checkRd: (-1) make_likelihood_matrix.Rd:16: Lost braces; missing escapes or markup?
    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.
       |                                                                             ^
checkRd: (-1) IndexComp.Rd:69: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) IndexComp.Rd:70: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) IndexComp.Rd:71: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) IndexComp.Rd:72: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) IndexComp.Rd:73: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) IndexComp.Rd:74: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) IndexComp.Rd:78: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) IndexComp.Rd:79: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) IndexComp.Rd:80: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) IndexComp.Rd:81: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) process_stats.Rd:11: Lost braces; missing escapes or markup?
    11 | the {janitor} package}
       |     ^
checkRd: (-1) theme_industRial.Rd:40: Lost braces; missing escapes or markup?
    40 | adapted from the package {cowplot} by Claus O.Wilke and reflects the principles
       |                          ^
checkRd: (-1) theme_industRial.Rd:45: Lost braces; missing escapes or markup?
    45 | It basically combines the half open theme with a grid background from {cowplot}
       |                                                                       ^
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'plot_functions.R'
checkRd: (-1) ask.user.yn.question.Rd:44: Lost braces; missing escapes or markup?
    44 | menu in the {utils} package, yesno in the {devtools} package.
       |             ^
checkRd: (-1) ask.user.yn.question.Rd:44: Lost braces; missing escapes or markup?
    44 | menu in the {utils} package, yesno in the {devtools} package.
       |                                           ^
checkRd: (-1) install.FFmpeg.Rd:25: Lost braces; missing escapes or markup?
    25 | This function is useful for saveVideo() in the {animation} package.
       |                                                ^
checkRd: (-1) install.SWFTools.Rd:27: Lost braces; missing escapes or markup?
    27 | This function is useful for saveSWF() in the {animation} package.
       |                                              ^
checkRd: (-1) os.shutdown.Rd:25: Lost braces; missing escapes or markup?
    25 | This function is a modified version of Yihui's shutdown function from the {fun} package.
       |                                                                           ^
Malformed Title field: should not end in a period.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'autoplot.restricted.Rd' 'autoplot.riskfactor.Rd' 'rating_factors.Rd'
checkRd: (-1) remit.Rd:32: Lost braces
    32 | A data set to replicate the findings of Escrib\`{a}-Folch,
       |                                                 ^
checkRd: (-1) remit.Rd:38: Lost braces
    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}
       |         ^
checkRd: (-1) interval-internal.Rd:40: Lost braces
    40 | \item{dqfunc}{function, density of the results of the quantile function, e.g., function(x){dnorm(qnorm(x))} (used for 'general' scores, 
       |                                                                                           ^
checkRd: (-1) decompose_volume.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) decompose_volume.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) decompose_volume.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) decompose_volume.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) fit_volume.Rd:44: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) fit_volume.Rd:45: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) fit_volume.Rd:46: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) fit_volume.Rd:47: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) forecast_volume.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) forecast_volume.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) forecast_volume.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) forecast_volume.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) generate_plots.Rd:15: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) generate_plots.Rd:16: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) generate_plots.Rd:17: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) intRvals-package.Rd:60: Lost braces
    60 | B\'{e}dard, J. & Gauthier, G. 1986. Assessment of faecal output in geese. Journal of Applied Ecology, 23, 77-90.
       |    ^
checkRd: (-1) partition.Rd:64: Lost braces
    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.
       |               ^
checkRd: (-1) f.influence.Rd:25: Lost braces; missing escapes or markup?
    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.
       |                                                               ^
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,
and section 'Moving into C API compliance' for issues with the use of
non-API entry points.
checkRd: (-1) check_convergence.Rd:47: Lost braces
    47 | \code{conv_plot}: code{ipm} invisibly.
       |                       ^
checkRd: (-1) init_ipm.Rd:50-51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) init_ipm.Rd:52-53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) init_ipm.Rd:57: Lost braces in \itemize; meant \describe ?
checkRd: (-1) init_ipm.Rd:58: Lost braces in \itemize; meant \describe ?
checkRd: (-1) init_ipm.Rd:62: Lost braces in \itemize; meant \describe ?
checkRd: (-1) init_ipm.Rd:63-65: Lost braces in \itemize; meant \describe ?
checkRd: (-1) init_ipm.Rd:70-74: Lost braces in \itemize; meant \describe ?
checkRd: (-1) init_ipm.Rd:75-78: Lost braces in \itemize; meant \describe ?
checkRd: (-1) make_ipm.Rd:276: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) make_ipm.Rd:277-281: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) make_ipm.Rd:282-286: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) make_ipm.Rd:287-291: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) make_ipm.Rd:292-293: Lost braces in \itemize; \value handles \item{}{} directly
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'calc.pvalues.R' 'helper.R' 'hypothesis_templates.R' 'irtpwr.R'
    'mml.fit.R' 'setup.data.R'
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'chain-simulation.R'
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'iso8601todataframe.R'
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'bicycle_theft.R' 'car_fleet.R' 'crimes_against_life.R'
    'gun_seizure.R' 'gun_seizure_historical.R' 'monthly_stats.R'
    'monthly_stats_dictionary.R' 'population.R' 'spatial_info.R'
    'upp_data.R' 'yearly_stats.R' 'yearly_stats_dictionary.R'
checkRd: (-1) is_israd_database.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) is_israd_database.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) is_israd_database.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) is_israd_database.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) is_israd_database.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) is_israd_database.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) is_israd_database.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) is_israd_database.Rd:26: Lost braces in \itemize; meant \describe ?
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'get_conservation_status.R' 'get_vernacularname.R'
checkRd: (-1) sTsls.Rd:17: Lost braces; missing escapes or markup?
    17 | \item{pi}{the matrix E[XZ']E[ZZ']^{-1}}
       |                                   ^
checkRd: (-1) sTslsSplines.Rd:20: Lost braces; missing escapes or markup?
    20 | \item{pi}{matrix, corresponds to E[XZ']E[ZZ']^{-1}, the first stage
       |                                               ^
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'.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'jdenticon.R'
Running examples in 'jewel-Ex.R' failed
The error most likely occurred in:

> ### Name: constructWeights
> ### Title: Construct weights for _jewel_ minimization problem from prior
> ###   information on vertices degrees.
> ### Aliases: constructWeights
> 
> ### ** Examples
> 
> {
+ K <- 3
+ p <- 50
+ n <- 20
+ data <- generateData_rewire(K = K, p = p, n = n, ncores = 1, verbose = FALSE)
+ G_list_true <- data$Graphs
+ true_degrees <- rowSums(G_list_true[[1]])
+ cut <- sort(true_degrees, decreasing = TRUE)[ceiling(p * 0.03)]
+ apriori_hubs <- ifelse(true_degrees >= cut, 10, 1)
+ W <- constructWeights(apriori_hubs, K = K)
+ }
Error in rewire_impl(rewire = graph, n = niter, mode = mode) : 
  The value 2.4500000000000002 is not representable as an integer. Invalid value
Source: rinterface_extra.c:83
Calls: generateData_rewire ... do_call -> eval -> eval -> <Anonymous> -> rewire_impl
Execution halted
Running examples in 'jlmerclusterperm-Ex.R' failed
The error most likely occurred in:

> ### Name: calculate_clusters_pvalues
> ### Title: Calculate bootstrapped p-values of cluster-mass statistics
> ### Aliases: calculate_clusters_pvalues clusters_are_comparable
> 
> ### ** Examples
> 
> ## Don't show: 
> if (julia_setup_ok()) (if (getRversion() >= "3.4") withAutoprint else force)({ # examplesIf
+ ## End(Don't show)
+ ## Don't show: 
+ }) # examplesIf
Starting Julia ...
> ## End(Don't show)
> 
> 
> 
> cleanEx()
Error: connections left open:
	->localhost:11980 (sockconn)
Execution halted
Running 'testthat.R' [1255m]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(jlview)
  > 
  > test_check("jlview")
  Julia version 1.11.3 at location C:\PROGRA~1\Julia\bin will be used.
  Loading setup script for JuliaCall...
checkRd: (-1) jmdem.control.Rd:42: Lost braces; missing escapes or markup?
    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.
       |                                                                                          ^
checkRd: (-1) jmdem.control.Rd:42: Lost braces; missing escapes or markup?
    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.
       |                                                                                                                                               ^
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'just.install.R'
Running 'testthat.R' [40s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > test_check("JWileymisc")
  Loading required package: JWileymisc
  $`1`
  
  $`2`
  
  attr(,"class")
  [1] "list"      "ggarrange"
  Saving _problems/test-descriptives-helpers-24.R
  Loading required namespace: GPArotation
  [ FAIL 1 | WARN 4 | SKIP 1 | PASS 418 ]
  
  ══ Skipped tests (1) ═══════════════════════════════════════════════════════════
  • On CRAN (1): 'test-distributions.R:75:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-descriptives-helpers.R:22:5'): .stylepairedwilcox works ──────
  Expected `res` to equal "Wilcoxon Paired V = 54.00, p = .004".
  Differences:
  `actual`:   "Wilcoxon Paired V = 45.00, p = .009"
  `expected`: "Wilcoxon Paired V = 54.00, p = .004"
  
  
  [ FAIL 1 | WARN 4 | SKIP 1 | PASS 418 ]
  Error:
  ! Test failures.
  Execution halted
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'kappa_inference.R'
checkRd: (-1) get.fit.Rd:46: Lost braces in \itemize; meant \describe ?
checkRd: (-1) get.fit.Rd:47: Lost braces in \itemize; meant \describe ?
checkRd: (-1) get.fit.Rd:48-49: Lost braces in \itemize; meant \describe ?
checkRd: (-1) get.fit.Rd:50-51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) get.fit.Rd:52-54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) get.fit.Rd:55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) get.fit.Rd:56: Lost braces in \itemize; meant \describe ?
checkRd: (-1) get.fit.Rd:57-60: Lost braces in \itemize; meant \describe ?
checkRd: (-1) get.fit.Rd:61-62: Lost braces in \itemize; meant \describe ?
checkRd: (-1) get.fit.Rd:63-64: Lost braces in \itemize; meant \describe ?
checkRd: (-1) get.fit.Rd:70: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get.fit.Rd:71: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get.fit.Rd:72: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get.fit.Rd:73: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get.fit.Rd:74: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get.fit.Rd:75: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get.fit.Rd:76: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get.fit.Rd:77: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get.fit.Rd:78: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get.fit.Rd:79: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get.fit.Rd:80: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get.sim.trajectories.Rd:66: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get.sim.trajectories.Rd:67: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) kdist.Rd:14: Lost braces; missing escapes or markup?
    14 | The {kdist} functions dk, pk, qk and rk, calculates the K-distribution
       |     ^
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.}
       |                                                                                                                                                                                                                                                                   ^
checkRd: (-1) subjOCCDIF.Rd:23: Lost braces
    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.
       |                                                                                                                                                                                                                                                                                                       ^
checkRd: (-1) useKeys.Rd:13: Lost braces; missing escapes or markup?
    13 | This function adds the {keys} dependencies to your application
       |                        ^
checkRd: (-1) kfda.Rd:26: Lost braces
    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}))}
       |                                                                                           ^
checkRd: (-1) kfino_plot.Rd:52: Lost braces; missing escapes or markup?
    52 |        plus the OK values. Prediction corresponds to E[X_{t} | Y_{1...t}] 
       |                                                          ^
checkRd: (-1) kfino_plot.Rd:52: Lost braces; missing escapes or markup?
    52 |        plus the OK values. Prediction corresponds to E[X_{t} | Y_{1...t}] 
       |                                                                  ^
checkRd: (-1) mount_appdata.Rd:10: Lost braces; missing escapes or markup?
    10 | \item{x}{An object of class \code{KinPairData} or {KinPairSimulation}}
       |                                                   ^
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'balance.R' 'data.R' 'order.R' 'revise.R' 'utils.R'
checkRd: (-1) klausuR.answ-class.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) klausuR.answ-class.Rd:18-22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) klausuR.answ-class.Rd:23-24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) klausuR.answ-class.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) klausuR.answ-class.Rd:35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) klausuR.answ-class.Rd:36-37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) klausur.Rd:107-109: Lost braces in \itemize; meant \describe ?
checkRd: (-1) klausur.Rd:110-111: Lost braces in \itemize; meant \describe ?
checkRd: (-1) klausur.Rd:112-113: Lost braces in \itemize; meant \describe ?
checkRd: (-1) klausur.Rd:114-116: Lost braces in \itemize; meant \describe ?
checkRd: (-1) klausur.Rd:117-118: Lost braces in \itemize; meant \describe ?
checkRd: (-1) klausur.Rd:119-120: Lost braces in \itemize; meant \describe ?
checkRd: (-1) klausur.Rd:121-123: Lost braces in \itemize; meant \describe ?
checkRd: (-1) klausur.Rd:124-126: Lost braces in \itemize; meant \describe ?
checkRd: (-1) klausur.Rd:147: Lost braces in \itemize; meant \describe ?
checkRd: (-1) klausur.Rd:148: Lost braces in \itemize; meant \describe ?
checkRd: (-1) klausur.Rd:149: Lost braces in \itemize; meant \describe ?
checkRd: (-1) klausur.Rd:150: Lost braces in \itemize; meant \describe ?
checkRd: (-1) klausur.Rd:151: Lost braces in \itemize; meant \describe ?
checkRd: (-1) klausur.Rd:152-155: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotkmc.Rd:21: Lost braces; missing escapes or markup?
    21 |     list of two functions,flist=list( f1=function( x ) { x } ,f2=function( x ) { x^2 } )  
       |                                                        ^
checkRd: (-1) plotkmc.Rd:21: Lost braces; missing escapes or markup?
    21 |     list of two functions,flist=list( f1=function( x ) { x } ,f2=function( x ) { x^2 } )  
       |                                                                                ^
checkRd: (-1) knockoff.Rd:22-24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) knockoff.Rd:25-27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MapPolygon.Rd:20: Lost braces
    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.}
       |                                                              ^
checkRd: (-1) SurveyQ.Rd:26: Lost braces
    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.}
       |                                                              ^
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'Koboconnect.R' 'other.R'
checkRd: (-1) compose.Rd:13: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) compose.Rd:14: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) EGIparallel.Rd:60: Lost braces; missing escapes or markup?
    60 | Finally, one can control the field {optim.option} in order to decide how to optimize the sampling criterion.
       |                                    ^
checkRd: (-1) max_sur_parallel.Rd:29: Lost braces; missing escapes or markup?
    29 | Finally, one can control the field {optim.option} in order to decide how to optimize the sampling criterion. 
       |                                    ^
checkRd: (-1) max_timse_parallel.Rd:30: Lost braces; missing escapes or markup?
    30 | Finally, one can control the field {optim.option} in order to decide how to optimize the sampling criterion. 
       |                                    ^
checkRd: (-1) max_vorob_parallel.Rd:30: Lost braces; missing escapes or markup?
    30 | Finally, one can control the field {optim.option} in order to decide how to optimize the sampling criterion.
       |                                    ^
checkRd: (-1) print_uncertainty_nd.Rd:72: Lost braces
    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.
       |                                    ^
checkRd: (-1) Predict_kernel_Ridge_MM.Rd:45: Lost braces; missing escapes or markup?
    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]) }
       |                                                                                                        ^
checkRd: (-1) ks_test_stat.Rd:14: Lost braces
    14 | are valid. See /code{LcKS} for accepted functions.}
       |                     ^
checkRd: (-1) GenSyntheticLogistic.Rd:46: Lost braces; missing escapes or markup?
    46 | 3) Every coordinate yi of the outcome vector y exists in {-1, 1}^n is sampled 
       |                                                          ^
checkRd: (-1) L0Learn-package.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) L0Learn-package.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) L0Learn-package.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) L0Learn-package.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) L0Learn-package.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) L0Learn-package.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) CreateDataSet.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) CreateDataSet.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) CreateDataSet.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) FindElement.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) FindElement.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) FindNbrClusters.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) FindNbrClusters.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) FindStructure.Rd:15: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) FindStructure.Rd:16: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) l1_spectralclustering.Rd:32: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) l1_spectralclustering.Rd:33: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) l1_spectralclustering.Rd:34: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) l1_spectralclustering.Rd:35: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) predict.l2boost.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) predict.l2boost.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) predict.l2boost.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) predict.l2boost.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) predict.l2boost.Rd:31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) predict.l2boost.Rd:32: Lost braces in \itemize; \value handles \item{}{} directly
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'as_base_data_frame.R' 'as_base_data_frame2.R'
    'as_labeled_data_frame.R' 'irregular2.R'
checkRd: (-1) ln_quantile_value.Rd:44: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ln_quantile_value.Rd:45: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ln_quantile_value.Rd:46: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ln_quantile_value.Rd:47: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ln_quantile_value.Rd:48: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ln_quantile_value.Rd:49: Lost braces in \itemize; \value handles \item{}{} directly
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.5/LABTNSCPSS.Rcheck/00install.out' for details.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'calculate_gaps_perc.Rd' 'get_cbh_metrics.Rd' 'get_cum_break.Rd'
    'get_depths.Rd' 'get_distance.Rd' 'get_effective_gap.Rd'
    'get_gaps_fbhs.Rd' 'get_layers_lad.Rd' 'get_real_depths.Rd'
    'get_real_fbh.Rd'
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'NDVI2LAI.R'
checkRd: (-1) lambda.r-package.Rd:71-74: Lost braces
    71 | x \%g\% y \%:=\% {
       |                  ^
Running 'testthat.R' [34s]
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.
       |                                 ^
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    '00methods.R' 'creg_datalist.R' 'creg_input.R' 'creg_partable.R'
    'creg_startvals.r'
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'lay.Rd'
File 'lazyeval/libs/x64/lazyeval.dll':
  Found non-API calls to R: 'PRENV', 'PRVALUE', 'R_PromiseExpr',
    'Rf_allocSExp', 'Rf_findVarInFrame3', 'SETLENGTH',
    'SET_GROWABLE_BIT', 'SET_PRCODE', 'SET_PRENV', 'SET_PRVALUE',
    'SET_TRUELENGTH'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual,
and section 'Moving into C API compliance' for issues with the use of
non-API entry points.
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
       |                                                        ^
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'legendSymbols.Rd'
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' }
       |                                               ^
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'},
       |                                                                                 ^
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.
       |                                                                                     ^
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'grab_crosswalk.R' 'lehdr.R'
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'letter_value.R' 'print_lv.R'
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
       |                           ^
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: \$
File 'lidR/libs/x64/lidR.dll':
  Found non-API calls to R: 'LEVELS', 'R_curErrorBuf', 'SETLENGTH',
    'SET_GROWABLE_BIT', 'SET_TRUELENGTH', 'TRUELENGTH', 'XTRUELENGTH'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual,
and section 'Moving into C API compliance' for issues with the use of
non-API entry points.
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 ?
Found the following significant warnings:
  Warning: src/Makevars.win: Unknown C++ standard '@CXX_STD@' was ignored
See 'd:/Rcompile/CRANpkg/local/4.5/lightgbm.Rcheck/00install.out' for details.
* used C++ compiler: 'g++.exe (GCC) 14.3.0'
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 ?
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'lineup-shiny.Rd' 'taggle-shiny.Rd'
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'auto.R'
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'list_bind.R'
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) 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 | $(n_{extreme} + 1) / (B + 1)$.
       |     ^
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}.}
       |                                                                                                                               ^
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'mod_carga_datos.R' 'mod_correlacion_utils.R' 'mod_dispersion.R'
    'mod_distribuciones.R' 'mod_distribuciones_fct.R'
    'mod_distribuciones_utils.R' 'mod_normal_utils.R'
File 'lobstr/libs/x64/lobstr.dll':
  Found non-API calls to R: 'PRENV', 'PRVALUE', 'R_PromiseExpr',
    'Rf_allocSExp', 'Rf_findVarInFrame3', 'SETLENGTH',
    'SET_GROWABLE_BIT', 'SET_PRCODE', 'SET_PRENV', 'SET_PRVALUE',
    'SET_TRUELENGTH'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual,
and section 'Moving into C API compliance' for issues with the use of
non-API entry points.
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
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'locate.R'
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'bittermelon.R' 'lofi.Rd'
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'emayili_emailer.R' 'login_server.R'
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'logger.R'
Malformed Description field: should contain one or more complete sentences.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'add_plot_labels.Rd' 'datasim_helpers.R' 'datasim_make.Rd'
    'model_eval.R' 'model_eval.Rd' 'model_plot.R' 'model_skeleton.Rd'
    'model_values.R' 'model_values.Rd' 'mosaic_cull_for_do.Rd' 'ntiles.R'
    'ntiles.Rd' 'point_plot.R' 'point_plot.Rd' 'print.R'
    'random_terms.Rd' 'regression_summaries.Rd' 'sims.R'
    'statistical_annotations.Rd' 'trials.R' 'trials.Rd' 'zero_one.Rd'
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'smr_custom.R' 'smr_major.R' 'smr_minor.R'
checkRd: (-1) k.Rd:27: Lost braces
    27 |  code{\link{ACSPlan-class}}, 
       |      ^
checkRd: (-1) Upload_to_db.Rd:43: Lost braces
    43 | lucas]{Connect_to_db}
       |       ^
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}.
       |                                                                                                        ^
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'classify.R' 'extract.R' 'score.R'
File 'magrittr/libs/x64/magrittr.dll':
  Found non-API calls to R: 'Rf_allocSExp', 'SET_PRCODE', 'SET_PRENV',
    'SET_PRVALUE'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual,
and section 'Moving into C API compliance' for issues with the use of
non-API entry points.
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
       |                                                   ^
checkRd: (-1) MangroveTree.Rd:37: Lost braces
    37 |       An object of class \\code{\link[Mangrove]{MangrovePed}}
       |                                ^
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.5/ManifoldOptim.Rcheck/00install.out' for details.
checkRd: (-1) EEGwide.Rd:30-33: Lost braces
    30 |   if(requireNamespace("ggplot2")){ 
       |                                  ^
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
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'data_analysis_descriptive.R' 'functions.R' 'main.R'
    'merge_quality_articles.R'
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: \&
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 ?
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).
       |     ^
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) {
       |                                                ^
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}}
       |                                                                                                                     ^
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. 
       |                                                                                                                                                    ^
checkRd: (-1) Match.Rd:90: Lost braces; missing escapes or markup?
    90 | expression in braces. For example, the condition "{[ab]*}" is equivalent
       |                                                   ^
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}.
       |                                        ^
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
       |                                                                   ^
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
       |                                                                                                                                                                                                           ^
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.
       |                                        ^
checkRd: (-1) MCbound.precalc1.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MCbound.precalc1.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MCbound.precalc1.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MCbound.precalc1.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MCbound.precalc1.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MCbound.precalc1.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MCbound.precalc1.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MCbound.precalc1.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MCbound.precalc1.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MCbound.precalc1.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MCbound.precalc1.Rd:26: Lost braces in \itemize; meant \describe ?
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: \#
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'summary.mcpmod_simulation.R'
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
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}.}
       |                                                                                                             ^
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.
       |     ^
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
       |     ^
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}}.
       |                                                                                     ^
checkRd: (-1) CVLasoelacox.Rd:68-69: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) CVLasoelacox.Rd:70-71: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) CVLasoelacox.Rd:72: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) CVLasoelacox.Rd:73: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) CVLasoelacox.Rd:74-76: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) CVLasoelacox.Rd:77-79: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) CVLasoelacox.Rd:80-81: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) CVLasoelacox.Rd:82-85: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) CVLasoelacox.Rd:86-87: Lost braces in \itemize; \value handles \item{}{} directly
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"}.
       |                                                                                                                                                                                                                                                                                                                                        ^
checkRd: (-1) asympVar_LinReg.Rd:52: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) asympVar_LinReg.Rd:53: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) asympVar_LinReg.Rd:54: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) asympVar_LinReg.Rd:55: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) asympVar_LinReg.Rd:56: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) asympVar_LogReg.Rd:55: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) asympVar_LogReg.Rd:56: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) asympVar_LogReg.Rd:57: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) asympVar_LogReg.Rd:58: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) asympVar_LogReg.Rd:59: Lost braces in \itemize; \value handles \item{}{} directly
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
checkRd: (-1) rland.graph.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rland.graph.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rland.graph.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rland.graph.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rland.graph.Rd:31: Lost braces in \itemize; \value handles \item{}{} directly
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
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'metalite_table1_to_rtf.R'
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'metaRangePriorityQueue.Rd' 'metaRangeProcess.Rd'
Missing dependency on R >= 4.2.0 because package code uses the pipe
  placeholder syntax added in R 4.2.0.
  File(s) using such syntax:
    'read_mgi_biotype_conflict_rpt.R'
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'api.R' 'handlers-static.R' 'static-assets.Rd'
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'get_dependencies.R' 'micromodal.R' 'micromodal.Rd'
    'use_micromodal.R'
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'cylinder-bundle-compartment.R' 'cylinder-bundle-geometry.R'
    'samplers.R' 'utils.R'
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'flexImputeModel.R'
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'detect_segments.R' 'find_best_split.R' 'identify_migrations.R'
    'utils.R'
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 ?
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'estimate.R' 'formula.R' 'toy_data.R'
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 ?
checkRd: (-1) gof.estimates.Rd:67-70: Lost braces in \itemize; meant \describe ?
checkRd: (-1) vcov.mipfp.Rd:63-66: Lost braces in \itemize; meant \describe ?
checkRd: (-1) vcov.mipfp.Rd:67-70: Lost braces in \itemize; meant \describe ?
checkRd: (-1) vcov.mipfp.Rd:71-74: Lost braces in \itemize; meant \describe ?
checkRd: (-1) vcov.mipfp.Rd:75-78: Lost braces in \itemize; meant \describe ?
checkRd: (-1) vcov.mipfp.Rd:89-91: Lost braces in \itemize; meant \describe ?
checkRd: (-1) vcov.mipfp.Rd:92-95: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sim.data.Rd:11: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) sim.data.Rd:12: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) sim.data.Rd:13: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) sim.data.Rd:14: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) sim.data.Rd:15: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) sim.data.Rd:16: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) sim.data.Rd:17: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) sim.data.Rd:18: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) sim.data.Rd:19: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) sim.data.Rd:20: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) sim.data.Rd:21: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) sim.data.Rd:22: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) sim.data.Rd:23: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) sim.data.Rd:24: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) sim.data.Rd:25: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) sim.data.Rd:26: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) sim.data.Rd:27: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) PV.Rd:14: Lost braces
    14 | plausible value in turn; with code{rewrite=FALSE} a new data set is
       |                                   ^
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) mlim.Rd:58: Lost braces
    58 |              Note that code{"XGB"} is only available in Mac OS and Linux. moreover,
       |                            ^
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'example.simfun.R' 'fit.surrogate.R'
Running 'testthat.R' [149s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > if (requireNamespace("testthat", quietly = TRUE)) {
  +   library("testthat")
  +   library("mlr3learners")
  +   test_check("mlr3learners")
  + }
  Loading required package: mlr3
  Saving _problems/test_regr_cv_glmnet-24.R
  Saving _problems/test_regr_glmnet-21.R
  [ FAIL 2 | WARN 0 | SKIP 4 | PASS 633 ]
  
  ══ Skipped tests (4) ═══════════════════════════════════════════════════════════
  • On CRAN (4): 'test_classif_nnet.R:2:1', 'test_classif_xgboost.R:2:1',
    'test_regr_nnet.R:2:1', 'test_regr_xgboost.R:2:1'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test_regr_cv_glmnet.R:21:3'): selected_features ───────────────────
  Expected `learner$selected_features(0)` to equal `task$feature_names`.
  Differences:
  `actual`:   "am"                                                        
  `expected`: "am" "carb" "cyl" "disp" "drat" "gear" "hp" "qsec" "vs" "wt"
  
  ── Failure ('test_regr_glmnet.R:18:3'): selected_features ──────────────────────
  Expected `learner$selected_features(0)` to equal `task$feature_names`.
  Differences:
  `actual`:   "am"                                                        
  `expected`: "am" "carb" "cyl" "disp" "drat" "gear" "hp" "qsec" "vs" "wt"
  
  
  [ FAIL 2 | WARN 0 | SKIP 4 | PASS 633 ]
  Error:
  ! Test failures.
  Execution halted
checkRd: (-1) MMD_attr.Rd:62: Lost braces; missing escapes or markup?
    62 | \item Probability of attribution of each unknown individual to each source $p_{u,s}$
       |                                                                               ^
checkRd: (-1) mmeln.Rd:69: Lost braces; missing escapes or markup?
    69 |   \item{obj$M}{Number of total observations sum_{i=1}^N(pi)}
       |                                                 ^
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'BF_for_everyone.R' 'rc_game_mgmt.R'
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'iht_interpreter.Rd' 'lr_pow.Rd' 'pj_pow.Rd' 'replext_helpers.R'
    'replext_helpers_pgsql.R' 'rm_interpreter.Rd'
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).
       |                                                                           ^
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: \&
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 ?
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'pop_sd.Rd' 'tidy_summary.R'
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 ?
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'define_extended_question.Rd' 'define_question.Rd'
    'define_questions_from_csv.Rd' 'define_questions_from_data_frame.Rd'
    'define_questions_from_excel.Rd' 'generate_xml.Rd'
    'generate_xml_file.Rd'
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'stopwords.R'
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 ?
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'compute-contribution.R' 'compute-headcount-ratio-adjusted.R'
    'compute-headcount-ratio.R' 'compute-mpi.R' 'compute_mpi.Rd'
    'create-deprivation-matrix.R' 'define-deprivation.R'
    'define-mpi-specs.R' 'define_deprivation.Rd' 'define_mpi_specs.Rd'
    'helpers.R' 'save_mpi.R' 'write-as-excel.R'
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}.
       |                                                           ^
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.}
       |                                      ^
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
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}}.
       |     ^
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.
       |                                                                                                                                                                                                                                                                                                ^
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 ?
checkRd: (-1) dbivCMP.Rd:14: Lost braces; missing escapes or markup?
    14 | \item{bivprob}{Bivariate probabilities, {p00, p01, p10, p11}.}
       |                                         ^
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'mlgraph.Rd'
Missing dependency on R >= 4.2.0 because package code uses the pipe
  placeholder syntax added in R 4.2.0.
  File(s) using such syntax:
    'predict.R' 'sensitivity.R' 'treatment_profile.R'
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}
       |                     ^
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'accessors.R' 'export_json.R' 'extract.R'
Codoc mismatches from Rd file 'multiview.control.Rd':
multiview.control
  Code: function(fdev = 1e-05, devmax = 0.999, eps = 1e-06, big =
                 9.9e+35, mnlam = 5, pmin = 1e-09, exmx = 250, prec =
                 1e-10, mxit = 100, itrace = 0, epsnr = 1e-06, mxitnr =
                 25, thresh = 1e-07, maxit = 1e+05, dfmax = NULL, pmax
                 = NULL, trace.it = 0, factory = FALSE)
  Docs: function(fdev = 1e-05, devmax = 0.999, eps = 1e-06, big =
                 9.9e+35, mnlam = 5, pmin = 1e-09, exmx = 250, prec =
                 1e-10, mxit = 100, itrace = 0, epsnr = 1e-06, mxitnr =
                 25, factory = FALSE)
  Argument names in code not in docs:
    thresh maxit dfmax pmax trace.it
  Mismatches in argument names:
    Position: 13 Code: thresh Docs: factory
Running examples in 'multiview-Ex.R' failed
The error most likely occurred in:

> ### Name: multiview.cox.path
> ### Title: Fit a Cox regression model with elastic net regularization for a
> ###   path of lambda values
> ### Aliases: multiview.cox.path
> 
> ### ** Examples
> 
> set.seed(2)
> nobs <- 100; nvars <- 15
> xvec <- rnorm(nobs * nvars)
> xvec[sample.int(nobs * nvars, size = 0.4 * nobs * nvars)] <- 0
> x <- matrix(xvec, nrow = nobs)
> beta <- rnorm(nvars / 3)
> fx <- x[, seq(nvars / 3)] %*% beta / 3
> ty <- rexp(nobs, exp(fx))
> tcens <- rbinom(n = nobs, prob = 0.3, size = 1)
> jsurv <- survival::Surv(ty, tcens)
> fit1 <- glmnet:::cox.path(x, jsurv)
Error: object 'cox.path' not found
Execution halted
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 ?
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'DFA.R' 'mvDFA.R' 'simulate_Lorenz_noise.R'
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.
       | ^
Missing dependency on R >= 4.2.0 because package code uses the pipe
  placeholder syntax added in R 4.2.0.
  File(s) using such syntax:
    'get_individual_algebra_results.R'
checkRd: (-1) mzipmed_data.Rd:22: Lost braces; missing escapes or markup?
    22 | @source {Simulated to serve as an example}
       |         ^
checkRd: (-1) M36NT2PM.dat.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) M36NT2PM.dat.Rd:38: Lost braces in \itemize; meant \describe ?
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.
       |                                                                                                                                                    ^
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'impute_below.Rd' 'impute_factor.Rd' 'impute_fixed.Rd'
    'impute_mean.Rd' 'impute_median.Rd' 'impute_mode.Rd' 'impute_zero.Rd'
    'replace_na_with.Rd'
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 ?
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'activate.Rd'
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 ?
Missing dependency on R >= 4.2.0 because package code uses the pipe
  placeholder syntax added in R 4.2.0.
  File(s) using such syntax:
    'functions.R'
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'neon_cloud.R'
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) networktree.Rd:56: Lost braces; missing escapes or markup?
    56 | with a matrix response {y}. \code{x1} and \code{x2} are used as
       |                        ^
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'visualizations.R'
Running 'testthat.R' [4s]
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(new.dist)
  > 
  > test_check("new.dist")
  Saving _problems/test_function-246.R
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 232 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_function.R:246:3'): functions returns a  vector with the expected size ──
  <rlib_error_package_not_found/rlang_error/error/condition>
  Error in `expect_vector(dbwd(10, alpha = 2, sigma = 2), ptype = double(), size = 1)`: The package "vctrs" is required.
  Backtrace:
      ▆
   1. └─testthat::expect_vector(...) at test_function.R:246:3
   2.   └─rlang::check_installed("vctrs")
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 232 ]
  Error:
  ! Test failures.
  Execution halted
checkRd: (-1) NHANES.Rd:278: Lost braces
   278 | \code{AgeFirstMarij}{Age participant first tried marijuana. Reported for participants aged 18 to 59 years.}
       |                     ^
checkRd: (-1) bootstrap_param_est.Rd:52: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bootstrap_param_est.Rd:53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bootstrap_param_est.Rd:54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) get_emission.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) get_emission.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) get_emission.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) impute.Rd:51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) impute.Rd:52: Lost braces in \itemize; meant \describe ?
checkRd: (-1) impute.Rd:53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) impute_ref.Rd:54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) impute_ref.Rd:55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) impute_ref.Rd:56: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sim_data.Rd:42: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sim_data.Rd:43: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sim_data.Rd:44: Lost braces in \itemize; \value handles \item{}{} directly
Malformed Description field: should contain one or more complete sentences.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'get_model_params.R' 'level_from_quantiles.R' 'make_request.R'
    'nixtla_client_cross_validation.R' 'nixtla_client_detect_anomalies.R'
    'nixtla_client_forecast.R' 'nixtla_client_historic.R'
    'nixtla_client_plot.R' 'nixtla_validate_api_key.R'
    'validate_exogenous.R'
checkRd: (-1) anova.Rd:19: Lost braces
    19 |   Returns an object of class code{anova}.  These objects represent
       |                                  ^
':::' call which should be '::': 'NMdata:::dcastSe'
  See the note in ?`:::` about the use of this operator.
checkRd: (-1) simulatePop.Rd:40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulatePop.Rd:41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulatePop.Rd:42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulatePop.Rd:43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulatePop.Rd:44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulatePop.Rd:45: Lost braces in \itemize; meant \describe ?
checkRd: (-1) imp_int_an.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) imp_int_an.Rd:25: Lost braces in \itemize; meant \describe ?
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 ?
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'libr_called.R' 'libr_unused.R' 'libr_used.R'
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 ?
Running examples in 'NSR-Ex.R' failed
The error most likely occurred in:

> ### Name: NSR_metadata
> ### Title: Get NSR metadata
> ### Aliases: NSR_metadata
> 
> ### ** Examples
> 
> {
+ metadata <- NSR_metadata()
+ }
There appears to be a problem reaching the API.
There appears to be a problem reaching the API.
There appears to be a problem reaching the API.
Error in names(output) <- c("citations", "version", "sources") : 
  'names' attribute [3] must be the same length as the vector [0]
Calls: NSR_metadata
Execution halted
Error(s) in re-building vignettes:
--- re-building 'NSR.Rmd' using rmarkdown

Quitting from NSR.Rmd:68-79 [unnamed-chunk-5]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `names(output) <- c("citations", "version", "sources")`:
! 'names' attribute [3] must be the same length as the vector [0]
---
Backtrace:
    ▆
 1. └─NSR::NSR_metadata()
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'NSR.Rmd' failed with diagnostics:
'names' attribute [3] must be the same length as the vector [0]
--- failed re-building 'NSR.Rmd'

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

Error: Vignette re-building failed.
Execution halted
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).}
       | ^
checkRd: (-1) OBMb.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) OBMb.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) OBMb.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) OBMb.Rd:31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) OBMb.Rd:32: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) OBMb.Rd:33: Lost braces in \itemize; \value handles \item{}{} directly
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: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.);
       |                  ^
checkRd: (-1) onlineCPD.Rd:35: Lost braces
    35 |  function(x, lambda){const_hazard(x, lambda=100)}
       |                     ^
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'duckdb_connection.R' 'get_database_functions.R' 'mysql_connection.R'
    'postgres_connection.R' 'snowflake_connection.R'
    'sqlite_connection.R' 'submit_query.R' 'vertica_connection.R'
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'octopus_api.R'
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'set_parameters.Rd'
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'OLStraj.R' 'cbc_lm.R'
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'app_server.R'
checkRd: (-1) oncotree.fit.Rd:63: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) oncotree.fit.Rd:64: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) oncotree.fit.Rd:65: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) oncotree.fit.Rd:66: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) oncotree.fit.Rd:67: Lost braces in \itemize; \value handles \item{}{} directly
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'global.R'
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'tab_onsv.R' 'tab_onsv.Rd'
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'format_search_term.R' 'openFDA.R'
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'acs12.Rd' 'arbuthnot.Rd' 'ask.Rd' 'biontech_adolescents.Rd'
    'birds.Rd' 'blizzard_salary.Rd' 'census.Rd' 'cia_factbook.Rd'
    'climber_drugs.Rd' 'comics.Rd' 'daycare_fines.Rd' 'dotPlot.Rd'
    'drone_blades.Rd' 'epa2021.Rd' 'exam_grades.Rd' 'fact_opinion.Rd'
    'family_college.Rd' 'fish_age.Rd' 'friday.Rd' 'gdp_countries.Rd'
    'gss_wordsum_class.Rd' 'house.Rd' 'iowa.Rd' 'ipo.Rd' 'iran.Rd'
    'labor_market_discriminiation.Rd' 'lecture_learning.Rd'
    'lego_population.Rd' 'lego_sample.Rd' 'lizard_run.Rd'
    'london_boroughs.Rd' 'london_murders.Rd' 'malaria.Rd' 'mariokart.Rd'
    'mlb_teams.Rd' 'mlbbat10.Rd' 'mn_police_use_of_force.Rd'
    'nba_finals.Rd' 'nba_finals_teams.Rd' 'nycflights.Rd' 'orings.Rd'
    'oscars.Rd' 'paralympic_1500.Rd' 'piracy.Rd' 'race_justice.Rd'
    'simpsons_paradox_covid.Rd' 'soda.Rd' 'sowc_child_mortality.Rd'
    'sowc_demographics.Rd' 'sowc_maternal_newborn.Rd' 'ssd_speed.Rd'
    'twins.Rd' 'ucla_textbooks_f18.Rd' 'us_temperature.Rd' 'usb_admit.Rd'
    'world_pop.Rd'
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'OpenRange_api_load_species.Rd' 'OpenRange_api_species.Rd'
    'OpenRange_load_species.Rd' 'OpenRange_sf.R' 'OpenRange_species.Rd'
checkRd: (-1) MonteCarlo.Rd:23: Lost braces
    23 | N is computed from \code{p} length. M is code{10^4} by default.
       |                                              ^
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 ?
checkRd: (-1) drawdesign.Rd:42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) drawdesign.Rd:43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) drawdesign.Rd:44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) orf.Rd:74: Lost braces
    74 | matrix of covariates \code{X} and a vector of outcomes 'code{Y} to the \code{orf}
       |                                                             ^
checkRd: (-1) hillEquation.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hillEquation.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hillEquation.Rd:30-31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hillEquation.Rd:31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hillEquation.Rd:32: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hillEquation.Rd:33: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hillEquation.Rd:34: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hillEquation.Rd:35: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) qiba.Rd:81-83: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) qiba.Rd:84-85: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) qiba.Rd:86-87: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) qiba.Rd:88-90: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) qiba.Rd:91-93: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) polynomial.derivatives.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) polynomial.derivatives.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) polynomial.derivatives.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) polynomial.integrals.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) polynomial.integrals.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) polynomial.integrals.Rd:21: Lost braces in \itemize; meant \describe ?
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'fitS4.R' 'helpers.R'
checkRd: (-1) oscar.Rd:44: Lost braces; missing escapes or markup?
    44 | \item{print}{Level of verbosity in Fortran (may not be visible on all terminals); should be an integer between {range, range}, Default: 3}
       |                                                                                                                ^
checkRd: (-1) oscar.control.Rd:41: Lost braces; missing escapes or markup?
    41 | \item{start}{Starting point generation method, see vignettes for details; should be an integer between {range,range}, Default: 2}
       |                                                                                                        ^
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/}
       |                                                                                                                                                                 ^
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}
       |                                               ^
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'owid.R'
checkRd: (-1) MICS2014Ch.Rd:296: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) MICS2014Ch.Rd:297: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) MICS2014HH.Rd:214: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) MICS2014HH.Rd:215: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) MICS2014HL.Rd:109: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) MICS2014HL.Rd:110: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) MICS2014Wm.Rd:336: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) MICS2014Wm.Rd:337: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) PakPMICS2018bh.Rd:88: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) PakPMICS2018bh.Rd:89: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) PakPMICS2018fs.Rd:308: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) PakPMICS2018fs.Rd:309: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) PakPMICS2018hh.Rd:362: Lost braces in \enumerate; meant \describe ?
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 ?
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}
       |                                                           ^
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 ?
checkRd: (-1) forbes400.Rd:9: Lost braces in \itemize; meant \describe ?
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 ?
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'evolve.Rd' 'genesis.Rd' 'simulate.Rd' 'wield.Rd'
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.}
       |                       ^
checkRd: (-1) plotHeat.Rd:113: Lost braces
   113 | code{\link[patternize]{patPCA}}, as 'one' when visualizing single image or as 'multi' for multi
       |     ^
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}  
       |                    ^
':::' 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.
Malformed Description field: should contain one or more complete sentences.
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 ?
checkRd: (-1) twoby2Calibrate.Rd:97-100: Lost braces in \itemize; meant \describe ?
checkRd: (-1) twoby2Calibrate.Rd:101-103: Lost braces in \itemize; meant \describe ?
checkRd: (-1) twoby2Calibrate.Rd:104-107: Lost braces in \itemize; meant \describe ?
checkRd: (-1) twoby2Calibrate.Rd:108-110: Lost braces in \itemize; meant \describe ?
checkRd: (-1) twoby2Calibrate.Rd:111-116: Lost braces in \itemize; meant \describe ?
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 ?
checkRd: (-1) PCM_ABC.Rd:114: Lost braces in \itemize; meant \describe ?
checkRd: (-1) PCM_ABC.Rd:115: Lost braces in \itemize; meant \describe ?
checkRd: (-1) PCM_ABC.Rd:117: Lost braces in \itemize; meant \describe ?
checkRd: (-1) PCM_ABC.Rd:205-207: Lost braces in \itemize; meant \describe ?
checkRd: (-1) PCM_ABC.Rd:208-211: Lost braces in \itemize; meant \describe ?
checkRd: (-1) PCM_ABC.Rd:212-216: Lost braces in \itemize; meant \describe ?
checkRd: (-1) PCM_ABC.Rd:221-224: Lost braces in \itemize; meant \describe ?
checkRd: (-1) PCM_ABC.Rd:225-228: Lost braces in \itemize; meant \describe ?
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 ?
checkRd: (-1) PCM_ABC.Rd:236: Lost braces in \itemize; meant \describe ?
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) 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.
       |     ^
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.
       |                                                                                                      ^
checkRd: (-1) variogramGuess.Rd:94: Lost braces
    94 | Method \code{"b"} was proposed by \doi{10.1016/0098-3004(95)00095-X}{Jian et al. (1996)} and
       |                                                                     ^
checkRd: (-1) variogramGuess.Rd:98: Lost braces
    98 | \doi{10.1016/j.cageo.2008.10.011}{Hiemstra et al. (2009)}.
       |                                  ^
checkRd: (-1) variogramGuess.Rd:100: Lost braces
   100 | Method \code{"d"} was developed by \doi{10.1007/s11004-012-9434-1}{Desassis & Renard (2012)}.
       |                                                                   ^
checkRd: (-1) DTV.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) DTV.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) DTV.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) DTV.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) DTV.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rosePlotsAct.Rd:19: Lost braces; missing escapes or markup?
    19 | A \code{plotly} {htmlwidget} with rose plots for locomotor activity.
       |                 ^
checkRd: (-1) rosePlotsSleep.Rd:19: Lost braces; missing escapes or markup?
    19 | #' @return A \code{plotly} {htmlwidget} with rose plots for sleep data.
       |                            ^
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'df_to_tier.R'
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'bake-par.R' 'bake.R' 'calculated-parameters.R' 'conductance.R'
    'constants.R' 'enviro-par.R' 'fit_aq_response.R'
    'fit_aq_response2.Rd' 'fit_photosynthesis.R' 'fit_r_light.R'
    'fit_r_light2.Rd' 'leaf-par.R' 'make_parameters.R' 'models.R'
    'parameter_names.R' 'photosynthesis.R' 'read_licor.R'
    'simulate_error.R' 'simulate_error.Rd' 'utils.R'
checkRd: (-1) 11_d.init.method.Rd:22-23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) 11_d.init.method.Rd:24-25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) 11_d.init.method.Rd:26-27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) 11_d.init.method.Rd:28-29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) 11_d.init.method.Rd:30-31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) 11_d.init.method.Rd:32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) 11_d.init.procedure.Rd:21-23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) 11_d.init.procedure.Rd:24-26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) 11_d.init.procedure.Rd:27-30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) 11_d.init.procedure.Rd:31-35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) as.star.tree.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) as.star.tree.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) as.star.tree.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) as.star.tree.Rd:29: Lost braces in \itemize; meant \describe ?
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
       |     ^
checkRd: (-1) IvesGodfray.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) IvesGodfray.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) IvesGodfray.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Kcalc.Rd:13: Escaped LaTeX specials: \$
checkRd: (-1) phylocom.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) phylocom.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) phylocom.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) phylosignal.Rd:13: Escaped LaTeX specials: \$
checkRd: (-1) sample2matrix.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sample2matrix.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sample2matrix.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) traitgram.Rd:14: Escaped LaTeX specials: \$
checkRd: (-1) utility.Rd:37: Escaped LaTeX specials: \$ \$
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'exr-read.R' 'exr-types-read.R' 'exr-write.R' 'utils.R'
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'piecenorm.R'
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'aliases.Rd' 'bind.Rd'
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'extract_col.Rd' 'na2empty.Rd' 'omit_na_cols.Rd' 'omit_na_rows.Rd'
    'pivot.R' 'pivot.Rd' 'utils.R' 'validate_col.Rd'
checkRd: (-1) get_pixels.Rd:27-29: Lost braces
    27 | if (interactive()) {
       |                    ^
checkRd: (-1) sprinkle_colnames.Rd:26-28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sprinkle_colnames.Rd:29-31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tidy_levels_labels.Rd:62: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tidy_levels_labels.Rd:63-68: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tidy_levels_labels.Rd:69-73: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tidy_levels_labels.Rd:74-77: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tidy_levels_labels.Rd:78-83: Lost braces in \itemize; meant \describe ?
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'buildPackageGraph.Rd' 'collectFunNames.Rd' 'functions.r'
    'plotPackageGraph.Rd' 'utils.r'
checkRd: (-1) one_design.Rd:125-126: Lost braces
   125 | function serves for the purpose of spot-testing for any pre-specified {n,
       |                                                                       ^
checkRd: (-1) plotluck.Rd:129: Lost braces
   129 |  in factors are are shown as a special factor level code{"?"}. They can be
       |                                                         ^
checkRd: (-1) domain_data.Rd:29: Lost braces
    29 | code{\link{help}}
       |     ^
checkRd: (-1) length_data.Rd:32: Lost braces
    32 | code{\link{help}}
       |     ^
checkRd: (-1) plotdomain.Rd:30: Lost braces
    30 | code{\link{help}}
       |     ^
checkRd: (-1) plotmutagensis.Rd:30: Lost braces
    30 | code{\link{help}}
       |     ^
checkRd: (-1) plotprotein-package.Rd:20: Lost braces
    20 | code{\link{help}}
       |     ^
checkRd: (-1) plotprotein.Rd:30: Lost braces
    30 | code{\link{help}}
       |     ^
checkRd: (-1) plotsite.Rd:30: Lost braces
    30 | code{\link{help}}
       |     ^
checkRd: (-1) site_data.Rd:30: Lost braces
    30 | code{\link{help}}
       |     ^
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'plug.R'
checkRd: (-1) plu_more.Rd:16: Lost braces; missing escapes or markup?
    16 | Additional arguments are replaced with "{n} more".
       |                                         ^
checkRd: (-1) PMCMR-deprecated.Rd:36: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) PMCMR-deprecated.Rd:37: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) PMCMR-deprecated.Rd:38: Lost braces in \itemize; \value handles \item{}{} directly
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
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'earned_value.R' 'planned_value.R' 'pmevR6.R'
checkRd: (-1) pmledecon.Rd:113: Lost braces; missing escapes or markup?
   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 $a_{ij} = 1/a_{ij}$.
       |                                                                                              ^
checkRd: (-1) estimate.functional.Rd:34: Lost braces; missing escapes or markup?
    34 | \item{bw}{function describing bandwidth selection (see ?gmm for alternatives). Standard is that the bandwidth depends on the sample length $T$ by $m(T)=T^{1/5}$.}
       |                                                                                                                                                           ^
checkRd: (-1) pois.fe.robust.Rd:47: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pois.fe.robust.Rd:48: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pois.fe.robust.Rd:49: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pois.fe.robust.Rd:50-51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pois.fe.robust.Rd:66: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pois.fe.robust.Rd:67: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pois.fe.robust.Rd:68-69: Lost braces in \itemize; \value handles \item{}{} directly
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'hiperfrac.R' 'rice.R'
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'hits.R' 'size.R' 'utils.R'
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}
       |        ^
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}}
       |                                                                                                     ^
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'getPrevalence.R'
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
       |                                                        ^
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'FSR.R' 'SR.R' 'helper_functions_model.R' 'plot.powerNLSEM.R'
    'smart_search.R'
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'save.R'
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})
       |                                                                                                                              ^
checkRd: (-1) dev_data.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dev_data.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dev_data.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dev_data.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dev_data.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gusto.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gusto.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gusto.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gusto.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gusto.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) val_data.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) val_data.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) val_data.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) val_data.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) val_data.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) preference-package.Rd:48-49: Lost braces in \itemize; meant \describe ?
checkRd: (-1) preference-package.Rd:50-51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) preference-package.Rd:52-53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) preference-package.Rd:58-60: Lost braces in \itemize; meant \describe ?
checkRd: (-1) preference-package.Rd:61-63: Lost braces in \itemize; meant \describe ?
checkRd: (-1) preference-package.Rd:68-69: Lost braces in \itemize; meant \describe ?
checkRd: (-1) preference-package.Rd:70-71: Lost braces in \itemize; meant \describe ?
checkRd: (-1) preference-package.Rd:72-73: Lost braces in \itemize; meant \describe ?
checkRd: (-1) preference-package.Rd:78-79: Lost braces in \itemize; meant \describe ?
checkRd: (-1) preference-package.Rd:80-81: Lost braces in \itemize; meant \describe ?
checkRd: (-1) preference.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) preference.Rd:22-23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) preference.Rd:24-25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) preference.Rd:26-27: Lost braces in \itemize; meant \describe ?
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 ?
Missing dependency on R >= 4.2.0 because package code uses the pipe
  placeholder syntax added in R 4.2.0.
  File(s) using such syntax:
    'estimate_risk.Rd'
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.
       |                                                                              ^
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.}
       |                                                                                                                                                                               ^
checkRd: (-1) proc.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) proc.Rd:28: Lost braces in \itemize; meant \describe ?
Unexported objects imported by ':::' calls:
  'bupaR:::allowed_lifecycles' 'bupaR:::apply_grouped_fun'
  See the note in ?`:::` about the use of this operator.
checkRd: (-1) paasche.Rd:91: Lost braces
    91 |     \code{OSME} \tab Output-oriented scale-mix efficiency score \emph{(code{orientation = "out"})}\cr
       |                                                                            ^
checkRd: (-1) PS.Rd:9: Lost braces
     9 |                 \item{CD}{}{Character disorder scale score}
       |                            ^
checkRd: (-1) proftools-package.Rd:40: Lost braces
    40 |   by the code{kcachegrind} program available on some operating
       |              ^
Found the following significant warnings:
  Warning: src/Makevars.ucrt: Unknown C++ standard 'CXX' was ignored
See 'd:/Rcompile/CRANpkg/local/4.5/PROJ.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 14.3.0'
checkRd: (-1) prolific_prescreener.Rd:254: Lost braces in \itemize; meant \describe ?
checkRd: (-1) prolific_prescreener.Rd:255: Lost braces in \itemize; meant \describe ?
checkRd: (-1) prolific_study.Rd:95: Lost braces in \itemize; meant \describe ?
checkRd: (-1) prolific_study.Rd:96: Lost braces in \itemize; meant \describe ?
checkRd: (-1) prolific_study.Rd:97: Lost braces in \itemize; meant \describe ?
checkRd: (-1) prolific_study.Rd:109: Lost braces in \itemize; meant \describe ?
checkRd: (-1) prolific_study.Rd:110: Lost braces in \itemize; meant \describe ?
checkRd: (-1) prolific_study.Rd:149: Lost braces in \itemize; meant \describe ?
checkRd: (-1) prolific_study.Rd:150: Lost braces in \itemize; meant \describe ?
checkRd: (-1) prolific_study.Rd:151: Lost braces in \itemize; meant \describe ?
checkRd: (-1) prolific_study.Rd:243: Lost braces in \itemize; meant \describe ?
checkRd: (-1) prolific_study.Rd:244: Lost braces in \itemize; meant \describe ?
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'complete_chat.R' 'complete_prompt.R' 'format_prompt.R'
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'build_url.R'
checkRd: (-1) struc_addSimData.Rd:15: Lost braces
    15 | \item{value}{code{data.frame} or code{data.table}}
       |                  ^
checkRd: (-1) struc_addSimData.Rd:15: Lost braces
    15 | \item{value}{code{data.frame} or code{data.table}}
       |                                      ^
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'nba_data.R' 'nba_data.Rd' 'nfl_data.R' 'nhl_data.R' 'nhl_data.Rd'
checkRd: (-1) prototest.univariate.Rd:21: Lost braces
    21 | response variable. Vector of length emph{n}, assumed to be quantitative.
       |                                         ^
checkRd: (-1) pr_stem_sentences.Rd:20: Lost braces; missing escapes or markup?
    20 | Implementation of the {SnowballC} stemmer. Note that punctuation and capital letters 
       |                       ^
checkRd: (-1) pr_stem_words.Rd:20: Lost braces; missing escapes or markup?
    20 | Implementation of the {SnowballC} stemmer. Note that punctuation and capitals letters 
       |                       ^
checkRd: (-1) proust_sentiments.Rd:7: Lost braces; missing escapes or markup?
     7 | See the {rfeel} package now: http://github.com/ColinFay/rfeel}
       |         ^
checkRd: (-1) proust_sentiments.Rd:20: Lost braces; missing escapes or markup?
    20 | See the {rfeel} package now: http://github.com/ColinFay/rfeel
       |         ^
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'get_proverbs.R'
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.}
       |  ^
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'pseudohouseholds.R'
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.}
       |                                                                                         ^
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}
       |                         ^
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){
       |                                                                                                              ^
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.}
       |                                        ^
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.
       |                                                                           ^
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}. 
       |                                                                                     ^
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'da.Rd' 'da_object_oriented_functions.R'
    'higher_level_disprop_analysis.R' 'lower_level_disprop_analysis.R'
    'print.da.Rd'
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
       |                                ^
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'pwrFDR.R'
checkRd: (-1) srswrRe.Rd:10: Lost braces
    10 |   \item{listRanef}{{\emph{ranef(model)}} object where {\emph{model}} is an { \emph{lmer}} object.}
       |                                                                            ^
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'qb_records.R'
checkRd: (-1) qif.Rd:45: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) qif.Rd:46: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) qif.Rd:47: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) qif.Rd:48: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) qif.Rd:49: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) qif.Rd:50: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) qif.Rd:51: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) qif.Rd:52: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) qif.Rd:53: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) qif.Rd:54: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) qif.Rd:55: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) qif.Rd:56: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) qif.Rd:57: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) qif.Rd:58: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) qif.Rd:59: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) qif.Rd:60: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) qif.Rd:61: Lost braces in \itemize; \value handles \item{}{} directly
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
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}.
       |                                                                                                                                                                                                                                                   ^
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}.}
       |                                                                  ^
Missing dependency on R >= 4.2.0 because package code uses the pipe
  placeholder syntax added in R 4.2.0.
  File(s) using such syntax:
    'qr_vcard.R'
Malformed Description field: should contain one or more complete sentences.
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 ?
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 ?
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'quax.Rd'
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
       |                                                      ^
checkRd: (-1) do_admb.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) do_admb.Rd:21: Lost braces in \itemize; meant \describe ?
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
checkRd: (-1) read_pars.Rd:32: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) read_pars.Rd:33: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) read_pars.Rd:34: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) read_pars.Rd:35: Lost braces in \itemize; \value handles \item{}{} directly
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
'library' or 'require' call to 'RDCOMClient' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
'library' or 'require' calls in package code:
  'RDCOMClient' 'rcom'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
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).
       |                                                                                                                                                                                                                                                                                                                                                                                                ^
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
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}
       |                                                                       ^
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'ao_get_leaners_progress_by_course.R'
Malformed Description field: should contain one or more complete sentences.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'add_element.Rd'
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
       |                                      ^
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}.}
       |                                 ^
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'evds_table_api.R' 'excel_internal.R' 'request_funcs.R'
    'sp_df_utils.R'
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'findblocks_bc.Rd' 'getdata_bc.Rd' 'listdata_bc.Rd' 'opendata_bc.Rd'
    'utils.R'
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}
       |                             ^
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'render_model.R'
Running 'run-all.R' [7s]
Running the tests in 'tests/run-all.R' failed.
Complete output:
  > library(testthat)
  > library(mlr)
  Loading required package: ParamHelpers
  > 
  > test_check("RBPcurve")
  Loading required package: RBPcurve
  Saving _problems/test_add-18.R
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 11 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_add.R:18:9'): add_functions ────────────────────────────────────
  Error in `rect(y1, x1, y2, x2, ...)`: invalid graphics state
  Backtrace:
      ▆
   1. └─RBPcurve (local) checkAdd(fun = k, obj = obj, plot.values = i, show.info = j) at test_add.R:18:9
   2.   ├─base::do.call(fun, fun.arg) at test_add.R:9:3
   3.   └─RBPcurve::addWellCalib(obj = `<S3: RBPObj>`, plot.values = TRUE)
   4.     ├─TeachingDemos::subplot(...)
   5.     ├─base::do.call(...)
   6.     ├─graphics::barplot(...)
   7.     └─graphics::barplot.default(...)
   8.       └─graphics (local) xyrect(...)
   9.         └─graphics::rect(y1, x1, y2, x2, ...)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 11 ]
  Error:
  ! Test failures.
  Execution halted
Running examples in 'rbranding-Ex.R' failed
The error most likely occurred in:

> ### Name: brand_add_logo
> ### Title: Add Brand Logo to ggplot2 Plot
> ### Aliases: brand_add_logo
> 
> ### ** Examples
> 
> {
+ # First set the brand theme to load configuration
+ old_wd <- getwd()
+ setwd(tempdir()) # Change to temp directory for example
+ brand_init()
+ get_brand_public()
+ get_template("blank")
+ brand_set_ggplot()
+ 
+ # Create a plot and add logo
+ library(ggplot2)
+ ggplot(mtcars, aes(x = mpg, y = wt)) +
+   geom_point() +
+   labs(title = "Example Plot") +
+   brand_add_logo()
+ 
+ # Customize logo position and size
+ ggplot(mtcars, aes(x = mpg, y = wt)) +
+   geom_point() +
+   labs(title = "Example Plot") +
+   brand_add_logo(x = 0.1, y = 0.9, size = 0.08)
+ 
+ setwd(old_wd) # Restore original working directory
+ }
Created files './rbranding_config.yml' and placeholder '_brand.yml' in current working directory
Checking remote version... 
Local branding file overwritten with remote file
Copied blank.txt to D:/temp/2026_05_04_16_41_50_24978/RtmpsHStC6
Copied icon.png to D:/temp/2026_05_04_16_41_50_24978/RtmpsHStC6
Copied logo.png to D:/temp/2026_05_04_16_41_50_24978/RtmpsHStC6
Brand theme applied successfully!
Error in brand_add_logo() : 
  No logo information found in brand configuration.
Execution halted
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"){
       |                        ^
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}. 
       |                                                                                                                                                                                                                                                 ^
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'utils.R'
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'print.rcpptimer.R'
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 
       |           ^
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 ?
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'helpers-process-tracing.R' 'process_tracing_estimator.Rd'
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)}.}
       |                                                                      ^
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). 
       |                                                           ^
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'gg_CD_local.R' 'gg_PIT_local.R'
checkRd: (-1) recombinator.Rd:32-34: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) recombinator.Rd:35-38: Lost braces in \enumerate; meant \describe ?
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
File 'rEDM/libs/x64/rEDM.dll':
  Found '_ZSt4cout', possibly from 'std::cout' (C++)
    Objects: 'cppEDM/lib/libEDM.a', 'cppEDM/src/libEDM.a'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
checkRd: (-1) make_refreshable.Rd:13: Lost braces
    13 | not that quotes need to be escaped (code{\"}).}
       |                                         ^
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".}}
       |                                  ^
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}.)
       |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  ^
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}.
       |                                                           ^
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.
       |                                                                                                                                   ^
Running examples in 'remstats-Ex.R' failed
The error most likely occurred in:

> ### Name: FEtype
> ### Title: FEtype
> ### Aliases: FEtype
> 
> ### ** Examples
> 
> history$type <- history$setting
> reh_tie <- remify::remify(history, model = "tie")
> effects <- ~ FEtype()
> remstats(reh = reh_tie, tie_effects = effects)
Error in if (attr(reh, "model") == "tie") { : argument is of length zero
Calls: remstats
Execution halted
Running 'tinytest.R' [1s]
Running the tests in 'tests/tinytest.R' failed.
Complete output:
  > 
  > if ( requireNamespace("tinytest", quietly=TRUE) ){
  + 	tinytest::test_package("remstats")
  + }
  
  test-bind-remstats.R..........    0 tests    
  test-bind-remstats.R..........    0 tests    Error in if (attr(reh, "model") == "tie") { : argument is of length zero
  Calls: <Anonymous> ... run_test_dir -> lapply -> FUN -> eval -> eval -> remstats
  Execution halted
Error(s) in re-building vignettes:
--- re-building 'remstats.Rmd' using rmarkdown

Quitting from remstats.Rmd:29-46 [unnamed-chunk-2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `if (attr(reh, "model") == "tie") ...`:
! argument is of length zero
---
Backtrace:
    ▆
 1. └─remstats::remstats(reh = rehObject, tie_effects = effects)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'remstats.Rmd' failed with diagnostics:
argument is of length zero
--- failed re-building 'remstats.Rmd'

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

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

> ### Name: aic
> ### Title: aic
> ### Aliases: aic aic.remstimate
> 
> ### ** Examples
> 
> 
> # ------------------------------------ #
> #       tie-oriented model: "MLE"      #
> # ------------------------------------ #
> 
> # loading data
> data(tie_data)
> 
> # processing event sequence with remify
> tie_reh <- remify::remify(edgelist = tie_data$edgelist, model = "tie")
>   
> # specifying linear predictor
> tie_model <- ~ 1 + 
+                remstats::indegreeSender()+
+                remstats::inertia()+
+                remstats::reciprocity() 
> 
> # calculating statistics
> tie_reh_stats <- remstats::remstats(reh = tie_reh, 
+                                     tie_effects = tie_model)
Error in if (attr(reh, "model") == "tie") { : argument is of length zero
Calls: <Anonymous>
Execution halted
Running 'tinytest.R' [1s]
Running the tests in 'tests/tinytest.R' failed.
Complete output:
  > if ( requireNamespace("tinytest", quietly=TRUE) ){
  +   tinytest::test_package("remstimate")
  + }
  
  test-remstimate-actor-oriented-pe.R    0 tests    
  test-remstimate-actor-oriented-pe.R    0 tests    
  test-remstimate-actor-oriented-pe.R    0 tests    
  test-remstimate-actor-oriented-pe.R    0 tests    
  test-remstimate-actor-oriented-pe.R    0 tests    Error in if (attr(reh, "model") == "tie") { : argument is of length zero
  Calls: <Anonymous> ... run_test_dir -> lapply -> FUN -> eval -> eval -> <Anonymous>
  Execution halted
Error(s) in re-building vignettes:
--- re-building 'remstimate.Rmd' using rmarkdown

Quitting from remstimate.Rmd:162-169 [unnamed-chunk-4]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `if (attr(reh, "model") == "tie") ...`:
! argument is of length zero
---
Backtrace:
    ▆
 1. └─remstats::remstats(reh = tie_reh, tie_effects = tie_model)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'remstimate.Rmd' failed with diagnostics:
argument is of length zero
--- failed re-building 'remstimate.Rmd'

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

Error: Vignette re-building failed.
Execution halted
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.
       |                                          ^
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
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'estimate_impact.R' 'plot_repsd.R' 'repsd_pval.R'
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'Require2.R' 'helpers.R' 'pak.R' 'pkgDep3.R'
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}
       |      ^
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'to_df.R'
checkRd: (-1) resistance.Rd:52: Lost braces
    52 |     \item B. Bollob\'{a}s, 1998.  \emph{Modern Graph Theory}.  Springer.
       |                      ^
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.5/restfulr.Rcheck/00install.out' for details.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'as_result.Rd' 'bind.R' 'bind.Rd' 'result.R' 'result.Rd'
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
       |                                                                         ^
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'define_an_exercise.Rd' 'define_exercises.Rd'
    'define_exercises_from_csv.Rd' 'define_exercises_from_excel.Rd'
checkRd: (-1) GenDataPopulation.Rd:21: Lost braces
    21 | {data}{Population of data}
       |       ^
checkRd: (-1) GenDataSample.Rd:23: Lost braces
    23 | {data}{Sample of data}
       |       ^
Malformed Description field: should contain one or more complete sentences.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'connection.R' 'level-set.R' 'lie-group.R' 'manifold.R' 'open-set.R'
    'spd-matrices.R' 'utils.R'
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 ?
Error(s) in re-building vignettes:
--- re-building 'Create_map_displaying_Ghana_2019_School_Attendance_Indicators.Rmd' using rmarkdown

Quitting from Create_map_displaying_Ghana_2019_School_Attendance_Indicators.Rmd:90-102 [plot_population_densities_of_school_drop_outs]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `[.data.frame`:
! undefined columns selected
---
Backtrace:
     ▆
  1. ├─base::withVisible(knit_print(x, ...))
  2. ├─knitr::knit_print(x, ...)
  3. └─tmap:::knit_print.tmap(x, ...)
  4.   └─tmap:::print.tmap(x, knit = TRUE, options = options, ...)
  5.     └─tmap:::step1_rearrange(x, knit_opts = options)
  6.       └─tmap:::step1_rearrange_facets(tmo, o)
  7.         └─base::lapply(...)
  8.           └─tmap (local) FUN(X[[i]], ...)
  9.             ├─tmap::tmapSubsetShp(shp, smvars)
 10.             └─tmap:::tmapSubsetShp.sf(shp, smvars)
 11.               ├─shp[, vars]
 12.               └─sf:::`[.sf`(shp, , vars)
 13.                 ├─x[i, j, drop = drop]
 14.                 └─base::`[.data.frame`(x, i, j, drop = drop)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'Create_map_displaying_Ghana_2019_School_Attendance_Indicators.Rmd' failed with diagnostics:
undefined columns selected
--- failed re-building 'Create_map_displaying_Ghana_2019_School_Attendance_Indicators.Rmd'

SUMMARY: processing the following file failed:
  'Create_map_displaying_Ghana_2019_School_Attendance_Indicators.Rmd'

Error: Vignette re-building failed.
Execution halted
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}
       |     ^
checkRd: (-1) rhandsontable-package.Rd:8: Lost braces
     8 | R interface for creating tables using Handsontable, url{https://handsontable.com/}
       |                                                        ^
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 ?
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'RHRVEasy.R' 'easyStatsFunctions.R'
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"}
       |                                                        ^
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,
and section 'Moving into C API compliance' for issues with the use of
non-API entry points.
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.}
       |                              ^
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'plotdensity.R'
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)
Found the following Makefile(s) with an include directive with a pathname using R_HOME:
  src/jri/src/Makefile.win
  src/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/4.5/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.
Error(s) in re-building vignettes:
--- re-building 'rjd3bench.Rmd' using rmarkdown

Quitting from rjd3bench.Rmd:98-131 [unnamed-chunk-2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `.jcall()`:
! RcallMethod: cannot determine object class
---
Backtrace:
    ▆
 1. └─rjd3bench::temporal_disaggregation(Y, indicators = x)
 2.   └─rjd3toolkit::.r2jd_tsdata(series)
 3.     └─rJava::.jcall(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'rjd3bench.Rmd' failed with diagnostics:
RcallMethod: cannot determine object class
--- failed re-building 'rjd3bench.Rmd'

SUMMARY: processing the following file failed:
  'rjd3bench.Rmd'

Error: Vignette re-building failed.
Execution halted
File 'rlang/libs/x64/rlang.dll':
  Found non-API calls to R: 'PRENV', 'PRVALUE', 'R_PromiseExpr',
    'Rf_allocSExp', 'Rf_findVarInFrame3', 'SETLENGTH',
    'SET_GROWABLE_BIT', 'SET_PRCODE', 'SET_PRENV', 'SET_PRVALUE',
    'SET_TRUELENGTH'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual,
and section 'Moving into C API compliance' for issues with the use of
non-API entry points.
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 ?
Missing dependency on R >= 4.2.0 because package code uses the pipe
  placeholder syntax added in R 4.2.0.
  File(s) using such syntax:
    'replace_doi.R'
File 'Rmixmod/libs/x64/Rmixmod.dll':
  Found '_ZSt4cout', possibly from 'std::cout' (C++)
    Object: 'mixmod.a'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
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)
       |                    ^
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'decrypt.Rd' 'encrypt.Rd' 'encrypt_raw.Rd'
checkRd: (-1) myTarGetClientList.Rd:33: Lost braces
    33 | {MyTarget API Documenation}{https://target.my.com/doc/api/detailed/#resource_agency_clients}
       |                            ^
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'compare_documents.Rd' 'term_char_sim.Rd' 'term_union.Rd'
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 ?
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
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.5/robregcc.Rcheck/00install.out' for details.
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 ?
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}".}
       |                                                                                                                                                                                                                                                                                                                                                               ^
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).}
       |                                                                                                                                 ^
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)
       |                                                         ^
checkRd: (-1) check_node.Rd:11: Lost braces
    11 | \item{x}{\\code{list}, the node to check}
       |                ^
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()}
       |                                                                                                            ^
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}
       |                      ^
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}.
       |                                                                                  ^
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'sort_tips.Rd' 'sort_tips.r' 'tips.r' 'validate_rankedPhylo.r'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.5/rsat.Rcheck/00install.out' for details.
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.
       |                                                                                                                                                          ^
Note: information on .o files for x64 is not available
File 'd:/Rcompile/CRANpkg/lib/4.5/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',
    'R_curErrorBuf', '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,
and section 'Moving into C API compliance' for issues with the use of
non-API entry points.
Running 'testthat.R' [8s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  > library(rsi)
  > 
  > test_check("rsi")
  Starting 2 test processes.
  > test-spectral_indices.R: 
  
  Error:
  ! testthat subprocess exited in file 'test-spectral_indices.R'.
  Caused by error:
  ! R session crashed with exit code -1073741819
  Backtrace:
       ▆
    1. └─testthat::test_check("rsi")
    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
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'geom-funs.R'
Found the following significant warnings:
  Warning: package 'foreign' was built under R version 4.6.0
See 'd:/Rcompile/CRANpkg/local/4.5/rsubgroup.Rcheck/00install.out' for details.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'lp.Rd'
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'add_row.Rd' 'delete_selected_rows.Rd' 'for_each_col.Rd' 'redo.Rd'
    'set_calculation.Rd' 'set_column_defaults.Rd' 'set_editor.Rd'
    'set_formatter_color.Rd' 'set_formatter_datetime.Rd'
    'set_formatter_html.Rd' 'set_formatter_image.Rd'
    'set_formatter_link.Rd' 'set_formatter_money.Rd'
    'set_formatter_plaintext.Rd' 'set_formatter_progress.Rd'
    'set_formatter_star.Rd' 'set_formatter_textarea.Rd'
    'set_formatter_tick_cross.Rd' 'set_formatter_toggle_switch.Rd'
    'set_formatter_traffic_light.Rd' 'set_header_filter.Rd'
    'set_multi_column_header.Rd' 'set_options_group_by.Rd'
    'set_options_pagination.Rd' 'set_tooltip.Rd' 'tabulatorContext.Rd'
    'titanic.Rd' 'trigger_download.Rd' 'trigger_get_data.Rd'
    'trigger_get_sheet_data.Rd' 'undo.Rd'
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}}.
       |                                                                    ^
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-65.R
  Saving _problems/test-td-101.R
  [ FAIL 2 | WARN 4 | SKIP 0 | PASS 10 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-td.R:65:3'): td_upload works with mock ─────────────────────────
  Error in `file(con, "w")`: cannot open the connection
  Backtrace:
      ▆
   1. └─RTD (local) setup_fake_embulk() at test-td.R:65:3
   2.   └─base::writeLines("@echo off\necho fake embulk", fake_embulk) at test-td.R:17:5
   3.     └─base::file(con, "w")
  ── Error ('test-td.R:101:3'): td_upload works with mock when the table already exists ──
  Error in `file(con, "w")`: cannot open the connection
  Backtrace:
      ▆
   1. └─RTD (local) setup_fake_embulk() at test-td.R:101:3
   2.   └─base::writeLines("@echo off\necho fake embulk", fake_embulk) at test-td.R:17:5
   3.     └─base::file(con, "w")
  
  [ FAIL 2 | WARN 4 | SKIP 0 | PASS 10 ]
  Error:
  ! Test failures.
  Execution halted
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'str_rtl.Rd'
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})}
       |     ^
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}}.
       |                                                                                                       ^
Found the following significant warnings:
  Warning: S3 methods '$<-.grouped_df', '[.fun_list', '[.grouped_df', '[.rowwise_df', '[<-.grouped_df', '[<-.rowwise_df', '[[<-.grouped_df', 'names<-.grouped_df', 'names<-.rowwise_df', 'add_count.data.frame', 'add_count.default', 'anti_join.data.frame', 'arrange.data.frame', 'as.data.frame.grouped_df', 'as_join_by.character', 'as_join_by.default', 'as_join_by.dplyr_join_by', 'as_join_by.list', 'as_tibble.grouped_df', 'as_tibble.rowwise_df', 'auto_copy.data.frame', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'count.data.frame', 'cross_join.data.frame', 'distinct.data.frame', 'do.NULL', 'do.data.frame', 'do.grouped_df', 'do.rowwise_df', 'dplyr_col_modify.data.frame', 'dplyr_col_modify.grouped_df', 'dplyr_col_modify.rowwise_df', 'dplyr_reconstruct.data.frame', 'dplyr_reconstruct.grouped_df', 'dplyr_reconstruct.rowwise_df', 'dplyr_row_slice.data.frame', ' [... truncated]
See 'd:/Rcompile/CRANpkg/local/4.5/rupturesRcpp.Rcheck/00install.out' for details.
* used C++ compiler: 'g++.exe (GCC) 14.3.0'
checkRd: (-1) RUVIII.Rd:51: Lost braces
    51 | If code{return.info} is \code{TRUE}, a list is returned that contains:
       |        ^
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) }
       |                                                                                   ^
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}).
       |                               ^
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'.
Malformed Title field: should not end in a period.
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.}
       |                                            ^
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    's3_check_for_file.R' 's3_file_size.R' 's3_get.Rd' 's3_get_files.R'
    's3_parse_uri.R'
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'fit_density_ratio.R' 'fit_plug_and_play.R'
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'class-2-differential.r' 'dual-apply.r' 'dual-math.r'
    'dual-summary.r' 'dual-test-near-equality.r' 'dual.r' 'dualFun1.Rd'
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'cmc_psat.Rd' 'h-fun.R' 'mc-test.R' 'tshift.R'
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.}
       |         ^
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'as_SpatRaster.Rd' 'clip_bands.Rd' 'get_band_names.Rd'
    'get_spatial_resolution.Rd' 'get_spectral_band_names.Rd'
    'merge_tiles.Rd' 'save_by_resolution.Rd' 'select_bands.Rd'
Running examples in 'savonliquide-Ex.R' failed
The error most likely occurred in:

> ### Name: check_contrast
> ### Title: Color Contrast Accessibility Report
> ### Aliases: check_contrast
> 
> ### ** Examples
> 
> 
> check_contrast(fg_col = "#21EA06", bg_col = "#483D3D")
Error:
! Failed to evaluate glue component {response$status_code}
Caused by error:
! object 'response' not found
Backtrace:
     ▆
  1. ├─savonliquide::check_contrast(fg_col = "#21EA06", bg_col = "#483D3D")
  2. │ └─base::tryCatch(...)
  3. │   └─base (local) tryCatchList(expr, classes, parentenv, handlers)
  4. │     └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
  5. │       └─value[[3L]](cond)
  6. │         ├─base::message(glue::glue("Error: here the API response status: {response$status_code}"))
  7. │         └─glue::glue("Error: here the API response status: {response$status_code}")
  8. │           └─glue::glue_data(...)
  9. ├─glue (local) `<fn>`("response$status_code")
 10. │ ├─.transformer(expr, env) %||% .null
 11. │ └─glue (local) .transformer(expr, env)
 12. │   ├─glue:::with_glue_error(...)
 13. │   │ └─base::withCallingHandlers(...)
 14. │   └─base::eval(expr, envir)
 15. │     └─base::eval(expr, envir)
 16. └─base::.handleSimpleError(...)
 17.   └─glue (local) h(simpleError(msg, call))
 18.     └─rlang::abort(message, parent = cnd, call = NULL)
Execution halted
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 ?
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.5/scAnnotate.Rcheck/00install.out' for details.
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}
       |                                              ^
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'nap.R' 'randomization_test.R' 'scdtb.R'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.5/scPOEM.Rcheck/00install.out' for details.
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]}}
       |                                                          ^
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.}
       |                 ^
Error(s) in re-building vignettes:
--- re-building 'spatial_matrices.Rmd' using rmarkdown
--- re-building 'spatial_model.Rmd' using rmarkdown
--- finished re-building 'spatial_model.Rmd'

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

Error: Vignette re-building failed.
Execution halted
checkRd: (-1) hyperpar.Rd:17: Lost braces
    17 | \item{c}{denotes the expected range of eqn{f} .}
       |                                           ^
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'assign_meta_data.Rd'
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'series.R'
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 PUBLIC "-//W3C//
                     (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"}.}
       |                                                                                                                                   ^
Malformed Title field: should not end in a period.
Malformed Description field: should contain one or more complete sentences.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'selcorr.R'
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'as.list.selenider_elements.Rd' 'elem_ancestors.Rd' 'elem_attr.Rd'
    'elem_cache.Rd' 'elem_click.Rd' 'elem_css_property.Rd'
    'elem_equal.Rd' 'elem_expect.Rd' 'elem_expect_all.Rd'
    'elem_filter.Rd' 'elem_flatten.Rd' 'elem_hover.Rd' 'elem_name.Rd'
    'elem_scroll_to.Rd' 'elem_select.Rd' 'elem_size.Rd' 'elem_text.Rd'
    'find_each_element.Rd' 'find_element.Rd' 'find_elements.Rd'
    'get_actual_element.Rd' 's.Rd'
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 ?
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'Joiner.Rd' 'Splitter.Rd' 'add_node.Rd' 'print.sewage_pipeline.Rd'
    'pull_output.Rd' 'run.Rd'
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'st_transform_outline.R'
Running 'testthat.R' [10s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  > library(sfislands)
  > 
  > test_check("sfislands")
Running 'testthat.R' [34s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(sfnetworks)
  > 
  > test_check("sfnetworks")
  Saving _problems/test_paths-45.R
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 276 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_paths.R:41:3'): Only the first from argument
            is used for shortest paths calculations ──
  Error in `all_shortest_paths(x, from, to, weights = weights, ...)`: `from` must specify exactly one vertex
  Backtrace:
       ▆
    1. ├─testthat::expect_warning(...) at test_paths.R:41:3
    2. │ └─testthat:::quasi_capture(...)
    3. │   ├─testthat (local) .capture(...)
    4. │   │ └─base::withCallingHandlers(...)
    5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
    6. ├─sfnetworks::st_network_paths(...)
    7. └─sfnetworks:::st_network_paths.sfnetwork(...)
    8.   └─sfnetworks:::get_all_shortest_paths(...)
    9.     └─igraph::all_shortest_paths(x, from, to, weights = weights, ...)
   10.       └─igraph:::get_all_shortest_paths_dijkstra_impl(...)
   11.         └─cli::cli_abort(...)
   12.           └─rlang::abort(...)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 276 ]
  Error:
  ! Test failures.
  Execution halted
Running examples in 'sftime-Ex.R' failed
The error most likely occurred in:

> ### Name: st_crop.sftime
> ### Title: Crop an 'sftime' object to a specific rectangle
> ### Aliases: st_crop.sftime
> 
> ### ** Examples
> 
> # modified from sf:
> box <- c(xmin = 0, ymin = 0, xmax = 1, ymax = 1)
> pol <- sf::st_sfc(sf::st_buffer(sf::st_point(c(0.5, 0.5)), 0.6))
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},
       |                                          ^
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'sgraph_utils.R'
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 ?
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})}
       |                              ^
checkRd: (-1) shiftrPrepare.Rd:37: Lost braces
    37 |     See code{\link{shiftrPermBinary}} function and the respective example.
       |             ^
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'destroyModule.R' 'makeModule.R'
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'continue_sequence.R' 'get_exchange_rates.R'
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.
       |                                                                                                    ^
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'lottie_addEventListener.Rd' 'lottie_button.Rd'
    'lottie_removeEventListener.Rd'
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}
       |            ^
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'fabs.Rd'
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 ?
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'app_server.R' 'function.R'
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 ?
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.'
       |                       ^
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
       |              ^
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'show_group_enrichment.R'
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/4.5/SIGN.Rcheck/00install.out' for details.
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
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'p_sie.R' 'prp.R' 'siie.R'
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))}
       |                                                     ^
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) {
       |                         ^
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'bootstrap-projection.R' 'bootstrap_CIs.Rd' 'bundle_sim.R'
    'calc_coverage.R' 'calc_rejection.R' 'extrapolate_coverage.Rd'
    'utilities.R'
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
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'si_calculate.Rd'
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'anon.R' 'anonymise.Rd'
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'markdown_block.R'
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'glimpse_na.Rd'
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
       |                                                     ^
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 ?
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.
       |                                                                                                  ^
Malformed Description field: should contain one or more complete sentences.
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.
       |                                        ^
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'SiZer.R'
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'ext-annotate_expr.R'
Running 'abind.R' [0s]
  Comparing 'abind.Rout' to 'abind.Rout.save' ... OK
  Running 'apply.R' [0s]
  Comparing 'apply.Rout' to 'apply.Rout.save' ... OK
  Running 'crossprod.R' [0s]
  Comparing 'crossprod.Rout' to 'crossprod.Rout.save' ... OK
  Running 'dimgets.R' [0s]
  Running 'extract.R' [0s]
  Comparing 'extract.Rout' to 'extract.Rout.save' ... OK
  Running 'matrix.R' [0s]
  Comparing 'matrix.Rout' to 'matrix.Rout.save' ... OK
  Running 'matrix_dimnames.R' [0s]
  Comparing 'matrix_dimnames.Rout' to 'matrix_dimnames.Rout.save' ... OK
  Running 'rollup.R' [0s]
  Comparing 'rollup.Rout' to 'rollup.Rout.save' ... OK
  Running 'split.R' [0s]
  Comparing 'split.Rout' to 'split.Rout.save' ... OK
  Running 'ssa_valid.R' [0s]
  Comparing 'ssa_valid.Rout' to 'ssa_valid.Rout.save' ... OK
  Running 'stm.R' [0s]
  Comparing 'stm.Rout' to 'stm.Rout.save' ... OK
  Running 'stm_apply.R' [0s]
  Comparing 'stm_apply.Rout' to 'stm_apply.Rout.save' ... OK
  Running 'stm_rollup.R' [0s]
  Comparing 'stm_rollup.Rout' to 'stm_rollup.Rout.save' ...113a114,115
> _row_tsums: reduced 1 (3) zeros
> _row_tsums: 0.000s [0.000s/0.000s]
  Running 'stm_subassign.R' [0s]
  Comparing 'stm_subassign.Rout' to 'stm_subassign.Rout.save' ... OK
  Running 'stm_ttcrossprod.R' [0s]
  Comparing 'stm_ttcrossprod.Rout' to 'stm_ttcrossprod.Rout.save' ... OK
  Running 'stm_valid.R' [0s]
  Comparing 'stm_valid.Rout' to 'stm_valid.Rout.save' ... OK
  Running 'stm_zeros.R' [0s]
  Comparing 'stm_zeros.Rout' to 'stm_zeros.Rout.save' ... OK
  Running 'subassign.R' [0s]
  Comparing 'subassign.Rout' to 'subassign.Rout.save' ... OK
  Running 'util.R' [0s]
  Comparing 'util.Rout' to 'util.Rout.save' ... OK
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] +
       |          ^
checkRd: (-1) cities_lon_lat.Rd:6: Lost braces
     6 | A subset of world.cities{maps}. Extracted in order to shink number of dependencies. 
       |                         ^
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 ?
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},....}
       |                                                                                ^
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)) 
       |                                                              ^
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'sk.R' 'sk_export.R' 'sk_index.R' 'sk_pars.R' 'sk_plot.R'
    'sk_plot.Rd' 'sk_sub.Rd' 'sk_var.Rd' 'sk_var_mult.Rd'
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.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'gtable_ld_associations_combine.Rd' 'gtable_ld_grobs.Rd'
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'PowerRelation.R' 'SocialRanking.R' 'copeland.R' 'doRanking.Rd'
    'elementLookup.Rd' 'generator.R' 'makePowerRelationMonotonic.R'
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
       |                                                  ^
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 ?
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'soundSpeed.Rd'
checkRd: (-1) load_sorvi_data.Rd:23: Lost braces in \itemize; meant \describe ?
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'SouthPark_Script_Data.Rd' 'app_server.R'
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
       |                             ^
Malformed Description field: should contain one or more complete sentences.
checkRd: (-1) cholsolveAQinvAT.Rd:5: Lost braces; missing escapes or markup?
     5 | \title{Solve the equation X = AQ^{-1}t(A) under permutations}
       |                                  ^
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.
       |                                                     ^
File 'sparsevctrs/libs/x64/sparsevctrs.dll':
  Found non-API call to R: 'DATAPTR'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual,
and section 'Moving into C API compliance' for issues with the use of
non-API entry points.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'sim_functional_process.R'
checkRd: (-1) distSG.Rd:40: Lost braces; missing escapes or markup?
    40 |   matrix and weight matrix (plus a matrix with {eID} identifiers
       |                                                ^
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'federov.R'
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.
       |                                                              ^
checkRd: (-1) FitAkdParameters.Rd:23: Lost braces; missing escapes or markup?
    23 |       p(y|ens) = 1 / K * sum {dnorm(y, z.i, s)} \cr
       |                              ^
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'analysis_age.R' 'analysis_alpha.R' 'analysis_helpers.R'
    'analysis_helpers_table.R' 'analysis_photo.R' 'analysis_radio.R'
    'analysis_setup.R' 'export_Output_Settings.R' 'export_download.R'
    'export_helpers.R' 'export_helpers_plot.R' 'export_helpers_table.R'
    'import_examples.R' 'import_examples_box.R'
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'innprod.R' 'utils.R'
checkRd: (-1) speech_recompiler.Rd:25: Lost braces; missing escapes or markup?
    25 | The default compilation is that of \ code {speech_build (., compiler = TRUE}).
       |                                           ^
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'import_qiime2_tax_table.R' 'import_sintax_tax_table.R'
checkRd: (-1) cylinder.counts.Rd:61-62: Lost braces
    61 | nucleotide, so that \code{a.c} represents the set {\code{aac}, \code{acc}, 
       |                                                   ^
checkRd: (-1) adaptIntegrateSpherePolar.Rd:14: Lost braces
    14 | code{adaptIntegrateBallPolar()} will likely miss these abrupt changes and give
       |     ^
checkRd: (-1) speedtestdata.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) speedtestdata.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) speedtestdata.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) speedtestdata.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) speedtestdata.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) speedtestdata.Rd:23: Lost braces in \itemize; meant \describe ?
Running 'testthat.R' [9s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(spMaps)
  Loading required package: sf
  Linking to GEOS 3.14.1, GDAL 3.12.1, PROJ 9.7.1; sf_use_s2() is TRUE
  Loading required package: sp
  > 
  > test_check("spMaps")
Missing dependency on R >= 4.2.0 because package code uses the pipe
  placeholder syntax added in R 4.2.0.
  File(s) using such syntax:
    'addlearn_local.R'
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).
       |                                                     ^
checkRd: (-1) new.distance.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) new.distance.Rd:31-32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) new.distance.Rd:33-34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) new.distance.Rd:35-36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) new.distance.Rd:37-38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) new.distance.Rd:39-40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sensitivity.plot.Rd:30-33: Lost braces in \itemize; meant \describe ?
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 ?
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
       |       ^
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}
       |                  ^
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'stamp.direction.r'
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
       |                                           ^
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}.
       |                                                                                                            ^
checkRd: (-1) stargazer.Rd:229: Lost braces
   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.}
       |                                                                         ^
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'stat_frequency.R'
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'character_dimensions.Rd' 'constellation_as_multistar.Rd'
    'constellation_as_tibble_list.Rd' 'define_dimension.Rd'
    'define_fact.Rd' 'dm_mrs_age.Rd' 'dm_mrs_cause.Rd'
    'filter_dimension.Rd' 'filter_fact_rows.Rd'
    'get_conformed_dimension.Rd' 'get_conformed_dimension_names.Rd'
    'get_dimension.Rd' 'get_dimension_attribute_names.Rd'
    'get_dimension_names.Rd' 'get_measure_names.Rd' 'get_star_schema.Rd'
    'get_star_schema_names.Rd' 'incremental_refresh_constellation.Rd'
    'incremental_refresh_star_schema.Rd' 'match_records.Rd'
    'modify_conformed_dimension_records.Rd' 'modify_dimension_records.Rd'
    'ms_mrs.Rd' 'ms_mrs_test.Rd' 'multistar_as_flat_table.Rd'
    'purge_dimensions_constellation.Rd' 'purge_dimensions_star_schema.Rd'
    'rename_dimension.Rd' 'rename_dimension_attributes.Rd'
    'rename_fact.Rd' 'rename_measures.Rd' 'role_playing_dimension.Rd'
    'run_query.Rd' 'select_dimension.Rd' 'select_fact.Rd' 'snake_case.Rd'
    'st_mrs_age.Rd' 'st_mrs_age_test.Rd' 'st_mrs_age_w10.Rd'
    'st_mrs_age_w11.Rd' 'st_mrs_age_w_test.Rd' 'st_mrs_cause.Rd'
    'st_mrs_cause_test.Rd' 'st_mrs_cause_w10.Rd' 'st_mrs_cause_w11.Rd'
    'st_mrs_cause_w_test.Rd' 'star_schema_as_flat_table.Rd'
    'star_schema_as_multistar.Rd' 'star_schema_as_tibble_list.Rd'
    'update_record.Rd' 'update_selection.Rd'
    'update_selection_general.Rd' 'updates_st_mrs_age.Rd'
    'updates_st_mrs_age_test.Rd'
checkRd: (-1) AutoPollution.Rd:16: Lost braces
    16 |     \code{Side} \tab {Side of vehicle: code{1}=right or \code{2}=left}\cr
       |                                            ^
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'od_list.R' 'od_resource.R' 'od_utils.R' 'other_endpoints.R'
    'sc_data.R' 'schema.R' 'schema_uri.R' 'sdmx_table.R' 'table.R'
    'table_as_data_frame.R' 'table_json.R' 'table_meta.R' 'table_saved.R'
Found the following possibly unsafe calls:
File 'statnet.common/R/control.utilities.R':
  unlockBinding("snctrl", environment(snctrl))
  unlockBinding("snctrl", environment(update_my_snctrl))
unable to reach CRAN

It looks like this package (or a package it requires) has a startup
message which cannot be suppressed: see ?packageStartupMessage.
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
       |                                                                ^
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")}
       | ^
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'Functions.R'
Malformed Title field: should not end in a period.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'defStormsList.R'
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}{
       |                            ^
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
       | ^
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'apportion_inverse.R' 'apportion_polygon.R' 'apportion_web.R'
    'prep_reach_dist.R'
Malformed Title field: should not end in a period.
efpFunctional: multiple local function definitions for 'plotProcess'
  with different formal arguments
mefp.efp: multiple local function definitions for 'computeEmpProc' with
  different formal arguments
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} ) |}
       |                                                                                                                                            ^
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'geom_glyph_ribbon.R' 'geom_glyph_ribbon.Rd' 'geom_glyph_segment.Rd'
    'theme_glyph.Rd'
checkRd: (-1) suggests.Rd:14: Lost braces; missing escapes or markup?
    14 | {suggests} aims to make that workflow as minimal and painless as possible,
       | ^
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) 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.}
       |                                                                          ^
checkRd: (-1) getFittedProbs.Rd:6-8: Lost braces
     6 | getFittedValues <- function(object) {
       |                                     ^
checkRd: (-1) getFittedProbs.Rd:14-16: Lost braces
    14 | getFittedValues <- function(object) {
       |                                     ^
checkRd: (-1) tprob.Rd:138: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tprob.Rd:139: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tprob.Rd:140: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tprob.Rd:141: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tprob.Rd:142: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tprob.Rd:143: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tprob.Rd:144: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tprob.Rd:145: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tprob.Rd:146: Lost braces in \itemize; meant \describe ?
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'censor_event.Rd' 'survival_class.R'
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
       |                                                        ^
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'suso_gql_helpers.R' 'suso_gql_uploadMap.R'
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
       |                     ^
checkRd: (-1) hyph.support.en.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) hyph.support.en.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) elliptical.ts.Rd:18: Lost braces; missing escapes or markup?
    18 |   \item{epsilon}{positive convergence tolerance \emph{e}; the iterations converge when |fit - fit_{old}|/|fit| < \emph{e}. Default is \emph{e=1e-04}.}
       |                                                                                                   ^
Missing or unexported objects:
  'harmony::HarmonyMatrix' 'harmony::moe_ridge_get_betas'
Error(s) in re-building vignettes:
--- re-building 'quickstart_tutorial.Rmd' using rmarkdown

Quitting from quickstart_tutorial.Rmd:142-154 [unnamed-chunk-11]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! 'HarmonyMatrix' is not an exported object from 'namespace:harmony'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'quickstart_tutorial.Rmd' failed with diagnostics:
'HarmonyMatrix' is not an exported object from 'namespace:harmony'
--- failed re-building 'quickstart_tutorial.Rmd'

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

Error: Vignette re-building failed.
Execution halted
checkRd: (-1) coord2dist.Rd:14: Lost braces; missing escapes or markup?
    14 | \code{n} x 4 matrix of coordinates consisting of {lat or y, lon or x} pairs for each each site
       |                                                  ^
checkRd: (-1) create_synthetic_example.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) create_synthetic_example.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) create_synthetic_example.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) initial_estimates_example.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) initial_estimates_example.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) initial_estimates_example.Rd:12: Lost braces in \itemize; meant \describe ?
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)")}.}
       |       ^
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}}]...'.
       |                      ^
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'add_lines.R' 'init.R' 'plots.R' 'report.R' 'tokenize.R'
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'auth0.R' 'config.R' 'entra_id.R' 'google.R' 'utils.R'
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 'counting.R' [0s]
  Comparing 'counting.Rout' to 'counting.Rout.save' ...26a27,28
> counting ... 9 string(s) using 19 nodes [0.00s]
> writing  ... 16 strings [0.00s]
47a50
> counting ... 9 string(s) using 19 nodes [0.00s]
49a53,54
> counting ... 9 string(s) using 19 nodes [0.00s]
> writing  ... 16 strings [0.00s]
70a76,77
> counting ... 2 string(s) using 5 nodes [0.00s]
> writing  ... 2 strings [0.00s]
77a85,86
> counting ... 2 string(s) using 5 nodes [0.00s]
> writing  ... 4 strings [0.00s]
86a96,97
> counting ... 2 string(s) using 6 nodes [0.00s]
> writing  ... 5 strings [0.00s]
96a108,109
> counting ... 2 string(s) using 6 nodes [0.00s]
> writing  ... 5 strings [0.00s]
106a120
> counting ... 2 string(s) using 5 nodes [0.00s]
108a123,124
> counting ... 2 string(s) using 5 nodes [0.00s]
> writing  ... 2 strings [0.00s]
  Running 'counting_useBytes.R' [1s]
  Comparing 'counting_useBytes.Rout' to 'counting_useBytes.Rout.save' ...32a33,34
> counting ... 10 string(s) using 19 nodes [0.00s]
> writing  ... 19 strings [0.00s]
56a59
> counting ... 10 string(s) using 19 nodes [0.00s]
58a62,63
> counting ... 10 string(s) using 19 nodes [0.00s]
> writing  ... 19 strings [0.00s]
82a88,89
> counting ... 2 string(s) using 5 nodes [0.00s]
> writing  ... 2 strings [0.00s]
89a97,98
> counting ... 2 string(s) using 5 nodes [0.00s]
> writing  ... 5 strings [0.00s]
99a109,110
> counting ... 2 string(s) using 6 nodes [0.00s]
> writing  ... 6 strings [0.00s]
110a122,123
> counting ... 2 string(s) using 6 nodes [0.00s]
> writing  ... 6 strings [0.00s]
121a135
> counting ... 2 string(s) using 5 nodes [0.00s]
123a138,139
> counting ... 2 string(s) using 5 nodes [0.00s]
> writing  ... 2 strings [0.00s]
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'parse_schema.R'
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'TaylorRussell.Rd'
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}.}
       |                                                                                                                                                                                                                                                                                                                                                  ^
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'mobius-strips.Rd'
checkRd: (-1) lognormConstCVCI.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) lognormConstCVCI.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) lognormConstCVCI.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) normConstCVCI.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) normConstCVCI.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) normConstCVCI.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) testassay.Rd:32: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) testassay.Rd:33: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) testassay.Rd:34: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) testassay.Rd:35: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) testassay.Rd:36: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) testassay.Rd:37: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) testassay.Rd:38: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) testassay.Rd:39: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) testassay.Rd:40: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) permucycle.Rd:37: Lost braces; missing escapes or markup?
    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.}
       |  ^
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'tex_preview.Rd'
Missing dependency on R >= 4.2.0 because package code uses the pipe
  placeholder syntax added in R 4.2.0.
  File(s) using such syntax:
    'textra.R'
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}{
       |                  ^
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
checkRd: (-1) shoulders.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'iterate.Rd' 'random_walk_rank.Rd'
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'tidymodl.R' 'tidymodl.Rd'
Found the following significant warnings:
  Warning: replacing previous import 'checkmate::check_data_frame' by 'rlang::check_data_frame' when loading 'tidynorm'
  Warning: replacing previous import 'checkmate::check_string' by 'rlang::check_string' when loading 'tidynorm'
See 'd:/Rcompile/CRANpkg/local/4.5/tidynorm.Rcheck/00install.out' for details.
* used C++ compiler: 'g++.exe (GCC) 14.3.0'
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'tidy_plate.R'
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'summarise2.Rd'
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'tcor.Rd'
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'base-lenses.R' 'where_il.Rd'
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.}
       |                                           ^
checkRd: (-1) tierChart.Rd:332: Lost braces
   332 |   If the input argument code{boxes} is \code{F}, the \code{lBox},
       |                             ^
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 ?
tmapGetShapeMeta1:
  function(shp, layer, o)
tmapGetShapeMeta1.sfnetwork:
  function(shp, o)

tmapShape:
  function(shp, is.main, crs, bbox, unit, filter, layer, shp_name,
           smeta, o, tmf)
tmapShape.sfnetwork:
  function(shp, is.main, crs, bbox, unit, filter, shp_name, smeta, o,
           tmf)
See section 'Generic functions and methods' in the 'Writing R
Extensions' manual.
Running examples in 'tmap.networks-Ex.R' failed
The error most likely occurred in:

> ### Name: tm_edges
> ### Title: Map layer: edges of a (sf)network
> ### Aliases: tm_edges opt_tm_edges
> 
> ### ** Examples
> 
> library(tmap)
> library(sfnetworks)
> 
> sfn = as_sfnetwork(roxel)
> 
> tm_shape(sfn) +
+ 	tm_network()
Error in tmapGetShapeMeta1.sfnetwork(shp, layer, c(o, tmg$tmf)) : 
  unused argument (c(o, tmg$tmf))
Calls: <Anonymous> ... step1_rearrange_facets -> lapply -> FUN -> tmapGetShapeMeta1
Execution halted
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.
       |                                                 ^
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 ?
Running 'testthat.R' [238s]
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(tnl.Test)
  > 
  > test_check("tnl.Test")
  Saving _problems/test_function-65.R
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 64 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_function.R:65:3'): functions returns a  vector with the expected size ──
  <rlib_error_package_not_found/rlang_error/error/condition>
  Error in `expect_vector(rtnl(10, 5, 10, 2), ptype = double(), size = 10)`: The package "vctrs" is required.
  Backtrace:
      ▆
   1. └─testthat::expect_vector(...) at test_function.R:65:3
   2.   └─rlang::check_installed("vctrs")
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 64 ]
  Error:
  ! Test failures.
  Execution halted
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'Get_time_entries.R'
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
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}}
       |                                                    ^
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'response_builder.R'
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
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'tree_mesh.R' 'tree_mesh.Rd' 'zzz.R'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.5/TreeDist.Rcheck/00install.out' for details.
File 'treesitter/libs/x64/treesitter.dll':
  Found non-API calls to R: 'PRENV', 'PRVALUE', 'R_PromiseExpr',
    'Rf_allocSExp', 'Rf_findVarInFrame3', 'SETLENGTH',
    'SET_GROWABLE_BIT', 'SET_PRCODE', 'SET_PRENV', 'SET_PRVALUE',
    'SET_TRUELENGTH'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual,
and section 'Moving into C API compliance' for issues with the use of
non-API entry points.
Malformed Title field: should not end in a period.
checkRd: (-1) summary.armasubsets.Rd:16: Lost braces
    16 | \item{matrix.logical}{With matrix=TRUE, the matrix is logical TRUE/FALSE or string "*"/code{" "}}
       |                                                                                            ^
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'calc_distance.R' 'reason_dataleaks.R' 'viz_dataleaks.R'
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'benchmark.R' 'print.R'
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.
       |                                                          ^
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'berkowitz.R' 'dac.R' 'gmm.R' 'hongli.R' 'minzar.R' 'nyblom.R'
    'shortfall_de.R' 'signbias.R' 'var.R' 'var_cp.R'
Malformed Description field: should contain one or more complete sentences.
checkRd: (-1) twosigmag.Rd:83: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) twosigmag.Rd:84: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) twosigmag.Rd:85: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) twosigmag.Rd:86: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) twosigmag.Rd:87: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) twosigmag.Rd:88: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) twosigmag.Rd:89: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) twosigmag.Rd:90: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) twosigmag.Rd:91: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) twosigmag.Rd:92: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) twosigmag.Rd:94: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) twosigmag.Rd:95: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) twosigmag.Rd:96: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) twoway.Rd:66: Lost braces
    66 | code{\link{twoway.formula}}, code{\link[stats]{medpolish}}
       |     ^
checkRd: (-1) twoway.Rd:66: Lost braces
    66 | code{\link{twoway.formula}}, code{\link[stats]{medpolish}}
       |                                  ^
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}).
       |                                ^
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'annotate_mf.R' 'annotate_mf_all.R'
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
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'runm.Rd' 'unm_summary.R'
Missing dependency on R >= 4.2.0 because package code uses the pipe
  placeholder syntax added in R 4.2.0.
  File(s) using such syntax:
    'available_version.R'
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'county_complete.Rd' 'fatal_police_shootings.Rd' 'gerrymander.Rd'
    'pierce_county_house_sales.Rd' 'pop_age_2019.Rd' 'pop_race_2019.Rd'
    'state_stats.Rd' 'us_temp.Rd'
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'intersection_powerset.R' 'powerset_icounts.Rd' 'pr.R' 'pr.boot.Rd'
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'usgas.Rd'
Malformed Title field: should not end in a period.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'build_model.coxph.Rd' 'build_table.coxph.Rd' 'build_table.lm.Rd'
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'cusum_failure.Rd' 'cusum_loglike.Rd' 'cusum_ome.Rd' 'cusum_sprt.Rd'
    'paste.R'
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'benchmark_event.R' 'benchmark_event.Rd' 'benchmark_score.R'
    'benchmark_score.Rd' 'benchmark_time.R'
    'compare_means_between_groups.R' 'compare_means_between_groups.Rd'
    'compare_means_within_groups.R' 'compare_rates_between_groups.R'
    'compare_rates_between_groups.Rd' 'compare_rates_within_groups.R'
    'get_concordant_discordant_pairs.R'
    'get_confidence_intervals_within_groups.R'
    'table_observed_expected.R' 'test_chisq_one.R' 'test_chisq_one.Rd'
    'test_chisq_two.Rd' 'test_fisher.Rd' 'test_mcnemar.R'
    'test_n_1_prop.R' 'test_n_1_prop.Rd' 'test_t.R' 'test_t_paired.R'
checkRd: (-1) sendTasks.Rd:41: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sendTasks.Rd:43: Lost braces in \itemize; \value handles \item{}{} directly
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})
       |                                                                                      ^
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
       |                                                                                                                                   ^
checkRd: (-1) simulateDCSIS.Rd:40: Lost braces
    40 |        Y = 6*X1 + 1.5*X2  + 9*1{X12 < 0} + exp(2*X22)*e
       |                                ^
checkRd: (-1) simulateDCSIS.Rd:42: Lost braces
    42 |        Y = 6*X1 + 1.5*X2  + 9*1{X12 < 0} + 6*X22 + e
       |                                ^
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.}
       |                                                                                             ^
checkRd: (-1) decomposition.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) decomposition.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) decomposition.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimation.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimation.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimation.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) moving.decomposition.Rd:27-28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) moving.decomposition.Rd:28: Lost braces
    28 | \item{W2}{nxn matrix of weights. Season is estimated as W2 \%}\% y, if y is the data vector}
       |      ^
checkRd: (-1) moving.decomposition.Rd:28: Lost braces
    28 | \item{W2}{nxn matrix of weights. Season is estimated as W2 \%}\% y, if y is the data vector}
       |          ^
checkRd: (-1) moving.estimation.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) moving.estimation.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) moving.estimation.Rd:31: Lost braces in \itemize; \value handles \item{}{} directly
File 'vctrs/libs/x64/vctrs.dll':
  Found non-API calls to R: 'PRENV', 'PRVALUE', 'R_PromiseExpr',
    'Rf_allocSExp', 'Rf_findVarInFrame3', 'SETLENGTH',
    'SET_GROWABLE_BIT', 'SET_PRCODE', 'SET_PRENV', 'SET_PRVALUE',
    'SET_TRUELENGTH'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual,
and section 'Moving into C API compliance' for issues with the use of
non-API entry points.
checkRd: (-1) additiveBeta.Rd:40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) additiveBeta.Rd:41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) additiveBeta.Rd:43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) additiveBeta.Rd:44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) additiveBeta.Rd:45: Lost braces in \itemize; meant \describe ?
checkRd: (-1) additiveBeta.Rd:47: Lost braces in \itemize; meant \describe ?
checkRd: (-1) downloadPBDB.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) downloadPBDB.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) downloadPBDB.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) downloadPBDB.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) downloadPBDB.Rd:31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) downloadPBDB.Rd:32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) downloadPBDB.Rd:33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) downloadPBDB.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) multiplicativeBeta.Rd:31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) multiplicativeBeta.Rd:32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) multiplicativeBeta.Rd:33: Lost braces in \itemize; meant \describe ?
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?}
       |                                                                                                   ^
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 ?
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'functions_upload.R' 'mod_hidecan.R'
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
checkRd: (-1) getTurnType.Rd:38: Lost braces; missing escapes or markup?
    38 | Return one of {Vocalisation, GrpVocalisation, ...} or identifier.
       |               ^
File 'vroom/libs/x64/vroom.dll':
  Found non-API calls to R: 'DATAPTR', 'SETLENGTH', 'SET_GROWABLE_BIT',
    'SET_TRUELENGTH'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual,
and section 'Moving into C API compliance' for issues with the use of
non-API entry points.
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 ?
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) 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
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'walkscore.R'
Missing or unexported object: 'tmap::tm_scale_bar'
Error(s) in re-building vignettes:
--- re-building 'waterquality_vignette.Rmd' using rmarkdown

Quitting from waterquality_vignette.Rmd:122-129 [unnamed-chunk-11]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! 'tm_scale_bar' is not an exported object from 'namespace:tmap'
---
Backtrace:
    ▆
 1. └─waterquality::Map_WQ_raster(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'waterquality_vignette.Rmd' failed with diagnostics:
'tm_scale_bar' is not an exported object from 'namespace:tmap'
--- failed re-building 'waterquality_vignette.Rmd'

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

Error: Vignette re-building failed.
Execution halted
checkRd: (-1) Session.Rd:146: Lost braces
   146 | sQuote{page load} timeout specifies a time to wait for the page loading
       |       ^
checkRd: (-1) busTrace.Rd:15: Lost braces
    15 | /href{https://crawdad.org/coppe-ufrj/RioBuses/20180319/}
       |      ^
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
       |                         ^
Running examples in 'WeightedTreemaps-Ex.R' failed
The error most likely occurred in:

> ### Name: drawTreemap
> ### Title: drawTreemap
> ### Aliases: drawTreemap
> 
> ### ** Examples
> 
> # load package
> library(WeightedTreemaps)
> 
> # generate dummy data
> df <- data.frame(
+   A = rep(c("abcd", "efgh"), each = 4),
+   B = letters[1:8],
+   size = c(37, 52, 58, 27, 49, 44, 34, 45)
+ )
> 
> # compute treemap
> tm <- voronoiTreemap(
+   data = df,
+   levels = c("B"),
+   cell_size = "size",
+   shape = "circle",
+   positioning = "regular",
+   seed = 123
+ )
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'coords_from_words.R' 'get_available_languages.R'
    'words_from_coords.R'
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'define_characteristics.Rd' 'define_instances.Rd' 'export.R'
    'generate_table.Rd' 'get_attribute_definition_function.Rd'
    'get_day_part.Rd' 'get_level_attribute_names.Rd' 'get_level_names.Rd'
    'get_table.Rd' 'get_table_attribute_names.Rd' 'get_table_csv.Rd'
    'get_table_rdb.Rd' 'get_table_xlsx.Rd' 'select_date_levels.Rd'
    'select_day_level.Rd' 'select_month_level.Rd'
    'select_quarter_level.Rd' 'select_semester_level.Rd'
    'select_time_level.Rd' 'select_week_level.Rd' 'select_year_level.Rd'
    'set_attribute_definition_function.Rd' 'set_day_part.Rd'
    'set_table_attribute_names.Rd' 'week.R'
Found the following significant warnings:
  Warning: replacing previous import 'bit64::setdiff' by 'dplyr::setdiff' when loading 'whSample'
  Warning: replacing previous import 'bit64::intersect' by 'dplyr::intersect' when loading 'whSample'
  Warning: replacing previous import 'bit64::union' by 'dplyr::union' when loading 'whSample'
  Warning: replacing previous import 'bit64::setequal' by 'dplyr::setequal' when loading 'whSample'
See 'd:/Rcompile/CRANpkg/local/4.5/whSample.Rcheck/00install.out' for details.
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 ?
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 ?
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'TWP.Rd'
Malformed Description field: should contain one or more complete sentences.
Malformed Description field: should contain one or more complete sentences.
Malformed Description field: should contain one or more complete sentences.
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 ?
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}
       |         ^
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'add_frag.R' 'data_frag.R' 'elem.Rd' 'list_as_xml_document.R'
    'read_fragment.R' 'tag.R' 'write_xml.R' 'xml_fragment.R'
    'xmlbuilder.R' 'xmlbuilder.Rd'
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}.}
       |                                                                                             ^
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'exhaustive_lhl.Rd' 'gaussian_fit.Rd' 'hyperbolic_fit.Rd'
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'zcta.R'
Malformed Description field: should contain one or more complete sentences.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'cache_report.R' 'list_deposit.R'
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'deposit_stats.R' 'scrap_stats.R'
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'external_fitters.Rd' 'zfunction.Rd' 'zlm.Rd' 'zprint.Rd'
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'notate.R'
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"}.
       |                                          ^