrix3")
+ ## Don't show: 
+ setwd(.old_wd)
+ ## End(Don't show)
+ ## Don't show: 
+ }) # examplesIf
> .old_wd <- setwd(tempdir())
> cormatrix_excel(mtcars, select = c("mpg", "cyl", "disp", "hp", "carb"), 
+     filename = "cormatrix1")
# Correlation Matrix (pearson-method)

Parameter |      mpg |      cyl |     disp |       hp |    carb
---------------------------------------------------------------
mpg       |          | -0.85*** | -0.85*** | -0.78*** | -0.55**
cyl       | -0.85*** |          |  0.90*** |  0.83*** |  0.53**
disp      | -0.85*** |  0.90*** |          |  0.79*** |   0.39*
hp        | -0.78*** |  0.83*** |  0.79*** |          | 0.75***
carb      |  -0.55** |   0.53** |    0.39* |  0.75*** |        

p-value adjustment method: none
Error: x must be class wbColour
Execution halted
Running 'testthat.R' [15s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(rempsyc)
  Suggested APA citation: Thériault, R. (2023). rempsyc: Convenience functions for psychology. 
  Journal of Open Source Software, 8(87), 5466. https://doi.org/10.21105/joss.05466
  > 
  > test_check("rempsyc")
  [ FAIL 1 | WARN 0 | SKIP 19 | PASS 46 ]
  
  ══ Skipped tests (19) ══════════════════════════════════════════════════════════
  • On CRAN (19): 'test-best_duplicate.R:8:3', 'test-extract_duplicates.R:8:3',
    'test-find_mad.R:2:3', 'test-format_value.R:2:3',
    'test-nice_assumptions.R:9:3', 'test-nice_contrasts.R:7:3',
    'test-nice_lm.R:5:3', 'test-nice_lm_contrasts.R:12:3',
    'test-nice_lm_slopes.R:5:3', 'test-nice_mod.R:4:3', 'test-nice_na.R:2:3',
    'test-nice_randomize.R:5:3', 'test-nice_reverse.R:3:3',
    'test-nice_slopes.R:4:3', 'test-nice_t_test.R:5:3', 'test-nice_table.R:13:3',
    'test-nice_var.R:2:3', 'test-scale_mad.R:2:3', 'test-winsorize_mad.R:2:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-cormatrix_excel.R:5:3'): cormatrix_excel ───────────────────────
  Error: x must be class wbColour
  Backtrace:
      ▆
   1. └─testthat::expect_snapshot(...) at test-cormatrix_excel.R:5:3
   2.   └─rlang::cnd_signal(state$error)
  
  [ FAIL 1 | WARN 0 | SKIP 19 | PASS 46 ]
  Error: Test failures
  Execution halted
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc    3.9Mb
    libs   1.4Mb
Package suggested but not available for checking: 'resourcecodedata'
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    include   2.4Mb
    libs      1.6Mb
    models    1.6Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/revert.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/Rfast2.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/Rfast.Rcheck/00install.out' for details.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data      1.9Mb
    doc       1.2Mb
    extdata   1.9Mb
installed size is 14.1Mb
  sub-directories of 1Mb or more:
    doc     7.1Mb
    fonts   1.5Mb
    libs    2.9Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    lib    3.1Mb
    libs   3.8Mb
File 'RInside/libs/x64/RInside.dll':
  Found 'srand', possibly from 'srand' (C)
    Object: 'RInside.o'
File 'RInside/libs/x64/libRInside.dll':
  Found 'srand', possibly from 'srand' (C)
    Object: 'RInside.o'
File 'RInside/libs/x64/RInside.dll':
  Found non-API calls to R: 'R_CleanTempDir', 'R_DefParams',
    'R_ReplDLLinit', 'R_RunExitFinalizers', 'R_SetParams', 'R_TempDir',
    'Rf_endEmbeddedR', 'Rf_initEmbeddedR', 'getRUser', 'get_R_HOME',
    'run_Rmainloop'
File 'RInside/libs/x64/libRInside.dll':
  Found non-API calls to R: 'R_CleanTempDir', 'R_DefParams',
    'R_ReplDLLinit', 'R_RunExitFinalizers', 'R_SetParams', 'R_TempDir',
    'Rf_endEmbeddedR', 'Rf_initEmbeddedR', 'getRUser', 'get_R_HOME',
    'run_Rmainloop'

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf.
Compiled code should not call non-API entry points in R.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
Note: information on .o files for x64 is not available
File 'd:/Rcompile/CRANpkg/lib/4.4/rJava/libs/x64/rJava.dll':
  Found '_exit', possibly from '_exit' (C)
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    include   3.4Mb
    libs      3.6Mb
installed size is 50.2Mb
  sub-directories of 1Mb or more:
    R     4.1Mb
    exe  45.7Mb
installed size is 24.6Mb
  sub-directories of 1Mb or more:
    extdata  23.8Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    lemon   2.9Mb
    libs    2.0Mb
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    libs  10.3Mb
installed size is 16.7Mb
  sub-directories of 1Mb or more:
    include   7.4Mb
    lib       3.0Mb
    libs      5.7Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    rmd   5.9Mb
Package suggested but not available for checking: 'bridgestan'
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs       1.0Mb
    minizinc   2.3Mb
installed size is 17.1Mb
  sub-directories of 1Mb or more:
    libs  16.9Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    extdata   2.0Mb
    libs      3.3Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    doc    1.7Mb
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    R  11.2Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc               1.7Mb
    libs              1.3Mb
    simulationStudy   1.6Mb
Found the following significant warnings:
  RODBC.c:294:31: warning: format '%d' expects argument of type 'int', but argument 3 has type 'SQLINTEGER' {aka 'long int'} [-Wformat=]
  RODBC.c:1078:59: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'SQLULEN' {aka 'long long unsigned int'} [-Wformat=]
See 'd:/Rcompile/CRANpkg/local/4.4/RODBC.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 13.2.0'
Error(s) in re-building vignettes:
--- re-building 'Bayesian.Rmd' using rmarkdown

Quitting from lines 57-75 [load-trees] (Bayesian.Rmd)
Error: processing vignette 'Bayesian.Rmd' failed with diagnostics:
cannot read from connection
--- failed re-building 'Bayesian.Rmd'

SUMMARY: processing the following file failed:
  'Bayesian.Rmd'

Error: Vignette re-building failed.
Execution halted
Package required but not available: 'Rcplex'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
installed size is 17.3Mb
  sub-directories of 1Mb or more:
    doc  15.2Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    R         3.2Mb
    extdata   2.7Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/ROracle.Rcheck/00install.out' for details.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    data   2.7Mb
    libs   1.4Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    R      4.7Mb
    help   1.0Mb
    libs   1.6Mb
Running 'testthat.R' [100s]
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(rplec)
  > 
  > test_check("rplec")
  trying URL 'https://raw.githubusercontent.com/herdiantrisufriyana/rplec/master/data/beta_values_case.rda'
  Content type 'application/octet-stream' length 18750575 bytes (17.9 MB)
  ==================================================
  downloaded 17.9 MB
  
  trying URL 'https://raw.githubusercontent.com/herdiantrisufriyana/rplec/master/data/beta_values_case.rda'
  Content type 'application/octet-stream' length 18750575 bytes (17.9 MB)
  ================================================
  downloaded 17.4 MB
  
  trying URL 'https://raw.githubusercontent.com/herdiantrisufriyana/rplec/master/data/beta_values_case.rda'
  Content type 'application/octet-stream' length 18750575 bytes (17.9 MB)
  ==================================================
  downloaded 17.9 MB
  
  [ FAIL 1 | WARN 2 | SKIP 0 | PASS 31 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-plec.R:5:3'): plec validates inputs correctly ──────────────────
  Error in `utils::download.file(url, temp, mode = "wb")`: download from 'https://raw.githubusercontent.com/herdiantrisufriyana/rplec/master/data/beta_values_case.rda' failed
  Backtrace:
      ▆
   1. └─rplec::download_beta_values_case() at test-plec.R:5:3
   2.   └─utils::download.file(url, temp, mode = "wb")
  
  [ FAIL 1 | WARN 2 | SKIP 0 | PASS 31 ]
  Error: Test failures
  Execution halted
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   1.3Mb
installed size is 16.4Mb
  sub-directories of 1Mb or more:
    libs  16.4Mb
installed size is 14.2Mb
  sub-directories of 1Mb or more:
    libs  13.6Mb
installed size is 18.9Mb
  sub-directories of 1Mb or more:
    libs  17.9Mb
Note: information on .o files for x64 is not available
File 'd:/Rcompile/CRANpkg/lib/4.4/Rserve/libs/x64/Rserve.dll':
  Found '_exit', possibly from '_exit' (C)
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'rand', possibly from 'rand' (C)
  Found 'srand', possibly from 'srand' (C)
File 'Rserve/libs/x64/Rserve.dll':
  Found non-API calls to R: 'R_Interactive', 'R_Visible',
    'Rf_initialize_R', 'setup_Rmainloop'

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.
Compiled code should not call non-API entry points in R.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    R      3.8Mb
    help   1.5Mb
installed size is 19.8Mb
  sub-directories of 1Mb or more:
    R      1.8Mb
    doc    4.7Mb
    libs  12.6Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    exec   1.7Mb
    lib    1.9Mb
    libs   1.4Mb
installed size is 18.2Mb
  sub-directories of 1Mb or more:
    libs   2.3Mb
installed size is 19.1Mb
  sub-directories of 1Mb or more:
    libs  18.7Mb
installed size is 42.7Mb
  sub-directories of 1Mb or more:
    libs    1.0Mb
    swipl  41.6Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    rmarkdown  11.0Mb
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    libs   7.6Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R   5.0Mb
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    doc    7.8Mb
    libs   2.5Mb
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    libs   9.8Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    R      3.0Mb
    libs   1.1Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
    libs   1.4Mb
Package which this enhances but not available for checking: 'glmmADMB'
Package suggested but not available for checking: 'gpuR'
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    include   5.2Mb
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    include   5.1Mb
    libs      5.2Mb
Package suggested but not available for checking: 'rWCVPdata'
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    java  10.7Mb
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    R         1.4Mb
    include   1.1Mb
    libs      4.7Mb
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    libs   7.6Mb
installed size is 15.3Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    libs  13.4Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    help   3.4Mb
    libs   1.3Mb
Package suggested but not available for checking: 'networkTomography'
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    bin   5.8Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   3.0Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    3.9Mb
    libs   1.1Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
    libs   1.2Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/scDHA.Rcheck/00install.out' for details.
installed size is 16.8Mb
  sub-directories of 1Mb or more:
    cppad     9.5Mb
    include   4.7Mb
    libs      1.9Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   3.8Mb
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    R   7.8Mb
installed size is 19.2Mb
  sub-directories of 1Mb or more:
    extdata  18.0Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    libs   2.0Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs     3.3Mb
    models   1.6Mb
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    doc    6.4Mb
    libs   1.8Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data        1.4Mb
    sequences   1.9Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   4.7Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs   3.2Mb
Package suggested but not available for checking: 'BPCells'
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    R     1.1Mb
    doc   5.2Mb
installed size is 112.7Mb
  sub-directories of 1Mb or more:
    doc      1.8Mb
    gdal     3.0Mb
    libs    94.2Mb
    proj     9.0Mb
    sqlite   1.5Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc    4.2Mb
    libs   1.3Mb
Package suggested but not available for checking: 'rCOSA'
Package unavailable to check Rd xrefs: 'rCOSA'
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc       1.7Mb
    extdata   4.2Mb
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    www   7.4Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    shinymgr    1.4Mb
    tutorials   3.6Mb
installed size is 13.3Mb
  sub-directories of 1Mb or more:
    R     1.5Mb
    www  10.1Mb
Running examples in 'shinyscholar-Ex.R' failed
The error most likely occurred in:

> ### Name: metadata
> ### Title: Add metadata lines to modules
> ### Aliases: metadata
> 
> ### ** Examples
> 
> td <- tempfile()
> dir.create(td, recursive = TRUE)
> 
> modules <- data.frame(
+   "component" = c("demo"),
+   "long_component" = c("demo"),
+   "module" = c("demo"),
+   "long_module" = c("demo"),
+   "map" = c(FALSE),
+   "result" = c(TRUE),
+   "rmd" = c(TRUE),
+   "save" = c(TRUE),
+   "async" = c(FALSE))
> 
> create_template(path = td, name = "demo",
+                 common_objects = c("demo"), modules = modules,
+                 author = "demo", include_map = FALSE,
+                 include_table = FALSE, include_code = FALSE, install = FALSE)
Warning in readRDS(con) :
  URL 'https://CRAN.R-project.org/web/packages/packages.rds': Timeout of 60 seconds was reached
Error in readRDS(con) : cannot read from connection
Calls: create_template ... <Anonymous> -> as.data.frame -> read_CRAN_object -> readRDS
Execution halted
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    extdata   1.0Mb
    help      1.7Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/SIGN.Rcheck/00install.out' for details.
installed size is 15.1Mb
  sub-directories of 1Mb or more:
    extdata  13.0Mb
    libs      1.5Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    R      2.2Mb
    libs   1.7Mb
Package which this enhances but not available for checking: 'kmndirs'
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
    libs   1.1Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   3.2Mb
    libs   1.0Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    doc    3.4Mb
    libs   1.6Mb
Check process probably crashed or hung up for 20 minutes ... killed
Most likely this happened in the example checks (?),
if not, ignore the following last lines of example output:
> cleanEx()
> nameEx("snvec")
> ### * snvec
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: snvec
> ### Title: Calculate Earth’s Obliquity and Precession in the Past
> ### Aliases: snvec
> 
> ### ** Examples
> 
> 
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()
> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
Time elapsed:  0.49 0.03 0.5 NA NA 
> grDevices::dev.off()
null device 
          1 
> ###
> ### Local variables: ***
> ### mode: outline-minor ***
> ### outline-regexp: "\\(> \\)?### [*]+" ***
> ### End: ***
> quit('no')
======== End of example output (where/before crash/hang up occured ?) ========
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R     3.2Mb
    doc   1.1Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    doc    1.3Mb
    libs   1.7Mb
Package suggested but not available for checking: 'SciencesPo'
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   4.1Mb
    doc    1.0Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   4.7Mb
    libs   1.0Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    extdata   6.0Mb
    libs      1.0Mb
Package suggested but not available for checking: 'NLMR'
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    R   5.0Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    R      2.8Mb
    libs   1.8Mb
installed size is 14.5Mb
  sub-directories of 1Mb or more:
    libs  13.6Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   2.5Mb
    help   1.7Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   4.5Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data     2.5Mb
    shapes   3.2Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   4.1Mb
    help   1.5Mb
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    doc   6.0Mb
    etc   2.1Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc   4.6Mb
Running 'testthat.R' [4s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(spectralGraphTopology)
  
  Attaching package: 'spectralGraphTopology'
  
  The following object is masked from 'package:stats':
  
      D
  
  > 
  > test_check("spectralGraphTopology")
  [ FAIL 3 | WARN 0 | SKIP 0 | PASS 43 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-learnGraphTopology.R:21:1'): (code run outside of `test_that()`) ──
  <purrr_error_indexed/rlang_error/error/condition>
  Error in `purrr::pmap(all_pars, build_and_run_test, desc = desc_stub, code = captured, 
      .interpret_glue = .interpret_glue)`: ℹ In index: 1.
  Caused by error:
  ! Failed to parse glue component
  Caused by error in `parse()`:
  ! <text>:1:1: unexpected ','
  1: ,
      ^
  ── Error ('test-learnSmoothSignalGraph.R:9:1'): (code run outside of `test_that()`) ──
  <purrr_error_indexed/rlang_error/error/condition>
  Error in `purrr::pmap(all_pars, build_and_run_test, desc = desc_stub, code = captured, 
      .interpret_glue = .interpret_glue)`: ℹ In index: 1.
  Caused by error:
  ! Failed to parse glue component
  Caused by error in `parse()`:
  ! <text>:1:1: unexpected ','
  1: ,
      ^
  ── Error ('test-operators.R:122:1'): (code run outside of `test_that()`) ───────
  <purrr_error_indexed/rlang_error/error/condition>
  Error in `purrr::pmap(all_pars, build_and_run_test, desc = desc_stub, code = captured, 
      .interpret_glue = .interpret_glue)`: ℹ In index: 1.
  Caused by error:
  ! Failed to parse glue component
  Caused by error in `parse()`:
  ! <text>:1:1: unexpected ','
  1: ,
      ^
  
  [ FAIL 3 | WARN 0 | SKIP 0 | PASS 43 ]
  Error: Test failures
  Execution halted
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc       1.1Mb
    extdata   2.6Mb
    libs      1.6Mb
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    doc   7.6Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    doc   5.5Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs   3.2Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    shiny-squid   5.3Mb
installed size is 14.8Mb
  sub-directories of 1Mb or more:
    libs  13.6Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
installed size is 14.1Mb
  sub-directories of 1Mb or more:
    include  11.3Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
Package suggested but not available for checking: 'starsdata'
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc   2.9Mb
    nc    1.7Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    libs   1.3Mb
Package suggested but not available for checking: 'asreml'
Package suggested but not available for checking: 'networksis'
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    shiny-apps   6.1Mb
installed size is 14.5Mb
  sub-directories of 1Mb or more:
    libs  13.4Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    data   6.3Mb
installed size is 14.6Mb
  sub-directories of 1Mb or more:
    joss_paper   1.2Mb
    libs        12.6Mb
Package suggested but not available for checking: 'StrathE2E2examples'
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    libs  10.6Mb
installed size is 35.4Mb
  sub-directories of 1Mb or more:
    libs  34.5Mb
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    doc    7.1Mb
    libs   1.1Mb
Package suggested but not available for checking: 'STRaitRazoR'
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   1.8Mb
    doc    3.1Mb
    help   1.0Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    lib    2.8Mb
    libs   1.5Mb
Package suggested but not available for checking: 'velocyto.R'
Package suggested but not available for checking: 'extraTrees'
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    R     1.7Mb
    doc   2.3Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   2.9Mb
    doc    2.5Mb
Packages suggested but not available for checking:
  'survHEinla', 'survHEhmc'
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    data   1.9Mb
    doc    5.3Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    dist3   2.0Mb
    dist4   1.7Mb
    dist5   2.1Mb
Package suggested but not available for checking: 'swephRdata'
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R         1.3Mb
    extdata   3.1Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   4.2Mb
    libs   1.4Mb
installed size is 13.6Mb
  sub-directories of 1Mb or more:
    java  12.7Mb
Package suggested but not available for checking: 'tashudata'
installed size is 13.2Mb
  sub-directories of 1Mb or more:
    doc  12.0Mb
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    doc    8.2Mb
    libs   1.1Mb
Check process probably crashed or hung up for 20 minutes ... killed
Most likely this happened in the example checks (?),
if not, ignore the following last lines of example output:
> if(interactive()){
+ 
+ with(iris, plot(Sepal.Length, Petal.Width,
+     col=c('red','green','blue')[Species]))
+ text( 6.5, 1.5, 'test' )
+ zoomplot( locator(2) ) # now click on 2 points in the plot to zoom in
+ 
+ plot( 1:10, rnorm(10) )
+ tmp <- rnorm(10,1,3)
+ lines( (1:10) + 0.5, tmp, col='red' )
+ zoomplot( c(0,11), range(tmp) )
+ }
> 
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()
> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
Time elapsed:  14.81 0.54 15.36 NA NA 
> grDevices::dev.off()
null device 
          1 
> ###
> ### Local variables: ***
> ### mode: outline-minor ***
> ### outline-regexp: "\\(> \\)?### [*]+" ***
> ### End: ***
> quit('no')
======== End of example output (where/before crash/hang up occured ?) ========
Running examples in 'teal.modules.general-Ex.R' failed
The error most likely occurred in:

> ### Name: tm_a_pca
> ### Title: 'teal' module: Principal component analysis
> ### Aliases: tm_a_pca
> 
> ### ** Examples
> 
> library(teal.widgets)
> 
> # general data example
> data <- teal_data()
> data <- within(data, {
+   require(nestcolor)
+   USArrests <- USArrests
+ })
> 
> datanames(data) <- "USArrests"
Warning: `datanames<-()` was deprecated in teal.data 0.7.0.
ℹ invalid to use `datanames()<-` or `names()<-` on an object of class
  `teal_data`. See ?names.teal_data
> 
> app <- init(
+   data = data,
+   modules = modules(
+     tm_a_pca(
+       "PCA",
+       dat = data_extract_spec(
+         dataname = "USArrests",
+         select = select_spec(
+           choices = variable_choices(
+             data = data[["USArrests"]], c("Murder", "Assault", "UrbanPop", "Rape")
+           ),
+           selected = c("Murder", "Assault"),
+           multiple = TRUE
+         ),
+         filter = NULL
+       ),
+       ggplot2_args = ggplot2_args(
+         labs = list(subtitle = "Plot generated by PCA Module")
+       )
+     )
+   )
+ )
[INFO] 2025-02-16 07:27:09.6412 pid:104740 token:[] teal.modules.general Initializing tm_a_pca
Error in as.list(data@env) : 
  no slot of name "env" for this object of class "teal_data"
Calls: init -> create_app_id -> as.list
Execution halted
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    doc    5.5Mb
    help   2.8Mb
installed size is 113.1Mb
  sub-directories of 1Mb or more:
    R      2.4Mb
    gdal   3.0Mb
    libs  97.2Mb
    proj   9.0Mb
installed size is 23.3Mb
  sub-directories of 1Mb or more:
    doc        1.1Mb
    libs       8.1Mb
    tessdata  14.0Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    R      4.0Mb
    data   3.0Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    R              1.2Mb
    threeBrainJS   2.9Mb
installed size is 23.4Mb
  sub-directories of 1Mb or more:
    libs  20.8Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   3.0Mb
Found the following significant warnings:
  tcltkimg.c:93:1: warning: function declaration isn't a prototype [-Wstrict-prototypes]
  tcltkimg.c:94:1: warning: function declaration isn't a prototype [-Wstrict-prototypes]
  tcltkimg.c:317:29: warning: format '%d' expects argument of type 'int', but argument 2 has type 'DWORD' {aka 'long unsigned int'} [-Wformat=]
See 'd:/Rcompile/CRANpkg/local/4.4/tkrplot.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 13.2.0'
installed size is 16.9Mb
  sub-directories of 1Mb or more:
    examples  12.6Mb
    include    3.6Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    data   7.2Mb
installed size is 28.4Mb
  sub-directories of 1Mb or more:
    R         5.9Mb
    help      1.8Mb
    include   1.9Mb
    libs     18.2Mb
Package suggested but not available for checking: 'toscaData'
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    data  12.0Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   2.2Mb
    doc    2.8Mb
Package suggested but not available for checking: 'taxidata'
installed size is 16.2Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    libs  13.3Mb
Packages suggested but not available for checking: 'fwelnet', 'doMC'
Package suggested but not available for checking: 'TreeDistData'
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    doc    4.9Mb
    libs   1.2Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    datasets   1.6Mb
    doc        1.3Mb
    libs       1.1Mb
installed size is 17.5Mb
  sub-directories of 1Mb or more:
    data      1.2Mb
    doc       1.3Mb
    extdata  14.8Mb
installed size is 12.3Mb
  sub-directories of 1Mb or more:
    doc    3.9Mb
    libs   7.3Mb
installed size is 14.6Mb
  sub-directories of 1Mb or more:
    libs  13.9Mb
installed size is 21.3Mb
  sub-directories of 1Mb or more:
    libs  20.2Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    data   4.6Mb
    libs   1.1Mb
Package which this enhances but not available for checking: 'sl3'
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    libs   4.4Mb
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    doc        1.4Mb
    shinyapp   4.9Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc         1.4Mb
    dummydata   1.4Mb
    libs        2.5Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    help   4.5Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    R      1.7Mb
    help   2.6Mb
installed size is 18.7Mb
  sub-directories of 1Mb or more:
    R      1.7Mb
    doc    1.3Mb
    libs  14.8Mb
Package suggested but not available for checking: 'USA.state.boundaries.data'
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   6.1Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    data   6.9Mb
Found the following significant warnings:
  randutils.c:60:12: warning: function declaration isn't a prototype [-Wstrict-prototypes]
See 'd:/Rcompile/CRANpkg/local/4.4/uuid.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 13.2.0'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/V8.Rcheck/00install.out' for details.
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    extdata   8.8Mb
installed size is 109.3Mb
  sub-directories of 1Mb or more:
    extdata   2.8Mb
    gdal      3.0Mb
    libs     93.1Mb
    proj      9.0Mb
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    R      4.3Mb
    help   3.3Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs   5.1Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    help          1.3Mb
    htmlwidgets   5.2Mb
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    doc           2.0Mb
    htmlwidgets   6.8Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc   5.5Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   5.8Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   4.3Mb
    help   1.3Mb
installed size is 24.0Mb
  sub-directories of 1Mb or more:
    extdata   1.6Mb
    libs     22.1Mb
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    extdata   8.5Mb
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    doc   6.6Mb
Package suggested but not available for checking: 'prepr'
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    client   9.1Mb
    doc      1.0Mb
Check process probably crashed or hung up for 20 minutes ... killed
Most likely this happened in the example checks (?),
if not, ignore the following last lines of example output:
> 	obj<-wblr.fit(wblr(rweibull(10,1,1)))
> 	xfit(obj)
$dist
[1] "weibull"

$fit
       Eta       Beta       Rsqr     AbPval 
 0.8259711  0.8737415  0.9526519 65.4679596 
attr(,"data_types")
 n  s  d  i 
10  0  0  0 

> 
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()
> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
Time elapsed:  4.13 0.11 4.24 NA NA 
> grDevices::dev.off()
null device 
          1 
> ###
> ### Local variables: ***
> ### mode: outline-minor ***
> ### outline-regexp: "\\(> \\)?### [*]+" ***
> ### End: ***
> quit('no')
======== End of example output (where/before crash/hang up occured ?) ========
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    data   4.2Mb
    libs   3.6Mb
Package suggested but not available for checking: 'wordnetDicts'
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    data   6.5Mb
installed size is 12.7Mb
  sub-directories of 1Mb or more:
    data  12.6Mb
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    data  11.1Mb
Package suggested but not available for checking: 'wmtsa'
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc   4.3Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    help   1.9Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    bin   5.5Mb
installed size is 28.7Mb
  sub-directories of 1Mb or more:
    java  26.1Mb
Found the following significant warnings:
  RSDTD.c:134:7: warning: 'xmlSkipBlankChars' is deprecated [-Wdeprecated-declarations]
  RSDTD.c:135:7: warning: 'xmlParseMarkupDecl' is deprecated [-Wdeprecated-declarations]
  RUtils.c:142:5: warning: 'xmlSubstituteEntitiesDefault' is deprecated [-Wdeprecated-declarations]
See 'd:/Rcompile/CRANpkg/local/4.4/XML.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 13.3.0'
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    exampleData   1.3Mb
    libs          2.1Mb
installed size is 31.1Mb
  sub-directories of 1Mb or more:
    libs  30.7Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   2.6Mb
    libs   2.5Mb
installed size is 13.2Mb
  sub-directories of 1Mb or more:
    data      1.0Mb
    extdata   2.9Mb
    libs      8.2Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   5.8Mb
installed size is 14.1Mb
  sub-directories of 1Mb or more:
    R  14.1Mb
Packages suggested but not available for checking: 'DeconRNASeq', 'WGCNA'
installed size is 13.5Mb
  sub-directories of 1Mb or more:
    libs  13.4Mb
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    data   3.0Mb
    libs   2.6Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R       2.0Mb
    data    1.3Mb
    files   1.7Mb
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    data  10.1Mb
Packages suggested but not available for checking: 'HiTC', 'snpStats'
Package unavailable to check Rd xrefs: ‘snpStats’
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    libs   8.8Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    data   1.6Mb
    libs   1.1Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    ShinyGR   4.3Mb
    doc       3.4Mb
installed size is 38.3Mb
  sub-directories of 1Mb or more:
    libs  37.1Mb
checkRd: (-1) ALF.Rd:47: Escaped LaTeX specials: \&
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs   3.6Mb
installed size is 27.3Mb
  sub-directories of 1Mb or more:
    libs  25.9Mb
installed size is 32.9Mb
  sub-directories of 1Mb or more:
    cereal   1.4Mb
    libs    31.4Mb
Bad \usage lines found in documentation object 'annmatrix':
  <unescaped bksl>method{@}{annmatrix}(object, name)
  <unescaped bksl>method{@}{annmatrix}(object, name) <- value

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Package suggested but not available for checking: ‘GEOquery’
installed size is 36.1Mb
  sub-directories of 1Mb or more:
    R  36.1Mb
installed size is 34.0Mb
  sub-directories of 1Mb or more:
    libs  33.7Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    libs   1.7Mb
installed size is 22.2Mb
  sub-directories of 1Mb or more:
    libs  21.9Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    data   2.1Mb
    doc    1.8Mb
sort_asap: no visible global function definition for ‘sort_by’
Undefined global functions or variables:
  sort_by
Found the following significant warnings:
  Warning: read_bcal.Rd:27: unknown macro '\abbr'
  Warning: read_chronomodel.Rd:36: unknown macro '\abbr'
  Warning: read_oxcal.Rd:27: unknown macro '\abbr'
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.3/ArchaeoPhases.Rcheck/00install.out’ for details.
prepare_Rd: read_bcal.Rd:27: unknown macro '\abbr'
prepare_Rd: read_chronomodel.Rd:36: unknown macro '\abbr'
prepare_Rd: read_oxcal.Rd:27: unknown macro '\abbr'
installed size is 18.2Mb
  sub-directories of 1Mb or more:
    libs  17.9Mb
Packages suggested but not available for checking:
  'affxparser', 'oligo', 'oligoClasses', 'pdInfoBuilder',
  'AffymetrixDataTestFiles'
Packages unavailable to check Rd xrefs: ‘affxparser’, ‘oligo’, ‘oligoClasses’
Package suggested but not available for checking: ‘affxparser’
Package unavailable to check Rd xrefs: ‘affxparser’
Package suggested but not available for checking: ‘GLAD’
Packages suggested but not available for checking:
  'GLAD', 'sfit', 'expectile', 'HaarSeg', 'mpcbs'
Package unavailable to check Rd xrefs: ‘GLAD’
installed size is 565.1Mb
  sub-directories of 1Mb or more:
    R       5.1Mb
    libs  559.4Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    libs   9.0Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   1.5Mb
installed size is 18.2Mb
  sub-directories of 1Mb or more:
    libs  18.0Mb
Running examples in ‘autogam-Ex.R’ failed
The error most likely occurred in:

> ### Name: autogam
> ### Title: Automate the creation of a Generalized Additive Model (GAM)
> ### Aliases: autogam
> 
> ### ** Examples
> 
> autogam(mtcars, 'mpg')
Error in magic(G$y, G$X, msp, G$S, G$off, L = G$L, lsp0 = G$lsp0, G$rank,  : 
  magic, the gcv/ubre optimizer, failed to converge after 400 iterations.
Calls: autogam ... do.call -> <Anonymous> -> estimate.gam -> am.fit -> magic
Execution halted
Packages required but not available: 'siggenes', 'clusterProfiler'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   6.0Mb
installed size is 90.2Mb
  sub-directories of 1Mb or more:
    doc    4.9Mb
    libs  83.8Mb
installed size is 114.9Mb
  sub-directories of 1Mb or more:
    libs  113.2Mb
installed size is 95.7Mb
  sub-directories of 1Mb or more:
    libs  93.9Mb
installed size is 63.5Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    libs  61.6Mb
Package suggested but not available for checking: ‘ArrayExpress’
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    libs   3.4Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    doc    3.9Mb
    help   2.2Mb
installed size is 13.6Mb
  sub-directories of 1Mb or more:
    libs  13.5Mb
installed size is 70.7Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs  67.2Mb
installed size is 118.1Mb
  sub-directories of 1Mb or more:
    doc     1.0Mb
    libs  116.6Mb
installed size is 24.4Mb
  sub-directories of 1Mb or more:
    doc   10.9Mb
    libs  12.5Mb
installed size is 87.0Mb
  sub-directories of 1Mb or more:
    libs  85.6Mb
installed size is 114.0Mb
  sub-directories of 1Mb or more:
    libs  113.5Mb
installed size is 45.9Mb
  sub-directories of 1Mb or more:
    libs  44.4Mb
installed size is 58.8Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    help   1.8Mb
    libs  54.6Mb
installed size is 244.5Mb
  sub-directories of 1Mb or more:
    libs  243.7Mb
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    libs   8.5Mb
installed size is 25.9Mb
  sub-directories of 1Mb or more:
    doc    2.8Mb
    libs  21.5Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    libs   8.0Mb
installed size is 87.5Mb
  sub-directories of 1Mb or more:
    libs  87.2Mb
installed size is 32.0Mb
  sub-directories of 1Mb or more:
    libs  31.8Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    extdata   2.3Mb
    libs      3.5Mb
Error(s) in re-building vignettes:
--- re-building ‘article.Rnw’ using Sweave
Setting levels: control = No, case = Yes
Loading required package: glmnet
Loading required package: Matrix
Loaded glmnet 4.1-7
Setting levels: control = No, case = Yes
Setting levels: control = No, case = Yes
Loading required package: Biostrings
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm,
    append, as.data.frame, basename, cbind, colnames, dirname,
    do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit, which.max, which.min

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following objects are masked from 'package:Matrix':

    expand, unname

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: XVector
Loading required package: GenomeInfoDb

Attaching package: 'Biostrings'

The following object is masked from 'package:base':

    strsplit

Error: processing vignette 'article.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'article.tex' failed.
LaTeX errors:
!pdfTeX error: pdflatex (file bbm10): Font bbm10 at 657 not found
 ==> Fatal error occurred, no output PDF file produced!
--- failed re-building 'article.Rnw'

SUMMARY: processing the following file failed:
  'article.Rnw'

Error: Vignette re-building failed.
Execution halted
installed size is 34.7Mb
  sub-directories of 1Mb or more:
    libs  34.0Mb
checkRd: (-1) Glendalough.Rd:19: Escaped LaTeX specials: \&
checkRd: (-1) Sluggan.Rd:19: Escaped LaTeX specials: \&
installed size is 96.7Mb
  sub-directories of 1Mb or more:
    libs  95.1Mb
installed size is 65.0Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    libs  61.7Mb
installed size is 36.5Mb
  sub-directories of 1Mb or more:
    libs  35.9Mb
installed size is 52.3Mb
  sub-directories of 1Mb or more:
    libs  51.7Mb
installed size is 25.4Mb
  sub-directories of 1Mb or more:
    libs  24.4Mb
installed size is 60.6Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    libs  57.4Mb
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    doc    2.9Mb
    libs   6.5Mb
installed size is 161.5Mb
  sub-directories of 1Mb or more:
    include  161.4Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   5.2Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc       1.8Mb
    extdata   1.9Mb
    libs      2.4Mb
installed size is 19.7Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs  18.1Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    libs   4.4Mb
installed size is 94.9Mb
  sub-directories of 1Mb or more:
    libs  94.4Mb
Package suggested but not available for checking: ‘msa’
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   3.0Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   1.7Mb
    help   2.6Mb
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    extdata   4.8Mb
    libs      2.9Mb
installed size is 48.3Mb
  sub-directories of 1Mb or more:
    extdata   1.5Mb
    libs     46.0Mb
Package suggested but not available for checking: ‘IHW’
installed size is 45.1Mb
  sub-directories of 1Mb or more:
    libs  44.1Mb
Found the following significant warnings:

  Warning: 'blandr.output.text' is deprecated.
  Warning: 'blandr.output.text' is deprecated.
  Warning: 'blandr.output.text' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
installed size is 14.1Mb
  sub-directories of 1Mb or more:
    libs  13.6Mb
installed size is 167.8Mb
  sub-directories of 1Mb or more:
    libs  167.0Mb
installed size is 97.6Mb
  sub-directories of 1Mb or more:
    libs  97.0Mb
installed size is 50.4Mb
  sub-directories of 1Mb or more:
    libs  50.0Mb
installed size is 90.8Mb
  sub-directories of 1Mb or more:
    libs  87.4Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
installed size is 16.2Mb
  sub-directories of 1Mb or more:
    libs  15.0Mb
installed size is 13.1Mb
  sub-directories of 1Mb or more:
    libs  12.2Mb
checkRd: (-1) bp_rats.Rd:41: Escaped LaTeX specials: \&
installed size is 52.5Mb
  sub-directories of 1Mb or more:
    libs  52.2Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc    2.7Mb
    libs   2.5Mb
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    components   1.0Mb
    fonts        2.8Mb
    lib          5.2Mb
installed size is 173.3Mb
  sub-directories of 1Mb or more:
    libs  172.4Mb
Package required but not available: ‘GENIE3’

Package suggested but not available for checking: ‘org.Mm.eg.db’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
pairwise.matrix: no visible global function definition for ‘%||%’
Undefined global functions or variables:
  %||%
Running examples in ‘bullseye-Ex.R’ failed
The error most likely occurred in:

> ### Name: pair_ace
> ### Title: Alternating conditional expectations correlation
> ### Aliases: pair_ace
> 
> ### ** Examples
> 
>  pair_ace(iris)
Error in rownames(m) %||% paste0("V", seq_along(xindex)) : 
  could not find function "%||%"
Calls: pair_ace -> pairwise -> pairwise.data.frame -> pairwise.matrix
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘calc_pairwise.Rmd’ using rmarkdown

Quitting from lines 44-46 [unnamed-chunk-3] (calc_pairwise.Rmd)
Error: processing vignette 'calc_pairwise.Rmd' failed with diagnostics:
could not find function "%||%"
--- failed re-building ‘calc_pairwise.Rmd’

--- re-building ‘integrating.Rmd’ using rmarkdown

Quitting from lines 57-62 [corrplot_assoc] (integrating.Rmd)
Error: processing vignette 'integrating.Rmd' failed with diagnostics:
could not find function "%||%"
--- failed re-building ‘integrating.Rmd’

--- re-building ‘vis_pairwise.Rmd’ using rmarkdown

Quitting from lines 52-53 [unnamed-chunk-3] (vis_pairwise.Rmd)
Error: processing vignette 'vis_pairwise.Rmd' failed with diagnostics:
could not find function "%||%"
--- failed re-building ‘vis_pairwise.Rmd’

SUMMARY: processing the following files failed:
  ‘calc_pairwise.Rmd’ ‘integrating.Rmd’ ‘vis_pairwise.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘bunching_examples.Rmd’ using rmarkdown
! kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 bbm10

! mkdir: ././opt/tex/texmf-var/fonts/pk/ljfour/public: Permission denied

! mktexpk: /opt/tex/texmf-dist/web2c/mktexdir /opt/tex/texmf-var/fonts/pk/ljfour/public/bbm failed.

! kpathsea: Appending font creation commands to missfont.log.

Error: processing vignette 'bunching_examples.Rmd' failed with diagnostics:
LaTeX failed to compile /Volumes/Builds/packages/big-sur-arm64/results/4.3/bunching.Rcheck/vign_test/bunching/vignettes/bunching_examples.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See bunching_examples.log for more info.
--- failed re-building ‘bunching_examples.Rmd’

--- re-building ‘bunching_theory.Rmd’ using rmarkdown
! kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 bbm10

! mkdir: ././opt/tex/texmf-var/fonts/pk/ljfour/public: Permission denied

! mktexpk: /opt/tex/texmf-dist/web2c/mktexdir /opt/tex/texmf-var/fonts/pk/ljfour/public/bbm failed.

! kpathsea: Appending font creation commands to missfont.log.

Error: processing vignette 'bunching_theory.Rmd' failed with diagnostics:
LaTeX failed to compile /Volumes/Builds/packages/big-sur-arm64/results/4.3/bunching.Rcheck/vign_test/bunching/vignettes/bunching_theory.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See bunching_theory.log for more info.
--- failed re-building ‘bunching_theory.Rmd’

SUMMARY: processing the following files failed:
  ‘bunching_examples.Rmd’ ‘bunching_theory.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    libs   6.9Mb
installed size is 21.5Mb
  sub-directories of 1Mb or more:
    libs  19.9Mb
installed size is 153.8Mb
  sub-directories of 1Mb or more:
    libs  151.7Mb
installed size is 44.3Mb
  sub-directories of 1Mb or more:
    libs  43.9Mb
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    data  10.1Mb
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    doc    1.1Mb
    libs   5.5Mb
installed size is 62.5Mb
  sub-directories of 1Mb or more:
    libs  62.4Mb
Package required but not available: ‘aroma.core’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    libs  10.7Mb
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    libs  10.2Mb
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    libs   5.9Mb
installed size is 38.3Mb
  sub-directories of 1Mb or more:
    libs  38.0Mb
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    R      2.3Mb
    libs   3.5Mb
installed size is 53.9Mb
  sub-directories of 1Mb or more:
    libs  52.8Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    data      1.6Mb
    extdata   1.1Mb
    libs      3.4Mb
installed size is 163.3Mb
  sub-directories of 1Mb or more:
    libs  162.9Mb
installed size is 24.4Mb
  sub-directories of 1Mb or more:
    libs  24.1Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    libs   3.4Mb
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    libs  11.1Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
Packages suggested but not available for checking:
  'GenomicInteractions', 'Gviz', 'countreg'
Packages suggested but not available for checking: 'entab', 'mzR'
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    R         2.8Mb
    extdata   4.3Mb
Packages required but not available:
  'ChIPseeker', 'TxDb.Hsapiens.UCSC.hg38.knownGene'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   1.8Mb
    libs   5.0Mb
installed size is 14.6Mb
  sub-directories of 1Mb or more:
    libs  14.3Mb
checkRd: (-1) clme.Rd:84: Escaped LaTeX specials: \&
installed size is 18.3Mb
  sub-directories of 1Mb or more:
    libs  16.4Mb
installed size is 31.5Mb
  sub-directories of 1Mb or more:
    libs  29.4Mb
Package required but not available: ‘GSVA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 18.8Mb
  sub-directories of 1Mb or more:
    libs  18.4Mb
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.3/cmmr.Rcheck/00install.out’ for details.
installed size is 35.6Mb
  sub-directories of 1Mb or more:
    libs  35.4Mb
Package required but not available: ‘GenomicInteractions’

Packages suggested but not available for checking:
  'InteractionSet', 'BSgenome.Hsapiens.UCSC.hg19'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 23.3Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    libs  19.2Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc       2.4Mb
    extdata   2.1Mb
installed size is 66.6Mb
  sub-directories of 1Mb or more:
    libs  65.5Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
installed size is 17.3Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs  15.2Mb
installed size is 30.5Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    libs  28.4Mb
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    libs  11.0Mb
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    libs   9.6Mb
Running examples in ‘conos-Ex.R’ failed
The error most likely occurred in:

> ### Name: Conos
> ### Title: Conos R6 class
> ### Aliases: Conos
> 
> ### ** Examples
> 
> 
> ## ------------------------------------------------
> ## Method `Conos$new`
> ## ------------------------------------------------
> 
> con <- Conos$new(small_panel.preprocessed, n.cores=1)
> 
> 
> ## ------------------------------------------------
> ## Method `Conos$buildGraph`
> ## ------------------------------------------------
> 
> con <- Conos$new(small_panel.preprocessed, n.cores=1)
> con$buildGraph(k=10, k.self=5, space='PCA', ncomps=10, n.odgenes=20, matching.method='mNN',
+     metric='angular', score.component.variance=TRUE, verbose=TRUE)
found 0 out of 1 cached PCA space pairs ... 
running 1 additional PCA space pairs 
Error in irlba::irlba(x, nv = ncomps, nu = 0, center = cm, right_only = FALSE,  : 
  function 'as_cholmod_sparse' not provided by package 'Matrix'
Calls: <Anonymous> ... FUN -> quickPlainPCA -> lapply -> FUN -> <Anonymous>
Execution halted
Running ‘testthat.R’ [3s/3s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(conos)
  Loading required package: Matrix
  Loading required package: igraph
  
  Attaching package: 'igraph'
  
  The following objects are masked from 'package:stats':
  
      decompose, spectrum
  
  The following object is masked from 'package:base':
  
      union
  
  > 
  > testthat::test_check("conos")
  
  Attaching package: 'testthat'
  
  The following object is masked from 'package:igraph':
  
      compare
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 1 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_functions.R:15:1'): (code run outside of `test_that()`) ────────
  Error in `irlba::irlba(x, nv = ncomps, nu = 0, center = cm, right_only = FALSE, 
      reorth = TRUE)`: function 'as_cholmod_sparse' not provided by package 'Matrix'
  Backtrace:
       ▆
    1. ├─base::suppressWarnings(con$buildGraph(ncomps = 25)) at test_functions.R:15:1
    2. │ └─base::withCallingHandlers(...)
    3. └─con$buildGraph(ncomps = 25)
    4.   └─private$updatePairs(...)
    5.     └─sccore::plapply(...)
    6.       └─base::lapply(...)
    7.         └─conos (local) FUN(X[[i]], ...)
    8.           └─conos:::quickPlainPCA(...)
    9.             └─base::lapply(...)
   10.               └─conos (local) FUN(X[[i]], ...)
   11.                 └─irlba::irlba(...)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 1 ]
  Error: Test failures
  Execution halted
installed size is 68.5Mb
  sub-directories of 1Mb or more:
    libs  67.3Mb
Package suggested but not available for checking: ‘phyloseq’
Package suggested but not available for checking: ‘xcms’
fishp: no visible binding for global variable ‘markname’
fishp: no visible binding for global variable ‘sum_chisq’
fishp: no visible binding for global variable ‘sum_z’
pvalues_to_zscores: no visible binding for global variable ‘markname’
tetracorr: no visible binding for global variable ‘PLCORR’
Undefined global functions or variables:
  PLCORR markname sum_chisq sum_z
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   5.3Mb
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    libs   9.2Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    doc    2.9Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘cplm.Rnw’ using Sweave
Loading required package: coda
Loading required package: Matrix
Loading required package: splines
Error: processing vignette 'cplm.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'cplm.tex' failed.
LaTeX errors:
!pdfTeX error: pdflatex (file bbm10): Font bbm10 at 600 not found
 ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘cplm.Rnw’

SUMMARY: processing the following file failed:
  ‘cplm.Rnw’

Error: Vignette re-building failed.
Execution halted
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
installed size is 41.5Mb
  sub-directories of 1Mb or more:
    libs  41.4Mb
installed size is 29.2Mb
  sub-directories of 1Mb or more:
    libs  27.6Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    data   8.0Mb
installed size is 201.8Mb
  sub-directories of 1Mb or more:
    R       2.1Mb
    data    1.7Mb
    libs  196.6Mb
Packages required and available but unsuitable versions:
  'stats', 'tools', 'utils'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 37.2Mb
  sub-directories of 1Mb or more:
    libs  37.1Mb
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    R      3.1Mb
    doc    1.2Mb
    help   1.0Mb
    libs   4.7Mb
installed size is 28.2Mb
  sub-directories of 1Mb or more:
    libs  27.3Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    doc    1.1Mb
    libs   3.0Mb
Found the following significant warnings:
  Warning: jpegReport.Rd:22: unknown macro '\abbr'
  Warning: jpegReport.Rd:50: unknown macro '\abbr'
  Warning: jpegReport.Rd:53: unknown macro '\abbr'
  Warning: jpegReport.Rd:56: unknown macro '\abbr'
  Warning: jpegReport.Rd:58: unknown macro '\abbr'
  Warning: jpegReport.Rd:62: unknown macro '\abbr'
  Warning: pdfReport.Rd:101: unknown macro '\abbr'
  Warning: pngReport.Rd:22: unknown macro '\abbr'
  Warning: pngReport.Rd:50: unknown macro '\abbr'
  Warning: pngReport.Rd:53: unknown macro '\abbr'
  Warning: pngReport.Rd:55: unknown macro '\abbr'
  Warning: pngReport.Rd:59: unknown macro '\abbr'
  Warning: readReportTable.Rd:35: unknown macro '\abbr'
  Warning: readReportTable.Rd:167: unknown macro '\abbr'
  Warning: scanReport.Rd:45: unknown macro '\abbr'
  Warning: scanReport.Rd:60: unknown macro '\abbr'
  Warning: scanReport.Rd:61: unknown macro '\abbr'
  Warning: scanReport.Rd:162: unknown macro '\abbr'
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.3/D4TAlink.light.Rcheck/00install.out’ for details.
prepare_Rd: jpegReport.Rd:22: unknown macro '\abbr'
prepare_Rd: jpegReport.Rd:50: unknown macro '\abbr'
prepare_Rd: jpegReport.Rd:53: unknown macro '\abbr'
prepare_Rd: jpegReport.Rd:56: unknown macro '\abbr'
prepare_Rd: jpegReport.Rd:58: unknown macro '\abbr'
prepare_Rd: jpegReport.Rd:62: unknown macro '\abbr'
prepare_Rd: pdfReport.Rd:101: unknown macro '\abbr'
prepare_Rd: pngReport.Rd:22: unknown macro '\abbr'
prepare_Rd: pngReport.Rd:50: unknown macro '\abbr'
prepare_Rd: pngReport.Rd:53: unknown macro '\abbr'
prepare_Rd: pngReport.Rd:55: unknown macro '\abbr'
prepare_Rd: pngReport.Rd:59: unknown macro '\abbr'
prepare_Rd: readReportTable.Rd:35: unknown macro '\abbr'
prepare_Rd: readReportTable.Rd:167: unknown macro '\abbr'
prepare_Rd: scanReport.Rd:45: unknown macro '\abbr'
prepare_Rd: scanReport.Rd:60: unknown macro '\abbr'
prepare_Rd: scanReport.Rd:61: unknown macro '\abbr'
prepare_Rd: scanReport.Rd:162: unknown macro '\abbr'
installed size is 29.3Mb
  sub-directories of 1Mb or more:
    libs  27.3Mb
Package suggested but not available for checking: ‘snpStats’
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   6.5Mb
Package required but not available: ‘dada2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘DBTC’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 53.3Mb
  sub-directories of 1Mb or more:
    libs  52.8Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    data   1.9Mb
    libs   5.5Mb
installed size is 24.3Mb
  sub-directories of 1Mb or more:
    libs  24.2Mb
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    libs   9.7Mb
installed size is 38.0Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs  35.8Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.1Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    extdata   2.1Mb
    libs      2.3Mb
installed size is 19.6Mb
  sub-directories of 1Mb or more:
    libs  18.8Mb
Packages suggested but not available for checking:
  'IHW', 'RNASeqPower', 'zFPKM'
installed size is 69.9Mb
  sub-directories of 1Mb or more:
    libs  69.0Mb
Package unavailable to check Rd xrefs: ‘airway’
checkRd: (-1) dataCensoring.Rd:78: Escaped LaTeX specials: \&
checkRd: (-1) dataLong.Rd:170: Escaped LaTeX specials: \&
checkRd: (-1) dataLongCompRisksTimeDep.Rd:130: Escaped LaTeX specials: \&
checkRd: (-1) dataLongMultiSpell.Rd:123: Escaped LaTeX specials: \&
checkRd: (-1) dataLongTimeDep.Rd:96: Escaped LaTeX specials: \&
Running ‘testthat.R’ [4s/4s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  realized_duration(...) not equal to c(...).
  1/4 mismatches
  [1] 29 - 28 == 1
  ── Failure ('test-realized_duration.R:158:2'): realized_duration works (realized_only = TRUE) ──
  realized_duration(...) not equal to c(...).
  1/4 mismatches
  [2] 29 - 28 == 1
  ── Failure ('test-realized_duration.R:161:2'): realized_duration works (realized_only = TRUE) ──
  realized_duration(...) not equal to c(...).
  1/4 mismatches
  [1] 29 - 28 == 1
  
  [ FAIL 36 | WARN 0 | SKIP 0 | PASS 331 ]
  Error: Test failures
  Execution halted
Package suggested but not available for checking: ‘distrEx’
installed size is 34.3Mb
  sub-directories of 1Mb or more:
    libs  33.6Mb
checkRd: (-1) dlsem.Rd:42: Escaped LaTeX specials: \&
checkRd: (-1) unirootTest.Rd:14: Escaped LaTeX specials: \&
checkRd: (-1) unirootTest.Rd:20: Escaped LaTeX specials: \&
checkRd: (-1) unirootTest.Rd:26: Escaped LaTeX specials: \&
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    data   5.1Mb
    libs   2.4Mb
installed size is 20.1Mb
  sub-directories of 1Mb or more:
    doc    6.7Mb
    libs  12.7Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    R         3.1Mb
    data      2.0Mb
    extdata   2.3Mb
installed size is 14.0Mb
  sub-directories of 1Mb or more:
    libs  13.9Mb
checkRd: (-1) EDcomp.Rd:88: Escaped LaTeX specials: \&
checkRd: (-1) LL.4.Rd:44: Escaped LaTeX specials: \&
checkRd: (-1) W4.Rd:37: Escaped LaTeX specials: \&
checkRd: (-1) algae.Rd:32: Escaped LaTeX specials: \&
checkRd: (-1) anova.drc.Rd:40: Escaped LaTeX specials: \&
checkRd: (-1) deguelin.Rd:33: Escaped LaTeX specials: \&
checkRd: (-1) gompertz.Rd:55: Escaped LaTeX specials: \&
checkRd: (-1) hatvalues.drc.Rd:44: Escaped LaTeX specials: \&
checkRd: (-1) llogistic.Rd:64: Escaped LaTeX specials: \&
checkRd: (-1) modelFit.Rd:36: Escaped LaTeX specials: \&
checkRd: (-1) weibull1.Rd:67: Escaped LaTeX specials: \&
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data      1.7Mb
    extdata   3.1Mb
Running examples in ‘dsem-Ex.R’ failed
The error most likely occurred in:

> ### Name: dsemRTMB
> ### Title: Fit dynamic structural equation model
> ### Aliases: dsemRTMB
> 
> ### ** Examples
> 
> # Define model
> sem = "
+   # Link, lag, param_name
+   cprofits -> consumption, 0, a1
+   cprofits -> consumption, 1, a2
+   pwage -> consumption, 0, a3
+   gwage -> consumption, 0, a3
+   cprofits -> invest, 0, b1
+   cprofits -> invest, 1, b2
+   capital -> invest, 0, b3
+   gnp -> pwage, 0, c2
+   gnp -> pwage, 1, c3
+   time -> pwage, 0, c1
+ "
> 
> # Load data
> data(KleinI, package="AER")
> TS = ts(data.frame(KleinI, "time"=time(KleinI) - 1931))
> tsdata = TS[,c("time","gnp","pwage","cprofits",'consumption',
+                "gwage","invest","capital")]
> 
> # Fit model
> fit = dsemRTMB( sem=sem,
+             tsdata = tsdata,
+             estimate_delta0 = TRUE,
+             control = dsem_control(quiet=TRUE) )
Read 10 records
Error in advector(e1) : 
  Invalid argument to 'advector' (lost class attribute?)
Calls: dsemRTMB ... dgmrf -> as.vector -> Ops.advector -> Arith2 -> advector
Execution halted
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    shiny_app   1.1Mb
installed size is 18.2Mb
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Package required but not available: ‘HDF5Array’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 224.7Mb
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Running ‘testthat.R’ [1s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  > library(EGRETci)
  > test_check("EGRETci")
  [ FAIL 1 | WARN 0 | SKIP 10 | PASS 16 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • On CRAN (10)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('tests_boot_tests.R:112:3'): paVector ──────────────────────────────
  `paIndexWinter` not equal to 11:13.
  Lengths differ: 4 is not 3
  
  [ FAIL 1 | WARN 0 | SKIP 10 | PASS 16 ]
  Error: Test failures
  Execution halted
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checkRd: (5) ePCR.Rd:0-17: Must have a \description
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Error(s) in re-building vignettes:
--- re-building ‘data_protocol.Rmd’ using rmarkdown
--- finished re-building ‘data_protocol.Rmd’

--- re-building ‘database.Rmd’ using rmarkdown
--- finished re-building ‘database.Rmd’

--- re-building ‘design_principles.Rmd’ using rmarkdown
--- finished re-building ‘design_principles.Rmd’

--- re-building ‘epiparameter.Rmd’ using rmarkdown
--- finished re-building ‘epiparameter.Rmd’

--- re-building ‘extract-bias.Rmd’ using rmarkdown
File figure/plot-results-percentiles-1.png not found in resource path
Error: processing vignette 'extract-bias.Rmd' failed with diagnostics:
pandoc document conversion failed with error 99
--- failed re-building ‘extract-bias.Rmd’

--- re-building ‘extract_convert.Rmd’ using rmarkdown
--- finished re-building ‘extract_convert.Rmd’

SUMMARY: processing the following file failed:
  ‘extract-bias.Rmd’

Error: Vignette re-building failed.
Execution halted
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Packages suggested but not available for checking: 'mzR', 'gcspikelite'
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Package required but not available: ‘PSCBS’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) calculateGLR.Rd:43: Escaped LaTeX specials: \&
CCRR: no visible global function definition for ‘%||%’
ITBiserial: no visible global function definition for ‘%||%’
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createBinaryFunction : <anonymous>: no visible global function
  definition for ‘%||%’
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stanine: no visible global function definition for ‘%||%’
Undefined global functions or variables:
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checkRd: (-1) ccF.Rd:5: Escaped LaTeX specials: \&
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checkRd: (-1) sp500.Rd:5: Escaped LaTeX specials: \&
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Error(s) in re-building vignettes:
--- re-building ‘jss.Rmd’ using rmarkdown
This is pdfTeX, Version 3.141592653-2.6-1.40.24 (TeX Live 2022) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode

kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+57/600 --dpi 657 bbm10
mkdir: ././opt/tex/texmf-var/fonts/pk/ljfour/public: Permission denied
mktexpk: /opt/tex/texmf-dist/web2c/mktexdir /opt/tex/texmf-var/fonts/pk/ljfour/public/bbm failed.
kpathsea: Appending font creation commands to missfont.log.
This is pdfTeX, Version 3.141592653-2.6-1.40.24 (TeX Live 2022) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode

kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+57/600 --dpi 657 bbm10
mkdir: ././opt/tex/texmf-var/fonts/pk/ljfour/public: Permission denied
mktexpk: /opt/tex/texmf-dist/web2c/mktexdir /opt/tex/texmf-var/fonts/pk/ljfour/public/bbm failed.
kpathsea: Appending font creation commands to missfont.log.
This is pdfTeX, Version 3.141592653-2.6-1.40.24 (TeX Live 2022) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode

kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+57/600 --dpi 657 bbm10
mkdir: ././opt/tex/texmf-var/fonts/pk/ljfour/public: Permission denied
mktexpk: /opt/tex/texmf-dist/web2c/mktexdir /opt/tex/texmf-var/fonts/pk/ljfour/public/bbm failed.
kpathsea: Appending font creation commands to missfont.log.
Error: processing vignette 'jss.Rmd' failed with diagnostics:
LaTeX failed to compile /Volumes/Builds/packages/big-sur-arm64/results/4.3/fairadapt.Rcheck/vign_test/fairadapt/vignettes/jss.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips.
--- failed re-building ‘jss.Rmd’

SUMMARY: processing the following file failed:
  ‘jss.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘familial-Ex.R’ failed
The error most likely occurred in:

> ### Name: center.test
> ### Title: Center test
> ### Aliases: center.test
> 
> ### ** Examples
> 
> set.seed(123)
> 
> test <- center.test(MASS::galaxies, mu = 21000, nboot = 100)
> print(test)
-----------------------------------------------
familial test of centers with huber family
-----------------------------------------------
mu = 21000 
posterior probabilities: 
  H0   H1 
0.59 0.41 
optimal decision: indeterminate 
> plot(test)
Error in validObject(.Object) : 
  invalid class “FncBand” object: superclass "mMatrix" not defined in the environment of the object's class
Calls: plot ... initialize -> initialize -> initMatrix -> validObject
Execution halted
Running ‘testthat.R’ [40s/44s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(familial)
  > 
  > test_check("familial")
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 34 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-center-test.R:27:3'): plot function returns a plot ─────────────
  Error in `validObject(.Object)`: invalid class "FncBand" object: superclass "mMatrix" not defined in the environment of the object's class
  Backtrace:
       ▆
    1. ├─testthat::expect_s3_class(plot(test), "ggplot") at test-center-test.R:27:3
    2. │ └─testthat::quasi_label(enquo(object), arg = "object")
    3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
    4. ├─base::plot(test)
    5. └─familial:::plot.center.test(test)
    6.   └─base::lapply(band, bands)
    7.     └─familial (local) FUN(X[[i]], ...)
    8.       ├─base::data.frame(...)
    9.       └─DepthProc::fncGetBand(DepthProc::fncDepth(boot.wide), level)
   10.         └─methods::new("FncBand", bands, index = obj@index, level = band)
   11.           ├─methods::initialize(value, ...)
   12.           └─methods::initialize(value, ...)
   13.             └─methods (local) initMatrix(.Object, ...)
   14.               └─methods::validObject(.Object)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 34 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
--- re-building ‘vignette.Rmd’ using rmarkdown

Quitting from lines 56-57 [unnamed-chunk-3] (vignette.Rmd)
Error: processing vignette 'vignette.Rmd' failed with diagnostics:
invalid class "FncBand" object: superclass "mMatrix" not defined in the environment of the object's class
--- failed re-building ‘vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
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checkRd: (-1) fermicatsR.Rd:31: Escaped LaTeX specials: \&
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Error(s) in re-building vignettes:
  ...
--- re-building ‘fitbitScraper-examples.Rmd’ using rmarkdown
Quitting from lines 22-24 (fitbitScraper-examples.Rmd) 
Error: processing vignette 'fitbitScraper-examples.Rmd' failed with diagnostics:
login failed
--- failed re-building ‘fitbitScraper-examples.Rmd’

SUMMARY: processing the following file failed:
  ‘fitbitScraper-examples.Rmd’

Error: Vignette re-building failed.
Execution halted
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Packages suggested but not available for checking:
  'benchden', 'reliaR', 'STAR'
installed size is 12.5Mb
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Package suggested but not available for checking: ‘ExperimentHub’
Error(s) in re-building vignettes:
--- re-building ‘FLASHMM-vignette.Rmd’ using rmarkdown
* installing *source* package ‘FLASHMM’ ...
** using staged installation
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (FLASHMM)

Quitting from lines 216-242 [Reference dataset] (FLASHMM-vignette.Rmd)
Error: processing vignette 'FLASHMM-vignette.Rmd' failed with diagnostics:
there is no package called 'ExperimentHub'
--- failed re-building ‘FLASHMM-vignette.Rmd’

SUMMARY: processing the following file failed:
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Error: Vignette re-building failed.
Execution halted
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installed size is 106.0Mb
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Package suggested but not available for checking: ‘WGCNA’
installed size is 37.7Mb
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installed size is 255.2Mb
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Package required but not available: ‘GEOquery’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘rrvgo’
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Package which this enhances but not available for checking: ‘simplifyEnrichment’
Package required but not available: ‘biocViews’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  6.8Mb
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Package required but not available: ‘snpStats’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 31.3Mb
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Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.3/GeoModels.Rcheck/00install.out’ for details.
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Running examples in ‘ggESDA-Ex.R’ failed
The error most likely occurred in:

> ### Name: Cardiological
> ### Title: Cardiological data example
> ### Aliases: Cardiological
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(Cardiological)
> ggInterval_index(Cardiological, aes(x = Syst))
Error in get(x, envir = ns, inherits = FALSE) : 
  object 'tbl_subset_col' not found
Calls: ggInterval_index ... as.data.frame -> [ -> [.symbolic_tbl -> getFromNamespace -> get
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘ggESDA.Rmd’ using rmarkdown
Quitting from lines 47-57 (ggESDA.Rmd) 
Error: processing vignette 'ggESDA.Rmd' failed with diagnostics:
object 'tbl_subset_col' not found
--- failed re-building ‘ggESDA.Rmd’

SUMMARY: processing the following file failed:
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Error: Vignette re-building failed.
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checkRd: (-1) coef.glmulti.Rd:26: Escaped LaTeX specials: \&
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checkRd: (-1) glmulti-class.Rd:26: Escaped LaTeX specials: \&
checkRd: (-1) glmulti.Rd:99: Escaped LaTeX specials: \&
checkRd: (-1) summary.glmulti.Rd:72: Escaped LaTeX specials: \&
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Error(s) in re-building vignettes:
--- re-building ‘custom_ocl_gpuR.Rnw’ using knitr
Error: processing vignette 'custom_ocl_gpuR.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'custom_ocl_gpuR.tex' failed.
LaTeX errors:
! Missing $ inserted.
<inserted text> 
                $
l.116 custom_
             ocl_gpuR.R\end{kframe}
! Emergency stop.
<inserted text> 
                $
l.116 custom_
             ocl_gpuR.R\end{kframe}
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘custom_ocl_gpuR.Rnw’

--- re-building ‘gpuR.Rnw’ using knitr
--- finished re-building ‘gpuR.Rnw’

SUMMARY: processing the following file failed:
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Error: Vignette re-building failed.
Execution halted
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jagam2greta: no visible global function definition for ‘%||%’
Undefined global functions or variables:
  %||%
Package required but not available: ‘DOSE’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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installed size is 275.7Mb
  sub-directories of 1Mb or more:
    R       2.1Mb
    java  272.1Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   3.0Mb
    libs   2.5Mb
Package required but not available: ‘handwriterRF’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   3.2Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    libs   7.2Mb
installed size is 168.2Mb
  sub-directories of 1Mb or more:
    libs  166.5Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    R         3.1Mb
    extdata   1.3Mb
Running examples in ‘HCD-Ex.R’ failed
The error most likely occurred in:

> ### Name: HCD
> ### Title: hierarchical community detection with recursive spectral methods
> ### Aliases: HCD
> ### Keywords: HCD BTSBM
> 
> ### ** Examples
> 
> dt <- BTSBM(n=1600,d=4,a.seq=0.2^seq(0,4),lambda=50)
> A <- dt$A.list[[1]]
> # you can try various versions of the algorithm as below: the Fix is fastest and ECV is slowest.
> system.time(HCD.result <- HCD(A,method="SC",stopping="Fix",D=4))
Begin clustering....
Error in irlba(f, nu = 2, nv = 2) : 
  function 'as_cholmod_sparse' not provided by package 'Matrix'
Calls: system.time -> HCD -> break.cl.sp -> irlba
Timing stopped at: 0.007 0.001 0.007
Execution halted
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    data   7.0Mb
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    libs  10.8Mb
Found the following significant warnings:
  Warning: ‘ndel’ is used uninitialized [-Wuninitialized]
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.3/hdsvm.Rcheck/00install.out’ for details.
* used C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used Fortran compiler: ‘GNU Fortran (GCC) 12.2.0’
* used SDK: ‘MacOSX11.3.sdk’
Running examples in ‘healthyR.ai-Ex.R’ failed
The error most likely occurred in:

> ### Name: hai_umap_list
> ### Title: UMAP Projection
> ### Aliases: hai_umap_list umap_list
> 
> ### ** Examples
> 
> library(healthyR.data)

== Welcome to healthyR.data ===========================================================================
If you find this package useful, please leave a star: 
   https://github.com/spsanderson/healthyR.data'

If you encounter a bug or want to request an enhancement please file an issue at:
   https://github.com/spsanderson/healthyR.data/issues

Thank you for using healthyR.data
> library(dplyr)

Attaching package: ‘dplyr’

The following objects are masked from ‘package:stats’:

    filter, lag

The following objects are masked from ‘package:base’:

    intersect, setdiff, setequal, union

> library(broom)
> 
> data_tbl <- healthyR_data %>%
+   filter(ip_op_flag == "I") %>%
+   filter(payer_grouping != "Medicare B") %>%
+   filter(payer_grouping != "?") %>%
+   select(service_line, payer_grouping) %>%
+   mutate(record = 1) %>%
+   as_tibble()
> 
> uit_tbl <- hai_kmeans_user_item_tbl(
+   .data = data_tbl,
+   .row_input = service_line,
+   .col_input = payer_grouping,
+   .record_input = record
+ )
> 
> kmm_tbl <- hai_kmeans_mapped_tbl(uit_tbl)
> 
> umap_list(.data = uit_tbl, kmm_tbl, 3)
Error in irlba::irlba(L, nv = n, nu = 0, maxit = iters) : 
  function 'as_cholmod_sparse' not provided by package 'Matrix'
Calls: umap_list ... irlba_tsvd_normalized_laplacian_init -> irlba_spectral_tsvd
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘auto-kmeans.Rmd’ using rmarkdown
--- finished re-building ‘auto-kmeans.Rmd’

--- re-building ‘getting-started.Rmd’ using rmarkdown
--- finished re-building ‘getting-started.Rmd’

--- re-building ‘kmeans-umap.Rmd’ using rmarkdown

Quitting from lines 147-148 [umap_list] (kmeans-umap.Rmd)
Error: processing vignette 'kmeans-umap.Rmd' failed with diagnostics:
function 'as_cholmod_sparse' not provided by package 'Matrix'
--- failed re-building ‘kmeans-umap.Rmd’

SUMMARY: processing the following file failed:
  ‘kmeans-umap.Rmd’

Error: Vignette re-building failed.
Execution halted
Package required and available but unsuitable version: ‘healthyR.ai’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Heatplus’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R      1.6Mb
    doc    1.9Mb
    libs   1.4Mb
installed size is 23.7Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs  19.7Mb
installed size is  5.2Mb
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    extdata   2.6Mb
    libs      2.4Mb
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    highlight   1.0Mb
    libs        8.4Mb
Found the following significant warnings:
  clang: warning: argument unused during compilation: '-mpopcnt' [-Wunused-command-line-argument]
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.3/highs.Rcheck/00install.out’ for details.
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
installed size is 83.4Mb
  sub-directories of 1Mb or more:
    libs  82.9Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    help   2.3Mb
    libs   2.7Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    libs   4.3Mb
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    libs  11.1Mb
installed size is 60.9Mb
  sub-directories of 1Mb or more:
    libs  59.4Mb
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.3/hoardeR.Rcheck/00install.out’ for details.
installed size is 15.1Mb
  sub-directories of 1Mb or more:
    libs  14.8Mb
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    data   8.0Mb
installed size is 68.3Mb
  sub-directories of 1Mb or more:
    libs  67.7Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   3.7Mb
Package suggested but not available for checking: ‘HTSFilter’
installed size is 44.0Mb
  sub-directories of 1Mb or more:
    libs  43.4Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    extdata   5.5Mb
    libs      1.8Mb
Package suggested but not available for checking: ‘flowCore’
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc    2.5Mb
    libs   2.8Mb
installed size is 31.1Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs  29.3Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    libs   4.6Mb
installed size is 22.8Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    doc    1.2Mb
    help   2.0Mb
    libs  17.1Mb
installed size is 32.9Mb
  sub-directories of 1Mb or more:
    data      1.4Mb
    doc       3.7Mb
    extdata   1.0Mb
    include   3.3Mb
    libs     22.9Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    R   6.4Mb
installed size is 93.4Mb
  sub-directories of 1Mb or more:
    libs  92.7Mb
installed size is 16.8Mb
  sub-directories of 1Mb or more:
    doc    3.1Mb
    libs  12.1Mb
Packages required but not available: 'siggenes', 'RankProd'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
installed size is 12.4Mb
  sub-directories of 1Mb or more:
    libs  11.1Mb
Package unavailable to check Rd xrefs: ‘minfi’
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   5.3Mb
installed size is 30.2Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs  28.8Mb
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    libs  11.2Mb
Package suggested but not available for checking: ‘rhdf5’
Running ‘edge.R’ [1s/1s]
  Running ‘prcomp.r’ [1s/1s]
  Running ‘ssvd.R’ [1s/1s]
  Running ‘svdr.R’ [1s/1s]
  Running ‘test.R’ [1s/1s]
Running the tests in ‘tests/test.R’ failed.
Last 13 lines of output:
  + 
  +   # test for https://github.com/bwlewis/irlba/issues/42
  +   set.seed(1234)
  +   a <- matrix(rnorm(10000), ncol=20)
  +   center <- runif(ncol(a))
  +   scale <- runif(ncol(a))
  +   L <- irlba(a, 5, scale=scale, center=center, fastpath=FAST)
  +   S <- svd(scale(a, center=center, scale=scale))
  +   if (isTRUE(max(abs(S$d[1:5] - L$d)) > 1e-3))
  +   {
  +     stop("Failed scale + center test fastpath=", FAST)
  +   }
  + }
  Error: Failed tprolate test fastpath=FALSE
  Execution halted
installed size is  9.9Mb
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    libs   8.1Mb
installed size is 93.6Mb
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    data   2.0Mb
    doc    2.3Mb
    libs  88.2Mb
installed size is 19.3Mb
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    art_profiles   1.5Mb
    libs          17.0Mb
installed size is 102.7Mb
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    libs  101.3Mb
installed size is  7.4Mb
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    extdata   5.5Mb
    libs      1.8Mb
installed size is  8.9Mb
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    libs   7.8Mb
installed size is 32.8Mb
  sub-directories of 1Mb or more:
    libs  32.3Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    libs   5.8Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    libs   4.1Mb
Package suggested but not available for checking: ‘PSCBS’
Package unavailable to check Rd xrefs: ‘PSCBS’
installed size is 16.9Mb
  sub-directories of 1Mb or more:
    libs  16.4Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs   4.0Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘Instruction_of_functions_of_R_package_KINSIMU.Rnw’ using Sweave
Error: processing vignette 'Instruction_of_functions_of_R_package_KINSIMU.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'Instruction_of_functions_of_R_package_KINSIMU.tex' failed.
LaTeX errors:
! LaTeX Error: Command \gather already defined.
               Or name \end... illegal, see p.192 of the manual.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
! Emergency stop.
 ...                                              
                                                  
l.1560 }
        
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘Instruction_of_functions_of_R_package_KINSIMU.Rnw’

SUMMARY: processing the following file failed:
  ‘Instruction_of_functions_of_R_package_KINSIMU.Rnw’

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘seqLogo’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 13.5Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    libs  10.9Mb
checkRd: (-1) LaplaceApproximation.Rd:485: Escaped LaTeX specials: \&
checkRd: (-1) LossMatrix.Rd:115: Escaped LaTeX specials: \&
checkRd: (-1) LossMatrix.Rd:117: Escaped LaTeX specials: \&
Error(s) in re-building vignettes:
  ...
--- re-building ‘using_latent2likert.Rmd’ using rmarkdown
File man/figures/courses-grouped-min.png not found in resource path
Error: processing vignette 'using_latent2likert.Rmd' failed with diagnostics:
pandoc document conversion failed with error 99
--- failed re-building ‘using_latent2likert.Rmd’

SUMMARY: processing the following file failed:
  ‘using_latent2likert.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking: 'xcms', 'MSnbase'
Package suggested but not available for checking: ‘VariantAnnotation’
installed size is 46.2Mb
  sub-directories of 1Mb or more:
    help   1.1Mb
    libs  43.3Mb
installed size is 12.8Mb
  sub-directories of 1Mb or more:
    data   1.8Mb
    libs  10.5Mb
installed size is 93.8Mb
  sub-directories of 1Mb or more:
    libs  92.5Mb
checkRd: (-1) hydro.Rd:17: Escaped LaTeX specials: \&
checkRd: (-1) predict.lb.Rd:16: Escaped LaTeX specials: \$
installed size is 13.5Mb
  sub-directories of 1Mb or more:
    R         2.0Mb
    doc       1.0Mb
    extdata   1.2Mb
    libs      8.7Mb
installed size is 68.4Mb
  sub-directories of 1Mb or more:
    libs  67.8Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction.Rmd’ using rmarkdown
Quitting from lines 22-30 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
there is no package called 'org.Mm.eg.db'
--- failed re-building ‘introduction.Rmd’

SUMMARY: processing the following file failed:
  ‘introduction.Rmd’

Error: Vignette re-building failed.
Execution halted
checkRd: (-1) lstats.liu.Rd:41: Escaped LaTeX specials: \&
installed size is 27.4Mb
  sub-directories of 1Mb or more:
    R          1.6Mb
    doc        1.6Mb
    libs      22.2Mb
    testdata   1.3Mb
installed size is 57.8Mb
  sub-directories of 1Mb or more:
    libs  56.8Mb
installed size is 34.7Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs  32.7Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘localsolver.Rmd’ using knitr
sh: localsolver: command not found
Quitting from lines 66-68 (localsolver.Rmd) 
Error: processing vignette 'localsolver.Rmd' failed with diagnostics:
has.localsolver(ls.path) is not TRUE
--- failed re-building ‘localsolver.Rmd’

SUMMARY: processing the following file failed:
  ‘localsolver.Rmd’

Error: Vignette re-building failed.
Execution halted
checkRd: (-1) TrafficFlow.Rd:25: Escaped LaTeX specials: \#
installed size is 27.3Mb
  sub-directories of 1Mb or more:
    libs  27.1Mb
checkRd: (-1) butstrap.Rd:44: Escaped LaTeX specials: \&
checkRd: (-1) butstrap.nri.Rd:42: Escaped LaTeX specials: \&
checkRd: (-1) butstrap.s.Rd:44: Escaped LaTeX specials: \&
checkRd: (-1) maxauc.Rd:39: Escaped LaTeX specials: \&
checkRd: (-1) maxauc.s.Rd:39: Escaped LaTeX specials: \&
checkRd: (-1) nri.Rd:33: Escaped LaTeX specials: \&
checkRd: (-1) roc.Rd:47: Escaped LaTeX specials: \&
checkRd: (-1) roc.s.Rd:47: Escaped LaTeX specials: \&
checkRd: (-1) sensspec.Rd:47: Escaped LaTeX specials: \&
checkRd: (-1) sensspec.s.Rd:47: Escaped LaTeX specials: \&
Package suggested but not available for checking: ‘RDRToolbox’
installed size is  5.6Mb
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    extdata   4.5Mb
    libs      1.0Mb
installed size is 92.5Mb
  sub-directories of 1Mb or more:
    libs  90.3Mb
installed size is 50.0Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs  47.8Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    libs   3.9Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    libs   2.0Mb
installed size is 32.2Mb
  sub-directories of 1Mb or more:
    libs  31.8Mb
Package suggested but not available for checking: ‘quitte’
Packages suggested but not available for checking:
  'ssize', 'GEOquery', 'GEOmetadb', 'WGCNA', 'pdInfoBuilder', 'lumi',
  'oligo', 'GOstats'
Package suggested but not available for checking: ‘BiocCheck’
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    data   2.3Mb
    libs   5.1Mb
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    libs  10.8Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
installed size is 11.8Mb
  sub-directories of 1Mb or more:
    R      2.7Mb
    data   2.4Mb
    libs   4.7Mb
checkRd: (-1) marima.Rd:223: Escaped LaTeX specials: \&
installed size is 15.3Mb
  sub-directories of 1Mb or more:
    examples   2.7Mb
    libs      11.3Mb
installed size is  5.3Mb
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    libs   3.4Mb
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    libs   9.1Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    libs   2.8Mb
Packages suggested but not available for checking:
  'BSgenome.Hsapiens.NCBI.GRCh38', 'clusterProfiler', 'org.Mm.eg.db',
  'wiggleplotr'
installed size is 13.2Mb
  sub-directories of 1Mb or more:
    java   3.3Mb
    libs   8.8Mb
qr.X: no visible binding for global variable ‘R’
Undefined global functions or variables:
  R
installed size is 17.8Mb
  sub-directories of 1Mb or more:
    doc    3.8Mb
    libs  13.7Mb
checkRd: (-1) MCtest.Rd:39: Escaped LaTeX specials: \#
checkRd: (-1) MCtest.Rd:40: Escaped LaTeX specials: \#
installed size is 17.2Mb
  sub-directories of 1Mb or more:
    libs  16.7Mb
installed size is 11.3Mb
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    libs  10.9Mb
installed size is 64.1Mb
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    libs  62.7Mb
installed size is 50.4Mb
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    libs  49.1Mb
installed size is 19.3Mb
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    libs  18.3Mb
installed size is 22.2Mb
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    libs  21.1Mb
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    libs   5.5Mb
installed size is 107.1Mb
  sub-directories of 1Mb or more:
    libs  106.3Mb
Packages suggested but not available for checking: 'ropls', 'xcms'
Packages suggested but not available for checking: 'phyloseq', 'biomformat'
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    R      3.0Mb
    help   2.2Mb
Packages suggested but not available for checking:
  'GEOquery', 'annaffy', 'hgu133plus2.db', 'hgu133a.db', 'hgu95av2.db'
installed size is 21.4Mb
  sub-directories of 1Mb or more:
    libs  21.0Mb
Package suggested but not available for checking: ‘InteractiveComplexHeatmap’
installed size is 60.3Mb
  sub-directories of 1Mb or more:
    libs  59.9Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    help   2.0Mb
    libs   2.7Mb
installed size is 29.7Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    doc    3.6Mb
    libs  22.1Mb
installed size is 19.7Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs  17.0Mb
Packages suggested but not available for checking: 'DAPAR', 'ProteoMM'
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    libs   8.6Mb
Package suggested but not available for checking: ‘dada2’
installed size is 15.3Mb
  sub-directories of 1Mb or more:
    libs  14.6Mb
installed size is 22.3Mb
  sub-directories of 1Mb or more:
    libs  22.2Mb
installed size is 42.7Mb
  sub-directories of 1Mb or more:
    libs  42.3Mb
installed size is 119.3Mb
  sub-directories of 1Mb or more:
    libs  118.7Mb
Package required but not available: ‘dada2’

Packages suggested but not available for checking: 'ANCOMBC', 'mia'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'karyoploteR', 'regioneR'
installed size is 26.5Mb
  sub-directories of 1Mb or more:
    libs  24.1Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
Packages suggested but not available for checking:
  'minfi', 'GEOquery', 'IlluminaHumanMethylation450kmanifest'
installed size is 134.9Mb
  sub-directories of 1Mb or more:
    doc     1.2Mb
    libs  132.9Mb
installed size is 17.6Mb
  sub-directories of 1Mb or more:
    doc    1.3Mb
    libs  15.9Mb
installed size is 20.7Mb
  sub-directories of 1Mb or more:
    libs  20.5Mb
Packages suggested but not available for checking: 'doMPI', 'alstructure'

Packages which this enhances but not available for checking:
  'miraculix', 'RandomFieldsUtils', 'MoBPSmaps'
Packages suggested but not available for checking:
  'ArchR', 'motifmatchr', 'TxDb.Hsapiens.UCSC.hg38.refGene',
  'BSgenome.Hsapiens.UCSC.hg19', 'chromVAR'
checkRd: (-1) modeest-package.Rd:150: Escaped LaTeX specials: \&
checkRd: (-1) vieu.Rd:56: Escaped LaTeX specials: \&
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   5.0Mb
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    doc    1.7Mb
    libs   4.6Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   2.6Mb
Error: package or namespace load failed for ‘movieROC’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
 there is no package called ‘knitr’
Call sequence:
6: stop(msg, call. = FALSE, domain = NA)
5: value[[3L]](cond)
4: tryCatchOne(expr, names, parentenv, handlers[[1L]])
3: tryCatchList(expr, classes, parentenv, handlers)
2: tryCatch({
       attr(package, "LibPath") <- which.lib.loc
       ns <- loadNamespace(package, lib.loc)
       env <- attachNamespace(ns, pos = pos, deps, exclude, include.only)
   }, error = function(e) {
       P <- if (!is.null(cc <- conditionCall(e))) 
           paste(" in", deparse(cc)[1L])
       else ""
       msg <- gettextf("package or namespace load failed for %s%s:\n %s", 
           sQuote(package), P, conditionMessage(e))
       if (logical.return && !quietly) 
           message(paste("Error:", msg), domain = NA)
       else stop(msg, call. = FALSE, domain = NA)
   })
1: library(package, lib.loc = lib.loc, cha
Execution halted
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Error: there is no package called ‘knitr’
Call sequence:
14: doWithOneRestart(return(expr), restart)
13: withOneRestart(expr, restarts[[1L]])
12: withRestarts(stop(cond), retry_loadNamespace = function() NULL)
11: loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
10: asNamespace(ns)
9: namespaceImportFrom(ns, loadNamespace(j <- i[[1L]], c(lib.loc, 
       .libPaths()), versionCheck = vI[[j]]), i[[2L]], from = package)
8: loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
7: asNamespace(ns)
6: namespaceImportFrom(ns, loadNamespace(j <- i[[1L]], c(lib.loc, 
       .libPaths()), versionCheck = vI[[j]]), i[[2L]], from = package)
5: loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
4: namespaceImport(ns, loadNamespace(i, c(lib.loc, .libPaths()), 
       versionCheck = vI[[i]]), from = package)
3: loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
2: namespaceImport(ns, loadNamespace(i, c(lib.loc, .libPat
Execution halted
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    libs   9.4Mb
installed size is 92.3Mb
  sub-directories of 1Mb or more:
    libs  91.9Mb
installed size is 14.2Mb
  sub-directories of 1Mb or more:
    data   1.6Mb
    libs  12.1Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
installed size is 49.3Mb
  sub-directories of 1Mb or more:
    libs  48.9Mb
installed size is 18.0Mb
  sub-directories of 1Mb or more:
    libs  17.0Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs   7.2Mb
Packages suggested but not available for checking:
  'switchBox', 'leukemiasEset'
installed size is 12.5Mb
  sub-directories of 1Mb or more:
    libs  11.6Mb
installed size is 271.4Mb
  sub-directories of 1Mb or more:
    R       2.0Mb
    doc     4.2Mb
    libs  264.5Mb
installed size is 35.8Mb
  sub-directories of 1Mb or more:
    libs  35.5Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    help   2.2Mb
    libs   2.1Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
checkRd: (-1) mvr.Rd:113: Escaped LaTeX specials: \#
checkRd: (-1) mvr.Rd:115: Escaped LaTeX specials: \#
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    libs   9.2Mb
installed size is 26.4Mb
  sub-directories of 1Mb or more:
    data     1.9Mb
    libs    23.3Mb
    models   1.1Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   4.6Mb
    doc    1.7Mb
installed size is 14.2Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    doc    6.5Mb
    libs   5.1Mb
Package suggested but not available for checking: ‘sSeq’
Package unavailable to check Rd xrefs: ‘sSeq’
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    libs   7.4Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    libs   4.3Mb
installed size is 24.8Mb
  sub-directories of 1Mb or more:
    libs  23.1Mb
installed size is 21.0Mb
  sub-directories of 1Mb or more:
    doc    2.8Mb
    libs  17.3Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs   4.9Mb
installed size is 243.5Mb
  sub-directories of 1Mb or more:
    libs  242.8Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc       4.0Mb
    extdata   1.8Mb
installed size is 21.6Mb
  sub-directories of 1Mb or more:
    libs  20.0Mb
Running ‘spelling.R’ [0s/0s]
  Running ‘testthat.R’ [12s/46s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
    6. └─npi::npi_search(city = "Atlanta", limit = 1)
    7.   └─npi:::npi_process_results(...)
    8.     └─npi:::npi_control_requests(params, user_n)
    9.       └─npi:::npi_get_results(results = results, query = query)
   10.         └─npi:::npi_get(npi_url(), query = ...)
   11.           └─npi:::npi_api("GET", url, ...)
   12.             └─httr (local) FUN(url, ..., config = c(npi_config(), config))
   13.               └─httr:::request_perform(req, hu$handle$handle)
   14.                 ├─httr:::request_fetch(req$output, req$url, handle)
   15.                 └─httr:::request_fetch.write_memory(req$output, req$url, handle)
   16.                   └─curl::curl_fetch_memory(url, handle = handle)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 74 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘advanced-use.Rmd’ using rmarkdown
Quitting from lines 39-46 (advanced-use.Rmd) 
Error: processing vignette 'advanced-use.Rmd' failed with diagnostics:
ℹ In index: 1.
Caused by error in `curl::curl_fetch_memory()`:
! Could not resolve host: npiregistry.cms.hhs.gov
--- failed re-building ‘advanced-use.Rmd’

--- re-building ‘npi.Rmd’ using rmarkdown
Quitting from lines 34-36 (npi.Rmd) 
Error: processing vignette 'npi.Rmd' failed with diagnostics:
Could not resolve host: npiregistry.cms.hhs.gov
--- failed re-building ‘npi.Rmd’

SUMMARY: processing the following files failed:
  ‘advanced-use.Rmd’ ‘npi.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 15.6Mb
  sub-directories of 1Mb or more:
    libs  15.2Mb
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    R         2.1Mb
    doc       5.7Mb
    extdata   1.6Mb
installed size is 15.6Mb
  sub-directories of 1Mb or more:
    R      3.0Mb
    data   1.0Mb
    doc    1.7Mb
    help   3.4Mb
    libs   5.9Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    libs   1.9Mb
installed size is 99.0Mb
  sub-directories of 1Mb or more:
    libs  98.0Mb
Fatal error: cannot create 'R_TempDir'
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
Warning in file(open = "w+") :
  cannot open file '/var/folders/k4/0jwzxmln0nb8y6rkzprptb640000gq/T//RtmpYdXjvw/Rfee3b1220180e': No space left on device
Error in file(open = "w+") : cannot open the connection
Calls: <Anonymous> -> .load_namespace_quietly -> .try_quietly -> file
Execution halted
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
installed size is 45.9Mb
  sub-directories of 1Mb or more:
    libs  44.0Mb
installed size is 42.3Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs  40.1Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc    3.2Mb
    libs   1.6Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    exampledata   1.5Mb
    libs          3.6Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   5.1Mb
installed size is 273.4Mb
  sub-directories of 1Mb or more:
    R         3.1Mb
    data      1.4Mb
    libs    261.6Mb
    models    4.7Mb
installed size is 37.3Mb
  sub-directories of 1Mb or more:
    extdata   2.1Mb
    libs     33.6Mb
Packages suggested but not available for checking: 'gurobi', 'lpsymphony'
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   4.0Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    doc       1.9Mb
    extdata   4.8Mb
Package suggested but not available for checking: ‘scde’
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    library   8.5Mb
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.3/PAMhm.Rcheck/00install.out’ for details.
installed size is 84.1Mb
  sub-directories of 1Mb or more:
    libs  83.6Mb
Package suggested but not available for checking: ‘anomalize’
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    R      7.9Mb
    help   3.1Mb
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    R      4.1Mb
    help   4.3Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    R      3.3Mb
    help   3.3Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    R      3.1Mb
    help   4.1Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    R      3.1Mb
    help   4.0Mb
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.3/pbdMPI.Rcheck/00install.out’ for details.
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    libs   6.6Mb
installed size is 133.1Mb
  sub-directories of 1Mb or more:
    doc     2.9Mb
    libs  129.4Mb
installed size is 36.1Mb
  sub-directories of 1Mb or more:
    libs  35.0Mb
installed size is 34.1Mb
  sub-directories of 1Mb or more:
    libs  33.9Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘tutorial.Rmd’ using rmarkdown
! kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 bbm10

! mkdir: ././opt/tex/texmf-var/fonts/pk/ljfour/public: Permission denied

! mktexpk: /opt/tex/texmf-dist/web2c/mktexdir /opt/tex/texmf-var/fonts/pk/ljfour/public/bbm failed.

! kpathsea: Appending font creation commands to missfont.log.

Error: processing vignette 'tutorial.Rmd' failed with diagnostics:
LaTeX failed to compile /Volumes/Builds/packages/big-sur-arm64/results/4.3/pcSteiner.Rcheck/vign_test/pcSteiner/vignettes/tutorial.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See tutorial.log for more info.
--- failed re-building ‘tutorial.Rmd’

SUMMARY: processing the following file failed:
  ‘tutorial.Rmd’

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘georob’
installed size is 136.3Mb
  sub-directories of 1Mb or more:
    libs  135.3Mb
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    data   1.8Mb
    libs   7.0Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    doc    1.9Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    doc   6.2Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   3.5Mb
installed size is 84.8Mb
  sub-directories of 1Mb or more:
    libs  84.4Mb
installed size is 12.8Mb
  sub-directories of 1Mb or more:
    doc    2.0Mb
    libs  10.2Mb
checkRd: (-1) Kcalc.Rd:13: Escaped LaTeX specials: \$
checkRd: (-1) phylosignal.Rd:13: Escaped LaTeX specials: \$
checkRd: (-1) traitgram.Rd:14: Escaped LaTeX specials: \$
checkRd: (-1) utility.Rd:37: Escaped LaTeX specials: \$ \$
installed size is 12.4Mb
  sub-directories of 1Mb or more:
    libs  12.1Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    doc    2.0Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    data   2.0Mb
Package required but not available: ‘VariantAnnotation’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘slingshot’
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs         3.8Mb
    tmp_images   1.9Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    tests   3.2Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    extdata   2.8Mb
    libs      2.9Mb
Package unavailable to check Rd xrefs: ‘VariantAnnotation’
installed size is 63.1Mb
  sub-directories of 1Mb or more:
    libs  62.7Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    libs   7.1Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    libs   8.3Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    R   4.2Mb
installed size is 15.4Mb
  sub-directories of 1Mb or more:
    libs  15.1Mb
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    libs   9.6Mb
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    doc    3.6Mb
    libs   5.7Mb
installed size is 20.1Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    doc    4.7Mb
    libs  11.3Mb
Package suggested but not available for checking: ‘glmSparseNet’
Error(s) in re-building vignettes:
--- re-building ‘priorityelasticnet-vignettes.Rmd’ using rmarkdown

Quitting from lines 427-450 [unnamed-chunk-23] (priorityelasticnet-vignettes.Rmd)
Error: processing vignette 'priorityelasticnet-vignettes.Rmd' failed with diagnostics:
there is no package called 'glmSparseNet'
--- failed re-building ‘priorityelasticnet-vignettes.Rmd’

SUMMARY: processing the following file failed:
  ‘priorityelasticnet-vignettes.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 227.4Mb
  sub-directories of 1Mb or more:
    libs  226.2Mb
installed size is 21.8Mb
  sub-directories of 1Mb or more:
    libs  21.6Mb
installed size is 15.6Mb
  sub-directories of 1Mb or more:
    data   2.2Mb
    libs  12.9Mb
installed size is 17.6Mb
  sub-directories of 1Mb or more:
    libs  17.5Mb
installed size is 120.3Mb
  sub-directories of 1Mb or more:
    libs  119.9Mb
Package suggested but not available for checking: ‘proDA’
installed size is 41.4Mb
  sub-directories of 1Mb or more:
    libs  41.1Mb
installed size is 127.4Mb
  sub-directories of 1Mb or more:
    libs  126.9Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs   3.0Mb
installed size is 51.3Mb
  sub-directories of 1Mb or more:
    libs  50.8Mb
installed size is 32.2Mb
  sub-directories of 1Mb or more:
    libs  31.7Mb
installed size is 16.6Mb
  sub-directories of 1Mb or more:
    libs  16.3Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R   5.1Mb
installed size is 119.7Mb
  sub-directories of 1Mb or more:
    libs  118.4Mb
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   7.8Mb
installed size is 16.7Mb
  sub-directories of 1Mb or more:
    libs  16.4Mb
Warning: package needs dependence on R (>= 2.10)
Packages suggested but not available for checking: 'batchelor', 'slingshot'
installed size is 25.5Mb
  sub-directories of 1Mb or more:
    doc           5.3Mb
    htmlwidgets   1.8Mb
    libs         16.3Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘ragtop_convertibles_in_r.Rmd’ using rmarkdown
Quitting from lines 425-461 (ragtop_convertibles_in_r.Rmd) 
Error: processing vignette 'ragtop_convertibles_in_r.Rmd' failed with diagnostics:
argument is of length zero
--- failed re-building ‘ragtop_convertibles_in_r.Rmd’

SUMMARY: processing the following file failed:
  ‘ragtop_convertibles_in_r.Rmd’

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘Spectra’
installed size is 16.6Mb
  sub-directories of 1Mb or more:
    doc       1.7Mb
    extdata   4.1Mb
    libs      9.9Mb
installed size is 12.9Mb
  sub-directories of 1Mb or more:
    R      4.1Mb
    libs   7.8Mb
installed size is 66.2Mb
  sub-directories of 1Mb or more:
    libs  65.4Mb
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    data   5.0Mb
    etc    1.9Mb
    po     1.2Mb
installed size is 16.6Mb
  sub-directories of 1Mb or more:
    data   4.1Mb
    libs  11.4Mb
installed size is 14.9Mb
  sub-directories of 1Mb or more:
    libs  14.1Mb
installed size is 14.6Mb
  sub-directories of 1Mb or more:
    libs  14.4Mb
installed size is 25.6Mb
  sub-directories of 1Mb or more:
    libs  24.7Mb
Package suggested but not available for checking: ‘raybevel’
installed size is 13.6Mb
  sub-directories of 1Mb or more:
    libs  12.8Mb
installed size is 58.2Mb
  sub-directories of 1Mb or more:
    libs  57.6Mb
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.3/rbm25.Rcheck/00install.out’ for details.
installed size is 14.0Mb
  sub-directories of 1Mb or more:
    libs  13.8Mb
installed size is 67.9Mb
  sub-directories of 1Mb or more:
    libs  67.1Mb
Package suggested but not available for checking: ‘rqubic’

Depends: includes the non-default packages:
  'biclust', 'fabia', 'iBBiG', 'superbiclust', 'BcDiag', 'BicARE',
  's4vd', 'BiBitR'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Packages suggested but not available for checking:
  'ROntoTools', 'hgu133plus2.db', 'pd.hg.u133.plus.2', 'oligo'
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.3/Rcplex.Rcheck/00install.out’ for details.
installed size is 20.1Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs  17.8Mb
installed size is 47.8Mb
  sub-directories of 1Mb or more:
    include  47.7Mb
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.3/RcppMeCab.Rcheck/00install.out’ for details.
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    libs   8.0Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    include   1.2Mb
    libs      5.6Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
installed size is 20.3Mb
  sub-directories of 1Mb or more:
    data   1.9Mb
    libs  16.6Mb
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    libs   8.6Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    data   1.7Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    2.5Mb
    libs   2.6Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    doc    3.3Mb
    libs   3.1Mb
installed size is 18.4Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    libs  14.5Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    libs   4.8Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    doc    3.4Mb
    libs   3.8Mb
installed size is 18.0Mb
  sub-directories of 1Mb or more:
    libs  16.6Mb
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    doc    3.9Mb
    libs   5.0Mb
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    libs  10.1Mb
Packages suggested but not available for checking: 'PADOG', 'GSVA'
Packages unavailable to check Rd xrefs: ‘GSVA’, ‘PADOG’
installed size is 17.4Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    doc    1.2Mb
    libs  13.9Mb
Package suggested but not available for checking: ‘RevGadgets’
installed size is 22.0Mb
  sub-directories of 1Mb or more:
    libs  21.2Mb
installed size is 14.1Mb
  sub-directories of 1Mb or more:
    data  14.1Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
Warning in py_initialize(config$python, config$libpython, config$pythonhome,  :
  Python 2 reached EOL on January 1, 2020. Python 2 compatability be removed in an upcoming reticulate release.

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file.
installed size is 35.7Mb
  sub-directories of 1Mb or more:
    doc     7.1Mb
    fonts   1.5Mb
    libs   23.8Mb
installed size is 18.6Mb
  sub-directories of 1Mb or more:
    data   1.6Mb
    libs  16.2Mb
installed size is 23.9Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs  22.4Mb
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    libs   8.7Mb
Note: information on .o files is not available
File ‘/Volumes/Builds/packages/big-sur-arm64/results/4.3/rJava.Rcheck/rJava/libs/rJava.so’:
  Found ‘___stderrp’, possibly from ‘stderr’ (C)
  Found ‘___stdoutp’, possibly from ‘stdout’ (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 19.9Mb
  sub-directories of 1Mb or more:
    libs  19.7Mb
installed size is 20.2Mb
  sub-directories of 1Mb or more:
    lemon   2.8Mb
    libs   17.1Mb
Error(s) in re-building vignettes:
--- re-building ‘RLescalation.Rmd’ using rmarkdown
File man/figures/logo.png not found in resource path
Error: processing vignette 'RLescalation.Rmd' failed with diagnostics:
pandoc document conversion failed with error 99
--- failed re-building ‘RLescalation.Rmd’

SUMMARY: processing the following file failed:
  ‘RLescalation.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 160.6Mb
  sub-directories of 1Mb or more:
    libs  159.6Mb
installed size is 71.2Mb
  sub-directories of 1Mb or more:
    include   7.3Mb
    lib      37.3Mb
    libs     26.2Mb
Packages suggested but not available for checking:
  'DoubletFinder', 'EnhancedVolcano', 'RcppPlanc', 'reactome.db'
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    libs   6.4Mb
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    libs   9.0Mb
Found the following significant warnings:
  Warning: Software mark not found in path.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.3/RMark.Rcheck/00install.out’ for details.
installed size is 132.0Mb
  sub-directories of 1Mb or more:
    libs  131.6Mb
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.3/RmecabKo.Rcheck/00install.out’ for details.
checkRd: (-1) cGARCHfilter-class.Rd:57: Escaped LaTeX specials: \&
checkRd: (-1) cGARCHfit-class.Rd:59: Escaped LaTeX specials: \&
checkRd: (-1) cGARCHsim-class.Rd:52: Escaped LaTeX specials: \&
checkRd: (-1) cGARCHspec-class.Rd:36: Escaped LaTeX specials: \&
checkRd: (-1) cgarchsim-methods.Rd:78: Escaped LaTeX specials: \&
checkRd: (-1) goGARCHfilter-class.Rd:155: Escaped LaTeX specials: \&
checkRd: (-1) goGARCHfit-class.Rd:166: Escaped LaTeX specials: \&
checkRd: (-1) rmgarch-package.Rd:73: Escaped LaTeX specials: \&
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    R          1.0Mb
    libs       1.2Mb
    minizinc   3.3Mb
installed size is 38.9Mb
  sub-directories of 1Mb or more:
    libs  38.0Mb
installed size is 27.5Mb
  sub-directories of 1Mb or more:
    libs  27.3Mb
installed size is 84.3Mb
  sub-directories of 1Mb or more:
    libs  83.7Mb
Package required but not available: ‘R4RNA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘recount3’
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    2.0Mb
    libs   1.7Mb
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    R  11.3Mb
installed size is 18.1Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs  15.4Mb
installed size is 22.1Mb
  sub-directories of 1Mb or more:
    libs  21.9Mb
installed size is 96.1Mb
  sub-directories of 1Mb or more:
    libs  95.3Mb
installed size is 26.6Mb
  sub-directories of 1Mb or more:
    libs  26.0Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R         3.0Mb
    extdata   2.7Mb
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.3/ROracle.Rcheck/00install.out’ for details.
installed size is 15.8Mb
  sub-directories of 1Mb or more:
    R      5.1Mb
    libs   9.6Mb
installed size is 24.2Mb
  sub-directories of 1Mb or more:
    libs  23.0Mb
installed size is 20.6Mb
  sub-directories of 1Mb or more:
    libs  19.6Mb
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   6.3Mb
installed size is 33.5Mb
  sub-directories of 1Mb or more:
    libs  32.2Mb
installed size is 103.5Mb
  sub-directories of 1Mb or more:
    libs  102.9Mb
Errors in running code in vignettes:
when running code in ‘Using.RRPP.Rmd’
  ...
> fit.par <- lm(fit$call$f1, data = fit$LM$data)

> all.equal(fit$LM$coefficients, fit.par$coefficients)
[1] TRUE

> summary(manova(fit.par))

  When sourcing ‘Using.RRPP.R’:
Error: residuals have rank 49 < 112
Execution halted

  ‘ANOVA.vs.MANOVA.Rmd’ using ‘UTF-8’... [18s/28s] OK
  ‘Using.RRPP.Rmd’ using ‘UTF-8’... failed
installed size is 19.8Mb
  sub-directories of 1Mb or more:
    libs  19.6Mb
Note: information on .o files is not available
File ‘/Volumes/Builds/packages/big-sur-arm64/results/4.3/Rserve.Rcheck/Rserve/libs/Rserve.so’:
  Found ‘___stderrp’, possibly from ‘stderr’ (C)
  Found ‘_abort’, possibly from ‘abort’ (C)
  Found ‘_exit’, possibly from ‘exit’ (C)
  Found ‘_rand’, possibly from ‘rand’ (C)
  Found ‘_random’, possibly from ‘random’ (C)
  Found ‘_sprintf’, possibly from ‘sprintf’ (C)
  Found ‘_srandom’, possibly from ‘srandom’ (C)
File ‘Rserve/libs/Rserve.so’:
  Found non-API calls to R: ‘R_Consolefile’, ‘R_Outputfile’,
    ‘R_TempDir’, ‘R_Visible’, ‘getInputHandler’, ‘ptr_R_Busy’,
    ‘ptr_R_ClearerrConsole’, ‘ptr_R_FlushConsole’, ‘ptr_R_ReadConsole’,
    ‘ptr_R_ResetConsole’, ‘ptr_R_ShowMessage’, ‘ptr_R_WriteConsole’,
    ‘ptr_R_WriteConsoleEx’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.
Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 27.4Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    libs  24.9Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    R      4.5Mb
    help   1.5Mb
installed size is 296.7Mb
  sub-directories of 1Mb or more:
    R       2.0Mb
    doc     4.7Mb
    libs  289.2Mb
installed size is 94.9Mb
  sub-directories of 1Mb or more:
    libs  94.6Mb
installed size is 57.4Mb
  sub-directories of 1Mb or more:
    libs  56.7Mb
installed size is 49.0Mb
  sub-directories of 1Mb or more:
    exec   1.7Mb
    lib   34.2Mb
    libs  11.4Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    external   1.6Mb
    libs       3.8Mb
Package suggested but not available for checking: ‘Gviz’
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs       2.3Mb
    projects   2.9Mb
installed size is 112.0Mb
  sub-directories of 1Mb or more:
    R       1.0Mb
    libs  110.1Mb
installed size is 29.9Mb
  sub-directories of 1Mb or more:
    doc    7.8Mb
    libs  21.2Mb
installed size is 217.7Mb
  sub-directories of 1Mb or more:
    data    1.5Mb
    libs  215.2Mb
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    R      3.0Mb
    libs   2.4Mb
Non-standard license specification:
  CECILL-2.1
Standardizable: FALSE
Package suggested but not available for checking: ‘gpuR’
installed size is 64.2Mb
  sub-directories of 1Mb or more:
    include   5.0Mb
    libs     58.8Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data      3.0Mb
    extdata   2.4Mb
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    libs  10.1Mb
Packages suggested but not available for checking:
  'BiocPkgTools', 'biocViews'
Packages unavailable to check Rd xrefs: ‘BiocPkgTools’, ‘biocViews’
installed size is 14.2Mb
  sub-directories of 1Mb or more:
    libs  14.1Mb
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    R         2.1Mb
    include   1.1Mb
    libs      5.8Mb
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    libs    8.4Mb
    yacas   1.3Mb
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    libs    9.1Mb
    yacas   1.3Mb
installed size is 16.1Mb
  sub-directories of 1Mb or more:
    libs  16.0Mb
installed size is 36.9Mb
  sub-directories of 1Mb or more:
    libs  35.8Mb
installed size is 16.4Mb
  sub-directories of 1Mb or more:
    libs  15.3Mb
installed size is 55.6Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    libs  53.0Mb
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    help   3.4Mb
    libs   4.0Mb
Packages suggested but not available for checking:
  'GOstats', 'networkTomography', 'org.Sc.sgd.db'
installed size is 46.8Mb
  sub-directories of 1Mb or more:
    libs  46.7Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    doc    3.9Mb
    libs   3.3Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   3.1Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    data   3.9Mb
    libs   3.7Mb
Packages suggested but not available for checking:
  'dittoSeq', 'DropletUtils', 'Nebulosa'
Packages unavailable to check Rd xrefs: ‘DropletUtils’, ‘Nebulosa’
Package required but not available: ‘glmGamPoi’

Package suggested but not available for checking: ‘Linnorm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    data   4.1Mb
    libs   3.0Mb
Running ‘testthat.R’ [2s/3s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(scDHA)
  libtorch is not installed. Use `torch::install_torch()` to download and install libtorch
  > 
  > on_cran <- function() !identical(Sys.getenv("NOT_CRAN"), "true")
  > 
  > if((!torch::torch_is_installed()) & 
  +    (tolower(Sys.info()[["sysname"]]) != "windows") & 
  +    (!on_cran()))
  + {
  +   torch::install_torch()
  + }
  > 
  > Sys.setenv(IN_TEST_scDHA="true")
  > 
  > test_check("scDHA")
  [ FAIL 1 | WARN 0 | SKIP 2 | PASS 3 ]
  
  ══ Skipped tests (2) ═══════════════════════════════════════════════════════════
  • On CRAN (2): 'test-scDHA.R:3:3', 'test-scDHA.R:41:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-scDHA.R:21:3'): scDHA.vis can run ──────────────────────────────
  Error in `irlba::irlba(L, nv = n, nu = 0, maxit = iters)`: function 'as_cholmod_sparse' not provided by package 'Matrix'
  Backtrace:
      ▆
   1. └─scDHA::scDHA.vis(result, ncores = 2, seed = 1) at test-scDHA.R:21:3
   2.   └─uwot::umap(data, n_threads = ncores)
   3.     └─uwot:::uwot(...)
   4.       └─uwot:::spectral_init(V, ndim = n_components, verbose = verbose)
   5.         └─uwot:::irlba_tsvd_normalized_laplacian_init(A, ndim, verbose = FALSE)
   6.           └─uwot:::irlba_spectral_tsvd(L, ndim + 1)
   7.             ├─base::suppressWarnings(...)
   8.             │ └─base::withCallingHandlers(...)
   9.             └─irlba::irlba(L, nv = n, nu = 0, maxit = iters)
  
  [ FAIL 1 | WARN 0 | SKIP 2 | PASS 3 ]
  Error: Test failures
  Execution halted
Packages suggested but not available for checking:
  'ontoProc', 'rrvgo', 'SingleCellSignalR'
Package required and available but unsuitable version: ‘UCell’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘batchelor’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘simplifyEnrichment’
Package required but not available: ‘scran’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'AUCell', 'decoupleR', 'infercnv', 'Nebulosa'
Package suggested but not available for checking: ‘glmGamPoi’
Package suggested but not available for checking: ‘oligoClasses’
Error(s) in re-building vignettes:
  ...
--- re-building ‘sdcSpatial.Rmd’ using rmarkdown
Quitting from lines 190-192 (sdcSpatial.Rmd) 
Error: processing vignette 'sdcSpatial.Rmd' failed with diagnostics:
different crs
--- failed re-building ‘sdcSpatial.Rmd’

SUMMARY: processing the following file failed:
  ‘sdcSpatial.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    libs   5.3Mb
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    R   9.0Mb
installed size is 20.4Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    libs  16.5Mb
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   8.4Mb
Packages required but not available: 'ggmsa', 'msa'

Package suggested but not available for checking: ‘org.Rn.eg.db’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'flowMerge', 'flowClust', 'flowCore'
Packages unavailable to check Rd xrefs: ‘flowClust’, ‘flowMerge’
Error(s) in re-building vignettes:
  ...
--- re-building ‘SEI_vignette.Rnw’ using knitr
Error: processing vignette 'SEI_vignette.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'SEI_vignette.tex' failed.
LaTeX errors:
!pdfTeX error: pdflatex (file bbm10): Font bbm10 at 657 not found
 ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘SEI_vignette.Rnw’

SUMMARY: processing the following file failed:
  ‘SEI_vignette.Rnw’

Error: Vignette re-building failed.
Execution halted
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘SemiCompRisks.ltx’ using tex
Error: processing vignette 'SemiCompRisks.ltx' failed with diagnostics:
Running 'texi2dvi' on 'SemiCompRisks.ltx' failed.
LaTeX errors:
!pdfTeX error: pdflatex (file bbm8): Font bbm8 at 600 not found
 ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘SemiCompRisks.ltx’

SUMMARY: processing the following file failed:
  ‘SemiCompRisks.ltx’

Error: Vignette re-building failed.
Execution halted
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    R      2.3Mb
    libs   2.6Mb
installed size is 22.8Mb
  sub-directories of 1Mb or more:
    libs    21.0Mb
    models   1.6Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   4.5Mb
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    libs   8.7Mb
Package suggested but not available for checking: ‘airway’
installed size is 17.6Mb
  sub-directories of 1Mb or more:
    doc    6.4Mb
    libs  10.3Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    data   5.1Mb
    libs   1.2Mb
installed size is 55.6Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs  53.4Mb
installed size is 17.2Mb
  sub-directories of 1Mb or more:
    libs  15.9Mb
Packages suggested but not available for checking: 'HDF5Array', 'BPCells'
Packages suggested but not available for checking:
  'BPCells', 'glmGamPoi', 'monocle', 'presto'
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    libs   8.3Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    data   6.8Mb
Packages suggested but not available for checking:
  'chromVAR', 'TFBSTools', 'motifmatchr'
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    libs   1.9Mb
Packages unavailable to check Rd xrefs: ‘motifmatchr’, ‘TFBSTools’, ‘chromVAR’
Error(s) in re-building vignettes:
  ...
--- re-building ‘sim.BA.Rmd’ using rmarkdown
File images/dag.png not found in resource path
Error: processing vignette 'sim.BA.Rmd' failed with diagnostics:
pandoc document conversion failed with error 99
--- failed re-building ‘sim.BA.Rmd’

SUMMARY: processing the following file failed:
  ‘sim.BA.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 19.1Mb
  sub-directories of 1Mb or more:
    extdata  13.0Mb
    libs      5.3Mb
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    libs   9.4Mb
installed size is 23.3Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs  20.9Mb
Package required but not available: ‘epiparameter’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    R      3.1Mb
    libs   6.8Mb
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    R         2.1Mb
    extdata   1.2Mb
    libs      6.5Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   5.2Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data   6.1Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘smm.Rnw’ using Sweave
Error: processing vignette 'smm.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'smm.tex' failed.
LaTeX errors:
!pdfTeX error: pdflatex (file bbm10): Font bbm10 at 657 not found
 ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘smm.Rnw’

SUMMARY: processing the following file failed:
  ‘smm.Rnw’

Error: Vignette re-building failed.
Execution halted
installed size is 16.5Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    doc    3.4Mb
    libs  10.6Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    extdata   3.1Mb
    libs      2.9Mb
Package required but not available: ‘GWASTools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    R     4.1Mb
    doc   1.1Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data      3.8Mb
    extdata   1.1Mb
installed size is 13.7Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    doc    1.3Mb
    libs   9.8Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   4.0Mb
    doc    1.0Mb
installed size is 17.8Mb
  sub-directories of 1Mb or more:
    data   4.7Mb
    libs  13.0Mb
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    extdata   5.9Mb
    libs      2.0Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    R   5.7Mb
installed size is 16.6Mb
  sub-directories of 1Mb or more:
    libs  16.5Mb
S3 methods shown with full name in documentation object 'SparseM.ontology':
  ‘as.matrix.csr’ ‘is.matrix.csr’ ‘is.matrix.csc’ ‘is.matrix.ssr’
  ‘is.matrix.ssc’ ‘is.matrix.coo’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
installed size is 35.3Mb
  sub-directories of 1Mb or more:
    libs  34.5Mb
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.3/spaths.Rcheck/00install.out’ for details.
Package required but not available: ‘SpatialExperiment’

Package suggested but not available for checking: ‘HDF5Array’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    help   1.9Mb
installed size is 13.7Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    libs  10.1Mb
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.3/spdep.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘scRNAseq’
Running examples in ‘speaq-Ex.R’ failed
The error most likely occurred in:

> ### Name: BWR
> ### Title: BW ratio calculation
> ### Aliases: BWR
> 
> ### ** Examples
> 
> res=makeSimulatedData();
> X=res$data;
> groupLabel=res$label;
> peakList <- detectSpecPeaks(X,
+                             nDivRange = c(128),
+                             scales = seq(1, 16, 2),
+                             baselineThresh = 50000,
+                             SNR.Th = -1,
+                             verbose=FALSE
+ );
> resFindRef<- findRef(peakList);
> refInd <- resFindRef$refInd;
> maxShift = 50;
> Y <- dohCluster(X,
+                 peakList = peakList,
+                 refInd = refInd,
+                 maxShift  = maxShift,
+                 acceptLostPeak = TRUE, verbose=FALSE);
Warning in min(peakList) :
  no non-missing arguments to min; returning Inf
Warning in max(peakList) :
  no non-missing arguments to max; returning -Inf
Error in startP:(minpeakList - 1) : result would be too long a vector
Calls: dohCluster -> .withMaxShift -> hClustAlign
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘classic_speaq_vignette.Rmd’ using rmarkdown
Quitting from lines 111-120 (classic_speaq_vignette.Rmd) 
Error: processing vignette 'classic_speaq_vignette.Rmd' failed with diagnostics:
result would be too long a vector
--- failed re-building ‘classic_speaq_vignette.Rmd’

--- re-building ‘speaq2_illustrations.Rmd’ using rmarkdown
Quitting from lines 71-83 (speaq2_illustrations.Rmd) 
Error: processing vignette 'speaq2_illustrations.Rmd' failed with diagnostics:
invalid 'times' argument
--- failed re-building ‘speaq2_illustrations.Rmd’

SUMMARY: processing the following files failed:
  ‘classic_speaq_vignette.Rmd’ ‘speaq2_illustrations.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    doc    3.1Mb
    libs   3.9Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    extdata   1.1Mb
    libs      3.9Mb
checkRd: (-1) shypEstFun.Rd:52: Escaped LaTeX specials: \$
checkRd: (-1) shypEstFun.Rd:54: Escaped LaTeX specials: \$
installed size is 52.3Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs  50.5Mb
installed size is 13.3Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    help   1.1Mb
    libs  10.9Mb
installed size is 104.3Mb
  sub-directories of 1Mb or more:
    libs  103.8Mb
installed size is 50.3Mb
  sub-directories of 1Mb or more:
    libs  50.0Mb
installed size is 90.0Mb
  sub-directories of 1Mb or more:
    libs  89.2Mb
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    data   3.6Mb
    libs   5.1Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    extdata   2.4Mb
    libs      4.2Mb
installed size is 62.7Mb
  sub-directories of 1Mb or more:
    libs  61.5Mb
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   6.9Mb
installed size is 28.3Mb
  sub-directories of 1Mb or more:
    libs  26.7Mb
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    libs   7.1Mb
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    libs   9.3Mb
installed size is 34.7Mb
  sub-directories of 1Mb or more:
    libs  33.9Mb
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    doc    7.1Mb
    libs   1.8Mb
installed size is 63.4Mb
  sub-directories of 1Mb or more:
    libs  62.1Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    doc    1.5Mb
    libs   2.0Mb
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    libs   8.8Mb
installed size is 30.9Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs  28.9Mb
installed size is 63.6Mb
  sub-directories of 1Mb or more:
    libs  63.0Mb
installed size is  9.0Mb
  sub-directories of 1Mb or more:
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    libs   7.2Mb
installed size is 45.7Mb
  sub-directories of 1Mb or more:
    libs  44.8Mb
installed size is 19.8Mb
  sub-directories of 1Mb or more:
    fonts   1.8Mb
    libs   17.9Mb
installed size is 22.7Mb
  sub-directories of 1Mb or more:
    libs  22.4Mb
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    libs  11.6Mb
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    data   4.3Mb
    libs   4.7Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
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    libs   4.5Mb
bold_search: no visible global function definition for ‘bold_tax_name’
bold_search: no visible global function definition for ‘bold_tax_id’
check_boldid: no visible global function definition for ‘bold_tax_id’
Undefined global functions or variables:
  bold_tax_id bold_tax_name
Packages suggested but not available for checking: 'dearseq', 'GEOquery'
Package unavailable to check Rd xrefs: ‘dearseq’
installed size is 33.8Mb
  sub-directories of 1Mb or more:
    libs  32.6Mb
installed size is 18.7Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    libs  16.0Mb
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    doc    4.5Mb
    help   2.7Mb
installed size is 301.5Mb
  sub-directories of 1Mb or more:
    R       3.0Mb
    libs  296.9Mb
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    libs   5.4Mb
installed size is 15.3Mb
  sub-directories of 1Mb or more:
    libs  13.7Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
installed size is  8.9Mb
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installed size is  8.1Mb
  sub-directories of 1Mb or more:
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installed size is 84.3Mb
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Running ‘testthat.R’ [8s/10s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(tidystats)
  This version of tidystats uses a new and improved way of structuring statistics. This breaks previous (major) versions of tidystats.
  > 
  > test_check("tidystats")
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 183 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test_glm.R:118:3'): glm anova works ───────────────────────────────
  `tidy_model` not equal to `expected_tidy_model`.
  Component "groups": Component 1: Component 2: Component 2: Component 2: Length mismatch: comparison on first 4 components
  Component "groups": Component 1: Component 2: Component 3: Component 2: Length mismatch: comparison on first 4 components
  Backtrace:
      ▆
   1. └─tidystats:::expect_equal_models(model = model, expected_tidy_model = expected_statistics$anova_glm) at test_glm.R:118:3
   2.   └─testthat::expect_equal(tidy_model, expected_tidy_model, tolerance = tolerance)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 183 ]
  Error: Test failures
  Execution halted
installed size is 55.8Mb
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    tiledb  37.1Mb
installed size is  6.9Mb
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    data   6.0Mb
installed size is 96.0Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs  92.1Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   3.8Mb
installed size is 16.5Mb
  sub-directories of 1Mb or more:
    examples  12.4Mb
    include    3.6Mb
installed size is 29.1Mb
  sub-directories of 1Mb or more:
    libs  28.8Mb
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    data   8.1Mb
installed size is 211.9Mb
  sub-directories of 1Mb or more:
    R          6.1Mb
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Running ‘testthat.R’ [8s/9s]
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(trace)
  > 
  > test_check("trace")
  [ FAIL 1 | WARN 0 | SKIP 1 | PASS 68 ]
  
  ══ Skipped tests (1) ═══════════════════════════════════════════════════════════
  • On CRAN (1): 'test-shinytest2.R:7:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-call_repeats.R:275:3'): batch correction ─────────────────────
  all.equal(...) is not TRUE
  
  `actual` is a character vector ('Mean relative difference: 1.364275e-05')
  `expected` is a logical vector (TRUE)
  
  [ FAIL 1 | WARN 0 | SKIP 1 | PASS 68 ]
  Error: Test failures
  Execution halted
Package suggested but not available for checking: ‘Capr’
Packages required but not available: 'csaw', 'HiCDOC'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 123.5Mb
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    libs  118.5Mb
installed size is 38.4Mb
  sub-directories of 1Mb or more:
    libs  37.9Mb
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.3/triptych.Rcheck/00install.out’ for details.
installed size is 27.4Mb
  sub-directories of 1Mb or more:
    libs  26.7Mb
installed size is 33.6Mb
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    libs  33.4Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘tsglm.Rnw’ using Sweave
Error: processing vignette 'tsglm.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'tsglm.tex' failed.
LaTeX errors:
!pdfTeX error: pdflatex (file bbm10): Font bbm10 at 657 not found
 ==> Fatal error occurred, no output PDF file produced!
--- failed re-building 'tsglm.Rnw'

SUMMARY: processing the following file failed:
  'tsglm.Rnw'

Error: Vignette re-building failed.
Execution halted
installed size is 10.6Mb
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    data   1.2Mb
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installed size is 15.4Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs  12.3Mb
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    data   4.6Mb
    libs   2.6Mb
installed size is 96.8Mb
  sub-directories of 1Mb or more:
    libs  95.8Mb
installed size is 128.9Mb
  sub-directories of 1Mb or more:
    R       2.1Mb
    libs  125.6Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    data       1.1Mb
    doc        1.4Mb
    shinyapp   4.9Mb
installed size is 27.7Mb
  sub-directories of 1Mb or more:
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    dummydata   1.4Mb
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installed size is  5.9Mb
  sub-directories of 1Mb or more:
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installed size is  5.5Mb
  sub-directories of 1Mb or more:
    R      1.8Mb
    help   2.6Mb
installed size is 14.0Mb
  sub-directories of 1Mb or more:
    libs  13.4Mb
installed size is 65.7Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    doc    1.1Mb
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installed size is 14.0Mb
  sub-directories of 1Mb or more:
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Running ‘testthat.R’ [39s/41s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(uwot)
  Loading required package: Matrix
  > 
  > test_check("uwot")
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 683 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_normlaplacian.R:36:5'): normalized laplacian ───────────────────
  Error in `irlba::irlba(L, nv = n, nu = 0, maxit = iters)`: function 'as_cholmod_sparse' not provided by package 'Matrix'
  Backtrace:
      ▆
   1. └─uwot:::irlba_tsvd_normalized_laplacian_init(sparse_m) at test_normlaplacian.R:36:5
   2.   └─uwot:::irlba_spectral_tsvd(L, ndim + 1)
   3.     ├─base::suppressWarnings(...)
   4.     │ └─base::withCallingHandlers(...)
   5.     └─irlba::irlba(L, nv = n, nu = 0, maxit = iters)
  ── Error ('test_output.R:315:3'): (code run outside of `test_that()`) ──────────
  Error in `irlba::irlba(L, nv = n, nu = 0, maxit = iters)`: function 'as_cholmod_sparse' not provided by package 'Matrix'
  Backtrace:
      ▆
   1. └─uwot::umap(...) at test_output.R:315:3
   2.   └─uwot:::uwot(...)
   3.     └─uwot:::spectral_init(...)
   4.       └─uwot:::irlba_tsvd_normalized_laplacian_init(A, ndim, verbose = FALSE)
   5.         └─uwot:::irlba_spectral_tsvd(L, ndim + 1)
   6.           ├─base::suppressWarnings(...)
   7.           │ └─base::withCallingHandlers(...)
   8.           └─irlba::irlba(L, nv = n, nu = 0, maxit = iters)
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 683 ]
  Error: Test failures
  Execution halted
installed size is 24.2Mb
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installed size is 250.9Mb
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    libs     246.7Mb
installed size is  8.9Mb
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installed size is  9.3Mb
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installed size is 32.5Mb
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installed size is  5.3Mb
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installed size is 31.9Mb
  sub-directories of 1Mb or more:
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    libs     30.0Mb
installed size is 115.7Mb
  sub-directories of 1Mb or more:
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installed size is 26.8Mb
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installed size is 92.2Mb
  sub-directories of 1Mb or more:
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installed size is 40.7Mb
  sub-directories of 1Mb or more:
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Package suggested but not available for checking: ‘ROTS’
installed size is  7.9Mb
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installed size is 32.5Mb
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installed size is 45.0Mb
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installed size is 43.1Mb
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installed size is  8.6Mb
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installed size is 40.6Mb
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checkRd: (-1) ZIClass.Rd:87: Escaped LaTeX specials: \_
checkRd: (-1) ZITrain.Rd:72: Escaped LaTeX specials: \_
checkRd: (-1) ZITrain.Rd:74: Escaped LaTeX specials: \_
checkRd: (-1) zid.Rd:45: Escaped LaTeX specials: \_
checkRd: (-1) zim.Rd:63: Escaped LaTeX specials: \_
installed size is 10.6Mb
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installed size is 30.1Mb
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installed size is  7.6Mb
  sub-directories of 1Mb or more:
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installed size is 15.0Mb
  sub-directories of 1Mb or more:
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Package suggested but not available for checking: ‘clinfun’
installed size is  9.3Mb
  sub-directories of 1Mb or more:
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    libs   2.7Mb
Package suggested but not available for checking: ‘HiTC’
Package unavailable to check Rd xrefs: ‘epiR’
Package which this enhances but not available for checking: ‘tripack’
Package unavailable to check Rd xrefs: ‘tripack’
Packages suggested but not available for checking: 'fBasics', 'Rmpfr'
Package suggested but not available for checking: ‘AICcmodavg’
installed size is 25.0Mb
  sub-directories of 1Mb or more:
    libs  23.5Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
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Package required but not available: ‘pwalign’

Package suggested but not available for checking: ‘msa’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘competitiontoolbox’
Package unavailable to check Rd xrefs: ‘competitiontoolbox’
installed size is 31.9Mb
  sub-directories of 1Mb or more:
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Found the following significant warnings:
  Warning: read_bcal.Rd:27: unknown macro '\abbr'
  Warning: read_chronomodel.Rd:36: unknown macro '\abbr'
  Warning: read_oxcal.Rd:27: unknown macro '\abbr'
See ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.3/ArchaeoPhases.Rcheck/00install.out’ for details.
installed size is 17.1Mb
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installed size is  6.2Mb
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installed size is 10.9Mb
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installed size is  5.6Mb
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installed size is 17.0Mb
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installed size is 91.3Mb
  sub-directories of 1Mb or more:
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installed size is 117.3Mb
  sub-directories of 1Mb or more:
    libs  115.5Mb
Package suggested but not available for checking: ‘xgboost’
installed size is 97.8Mb
  sub-directories of 1Mb or more:
    libs  96.0Mb
installed size is 65.3Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
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installed size is 12.7Mb
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installed size is 71.8Mb
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installed size is 133.2Mb
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installed size is 24.5Mb
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installed size is 11.4Mb
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installed size is 67.1Mb
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Package unavailable to check Rd xrefs: ‘fGarch’
installed size is 107.0Mb
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installed size is 46.7Mb
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installed size is 59.9Mb
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Package suggested but not available for checking: ‘sensitivity’
installed size is  7.9Mb
  sub-directories of 1Mb or more:
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installed size is 254.0Mb
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installed size is 24.8Mb
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installed size is  6.1Mb
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installed size is 70.0Mb
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installed size is 32.7Mb
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installed size is 35.3Mb
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Package unavailable to check Rd xrefs: ‘betareg’
installed size is 100.0Mb
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installed size is 66.4Mb
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installed size is 14.4Mb
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installed size is 37.1Mb
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installed size is 53.6Mb
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installed size is 25.7Mb
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Package which this enhances but not available for checking: ‘caret’
installed size is 55.8Mb
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installed size is  9.7Mb
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installed size is 18.4Mb
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Package listed in more than one of Depends, Imports, Suggests, Enhances:
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A package should be listed in only one of these fields.
Packages in Depends field not imported from:
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  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
checkRd: (-1) FighterAircraft.Rd:32: Escaped LaTeX specials: \&
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
installed size is 49.3Mb
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Package suggested but not available for checking: ‘Seurat’
installed size is 45.6Mb
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Package suggested but not available for checking: ‘reldist’
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Error(s) in re-building vignettes:
  ...
--- re-building ‘BonEV.Rnw’ using Sweave
Error: processing vignette 'BonEV.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'BonEV.tex' failed.
LaTeX errors:
! LaTeX Error: File `underscore.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.6 \parindent
               0in^^M
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘BonEV.Rnw’

SUMMARY: processing the following file failed:
  ‘BonEV.Rnw’

Error: Vignette re-building failed.
Execution halted
installed size is 12.9Mb
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Package suggested but not available for checking: ‘sparsenet’
installed size is 53.6Mb
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Packages suggested but not available for checking:
  'BayesFactor', 'rstan', 'rstanarm', 'MCMCpack'
installed size is  9.2Mb
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Error(s) in re-building vignettes:
--- re-building ‘Brobdingnag.Rnw’ using Sweave
Loading required package: Brobdingnag
Loading required package: Matrix

Attaching package: ‘Brobdingnag’

The following objects are masked from ‘package:Matrix’:

    diag, t

The following objects are masked from ‘package:base’:

    diag, t

Error: processing vignette 'Brobdingnag.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'Brobdingnag.tex' failed.
LaTeX errors:
! LaTeX Error: File `dsfont.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.4 \usepackage
               {bbm}^^M
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘Brobdingnag.Rnw’

--- re-building ‘S4_brob.Rnw’ using Sweave
Creating a new generic function for ‘max’ in the global environment
Creating a new generic function for ‘min’ in the global environment
Creating a new generic function for ‘range’ in the global environment
Creating a new generic function for ‘prod’ in the global environment
Creating a new generic function for ‘sum’ in the global environment
Error: processing vignette 'S4_brob.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'S4_brob.tex' failed.
LaTeX errors:
! LaTeX Error: File `dsfont.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.4 \usepackage
               {bbm}^^M
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘S4_brob.Rnw’

SUMMARY: processing the following files failed:
  ‘Brobdingnag.Rnw’ ‘S4_brob.Rnw’

Error: Vignette re-building failed.
Execution halted
installed size is  9.4Mb
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installed size is 32.2Mb
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installed size is 177.1Mb
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Package suggested but not available for checking: ‘gsl’
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installed size is 18.8Mb
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installed size is 36.0Mb
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installed size is  5.5Mb
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installed size is  7.2Mb
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installed size is  6.6Mb
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installed size is 149.7Mb
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installed size is 17.9Mb
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Package which this enhances but not available for checking: ‘mirt’
Package unavailable to check Rd xrefs: ‘mirt’
Error(s) in re-building vignettes:
--- re-building ‘cem.Rnw’ using Sweave
Loading required package: cem
Loading required package: tcltk
Loading required package: lattice

How to use CEM? Type vignette("cem")

Loading required package: Amelia
Loading required package: Rcpp
## 
## Amelia II: Multiple Imputation
## (Version 1.8.1, built: 2022-11-18)
## Copyright (C) 2005-2023 James Honaker, Gary King and Matthew Blackwell
## Refer to http://gking.harvard.edu/amelia/ for more information
## 
Error: processing vignette 'cem.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'cem.tex' failed.
BibTeX errors:
The top-level auxiliary file: cem.aux
I couldn't open style file apsr.bst
---line 66 of file cem.aux
 : \bibstyle{apsr
 :               }
I'm skipping whatever remains of this command
I found no style file---while reading file cem.aux
--- failed re-building ‘cem.Rnw’

SUMMARY: processing the following file failed:
  ‘cem.Rnw’

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘linkcomm’
Found the following significant warnings:

  Warning: 'process_marker_data' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Packages suggested but not available for checking: 'drc', 'qpcR'
Package unavailable to check Rd xrefs: ‘qpcR’
Packages suggested but not available for checking: 'clustree', 'Seurat'
Packages required but not available:
  'TxDb.Hsapiens.UCSC.hg38.knownGene',
  'TxDb.Mmusculus.UCSC.mm10.knownGene'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    data   1.8Mb
    libs   4.8Mb
installed size is 13.5Mb
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    libs  13.2Mb
Package suggested but not available for checking: ‘seqHMM’
installed size is 17.7Mb
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    libs  15.8Mb
installed size is 32.7Mb
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    libs  30.6Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘cloudUtil.Rnw’ using Sweave
Error: processing vignette 'cloudUtil.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'cloudUtil.tex' failed.
LaTeX errors:
! LaTeX Error: File `pstricks.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.10 \usepackage
                {hyperref}^^M
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘cloudUtil.Rnw’

SUMMARY: processing the following file failed:
  ‘cloudUtil.Rnw’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘clValid.Rnw’ using Sweave
Loading required package: cluster
Read 7 items

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:stats’:

    IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: ‘S4Vectors’

The following object is masked from ‘package:utils’:

    findMatches

The following objects are masked from ‘package:base’:

    I, expand.grid, unname

Warning: replacing previous import ‘utils::findMatches’ by ‘S4Vectors::findMatches’ when loading ‘AnnotationDbi’

Loading required package: RankAggreg
Error: processing vignette 'clValid.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'clValid.tex' failed.
LaTeX errors:
! LaTeX Error: File `relsize.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.28 \usepackage
                [mathcal]{euscript}^^M
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘clValid.Rnw’

SUMMARY: processing the following file failed:
  ‘clValid.Rnw’

Error: Vignette re-building failed.
Execution halted
installed size is 17.1Mb
  sub-directories of 1Mb or more:
    libs  15.4Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘weight_cause_cox.rnw’ using Sweave
Error: processing vignette 'weight_cause_cox.rnw' failed with diagnostics:
Running 'texi2dvi' on 'weight_cause_cox.tex' failed.
LaTeX errors:
! LaTeX Error: File `pgfplots.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.28 \pgfplotsset
                 {compat=1.10}^^M
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘weight_cause_cox.rnw’

SUMMARY: processing the following file failed:
  ‘weight_cause_cox.rnw’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘cmvnorm.Rnw’ using Sweave

Attaching package: ‘cmvnorm’

The following objects are masked from ‘package:stats’:

    sd, var


Attaching package: ‘elliptic’

The following objects are masked from ‘package:cmvnorm’:

    Im<-, Re<-, sd

The following objects are masked from ‘package:stats’:

    sd, sigma

The following object is masked from ‘package:base’:

    is.primitive

Error: processing vignette 'cmvnorm.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'cmvnorm.tex' failed.
LaTeX errors:
! LaTeX Error: File `dsfont.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.4 \usepackage
               {bbm}^^M
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘cmvnorm.Rnw’

SUMMARY: processing the following file failed:
  ‘cmvnorm.Rnw’

Error: Vignette re-building failed.
Execution halted
installed size is 33.3Mb
  sub-directories of 1Mb or more:
    libs  33.1Mb
.stop_not_number: no visible global function definition for ‘%||%’
Undefined global functions or variables:
  %||%
Package suggested but not available for checking: ‘wTO’
Package suggested but not available for checking: ‘car’
installed size is 17.0Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    libs  12.9Mb
installed size is 94.7Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs  92.4Mb
installed size is 16.4Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs  14.4Mb
Packages suggested but not available for checking:
  'pcalg', 'InvariantCausalPrediction', 'backShift', 'CAM', 'mboost',
  'huge', 'flare'
Error(s) in re-building vignettes:
--- re-building ‘compare-intro.Rnw’ using Sweave
Error: processing vignette 'compare-intro.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'compare-intro.tex' failed.
LaTeX errors:
! LaTeX Error: File `boxedminipage.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.4 \usepackage
               {hyperref} % for \url^^M
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘compare-intro.Rnw’

--- re-building ‘fundamentals.Rnw’ using Sweave

Attaching package: ‘compare’

The following object is masked from ‘package:base’:

    isTRUE

--- finished re-building ‘fundamentals.Rnw’

SUMMARY: processing the following file failed:
  ‘compare-intro.Rnw’

Error: Vignette re-building failed.
Execution halted
installed size is 28.0Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    libs  26.4Mb
Packages suggested but not available for checking:
  'scagnostics', 'parsnip', 'C50', 'bartMachine', 'caret'
Packages suggested but not available for checking:
  'conosPanel', 'org.Mm.eg.db', 'p2data', 'rhdf5'
installed size is 11.3Mb
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    libs   9.6Mb
installed size is 70.2Mb
  sub-directories of 1Mb or more:
    libs  68.9Mb
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    R     2.4Mb
    doc   3.2Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    data   4.7Mb
    doc    1.6Mb
installed size is  7.0Mb
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    libs   6.9Mb
installed size is 41.6Mb
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    libs  41.5Mb
installed size is 26.9Mb
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    libs  25.2Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   4.1Mb
    doc    1.6Mb
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    data   8.5Mb
installed size is 180.8Mb
  sub-directories of 1Mb or more:
    R       2.1Mb
    data    2.0Mb
    libs  175.5Mb
Running ‘testthat.R’ [73s/114s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  Chain 1: Iteration: 290 / 300 [ 96%]  (Sampling)
  Chain 2: Iteration: 190 / 300 [ 63%]  (Sampling)
  Chain 1: Iteration: 300 / 300 [100%]  (Sampling)
  Chain 1: 
  Chain 1:  Elapsed Time: 22.012 seconds (Warm-up)
  Chain 1:                17.161 seconds (Sampling)
  Chain 1:                39.173 seconds (Total)
  Chain 1: 
  Chain 2: Iteration: 210 / 300 [ 70%]  (Sampling)
  Chain 2: Iteration: 230 / 300 [ 76%]  (Sampling)
  Chain 2: Iteration: 250 / 300 [ 83%]  (Sampling)
  Chain 2: Iteration: 270 / 300 [ 90%]  (Sampling)
  Chain 2: Iteration: 290 / 300 [ 96%]  (Sampling)
  
  Execution halted
installed size is 38.7Mb
  sub-directories of 1Mb or more:
    libs  38.6Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    doc    2.4Mb
installed size is 29.0Mb
  sub-directories of 1Mb or more:
    libs  28.2Mb
Found the following significant warnings:
  Warning: jpegReport.Rd:22: unknown macro '\abbr'
  Warning: jpegReport.Rd:50: unknown macro '\abbr'
  Warning: jpegReport.Rd:53: unknown macro '\abbr'
  Warning: jpegReport.Rd:56: unknown macro '\abbr'
  Warning: jpegReport.Rd:58: unknown macro '\abbr'
  Warning: jpegReport.Rd:62: unknown macro '\abbr'
  Warning: pdfReport.Rd:101: unknown macro '\abbr'
  Warning: pngReport.Rd:22: unknown macro '\abbr'
  Warning: pngReport.Rd:50: unknown macro '\abbr'
  Warning: pngReport.Rd:53: unknown macro '\abbr'
  Warning: pngReport.Rd:55: unknown macro '\abbr'
  Warning: pngReport.Rd:59: unknown macro '\abbr'
  Warning: readReportTable.Rd:35: unknown macro '\abbr'
  Warning: readReportTable.Rd:167: unknown macro '\abbr'
  Warning: scanReport.Rd:45: unknown macro '\abbr'
  Warning: scanReport.Rd:60: unknown macro '\abbr'
  Warning: scanReport.Rd:61: unknown macro '\abbr'
  Warning: scanReport.Rd:162: unknown macro '\abbr'
See ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.3/D4TAlink.light.Rcheck/00install.out’ for details.
installed size is 35.9Mb
  sub-directories of 1Mb or more:
    libs  33.7Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc    2.7Mb
    libs   4.4Mb
Error(s) in re-building vignettes:
--- re-building ‘DBR.Rnw’ using Sweave
DBR 1.4.1
Bayesian Discretized Beta Regression for the Analysis of Ratings Data
Warning in cor.test.default(pain$severity, pain$interference, method = "spearman") :
  Cannot compute exact p-value with ties
Warning in cor.test.default(pain$age, pain$interference, method = "spearman") :
  Cannot compute exact p-value with ties
Warning in ks.test.default(pred_sample, pain$interference) :
  p-value will be approximate in the presence of ties
Error: processing vignette 'DBR.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'DBR.tex' failed.
LaTeX errors:
! LaTeX Error: File `breqn.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.18 \usepackage
                {atbegshi}% http://ctan.org/pkg/atbegshi^^M
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘DBR.Rnw’

SUMMARY: processing the following file failed:
  ‘DBR.Rnw’

Error: Vignette re-building failed.
Execution halted
installed size is 51.1Mb
  sub-directories of 1Mb or more:
    libs  50.7Mb
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    data   1.9Mb
    libs   5.3Mb
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    libs   9.9Mb
Packages suggested but not available for checking: 'EMD', 'astrochron'
installed size is 17.6Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    help   2.2Mb
    libs  12.9Mb
Package suggested but not available for checking: ‘missMDA’
installed size is 35.9Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs  33.7Mb
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    doc    1.8Mb
    help   2.4Mb
    libs   3.5Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘desirability.Rnw’ using Sweave
Error: processing vignette 'desirability.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'desirability.tex' failed.
LaTeX errors:
! LaTeX Error: File `algorithm2e.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.14 \usepackage
                [^^M
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘desirability.Rnw’

SUMMARY: processing the following file failed:
  ‘desirability.Rnw’

Error: Vignette re-building failed.
Execution halted
installed size is 18.3Mb
  sub-directories of 1Mb or more:
    libs  17.5Mb
Packages suggested but not available for checking: 'psych', 'sirt'
Packages suggested but not available for checking: 'KrigInv', 'GPareto'
Package unavailable to check Rd xrefs: ‘KrigInv’
Error(s) in re-building vignettes:
  ...
--- re-building ‘dirmcmc_vignette.Rnw’ using Sweave
Error: processing vignette 'dirmcmc_vignette.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'dirmcmc_vignette.tex' failed.
LaTeX errors:
! LaTeX Error: File `todonotes.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.14 \usepackage
                {Sweave}^^M
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘dirmcmc_vignette.Rnw’

SUMMARY: processing the following file failed:
  ‘dirmcmc_vignette.Rnw’

Error: Vignette re-building failed.
Execution halted
installed size is 87.5Mb
  sub-directories of 1Mb or more:
    libs  86.7Mb
Running ‘testthat.R’ [6s/9s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  realized_duration(...) not equal to c(...).
  1/4 mismatches
  [1] 31 - 28 == 3
  ── Failure ('test-realized_duration.R:158:2'): realized_duration works (realized_only = TRUE) ──
  realized_duration(...) not equal to c(...).
  1/4 mismatches
  [2] 31 - 28 == 3
  ── Failure ('test-realized_duration.R:161:2'): realized_duration works (realized_only = TRUE) ──
  realized_duration(...) not equal to c(...).
  1/4 mismatches
  [1] 31 - 28 == 3
  
  [ FAIL 36 | WARN 0 | SKIP 0 | PASS 331 ]
  Error: Test failures
  Execution halted
installed size is 32.7Mb
  sub-directories of 1Mb or more:
    libs  31.9Mb
Error(s) in re-building vignettes:
--- re-building ‘dlsem_vignette.Rnw’ using Sweave
Loading required package: dlsem
Loading required package: graph
Loading required package: BiocGenerics

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:stats’:

    IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: Rgraphviz
Loading required package: grid
Error: processing vignette 'dlsem_vignette.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'dlsem_vignette.tex' failed.
LaTeX errors:
! LaTeX Error: File `boxedminipage.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.9 ^^M
       
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘dlsem_vignette.Rnw’

SUMMARY: processing the following file failed:
  ‘dlsem_vignette.Rnw’

Error: Vignette re-building failed.
Execution halted
installed size is 19.9Mb
  sub-directories of 1Mb or more:
    doc    6.7Mb
    libs  12.4Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    R         3.0Mb
    data      2.0Mb
    extdata   2.3Mb
Package suggested but not available for checking: ‘PerformanceAnalytics’
Package required but not available: ‘TxDb.Hsapiens.UCSC.hg38.knownGene’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 85.5Mb
  sub-directories of 1Mb or more:
    libs  84.7Mb
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    data   2.5Mb
    doc    1.4Mb
    libs   3.6Mb
installed size is 11.8Mb
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    data   3.1Mb
    libs   8.1Mb
installed size is 10.3Mb
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    libs        8.9Mb
    shiny_app   1.1Mb
Package suggested but not available for checking: ‘qs’
installed size is 13.5Mb
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    doc    1.3Mb
    libs  11.6Mb
installed size is 227.9Mb
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    doc     3.5Mb
    libs  223.3Mb
Package suggested but not available for checking: ‘seacarb’
Package suggested but not available for checking: ‘untb’
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    libs  10.6Mb
Error in load(p, envir = env) : empty (zero-byte) input file
  Calls: <Anonymous> ... suppressPackageStartupMessages -> withCallingHandlers -> load
  Execution halted
installed size is 94.3Mb
  sub-directories of 1Mb or more:
    help   2.7Mb
    libs  91.1Mb
Packages suggested but not available for checking: 'DIFboost', 'VGAMdata'
Package unavailable to check Rd xrefs: ‘DIFboost’
Package unavailable to check Rd xrefs: ‘faraway’
installed size is 26.4Mb
  sub-directories of 1Mb or more:
    libs  26.3Mb
installed size is 95.9Mb
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    libs  95.2Mb
Package unavailable to check Rd xrefs: ‘eRm’
installed size is 25.8Mb
  sub-directories of 1Mb or more:
    libs  25.7Mb
Error(s) in re-building vignettes:
--- re-building ‘ellipticpaper.Rnw’ using Sweave

Attaching package: ‘elliptic’

The following objects are masked from ‘package:stats’:

    sd, sigma

The following object is masked from ‘package:base’:

    is.primitive

Loading required package: emulator
Loading required package: mvtnorm
Loading required package: calibrator
Error: processing vignette 'ellipticpaper.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'ellipticpaper.tex' failed.
LaTeX errors:
! LaTeX Error: File `dsfont.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.4 \usepackage
               {bbm}^^M
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘ellipticpaper.Rnw’

--- re-building ‘residuetheorem.Rnw’ using Sweave

Attaching package: ‘elliptic’

The following objects are masked from ‘package:stats’:

    sd, sigma

The following object is masked from ‘package:base’:

    is.primitive

Error: processing vignette 'residuetheorem.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'residuetheorem.tex' failed.
LaTeX errors:
! LaTeX Error: File `dsfont.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.4 \usepackage
               {bbm}^^M
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘residuetheorem.Rnw’

SUMMARY: processing the following files failed:
  ‘ellipticpaper.Rnw’ ‘residuetheorem.Rnw’

Error: Vignette re-building failed.
Execution halted
installed size is 63.2Mb
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    libs  61.9Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   7.3Mb
Packages suggested but not available for checking:
  'fields', 'lme4', 'rworldmap', 'statnet'
Packages suggested but not available for checking:
  'fields', 'forecast', 'imputeTS', 'lme4', 'statnet'
installed size is 149.6Mb
  sub-directories of 1Mb or more:
    doc     1.5Mb
    libs  145.6Mb
installed size is 17.6Mb
  sub-directories of 1Mb or more:
    libs  15.0Mb
Package suggested but not available for checking: ‘semTools’
Packages unavailable to check Rd xrefs: ‘OpenMx’, ‘semTools’
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    doc    1.3Mb
    libs   3.8Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   3.4Mb
    help   1.5Mb
Packages suggested but not available for checking:
  'SimComp', 'multcomp', 'mratios'
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R     2.0Mb
    doc   2.9Mb
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    libs  11.1Mb
Running ‘testthat.R’ [74s/116s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(familial)
  > 
  > test_check("familial")
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 34 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-center-test.R:27:3'): plot function returns a plot ─────────────
  Error in `validObject(.Object)`: invalid class "FncBand" object: superclass "mMatrix" not defined in the environment of the object's class
  Backtrace:
       ▆
    1. ├─testthat::expect_s3_class(plot(test), "ggplot") at test-center-test.R:27:3
    2. │ └─testthat::quasi_label(enquo(object), arg = "object")
    3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
    4. ├─base::plot(test)
    5. └─familial:::plot.center.test(test)
    6.   └─base::lapply(band, bands)
    7.     └─familial (local) FUN(X[[i]], ...)
    8.       ├─base::data.frame(...)
    9.       └─DepthProc::fncGetBand(DepthProc::fncDepth(boot.wide), level)
   10.         └─methods::new("FncBand", bands, index = obj@index, level = band)
   11.           ├─methods::initialize(value, ...)
   12.           └─methods::initialize(value, ...)
   13.             └─methods (local) initMatrix(.Object, ...)
   14.               └─methods::validObject(.Object)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 34 ]
  Error: Test failures
  Execution halted
installed size is  6.0Mb
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installed size is  7.3Mb
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installed size is 43.9Mb
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installed size is 36.1Mb
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installed size is 16.8Mb
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installed size is 10.2Mb
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Package suggested but not available for checking: ‘DESeq2’
installed size is 32.1Mb
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Installation failed.
See ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.3/fcl.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘fields’
installed size is 15.6Mb
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    doc    1.5Mb
    help   2.1Mb
    libs   9.1Mb
installed size is 17.7Mb
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installed size is 25.0Mb
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installed size is  8.8Mb
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search_finna : <anonymous>: no visible global function definition for
  ‘%||%’
search_finna : <anonymous> : <anonymous>: no visible global function
  definition for ‘%||%’
search_publisher : <anonymous>: no visible global function definition
  for ‘%||%’
Undefined global functions or variables:
  %||%
Running examples in ‘finna-Ex.R’ failed
The error most likely occurred in:

> ### Name: analyze_metadata
> ### Title: Analyze Refined Finna Metadata
> ### Aliases: analyze_metadata
> 
> ### ** Examples
> 
> library(finna)
> sibelius_data <- search_finna("sibelius")
Warning in search_finna("sibelius") :
  Default limit of 100 records is being used. Specify 'limit' argument for more records.
Error in record$id %||% NA : could not find function "%||%"
Calls: search_finna -> lapply -> FUN
Execution halted
Running ‘testthat.R’ [2s/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(finna)
  > 
  > test_check("finna")
  Total results found: 2062423
  Data fetching completed in 2.25 seconds.
  Total results found: 3
  Data fetching completed in 0.47 seconds.
  Total results found: 2062423
  Data fetching completed in 0.76 seconds.
  No encoding supplied: defaulting to UTF-8.
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 61 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-search_publisher.R:3:3'): search_publisher performs a basic search correctly ──
  Error in `record$id %||% NA`: could not find function "%||%"
  Backtrace:
      ▆
   1. ├─base::suppressWarnings(search_publisher("sibelius", limit = 10)) at test-search_publisher.R:3:3
   2. │ └─base::withCallingHandlers(...)
   3. └─finna::search_publisher("sibelius", limit = 10)
   4.   └─base::lapply(...)
   5.     └─finna (local) FUN(X[[i]], ...)
  ── Error ('test_search_finna.R:3:3'): search_finna performs a basic search correctly ──
  Error in `record$id %||% NA`: could not find function "%||%"
  Backtrace:
      ▆
   1. ├─base::suppressWarnings(search_finna("sibelius", type = "Author")) at test_search_finna.R:3:3
   2. │ └─base::withCallingHandlers(...)
   3. └─finna::search_finna("sibelius", type = "Author")
   4.   └─base::lapply(...)
   5.     └─finna (local) FUN(X[[i]], ...)
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 61 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
--- re-building ‘vignette.Rmd’ using rmarkdown

Quitting from lines 23-26 [unnamed-chunk-1] (vignette.Rmd)
Error: processing vignette 'vignette.Rmd' failed with diagnostics:
could not find function "%||%"
--- failed re-building ‘vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 48.3Mb
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    libs  47.0Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘fitbitScraper-examples.Rmd’ using rmarkdown
Pandoc is required to build R Markdown vignettes but not available. Please make sure it is installed.
Quitting from lines 22-24 (fitbitScraper-examples.Rmd) 
Error: processing vignette 'fitbitScraper-examples.Rmd' failed with diagnostics:
login failed
--- failed re-building ‘fitbitScraper-examples.Rmd’

SUMMARY: processing the following file failed:
  ‘fitbitScraper-examples.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 11.9Mb
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    R      2.0Mb
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installed size is 315.7Mb
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installed size is  7.7Mb
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    libs   6.5Mb
installed size is  6.2Mb
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Package suggested but not available for checking: ‘minet’
installed size is 19.0Mb
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    doc    1.1Mb
    help   1.0Mb
    libs  13.8Mb
Package suggested but not available for checking: ‘Mcomp’
Error(s) in re-building vignettes:
--- re-building ‘lala2015frbs.ltx’ using tex
--- finished re-building ‘lala2015frbs.ltx’

--- re-building ‘lala2015pmml.Rtex’ using Sweave
Warning in mean.default((real.val - res.test)^2) :
  argument is not numeric or logical: returning NA
Error: processing vignette 'lala2015pmml.Rtex' failed with diagnostics:
Running 'texi2dvi' on 'lala2015pmml.tex' failed.
LaTeX errors:
! LaTeX Error: File `elsarticle.cls' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: cls)

! Emergency stop.
<read *> 
         
l.4 \usepackage
               {setspace}^^M
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building 'lala2015pmml.Rtex'

SUMMARY: processing the following file failed:
  ‘lala2015pmml.Rtex’

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘MARSS’
installed size is 106.6Mb
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installed size is 26.3Mb
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Error(s) in re-building vignettes:
--- re-building ‘gamboostLSS_Tutorial.Rnw’ using Sweave
Loading required package: R2BayesX
Loading required package: BayesXsrc
Loading required package: colorspace
Loading required package: mgcv
Loading required package: nlme
This is mgcv 1.8-42. For overview type 'help("mgcv-package")'.
Loading required package: gamboostLSS
Loading required package: mboost
Loading required package: parallel
Loading required package: stabs

Attaching package: 'gamboostLSS'

The following object is masked from 'package:stats':

    model.weights

Loading required namespace: BayesX
Error: processing vignette 'gamboostLSS_Tutorial.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'gamboostLSS_Tutorial.tex' failed.
LaTeX errors:
! LaTeX Error: File `dsfont.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.18 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building 'gamboostLSS_Tutorial.Rnw'

SUMMARY: processing the following file failed:
  'gamboostLSS_Tutorial.Rnw'

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘caret’
installed size is 36.2Mb
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installed size is 12.0Mb
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    data   1.4Mb
    libs  10.0Mb
installed size is 114.3Mb
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    libs  113.8Mb
installed size is 60.6Mb
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    extdata   1.6Mb
    libs     57.0Mb
installed size is 16.7Mb
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    doc    1.1Mb
    libs  15.3Mb
installed size is  6.6Mb
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    doc    2.0Mb
    libs   4.0Mb
installed size is 31.5Mb
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    libs  30.8Mb
installed size is 105.4Mb
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    R       1.1Mb
    libs  104.0Mb
installed size is 23.5Mb
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    R        13.0Mb
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    help      4.1Mb
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.3/GeoModels.Rcheck/00install.out’ for details.
installed size is 113.8Mb
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installed size is 31.0Mb
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    libs  30.7Mb
installed size is  7.9Mb
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    libs   7.9Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘ggESDA.Rmd’ using rmarkdown
Pandoc is required to build R Markdown vignettes but not available. Please make sure it is installed.
Quitting from lines 47-57 (ggESDA.Rmd) 
Error: processing vignette 'ggESDA.Rmd' failed with diagnostics:
object 'tbl_subset_col' not found
--- failed re-building ‘ggESDA.Rmd’

SUMMARY: processing the following file failed:
  ‘ggESDA.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 19.7Mb
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Packages suggested but not available for checking:
  'car', 'NetworkToolbox', 'NetworkComparisonTest'
installed size is  6.6Mb
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    doc    2.3Mb
    help   1.2Mb
installed size is  7.6Mb
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    libs   2.1Mb
Packages suggested but not available for checking: 'psych', 'psychTools'
installed size is  6.6Mb
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    libs   6.2Mb
installed size is 209.7Mb
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    doc     1.9Mb
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Package suggested but not available for checking: ‘mlmRev’
installed size is 67.4Mb
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installed size is 164.5Mb
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installed size is 45.9Mb
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    libs  45.7Mb
installed size is 99.5Mb
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    libs           93.0Mb
    test_data       2.3Mb
    vignette_data   2.1Mb
installed size is 34.8Mb
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    libs  32.9Mb
installed size is 11.5Mb
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    doc    1.3Mb
    libs   9.8Mb
Package unavailable to check Rd xrefs: ‘caret’
Package suggested but not available for checking: ‘SeqVarTools’
Package unavailable to check Rd xrefs: ‘repeated’
installed size is 51.9Mb
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    i     48.7Mb
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Error(s) in re-building vignettes:
  ...
--- re-building ‘Overview.Rmd’ using rmarkdown
Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Warning in close.connection(con) :
  Problem closing connection:  No space left on device
[WARNING] This document format requires a nonempty <title> element.
  Defaulting to 'Overview.knit' as the title.
  To specify a title, use 'title' in metadata or --metadata title="...".
pandoc: /Volumes/Builds/packages/big-sur-x86_64/results/4.3/governor.Rcheck/vign_test/governor/vignettes/Overview.html: withFile: resource exhausted (No space left on device)
Error: processing vignette 'Overview.Rmd' failed with diagnostics:
pandoc document conversion failed with error 1
--- failed re-building ‘Overview.Rmd’

SUMMARY: processing the following file failed:
  ‘Overview.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 36.8Mb
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    libs  36.3Mb
Running ‘testthat.R’ [6s/13s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  ── 1. Failure ('test_predict.GP.R:64:9'): check predict.GP ─────────────────────
  smse2 >= 0 & smse2 < 30 is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  
  ── 2. Failure ('test_predict.GP.R:81:9'): check predict.GP ─────────────────────
  sum(gpp2$complete_data[, 5] - ms2 < 1e-05) >= 10 is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  
  ══ DONE ════════════════════════════════════════════════════════════════════════
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
--- re-building ‘gplm-examples.Rnw’ using Sweave
Loading required package: AER
Loading required package: car
Loading required package: carData
Loading required package: lmtest
Loading required package: zoo

Attaching package: ‘zoo’

The following objects are masked from ‘package:base’:

    as.Date, as.Date.numeric

Loading required package: sandwich
Loading required package: survival
Error: processing vignette 'gplm-examples.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'gplm-examples.tex' failed.
LaTeX errors:
! LaTeX Error: File `wasysym.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.20 \usepackage
                {comment}^^M
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘gplm-examples.Rnw’

SUMMARY: processing the following file failed:
  ‘gplm-examples.Rnw’

Error: Vignette re-building failed.
Execution halted
installed size is 54.4Mb
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installed size is 11.0Mb
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installed size is 18.8Mb
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installed size is 51.4Mb
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installed size is  8.8Mb
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    libs   8.4Mb
Packages unavailable to check Rd xrefs: ‘repeated’, ‘gnlm’
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    doc    4.1Mb
    libs   3.4Mb
installed size is  7.4Mb
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    help   2.2Mb
installed size is 69.4Mb
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installed size is 87.4Mb
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    libs  86.0Mb
installed size is  8.3Mb
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    R      1.0Mb
    libs   5.6Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘HDXBoxeR.Rmd’ using rmarkdown
Error: processing vignette 'HDXBoxeR.Rmd' failed with diagnostics:
Error writing to connection:  No space left on device
--- failed re-building ‘HDXBoxeR.Rmd’

SUMMARY: processing the following file failed:
  ‘HDXBoxeR.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.2Mb
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    R      1.7Mb
    doc    1.9Mb
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Package suggested but not available for checking: ‘geojsonio’
installed size is  7.3Mb
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    libs   3.9Mb
installed size is 84.0Mb
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    libs  83.4Mb
installed size is 60.4Mb
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    libs  58.9Mb
Note: skipping ‘Ch_cluster_analysis.Rnw’ due to unavailable dependencies:
  'mvtnorm'
installed size is 69.9Mb
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    libs  69.4Mb
installed size is  9.3Mb
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    libs   7.9Mb
plotHVT: no visible global function definition for ‘%||%’
Undefined global functions or variables:
  %||%
installed size is 41.2Mb
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Error(s) in re-building vignettes:
--- re-building ‘hypergeometric.Rnw’ using Sweave
Loading required package: hypergeo
Loading required package: elliptic

Attaching package: ‘elliptic’

The following objects are masked from ‘package:stats’:

    sd, sigma

The following object is masked from ‘package:base’:

    is.primitive

Error: processing vignette 'hypergeometric.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'hypergeometric.tex' failed.
LaTeX errors:
! LaTeX Error: File `dsfont.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.4 \usepackage
               {bbm}^^M
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘hypergeometric.Rnw’

SUMMARY: processing the following file failed:
  ‘hypergeometric.Rnw’

Error: Vignette re-building failed.
Execution halted
installed size is  6.4Mb
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Package suggested but not available for checking: ‘LTRCtrees’
Package unavailable to check Rd xrefs: ‘LTRCtrees’
installed size is 15.6Mb
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installed size is 32.2Mb
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installed size is 24.8Mb
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    help   2.4Mb
    libs  18.7Mb
installed size is  7.3Mb
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    data   3.4Mb
    doc    1.6Mb
installed size is 95.2Mb
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installed size is  6.7Mb
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installed size is 30.6Mb
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installed size is 10.9Mb
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installed size is  5.1Mb
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installed size is 10.5Mb
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installed size is 95.2Mb
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installed size is 103.7Mb
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installed size is 33.9Mb
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installed size is 15.3Mb
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installed size is 12.2Mb
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installed size is  5.1Mb
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    help   2.1Mb
installed size is 13.2Mb
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    libs  10.6Mb
installed size is  5.3Mb
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    data      2.2Mb
    doc       1.5Mb
    extdata   1.1Mb
installed size is 11.9Mb
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installed size is 95.4Mb
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installed size is 11.9Mb
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    doc       1.0Mb
    extdata   1.2Mb
    libs      8.2Mb
installed size is 72.3Mb
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Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction.Rmd’ using rmarkdown
Pandoc is required to build R Markdown vignettes but not available. Please make sure it is installed.
Quitting from lines 22-30 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
there is no package called 'org.Mm.eg.db'
--- failed re-building ‘introduction.Rmd’

SUMMARY: processing the following file failed:
  ‘introduction.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 27.6Mb
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    R          1.5Mb
    doc        1.6Mb
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    testdata   1.3Mb
Package suggested but not available for checking: ‘pbkrtest’
Package unavailable to check Rd xrefs: ‘pbkrtest’
installed size is 55.3Mb
  sub-directories of 1Mb or more:
    libs  54.3Mb
Packages suggested but not available for checking: 'car', 'dynlm', 'AER'
Package unavailable to check Rd xrefs: ‘car’
installed size is  9.7Mb
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installed size is 25.1Mb
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gg_scatter: no visible global function definition for '%||%'
Undefined global functions or variables:
  %||%
Packages suggested but not available for checking:
  'sirt', 'kerdiest', 'car', 'mitml'
installed size is 45.9Mb
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installed size is 26.1Mb
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installed size is 32.8Mb
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installed size is 25.1Mb
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Packages suggested but not available for checking:
  'ssize', 'WGCNA', 'KEGGgraph', 'pdInfoBuilder', 'lumi', 'oligo',
  'affy', 'genefilter', 'beadarray', 'GOstats', 'Category', 'impute'
installed size is 10.4Mb
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    R      2.1Mb
    data   3.1Mb
    libs   4.9Mb
installed size is 11.0Mb
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Package suggested but not available for checking: ‘DescTools’
installed size is 21.9Mb
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    htmlwidgets   3.5Mb
    libs         15.0Mb
installed size is 12.5Mb
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    data   3.0Mb
    libs   4.7Mb
Packages suggested but not available for checking: 'csampling', 'nlreg'
installed size is 14.5Mb
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    libs      10.5Mb
installed size is  5.4Mb
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installed size is 10.2Mb
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    libs   8.6Mb
Package required and available but unsuitable version: ‘systemfonts’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 14.2Mb
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Package suggested but not available for checking: ‘MBSP’
installed size is  6.1Mb
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    R      2.0Mb
    data   3.9Mb
Errors in running code in vignettes:
when running code in ‘mcemGLM-vignette.Rnw’
  ...
         6      :  6   6      :  6   Max.   :1.000  
         (Other):324   (Other):324                  

> fitBernoulli <- mcemGLMM(fixed = Mate ~ 0 + Cross, 
+     random = list(~0 + Female, ~0 + Male), data = salamander, 
+     family = "bernoulli", vcD .... [TRUNCATED] 

Execution halted

... incomplete output.  Crash?

  ‘mcemGLM-vignette.Rnw’... failed to complete the test
* checking re-building of vignette outputs ...* using check arguments '--no-clean-on-error '
installed size is 64.7Mb
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installed size is 157.0Mb
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installed size is 109.1Mb
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installed size is  7.1Mb
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    R      3.0Mb
    help   3.2Mb
Packages suggested but not available for checking:
  'org.Hs.eg.db', 'annaffy', 'hgu133plus2.db', 'hgu133a.db',
  'hgu95av2.db'
installed size is 56.8Mb
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    libs  56.3Mb
installed size is 19.9Mb
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installed size is 10.2Mb
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installed size is 20.9Mb
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installed size is 43.5Mb
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installed size is 112.9Mb
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Packages unavailable to check Rd xrefs: ‘lme4’, ‘mixAK’
Packages suggested but not available for checking:
  'clustree', 'karyoploteR', 'regioneR'
Package unavailable to check Rd xrefs: ‘genefilter’
Packages suggested but not available for checking:
  'minfi', 'IlluminaHumanMethylation450kmanifest'
installed size is 141.3Mb
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installed size is 16.6Mb
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installed size is 19.0Mb
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Package required and available but unsuitable version: ‘tinytable’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘survey’
installed size is  8.8Mb
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Packages suggested but not available for checking: 'fftw', 'RODBC'
Packages unavailable to check Rd xrefs: ‘seewave’, ‘RODBC’
installed size is 11.0Mb
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Package suggested but not available for checking: ‘ergm’
Error: there is no package called ‘knitr’
Call sequence:
14: doWithOneRestart(return(expr), restart)
13: withOneRestart(expr, restarts[[1L]])
12: withRestarts(stop(cond), retry_loadNamespace = function() NULL)
11: loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
10: asNamespace(ns)
9: namespaceImportFrom(ns, loadNamespace(j <- i[[1L]], c(lib.loc, 
       .libPaths()), versionCheck = vI[[j]]), i[[2L]], from = package)
8: loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
7: asNamespace(ns)
6: namespaceImportFrom(ns, loadNamespace(j <- i[[1L]], c(lib.loc, 
       .libPaths()), versionCheck = vI[[j]]), i[[2L]], from = package)
5: loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
4: namespaceImport(ns, loadNamespace(i, c(lib.loc, .libPaths()), 
       versionCheck = vI[[i]]), from = package)
3: loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
2: namespaceImport(ns, loadNamespace(i, c(lib.loc, .libPat
Execution halted
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : 
  there is no package called ‘knitr’
Calls: <Anonymous>
Execution halted
Packages suggested but not available for checking: 'mvoutlier', 'glmulti'
installed size is  9.7Mb
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installed size is 94.2Mb
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installed size is 14.5Mb
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    data   1.6Mb
    libs  12.5Mb
installed size is 11.1Mb
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    R      2.1Mb
    data   4.5Mb
    libs   3.6Mb
Package suggested but not available for checking: ‘ICAMS’
installed size is 17.7Mb
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installed size is 16.0Mb
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Package suggested but not available for checking: ‘statnet’
installed size is 278.5Mb
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installed size is 36.5Mb
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installed size is 13.1Mb
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Package unavailable to check Rd xrefs: ‘sampleSelection’
installed size is 28.1Mb
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    data     2.9Mb
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    models   1.1Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘NBLAST-Clustering.Rmd’ using rmarkdown
Pandoc is required to build R Markdown vignettes but not available. Please make sure it is installed.
2023-07-10 21:31:32.757 R[43986:2287591920] XType: Using static font registry.

Quitting from lines 57-60 [unnamed-chunk-5] (NBLAST-Clustering.Rmd)
Error: processing vignette 'NBLAST-Clustering.Rmd' failed with diagnostics:
Saving a widget with selfcontained = TRUE requires pandoc. See here to learn more https://bookdown.org/yihui/rmarkdown-cookbook/install-pandoc.html
--- failed re-building ‘NBLAST-Clustering.Rmd’

SUMMARY: processing the following file failed:
  ‘NBLAST-Clustering.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  6.3Mb
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installed size is 25.6Mb
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installed size is 233.3Mb
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Package suggested but not available for checking: ‘csampling’
Package unavailable to check Rd xrefs: ‘csampling’
installed size is  6.3Mb
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installed size is 14.8Mb
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    R      3.0Mb
    data   1.0Mb
    doc    1.7Mb
    help   3.4Mb
    libs   5.1Mb
installed size is  6.5Mb
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    data   3.2Mb
    libs   1.9Mb
installed size is 47.2Mb
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installed size is 39.6Mb
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    doc    1.1Mb
    libs  37.4Mb
installed size is 277.5Mb
  sub-directories of 1Mb or more:
    R         3.1Mb
    data      1.4Mb
    libs    265.8Mb
    models    4.7Mb
installed size is  9.3Mb
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installed size is  7.2Mb
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installed size is 34.9Mb
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installed size is  7.9Mb
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installed size is  5.9Mb
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    libs      3.0Mb
installed size is  8.1Mb
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    data   6.1Mb
    doc    1.8Mb
posterior_epred_ordbeta_prep: no visible global function definition for
  ‘%||%’
Undefined global functions or variables:
  %||%
Running examples in ‘ordbetareg-Ex.R’ failed
The error most likely occurred in:

> ### Name: posterior_epred_ordbeta.brmsfit
> ### Title: Calculate Probability of Response Components
> ### Aliases: posterior_epred_ordbeta.brmsfit posterior_epred_ordbeta
> 
> ### ** Examples
> 
> 
> data('ord_fit_mean')
> 
> # use function to calculate probability of top end of scale
> 
> pr_1s <- posterior_epred_ordbeta(ord_fit_mean,component="top")
Error in incl_thres %||% FALSE : could not find function "%||%"
Calls: posterior_epred_ordbeta ... posterior_epred_ordbeta.brmsfit -> posterior_epred_ordbeta_prep -> as_one_logical
Execution halted
installed size is 10.0Mb
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Packages suggested but not available for checking:
  'org.Dr.eg.db', 'org.Mm.eg.db', 'scde'
installed size is  9.6Mb
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    library   8.7Mb
installed size is 16.2Mb
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    libs  15.8Mb
installed size is 46.0Mb
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installed size is 84.5Mb
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installed size is  5.9Mb
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    libs   4.0Mb
Error(s) in re-building vignettes:
--- re-building ‘partitionspaper.Rnw’ using Sweave
Loading required package: partitions
Error: processing vignette 'partitionspaper.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'partitionspaper.tex' failed.
LaTeX errors:
! LaTeX Error: File `dsfont.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.4 \usepackage
               {bbm}^^M
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘partitionspaper.Rnw’

--- re-building ‘scrabble.Rnw’ using Sweave
Error: processing vignette 'scrabble.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'scrabble.tex' failed.
LaTeX errors:
! LaTeX Error: File `dsfont.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.4 \usepackage
               {bbm}^^M
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘scrabble.Rnw’

--- re-building ‘setpartitions.Rnw’ using Sweave
Loading required package: partitions
Error: processing vignette 'setpartitions.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'setpartitions.tex' failed.
LaTeX errors:
! LaTeX Error: File `dsfont.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.4 \usepackage
               {bbm}^^M
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘setpartitions.Rnw’

SUMMARY: processing the following files failed:
  ‘partitionspaper.Rnw’ ‘scrabble.Rnw’ ‘setpartitions.Rnw’

Error: Vignette re-building failed.
Execution halted
installed size is  8.7Mb
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installed size is  6.4Mb
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    R      3.1Mb
    help   3.2Mb
installed size is  7.6Mb
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    help   3.3Mb
installed size is  7.9Mb
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    R      3.1Mb
    help   4.5Mb
installed size is  5.5Mb
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    R      3.1Mb
    help   2.3Mb
Package required and available but unsuitable version: ‘paws.analytics’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    R      3.1Mb
    help   4.4Mb
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.3/pbdMPI.Rcheck/00install.out’ for details.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    doc    1.7Mb
    help   2.3Mb
installed size is 140.0Mb
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    doc     2.9Mb
    libs  136.3Mb
Packages suggested but not available for checking:
  'car', 'fields', 'georob', 'gstat'
Packages unavailable to check Rd xrefs: ‘fields’, ‘gstat’, ‘car’
installed size is 126.0Mb
  sub-directories of 1Mb or more:
    libs  125.0Mb
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    data   1.8Mb
    libs   9.2Mb
installed size is 51.5Mb
  sub-directories of 1Mb or more:
    libs  50.4Mb
installed size is 11.3Mb
  sub-directories of 1Mb or more:
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Package suggested but not available for checking: ‘lme4’
Package unavailable to check Rd xrefs: ‘lme4’
Package unavailable to check Rd xrefs: ‘phase1RMD’
Package suggested but not available for checking: ‘BiocParallel’
Packages suggested but not available for checking:
  'randomForestSRC', 'xgboost'
installed size is 86.7Mb
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Packages suggested but not available for checking: 'INLA', 'DHARMa', 'rr2'
installed size is 12.4Mb
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    libs   9.9Mb
installed size is 11.5Mb
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    libs  11.1Mb
installed size is 24.1Mb
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    libs  23.9Mb
installed size is  6.1Mb
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    R      2.1Mb
    data   2.8Mb
Package suggested but not available for checking: ‘httk’
installed size is 23.5Mb
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Package suggested but not available for checking: ‘ellipse’
installed size is 18.8Mb
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    doc    2.1Mb
    libs  12.6Mb
installed size is  5.5Mb
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    data   3.6Mb
    doc    1.5Mb
installed size is 13.2Mb
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    R      7.1Mb
    data   5.0Mb
installed size is  6.4Mb
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    data   2.6Mb
    doc    1.8Mb
    libs   1.5Mb
installed size is 18.0Mb
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    libs  17.6Mb
installed size is 64.6Mb
  sub-directories of 1Mb or more:
    libs  64.2Mb
installed size is 39.4Mb
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Package suggested but not available for checking: ‘rstan’
Package unavailable to check Rd xrefs: ‘rstan’
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
installed size is  9.5Mb
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    libs   9.0Mb
Package suggested but not available for checking: ‘bipartite’
Package suggested but not available for checking: ‘AER’
installed size is 10.7Mb
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    doc    3.6Mb
    libs   5.8Mb
installed size is 235.4Mb
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    libs  234.2Mb
installed size is 20.7Mb
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    libs  20.3Mb
installed size is  5.0Mb
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    doc    1.4Mb
    libs   2.6Mb
installed size is 123.0Mb
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    libs  122.6Mb
installed size is 34.4Mb
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    libs  33.7Mb
installed size is  6.7Mb
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    data   2.3Mb
    libs   3.2Mb
installed size is 139.0Mb
  sub-directories of 1Mb or more:
    libs  138.5Mb
installed size is  5.1Mb
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    libs   4.8Mb
installed size is 27.6Mb
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    libs  26.5Mb
installed size is 47.6Mb
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installed size is 33.2Mb
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    libs  32.8Mb
installed size is  7.7Mb
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    data   7.6Mb
installed size is 108.7Mb
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    libs  107.4Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   3.7Mb
installed size is 15.7Mb
  sub-directories of 1Mb or more:
    libs  15.7Mb
Packages suggested but not available for checking: 'glmmTMB', 'DHARMa'
installed size is 15.2Mb
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    libs  14.9Mb
installed size is 44.3Mb
  sub-directories of 1Mb or more:
    extdata   3.3Mb
    libs     39.7Mb
Packages suggested but not available for checking:
  'faraway', 'quantoptr', 'survminer'
installed size is 16.0Mb
  sub-directories of 1Mb or more:
    libs  14.2Mb
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    libs   6.7Mb
Package unavailable to check Rd xrefs: ‘survey’
'library' or 'require' call to ‘RDCOMClient’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
'library' or 'require' calls in package code:
  ‘RDCOMClient’ ‘rcom’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
installed size is 35.7Mb
  sub-directories of 1Mb or more:
    libs  34.3Mb
Package suggested but not available for checking: ‘quanteda.textmodels’
Error(s) in re-building vignettes:
--- re-building ‘RankAggreg.Rnw’ using Sweave
Loading required package: cluster
Package 'mclust' version 6.0.0
Type 'citation("mclust")' for citing this R package in publications.

Attaching package: ‘kohonen’

The following object is masked from ‘package:mclust’:

    map

Error: processing vignette 'RankAggreg.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'RankAggreg.tex' failed.
LaTeX errors:
! LaTeX Error: File `relsize.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.28 \usepackage
                [mathcal]{euscript}^^M
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘RankAggreg.Rnw’

SUMMARY: processing the following file failed:
  ‘RankAggreg.Rnw’

Error: Vignette re-building failed.
Execution halted
installed size is 16.5Mb
  sub-directories of 1Mb or more:
    doc       1.7Mb
    extdata   4.1Mb
    libs      9.9Mb
installed size is 12.3Mb
  sub-directories of 1Mb or more:
    R      4.1Mb
    libs   7.2Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
installed size is 68.5Mb
  sub-directories of 1Mb or more:
    libs  67.6Mb
installed size is 16.2Mb
  sub-directories of 1Mb or more:
    data   4.5Mb
    libs  10.7Mb
installed size is 16.4Mb
  sub-directories of 1Mb or more:
    libs  15.6Mb
installed size is 67.3Mb
  sub-directories of 1Mb or more:
    libs  65.4Mb
installed size is 60.1Mb
  sub-directories of 1Mb or more:
    libs  59.5Mb
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.3/Rblpapi.Rcheck/00install.out’ for details.
installed size is 15.2Mb
  sub-directories of 1Mb or more:
    libs  15.0Mb
installed size is 64.3Mb
  sub-directories of 1Mb or more:
    libs  63.6Mb
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.3/Rcplex.Rcheck/00install.out’ for details.
installed size is 23.0Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs  20.6Mb
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.3/RcppMeCab.Rcheck/00install.out’ for details.
installed size is 20.0Mb
  sub-directories of 1Mb or more:
    data   1.9Mb
    libs  16.3Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    data   1.7Mb
    libs   1.1Mb
installed size is 19.4Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    libs  14.6Mb
Packages suggested but not available for checking: 'cdparcoord', 'partools'
Package suggested but not available for checking: ‘ggpubr’
installed size is 18.5Mb
  sub-directories of 1Mb or more:
    libs  17.1Mb
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    libs   9.7Mb
installed size is 17.2Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    doc    1.2Mb
    libs  13.7Mb
installed size is 24.2Mb
  sub-directories of 1Mb or more:
    libs  23.4Mb
installed size is 47.2Mb
  sub-directories of 1Mb or more:
    libs  45.8Mb
Running ‘testthat.R’ [64s/56s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
       ▆
    1. ├─testthat::expect_error(...) at test-forestry.R:48:2
    2. │ └─testthat:::quasi_capture(...)
    3. │   ├─testthat (local) .capture(...)
    4. │   │ └─base::withCallingHandlers(...)
    5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
    6. └─Rforestry::forestry(x = iris[, -1], y = iris[, 1], seed = seed_i)
    7.   └─base::tryCatch(...)
    8.     └─base (local) tryCatchList(expr, classes, parentenv, handlers)
    9.       └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
   10.         └─value[[3L]](cond)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 1422 ]
  Error: Test failures
  Execution halted
Running examples in ‘ridge-Ex.R’ failed
The error most likely occurred in:

> ### Name: pvals
> ### Title: Compute p-values for ridgeLinear and ridgeLogistic models
> ### Aliases: pvals pvals.ridgeLinear pvals.ridgeLogistic
> ###   plot.pvalsRidgeLinear plot.pvalsRidgeLogistic print.pvalsRidgeLinear
> ###   print.pvalsRidgeLogistic
> 
> ### ** Examples
> 
> data(GenBin)
> mod <- logisticRidge(Phenotypes ~ ., data = as.data.frame(GenBin))

Execution halted
installed size is 18.4Mb
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    data   1.6Mb
    libs  16.0Mb
Package suggested but not available for checking: ‘portfolioBacktest’
installed size is 21.8Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs  20.3Mb
Note: information on .o files is not available
File ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.3/rJava.Rcheck/rJava/libs/rJava.so’:
  Found ‘___stderrp’, possibly from ‘stderr’ (C)
  Found ‘___stdoutp’, possibly from ‘stdout’ (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 20.1Mb
  sub-directories of 1Mb or more:
    lemon   2.8Mb
    libs   17.0Mb
installed size is 165.9Mb
  sub-directories of 1Mb or more:
    libs  164.9Mb
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    libs  12.0Mb
Found the following significant warnings:
  Warning: Software mark not found in path.
See ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.3/RMark.Rcheck/00install.out’ for details.
installed size is 135.1Mb
  sub-directories of 1Mb or more:
    libs  134.7Mb
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.3/RmecabKo.Rcheck/00install.out’ for details.
installed size is 39.4Mb
  sub-directories of 1Mb or more:
    libs  38.4Mb
installed size is 27.7Mb
  sub-directories of 1Mb or more:
    libs  27.6Mb
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.3/Rmpi.Rcheck/00install.out’ for details.
installed size is 85.0Mb
  sub-directories of 1Mb or more:
    libs  84.4Mb
installed size is 32.6Mb
  sub-directories of 1Mb or more:
    libs  31.4Mb
installed size is 13.8Mb
  sub-directories of 1Mb or more:
    libs  12.6Mb
installed size is 18.4Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs  15.8Mb
Error(s) in re-building vignettes:
--- re-building ‘RobPer_vignette.Rnw’ using Sweave
Loading required package: robustbase
Loading required package: quantreg
Loading required package: SparseM

Attaching package: 'SparseM'

The following object is masked from 'package:base':

    backsolve

Loading required package: splines
Loading required package: BB
Loading required package: rgenoud
##  rgenoud (Version 5.9-0.3, Build Date: 2022-04-19)
##  See http://sekhon.berkeley.edu/rgenoud for additional documentation.
##  Please cite software as:
##   Walter Mebane, Jr. and Jasjeet S. Sekhon. 2011.
##   ``Genetic Optimization Using Derivatives: The rgenoud package for R.''
##   Journal of Statistical Software, 42(11): 1-26. 
##

Error: processing vignette 'RobPer_vignette.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'RobPer_vignette.tex' failed.
LaTeX errors:
! LaTeX Error: File `dsfont.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.4 \usepackage
               {thumbpdf,lmodern}^^M
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building 'RobPer_vignette.Rnw'

SUMMARY: processing the following file failed:
  'RobPer_vignette.Rnw'

Error: Vignette re-building failed.
Execution halted
installed size is 97.5Mb
  sub-directories of 1Mb or more:
    libs  96.7Mb
Package suggested but not available for checking: ‘ivgets’
Package unavailable to check Rd xrefs: ‘ivgets’
installed size is 27.1Mb
  sub-directories of 1Mb or more:
    libs  26.5Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    libs   4.9Mb
Packages suggested but not available for checking: 'car', 'HH'
Package unavailable to check Rd xrefs: ‘HH’
installed size is 17.5Mb
  sub-directories of 1Mb or more:
    doc  15.2Mb
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.3/ROracle.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘MBESS’
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    data   2.7Mb
    libs   5.3Mb
installed size is 61.1Mb
  sub-directories of 1Mb or more:
    libs  59.9Mb
installed size is 21.1Mb
  sub-directories of 1Mb or more:
    libs  20.2Mb
installed size is 102.8Mb
  sub-directories of 1Mb or more:
    libs  102.2Mb
Errors in running code in vignettes:
when running code in ‘Using.RRPP.Rmd’
  ...
> fit.par <- lm(fit$call$f1, data = fit$LM$data)

> all.equal(fit$LM$coefficients, fit.par$coefficients)
[1] TRUE

> summary(manova(fit.par))

  When sourcing ‘Using.RRPP.R’:
Error: residuals have rank 49 < 112
Execution halted

  ‘ANOVA.vs.MANOVA.Rmd’ using ‘UTF-8’... [28s/42s] OK
  ‘Using.RRPP.Rmd’ using ‘UTF-8’... failed
Packages suggested but not available for checking: 'fields', 'qgraph'
Note: information on .o files is not available
File ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.3/Rserve.Rcheck/Rserve/libs/Rserve.so’:
  Found ‘___stderrp’, possibly from ‘stderr’ (C)
  Found ‘_abort’, possibly from ‘abort’ (C)
  Found ‘_exit’, possibly from ‘exit’ (C)
  Found ‘_rand’, possibly from ‘rand’ (C)
  Found ‘_random’, possibly from ‘random’ (C)
  Found ‘_sprintf’, possibly from ‘sprintf’ (C)
  Found ‘_srandom’, possibly from ‘srandom’ (C)
File ‘Rserve/libs/Rserve.so’:
  Found non-API calls to R: ‘R_Consolefile’, ‘R_Outputfile’,
    ‘R_TempDir’, ‘R_Visible’, ‘getInputHandler’, ‘ptr_R_Busy’,
    ‘ptr_R_ClearerrConsole’, ‘ptr_R_FlushConsole’, ‘ptr_R_ReadConsole’,
    ‘ptr_R_ResetConsole’, ‘ptr_R_ShowMessage’, ‘ptr_R_WriteConsole’,
    ‘ptr_R_WriteConsoleEx’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.
Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 299.3Mb
  sub-directories of 1Mb or more:
    R       2.0Mb
    doc     4.7Mb
    libs  291.8Mb
installed size is 96.4Mb
  sub-directories of 1Mb or more:
    libs  96.1Mb
installed size is 58.4Mb
  sub-directories of 1Mb or more:
    libs  57.7Mb
installed size is 49.8Mb
  sub-directories of 1Mb or more:
    exec   1.7Mb
    lib   34.7Mb
    libs  11.5Mb
installed size is 123.1Mb
  sub-directories of 1Mb or more:
    R       1.1Mb
    libs  121.2Mb
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    libs   7.5Mb
installed size is 28.6Mb
  sub-directories of 1Mb or more:
    doc    7.8Mb
    libs  19.9Mb
installed size is 224.1Mb
  sub-directories of 1Mb or more:
    data    1.5Mb
    libs  221.6Mb
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    data   4.6Mb
    libs   6.6Mb
installed size is 48.6Mb
  sub-directories of 1Mb or more:
    libs  47.4Mb
installed size is 66.3Mb
  sub-directories of 1Mb or more:
    include   5.1Mb
    libs     60.8Mb
Package suggested but not available for checking: ‘partykit’
Package unavailable to check Rd xrefs: ‘partykit’
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   5.4Mb
installed size is 38.0Mb
  sub-directories of 1Mb or more:
    libs  36.8Mb
installed size is 16.6Mb
  sub-directories of 1Mb or more:
    libs  15.4Mb
Note: skipping ‘my-vignette.Rnw’ due to unavailable dependencies: 'lme4'
installed size is 20.5Mb
  sub-directories of 1Mb or more:
    libs  20.3Mb
Packages suggested but not available for checking:
  'GO.db', 'GOstats', 'car', 'ergm', 'networkTomography',
  'org.Sc.sgd.db'
installed size is 47.7Mb
  sub-directories of 1Mb or more:
    libs  47.6Mb
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    data   4.9Mb
    libs   3.6Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   4.1Mb
    libs   2.9Mb
installed size is 21.2Mb
  sub-directories of 1Mb or more:
    libs  20.5Mb
Error(s) in re-building vignettes:
--- re-building ‘intro.Rnw’ using Sweave
scuba 1.11-1 
Type ‘help(scuba)’ for an introduction 
Read the warnings in ‘help(scuba.disclaimer)’ 
For news about changes to the package, type ‘news(package='scuba')’
scuba 1.11-1 
Type ‘help(scuba)’ for an introduction 
Read the warnings in ‘help(scuba.disclaimer)’ 
For news about changes to the package, type ‘news(package='scuba')’

Attaching package: ‘scuba’

The following objects are masked _by_ ‘.GlobalEnv’:

    pedro902, pedro903, pedro904, pedro922, pedro943, pedro944,
    pedro945, pedro946, pedro948, pedro949, pedro950

Error: processing vignette 'intro.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'intro.tex' failed.
LaTeX errors:
! LaTeX Error: File `anysize.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.9 \marginsize
               {2cm}{2cm}{2cm}{2cm}^^M
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘intro.Rnw’

SUMMARY: processing the following file failed:
  ‘intro.Rnw’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘sdcSpatial.Rmd’ using rmarkdown
Pandoc is required to build R Markdown vignettes but not available. Please make sure it is installed.
Quitting from lines 190-192 (sdcSpatial.Rmd) 
Error: processing vignette 'sdcSpatial.Rmd' failed with diagnostics:
different crs
--- failed re-building ‘sdcSpatial.Rmd’

SUMMARY: processing the following file failed:
  ‘sdcSpatial.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    libs   5.5Mb
installed size is 89.3Mb
  sub-directories of 1Mb or more:
    libs  87.4Mb
Error(s) in re-building vignettes:
--- re-building ‘sdmvspecies.Rnw’ using Sweave
Loading required package: sp
[1] "/Volumes/Builds/packages/big-sur-x86_64/results/4.3/sdmvspecies.Rcheck/sdmvspecies/external/env/bio1.bil" 
[2] "/Volumes/Builds/packages/big-sur-x86_64/results/4.3/sdmvspecies.Rcheck/sdmvspecies/external/env/bio11.bil"
[3] "/Volumes/Builds/packages/big-sur-x86_64/results/4.3/sdmvspecies.Rcheck/sdmvspecies/external/env/bio12.bil"
[4] "/Volumes/Builds/packages/big-sur-x86_64/results/4.3/sdmvspecies.Rcheck/sdmvspecies/external/env/bio14.bil"
[5] "/Volumes/Builds/packages/big-sur-x86_64/results/4.3/sdmvspecies.Rcheck/sdmvspecies/external/env/bio16.bil"
[6] "/Volumes/Builds/packages/big-sur-x86_64/results/4.3/sdmvspecies.Rcheck/sdmvspecies/external/env/bio5.bil" 
[7] "/Volumes/Builds/packages/big-sur-x86_64/results/4.3/sdmvspecies.Rcheck/sdmvspecies/external/env/bio7.bil" 
Error: processing vignette 'sdmvspecies.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'sdmvspecies.tex' failed.
LaTeX errors:
! LaTeX Error: File `hanging.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.9 \usepackage
               [utf8]{inputenc}^^M
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘sdmvspecies.Rnw’

SUMMARY: processing the following file failed:
  ‘sdmvspecies.Rnw’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘sealasso.Rnw’ using Sweave
Loading required package: lars
Loaded lars 1.3

Error: processing vignette 'sealasso.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'sealasso.tex' failed.
LaTeX errors:
! LaTeX Error: File `anysize.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.4 \marginsize
               {2.5cm}{2.5cm}{2.5cm}{2.5cm}^^M
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘sealasso.Rnw’

SUMMARY: processing the following file failed:
  ‘sealasso.Rnw’

Error: Vignette re-building failed.
Execution halted
installed size is 19.1Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    libs  15.2Mb
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   8.6Mb
Package suggested but not available for checking: ‘Rmpfr’
Packages suggested but not available for checking: 'blavaan', 'emmeans'
Package unavailable to check Rd xrefs: ‘blavaan’
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    R      2.3Mb
    libs   2.5Mb
Packages suggested but not available for checking:
  'FactoMineR', 'descriptio'
installed size is 17.7Mb
  sub-directories of 1Mb or more:
    doc    6.4Mb
    libs  10.4Mb
installed size is 19.9Mb
  sub-directories of 1Mb or more:
    libs  18.4Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    libs   4.2Mb
installed size is 56.7Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs  54.5Mb
installed size is 16.0Mb
  sub-directories of 1Mb or more:
    libs  14.7Mb
Package suggested but not available for checking: ‘ggraph’
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    ShinyItemAnalysis   2.3Mb
    data                2.0Mb
installed size is 12.8Mb
  sub-directories of 1Mb or more:
    libs  11.8Mb
Package suggested but not available for checking: ‘edgeR’
Note: skipping ‘SIBER.Rnw’ due to unavailable dependencies: 'edgeR'
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    extdata   1.0Mb
    help      1.7Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    libs   1.9Mb
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    libs   8.9Mb
Packages suggested but not available for checking:
  'quantreg', 'semTools', 'OpenMx', 'copula'
Package unavailable to check Rd xrefs: ‘copula’
installed size is 22.7Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs  20.3Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   2.8Mb
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    R      2.2Mb
    libs   6.8Mb
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    R         2.0Mb
    extdata   1.3Mb
    libs      7.6Mb
installed size is 13.1Mb
  sub-directories of 1Mb or more:
    libs  12.9Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   4.9Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
installed size is 16.7Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    doc    3.4Mb
    libs  10.8Mb
Packages suggested but not available for checking:
  'raster', 'rasterVis', 'meteoForecast'
installed size is 14.2Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    doc    1.3Mb
    libs  10.4Mb
installed size is 16.8Mb
  sub-directories of 1Mb or more:
    data   4.7Mb
    libs  11.9Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    R   5.0Mb
installed size is 15.1Mb
  sub-directories of 1Mb or more:
    libs  15.1Mb
installed size is 47.6Mb
  sub-directories of 1Mb or more:
    libs  46.8Mb
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.3/spaths.Rcheck/00install.out’ for details.
installed size is 14.1Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs  12.5Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    help   2.2Mb
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    libs   8.0Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘classic_speaq_vignette.Rmd’ using rmarkdown
Pandoc is required to build R Markdown vignettes but not available. Please make sure it is installed.
2023-07-10 23:48:34.091 R[19637:2290508776] XType: Using static font registry.

Quitting from lines 111-120 [Spectral_alignment] (classic_speaq_vignette.Rmd)
Error: processing vignette 'classic_speaq_vignette.Rmd' failed with diagnostics:
result would be too long a vector
--- failed re-building ‘classic_speaq_vignette.Rmd’

--- re-building ‘speaq2_illustrations.Rmd’ using rmarkdown
Pandoc is required to build R Markdown vignettes but not available. Please make sure it is installed.
2023-07-10 23:48:40.223 R[20964:2290511430] XType: Using static font registry.

Quitting from lines 71-83 [detect winepeaks] (speaq2_illustrations.Rmd)
Error: processing vignette 'speaq2_illustrations.Rmd' failed with diagnostics:
invalid 'times' argument
--- failed re-building ‘speaq2_illustrations.Rmd’

SUMMARY: processing the following files failed:
  ‘classic_speaq_vignette.Rmd’ ‘speaq2_illustrations.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc    3.1Mb
    libs   3.7Mb
installed size is 22.6Mb
  sub-directories of 1Mb or more:
    libs  22.2Mb
installed size is 18.3Mb
  sub-directories of 1Mb or more:
    libs  17.1Mb
installed size is 50.2Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs  48.3Mb
Running examples in ‘spsurv-Ex.R’ failed
The error most likely occurred in:

> ### Name: bppo
> ### Title: Bernstein Polynomial Based Proportional Odds Model
> ### Aliases: bppo
> 
> ### ** Examples
> 
> 
> library("spsurv")
> data("veteran")
Warning in data("veteran") : data set ‘veteran’ not found
> 
> fit <- bppo(Surv(time, status) ~ karno + celltype,
+ data = veteran)
Error in optimHess(theta, fn, gr, control = list(fnscale = -1)) : 
  non-finite value supplied by optim
Calls: bppo ... spbp.mle -> <Anonymous> -> <Anonymous> -> .local -> optimHess
Execution halted
Running ‘testthat.R’ [17s/31s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  ── Error ('test.R:33:1'): (code run outside of `test_that()`) ──────────────────
  Error in `optimHess(theta, fn, gr, control = list(fnscale = -1))`: non-finite value supplied by optim
  Backtrace:
      ▆
   1. └─spsurv::bppo(Surv(time, status) ~ karno + factor(celltype), data = veteran) at test.R:33:0
   2.   └─spsurv:::spbp.default(...)
   3.     └─spsurv:::spbp.mle(standata = standata, ...)
   4.       ├─rstan::optimizing(...)
   5.       └─rstan::optimizing(...)
   6.         └─rstan (local) .local(object, ...)
   7.           └─stats::optimHess(theta, fn, gr, control = list(fnscale = -1))
  
  [ FAIL 1 | WARN 7 | SKIP 0 | PASS 0 ]
  Error: Test failures
  Execution halted
Package suggested but not available for checking: ‘ecpc’
installed size is 41.8Mb
  sub-directories of 1Mb or more:
    libs  40.7Mb
installed size is 99.2Mb
  sub-directories of 1Mb or more:
    libs  98.7Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘SSsimple.Snw’ using Sweave
Loading required package: mvtnorm
Error: processing vignette 'SSsimple.Snw' failed with diagnostics:
Running 'texi2dvi' on 'SSsimple.tex' failed.
LaTeX errors:
! LaTeX Error: File `supertabular.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.8 \usepackage
               {wasysym}^^M
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘SSsimple.Snw’

SUMMARY: processing the following file failed:
  ‘SSsimple.Snw’

Error: Vignette re-building failed.
Execution halted
installed size is 51.2Mb
  sub-directories of 1Mb or more:
    libs  50.8Mb
installed size is 92.5Mb
  sub-directories of 1Mb or more:
    libs  91.7Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    data   3.6Mb
    libs   5.2Mb
Package suggested but not available for checking: ‘tweedie’
Package unavailable to check Rd xrefs: ‘tweedie’
Packages suggested but not available for checking:
  'semPlot', 'FactoMineR', 'FactoInvestigate', 'factoextra'
installed size is 63.4Mb
  sub-directories of 1Mb or more:
    libs  62.2Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘StMoMoVignette.Rnw’ using Sweave
Loading required package: gnm
Loading required package: forecast
Error: processing vignette 'StMoMoVignette.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'StMoMoVignette.tex' failed.
LaTeX errors:
! LaTeX Error: File `ctable.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.7 \usepackage
               [caption = false]{subfig}^^M
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building 'StMoMoVignette.Rnw'

SUMMARY: processing the following file failed:
  'StMoMoVignette.Rnw'

Error: Vignette re-building failed.
Execution halted
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   2.5Mb
    libs   2.5Mb
installed size is 34.9Mb
  sub-directories of 1Mb or more:
    libs  33.9Mb
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    libs   9.0Mb
Package unavailable to check Rd xrefs: ‘HDoutliers’
installed size is 12.9Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs  10.0Mb
Packages suggested but not available for checking: 'arm', 'caret', 'party'
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data   2.2Mb
    doc    3.1Mb
    help   1.0Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
Packages suggested but not available for checking:
  'arm', 'bartMachine', 'extraTrees', 'party', 'xgboost'
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    libs   7.3Mb
installed size is 64.9Mb
  sub-directories of 1Mb or more:
    libs  63.6Mb
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    data   2.3Mb
    doc    5.3Mb
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    help   1.0Mb
    libs   6.8Mb
installed size is 22.1Mb
  sub-directories of 1Mb or more:
    libs  21.5Mb
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.3/systemfonts.Rcheck/00install.out’ for details.
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    data   5.3Mb
    libs   4.7Mb
installed size is 15.5Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs  13.8Mb
Package suggested but not available for checking: ‘dearseq’
installed size is 13.6Mb
  sub-directories of 1Mb or more:
    doc  12.0Mb
installed size is 38.5Mb
  sub-directories of 1Mb or more:
    doc    1.3Mb
    libs  36.8Mb
installed size is 17.9Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    libs  15.2Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    doc   5.9Mb
installed size is 309.6Mb
  sub-directories of 1Mb or more:
    R       3.0Mb
    libs  305.0Mb
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    libs   5.3Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   3.4Mb
Package suggested but not available for checking: ‘ggplot2’
installed size is 47.2Mb
  sub-directories of 1Mb or more:
    libs  46.2Mb
Running ‘testthat.R’ [14s/19s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(tidystats)
  This version of tidystats uses a new and improved way of structuring statistics. This breaks previous (major) versions of tidystats.
  > 
  > test_check("tidystats")
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 183 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test_glm.R:118:3'): glm anova works ───────────────────────────────
  `tidy_model` not equal to `expected_tidy_model`.
  Component "groups": Component 1: Component 2: Component 2: Component 2: Length mismatch: comparison on first 4 components
  Component "groups": Component 1: Component 2: Component 3: Component 2: Length mismatch: comparison on first 4 components
  Backtrace:
      ▆
   1. └─tidystats:::expect_equal_models(model = model, expected_tidy_model = expected_statistics$anova_glm) at test_glm.R:118:3
   2.   └─testthat::expect_equal(tidy_model, expected_tidy_model, tolerance = tolerance)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 183 ]
  Error: Test failures
  Execution halted
installed size is 58.4Mb
  sub-directories of 1Mb or more:
    libs    14.9Mb
    tiledb  41.0Mb
Found the following significant warnings:
  Warning: type_boxplot.Rd:35: unknown macro '\abbr'
See ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.3/tinyplot.Rcheck/00install.out’ for details.
prepare_Rd: type_boxplot.Rd:35: unknown macro '\abbr'
installed size is 98.9Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs  94.9Mb
installed size is 16.7Mb
  sub-directories of 1Mb or more:
    examples  12.6Mb
    include    3.6Mb
installed size is 30.3Mb
  sub-directories of 1Mb or more:
    libs  30.0Mb
Package suggested but not available for checking: ‘stm’
Package unavailable to check Rd xrefs: ‘stm’
installed size is 203.3Mb
  sub-directories of 1Mb or more:
    R          6.1Mb
    help       2.5Mb
    include    1.9Mb
    libs     192.1Mb
Package suggested but not available for checking: ‘brms’
Package unavailable to check Rd xrefs: ‘brms’
installed size is 18.7Mb
  sub-directories of 1Mb or more:
    data      2.3Mb
    doc       1.3Mb
    extdata  14.8Mb
installed size is 114.4Mb
  sub-directories of 1Mb or more:
    doc     3.9Mb
    libs  109.4Mb
installed size is 39.5Mb
  sub-directories of 1Mb or more:
    libs  39.0Mb
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.3/triptych.Rcheck/00install.out’ for details.
Package unavailable to check Rd xrefs: ‘fpc’
Error(s) in re-building vignettes:
  ...
--- re-building ‘tsglm.Rnw’ using Sweave
Error: processing vignette 'tsglm.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'tsglm.tex' failed.
LaTeX errors:
! LaTeX Error: File `mathabx.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.13 \usepackage
                {microtype}^^M
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building 'tsglm.Rnw'

SUMMARY: processing the following file failed:
  'tsglm.Rnw'

Error: Vignette re-building failed.
Execution halted
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    libs   8.5Mb
installed size is 15.1Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs  12.1Mb
installed size is 96.9Mb
  sub-directories of 1Mb or more:
    libs  95.9Mb
Package unavailable to check Rd xrefs: ‘twang’
installed size is 132.0Mb
  sub-directories of 1Mb or more:
    R       2.1Mb
    libs  128.8Mb
installed size is 27.2Mb
  sub-directories of 1Mb or more:
    doc         1.4Mb
    dummydata   1.4Mb
    libs       22.6Mb
Package suggested but not available for checking: ‘adespatial’
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    libs   7.6Mb
Package suggested but not available for checking: ‘ggtern’
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    R      5.0Mb
    help   3.1Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc   2.7Mb
installed size is 33.0Mb
  sub-directories of 1Mb or more:
    libs  32.4Mb
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    doc           2.0Mb
    htmlwidgets   6.9Mb
installed size is 33.1Mb
  sub-directories of 1Mb or more:
    extdata   1.6Mb
    libs     31.1Mb
installed size is 117.8Mb
  sub-directories of 1Mb or more:
    libs  116.4Mb
installed size is 27.8Mb
  sub-directories of 1Mb or more:
    libs  27.6Mb
installed size is 94.2Mb
  sub-directories of 1Mb or more:
    data   4.2Mb
    libs  89.4Mb
combine_filters : <anonymous>: no visible global function definition
  for ‘%||%’
Undefined global functions or variables:
  %||%
installed size is 58.8Mb
  sub-directories of 1Mb or more:
    libs  58.4Mb
Package suggested but not available for checking: ‘classInt’
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    libs   7.9Mb
installed size is 44.0Mb
  sub-directories of 1Mb or more:
    libs  43.0Mb
Package suggested but not available for checking: ‘preprocessCore’
installed size is 32.6Mb
  sub-directories of 1Mb or more:
    java  30.1Mb
Package suggested but not available for checking: ‘nlmixr2’
installed size is 40.3Mb
  sub-directories of 1Mb or more:
    libs  40.0Mb
installed size is 41.2Mb
  sub-directories of 1Mb or more:
    libs  40.7Mb
Files named as vignettes but with no recognized vignette engine:
   ‘vignettes/getting-started.Rmd’
   ‘vignettes/project-owners.Rmd’
(Is a VignetteBuilder field missing?)
Package suggested but not available for checking: ‘rJava’
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.3/zoomerjoin.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘partitions’
Package suggested but not available for checking: 'INLA'
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    data      1.0Mb
    extdata   2.9Mb
    libs      2.0Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    data   2.9Mb
    libs   1.2Mb
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    adelie   1.8Mb
    doc      1.4Mb
    libs     5.5Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    data   1.6Mb
    libs   1.0Mb
Error(s) in re-building vignettes:
--- re-building 'ascariasis.Rmd' using rmarkdown
File figure/asc_plot_mixt-1.png not found in resource path
Error: processing vignette 'ascariasis.Rmd' failed with diagnostics:
pandoc document conversion failed with error 99
--- failed re-building 'ascariasis.Rmd'

--- re-building 'simulation_study.Rmd' using rmarkdown
File figure/sim_plot_true_data-1.png not found in resource path
Error: processing vignette 'simulation_study.Rmd' failed with diagnostics:
pandoc document conversion failed with error 99
--- failed re-building 'simulation_study.Rmd'

SUMMARY: processing the following files failed:
  'ascariasis.Rmd' 'simulation_study.Rmd'

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building 'andurinha.Rmd' using rmarkdown
Could not fetch https://fonts.googleapis.com/css?family=Montserrat&display=swap
HttpExceptionRequest Request {
  host                 = "fonts.googleapis.com"
  port                 = 443
  secure               = True
  requestHeaders       = []
  path                 = "/css"
  queryString          = "?family=Montserrat&display=swap"
  method               = "GET"
  proxy                = Nothing
  rawBody              = False
  redirectCount        = 10
  responseTimeout      = ResponseTimeoutDefault
  requestVersion       = HTTP/1.1
}
 NoResponseDataReceived
Error: processing vignette 'andurinha.Rmd' failed with diagnostics:
pandoc document conversion failed with error 61
--- failed re-building 'andurinha.Rmd'

SUMMARY: processing the following file failed:
  'andurinha.Rmd'

Error: Vignette re-building failed.
Execution halted
installed size is 35.3Mb
  sub-directories of 1Mb or more:
    R  35.3Mb
Package required but not available: 'pwalign'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    documents     2.4Mb
    libs          1.4Mb
    screenshots   1.6Mb
sort_asap: no visible global function definition for 'sort_by'
Undefined global functions or variables:
  sort_by
Found the following significant warnings:
  Warning: read_bcal.Rd:27: unknown macro '\abbr'
  Warning: read_chronomodel.Rd:36: unknown macro '\abbr'
  Warning: read_oxcal.Rd:27: unknown macro '\abbr'
See 'd:/Rcompile/CRANpkg/local/4.3/ArchaeoPhases.Rcheck/00install.out' for details.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R      2.3Mb
    help   1.1Mb
installed size is 14.3Mb
  sub-directories of 1Mb or more:
    bin   11.3Mb
    misc   2.1Mb
Running 'testthat.R' [57s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(ARUtools)
  > 
  > test_check("ARUtools")
  ERROR: Unknown command "TMPDIR=D:/temp/2025_02_14_01_50_00_25053/RtmpkjJueQ/file2a12439813cdd". Did you mean command "preview"?
  ERROR: Unknown command "TMPDIR=D:/temp/2025_02_14_01_50_00_25053/RtmpkjJueQ/file2a124208a4425". Did you mean command "preview"?
  Extracting Dates and Times...
  ! Omitted 1 extra, non-json/GPS files
  ! Detected 2 log files
  [ FAIL 2 | WARN 0 | SKIP 6 | PASS 566 ]
  
  ══ Skipped tests (6) ═══════════════════════════════════════════════════════════
  • On CRAN (5): 'test-08_selections.R:27:3', 'test-08_selections.R:91:3',
    'test-08_selections.R:198:3', 'test-10_clean_logs.R:29:3',
    'test-10_clean_logs.R:61:3'
  • SoX not available (1): 'test-07_wave_files.R:193:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-09_create_dirs.R:35:3'): create_dirs() ───────────────────────
  `... <- NULL` produced warnings.
  ── Failure ('test-09_create_dirs.R:78:3'): create_dirs() ───────────────────────
  `... <- NULL` produced warnings.
  
  [ FAIL 2 | WARN 0 | SKIP 6 | PASS 566 ]
  Deleting unused snapshots:
  • 08_selections/sim-selection-weights2.svg
  • 08_selections/sim-selection-weights3.svg
  Error: Test failures
  Execution halted
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   1.1Mb
Check process probably crashed or hung up for 20 minutes ... killed
Most likely this happened in the example checks (?),
if not, ignore the following last lines of example output:
> 
> ### ** Examples
> 
> ## Not run: 
> ##D #get veg.PI data for selected plots:
> ##D my.data <- get_ausplots(my.Plot_IDs=c("SATFLB0004", "QDAMGD0022", "NTASTU0002"),
> ##D 	veg.PI=TRUE, site_info=FALSE)
> ##D 
> ##D #generate a percent cover occurrence matrix using "genus_species" species identification:
> ##D species_table(my.data$veg.PI, m_kind="percent_cover", cover_type="PFC", 
> ##D species_name="GS")
> ## End(Not run)
> 
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()
> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
Time elapsed:  6.6 0.39 7 NA NA 
> grDevices::dev.off()
null device 
          1 
> ###
> ### Local variables: ***
> ### mode: outline-minor ***
> ### outline-regexp: "\\(> \\)?### [*]+" ***
> ### End: ***
> quit('no')
======== End of example output (where/before crash/hang up occured ?) ========
installed size is 30.3Mb
  sub-directories of 1Mb or more:
    libs  29.5Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    libs   3.5Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    libs   1.4Mb
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    doc    4.4Mb
    help   2.2Mb
Package unavailable to check Rd xrefs: 'INLA'
installed size is 13.4Mb
  sub-directories of 1Mb or more:
    doc   10.8Mb
    libs   1.5Mb
installed size is 13.9Mb
  sub-directories of 1Mb or more:
    libs  12.8Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    help   1.8Mb
    libs   3.3Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   3.3Mb
    doc    1.2Mb
    libs   1.4Mb
Found the following significant warnings:

  Warning: 'adonis' is deprecated.
  Warning: 'adonis' is deprecated.
  Warning: 'adonis' is deprecated.
  Warning: 'adonis' is deprecated.
  Warning: 'adonis' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc    3.3Mb
    help   1.1Mb
    libs   1.6Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc    2.9Mb
    libs   1.4Mb
installed size is 15.8Mb
  sub-directories of 1Mb or more:
    libs  15.5Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   1.7Mb
    help   2.4Mb
    libs   1.0Mb
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    R          1.2Mb
    libs       5.2Mb
    testdata   1.4Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    libs   1.2Mb
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    data   7.7Mb
    libs   1.2Mb
installed size is 40.9Mb
  sub-directories of 1Mb or more:
    include  10.5Mb
    lib      29.9Mb
Error(s) in re-building vignettes:
--- re-building 'brea.Rmd' using rmarkdown

Quitting from lines 303-305 [unnamed-chunk-18] (brea.Rmd)
Error: processing vignette 'brea.Rmd' failed with diagnostics:
package 'MASS' must be installed
--- failed re-building 'brea.Rmd'

SUMMARY: processing the following file failed:
  'brea.Rmd'

Error: Vignette re-building failed.
Execution halted
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    R     3.8Mb
    doc   3.6Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.3/BRugs.Rcheck/00install.out' for details.
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    components   1.0Mb
    fonts        2.4Mb
    lib          5.0Mb
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    doc    2.8Mb
    libs   3.3Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.3/btb.Rcheck/00install.out' for details.
Running 'testthat.R' [45s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library("testthat")
  > 
  > test_check("btergm")
  Loading required package: btergm
  Registered S3 methods overwritten by 'btergm':
    method    from
    plot.gof  ergm
    print.gof ergm
  Package:  btergm
  Version:  1.10.12
  Date:     2024-03-31
  Authors:  Philip Leifeld (University of Manchester)
            Skyler J. Cranmer (The Ohio State University)
            Bruce A. Desmarais (Pennsylvania State University)
  
  [ FAIL 1 | WARN 2 | SKIP 8 | PASS 51 ]
  
  ══ Skipped tests (8) ═══════════════════════════════════════════════════════════
  • On CRAN (8): 'test-btergm.R:82:3', 'test-btergm.R:180:3',
    'test-btergm.R:197:3', 'test-data.R:4:3', 'test-interpret.R:4:3',
    'test-interpret.R:32:3', 'test-interpret.R:59:3', 'test-interpret.R:87:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-btergm.R:73:3'): offset argument in btergm works without composition change ──
  Error in `ergm::ergm.pl(nw, Clist.miss, model, theta.offset = c(rep(FALSE, 
      length(l$rhs.terms) - 1), TRUE), verbose = FALSE, control = control.ergm)`: VECTOR_ELT() can only be applied to a 'list', not a 'NULL'
  Backtrace:
      ▆
   1. ├─base::suppressWarnings(...) at test-btergm.R:73:3
   2. │ └─base::withCallingHandlers(...)
   3. └─btergm::btergm(...)
   4.   └─ergm::ergm.pl(...)
  
  [ FAIL 1 | WARN 2 | SKIP 8 | PASS 51 ]
  Error: Test failures
  Execution halted
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   3.2Mb
Check process probably crashed or hung up for 20 minutes ... killed
Most likely this happened in the example checks (?),
if not, ignore the following last lines of example output:
> ##D #...or calculate the DI and LPD of the trained model:
> ##D # DI = trainDI(model=model, LPD = TRUE)
> ##D 
> ##D # the DI can now be used to compute the AOA (here with LPD):
> ##D studyArea = rast(system.file("extdata/predictors_chile.tif", package = "CAST"))
> ##D AOA = aoa(studyArea, model = model, trainDI = DI, LPD = TRUE, maxLPD = 1)
> ##D print(AOA)
> ##D plot(AOA)
> ##D plot(AOA$AOA)
> ##D plot(AOA$LPD)
> ## End(Not run)
> 
> 
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()
> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
Time elapsed:  14.27 0.59 14.86 NA NA 
> grDevices::dev.off()
null device 
          1 
> ###
> ### Local variables: ***
> ### mode: outline-minor ***
> ### outline-regexp: "\\(> \\)?### [*]+" ***
> ### End: ***
> quit('no')
======== End of example output (where/before crash/hang up occured ?) ========
installed size is 17.6Mb
  sub-directories of 1Mb or more:
    doc   16.4Mb
    libs   1.1Mb
Error(s) in re-building vignettes:
--- re-building 'atp_calculation.Rmd' using rmarkdown
File mito_glyco_tests.png not found in resource path
Error: processing vignette 'atp_calculation.Rmd' failed with diagnostics:
pandoc document conversion failed with error 99
--- failed re-building 'atp_calculation.Rmd'

--- re-building 'ceas.Rmd' using rmarkdown
--- finished re-building 'ceas.Rmd'

SUMMARY: processing the following file failed:
  'atp_calculation.Rmd'

Error: Vignette re-building failed.
Execution halted
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    data   3.2Mb
    doc    2.0Mb
    libs   1.7Mb
Error(s) in re-building vignettes:
--- re-building 'chain_glm.Rmd' using rmarkdown

Quitting from lines 173-174 [glm1_3] (chain_glm.Rmd)
Error: processing vignette 'chain_glm.Rmd' failed with diagnostics:
package 'MASS' must be installed
--- failed re-building 'chain_glm.Rmd'

--- re-building 'introduction.Rmd' using rmarkdown
--- finished re-building 'introduction.Rmd'

SUMMARY: processing the following file failed:
  'chain_glm.Rmd'

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building 'README.Rmd' using rmarkdown
File man/figures/logo.png not found in resource path
Error: processing vignette 'README.Rmd' failed with diagnostics:
pandoc document conversion failed with error 99
--- failed re-building 'README.Rmd'

SUMMARY: processing the following file failed:
  'README.Rmd'

Error: Vignette re-building failed.
Execution halted
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    doc    3.6Mb
    libs   1.1Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    extdata   5.3Mb
    libs      1.0Mb
.stop_not_number: no visible global function definition for '%||%'
Undefined global functions or variables:
  %||%
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc   5.4Mb
Error(s) in re-building vignettes:
--- re-building 'cran.Rmd' using rmarkdown

Quitting from lines 42-45 [get_dep_all_packages] (cran.Rmd)
Error: processing vignette 'cran.Rmd' failed with diagnostics:
no applicable method for 'count' applied to an object of class "NULL"
--- failed re-building 'cran.Rmd'

--- re-building 'degree.Rmd' using rmarkdown

Quitting from lines 46-52 [unnamed-chunk-2] (degree.Rmd)
Error: processing vignette 'degree.Rmd' failed with diagnostics:
no applicable method for 'inner_join' applied to an object of class "NULL"
--- failed re-building 'degree.Rmd'

--- re-building 'introduction.Rmd' using rmarkdown
--- finished re-building 'introduction.Rmd'

SUMMARY: processing the following files failed:
  'cran.Rmd' 'degree.Rmd'

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: 'BSgenome.Scerevisiae.UCSC.sacCer3'
Package suggested but not available for checking: 'EnsDb.Hsapiens.v86'
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   5.7Mb
installed size is 13.0Mb
  sub-directories of 1Mb or more:
    doc   11.7Mb
    help   1.2Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    data   7.6Mb
Packages required and available but unsuitable versions:
  'stats', 'tools', 'utils'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    R      2.6Mb
    doc    1.2Mb
    help   1.0Mb
    libs   1.3Mb
Found the following significant warnings:
  Warning: jpegReport.Rd:22: unknown macro '\abbr'
  Warning: jpegReport.Rd:50: unknown macro '\abbr'
  Warning: jpegReport.Rd:53: unknown macro '\abbr'
  Warning: jpegReport.Rd:56: unknown macro '\abbr'
  Warning: jpegReport.Rd:58: unknown macro '\abbr'
  Warning: jpegReport.Rd:62: unknown macro '\abbr'
  Warning: pdfReport.Rd:101: unknown macro '\abbr'
  Warning: pngReport.Rd:22: unknown macro '\abbr'
  Warning: pngReport.Rd:50: unknown macro '\abbr'
  Warning: pngReport.Rd:53: unknown macro '\abbr'
  Warning: pngReport.Rd:55: unknown macro '\abbr'
  Warning: pngReport.Rd:59: unknown macro '\abbr'
  Warning: readReportTable.Rd:35: unknown macro '\abbr'
  Warning: readReportTable.Rd:167: unknown macro '\abbr'
  Warning: scanReport.Rd:45: unknown macro '\abbr'
  Warning: scanReport.Rd:60: unknown macro '\abbr'
  Warning: scanReport.Rd:61: unknown macro '\abbr'
  Warning: scanReport.Rd:162: unknown macro '\abbr'
See 'd:/Rcompile/CRANpkg/local/4.3/D4TAlink.light.Rcheck/00install.out' for details.
Running 'testthat.R' [6s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(mockery)
  > library(DataFakeR)
  > 
  > test_check("DataFakeR")
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 58 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-lint_check.R:3:3'): Linting package ────────────────────────────
  Error: Function with_defaults was deprecated in lintr version 3.0.0. Use linters_with_defaults or modify_defaults instead.
  Backtrace:
      ▆
   1. └─lintr::with_defaults(...) at test-lint_check.R:3:3
   2.   └─lintr:::lintr_deprecated(...)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 58 ]
  Error: Test failures
  Execution halted
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    3.0Mb
    libs   1.5Mb
Running 'testthat.R' [24s]
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/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  > library(defineR)
  Loading required package: common
  Loading required package: glue
  > 
  > test_check("defineR")
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    R      1.7Mb
    doc    1.8Mb
    help   1.6Mb
    libs   1.2Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data          1.8Mb
    htmlwidgets   3.6Mb
Package required but not available: 'signatureSearchData'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Error(s) in re-building vignettes:
--- re-building 'diffenrich_vignette.Rmd' using rmarkdown

Quitting from lines 161-163 [get_kegg_exp1] (diffenrich_vignette.Rmd)
Error: processing vignette 'diffenrich_vignette.Rmd' failed with diagnostics:
cannot read from connection
--- failed re-building 'diffenrich_vignette.Rmd'

SUMMARY: processing the following file failed:
  'diffenrich_vignette.Rmd'

Error: Vignette re-building failed.
Execution halted
installed size is 13.5Mb
  sub-directories of 1Mb or more:
    libs  12.9Mb
Package which this enhances but not available for checking: 'INLA'
installed size is 17.0Mb
  sub-directories of 1Mb or more:
    include  15.8Mb
installed size is 14.4Mb
  sub-directories of 1Mb or more:
    libs  13.7Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    libs   2.6Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
    libs   1.2Mb
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    doc    6.7Mb
    libs   1.7Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    R         2.0Mb
    data      2.0Mb
    extdata   2.3Mb
Package suggested but not available for checking: 'pwalign'
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data      1.7Mb
    extdata   3.2Mb
Running examples in 'dsem-Ex.R' failed
The error most likely occurred in:

> ### Name: dsemRTMB
> ### Title: Fit dynamic structural equation model
> ### Aliases: dsemRTMB
> 
> ### ** Examples
> 
> # Define model
> sem = "
+   # Link, lag, param_name
+   cprofits -> consumption, 0, a1
+   cprofits -> consumption, 1, a2
+   pwage -> consumption, 0, a3
+   gwage -> consumption, 0, a3
+   cprofits -> invest, 0, b1
+   cprofits -> invest, 1, b2
+   capital -> invest, 0, b3
+   gnp -> pwage, 0, c2
+   gnp -> pwage, 1, c3
+   time -> pwage, 0, c1
+ "
> 
> # Load data
> data(KleinI, package="AER")
> TS = ts(data.frame(KleinI, "time"=time(KleinI) - 1931))
> tsdata = TS[,c("time","gnp","pwage","cprofits",'consumption',
+                "gwage","invest","capital")]
> 
> # Fit model
> fit = dsemRTMB( sem=sem,
+             tsdata = tsdata,
+             estimate_delta0 = TRUE,
+             control = dsem_control(quiet=TRUE) )
Read 10 records
Error in advector(e1) : 
  Invalid argument to 'advector' (lost class attribute?)
Calls: dsemRTMB ... dgmrf -> as.vector -> Ops.advector -> Arith2 -> advector
Execution halted
installed size is 31.1Mb
  sub-directories of 1Mb or more:
    libs  30.4Mb
installed size is 12.4Mb
  sub-directories of 1Mb or more:
    R      3.6Mb
    data   7.3Mb
    doc    1.1Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   3.9Mb
    libs   1.1Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    libs   1.8Mb
installed size is 15.6Mb
  sub-directories of 1Mb or more:
    doc    3.5Mb
    libs  11.0Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    R      2.3Mb
    help   3.4Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    2.8Mb
    libs   1.0Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    extdata   4.0Mb
    libs      1.0Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.3/excel.link.Rcheck/00install.out' for details.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    R      3.5Mb
    help   1.2Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    3.0Mb
    help   1.2Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    doc    2.5Mb
    help   1.8Mb
    libs   1.9Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    R      2.8Mb
    help   1.7Mb
Missing link or links in documentation object 'fast.Rd':
  '[rgrass:readRAST]{rgrass::read_RAST()}'
  '[rgrass:readVECT]{rgrass::read_VECT()}'

See section 'Cross-references' in the 'Writing R Extensions' manual.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    doc    1.1Mb
    libs   1.1Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
    libs   1.2Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    Rcgi      3.0Mb
    cgi-bin   2.8Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   3.7Mb
    libs   1.3Mb
Running 'spelling.R' [0s]
  Running 'testthat.R' [149s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > suppressMessages(library(testthat))
  > 
  > test_check("fbar")
  Loading required package: fbar
  [ FAIL 1 | WARN 12 | SKIP 2 | PASS 45 ]
  
  ══ Skipped tests (2) ═══════════════════════════════════════════════════════════
  • known theoretical issue (2): 'test-full-size.R:36:3', 'test-full-size.R:46:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-utilities.R:27:5'): Works correctly with http://bigg.ucsd.edu/static/models/iJO1366.json ──
  Error in `readBin(structure(4L, class = c("url", "connection"), conn_id = <pointer: 0x00000000000001e5>), 
      raw(0), 32768L)`: cannot read from connection
  Backtrace:
      ▆
   1. ├─fbar::get_BiGG(address) at test-utilities.R:27:5
   2. │ └─jsonlite::fromJSON(address)
   3. │   └─jsonlite:::parse_and_simplify(...)
   4. │     └─jsonlite:::parseJSON(txt, bigint_as_char)
   5. │       └─jsonlite:::parse_con(txt, bigint_as_char)
   6. └─base::readBin(`<url>`, `<raw>`, 32768L)
  
  [ FAIL 1 | WARN 12 | SKIP 2 | PASS 45 ]
  Error: Test failures
  Execution halted
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    R      1.8Mb
    doc    1.5Mb
    help   2.1Mb
    libs   1.6Mb
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    libs   8.0Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   1.4Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   1.8Mb
    libs   1.2Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   1.9Mb
    libs   2.3Mb
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    R         4.7Mb
    doc       2.1Mb
    extdata   2.1Mb
search_finna : <anonymous>: no visible global function definition for
  '%||%'
search_finna : <anonymous> : <anonymous>: no visible global function
  definition for '%||%'
search_publisher : <anonymous>: no visible global function definition
  for '%||%'
Undefined global functions or variables:
  %||%
Running examples in 'finna-Ex.R' failed
The error most likely occurred in:

> ### Name: analyze_metadata
> ### Title: Analyze Refined Finna Metadata
> ### Aliases: analyze_metadata
> 
> ### ** Examples
> 
> library(finna)
> sibelius_data <- search_finna("sibelius")
Warning in search_finna("sibelius") :
  Default limit of 100 records is being used. Specify 'limit' argument for more records.
Error in record$id %||% NA : could not find function "%||%"
Calls: search_finna -> lapply -> FUN
Execution halted
Running 'testthat.R' [6s]
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(finna)
  > 
  > test_check("finna")
  Total results found: 2062421
  Data fetching completed in 0.58 seconds.
  Total results found: 3
  Data fetching completed in 0.12 seconds.
  Total results found: 2062421
  Data fetching completed in 0.15 seconds.
  No encoding supplied: defaulting to UTF-8.
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 61 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-search_publisher.R:3:3'): search_publisher performs a basic search correctly ──
  Error in `record$id %||% NA`: could not find function "%||%"
  Backtrace:
      ▆
   1. ├─base::suppressWarnings(search_publisher("sibelius", limit = 10)) at test-search_publisher.R:3:3
   2. │ └─base::withCallingHandlers(...)
   3. └─finna::search_publisher("sibelius", limit = 10)
   4.   └─base::lapply(...)
   5.     └─finna (local) FUN(X[[i]], ...)
  ── Error ('test_search_finna.R:3:3'): search_finna performs a basic search correctly ──
  Error in `record$id %||% NA`: could not find function "%||%"
  Backtrace:
      ▆
   1. ├─base::suppressWarnings(search_finna("sibelius", type = "Author")) at test_search_finna.R:3:3
   2. │ └─base::withCallingHandlers(...)
   3. └─finna::search_finna("sibelius", type = "Author")
   4.   └─base::lapply(...)
   5.     └─finna (local) FUN(X[[i]], ...)
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 61 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
--- re-building 'vignette.Rmd' using rmarkdown

Quitting from lines 23-26 [unnamed-chunk-1] (vignette.Rmd)
Error: processing vignette 'vignette.Rmd' failed with diagnostics:
could not find function "%||%"
--- failed re-building 'vignette.Rmd'

SUMMARY: processing the following file failed:
  'vignette.Rmd'

Error: Vignette re-building failed.
Execution halted
installed size is 14.2Mb
  sub-directories of 1Mb or more:
    libs  12.8Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    doc    3.6Mb
    libs   1.6Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    help   2.3Mb
    libs   1.3Mb
installed size is 22.8Mb
  sub-directories of 1Mb or more:
    libs  21.7Mb
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    doc    9.1Mb
    libs   1.0Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R      2.8Mb
    help   1.3Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    doc    1.1Mb
    libs   1.2Mb
installed size is 20.8Mb
  sub-directories of 1Mb or more:
    data   5.0Mb
    doc    1.8Mb
    libs  13.0Mb
installed size is 33.6Mb
  sub-directories of 1Mb or more:
    doc   31.8Mb
    libs   1.3Mb
installed size is 106.0Mb
  sub-directories of 1Mb or more:
    L8NY18   2.3Mb
    gdal     3.0Mb
    libs    91.0Mb
    proj     8.4Mb
installed size is 103.9Mb
  sub-directories of 1Mb or more:
    extdata   1.3Mb
    gdal      3.0Mb
    libs     89.6Mb
    proj      8.4Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    extdata   3.8Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc       1.5Mb
    extdata   3.2Mb
    libs      1.1Mb
installed size is 13.6Mb
  sub-directories of 1Mb or more:
    libs  12.9Mb
Error(s) in re-building vignettes:
--- re-building 'geoAr_geofacet.Rmd' using rmarkdown
File figure/tucmap-1.png not found in resource path
Error: processing vignette 'geoAr_geofacet.Rmd' failed with diagnostics:
pandoc document conversion failed with error 99
--- failed re-building 'geoAr_geofacet.Rmd'

--- re-building 'geoAr_leaflet.Rmd' using rmarkdown
File figure/map-1.png not found in resource path
Error: processing vignette 'geoAr_leaflet.Rmd' failed with diagnostics:
pandoc document conversion failed with error 99
--- failed re-building 'geoAr_leaflet.Rmd'

--- re-building 'georefar.Rmd' using rmarkdown
--- finished re-building 'georefar.Rmd'

SUMMARY: processing the following files failed:
  'geoAr_geofacet.Rmd' 'geoAr_leaflet.Rmd'

Error: Vignette re-building failed.
Execution halted
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    extdata   3.0Mb
    libs      1.5Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    libs   4.4Mb
installed size is 21.8Mb
  sub-directories of 1Mb or more:
    R        12.1Mb
    extdata   6.3Mb
    help      3.2Mb
Check process probably crashed or hung up for 20 minutes ... killed
Most likely this happened in the example checks (?),
if not, ignore the following last lines of example output:
> cleanEx()
> nameEx("setMetadataStandard")
> ### * setMetadataStandard
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: setMetadataStandard
> ### Title: setMetadataStandard
> ### Aliases: setMetadataStandard
> 
> ### ** Examples
> 
> 
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()
> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
Time elapsed:  231.26 2.06 246.78 NA NA 
> grDevices::dev.off()
null device 
          1 
> ###
> ### Local variables: ***
> ### mode: outline-minor ***
> ### outline-regexp: "\\(> \\)?### [*]+" ***
> ### End: ***
> quit('no')
======== End of example output (where/before crash/hang up occured ?) ========
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.3/GeoModels.Rcheck/00install.out' for details.
Package suggested but not available for checking: 'RandomFields'

Package which this enhances but not available for checking: 'INLA'
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc       3.0Mb
    extdata   1.6Mb
    libs      1.1Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    doc    2.3Mb
    help   1.1Mb
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    doc        1.1Mb
    help       2.4Mb
    testdata   4.8Mb
installed size is 46.0Mb
  sub-directories of 1Mb or more:
    i     43.7Mb
    libs   1.2Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    R   6.1Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data   3.9Mb
    libs   1.7Mb
jagam2greta: no visible global function definition for '%||%'
Undefined global functions or variables:
  %||%
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    doc    2.8Mb
    libs   1.0Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs                     1.3Mb
    supplementary_material   3.1Mb
Package required but not available: 'EnsDb.Hsapiens.v75'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc    4.1Mb
    libs   1.2Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    data   1.1Mb
    help   1.8Mb
Running examples in 'GVS-Ex.R' failed
The error most likely occurred in:

> ### Name: GVS_metadata
> ### Title: Get GVS metadata
> ### Aliases: GVS_metadata
> 
> ### ** Examples
> 
> {
+ metadata <- GVS_metadata()
+ }
There appears to be a problem reaching the API.
There appears to be a problem reaching the API.
There appears to be a problem reaching the API.
Error in names(output) <- c("citations", "version", "sources") : 
  'names' attribute [3] must be the same length as the vector [0]
Calls: GVS_metadata
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.3/h2o.Rcheck/00install.out' for details.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs    1.0Mb
    shiny   4.3Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    doc    2.5Mb
    libs   1.3Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
    libs   1.4Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   2.5Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    libs   1.3Mb
installed size is 15.0Mb
  sub-directories of 1Mb or more:
    libs  13.8Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    doc    4.0Mb
Error(s) in re-building vignettes:
--- re-building 'htrSPRanalysis-vignette.Rmd' using knitr
trying URL 'https://gitlab.oit.duke.edu/janice/htrspranalysis/-/raw/master/inst/extdata/titration_data.xlsx?ref_type=heads'
Content type 'application/octet-stream' length 4816423 bytes (4.6 MB)
======================
downloaded 2.1 MB


Quitting from lines 93-121 [unnamed-chunk-3] (htrSPRanalysis-vignette.Rmd)
Error: processing vignette 'htrSPRanalysis-vignette.Rmd' failed with diagnostics:
download from 'https://gitlab.oit.duke.edu/janice/htrspranalysis/-/raw/master/inst/extdata/titration_data.xlsx?ref_type=heads' failed
--- failed re-building 'htrSPRanalysis-vignette.Rmd'

SUMMARY: processing the following file failed:
  'htrSPRanalysis-vignette.Rmd'

Error: Vignette re-building failed.
Execution halted
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   1.9Mb
    doc    2.3Mb
    help   1.1Mb
plotHVT: no visible global function definition for '%||%'
Undefined global functions or variables:
  %||%
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    extdata   5.5Mb
    libs      1.1Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc    2.8Mb
    libs   1.1Mb
Packages suggested but not available for checking:
  'BSgenome.Hsapiens.1000genomes.hs37d5',
  'BSgenome.Mmusculus.UCSC.mm10'
Found the following significant warnings:
  D:/rtools43/usr/lib/mxe/usr/x86_64-w64-mingw32.static.posix/include/winnt.h:8404:37: warning: ISO C++ forbids flexible array member 'Elements' [-Wpedantic]
  D:/rtools43/usr/lib/mxe/usr/x86_64-w64-mingw32.static.posix/include/winnt.h:8667:22: warning: ISO C++ forbids flexible array member 'pEventLogRecords' [-Wpedantic]
  D:/rtools43/usr/lib/mxe/usr/x86_64-w64-mingw32.static.posix/include/winnt.h:8673:13: warning: ISO C++ forbids flexible array member 'ulOffsets' [-Wpedantic]
  D:/rtools43/usr/lib/mxe/usr/x86_64-w64-mingw32.static.posix/include/minwindef.h:196:3: warning: function declaration isn't a prototype [-Wstrict-prototypes]
  D:/rtools43/usr/lib/mxe/usr/x86_64-w64-mingw32.static.posix/include/minwindef.h:197:3: warning: function declaration isn't a prototype [-Wstrict-prototypes]
  D:/rtools43/usr/lib/mxe/usr/x86_64-w64-mingw32.static.posix/include/minwindef.h:198:3: warning: function declaration isn't a prototype [-Wstrict-prototypes]
  D:/rtools43/usr/lib/mxe/usr/x86_64-w64-mingw32.static.posix/include/processthreadsapi.h:130:47: warning: ISO C does not allow extra ';' outside of a function [-Wpedantic]
  D:/rtools43/usr/lib/mxe/usr/x86_64-w64-mingw32.static.posix/include/rpcndr.h:451:3: warning: function declaration isn't a prototype [-Wstrict-prototypes]
  D:/rtools43/usr/lib/mxe/usr/x86_64-w64-mingw32.static.posix/include/urlmon.h:1333:24: warning: ISO C restricts enumerator values to range of 'int' [-Wpedantic]
  D:/rtools43/usr/lib/mxe/usr/x86_64-w64-mingw32.static.posix/include/urlmon.h:1745:25: warning: ISO C restricts enumerator values to range of 'int' [-Wpedantic]
  D:/rtools43/usr/lib/mxe/usr/x86_64-w64-mingw32.static.posix/include/winioctl.h:359:11: warning: ISO C forbids zero-size array 'SerialNumber' [-Wpedantic]
See 'd:/Rcompile/CRANpkg/local/4.3/igraph.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 12.3.0'
* used C++ compiler: 'g++.exe (GCC) 12.3.0'
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    doc    1.2Mb
    help   2.0Mb
    libs   6.4Mb
Found the following significant warnings:
  D:/rtools43/usr/lib/mxe/usr/x86_64-w64-mingw32.static.posix/include/winnt.h:8404:37: warning: ISO C++ forbids flexible array member 'Elements' [-Wpedantic]
  D:/rtools43/usr/lib/mxe/usr/x86_64-w64-mingw32.static.posix/include/winnt.h:8667:22: warning: ISO C++ forbids flexible array member 'pEventLogRecords' [-Wpedantic]
  D:/rtools43/usr/lib/mxe/usr/x86_64-w64-mingw32.static.posix/include/winnt.h:8673:13: warning: ISO C++ forbids flexible array member 'ulOffsets' [-Wpedantic]
  D:/rtools43/usr/lib/mxe/usr/x86_64-w64-mingw32.static.posix/include/rpcndr.h:447:19: warning: ISO C++ forbids flexible array member 'Format' [-Wpedantic]
  D:/rtools43/usr/lib/mxe/usr/x86_64-w64-mingw32.static.posix/include/oaidl.h:548:37: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
  D:/rtools43/usr/lib/mxe/usr/x86_64-w64-mingw32.static.posix/include/oaidl.h:499:29: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
See 'd:/Rcompile/CRANpkg/local/4.3/imager.Rcheck/00install.out' for details.
* used C++ compiler: 'g++.exe (GCC) 12.3.0'
installed size is 20.8Mb
  sub-directories of 1Mb or more:
    data      1.4Mb
    doc       3.7Mb
    extdata   1.0Mb
    include   3.3Mb
    libs     10.7Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    data   3.3Mb
    doc    1.6Mb
    libs   1.0Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc    4.1Mb
    libs   1.1Mb
Error(s) in re-building vignettes:
--- re-building 'NAME-OF-VIGNETTE.Rmd' using rmarkdown

Quitting from lines 31-37 [unnamed-chunk-3] (NAME-OF-VIGNETTE.Rmd)
Error: processing vignette 'NAME-OF-VIGNETTE.Rmd' failed with diagnostics:
cannot read from connection
--- failed re-building 'NAME-OF-VIGNETTE.Rmd'

SUMMARY: processing the following file failed:
  'NAME-OF-VIGNETTE.Rmd'

Error: Vignette re-building failed.
Execution halted
Running 'testthat.R' [62s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(IsoMemo)
  > 
  > test_check("IsoMemo")
  [ FAIL 1 | WARN 3 | SKIP 0 | PASS 0 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-01-getData.R:3:3'): getData() actually retrieves all data ──────
  Error in `expect_match(levels(df$source)[1], "14CSea")`: is.character(act$val) is not TRUE
  Backtrace:
      ▆
   1. └─testthat::expect_match(levels(df$source)[1], "14CSea") at test-01-getData.R:3:3
   2.   └─base::stopifnot(is.character(act$val))
  
  [ FAIL 1 | WARN 3 | SKIP 0 | PASS 0 ]
  Error: Test failures
  Execution halted
Running examples in 'ISRaD-Ex.R' failed
The error most likely occurred in:

> ### Name: ISRaD.getdata
> ### Title: ISRaD.getdata
> ### Aliases: ISRaD.getdata
> 
> ### ** Examples
> 
> # Return full dataset ("full")
> ISRaD_full <- ISRaD.getdata(tempdir(), dataset = "full", extra = FALSE)

 ISRaD_database_files not found...

 Downloading database files from: https://github.com/International-Soil-Radiocarbon-Database/ISRaD/raw/main/ISRaD_data_files/database/ISRaD_database_files.zip

trying URL 'https://github.com/International-Soil-Radiocarbon-Database/ISRaD/raw/main/ISRaD_data_files/database/ISRaD_database_files.zip'
Content type 'application/zip' length 22960279 bytes (21.9 MB)
====================================
downloaded 16.0 MB

Warning in download.file(dataURL, file.path(directory, "ISRaD_database_files.zip")) :
  downloaded length 0 != reported length 0
Warning in download.file(dataURL, file.path(directory, "ISRaD_database_files.zip")) :
  URL 'https://raw.githubusercontent.com/International-Soil-Radiocarbon-Database/ISRaD/main/ISRaD_data_files/database/ISRaD_database_files.zip': Timeout of 60 seconds was reached
Error in download.file(dataURL, file.path(directory, "ISRaD_database_files.zip")) : 
  download from 'https://github.com/International-Soil-Radiocarbon-Database/ISRaD/raw/main/ISRaD_data_files/database/ISRaD_database_files.zip' failed
Calls: ISRaD.getdata -> download.file
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.3/iTensor.Rcheck/00install.out' for details.
installed size is 13.3Mb
  sub-directories of 1Mb or more:
    art_profiles   1.5Mb
    libs          11.0Mb
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    doc       2.3Mb
    extdata   4.0Mb
    help      1.9Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    extdata   5.5Mb
    libs      1.1Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   3.6Mb
installed size is 11.9Mb
  sub-directories of 1Mb or more:
    doc    3.3Mb
    help   7.8Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    3.1Mb
    libs   1.3Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs   1.7Mb
Error(s) in re-building vignettes:
--- re-building 'using_latent2likert.Rmd' using rmarkdown
File man/figures/courses-grouped-min.png not found in resource path
Error: processing vignette 'using_latent2likert.Rmd' failed with diagnostics:
pandoc document conversion failed with error 99
--- failed re-building 'using_latent2likert.Rmd'

SUMMARY: processing the following file failed:
  'using_latent2likert.Rmd'

Error: Vignette re-building failed.
Execution halted
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    doc    2.5Mb
    libs   5.7Mb
Found the following significant warnings:
  D:/rtools43/usr/lib/mxe/usr/x86_64-w64-mingw32.static.posix/include/winnt.h:8404:37: warning: ISO C++ forbids flexible array member 'Elements' [-Wpedantic]
  D:/rtools43/usr/lib/mxe/usr/x86_64-w64-mingw32.static.posix/include/winnt.h:8667:22: warning: ISO C++ forbids flexible array member 'pEventLogRecords' [-Wpedantic]
  D:/rtools43/usr/lib/mxe/usr/x86_64-w64-mingw32.static.posix/include/winnt.h:8673:13: warning: ISO C++ forbids flexible array member 'ulOffsets' [-Wpedantic]
  D:/rtools43/usr/lib/mxe/usr/x86_64-w64-mingw32.static.posix/include/minwindef.h:196:3: warning: function declaration isn't a prototype [-Wstrict-prototypes]
  D:/rtools43/usr/lib/mxe/usr/x86_64-w64-mingw32.static.posix/include/minwindef.h:197:3: warning: function declaration isn't a prototype [-Wstrict-prototypes]
  D:/rtools43/usr/lib/mxe/usr/x86_64-w64-mingw32.static.posix/include/minwindef.h:198:3: warning: function declaration isn't a prototype [-Wstrict-prototypes]
  D:/rtools43/usr/lib/mxe/usr/x86_64-w64-mingw32.static.posix/include/processthreadsapi.h:130:47: warning: ISO C does not allow extra ';' outside of a function [-Wpedantic]
  D:/rtools43/usr/lib/mxe/usr/x86_64-w64-mingw32.static.posix/include/rpcndr.h:451:3: warning: function declaration isn't a prototype [-Wstrict-prototypes]
  D:/rtools43/usr/lib/mxe/usr/x86_64-w64-mingw32.static.posix/include/urlmon.h:1333:24: warning: ISO C restricts enumerator values to range of 'int' [-Wpedantic]
  D:/rtools43/usr/lib/mxe/usr/x86_64-w64-mingw32.static.posix/include/urlmon.h:1745:25: warning: ISO C restricts enumerator values to range of 'int' [-Wpedantic]
  D:/rtools43/usr/lib/mxe/usr/x86_64-w64-mingw32.static.posix/include/winioctl.h:359:11: warning: ISO C forbids zero-size array 'SerialNumber' [-Wpedantic]
See 'd:/Rcompile/CRANpkg/local/4.3/leidenbase.Rcheck/00install.out' for details.
* used C++ compiler: 'g++.exe (GCC) 12.3.0'
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    help   1.1Mb
    libs   4.1Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    R         1.0Mb
    doc       1.0Mb
    extdata   1.1Mb
    libs      1.7Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    R          1.5Mb
    doc        1.6Mb
    libs       1.4Mb
    testdata   1.3Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc    4.0Mb
    libs   1.4Mb
installed size is 13.8Mb
  sub-directories of 1Mb or more:
    libs  13.4Mb
Package suggested but not available for checking: 'EnsDb.Hsapiens.v75'
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R      4.0Mb
    libs   1.1Mb
installed size is 29.0Mb
  sub-directories of 1Mb or more:
    gdal   3.0Mb
    libs  17.4Mb
    proj   8.4Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.3/magick.Rcheck/00install.out' for details.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    data   2.3Mb
    libs   1.3Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.3/manifold.Rcheck/00install.out' for details.
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    data          1.3Mb
    doc           1.6Mb
    htmlwidgets   3.5Mb
    libs          3.1Mb
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    R      2.7Mb
    data   2.4Mb
    libs   1.3Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    examples   2.7Mb
    libs       1.3Mb
Package suggested but not available for checking: 'BSgenome.Hsapiens.NCBI.GRCh38'
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    java   3.3Mb
    libs   1.8Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc    3.8Mb
    libs   1.5Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    R      1.9Mb
    doc    3.6Mb
    libs   2.4Mb
Package suggested but not available for checking: 'BSgenome.Mmusculus.UCSC.mm10'
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    doc    5.5Mb
    lib    1.2Mb
    libs   1.2Mb
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    libs   7.1Mb
installed size is 27.8Mb
  sub-directories of 1Mb or more:
    include  10.1Mb
    libs     17.2Mb
Found the following significant warnings:

  Warning: 'maximization_to_minimization' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs   6.4Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc    3.3Mb
    libs   1.1Mb
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    data   4.5Mb
    libs   1.3Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    R   5.8Mb
Error(s) in re-building vignettes:
--- re-building 'Introduction.Rmd' using rmarkdown
File ./man/figures/plot_peje.png not found in resource path
Error: processing vignette 'Introduction.Rmd' failed with diagnostics:
pandoc document conversion failed with error 99
--- failed re-building 'Introduction.Rmd'

SUMMARY: processing the following file failed:
  'Introduction.Rmd'

Error: Vignette re-building failed.
Execution halted
installed size is 17.5Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    doc    4.2Mb
    libs  11.3Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    help   2.0Mb
    libs   1.1Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    R      1.9Mb
    doc    2.0Mb
    libs   1.0Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    doc    3.5Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.3/nbfar.Rcheck/00install.out' for details.
installed size is 15.7Mb
  sub-directories of 1Mb or more:
    libs  15.4Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc    2.5Mb
    libs   1.5Mb
installed size is 14.7Mb
  sub-directories of 1Mb or more:
    libs  13.9Mb
installed size is 27.6Mb
  sub-directories of 1Mb or more:
    CppCode   4.8Mb
    R         8.2Mb
    include  11.7Mb
    libs      1.2Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   2.6Mb
    mods   3.3Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   4.2Mb
    libs   1.0Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    doc    5.3Mb
    libs   1.6Mb
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    R      2.7Mb
    data   1.0Mb
    doc    1.7Mb
    help   3.1Mb
    libs   1.5Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   2.6Mb
    libs   1.2Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   4.6Mb
installed size is 16.5Mb
  sub-directories of 1Mb or more:
    R        2.6Mb
    data     1.4Mb
    libs     5.1Mb
    models   4.8Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   4.7Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    libs   1.7Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    extdata   2.1Mb
    libs      1.4Mb
Error(s) in re-building vignettes:
--- re-building 'OptimModel_vignette.Rmd' using rmarkdown

Quitting from lines 393-408 [unnamed-chunk-10] (OptimModel_vignette.Rmd)
Error: processing vignette 'OptimModel_vignette.Rmd' failed with diagnostics:
<text>:11:1: unexpected '<'
10: attr(f.model,"srcref") <- 
11: <
    ^
--- failed re-building 'OptimModel_vignette.Rmd'

SUMMARY: processing the following file failed:
  'OptimModel_vignette.Rmd'

Error: Vignette re-building failed.
Execution halted
posterior_epred_ordbeta_prep: no visible global function definition for
  '%||%'
Undefined global functions or variables:
  %||%
Running examples in 'ordbetareg-Ex.R' failed
The error most likely occurred in:

> ### Name: posterior_epred_ordbeta.brmsfit
> ### Title: Calculate Probability of Response Components
> ### Aliases: posterior_epred_ordbeta.brmsfit posterior_epred_ordbeta
> 
> ### ** Examples
> 
> 
> data('ord_fit_mean')
> 
> # use function to calculate probability of top end of scale
> 
> pr_1s <- posterior_epred_ordbeta(ord_fit_mean,component="top")
Error in incl_thres %||% FALSE : could not find function "%||%"
Calls: posterior_epred_ordbeta ... posterior_epred_ordbeta.brmsfit -> posterior_epred_ordbeta_prep -> as_one_logical
Execution halted
Error(s) in re-building vignettes:
--- re-building 'package_introduction.qmd' using html


processing file: package_introduction.qmd
Error in `incl_thres %||% FALSE`:
! could not find function "%||%"
Backtrace:
    ▆
 1. ├─... %>% hist
 2. ├─graphics::hist(.)
 3. ├─ordbetareg::posterior_epred_ordbeta(ord_fit_mean, component = "top")
 4. └─ordbetareg:::posterior_epred_ordbeta.brmsfit(ord_fit_mean, component = "top")
 5.   └─ordbetareg:::posterior_epred_ordbeta_prep(...)
 6.     └─ordbetareg:::as_one_logical(incl_thres %||% FALSE)



Quitting from lines 260-269 [posterior_epred_ordbeta] (package_introduction.qmd)
Execution halted
Error: processing vignette 'package_introduction.qmd' failed with diagnostics:
✖ Error running quarto cli.
Caused by error:
! System command 'quarto.exe' failed
--- failed re-building 'package_introduction.qmd'

SUMMARY: processing the following file failed:
  'package_introduction.qmd'

Error: Vignette re-building failed.
Execution halted
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc    5.0Mb
    libs   1.4Mb
installed size is 15.2Mb
  sub-directories of 1Mb or more:
    library  14.3Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc    3.1Mb
    libs   2.8Mb
Check process probably crashed or hung up for 20 minutes ... killed
Most likely this happened in the example checks (?),
if not, ignore the following last lines of example output:
> ### Aliases: ybp2date date2ybp
> 
> ### ** Examples
> 
> ybp2date(-10000)
[1] "-8050-01-01 UTC"
> ybp2date(0)
[1] "1950-01-01 UTC"
> # back and forth
> date2ybp(ybp2date(-10000))
[1] -10000
> 
> 
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()
> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
Time elapsed:  8.64 0.34 9 NA NA 
> grDevices::dev.off()
null device 
          1 
> ###
> ### Local variables: ***
> ### mode: outline-minor ***
> ### outline-regexp: "\\(> \\)?### [*]+" ***
> ### End: ***
> quit('no')
======== End of example output (where/before crash/hang up occured ?) ========
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    R      7.8Mb
    help   2.8Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    R      3.3Mb
    help   3.4Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    R      3.1Mb
    help   3.0Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    R      2.8Mb
    help   3.6Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    R      3.1Mb
    help   3.6Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    lib    2.8Mb
    libs   2.3Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    libs   1.5Mb
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    doc    2.9Mb
    libs   8.4Mb
installed size is 13.3Mb
  sub-directories of 1Mb or more:
    include  11.2Mb
    libs      1.8Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs   1.3Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc       1.5Mb
    extdata   3.1Mb
    libs      1.0Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   1.6Mb
    doc    2.1Mb
    libs   1.0Mb
Package suggested but not available for checking: 'pinnacle.API'
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    doc    2.1Mb
    libs   1.6Mb
Running examples in 'pollimetry-Ex.R' failed
The error most likely occurred in:

> ### Name: bodysize
> ### Title: Converts the intertegular distance (IT) and co-variates to body
> ###   size in dry weight (mg) for bees or hoverflies.
> ### Aliases: bodysize
> 
> ### ** Examples
> 
> example=cbind.data.frame(IT=c(1.3,2.3),
+                          Sex=c("Female","Male"), 
+                          Subfamily=c("Syrphinae","Eristalinae"),
+                          Region=c("Australasia","Europe"),
+                          Species=c("Sphaerophoria_macrogaster","Myathropa_florea"))
> bodysize(x=example,taxa="hov",type="taxo")
Loading required namespace: pollimetrydata
Failed with error:  'there is no package called 'pollimetrydata''
Downloading data from: https://github.com/liamkendall/pollimetrydata/raw/master/data/hov_tax_mod.rdata 

SHA-1 hash of the downloaded data file is:
8fabe989dfed6c91d8e5834ad224ff4865b76b7f
Loading required package: rstan
Loading required package: StanHeaders
Error: package or namespace load failed for 'rstan' in .doLoadActions(where, attach):
 error in load action .__A__.1 for package rstan: Rcpp::loadModule(module = "class_model_base", what = TRUE, env = ns, : Unable to load module "class_model_base": attempt to apply non-function
Error in .requirePackage(package) : 
  unable to find required package 'rstan'
Calls: bodysize ... .findInheritedMethods -> getClass -> getClassDef -> .requirePackage
Execution halted
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    R      6.5Mb
    data   4.6Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   2.6Mb
    doc    1.8Mb
    libs   1.0Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    extdata   2.8Mb
    libs      1.3Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc    3.6Mb
    libs   1.4Mb
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    doc    4.7Mb
    libs   1.7Mb
installed size is 15.0Mb
  sub-directories of 1Mb or more:
    libs  14.9Mb
installed size is 23.6Mb
  sub-directories of 1Mb or more:
    libs  15.0Mb
    proj   8.4Mb
Running examples in 'promor-Ex.R' failed
The error most likely occurred in:

> ### Name: impute_plot
> ### Title: Visualize the impact of imputation
> ### Aliases: impute_plot
> 
> ### ** Examples
> 
> 
> ## Generate a raw_df object with default settings. No technical replicates.
> raw_df <- create_df(
+   prot_groups = "https://raw.githubusercontent.com/caranathunge/promor_example_data/main/pg1.txt",
+   exp_design = "https://raw.githubusercontent.com/caranathunge/promor_example_data/main/ed1.txt"
+ )
Warning in scan(file = file, what = what, sep = sep, quote = quote, dec = dec,  :
  URL 'https://raw.githubusercontent.com/caranathunge/promor_example_data/main/pg1.txt': Timeout of 60 seconds was reached
Error in scan(file = file, what = what, sep = sep, quote = quote, dec = dec,  : 
  cannot read from connection
Calls: create_df -> read.csv -> read.table -> scan
Execution halted
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    doc        4.0Mb
    examples   2.6Mb
installed size is 26.5Mb
  sub-directories of 1Mb or more:
    libs  25.8Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc    4.4Mb
    libs   1.0Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    extdata   3.3Mb
    libs      2.9Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    extdata   3.0Mb
    libs      1.0Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
    libs   1.2Mb
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    doc    6.6Mb
    libs   1.1Mb
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    doc           5.3Mb
    htmlwidgets   1.8Mb
    libs          2.2Mb
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    htmlwidgets  10.0Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    doc       1.7Mb
    extdata   4.1Mb
    libs      1.4Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    R      3.1Mb
    libs   1.5Mb
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    data   4.6Mb
    etc    1.9Mb
    po     1.2Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data   3.9Mb
    libs   1.6Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   2.9Mb
    libs   1.3Mb
installed size is 12.6Mb
  sub-directories of 1Mb or more:
    libs  11.4Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.3/Rcplex.Rcheck/00install.out' for details.
installed size is 39.8Mb
  sub-directories of 1Mb or more:
    include  38.1Mb
    libs      1.4Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   3.8Mb
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    include   9.6Mb
    libs      1.2Mb
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    libs   8.3Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   1.8Mb
    libs   2.2Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    R      4.0Mb
    data   1.5Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc    3.3Mb
    libs   1.1Mb
installed size is 17.7Mb
  sub-directories of 1Mb or more:
    redengine  16.6Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc    3.5Mb
    libs   1.4Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.3/restfulr.Rcheck/00install.out' for details.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    include   2.4Mb
    libs      1.7Mb
    models    1.6Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.3/Rfast2.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.3/Rfast.Rcheck/00install.out' for details.
installed size is 13.1Mb
  sub-directories of 1Mb or more:
    data  13.1Mb
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    doc   6.9Mb
installed size is 13.8Mb
  sub-directories of 1Mb or more:
    doc     7.1Mb
    fonts   1.5Mb
    libs    2.7Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.3/Riemann.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.3/RiemBase.Rcheck/00install.out' for details.
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    lib    3.3Mb
    libs   4.1Mb
Note: information on .o files for x64 is not available
File 'd:/Rcompile/CRANpkg/lib/4.3/rJava/libs/x64/rJava.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    lemon   2.9Mb
    libs    2.1Mb
Error(s) in re-building vignettes:
--- re-building 'RLescalation.Rmd' using rmarkdown
File man/figures/logo.png not found in resource path
Error: processing vignette 'RLescalation.Rmd' failed with diagnostics:
pandoc document conversion failed with error 99
--- failed re-building 'RLescalation.Rmd'

SUMMARY: processing the following file failed:
  'RLescalation.Rmd'

Error: Vignette re-building failed.
Execution halted
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    libs  10.3Mb
installed size is 16.6Mb
  sub-directories of 1Mb or more:
    include   7.4Mb
    lib       3.0Mb
    libs      5.7Mb
Running examples in 'rllama-Ex.R' failed
The error most likely occurred in:

> ### Name: get_defillama_chain_hist_tvl
> ### Title: Chain History Data
> ### Aliases: get_defillama_chain_hist_tvl
> 
> ### ** Examples
> 
> # total tvl by date
> chain_tvl = get_defillama_chain_hist_tvl( "Ethereum" )
Error in curl::curl_fetch_memory(url, handle = handle) : 
  Timeout was reached [api.llama.fi]: SSL/TLS connection timeout
Calls: get_defillama_chain_hist_tvl ... request_fetch.write_memory -> <Anonymous> -> raise_libcurl_error
Execution halted
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    libs   8.8Mb
Error(s) in re-building vignettes:
--- re-building 'rnaCrosslinkOO.Rmd' using rmarkdown
File rnaCrosslinkProtocol.jpg not found in resource path
Error: processing vignette 'rnaCrosslinkOO.Rmd' failed with diagnostics:
pandoc document conversion failed with error 99
--- failed re-building 'rnaCrosslinkOO.Rmd'

SUMMARY: processing the following file failed:
  'rnaCrosslinkOO.Rmd'

Error: Vignette re-building failed.
Execution halted
installed size is 15.9Mb
  sub-directories of 1Mb or more:
    libs  15.6Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    extdata   2.0Mb
    libs      3.3Mb
Found the following significant warnings:
  d:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.3.0\include\emmintrin.h:134:24: warning: array subscript '__m128d_u[0]' is partly outside array bounds of 'Eigen::internal::plain_matrix_type<Eigen::Product<Eigen::Block<Eigen::Matrix<double, -1, -1>, 1, -1, false>, Eigen::Transpose<Eigen::Block<Eigen::Matrix<double, -1, -1>, 1, -1, false> >, 0>, Eigen::Dense>::type [1]' {aka 'Eigen::Matrix<double, 1, 1, 0, 1, 1> [1]'} [-Warray-bounds]
See 'd:/Rcompile/CRANpkg/local/4.3/RobustGaSP.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 12.3.0'
* used C++ compiler: 'g++.exe (GCC) 12.3.0'
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc               1.7Mb
    libs              1.3Mb
    simulationStudy   1.6Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    R         2.7Mb
    extdata   2.7Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.3/ROracle.Rcheck/00install.out' for details.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    data   2.7Mb
    libs   1.5Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    R      4.7Mb
    libs   1.7Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   1.4Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.3/Rpoppler.Rcheck/00install.out' for details.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   3.9Mb
installed size is 14.2Mb
  sub-directories of 1Mb or more:
    libs  13.7Mb
Error(s) in re-building vignettes:
--- re-building 'benchmarks.Rmd' using rmarkdown
--- finished re-building 'benchmarks.Rmd'

--- re-building 'research_workflows.Rmd' using rmarkdown
File figure/unnamed-chunk-7-1.png not found in resource path
Error: processing vignette 'research_workflows.Rmd' failed with diagnostics:
pandoc document conversion failed with error 99
--- failed re-building 'research_workflows.Rmd'

--- re-building 'rredlist.Rmd' using rmarkdown
--- finished re-building 'rredlist.Rmd'

SUMMARY: processing the following file failed:
  'research_workflows.Rmd'

Error: Vignette re-building failed.
Execution halted
installed size is 17.3Mb
  sub-directories of 1Mb or more:
    libs  16.3Mb
Note: information on .o files for x64 is not available
File 'd:/Rcompile/CRANpkg/lib/4.3/Rserve/libs/x64/Rserve.dll':
  Found '_exit', possibly from '_exit' (C)
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'rand', possibly from 'rand' (C)
  Found 'srand', possibly from 'srand' (C)
File 'Rserve/libs/x64/Rserve.dll':
  Found non-API calls to R: 'R_Interactive', 'R_Visible',
    'Rf_initialize_R', 'setup_Rmainloop'

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.
Compiled code should not call non-API entry points in R.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    R      3.9Mb
    help   1.5Mb
installed size is 18.9Mb
  sub-directories of 1Mb or more:
    R      1.9Mb
    doc    4.7Mb
    libs  11.6Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    exec   1.7Mb
    lib    1.9Mb
    libs   1.5Mb
installed size is 18.3Mb
  sub-directories of 1Mb or more:
    libs   2.4Mb
installed size is 19.1Mb
  sub-directories of 1Mb or more:
    libs  18.6Mb
installed size is 41.7Mb
  sub-directories of 1Mb or more:
    libs    1.1Mb
    swipl  40.5Mb
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    libs   7.7Mb
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    doc    7.8Mb
    libs   2.6Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    R      3.0Mb
    libs   1.1Mb
Found the following significant warnings:

  Warning: 'adonis' is deprecated.
  Warning: 'adonis' is deprecated.
  Warning: 'vegan::adonis' is deprecated.
  Warning: 'vegan::adonis' is deprecated.
  Warning: 'vegan::adonis' is deprecated.
  Warning: 'vegan::adonis' is deprecated.
  Warning: 'vegan::adonis' is deprecated.
  Warning: 'vegan::adonis' is deprecated.
  Warning: 'vegan::adonis' is deprecated.
  Warning: 'vegan::adonis' is deprecated.
  Warning: 'adonis' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    include   5.1Mb
    libs      5.3Mb
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    R         1.4Mb
    include   1.1Mb
    libs      4.8Mb
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    libs   7.3Mb
installed size is 15.4Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    libs  13.6Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc    3.9Mb
    libs   1.2Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   3.9Mb
    libs   1.2Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.3/scDHA.Rcheck/00install.out' for details.
installed size is 16.8Mb
  sub-directories of 1Mb or more:
    cppad     9.5Mb
    include   4.7Mb
    libs      2.0Mb
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    R   8.1Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    R      1.6Mb
    libs   2.1Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   4.7Mb
    libs   1.0Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc   5.1Mb
installed size is 107.6Mb
  sub-directories of 1Mb or more:
    doc      1.8Mb
    gdal     3.0Mb
    libs    89.8Mb
    proj     8.4Mb
    sqlite   1.5Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc    4.2Mb
    libs   1.4Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    extdata   1.0Mb
    help      1.7Mb
    libs      1.0Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.3/SIGN.Rcheck/00install.out' for details.
Found the following significant warnings:

  Warning: 'adonis' is deprecated.
  Warning: 'adonis' is deprecated.
  Warning: 'adonis' is deprecated.
  Warning: 'adonis' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Error(s) in re-building vignettes:
--- re-building 'sim.BA.Rmd' using rmarkdown
File images/dag.png not found in resource path
Error: processing vignette 'sim.BA.Rmd' failed with diagnostics:
pandoc document conversion failed with error 99
--- failed re-building 'sim.BA.Rmd'

SUMMARY: processing the following file failed:
  'sim.BA.Rmd'

Error: Vignette re-building failed.
Execution halted
installed size is 15.2Mb
  sub-directories of 1Mb or more:
    extdata  13.0Mb
    libs      1.5Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    R      2.2Mb
    libs   1.8Mb
Running 'testthat.R' [10s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(sjtable2df)
  > 
  > test_check("sjtable2df")
  boundary (singular) fit: see help('isSingular')
  boundary (singular) fit: see help('isSingular')
  boundary (singular) fit: see help('isSingular')
  boundary (singular) fit: see help('isSingular')
  [ FAIL 1 | WARN 5 | SKIP 5 | PASS 18 ]
  
  ══ Skipped tests (5) ═══════════════════════════════════════════════════════════
  • On CRAN (5): 'test-mtab2df.R:48:5', 'test-mtab2df.R:136:5',
    'test-xtab2df.R:36:5', 'test-xtab2df.R:206:5', 'test-xtab2df.R:253:5'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-mtab2df.R:134:5'): correct functioning of mtab2df: glmer ─────
  nrow(final_tab) == 10 is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  
  [ FAIL 1 | WARN 5 | SKIP 5 | PASS 18 ]
  Error: Test failures
  Execution halted
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
    libs   1.1Mb
Found the following significant warnings:

  Warning: 'vegan::adonis' is deprecated.
  Warning: 'vegan::adonis' is deprecated.
  Warning: 'vegan::adonis' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.3/SmartSVA.Rcheck/00install.out' for details.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   3.3Mb
    libs   1.1Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    doc    3.4Mb
    libs   1.7Mb
Check process probably crashed or hung up for 20 minutes ... killed
Most likely this happened in the example checks (?),
if not, ignore the following last lines of example output:
> cleanEx()
> nameEx("snvec")
> ### * snvec
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: snvec
> ### Title: Calculate Earth’s Obliquity and Precession in the Past
> ### Aliases: snvec
> 
> ### ** Examples
> 
> 
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()
> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
Time elapsed:  0.47 0.05 0.52 NA NA 
> grDevices::dev.off()
null device 
          1 
> ###
> ### Local variables: ***
> ### mode: outline-minor ***
> ### outline-regexp: "\\(> \\)?### [*]+" ***
> ### End: ***
> quit('no')
======== End of example output (where/before crash/hang up occured ?) ========
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R     3.3Mb
    doc   1.1Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    doc    1.3Mb
    libs   1.7Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   4.7Mb
    libs   1.1Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    extdata   6.0Mb
    libs      1.1Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    R   4.8Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    R      2.8Mb
    libs   1.9Mb
S3 methods shown with full name in documentation object 'SparseM.ontology':
  'as.matrix.csr' 'is.matrix.csr' 'is.matrix.csc' 'is.matrix.ssr'
  'is.matrix.ssc' 'is.matrix.coo'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
installed size is 14.6Mb
  sub-directories of 1Mb or more:
    libs  13.7Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   2.6Mb
    help   1.7Mb
    libs   1.1Mb
Running 'testthat.R' [5s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(spectralGraphTopology)
  
  Attaching package: 'spectralGraphTopology'
  
  The following object is masked from 'package:stats':
  
      D
  
  > 
  > test_check("spectralGraphTopology")
  [ FAIL 3 | WARN 0 | SKIP 0 | PASS 43 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-learnGraphTopology.R:21:1'): (code run outside of `test_that()`) ──
  <purrr_error_indexed/rlang_error/error/condition>
  Error in `purrr::pmap(all_pars, build_and_run_test, desc = desc_stub, code = captured, 
      .interpret_glue = .interpret_glue)`: ℹ In index: 1.
  Caused by error:
  ! Failed to parse glue component
  Caused by error in `parse()`:
  ! <text>:1:1: unexpected ','
  1: ,
      ^
  ── Error ('test-learnSmoothSignalGraph.R:9:1'): (code run outside of `test_that()`) ──
  <purrr_error_indexed/rlang_error/error/condition>
  Error in `purrr::pmap(all_pars, build_and_run_test, desc = desc_stub, code = captured, 
      .interpret_glue = .interpret_glue)`: ℹ In index: 1.
  Caused by error:
  ! Failed to parse glue component
  Caused by error in `parse()`:
  ! <text>:1:1: unexpected ','
  1: ,
      ^
  ── Error ('test-operators.R:122:1'): (code run outside of `test_that()`) ───────
  <purrr_error_indexed/rlang_error/error/condition>
  Error in `purrr::pmap(all_pars, build_and_run_test, desc = desc_stub, code = captured, 
      .interpret_glue = .interpret_glue)`: ℹ In index: 1.
  Caused by error:
  ! Failed to parse glue component
  Caused by error in `parse()`:
  ! <text>:1:1: unexpected ','
  1: ,
      ^
  
  [ FAIL 3 | WARN 0 | SKIP 0 | PASS 43 ]
  Error: Test failures
  Execution halted
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    data   1.8Mb
    doc    1.5Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc       1.1Mb
    extdata   2.6Mb
    libs      1.7Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    R      1.9Mb
    libs   1.8Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    libs   1.4Mb
installed size is 14.6Mb
  sub-directories of 1Mb or more:
    libs  13.5Mb
Error(s) in re-building vignettes:
--- re-building 'stmVignette.Rnw' using Sweave
stm v1.3.7 successfully loaded. See ?stm for help. 
 Papers, resources, and other materials at structuraltopicmodel.com
Warning in load(url("https://github.com/bstewart/stm/blob/gh-pages/files/VignetteObjects.RData?raw=true")) :
  URL 'https://raw.githubusercontent.com/bstewart/stm/refs/heads/gh-pages/files/VignetteObjects.RData': Timeout of 60 seconds was reached

Error: processing vignette 'stmVignette.Rnw' failed with diagnostics:
 chunk 7 
Error in load(url("https://github.com/bstewart/stm/blob/gh-pages/files/VignetteObjects.RData?raw=true")) : 
  cannot read from connection

--- failed re-building 'stmVignette.Rnw'

SUMMARY: processing the following file failed:
  'stmVignette.Rnw'

Error: Vignette re-building failed.
Execution halted
installed size is 14.7Mb
  sub-directories of 1Mb or more:
    joss_paper   1.2Mb
    libs        12.7Mb
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    libs   9.3Mb
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    doc    7.1Mb
    libs   1.1Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    doc    3.1Mb
    help   1.0Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    lib    2.8Mb
    libs   1.6Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   4.3Mb
    libs   1.4Mb
Running examples in 'teal.modules.general-Ex.R' failed
The error most likely occurred in:

> ### Name: tm_a_pca
> ### Title: 'teal' module: Principal component analysis
> ### Aliases: tm_a_pca
> 
> ### ** Examples
> 
> library(teal.widgets)
> 
> # general data example
> data <- teal_data()
> data <- within(data, {
+   require(nestcolor)
+   USArrests <- USArrests
+ })
> 
> datanames(data) <- "USArrests"
Warning: `datanames<-()` was deprecated in teal.data 0.7.0.
ℹ invalid to use `datanames()<-` or `names()<-` on an object of class
  `teal_data`. See ?names.teal_data
> 
> app <- init(
+   data = data,
+   modules = modules(
+     tm_a_pca(
+       "PCA",
+       dat = data_extract_spec(
+         dataname = "USArrests",
+         select = select_spec(
+           choices = variable_choices(
+             data = data[["USArrests"]], c("Murder", "Assault", "UrbanPop", "Rape")
+           ),
+           selected = c("Murder", "Assault"),
+           multiple = TRUE
+         ),
+         filter = NULL
+       ),
+       ggplot2_args = ggplot2_args(
+         labs = list(subtitle = "Plot generated by PCA Module")
+       )
+     )
+   )
+ )
[INFO] 2025-02-14 08:17:48.8266 pid:56656 token:[] teal.modules.general Initializing tm_a_pca
Error in as.list(data@env) : 
  no slot of name "env" for this object of class "teal_data"
Calls: init -> create_app_id -> as.list
Execution halted
installed size is 108.2Mb
  sub-directories of 1Mb or more:
    R      2.4Mb
    gdal   3.0Mb
    libs  92.9Mb
    proj   8.4Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    R      4.1Mb
    data   3.0Mb
Error(s) in re-building vignettes:
--- re-building 'creating_prompt_wraps.Rmd' using rmarkdown
--- finished re-building 'creating_prompt_wraps.Rmd'

--- re-building 'getting_started.Rmd' using rmarkdown
File ../man/figures/answer_using_r1-1.png not found in resource path
Error: processing vignette 'getting_started.Rmd' failed with diagnostics:
pandoc document conversion failed with error 99
--- failed re-building 'getting_started.Rmd'

--- re-building 'sentiment_analysis.Rmd' using rmarkdown
File ../man/figures/plot_sentiment_analysis-1.png not found in resource path
Error: processing vignette 'sentiment_analysis.Rmd' failed with diagnostics:
pandoc document conversion failed with error 99
--- failed re-building 'sentiment_analysis.Rmd'

SUMMARY: processing the following files failed:
  'getting_started.Rmd' 'sentiment_analysis.Rmd'

Error: Vignette re-building failed.
Execution halted
Running 'testthat.R' [25s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(tidystats)
  This version of tidystats uses a new and improved way of structuring statistics. This breaks previous (major) versions of tidystats.
  > 
  > test_check("tidystats")
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 183 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test_glm.R:118:3'): glm anova works ───────────────────────────────
  `tidy_model` not equal to `expected_tidy_model`.
  Component "groups": Component 1: Component 2: Component 2: Component 2: Length mismatch: comparison on first 4 components
  Component "groups": Component 1: Component 2: Component 3: Component 2: Length mismatch: comparison on first 4 components
  Backtrace:
      ▆
   1. └─tidystats:::expect_equal_models(model = model, expected_tidy_model = expected_statistics$anova_glm) at test_glm.R:118:3
   2.   └─testthat::expect_equal(tidy_model, expected_tidy_model, tolerance = tolerance)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 183 ]
  Error: Test failures
  Execution halted
Found the following significant warnings:
  Warning: type_boxplot.Rd:35: unknown macro '\abbr'
See 'd:/Rcompile/CRANpkg/local/4.3/tinyplot.Rcheck/00install.out' for details.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   5.1Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   3.1Mb
Found the following significant warnings:
  D:/RCompile/recent/R-4.3.3/Tcl/include/X11/Xlib.h:131:9: warning: function declaration isn't a prototype [-Wstrict-prototypes]
  D:/RCompile/recent/R-4.3.3/Tcl/include/X11/Xlib.h:334:16: warning: function declaration isn't a prototype [-Wstrict-prototypes]
  D:/RCompile/recent/R-4.3.3/Tcl/include/X11/Xlib.h:453:9: warning: function declaration isn't a prototype [-Wstrict-prototypes]
  D:/RCompile/recent/R-4.3.3/Tcl/include/X11/Xlib.h:471:9: warning: function declaration isn't a prototype [-Wstrict-prototypes]
  D:/RCompile/recent/R-4.3.3/Tcl/include/X11/Xlib.h:496:9: warning: function declaration isn't a prototype [-Wstrict-prototypes]
  D:/RCompile/recent/R-4.3.3/Tcl/include/X11/Xlib.h:497:9: warning: function declaration isn't a prototype [-Wstrict-prototypes]
  D:/RCompile/recent/R-4.3.3/Tcl/include/X11/Xlib.h:509:9: warning: function declaration isn't a prototype [-Wstrict-prototypes]
  D:/RCompile/recent/R-4.3.3/Tcl/include/X11/Xlib.h:522:9: warning: function declaration isn't a prototype [-Wstrict-prototypes]
  D:/RCompile/recent/R-4.3.3/Tcl/include/X11/Xlib.h:1053:1: warning: function declaration isn't a prototype [-Wstrict-prototypes]
  tcltkimg.c:93:1: warning: function declaration isn't a prototype [-Wstrict-prototypes]
  tcltkimg.c:94:1: warning: function declaration isn't a prototype [-Wstrict-prototypes]
See 'd:/Rcompile/CRANpkg/local/4.3/tkrplot.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 12.3.0'
installed size is 17.0Mb
  sub-directories of 1Mb or more:
    examples  12.7Mb
    include    3.6Mb
Packages suggested but not available for checking:
  'Rcampdf', 'Rpoppler', 'tm.lexicon.GeneralInquirer'
installed size is 28.4Mb
  sub-directories of 1Mb or more:
    R         5.9Mb
    help      1.7Mb
    include   1.9Mb
    libs     18.3Mb
installed size is 16.3Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    libs  13.4Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc    4.9Mb
    libs   1.3Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    datasets   1.6Mb
    doc        1.3Mb
    libs       1.1Mb
installed size is 14.7Mb
  sub-directories of 1Mb or more:
    libs  14.1Mb
installed size is 21.5Mb
  sub-directories of 1Mb or more:
    libs  20.4Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    data   4.6Mb
    libs   1.2Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc         1.4Mb
    dummydata   1.4Mb
    libs        2.6Mb
installed size is 18.9Mb
  sub-directories of 1Mb or more:
    R      1.7Mb
    doc    1.3Mb
    libs  14.9Mb
Found the following significant warnings:
  randutils.c:60:12: warning: function declaration isn't a prototype [-Wstrict-prototypes]
See 'd:/Rcompile/CRANpkg/local/4.3/uuid.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 12.3.0'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.3/V8.Rcheck/00install.out' for details.
installed size is 104.5Mb
  sub-directories of 1Mb or more:
    extdata   2.8Mb
    gdal      3.0Mb
    libs     88.9Mb
    proj      8.4Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.3/vctrs.Rcheck/00install.out' for details.
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    R      4.3Mb
    help   3.1Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    2.7Mb
    libs   1.1Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs   5.2Mb
Found the following significant warnings:
  Warning: replacing previous import 'hardhat::contr_one_hot' by 'parsnip::contr_one_hot' when loading 'viralmodels'
See 'd:/Rcompile/CRANpkg/local/4.3/viralmodels.Rcheck/00install.out' for details.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   5.8Mb
installed size is 21.8Mb
  sub-directories of 1Mb or more:
    extdata   1.6Mb
    libs     19.9Mb
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    doc    6.6Mb
    libs   1.0Mb
Error(s) in re-building vignettes:
--- re-building 'use_case.Rmd' using rmarkdown
--- finished re-building 'use_case.Rmd'

--- re-building 'weatherOz.Rmd' using rmarkdown_notangle
--- finished re-building 'weatherOz.Rmd'

--- re-building 'weatherOz_for_BOM.Rmd' using rmarkdown_notangle
--- finished re-building 'weatherOz_for_BOM.Rmd'

--- re-building 'weatherOz_for_DPIRD.Rmd' using rmarkdown_notangle
File vignettes/view_sw_ag_region-1.png not found in resource path
Error: processing vignette 'weatherOz_for_DPIRD.Rmd' failed with diagnostics:
pandoc document conversion failed with error 99
--- failed re-building 'weatherOz_for_DPIRD.Rmd'

--- re-building 'weatherOz_for_SILO.Rmd' using rmarkdown_notangle
--- finished re-building 'weatherOz_for_SILO.Rmd'

SUMMARY: processing the following file failed:
  'weatherOz_for_DPIRD.Rmd'

Error: Vignette re-building failed.
Execution halted
combine_filters : <anonymous>: no visible global function definition
  for '%||%'
Undefined global functions or variables:
  %||%
Error(s) in re-building vignettes:
--- re-building 'WindCurves_Info.Rmd' using rmarkdown

Quitting from lines 66-77 [unnamed-chunk-3] (WindCurves_Info.Rmd)
Error: processing vignette 'WindCurves_Info.Rmd' failed with diagnostics:
dumpdata.R:2:1: unexpected '<'
1: random <-
2: <
   ^
--- failed re-building 'WindCurves_Info.Rmd'

SUMMARY: processing the following file failed:
  'WindCurves_Info.Rmd'

Error: Vignette re-building failed.
Execution halted
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
    libs   1.1Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    help   1.9Mb
    libs   1.0Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    bin   5.6Mb
Found the following significant warnings:
  DocParse.c:1334:5: warning: 'xmlKeepBlanksDefault' is deprecated [-Wdeprecated-declarations]
  RSDTD.c:134:7: warning: 'xmlSkipBlankChars' is deprecated [-Wdeprecated-declarations]
  RSDTD.c:135:7: warning: 'xmlParseMarkupDecl' is deprecated [-Wdeprecated-declarations]
  RUtils.c:142:5: warning: 'xmlSubstituteEntitiesDefault' is deprecated [-Wdeprecated-declarations]
See 'd:/Rcompile/CRANpkg/local/4.3/XML.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 12.3.0'
Running examples in 'Xplortext-Ex.R' failed
The error most likely occurred in:

> ### Name: plot.LexChar
> ### Title: Plot LexChar objects
> ### Aliases: plot.LexChar
> ### Keywords: plot
> 
> ### ** Examples
> 
> data(open.question)
> res.TD<-TextData(open.question, var.text=c(9,10), var.agg="Gen_Edu", Fmin=10, Dmin=10,
+         remov.number=TRUE, stop.word.tm=TRUE)
> LD<-LexChar(res.TD,maxCharDoc = 0)
> plot(LD)
Error in `gtable_add_grob()`:
! `grobs` must be a single grob or a list of grobs, not a list.
Backtrace:
     ▆
  1. ├─base::plot(LD)
  2. └─Xplortext:::plot.LexChar(LD)
  3.   ├─base::suppressWarnings(...)
  4.   │ └─base::withCallingHandlers(...)
  5.   └─Xplortext (local) marrangeGrob2(grobs = pword, nrow = numr, ncol = numc, top = top)
  6.     ├─base::do.call(gridExtra::arrangeGrob, c(grobs[groups[[g]]], params))
  7.     └─gridExtra (local) `<fn>`(...)
  8.       └─gtable::gtable_add_grob(grobs = grobs)
  9.         └─gtable:::stop_input_type(grobs, "a single grob or a list of grobs")
 10.           └─rlang::abort(message, ..., call = call, arg = arg)
Execution halted