installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc       1.5Mb
    extdata   1.1Mb
    libs      1.6Mb
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'

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

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

Error: Vignette re-building failed.
Execution halted
Error loading dataset 'lacerta_ensemble':
   Error in xgb.get.handle(model) : 
    'xgb.Booster' object is corrupted or is from an incompatible XGBoost version.
Running examples in 'tidysdm-Ex.R' failed
The error most likely occurred in:

> ### Name: make_mask_from_presence
> ### Title: Make a mask from presence data
> ### Aliases: make_mask_from_presence
> 
> ### ** Examples
> 
> lacerta_sf <- lacerta %>%
+   sf::st_as_sf(coords = c("longitude", "latitude")) %>%
+   sf::st_set_crs(4326)
> land_mask <- terra::readRDS(system.file("extdata/lacerta_land_mask.rds",
+   package = "tidysdm"
+ ))
Warning: PROJ: proj_create_from_database: Cannot find proj.db (GDAL error 1)
Error: [rast] empty srs
Execution halted
Packages suggested but not available for checking: 'umx', 'OpenMx'
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc   5.4Mb
'LazyData' is specified without a 'data' directory
Running examples in 'tidyterra-Ex.R' failed
The error most likely occurred in:

> ### Name: as_spatraster
> ### Title: Coerce a data frame to 'SpatRaster'
> ### Aliases: as_spatraster
> 
> ### ** Examples
> 
> library(terra)
terra 1.8.86
> 
> r <- rast(matrix(1:90, ncol = 3), crs = "EPSG:3857")
Warning: PROJ: proj_create_from_database: Cannot find proj.db (GDAL error 1)
Error: [rast] empty srs
Execution halted
Package suggested but not available for checking: 'rrelaxiv'
installed size is 26.1Mb
  sub-directories of 1Mb or more:
    libs    22.2Mb
    tiledb   1.4Mb
checkRd: (-1) compare.Rd:46: Escaped LaTeX specials: \&
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
checkRd: (-1) setup_sql_functions.Rd:5: Lost braces; missing escapes or markup?
     5 | \title{Install {timeseriesdb} System Functions}
       |                ^
checkRd: (-1) setup_sql_functions.Rd:17: Lost braces; missing escapes or markup?
    17 | Installs functions needed to operated {timeseriesdb} in
       |                                       ^
checkRd: (-1) setup_sql_grant_rights.Rd:5: Lost braces; missing escapes or markup?
     5 | \title{Grant execute on {timeseriesdb} functions}
       |                         ^
checkRd: (-1) setup_sql_grant_rights.Rd:17: Lost braces; missing escapes or markup?
    17 | Grant execute on {timeseriesdb} functions
       |                  ^
checkRd: (-1) setup_sql_tables.Rd:5: Lost braces; missing escapes or markup?
     5 | \title{Install {timeseriesdb} System Tables}
       |                ^
checkRd: (-1) setup_sql_tables.Rd:17: Lost braces; missing escapes or markup?
    17 | Installs tables needed to operated {timeseriesdb} in
       |                                    ^
checkRd: (-1) setup_sql_triggers.Rd:5: Lost braces; missing escapes or markup?
     5 | \title{Install {timeseriesdb} Triggers}
       |                ^
checkRd: (-1) alcohol.Rd:16-18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) alcohol.Rd:19-21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) alcohol.Rd:22-26: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
Running 'testthat.R' [3s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(tinyProject)
  > 
  > test_check("tinyProject")
  Saving _problems/test-commandArgs-41.R
  [ FAIL 1 | WARN 5 | SKIP 0 | PASS 73 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-commandArgs.R:3:1'): (code run outside of `test_that()`) ───────
  <lifecycle_error_deprecated/defunctError/rlang_error/error/condition>
  Error: `with_mock()` was deprecated in testthat 3.2.0 and is now defunct.
  ℹ Please use `with_mocked_bindings()` instead.
  Backtrace:
      ▆
   1. └─testthat::with_mock(...) at test-commandArgs.R:3:1
   2.   └─lifecycle::deprecate_stop("3.2.0", "with_mock()", "with_mocked_bindings()")
   3.     └─lifecycle:::deprecate_stop0(msg)
   4.       └─rlang::cnd_signal(...)
  
  [ FAIL 1 | WARN 5 | SKIP 0 | PASS 73 ]
  Error:
  ! Test failures.
  Execution halted
'LazyData' is specified without a 'data' directory
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    data   2.2Mb
    help   1.1Mb
    libs   4.0Mb
Specified C++14: please drop specification unless essential
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   5.1Mb
'LazyData' is specified without a 'data' directory
checkRd: (-1) partition_undirected_graph.Rd:20: Lost braces; missing escapes or markup?
    20 | \item{cutoff}{Numeric. The value max(0, g_{i,j} - cutoff) so that there are <\code{.num_components}> components in the graph.}
       |                                           ^
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   3.0Mb
GNU make is a SystemRequirements.
checkRd: (-1) tierChart.Rd:332: Lost braces
   332 |   If the input argument code{boxes} is \code{F}, the \code{lBox},
       |                             ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
checkRd: (-1) pmvn.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pmvn.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pmvn.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pmvt.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pmvt.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pmvt.Rd:25: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
installed size is 16.9Mb
  sub-directories of 1Mb or more:
    examples  12.6Mb
    include    3.6Mb
GNU make is a SystemRequirements.
checkRd: (-1) tv_episode_changes.Rd:29: Lost braces; missing escapes or markup?
    29 | This method is used in conjunction with the /tv/{id}/changes method. This method uses the episode_id value found in the change entries.
       |                                                 ^
checkRd: (-1) tv_season_changes.Rd:29: Lost braces; missing escapes or markup?
    29 | This method is used in conjunction with the /tv/{id}/changes method. This method uses the season_id value found in the change entries.
       |                                                 ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) pvalEffectPlot.Rd:90: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pvalEffectPlot.Rd:91: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pvalEffectPlot.Rd:92: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pvalEffectPlot.Rd:93: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pvalEffectPlot.Rd:94: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'Rcampdf', 'tm.lexicon.GeneralInquirer'
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  Warning: namespace 'seqHMM' is not available and has been replaced
See 'd:/Rcompile/CRANpkg/local/4.4/tna.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   4.3Mb
checkRd: (-1) jsonStr.Rd:5: Lost braces; missing escapes or markup?
     5 | \title{Format data as a JSON object (like this: {"x": "120"}).}
       |                                                 ^
checkRd: (-1) jsonStr.Rd:18: Lost braces; missing escapes or markup?
    18 | Format data as a JSON object (like this: {"x": "120"}).
       |                                          ^
checkRd: (-1) fixed_width_no_modeling.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) fixed_width_no_modeling.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) fixed_width_no_modeling.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
checkRd: (-1) TopDom.Rd:21: Lost braces; missing escapes or markup?
    21 | Recommended range is in {5, ..., 20}.}
       |                         ^
checkRd: (-1) getSegsExtra.Rd:14: Lost braces
    14 | \item{data}{data.table returned from function /code{tdtr}}
       |                                                    ^
Packages suggested but not available for checking:
  'RGtk2', 'gWidgets2RGtk2'
Package suggested but not available for checking: 'gurobi'
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    data   7.2Mb
installed size is 19.2Mb
  sub-directories of 1Mb or more:
    R         5.9Mb
    help      1.8Mb
    include   1.9Mb
    libs      9.3Mb
Package suggested but not available for checking: 'toscaData'
Problems with news in 'NEWS.md':
No news entries found.
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    data  12.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) parse_beast_output_files.Rd:23: Lost braces
    23 |     item{\code{estimates}: parameter estimates}
       |         ^
checkRd: (-1) parse_beast_output_files.Rd:24-28: Lost braces
    24 |     item{
       |         ^
checkRd: (-1) parse_beast_output_files.Rd:29-31: Lost braces
    29 |     item{\code{operators}: the BEAST2 MCMC operator
       |         ^
checkRd: (-1) parse_beast_posterior.Rd:28: Lost braces
    28 |     item{\code{estimates}: parameter estimates}
       |         ^
checkRd: (-1) parse_beast_posterior.Rd:29-33: Lost braces
    29 |     item{
       |         ^
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   2.2Mb
    doc    2.6Mb
'LazyData' is specified without a 'data' directory
train.xgboost: warning in xgb.train(params = params, data = train_aux,
  eval_metric = "mlogloss", nrounds = nrounds, watchlist = watchlist,
  obj = obj, feval = feval, verbose = verbose, print_every_n =
  print_every_n, early_stopping_rounds = early_stopping_rounds,
  maximize = maximize, save_period = save_period, save_name =
  save_name, xgb_model = xgb_model, callbacks = callbacks, ... = ...):
  partial argument match of 'obj' to 'objective'
train.xgboost: warning in xgb.train(params = params, data = train_aux,
  nrounds = nrounds, watchlist = watchlist, obj = obj, feval = feval,
  verbose = verbose, print_every_n = print_every_n,
  early_stopping_rounds = early_stopping_rounds, maximize = maximize,
  save_period = save_period, save_name = save_name, xgb_model =
  xgb_model, callbacks = callbacks, ... = ...): partial argument match
  of 'obj' to 'objective'
checkRd: (-1) trait_missing.Rd:17-18: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) trait_missing.Rd:19-20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) trait_missing.Rd:21-22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) trait_missing.Rd:23-24: Lost braces in \itemize; \value handles \item{}{} directly
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
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Packages suggested but not available for checking: 'fwelnet', 'doMC'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    doc   5.0Mb
checkRd: (-1) trtsel.Rd:69: Lost braces; missing escapes or markup?
    69 | numeric with two values {0,1} and gaussian(link = "identity") otherwise.
       |                         ^
Package suggested but not available for checking: 'TreeDistData'
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    datasets   1.6Mb
    doc        1.3Mb
    libs       1.1Mb
installed size is 17.6Mb
  sub-directories of 1Mb or more:
    data      1.2Mb
    doc       1.3Mb
    extdata  14.8Mb
Problems with news in 'NEWS.md':
No news entries found.
installed size is 12.3Mb
  sub-directories of 1Mb or more:
    doc    3.9Mb
    libs   7.3Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'rrelaxiv', 'gurobi'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) summary.armasubsets.Rd:16: Lost braces
    16 | \item{matrix.logical}{With matrix=TRUE, the matrix is logical TRUE/FALSE or string "*"/code{" "}}
       |                                                                                            ^
checkRd: (-1) tsBSS-package.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tsBSS-package.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tsBSS-package.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tsBSS-package.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tsBSS-package.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tsBSS-package.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tsBSS-package.Rd:34: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) TempDisaggDGP.Rd:79: Escaped LaTeX specials: \&
checkRd: (-1) disaggregate.Rd:56: Escaped LaTeX specials: \&
checkRd: (-1) example.database2.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) example.database2.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) example.database3.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) example.database3.Rd:19: Lost braces in \itemize; meant \describe ?
installed size is 14.6Mb
  sub-directories of 1Mb or more:
    libs  13.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 21.3Mb
  sub-directories of 1Mb or more:
    libs  20.2Mb
'LazyData' is specified without a 'data' directory
installed size is 16.0Mb
  sub-directories of 1Mb or more:
    libs  14.3Mb
GNU make is a SystemRequirements.
Error(s) in re-building vignettes:
--- re-building 'feasible_multivariate_garch.Rmd' using rmarkdown
--- finished re-building 'feasible_multivariate_garch.Rmd'

--- re-building 'tsmarch_demo.Rmd' using rmarkdown
SUMMARY: processing the following file failed:
  'tsmarch_demo.Rmd'

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    data   4.6Mb
    libs   1.1Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
'LazyData' is specified without a 'data' directory
checkRd: (-1) repr_dwt.Rd:28: Lost braces; missing escapes or markup?
    28 | The final representation has length equal to floor(n / 2^{level}), where n is a length of original time series.
       |                                                          ^
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
ps.fast: warning in xgboost(data = sparse.data, label = data[,
  treat.var], params = params, tree_method = tree_method, feval =
  pred.xgboost, nrounds = n.trees, verbose = verbose, weight = sampW,
  callbacks = callback.list): partial argument match of 'weight' to
  'weights'
checkRd: (-1) tweedie-internal.Rd:74: Lost braces
    74 |         doi{10.1093/biomet/74.2.221}
       |            ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) twosigmag.Rd:83: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) twosigmag.Rd:84: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) twosigmag.Rd:85: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) twosigmag.Rd:86: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) twosigmag.Rd:87: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) twosigmag.Rd:88: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) twosigmag.Rd:89: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) twosigmag.Rd:90: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) twosigmag.Rd:91: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) twosigmag.Rd:92: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) twosigmag.Rd:94: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) twosigmag.Rd:95: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) twosigmag.Rd:96: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) twoway.Rd:66: Lost braces
    66 | code{\link{twoway.formula}}, code{\link[stats]{medpolish}}
       |     ^
checkRd: (-1) twoway.Rd:66: Lost braces
    66 | code{\link{twoway.formula}}, code{\link[stats]{medpolish}}
       |                                  ^
Package which this enhances but not available for checking: 'sl3'
checkRd: (-1) est_g_exp.Rd:55: Lost braces; missing escapes or markup?
    55 |  {A - delta}, {A + delta}, and {A + 2 * delta}).
       |  ^
checkRd: (-1) est_g_exp.Rd:55: Lost braces; missing escapes or markup?
    55 |  {A - delta}, {A + delta}, and {A + 2 * delta}).
       |               ^
checkRd: (-1) est_g_exp.Rd:55: Lost braces; missing escapes or markup?
    55 |  {A - delta}, {A + delta}, and {A + 2 * delta}).
       |                                ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
checkRd: (-1) cambodia.Rd:47: Lost braces
    47 | (\doi{10.1371/journal.pmed.1000253}{10.1371/journal.pmed.1000253})
       |                                    ^
checkRd: (-1) microdata.Rd:33: Lost braces
    33 | (\doi{10.1371/journal.pmed.1000253}{10.1371/journal.pmed.1000253})
       |                                    ^
checkRd: (-1) u5mr_cohort.Rd:111: Lost braces
   111 | (\doi{10.1371/journal.pmed.1000253}{10.1371/journal.pmed.1000253})
       |                                    ^
Problems with news in 'NEWS.md':
No news entries found.
Error(s) in re-building vignettes:
--- re-building 'neun_euro_ticket_demonstrator.Rmd' using rmarkdown
--- finished re-building 'neun_euro_ticket_demonstrator.Rmd'

--- re-building 'user_sample_1.Rmd' using rmarkdown
File figure/plot_counter_1-1.png not found in resource path
Error: processing vignette 'user_sample_1.Rmd' failed with diagnostics:
pandoc document conversion failed with error 99
--- failed re-building 'user_sample_1.Rmd'

--- re-building 'user_sample_2.Rmd' using rmarkdown
--- finished re-building 'user_sample_2.Rmd'

--- re-building 'user_sample_3.Rmd' using rmarkdown
File figure/bias_plot-1.png not found in resource path
Error: processing vignette 'user_sample_3.Rmd' failed with diagnostics:
pandoc document conversion failed with error 99
--- failed re-building 'user_sample_3.Rmd'

SUMMARY: processing the following files failed:
  'user_sample_1.Rmd' 'user_sample_3.Rmd'

Error: Vignette re-building failed.
Execution halted
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc     4.5Mb
    ubinc   2.0Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    doc    1.1Mb
    libs   4.4Mb
GNU make is a SystemRequirements.
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    doc        1.3Mb
    shinyapp   5.6Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    doc         1.3Mb
    dummydata   1.4Mb
    libs        2.5Mb
Package suggested but not available for checking: 'MBESS'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
Package required but not available: 'OpenMx'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running 'testthat.R' [12s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(unifir)
  > Sys.setenv("unifir_debugmode" = "true")
  > test_check("unifir")
  Starting 2 test processes.
  Saving _problems/test-associate_coordinates-11.R
  [ FAIL 1 | WARN 1 | SKIP 6 | PASS 189 ]
  
  ══ Skipped tests (6) ═══════════════════════════════════════════════════════════
  • On CRAN (6): 'test-add_default_tree.R:2:3', 'test-add_default_tree.R:87:3',
    'test-add_player.R:2:3', 'test-add_player.R:86:3', 'test-get_asset.R:2:3',
    'test-not_on_ci.R:3:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-associate_coordinates.R:8:3'): associate_coordinates is stable ──
  Error in `h(simpleError(msg, call))`: error in evaluating the argument 'x' in selecting a method for function 'crs': error in evaluating the argument 'x' in selecting a method for function 'rast': [rast] empty srs
  Backtrace:
       ▆
    1. ├─unifir::associate_coordinates(...) at test-associate_coordinates.R:8:3
    2. │ ├─terra::crs(terra::rast(raster))
    3. │ └─terra::rast(raster)
    4. ├─terra::rast(matrix(data = rep(1, 100), nrow = 10), crs = "EPSG:5071")
    5. ├─terra::rast(matrix(data = rep(1, 100), nrow = 10), crs = "EPSG:5071")
    6. │ └─terra (local) .local(x, ...)
    7. │   ├─terra::rast(...)
    8. │   └─terra::rast(...)
    9. │     └─terra (local) .local(x = x, ...)
   10. │       └─terra:::new_rast(...)
   11. │         └─terra:::messages(r, "rast")
   12. │           └─terra:::error(f, x@pntr$getError())
   13. │             └─base::stop("[", f, "] ", emsg, ..., call. = FALSE)
   14. ├─base::.handleSimpleError(`<fn>`, "[rast] empty srs", base::quote(NULL))
   15. │ └─base (local) h(simpleError(msg, call))
   16. └─base::.handleSimpleError(...)
   17.   └─base (local) h(simpleError(msg, call))
  
  [ FAIL 1 | WARN 1 | SKIP 6 | PASS 189 ]
  Error:
  ! Test failures.
  Execution halted
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    libs   9.9Mb
checkRd: (-1) reg_1d.Rd:42: Lost braces; missing escapes or markup?
    42 |         \item Metric input is not in {1,2,3}: Metric does not exist
       |                                      ^
checkRd: (-1) reg_2d.Rd:33: Lost braces; missing escapes or markup?
    33 |         \item Metric input is not in {1,2,3}: Metric does not exist
       |                                      ^
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) simRedCard.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simRedCard.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 18.8Mb
  sub-directories of 1Mb or more:
    R      1.6Mb
    doc    1.4Mb
    libs  14.9Mb
GNU make is a SystemRequirements.
checkRd: (-1) UNPaC_Copula.Rd:59: Lost braces; missing escapes or markup?
    59 | \item{\code{selected_features}}: {A vector of integers indicating the features retained by the feature filtering process.}
       |                                  ^
checkRd: (-1) UNPaC_Copula.Rd:60: Lost braces; missing escapes or markup?
    60 | \item{\code{sim_CI}}: {vector containing the cluster indices for each generated unimodal reference distribution}
       |                       ^
checkRd: (-1) UNPaC_Copula.Rd:61-62: Lost braces
    61 | \item{\code{pvalue_emp}}: {the empirical p-value:  the proportion of times the cluster index from the reference
       |                           ^
checkRd: (-1) UNPaC_Copula.Rd:63: Lost braces; missing escapes or markup?
    63 | \item{\code{pvalue_norm}}: {the normalized p-value: the simulated p-value based on comparison to a standard normal distribution }
       |                            ^
checkRd: (-1) UNPaC_num_clust.Rd:58-62: Lost braces
    58 | \item{\code{BestK}}: {A matrix with 1 row and 4 columns named: "Max_CI","Max_CI_wi_1SE","Max_scaled_CI" and "Max_logWCSS_wi_1SE".
       |                      ^
checkRd: (-1) UNPaC_num_clust.Rd:63-65: Lost braces
    63 | \item{\code{full_process}}: {A matrix containing the number of clusters, K, evaluated, the CI from the data, the average CI from the null
       |                             ^
checkRd: (-1) UNPaC_num_clust.Rd:66: Lost braces; missing escapes or markup?
    66 | \item{\code{selected_features}}: {A vector of integers indicating the features retained by the feature filtering process.}}
       |                                  ^
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    doc   7.6Mb
'LazyData' is specified without a 'data' directory
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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc   3.8Mb
checkRd: (-1) aosat.Rd:20: Escaped LaTeX specials: \_ \_ \_
checkRd: (-1) aosat.Rd:21: Escaped LaTeX specials: \_
checkRd: (-1) arctic.oscillations.Rd:19: Escaped LaTeX specials: \_ \_ \_
checkRd: (-1) arctic.oscillations.Rd:20: Escaped LaTeX specials: \_
checkRd: (-1) babies.Rd:28: Escaped LaTeX specials: \&
checkRd: (-1) babies.Rd:41: Escaped LaTeX specials: \$
checkRd: (-1) cabinet.Rd:25: Escaped LaTeX specials: \$
checkRd: (-1) cabinet.Rd:43: Escaped LaTeX specials: \$
checkRd: (-1) cabinet.Rd:48: Escaped LaTeX specials: \$
checkRd: (-1) exec.pay.Rd:5: Escaped LaTeX specials: \$
checkRd: (-1) sp500.excess.Rd:4: Escaped LaTeX specials: \&
checkRd: (-1) sp500.excess.Rd:6: Escaped LaTeX specials: \&
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    extdata   9.8Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    data   6.9Mb
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
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'
installed size is 24.5Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs  22.5Mb
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'vaers', 'vaersND'
Packages suggested but not available for checking: 'vaers', 'vaersND'
'LazyData' is specified without a 'data' directory
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    extdata   8.8Mb
'LazyData' is specified without a 'data' directory
checkRd: (-1) sendTasks.Rd:41: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sendTasks.Rd:43: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
installed size is 109.3Mb
  sub-directories of 1Mb or more:
    extdata   2.8Mb
    gdal      3.0Mb
    libs     93.1Mb
    proj      9.0Mb
checkRd: (-1) sample_gen.Rd:18: Lost braces; missing escapes or markup?
    18 | Generate \code{n} random samples from multivariate Gaussian distribution N(0, (L^TL)^{-1})
       |                                                                                      ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
checkRd: (-1) vardannual.Rd:97: Lost braces
    97 | \item{ID_level2}{Optional}{variable for unit ID codes. One dimensional object convertible to one-column \code{data.table} or variable name as character, column number.}
       |                           ^
checkRd: (-1) vardannual.Rd:99: Lost braces
    99 | \item{dataset}{Optional}{survey data object convertible to \code{data.table}.}
       |                         ^
checkRd: (-1) vardcrospoor.Rd:122: Lost braces
   122 | \item{ind_gr}{Optional}{variable by which divided independently X matrix of the auxiliary variables for the calibration. One dimensional object convertible to one-column \code{data.table} or variable name as character, column number.}
       |                        ^
checkRd: (-1) vardcrospoor.Rd:124: Lost braces
   124 | \item{use.estVar}{Logical}{value. If value is \code{TRUE}, then \code{R} function \code{estVar} is used for the  estimation of covariance matrix of the residuals. If value is \code{FALSE}, then \code{R} function \code{estVar} is not used for the estimation of covariance matrix of the residuals.}
       |                           ^
checkRd: (-1) vardom_othstr.Rd:69: Lost braces
    69 | \item{percentratio}{Positive}{numeric value. All linearized variables are multiplied with \code{percentratio} value, by default - 1.}
       |                              ^
checkRd: (-1) varpoord.Rd:121: Lost braces
   121 | \item{month_at_work}{Variable}{for total number of month at work (sum of the number of months spent at full-time work as employee, number of months spent at part-time work as employee, number of months spent at full-time work as self-employed (including family worker), number of months spent at part-time work as self-employed (including family worker)).  One dimensional object convertible to one-column \code{data.table} or variable name as character, column number.}
       |                               ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) betaburr.Rd:7: Lost braces
     7 | \description{Computes the pdf, cdf, value at risk and expected shortfall for the beta Burr distribution due to Parana\'{i}ba et al. (2011) given by
       |                                                                                                                        ^
checkRd: (-1) betafrechet.Rd:7: Lost braces
     7 | \description{Computes the pdf, cdf, value at risk and expected shortfall for the beta Fr\'{e}chet distribution due to Barreto-Souza et al. (2011) given by
       |                                                                                           ^
checkRd: (-1) frechet.Rd:7: Lost braces
     7 | \description{Computes the pdf, cdf, value at risk and expected shortfall for the Fr\'{e}chet distribution due to Fr\'{e}chet (1927) given by
       |                                                                                      ^
checkRd: (-1) frechet.Rd:7: Lost braces
     7 | \description{Computes the pdf, cdf, value at risk and expected shortfall for the Fr\'{e}chet distribution due to Fr\'{e}chet (1927) given by
       |                                                                                                                      ^
checkRd: (-1) kumburr7.Rd:7: Lost braces
     7 | \description{Computes the pdf, cdf, value at risk and expected shortfall for the Kumaraswamy Burr XII distribution due to Parana\'{i}ba et al. (2013) given by
       |                                                                                                                                   ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) simulateDCSIS.Rd:40: Lost braces
    40 |        Y = 6*X1 + 1.5*X2  + 9*1{X12 < 0} + exp(2*X22)*e
       |                                ^
checkRd: (-1) simulateDCSIS.Rd:42: Lost braces
    42 |        Y = 6*X1 + 1.5*X2  + 9*1{X12 < 0} + 6*X22 + e
       |                                ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) get.miniseq.sample.files.Rd:15: Lost braces
    15 | \item{file.suffix}{Regex expression for end of file name. For example, `file.suffix = '_S\\d{1,2}_.*_R1_.*'` will match R1 files.1 files.}
       |                                                                                             ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) randomVarImpsRFplot.Rd:97: Escaped LaTeX specials: \&
checkRd: (-1) varSelImpSpecRF.Rd:83: Escaped LaTeX specials: \&
checkRd: (-1) Acoef_sh.Rd:23: Lost braces; missing escapes or markup?
    23 | The function returns the K-by-K matrices {A_1, ..., A_p} as a list object.
       |                                          ^
checkRd: (-1) VARshrink.Rd:58: Lost braces; missing escapes or markup?
    58 | Consider VAR(p) model: y_t = A_1 y_{t-1} + ... + A_p y_{t-p} + C d_t + e_t,
       |                                    ^
checkRd: (-1) VARshrink.Rd:58: Lost braces; missing escapes or markup?
    58 | Consider VAR(p) model: y_t = A_1 y_{t-1} + ... + A_p y_{t-p} + C d_t + e_t,
       |                                                        ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
checkRd: (-1) decomposition.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) decomposition.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) decomposition.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimation.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimation.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimation.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) moving.decomposition.Rd:27-28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) moving.decomposition.Rd:28: Lost braces
    28 | \item{W2}{nxn matrix of weights. Season is estimated as W2 \%}\% y, if y is the data vector}
       |      ^
checkRd: (-1) moving.decomposition.Rd:28: Lost braces
    28 | \item{W2}{nxn matrix of weights. Season is estimated as W2 \%}\% y, if y is the data vector}
       |          ^
checkRd: (-1) moving.estimation.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) moving.estimation.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) moving.estimation.Rd:31: Lost braces in \itemize; \value handles \item{}{} directly
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) additiveBeta.Rd:40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) additiveBeta.Rd:41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) additiveBeta.Rd:43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) additiveBeta.Rd:44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) additiveBeta.Rd:45: Lost braces in \itemize; meant \describe ?
checkRd: (-1) additiveBeta.Rd:47: Lost braces in \itemize; meant \describe ?
checkRd: (-1) downloadPBDB.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) downloadPBDB.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) downloadPBDB.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) downloadPBDB.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) downloadPBDB.Rd:31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) downloadPBDB.Rd:32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) downloadPBDB.Rd:33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) downloadPBDB.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) multiplicativeBeta.Rd:31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) multiplicativeBeta.Rd:32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) multiplicativeBeta.Rd:33: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) ex121.Rd:18: Escaped LaTeX specials: \&
checkRd: (-1) ex124.Rd:18: Escaped LaTeX specials: \&
checkRd: (-1) ex125.Rd:18: Escaped LaTeX specials: \&
checkRd: (-1) ex127.Rd:18: Escaped LaTeX specials: \&
checkRd: (-1) ex32.Rd:18: Escaped LaTeX specials: \&
checkRd: (-1) ex33.Rd:18: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    R      4.3Mb
    help   3.3Mb
'LazyData' is specified without a 'data' directory
checkRd: (-1) VirtualArray-single-bracket-method.Rd:6: Lost braces
     6 | \title{Indexing to extract subsets of a 'code{\link[via:XArray-class]{VirtualArray}}'-class object}
       |                                              ^
checkRd: (-1) subset.Rd:20: Lost braces
    20 | \item{drop}{\code{logical} in case the result of subsetting is a single element, should the \\code{\link[via:XArray-class]{VirtualArray}} wrapper be dropped?}
       |                                                                                                   ^
Running examples in 'via-Ex.R' failed
The error most likely occurred in:

> ### Name: project
> ### Title: Project a "RasterArray"-class object
> ### Aliases: project project,RasterArray-method
> ### Keywords: datasets
> 
> ### ** Examples
> 
> # project first three to mollweide
> ex <- rastex() 
> mollEx <- project(ex[1:3], y="ESRI:54009")
Warning: PROJ: proj_get_authorities_from_database: Cannot find proj.db (GDAL error 1)
Warning: PROJ: proj_get_authorities_from_database: Cannot find proj.db (GDAL error 1)
Warning: [project] Cannot set raster SRS: empty srs
Error: [project] cannot get output boundaries for the target crs
Execution halted
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    doc   9.5Mb
checkRd: (-1) vic_param.Rd:311: Lost braces
   311 | albedo must be supplied in code{forcing_veg}. Default = 1.}
       |                                ^
checkRd: (-1) vic_param.Rd:323: Lost braces
   323 | supplied in code{forcing_veg}. Default = 1.}
       |                 ^
checkRd: (-1) vic_param.Rd:341: Lost braces
   341 | be supplied in code{forcing_veg} Default = 0.}
       |                    ^
checkRd: (-1) vietnamcode.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) vietnamcode.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) vietnamcode_data.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) vietnamcode_data.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) vietnamcode_data.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) vietnamcode_data.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) vietnamcode_data.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) vietnamcode_data.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) vietnamcode_data.Rd:16: Lost braces in \itemize; meant \describe ?
Running 'testthat.R' [27s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(viewscape)
  > 
  > testthat::test_check("viewscape")
  Saving _problems/test-calculate_feature-25.R
  Saving _problems/test-calculate_viewmetrics-32.R
  [ FAIL 2 | WARN 3 | SKIP 0 | PASS 5 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-calculate_feature.R:22:3'): runs correctly ─────────────────────
  Error: [project] cannot get output boundaries for the target crs
  Backtrace:
      ▆
   1. └─viewscape::calculate_feature(...) at test-calculate_feature.R:22:3
   2.   ├─terra::project(feature, y = terra::crs(viewshed@crs))
   3.   └─terra::project(feature, y = terra::crs(viewshed@crs))
   4.     └─terra (local) .local(x, ...)
   5.       └─terra:::messages(x, "project")
   6.         └─terra:::error(f, x@pntr$getError())
  ── Error ('test-calculate_viewmetrics.R:29:3'): runs correctly ─────────────────
  Error: [project] cannot get output boundaries for the target crs
  Backtrace:
      ▆
   1. └─viewscape::calculate_viewmetrics(...) at test-calculate_viewmetrics.R:29:3
   2.   ├─terra::project(dtm, y = terra::crs(viewshed@crs))
   3.   └─terra::project(dtm, y = terra::crs(viewshed@crs))
   4.     └─terra (local) .local(x, ...)
   5.       └─terra:::messages(x, "project")
   6.         └─terra:::error(f, x@pntr$getError())
  
  [ FAIL 2 | WARN 3 | SKIP 0 | PASS 5 ]
  Error:
  ! Test failures.
  Execution halted
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc   4.7Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc   2.7Mb
'LazyData' is specified without a 'data' directory
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs   5.1Mb
checkRd: (-1) viridis.Rd:50: Lost braces in \itemize; meant \describe ?
checkRd: (-1) viridis.Rd:51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) viridis.Rd:52: Lost braces in \itemize; meant \describe ?
checkRd: (-1) viridis.Rd:53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) viridis.Rd:54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) viridis.Rd:55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) viridis.Rd:56: Lost braces in \itemize; meant \describe ?
checkRd: (-1) viridis.Rd:57: Lost braces in \itemize; meant \describe ?
checkRd: (-1) viridis.map.Rd:24-30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) viridis.map.Rd:31-34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) viridis.map.Rd:35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) viridis.map.Rd:36-37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) viridis.map.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) viridis.map.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) viridis.map.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) viridis.map.Rd:13-14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) viridis.map.Rd:42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) viridis.map.Rd:43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) viridis.map.Rd:44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) viridis.map.Rd:45: Lost braces in \itemize; meant \describe ?
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    help          1.3Mb
    htmlwidgets   5.2Mb
Running examples in 'visaOTR-Ex.R' failed
The error most likely occurred in:

> ### Name: visa.est
> ### Title: Valid Improved Sparsity A-Learning for Optimal Treatment
> ###   Decision
> ### Aliases: visa.est
> 
> ### ** Examples
> 
> data(visa_SimuData)
> y = visa_SimuData$y
> a = visa_SimuData$a
> x = visa_SimuData$x
> # estimation
> result <- visa.est(y, x, a, IC = "BIC", lambda.list = c(0.1, 0.5))
Warning in throw_err_or_depr_msg("Passed unrecognized parameters: ", paste(head(names_unrecognized),  :
  Passed unrecognized parameters: verbose. This warning will become an error in a future version.
Warning in throw_err_or_depr_msg("Parameter '", match_old, "' has been renamed to '",  :
  Parameter 'data' has been renamed to 'x'. This warning will become an error in a future version.
Error in xgboost::xgboost(data = xgmat1, objective = "binary:logistic",  : 
  argument "y" is missing, with no default
Calls: visa.est ... <Anonymous> -> process.y.margin.and.objective -> NROW
Execution halted
checkRd: (-1) compdesc.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) compdesc.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) compdesc.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) compdesc.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly
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checkRd: (-1) compdesc.Rd:32: Lost braces in \itemize; \value handles \item{}{} directly
Problems with news in 'NEWS.md':
No news entries found.
checkRd: (-1) ViSiElse.Rd:101-107: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ViSiElse.Rd:102: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) dim-ViSibook-methods.Rd:16: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dim-ViSibook-methods.Rd:17-18: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) summary-ViSigrid-methods.Rd:16: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) summary-ViSigrid-methods.Rd:17: Lost braces in \itemize; \value handles \item{}{} directly
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    doc           2.0Mb
    htmlwidgets   6.8Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    help   3.0Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc   5.5Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   5.8Mb
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    dist   7.6Mb
'LazyData' is specified without a 'data' directory
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc       5.4Mb
    extdata   1.1Mb
'LazyData' is specified without a 'data' directory
checkRd: (-1) getTurnType.Rd:38: Lost braces; missing escapes or markup?
    38 | Return one of {Vocalisation, GrpVocalisation, ...} or identifier.
       |               ^
installed size is 24.0Mb
  sub-directories of 1Mb or more:
    extdata   1.6Mb
    libs     22.1Mb
GNU make is a SystemRequirements.
Running examples in 'voluModel-Ex.R' failed
The error most likely occurred in:

> ### Name: diversityStack
> ### Title: Diversity stack
> ### Aliases: diversityStack
> ### Keywords: plotting
> 
> ### ** Examples
> 
> library(terra)
terra 1.8.86
> rast1 <- rast(ncol=10, nrow=10)
> values(rast1) <- rep(0:1, 50)
> 
> rast2 <- rast(ncol=10, nrow=10)
> values(rast2) <- c(rep(0, 50), rep(1,50))
> 
> rastList <- list(rast1, rast2)
> result <- diversityStack(rasterList = rastList,
+                          template = rast2)
Warning: PROJ: proj_create: no database context specified (GDAL error 1)
Warning: PROJ: proj_create: no database context specified (GDAL error 1)
Warning: PROJ: proj_create: no database context specified (GDAL error 1)
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    vortexRdata pre-1.0.3
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) compute.means.Rd:23: Escaped LaTeX specials: \&
checkRd: (-1) norm.wattfabricius.Rd:5: Escaped LaTeX specials: \&
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) Data-Examples.Rd:39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Data-Examples.Rd:40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Data-Examples.Rd:41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Data-Examples.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Data-Examples.Rd:31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Data-Examples.Rd:32: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Data.trafo.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Data.trafo.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Data.trafo.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Toep.estimator.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Toep.estimator.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
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checkRd: (-1) Toep.estimator.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
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checkRd: (-1) vsts_create_release.Rd:33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) vsts_create_release.Rd:34: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) WACS.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) WACS.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) WACS.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) WACS.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) WACS.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) WACS.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) WACS.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) WACS.Rd:36-37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) WACS.Rd:38-39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) WACSreadAgroclim.Rd:15: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) WACSreadAgroclim.Rd:16-17: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
'LazyData' is specified without a 'data' directory
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    doc   5.4Mb
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    help   4.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running 'testthat.R' [19s]
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(wbids)
  The tzdb package is not installed. Timezones will not be available to Arrow compute functions.
  > 
  > test_check("wbids")
  Reading in file.
  Processing file.
  Downloading file to: D:\temp\2025_12_05_01_50_00_7414\Rtmpe2Ll10\file8524cb31...
  Processing file.
  Downloading file to: D:\temp\2025_12_05_01_50_00_7414\Rtmpe2Ll10\file85247aa1...
  Reading in file.
  Downloading file to: D:\temp\2025_12_05_01_50_00_7414\Rtmpe2Ll10\file8524768f...
  Saving _problems/test-ids_get-474.R
  [ FAIL 1 | WARN 0 | SKIP 6 | PASS 153 ]
  
  ══ Skipped tests (6) ═══════════════════════════════════════════════════════════
  • On CRAN (6): 'test-ids_bulk.R:161:3', 'test-ids_bulk.R:215:3',
    'test-ids_bulk.R:248:3', 'test-ids_bulk.R:301:3', 'test-ids_bulk.R:368:3',
    'test-ids_get_ed.R:2:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-ids_get.R:472:3'): ids_get filters post-observed-year NAs correctly ──
  Expected `all(result$year <= as.numeric(format(Sys.Date(), "%Y")) | !is.na(result$value))` to be TRUE.
  Differences:
  `actual`:   FALSE
  `expected`: TRUE 
  
  
  [ FAIL 1 | WARN 0 | SKIP 6 | PASS 153 ]
  Error:
  ! Test failures.
  Execution halted
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'prepr'
Problems with news in 'NEWS.md':
No news entries found.
checkRd: (-1) Session.Rd:146: Lost braces
   146 | sQuote{page load} timeout specifies a time to wait for the page loading
       |       ^
'LazyData' is specified without a 'data' directory
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    client   9.1Mb
    doc      1.0Mb
Packages suggested but not available for checking: 'iptools', 'rgeolocate'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   7.1Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
checkRd: (-1) busTrace.Rd:15: Lost braces
    15 | /href{https://crawdad.org/coppe-ufrj/RioBuses/20180319/}
       |      ^
train.xgboost1: no visible global function definition for
  'cb.evaluation.log'
Undefined global functions or variables:
  cb.evaluation.log
checkRd: (-1) WeightedROC.Rd:10: Lost braces; missing escapes or markup?
    10 | integer/numeric with values all in {0=negative,1=positive} or
       |                                    ^
checkRd: (-1) WeightedROC.Rd:11: Lost braces; missing escapes or markup?
    11 | {1=negative,2=positive} or {-1=negative,1=positive}.}
       | ^
checkRd: (-1) WeightedROC.Rd:11: Lost braces; missing escapes or markup?
    11 | {1=negative,2=positive} or {-1=negative,1=positive}.}
       |                            ^
checkRd: (-1) CLIC.Rd:149: Lost braces
   149 | Composite likelihood {E}{M} algorithm with applications to
       |                         ^
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Major changes
    Minor changes
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    extdata   5.6Mb
Running 'testthat.R' [11m]
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(whirl)
  > 
  > test_check("whirl")
  Saving _problems/test-mdformats-35.R
  
                              
  [ FAIL 1 | WARN 0 | SKIP 15 | PASS 150 ]
  
  ══ Skipped tests (15) ══════════════════════════════════════════════════════════
  • On CRAN (15): 'test-biocompute.R:1:1', 'test-custom_logging.R:19:1',
    'test-examples.R:1:1', 'test-python.R:2:3', 'test-python.R:44:3',
    'test-run.R:33:3', 'test-run.R:76:3', 'test-run.R:87:3', 'test-run.R:95:3',
    'test-run.R:112:3', 'test-run.R:134:3', 'test-run.R:151:3',
    'test-strace.R:42:3', 'test-util_queue_summary.R:11:3',
    'test-whirl_queue.R:1:1'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-mdformats.R:29:3'): pandoc works ─────────────────────────────
  Expected `all(...)` to be TRUE.
  Differences:
  `actual`:   FALSE
  `expected`: TRUE 
  
  
  [ FAIL 1 | WARN 0 | SKIP 15 | PASS 150 ]
  Error:
  ! Test failures.
  Execution halted
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    data   4.2Mb
    libs   3.6Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) get_geo_box.Rd:37-38: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get_geo_box.Rd:39-40: Lost braces in \itemize; \value handles \item{}{} directly
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checkRd: (-1) get_geo_box.Rd:43-44: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get_geo_entity.Rd:27-28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get_geo_entity.Rd:29-30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get_geo_entity.Rd:31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get_geo_entity.Rd:32: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get_geo_entity.Rd:33-34: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) milakes.Rd:10: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) milakes.Rd:12: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) milakes.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) milakes.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) milakes.Rd:22: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  stop.c:10:6: warning: function declaration isn't a prototype [-Wstrict-prototypes]
See 'd:/Rcompile/CRANpkg/local/4.4/winch.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 13.3.0'
checkRd: (-1) secondDerivative.Rd:14: Lost braces
    14 | This must be a function of the form FUN <- function(x, ...){...}
       |                                                            ^
checkRd: (-1) windAC.Rd:31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) windAC.Rd:32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) windAC.Rd:33: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'wordnetDicts'
checkRd: (-1) wordpiece_cache_dir.Rd:16-17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) wordpiece_cache_dir.Rd:18-19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) wordpiece_cache_dir.Rd:20-21: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    data   6.5Mb
Malformed Description field: should contain one or more complete sentences.
installed size is 12.7Mb
  sub-directories of 1Mb or more:
    data  12.6Mb
Malformed Description field: should contain one or more complete sentences.
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    data  11.1Mb
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    data  11.3Mb
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    data  11.1Mb
Package suggested but not available for checking: 'wmtsa'
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  'tidyr'
A package should be listed in only one of these fields.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    doc       2.8Mb
    extdata   2.5Mb
checkRd: (-1) createDemandSite.Rd:26: Lost braces
    26 |   \item{suppliers}{(optional) A list of object(s) inherited from the folowing classes: \code{\link[WRSS]{createAquifer}}, \code{\link[WRSS]{createRiver}}, \code{\link[WRSS]{createReservoir}}, code{\link[WRSS]{createDiversion}}.}
       |                                                                                                                                                                                                     ^
checkRd: (-1) createDemandSite.base.Rd:26: Lost braces
    26 |   \item{suppliers}{(optional) A list of object(s) inherited from the folowing classes: \code{\link[WRSS]{createAquifer}}, \code{\link[WRSS]{createRiver}}, \code{\link[WRSS]{createReservoir}}, code{\link[WRSS]{createDiversion}}.}
       |                                                                                                                                                                                                     ^
checkRd: (-1) createDemandSite.default.Rd:32: Lost braces
    32 |   \item{suppliers}{(optional) A list of object(s) inherited from the folowing classes: \code{\link[WRSS]{createAquifer}}, \code{\link[WRSS]{createRiver}}, \code{\link[WRSS]{createReservoir}}, code{\link[WRSS]{createDiversion}}.}
       |                                                                                                                                                                                                     ^
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
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) wtest.Rd:61-64: Lost braces
    61 | {When \code{w.order} =2, the \code{wtest()} will automatically calculate the main effect first and then do a pre-filter before calculating interactions.
       | ^
checkRd: (-1) wtest.high.Rd:61-64: Lost braces
    61 | {When \code{w.order} > 2, the \code{wtest()} will automatically calculate the main effect first and then do a pre-filter before calculating interactions.
       | ^
checkRd: (-1) exploreSignatures.Rd:47: Lost braces in \itemize; \value handles \item{}{} directly
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checkRd: (-1) exploreSignatures.Rd:56: Lost braces in \itemize; \value handles \item{}{} directly
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checkRd: (-1) exploreSignatures.Rd:58-59: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) exploreSignatures.Rd:65-66: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) exploreSignatures.Rd:67-69: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) generateData.Rd:47: Lost braces
    47 | \bold{code{data}} \tab the generated data \cr
       |           ^
checkRd: (-1) generateData.Rd:53: Lost braces
    53 | Refer to \bold{\emph{code{\link{retrieveDataFactory}}}} and to
       |                          ^
checkRd: (-1) qualifyFunctionArguments.Rd:14: Lost braces
    14 | A emph{\code{list}} with following names
       |       ^
checkRd: (-1) qualifyFunctionArguments.Rd:26: Lost braces
    26 | \item{code{arguments}}{a \code{pairList} of argument names and values.
       |           ^
checkRd: (-1) completeManualPage.Rd:12: Lost braces
    12 | See \emph{\bold{code{\link{ProcessingContext}}}}. Only
       |                     ^
checkRd: (-1) produceAllManualPagesFromObject.Rd:14: Lost braces
    14 | See \emph{\bold{\\code{\link{ProcessingContext}}}}.}
       |                       ^
checkRd: (-1) chemnet.Rd:111: Lost braces in \itemize; meant \describe ?
checkRd: (-1) chemnet.Rd:112: Lost braces in \itemize; meant \describe ?
checkRd: (-1) knecht.Rd:103: Lost braces in \itemize; meant \describe ?
checkRd: (-1) knecht.Rd:104: Lost braces in \itemize; meant \describe ?
checkRd: (-1) knecht.Rd:105: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building 'xgb2sql.Rmd' using rmarkdown

Quitting from xgb2sql.Rmd:221-231 [unnamed-chunk-6]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `process.y.margin.and.objective()`:
! Got numeric 'y' - supported objectives for this data are: reg:squarederror, reg:squaredlogerror, reg:logistic, reg:pseudohubererror, reg:absoluteerror, reg:quantileerror, count:poisson, reg:gamma, reg:tweedie. Was passed: reg:linear
---
Backtrace:
    ▆
 1. └─xgboost::xgboost(...)
 2.   └─xgboost:::process.y.margin.and.objective(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'xgb2sql.Rmd' failed with diagnostics:
Got numeric 'y' - supported objectives for this data are: reg:squarederror, reg:squaredlogerror, reg:logistic, reg:pseudohubererror, reg:absoluteerror, reg:quantileerror, count:poisson, reg:gamma, reg:tweedie. Was passed: reg:linear
--- failed re-building 'xgb2sql.Rmd'

SUMMARY: processing the following file failed:
  'xgb2sql.Rmd'

Error: Vignette re-building failed.
Execution halted
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   8.3Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is 28.9Mb
  sub-directories of 1Mb or more:
    java  26.5Mb
'LazyData' is specified without a 'data' directory
installed size is 11.8Mb
  sub-directories of 1Mb or more:
    java  11.7Mb
checkRd: (-1) xml_to_df.Rd:144: Lost braces; missing escapes or markup?
   144 | Default {NULL} means the workbook will not be protected with a password}
       |         ^
'LazyData' is specified without a 'data' directory
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          2.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    data   3.4Mb
    doc    3.2Mb
'LazyData' is specified without a 'data' directory
checkRd: (-1) xwfGridsearch.Rd:27: Lost braces; missing escapes or markup?
    27 | \item{iter}{Number of levels in the adaptive grid search. The resolution in b obtained is 2^{-1-iter}.}
       |                                                                                             ^
checkRd: (-1) cat_sim.Rd:110: Lost braces; missing escapes or markup?
   110 | \code{min} and {max} are mandatory for setting limits on the test length. User-defined
       |                ^
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc   2.1Mb
Package suggested but not available for checking: 'MBESS'
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'RNRCS', 'metScanR'
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building 'z22.Rmd' using rmarkdown
File man/figures/vignette/unnamed-chunk-5-1.png not found in resource path
Error: processing vignette 'z22.Rmd' failed with diagnostics:
pandoc document conversion failed with error 99
--- failed re-building 'z22.Rmd'

SUMMARY: processing the following file failed:
  'z22.Rmd'

Error: Vignette re-building failed.
Execution halted
Malformed Description field: should contain one or more complete sentences.
checkRd: (-1) glm.cons.Rd:54: Lost braces; missing escapes or markup?
    54 | \item{method}{the method used in fitting the model. The default method "\code{glm.fit.cons}" uses function {nnnpls} from package nnls instead of \code{lm.fit} to impose the sign of the coefficients. As in \code{glm}, the alternative method "\code{model.frame}" returns the model frame and does no fitting.}
       |                                                                                                            ^
Running examples in 'zetadiv-Ex.R' failed
The error most likely occurred in:

> ### Name: Zeta.order.ex
> ### Title: Expectation of zeta diversity for a specific number of
> ###   assemblages or sites
> ### Aliases: Zeta.order.ex
> 
> ### ** Examples
> 
> 
> utils::data(bird.spec.coarse)
> data.spec.bird <- bird.spec.coarse[,3:193]
> 
> zeta.bird <- Zeta.order.ex(data.spec.bird, order = 3)
> zeta.bird
$zeta.order
[1] 3

$combinations
[1] 302621

$zeta.val
[1] 57.61204

$zeta.val.sd
[1] 13.10351

> 
> ##########
> s
Error: object 's' not found
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc   5.2Mb
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: \_
checkRd: (-1) zim.Rd:182: Lost braces
   182 |   dQuote{tab-delimited text file} when you have done and close the spreadsheet
       |         ^
checkRd: (-1) in.zoom.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) in.zoom.Rd:35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) in.zoom.Rd:36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) in.zoom.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) in.zoom.Rd:38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) in.zoom.Rd:39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) zm.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) zm.Rd:31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) zm.Rd:32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) zm.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) zm.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) update_ztable.Rd:75: Lost braces; missing escapes or markup?
    75 | must be NULL or contain only elements of {"h","t","b","p","!","H"}.}
       |                                          ^
checkRd: (-1) ztable_sub.Rd:78: Lost braces; missing escapes or markup?
    78 | must be NULL or contain only elements of {"h","t","b","p","!","H"}.
       |                                          ^
'LazyData' is specified without a 'data' directory