'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Depends: includes the non-default packages:
  'combinat', 'matrixcalc', 'mvtnorm', 'expm', 'CompQuadForm',
  'ggplot2'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
'LazyData' is specified without a 'data' directory
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs   6.9Mb
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.
'LazyData' is specified without a 'data' directory
'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
Package which this enhances but not available for checking: 'RGtk2'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages which this enhances but not available for checking:
  'Rcplex', 'gurobi', 'rcbc'
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
checkRd: (-1) fit.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fit.Rd:38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fit.Rd:39: 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
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    data   2.5Mb
    doc    5.4Mb
checkRd: (-1) fpiter.Rd:55-58: Lost braces
    55 |     \code{tol}{  A small, positive scalar that determines when iterations
       |               ^
checkRd: (-1) fpiter.Rd:60-61: Lost braces
    60 |     \code{maxiter}{  An integer denoting the maximum limit on the number of
       |                   ^
checkRd: (-1) fpiter.Rd:63-65: Lost braces
    63 |     \code{trace}{  A logical variable denoting whether some of the intermediate
       |                 ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) formatScientificTeX.Rd:33: Lost braces; missing escapes or markup?
    33 | function will return  " 3.0\\\\times 10^{2}"
       |                                         ^
Package which this enhances but not available for checking: 'doMC'
Running examples in 'DALEXtra-Ex.R' failed
The error most likely occurred in:

> ### Name: explain_xgboost
> ### Title: Create explainer from your xgboost model
> ### Aliases: explain_xgboost
> 
> ### ** Examples
> 
> library("xgboost")
> library("DALEXtra")
> library("mlr")
Loading required package: ParamHelpers
> # 8th column is target that has to be omitted in X data
> data <- as.matrix(createDummyFeatures(titanic_imputed[,-8]))
> model <- xgboost(data, titanic_imputed$survived, nrounds = 10,
+                  params = list(objective = "binary:logistic"),
+                 prediction = TRUE)
Warning in throw_err_or_depr_msg("Parameter(s) have been removed from this function: ",  :
  Parameter(s) have been removed from this function: params. This warning will become an error in a future version.
Warning in throw_err_or_depr_msg("Passed unrecognized parameters: ", paste(head(names_unrecognized),  :
  Passed unrecognized parameters: prediction. This warning will become an error in a future version.
> # explainer with encode functiom
> explainer_1 <- explain_xgboost(model, data = titanic_imputed[,-8],
+                                titanic_imputed$survived,
+                                encode_function = function(data) {
+  as.matrix(createDummyFeatures(data))
+ })
Preparation of a new explainer is initiated
  -> model label       :  xgb.Booster  ( [33m default [39m )
  -> data              :  2207  rows  7  cols 
  -> target variable   :  2207  values 
  -> predict function  :  yhat.xgb.Booster  will be used ( [33m default [39m )
  -> predicted values  :  No value for predict function target column. ( [33m default [39m )
Error in strsplit(model$params$objective, ":", fixed = TRUE) : 
  non-character argument
Calls: explain_xgboost ... explain -> model_info -> model_info.xgb.Booster -> strsplit
Execution halted
Running 'testthat.R' [69s]
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(damAOI)
  > 
  > test_check("damAOI")
  Saving _problems/test-makesystem-5.R
  [ FAIL 1 | WARN 25 | SKIP 0 | PASS 14 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-makesystem.R:5:3'): makesystem ─────────────────────────────────
  Error in `data.frame(name = vect(system[system$area == "reservoir", ])$name, elev = extract(dem, vect(system[system$area == "reservoir", ]), fun = "mean", ID = FALSE))`: arguments imply differing number of rows: 2, 0
  Backtrace:
      ▆
   1. └─damAOI::makesystem(names, system, dem_system) at test-makesystem.R:5:3
   2.   └─base::data.frame(...)
  
  [ FAIL 1 | WARN 25 | SKIP 0 | PASS 14 ]
  Error:
  ! Test failures.
  Execution halted
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   4.4Mb
'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   4.4Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    R      1.7Mb
    help   2.6Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    java   7.5Mb
GNU make is a SystemRequirements.
checkRd: (-1) processFlow.Rd:14: Lost braces
    14 | \item{roundDigits}{Integer. If NA, numerics are not rounded before comparison. If /code{roundDigits} is specified, numerics are 
       |                                                                                        ^
checkRd: (-1) processFlow.Rd:15: Lost braces
    15 | rounded to /code{roundDigits} decimal places using \link[base]{round}.}
       |                 ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) data_edit.Rd:137: Lost braces
   137 | code{data_edit} is a shiny application built on \code{rhandsontable} that is
       |     ^
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/DataGraph.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
Running examples in 'DataMetProcess-Ex.R' failed
The error most likely occurred in:

> ### Name: list_inmet
> ### Title: List of data available at INMET by year
> ### Aliases: list_inmet
> 
> ### ** Examples
> 
> 
> file.down <- tempfile()
> file.save <- tempfile()
> 
> info.inmet <-
+   DataMetProcess::list_inmet(year="2000",file.down)
trying URL 'https://portal.inmet.gov.br/uploads/dadoshistoricos/2000.zip'
Warning in utils::download.file(url = base::paste0("https://portal.inmet.gov.br/uploads/dadoshistoricos/",  :
  cannot open URL 'https://portal.inmet.gov.br/uploads/dadoshistoricos/2000.zip': HTTP status was '403 Forbidden'
Error: Error downloading data for year 2000.
Possible cause: download timeout exceeded.
Suggested solution: increase the maximum download time, e.g.:
options(timeout = 1000)

Original error message: cannot open URL 'https://portal.inmet.gov.br/uploads/dadoshistoricos/2000.zip'
Execution halted
Error(s) in re-building vignettes:
--- re-building 'DataMetProcess-vignette.Rmd' using rmarkdown
trying URL 'https://portal.inmet.gov.br/uploads/dadoshistoricos/2000.zip'

Quitting from DataMetProcess-vignette.Rmd:26-35 [unnamed-chunk-2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! Error downloading data for year 2000.
Possible cause: download timeout exceeded.
Suggested solution: increase the maximum download time, e.g.:
options(timeout = 1000)

Original error message: cannot open URL 'https://portal.inmet.gov.br/uploads/dadoshistoricos/2000.zip'
---
Backtrace:
    ▆
 1. └─DataMetProcess::list_inmet(year = "2000", filename = file.down)
 2.   └─base::tryCatch(...)
 3.     └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 4.       └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 5.         └─value[[3L]](cond)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'DataMetProcess-vignette.Rmd' failed with diagnostics:
Error downloading data for year 2000.
Possible cause: download timeout exceeded.
Suggested solution: increase the maximum download time, e.g.:
options(timeout = 1000)

Original error message: cannot open URL 'https://portal.inmet.gov.br/uploads/dadoshistoricos/2000.zip'
--- failed re-building 'DataMetProcess-vignette.Rmd'

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   4.7Mb
'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:
    po   1.5Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc   3.3Mb
GNU make is a SystemRequirements.
Package suggested but not available for checking: 'SASxport'
'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
Error(s) in re-building vignettes:
--- re-building 'daymetr-vignette.Rmd' using knitr
proj_uom_get_info_from_database: Cannot find proj.db

Quitting from daymetr-vignette.Rmd:189-208 [unnamed-chunk-10]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! [project] cannot get output boundaries for the target crs
---
Backtrace:
    ▆
 1. ├─terra::project(r, "+init=epsg:4326")
 2. └─terra::project(r, "+init=epsg:4326")
 3.   └─terra (local) .local(x, ...)
 4.     └─terra:::messages(x, "project")
 5.       └─terra:::error(f, x@pntr$getError())
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'daymetr-vignette.Rmd' failed with diagnostics:
[project] cannot get output boundaries for the target crs
--- failed re-building 'daymetr-vignette.Rmd'

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

Error: Vignette re-building failed.
Execution halted
checkRd: (-1) plot.mleBb.Rd:48: Lost braces
    48 |   \ code{size} is extracted from argument \code{x}.
       |         ^
checkRd: (-1) value_missing_table.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) value_missing_table.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in 'dblr-Ex.R' failed
The error most likely occurred in:

> ### Name: dblr_train
> ### Title: Discrete Boosting Logistic Regression Training
> ### Aliases: dblr_train
> 
> ### ** Examples
> 
> # use iris data for example
> dat <- iris
> # create two categorical variables
> dat$Petal.Width <- as.factor((iris$Petal.Width<=0.2)*1+(iris$Petal.Width>1.0)*2)
> dat$Sepal.Length <- (iris$Sepal.Length<=3.0)*2+(iris$Sepal.Length>6.0)*1.25
> # create the response variable
> dat$Species <- as.numeric(dat$Species=='versicolor')
> set.seed(123)
> # random sampling
> index <- sample(1:150,100,replace = FALSE)
> # train the dblr model using the training data
> dblr_fit <- dblr_train(train_x=dat[index,c(1:4)],
+ train_y=dat[index,5],category_cols = c('Petal.Width','Sepal.Length'),
+ metric = 'logloss',subsample = 0.5,eta = 0.05,colsample = 1.0,
+ lambda = 1.0,cv_early_stops = 10,verbose=FALSE)
Warning in throw_err_or_depr_msg("Passed unrecognized parameters: ", paste(head(names_unrecognized),  :
  Passed unrecognized parameters: metrics. This warning will become an error in a future version.
Error in begin_iteration:end_iteration : argument of length 0
Calls: dblr_train -> <Anonymous>
Execution halted
checkRd: (-1) CI_mc.Rd:10: Lost braces; missing escapes or markup?
    10 | \item{i}{the row index of the interest entry X_{i,j}}
       |                                                ^
checkRd: (-1) CI_mc.Rd:12: Lost braces; missing escapes or markup?
    12 | \item{j}{the row index of the interest entry X_{i,j}}
       |                                                ^
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    3.0Mb
    libs   1.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) data.Rd:11: Lost braces
    11 | \doi{10.1007/s40258-021-00647-3}{DOI}
       |                                 ^
Problems with news in 'NEWS.md':
No news entries found.
Package suggested but not available for checking: 'BRugs'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'cmdstanr'
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Running 'testthat.R' [49s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(ddml)
  > 
  > test_check("ddml")
  Saving _problems/test-ml_wrappers-35.R
  
  sample fold 1/3
  sample fold 2/3
  sample fold 3/3[ FAIL 1 | WARN 6 | SKIP 0 | PASS 134 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-ml_wrappers.R:35:3'): mdl_xgboost is working ───────────────────
  Error in `process.y.margin.and.objective(as.vector(y), base_margin, objective, params)`: 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: binary:logistic
  Backtrace:
      ▆
   1. └─ddml::mdl_xgboost(y, X, objective = "binary:logistic") at test-ml_wrappers.R:35:3
   2.   └─xgboost::xgboost(...)
   3.     └─xgboost:::process.y.margin.and.objective(...)
   4.       └─xgboost:::process.y.margin.and.objective(...)
  
  [ FAIL 1 | WARN 6 | SKIP 0 | PASS 134 ]
  Error:
  ! Test failures.
  Execution halted
checkRd: (-1) detectAgeInterval.Rd:10: Lost braces
    10 | \item{Dat}{a \code{data.frame} containing a column called \code{Age}, or code{age}.}
       |                                                                              ^
checkRd: (-1) detectSex.Rd:10: Lost braces
    10 | \item{Dat}{a \code{data.frame} containing a column called \code{Sex}, or code{sex}.}
       |                                                                              ^
checkRd: (-1) ggbgetAgesFit.Rd:28: Lost braces
    28 | code{\link{ggbChooseAges}}
       |     ^
checkRd: (-1) plot.ddpcr_plate.Rd:136-137: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.ddpcr_plate.Rd:138-139: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.ddpcr_plate.Rd:140-141: Lost braces in \itemize; meant \describe ?
Specified C++11: please drop specification unless essential
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   4.2Mb
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) deconv.Rd:85: Lost braces; missing escapes or markup?
    85 |     \code{tg}, std. error of \eqn{g}, \eqn{G} (the cdf of {g}),
       |                                                           ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) deepNN-package.Rd:18: Lost braces
    18 | section{Dependencies}{
       |        ^
checkRd: (-1) deepNN-package.Rd:18-21: Lost braces
    18 | section{Dependencies}{
       |                      ^
checkRd: (-1) deepNN-package.Rd:23: Lost braces
    23 | section{Citation}{
       |        ^
checkRd: (-1) deepNN-package.Rd:23-25: Lost braces
    23 | section{Citation}{
       |                  ^
checkRd: (-1) deepNN-package.Rd:27-38: Lost braces
    27 | references{
       |           ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Packages suggested but not available for checking: 'bGMYC', 'splits'
Package unavailable to check Rd xrefs: 'bGMYC'
Unknown package 'splits' in Rd xrefs
checkRd: (-1) deltaPlot.Rd:28: Lost braces
    28 |  \item{purify}{logical: should item purification be performed? (Default is code{FALSE}). See \bold{Details}.}
       |                                                                                ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    doc    3.1Mb
    help   1.3Mb
checkRd: (-1) kin.Rd:49-50: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) kin.Rd:51-52: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) kin.Rd:53-61: Lost braces
    53 | {\itemize{
       | ^
checkRd: (-1) kin.Rd:54: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) kin.Rd:55: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) kin.Rd:56: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) kin.Rd:57: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) kin.Rd:58: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) kin.Rd:59: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) kin2sex.Rd:56-57: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) kin2sex.Rd:58: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) kin2sex.Rd:59-67: Lost braces
    59 | {\itemize{
       | ^
checkRd: (-1) kin2sex.Rd:60: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) kin2sex.Rd:61: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) kin2sex.Rd:62: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) kin2sex.Rd:63: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) kin2sex.Rd:64: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) kin2sex.Rd:65: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
checkRd: (-1) scramb.Rd:44: Escaped LaTeX specials: \&
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc   5.8Mb
checkRd: (-1) DendSer.Rd:50: Escaped LaTeX specials: \&
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    help   1.5Mb
    libs   1.9Mb
GNU make is a SystemRequirements.
Package suggested but not available for checking: 'OpenMx'
'LazyData' is specified without a 'data' directory
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    doc       4.8Mb
    extdata   2.1Mb
Package suggested but not available for checking: 'Rdonlp2'
checkRd: (-1) barriers.Rd:127: Escaped LaTeX specials: \$
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'RDCOMClient'
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    R      1.7Mb
    doc    1.8Mb
    help   1.7Mb
    libs   1.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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
'LazyData' is specified without a 'data' directory
checkRd: (-1) runContrasts.Rd:79: Lost braces in \itemize; meant \describe ?
checkRd: (-1) runContrasts.Rd:80: Lost braces in \itemize; meant \describe ?
checkRd: (-1) runContrasts.Rd:81: Lost braces in \itemize; meant \describe ?
checkRd: (-1) runContrasts.Rd:82: Lost braces in \itemize; meant \describe ?
checkRd: (-1) AIC.dglars.Rd:47: Lost braces
    47 | \item{comp}{the measures of model complexity used to compute the measure of goodness-of-fit. It is equal to \code{npar} when code{complexity = "df"};}
       |                                                                                                                                  ^
checkRd: (-1) dglars.Rd:258: Lost braces
   258 |                 \item{\code{7}}{maximum number of solution points ('code{np}') reached.}
       |                                                                         ^
Specified C++11: please drop specification unless essential
Error(s) in re-building vignettes:
--- re-building 'dgpsi.Rmd' using rmarkdown
File ./images/step_fct_loo.png not found in resource path
Error: processing vignette 'dgpsi.Rmd' failed with diagnostics:
pandoc document conversion failed with error 99
--- failed re-building 'dgpsi.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Specified C++11: please drop specification unless essential
checkRd: (-1) dHSIC-package.Rd:32: Lost braces
    32 |   Gretton, A., K. Fukumizu, C. H. Teo, L. Song, B. Sch{\"o}lkopf and
       |                                                       ^
checkRd: (-1) dHSIC-package.Rd:36: Lost braces
    36 |   Pfister, N., P. B{\"u}hlmann, B. Sch{\"o}lkopf and J. Peters (2017).
       |                    ^
checkRd: (-1) dHSIC-package.Rd:36: Lost braces
    36 |   Pfister, N., P. B{\"u}hlmann, B. Sch{\"o}lkopf and J. Peters (2017).
       |                                       ^
checkRd: (-1) dhsic.Rd:84: Lost braces
    84 |   Gretton, A., K. Fukumizu, C. H. Teo, L. Song, B. Sch{\"o}lkopf and
       |                                                       ^
checkRd: (-1) dhsic.Rd:88: Lost braces
    88 |   Pfister, N., P. B{\"u}hlmann, B. Sch{\"o}lkopf and J. Peters (2017).
       |                    ^
checkRd: (-1) dhsic.Rd:88: Lost braces
    88 |   Pfister, N., P. B{\"u}hlmann, B. Sch{\"o}lkopf and J. Peters (2017).
       |                                       ^
checkRd: (-1) dhsic.test.Rd:124: Lost braces
   124 |   Gretton, A., K. Fukumizu, C. H. Teo, L. Song, B. Sch{\"o}lkopf and
       |                                                       ^
checkRd: (-1) dhsic.test.Rd:128: Lost braces
   128 |   Pfister, N., P. B{\"u}hlmann, B. Sch{\"o}lkopf and J. Peters (2017).
       |                    ^
checkRd: (-1) dhsic.test.Rd:128: Lost braces
   128 |   Pfister, N., P. B{\"u}hlmann, B. Sch{\"o}lkopf and J. Peters (2017).
       |                                       ^
checkRd: (-1) DIconvex.Rd:40: Lost braces; missing escapes or markup?
    40 |  {Paul Schneider <paul.schneider@usi.ch>}{}
       |  ^
checkRd: (-1) define.Rd:16: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) define.Rd:17-18: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) define.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) define.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) define.Rd:21-22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) define.Rd:23-24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) define.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) define.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) define.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) define.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) define.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) did_imputation.Rd:74: Lost braces; missing escapes or markup?
    74 | form average treatment effects for groups of {it}.
       |                                              ^
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  'fixest'
A package should be listed in only one of these fields.
'LazyData' is specified without a 'data' directory
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    doc  10.8Mb
checkRd: (-1) sensitivitySamplerManual-DPMech-function-numeric-numeric-numeric-method.Rd:25: Lost braces
    25 | \item{k}{order statistic index in {1,...,\code{m}}.}
       |                                   ^
checkRd: (-1) sensitivitySamplerManual-DPMechNumeric-function-numeric-numeric-numeric-method.Rd:25: Lost braces
    25 | \item{k}{order statistic index in {1,...,\code{m}}.}
       |                                   ^
checkRd: (-1) sensitivitySamplerManual.Rd:22: Lost braces
    22 | \item{k}{order statistic index in {1,...,\code{m}}.}
       |                                   ^
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'gurobi'
checkRd: (-1) simulate_diff_tables.Rd:72: Lost braces; missing escapes or markup?
    72 |   {The Sharma-Song test} {\code{\link[DiffXTables]{sharma.song.test}}}
       |   ^
checkRd: (-1) simulate_diff_tables.Rd:74: Lost braces; missing escapes or markup?
    74 |   {The comparative chi-squared test} {\code{\link[DiffXTables]{cp.chisq.test}}}
       |   ^
checkRd: (-1) simulate_diff_tables.Rd:76: Lost braces; missing escapes or markup?
    76 |   {The heterogeneity test} {\code{\link[DiffXTables]{heterogeneity.test}}}
       |   ^
'LazyData' is specified without a 'data' directory
Running 'testthat.R' [2s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(digitize)
  > 
  > test_check("digitize")
  Saving _problems/test-reverse_compatible-38.R
  Saving _problems/test-unit-15.R
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 1 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-reverse_compatible.r:32:13'): `digitize` gives same ────────────
  <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-reverse_compatible.r:32:13
   2.   └─lifecycle::deprecate_stop("3.2.0", "with_mock()", "with_mocked_bindings()")
   3.     └─lifecycle:::deprecate_stop0(msg)
   4.       └─rlang::cnd_signal(...)
  ── Error ('test-unit.r:9:13'): Digitize skips point input ──────────────────────
  <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-unit.r:9:13
   2.   └─lifecycle::deprecate_stop("3.2.0", "with_mock()", "with_mocked_bindings()")
   3.     └─lifecycle:::deprecate_stop0(msg)
   4.       └─rlang::cnd_signal(...)
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 1 ]
  Error:
  ! Test failures.
  Execution halted
checkRd: (-1) DIME.Rd:272: Lost braces; missing escapes or markup?
   272 | \item{name}{the name of the model {"GNG", "iNUDGE","NUDGE"} where
       |                                   ^
Package suggested but not available for checking: 'rrelaxiv'
'LazyData' is specified without a 'data' directory
installed size is 13.4Mb
  sub-directories of 1Mb or more:
    libs  12.8Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   4.2Mb
GNU make is a SystemRequirements.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    tutorials   4.2Mb
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) mc_attitudes.Rd:52: Lost braces
    52 | P\'{a}ez, A. (2013). Mapping travelers’ attitudes: does space matter?. Journal of Transport Geography, 26, 117-125. (https://doi.org/10.1016/j.jtrangeo.2012.09.002)
       |    ^
checkRd: (-1) mc_commute.csv.Rd:49: Lost braces
    49 | Whalen, K. E., P\'{a}ez, A., & Carrasco, J. A. (2013). Mode choice of university students commuting to school and the role of active travel. Journal of Transport Geography, 31, 132-142. (https://doi.org/10.1016/j.jtrangeo.2013.06.008)
       |                   ^
checkRd: (-1) mc_commute_long.Rd:74: Lost braces
    74 | Whalen, K. E., P\'{a}ez, A., & Carrasco, J. A. (2013). Mode choice of university students commuting to school and the role of active travel. Journal of Transport Geography, 31, 132-142. (https://doi.org/10.1016/j.jtrangeo.2013.06.008)
       |                   ^
checkRd: (-1) mc_commute_wide.Rd:87: Lost braces
    87 | Whalen, K. E., P\'{a}ez, A., & Carrasco, J. A. (2013). Mode choice of university students commuting to school and the role of active travel. Journal of Transport Geography, 31, 132-142. (https://doi.org/10.1016/j.jtrangeo.2013.06.008)
       |                   ^
checkRd: (-1) mc_modality.Rd:50: Lost braces
    50 | Lavery, T., P\'{a}ez, A., & Kanaroglou, P.S. (2013). Driving out of choices: An investigation of transport modality in a university sample. Transportation Research Part A: Policy and Practice, 57:37-46 (https://doi.org/10.1016/j.tra.2013.09.010)
       |                ^
checkRd: (-1) cIndex.Rd:32: Lost braces; missing escapes or markup?
    32 | [a_{q-1}, a_q) are available.
       |    ^
checkRd: (-1) cIndexCompRisks.Rd:31: Lost braces; missing escapes or markup?
    31 | [a_{q-1}, a_q) are available.
       |    ^
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: \&
checkRd: (-1) estMargProb.Rd:23: Lost braces; missing escapes or markup?
    23 | a_2), ..., [a_{q-1}, a_q), [a_q, Inf).
       |               ^
checkRd: (-1) estMargProbCompRisks.Rd:24: Lost braces; missing escapes or markup?
    24 | a_2), ..., [a_{q-1}, a_q), [a_q, Inf).
       |               ^
checkRd: (-1) estSurv.Rd:23: Lost braces; missing escapes or markup?
    23 | a_2), ..., [a_{q-1}, a_q), [a_q, Inf).
       |               ^
checkRd: (-1) estSurvCompRisks.Rd:24: Lost braces; missing escapes or markup?
    24 | a_2), ..., [a_{q-1}, a_q), [a_q, Inf).
       |               ^
checkRd: (-1) lifeTable.Rd:21: Lost braces; missing escapes or markup?
    21 | [a_0, a_1), [a_1, a_2), ..., [a_{q-1}, a_q) ("character vector")}
       |                                 ^
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc       1.5Mb
    extdata   4.2Mb
'LazyData' is specified without a 'data' directory
checkRd: (-1) csv_to_disk.frame.Rd:56: Lost braces; missing escapes or markup?
    56 | strings, and you are encouraged to use {fasttime} to convert the strings to
       |                                        ^
checkRd: (-1) purrr_as_mapper.Rd:10: Lost braces; missing escapes or markup?
    10 | \item{.f}{a normal function or purrr syntax function i.e. `~{ ...code...}`}
       |                                                             ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Problems with news in 'NEWS.md':
No news entries found.
checkRd: (-1) dapply.Rd:27-30: Lost braces
    27 | udf <- function(x){
       |                   ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'BOLTSSIRR'
Running 'testthat.R' [102s]
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(divraster)
  Welcome to divraster!
  To acknowledge our work use: citation('divraster')
  > 
  > test_check("divraster")
  Saving _problems/test-alpha-22.R
  Saving _problems/test-beta_spatial-25.R
  Saving _problems/test-beta_temporal-37.R
  Saving _problems/test-rand-22.R
  [ FAIL 4 | WARN 383 | SKIP 0 | PASS 84 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-alpha.R:22:3'): function spat.alpha works ────────────────────
  Expected `spat.alpha(bin.crs)` to throw a error.
  ── Failure ('test-beta_spatial.R:25:3'): function spat.beta works ──────────────
  Expected `spat.beta(bin.crs)` to throw a error.
  ── Failure ('test-beta_temporal.R:37:3'): function temp.beta works ─────────────
  Expected `temp.beta(bin.crs, bin2)` to throw a error.
  ── Failure ('test-rand.R:22:3'): function spat.rand works ──────────────────────
  Expected `spat.rand(bin.crs, traits, 3, "spat")` to throw a error.
  
  [ FAIL 4 | WARN 383 | SKIP 0 | PASS 84 ]
  Error:
  ! Test failures.
  Execution halted
Running examples in 'divvy-Ex.R' failed
The error most likely occurred in:

> ### Name: bandit
> ### Title: Rarefy localities within latitudinal bands
> ### Aliases: bandit
> 
> ### ** Examples
> 
> # load bivalve occurrences to rasterise
> library(terra)
terra 1.8.86
> data(bivalves)
> 
> # initialise Equal Earth projected coordinates
> rWorld <- rast()
> prj <- 'EPSG:8857'
> rPrj <- project(rWorld, prj, res = 200000) # 200,000m is approximately 2 degrees
Warning: PROJ: proj_create_from_database: Cannot find proj.db (GDAL error 1)
Warning: PROJ: proj_create_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
Running 'testthat.R' [97s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(divvy)
  > 
  > test_check("divvy")
  Saving _problems/test_calc_eco_variables-32.R
  Saving _problems/test_subsample-50.R
  [ FAIL 2 | WARN 6 | SKIP 0 | PASS 28 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_calc_eco_variables.R:32:1'): (code run outside of `test_that()`) ──
  Error: [project] cannot get output boundaries for the target crs
  Backtrace:
      ▆
   1. ├─terra::project(rWorld, prj, res = 2e+05) at test_calc_eco_variables.R:32:1
   2. └─terra::project(rWorld, prj, res = 2e+05)
   3.   └─terra (local) .local(x, ...)
   4.     ├─terra::project(rast(x), y)
   5.     └─terra::project(rast(x), y)
   6.       └─terra (local) .local(x, ...)
   7.         └─terra:::messages(x, "project")
   8.           └─terra:::error(f, x@pntr$getError())
  ── Error ('test_subsample.R:50:1'): (code run outside of `test_that()`) ────────
  Error: [project] cannot get output boundaries for the target crs
  Backtrace:
      ▆
   1. ├─terra::project(rWorld, prj, res = 2e+05) at test_subsample.R:50:1
   2. └─terra::project(rWorld, prj, res = 2e+05)
   3.   └─terra (local) .local(x, ...)
   4.     ├─terra::project(rast(x), y)
   5.     └─terra::project(rast(x), y)
   6.       └─terra (local) .local(x, ...)
   7.         └─terra:::messages(x, "project")
   8.           └─terra:::error(f, x@pntr$getError())
  
  [ FAIL 2 | WARN 6 | SKIP 0 | PASS 28 ]
  Error:
  ! Test failures.
  Execution halted
Error(s) in re-building vignettes:
--- re-building 'habitat-rangesize-case-study.Rmd' using rmarkdown
--- finished re-building 'habitat-rangesize-case-study.Rmd'

--- re-building 'subsampling-vignette.Rmd' using rmarkdown

Quitting from subsampling-vignette.Rmd:84-100 [rasterise]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! [project] cannot get output boundaries for the target crs
---
Backtrace:
    ▆
 1. ├─terra::project(rWorld, prj, res = 2e+05)
 2. └─terra::project(rWorld, prj, res = 2e+05)
 3.   └─terra (local) .local(x, ...)
 4.     ├─terra::project(rast(x), y)
 5.     └─terra::project(rast(x), y)
 6.       └─terra (local) .local(x, ...)
 7.         └─terra:::messages(x, "project")
 8.           └─terra:::error(f, x@pntr$getError())
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'subsampling-vignette.Rmd' failed with diagnostics:
[project] cannot get output boundaries for the target crs
--- failed re-building 'subsampling-vignette.Rmd'

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Changes to previous versions
    Minor changes
    Fixes
    Previous Versions
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    libs   2.5Mb
Running 'testthat.R' [70s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(dmlalg)
  > 
  > test_check("dmlalg")
  Saving _problems/test-data_formats_regsdml-1332.R
  [ FAIL 1 | WARN 0 | SKIP 1 | PASS 1096 ]
  
  ══ Skipped tests (1) ═══════════════════════════════════════════════════════════
  • empty test (1): 'test-data_formats_regsdml.R:1385:1'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-data_formats_regsdml.R:1332:5'): return_results outputs right data formats ──
  Error in `expect(nrow(results$beta_test), d)`: `ok` must be `TRUE` or `FALSE`, not the number 3.
  Backtrace:
      ▆
   1. └─dmlalg (local) check_return_results_format(beta = beta, var = var, xx_colnames = xx_colnames) at test-data_formats_regsdml.R:1356:3
   2.   └─testthat::expect(ok = nrow(results$beta_test)) at test-data_formats_regsdml.R:1332:5
   3.     └─testthat:::check_bool(ok)
   4.       └─testthat:::stop_input_type(...)
   5.         └─rlang::abort(message, ..., call = call, arg = arg)
  
  [ FAIL 1 | WARN 0 | SKIP 1 | PASS 1096 ]
  Error:
  ! Test failures.
  Execution halted
checkRd: (-1) dca.Rd:24: Lost braces; missing escapes or markup?
    24 | \eqn{neglinks_{ij} = 1} means chunklet \code{i} and chunklet {j}
       |                                                              ^
checkRd: (-1) dca.Rd:26: Lost braces; missing escapes or markup?
    26 | \eqn{neglinks_{ij} = 0} means chunklet \code{i} and chunklet {j}
       |                                                              ^
checkRd: (-1) rca.Rd:57: Lost braces; missing escapes or markup?
    57 |       e.g. {1, 3, 7} and {4, 6}, might belong to the
       |            ^
checkRd: (-1) rca.Rd:57: Lost braces; missing escapes or markup?
    57 |       e.g. {1, 3, 7} and {4, 6}, might belong to the
       |                          ^
checkRd: (-1) scale_color_dMod.Rd:10: Lost braces
    10 | \item{...}{arguments goint to code{scale_color_manual()}}
       |                                   ^
checkRd: (-1) scale_fill_dMod.Rd:10: Lost braces
    10 | \item{...}{arguments goint to code{scale_color_manual()}}
       |                                   ^
checkRd: (-1) trust.Rd:103: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) trust.Rd:104: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) trust.Rd:105: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) trust.Rd:106: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) trust.Rd:107-108: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) trust.Rd:109-110: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) trust.Rd:111-112: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) trust.Rd:113-114: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) trust.Rd:115-122: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) trust.Rd:123-126: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) trust.Rd:127: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) trust.Rd:128-131: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) trust.Rd:132-133: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) trust.Rd:134-135: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) trust.Rd:136-138: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) trust.Rd:139-141: Lost braces in \itemize; \value handles \item{}{} directly
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) setCPT.O.Rd:85: Lost braces; missing escapes or markup?
    85 | statespace {0,1,2}, which this is *not* checked anywhere. Thus, if
       |            ^
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
checkRd: (-1) dnr.Rd:12: Escaped LaTeX specials: \#
checkRd: (-1) beetle.Rd:13: Lost braces; missing escapes or markup?
    13 |     \item{\code{x}}{dose (log base 10 CS2mgl^{-1})}
       |                                              ^
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
    libs   1.1Mb
'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
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    doc    6.7Mb
    libs   1.6Mb
GNU make is a SystemRequirements.
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
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    New features
Package suggested but not available for checking: 'gurobi'
'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) confint.dr4pl.Rd:49: Escaped LaTeX specials: \&
checkRd: (-1) gof-dr4pl.Rd:40: Escaped LaTeX specials: \&
checkRd: (-1) vcov.dr4pl.Rd:61: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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:43: Lost braces
    43 |   emph{Generalized Linear Models}, 
       |       ^
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: \&
checkRd: (-1) excalibur.Rd:18: Lost braces; missing escapes or markup?
    18 |     \item{\code{GR}}{a numeric vector: germination rates in d^{-1}}
       |                                                               ^
checkRd: (-1) festuca.Rd:16: Lost braces; missing escapes or markup?
    16 |     \item{\code{GR}}{a numeric vector: germination rates in d^{-1}}
       |                                                               ^
Specified C++11: please drop specification unless essential
checkRd: (-1) predict.drf.Rd:30-31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) predict.drf.Rd:32-33: Lost braces in \itemize; meant \describe ?
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GNU make is a SystemRequirements.
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Problems with news in 'NEWS.md':
No news entries found.
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    extdata   3.2Mb
installed size is  5.7Mb
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installed size is  5.2Mb
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    appinformation   4.1Mb
installed size is  5.7Mb
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    help   1.3Mb
    libs   3.7Mb
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    22 |   \item{error}{ Numeric value. Maximum pointwise error when estimating the density associated to X (f) in two consecutive steps. If this is missing, it is $1e{-06}$.}
       |                                                                                                                                                               ^
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    21 |    \item{error}{ Numeric value. Maximum pointwise error when estimating the density associated to X (f) in two consecutive steps. If this is missing, it is $1e{-06}$.}
       |                                                                                                                                                                ^
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    24 |   \item{error}{ Numeric value. Maximum pointwise error when estimating the density associated to X (f) in two consecutive steps. If this is missing, it is $1e{-06}$.}
       |                                                                                                                                                               ^
Specified C++11: please drop specification unless essential
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    64 | The empiric model is specified as F(d, beta) = d^{exp(beta)}. The logistic model is
       |                                                  ^
'LazyData' is specified without a 'data' directory
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GNU make is a SystemRequirements.
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    libs  35.6Mb
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'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
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
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    extdata   5.1Mb
Package suggested but not available for checking: 'cmdstanr'
installed size is 12.2Mb
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    R      3.5Mb
    data   7.3Mb
Problems with news in 'NEWS.md':
No news entries found.
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    27 |      For example, the order {a, b, c} implies that a > b, a  > c, and b > c.
       |                             ^
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    57 | By default, sampled from {-1, 1} with probabilities {.25, .75}.
       |                          ^
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    57 | By default, sampled from {-1, 1} with probabilities {.25, .75}.
       |                                                     ^
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installed size is  5.6Mb
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    data   2.5Mb
    doc    1.4Mb
Package required but not available: 'semPlot'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
installed size is  5.0Mb
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    data   3.9Mb
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    libs   1.8Mb
checkRd: (-1) monitor_long_1d.Rd:33: Lost braces
    33 | If \code{side="upward"}{apply control charts that aim to detect upward shifts.} \cr
       |                        ^
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    34 | If \code{side="downward"}{apply control charts that aim to detect downward shifts.} \cr
       |                          ^
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    35 | If \code{side="both"}{apply control charts that aim to detect shifts in both sides}}
       |                      ^
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    38 | If \code{chart="CUSUM"}{apply CUSUM charts.} \cr
       |                        ^
checkRd: (-1) monitor_long_1d.Rd:39: Lost braces
    39 | If \code{chart="EWMA"}{apply EWMA charts.}}
       |                       ^
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
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    34 | if (require(incidence)) {
       |                         ^
'LazyData' is specified without a 'data' directory
Running 'testthat.R' [10s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(earthtones)
  > 
  > test_check("earthtones")
  Saving _problems/test-earth-5.R
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 2 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-earth.R:5:3'): returns normal ──────────────────────────────────
  Error: [rast] empty srs
  Backtrace:
       ▆
    1. ├─testthat::expect_is(get_earthtones(), "palette") at test-earth.R:5:3
    2. │ └─testthat::quasi_label(enquo(object), label)
    3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
    4. └─earthtones::get_earthtones()
    5.   └─maptiles::get_tiles(...)
    6.     └─maptiles:::get_bbox_and_proj(x)
    7.       ├─terra::crs("epsg:4326")
    8.       └─terra::crs("epsg:4326")
    9.         └─terra (local) .local(x, ...)
   10.           ├─terra::rast(crs = x)
   11.           └─terra::rast(crs = x)
   12.             └─terra (local) .local(x = x, ...)
   13.               └─terra:::new_rast(...)
   14.                 └─terra:::messages(r, "rast")
   15.                   └─terra:::error(f, x@pntr$getError())
  
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 2 ]
  Error:
  ! Test failures.
  Execution halted
'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
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: 'gurobi'
Running examples in 'ebirdst-Ex.R' failed
The error most likely occurred in:

> ### Name: assign_to_grid
> ### Title: Assign points to a spacetime grid
> ### Aliases: assign_to_grid
> 
> ### ** Examples
> 
> set.seed(1)
> 
> # generate some example points
> points_xyt <- data.frame(x = runif(100), y = runif(100), t = rnorm(100))
> # assign to grid
> cells <- assign_to_grid(points_xyt, res = c(0.1, 0.1, 0.5))
> 
> # assign a second set of points to the same grid
> assign_to_grid(points_xyt, grid_definition = attr(cells, "grid_definition"))
# A tibble: 100 × 2
   cell_xy cell_xyt
   <chr>   <chr>   
 1 4-7     4-7-4   
 2 5-4     5-4-5   
 3 7-3     7-3-3   
 4 10-10   10-10-6 
 5 3-7     3-7-4   
 6 10-3    10-3-9  
 7 10-2    10-2-7  
 8 8-5     8-5-7   
 9 7-10    7-10-6  
10 2-7     2-7-9   
# ℹ 90 more rows
> 
> # assign lon-lat points to a 10km space-only grid
> points_ll <- data.frame(longitude = runif(100, min = -180, max = 180),
+                         latitude = runif(100, min = -90, max = 90))
> assign_to_grid(points_ll, res = c(10000, 10000), is_lonlat = TRUE)
Warning: PROJ: proj_create_from_database: Cannot find proj.db (GDAL error 1)
Warning: [vect] Cannot set SRS to vector: empty srs
Error: [project] input crs is not valid
Execution halted
'LazyData' is specified without a 'data' directory
Running 'testthat.R' [35s]
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(ebvcube)
  ebvcube 0.5.2
  > 
  > test_check("ebvcube")
  Saving _problems/test-ebv_create_taxonomy-31.R
  Saving _problems/test-ebv_create_taxonomy-101.R
  Saving _problems/test-ebv_manipulate-30.R
'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
Error(s) in re-building vignettes:
--- re-building 'ecoCopula.Rmd' using rmarkdown
File figure/unnamed-chunk-8-1.png not found in resource path
Error: processing vignette 'ecoCopula.Rmd' failed with diagnostics:
pandoc document conversion failed with error 99
--- failed re-building 'ecoCopula.Rmd'

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

Error: Vignette re-building failed.
Execution halted
installed size is 15.6Mb
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    doc    3.5Mb
    libs  11.1Mb
'LazyData' is specified without a 'data' directory
checkRd: (-1) ecolRxC.Rd:161-166: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) ecolRxC.Rd:217-221: Lost braces in \itemize; meant \describe ?
Package suggested but not available for checking: 'cmdstanr'
'LazyData' is specified without a 'data' directory
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'.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  6.0Mb
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    data   1.1Mb
    doc    4.4Mb
checkRd: (-1) transformFitness.Rd:25: Lost braces; missing escapes or markup?
    25 | minimization (most others). This function computes a factor from {-1, 1} for
       |                                                                  ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) read.edf.Rd:30: Lost braces
    30 | Kemp B., V\"{a}rri, A., Rosa, A.C., Nielsen, K.D. and Gade, J. (1992).
       |             ^
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    TODO:
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running 'test-all.R' [6s]
Running the tests in 'tests/test-all.R' failed.
Complete output:
  > library(testthat)
  > test_check("EDISON")
  Loading required package: EDISON
  Loading required package: corpcor
  Loading required package: MASS
  [1] "Initialisation successful."
  [1] "Starting tvDBN iterations..."
  5 % 10 % 15 % 20 % 25 % 30 % 35 % 40 % 45 % 50 % 55 % 60 % 65 % 70 % 75 % 80 % 85 % 90 % 95 % 100 % [1] ""
  [1] "End of iterations"
  [1] "Initialisation successful."
  [1] "Starting tvDBN iterations..."
  5 % 10 % 15 % 20 % 25 % 30 % 35 % 40 % 45 % 50 % 55 % 60 % 65 % 70 % 75 % 80 % 85 % 90 % 95 % 100 % [1] ""
  [1] "End of iterations"
  Saving _problems/test-structure-moves-329.R
  Saving _problems/test-structure-moves-333.R
  Saving _problems/test-structure-moves-337.R
  [ FAIL 3 | WARN 0 | SKIP 0 | PASS 17 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-structure-moves.r:328:1'): network info the same before and after  ──
  Error in `is_true()`: could not find function "is_true"
  Backtrace:
      ▆
   1. └─testthat::expect_that(updateCorrectly(), is_true())
  ── Error ('test-structure-moves.r:332:1'): rejected moves make no change ───────
  Error in `is_true()`: could not find function "is_true"
  Backtrace:
      ▆
   1. └─testthat::expect_that(noChangeOnReject(), is_true())
  ── Error ('test-structure-moves.r:336:1'): output not null ─────────────────────
  Error in `is_false()`: could not find function "is_false"
  Backtrace:
      ▆
   1. └─testthat::expect_that(...)
  
  [ FAIL 3 | WARN 0 | SKIP 0 | PASS 17 ]
  Error:
  ! Test failures.
  Execution halted
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    help   2.7Mb
    libs   4.3Mb
GNU make is a SystemRequirements.
checkRd: (-1) eesim.Rd:148-151: Lost braces in \itemize; \value handles \item{}{} directly
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checkRd: (-1) eesim.Rd:156-158: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
Error loading dataset 'model.xgb':
   Error in xgb.get.handle(model) : 
    'xgb.Booster' object is corrupted or is from an incompatible XGBoost version.
'LazyData' is specified without a 'data' directory
installed size is 12.6Mb
  sub-directories of 1Mb or more:
    libs  12.5Mb
Package required but not available: 'semPlot'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'eggCountsExtra'
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    doc       5.1Mb
    extdata   5.1Mb
Problems with news in 'NEWS.md':
No news entries found.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/EIX.Rcheck/00install.out' for details.
Running examples in 'eks-Ex.R' failed
The error most likely occurred in:

> ### Name: tidyst_kdr
> ### Title: Tidy and geospatial kernel density ridge estimates
> ### Aliases: tidy_kdr st_kdr
> ### Keywords: smooth
> 
> ### ** Examples
> ## tidy density ridge estimate
> library(ggplot2)
>  
> 
> ## geospatial density ridge estimate
> data(wa)
> data(grevilleasf)
> hakeoides <- dplyr::filter(grevilleasf, species=="hakeoides")
> ## gridsize=c(21,21) is for illustrative purposes only 
> ## remove for more complete KDR
> s1 <- st_kdr(hakeoides, gridsize=c(21,21))
> 
> ## base R plot
> xlim <- c(1.2e5, 1.1e6); ylim <- c(6.1e6, 7.2e6)
> plot(wa, xlim=xlim, ylim=ylim)
> plot(sf::st_geometry(hakeoides), add=TRUE, col=3, pch=16, cex=0.5)
> plot(s1, add=TRUE)
Error in center_h[i] <- center_h[i - 1] - max_sizes[i - 1]/2 - y_spacing -  : 
  replacement has length zero
Calls: plot ... <Anonymous> -> <Anonymous> -> do.call -> <Anonymous>
Execution halted
'LazyData' is specified without a 'data' directory
checkRd: (-1) fit_mean.Rd:54: Lost braces
    54 | \code{t_optims}{optimal parametrizations}
       |                ^
checkRd: (-1) fit_mean.Rd:55: Lost braces
    55 | \code{G_optims}{optimal rotations}
       |                ^
checkRd: (-1) fit_mean.Rd:56: Lost braces
    56 | \code{b_optims}{optimal scalings}
       |                ^
checkRd: (-1) fit_mean.Rd:57: Lost braces
    57 | \code{n_optims}{optimal re-normalization}
       |                ^
checkRd: (-1) fit_mean.Rd:58: Lost braces
    58 | \code{n_iter}{number of iterations until convergence}
       |              ^
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    47 | as a document at .tasks/task/${taskId}. This is yours to keep or remove
       |                               ^
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    48 | as a document at .tasks/task/${taskId}. This is yours to keep or remove
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    16 | Variables: \code{id}  = {identification number},
       |                         ^
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    17 | \code{state} = {state}, \code{age} = age in years on a shifted scale (current age minus 70),
       |                ^
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    25 |  TRUE for output on start-state totals e_{r.} (for \code{S}>0)
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    80 | \code{\link{score}}, \link{elo.run.helpers}{elo.run helpers}, \code{\link{elo.calc}},
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    41 |   \code{family="binomial"} should be a factor with two levels which is coded as \code{0} and {1}.
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    22 | less memory. Genetic data consists of nucleotide data {A,T,C,G} and are usually saved
       |                                                       ^
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   124 | Avg = 0.5 (sum | P_i - Q_i| + max{ | P_i - Q_i |})
       |                                  ^
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    18 | Compute the empirical MCR, assuming that #{cluster} = #{block},
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    18 | Compute the empirical MCR, assuming that #{cluster} = #{block},
       |                                                        ^
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   111 | \ifelse{html}{\out{<i>r</i><sub>1</sub> = 1}}{{\eqn{r_1 = 1}}{r_1 = 1}} while the individual with the lowest phenotypic value
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   112 | is given the rank \ifelse{html}{\out{<i>r<sub>n</sub></i> = <i>n</i>}}{{\eqn{r_n = n}}{r_n = n}}), the probability of an individual
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    16 | If Sigma has the q-factor decomposition Sigma=diag(Psi)+BB', then Sigma^{-1} 
       |                                                                         ^
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    17 | has the corresponding q-factor decomposition Sigma^{-1}=diag(phi)(I-theta theta')diag(phi), where theta is a mxq matrix and phi the vector of 
       |                                                    ^
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    21 | \item{iSB}{m x q matrix (diag(Psi)+BB')^{-1}B.}
       |                                         ^
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    15 | If Sigma has the q-factor decomposition Sigma=diag(Psi)+BB', then the function returns a matrix Omega such that Sigma^{-1} = Omega Omega'. Equivalently,
       |                                                                                                                       ^
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    24 | \item Graphs: Erd\"{o}s-R\'{e}nyi graphs with connection probability 0.10 for
       |                    ^
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       |                            ^
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    21 | \item Graphs: Erd\"{o}s-R\'{e}nyi graphs with connection probability given by
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       |                            ^
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    15 | A list of cluster labels and a R object of class "fcm {ppclust}"
       |                                                       ^
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    15 | A list of cluster labels and a R object of class "pam {cluster}"
       |                                                       ^
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     5 |   Conducts a generalized likelihood ratio test testing whether {\eqn{\beta \in}  (-\code{c},\code{c})}. Covariates can be accommodated.
       |                                                                ^
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    34 |   This is a similar function to the main function \code{evian}. Instead of testing H0: \eqn{\beta}=0, it tests for whether H0:{\eqn{\beta \in} (-\code{c},\code{c})}.
       |                                                                                                                               ^
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   183 |  \item {nlumgammagpd} and {proflumgammagpd} - \code{c(mgshape, mgscale, mgweight[1:(M-1)], sigmau, xi)}
       |                           ^
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   181 |  \item {nlumgammagpdcon} and {proflumgammagpdcon} - \code{c(mgshape, mgscale, mgweight[1:(M-1)], xi)}
       |                              ^
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    87 | code{\link[evmix:kernels]{kd*}}  and \code{\link[evmix:kernels]{kp*}} give the
       |     ^
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    18 | Procrustes distance provides a measure of coincidence of two point sets {xi} and {yi}, i=1..N. For this purpose the variance of point deviations is calculated at the optimal superposition of the sets. It allows to characterize the shape proximity of a given simplex to shape of a reference one.
       |                                                                         ^
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    18 | Procrustes distance provides a measure of coincidence of two point sets {xi} and {yi}, i=1..N. For this purpose the variance of point deviations is calculated at the optimal superposition of the sets. It allows to characterize the shape proximity of a given simplex to shape of a reference one.
       |                                                                                  ^
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    42 | CALI\'{N}SKI, T.; CORSTEN, L. C. A. Clustering
       |       ^
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    41 | CALI\'{N}SKI, T.; CORSTEN, L. C. A. Clustering
       |       ^
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Running examples in 'explore-Ex.R' failed
The error most likely occurred in:

> ### Name: explain_xgboost
> ### Title: Explain a binary target using xgboost
> ### Aliases: explain_xgboost
> 
> ### ** Examples
> 
> data <- use_data_iris()
> data$is_versicolor <- ifelse(data$Species == "versicolor", 1, 0)
> data$Species <- NULL
> explain_xgboost(data, target = is_versicolor, log = FALSE)
Warning in check.deprecation(deprecated_cv_params, match.call(), ...) :
  Passed invalid function arguments: eval_metric, nthread. These should be passed as a list to argument 'params'. Conversion from argument to 'params' entry will be done automatically, but this behavior will become an error in a future version.
Warning in check.custom.obj(params, objective) :
  Argument 'objective' is only for custom objectives. For built-in objectives, pass the objective under 'params'. This warning will become an error in a future version.
Error in all_nrounds[k] <- cv$best_iteration : 
  replacement has length zero
Calls: explain_xgboost
Execution halted
Error(s) in re-building vignettes:
--- re-building 'abtest.Rmd' using rmarkdown
--- finished re-building 'abtest.Rmd'

--- re-building 'clean-drop.Rmd' using rmarkdown
--- finished re-building 'clean-drop.Rmd'

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--- finished re-building 'data.Rmd'

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

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

Quitting from explain.Rmd:65-69 [unnamed-chunk-6]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `all_nrounds[k] <- cv$best_iteration`:
! replacement has length zero
---
Backtrace:
    ▆
 1. └─explore::explain_xgboost(data %>% drop_var_not_numeric(), target = buy)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'explain.Rmd' failed with diagnostics:
replacement has length zero
--- failed re-building 'explain.Rmd'

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--- finished re-building 'explore-mtcars.Rmd'

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SUMMARY: processing the following file failed:
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Error: Vignette re-building failed.
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     6 | Computation of aggregation matrices for generalized interactions that are used in code{\link{extRC}} to estimate extended RC models.
       |                                                                                       ^
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     5 | \description{It plots the output of code{\link{extRC}} function for a vector of lambda values.}
       |                                         ^
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     5 | \description{Given the output of code{\link{extRC}} function, it is written in a readable form.}
       |                                      ^
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     5 | \description{Summary method for the output of code{\link{extRC}} function.}
       |                                                   ^
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    80 | \doi{10.1016/s0002-9394(02)01825-1}{Beck et al.}, and
       |                                    ^
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checkRd: (-1) fmCov.Rd:37: Lost braces; missing escapes or markup?
    37 | where, \code{alpha(i)} is the intercept, \code{f(t)} is a {K x 1} vector of 
       |                                                           ^
checkRd: (-1) plot.ffm.Rd:82: Lost braces; missing escapes or markup?
    82 | \item{las}{one of {0, 1, 2, 3} to set the direction of axis labels, same as
       |                   ^
checkRd: (-1) summary.ffm.Rd:39: Lost braces; missing escapes or markup?
    39 | Returned object is of class {summary.ffm}.
       |                             ^
checkRd: (-1) fviz_nbclust.Rd:75: Lost braces; missing escapes or markup?
    75 | (2001) proposed: "the smallest k such that gap(k) >= gap(k+1) - s_{k+1}". 
       |                                                                   ^
checkRd: (-1) fviz_nbclust.Rd:77: Lost braces; missing escapes or markup?
    77 | SE.factor*s_{k+1}" where SE.factor is a numeric value which can be 1
       |             ^
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    minor changes
'LazyData' is specified without a 'data' directory
checkRd: (-1) FADPclust.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly
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checkRd: (-1) FADPclust.Rd:37: Lost braces in \itemize; \value handles \item{}{} directly
Packages required but not available: 'EGAnet', 'MBESS', 'semPlot'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
checkRd: (-1) happy.Rd:14: Lost braces
    14 |                  code{Pretty happy} <  \code{Very happy}}
       |                      ^
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    22 | A map of France as {sf} object. Can be used as dataset or for maps
       |                    ^
installed size is  5.8Mb
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    R      3.5Mb
    help   1.2Mb
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'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
installed size is  5.2Mb
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    doc    3.0Mb
    help   1.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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    doc    2.4Mb
    help   1.8Mb
    libs   2.4Mb
Specified C++11: please drop specification unless essential
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    R      2.8Mb
    help   2.1Mb
Error(s) in re-building vignettes:
--- re-building 'benchmark.Rmd' using rmarkdown

Quitting from benchmark.Rmd:53-62 [unnamed-chunk-2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! [rast] empty srs
---
Backtrace:
    ▆
 1. └─base::lapply(...)
 2.   └─global FUN(X[[i]], ...)
 3.     ├─terra::rast(...)
 4.     └─terra::rast(...)
 5.       └─terra (local) .local(x = x, ...)
 6.         └─terra:::new_rast(...)
 7.           └─terra:::messages(r, "rast")
 8.             └─terra:::error(f, x@pntr$getError())
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'benchmark.Rmd' failed with diagnostics:
[rast] empty srs
--- failed re-building 'benchmark.Rmd'

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

Quitting from index.Rmd:158-179 [visualize-kernels]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! [rast] empty srs
---
Backtrace:
    ▆
 1. ├─terra::rast(ext(0, 90, 0, 90), resolution = 30, crs = "EPSG:32611")
 2. └─terra::rast(ext(0, 90, 0, 90), resolution = 30, crs = "EPSG:32611")
 3.   ├─base::do.call(new_rast, dots)
 4.   └─terra (local) `<fn>`(...)
 5.     └─terra:::messages(r, "rast")
 6.       └─terra:::error(f, x@pntr$getError())
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'index.Rmd' failed with diagnostics:
[rast] empty srs
--- failed re-building 'index.Rmd'

SUMMARY: processing the following files failed:
  'benchmark.Rmd' 'index.Rmd'

Error: Vignette re-building failed.
Execution halted
installed size is  5.6Mb
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    images   3.1Mb
    libs     1.3Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    doc    1.0Mb
    libs   1.1Mb
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: 'coxKM'
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
    libs   1.2Mb
checkRd: (-1) eigen_compute_single_entry_of_diagonal_matrix.Rd:17: Lost braces; missing escapes or markup?
    17 | The value of m^{-1}_{j,j}
       |                ^
checkRd: (-1) eigen_compute_single_entry_of_diagonal_matrix.Rd:17: Lost braces; missing escapes or markup?
    17 | The value of m^{-1}_{j,j}
       |                     ^
'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
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/fastplyr.Rcheck/00install.out' for details.
checkRd: (-1) update_nhl_db.Rd:51-53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) update_nhl_db.Rd:54-57: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) update_phf_db.Rd:54-57: Lost braces in \itemize; meant \describe ?
installed size is 15.7Mb
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    data  15.7Mb
installed size is  5.3Mb
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    cgi-bin   2.5Mb
Running examples in 'faunabr-Ex.R' failed
The error most likely occurred in:

> ### Name: filter_faunabr
> ### Title: Identify records outside natural ranges according to Fauna do
> ###   Brasil
> ### Aliases: filter_faunabr
> 
> ### ** Examples
> 
> data("fauna_data") #Load fauna e Funga do Brasil data
> data("occurrences") #Load occurrences
> pts <- subset(occurrences, species == "Panthera onca")
> fd <- filter_faunabr(data = fauna_data,
+                      occ = pts, long = "x", lat = "y", species = "species",
+                      by_state = TRUE, buffer_state = 20,
+                      by_country = TRUE, buffer_country = 20,
+                      value = "flag&clean", keep_columns = TRUE,
+                      verbose = FALSE)
Warning: PROJ: proj_create: no database context specified (GDAL error 1)
Warning: [vect] Cannot set SRS to vector: empty srs
Error: [distance] crs not defined
Execution halted
checkRd: (-1) Error-Classes.Rd:107-119: Lost braces
   107 |   \item \code{do_verbose(response, template)} {
       |                                               ^
checkRd: (-1) Error.Rd:33-45: Lost braces
    33 |   \item \code{do(response, mssg)} {
       |                                   ^
installed size is  5.9Mb
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checkRd: (-1) FBN.histogramMaxima.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FBN.histogramMaxima.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FBN.histogramMaxima.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FBN.histogramMaxima.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FBN.kmeans.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FBN.kmeans.Rd:20: Lost braces in \itemize; meant \describe ?
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'LazyData' is specified without a 'data' directory
checkRd: (-1) fbad_copy_ad.Rd:25: Lost braces; missing escapes or markup?
    25 | \item{status_option}{(string) enum {ACTIVE, PAUSED, INHERITED_FROM_SOURCE}}
       |                                    ^
checkRd: (-1) fbad_copy_ad.Rd:27: Lost braces; missing escapes or markup?
    27 | \item{rename_strategy}{(string) enum {DEEP_RENAME, ONLY_TOP_LEVEL_RENAME, NO_RENAME}}
       |                                      ^
checkRd: (-1) fbad_copy_adset.Rd:34: Lost braces; missing escapes or markup?
    34 | \item{status_option}{(string) enum {ACTIVE, PAUSED, INHERITED_FROM_SOURCE}}
       |                                    ^
checkRd: (-1) fbad_copy_adset.Rd:36: Lost braces; missing escapes or markup?
    36 | \item{rename_strategy}{(string) enum {DEEP_RENAME, ONLY_TOP_LEVEL_RENAME, NO_RENAME}}
       |                                      ^
checkRd: (-1) fbad_copy_campaign.Rd:31: Lost braces; missing escapes or markup?
    31 | \item{status_option}{(string) enum {ACTIVE, PAUSED, INHERITED_FROM_SOURCE}}
       |                                    ^
checkRd: (-1) fbad_copy_campaign.Rd:33: Lost braces; missing escapes or markup?
    33 | \item{rename_strategy}{(string) enum {DEEP_RENAME, ONLY_TOP_LEVEL_RENAME, NO_RENAME}}
       |                                      ^
checkRd: (-1) plot.fbroc.conf.Rd:5: Lost braces
     5 | \title{Plots function for object of class{fbroc.conf}}
       |                                          ^
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    doc    4.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) simulation_model9.Rd:47: Lost braces; missing escapes or markup?
    47 | \item{ci}{A vector of 2 values containing $c_{1i}$ and $c_{2i}$ in the contamination
       |                                              ^
checkRd: (-1) simulation_model9.Rd:47: Lost braces; missing escapes or markup?
    47 | \item{ci}{A vector of 2 values containing $c_{1i}$ and $c_{2i}$ in the contamination
       |                                                           ^
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    libs   8.0Mb
GNU make is a SystemRequirements.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   1.4Mb
checkRd: (-1) NASAtemp.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) NASAtemp.Rd:15: Lost braces in \itemize; meant \describe ?
Error(s) in re-building vignettes:
--- re-building 'fdesigns_vignette.Rmd' using rmarkdown
! LaTeX Error: \begin{document} ended by \end{verbatim}.

Error: processing vignette 'fdesigns_vignette.Rmd' failed with diagnostics:
LaTeX failed to compile D:/RCompile/CRANpkg/local/4.4/fdesigns.Rcheck/vign_test/fdesigns/vignettes/fdesigns_vignette.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See fdesigns_vignette.log for more info.
--- failed re-building 'fdesigns_vignette.Rmd'

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
checkRd: (-1) p.fdr.Rd:30: Lost braces
    30 | \item{adjust.method}{A string used to identify the p-value and false discovery rate adjustment method. Defaults to \code{BH}. Options are \code{BH}, \code{BY}, code{Bon},\code{Holm}, \code{Hoch}, and \code{Sidak}.}
       |                                                                                                                                                                     ^
checkRd: (-1) mutlicol_terminator.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mutlicol_terminator.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mutlicol_terminator.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mutlicol_terminator.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rfeTerminator.Rd:42: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rfeTerminator.Rd:43: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rfeTerminator.Rd:44: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rfeTerminator.Rd:45: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
checkRd: (-1) morse.Rd:40: Escaped LaTeX specials: \#
checkRd: (-1) noRegMin.Rd:23: Escaped LaTeX specials: \#
checkRd: (-1) noRegMin.Rd:24: Escaped LaTeX specials: \#
checkRd: (-1) regMin.Rd:24: Escaped LaTeX specials: \#
Package suggested but not available for checking: 'HonestDiDFEct'
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'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
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    doc    2.3Mb
    help   2.5Mb
Unexported object imported by a ':::' call: 'bit:::R_bit_as_hi'
  See the note in ?`:::` about the use of this operator.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) contemParametros.Rd:19: Lost braces
    19 | \item{exclui3pontos}{verify por ... ? in f<-function(a, ...){ }}
       |                                                             ^
'LazyData' is specified without a 'data' directory
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installed size is  6.0Mb
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    data   1.8Mb
    libs   2.2Mb
Missing link or links in Rd file 'offGridWeights.Rd':
  ' predictSurface'

See section 'Cross-references' in the 'Writing R Extensions' manual.
installed size is  9.6Mb
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    R         4.6Mb
    doc       1.4Mb
    extdata   2.1Mb
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    doc   5.0Mb
'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
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checkRd: (-1) bitspec.Rd:8: Escaped LaTeX specials: \&
Running examples in 'fireexposuR-Ex.R' failed
The error most likely occurred in:

> ### Name: fire_exp_dir
> ### Title: Conduct a directional exposure assessment
> ### Aliases: fire_exp_dir
> 
> ### ** Examples
> 
> # read example hazard data
> hazard_file_path <- "extdata/hazard.tif"
> hazard <- terra::rast(system.file(hazard_file_path, package = "fireexposuR"))
> 
> # generate an example point
> point_wkt <- "POINT (345000 5876000)"
> point <- terra::vect(point_wkt, crs = hazard)
> 
> # compute exposure metric
> exposure <- fire_exp(hazard)
> 
> # assess directional exposure
> fire_exp_dir(exposure, point)
Warning: PROJ: proj_create_from_database: Cannot find proj.db (GDAL error 1)
Error: [project] output crs is not valid
Execution halted
Error(s) in re-building vignettes:
--- re-building 'fireexposuR.Rmd' using rmarkdown

Quitting from fireexposuR.Rmd:178-189 [example2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `fire_exp_dir()`:
! `exposure` and `value` must have the same CRS
---
Backtrace:
    ▆
 1. └─fireexposuR::fire_exp_dir(exposure, aoi)
 2.   └─base::stopifnot(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'fireexposuR.Rmd' failed with diagnostics:
`exposure` and `value` must have the same CRS
--- failed re-building 'fireexposuR.Rmd'

--- re-building 'prep-input-data.Rmd' using rmarkdown
--- finished re-building 'prep-input-data.Rmd'

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

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

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

Error: Vignette re-building failed.
Execution halted
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checkRd: (-1) FiSh-package.Rd:19: Lost braces
    19 | \doi{10.3389/feart.2020.00255}{Frontiers in Earth Science, 8:255}.
       |                               ^
checkRd: (-1) FiSh-package.Rd:32: Lost braces
    32 | \doi{10.3389/feart.2020.00255}{Frontiers in Earth Science, 8:255}.
       |                               ^
checkRd: (-1) SEP_FIM.Rd:46: Lost braces
    46 | \doi{10.3389/feart.2020.00255}{Frontiers in Earth Science, 8:255}.
       |                               ^
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checkRd: (-1) fitConic.Rd:66-73: Lost braces
    66 | \code{parA }{vector of the six "ABCDEF" coefficients
       |             ^
checkRd: (-1) fitConic.Rd:67: Lost braces
    67 | \code{RSS }{'root sum square' figure of merit describing the relative fit quality}
       |            ^
checkRd: (-1) fitConic.Rd:68: Lost braces
    68 | \code{iters }{number of iterations at convergence}
       |              ^
checkRd: (-1) fitConic.Rd:69-71: Lost braces
    69 | \code{exitCode }{1 means ellipse, 2 means hyperbola, 3 means parabola.
       |                 ^
checkRd: (-1) rotateA.Rd:59: Lost braces; missing escapes or markup?
    59 | For \code{xyrot} {a Nx2 array of the x,y coordinates of the rotated data set. }
       |                  ^
checkRd: (-1) fitmixEM.Rd:51: Escaped LaTeX specials: \&
Package suggested but not available for checking: 'gridlayout'
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   5.3Mb
Specified C++11: please drop specification unless essential
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Package suggested but not available for checking: 'STAR'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'fivethirtyeightdata'
checkRd: (-1) food_world_cup.Rd:70: Lost braces in \itemize; meant \describe ?
checkRd: (-1) food_world_cup.Rd:71: Lost braces in \itemize; meant \describe ?
checkRd: (-1) food_world_cup.Rd:72: Lost braces in \itemize; meant \describe ?
checkRd: (-1) food_world_cup.Rd:73: Lost braces in \itemize; meant \describe ?
checkRd: (-1) food_world_cup.Rd:74: Lost braces in \itemize; meant \describe ?
checkRd: (-1) food_world_cup.Rd:75: Lost braces in \itemize; meant \describe ?
Package unavailable to check Rd xrefs: 'fivethirtyeightdata'
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    R      1.4Mb
    doc    4.6Mb
    libs   1.6Mb
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    14 | All standard distributions from {stats} package are covered. For a list
       |                                 ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) convertInitDesignToGrid.Rd:11: Lost braces; missing escapes or markup?
    11 | The initial design, consisting of \code{d + 1} columns ({d} dimensions and
       |                                                         ^
Specified C++11: please drop specification unless essential
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    doc    1.9Mb
    help   2.3Mb
    libs   1.2Mb
checkRd: (-1) ModelMixHMM-class.Rd:31: Lost braces; missing escapes or markup?
    31 |         \code{smoothed} of class {StatMixHMM}).
       |                                  ^
checkRd: (-1) ModelMixHMMR-class.Rd:31: Lost braces; missing escapes or markup?
    31 |         \code{smoothed} of class {StatMixHMMR}).
       |                                  ^
checkRd: (-1) summary.flamcv.rd:8: Lost braces
     8 | This function summarizes a call to code{\link{flamCV}} and identifies the tuning parameter chosen by cross-validation.
       |                                        ^
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
checkRd: (-1) flashClust.Rd:92: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
checkRd: (-1) flex_dashboard.Rd:96: Lost braces; missing escapes or markup?
    96 | the `{.storyboard}` attribute to individual pages rather than using the
       |      ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) fmp.Rd:45: Lost braces; missing escapes or markup?
    45 | If k = 0: (xi_1, ..., x_{C_i - 1}, omega)
       |                         ^
checkRd: (-1) fmp.Rd:47: Lost braces; missing escapes or markup?
    47 | If k = 1: (xi_1, ..., x_{C_i - 1}, omega, alpha1, tau1)
       |                         ^
checkRd: (-1) fmp.Rd:49: Lost braces; missing escapes or markup?
    49 | If k = 2: (xi_1, ..., x_{C_i - 1}, omega, alpha1, tau1, alpha2, tau2)
       |                         ^
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    libs   9.6Mb
Running examples in 'flexurba-Ex.R' failed
The error most likely occurred in:

> ### Name: DoU_classify_grid
> ### Title: Create the DEGURBA grid cell classification
> ### Aliases: DoU_classify_grid
> 
> ### ** Examples
> 
> # load the data
> data_belgium <- DoU_load_grid_data_belgium()
Warning: PROJ: proj_get_authorities_from_database: Cannot find proj.db (GDAL error 1)
Error: [rast] empty srs
Execution halted
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    libs   8.1Mb
'LazyData' is specified without a 'data' directory
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    doc   9.1Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R      1.6Mb
    doc    1.2Mb
    libs   1.4Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    R   7.0Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R      2.7Mb
    help   1.4Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    htmlwidgets   3.9Mb
checkRd: (-1) flow_embed.Rd:30: Lost braces; missing escapes or markup?
    30 | \item Don't forget to add {flow} to Suggests in your DESCRIPTION file.
       |                           ^
checkRd: (-1) flowdata.Rd:10: Lost braces; missing escapes or markup?
    10 | \item{Flow}{Water flow, in m^{3}/s}
       |                              ^
Malformed Description field: should contain one or more complete sentences.
GNU make is a SystemRequirements.
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    libs   8.6Mb
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) FMP.Rd:30: Lost braces; missing escapes or markup?
    30 | \eqn{m(\theta) = b_0 + b_1 \theta + b_2 \theta^2 + b_3 \theta^3}. Acceptable values of k = {0,1,2,3}. According to 
       |                                                                                            ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) Estable.Rd:40: Lost braces
    40 |   \code{dEstable}{ gives the density function;}
       |                  ^
checkRd: (-1) Estable.Rd:41: Lost braces
    41 |   \code{pEstable}{ gives the distribution function or its complement;}
       |                  ^
checkRd: (-1) Estable.Rd:42: Lost braces
    42 |   \code{qEstable}{ gives quantiles;}
       |                  ^
checkRd: (-1) Estable.Rd:43-56: Lost braces
    43 |   \code{tailsEstable}{ returns a list with the following components
       |                      ^
checkRd: (-1) FMstable.Rd:50: Lost braces
    50 |   \code{dFMstable}{ gives the density function;}
       |                   ^
checkRd: (-1) FMstable.Rd:51: Lost braces
    51 |   \code{pFMstable}{ gives the distribution function or its complement;}
       |                   ^
checkRd: (-1) FMstable.Rd:52: Lost braces
    52 |   \code{qFMstable}{ gives quantiles;}
       |                   ^
checkRd: (-1) FMstable.Rd:53-66: Lost braces
    53 |   \code{tailsFMstable}{  returns a list with the following components
       |                       ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) navbar_page.Rd:36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) navbar_page.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) navbar_page.Rd:38: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    fonts   6.6Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    fonts   6.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'cmdstanr'
Package unavailable to check Rd xrefs: 'cmdstanr'
Package suggested but not available for checking: 'doMC'
checkRd: (-1) foreca.Rd:77: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) foreca.Rd:78-80: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) foreca.Rd:81-83: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) foreca.Rd:84-87: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) foreca.Rd:88-90: Lost braces in \itemize; \value handles \item{}{} directly
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checkRd: (-1) foreca.Rd:93: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) initialize_weightvector.Rd:53-54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) initialize_weightvector.Rd:55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) initialize_weightvector.Rd:56: Lost braces in \itemize; meant \describe ?
checkRd: (-1) initialize_weightvector.Rd:57: Lost braces in \itemize; meant \describe ?
checkRd: (-1) initialize_weightvector.Rd:58: Lost braces in \itemize; meant \describe ?
checkRd: (-1) initialize_weightvector.Rd:59: Lost braces in \itemize; meant \describe ?
checkRd: (-1) initialize_weightvector.Rd:60-61: Lost braces in \itemize; meant \describe ?
checkRd: (-1) initialize_weightvector.Rd:62: Lost braces in \itemize; meant \describe ?
checkRd: (-1) initialize_weightvector.Rd:63: Lost braces in \itemize; meant \describe ?
checkRd: (-1) initialize_weightvector.Rd:64-65: Lost braces in \itemize; meant \describe ?
Depends: includes the non-default packages:
  'distributional', 'doParallel', 'dplyr', 'fable', 'fabletools',
  'fable.prophet', 'feasts', 'fracdiff', 'ggplot2', 'gt', 'lubridate',
  'magrittr', 'parallel', 'readr', 'scales', 'tibble', 'tidyr',
  'tsibble', 'urca'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    doc   6.3Mb
    js    3.4Mb
'LazyData' is specified without a 'data' directory
checkRd: (-1) process_pcl.Rd:28: Lost braces; missing escapes or markup?
    28 | \item{pavd}{logical input to include Plant Area Volume Density Plot from {plot_pavd},
       |                                                                          ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) FGf.Rd:15: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) FGf.Rd:16: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) FGf.Rd:17: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) FGf.Rd:18: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) FGf.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) FourgameteP.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FourgameteP.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FourgameteP.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FourgameteP.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FourgameteP.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FourgameteP.Rd:32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FourgameteP.Rd:33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FourgameteP.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FourgameteP.Rd:35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FourgameteP.Rd:36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FourgameteP.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FourgameteP.Rd:38: Lost braces in \itemize; meant \describe ?
'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) plot_lines.Rd:66: Lost braces
    66 | moderator. By default it is equal to \8code{c(19, 17, 15, 8, 5, 4, 3, 1)}.}
       |                                            ^
checkRd: (-1) Fpop.Rd:8: Lost braces; missing escapes or markup?
     8 | sum_{i=1}^n (x_i-m_i)^2 + lambda * sum_{i=1}^{n-1} I(m_i !=
       |     ^
checkRd: (-1) Fpop.Rd:8: Lost braces; missing escapes or markup?
     8 | sum_{i=1}^n (x_i-m_i)^2 + lambda * sum_{i=1}^{n-1} I(m_i !=
       |                                        ^
checkRd: (-1) Fpop.Rd:8: Lost braces; missing escapes or markup?
     8 | sum_{i=1}^n (x_i-m_i)^2 + lambda * sum_{i=1}^{n-1} I(m_i !=
       |                                              ^
checkRd: (-1) Fpop.Rd:9: Lost braces; missing escapes or markup?
     9 | m_{i+1}), where the indicator function I counts the number of
       |   ^
Package suggested but not available for checking: 'RandomFields'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) emfrail_control.Rd:49: Lost braces in \itemize; meant \describe ?
checkRd: (-1) emfrail_control.Rd:50: Lost braces in \itemize; meant \describe ?
checkRd: (-1) emfrail_control.Rd:51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) emfrail_control.Rd:52: Lost braces in \itemize; meant \describe ?
checkRd: (-1) emfrail_control.Rd:53-54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) emfrail_control.Rd:55-57: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
installed size is  9.8Mb
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    R      1.7Mb
    help   2.8Mb
    libs   3.6Mb
checkRd: (-1) MultiAsset.Rd:26: Escaped LaTeX specials: \&
checkRd: (-1) summary.frbs.Rd:32: Lost braces
    32 |                           \code{"GAUSSIAN"}, code{"TRIANGLE"}, \code{"TRAPEZOID"}, \code{"SIGMOID"}, and \code{"BELL"}.
       |                                                  ^
checkRd: (-1) summary.frbs.Rd:60: Lost braces; missing escapes or markup?
    60 |          {4.0, 0.23, 0.43, 0.53, 0.73} on its column. It means that the label a.2 of variable v.1 
       |          ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) maximin.Rd:197: Lost braces
   197 | Meinshausen, N and P. B{u}hlmann (2015). Maximin effects in inhomogeneous large-scale data.
       |                        ^
installed size is  5.7Mb
  sub-directories of 1Mb or more:
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checkRd: (-1) NEWS.Rd:234: Escaped LaTeX specials: \_
checkRd: (-1) NEWS.Rd:257: Escaped LaTeX specials: \_ \_
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checkRd: (-1) NEWS.Rd:262: Escaped LaTeX specials: \_
checkRd: (-1) NEWS.Rd:265: Escaped LaTeX specials: \_
Package suggested but not available for checking: 'dggrids'
installed size is 20.6Mb
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    data   4.8Mb
    doc    1.8Mb
    libs  12.8Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
'LazyData' is specified without a 'data' directory
checkRd: (-1) FSelector-package.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FSelector-package.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FSelector-package.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FSelector-package.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) relief.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) relief.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) report.Rd:18: Lost braces; missing escapes or markup?
    18 |         \item{las}{numeric in {0,1,2,3}; the style of axis labels (see \code{\link{par}}).}
       |                               ^
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) Spec_compare_localize_freq.Rd:49: Escaped LaTeX specials: \&
checkRd: (-1) Spec_compare_localize_freq.Rd:52: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Package required but not available: 'MBESS'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    data   4.4Mb
    libs   1.6Mb
'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
'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
'LazyData' is specified without a 'data' directory
checkRd: (-1) trapezoidalApproximation-methods.Rd:49: Lost braces; missing escapes or markup?
    49 | For example, if Val(A) < EV_{1/3}(A) or Val(A) > EV_{2/3}(A),
       |                             ^
checkRd: (-1) trapezoidalApproximation-methods.Rd:49: Lost braces; missing escapes or markup?
    49 | For example, if Val(A) < EV_{1/3}(A) or Val(A) > EV_{2/3}(A),
       |                                                     ^
checkRd: (-1) genmf.Rd:26: Lost braces; missing escapes or markup?
    26 | \item 'gbellmf' is c(\code{a, b, c}), where \code{a} denotes the width, \code{b} is usually positive and {c} locates the center of the curve.
       |                                                                                                          ^
Found the following significant warnings:
  Note: possible error in 'findInterval(null, ti, ': unused arguments (checkSorted = FALSE, checkNA = FALSE) 
See 'd:/Rcompile/CRANpkg/local/4.4/fwb.Rcheck/00install.out' for details.
Information on the location(s) of code generating the 'Note's can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to 'yes'.
norm_inter_invert: possible error in findInterval(null, ti, checkSorted
  = FALSE, checkNA = FALSE): unused arguments (checkSorted = FALSE,
  checkNA = FALSE)
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    help   4.6Mb
checkRd: (-1) min_hpd_inc_area_df.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) min_hpd_inc_area_df.Rd:21-22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) min_hpd_inc_area_df.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) vza_mean_and_var_rasters.Rd:20: Lost braces
    20 | of the paper on Wilson's warbler, this function computes $tilde{T}^{(mu)}$ (returned as
       |                                                                ^
checkRd: (-1) vza_mean_and_var_rasters.Rd:20: Lost braces; missing escapes or markup?
    20 | of the paper on Wilson's warbler, this function computes $tilde{T}^{(mu)}$ (returned as
       |                                                                    ^
checkRd: (-1) vza_mean_and_var_rasters.Rd:21: Lost braces; missing escapes or markup?
    21 | list component \code{mean.raster}) and $R^{(sigma^2)}$ (returned as list component
       |                                           ^
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/galvanizer.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
checkRd: (-1) naref.Rd:13: Lost braces
    13 | \details{ For every \code{factor} or \code{character} column in \code{x}, \code{naref} sets \code{NA} as the reference level for a \code{factor} variable. Columns coded as \code{character} class are first converted to factors via \R{factor(x)}.  If \code{impute=TRUE} then the numeric columns are converted to two columns, one appended \code{.x} that contains imputed values and another appended \code{.miss} which is a binary variable indicating whether the original value was missing.  Numeric columns are returned without change if \code{impute=FALSE} or if they do not contain any missing values.  
       |                                                                                                                                                                                                                                         ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) pc.Rd:17: Lost braces
    17 | The functions \code{gamlss.pcr()} and \code{gamlss.pc()} are supporting functions. The  are not intended to be called directly by users. The function \code{gamlss.pc()} is using the linear model function \code{lm()} to fit the first principal components while the function code{gamlss.pcr()} uses \code{fitPCR()}.
       |                                                                                                                                                                                                                                                                                      ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.6Mb
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    doc   7.4Mb
installed size is 33.5Mb
  sub-directories of 1Mb or more:
    doc   31.8Mb
    libs   1.2Mb
'LazyData' is specified without a 'data' directory
checkRd: (-1) read.ctable.Rd:19: Lost braces; missing escapes or markup?
    19 | a integer scalar which is the index ({icol,irow}) of {row,col}-header
       |                                      ^
checkRd: (-1) read.ctable.Rd:19: Lost braces; missing escapes or markup?
    19 | a integer scalar which is the index ({icol,irow}) of {row,col}-header
       |                                                      ^
checkRd: (-1) read.ctable.Rd:29: Lost braces; missing escapes or markup?
    29 | output array, {row,col}.names are not necessary \code{dimnames[[1]]} and
       |               ^
installed size is  6.5Mb
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    extdata   1.6Mb
    libs      2.9Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
checkRd: (-1) fitgbd.Rd:29: Escaped LaTeX specials: \&
checkRd: (-1) fitgld.Rd:30: Escaped LaTeX specials: \&
checkRd: (-1) gb.Rd:28: Escaped LaTeX specials: \&
checkRd: (-1) gbd.Rd:37: Escaped LaTeX specials: \&
checkRd: (-1) gld.Rd:36: Escaped LaTeX specials: \&
checkRd: (-1) estprops.Rd:40: Escaped LaTeX specials: \&
Package suggested but not available for checking: 'paleofire'
checkRd: (-1) listInverseBlocks.Rd:5: Lost braces; missing escapes or markup?
     5 | \title{List all the inverse matrices of the leading sub-matrix of P=Sigma^{-1}
       |                                                                           ^
checkRd: (-1) listInverseBlocks.Rd:17: Lost braces; missing escapes or markup?
    17 | List all the inverse matrices of the leading sub-matrix of P=Sigma^{-1}
       |                                                                    ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) gconsensus.Rd:48-54: Lost braces
    48 | {\code{display.signif.digits} an integer representing the number of significant digits to be obtained in the adaptative approach of the Monte Carlo simulation,
       | ^
checkRd: (-1) GCTF.Rd:56: Lost braces; missing escapes or markup?
    56 |   U : A matrix which has N-rows and J-columns (J < {N, M}).
       |                                                    ^
checkRd: (-1) GCTF.Rd:57: Lost braces; missing escapes or markup?
    57 |   V : A matrix which has M-rows and J-columns (J < {N, M}).
       |                                                    ^
checkRd: (-1) GCTF.Rd:58: Lost braces; missing escapes or markup?
    58 |   J : The number of dimension (J < {N, M}).
       |                                    ^
installed size is 110.9Mb
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    L8NY18   2.3Mb
    gdal     3.0Mb
    libs    95.3Mb
    proj     9.0Mb
installed size is 110.9Mb
  sub-directories of 1Mb or more:
    extdata   2.0Mb
    gdal      3.0Mb
    libs     94.8Mb
    proj      9.0Mb
checkRd: (-1) nearblack.Rd:30: Lost braces
    30 | code{infile=}, indicating that the input file should be
       |     ^
Running examples in 'gdim-Ex.R' failed
The error most likely occurred in:

> ### Name: eigcv
> ### Title: Compute cross-validate eigenvalues
> ### Aliases: eigcv
> 
> ### ** Examples
> 
> 
> library(fastRG)
> 
> set.seed(27)
> 
> B <- matrix(0.1, 5, 5)
> diag(B) <- 0.3
> 
> model <- sbm(
+   n = 1000,
+   k = 5,
+   B = B,
+   expected_degree = 40,
+   poisson_edges = FALSE,
+   allow_self_loops = FALSE
+ )
Error: Must specify only one of `B` and `k`, not both.
Execution halted
Running 'testthat.R' [21s]
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(gdim)
  Loading required package: Matrix
  > 
  > test_check("gdim")
  
  Attaching package: 'fastRG'
  
  The following object is masked from 'package:testthat':
  
      expectation
  
  Saving _problems/test-eigcv-17.R
  Saving _problems/test-eigcv-81.R
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 3 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-eigcv.R:10:3'): symmetric eigcv, calculations on A ─────────────
  Error: Must specify only one of `B` and `k`, not both.
  Backtrace:
      ▆
   1. └─fastRG::sbm(...) at test-eigcv.R:10:3
   2.   └─fastRG::dcsbm(...)
  ── Error ('test-eigcv.R:74:3'): symmetric eigcv, calculations on L ─────────────
  Error: Must specify only one of `B` and `k`, not both.
  Backtrace:
      ▆
   1. └─fastRG::sbm(...) at test-eigcv.R:74:3
   2.   └─fastRG::dcsbm(...)
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 3 ]
  Error:
  ! Test failures.
  Execution halted
Package suggested but not available for checking: 'cdmTools'
installed size is  5.7Mb
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    extdata   3.8Mb
checkRd: (-1) GDSARM.Rd:7: Lost braces
     7 | Cand{\`e}s, E. and Tao, T. (2007). The Dantzig selector: Statistical estimation when p is much
       |     ^
checkRd: (-1) GDSARM.Rd:10: Lost braces
    10 | Dopico-Garc{\' i}a, M.S., Valentao, P., Guerra, L., Andrade, P. B., and Seabra, R. M. (2007).
       |            ^
checkRd: (-1) GDS_givencols.Rd:7: Lost braces
     7 | Cand{\`e}s, E. and Tao, T. (2007). The Dantzig selector: Statistical estimation when p is much
       |     ^
checkRd: (-1) GDS_givencols.Rd:10: Lost braces
    10 | Dopico-Garc{\' i}a, M.S., Valentao, P., Guerra, L., Andrade, P. B., and Seabra, R. M. (2007).
       |            ^
checkRd: (-1) dantzig.delta.Rd:7: Lost braces
     7 | Cand{\`e}s, E. and Tao, T. (2007). The Dantzig selector: Statistical estimation when p is much
       |     ^
checkRd: (-1) dantzigS.Rd:7: Lost braces
     7 | Cand{\`e}s, E. and Tao, T. (2007). The Dantzig selector: Statistical estimation when p is much
       |     ^
checkRd: (-1) dataCompoundExt.Rd:6: Lost braces
     6 | \title{Compound Extraction experiment of Dopico-Garc{\' i}a et al. (2007)}
       |                                                     ^
checkRd: (-1) dataCompoundExt.Rd:35: Lost braces
    35 | An analytical experiment conducted by Dopico-Garc{\' i}a et al. (2007) to
       |                                                  ^
checkRd: (-1) dataCompoundExt.Rd:22: Lost braces
    22 | Dopico-Garc{\' i}a, M.S., Valentao, P., Guerra, L., Andrade, P. B., and Seabra, R. M. (2007).
       |            ^
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
Package suggested but not available for checking: 'gdxrrw'
'LazyData' is specified without a 'data' directory
checkRd: (-1) dental.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dental.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dental.Rd:17: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) dental.Rd:19: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) seizure.Rd:15: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) geexex.Rd:14: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) geexex.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gelnet.logreg.obj.Rd:17: Lost braces; missing escapes or markup?
    17 | \item{y}{n-by-1 binary response vector sampled from {0,1}}
       |                                                     ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc       1.3Mb
    extdata   3.2Mb
    libs      1.0Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'genderdata'
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    doc       1.1Mb
    extdata   8.2Mb
checkRd: (-1) GeneF-internal.Rd:40: Lost braces; missing escapes or markup?
    40 | \author{Yinglei Lai {ylai@gwu.edu}}
       |                     ^
checkRd: (-1) flexorhtest.Rd:57: Lost braces; missing escapes or markup?
    57 | \author{Yinglei Lai {ylai@gwu.edu}}
       |                     ^
checkRd: (-1) flexorhtest.pvalue.Rd:57: Lost braces; missing escapes or markup?
    57 | \author{Yinglei Lai {ylai@gwu.edu}}
       |                     ^
train.xgboost: no visible global function definition for
  'cb.evaluation.log'
Undefined global functions or variables:
  cb.evaluation.log
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
checkRd: (-1) cpm.Rd:70: Lost braces; missing escapes or markup?
    70 | covariates included in \code{formula_l} or {formula_s} (required).}
       |                                            ^
checkRd: (-1) LD.Rd:37-46: Lost braces in \itemize; meant \describe ?
checkRd: (-1) LD.Rd:47-64: Lost braces in \itemize; meant \describe ?
checkRd: (-1) LD.Rd:66-73: Lost braces in \itemize; meant \describe ?
checkRd: (-1) LD.Rd:78-79: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) diseq.Rd:126-128: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) diseq.Rd:129: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
checkRd: (-1) barto.Rd:15-18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) barto.Rd:19-22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) barto.Rd:23-26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) chrY_subseg.Rd:16-17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) chrY_subseg.Rd:18-19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mauve_bbone.Rd:16-17: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) three_genes.Rd:17-18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) three_genes.Rd:19-20: Lost braces in \itemize; meant \describe ?
Problems with news in 'NEWS.md':
No news entries found.
checkRd: (-1) cfunc.new.Rd:57: Lost braces in \itemize; meant \describe ?
checkRd: (-1) cfunc.new.Rd:58-59: Lost braces in \itemize; meant \describe ?
checkRd: (-1) cfunc.new.Rd:60-61: Lost braces in \itemize; meant \describe ?
checkRd: (-1) cfunc.new.Rd:62: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) cfunc.new.Rd:65: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gensvm.grid.Rd:125: Lost braces
   125 | "Kernels in GenSVM" in the code{ink{gensvm-package}} page for more info.}
       |                                ^
checkRd: (-1) gensvm.grid.Rd:125: Lost braces
   125 | "Kernels in GenSVM" in the code{ink{gensvm-package}} page for more info.}
       |                                    ^
checkRd: (-1) gensvm.grid.Rd:127: Lost braces
   127 | GenSVM" in the code{ink{gensvm-package}} page for more info.}
       |                    ^
checkRd: (-1) gensvm.grid.Rd:127: Lost braces
   127 | GenSVM" in the code{ink{gensvm-package}} page for more info.}
       |                        ^
checkRd: (-1) gensvm.grid.Rd:129: Lost braces
   129 | section "Kernels in GenSVM" in the code{ink{gensvm-package}} page for more 
       |                                        ^
checkRd: (-1) gensvm.grid.Rd:129: Lost braces
   129 | section "Kernels in GenSVM" in the code{ink{gensvm-package}} page for more 
       |                                            ^
installed size is 13.5Mb
  sub-directories of 1Mb or more:
    libs  12.8Mb
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
'LazyData' is specified without a 'data' directory
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    extdata   3.0Mb
    libs      1.4Mb
'LazyData' is specified without a 'data' directory
checkRd: (-1) calvaria.Rd:8: Lost braces; missing escapes or markup?
     8 | A named list containing \code{x} {a vector containing the ages}
       |                                  ^
checkRd: (-1) calvaria.Rd:9: Lost braces; missing escapes or markup?
     9 |   \code{y} {a matrix where each column is a preshape.} The 23rd, 101st,
       |            ^
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    libs   4.4Mb
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  'mime'
A package should be listed in only one of these fields.
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:

R version 4.4.3 (2025-02-28 ucrt) -- "Trophy Case"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> pkgname <- "geoflow"
> source(file.path(R.home("share"), "R", "examples-header.R"))
> options(warn = 1)
> options(pager = "console")
> library('geoflow')
Loading ISO 19139 XML schemas...
Loading ISO 19115-3 XML schemas...
Loading ISO 19139 codelists...
======== End of example output (where/before crash/hang up occured ?) ========
Specified C++11: please drop specification unless essential
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    doc       2.1Mb
    extdata   3.5Mb
Running examples in 'geomander-Ex.R' failed
The error most likely occurred in:

> ### Name: get_lewis
> ### Title: Get historical United States Congressional District Shapefiles
> ### Aliases: get_lewis
> 
> ### ** Examples
> 
> get_lewis(state = 'NM', congress = 111)
Data sourced from the United States Congressional District Shapefiles
<https://cdmaps.polisci.ucla.edu/>.
This message is displayed once per session.
Warning in CPL_read_ogr(dsn, layer, query, as.character(options), quiet,  :
  GDAL Error 1: HTTP error code : 404
Error: Cannot open "https://raw.githubusercontent.com/JeffreyBLewis/congressional-district-boundaries/master/New_Mexico_108_to_112.geojson"; The file doesn't seem to exist.
Execution halted
Package suggested but not available for checking: 'geomarocdata'
installed size is 22.1Mb
  sub-directories of 1Mb or more:
    R        12.1Mb
    extdata   6.4Mb
    help      3.4Mb
Running examples in 'geoprofiler-Ex.R' failed
The error most likely occurred in:

> ### Name: swath_stats
> ### Title: Summary Statistics on Swath Elevation Profile
> ### Aliases: swath_stats
> 
> ### ** Examples
> 
> # Create a random raster
> r <- terra::rast(ncol = 10, nrow = 10, xmin = -150, xmax = -80, ymin = 20, ymax = 60)
> terra::values(r) <- runif(terra::ncell(r))
> 
> # Create a random profile
> profile <- data.frame(lon = c(-140, -90), lat = c(55, 25)) |>
+   sf::st_as_sf(coords = c("lon", "lat"), crs = "WGS84")
> swath <- swath_profile(profile, r, k = 5, dist = 10)
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)
Error: [project] cannot get output boundaries for the target crs
Execution halted
Error(s) in re-building vignettes:
--- re-building 'A_Distances.Rmd' using rmarkdown
--- finished re-building 'A_Distances.Rmd'

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

Quitting from B_Swath.Rmd:58-69 [load_data]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! [project] cannot get output boundaries for the target crs
---
Backtrace:
    ▆
 1. ├─terra::project(...)
 2. └─terra::project(...)
 3.   └─terra (local) .local(x, ...)
 4.     └─terra:::messages(x, "project")
 5.       └─terra:::error(f, x@pntr$getError())
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'B_Swath.Rmd' failed with diagnostics:
[project] cannot get output boundaries for the target crs
--- failed re-building 'B_Swath.Rmd'

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs   3.3Mb
GNU make is a SystemRequirements.
Package suggested but not available for checking: 'RandomFields'
Running examples in 'geostatsp-Ex.R' failed
The error most likely occurred in:

> ### Name: simLgcp
> ### Title: Simulate a log-Gaussian Cox process
> ### Aliases: simLgcp simPoissonPP
> 
> ### ** Examples
> 
> mymodel = c(mean=-0.5, variance=1, 
+ 				range=2, shape=2)
> 
> myraster = rast(nrows=15,ncols=20,xmin=0,xmax=10,ymin=0,ymax=7.5)
> 
> # some covariates, deliberately with a different resolution than myraster
> covA = covB = myoffset = rast(ext(myraster), 10, 10)
> values(covA) = as.vector(matrix(1:10, 10, 10))
> values(covB) = as.vector(matrix(1:10, 10, 10, byrow=TRUE))
> values(myoffset) = round(seq(-1, 1, len=ncell(myoffset)))
> 
> myCovariate = list(a=covA, b=covB, offsetFooBar = myoffset)
> 
> myLgcp=simLgcp(param=mymodel, 
+ 	covariates=myCovariate, 
+ 	betas=c(a=-0.1, b=0.25), 
+ 	offset='offsetFooBar',
+ 	rasterTemplate=myraster)
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)
Error(s) in re-building vignettes:
--- re-building 'geotargets.Rmd' using rmarkdown

Quitting from geotargets.Rmd:175-182 [make_vect]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
NULL
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'geotargets.Rmd' failed with diagnostics:
Error in tar_make():
  [project] output crs is not valid
  See https://books.ropensci.org/targets/debugging.html
--- failed re-building 'geotargets.Rmd'

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

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

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

> ### Name: grid_thinning
> ### Title: Perform Grid-Based Thinning of Spatial Points
> ### Aliases: grid_thinning
> 
> ### ** Examples
> 
> # Example: Grid thinning using thin_dist
> coords <- matrix(c(-122.4194, 37.7749,
+                         -122.4195, 37.7740,
+                         -122.4196, 37.7741), ncol = 2, byrow = TRUE)
> 
> result <- grid_thinning(coords, thin_dist = 10, trials = 5, all_trials = TRUE)
Warning: PROJ: proj_create_from_database: Cannot find proj.db (GDAL error 1)
Error: [rast] empty srs
Execution halted
Error(s) in re-building vignettes:
--- re-building 'GeoThinneR.Rmd' using rmarkdown

Quitting from GeoThinneR.Rmd:308-322 [unnamed-chunk-17]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! [rast] empty srs
---
Backtrace:
     ▆
  1. ├─base::system.time(...)
  2. └─GeoThinneR::thin_points(...)
  3.   └─GeoThinneR (local) perform_thinning(data)
  4.     └─GeoThinneR::grid_thinning(...)
  5.       ├─terra::rast(...)
  6.       └─terra::rast(...)
  7.         └─terra (local) .local(x = x, ...)
  8.           └─terra:::new_rast(...)
  9.             └─terra:::messages(r, "rast")
 10.               └─terra:::error(f, x@pntr$getError())
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'GeoThinneR.Rmd' failed with diagnostics:
[rast] empty srs
--- failed re-building 'GeoThinneR.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Malformed Description field: should contain one or more complete sentences.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc   5.7Mb
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    libs   8.4Mb
Specified C++11: please drop specification unless essential
checkRd: (-1) gesso.cv.Rd:46: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gesso.cv.Rd:47: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gesso.cv.Rd:48: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gesso.cv.Rd:49: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gesso.cv.Rd:50: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    extdata   4.9Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc   4.9Mb
Package suggested but not available for checking: 'RGtk2'
checkRd: (-1) QANOVA.Rd:62: Lost braces in \itemize; meant \describe ?
checkRd: (-1) QANOVA.Rd:63: Lost braces in \itemize; meant \describe ?
checkRd: (-1) QANOVA.Rd:64-66: Lost braces in \itemize; meant \describe ?
checkRd: (-1) QANOVA.Rd:67: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) gfonts.Rd:8: Lost braces; missing escapes or markup?
     8 | Download Google fonts and generate CSS to use in {rmarkdown} documents and
       |                                                  ^
checkRd: (-1) gfonts.Rd:9: Lost braces; missing escapes or markup?
     9 | {shiny} applications. Some popular fonts are included and ready to use.
       | ^
checkRd: (-1) use_pkg_gfont.Rd:5: Lost braces; missing escapes or markup?
     5 | \title{Use a Google Font included in {gfonts}}
       |                                      ^
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc       1.7Mb
    extdata   2.2Mb
    libs      1.0Mb
'LazyData' is specified without a 'data' directory
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    R   8.8Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   2.2Mb
    doc    1.9Mb
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    R     1.3Mb
    doc   2.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    R     1.2Mb
    doc   7.3Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    doc   7.0Mb
'LazyData' is specified without a 'data' directory
checkRd: (-1) pcp_scale.Rd:50: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pcp_scale.Rd:51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pcp_scale.Rd:52: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pcp_scale.Rd:53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pcp_scale.Rd:54-55: Lost braces in \itemize; meant \describe ?
Package suggested but not available for checking: 'OpenMx'
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    doc    7.4Mb
    help   1.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'lixoftConnectors'
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    help       2.4Mb
    testdata   3.0Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    help   5.7Mb
'LazyData' is specified without a 'data' directory
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    R     1.0Mb
    doc   4.0Mb
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    extdata   9.1Mb
Package suggested but not available for checking: 'semPlot'
'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:
    Win CRAN check results - R Windows
checkRd: (-1) MODFIT.Rd:33: Lost braces; missing escapes or markup?
    33 |   {chisq_i = sum( (O_iz - E_iz)^2 / E_iz; z = 0, ..., C ), }
       |   ^
checkRd: (-1) probs.GGUM.Rd:27: Lost braces; missing escapes or markup?
    27 |   GUM-based probabilities just constrain alpha to a unit vector of length {I}
       |                                                                           ^
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    doc    9.5Mb
    help   1.1Mb
'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc        1.9Mb
    examples   3.5Mb
'LazyData' is specified without a 'data' directory
installed size is 18.2Mb
  sub-directories of 1Mb or more:
    Giac  18.1Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc    3.1Mb
    help   3.0Mb
checkRd: (-1) gigg.Rd:70-77: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gigg.Rd:78: Lost braces in \itemize; \value handles \item{}{} directly
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No news entries found.
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: 'doMC'
Running examples in 'GLCMTextures-Ex.R' failed
The error most likely occurred in:

> ### Name: glcm_textures
> ### Title: Calculates GLCM texture metrics of a Raster Layer
> ### Aliases: glcm_textures
> 
> ### ** Examples
> 
> r<- rast(volcano, extent= ext(2667400, 2667400 + ncol(volcano)*10,
+ 6478700, 6478700 + nrow(volcano)*10), crs = "EPSG:27200")
Warning: PROJ: proj_create_from_database: Cannot find proj.db (GDAL error 1)
Error: [rast] empty srs
Execution halted
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    libs   5.1Mb
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    16 |         \item Now \code{AICc == Inf} when {n <= p + 1}.
       |                                           ^
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     4 | \description{Section 4.1.2 of the refence below descries a simulation study with data generated from a probit mixed model with six fixed effects parameters and a bivariate random effects vector having a 2 by 2 symmetric positive definite covariance matrix. The function simulates a data set from this model with 2500 groups and the number of observation in each group being a random draw from {20,21,...,30}.}
       |                                                                                                                                                                                                                                                                                                                                                                                                          ^
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
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GNU make is a SystemRequirements.
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    libs        4.5Mb
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    16 |                          a factor with levels either \\code{F} (female) or code{M} (male)}
       |                                                            ^
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    16 |                          a factor with levels either \\code{F} (female) or code{M} (male)}
       |                                                                                ^
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     4 | \title{{Gal\'{a}pagos} Island species data}
       |              ^
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     6 |   The number of species on the {Gal\'{a}pagos} Islands
       |                                ^
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     6 |   The number of species on the {Gal\'{a}pagos} Islands
       |                                      ^
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    40 |    {Gal\'{a}pagos} (the endemics). 
       |    ^
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    40 |    {Gal\'{a}pagos} (the endemics). 
       |          ^
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    44 |   Species number and endemism: The {Gal\'{a}pagos} Archipelago revisited.
       |                                          ^
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    14 |   \item{object}{A fitted model object, of class \code{glm}, \code{lm} or code{glm.nb}}
       |                                                                              ^
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    14 | code{glmulti} finds what are the \code{n} best models (the confidence set of models) among all possible models (the candidate set, as specified by the user).
       |     ^
checkRd: (-1) glmulti.Rd:99: Escaped LaTeX specials: \&
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Malformed Description field: should contain one or more complete sentences.
Package suggested but not available for checking: 'flexsdm'
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checkRd: (-1) rtheta.Rd:50-76: Lost braces in \itemize; meant \describe ?
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GNU make is a SystemRequirements.
Package suggested but not available for checking: 'doMC'
installed size is  6.3Mb
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    libs   1.1Mb
'LazyData' is specified without a 'data' directory
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    54 | of `{sf}` objects).}
       |     ^
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Malformed Description field: should contain one or more complete sentences.
installed size is  6.3Mb
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    R   5.7Mb
installed size is  9.1Mb
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    libs   8.2Mb
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    doc    3.5Mb
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Package suggested but not available for checking: 'cmdstanr'
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Malformed Title field: should not end in a period.
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    65 |         least one root larger than one) on bootstrapped \verb{x} and {y}.
       |                                                                      ^
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    68 |         least one root larger than one) on bootstrapped \verb{x} and {z}.
       |                                                                      ^
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    71 |         least one root larger than one) on bootstrapped \verb{x}, \verb{y} and {z}.
       |                                                                                ^
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Running 'testthat.R' [7s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(graphhopper)
  > 
  > test_check("graphhopper")
  Saving _problems/test_route-22.R
  [ FAIL 1 | WARN 0 | SKIP 2 | PASS 6 ]
  
  ══ Skipped tests (2) ═══════════════════════════════════════════════════════════
  • gh_is_avialable() is not TRUE (2): 'test_route-local-gh-instance.R:10:3',
    'test_spt-local-gh-instance.R:4:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_route.R:9:3'): sf LINESTRING ───────────────────────────────────
  <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_route.R:9:3
   2.   └─lifecycle::deprecate_stop("3.2.0", "with_mock()", "with_mocked_bindings()")
   3.     └─lifecycle:::deprecate_stop0(msg)
   4.       └─rlang::cnd_signal(...)
  
  [ FAIL 1 | WARN 0 | SKIP 2 | PASS 6 ]
  Error:
  ! Test failures.
  Execution halted
Specified C++11: please drop specification unless essential
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GNU make is a SystemRequirements.
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accrualReport: multiple local function definitions for 'gg' with
  different formal arguments
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    24 | \item{code{figpos}:}{LaTeX figure environment position; default is \code{"htb!"}}
       |           ^
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Package suggested but not available for checking: 'doMC'
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R     1.2Mb
    doc   2.8Mb
GNU make is a SystemRequirements.
Malformed Description field: should contain one or more complete sentences.
Specified C++11: please drop specification unless essential
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs                     1.2Mb
    supplementary_material   3.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    extdata   5.0Mb
Missing link or links in Rd file 'growthPheno-pkg.Rd':
  'byIndv4Times_periodicRates '

See section 'Cross-references' in the 'Writing R Extensions' manual.
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
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    14 | \item{refpts}{a numeric vector used as a reference point to determine the correct side of the \code{qdb} for classifying \code{x}. The \code{length(refpts)} should be equal to {ncol(x)}. Default to \code{colMeans(x)}. }
       |                                                                                                                                                                                 ^
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checkRd: (-1) artset1987.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tumor.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tumor.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tumor.Rd:12: Lost braces in \itemize; meant \describe ?
installed size is  5.6Mb
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    extdata   4.5Mb
    libs      1.0Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc    4.1Mb
    libs   1.1Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    data   1.0Mb
    help   2.0Mb
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
checkRd: (-1) guild_merge.Rd:38: Lost braces; missing escapes or markup?
    38 |     \item{\code{summary_name}}{Name used for the run summary. Use '${run_id}' in the name to include the run ID.}
       |                                                                     ^
checkRd: (-1) guild_merge_cli.Rd:88: Lost braces; missing escapes or markup?
    88 | \item{summary_name}{Name used for the run summary. Use '${run_id}' in the name to include the run ID.}
       |                                                          ^
installed size is  8.3Mb
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    htmlwidgets   8.2Mb
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    81 | \eqn{83} SNPs are in cluster {-}, \eqn{714} SNPs are in cluster \eqn{0},
       |                              ^
checkRd: (-1) esSimDiffPriors.Rd:91: Lost braces; missing escapes or markup?
    91 | \eqn{64} SNPs are in cluster {-}, \eqn{708} SNPs are in cluster \eqn{0},
       |                              ^
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'LazyData' is specified without a 'data' directory
installed size is 267.8Mb
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    R       1.5Mb
    help    1.1Mb
    java  264.7Mb
Package required and available but unsuitable version: 'h3lib'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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installed size is  7.7Mb
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    doc     3.6Mb
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  '.ga.breed' '.ga.fitness' '.ga.init' '.ga.mutate' '.ga.step'
  '.ga.weight'
Found the following significant warnings:
  hann.h:18:1: warning: function declaration isn't a prototype [-Wstrict-prototypes]
  common_utils.c:31:8: warning: function declaration isn't a prototype [-Wstrict-prototypes]
See 'd:/Rcompile/CRANpkg/local/4.4/hann.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 13.3.0'
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    data   2.7Mb
    doc    2.5Mb
    libs   1.3Mb
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  init.c:5:1: warning: function declaration isn't a prototype [-Wstrict-prototypes]
See 'd:/Rcompile/CRANpkg/local/4.4/hashmapR.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 13.3.0'
* used C++ compiler: 'g++.exe (GCC) 13.3.0'
installed size is  5.4Mb
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    data   2.4Mb
    doc    2.7Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Specified C++14: please drop specification unless essential
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R         2.6Mb
    extdata   1.3Mb
GNU make is a SystemRequirements.
checkRd: (-1) deff.sigma.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) deff.sigma.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) deff.sigma.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) deff.sigma.Rd:31: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) deff.sigma.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) deff.sigma.Rd:35: Lost braces in \itemize; meant \describe ?
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc   5.4Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc           2.7Mb
    htmlwidgets   2.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   6.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'cmdstanr'
checkRd: (-1) phenowheat.Rd:18: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) phenowheat.Rd:19: Lost braces in \enumerate; meant \describe ?
installed size is 13.5Mb
  sub-directories of 1Mb or more:
    include   2.3Mb
    lib      11.0Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
'LazyData' is specified without a 'data' directory
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   4.7Mb
    libs   1.3Mb
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is 15.4Mb
  sub-directories of 1Mb or more:
    R      8.9Mb
    data   6.2Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    doc    3.7Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc   5.3Mb
Malformed Title field: should not end in a period.
checkRd: (-1) colByValue.Rd:20: Lost braces; missing escapes or markup?
    20 | \item{las}{numeric in {0,1,2,3}; the style of axis labels.}
       |                       ^
'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc   5.4Mb
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   5.0Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) marker_h2.Rd:92: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) marker_h2.Rd:93: Lost braces in \itemize; \value handles \item{}{} directly
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checkRd: (-1) repeatability.Rd:45: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) glm.hermite.Rd:46-48: Lost braces in \itemize; \value handles \item{}{} directly
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checkRd: (-1) phermite.Rd:38: Lost braces; missing escapes or markup?
    38 |   {b} and \code{m} to be lower (or greater) than \code{q}.
       |   ^
GNU make is a SystemRequirements.
checkRd: (-1) hero.Rd:67-68: Lost braces
    67 | then \code{\link[pbapply]{pblapply}} is used. If code{package ==
       |                                                      ^
checkRd: (-1) hero.Rd:69: Lost braces
    69 | code{package == "Rmpi"}, then \code{\link[Rmpi]{mpi.applyLB}} is used.}
       |     ^
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   2.4Mb
'LazyData' is specified without a 'data' directory
checkRd: (-1) predictPair.Rd:20: Lost braces; missing escapes or markup?
    20 | A number in the set {-1, 0, 1}, where 1 means row1 is predicted to
       |                     ^
checkRd: (-1) predictPairInternal.Rd:18: Lost braces; missing escapes or markup?
    18 | A number in the set {-1, 0, 1}, where 1 means row1 is predicted to
       |                     ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) ohio.Rd:104: Escaped LaTeX specials: \&
checkRd: (-1) ohio.Rd:105: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    extdata   7.6Mb
checkRd: (-1) read.VCF.Rd:21: Lost braces
    21 | Reads a \url{https://samtools.github.io/hts-specs/}{Variant Call Format (VCF)} file into a BED object,
       |                                                    ^
checkRd: (-1) hierNet.Rd:28: Lost braces; missing escapes or markup?
    28 |     terms, th_{jj}X_j^2, in the model.  Default TRUE.}
       |               ^
checkRd: (-1) hierNet.logistic.Rd:30: Lost braces; missing escapes or markup?
    30 |     terms, th_{jj}X_j^2, in the model.  Default TRUE.}  
       |               ^
checkRd: (-1) hierNet.logistic.Rd:63: Lost braces
    63 | \seealso{\link{predict.hierNet.logistic},link{hierNet.logistic.path}}
       |                                              ^
checkRd: (-1) hierNet.logistic.path.Rd:39: Lost braces; missing escapes or markup?
    39 |   terms, th_{jj}X_j^2, in the model.  Default TRUE.}
       |             ^
checkRd: (-1) hierNet.path.Rd:38: Lost braces; missing escapes or markup?
    38 |   terms, th_{jj}X_j^2, in the model.  Default TRUE.}
       |             ^
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Package which this enhances but not available for checking: 'HadoopStreaming'
mdffits:
  function(model, ...)
mdffits.mer:
  function(object, level, delete, ...)
See section 'Generic functions and methods' in the 'Writing R
Extensions' manual.
checkRd: (-1) hlt.Rd:64: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) hltsim.Rd:38: Lost braces in \itemize; \value handles \item{}{} directly
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    article   3.2Mb
    doc       1.1Mb
    libs      6.1Mb
GNU make is a SystemRequirements.
Fdebug: multiple local function definitions for 'deb' with different
  formal arguments
html_describe_con: multiple local function definitions for 'g' with
  different formal arguments
checkRd: (-1) nafracCalc.Rd:45: Lost braces
    45 |   as if code{y} were not of class \code{"multipleHmmDataSets"}.
       |             ^
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is 15.2Mb
  sub-directories of 1Mb or more:
    libs  13.9Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   1.9Mb
    doc    4.0Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'glmmADMB'
checkRd: (-1) HOasso.Rd:43: Lost braces; missing escapes or markup?
    43 | Arguments \code{x} and {y} are \code{character} objects and can assume values   \code{"sout"}, \code{"dout"}, \code{"lout"}, \code{"sin"}, \code{"din"}, \code{"lin"} representing the out-strength, out-degree, out-log-strength, in-strength, in-degree, and in-log-strength respectively.
       |                        ^
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    app   1.7Mb
    doc   3.2Mb
'LazyData' is specified without a 'data' directory
checkRd: (-1) hd.ord.Rd:43: Lost braces in \itemize; \value handles \item{}{} directly
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checkRd: (-1) hd.ord.Rd:47: Lost braces in \itemize; \value handles \item{}{} directly
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checkRd: (-1) hd.ord.Rd:49: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hd.ord.Rd:50: Lost braces in \itemize; \value handles \item{}{} directly
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checkRd: (-1) hd.ord.Rd:55: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hd.ord.Rd:56: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hot.deck.Rd:39: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hot.deck.Rd:40: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hot.deck.Rd:41: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hot.deck.Rd:42: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hot.deck.Rd:43: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hot.deck.Rd:44: Lost braces in \itemize; \value handles \item{}{} directly
Running 'apply.r' [1s]
  Running 'arithmetic.r' [1s]
  Running 'as-array.r' [1s]
  Running 'colSums.r' [1s]
  Running 'copy.r' [1s]
  Running 'create.r' [1s]
  Running 'dim.r' [1s]
  Running 'extract-replace.r' [1s]
  Running 'inplace.r' [1s]
  Running 'marray.r' [1s]
  Running 'restore.r' [1s]
Running the tests in 'tests/marray.r' failed.
Complete output:
  > require(houba)
  Loading required package: houba
  > 
  > a <- mvector("int", 2)
  > a[2] <- 1
  > stopifnot( a[2] == 1 )
  > 
  > a <- mmatrix("float", 6, 3)
  > a[] <- 1:18
  > stopifnot( all(a[1,] == c(1, 7, 13)) )
  > 
  > a <- marray("double", 2:4)
  > a[] <- 1:24
  > stopifnot( all(a[2,1,] == c(2, 8, 14, 20)) )
  Error in a[2, 1, ] : argument is missing, with no default
  Calls: stopifnot -> [ -> [ -> myMissing
  Execution halted
Running 'testthat.R' [2s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(howzatR)
  > 
  > test_check("howzatR")
  Saving _problems/test-batting_basics-7.R
  Saving _problems/test-batting_basics-22.R
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 16 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-batting_basics.R:7:3'): bat_avg works ──────────────────────────
  Error in `expect(bat_avg(runs_scored = 50, no_dismissals = 2), 25)`: `ok` must be `TRUE` or `FALSE`, not the number 25.
  Backtrace:
      ▆
   1. └─testthat::expect(ok = bat_avg(runs_scored = 50, no_dismissals = 2)) at test-batting_basics.R:7:3
   2.   └─testthat:::check_bool(ok)
   3.     └─testthat:::stop_input_type(...)
   4.       └─rlang::abort(message, ..., call = call, arg = arg)
  ── Error ('test-batting_basics.R:22:3'): bat_sr works ──────────────────────────
  Error in `expect(bat_sr(runs_scored = 250, balls_faced = 200), 125)`: `ok` must be `TRUE` or `FALSE`, not the number 125.
  Backtrace:
      ▆
   1. └─testthat::expect(ok = bat_sr(runs_scored = 250, balls_faced = 200)) at test-batting_basics.R:22:3
   2.   └─testthat:::check_bool(ok)
   3.     └─testthat:::stop_input_type(...)
   4.       └─rlang::abort(message, ..., call = call, arg = arg)
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 16 ]
  Error:
  ! Test failures.
  Execution halted
checkRd: (-1) HPLB.Rd:33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) HPLB.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) HPLB.Rd:35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) HPLB.Rd:36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) HPLB.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) HPLB.Rd:38: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    data   7.0Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    doc    2.0Mb
    help   1.5Mb
checkRd: (-1) simplePostToHost.Rd:14: Escaped LaTeX specials: \&
GNU make is a SystemRequirements.
Packages suggested but not available for checking: 'hubExamples', 'hubVis'
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   4.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running 'testthat.R' [3s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(humanize)
  > 
  > test_check("humanize")
  Saving _problems/test_time-150.R
  Saving _problems/test_time-219.R
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 96 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_time.R:145:3'): natural_time works as expected ─────────────────
  <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_time.R:145:3
   2.   └─lifecycle::deprecate_stop("3.2.0", "with_mock()", "with_mocked_bindings()")
   3.     └─lifecycle:::deprecate_stop0(msg)
   4.       └─rlang::cnd_signal(...)
  ── Error ('test_time.R:214:3'): natural_time no months works as expected ───────
  <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_time.R:214:3
   2.   └─lifecycle::deprecate_stop("3.2.0", "with_mock()", "with_mocked_bindings()")
   3.     └─lifecycle:::deprecate_stop0(msg)
   4.       └─rlang::cnd_signal(...)
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 96 ]
  Error:
  ! Test failures.
  Execution halted
checkRd: (-1) CalcROC.Rd:47: Lost braces
    47 | The accuracy of the classifier is the mean value of dQuote{(optSn, optSp)} for two-class problem and the mean value of \dQuote{(optSn, optSp,optS3)} for three-class problem.
       |                                                           ^
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'hurricaneexposuredata'
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'microViz'
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    extdata   5.5Mb
    libs      1.0Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    extdata   4.8Mb
'LazyData' is specified without a 'data' directory
checkRd: (-1) extractPeriod.Rd:57: Lost braces
    57 | NOTE: all the dates in the datalist should follow the format in ?as.Date{base}.
       |                                                                         ^
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    extdata   5.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) IATData.Rd:24: Lost braces; missing escapes or markup?
    24 | Dan Martin {dpmartin42@gmail.com}
       |            ^
Running examples in 'IBLM-Ex.R' failed
The error most likely occurred in:

> ### Name: beta_corrected_density
> ### Title: Density Plot of Beta Corrections for a Variable
> ### Aliases: beta_corrected_density
> 
> ### ** Examples
> 
> # This function is created inside explain_iblm() and is output as an item
> 
> df_list <- freMTPLmini |> split_into_train_validate_test(seed = 9000)
> 
> iblm_model <- train_iblm_xgb(
+   df_list,
+   response_var = "ClaimRate",
+   family = "poisson"
+ )
Warning in throw_err_or_depr_msg("Parameter '", match_old, "' has been renamed to '",  :
  Parameter 'watchlist' has been renamed to 'evals'. This warning will become an error in a future version.
> 
> explain_objects <- explain_iblm(iblm_model, df_list$test)
Error in predict.xgb.Booster(booster_model, newdata = xgboost::xgb.DMatrix(data.matrix(data)),  : 
  [09:32:10] src/c_api/c_api_utils.h:127: Check failed: std::accumulate(shape.cbegin(), shape.cend(), static_cast<bst_ulong>(1), std::multiplies<>{}) == chunksize * rows (3764 vs. 30112) : 
Calls: explain_iblm ... extract_booster_shap.xgb.Booster -> data.frame -> <Anonymous> -> predict.xgb.Booster
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'SparkR'
checkRd: (-1) setServerLogLevel.Rd:20: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) setServerLogLevel.Rd:21: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) setServerLogLevel.Rd:22: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) setServerLogLevel.Rd:23: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) setServerLogLevel.Rd:24: Lost braces in \enumerate; meant \describe ?
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   5.6Mb
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    29 | \item A numeric p_norm, giving the factor between p_{gs} and phi_{0gs} (see paper for details).
       |                                                     ^
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    29 | \item A numeric p_norm, giving the factor between p_{gs} and phi_{0gs} (see paper for details).
       |                                                                  ^
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    39 | stocks. \doi{10.17895/ices.pub.3036}{\emph{ICES Advice
       |                                     ^
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    42 | stocks. \doi{10.17895/ices.pub.3036}{\emph{ICES Advice
       |                                     ^
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    64 | \doi{10.17895/ices.pub.3038}{\emph{ICES Advice Technical
       |                             ^
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    71 | \doi{10.17895/ices.pub.5997}{\emph{ICES Scientific Reports
       |                             ^
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See section 'The DESCRIPTION file' in the 'Writing R Extensions'
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    35 | distribution; 'd${dis}' gives the density function \eqn{g(\cdot)}.}
       |                  ^
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    24 | It develops an object of \code{lab.qcs}-code{link{class}} to perform statistical quality control.
       |                                             ^
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    24 | It develops an object of \code{lab.qcs}-code{link{class}} to perform statistical quality control.
       |                                                  ^
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    41 | be done either as a single vector of values (e.g. `function(x) { ... }`), or individual inputs for each parameter
       |                                                                ^
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       |                         ^
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    23 | \item{grayscale}{logical. Defines color channels of images: 1 if code{TRUE}, 3 if \code{FALSE}.}
       |                                                                      ^
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    23 | minority examples and majority ones, that is, the quotient {size of
       |                                                            ^
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    24 | minority class}/{size of majority class}. There are methods, such as
       |                 ^
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See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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GNU make is a SystemRequirements.
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    16 | This function creates a matrix such that P[t, s] = P(C = t | I = s) = theta_{t-s} for s <= t and 0 otherwise.
       |                                                                             ^
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    11 | the {janitor} package}
       |     ^
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    40 | adapted from the package {cowplot} by Claus O.Wilke and reflects the principles
       |                          ^
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    45 | It basically combines the half open theme with a grid background from {cowplot}
       |                                                                       ^
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Problems with news in 'NEWS.md':
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    INSPECTumours (development version)
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    44 | menu in the {utils} package, yesno in the {devtools} package.
       |             ^
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    44 | menu in the {utils} package, yesno in the {devtools} package.
       |                                           ^
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    25 | This function is useful for saveVideo() in the {animation} package.
       |                                                ^
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    27 | This function is useful for saveSWF() in the {animation} package.
       |                                              ^
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    25 | This function is a modified version of Yihui's shutdown function from the {fun} package.
       |                                                                           ^
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    32 | A data set to replicate the findings of Escrib\`{a}-Folch,
       |                                                 ^
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    38 | Escrib\`{a}-Folch, A., Meseguer, C. and Wright, J. (2018), Remittances and Protest in Dictatorships. American Journal of Political Science, 62: 889-904. \doi{10.1111/ajps.12382}
       |         ^
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    40 | \item{dqfunc}{function, density of the results of the quantile function, e.g., function(x){dnorm(qnorm(x))} (used for 'general' scores, 
       |                                                                                           ^
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Running examples in 'inTrees-Ex.R' failed
The error most likely occurred in:

> ### Name: XGB2List
> ### Title: Transform an xgboost object to a list of trees
> ### Aliases: XGB2List
> ### Keywords: xgboost
> 
> ### ** Examples
> 
> 	library(data.table)
> 	library(xgboost)
> 	# test data set 1: iris
> 	X <- within(iris,rm("Species")); Y <- iris[,"Species"]
> 	X <- within(iris,rm("Species")); Y <- iris[,"Species"]
> 	model_mat <- model.matrix(~. -1, data=X)
> 	xgb <- xgboost(model_mat, label = as.numeric(Y) - 1, nrounds = 20, 
+ 		objective = "multi:softprob", num_class = 3 )
Warning in throw_err_or_depr_msg("Passed unrecognized parameters: ", paste(head(names_unrecognized),  :
  Passed unrecognized parameters: num_class. 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 'label' has been renamed to 'y'. This warning will become an error in a future version.
Error in process.y.margin.and.objective(y, base_margin, objective, params) : 
  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: multi:softprob
Calls: xgboost -> process.y.margin.and.objective
Execution halted
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    60 | B\'{e}dard, J. & Gauthier, G. 1986. Assessment of faecal output in geese. Journal of Applied Ecology, 23, 77-90.
       |    ^
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    64 | Bates, D., M\"{a}chler, M., Bolker, B.M. & Walker, S.C. (2015). Fitting linear mixed-effects models using lme4. Journal of Statistical Software, 67, 1-48.
       |               ^
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    25 | where F is the field of influence, k is order of influence, l_{ij} is the ith row and jth column element of the Leontief Inverse and -s indicates the sth element has been removed.
       |                                                               ^
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    19 | impact. emph{Journal of Applied Psychology}, 92(5), 1380.
       |             ^
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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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    47 | \code{conv_plot}: code{ipm} invisibly.
       |                       ^
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Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/IsoriX.Rcheck/00install.out' for details.
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Running 'testthat.R' [21s]
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(IVDML)
  > 
  > test_check("IVDML")
  Saving _problems/test-fit_IVDML-86.R
  Saving _problems/test-fit_IVDML-98.R
  Fitted IVDML object
  Machine learning method:  gam 
  IV methods:  linearIV, mlIV 
  Number of cross-fitting sample splits:  1[ FAIL 2 | WARN 6 | SKIP 0 | PASS 31 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-fit_IVDML.R:86:3'): fit_IVDML works when ml_par are set globally. ──
  Expected `fit_IVDML(...)` not to throw any errors.
  Actually got a <simpleError> with message:
    argument "y" is missing, with no default
  ── Failure ('test-fit_IVDML.R:98:3'): fit_IVDML works when ml_par is set differently for the different nuisance functions. ──
  Expected `fit_IVDML(...)` not to throw any errors.
  Actually got a <simpleError> with message:
    argument "y" is missing, with no default
  
  [ FAIL 2 | WARN 6 | SKIP 0 | PASS 31 ]
  Error:
  ! Test failures.
  Execution halted
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    17 | \item{pi}{the matrix E[XZ']E[ZZ']^{-1}}
       |                                   ^
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    20 | \item{pi}{matrix, corresponds to E[XZ']E[ZZ']^{-1}, the first stage
       |                                               ^
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    extdata   1.0Mb
Error(s) in re-building vignettes:
--- re-building 'ivo_table.Rmd' using rmarkdown
File man/figures/logo.png not found in resource path
Error: processing vignette 'ivo_table.Rmd' failed with diagnostics:
pandoc document conversion failed with error 99
--- failed re-building 'ivo_table.Rmd'

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

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

Error: Vignette re-building failed.
Execution halted
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    41 | The {bootstrap} method uses resampling with replacement binary vectors to compute a p-value (see optional arguments).
       |     ^
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GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Found the following Makefile(s) with an include directive with a pathname using R_HOME:
  src/jvm-w32/Makefile
Even though not recommended, variable R_HOME may contain spaces.
Makefile directives use space as a separator and there is no portable
way to quote/escape the space in Make rules and directives.  However,
one can and should quote pathnames when passed from Makefile to the
shell, and this can be done specifically when invoking Make recursively.
It is therefore recommended to use the Make '-f' option to include files
in directories specified using R_HOME.  This option can be specified
multiple times to include multiple Makefiles.  Note that 'Makeconf' is
included automatically into top-level makefile of a package.
More information can be found in 'Writing R Extensions'.
installed size is  6.1Mb
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Package suggested but not available for checking: 'clonevol'
installed size is  6.0Mb
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GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
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   298 | following transformation b_1 + b_2*I_1(Y(t)) + ... + b_{n+2}*I_{n+1}(Y(t)),
       |                                                        ^
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   298 | following transformation b_1 + b_2*I_1(Y(t)) + ... + b_{n+2}*I_{n+1}(Y(t)),
       |                                                                ^
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   299 | where I_1,...,I_{n+1} is the basis of quadratic I-splines. To constraint the
       |                 ^
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    42 |     The control argument of \code{jmdem} is by default passed to the control argument of {jmdem.fit}, which uses its elements as arguments to {jmdem.control}: the latter provides defaults and sanity checking.
       |                                                                                          ^
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    42 |     The control argument of \code{jmdem} is by default passed to the control argument of {jmdem.fit}, which uses its elements as arguments to {jmdem.control}: the latter provides defaults and sanity checking.
       |                                                                                                                                               ^
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    libs   3.7Mb
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installed size is 16.4Mb
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'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    pre-release juicr (2017 - 2021)
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    14 | The {kdist} functions dk, pk, qk and rk, calculates the K-distribution
       |     ^
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    help  10.8Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/kerastuneR.Rcheck/00install.out' for details.
checkRd: (-1) kernelFactory.Rd:21: Lost braces; missing escapes or markup?
    21 | \item{method}{Can be one of the following: POLynomial kernel function (\code{pol}), LINear kernel function (\code{lin}), Radial Basis kernel Function \code{rbf}), random choice (random={pol, lin, rbf}) (\code{random}), burn- in choice of best function (burn={pol, lin, rbf }) (\code{burn}). Use \code{random} or \code{burn} if you don't know in advance which kernel function is best.}
       |                                                                                                                                                                                          ^
checkRd: (-1) kernelFactory.Rd:21: Lost braces; missing escapes or markup?
    21 | \item{method}{Can be one of the following: POLynomial kernel function (\code{pol}), LINear kernel function (\code{lin}), Radial Basis kernel Function \code{rbf}), random choice (random={pol, lin, rbf}) (\code{random}), burn- in choice of best function (burn={pol, lin, rbf }) (\code{burn}). Use \code{random} or \code{burn} if you don't know in advance which kernel function is best.}
       |                                                                                                                                                                                                                                                                   ^
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    23 | the scale on which to evaluate each subject. \code{stype = "ObsScore"} uses the subject's total score. \code{stype = "Theta"} uses the subject's rank on the \code{thetadist} scale. \code{stype = "ThetaML"} uses the maximum likelihood estimate for the subject on the \code{thetadist} scale. code{stype = "ScoreML"} uses the maximum likelihood estimate for the subject on the overall test score scale.
       |                                                                                                                                                                                                                                                                                                       ^
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    13 | This function adds the {keys} dependencies to your application
       |                        ^
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Minor Changes
Package suggested but not available for checking: 'semPlot'
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    26 |  \item{kpca.train}{An object of class "kpca". It has results of \code{kpca} function. (see{\code{\link[kernlab]{kpca}}} (in package \pkg{kernlab}))}
       |                                                                                           ^
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    52 |        plus the OK values. Prediction corresponds to E[X_{t} | Y_{1...t}] 
       |                                                          ^
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    52 |        plus the OK values. Prediction corresponds to E[X_{t} | Y_{1...t}] 
       |                                                                  ^
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    10 | \item{x}{An object of class \code{KinPairData} or {KinPairSimulation}}
       |                                                   ^
Package which this enhances but not available for checking: 'rkward'
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    21 |     list of two functions,flist=list( f1=function( x ) { x } ,f2=function( x ) { x^2 } )  
       |                                                        ^
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    21 |     list of two functions,flist=list( f1=function( x ) { x } ,f2=function( x ) { x^2 } )  
       |                                                                                ^
Specified C++11: please drop specification unless essential
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GNU make is a SystemRequirements.
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    20 |   \item{shape}{If the estimators in the function link[KnowBR]{KnowBPolygon} were calculated using an external shape file, it is necessary to indicate the file in this argument. It is not necessary to select any polygon within the file, just to load the whole shape file.}
       |                                                              ^
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    26 |   \item{shape}{If the estimators in the function link[KnowBR]{KnowBPolygon} were calculated using an external shape file, it is necessary to indicate the file in this argument. It is not necessary to select any polygon within the file, just to load the whole shape file.}
       |                                                              ^
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  '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'
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    60 | Finally, one can control the field {optim.option} in order to decide how to optimize the sampling criterion.
       |                                    ^
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    29 | Finally, one can control the field {optim.option} in order to decide how to optimize the sampling criterion. 
       |                                    ^
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    30 | Finally, one can control the field {optim.option} in order to decide how to optimize the sampling criterion. 
       |                                    ^
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    30 | Finally, one can control the field {optim.option} in order to decide how to optimize the sampling criterion.
       |                                    ^
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    72 | Optional argument. When set to code{NULL} (default) the function performs the projections on plans spanned by each pair (i,j) of dimension. Otherwise, the argument is an array of size 2 corresponding to the dimensions spanning the (only) plan on which the projection is performed.
       |                                    ^
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    45 |   and alpha_train is the BLUP of alpha for the model, i.e. alpha_train=Cov(alpha,Y_train)*Var(Y_train)^{-1}*(Y_train - E[Y_train]) }
       |                                                                                                        ^
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    14 | are valid. See /code{LcKS} for accepted functions.}
       |                     ^
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    46 | 3) Every coordinate yi of the outcome vector y exists in {-1, 1}^n is sampled 
       |                                                          ^
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checkRd: (-1) lambda.r-package.Rd:71-74: Lost braces
    71 | x \%g\% y \%:=\% {
       |                  ^
GNU make is a SystemRequirements.
Running 'testthat.R' [35s]
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(LandComp)
  > 
  > test_check("LandComp")
  Saving _problems/test-LandComp-17.R
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 86 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-LandComp.R:17:13'): inappropriate x ────────────────────────────
  Error in `stop_if_not(length(maxSizeOfObjects) == 1L, is.numeric(maxSizeOfObjects), !is.na(maxSizeOfObjects), maxSizeOfObjects >= 0)`: 'list' object cannot be coerced to type 'double'
  Backtrace:
       ▆
    1. ├─testthat::expect_warning(...) at test-LandComp.R:17:13
    2. │ └─testthat:::quasi_capture(...)
    3. │   ├─testthat (local) .capture(...)
    4. │   │ └─base::withCallingHandlers(...)
    5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
    6. ├─LandComp::LandComp(x = hexagonal_data_logi, aggregation_steps = 0)
    7. │ └─future::plan("future::multisession")
    8. │   └─future (local) plan_set(...)
    9. │     └─future:::plan_init(stack[[1]], debug = debug)
   10. │       └─future:::makeFutureBackend(evaluator, debug = debug)
   11. │         └─base::do.call(factory, args = args, envir = envir)
   12. └─future (local) `<fn>`(...)
   13.   └─future::ClusterFutureBackend(...)
   14.     └─future::MultiprocessFutureBackend(...)
   15.       └─future::FutureBackend(...)
   16.         └─future:::stop_if_not(...)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 86 ]
  Error:
  ! Test failures.
  Execution halted
Error(s) in re-building vignettes:
--- re-building 'LandComp.Rmd' using rmarkdown

Quitting from LandComp.Rmd:66-68 [square_example2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `stop_if_not()`:
! 'list' object cannot be coerced to type 'double'
---
Backtrace:
     ▆
  1. ├─LandComp::LandComp(...)
  2. │ └─future::plan("future::multisession")
  3. │   └─future (local) plan_set(...)
  4. │     └─future:::plan_init(stack[[1]], debug = debug)
  5. │       └─future:::makeFutureBackend(evaluator, debug = debug)
  6. │         └─base::do.call(factory, args = args, envir = envir)
  7. └─future (local) `<fn>`(...)
  8.   └─future::ClusterFutureBackend(...)
  9.     └─future::MultiprocessFutureBackend(...)
 10.       └─future::FutureBackend(...)
 11.         └─future:::stop_if_not(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'LandComp.Rmd' failed with diagnostics:
'list' object cannot be coerced to type 'double'
--- failed re-building 'LandComp.Rmd'

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

Error: Vignette re-building failed.
Execution halted
checkRd: (-1) GenerateData.Rd:35-36: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) GenerateData.Rd:37-38: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) GenerateData.Rd:39-40: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) GenerateData.Rd:41-42: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) GenerateData.Rd:43-44: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) GenerateData.Rd:45: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) landmix.estimator.Rd:59-65: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) landmix.estimator.Rd:67-74: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) DOS.Rd:34: Lost braces; missing escapes or markup?
    34 |         Band-specific sensor $G_{rescale}$ (gain). Require either gain and offset or Grescale and Brescale to convert DN to radiance.
       |                                 ^
checkRd: (-1) DOS.Rd:37: Lost braces; missing escapes or markup?
    37 |         Band-specific sensor $B_{rescale}$ (bias). Require either gain and offset or Grescale and Brescale to convert DN to radiance.
       |                                 ^
Running examples in 'landscapemetrics-Ex.R' failed
The error most likely occurred in:

> ### Name: check_landscape
> ### Title: Check input landscape
> ### Aliases: check_landscape
> 
> ### ** Examples
> 
> augusta_nlcd <- terra::rast(landscapemetrics::augusta_nlcd)
> check_landscape(augusta_nlcd)
  layer       crs units   class n_classes OK
1     1 projected     m integer        15  ✔
> podlasie_ccilc <- terra::rast(landscapemetrics::podlasie_ccilc)
Warning: PROJ: proj_create_from_database: Cannot find proj.db (GDAL error 1)
Error: [rast] empty srs
Execution halted
Error(s) in re-building vignettes:
--- re-building 'get_started.Rmd' using rmarkdown

Quitting from get_started.Rmd:20-29 [load_libraries_hidden]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! [rast] empty srs
---
Backtrace:
     ▆
  1. ├─terra::rast(landscapemetrics::podlasie_ccilc)
  2. └─terra::rast(landscapemetrics::podlasie_ccilc)
  3.   └─terra (local) .local(x, ...)
  4.     ├─terra::unwrap(x)
  5.     └─terra::unwrap(x)
  6.       └─terra (local) .local(x, ...)
  7.         ├─base::eval(parse(text = x@definition))
  8.         │ └─base::eval(parse(text = x@definition))
  9.         ├─terra::rast(...)
 10.         └─terra::rast(...)
 11.           └─terra (local) .local(x = x, ...)
 12.             └─terra:::new_rast(...)
 13.               └─terra:::messages(r, "rast")
 14.                 └─terra:::error(f, x@pntr$getError())
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'get_started.Rmd' failed with diagnostics:
[rast] empty srs
--- failed re-building 'get_started.Rmd'

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

Error: Vignette re-building failed.
Execution halted
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   1.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) LML.Rd:43: Lost braces
    43 |     is specified only with the \code{GD}, code{HME}, or \code{NSIS}
       |                                               ^
checkRd: (-1) LaplaceApproximation.Rd:485: Escaped LaTeX specials: \&
checkRd: (-1) LossMatrix.Rd:115: Escaped LaTeX specials: \&
checkRd: (-1) LossMatrix.Rd:117: Escaped LaTeX specials: \&
checkRd: (-1) MISS.Rd:106: Lost braces
   106 |   code{Fit$Imp}. In the presence of numerous missing values, say more
       |       ^
checkRd: (-1) Matrices.Rd:316: Lost braces
   316 |   Gauss-Hermite quadrature rules. A grid of order eqn{K} provides an
       |                                                      ^
checkRd: (-1) PMC.Rd:214: Lost braces
   214 |   item{nu}{This is the degrees of freedom parameter \eqn{\nu}{nu} for
       |       ^
checkRd: (-1) PMC.Rd:214-215: Lost braces
   214 |   item{nu}{This is the degrees of freedom parameter \eqn{\nu}{nu} for
       |           ^
checkRd: (-1) caterpillar.plot.Rd:15: Lost braces
    15 |     code{demonoid.hpc}, \code{iterquad}, \code{laplace}, \code{pmc},
       |         ^
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
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
Package required but not available: 'EGAnet'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Running 'testthat.R' [9s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(latex2exp)
  > 
  > test_check("latex2exp")
  Saving _problems/test_simple-166.R
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 100 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_simple.R:166:3'): Escaped symbols renders correctly ────────────
  Error in `str_replace_all(., "\\\\['\\$\\{\\}\\[\\]\\!\\?\\_\\^]", function(char) {     str_c("\\ESCAPED@", as.integer(charToRaw(str_replace_fixed(char, "\\", ""))), "{}") })`: `replacement` function must return a vector the same length as the input
  (2), not length 1.
  Backtrace:
       ▆
    1. ├─latex2exp:::expect_renders_same(...) at test_simple.R:166:3
    2. │ └─latex2exp:::.expect_renders(object, expected_expression, negate = FALSE) at ./setup.R:30:3
    3. │   └─latex2exp::TeX(act$val) at ./setup.R:65:5
    4. │     └─latex2exp:::parse_latex(input)
    5. │       └─... %>% ...
    6. ├─stringr::str_replace_all(., "([^\\\\]?)\\\\\\s", "\\1\\\\@SPACE2{}")
    7. │ └─stringr:::check_lengths(string, pattern, replacement)
    8. │   └─vctrs::vec_size_common(...)
    9. ├─stringr::str_replace_all(., "([^\\\\]?)\\\\;", "\\1\\\\@SPACE2{}")
   10. │ └─stringr:::check_lengths(string, pattern, replacement)
   11. │   └─vctrs::vec_size_common(...)
   12. ├─stringr::str_replace_all(., "([^\\\\]?)\\\\,", "\\1\\\\@SPACE1{}")
   13. │ └─stringr:::check_lengths(string, pattern, replacement)
   14. │   └─vctrs::vec_size_common(...)
   15. └─stringr::str_replace_all(...)
   16.   └─stringr:::str_transform_all(string, pattern, replacement)
   17.     └─cli::cli_abort(...)
   18.       └─rlang::abort(...)
  
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 100 ]
  Error:
  ! Test failures.
  Execution halted
Error(s) in re-building vignettes:
--- re-building 'supported-commands.Rmd' using rmarkdown
--- finished re-building 'supported-commands.Rmd'

--- re-building 'using-latex2exp.Rmd' using rmarkdown

Quitting from using-latex2exp.Rmd:55-71 [base-plot]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
NULL
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'using-latex2exp.Rmd' failed with diagnostics:
`replacement` function must return a vector the same length as the input
(2), not length 1.
--- failed re-building 'using-latex2exp.Rmd'

SUMMARY: processing the following file failed:
  'using-latex2exp.Rmd'

Error: Vignette re-building failed.
Execution halted
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    doc   6.4Mb
Package required but not available: 'semPlot'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Specified C++11: please drop specification unless essential
'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
Package required but not available: 'semPlot'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
checkRd: (-1) TS_diagnostics_plot.Rd:19: Lost braces
    19 | \item{interactive}{\code{logical} input, should be code{TRUE} unless
       |                                                        ^
checkRd: (-1) plot.TS_fit.Rd:29: Lost braces
    29 | \item{interactive}{\code{logical} input, should be code{TRUE} unless
       |                                                        ^
'LazyData' is specified without a 'data' directory
Running examples in 'ldmppr-Ex.R' failed
The error most likely occurred in:

> ### Name: predict_marks
> ### Title: Predict values from the mark distribution
> ### Aliases: predict_marks
> 
> ### ** Examples
> 
> # Simulate a realization
> generating_parameters <- c(2, 8, .02, 2.5, 3, 1, 2.5, .2)
> M_n <- matrix(c(10, 14), ncol = 1)
> generated_locs <- simulate_sc(
+   t_min = 0,
+   t_max = 1,
+   sc_params = generating_parameters,
+   anchor_point = M_n,
+   xy_bounds = c(0, 25, 0, 25)
+ )
> 
> # Load the raster files
> raster_paths <- list.files(system.file("extdata", package = "ldmppr"),
+   pattern = "\\.tif$", full.names = TRUE
+ )
> rasters <- lapply(raster_paths, terra::rast)
> 
> # Scale the rasters
> scaled_raster_list <- scale_rasters(rasters)
> 
> # Load the example mark model
> file_path <- system.file("extdata", "example_mark_model.rds", package = "ldmppr")
> example_mark_model <- readRDS(file_path)
> 
> # Unbundle the model
> mark_model <- bundle::unbundle(example_mark_model)
Error in xgboost::xgb.load.raw(object, as_booster = TRUE) : 
  unused argument (as_booster = TRUE)
Calls: <Anonymous> ... <Anonymous> -> unbundle -> unbundle.bundle -> <Anonymous>
Execution halted
Error(s) in re-building vignettes:
--- re-building 'ldmppr_howto.Rmd' using rmarkdown

Quitting from ldmppr_howto.Rmd:100-130 [train_mark_model]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `xgboost::xgb.load.raw()`:
! unused argument (as_booster = TRUE)
---
Backtrace:
    ▆
 1. ├─bundle::unbundle(example_mark_model$bundled_model)
 2. └─bundle:::unbundle.bundle(example_mark_model$bundled_model)
 3.   └─x$situate(get_object(x))
 4.     └─bundle::swap_element(object, "fit")
 5.       ├─bundle::unbundle(component)
 6.       └─bundle:::unbundle.bundle(component)
 7.         └─x$situate(get_object(x))
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'ldmppr_howto.Rmd' failed with diagnostics:
unused argument (as_booster = TRUE)
--- failed re-building 'ldmppr_howto.Rmd'

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
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:
    light.interception.voxels() - This function create the Fraction absorbed incident light
    light.interception.raster() - Create a raster of Fraction absorbed incident light
    light.incident.voxels() - This function create the Fraction incident light
    light.incident.raster() - Create a raster of the Fraction incident light
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) IPODFUN.Rd:18: Lost braces; missing escapes or markup?
    18 |   \item{H}{an N by N projection matrix X(X'X)^{-1}X' }
       |                                               ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) clusterDistance.Rd:28-29: Lost braces
    28 | \code{approach} indicates the algorithm used to get the value. \code{distance} indicates the distance used to get the value. Possible values: {\code{'MAX'},
       |                                                                                                                                               ^
checkRd: (-1) clusterDistance.details.Rd:28-29: Lost braces
    28 | \code{approach} indicates the algorithm used to get the value. \code{distance} indicates the distance used to get the value. Possible values: {\code{'MAX'},
       |                                                                                                                                               ^
checkRd: (-1) clusterDistanceByApproach.Rd:24-25: Lost braces
    24 | \code{approach} indicates the algorithm used to get the value. Possible values: {\code{'MAX'},
       |                                                                                 ^
checkRd: (-1) clusterDistanceByApproach.details.Rd:24-25: Lost braces
    24 | \code{approach} indicates the algorithm used to get the value. Possible values: {\code{'MAX'},
       |                                                                                 ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) S2mu.Rd:18: Lost braces; missing escapes or markup?
    18 | \code{S2mu} computes a estimation of the variance, given a sample {x} with known population mean (denoted by \code{mu}).
       |                                                                   ^
checkRd: (-1) sample.quantile.Rd:20: Lost braces; missing escapes or markup?
    20 | \code{sample.quantile} computes a estimation of different quantiles, given a sample {x}, using order statistics.
       |                                                                                     ^
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   5.9Mb
Package suggested but not available for checking: 'doMC'
GNU make is a SystemRequirements.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc   5.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    help   1.2Mb
    libs   4.0Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
checkRd: (-1) hash_sentiment_slangsd.Rd:28-37: Lost braces
    28 | article{DBLP:journals/corr/Wu-etal16,
       |        ^
checkRd: (-1) hash_sentiment_slangsd.Rd:29: Lost braces; missing escapes or markup?
    29 |   author    = {Liang Wu and Fred Morstatter and Huan Liu},
       |               ^
checkRd: (-1) hash_sentiment_slangsd.Rd:30-31: Lost braces
    30 |   title     = {SlangSD: Building and Using a Sentiment Dictionary of Slang 
       |               ^
checkRd: (-1) hash_sentiment_slangsd.Rd:32: Lost braces; missing escapes or markup?
    32 |   journal   = {CoRR},
       |               ^
checkRd: (-1) hash_sentiment_slangsd.Rd:33: Lost braces; missing escapes or markup?
    33 |   volume    = {abs/1608.05129},
       |               ^
checkRd: (-1) hash_sentiment_slangsd.Rd:34: Lost braces; missing escapes or markup?
    34 |   year      = {2016},
       |               ^
checkRd: (-1) hash_sentiment_slangsd.Rd:35: Lost braces; missing escapes or markup?
    35 |   url       = {http://arxiv.org/abs/1608.05129},
       |               ^
checkRd: (-1) hash_sentiment_slangsd.Rd:36: Lost braces; missing escapes or markup?
    36 |   timestamp = {Wed, 17 Aug 2016 23:32:57 GMT}
       |               ^
checkRd: (-1) sw_python.Rd:32: Lost braces; missing escapes or markup?
    32 | * Neither the name of the {organization} nor the names of its
       |                           ^
Package suggested but not available for checking: 'doMC'
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'rsyslog'
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    include   1.0Mb
    lib       4.8Mb
    libs      2.9Mb
GNU make is a SystemRequirements.
checkRd: (-1) isingdata.Rd:14: Lost braces; missing escapes or markup?
    14 |     \item{X}{a 5000-by-100 matrix, each entry is in {-1,1}.}
       |                                                     ^
checkRd: (-1) predict.lb.Rd:16: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
Running examples in 'lidaRtRee-Ex.R' failed
The error most likely occurred in:

> ### Name: raster_chull_mask
> ### Title: Raster mask of convex hull
> ### Aliases: raster_chull_mask
> 
> ### ** Examples
> 
> # create raster
> r <- terra::rast(extent = c(0, 40, 0, 40), resolution = 1, crs = "epsg:2154")
Warning: PROJ: proj_create_from_database: Cannot find proj.db (GDAL error 1)
Error: [rast] empty srs
Execution halted
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    R         1.1Mb
    doc       1.0Mb
    extdata   1.2Mb
    libs      1.8Mb
checkRd: (-1) lx_list_lights.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) lx_list_lights.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) lx_list_lights.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) lx_list_lights.Rd:27: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
'LazyData' is specified without a 'data' directory
checkRd: (-1) likelihood_calculation.Rd:24: Lost braces
    24 | For eqn{i = 1\dots N} independent observations in a vector \var{X}, with individual observations \eqn{x_i}{xi}, and a set of parameter values \eqn{\theta}:
       |        ^
checkRd: (-1) simulated_annealing_algorithm.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulated_annealing_algorithm.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulated_annealing_algorithm.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulated_annealing_algorithm.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulated_annealing_algorithm.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulated_annealing_algorithm.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulated_annealing_algorithm.Rd:27: Lost braces in \itemize; meant \describe ?
Running 'testthat.R' [45s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(lime)
  > 
  > test_check("lime")
  Saving _problems/test-text-28.R
  [ FAIL 1 | WARN 6 | SKIP 1 | PASS 21 ]
  
  ══ Skipped tests (1) ═══════════════════════════════════════════════════════════
  • On CRAN (1): 'test-h2o.R:3:1'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-text.R:28:3'): single sentence explanation ───────────────────
  Expected `explanation` to have length 13.
  Actual length: 11.
  
  [ FAIL 1 | WARN 6 | SKIP 1 | PASS 21 ]
  Error:
  ! Test failures.
  Execution halted
'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
'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) solveLP.Rd:119: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) lstats.liu.Rd:41: Escaped LaTeX specials: \&
checkRd: (-1) vcov.liu.Rd:20: Lost braces
    20 | A list of matrix of estimated covariances in the linear Liu regression model for scalar or vector biasing parameter \code{d}{d} is produced. Each list element has row and column names corresponding to the parameter names given by the \code{coef(mod)}. List items are named correspond to values of biasing parameter \eqn{d}{d}.}
       |                                                                                                                             ^
checkRd: (-1) MHDI.Rd:23: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    R          1.5Mb
    doc        1.6Mb
    libs       1.3Mb
    testdata   1.3Mb
checkRd: (-1) relLik.Rd:16: Lost braces
    16 | \item{AIC(x), BIC(x) }{The \code{AIC} or ]code{BIC} value of the first model object.}
       |                                               ^
checkRd: (-1) relLik.Rd:17: Lost braces
    17 | \item{AIC(y), BIC(y) }{The \code{AIC} or ]code{BIC} value of the second model object.}
       |                                               ^
checkRd: (-1) bootstrap_pvals.Rd:78: Lost braces; missing escapes or markup?
    78 | $(n_{extreme} + 1) / (B + 1)$.
       |     ^
Package suggested but not available for checking: 'semPlot'
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs       1.1Mb
    tinytest   3.5Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    R              1.4Mb
    doc-overview   2.2Mb
checkRd: (-1) vcov.Rd:20: Lost braces
    20 | A list of matrix of estimated covariances in the linear ridge regression model for scalar or vector biasing parameter \code{K}{K} is produced. Each list element has row and column names corresponding to the parameter names given by the \code{coef(mod)}. List items are named correspond to values of biasing parameter \eqn{K}{K}.}
       |                                                                                                                               ^
Specified C++11: please drop specification unless essential
checkRd: (-1) lmSubsets-package.Rd:48: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc    4.0Mb
    libs   1.3Mb
GNU make is a SystemRequirements.
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Author
    Maintainer
installed size is 13.7Mb
  sub-directories of 1Mb or more:
    libs  13.3Mb
'LazyData' is specified without a 'data' directory
checkRd: (-1) mte_tilde_at.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mte_tilde_at.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mte_tilde_at.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mte_tilde_at.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mte_tilde_at.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
checkRd: (-1) FootballBrain.Rd:15: Lost braces; missing escapes or markup?
    15 |     { } \tab {or \code{FBConcuss}=football player with concussion history} \cr
       |     ^
checkRd: (-1) HappyPlanetIndex.Rd:14: Lost braces; missing escapes or markup?
    14 |     { } \tab {\code{5}=South Asia, \code{6}=East Asia, \code{7}=former Communist countries}\cr
       |     ^
checkRd: (-1) RockandRoll2012.Rd:17: Lost braces; missing escapes or markup?
    17 |     { } \tab {\code{Lifetime Achievement}, \code{Sideman}} \cr
       |     ^
checkRd: (-1) RockandRoll2015.Rd:17: Lost braces; missing escapes or markup?
    17 |     { } \tab {\code{Lifetime Achievement}, \code{Sideman}} \cr
       |     ^
checkRd: (-1) StudentSurvey.Rd:12: Lost braces; missing escapes or markup?
    12 |     \item{\code{Sex}}{code {F}=female or \code{M}=male}
       |                            ^
checkRd: (-1) SynchronizedMovement.Rd:16: Lost braces; missing escapes or markup?
    16 |     { } \tab {for High/Low Synchronization + High/Low Exertion}\cr
       |     ^
checkRd: (-1) TrafficFlow.Rd:25: Escaped LaTeX specials: \#
Package suggested but not available for checking: 'rsyslog'
Package suggested but not available for checking: 'rsyslog'
Depends: includes the non-default packages:
  'adabag', 'arm', 'brnn', 'C50', 'car', 'corrplot', 'Cubist',
  'doParallel', 'dplyr', 'e1071', 'gam', 'gbm', 'ggplot2', 'ggplotify',
  'glmnet', 'gridExtra', 'gt', 'ipred', 'klaR', 'MachineShop',
  'magrittr', 'MASS', 'mda', 'parallel', 'pls', 'pROC', 'purrr',
  'randomForest', 'ranger', 'reactable', 'reactablefmtr', 'readr',
  'rpart', 'scales', 'tidyr', 'tree', 'xgboost'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
'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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'scio'
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    extdata   4.5Mb
'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
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    help   1.1Mb
    libs   4.5Mb
Package suggested but not available for checking: 'kerdiest'
checkRd: (-1) specialchars.Rd:6: Escaped LaTeX specials: \&
'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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) LS.kalman.Rd:65: Escaped LaTeX specials: \&
checkRd: (-1) spectral.density.Rd:55: Escaped LaTeX specials: \&
checkRd: (-1) k.Rd:27: Lost braces
    27 |  code{\link{ACSPlan-class}}, 
       |      ^
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
checkRd: (-1) Upload_to_db.Rd:43: Lost braces
    43 | lucas]{Connect_to_db}
       |       ^
'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R      1.8Mb
    help   1.1Mb
    libs   1.1Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R      4.0Mb
    libs   1.0Mb
checkRd: (-1) LVGP_fit.Rd:47: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) LVGP_fit.Rd:48: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) LVGP_fit.Rd:49: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) LVGP_fit.Rd:50: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) LVGP_fit.Rd:51: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) LVGP_fit.Rd:52: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) LVGP_predict.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) LVGP_predict.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) math_example.Rd:21: Lost braces
    21 | Data are sampled from the modified math function based on the first example in the paper listed in code{references}.
       |                                                                                                        ^
Specified C++11: please drop specification unless essential
checkRd: (-1) StEM_pcirt.Rd:11: Lost braces; missing escapes or markup?
    11 | \item{response}{N by J matrix containing {0,1,...,M-1} responses, where N is the number of respondents and J is the number of items.}
       |                                          ^
Packages required but not available: 'OpenMx', 'semPlot'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
installed size is 32.4Mb
  sub-directories of 1Mb or more:
    gdal   3.0Mb
    libs  20.2Mb
    proj   9.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'rnaturalearthhires'
Running examples in 'macroBiome-Ex.R' failed
The error most likely occurred in:

> ### Name: cliBioCliIdxGrid
> ### Title: Calculator for Bioclimatic Indices
> ### Aliases: cliBioCliIdxGrid
> 
> ### ** Examples
> 
> # Loading mandatory data for the Example 'Climate Normal Grid'
> data(inp_exClnrGrid)
> 
> # Calculate values of all default bioclimatic indices with default settings
> # for Csongrad-Csanad County (for the normal period 1981-2010)
> with(inp_exClnrGrid, {
+ rs.bci1 <- cliBioCliIdxGrid(temp, prec)
+ rs.bci1
+ })
Warning: PROJ: proj_create: no database context specified (GDAL error 1)
Error: [rast] empty srs
Execution halted
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'quitte'
Package suggested but not available for checking: 'doMC'
installed size is 67.5Mb
  sub-directories of 1Mb or more:
    doc    6.3Mb
    libs  60.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    data   2.3Mb
    libs   1.3Mb
'LazyData' is specified without a 'data' directory
checkRd: (-1) create_terminal_dir.Rd:11: Lost braces; missing escapes or markup?
    11 | the following child folders: {repo_base}/bin/ and {repo_base}/src/. A
       |                              ^
checkRd: (-1) create_terminal_dir.Rd:11: Lost braces; missing escapes or markup?
    11 | the following child folders: {repo_base}/bin/ and {repo_base}/src/. A
       |                                                   ^
checkRd: (-1) full_repo_dir.Rd:11: Lost braces; missing escapes or markup?
    11 | the following child folders: {repo_base}/bin/ and {repo_base}/src/. A
       |                              ^
checkRd: (-1) full_repo_dir.Rd:11: Lost braces; missing escapes or markup?
    11 | the following child folders: {repo_base}/bin/ and {repo_base}/src/. A
       |                                                   ^
'LazyData' is specified without a 'data' directory
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    doc   6.9Mb
checkRd: (-1) manet.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) manet.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) manet.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) manet.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) manet.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) manet.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mixtbern.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mixtbern.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mixtbern.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mixtbern.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mixtbern.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) MangroveTree.Rd:37: Lost braces
    37 |       An object of class \\code{\link[Mangrove]{MangrovePed}}
       |                                ^
checkRd: (-1) manipulateWidget.Rd:113-117: Lost braces in \itemize; meant \describe ?
checkRd: (-1) manipulateWidget.Rd:118-120: Lost braces in \itemize; meant \describe ?
checkRd: (-1) manipulateWidget.Rd:121-123: Lost braces in \itemize; meant \describe ?
checkRd: (-1) manipulateWidget.Rd:124-127: Lost braces in \itemize; meant \describe ?
Running 'testthat.R' [8s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(manipulateWidget)
  > 
  > test_check("manipulateWidget")
  Saving _problems/test-on_done-20.R
  Saving _problems/test-on_done-42.R
  [ FAIL 2 | WARN 0 | SKIP 1 | PASS 650 ]
  
  ══ Skipped tests (1) ═══════════════════════════════════════════════════════════
  • empty test (1): 'test-inputs.R:97:1'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-on_done.R:5:5'): onDone / stops the shiny gadget and returns a htmlwidget ──
  <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-on_done.R:5:5
   2.   └─lifecycle::deprecate_stop("3.2.0", "with_mock()", "with_mocked_bindings()")
   3.     └─lifecycle:::deprecate_stop0(msg)
   4.       └─rlang::cnd_signal(...)
  ── Error ('test-on_done.R:24:23'): onDone / returns a combined widget if comparison ──
  <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. ├─base::suppressWarnings(...) at test-on_done.R:24:5
   2. │ └─base::withCallingHandlers(...)
   3. └─testthat::with_mock(...) at test-on_done.R:24:23
   4.   └─lifecycle::deprecate_stop("3.2.0", "with_mock()", "with_mocked_bindings()")
   5.     └─lifecycle:::deprecate_stop0(msg)
   6.       └─rlang::cnd_signal(...)
  
  [ FAIL 2 | WARN 0 | SKIP 1 | PASS 650 ]
  Error:
  ! Test failures.
  Execution halted
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    doc    3.5Mb
checkRd: (-1) EEGwide.Rd:30-33: Lost braces
    30 |   if(requireNamespace("ggplot2")){ 
       |                                  ^
Packages suggested but not available for checking: 'semPlot', 'semptools'
'LazyData' is specified without a 'data' directory
installed size is 33.5Mb
  sub-directories of 1Mb or more:
    mapdata  33.4Mb
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    data          1.3Mb
    doc           1.6Mb
    htmlwidgets   3.5Mb
    libs          3.0Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    R   7.9Mb
Found the following significant warnings:
  Warning: PROJ: proj_create_from_name: Cannot find proj.db (GDAL error 1)
See 'd:/Rcompile/CRANpkg/local/4.4/mapme.biodiversity.Rcheck/00install.out' for details.
Warning: PROJ: proj_create_from_name: Cannot find proj.db (GDAL error 1)

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.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/mapmisc.Rcheck/00install.out' for details.
Running examples in 'mapsRinteractive-Ex.R' failed
The error most likely occurred in:

> ### Name: mri
> ### Title: mri
> ### Aliases: mri
> 
> ### ** Examples
> 
> #load package
> require(terra)
Loading required package: terra
terra 1.8.86
> 
> #create a synthetic example raster dataset
> rr1<-rast(nrow=10, ncol=10, 
+   vals= sample(1:4, 100, replace=TRUE), 
+   crs=crs("EPSG:3857")
+   )
Warning: PROJ: proj_create_from_database: Cannot find proj.db (GDAL error 1)
Error: [rast] empty srs
Execution halted
Running 'tinytest.R' [9s]
Running the tests in 'tests/tinytest.R' failed.
Complete output:
  > if (requireNamespace("tinytest", quietly = TRUE)) {
  +   tinytest::test_package("maptiles")
  + }
  
  test_maptiles.R...............    0 tests    
  test_maptiles.R...............    0 tests    
  test_maptiles.R...............    0 tests    
  test_maptiles.R...............    0 tests    
  test_maptiles.R...............    0 tests    
  test_maptiles.R...............    0 tests    
  test_maptiles.R...............    0 tests    
  test_maptiles.R...............    0 tests    
  test_maptiles.R...............    0 tests    Error in h(simpleError(msg, call)) : 
    error in evaluating the argument 'x' in selecting a method for function 'ext': [project] output crs is not valid
  Calls: <Anonymous> ... ext -> project -> project -> .local -> messages -> error
  In addition: Warning message:
  PROJ: proj_create_from_database: Cannot find proj.db (GDAL error 1) 
  Execution halted
GNU make is a SystemRequirements.
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    doc  10.0Mb
checkRd: (-1) locate_shift.Rd:29: Lost braces
    29 | \code{\link{quickfit}}, code{\link{locator}}
       |                             ^
checkRd: (-1) marcher-package.Rd:14: Lost braces; missing escapes or markup?
    14 | 1. \code{\link{estimate_shift}} {Estimate a range shift process.}
       |                                 ^
checkRd: (-1) marcher-package.Rd:16: Lost braces; missing escapes or markup?
    16 | 2. \code{\link{simulate_shift}} {Simulate a range shift process.}
       |                                 ^
checkRd: (-1) marcher-package.Rd:18: Lost braces; missing escapes or markup?
    18 | 3. \code{\link{plot.shiftfit}} {Visualize a range shift process.}
       |                                ^
checkRd: (-1) marcher-package.Rd:20: Lost braces; missing escapes or markup?
    20 | 4. \code{\link{test_rangeshift}} {Test whether a range shift occurred.}
       |                                  ^
checkRd: (-1) marcher-package.Rd:22: Lost braces; missing escapes or markup?
    22 | 5. \code{\link{test_return}} {Test whether a migration was a return migration.}
       |                              ^
checkRd: (-1) marcher-package.Rd:24: Lost braces; missing escapes or markup?
    24 | 6. \code{\link{test_stopover}} {Test whether a stopover occurred during a migration.}
       |                                ^
checkRd: (-1) quickfit.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) quickfit.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) test_rangeshift.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) test_rangeshift.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) test_rangeshift.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) test_rangeshift.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mma.Rd:67: Escaped LaTeX specials: \&
checkRd: (-1) marima.Rd:28: Lost braces; missing escapes or markup?
    28 | ( if(is.ts(DATA)) { DATA <- as.matrix(data.frame(DATA)) } and a message
       |                   ^
checkRd: (-1) marima.Rd:223: Escaped LaTeX specials: \&
Error(s) in re-building vignettes:
--- re-building 'my-vignette.Rmd' using rmarkdown
The magick package is required to crop "D:/RCompile/CRANpkg/local/4.4/MariNET.Rcheck/vign_test/MariNET/vignettes/my-vignette_files/figure-html/qgraph-plot2-1.png" but not available.
The magick package is required to crop "D:/RCompile/CRANpkg/local/4.4/MariNET.Rcheck/vign_test/MariNET/vignettes/my-vignette_files/figure-html/qgraph-plot3-1.png" but not available.
The magick package is required to crop "D:/RCompile/CRANpkg/local/4.4/MariNET.Rcheck/vign_test/MariNET/vignettes/my-vignette_files/figure-html/qgraph-plot4-1.png" but not available.
File styles.css not found in resource path
Error: processing vignette 'my-vignette.Rmd' failed with diagnostics:
pandoc document conversion failed with error 99
--- failed re-building 'my-vignette.Rmd'

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

Error: Vignette re-building failed.
Execution halted
checkRd: (-1) markdownInput.Rd:17: Lost braces
    17 | \item{inputId}{The code{input} slot that will be used to access the value.}
       |                        ^
checkRd: (-1) markdownInput.Rd:35: Lost braces in \enumerate; \value handles \item{}{} directly
checkRd: (-1) markdownInput.Rd:36: Lost braces in \enumerate; \value handles \item{}{} directly
checkRd: (-1) markdownInput.Rd:81-82: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) markdownInput.Rd:84-86: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) markdownInput.Rd:89-90: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) moduleMarkdownInput.Rd:64-65: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) moduleMarkdownInput.Rd:67-69: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) moduleMarkdownInput.Rd:72-73: Lost braces in \enumerate; meant \describe ?
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    examples   2.7Mb
    libs       1.3Mb
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
checkRd: (-1) Markovchart.Rd:154: Lost braces
   154 | If either \code{h} or \code{k} have length greater than 1, then the \code{G-value} (weighted average of average cost and cost standard deviation) is calculated for all given values without optimisation. The value of the function in this case is a data frame of class code{Markov_grid} with \code{length(h)*length(k)} number of rows and three columns for \code{h}, \code{k} and the \code{G-value}.
       |                                                                                                                                                                                                                                                                                ^
checkRd: (-1) marqLevAlg-package.Rd:14: Lost braces; missing escapes or markup?
    14 | (GH^{-1}G).
       |     ^
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'marssTMB'
'LazyData' is specified without a 'data' directory
checkRd: (-1) focalCompare.Rd:14: Lost braces
    14 | \item{fun}{The function fun should take multiple numbers, and return a single number. For example mean, modal, min or max. It should also accept a na.rm argument (or ignore it, e.g. as one of the 'dots' arguments. For example, length will fail, but function(x, ...){na.omit(length(x))} works. (Specifications from `raster::focal`)}
       |                                                                                                                                                                                                                                                                          ^
checkRd: (-1) hr_levels.Rd:9-12: Lost braces
     9 | kernelBiweight <- function(x, mean = 0, sd = 1) {
       |                                                 ^
checkRd: (-1) hr_levels.Rd:33-36: Lost braces
    33 | kernelCosine <- function(x, mean = 0, sd = 1) {
       |                                               ^
checkRd: (-1) hr_levels.Rd:41-44: Lost braces
    41 | kernelEpanechnikov <- function(x, mean = 0, sd = 1) {
       |                                                     ^
checkRd: (-1) hr_levels.Rd:58-61: Lost braces
    58 | kernelOptCosine <- function(x, mean = 0, sd = 1) {
       |                                                  ^
checkRd: (-1) hr_levels.Rd:65-68: Lost braces
    65 | kernelRectangular <- function(x, mean = 0, sd = 1) {
       |                                                    ^
checkRd: (-1) hr_levels.Rd:72-75: Lost braces
    72 | kernelSquaredCosine <- function(x, mean = 0, sd = 1) {
       |                                                      ^
checkRd: (-1) hr_levels.Rd:79-82: Lost braces
    79 | kernelTriangular <- function(x, mean = 0, sd = 1) {
       |                                                   ^
checkRd: (-1) hr_levels.Rd:86-89: Lost braces
    86 | kernelTricube <- function(x, mean = 0, sd = 1) {
       |                                                ^
checkRd: (-1) hr_levels.Rd:93-96: Lost braces
    93 | kernelTriweight <- function(x, mean = 0, sd = 1) {
       |                                                  ^
checkRd: (-1) hr_levels.Rd:100-103: Lost braces
   100 | kernelUniform <- function(x, mean = 0, sd = 1) {
       |                                                ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) CF2004.Rd:8: Lost braces; missing escapes or markup?
     8 |   \item{X2}{an optional second variable with same length as \code{X}, should the equation be multiple (see Details) {in mm}}
       |                                                                                                                     ^
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'gurobi'
checkRd: (-1) Rand.index.Rd:22: Lost braces; missing escapes or markup?
    22 | The two vectors \code{x} and \code{y} must have equal length. Given a set \eqn{S} and two partitions \eqn{X} and \eqn{Y} of \eqn{S}, the Rand index is the proportion of pairs of elements in \eqn{S} (out of all pairs) that are either concordant in both \eqn{X} and \eqn{Y} (i.e., they belong to the same member of \eqn{X} and to the same member of \eqn{Y}) or discordant (i.e., not concordant) in both \eqn{X} and {Y}.  
       |                                                                                                                                                                                                                                                                                                                                                                                                                              ^
checkRd: (-1) predict.matchFeat.Rd:21: Lost braces
    21 | The function \code{predict.matchFeat} finds the best matching for new feature vectors relative to an existing set of cluster/class centers. If code{object} results from a call to \code{\link{match.gaussmix}}, the same function is used for prediction (with fixed mean vectors and covariance matrices). In other cases, the function \code{\link{match.template}} is used for prediction. 
       |                                                                                                                                                    ^
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    java   3.3Mb
    libs   1.7Mb
Package suggested but not available for checking: 'gurobi'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'rrelaxiv'
checkRd: (-1) Match.Rd:90: Lost braces; missing escapes or markup?
    90 | expression in braces. For example, the condition "{[ab]*}" is equivalent
       |                                                   ^
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    doc   7.9Mb
'LazyData' is specified without a 'data' directory
checkRd: (-1) Matrix_eQTL_main.Rd:31: Lost braces; missing escapes or markup?
    31 |     {genepos} in the call of \code{Matrix_eQTL_main} function.
       |     ^
checkRd: (-1) Matrix_eQTL_main.Rd:35: Lost braces; missing escapes or markup?
    35 |     the data frames \code{snpspos} and {genepos}.
       |                                        ^
Running examples in 'MatrixHMM-Ex.R' failed
The error most likely occurred in:

> ### Name: Eigen.HMM_fit
> ### Title: Fitting Parsimonious Hidden Markov Models for Matrix-Variate
> ###   Longitudinal Data
> ### Aliases: Eigen.HMM_fit
> 
> ### ** Examples
> 
> data(simData)
> Y <- simData$Y
> init <- Eigen.HMM_init(Y = Y, k = 2, density = "MVT", mod.row = "EEE", mod.col = "EE", nstartR = 10)
Warning in socketConnection(port = port, server = TRUE, blocking = TRUE,  :
  port 11755 cannot be opened
Error in socketConnection(port = port, server = TRUE, blocking = TRUE,  : 
  cannot open the connection
Calls: Eigen.HMM_init ... <Anonymous> -> makeSOCKcluster -> newSOCKnode -> socketConnection
Execution halted
'LazyData' is specified without a 'data' directory
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  'Matrix'
A package should be listed in only one of these fields.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
checkRd: (-1) MaxentVariableSelection-package.Rd:46: Lost braces; missing escapes or markup?
    46 | \tab Tyberghein L, Verbruggen H, Pauly K, Troupin C, Mineur F and {De Clerck}, O (2012)\cr
       |                                                                   ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'doMC'
Running 'testthat.R' [40s]
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(mbbe)
  > 
  > test_check("mbbe")
  Saving _problems/test-check_requirements-52.R
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 11 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-check_requirements.R:39:3'): check_requirements works ──────────
  <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-check_requirements.R:39:3
   2.   └─lifecycle::deprecate_stop("3.2.0", "with_mock()", "with_mocked_bindings()")
   3.     └─lifecycle:::deprecate_stop0(msg)
   4.       └─rlang::cnd_signal(...)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 11 ]
  Error:
  ! Test failures.
  Execution halted
'LazyData' is specified without a 'data' directory
Package required but not available: 'OpenMx'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
checkRd: (-1) findDescendingTrans.Rd:29: Lost braces
    29 |    Foster, S.D., Hosack, G.R., J. Monk, Lawrence, E., Barrett, N.S., Williams, A. and Przeslawski, P. (2020) Spatially-Balanced Designs for Transect-Based Surveys. Methods in Ecology and Evolution. emph{11}: 95--105
       |                                                                                                                                                                                                           ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) SIGMAS.Rd:17: Lost braces; missing escapes or markup?
    17 | Sigmahat =  (Y^{T} Y)/n;
       |                ^
checkRd: (-1) SIGMAS.Rd:18: Lost braces; missing escapes or markup?
    18 | Sigmahat_fit = (Y^{T}  P_fx  Y)/n;
       |                   ^
checkRd: (-1) matpower.Rd:17: Lost braces; missing escapes or markup?
    17 | The function computes M^{power} for a symmetric matrix M. }
       |                         ^
checkRd: (-1) satisfaction.Rd:28: Lost braces
    28 | Della Valle E (2010) Della Valle E 2010 Analisi Multidimensionale dei Dati: la Qualit\'{a} del Lavoro nelle Cooperative Sociali. 
       |                                                                                        ^
checkRd: (-1) satisfaction.Rd:29: Lost braces
    29 | Unpublished thesis, Seconda Universit\'{a}  degli Studi di Napoli, Capua Italy.
       |                                        ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc    3.8Mb
    libs   1.4Mb
checkRd: (-1) mc.lnOR.Rd:7: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
checkRd: (-1) MCbound.precalc1.Rd:16: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) MCbound.precalc1.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MCtest.Rd:39: Escaped LaTeX specials: \#
checkRd: (-1) MCtest.Rd:40: Escaped LaTeX specials: \#
installed size is  5.1Mb
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    doc   2.9Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    doc   6.8Mb
Package suggested but not available for checking: 'cmdstanr'
'LazyData' is specified without a 'data' directory
checkRd: (-1) eigp.Rd:34: Escaped LaTeX specials: \&
checkRd: (-1) imcdiag.Rd:50: Escaped LaTeX specials: \&
checkRd: (-1) imcdiag.Rd:52: Escaped LaTeX specials: \&
checkRd: (-1) mc.plot.Rd:23: Escaped LaTeX specials: \&
checkRd: (-1) mc.plot.Rd:25: Escaped LaTeX specials: \&
checkRd: (-1) mctest.Rd:39: Escaped LaTeX specials: \&
checkRd: (-1) mctest.Rd:41: Escaped LaTeX specials: \&
checkRd: (-1) omcdiag.Rd:39: Escaped LaTeX specials: \&
checkRd: (-1) omcdiag.Rd:41: Escaped LaTeX specials: \&
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Initial version.
checkRd: (-1) mcvis.Rd:32: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mcvis.Rd:33: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mcvis.Rd:34: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
checkRd: (-1) get_mdgc.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) get_mdgc.Rd:35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) get_mdgc.Rd:36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) get_mdgc.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) normalizeWithMA.Rd:19: Lost braces
    19 |         \item{expGroup}{ a \code{vector} of experimental grouping variable such as plate. The length of code{expGroup} must be same as the number of rows of \code{mD}.}
       |                                                                                                             ^
Package suggested but not available for checking: 'RGtk2'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) mdp_example_forest.Rd:36: Lost braces; missing escapes or markup?
    36 | Let {1, ... S} be the states of the forest. the Sth state being the oldest.
       |     ^
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'cmdstanr'
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   4.1Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
checkRd: (-1) bhm.mcmc.Rd:37: Lost braces; missing escapes or markup?
    37 |   where \eqn{N_{ij}} denotes the number of times that the error profile \eqn{i} is cited on a report from hospital {j} and \eqn{y_{ij}} is the corresponding number of times that profile \eqn{i} in hospital \eqn{j} was reported with harm.
       |                                                                                                                    ^
checkRd: (-1) strings-internal.Rd:14: Lost braces
    14 | code{stringPlaceExact}: find location of string, using exact match
       |     ^
checkRd: (-1) strings-internal.Rd:17: Lost braces
    17 | code{stringPlaceFuzzy}: find location of string, using partial match
       |     ^
checkRd: (-1) strings-internal.Rd:19: Lost braces
    19 | code{stringPlace}: find location of string, generic
       |     ^
checkRd: (-1) strings-internal.Rd:21: Lost braces
    21 | code{checkFuzzy}: check for "close" string matches
       |     ^
Running examples in 'medfateland-Ex.R' failed
The error most likely occurred in:

> ### Name: overland_routing
> ### Title: Overland routing for TETIS sub-model
> ### Aliases: overland_routing cell_neighbors
> 
> ### ** Examples
> 
> # Load example watershed data
> data("example_watershed")
> 
> # Get bounding box to determine limits
> b <- sf::st_bbox(example_watershed)
> b
   xmin    ymin    xmax    ymax 
 401430 4671870  402830 4672570 
> 
> # Define a raster topology, using terra package, 
> # with the same CRS as the watershed. In this example cells have 100 m side.
> # Coordinates in the 'sf' object are assumed to be cell centers
> r <-terra::rast(xmin = 401380, ymin = 4671820, xmax = 402880, ymax = 4672620, 
+                 nrow = 8, ncol = 15, crs = "epsg:32631")
Warning: PROJ: proj_create_from_database: Cannot find proj.db (GDAL error 1)
Error: [rast] empty srs
Execution halted
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
'LazyData' is specified without a 'data' directory
checkRd: (-1) MED.Rd:25: Lost braces
    25 | The vector of treatment assignments of length \eqn{n}. Must be coded as \eqn{\{0,1} {{0,1}}.
       |                                                                                     ^
'LazyData' is specified without a 'data' directory
'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) Soybean.Rd:15: Escaped LaTeX specials: \#
checkRd: (-1) Soybean.Rd:33: Escaped LaTeX specials: \#
'LazyData' is specified without a 'data' directory
'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
'LazyData' is specified without a 'data' directory
installed size is  7.9Mb
  sub-directories of 1Mb or more:
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Package suggested but not available for checking: 'mdrb'
checkRd: (-1) CVLasoelacox.Rd:68-69: Lost braces in \itemize; \value handles \item{}{} directly
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    help   2.3Mb
checkRd: (-1) datagenerator.Rd:17: Lost braces; missing escapes or markup?
    17 | Returns data frame with \code{n*K} rows (if \code{n} is a scalar), or \code{sum(n)} rows (if \code{n} is a \code{K}-element vector). The data frame contains columns "y", "x1", \dots, "x_{p-1}" and "group" if \code{family="gaussian"}, \code{"binomial"} or \code{"poisson"}; or contains columns "time", "status", "x1", \dots, "x_{p-1}" and "group" if \code{family="cox"}.
       |                                                                                                                                                                                           ^
checkRd: (-1) datagenerator.Rd:17: Lost braces; missing escapes or markup?
    17 | Returns data frame with \code{n*K} rows (if \code{n} is a scalar), or \code{sum(n)} rows (if \code{n} is a \code{K}-element vector). The data frame contains columns "y", "x1", \dots, "x_{p-1}" and "group" if \code{family="gaussian"}, \code{"binomial"} or \code{"poisson"}; or contains columns "time", "status", "x1", \dots, "x_{p-1}" and "group" if \code{family="cox"}.
       |                                                                                                                                                                                                                                                                                                                                        ^
installed size is  5.2Mb
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    data   4.1Mb
'LazyData' is specified without a 'data' directory
checkRd: (-1) asympVar_LinReg.Rd:52: Lost braces in \itemize; \value handles \item{}{} directly
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checkRd: (-1) asympVar_LinReg.Rd:54: Lost braces in \itemize; \value handles \item{}{} directly
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checkRd: (-1) asympVar_LogReg.Rd:55: Lost braces in \itemize; \value handles \item{}{} directly
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checkRd: (-1) get_gamma_EB.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get_gamma_EB.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get_gamma_EB.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
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    examples  10.3Mb
checkRd: (-1) rland.graph.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly
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checkRd: (-1) rland.graph.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
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checkRd: (-1) rland.graph.Rd:32: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rland.graph.Rd:33-34: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
Package required but not available: 'OpenMx'

Package suggested but not available for checking: 'semPlot'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   3.5Mb
GNU make is a SystemRequirements.
Package suggested but not available for checking: 'metaSEM'
Running examples in 'meteo-Ex.R' failed
The error most likely occurred in:

> ### Name: dem_twi_srb
> ### Title: Digital Elevation Model (DEM) and Topographic Wetness Index
> ###   (TWI) for Serbia
> ### Aliases: dem_twi_srb
> ### Keywords: datasets
> 
> ### ** Examples
> 
> library(terra)
terra 1.8.86
> # load data 
> data(dem_twi_srb)
> terra::unwrap(dem_twi_srb)
Warning: PROJ: proj_create_from_database: Cannot find proj.db (GDAL error 1)
Error: [rast] empty srs
Execution halted
'LazyData' is specified without a 'data' directory
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    R      1.8Mb
    doc    3.4Mb
    libs   2.3Mb
'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
'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc    3.9Mb
    libs   1.2Mb
'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
Error(s) in re-building vignettes:
--- re-building 'NCEAS.Rmd' using rmarkdown

Quitting from NCEAS.Rmd:376-430 [reconstruct-spatial]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! [rast] empty srs
---
Backtrace:
    ▆
 1. ├─terra::rast(...)
 2. └─terra::rast(...)
 3.   └─terra (local) .local(x = x, ...)
 4.     └─terra:::new_rast(...)
 5.       └─terra:::messages(r, "rast")
 6.         └─terra:::error(f, x@pntr$getError())
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'NCEAS.Rmd' failed with diagnostics:
[rast] empty srs
--- failed re-building 'NCEAS.Rmd'

--- re-building 'a-modeling-example.Rmd' using rmarkdown
--- finished re-building 'a-modeling-example.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: 'MBESS'
Running 'testthat.R' [92s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(mice)
  
  Attaching package: 'mice'
  
  The following object is masked from 'package:stats':
  
      filter
  
  The following objects are masked from 'package:base':
  
      cbind, rbind
  
  > 
  > test_check("mice")
  Saving _problems/test-mice.impute.2l.bin-32.R
  [ FAIL 1 | WARN 0 | SKIP 2 | PASS 379 ]
  
  ══ Skipped tests (2) ═══════════════════════════════════════════════════════════
  • empty test (2): ,
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-mice.impute.2l.bin.R:30:1'): (code run outside of `test_that()`) ──
  Error: object 'ID' not found
  Backtrace:
      ▆
   1. ├─... %>% dplyr::select(-month) at test-mice.impute.2l.bin.R:30:1
   2. ├─dplyr::select(., -month)
   3. ├─tidyr::fill(., treatment)
   4. ├─tidyr::complete(toenail, ID, visit)
   5. └─tidyr:::complete.data.frame(toenail, ID, visit)
   6.   ├─tidyr::expand(data, ...)
   7.   └─tidyr:::expand.data.frame(data, ...)
   8.     └─tidyr:::grid_dots(..., `_data` = data)
   9.       └─rlang::eval_tidy(dot, data = mask)
  
  [ FAIL 1 | WARN 0 | SKIP 2 | PASS 379 ]
  Error:
  ! Test failures.
  Execution halted
'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   3.7Mb
    help   1.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    doc    5.5Mb
    lib    1.2Mb
    libs   1.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'midfielddata'
checkRd: (-1) miive.Rd:120-239: Lost braces in \itemize; meant \describe ?
checkRd: (-1) miive.Rd:241-264: Lost braces in \itemize; meant \describe ?
checkRd: (-1) miive.Rd:266-277: Lost braces in \itemize; meant \describe ?
checkRd: (-1) miive.Rd:279-286: Lost braces in \itemize; meant \describe ?
checkRd: (-1) miive.Rd:288-293: Lost braces in \itemize; meant \describe ?
checkRd: (-1) miive.Rd:295-311: Lost braces in \itemize; meant \describe ?
checkRd: (-1) miive.Rd:313-337: Lost braces in \itemize; meant \describe ?
checkRd: (-1) miive.Rd:339-352: Lost braces in \itemize; meant \describe ?
checkRd: (-1) miive.Rd:353-370: Lost braces in \itemize; meant \describe ?
checkRd: (-1) miive.Rd:426: Lost braces
   426 | \link{MIIVsem}{miivs}
       |               ^
checkRd: (-1) miivs.Rd:33-160: Lost braces in \itemize; meant \describe ?
Error loading dataset 'otu_mini_bin_results_xgbTree':
   Error in xgb.get.handle(model) : 
    'xgb.Booster' object is corrupted or is from an incompatible XGBoost version.
Package suggested but not available for checking: 'gurobi'
checkRd: (-1) acs2016.Rd:14: Lost braces
    14 |   \item{BROADBND}{Cellular data plan for a smartphone or other mobile device}{1 yes 2 no}
       |                                                                              ^
checkRd: (-1) acs2016.Rd:21: Lost braces
    21 |   \item{MHP}{Mobile home costs}{$, yearly}
       |                                ^
'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
installed size is 25.4Mb
  sub-directories of 1Mb or more:
    libs        1.1Mb
    redengine  24.2Mb
checkRd: (-1) gof.estimates.Rd:59-62: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gof.estimates.Rd:63-66: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) sim.data.Rd:15: Lost braces in \enumerate; meant \describe ?
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checkRd: (-1) sim.data.Rd:23: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) sim.data.Rd:24: Lost braces in \enumerate; meant \describe ?
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checkRd: (-1) sim.data.Rd:26: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) sim.data.Rd:27: Lost braces in \enumerate; meant \describe ?
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    libs   7.2Mb
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Problems with news in 'NEWS.md':
No news entries found.
Package suggested but not available for checking: 'BRugs'
checkRd: (-1) sumKeepAttr.Rd:19: Lost braces
    19 |       (only relevant if code{x} has only one element).}
       |                             ^
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc   6.2Mb
checkRd: (-1) PV.Rd:14: Lost braces
    14 | plausible value in turn; with code{rewrite=FALSE} a new data set is
       |                                   ^
checkRd: (-1) SLD.Rd:20: Escaped LaTeX specials: \&
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Bug Fix
    Update Vignettes
    Function Optimizing
    New Functions
    Vignette
    Optimization
    Fix Bugs
    Add New Function
    Update Description Files
    Fix bugs
    New .R files
    Update Old .R files
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'mixRasch'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running 'testthat.R' [3s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > suppressPackageStartupMessages({
  +   library(testthat)
  +   library(data.table)
  + })
  > 
  > test_check("mknapsack")
  Loading required package: mknapsack
  Saving _problems/test-packing-153.R
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 21 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-packing.R:146:5'): solver / calls correct method based on the option value ──
  <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-packing.R:146:5
   2.   └─lifecycle::deprecate_stop("3.2.0", "with_mock()", "with_mocked_bindings()")
   3.     └─lifecycle:::deprecate_stop0(msg)
   4.       └─rlang::cnd_signal(...)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 21 ]
  Error:
  ! Test failures.
  Execution halted
installed size is 12.9Mb
  sub-directories of 1Mb or more:
    libs  12.6Mb
'LazyData' is specified without a 'data' directory
checkRd: (-1) Texture.Rd:35: Escaped LaTeX specials: \&
checkRd: (-1) binom.diagnostics.Rd:33: Escaped LaTeX specials: \&
checkRd: (-1) mldrGUI.Rd:22-25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mldrGUI.Rd:26-28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mldrGUI.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mldrGUI.Rd:30-31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mldrGUI.Rd:32-34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gp.list.Rd:16: Escaped LaTeX specials: \#
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
checkRd: (-1) mlim.Rd:58: Lost braces
    58 |              Note that code{"XGB"} is only available in Mac OS and Linux. moreover,
       |                            ^
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc   4.9Mb
Error(s) in re-building vignettes:
--- re-building 'getting-started.Rmd' using rmarkdown
File ../man/figures/logo.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 'introduction.Rmd' using rmarkdown
File ../man/figures/logo.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'

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

--- re-building 'visualization-guide.Rmd' using rmarkdown
--- finished re-building 'visualization-guide.Rmd'

SUMMARY: processing the following files failed:
  'getting-started.Rmd' 'introduction.Rmd' 'usage-tutorial.Rmd'

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking:
  'ueadata1', 'ueadata2', 'ueadata3', 'ueadata4', 'ueadata5',
  'ueadata6', 'ueadata7', 'ueadata8'
installed size is 29.0Mb
  sub-directories of 1Mb or more:
    include  10.7Mb
    libs     17.8Mb
Package suggested but not available for checking: 'polars'
Package unavailable to check Rd xrefs: 'polars'
Running examples in 'mlr3pipelines-Ex.R' failed
The error most likely occurred in:

> ### Name: mlr_pipeops_nmf
> ### Title: Non-negative Matrix Factorization
> ### Aliases: mlr_pipeops_nmf PipeOpNMF
> 
> ### ** Examples
> 
> ## Don't show: 
> if (mlr3misc::require_namespaces(c("NMF", "MASS"), quietly = TRUE)) withAutoprint({ # examplesIf
+ ## End(Don't show)
+ ## Don't show: 
+ # NMF attaches these packages to search path on load, #929
+ lapply(c("package:Biobase", "package:BiocGenerics", "package:generics"), detach, character.only = TRUE)
+ ## End(Don't show)
+ library("mlr3")
+ 
+ task = tsk("iris")
+ pop = po("nmf")
+ 
+ task$data()
+ pop$train(list(task))[[1]]$data()
+ 
+ pop$state
+ ## Don't show: 
+ # BiocGenerics overwrites printer for our tables mlr-org/mlr3#1112
+ # Necessary as detaching packages does not remove registered S3 methods
+ suppressWarnings(try(rm("format.list", envir = .BaseNamespaceEnv$.__S3MethodsTable__.), silent = TRUE))
+ ## End(Don't show)
+ ## Don't show: 
+ }) # examplesIf
> lapply(c("package:Biobase", "package:BiocGenerics", "package:generics"), 
+     detach, character.only = TRUE)
Error in FUN(X[[i]], ...) : invalid 'name' argument
Calls: withAutoprint ... withVisible -> eval -> eval -> lapply -> lapply -> FUN
Execution halted
Package suggested but not available for checking: 'mlr3proba'
Package suggested but not available for checking: 'mlr3proba'
checkRd: (-1) MBOMultiObjResult.Rd:8: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MBOMultiObjResult.Rd:9: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MBOMultiObjResult.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MBOMultiObjResult.Rd:11-13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MBOMultiObjResult.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MBOSingleObjResult.Rd:8: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MBOSingleObjResult.Rd:9-11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MBOSingleObjResult.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MBOSingleObjResult.Rd:13-15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MBOSingleObjResult.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MBOSingleObjResult.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) error_handling.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) error_handling.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) error_handling.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) error_handling.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) error_handling.Rd:16-17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) error_handling.Rd:18-20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) error_handling.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mbo_parallel.Rd:9: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mbo_parallel.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) setMBOControlMultiObj.Rd:119-120: Lost braces
   119 | Notes in Computer Science, ISBN 978-3-642-37139-4, pp. 756{770,
       |                                                           ^
checkRd: (-1) trafos.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) trafos.Rd:29: Lost braces in \itemize; meant \describe ?
Error(s) in re-building vignettes:
--- re-building 'mlspatial.Rmd' using rmarkdown

Quitting from mlspatial.Rmd:127-181 [unnamed-chunk-7]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `xgboost()`:
! argument "y" is missing, with no default
---
Backtrace:
    ▆
 1. └─xgboost::xgboost(...)
 2.   └─xgboost:::process.y.margin.and.objective(...)
 3.     └─base::NROW(y)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'mlspatial.Rmd' failed with diagnostics:
argument "y" is missing, with no default
--- failed re-building 'mlspatial.Rmd'

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

Error: Vignette re-building failed.
Execution halted
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs   6.3Mb
GNU make is a SystemRequirements.
checkRd: (-1) simpopmlx.Rd:21: Lost braces; missing escapes or markup?
    21 | \item{fim}{the Fisher Information Matrix estimated by Monolix. fim={"sa", "lin"} (default="sa")}
       |                                                                    ^
installed size is 13.6Mb
  sub-directories of 1Mb or more:
    libs  13.2Mb
installed size is 15.6Mb
  sub-directories of 1Mb or more:
    images   1.1Mb
    shiny   14.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   5.8Mb
checkRd: (-1) MMD_attr.Rd:62: Lost braces; missing escapes or markup?
    62 | \item Probability of attribution of each unknown individual to each source $p_{u,s}$
       |                                                                               ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) mmeln.Rd:69: Lost braces; missing escapes or markup?
    69 |   \item{obj$M}{Number of total observations sum_{i=1}^N(pi)}
       |                                                 ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) average.fit.models.Rd:6: Lost braces; missing escapes or markup?
     6 | These function takes the output of pgls.iter and uses its list of objects { model fits, optimzations (e.g.AICc)} and performs a weighted average on the ctoefficients estimated in the former by weighting by the latter. The parameters can also optionally be converted to binary by specifying "binary=FALSE" or just running the alias wraper function for assessing evidence of variable importance (Burnham & Anderson 2000).
       |                                                                           ^
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
checkRd: (-1) k2d.Rd:26: Lost braces
    26 | d_ND(x,y) = sqrt{ k(x,x) - 2k(x,y) + k(y,y)}.
       |                 ^
checkRd: (-1) k2d.Rd:34: Lost braces
    34 | d_n(x,y) = 1 - k(x,y)/sqrt{ k(x,x)k(y,y)},
       |                           ^
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
'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
'LazyData' is specified without a 'data' directory
checkRd: (-1) mom.mtruncnorm.Rd:35: Lost braces
    35 |   \item{cum}{a logical value; if  code{TRUE}  (default value), cumulants 
       |                                       ^
checkRd: (-1) mom.mtruncnorm.Rd:43: Lost braces; missing escapes or markup?
    43 | The maximal value of {d} is \code{20}. If this threshold is exceeded, \code{NA}s
       |                      ^
checkRd: (-1) mt.Rd:110: Lost braces
   110 |   and code{tvpack}, downloaded in 2005 and again in 2007 from his webpage, 
       |           ^
Problems with news in 'NEWS.md':
No news entries found.
Packages suggested but not available for checking:
  'alstructure', 'visPedigree'

Packages which this enhances but not available for checking:
  'miraculix', 'RandomFieldsUtils', 'MoBPSmaps'
'LazyData' is specified without a 'data' directory
checkRd: (-1) lientz.Rd:45: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) lientz.Rd:46: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) lientz.Rd:47: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) modeest-package.Rd:150: Escaped LaTeX specials: \&
checkRd: (-1) vieu.Rd:56: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
checkRd: (-1) modelDown.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) modelDown.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) modelDown.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) modelDown.Rd:31: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building 'getting-started-with-modeltime.Rmd' using rmarkdown

Quitting from getting-started-with-modeltime.Rmd:162-171 [unnamed-chunk-9]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `switch()`:
! EXPR must be a length 1 vector
---
Backtrace:
    ▆
 1. ├─... %>% ...
 2. ├─generics::fit(...)
 3. ├─parsnip::fit.model_spec(...)
 4. │ └─parsnip:::form_xy(...)
 5. │   └─parsnip:::xy_xy(...)
 6. │     └─parsnip:::eval_mod(...)
 7. │       └─rlang::eval_tidy(e, env = envir, ...)
 8. └─modeltime::auto_arima_xgboost_fit_impl(...)
 9.   └─modeltime::xgboost_predict(fit_xgboost, newdata = xreg_tbl)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'getting-started-with-modeltime.Rmd' failed with diagnostics:
EXPR must be a length 1 vector
--- failed re-building 'getting-started-with-modeltime.Rmd'

SUMMARY: processing the following file failed:
  'getting-started-with-modeltime.Rmd'

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building 'getting-started.Rmd' using rmarkdown
--- finished re-building 'getting-started.Rmd'

--- re-building 'panel-data.Rmd' using rmarkdown

Quitting from panel-data.Rmd:182-194 [unnamed-chunk-9]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `switch()`:
! EXPR must be a length 1 vector
---
Backtrace:
     ▆
  1. ├─... %>% fit(training(walmart_tscv$splits[[1]]))
  2. ├─generics::fit(., training(walmart_tscv$splits[[1]]))
  3. ├─workflows:::fit.workflow(., training(walmart_tscv$splits[[1]]))
  4. │ └─workflows::.fit_model(workflow, control)
  5. │   ├─generics::fit(action_model, workflow = workflow, control = control)
  6. │   └─workflows:::fit.action_model(...)
  7. │     └─workflows:::fit_from_xy(spec, mold, case_weights, control_parsnip)
  8. │       ├─generics::fit_xy(...)
  9. │       └─parsnip::fit_xy.model_spec(...)
 10. │         └─parsnip:::xy_xy(...)
 11. │           └─parsnip:::eval_mod(...)
 12. │             └─rlang::eval_tidy(e, env = envir, ...)
 13. └─modeltime::prophet_xgboost_fit_impl(...)
 14.   └─modeltime::xgboost_predict(fit_xgboost, newdata = xreg_tbl)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'panel-data.Rmd' failed with diagnostics:
EXPR must be a length 1 vector
--- failed re-building 'panel-data.Rmd'

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'MBESS'
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
checkRd: (-1) CHECKSUCCESS.Rd:44: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
installed size is 14.7Mb
  sub-directories of 1Mb or more:
    htmlwidgets  14.7Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
checkRd: (-1) circ_dist.Rd:21: Lost braces; missing escapes or markup?
    21 | The distance between two observations {i} and {j} of a circular variable {q}
       |                                       ^
checkRd: (-1) circ_dist.Rd:21: Lost braces; missing escapes or markup?
    21 | The distance between two observations {i} and {j} of a circular variable {q}
       |                                               ^
checkRd: (-1) circ_dist.Rd:21: Lost braces; missing escapes or markup?
    21 | The distance between two observations {i} and {j} of a circular variable {q}
       |                                                                          ^
checkRd: (-1) legacy.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) legacy.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) legacy.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) legacy.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) legacy.Rd:31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) legacy.Rd:32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) legacy.Rd:33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) legacy.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) legacy.Rd:35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) legacy.Rd:36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) legacy.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) legacy.Rd:38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) legacy.Rd:40: Lost braces in \itemize; meant \describe ?
GNU make is a SystemRequirements.
checkRd: (-1) morphemepiece_cache_dir.Rd:17-19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) morphemepiece_cache_dir.Rd:20-21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) morphemepiece_cache_dir.Rd:22-24: Lost braces in \itemize; meant \describe ?
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   1.5Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs   4.4Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package required but not available: 'MBESS'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Specified C++11: please drop specification unless essential
Error(s) in re-building vignettes:
--- re-building 'moveEZ.Rmd' using rmarkdown
File anim1.gif not found in resource path
Error: processing vignette 'moveEZ.Rmd' failed with diagnostics:
pandoc document conversion failed with error 99
--- failed re-building 'moveEZ.Rmd'

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

Error: Vignette re-building failed.
Execution halted
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    doc       4.8Mb
    extdata   1.9Mb
    libs      1.0Mb
checkRd: (-1) genotype_data.Rd:7: Escaped LaTeX specials: \_
checkRd: (-1) genotype_data.Rd:18: Escaped LaTeX specials: \_
checkRd: (-1) phenotype_data.Rd:15: Escaped LaTeX specials: \_
checkRd: (-1) glmfence.Rd:21: Lost braces; missing escapes or markup?
    21 | is performed where the boundary is cstar*hat(sigma)_{M,tildeM}.}
       |                                                     ^
checkRd: (-1) lmfence.Rd:21: Lost braces; missing escapes or markup?
    21 | is performed where the boundary is cstar*hat(sigma)_{M,tildeM}.}
       |                                                     ^
checkRd: (-1) get.mpt.fia.Rd:60: Lost braces
    60 | \item{lnconst}{When inequality constraints are present, \code{lnconst} serves as an adjustment of code{lnInt}. It estimates the logarithm of the proportion of parameter space [0,1]^S that satisfies those inequality constraints, and the log integral term is given by \code{lnInt+lnconst}.
       |                                                                                                       ^
checkRd: (-1) prediction.plot.Rd:38: Lost braces
    38 | The labels on the x-axis. Default is \code{Tree 1} to code{Tree n}.
       |                                                           ^
GNU make is a SystemRequirements.
Running 'multiResGrid.R' [17s]
Running the tests in 'tests/multiResGrid.R' failed.
Complete output:
  > s1 = Sys.time()
  > library(MRG)
  > library(tidyr)
  > 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
  
  > # Neccessary to silence sf startup messages
  > suppressMessages(library(sf))
  > if (require(giscoR, quietly = TRUE)) {
  + # Read nuts borders, used for extracting smaller data set 
  +   borders = gisco_get_nuts(nuts_level = 2)
  +   dkb = borders[borders$CNTR_CODE == "DK",] %>% st_transform(crs = 3035)
  + } else {
  +   mrgpath = find.package("MRG")
  +   load(file.path(mrgpath, "ex/dkb.rda"))
  + }
  > #'
  > # These are SYNTHETIC agricultural FSS data 
  > data(ifs_dk) # Census data
  > ifs_weight = ifs_dk %>% dplyr::filter(Sample == 1) # Extract weighted subsample
  > 
  > # Create spatial data
  > ifg = fssgeo(ifs_dk, locAdj = "LL")
  > fsg = fssgeo(ifs_weight, locAdj = "LL")
  > 
  > ifg$dkb = st_join(ifg, dkb)$NUTS_ID
  > ifg = ifg[!is.na(ifg$dkb) & ifg$dkb == "DK01",]
  > fsg$dkb = st_join(fsg, dkb)$NUTS_ID
  > fsg = fsg[!is.na(fsg$dkb) & fsg$dkb == "DK01",]
  > 
  > ifg$ft = as.numeric(substr(ifg$FARMTYPE, 3, 4))^2
  > 
  > s2 = Sys.time()
  > #'
  > # Set the base resolutions, and create a hierarchical list with gridded data
  > ress = c(1,5,10,20,40)*1000
  > # Gridding Utilized agricultural area (UAA), organic UAA and ft together
  > ifl = gridData(ifg, c("UAA", "UAAXK0000_ORG", "ft"), res = ress)
  Error: [rast] empty srs
  In addition: Warning message:
  PROJ: proj_create_from_database: Cannot find proj.db (GDAL error 1) 
  Execution halted
checkRd: (-1) MultiManhattan.Rd:33: Lost braces; missing escapes or markup?
    33 |         \item{LogTimes}{Magnification of {-log10(P-value)}; the default is
       |                                          ^
checkRd: (-1) MultiManhattan.Rd:35: Lost braces; missing escapes or markup?
    35 |     \item{LODTimes}{Magnification of {LOD score}; the default is 1.2.}
       |                                      ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) n.Rd:46: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) n.Rd:47-48: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) n.Rd:49-50: Lost braces in \itemize; \value handles \item{}{} directly
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc    3.3Mb
    libs   1.0Mb
'LazyData' is specified without a 'data' directory
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    data   4.5Mb
    libs   1.2Mb
installed size is  5.2Mb
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    libs   4.8Mb
'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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) multivar_joint_shannon_entropy.Rd:20: Lost braces
    20 |     {\code{table.variables}, \code{table.class}}.
       |     ^
checkRd: (-1) total_correlation.Rd:20: Lost braces
    20 |     {\code{table.variables}, \code{table.class}}.
       |     ^
'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
'LazyData' is specified without a 'data' directory
checkRd: (-1) coef.mdf.Rd:17: Lost braces; missing escapes or markup?
    17 |   \item{type}{: Argument that controls the type of parameters to be returned. If \code{type="persons"} (default), a vector with the person parameters is returned. When \code{type="items"} then a vector with the item ranks obtained by the MUDFOLD item selection algorithm is returned. If {type="all"} then a list with both person and item coefficients is returned to the user.
       |                                                                                                                                                                                                                                                                                                ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
Package required but not available: 'OpenMx'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
checkRd: (-1) MultEq-package.Rd:26-27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MultEq-package.Rd:28-29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MultEq-package.Rd:30: Lost braces in \itemize; meant \describe ?
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    14 | \item{bivprob}{Bivariate probabilities, {p00, p01, p10, p11}.}
       |                                         ^
Package required but not available: 'OpenMx'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running examples in 'multilandr-Ex.R' failed
The error most likely occurred in:

> ### Name: mland
> ### Title: Generates object of class 'MultiLand'
> ### Aliases: mland
> 
> ### ** Examples
> 
> # Loads main raster with land covers
> elchaco <- terra::rast(system.file("extdata", "elchaco.tif", package = "multilandr"))
> 
> # Main raster should have discrete values (e.g. land covers). This can be
> # checked with the function check_raster():
> 
> check_raster(elchaco)
  layer       crs units   class n_classes OK
1     1 projected     m integer         6  ✔
> 
> # Loads extra raster with NDVI values
> elchaco_ndvi <- terra::rast(system.file("extdata", "elchaco_ndvi.tif", package = "multilandr"))
> 
> # Classes names
> cl_names <- c(1, "Forest",
+               2, "Grassland",
+               3, "Crops",
+               4, "Pastures",
+               5, "Water",
+               6, "Urban")
> 
> # Loads points
> elchaco_sites <- terra::vect(system.file("extdata", "elchaco_sites.gpkg", package = "multilandr"))
> 
> # Creates 'MultiLand' object by loading main raster, an extra raster and points.
> ernesdesign <- mland(points_layer = elchaco_sites,
+                      rast_layer = elchaco,
+                      radii = seq(1000, 5000, 1000),
+                      class_names = list(cl_names),
+                      site_ref = "name",
+                      ext_rast_layer = elchaco_ndvi,
+                      rast_names = c("landcover", "NDVI"),
+                      segs = 20)
Loading layers

Error: - rasters CRS must be equal to points layer CRS.
Execution halted
Running 'testthat.R' [55s]
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(multilandr)
  > 
  > test_check("multilandr")
  
  Saving _problems/test-mland-13.R
  - condition 1: raster layers included in the filtering process: 1
  140 points were retained out of 607 initial points (23.06%).
  
  - condition 1: raster layers included in the filtering process: 1
  - condition 2: raster layers included in the filtering process: 1
  67 points were retained out of 607 initial points (11.04%).
  
  [ FAIL 1 | WARN 5 | SKIP 0 | PASS 13 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-mland.R:7:5'): loads MultiLand successfully ────────────────────
  Error: - rasters CRS must be equal to points layer CRS.
  Backtrace:
      ▆
   1. ├─testthat::expect_s4_class(...) at test-mland.R:4:3
   2. │ └─testthat::quasi_label(enquo(object))
   3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
   4. └─multilandr::mland(...) at test-mland.R:7:5
   5.   └─base::tryCatch(...)
   6.     └─base (local) tryCatchList(expr, classes, parentenv, handlers)
   7.       └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
   8.         └─value[[3L]](cond)
  
  [ FAIL 1 | WARN 5 | SKIP 0 | PASS 13 ]
  Error:
  ! Test failures.
  Execution halted
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
Package suggested but not available for checking: 'cmdstanr'
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    data   1.0Mb
    doc    6.4Mb
'LazyData' is specified without a 'data' directory
Package required but not available: 'MBESS'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
installed size is 19.3Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    doc    4.5Mb
    libs  12.6Mb
GNU make is a SystemRequirements.
Package suggested but not available for checking: 'rrelaxiv'
checkRd: (-1) mPhen.defineOptions.Rd:4: Escaped LaTeX specials: \$
GNU make is a SystemRequirements.
checkRd: (-1) nullestimation.Rd:17: Lost braces; missing escapes or markup?
    17 |           \code{U}        \tab The common latent space vectors. U in R^{n x d}\cr
       |                                                                        ^
'LazyData' is specified without a 'data' directory
installed size is  7.1Mb
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    doc    2.7Mb
    help   2.3Mb
    libs   1.0Mb
Running examples in 'MultiscaleDTM-Ex.R' failed
The error most likely occurred in:

> ### Name: AdjSD
> ### Title: Calculates standard deviation of bathymetry (a measure of
> ###   rugosity) adjusted for slope
> ### Aliases: AdjSD
> 
> ### ** Examples
> 
> r<- erupt()
Warning: PROJ: proj_create_from_database: Cannot find proj.db (GDAL error 1)
Error: [rast] empty srs
Execution halted
Running 'testthat.R' [11s]
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(MultiscaleDTM)
  Loading required package: terra
  terra 1.8.86
  
  Attaching package: 'terra'
  
  The following objects are masked from 'package:testthat':
  
      compare, describe
  
  > 
  > test_check("MultiscaleDTM")
  Saving _problems/test-functions-1.R
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 0 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-functions.R:1:1'): (code run outside of `test_that()`) ─────────
  Error: [rast] empty srs
  Backtrace:
       ▆
    1. └─MultiscaleDTM::erupt() at test-functions.R:1:1
    2.   ├─terra::rast(...)
    3.   └─terra::rast(...)
    4.     └─terra (local) .local(x, ...)
    5.       ├─terra::rast(nrows = nrow(x), ncols = ncol(x), crs = crs, extent = extent)
    6.       └─terra::rast(nrows = nrow(x), ncols = ncol(x), crs = crs, extent = extent)
    7.         └─terra (local) .local(x = x, ...)
    8.           └─terra:::new_rast(...)
    9.             └─terra:::messages(r, "rast")
   10.               └─terra:::error(f, x@pntr$getError())
  
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 0 ]
  Error:
  ! Test failures.
  Execution halted
'LazyData' is specified without a 'data' directory
checkRd: (-1) biomasse.Rd:30: Lost braces
    30 | Makowski, D., Jeuffroy, M.-H., Gu\'{e}rif, M., 2004 Bayesian methods for
       |                                    ^
checkRd: (-1) climat.Rd:20: Lost braces
    20 | Makowski, D., Jeuffroy, M.-H., Gu\'{e}rif, M., 2004 Bayesian methods for
       |                                    ^
checkRd: (-1) simulmodel.Rd:15: Lost braces
    15 |   \item{\dots}{... }{possible fixed parameters of the R-function}
       |                     ^
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   4.3Mb
Specified C++11: please drop specification unless essential
checkRd: (-1) metricUnfolding.Rd:69-70: Lost braces in \itemize; meant \describe ?
checkRd: (-1) metricUnfolding.Rd:71-72: Lost braces in \itemize; meant \describe ?
checkRd: (-1) metricUnfolding.Rd:73-74: Lost braces in \itemize; meant \describe ?
checkRd: (-1) metricUnfolding.Rd:75-79: Lost braces in \itemize; meant \describe ?
checkRd: (-1) metricUnfolding.Rd:80-86: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) cv.glm1path.Rd:74: Lost braces
    74 | \code{\link{glm1path}}, \\code{\link{glm1}}, \code{\link{glm}}, \code{\link{family}}
       |                               ^
Package suggested but not available for checking: 'cmdstanr'
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    R     7.4Mb
    doc   2.0Mb
checkRd: (-1) bal.Rd:156: Escaped LaTeX specials: \&
checkRd: (-1) MVNtestchar-package.Rd:16-17: Lost braces; missing escapes or markup?
    16 | {Provides a test of multivariate normality of a sample which does not require estimation of the nuisance parameters, the mean      vector and covariance matrix.  Rather, a sequence of transformations removes these nuisance parameters, resulting in a set of    sample matrices that are positive definite.  If, and only if the original data is multivariate normal, these matrices are       uniformly distributed on the space of positive definite matrices in the unit hyper-rectangle.  The package performs a goodness    of fit test of this hypothesis. In addition to the test, functions in the package give visualizations of the  support region    of positive definite matrices for p equals 2.
       | ^
checkRd: (-1) pkb.Rd:14: Escaped LaTeX specials: \# \# \#
'LazyData' is specified without a 'data' directory
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Package required but not available: 'OpenMx'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'OpenMx'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'rTubeDB'
Package unavailable to check Rd xrefs: 'rTubeDB'
Error(s) in re-building vignettes:
--- re-building 'use-mycolors.Rmd' using rmarkdown

Quitting from use-mycolors.Rmd:77-80 [unnamed-chunk-3]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
NULL
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'use-mycolors.Rmd' failed with diagnostics:
Problem while converting geom to grob.
ℹ Error occurred in the 4th layer.
Caused by error in `is.waive()`:
! could not find function "is.waive"
--- failed re-building 'use-mycolors.Rmd'

SUMMARY: processing the following file failed:
  'use-mycolors.Rmd'

Error: Vignette re-building failed.
Execution halted
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checkRd: (-1) mzipmed_data.Rd:22: Lost braces; missing escapes or markup?
    22 | @source {Simulated to serve as an example}
       |         ^
Package which this enhances but not available for checking: 'asreml'
installed size is 16.2Mb
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    extdata  16.2Mb
checkRd: (-1) M36NT2PM.dat.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) M36NT2PM.dat.Rd:38: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
checkRd: (-1) DSIVdata.Rd:15-23: Lost braces
    15 | for(i in 1:50){
       |               ^
checkRd: (-1) DSIVdata.Rd:17-21: Lost braces
    17 |   for(j in 1:50){
       |                 ^
checkRd: (-1) DSIVdata.Rd:31-39: Lost braces
    31 | for(i in 1:20){
       |               ^
checkRd: (-1) DSIVdata.Rd:33-37: Lost braces
    33 |   for(j in 1:20){
       |                 ^
checkRd: (-1) DSLIVEdata.Rd:10-18: Lost braces
    10 | for(i in 1:200){
       |                ^
checkRd: (-1) DSLIVEdata.Rd:12-16: Lost braces
    12 |   for(j in 1:200){
       |                  ^
checkRd: (-1) DSLIVEdata.Rd:26-34: Lost braces
    26 | for(i in 1:20){
       |               ^
checkRd: (-1) DSLIVEdata.Rd:28-32: Lost braces
    28 |   for(j in 1:20){
       |                 ^
checkRd: (-1) DSLIVEdata.Rd:50-54: Lost braces
    50 | for(kk in 1:length(p)){
       |                       ^
checkRd: (-1) drop_name_crossref.Rd:49: Lost braces; missing escapes or markup?
    49 | Takes one or several dois and extracts information from Crossref, then processes them into visual citations with \code{\link{drop_name}}. Requires {rcrossref} > v1.1, see README for further details.
       |                                                                                                                                                    ^
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    data     1.9Mb
    libs     2.4Mb
    models   1.1Mb
checkRd: (-1) fod.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fod.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fod.Rd:14: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Version (2018-01-22)
    Version  (2017-08-22)
    Version
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    doc    6.5Mb
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GNU make is a SystemRequirements.
checkRd: (-1) NbClust.Rd:50: Lost braces; missing escapes or markup?
    50 |       \item \bold{Average} : The distance \eqn{D_{ij}}{D_ij} between two clusters \eqn{C_{i}}{C_i} and \eqn{C_{j}}{C_j} is the mean of the distances between the pair of points {x} and {y}, where \eqn{x \in C_{i}, y \in C_{j}}{x in C_i, y in C_j}.
       |                                                                                                                                                                                 ^
checkRd: (-1) NbClust.Rd:50: Lost braces; missing escapes or markup?
    50 |       \item \bold{Average} : The distance \eqn{D_{ij}}{D_ij} between two clusters \eqn{C_{i}}{C_i} and \eqn{C_{j}}{C_j} is the mean of the distances between the pair of points {x} and {y}, where \eqn{x \in C_{i}, y \in C_{j}}{x in C_i, y in C_j}.
       |                                                                                                                                                                                         ^
checkRd: (-1) nbconvert.Rd:49: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) nbconvert.Rd:50: Lost braces in \enumerate; meant \describe ?
Package suggested but not available for checking: 'NBDCtoolsData'
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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installed size is  9.5Mb
  sub-directories of 1Mb or more:
    data   9.4Mb
installed size is 16.9Mb
  sub-directories of 1Mb or more:
    libs  16.6Mb
Problems with news in 'NEWS.md':
No news entries found.
Problems with news in 'NEWS.md':
No news entries found.
checkRd: (-1) ncpen.Rd:108: Lost braces; missing escapes or markup?
   108 |   \item{gamma}{extra shrinkage parameter for \code{classo} and {sridge} only.}
       |                                                                ^
checkRd: (-1) ncpen.reg.Rd:109: Lost braces; missing escapes or markup?
   109 |   \item{gamma}{extra shrinkage parameter for \code{classo} and {sridge} only.}
       |                                                                ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.2Mb
Package required but not available: 'MBESS'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    data   7.1Mb
'LazyData' is specified without a 'data' directory
Packages required but not available: 'fungible', 'MBESS'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'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
GNU make is a SystemRequirements.
checkRd: (-1) GSS.Rd:17: Lost braces
    17 | code{2016}.}
       |     ^
Specified C++11: please drop specification unless essential
Error(s) in re-building vignettes:
--- re-building 'netseer.Rmd' using rmarkdown
File man/figures/logo.png not found in resource path
Error: processing vignette 'netseer.Rmd' failed with diagnostics:
pandoc document conversion failed with error 99
--- failed re-building 'netseer.Rmd'

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

Error: Vignette re-building failed.
Execution halted
checkRd: (-1) PVmodule.Rd:27: Lost braces; missing escapes or markup?
    27 | In the resulting netSEM model, time was used as a proxy for damp heat exposure stress (S) variable and $P_{max}$ (maximum power generated by the modules) was used as the performance level response ($R$) variable, several mechanistic variables ($M$) were obtained through chemical evaluation methods, including FTIR and TGA  on EVA encapsulant. 
       |                                                                                                           ^
checkRd: (-1) netSEMp1.Rd:55: Lost braces
    55 | For example, in the quadratic functional form y ~ b0 + b1x + b2x^2, the three P-values correspond two those of \\hat{b0}, \\hat{b1} and \\hat{b2}, respectively. 
       |                                                                                                                     ^
checkRd: (-1) netSEMp1.Rd:55: Lost braces
    55 | For example, in the quadratic functional form y ~ b0 + b1x + b2x^2, the three P-values correspond two those of \\hat{b0}, \\hat{b1} and \\hat{b2}, respectively. 
       |                                                                                                                                ^
checkRd: (-1) netSEMp1.Rd:55: Lost braces
    55 | For example, in the quadratic functional form y ~ b0 + b1x + b2x^2, the three P-values correspond two those of \\hat{b0}, \\hat{b1} and \\hat{b2}, respectively. 
       |                                                                                                                                              ^
checkRd: (-1) spec_clust.Rd:33: Lost braces; missing escapes or markup?
    33 | A label vector of size n x 1 with elements in {1,2,...,K}
       |                                               ^
checkRd: (-1) rc.plot.ideogram.Rd:20: Lost braces; missing escapes or markup?
    20 |  \item{las}{numeric in {0,1,2,3}; the style of chromosome labels. 0, always parallel to the track [default]; 1, always horizontal; 2, always perpendicular to the track; 3, always vertical.}
       |                        ^
checkRd: (-1) NetworkChange.Rd:163: Escaped LaTeX specials: \&
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checkRd: (-1) networktree.Rd:56: Lost braces; missing escapes or markup?
    56 | with a matrix response {y}. \code{x1} and \code{x2} are used as
       |                        ^
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    data   7.8Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R         1.4Mb
    extdata   1.6Mb
    libs      1.3Mb
Packages suggested but not available for checking:
  'BPST', 'ImageSCC', 'Triangulation'
'LazyData' is specified without a 'data' directory
Packages which this enhances but not available for checking:
  'NGCHMDemoData', 'NGCHMSupportFiles'
'LazyData' is specified without a 'data' directory
checkRd: (-1) NHANES.Rd:278: Lost braces
   278 | \code{AgeFirstMarij}{Age participant first tried marijuana. Reported for participants aged 18 to 59 years.}
       |                     ^
'LazyData' is specified without a 'data' directory
The following files should probably not be installed:
  'nhm-manual.tex'

Consider the use of a .Rinstignore file: see 'Writing R Extensions',
or move the vignette sources from 'inst/doc' to 'vignettes'.
checkRd: (-1) graphresU.fun.Rd:72: Escaped LaTeX specials: \&
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checkRd: (-1) sim_data.Rd:44: Lost braces in \itemize; \value handles \item{}{} directly
installed size is  5.3Mb
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    doc   4.0Mb
'LazyData' is specified without a 'data' directory
installed size is 27.8Mb
  sub-directories of 1Mb or more:
    CppCode   4.8Mb
    R         8.5Mb
    include  11.7Mb
    libs      1.2Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc       4.0Mb
    extdata   1.8Mb
Package which this enhances but not available for checking: 'jpndistrict'
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) dot-make_long_data.Rd:44: Lost braces; missing escapes or markup?
    44 | training sample), psi (the value of this observations Psihat(P_{n,B_n}^0)),
       |                                                                ^
checkRd: (-1) dot-make_long_data_nested_cv.Rd:49: Lost braces; missing escapes or markup?
    49 | training sample), psi (the value of this observations Psihat(P_{n,B_n}^0)),
       |                                                                ^
Running examples in 'nlpred-Ex.R' failed
The error most likely occurred in:

> ### Name: xgboost_wrapper
> ### Title: Wrapper for fitting eXtreme gradient boosting via 'xgboost'
> ### Aliases: xgboost_wrapper
> 
> ### ** Examples
> 
> # simulate data
> # make list of training data
> train_X <- data.frame(x1 = runif(50))
> train_Y <- rbinom(50, 1, plogis(train_X$x1))
> train <- list(Y = train_Y, X = train_X)
> # make list of test data
> test_X <- data.frame(x1 = runif(50))
> test_Y <- rbinom(50, 1, plogis(train_X$x1))
> test <- list(Y = test_Y, X = test_X)
> # fit xgboost
> xgb_wrap <- xgboost_wrapper(train = train, test = test)
Warning in throw_err_or_depr_msg("Parameter(s) have been removed from this function: ",  :
  Parameter(s) have been removed from this function: params, save_period. This warning will become an error in a future version.
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.
Warning in throw_err_or_depr_msg("Parameter '", match_old, "' has been renamed to '",  :
  Parameter 'eta' has been renamed to 'learning_rate'. This warning will become an error in a future version.
Error in xgboost::xgboost(data = xgmat, objective = "binary:logistic",  : 
  argument "y" is missing, with no default
Calls: xgboost_wrapper ... <Anonymous> -> process.y.margin.and.objective -> NROW
Execution halted
Package required but not available: 'OpenMx'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
checkRd: (-1) anova.Rd:19: Lost braces
    19 |   Returns an object of class code{anova}.  These objects represent
       |                                  ^
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc   5.5Mb
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: 'simpar'
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) simulatePop.Rd:40: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) plot.ndmodel.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.ndmodel.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.ndmodel.Rd:18: 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
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   2.6Mb
    mods   3.3Mb
Package suggested but not available for checking: 'OpenMx'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    doc    2.8Mb
    help   5.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) DiscHazRateAuxFunctions.Rd:46: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DiscHazRateAuxFunctions.Rd:47: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DiscHazRateAuxFunctions.Rd:48: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nppbib.Rd:28: Escaped LaTeX specials: \#
'LazyData' is specified without a 'data' directory
checkRd: (-1) np.reg.test.Rd:148: Lost braces
   148 | ter Braak, C. J. F. (1992). Permutation versus bootstrap significance tests in multiple regression and ANOVA. In K. H. J\"{o}ckel, G. Rothe, & W. Sendler (Eds.), Bootstrapping and related techniques. lecture notes in economics and mathematical systems, vol 376 (pp. 79-86). Springer.
       |                                                                                                                           ^
checkRd: (-1) nptest-package.Rd:73: Lost braces
    73 | ter Braak, C. J. F. (1992). Permutation versus bootstrap significance tests in multiple regression and ANOVA. In K. H. J\"{o}ckel, G. Rothe, & W. Sendler (Eds.), Bootstrapping and related techniques. lecture notes in economics and mathematical systems, vol 376 (pp. 79-86). Springer.
       |                                                                                                                           ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) MSM.fit.Rd:21: Lost braces
    21 | \code{MSM.fit} returns an object of class code{MSM.lm} or \code{MSM.glm}, depending on the input model.
       |                                               ^
checkRd: (-1) SMC.Smooth.Rd:25: Lost braces; missing escapes or markup?
    25 | observation at current time step. It should return {xx} (the samples xt) and
       |                                                    ^
checkRd: (-1) SMC.Smooth.Rd:26: Lost braces; missing escapes or markup?
    26 | {logww} (their corresponding log weight).}
       | ^
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   4.1Mb
GNU make is a SystemRequirements.
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
Depends: includes the non-default packages:
  'Cubist', 'Metrics', 'arm', 'brnn', 'broom', 'car', 'caret',
  'corrplot', 'doParallel', 'dplyr', 'e1071', 'earth', 'gam', 'gbm',
  'ggplot2', 'glmnet', 'gridExtra', 'ipred', 'leaps', 'nnet', 'olsrr',
  'parallel', 'pls', 'purrr', 'randomForest', 'reactable',
  'reactablefmtr', 'readr', 'rpart', 'tidyr', 'tree', 'xgboost'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc    5.5Mb
    libs   1.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) xyz2R.Rd:31: Lost braces
    31 |    \item Finally, code{T} is rotated an angle \code{z} about its NEWEST z-axis.
       |                       ^
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
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installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   4.2Mb
    doc    1.4Mb
checkRd: (-1) OBMb.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly
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    93 | \code{'sparse'}, then only (S^{diag}, S^{off,d})
       |                               ^
checkRd: (-1) ChangepointDetector.Rd:93: Lost braces; missing escapes or markup?
    93 | \code{'sparse'}, then only (S^{diag}, S^{off,d})
       |                                         ^
checkRd: (-1) ChangepointDetector.Rd:94: Lost braces; missing escapes or markup?
    94 | and (S^{diag}, S^{off,s}) are included in \code{stat} respectively.);
       |        ^
checkRd: (-1) ChangepointDetector.Rd:94: Lost braces; missing escapes or markup?
    94 | and (S^{diag}, S^{off,s}) are included in \code{stat} respectively.);
       |                  ^
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
checkRd: (-1) onlineCPD.Rd:35: Lost braces
    35 |  function(x, lambda){const_hazard(x, lambda=100)}
       |                     ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc   6.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   4.7Mb
installed size is 31.7Mb
  sub-directories of 1Mb or more:
    doc   29.4Mb
    help   2.0Mb
'LazyData' is specified without a 'data' directory
checkRd: (-1) dot-discoveryRequest.Rd:15-16: Lost braces
    15 | \item{service}{One of {"locations", "deployments", "deviceCategories", "devices",
       |                       ^
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    18 | \item{method}{One of {"get", "getTree"}}
       |                      ^
checkRd: (-1) dot-saveAsFile.Rd:19: Lost braces; missing escapes or markup?
    19 | (numeric) Result code from {0: done, -1: error, -2: fileExists}
       |                            ^
Package suggested but not available for checking: 'cmdstanr'
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
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GNU make is a SystemRequirements.
installed size is 30.3Mb
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    libs   19.9Mb
    share  10.2Mb
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installed size is  5.1Mb
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    doc    2.4Mb
    libs   1.6Mb
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    data   4.6Mb
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'umx', 'ifaTools'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/OpenMx.Rcheck/00install.out' for details.
installed size is  7.2Mb
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    java     1.2Mb
    models   6.0Mb
Package suggested but not available for checking: 'openNLPmodels.en'
installed size is  8.4Mb
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    doc    2.6Mb
    libs   5.3Mb
installed size is  5.3Mb
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    doc   4.9Mb
installed size is  5.2Mb
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    R      1.1Mb
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Running 'testthat.R' [2s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(operator.tools)
  > 
  > test_check("operator.tools")
  Saving _problems/test-operators-11.R
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 27 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-operators.R:6:1'): opetators ───────────────────────────────────
  Error in `is_true()`: could not find function "is_true"
  Backtrace:
      ▆
   1. └─testthat::expect_that(...) at test-operators.R:6:1
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 27 ]
  Error:
  ! Test failures.
  Execution halted
Problems with news in 'NEWS.md':
No news entries found.
checkRd: (-1) word_imp.Rd:14: Lost braces
    14 | number of individual records. An \code{n} x code{2} dataframe can
       |                                                 ^
checkRd: (-1) MonteCarlo.Rd:23: Lost braces
    23 | N is computed from \code{p} length. M is code{10^4} by default.
       |                                              ^
Package suggested but not available for checking: 'gurobi'
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
checkRd: (-1) drawdesign.Rd:39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) drawdesign.Rd:40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) drawdesign.Rd:41: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) drawdesign.Rd:44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gnu_style.Rd:24: Lost braces
    24 | [GNU Command Line Standards]{http://www.gnu.org/prep/standards/standards.html}
       |                             ^
Running 'testthat.R' [2s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(optigrab)
  > 
  > test_check("optigrab")
  Saving _problems/test-opt_expand-98.R
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 106 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-opt_expand.r:98:1'): (code run outside of `test_that()`) ───────
  Error in `is_true()`: could not find function "is_true"
  Backtrace:
      ▆
   1. └─testthat::expect_that(is.character(expanded), is_true()) at test-opt_expand.r:98:1
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 106 ]
  Error:
  ! Test failures.
  Execution halted
Package which this enhances but not available for checking: 'gurobi'
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Package suggested but not available for checking: 'rrelaxiv'
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    74 | matrix of covariates \code{X} and a vector of outcomes 'code{Y} to the \code{orf}
       |                                                             ^
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    44 | \item{print}{Level of verbosity in Fortran (may not be visible on all terminals); should be an integer between {range, range}, Default: 3}
       |                                                                                                                ^
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    41 | \item{start}{Starting point generation method, see vignettes for details; should be an integer between {range,range}, Default: 2}
       |                                                                                                        ^
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installed size is  6.8Mb
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    doc    5.0Mb
    libs   1.3Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   3.6Mb
    help   1.1Mb
'LazyData' is specified without a 'data' directory
installed size is 15.2Mb
  sub-directories of 1Mb or more:
    libs  14.8Mb
GNU make is a SystemRequirements.
Package suggested but not available for checking: 'Rcplex'
checkRd: (-1) otp_create_surface.Rd:33: Lost braces; missing escapes or markup?
    33 | The file will be named surface_{id}.tiff, with {id} replaced by the OTP id assigned
       |                                ^
checkRd: (-1) otp_create_surface.Rd:33: Lost braces; missing escapes or markup?
    33 | The file will be named surface_{id}.tiff, with {id} replaced by the OTP id assigned
       |                                                ^
checkRd: (-1) imput_cov.Rd:79: Lost braces
    79 | \item van Buuren, S., Groothuis-Oudshoorn, K. (2011). mice: Multivariate Imputation by Chained Equations in R. Journal of Statistical Software, 45(3), 1–67. url{https://www.jstatsoft.org/v45/i03/}
       |                                                                                                                                                                 ^
checkRd: (-1) indiv_grp_closest.Rd:47: Lost braces; missing escapes or markup?
    47 | The function \code{indiv_grp_closest} is an intermediate function used in the implementation of an algorithm called {OUTCOME} (and its enrichment {R-OUTCOME}, see the reference (2) for more details) dedicated to the solving of recoding problems in data fusion using Optimal Transportation theory.
       |                                                                                                                     ^
checkRd: (-1) indiv_grp_closest.Rd:47: Lost braces; missing escapes or markup?
    47 | The function \code{indiv_grp_closest} is an intermediate function used in the implementation of an algorithm called {OUTCOME} (and its enrichment {R-OUTCOME}, see the reference (2) for more details) dedicated to the solving of recoding problems in data fusion using Optimal Transportation theory.
       |                                                                                                                                                   ^
checkRd: (-1) merge_dbs.Rd:179: Lost braces
   179 | \item van Buuren, S., Groothuis-Oudshoorn, K. (2011). mice: Multivariate Imputation by Chained Equations in R. Journal of Statistical Software, 45(3), 1–67. url{https://www.jstatsoft.org/v45/i03/}
       |                                                                                                                                                                 ^
Specified C++11: please drop specification unless essential
checkRd: (-1) fmat.Rd:15: Lost braces; missing escapes or markup?
    15 | \item outcome: codes {I, P, R, NC, O, UH, UO, eUH, eUO, NE}
       |                      ^
checkRd: (-1) fmat.Rd:24: Lost braces; missing escapes or markup?
    24 | The input parameters given by the user are {I, P, R, NC, O, UH, UO} and
       |                                            ^
checkRd: (-1) fmat.Rd:25: Lost braces; missing escapes or markup?
    25 | the parameter 'e'. The parameter e is multiplied by {UH, UO} internally so as to
       |                                                     ^
checkRd: (-1) fmat.Rd:26: Lost braces; missing escapes or markup?
    26 | produce {eUH, eUO}.
       |         ^
checkRd: (-1) middleearth.Rd:14: Lost braces; missing escapes or markup?
    14 | \item \strong{code:} one of the outcome codes {I, P, R, NC, O, UH, UO, UH, UO, NE}
       |                                               ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running 'testthat.R' [3s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(owmr)
  owmr 0.8.2
     another crazy way to talk to OpenWeatherMap's API
     Documentation: type ?owmr or https://crazycapivara.github.io/owmr/
     Issues, notes and bleeding edge: https://github.com/crazycapivara/owmr/
  
  It is recommended that you store your api key in an environment variable called OWM_API_KEY.
  
  > 
  > test_check("owmr")
  Saving _problems/test_current_mocks-30.R
  Saving _problems/test_forecast-29.R
  [ FAIL 2 | WARN 3 | SKIP 0 | PASS 28 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_current_mocks.R:8:3'): current weather data ────────────────────
  <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_current_mocks.R:8:3
   2.   └─lifecycle::deprecate_stop("3.2.0", "with_mock()", "with_mocked_bindings()")
   3.     └─lifecycle:::deprecate_stop0(msg)
   4.       └─rlang::cnd_signal(...)
  ── Error ('test_forecast.R:8:3'): forecast data ────────────────────────────────
  <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_forecast.R:8:3
   2.   └─lifecycle::deprecate_stop("3.2.0", "with_mock()", "with_mocked_bindings()")
   3.     └─lifecycle:::deprecate_stop0(msg)
   4.       └─rlang::cnd_signal(...)
  
  [ FAIL 2 | WARN 3 | SKIP 0 | PASS 28 ]
  Error:
  ! Test failures.
  Execution halted
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Changes
checkRd: (-1) residuals_paco.Rd:10: Escaped LaTeX specials: \$
Specified C++11: please drop specification unless essential
installed size is  7.2Mb
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    doc       2.0Mb
    extdata   4.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) MICS2014Ch.Rd:296: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) MICS2014Ch.Rd:297: Lost braces in \enumerate; meant \describe ?
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checkRd: (-1) PakPMICS2018hh.Rd:363: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) PakPMICS2018mm.Rd:69: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) PakPMICS2018mm.Rd:70: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) PakPMICS2018mn.Rd:243: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) PakPMICS2018mn.Rd:244: Lost braces in \enumerate; meant \describe ?
installed size is 17.9Mb
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    library  17.0Mb
Package suggested but not available for checking: 'CorShrink'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running 'testthat.R' [78s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(panelr)
  Loading required package: lme4
  Loading required package: Matrix
  
  Attaching package: 'panelr'
  
  The following object is masked from 'package:stats':
  
      filter
  
  > 
  > test_check("panelr")
  Saving _problems/test-utils-298.R
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 292 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-utils.R:298:3'): extractors work ─────────────────────────────
  Expected `predict(mod)` to run silently.
  Actual noise: warnings.
  
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 292 ]
  Error:
  ! Test failures.
  Execution halted
checkRd: (-1) panelsummary.Rd:112: Lost braces; missing escapes or markup?
   112 | \item `"{exp(estimate) * std.error}"
       |         ^
checkRd: (-1) panelsummary_raw.Rd:90: Lost braces; missing escapes or markup?
    90 | \item `"{exp(estimate) * std.error}"
       |         ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) hvidovre.Rd:11: Lost braces
    11 |     \item{\code{roof_tile}}{a numeric vector, roof_tile}{dummy, roof made out of tiles =1}
       |                                                         ^
checkRd: (-1) hvidovre.Rd:25: Lost braces
    25 |     \item{\code{railways}}{a numeric vector, railways}{distance to nearest railway in meters}
       |                                                       ^
checkRd: (-1) hvidovre.Rd:26: Lost braces
    26 |     \item{\code{nature_SLD}}{a numeric vector, nature_SLD}{distance to nearest nature area in meters}
       |                                                           ^
Package suggested but not available for checking: 'EGAnet'
checkRd: (-1) returns.Rd:21: Lost braces; missing escapes or markup?
    21 |   \item{...}{Other options including {type} which refers to the
       |                                      ^
Malformed Description field: should contain one or more complete sentences.
checkRd: (-1) PPS.fit.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) PPS.fit.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) PPS.fit.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) PPS.fit.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) PPS.fit.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) PPS.fit.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) forbes400.Rd:8: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) turkey.Rd:8: Lost braces in \itemize; meant \describe ?
checkRd: (-1) turkey.Rd:9: Lost braces in \itemize; meant \describe ?
checkRd: (-1) turkey.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) turkey.Rd:11: Lost braces in \itemize; meant \describe ?
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
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    doc    2.8Mb
    libs   2.8Mb
'LazyData' is specified without a 'data' directory
checkRd: (-1) PAS-package.Rd:30: Lost braces
    30 |     {\code{bin model}}{\cr Zhiqiu Hu, Zhiquan Wang, and Shizhong Xu (2012) An infinitesimal model for quantitative trait genomic value prediction. PloS ONE 7: e41336.}
       |                       ^
Running 'testthat.R' [2s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(passport)
  > 
  > test_check("passport")
  Saving _problems/test_parse_country-49.R
  [ FAIL 1 | WARN 4 | SKIP 1 | PASS 37 ]
  
  ══ Skipped tests (1) ═══════════════════════════════════════════════════════════
  • On CRAN (1): 'test_parse_country.R:91:5'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test_parse_country.R:43:5'): parsing country names with simulated geocoding APIs works ──
  `with_mock(...)` threw an error with unexpected message.
  Expected match: "jsonlite"
  Actual message: "`with_mock()` was deprecated in testthat 3.2.0 and is now defunct.\nℹ Please use `with_mocked_bindings()` instead."
  Backtrace:
      ▆
   1. ├─testthat::expect_error(...) at test_parse_country.R:43:5
   2. │ └─testthat:::quasi_capture(...)
   3. │   ├─testthat (local) .capture(...)
   4. │   │ └─base::withCallingHandlers(...)
   5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
   6. └─testthat::with_mock(...)
   7.   └─lifecycle::deprecate_stop("3.2.0", "with_mock()", "with_mocked_bindings()")
   8.     └─lifecycle:::deprecate_stop0(msg)
   9.       └─rlang::cnd_signal(...)
  
  [ FAIL 1 | WARN 4 | SKIP 1 | PASS 37 ]
  Error:
  ! Test failures.
  Execution halted
Error(s) in re-building vignettes:
--- re-building 'a0_pastclim_overview.Rmd' using rmarkdown
--- re-building 'a1_available_datasets.Rmd' using rmarkdown
--- finished re-building 'a1_available_datasets.Rmd'

--- re-building 'a2_custom_datasets.Rmd' using rmarkdown
--- finished re-building 'a2_custom_datasets.Rmd'

--- re-building 'a3_pastclim_present_and_future.Rmd' using rmarkdown
--- finished re-building 'a3_pastclim_present_and_future.Rmd'

--- re-building 'a4_delta_downscale_d.Rmd' using rmarkdown

Quitting from a4_delta_downscale_d.Rmd:134-140 [unnamed-chunk-10]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! [rast] empty srs
---
Backtrace:
     ▆
  1. ├─terra::readRDS(...)
  2. └─terra::readRDS(...)
  3.   ├─terra::unwrap(x)
  4.   └─terra::unwrap(x)
  5.     └─terra (local) .local(x, ...)
  6.       └─base::lapply(x@rasters, unwrap)
  7.         ├─terra (local) FUN(X[[i]], ...)
  8.         └─terra (local) FUN(X[[i]], ...)
  9.           └─terra (local) .local(x, ...)
 10.             ├─base::eval(parse(text = x@definition))
 11.             │ └─base::eval(parse(text = x@definition))
 12.             ├─terra::rast(...)
 13.             └─terra::rast(...)
 14.               └─terra (local) .local(x = x, ...)
 15.                 └─terra:::new_rast(...)
 16.                   └─terra:::messages(r, "rast")
 17.                     └─terra:::error(f, x@pntr$getError())
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'a4_delta_downscale_d.Rmd' failed with diagnostics:
[rast] empty srs
--- failed re-building 'a4_delta_downscale_d.Rmd'

SUMMARY: processing the following files failed:
  'a0_pastclim_overview.Rmd' 'a4_delta_downscale_d.Rmd'

Error: Vignette re-building failed.
Execution halted
installed size is  5.1Mb
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    R      3.5Mb
    data   1.5Mb
installed size is  7.1Mb
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    doc   6.7Mb
checkRd: (-1) plotHeat.Rd:113: Lost braces
   113 | code{\link[patternize]{patPCA}}, as 'one' when visualizing single image or as 'multi' for multi
       |     ^
GNU make is a SystemRequirements.
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    R      8.0Mb
    help   2.9Mb
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
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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
checkRd: (-1) pbd_loglik.Rd:31: Lost braces
    31 |     \code{pars2[1]} {set the conditioning on non-extinction of the clade (1) or not (0) \cr \cr}
       |                     ^
checkRd: (-1) pbd_loglik.Rd:32: Lost braces
    32 |     \code{pars2[2]} {sets whether the likelihood is for the branching times (0) or the phylogeny (1) \cr \cr}
       |                     ^
checkRd: (-1) pbd_loglik.Rd:33: Lost braces
    33 |     \code{pars2[3]} {sets whether the first element of the branching times is the stem (1) or the crown (2) age \cr \cr}
       |                     ^
checkRd: (-1) pbd_loglik.Rd:34: Lost braces
    34 |     \code{pars2[4]} {sets whether the parameters and likelihood should be shown on screen (1) or not (0) \cr \cr}
       |                     ^
checkRd: (-1) pbd_loglik.Rd:35: Lost braces
    35 |     \code{pars2[5]} {sets which method should be used in the ode-solver. Default is 'lsoda'. See package deSolve for details. \cr \cr}
       |                     ^
checkRd: (-1) pbd_loglik.Rd:36: Lost braces
    36 |     \code{pars2[6]}{Sets the lower bound of the number of species on which conditioning should be done when cond = 2. Set this to 0 when conditioning should be done on precisely the number of species (default)\cr \cr}
       |                    ^
checkRd: (-1) pbd_loglik.Rd:37: Lost braces
    37 |     \code{pars2[7]}{Sets the upper bound of the number of species on which conditioning should be done when cond = 2. Set this to 0 when conditioning should be done on precisely the number of species (default)\cr \cr}  
       |                    ^
installed size is  5.6Mb
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    lib    2.9Mb
    libs   2.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
':::' calls which should be '::':
  'PBSmodelling:::.findSquare' 'PBSmodelling:::.getHiddenEnv'
  'PBSmodelling:::.makeCleanVec' 'PBSmodelling:::.readList.P'
  'PBSmodelling:::.trimWhiteSpace'
  See the note in ?`:::` about the use of this operator.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/PBSddesolve.Rcheck/00install.out' for details.
installed size is  6.3Mb
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    data   2.7Mb
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installed size is  5.2Mb
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    doc        1.4Mb
    examples   1.7Mb
Malformed Description field: should contain one or more complete sentences.
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installed size is  6.2Mb
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    data   2.1Mb
    libs   1.4Mb
checkRd: (-1) twoby2Calibrate.Rd:84: Lost braces in \itemize; meant \describe ?
checkRd: (-1) twoby2Calibrate.Rd:85-86: Lost braces in \itemize; meant \describe ?
checkRd: (-1) twoby2Calibrate.Rd:87-92: Lost braces in \itemize; meant \describe ?
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'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
installed size is 12.1Mb
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    doc    2.9Mb
    libs   8.5Mb
GNU make is a SystemRequirements.
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checkRd: (-1) PCM_ABC.Rd:106: Lost braces in \itemize; meant \describe ?
checkRd: (-1) PCM_ABC.Rd:108-109: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) PCM_ABC.Rd:205-207: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) PCM_ABC.Rd:212-216: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) PCM_ABC.Rd:229-231: Lost braces in \itemize; meant \describe ?
checkRd: (-1) PCM_ABC.Rd:232: Lost braces in \itemize; meant \describe ?
checkRd: (-1) PCM_ABC.Rd:233: Lost braces in \itemize; meant \describe ?
checkRd: (-1) PCM_ABC.Rd:234: Lost braces in \itemize; meant \describe ?
checkRd: (-1) PCM_ABC.Rd:235: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) PCM_ABC.Rd:237: Lost braces in \itemize; meant \describe ?
checkRd: (-1) PCM_ABC.Rd:238: Lost braces in \itemize; meant \describe ?
checkRd: (-1) PCM_ABC.Rd:239: Lost braces in \itemize; meant \describe ?
checkRd: (-1) PCM_ABC.Rd:240: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulate_phylproc.Rd:56: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulate_phylproc.Rd:58-59: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulate_phylproc.Rd:64: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulate_phylproc.Rd:65: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulate_phylproc.Rd:67: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getPCRAData.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getPCRAData.Rd:29: Lost braces in \itemize; meant \describe ?
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
checkRd: (-1) pcvpcr.Rd:42: Lost braces; missing escapes or markup?
    42 | set {X, y} and cross-validation.
       |     ^
checkRd: (-1) pcvpls.Rd:42: Lost braces; missing escapes or markup?
    42 | set {X, y} and cross-validation.
       |     ^
Package suggested but not available for checking: 'cmdstanr'
Package suggested but not available for checking: 'PythonInR'
installed size is 20.3Mb
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    share  12.8Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) embedded.blocks.Rd:39: Lost braces
    39 | \item{miv.threshold}{MIV (marginal information value) entrance threshold applicable only for code{"stepMIV"} method.
       |                                                                                                  ^
checkRd: (-1) embedded.blocks.Rd:44: Lost braces
    44 | \item{m.ch.p.val}{Significance level of p-value for marginal chi-square test applicable only for code{"stepMIV"} method.
       |                                                                                                      ^
checkRd: (-1) ensemble.blocks.Rd:39: Lost braces
    39 | \item{miv.threshold}{MIV (marginal information value) entrance threshold applicable only for code{"stepMIV"} method.
       |                                                                                                  ^
checkRd: (-1) ensemble.blocks.Rd:44: Lost braces
    44 | \item{m.ch.p.val}{Significance level of p-value for marginal chi-square test applicable only for code{"stepMIV"} method.
       |                                                                                                      ^
checkRd: (-1) staged.blocks.Rd:39: Lost braces
    39 | \item{miv.threshold}{MIV (marginal information value) entrance threshold applicable only for code{"stepMIV"} method.
       |                                                                                                  ^
checkRd: (-1) staged.blocks.Rd:44: Lost braces
    44 | \item{m.ch.p.val}{Significance level of p-value for marginal chi-square test applicable only for code{"stepMIV"} method.
       |                                                                                                      ^
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    94 | Method \code{"b"} was proposed by \doi{10.1016/0098-3004(95)00095-X}{Jian et al. (1996)} and
       |                                                                     ^
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    98 | \doi{10.1016/j.cageo.2008.10.011}{Hiemstra et al. (2009)}.
       |                                  ^
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   100 | Method \code{"d"} was developed by \doi{10.1007/s11004-012-9434-1}{Desassis & Renard (2012)}.
       |                                                                   ^
installed size is 10.3Mb
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GNU make is a SystemRequirements.
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Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/personalized2part.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/personalized.Rcheck/00install.out' for details.
'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:
    Fixed issues
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    15 | A code{\link{marked_petrinet}}
       |       ^
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   100 | "Result": {
       |           ^
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   105 | "BacteriaLysed": {
       |                  ^
installed size is  5.2Mb
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    19 | A \code{plotly} {htmlwidget} with rose plots for locomotor activity.
       |                 ^
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    19 | #' @return A \code{plotly} {htmlwidget} with rose plots for sleep data.
       |                            ^
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GNU make is a SystemRequirements.
Running examples in 'phyloregion-Ex.R' failed
The error most likely occurred in:

> ### Name: rast2comm
> ### Title: Convert raw input distribution data to community
> ### Aliases: rast2comm polys2comm points2comm
> 
> ### ** Examples
> 
> 
> 
> library(terra)
terra 1.8.86
> s <- vect(system.file("ex/nigeria.json", package="phyloregion"))
> set.seed(1)
> m <- as.data.frame(spatSample(s, 1000, method = "random"),
+                    geom = "XY")[-1]
> names(m) <- c("lon", "lat")
> species <- paste0("sp", sample(1:100))
> m$taxon <- sample(species, size = nrow(m), replace = TRUE)
> 
> pt <- points2comm(dat = m, res = 0.5) # This generates a list of two objects
Warning: PROJ: proj_create_from_database: Cannot find proj.db (GDAL error 1)
Warning: [crs<-] Cannot set raster SRS: empty srs
Error: [project] output crs is not valid
Execution halted
Error(s) in re-building vignettes:
--- re-building 'Benchmark.Rmd' using rmarkdown
--- finished re-building 'Benchmark.Rmd'

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

--- re-building 'phyloregion-intro.Rmd' using rmarkdown

Quitting from phyloregion-intro.Rmd:74-87 [unnamed-chunk-3]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! [project] output crs is not valid
---
Backtrace:
    ▆
 1. └─phyloregion::points2comm(...)
 2.   ├─base::suppressWarnings(invisible(project(m, "epsg:4326")))
 3.   │ └─base::withCallingHandlers(...)
 4.   ├─terra::project(m, "epsg:4326")
 5.   └─terra::project(m, "epsg:4326")
 6.     └─terra (local) .local(x, ...)
 7.       └─terra:::messages(x, "project")
 8.         └─terra:::error(f, x@pntr$getError())
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'phyloregion-intro.Rmd' failed with diagnostics:
[project] output crs is not valid
--- failed re-building 'phyloregion-intro.Rmd'

SUMMARY: processing the following file failed:
  'phyloregion-intro.Rmd'

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: 'semPlot'
installed size is  5.5Mb
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    data   1.6Mb
    doc    2.1Mb
checkRd: (-1) pa-internal.Rd:11: Lost braces
    11 | code{l2df}: convert list to data.frame
       |     ^
checkRd: (-1) pa-internal.Rd:14: Lost braces
    14 | code{convertTZ}: force a new timezone on datetime
       |     ^
checkRd: (-1) pa-internal.Rd:16: Lost braces
    16 | code{createTime}: create datetime variable
       |     ^
checkRd: (-1) pa-internal.Rd:18: Lost braces
    18 | code{addDayIndex}: create ID_day variable from timestamp
       |     ^
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checkRd: (-1) utility.Rd:37: Escaped LaTeX specials: \$ \$
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    27 | if (interactive()) {
       |                    ^
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checkRd: (-1) tidy_levels_labels.Rd:78-83: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running 'testthat.R' [126s]
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(pkgdown)
  > 
  > test_check("pkgdown")
  Starting 2 test processes.
  > test-tweak-homepage.R: 
  
  Error:
  ! testthat subprocess exited in file 'test-tweak-homepage.R'.
  Caused by error:
  ! R session crashed with exit code -1073741819
  Backtrace:
       ▆
    1. └─testthat::test_check("pkgdown")
    2.   └─testthat::test_dir(...)
    3.     └─testthat:::test_files(...)
    4.       └─testthat:::test_files_parallel(...)
    5.         ├─withr::with_dir(...)
    6.         │ └─base::force(code)
    7.         ├─testthat::with_reporter(...)
    8.         │ └─base::tryCatch(...)
    9.         │   └─base (local) tryCatchList(expr, classes, parentenv, handlers)
   10.         │     └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
   11.         │       └─base (local) doTryCatch(return(expr), name, parentenv, handler)
   12.         └─testthat:::parallel_event_loop_chunky(queue, reporters, ".")
   13.           └─queue$poll(Inf)
   14.             └─base::lapply(...)
   15.               └─testthat (local) FUN(X[[i]], ...)
   16.                 └─private$handle_error(msg, i)
   17.                   └─cli::cli_abort(...)
   18.                     └─rlang::abort(...)
  Execution halted
Problems with news in 'NEWS.md':
No news entries found.
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   125 | function serves for the purpose of spot-testing for any pre-specified {n,
       |                                                                       ^
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installed size is  6.0Mb
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    libs         2.5Mb
    tmp_images   1.9Mb
installed size is  7.0Mb
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    data   1.4Mb
    doc    2.4Mb
    libs   1.6Mb
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    21 | delta_k = log(a_k - a_{k+1})
       |                       ^
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    29 | logical. If code{TRUE} all the q variable are assumed to have the same mean.
       |                 ^
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    15 | When \\code{y0} is not specified, the lowest value of the y-axis is used.}
       |            ^
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    24 | \\code{\\link[graphics]{par}}.}
       |       ^
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    24 | \\code{\\link[graphics]{par}}.}
       |                        ^
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checkRd: (-1) plotluck.Rd:129: Lost braces
   129 |  in factors are are shown as a special factor level code{"?"}. They can be
       |                                                         ^
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checkRd: (-1) domain_data.Rd:29: Lost braces
    29 | code{\link{help}}
       |     ^
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    32 | code{\link{help}}
       |     ^
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    30 | code{\link{help}}
       |     ^
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    30 | code{\link{help}}
       |     ^
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    20 | code{\link{help}}
       |     ^
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    30 | code{\link{help}}
       |     ^
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    30 | code{\link{help}}
       |     ^
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    30 | code{\link{help}}
       |     ^
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    16 | Additional arguments are replaced with "{n} more".
       |                                         ^
Package suggested but not available for checking: 'pmartRdata'
checkRd: (-1) PMCMR-deprecated.Rd:36: Lost braces in \itemize; \value handles \item{}{} directly
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checkRd: (-1) PMCMR-deprecated.Rd:39-40: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) PMCMR-deprecated.Rd:41: Lost braces in \itemize; \value handles \item{}{} directly
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   113 |     likelihood less than $10^{-10}$ are replaced by $10^{-10}$.
       |                              ^
checkRd: (-1) pmledecon.Rd:113: Lost braces; missing escapes or markup?
   113 |     likelihood less than $10^{-10}$ are replaced by $10^{-10}$.
       |                                                         ^
checkRd: (-1) ahp.Rd:16: Lost braces; missing escapes or markup?
    16 | an ``A'' matrix. It should be a square matrix with diagonal values equal 1 and $a_{ij} = 1/a_{ij}$.
       |                                                                                   ^
checkRd: (-1) ahp.Rd:16: Lost braces; missing escapes or markup?
    16 | an ``A'' matrix. It should be a square matrix with diagonal values equal 1 and $a_{ij} = 1/a_{ij}$.
       |                                                                                              ^
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'lixoftConnectors'
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Problems with news in 'NEWS.md':
No news entries found.
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    34 | \item{bw}{function describing bandwidth selection (see ?gmm for alternatives). Standard is that the bandwidth depends on the sample length $T$ by $m(T)=T^{1/5}$.}
       |                                                                                                                                                           ^
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checkRd: (-1) pois.fe.robust.Rd:50-51: Lost braces in \itemize; meant \describe ?
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    R      6.3Mb
    data   4.3Mb
checkRd: (-1) inputData.Rd:94: Lost braces
    94 | recommend using either \sQuote{code{.}} (a period) or
       |                                    ^
checkRd: (-1) inputData.Rd:95: Lost braces
    95 | \sQuote{code{_}} (an underscore) rather than a space.
       |             ^
checkRd: (-1) preprocessData.Rd:81: Lost braces
    81 | recommend using either \sQuote{code{.}} (a period) or
       |                                    ^
checkRd: (-1) preprocessData.Rd:82: Lost braces
    82 | \sQuote{code{_}} (an underscore) rather than a space.
       |             ^
checkRd: (-1) stat_quantile_prob.Rd:14: Lost braces; missing escapes or markup?
    14 | Number {25, 50, 75}
       |        ^
installed size is  5.8Mb
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    data   2.6Mb
    doc    1.8Mb
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checkRd: (-1) calculateDIC.Rd:30-31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) calculateDIC.Rd:32-33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) polySegratioMM-package.Rd:70-72: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MLM_Model.Rd:31: Lost braces; missing escapes or markup?
    31 |   the weight vectors \bold{{w}^{i}} corresponds to class \eqn{i}{i}.
       |                                ^
checkRd: (-1) MLM_Model.Rd:33: Lost braces; missing escapes or markup?
    33 | We set \eqn{{\bold{{w}}^{h}} = 0} and the parameters to be learned are the weight vectors \bold{{w}^{i}}
       |                                                                                                     ^
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
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    doc   5.1Mb
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
Running 'testthat.R' [8s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > if (requireNamespace("testthat", quietly = TRUE)) {
  +   library(testthat)
  +   library(PortfolioTesteR)
  +   test_check("PortfolioTesteR")
  + } else {
  +   message("Skipping tests: 'testthat' not installed")
  + }
  Saving _problems/test-ml-helpers-101.R
  [ FAIL 1 | WARN 0 | SKIP 3 | PASS 55 ]
  
  ══ Skipped tests (3) ═══════════════════════════════════════════════════════════
  • On CRAN (3): 'test-optimization.R:2:3', 'test-optimization.R:46:3',
    'test-walk-forward.R:2:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-ml-helpers.R:92:3'): backtest invariants hold on active dates (smoke, linear) ──
  Error in `.roll_align_common(c(features_list, list(label)))`: No common dates across panels.
  Backtrace:
      ▆
   1. └─PortfolioTesteR::ml_backtest(...) at test-ml-helpers.R:92:3
   2.   └─PortfolioTesteR::roll_fit_predict(...)
   3.     └─PortfolioTesteR:::.roll_align_common(c(features_list, list(label)))
  
  [ FAIL 1 | WARN 0 | SKIP 3 | PASS 55 ]
  Error:
  ! Test failures.
  Execution halted
Error(s) in re-building vignettes:
--- re-building 'Getting_Started_Advanced.Rmd' using rmarkdown

Quitting from Getting_Started_Advanced.Rmd:84-108 [baseline_pooled]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `.roll_align_common()`:
! No common dates across panels.
---
Backtrace:
    ▆
 1. └─PortfolioTesteR::ml_backtest(...)
 2.   └─PortfolioTesteR::roll_fit_predict(...)
 3.     └─PortfolioTesteR:::.roll_align_common(c(features_list, list(label)))
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'Getting_Started_Advanced.Rmd' failed with diagnostics:
No common dates across panels.
--- failed re-building 'Getting_Started_Advanced.Rmd'

--- re-building 'getting-started.Rmd' using rmarkdown
--- finished re-building 'getting-started.Rmd'

--- re-building 'optimization-walkforward.Rmd' using rmarkdown
--- finished re-building 'optimization-walkforward.Rmd'

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

Error: Vignette re-building failed.
Execution halted
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
'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
'LazyData' is specified without a 'data' directory
Running examples in 'PoweREST-Ex.R' failed
The error most likely occurred in:

> ### Name: fit_XGBoost
> ### Title: Fit with XGBoost
> ### Aliases: fit_XGBoost
> 
> ### ** Examples
> 
> data(power_example)
> # Fit the local power surface of avg_log2FC_abs between 1 and 2
> avg_log2FC_abs_1_2<-dplyr::filter(power_example,avg_log2FC_abs>1 & avg_log2FC_abs<2)
> # Fit the model
> bst<-fit_XGBoost(power_example$power,avg_log2FC=power_example$avg_log2FC_abs,
+ avg_PCT=power_example$mean_pct,replicates=power_example$sample_size)
Warning in throw_err_or_depr_msg("Passed unrecognized parameters: ", paste(head(names_unrecognized),  :
  Passed unrecognized parameters: max.depth, 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.
Warning in throw_err_or_depr_msg("Parameter '", match_old, "' has been renamed to '",  :
  Parameter 'eta' has been renamed to 'learning_rate'. This warning will become an error in a future version.
Error in xgboost::xgboost(data = dtrain, max.depth = max.depth, eta = eta,  : 
  argument "y" is missing, with no default
Calls: fit_XGBoost ... <Anonymous> -> process.y.margin.and.objective -> NROW
Execution halted
checkRd: (-1) coalesce_xy.Rd:22: Lost braces; missing escapes or markup?
    22 | the \code{conflict} argument of {powerjoin}'s join functions. \code{coalesce_xy()} is
       |                                 ^
checkRd: (-1) power_left_join.Rd:67: Lost braces; missing escapes or markup?
    67 | \item{by}{As in {dplyr}, but extended so user can supply a formula or a list
       |                 ^
checkRd: (-1) power_left_join.Rd:79: Lost braces; missing escapes or markup?
    79 | \item{keep}{A boolean for compatibility with {dplyr}, or a value among "left",
       |                                              ^
checkRd: (-1) preprocess_inputs.Rd:37: Lost braces; missing escapes or markup?
    37 | only be used in the \code{x} and \code{y} arguments of {powerjoin} join functions. No
       |                                                        ^
checkRd: (-1) bira2.Rd:91: Escaped LaTeX specials: \&
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checkRd: (-1) med_pn.Rd:129: Escaped LaTeX specials: \&
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    doc   6.2Mb
Package suggested but not available for checking: 'MBESS'
Running examples in 'pplot-Ex.R' failed
The error most likely occurred in:

> ### Name: pplot.t.test
> ### Title: Generate p-plot from a series of data points
> ### Aliases: pplot.t.test
> ### Keywords: utilities
> 
> ### ** Examples
> 
> # Show p-plot for significant test (the simulation 
> # has a power of > 88% to return a significant 
> # effect).
> testdata <- rnorm(64, mean = 0.4, sd = 1)
> pplot.t.test(testdata)
Warning in pplot.t.test(testdata) :
  Package 'MBESS' is not installed but required for computing confidence intervals for effect sizes (for plottype >= 2).
Error in pplot.t.test(testdata) : 
Execution halted
checkRd: (-1) ccp_ppm.Rd:26: Lost braces; missing escapes or markup?
    26 | \item{model}{Determines of model fit is such that there are p_{it}s (model=1) or
       |                                                               ^
checkRd: (-1) curve_ppmx.Rd:145: Lost braces; missing escapes or markup?
   145 | \item sig2 - a matrix of dimension (T, N) containing MCMC iterates associated with each subjects variance parameter (sigma2*_{c_i})
       |                                                                                                                              ^
checkRd: (-1) gaussian_ppmx.Rd:143: Lost braces; missing escapes or markup?
   143 | \item mu - a matrix  of dimension (T, N) containing MCMC iterates associated with each subjects mean parameter (mu*_{c_i}).
       |                                                                                                                     ^
checkRd: (-1) gaussian_ppmx.Rd:145: Lost braces; missing escapes or markup?
   145 | \item sig2 - a matrix of dimension (T, N) containing MCMC iterates associated with each subjects variance parameter (sigma2*_{c_i})
       |                                                                                                                              ^
checkRd: (-1) ordinal_ppmx.Rd:145: Lost braces; missing escapes or markup?
   145 | \item mu - a matrix  of dimension (T, N) containing MCMC iterates associated with each subjects mean parameter (mu*_{c_i}).
       |                                                                                                                     ^
checkRd: (-1) ordinal_ppmx.Rd:147: Lost braces; missing escapes or markup?
   147 | \item sig2 - a matrix of dimension (T, N) containing MCMC iterates associated with each sujbects variance parameter (sigma2*_{c_i})
       |                                                                                                                              ^
installed size is 12.1Mb
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'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    doc  10.5Mb
Specified C++11: please drop specification unless essential
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  'knitr' 'rmarkdown'
A package should be listed in only one of these fields.
'LazyData' is specified without a 'data' directory
checkRd: (-1) diagnose_expressions.Rd:39: Lost braces
    39 | \item wrapping a function argument in two curly braces (e.g. `{{arg}} > 0) means
       |                                                               ^
Package required but not available: 'MBESS'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Running examples in 'predictoR-Ex.R' failed
The error most likely occurred in:

> ### Name: e_xgb_importance
> ### Title: Var importance XGBoosting
> ### Aliases: e_xgb_importance
> 
> ### ** Examples
> 
> model <- traineR::train.xgboost(Species ~ ., data = iris, nrounds = 20)
Warning in check.deprecation(deprecated_train_params, match.call(), ...) :
  Passed invalid function arguments: eval_metric. These should be passed as a list to argument 'params'. Conversion from argument to 'params' entry will be done automatically, but this behavior will become an error in a future version.
Warning in throw_err_or_depr_msg("Parameter '", match_old, "' has been renamed to '",  :
  Parameter 'watchlist' has been renamed to 'evals'. 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 'feval' has been renamed to 'custom_metric'. This warning will become an error in a future version.
[1]	train-mlogloss:0.736115 
[2]	train-mlogloss:0.524235 
[3]	train-mlogloss:0.387996 
[4]	train-mlogloss:0.294146 
[5]	train-mlogloss:0.226824 
[6]	train-mlogloss:0.177835 
[7]	train-mlogloss:0.141766 
[8]	train-mlogloss:0.115002 
[9]	train-mlogloss:0.094791 
[10]	train-mlogloss:0.078860 
[11]	train-mlogloss:0.066746 
[12]	train-mlogloss:0.057845 
[13]	train-mlogloss:0.050360 
[14]	train-mlogloss:0.044290 
[15]	train-mlogloss:0.039567 
[16]	train-mlogloss:0.035267 
[17]	train-mlogloss:0.032581 
[18]	train-mlogloss:0.030403 
[19]	train-mlogloss:0.028410 
[20]	train-mlogloss:0.026969 
Error in model$prmdt <- `*vtmp*` : 
  ALTLIST classes must provide a Set_elt method [class: XGBAltrepPointerClass, pkg: xgboost]
Calls: <Anonymous> -> create.model
Execution halted
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    R   3.7Mb
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checkRd: (-1) dev_data.Rd:10: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) prereg_initialize.Rd:20: Lost braces; missing escapes or markup?
    20 | the (pre)registration form specification (in {preregr} format), see the
       |                                              ^
checkRd: (-1) prereg_initialize.Rd:23: Lost braces; missing escapes or markup?
    23 | specification, or a loaded or imported {preregr} (pre)registration form.
       |                                        ^
checkRd: (-1) prereg_initialize.Rd:26: Lost braces; missing escapes or markup?
    26 | For an introduction to working with {preregr} (pre)registrations,
       |                                     ^
checkRd: (-1) rmd_templates.Rd:75: Lost braces; missing escapes or markup?
    75 | This function creates an R Markdown template from a {preregr}
       |                                                     ^
checkRd: (-1) rmd_templates.Rd:77: Lost braces; missing escapes or markup?
    77 | Sheet holding the (pre)registration form specification (in {preregr}
       |                                                            ^
checkRd: (-1) rmd_templates.Rd:81: Lost braces; missing escapes or markup?
    81 | specification, or a loaded or imported {preregr} (pre)registration form.
       |                                        ^
checkRd: (-1) format_number.Rd:36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) format_number.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) format_number.Rd:38: Lost braces in \itemize; meant \describe ?
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installed size is 10.0Mb
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    extdata   9.7Mb
'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
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'cmdstanr'
'LazyData' is specified without a 'data' directory
checkRd: (-1) alogistic.Rd:20: Lost braces
    20 | The user does not put these directly into this function, but rather uses code{ode} in the \code{deSolve} package.
       |                                                                              ^
Running 'testthat.R' [21s]
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(prior3D)
  > 
  > test_check("prior3D")
  terra 1.8.86
  
  Attaching package: 'terra'
  
  The following objects are masked from 'package:testthat':
  
      compare, describe
  
  Saving _problems/test-split_rast-102.R
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 21 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-split_rast.r:97:3'): split_rast works ──────────────────────────
  Error: [project] cannot get output boundaries for the target crs
  Backtrace:
      ▆
   1. ├─base::suppressWarnings(...) at test-split_rast.r:97:3
   2. │ └─base::withCallingHandlers(...)
   3. ├─prior3D::split_rast(...)
   4. ├─terra::project(depth_raster, "epsg:3857", method = "average")
   5. └─terra::project(depth_raster, "epsg:3857", method = "average")
   6.   └─terra (local) .local(x, ...)
   7.     └─terra:::messages(x, "project")
   8.       └─terra:::error(f, x@pntr$getError())
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 21 ]
  Error:
  ! Test failures.
  Execution halted
checkRd: (-1) findbeta.Rd:20: Lost braces; missing escapes or markup?
    20 | \item{lower.v}{logical, if TRUE the specified percentile.value is the upper limit for the mean (or the median or the mode) at the specified confidence level (percentile). If {FALSE} the specified percentile.value is the lower limit for the mean (or the median or the mode) at the specified confidence level (percentile). The default is FALSE.}
       |                                                                                                                                                                               ^
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  'gurobi', 'Rcplex', 'rcbc'
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    doc    3.6Mb
    libs   1.3Mb
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  'gurobi', 'rcbc', 'cplexAPI'
installed size is 10.4Mb
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    R      1.5Mb
    doc    4.7Mb
    help   1.3Mb
    libs   1.6Mb
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Unexported objects imported by ':::' calls:
  'bupaR:::allowed_lifecycles' 'bupaR:::apply_grouped_fun'
  See the note in ?`:::` about the use of this operator.
Unexported object imported by a ':::' call: 'bupaR:::apply_grouped_fun'
  See the note in ?`:::` about the use of this operator.
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    91 |     \code{OSME} \tab Output-oriented scale-mix efficiency score \emph{(code{orientation = "out"})}\cr
       |                                                                            ^
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     9 |                 \item{CD}{}{Character disorder scale score}
       |                            ^
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    40 |   by the code{kcachegrind} program available on some operating
       |              ^
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GNU make is a SystemRequirements.
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    15 | \item{value}{code{data.frame} or code{data.table}}
       |                  ^
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    15 | \item{value}{code{data.frame} or code{data.table}}
       |                                      ^
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    21 | response variable. Vector of length emph{n}, assumed to be quantitative.
       |                                         ^
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    20 | Implementation of the {SnowballC} stemmer. Note that punctuation and capital letters 
       |                       ^
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    20 | Implementation of the {SnowballC} stemmer. Note that punctuation and capitals letters 
       |                       ^
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     7 | See the {rfeel} package now: http://github.com/ColinFay/rfeel}
       |         ^
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    20 | See the {rfeel} package now: http://github.com/ColinFay/rfeel
       |         ^
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    doc   5.6Mb
installed size is  9.2Mb
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    libs   8.8Mb
GNU make is a SystemRequirements.
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installed size is  5.3Mb
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checkRd: (-1) qpc.Rd:43: Lost braces
    43 | S{Sulewski, P. (2020). \emph{Normal Distribution with Plasticizing Component,} Communications in Statistics ? Theory and Method 51(11), 3806-3835.}
       |  ^
checkRd: (-1) data1.Rd:14: Lost braces
    14 | The data set from {AbouRizk, S.M., Halpin, D.W., Wilson, J. R. (1994). \emph{Fitting beta distributions based on sample data.} Journal of Construction Engineering and Management 120(2), 288–305.}
       |                   ^
checkRd: (-1) data2.Rd:14: Lost braces; missing escapes or markup?
    14 | The data set presents the height of 99 five-year-old British boys in cm downloaded from {http://www.mas.ncl.ac.uk/njnsm/medfac/docs/intro.pdf.}
       |                                                                                         ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) table1.Rd:14: Lost braces
    14 | The first data set from {Sulewski, P. (2017) \emph{A new test for independence in 2x2 contingency tables,} Acta Universitatis Lodziensis. Folia Oeconomica, 4(330), 55–75}
       |                         ^
checkRd: (-1) table3.Rd:14: Lost braces
    14 | The third data set from {Sulewski, P. (2021). \emph{Logarithmic Minimum Test for Independence in Three Way Con-tingency Table of Small Sizes.} Journal of Statistical Computation and Simulation 91(13), 2780-2799}
       |                         ^
GNU make is a SystemRequirements.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/psp.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'semPlot', 'metaSEM'
checkRd: (-1) dprime.Rd:37: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dprime.Rd:38: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dprime.Rd:39: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dprime.Rd:40: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dprime.Rd:41: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) PTE_bootstrap_inference.Rd:39-42: Lost braces
    39 |                                                         continuous = function(Xytrain){ #defalt is OLS regression
       |                                                                                       ^
checkRd: (-1) PTE_bootstrap_inference.Rd:43-47: Lost braces
    43 |                                                         incidence = function(Xytrain){ #default is logistic regression
       |                                                                                      ^
checkRd: (-1) PTE_bootstrap_inference.Rd:48-52: Lost braces
    48 |                                                         survival = function(Xytrain){ #default is Weibull regression
       |                                                                                     ^
checkRd: (-1) PTE_bootstrap_inference.Rd:66-68: Lost braces
    66 |                                         function(mod, Xyleftout){
       |                                                                 ^
checkRd: (-1) PTE_bootstrap_inference.Rd:74-77: Lost braces
    74 |                                         function(results, indices_1_1, indices_0_0, indices_0_1, indices_1_0){
       |                                                                                                              ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) ptw-package.Rd:20-28: Lost braces
    20 | @Article{Bloemberg2010,
       |         ^
checkRd: (-1) ptw-package.Rd:30-38: Lost braces
    30 | Article{Wehrens2015,
       |        ^
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    doc        4.0Mb
    examples   2.6Mb
Running examples in 'pubh-Ex.R' failed
The error most likely occurred in:

> ### Name: axis_labs
> ### Title: Apply labels from variables to axis-labels in plots.
> ### Aliases: axis_labs
> 
> ### ** Examples
> 
> data(kfm, package = "ISwR")
> require(sjlabelled, quietly = TRUE)

Attaching package: 'sjlabelled'

The following object is masked from 'package:ggplot2':

    as_label

> kfm <- kfm |>
+   var_labels(
+     dl.milk = "Breast-milk intake (dl/day)",
+     sex = "Sex",
+     weight = "Child weight (kg)",
+     ml.suppl = "Milk substitute (ml/day)",
+     mat.weight = "Maternal weight (kg)",
+     mat.height = "Maternal height (cm)"
+   )
> 
> kfm |>
+   gf_point(weight ~ dl.milk) |>
+   gf_lm(col = 2, interval = "confidence", col = 2) |>
+   axis_labs()
Warning in rep(yes, length.out = len) :
  'x' is NULL so the result will be NULL
Error in ans[ypos] <- rep(yes, length.out = len)[ypos] : 
  replacement has length zero
Calls: axis_labs -> ifelse
Execution halted
checkRd: (-1) ma.Rd:62: Lost braces
    62 | \item{yi}{Numeric vector of length code{k} with observed effect size
       |                                        ^
checkRd: (-1) ma.Rd:65: Lost braces
    65 | \item{vi}{Numeric vector of length code{k} with sampling variances.}
       |                                        ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) plotWordCloud.Rd:5: Lost braces; missing escapes or markup?
     5 | \title{PubMed wordcloud using function 'wordcloud' of package {wordcloud}}
       |                                                               ^
checkRd: (-1) plotWordCloud.Rd:32: Lost braces; missing escapes or markup?
    32 | This function just call 'wordcloud' from package {wordcloud}. See package {wordcloud} for more details about the parameters.
       |                                                  ^
checkRd: (-1) plotWordCloud.Rd:32: Lost braces; missing escapes or markup?
    32 | This function just call 'wordcloud' from package {wordcloud}. See package {wordcloud} for more details about the parameters.
       |                                                                           ^
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  three_utility_probit_helper_functions.cpp:119:30: warning: overflow in conversion from 'double' to 'int' changes value from '-Inf' to '-2147483648' [-Woverflow]
  three_utility_probit_helper_functions.cpp:119:70: warning: overflow in conversion from 'double' to 'int' changes value from '-Inf' to '-2147483648' [-Woverflow]
  three_utility_probit_helper_functions.cpp:139:68: warning: overflow in conversion from 'double' to 'int' changes value from '-Inf' to '-2147483648' [-Woverflow]
  three_utility_probit_helper_functions.cpp:158:50: warning: overflow in conversion from 'double' to 'int' changes value from '-Inf' to '-2147483648' [-Woverflow]
  three_utility_probit_helper_functions.cpp:162:38: warning: overflow in conversion from 'double' to 'int' changes value from '-Inf' to '-2147483648' [-Woverflow]
  three_utility_probit_helper_functions.cpp:162:77: warning: overflow in conversion from 'double' to 'int' changes value from '-Inf' to '-2147483648' [-Woverflow]
See 'd:/Rcompile/CRANpkg/local/4.4/pumBayes.Rcheck/00install.out' for details.
* used C++ compiler: 'g++.exe (GCC) 13.3.0'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) DataSets.Rd:10: Lost braces; missing escapes or markup?
    10 | \format{the \code{PvarQuantileDF} is a \code{data.frame} with fields \code{prob} an {Qaunt}. 
       |                                                                                     ^
checkRd: (-1) pvlrt.Rd:42: Lost braces; missing escapes or markup?
    42 | \item{no_zi_idx}{List of pairs {(i, j)} where zero inflation is not allowed. To
       |                                ^
checkRd: (-1) r_contin_table_zip.Rd:35: Lost braces; missing escapes or markup?
    35 | \item{no_zi_idx}{List of pairs {(i, j)} where zero inflation is not allowed. To
       |                                ^
Package required but not available: 'MBESS'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
checkRd: (-1) aid_st2.Rd:6: Escaped LaTeX specials: \&
installed size is  7.3Mb
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    data   7.2Mb
'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) srswrRe.Rd:10: Lost braces
    10 |   \item{listRanef}{{\emph{ranef(model)}} object where {\emph{model}} is an { \emph{lmer}} object.}
       |                                                                            ^
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    gui          1.6Mb
    staticdocs   3.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 26.3Mb
  sub-directories of 1Mb or more:
    libs  25.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc   5.2Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'spDataLarge'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) qif.Rd:45: Lost braces in \itemize; \value handles \item{}{} directly
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checkRd: (-1) qif.Rd:47: Lost braces in \itemize; \value handles \item{}{} directly
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checkRd: (-1) qif.Rd:50: Lost braces in \itemize; \value handles \item{}{} directly
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checkRd: (-1) qif.Rd:52: Lost braces in \itemize; \value handles \item{}{} directly
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checkRd: (-1) qif.Rd:60: Lost braces in \itemize; \value handles \item{}{} directly
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checkRd: (-1) qif.Rd:62: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) qif.Rd:63: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) qif.Rd:64: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) qif.Rd:65: Lost braces in \itemize; \value handles \item{}{} directly
'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) qmethod-package.Rd:109: Lost braces
   109 |   \item Van Exel, J., and G. de Graaf, 2005. \emph{Q Methodology: A Sneak Preview}\cr \url{https://qmethodblog.files.wordpress.com/2016/01/qmethodologyasneakpreviewreferenceupdate.pdf}{Available at this link}.
       |                                                                                                                                                                                         ^
checkRd: (-1) qmethod-package.Rd:110: Lost braces
   110 |   \item Brown, S. R., 1980. \emph{Political subjectivity: Applications of Q methodology in political science}, New Haven, CT: Yale University Press.\cr \url{https://qmethodblog.files.wordpress.com/2016/01/brown-1980-politicalsubjectivity.pdf}{Available at this link}.
       |                                                                                                                                                                                                                                                   ^
Specified C++11: please drop specification unless essential
checkRd: (-1) hideLocation.Rd:10: Lost braces; missing escapes or markup?
    10 | \item{trueLoc}{A vector of one or more numbers in the set {1, 2, ..., nSubjects} whose locations are to be hidden.}
       |                                                           ^
checkRd: (-1) hideLocation.Rd:12: Lost braces; missing escapes or markup?
    12 | \item{nSubjects}{An integer larger than 1 used to define the set {1, 2, ..., nSubjects}.}
       |                                                                  ^
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    data  10.8Mb
GNU make is a SystemRequirements.
installed size is 12.6Mb
  sub-directories of 1Mb or more:
    data  12.5Mb
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building 'QTE_RD.Rmd' using rmarkdown
Error reading bibliography file qte_rdd.bib:
(line 11, column 3):
unexpected '%'
expecting white space
Error: processing vignette 'QTE_RD.Rmd' failed with diagnostics:
pandoc document conversion failed with error 25
--- failed re-building 'QTE_RD.Rmd'

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc   4.4Mb
'LazyData' is specified without a 'data' directory
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
checkRd: (-1) IPWE_mean_IndCen.Rd:54-57: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) IPWE_mean_IndCen.Rd:58: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) IPWE_mean_IndCen.Rd:59: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) IPWE_mean_IndCen.Rd:60: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) IPWE_mean_IndCen.Rd:61-62: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) IPWE_mean_IndCen.Rd:63: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simJLSDdata.Rd:14: Lost braces; missing escapes or markup?
    14 | \item{case}{string. One of {"a", "b", "c"}, corresponding to three models.}
       |                            ^
checkRd: (-1) simJLSDdata.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simJLSDdata.Rd:31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simJLSDdata.Rd:32-34: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simJLSDdata.Rd:35: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
checkRd: (-1) find_lcp.Rd:60: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) find_lcp.Rd:61: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) find_lcp.Rd:62: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) find_lcp.Rd:63-65: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) find_lcp.Rd:66: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) find_lcp.Rd:67: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) summarize_lcps.Rd:17: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) summarize_lcps.Rd:18-19: Lost braces in \itemize; \value handles \item{}{} directly
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checkRd: (-1) summarize_lcps.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) summarize_lcps.Rd:23-25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) als_data.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) als_data.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) als_data.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) als_data.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) als_data.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) als_data.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) als_data.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) als_data.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) als_data.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) als_data.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) als_data.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) als_data.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) als_data.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) als_data.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) als_data.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) als_data.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) als_data.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) als_data.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) als_data_qc_mapping.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) als_data_qc_mapping.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) als_data_qc_mapping.Rd:13: Lost braces in \itemize; meant \describe ?
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
    libs   1.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) quarries.Rd:17-19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) quarries.Rd:20-22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) quarries.Rd:23-25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) quarries.Rd:26-28: Lost braces in \itemize; meant \describe ?
Package required but not available: 'MBESS'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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
Running examples in 'quincunx-Ex.R' failed
The error most likely occurred in:

> ### Name: get_cohorts
> ### Title: Get PGS Catalog Cohorts
> ### Aliases: get_cohorts
> 
> ### ** Examples
> 
> # Get information about specific cohorts by their symbols (acronyms)
> get_cohorts(cohort_symbol = c('23andMe', 'IPOBCS'))
Error in `purrr::map()`:
ℹ In index: 1.
Caused by error:
! object 'at_depth' is not exported by 'namespace:purrr'
Backtrace:
     ▆
  1. ├─quincunx::get_cohorts(cohort_symbol = c("23andMe", "IPOBCS"))
  2. │ ├─quincunx:::coerce_to_s4_cohorts(...)
  3. │ └─quincunx:::get_cohort_by_cohort_symbol(...)
  4. │   ├─purrr::pmap(...)
  5. │   │ └─purrr:::pmap_("list", .l, .f, ..., .progress = .progress)
  6. │   │   └─purrr:::vctrs_list_compat(.l, error_call = .purrr_error_call)
  7. │   │     └─purrr:::vctrs_vec_compat(x, user_env)
  8. │   └─purrr::map(...)
  9. │     └─purrr:::map_("list", .x, .f, ..., .progress = .progress)
 10. │       ├─purrr:::with_indexed_errors(...)
 11. │       │ └─base::withCallingHandlers(...)
 12. │       ├─purrr:::call_with_cleanup(...)
 13. │       └─purrr (local) .f(.x[[i]], ...)
 14. │         └─quincunx (local) f(...)
 15. │           └─quincunx:::get(...)
 16. │             └─quincunx:::request_all(...)
 17. │               └─quincunx:::is_paginated(obj$json)
 18. │                 └─quincunx:::count(json_string)
 19. ├─base::loadNamespace(x)
 20. │ └─base::namespaceImportFrom(...)
 21. │   └─base::importIntoEnv(impenv, impnames, ns, impvars)
 22. │     └─base::stop(...)
 23. └─base::.handleSimpleError(...)
 24.   └─purrr (local) h(simpleError(msg, call))
 25.     └─cli::cli_abort(...)
 26.       └─rlang::abort(...)
Execution halted
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
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    doc         2.1Mb
    shiny_app   1.2Mb
checkRd: (-1) est.R0.ML.Rd:98: Lost braces
    98 | Supplementary Material S1 from \doi{10.1186/1472-6947-12-147}{Obadia et al., 2012}.
       |                                                              ^
checkRd: (-1) plot.R0.R.Rd:20: Lost braces
    20 | Called for side effect. Draws all \eqn{R_{0}} or /eqn{R(t)} values from one estimation method.
       |                                                      ^
checkRd: (-1) plot.R0.sR.Rd:20: Lost braces
    20 | Called for side effect. Draws all \eqn{R_{0}} or /eqn{R(t)} values from an
       |                                                      ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) do_admb.Rd:20: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) do_admb.Rd:49: Lost braces in \itemize; meant \describe ?
checkRd: (-1) read_pars.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) read_pars.Rd:31: Lost braces in \itemize; \value handles \item{}{} directly
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checkRd: (-1) read_pars.Rd:36: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) read_pars.Rd:37: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) read_pars.Rd:38: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) read_pars.Rd:39: Lost braces in \itemize; \value handles \item{}{} directly
Package suggested but not available for checking: 'ReGenesees'
GNU make is a SystemRequirements.
installed size is  5.0Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'bootmlm'
Package suggested but not available for checking: 'RDCOMClient'
'library' or 'require' call to 'RDCOMClient' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages suggested but not available for checking: 'rcom', 'RDCOMClient'
'library' or 'require' calls in package code:
  'RDCOMClient' 'rcom'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package suggested but not available for checking: 'BRugs'
installed size is 11.5Mb
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    doc   9.9Mb
installed size is  7.3Mb
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    htmlwidgets   1.8Mb
checkRd: (-1) r4ss-package.Rd:9: Lost braces; missing escapes or markup?
     9 | A collection of R functions for use with Stock Synthesis, a fisheries stock assessment modeling platform written in ADMB by Dr. Richard D. Methot at the NOAA Northwest Fisheries Science Center. The functions include tools for summarizing and plotting results, manipulating files, visualizing model parameterizations, and various other common stock assessment tasks. This version of '{r4ss}' is compatible with Stock Synthesis versions 3.24 through 3.30 (specifically version 3.30.19.01, from April 2022).
       |                                                                                                                                                                                                                                                                                                                                                                                                ^
installed size is  6.6Mb
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    extdata   3.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) extract_class.Rd:18: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) extract_class.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) extract_class.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
checkRd: (-1) post_RA_fits.Rd:61: Lost braces; missing escapes or markup?
    61 |     \item{\code{H(po_{bm_{n.bm}}, po_act)}:}{ last benchmark prior bm_{n.bm} inducing the fit \code{fits.bm[[n.bm]]} and actual prior}
       |                                                                       ^
'LazyData' is specified without a 'data' directory
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    doc    6.6Mb
    libs   1.0Mb
'LazyData' is specified without a 'data' directory
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    doc           5.3Mb
    htmlwidgets   1.8Mb
    libs          2.1Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc   5.5Mb
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    app  10.0Mb
Running examples in 'radiant.model-Ex.R' failed
The error most likely occurred in:

> ### Name: gbt
> ### Title: Gradient Boosted Trees using XGBoost
> ### Aliases: gbt
> 
> ### ** Examples
> 
> ## Not run: 
> ##D gbt(titanic, "survived", c("pclass", "sex"), lev = "Yes") %>% summary()
> ##D gbt(titanic, "survived", c("pclass", "sex")) %>% str()
> ## End(Not run)
> gbt(
+   titanic, "survived", c("pclass", "sex"), lev = "Yes",
+   early_stopping_rounds = 0, nthread = 1
+ ) %>% summary()
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.
Warning in throw_err_or_depr_msg("Parameter '", match_old, "' has been renamed to '",  :
  Parameter 'label' has been renamed to 'y'. This warning will become an error in a future version.
Error in process.y.margin.and.objective(y, base_margin, objective, params) : 
  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: binary:logistic
Calls: %>% ... do.call -> <Anonymous> -> process.y.margin.and.objective
Execution halted
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data      2.2Mb
    extdata   1.4Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   3.9Mb
Error(s) in re-building vignettes:
--- re-building 'vign-01-overview.Rmd' using rmarkdown
--- finished re-building 'vign-01-overview.Rmd'

--- re-building 'vign-02-export-spatial.Rmd' using rmarkdown

Quitting from vign-02-export-spatial.Rmd:103-112 [terra]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! [rast] empty srs
---
Backtrace:
    ▆
 1. ├─terra::rast(h, crs = paste("epsg", epsg, sep = ":"), extent = ext(extent))
 2. └─terra::rast(h, crs = paste("epsg", epsg, sep = ":"), extent = ext(extent))
 3.   └─terra (local) .local(x, ...)
 4.     ├─terra::rast(nrows = nrow(x), ncols = ncol(x), crs = crs, extent = extent)
 5.     └─terra::rast(nrows = nrow(x), ncols = ncol(x), crs = crs, extent = extent)
 6.       └─terra (local) .local(x = x, ...)
 7.         └─terra:::new_rast(...)
 8.           └─terra:::messages(r, "rast")
 9.             └─terra:::error(f, x@pntr$getError())
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'vign-02-export-spatial.Rmd' failed with diagnostics:
[rast] empty srs
--- failed re-building 'vign-02-export-spatial.Rmd'

SUMMARY: processing the following file failed:
  'vign-02-export-spatial.Rmd'

Error: Vignette re-building failed.
Execution halted
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    libs   7.4Mb
'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
'LazyData' is specified without a 'data' directory
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
'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:
    data   4.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) makeDesignMatrix.Rd:16: Lost braces; missing escapes or markup?
    16 | is randomized to a certain treatment {j}, the entry of \code{(i,j)} of the
       |                                      ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in 'rangeBuilder-Ex.R' failed
The error most likely occurred in:

> ### Name: filterByLand
> ### Title: Filter occurrences based on land vs ocean
> ### Aliases: filterByLand
> 
> ### ** Examples
> 
> 
> data(crotalus)
> 
> #identify points that fall off land
> filterByLand(crotalus[,c('decimallongitude','decimallatitude')])
Warning: PROJ: proj_create_from_database: Cannot find proj.db (GDAL error 1)
Error in h(simpleError(msg, call)) : 
  error in evaluating the argument 'x' in selecting a method for function 'extract': [rast] empty srs
Calls: filterByLand ... rast -> rast -> .local -> new_rast -> messages -> error
Execution halted
'LazyData' is specified without a 'data' directory
checkRd: (-1) grottaBar.Rd:69: Lost braces in \itemize; meant \describe ?
checkRd: (-1) grottaBar.Rd:70: Lost braces in \itemize; meant \describe ?
checkRd: (-1) grottaBar.Rd:71: Lost braces in \itemize; meant \describe ?
checkRd: (-1) grottaBar.Rd:79: Lost braces in \itemize; meant \describe ?
checkRd: (-1) grottaBar.Rd:80: Lost braces in \itemize; meant \describe ?
checkRd: (-1) grottaBar.Rd:81: Lost braces in \itemize; meant \describe ?
checkRd: (-1) grottaBar.Rd:82: Lost braces in \itemize; meant \describe ?
checkRd: (-1) grottaBar.Rd:83: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rankL2R.Rd:18: Lost braces; missing escapes or markup?
    18 | where the vector dimension is 2^{response.number}.}
       |                                 ^
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'
'LazyData' is specified without a 'data' directory
checkRd: (-1) user_log_dir.Rd:48: Lost braces
    48 | \\env{$XDG_CACHE_HOME} if defined
       |      ^
'LazyData' is specified without a 'data' directory
Running examples in 'rapr-Ex.R' failed
The error most likely occurred in:

> ### Name: rap_projection
> ### Title: Select Projection System for RAP Extent
> ### Aliases: rap_projection
> 
> ### ** Examples
> 
> ## Don't show: 
> if (requireNamespace("terra")) (if (getRversion() >= "3.4") withAutoprint else force)({ # examplesIf
+ ## End(Don't show)
+ 
+ rap_projection("CONUS_AEA", 10)
+ 
+ rap_projection("CONUS_IGH", 100)
+ ## Don't show: 
+ }) # examplesIf
> rap_projection("CONUS_AEA", 10)
Warning: PROJ: proj_create_from_database: Cannot find proj.db (GDAL error 1)
Error: [rast] empty srs
Execution halted
Running 'tinytest.R' [8s]
Running the tests in 'tests/tinytest.R' failed.
Complete output:
  > 
  > if ( requireNamespace("tinytest", quietly=TRUE) ){
  +   tinytest::test_package("rapr")
  + }
  
  test_rapr.R...................    0 tests    
  test_rapr.R...................    0 tests    
  test_rapr.R...................    0 tests    Error: [project] input crs is not valid
  In addition: Warning messages:
  1: PROJ: proj_create_from_database: Cannot find proj.db (GDAL error 1) 
  2: [as.polygons] Cannot set SRS to vector: empty srs 
  Execution halted
Package suggested but not available for checking: 'gurobi'
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    doc       1.7Mb
    extdata   4.1Mb
    libs      1.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in 'rasterdiv-Ex.R' failed
The error most likely occurred in:

> ### Name: copNDVI
> ### Title: Copernicus Long Term (1999-2017) NDVI Overview (5km)
> ### Aliases: copNDVI
> ### Keywords: datasets
> 
> ### ** Examples
> 
> copNDVI <- load_copNDVI()
Warning: PROJ: proj_create_from_database: Cannot find proj.db (GDAL error 1)
Error: [rast] empty srs
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    R      3.1Mb
    libs   1.4Mb
Running 'tinytest.R' [12s]
Running the tests in 'tests/tinytest.R' failed.
Complete output:
  > 
  > if ( requireNamespace("tinytest", quietly=TRUE) ){
  + 	tinytest::test_package("raster")
  + }
  Loading required package: sp
  
  test_getvaluesblock.R.........    0 tests    
  test_getvaluesblock.R.........    0 tests    
  test_getvaluesblock.R.........    1 tests [0;32mOK[0m [0;34m0.3s[0m
  
  test_rasterize.R..............    0 tests    
  test_rasterize.R..............    0 tests    
  test_rasterize.R..............    0 tests    
  test_rasterize.R..............    0 tests    
  test_rasterize.R..............    0 tests    
  test_rasterize.R..............    0 tests    
  test_rasterize.R..............    0 tests    
  test_rasterize.R..............    0 tests    
  test_rasterize.R..............    1 tests [0;32mOK[0m [0;34m1.4s[0m
  [0;36m3ms[0m
  
  test_subset.R.................    0 tests    
  test_subset.R.................    0 tests    
  test_subset.R.................    0 tests    
  test_subset.R.................    0 tests    
  test_subset.R.................    1 tests [0;32mOK[0m 
  test_subset.R.................    2 tests [0;32mOK[0m 
  test_subset.R.................    3 tests [0;32mOK[0m 
  test_subset.R.................    4 tests [0;32mOK[0m 
  test_subset.R.................    5 tests [0;32mOK[0m 
  test_subset.R.................    6 tests [0;32mOK[0m [0;34m0.4s[0m
  
  test_wkt_grd.R................    0 tests    
  test_wkt_grd.R................    0 tests    Error: [rast] empty srs
  In addition: Warning message:
  PROJ: proj_create_from_database: Cannot find proj.db (GDAL error 1) 
  Execution halted
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   4.3Mb
GNU make is a SystemRequirements.
checkRd: (-1) S1.Rd:10: Lost braces; missing escapes or markup?
    10 | \item{m_bar}{the sample vector of moments for a specified vector $(h_{a,r},y)$}
       |                                                                      ^
checkRd: (-1) S1.Rd:16: Lost braces; missing escapes or markup?
    16 | \item{N_k}{index of the $ h_{a,r}$ function considered}
       |                             ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'cairoDevice', 'RGtk2'
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    data   4.5Mb
    etc    1.9Mb
    po     1.2Mb
checkRd: (-1) acquireAuditData.Rd:24: Escaped LaTeX specials: \_
checkRd: (-1) rattle.Rd:44: Escaped LaTeX specials: \_
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   3.9Mb
    libs   1.5Mb
checkRd: (-1) rbm.haplos.power.Rd:35: Lost braces; missing escapes or markup?
    35 |   \item{simus.haplos}{ Which method to simulate the data, if \code{simus.haplos="freqs"}, {rbm.haplos.freqs()} is used, otherwise \code{rbm.haplos.thresholds()} is used.}
       |                                                                                           ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is 12.5Mb
  sub-directories of 1Mb or more:
    libs  11.3Mb
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in 'rcaiman-Ex.R' failed
The error most likely occurred in:

> ### Name: compute_canopy_openness
> ### Title: Calculate canopy openness
> ### Aliases: compute_canopy_openness
> 
> ### ** Examples
> 
> caim <- read_caim()
Warning: PROJ: proj_create_from_database: Cannot find proj.db (GDAL error 1)
Warning: [crs<-] Cannot set raster SRS: empty srs
> z <- zenith_image(ncol(caim), lens())
Warning: PROJ: proj_create_from_database: Cannot find proj.db (GDAL error 1)
Warning: [crs<-] Cannot set raster SRS: empty srs
> a <- azimuth_image(z)
> m <- select_sky_region(z, 0, 70)
> bin <- binarize_with_thr(caim$Blue, thr_isodata(caim$Blue[m]))
The threshold value was computed with a subsample of size 500.
> plot(bin)
> compute_canopy_openness(bin, z, a, m, 10)
Error: `r` and `segmentation` must have the same geometry.
Execution halted
Package suggested but not available for checking: 'rrelaxiv'
'LazyData' is specified without a 'data' directory
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
GNU make is a SystemRequirements.
Package suggested but not available for checking: 'rrelaxiv'
'LazyData' is specified without a 'data' directory
installed size is 20.2Mb
  sub-directories of 1Mb or more:
    cont  20.1Mb
checkRd: (-1) nc_open_CGLS.Rd:29-32: Lost braces
    29 | if(resolution == "300m"){
       |                         ^
checkRd: (-1) nc_open_CGLS.Rd:33-36: Lost braces
    33 | if(resolution == "1km"){
       |                        ^
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   4.2Mb
'LazyData' is specified without a 'data' directory
checkRd: (-1) Rchoice.Rd:159: Lost braces; missing escapes or markup?
   159 |  \code{ranp}. If the parameters are assumed to be normally distributed \eqn{\beta_i ~ N(\beta, \Sigma)}, then the random parameter are constructed as: \deqn{\beta_{ir}=\beta+L\omega_{ir}} where \eqn{LL'=\Sigma} and \eqn{\omega_{ir}} is the {r}-th draw from standard normal distribution for individual \eqn{i}. 
       |                                                                                                                                                                                                                                                 ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) RcmdrPlugin.MA-package.Rd:21: Escaped LaTeX specials: \&
checkRd: (-1) RcmdrPlugin.MA-package.Rd:23: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
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.
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    R     1.2Mb
    doc   4.5Mb
    po    2.4Mb
checkRd: (-1) nonlinearAR1.sim.Rd:8: Lost braces; missing escapes or markup?
     8 | of the form z_n = g(z_{n-1}) + epsilon. A normal distribution is assumed for the innovations.
       |                       ^
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    corpora   7.4Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/Rcplex.Rcheck/00install.out' for details.
installed size is 15.6Mb
  sub-directories of 1Mb or more:
    include  13.5Mb
    libs      1.2Mb
installed size is 39.7Mb
  sub-directories of 1Mb or more:
    include  38.1Mb
    libs      1.4Mb
Specified C++11: please drop specification unless essential
Problems with news in 'NEWS.md':
No news entries found.
installed size is 48.7Mb
  sub-directories of 1Mb or more:
    include  48.3Mb
Specified C++11: please drop specification unless essential
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   3.8Mb
GNU make is a SystemRequirements.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    include   4.4Mb
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    include   9.6Mb
    libs      1.2Mb
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    include   6.4Mb
    libs      1.1Mb
GNU make is a SystemRequirements.
installed size is 52.2Mb
  sub-directories of 1Mb or more:
    libs  50.1Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc       1.2Mb
    include   2.2Mb
    libs      1.3Mb
installed size is 14.0Mb
  sub-directories of 1Mb or more:
    include        8.0Mb
    jsonexamples   3.8Mb
    libs           2.0Mb
Running examples in 'rcrisp-Ex.R' failed
The error most likely occurred in:

> ### Name: reproject
> ### Title: Reproject a raster or vector dataset to the specified coordinate
> ###   reference system (CRS)
> ### Aliases: reproject
> 
> ### ** Examples
> 
> # Reproject a raster to EPSG:4326
> r <- terra::rast(matrix(1:12, nrow = 3, ncol = 4), crs = "EPSG:32633")
Warning: PROJ: proj_create_from_database: Cannot find proj.db (GDAL error 1)
Error: [rast] empty srs
Execution halted
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    libs   9.6Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   1.7Mb
    libs   2.2Mb
'LazyData' is specified without a 'data' directory
checkRd: (-1) farthest_point_sampling.Rd:28: Lost braces; missing escapes or markup?
    28 | space P = {p_1, ..., p_k}, such that each p_i is the farthest 
       |           ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) computeCBMeasure.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) computeCBMeasure.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) computeCBMeasure.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) computeCBMeasure.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) computeCBMeasure.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rdm.Rd:52: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rdm.Rd:53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rdm.Rd:54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rdm.Rd:55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rdm.Rd:56: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    R      4.4Mb
    data   1.7Mb
Package suggested but not available for checking: 'dataui'
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc   5.9Mb
checkRd: (-1) reader-package.Rd:38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) reader-package.Rd:39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) reader-package.Rd:40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) reader-package.Rd:41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) reader-package.Rd:42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) reader-package.Rd:43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) reader-package.Rd:44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) reader-package.Rd:45: Lost braces in \itemize; meant \describe ?
checkRd: (-1) reader-package.Rd:46: Lost braces in \itemize; meant \describe ?
checkRd: (-1) reader-package.Rd:47: Lost braces in \itemize; meant \describe ?
checkRd: (-1) reader-package.Rd:48: Lost braces in \itemize; meant \describe ?
checkRd: (-1) reader-package.Rd:49: Lost braces in \itemize; meant \describe ?
checkRd: (-1) reader-package.Rd:50: Lost braces in \itemize; meant \describe ?
checkRd: (-1) reader-package.Rd:51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) reader-package.Rd:52: Lost braces in \itemize; meant \describe ?
checkRd: (-1) reader-package.Rd:53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) reader-package.Rd:54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) reader-package.Rd:55: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) ReAD.Rd:19: Lost braces; missing escapes or markup?
    19 | \item{pi}{An estimate of the stationary probabilities of four states {(0,0), (0,1), (1,0), (1,1)}.}
       |                                                                      ^
checkRd: (-1) em_hmm.Rd:22: Lost braces; missing escapes or markup?
    22 | \item{pi}{An estimate of the stationary probabilities of four states {(0,0), (0,1), (1,0), (1,1)}.}
       |                                                                      ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) Automotive.Rd:29: Lost braces
    29 | Wikipedia (2018): \dQuote{Automobilindustrie --- Wikipedia{,} Die freie Enzyklopaedie}. \url{https://de.wikipedia.org/wiki/Automobilindustrie} (accessed October 14, 2018). Own postprocessing.
       |                                                           ^
checkRd: (-1) Automotive.Rd:33: Lost braces
    33 | Wikipedia (2018): \dQuote{Automobilindustrie --- Wikipedia{,} Die freie Enzyklopaedie}. \url{https://de.wikipedia.org/wiki/Automobilindustrie} (accessed October 14, 2018). 
       |                                                           ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    htmlwidgets   9.8Mb
checkRd: (-1) recombinator.Rd:32-34: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) recombinator.Rd:35-38: Lost braces in \enumerate; meant \describe ?
'LazyData' is specified without a 'data' directory
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    data   9.0Mb
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
checkRd: (-1) pseudo.geefit.Rd:17: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pseudo.geefit.Rd:18: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pseudo.onedim.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pseudo.onedim.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pseudo.onedim.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pseudo.onedim.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pseudo.onedim.Rd:31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pseudo.threedim.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pseudo.threedim.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pseudo.threedim.Rd:31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pseudo.threedim.Rd:32: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pseudo.threedim.Rd:33: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pseudo.twodim.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pseudo.twodim.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pseudo.twodim.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pseudo.twodim.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pseudo.twodim.Rd:31: Lost braces in \itemize; \value handles \item{}{} directly
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc    3.4Mb
    libs   1.2Mb
installed size is 28.7Mb
  sub-directories of 1Mb or more:
    redengine  28.3Mb
'LazyData' is specified without a 'data' directory
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    libs   2.0Mb
installed size is 13.3Mb
  sub-directories of 1Mb or more:
    libs  12.3Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    doc    1.8Mb
checkRd: (-1) make_refreshable.Rd:13: Lost braces
    13 | not that quotes need to be escaped (code{\"}).}
       |                                         ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) impute_down_nuts.Rd:21: Lost braces
    21 | NUTS typologies, defaults to code{"geo_var".}}
       |                                  ^
checkRd: (-1) validate_data_frame.Rd:19: Lost braces
    19 | NUTS typologies, defaults to code{"geo_var".}}
       |                                  ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) fbase1.binomial.Rd:32: Lost braces; missing escapes or markup?
    32 | In all base log-likelihood functions, we have dropped any additive terms that are independent of the distribution parameter, e.g. constant terms or those terms that are dependent on the response variable only. This is done for computational efficiency. Therefore, these functions cannot be used to obtain the absolute values of log-likelihood functions but only in the context of optimization and/or sampling. Users can write thin wrappers around these functions to add the constant terms to the function value. (Derivatives do not need correction. For binomial family, all factorial terms are ignored since they only depend on \code{n} and {y}.)
       |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  ^
Package suggested but not available for checking: 'semPlot'
Error(s) in re-building vignettes:
--- re-building 'short_intro.Rmd' using knitr

Quitting from short_intro.Rmd:44-46 [unnamed-chunk-3]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `loadNamespace()`:
! there is no package called 'semPlot'
---
Backtrace:
    ▆
 1. └─base::loadNamespace(x)
 2.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
 3.     └─base (local) withOneRestart(expr, restarts[[1L]])
 4.       └─base (local) doWithOneRestart(return(expr), restart)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'short_intro.Rmd' failed with diagnostics:
there is no package called 'semPlot'
--- failed re-building 'short_intro.Rmd'

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

Error: Vignette re-building failed.
Execution halted
checkRd: (-1) plot.ehh.Rd:27: Lost braces
    27 | \item{type}{plot type (see code{\link[graphics]{plot.default}} and \code{\link[graphics]{matplot}}). 
       |                                ^
checkRd: (-1) plot.ehhs.Rd:27: Lost braces
    27 | \item{type}{plot type (see code{\link[graphics]{plot.default}}.
       |                                ^
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: 'Rcplex'
checkRd: (-1) polarizacion_Dalton.Rd:26: Lost braces; missing escapes or markup?
    26 | {Pd = sqrt(sum(p_j*(x_j-mean(x_p))/4.5)^2)}
       | ^
checkRd: (-1) reparto_div.Rd:37: Lost braces; missing escapes or markup?
    37 | The set of divisors is formed by the odd numbers, that is {1,3,..,2n+1}.
       |                                                           ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) rem.dyad.Rd:121: Lost braces; missing escapes or markup?
   121 | \item Single or multiple covariates, time varying: For \code{CovSnd}, \code{CovRec}, or \code{CovInt}, an \code{m} by \code{p} by {n} array whose respective dimensions index time (i.e., event number), covariate, and actor.  For \code{CovEvent}, a \code{m} by \code{p} by \code{n} by \code{n} array, whose dimensions are analogous to the previous case.
       |                                                                                                                                   ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc    3.5Mb
    libs   1.3Mb
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc    3.9Mb
    libs   1.4Mb
'LazyData' is specified without a 'data' directory
'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) twosidedPValuestobins.Rd:84: Lost braces; missing escapes or markup?
    84 | A matrix with \code{n.bins + 1} rows and {ncol(zmat)} columns, representing for each study the discretization chosed. Values are the between bin breaks. First and last values are the edges of the outmost bins.
       |                                          ^
checkRd: (-1) ztobins.Rd:90: Lost braces; missing escapes or markup?
    90 | A matrix with \code{n.bins + 1} rows and {ncol(zmat)} columns, representing for each study the discretization chosed. Values are the between bin breaks. First and last values are the edges of the outmost bins.
       |                                          ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) method.A.Rd:200-205: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) method.A.Rd:206-211: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) method.A.Rd:231-236: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) method.A.Rd:237-242: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) method.B.Rd:201-206: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) method.B.Rd:207-212: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) method.B.Rd:232-237: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) method.B.Rd:238-243: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
checkRd: (-1) repo_build.Rd:44-47: Lost braces
    44 | ## chunk "item 1" {
       |                   ^
checkRd: (-1) repo_dependencies.Rd:48: Lost braces in \itemize; meant \describe ?
checkRd: (-1) repo_dependencies.Rd:49-50: Lost braces in \itemize; meant \describe ?
checkRd: (-1) repo_dependencies.Rd:51-53: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in 'reproducible-Ex.R' failed
The error most likely occurred in:

> ### Name: gdalProject
> ### Title: 3-Step postProcess sequence for SpatRasters using 'gdalwarp'
> ### Aliases: gdalProject gdalResample gdalMask
> 
> ### ** Examples
> 
> # prepare dummy data -- 3 SpatRasters, 2 SpatVectors
> # need 2 SpatRaster
> rf <- system.file("ex/elev.tif", package = "terra")
> elev1 <- terra::rast(rf)
> #'
> ras2 <- terra::deepcopy(elev1)
> ras2[ras2 > 200 & ras2 < 300] <- NA_integer_
> terra::values(elev1) <- rep(1L, terra::ncell(ras2))
> #'
> # a polygon vector
> f <- system.file("ex/lux.shp", package = "terra")
> vOrig <- terra::vect(f)
Warning: PROJ: proj_identify: Cannot find proj.db (GDAL error 1)
> v <- vOrig[1:2, ]
> #'
> utm <- terra::crs("epsg:23028") # $wkt
Warning: PROJ: proj_create_from_database: Cannot find proj.db (GDAL error 1)
Error: [rast] empty srs
Execution halted
Error(s) in re-building vignettes:
--- re-building 'Intro-to-Cache.Rmd' using rmarkdown

Quitting from Intro-to-Cache.Rmd:65-97 [function-level]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! [project] cannot get output boundaries for the target crs
---
Backtrace:
    ▆
 1. ├─base::system.time(...)
 2. ├─base::suppressWarnings(map1 <- terra::project(ras, newCRS))
 3. │ └─base::withCallingHandlers(...)
 4. ├─terra::project(ras, newCRS)
 5. └─terra::project(ras, newCRS)
 6.   └─terra (local) .local(x, ...)
 7.     └─terra:::messages(x, "project")
 8.       └─terra:::error(f, x@pntr$getError())
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'Intro-to-Cache.Rmd' failed with diagnostics:
[project] cannot get output boundaries for the target crs
--- failed re-building 'Intro-to-Cache.Rmd'

SUMMARY: processing the following file failed:
  'Intro-to-Cache.Rmd'

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
checkRd: (-1) NCBirths2004.Rd:16: Lost braces
    16 |     \item{\code{Smoker}}{Mother a smoker? code{No}, \code{Yes}}
       |                                               ^
checkRd: (-1) ExpandProbs.Rd:35: Lost braces; missing escapes or markup?
    35 |      {z_probs2 sqrt((n-1)/n) = t_probs,n-1}
       |      ^
GNU make is a SystemRequirements.
checkRd: (-1) resistance.Rd:52: Lost braces
    52 |     \item B. Bollob\'{a}s, 1998.  \emph{Modern Graph Theory}.  Springer.
       |                      ^
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    data   7.3Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/restfulr.Rcheck/00install.out' for details.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    include   2.4Mb
    libs      1.7Mb
    models    1.6Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc        1.1Mb
    examples   1.9Mb
checkRd: (-1) harmonize_values.Rd:44: Lost braces; missing escapes or markup?
    44 | \item{perl}{Use perl-like regex? Defaults to {FALSE}.}
       |                                              ^
checkRd: (-1) cpUpper.Rd:39: Lost braces
    39 | \code{"fastfloyd"}{ (default) uses an iterative variant of the Floyd-Warshall algorithm, in which the check of consistency of the current observation with a given cluster is done in a single step of the Floyd-Warshall algorithm. Much faster than \code{"floyd"}.}
       |                   ^
checkRd: (-1) cpUpper.Rd:41: Lost braces
    41 | \code{"floyd"}{ uses the algorithm described in Crawford and Pendakur (2013): at each step the complete Floyd-Warshall algorithm is run to check whether each cluster can accomodate the current observation.}
       |               ^
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    reveal.js-4.2.1   4.9Mb
checkRd: (-1) rec.Rd:23: Escaped LaTeX specials: \$
checkRd: (-1) saveRev.Rd:12: Lost braces; missing escapes or markup?
    12 | \item{use_wd}{logical - If TRUE, the history will be prepended by setwd({'users current working directory'}). This function will set the script's working directory to
       |                                                                         ^
'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
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    data   4.8Mb
    help   1.1Mb
checkRd: (-1) fs_search.Rd:76: Lost braces
    76 | \\code{\link{fs_auth}} \code{\link{fs_browse}}
       |       ^
Problems with news in 'NEWS.md':
No news entries found.
installed size is 13.4Mb
  sub-directories of 1Mb or more:
    data  13.3Mb
Error(s) in re-building vignettes:
--- re-building 'FAQ.Rmd' using rmarkdown_notangle
--- finished re-building 'FAQ.Rmd'

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

--- re-building 'UseCase1.Rmd' using rmarkdown_notangle

Quitting from UseCase1.Rmd:93-96 [unnamed-chunk-6]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! [rast] empty srs
---
Backtrace:
    x
 1. \-rflsgen::flsgen_generate(structure, verbose = FALSE)
 2.   +-terra::rast(...)
 3.   \-terra::rast(...)
 4.     \-terra (local) .local(x = x, ...)
 5.       \-terra:::new_rast(...)
 6.         \-terra:::messages(r, "rast")
 7.           \-terra:::error(f, x@pntr$getError())
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'UseCase1.Rmd' failed with diagnostics:
[rast] empty srs
--- failed re-building 'UseCase1.Rmd'

--- re-building 'UseCase2.Rmd' using rmarkdown_notangle
--- finished re-building 'UseCase2.Rmd'

--- re-building 'UseCase3.Rmd' using rmarkdown_notangle
--- finished re-building 'UseCase3.Rmd'

SUMMARY: processing the following file failed:
  'UseCase1.Rmd'

Error: Vignette re-building failed.
Execution halted
'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
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data      1.9Mb
    doc       1.2Mb
    extdata   1.9Mb
Problems with news in 'NEWS.md':
No news entries found.
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    doc   7.0Mb
checkRd: (-1) GenDataPopulation.Rd:21: Lost braces
    21 | {data}{Population of data}
       |       ^
checkRd: (-1) GenDataSample.Rd:23: Lost braces
    23 | {data}{Sample of data}
       |       ^
'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
Running 'tinytest.R' [7s]
Running the tests in 'tests/tinytest.R' failed.
Complete output:
  > 
  > if ( requireNamespace("tinytest", quietly=TRUE) ){
  +   tinytest::test_package("rgeomorphon")
  + }
  
  test_rgeomorphon.R............    0 tests    
  test_rgeomorphon.R............    0 tests    
  test_rgeomorphon.R............    0 tests    
  test_rgeomorphon.R............    0 tests    
  test_rgeomorphon.R............    0 tests    
  test_rgeomorphon.R............    0 tests    
  test_rgeomorphon.R............    0 tests    
  test_rgeomorphon.R............    0 tests    
  test_rgeomorphon.R............    0 tests    
  test_rgeomorphon.R............    1 tests [0;32mOK[0m Error: [rast] empty srs
  In addition: Warning message:
  PROJ: proj_create_from_database: Cannot find proj.db (GDAL error 1) 
  Execution halted
checkRd: (-1) RiemannianMetric.Rd:450-453: Lost braces
   450 | if (reticulate::py_module_available("geomstats")) {
       |                                                   ^
checkRd: (-1) RiemannianMetric.Rd:484-487: Lost braces
   484 | if (reticulate::py_module_available("geomstats")) {
       |                                                   ^
checkRd: (-1) RiemannianMetric.Rd:588-591: Lost braces
   588 | if (reticulate::py_module_available("geomstats")) {
       |                                                   ^
checkRd: (-1) Ghana_2021_school_attendance.Rd:75: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Ghana_2021_school_attendance_geometry.Rd:75: Lost braces in \itemize; meant \describe ?
installed size is 14.2Mb
  sub-directories of 1Mb or more:
    doc     7.2Mb
    fonts   1.5Mb
    libs    2.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) code_sawtooth_design.Rd:53: Lost braces
    53 | /url{http://www.sawtoothsoftware.com/help/lighthouse-studio/manual/index.html?hid_web_cbc_exporting.html}
       |     ^
'LazyData' is specified without a 'data' directory
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    doc          10.3Mb
    htmlwidgets   1.2Mb
checkRd: (-1) rhandsontable-package.Rd:8: Lost braces
     8 | R interface for creating tables using Handsontable, url{https://handsontable.com/}
       |                                                        ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) GenerateClusterData.Rd:34: Lost braces; missing escapes or markup?
    34 | origin, v_1, -v_1, v_2, -v_2, v_3, -v_3,..., v_{(numberOfClusters-1)/2},
       |                                                ^
checkRd: (-1) GenerateClusterData.Rd:35: Lost braces; missing escapes or markup?
    35 | -v_{(numberOfClusters-1)/2} (if \code{numberOfClusters} is odd)
       |    ^
checkRd: (-1) GenerateClusterData.Rd:36: Lost braces; missing escapes or markup?
    36 | origin, v_1, -v_1, v_2, -v_2, v_3, -v_3,..., v_{(numberOfClusters-1)/2}
       |                                                ^
checkRd: (-1) GetClusteringDefaultMicrobenchmarks.Rd:21-22: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) GetClusteringDefaultMicrobenchmarks.Rd:23-24: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) GetClusteringDefaultMicrobenchmarks.Rd:25-26: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) GetClusteringDefaultMicrobenchmarks.Rd:27-28: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) GetClusteringDefaultMicrobenchmarks.Rd:29-30: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) GetClusteringDefaultMicrobenchmarks.Rd:31-32: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) GetClusteringDefaultMicrobenchmarks.Rd:33-34: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) GetClusteringDefaultMicrobenchmarks.Rd:35-36: Lost braces
    35 |    \item{pam_cluster_64_7_5715},{N=64, seven clusters with 5715 vectors per
       |                                 ^
checkRd: (-1) GetClusteringDefaultMicrobenchmarks.Rd:37-38: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) GetClusteringDefaultMicrobenchmarks.Rd:39-40: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) GetClusteringExampleMicrobenchmarks.Rd:21-22: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) GetClusteringExampleMicrobenchmarks.Rd:23-24: Lost braces in \enumerate; meant \describe ?
'LazyData' is specified without a 'data' directory
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    extdata   5.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'mimic.demo', 'eicu.demo'
checkRd: (-1) iex.chart.Rd:23: Lost braces; missing escapes or markup?
    23 | r takes only of of the values accepted IN API request. {"5y", "2y", "1y", "ytd", "6m", "3m", "1m", "1d"}
       |                                                        ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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.
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) riskParityPortfolio.Rd:163: Lost braces in \itemize; meant \describe ?
checkRd: (-1) riskParityPortfolio.Rd:164: Lost braces in \itemize; meant \describe ?
checkRd: (-1) riskParityPortfolio.Rd:165: Lost braces in \itemize; meant \describe ?
checkRd: (-1) riskParityPortfolio.Rd:166: Lost braces in \itemize; meant \describe ?
checkRd: (-1) riskParityPortfolio.Rd:167: Lost braces in \itemize; meant \describe ?
checkRd: (-1) riskParityPortfolio.Rd:168: Lost braces in \itemize; meant \describe ?
checkRd: (-1) riskParityPortfolio.Rd:169: Lost braces in \itemize; meant \describe ?
checkRd: (-1) riskParityPortfolio.Rd:170: Lost braces in \itemize; meant \describe ?
checkRd: (-1) riskPredict.Rd:38: Lost braces
    38 | {hat{eta}_c^{(1)}} based on the prediction rule.}
       | ^
checkRd: (-1) riskPredict.Rd:38: Lost braces
    38 | {hat{eta}_c^{(1)}} based on the prediction rule.}
       |     ^
checkRd: (-1) riskPredict.Rd:38: Lost braces; missing escapes or markup?
    38 | {hat{eta}_c^{(1)}} based on the prediction rule.}
       |             ^
checkRd: (-1) riskPredictDiff.Rd:34: Lost braces
    34 | {hat{eta}_c^{(1)}-hat{eta}_c^{(2)}} based on the 2 prediction rules.}
       | ^
checkRd: (-1) riskPredictDiff.Rd:34: Lost braces
    34 | {hat{eta}_c^{(1)}-hat{eta}_c^{(2)}} based on the 2 prediction rules.}
       |     ^
checkRd: (-1) riskPredictDiff.Rd:34: Lost braces; missing escapes or markup?
    34 | {hat{eta}_c^{(1)}-hat{eta}_c^{(2)}} based on the 2 prediction rules.}
       |             ^
checkRd: (-1) riskPredictDiff.Rd:34: Lost braces
    34 | {hat{eta}_c^{(1)}-hat{eta}_c^{(2)}} based on the 2 prediction rules.}
       |                      ^
checkRd: (-1) riskPredictDiff.Rd:34: Lost braces; missing escapes or markup?
    34 | {hat{eta}_c^{(1)}-hat{eta}_c^{(2)}} based on the 2 prediction rules.}
       |                              ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) RivivcA.Rd:7: Lost braces
     7 | This is the major function to be called where numerical convolution ad/or deconvolution might be used for a linear in vitro in vivo correlation level A. It performes either numerical convolution via /code{NumConv()} or deconvolution via /code{NumDeconv()} and correlates their results with the known.data object via linear regression \code{lm()}. If you just want raw results of convolution/deconvolution then call explicitely \code{\link{NumConv}} or \code{link{NumDeconv}}
       |                                                                                                                                                                                                             ^
checkRd: (-1) RivivcA.Rd:7: Lost braces
     7 | This is the major function to be called where numerical convolution ad/or deconvolution might be used for a linear in vitro in vivo correlation level A. It performes either numerical convolution via /code{NumConv()} or deconvolution via /code{NumDeconv()} and correlates their results with the known.data object via linear regression \code{lm()}. If you just want raw results of convolution/deconvolution then call explicitely \code{\link{NumConv}} or \code{link{NumDeconv}}
       |                                                                                                                                                                                                                                                   ^
Found the following possibly unsafe calls:
File 'rJava/R/import.R':
  unlockBinding(IMPORTER, env = env)
  assignInNamespace(IMPORTER, importer, envir = env)
File 'rJava/R/jinit.R':
  unlockBinding(x, .env)
  unlockBinding(x, pe)
GNU make is a SystemRequirements.
Found the following Makefile(s) with an include directive with a pathname using R_HOME:
  jri/src/Makefile.win
  jri/src/win32/Makefile
  src/jvm-w32/Makefile
Even though not recommended, variable R_HOME may contain spaces.
Makefile directives use space as a separator and there is no portable
way to quote/escape the space in Make rules and directives.  However,
one can and should quote pathnames when passed from Makefile to the
shell, and this can be done specifically when invoking Make recursively.
It is therefore recommended to use the Make '-f' option to include files
in directories specified using R_HOME.  This option can be specified
multiple times to include multiple Makefiles.  Note that 'Makeconf' is
included automatically into top-level makefile of a package.
More information can be found in 'Writing R Extensions'.
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  5.1Mb
  sub-directories of 1Mb or more:
    java   4.2Mb
'LazyData' is specified without a 'data' directory
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    include   3.4Mb
    libs      3.6Mb
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 50.2Mb
  sub-directories of 1Mb or more:
    R     4.1Mb
    exe  45.7Mb
'LazyData' is specified without a 'data' directory
installed size is 24.6Mb
  sub-directories of 1Mb or more:
    extdata  23.8Mb
'LazyData' is specified without a 'data' directory
checkRd: (-1) Exponential.Rd:52: Escaped LaTeX specials: \&
checkRd: (-1) Gamma.Rd:80: Escaped LaTeX specials: \&
checkRd: (-1) college.Rd:13: Escaped LaTeX specials: \$
checkRd: (-1) college.Rd:15: Escaped LaTeX specials: \$
Running examples in 'rLakeHabitat-Ex.R' failed
The error most likely occurred in:

> ### Name: crossValidate
> ### Title: Cross Validate Interpolated Bathymetry
> ### Aliases: crossValidate
> 
> ### ** Examples
> 
> #load example outline
> outline <- terra::vect(system.file("extdata", "example_outline.shp", package = 'rLakeHabitat'))
Warning: PROJ: proj_identify: Cannot find proj.db (GDAL error 1)
Warning: [vect] Z coordinates ignored
> #load example xyz data
> data <- read.csv(system.file("extdata", "example_depths.csv", package = 'rLakeHabitat'))
> #run function
> crossValidate(outline, data, "x", "y", "z", zeros = FALSE, separation = 10, k = 5, crsUnit = "dd",
+ res = 50, method = "IDW", nmax = 4, idp = 1.5)
Warning: PROJ: proj_create_from_database: Cannot find proj.db (GDAL error 1)
Error: [rast] empty srs
Execution halted
Running examples in 'rlandfire-Ex.R' failed
The error most likely occurred in:

> ### Name: getAOI
> ### Title: Create extent vector for 'landfireAPI()'
> ### Aliases: getAOI
> 
> ### ** Examples
> 
> r <- terra::rast(nrows = 50, ncols = 50,
+   xmin = -123.7835, xmax = -123.6352,
+   ymin = 41.7534, ymax = 41.8042,
+   crs = terra::crs("epsg:4326"),
+   vals = rnorm(2500))
Warning: PROJ: proj_create_from_database: Cannot find proj.db (GDAL error 1)
Error: [rast] empty srs
Execution halted
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    lemon   2.9Mb
    libs    2.0Mb
'LazyData' is specified without a 'data' directory
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    libs  10.3Mb
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
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'rnaturalearthhires'
'LazyData' is specified without a 'data' directory
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    rmd   5.9Mb
checkRd: (-1) setOption.Matlab.Rd:37-39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) setOption.Matlab.Rd:40-41: Lost braces in \itemize; meant \describe ?
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    libs   8.8Mb
GNU make is a SystemRequirements.
Package suggested but not available for checking: 'bridgestan'
Running 'testthat.R' [18s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(rmdl)
  Loading required package: vctrs
  Loading required package: tibble
  
  Attaching package: 'tibble'
  
  The following object is masked from 'package:vctrs':
  
      data_frame
  
  
  Attaching package: 'rmdl'
  
  The following object is masked from 'package:testthat':
  
      describe
  
  > 
  > test_check("rmdl")
  Interaction term `green` was applied to exposure term `witch`
  Interaction term `green` was applied to exposure term `witch`
  Interaction term `west` was applied to exposure term `witch`
  Using `fundamental` decomposition pattern: 
  - Mediation term: NA
  - Stratifying term: NA
  Using `fundamental` decomposition pattern: 
  - Mediation term: NA
  - Stratifying term: NA
  Interaction term `green` was applied to exposure term `witch`
  Saving _problems/test-terms-213.R
  [ FAIL 1 | WARN 0 | SKIP 4 | PASS 206 ]
  
  ══ Skipped tests (4) ═══════════════════════════════════════════════════════════
  • Skipping (1): 'test-formulas.R:57:2'
  • empty test (3): 'test-interaction.R:41:1', 'test-model-table.R:272:1',
    'test-patterns.R:36:1'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-terms.R:213:2'): interaction terms are appropriately made ──────
  Error in `expect(length(t), 5)`: `ok` must be `TRUE` or `FALSE`, not the number 5.
  Backtrace:
      ▆
   1. └─testthat::expect(ok = length(t)) at test-terms.R:213:9
   2.   └─testthat:::check_bool(ok)
   3.     └─testthat:::stop_input_type(...)
   4.       └─rlang::abort(message, ..., call = call, arg = arg)
  
  [ FAIL 1 | WARN 0 | SKIP 4 | PASS 206 ]
  Error:
  ! Test failures.
  Execution halted
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: 'OpenMx'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Missing link or links in Rd file 'LFD.Rd':
  'plot.H_LFD '

See section 'Cross-references' in the 'Writing R Extensions' manual.
Specified C++11: please drop specification unless essential
checkRd: (-1) histMisclassif.Rd:22: Lost braces
    22 | err_i = 1 - max_{k={1,\ldots,K}} P(Z_i=k|x_i)
       |                 ^
checkRd: (-1) histMisclassif.Rd:22: Lost braces
    22 | err_i = 1 - max_{k={1,\ldots,K}} P(Z_i=k|x_i)
       |                    ^
checkRd: (-1) nsgaControl.Rd:20-27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nsgaControl.Rd:28-35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nsgaControl.Rd:36-43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nsgaControl.Rd:45: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot-methods.Rd:53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot-methods.Rd:54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot-methods.Rd:55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot-methods.Rd:56: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'cmdstanr'
Package unavailable to check Rd xrefs: 'cmdstanr'
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
GNU make is a SystemRequirements.
checkRd: (-1) myTarGetClientList.Rd:33: Lost braces
    33 | {MyTarget API Documenation}{https://target.my.com/doc/api/detailed/#resource_agency_clients}
       |                            ^
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
Package suggested but not available for checking: 'rnaturalearthhires'
checkRd: (-1) rncl.Rd:53-55: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rncl.Rd:57: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rncl.Rd:59-63: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rncl.Rd:65-71: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rncl.Rd:73-78: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rncl.Rd:80-84: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rncl.Rd:86-90: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rncl.Rd:92-93: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rncl.Rd:95-96: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rncl.Rd:98-99: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rncl.Rd:101-102: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rncl.Rd:104-105: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rncl.Rd:107-110: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rncl.Rd:112-115: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rncl.Rd:117-119: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rncl.Rd:121-124: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) NlistServersInCategory.Rd:11: Escaped LaTeX specials: \_
installed size is 17.1Mb
  sub-directories of 1Mb or more:
    libs  16.9Mb
checkRd: (-1) nexml_get.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nexml_get.Rd:31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nexml_get.Rd:32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nexml_get.Rd:33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nexml_get.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nexml_get.Rd:35: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    extdata   2.0Mb
    libs      3.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in 'roads-Ex.R' failed
The error most likely occurred in:

> ### Name: CLUSexample
> ### Title: Data from the CLUS example
> ### Aliases: CLUSexample
> ### Keywords: datasets
> 
> ### ** Examples
> 
> CLUSexample
$cost
[1] "This is a PackedSpatRaster object. Use 'terra::unwrap()' to unpack it"

$landings
Simple feature collection with 4 features and 0 fields
Geometry type: POINT
Dimension:     XY
Bounding box:  xmin: 0.5 ymin: 0.5 xmax: 4.5 ymax: 2.5
Projected CRS: NAD83 / Statistics Canada Lambert
         geometry
1 POINT (0.5 2.5)
2 POINT (2.5 2.5)
3 POINT (1.5 0.5)
4 POINT (4.5 0.5)

$roads
[1] "This is a PackedSpatRaster object. Use 'terra::unwrap()' to unpack it"

> prepExData(CLUSexample)
Warning: PROJ: proj_create_from_database: Cannot find proj.db (GDAL error 1)
Error: [rast] empty srs
Execution halted
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    doc    1.7Mb
checkRd: (-1) fData.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) fData.Rd:23-24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) fData.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) fData.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) fData.Rd:27-28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mfData.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mfData.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mfData.Rd:24-25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mfData.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mfData.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mfData.Rd:28-29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) outliergram.Rd:45-48: Lost braces in \itemize; meant \describe ?
checkRd: (-1) outliergram.Rd:49-51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) outliergram.Rd:52-54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) outliergram.Rd:55-58: Lost braces in \itemize; meant \describe ?
checkRd: (-1) outliergram.Rd:59-62: Lost braces in \itemize; meant \describe ?
checkRd: (-1) outliergram.Rd:63-65: Lost braces in \itemize; meant \describe ?
checkRd: (-1) outliergram.Rd:66-69: Lost braces in \itemize; meant \describe ?
checkRd: (-1) outliergram.Rd:70-71: Lost braces in \itemize; meant \describe ?
checkRd: (-1) outliergram.Rd:94: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) outliergram.Rd:95-96: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) outliergram.Rd:97: Lost braces in \itemize; \value handles \item{}{} directly
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    R  11.2Mb
Specified C++11: please drop specification unless essential
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
checkRd: (-1) predict.robu.Rd:36-42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) predict.robu.Rd:43-49: Lost braces in \itemize; meant \describe ?
checkRd: (-1) predict.robu.Rd:50-55: Lost braces in \itemize; meant \describe ?
Found the following significant warnings:
  extrafuns_cpp.cpp:92:35: warning: overflow in conversion from 'double' to 'arma::uword' {aka 'unsigned int'} changes value from '+QNaN' to '0' [-Woverflow]
  robust_lmm.cpp:836:34: warning: overflow in conversion from 'double' to 'arma::uword' {aka 'unsigned int'} changes value from '+QNaN' to '0' [-Woverflow]
  robust_lmm.cpp:836:52: warning: overflow in conversion from 'double' to 'arma::uword' {aka 'unsigned int'} changes value from '+QNaN' to '0' [-Woverflow]
See 'd:/Rcompile/CRANpkg/local/4.4/robustBLME.Rcheck/00install.out' for details.
* used C++ compiler: 'g++.exe (GCC) 13.3.0'
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc               1.7Mb
    libs              1.3Mb
    simulationStudy   1.6Mb
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
checkRd: (-1) descriptiveTable.Rd:18: Lost braces
    18 | other object type that does not fail in code{model.frame(object)}.}
       |                                             ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) performance.Rd:35: Escaped LaTeX specials: \#
checkRd: (-1) performance.Rd:36: Escaped LaTeX specials: \# \# \#
checkRd: (-1) performance.Rd:37: Escaped LaTeX specials: \# \#
'LazyData' is specified without a 'data' directory
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'
'LazyData' is specified without a 'data' directory
Package required but not available: 'Rcplex'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
checkRd: (-1) ROI_plugin_build_equality_constraints.Rd:27: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) ROI_plugin_build_equality_constraints.Rd:28: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) ROI_plugin_build_inequality_constraints.Rd:27: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) ROI_plugin_build_inequality_constraints.Rd:28: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) ROI_plugin_build_inequality_constraints.Rd:29: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) ROI_solve.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ROI_solve.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ROI_solve.Rd:28-30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ROI_solve.Rd:31: Lost braces in \itemize; \value handles \item{}{} directly
installed size is 17.3Mb
  sub-directories of 1Mb or more:
    doc  15.2Mb
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    R         3.2Mb
    extdata   2.7Mb
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
'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
'LazyData' is specified without a 'data' directory
checkRd: (-1) read_ascii.Rd:33: Lost braces
    33 | \item{respondent_pattern}{For use when the file does not contain a line for every card for every respondent (or contains extra lines that correspond to no respondent), a regular expression that matches the file's respondent identifier; e.g., if the respondent number is stored in the first four digits of each line, preceded by a space, "(?<=^\\s)\\d{4}".}
       |                                                                                                                                                                                                                                                                                                                                                               ^
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/ROracle.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
checkRd: (-1) osm_url_spec.Rd:23: Lost braces; missing escapes or markup?
    23 | \item{server_url}{A url using `{x}`, `{y}`, and `{z}` for the x, y, and
       |                                ^
checkRd: (-1) osm_url_spec.Rd:23: Lost braces; missing escapes or markup?
    23 | \item{server_url}{A url using `{x}`, `{y}`, and `{z}` for the x, y, and
       |                                       ^
checkRd: (-1) osm_url_spec.Rd:23: Lost braces; missing escapes or markup?
    23 | \item{server_url}{A url using `{x}`, `{y}`, and `{z}` for the x, y, and
       |                                                  ^
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    R      1.6Mb
    data   2.7Mb
    libs   1.4Mb
'LazyData' is specified without a 'data' directory
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    R      4.8Mb
    help   1.1Mb
    libs   1.6Mb
Package suggested but not available for checking: 'RandomFields'
checkRd: (-1) Clyde.Rd:8: Lost braces
     8 | These data record the water quality, in terms of dissolved oxygen (\code{DO}) on a percentage scale, at a number of sampling stations (\code{Station}) on the River Clyde.  The date (\code{Day}, \\code{Month}, \code{Year}) is also available, along with the day of the year (\code{Doy} between 1 and 365) and an identified (\code{id}) of the survey on which each measurement was made.
       |                                                                                                                                                                                                         ^
checkRd: (-1) rp.pos.Rd:22-24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rp.pos.Rd:25-27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rp.pos.Rd:28-30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rp.pos.Rd:31-49: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rp.pos.Rd:35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rp.pos.Rd:36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rp.pos.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rp.pos.Rd:38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rp.pos.Rd:39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rp.pos.Rd:40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rp.pos.Rd:41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rp.pos.Rd:42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rp.pos.Rd:43: Lost braces in \itemize; meant \describe ?
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    extdata   4.9Mb
    help      1.4Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
checkRd: (-1) rpivotTable.Rd:60: Lost braces; missing escapes or markup?
    60 | An example is: onRefresh=htmlwidgets::JS("function(config) { Shiny.onInputChange('myPivotData', config); }")
       |                                                            ^
checkRd: (-1) plotImage.blcTree.Rd:17: Lost braces
    17 |   \item{method}{Method to determine width of columns that represent classes: \dQuote{weight} (subject weight in class) or dQuote{binary} (depth in tree).}
       |                                                                                                                                 ^
checkRd: (-1) plotImage.glcTree.Rd:16: Lost braces
    16 |   \item{method}{Method to determine width of columns that represent classes: \dQuote{weight} (subject weight in class) or dQuote{binary} (depth in tree).}
       |                                                                                                                                 ^
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   1.3Mb
checkRd: (-1) get.poetry.Rd:17: Lost braces; missing escapes or markup?
    17 | \item{output}{Can be any or a combination of the input terms {'author', 'title', 'lines', 'linecount'}. If NULL, all
       |                                                              ^
'LazyData' is specified without a 'data' directory
Running 'testthat.R' [25s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(Rpolyhedra)
  > library(stringr)
  > library(lgr)
  > library(rgl)
  > library(geometry)
  > library(testthat)
  > 
  > # Change threshold to ERROR. Comment out/change if verbosity required for development
  > lgr::basic_config(threshold = "error")
  <LoggerRoot> [error] root
  
  appenders:
    console: <AppenderConsole> [all] -> console
  > #' getDataDirMockedTest mocked function for a temp dest folder for testing proposes
  > 
  > 
  > 
  > testthat::test_check("Rpolyhedra")
  Saving _problems/test_package_lib-41.R
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 646 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_package_lib.R:22:3'): test on package lib functions ────────────
  <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_package_lib.R:22:3
   2.   └─lifecycle::deprecate_stop("3.2.0", "with_mock()", "with_mocked_bindings()")
   3.     └─lifecycle:::deprecate_stop0(msg)
   4.       └─rlang::cnd_signal(...)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 646 ]
  Error:
  ! Test failures.
  Execution halted
installed size is 16.4Mb
  sub-directories of 1Mb or more:
    libs  16.4Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/RPostgreSQL.Rcheck/00install.out' for details.
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    extdata   4.5Mb
checkRd: (-1) as.tg.Rd:18: Lost braces; missing escapes or markup?
    18 | Renames the \code{class(tg)["name"]} attribute and sets {class(tg)["type"] <- "TextGrid"} (if it is not already set)
       |                                                         ^
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
checkRd: (-1) check_node.Rd:11: Lost braces
    11 | \item{x}{\\code{list}, the node to check}
       |                ^
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   4.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 14.2Mb
  sub-directories of 1Mb or more:
    libs  13.6Mb
checkRd: (-1) ex.Rd:20: Lost braces
    20 | Execute a ops-dag using `code{wrap()}` data as values.
       |                              ^
checkRd: (-1) sql_node.Rd:29: Lost braces; missing escapes or markup?
    29 | \item{expand_braces}{logical if TRUE use {col} notation to ensure {col} is a column name.}
       |                                          ^
checkRd: (-1) sql_node.Rd:29: Lost braces; missing escapes or markup?
    29 | \item{expand_braces}{logical if TRUE use {col} notation to ensure {col} is a column name.}
       |                                                                   ^
checkRd: (-1) R2_lik.Rd:37: Lost braces; missing escapes or markup?
    37 | \code{R2_lik()} is also computed for LMMs and GLMMs in the {MuMIn} package.
       |                                                            ^
checkRd: (-1) R2_pred.Rd:32: Lost braces; missing escapes or markup?
    32 | Note that the version of \code{binaryPGLMM()} in the package ape is replaced by a version contained within {rr2} that outputs all of the required information for the calculation of R2_resid.
       |                                                                                                            ^
checkRd: (-1) R2_resid.Rd:69: Lost braces; missing escapes or markup?
    69 | Note that the version of \code{binaryPGLMM()} in the package ape is replaced by a version contained within {rr2} that outputs all of the required information for the calculation of \code{R2_resid()}
       |                                                                                                            ^
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc   5.3Mb
checkRd: (-1) rrecsys.Rd:72: Lost braces; missing escapes or markup?
    72 |  The average deviation rating $dev_{ij}$ between co-rated items is defined by:
       |                                    ^
checkRd: (-1) rrecsys.Rd:76: Lost braces; missing escapes or markup?
    76 |  Where $c_{ij}$ is the number of co-ratings between items $i$ and $j$ and $r_{ui}$ is an existing rating for user $u$ on item $i$. The Weighted Slope One takes into account both, information from users who rated the same item and the number of observed ratings.
       |           ^
checkRd: (-1) rrecsys.Rd:76: Lost braces; missing escapes or markup?
    76 |  Where $c_{ij}$ is the number of co-ratings between items $i$ and $j$ and $r_{ui}$ is an existing rating for user $u$ on item $i$. The Weighted Slope One takes into account both, information from users who rated the same item and the number of observed ratings.
       |                                                                              ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) lateformeeting.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) lateformeeting.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) lateformeeting.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) lateformeeting.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) lfm_clean.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) lfm_clean.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) lfm_clean.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) lfm_clean.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) regrad.Rd:46: Lost braces; missing escapes or markup?
    46 |  \item \code{x-axis} {1st column: The names of the different institutions}
       |                      ^
checkRd: (-1) regrad.Rd:47: Lost braces; missing escapes or markup?
    47 |  \item \code{y-axis} {2nd column: The value to show completeness}
       |                      ^
Package suggested but not available for checking: 'rnaturalearthhires'
checkRd: (-1) rrinf_clust.Rd:24: Lost braces; missing escapes or markup?
    24 | \item{clustering}{A \code{List} that specifies a clustering of datapoint indexes {1, ..., n}. See \link{example_clustering} for details.}
       |                                                                                  ^
checkRd: (-1) rrtest_clust.Rd:21: Lost braces; missing escapes or markup?
    21 | \item{clustering}{A \code{List} that specifies a clustering of datapoint indexes {1, ..., n}.
       |                                                                                  ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) rSCA.modeling.Rd:61: Lost braces; missing escapes or markup?
    61 |                 a predefined string to specify how the information of leaf nodes will be stored in the map file. A full list of options for mapvalue is: {mean, max, min, median, interval, radius, variation, random}. Default value is "mean". Use "interval" to get an interval bounded by the minimum and maximum values, (i.e., [min, max]). The option of "radius" will output the mean and the radius [i.e., (max - min) / 2] at the same time. Use "variation" to output the mean and the standard deviation. The option of "random" will output the information as an interval like the "interval" option, but it will use a random value within the interval as the predicted value.
       |                                                                                                                                                          ^
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   4.2Mb
checkRd: (-1) remoteDriver-class.Rd:39-40: Lost braces
    39 | browser being used; should be one of {chrome|firefox|htmlunit|
       |                                      ^
checkRd: (-1) remoteDriver-class.Rd:50: Lost braces; missing escapes or markup?
    50 | of {WINDOWS|XP|VISTA|MAC|LINUX|UNIX}. When requesting a new session,
       |    ^
checkRd: (-1) remoteDriver-class.Rd:194-196: Lost braces
   194 |   element, available schemes: {"class name", "css selector",
       |                               ^
checkRd: (-1) webElement-class.Rd:50-52: Lost braces
    50 |     element, available schemes: {"class name", "css selector",
       |                                 ^
checkRd: (-1) webElement-class.Rd:67-69: Lost braces
    67 |     element, available schemes: {"class name", "css selector",
       |                                 ^
'LazyData' is specified without a 'data' directory
installed size is 19.3Mb
  sub-directories of 1Mb or more:
    libs  18.3Mb
GNU make is a SystemRequirements.
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'gurobi'
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    R      4.0Mb
    help   1.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/RSQLite.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 20.9Mb
  sub-directories of 1Mb or more:
    R      1.8Mb
    doc    4.8Mb
    libs  13.2Mb
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    exec   1.7Mb
    lib    1.9Mb
    libs   1.4Mb
GNU make is a SystemRequirements.
Package suggested but not available for checking: 'cmdstanr'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/RStoolbox.Rcheck/00install.out' for details.
installed size is 20.1Mb
  sub-directories of 1Mb or more:
    libs  19.6Mb
installed size is 55.6Mb
  sub-directories of 1Mb or more:
    libs    1.0Mb
    swipl  54.3Mb
GNU make is a SystemRequirements.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
'LazyData' is specified without a 'data' directory
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    R     1.5Mb
    doc   6.4Mb
checkRd: (-1) LBA-race.Rd:157: Lost braces
   157 |   corresponding (and not first) accumulator winning see /code{/link{LBA}}.
       |                                                              ^
checkRd: (-1) LBA-race.Rd:157: Lost braces
   157 |   corresponding (and not first) accumulator winning see /code{/link{LBA}}.
       |                                                                    ^
'LazyData' is specified without a 'data' directory
Running 'testthat.R' [5s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(mockery)
  > library(RTD)
  > 
  > test_check("RTD")
  Saving _problems/test-td-24.R
  Saving _problems/test-td-45.R
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 10 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-td.R:12:3'): td_upload works with mock ─────────────────────────
  <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-td.R:12:3
   2.   └─lifecycle::deprecate_stop("3.2.0", "with_mock()", "with_mocked_bindings()")
   3.     └─lifecycle:::deprecate_stop0(msg)
   4.       └─rlang::cnd_signal(...)
  ── Error ('test-td.R:32:3'): td_upload works with mock when the table already exists ──
  <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-td.R:32:3
   2.   └─lifecycle::deprecate_stop("3.2.0", "with_mock()", "with_mocked_bindings()")
   3.     └─lifecycle:::deprecate_stop0(msg)
   4.       └─rlang::cnd_signal(...)
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 10 ]
  Error:
  ! Test failures.
  Execution halted
'LazyData' is specified without a 'data' directory
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    rmarkdown  11.0Mb
GNU make is a SystemRequirements.
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    libs   9.8Mb
Specified C++11: please drop specification unless essential
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    libs   8.1Mb
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R   5.0Mb
checkRd: (-1) rt_GET.Rd:13: Lost braces
    13 | code{\link[httr]{GET}} (\code{TRUE}) or not (\code{FALSE})}
       |     ^
checkRd: (-1) rt_POST.Rd:13: Lost braces
    13 | code{\link[httr]{POST}} (\code{TRUE}) or not (\code{FALSE})}
       |     ^
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    doc    7.8Mb
    libs   2.5Mb
GNU make is a SystemRequirements.
Package suggested but not available for checking: 'cmdstanr'
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    libs   6.3Mb
GNU make is a SystemRequirements.
checkRd: (-1) rts.Rd:32: Lost braces
    32 | If a name of a raster time series file is provided for the \code{x} argument, it acts the same as code{\link[rts]{read.rts}}.
       |                                                                                                       ^
Problems with news in 'NEWS.md':
No news entries found.
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    R      3.0Mb
    libs   1.1Mb
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc   4.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) RUVIII.Rd:51: Lost braces
    51 | If code{return.info} is \code{TRUE}, a list is returned that contains:
       |        ^
Package which this enhances but not available for checking: 'glmmADMB'
checkRd: (-1) Valpha.Rd:15: Lost braces; missing escapes or markup?
    15 |   \item{V}{a numeric vector with (i,j) entry: V[i,j] = P(theta_{i} >= theta[alpha_{j}]|data) }
       |                                                                ^
checkRd: (-1) Valpha.Rd:15: Lost braces; missing escapes or markup?
    15 |   \item{V}{a numeric vector with (i,j) entry: V[i,j] = P(theta_{i} >= theta[alpha_{j}]|data) }
       |                                                                                   ^
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
Problems with news in 'NEWS.md':
No news entries found.
checkRd: (-1) HardThresh.Rd:15: Lost braces; missing escapes or markup?
    15 | \code{x} filtered result (y 1_{|y|>t}).
       |                               ^
checkRd: (-1) SoftThresh.Rd:15: Lost braces; missing escapes or markup?
    15 | \code{x} filtered result (y 1_{|y|>t}).
       |                               ^
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    java  10.7Mb
'LazyData' is specified without a 'data' directory
File 'RWinEdt/R/zzz.R':
  .onAttach calls:
    writeLines(edtFile, con = send2RedtLoc)
    writeLines(edtFile, con = send2RedtLoc)

Package startup functions should use 'packageStartupMessage' to
  generate messages.
See section 'Good practice' in '?.onAttach'.
'LazyData' is specified without a 'data' directory
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
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    R         1.4Mb
    include   1.3Mb
    libs      4.9Mb
Specified C++14: please drop specification unless essential
Package suggested but not available for checking: 'unix'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) ZigZagLogistic.Rd:11: Lost braces; missing escapes or markup?
    11 | \item{dataX}{Design matrix containing observations of the independent variables x. The i-th row represents the i-th observation with components x_{i,1}, ..., x_{i,d}.}
       |                                                                                                                                                   ^
checkRd: (-1) ZigZagLogistic.Rd:11: Lost braces; missing escapes or markup?
    11 | \item{dataX}{Design matrix containing observations of the independent variables x. The i-th row represents the i-th observation with components x_{i,1}, ..., x_{i,d}.}
       |                                                                                                                                                                 ^
checkRd: (-1) ZigZagLogistic.Rd:13: Lost braces; missing escapes or markup?
    13 | \item{dataY}{Vector of length n containing {0, 1}-valued observations of the dependent variable y.}
       |                                            ^
checkRd: (-1) ciReg.Rd:10: Lost braces
    10 | \item{fit}{an object of class{lm}, i.e. the output from \code{\link{lm}}.}
       |                              ^
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    libs   8.0Mb
checkRd: (-1) BootsChapt.Rd:38: Escaped LaTeX specials: \&
checkRd: (-1) SemiparChangePoint.Rd:30: Escaped LaTeX specials: \&
checkRd: (-1) schapt.Rd:44: Escaped LaTeX specials: \&
'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
checkRd: (-1) binaryChoice.Rd:105: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) binaryChoice.Rd:106: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) binaryChoice.Rd:111: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) binaryChoice.Rd:112: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) binaryChoice.Rd:113: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) binaryChoice.Rd:114: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) SAM.Rd:67: Escaped LaTeX specials: \$
checkRd: (-1) samr.Rd:59: Escaped LaTeX specials: \$
checkRd: (-1) samr.Rd:84: Escaped LaTeX specials: \# \$
checkRd: (-1) samr.Rd:88: Escaped LaTeX specials: \$
checkRd: (-1) samr.Rd:92: Escaped LaTeX specials: \$
checkRd: (-1) samr.Rd:97: Escaped LaTeX specials: \#
checkRd: (-1) samr.assess.samplesize.plot.Rd:12: Escaped LaTeX specials: \#
installed size is 15.3Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    libs  13.5Mb
Specified C++11: please drop specification unless essential
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    help   3.4Mb
    libs   1.3Mb
checkRd: (-1) ModelHMMR-class.Rd:37: Lost braces; missing escapes or markup?
    37 |         class {StatHMMR}).
       |               ^
Package suggested but not available for checking: 'networkTomography'
'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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
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
GNU make is a SystemRequirements.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc       5.1Mb
    extdata   1.1Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    3.9Mb
    libs   1.1Mb
checkRd: (-1) gen.ds.Rd:43-48: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gen.ds.Rd:50-53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gen.ds.Rd:64-65: Lost braces
    64 |    \item{the dependence parameter \code{dep} or the vector of dependence parameters \code{dep}. When missing, these coefficients are obtained from independent standard uniform sampling.
       |         ^
checkRd: (-1) gen.ds.Rd:66: Lost braces
    66 |    \item{the list \code{asy} of asymmetric weights \eqn{\beta_{i,b}} for \eqn{b \in B}  and \eqn{i \in b}. When missing, these coefficients are obtained from independent standard uniform sampling followed by renormalization in order to satisfy the sum-to-one constraints.}
       |         ^
'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) setData.ReducedRankRegressions.Rd:14-16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) setData.ReducedRankRegressions.Rd:17-18: Lost braces in \itemize; meant \describe ?
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Updated help pages with examples
    Updated conjugate model sampler
'LazyData' is specified without a 'data' directory
Packages which this enhances but not available for checking:
  'gurobi', 'Rcplex', 'pogs'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
checkRd: (-1) get.events.Rd:51: Lost braces
    51 |   code{\link[deSolve]{events}}
       |       ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) scatterD3.Rd:209: Lost braces; missing escapes or markup?
   209 | {https://github.com/skokenes/D3-Lasso-Plugin}{d3-lasso-plugin} feature}
       | ^
checkRd: (-1) scatterD3.Rd:209: Lost braces
   209 | {https://github.com/skokenes/D3-Lasso-Plugin}{d3-lasso-plugin} feature}
       |                                              ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'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
'LazyData' is specified without a 'data' directory
installed size is 17.0Mb
  sub-directories of 1Mb or more:
    cppad     9.5Mb
    include   4.7Mb
    libs      2.1Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   4.0Mb
    lib    1.1Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'gpuR'
'LazyData' is specified without a 'data' directory
installed size is 16.8Mb
  sub-directories of 1Mb or more:
    extdata  16.7Mb
'LazyData' is specified without a 'data' directory
checkRd: (-1) simulateSNPs.Rd:46: Escaped LaTeX specials: \& \& \&
checkRd: (-1) simulateSNPs.Rd:80: Escaped LaTeX specials: \& \& \&
checkRd: (-1) scriptloc.Rd:5: Lost braces; missing escapes or markup?
     5 | \title{Get location of script in a fashion analagous to ${BASH_SOURCE[0]}}
       |                                                          ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) cln.Rd:27: Lost braces
    27 |    case for text \code{1} for 1st uppercase, code{2} for lowercase, code{3} for uppercase (optional)
       |                                                  ^
checkRd: (-1) cln.Rd:27: Lost braces
    27 |    case for text \code{1} for 1st uppercase, code{2} for lowercase, code{3} for uppercase (optional)
       |                                                                         ^
checkRd: (-1) geom_flat_violin.Rd:7: Lost braces
     7 | url{https://gist.github.com/dgrtwo/eb7750e74997891d7c20}
       |    ^
checkRd: (-1) sdc_extabs.Rd:59: Lost braces
    59 | (including ]code{forcelist} variables) that can be used to form tables.}
       |                 ^
Problems with news in 'NEWS.md':
No news entries found.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   3.9Mb
Specified C++11: please drop specification unless essential
checkRd: (-1) msdpd.Rd:69: Lost braces in \itemize; meant \describe ?
checkRd: (-1) msdpd.Rd:76: Lost braces in \itemize; meant \describe ?
checkRd: (-1) msdpd.Rd:77: Lost braces in \itemize; meant \describe ?
checkRd: (-1) msdpd.Rd:78: Lost braces in \itemize; meant \describe ?
checkRd: (-1) msdpd.Rd:53: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) msdpd.Rd:54: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) msdpd.Rd:55: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) msdpd.Rd:56: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) msdpdth.Rd:84: Lost braces in \itemize; meant \describe ?
checkRd: (-1) msdpdth.Rd:91: Lost braces in \itemize; meant \describe ?
checkRd: (-1) msdpdth.Rd:92: Lost braces in \itemize; meant \describe ?
checkRd: (-1) msdpdth.Rd:93: Lost braces in \itemize; meant \describe ?
checkRd: (-1) msdpdth.Rd:65: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) msdpdth.Rd:66: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) msdpdth.Rd:67: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) msdpdth.Rd:68: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) msdpdth.Rd:69: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) msdpdth.Rd:70: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hyperpar.Rd:17: Lost braces
    17 | \item{c}{denotes the expected range of eqn{f} .}
       |                                           ^
'LazyData' is specified without a 'data' directory
Running 'testthat.R' [26s]
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(SeaGraphs)
  > 
  > test_check("SeaGraphs")
  Reading layer `mask_shapefile' from data source 
    `D:\RCompile\CRANpkg\lib\4.4\SeaGraphs\external\mask_shapefile\mask_shapefile.shp' 
    using driver `ESRI Shapefile'
  Simple feature collection with 1 feature and 1 field
  Geometry type: POLYGON
  Dimension:     XY
  Bounding box:  xmin: 34.43481 ymin: 43.74194 xmax: 34.89778 ymax: 43.9225
  Geodetic CRS:  WGS 84
  Reading layer `mask_shapefile' from data source 
    `D:\RCompile\CRANpkg\lib\4.4\SeaGraphs\external\mask_shapefile\mask_shapefile.shp' 
    using driver `ESRI Shapefile'
  Simple feature collection with 1 feature and 1 field
  Geometry type: POLYGON
  Dimension:     XY
  Bounding box:  xmin: 34.43481 ymin: 43.74194 xmax: 34.89778 ymax: 43.9225
  Geodetic CRS:  WGS 84
  Saving _problems/test-seagraph-68.R
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 28 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-seagraph.r:68:3'): seagraph works ──────────────────────────────
  Error: [project] output crs is not valid
  Backtrace:
      ▆
   1. ├─terra::project(vect_mask_shapefile, "+init=EPSG:4269") at test-seagraph.r:68:3
   2. └─terra::project(vect_mask_shapefile, "+init=EPSG:4269")
   3.   └─terra (local) .local(x, ...)
   4.     └─terra:::messages(x, "project")
   5.       └─terra:::error(f, x@pntr$getError())
  
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 28 ]
  Error:
  ! Test failures.
  Execution halted
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    R   7.8Mb
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    css_data   8.7Mb
installed size is 19.2Mb
  sub-directories of 1Mb or more:
    extdata  18.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    R      1.6Mb
    libs   2.0Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Running examples in 'seeclickfixr-Ex.R' failed
The error most likely occurred in:

> ### Name: list_places
> ### Title: Query sub-city neighborhoods in which issues can be reported.
> ### Aliases: list_places
> 
> ### ** Examples
> 
> list_places("Boston, MA",limit = 5)
Error: lexical error: invalid char in json text.
                                       <!DOCTYPE html><html lang="en-U
                     (right here) ------^
Execution halted
checkRd: (-1) seedCCA.Rd:17: Lost braces; missing escapes or markup?
    17 | \item{u}{numeric, maximum number of projections. The default is 10. This is used for \code{type="seed1"}, \code{type="seed2"} and {tyepe="pls"}.}
       |                                                                                                                                   ^
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 34.5Mb
  sub-directories of 1Mb or more:
    www  34.4Mb
'LazyData' is specified without a 'data' directory
Package required but not available: 'semPlot'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Problems with news in 'NEWS.md':
No news entries found.
Package which this enhances but not available for checking: 'semPlot'
Package required but not available: 'OpenMx'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'semPlot'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'OpenMx'

Package suggested but not available for checking: 'ctsemOMX'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Specified C++11: please drop specification unless essential
'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) sendmail_options.Rd:32-35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sendmail_options.Rd:36-37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sendmail_options.Rd:38-39: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
checkRd: (-1) match_dataphy.Rd:37-38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) match_dataphy.Rd:39-41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) match_dataphy.Rd:42-44: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs     3.3Mb
    models   1.6Mb
GNU make is a SystemRequirements.
Specified C++14: please drop specification unless essential
checkRd: (-1) process,HybridSequenceClassifier-method.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) process,HybridSequenceClassifier-method.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) process,HybridSequenceClassifier-method.Rd:32: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data        1.4Mb
    sequences   1.9Mb
Package suggested but not available for checking: 'doMC'
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
GNU make is a SystemRequirements.
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    help   1.3Mb
    libs   3.9Mb
GNU make is a SystemRequirements.
checkRd: (-1) SEset_to_network.Rd:50: Escaped LaTeX specials: \&
checkRd: (-1) network_to_SEset.Rd:72: Escaped LaTeX specials: \&
checkRd: (-1) network_to_path.Rd:50: Escaped LaTeX specials: \&
checkRd: (-1) path_to_network.Rd:29: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'BPCells'
Packages suggested but not available for checking: 'BPCells', 'presto'
Package unavailable to check Rd xrefs: 'BPCells'
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    R     1.2Mb
    doc   6.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc   5.1Mb
installed size is 123.4Mb
  sub-directories of 1Mb or more:
    doc     12.6Mb
    gdal     3.0Mb
    libs    94.2Mb
    proj     9.0Mb
    sqlite   1.5Mb
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) bisee.Rd:127: Lost braces
   127 | values including \code{x}, \code{y}, code{family}, \code{clusterID},
       |                                          ^
checkRd: (-1) hisee.Rd:101: Lost braces
   101 | values including \code{x}, \code{y}, code{family}, \code{clusterID},
       |                                          ^
checkRd: (-1) isee.Rd:116: Lost braces
   116 | values including \code{x}, \code{y}, code{family}, \code{clusterID},
       |                                          ^
checkRd: (-1) see.Rd:98: Lost braces
    98 | values including \code{x}, \code{y}, code{family}, \code{clusterID},
       |                                          ^
'LazyData' is specified without a 'data' directory
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    data   6.7Mb
checkRd: (-1) sgt.Rd:55: Lost braces
    55 |   \code{sigma <= 0}, \code{lambda <= -1}, \code{lambda >= 1}, \code{p <= 0}, and \code{q <= 0} are errors and return \code{NaN}. Also, if \code{mean.cent} is \code{TRUE} but code{p*q <= 1}, the result is an error and \code{NaNs} are produced. Similarly, if \code{var.adj} is \code{TRUE} but code{p*q <= 2}, the result is an error and \code{NaNs} are produced.
       |                                                                                                                                                                                   ^
checkRd: (-1) sgt.Rd:55: Lost braces
    55 |   \code{sigma <= 0}, \code{lambda <= -1}, \code{lambda >= 1}, \code{p <= 0}, and \code{q <= 0} are errors and return \code{NaN}. Also, if \code{mean.cent} is \code{TRUE} but code{p*q <= 1}, the result is an error and \code{NaNs} are produced. Similarly, if \code{var.adj} is \code{TRUE} but code{p*q <= 2}, the result is an error and \code{NaNs} are produced.
       |                                                                                                                                                                                                                                                                                                        ^
checkRd: (-1) changept.Rd:17-19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) changept.Rd:20-21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) changept.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) powerShape.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) powerShape.Rd:31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) powerShape.Rd:32-33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) powerShapeNA.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) powerShapeNA.Rd:31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) powerShapeNA.Rd:32-33: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
Running examples in 'ShapePattern-Ex.R' failed
The error most likely occurred in:

> ### Name: ssr
> ### Title: Decompose a planar shape (polygon) to produce area, perimeter,
> ###   and number of parts spectra
> ### Aliases: ssr
> ### Keywords: manip
> 
> ### ** Examples
> 
> # ALTERNATE DEMO DATASETS
> # shpfileobj <- terra::vect(data$p4no)
> # shpfileobj <- terra::vect(data$p4is)
> 
> # PATH TO DEMO SHAPEFILE
> f <- system.file("ex/lux.shp", package="terra")
> # IMPORT SHAPEFILE TO SpatVect FORMAT WITH terra PACKAGE
> v <- terra::vect(f)
Warning: PROJ: proj_identify: Cannot find proj.db (GDAL error 1)
> # REPROJECT TO A VALID PROEJCTION
> shpfileobj <- terra::project(v, "EPSG:2150")
Warning: PROJ: proj_create_from_database: Cannot find proj.db (GDAL error 1)
Error: [project] output crs is not valid
Execution halted
Error(s) in re-building vignettes:
--- re-building 'basic_workflow.Rmd' using rmarkdown

Quitting from basic_workflow.Rmd:62-87 [unnamed-chunk-3]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `[.data.table`:
! column not found: [(Intercept)]
---
Backtrace:
    ▆
 1. └─SHAPforxgboost::shap.prep(fit, X_train = X)
 2.   ├─...[]
 3.   └─data.table:::`[.data.table`(...)
 4.     └─data.table:::stopf(...)
 5.       └─data.table:::raise_condition(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'basic_workflow.Rmd' failed with diagnostics:
column not found: [(Intercept)]
--- failed re-building 'basic_workflow.Rmd'

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc    3.3Mb
    libs   1.3Mb
Packages suggested but not available for checking: 'OpenMx', 'rCOSA'
Package unavailable to check Rd xrefs: 'rCOSA'
Package suggested but not available for checking: 'hydromad'
checkRd: (-1) age_corr.Rd:15: Lost braces
    15 | \item{plot}{Should the results be plotted? (/code{TRUE/FALSE})}
       |                                                  ^
checkRd: (-1) age_corr.Rd:17: Lost braces
    17 | \item{agecorrection}{Correct for jumps in age (/code{TRUE}) or
       |                                                     ^
checkRd: (-1) age_corr.Rd:18: Lost braces
    18 | only for starting time (/code{FALSE})}
       |                              ^
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc       1.7Mb
    extdata   4.2Mb
'LazyData' is specified without a 'data' directory
checkRd: (-1) shiftrPrepare.Rd:37: Lost braces
    37 |     See code{\link{shiftrPermBinary}} function and the respective example.
       |             ^
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    www   7.4Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'cmdstanr'
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    www   9.4Mb
'LazyData' is specified without a 'data' directory
installed size is 20.5Mb
  sub-directories of 1Mb or more:
    www  19.7Mb
'LazyData' is specified without a 'data' directory
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    www   7.6Mb
'LazyData' is specified without a 'data' directory
checkRd: (-1) js_calls.Rd:63: Lost braces in \itemize; meant \describe ?
checkRd: (-1) js_calls.Rd:64: Lost braces in \itemize; meant \describe ?
checkRd: (-1) js_calls.Rd:65-66: Lost braces in \itemize; meant \describe ?
checkRd: (-1) js_calls.Rd:67: Lost braces in \itemize; meant \describe ?
checkRd: (-1) js_calls.Rd:68: Lost braces in \itemize; meant \describe ?
checkRd: (-1) js_calls.Rd:69: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pickCheckboxNamesAndLabels.Rd:14: Lost braces
    14 | \item{choices}{link{pickCheckboxInput} choices list.}
       |                    ^
Running 'testthat.R' [4s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(shinyGovstyle)
  > 
  > test_check("shinyGovstyle")
  Saving _problems/test-backlink_Input-7.R
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 125 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-backlink_Input.R:4:3'): backlink works ───────────────────────
  Expected `backlink_check$children[[1]][[2]]` to be identical to "Back".
  Differences:
  target is NULL, current is character
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 125 ]
  Error:
  ! Test failures.
  Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) shinyjs-defunct.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) shinyjs-defunct.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) shinyjs-defunct.Rd:20: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) store_googledrive.Rd:19: Lost braces; missing escapes or markup?
    19 | See the {gargle} package to manage authentication, and especially
       |         ^
checkRd: (-1) store_googledrive.Rd:20: Lost braces; missing escapes or markup?
    20 | \href{https://gargle.r-lib.org/articles/articles/managing-tokens-securely.html}{this vignette from {gargle} package} to manage the process.
       |                                                                                                    ^
checkRd: (-1) custom-labels.Rd:7: Lost braces; missing escapes or markup?
     7 | \title{Modify {shinymanager} labels to use custom text}
       |               ^
checkRd: (-1) use_language.Rd:5: Lost braces; missing escapes or markup?
     5 | \title{Use {shinymanager} labels}
       |            ^
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    shinymgr    1.4Mb
    tutorials   3.6Mb
'LazyData' is specified without a 'data' directory
installed size is 21.1Mb
  sub-directories of 1Mb or more:
    shinyApp  21.0Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'cmdstanr'
'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) shiny_pivot_table.Rd:58: Lost braces in \itemize; meant \describe ?
checkRd: (-1) shiny_pivot_table.Rd:59: Lost braces in \itemize; meant \describe ?
checkRd: (-1) shiny_pivot_table.Rd:60: Lost braces in \itemize; meant \describe ?
checkRd: (-1) shiny_pivot_table.Rd:61: Lost braces in \itemize; meant \describe ?
checkRd: (-1) shiny_pivot_table.Rd:62: Lost braces in \itemize; meant \describe ?
checkRd: (-1) shiny_pivot_table.Rd:63: Lost braces in \itemize; meant \describe ?
checkRd: (-1) shiny_pivot_table.Rd:64: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    R     1.6Mb
    www   6.5Mb
'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
Running 'testthat.R' [2s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(shinyShortcut)
  > 
  > test_check("shinyShortcut")
  Saving _problems/test-shinyShortcut-31.R
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-shinyShortcut.R:5:3'): ShinyShorcut returns the correct files ──
  <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-shinyShortcut.R:5:3
   2.   └─lifecycle::deprecate_stop("3.2.0", "with_mock()", "with_mocked_bindings()")
   3.     └─lifecycle:::deprecate_stop0(msg)
   4.       └─rlang::cnd_signal(...)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ]
  Error:
  ! Test failures.
  Execution halted
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'cmdstanr'
'LazyData' is specified without a 'data' directory
checkRd: (-1) run_shinytitle_example.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) run_shinytitle_example.Rd:19: 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
checkRd: (-1) shutterplot.Rd:59: Lost braces; missing escapes or markup?
    59 | \item{las}{numeric in {0,1,2,3}; the style of axis labels.'
       |                       ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) drr.Rd:36: Lost braces; missing escapes or markup?
    36 |   \code{drr} {is Rosin - Rammler probability density function}\cr
       |              ^
checkRd: (-1) drr.Rd:37: Lost braces; missing escapes or markup?
    37 |   \code{urr} {is Rosin - Rammler cumulative distribution function (CDF) representing undersize mass fraction}\cr
       |              ^
checkRd: (-1) drr.Rd:38: Lost braces
    38 |   \code{orr} {is Rosin - Rammler complementary CDF representing oversize mass fraction ie. relative remainder on the sieve with the mesh size \code{x}}\cr
       |              ^
Specified C++11: please drop specification unless essential
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    extdata   1.0Mb
    help      1.7Mb
installed size is 13.1Mb
  sub-directories of 1Mb or more:
    R         1.1Mb
    extdata   9.8Mb
    libs      1.1Mb
checkRd: (-1) add_k_mer_state.Rd:33: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) add_k_mer_state.Rd:34: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) add_k_mer_state.Rd:35: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) add_k_mer_state.Rd:36: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) duration_viterbi.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) duration_viterbi.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) duration_viterbi.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) duration_viterbi.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/SIGN.Rcheck/00install.out' for details.
'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) sig.Rd:35: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sig.Rd:36: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sig_report.Rd:41: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sig_report.Rd:42: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sig_report.Rd:43: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sig_report.Rd:44: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sig_report.Rd:45-46: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sig_report.Rd:47: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sig_report.Rd:48: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sig_report.Rd:49-50: Lost braces in \itemize; \value handles \item{}{} directly
Error(s) in re-building vignettes:
--- re-building 'sigugr.Rmd' using rmarkdown

Quitting from sigugr.Rmd:135-139 [clip]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! OGRCreateCoordinateTransformation(): transformation not available
---
Backtrace:
    ▆
 1. └─sigugr::clip_raster(mdt, bbox, keep_crs = FALSE)
 2.   ├─sf::st_transform(polygon_bbox, terra::crs(raster))
 3.   └─sf:::st_transform.sf(polygon_bbox, terra::crs(raster))
 4.     ├─sf::st_transform(st_geometry(x), crs, ...)
 5.     └─sf:::st_transform.sfc(st_geometry(x), crs, ...)
 6.       ├─sf::st_sfc(...)
 7.       ├─base::structure(...)
 8.       └─sf:::CPL_transform(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'sigugr.Rmd' failed with diagnostics:
OGRCreateCoordinateTransformation(): transformation not available
--- failed re-building 'sigugr.Rmd'

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

Error: Vignette re-building failed.
Execution halted
checkRd: (-1) siland.Rd:64: Lost braces; missing escapes or markup?
    64 | \item x_{l,i}, local variable l,
       |         ^
checkRd: (-1) siland.Rd:70: Lost braces; missing escapes or markup?
    70 | \item d_{r,i} the distance between the center of pixel r and the observation at site i.
       |         ^
checkRd: (-1) inlandwaters.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) inlandwaters.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) inlandwaters.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) inlandwaters.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) inlandwaters.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) inlandwaters.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sim_Y_Binary_X.Rd:51: Lost braces
    51 |     \item \code{dist = "binomial"} is drawn from eqn{Bin(XB, XB(1-XB))}
       |                                                     ^
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
'LazyData' is specified without a 'data' directory
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    doc   6.5Mb
installed size is 15.1Mb
  sub-directories of 1Mb or more:
    extdata  13.0Mb
    libs      1.5Mb
Running 'ex_cvx.R' [90s]
  Running 'fastmerge-ex.R' [7s]
  Running 'smooth.pen_agcv.R' [3s]
Running the tests in 'tests/smooth.pen_agcv.R' failed.
Complete output:
  > library(simest)
  > 
  > ## Test smooth.pen.reg(*, agcv=TRUE) ---------------
  > 
  > ## -- Using a subset of R's sunspots data  ------
  > osV <- abbreviate(gsub("[^[:alnum:]]", '', sub("\\(.*", '', osVersion)), 12)
  > 
  > if(!dev.interactive(TRUE)) pdf(paste0("smooth.pen_sunsp__", osV, ".pdf"), width = 9, height=5)
  > 
  > str(ssp <- window(sunspot.m2014, start = 1900))
  Error: object 'sunspot.m2014' not found
  Execution halted
checkRd: (-1) create_modelDF.Rd:25-38: Lost braces
    25 | convert_xlsx_to_csv<-function(xlsx_file){
       |                                         ^
checkRd: (-1) create_modelDF.Rd:33-36: Lost braces
    33 |   for (i in Sheetnames) {
       |                         ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) internal.statistics.one.lm.Rd:18: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) internal.statistics.one.lm.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simstudy.logistic.Rd:64: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simstudy.logistic.Rd:65: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simstudy.logistic.Rd:66: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simstudy.logistic.Rd:67: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simstudy.prop.Rd:51: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simstudy.prop.Rd:52: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simstudy.prop.Rd:53: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simstudy.prop2.Rd:66: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simstudy.prop2.Rd:67: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simstudy.prop2.Rd:68: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simstudy.t.Rd:51: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simstudy.t.Rd:52: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simstudy.t.Rd:53: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simstudy.t2.Rd:72: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simstudy.t2.Rd:73: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simstudy.t2.Rd:74: Lost braces in \itemize; \value handles \item{}{} directly
GNU make is a SystemRequirements.
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    simpleCache [0.0.1]
'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
Package suggested but not available for checking: 'OpenMx'
Specified C++14: please drop specification unless essential
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Version (Date)
'LazyData' is specified without a 'data' directory
checkRd: (-1) make_one_dataset.Rd:67: Lost braces; missing escapes or markup?
    67 |  \code{within.SD} to be extremely small (e.g., $1 * 10^{-7}$) and all corresponding correlations in matrix
       |                                                        ^
checkRd: (-1) add_bold.Rd:15: Lost braces; missing escapes or markup?
    15 | For example, in latex it would take "2" and output "{\\bf 2}"; in html
       |                                                     ^
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    doc   6.9Mb
checkRd: (-1) sim.bdh.age.Rd:66: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sim.bdh.age.Rd:67: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sim.bdh.age.Rd:68: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sim.bdh.age.Rd:69: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sim.bdh.age.Rd:70: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sim.bdh.taxa.gsa.Rd:69: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sim.bdh.taxa.gsa.Rd:70: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sim.bdh.taxa.gsa.Rd:71: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sim.bdh.taxa.gsa.Rd:72: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sim.bdh.taxa.gsa.Rd:73: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sim.bdh.taxa.ssa.Rd:66: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sim.bdh.taxa.ssa.Rd:67: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sim.bdh.taxa.ssa.Rd:68: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sim.bdh.taxa.ssa.Rd:69: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sim.bdh.taxa.ssa.Rd:70: Lost braces in \itemize; meant \describe ?
Problems with news in 'NEWS.md':
No news entries found.
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    R      2.3Mb
    data   4.8Mb
    libs   1.7Mb
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) rawCCD.Rd:20: Lost braces; missing escapes or markup?
    20 |   \item{distr.type}{school district type (constructed for illustration purposes; (values={"A", "B", "C", "D"})).}
       |                                                                                          ^
checkRd: (-1) selectMatch.Rd:61: Lost braces; missing escapes or markup?
    61 | \item{replacementUnitsFilename}{character; csv filename for saving {unit:replacement} directory when writeOut == TRUE; default = "replacementUnits.csv"}
       |                                                                    ^
checkRd: (-1) selectMatch.Rd:63: Lost braces; missing escapes or markup?
    63 | \item{subUnitTableFilename}{character; csv filename for saving {unit:replacement} directory when writeOut == TRUE; default = "subUnitTable.csv"}
       |                                                                ^
checkRd: (-1) selectMatch.Rd:66: Lost braces; missing escapes or markup?
    66 | list with: 1) table of the form: {selected unit i: (unit i replacements)}, 2) table of the form: {potential unit i:(unit i sub-units)}, 3) balance diagnostics.
       |                                  ^
checkRd: (-1) selectMatch.Rd:66: Lost braces; missing escapes or markup?
    66 | list with: 1) table of the form: {selected unit i: (unit i replacements)}, 2) table of the form: {potential unit i:(unit i sub-units)}, 3) balance diagnostics.
       |                                                                                                  ^
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
checkRd: (-1) ss.cc.Rd:44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ss.ci.Rd:26: Lost braces
    26 | \item{alpha}{The eqn{\\alpha} error used to compute the \eqn{100*(1-\\alpha)\%} confidence interval}
       |                     ^
checkRd: (-1) ss.rr.Rd:84: Lost braces; missing escapes or markup?
    84 | $MS_{factor}/MS_{interaction}$, e.g. in appendix A of AIAG MSA manual, 
       |     ^
checkRd: (-1) ss.rr.Rd:84: Lost braces; missing escapes or markup?
    84 | $MS_{factor}/MS_{interaction}$, e.g. in appendix A of AIAG MSA manual, 
       |                 ^
checkRd: (-1) ss.rr.Rd:87: Lost braces; missing escapes or markup?
    87 | F test is performed as $MS_{factor}/MS_{equipment}$, i.e., repeatability.
       |                            ^
checkRd: (-1) ss.rr.Rd:87: Lost braces; missing escapes or markup?
    87 | F test is performed as $MS_{factor}/MS_{equipment}$, i.e., repeatability.
       |                                        ^
Package which this enhances but not available for checking: 'kmndirs'
Running 'testthat.r' [11s]
Running the tests in 'tests/testthat.r' failed.
Complete output:
  > # Run all unit tests
  > 
  > # This is a wrapper around all the tests specified
  > # in the tests/testthat directory. These tests are visible
  > # to users and serve as small examples as well.
  > testthat::test_check("skytrackr")
  Loading required package: skytrackr
  
  Attaching package: 'skytrackr'
  
  The following object is masked from 'package:datasets':
  
      rivers
  
  Saving _problems/test_skytrackr-10.R
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 0 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_skytrackr.R:6:1'): (code run outside of `test_that()`) ─────────
  Error: [rast] empty srs
  Backtrace:
      ▆
   1. └─skytrackr::stk_mask(bbox = bbox, buffer = 150, resolution = 0.5) at test_skytrackr.R:6:1
   2.   ├─terra::rast(...)
   3.   └─terra::rast(...)
   4.     └─terra (local) .local(x = x, ...)
   5.       └─terra:::new_rast(...)
   6.         └─terra:::messages(r, "rast")
   7.           └─terra:::error(f, x@pntr$getError())
  
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 0 ]
  Error:
  ! Test failures.
  Execution halted
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   5.1Mb
checkRd: (-1) outliers.hdts.Rd:44: Lost braces; missing escapes or markup?
    44 |   \item I.cov.rob - The matrix (V'GnV)^{-1} used to compute the statistics to detect the idiosyncratic outliers.
       |                                        ^
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
    libs   1.1Mb
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   4.4Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc   4.5Mb
checkRd: (-1) fit_slim.Rd:24: Lost braces; missing escapes or markup?
    24 | sum(x' V^{-1} (y - x beta)) = 0 as the covariance V tends from V[, , 1] +
       |          ^
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) slp-package.Rd:38: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'gurobi'
GNU make is a SystemRequirements.
checkRd: (-1) cities_lon_lat.Rd:6: Lost braces
     6 | A subset of world.cities{maps}. Extracted in order to shink number of dependencies. 
       |                         ^
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building 'Converting_VCF_and_PLINK_formats.Rmd' using rmarkdown
File figure/data_transformation_example_plot-1.png not found in resource path
Error: processing vignette 'Converting_VCF_and_PLINK_formats.Rmd' failed with diagnostics:
pandoc document conversion failed with error 99
--- failed re-building 'Converting_VCF_and_PLINK_formats.Rmd'

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

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

SUMMARY: processing the following files failed:
  'Converting_VCF_and_PLINK_formats.Rmd' 'aDNA_smartpca_analysis.Rmd'
  'mallard_smartpca_analysis.Rmd'

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
checkRd: (-1) customerRetentionDemographics.Rd:10: Escaped LaTeX specials: \$
checkRd: (-1) customerRetentionDemographics.Rd:11: Escaped LaTeX specials: \$ \$
checkRd: (-1) customerRetentionDemographics.Rd:12: Escaped LaTeX specials: \$ \$
checkRd: (-1) customerRetentionDemographics.Rd:13: Escaped LaTeX specials: \$ \$
checkRd: (-1) customerRetentionDemographics.Rd:14: Escaped LaTeX specials: \$ \$
checkRd: (-1) customerRetentionDemographics.Rd:15: Escaped LaTeX specials: \$
checkRd: (-1) trlong.Rd:17: Lost braces
    17 |     \item{\code{resp}}{a factor indicating the transport mode choice, and \code{B} denotes taking the bus, code{D} denotes driving one's own vehicle, \code{F} denotes getting a ride with a friend, \code{O} denotes other, and \code{W} denotes walking}
       |                                                                                                                ^
checkRd: (-1) smdocker_log.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) smdocker_log.Rd:35-37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) smdocker_log.Rd:38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) smdocker_log.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) smdocker_log.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) smdocker_log.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) smdocker_log.Rd:19: Lost braces in \itemize; meant \describe ?
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
GNU make is a SystemRequirements.
checkRd: (-1) SimModel1.Rd:21: Lost braces; missing escapes or markup?
    21 | \item{beta}{the \eqn{\beta} matrix, iqx+ip*ik, y_{1,t-1},y_{1,t-2},...,y_{2,t-1},y_{2,t-2},...}
       |                                                  ^
checkRd: (-1) SimModel1.Rd:21: Lost braces; missing escapes or markup?
    21 | \item{beta}{the \eqn{\beta} matrix, iqx+ip*ik, y_{1,t-1},y_{1,t-2},...,y_{2,t-1},y_{2,t-2},...}
       |                                                            ^
checkRd: (-1) SimModel1.Rd:21: Lost braces; missing escapes or markup?
    21 | \item{beta}{the \eqn{\beta} matrix, iqx+ip*ik, y_{1,t-1},y_{1,t-2},...,y_{2,t-1},y_{2,t-2},...}
       |                                                                          ^
checkRd: (-1) SimModel1.Rd:21: Lost braces; missing escapes or markup?
    21 | \item{beta}{the \eqn{\beta} matrix, iqx+ip*ik, y_{1,t-1},y_{1,t-2},...,y_{2,t-1},y_{2,t-2},...}
       |                                                                                    ^
checkRd: (-1) SimModel2.Rd:19: Lost braces; missing escapes or markup?
    19 | \item{beta_0}{the initial beta, iqx+ip*ik, y_{1,t-1},y_{1,t-2},...,y_{2,t-1},y_{2,t-2},....}
       |                                              ^
checkRd: (-1) SimModel2.Rd:19: Lost braces; missing escapes or markup?
    19 | \item{beta_0}{the initial beta, iqx+ip*ik, y_{1,t-1},y_{1,t-2},...,y_{2,t-1},y_{2,t-2},....}
       |                                                        ^
checkRd: (-1) SimModel2.Rd:19: Lost braces; missing escapes or markup?
    19 | \item{beta_0}{the initial beta, iqx+ip*ik, y_{1,t-1},y_{1,t-2},...,y_{2,t-1},y_{2,t-2},....}
       |                                                                      ^
checkRd: (-1) SimModel2.Rd:19: Lost braces; missing escapes or markup?
    19 | \item{beta_0}{the initial beta, iqx+ip*ik, y_{1,t-1},y_{1,t-2},...,y_{2,t-1},y_{2,t-2},....}
       |                                                                                ^
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   3.2Mb
    libs   1.0Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
checkRd: (-1) SMMA.Rd:115: Lost braces
   115 |  is the empirical explained variance from \cite{Meinshausen and B{u}hlmann, 2015}.  See \cite{Lund et al., 2020} for more details and references.
       |                                                                  ^
checkRd: (-1) SMMA.Rd:170: Lost braces
   170 | Meinshausen, N and P. B{u}hlmann (2015). Maximin effects in inhomogeneous large-scale data.
       |                        ^
Specified C++11: please drop specification unless essential
checkRd: (-1) estimMk.Rd:44: Lost braces; missing escapes or markup?
    44 | estimMk returns the transition probability matrix of size (S^{k})xS (with S = length(E)) 
       |                                                              ^
checkRd: (-1) getGlobalOptimum.Rd:16: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) getGlobalOptimum.Rd:17: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) getGlobalOptimum.Rd:18: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) getLocalOptimum.Rd:16: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) getLocalOptimum.Rd:17: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) getLocalOptimum.Rd:18: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) smoof_function.Rd:10: Lost braces
    10 | or code{smoof_multi_objective_function}. Both single- and multi-objective functions share the following attributes.
       |        ^
Package suggested but not available for checking: 'doMC'
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    doc    3.5Mb
    libs   1.7Mb
Problems with news in 'NEWS.md':
No news entries found.
checkRd: (-1) SnakesAndLaddersGame.Rd:25: Lost braces; missing escapes or markup?
    25 | {Hector Haffenden} {haffendenh@cardiff.ac.uk}
       |                    ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) sk_GLS.Rd:34: Lost braces; missing escapes or markup?
    34 | The GLS solution is: b = ( X^T V^{-1} X )^{-1} X^T V^{-1} z,
       |                                  ^
checkRd: (-1) sk_GLS.Rd:34: Lost braces; missing escapes or markup?
    34 | The GLS solution is: b = ( X^T V^{-1} X )^{-1} X^T V^{-1} z,
       |                                           ^
checkRd: (-1) sk_GLS.Rd:34: Lost braces; missing escapes or markup?
    34 | The GLS solution is: b = ( X^T V^{-1} X )^{-1} X^T V^{-1} z,
       |                                                      ^
checkRd: (-1) sk_GLS.Rd:40: Lost braces; missing escapes or markup?
    40 | Operations with V^{-1} are computed using the factorization \code{fac} (see \code{sk_var}), or
       |                   ^
checkRd: (-1) sk_LL.Rd:37: Lost braces; missing escapes or markup?
    37 | \code{quad_form} is z^T V^{-1} z, for the observed response vector z, which is constructed
       |                           ^
checkRd: (-1) sk_var.Rd:41: Lost braces; missing escapes or markup?
    41 | returns the quadratic form X^T V^{-1} X.
       |                                  ^
checkRd: (-1) sk_var.Rd:33: Lost braces; missing escapes or markup?
    33 | either matrix \code{V}, or X^T V^{-1} X, or a factorization ('chol' or 'eigen')
       |                                  ^
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    demo-geotiff   1.3Mb
    doc            3.2Mb
Running examples in 'snic-Ex.R' failed
The error most likely occurred in:

> ### Name: seeds_api
> ### Title: Convert seed coordinates between raster index, map, and WGS84
> ###   systems
> ### Aliases: seeds_api as_seeds_rc as_seeds_xy as_seeds_wgs84
> 
> ### ** Examples
> 
> if (requireNamespace("terra", quietly = TRUE)) {
+     # Load a test Sentinel-2 band
+     s2_file <- system.file(
+         "demo-geotiff/S2_20LMR_B04_20220630.tif",
+         package = "snic"
+     )
+     s2_rast <- terra::rast(s2_file)
+ 
+     # Create some test coordinates in pixel space
+     seeds_rc <- data.frame(r = c(10, 20, 30), c = c(15, 25, 35))
+ 
+     # Convert to map coordinates (x,y)
+     seeds_xy <- as_seeds_xy(seeds_rc, s2_rast)
+ 
+     # Convert to geographic coordinates (lat,lon)
+     seeds_wgs84 <- as_seeds_wgs84(seeds_rc, s2_rast)
+ }
Warning: PROJ: proj_create_from_database: Cannot find proj.db (GDAL error 1)
Error: [project] output crs is not valid
Execution halted
Error(s) in re-building vignettes:
--- re-building 'snic-array-pipeline.Rmd' using rmarkdown
--- finished re-building 'snic-array-pipeline.Rmd'

--- re-building 'snic-spatraster-pipeline.Rmd' using rmarkdown

Quitting from snic-spatraster-pipeline.Rmd:70-74 [seeds]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! [project] output crs is not valid
---
Backtrace:
    ▆
 1. └─snic::snic_grid(s2, type = "rectangular", spacing = 24, padding = 2)
 2.   └─snic:::.rc_to_wgs84(x, seeds)
 3.     ├─snic:::.xy_to_wgs84(x, seeds_xy)
 4.     └─snic:::.xy_to_wgs84.SpatRaster(x, seeds_xy)
 5.       ├─terra::project(v, "EPSG:4326")
 6.       └─terra::project(v, "EPSG:4326")
 7.         └─terra (local) .local(x, ...)
 8.           └─terra:::messages(x, "project")
 9.             └─terra:::error(f, x@pntr$getError())
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'snic-spatraster-pipeline.Rmd' failed with diagnostics:
[project] output crs is not valid
--- failed re-building 'snic-spatraster-pipeline.Rmd'

SUMMARY: processing the following file failed:
  'snic-spatraster-pipeline.Rmd'

Error: Vignette re-building failed.
Execution halted
Specified C++11: please drop specification unless essential
checkRd: (-1) knockoffGenotypes.Rd:32: Lost braces; missing escapes or markup?
    32 | This function efficiently constructs group-knockoffs of {0,1,2} variables distributed
       |                                                         ^
checkRd: (-1) knockoffGenotypes.Rd:11: Lost braces; missing escapes or markup?
    11 | \item{X}{a {0,1,2} matrix of size n-by-p containing the original variables.}
       |            ^
checkRd: (-1) knockoffGenotypes.Rd:29: Lost braces; missing escapes or markup?
    29 | A {0,1,2} matrix of size n-by-p containing the knockoff variables.
       |   ^
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc   4.2Mb
checkRd: (-1) plot.selm.Rd:101: Lost braces
   101 | data. Default value for code{which} is \code{2:4} if \code{p>1}, otherwise
       |                             ^
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'cmdstanr'
checkRd: (-1) preg2.Rd:8: Lost braces
     8 | An object of class \\code{tbl_df} (inherits from \\code{tbl}, \\code{data.frame}) with 2 rows and 4 columns.
       |                          ^
checkRd: (-1) preg2.Rd:8: Lost braces
     8 | An object of class \\code{tbl_df} (inherits from \\code{tbl}, \\code{data.frame}) with 2 rows and 4 columns.
       |                                                        ^
checkRd: (-1) preg2.Rd:8: Lost braces
     8 | An object of class \\code{tbl_df} (inherits from \\code{tbl}, \\code{data.frame}) with 2 rows and 4 columns.
       |                                                                     ^
checkRd: (-1) s_soda_pred.Rd:8: Lost braces; missing escapes or markup?
     8 | S-SODA assumes within each slice the X vector follow multivariate normal distribution. This function predicts the response y by reverting the P(X | slice(y)) to P(slice(y) | X), and estimates the E(y|X) as sum_{h} E(y | slice(y)=h, X) P (slice(y)=h | X)
       |                                                                                                                                                                                                                   ^
checkRd: (-1) db_compact.Rd:41: Lost braces; missing escapes or markup?
    41 | database structure will be set to true. See GET /{db}. You can also obtain a list of
       |                                                  ^
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R     3.2Mb
    doc   1.1Mb
checkRd: (-1) llwrPTF.Rd:7: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) solr_mlt.Rd:70: Lost braces; missing escapes or markup?
    70 | TermVector DEFAULT_FIELD_NAMES = new String[] {"contents"}
       |                                               ^
checkRd: (-1) solve_pH_from_AT.Rd:83: Lost braces in \itemize; meant \describe ?
checkRd: (-1) solve_pH_from_AT.Rd:84: Lost braces in \itemize; meant \describe ?
checkRd: (-1) solve_pH_from_AT.Rd:85: Lost braces in \itemize; meant \describe ?
checkRd: (-1) solve_pH_from_AT.Rd:86: Lost braces in \itemize; meant \describe ?
checkRd: (-1) solve_pH_from_AT.Rd:87: Lost braces in \itemize; meant \describe ?
checkRd: (-1) solve_pH_from_AT.Rd:88: Lost braces in \itemize; meant \describe ?
checkRd: (-1) solve_pH_from_AT.Rd:89: Lost braces in \itemize; meant \describe ?
checkRd: (-1) solve_pH_from_AT.Rd:90: Lost braces in \itemize; meant \describe ?
checkRd: (-1) solve_pH_from_AT.Rd:91: Lost braces in \itemize; meant \describe ?
checkRd: (-1) solve_pH_from_AT.Rd:92: Lost braces in \itemize; meant \describe ?
checkRd: (-1) solve_pH_from_AT.Rd:93: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
checkRd: (-1) load_sorvi_data.Rd:23: Lost braces in \itemize; meant \describe ?
Package suggested but not available for checking: 'SciencesPo'
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   3.9Mb
    doc    1.0Mb
Package suggested but not available for checking: 'gridlayout'
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   4.7Mb
    libs   1.0Mb
'LazyData' is specified without a 'data' directory
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    extdata   6.0Mb
    libs      1.0Mb
installed size is 15.2Mb
  sub-directories of 1Mb or more:
    include  10.1Mb
    libs      5.1Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'NLMR'
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    R   5.1Mb
Package suggested but not available for checking: 'NLMR'
Running examples in 'SpaDES.tools-Ex.R' failed
The error most likely occurred in:

> ### Name: randomPolygons
> ### Title: Produce a 'SpatRaster' of random polygons
> ### Aliases: randomPolygons randomPolygon randomPolygon.default
> 
> ### ** Examples
> 
> origDTThreads <- data.table::setDTthreads(2L)
> origNcpus <- options(Ncpus = 2L)
> 
> set.seed(1234)
> Ras <- randomPolygons(numTypes = 5)
> if (interactive() ) {
+   terra::plot(Ras, col = c("yellow", "dark green", "blue", "dark red"))
+ }
> 
> # more complex patterning, with a range of patch sizes
> r <- terra::rast(terra::ext(0, 50, 0, 50), resolution = 1, vals = 0)
> a <- randomPolygons(numTypes = 400, r)
duplicate initial loci are provided
> a[a < 320] <- 0
> a[a >= 320] <- 1
> clumped <- terra::patches(a)
> if (interactive()) {
+   terra::plot(a)
+ }
> 
> # clean up
> data.table::setDTthreads(origDTThreads)
> options(Ncpus = origNcpus)
> 
> a1 <- terra::vect(cbind(-110, 59), crs = "epsg:4326")
Warning: PROJ: proj_create_from_database: Cannot find proj.db (GDAL error 1)
Warning: [crs<-] Cannot set SRS to vector: empty srs
> a2 <- randomPolygon(a1, area = 1e7)
Error: [project] input crs is not valid
Execution halted
'LazyData' is specified without a 'data' directory
Running 'testthat.R' [16s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(spaero)
  > 
  > test_check("spaero")
  Saving _problems/test-simulator-8.R
  [ FAIL 1 | WARN 4 | SKIP 7 | PASS 47 ]
  
  ══ Skipped tests (7) ═══════════════════════════════════════════════════════════
  • On CRAN (7): 'test-simulator.R:60:3', 'test-simulator.R:82:3',
    'test-simulator.R:157:3', 'test-simulator.R:190:3', 'test-stats.R:118:3',
    'test-stats.R:237:3', 'test-stats.R:304:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-simulator.R:6:3'): Argument checking works ─────────────────────
  <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-simulator.R:6:3
   2.   └─lifecycle::deprecate_stop("3.2.0", "with_mock()", "with_mocked_bindings()")
   3.     └─lifecycle:::deprecate_stop0(msg)
   4.       └─rlang::cnd_signal(...)
  
  [ FAIL 1 | WARN 4 | SKIP 7 | PASS 47 ]
  Error:
  ! Test failures.
  Execution halted
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    R      2.9Mb
    libs   1.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) sdf_unnest.Rd:20: Lost braces
    20 | \code{a1, a2, a3}, then code{sdf_explode(df, a)} will produce output with each record replicated
       |                             ^
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Specified C++11: please drop specification unless essential
checkRd: (-1) Coord.to.Pointers.Rd:54: Lost braces; missing escapes or markup?
    54 | \item{triangle=TRUE}{Input \code{rows} and {cols} represent lower
       |                                            ^
checkRd: (-1) Coord.to.Pointers.Rd:59: Lost braces; missing escapes or markup?
    59 | \item{triangle=FALSE}{Input \code{rows} and {cols} represent a full
       |                                             ^
checkRd: (-1) cholsolveAQinvAT.Rd:5: Lost braces; missing escapes or markup?
     5 | \title{Solve the equation X = AQ^{-1}t(A) under permutations}
       |                                  ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) mu_calc.Rd:32: Lost braces; missing escapes or markup?
    32 | mu_{d} | mu_{d} < mu_{d-1} and mu_{d} | mu_{d} > mu_{d-1} respecitively.
       |    ^
checkRd: (-1) mu_calc.Rd:32: Lost braces; missing escapes or markup?
    32 | mu_{d} | mu_{d} < mu_{d-1} and mu_{d} | mu_{d} > mu_{d-1} respecitively.
       |             ^
checkRd: (-1) mu_calc.Rd:32: Lost braces; missing escapes or markup?
    32 | mu_{d} | mu_{d} < mu_{d-1} and mu_{d} | mu_{d} > mu_{d-1} respecitively.
       |                      ^
checkRd: (-1) mu_calc.Rd:32: Lost braces; missing escapes or markup?
    32 | mu_{d} | mu_{d} < mu_{d-1} and mu_{d} | mu_{d} > mu_{d-1} respecitively.
       |                                   ^
checkRd: (-1) mu_calc.Rd:32: Lost braces; missing escapes or markup?
    32 | mu_{d} | mu_{d} < mu_{d-1} and mu_{d} | mu_{d} > mu_{d-1} respecitively.
       |                                            ^
checkRd: (-1) mu_calc.Rd:32: Lost braces; missing escapes or markup?
    32 | mu_{d} | mu_{d} < mu_{d-1} and mu_{d} | mu_{d} > mu_{d-1} respecitively.
       |                                                     ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) plot.sparsereg.Rd:22-23: Lost braces
    22 | \env{main1, main2, main3}{
       |                          ^
checkRd: (-1) plot.sparsereg.Rd:25-27: Lost braces
    25 | \env{xlabel}{
       |             ^
checkRd: (-1) plot.sparsereg.Rd:29-31: Lost braces
    29 | \env{plot.one}{
       |               ^
checkRd: (-1) summary.sparsereg.Rd:27-29: Lost braces
    27 | \env{interval}{
       |               ^
checkRd: (-1) summary.sparsereg.Rd:31-33: Lost braces
    31 | \env{ci}{
       |         ^
checkRd: (-1) summary.sparsereg.Rd:35-37: Lost braces
    35 | \env{order}{
       |            ^
checkRd: (-1) summary.sparsereg.Rd:39-41: Lost braces
    39 | \env{normal}{
       |             ^
checkRd: (-1) summary.sparsereg.Rd:43-45: Lost braces
    43 | \env{select}{
       |             ^
checkRd: (-1) summary.sparsereg.Rd:47-48: Lost braces
    47 | \env{printit}{
       |              ^
checkRd: (-1) summary.sparsereg.Rd:50-52: Lost braces
    50 | \env{stage}{
       |            ^
installed size is 13.4Mb
  sub-directories of 1Mb or more:
    libs  12.6Mb
'LazyData' is specified without a 'data' directory
Running examples in 'spaths-Ex.R' failed
The error most likely occurred in:

> ### Name: max_edges
> ### Title: Maximum number of edges in your grid
> ### Aliases: max_edges
> 
> ### ** Examples
> 
> # Generate example data
> set.seed(2L)
> input_grid <- terra::rast(crs = "epsg:4326", resolution = 2, vals = sample(c(1L, NA_integer_),
+   16200L, TRUE, c(0.8, 0.2)))
Warning: PROJ: proj_create_from_database: Cannot find proj.db (GDAL error 1)
Error: [rast] empty srs
Execution halted
installed size is 14.5Mb
  sub-directories of 1Mb or more:
    libs  13.6Mb
checkRd: (-1) distSG.Rd:40: Lost braces; missing escapes or markup?
    40 |   matrix and weight matrix (plus a matrix with {eID} identifiers
       |                                                ^
Specified C++11: please drop specification unless essential
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   2.5Mb
    help   1.4Mb
    libs   1.0Mb
Running examples in 'spatialrisk-Ex.R' failed
The error most likely occurred in:

> ### Name: plot.concentration
> ### Title: Automatically create a plot for objects obtained from
> ###   'find_highest_concentration()'
> ### Aliases: plot.concentration
> 
> ### ** Examples
> 
> x <- find_highest_concentration(Groningen, "amount")
Warning: PROJ: proj_create_from_database: Cannot find proj.db (GDAL error 1)
Warning: [vect] Cannot set SRS to vector: empty srs
> plot(x, "concentration")
> plot(x, "rasterized")
Error in st_transform.sfc(sf::st_as_sfc(sf::st_bbox(x)), crs = 4326) : 
  cannot transform sfc object with missing crs
Calls: plot ... leaflet_stars -> createExtent -> <Anonymous> -> st_transform.sfc
Execution halted
GNU make is a SystemRequirements.
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.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   4.7Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'spDataLarge'
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
checkRd: (-1) findRef.Rd:39: Lost braces
    39 | Vu TN, Valkenborg D, Smets K, Verwaest KA, Dommisse R, Lemi\`{e}re F, Verschoren A, Goethals B, Laukens K. (2011) An integrated workflow for robust alignment and simplified quantitative analysis of NMR spectrometry data. BMC Bioinformatics. 2011 Oct 20;12:405.
       |                                                              ^
checkRd: (-1) hClustAlign.Rd:70: Lost braces
    70 | Vu TN, Valkenborg D, Smets K, Verwaest KA, Dommisse R, Lemi\`{e}re F, Verschoren A, Goethals B, Laukens K. (2011) An integrated workflow for robust alignment and simplified quantitative analysis of NMR spectrometry data. BMC Bioinformatics. 2011 Oct 20;12:405.
       |                                                              ^
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Roadmap of specklestar package
'LazyData' is specified without a 'data' directory
checkRd: (-1) FitAkdParameters.Rd:23: Lost braces; missing escapes or markup?
    23 |       p(y|ens) = 1 / K * sum {dnorm(y, z.i, s)} \cr
       |                              ^
checkRd: (-1) image.plot.Rd:78: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) speech_recompiler.Rd:25: Lost braces; missing escapes or markup?
    25 | The default compilation is that of \ code {speech_build (., compiler = TRUE}).
       |                                           ^
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) cylinder.counts.Rd:61-62: Lost braces
    61 | nucleotide, so that \code{a.c} represents the set {\code{aac}, \code{acc}, 
       |                                                   ^
Package required but not available: 'semPlot'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
checkRd: (-1) adaptIntegrateSpherePolar.Rd:14: Lost braces
    14 | code{adaptIntegrateBallPolar()} will likely miss these abrupt changes and give
       |     ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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checkRd: (-1) speedtestdata.Rd:23: Lost braces in \itemize; meant \describe ?
Specified C++11: please drop specification unless essential
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Feature Changes
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    data   1.7Mb
    doc    1.5Mb
installed size is  6.8Mb
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    extdata   2.6Mb
    libs      1.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    doc   7.6Mb
Specified C++11: please drop specification unless essential
Package required but not available: 'MBESS'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
installed size is  6.8Mb
  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
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
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   248 | and code{port} arguments of sqldf.
       |         ^
'LazyData' is specified without a 'data' directory
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    55 |     \code{tol}{ - a small, positive scalar that determines when iterations 
       |               ^
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    60 |     \code{maxiter}{ - an integer denoting the maximum limit on the number of 
       |                   ^
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    63 |     \code{trace}{ - a logical variable denoting whether some of the intermediate 
       |                 ^
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    67 |     \code{intermed}}{ - a logical variable denoting whether the intermediate 
       |                     ^
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   134 |       along with the corresponding log-likelihood value.  When the code{objfn} is not specified it will return the fixed-point residual instead of the objective function values. 
       |                                                                        ^
installed size is  8.7Mb
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installed size is  5.4Mb
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checkRd: (-1) squidR.Rd:83: Lost braces; missing escapes or markup?
    83 |   \item \code{X1_sto_shared} (default \code{TRUE}): {logical}; if \code{TRUE}, the stochastic environmental effect included in the environmental effect x1 will be shared between individuals. If \code{FALSE}, each individual will experience a different stochastic environmental effect x1 (i.e. a new stochastic environmental effect is generated for each individual).
       |                                                     ^
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checkRd: (-1) plot.SRCS.Rd:55: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) plot.SRCS.Rd:61-62: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.SRCS.Rd:63-64: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.SRCS.Rd:65-66: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.SRCS.Rd:72-73: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.SRCS.Rd:74-75: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.SRCS.Rd:76: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.SRCS.Rd:77-79: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) plot.SRCS.Rd:82: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.SRCS.Rd:87-88: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.SRCS.Rd:89: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.SRCS.Rd:143-144: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.SRCS.Rd:145: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.SRCS.Rd:146-148: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.SRCS.Rd:149: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
Running 'testthat.R' [11s]
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(srppp)
  Loading required package: dm
  
  Attaching package: 'dm'
  
  The following object is masked from 'package:stats':
  
      filter
  
  > 
  > test_check("srppp")
checkRd: (-1) ssaBSS-package.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ssaBSS-package.Rd:23: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) ssaBSS-package.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ssaBSS-package.Rd:26: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
installed size is 15.4Mb
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'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
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installed size is  6.8Mb
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GNU make is a SystemRequirements.
checkRd: (-1) new.distance.Rd:30: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) new.distance.Rd:33-34: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) sensitivity.plot.Rd:34-35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sensitivity.plot.Rd:36-37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sensitivity.plot.Rd:38-40: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) SRanalysis.Rd:100: Lost braces
   100 |   P. B{\"u}hlmann (2019). Stabilizing Variable Selection and
       |       ^
checkRd: (-1) StabilizedRegression.Rd:109: Lost braces
   109 |   P. B{\"u}hlmann (2019). Stabilizing Variable Selection and
       |       ^
Problems with news in 'NEWS.md':
No news entries found.
checkRd: (-1) stabsel_parameters.Rd:42: Lost braces
    42 |     always use code{"none"}.}
       |                    ^
checkRd: (-1) stabsel_stabsel.Rd:25: Lost braces
    25 |     always use code{"none"}.}
       |                    ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) stackExample.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) stackExample.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) stamppFst.Rd:20: Lost braces
    20 | \code{Fsts}{a matrix of pairwise Fst values between populations}
       |            ^
checkRd: (-1) stamppFst.Rd:21: Lost braces
    21 | \code{Pvalues}{a matrix of p-values for each of the pairwise Fst values containined in the 'Fsts' matrix}
       |               ^
checkRd: (-1) stamppFst.Rd:22: Lost braces
    22 | \code{Bootstraps}{a dataframe of each Fst value generated during Bootstrapping and the associated confidence intervals}
       |                  ^
checkRd: (-1) standardize.Rd:94: Lost braces; missing escapes or markup?
    94 | take on values {-0.5, 0, 0.5} rather than {-1, 0, 1}, the standard deviation
       |                ^
checkRd: (-1) standardize.Rd:94: Lost braces; missing escapes or markup?
    94 | take on values {-0.5, 0, 0.5} rather than {-1, 0, 1}, the standard deviation
       |                                           ^
installed size is 14.1Mb
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    include  11.3Mb
GNU make is a SystemRequirements.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
GNU make is a SystemRequirements.
checkRd: (-1) get_fields.Rd:27: Lost braces
    27 | codes, the function will return a warning by default, suggesting setting \code{convert_field_names} to code{TRUE}.
       |                                                                                                            ^
checkRd: (-1) identify_form_fields.Rd:34: Lost braces
    34 | codes, the function will return a warning by default, suggesting setting \code{convert_field_names} to code{TRUE}.
       |                                                                                                            ^
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   229 |   \item{report}{a character string containing only elements of {\code{"v"}, \code{"c"}, \code{"s"},\code{"t"}, \code{"p"}, \code{"*"}} that determines whether, and in which order, variable names (\code{"v"}), coefficients (\code{"c"}), standard errors/confidence intervals (\code{"s"}), test statistics (\code{"t"}) and p-values (\code{"p"}) should be reported in regression tables. If one of the aforementioned letters is followed by an asterisk (\code{"*"}), significance stars will be reported next to the corresponding statistic.}
       |                                                                ^
checkRd: (-1) stargazer.Rd:246: Lost braces
   246 |   \item{table.placement}{a character string containing only elements of {\code{"h"}, \code{"t"},\code{"b"}, \code{"p"}, \code{"!"}, \code{"H"}} that determines the table placement in its LaTeX floating environment.}
       |                                                                         ^
Package suggested but not available for checking: 'starsdata'
installed size is  6.8Mb
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    nc    1.7Mb
checkRd: (-1) multiCUMSUM.Rd:33: Escaped LaTeX specials: \&
checkRd: (-1) AutoPollution.Rd:16: Lost braces
    16 |     \code{Side} \tab {Side of vehicle: code{1}=right or \code{2}=left}\cr
       |                                            ^
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
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Package suggested but not available for checking: 'asreml'
Package suggested but not available for checking: 'asreml'
Package suggested but not available for checking: 'asreml'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following possibly unsafe calls:
File 'statnet.common/R/control.utilities.R':
  unlockBinding("snctrl", environment(snctrl))
  unlockBinding("snctrl", environment(update_my_snctrl))
Package suggested but not available for checking: 'networksis'
unable to reach CRAN

It looks like this package (or a package it requires) has a startup
message which cannot be suppressed: see ?packageStartupMessage.
'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
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    help   1.6Mb
checkRd: (-1) sample2indp.pow.Rd:48: Lost braces
    48 | Pooled standard deviation= \code{sp} = sqrt{((n1 - 1) sigma1^2 +(n2 - 1) sigma2^2) / (n1 + n2 - 2)}
       |                                            ^
checkRd: (-1) tuneParam.Rd:28: Lost braces; missing escapes or markup?
    28 | It supports the BFGS optimization method ('QN') from the optim {stats} function, the Hooke-Jeeves derivative-free
       |                                                                ^
checkRd: (-1) tuneParamCL2.Rd:28: Lost braces; missing escapes or markup?
    28 | It supports the BFGS optimization method ('QN') from the optim {stats} function, the Hooke-Jeeves derivative-free
       |                                                                ^
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) landmarkMatrixToList.Rd:10: Lost braces
    10 |   \item{semilandmark.pattern}{a regular expression pattern passed to \code{sub()} for identifying and grouping curve points. The default is landmark names ending in one or more numbers. To disable grouping, set to code{''}.}
       |                                                                                                                                                                                                                           ^
checkRd: (-1) docker_config_collection.Rd:11: Lost braces; missing escapes or markup?
    11 | \Sexpr[results=rd,stage=render]{stevedore:::generate_help("config")}
       | ^
checkRd: (-1) docker_container.Rd:13: Lost braces
    13 | \Sexpr[results=rd,stage=render]{stevedore:::generate_help("docker_container")}
       | ^
checkRd: (-1) docker_image_collection.Rd:11: Lost braces
    11 | \Sexpr[results=rd,stage=render]{stevedore:::generate_help("image")}
       | ^
checkRd: (-1) docker_plugin_collection.Rd:11: Lost braces
    11 | \Sexpr[results=rd,stage=render]{stevedore:::generate_help("plugin")}
       | ^
checkRd: (-1) docker_service_collection.Rd:11: Lost braces
    11 | \Sexpr[results=rd,stage=render]{stevedore:::generate_help("service")}
       | ^
checkRd: (-1) docker_task.Rd:13: Lost braces
    13 | \Sexpr[results=rd,stage=render]{stevedore:::generate_help("docker_task")}
       | ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
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
Malformed Title field: should not end in a period.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/stoRy.Rcheck/00install.out' for details.
checkRd: (-1) powderymildew.Rd:14-16: Lost braces
    14 | \code{$demographic.coord}{
       |                          ^
checkRd: (-1) powderymildew.Rd:18-20: Lost braces
    18 | \code{$genetic.coord}{
       |                      ^
checkRd: (-1) powderymildew.Rd:22-24: Lost braces
    22 | \code{$demographic.measures}{
       |                             ^
checkRd: (-1) powderymildew.Rd:26-28: Lost braces
    26 | \code{$genetic.frequencies}{
       |                            ^
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'StrathE2E2examples'
checkRd: (-1) StrathE2E2-package.Rd:70: Lost braces; missing escapes or markup?
    70 | {Basic model operations:} \cr
       | ^
checkRd: (-1) StrathE2E2-package.Rd:79: Lost braces; missing escapes or markup?
    79 | {Parameter estimation:} \cr
       | ^
checkRd: (-1) StrathE2E2-package.Rd:88: Lost braces; missing escapes or markup?
    88 | {Sensitivity and Monte Carlo analyses:} \cr
       | ^
checkRd: (-1) StrathE2E2-package.Rd:98: Lost braces; missing escapes or markup?
    98 | {Compare model runs:} \cr
       | ^
checkRd: (-1) StrathE2E2-package.Rd:105: Lost braces; missing escapes or markup?
   105 | {Fishery yield analysis:} \cr
       | ^
checkRd: (-1) StrathE2E2-package.Rd:111: Lost braces; missing escapes or markup?
   111 | {Visualize model inputs:} \cr
       | ^
checkRd: (-1) StrathE2E2-package.Rd:117: Lost braces; missing escapes or markup?
   117 | {Visualize model outputs:} \cr
       | ^
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
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    doc   5.0Mb
'LazyData' is specified without a 'data' directory
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    libs  10.6Mb
Malformed Title field: should not end in a period.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is 35.4Mb
  sub-directories of 1Mb or more:
    libs  34.5Mb
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    doc    7.2Mb
    libs   1.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc       2.0Mb
    extdata   2.9Mb
efpFunctional: multiple local function definitions for 'plotProcess'
  with different formal arguments
mefp.efp: multiple local function definitions for 'computeEmpProc' with
  different formal arguments
Found the following significant warnings:
  functions.c:46:39: warning: ISO C forbids empty initializer braces before C2X [-Wpedantic]
  functions.c:51:28: warning: ISO C forbids empty initializer braces before C2X [-Wpedantic]
  functions.c:107:33: warning: ISO C forbids empty initializer braces before C2X [-Wpedantic]
  functions.c:108:33: warning: ISO C forbids empty initializer braces before C2X [-Wpedantic]
See 'd:/Rcompile/CRANpkg/local/4.4/structenforcement.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 13.3.0'
checkRd: (-1) cmss.Rd:21: Lost braces
    21 | \item{sim.fn}{Optional function to be used as similarity measure for accept/reject step. Default function is: |cor( bar{x}^{(r)}|,~ bar{x}_{target} ) |}
       |                                                                                                                        ^
checkRd: (-1) cmss.Rd:21: Lost braces; missing escapes or markup?
    21 | \item{sim.fn}{Optional function to be used as similarity measure for accept/reject step. Default function is: |cor( bar{x}^{(r)}|,~ bar{x}_{target} ) |}
       |                                                                                                                            ^
checkRd: (-1) cmss.Rd:21: Lost braces
    21 | \item{sim.fn}{Optional function to be used as similarity measure for accept/reject step. Default function is: |cor( bar{x}^{(r)}|,~ bar{x}_{target} ) |}
       |                                                                                                                                        ^
checkRd: (-1) cmss.Rd:21: Lost braces; missing escapes or markup?
    21 | \item{sim.fn}{Optional function to be used as similarity measure for accept/reject step. Default function is: |cor( bar{x}^{(r)}|,~ bar{x}_{target} ) |}
       |                                                                                                                                            ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) suggests.Rd:14: Lost braces; missing escapes or markup?
    14 | {suggests} aims to make that workflow as minimal and painless as possible,
       | ^
'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
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    data   1.8Mb
    doc    3.1Mb
    help   1.0Mb
Package suggested but not available for checking: 'MOFAdata'
installed size is  9.6Mb
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    extdata   9.3Mb
checkRd: (-1) sunburst.Rd:30: Lost braces; missing escapes or markup?
    30 | nested d3 JSON hierarchy with `{name:...,  children:[];}`.  \code{csvdata}
       |                                ^
checkRd: (-1) sunburst.Rd:88: Lost braces; missing escapes or markup?
    88 | \item{jsondata}{\code{deprecated} use data argument instead; data in nested d3 JSON hierarchy with `{name:...,  children:[];}`}
       |                                                                                                     ^
checkRd: (-1) sund2b.Rd:22: Lost braces; missing escapes or markup?
    22 | nested d3 JSON hierarchy with `{name:...,  children:[];}`.  \code{list}, \code{character},
       |                                ^
checkRd: (-1) BiclustSet-class.Rd:19: Lost braces
    19 |     \item{\code{Number}:}{code{"numeric"}, number of biclusters in the set}
       |                               ^
Package suggested but not available for checking: 'velocyto.R'
checkRd: (-1) plot.Rd:42: Lost braces; missing escapes or markup?
    42 |  \item{color.off}{color code; specifying the color for set(s) which are "{absent}" for an intersection.}
       |                                                                          ^
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  D:/RCompile/CRANpkg/lib/4.4/ClusterR/include/affinity_propagation.h:360:34: warning: overflow in conversion from 'double' to 'long long unsigned int' changes value from '+QNaN' to '0' [-Woverflow]
  D:/RCompile/CRANpkg/lib/4.4/ClusterR/include/affinity_propagation.h:448:30: warning: overflow in conversion from 'double' to 'long long unsigned int' changes value from '+QNaN' to '0' [-Woverflow]
See 'd:/Rcompile/CRANpkg/local/4.4/SuperpixelImageSegmentation.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 13.3.0'
* used C++ compiler: 'g++.exe (GCC) 13.3.0'
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) getFittedProbs.Rd:6-8: Lost braces
     6 | getFittedValues <- function(object) {
       |                                     ^
checkRd: (-1) getFittedProbs.Rd:14-16: Lost braces
    14 | getFittedValues <- function(object) {
       |                                     ^
Running examples in 'SurfaceTortoise-Ex.R' failed
The error most likely occurred in:

> ### Name: tortoise
> ### Title: tortoise
> ### Aliases: tortoise
> 
> ### ** Examples
> 
> #load packages
> require(terra)
Loading required package: terra
terra 1.8.86
> require(gstat)
Loading required package: gstat
> require(sf)
Loading required package: sf
Linking to GEOS 3.13.0, GDAL 3.10.1, PROJ 9.5.1; sf_use_s2() is TRUE
> #create an example raster dataset
> x<-rast(nrow=5, ncol=10, vals= sample(1:4, 50, replace=TRUE),crs=crs("EPSG:3857"))
Warning: PROJ: proj_create_from_database: Cannot find proj.db (GDAL error 1)
Error: [rast] empty srs
Execution halted
installed size is  5.4Mb
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    tinytest   4.1Mb
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    doc       1.5Mb
    extdata   4.0Mb
    shiny     3.1Mb
Package required but not available: 'MBESS'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    R     1.7Mb
    doc   2.2Mb
GNU make is a SystemRequirements.
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    doc    3.9Mb
    libs   2.6Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   2.9Mb
    doc    2.5Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc   4.7Mb
Package suggested but not available for checking: 'gurobi'
Packages suggested but not available for checking:
  'survHEinla', 'survHEhmc'
checkRd: (-1) tprob.Rd:138: Lost braces in \itemize; meant \describe ?
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    24 | \item{mpl_h0t}{MPL estimates of the baseline hazard for T, i.e. h_{0T}(x_i)}
       |                                                                   ^
checkRd: (-1) coxph_mpl_dc.Rd:25: Lost braces; missing escapes or markup?
    25 | \item{mpl_h0c}{MPL estimates of the baseline hazard for C, i.e. h_{0C}(x_i)}
       |                                                                   ^
checkRd: (-1) coxph_mpl_dc.Rd:26: Lost braces; missing escapes or markup?
    26 | \item{mpl_H0t}{MPL estimates of the baseline cumulative hazard for T, i.e. H_{0T}(x_i)}
       |                                                                              ^
checkRd: (-1) coxph_mpl_dc.Rd:27: Lost braces; missing escapes or markup?
    27 | \item{mpl_H0c}{MPL estimates of the baseline cumulative hazard for C, i.e. H_{0c}(x_i)}
       |                                                                              ^
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    28 | \item{mpl_S0t}{MPL estimates of the baseline survival for T, i.e. S_{0T}(x_i)}
       |                                                                     ^
checkRd: (-1) coxph_mpl_dc.Rd:29: Lost braces; missing escapes or markup?
    29 | \item{mpl_S0c}{MPL estimates of the baseline survival for C, i.e. S_{0C}(x_i)}
       |                                                                     ^
installed size is  9.4Mb
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    data   1.9Mb
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installed size is  6.0Mb
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checkRd: (-1) sf.Rd:66: Lost braces; missing escapes or markup?
    66 | A {data.table} which is stored as an attribute of
       |   ^
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
checkRd: (-1) coxDT.Rd:76: Lost braces; missing escapes or markup?
    76 | The estimation procedure here is performed using coxph {survival} and inserting these estimated
       |                                                        ^
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installed size is  5.6Mb
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checkRd: (-1) koInstall.Rd:24: Lost braces; missing escapes or markup?
    24 | set, svKomodo loads {svSocket}, starts the socket server listening to the
       |                     ^
checkRd: (-1) svKomodo-package.Rd:18: Lost braces; missing escapes or markup?
    18 | Komodo and (2) the present {svKomodo} R package that work hand in hand to
       |                            ^
checkRd: (-1) svKomodo-package.Rd:28: Lost braces; missing escapes or markup?
    28 | Nevertheless, the SciViews-K Komodo addin and the {svKomodo} R package
       |                                                   ^
checkRd: (-1) svKomodo-package.Rd:31: Lost braces; missing escapes or markup?
    31 | communication protocols developed in the {svSocket} and {svHttp} R packages.
       |                                          ^
checkRd: (-1) svKomodo-package.Rd:31: Lost braces; missing escapes or markup?
    31 | communication protocols developed in the {svSocket} and {svHttp} R packages.
       |                                                         ^
checkRd: (-1) svKomodo-package.Rd:37: Lost braces; missing escapes or markup?
    37 | Both SciViews-K and {svKomodo} should be considered archived items. I keep
       |                     ^
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    32 | \code{\link[survey:surveysummary]{survey::svymean()}} and related functions from the {survey}
       |                                                                                      ^
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installed size is  5.2Mb
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    data   4.8Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'swephRdata'
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Additional functions and data sets
    Amendments to functions
'LazyData' is specified without a 'data' directory
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checkRd: (-1) hyph.support.en.Rd:20: Lost braces in \itemize; meant \describe ?
Packages suggested but not available for checking: 'sylly.de', 'sylly.es'
checkRd: (-1) kRp.hyphen-methods.Rd:84: Lost braces in \itemize; meant \describe ?
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    18 |   \item{epsilon}{positive convergence tolerance \emph{e}; the iterations converge when |fit - fit_{old}|/|fit| < \emph{e}. Default is \emph{e=1e-04}.}
       |                                                                                                   ^
'LazyData' is specified without a 'data' directory
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Packages required but not available: 'OpenMx', 'metaSEM'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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    14 | \code{n} x 4 matrix of coordinates consisting of {lat or y, lon or x} pairs for each each site
       |                                                  ^
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checkRd: (-1) initial_estimates_example.Rd:12: Lost braces in \itemize; meant \describe ?
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    data   4.5Mb
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Package required but not available: 'MOTE'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
installed size is  5.6Mb
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checkRd: (-1) tabmulti.Rd:68: Lost braces
    68 | \\code{yvarlabels = list(race = "Race/ethnicity", age_yrs = "Age (years)")}.}
       |       ^
checkRd: (-1) tabmulti.svy.Rd:67: Lost braces
    67 | \\code{yvarlabels = list(race = "Race/ethnicity", age_yrs = "Age (years)")}.}
       |       ^
Running examples in 'tabs-Ex.R' failed
The error most likely occurred in:

> ### Name: explore
> ### Title: Leaflet map of present and paleo configurations for
> ###   biogeographic systems
> ### Aliases: explore
> 
> ### ** Examples
> 
> 
> # load data samples
> sporades <- sporades()
Warning: PROJ: proj_create_from_database: Cannot find proj.db (GDAL error 1)
Error: [rast] empty srs
Execution halted
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checkRd: (-1) parse_logs.Rd:38: Lost braces
    38 |  '{{ip ip_address}} [{{date access_date}}]...'.
       |   ^
checkRd: (-1) parse_logs.Rd:38: Lost braces
    38 |  '{{ip ip_address}} [{{date access_date}}]...'.
       |                      ^
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) tapnet-package.Rd:40: Escaped LaTeX specials: \&
checkRd: (-1) TAQ-functions.Rd:119: Lost braces
   119 | Brownlees, C. T., and Gallo, G. M. (2006). Financial Econometric Analysis at Ultra{--}High Frequency: Data Handling Concerns, \emph{Computational Statistics and Data Analysis} \bold{51}, 2232--2245.
       |                                                                                   ^
checkRd: (-1) TAQ-package.Rd:59: Lost braces
    59 | Brownlees, C. T., and Gallo, G. M. (2006). Financial Econometric Analysis at Ultra{--}High Frequency: Data Handling Concerns, \emph{Computational Statistics and Data Analysis} \bold{51}, 2232--2245.
       |                                                                                   ^
Running examples in 'targeted-Ex.R' failed
The error most likely occurred in:

> ### Name: learner_xgboost
> ### Title: Construct a learner
> ### Aliases: learner_xgboost
> 
> ### ** Examples
> 
> n  <- 1e3
> x1 <- rnorm(n, sd = 2)
> x2 <- rnorm(n)
> lp <- x2*x1 + cos(x1)
> yb <- rbinom(n, 1, lava::expit(lp))
> y <-  lp + rnorm(n, sd = 0.5**.5)
> d0 <- data.frame(y, yb, x1, x2)
> 
> # regression
> lr <- learner_xgboost(y ~ x1 + x2, nrounds = 5)
> lr$estimate(d0)
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.
Warning in throw_err_or_depr_msg("Parameter '", match_old, "' has been renamed to '",  :
  Parameter 'eta' has been renamed to 'learning_rate'. 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 'lambda' has been renamed to 'reg_lambda'. This warning will become an error in a future version.
Error in (function (x, y, objective = NULL, nrounds = 100L, max_depth = NULL,  : 
  argument "y" is missing, with no default
Calls: <Anonymous> ... <Anonymous> -> process.y.margin.and.objective -> NROW
Execution halted
Error(s) in re-building vignettes:
--- re-building 'predictionclass.Rmd' using rmarkdown

Quitting from predictionclass.Rmd:143-145 [unnamed-chunk-5]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! argument "y" is missing, with no default
---
Backtrace:
    ▆
 1. └─lr_xgboost$estimate(data = pbc)
 2.   └─private$fitfun(data, ...)
 3.     ├─base::structure(do.call(private$init.estimate, args), design = summary(xx))
 4.     ├─base::do.call(private$init.estimate, args)
 5.     └─targeted (local) `<fn>`(...)
 6.       ├─base::do.call(...)
 7.       └─xgboost (local) `<fn>`(...)
 8.         └─xgboost:::process.y.margin.and.objective(...)
 9.           └─base::NROW(y)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'predictionclass.Rmd' failed with diagnostics:
argument "y" is missing, with no default
--- failed re-building 'predictionclass.Rmd'

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

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

Error: Vignette re-building failed.
Execution halted
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Package suggested but not available for checking: 'tashudata'
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Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/TaxaNorm.Rcheck/00install.out' for details.
checkRd: (-1) tca.Rd:35: Lost braces; missing escapes or markup?
    35 | \item{C1.map}{An \code{p1} by \code{k} matrix of 0/1 values, indicating for each of the \code{p1} covariates in \code{C1} whether to consider its potential effects on the values of each of the \code{k} sources (e.g., if position \code{i,j} in \code{C1.map} is 1 then the potential effect of the \code{i}-th covariate in \code{C1} on the {j}-th source will be considered). If \code{C1.map == NULL} then effects for all covariates in \code{C1} will be considered in each of the sources. Note that \code{C1.map} is available only if \code{constrain_mu == TRUE}.}
       |                                                                                                                                                                                                                                                                                                                                                  ^
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    libs   1.1Mb
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
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Running examples in 'terra-Ex.R' failed
The error most likely occurred in:

> ### Name: cellSize
> ### Title: Area covered by each raster cell
> ### Aliases: cellSize cellSize,SpatRaster-method
> ### Keywords: methods spatial
> 
> ### ** Examples
> 
> 
> # SpatRaster 
> r <- rast(nrows=18, ncols=36)
> v <- 1:ncell(r)
> v[200:400] <- NA
> values(r) <- v
> 
> # size of each raster cell
> a <- cellSize(r)
> 
> # illustration of distortion
> r <- rast(ncols=90, nrows=45, ymin=-80, ymax=80)
> m <- project(r, "+proj=merc")
Warning: PROJ: proj_create: no database context specified (GDAL error 1)
Warning: PROJ: proj_create: no database context specified (GDAL error 1)
Error: [project] cannot get output boundaries for the target crs
Execution halted
checkRd: (-1) MC_CRUDE.Rd:19: Lost braces; missing escapes or markup?
    19 | \item{lsf}{objective function with limit state function in form of function(x) {x[1]+x[2]...}}
       |                                                                                ^
checkRd: (-1) MC_IS.Rd:23: Lost braces; missing escapes or markup?
    23 | \item{lsf}{objective function with limit state function in form of function(x) {x[1]+x[2]...}}
       |                                                                                ^
checkRd: (-1) PROB_BASEVAR-class.Rd:14: Lost braces
    14 | \item{\code{Id}}{Place in vector of objective functional expression function(x){x[id]}}
       |                                                                                ^
checkRd: (-1) PROB_DETVAR-class.Rd:14: Lost braces
    14 | \item{\code{Id}}{Place in vector of objective functional expression function(x){x[id]}}
       |                                                                                ^
checkRd: (-1) SORM.Rd:10: Lost braces; missing escapes or markup?
    10 | \item{lsf}{objective function with limit state function in form of function(x) {x[1]+x[2]...}}
       |                                                                                ^
checkRd: (-1) SYS_LSF-class.Rd:16: Lost braces
    16 | \item{\code{func}}{prepared for objective functions like SYS_LSF$func <- function(x){return(x[1] + x[2])}}
       |                                                                                     ^
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    tessdata  14.0Mb
Package required but not available: 'semPlot'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
checkRd: (-1) lognormConstCVCI.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
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Package suggested but not available for checking: 'gurobi'
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    37 |  {The 2 in the first row means there are two cycles;}
       |  ^
checkRd: (-1) permucycle.Rd:38: Lost braces; missing escapes or markup?
    38 |   {The second row means there is a cycle of length 2, with members  (1,3);}
       |   ^
checkRd: (-1) permucycle.Rd:39: Lost braces; missing escapes or markup?
    39 |  {The third row means  there is a cycle of length 1, with member  (2);}
       |  ^
checkRd: (-1) permucycle.Rd:40: Lost braces; missing escapes or markup?
    40 |  {The fourth row is redundant for this specific case.}
       |  ^
checkRd: (-1) permucycle.Rd:41: Lost braces; missing escapes or markup?
    41 |  {One can read from the output of permucycle() to obtain cycle notation (13)(2) of the permutation, and other information.}
       |  ^
Package which this enhances but not available for checking: 'metaSEM'
installed size is  5.2Mb
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    data   5.2Mb
checkRd: (-1) infer_Z.Rd:16: Lost braces; missing escapes or markup?
    16 |   \item{nu}{Informally, the probability that the row document has the column treatment.  Formally, the parameter for the variatioanl approximation of z_{i,k}, which is a Bernoulli distribution.}
       |                                                                                                                                                         ^
checkRd: (-1) sibp.Rd:26: Lost braces
    26 | It is recommended to use link{sibp_param_search} instead of this function to search over multiple configurations of the most important parameters.  So long as only the training data is used, the analyst can freely experimient with as many parameter configurations as he likes without corrupting his causal inferences.  Once a parameter configuration is chosen, the user can then use \link{sibp_amce} on the test set to estimate the average marginal component effect (AMCE) for each treatment.}
       |                              ^
checkRd: (-1) sibp.Rd:28: Lost braces; missing escapes or markup?
    28 |   \item{nu}{Informally, the probability that the row document has the column treatment.  Formally, the parameter for the variational approximation of z_{i,k}, which is a Bernoulli distribution.}
       |                                                                                                                                                         ^
checkRd: (-1) sibp_amce.Rd:19: Lost braces
    19 |   \item{sibp.amce}{The table returned by code{sibp_amce}.}
       |                                              ^
Problems with news in 'NEWS.md':
No news entries found.
checkRd: (-1) make.phrase.matrix.Rd:20: Lost braces
    20 |  \\tabular{rrrrr}{
       |           ^
checkRd: (-1) make.phrase.matrix.Rd:20-23: Lost braces
    20 |  \\tabular{rrrrr}{
       |                  ^
'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
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Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
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checkRd: (-1) shoulders.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) shoulders.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running 'testthat.R' [1s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(ThankYouStars)
  > 
  > test_check("ThankYouStars")
  Saving _problems/test-starring-12.R
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-starring.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-starring.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 0 | SKIP 0 | PASS 0 ]
  Error:
  ! Test failures.
  Execution halted
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    rda    7.1Mb
'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:
    R      4.0Mb
    data   3.0Mb
'LazyData' is specified without a 'data' directory
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    R              1.2Mb
    threeBrainJS   2.9Mb
'LazyData' is specified without a 'data' directory
checkRd: (-1) CPdimensionalityplot.Rd:18: Escaped LaTeX specials: \&
checkRd: (-1) CPdimensionalityplot.Rd:19: Escaped LaTeX specials: \&
checkRd: (-1) Kinship.Rd:15: Escaped LaTeX specials: \&
checkRd: (-1) Kinship.Rd:23: Escaped LaTeX specials: \&
checkRd: (-1) T2func.Rd:44: Escaped LaTeX specials: \&
checkRd: (-1) T2funcrep.Rd:44: Escaped LaTeX specials: \&
checkRd: (-1) T3dimensionalityplot.Rd:18: Escaped LaTeX specials: \&
checkRd: (-1) T3func.Rd:43: Escaped LaTeX specials: \&
checkRd: (-1) T3func.Rd:44: Escaped LaTeX specials: \&
checkRd: (-1) T3funcrep.Rd:43: Escaped LaTeX specials: \&
checkRd: (-1) T3funcrep.Rd:44: Escaped LaTeX specials: \&
checkRd: (-1) TV.Rd:26: Escaped LaTeX specials: \& \& \&
checkRd: (-1) TV.Rd:30: Escaped LaTeX specials: \&
checkRd: (-1) TV.Rd:31: Escaped LaTeX specials: \&
checkRd: (-1) TV.Rd:32: Escaped LaTeX specials: \&
checkRd: (-1) TV.Rd:33: Escaped LaTeX specials: \&
checkRd: (-1) pcamean.Rd:33: Escaped LaTeX specials: \&
checkRd: (-1) threewayanova.Rd:24: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/tibble.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
Running examples in 'tidybins-Ex.R' failed
The error most likely occurred in:

> ### Name: bin_cols
> ### Title: Bin Cols
> ### Aliases: bin_cols
> 
> ### ** Examples
> 
> 
> iris %>%
+ bin_cols(Sepal.Width, n_bins = 5, pretty_labels = TRUE) %>%
+ bin_cols(Petal.Width, n_bins = 3, bin_type = c("width", "kmeans")) %>%
+ bin_cols(Sepal.Width, bin_type = "xgboost", target = Species, seed = 1) -> iris1
Error in `purrr::map_chr()`:
ℹ In index: 1.
ℹ With name: Sepal.Width.
Caused by error:
! Can't coerce from an integer to a string.
Backtrace:
     ▆
  1. ├─... %>% ...
  2. ├─tidybins::bin_cols(...)
  3. │ └─.data %>% ...
  4. ├─framecleaner::select_otherwise(...)
  5. │ └─tidyselect::eval_select(.dots, data = .data)
  6. │   └─tidyselect::tidyselect_data_has_predicates(data)
  7. ├─tidybins::bin_cols(...)
  8. │ └─.data %>% ...
  9. ├─framecleaner::select_otherwise(...)
 10. │ └─tidyselect::eval_select(.dots, data = .data)
 11. │   └─tidyselect::tidyselect_data_has_predicates(data)
 12. ├─tidybins::bin_cols(., Sepal.Width, n_bins = 5, pretty_labels = TRUE)
 13. │ └─tidybins:::oner_wrapper(...)
 14. │   └─bin_df %>% rename_bin_lens(abbv = abbv, cols = tidyselect::everything())
 15. ├─tidybins:::rename_bin_lens(., abbv = abbv, cols = tidyselect::everything())
 16. │ └─... %>% stringr::str_c("_", abbv, .)
 17. ├─stringr::str_c("_", abbv, .)
 18. ├─purrr::map_chr(., 1)
 19. │ └─purrr:::map_("character", .x, .f, ..., .progress = .progress)
 20. │   ├─purrr:::with_indexed_errors(...)
 21. │   │ └─base::withCallingHandlers(...)
 22. │   └─purrr:::call_with_cleanup(...)
 23. └─base::.handleSimpleError(...)
 24.   └─purrr (local) h(simpleError(msg, call))
 25.     └─cli::cli_abort(...)
 26.       └─rlang::abort(...)
Execution halted
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
    doc    1.0Mb
    help   6.0Mb
Error(s) in re-building vignettes:
--- re-building 'v01_intro.Rmd' using rmarkdown
File man/figures/korea_map.png not found in resource path
Error: processing vignette 'v01_intro.Rmd' failed with diagnostics:
pandoc document conversion failed with error 99
--- failed re-building 'v01_intro.Rmd'

--- re-building 'v02_regional_analysis.Rmd' using rmarkdown
--- finished re-building 'v02_regional_analysis.Rmd'

--- re-building 'v03_gallery.Rmd' using rmarkdown
--- finished re-building 'v03_gallery.Rmd'

--- re-building 'v04_data_cleaning_kosis.Rmd' using rmarkdown
--- finished re-building 'v04_data_cleaning_kosis.Rmd'

--- re-building 'v05_contributors_guide.Rmd' using rmarkdown
--- finished re-building 'v05_contributors_guide.Rmd'

SUMMARY: processing the following file failed:
  'v01_intro.Rmd'

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Package required but not available: 'MBESS'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Initial Release (v0.1.0)
'LazyData' is specified without a 'data' directory
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc   5.1Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/tidyjson.Rcheck/00install.out' for details.
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Minor changes:
checkRd: (-1) single_imputation.Rd:21-22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) single_imputation.Rd:23-27: Lost braces in \itemize; meant \describe ?
Package suggested but not available for checking: 'admixtools'
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
'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.
'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
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    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
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    ubinc   2.0Mb
installed size is  6.9Mb
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    R      1.1Mb
    doc    1.1Mb
    libs   4.4Mb
GNU make is a SystemRequirements.
installed size is  8.6Mb
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    doc        1.3Mb
    shinyapp   5.6Mb
installed size is  7.1Mb
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    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
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    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
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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
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installed size is 18.8Mb
  sub-directories of 1Mb or more:
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    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
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    doc   7.6Mb
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Package suggested but not available for checking: 'USA.state.boundaries.data'
installed size is  6.1Mb
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    data   6.1Mb
'LazyData' is specified without a 'data' directory
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installed size is  5.2Mb
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installed size is  7.0Mb
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    data   6.9Mb
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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
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    libs  22.5Mb
Problems with news in 'NEWS.md':
No news entries found.
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Packages suggested but not available for checking: 'vaers', 'vaersND'
Packages suggested but not available for checking: 'vaers', 'vaersND'
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checkRd: (-1) sendTasks.Rd:43: Lost braces in \itemize; \value handles \item{}{} directly
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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})
       |                                                                                      ^
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'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
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    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.}
       |                                                                                             ^
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'LazyData' is specified without a 'data' directory
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    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,
       |                                                        ^
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Problems with news in 'NEWS.md':
No news entries found.
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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
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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.
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'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 ?
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checkRd: (-1) additiveBeta.Rd:47: Lost braces in \itemize; meant \describe ?
checkRd: (-1) downloadPBDB.Rd:27: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) multiplicativeBeta.Rd:33: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) ex121.Rd:18: Escaped LaTeX specials: \&
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    R      4.3Mb
    help   3.3Mb
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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' [28s]
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
checkRd: (-1) compdesc.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) compdesc.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) compdesc.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) compdesc.Rd:31: Lost braces in \itemize; \value handles \item{}{} directly
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 ?
checkRd: (-1) ViSiElse.Rd:103: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ViSiElse.Rd:104: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ViSiElse.Rd:105-106: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ViSiElse.Rd:108-127: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ViSiElse.Rd:112-113: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ViSiElse.Rd:114-115: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ViSiElse.Rd:116: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ViSiElse.Rd:128-134: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ViSiElse.Rd:135-147: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ViSiElse.Rd:148-157: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ViSiElse.Rd:152-153: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ViSiElse.Rd:154-155: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ViSibook-class.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ViSibook-class.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ViSibook-class.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ViSibook-class.Rd:30: Lost braces in \itemize; meant \describe ?
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
checkRd: (-1) Toep.estimator.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Toep.estimator.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) aquaporin.Rd:10: Lost braces in \itemize; meant \describe ?
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' [20s]
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_08_01_50_00_1885\RtmpojieKo\file156bc3aa...
  Processing file.
  Downloading file to: D:\temp\2025_12_08_01_50_00_1885\RtmpojieKo\file156bc56a...
  Reading in file.
  Downloading file to: D:\temp\2025_12_08_01_50_00_1885\RtmpojieKo\file156bc73a...
  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
checkRd: (-1) get_geo_box.Rd:41: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get_geo_box.Rd:42: Lost braces in \itemize; \value handles \item{}{} directly
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 ?
checkRd: (-1) milakes.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) milakes.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) milakes.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) milakes.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) milakes.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) milakes.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) milakes.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) milakes.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) milakes.Rd:19: Lost braces in \itemize; meant \describe ?
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
checkRd: (-1) exploreSignatures.Rd:48: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) exploreSignatures.Rd:49-50: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) exploreSignatures.Rd:56: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) exploreSignatures.Rd:57: Lost braces in \itemize; \value handles \item{}{} directly
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