Package unavailable to check Rd xrefs: ‘INLA’
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    34 | email{noahsilverman@ucla.edu}
       |      ^
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    11 | the following child folders: {repo_base}/bin/ and {repo_base}/src/. A
       |                              ^
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    11 | the following child folders: {repo_base}/bin/ and {repo_base}/src/. A
       |                                                   ^
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    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
       |                                                   ^
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checkRd: (-1) breast_cancer_clean_features.Rd:45: Escaped LaTeX specials: \&
checkRd: (-1) MangroveTree.Rd:37: Lost braces
    37 |       An object of class \\code{\link[Mangrove]{MangrovePed}}
       |                                ^
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) manipulateWidget.Rd:113-117: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) EEGwide.Rd:30-33: Lost braces
    30 |   if(requireNamespace("ggplot2")){ 
       |                                  ^
Package suggested but not available for checking: ‘RSiena’
'LazyData' is specified without a 'data' directory
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    19 | \eqn{0} means there exists no path for node \eqn{i} and {j}.
       |                                                         ^
Found the following significant warnings:

  Warning in plotmapa(mapafit) : 'plotmapa' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU (user + system) or elapsed time > 5s
         user system elapsed
mapa    2.935  0.135   5.099
mapafor 2.925  0.040   5.161
Specified C++14: please drop specification unless essential
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Bug Fixes
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
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    53 | When {sparse=TRUE} (default), spike--and--slab priors are imposed to identify important main and interaction effects. If {sparse=FALSE}, Laplacian shrinkage will be used.
       |      ^
checkRd: (-1) marble.Rd:53: Lost braces; missing escapes or markup?
    53 | When {sparse=TRUE} (default), spike--and--slab priors are imposed to identify important main and interaction effects. If {sparse=FALSE}, Laplacian shrinkage will be used.
       |                                                                                                                          ^
checkRd: (-1) marble.Rd:55: Lost braces; missing escapes or markup?
    55 | When {robust=TRUE} (default), the distribution of \eqn{\epsilon_{i}} is defined as a Laplace distribution with density
       |      ^
checkRd: (-1) marble.Rd:58: Lost braces; missing escapes or markup?
    58 | }, (\eqn{i=1,\dots,n}), which leads to a Bayesian formulation of LAD regression. If {robust=FALSE}, \eqn{\epsilon_{i}} follows a normal distribution.
       |                                                                                     ^
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    29 | \code{\link{quickfit}}, code{\link{locator}}
       |                             ^
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    14 | 1. \code{\link{estimate_shift}} {Estimate a range shift process.}
       |                                 ^
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    16 | 2. \code{\link{simulate_shift}} {Simulate a range shift process.}
       |                                 ^
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    18 | 3. \code{\link{plot.shiftfit}} {Visualize a range shift process.}
       |                                ^
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    20 | 4. \code{\link{test_rangeshift}} {Test whether a range shift occurred.}
       |                                  ^
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    22 | 5. \code{\link{test_return}} {Test whether a migration was a return migration.}
       |                              ^
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    24 | 6. \code{\link{test_stopover}} {Test whether a stopover occurred during a migration.}
       |                                ^
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checkRd: (-1) mma.Rd:67: Escaped LaTeX specials: \&
Package vignette with \VignetteEngine{} not specifying an engine package:
  ‘TechnicalDetails.Rnw’
Engines should be specified as \VignetteEngine{PKG::ENG}.
checkRd: (-1) residuals.rsm.Rd:74: Escaped LaTeX specials: \&
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    28 | ( if(is.ts(DATA)) { DATA <- as.matrix(data.frame(DATA)) } and a message
       |                   ^
checkRd: (-1) marima.Rd:223: Escaped LaTeX specials: \&
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    17 | \item{inputId}{The code{input} slot that will be used to access the value.}
       |                        ^
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'LazyData' is specified without a 'data' directory
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    31 | \item{stringchar}{It can be a {n x n} matrix or a character vector or a list}
       |                               ^
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    39 | \item{data}{It can be a character vector or a {n x n} matrix or a {n x n} data frame or a list}
       |                                               ^
checkRd: (-1) markovchainFit.Rd:39: Lost braces; missing escapes or markup?
    39 | \item{data}{It can be a character vector or a {n x n} matrix or a {n x n} data frame or a list}
       |                                                                   ^
checkRd: (-1) markovchainFit.Rd:61: Lost braces; missing escapes or markup?
    61 | {k x k} where k is the number of states in the chain and the values
       | ^
GNU make is a SystemRequirements.
checkRd: (-1) Markovchart.Rd:154: Lost braces
   154 | If either \code{h} or \code{k} have length greater than 1, then the \code{G-value} (weighted average of average cost and cost standard deviation) is calculated for all given values without optimisation. The value of the function in this case is a data frame of class code{Markov_grid} with \code{length(h)*length(k)} number of rows and three columns for \code{h}, \code{k} and the \code{G-value}.
       |                                                                                                                                                                                                                                                                                ^
checkRd: (-1) marqLevAlg-package.Rd:14: Lost braces; missing escapes or markup?
    14 | (GH^{-1}G).
       |     ^
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘marssTMB’
'LazyData' is specified without a 'data' directory
checkRd: (-1) focalCompare.Rd:14: Lost braces
    14 | \item{fun}{The function fun should take multiple numbers, and return a single number. For example mean, modal, min or max. It should also accept a na.rm argument (or ignore it, e.g. as one of the 'dots' arguments. For example, length will fail, but function(x, ...){na.omit(length(x))} works. (Specifications from `raster::focal`)}
       |                                                                                                                                                                                                                                                                          ^
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     9 | kernelBiweight <- function(x, mean = 0, sd = 1) {
       |                                                 ^
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    33 | kernelCosine <- function(x, mean = 0, sd = 1) {
       |                                               ^
checkRd: (-1) hr_levels.Rd:41-44: Lost braces
    41 | kernelEpanechnikov <- function(x, mean = 0, sd = 1) {
       |                                                     ^
checkRd: (-1) hr_levels.Rd:58-61: Lost braces
    58 | kernelOptCosine <- function(x, mean = 0, sd = 1) {
       |                                                  ^
checkRd: (-1) hr_levels.Rd:65-68: Lost braces
    65 | kernelRectangular <- function(x, mean = 0, sd = 1) {
       |                                                    ^
checkRd: (-1) hr_levels.Rd:72-75: Lost braces
    72 | kernelSquaredCosine <- function(x, mean = 0, sd = 1) {
       |                                                      ^
checkRd: (-1) hr_levels.Rd:79-82: Lost braces
    79 | kernelTriangular <- function(x, mean = 0, sd = 1) {
       |                                                   ^
checkRd: (-1) hr_levels.Rd:86-89: Lost braces
    86 | kernelTricube <- function(x, mean = 0, sd = 1) {
       |                                                ^
checkRd: (-1) hr_levels.Rd:93-96: Lost braces
    93 | kernelTriweight <- function(x, mean = 0, sd = 1) {
       |                                                  ^
checkRd: (-1) hr_levels.Rd:100-103: Lost braces
   100 | kernelUniform <- function(x, mean = 0, sd = 1) {
       |                                                ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) CF2004.Rd:8: Lost braces; missing escapes or markup?
     8 |   \item{X2}{an optional second variable with same length as \code{X}, should the equation be multiple (see Details) {in mm}}
       |                                                                                                                     ^
'LazyData' is specified without a 'data' directory
Invalid package aliases in Rd file 'NewPackage-package.Rd':
  ‘NewPackage-package’
Auto-generated content requiring editing in Rd file 'NewPackage-package.Rd':
  \references: ‘This optional section can contain literature or other refere...’
  \seealso: ‘Optional links to other man pages’
  \examples: ‘\dontrun{      ## Optional simple examples of the most impor...’
Package suggested but not available for checking: ‘gurobi’
checkRd: (-1) Rand.index.Rd:22: Lost braces; missing escapes or markup?
    22 | The two vectors \code{x} and \code{y} must have equal length. Given a set \eqn{S} and two partitions \eqn{X} and \eqn{Y} of \eqn{S}, the Rand index is the proportion of pairs of elements in \eqn{S} (out of all pairs) that are either concordant in both \eqn{X} and \eqn{Y} (i.e., they belong to the same member of \eqn{X} and to the same member of \eqn{Y}) or discordant (i.e., not concordant) in both \eqn{X} and {Y}.  
       |                                                                                                                                                                                                                                                                                                                                                                                                                              ^
checkRd: (-1) predict.matchFeat.Rd:21: Lost braces
    21 | The function \code{predict.matchFeat} finds the best matching for new feature vectors relative to an existing set of cluster/class centers. If code{object} results from a call to \code{\link{match.gaussmix}}, the same function is used for prediction (with fixed mean vectors and covariance matrices). In other cases, the function \code{\link{match.template}} is used for prediction. 
       |                                                                                                                                                    ^
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘gurobi’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rrelaxiv’
checkRd: (-1) matchMulti-package.Rd:75: Lost braces
    75 | c("\\Sexpr[results=rd,stage=build]{tools:::Rd_package_author(\"#1\")}",
       |                                   ^
checkRd: (-1) matchMulti-package.Rd:79: Lost braces
    79 | c("\\Sexpr[results=rd,stage=build]{tools:::Rd_package_maintainer(\"#1\")}",
       |                                   ^
checkRd: (-1) Match.Rd:90: Lost braces; missing escapes or markup?
    90 | expression in braces. For example, the condition "{[ab]*}" is equivalent
       |                                                   ^
checkRd: (-1) size_t-class.Rd:6: Escaped LaTeX specials: \_
checkRd: (-1) vectors3d.Rd:86: Lost braces
    86 | \code{\link{arrows3d}}, code{\link[rgl]{texts3d}}, code{\link[rgl]{rgl.material}}
       |                             ^
checkRd: (-1) vectors3d.Rd:86: Lost braces
    86 | \code{\link{arrows3d}}, code{\link[rgl]{texts3d}}, code{\link[rgl]{rgl.material}}
       |                                                        ^
'LazyData' is specified without a 'data' directory
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checkRd: (-1) r1.Rd:71: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) r1.Rd:75: Lost braces in \itemize; meant \describe ?
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}.
       |                                        ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘utilities.R’
checkRd: (-1) MaxentVariableSelection-package.Rd:46: Lost braces; missing escapes or markup?
    46 | \tab Tyberghein L, Verbruggen H, Pauly K, Troupin C, Mineur F and {De Clerck}, O (2012)\cr
       |                                                                   ^
'LazyData' is specified without a 'data' directory
Package vignettes without corresponding tangle output:
  ‘intro-to-maximum-likelihood.Rnw’
  ‘stochastic-gradient-maxLik.Rnw’
  ‘using-maxlik.Rnw’
'LazyData' is specified without a 'data' directory
Found export directive that requires package ‘methods’:
  ‘exportClasses’
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains ‘methods’.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘map_5.png’ ‘maze_5.html’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) findDescendingTrans.Rd:29: Lost braces
    29 |    Foster, S.D., Hosack, G.R., J. Monk, Lawrence, E., Barrett, N.S., Williams, A. and Przeslawski, P. (2020) Spatially-Balanced Designs for Transect-Based Surveys. Methods in Ecology and Evolution. emph{11}: 95--105
       |                                                                                                                                                                                                           ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) SIGMAS.Rd:17: Lost braces; missing escapes or markup?
    17 | Sigmahat =  (Y^{T} Y)/n;
       |                ^
checkRd: (-1) SIGMAS.Rd:18: Lost braces; missing escapes or markup?
    18 | Sigmahat_fit = (Y^{T}  P_fx  Y)/n;
       |                   ^
checkRd: (-1) matpower.Rd:17: Lost braces; missing escapes or markup?
    17 | The function computes M^{power} for a symmetric matrix M. }
       |                         ^
Error(s) in re-building vignettes:
  ...
--- re-building ‘examples_mbreaks.Rmd’ using rmarkdown
Could not fetch http://www.zotero.org/styles/elsevier-harvard
HttpExceptionRequest Request {
  host                 = "www.zotero.org"
  port                 = 80
  secure               = False
  requestHeaders       = []
  path                 = "/styles/elsevier-harvard"
  queryString          = ""
  method               = "GET"
  proxy                = Nothing
  rawBody              = False
  redirectCount        = 10
  responseTimeout      = ResponseTimeoutDefault
  requestVersion       = HTTP/1.1
  proxySecureMode      = ProxySecureWithConnect
}
 (InternalException (HandshakeFailed (Error_Protocol "peer does not support Extended Main Secret" HandshakeFailure)))
Error: processing vignette 'examples_mbreaks.Rmd' failed with diagnostics:
pandoc document conversion failed with error 61
--- failed re-building ‘examples_mbreaks.Rmd’

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

Error: Vignette re-building failed.
Execution halted
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.
       |                                        ^
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'LazyData' is specified without a 'data' directory
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checkRd: (-1) mc.lnOR.Rd:7: Escaped LaTeX specials: \&
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checkRd: (-1) MCtest.Rd:39: Escaped LaTeX specials: \#
checkRd: (-1) MCtest.Rd:40: Escaped LaTeX specials: \#
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'LazyData' is specified without a 'data' directory
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checkRd: (-1) ess.Rd:14: Lost braces
    14 | \code{g} should take a vector input only. Ifcode{g} is \code{NULL}, \code{g} is set to be identity, which is estimation
       |                                                 ^
Package suggested but not available for checking: ‘cmdstanr’
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Documented arguments not in \usage in Rd file 'geom_cp_density.Rd':
  ‘include’

Documented arguments not in \usage in Rd file 'get_simulate.Rd':
  ‘par_trials’ ‘pars_pop’ ‘pars_varying’

Documented arguments not in \usage in Rd file 'pp_eval.Rd':
  ‘...’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
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'LazyData' is specified without a 'data' directory
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Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Initial version.
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checkRd: (-1) mcvis.Rd:34: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) pBED.Rd:34: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) get_mdgc.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) get_mdgc.Rd:35: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) get_mdgc.Rd:37: Lost braces in \itemize; meant \describe ?
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    19 | 	\item{expGroup}{ a \code{vector} of experimental grouping variable such as plate. The length of code{expGroup} must be same as the number of rows of \code{mD}.}
       |                                                                                                             ^
Package suggested but not available for checking: ‘RGtk2’
'LazyData' is specified without a 'data' directory
checkRd: (-1) data.mb.Rd:76: Lost braces
    76 | level-1 variables code{y}, \code{x} and the level-2 variable \code{w}.
       |                       ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) mdp_example_forest.Rd:36: Lost braces; missing escapes or markup?
    36 | Let {1, ... S} be the states of the forest. the Sth state being the oldest.
       |     ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) Elections.Rd:8: Lost braces
     8 | An object of class \\code{tbl_df} (inherits from \\code{tbl}, \\code{data.frame}) 
       |                          ^
checkRd: (-1) Elections.Rd:8: Lost braces
     8 | An object of class \\code{tbl_df} (inherits from \\code{tbl}, \\code{data.frame}) 
       |                                                        ^
checkRd: (-1) Elections.Rd:8: Lost braces
     8 | An object of class \\code{tbl_df} (inherits from \\code{tbl}, \\code{data.frame}) 
       |                                                                     ^
checkRd: (-1) Violations.Rd:39-45: Lost braces
    39 | {
       | ^
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘MethylCapSig’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘cmdstanr’
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) bhm.mcmc.Rd:37: Lost braces; missing escapes or markup?
    37 |   where \eqn{N_{ij}} denotes the number of times that the error profile \eqn{i} is cited on a report from hospital {j} and \eqn{y_{ij}} is the corresponding number of times that profile \eqn{i} in hospital \eqn{j} was reported with harm.
       |                                                                                                                    ^
checkRd: (-1) strings-internal.Rd:14: Lost braces
    14 | code{stringPlaceExact}: find location of string, using exact match
       |     ^
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    17 | code{stringPlaceFuzzy}: find location of string, using partial match
       |     ^
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    19 | code{stringPlace}: find location of string, generic
       |     ^
checkRd: (-1) strings-internal.Rd:21: Lost braces
    21 | code{checkFuzzy}: check for "close" string matches
       |     ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) MED.Rd:25: Lost braces
    25 | The vector of treatment assignments of length \eqn{n}. Must be coded as \eqn{\{0,1} {{0,1}}.
       |                                                                                     ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) medScan.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) medScan.Rd:24-26: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘Data_Correlation.txt’ ‘correlation_FDR_table.txt’
'LazyData' is specified without a 'data' directory
checkRd: (-1) mgLandscape.Rd:79: Lost braces
    79 | A code{$summary} table giving the results of the variation partitioning.  The following table
       |       ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) Soybean.Rd:15: Escaped LaTeX specials: \#
checkRd: (-1) Soybean.Rd:33: Escaped LaTeX specials: \#
'LazyData' is specified without a 'data' directory
checkRd: (-1) Mercator-class.Rd:91-92: Lost braces
    91 |     \item{barplot{height, main = '', sub = NULL, border = NA, space =
       |                  ^
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   109 |     \item{hist:}{\code{signature(object = "Mercator")}}{
       |                                                        ^
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   113 |     \item{summary:}{\code{signature(object = "Mercator")}}{
       |                                                           ^
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   117 |     \item{dim:}{\code{signature(object = "Mercator")}}{
       |                                                       ^
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   120 |     \item{[:}{\code{signature(object = "Mercator")}}{
       |                                                     ^
checkRd: (-1) threshLGF.Rd:21: Lost braces; missing escapes or markup?
    21 |   \item{object}{An object of class {BinaryMatrix}
       |                                    ^
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) expand.Rd:28: Lost braces; missing escapes or markup?
    28 | approximate dates (annotated with '..', '{ , }', 'XX' or '~').
       |                                          ^
Package suggested but not available for checking: ‘INLA’
'LazyData' is specified without a 'data' directory
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
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checkRd: (-1) CVLasoelacox.Rd:86-87: Lost braces in \itemize; \value handles \item{}{} directly
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    14 | * `"{{index}}"` : This means to use the index of rows/items
       |     ^
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    15 | * `"{{name}}"`  : This means to use row/item names.
       |     ^
checkRd: (-1) get_sort_var.Rd:16: Lost braces
    16 | * `"{{value}}"` : This means to use the values in vectors or lists. Lists}
       |     ^
checkRd: (-1) lookup_tax_data.Rd:57: Lost braces
    57 | * `"{{index}}"` : This means to use the index of rows/items
       |     ^
checkRd: (-1) lookup_tax_data.Rd:58: Lost braces
    58 | * `"{{name}}"`  : This means to use row/item names.
       |     ^
checkRd: (-1) lookup_tax_data.Rd:59: Lost braces
    59 | * `"{{value}}"` : This means to use the values in vectors or lists. Lists
       |     ^
checkRd: (-1) parse_tax_data.Rd:82: Lost braces
    82 | following: * For tables, the names of columns can be used. * `"{{index}}"` : This means to use
       |                                                                ^
checkRd: (-1) parse_tax_data.Rd:83: Lost braces
    83 | the index of rows/items * `"{{name}}"`  : This means to use row/item names. * `"{{value}}"` :
       |                             ^
checkRd: (-1) parse_tax_data.Rd:83: Lost braces
    83 | the index of rows/items * `"{{name}}"`  : This means to use row/item names. * `"{{value}}"` :
       |                                                                                 ^
Invalid package aliases in Rd file 'taxa-package.Rd':
  ‘taxa-package’
Documented arguments not in \usage in Rd file 'limited_print.Rd':
  ‘trunc’

Documented arguments not in \usage in Rd file 'parse_heirarchies_to_taxonomy.Rd':
  ‘A’

Documented arguments not in \usage in Rd file 'parse_raw_heirarchies_to_taxonomy.Rd':
  ‘A’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘cycHumanBloodData.csv’ ‘cycHumanBloodDesign.csv’
  ‘cycMouseLiverProtein.txt’ ‘cycMouseLiverRNA.csv’ ‘cycSimu4h2d.csv’
  ‘cycYeastCycle.csv’ ‘example’
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'Rcgmin', 'Rvmmin'
checkRd: (-1) conv.wald.Rd:109: Lost braces; missing escapes or markup?
   109 |       Note that the back-calculated sampling variance for study 2 is not identical in these two examples, because the CI bounds and p-value are rounded to two decimal places, which introduces some inaccuracies. Also, if both (\code{ci.lb}, \code{ci.ub}) and either \code{zval} or {pval} is available for a study, then the back-calculation of \mjseqn{v_i} via the confidence interval is preferred.
       |                                                                                                                                                                                                                                                                                         ^
Unknown packages ‘Rcgmin’, ‘Rvmmin’ in Rd xrefs
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"}.
       |                                                                                                                                                                                                                                                                                                                                        ^
'LazyData' is specified without a 'data' directory
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
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checkRd: (-1) asympVar_LinReg.Rd:55: Lost braces in \itemize; \value handles \item{}{} directly
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checkRd: (-1) asympVar_LogReg.Rd:55: Lost braces in \itemize; \value handles \item{}{} directly
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
'LazyData' is specified without a 'data' directory
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
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checkRd: (-1) rland.graph.Rd:33-34: Lost braces in \itemize; \value handles \item{}{} directly
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checkRd: (-1) param.Rd:29: Lost braces
    29 | T. Strub, S. Giuliano, T. Ye, et al. (2011) Essential role of microphthalmia transcription factor for DNA replication, mitosis and genomic stability in melanoma. emph{Oncogene} \bold{30}:2319-32.
       |                                                                                                                                                                       ^
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
checkRd: (-1) cardiac.Rd:15: Escaped LaTeX specials: \&
checkRd: (-1) plvol.Rd:14: Escaped LaTeX specials: \&
checkRd: (-1) sbp.Rd:16: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘MetProc_output.pdf’ ‘sample_removed.csv’ ‘sample_retained.csv’
Package suggested but not available for checking: ‘INLA’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Argument items with no description in Rd file 'predict.mfp.Rd':
  ‘safe’
'LazyData' is specified without a 'data' directory
checkRd: (-1) summarize_stats_CSV.Rd:81: Lost braces; missing escapes or markup?
    81 | {stage}\emph{Mean}(patchNum).csv and {stage}\emph{Quantile}(quantNum)_(patchNum).csv.
       | ^
checkRd: (-1) summarize_stats_CSV.Rd:81: Lost braces; missing escapes or markup?
    81 | {stage}\emph{Mean}(patchNum).csv and {stage}\emph{Quantile}(quantNum)_(patchNum).csv.
       |                                      ^
checkRd: (-1) summarize_stats_CSV_decoupled.Rd:84: Lost braces; missing escapes or markup?
    84 | {stage}\emph{Mean}(patchNum).csv and {stage}\emph{Quantile}(quantNum)_(patchNum).csv.
       | ^
checkRd: (-1) summarize_stats_CSV_decoupled.Rd:84: Lost braces; missing escapes or markup?
    84 | {stage}\emph{Mean}(patchNum).csv and {stage}\emph{Quantile}(quantNum)_(patchNum).csv.
       |                                      ^
checkRd: (-1) calcQuantiles.Rd:52: Lost braces; missing escapes or markup?
    52 | {M/F}\emph{Mean}(patchNum).csv and {M/F}\emph{Quantile}(quantNum)_(patchNum).csv.
       | ^
checkRd: (-1) calcQuantiles.Rd:52: Lost braces; missing escapes or markup?
    52 | {M/F}\emph{Mean}(patchNum).csv and {M/F}\emph{Quantile}(quantNum)_(patchNum).csv.
       |                                    ^
checkRd: (-1) mgm.Rd:75: Lost braces; missing escapes or markup?
    75 | If \code{binarySign = TRUE}, a sign for the interaction within binary nodes and between binary and continuous nodes is provided in the output. Note that in this case the two categories of the binary variables have to be coded in {0,1}. This is to ensure that the interpretation of the sign is unambigous: a positive sign of a parameter means that increasing the associated predictor results in a higher probability for category 1.
       |                                                                                                                                                                                                                                      ^
checkRd: (-1) mvar.Rd:75: Lost braces; missing escapes or markup?
    75 | If \code{binarySign = TRUE}, a sign for the interaction within binary nodes and between binary and continuous nodes is provided in the output. Note that in this case the two categories of the binary variables have to be coded in {0,1}. This is to ensure that the interpretation of the sign is unambigous: a positive sign of a parameter means that increasing the associated predictor results in a higher probability for category 1.
       |                                                                                                                                                                                                                                      ^
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘structSSI’
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Specified C++11: please drop specification unless essential
checkRd: (-1) VIF.Rd:47: Lost braces; missing escapes or markup?
    47 | vif_corrected = vif_basic^{(1/(2*df))}
       |                           ^
checkRd: (-1) ampute.Rd:143: Lost braces
   143 | we refer to \doi{10.1177/0049124118799376}{Schouten and Vink, 2018}.
       |                                           ^
checkRd: (-1) ampute.Rd:188: Lost braces
   188 | \doi{10.1080/00949655.2018.1491577}{Schouten, Lugtig and Vink, 2018}.
       |                                    ^
checkRd: (-1) ampute.Rd:223: Lost braces
   223 | Schouten, R.M. and Vink, G. (2018){The Dance of the Mechanisms: How Observed Information Influences the Validity of Missingness Assumptions}.
       |                                   ^
checkRd: (-1) mice.Rd:348: Lost braces; missing escapes or markup?
   348 | The \pkg{mice} software was published in the {Journal of Statistical Software} (Van Buuren and Groothuis-Oudshoorn, 2011). \doi{10.18637/jss.v045.i03}
       |                                              ^
checkRd: (-1) mice.impute.pmm.Rd:87: Lost braces; missing escapes or markup?
    87 | \item{Construct \eqn{n_0} sets \eqn{Z_j}, each containing \eqn{d} candidate donors, from Y_{obs} such that \eqn{\sum_d\dot\eta(i,j)} is minimum for all \eqn{j=1,\dots,n_0}. Break ties randomly.}
       |                                                                                            ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) linda.Rd:106: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) linda.Rd:107: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) linda.Rd:108: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) linda.Rd:109: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) linda.Rd:110: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) linda.Rd:111: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) linda.Rd:112: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) linda.Rd:113-114: Lost braces in \itemize; \value handles \item{}{} directly
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘microcontax.data’
Package unavailable to check Rd xrefs: ‘microcontax.data’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) addSchemes.Rd:13: Lost braces
    13 | \item{extraSchemes}{array of schemes to add, see code{\link{SetOfSchemes-class}}}
       |                                                      ^
checkRd: (-1) pkCurveStat.Rd:30: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) pkCurveStat.Rd:32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rankObject.Rd:33-36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rankObject.Rd:37: Lost braces in \itemize; meant \describe ?
Documented arguments not in \usage in Rd file 'changeDevSettings.Rd':
  ‘defaultsSettings’

Documented arguments not in \usage in Rd file 'getResultPerScheme.Rd':
  ‘criteria’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
checkRd: (-1) readFastq.Rd:62: Lost braces
    62 | code{\link{readFasta}}.
       |     ^
checkRd: (-1) RNGStream.Rd:29: Lost braces
    29 | item{open}{function to use the current seed}
       |     ^
checkRd: (-1) RNGStream.Rd:29: Lost braces
    29 | item{open}{function to use the current seed}
       |           ^
checkRd: (-1) RNGStream.Rd:30: Lost braces
    30 | item{close}{function to make the current seed equal to .Random.seed}
       |     ^
checkRd: (-1) RNGStream.Rd:30: Lost braces
    30 | item{close}{function to make the current seed equal to .Random.seed}
       |            ^
checkRd: (-1) RNGStream.Rd:31: Lost braces
    31 | item{resetStream}{function to move back to start of stream}
       |     ^
checkRd: (-1) RNGStream.Rd:31: Lost braces
    31 | item{resetStream}{function to move back to start of stream}
       |                  ^
checkRd: (-1) RNGStream.Rd:32: Lost braces
    32 | item{resetSubStream}{function to move back to start of sub-stream}
       |     ^
checkRd: (-1) RNGStream.Rd:32: Lost braces
    32 | item{resetSubStream}{function to move back to start of sub-stream}
       |                     ^
checkRd: (-1) RNGStream.Rd:33: Lost braces
    33 | item{nextSubStream}{function to move to next sub-stream}
       |     ^
checkRd: (-1) RNGStream.Rd:33: Lost braces
    33 | item{nextSubStream}{function to move to next sub-stream}
       |                    ^
checkRd: (-1) RNGStream.Rd:34: Lost braces
    34 | item{nextStream}{function to move to next stream}
       |     ^
checkRd: (-1) RNGStream.Rd:34: Lost braces
    34 | item{nextStream}{function to move to next stream}
       |                 ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Auto-generated content requiring editing in Rd file 'MIDASwrappeR-package.Rd':
  \references: ‘This optional section can contain literature or other refere...’
  \seealso: ‘Optional links to other man pages’
  \examples: ‘## Optional simple examples of the most important functions ...’
Package suggested but not available for checking: ‘midfielddata’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
checkRd: (-1) discretizeMutual.Rd:58: Lost braces
    58 | \item{two vectors containing the cutpoints for each variable : \emph{cutpoints1} corresponds to /emph{myDist1}, /emph{cutpoints2} corresponds to /emph{myDist2}.}
       |                                                                                                      ^
checkRd: (-1) discretizeMutual.Rd:58: Lost braces
    58 | \item{two vectors containing the cutpoints for each variable : \emph{cutpoints1} corresponds to /emph{myDist1}, /emph{cutpoints2} corresponds to /emph{myDist2}.}
       |                                                                                                                      ^
checkRd: (-1) discretizeMutual.Rd:58: Lost braces
    58 | \item{two vectors containing the cutpoints for each variable : \emph{cutpoints1} corresponds to /emph{myDist1}, /emph{cutpoints2} corresponds to /emph{myDist2}.}
       |                                                                                                                                                       ^
checkRd: (-1) discretizeMutual.Rd:62: Lost braces
    62 | \item{if $emph{plot} == TRUE, a plot object (requires ggplot2 and gridExtra).}
       |               ^
checkRd: (-1) miic.Rd:158-209: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) miic.Rd:211: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) miic.Rd:213-214: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) miive.Rd:120-239: Lost braces in \itemize; meant \describe ?
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   426 | \link{MIIVsem}{miivs}
       |               ^
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    60 | Zena Lapp, {zenalapp@umich.edu}
       |            ^
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    62 | Kelly Sovacool, {sovacool@umich.edu}
       |                 ^
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    30 | Zena Lapp, {zenalapp@umich.edu}
       |            ^
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    58 | Kelly Sovacool, {sovacool@umich.edu}
       |                 ^
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    16 | Zena Lapp, {zenalapp@umich.edu}
       |            ^
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Specified C++11: please drop specification unless essential
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    14 |   \item{BROADBND}{Cellular data plan for a smartphone or other mobile device}{1 yes 2 no}
       |                                                                              ^
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    21 |   \item{MHP}{Mobile home costs}{$, yearly}
       |                                ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
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'LazyData' is specified without a 'data' directory
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    19 |       (only relevant if code{x} has only one element).}
       |                             ^
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    47 | of \code{nlambda} and code{lambda.min.ratio}. Default is NULL}
       |                           ^
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    55 | of \code{nlambda} and code{lambda.min.ratio}. Default is NULL}
       |                           ^
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    45 | of \code{nlambda} and code{lambda.min.ratio}. Default is NULL}
       |                           ^
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    53 | of \code{nlambda} and code{lambda.min.ratio}. Default is NULL}
       |                           ^
Documented arguments not in \usage in Rd file 'logAdd.Rd':
  ‘x’ ‘y’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Argument items with no description in Rd file 'randomizationTest.Rd':
  ‘R’
checkRd: (-1) PV.Rd:14: Lost braces
    14 | plausible value in turn; with code{rewrite=FALSE} a new data set is
       |                                   ^
Documented arguments not in \usage in Rd file 'rigaussian.Rd':
  ‘mu’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
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    35 |   \code{t * 1} and \code{B} is of dimension{t * N}. Ideally, \code{fun.sim}()
       |                                            ^
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Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Bug Fix
    Update Vignettes
    Function Optimizing
    New Functions
    Vignette
    Optimization
    Fix Bugs
    Add New Function
    Update Description Files
    Fix bugs
    New .R files
    Update Old .R files
Specified C++11: please drop specification unless essential
checkRd: (-1) mixmeta-package.Rd:115: Escaped LaTeX specials: \&
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checkRd: (-1) ml.igls.Rd:62: Escaped LaTeX specials: \&
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Package suggested but not available for checking: ‘mixRasch’
Found the following significant warnings:

  Warning in is.R() : 'is.R' is deprecated.
  Warning in is.R() : 'is.R' is deprecated.
  Warning in is.R() : 'is.R' is deprecated.
  Warning in is.R() : 'is.R' is deprecated.
  Warning in is.R() : 'is.R' is deprecated.
  Warning in is.R() : 'is.R' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU (user + system) or elapsed time > 5s
          user system elapsed
ncMcTest 7.750  0.003  12.626
kilns    4.434  0.024   8.446
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    18 | The function \code{print.selectEM} is the print method for the class{selectEM}, which is the output
       |                                                                     ^
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Package has ‘vignettes’ subdirectory but apparently no vignettes.
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     9 |       (2) All x-coordinates of R1',..,Rn' are distinct, and take values in {1,..,2n}.
       |                                                                            ^
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    10 |       (3) All y-coordinates of R1',..,Rn' are distinct, and take values in {1,..,2n}.
       |                                                                            ^
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    43 | \item{y}{vector of size n. If loss = "logit", elements of y must be in {-1,1}}
       |                                                                        ^
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    25 | \item{y}{vector of size n. If loss = "logit", elements of y must be in {-1,1}}
       |                                                                        ^
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    26 | \item{y}{vector of size n. If loss = "logit", elements of y must be in {-1,1}}
       |                                                                        ^
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    25 | \item{y}{vector of size n. If loss = "logit", elements of y must be in {-1,1}}
       |                                                                        ^
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    58 |              Note that code{"XGB"} is only available in Mac OS and Linux. moreover,
       |                            ^
'LazyData' is specified without a 'data' directory
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    44 | using reference based imputation as proposed by \doi{10.1080/10543406.2013.834911}{Carpenter et al (2013)}. This approach
       |                                                                                   ^
Packages suggested but not available for checking:
  'ueadata1', 'ueadata2', 'ueadata3', 'ueadata4', 'ueadata5',
  'ueadata6', 'ueadata7', 'ueadata8'
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    23 | \code{groupdiff_tau()} computes \eqn{min(x/y, y/x)}, i.e. the smallest symmetric ratio between \eqn{x} and eqn{y}
       |                                                                                                               ^
Package suggested but not available for checking: ‘nc’
Error(s) in re-building vignettes:
  ...
--- re-building ‘ResamplingSameOtherCV.Rmd’ using rmarkdown

Quitting from lines 95-99 [unnamed-chunk-2] (ResamplingSameOtherCV.Rmd)
Error: processing vignette 'ResamplingSameOtherCV.Rmd' failed with diagnostics:
there is no package called 'nc'
--- failed re-building ‘ResamplingSameOtherCV.Rmd’

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

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

Error: Vignette re-building failed.
Execution halted
Documented arguments not in \usage in Rd file 'cpoTemplate.Rd':
  ‘affect.names’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Problems with news in ‘NEWS.md’:
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   119 | Notes in Computer Science, ISBN 978-3-642-37139-4, pp. 756{770,
       |                                                           ^
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checkRd: (-1) trafos.Rd:29: Lost braces in \itemize; meant \describe ?
Package suggested but not available for checking: ‘SwarmSVM’
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'LazyData' is specified without a 'data' directory
checkRd: (-1) simpopmlx.Rd:21: Lost braces; missing escapes or markup?
    21 | \item{fim}{the Fisher Information Matrix estimated by Monolix. fim={"sa", "lin"} (default="sa")}
       |                                                                    ^
Problems with news in ‘NEWS.md’:
No news entries found.
Package suggested but not available for checking: ‘mosaicCalc’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) get_mean_sd_hour.Rd:20: Lost braces
    20 | A function for calcualting the average timing of variables (in this case the M10 and L5).  Find the average timing mu that min{ sum { min[ (tind_i - mu)^2, (1440 + mu - tind_i )^2 ]}}
       |                                                                                                                               ^
checkRd: (-1) get_mean_sd_hour.Rd:20: Lost braces; missing escapes or markup?
    20 | A function for calcualting the average timing of variables (in this case the M10 and L5).  Find the average timing mu that min{ sum { min[ (tind_i - mu)^2, (1440 + mu - tind_i )^2 ]}}
       |                                                                                                                                     ^
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    62 | \item Probability of attribution of each unknown individual to each source $p_{u,s}$
       |                                                                               ^
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checkRd: (-1) mmeln.Rd:69: Lost braces; missing escapes or markup?
    69 |   \item{obj$M}{Number of total observations sum_{i=1}^N(pi)}
       |                                                 ^
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     6 | These function takes the output of pgls.iter and uses its list of objects { model fits, optimzations (e.g.AICc)} and performs a weighted average on the ctoefficients estimated in the former by weighting by the latter. The parameters can also optionally be converted to binary by specifying "binary=FALSE" or just running the alias wraper function for assessing evidence of variable importance (Burnham & Anderson 2000).
       |                                                                           ^
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
Problems with news in ‘NEWS.md’:
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checkRd: (-1) k2d.Rd:26: Lost braces
    26 | d_ND(x,y) = sqrt{ k(x,x) - 2k(x,y) + k(y,y)}.
       |                 ^
checkRd: (-1) k2d.Rd:34: Lost braces
    34 | d_n(x,y) = 1 - k(x,y)/sqrt{ k(x,x)k(y,y)},
       |                           ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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checkRd: (-1) association.Rd:82: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) association.Rd:96: Lost braces in \itemize; meant \describe ?
checkRd: (-1) association.Rd:97: Lost braces in \itemize; meant \describe ?
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'LazyData' is specified without a 'data' directory
checkRd: (-1) rMNB.Rd:23: Lost braces; missing escapes or markup?
    23 | It simulates a multivariate response variable, Y_{ij}, that is jth measurement
       |                                                  ^
'LazyData' is specified without a 'data' directory
Package vignette with \VignetteEngine{} not specifying an engine package:
  ‘vignette.Rmd’
Engines should be specified as \VignetteEngine{PKG::ENG}.
'LazyData' is specified without a 'data' directory
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    35 |   \item{cum}{a logical value; if  code{TRUE}  (default value), cumulants 
       |                                       ^
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    43 | The maximal value of {d} is \code{20}. If this threshold is exceeded, \code{NA}s
       |                      ^
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   110 |   and code{tvpack}, downloaded in 2005 and again in 2007 from his webpage, 
       |           ^
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Packages which this enhances but not available for checking:
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    20 | trafo <- function(x){ return(x^2)}
       |                     ^
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   139 | For binary CF models, if{importance.type = 2}, function uses AUC-based variables importances as described by Janitza et al. (2012). Here, the area under the curve instead of the accuracy is used to calculate the importance of each variable. This AUC-based variable importance measure is more robust towards class imbalance. 
       |                         ^
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    75 | the {ggplot2} package, but provides functionality that \code{geom_smooth()}
       |     ^
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    85 | {ggplot2} grouping aesthetics: \code{group}, \code{color}, \code{fill},
       | ^
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    87 | {ggplot2} package, but provides functionality that \code{geom_smooth()}
       | ^
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    21 | The distance between two observations {i} and {j} of a circular variable {q}
       |                                       ^
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    21 | The distance between two observations {i} and {j} of a circular variable {q}
       |                                               ^
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    21 | The distance between two observations {i} and {j} of a circular variable {q}
       |                                                                          ^
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    34 | \\code{LCx} class. It plots the survival probability as a function of concentration.
       |       ^
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     7 | \title{{mortaar_life_table} and {mortaar_life_table_list}}
       |                                 ^
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    58 | \item{tol}{Convergence is determined when ||U_j - U_{j-1}||_F < tol,
       |                                                     ^
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    59 | \item{tol}{Convergence is determined when ||U_j - U_{j-1}||_F < tol,
       |                                                     ^
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    39 | 	\link{brownian.bridge.dyn}, link{dynBGBvariance}
       |                                         ^
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    16 |   Calculates the stimulus level(s) for a probit model of a psychometric function for given levels of performance.  For a more general version, see \link[MASS]{dose.p} in pkg{MASS}.
       |                                                                                                                                                                              ^
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    21 | is performed where the boundary is cstar*hat(sigma)_{M,tildeM}.}
       |                                                     ^
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    21 | is performed where the boundary is cstar*hat(sigma)_{M,tildeM}.}
       |                                                     ^
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    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}.
       |                                                                                                       ^
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    38 | The labels on the x-axis. Default is \code{Tree 1} to code{Tree n}.
       |                                                           ^
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    51 | if (requireNamespace("rjags", quietly = TRUE)) {
       |                                                ^
GNU make is a SystemRequirements.
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    33 | 	\item{LogTimes}{Magnification of {-log10(P-value)}; the default is
       |                                          ^
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    35 |     \item{LODTimes}{Magnification of {LOD score}; the default is 1.2.}
       |                                      ^
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    10 |            log E(Y_{t+1} | A_t = 0, I_t = 1) = alpha_0 + alpha_1 * time / total_T
       |                    ^
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    64 | default is {FALSE}. To enable parallel tuning, load the
       |            ^
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    59 | default is {FALSE}. To enable parallel tuning, load the
       |            ^
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    59 | default is {FALSE}. To enable parallel tuning, load the
       |            ^
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    80 | default is {FALSE}. To enable parallel tuning, load the
       |            ^
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    74 | default is {FALSE}. To enable parallel tuning, load the
       |            ^
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    74 | default is {FALSE}. To enable parallel tuning, load the
       |            ^
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    42 |   \item{calibrateIntensity_method}{a \code{character} indicating the intensities calibration method used (\code{"TIC"} method by default).  This calibration method can be remplaced by \code{"PQN"} or {"median"}.See \code{calibrateIntensity-methods} of the \code{MALDIquant} R package for details.}
       |                                                                                                                                                                                                         ^
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Argument items with no description in Rd file 'larg.ellip.Rd':
  ‘n’ ‘box’ ‘add’ ‘xlim’ ‘ylim’ ‘zlim’ ‘xlab’ ‘ylab’ ‘zlab’ ‘col’
  ‘alpha’ ‘\dots’
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    20 |     {\code{table.variables}, \code{table.class}}.
       |     ^
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    20 |     {\code{table.variables}, \code{table.class}}.
       |     ^
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    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.
       |                                                                                                                                                                                                                                                                                                ^
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  ‘width’ ‘lwd’ ‘label.groups’ ‘T.base’ ‘orientation’

Documented arguments not in \usage in Rd file 'plotTs.Rd':
  ‘font.family’ ‘fig’ ‘mar’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
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    14 | \item{bivprob}{Bivariate probabilities, {p00, p01, p10, p11}.}
       |                                         ^
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    35 | Returns an object of class 'pcaRes.'  See documentation in the package code{\link[pcaMethods:pcaMethods]{ pcaMethods}}
       |                                                                            ^
Documented arguments not in \usage in Rd file 'Trace.Rd':
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Documented arguments not in \usage in Rd file 'iteraite_fun_Iter.Rd':
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Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Package suggested but not available for checking: ‘cmdstanr’
diagnostic_posterior:
  function(posterior, ...)
diagnostic_posterior.brmcoda:
  function(posteriors, diagnostic, ...)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
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    38 | \item{vertex.shape}{Symbol to use for nodes, corresponding to the parameter {pch} of the R \code{points} function.  This can either
       |                                                                             ^
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    21 | for all 10 paired comparisons of 5 choice elements {a,b,c,d,e} in a
       |                                                    ^
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    17 |           \code{U}        \tab The common latent space vectors. U in R^{n x d}\cr
       |                                                                        ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) biomasse.Rd:30: Lost braces
    30 | Makowski, D., Jeuffroy, M.-H., Gu\'{e}rif, M., 2004 Bayesian methods for
       |                                    ^
checkRd: (-1) climat.Rd:20: Lost braces
    20 | Makowski, D., Jeuffroy, M.-H., Gu\'{e}rif, M., 2004 Bayesian methods for
       |                                    ^
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    15 |   \item{\dots}{... }{possible fixed parameters of the R-function}
       |                     ^
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   148 | /code{/link{dist}/}
       |      ^
checkRd: (-1) Distancia.Rd:148: Lost braces
   148 | /code{/link{dist}/}
       |            ^
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    81 | /code{/link{Distancia}/} ,/code{/link{Dendrograma}/}, /code{/link{heatplot}/}
       |      ^
checkRd: (-1) HeatPlot.Rd:81: Lost braces
    81 | /code{/link{Distancia}/} ,/code{/link{Dendrograma}/}, /code{/link{heatplot}/}
       |            ^
checkRd: (-1) HeatPlot.Rd:81: Lost braces
    81 | /code{/link{Distancia}/} ,/code{/link{Dendrograma}/}, /code{/link{heatplot}/}
       |                                ^
checkRd: (-1) HeatPlot.Rd:81: Lost braces
    81 | /code{/link{Distancia}/} ,/code{/link{Dendrograma}/}, /code{/link{heatplot}/}
       |                                      ^
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    81 | /code{/link{Distancia}/} ,/code{/link{Dendrograma}/}, /code{/link{heatplot}/}
       |                                                            ^
checkRd: (-1) HeatPlot.Rd:81: Lost braces
    81 | /code{/link{Distancia}/} ,/code{/link{Dendrograma}/}, /code{/link{heatplot}/}
       |                                                                  ^
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    55 | /code{/link{dist}/}
       |      ^
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    55 | /code{/link{dist}/}
       |            ^
checkRd: (-1) SummaryDistancia.Rd:98: Lost braces
    98 | /code{/link{dist}/}
       |      ^
checkRd: (-1) SummaryDistancia.Rd:98: Lost braces
    98 | /code{/link{dist}/}
       |            ^
Specified C++11: please drop specification unless essential
checkRd: (-1) durante.Rd:60-61: Lost braces
    60 | in their study, \doi{10.1177/0956797612466416}{\emph{The
       |                                               ^
checkRd: (-1) hurricane.Rd:34: Lost braces
    34 | in their study, \doi{10.1073/pnas.1402786111}{\emph{Female hurricanes are deadlier than male hurricanes}}.
       |                                              ^
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    33 | \doi{10.1145/2470654.2481359}{Evaluating the Efficiency of Physical Visualizations}
       |                              ^
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checkRd: (-1) metricUnfolding.Rd:73-74: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) plotLociHC.Rd:55: Lost braces; missing escapes or markup?
    55 | If \code{value} is one of {0.2,0.4,0.6,0.8,1,2,3,4,5,6,7,8,9,10}
       |                           ^
Documented arguments not in \usage in Rd file 'check_mnsl.Rd':
  ‘fix’

Documented arguments not in \usage in Rd file 'text_colour.Rd':
  ‘a’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) cv.glm1path.Rd:74: Lost braces
    74 | \code{\link{glm1path}}, \\code{\link{glm1}}, \code{\link{glm}}, \code{\link{family}}
       |                               ^
checkRd: (-1) hurricane.Rd:47-48: Lost braces
    47 | \doi{10.1073/pnas.1402786111}{Female hurricanes are
       |                              ^
checkRd: (-1) hurricane.Rd:55: Lost braces
    55 | \doi{10.1038/s41562-020-0912-z}{Specification curve analysis}
       |                                ^
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    67 | {rater1} and {rater2}, and the 5-point scale values were
       | ^
checkRd: (-1) soccer.Rd:67: Lost braces; missing escapes or markup?
    67 | {rater1} and {rater2}, and the 5-point scale values were
       |              ^
checkRd: (-1) bal.Rd:156: Escaped LaTeX specials: \&
checkRd: (-1) MVNtestchar-package.Rd:16-17: Lost braces; missing escapes or markup?
    16 | {Provides a test of multivariate normality of a sample which does not require estimation of the nuisance parameters, the mean      vector and covariance matrix.  Rather, a sequence of transformations removes these nuisance parameters, resulting in a set of    sample matrices that are positive definite.  If, and only if the original data is multivariate normal, these matrices are       uniformly distributed on the space of positive definite matrices in the unit hyper-rectangle.  The package performs a goodness    of fit test of this hypothesis. In addition to the test, functions in the package give visualizations of the  support region    of positive definite matrices for p equals 2.
       | ^
checkRd: (-1) pkb.Rd:14: Escaped LaTeX specials: \# \# \#
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checkRd: (-1) pmvss.Rd:101: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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    39 | The "nbdev.mxm" (negative binomial deviance) is missing. For more information on these see \code{\link{cv.ses}}. bold{Note} that they come with "".
       |                                                                                                                      ^
checkRd: (-1) cv.fbed.lmm.reg.Rd:32: Lost braces; missing escapes or markup?
    32 | The folds of the data to use (a list generated by the function generateCVRuns {TunePareto}). If NULL the folds are created internally with the same function.
       |                                                                               ^
checkRd: (-1) cv.gomp.Rd:29: Lost braces; missing escapes or markup?
    29 | The folds of the data to use (a list generated by the function generateCVRuns {TunePareto}). If NULL the folds are created internally with the same function.
       |                                                                               ^
checkRd: (-1) cv.ses.Rd:94: Lost braces; missing escapes or markup?
    94 | The folds of the data to use (a list generated by the function generateCVRuns {TunePareto}). If NULL the folds are created internally with the same function.
       |                                                                               ^
Package suggested but not available for checking: ‘rTubeDB’
Package unavailable to check Rd xrefs: ‘rTubeDB’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) mzipmed_data.Rd:22: Lost braces; missing escapes or markup?
    22 | @source {Simulated to serve as an example}
       |         ^
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
checkRd: (-1) PipeOpMice.Rd:33: Lost braces; missing escapes or markup?
    33 | set of methods to chose. Avalible methods {"pmm", "midastouch", "sample", "cart", "rf"} Default 'pmm'. If seted on NULL this methods are used predictive mean matching (numeric data) logreg, logistic regression imputation (binary data, factor with 2 levels) polyreg, polytomous regression imputation for unordered categorical data (factor > 2 levels) polr, proportional odds model for (ordered, > 2 levels).
       |                                           ^
checkRd: (-1) M36NT2PM.dat.Rd:37: Lost braces in \itemize; meant \describe ?
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'LazyData' is specified without a 'data' directory
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    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){
       |               ^
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    33 |   for(j in 1:20){
       |                 ^
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    10 | for(i in 1:200){
       |                ^
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    12 |   for(j in 1:200){
       |                  ^
checkRd: (-1) DSLIVEdata.Rd:26-34: Lost braces
    26 | for(i in 1:20){
       |               ^
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    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.
       |                                                                                                                                                    ^
checkRd: (-1) mcar_test.Rd:28: Lost braces; missing escapes or markup?
    28 | Code is adapted from LittleMCAR() in the now-orphaned {BaylorEdPsych}
       |                                                       ^
checkRd: (-1) mcar_test.Rd:31: Lost braces; missing escapes or markup?
    31 | using Maximum likelihood estimation from {norm}.
       |                                          ^
Specified C++11: please drop specification unless essential
checkRd: (-1) nanoperiod.Rd:268: Lost braces
   268 | possible to use the binary operator `code{+}`. Instead the
       |                                          ^
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Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘spatialClust’
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Version (2018-01-22)
    Version  (2017-08-22)
    Version
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘gurobi’
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Invalid package aliases in Rd file 'NBBttest-package.Rd':
  ‘NBBtatest-package’
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 ?
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Documented arguments not in \usage in Rd file 'Moth.Rd':
  ‘delta.ident’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) ncpen.Rd:108: Lost braces; missing escapes or markup?
   108 |   \item{gamma}{extra shrinkage parameter for \code{classo} and {sridge} only.}
       |                                                                ^
checkRd: (-1) ncpen.reg.Rd:109: Lost braces; missing escapes or markup?
   109 |   \item{gamma}{extra shrinkage parameter for \code{classo} and {sridge} only.}
       |                                                                ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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   153 | c("\\Sexpr[results=rd]{tools:::Rd_expr_doi(\"#1\")}",
       |                       ^
checkRd: (-1) ncvreg.Rd:207: Lost braces
   207 | c("\\Sexpr[results=rd]{tools:::Rd_expr_doi(\"#1\")}",
       |                       ^
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   178 | \strong{5}: 232-253.  c("\\Sexpr[results=rd]{tools:::Rd_expr_doi(\"#1\")}",
       |                                             ^
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   184 | c("\\Sexpr[results=rd]{tools:::Rd_expr_doi(\"#1\")}",
       |                       ^
checkRd: (-1) plot.cv.ncvreg.Rd:81: Lost braces
    81 | c("\\Sexpr[results=rd]{tools:::Rd_expr_doi(\"#1\")}",
       |                       ^
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    40 | c("\\Sexpr[results=rd]{tools:::Rd_expr_doi(\"#1\")}",
       |                       ^
checkRd: (-1) predict.ncvreg.Rd:92: Lost braces
    92 | c("\\Sexpr[results=rd]{tools:::Rd_expr_doi(\"#1\")}",
       |                       ^
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    88 | \strong{5}: 232-253.  c("\\Sexpr[results=rd]{tools:::Rd_expr_doi(\"#1\")}",
       |                                             ^
checkRd: (-1) summary.cv.ncvreg.Rd:64: Lost braces
    64 | c("\\Sexpr[results=rd]{tools:::Rd_expr_doi(\"#1\")}",
       |                       ^
'LazyData' is specified without a 'data' directory
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    69 | Anderson-Darling test." See url{https://github.com/Lakens/perfect-t-test} for
       |                                ^
checkRd: (-1) t_neat.Rd:243: Lost braces
   243 | Anderson-Darling test." See url{https://github.com/Lakens/perfect-t-test} for
       |                                ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘manual.Rmd’ using rmarkdown
Could not fetch http://www.zotero.org/styles/springer-vancouver-brackets
HttpExceptionRequest Request {
  host                 = "www.zotero.org"
  port                 = 80
  secure               = False
  requestHeaders       = []
  path                 = "/styles/springer-vancouver-brackets"
  queryString          = ""
  method               = "GET"
  proxy                = Nothing
  rawBody              = False
  redirectCount        = 10
  responseTimeout      = ResponseTimeoutDefault
  requestVersion       = HTTP/1.1
  proxySecureMode      = ProxySecureWithConnect
}
 (InternalException (HandshakeFailed (Error_Protocol "peer does not support Extended Main Secret" HandshakeFailure)))
Error: processing vignette 'manual.Rmd' failed with diagnostics:
pandoc document conversion failed with error 61
--- failed re-building ‘manual.Rmd’

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
checkRd: (-1) color_palette.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) color_palette.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) color_palette.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) color_palette.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) color_palette.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) color_palette.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) color_palette.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) color_palette.Rd:29: Lost braces in \itemize; meant \describe ?
Specified C++11: please drop specification unless essential
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GNU make is a SystemRequirements.
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    17 | code{2016}.}
       |     ^
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Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘RSiena’
Package suggested but not available for checking: ‘fastshp’
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    27 | In the resulting netSEM model, time was used as a proxy for damp heat exposure stress (S) variable and $P_{max}$ (maximum power generated by the modules) was used as the performance level response ($R$) variable, several mechanistic variables ($M$) were obtained through chemical evaluation methods, including FTIR and TGA  on EVA encapsulant. 
       |                                                                                                           ^
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    55 | For example, in the quadratic functional form y ~ b0 + b1x + b2x^2, the three P-values correspond two those of \\hat{b0}, \\hat{b1} and \\hat{b2}, respectively. 
       |                                                                                                                     ^
checkRd: (-1) netSEMp1.Rd:55: Lost braces
    55 | For example, in the quadratic functional form y ~ b0 + b1x + b2x^2, the three P-values correspond two those of \\hat{b0}, \\hat{b1} and \\hat{b2}, respectively. 
       |                                                                                                                                ^
checkRd: (-1) netSEMp1.Rd:55: Lost braces
    55 | For example, in the quadratic functional form y ~ b0 + b1x + b2x^2, the three P-values correspond two those of \\hat{b0}, \\hat{b1} and \\hat{b2}, respectively. 
       |                                                                                                                                              ^
checkRd: (-1) spec_clust.Rd:33: Lost braces; missing escapes or markup?
    33 | A label vector of size n x 1 with elements in {1,2,...,K}
       |                                               ^
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    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.}
       |                        ^
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checkRd: (-1) NetworkChangeRobust.Rd:144: Escaped LaTeX specials: \&
checkRd: (-1) NetworkStatic.Rd:142: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
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checkRd: (-1) harry_potter.Rd:45: Lost braces in \itemize; meant \describe ?
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Found the following files/directories:
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GNU make is a SystemRequirements.
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    56 | with a matrix response {y}. \code{x1} and \code{x2} are used as
       |                        ^
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    35 |       parameters \code{L} and {M} (in that order).}
       |                               ^
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   278 | \code{AgeFirstMarij}{Age participant first tried marijuana. Reported for participants aged 18 to 59 years.}
       |                     ^
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    25 | See /link{download_nhdplusv2} for documentation of that dataset.}
       |          ^
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    15 | See /link{download_nhdplusv2} for documentation of that dataset.}
       |          ^
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    56 | with \eqn{Z} the covariate and eqn{d_Z} its dimension (number of covariates)
       |                                   ^
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    47 | 	Marginal distribution: {\deqn{ S = \int_{-\infty}^{\infty} \left| F_n(x)-F(x) \right| dx} } 
       |                                ^
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    49 | 	Marginal distribution, based on Anderson Darling statistic: {\deqn{ S = \int_{-\infty}^{\infty} \left| \frac{F_n(x)-F(x)}{F(x)(1-F(x))} \right| dx} } 
       |                                                                     ^
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    51 | 		Correlation function: {\deqn{ S = \int_0^L\left|C_n(l)-C(l)\right|dl} } 
       |                                       ^
Invalid package aliases in Rd file 'NH-MSAR-package.Rd':
  ‘NH-MSAR-package’
Argument items with no description in Rd file 'ENu_graph.Rd':
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Argument items with no description in Rd file 'Estep.MSAR.VM.Rd':
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Auto-generated content requiring editing in Rd file 'NH-MSAR-package.Rd':
  \details: ‘...the package, including the most important ~~ ~~ functions ~~’
Argument items with no description in Rd file 'init.theta.MSAR.Rd':
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   105 | Ionides, E.L., D. Nguyen, Y. Atchad{\'e}, S. Stoev, and A.A. King (2015). Inference for dynamic and latent variable models via iterated, perturbed Bayes maps. \emph{Proceedings of the National Academy of Sciences}, 112(3), 719-724.
       |                                    ^
Package which this enhances but not available for checking: ‘jpndistrict’
Malformed Description field: should contain one or more complete sentences.
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    44 | training sample), psi (the value of this observations Psihat(P_{n,B_n}^0)),
       |                                                                ^
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    49 | training sample), psi (the value of this observations Psihat(P_{n,B_n}^0)),
       |                                                                ^
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    19 |   Returns an object of class code{anova}.  These objects represent
       |                                  ^
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    34 | Given \eqn{n} points on a line, \env{input}, each with a corresponding env{f} value this algorithm computes a lifting transform of the (\env{input},\env{f}) data. If lengths are inputted (\env{inputtype="lengths"}), then the gridpoints are taken to be the left endpoints of the intervals defined by the lengths inputted. 
       |                                                                           ^
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'LazyData' is specified without a 'data' directory
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    23 | The number of low-dimension (J < {N, M}).
       |                                  ^
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    71 | The number of low-dimension (J < {N, M}). If a numerical vector is specified
       |                                  ^
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   119 |   U : A matrix which has N-rows and J-columns (J < {N, M}).
       |                                                    ^
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   120 |   V : A matrix which has M-rows and J-columns (J < {N, M}).
       |                                                    ^
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   121 |   J : The number of dimension (J < {N, M}).
       |                                    ^
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Auto-generated content requiring editing in Rd file 'noise-package.Rd':
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Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
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    23 | If psn is not available system{base} is used.
       |                               ^
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    91 | The fy and fx arguments can be used to alter the scale of data plotted. For example, using fy=function(y){log(y+1)}
       |                                                                                                          ^
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  ‘inherit.aes’ ‘...’

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  ‘mapping’ ‘data’ ‘geom’ ‘position’ ‘na.rm’ ‘show.legend’
  ‘inherit.aes’ ‘...’

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  ‘inherit.aes’ ‘...’

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Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
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    14 |   \item{shape}{either \code{wide} or {long}. Default \code{wide}. See Details.}
       |                                      ^
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    75 |     \item{\code{GetTrace()}:}{retrieve all traced iterations. Returns a list with all the parameters set using the method SetTrace(). See description of snapshot{reference} method for a description of the parameters.  }
       |                                                                                                                                                                  ^
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    35 |               code{plot.type="circle"} and \code{x} is the output of \code{\link{kern.reg.circ.lin}}) or to \code{\link{lines3d}} (if \code{plot.type="circle"})
       |                   ^
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    59 | Default: function(x) {
       |                      ^
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    60 | Default: function(x) {
       |                      ^
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  ‘y_zx_dependent’

Documented arguments not in \usage in Rd file 'make_proposer.Rd':
  ‘N’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
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   148 | ter Braak, C. J. F. (1992). Permutation versus bootstrap significance tests in multiple regression and ANOVA. In K. H. J\"{o}ckel, G. Rothe, & W. Sendler (Eds.), Bootstrapping and related techniques. lecture notes in economics and mathematical systems, vol 376 (pp. 79-86). Springer.
       |                                                                                                                           ^
checkRd: (-1) nptest-package.Rd:73: Lost braces
    73 | ter Braak, C. J. F. (1992). Permutation versus bootstrap significance tests in multiple regression and ANOVA. In K. H. J\"{o}ckel, G. Rothe, & W. Sendler (Eds.), Bootstrapping and related techniques. lecture notes in economics and mathematical systems, vol 376 (pp. 79-86). Springer.
       |                                                                                                                           ^
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    14 | {Maintainer}: Saurav Guha \email{saurav.iasri@gmail.com}
       | ^
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    13 | \item{z}{the vector of zi = min{Xi, Yi}}
       |                                ^
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    21 | \code{MSM.fit} returns an object of class code{MSM.lm} or \code{MSM.glm}, depending on the input model.
       |                                               ^
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    25 | observation at current time step. It should return {xx} (the samples xt) and
       |                                                    ^
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    26 | {logww} (their corresponding log weight).}
       | ^
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    17 | \item{exp_counts}{dataframe Single-cell expression counts {CHROM, seg, cnv_state, gene, Y_obs, lambda_ref}}
       |                                                           ^
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  ‘msg’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
GNU make is a SystemRequirements.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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    31 |    \item Finally, code{T} is rotated an angle \code{z} about its NEWEST z-axis.
       |                       ^
'LazyData' is specified without a 'data' directory
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checkRd: (-1) plsda.Rd:39: Lost braces
    39 | \item{code{PRESS}}{The residual sum of squares for the samples which were not used to fit the model}
       |           ^
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checkRd: (-1) plsda.Rd:40: Lost braces
    40 | \item{code{Q2}}{quality of  cross-validation}}
       |           ^
checkRd: (-1) plsda.Rd:40: Lost braces in \itemize; \value handles \item{}{} directly
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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    93 | \code{'sparse'}, then only (S^{diag}, S^{off,d})
       |                               ^
checkRd: (-1) ChangepointDetector.Rd:93: Lost braces; missing escapes or markup?
    93 | \code{'sparse'}, then only (S^{diag}, S^{off,d})
       |                                         ^
checkRd: (-1) ChangepointDetector.Rd:94: Lost braces; missing escapes or markup?
    94 | and (S^{diag}, S^{off,s}) are included in \code{stat} respectively.);
       |        ^
checkRd: (-1) ChangepointDetector.Rd:94: Lost braces; missing escapes or markup?
    94 | and (S^{diag}, S^{off,s}) are included in \code{stat} respectively.);
       |                  ^
Argument items with no description in Rd file 'plot.comphat.Rd':
  ‘\dots’
checkRd: (-1) onlineCPD.Rd:35: Lost braces
    35 |  function(x, lambda){const_hazard(x, lambda=100)}
       |                     ^
checkRd: (-1) ocsApiUserProvisioningManager.Rd:87: Lost braces
    87 |  \item{code{addToGroup(userid, groupid)}}{
       |            ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) plot.ODEmorris.Rd:62-63: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.ODEmorris.Rd:64-65: Lost braces in \itemize; meant \describe ?
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) formula.oglmx.Rd:49: Lost braces
    49 |   \code{\link{oglmx}}, code{\link[lmtest]{lrtest}}, code{\link{formula}}.
       |                            ^
checkRd: (-1) formula.oglmx.Rd:49: Lost braces
    49 |   \code{\link{oglmx}}, code{\link[lmtest]{lrtest}}, code{\link{formula}}.
       |                                                         ^
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) dot-discoveryRequest.Rd:15-16: Lost braces
    15 | \item{service}{One of {"locations", "deployments", "deviceCategories", "devices",
       |                       ^
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    18 | \item{method}{One of {"get", "getTree"}}
       |                      ^
checkRd: (-1) dot-saveAsFile.Rd:19: Lost braces; missing escapes or markup?
    19 | (numeric) Result code from {0: done, -1: error, -2: fileExists}
       |                            ^
Package suggested but not available for checking: ‘cmdstanr’
checkRd: (-1) summary.blrm_trial.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) summary.blrm_trial.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) summary.blrm_trial.Rd:22: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) summary.blrm_trial.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) summary.blrm_trial.Rd:31-33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) summary.blrm_trial.Rd:34: Lost braces in \itemize; meant \describe ?
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) one_sample.Rd:40: Lost braces; missing escapes or markup?
    40 | In two sided or one sided interval estimation of \code{sigma^2} of one normal sample, {side} is a parameter used to control whether to compute two sided or one sided interval estimation. When computing the one sided upper limit, input \code{side = -1}; when computing the one sided lower limit, input \code{side = 1}; when computing the two sided limits, input \code{side = 0} (default).
       |                                                                                       ^
Rd files without \alias:
  ‘ontologyPlot-package.Rd’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
License stub is invalid DCF.
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘openNLPmodels.en’
checkRd: (-1) constructD.Rd:18: Lost braces
    18 | values for code{"columns"} and \code{"rows"}).}
       |                ^
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    43 |                { Z_max x Z_mdn - Z_min <= crit }.
       |                ^
checkRd: (-1) indexConflict2.Rd:46: Lost braces; missing escapes or markup?
    46 |                { Z_min - Z_max x Z_mdn <= crit }.
       |                ^
checkRd: (-1) indexConflict2.Rd:56: Lost braces; missing escapes or markup?
    56 |        { a x Z_max x Z_mdn =< crit/a + Z_min}. This shows that a bigger value of \code{a}
       |        ^
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    18 | range. Usually {-1, 1} are reasonable settings}
       |                ^
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checkRd: (-1) settings.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) settings.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) settings.Rd:28: Lost braces in \itemize; meant \describe ?
Documented arguments not in \usage in Rd file 'bertinBase.Rd':
  ‘x’ ‘ratings’ ‘trim’

Documented arguments not in \usage in Rd file 'biplot3dBase2.Rd':
  ‘ext.sphere’

Documented arguments not in \usage in Rd file 'convertImportObjectToRepGridObject.Rd':
  ‘x’

Documented arguments not in \usage in Rd file 'convertScivescoImportObjectToRepGridObject.Rd':
  ‘x’

Documented arguments not in \usage in Rd file 'mapCoordinatesToColor.Rd':
  ‘color’

Documented arguments not in \usage in Rd file 'quasiDistributionDistanceSlater.Rd':
  ‘rep’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Running examples in ‘openscoring-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: oscai
> ### Title: Score with an AI A basic function to score the creativity with
> ###   an AI. See the OpenScoring site for more information. Requires an
> ###   internet connection.
> ### Aliases: oscai
> 
> ### ** Examples
> 
> df <- data.frame(
+   stimulus = c("brick", "hammer", "sponge"),
+   response = c("butter for trolls", "make Thor jealous", "make it play in a kids show")
+ )
> 
> df <- oscai(df, stimulus, response, model = "davinci2")
Error: lexical error: invalid char in json text.
                                       <html>  <head><title>502 Bad Ga
                     (right here) ------^
Execution halted
checkRd: (-1) loss.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) loss.Rd:25-26: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) mixture-opera.Rd:82: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mixture-opera.Rd:83: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) plot.mixture.Rd:34: Lost braces in \itemize; meant \describe ?
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) word_imp.Rd:14: Lost braces
    14 | number of individual records. An \code{n} x code{2} dataframe can
       |                                                 ^
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    23 | N is computed from \code{p} length. M is code{10^4} by default.
       |                                              ^
Package suggested but not available for checking: ‘gurobi’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘Graph_layout_Doptbd_trtE’
Malformed Title field: should not end in a period.
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    30 | List/data frame of dimension (number of evaluations) x (4 + n_par) containing input data and results. Columns \code{size} and \code{cost} are optimal holdout size and cost at this size respectively. Parameters N, k1, theta.1, theta.2,...,theta.{n_par} are input data.
       |                                                                                                                                                                                                                                                     ^
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checkRd: (-1) lorenz.Rd:82: Lost braces; missing escapes or markup?
    82 | L_i = sum_{j=1}^{i} x_j * n_j / sum_{j=1}^{n} x_j * n_j.
       |           ^
checkRd: (-1) lorenz.Rd:82: Lost braces; missing escapes or markup?
    82 | L_i = sum_{j=1}^{i} x_j * n_j / sum_{j=1}^{n} x_j * n_j.
       |                 ^
checkRd: (-1) lorenz.Rd:82: Lost braces; missing escapes or markup?
    82 | L_i = sum_{j=1}^{i} x_j * n_j / sum_{j=1}^{n} x_j * n_j.
       |                                     ^
checkRd: (-1) lorenz.Rd:82: Lost braces; missing escapes or markup?
    82 | L_i = sum_{j=1}^{i} x_j * n_j / sum_{j=1}^{n} x_j * n_j.
       |                                           ^
checkRd: (-1) lorenz.Rd:83: Lost braces; missing escapes or markup?
    83 | where x_i are indexed in non-decreasing order (x_i <= x_{i+1}).
       |                                                         ^
checkRd: (-1) gnu_style.Rd:24: Lost braces
    24 | [GNU Command Line Standards]{http://www.gnu.org/prep/standards/standards.html}
       |                             ^
Package which this enhances but not available for checking: ‘gurobi’
'LazyData' is specified without a 'data' directory
checkRd: (-1) calc_n_from_c.Rd:5: Lost braces; missing escapes or markup?
     5 | \title{Helper function to calculate other n's given n_{1,T} and allocation ratios}
       |                                                       ^
checkRd: (-1) calc_n_from_c.Rd:15: Lost braces; missing escapes or markup?
    15 | Helper function to calculate other n's given n_{1,T} and allocation ratios
       |                                                ^
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘manual.Rmd’ using rmarkdown
Could not fetch http://www.zotero.org/styles/springer-vancouver-brackets
HttpExceptionRequest Request {
  host                 = "www.zotero.org"
  port                 = 80
  secure               = False
  requestHeaders       = []
  path                 = "/styles/springer-vancouver-brackets"
  queryString          = ""
  method               = "GET"
  proxy                = Nothing
  rawBody              = False
  redirectCount        = 10
  responseTimeout      = ResponseTimeoutDefault
  requestVersion       = HTTP/1.1
  proxySecureMode      = ProxySecureWithConnect
}
 (InternalException (HandshakeFailed (Error_Protocol "peer does not support Extended Main Secret" HandshakeFailure)))
Error: processing vignette 'manual.Rmd' failed with diagnostics:
pandoc document conversion failed with error 61
--- failed re-building ‘manual.Rmd’

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Found export directive that requires package ‘methods’:
  ‘exportClasses’
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains ‘methods’.
Package suggested but not available for checking: ‘rrelaxiv’
Found the following files/directories:
  ‘Graph_layout_Doptrcd_trtE’
Package suggested but not available for checking: ‘gurobi’
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) internal.Rd:26-27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) internal.Rd:29-31: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) internal.Rd:48: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) internal.Rd:56-57: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) internal.Rd:62-63: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) internal.Rd:68: Lost braces in \itemize; meant \describe ?
checkRd: (-1) internal.Rd:70: Lost braces in \itemize; meant \describe ?
checkRd: (-1) minK.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) minK.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) minK.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) lra-ord.Rd:54: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) lra-ord.Rd:55-56: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) lra-ord.Rd:57-58: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) lra-ord.Rd:59: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) lra-ord.Rd:60: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) orf.Rd:74: Lost braces
    74 | matrix of covariates \code{X} and a vector of outcomes 'code{Y} to the \code{orf}
       |                                                             ^
Found the following files/directories:
  ‘cluster of fitted mean data.eps’ ‘cluster of fitted mean data.txt’
  ‘cluster of raw data.txt’
checkRd: (-1) distsumlpmin.Rd:69: Lost braces
    69 |   \code{Véase}{Vease} \enc{también}{tambien} \code{\link{distsummin}}, \code{\link{orloca.es-package}}, \code{\link{loca.p}} y \code{\link{distsum}}.
       |               ^
checkRd: (-1) distsummin.Rd:80: Lost braces
    80 | \code{Véase}{Vease} \enc{también}{tambien} \code{\link{orloca.es-package}}, \code{\link{loca.p}} y \code{\link{distsum}}.
       |             ^
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
Documented arguments not in \usage in Rd file 'dosepred.Rd':
  ‘w’

Documented arguments not in \usage in Rd file 'surv_dm_solver.Rd':
  ‘bw_optim’

Documented arguments not in \usage in Rd file 'surv_forward_solver.Rd':
  ‘Phit’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
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 ?
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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}
       |                                                                                                        ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) RLum.OSL_decomposition.Rd:90-91: Lost braces
    90 | \item \link{optimise_OSLintervals}: {Approximates the optimal integration intervals. Uses the global
       |                                     ^
checkRd: (-1) RLum.OSL_decomposition.Rd:92-94: Lost braces
    92 | \item \link{decompose_OSLcurve}: {Calculates component intensities for \strong{all} \code{record_type} measurements.
       |                                  ^
checkRd: (-1) fit_OSLcurve.Rd:97: Lost braces; missing escapes or markup?
    97 | fitting with the \emph{RSS_{K-1}} value of the previous fitting and calculates
       |                            ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) otp_create_surface.Rd:33: Lost braces; missing escapes or markup?
    33 | The file will be named surface_{id}.tiff, with {id} replaced by the OTP id assigned
       |                                ^
checkRd: (-1) otp_create_surface.Rd:33: Lost braces; missing escapes or markup?
    33 | The file will be named surface_{id}.tiff, with {id} replaced by the OTP id assigned
       |                                                ^
checkRd: (-1) imput_cov.Rd:79: Lost braces
    79 | \item van Buuren, S., Groothuis-Oudshoorn, K. (2011). mice: Multivariate Imputation by Chained Equations in R. Journal of Statistical Software, 45(3), 1–67. url{https://www.jstatsoft.org/v45/i03/}
       |                                                                                                                                                                 ^
checkRd: (-1) indiv_grp_closest.Rd:47: Lost braces; missing escapes or markup?
    47 | The function \code{indiv_grp_closest} is an intermediate function used in the implementation of an algorithm called {OUTCOME} (and its enrichment {R-OUTCOME}, see the reference (2) for more details) dedicated to the solving of recoding problems in data fusion using Optimal Transportation theory.
       |                                                                                                                     ^
checkRd: (-1) indiv_grp_closest.Rd:47: Lost braces; missing escapes or markup?
    47 | The function \code{indiv_grp_closest} is an intermediate function used in the implementation of an algorithm called {OUTCOME} (and its enrichment {R-OUTCOME}, see the reference (2) for more details) dedicated to the solving of recoding problems in data fusion using Optimal Transportation theory.
       |                                                                                                                                                   ^
checkRd: (-1) merge_dbs.Rd:179: Lost braces
   179 | \item van Buuren, S., Groothuis-Oudshoorn, K. (2011). mice: Multivariate Imputation by Chained Equations in R. Journal of Statistical Software, 45(3), 1–67. url{https://www.jstatsoft.org/v45/i03/}
       |                                                                                                                                                                 ^
Specified C++11: please drop specification unless essential
checkRd: (-1) fmat.Rd:15: Lost braces; missing escapes or markup?
    15 | \item outcome: codes {I, P, R, NC, O, UH, UO, eUH, eUO, NE}
       |                      ^
checkRd: (-1) fmat.Rd:24: Lost braces; missing escapes or markup?
    24 | The input parameters given by the user are {I, P, R, NC, O, UH, UO} and
       |                                            ^
checkRd: (-1) fmat.Rd:25: Lost braces; missing escapes or markup?
    25 | the parameter 'e'. The parameter e is multiplied by {UH, UO} internally so as to
       |                                                     ^
checkRd: (-1) fmat.Rd:26: Lost braces; missing escapes or markup?
    26 | produce {eUH, eUO}.
       |         ^
checkRd: (-1) middleearth.Rd:14: Lost braces; missing escapes or markup?
    14 | \item \strong{code:} one of the outcome codes {I, P, R, NC, O, UH, UO, UH, UO, NE}
       |                                               ^
Specified C++11: please drop specification unless essential
checkRd: (-1) BFGS_lpdf.Rd:37: Lost braces
    37 | A wrapper for code{\link{BFGS_std}} that is useful for easily calling 
       |                   ^
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) lint_package.Rd:20: Lost braces
    20 | code{\link[lintr:lint_package]{lintr::lint_package}} where we hardcode the
       |     ^
checkRd: (-1) provide_news_rd.Rd:22: Lost braces
    22 | Christian Vonderach uses the index thus wants file{inst/NEWS.rd} to
       |                                                   ^
checkRd: (-1) provide_news_rd.Rd:23: Lost braces
    23 | automatically be in sync with file{./NEWS.md}.
       |                                   ^
Documented arguments not in \usage in Rd file 'prediction_regression.Rd':
  ‘dataset’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Changes
'LazyData' is specified without a 'data' directory
checkRd: (-1) residuals_paco.Rd:10: Escaped LaTeX specials: \$
Specified C++11: please drop specification unless essential
Package vignette with \VignetteEngine{} not specifying an engine package:
  ‘pacviz.Rmd’
Engines should be specified as \VignetteEngine{PKG::ENG}.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) pagoo.Rd:107-110: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pagoo.Rd:112-115: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pagoo.Rd:117-119: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pagoo.Rd:121-125: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) pagoo.Rd:131-133: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) pagoo.Rd:165-167: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pagoo.Rd:169-170: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pagoo.Rd:172-173: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
checkRd: (-1) MICS2014Ch.Rd:296: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) MICS2014Ch.Rd:297: Lost braces in \enumerate; meant \describe ?
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) PakPMICS2018bh.Rd:90: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) PakPMICS2018ch.Rd:454: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) PakPMICS2018fs.Rd:310: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) PakPMICS2018hh.Rd:364: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) PakPMICS2018hl.Rd:132: Lost braces in \enumerate; meant \describe ?
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checkRd: (-1) PakPMICS2018mn.Rd:245: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) PakPMICS2018wm.Rd:448: Lost braces in \enumerate; meant \describe ?
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘CorShrink’
'LazyData' is specified without a 'data' directory
checkRd: (-1) branchClasses.Rd:15: Lost braces; missing escapes or markup?
    15 | \item{whichExtant}{A logical vector with length equal to number of tips in the tree. A {TRUE} value indicates
       |                                                                                        ^
checkRd: (-1) minCharChange.Rd:134: Lost braces; missing escapes or markup?
   134 | an identical name in function \code{phyDat} in package {phangorn}.
       |                                                        ^
checkRd: (-1) resolveTreeChar.Rd:98: Lost braces; missing escapes or markup?
    98 | an identical name in function \code{phyDat} in package {phangorn}.
       |                                                        ^
checkRd: (-1) simFossilRecord.Rd:44: Lost braces
    44 | since its origination time is code{D},
       |                                   ^
checkRd: (-1) as_ped.Rd:91: Lost braces
    91 | variables that were used to create the PED object (code{data}).}
       |                                                        ^
Documented arguments not in \usage in Rd file 'dplyr_verbs.Rd':
  ‘funs’ ‘.dots’ ‘keep_attributes’

Documented arguments not in \usage in Rd file 'nest_tdc.Rd':
  ‘vars’ ‘id’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
checkRd: (-1) addFPOD.Rd:42: Lost braces
    42 |   has FPOD detections, these events may not work with a variety of other ]code{PAMpal}
       |                                                                               ^
S3 methods shown with full name in Rd file 'pamr.internal.Rd':
  ‘print.nsc’ ‘print.nsccv’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
checkRd: (-1) checkSoundscapeInput.Rd:40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) checkSoundscapeInput.Rd:41-42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) checkSoundscapeInput.Rd:43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) checkSoundscapeInput.Rd:44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotPSD.Rd:77: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotPSD.Rd:78-79: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotPSD.Rd:80-81: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotPSD.Rd:82-85: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotPSD.Rd:86-89: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
checkRd: (-1) Pandoc.convert.Rd:42: Lost braces
    42 | Calling John MacFarlane's great program to convert specified file (see \code{f} parameter below) or character vector {see \code{text} paramater} to other formats like \code{HTML}, \code{pdf}, \code{docx}, \code{odt} etc.
       |                                                                                                                      ^
Running ‘testthat.R’ [9s/33s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(Pandora)
  > 
  > test_check("Pandora")
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 25 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-getData.R:57:3'): Test getData() ───────────────────────────────
  Error in `getData(name = "SAAID_V.2.0_2023 Animals (CSV)")`: Error in filterResourceByName(., name = name) : 
    No resource found with name 'SAAID_V.2.0_2023 Animals (CSV)'
  
  Backtrace:
      ▆
   1. ├─testthat::expect_true(...) at test-getData.R:57:3
   2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
   3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
   4. ├─base::nrow(getData(name = "SAAID_V.2.0_2023 Animals (CSV)"))
   5. └─Pandora::getData(name = "SAAID_V.2.0_2023 Animals (CSV)")
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 25 ]
  Error: Test failures
  Execution halted
checkRd: (-1) btsdemo.Rd:22: Escaped LaTeX specials: \_
checkRd: (-1) btsdemo.Rd:23: Escaped LaTeX specials: \_
checkRd: (-1) btsdemo.Rd:24: Escaped LaTeX specials: \_
checkRd: (-1) btsdemo.Rd:25: Escaped LaTeX specials: \_
checkRd: (-1) btsdemo.Rd:26: Escaped LaTeX specials: \_
checkRd: (-1) btsdemo.Rd:30: Escaped LaTeX specials: \_
Specified C++11: please drop specification unless essential
checkRd: (-1) panelsummary.Rd:112: Lost braces; missing escapes or markup?
   112 | \item `"{exp(estimate) * std.error}"
       |         ^
checkRd: (-1) panelsummary_raw.Rd:90: Lost braces; missing escapes or markup?
    90 | \item `"{exp(estimate) * std.error}"
       |         ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) hvidovre.Rd:11: Lost braces
    11 |     \item{\code{roof_tile}}{a numeric vector, roof_tile}{dummy, roof made out of tiles =1}
       |                                                         ^
checkRd: (-1) hvidovre.Rd:25: Lost braces
    25 |     \item{\code{railways}}{a numeric vector, railways}{distance to nearest railway in meters}
       |                                                       ^
checkRd: (-1) hvidovre.Rd:26: Lost braces
    26 |     \item{\code{nature_SLD}}{a numeric vector, nature_SLD}{distance to nearest nature area in meters}
       |                                                           ^
checkRd: (-1) apa_print.htest.Rd:58: Lost braces
    58 | [here]{https://github.com/crsh/papaja/issues} (please include
       |       ^
checkRd: (-1) init_apa_results.Rd:15-16: Lost braces
    15 | \item{\code{full_result}}{A (named list of) character strings comprised of \code{estimate} and \verb{statistic`` for each factor.\} \\item\{}table`}{A data frame containing all results; can, for example, be passed to \code{\link[=apa_table]{apa_table()}}.
       |                                                                                                                                                     ^
checkRd: (-1) agreement.Rd:52: Lost braces in \itemize; meant \describe ?
checkRd: (-1) agreement.Rd:53-54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) agreement.Rd:55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) agreement.Rd:56: Lost braces in \itemize; meant \describe ?
checkRd: (-1) agreement.Rd:57: Lost braces in \itemize; meant \describe ?
checkRd: (-1) agreement.Rd:58: Lost braces in \itemize; meant \describe ?
checkRd: (-1) papciUI.Rd:33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) papciUI.Rd:34-35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) papciUI.Rd:36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) papciUI.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) papciUI.Rd:38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) papciUI.Rd:39: Lost braces in \itemize; meant \describe ?
Specified C++11: please drop specification unless essential
checkRd: (-1) getParamNr.Rd:15: Lost braces
    15 | Default is code{FALSE}.}
       |                ^
checkRd: (-1) getRequirements.Rd:16: Lost braces
    16 | code{TRUE}.}
       |     ^
checkRd: (-1) sampleValue.Rd:15: Lost braces; missing escapes or markup?
    15 | Default is code {FALSE}.}
       |                 ^
checkRd: (-1) sampleValues.Rd:18: Lost braces; missing escapes or markup?
    18 | Default is code {FALSE}.}
       |                 ^
'LazyData' is specified without a 'data' directory
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) Code.Rd:68: Lost braces
    68 | ([base]{character})
       |        ^
checkRd: (-1) printMessage.Rd:10: Lost braces
    10 | \item{notPermitted}{([base]{data.frame})}
       |                            ^
checkRd: (-1) printMessage.Rd:12: Lost braces
    12 | \item{versionCheck}{([base]{data.frame})}
       |                            ^
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 ?
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in Rd file 'expect_missing_argument.Rd':
  ‘message’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
checkRd: (-1) summary.parsec.Rd:13-14: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘co2’ ‘co2.1’ ‘co2.2’ ‘co2s.1’ ‘co2s.2’ ‘ctm.1’ ‘ctm.2’ ‘m’ ‘m.1’
  ‘m.2’ ‘test’ ‘test.1’ ‘test.2’ ‘testa.1’ ‘testa.2’ ‘xfile.1’
  ‘xfile.2’
Documented arguments not in \usage in Rd file 'fixvar_of_red_mod.Rd':
  ‘data’

Documented arguments not in \usage in Rd file 'get_ndf.Rd':
  ‘data’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
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) as_config.Rd:32: Lost braces; missing escapes or markup?
    32 | with `{config}` package, which requires existence of default key.
       |       ^
checkRd: (-1) as_config.Rd:28: Lost braces; missing escapes or markup?
    28 | list compatible with `{config}` package
       |                       ^
'LazyData' is specified without a 'data' directory
Package vignette with \VignetteEngine{} not specifying an engine package:
  ‘intro-pathdiagram.Rnw’
Engines should be specified as \VignetteEngine{PKG::ENG}.
checkRd: (-1) plotHeat.Rd:113: Lost braces
   113 | code{\link[patternize]{patPCA}}, as 'one' when visualizing single image or as 'multi' for multi
       |     ^
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
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}  
       |                    ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
checkRd: (-1) 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 ?
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
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 ?
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checkRd: (-1) simulate_phylproc.Rd:67: Lost braces in \itemize; meant \describe ?
Specified C++11: please drop specification unless essential
checkRd: (-1) MiniBenchmarkRvsCpp.Rd:16: Lost braces in \itemize; meant \describe ?
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Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
checkRd: (-1) pcoxtimecv.Rd:51: Lost braces; missing escapes or markup?
    51 | \item{foldids}{an optional sequence of values between \code{1} and {nfolds} specifying what fold each observation is in. This is important when comparing performance across models. If specified, \code{nfolds} can be missing.}
       |                                                                    ^
checkRd: (-1) pcoxtimecv.Rd:89: Lost braces
    89 | If more than one \code{alphas} is specified, say code{(0.2, 0.5, 1)}, the \code{pcoxtimecv} will search (experimental) for optimal values for alpha with respect to the corresponding lambda values. In this case, optimal alpha and lambda sequence will be returned, i.e., the \code{(alphas, lambdas)} pair that corresponds to the lowest predicted cross-validated error (likelihood deviance).
       |                                                      ^
checkRd: (-1) simtdc.Rd:67: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simtdc.Rd:69: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simtdc.Rd:70: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simtdc.Rd:71: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simtdc.Rd:72: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simtdc.Rd:73: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simtdc.Rd:74: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simtdc.Rd:76: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simtdc.Rd:77: Lost braces in \itemize; \value handles \item{}{} directly
Documented arguments not in \usage in Rd file 'getResponse.Rd':
  ‘model’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
checkRd: (-1) getPCRAData.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getPCRAData.Rd:29: Lost braces in \itemize; meant \describe ?
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
checkRd: (-1) pcvpcr.Rd:42: Lost braces; missing escapes or markup?
    42 | set {X, y} and cross-validation.
       |     ^
checkRd: (-1) pcvpls.Rd:42: Lost braces; missing escapes or markup?
    42 | set {X, y} and cross-validation.
       |     ^
Objects in \usage without \alias in Rd file 'ODACATH.estimate.Rd':
  ‘ODACAT.estimate’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Package suggested but not available for checking: ‘PythonInR’
checkRd: (-1) keyword_directory.Rd:48: Lost braces
    48 | Default pattern is "\\p{WHITE_SPACE}{3,}" which can be interpreted as: 
       |                        ^
checkRd: (-1) keyword_directory.Rd:48: Lost braces
    48 | Default pattern is "\\p{WHITE_SPACE}{3,}" which can be interpreted as: 
       |                                     ^
checkRd: (-1) keyword_search.Rd:59: Lost braces
    59 | Default pattern is "\\p{WHITE_SPACE}{3,}" which can be interpreted as: 
       |                        ^
checkRd: (-1) keyword_search.Rd:59: Lost braces
    59 | Default pattern is "\\p{WHITE_SPACE}{3,}" which can be interpreted as: 
       |                                     ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) get_training_data.Rd:6-14: Lost braces
     6 | where <- function(name, env = parent.frame()) {
       |                                               ^
checkRd: (-1) get_training_data.Rd:7-9: Lost braces
     7 |   if (identical(env, emptyenv())) {
       |                                   ^
checkRd: (-1) get_training_data.Rd:9-11: Lost braces
     9 |   } else if (exists(name, envir = env, inherits = FALSE)) {
       |                                                           ^
checkRd: (-1) get_training_data.Rd:11-13: Lost braces
    11 |   } else {
       |          ^
checkRd: (-1) get_training_data.Rd:20-28: Lost braces
    20 | where <- function(name, env = parent.frame()) {
       |                                               ^
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    21 |   if (identical(env, emptyenv())) {
       |                                   ^
checkRd: (-1) get_training_data.Rd:23-25: Lost braces
    23 |   } else if (exists(name, envir = env, inherits = FALSE)) {
       |                                                           ^
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    25 |   } else {
       |          ^
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) pdkMeans.Rd:63: Lost braces
    63 | \cite{C18}{pdSpecEst} for more details. Note that this comes at the cost of increased computation time in comparison to one
       |           ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) embedded.blocks.Rd:39: Lost braces
    39 | \item{miv.threshold}{MIV (marginal information value) entrance threshold applicable only for code{"stepMIV"} method.
       |                                                                                                  ^
checkRd: (-1) embedded.blocks.Rd:44: Lost braces
    44 | \item{m.ch.p.val}{Significance level of p-value for marginal chi-square test applicable only for code{"stepMIV"} method.
       |                                                                                                      ^
checkRd: (-1) ensemble.blocks.Rd:39: Lost braces
    39 | \item{miv.threshold}{MIV (marginal information value) entrance threshold applicable only for code{"stepMIV"} method.
       |                                                                                                  ^
checkRd: (-1) ensemble.blocks.Rd:44: Lost braces
    44 | \item{m.ch.p.val}{Significance level of p-value for marginal chi-square test applicable only for code{"stepMIV"} method.
       |                                                                                                      ^
checkRd: (-1) staged.blocks.Rd:39: Lost braces
    39 | \item{miv.threshold}{MIV (marginal information value) entrance threshold applicable only for code{"stepMIV"} method.
       |                                                                                                  ^
checkRd: (-1) staged.blocks.Rd:44: Lost braces
    44 | \item{m.ch.p.val}{Significance level of p-value for marginal chi-square test applicable only for code{"stepMIV"} method.
       |                                                                                                      ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) Peacock.test-package.Rd:28: Escaped LaTeX specials: \_
'LazyData' is specified without a 'data' directory
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checkRd: (-1) est_norm.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) est_norm.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) est_norm.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) example.geno.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) example.geno.Rd:25-26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) example.geno.Rd:27-28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) example.geno.Rd:33: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) example.geno.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) example.geno.Rd:38-40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) example.geno.Rd:41-45: Lost braces in \itemize; meant \describe ?
checkRd: (-1) example.geno.Rd:49: Lost braces in \itemize; meant \describe ?
checkRd: (-1) example.geno.Rd:50: Lost braces in \itemize; meant \describe ?
checkRd: (-1) example.geno.Rd:55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) example.geno.Rd:56-57: Lost braces in \itemize; meant \describe ?
checkRd: (-1) example.geno.Rd:58-59: Lost braces in \itemize; meant \describe ?
checkRd: (-1) example.geno.Rd:60-61: Lost braces in \itemize; meant \describe ?
S3 methods shown with full name in Rd file 'format.relation.Rd':
  ‘format.relation’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
checkRd: (-1) pedigree_ll_terms.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pedigree_ll_terms.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pedigree_ll_terms.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pedigree_ll_terms.Rd:19-20: Lost braces in \itemize; meant \describe ?
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)}.
       |                                                                   ^
GNU make is a SystemRequirements.
checkRd: (-1) 5.1.pems.plots.Rd:212: Lost braces; missing escapes or markup?
   212 |   (Logical or character) For {WatsonPlot}, how to 
       |                              ^
checkRd: (-1) 5.1.pems.plots.Rd:221: Lost braces; missing escapes or markup?
   221 |   (numeric) For {WatsonPlot}, pre-set plot types: 
       |                 ^
checkRd: (-1) 6.2.check.functions.Rd:189: Lost braces
   189 |   If a parent function is identified as \code{fun.name} and the check case (code{input}, 
       |                                                                                 ^
checkRd: (-1) 7.1.vsp.code.Rd:89: Lost braces
    89 |   code{\link{common.calculations}} for further details.
       |       ^
checkRd: (-1) 7.2.emissions.code.Rd:90: Lost braces
    90 |   emissions calculation methods. It accepts an input code{conc} which it checks and passes 
       |                                                          ^
checkRd: (-1) 8.1.tidyverse.tools.Rd:139: Lost braces
   139 |    (\code{pems}, code{data.frame}, etc) to 
       |                      ^
Specified C++11: please drop specification unless essential
checkRd: (-1) breslow.Rd:27: Escaped LaTeX specials: \# \#
checkRd: (-1) my.bspline.Rd:38: Escaped LaTeX specials: \$ \$ \$
Specified C++11: please drop specification unless essential
checkRd: (-1) my.bspline.Rd:21: Escaped LaTeX specials: \$ \$ \$ \$ \$ \$
checkRd: (-1) my.bspline.Rd:27: Escaped LaTeX specials: \$ \$ \$
checkRd: (-1) pendensity.Rd:52: Escaped LaTeX specials: \$
checkRd: (-1) pendensity.Rd:57: Escaped LaTeX specials: \$ \$
checkRd: (-1) pendensity.Rd:66: Escaped LaTeX specials: \$
checkRd: (-1) pendensity.Rd:82: Escaped LaTeX specials: \$ \$
checkRd: (-1) pendensity.Rd:96: Escaped LaTeX specials: \$
checkRd: (-1) pendensity.Rd:100: Escaped LaTeX specials: \$
checkRd: (-1) pendensity.Rd:105: Escaped LaTeX specials: \$
checkRd: (-1) pendensity.Rd:109: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) mc3_pep.Rd:53: Lost braces; missing escapes or markup?
    53 | is not 2^{p} but the number of unique models `visited' by the 
       |          ^
Argument items with no description in Rd file 'lmres.Rd':
  ‘\dots’
Argument items with no description in Rd file 'simpleSlope.Rd':
  ‘\dots’
Argument items with no description in Rd file 'summary.lmres.Rd':
  ‘\dots’
checkRd: (-1) CAPM.RiskPremium.Rd:67: Escaped LaTeX specials: \&
checkRd: (-1) Return.portfolio.Rd:109: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Return.portfolio.Rd:110-113: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Return.portfolio.Rd:114-118: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Return.portfolio.Rd:119-122: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Return.portfolio.Rd:123-129: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Return.portfolio.Rd:130-132: Lost braces in \itemize; meant \describe ?
checkRd: (-1) chart.ECDF.Rd:31: Escaped LaTeX specials: \#
checkRd: (-1) managers.Rd:8: Escaped LaTeX specials: \&
Package suggested but not available for checking: ‘DMwR’
checkRd: (-1) classificationMetrics.Rd:85: Lost braces; missing escapes or markup?
    85 |   will use some extra notation, namely: TP = #{p == + & t == +} ; FP =
       |                                               ^
checkRd: (-1) classificationMetrics.Rd:86: Lost braces; missing escapes or markup?
    86 |   #{p == + & t == -} ; TN = #{p == - & t == -}; FN = #{p == - & t == +}
       |    ^
checkRd: (-1) classificationMetrics.Rd:86: Lost braces; missing escapes or markup?
    86 |   #{p == + & t == -} ; TN = #{p == - & t == -}; FN = #{p == - & t == +}
       |                              ^
checkRd: (-1) classificationMetrics.Rd:86: Lost braces; missing escapes or markup?
    86 |   #{p == + & t == -} ; TN = #{p == - & t == -}; FN = #{p == - & t == +}
       |                                                       ^
checkRd: (-1) classificationMetrics.Rd:87: Lost braces; missing escapes or markup?
    87 |   ; P = #{t == +} ; N = #{t == -}; Finally, for some descriptions
       |          ^
checkRd: (-1) classificationMetrics.Rd:87: Lost braces; missing escapes or markup?
    87 |   ; P = #{t == +} ; N = #{t == -}; Finally, for some descriptions
       |                          ^
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘dendextendRcpp’
Documented arguments not in \usage in Rd file 'allTrees.Rd':
  ‘dist’

Documented arguments not in \usage in Rd file 'getNode.Rd':
  ‘hc’ ‘pair’

Documented arguments not in \usage in Rd file 'switchEntries.Rd':
  ‘pair’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
checkRd: (-1) jackal.Rd:32: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Invalid package aliases in Rd file 'perspective-package.Rd':
  ‘perspective-package’
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Fixed issues
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) read_PN.Rd:15: Lost braces
    15 | A code{\link{marked_petrinet}}
       |       ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) ReadHardcalls.Rd:5: Lost braces; missing escapes or markup?
     5 | \title{Loads the variant_numth variant, and then fills buf with {0, 1, 2, NA}
       |                                                                 ^
checkRd: (-1) ReadIntList.Rd:17: Lost braces; missing escapes or markup?
    17 | correspond to variant_subset, and values are in {0, 1, 2, NA} indicating
       |                                                 ^
checkRd: (-1) PatentsRD.Rd:4: Escaped LaTeX specials: \&
checkRd: (-1) PatentsRD.Rd:30: Escaped LaTeX specials: \&
checkRd: (-1) PatentsRDUS.Rd:4: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
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
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘animation.gif’
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
checkRd: (-1) PhageCocktail.Rd:100-103: Lost braces
   100 | "Result": {
       |           ^
checkRd: (-1) PhageCocktail.Rd:105-112: Lost braces
   105 | "BacteriaLysed": {
       |                  ^
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
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.
       |                            ^
checkRd: (-1) phasePlaneAnalysis.Rd:84: Lost braces; missing escapes or markup?
    84 | identified {see (3) above}, if this point is a saddle then the manifolds are
       |            ^
Found the following files/directories:
  ‘test.pdf’
'LazyData' is specified without a 'data' directory
checkRd: (-1) connectedSets.Rd:27: Escaped LaTeX specials: \_ \_
checkRd: (-1) connectedSets.Rd:29: Escaped LaTeX specials: \_ \_
checkRd: (-1) connectedSets.Rd:31: Escaped LaTeX specials: \_ \_
checkRd: (-1) maxConnectedSet.Rd:35: Escaped LaTeX specials: \_ \_ \_ \_ \_ \_ \_ \_
checkRd: (-1) maxConnectedSet.Rd:37: Escaped LaTeX specials: \_ \_ \_ \_ \_ \_ \_ \_ \_ \_
checkRd: (-1) maxConnectedSet.Rd:39: Escaped LaTeX specials: \_ \_ \_ \_ \_ \_ \_ \_ \_ \_
checkRd: (-1) maxConnectedSet.Rd:41: Escaped LaTeX specials: \_ \_ \_ \_ \_ \_ \_ \_ \_ \_
checkRd: (-1) maxConnectedSet.Rd:45: Escaped LaTeX specials: \_ \_ \_ \_ \_ \_ \_ \_ \_ \_
checkRd: (-1) maxConnectedSet.Rd:47: Escaped LaTeX specials: \_ \_
Specified C++11: please drop specification unless essential
checkRd: (-1) read_cid_spectravue_csv.Rd:46: Lost braces
    46 | function code{range()} will return range of wavelengths expressed in
       |              ^
checkRd: (-1) read_fmi2mspct.Rd:78: Lost braces; missing escapes or markup?
    78 |   \code{tz = UTC} and {time.shift.min = 120} to convert times to UTC. This
       |                       ^
checkRd: (-1) McCree_photosynthesis.mspct.Rd:18: Lost braces; missing escapes or markup?
    18 |   Irradiance was in the range 10 to 15 W m$^{-2}$.
       |                                             ^
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 ?
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checkRd: (-1) 11_d.init.procedure.Rd:21-23: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) as.star.tree.Rd:26: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) as.star.tree.Rd:29: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) GarlandJanis.IC.Rd:4: Escaped LaTeX specials: \&
checkRd: (-1) GarlandJanis.IC.Rd:6: Escaped LaTeX specials: \&
checkRd: (-1) GarlandJanis.Original.Rd:4: Escaped LaTeX specials: \&
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checkRd: (-1) GarlandJanis.varcov.Rd:7: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
checkRd: (-1) fitgom.Rd:87: Lost braces
    87 |   \item \code{theta} The ncol{counts} by K matrix of estimated
       |                              ^
checkRd: (-1) fitgom.Rd:89: Lost braces
    89 |   \item \code{omega} The nrow{counts} by K matrix of estimated
       |                              ^
checkRd: (-1) phylter.Rd:51: Lost braces; missing escapes or markup?
    51 | the output ({out$DiscardedGenes}).}
       |             ^
Package suggested but not available for checking: ‘INLA’
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
       |     ^
'LazyData' is specified without a 'data' directory
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: \$ \$
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘pinnacle.API’
checkRd: (-1) pinp.Rd:60: Lost braces; missing escapes or markup?
    60 |   {current date}"}
       |   ^
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Invalid package aliases in Rd file 'pipegs.Rd':
  ‘pipegs-package’
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Documented arguments not in \usage in Rd file 'TungUbRF.Rd':
  ‘feature_num_tree’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) get_pixels.Rd:27-29: Lost braces
    27 | if (interactive()) {
       |                    ^
'LazyData' is specified without a 'data' directory
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 ?
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) deps.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) deps.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) deps.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pkgdepR-package.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pkgdepR-package.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pkgdepR-package.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) build_reference.Rd:157: Lost braces; missing escapes or markup?
   157 | a top-level \code{icons} directory. This should contain {.png} files that are
       |                                                         ^
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) write.pkgbib.Rd:44: Lost braces; missing escapes or markup?
    44 | The Old version of this function {write.bib} has now been integrated
       |                                  ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) cov_holder.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) cov_holder.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) cov_holder.Rd:31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) cov_holder.Rd:32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) cov_holder.Rd:33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pk.calc.sparse_auc.Rd:49: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pk.calc.sparse_auc.Rd:50: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pk.calc.sparse_auc.Rd:51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sparse_auc_weight_linear.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sparse_auc_weight_linear.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sparse_auc_weight_linear.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sparse_mean.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sparse_mean.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) time_calc.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) time_calc.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) time_calc.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) time_calc.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) time_calc.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) adjacency.Rd:27: Lost braces; missing escapes or markup?
    27 | item j. For example, in the ranking \\{1\\} > \\{3, 4\\} > \\{2\\},
       |                                       ^
checkRd: (-1) adjacency.Rd:27: Lost braces; missing escapes or markup?
    27 | item j. For example, in the ranking \\{1\\} > \\{3, 4\\} > \\{2\\},
       |                                                 ^
checkRd: (-1) adjacency.Rd:27: Lost braces; missing escapes or markup?
    27 | item j. For example, in the ranking \\{1\\} > \\{3, 4\\} > \\{2\\},
       |                                                              ^
checkRd: (-1) rankings.Rd:127: Lost braces; missing escapes or markup?
   127 | rank skipped. For example {1, 0, 2, 1}, ranks the first and fourth items in
       |                           ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) 01-TCGA-ESCA-data.Rd:47: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) 01-TCGA-ESCA-data.Rd:48: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) 01-TCGA-ESCA-data.Rd:49-51: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) 01-TCGA-ESCA-data.Rd:52-55: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) 01-TCGA-ESCA-data.Rd:56-58: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) 01-TCGA-ESCA-data.Rd:59-62: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) 01-TCGA-ESCA-data.Rd:63-64: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) 02-fitCoxModel.Rd:87: Lost braces; missing escapes or markup?
    87 |   returns the value on which it was invoked. The {summary} method
       |                                                  ^
Found the following files/directories:
  ‘P2Run.csv’ ‘P2Run.html’ ‘P2Run.png’
checkRd: (-1) one_design.Rd:125-126: Lost braces
   125 | function serves for the purpose of spot-testing for any pre-specified {n,
       |                                                                       ^
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
checkRd: (-1) plgraphics-internal.Rd:19: Lost braces
    19 |     \item{RNAMES}{code{row.names} if \code{x} is a matrix or data.frame,
       |                       ^
checkRd: (-1) check_hwe.Rd:103: Lost braces; missing escapes or markup?
   103 | {'ALL', 'AFF', 'UNAFF', 'ALL(QT)', 'ALL(NP)'}), A1 (Allele 1; usually minor),
       | ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) delta2a.Rd:21: Lost braces; missing escapes or markup?
    21 | delta_k = log(a_k - a_{k+1})
       |                       ^
checkRd: (-1) ordprob.mple.Rd:29: Lost braces
    29 | logical. If code{TRUE} all the q variable are assumed to have the same mean.
       |                 ^
Package vignette without corresponding tangle output:
  ‘plot3logit-overview.Rmd’
'LazyData' is specified without a 'data' directory
checkRd: (-1) add_bars.Rd:15: Lost braces
    15 | When \\code{y0} is not specified, the lowest value of the y-axis is used.}
       |            ^
checkRd: (-1) add_bars.Rd:24: Lost braces
    24 | \\code{\\link[graphics]{par}}.}
       |       ^
checkRd: (-1) add_bars.Rd:24: Lost braces
    24 | \\code{\\link[graphics]{par}}.}
       |                        ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) plotluck.Rd:129: Lost braces
   129 |  in factors are are shown as a special factor level code{"?"}. They can be
       |                                                         ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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}}
       |     ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) spls.cv.Rd:70-72: Lost braces
    70 | \item{scale.X}{aa}{boolean value indicating whether the data matrices 
       |                   ^
checkRd: (-1) spls.stab.Rd:65-67: Lost braces
    65 | \item{scale.X}{aa}{boolean value indicating whether the data matrices 
       |                   ^
Invalid package aliases in Rd file 'plsgenomics-deprecated.Rd':
  ‘plsgenomics-deprecated-package’
Invalid package aliases in Rd file 'plsgenomics-internal.Rd':
  ‘plsgenomics-internal-package’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Package vignette without corresponding tangle output:
  ‘Why-pluralize.Rmd’
checkRd: (-1) plu_more.Rd:16: Lost braces; missing escapes or markup?
    16 | Additional arguments are replaced with "{n} more".
       |                                         ^
Package suggested but not available for checking: ‘pmartRdata’
checkRd: (-1) PMCMR-deprecated.Rd:36: Lost braces in \itemize; \value handles \item{}{} directly
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
'LazyData' is specified without a 'data' directory
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 $a_{ij} = 1/a_{ij}$.
       |                                                                                              ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) plot_scm.Rd:106: Lost braces; missing escapes or markup?
   106 | \item{lookupDF}{A data frame containing a lookup table for node labels. By default, {plot_scm} will use the PSN model names. If a lookup table containing the fields `Model` and `Alias` is provided, model names in `Model` will be replaced in the output plots by mtaching labels in `Alias`.}
       |                                                                                     ^
checkRd: (-1) rnm.Rd:56: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rnm.Rd:57: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rnm.Rd:58: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rnm.Rd:59: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rnm.Rd:60: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rnm.Rd:61: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rnm.Rd:62: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rnm.Rd:63: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rnm.Rd:64: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rnm.Rd:65: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rnm.Rd:66: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rnm.Rd:67: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rnm.Rd:68: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rnm.Rd:69: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rnm.Rd:70: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rnm.Rd:71: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
Package unavailable to check Rd xrefs: ‘INLA’
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 $m(T)=T^{1/5}$.}
       |                                                                                                                                                           ^
'LazyData' is specified without a 'data' directory
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
checkRd: (-1) carcinoma.Rd:8: Escaped LaTeX specials: \&
checkRd: (-1) poLCA.Rd:63: Escaped LaTeX specials: \&
checkRd: (-1) poLCA.Rd:69: Escaped LaTeX specials: \&
checkRd: (-1) nuisance_functions.Rd:18-19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) policy.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) policy_data.Rd:124-125: Lost braces in \itemize; meant \describe ?
checkRd: (-1) policy_data.Rd:126: Lost braces in \itemize; meant \describe ?
checkRd: (-1) policy_data.Rd:127-128: Lost braces in \itemize; meant \describe ?
checkRd: (-1) policy_data.Rd:129: Lost braces in \itemize; meant \describe ?
checkRd: (-1) policy_data.Rd:130: Lost braces in \itemize; meant \describe ?
checkRd: (-1) policy_data.Rd:131: Lost braces in \itemize; meant \describe ?
checkRd: (-1) policy_data.Rd:132: Lost braces in \itemize; meant \describe ?
checkRd: (-1) policy_eval.Rd:193: Lost braces in \itemize; meant \describe ?
checkRd: (-1) policy_eval.Rd:194: Lost braces in \itemize; meant \describe ?
checkRd: (-1) policy_eval.Rd:195: Lost braces in \itemize; meant \describe ?
checkRd: (-1) policy_eval.Rd:196-197: Lost braces in \itemize; meant \describe ?
checkRd: (-1) policy_eval.Rd:198: Lost braces in \itemize; meant \describe ?
checkRd: (-1) policy_eval.Rd:199: Lost braces in \itemize; meant \describe ?
checkRd: (-1) policy_learn.Rd:129: Lost braces in \itemize; meant \describe ?
checkRd: (-1) policy_learn.Rd:130: Lost braces in \itemize; meant \describe ?
checkRd: (-1) policy_learn.Rd:131: Lost braces in \itemize; meant \describe ?
checkRd: (-1) policy_learn.Rd:132-133: Lost braces in \itemize; meant \describe ?
checkRd: (-1) policy_learn.Rd:134: Lost braces in \itemize; meant \describe ?
Package suggested but not available for checking: ‘pollimetrydata’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
zap:
  function(x, digits)
zap.default:
  function(x, digits, mFUN, min.d)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Codoc mismatches from Rd file 'zap.Rd':
zap.default
  Code: function(x, digits = getOption("digits"), mFUN = function(x,
                 ina) max(abs(x[!ina])), min.d = 0L)
  Docs: function(x, digits = getOption("digits"))
  Argument names in code not in docs:
    mFUN min.d
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) calculateDIC.Rd:30-31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) calculateDIC.Rd:32-33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) polySegratioMM-package.Rd:70-72: Lost braces in \itemize; meant \describe ?
Found the following files/directories:
  ‘test-data.R’ ‘test-inits.R’ ‘test.bug’ ‘test.cmd’
checkRd: (-1) MLM_Model.Rd:31: Lost braces; missing escapes or markup?
    31 |   the weight vectors \bold{{w}^{i}} corresponds to class \eqn{i}{i}.
       |                                ^
checkRd: (-1) MLM_Model.Rd:33: Lost braces; missing escapes or markup?
    33 | We set \eqn{{\bold{{w}}^{h}} = 0} and the parameters to be learned are the weight vectors \bold{{w}^{i}}
       |                                                                                                     ^
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Found export directive that requires package ‘methods’:
  ‘exportClasses’
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains ‘methods’.
checkRd: (-1) Kendall.Rd:12-13: Lost braces
    12 | \item{rates}{a}{matrix or dataframe with four columns: Rate identifier, Year,
       |                ^
checkRd: (-1) Kendall.Rd:15: Lost braces
    15 | \item{grades}{number}{of different levels of means and variances to try, default is 1000}
       |                      ^
checkRd: (-1) Kendall.Rd:17-18: Lost braces
    17 | \item{maxvar}{maximum}{variance to search over, default is 0.20. The maximum
       |                       ^
checkRd: (-1) Kendall.Rd:20: Lost braces
    20 | \item{minvar}{minimum}{variance to search, default is 0.00001}
       |                       ^
checkRd: (-1) Kendall.Rd:22: Lost braces
    22 | \item{maxmean}{maximum}{limit on the mean values to search, default 1}
       |                        ^
checkRd: (-1) Kendall.Rd:24: Lost braces
    24 | \item{minmean}{minimum}{limit on the mean values to search, default 0.01}
       |                        ^
checkRd: (-1) Kendall.Rd:73: Escaped LaTeX specials: \&
checkRd: (-1) countCDFxt.Rd:63: Escaped LaTeX specials: \&
checkRd: (-1) plot.tfam.Rd:17: Lost braces
    17 | objects created using code{tfam_inertia}.}
       |                           ^
checkRd: (-1) popdemo-package.Rd:32: Lost braces
    32 |        code{\link{inertia}} measures asymptotic population density relative to stable
       |            ^
checkRd: (-1) tfa_inertia.Rd:33: Lost braces
    33 | item{inertia}{inertias of perturbed matrices}
       |     ^
checkRd: (-1) tfa_inertia.Rd:33: Lost braces
    33 | item{inertia}{inertias of perturbed matrices}
       |              ^
checkRd: (-1) survmean.Rd:83: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) survmean.Rd:84: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) survmean.Rd:85: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) survmean.Rd:86-88: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘ragt2ridges’
Unknown package ‘ragt2ridges’ in Rd xrefs
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
checkRd: (-1) tradelist-class.Rd:91: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) summary.POUMM.Rd:28: Lost braces; missing escapes or markup?
    28 | \item{stats}{a named list of functions of the form function(par) { number },
       |                                                                  ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) coalesce_xy.Rd:22: Lost braces; missing escapes or markup?
    22 | the \code{conflict} argument of {powerjoin}'s join functions. \code{coalesce_xy()} is
       |                                 ^
checkRd: (-1) power_left_join.Rd:67: Lost braces; missing escapes or markup?
    67 | \item{by}{As in {dplyr}, but extended so user can supply a formula or a list
       |                 ^
checkRd: (-1) power_left_join.Rd:79: Lost braces; missing escapes or markup?
    79 | \item{keep}{A boolean for compatibility with {dplyr}, or a value among "left",
       |                                              ^
checkRd: (-1) preprocess_inputs.Rd:37: Lost braces; missing escapes or markup?
    37 | only be used in the \code{x} and \code{y} arguments of {powerjoin} join functions. No
       |                                                        ^
checkRd: (-1) equal.ordered.Rd:27: Lost braces; missing escapes or markup?
    27 | A vector of values for one in {kappa, N, power} that is not supplied by the user.
       |                               ^
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    33 | A vector of values for one in {kappa, N, power} that is not supplied by the user.
       |                               ^
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    27 | A vector of values for one in {kappa, N, power} that is not supplied by the user.
       |                               ^
checkRd: (-1) equal.unordered.cov.Rd:33: Lost braces; missing escapes or markup?
    33 | A vector of values for one in {kappa, N, power} that is not supplied by the user.
       |                               ^
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    30 | A vector of values for one in {kappa, N, power} that is not supplied by the user.
       |                               ^
checkRd: (-1) unequal.ordered.cov.Rd:36: Lost braces; missing escapes or markup?
    36 | A vector of values for one in {kappa, N, power} that is not supplied by the user.
       |                               ^
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    30 | A vector of values for one in {kappa, N, power} that is not supplied by the user.
       |                               ^
checkRd: (-1) unequal.unordered.cov.Rd:36: Lost braces; missing escapes or markup?
    36 | A vector of values for one in {kappa, N, power} that is not supplied by the user.
       |                               ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) bira2.Rd:91: Escaped LaTeX specials: \&
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Specified C++11: please drop specification unless essential
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})
       |                                                                                                                              ^
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   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})
       |                                                                                                                              ^
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
checkRd: (-1) pqrBayes.Rd:58: Lost braces; missing escapes or markup?
    58 | When {sparse=TRUE} (default), spike--and--slab priors are adopted. Otherwise, Laplacian shrinkage will be used.
       |      ^
checkRd: (-1) pqrBayes.Rd:62: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pqrBayes.Rd:63: Lost braces in \itemize; meant \describe ?
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) PRDA.Rd:8: Lost braces; missing escapes or markup?
     8 | Given an hypothetical value of effect size, {PRDA} performs a prospective
       |                                             ^
checkRd: (-1) PRDA.Rd:22: Lost braces; missing escapes or markup?
    22 | In {PRDA} there are two main functions:
       |    ^
checkRd: (-1) PRDA.Rd:51: Lost braces; missing escapes or markup?
    51 | Alternatively, {PRDA} allows users to specify a distribution of plausible
       |                ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) diagnose_expressions.Rd:39: Lost braces
    39 | \item wrapping a function argument in two curly braces (e.g. `{{arg}} > 0) means
       |                                                               ^
Package which this enhances but not available for checking: ‘ffbase’
Unknown package ‘ffbase’ in Rd xrefs
'LazyData' is specified without a 'data' directory
checkRd: (-1) app_server.Rd:10: Lost braces; missing escapes or markup?
    10 | \item{input, output, session}{Internal parameters for {shiny}. 
       |                                                       ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) dev_data.Rd:10: Lost braces in \itemize; meant \describe ?
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'LazyData' is specified without a 'data' directory
checkRd: (-1) preference-package.Rd:48-49: Lost braces in \itemize; meant \describe ?
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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 ?
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'maptools', 'rgdal'
Found the following files/directories:
  ‘hista.png’ ‘plotcd.png’ ‘test.R’ ‘test.html’ ‘testR2html.R’
  ‘testglm.csv’ ‘testglm.html’ ‘testglm.tab’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) alogistic.Rd:20: Lost braces
    20 | The user does not put these directly into this function, but rather uses code{ode} in the \code{deSolve} package.
       |                                                                              ^
checkRd: (-1) prim.box.Rd:66: Lost braces in \itemize; meant \describe ?
checkRd: (-1) prim.box.Rd:68: Lost braces in \itemize; meant \describe ?
checkRd: (-1) prim.box.Rd:70: Lost braces in \itemize; meant \describe ?
checkRd: (-1) NesPrInDT.Rd:17: Lost braces
    17 | {see function \code{\link{PrInDT}} for details.}\cr
       | ^
checkRd: (-1) PrInDTAll.Rd:16: Lost braces
    16 | {see function \code{\link{PrInDT}} for details.}\cr
       | ^
checkRd: (-1) PrInDTAllparts.Rd:17: Lost braces
    17 | {see function \code{\link{PrInDT}} for details.}\cr
       | ^
checkRd: (-1) PrInDTMulab.Rd:17: Lost braces
    17 | {see function \code{\link{PrInDT}} for details.}\cr
       | ^
checkRd: (-1) PrInDTMulabAll.Rd:17: Lost braces
    17 | {see function \code{\link{PrInDT}} for details.}\cr
       | ^
checkRd: (-1) PrInDTMulev.Rd:16: Lost braces
    16 | {see function \code{\link{PrInDT}} for details.}\cr
       | ^
checkRd: (-1) PrInDTMulevAll.Rd:16: Lost braces
    16 | {see function \code{\link{PrInDT}} for details.}\cr
       | ^
checkRd: (-1) PrInDTreg.Rd:16: Lost braces
    16 | {see function \code{\link{PrInDT}} for details.}\cr
       | ^
checkRd: (-1) PrInDTregAll.Rd:16: Lost braces
    16 | {see function \code{\link{PrInDT}} for details.}\cr
       | ^
checkRd: (-1) RePrInDT.Rd:17: Lost braces
    17 | {see function \code{\link{PrInDT}} for details.}\cr
       | ^
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.}
       |                                                                                                                                                                               ^
Packages suggested but not available for checking: 'gurobi', 'rcbc'
Packages suggested but not available for checking:
  'gurobi', 'rcbc', 'cplexAPI'
'LazyData' is specified without a 'data' directory
checkRd: (-1) clr_darken.Rd:50: Lost braces; missing escapes or markup?
    50 |   information regarding use of color spaces, please refer to the {colorspace}
       |                                                                  ^
checkRd: (-1) clr_lighten.Rd:50: Lost braces; missing escapes or markup?
    50 |   information regarding use of color spaces, please refer to the {colorspace}
       |                                                                  ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) proc.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) proc.Rd:28: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
checkRd: (-1) paasche.Rd:91: Lost braces
    91 |     \code{OSME} \tab Output-oriented scale-mix efficiency score \emph{(code{orientation = "out"})}\cr
       |                                                                            ^
checkRd: (-1) plot.profileModel.Rd:69: Escaped LaTeX specials: \&
checkRd: (-1) profileModel.Rd:277: Escaped LaTeX specials: \&
checkRd: (-1) PS.Rd:9: Lost braces
     9 | 		\item{CD}{}{Character disorder scale score}
       |                            ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) proftools-package.Rd:40: Lost braces
    40 |   by the code{kcachegrind} program available on some operating
       |              ^
checkRd: (-1) summary.projections.Rd:33-48: Lost braces
    33 | if (require(incidence)) {
       |                         ^
checkRd: (-1) organize.Rd:17: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) organize.Rd:18: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rebuild.Rd:17: Lost braces in \itemize; \value handles \item{}{} directly
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checkRd: (-1) rebuild.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rebuild.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
Package suggested but not available for checking: ‘cmdstanr’
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 ?
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
checkRd: (-1) impute_plot.Rd:32: Lost braces; missing escapes or markup?
    32 | \item{global}{Logical. If \code{TRUE} ({default}), a global density plot is
       |                                        ^
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘cin’
checkRd: (-1) computeResponseProbability.Rd:12: Lost braces; missing escapes or markup?
    12 | \item{model}{the item model to use. Accepts \code{grm} or {gpcm}.}
       |                                                           ^
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}}
       |                                      ^
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
       |         ^
Package suggested but not available for checking: ‘rdt’
Package suggested but not available for checking: ‘rdt’
Package suggested but not available for checking: ‘rdt’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rdt’
checkRd: (-1) papionin.Rd:21: Lost braces; missing escapes or markup?
    21 | \item \strong{coords} {The 3D array of landamrk coordinates}
       |                       ^
checkRd: (-1) papionin.Rd:22: Lost braces; missing escapes or markup?
    22 | \item \strong{species} {The vector of species names}
       |                        ^
checkRd: (-1) papionin.Rd:23: Lost braces; missing escapes or markup?
    23 | \item \strong{semi_lm} {The vector of semilandmark numbers of the full dataset}
       |                        ^
checkRd: (-1) papionin.Rd:24: Lost braces; missing escapes or markup?
    24 | \item \strong{curves} {The list of curves for sliding semilandmarks of the full dataset}
       |                       ^
checkRd: (-1) papionin.Rd:25: Lost braces; missing escapes or markup?
    25 | \item \strong{links} {The matrix of links between landmarks for the full dataset}
       |                      ^
checkRd: (-1) papionin.Rd:26-30: Lost braces
    26 | \item \strong{outline} {A list of 4 elements for the analysis of the outline shape:
       |                        ^
Invalid package aliases in Rd file 'granova-package.Rd':
  ‘granova-package’
GNU make is a SystemRequirements.
checkRd: (-1) qpc.Rd:43: Lost braces
    43 | S{Sulewski, P. (2020). \emph{Normal Distribution with Plasticizing Component,} Communications in Statistics ? Theory and Method 51(11), 3806-3835.}
       |  ^
checkRd: (-1) riedsid.Rd:92-93: Lost braces in \itemize; meant \describe ?
checkRd: (-1) riedsid.Rd:94-96: Lost braces in \itemize; meant \describe ?
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in Rd file 'kepner_robinson_test_internal.Rd':
  ‘group’ ‘alternative’ ‘trend’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
checkRd: (-1) data1.Rd:14: Lost braces
    14 | The data set from {AbouRizk, S.M., Halpin, D.W., Wilson, J. R. (1994). \emph{Fitting beta distributions based on sample data.} Journal of Construction Engineering and Management 120(2), 288–305.}
       |                   ^
checkRd: (-1) data2.Rd:14: Lost braces; missing escapes or markup?
    14 | The data set presents the height of 99 five-year-old British boys in cm downloaded from {http://www.mas.ncl.ac.uk/njnsm/medfac/docs/intro.pdf.}
       |                                                                                         ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) get.psid.Rd:14: Lost braces
    14 | \item{params}{postForm{RCurl} parameters}
       |                       ^
checkRd: (-1) get.psid.Rd:16: Lost braces
    16 | \item{curl}{postForm{RCurl} curl handle}
       |                     ^
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}
       |                         ^
Documented arguments not in \usage in Rd file 'pspline.sample.scalars.Rd':
  ‘time’

Documented arguments not in \usage in Rd file 'pspline.sample.timeseries.Rd':
  ‘time’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
checkRd: (-1) pspGlobal.Rd:65-67: Lost braces
    65 |     \code{population}{The number of parameter sets in each ordinal region,
       |                      ^
checkRd: (-1) pspGlobal.Rd:68: Lost braces
    68 |     \code{iterations}{The number of global iterations. It has to be an integer. If emph{population} is not set or the regions have population less then the upper bound on their size, the function will stop after the set number of \emph{iterations}.}
       |                      ^
checkRd: (-1) pspGlobal.Rd:68: Lost braces
    68 |     \code{iterations}{The number of global iterations. It has to be an integer. If emph{population} is not set or the regions have population less then the upper bound on their size, the function will stop after the set number of \emph{iterations}.}
       |                                                                                        ^
checkRd: (-1) pspGlobal.Rd:69-71: Lost braces
    69 |     \code{lower, upper}{Vectors specifiying the lower and upper boundaries of
       |                        ^
checkRd: (-1) pspGlobal.Rd:72-74: Lost braces
    72 |     \code{init}{A marix of parameters to use as the first jumping distribution. 
       |                ^
checkRd: (-1) pspGlobal.Rd:75-76: Lost braces
    75 |     \code{radius}{The radius of the hypershere with n-dimensions to sample from.
       |                  ^
checkRd: (-1) pspGlobal.Rd:77-79: Lost braces
    77 |     \code{parameter_names}{A character vector that includes the names of each parameter.
       |                           ^
checkRd: (-1) pspGlobal.Rd:80-83: Lost braces
    80 |     \code{dimensionality}{A single integer that specifies the number of
       |                          ^
checkRd: (-1) pspGlobal.Rd:84-85: Lost braces
    84 |     \code{responses}{It is an integer that specifies the number of continuous
       |                     ^
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) SumStat.Rd:107: Lost braces
   107 | Current version of \code{PSweight} allows for five types of propensity score weights used to estimate ATE (\code{"IPW"}), ATT {(\code{"treated"})}, and
       |                                                                                                                               ^
checkRd: (-1) SumStat.Rd:108: Lost braces
   108 | ATO{(\code{"overlap"})}, ATM {\code{"matching"}} and ATEN \code{"entropy"}. These weights are members of a larger class of balancing weights defined in Li, Morgan, and Zaslavsky (2018).
       |    ^
checkRd: (-1) SumStat_cl.Rd:72: Lost braces
    72 | Current version of \code{PSweight} allows for five types of propensity score weights used to estimate ATE (\code{"IPW"}), ATT {(\code{"treated"})}, and
       |                                                                                                                               ^
checkRd: (-1) SumStat_cl.Rd:73: Lost braces
    73 | ATO{(\code{"overlap"})}, ATM {\code{"matching"}} and ATEN \code{"entropy"}. These weights are members of a larger class of balancing weights defined in Li, Morgan, and Zaslavsky (2018).
       |    ^
checkRd: (-1) dprime.Rd:37: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dprime.Rd:38: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dprime.Rd:39: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dprime.Rd:40: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dprime.Rd:41: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) PTE_bootstrap_inference.Rd:39-42: Lost braces
    39 |                                                         continuous = function(Xytrain){ #defalt is OLS regression
       |                                                                                       ^
checkRd: (-1) PTE_bootstrap_inference.Rd:43-47: Lost braces
    43 |                                                         incidence = function(Xytrain){ #default is logistic regression
       |                                                                                      ^
checkRd: (-1) PTE_bootstrap_inference.Rd:48-52: Lost braces
    48 |                                                         survival = function(Xytrain){ #default is Weibull regression
       |                                                                                     ^
checkRd: (-1) PTE_bootstrap_inference.Rd:66-68: Lost braces
    66 |                                         function(mod, Xyleftout){
       |                                                                 ^
checkRd: (-1) PTE_bootstrap_inference.Rd:74-77: Lost braces
    74 |                                         function(results, indices_1_1, indices_0_0, indices_0_1, indices_1_0){
       |                                                                                                              ^
checkRd: (-1) pgram.Rd:12: Lost braces; missing escapes or markup?
    12 | \item{fr}{use "default" for usual Fourier frequencies, {1/n, ..., floor(n/2)/n}. 
       |                                                        ^
Documented arguments not in \usage in Rd file 'GetFitHReg.Rd':
  ‘z’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
checkRd: (-1) imutant.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) imutant.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) imutant.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) imutant.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) imutant.Rd:31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) imutant.Rd:32: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) imutant.Rd:33: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ptm.plot.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ptm.plot.Rd:35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ptm.plot.Rd:36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ptm.plot.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ptm.plot.Rd:38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ptm.plot.Rd:39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ptm.plot.Rd:40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ptm.plot.Rd:41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ptm.plot.Rd:42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ptm.plot.Rd:43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ptm.plot.Rd:44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ptm.plot.Rd:45: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ptm.plot.Rd:46: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ptm.plot.Rd:47: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
checkRd: (-1) ptw-package.Rd:20-28: Lost braces
    20 | @Article{Bloemberg2010,
       |         ^
checkRd: (-1) ptw-package.Rd:30-38: Lost braces
    30 | Article{Wehrens2015,
       |        ^
checkRd: (-1) ma.Rd:62: Lost braces
    62 | \item{yi}{Numeric vector of length code{k} with observed effect size
       |                                        ^
checkRd: (-1) ma.Rd:65: Lost braces
    65 | \item{vi}{Numeric vector of length code{k} with sampling variances.}
       |                                        ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) plotWordCloud.Rd:5: Lost braces; missing escapes or markup?
     5 | \title{PubMed wordcloud using function 'wordcloud' of package {wordcloud}}
       |                                                               ^
checkRd: (-1) plotWordCloud.Rd:32: Lost braces; missing escapes or markup?
    32 | This function just call 'wordcloud' from package {wordcloud}. See package {wordcloud} for more details about the parameters.
       |                                                  ^
checkRd: (-1) plotWordCloud.Rd:32: Lost braces; missing escapes or markup?
    32 | This function just call 'wordcloud' from package {wordcloud}. See package {wordcloud} for more details about the parameters.
       |                                                                           ^
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [7s/13s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(PUlasso)
  > 
  > test_check("PUlasso")
  Fitting 0th lambda
  converged at 1th iterations
  Fitting 1th lambda
  converged at 62th iterations
  Fitting 2th lambda
  converged at 117th iterations
  Fitting 3th lambda
  converged at 136th iterations
  Fitting 4th lambda
  converged at 125th iterations
  Fitting 0th lambda
  converged at 1th iterations
  Fitting 1th lambda
  converged at 41th iterations
  Fitting 2th lambda
  converged at 41th iterations
  Fitting 3th lambda
  converged at 37th iterations
  Fitting 4th lambda
  converged at 31th iterations
  Fitting 0th lambda
  converged at 1th iterations
  Fitting 1th lambda
  converged at 41th iterations
  Fitting 2th lambda
  converged at 41th iterations
  Fitting 3th lambda
  converged at 37th iterations
  Fitting 4th lambda
  converged at 31th iterations
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 14 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test.R:47:3'): Input : Dense matrix ───────────────────────────────
  max(abs(gn.svrg$coef - gn$coef)) is not strictly less than 0.001. Difference: 1.18e-05
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 14 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) DataSets.Rd:10: Lost braces; missing escapes or markup?
    10 | \format{the \code{PvarQuantileDF} is a \code{data.frame} with fields \code{prob} an {Qaunt}. 
       |                                                                                     ^
checkRd: (-1) pvlrt.Rd:42: Lost braces; missing escapes or markup?
    42 | \item{no_zi_idx}{List of pairs {(i, j)} where zero inflation is not allowed. To
       |                                ^
checkRd: (-1) r_contin_table_zip.Rd:35: Lost braces; missing escapes or markup?
    35 | \item{no_zi_idx}{List of pairs {(i, j)} where zero inflation is not allowed. To
       |                                ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) Ch05-detail.Rd:23: Escaped LaTeX specials: \#
checkRd: (-1) Ch05-detail.Rd:24: Escaped LaTeX specials: \#
checkRd: (-1) Ch05-detail.Rd:25: Escaped LaTeX specials: \#
checkRd: (-1) Ch05-detail.Rd:31: Escaped LaTeX specials: \#
checkRd: (-1) Ch05-detail.Rd:32: Escaped LaTeX specials: \#
checkRd: (-1) Ch09-CDF-Pval.Rd:72: Lost braces; missing escapes or markup?
    72 |   G(u) = (1-r) u  + r Fc_A(Fc_0^{-1}(u))
       |                                 ^
checkRd: (-1) Ch10-CDF-Pval-HA.Rd:62: Lost braces; missing escapes or markup?
    62 |   G_A(u) = Fc_A(Fc_0^{-1}(u))
       |                      ^
checkRd: (-1) Ch0C-plot.cpd.PwrGSD.Rd:40: Escaped LaTeX specials: \&
checkRd: (-1) Ch17-CRRtoRR.Rd:15: Lost braces; missing escapes or markup?
    15 |     \ldots, [t_m, t_{m+1})$ then \code{DT} will be c($t_2-t_1,t_3 -t_2,
       |                     ^
checkRd: (-1) Ch17-CRRtoRR.Rd:16: Lost braces; missing escapes or markup?
    16 |     \ldots, t_{m+1} - t_m )$
       |               ^
checkRd: (-1) aid_st2.Rd:6: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) crosstab.Rd:45: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) crosstab.Rd:46: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) crosstab.Rd:47: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) crosstab.Rd:48: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) crosstab.Rd:49: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) crosstab.Rd:50: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) crosstab.Rd:51-52: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
checkRd: (-1) srswrRe.Rd:10: Lost braces
    10 |   \item{listRanef}{{\emph{ranef(model)}} object where {\emph{model}} is an { \emph{lmer}} object.}
       |                                                                            ^
Documented arguments not in \usage in Rd file 'lagm.Rd':
  ‘x’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) qgcomp.survcurve.boot.Rd:17-19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) qgcomp.survcurve.boot.Rd:20-21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) qgcomp.survcurve.boot.Rd:22-23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) qgcomp.survcurve.boot.Rd:24-25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) QGlink.funcs.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) QGlink.funcs.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) QGlink.funcs.Rd:31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) QGmvpred.Rd:39: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) QGmvpred.Rd:40: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) QGmvpred.Rd:41: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) QGmvpred.Rd:42: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) QGpred.Rd:36: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) QGpred.Rd:37: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) QGpred.Rd:38: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) QGpred.Rd:39: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gmap.Rd:195: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gmap.Rd:196: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gmap.Rd:197: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gmap.Rd:198: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gmap.Rd:199: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gmap.Rd:200: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gmap.Rd:201: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gmap.Rd:202: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gmap.Rd:203: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gmap.Rd:204: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gmap.Rd:205: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gmap.Rd:206: Lost braces in \itemize; \value handles \item{}{} directly
Package suggested but not available for checking: ‘spDataLarge’
'LazyData' is specified without a 'data' directory
Argument items with no description in Rd file 'ad.simudata.Rd':
  ‘SimuNum’
'LazyData' is specified without a 'data' directory
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
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
checkRd: (-1) qmethod-package.Rd:109: Lost braces
   109 |   \item Van Exel, J., and G. de Graaf, 2005. \emph{Q Methodology: A Sneak Preview}\cr \url{https://qmethodblog.files.wordpress.com/2016/01/qmethodologyasneakpreviewreferenceupdate.pdf}{Available at this link}.
       |                                                                                                                                                                                         ^
checkRd: (-1) qmethod-package.Rd:110: Lost braces
   110 |   \item Brown, S. R., 1980. \emph{Political subjectivity: Applications of Q methodology in political science}, New Haven, CT: Yale University Press.\cr \url{https://qmethodblog.files.wordpress.com/2016/01/brown-1980-politicalsubjectivity.pdf}{Available at this link}.
       |                                                                                                                                                                                                                                                   ^
Specified C++11: please drop specification unless essential
checkRd: (-1) hideLocation.Rd:10: Lost braces; missing escapes or markup?
    10 | \item{trueLoc}{A vector of one or more numbers in the set {1, 2, ..., nSubjects} whose locations are to be hidden.}
       |                                                           ^
checkRd: (-1) hideLocation.Rd:12: Lost braces; missing escapes or markup?
    12 | \item{nSubjects}{An integer larger than 1 used to define the set {1, 2, ..., nSubjects}.}
       |                                                                  ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) setqreportOption.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) setqreportOption.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) setqreportOption.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) setqreportOption.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) setqreportOption.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) setqreportOption.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) setqreportOption.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) setqreportOption.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) setqreportOption.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) setqreportOption.Rd:21: Lost braces in \itemize; meant \describe ?
Specified C++11: please drop specification unless essential
checkRd: (-1) NEWS.Rd:15: Escaped LaTeX specials: \&
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in Rd file 'mmer_adapted.Rd':
  ‘void’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
checkRd: (-1) IPWE_mean_IndCen.Rd:54-57: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) IPWE_mean_IndCen.Rd:58: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) IPWE_mean_IndCen.Rd:59: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) IPWE_mean_IndCen.Rd:60: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) IPWE_mean_IndCen.Rd:61-62: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) IPWE_mean_IndCen.Rd:63: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simJLSDdata.Rd:14: Lost braces; missing escapes or markup?
    14 | \item{case}{string. One of {"a", "b", "c"}, corresponding to three models.}
       |                            ^
checkRd: (-1) simJLSDdata.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simJLSDdata.Rd:31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simJLSDdata.Rd:32-34: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simJLSDdata.Rd:35: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) find_lcp.Rd:60: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) find_lcp.Rd:61: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) find_lcp.Rd:62: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) find_lcp.Rd:63-65: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) find_lcp.Rd:66: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) find_lcp.Rd:67: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) summarize_lcps.Rd:17: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) summarize_lcps.Rd:18-19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) summarize_lcps.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) summarize_lcps.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) summarize_lcps.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) summarize_lcps.Rd:23-25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) als_data.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) als_data.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) als_data.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) als_data.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) als_data.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) als_data.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) als_data.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) als_data.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) als_data.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) als_data.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) als_data.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) als_data.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) als_data.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) als_data.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) als_data.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) als_data.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) als_data.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) als_data.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) als_data_qc_mapping.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) als_data_qc_mapping.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) als_data_qc_mapping.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) qualpal.Rd:22-28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) qualpal.Rd:30-50: Lost braces in \itemize; meant \describe ?
checkRd: (-1) cqs.Rd:30-31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) cqs.Rd:33-35: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) cqs.Rd:37-45: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) llqr.Rd:35-36: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) llqr.Rd:38-41: Lost braces in \itemize; \value handles \item{}{} directly
Documented arguments not in \usage in Rd file 'convert-wrappers.Rd':
  ‘...’

Documented arguments not in \usage in Rd file 'corpus-class.Rd':
  ‘if’

Documented arguments not in \usage in Rd file 'dfm-class.Rd':
  ‘drop_docid’

Documented arguments not in \usage in Rd file 'dictionary-class.Rd':
  ‘object’

Documented arguments not in \usage in Rd file 'matrix2fcm.Rd':
  ‘slots’

Documented arguments not in \usage in Rd file 'meta_system.Rd':
  ‘source’

Documented arguments not in \usage in Rd file 'search_index.Rd':
  ‘regex’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Found the following calls to attach():
File ‘quantmod/R/attachSymbols.R’:
  attach(NULL, pos = pos, name = DB$name)
  attach(NULL, pos = pos, name = DB$name)
See section ‘Good practice’ in ‘?attach’.
'LazyData' is specified without a 'data' directory
checkRd: (-1) ps.Rd:77: Lost braces; missing escapes or markup?
    77 | such as [x, ..., x^{d-1}, Z], where \eqn{Z= B D'(DD')^{-1}}{Z= B D'(DD')^{-1}}, \eqn{d}{d} is the difference order and \eqn{B}{B} is the B-spline basis. Only the coefficients of Z are penalized via an identity matrix. Currently \code{decom=TRUE} does not work with shape (monotonicity and concavity) restrictions and noncrossing constraints.
       |                    ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) boot.rq.pwxy.Rd:52: Lost braces in \enumerate; \value handles \item{}{} directly
checkRd: (-1) boot.rq.pwxy.Rd:53: Lost braces in \enumerate; \value handles \item{}{} directly
checkRd: (-1) boot.rq.pwxy.Rd:54: Lost braces in \enumerate; \value handles \item{}{} directly
checkRd: (-1) plot.rqss.Rd:16: Lost braces; missing escapes or markup?
    16 | to plot {summary.rqss}  objects just generates a warning message.
       |         ^
checkRd: (-1) rq.fit.conquer.Rd:22: Lost braces
    22 |       objective function.  Default is max{((log(n) + p) / n)^0.4, 0.05}. 
       |                                          ^
checkRd: (-1) rq.fit.pfnb.Rd:37-38: Lost braces in \enumerate; \value handles \item{}{} directly
checkRd: (-1) rq.fit.pfnb.Rd:39-43: Lost braces in \enumerate; \value handles \item{}{} directly
checkRd: (-1) rq.fit.pfnb.Rd:44: Lost braces in \enumerate; \value handles \item{}{} directly
checkRd: (-1) rq.fit.qfnb.Rd:31-32: Lost braces in \enumerate; \value handles \item{}{} directly
checkRd: (-1) rq.fit.qfnb.Rd:33: Lost braces in \enumerate; \value handles \item{}{} directly
checkRd: (-1) rq.fit.qfnb.Rd:34: Lost braces in \enumerate; \value handles \item{}{} directly
checkRd: (-1) MovingBlocks-class.Rd:11: Lost braces
    11 | bootstrap described in K{\"u}nsch (1989).
       |                         ^
checkRd: (-1) MovingBlocks-class.Rd:18: Lost braces
    18 | The Moving Blocks Bootstrap method of K{\"u}nsch (1989) resamples blocks
       |                                        ^
checkRd: (-1) MovingBlocks-class.Rd:25: Lost braces
    25 | K{\"u}nsch, H. R. (1989). The jackknife and the bootstrap for general stationary
       |  ^
checkRd: (-1) frequenciesValidator.Rd:16: Lost braces; missing escapes or markup?
    16 | \item{steps}{a vector containing a subset of {1,2,3,4,5,6}, indicating
       |                                              ^
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 ?
Auto-generated content requiring editing in Rd file 'quhomology-package.Rd':
  \details: ‘...o use the package, including the most important functions ~~’
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘fastshp’
checkRd: (-1) display_table.Rd:37: Lost braces; missing escapes or markup?
    37 | \item{normtest}{A character indicating test of normality, the default method is \code{\link{shapiro.test}} when sample size no more than 5000, otherwise \code{\link[nortest]{lillie.test}} {Kolmogorov-Smirnov} is used, see package \strong{nortest} for more methods.Use 'shapiro.test', 'lillie.test', 'ad.test', etc to specify methods.}
       |                                                                                                                                                                                             ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) qut.Rd:25: Lost braces; missing escapes or markup?
    25 |      a user supplied \code{glmnet} or {lars} object.  Typical usage is to leave it empty so that the program computes the regularization path using the algorithm selected in \code{type}. WARNING: use with care, if supplied, object options must match with user supplied options.
       |                                       ^
checkRd: (-1) sigmarcv.Rd:25: Lost braces; missing escapes or markup?
    25 | A user supplied \code{glmnet} or {lars} object.  Typical usage is to leave it empty so that the program computes the regularization path using the algorithm selected in \code{type}. WARNING: use with care, if supplied, object options must match with user supplied options.
       |                                  ^
Invalid package aliases in Rd file 'qut-package.Rd':
  ‘QUT-package’
Specified C++11: please drop specification unless essential
checkRd: (-1) est.R0.ML.Rd:98: Lost braces
    98 | Supplementary Material S1 from \doi{10.1186/1472-6947-12-147}{Obadia et al., 2012}.
       |                                                              ^
checkRd: (-1) plot.R0.R.Rd:20: Lost braces
    20 | Called for side effect. Draws all \eqn{R_{0}} or /eqn{R(t)} values from one estimation method.
       |                                                      ^
checkRd: (-1) plot.R0.sR.Rd:20: Lost braces
    20 | Called for side effect. Draws all \eqn{R_{0}} or /eqn{R(t)} values from an
       |                                                      ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) do_admb.Rd:20: Lost braces in \itemize; meant \describe ?
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
Package suggested but not available for checking: ‘ReGenesees’
checkRd: (-1) conf2d.Rd:64: Lost braces; missing escapes or markup?
    64 |   compute a smooth surface from \code{x} and {y}. If users already have
       |                                              ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) HTML.data.frame.Rd:54: Lost braces; missing escapes or markup?
    54 | 	\code{getOption("R2HTML.format.decimal.mark")} and {options("R2HTML.format.decimal.mark"=",")}
       |                                                            ^
checkRd: (-1) jags.Rd:128: Lost braces in \itemize; meant \describe ?
Package suggested but not available for checking: ‘bootmlm’
Found the following calls to attach():
File ‘R2OpenBUGS/R/attach.all.R’:
  attach(x, name = name)
See section ‘Good practice’ in ‘?attach’.
checkRd: (-1) bugs.Rd:158: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bugs.Rd:163: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bugs.Rd:164: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bugs.Rd:166: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
Found the following calls to attach():
File ‘R2WinBUGS/R/attach.all.R’:
  attach(x, name = name)
See section ‘Good practice’ in ‘?attach’.
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).
       |                                                                                                                                                                                                                                                                                                                                                                                                ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) extract_class.Rd:18: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) extract_class.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) extract_class.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
checkRd: (-1) post_RA_fits.Rd:61: Lost braces; missing escapes or markup?
    61 |     \item{\code{H(po_{bm_{n.bm}}, po_act)}:}{ last benchmark prior bm_{n.bm} inducing the fit \code{fits.bm[[n.bm]]} and actual prior}
       |                                                                       ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
checkRd: (-1) plot-methods.Rd:98: Lost braces
    98 | 			The line width, a emph{positive} number, defaulting to \code{1}. The interpretation is device-specific, and some devices do not implement line widths less than one (see the help on the device for details of the interpretation). Note that this paramater can also represent a list of different line widths, with length of the list corresponding to the number of \code{DVH} or \code{DVH.list} objects (if \code{plot.type="individual"}, number of line widths should correspond to number of individual \code{DVH} objects).
       |                                               ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) DataSet-class.Rd:25: Lost braces; missing escapes or markup?
    25 | Example: {fromField:"val1", toField:"value"}.}
       |          ^
checkRd: (-1) amTimeSeries.Rd:119: Lost braces in \itemize; meant \describe ?
checkRd: (-1) amTimeSeries.Rd:120: Lost braces in \itemize; meant \describe ?
checkRd: (-1) amTimeSeries.Rd:121: Lost braces in \itemize; meant \describe ?
checkRd: (-1) amTimeSeries.Rd:122: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getCurrentStockData.Rd:56: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getCurrentStockData.Rd:57: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getTransformTS.Rd:59: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getTransformTS.Rd:60: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rAmCharts-shinymodules-ts.Rd:114: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rAmCharts-shinymodules-ts.Rd:115: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rAmCharts-shinymodules-ts.Rd:155: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rAmCharts-shinymodules-ts.Rd:156: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rAmCharts-shinymodules-ts.Rd:157: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rAmCharts-shinymodules-ts.Rd:158: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rAmCharts-shinymodules.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rAmCharts-shinymodules.Rd:35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rAmCharts-shinymodules.Rd:36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rAmCharts-shinymodules.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rAmCharts-shinymodules.Rd:38: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) makeDesignMatrix.Rd:16: Lost braces; missing escapes or markup?
    16 | is randomized to a certain treatment {j}, the entry of \code{(i,j)} of the
       |                                      ^
checkRd: (-1) outcomeProbs.Rd:18: Lost braces
    18 |   \item{scale}{either "prob" where probabilities are returned, the default, or "raw" where the probabilities are returned on the logit or probit scale, depending on which scale was selected in the texttt{randomLCA} function}
       |                                                                                                                                                                                                            ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Invalid package aliases in Rd file 'randtests-package.Rd':
  ‘randomtests-package’
checkRd: (-1) auxfun.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) auxfun.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) auxfun.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) auxfun.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) auxfun.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) auxfun.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) auxfun.Rd:35-37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) auxfun.Rd:38-44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) addRasterLegend.Rd:89: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) addRasterLegend.Rd:90: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) addRasterLegend.Rd:91: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) addRasterLegend.Rd:92: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) addRasterLegend.Rd:93: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
checkRd: (-1) grottaBar.Rd:69: Lost braces in \itemize; meant \describe ?
checkRd: (-1) grottaBar.Rd:70: Lost braces in \itemize; meant \describe ?
checkRd: (-1) grottaBar.Rd:71: Lost braces in \itemize; meant \describe ?
checkRd: (-1) grottaBar.Rd:79: Lost braces in \itemize; meant \describe ?
checkRd: (-1) grottaBar.Rd:80: Lost braces in \itemize; meant \describe ?
checkRd: (-1) grottaBar.Rd:81: Lost braces in \itemize; meant \describe ?
checkRd: (-1) grottaBar.Rd:82: Lost braces in \itemize; meant \describe ?
checkRd: (-1) grottaBar.Rd:83: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rankL2R.Rd:18: Lost braces; missing escapes or markup?
    18 | where the vector dimension is 2^{response.number}.}
       |                                 ^
Documented arguments not in \usage in Rd file 'get_parameters.Rd':
  ‘parameters_def’

Documented arguments not in \usage in Rd file 'print.rapi_api.Rd':
  ‘...further’

Documented arguments not in \usage in Rd file 'print.rapi_operation.Rd':
  ‘...further’

Documented arguments not in \usage in Rd file 'print.rapi_schema_function.Rd':
  ‘...further’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) user_log_dir.Rd:48: Lost braces
    48 | \\env{$XDG_CACHE_HOME} if defined
       |      ^
checkRd: (-1) max.Rd:17: Lost braces
    17 | Returns the maximum of all values in a vector by passing \{code{\link{max}} as \code{fn} argument to \code{\link{univar}} function.
       |                                                                ^
checkRd: (-1) min.Rd:17: Lost braces
    17 | Returns the minimum of all values in a vector by passing \{code{\link{min}} as \code{fn} argument to \code{\link{univar}} function.
       |                                                                ^
checkRd: (-1) rapport.inputs.Rd:26: Lost braces
    26 |     \item \emph{dataset inputs}, i.e. the inputs that refer to named element of an |code{R} object provided in \code{data} argument in \code{rapport} call. Currently, \code{rapport} supports only \code{data.frame} objects, but that may change in the (near) future.
       |                                                                                         ^
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘gurobi’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'mpaRaoS.Rd':
  ‘rasterm’

Objects in \usage without \alias in Rd file 'paRaoP.Rd':
  ‘paRaoS’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
checkRd: (-1) RasterList-Package.Rd:20: Lost braces
    20 | {\code{\link{rasterList}}}{: it is the constructor of a  \code{\link{RasterList-class}} object from a generic \code{object}, it also transforms a \code{\link{RasterList-class}} into another one throungh a function argument. }
       |                           ^
checkRd: (-1) RasterList-Package.Rd:22: Lost braces
    22 | {\code{\link{rasterListFun}}}{: it is a function that constructs  a  particular \code{\link{RasterList-class}} object in which the objects are \code{function}-type. }
       |                              ^
checkRd: (-1) RasterList-Package.Rd:24: Lost braces
    24 | {\code{\link{RasterListApply}}}{: it is a function that allows to operate among two or more \code{\link{RasterList-class}} objects defined in the same spatial extent through a generic function \code{fun(x,y,...)} where \code{x} and \code{y} are each cell/element of two \code{\link{RasterList-class}} objects given as arguments \code{x} and \code{y} of \code{\link{RasterListApply}}.}
       |                                ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) as_mcmc.list.Rd:5: Lost braces; missing escapes or markup?
     5 | \title{Convert a rater_fit object to a {coda} \code{mcmc.list} object.}
       |                                        ^
checkRd: (-1) as_mcmc.list.Rd:16: Lost braces; missing escapes or markup?
    16 | Convert a rater_fit object to a {coda} \code{mcmc.list} object.
       |                                 ^
checkRd: (-1) as_mcmc.list.Rd:13: Lost braces; missing escapes or markup?
    13 | A {coda} mcmc.list object.
       |   ^
GNU make is a SystemRequirements.
checkRd: (-1) dbConnect-AthenaDriver-method.Rd:109-111: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dbConnect-AthenaDriver-method.Rd:115-120: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dbConnect-AthenaDriver-method.Rd:121-124: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dbConnect-AthenaDriver-method.Rd:125-127: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dbConnect-AthenaDriver-method.Rd:128-138: Lost braces in \itemize; meant \describe ?
checkRd: (-1) S1.Rd:10: Lost braces; missing escapes or markup?
    10 | \item{m_bar}{the sample vector of moments for a specified vector $(h_{a,r},y)$}
       |                                                                      ^
checkRd: (-1) S1.Rd:16: Lost braces; missing escapes or markup?
    16 | \item{N_k}{index of the $ h_{a,r}$ function considered}
       |                             ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'cairoDevice', 'RGtk2'
checkRd: (-1) acquireAuditData.Rd:24: Escaped LaTeX specials: \_
checkRd: (-1) rattle.Rd:44: Escaped LaTeX specials: \_
checkRd: (-1) rbm.haplos.power.Rd:35: Lost braces; missing escapes or markup?
    35 |   \item{simus.haplos}{ Which method to simulate the data, if \code{simus.haplos="freqs"}, {rbm.haplos.freqs()} is used, otherwise \code{rbm.haplos.thresholds()} is used.}
       |                                                                                           ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) rvn_dist_lonlat.Rd:14: Lost braces; missing escapes or markup?
    14 | \item{method}{calculation method as either \code{haversine} (default) or {vincentysphere}}
       |                                                                          ^
checkRd: (-1) rvn_gen_obsweights.Rd:29: Lost braces
    29 | {wts}{returns numeric vector of weights}
       |      ^
checkRd: (-1) rvn_hyd_dygraph.Rd:27: Lost braces
    27 | {res}{ a list of plot handles to dygraph plots}
       |      ^
checkRd: (-1) rvn_hydrograph_data.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rvn_hydrograph_data.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rvn_hydrograph_data.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rvn_hydrograph_data.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rvn_hydrograph_data.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rvn_rvh_query.Rd:17: Lost braces
    17 | {rvh}{rvh object in same format, but queried to condition and all features (SBtable, HRUtable, SBnetwork) updated.}
       |      ^
checkRd: (-1) rvn_rvh_subbasin_visnetwork_plot.Rd:15: Lost braces
    15 | {p1}{returns visNetwork plot object}
       |     ^
checkRd: (-1) rvn_rvi_process_ggplot.Rd:40: Lost braces
    40 | {p1}{returns ggplot object. Also generates a .pdf file in working directory if pdfplot argument is not NULL.}
       |     ^
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'onb_from_w.Rd':
  ‘v’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Documented arguments not in \usage in Rd file 'gen_fractal_perlin.Rd':
  ‘image’

Documented arguments not in \usage in Rd file 'generate_base_shape.Rd':
  ‘image’

Documented arguments not in \usage in Rd file 'generate_cloud_layer.Rd':
  ‘image’

Documented arguments not in \usage in Rd file 'make_base_triangulated.Rd':
  ‘zscale’

Documented arguments not in \usage in Rd file 'raymarch_cloud_layer.Rd':
  ‘image’

Documented arguments not in \usage in Rd file 'render_snapshot_software.Rd':
  ‘ground_size’

Documented arguments not in \usage in Rd file 'transform_into_heightmap_coords.Rd':
  ‘image’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Documented arguments not in \usage in Rd file 'Min_Max_Inverse_Scale_Vec.Rd':
  ‘mat’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
checkRd: (-1) ecoperators-methods.Rd:50: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ecoperators-methods.Rd:51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ecoperators-methods.Rd:52: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ecoperators-methods.Rd:53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ecoperators-methods.Rd:54: Lost braces in \itemize; meant \describe ?
GNU make is a SystemRequirements.
checkRd: (-1) rbeta.Rd:31-32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rbeta.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rbeta.Rd:35-37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dot-is_equal_rmInf.Rd:5: Lost braces; missing escapes or markup?
     5 | \title{Check if two vectors \code{x} and {y} are equal after remove \code{Inf}}
       |                                          ^
checkRd: (-1) dot-is_equal_rmInf.Rd:18: Lost braces; missing escapes or markup?
    18 | Check if two vectors \code{x} and {y} are equal after remove \code{Inf}
       |                                   ^
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) ecoperators-methods.Rd:50: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ecoperators-methods.Rd:51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ecoperators-methods.Rd:52: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ecoperators-methods.Rd:53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ecoperators-methods.Rd:54: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) R.cache-package.Rd:28-30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) R.cache-package.Rd:31-34: Lost braces in \itemize; meant \describe ?
Package suggested but not available for checking: ‘rrelaxiv’
'LazyData' is specified without a 'data' directory
checkRd: (-1) mig_calculate_rc.Rd:28: Lost braces; missing escapes or markup?
    28 | \item pre-working age: {a1, alpha1}
       |                        ^
checkRd: (-1) mig_calculate_rc.Rd:29: Lost braces; missing escapes or markup?
    29 | \item working age: {a2, alpha2, mu2, lambda2}
       |                    ^
checkRd: (-1) mig_calculate_rc.Rd:30: Lost braces; missing escapes or markup?
    30 | \item retirement: {a3, alpha3, mu3, lambda3}
       |                   ^
checkRd: (-1) mig_calculate_rc.Rd:31: Lost braces; missing escapes or markup?
    31 | \item post retirement: {a4, lambda4}
       |                        ^
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘rrelaxiv’
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘temp.RData’
'LazyData' is specified without a 'data' directory
checkRd: (-1) nc_open_CGLS.Rd:29-32: Lost braces
    29 | if(resolution == "300m"){
       |                         ^
checkRd: (-1) nc_open_CGLS.Rd:33-36: Lost braces
    33 | if(resolution == "1km"){
       |                        ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) Rchoice.Rd:159: Lost braces; missing escapes or markup?
   159 |  \code{ranp}. If the parameters are assumed to be normally distributed \eqn{\beta_i ~ N(\beta, \Sigma)}, then the random parameter are constructed as: \deqn{\beta_{ir}=\beta+L\omega_{ir}} where \eqn{LL'=\Sigma} and \eqn{\omega_{ir}} is the {r}-th draw from standard normal distribution for individual \eqn{i}. 
       |                                                                                                                                                                                                                                                 ^
Found the following files/directories:
  ‘data.csv’
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'makeTitle.Rd':
  ‘string:’ ‘length:’ ‘prefix.length:’ ‘char:’

Documented arguments not in \usage in Rd file 'messageConsole.Rd':
  ‘message:’

Documented arguments not in \usage in Rd file 'tkEmptyLine.Rd':
  ‘tk.object:’ ‘row:’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Found the following files/directories:
  ‘outcmaesdisp.dat’
checkRd: (-1) indexplot.Rd:28: Lost braces
    28 |   \item{legend}{keyword (see \code{link}[grapics]{legend}) giving location of the legend if \code{groups} are specified; 
       |                                                  ^
Depends: includes the non-default packages:
  'biclust', 'fabia', 'iBBiG', 'superbiclust', 'BcDiag', 'BicARE',
  's4vd', 'BiBitR'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Invalid package aliases in Rd file 'RcmdrPlugin.coin-package.Rd':
  ‘RcmdrcoinPlugin-package’
'LazyData' is specified without a 'data' directory
Invalid package aliases in Rd file 'Rcmdr.HH-package.Rd':
  ‘Rcmdr.HH-package’
checkRd: (-1) RcmdrPlugin.MA-package.Rd:21: Escaped LaTeX specials: \&
checkRd: (-1) RcmdrPlugin.MA-package.Rd:23: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Invalid package aliases in Rd file 'RcmdrPlugin.SCDA-package.Rd':
  ‘RcmdrSCDAPlugin-package’
Package suggested but not available for checking: ‘ROpenOffice’
checkRd: (-1) plotCorpusCa.rd:53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotCorpusCa.rd:56: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotCorpusCa.rd:59: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotCorpusCa.rd:62: Lost braces in \itemize; meant \describe ?
checkRd: (-1) recodeTimeVarDlg.Rd:11-13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) recodeTimeVarDlg.Rd:14-16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) recodeTimeVarDlg.Rd:17-18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) vocabularyTable.rd:46-47: Lost braces in \itemize; meant \describe ?
checkRd: (-1) vocabularyTable.rd:48-50: Lost braces in \itemize; meant \describe ?
checkRd: (-1) vocabularyTable.rd:55: Lost braces
    55 | \seealso{\code{\link{vocabularyDlg}}, code{\link{DocumentTermMatrix}}, \code{\link{table}}, }
       |                                           ^
Depends: includes the non-default packages:
  'IQCC', 'qcc', 'qicharts2', 'randtests', 'rmarkdown',
  'TeachingDemos', 'tseries'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
checkRd: (-1) nonlinearAR1.sim.Rd:8: Lost braces; missing escapes or markup?
     8 | of the form z_n = g(z_{n-1}) + epsilon. A normal distribution is assumed for the innovations.
       |                       ^
checkRd: (-1) hetTgen.Rd:16: Lost braces; missing escapes or markup?
    16 | \item{info.type}{character. \code{AD}: allele depth value, {AD-tot}:total
       |                                                            ^
Package suggested but not available for checking: ‘conics’
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
checkRd: (-1) cSMCexamples.Rd:78-80: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) cSMCexamples.Rd:81-83: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) cSMCexamples.Rd:89: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) cSMCexamples.Rd:90: Lost braces in \itemize; \value handles \item{}{} directly
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++14: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Invalid package aliases in Rd file 'Rd2markdown-package.Rd':
  ‘Rd2markdown-package’
'LazyData' is specified without a 'data' directory
checkRd: (-1) plot.rdaccahp.Rd:38: Lost braces; missing escapes or markup?
    38 | {Yao Liu} \email{liuyao@stu.xmu.edu.cn}
       | ^
checkRd: (-1) rdacca.hp.Rd:86: Lost braces; missing escapes or markup?
    86 | {Pedro Peres-Neto} \email{pedro.peres-neto@concordia.ca}
       | ^
checkRd: (-1) rdacca.hp.Rd:88: Lost braces; missing escapes or markup?
    88 | {Kim Nimon} \email{kim.nimon@gmail.com}
       | ^
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) linear_RNDPROJ.Rd:45: Lost braces; missing escapes or markup?
    45 | there is a linear map \eqn{f:R^N} to {R^n} such that
       |                                      ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) halfnorm.like.Rd:105: Lost braces; missing escapes or markup?
   105 |   {f(x|a,b,c_1,c_2,...,c_k) = f(x|a,b)(1 + c(1) h_i1(x) + c(2) h_i2(x) + ... + c(k) h_ik(x)). }
       |   ^
checkRd: (-1) secondDeriv.Rd:15: Lost braces
    15 | This must be a function of the form FUN <- function(x, ...){...}
       |                                                            ^
checkRd: (-1) farthest_point_sampling.Rd:28: Lost braces; missing escapes or markup?
    28 | space P = {p_1, ..., p_k}, such that each p_i is the farthest 
       |           ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) computeCBMeasure.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) computeCBMeasure.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) computeCBMeasure.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) computeCBMeasure.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) computeCBMeasure.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rdm.Rd:52: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rdm.Rd:53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rdm.Rd:54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rdm.Rd:55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rdm.Rd:56: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
Invalid package aliases in Rd file 'rdoc_options.Rd':
  ‘rdoc_options-package’
'LazyData' is specified without a 'data' directory
Auto-generated content requiring editing in Rd file 'RDocumentation-package.Rd':
  \details: ‘...o use the package, including the most important functions ~~’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘dataui’
'LazyData' is specified without a 'data' directory
checkRd: (-1) read_awe.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) read_awe.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) read_awe.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) read_payrolls.Rd:16-17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) read_payrolls.Rd:18-19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) read_payrolls.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) read_payrolls.Rd:21-22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) read_payrolls.Rd:23-24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) read_payrolls.Rd:25-26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) read_payrolls.Rd:27-28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) read_payrolls.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) reader-package.Rd:38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) reader-package.Rd:39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) reader-package.Rd:40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) reader-package.Rd:41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) reader-package.Rd:42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) reader-package.Rd:43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) reader-package.Rd:44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) reader-package.Rd:45: Lost braces in \itemize; meant \describe ?
checkRd: (-1) reader-package.Rd:46: Lost braces in \itemize; meant \describe ?
checkRd: (-1) reader-package.Rd:47: Lost braces in \itemize; meant \describe ?
checkRd: (-1) reader-package.Rd:48: Lost braces in \itemize; meant \describe ?
checkRd: (-1) reader-package.Rd:49: Lost braces in \itemize; meant \describe ?
checkRd: (-1) reader-package.Rd:50: Lost braces in \itemize; meant \describe ?
checkRd: (-1) reader-package.Rd:51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) reader-package.Rd:52: Lost braces in \itemize; meant \describe ?
checkRd: (-1) reader-package.Rd:53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) reader-package.Rd:54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) reader-package.Rd:55: Lost braces in \itemize; meant \describe ?
Found the following files/directories:
  ‘temp.txt’ ‘temp2.csv’ ‘temp3.rda’
'LazyData' is specified without a 'data' directory
checkRd: (-1) Read.mnist.Rd:31: Lost braces
    31 | item{mark}{the remark of the Info}
       |     ^
checkRd: (-1) Read.mnist.Rd:31: Lost braces
    31 | item{mark}{the remark of the Info}
       |           ^
Auto-generated content requiring editing in Rd file 'readmnist-package.Rd':
  \details: ‘...the package, including the most important ~~ ~~ functions ~~’
'LazyData' is specified without a 'data' directory
checkRd: (-1) get.skip.Rd:15: Lost braces
    15 | line in the file to determine the {code{skip}} value.}
       |                                   ^
checkRd: (-1) get.skip.Rd:15: Lost braces
    15 | line in the file to determine the {code{skip}} value.}
       |                                        ^
checkRd: (-1) readMzXmlDir.Rd:39: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) readMzXmlDir.Rd:40: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) readMzXmlDir.Rd:41: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) readMzXmlFile.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) readMzXmlFile.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) readMzXmlFile.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
checkRd: (-1) ReAD.Rd:19: Lost braces; missing escapes or markup?
    19 | \item{pi}{An estimate of the stationary probabilities of four states {(0,0), (0,1), (1,0), (1,1)}.}
       |                                                                      ^
checkRd: (-1) em_hmm.Rd:22: Lost braces; missing escapes or markup?
    22 | \item{pi}{An estimate of the stationary probabilities of four states {(0,0), (0,1), (1,0), (1,1)}.}
       |                                                                      ^
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) get_temp.Rd:18: Lost braces
    18 | \item{seed}{a seed value for \code{digest::digest}. If code{NULL}, a random
       |                                                            ^
Documented arguments not in \usage in Rd file 'add_docid.Rd':
  ‘impute_types’

Documented arguments not in \usage in Rd file 'texts.Rd':
  ‘spacer’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
checkRd: (-1) RealVAMS.Rd:133: Lost braces; missing escapes or markup?
   133 | \code{diag(sqrt.w)\%*\%R\%*\%diag(sqrt.w)}. The matrix R assumes a variance of 1 for all of the binomial responses, while R.full includes the variance from the binomial distribution (in Wolfinger (1993), diag(sqrt.w) is called R_{mu}).}
       |                                                                                                                                                                                                                                      ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) Automotive.Rd:29: Lost braces
    29 | Wikipedia (2018): \dQuote{Automobilindustrie --- Wikipedia{,} Die freie Enzyklopaedie}. \url{https://de.wikipedia.org/wiki/Automobilindustrie} (accessed October 14, 2018). Own postprocessing.
       |                                                           ^
checkRd: (-1) Automotive.Rd:33: Lost braces
    33 | Wikipedia (2018): \dQuote{Automobilindustrie --- Wikipedia{,} Die freie Enzyklopaedie}. \url{https://de.wikipedia.org/wiki/Automobilindustrie} (accessed October 14, 2018). 
       |                                                           ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) recombinator.Rd:32-34: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) recombinator.Rd:35-38: Lost braces in \enumerate; meant \describe ?
'LazyData' is specified without a 'data' directory
Auto-generated content requiring editing in Rd file 'recom-package.Rd':
  \examples: ‘\dontrun{      ## Optional simple examples of the most impor...’
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
checkRd: (-1) pseudo.geefit.Rd:17: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pseudo.geefit.Rd:18: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pseudo.onedim.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pseudo.onedim.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pseudo.onedim.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pseudo.onedim.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pseudo.onedim.Rd:31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pseudo.threedim.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pseudo.threedim.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pseudo.threedim.Rd:31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pseudo.threedim.Rd:32: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pseudo.threedim.Rd:33: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pseudo.twodim.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pseudo.twodim.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pseudo.twodim.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pseudo.twodim.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pseudo.twodim.Rd:31: Lost braces in \itemize; \value handles \item{}{} directly
Specified C++11: please drop specification unless essential
checkRd: (-1) simEvent.Rd:112: Lost braces; missing escapes or markup?
   112 | and another argument named {zCoef} for covariate coefficient vector.
       |                            ^
'LazyData' is specified without a 'data' directory
Invalid package aliases in Rd file 'RED.Rd':
  ‘RED-package’
checkRd: (-1) refdb_import_BOLD.Rd:63: Lost braces
    63 | link[bold]{bold_stats} and \link[bold]{bold_seqspec}
       |           ^
Auto-generated content requiring editing in Rd file 'referenceIntervals-package.Rd':
  \references: ‘~~ Literature or other references for background information ~~’
checkRd: (-1) make_refreshable.Rd:13: Lost braces
    13 | not that quotes need to be escaped (code{\"}).}
       |                                         ^
'LazyData' is specified without a 'data' directory
Found export directive that requires package ‘methods’:
  ‘exportMethods’
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains ‘methods’.
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in Rd file 'Estep.Rd':
  ‘adaptive_quad’

Documented arguments not in \usage in Rd file 'd_bernoulli.Rd':
  ‘pred.data’ ‘num.quad’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Found the following files/directories:
  ‘EnvironmentalA.txt’ ‘EnvironmentalB.txt’ ‘Example.txt’
  ‘Example_Predictions.txt’ ‘Example_RRDist.txt’
  ‘Example_RRDistCol.TIF’ ‘Example_RRDistGrey.TIF’ ‘GeneticA.txt’
  ‘GeneticB.txt’ ‘Inds.txt’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) regCVCF.Rd:52: Lost braces; missing escapes or markup?
    52 | a decision tree with {C4.5} on each one. Using each classifier, a prediction of the whole dataset is obtained.
       |                      ^
checkRd: (-1) summary.rfdata.Rd:17: Lost braces; missing escapes or markup?
    17 | A list including information related to the noise filtering process contained in the object \code{object} of class {rfdata} with the following elements:
       |                                                                                                                    ^
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".}}
       |                                  ^
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) fbase1.binomial.Rd:32: Lost braces; missing escapes or markup?
    32 | In all base log-likelihood functions, we have dropped any additive terms that are independent of the distribution parameter, e.g. constant terms or those terms that are dependent on the response variable only. This is done for computational efficiency. Therefore, these functions cannot be used to obtain the absolute values of log-likelihood functions but only in the context of optimization and/or sampling. Users can write thin wrappers around these functions to add the constant terms to the function value. (Derivatives do not need correction. For binomial family, all factorial terms are ignored since they only depend on \code{n} and {y}.)
       |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  ^
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    10 | \item{input, output, session}{Internal parameters for {shiny}.
       |                                                       ^
checkRd: (-1) plot.ehh.Rd:27: Lost braces
    27 | \item{type}{plot type (see code{\link[graphics]{plot.default}} and \code{\link[graphics]{matplot}}). 
       |                                ^
checkRd: (-1) plot.ehhs.Rd:27: Lost braces
    27 | \item{type}{plot type (see code{\link[graphics]{plot.default}}.
       |                                ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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)}
       | ^
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    37 | The set of divisors is formed by the odd numbers, that is {1,3,..,2n+1}.
       |                                                           ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) rem.dyad.Rd:121: Lost braces; missing escapes or markup?
   121 | \item Single or multiple covariates, time varying: For \code{CovSnd}, \code{CovRec}, or \code{CovInt}, an \code{m} by \code{p} by {n} array whose respective dimensions index time (i.e., event number), covariate, and actor.  For \code{CovEvent}, a \code{m} by \code{p} by \code{n} by \code{n} array, whose dimensions are analogous to the previous case.
       |                                                                                                                                   ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) REndo.Rd:19: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) rentrez.Rd:17-21: Lost braces
    17 | /enumerated{
       |            ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) twosidedPValuestobins.Rd:84: Lost braces; missing escapes or markup?
    84 | A matrix with \code{n.bins + 1} rows and {ncol(zmat)} columns, representing for each study the discretization chosed. Values are the between bin breaks. First and last values are the edges of the outmost bins.
       |                                          ^
checkRd: (-1) ztobins.Rd:90: Lost braces; missing escapes or markup?
    90 | A matrix with \code{n.bins + 1} rows and {ncol(zmat)} columns, representing for each study the discretization chosed. Values are the between bin breaks. First and last values are the edges of the outmost bins.
       |                                          ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) method.A.Rd:200-205: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) method.A.Rd:206-211: Lost braces in \itemize; \value handles \item{}{} directly
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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
Found the following files/directories:
  ‘PackageCites.bib’
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) repo_build.Rd:44-47: Lost braces
    44 | ## chunk "item 1" {
       |                   ^
checkRd: (-1) repo_dependencies.Rd:48: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) repo_dependencies.Rd:51-53: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) NCBirths2004.Rd:16: Lost braces
    16 |     \item{\code{Smoker}}{Mother a smoker? code{No}, \code{Yes}}
       |                                               ^
checkRd: (-1) ExpandProbs.Rd:35: Lost braces; missing escapes or markup?
    35 |      {z_probs2 sqrt((n-1)/n) = t_probs,n-1}
       |      ^
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
checkRd: (-1) cast.Rd:45: Escaped LaTeX specials: \_
checkRd: (-1) cast.Rd:46: Escaped LaTeX specials: \_
checkRd: (-1) as-data-frame-cast-df-v7.rd:3: Escaped LaTeX specials: \_
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checkRd: (-1) as-matrix-cast-df-bu.rd:3: Escaped LaTeX specials: \_
checkRd: (-1) as-matrix-cast-matrix-2y.rd:3: Escaped LaTeX specials: \_
checkRd: (-1) cast-9g.rd:19: Escaped LaTeX specials: \_ \_
checkRd: (-1) cast-9g.rd:41: Escaped LaTeX specials: \_
checkRd: (-1) cast-9g.rd:46: Escaped LaTeX specials: \_ \_
checkRd: (-1) clean-vars-rc.rd:13: Escaped LaTeX specials: \_
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checkRd: (-1) reshape-4u.rd:17: Escaped LaTeX specials: \_ \_
checkRd: (-1) resistance.Rd:52: Lost braces
    52 |     \item B. Bollob\'{a}s, 1998.  \emph{Modern Graph Theory}.  Springer.
       |                      ^
Specified C++11: please drop specification unless essential
checkRd: (-1) harmonize_values.Rd:44: Lost braces; missing escapes or markup?
    44 | \item{perl}{Use perl-like regex? Defaults to {FALSE}.}
       |                                              ^
checkRd: (-1) getPartialGamelog.Rd:27-28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) getPartialGamelog.Rd:29-30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) elink.Rd:70-71: Lost braces in \itemize; meant \describe ?
checkRd: (-1) elink.Rd:72-73: Lost braces in \itemize; meant \describe ?
checkRd: (-1) elink.Rd:74-76: Lost braces in \itemize; meant \describe ?
checkRd: (-1) reutils-package.Rd:114: Lost braces
   114 |      code{reutils.test.remote} to \code{TRUE} to run the full suite of tests.
       |          ^
checkRd: (-1) cpUpper.Rd:39: Lost braces
    39 | \code{"fastfloyd"}{ (default) uses an iterative variant of the Floyd-Warshall algorithm, in which the check of consistency of the current observation with a given cluster is done in a single step of the Floyd-Warshall algorithm. Much faster than \code{"floyd"}.}
       |                   ^
checkRd: (-1) cpUpper.Rd:41: Lost braces
    41 | \code{"floyd"}{ uses the algorithm described in Crawford and Pendakur (2013): at each step the complete Floyd-Warshall algorithm is run to check whether each cluster can accomodate the current observation.}
       |               ^
checkRd: (-1) rec.Rd:23: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) saveRev.Rd:12: Lost braces; missing escapes or markup?
    12 | \item{use_wd}{logical - If TRUE, the history will be prepended by setwd({'users current working directory'}). This function will set the script's working directory to
       |                                                                         ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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    76 | \\code{\link{fs_auth}} \code{\link{fs_browse}}
       |       ^
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) disp.Rd:20: Lost braces; missing escapes or markup?
    20 | sum_{i=1}^n a(R(e_i)) * e_i where 
       |     ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found export directive that requires package ‘methods’:
  ‘exportClasses’
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains ‘methods’.
checkRd: (-1) logLoss.Rd:11: Lost braces; missing escapes or markup?
    11 | \item{y}{vector of observed binomial values {0,1}}
       |                                             ^
checkRd: (-1) logLoss.Rd:13: Lost braces; missing escapes or markup?
    13 | \item{p}{vector of predicted probabilities {0-1}}
       |                                            ^
checkRd: (-1) logLoss.Rd:35: Lost braces; missing escapes or markup?
    35 |       in {0,1} and estimated probability yp that yt = 1, the log loss is derived as: 
       |          ^
checkRd: (-1) rf.modelSel.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rf.modelSel.Rd:31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rf.modelSel.Rd:32: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rf.modelSel.Rd:33: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rf.modelSel.Rd:34: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rf.modelSel.Rd:35: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rf.modelSel.Rd:36: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
checkRd: (-1) tk.browse.Rd:29: Lost braces
    29 |     Single logical value, whether to wait for the interface window to be closed before unfreezing the R console. The \code{FALSE} default let you use R and the interface in parallel (see the 'Typing R commands while browsing' section below), the code{TRUE} value is used essentially in the stand alone version.
       |                                                                                                                                                                                                                                                           ^
checkRd: (-1) tk.convert.Rd:17: Lost braces
    17 |     Single logical value, whether to wait for the interface window to be closed before unfreezing the R console. The \code{FALSE} default let you use R and the interface in parallel, the code{TRUE} is used essentially in the stand alone version.
       |                                                                                                                                                                                                ^
checkRd: (-1) tk.tracks.Rd:8: Lost braces
     8 |   This function allows to load and edit the \code{\linkS4class{drawable.list}} object that is to be passed to \code{\link{tk.browse}} and code{\link{browsePlot}}, using a Tcl-tk interface
       |                                                                                                                                               ^
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) GenDataPopulation.Rd:21: Lost braces
    21 | {data}{Population of data}
       |       ^
checkRd: (-1) GenDataSample.Rd:23: Lost braces
    23 | {data}{Sample of data}
       |       ^
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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")) {
       |                                                   ^
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checkRd: (-1) Ghana_2021_school_attendance_geometry.Rd:75: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
checkRd: (-1) regCVCF.Rd:52: Lost braces; missing escapes or markup?
    52 | a decision tree with {C4.5} on each one. Using each classifier, a prediction of the whole dataset is obtained.
       |                      ^
checkRd: (-1) summary.rfdata.Rd:17: Lost braces; missing escapes or markup?
    17 | A list including information related to the noise filtering process contained in the object \code{object} of class {rfdata} with the following elements:
       |                                                                                                                    ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) code_sawtooth_design.Rd:53: Lost braces
    53 | /url{http://www.sawtoothsoftware.com/help/lighthouse-studio/manual/index.html?hid_web_cbc_exporting.html}
       |     ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) rhandsontable-package.Rd:8: Lost braces
     8 | R interface for creating tables using Handsontable, url{https://handsontable.com/}
       |                                                        ^
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘mydata.rda’ ‘thedata.rda’
checkRd: (-1) GenerateClusterData.Rd:34: Lost braces; missing escapes or markup?
    34 | origin, v_1, -v_1, v_2, -v_2, v_3, -v_3,..., v_{(numberOfClusters-1)/2},
       |                                                ^
checkRd: (-1) GenerateClusterData.Rd:35: Lost braces; missing escapes or markup?
    35 | -v_{(numberOfClusters-1)/2} (if \code{numberOfClusters} is odd)
       |    ^
checkRd: (-1) GenerateClusterData.Rd:36: Lost braces; missing escapes or markup?
    36 | origin, v_1, -v_1, v_2, -v_2, v_3, -v_3,..., v_{(numberOfClusters-1)/2}
       |                                                ^
checkRd: (-1) GetClusteringDefaultMicrobenchmarks.Rd:21-22: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) GetClusteringDefaultMicrobenchmarks.Rd:23-24: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) GetClusteringDefaultMicrobenchmarks.Rd:25-26: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) GetClusteringDefaultMicrobenchmarks.Rd:27-28: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) GetClusteringDefaultMicrobenchmarks.Rd:29-30: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) GetClusteringDefaultMicrobenchmarks.Rd:31-32: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) GetClusteringDefaultMicrobenchmarks.Rd:33-34: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) GetClusteringDefaultMicrobenchmarks.Rd:35-36: Lost braces
    35 |    \item{pam_cluster_64_7_5715},{N=64, seven clusters with 5715 vectors per
       |                                 ^
checkRd: (-1) GetClusteringDefaultMicrobenchmarks.Rd:37-38: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) GetClusteringDefaultMicrobenchmarks.Rd:39-40: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) GetClusteringExampleMicrobenchmarks.Rd:21-22: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) GetClusteringExampleMicrobenchmarks.Rd:23-24: Lost braces in \enumerate; meant \describe ?
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'mimic.demo', 'eicu.demo'
Specified C++11: please drop specification unless essential
checkRd: (-1) acg.Rd:72: Escaped LaTeX specials: \&
checkRd: (-1) gorilla.Rd:41: Escaped LaTeX specials: \&
checkRd: (-1) grassmann.utest.Rd:63: Escaped LaTeX specials: \&
checkRd: (-1) macg.Rd:71: Escaped LaTeX specials: \&
checkRd: (-1) sphere.utest.Rd:47: Escaped LaTeX specials: \&
checkRd: (-1) stiefel.utest.Rd:64: Escaped LaTeX specials: \&
checkRd: (-1) wrap.landmark.Rd:41: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
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"}
       |                                                        ^
checkRd: (-1) descrip.Rd:122: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) descrip.Rd:123: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) descrip.Rd:124-125: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) descrip.Rd:126-128: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) descrip.Rd:129-133: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) descrip.Rd:134-135: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) descrip.Rd:136-138: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) descrip.Rd:139-140: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) descrip.Rd:141-144: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) descrip.Rd:145-146: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) descrip.Rd:147: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) descrip.Rd:148: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) descrip.Rd:149: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) correct_sign.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) correct_sign.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
File ‘RInside/libs/RInside.so’:
  Found ‘srand’, possibly from ‘srand’ (C)
    Object: ‘RInside.o’
File ‘RInside/libs/RInside.so’:
  Found non-API calls to R: ‘R_CStackLimit’, ‘R_CleanTempDir’,
    ‘R_DefParams’, ‘R_ReplDLLinit’, ‘R_RunExitFinalizers’,
    ‘R_SetParams’, ‘R_SignalHandlers’, ‘R_TempDir’, ‘Rf_endEmbeddedR’,
    ‘Rf_initEmbeddedR’, ‘run_Rmainloop’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
checkRd: (-1) ipc_get_analyses.Rd:46: Lost braces; missing escapes or markup?
    46 | available on the \strong{analyses/{id}/{period}} advanced API endpoint,
       |                                   ^
checkRd: (-1) ipc_get_analyses.Rd:46: Lost braces; missing escapes or markup?
    46 | available on the \strong{analyses/{id}/{period}} advanced API endpoint,
       |                                        ^
checkRd: (-1) ipc_get_areas.Rd:50: Lost braces; missing escapes or markup?
    50 | and period, available on the \strong{areas/{id}/{period}} advanced API endpoint,
       |                                            ^
checkRd: (-1) ipc_get_areas.Rd:50: Lost braces; missing escapes or markup?
    50 | and period, available on the \strong{areas/{id}/{period}} advanced API endpoint,
       |                                                 ^
checkRd: (-1) ipc_get_icons.Rd:49: Lost braces; missing escapes or markup?
    49 | and period, available on the \strong{types/{id}/{period}} advanced API endpoint,
       |                                            ^
checkRd: (-1) ipc_get_icons.Rd:49: Lost braces; missing escapes or markup?
    49 | and period, available on the \strong{types/{id}/{period}} advanced API endpoint,
       |                                                 ^
checkRd: (-1) ipc_get_points.Rd:47: Lost braces; missing escapes or markup?
    47 | and period, available on the \strong{types/{id}/{period}} advanced API endpoint,
       |                                            ^
checkRd: (-1) ipc_get_points.Rd:47: Lost braces; missing escapes or markup?
    47 | and period, available on the \strong{types/{id}/{period}} advanced API endpoint,
       |                                                 ^
checkRd: (-1) ipc_get_population.Rd:49: Lost braces; missing escapes or markup?
    49 | analysis, available on the \strong{types/{id}} advanced API endpoint,
       |                                          ^
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) riskParityPortfolio.Rd:163: Lost braces in \itemize; meant \describe ?
checkRd: (-1) riskParityPortfolio.Rd:164: Lost braces in \itemize; meant \describe ?
checkRd: (-1) riskParityPortfolio.Rd:165: Lost braces in \itemize; meant \describe ?
checkRd: (-1) riskParityPortfolio.Rd:166: Lost braces in \itemize; meant \describe ?
checkRd: (-1) riskParityPortfolio.Rd:167: Lost braces in \itemize; meant \describe ?
checkRd: (-1) riskParityPortfolio.Rd:168: Lost braces in \itemize; meant \describe ?
checkRd: (-1) riskParityPortfolio.Rd:169: Lost braces in \itemize; meant \describe ?
checkRd: (-1) riskParityPortfolio.Rd:170: Lost braces in \itemize; meant \describe ?
checkRd: (-1) riskPredict.Rd:38: Lost braces
    38 | {hat{eta}_c^{(1)}} based on the prediction rule.}
       | ^
checkRd: (-1) riskPredict.Rd:38: Lost braces
    38 | {hat{eta}_c^{(1)}} based on the prediction rule.}
       |     ^
checkRd: (-1) riskPredict.Rd:38: Lost braces; missing escapes or markup?
    38 | {hat{eta}_c^{(1)}} based on the prediction rule.}
       |             ^
checkRd: (-1) riskPredictDiff.Rd:34: Lost braces
    34 | {hat{eta}_c^{(1)}-hat{eta}_c^{(2)}} based on the 2 prediction rules.}
       | ^
checkRd: (-1) riskPredictDiff.Rd:34: Lost braces
    34 | {hat{eta}_c^{(1)}-hat{eta}_c^{(2)}} based on the 2 prediction rules.}
       |     ^
checkRd: (-1) riskPredictDiff.Rd:34: Lost braces; missing escapes or markup?
    34 | {hat{eta}_c^{(1)}-hat{eta}_c^{(2)}} based on the 2 prediction rules.}
       |             ^
checkRd: (-1) riskPredictDiff.Rd:34: Lost braces
    34 | {hat{eta}_c^{(1)}-hat{eta}_c^{(2)}} based on the 2 prediction rules.}
       |                      ^
checkRd: (-1) riskPredictDiff.Rd:34: Lost braces; missing escapes or markup?
    34 | {hat{eta}_c^{(1)}-hat{eta}_c^{(2)}} based on the 2 prediction rules.}
       |                              ^
Found the following files/directories:
  ‘B110711CD4.CSV’ ‘inputparam2.txt’ ‘itcout0.pdf’ ‘itcout1.eps’
  ‘origin_data.csv’
checkRd: (-1) CovsAlignedToADesign-class.Rd:22: Lost braces; missing escapes or markup?
    22 | specified stratum weight to the product of h_b (the harmonic mean of n_{tb} and
       |                                                                        ^
checkRd: (-1) CovsAlignedToADesign-class.Rd:23: Lost braces; missing escapes or markup?
    23 | n_{cb}, the counts of treatment and control clusters in stratum b) with bar-w_b,
       |   ^
checkRd: (-1) DesignWeights.Rd:39: Lost braces; missing escapes or markup?
    39 | mean of n_{tb} and n_{cb}, the number of treatment and control
       |           ^
checkRd: (-1) DesignWeights.Rd:39: Lost braces; missing escapes or markup?
    39 | mean of n_{tb} and n_{cb}, the number of treatment and control
       |                      ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) RivivcA.Rd:7: Lost braces
     7 | This is the major function to be called where numerical convolution ad/or deconvolution might be used for a linear in vitro in vivo correlation level A. It performes either numerical convolution via /code{NumConv()} or deconvolution via /code{NumDeconv()} and correlates their results with the known.data object via linear regression \code{lm()}. If you just want raw results of convolution/deconvolution then call explicitely \code{\link{NumConv}} or \code{link{NumDeconv}}
       |                                                                                                                                                                                                             ^
checkRd: (-1) RivivcA.Rd:7: Lost braces
     7 | This is the major function to be called where numerical convolution ad/or deconvolution might be used for a linear in vitro in vivo correlation level A. It performes either numerical convolution via /code{NumConv()} or deconvolution via /code{NumDeconv()} and correlates their results with the known.data object via linear regression \code{lm()}. If you just want raw results of convolution/deconvolution then call explicitely \code{\link{NumConv}} or \code{link{NumDeconv}}
       |                                                                                                                                                                                                                                                   ^
Non-standard file/directory found at top level:
  ‘jri’
Found the following possibly unsafe calls:
File ‘rJava/R/import.R’:
  unlockBinding(IMPORTER, env = env)
  assignInNamespace(IMPORTER, importer, envir = env)
File ‘rJava/R/jinit.R’:
  unlockBinding(x, .env)
  unlockBinding(x, pe)
GNU make is a SystemRequirements.
Found the following Makefile(s) with an include directive with a pathname using R_HOME:
  jri/src/Makefile.win
  jri/src/win32/Makefile
  src/jvm-w32/Makefile
Even though not recommended, variable R_HOME may contain spaces.
Makefile directives use space as a separator and there is no portable
way to quote/escape the space in Make rules and directives.  However,
one can and should quote pathnames when passed from Makefile to the
shell, and this can be done specifically when invoking Make recursively.
It is therefore recommended to use the Make '-f' option to include files
in directories specified using R_HOME.  This option can be specified
multiple times to include multiple Makefiles.  Note that 'Makeconf' is
included automatically into top-level makefile of a package.
More information can be found in 'Writing R Extensions'.
Note: information on .o files is not available
File ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/rJava/libs/rJava.so’:
  Found ‘_exit’, possibly from ‘_exit’ (C)
  Found ‘stderr’, possibly from ‘stderr’ (C)
  Found ‘stdout’, possibly from ‘stdout’ (C)
File ‘rJava/libs/rJava.so’:
  Found non-API calls to R: ‘R_CStackLimit’, ‘R_CStackStart’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Specified C++11: please drop specification unless essential
License stub is invalid DCF.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) Exponential.Rd:52: Escaped LaTeX specials: \&
checkRd: (-1) Gamma.Rd:80: Escaped LaTeX specials: \&
checkRd: (-1) college.Rd:13: Escaped LaTeX specials: \$
checkRd: (-1) college.Rd:15: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) basic_GS.Rd:42: Lost braces; missing escapes or markup?
    42 | \eqn{L} and {U} are strictly lower/upper triangular matrix respectively.
       |             ^
checkRd: (-1) basic_SOR.Rd:45: Lost braces; missing escapes or markup?
    45 | \eqn{L} and {U} are strictly lower/upper triangular matrix respectively.
       |             ^
checkRd: (-1) basic_SSOR.Rd:45: Lost braces; missing escapes or markup?
    45 | \eqn{L} and {U} are strictly lower/upper triangular matrix respectively.
       |             ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) ms_simplify.Rd:36: Lost braces
    36 | \url{https://github.com/mbloch/mapshaper/wiki/Simplification-Tips}{link}
       |                                                                   ^
Specified C++11: please drop specification unless essential
checkRd: (-1) ioslides_presentation.Rd:239: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ioslides_presentation.Rd:240: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ioslides_presentation.Rd:241: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ioslides_presentation.Rd:242: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ioslides_presentation.Rd:243: Lost braces in \itemize; meant \describe ?
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 ?
checkRd: (-1) ComprehensiveTemperatureGenerator.Rd:68: Lost braces; missing escapes or markup?
    68 | \item{exogen_all}{data frame containing exogenous variable formatted like \code{Tx_all} and {Tn_all}. Default is \code{NULL}. 
       |                                                                                             ^
checkRd: (-1) qqplot_RMAWGEN_Tx.Rd:70: Lost braces; missing escapes or markup?
    70 | \code{Tx_gen},{Tn_gen} and \code{main} must have an even number of elements.
       |               ^
GNU make is a SystemRequirements.
checkRd: (-1) RMBC.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) RMBC.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) RMBC.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) RMBC.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) RMBC.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) RMBC.Rd:29-30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) RMBC.Rd:31-34: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) RMBCaux.Rd:50-51: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) RMBCaux.Rd:52-53: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) RMBCaux.Rd:54-55: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) RMBCaux.Rd:56-57: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) RMBCaux.Rd:58-59: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) RMBCaux.Rd:60-61: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) RMBCaux.Rd:62-63: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) robustINIT.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) robustINIT.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) robustINIT.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) robustINIT.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) weightedSestimator.Rd:38: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) weightedSestimator.Rd:39: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) weightedSestimator.Rd:40: Lost braces in \itemize; \value handles \item{}{} directly
Specified C++11: please drop specification unless essential
checkRd: (-1) plot.mcfs.Rd:24: Lost braces; missing escapes or markup?
    24 |     \item\code{ri} {plots top features set with their RIs as well as max RI obtained from permutation experiments. Red color denotes important features.}
       |                    ^
checkRd: (-1) rmdcev.Rd:11: Lost braces
    11 | Lloyd-Smith, P. (2020). Kuhn-Tucker and Multiple Discrete-Continuous Extreme Value (MDCEV) Model Estimation and Simulation in R: The rmdcev Package. R Journal. 12(2): 251-265. \doi{doi.org/10.32614/RJ-2021-015}{(link)}
       |                                                                                                                                                                                                                   ^
checkRd: (-1) rmdcev.Rd:12: Lost braces
    12 | Bhat, CR (2008). The multiple discrete-continuous extreme value (MDCEV) model: Role of utility function parameters, identification considerations, and model extensions. Transportation Research Part B: Methodological, 42(3): 274-303.\doi{10.1016/j.trb.2007.06.002}{(link)}
       |                                                                                                                                                                                                                                                                        ^
checkRd: (-1) rmdcev.Rd:13: Lost braces
    13 | Lloyd-Smith, P (2018). A new approach to calculating welfare measures in Kuhn-Tucker demand models. Journal of Choice Modeling 26:19–27. \doi{10.1016/j.jocm.2017.12.002}{(link)}
       |                                                                                                                                                                          ^
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) cGARCHfilter-class.Rd:57: Escaped LaTeX specials: \&
checkRd: (-1) cGARCHfit-class.Rd:59: Escaped LaTeX specials: \&
checkRd: (-1) cGARCHsim-class.Rd:52: Escaped LaTeX specials: \&
checkRd: (-1) cGARCHspec-class.Rd:36: Escaped LaTeX specials: \&
checkRd: (-1) cgarchsim-methods.Rd:78: Escaped LaTeX specials: \&
checkRd: (-1) goGARCHfft-class.Rd:65: Lost braces
    65 | code{dfft(object, index=0)} on an object created from a forecast with 
       |     ^
checkRd: (-1) goGARCHfilter-class.Rd:155: Escaped LaTeX specials: \&
checkRd: (-1) goGARCHfit-class.Rd:166: Escaped LaTeX specials: \&
checkRd: (-1) rmgarch-package.Rd:73: Escaped LaTeX specials: \&
checkRd: (-1) mgraph.Rd:62: Lost braces
    62 |   \item{TC}{target class (for multi-class classification class) within {1,...,\emph{Nc}}, where \emph{Nc} is the number of classes. If multi-class and TC==-1 then TC is set to 
       |                                                                        ^
checkRd: (-1) mmetric.Rd:112: Lost braces
   112 |   \item{TC}{target class index or vector of indexes (for multi-class classification class) within {1,...,\emph{Nc}}, where \emph{Nc} is the number of classes:<cr>
       |                                                                                                   ^
checkRd: (-1) mparheuristic.Rd:27: Lost braces
    27 | except for SVM several \code{rbfdot} kernel based models (\code{"ksvm"},\code{"rsvm"},\code{"lssvm"}, which can assume \code{2^}{search-range}; please check the result of this function to confirm if the search is linear or \code{2^}{search-range}). 
       |                                                                                                                                 ^
checkRd: (-1) mparheuristic.Rd:27: Lost braces
    27 | except for SVM several \code{rbfdot} kernel based models (\code{"ksvm"},\code{"rsvm"},\code{"lssvm"}, which can assume \code{2^}{search-range}; please check the result of this function to confirm if the search is linear or \code{2^}{search-range}). 
       |                                                                                                                                                                                                                                         ^
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
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)
       |                    ^
Documented arguments not in \usage in Rd file 'bind.Rd':
  ‘.single_on_bind’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
checkRd: (-1) nsgaControl.Rd:20-27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nsgaControl.Rd:28-35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nsgaControl.Rd:36-43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nsgaControl.Rd:45: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot-methods.Rd:53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot-methods.Rd:54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot-methods.Rd:55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot-methods.Rd:56: Lost braces in \itemize; meant \describe ?
Found the following calls to attach():
File ‘Rmosek/R/builder.R’:
  attach(builderenv, pos, name, warn.conflicts)
See section ‘Good practice’ in ‘?attach’.
'LazyData' is specified without a 'data' directory
checkRd: (-1) DO.unit.convert.Rd:24: Lost braces; missing escapes or markup?
    24 |     Units of dissolved oxygen concentration desired, i.e. to be converted to. Must be \code{"mg/L"}, \code{"PP"}, or {"pct"}.
       |                                                                                                                      ^
checkRd: (-1) MR.loops.Rd:80: Lost braces; missing escapes or markup?
    80 | Returns a list of 2. \code{$MR.summary} is of class {data.frame} with 3 columns: \code{$MR} (metabolic rate in user specified units, this is the same as the slope in each linear model), \code{$sd.slope} (standard deviation of slopes calculation), \code{$r.square} (adjusted r square value from each model). This second object is a list of \code{biglm} objects, each one representing a metabolic loop (see McDonnell and Chapman 2016). 
       |                                                     ^
checkRd: (-1) get.pcrit.Rd:27: Lost braces; missing escapes or markup?
    27 | Metabolic rate variable name, formatted as character. Default = \code{NULL}. If this argument takes a value, Pcrit will be calculated by regressing \code{MR.var.name} on \code{DO.var.name}. \code{time.var} and {time.interval} should, in this case, take no value. If \code{MR.var.name} is left as\code{NULL}, then instantaneous metabolic rates (MR) at specified time intervals (see \code{time.interval}) from \code{DO.var.name} and \code{time.var}.
       |                                                                                                                                                                                                                   ^
checkRd: (-1) tot.rss.Rd:35: Lost braces
    35 | code{\link{sumsq}}
       |     ^
checkRd: (-1) tot.rss.Rd:36: Lost braces
    36 | code{\link{get.pcrit}}
       |     ^
Package suggested but not available for checking: ‘cmdstanr’
Package unavailable to check Rd xrefs: ‘cmdstanr’
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
GNU make is a SystemRequirements.
checkRd: (-1) myTarGetClientList.Rd:33: Lost braces
    33 | {MyTarget API Documenation}{https://target.my.com/doc/api/detailed/#resource_agency_clients}
       |                            ^
checkRd: (-1) validateFromString.Rd:6: Lost braces
     6 | e.g. the string "{ mzQC : {}}"}
       |                  ^
checkRd: (-1) GLMnetwork.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) GLMnetwork.Rd:24-25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) imputeHD.Rd:26-27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) imputeHD.Rd:28-29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) imputeHD.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) imputedGLMnetwork.Rd:27-29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) imputedGLMnetwork.Rd:30-32: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) stabilitySelection.Rd:21-22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) stabilitySelection.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) stabilitySelection.Rd:24-25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) stabilitySelection.Rd:26-27: Lost braces in \itemize; \value handles \item{}{} directly
Package suggested but not available for checking: ‘rnaturalearthhires’
Malformed Title field: should not end in a period.
checkRd: (-1) NCEP.track2kml.Rd:36: Lost braces
    36 |   There are several options for specifying \code{col.scheme}.  A single color may be specified for all points (using e.g. \code{'red'}, \code{2}, or \code{"#FF0000"}), specific colors may be given for each point (e.g. \code{c('red','blue','green', etc.)} or code{c('#FF0000','#0000FF','#00FF00', etc.)}), or the function can automatically assign colors, according to the values in \code{clo.variable}, if \code{col.scheme} is any color palette in \code{\link[RColorBrewer]{display.brewer.all}} or one of the recognizezd R color palettes (i.e. \code{'rainbow'}, \code{'heat.colors'}, \code{'terrain.colors'}, \code{'topo.colors'}, \code{'cm.colors'}, or \code{'bpy.colors'}).  An alpha value (0-255) may be supplied to \code{point.alpha} to adjust transparencies.
       |                                                                                                                                                                                                                                                                       ^
checkRd: (-1) rncl.Rd:53-55: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rncl.Rd:57: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rncl.Rd:59-63: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rncl.Rd:65-71: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rncl.Rd:73-78: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rncl.Rd:80-84: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rncl.Rd:86-90: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rncl.Rd:92-93: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rncl.Rd:95-96: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rncl.Rd:98-99: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rncl.Rd:101-102: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rncl.Rd:104-105: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rncl.Rd:107-110: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rncl.Rd:112-115: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rncl.Rd:117-119: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rncl.Rd:121-124: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) NlistServersInCategory.Rd:11: Escaped LaTeX specials: \_
checkRd: (-1) term_day_dist.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) term_day_dist.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) term_day_dist.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) term_day_dist.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) term_day_dist.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) term_day_dist.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) nexml_get.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nexml_get.Rd:31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nexml_get.Rd:32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nexml_get.Rd:33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nexml_get.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nexml_get.Rd:35: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rgdal’
'LazyData' is specified without a 'data' directory
checkRd: (-1) projectRoads.Rd:116-117: Lost braces in \itemize; meant \describe ?
checkRd: (-1) projectRoads.Rd:118-120: Lost braces in \itemize; meant \describe ?
checkRd: (-1) projectRoads.Rd:121-125: Lost braces in \itemize; meant \describe ?
checkRd: (-1) projectRoads.Rd:126-128: Lost braces in \itemize; meant \describe ?
checkRd: (-1) projectRoads.Rd:98: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) projectRoads.Rd:99-100: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) projectRoads.Rd:101: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) projectRoads.Rd:102: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) projectRoads.Rd:103-106: Lost braces in \itemize; \value handles \item{}{} directly
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
checkRd: (-1) cubinf.summaries.Rd:46: Lost braces
    46 | The class "lm" functions \code{effects}, \code{alias}, \code{add1}, \code{drop1}, code{kappa},
       |                                                                                       ^
Specified C++11: please drop specification unless essential
Error(s) in re-building vignettes:
  ...
--- re-building ‘m_tests.Rmd’ using rmarkdown
Could not fetch http://www.zotero.org/styles/elsevier-harvard
HttpExceptionRequest Request {
  host                 = "www.zotero.org"
  port                 = 80
  secure               = False
  requestHeaders       = []
  path                 = "/styles/elsevier-harvard"
  queryString          = ""
  method               = "GET"
  proxy                = Nothing
  rawBody              = False
  redirectCount        = 10
  responseTimeout      = ResponseTimeoutDefault
  requestVersion       = HTTP/1.1
  proxySecureMode      = ProxySecureWithConnect
}
 (InternalException (HandshakeFailed (Error_Protocol "peer does not support Extended Main Secret" HandshakeFailure)))
Error: processing vignette 'm_tests.Rmd' failed with diagnostics:
pandoc document conversion failed with error 61
--- failed re-building ‘m_tests.Rmd’

--- re-building ‘robnptests.Rmd’ using rmarkdown
Could not fetch http://www.zotero.org/styles/elsevier-harvard
HttpExceptionRequest Request {
  host                 = "www.zotero.org"
  port                 = 80
  secure               = False
  requestHeaders       = []
  path                 = "/styles/elsevier-harvard"
  queryString          = ""
  method               = "GET"
  proxy                = Nothing
  rawBody              = False
  redirectCount        = 10
  responseTimeout      = ResponseTimeoutDefault
  requestVersion       = HTTP/1.1
  proxySecureMode      = ProxySecureWithConnect
}
 (InternalException (HandshakeFailed (Error_Protocol "peer does not support Extended Main Secret" HandshakeFailure)))
Error: processing vignette 'robnptests.Rmd' failed with diagnostics:
pandoc document conversion failed with error 61
--- failed re-building ‘robnptests.Rmd’

SUMMARY: processing the following files failed:
  ‘m_tests.Rmd’ ‘robnptests.Rmd’

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
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) rcalibration_MS-class.Rd:21: Lost braces; missing escapes or markup?
    21 |     \item{\code{input}:}{Object of class \code{list}. Each element is a \code{matrix} of the design of experiments in each source with dimension n_i x p_{x,i}, for i=1,...,num_sources.}
       |                                                                                                                                                          ^
checkRd: (-1) separable_kernel.Rd:26: Lost braces
    26 | A vector specifying the type of kernels of each coordinate of the input. \code{matern_3_2} and \code{matern_5_2} are \code{Matern correlation} with roughness parameter 3/2 and 5/2 respectively. \code{pow_exp} is power exponential correlation with roughness parameter alpha. If \code{pow_exp} is to be used, one needs to specify its roughness parameter alpha. The default choice is \code{matern_5_2}. The \code{periodic_gauss} means the Gaussian kernel with periodic folding method with be used. The code{periodic_exp} means the exponential kernel with periodic folding method will be used.
       |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        ^
Specified C++11: please drop specification unless essential
checkRd: (-1) coefPlot.Rd:64: Lost braces
    64 | for the degrees of freedom.  For code{"sparseLTS"} objects, possible values
       |                                      ^
checkRd: (-1) coefPlot.Rd:65: Lost braces
    65 | are code{"lambda"} for the value of the penalty parameter (the default), or
       |         ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) hyper_names.Rd:37-38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) hyper_names.Rd:39-41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) hyper_names.Rd:42-44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) hyper_names.Rd:45-47: Lost braces in \itemize; meant \describe ?
Problems with news in ‘NEWS.md’:
No news entries found.
Objects in \usage without \alias in Rd file 'gettptnfpfn-defunct.Rd':
  ‘gettptnfpfn’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
checkRd: (-1) descriptiveTable.Rd:18: Lost braces
    18 | other object type that does not fail in code{model.frame(object)}.}
       |                                             ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) performance.Rd:35: Escaped LaTeX specials: \#
checkRd: (-1) performance.Rd:36: Escaped LaTeX specials: \# \# \#
checkRd: (-1) performance.Rd:37: Escaped LaTeX specials: \# \#
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) ROI_plugin_build_equality_constraints.Rd:27: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) ROI_plugin_build_equality_constraints.Rd:28: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) ROI_plugin_build_inequality_constraints.Rd:27: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) ROI_plugin_build_inequality_constraints.Rd:28: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) ROI_plugin_build_inequality_constraints.Rd:29: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) ROI_solve.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ROI_solve.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ROI_solve.Rd:28-30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ROI_solve.Rd:31: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) update_tidy_omic.Rd:16-17: Lost braces
    16 | in \code{updated_tidy_data} (names) and the table {features, samples,
       |                                                   ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) read_ascii.Rd:33: Lost braces
    33 | \item{respondent_pattern}{For use when the file does not contain a line for every card for every respondent (or contains extra lines that correspond to no respondent), a regular expression that matches the file's respondent identifier; e.g., if the respondent number is stored in the first four digits of each line, preceded by a space, "(?<=^\\s)\\d{4}".}
       |                                                                                                                                                                                                                                                                                                                                                               ^
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) osm_url_spec.Rd:23: Lost braces; missing escapes or markup?
    23 | \item{server_url}{A url using `{x}`, `{y}`, and `{z}` for the x, y, and
       |                                ^
checkRd: (-1) osm_url_spec.Rd:23: Lost braces; missing escapes or markup?
    23 | \item{server_url}{A url using `{x}`, `{y}`, and `{z}` for the x, y, and
       |                                       ^
checkRd: (-1) osm_url_spec.Rd:23: Lost braces; missing escapes or markup?
    23 | \item{server_url}{A url using `{x}`, `{y}`, and `{z}` for the x, y, and
       |                                                  ^
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘RandomFields’
checkRd: (-1) Clyde.Rd:8: Lost braces
     8 | These data record the water quality, in terms of dissolved oxygen (\code{DO}) on a percentage scale, at a number of sampling stations (\code{Station}) on the River Clyde.  The date (\code{Day}, \\code{Month}, \code{Year}) is also available, along with the day of the year (\code{Doy} between 1 and 365) and an identified (\code{id}) of the survey on which each measurement was made.
       |                                                                                                                                                                                                         ^
checkRd: (-1) rp.pos.Rd:22-24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rp.pos.Rd:25-27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rp.pos.Rd:28-30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rp.pos.Rd:31-49: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rp.pos.Rd:35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rp.pos.Rd:36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rp.pos.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rp.pos.Rd:38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rp.pos.Rd:39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rp.pos.Rd:40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rp.pos.Rd:41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rp.pos.Rd:42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rp.pos.Rd:43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) prp.Rd:565: Lost braces
   565 |      The border is by default invisible, see code{split.border.col}.
       |                                                  ^
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
checkRd: (-1) rpivotTable.Rd:60: Lost braces; missing escapes or markup?
    60 | An example is: onRefresh=htmlwidgets::JS("function(config) { Shiny.onInputChange('myPivotData', config); }")
       |                                                            ^
checkRd: (-1) plotImage.blcTree.Rd:17: Lost braces
    17 |   \item{method}{Method to determine width of columns that represent classes: \dQuote{weight} (subject weight in class) or dQuote{binary} (depth in tree).}
       |                                                                                                                                 ^
checkRd: (-1) plotImage.glcTree.Rd:16: Lost braces
    16 |   \item{method}{Method to determine width of columns that represent classes: \dQuote{weight} (subject weight in class) or dQuote{binary} (depth in tree).}
       |                                                                                                                                 ^
checkRd: (-1) fauxmatching.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fauxmatching.Rd:17-18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fauxmatching.Rd:48-49: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fauxmatching.Rd:50-51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fauxmatching.Rd:52: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rpm.Rd:112-113: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rpm.Rd:114-115: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rpm.Rd:116: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rpm_MLPLE.Rd:110-111: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rpm_MLPLE.Rd:112-113: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rpm_MLPLE.Rd:114: Lost braces in \itemize; meant \describe ?
checkRd: (-1) summary_rpm.Rd:95-96: Lost braces in \itemize; meant \describe ?
checkRd: (-1) summary_rpm.Rd:97-98: Lost braces in \itemize; meant \describe ?
checkRd: (-1) summary_rpm.Rd:99: Lost braces in \itemize; meant \describe ?
checkRd: (-1) get.poetry.Rd:17: Lost braces; missing escapes or markup?
    17 | \item{output}{Can be any or a combination of the input terms {'author', 'title', 'lines', 'linecount'}. If NULL, all
       |                                                              ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) rpql.Rd:64: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rpql.Rd:66: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rpql.Rd:68: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rpql.Rd:70: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rpql.Rd:72: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rpql.Rd:74: Lost braces in \itemize; meant \describe ?
checkRd: (-1) as.tg.Rd:18: Lost braces; missing escapes or markup?
    18 | Renames the \code{class(tg)["name"]} attribute and sets {class(tg)["type"] <- "TextGrid"} (if it is not already set)
       |                                                         ^
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) psel.Rd:83: Lost braces; missing escapes or markup?
    83 | For example, a \code{top=1} preference selection on the tuples {(a=1, b=1), (a=1, b=2)}
       |                                                                ^
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) check_node.Rd:11: Lost braces
    11 | \item{x}{\\code{list}, the node to check}
       |                ^
checkRd: (-1) rptBinary.Rd:89: Lost braces
    89 |      Note that the distribution might not be symmetrical, in which case the emph{se} is less informative.}
       |                                                                                 ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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()}
       |                                                                                                            ^
Found the following files/directories:
  ‘HL_H0.pdf’ ‘pi0infer.pdf’ ‘rate.txt’ ‘summary.txt’
checkRd: (-1) Boost.Rd:40: Lost braces; missing escapes or markup?
    40 | \item{niter}{number of boosting iterations (for RRBoost: T_{1,max} + T_{2,max}) (numeric)}
       |                                                            ^
checkRd: (-1) Boost.Rd:40: Lost braces; missing escapes or markup?
    40 | \item{niter}{number of boosting iterations (for RRBoost: T_{1,max} + T_{2,max}) (numeric)}
       |                                                                        ^
checkRd: (-1) Boost.Rd:54: Lost braces; missing escapes or markup?
    54 | \item{niter}{number of iterations for the boosting algorithm (for RRBoost T_{1,max} + T_{2,max}) (numeric)}
       |                                                                             ^
checkRd: (-1) Boost.Rd:54: Lost braces; missing escapes or markup?
    54 | \item{niter}{number of iterations for the boosting algorithm (for RRBoost T_{1,max} + T_{2,max}) (numeric)}
       |                                                                                         ^
checkRd: (-1) Boost.control.Rd:25: Lost braces; missing escapes or markup?
    25 | \item{n_init}{number of iterations for the SBoost step of RRBoost ($T_{1,max}$) (int)}
       |                                                                       ^
checkRd: (-1) Boost.validation.Rd:41: Lost braces; missing escapes or markup?
    41 | \item{niter}{number of iterations (for RRBoost T_{1,max} + T_{2,max}) (numeric)}
       |                                                  ^
checkRd: (-1) Boost.validation.Rd:41: Lost braces; missing escapes or markup?
    41 | \item{niter}{number of iterations (for RRBoost T_{1,max} + T_{2,max}) (numeric)}
       |                                                              ^
checkRd: (-1) rrecsys.Rd:72: Lost braces; missing escapes or markup?
    72 |  The average deviation rating $dev_{ij}$ between co-rated items is defined by:
       |                                    ^
checkRd: (-1) rrecsys.Rd:76: Lost braces; missing escapes or markup?
    76 |  Where $c_{ij}$ is the number of co-ratings between items $i$ and $j$ and $r_{ui}$ is an existing rating for user $u$ on item $i$. The Weighted Slope One takes into account both, information from users who rated the same item and the number of observed ratings.
       |           ^
checkRd: (-1) rrecsys.Rd:76: Lost braces; missing escapes or markup?
    76 |  Where $c_{ij}$ is the number of co-ratings between items $i$ and $j$ and $r_{ui}$ is an existing rating for user $u$ on item $i$. The Weighted Slope One takes into account both, information from users who rated the same item and the number of observed ratings.
       |                                                                              ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) lateformeeting.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) lateformeeting.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) lateformeeting.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) lateformeeting.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) lfm_clean.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) lfm_clean.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) lfm_clean.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) lfm_clean.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) regrad.Rd:46: Lost braces; missing escapes or markup?
    46 |  \item \code{x-axis} {1st column: The names of the different institutions}
       |                      ^
checkRd: (-1) regrad.Rd:47: Lost braces; missing escapes or markup?
    47 |  \item \code{y-axis} {2nd column: The value to show completeness}
       |                      ^
checkRd: (-1) rrinf_clust.Rd:24: Lost braces; missing escapes or markup?
    24 | \item{clustering}{A \code{List} that specifies a clustering of datapoint indexes {1, ..., n}. See \link{example_clustering} for details.}
       |                                                                                  ^
checkRd: (-1) rrtest_clust.Rd:21: Lost braces; missing escapes or markup?
    21 | \item{clustering}{A \code{List} that specifies a clustering of datapoint indexes {1, ..., n}.
       |                                                                                  ^
'LazyData' is specified without a 'data' directory
Argument items with no description in Rd file 'RNAPlot.Rd':
  ‘seqTF’
Argument items with no description in Rd file 'aptPlotCT.Rd':
  ‘seqTF’
Found the following files/directories:
  ‘test.bpl’ ‘test.cr’ ‘test.ct’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) mrrr.Rd:67: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mrrr.Rd:68: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mrrr.Rd:69-70: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mrrr.Rd:71-72: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mrrr.Rd:73: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mrrr.Rd:74: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
checkRd: (-1) landslides.Rd:11-21: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) landslides.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) landslides.Rd:17-18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) landslides.Rd:22-26: Lost braces
    22 | \item \code{dem} {Digital elevation model given as a .Rd grid, i.e. a list
       |                  ^
checkRd: (-1) landslides.Rd:27-28: Lost braces
    27 | \item \code{study_area} {An \code{sf}-object representing the outlines of
       |                         ^
checkRd: (-1) rsaga.get.modules.Rd:68: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rsaga.get.modules.Rd:69: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rsaga.get.modules.Rd:70: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
Running examples in ‘rsbp-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: getPart
> ### Title: Retrieve information for a part from the Registry of Standard
> ###   Biological Parts
> ### Aliases: getPart
> 
> ### ** Examples
> 
> getPart("BBa_R0040")
Warning in open.connection(x, "rb") :
  URL 'http://parts.igem.org/cgi/xml/part.cgi?part=BBa_R0040': status was 'Couldn't connect to server'
Error in open.connection(x, "rb") : 
  cannot open the connection to 'http://parts.igem.org/cgi/xml/part.cgi?part=BBa_R0040'
Calls: getPart ... read_xml.character -> read_xml.connection -> open -> open.connection
Execution halted
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.
       |                                                                                                                                                          ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) remoteDriver-class.Rd:39-40: Lost braces
    39 | browser being used; should be one of {chrome|firefox|htmlunit|
       |                                      ^
checkRd: (-1) remoteDriver-class.Rd:50: Lost braces; missing escapes or markup?
    50 | of {WINDOWS|XP|VISTA|MAC|LINUX|UNIX}. When requesting a new session,
       |    ^
checkRd: (-1) remoteDriver-class.Rd:194-196: Lost braces
   194 |   element, available schemes: {"class name", "css selector",
       |                               ^
checkRd: (-1) webElement-class.Rd:50-52: Lost braces
    50 |     element, available schemes: {"class name", "css selector",
       |                                 ^
checkRd: (-1) webElement-class.Rd:67-69: Lost braces
    67 |     element, available schemes: {"class name", "css selector",
       |                                 ^
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Note: information on .o files is not available
File ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rserve/libs/Rserve.so’:
  Found ‘exit’, possibly from ‘exit’ (C)
  Found ‘rand’, possibly from ‘rand’ (C)
  Found ‘random’, possibly from ‘random’ (C)
  Found ‘srandom’, possibly from ‘srandom’ (C)
  Found ‘stderr’, possibly from ‘stderr’ (C)
File ‘Rserve/libs/Rserve.so’:
  Found non-API calls to R: ‘R_Consolefile’, ‘R_InputHandlers’,
    ‘R_Outputfile’, ‘R_TempDir’, ‘R_Visible’, ‘addInputHandler’,
    ‘ptr_R_Busy’, ‘ptr_R_ClearerrConsole’, ‘ptr_R_FlushConsole’,
    ‘ptr_R_ReadConsole’, ‘ptr_R_ResetConsole’, ‘ptr_R_ShowMessage’,
    ‘ptr_R_WriteConsole’, ‘ptr_R_WriteConsoleEx’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘gurobi’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) simpopmlx.Rd:24: Lost braces; missing escapes or markup?
    24 | \item{fim}{the (\emph{string}) Fisher Information Matrix estimated by Monolix. fim={"sa", "lin"} (default="sa")}
       |                                                                                    ^
checkRd: (-1) writeData.Rd:18: Lost braces; missing escapes or markup?
    18 | It must be one of {"\\t", " ", ";", ","}}
       |                   ^
checkRd: (-1) writeData.Rd:21: Lost braces; missing escapes or markup?
    21 | It must be one of {"csv", "txt"}
       |                   ^
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
checkRd: (-1) box_m.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) box_m.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) box_m.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) box_m.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) wilcox_test.Rd:91: Lost braces; missing escapes or markup?
    91 |  distribution of \code{(u+v)/2}, where \code{u} and {v} are independent, each
       |                                                     ^
checkRd: (-1) ChangeSpout.Rd:22: Lost braces
    22 | 	a new spout. E.g., a new code{data.frame}.
       |                                      ^
checkRd: (-1) Topology.Rd:11: Lost braces
    11 | By passing a spout (dataframe) to this function and storing its return object you can start building a topology for a RStorm stream. See code{\link{RStorm}} for more detailed examples of the use of Topology. The Topology is the most important concept when defining a RStorm stream.
       |                                                                                                                                              ^
Argument items with no description in Rd file 'SetHash.Rd':
  ‘\dots’
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
checkRd: (-1) RTDE.Rd:78: Lost braces in \itemize; meant \describe ?
checkRd: (-1) RTDE.Rd:79: Lost braces in \itemize; meant \describe ?
checkRd: (-1) LBA-race.Rd:157: Lost braces
   157 |   corresponding (and not first) accumulator winning see /code{/link{LBA}}.
       |                                                              ^
checkRd: (-1) LBA-race.Rd:157: Lost braces
   157 |   corresponding (and not first) accumulator winning see /code{/link{LBA}}.
       |                                                                    ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘test_addPageBreak.doc’ ‘test_addPlot.doc’ ‘test_addSessionInfo.doc’
  ‘test_addTable.doc’
GNU make is a SystemRequirements.
checkRd: (-1) tw_options.Rd:22: Lost braces in \itemize; meant \describe ?
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) grapes-.-times-grapes.Rd:6-9: Lost braces
     6 | "round.torch.Tensor" <- function(input) {
       |                                         ^
'LazyData' is specified without a 'data' directory
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) read_vcv.Rd:10: Lost braces
    10 | \item{file}{\\code{[character]} filename}
       |                   ^
Documented arguments not in \usage in Rd file 'summary.trimbatch.Rd':
  ‘x’

Documented arguments not in \usage in Rd file 'trim_workhorse.Rd':
  ‘max_beta’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘cmdstanr’
GNU make is a SystemRequirements.
checkRd: (-1) rts.Rd:32: Lost braces
    32 | If a name of a raster time series file is provided for the \code{x} argument, it acts the same as code{\link[rts]{read.rts}}.
       |                                                                                                       ^
Problems with news in ‘NEWS.md’:
No news entries found.
Found the following files/directories:
  ‘Tsttwalk.dat’
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
checkRd: (-1) starspace.Rd:108: Lost braces; missing escapes or markup?
   108 | \item loss:            loss function {hinge, softmax} [hinge]
       |                                      ^
checkRd: (-1) starspace_dictionary.Rd:15: Lost braces in \enumerate; \value handles \item{}{} directly
checkRd: (-1) starspace_dictionary.Rd:16: Lost braces in \enumerate; \value handles \item{}{} directly
checkRd: (-1) starspace_dictionary.Rd:17: Lost braces in \enumerate; \value handles \item{}{} directly
checkRd: (-1) starspace_dictionary.Rd:18: Lost braces in \enumerate; \value handles \item{}{} directly
checkRd: (-1) starspace_dictionary.Rd:19: Lost braces in \enumerate; \value handles \item{}{} directly
checkRd: (-1) starspace_dictionary.Rd:20-21: Lost braces in \enumerate; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
checkRd: (-1) rules.Rd:24: Lost braces; missing escapes or markup?
    24 | \item Absent names are replaced with the 'rule__\\{ind\\}' where \\{ind\\} is the
       |                                                   ^
checkRd: (-1) rules.Rd:24: Lost braces; missing escapes or markup?
    24 | \item Absent names are replaced with the 'rule__\\{ind\\}' where \\{ind\\} is the
       |                                                                    ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) tracker.Rd:70: Escaped LaTeX specials: \&
checkRd: (-1) tracker.Rd:73: Escaped LaTeX specials: \&
S3 methods shown with full name in Rd file 'printHTML.trackinfo.Rd':
  ‘printHTML.trackInfo’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Found the following files/directories:
  ‘results’
checkRd: (-1) max_run.Rd:57: Lost braces; missing escapes or markup?
    57 | max {numeric} vector of length equals length of \code{x}.
       |     ^
checkRd: (-1) mean_run.Rd:48: Lost braces; missing escapes or markup?
    48 | mean {numeric} vector of length equals length of \code{x}.
       |      ^
checkRd: (-1) min_run.Rd:57: Lost braces; missing escapes or markup?
    57 | min {numeric} vector of length equals length of \code{x}.
       |     ^
checkRd: (-1) runner.Rd:160-165: Lost braces in \itemize; meant \describe ?
checkRd: (-1) runner.Rd:166-172: Lost braces in \itemize; meant \describe ?
checkRd: (-1) runner.Rd:173-182: Lost braces in \itemize; meant \describe ?
checkRd: (-1) runner.Rd:183-194: Lost braces in \itemize; meant \describe ?
Documented arguments not in \usage in Rd file 'dot-is_datetime_valid.Rd':
  ‘(`character`)’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) RUVIII.Rd:51: Lost braces
    51 | If code{return.info} is \code{TRUE}, a list is returned that contains:
       |        ^
Package which this enhances but not available for checking: ‘glmmADMB’
checkRd: (-1) Valpha.Rd:15: Lost braces; missing escapes or markup?
    15 |   \item{V}{a numeric vector with (i,j) entry: V[i,j] = P(theta_{i} >= theta[alpha_{j}]|data) }
       |                                                                ^
checkRd: (-1) Valpha.Rd:15: Lost braces; missing escapes or markup?
    15 |   \item{V}{a numeric vector with (i,j) entry: V[i,j] = P(theta_{i} >= theta[alpha_{j}]|data) }
       |                                                                                   ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘gpuR’
Problems with news in ‘NEWS.md’:
No news entries found.
Documented arguments not in \usage in Rd file 'summary.rv.Rd':
  ‘all.levels’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
S3 methods shown with full name in Rd file 'matmult.Rd':
  ‘%*%.rv’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
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}).
       |                               ^
checkRd: (-1) dGenWish.Rd:48: Lost braces
    48 |   -df/2*log|L(2*Sigma)L'| -1/2*tr{ (L(2*Sigma)L')^-1 L(-D)L' }
       |                                  ^
checkRd: (-1) get.Q.Rd:9: Lost braces
     9 |   equal to exp{b1*x_1ij + ... + bp*x_pij}, where beta=(b1,b2,...,bp) is
       |               ^
checkRd: (-1) get.Q.Rd:10: Lost braces; missing escapes or markup?
    10 |   a vector of log-conductance values of the covariates {x_kij}.  Each
       |                                                        ^
checkRd: (-1) mcmc.wish.icar.Rd:73: Lost braces; missing escapes or markup?
    73 |   a vector of log-conductance values of the covariates {x_kij}.  Each
       |                                                        ^
Package suggested but not available for checking: ‘rWCVPdata’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'wind.fit_int.Rd':
  ‘X’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Malformed Title field: should not end in a period.
checkRd: (-1) s_crandb_tvdb.Rd:63: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) s_crandb_tvdb.Rd:64: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) s_crandb_tvdb.Rd:65: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) s_crandb_tvdb.Rd:66: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) s_crandb_tvdb.Rd:67: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) s_crandb_tvdb.Rd:68: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) s_crandb_tvdb.Rd:69: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) wtss_to_ts.Rd:31: Lost braces; missing escapes or markup?
    31 | This period can be either {"month", "week", "day"}, 
       |                           ^
checkRd: (-1) wtss_to_ts.Rd:32: Lost braces; missing escapes or markup?
    32 | {"months", "weeks", "days"} or
       | ^
checkRd: (-1) wtss_to_ts.Rd:33: Lost braces; missing escapes or markup?
    33 | {12, 52, 365}. This function creates a new time series with the required 
       | ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) plot.eff.ridge.Rd:6: Lost braces
     6 |  emph{Single Interior Knot} at the MSE Optimal m-Extent of Shrinkage. The
       |      ^
Specified C++11: please drop specification unless essential
Specified C++14: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) ZigZagLogistic.Rd:11: Lost braces; missing escapes or markup?
    11 | \item{dataX}{Design matrix containing observations of the independent variables x. The i-th row represents the i-th observation with components x_{i,1}, ..., x_{i,d}.}
       |                                                                                                                                                   ^
checkRd: (-1) ZigZagLogistic.Rd:11: Lost braces; missing escapes or markup?
    11 | \item{dataX}{Design matrix containing observations of the independent variables x. The i-th row represents the i-th observation with components x_{i,1}, ..., x_{i,d}.}
       |                                                                                                                                                                 ^
checkRd: (-1) ZigZagLogistic.Rd:13: Lost braces; missing escapes or markup?
    13 | \item{dataY}{Vector of length n containing {0, 1}-valued observations of the dependent variable y.}
       |                                            ^
checkRd: (-1) ciReg.Rd:10: Lost braces
    10 | \item{fit}{an object of class{lm}, i.e. the output from \code{\link{lm}}.}
       |                              ^
Documented arguments not in \usage in Rd file 'LoadDataFile.Rd':
  ‘remapcells’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
checkRd: (-1) s2Data.Rd:33: Lost braces
    33 | \code{TRUE}{ (default) The data is converted to a matrix. Factor variables are automatically coded using \code{\link{model.matrix}}. The data is scaled, and constant columns are removed.}
       |            ^
checkRd: (-1) s2Data.Rd:35: Lost braces
    35 | \code{FALSE}{ Do nothing. Keep in mind that the theoretical framework assumes that \code{xL} is centered. Unless you are absolutely sure, avoid this.}
       |             ^
Argument items with no description in Rd file 'predict.s2netR.Rd':
  ‘...’
Argument items with no description in Rd file 'print_misc.Rd':
  ‘\dots’
Specified C++11: please drop specification unless essential
checkRd: (-1) BootsChapt.Rd:38: Escaped LaTeX specials: \&
checkRd: (-1) SemiparChangePoint.Rd:30: Escaped LaTeX specials: \&
checkRd: (-1) schapt.Rd:44: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
checkRd: (-1) default.saemix.plots.Rd:21-25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) default.saemix.plots.Rd:26-28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) default.saemix.plots.Rd:29-30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) default.saemix.plots.Rd:31-32: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) default.saemix.plots.Rd:33-34: Lost braces in \itemize; \value handles \item{}{} directly
Specified C++11: please drop specification unless essential
checkRd: (-1) sim_setup_preconfigured.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sim_setup_preconfigured.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sim_setup_preconfigured.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sim_setup_preconfigured.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sim_setup_preconfigured.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sim_setup_preconfigured.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sim_setup_preconfigured.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sim_setup_preconfigured.Rd:31: Lost braces in \itemize; meant \describe ?
Documented arguments not in \usage in Rd file 'file_status.Rd':
  ‘A’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) sf_get_all_jobs_bulk.Rd:42-43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sf_get_all_jobs_bulk.Rd:44-46: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sf_get_all_query_jobs_bulk.Rd:43-44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sf_get_all_query_jobs_bulk.Rd:45-47: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sf_get_all_query_jobs_bulk.Rd:48-50: Lost braces in \itemize; meant \describe ?
checkRd: (-1) valid_metadata_list.Rd:10: Lost braces
    10 | code{list}; contains name and valid inputs for data types
       |     ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Auto-generated content requiring editing in Rd file 'SAMM-package.Rd':
  \seealso: ‘~~ Optional links to other man pages, e.g. ~~’
checkRd: (-1) binaryChoice.Rd:105: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) binaryChoice.Rd:106: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) binaryChoice.Rd:111: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) binaryChoice.Rd:112: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) binaryChoice.Rd:113: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) binaryChoice.Rd:114: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) SAM.Rd:67: Escaped LaTeX specials: \$
checkRd: (-1) samr.Rd:59: Escaped LaTeX specials: \$
checkRd: (-1) samr.Rd:84: Escaped LaTeX specials: \# \$
checkRd: (-1) samr.Rd:88: Escaped LaTeX specials: \$
checkRd: (-1) samr.Rd:92: Escaped LaTeX specials: \$
checkRd: (-1) samr.Rd:97: Escaped LaTeX specials: \#
checkRd: (-1) samr.assess.samplesize.plot.Rd:12: Escaped LaTeX specials: \#
Specified C++11: please drop specification unless essential
checkRd: (-1) ModelHMMR-class.Rd:37: Lost braces; missing escapes or markup?
    37 |         class {StatHMMR}).
       |               ^
Package suggested but not available for checking: ‘networkTomography’
‘sandwich-CL.Rnw’... [10s/17s] NOTE
differences from ‘sandwich-CL.Rout.save’
82c82
< Classes and Methods for R originally developed in the
---
> Classes and Methods for R developed in the
85,87c85,87
< Stanford University (2002-2015),
< by and under the direction of Simon Jackman.
< hurdle and zeroinfl functions by Achim Zeileis.
---
> Stanford University
> Simon Jackman
> hurdle and zeroinfl functions by Achim Zeileis
  ‘sandwich-OOP.Rnw’... [2s/3s] OK
  ‘sandwich.Rnw’... [1s/2s] OK
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) santaR_auto_summary.Rd:54: Lost braces; missing escapes or markup?
    54 | A list: \code{result$pval.all} \code{data.frame} of \emph{p}-values, with all variables as rows and different \emph{p}-value corrections as columns. \code{result$pval.summary} \code{data.frame} of number of variables with a \emph{p}-value inferior to a cut-off. Different metric and {p}-value correction as rows, different cut-off (\emph{Inf 0.05}, \emph{Inf 0.01}, \emph{Inf 0.001}) as columns.
       |                                                                                                                                                                                                                                                                                            ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘FitARMA’
Specified C++11: please drop specification unless essential
checkRd: (-1) generef.Rd:29: Escaped LaTeX specials: \&
Argument items with no description in Rd file 'creer_graphe.Rd':
  ‘groupes’
Argument items with no description in Rd file 'fichiers.Rd':
  ‘groupes’
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
checkRd: (-1) gen.ds.Rd:43-48: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gen.ds.Rd:50-53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gen.ds.Rd:64-65: Lost braces
    64 |    \item{the dependence parameter \code{dep} or the vector of dependence parameters \code{dep}. When missing, these coefficients are obtained from independent standard uniform sampling.
       |         ^
checkRd: (-1) gen.ds.Rd:66: Lost braces
    66 |    \item{the list \code{asy} of asymmetric weights \eqn{\beta_{i,b}} for \eqn{b \in B}  and \eqn{i \in b}. When missing, these coefficients are obtained from independent standard uniform sampling followed by renormalization in order to satisfy the sum-to-one constraints.}
       |         ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) OTC.Rd:42: Lost braces; missing escapes or markup?
    42 | discretizing R^{numbers of variables}. If NULL, it is estimating
       |                ^
checkRd: (-1) OTC.Rd:83: Lost braces; missing escapes or markup?
    83 | discretizing R^{numbers of variables}. If NULL, it is estimating
       |                ^
checkRd: (-1) OTHist.Rd:29: Lost braces; missing escapes or markup?
    29 | discretizing R^{numbers of variables}. If NULL, it is estimating
       |                ^
checkRd: (-1) dOTC.Rd:72: Lost braces; missing escapes or markup?
    72 | discretizing R^{numbers of variables}. If NULL, it is estimating
       |                ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) setData.ReducedRankRegressions.Rd:14-16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) setData.ReducedRankRegressions.Rd:17-18: Lost braces in \itemize; meant \describe ?
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Updated help pages with examples
    Updated conjugate model sampler
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Packages which this enhances but not available for checking:
  'gurobi', 'pogs'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
License stub is invalid DCF.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) getSigmaR.Rd:13-14: Lost braces
    13 |   \item{digits}{digits}{number of decimal places to use when rounding,
       |                        ^
checkRd: (-1) x.oreo.Rd:48: Escaped LaTeX specials: \_ \_
checkRd: (-1) get.events.Rd:51: Lost braces
    51 |   code{\link[deSolve]{events}}
       |       ^
Error(s) in re-building vignettes:
  ...
--- re-building ‘manual.Rmd’ using rmarkdown
Could not fetch http://www.zotero.org/styles/springer-vancouver-brackets
HttpExceptionRequest Request {
  host                 = "www.zotero.org"
  port                 = 80
  secure               = False
  requestHeaders       = []
  path                 = "/styles/springer-vancouver-brackets"
  queryString          = ""
  method               = "GET"
  proxy                = Nothing
  rawBody              = False
  redirectCount        = 10
  responseTimeout      = ResponseTimeoutDefault
  requestVersion       = HTTP/1.1
  proxySecureMode      = ProxySecureWithConnect
}
 (InternalException (HandshakeFailed (Error_Protocol "peer does not support Extended Main Secret" HandshakeFailure)))
Error: processing vignette 'manual.Rmd' failed with diagnostics:
pandoc document conversion failed with error 61
--- failed re-building ‘manual.Rmd’

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
checkRd: (-1) scatterD3.Rd:209: Lost braces; missing escapes or markup?
   209 | {https://github.com/skokenes/D3-Lasso-Plugin}{d3-lasso-plugin} feature}
       | ^
checkRd: (-1) scatterD3.Rd:209: Lost braces
   209 | {https://github.com/skokenes/D3-Lasso-Plugin}{d3-lasso-plugin} feature}
       |                                              ^
checkRd: (-1) PermBiclust.beta.ks.Rd:29: Lost braces; missing escapes or markup?
    29 | \item{\code{num.bicluster}}: {The number of biclusters estimated by the procedure.}
       |                              ^
checkRd: (-1) PermBiclust.beta.ks.Rd:30: Lost braces
    30 | \item{\code{x.residual}}: {The data matrix \code{x} after removing the signals}
       |                           ^
checkRd: (-1) PermBiclust.sigclust.Rd:32: Lost braces; missing escapes or markup?
    32 | \item{\code{num.bicluster}}: {The number of biclusters estimated by the procedure.}
       |                              ^
checkRd: (-1) PermBiclust.sigclust.Rd:33: Lost braces
    33 | \item{\code{x.residual}}: {The data matrix \code{x} after removing the signals}
       |                           ^
checkRd: (-1) PermBiclust.sigclust_stop.Rd:35: Lost braces; missing escapes or markup?
    35 | \item{\code{num.bicluster}}: {The number of biclusters estimated by the procedure.}
       |                              ^
checkRd: (-1) PermBiclust.sigclust_stop.Rd:36: Lost braces
    36 | \item{\code{x.residual}}: {The data matrix \code{x} after removing the signals}
       |                           ^
'LazyData' is specified without a 'data' directory
Found the following significant warnings:

  Warning in is.R() : 'is.R' is deprecated.
  Warning in is.R() : 'is.R' is deprecated.
  Warning in is.R() : 'is.R' is deprecated.
  Warning in is.R() : 'is.R' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
checkRd: (-1) scdensity.Rd:119-120: Lost braces in \itemize; meant \describe ?
checkRd: (-1) scdensity.Rd:121-123: Lost braces in \itemize; meant \describe ?
checkRd: (-1) scdensity.Rd:124-126: Lost braces in \itemize; meant \describe ?
checkRd: (-1) scdensity.Rd:127-130: Lost braces in \itemize; meant \describe ?
checkRd: (-1) scdensity.Rd:131-135: Lost braces in \itemize; meant \describe ?
checkRd: (-1) scdensity.Rd:136-138: Lost braces in \itemize; meant \describe ?
checkRd: (-1) scdensity.Rd:139-142: Lost braces in \itemize; meant \describe ?
checkRd: (-1) scdensity.Rd:143-144: Lost braces in \itemize; meant \describe ?
checkRd: (-1) scdensity.Rd:145-147: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'sceasy', 'SeuratDisk', 'SeuratWrappers'
checkRd: (-1) get_profile.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get_profile.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get_profile.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get_profile.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get_profile.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) schoRsch.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) schoRsch.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) schoRsch.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) schoRsch.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) schoRsch.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) schoRsch.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) schoRsch.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) schoRsch.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) schoRsch.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) schoRsch.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) schoRsch.Rd:31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) schoRsch.Rd:35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) schoRsch.Rd:36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) schoRsch.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) schoRsch.Rd:38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) schoRsch.Rd:39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) schoRsch.Rd:40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) schoRsch.Rd:41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) schoRsch.Rd:42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) schoRsch.Rd:43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) schoRsch.Rd:44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) schoRsch.Rd:45: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
S3 methods shown with full name in Rd file 'plot.Rd':
  ‘plot.discretization’

S3 methods shown with full name in Rd file 'predict.Rd':
  ‘predict.discretization’ ‘predict.reject_infered’

S3 methods shown with full name in Rd file 'summary.Rd':
  ‘summary.discretization’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
checkRd: (-1) reduce_dimensionality.Rd:19: Lost braces
    19 | \item{ndim}{the maximum dimension of the space which the data are to be represented in; must be in {1, 2, \ldots, n-1}.}
       |                                                                                                    ^
checkRd: (-1) ti_scorpius.Rd:18: Lost braces; missing escapes or markup?
    18 | \item{distance_method}{A character string indicating which correlationcoefficient (or covariance) is to be computed. One of "pearson", "spearman" (default), or "cosine". Domain: {spearman, pearson, cosine}. Default: spearman. Format: character.}
       |                                                                                                                                                                                   ^
checkRd: (-1) ti_scorpius.Rd:30: Lost braces; missing escapes or markup?
    30 | \item{smoother}{\code{principal_curve} parameter; choice of smoother. Domain: {smooth_spline, lowess, periodic_lowess}. Default: smooth_spline. Format: character.}
       |                                                                               ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) simulateSNPs.Rd:46: Escaped LaTeX specials: \& \& \&
checkRd: (-1) simulateSNPs.Rd:80: Escaped LaTeX specials: \& \& \&
checkRd: (-1) scriptloc.Rd:5: Lost braces; missing escapes or markup?
     5 | \title{Get location of script in a fashion analagous to ${BASH_SOURCE[0]}}
       |                                                          ^
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘untitled_consensus_cluster’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘glmGamPoi’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) cln.Rd:27: Lost braces
    27 |    case for text \code{1} for 1st uppercase, code{2} for lowercase, code{3} for uppercase (optional)
       |                                                  ^
checkRd: (-1) cln.Rd:27: Lost braces
    27 |    case for text \code{1} for 1st uppercase, code{2} for lowercase, code{3} for uppercase (optional)
       |                                                                         ^
checkRd: (-1) geom_flat_violin.Rd:7: Lost braces
     7 | url{https://gist.github.com/dgrtwo/eb7750e74997891d7c20}
       |    ^
checkRd: (-1) sda.Rd:36-37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sda.Rd:38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sda.Rd:40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sda.package.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sda.package.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sda.package.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sdc_extabs.Rd:59: Lost braces
    59 | (including ]code{forcelist} variables) that can be used to form tables.}
       |                 ^
Problems with news in ‘NEWS.md’:
No news entries found.
Specified C++11: please drop specification unless essential
checkRd: (-1) msdpd.Rd:69: Lost braces in \itemize; meant \describe ?
checkRd: (-1) msdpd.Rd:76: Lost braces in \itemize; meant \describe ?
checkRd: (-1) msdpd.Rd:77: Lost braces in \itemize; meant \describe ?
checkRd: (-1) msdpd.Rd:78: Lost braces in \itemize; meant \describe ?
checkRd: (-1) msdpd.Rd:53: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) msdpd.Rd:54: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) msdpd.Rd:55: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) msdpd.Rd:56: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) msdpdth.Rd:84: Lost braces in \itemize; meant \describe ?
checkRd: (-1) msdpdth.Rd:91: Lost braces in \itemize; meant \describe ?
checkRd: (-1) msdpdth.Rd:92: Lost braces in \itemize; meant \describe ?
checkRd: (-1) msdpdth.Rd:93: Lost braces in \itemize; meant \describe ?
checkRd: (-1) msdpdth.Rd:65: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) msdpdth.Rd:66: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) msdpdth.Rd:67: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) msdpdth.Rd:68: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) msdpdth.Rd:69: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) msdpdth.Rd:70: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hyperpar.Rd:17: Lost braces
    17 | \item{c}{denotes the expected range of eqn{f} .}
       |                                           ^
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'parse_search_analytics.Rd':
  ‘pn’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'pipe.Rd':
  ‘...’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
checkRd: (-1) seas.check.Rd:48-49: Lost braces in \itemize; meant \describe ?
checkRd: (-1) seas.check.Rd:50: Lost braces in \itemize; meant \describe ?
checkRd: (-1) seas.check.Rd:51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) seas.check.Rd:52-54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) seas.check.Rd:55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) seas.check.Rd:56: Lost braces in \itemize; meant \describe ?
checkRd: (-1) seas.check.Rd:57: Lost braces in \itemize; meant \describe ?
checkRd: (-1) seas.check.Rd:58: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) 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"}.}
       |                                                                                                                                   ^
checkRd: (-1) Gmixt_simultanee.Rd:21: Lost braces
    21 | { \\sum{p=1 -> P} log( \\pi{p} f( y{ij} ; \\theta{p} ) ) }
       | ^
checkRd: (-1) Gmixt_simultanee.Rd:21: Lost braces
    21 | { \\sum{p=1 -> P} log( \\pi{p} f( y{ij} ; \\theta{p} ) ) }
       |        ^
checkRd: (-1) Gmixt_simultanee.Rd:21: Lost braces
    21 | { \\sum{p=1 -> P} log( \\pi{p} f( y{ij} ; \\theta{p} ) ) }
       |                            ^
checkRd: (-1) Gmixt_simultanee.Rd:21: Lost braces
    21 | { \\sum{p=1 -> P} log( \\pi{p} f( y{ij} ; \\theta{p} ) ) }
       |                                    ^
checkRd: (-1) Gmixt_simultanee.Rd:21: Lost braces
    21 | { \\sum{p=1 -> P} log( \\pi{p} f( y{ij} ; \\theta{p} ) ) }
       |                                                  ^
checkRd: (-1) segclust2d.Rd:37: Lost braces
    37 | Patin, R., Etienne, M. P., Lebarbier, E., Chamaill{\'e}-Jammes, S., 
       |                                                   ^
Packages suggested but not available for checking: 'spgrass6', 'rgdal'
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
checkRd: (-1) SVbound.Rd:26: Lost braces; missing escapes or markup?
    26 | \item{RR_UY_T1}{Input value. The sensitivity parameter RR_{UY|T=1}. Must be
       |                                                           ^
checkRd: (-1) SVbound.Rd:29: Lost braces; missing escapes or markup?
    29 | \item{RR_UY_T0}{Input value. The sensitivity parameter RR_{UY|T=0}. Must be
       |                                                           ^
checkRd: (-1) SVbound.Rd:32: Lost braces; missing escapes or markup?
    32 | \item{RR_SU_T1}{Input value. The sensitivity parameter RR_{SU|T=1}. Must be
       |                                                           ^
checkRd: (-1) SVbound.Rd:35: Lost braces; missing escapes or markup?
    35 | \item{RR_SU_T0}{Input value. The sensitivity parameter RR_{SU|T=0}. Must be
       |                                                           ^
checkRd: (-1) SVbound.Rd:38: Lost braces; missing escapes or markup?
    38 | \item{RR_UY_S1}{Input value. The sensitivity parameter RR_{UY|S=1}. Must be
       |                                                           ^
checkRd: (-1) SVbound.Rd:41: Lost braces; missing escapes or markup?
    41 | \item{RR_TU_S1}{Input value. The sensitivity parameter RR_{TU|S=1}. Must be
       |                                                           ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) convert2snafu.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) convert2snafu.Rd:28-29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) convert2snafu.Rd:31-32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) convert2snafu.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) convert2snafu.Rd:36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) convert2snafu.Rd:38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) convert2snafu.Rd:40-41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) correct.changes.Rd:24-25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) correct.changes.Rd:28-29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) correct.changes.Rd:40: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) correct.changes.Rd:43: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) correct.changes.Rd:46: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) correct.changes.Rd:57: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) correct.changes.Rd:60: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) textcleaner.Rd:50: Lost braces in \itemize; meant \describe ?
checkRd: (-1) textcleaner.Rd:53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) textcleaner.Rd:100-101: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) textcleaner.Rd:104-105: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) textcleaner.Rd:116: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) textcleaner.Rd:119: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) textcleaner.Rd:130: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) textcleaner.Rd:133: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) append.dictionary.Rd:33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) append.dictionary.Rd:36-37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) append.dictionary.Rd:40-41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) append.dictionary.Rd:44-47: Lost braces in \itemize; meant \describe ?
checkRd: (-1) append.dictionary.Rd:89-92: Lost braces in \itemize; meant \describe ?
checkRd: (-1) append.dictionary.Rd:95-98: Lost braces in \itemize; meant \describe ?
checkRd: (-1) append.dictionary.Rd:107: Lost braces in \itemize; meant \describe ?
checkRd: (-1) append.dictionary.Rd:110: Lost braces in \itemize; meant \describe ?
checkRd: (-1) append.dictionary.Rd:113: Lost braces in \itemize; meant \describe ?
checkRd: (-1) NRW.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) NRW.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bootSemNeT.Rd:31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bootSemNeT.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bootSemNeT.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bootSemNeT.Rd:40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bootSemNeT.Rd:53-54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bootSemNeT.Rd:57-58: Lost braces in \itemize; meant \describe ?
checkRd: (-1) compare_nets.Rd:62: Lost braces in \itemize; meant \describe ?
checkRd: (-1) compare_nets.Rd:64: Lost braces in \itemize; meant \describe ?
checkRd: (-1) compare_nets.Rd:66: Lost braces in \itemize; meant \describe ?
checkRd: (-1) compare_nets.Rd:32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) compare_nets.Rd:35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.compareShiny.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.compareShiny.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.compareShiny.Rd:31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) test.bootSemNeT.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) test.bootSemNeT.Rd:27-28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) test.bootSemNeT.Rd:31-33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) test.bootSemNeT.Rd:41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) test.bootSemNeT.Rd:44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) test.bootSemNeT.Rd:47: Lost braces in \itemize; meant \describe ?
checkRd: (-1) information.criteria.Rd:33: Lost braces
    33 | 	\emph{Psychometrika}  bold{52}, 345--370.
       |                                   ^
checkRd: (-1) specifyModel.Rd:49: Lost braces
    49 |     to specifying the ]code{file} argument or reading the model specification from
       |                            ^
checkRd: (-1) escape.Rd:28: Escaped LaTeX specials: \$
checkRd: (-1) markupConvert.Rd:16: Lost braces
    16 | \item{table.float}{TRUE if you want insertion of '\\begin{table}'}
       |                                                          ^
'LazyData' is specified without a 'data' directory
Package vignette with \VignetteEngine{} not specifying an engine package:
  ‘semtable.Rnw’
Engines should be specified as \VignetteEngine{PKG::ENG}.
checkRd: (-1) PAVranking.Rd:77-79: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) PAVranking.Rd:80-82: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) PAVranking.Rd:83-85: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) PAVranking.Rd:86-87: Lost braces in \itemize; \value handles \item{}{} directly
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
checkRd: (-1) sendmail_options.Rd:32-35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sendmail_options.Rd:36-37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sendmail_options.Rd:38-39: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
checkRd: (-1) match_dataphy.Rd:37-38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) match_dataphy.Rd:39-41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) match_dataphy.Rd:42-44: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Auto-generated content requiring editing in Rd file 'seqCBS-package.Rd':
  \details: ‘...the package, including the most important ~~ ~~ functions ~~’
Specified C++14: please drop specification unless essential
checkRd: (-1) process,HybridSequenceClassifier-method.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) process,HybridSequenceClassifier-method.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) process,HybridSequenceClassifier-method.Rd:32: Lost braces in \itemize; \value handles \item{}{} directly
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) SeqDesignInference.Rd:319: Lost braces; missing escapes or markup?
   319 | (a) difference in means estimator i.e. [ybar_T - ybar_C +/- t_{alpha/2, n_T + n_C - 2} s_{ybar_T - ybar_C}] or
       |                                                               ^
checkRd: (-1) SeqDesignInference.Rd:319: Lost braces; missing escapes or markup?
   319 | (a) difference in means estimator i.e. [ybar_T - ybar_C +/- t_{alpha/2, n_T + n_C - 2} s_{ybar_T - ybar_C}] or
       |                                                                                          ^
checkRd: (-1) SeqDesignInference.Rd:320: Lost braces; missing escapes or markup?
   320 | (b) the OLS estimator i.e. [beta_hat_T +/- t_{alpha/2, n + p - 2} s_{beta_hat_T}]
       |                                              ^
checkRd: (-1) SeqDesignInference.Rd:320: Lost braces; missing escapes or markup?
   320 | (b) the OLS estimator i.e. [beta_hat_T +/- t_{alpha/2, n + p - 2} s_{beta_hat_T}]
       |                                                                     ^
Found the following files/directories:
  ‘assocpointpair_result.csv’ ‘foundereffectfinder_result.csv’
  ‘getfreqs_result.csv’ ‘getfreqs_result.png’ ‘orPlot.pdf1_1.pdf’
  ‘orPlot.pdf2_1.pdf’ ‘orPlot.pdf3_1.pdf’ ‘orPlot.pdf4_1.pdf’
  ‘orPlot.pdf5_1.pdf’ ‘orPlot.pdf6_1.pdf’ ‘orPlot.pdf7_1.pdf’
  ‘orPlot.pdf8_1.pdf’ ‘q-values_result.csv’ ‘rewritetuple_result.csv’
  ‘tartan_plot.pdf’ ‘vispair_plot.pdf’ ‘vispairfeat_plot.pdf’
  ‘volcano_plot.pdf’
checkRd: (-1) poisthin.Rd:82-83: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) poisthin.Rd:84-85: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) poisthin.Rd:86: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) poisthin.Rd:87-88: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Argument items with no description in Rd file 'sequential.design.Rd':
  ‘\dots’
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) SEset_to_network.Rd:50: Escaped LaTeX specials: \&
checkRd: (-1) network_to_SEset.Rd:72: Escaped LaTeX specials: \&
checkRd: (-1) network_to_path.Rd:50: Escaped LaTeX specials: \&
checkRd: (-1) path_to_network.Rd:29: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘BPCells’
Packages suggested but not available for checking:
  'BPCells', 'monocle', 'presto'
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) kernels.Rd:28: Lost braces; missing escapes or markup?
    28 | \item \code{guassian}: K(z) = (2pi)^{1/2} * exp(-z^2/2)
       |                                     ^
Documented arguments not in \usage in Rd file 'jc_clc_perm_impl.Rd':
  ‘a’

Documented arguments not in \usage in Rd file 'local_g_spt.Rd':
  ‘n_sim’

Documented arguments not in \usage in Rd file 'permute_listw.Rd':
  ‘a’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
checkRd: (-1) spatial_morphers.Rd:112: Lost braces
   112 | geospatial features as object of class code{\link[sf]{sf}} or
       |                                            ^
Specified C++11: please drop specification unless essential
checkRd: (-1) st_as_sftime.Rd:71: Lost braces
    71 | remove these columns from code{data.frame}?}
       |                               ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) bisee.Rd:127: Lost braces
   127 | values including \code{x}, \code{y}, code{family}, \code{clusterID},
       |                                          ^
checkRd: (-1) hisee.Rd:101: Lost braces
   101 | values including \code{x}, \code{y}, code{family}, \code{clusterID},
       |                                          ^
checkRd: (-1) isee.Rd:116: Lost braces
   116 | values including \code{x}, \code{y}, code{family}, \code{clusterID},
       |                                          ^
checkRd: (-1) see.Rd:98: Lost braces
    98 | values including \code{x}, \code{y}, code{family}, \code{clusterID},
       |                                          ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) generate_toy_data.Rd:35: Lost braces
    35 | \item{groups}{If item{grouped=TRUE}, the grouping structure is required. Each input variable should have a group id.}
       |                      ^
checkRd: (-1) generate_toy_data.Rd:58: Lost braces
    58 | \item{true_grp_id}{Indices of which groups are non-zero in item{true_beta}.}
       |                                                                ^
checkRd: (-1) predict.sgs.Rd:18: Lost braces
    18 | item{response}{The predicted response. In the logistic case, this represents the predicted class probabilities.}
       |     ^
checkRd: (-1) predict.sgs.Rd:18: Lost braces
    18 | item{response}{The predicted response. In the logistic case, this represents the predicted class probabilities.}
       |               ^
checkRd: (-1) predict.sgs.Rd:19: Lost braces
    19 | item{class}{The predicted class assignments. Only returned if type = "logistic" in the \code{"sgs"} object.}
       |     ^
checkRd: (-1) predict.sgs.Rd:19: Lost braces
    19 | item{class}{The predicted class assignments. Only returned if type = "logistic" in the \code{"sgs"} object.}
       |            ^
checkRd: (-1) calculate_sampsize.Rd:42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) calculate_sampsize.Rd:43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) calculate_sampsize.Rd:44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sgt.Rd:55: Lost braces
    55 |   \code{sigma <= 0}, \code{lambda <= -1}, \code{lambda >= 1}, \code{p <= 0}, and \code{q <= 0} are errors and return \code{NaN}. Also, if \code{mean.cent} is \code{TRUE} but code{p*q <= 1}, the result is an error and \code{NaNs} are produced. Similarly, if \code{var.adj} is \code{TRUE} but code{p*q <= 2}, the result is an error and \code{NaNs} are produced.
       |                                                                                                                                                                                   ^
checkRd: (-1) sgt.Rd:55: Lost braces
    55 |   \code{sigma <= 0}, \code{lambda <= -1}, \code{lambda >= 1}, \code{p <= 0}, and \code{q <= 0} are errors and return \code{NaN}. Also, if \code{mean.cent} is \code{TRUE} but code{p*q <= 1}, the result is an error and \code{NaNs} are produced. Similarly, if \code{var.adj} is \code{TRUE} but code{p*q <= 2}, the result is an error and \code{NaNs} are produced.
       |                                                                                                                                                                                                                                                                                                        ^
checkRd: (-1) changept.Rd:17-19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) changept.Rd:20-21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) changept.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) powerShape.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) powerShape.Rd:31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) powerShape.Rd:32-33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) powerShapeNA.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) powerShapeNA.Rd:31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) powerShapeNA.Rd:32-33: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
Package vignette without corresponding tangle output:
  ‘shape.Rnw’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rCOSA’
Package unavailable to check Rd xrefs: ‘rCOSA’
Package suggested but not available for checking: ‘hydromad’
checkRd: (-1) monthlyWB.Rd:41: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) monthlyWB.Rd:42: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) monthlyWB.Rd:43: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) monthlyWB.Rd:44: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) monthlyWB.Rd:45: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) monthlyWB.Rd:46: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) monthlyWB.Rd:47: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) monthlyWB.Rd:48: Lost braces in \itemize; \value handles \item{}{} directly
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})}
       |                              ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) shiftrPrepare.Rd:37: Lost braces
    37 |     See code{\link{shiftrPermBinary}} function and the respective example.
       |             ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) shinyalert.Rd:159: Lost braces; missing escapes or markup?
   159 | Modals created with {shinyalert} have a return value when they exit.
       |                     ^
checkRd: (-1) shinyalert.Rd:180: Lost braces; missing escapes or markup?
   180 | For example, using the following {shinyalert} code will result in a modal with
       |                                  ^
checkRd: (-1) useShinyalert.Rd:21: Lost braces; missing escapes or markup?
    21 | The first time a {shinyalert} message is shown, the required scripts are
       |                  ^
checkRd: (-1) useShinyalert.Rd:12: Lost braces; missing escapes or markup?
    12 | \item{force}{Set to \code{TRUE} to force pre-loading the {shinyalert} scripts. If
       |                                                          ^
Package suggested but not available for checking: ‘cmdstanr’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) js_calls.Rd:63: Lost braces in \itemize; meant \describe ?
checkRd: (-1) js_calls.Rd:64: Lost braces in \itemize; meant \describe ?
checkRd: (-1) js_calls.Rd:65-66: Lost braces in \itemize; meant \describe ?
checkRd: (-1) js_calls.Rd:67: Lost braces in \itemize; meant \describe ?
checkRd: (-1) js_calls.Rd:68: Lost braces in \itemize; meant \describe ?
checkRd: (-1) js_calls.Rd:69: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pickCheckboxNamesAndLabels.Rd:14: Lost braces
    14 | \item{choices}{link{pickCheckboxInput} choices list.}
       |                    ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) display.Rd:17: Lost braces; missing escapes or markup?
    17 | div which wraps your message to display it in the {position} corner of your shiny app.
       |                                                   ^
checkRd: (-1) info_value.Rd:15: Lost braces; missing escapes or markup?
    15 | div which wraps rendered value to display it in the {position} corner of your shiny app.
       |                                                     ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) shinyjs-defunct.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) shinyjs-defunct.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) shinyjs-defunct.Rd:20: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) store_googledrive.Rd:19: Lost braces; missing escapes or markup?
    19 | See the {gargle} package to manage authentication, and especially
       |         ^
checkRd: (-1) store_googledrive.Rd:20: Lost braces; missing escapes or markup?
    20 | \href{https://gargle.r-lib.org/articles/articles/managing-tokens-securely.html}{this vignette from {gargle} package} to manage the process.
       |                                                                                                    ^
checkRd: (-1) custom-labels.Rd:7: Lost braces; missing escapes or markup?
     7 | \title{Modify {shinymanager} labels to use custom text}
       |               ^
checkRd: (-1) use_language.Rd:5: Lost braces; missing escapes or markup?
     5 | \title{Use {shinymanager} labels}
       |            ^
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘uchardet’
'LazyData' is specified without a 'data' directory
checkRd: (-1) messages.Rd:40: Lost braces
    40 | \item{id}{Reference to link{f7Messages} container.}
       |                            ^
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘uchardet’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
checkRd: (-1) shiny_pivot_table.Rd:58: Lost braces in \itemize; meant \describe ?
checkRd: (-1) shiny_pivot_table.Rd:59: Lost braces in \itemize; meant \describe ?
checkRd: (-1) shiny_pivot_table.Rd:60: Lost braces in \itemize; meant \describe ?
checkRd: (-1) shiny_pivot_table.Rd:61: Lost braces in \itemize; meant \describe ?
checkRd: (-1) shiny_pivot_table.Rd:62: Lost braces in \itemize; meant \describe ?
checkRd: (-1) shiny_pivot_table.Rd:63: Lost braces in \itemize; meant \describe ?
checkRd: (-1) shiny_pivot_table.Rd:64: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
checkRd: (-1) addValidationSuffix.Rd:13: Lost braces; missing escapes or markup?
    13 | A string `"{tagId}-shinyreforms-validation"`.
       |            ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘.shiny_run’ ‘shinyShortcut.desktop’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘cmdstanr’
checkRd: (-1) add_class.Rd:18: Lost braces; missing escapes or markup?
    18 | Custom function for adding a CSS class used in {shinysurveys}.
       |                                                ^
checkRd: (-1) disable_element.Rd:16: Lost braces; missing escapes or markup?
    16 | Custom function for disabling an HTML element in {shinysurveys}.
       |                                                  ^
checkRd: (-1) enable_element.Rd:16: Lost braces; missing escapes or markup?
    16 | Custom function for disabling an HTML element in {shinysurveys}.
       |                                                  ^
checkRd: (-1) extendInputType.Rd:12: Lost braces; missing escapes or markup?
    12 | \item{extension}{A shiny input type not natively supported by {shinysurveys}. See the examples section for more information.}
       |                                                               ^
checkRd: (-1) getSurveyData.Rd:15: Lost braces; missing escapes or markup?
    15 | default, and the built-in {shinysurveys} userID will be used.}
       |                           ^
checkRd: (-1) radioMatrixInput.Rd:18: Lost braces; missing escapes or markup?
    18 | \item{...}{Additional arguments specific to {shinysurveys} required questions.}
       |                                             ^
checkRd: (-1) remove_class.Rd:18: Lost braces; missing escapes or markup?
    18 | Custom function for removing a CSS class used in {shinysurveys}.
       |                                                  ^
checkRd: (-1) toggle_element.Rd:18: Lost braces; missing escapes or markup?
    18 | Custom function for toggling enable/disable state of HTML element in {shinysurveys}.
       |                                                                      ^
checkRd: (-1) AppDriver.Rd:1087: Lost braces; missing escapes or markup?
  1087 | _snaps/{variant}/{test.md}\verb{, so }variant` must be a single
       |        ^
checkRd: (-1) AppDriver.Rd:1087: Lost braces; missing escapes or markup?
  1087 | _snaps/{variant}/{test.md}\verb{, so }variant` must be a single
       |                  ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) run_shinytitle_example.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) run_shinytitle_example.Rd:19: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
checkRd: (-1) MrBayes.Rd:24: Lost braces
    24 | \item{contype}{A character string; the type of consensus tree calculated from the posterior distribution of trees}{either "halfcompat" (majority-rule consensus tree) or "allcombat" (strict consensus tree)}
       |                                                                                                                   ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) shutterplot.Rd:59: Lost braces; missing escapes or markup?
    59 | \item{las}{numeric in {0,1,2,3}; the style of axis labels.'
       |                       ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) pop.dist.Rd:41: Lost braces; missing escapes or markup?
    41 | where \emph{dist(i,j)} represents the distance between populations \emph{i} and \emph{j}, \emph{m} and \emph{n} are the number of sequences in populations \emph{i} and \emph{j}, respectively, and \emph{dist(H_{ki},H_{lj})} is the distance between the \emph{k-th} sequence found in population \emph{i} and the \emph{l-th} sequence found in population \emph{j}. 
       |                                                                                                                                                                                                                  ^
checkRd: (-1) pop.dist.Rd:41: Lost braces; missing escapes or markup?
    41 | where \emph{dist(i,j)} represents the distance between populations \emph{i} and \emph{j}, \emph{m} and \emph{n} are the number of sequences in populations \emph{i} and \emph{j}, respectively, and \emph{dist(H_{ki},H_{lj})} is the distance between the \emph{k-th} sequence found in population \emph{i} and the \emph{l-th} sequence found in population \emph{j}. 
       |                                                                                                                                                                                                                         ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) drr.Rd:36: Lost braces; missing escapes or markup?
    36 |   \code{drr} {is Rosin - Rammler probability density function}\cr
       |              ^
checkRd: (-1) drr.Rd:37: Lost braces; missing escapes or markup?
    37 |   \code{urr} {is Rosin - Rammler cumulative distribution function (CDF) representing undersize mass fraction}\cr
       |              ^
checkRd: (-1) drr.Rd:38: Lost braces
    38 |   \code{orr} {is Rosin - Rammler complementary CDF representing oversize mass fraction ie. relative remainder on the sieve with the mesh size \code{x}}\cr
       |              ^
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘qlcMatrix’
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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) 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
Found the following files/directories:
  ‘ExportFigtree1.tre’
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))}
       |                                                     ^
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) fptsde1d.Rd:69: Lost braces; missing escapes or markup?
    69 | \code{dfptsde1d} {gives the density estimate of fpt.}
       |                  ^
checkRd: (-1) fptsde1d.Rd:70: Lost braces; missing escapes or markup?
    70 | \code{fptsde1d} {generates random of fpt.}
       |                 ^
checkRd: (-1) fptsde2d.Rd:75: Lost braces; missing escapes or markup?
    75 | \code{dfptsde2d} {gives the kernel density approximation for fpt.}
       |                  ^
checkRd: (-1) fptsde2d.Rd:76: Lost braces; missing escapes or markup?
    76 | \code{fptsde2d} {generates random of fpt.}
       |                 ^
checkRd: (-1) fptsde3d.Rd:77: Lost braces; missing escapes or markup?
    77 | \code{dfptsde3d} {gives the marginal kernel density approximation for fpt.}
       |                  ^
checkRd: (-1) fptsde3d.Rd:78: Lost braces; missing escapes or markup?
    78 | \code{fptsde3d} {generates random of fpt.}
       |                 ^
checkRd: (-1) rsde1d.Rd:54: Lost braces
    54 | \code{dsde1d} {gives the transition density estimate of \code{X(t-s) | X(s)=x0}.}
       |               ^
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    55 | \code{rsde1d} {generates random of \code{X(t-s) | X(s)=x0}.}
       |               ^
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    46 | \code{dsde2d} {gives the bivariate density approximation for \code{(X(t-s),Y(t-s) | X(s)=x0,Y(s)=y0)}.}
       |               ^
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    47 | \code{rsde2d} {generates random of the couple \code{(X(t-s),Y(t-s) | X(s)=x0,Y(s)=y0)}.}
       |               ^
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    46 | \code{dsde3d} {gives the trivariate density approximation \code{(X(t-s),Y(t-s),Z(t-s) | X(s)=x0,Y(s)=y0,Z(s)=z0)}.}
       |               ^
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    47 | \code{rsde3d} {generates random of the \code{(X(t-s),Y(t-s),Z(t-s) | X(s)=x0,Y(s)=y0,Z(s)=z0)}.}
       |               ^
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    25 | convert_xlsx_to_csv<-function(xlsx_file){
       |                                         ^
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    33 |   for (i in Sheetnames) {
       |                         ^
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    93 | {FD(h[i](t)) = (exp(g(x[j]) - g(x[l])) - 1) * 100}
       | ^
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Auto-generated content requiring editing in Rd file 'SimplifyStats-package.Rd':
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    11 | \item{x}{\code{\link{Pop-class}} or code{\link{Colony-class}} or \code{\link{MultiColony-class}},
       |                                         ^
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     7 | 	This function can be used to create data from a set of parameters created from \code{\link{draw}}, called a code{paramSet}. This function is used internally to create data, and is available publicly for accessibility and debugging.
       |                                                                                                                         ^
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     7 | 	This function can be used to export data created from a set of parameters created from \code{\link{draw}}, called a code{paramSet}. This function can export data to be analyzed with either Mplus or LISREL.
       |                                                                                                                                 ^
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    67 |  \code{within.SD} to be extremely small (e.g., $1 * 10^{-7}$) and all corresponding correlations in matrix
       |                                                        ^
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    15 | For example, in latex it would take "2" and output "{\\bf 2}"; in html
       |                                                     ^
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   109 | bounds for P{X<Y}, based on two independent samples. \emph{The Annals of
       |             ^
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    27 | individual curves, adjusted for {abcd} to lie on top of (i.e. be
       |                                 ^
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   110 | \code{\link{nlme}}) (default {nlmeControl(returnObject = TRUE)}).}
       |                              ^
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    20 |   \item{distr.type}{school district type (constructed for illustration purposes; (values={"A", "B", "C", "D"})).}
       |                                                                                          ^
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    61 | \item{replacementUnitsFilename}{character; csv filename for saving {unit:replacement} directory when writeOut == TRUE; default = "replacementUnits.csv"}
       |                                                                    ^
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    63 | \item{subUnitTableFilename}{character; csv filename for saving {unit:replacement} directory when writeOut == TRUE; default = "subUnitTable.csv"}
       |                                                                ^
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    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.
       |                                  ^
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    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.
       |                                                                                                  ^
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    26 | \item{alpha}{The eqn{\\alpha} error used to compute the \eqn{100*(1-\\alpha)\%} confidence interval}
       |                     ^
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    84 | $MS_{factor}/MS_{interaction}$, e.g. in appendix A of AIAG MSA manual, 
       |     ^
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    84 | $MS_{factor}/MS_{interaction}$, e.g. in appendix A of AIAG MSA manual, 
       |                 ^
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    87 | F test is performed as $MS_{factor}/MS_{equipment}$, i.e., repeatability.
       |                            ^
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    87 | F test is performed as $MS_{factor}/MS_{equipment}$, i.e., repeatability.
       |                                        ^
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    44 |   \item I.cov.rob - The matrix (V'GnV)^{-1} used to compute the statistics to detect the idiosyncratic outliers.
       |                                        ^
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    22 | https://i.cdn.turner.com/nba/nba/.element/img/4.0/global/logos/512x512/bg.white/svg/{team_short_name}.svg
       |                                                                                     ^
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    24 | sum(x' V^{-1} (y - x beta)) = 0 as the covariance V tends from V[, , 1] +
       |          ^
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   111 | This function minimizes the Box-Cox Stress of Chen & Buja (2013) via gradient descent. This is a ratio metric scaling method. The transformations are not straightforward to interpret but mu is associated with fitted distances in the configuration and lambda with the dissimilarities. Concretely for fitted distances (attraction part) it is BC_{mu+lambda}(d(X)) and for the repulsion part it is delta^lambdaBC_{mu}(d(X)) with BC being the one-parameter Box Cox transformation.
       |                                                                                                                                                                                                                                                                                                                                                        ^
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   111 | This function minimizes the Box-Cox Stress of Chen & Buja (2013) via gradient descent. This is a ratio metric scaling method. The transformations are not straightforward to interpret but mu is associated with fitted distances in the configuration and lambda with the dissimilarities. Concretely for fitted distances (attraction part) it is BC_{mu+lambda}(d(X)) and for the repulsion part it is delta^lambdaBC_{mu}(d(X)) with BC being the one-parameter Box Cox transformation.
       |                                                                                                                                                                                                                                                                                                                                                                                                                          ^
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    14 | \item{d}{A list d{[[j]]} whose elements are vectors of variable names from A defining marginal tables/cubes 
       |                  ^
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    24 | D = {D[[j]]} of marginal tables/cubes of A spesified by the list d = d{[[j]]} generated 
       |     ^
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    24 | D = {D[[j]]} of marginal tables/cubes of A spesified by the list d = d{[[j]]} generated 
       |                                                                       ^
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    31 | \item{d}{A list d{[[j]]} whose elements are vectors of variable names from A defining marginal tables/cubes D
       |                  ^
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    15 | \item{d}{A list d{[[j]]} whose elements are vectors of variable names from A defining marginal tables/cubes D
       |                  ^
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     6 | A subset of world.cities{maps}. Extracted in order to shink number of dependencies. 
       |                         ^
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    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}
       |                                                                                                                ^
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    49 | \item asmd_{mean/median}: average/median absolute standardized mean difference (and min, max) of patient characteristics between those without (1) and with (0) observed covariate
       |            ^
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    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},...}
       |                                                  ^
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    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},...}
       |                                                            ^
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    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},...}
       |                                                                          ^
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    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},...}
       |                                                                                    ^
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    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},....}
       |                                              ^
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    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},....}
       |                                                        ^
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    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},....}
       |                                                                      ^
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    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},....}
       |                                                                                ^
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    73 | algorithm to be used. For details, see {optim}.}
       |                                        ^
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    76 | the optimization algorithm to be used. For details, see {optim}.}
       |                                                         ^
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   101 | the control parameters from the {optim} function through the argument
       |                                 ^
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Functions with \usage entries need to have the appropriate \alias
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The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
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   115 |  is the empirical explained variance from \cite{Meinshausen and B{u}hlmann, 2015}.  See \cite{Lund et al., 2020} for more details and references.
       |                                                                  ^
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   170 | Meinshausen, N and P. B{u}hlmann (2015). Maximin effects in inhomogeneous large-scale data.
       |                        ^
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    44 | estimMk returns the transition probability matrix of size (S^{k})xS (with S = length(E)) 
       |                                                              ^
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    10 | or code{smoof_multi_objective_function}. Both single- and multi-objective functions share the following attributes.
       |        ^
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checkRd: (-1) cma.Rd:53: Lost braces; missing escapes or markup?
    53 | phi_i = {0.5,1,1,...,0.5} / order
       |         ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) smoothtail-package.Rd:63: Lost braces
    63 | Kaspar Ru{f}{i}bach (maintainer), \email{kaspar.rufibach@gmail.com} , \cr \url{http://www.kasparrufibach.ch}
       |          ^
checkRd: (-1) smoothtail-package.Rd:63: Lost braces
    63 | Kaspar Ru{f}{i}bach (maintainer), \email{kaspar.rufibach@gmail.com} , \cr \url{http://www.kasparrufibach.ch}
       |             ^
Problems with news in ‘NEWS.md’:
No news entries found.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘lseq’
Auto-generated content requiring editing in Rd file 'smotefamily-package.Rd':
  \references: ‘This optional section can contain literature or other refere...’
  \seealso: ‘Optional links to other man pages’
  \examples: ‘\dontrun{      ## Optional simple examples of the most impor...’
Found the following files/directories:
  ‘my_new_social_media_plot.png’
checkRd: (-1) SnakesAndLaddersGame.Rd:25: Lost braces; missing escapes or markup?
    25 | {Hector Haffenden} {haffendenh@cardiff.ac.uk}
       |                    ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) sk_GLS.Rd:34: Lost braces; missing escapes or markup?
    34 | The GLS solution is: b = ( X^T V^{-1} X )^{-1} X^T V^{-1} z,
       |                                  ^
checkRd: (-1) sk_GLS.Rd:34: Lost braces; missing escapes or markup?
    34 | The GLS solution is: b = ( X^T V^{-1} X )^{-1} X^T V^{-1} z,
       |                                           ^
checkRd: (-1) sk_GLS.Rd:34: Lost braces; missing escapes or markup?
    34 | The GLS solution is: b = ( X^T V^{-1} X )^{-1} X^T V^{-1} z,
       |                                                      ^
checkRd: (-1) sk_GLS.Rd:40: Lost braces; missing escapes or markup?
    40 | Operations with V^{-1} are computed using the factorization \code{fac} (see \code{sk_var}), or
       |                   ^
checkRd: (-1) sk_LL.Rd:37: Lost braces; missing escapes or markup?
    37 | \code{quad_form} is z^T V^{-1} z, for the observed response vector z, which is constructed
       |                           ^
checkRd: (-1) sk_var.Rd:41: Lost braces; missing escapes or markup?
    41 | returns the quadratic form X^T V^{-1} X.
       |                                  ^
checkRd: (-1) sk_var.Rd:33: Lost braces; missing escapes or markup?
    33 | either matrix \code{V}, or X^T V^{-1} X, or a factorization ('chol' or 'eigen')
       |                                  ^
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘tutorial.Rmd’ using rmarkdown
Could not fetch http://www.zotero.org/styles/nature
HttpExceptionRequest Request {
  host                 = "www.zotero.org"
  port                 = 80
  secure               = False
  requestHeaders       = []
  path                 = "/styles/nature"
  queryString          = ""
  method               = "GET"
  proxy                = Nothing
  rawBody              = False
  redirectCount        = 10
  responseTimeout      = ResponseTimeoutDefault
  requestVersion       = HTTP/1.1
  proxySecureMode      = ProxySecureWithConnect
}
 (InternalException (HandshakeFailed (Error_Protocol "peer does not support Extended Main Secret" HandshakeFailure)))
Error: processing vignette 'tutorial.Rmd' failed with diagnostics:
pandoc document conversion failed with error 61
--- failed re-building ‘tutorial.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Specified C++11: please drop specification unless essential
checkRd: (-1) knockoffGenotypes.Rd:32: Lost braces; missing escapes or markup?
    32 | This function efficiently constructs group-knockoffs of {0,1,2} variables distributed
       |                                                         ^
checkRd: (-1) knockoffGenotypes.Rd:11: Lost braces; missing escapes or markup?
    11 | \item{X}{a {0,1,2} matrix of size n-by-p containing the original variables.}
       |            ^
checkRd: (-1) knockoffGenotypes.Rd:29: Lost braces; missing escapes or markup?
    29 | A {0,1,2} matrix of size n-by-p containing the knockoff variables.
       |   ^
checkRd: (-1) maize.line.Rd:9: Lost braces in \itemize; meant \describe ?
checkRd: (-1) maize.line.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) maize.line.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) maize.line.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) raw.data.Rd:26: Lost braces; missing escapes or markup?
    26 | \item{call.rate}{\code{numeric}. Threshold for removing marker by missing genotype rate. SNP with \code{call rate} below threshold are removed from dataset. Must be between {0, 1}}
       |                                                                                                                                                                              ^
checkRd: (-1) raw.data.Rd:28: Lost braces; missing escapes or markup?
    28 | \item{maf}{Threshold for removing SNP by minor allele frequency. Must be between {0, 1}}
       |                                                                                  ^
checkRd: (-1) plot.selm.Rd:101: Lost braces
   101 | data. Default value for code{which} is \code{2:4} if \code{p>1}, otherwise
       |                             ^
Found the following calls to attach():
File ‘SOAR/R/SOAR.R’:
  attach(NULL, pos, basename(directory))
See section ‘Good practice’ in ‘?attach’.
Found the following files/directories:
  ‘.R_Test’
'LazyData' is specified without a 'data' directory
checkRd: (-1) map.active.Rd:82: Lost braces
    82 | \link{guides}, \link{theme} and link{guide_legend} functions from the
       |                                     ^
checkRd: (-1) map.add.Rd:99: Lost braces
    99 | \link{guides}, \link{theme} and link{guide_legend} functions from the
       |                                     ^
checkRd: (-1) map.csa.mca.Rd:35: Lost braces
    35 | \link{soc.csa}, \link{map.csa.all}, link{map.csa.mca.array}
       |                                         ^
checkRd: (-1) map.ctr.Rd:85: Lost braces
    85 | \link{guides}, \link{theme} and link{guide_legend} functions from the
       |                                     ^
checkRd: (-1) map.ind.Rd:80: Lost braces
    80 | \link{guides}, \link{theme} and link{guide_legend} functions from the
       |                                     ^
checkRd: (-1) map.mod.Rd:82: Lost braces
    82 | \link{guides}, \link{theme} and link{guide_legend} functions from the
       |                                     ^
checkRd: (-1) map.sup.Rd:82: Lost braces
    82 | \link{guides}, \link{theme} and link{guide_legend} functions from the
       |                                     ^
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
       |                                                  ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) llwrPTF.Rd:7: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) solr_mlt.Rd:70: Lost braces; missing escapes or markup?
    70 | TermVector DEFAULT_FIELD_NAMES = new String[] {"contents"}
       |                                               ^
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘.solveEnv’
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 ?
Documented arguments not in \usage in Rd file 'som.nn.do.train.Rd':
  ‘model’

Documented arguments not in \usage in Rd file 'som.nn.som.internal.Rd':
  ‘rlen’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
S3 methods shown with full name in Rd file 'plot.predictions.Rd':
  ‘plot.predictions’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
checkRd: (-1) plot.som.Rd:27: Escaped LaTeX specials: \_
checkRd: (-1) som.Rd:128: Escaped LaTeX specials: \_
'LazyData' is specified without a 'data' directory
checkRd: (-1) spe.Rd:101: Lost braces
   101 | code{spe} command; (4) \code{alpha} stores significance level as in
       |     ^
checkRd: (-1) load_sorvi_data.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) findFn.Rd:101-102: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) findFn.Rd:103-109: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) findFn.Rd:110-116: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) findFn.Rd:117-120: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) findFn.Rd:121-124: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) findFn.Rd:125: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) findFn.Rd:126-130: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) findFn.Rd:131-133: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) findFn.Rd:134-137: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) findFn.Rd:144-150: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) findFn.Rd:151-157: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) findFn.Rd:158-161: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) findFn.Rd:162: Lost braces in \itemize; \value handles \item{}{} directly
Documented arguments not in \usage in Rd file 'path2name.Rd':
  ‘x’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘SciencesPo’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) SpaceTimeBSS-package.Rd:23: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘NLMR’
Package suggested but not available for checking: ‘NLMR’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) sdf_unnest.Rd:20: Lost braces
    20 | \code{a1, a2, a3}, then code{sdf_explode(df, a)} will produce output with each record replicated
       |                             ^
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) xgboost_classifier.Rd:92: Lost braces; missing escapes or markup?
    92 | \item{tree_method}{The tree construction algorithm used in XGBoost. options: {'auto', 'exact', 'approx'} [default='auto']}
       |                                                                              ^
checkRd: (-1) xgboost_classifier.Rd:100: Lost braces; missing escapes or markup?
   100 | \item{normalize_type}{Parameter of Dart booster. type of normalization algorithm, options: {'tree', 'forest'}. [default="tree"]}
       |                                                                                            ^
checkRd: (-1) xgboost_classifier.Rd:116: Lost braces; missing escapes or markup?
   116 | \item{use_external_memory}{The tree construction algorithm used in XGBoost. options: {'auto', 'exact', 'approx'} [default='auto']}
       |                                                                                      ^
checkRd: (-1) xgboost_regressor.Rd:88: Lost braces; missing escapes or markup?
    88 | \item{tree_method}{The tree construction algorithm used in XGBoost. options: {'auto', 'exact', 'approx'} [default='auto']}
       |                                                                              ^
checkRd: (-1) xgboost_regressor.Rd:96: Lost braces; missing escapes or markup?
    96 | \item{normalize_type}{Parameter of Dart booster. type of normalization algorithm, options: {'tree', 'forest'}. [default="tree"]}
       |                                                                                            ^
checkRd: (-1) xgboost_regressor.Rd:112: Lost braces; missing escapes or markup?
   112 | \item{use_external_memory}{The tree construction algorithm used in XGBoost. options: {'auto', 'exact', 'approx'} [default='auto']}
       |                                                                                      ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) counterfactual_yhat.Rd:47: Lost braces; missing escapes or markup?
    47 | We want the counterfactual Yhat_{g' <- G} |X=x,G=g (or alternatively
       |                                 ^
checkRd: (-1) counterfactual_yhat.Rd:48: Lost braces; missing escapes or markup?
    48 | Yhat_{g' <- G} |G=g).
       |      ^
checkRd: (-1) counterfactual_yhat.Rd:58: Lost braces; missing escapes or markup?
    58 | To estimate Y'=Yhat_{g' <- G} | G=g, we need to
       |                     ^
checkRd: (-1) counterfactual_yhat.Rd:65: Lost braces; missing escapes or markup?
    65 | To estimate Y'=Yhat_{g' <- G} |X=x, G=g, we need to
       |                     ^
checkRd: (-1) counterfactual_yhat.Rd:27: Lost braces; missing escapes or markup?
    27 | indices representing sample(s) from counterfactual  Yhat_{g' <- G} |X=x,G=g
       |                                                          ^
Unknown package ‘sparsebn’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Malformed Description field: should contain one or more complete sentences.
Specified C++11: please drop specification unless essential
checkRd: (-1) Coord.to.Pointers.Rd:54: Lost braces; missing escapes or markup?
    54 | \item{triangle=TRUE}{Input \code{rows} and {cols} represent lower
       |                                            ^
checkRd: (-1) Coord.to.Pointers.Rd:59: Lost braces; missing escapes or markup?
    59 | \item{triangle=FALSE}{Input \code{rows} and {cols} represent a full
       |                                             ^
checkRd: (-1) cholsolveAQinvAT.Rd:5: Lost braces; missing escapes or markup?
     5 | \title{Solve the equation X = AQ^{-1}t(A) under permutations}
       |                                  ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) mu_calc.Rd:32: Lost braces; missing escapes or markup?
    32 | mu_{d} | mu_{d} < mu_{d-1} and mu_{d} | mu_{d} > mu_{d-1} respecitively.
       |    ^
checkRd: (-1) mu_calc.Rd:32: Lost braces; missing escapes or markup?
    32 | mu_{d} | mu_{d} < mu_{d-1} and mu_{d} | mu_{d} > mu_{d-1} respecitively.
       |             ^
checkRd: (-1) mu_calc.Rd:32: Lost braces; missing escapes or markup?
    32 | mu_{d} | mu_{d} < mu_{d-1} and mu_{d} | mu_{d} > mu_{d-1} respecitively.
       |                      ^
checkRd: (-1) mu_calc.Rd:32: Lost braces; missing escapes or markup?
    32 | mu_{d} | mu_{d} < mu_{d-1} and mu_{d} | mu_{d} > mu_{d-1} respecitively.
       |                                   ^
checkRd: (-1) mu_calc.Rd:32: Lost braces; missing escapes or markup?
    32 | mu_{d} | mu_{d} < mu_{d-1} and mu_{d} | mu_{d} > mu_{d-1} respecitively.
       |                                            ^
checkRd: (-1) mu_calc.Rd:32: Lost braces; missing escapes or markup?
    32 | mu_{d} | mu_{d} < mu_{d-1} and mu_{d} | mu_{d} > mu_{d-1} respecitively.
       |                                                     ^
checkRd: (-1) lsq.Rd:12-13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) lsq.Rd:13-14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) lsq.Rd:14-15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) lsq.Rd:15-16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) lsq.Rd:17-18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) lsq.Rd:19-20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) lsq.Rd:21-22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) lsq.Rd:22-23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) lsq.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) lsq.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) lsq.Rd:26-27: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
checkRd: (-1) plot.sparsereg.Rd:22-23: Lost braces
    22 | \env{main1, main2, main3}{
       |                          ^
checkRd: (-1) plot.sparsereg.Rd:25-27: Lost braces
    25 | \env{xlabel}{
       |             ^
checkRd: (-1) plot.sparsereg.Rd:29-31: Lost braces
    29 | \env{plot.one}{
       |               ^
checkRd: (-1) summary.sparsereg.Rd:27-29: Lost braces
    27 | \env{interval}{
       |               ^
checkRd: (-1) summary.sparsereg.Rd:31-33: Lost braces
    31 | \env{ci}{
       |         ^
checkRd: (-1) summary.sparsereg.Rd:35-37: Lost braces
    35 | \env{order}{
       |            ^
checkRd: (-1) summary.sparsereg.Rd:39-41: Lost braces
    39 | \env{normal}{
       |             ^
checkRd: (-1) summary.sparsereg.Rd:43-45: Lost braces
    43 | \env{select}{
       |             ^
checkRd: (-1) summary.sparsereg.Rd:47-48: Lost braces
    47 | \env{printit}{
       |              ^
checkRd: (-1) summary.sparsereg.Rd:50-52: Lost braces
    50 | \env{stage}{
       |            ^
checkRd: (-1) elasticNetSEMcv.Rd:69: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) elasticNetSEMcv.Rd:71-74: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) elasticNetSEMcv.Rd:75-82: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) elasticNetSEMcv.Rd:83-92: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) elasticNetSEMcv.Rd:93: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) elasticNetSEMcv.Rd:94: Lost braces in \itemize; \value handles \item{}{} directly
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) SpatialBSS-package.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) SpatialBSS-package.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) SpatialBSS-package.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) SpatialBSS-package.Rd:28: Lost braces in \itemize; meant \describe ?
Package suggested but not available for checking: ‘INLA’
checkRd: (-1) distSG.Rd:40: Lost braces; missing escapes or markup?
    40 |   matrix and weight matrix (plus a matrix with {eID} identifiers
       |                                                ^
Specified C++11: please drop specification unless essential
Specified C++14: please drop specification unless essential
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
Depends: includes the non-default packages:
  'spatstat.geom', 'spatstat.random', 'spatstat.explore',
  'spatstat.model', 'spatstat.linnet', 'spatstat.data', 'spatstat',
  'rpanel', 'tcltk'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Depends: includes the non-default packages:
  'spatstat.data', 'spatstat.sparse', 'spatstat.geom',
  'spatstat.random', 'spatstat.explore', 'spatstat.model',
  'spatstat.linnet', 'spatstat'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Depends: includes the non-default packages:
  'spatstat.data', 'spatstat.sparse', 'spatstat.geom',
  'spatstat.random', 'spatstat.explore', 'spatstat.model', 'spatstat'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Depends: includes the non-default packages:
  'spatstat.data', 'spatstat.geom', 'spatstat.random',
  'spatstat.explore', 'nlme', 'rpart'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Depends: includes the non-default packages:
  'spatstat.data', 'spatstat.geom', 'spatstat.random',
  'spatstat.explore', 'spatstat.model', 'spatstat.linnet'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Found the following significant warnings:

  Warning in is.R() : 'is.R' is deprecated.
  Warning in is.R() : 'is.R' is deprecated.
  Warning in is.R() : 'is.R' is deprecated.
  Warning in is.R() : 'is.R' is deprecated.
  Warning in is.R() : 'is.R' is deprecated.
  Warning in is.R() : 'is.R' is deprecated.
  Warning in is.R() : 'is.R' is deprecated.
  Warning in is.R() : 'is.R' is deprecated.
  Warning in is.R() : 'is.R' is deprecated.
  Warning in is.R() : 'is.R' is deprecated.
  Warning in is.R() : 'is.R' is deprecated.
  Warning in is.R() : 'is.R' is deprecated.
  Warning in is.R() : 'is.R' is deprecated.
  Warning in is.R() : 'is.R' is deprecated.
  Warning in is.R() : 'is.R' is deprecated.
  Warning in is.R() : 'is.R' is deprecated.
  Warning in is.R() : 'is.R' is deprecated.
  Warning in is.R() : 'is.R' is deprecated.
  Warning in is.R() : 'is.R' is deprecated.
  Warning in is.R() : 'is.R' is deprecated.
  Warning in is.R() : 'is.R' is deprecated.
  Warning in is.R() : 'is.R' is deprecated.
  Warning in is.R() : 'is.R' is deprecated.
  Warning in is.R() : 'is.R' is deprecated.
  Warning in is.R() : 'is.R' is deprecated.
  Warning in is.R() : 'is.R' is deprecated.
  Warning in is.R() : 'is.R' is deprecated.
  Warning in is.R() : 'is.R' is deprecated.
  Warning in is.R() : 'is.R' is deprecated.
  Warning in is.R() : 'is.R' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU (user + system) or elapsed time > 5s
             user system elapsed
SpatDensReg 3.187  0.103   5.392
'LazyData' is specified without a 'data' directory
checkRd: (-1) NEWS.Rd:137: Escaped LaTeX specials: \&
checkRd: (-1) dphat.Rd:25: Lost braces
    25 | These results were heavily used in Krumbholz/Z\"{o}ller (1995) for Shewhart and in Knoth/Steinmetz (2013) for EWMA control charts.
       |                                                 ^
checkRd: (-1) dphat.Rd:38: Lost braces
    38 | W. Krumbholz and A. Z\"{o}ller (1995),
       |                        ^
checkRd: (-1) dphat.Rd:39: Lost braces
    39 | \code{p}-Karten vom Shewhartschen Typ f\"{u}r die messende Pr\"{u}fung,
       |                                          ^
checkRd: (-1) dphat.Rd:39: Lost braces
    39 | \code{p}-Karten vom Shewhartschen Typ f\"{u}r die messende Pr\"{u}fung,
       |                                                                ^
checkRd: (-1) xshewhartrunsrules.arl.Rd:37-38: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) xshewhartrunsrules.arl.Rd:43-44: Lost braces in \itemize; meant \describe ?
Package suggested but not available for checking: ‘spDataLarge’
checkRd: (-1) findRef.Rd:39: Lost braces
    39 | Vu TN, Valkenborg D, Smets K, Verwaest KA, Dommisse R, Lemi\`{e}re F, Verschoren A, Goethals B, Laukens K. (2011) An integrated workflow for robust alignment and simplified quantitative analysis of NMR spectrometry data. BMC Bioinformatics. 2011 Oct 20;12:405.
       |                                                              ^
checkRd: (-1) hClustAlign.Rd:70: Lost braces
    70 | Vu TN, Valkenborg D, Smets K, Verwaest KA, Dommisse R, Lemi\`{e}re F, Verschoren A, Goethals B, Laukens K. (2011) An integrated workflow for robust alignment and simplified quantitative analysis of NMR spectrometry data. BMC Bioinformatics. 2011 Oct 20;12:405.
       |                                                              ^
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Roadmap of specklestar package
'LazyData' is specified without a 'data' directory
checkRd: (-1) FitAkdParameters.Rd:23: Lost braces; missing escapes or markup?
    23 |       p(y|ens) = 1 / K * sum {dnorm(y, z.i, s)} \cr
       |                              ^
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checkRd: (-1) image.plot.Rd:78: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
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Unknown package ‘cooltools’ in Rd xrefs
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Documented arguments not in \usage in Rd file 'i_is_index.Rd':
  ‘max_length’

Documented arguments not in \usage in Rd file 'i_read_asd_spectra.Rd':
  ‘format’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
checkRd: (-1) speech_recompiler.Rd:25: Lost braces; missing escapes or markup?
    25 | The default compilation is that of \ code {speech_build (., compiler = TRUE}).
       |                                           ^
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘.neig’
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    15 | {alpha, alpha_I, beta, gamma}.
       | ^
Objects in \usage without \alias in Rd file 'add_details.Rd':
  ‘\S4method{add_details}{spflow_model}’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
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    61 | nucleotide, so that \code{a.c} represents the set {\code{aac}, \code{acc}, 
       |                                                   ^
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    14 | code{adaptIntegrateBallPolar()} will likely miss these abrupt changes and give
       |     ^
Found the following files/directories:
  ‘AlphaGA_3.txt’ ‘AlphaML_3.txt’ ‘BetaGA_3.txt’ ‘BetaML_3.txt’
  ‘Performance_GA_ML_ 3 .pdf’ ‘SPIGA_3Pmon.Pm_St1.pdf’
  ‘SPIGA_3Pmon.Pm_St2.pdf’ ‘SPI_AG_3.txt’ ‘SPI_ML_3.txt’
  ‘SPI_ML_3Pm_St1.pdf’ ‘SPI_ML_3Pm_St2.pdf’ ‘SPI_ML_3Pm_St3.pdf’
  ‘SPI_ML_3Pm_St4.pdf’ ‘SPI_PARAM_3.txt’ ‘SPI_PARAM_3Pm_St1.pdf’
  ‘SPI_PARAM_3Pm_St2.pdf’ ‘SPI_PARAM_3Pm_St3.pdf’
  ‘SPI_PARAM_3Pm_St4.pdf’
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checkRd: (-1) BVCfit.Rd:71: Lost braces in \itemize; meant \describe ?
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    21 | in the polar coordinate system, r_k and r_{k+1} are the radius of the two loops at theta + 2*pi*a and theta + 2*pi*(a+1) that below and above the data point,
       |                                           ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) wood_inv_solve.Rd:7: Lost braces; missing escapes or markup?
     7 | using the Woodbury formula. The function \code{mmqn_step} invokes \code{wood_inv_solve} instead of {ddg} if the argument
       |                                                                                                    ^
checkRd: (-1) wood_inv_solve.Rd:26: Lost braces; missing escapes or markup?
    26 | using the Woodbury formula. The function \code{mmqn_step} invokes \code{wood_inv_solve} instead of {ddg} if the argument
       |                                                                                                    ^
Invalid package aliases in Rd file 'split_feasibility.Rd':
  ‘split_feasibility-package’
'LazyData' is specified without a 'data' directory
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    16 | \doi{10.1111/add.14071}{Boffo et al., 2018}. Participants were presented stimuli from a "test"
       |                        ^
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    16 | described in detail in \doi{10.1016/j.tate.2019.102887}{Hedge, Powell, and Sumner (2018)}. 
       |                                                        ^
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    19 | \doi{10.1016/j.tate.2019.102887}{Abacioglu and colleagues (2019)}. 
       |                                 ^
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    15 | problems within the last year (\doi{https://doi.org/10.15288/jsa.1989.50.30}{White & Labouvie, 1989}).
       |                                                                             ^
checkRd: (-1) ds_sst.Rd:17: Lost braces
    17 | described in detail in \doi{10.1016/j.tate.2019.102887}{Hedge, Powell, and Sumner (2018)}. 
       |                                                        ^
checkRd: (-1) ds_vpt.Rd:22: Lost braces
    22 | \doi{10.1111/acer.12853}{(Pronk, Deursen, Beraha, Larsen, & Wiers, 2015)}.
       |                         ^
checkRd: (-1) splithalfr.Rd:15: Lost braces
    15 |   \item \code{vignette("rapi_sum")} Sum-score for data of the 23-item version of the Rutgers Alcohol Problem Index (\doi{https://doi.org/10.15288/jsa.1989.50.30}{White & Labouvie, 1989})
       |                                                                                                                                                                  ^
Specified C++11: please drop specification unless essential
checkRd: (-1) softening.optimized.Rd:42-43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) softening.optimized.Rd:44: Lost braces in \itemize; meant \describe ?
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Feature Changes
Specified C++11: please drop specification unless essential
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   118 | rfcv{randomForest} and gbm
       |     ^
checkRd: (-1) gbmokgbmidwcv.Rd:108: Lost braces
   108 | variable and anisotropy parameters. see notes vgm{gstat} for details.
       |                                                  ^
Error(s) in re-building vignettes:
  ...
--- re-building ‘Introduction_to_spnaf.Rmd’ using rmarkdown

Quitting from lines 49-66 [unnamed-chunk-5] (Introduction_to_spnaf.Rmd)
Error: processing vignette 'Introduction_to_spnaf.Rmd' failed with diagnostics:
row.names wrong length
--- failed re-building ‘Introduction_to_spnaf.Rmd’

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

Error: Vignette re-building failed.
Execution halted
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Documented arguments not in \usage in Rd file 'obis_search.Rd':
  ‘scientificname’

Documented arguments not in \usage in Rd file 'spocc_objects.Rd':
  ‘n’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) get_my_currently_playing.Rd:15: Lost braces
    15 | href{https://developer.spotify.com/documentation/general/guides/track-relinking-guide/}{Track Relinking}}
       |     ^
checkRd: (-1) get_my_currently_playing.Rd:15: Lost braces
    15 | href{https://developer.spotify.com/documentation/general/guides/track-relinking-guide/}{Track Relinking}}
       |                                                                                        ^
Documented arguments not in \usage in Rd file 'checkFunEvalsDesignSize.Rd':
  ‘fun’ ‘upper’

Documented arguments not in \usage in Rd file 'print.spotBOModel.Rd':
  ‘object’

Documented arguments not in \usage in Rd file 'print.spotGaussianProcessModel.Rd':
  ‘object’

Documented arguments not in \usage in Rd file 'print.spotLOESS.Rd':
  ‘object’

Documented arguments not in \usage in Rd file 'print.spotLassoModel.Rd':
  ‘object’

Documented arguments not in \usage in Rd file 'print.spotLinearModel.Rd':
  ‘object’

Documented arguments not in \usage in Rd file 'print.spotRSM.Rd':
  ‘object’

Documented arguments not in \usage in Rd file 'print.spotRandomForest.Rd':
  ‘object’

Documented arguments not in \usage in Rd file 'print.spotRanger.Rd':
  ‘object’

Documented arguments not in \usage in Rd file 'print.spotSeverity.Rd':
  ‘object’

Documented arguments not in \usage in Rd file 'print.spotTreeModel.Rd':
  ‘object’

Documented arguments not in \usage in Rd file 'simulationSpectral.Rd':
  ‘...’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    updates of 10th May 2021
Specified C++11: please drop specification unless essential
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     7 | \format{An object of class /code{"list"}.}
       |                                 ^
checkRd: (-1) shypEstFun.Rd:52: Escaped LaTeX specials: \$
checkRd: (-1) shypEstFun.Rd:54: Escaped LaTeX specials: \$
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    27 | The function is Eq. Table 1-C1 in insertRef{Streck.2020}{spsh} using eq 21 which can be used
       |                                            ^
checkRd: (-1) sncFun.01110.Rd:27: Lost braces
    27 | The function is Eq. Table 1-C1 in insertRef{Streck.2020}{spsh} using eq 21 which can be used
       |                                                         ^
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    27 | The function is Eq. Table 1-B in insertRef{Streck.2020}{spsh}
       |                                           ^
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    27 | The function is Eq. Table 1-B in insertRef{Streck.2020}{spsh}
       |                                                        ^
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    27 | The function is Eq. Table 1-A  in insertRef{Streck.2020}{spsh}
       |                                            ^
checkRd: (-1) sncFun.04110.Rd:27: Lost braces
    27 | The function is Eq. Table 1-A  in insertRef{Streck.2020}{spsh}
       |                                                         ^
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    42 | and a matching \code{Qres} list attribute if {Q} was given.
       |                                              ^
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   158 |   the matrix of regressors, of order \emph{(Nxp_{g})}. Moreover, 
       |                                                 ^
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    67 | \item{het}{default {FALSE}: if {TRUE} uses the methods 
       |                    ^
checkRd: (-1) spsurgs3sls.Rd:67: Lost braces; missing escapes or markup?
    67 | \item{het}{default {FALSE}: if {TRUE} uses the methods 
       |                                ^
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
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    29 | Some functions in {spsUtil}, {spsComps} and {systempPipeShiny} will behave
       |                   ^
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    29 | Some functions in {spsUtil}, {spsComps} and {systempPipeShiny} will behave
       |                              ^
checkRd: (-1) spsOption.Rd:29: Lost braces; missing escapes or markup?
    29 | Some functions in {spsUtil}, {spsComps} and {systempPipeShiny} will behave
       |                                             ^
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    36 | \item{...}{Other values "obsData", "fittedData" and "residuals" are provided only for temporal prediction. This is to analyse the code{spTimer} forecast output using package \code{forecast} through function \code{\link{as.forecast.object}}.}
       |                                                                                                                                       ^
Argument items with no description in Rd file 'sim.kong.Rd':
  ‘gamma’ ‘beta’ ‘design’ ‘rho’ ‘seed’ ‘impute’ ‘ppi’
'LazyData' is specified without a 'data' directory
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   248 | and code{port} arguments of sqldf.
       |         ^
'LazyData' is specified without a 'data' directory
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    55 |     \code{tol}{ - a small, positive scalar that determines when iterations 
       |               ^
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    60 |     \code{maxiter}{ - an integer denoting the maximum limit on the number of 
       |                   ^
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    63 |     \code{trace}{ - a logical variable denoting whether some of the intermediate 
       |                 ^
checkRd: (-1) fpiter.Rd:67-70: Lost braces
    67 |     \code{intermed}}{ - a logical variable denoting whether the intermediate 
       |                     ^
checkRd: (-1) squarem.Rd:134: Lost braces
   134 |       along with the corresponding log-likelihood value.  When the code{objfn} is not specified it will return the fixed-point residual instead of the objective function values. 
       |                                                                        ^
checkRd: (-1) squidR.Rd:83: Lost braces; missing escapes or markup?
    83 |   \item \code{X1_sto_shared} (default \code{TRUE}): {logical}; if \code{TRUE}, the stochastic environmental effect included in the environmental effect x1 will be shared between individuals. If \code{FALSE}, each individual will experience a different stochastic environmental effect x1 (i.e. a new stochastic environmental effect is generated for each individual).
       |                                                     ^
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    33 | Otherwise, if {pdim=TRUE}, the pxp SSCM is computed, and then from the SSCM an estimator of the correlation matrix, which is done by the function \code{\link{SSCM2Shape}}, see there for details.
       |               ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
checkRd: (-1) new.distance.Rd:30: Lost braces in \itemize; meant \describe ?
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'LazyData' is specified without a 'data' directory
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Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) readratdatafixed.Rd:25: Lost braces; missing escapes or markup?
    25 | number of the set {1, 2, 3}, {1..5}, {1..7} or {1..9}. When there are 10
       |                   ^
checkRd: (-1) readratdatafixed.Rd:25: Lost braces; missing escapes or markup?
    25 | number of the set {1, 2, 3}, {1..5}, {1..7} or {1..9}. When there are 10
       |                              ^
checkRd: (-1) readratdatafixed.Rd:25: Lost braces; missing escapes or markup?
    25 | number of the set {1, 2, 3}, {1..5}, {1..7} or {1..9}. When there are 10
       |                                      ^
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    25 | number of the set {1, 2, 3}, {1..5}, {1..7} or {1..9}. When there are 10
       |                                                ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) SRanalysis.Rd:100: Lost braces
   100 |   P. B{\"u}hlmann (2019). Stabilizing Variable Selection and
       |       ^
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   109 |   P. B{\"u}hlmann (2019). Stabilizing Variable Selection and
       |       ^
'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
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    42 |     always use code{"none"}.}
       |                    ^
checkRd: (-1) stabsel_stabsel.Rd:25: Lost braces
    25 |     always use code{"none"}.}
       |                    ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) stackExample.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) stackExample.Rd:11: Lost braces in \itemize; meant \describe ?
Documented arguments not in \usage in Rd file 'connect-report_mig-method.Rd':
  ‘h’ ‘...’

Documented arguments not in \usage in Rd file 'print-report_mig-method.Rd':
  ‘h’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
checkRd: (-1) stamppFst.Rd:20: Lost braces
    20 | \code{Fsts}{a matrix of pairwise Fst values between populations}
       |            ^
checkRd: (-1) stamppFst.Rd:21: Lost braces
    21 | \code{Pvalues}{a matrix of p-values for each of the pairwise Fst values containined in the 'Fsts' matrix}
       |               ^
checkRd: (-1) stamppFst.Rd:22: Lost braces
    22 | \code{Bootstraps}{a dataframe of each Fst value generated during Bootstrapping and the associated confidence intervals}
       |                  ^
checkRd: (-1) standardize.Rd:94: Lost braces; missing escapes or markup?
    94 | take on values {-0.5, 0, 0.5} rather than {-1, 0, 1}, the standard deviation
       |                ^
checkRd: (-1) standardize.Rd:94: Lost braces; missing escapes or markup?
    94 | take on values {-0.5, 0, 0.5} rather than {-1, 0, 1}, the standard deviation
       |                                           ^
checkRd: (-1) alertify.Rd:69: Lost braces
    69 | \item{closable}{Logical; if \code{TRUE} (the default), a |code{Close} button is displayed in the header of the dialog.}
       |                                                               ^
checkRd: (-1) notify.Rd:47: Lost braces
    47 | \item{hide}{Logical; if \code{TRUE} (the default), notice is closed after |code{delay} specified in milliseconds.}
       |                                                                                ^
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
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) abs_parms.Rd:67: Lost braces; missing escapes or markup?
    67 |    \item $S_{275-295}$ slope between 275 and 295 nm calculated with nonlinear regression
       |             ^
checkRd: (-1) abs_parms.Rd:68: Lost braces; missing escapes or markup?
    68 |    \item $S_{350-400}$ slope between 350 and 400 nm calculated with nonlinear regression
       |             ^
checkRd: (-1) abs_parms.Rd:69: Lost braces; missing escapes or markup?
    69 |    \item $S_{300-700}$ slope between 275 and 295 nm calculated with nonlinear regression
       |             ^
checkRd: (-1) abs_parms.Rd:70: Lost braces; missing escapes or markup?
    70 |    \item SR slope ratio, calculated by $S_{275-295}$/$S_{350-400}$
       |                                           ^
checkRd: (-1) abs_parms.Rd:70: Lost braces; missing escapes or markup?
    70 |    \item SR slope ratio, calculated by $S_{275-295}$/$S_{350-400}$
       |                                                         ^
checkRd: (-1) abs_parms.Rd:71: Lost braces; missing escapes or markup?
    71 |    \item E2:E3 ratio $a_{250}$/$a_{365}$
       |                         ^
checkRd: (-1) abs_parms.Rd:71: Lost braces; missing escapes or markup?
    71 |    \item E2:E3 ratio $a_{250}$/$a_{365}$
       |                                   ^
checkRd: (-1) abs_parms.Rd:72: Lost braces; missing escapes or markup?
    72 |    \item E4:E6 ratio $a_{465}$/$a_{665}$
       |                         ^
checkRd: (-1) abs_parms.Rd:72: Lost braces; missing escapes or markup?
    72 |    \item E4:E6 ratio $a_{465}$/$a_{665}$
       |                                   ^
checkRd: (-1) abs_parms.Rd:73: Lost braces; missing escapes or markup?
    73 |    \item $a_{254}$ absorbance at 254 nm
       |             ^
checkRd: (-1) abs_parms.Rd:74: Lost braces; missing escapes or markup?
    74 |    \item $a_{300}$ absorbance at 300 nm
       |             ^
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.}
       |                                                                         ^
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘starsdata’
checkRd: (-1) multiCUMSUM.Rd:33: Escaped LaTeX specials: \&
checkRd: (-1) AutoPollution.Rd:16: Lost braces
    16 |     \code{Side} \tab {Side of vehicle: code{1}=right or \code{2}=left}\cr
       |                                            ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) statcan_data.Rd:22: Lost braces; missing escapes or markup?
    22 | \code{statcan_data()} function has 2 arguments to fulfill to get data: {tableNumber} & {lang}.
       |                                                                        ^
checkRd: (-1) statcan_data.Rd:22: Lost braces; missing escapes or markup?
    22 | \code{statcan_data()} function has 2 arguments to fulfill to get data: {tableNumber} & {lang}.
       |                                                                                        ^
checkRd: (-1) statcan_search.Rd:18: Lost braces; missing escapes or markup?
    18 | The \code{statcan_search()} function has 2 arguments to fulfill to find a database: {keywords} and {lang}.
       |                                                                                     ^
checkRd: (-1) statcan_search.Rd:18: Lost braces; missing escapes or markup?
    18 | The \code{statcan_search()} function has 2 arguments to fulfill to find a database: {keywords} and {lang}.
       |                                                                                                    ^
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘asreml’
Package suggested but not available for checking: ‘asreml’
checkRd: (-1) plot.QTLMPP.Rd:33-34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.QTLMPP.Rd:35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.QTLMPP.Rd:36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.QTLMPP.Rd:37-38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.gDataMPP.Rd:40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.gDataMPP.Rd:41-42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.gDataMPP.Rd:43-44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.gDataMPP.Rd:45-46: Lost braces in \itemize; meant \describe ?
Package suggested but not available for checking: ‘asreml’
'LazyData' is specified without a 'data' directory
Package vignette with \VignetteEngine{} not specifying an engine package:
  ‘stationery.Rnw’
Engines should be specified as \VignetteEngine{PKG::ENG}.
'LazyData' is specified without a 'data' directory
Found the following possibly unsafe calls:
File ‘statnet.common/R/control.utilities.R’:
  unlockBinding("snctrl", environment(snctrl))
  unlockBinding("snctrl", environment(update_my_snctrl))
Package suggested but not available for checking: ‘networksis’
There are updates for the following statnet packages on CRAN:
          Installed ReposVer Built  
latentnet "2.10.6"  "2.11.0" "4.4.0"
Restart R and use "statnet::update_statnet()" to get the updates.

It looks like this package (or a package it requires) has a startup
message which cannot be suppressed: see ?packageStartupMessage.
'LazyData' is specified without a 'data' directory
checkRd: (-1) sp_get_codelist_file.Rd:29: Lost braces; missing escapes or markup?
    29 | finer-grained control of intermediate outputs is needed, e.g. in a {targets} workflow.
       |                                                                    ^
checkRd: (-1) sp_get_codelist_url.Rd:19: Lost braces; missing escapes or markup?
    19 | finer-grained control of intermediate outputs is needed, e.g. in a {targets} workflow.
       |                                                                    ^
checkRd: (-1) sp_get_table_file.Rd:21: Lost braces; missing escapes or markup?
    21 | finer-grained control of intermediate outputs is needed, e.g. in a {targets} workflow.
       |                                                                    ^
checkRd: (-1) sp_load_codelist.Rd:19: Lost braces; missing escapes or markup?
    19 | finer-grained control of intermediate outputs is needed, e.g. in a {targets} workflow.
       |                                                                    ^
checkRd: (-1) sp_load_table.Rd:19: Lost braces; missing escapes or markup?
    19 | finer-grained control of intermediate outputs is needed, e.g. in a {targets} workflow.
       |                                                                    ^
'LazyData' is specified without a 'data' directory
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)}
       |                                            ^
Package suggested but not available for checking: ‘imputeMissings’
checkRd: (-1) rankSTB.Rd:31: Lost braces; missing escapes or markup?
    31 | are transformed to min. rank-values. In step 6) the "N_{k-1}-(1-alpha)*N largest" elements of "d_{l}^{theta}" have to
       |                                                        ^
checkRd: (-1) rankSTB.Rd:31: Lost braces; missing escapes or markup?
    31 | are transformed to min. rank-values. In step 6) the "N_{k-1}-(1-alpha)*N largest" elements of "d_{l}^{theta}" have to
       |                                                                                                  ^
checkRd: (-1) rankSTB.Rd:31: Lost braces; missing escapes or markup?
    31 | are transformed to min. rank-values. In step 6) the "N_{k-1}-(1-alpha)*N largest" elements of "d_{l}^{theta}" have to
       |                                                                                                      ^
checkRd: (-1) stb.default.Rd:43: Lost braces
    43 | sampling from the standard normal distribution. Another example is defining func=function(n){rchisq(n=n, df=3, ncp=2)}
       |                                                                                             ^
checkRd: (-1) stdGlm.Rd:93: Escaped LaTeX specials: \&
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checkRd: (-1) keypoints.Rd:63-65: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) keypoints.Rd:66-67: Lost braces in \enumerate; meant \describe ?
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) STEPCAM_ABC.Rd:19: Lost braces
    19 |   \code{rows}{ every row corresponds to a different plot or community} \cr
       |              ^
checkRd: (-1) STEPCAM_ABC.Rd:20: Lost braces
    20 |   \code{columns}{ every column corresponds to a different species.} \cr
       |                 ^
checkRd: (-1) STEPCAM_ABC.Rd:25: Lost braces
    25 |   \code{rows}{ every row corresponds to a different species} \cr
       |              ^
checkRd: (-1) STEPCAM_ABC.Rd:26: Lost braces
    26 |   \code{columns}{ the first column contains the name of the species, every consecutive column corresponds to a different trait} \cr
       |                 ^
checkRd: (-1) plotSTEPCAM.Rd:16: Lost braces
    16 |             - \code{DA}{ a vector containing the posterior distribution for the parameter dispersal assembly} \cr
       |                        ^
checkRd: (-1) plotSTEPCAM.Rd:17: Lost braces
    17 |             - \code{HF}{ a vector containing the posterior distribution for the parameter habitat filtering} \cr
       |                        ^
checkRd: (-1) plotSTEPCAM.Rd:18: Lost braces
    18 |             - \code{LS}{ a vector containing the posterior distribution for the parameter limiting similarity} \cr
       |                        ^
checkRd: (-1) tuneParam.Rd:28: Lost braces; missing escapes or markup?
    28 | It supports the BFGS optimization method ('QN') from the optim {stats} function, the Hooke-Jeeves derivative-free
       |                                                                ^
checkRd: (-1) tuneParamCL2.Rd:28: Lost braces; missing escapes or markup?
    28 | It supports the BFGS optimization method ('QN') from the optim {stats} function, the Hooke-Jeeves derivative-free
       |                                                                ^
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
checkRd: (-1) landmarkMatrixToList.Rd:10: Lost braces
    10 |   \item{semilandmark.pattern}{a regular expression pattern passed to \code{sub()} for identifying and grouping curve points. The default is landmark names ending in one or more numbers. To disable grouping, set to code{''}.}
       |                                                                                                                                                                                                                           ^
checkRd: (-1) docker_config_collection.Rd:11: Lost braces; missing escapes or markup?
    11 | \Sexpr[results=rd,stage=render]{stevedore:::generate_help("config")}
       | ^
checkRd: (-1) docker_container.Rd:13: Lost braces
    13 | \Sexpr[results=rd,stage=render]{stevedore:::generate_help("docker_container")}
       | ^
checkRd: (-1) docker_image_collection.Rd:11: Lost braces
    11 | \Sexpr[results=rd,stage=render]{stevedore:::generate_help("image")}
       | ^
checkRd: (-1) docker_plugin_collection.Rd:11: Lost braces
    11 | \Sexpr[results=rd,stage=render]{stevedore:::generate_help("plugin")}
       | ^
checkRd: (-1) docker_service_collection.Rd:11: Lost braces
    11 | \Sexpr[results=rd,stage=render]{stevedore:::generate_help("service")}
       | ^
checkRd: (-1) docker_task.Rd:13: Lost braces
    13 | \Sexpr[results=rd,stage=render]{stevedore:::generate_help("docker_task")}
       | ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘corrviz.html’
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Argument items with no description in Rd file 'd.sum.of.mixtures.EXPLN.Rd':
  ‘p.vector’
Malformed Title field: should not end in a period.
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checkRd: (-1) geo_toptail.Rd:26: Lost braces; missing escapes or markup?
    26 | in {stplanr} v0.8.5 for an implementation that uses the geosphere
       |    ^
checkRd: (-1) powderymildew.Rd:14-16: Lost braces
    14 | \code{$demographic.coord}{
       |                          ^
checkRd: (-1) powderymildew.Rd:18-20: Lost braces
    18 | \code{$genetic.coord}{
       |                      ^
checkRd: (-1) powderymildew.Rd:22-24: Lost braces
    22 | \code{$demographic.measures}{
       |                             ^
checkRd: (-1) powderymildew.Rd:26-28: Lost braces
    26 | \code{$genetic.frequencies}{
       |                            ^
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘myNewStrat.R’
Package suggested but not available for checking: ‘StrathE2E2examples’
checkRd: (-1) StrathE2E2-package.Rd:70: Lost braces; missing escapes or markup?
    70 | {Basic model operations:} \cr
       | ^
checkRd: (-1) StrathE2E2-package.Rd:79: Lost braces; missing escapes or markup?
    79 | {Parameter estimation:} \cr
       | ^
checkRd: (-1) StrathE2E2-package.Rd:88: Lost braces; missing escapes or markup?
    88 | {Sensitivity and Monte Carlo analyses:} \cr
       | ^
checkRd: (-1) StrathE2E2-package.Rd:98: Lost braces; missing escapes or markup?
    98 | {Compare model runs:} \cr
       | ^
checkRd: (-1) StrathE2E2-package.Rd:105: Lost braces; missing escapes or markup?
   105 | {Fishery yield analysis:} \cr
       | ^
checkRd: (-1) StrathE2E2-package.Rd:111: Lost braces; missing escapes or markup?
   111 | {Visualize model inputs:} \cr
       | ^
checkRd: (-1) StrathE2E2-package.Rd:117: Lost braces; missing escapes or markup?
   117 | {Visualize model outputs:} \cr
       | ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) isle.Rd:38: Lost braces
    38 | \code{\link[streamDAG]{stream.order}}, \code{\link[igraph]{delete.vertices}}, code{\link[igraph]{add.vertices}}, code{\link[igraph]{add.edges}}
       |                                                                                   ^
checkRd: (-1) isle.Rd:38: Lost braces
    38 | \code{\link[streamDAG]{stream.order}}, \code{\link[igraph]{delete.vertices}}, code{\link[igraph]{add.vertices}}, code{\link[igraph]{add.edges}}
       |                                                                                                                      ^
Malformed Title field: should not end in a period.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'get_groups.Rd':
  ‘groups’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
checkRd: (-1) string_magic.Rd:176: Lost braces; missing escapes or markup?
   176 | each of them. Do you think we can do that? Of course yes: string_magic("hello {upper, ''s, c ? x}"). And that's it.
       |                                                                               ^
checkRd: (-1) string_magic.Rd:186: Lost braces; missing escapes or markup?
   186 | The syntax is always the same: {operations ? expression}, where the operations section
       |                                ^
checkRd: (-1) string_magic.Rd:213: Lost braces; missing escapes or markup?
   213 | expression only begins after it. Ex: "{upper! hi}" leads to " HI" while \code{"{upper ! hi}"}
       |                                       ^
checkRd: (-1) string_magic.Rd:751: Lost braces
   751 | Ex.3: string_magic("I {'can {write} {{what}} I want'}") leads to \code{"I can {write} {{what}} I want"}.
       |                       ^
checkRd: (-1) string_magic.Rd:751: Lost braces; missing escapes or markup?
   751 | Ex.3: string_magic("I {'can {write} {{what}} I want'}") leads to \code{"I can {write} {{what}} I want"}.
       |                             ^
checkRd: (-1) string_magic.Rd:751: Lost braces
   751 | Ex.3: string_magic("I {'can {write} {{what}} I want'}") leads to \code{"I can {write} {{what}} I want"}.
       |                                     ^
checkRd: (-1) string_magic_alias.Rd:98: Lost braces
    98 | if you want the interpolation to be done with "{{}}" (instead of \code{{}}) or if you want the
       |                                                ^
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'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘STRaitRazoR’
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) Grossarl.Rd:53: Lost braces
    53 | \emph{Festschrift 50 Jahre \"{O}sterreichische Statistische Gesellschaft}, 133-146,
       |                              ^
checkRd: (-1) Grossarl.Rd:54: Lost braces
    54 | \"{O}sterreichische Statistische Gesellschaft.
       |   ^
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checkRd: (-1) SP2001.Rd:5: Escaped LaTeX specials: \&
checkRd: (-1) SP2001.Rd:12: Escaped LaTeX specials: \&
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   223 | Zeileis A., Kleiber C., Kr\"{a}mer W., Hornik K. (2003), Testing and Dating of
       |                             ^
checkRd: (-1) efp.Rd:109: Lost braces
   109 | Kr\"{a}mer W., Ploberger W., Alt R. (1988), Testing for structural change in
       |     ^
checkRd: (-1) efp.Rd:119: Lost braces
   119 | Ploberger W., Kr\"{a}mer W. (1992), The CUSUM test with OLS residuals,
       |                   ^
Specified C++11: please drop specification unless essential
Invalid package aliases in Rd file 'StructFDR-package.Rd':
  ‘TreeFDR-package’
checkRd: (-1) calculateStatistics.Rd:22: Lost braces; missing escapes or markup?
    22 | \item{quant}{numeric quantile to calculate {0,1}, default 0.95.}
       |                                            ^
checkRd: (-1) cmss.Rd:21: Lost braces
    21 | \item{sim.fn}{Optional function to be used as similarity measure for accept/reject step. Default function is: |cor( bar{x}^{(r)}|,~ bar{x}_{target} ) |}
       |                                                                                                                        ^
checkRd: (-1) cmss.Rd:21: Lost braces; missing escapes or markup?
    21 | \item{sim.fn}{Optional function to be used as similarity measure for accept/reject step. Default function is: |cor( bar{x}^{(r)}|,~ bar{x}_{target} ) |}
       |                                                                                                                            ^
checkRd: (-1) cmss.Rd:21: Lost braces
    21 | \item{sim.fn}{Optional function to be used as similarity measure for accept/reject step. Default function is: |cor( bar{x}^{(r)}|,~ bar{x}_{target} ) |}
       |                                                                                                                                        ^
checkRd: (-1) cmss.Rd:21: Lost braces; missing escapes or markup?
    21 | \item{sim.fn}{Optional function to be used as similarity measure for accept/reject step. Default function is: |cor( bar{x}^{(r)}|,~ bar{x}_{target} ) |}
       |                                                                                                                                            ^
'LazyData' is specified without a 'data' directory
S3 methods shown with full name in Rd file 'size.penalize.Rd':
  ‘size.penalize’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
checkRd: (-1) subdetect-package.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) subdetect-package.Rd:12: Lost braces in \itemize; meant \describe ?
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Documented arguments not in \usage in Rd file 'subsamp.Rd':
  ‘x:’ ‘y:’ ‘s:’ ‘m:’ ‘qnum:’ ‘wplot:’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
checkRd: (-1) P3C.Rd:18: Lost braces; missing escapes or markup?
    18 |  used for this will be 1.00*10^{-PoissonThreshold}.}
       |                                ^
Package suggested but not available for checking: ‘vlad’
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checkRd: (-1) fp19.Rd:12-13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fp19.Rd:14: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) fp19.Rd:23-24: Lost braces in \itemize; meant \describe ?
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    14 | {suggests} aims to make that workflow as minimal and painless as possible,
       | ^
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checkRd: (-1) plot.SUMMERproj.Rd:62: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.SUMMERproj.Rd:63: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.SUMMERproj.Rd:64: Lost braces in \itemize; meant \describe ?
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:[];}`}
       |                                                                                                     ^
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    22 | nested d3 JSON hierarchy with `{name:...,  children:[];}`.  \code{list}, \code{character},
       |                                ^
Auto-generated content requiring editing in Rd file 'supcluster-package.Rd':
  \references: ‘~~ Literature or other references for background information ~~’
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checkRd: (-1) plot.supc.Rd:13: Lost braces in \itemize; meant \describe ?
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    19 |     \item{\code{Number}:}{code{"numeric"}, number of biclusters in the set}
       |                               ^
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    42 |  \item{color.off}{color code; specifying the color for set(s) which are "{absent}" for an intersection.}
       |                                                                          ^
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checkRd: (-1) SL.bartMachine.Rd:41: Lost braces; missing escapes or markup?
    41 | contained in the interval (y_{min}, y_{max}), based on a normal
       |                              ^
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    41 | contained in the interval (y_{min}, y_{max}), based on a normal
       |                                       ^
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     5 | \title{cforest {party}}
       |                ^
Unknown package ‘extraTrees’ in Rd xrefs
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     6 | getFittedValues <- function(object) {
       |                                     ^
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    14 | getFittedValues <- function(object) {
       |                                     ^
surfaceSimulate : phytransform: no visible global function definition
  for ‘rescale’
Undefined global functions or variables:
  rescale
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GNU make is a SystemRequirements.
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    58 | quantile interval; \code{"hf1"} to {"hf9"} are weighted analogues of
       |                                    ^
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    19 | using \link{set.seed} as usual but also in {numpy} and {torch} via {reticulate}.
       |                                            ^
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    19 | using \link{set.seed} as usual but also in {numpy} and {torch} via {reticulate}.
       |                                                        ^
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    19 | using \link{set.seed} as usual but also in {numpy} and {torch} via {reticulate}.
       |                                                                    ^
Unknown package ‘distr6’ in Rd xrefs
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    24 | \item{mpl_h0t}{MPL estimates of the baseline hazard for T, i.e. h_{0T}(x_i)}
       |                                                                   ^
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    25 | \item{mpl_h0c}{MPL estimates of the baseline hazard for C, i.e. h_{0C}(x_i)}
       |                                                                   ^
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    26 | \item{mpl_H0t}{MPL estimates of the baseline cumulative hazard for T, i.e. H_{0T}(x_i)}
       |                                                                              ^
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    27 | \item{mpl_H0c}{MPL estimates of the baseline cumulative hazard for C, i.e. H_{0c}(x_i)}
       |                                                                              ^
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    28 | \item{mpl_S0t}{MPL estimates of the baseline survival for T, i.e. S_{0T}(x_i)}
       |                                                                     ^
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    29 | \item{mpl_S0c}{MPL estimates of the baseline survival for C, i.e. S_{0C}(x_i)}
       |                                                                     ^
Specified C++11: please drop specification unless essential
Unknown package ‘survJamda’ in Rd xrefs
Error(s) in re-building vignettes:
  ...
--- re-building ‘SurvMetrics-vignette.Rmd’ using rmarkdown
Could not fetch http://www.zotero.org/styles/association-for-computing-machinery
HttpExceptionRequest Request {
  host                 = "www.zotero.org"
  port                 = 80
  secure               = False
  requestHeaders       = []
  path                 = "/styles/association-for-computing-machinery"
  queryString          = ""
  method               = "GET"
  proxy                = Nothing
  rawBody              = False
  redirectCount        = 10
  responseTimeout      = ResponseTimeoutDefault
  requestVersion       = HTTP/1.1
  proxySecureMode      = ProxySecureWithConnect
}
 (InternalException (HandshakeFailed (Error_Protocol "peer does not support Extended Main Secret" HandshakeFailure)))
Error: processing vignette 'SurvMetrics-vignette.Rmd' failed with diagnostics:
pandoc document conversion failed with error 61
--- failed re-building ‘SurvMetrics-vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
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    66 | A {data.table} which is stored as an attribute of
       |   ^
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    79 | estimating coefficients for the Super Learner, defaults to \code{"method.NNLS"}), code{stratifyCV}
       |                                                                                       ^
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    87 | estimate the survival function of \code{tau - time}. Defaults to code{NULL},
       |                                                                      ^
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    68 | code{stratifyCV} (logical indicating whether to stratify by outcome in \code{SuperLearner}'s cross-validation
       |     ^
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    75 | estimate the survival function of \code{tau - time}. Defaults to code{NULL},
       |                                                                      ^
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
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    76 | The estimation procedure here is performed using coxph {survival} and inserting these estimated
       |                                                        ^
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    24 | set, svKomodo loads {svSocket}, starts the socket server listening to the
       |                     ^
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    18 | Komodo and (2) the present {svKomodo} R package that work hand in hand to
       |                            ^
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    28 | Nevertheless, the SciViews-K Komodo addin and the {svKomodo} R package
       |                                                   ^
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    31 | communication protocols developed in the {svSocket} and {svHttp} R packages.
       |                                          ^
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    31 | communication protocols developed in the {svSocket} and {svHttp} R packages.
       |                                                         ^
checkRd: (-1) svKomodo-package.Rd:37: Lost braces; missing escapes or markup?
    37 | Both SciViews-K and {svKomodo} should be considered archived items. I keep
       |                     ^
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checkRd: (-1) svSocket-package.Rd:12: Lost braces; missing escapes or markup?
    12 | The SciViews {svSocket} package provides a stateful, multi-client and
       |              ^
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    16 | thus, it needs a working version of Tcl/Tk (>= 8.4) and of the {tcltk} R
       |                                                                ^
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    33 | efficient as, say {Rserver} ({Rserver} exchanges R objects in binary format,
       |                   ^
checkRd: (-1) svSocket-package.Rd:33: Lost braces; missing escapes or markup?
    33 | efficient as, say {Rserver} ({Rserver} exchanges R objects in binary format,
       |                              ^
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    34 | but {Rserver} is not stateful, clients do not share the same global workspace
       |     ^
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    32 | \code{\link[survey:surveysummary]{survey::svymean()}} and related functions from the {survey}
       |                                                                                      ^
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checkRd: (-1) swDsn.Rd:28: Lost braces
    28 | numeric (scalar or vector): Relative treatment effect upon crossing over from control. Note that this is not the treatment effect (the treatment effect is specified in the call to other functions such as \code{swPwr} or \code{swSim})!  If \code{tx.effect.frac} is set to a scalar with value of 1, the standard SW CRT treatment effect will be presumed. If code{tx.effect.frac} is set to a scalar with a fractional value between 0 and 1, then only the first time point upon crossing over from control will have fractional relative treatment effect; the remaining exposure times will have a relative treatment effect of 1. If a vector of fractional treatment effect is specified, each element of the vector corresponds to the (fractional) treatment effect upon crossing over from control; if the length of the vector is less than total number of exposure times, the remaining time points will have a relative treatment effect value of 1; if the length of the vector is greater than total number of time points after crossing over, not all elements of \code{tx.effect.frac} will be used. The default value is (scalar) 1.
       |                                                                                                                                                                                                                                                                                                                                                                        ^
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Package suggested but not available for checking: ‘swephRdata’
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Additional functions and data sets
    Amendments to functions
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    pre-release switchboard (2020 - 2021)
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Packages suggested but not available for checking: 'sylly.de', 'sylly.es'
checkRd: (-1) kRp.hyphen-methods.Rd:84: Lost braces in \itemize; meant \describe ?
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    18 |   \item{epsilon}{positive convergence tolerance \emph{e}; the iterations converge when |fit - fit_{old}|/|fit| < \emph{e}. Default is \emph{e=1e-04}.}
       |                                                                                                   ^
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Package suggested but not available for checking: ‘odeintr’
Error(s) in re-building vignettes:
  ...
--- re-building ‘odesystem.Rmd’ using rmarkdown

Quitting from lines 72-78 [unnamed-chunk-4] (odesystem.Rmd)
Error: processing vignette 'odesystem.Rmd' failed with diagnostics:
'odeintr' package needs to be installed for this functionality
--- failed re-building ‘odesystem.Rmd’

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

SUMMARY: processing the following file failed:
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Error: Vignette re-building failed.
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    14 | \code{n} x 4 matrix of coordinates consisting of {lat or y, lon or x} pairs for each each site
       |                                                  ^
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    28 | before plotting {ex: \code{trans = c(s = "exp", d = "exp")}}/}
       |                 ^
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'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘test.csv’
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'table_params_circle.Rd':
  ‘d’

Documented arguments not in \usage in Rd file 'table_params_rect.Rd':
  ‘d’ ‘scale_breaks’ ‘r_max’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
checkRd: (-1) table_ester.Rd:32: Lost braces; missing escapes or markup?
    32 | inside of curly brackets, i.e., { } . For instance, if estimate = 1.23
       |                                 ^
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    33 | and error = 0.45, then \code{form} = "{estimate} ({error})" will return
       |                                       ^
checkRd: (-1) table_ester.Rd:33: Lost braces; missing escapes or markup?
    33 | and error = 0.45, then \code{form} = "{estimate} ({error})" will return
       |                                                   ^
checkRd: (-1) tmCtypes.Rd:22: Escaped LaTeX specials: \#
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    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)")}.}
       |       ^
Specified C++11: please drop specification unless essential
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checkRd: (-1) parse_logs.Rd:38: Lost braces
    38 |  '{{ip ip_address}} [{{date access_date}}]...'.
       |   ^
checkRd: (-1) parse_logs.Rd:38: Lost braces
    38 |  '{{ip ip_address}} [{{date access_date}}]...'.
       |                      ^
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
S3 methods shown with full name in Rd file 'designMatrices.Rd':
  ‘print.designMatrices’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
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checkRd: (-1) SKPar.Rd:36: Lost braces in \itemize; meant \describe ?
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   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.
       |                                                                                   ^
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'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'default_db_ref.Rd':
  ‘name’ ‘url’ ‘desc’ ‘id_regex’

Documented arguments not in \usage in Rd file 'limited_print.Rd':
  ‘trunc’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
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checkRd: (-1) mean_ci.Rd:24: Lost braces
    24 | \item{na.rm}{logical code{TRUE/FALSE}. Remove NAs from the dataset. Defaults
       |                          ^
checkRd: (-1) median_ci.Rd:24: Lost braces
    24 | \item{na.rm}{logical code{TRUE/FALSE}. Remove NAs from the dataset. Defaults
       |                          ^
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}.}
       |                                                                                                                                                                                                                                                                                                                                                  ^
'LazyData' is specified without a 'data' directory
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Malformed Description field: should contain one or more complete sentences.
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GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Found the following significant warnings:
  /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/math/tools/config.hpp:23:6: warning: #warning before C++23 is a GCC extension
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/teachingApps.Rcheck/00install.out’ for details.
* used C++ compiler: ‘g++-13 (Debian 13.2.0-13) 13.2.0’
Specified C++11: please drop specification unless essential
checkRd: (-1) teachingApp.Rd:66: Lost braces
    66 | code{link{create_logo}}
       |     ^
checkRd: (-1) teachingApp.Rd:66: Lost braces
    66 | code{link{create_logo}}
       |          ^
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    68 | code{link{add_logo}}
       |     ^
checkRd: (-1) teachingApp.Rd:68: Lost braces
    68 | code{link{add_logo}}
       |          ^
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘R2wd’
checkRd: (-1) crossEntropy.Rd:32: Lost braces
    32 | link{squaredError}
       |     ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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checkRd: (-1) sendChatAction.Rd:17: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) sendChatAction.Rd:25: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
'LazyData' is specified without a 'data' directory
checkRd: (-1) tcata.line.plot.Rd:72: Lost braces; missing escapes or markup?
    72 | \item{las}{numeric in {0,1,2,3}; the style of the axis labels. See \code{\link[graphics]{par}}.}
       |                       ^
checkRd: (-1) tds.plot.Rd:27: Lost braces; missing escapes or markup?
    27 | \item{las}{numeric in {0,1,2,3}; the style of the axis labels. See: \code{\link[graphics]{par}}}
       |                       ^
checkRd: (-1) Tendril.Rd:53: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Tendril.Rd:54: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Tendril.Rd:55: Lost braces in \itemize; \value handles \item{}{} directly
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checkRd: (-1) Tendril.Rd:57: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Tendril.Rd:58: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Tendril.Rd:59: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Tendril.Rd:60: Lost braces in \itemize; \value handles \item{}{} directly
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checkRd: (-1) Tendril.Rd:63: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Tendril.Rd:64: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Tendril.Rd:65: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Tendril.Rd:66: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Tendril.Rd:67: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
checkRd: (-1) tenFM.rank.Rd:31: Lost braces; missing escapes or markup?
    31 | \item{penalty}{takes value in {1,2,3,4,5}, decides which penalty function to use for each tesnor mode \eqn{k}. Here \eqn{\nu} is a tuning parameter defined in the argument "\code{delta1}", and \eqn{d=\prod_{i=1}^{K} d_k }.
       |                               ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) NEWS.Rd:427: Lost braces; missing escapes or markup?
   427 |       \item  Changes to \code{simulate.stergm} parameters: addition of \code{duration.dependent} parameter: {Logical: Whether the model terms in formula or model are duration dependent. E.g., if a duration-dependent term  is used in estimation/simulation model, the probability of forming or dissolving a tie may dependent on the age the dyad status. If TRUE, the matrix of tie ages will be allocated.}
       |                                                                                                             ^
checkRd: (-1) discordBDStratTNT-ergmProposal-9267ec8b.Rd:18: Lost braces
    18 | code{\link[ergm:blocks-ergmConstraint]{blocks}} constraints and
       |     ^
checkRd: (-1) discordTNT-ergmProposal-bc75dff0.Rd:9: Lost braces
     9 | code{discordance_fraction} of proposed toggles being made on the set of discordant dyads,
       |     ^
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) MC_CRUDE.Rd:19: Lost braces; missing escapes or markup?
    19 | \item{lsf}{objective function with limit state function in form of function(x) {x[1]+x[2]...}}
       |                                                                                ^
checkRd: (-1) MC_IS.Rd:23: Lost braces; missing escapes or markup?
    23 | \item{lsf}{objective function with limit state function in form of function(x) {x[1]+x[2]...}}
       |                                                                                ^
checkRd: (-1) PROB_BASEVAR-class.Rd:14: Lost braces
    14 | \item{\code{Id}}{Place in vector of objective functional expression function(x){x[id]}}
       |                                                                                ^
checkRd: (-1) PROB_DETVAR-class.Rd:14: Lost braces
    14 | \item{\code{Id}}{Place in vector of objective functional expression function(x){x[id]}}
       |                                                                                ^
checkRd: (-1) SORM.Rd:10: Lost braces; missing escapes or markup?
    10 | \item{lsf}{objective function with limit state function in form of function(x) {x[1]+x[2]...}}
       |                                                                                ^
checkRd: (-1) SYS_LSF-class.Rd:16: Lost braces
    16 | \item{\code{func}}{prepared for objective functions like SYS_LSF$func <- function(x){return(x[1] + x[2])}}
       |                                                                                     ^
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
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checkRd: (-1) normConstCVCI.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
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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
Package suggested but not available for checking: ‘gurobi’
checkRd: (-1) getSolution-methods.Rd:23: Lost braces; missing escapes or markup?
    23 | \item{index_only}{if \code{TRUE}, only print item indices. if \code{FALSE}, print all item attributes. (default = {TRUE})}
       |                                                                                                                   ^
Package vignette with \VignetteEngine{} not specifying an engine package:
  ‘tester_introduction.Rnw’
Engines should be specified as \VignetteEngine{PKG::ENG}.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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.}
       |  ^
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    25 | \\renewcommand{\\multicolumnx}[3]{\\multicolumn{#1}{c}{#3}}
       |               ^
checkRd: (-1) patch_table_env.Rd:25: Lost braces
    25 | \\renewcommand{\\multicolumnx}[3]{\\multicolumn{#1}{c}{#3}}
       |                                  ^
checkRd: (-1) patch_table_env.Rd:25: Lost braces
    25 | \\renewcommand{\\multicolumnx}[3]{\\multicolumn{#1}{c}{#3}}
       |                                                ^
checkRd: (-1) patch_table_env.Rd:25: Lost braces
    25 | \\renewcommand{\\multicolumnx}[3]{\\multicolumn{#1}{c}{#3}}
       |                                                    ^
checkRd: (-1) patch_table_env.Rd:25: Lost braces
    25 | \\renewcommand{\\multicolumnx}[3]{\\multicolumn{#1}{c}{#3}}
       |                                                       ^
Packages which this enhances but not available for checking:
  'mnlogit', 'Zelig'
checkRd: (-1) lexicon_afinn.Rd:48: Lost braces; missing escapes or markup?
    48 | ``A new {ANEW:} Evaluation of a word list for sentiment analysis in
       |         ^
checkRd: (-1) lexicon_afinn.Rd:54: Lost braces; missing escapes or markup?
    54 | title     = \{A new {ANEW:} Evaluation of a word list for sentiment analysis in microblogs\}, \cr
       |                     ^
checkRd: (-1) infer_Z.Rd:16: Lost braces; missing escapes or markup?
    16 |   \item{nu}{Informally, the probability that the row document has the column treatment.  Formally, the parameter for the variatioanl approximation of z_{i,k}, which is a Bernoulli distribution.}
       |                                                                                                                                                         ^
checkRd: (-1) sibp.Rd:26: Lost braces
    26 | It is recommended to use link{sibp_param_search} instead of this function to search over multiple configurations of the most important parameters.  So long as only the training data is used, the analyst can freely experimient with as many parameter configurations as he likes without corrupting his causal inferences.  Once a parameter configuration is chosen, the user can then use \link{sibp_amce} on the test set to estimate the average marginal component effect (AMCE) for each treatment.}
       |                              ^
checkRd: (-1) sibp.Rd:28: Lost braces; missing escapes or markup?
    28 |   \item{nu}{Informally, the probability that the row document has the column treatment.  Formally, the parameter for the variational approximation of z_{i,k}, which is a Bernoulli distribution.}
       |                                                                                                                                                         ^
checkRd: (-1) sibp_amce.Rd:19: Lost braces
    19 |   \item{sibp.amce}{The table returned by code{sibp_amce}.}
       |                                              ^
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) make.phrase.matrix.Rd:20: Lost braces
    20 |  \\tabular{rrrrr}{
       |           ^
checkRd: (-1) make.phrase.matrix.Rd:20-23: Lost braces
    20 |  \\tabular{rrrrr}{
       |                  ^
'LazyData' is specified without a 'data' directory
Unknown package ‘textreadr’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) tfd_von_mises_fisher.Rd:63: Lost braces; missing escapes or markup?
    63 | NOTE: Currently only n in {2, 3, 4, 5} are supported. For n=5 some numerical
       |                           ^
checkRd: (-1) predict.tfunHDDC.Rd:31-39: Lost braces
    31 | The teigen family. Stat Comput 22:1021{1029. <doi.org/10.1007/
       |                                       ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) resampled_ttest.Rd:5: Lost braces; missing escapes or markup?
     5 | \title{Compute correlated t-statistic and p-value for resampled data from {correctR} package}
       |                                                                           ^
checkRd: (-1) resampled_ttest.Rd:24: Lost braces; missing escapes or markup?
    24 | Compute correlated t-statistic and p-value for resampled data from {correctR} package
       |                                                                    ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'witcher.Rd':
  ‘palettes’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'poisson_likelihood.Rd':
  ‘rate_exp’ ‘rate_ref’ ‘rate_pla’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
checkRd: (-1) CPdimensionalityplot.Rd:18: Escaped LaTeX specials: \&
checkRd: (-1) CPdimensionalityplot.Rd:19: Escaped LaTeX specials: \&
checkRd: (-1) Kinship.Rd:15: Escaped LaTeX specials: \&
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checkRd: (-1) T2func.Rd:44: Escaped LaTeX specials: \&
checkRd: (-1) T2funcrep.Rd:44: Escaped LaTeX specials: \&
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checkRd: (-1) T3func.Rd:43: Escaped LaTeX specials: \&
checkRd: (-1) T3func.Rd:44: Escaped LaTeX specials: \&
checkRd: (-1) T3funcrep.Rd:43: Escaped LaTeX specials: \&
checkRd: (-1) T3funcrep.Rd:44: Escaped LaTeX specials: \&
checkRd: (-1) TV.Rd:26: Escaped LaTeX specials: \& \& \&
checkRd: (-1) TV.Rd:30: Escaped LaTeX specials: \&
checkRd: (-1) TV.Rd:31: Escaped LaTeX specials: \&
checkRd: (-1) TV.Rd:32: Escaped LaTeX specials: \&
checkRd: (-1) TV.Rd:33: Escaped LaTeX specials: \&
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checkRd: (-1) threewayanova.Rd:24: Escaped LaTeX specials: \&
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'LazyData' is specified without a 'data' directory
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    18 |   \item \code{sigma}{: A list of length five; each entry is a covariance matrix
       |                     ^
checkRd: (-1) 01-dataObjects.Rd:20-23: Lost braces
    20 |   \item \code{savedSims}{: A list of length five; each entry is a
       |                         ^
checkRd: (-1) 01-dataObjects.Rd:24-26: Lost braces
    24 |   \item \code{savedReap}{: A list of length five; each entry is a
       |                         ^
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
checkRd: (-1) bin_cols.Rd:50: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bin_cols.Rd:51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bin_cols.Rd:52: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bin_cols.Rd:53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bin_cols.Rd:54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bin_cols.Rd:55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bin_cols.Rd:56: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bin_cols.Rd:57: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bin_cols.Rd:58: Lost braces in \itemize; meant \describe ?
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘introdution.Rmd’ using knitr
Failed to parse YAML:

title: "tidygate: high-level data analysis and manipulation in tidyverse style"
output: github_documentdate: "2024-02-20"
                            ^~~~~~
package: tidygate
output:
  BiocStyle::html_document:
    toc_float: true
vignette: >
  %\VignetteEngine{knitr::knitr}
  %\VignetteIndexEntry{Overview of the tidybulk package}
  %\usepackage[UTF-8]{inputenc}

Error: processing vignette 'introdution.Rmd' failed with diagnostics:
Scanner error: mapping values are not allowed in this context at line 2, column 28
--- failed re-building ‘introdution.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Initial Release (v0.1.0)
'LazyData' is specified without a 'data' directory
checkRd: (-1) json_schema.Rd:33: Lost braces; missing escapes or markup?
    33 |   \item object  -> {"name": <type>} e.g., {"age": 32} -> {"age": "number"}
       |                    ^
checkRd: (-1) json_schema.Rd:33: Lost braces; missing escapes or markup?
    33 |   \item object  -> {"name": <type>} e.g., {"age": 32} -> {"age": "number"}
       |                                           ^
checkRd: (-1) json_schema.Rd:33: Lost braces; missing escapes or markup?
    33 |   \item object  -> {"name": <type>} e.g., {"age": 32} -> {"age": "number"}
       |                                                          ^
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Minor changes:
checkRd: (-1) single_imputation.Rd:21-22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) single_imputation.Rd:23-27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) separate_genes.Rd:14: Lost braces
    14 | microbial genes like AbcD, default [A-Za-z][a-z]{2}[A-Z0-9]+}
       |                                                 ^
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'vars_select.Rd':
  ‘args’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
checkRd: (-1) get_tidysq_options.Rd:37: Lost braces
    37 | \item tidysq_pillar_max_width [code{integer(1)}]\cr
       |                                    ^
checkRd: (-1) read_fasta.Rd:54-55: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) read_fasta.Rd:56: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rrelaxiv’
checkRd: (-1) compare.Rd:46: Escaped LaTeX specials: \&
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Invalid package aliases in Rd file 'timeSeq_1.0.4-package.Rd':
  ‘timeSeq_1.0.4-package’
checkRd: (-1) setup_sql_functions.Rd:5: Lost braces; missing escapes or markup?
     5 | \title{Install {timeseriesdb} System Functions}
       |                ^
checkRd: (-1) setup_sql_functions.Rd:17: Lost braces; missing escapes or markup?
    17 | Installs functions needed to operated {timeseriesdb} in
       |                                       ^
checkRd: (-1) setup_sql_grant_rights.Rd:5: Lost braces; missing escapes or markup?
     5 | \title{Grant execute on {timeseriesdb} functions}
       |                         ^
checkRd: (-1) setup_sql_grant_rights.Rd:17: Lost braces; missing escapes or markup?
    17 | Grant execute on {timeseriesdb} functions
       |                  ^
checkRd: (-1) setup_sql_tables.Rd:5: Lost braces; missing escapes or markup?
     5 | \title{Install {timeseriesdb} System Tables}
       |                ^
checkRd: (-1) setup_sql_tables.Rd:17: Lost braces; missing escapes or markup?
    17 | Installs tables needed to operated {timeseriesdb} in
       |                                    ^
checkRd: (-1) setup_sql_triggers.Rd:5: Lost braces; missing escapes or markup?
     5 | \title{Install {timeseriesdb} Triggers}
       |                ^
checkRd: (-1) POSIXst-class.Rd:247: Lost braces
   247 |   do any conversion on the POSIX{l,c}t objects).
       |                                 ^
checkRd: (-1) alcohol.Rd:16-18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) alcohol.Rd:19-21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) alcohol.Rd:22-26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) add_md.Rd:10: Lost braces; missing escapes or markup?
    10 | \item{body}{an XML object generated via {tinkr}}
       |                                         ^
checkRd: (-1) md_ns.Rd:13: Lost braces; missing escapes or markup?
    13 | The {commonmark} package is used to translate markdown to XML, but it does
       |     ^
checkRd: (-1) md_ns.Rd:14: Lost braces; missing escapes or markup?
    14 | not assign a namespace prefix, which means that {xml2} will auto-assign a
       |                                                 ^
checkRd: (-1) stylesheet.Rd:5: Lost braces; missing escapes or markup?
     5 | \title{The {tinkr} stylesheet}
       |            ^
checkRd: (-1) stylesheet.Rd:14: Lost braces; missing escapes or markup?
    14 | This function returns the path to the {tinkr} stylesheet
       |                                       ^
checkRd: (-1) stylesheet.Rd:11: Lost braces; missing escapes or markup?
    11 | stylesheet used by {tinkr}.
       |                    ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) partition_undirected_graph.Rd:20: Lost braces; missing escapes or markup?
    20 | \item{cutoff}{Numeric. The value max(0, g_{i,j} - cutoff) so that there are <\code{.num_components}> components in the graph.}
       |                                           ^
GNU make is a SystemRequirements.
checkRd: (-1) tierChart.Rd:332: Lost braces
   332 |   If the input argument code{boxes} is \code{F}, the \code{lBox},
       |                             ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found an obsolete/platform-specific call in the following function:
  ‘.my.tkdev’
Found the platform-specific device:
  ‘X11’
dev.new() is the preferred way to open a new device, in the unlikely
event one is needed.
Specified C++11: please drop specification unless essential
Error(s) in re-building vignettes:
  ...
--- re-building ‘tlars_variable_selection.Rmd’ using rmarkdown
Could not fetch http://www.zotero.org/styles/institute-of-mathematical-statistics
HttpExceptionRequest Request {
  host                 = "www.zotero.org"
  port                 = 80
  secure               = False
  requestHeaders       = []
  path                 = "/styles/institute-of-mathematical-statistics"
  queryString          = ""
  method               = "GET"
  proxy                = Nothing
  rawBody              = False
  redirectCount        = 10
  responseTimeout      = ResponseTimeoutDefault
  requestVersion       = HTTP/1.1
  proxySecureMode      = ProxySecureWithConnect
}
 (InternalException (HandshakeFailed (Error_Protocol "peer does not support Extended Main Secret" HandshakeFailure)))
Error: processing vignette 'tlars_variable_selection.Rmd' failed with diagnostics:
pandoc document conversion failed with error 61
--- failed re-building ‘tlars_variable_selection.Rmd’

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

Error: Vignette re-building failed.
Execution halted
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    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.
       |                                                 ^
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    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.
       |                                                 ^
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    22 |   \item{SL.library}{specification of prediction algorithms, default is {(\sQuote{SL.glm}, \sQuote{SL.glmnet}, \sQuote{tmle.SL.dbarts2})}. In practice, including more prediction algorithms in the library improves results.}
       |                                                                        ^
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    26 | \item{id}{id}{id to group observations, not used}
       |              ^
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    51 | {object}{an object of type tmle.SL.dbarts2 used internally by \code{Super Learner}}
       |         ^
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Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
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     5 | \title{Format data as a JSON object (like this: {"x": "120"}).}
       |                                                 ^
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    18 | Format data as a JSON object (like this: {"x": "120"}).
       |                                          ^
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    21 | Recommended range is in {5, ..., 20}.}
       |                         ^
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    14 | \item{data}{data.table returned from function /code{tdtr}}
       |                                                    ^
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    23 |     item{\code{estimates}: parameter estimates}
       |         ^
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    24 |     item{
       |         ^
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    29 |     item{\code{operators}: the BEAST2 MCMC operator
       |         ^
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    28 |     item{\code{estimates}: parameter estimates}
       |         ^
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    29 |     item{
       |         ^
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Running ‘testthat.R’ [11s/17s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(tractor.base)
  
  Attaching package: 'tractor.base'
  
  The following object is masked from 'package:base':
  
      %||%
  
  > 
  > test_check("tractor.base")
  [ FAIL 1 | WARN 0 | SKIP 1 | PASS 114 ]
  
  ══ Skipped tests (1) ═══════════════════════════════════════════════════════════
  • oro.nifti cannot be loaded (1): 'test-35-coerce.R:29:5'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-05-files.R:107:5'): we can sort and read DICOM files ───────────
  Error in `as(images[[1]], "MriImage")`: no method or default for coercing "divestImage" to "MriImage"
  Backtrace:
       ▆
    1. ├─testthat::expect_output(...) at test-05-files.R:107:5
    2. │ └─testthat:::quasi_capture(...)
    3. │   ├─testthat (local) .capture(...)
    4. │   │ └─testthat::capture_output_lines(code, print, width = width)
    5. │   │   └─testthat:::eval_with_output(code, print = print, width = width)
    6. │   │     ├─withr::with_output_sink(path, withVisible(code))
    7. │   │     │ └─base::force(code)
    8. │   │     └─base::withVisible(code)
    9. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
   10. └─tractor.base::readDicomDirectory(...)
   11.   └─methods::as(images[[1]], "MriImage")
  
  [ FAIL 1 | WARN 0 | SKIP 1 | PASS 114 ]
  Error: Test failures
  Execution halted
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    46 | "Found {trans("file", .n = n_files)} in {trans("directory", .n = n_dirs)}".
       |        ^
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    46 | "Found {trans("file", .n = n_files)} in {trans("directory", .n = n_dirs)}".
       |                                         ^
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    69 | numeric with two values {0,1} and gaussian(link = "identity") otherwise.
       |                         ^
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  ‘p’

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  ‘p’

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  ‘moving’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
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    19 | column (\code{yprob}) gives the true probabilities (i.e., Pr{Y = 1 | X = x}). 
       |                                                             ^
Auto-generated content requiring editing in Rd file 'treemisc-package.Rd':
  \references: ‘This optional section can contain literature or other refere...’
  \seealso: ‘Optional links to other man pages’
  \examples: ‘## Optional simple examples of the most important functions ...’
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    37 | \link{TNTOrder}{\code{tnt} order},
       |                ^
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    64 | (default: minimum{Number of random experiments K, number of physical cores}).}
       |                  ^
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    51 | (default: minimum{Number of random experiments K, number of physical cores}).}
       |                  ^
Error(s) in re-building vignettes:
  ...
--- re-building ‘TRexSelector_usage_and_simulations.Rmd’ using rmarkdown
Could not fetch http://www.zotero.org/styles/institute-of-mathematical-statistics
HttpExceptionRequest Request {
  host                 = "www.zotero.org"
  port                 = 80
  secure               = False
  requestHeaders       = []
  path                 = "/styles/institute-of-mathematical-statistics"
  queryString          = ""
  method               = "GET"
  proxy                = Nothing
  rawBody              = False
  redirectCount        = 10
  responseTimeout      = ResponseTimeoutDefault
  requestVersion       = HTTP/1.1
  proxySecureMode      = ProxySecureWithConnect
}
 (InternalException (HandshakeFailed (Error_Protocol "peer does not support Extended Main Secret" HandshakeFailure)))
Error: processing vignette 'TRexSelector_usage_and_simulations.Rmd' failed with diagnostics:
pandoc document conversion failed with error 61
--- failed re-building ‘TRexSelector_usage_and_simulations.Rmd’

SUMMARY: processing the following file failed:
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Error: Vignette re-building failed.
Execution halted
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GNU make is a SystemRequirements.
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    31 | If summary=TRUE, a data.frame with columns "dv{index}" with mean for each dependent
       |                                               ^
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    32 | variable plus optional quantiles columns with names "dv{index}_{quantile}".
       |                                                        ^
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    32 | variable plus optional quantiles columns with names "dv{index}_{quantile}".
       |                                                                ^
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    24 | If summary=TRUE, a data.frame with columns "dv{index}" with mean for each dependent
       |                                               ^
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    25 | variable plus optional quantiles columns with names "dv{index}_{quantile}".
       |                                                        ^
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    25 | variable plus optional quantiles columns with names "dv{index}_{quantile}".
       |                                                                ^
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    18 | data.frame with "{var_name}" column for the mean and
       |                  ^
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    19 | "{var_name}_{prob}" columns for each probability.
       |  ^
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    19 | "{var_name}_{prob}" columns for each probability.
       |             ^
GNU make is a SystemRequirements.
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Malformed Title field: should not end in a period.
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  Cannot extract version info from the following section titles:
    Changes
GNU make is a SystemRequirements.
Malformed Description field: should contain one or more complete sentences.
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There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘log2console’
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    16 | \item{matrix.logical}{With matrix=TRUE, the matrix is logical TRUE/FALSE or string "*"/code{" "}}
       |                                                                                            ^
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    39 | If \code{order.x} or {order.y} are \code{NULL}, their respective series will be fitted automatically using a AR model.
       |                      ^
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    31 | If \code{order.x} or {order.y} are \code{NULL}, their respective series will be fitted automatically using a AR model. If \code{permissive} is \code{TRUE} and no AR order is found automatically, an AR order of 1 will be imposed, if this case fails, then no order can be found and the function produces an error.
       |                      ^
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    16 | Converts any variable with two possible values to a {0,1} binary
       |                                                     ^
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    13 | A vector with values in {0,1}.
       |                         ^
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    28 | The final representation has length equal to floor(n / 2^{level}), where n is a length of original time series.
       |                                                          ^
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  ‘turner_introduction.Rnw’
Engines should be specified as \VignetteEngine{PKG::ENG}.
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    74 | 	doi{10.1093/biomet/74.2.221}
       |            ^
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    25 | \item{xcov}{Either a \[stats]{formula} with an empty left-hand side specifying external covariates
       |                              ^
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    30 | \item{threshold_estimate_explanatory}{Point estimate of d_{0}}
       |                                                           ^
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    31 | \item{threshold_estimate_response}{Estimate of f(d_{0}), which may not be 
       |                                                    ^
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    66 | code{\link{twoway.formula}}, code{\link[stats]{medpolish}}
       |     ^
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    66 | code{\link{twoway.formula}}, code{\link[stats]{medpolish}}
       |                                  ^
Package which this enhances but not available for checking: ‘sl3’
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    55 |  {A - delta}, {A + delta}, and {A + 2 * delta}).
       |  ^
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    55 |  {A - delta}, {A + delta}, and {A + 2 * delta}).
       |               ^
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    55 |  {A - delta}, {A + delta}, and {A + 2 * delta}).
       |                                ^
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No news entries found.
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    47 | (\doi{10.1371/journal.pmed.1000253}{10.1371/journal.pmed.1000253})
       |                                    ^
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    33 | (\doi{10.1371/journal.pmed.1000253}{10.1371/journal.pmed.1000253})
       |                                    ^
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   111 | (\doi{10.1371/journal.pmed.1000253}{10.1371/journal.pmed.1000253})
       |                                    ^
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    35 | Lp<- function(a, data, sgl){
       |                            ^
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    38 | sapply(a,FUN=function(a){prod((psip(sgl,a)^ndlt)*((1-psip(sgl,a))^(npt-ndlt)))})
       |                         ^
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    42 | Lt<- function(a, data, sgl){
       |                            ^
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    45 | sapply(a,FUN=function(a){prod((psit(sgl,a)^ndlt)*((1-psit(sgl,a))^(npt-ndlt)))})
       |                         ^
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    49 | Ll<- function(a, data, sgl){
       |                            ^
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    52 | sapply(a,FUN=function(a){prod((psil(sgl,a)^ndlt)*((1-psil(sgl,a))^(npt-ndlt)))})
       |                         ^
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    39 | to \code{\link[ggplot2:ggsave]{ggplot2::ggsave()}}. This is prevented by default since {gglot} switched
       |                                                                                        ^
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    50 |   In addition to the S3 methods listed under the topic "Methods (by generic)", the \code{predict} and {simulate} methods
       |                                                                                                       ^
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  Cannot extract version info from the following section titles:
    uktrans_get is fixed when start_date is used (#2)
    Extra layer of of NULL returns to fail gracefully with an informative message.
    Removed travis & appveyor and using gh_actions instead.
    Using gh-pages to create the pkgdown website.
    Create an app as vignette page to search with the help of uklr.
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  ‘U’ ‘relabel_technique’ ‘w’ ‘X’ ‘distCriterion’ ‘K’ ‘GDM’
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  ‘U’
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Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
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    42 |         \item Metric input is not in {1,2,3}: Metric does not exist
       |                                      ^
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    33 |         \item Metric input is not in {1,2,3}: Metric does not exist
       |                                      ^
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    45 | link[dlogitnorm]{dlogitnorm}for the normal density.
       |                 ^
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    59 | \item{\code{selected_features}}: {A vector of integers indicating the features retained by the feature filtering process.}
       |                                  ^
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    60 | \item{\code{sim_CI}}: {vector containing the cluster indices for each generated unimodal reference distribution}
       |                       ^
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    61 | \item{\code{pvalue_emp}}: {the empirical p-value:  the proportion of times the cluster index from the reference
       |                           ^
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    63 | \item{\code{pvalue_norm}}: {the normalized p-value: the simulated p-value based on comparison to a standard normal distribution }
       |                            ^
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    58 | \item{\code{BestK}}: {A matrix with 1 row and 4 columns named: "Max_CI","Max_CI_wi_1SE","Max_scaled_CI" and "Max_logWCSS_wi_1SE".
       |                      ^
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    63 | \item{\code{full_process}}: {A matrix containing the number of clusters, K, evaluated, the CI from the data, the average CI from the null
       |                             ^
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    66 | \item{\code{selected_features}}: {A vector of integers indicating the features retained by the feature filtering process.}}
       |                                  ^
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    35 | defaults to "{package name} authors"; you should only change this if you
       |              ^
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    54 | defaults to "{package name} authors"; you should only change this if you
       |              ^
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  ‘destdir’ ‘zipfile’

Documented arguments not in \usage in Rd file 'write-this.Rd':
  ‘contents’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
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    21 |    \code{train}{The mldr dataset with train examples, that includes all
       |                ^
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    23 |    \code{test}{The mldr dataset with test examples, defined by the
       |               ^
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    25 |    \code{validation}{Optionally, only if \code{has.validation = TRUE}.
       |                     ^
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    18 | Generate \code{n} random samples from multivariate Gaussian distribution N(0, (L^TL)^{-1})
       |                                                                                      ^
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    97 | \item{ID_level2}{Optional}{variable for unit ID codes. One dimensional object convertible to one-column \code{data.table} or variable name as character, column number.}
       |                           ^
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    99 | \item{dataset}{Optional}{survey data object convertible to \code{data.table}.}
       |                         ^
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   122 | \item{ind_gr}{Optional}{variable by which divided independently X matrix of the auxiliary variables for the calibration. One dimensional object convertible to one-column \code{data.table} or variable name as character, column number.}
       |                        ^
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   124 | \item{use.estVar}{Logical}{value. If value is \code{TRUE}, then \code{R} function \code{estVar} is used for the  estimation of covariance matrix of the residuals. If value is \code{FALSE}, then \code{R} function \code{estVar} is not used for the estimation of covariance matrix of the residuals.}
       |                           ^
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    69 | \item{percentratio}{Positive}{numeric value. All linearized variables are multiplied with \code{percentratio} value, by default - 1.}
       |                              ^
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   121 | \item{month_at_work}{Variable}{for total number of month at work (sum of the number of months spent at full-time work as employee, number of months spent at part-time work as employee, number of months spent at full-time work as self-employed (including family worker), number of months spent at part-time work as self-employed (including family worker)).  One dimensional object convertible to one-column \code{data.table} or variable name as character, column number.}
       |                               ^
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     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
       |                                                                                                                        ^
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     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
       |                                                                                           ^
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     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
       |                                                                                      ^
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     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
       |                                                                                                                      ^
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     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
       |                                                                                                                                   ^
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    40 |        Y = 6*X1 + 1.5*X2  + 9*1{X12 < 0} + exp(2*X22)*e
       |                                ^
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    42 |        Y = 6*X1 + 1.5*X2  + 9*1{X12 < 0} + 6*X22 + e
       |                                ^
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    15 | \item{file.suffix}{Regex expression for end of file name. For example, `file.suffix = '_S\\d{1,2}_.*_R1_.*'` will match R1 files.1 files.}
       |                                                                                             ^
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    23 | The function returns the K-by-K matrices {A_1, ..., A_p} as a list object.
       |                                          ^
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    58 | Consider VAR(p) model: y_t = A_1 y_{t-1} + ... + A_p y_{t-p} + C d_t + e_t,
       |                                    ^
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    58 | Consider VAR(p) model: y_t = A_1 y_{t-1} + ... + A_p y_{t-p} + C d_t + e_t,
       |                                                        ^
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    28 | \item{W2}{nxn matrix of weights. Season is estimated as W2 \%}\% y, if y is the data vector}
       |      ^
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    28 | \item{W2}{nxn matrix of weights. Season is estimated as W2 \%}\% y, if y is the data vector}
       |          ^
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    15 | and dimension information (\code{dim} or code{length}) of each item,
       |                                              ^
GNU make is a SystemRequirements.
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    35 | link[vcmeta]{meta.lm.gen} functions in application where compatible
       |             ^
Running ‘test-all.R’ [2s/9s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library("testthat")
  > library('vcr')
  > test_check("vcr")
  https://hb.opencpu.org is down Timeout was reached: [hb.opencpu.org] Connection timed out after 5002 milliseconds
  Error in `FUN()`:
  ! In path: "/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/vcr.Rcheck/tests/testthat/helper-vcr.R"
  Caused by error in `vapply()`:
  ! values must be length 1,
   but FUN(X[[1]]) result is length 0
  Backtrace:
       ▆
    1. ├─testthat::test_check("vcr")
    2. │ └─testthat::test_dir(...)
    3. │   └─testthat:::test_files(...)
    4. │     └─testthat:::test_files_serial(...)
    5. │       └─testthat:::test_files_setup_state(...)
    6. │         └─testthat::source_test_helpers(".", env)
    7. │           └─testthat::source_dir(path, "^helper.*\\.[rR]$", env = env, wrap = FALSE)
    8. │             └─base::lapply(...)
    9. │               └─testthat (local) FUN(X[[i]], ...)
   10. │                 └─testthat::source_file(path, env = env, chdir = chdir, wrap = wrap)
   11. │                   ├─base::withCallingHandlers(...)
   12. │                   └─base::eval(exprs, env)
   13. │                     └─base::eval(exprs, env)
   14. │                       └─base::vapply(out, "[[", 1, "status_code") at tests/testthat/helper-vcr.R:82:1
   15. └─base::.handleSimpleError(...)
   16.   └─testthat (local) h(simpleError(msg, call))
   17.     └─rlang::abort(...)
  Execution halted
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Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
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    51 | S = dbar/sqrt(2*pi*se_{d}(0)/N),
       |                       ^
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    53 | where d is the loss differential, d = e1 - e2 (e1 = loss(x, xhat1) and e2 = loss(x, xhat2)), dbar is its sample mean, and se_{d}(0) is the standard error for d, which must be estimated, and N is the length of the series investigated.  Let V = 2*pi*se_{d}(0), then V is estimated by
       |                                                                                                                              ^
checkRd: (-1) predcomp.test.Rd:53: Lost braces; missing escapes or markup?
    53 | where d is the loss differential, d = e1 - e2 (e1 = loss(x, xhat1) and e2 = loss(x, xhat2)), dbar is its sample mean, and se_{d}(0) is the standard error for d, which must be estimated, and N is the length of the series investigated.  Let V = 2*pi*se_{d}(0), then V is estimated by
       |                                                                                                                                                                                                                                                            ^
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checkRd: (-1) fit.vfp.Rd:87: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fit.vfp.Rd:88: Lost braces in \itemize; meant \describe ?
Found the following significant warnings:
  Warning in is.R() : 'is.R' is deprecated.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/VGAM.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-13 (Debian 13.2.0-13) 13.2.0’
* used Fortran compiler: ‘GNU Fortran (Debian 13.2.0-13) 13.2.0’
checkRd: (-1) CommonVGAMffArguments.Rd:597: Lost braces
   597 |   Changes relating to the code{lss} argument have very important
       |                               ^
checkRd: (-1) ucberk.Rd:20: Lost braces
    20 |                 called \code{A}, code{B}, \dots, code{F}.
       |                                      ^
checkRd: (-1) ucberk.Rd:20: Lost braces
    20 |                 called \code{A}, code{B}, \dots, code{F}.
       |                                                      ^
checkRd: (-1) LinRegChol.Rd:21: Lost braces; missing escapes or markup?
    21 | Do linear regression of form (X^T O X + P)^{-1} X^T y where O is omega, P is
       |                                            ^
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
Argument items with no description in Rd file 'learnPartitionWithLLR.Rd':
  ‘type’ ‘procedure’ ‘ql’ ‘qq’ ‘BinaryLearningProcedure’
Argument items with no description in Rd file 'plotClassifRule.Rd':
  ‘object’
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) show_query.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) show_query.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) show_query.Rd:29: Lost braces in \itemize; meant \describe ?
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 ?
Documented arguments not in \usage in Rd file 'draw_map_shiny.Rd':
  ‘rigth.lim’

Documented arguments not in \usage in Rd file 'map_summary.Rd':
  ‘rigth.lim’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
checkRd: (-1) RVineMatrix.Rd:90: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) RVineMatrix.Rd:91: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) RVineMatrix.Rd:92: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
checkRd: (-1) viridis.Rd:50: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) viridis.Rd:57: Lost braces in \itemize; meant \describe ?
checkRd: (-1) viridis.map.Rd:24-30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) viridis.map.Rd:31-34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) viridis.map.Rd:35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) viridis.map.Rd:36-37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) viridis.map.Rd:10: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) viridis.map.Rd:13-14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) viridis.map.Rd:42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) viridis.map.Rd:43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) viridis.map.Rd:44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) viridis.map.Rd:45: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulatePopulation.Rd:75: Lost braces; missing escapes or markup?
    75 |   \item \strong{Pollen productivity}: In each time step the model computes the pollen productivity (in relative values) of the population using the equation \eqn{P_{t} = \sum x_{it} \times max(S_{t}, B)}, where \emph{t} is time (a given simulation time step), \emph{P} is the pollen productivity of the population at a given time, \emph{x_{i}} represents the biomass of every adult individual, \emph{S} is the environmental suitability at the given time, \emph{B} is the contribution of biomass to pollen productivity regardless of environmental suitability (\emph{pollen.control} parameter in the simulation, 0 by default). If \emph{B} equals 1, \emph{P} is equal to the total biomass sum of the adult population, regardless of the environmental suitability. If \emph{B} equals 0, pollen productivity depends entirely on environmental suitability values.
       |                                                                                                                                                                                                                                                                                                                                                    ^
checkRd: (-1) NSpec.DB.Rd:16: Lost braces; missing escapes or markup?
    16 |   ...{currently not used}
       |      ^
checkRd: (-1) wavelength-methods.Rd:32: Lost braces; missing escapes or markup?
    32 | A call to {new} returns a newly allocated object from the class identified by the first argument.
       |           ^
checkRd: (-1) phasePortrait.Rd:350: Lost braces; missing escapes or markup?
   350 |   \code{vMod = xMod^(1/lambda)} and {vArg = xArg^(1/lambda)}\cr\cr
       |                                     ^
checkRd: (-1) compdesc.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) compdesc.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) compdesc.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) compdesc.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) compdesc.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) compdesc.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) compdesc.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) compdesc.Rd:31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) compdesc.Rd:32: Lost braces in \itemize; \value handles \item{}{} directly
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) ViSiElse.Rd:101-107: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ViSiElse.Rd:102: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ViSiElse.Rd:103: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ViSiElse.Rd:104: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ViSiElse.Rd:105-106: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ViSiElse.Rd:108-127: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ViSiElse.Rd:112-113: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ViSiElse.Rd:114-115: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ViSiElse.Rd:116: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ViSiElse.Rd:128-134: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ViSiElse.Rd:135-147: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ViSiElse.Rd:148-157: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ViSiElse.Rd:152-153: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ViSiElse.Rd:154-155: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ViSibook-class.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ViSibook-class.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ViSibook-class.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ViSibook-class.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dim-ViSibook-methods.Rd:16: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dim-ViSibook-methods.Rd:17-18: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) summary-ViSigrid-methods.Rd:16: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) summary-ViSigrid-methods.Rd:17: Lost braces in \itemize; \value handles \item{}{} directly
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) aminoAcidFun.Rd:37: Lost braces
    37 | \item{ownVLFreduced}{ownVLFMatrix}{A matrix containing only those specimen that have VLFs as well as the amino acids at the positions that contain VLFs and NAs in all other positions of the sequence.  Only appears if own is not NULL.}
       |                                   ^
checkRd: (-1) vlfFun.Rd:36: Lost braces
    36 | \item{ownVLFreduced}{ownVLFMatrix}{A matrix containing only those specimen that have VLFs as well as the nucleotides at the positions that contain VLFs and NAs in all other positions of the sequence.  Only appears if own is not NULL.}
       |                                   ^
Specified C++11: please drop specification unless essential
checkRd: (-1) getTurnType.Rd:38: Lost braces; missing escapes or markup?
    38 | Return one of {Vocalisation, GrpVocalisation, ...} or identifier.
       |               ^
Package suggested but not available for checking: ‘INLA’
Package unavailable to check Rd xrefs: ‘INLA’
GNU make is a SystemRequirements.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    vortexRdata pre-1.0.3
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) compute.means.Rd:23: Escaped LaTeX specials: \&
checkRd: (-1) norm.wattfabricius.Rd:5: Escaped LaTeX specials: \&
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) Data-Examples.Rd:39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Data-Examples.Rd:40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Data-Examples.Rd:41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Data-Examples.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Data-Examples.Rd:31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Data-Examples.Rd:32: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Data.trafo.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Data.trafo.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Data.trafo.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Toep.estimator.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Toep.estimator.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Toep.estimator.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Toep.estimator.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) aquaporin.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) vsts_create_release.Rd:33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) vsts_create_release.Rd:34: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) WACS.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) WACS.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) WACS.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) WACS.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) WACS.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) WACS.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) WACS.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) WACS.Rd:36-37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) WACS.Rd:38-39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) WACSreadAgroclim.Rd:15: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) WACSreadAgroclim.Rd:16-17: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) anchor_points_grey.Rd:9: Lost braces
     9 | Zeeden et al., (2013) and anchored to the code{\link{astrosignal_example}} \cr
       |                                               ^
checkRd: (-1) retrack_wt_MC.Rd:206: Lost braces
   206 | be off in certain intervals. the link[WaverideR]{retrack_wt_MC} mitigates
       |                                                 ^
checkRd: (-1) retrack_wt_MC.Rd:40: Lost braces
    40 | link[WaverideR]{analyze_wavelet} wavelet function
       |                ^
checkRd: (-1) retrack_wt_MC.Rd:41: Lost braces
    41 | To create a list use the link[base]{list} function}
       |                                    ^
checkRd: (-1) retrack_wt_MC.Rd:44: Lost braces
    44 | To create the matrix use the link[base]{cbind} function and only add the
       |                                        ^
Found the following files/directories:
  ‘ReconstructedData.txt’ ‘ReconstructedDataStDev.txt’
  ‘ResampledReconstructions.txt’
  ‘ResampledReconstructionsStandardVariation.txt’
Specified C++11: please drop specification unless essential
checkRd: (-1) accessC.wst.rd:24: Lost braces
    24 | Note that coefficients returned by this function are in emph{packet order}. They can be used \emph{as is} but for many applications it might be more useful to deal with the coefficients in packets: see the function \code{\link{getpacket.wst}} for further details. 
       |                                                             ^
checkRd: (-1) griddata.rd:18: Lost braces
    18 | \code{G}{Codes the value of the linear interpolant matrix for the corresponding entry in \code{gridt}. The value at each point corresponds to the proportion of the original data point pointed to by \code{Gindex} that contributes to the new value at the corresponding \code{gridt} value. See Kovac, (1997), page 81 for further information.}
       |         ^
checkRd: (-1) makegrid.rd:13: Lost braces; missing escapes or markup?
    13 | \item{gridn}{The number of grid points in the dyadic grid that the (x,y) gets interpolated to. By default this is the next power of two larger than the length of {x}.}
       |                                                                                                                                                                   ^
checkRd: (-1) makewpstDO.rd:29: Lost braces
    29 | /bold{12}, 45-56.
       |      ^
checkRd: (-1) wd.object.rd:47: Lost braces
    47 | The wd class of objects has methods for the following generic functions: \code{\link{plot}}, \code{\link{threshold}}, \code{\link{summary}}, \code{\link{print}}, code{\link{draw}}.
       |                                                                                                                                                                       ^
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) centrality.Rd:42-43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) centrality.Rd:44-45: Lost braces in \itemize; meant \describe ?
checkRd: (-1) centrality.Rd:50-52: Lost braces in \itemize; meant \describe ?
checkRd: (-1) centrality.Rd:53-54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) centrality.Rd:55-56: Lost braces in \itemize; meant \describe ?
checkRd: (-1) centrality.Rd:57-59: Lost braces in \itemize; meant \describe ?
checkRd: (-1) centrality.Rd:65-66: Lost braces in \itemize; meant \describe ?
checkRd: (-1) centrality.Rd:67-69: Lost braces in \itemize; meant \describe ?
checkRd: (-1) centrality.Rd:70-72: Lost braces in \itemize; meant \describe ?
checkRd: (-1) clustcoef.Rd:67: Lost braces
    67 |   \item Barrat, A., Barth\'{e}lemy, M., Pastor-Satorras,
       |                            ^
checkRd: (-1) dprewire.Rd:37-40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dprewire.Rd:41-43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dprewire.Rd:44-45: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dprewire.Rd:45-48: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dprewire.Rd:48-50: Lost braces
    48 | is provided.} \item{\code{cvxr_control} {A list of parameters passed to
       |                                         ^
checkRd: (-1) rpa_control_preference.Rd:69-76: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rpa_control_preference.Rd:77-87: Lost braces in \itemize; meant \describe ?
Package suggested but not available for checking: ‘prepr’
checkRd: (-1) wdpa_clean.Rd:23: Lost braces
    23 | \item{crs}{\code{character} or code{integer} object representing a
       |                                    ^
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) get_cid.Rd:58-59: Lost braces
    58 | <structure search> is assembled as "{\code{substructure} |
       |                                     ^
checkRd: (-1) get_cid.Rd:59-60: Lost braces
    59 | \code{superstructure} | \code{similarity} | \code{identity}} / {\code{smiles}
       |                                                                ^
checkRd: (-1) get_cid.Rd:70-71: Lost braces
    70 | "{\code{fastidentity} | \code{fastsimilarity_2d} | \code{fastsimilarity_3d} |
       |  ^
checkRd: (-1) get_cid.Rd:71-72: Lost braces
    71 | \code{fastsubstructure} | \code{fastsuperstructure}}/{\code{smiles} |
       |                                                      ^
checkRd: (-1) Session.Rd:146: Lost braces
   146 | sQuote{page load} timeout specifies a time to wait for the page loading
       |       ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) image_func.Rd:20: Lost braces; missing escapes or markup?
    20 | This is a convenience function for applying {magick} functions that take an image as the first argument and return an image. It's fully vectorised, so you can set separate argument values for each image.
       |                                             ^
Documented arguments not in \usage in Rd file 'read_img.Rd':
  ‘imgfile’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Packages suggested but not available for checking: 'iptools', 'rgeolocate'
'LazyData' is specified without a 'data' directory
checkRd: (-1) predict.SDMfit.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) predict.SDMfit.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
checkRd: (-1) busTrace.Rd:15: Lost braces
    15 | /href{https://crawdad.org/coppe-ufrj/RioBuses/20180319/}
       |      ^
Specified C++11: please drop specification unless essential
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
       |                         ^
Argument items with no description in Rd file 'zdifference_ordinal.Rd':
  ‘na.rm’
'LazyData' is specified without a 'data' directory
S3 methods shown with full name in Rd file 'QIC.gee.Rd':
  ‘QIC.gee’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Major changes
    Minor changes
'LazyData' is specified without a 'data' directory
checkRd: (-1) get.deriv.smooth.hist.Rd:5: Lost braces; missing escapes or markup?
     5 | \title{Gets $n^{th}$ derivative of smoothed histogram}
       |                ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘pageviews’
checkRd: (-1) get_geo_box.Rd:37-38: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get_geo_box.Rd:39-40: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get_geo_box.Rd:41: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get_geo_box.Rd:42: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get_geo_box.Rd:43-44: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get_geo_entity.Rd:27-28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get_geo_entity.Rd:29-30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get_geo_entity.Rd:31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get_geo_entity.Rd:32: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get_geo_entity.Rd:33-34: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) milakes.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) milakes.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) milakes.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) milakes.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) milakes.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) milakes.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) milakes.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) milakes.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) milakes.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) milakes.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) milakes.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) milakes.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) milakes.Rd:22: Lost braces in \itemize; meant \describe ?
Package suggested but not available for checking: ‘pageviews’
'LazyData' is specified without a 'data' directory
checkRd: (-1) secondDerivative.Rd:14: Lost braces
    14 | This must be a function of the form FUN <- function(x, ...){...}
       |                                                            ^
checkRd: (-1) windAC.Rd:31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) windAC.Rd:32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) windAC.Rd:33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Hoover.Rd:21: Lost braces; missing escapes or markup?
    21 | Let x_{i} be the income of the i-th person and \eqn{\overline{x}} be the mean income. Then the Hoover index H is:
       |       ^
checkRd: (-1) RicciSchutz.Rd:21: Lost braces; missing escapes or markup?
    21 | In the case of an empirical distribution with n elements where y_{i} denotes the wealth of household i and \eqn{\overline{y}} the sample average, the Ricci and Schutz coefficient can be expressed as:
       |                                                                  ^
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) word2vec_similarity.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) word2vec_similarity.Rd:31: 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 ?
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'new_givens_path.Rd':
  ‘generate’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
checkRd: (-1) theme_wpa.Rd:16: Lost braces; missing escapes or markup?
    16 | you can use this font, install and load {extrafont} prior to
       |                                         ^
'LazyData' is specified without a 'data' directory
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) wql-package.Rd:7: Lost braces
     7 | \title{c("\\Sexpr[results=rd,stage=build]{tools:::Rd_package_title(\"#1\")}",
       |                                          ^
checkRd: (-1) wql-package.Rd:10: Lost braces
    10 | c("\\Sexpr[results=rd,stage=build]{tools:::Rd_package_description(\"#1\")}",
       |                                   ^
checkRd: (-1) wql-package.Rd:61: Lost braces
    61 | c("\\Sexpr[results=rd,stage=build]{tools:::Rd_package_author(\"#1\")}",
       |                                   ^
checkRd: (-1) wql-package.Rd:65: Lost braces
    65 | c("\\Sexpr[results=rd,stage=build]{tools:::Rd_package_maintainer(\"#1\")}",
       |                                   ^
checkRd: (-1) item.side.Rd:35: Lost braces
    35 |   	code{TRUE}. If any other value, the axis is not drawn.}
       |             ^
Malformed Title field: should not end in a period.
checkRd: (-1) createDemandSite.Rd:26: Lost braces
    26 |   \item{suppliers}{(optional) A list of object(s) inherited from the folowing classes: \code{\link[WRSS]{createAquifer}}, \code{\link[WRSS]{createRiver}}, \code{\link[WRSS]{createReservoir}}, code{\link[WRSS]{createDiversion}}.}
       |                                                                                                                                                                                                     ^
checkRd: (-1) createDemandSite.base.Rd:26: Lost braces
    26 |   \item{suppliers}{(optional) A list of object(s) inherited from the folowing classes: \code{\link[WRSS]{createAquifer}}, \code{\link[WRSS]{createRiver}}, \code{\link[WRSS]{createReservoir}}, code{\link[WRSS]{createDiversion}}.}
       |                                                                                                                                                                                                     ^
checkRd: (-1) createDemandSite.default.Rd:32: Lost braces
    32 |   \item{suppliers}{(optional) A list of object(s) inherited from the folowing classes: \code{\link[WRSS]{createAquifer}}, \code{\link[WRSS]{createRiver}}, \code{\link[WRSS]{createReservoir}}, code{\link[WRSS]{createDiversion}}.}
       |                                                                                                                                                                                                     ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) wtest.Rd:61-64: Lost braces
    61 | {When \code{w.order} =2, the \code{wtest()} will automatically calculate the main effect first and then do a pre-filter before calculating interactions.
       | ^
checkRd: (-1) wtest.high.Rd:61-64: Lost braces
    61 | {When \code{w.order} > 2, the \code{wtest()} will automatically calculate the main effect first and then do a pre-filter before calculating interactions.
       | ^
Documented arguments not in \usage in Rd file 'Cut.off.Rd':
  ‘main’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
checkRd: (-1) batch_modwt_wvar_cpp.Rd:36: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) batch_modwt_wvar_cpp.Rd:37: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) batch_modwt_wvar_cpp.Rd:38: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ci_eta3.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ci_eta3.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ci_eta3.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ci_eta3_robust.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ci_eta3_robust.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ci_eta3_robust.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ci_wave_variance.Rd:32: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ci_wave_variance.Rd:33: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ci_wave_variance.Rd:34: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) modwt_wvar_cpp.Rd:36: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) modwt_wvar_cpp.Rd:37: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) modwt_wvar_cpp.Rd:38: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) wvar_cpp.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) wvar_cpp.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) wvar_cpp.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
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) xbrlSECdev01.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) xshow.Rd:19: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) xshow.Rd:20: Lost braces in \enumerate; meant \describe ?
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 ?
Unknown package ‘RSiena’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘xgb.txt’
GNU make is a SystemRequirements.
checkRd: (-1) XMLGetters-methods.Rd:165: Lost braces in \itemize; meant \describe ?
checkRd: (-1) XMLGetters-methods.Rd:166: Lost braces in \itemize; meant \describe ?
checkRd: (-1) XMLGetters-methods.Rd:167: Lost braces in \itemize; meant \describe ?
checkRd: (-1) XMLGetters-methods.Rd:168-169: Lost braces in \itemize; meant \describe ?
checkRd: (-1) XMLGetters-methods.Rd:170: Lost braces in \itemize; meant \describe ?
checkRd: (-1) XMLGetters-methods.Rd:171: Lost braces in \itemize; meant \describe ?
checkRd: (-1) XMLGetters-methods.Rd:172: Lost braces in \itemize; meant \describe ?
checkRd: (-1) XMLGetters-methods.Rd:179-182: Lost braces in \itemize; meant \describe ?
checkRd: (-1) XMLGetters-methods.Rd:191: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
checkRd: (-1) xml_to_df.Rd:144: Lost braces; missing escapes or markup?
   144 | Default {NULL} means the workbook will not be protected with a password}
       |         ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rbokeh’
checkRd: (-1) read.npc.vpc.results.Rd:16: Escaped LaTeX specials: \_
checkRd: (-1) read.npc.vpc.results.Rd:19: Escaped LaTeX specials: \_ \_ \_ \_ \_ \_
checkRd: (-1) read.npc.vpc.results.Rd:22: Escaped LaTeX specials: \_
Documented arguments not in \usage in Rd file 'xpose.create.title.Rd':
  ‘plot.text’ ‘main’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Invalid package aliases in Rd file 'XRjulia-package.Rd':
  ‘XRjulia-package’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘xtable.html’ ‘xtable.tex’
Argument items with no description in Rd file 'getCondition.Rd':
  ‘object’
Argument items with no description in Rd file 'screen.Rd':
  ‘fac’ ‘condition’ ‘position’
Found the following files/directories:
  ‘OPT.csv’ ‘testTecan_defaultLiquid.csv’ ‘testTecan_setLiquid.csv’
checkRd: (-1) xwfGridsearch.Rd:27: Lost braces; missing escapes or markup?
    27 | \item{iter}{Number of levels in the adaptive grid search. The resolution in b obtained is 2^{-1-iter}.}
       |                                                                                             ^
checkRd: (-1) cat_sim.Rd:110: Lost braces; missing escapes or markup?
   110 | \code{min} and {max} are mandatory for setting limits on the test length. User-defined
       |                ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) boot.yhat.Rd:3: Lost braces
     3 | \title{Bootstrap metrics produced from /code{calc.yhat}}
       |                                             ^
checkRd: (-1) boot.yhat.Rd:19: Lost braces
    19 |     Ouput of /code{lm}
       |                   ^
checkRd: (-1) boot.yhat.Rd:22: Lost braces
    22 |     Output of /code{calc.yhat}
       |                    ^
checkRd: (-1) booteval.yhat.rd:3: Lost braces
     3 | \title{Evaluate bootstrap metrics produced from /code{calc.yhat}}
       |                                                      ^
checkRd: (-1) booteval.yhat.rd:5: Lost braces
     5 |   This function evaluates the bootstrap metrics produced from /code{boot.yhat}.   
       |                                                                    ^
checkRd: (-1) combCI.rd:26: Lost braces
    26 |   This function evaluates the bootstrap metrics produced from /code{boot.yhat}.   
       |                                                                    ^
checkRd: (-1) commonality.rd:12: Lost braces
    12 |     Output from /code{aps}
       |                      ^
checkRd: (-1) dombin.rd:12: Lost braces
    12 |     Output from /code{dominance}
       |                      ^
checkRd: (-1) dominance.rd:12: Lost braces
    12 |     Output from /code{aps}
       |                      ^
checkRd: (-1) plotCI.yhat.rd:5: Lost braces
     5 |   This function plots CIs that have been produced from /code{booteval.yhat}.
       |                                                             ^
checkRd: (-1) plotCI.yhat.rd:32: Lost braces
    32 |   This function plots CIs that have been produced from /code{booteval.yhat}.   
       |                                                             ^
checkRd: (-1) plotCI.yhat.rd:35: Lost braces
    35 | This returns a plot of CIs that have been produced from /code{booteval.yhat}.
       |                                                              ^
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Argument items with no description in Rd file 'IC.Rd':
  ‘\dots’
Packages suggested but not available for checking: 'RNRCS', 'metScanR'
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
checkRd: (-1) glm.cons.Rd:54: Lost braces; missing escapes or markup?
    54 | \item{method}{the method used in fitting the model. The default method "\code{glm.fit.cons}" uses function {nnnpls} from package nnls instead of \code{lm.fit} to impose the sign of the coefficients. As in \code{glm}, the alternative method "\code{model.frame}" returns the model frame and does no fitting.}
       |                                                                                                            ^
Auto-generated content requiring editing in Rd file 'ZIBseq-package.Rd':
  \seealso: ‘~~ Optional links to other man pages, e.g. ~~ ~~ \code{\link...’
checkRd: (-1) label_kansuji.Rd:48: Lost braces; missing escapes or markup?
    48 | but if TRUE and installed '{scales}` package, 1.10 will be displayed.}
       |                            ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
checkRd: (-1) inside2trans.Rd:124: Lost braces
   124 | \bold{Linking number --- {Wikipedia}{,} The Free Encyclopedia}.
       |                                     ^
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"}.
       |                                          ^
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 134469 marked UTF-8 strings
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 13.7Mb
  sub-directories of 1Mb or more:
    include  13.6Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
checkRd: (-1) bind_tweets.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bind_tweets.Rd:22: Lost braces in \itemize; meant \describe ?
Undeclared package ‘CCA’ in Rd xrefs
Found the following files/directories:
  ‘acceldata2.RData’
File ‘acc/libs/acc.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Documented arguments not in \usage in Rd file 'ADMM_EN2.Rd':
  ‘alpha’

Documented arguments not in \usage in Rd file 'ADMM_EN_SMW.Rd':
  ‘alpha’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Argument items with no description in Rd file 'testRmACD.Rd':
  ‘pStar’
File ‘ACDm/libs/ACDm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    htmlwidgets  11.6Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘hunspell’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
‘configure’: /bin/bash is not portable
installed size is 13.7Mb
  sub-directories of 1Mb or more:
    R  13.6Mb
Problems with news in ‘NEWS.md’:
No news entries found.
Namespace in Imports field not imported from: ‘svglite’
  All declared Imports should be used.
Problems with news in ‘NEWS.md’:
No news entries found.
Namespace in Imports field not imported from: ‘tidyr’
  All declared Imports should be used.
Imports includes 25 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘RcppProgress’
  All declared Imports should be used.
Documented arguments not in \usage in Rd file 'd1.Rd':
  ‘The’ ‘A’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 305 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘Example.jpeg’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Invalid package aliases in Rd file 'aslm-package.Rd':
  ‘aslm-package’ ‘asggm-package’
Argument items with no description in Rd file 'asggm-internal.Rd':
  ‘ansL’ ‘kNodes’ ‘spP’
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    doc   7.1Mb
checkRd: (-1) ada.Rd:171: Escaped LaTeX specials: \&
Package suggested but not available for checking: ‘arrow’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Benchmarking’
  All declared Imports should be used.
Documented arguments not in \usage in Rd file 'print.aTest.Rd':
  ‘how’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    data   3.0Mb
Namespace in Imports field not imported from: ‘sp’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘jsonlite’
  All declared Imports should be used.
Documented arguments not in \usage in Rd file 'ae_count.Rd':
  ‘patients’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    data   9.3Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   4.7Mb
'LazyData' is specified without a 'data' directory
Undeclared package ‘future’ in Rd xrefs
Malformed Description field: should contain one or more complete sentences.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc   3.7Mb
'LazyData' is specified without a 'data' directory
Undeclared packages ‘timereg’, ‘rms’, ‘ranger’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Note: found 12 marked UTF-8 strings
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Undeclared package ‘tibble’ in Rd xrefs
Namespaces in Imports field not imported from:
  ‘fields’ ‘knitr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    tutorials   5.6Mb
Namespaces in Imports field not imported from:
  ‘BayesFactor’ ‘GGally’ ‘Hmisc’ ‘WRS2’ ‘boot’ ‘car’ ‘dplyr’ ‘effects’
  ‘effsize’ ‘forcats’ ‘ggplot2’ ‘lm.beta’ ‘nlme’ ‘readr’ ‘robust’
  ‘sandwich’ ‘sjstats’ ‘tidyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘table_AeRobiology’
Namespace in Imports field not imported from: ‘flextable’
  All declared Imports should be used.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘DBI’ ‘assertthat’ ‘tibble’
  All declared Imports should be used.
Note: found 11 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘docstring’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘mathjaxr’
  All declared Imports should be used.
Undeclared packages ‘epiR’, ‘cccrm’ in Rd xrefs
Package which this enhances but not available for checking: ‘asreml’
Specified C++11: please drop specification unless essential
File ‘ahaz/libs/ahaz.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘devtools’ ‘mixexp’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘knitr’ ‘randomNames’ ‘tidyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Undeclared packages ‘multcomp’, ‘gmodels’ in Rd xrefs
Undeclared package ‘R6’ in Rd xrefs
Undeclared package ‘era’ in Rd xrefs
Namespaces in Imports field not imported from:
  ‘Rsolnp’ ‘SuperLearner’ ‘future.apply’ ‘ggplot2’ ‘progressr’ ‘stats’
  ‘utils’
  All declared Imports should be used.
Note: found 53 marked UTF-8 strings
Note: found 17 marked UTF-8 strings
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    ShinyGR   4.3Mb
    doc       3.5Mb
'LazyData' is specified without a 'data' directory
Note: found 1 marked UTF-8 string
Note: found 710 marked UTF-8 strings
Found the following files/directories:
  ‘stuve.pdf’
'LazyData' is specified without a 'data' directory
Undeclared package ‘SnowballC’ in Rd xrefs
'LazyData' is specified without a 'data' directory
checkRd: (-1) ALF.Rd:47: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
File ‘AlgDesign/libs/AlgDesign.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
checkRd: (-1) optimalfrequency.Rd:29: Escaped LaTeX specials: \$
checkRd: (-1) optimalfrequency.Rd:30: Escaped LaTeX specials: \$
checkRd: (-1) optimalfrequency.Rd:31: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Undeclared package ‘hyperSpec’ in Rd xrefs
Note: found 115 marked UTF-8 strings
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
File ‘alphabetr/libs/alphabetr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) UN1.Rd:16: Escaped LaTeX specials: \$
checkRd: (-1) rateprof.Rd:64: Escaped LaTeX specials: \&
Malformed Title field: should not end in a period.
Argument items with no description in Rd file 'MLS.Rd':
  ‘MSE1’
'LazyData' is specified without a 'data' directory
Note: found 171 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘metaboliteIDmapping’
Namespaces in Imports field not imported from:
  ‘magrittr’ ‘tidyverse’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘jsonlite’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Invalid package aliases in Rd file 'amelia.package.Rd':
  ‘amelia-package’
'LazyData' is specified without a 'data' directory
'library' or 'require' call to ‘network’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Malformed Title field: should not end in a period.
Note: found 7 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘devtools’ ‘dplyr’ ‘gridExtra’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘kernlab’
  All declared Imports should be used.
Failed to query server: Failed to read RTC: Input/output error
checkRd: (-1) diff.Rd:14: Lost braces
    14 | \item{x}{A track_xy{t}.}
       |                    ^
checkRd: (-1) nsd.Rd:22: Lost braces
    22 | \item{x}{A track_xy{t}.}
       |                    ^
Documented arguments not in \usage in Rd file 'check_factors.Rd':
  ‘object’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘arrow’
checkRd: (-1) deshrink.Rd:55: Escaped LaTeX specials: \&
checkRd: (-1) deshrink.Rd:51: Escaped LaTeX specials: \&
checkRd: (-1) plot.mat.Rd:60: Escaped LaTeX specials: \&
checkRd: (-1) plot.wa.Rd:46: Escaped LaTeX specials: \&
checkRd: (-1) predict.prcurve.Rd:5: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Auto-generated content requiring editing in Rd file 'rowVars.Rd':
  \arguments: \dots: ‘~~Describe \code{\dots} here~~’
Found the following files/directories:
  ‘BH-0.05-ListOfGenes.txt’ ‘BH-0.05-VM-ListOfGenes.txt’
  ‘CompleteListOfGenes.txt’ ‘GenesOutOfAnalysis.txt’
  ‘GenesOutOfAnalysis_NotEnoughObs.txt’
  ‘GenesOutOfAnalysis_NullVar.txt’ ‘VM-CompleteListOfGenes.txt’
  ‘bonferroni-0.05-ListOfGenes.txt’
  ‘bonferroni-0.05-VM-ListOfGenes.txt’
checkRd: (-1) AncestryMapper2.0-package.Rd:33: Escaped LaTeX specials: \~
checkRd: (-1) AncestryMapper2.0-package.Rd:38: Escaped LaTeX specials: \~
Note: found 237 marked UTF-8 strings
Package suggested but not available for checking: ‘arrow’
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) PV_post_triang_3.Rd:7: Escaped LaTeX specials: \_ \_
checkRd: (-1) PV_post_triang_3.Rd:22: Escaped LaTeX specials: \_ \_
checkRd: (-1) PV_pre_triang_3.Rd:7: Escaped LaTeX specials: \_ \_
checkRd: (-1) PV_pre_triang_3.Rd:22: Escaped LaTeX specials: \_ \_
Namespaces in Imports field not imported from:
  ‘car’ ‘datasets’ ‘dplyr’ ‘ggplot2’ ‘plotly’ ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘DescTools’ ‘HH’ ‘datasets’ ‘dplyr’ ‘rhandsontable’ ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘DescTools’ ‘HH’ ‘datasets’ ‘dplyr’ ‘rhandsontable’ ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 34.5Mb
  sub-directories of 1Mb or more:
    R  34.4Mb
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘Rdpack’ ‘mcclust’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘curl’ ‘httr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Undeclared packages ‘geepack’, ‘dispmod’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Imports includes 22 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Namespace in Imports field not imported from: ‘RcppParallel’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Package required but not available: ‘arrow’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘AER’ ‘ChainLadder’ ‘ISLR’ ‘ggplot2’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘pls’
  All declared Imports should be used.
Documented arguments not in \usage in Rd file 'apercu.Rd':
  ‘c’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Package required but not available: ‘bgw’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Note: found 1 marked UTF-8 string
'LazyData' is specified without a 'data' directory
Undeclared package ‘lme4’ in Rd xrefs
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    extdata   5.4Mb
Found the following files/directories:
  ‘APBinary_PPV.csv’ ‘APBinary_TPF.csv’
  ‘APBinary_ap_summary(method=perturbation,B=1500).csv’
  ‘APBinary_auc_summary(method=perturbation,B=1500).csv’
  ‘APSurv_PPV.csv’ ‘APSurv_TPF.csv’
  ‘APSurv_ap_summary(method=bootstrap,B=500).csv’
  ‘APSurv_auc_summary(method=bootstrap,B=500).csv’
  ‘CompareAP_Binary_dap_summary(method=none).csv’
  ‘CompareAP_Survival_dap_summary(method=bootstrap,B=500).csv’
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    data   1.6Mb
    doc    1.7Mb
Package suggested but not available for checking: ‘arcgisbinding’
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc   5.8Mb
checkRd: (-1) MultiPhasesTransition.Rd:23: Lost braces
    23 | code{position_minimum}.}
       |     ^
Undeclared package ‘RCurl’ in Rd xrefs
Note: found 76 marked Latin-1 strings
Namespaces in Imports field not imported from:
  ‘bannerCommenter’ ‘config’ ‘feather’ ‘here’ ‘knitr’ ‘log4r’ ‘ps’
  ‘rmarkdown’ ‘skimr’ ‘snakecase’ ‘testthat’ ‘tidyverse’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Undeclared package ‘rmarkdown’ in Rd xrefs
Specified C++11: please drop specification unless essential
Found export directive that requires package ‘methods’:
  ‘exportMethods’
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains ‘methods’.
'LazyData' is specified without a 'data' directory
Undeclared package ‘beepr’ in Rd xrefs
Namespaces in Imports field not imported from:
  ‘purrr’ ‘shinyBS’ ‘shinydashboard’ ‘shinyjs’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘arrow’
Namespace in Imports field not imported from: ‘mvtnorm’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘sp’
  All declared Imports should be used.
Undeclared packages ‘survey’, ‘Matching’ in Rd xrefs
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    R             2.3Mb
    help          1.2Mb
    testScripts   1.3Mb
Packages suggested but not available for checking:
  'sfit', 'expectile', 'HaarSeg', 'mpcbs'
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   5.1Mb
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/data/gannet/ripley/R/packages/tests-clang/arrow.Rcheck/00install.out’ for details.
Note: found 1409 marked UTF-8 strings
checkRd: (-1) breast_cancer_clean_features.Rd:45: Escaped LaTeX specials: \&
Note: found 328 marked UTF-8 strings
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘purrr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
File ‘ash/libs/ash.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    include   6.5Mb
Package which this enhances but not available for checking: ‘asreml’
'LazyData' is specified without a 'data' directory
Undeclared packages ‘assertive.properties’, ‘assertive.types’ in Rd xrefs
Unknown packages ‘assertive.properties’, ‘assertive.types’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Undeclared package ‘rstudioapi’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Found the following significant warnings:

  Warning in is.R() : 'is.R' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Undeclared package ‘sets’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
Package suggested but not available for checking: ‘asteRiskData’
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Running examples in ‘astrochron-Ex.R’ failed
The error most likely occurred in:

> ### Name: asm
> ### Title: Average Spectral Misfit
> ### Aliases: asm
> 
> ### ** Examples
> 
> ## These frequencies are from modelA (type '?astrochron' for more information). 
> ## They are for an 8 meter window, centered at 22 meters height. Units are cycles/m . 
> freq <- c(0.1599833,0.5332776,1.5998329,2.6797201,3.2796575,3.8795948,5.5194235,6.5459830)
> freq <- data.frame(freq)
> 
> ## Rayleigh frequency in cycles/m
> rayleigh <- 0.1245274
> 
> ## Nyquist frequency in cycles/m
> nyquist <- 6.66597
> 
> ## orbital target in 1/ky. Predicted periods for 94 Ma (see Meyers et al., 2012)
> target <- c(1/405.47,1/126.98,1/96.91,1/37.66,1/22.42,1/18.33)
> 
> ## percent uncertainty in orbital target
> fper=c(0.023,0.046,0.042,0.008,0.035,0.004)
> 
> asm(freq=freq,target=target,fper=fper,rayleigh=rayleigh,nyquist=nyquist,sedmin=0.5,sedmax=3,
+     numsed=100,linLog=1,iter=100000,output=FALSE)

----- PERFORMING AVERAGE SPECTRAL MISFIT ANALYSIS -----

 *** caught segfault ***
address 0x7ffc2c8fb7a0, cause 'memory not mapped'

Traceback:
 1: asm1.8(freq[, 1], numfreq, target[, 1], numtarg, fper[, 1], rayleigh,     nyquist, sedmin, sedmax, numsed, linLog, ispecgen, irepl,     isetfreq, iter)
 2: asm(freq = freq, target = target, fper = fper, rayleigh = rayleigh,     nyquist = nyquist, sedmin = 0.5, sedmax = 3, numsed = 100,     linLog = 1, iter = 1e+05, output = FALSE)
An irrecoverable exception occurred. R is aborting now ...
Note: found 17 marked UTF-8 strings
Undeclared package ‘iterators’ in Rd xrefs
Package suggested but not available for checking: ‘nc’
Running ‘testthat.R’ [9s/17s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > if(require(testthat))test_check("atime")
  Loading required package: testthat
  Loading required package: atime
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 38 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-CRAN.R:184:5'): error for expr.list not list ───────────────────
  <packageNotFoundError/error/condition>
  Error: there is no package called 'nc'
  Backtrace:
      ▆
   1. └─atime (local) dolist(expr.list) at test-CRAN.R:193:3
   2.   └─atime::atime(...) at test-CRAN.R:184:5
   3.     └─base::eval(m.call, N.env)
   4.       └─base::eval(m.call, N.env)
   5.         └─bench::mark(...)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 38 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
--- re-building ‘Custom_Plots.Rmd’ using knitr
--- finished re-building ‘Custom_Plots.Rmd’

--- re-building ‘Custom_References.Rmd’ using knitr
--- finished re-building ‘Custom_References.Rmd’

--- re-building ‘Custom_Units.Rmd’ using knitr
--- finished re-building ‘Custom_Units.Rmd’

--- re-building ‘cum_median.Rmd’ using knitr
--- finished re-building ‘cum_median.Rmd’

--- re-building ‘regex.Rmd’ using knitr

Quitting from lines 80-96 [unnamed-chunk-5] (regex.Rmd)
Error: processing vignette 'regex.Rmd' failed with diagnostics:
there is no package called 'nc'
--- failed re-building ‘regex.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘DT’ ‘lubridate’ ‘openair’ ‘plotly’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘R.rsp’
  All declared Imports should be used.
Undeclared package ‘snpar’ in Rd xrefs
Unknown package ‘snpar’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘dlnm’ ‘ggplot2’ ‘mvmeta’ ‘pbs’ ‘tsModel’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘tidyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Undeclared package ‘gtable’ in Rd xrefs
Note: found 1 marked UTF-8 string
Note: found 54582 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building ‘my-vignette.Rmd’ using knitr
Failed to parse YAML:

title: "AugmenterR package"
author: "Rafael S. Pereira"
date: "2024-02-09"
output: pdf_document
 vignette: >
          ^~~~~~
   %\VignetteIndexEntry{AugmenterR} 
   %\VignetteEngine{knitr::knitr}
   %\VignetteEncoding{UTF-8}

Error: processing vignette 'my-vignette.Rmd' failed with diagnostics:
Scanner error: mapping values are not allowed in this context at line 5, column 10
--- failed re-building ‘my-vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘nc’
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘abind’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘broom’ ‘diptest’ ‘ggplot2’ ‘hexbin’ ‘moments’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Undeclared package ‘tensorflow’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘usethis’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘plotly’ ‘shinycssloaders’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Hmisc’
  All declared Imports should be used.
Note: found 610 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘readxl’ ‘reshape2’ ‘stringr’ ‘tidyr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DT’ ‘bslib’ ‘rclipboard’ ‘rmarkdown’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
checkRd: (-1) ec2_create_security_group.Rd:66: Escaped LaTeX specials: \#
checkRd: (-1) ec2_create_security_group.Rd:66: Escaped LaTeX specials: \$
checkRd: (-1) ec2_create_security_group.Rd:79: Escaped LaTeX specials: \#
checkRd: (-1) ec2_create_security_group.Rd:79: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘qpdf’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘openssl’
  All declared Imports should be used.
Undeclared package ‘AzureAuth’ in Rd xrefs
Namespace in Imports field not imported from: ‘curl’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘R6’ ‘jose’ ‘openssl’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘httr’ ‘openssl’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
Package suggested but not available for checking: ‘lixoftConnectors’
Found the following files/directories:
  ‘containers-user-1234’
Note: found 64209 marked UTF-8 strings
Note: found 135648 marked UTF-8 strings
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   5.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Undeclared packages ‘InvariantCausalPrediction’, ‘CompareCausalNetworks’ in Rd xrefs
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    libs   7.1Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Note: found 260 marked UTF-8 strings
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    libs   7.6Mb
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    libs   4.1Mb
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
Undeclared package ‘tidyselect’ in Rd xrefs
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    R      2.5Mb
    data   1.3Mb
    doc    1.8Mb
Undeclared package ‘akima’ in Rd xrefs
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘fdpbandsdata’
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   4.7Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Note: found 148 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
checkRd: (-1) barcode.Rd:52: Escaped LaTeX specials: \&
Undeclared package ‘YaleToolkit’ in Rd xrefs
Note: found 13825 marked UTF-8 strings
File ‘Barnard/libs/Barnard.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    java   9.4Mb
Undeclared package ‘Rraven’ in Rd xrefs
File ‘base64enc/libs/base64enc.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Undeclared packages ‘jsonlite’, ‘arrow’ in Rd xrefs
Namespace in Imports field not imported from: ‘splines’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Earlier versions
Imports includes 25 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Namespaces in Imports field not imported from:
  ‘circlize’ ‘hexbin’ ‘scales’ ‘sna’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Undeclared package ‘Rmpi’ in Rd xrefs
Namespace in Imports field not imported from: ‘vtable’
  All declared Imports should be used.
Note: found 19 marked UTF-8 strings
File ‘batman/libs/batman.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Note: found 493 marked UTF-8 strings
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   6.4Mb
GNU make is a SystemRequirements.
Invalid package aliases in Rd file 'bayesANOVA-package.Rd':
  ‘bayesANOVA-package’
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘magrittr’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
checkRd: (-1) BayesComm-package.Rd:33: Escaped LaTeX specials: \&
File ‘BayesComm/libs/BayesComm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Specified C++11: please drop specification unless essential
checkRd: (-1) dilution.Rd:13: Escaped LaTeX specials: \$
checkRd: (-1) dilution.Rd:15: Escaped LaTeX specials: \$
checkRd: (-1) dilution.Rd:16: Escaped LaTeX specials: \$
checkRd: (-1) dilution.Rd:17: Escaped LaTeX specials: \$
checkRd: (-1) personality.Rd:15: Escaped LaTeX specials: \$
checkRd: (-1) personality.Rd:16: Escaped LaTeX specials: \$
checkRd: (-1) personality.Rd:17: Escaped LaTeX specials: \$
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs   8.1Mb
Namespace in Imports field not imported from: ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘MASS’ ‘MatrixModels’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 12.5Mb
  sub-directories of 1Mb or more:
    doc  10.9Mb
Installation failed.
See ‘/data/gannet/ripley/R/packages/tests-clang/BayesFM.Rcheck/00install.out’ for details.
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    libs   7.9Mb
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘StanHeaders’ ‘astsa’
  All declared Imports should be used.
GNU make is a SystemRequirements.
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    libs   7.8Mb
Namespaces in Imports field not imported from:
  ‘MASS’ ‘RcppParallel’ ‘mlbench’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Undeclared package ‘fGarch’ in Rd xrefs
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    libs   9.2Mb
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   3.5Mb
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘plyr’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
File ‘bayesianETAS/libs/bayesianETAS.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    help   1.9Mb
    libs   3.8Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Problems with news in ‘NEWS.md’:
No news entries found.
Namespace in Imports field not imported from: ‘FastGP’
  All declared Imports should be used.
Undeclared packages ‘rworldmap’, ‘snowFT’ in Rd xrefs
checkRd: (-1) insert_NAs.Rd:22: Lost braces; missing escapes or markup?
    22 | A data frame where new rows have been inserted to regularize the \code{date} column. This results in values provided for \code{id}, \code{date}, and {dt} while inserting NAs for all other columns. Additionally, observations with duplicate date-times are removed.
       |                                                                                                                                                      ^
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc    2.9Mb
    libs   1.4Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    help   6.0Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
    doc    1.0Mb
'LazyData' is specified without a 'data' directory
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    R     1.9Mb
    doc   3.8Mb
Namespaces in Imports field not imported from:
  ‘HDInterval’ ‘MCMCpack’ ‘R2WinBUGS’ ‘R2jags’ ‘carData’ ‘rjags’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) pulse_of_the_nation.Rd:10: Escaped LaTeX specials: \$
Note: found 1924 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘MASS’ ‘Matrix’ ‘matrixcalc’ ‘stats’
  All declared Imports should be used.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Argument items with no description in Rd file 'hmmeantemp.Rd':
  ‘dat’
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    doc    1.4Mb
    libs   1.6Mb
Undeclared package ‘mvtnorm’ in Rd xrefs
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    ex-data   4.7Mb
File ‘BayesTree/libs/BayesTree.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Note: found 385 marked UTF-8 strings
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
installed size is 11.8Mb
  sub-directories of 1Mb or more:
    libs  11.7Mb
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘ggfortify’ ‘ggplot2’ ‘matrixStats’ ‘reshape2’ ‘scales’
  All declared Imports should be used.
Undeclared package ‘formula.tools’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Undeclared package ‘betareg’ in Rd xrefs
File ‘BCBCSF/libs/BCBCSF.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following files/directories:
  ‘.fitbcbcsf_alpha1_mu_3_n_31_p_4026_nfsel_20_biascor_1.RData’
  ‘.fitbcbcsf_alpha1_mu_3_n_31_p_4026_nfsel_50_biascor_1.RData’
  ‘.fitbcbcsf_alpha1_mu_3_n_53_p_4026_nfsel_20_biascor_1.RData’
  ‘.fitbcbcsf_alpha1_mu_3_n_53_p_4026_nfsel_50_biascor_1.RData’
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc       1.2Mb
    extdata   3.3Mb
Found the following files/directories:
  ‘fabiabreast.txt’
checkRd: (-1) tlsce.Rd:51: Escaped LaTeX specials: \_
checkRd: (-1) tlsce.Rd:55: Escaped LaTeX specials: \_
checkRd: (-1) tlsce.Rd:90: Escaped LaTeX specials: \_
checkRd: (-1) tlsce.Rd:93: Escaped LaTeX specials: \_
S3 methods shown with full name in Rd file 'export.bce.Rd':
  ‘export.bce’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘coda’ ‘knitr’ ‘plyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
checkRd: (-1) BchronDensity.Rd:47: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) BchronDensity.Rd:48: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) BchronDensity.Rd:49: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) BchronDensity.Rd:50: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) BchronDensity.Rd:51: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) BchronDensity.Rd:52: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) BchronDensity.Rd:53: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) BchronRSL.Rd:34-41: Lost braces
    34 | itemize{
       |        ^
checkRd: (-1) Glendalough.Rd:19: Escaped LaTeX specials: \&
checkRd: (-1) Sluggan.Rd:19: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘knitr’ ‘rlang’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc       3.6Mb
    extdata   1.2Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Note: found 2666 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘dump.txt’
Found the following significant warnings:
  Warning in is.R() : 'is.R' is deprecated.
See ‘/data/gannet/ripley/R/packages/tests-clang/bdsmatrix.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 18.1.0rc’
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    libs   7.5Mb
GNU make is a SystemRequirements.
Imports includes 22 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘chron’ ‘colorspace’ ‘gtable’ ‘htmltools’ ‘htmlwidgets’
  ‘httpuv’ ‘magrittr’ ‘munsell’ ‘plyr’ ‘scales’ ‘stringi’ ‘xtable’
  ‘yaml’
  All declared Imports should be used.
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    java   7.7Mb
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘beast_plot_toy.pdf’
Note: found 107 marked UTF-8 strings
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   1.7Mb
    libs   3.4Mb
GNU make is a SystemRequirements.
Found the following files/directories:
  ‘pulse-PKdhtXMmr18n’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
File ‘BenfordTests/libs/BenfordTests.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Undeclared package ‘tibble’ in Rd xrefs
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘BiDAG’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘compiler’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘DT’ ‘dplyr’ ‘ggplot2’ ‘readxl’ ‘rlist’ ‘shinyBS’ ‘shinyWidgets’
  ‘shinydashboard’ ‘shinyjs’ ‘shinythemes’ ‘stringr’ ‘tidyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 42 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
File ‘betategarch/libs/betategarch.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Malformed Title field: should not end in a period.
Imports includes 27 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'print_summary_gibbs_psd_help.Rd':
  ‘flag=T:’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    libs   7.3Mb
Note: found 379 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
checkRd: (-1) bgmm-package.Rd:23: Escaped LaTeX specials: \&
Note: found 582 marked UTF-8 strings
GNU make is a SystemRequirements.
Installation failed.
See ‘/data/gannet/ripley/R/packages/tests-clang/bgw.Rcheck/00install.out’ for details.
checkRd: (-1) dotPlot.Rd:56: Escaped LaTeX specials: \&
Undeclared package ‘conf.design’ in Rd xrefs
Specified C++11: please drop specification unless essential
installed size is 153.3Mb
  sub-directories of 1Mb or more:
    include  153.2Mb
Specified C++11: please drop specification unless essential
Argument items with no description in Rd file 'h.pr.u.Rd':
  ‘z’ ‘ih’ ‘mu’ ‘sigma’ ‘pk’ ‘K’ ‘H’ ‘n’
Argument items with no description in Rd file 'hatpai.u.Rd':
  ‘z’ ‘hk1’ ‘hk0’ ‘ph1’ ‘ph0’ ‘sigma1’ ‘sigma0’ ‘mu1’ ‘mu0’ ‘pai’ ‘H’
  ‘n’
Argument items with no description in Rd file 'ind.u.Rd':
  ‘pr’
Argument items with no description in Rd file 'lambda.u.Rd':
  ‘nu’
Argument items with no description in Rd file 'mu.k.u.Rd':
  ‘k’ ‘ik’ ‘z’ ‘sigma’ ‘mu0’
Argument items with no description in Rd file 'nu.u.Rd':
  ‘ind’ ‘tau’ ‘H’
Argument items with no description in Rd file 'pai.u.Rd':
  ‘b’ ‘a.pai’ ‘b.pai’
Argument items with no description in Rd file 'sig.k.u.Rd':
  ‘k’ ‘ik’ ‘z’ ‘mu0’ ‘a0’ ‘b0’
Argument items with no description in Rd file 'z.pr.u.Rd':
  ‘z’ ‘hk’ ‘mu’ ‘sigma’ ‘ph’ ‘H’ ‘n’
File ‘BiasedUrn/libs/BiasedUrn.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Imports includes 23 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Note: found 99 marked UTF-8 strings
Note: found 1904 marked UTF-8 strings
Note: found 573 marked UTF-8 strings
checkRd: (-1) Jeffreysbs.Rd:17: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘DAAG’ ‘datasets’ ‘expm’ ‘mvtnorm’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘nycflights13’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘RBGL’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Found export directive that requires package ‘methods’:
  ‘exportMethods’
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains ‘methods’.
Package suggested but not available for checking: ‘ffbase’
Namespace in Imports field not imported from: ‘httr’
  All declared Imports should be used.
Invalid package aliases in Rd file 'package_bigdist.Rd':
  ‘package_bigdist-package’
Note: found 940 marked Latin-1 strings
Specified C++11: please drop specification unless essential
Found the following calls to data() loading into the global environment:
File ‘biglm/R/bigglm.R’:
  data(reset = TRUE)
  data(reset = FALSE)
See section ‘Good practice’ in ‘?data’.
File ‘biglm/libs/biglm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Specified C++14: please drop specification unless essential
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘rrelaxiv’
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘rmio’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘rmio’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘survival’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
Note: found 660 marked UTF-8 strings
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Undeclared packages ‘tint’, ‘pinp’, ‘linl’ in Rd xrefs
Found the following files/directories:
  ‘ccf_ccf_ID31_ID32_res.jpg’ ‘ccf_ccf_ID31_ID32_res.pdf’
  ‘output_ENSO_NHSST.tmp’ ‘plot_plot_ts_RAW_BIN_enso_sst.pdf’
  ‘plot_plot_ts_RAW_BIN_enso_sst01.png’
  ‘plot_plot_ts_RAW_BIN_enso_sst02.png’
  ‘plot_plot_ts_RAW_BIN_enso_sst03.png’
  ‘plot_plot_ts_RAW_BIN_enso_sst04.png’ ‘plot_ts_ACER_ABRUPT.pdf’
  ‘plot_ts_ACER_ABRUPT01.png’ ‘plot_ts_ACER_ABRUPT02.png’
  ‘plot_ts_ACER_ABRUPT03.png’ ‘plot_ts_ACER_ABRUPT04.png’
  ‘salida_ACER_ABRUPT.tmp’ ‘scaterplot_scatterplot_ENSO_SST.jpg’
  ‘scaterplot_scatterplot_ENSO_SST.pdf’
'LazyData' is specified without a 'data' directory
Undeclared package ‘genalg’ in Rd xrefs
'LazyData' is specified without a 'data' directory
File ‘binom/libs/binom.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘gtools’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    libs   7.1Mb
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
S3 methods shown with full name in Rd file 'select.cfs.Rd':
  ‘select.cfs’

S3 methods shown with full name in Rd file 'select.fast.filter.Rd':
  ‘select.fast.filter’

S3 methods shown with full name in Rd file 'select.forward.Corr.Rd':
  ‘select.forward.Corr’

S3 methods shown with full name in Rd file 'select.forward.wrapper.Rd':
  ‘select.forward.wrapper’

S3 methods shown with full name in Rd file 'select.inf.chi2.Rd':
  ‘select.inf.chi2’

S3 methods shown with full name in Rd file 'select.inf.gain.Rd':
  ‘select.inf.gain’

S3 methods shown with full name in Rd file 'select.inf.symm.Rd':
  ‘select.inf.symm’

S3 methods shown with full name in Rd file 'select.process.Rd':
  ‘select.process’

S3 methods shown with full name in Rd file 'select.relief.Rd':
  ‘select.relief’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Undeclared package ‘seqinr’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘asreml’
Documented arguments not in \usage in Rd file 'predict2.em.Rd':
  ‘na.rm’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
File ‘bioPN/libs/bioPN.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data      1.6Mb
    extdata   2.0Mb
Undeclared package ‘vegan’ in Rd xrefs
Invalid package aliases in Rd file 'bios2cor-package.Rd':
  ‘bios2cor-package’
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    extdata   4.8Mb
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc   5.6Mb
Problems with news in ‘NEWS.md’:
No news entries found.
Note: found 46 marked UTF-8 strings
checkRd: (-1) tocher.Rd:13: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘stats’ ‘utils’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Undeclared package ‘RColorBrewer’ in Rd xrefs
Package suggested but not available for checking: ‘RQuantLib’
Note: found 516 marked UTF-8 strings
Argument items with no description in Rd file 'ONA_compiled.Rd':
  ‘ATN’
Namespaces in Imports field not imported from:
  ‘R6’ ‘knitr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘digest’ ‘ergm’ ‘foreign’ ‘gWidgets2’ ‘gWidgets2tcltk’ ‘haven’
  ‘plot3D’ ‘plot3Drgl’ ‘rgl’ ‘sna’ ‘statnet.common’
  All declared Imports should be used.
Argument items with no description in Rd file 'export.dyadic.Rd':
  ‘blauObj’
Package suggested but not available for checking: ‘cmdstanr’
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    R          1.2Mb
    libs       8.4Mb
    testdata   1.4Mb
GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
  ‘knitr’ ‘rmarkdown’
  All declared Imports should be used.
checkRd: (-1) posteriorFeasibility.Rd:25: Escaped LaTeX specials: \#
checkRd: (-1) sp500Returns.Rd:4: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
Namespace in Imports field not imported from: ‘RcppArmadillo’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Undeclared package ‘np’ in Rd xrefs
File ‘blockTools/libs/blockTools.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘shiny’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘caret’ ‘datasets’ ‘dplyr’ ‘e1071’ ‘ggplot2’ ‘rhandsontable’ ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘caret’ ‘datasets’ ‘dplyr’ ‘e1071’ ‘ggplot2’ ‘rhandsontable’ ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 7 marked UTF-8 strings
Specified C++11: please drop specification unless essential
installed size is 13.0Mb
  sub-directories of 1Mb or more:
    libs  12.2Mb
GNU make is a SystemRequirements.
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    libs   7.8Mb
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Documented arguments not in \usage in Rd file 'id2rownum.Rd':
  ‘ids’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
GNU make is a SystemRequirements.
Found the following significant warnings:

  Warning in is.R() : 'is.R' is deprecated.
  Warning in is.R() : 'is.R' is deprecated.
  Warning in is.R() : 'is.R' is deprecated.
  Warning in is.R() : 'is.R' is deprecated.
  Warning in is.R() : 'is.R' is deprecated.
  Warning in is.R() : 'is.R' is deprecated.
  Warning in is.R() : 'is.R' is deprecated.
  Warning in is.R() : 'is.R' is deprecated.
  Warning in is.R() : 'is.R' is deprecated.
  Warning in is.R() : 'is.R' is deprecated.
  Warning in is.R() : 'is.R' is deprecated.
  Warning in is.R() : 'is.R' is deprecated.
  Warning in is.R() : 'is.R' is deprecated.
  Warning in is.R() : 'is.R' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Namespace in Imports field not imported from: ‘curl’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Rgraphviz’ ‘fastDummies’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘caret’ ‘e1071’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    data   7.0Mb
Note: found 21550 marked UTF-8 strings
Package suggested but not available for checking: ‘sangerseqR’
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
installed size is 46.5Mb
  sub-directories of 1Mb or more:
    include  10.7Mb
    lib      35.4Mb
GNU make is a SystemRequirements.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
Namespace in Imports field not imported from: ‘sna’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘HSAUR3’ ‘knitr’ ‘rmarkdown’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Undeclared package ‘psych’ in Rd xrefs
File ‘bootruin/libs/bootruin.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
GNU make is a SystemRequirements.
Packages suggested but not available for checking: 'cplexAPI', 'bestsubset'
Documented arguments not in \usage in Rd file 'InternalFunctions.Rd':
  ‘metric’ ‘matrix’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Undeclared packages ‘data.table’, ‘readxl’, ‘openxlsx’ in Rd xrefs
Specified C++11: please drop specification unless essential
checkRd: (-1) bp_rats.Rd:41: Escaped LaTeX specials: \&
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘graphics’
  All declared Imports should be used.
Packages suggested but not available for checking: 'RGtk2', 'cairoDevice'
Documented arguments not in \usage in Rd file 'utils.Rd':
  ‘max.len’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘CCA’ ‘brainR’ ‘elasticnet’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
File ‘Branching/libs/Branching.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
Package required but not available: ‘arrow’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Undeclared package ‘generics’ in Rd xrefs
GNU make is a SystemRequirements.
Note: found 108 marked UTF-8 strings
Namespace in Imports field not imported from: ‘kableExtra’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘profileModel’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘cmdstanr’
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    R     3.0Mb
    doc   3.6Mb
Package suggested but not available for checking: ‘glmmADMB’
Found the following significant warnings:
  Warning in is.R() : 'is.R' is deprecated.
See ‘/data/gannet/ripley/R/packages/tests-clang/BRugs.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 18.1.0rc’
Found the following Makefile(s) with an include directive with a pathname using R_HOME:
  src/Makefile.win
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'.
Found the following significant warnings:

  Warning in is.R() : 'is.R' is deprecated.
  Warning in is.R() : 'is.R' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
'LazyData' is specified without a 'data' directory
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
Namespaces in Imports field not imported from:
  ‘rworldxtra’ ‘sp’
  All declared Imports should be used.
Undeclared package ‘data.table’ in Rd xrefs
Undeclared package ‘weibullness’ in Rd xrefs
Argument items with no description in Rd file 'plot.bshazard.Rd':
  ‘\dots’
Argument items with no description in Rd file 'print.bshazard.Rd':
  ‘\dots’
Argument items with no description in Rd file 'summary.bshazard.Rd':
  ‘\dots’
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   2.9Mb
    doc    1.4Mb
installed size is 12.6Mb
  sub-directories of 1Mb or more:
    fonts   3.7Mb
    lib     5.4Mb
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Imports includes 23 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘grDevices’ ‘graphics’
  All declared Imports should be used.
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    doc    2.8Mb
    libs   2.6Mb
Namespaces in Imports field not imported from:
  ‘mvtnorm’ ‘ssmn’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    libs   8.6Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘RSiena’
Note: found 89 marked UTF-8 strings
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc   4.9Mb
'LazyData' is specified without a 'data' directory
Undeclared package ‘mitools’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Imports includes 32 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc       2.3Mb
    extdata   3.4Mb
Undeclared package ‘googledrive’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Hmisc’ ‘magrittr’ ‘rmarkdown’
  All declared Imports should be used.
checkRd: (-1) kink_estimator.Rd:60: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'count.Rd':
  ‘.data’

Documented arguments not in \usage in Rd file 'unite.Rd':
  ‘.data’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Undeclared packages ‘Hmisc’, ‘gtools’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
File ‘bvarsv/libs/bvarsv.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Undeclared package ‘tibble’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Undeclared packages ‘quadprog’, ‘nnls’ in Rd xrefs
File ‘bvls/libs/bvls.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Note: found 179 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘markdown’
  All declared Imports should be used.
checkRd: (-1) deleteZeroComponents.Rd:70: Escaped LaTeX specials: \& \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘ReGenesees’
Note: found 58 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
File ‘CAMAN/libs/CAMAN.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 287 marked UTF-8 strings
Namespace in Imports field not imported from: ‘sf’
  All declared Imports should be used.
Note: found 2992 marked UTF-8 strings
Note: found 23 marked UTF-8 strings
Argument items with no description in Rd file 'makeEventHistory.Rd':
  ‘type’
Argument items with no description in Rd file 'plotSeqCount.Rd':
  ‘segColors’
Undeclared packages ‘yacca’, ‘CCA’ in Rd xrefs
Found the following files/directories:
  ‘MDA231_tree.pdf’
'LazyData' is specified without a 'data' directory
Note: found 59 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘htmltools’ ‘shinydashboard’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    captr .1.4
    captr .1.3
    captr .1.2
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc   5.7Mb
Note: found 1 marked UTF-8 string
checkRd: (-1) States.Rd:48: Escaped LaTeX specials: \$
Problems with news in ‘NEWS.md’:
No news entries found.
Namespaces in Imports field not imported from:
  ‘Hmisc’ ‘methods’ ‘readr’ ‘recipes’ ‘sf’ ‘stringr’ ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Undeclared package ‘plotrix’ in Rd xrefs
Package suggested but not available for checking: ‘rnaturalearthhires’
Namespace in Imports field not imported from: ‘R.utils’
  All declared Imports should be used.
installed size is 12.4Mb
  sub-directories of 1Mb or more:
    www  12.3Mb
Namespace in Imports field not imported from: ‘shiny’
  All declared Imports should be used.
GNU make is a SystemRequirements.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    doc   5.4Mb
Namespaces in Imports field not imported from:
  ‘R6’ ‘crayon’ ‘dplyr’ ‘tidyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘pulse-PKdhtXMmr18n’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Invalid package aliases in Rd file 'EcoLinkPredict.Rd':
  ‘EcoLinkPredict-package’
'LazyData' is specified without a 'data' directory
Note: found 3 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Matrix’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
checkRd: (-1) gen.sim.data.Rd:73: Lost braces; missing escapes or markup?
    73 | Y = X_0 Beta_0^T + X_1 Beta_1^T + Z Gamma^T + E Sigma^{1/2},
       |                                                       ^
Namespaces in Imports field not imported from:
  ‘broom’ ‘epitools’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 20.3Mb
  sub-directories of 1Mb or more:
    doc  19.9Mb
Found the following files/directories:
  ‘catmapdata.fixed.effects.plot.pdf’ ‘catmapdata.funnel.plot.pdf’
  ‘catmapdata.output.txt’ ‘catmapdata.random.effects.plot.pdf’
Undeclared packages ‘pixmap’, ‘XML’, ‘exactRankTests’, ‘coin’, ‘ROCR’, ‘Epi’, ‘verification’, ‘Hmisc’, ‘gtools’, ‘magic’, ‘zoo’ in Rd xrefs
Specified C++14: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘epitools’ ‘forcats’ ‘purrr’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Undeclared packages ‘extraDistr’, ‘mvtnorm’ in Rd xrefs
Note: found 32 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘CBPS’ ‘spelling’
  All declared Imports should be used.
checkRd: (-1) tpcExample.Rd:30: Escaped LaTeX specials: \&
Undeclared package ‘graph’ in Rd xrefs
Package suggested but not available for checking: ‘rkeops’
GNU make is a SystemRequirements.
Package vignette with \VignetteEngine{} not specifying an engine package:
  ‘causalsens.Rnw’
Engines should be specified as \VignetteEngine{PKG::ENG}.
Note: found 1045 marked UTF-8 strings
Undeclared package ‘sitmo’ in Rd xrefs
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is 16.1Mb
  sub-directories of 1Mb or more:
    libs  15.6Mb
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘GeneNet’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘fields’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘hotcold.csv’
Problems with news in ‘NEWS.md’:
No news entries found.
Specified C++11: please drop specification unless essential
Packages which this enhances but not available for checking:
  'arrow', 'CirceR', 'Capr'
Package vignette without corresponding tangle output:
  ‘CDNmoney.Stex’
OMP: Warning #96: Cannot form a team with 24 threads, using 2 instead.
OMP: Hint Consider unsetting KMP_DEVICE_THREAD_LIMIT (KMP_ALL_THREADS), KMP_TEAMS_THREAD_LIMIT, and OMP_THREAD_LIMIT (if any are set).

It looks like this package (or a package it requires) has a startup
message which cannot be suppressed: see ?packageStartupMessage.
Found the following files/directories:
  ‘figure01ceg.pdf’ ‘figure02ceg.pdf’ ‘staged.tree.graph.pdf’
  ‘stratified-event-tree-plot.pdf’
'LazyData' is specified without a 'data' directory
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    data   3.2Mb
    doc    2.0Mb
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
Auto-generated content requiring editing in Rd file 'CensMFM-package.Rd':
  \details: ‘...o use the package, including the most important functions ~~’
Package required but not available: ‘arrow’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Unexported objects imported by ':::' calls:
  ‘copula:::dCdu’ ‘copula:::fitCopStart’
  See the note in ?`:::` about the use of this operator.
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘data.table’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Argument items with no description in Rd file 'centralplot.Rd':
  ‘alpha’
'LazyData' is specified without a 'data' directory
Note: found 104 marked UTF-8 strings
Undeclared package ‘vegan’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘base’ ‘stats’ ‘tidyr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DT’ ‘batchtools’ ‘data.table’ ‘dplyr’ ‘ggplot2’ ‘htmltools’
  ‘jsonlite’ ‘magrittr’ ‘methods’ ‘plotly’ ‘reshape’ ‘rlang’ ‘shiny’
  ‘shinyWidgets’ ‘shinyjqui’ ‘shinyjs’ ‘shinymaterial’ ‘sortable’ ‘ssh’
  ‘xml2’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘lmtest’
  All declared Imports should be used.
Problems with news in ‘NEWS.md’:
No news entries found.
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Major refactoring of the code
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) helpers_pbp.Rd:336: Lost braces in \itemize; meant \describe ?
checkRd: (-1) helpers_pbp.Rd:337: Lost braces in \itemize; meant \describe ?
checkRd: (-1) helpers_pbp.Rd:338: Lost braces in \itemize; meant \describe ?
checkRd: (-1) helpers_pbp.Rd:339: Lost braces in \itemize; meant \describe ?
checkRd: (-1) helpers_pbp.Rd:340: Lost braces in \itemize; meant \describe ?
checkRd: (-1) helpers_pbp.Rd:341: Lost braces in \itemize; meant \describe ?
checkRd: (-1) helpers_pbp.Rd:390: Lost braces in \itemize; meant \describe ?
checkRd: (-1) helpers_pbp.Rd:391: Lost braces in \itemize; meant \describe ?
checkRd: (-1) helpers_pbp.Rd:392: Lost braces in \itemize; meant \describe ?
checkRd: (-1) helpers_pbp.Rd:393: Lost braces in \itemize; meant \describe ?
checkRd: (-1) helpers_pbp.Rd:394: Lost braces in \itemize; meant \describe ?
checkRd: (-1) update_cfb_db.Rd:46-48: Lost braces in \itemize; meant \describe ?
checkRd: (-1) update_cfb_db.Rd:49-52: Lost braces in \itemize; meant \describe ?
Documented arguments not in \usage in Rd file 'create_epa.Rd':
  ‘clean_pbp_dat’ ‘df’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
installed size is 38.5Mb
  sub-directories of 1Mb or more:
    include  38.4Mb
Malformed Title field: should not end in a period.
File ‘cgAUC/libs/cgAUC.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘tidyverse’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘grDevices’
  All declared Imports should be used.
Undeclared packages ‘bigBits’, ‘dplyr’, ‘matrixStats’, ‘filesstrings’, ‘pracma’, ‘sf’ in Rd xrefs
Namespaces in Imports field not imported from:
  ‘bench’ ‘ggplot2’
  All declared Imports should be used.
Invalid package aliases in Rd file 'ChangePointAnalyzer-package.Rd':
  ‘ChangePointAnalyzer-package’
Auto-generated content requiring editing in Rd file 'ChangePointAnalyzer-package.Rd':
  \references: ‘This optional section can contain literature or other refere...’
  \seealso: ‘Optional links to other man pages’
  \examples: ‘\dontrun{      ## Optional simple examples of the most impor...’
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    extdata   4.7Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘AER’ ‘graphics’ ‘lmtest’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘darts’
Namespace in Imports field not imported from: ‘jsonlite’
  All declared Imports should be used.
Note: found 200 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘countreg’
Namespaces in Imports field not imported from:
  'knitr' 'rmarkdown'
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘dbplyr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘gamlss.dist’
  All declared Imports should be used.
Note: found 32 marked UTF-8 strings
Imports includes 29 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
'LazyData' is specified without a 'data' directory
Note: found 8119 marked UTF-8 strings
Invalid package aliases in Rd file 'ChIPtest-package.Rd':
  ‘ChIPtest_1.0-package’
File ‘ChIPtest/libs/ChIPtest.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘cmdstanr’
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
Package unavailable to check Rd xrefs: ‘cmdstanr’
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs   2.0Mb
Problems with news in ‘NEWS.md’:
No news entries found.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    help   2.2Mb
installed size is 18.0Mb
  sub-directories of 1Mb or more:
    data  17.9Mb
Note: found 10 marked UTF-8 strings
Package vignettes with \VignetteEngine{} not specifying an engine package:
  ‘a-introduction.Rmd’
  ‘b-state-choropleth.Rmd’
  ‘c-county-choropleth.Rmd’
  ‘d-country-choropleth.Rmd’
  ‘e-admin1-choropleths.Rmd’
  ‘f-creating-your-own-maps.Rmd’
  ‘g-mapping-us-census-data.Rmd’
  ‘h-world-bank-data.Rmd’
  ‘i-animated-choropleths.Rmd’
Engines should be specified as \VignetteEngine{PKG::ENG}.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘entab’
Namespace in Imports field not imported from: ‘readr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘htmltools’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘base’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DT’ ‘dplyr’ ‘prettydoc’ ‘rmdformats’ ‘skimr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘stringr’
  All declared Imports should be used.
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    doc       5.7Mb
    extdata   2.1Mb
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    R         1.7Mb
    extdata   4.3Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘magrittr’
  All declared Imports should be used.
Note: found 28982 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘circlize’ ‘utils’
  All declared Imports should be used.
Package suggested but not available for checking: ‘userfriendlyscience’
Package vignette with \VignetteEngine{} not specifying an engine package:
  ‘circlize.Rmd’
Engines should be specified as \VignetteEngine{PKG::ENG}.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘RInside’ ‘circular’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc   7.3Mb
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘RColorBrewer’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘networkD3’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 29 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    doc    3.6Mb
    help   1.0Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
Undeclared package ‘reshape’ in Rd xrefs
Note: found 9 marked UTF-8 strings
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Undeclared packages ‘bslib’, ‘shiny’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    clhs_0.7-2
    clhs_0.7-0
    clhs_0.6-0
    clhs_0.5-7
    clhs_0.5-6
    clhs_0.5-3
    clhs_0.5-2
    clhs_0.5-1
    clhs_0.5-0
    clhs_0.4-3
    clhs_0.4-2
    clhs_0.4-1
    clhs_0.4-0
    clhs_0.3-2
    clhs_0.3-1
    clhs_0.3-0
    clhs_0.2-1
    clhs_0.2-0
    clhs_0.1-0
Namespace in Imports field not imported from: ‘sp’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
File ‘ClickClust/libs/ClickClust.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package required but not available: ‘arrow’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Note: found 1 marked UTF-8 string
Note: found 494 marked Latin-1 strings
  Note: found 11871 marked UTF-8 strings
Note: found 10332 marked UTF-8 strings
Specified C++11: please drop specification unless essential
Note: found 8737 marked UTF-8 strings
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   3.4Mb
    doc    1.9Mb
installed size is 48.7Mb
  sub-directories of 1Mb or more:
    extdata  48.5Mb
Undeclared package ‘s2dv’ in Rd xrefs
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc   4.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    doc   5.4Mb
checkRd: (-1) clme.Rd:84: Escaped LaTeX specials: \&
File ‘clogitboost/libs/clogitboost.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘clogitL1/libs/clogitL1.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Problems with news in ‘NEWS.md’:
No news entries found.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Objects in \usage without \alias in Rd file 'clpm-internal.Rd':
  ‘lpm.newton2’ ‘lpm.fit’ ‘lpm.newton’ ‘L_lambda’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Undeclared packages ‘mlbench’, ‘fpc’ in Rd xrefs
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘DT’
  All declared Imports should be used.
Found the following files/directories:
  ‘clusterhap_reports’
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in Rd file 'calculate_connectivity.Rd':
  ‘datdf’

Documented arguments not in \usage in Rd file 'dunn_metric.Rd':
  ‘distance’ ‘method’

Documented arguments not in \usage in Rd file 'evaluate_all_column_dataset.Rd':
  ‘data’

Documented arguments not in \usage in Rd file 'information_external.Rd':
  ‘info’

Documented arguments not in \usage in Rd file 'information_internal.Rd':
  ‘info’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
File ‘clustering.sc.dp/libs/clustering.sc.dp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
File ‘ClusterStability/libs/ClusterStability.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘sp’ ‘spdep’
  All declared Imports should be used.
checkRd: (-1) dtmvnom.Rd:30: Escaped LaTeX specials: \&
Namespace in Imports field not imported from: ‘stringi’
  All declared Imports should be used.
Note: found 5626 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘MASS’ ‘cluster’ ‘datasets’ ‘dplyr’ ‘klaR’ ‘psycho’ ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
File ‘clv/libs/clv.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   5.2Mb
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘MPV’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
Note: found 4622 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
checkRd: (-1) plot.predict.crrQR.Rd:18: Escaped LaTeX specials: \#
checkRd: (-1) plot.predict.crrQR.Rd:22: Escaped LaTeX specials: \#
checkRd: (-1) plot.predict.crr.Rd:18: Escaped LaTeX specials: \#
checkRd: (-1) plot.predict.crr.Rd:22: Escaped LaTeX specials: \#
File ‘cmprsk/libs/cmprsk.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘FNN’ ‘R.utils’ ‘SearchTrees’ ‘colorspace’ ‘colourpicker’
  ‘data.table’ ‘maps’ ‘ncdf4’ ‘raster’ ‘shinyFiles’ ‘shinyWidgets’
  ‘shinyjs’ ‘shinythemes’ ‘tcltk’ ‘xml2’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘caret’ ‘e1071’ ‘epitools’ ‘shiny’ ‘shinyMatrix’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘tobit1’
'LazyData' is specified without a 'data' directory
Undeclared package ‘wavethresh’ in Rd xrefs
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc       3.2Mb
    extdata   1.7Mb
Namespace in Imports field not imported from: 'Hmisc'
  All declared Imports should be used.
Package suggested but not available for checking: ‘PopGenome’
Documented arguments not in \usage in Rd file 'feat_sample.Rd':
  ‘locus_group’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Documented arguments not in \usage in Rd file 'get_superior.Rd':
  ‘stirng’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Package suggested but not available for checking: ‘disttree’
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘nnet’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 14729 marked UTF-8 strings
Package which this enhances but not available for checking: ‘rkward’
Undeclared package ‘pls’ in Rd xrefs
Documented arguments not in \usage in Rd file 'cocorresp-internal.Rd':
  ‘Y’ ‘eps’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Package which this enhances but not available for checking: ‘rkward’
Note: found 27 marked UTF-8 strings
Package suggested but not available for checking: ‘userfriendlyscience’
Namespaces in Imports field not imported from:
  ‘graphics’ ‘jsonlite’ ‘rlang’ ‘tidyselect’ ‘vctrs’
  All declared Imports should be used.
Note: found 65 marked UTF-8 strings
Note: found 30244 marked UTF-8 strings
Found the following files/directories:
  ‘foo.R’ ‘foo.html’
Note: found 6 marked UTF-8 strings
Package suggested but not available for checking: ‘bvpSolve’
'LazyData' is specified without a 'data' directory
File ‘coenoflex/libs/coenoflex.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Namespaces in Imports field not imported from:
  ‘Rdpack’ ‘coin’ ‘ggplot2’ ‘plyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 4186 marked UTF-8 strings
Note: found 89 marked Latin-1 strings
  Note: found 1203 marked UTF-8 strings
File ‘collUtils/libs/collUtils.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc   4.9Mb
Namespaces in Imports field not imported from:
  ‘magrittr’ ‘qpdf’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 742 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘grid’ ‘gridExtra’
  All declared Imports should be used.
Found the following significant warnings:

  Warning in is.R() : 'is.R' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc       2.4Mb
    extdata   2.1Mb
Note: found 2 marked UTF-8 strings
Unexported object imported by a ':::' call: ‘crayon:::mypaste’
  See the note in ?`:::` about the use of this operator.
Problems with news in ‘NEWS.md’:
No news entries found.
Namespaces in Imports field not imported from:
  ‘chi’ ‘dplyr’ ‘spatstat.utils’ ‘utils’
  All declared Imports should be used.
Malformed Description field: should contain one or more complete sentences.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘cometExactTest_plot.pdf’
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘GGally’ ‘RColorBrewer’ ‘abind’ ‘diagram’ ‘ggplot2’ ‘grid’ ‘gtable’
  ‘igraph’ ‘magrittr’ ‘plyr’ ‘purrr’ ‘reshape2’ ‘scales’ ‘useful’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘CAM’
File ‘compareC/libs/compareC.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Skipping checking math rendering: package 'V8' unavailable
Namespaces in Imports field not imported from:
  ‘PearsonDS’ ‘VGAM’ ‘actuar’ ‘fExtremes’ ‘rmutil’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 11 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
File ‘ConConPiWiFun/libs/ConConPiWiFun.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Note: found 92 marked UTF-8 strings
Undeclared packages ‘DescTools’, ‘epiR’ in Rd xrefs
Auto-generated content requiring editing in Rd file 'concordancer-package.Rd':
  \references: ‘This optional section can contain literature or other refere...’
  \seealso: ‘Optional links to other man pages’
  \examples: ‘\dontrun{      ## Optional simple examples of the most impor...’
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘kernlab’ ‘purrr’ ‘survminer’ ‘tidyverse’
  All declared Imports should be used.
checkRd: (-1) babies.Rd:35: Escaped LaTeX specials: \&
Problems with news in ‘NEWS.md’:
No news entries found.
Undeclared package ‘mvtnorm’ in Rd xrefs
'LazyData' is specified without a 'data' directory
run_pipeline_gbq: no visible global function definition for
  ‘query_exec’
Undefined global functions or variables:
  query_exec
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found export directive that requires package ‘methods’:
  ‘exportClasses’
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains ‘methods’.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘mvtnorm’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
checkRd: (-1) clResults.Rd:58: Lost braces in \itemize; meant \describe ?
checkRd: (-1) clResults.Rd:59: Lost braces in \itemize; meant \describe ?
checkRd: (-1) clResults.Rd:60-61: Lost braces in \itemize; meant \describe ?
checkRd: (-1) clResults.Rd:62-63: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘design_names.csv’ ‘design_numbers.csv’
  ‘encoded_orthogonal_factorial_design.csv’
  ‘orthogonal_factorial_design.csv’
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘base’ ‘lwgeom’ ‘s2’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DT’ ‘Hmisc’ ‘dplyr’ ‘foreign’ ‘lavaan’ ‘openxlsx’ ‘purrr’ ‘semTools’
  ‘shinyWidgets’ ‘stringr’ ‘summarytools’ ‘waiter’
  All declared Imports should be used.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    htmlwidgets   3.9Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘scales’ ‘sna’
  All declared Imports should be used.
Note: found 244 marked UTF-8 strings
Undeclared package ‘ggplot2’ in Rd xrefs
File ‘ConsReg/libs/ConsReg.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
File ‘contoureR/libs/contoureR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Note: found 3 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 1 marked UTF-8 string
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Invalid package aliases in Rd file 'coopProductGame-package.Rd':
  ‘coopProducGame-package’
Note: found 144 marked UTF-8 strings
checkRd: (-1) condQestCopC.Rd:45: Lost braces; missing escapes or markup?
    45 | obtain the conditional qth quantile of Y_{n+1} given {Y1,...,Yn}.
       |                                          ^
checkRd: (-1) condQestCopC.Rd:45: Lost braces; missing escapes or markup?
    45 | obtain the conditional qth quantile of Y_{n+1} given {Y1,...,Yn}.
       |                                                      ^
checkRd: (-1) condQestCopC.Rd:40: Lost braces; missing escapes or markup?
    40 | \code{condQestCopC} returns the conditional tao-th quantile of Y_{n+1} given {Y1,...,Yn}
       |                                                                  ^
checkRd: (-1) condQestCopC.Rd:40: Lost braces; missing escapes or markup?
    40 | \code{condQestCopC} returns the conditional tao-th quantile of Y_{n+1} given {Y1,...,Yn}
       |                                                                              ^
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc             2.3Mb
    vignette_data   2.6Mb
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'ft.Rd':
  ‘theta’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Packages suggested but not available for checking:
  'cec2005benchmark', 'cec2013'
'LazyData' is specified without a 'data' directory
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    R     2.1Mb
    doc   3.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
File ‘cord/libs/cord.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘readr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘devtools’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘ggplot2’ ‘re2’ ‘rmarkdown’ ‘shinyWidgets’
  ‘shinydashboard’ ‘shinyjs’
  All declared Imports should be used.
Note: found 1187 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Note: found 438 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘data.table’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘xcms’
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 18.1Mb
  sub-directories of 1Mb or more:
    extdata  17.8Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc   4.8Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc   6.7Mb
Namespace in Imports field not imported from: ‘graphics’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘knitr’ ‘rmarkdown’
  All declared Imports should be used.
checkRd: (-1) cosmoFns-package.Rd:34: Escaped LaTeX specials: \&
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
Note: found 59 marked UTF-8 strings
Namespace in Imports field not imported from: ‘jpeg’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Undeclared packages ‘xaringan’, ‘beepr’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 9044 marked UTF-8 strings
Note: found 140280 marked UTF-8 strings
Undeclared package ‘betareg’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘gstat’
  All declared Imports should be used.
File ‘covBM/libs/covBM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘covfefe_inauguration.txt’
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc       1.6Mb
    extdata   2.7Mb
Note: found 1934235 marked UTF-8 strings
Note: found 2385 marked UTF-8 strings
Namespace in Imports field not imported from: ‘lubridate’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘httr’ ‘stringr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘mapview’ ‘plotly’
  All declared Imports should be used.
Note: found 20 marked UTF-8 strings
Note: found 213180 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘gsl’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘misc3d’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘mediation’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Found the following significant warnings:

  Warning in is.R() : 'is.R' is deprecated.
  Warning in is.R() : 'is.R' is deprecated.
  Warning in is.R() : 'is.R' is deprecated.
  Warning in is.R() : 'is.R' is deprecated.
  Warning in is.R() : 'is.R' is deprecated.
  Warning in is.R() : 'is.R' is deprecated.
  Warning in is.R() : 'is.R' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    libs   7.4Mb
'LazyData' is specified without a 'data' directory
Found the following significant warnings:

  Warning in is.R() : 'is.R' is deprecated.
  Warning in is.R() : 'is.R' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    libs   9.8Mb
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
File ‘CoxPlus/libs/CoxPlus.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Rdpack’ ‘grDevices’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘BEST’
File ‘cpm/libs/cpm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Specified C++14: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘RcppProgress’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
File ‘cqrReg/libs/cqrReg.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   5.1Mb
Note: found 11 marked Latin-1 strings
  Note: found 57 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
File ‘credule/libs/credule.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Note: found 37 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘BSgenome.Scerevisiae.UCSC.sacCer3’
Namespaces in Imports field not imported from:
  ‘DT’ ‘gbm’
  All declared Imports should be used.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    doc   6.4Mb
Packages suggested but not available for checking: 'conos', 'pagoda2'
‘cleanup’: /bin/bash is not portable
'LazyData' is specified without a 'data' directory
Note: found 3 marked UTF-8 strings
Found the following files/directories:
  ‘crop.eps’ ‘crop.pdf’ ‘crop.png’ ‘crop.ps’
Undeclared package ‘R2jags’ in Rd xrefs
Namespaces in Imports field not imported from:
  ‘R6’ ‘dplyr’ ‘r6extended’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
File ‘crrSC/libs/crrSC.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Note: found 500 marked UTF-8 strings
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   5.7Mb
Namespaces in Imports field not imported from:
  ‘DT’ ‘dplyr’ ‘geosphere’ ‘mapdata’ ‘maps’ ‘marmap’ ‘shinydashboard’
  ‘shinyjs’ ‘stringr’ ‘swfscDAS’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Undeclared package ‘copula’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Imports includes 21 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘extrafont’ ‘future’
  All declared Imports should be used.
Note: found 282 marked UTF-8 strings
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
    doc    1.6Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    doc   7.7Mb
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    data   7.6Mb
Note: found 3031 marked UTF-8 strings
Note: found 2 marked UTF-8 strings
Documented arguments not in \usage in Rd file 'tool.Rd':
  ‘seq’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    data   1.9Mb
    doc    1.6Mb
    libs   2.2Mb
Namespaces in Imports field not imported from:
  ‘epitools’ ‘rpivotTable’ ‘shinyMatrix’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 1350 marked UTF-8 strings
installed size is 16.1Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    data   1.7Mb
    libs  12.0Mb
Namespace in Imports field not imported from: ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Found the following files/directories:
  ‘par-7269706c6579’
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘caret’ ‘datasets’ ‘dplyr’ ‘e1071’ ‘party’ ‘rhandsontable’ ‘rpart’
  ‘rpart.plot’ ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘caret’ ‘datasets’ ‘dplyr’ ‘e1071’ ‘party’ ‘rhandsontable’ ‘rpart’
  ‘rpart.plot’ ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘Hello.csv’
'LazyData' is specified without a 'data' directory
Undeclared package ‘caret’ in Rd xrefs
Documented arguments not in \usage in Rd file 'chi2cub2cov.Rd':
  ‘covar’

Documented arguments not in \usage in Rd file 'cubpq.Rd':
  ‘summary’

Documented arguments not in \usage in Rd file 'cubshe.Rd':
  ‘makeplot’ ‘summary’

Documented arguments not in \usage in Rd file 'kkk.Rd':
  ‘Vector’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Namespace in Imports field not imported from: ‘pspearman’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
File ‘curl/libs/curl.so’:
  Found non-API call to R: ‘R_new_custom_connection’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Note: found 459 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘Adjusted_p_values.pdf’ ‘Effect_Size_Curves.pdf’
  ‘Mean_Difference_Curves.pdf’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Misc
checkRd: (-1) abs_d_ppv_npv.Rd:27: Escaped LaTeX specials: \_ \_ \_
Package which this enhances but not available for checking: ‘RGtk2’
Documented arguments not in \usage in Rd file 'compute_stat.Rd':
  ‘K_0’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘lattice’ ‘robustbase’
A package should be listed in only one of these fields.
Packages which this enhances but not available for checking:
  'Rcplex', 'gurobi', 'rcbc'
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    R     2.7Mb
    doc   1.2Mb
File ‘cycleRtools/libs/cycleRtools.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Problems with news in ‘NEWS.md’:
No news entries found.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    docs          1.0Mb
    extdata       1.4Mb
    htmlwidgets   1.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘stringi’
  All declared Imports should be used.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc   4.9Mb
Namespace in Imports field not imported from: ‘titanic’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 469 marked UTF-8 strings
checkRd: (-1) D4TAlinkTask.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) D4TAlinkTask.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) D4TAlinkTask.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) D4TAlinkTask.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) D4TAlinkTask.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) D4TAlinkTask.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) D4TAlinkTask.Rd:19-20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) D4TAlinkTask.Rd:21-22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) D4TAlinkTask.Rd:23-24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) D4TAlinkTask.Rd:25-26: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 109157 marked UTF-8 strings
Note: found 4 marked Latin-1 strings
  Note: found 21 marked UTF-8 strings
Note: found 2020 marked UTF-8 strings
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
Note: found 212 marked Latin-1 strings
  Note: found 12719 marked UTF-8 strings
File ‘DALY/libs/DALY.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Documented arguments not in \usage in Rd file 'mm_run_reg.Rd':
  ‘all_params’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Note: found 5 marked UTF-8 strings
Invalid package aliases in Rd file 'dap-package.Rd':
  ‘dap-package’
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   4.4Mb
'LazyData' is specified without a 'data' directory
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    java   7.5Mb
Undeclared package ‘DRquality’ in Rd xrefs
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘htmltools’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘purrr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘my new data set.rds’
Namespace in Imports field not imported from: ‘lattice’
  All declared Imports should be used.
Note: found 72720 marked Latin-1 strings
'LazyData' is specified without a 'data' directory
Note: found 2 marked UTF-8 strings
Package vignette with \VignetteEngine{} not specifying an engine package:
  ‘Multiclass.Rmd’
Engines should be specified as \VignetteEngine{PKG::ENG}.
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Note: found 8 marked Latin-1 strings
Undeclared package ‘tidyselect’ in Rd xrefs
Package suggested but not available for checking: ‘arrow’
Undeclared package ‘FCPS’ in Rd xrefs
Undeclared package ‘performance’ in Rd xrefs
Imports includes 22 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
checkRd: (-1) is_datelife_query.Rd:17: Lost braces; missing escapes or markup?
    17 | First, that \code{input} is of class {datelifeQuery}.
       |                                      ^
Note: found 2596 marked UTF-8 strings
Package suggested but not available for checking: ‘SASxport’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 54339 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Undeclared package ‘sfsmisc’ in Rd xrefs
Namespaces in Imports field not imported from:
  ‘knitr’ ‘tidyverse’ ‘vctrs’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘arrow’
Undeclared package ‘withr’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘softImpute’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘ggplot2’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘html5’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘lubridate’ ‘tseries’
  All declared Imports should be used.
Documented arguments not in \usage in Rd file 'a_dcc_mat_est.Rd':
  ‘param’

Documented arguments not in \usage in Rd file 'dcc_mat_est.Rd':
  ‘param’

Documented arguments not in \usage in Rd file 'deco_mat_est.Rd':
  ‘param’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Note: found 122 marked UTF-8 strings
Problems with news in ‘NEWS.md’:
No news entries found.
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
Note: found 2 marked Latin-1 strings
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Note: found 38 marked UTF-8 strings
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Undeclared package ‘fda.usc’ in Rd xrefs
Namespaces in Imports field not imported from:
  ‘MASS’ ‘qpdf’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    sample_data   3.1Mb
Namespace in Imports field not imported from: ‘shinydisconnect’
  All declared Imports should be used.
Auto-generated content requiring editing in Rd file 'DDPNA-package.Rd':
  \details: ‘...o use the package, including the most important functions ~~’
Argument items with no description in Rd file 'DEP_Mod_net_plot.Rd':
  ‘\dots’
Specified C++11: please drop specification unless essential
Note: found 53 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    extdata   4.9Mb
Note: found 1 marked Latin-1 string
  Note: found 46826 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘reticulate’ ‘tensorflow’
  All declared Imports should be used.
Documented arguments not in \usage in Rd file 'getTriContextFraction.Rd':
  ‘trimer.counts.ref’

Documented arguments not in \usage in Rd file 'norm.it.Rd':
  ‘trimer.counts’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 7 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
Undeclared packages ‘e1071’, ‘nloptr’ in Rd xrefs
Namespaces in Imports field not imported from:
  ‘knitr’ ‘shinyBS’ ‘shinyMatrix’
  All declared Imports should be used.
Found the following files/directories:
  ‘res.pdf’ ‘res1.jpg’
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘Matrix’
  All declared Imports should be used.
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Changes from previous package DecompHoriuchi
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘smd_table.docx’
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    doc    3.1Mb
    help   1.3Mb
'LazyData' is specified without a 'data' directory
checkRd: (-1) scramb.Rd:44: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   4.2Mb
checkRd: (-1) DendSer.Rd:50: Escaped LaTeX specials: \&
Note: found 3 marked UTF-8 strings
Problems with news in ‘NEWS.md’:
No news entries found.
Namespace in Imports field not imported from: ‘mvtnorm’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Note: found 2534 marked UTF-8 strings
Undeclared package ‘DEoptim’ in Rd xrefs
'LazyData' is specified without a 'data' directory
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    doc       4.8Mb
    extdata   2.1Mb
Package suggested but not available for checking: ‘Rdonlp2’
checkRd: (-1) discrimination.Rd:19: Escaped LaTeX specials: \&
checkRd: (-1) fitdmm.Rd:59: Escaped LaTeX specials: \$
Package suggested but not available for checking: ‘Rdonlp2’
Specified C++11: please drop specification unless essential
checkRd: (-1) barriers.Rd:127: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Undeclared packages ‘FactoMineR’, ‘vcd’ in Rd xrefs
Note: found 5764 marked UTF-8 strings
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘.N’ ‘.Nmiss’ ‘.Q1’ ‘.Q3’ ‘.factorN’ ‘.factorNmiss’ ‘.factorQ1’
  ‘.factorQ3’ ‘.factormax’ ‘.factormean’ ‘.factormedian’ ‘.factormin’
  ‘.factorsd’ ‘.max’ ‘.mean’ ‘.median’ ‘.min’ ‘.sd’
Namespace in Imports field not imported from: ‘datasets’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Undeclared package ‘htmlwidgets’ in Rd xrefs
Package suggested but not available for checking: ‘RDCOMClient’
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    R      1.7Mb
    doc    1.8Mb
    help   1.6Mb
Undeclared packages ‘ineq’, ‘randtests’, ‘Hmisc’, ‘plotrix’, ‘caret’, ‘pcaPP’, ‘polycor’, ‘lmtest’, ‘car’, ‘gmp’, ‘vcdExtra’, ‘chron’, ‘coin’, ‘caTools’, ‘forecast’, ‘sfsmisc’, ‘vcd’, ‘areaplot’, ‘corrgram’, ‘UsingR’, ‘memisc’, ‘gtools’, ‘BSDA’, ‘prettyR’ in Rd xrefs
Undeclared package ‘RcppArmadillo’ in Rd xrefs
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
Packages which this enhances but not available for checking:
  'gurobi', 'Rcplex'
Note: found 47 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data          1.8Mb
    htmlwidgets   3.7Mb
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘RColorBrewer’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DT’ ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Imports includes 22 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Note: found 1 marked UTF-8 string
'LazyData' is specified without a 'data' directory
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    libs   9.7Mb
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) runContrasts.Rd:79: Lost braces in \itemize; meant \describe ?
checkRd: (-1) runContrasts.Rd:80: Lost braces in \itemize; meant \describe ?
checkRd: (-1) runContrasts.Rd:81: Lost braces in \itemize; meant \describe ?
checkRd: (-1) runContrasts.Rd:82: Lost braces in \itemize; meant \describe ?
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc   5.1Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘rlang’
  All declared Imports should be used.
Note: found 1 marked UTF-8 string
Documented arguments not in \usage in Rd file 'encode_unit.Rd':
  ‘original’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Note: found 8014 marked UTF-8 strings
Package suggested but not available for checking: ‘blockcluster’
Namespaces in Imports field not imported from:
  ‘R6’ ‘dplyr’ ‘purrr’
  All declared Imports should be used.
Undeclared package ‘tibble’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: ‘arrow’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    doc  10.8Mb
File ‘diffIRT/libs/diffIRT.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'Nortonbass_startvalgen.Rd':
  ‘param’ ‘startvalgen’

Documented arguments not in \usage in Rd file 'seqdiffusion.Rd':
  ‘w’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Package suggested but not available for checking: ‘gurobi’
Note: found 15 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building ‘DImodelsVis-with-complex-models.Rmd’ using rmarkdown

Quitting from lines 253-254 [conditional-ternary-plot] (DImodelsVis-with-complex-models.Rmd)
Error: processing vignette 'DImodelsVis-with-complex-models.Rmd' failed with diagnostics:
! Error in a deferred `on.exit()` clause
Caused by error in `"id" %in% names(args)`:
! Could not evaluate cli `{}` expression: `pb_spin`.
Caused by error in `eval(expr, envir = envir)`:
! object 'pb_spin' not found
--- failed re-building ‘DImodelsVis-with-complex-models.Rmd’

SUMMARY: processing the following file failed:
  ‘DImodelsVis-with-complex-models.Rmd’

Error: Vignette re-building failed.
Execution halted
Undeclared package ‘CVST’ in Rd xrefs
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘rrelaxiv’
Namespace in Imports field not imported from: ‘sandwich’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
checkRd: (-1) TempDisaggDGP.Rd:79: Escaped LaTeX specials: \&
checkRd: (-1) disaggregate.Rd:56: Escaped LaTeX specials: \&
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘readr’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Invalid package aliases in Rd file 'RV.Rd':
  ‘RV-package’
'LazyData' is specified without a 'data' directory
checkRd: (-1) dataCensoring.Rd:78: Escaped LaTeX specials: \&
checkRd: (-1) dataLong.Rd:170: Escaped LaTeX specials: \&
checkRd: (-1) dataLongCompRisksTimeDep.Rd:130: Escaped LaTeX specials: \&
checkRd: (-1) dataLongMultiSpell.Rd:123: Escaped LaTeX specials: \&
checkRd: (-1) dataLongTimeDep.Rd:96: Escaped LaTeX specials: \&
Undeclared package ‘Hmisc’ in Rd xrefs
Note: found 270 marked UTF-8 strings
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc       1.5Mb
    extdata   4.2Mb
'LazyData' is specified without a 'data' directory
Package required but not available: ‘arrow’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Note: found 106 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 12 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
checkRd: (-1) booter.Rd:68: Escaped LaTeX specials: \&
checkRd: (-1) ci.booted.Rd:53: Escaped LaTeX specials: \&
checkRd: (-1) pbooter.Rd:57: Escaped LaTeX specials: \&
GNU make is a SystemRequirements.
Problems with news in ‘NEWS.md’:
No news entries found.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘proxy’
  All declared Imports should be used.
Undeclared package ‘robustbase’ in Rd xrefs
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘rlang’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Undeclared package ‘RobAStBase’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Undeclared package ‘distrTEst’ in Rd xrefs
Undeclared package ‘distr’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘truncnorm’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘ggmulti’ ‘loon’ ‘loon.data’ ‘loon.ggplot’ ‘loon.shiny’ ‘loon.tourr’
  ‘stats’ ‘zenplots’
  All declared Imports should be used.
Package suggested but not available for checking: ‘BOLTSSIRR’
Namespaces in Imports field not imported from:
  ‘gridExtra’ ‘plotly’ ‘pryr’ ‘rpart’
  All declared Imports should be used.
Undeclared package ‘palaeoverse’ in Rd xrefs
'LazyData' is specified without a 'data' directory
File ‘dkDNA/libs/dkDNA.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
installed size is 16.6Mb
  sub-directories of 1Mb or more:
    include  16.3Mb
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Changes to previous versions
    Minor changes
    Fixes
    Previous Versions
checkRd: (-1) dlsem.Rd:42: Escaped LaTeX specials: \&
checkRd: (-1) unirootTest.Rd:14: Escaped LaTeX specials: \&
checkRd: (-1) unirootTest.Rd:20: Escaped LaTeX specials: \&
checkRd: (-1) unirootTest.Rd:26: Escaped LaTeX specials: \&
Invalid package aliases in Rd file 'dmaiIntro.Rd':
  ‘dmaiIntro-package’
'LazyData' is specified without a 'data' directory
Argument items with no description in Rd file 'dml_bagging.Rd':
  ‘y,x,d,data,sed’
Argument items with no description in Rd file 'dml_boosting.Rd':
  ‘y,x,d,data,sed’
Argument items with no description in Rd file 'dml_ensemble_lm.Rd':
  ‘y,x,d,data,sed’
Argument items with no description in Rd file 'dml_ensemble_rf.Rd':
  ‘y,x,d,data,sed’
Argument items with no description in Rd file 'dml_neural_network.Rd':
  ‘y,x,d,data,sed’
Argument items with no description in Rd file 'dml_random_forest.Rd':
  ‘y,x,d,data,sed’
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Invalid package aliases in Rd file 'dnapath2-package.Rd':
  ‘dnapath2-package’
Auto-generated content requiring editing in Rd file 'dnapath2-package.Rd':
  \references: ‘This optional section can contain literature or other refere...’
  \seealso: ‘Optional links to other man pages’
  \examples: ‘\dontrun{      ## Optional simple examples of the most impor...’
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Note: found 175 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘GOstats’ ‘caTools’ ‘fdrtool’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) dnr.Rd:12: Escaped LaTeX specials: \#
S3 methods shown with full name in Rd file 'add.joint.mean.many.Rd':
  ‘all.cond.mean.PO’ ‘all.cond.mean2.PO’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Argument items with no description in Rd file 'derivType.Rd':
  ‘L’ ‘mu’ ‘eps’
Argument items with no description in Rd file 'getNewParams.SC.Rd':
  ‘n.fft’
Argument items with no description in Rd file 'graph.CTMC.Rd':
  ‘\dots’
Argument items with no description in Rd file 'num.deriv.Rd':
  ‘\dots’
Argument items with no description in Rd file 'power.coef.one.Rd':
  ‘\dots’
Specified C++11: please drop specification unless essential
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
Note: found 9796 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'check_results.Rd':
  ‘error_on_failure’ ‘error_on_warning’

Documented arguments not in \usage in Rd file 'function_get_comments.Rd':
  ‘thresholds’

Documented arguments not in \usage in Rd file 'vignette_results_display.Rd':
  ‘vignette_results’ ‘error_on_failure’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    doc   6.5Mb
checkRd: (-1) compare_heaps.Rd:11: Lost braces
    11 | sub-sample selected with code{dodgr_sample})}
       |                              ^
checkRd: (-1) dodgr_save_streetnet.Rd:24: Lost braces
    24 | result of a link{weight_streetnet} call can be rapidly loaded into a
       |                 ^
checkRd: (-1) weight_railway.Rd:23: Lost braces
    23 | \item{id_col}{Specify column of the code{sf} \code{data.frame} object which
       |                                         ^
checkRd: (-1) weight_streetnet.Rd:85: Lost braces
    85 | \item{id_col}{For \code{sf}-formatted data only: Specify column of the code{sf}
       |                                                                            ^
GNU make is a SystemRequirements.
Package which this enhances but not available for checking: ‘gurobi’
'LazyData' is specified without a 'data' directory
Note: found 3 marked UTF-8 strings
Package required but not available: ‘arrow’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    R         2.0Mb
    data      1.9Mb
    extdata   2.3Mb
Undeclared package ‘molaR’ in Rd xrefs
Note: found 100 marked UTF-8 strings
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    New features
Namespace in Imports field not imported from: ‘gridExtra’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘DT’ ‘DoseFinding’ ‘Rsolnp’ ‘ggplot2’ ‘kableExtra’ ‘knitr’
  ‘latticeExtra’ ‘purrr’ ‘readxl’ ‘shinyBS’ ‘shinyWidgets’ ‘shinyjs’
  ‘stringr’ ‘utils’
  All declared Imports should be used.
Package suggested but not available for checking: ‘gurobi’
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
Found the following files/directories:
  ‘myfile.ps’ ‘myfile.svg’
Note: found 2 marked UTF-8 strings
Note: found 2 marked UTF-8 strings
Undeclared package ‘broomExtra’ in Rd xrefs
Unknown package ‘broomExtra’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    assets   2.9Mb
    doc      2.1Mb
Namespaces in Imports field not imported from:
  ‘tidyr’ ‘tidyverse’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 4 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘R6’ ‘dplyr’ ‘ggplot2’ ‘nloptr’
  All declared Imports should be used.
Found export directive that requires package ‘methods’:
  ‘exportMethods’
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains ‘methods’.
Undeclared package ‘RcppEigen’ in Rd xrefs
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
checkRd: (-1) confint.dr4pl.Rd:49: Escaped LaTeX specials: \&
checkRd: (-1) gof-dr4pl.Rd:40: Escaped LaTeX specials: \&
checkRd: (-1) vcov.dr4pl.Rd:61: Escaped LaTeX specials: \&
Note: found 103 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘disk.frame’
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘drawBox.pdf’ ‘drawCircle.pdf’ ‘drawCurve.pdf’ ‘drawLine.pdf’
  ‘drawPoint.pdf’ ‘drawSettingsExample.pdf’ ‘drawText.pdf’ ‘export.pdf’
Undeclared package ‘SimMultiCorrData’ in Rd xrefs
'LazyData' is specified without a 'data' directory
checkRd: (-1) EDcomp.Rd:88: Escaped LaTeX specials: \&
checkRd: (-1) LL.4.Rd:44: Escaped LaTeX specials: \&
checkRd: (-1) W4.Rd:37: Escaped LaTeX specials: \&
checkRd: (-1) algae.Rd:32: Escaped LaTeX specials: \&
checkRd: (-1) anova.drc.Rd:40: Escaped LaTeX specials: \&
checkRd: (-1) deguelin.Rd:33: Escaped LaTeX specials: \&
checkRd: (-1) gompertz.Rd:55: Escaped LaTeX specials: \&
checkRd: (-1) hatvalues.drc.Rd:44: Escaped LaTeX specials: \&
checkRd: (-1) llogistic.Rd:64: Escaped LaTeX specials: \&
checkRd: (-1) modelFit.Rd:36: Escaped LaTeX specials: \&
checkRd: (-1) weibull1.Rd:67: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data      1.6Mb
    extdata   3.2Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc   2.9Mb
'LazyData' is specified without a 'data' directory
Undeclared package ‘data.table’ in Rd xrefs
Namespace in Imports field not imported from: ‘base’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘pulse-PKdhtXMmr18n’
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    appinformation   4.1Mb
Namespace in Imports field not imported from: ‘mnormt’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘rJava’ ‘tools’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
Undeclared package ‘EvalEst’ in Rd xrefs
Documented arguments not in \usage in Rd file 'forecastCovCompiled.Rd':
  ‘obj’ ‘zero’ ‘trend’ ‘estimation.sample’ ‘...’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
File ‘dse/libs/dse.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:

  Warning in is.R() : 'is.R' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Note: found 386 marked UTF-8 strings
Note: found 4891 marked UTF-8 strings
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘dsBaseClient’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Undeclared packages ‘dstat’, ‘sensitivity2x2xk’ in Rd xrefs
Note: found 1 marked Latin-1 string
'LazyData' is specified without a 'data' directory
Note: found 281 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Undeclared package ‘vctrs’ in Rd xrefs
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    htmlwidgets   5.8Mb
GNU make is a SystemRequirements.
Objects in \usage without \alias in Rd file 'd.spls.norm1.Rd':
  ‘d.spls.norm2’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
File ‘dualtrees/libs/dualtrees.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘digest’ ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘arrow’
installed size is 38.7Mb
  sub-directories of 1Mb or more:
    libs  38.1Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘arrow’
'LazyData' is specified without a 'data' directory
Note: found 2854 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘Rdpack’ ‘dogesr’ ‘knitr’ ‘qpdf’ ‘rmarkdown’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘DT’
  All declared Imports should be used.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Undeclared package ‘rdwd’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘GenEst’ ‘expint’ ‘numDeriv’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Undeclared package ‘quadprog’ in Rd xrefs
Undeclared package ‘stringdist’ in Rd xrefs
Package suggested but not available for checking: ‘cmdstanr’
installed size is 13.4Mb
  sub-directories of 1Mb or more:
    R      3.5Mb
    data   9.0Mb
Package unavailable to check Rd xrefs: ‘cmdstanr’
Problems with news in ‘NEWS.md’:
No news entries found.
Namespaces in Imports field not imported from:
  ‘NatureSounds’ ‘av’ ‘magrittr’ ‘stats’
  All declared Imports should be used.
Undeclared package ‘warbleR’ in Rd xrefs
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘lle’
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘graphics’
  All declared Imports should be used.
checkRd: (-1) generate_kinetics.Rd:57: Lost braces; missing escapes or markup?
    57 | By default, sampled from {-1, 1} with probabilities {.25, .75}.
       |                          ^
checkRd: (-1) generate_kinetics.Rd:57: Lost braces; missing escapes or markup?
    57 | By default, sampled from {-1, 1} with probabilities {.25, .75}.
       |                                                     ^
checkRd: (-1) new_log_level.Rd:19: Lost braces; missing escapes or markup?
    19 | \item{log_style}{is a {crayon::style()} that will colorize
       |                       ^
checkRd: (-1) new_log_level.Rd:22: Lost braces; missing escapes or markup?
    22 | \item{msg_style}{is a {crayon::style()} style that will gray scale the
       |                       ^
checkRd: (-1) sys_context.Rd:22: Lost braces; missing escapes or markup?
    22 | \item{"sysname"} : {The operating system name.}
       |                    ^
checkRd: (-1) sys_context.Rd:23: Lost braces; missing escapes or markup?
    23 | \item{"release"} : {The OS release.}
       |                    ^
checkRd: (-1) sys_context.Rd:24: Lost braces; missing escapes or markup?
    24 | \item{"version"} : {The OS version.}
       |                    ^
checkRd: (-1) sys_context.Rd:25: Lost braces; missing escapes or markup?
    25 | \item{"nodename"} : {A name by which the machine is known on the network (if any).}
       |                     ^
checkRd: (-1) sys_context.Rd:26: Lost braces; missing escapes or markup?
    26 | \item{"machine"} : {A concise description of the hardware, often the CPU type.}
       |                    ^
checkRd: (-1) sys_context.Rd:27: Lost braces; missing escapes or markup?
    27 | \item{"login"} : {The user's login name, or "unknown" if it cannot be ascertained.}
       |                  ^
checkRd: (-1) sys_context.Rd:28: Lost braces; missing escapes or markup?
    28 | \item{"user"} : {The name of the real user ID, or "unknown" if it cannot be ascertained.}
       |                 ^
checkRd: (-1) sys_context.Rd:29: Lost braces; missing escapes or markup?
    29 | \item{"r-ver"} : {R Version in (major).(minor) format.}
       |                  ^
Undeclared package ‘CausalImpact’ in Rd xrefs
'LazyData' is specified without a 'data' directory
checkRd: (-1) NKI-breast-cancer-clinical-data.Rd:26: Escaped LaTeX specials: \&
checkRd: (-1) NKI-breast-cancer-clinical-data.Rd:33: Escaped LaTeX specials: \&
checkRd: (-1) NKI-breast-cancer-clinical-data.Rd:37: Escaped LaTeX specials: \&
checkRd: (-1) WBC-follow-up-data.Rd:13: Escaped LaTeX specials: \&
checkRd: (-1) WBC-follow-up-data.Rd:14: Escaped LaTeX specials: \&
checkRd: (-1) WBC-follow-up-data.Rd:26: Escaped LaTeX specials: \&
checkRd: (-1) WBC-follow-up-data.Rd:31: Escaped LaTeX specials: \&
checkRd: (-1) WBC-follow-up-data.Rd:41: Escaped LaTeX specials: \&
checkRd: (-1) WBC-measurements-data.Rd:13: Escaped LaTeX specials: \&
checkRd: (-1) WBC-measurements-data.Rd:14: Escaped LaTeX specials: \&
checkRd: (-1) WBC-measurements-data.Rd:25: Escaped LaTeX specials: \&
checkRd: (-1) WBC-measurements-data.Rd:30: Escaped LaTeX specials: \&
checkRd: (-1) WBC-measurements-data.Rd:40: Escaped LaTeX specials: \&
File ‘dynpred/libs/dynpred.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   2.5Mb
    doc    1.4Mb
Found the following files/directories:
  ‘containers-user-1234’
Note: found 9 marked UTF-8 strings
Specified C++11: please drop specification unless essential
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    extdata   4.8Mb
Namespace in Imports field not imported from: ‘hms’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
Undeclared package ‘leaps’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 10 marked UTF-8 strings
Undeclared package ‘tibble’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘example_table1.csv’ ‘example_table1.txt’ ‘example_table2.csv’
  ‘example_table2.txt’ ‘example_table3.csv’ ‘example_table3.txt’
  ‘table1.csv’ ‘table2.csv’ ‘table2.txt’ ‘table3.txt’ ‘table4.txt’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘rprojroot’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘gurobi’
Namespace in Imports field not imported from: ‘qcr’
  All declared Imports should be used.
Package required but not available: ‘arrow’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Note: found 2 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 1281 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘pander’
  All declared Imports should be used.
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    libs   7.9Mb
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘graphics’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Rmisc’ ‘rlang’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 42 marked UTF-8 strings
Note: found 5 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Undeclared package ‘magrittr’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    TODO:
'LazyData' is specified without a 'data' directory
Note: found 22 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Undeclared packages ‘tidyr’, ‘scales’ in Rd xrefs
Note: found 6 marked UTF-8 strings
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Undeclared package ‘htmlwidgets’ in Rd xrefs
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘magrittr’ ‘tibble’
  All declared Imports should be used.
Note: found 74 marked UTF-8 strings
Documented arguments not in \usage in Rd file 'fcf.env.Rd':
  ‘vars’

Documented arguments not in \usage in Rd file 'getlevels.Rd':
  ‘editarray’

Documented arguments not in \usage in Rd file 'parseCatEdit.Rd':
  ‘e’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
Undeclared package ‘ndl’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Undeclared package ‘T2EQ’ in Rd xrefs
Note: found 136358 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘reticulate’ ‘tensorflow’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘PCovR’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘progress’
  All declared Imports should be used.
Package suggested but not available for checking: ‘lavaan.survey’
Namespace in Imports field not imported from: ‘rmarkdown’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Undeclared package ‘carData’ in Rd xrefs
Undeclared packages ‘carData’, ‘faraway’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Note: found 24 marked UTF-8 strings
Found the following files/directories:
  ‘eval_test_LG_ROC.pdf’ ‘test.pdf’
Package suggested but not available for checking: ‘eggCountsExtra’
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    libs   7.9Mb
GNU make is a SystemRequirements.
Note: found 7 marked UTF-8 strings
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    doc       5.1Mb
    extdata   5.1Mb
Namespace in Imports field not imported from: ‘snow’
  All declared Imports should be used.
Running ‘testthat.R’ [10s/15s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(eiCompare)
  Loading required package: eiPack
  Loading required package: ei
  Loading required package: wru
  
  Please cite as:
  
  Khanna K, Bertelsen B, Olivella S, Rosenman E, Rossell Hayes A, Imai K
  (2024). _wru: Who are You? Bayesian Prediction of Racial Category Using
  Surname, First Name, Middle Name, and Geolocation_. R package version
  3.0.0, <https://CRAN.R-project.org/package=wru>.
  
  Note that wru 2.0.0 uses 2020 census data by default.
  Use the argument `year = "2010"`, to replicate analyses produced with earlier package versions.
  
  > 
  > test_check("eiCompare")
  Error in wru::predict_race(voter.file = wru_voter_file, census.surname = use_surname,  : 
    unused argument (surname.year = surname_year)
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 75 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_wru_predict_race_wrapper.R:19:3'): WRU wrapper correctly calculates probabilities. ──
  Error in `if (grep("cannot open the connection", error_type$message)) {
      message("Failed to connect to the remote data sources. Check internet connection. Returning NULL")
      return()
  } else {
      stop()
  }`: argument is of length zero
  Backtrace:
      ▆
   1. └─eiCompare::wru_predict_race_wrapper(...) at test_wru_predict_race_wrapper.R:19:3
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 75 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
--- re-building ‘bisg.Rmd’ using rmarkdown

Quitting from lines 127-149 [unnamed-chunk-13] (bisg.Rmd)
Error: processing vignette 'bisg.Rmd' failed with diagnostics:
argument is of length zero
--- failed re-building ‘bisg.Rmd’

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

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

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

Quitting from lines 166-191 [apply_bisg] (performance_analysis.Rmd)
Error: processing vignette 'performance_analysis.Rmd' failed with diagnostics:
argument is of length zero
--- failed re-building ‘performance_analysis.Rmd’

SUMMARY: processing the following files failed:
  ‘bisg.Rmd’ ‘performance_analysis.Rmd’

Error: Vignette re-building failed.
Execution halted
Note: found 1 marked UTF-8 string
Problems with news in ‘NEWS.md’:
No news entries found.
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘mathjaxr’
  All declared Imports should be used.
Undeclared package ‘eRm’ in Rd xrefs
Documented arguments not in \usage in Rd file 'colBoxplot4.Rd':
  ‘id’

Documented arguments not in \usage in Rd file 'elaborator_server.Rd':
  ‘id’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) AuditErrors.Rd:40: Escaped LaTeX specials: \_
checkRd: (-1) compute.audit.errors.Rd:24: Escaped LaTeX specials: \_
checkRd: (-1) compute.stark.t.Rd:35: Escaped LaTeX specials: \_ \_
checkRd: (-1) find.q.Rd:44: Escaped LaTeX specials: \_
checkRd: (-1) find.q.Rd:56: Escaped LaTeX specials: \_
checkRd: (-1) stark.test.Rd:50: Escaped LaTeX specials: \$
checkRd: (-1) stark.test.Rd:101: Escaped LaTeX specials: \$ \$
checkRd: (-1) tri.audit.sim.Rd:47: Escaped LaTeX specials: \_
checkRd: (-1) tri.calc.sample.Rd:34: Escaped LaTeX specials: \_
checkRd: (-1) tri.sample.Rd:34: Escaped LaTeX specials: \$
checkRd: (-1) tri.sample.Rd:36: Escaped LaTeX specials: \$
checkRd: (-1) tri.sample.Rd:49: Escaped LaTeX specials: \$
checkRd: (-1) weight.function.Rd:16: Escaped LaTeX specials: \_
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘datasets’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Undeclared package ‘EloRating’ in Rd xrefs
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
GNU make is a SystemRequirements.
File ‘elsa/libs/elsa.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Undeclared package ‘textrecipes’ in Rd xrefs
Namespace in Imports field not imported from: ‘Matrix’
  All declared Imports should be used.
Note: found 155 marked UTF-8 strings
Note: found 50 marked Latin-1 strings
License stub is invalid DCF.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    emoji_fonts   6.5Mb
Note: found 16919 marked UTF-8 strings
Undeclared packages ‘Kendall’, ‘geoR’ in Rd xrefs
Specified C++11: please drop specification unless essential
Note: found 23639 marked Latin-1 strings
checkRd: (-1) encode.character.Rd:22: Escaped LaTeX specials: \~
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
Found the following files/directories:
  ‘file.path(temp_dir, gp2.csv)’
Note: found 2 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘Biostrings’ ‘DECIPHER’ ‘ggplot2’ ‘reshape2’ ‘usethis’
  All declared Imports should be used.
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    data   7.3Mb
Package vignette with \VignetteEngine{} not specifying an engine package:
  ‘ensurer.Rmd’
Engines should be specified as \VignetteEngine{PKG::ENG}.
File ‘EntropyEstimation/libs/EntropyEstimation.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'xcms', 'MSnbase'
Auto-generated content requiring editing in Rd file 'EnviroPRA-package.Rd':
  \details: ‘...o use the package, including the most important functions ~~’
'LazyData' is specified without a 'data' directory
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    R      2.3Mb
    help   3.6Mb
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘Net1-fromR.inp’
Imports includes 21 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Note: found 1 marked Latin-1 string
  Note: found 1508 marked UTF-8 strings
Package suggested but not available for checking: ‘arrow’
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc    2.9Mb
    help   2.5Mb
Namespace in Imports field not imported from: ‘colorspace’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘tinytest’
  All declared Imports should be used.
checkRd: (-1) risk.display.rd:98: Escaped LaTeX specials: \$
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
Package suggested but not available for checking: ‘epidict’
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    help   2.1Mb
    libs   8.4Mb
GNU make is a SystemRequirements.
S3 methods shown with full name in Rd file 'addDrug.Lexis.Rd':
  ‘addDrug.Lexis’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘episcan_1geno_cc.txt’ ‘episcan_1geno_quant.txt’
  ‘episcan_2geno_cc.txt’ ‘episcan_2geno_quant.txt’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘taskscheduleR’

Imports includes 34 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Namespaces in Imports field not imported from:
  ‘httpuv’ ‘knitr’ ‘plyr’ ‘tidyverse’ ‘xml2’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘xts’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
Note: found 15 marked UTF-8 strings
Note: found 1 marked UTF-8 string
'LazyData' is specified without a 'data' directory
Undeclared package ‘OpenMx’ in Rd xrefs
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
File ‘equivalence/libs/equivalence.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘cubature’ ‘rootSolve’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘gcspikelite’
Undeclared package ‘margins’ in Rd xrefs
Documented arguments not in \usage in Rd file 'subnetwork_templates.Rd':
  ‘nams.vattr’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    R     1.0Mb
    doc   1.7Mb
Namespace in Imports field not imported from: ‘signal’
  All declared Imports should be used.
S3 methods shown with full name in Rd file 'summary.error_interval.Rd':
  ‘summary.error_interval’

S3 methods shown with full name in Rd file 'summary.measure.Rd':
  ‘summary.measure’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Invalid package aliases in Rd file 'esaBcv_package.Rd':
  ‘esaBcv_package-package’
installed size is 13.7Mb
  sub-directories of 1Mb or more:
    doc  13.1Mb
Undeclared package ‘metafor’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Note: found 3 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
checkRd: (-1) aic.Rd:25: Escaped LaTeX specials: \&
checkRd: (-1) aic.Rd:29: Escaped LaTeX specials: \&
checkRd: (-1) ictab.Rd:56: Escaped LaTeX specials: \&
checkRd: (-1) ictab.Rd:60: Escaped LaTeX specials: \&
checkRd: (-1) ictab.Rd:64: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
S3 methods shown with full name in Rd file 'ETAS-internal.Rd':
  ‘Smooth.catalog’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Found export directive that requires package ‘methods’:
  ‘exportClasses’
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains ‘methods’.
'LazyData' is specified without a 'data' directory
Note: found 1350 marked UTF-8 strings
Note: found 1054 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘forcats’ ‘rqPen’ ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘metadat’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘EnvStats’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘KMsurv’ ‘MLEcens’ ‘lubridate’ ‘msm’ ‘perm’
  All declared Imports should be used.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    doc   6.0Mb
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘curl’ ‘scales’ ‘stringr’
  All declared Imports should be used.
Undeclared package ‘R6’ in Rd xrefs
Documented arguments not in \usage in Rd file 'doHttrRequest.Rd':
  ‘params’ ‘customConfig’

Documented arguments not in \usage in Rd file 'errorMessage.Rd':
  ‘test_me’

Documented arguments not in \usage in Rd file 'isError.Rd':
  ‘test_me’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
checkRd: (-1) calculateGLR.Rd:43: Escaped LaTeX specials: \&
checkRd: (-1) Snoring.Rd:21: Escaped LaTeX specials: \&
Undeclared packages ‘ks’, ‘evd’, ‘ismev’, ‘mixtools’, ‘evir’, ‘smoothtail’ in Rd xrefs
Found the following files/directories:
  ‘sample .nwk’
Note: found 10 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    data      2.5Mb
    doc       1.6Mb
    extdata   2.4Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘parallel’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
Package suggested but not available for checking: ‘ExactData’
checkRd: (-1) exams2sakai.Rd:152: Escaped LaTeX specials: \&
Undeclared package ‘tth’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 342 marked UTF-8 strings
Namespace in Imports field not imported from: ‘gamlss.dist’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
File ‘exif/libs/exif.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘polynom’
  All declared Imports should be used.
Undeclared packages ‘tseriesChaos’, ‘rSFA’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘tidyverse’
  All declared Imports should be used.
Package suggested but not available for checking: ‘cec2013’
checkRd: (-1) ccF.Rd:5: Escaped LaTeX specials: \&
checkRd: (-1) ccF.Rd:32: Escaped LaTeX specials: \&
checkRd: (-1) ccF.Rd:29: Escaped LaTeX specials: \&
Undeclared package ‘quantreg’ in Rd xrefs
'LazyData' is specified without a 'data' directory
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   7.0Mb
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc      3.4Mb
    images   1.1Mb
Namespace in Imports field not imported from: ‘ggpmisc’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 1 marked UTF-8 string
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
checkRd: (-1) sp500.Rd:5: Escaped LaTeX specials: \&
File ‘extremis/libs/extremis.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package suggested but not available for checking: ‘exuberdata’
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Functions and objects (details)
checkRd: (-1) codePasses.Rd:64: Escaped LaTeX specials: \#
Namespace in Imports field not imported from: ‘rlang’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘BiocStyle’
  All declared Imports should be used.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Undeclared package ‘tibble’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Undeclared package ‘strucchange’ in Rd xrefs
Undeclared package ‘pyinit’ in Rd xrefs
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    minor changes
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘R6’ ‘caTools’ ‘httr’ ‘jsonlite’ ‘rlang’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘base’ ‘data.table’
  All declared Imports should be used.
Note: found 55 marked UTF-8 strings
File ‘falcon/libs/falcon.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:

  Warning in is.R() : 'is.R' is deprecated.
  Warning in is.R() : 'is.R' is deprecated.
  Warning in is.R() : 'is.R' is deprecated.
  Warning in is.R() : 'is.R' is deprecated.
  Warning in is.R() : 'is.R' is deprecated.
  Warning in is.R() : 'is.R' is deprecated.
  Warning in is.R() : 'is.R' is deprecated.
  Warning in is.R() : 'is.R' is deprecated.
  Warning in is.R() : 'is.R' is deprecated.
  Warning in is.R() : 'is.R' is deprecated.
  Warning in is.R() : 'is.R' is deprecated.
  Warning in is.R() : 'is.R' is deprecated.
  Warning in is.R() : 'is.R' is deprecated.
  Warning in is.R() : 'is.R' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    R      3.5Mb
    doc    1.0Mb
    help   1.2Mb
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'cache.Rd':
  ‘data’ ‘reset’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Note: found 179 marked UTF-8 strings
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Undeclared package ‘RWeka’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘rlang’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 1430 marked UTF-8 strings
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    3.0Mb
    help   1.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
File ‘FastBandChol/libs/FastBandChol.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Specified C++11: please drop specification unless essential
File ‘fastcmh/libs/fastcmh.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    libs   7.2Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    help   1.8Mb
    libs   1.4Mb
Documented arguments not in \usage in Rd file 'kkk.Rd':
  ‘Vector’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
File ‘fastdigest/libs/fastdigest.so’:
  Found no call to: ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘RobustGaSP’
  All declared Imports should be used.
Documented arguments not in \usage in Rd file 'Get_C_R_K_Q.Rd':
  ‘have_noise’

Documented arguments not in \usage in Rd file 'Sample_KF_post.Rd':
  ‘C0’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
File ‘FastGP/libs/FastGP.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘coxKM’
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   4.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Undeclared packages ‘ICSNP’, ‘ICS’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) FastPCS-package.Rd:29: Escaped LaTeX specials: \&
checkRd: (-1) FastPCS.Rd:104: Escaped LaTeX specials: \&
Rd files without \alias:
  ‘FastPCS-package.Rd’
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘mosaicCalc’
Specified C++11: please drop specification unless essential
checkRd: (-1) Lemons.Rd:3: Escaped LaTeX specials: \&
checkRd: (-1) Lemons.Rd:5: Escaped LaTeX specials: \&
Invalid package aliases in Rd file 'FastRCS-package.Rd':
  ‘FastPCS-package’
Namespace in Imports field not imported from: ‘ggplot2’
  All declared Imports should be used.
checkRd: (-1) update_nhl_db.Rd:51-53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) update_nhl_db.Rd:54-57: Lost braces in \itemize; meant \describe ?
checkRd: (-1) update_phf_db.Rd:51-53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) update_phf_db.Rd:54-57: Lost braces in \itemize; meant \describe ?
installed size is 15.8Mb
  sub-directories of 1Mb or more:
    data  15.7Mb
.run: no visible binding for global variable ‘init’
.run: no visible global function definition for ‘init’
.run: no visible binding for global variable ‘run’
Undefined global functions or variables:
  init run
Note: information on .o files is not available
File ‘FastRWeb/libs/null.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Undeclared package ‘earth’ in Rd xrefs
Documented arguments not in \usage in Rd file 'bin.Rd':
  ‘Integer’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Package suggested but not available for checking: ‘NNLM’
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   4.3Mb
GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
  ‘collapse’ ‘data.table’ ‘kit’ ‘magrittr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘assertthat’ ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Undeclared package ‘magrittr’ in Rd xrefs
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    doc    3.9Mb
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘test2delete.txt’ ‘test2delete2_values.txt’ ‘test2delete_values.txt’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘.Rprofile’
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    R      1.8Mb
    doc    1.5Mb
    help   2.1Mb
Unexported object imported by a ':::' call: ‘fdapace:::interp2lin’
  See the note in ?`:::` about the use of this operator.
installed size is 14.2Mb
  sub-directories of 1Mb or more:
    libs  13.0Mb
GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
  ‘FastGP’ ‘MASS’ ‘fdapace’
  All declared Imports should be used.
Argument items with no description in Rd file 'getbasispenalty.Rd':
  ‘Lfdobj’
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    libs   1.9Mb
Note: found 76 marked UTF-8 strings
Specified C++11: please drop specification unless essential
Note: found 3 marked Latin-1 strings
  Note: found 3 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘data.table’ ‘ggplot2’ ‘randomcoloR’ ‘sqldf’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
File ‘FD/libs/FD.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following files/directories:
  ‘vert.txt’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘treesAll.txt’
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘e1071’ ‘lattice’ ‘randomForest’ ‘tibble’ ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 20 marked UTF-8 strings
checkRd: (-1) morse.Rd:40: Escaped LaTeX specials: \#
checkRd: (-1) noRegMin.Rd:23: Escaped LaTeX specials: \#
checkRd: (-1) noRegMin.Rd:24: Escaped LaTeX specials: \#
checkRd: (-1) regMin.Rd:24: Escaped LaTeX specials: \#
File ‘fechner/libs/fechner.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘panelView’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    New Stuff
Namespaces in Imports field not imported from:
  ‘rvest’ ‘stringi’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 43825 marked UTF-8 strings
Note: found 134 marked UTF-8 strings
checkRd: (-1) fermicatsR.Rd:31: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Missing or unexported object: ‘tidytable::unnest.’
Running ‘testthat.R’ [12s/18s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(ffsimulator)
  > library(checkmate)
  > 
  > test_check("ffsimulator")
  [ FAIL 2 | WARN 1 | SKIP 7 | PASS 18 ]
  
  ══ Skipped tests (7) ═══════════════════════════════════════════════════════════
  • On CRAN (7): 'test-ffs_autoplot.R:13:3', 'test-integration.R:2:3',
    'test-integration.R:17:3', 'test-integration.R:37:3',
    'test-integration.R:49:3', 'test-integration.R:61:3',
    'test-integration.R:70:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-ffs_components.R:8:3'): ffs_adp_outcomes() works for both the simple and none injury models ──
  Error: 'unnest.' is not an exported object from 'namespace:tidytable'
  Backtrace:
      ▆
   1. ├─ffsimulator::ffs_adp_outcomes(...) at test-ffs_components.R:8:3
   2. │ └─tidytable::unnest.(ao, "rank", .drop = FALSE) %>% ...
   3. └─ffsimulator:::.ff_apply_gp_model(., gp_model)
  ── Error ('test-ffs_components.R:136:3'): schedules returns a tibble and specific columns ──
  Error: 'unnest.' is not an exported object from 'namespace:tidytable'
  Backtrace:
      ▆
   1. └─ffsimulator::ffs_build_schedules(...) at test-ffs_components.R:136:3
   2.   ├─ffsimulator:::.ff_roundrobin_size(...)
   3.   └─ffsimulator:::.ff_roundrobin_build(n_teams)
  
  [ FAIL 2 | WARN 1 | SKIP 7 | PASS 18 ]
  Deleting unused snapshots:
  • ffs_autoplot/points-plot.svg
  • ffs_autoplot/rank-plot.new.svg
  • ffs_autoplot/rank-plot.svg
  • ffs_autoplot/weekly-luck-plot.svg
  • ffs_autoplot/weekly-points-plot.svg
  Error: Test failures
  Execution halted
Documented arguments not in \usage in Rd file 'checkStream.Rd':
  ‘skipChecks’

Documented arguments not in \usage in Rd file 'cpp_detectCUSUMMeanSinglePrechange.Rd':
  ‘BL’

Documented arguments not in \usage in Rd file 'cpp_detectEWMAMeanSinglePrechange.Rd':
  ‘BL’

Documented arguments not in \usage in Rd file 'makeStreamMeanChangeR.Rd':
  ‘x’

Documented arguments not in \usage in Rd file 'update_Omega.Rd':
  ‘m_new’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Package vignette without corresponding tangle output:
  ‘intro.Rmd’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data      1.9Mb
    extdata   2.8Mb
Undeclared packages ‘MLEcens’, ‘Icens’ in Rd xrefs
Namespace in Imports field not imported from: ‘numDeriv’
  All declared Imports should be used.
Package suggested but not available for checking: ‘MicrobeDS’
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    doc    3.0Mb
    help   1.1Mb
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    R         4.6Mb
    doc       2.1Mb
    extdata   2.1Mb
Package suggested but not available for checking: ‘arrow’
Invalid package aliases in Rd file 'filename.Rd':
  ‘filename-package’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘rclipboard’ ‘shinyBS’ ‘shinyWidgets’ ‘shinyjs’
  All declared Imports should be used.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc   4.9Mb
Namespace in Imports field not imported from: ‘tidyselect’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Undeclared package ‘lubridate’ in Rd xrefs
Namespace in Imports field not imported from: ‘mvtnorm’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 222 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Undeclared package ‘FinePop’ in Rd xrefs
Package suggested but not available for checking: ‘diveRsity’
Unknown package ‘diveRsity’ in Rd xrefs
Found the following files/directories:
  ‘AH_genepop.txt’ ‘AH_popname.txt’ ‘JSM_MS_freq.txt’
  ‘JSM_MS_genepop.txt’ ‘JSM_genepop_clipped_both.txt’
  ‘JSM_genepop_clipped_maf.txt’ ‘JSM_genepop_clipped_name.txt’
  ‘JSM_mtDNA_freq.txt’ ‘JSM_popname.txt’ ‘result_DJ.csv’
  ‘result_EBDJ.csv’ ‘result_EBFST.csv’ ‘result_EBFST_mtDNA.csv’
  ‘result_EBGstH.csv’ ‘result_GstH.csv’ ‘result_GstN.csv’
  ‘result_GstNC.csv’ ‘result_thetaWCpair.csv’
checkRd: (-1) bitspec.Rd:8: Escaped LaTeX specials: \&
Namespace in Imports field not imported from: ‘RcppProgress’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘mvtnorm’
  All declared Imports should be used.
Note: found 68047 marked UTF-8 strings
Package suggested but not available for checking: ‘arrow’

Imports includes 33 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Note: found 7 marked UTF-8 strings
Specified C++11: please drop specification unless essential
File ‘fishMod/libs/fishMod.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘knitr’ ‘rmarkdown’ ‘utils’
  All declared Imports should be used.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data      1.3Mb
    extdata   3.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Imports includes 25 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc   4.1Mb
Undeclared package ‘conicfit’ in Rd xrefs
Undeclared package ‘ks’ in Rd xrefs
checkRd: (-1) fitmixEM.Rd:51: Escaped LaTeX specials: \&
Undeclared package ‘extraDistr’ in Rd xrefs
Package suggested but not available for checking: ‘gridlayout’
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘MASS’ ‘XML’ ‘gglasso’ ‘methods’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'nCDunnett', 'reliaR', 'STAR'
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘rstudioapi’
  All declared Imports should be used.
Package suggested but not available for checking: ‘fivethirtyeightdata’
Package unavailable to check Rd xrefs: ‘fivethirtyeightdata’
Note: found 584 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    R     1.3Mb
    doc   3.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘mathjaxr’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
checkRd: (-1) flashClust.Rd:92: Escaped LaTeX specials: \&
File ‘flashClust/libs/flashClust.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘RCurl’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
checkRd: (-1) cclust.Rd:78: Escaped LaTeX specials: \&
checkRd: (-1) randIndex.Rd:53: Escaped LaTeX specials: \&
checkRd: (-1) vacmot.Rd:25: Escaped LaTeX specials: \&
checkRd: (-1) vacmot.Rd:28: Escaped LaTeX specials: \&
Undeclared package ‘mixture’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 710 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    doc   9.1Mb
Undeclared package ‘flip’ in Rd xrefs
File ‘flock/libs/flock.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Note: found 3549 marked UTF-8 strings
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    R   7.0Mb
Undeclared package ‘Kendall’ in Rd xrefs
Malformed Description field: should contain one or more complete sentences.
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Undeclared package ‘HMR’ in Rd xrefs
Found the following files/directories:
  ‘flux.CH4.txt’
Namespaces in Imports field not imported from:
  ‘kableExtra’ ‘knitr’ ‘rmarkdown’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘kableExtra’ ‘knitr’ ‘rmarkdown’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Undeclared package ‘XICOR’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 446 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    fonts   6.6Mb
Malformed Description field: should contain one or more complete sentences.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    fonts   6.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Namespace in Imports field not imported from: ‘grid’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 234 marked UTF-8 strings
Namespace in Imports field not imported from: ‘tidyverse’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Undeclared package ‘ForecastCombinations’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘dtplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘decomposedPSF’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Previous versions (not tagged nor released)
Namespaces in Imports field not imported from:
  ‘blockCV’ ‘patchwork’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘pkgKitten’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘tibble’ ‘viridis’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘R6’ ‘httr’ ‘jsonlite’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    doc    1.1Mb
    help   1.0Mb
Note: found 31 marked UTF-8 strings
Package required but not available: ‘arrow’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘LaplacesDemon’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
Package suggested but not available for checking: ‘bcp’
File ‘fpow/libs/fpow.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘psych’
  All declared Imports should be used.
Package suggested but not available for checking: ‘RandomFields’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
File ‘fractional/libs/fractional.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is 17.9Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    help   2.3Mb
    libs  12.9Mb
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) MultiAsset.Rd:26: Escaped LaTeX specials: \&
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
Note: found 1 marked UTF-8 string
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'freqdom.transpose.Rd':
  ‘S’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R   5.7Mb
Note: found 50 marked UTF-8 strings
Package suggested but not available for checking: ‘dggrids’
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    data   4.9Mb
    doc    1.9Mb
    libs   1.6Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    libs   7.5Mb
'LazyData' is specified without a 'data' directory
Undeclared package ‘chillR’ in Rd xrefs
Packages suggested but not available for checking:
  'extraTrees', 'foba', 'nodeHarvest', 'obliqueRF', 'penalizedLDA',
  'relaxo', 'rrlda'
Argument items with no description in Rd file 'plot.classes.Rd':
  ‘\dots’
Argument items with no description in Rd file 'predict.fsim.Rd':
  ‘\dots’
Argument items with no description in Rd file 'predict.lm.Rd':
  ‘\dots’
Argument items with no description in Rd file 'predict.sfpl.Rd':
  ‘\dots’
Argument items with no description in Rd file 'predict.sfplsim.FASSMR.Rd':
  ‘\dots’
Argument items with no description in Rd file 'print.summary.mfplsim.Rd':
  ‘\dots’
Namespaces in Imports field not imported from:
  ‘class’ ‘mlbench’ ‘neuralnet’ ‘rpart’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Error(s) in re-building vignettes:
--- re-building ‘simulated.Rmd’ using rmarkdown
OMP: Warning #96: Cannot form a team with 24 threads, using 2 instead.
OMP: Hint Consider unsetting KMP_DEVICE_THREAD_LIMIT (KMP_ALL_THREADS), KMP_TEAMS_THREAD_LIMIT, and OMP_THREAD_LIMIT (if any are set).

fatal Fortran runtime error(/tmp/Rtmp8uXEZf/R.INSTALL1593a33eb7175e/mpmi/src/cminjk.f95:187): Assign: mismatching element counts in array assignment (to 509, from 508)
--- re-building ‘traffic.Rmd’ using rmarkdown
OMP: Warning #96: Cannot form a team with 24 threads, using 2 instead.
OMP: Hint Consider unsetting KMP_DEVICE_THREAD_LIMIT (KMP_ALL_THREADS), KMP_TEAMS_THREAD_LIMIT, and OMP_THREAD_LIMIT (if any are set).
--- finished re-building ‘traffic.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Documented arguments not in \usage in Rd file 'imp_small_gaps_WMA.Rd':
  ‘Data’ ‘univariate’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘qpdf’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Note: found 39 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
checkRd: (-1) Spec_compare_localize_freq.Rd:49: Escaped LaTeX specials: \&
checkRd: (-1) Spec_compare_localize_freq.Rd:52: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Note: found 7921 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘foreach’
  All declared Imports should be used.
Malformed Description field: should contain one or more complete sentences.
Note: found 120 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Note: found 36 marked UTF-8 strings
Documented arguments not in \usage in Rd file 'build_limits_lookup.Rd':
  ‘min_preds’ ‘max_preds’ ‘min_ratio’ ‘max_ratio’ ‘draw_unadjusted’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) add_flat_template.Rd:81: Lost braces; missing escapes or markup?
    81 | \item "minimal_package": Minimal template to start a new package when you already know {fusen}, along with the "dev_history" template. Note that this is called "minimal" in \code{create_fusen()}.
       |                                                                                        ^
checkRd: (-1) init_share_on_github.Rd:17: Lost braces; missing escapes or markup?
    17 | This uses {pkgdown} to share the documentation of the package through GitHub Actions.
       |           ^
checkRd: (-1) init_share_on_github.Rd:36: Lost braces; missing escapes or markup?
    36 | \item Init continuous deployment (CD) of the {pkgdown} website documentation
       |                                              ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘completeTrial_byArm_eventPriorRateC3=0.001_eventPriorRateT1=0_eventPriorRateT2=0_eventPriorWt=0.5.RData’
  ‘completeTrial_byArm_eventPriorRateC3=0.06_eventPriorRateT1=0.03_eventPriorRateT2=0.03_eventPriorWt=0.2.RData’
  ‘completeTrial_byArm_eventPriorRateC3=0.06_eventPriorRateT1=0.03_eventPriorRateT2=0.03_eventPriorWt=0.4.RData’
  ‘completeTrial_byArm_eventPriorRateC3=0.06_eventPriorRateT1=0.03_eventPriorRateT2=0.03_eventPriorWt=0.6.RData’
  ‘completeTrial_pooled_eventPriorRate=0.001_eventPriorWt=0.5.RData’
  ‘completeTrial_pooled_eventPriorRate=0.06_eventPriorWt=0.2.RData’
  ‘completeTrial_pooled_eventPriorRate=0.06_eventPriorWt=0.4.RData’
  ‘completeTrial_pooled_eventPriorRate=0.06_eventPriorWt=0.6.RData’
  ‘rcdf_byArm_arm=T1_eventPriorRateC3=0.06_eventPriorRateT1=0.03_eventPriorRateT2=0.03.pdf’
  ‘rcdf_pooled_eventPriorRate=0.06.pdf’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    help   4.3Mb
Invalid package aliases in Rd file 'GAabbreviate-internal.Rd':
  ‘GAabbreviation-package’
Undeclared package ‘mfdb’ in Rd xrefs
File ‘gafit/libs/gafit.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘gargle’ ‘getProxy’ ‘rappsflyer’ ‘rfacebookstat’ ‘rgoogleads’
  ‘rmytarget’ ‘rvkstat’ ‘ryandexdirect’ ‘rym’ ‘tidyr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DT’ ‘webshot’
  All declared Imports should be used.
Documented arguments not in \usage in Rd file 'splitQTL_comment.Rd':
  ‘output_qtls’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Namespace in Imports field not imported from: ‘grDevices’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘MASS’ ‘gamlss’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) LGAclaims.Rd:30: Escaped LaTeX specials: \_
checkRd: (-1) LGAclaims.Rd:34: Escaped LaTeX specials: \_
checkRd: (-1) LGAclaims.Rd:35: Escaped LaTeX specials: \_
checkRd: (-1) LGAclaims.Rd:36: Escaped LaTeX specials: \_
Undeclared package ‘gamlss’ in Rd xrefs
Undeclared packages ‘gamlss.dist’, ‘gamlss.add’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) GSE.Test.Main.Rd:23: Escaped LaTeX specials: \_
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    doc    7.9Mb
    libs   2.3Mb
Undeclared package ‘car’ in Rd xrefs
installed size is 32.9Mb
  sub-directories of 1Mb or more:
    doc  31.8Mb
'LazyData' is specified without a 'data' directory
Undeclared package ‘purrr’ in Rd xrefs
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
GNU make is a SystemRequirements.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    extdata   1.6Mb
    libs      1.8Mb
Undeclared packages ‘fortunes’, ‘rmsfact’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Package required but not available: ‘arrow’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
File ‘gbp/libs/gbp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
checkRd: (-1) fitgbd.Rd:29: Escaped LaTeX specials: \&
checkRd: (-1) fitgld.Rd:30: Escaped LaTeX specials: \&
checkRd: (-1) gb.Rd:28: Escaped LaTeX specials: \&
checkRd: (-1) gbd.Rd:37: Escaped LaTeX specials: \&
checkRd: (-1) gld.Rd:36: Escaped LaTeX specials: \&
Package in Depends field not imported from: ‘tools’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Unexported objects imported by ':::' calls:
  ‘tools:::.Rd_get_argument_names’ ‘tools:::RdTags’ ‘tools:::fetchRdDB’
  See the note in ?`:::` about the use of this operator.
checkRd: (-1) estprops.Rd:40: Escaped LaTeX specials: \&
Package suggested but not available for checking: ‘gputools’
Package suggested but not available for checking: ‘paleofire’
Namespace in Imports field not imported from: ‘raster’
  All declared Imports should be used.
Note: found 103 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Undeclared package ‘gcmr’ in Rd xrefs
'LazyData' is specified without a 'data' directory
File ‘GCPM/libs/GCPM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Specified C++11: please drop specification unless essential
installed size is 17.8Mb
  sub-directories of 1Mb or more:
    extdata   9.0Mb
    proj      8.3Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    L8NY18   2.3Mb
    libs     3.5Mb
checkRd: (-1) GMSCDM.Rd:25: Lost braces; missing escapes or markup?
    25 | representing restricted GMS-DINA and GMS-DINO models where delta_{jm1} are equal for all strategies. Note that only a single model can be used
       |                                                                  ^
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘gdxrrw’
'LazyData' is specified without a 'data' directory
Note: found 3 marked UTF-8 strings
Undeclared packages ‘palmerpenguins’, ‘readxl’ in Rd xrefs
File ‘GEEaSPU/libs/GEEaSPU.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘rootSolve’
  All declared Imports should be used.
File ‘gelnet/libs/gelnet.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Auto-generated content requiring editing in Rd file 'gemlog-package.Rd':
  \details: ‘...the package, including the most important ~~ ~~ functions ~~’
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc       1.5Mb
    extdata   3.5Mb
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘pracma’ ‘rlang’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 17 marked UTF-8 strings
Imports includes 21 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Invalid package aliases in Rd file 'GenBinom-package.Rd':
  ‘GenbinomApps-package’
Undeclared package ‘poibin’ in Rd xrefs
Namespace in Imports field not imported from: ‘purrr’
  All declared Imports should be used.
Package suggested but not available for checking: ‘genderdata’
Undeclared package ‘mmap’ in Rd xrefs
Documented arguments not in \usage in Rd file 'expand.Rd':
  ‘x’

Documented arguments not in \usage in Rd file 'grapes-bq-grapes.Rd':
  ‘x’

Documented arguments not in \usage in Rd file 'grapes-bt-grapes.Rd':
  ‘x’

Documented arguments not in \usage in Rd file 'stftcalc.Rd':
  ‘x’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘BiocManager’ ‘R.utils’ ‘markdown’
  All declared Imports should be used.
Package suggested but not available for checking: ‘rrvgo’
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Namespaces in Imports field not imported from:
  ‘GGEBiplots’ ‘calibrate’ ‘graphics’ ‘matrixStats’ ‘prettydoc’
  ‘reshape2’
  All declared Imports should be used.
Skipping checking math rendering: package 'V8' unavailable
Undeclared package ‘bootstrap’ in Rd xrefs
Specified C++11: please drop specification unless essential
Specified C++14: please drop specification unless essential
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘censobr’
Note: found 58 marked UTF-8 strings
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    extdata   3.0Mb
Note: found 4828 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Undeclared package ‘RiemBase’ in Rd xrefs
Note: found 646 marked UTF-8 strings
Note: found 93994 marked UTF-8 strings
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc       2.1Mb
    extdata   3.5Mb
Found the following files/directories:
  ‘pulse-PKdhtXMmr18n’
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘geomarocdata’
'LazyData' is specified without a 'data' directory
installed size is 14.8Mb
  sub-directories of 1Mb or more:
    R         9.5Mb
    extdata   2.6Mb
    help      2.6Mb
Package required but not available: ‘GPvecchia’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Namespace in Imports field not imported from: ‘velociraptr’
  All declared Imports should be used.
Note: found 2085 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘dbplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   4.1Mb
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
Undeclared package ‘loo’ in Rd xrefs
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘RandomFields’
Unknown package ‘RandomFields’ in Rd xrefs
Note: found 4 marked UTF-8 strings
Malformed Description field: should contain one or more complete sentences.
Found the following calls to data() loading into the global environment:
File ‘geotools/R/zzz.R’:
  data(fr_geo_rad)
See section ‘Good practice’ in ‘?data’.
Note: found 64 marked Latin-1 strings
  Note: found 25 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Package required but not available: ‘arrow’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘pipeR’ ‘rlang’
  All declared Imports should be used.
Package suggested but not available for checking: ‘RGtk2’
Namespaces in Imports field not imported from:
  ‘googlesheets4’ ‘tidyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘plotly’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'attract_by_distance.Rd':
  ‘prop_start’ ‘prop_end’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Undeclared packages ‘FactoMineR’, ‘ade4’, ‘factoextra’ in Rd xrefs
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc       3.0Mb
    extdata   1.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    doc    6.6Mb
    help   1.1Mb
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'labels.rpart.Rd':
  ‘pretty:’

Documented arguments not in \usage in Rd file 'rpart_labels.Rd':
  ‘model’ ‘...’

Documented arguments not in \usage in Rd file 'rpart_segments.Rd':
  ‘model’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Undeclared package ‘gge’ in Rd xrefs
Namespace in Imports field not imported from: ‘magrittr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘R6’ ‘scales’ ‘utils’
  All declared Imports should be used.
Found the following assignments to the global environment:
File ‘ggExtra/R/ggMarginalGadget.R’:
  assign(plotname, eval(parse(text = origPlot)), envir = .GlobalEnv)
'LazyData' is specified without a 'data' directory
Undeclared packages ‘akima’, ‘ggforce’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘grDevices’ ‘gtable’
  All declared Imports should be used.
Undeclared package ‘rlang’ in Rd xrefs
Specified C++11: please drop specification unless essential
Undeclared package ‘rlang’ in Rd xrefs
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    R     1.0Mb
    doc   7.0Mb
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
Package vignette without corresponding tangle output:
  ‘Introduction_to_gglasso_package.Rmd’
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘Rdpack’ ‘mathjaxr’
  All declared Imports should be used.
checkRd: (-1) boot_eip.Rd:50: Escaped LaTeX specials: \&
checkRd: (-1) constrained.Rd:93: Escaped LaTeX specials: \&
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘Rdpack’
  All declared Imports should be used.
checkRd: (-1) constrained.Rd:37: Escaped LaTeX specials: \&
':::' call which should be '::': ‘scales:::censor’
  See the note in ?`:::` about the use of this operator.
Unexported object imported by a ':::' call: ‘productplots:::bound’
  See the note in ?`:::` about the use of this operator.
Undeclared package ‘dwlm’ in Rd xrefs
Namespaces in Imports field not imported from:
  ‘sna’ ‘utils’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘grid’ ‘scales’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Undeclared packages ‘scales’, ‘labeling’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Note: found 1 marked UTF-8 string
Namespace in Imports field not imported from: ‘survival’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Undeclared package ‘ggdensity’ in Rd xrefs
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R     1.3Mb
    doc   1.9Mb
Undeclared packages ‘interp’, ‘akima’ in Rd xrefs
Namespaces in Imports field not imported from:
  ‘gcookbook’ ‘ggthemes’ ‘moonBook’ ‘tidyverse’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘lixoftConnectors’
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    doc        1.1Mb
    help       2.4Mb
    testdata   4.8Mb
'LazyData' is specified without a 'data' directory
Note: found 35 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘grDevices’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Undeclared package ‘car’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Imports includes 37 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Namespaces in Imports field not imported from:
  ‘DT’ ‘Formula’ ‘GGally’ ‘Hmisc’ ‘RPostgres’ ‘colourpicker’ ‘ggpmisc’
  ‘ggpubr’ ‘glue’ ‘gridExtra’ ‘markdown’ ‘patchwork’ ‘plotly’
  ‘quantreg’ ‘shinyFiles’ ‘shinyjqui’ ‘shinyjs’ ‘table1’ ‘zoo’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   3.6Mb
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    extdata   9.1Mb
Undeclared package ‘vipor’ in Rd xrefs
Note: found 6242 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘nomogramFormula’ ‘survival’
  All declared Imports should be used.
Note: found 19 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘magrittr’ ‘utils’
  All declared Imports should be used.
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    * Changes all data options to .data to decrease possibility of column naming overlap
Undeclared package ‘RColorBrewer’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Undeclared package ‘rlang’ in Rd xrefs
Namespace in Imports field not imported from: ‘tidyr’
  All declared Imports should be used.
Undeclared packages ‘chemometrics’, ‘rlang’ in Rd xrefs
Documented arguments not in \usage in Rd file 'ggplot_gtable.Rd':
  ‘plot’

Documented arguments not in \usage in Rd file 'undocumented.Rd':
  ‘latex’ ‘ggplot’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Note: found 138 marked UTF-8 strings
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Win CRAN check results - R Windows
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    doc    9.5Mb
    help   1.1Mb
Note: found 208 marked UTF-8 strings
Namespace in Imports field not imported from: ‘ggplot2’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘class’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Note: found 11 marked UTF-8 strings
installed size is 18.1Mb
  sub-directories of 1Mb or more:
    Giac  17.9Mb
Note: found 553 marked UTF-8 strings
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc    3.4Mb
    help   2.5Mb
Undeclared package ‘Runuran’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘Pictures_analyzed’ ‘cutoff_vals’ ‘cutoff_vals1’ ‘gina_cran.JPG’
Undeclared packages ‘ineq’, ‘IC2’ in Rd xrefs
Unknown package ‘IC2’ in Rd xrefs
Specified C++11: please drop specification unless essential
File ‘GiRaF/libs/GiRaF.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Note: found 1178 marked UTF-8 strings
Note: found 866 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘mockery’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘mockery’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘MASS’ ‘MCMCpack’ ‘ggplot2’ ‘moments’
  All declared Imports should be used.
Problems with news in ‘NEWS.md’:
No news entries found.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) randPIT.Rd:52: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
File ‘gllm/libs/gllm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs   5.9Mb
File ‘GLMaSPU/libs/GLMaSPU.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘ordinal’
  All declared Imports should be used.
checkRd: (-1) glmc.Rd:232: Escaped LaTeX specials: \&
checkRd: (-1) glmc.Rd:241: Escaped LaTeX specials: \&
checkRd: (-1) glmc.control.Rd:29: Escaped LaTeX specials: \$
checkRd: (-1) glmc.control.Rd:31: Escaped LaTeX specials: \$
checkRd: (-1) glmc.summaries.Rd:79: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Undeclared package ‘GMMBoost’ in Rd xrefs
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   4.0Mb
Namespace in Imports field not imported from: ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.0Mb
installed size is 11.8Mb
  sub-directories of 1Mb or more:
    doc             1.4Mb
    libs            6.4Mb
    test_data       2.2Mb
    vignette_data   1.2Mb
Namespaces in Imports field not imported from:
  ‘AER’ ‘MASS’ ‘Matrix’ ‘censReg’ ‘effects’ ‘foreign’ ‘lme4’ ‘lmtest’
  ‘nnet’ ‘pBrackets’ ‘plm’ ‘pscl’ ‘sandwich’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
checkRd: (-1) coef.glmulti.Rd:26: Escaped LaTeX specials: \&
checkRd: (-1) coef.glmulti.Rd:27: Escaped LaTeX specials: \&
checkRd: (-1) coef.glmulti.Rd:51: Escaped LaTeX specials: \&
checkRd: (-1) coef.glmulti.Rd:60: Escaped LaTeX specials: \&
checkRd: (-1) coef.glmulti.Rd:61: Escaped LaTeX specials: \&
checkRd: (-1) consensus.Rd:29: Escaped LaTeX specials: \&
checkRd: (-1) getfit.Rd:26: Escaped LaTeX specials: \&
checkRd: (-1) glmulti-class.Rd:26: Escaped LaTeX specials: \&
checkRd: (-1) glmulti.Rd:99: Escaped LaTeX specials: \&
checkRd: (-1) summary.glmulti.Rd:72: Escaped LaTeX specials: \&
Malformed Description field: should contain one or more complete sentences.
File ‘globalOptTests/libs/globalOptTests.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Note: found 2 marked UTF-8 strings
Namespace in Imports field not imported from: ‘rnaturalearthdata’
  All declared Imports should be used.
Note: found 1191 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Undeclared package ‘caret’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Note: found 2629 marked UTF-8 strings
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Packages suggested but not available for checking:
  'SeqArray', 'SeqVarTools'
Undeclared package ‘glmmLasso’ in Rd xrefs
Undeclared package ‘sandwich’ in Rd xrefs
Found the following significant warnings:
  Warning in is.R() : 'is.R' is deprecated.
See ‘/data/gannet/ripley/R/packages/tests-clang/gmodels.Rcheck/00install.out’ for details.
Undeclared package ‘rms’ in Rd xrefs
Found the following significant warnings:

  Warning in is.R() : 'is.R' is deprecated.
  Warning in is.R() : 'is.R' is deprecated.
  Warning in is.R() : 'is.R' is deprecated.
  Warning in is.R() : 'is.R' is deprecated.
  Warning in is.R() : 'is.R' is deprecated.
  Warning in is.R() : 'is.R' is deprecated.
  Warning in is.R() : 'is.R' is deprecated.
  Warning in is.R() : 'is.R' is deprecated.
  Warning in is.R() : 'is.R' is deprecated.
  Warning in is.R() : 'is.R' is deprecated.
  Warning in is.R() : 'is.R' is deprecated.
  Warning in is.R() : 'is.R' is deprecated.
  Warning in is.R() : 'is.R' is deprecated.
  Warning in is.R() : 'is.R' is deprecated.
  Warning in is.R() : 'is.R' is deprecated.
  Warning in is.R() : 'is.R' is deprecated.
  Warning in is.R() : 'is.R' is deprecated.
  Warning in is.R() : 'is.R' is deprecated.
  Warning in is.R() : 'is.R' is deprecated.
  Warning in is.R() : 'is.R' is deprecated.
  Warning in is.R() : 'is.R' is deprecated.
  Warning in is.R() : 'is.R' is deprecated.
  Warning in is.R() : 'is.R' is deprecated.
  Warning in is.R() : 'is.R' is deprecated.
  Warning in is.R() : 'is.R' is deprecated.
  Warning in is.R() : 'is.R' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
'LazyData' is specified without a 'data' directory
checkRd: (-1) replace_in_file.Rd:40: Escaped LaTeX specials: \#
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Undeclared package ‘repeated’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 3 marked UTF-8 strings
Undeclared packages ‘openxlsx’, ‘readxl’ in Rd xrefs
Namespaces in Imports field not imported from:
  ‘base’ ‘methods’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
Undeclared package ‘goftest’ in Rd xrefs
Note: found 1352 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘rhandsontable’ ‘shiny’ ‘stats’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
checkRd: (-1) BVDWSTOXX.Rd:14: Escaped LaTeX specials: \&
checkRd: (-1) BVDWSTOXX.Rd:15: Escaped LaTeX specials: \&
checkRd: (-1) BVDWSTOXX.Rd:16: Escaped LaTeX specials: \& \&
checkRd: (-1) BVDWSTOXX.Rd:26: Escaped LaTeX specials: \&
checkRd: (-1) BVDWSTOXX.Rd:31: Escaped LaTeX specials: \&
checkRd: (-1) BVDWSTOXX.Rd:34: Escaped LaTeX specials: \&
checkRd: (-1) BVDWSTOXX.Rd:37: Escaped LaTeX specials: \&
Undeclared package ‘fBasics’ in Rd xrefs
Specified C++11: please drop specification unless essential
checkRd: (-1) create_golem.Rd:30: Lost braces; missing escapes or markup?
    30 | \item{package_name}{Package name to use. By default, {golem} uses
       |                                                      ^
checkRd: (-1) fill_desc.Rd:42: Lost braces; missing escapes or markup?
    42 | The {desc} object, invisibly.
       |     ^
checkRd: (-1) get_sysreqs.Rd:23: Lost braces; missing escapes or markup?
    23 | {dockerfiler}.
       | ^
checkRd: (-1) golem_opts.Rd:80: Lost braces; missing escapes or markup?
    80 | \item{config_file}{path to the {golem} config file}
       |                                ^
checkRd: (-1) install_dev_deps.Rd:5: Lost braces; missing escapes or markup?
     5 | \title{Install {golem} dev dependencies}
       |                ^
checkRd: (-1) project_hook.Rd:13: Lost braces; missing escapes or markup?
    13 | \item{package_name}{Package name to use. By default, {golem} uses
       |                                                      ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Rd files without \alias:
  ‘goodpractice-package.Rd’
Note: found 1 marked UTF-8 string
Packages suggested but not available for checking:
  'bigQueryR', 'ganalytics'
Unknown package ‘bigQueryR’ in Rd xrefs
Package suggested but not available for checking: ‘bigQueryR’
Documented arguments not in \usage in Rd file 'doHttrRequest.Rd':
  ‘session’ ‘params’

Documented arguments not in \usage in Rd file 'get_google_token.Rd':
  ‘shiny_return_token’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
checkRd: (-1) GitHubEventsConfig.Rd:16: Lost braces; missing escapes or markup?
    16 | \item{x}{The repository in format {owner}/{repo} e.g. MarkEdmondson1234/googleCloudRunner}
       |                                   ^
checkRd: (-1) GitHubEventsConfig.Rd:16: Lost braces; missing escapes or markup?
    16 | \item{x}{The repository in format {owner}/{repo} e.g. MarkEdmondson1234/googleCloudRunner}
       |                                           ^
checkRd: (-1) cr_buildstep_targets.Rd:27: Lost braces
    27 | \item{id}{The id of the buildstep.  In link{cr_buildstep_targets_multi} this is used along with \code{waitFor} to determine the order of execution}
       |                                            ^
checkRd: (-1) cr_setup_service.Rd:21: Lost braces; missing escapes or markup?
    21 | \item{account_email}{The service account email e.g. \code{accountId@projectid.iam.gserviceaccount.com} or {12345678@cloudbuild.gserviceaccount.com}}
       |                                                                                                           ^
Undeclared packages ‘rcmdcheck’, ‘covr’, ‘devtools’, ‘pkgdown’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Undeclared package ‘jsonlite’ in Rd xrefs
Namespaces in Imports field not imported from:
  ‘assertthat’ ‘future’ ‘httr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    R   5.7Mb
installed size is 12.3Mb
  sub-directories of 1Mb or more:
    libs  11.4Mb
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
File ‘gplm/libs/gplm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
checkRd: (-1) barplot2.Rd:219: Escaped LaTeX specials: \_
checkRd: (-1) colorpanel.Rd:31: Escaped LaTeX specials: \#
checkRd: (-1) qqnorm.aov.Rd:33: Escaped LaTeX specials: \&
checkRd: (-1) venn.Rd:59: Escaped LaTeX specials: \_
Specified C++11: please drop specification unless essential
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    doc    3.5Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘cmdstanr’
Undeclared package ‘speedglm’ in Rd xrefs
Installation failed.
See ‘/data/gannet/ripley/R/packages/tests-clang/GPvecchia.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    help   5.3Mb
Undeclared package ‘gratia’ in Rd xrefs
Note: found 5030 marked UTF-8 strings
Package suggested but not available for checking: ‘monocle’
Package unavailable to check Rd xrefs: ‘monocle’
'LazyData' is specified without a 'data' directory
Imports includes 21 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Namespaces in Imports field not imported from:
  ‘Hmisc’ ‘PairedData’ ‘RColorBrewer’ ‘agricolae’ ‘corrplot’ ‘desplot’
  ‘dplyr’ ‘ggplot2’ ‘ggpubr’ ‘gridGraphics’ ‘gtools’ ‘kableExtra’
  ‘knitr’ ‘magrittr’ ‘pastecs’ ‘reshape2’ ‘rmarkdown’ ‘shinyWidgets’
  ‘summarytools’
  All declared Imports should be used.
checkRd: (-1) corrApp.Rd:40: Escaped LaTeX specials: \&
checkRd: (-1) crdApp.Rd:46: Escaped LaTeX specials: \&
checkRd: (-1) descApp.Rd:55: Escaped LaTeX specials: \&
checkRd: (-1) layoutApp.Rd:50: Escaped LaTeX specials: \&
checkRd: (-1) rbdApp.Rd:46: Escaped LaTeX specials: \&
checkRd: (-1) ttApp.Rd:43: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘reshape2’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Undeclared package ‘glasso’ in Rd xrefs
Specified C++11: please drop specification unless essential
Note: found 22 marked UTF-8 strings
Argument items with no description in Rd file 'HistPCA.Rd':
  ‘ggplot’
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Note: found 989 marked UTF-8 strings
GNU make is a SystemRequirements.
accrualReport: multiple local function definitions for ‘gg’ with
  different formal arguments
checkRd: (-1) iterate_matrix.Rd:32-33: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) iterate_matrix.Rd:34-36: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) iterate_matrix.Rd:37-38: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) iterate_matrix.Rd:39-41: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) iterate_matrix.Rd:42-44: Lost braces in \itemize; \value handles \item{}{} directly
GNU make is a SystemRequirements.
Malformed Description field: should contain one or more complete sentences.
Specified C++14: please drop specification unless essential
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘BiasedUrn’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘usethis’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘msm’
  All declared Imports should be used.
S3 methods shown with full name in Rd file 'groc.fit.Rd':
  ‘groc.fit’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘MASS’ ‘rjags’
  All declared Imports should be used.
File ‘grove/libs/grove.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Problems with news in ‘NEWS.md’:
No news entries found.
Undeclared packages ‘repeated’, ‘gnlm’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Invalid package aliases in Rd file 'fit_grp.Rd':
  ‘grplasso-package’
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    libs  10.0Mb
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
Found the following files/directories:
  ‘p1_20up-vs-p2_25up_in_str1.txt’ ‘p1_20up-vs-p2_25up_in_str2.txt’
  ‘p2_25up-vs-p1_20up_in_str1.txt’ ‘p2_25up-vs-p1_20up_in_str2.txt’
  ‘s0_20up.txt’ ‘s0_30up.txt’ ‘s0_f2up.txt’ ‘strs.vec_01mx.txt’
  ‘strs.vec_02mx.txt’ ‘strs.vec_03mx.txt’ ‘strs.vec_04mx.txt’
  ‘strs.vec_05mx.txt’ ‘strs.vec_06mx.txt’ ‘strs.vec_30up.txt’
  ‘strs.vec_50up.txt’ ‘strs.vec_f2up.txt’ ‘uni_p1_20up-p2_25up.txt’
File ‘grr/libs/grr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Imports includes 21 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
checkRd: (-1) runGRM.Rd:24: Lost braces
    24 |    from \code{\link{mirt}} or code{\linkS4class{lavaan}} from from
       |                                   ^
checkRd: (-1) fmddisc.Rd:23: Escaped LaTeX specials: \_
checkRd: (-1) schuster.Rd:46: Escaped LaTeX specials: \_
checkRd: (-1) schuster.Rd:54: Escaped LaTeX specials: \&
Found the following files/directories:
  ‘FMD mag discontinuities_disc.png’ ‘FMD mag
  discontinuities_disc1.res’ ‘FMD mag discontinuities_disc2.res’
  ‘IDYLLWILD_bvmed.png’ ‘IDYLLWILD_fig.png’ ‘Schuster's
  diagram_schu.png’ ‘hour.res’
Objects in \usage without \alias in Rd file 'GSA.internal.Rd':
  ‘est.s0’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Undeclared package ‘nflfastR’ in Rd xrefs
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
Malformed Description field: should contain one or more complete sentences.
File ‘gsmoothr/libs/gsmoothr.so’:
  Found no call to: ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   3.4Mb
    doc    1.3Mb
Namespace in Imports field not imported from: ‘devtools’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   4.1Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    help   1.9Mb
Note: found 146 marked UTF-8 strings
Note: found 269 marked UTF-8 strings
Note: found 42384 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘RRprof.out’
Namespace in Imports field not imported from: ‘RUnit’
  All declared Imports should be used.
Undeclared package ‘permute’ in Rd xrefs
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
Note: found 20255 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
File ‘GWASExactHW/libs/GWASExactHW.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Package required but not available: ‘nhdplusTools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Note: found 275 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘doParallel’ ‘foreach’ ‘spgwr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘sf’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘DT’ ‘attempt’ ‘corpcor’ ‘glue’ ‘htmltools’ ‘pkgload’ ‘processx’
  ‘tools’
  All declared Imports should be used.
Imports includes 21 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Found the following files/directories:
  ‘testdata1.txt’ ‘testdata2.txt’ ‘testdata3.txt’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is 267.8Mb
  sub-directories of 1Mb or more:
    R       1.5Mb
    help    1.0Mb
    java  264.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    HaDeX   4.1Mb
    doc     4.0Mb
Namespaces in Imports field not imported from:
  ‘DT’ ‘gsubfn’ ‘stringr’
  All declared Imports should be used.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘.ga.breed’ ‘.ga.fitness’ ‘.ga.init’ ‘.ga.mutate’ ‘.ga.step’
  ‘.ga.weight’
Undeclared package ‘mnis’ in Rd xrefs
Note: found 7592 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
checkRd: (-1) HWAlr.Rd:25: Escaped LaTeX specials: \&
checkRd: (-1) HWAlrPlot.Rd:25: Escaped LaTeX specials: \&
checkRd: (-1) HWClr.Rd:23: Escaped LaTeX specials: \&
checkRd: (-1) HWClrPlot.Rd:25: Escaped LaTeX specials: \&
checkRd: (-1) HWIlr.Rd:30: Escaped LaTeX specials: \&
checkRd: (-1) HWf.Rd:25: Escaped LaTeX specials: \&
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    doc    2.6Mb
'LazyData' is specified without a 'data' directory
Undeclared package ‘dplyr’ in Rd xrefs
GNU make is a SystemRequirements.
File ‘hawkes/libs/hawkes.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
installed size is 14.6Mb
  sub-directories of 1Mb or more:
    libs  13.0Mb
GNU make is a SystemRequirements.
Specified C++14: please drop specification unless essential
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R         2.6Mb
    extdata   1.3Mb
GNU make is a SystemRequirements.
Note: found 3 marked UTF-8 strings
Note: found 104392 marked UTF-8 strings
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc   4.7Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc           2.7Mb
    htmlwidgets   2.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   6.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
File ‘HDGLM/libs/HDGLM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Imports includes 24 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Namespaces in Imports field not imported from:
  ‘MCMCpack’ ‘ggjoy’ ‘isotone’ ‘png’ ‘questionr’ ‘rprojroot’
  ‘tidyverse’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    doc    3.8Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc   5.2Mb
Namespaces in Imports field not imported from:
  ‘TidyDensity’ ‘healthyR’ ‘healthyR.ai’ ‘healthyR.data’ ‘healthyR.ts’
  ‘tidyAML’
  All declared Imports should be used.
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc   5.1Mb
Specified C++11: please drop specification unless essential
Undeclared package ‘tibble’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Undeclared package ‘sp’ in Rd xrefs
Specified C++11: please drop specification unless essential
Undeclared packages ‘Sleuth2’, ‘rrcov’, ‘archdata’, ‘qqtest’ in Rd xrefs
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   2.1Mb
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) ohio.Rd:104: Escaped LaTeX specials: \&
checkRd: (-1) ohio.Rd:105: Escaped LaTeX specials: \&
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘usethis’
  All declared Imports should be used.
Undeclared package ‘lme4’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Note: found 52 marked UTF-8 strings
File ‘HiCseg/libs/HiCseg.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package vignette without corresponding tangle output:
  ‘HiCseg.Rnw’
Found export directives that require package ‘methods’:
  ‘exportClasses’ ‘exportMethods’
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains ‘methods’.
File ‘HiDimDA/libs/HiDimDA.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘RiskPortfolios’
  All declared Imports should be used.
Note: found 11 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Argument items with no description in Rd file 'qcplate.Rd':
  ‘dat’
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘colorfulVennPlot’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Undeclared packages ‘Guerry’, ‘alr4’, ‘agridat’, ‘coin’ in Rd xrefs
Invalid package aliases in Rd file 'histogram-package.Rd':
  ‘histogramtools-package’
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘trackr’
Package which this enhances but not available for checking: ‘HadoopStreaming’
Note: found 9638 marked UTF-8 strings
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
html_describe_con: multiple local function definitions for ‘g’ with
  different formal arguments
Documented arguments not in \usage in Rd file 'bootstrapfun.Rd':
  ‘DoF’ ‘n_sample’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) disc42.Rd:28: Escaped LaTeX specials: \&
checkRd: (-1) discrimination.Rd:31: Escaped LaTeX specials: \&
Undeclared package ‘genalg’ in Rd xrefs
Auto-generated content requiring editing in Rd file 'HMVD-package.Rd':
  \details: ‘...o use the package, including the most important functions ~~’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘glmmADMB’
Namespaces in Imports field not imported from:
  ‘knitr’ ‘rmarkdown’
  All declared Imports should be used.
Invalid package aliases in Rd file 'hoardeR-package.Rd':
  ‘R/hoardeR-package’
Argument items with no description in Rd file 'bid2.Rd':
  ‘numattable1’ ‘playerseats1’ ‘blinds1’ ‘dealer1’ ‘b3’ ‘b4’ ‘round1’
  ‘ntable1’ ‘decision1’
Argument items with no description in Rd file 'calcwin1.Rd':
  ‘numattable1’ ‘playerseats1’ ‘b3’ ‘b7’
Argument items with no description in Rd file 'mycount1.Rd':
  ‘x’
Argument items with no description in Rd file 'mygraphics1.Rd':
  ‘numattable1’ ‘playerseats1’ ‘chips1’ ‘blinds1’ ‘dealer1’ ‘b3’ ‘b4’
  ‘b5’ ‘b6’ ‘b7’ ‘chips2’ ‘ntable1’ ‘myfast1’ ‘chipstart1’ ‘name1’
  ‘lowercut1’
Argument items with no description in Rd file 'nothing1.Rd':
  ‘x’
Argument items with no description in Rd file 'onepair1.Rd':
  ‘x’
Argument items with no description in Rd file 'straight1.Rd':
  ‘x’
Argument items with no description in Rd file 'straightdraw1.Rd':
  ‘x’
Argument items with no description in Rd file 'strflsh1.Rd':
  ‘x’ ‘y’
Argument items with no description in Rd file 'trip1.Rd':
  ‘x’
Argument items with no description in Rd file 'twopair1.Rd':
  ‘x’
Argument items with no description in Rd file 'writebets1.Rd':
  ‘b9’ ‘y1’ ‘numattable1’ ‘b3’ ‘playerseats1’ ‘chips1’ ‘chips2’ ‘over1’
  ‘myfast1’ ‘name1’
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    app   1.7Mb
    doc   3.3Mb
Undeclared package ‘rgl’ in Rd xrefs
Namespace in Imports field not imported from: ‘survival’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 124 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Rd files without \alias:
  ‘hpoPlot-package.Rd’
Package vignette without corresponding tangle output:
  ‘why_hrbrthemes.Rmd’
Packages suggested but not available for checking: 'RGtk2', 'cairoDevice'
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in Rd file 'dot-E3.Rd':
  ‘i’ ‘M’

Documented arguments not in \usage in Rd file 'dot-E4.Rd':
  ‘i’ ‘M’

Documented arguments not in \usage in Rd file 'hrm.0w.2s.Rd':
  ‘group’

Documented arguments not in \usage in Rd file 'hrm.0w.3s.Rd':
  ‘group’

Documented arguments not in \usage in Rd file 'hrm.0w.4s.Rd':
  ‘group’

Documented arguments not in \usage in Rd file 'hrm.0w.5s.Rd':
  ‘group’

Documented arguments not in \usage in Rd file 'hrm.1f.Rd':
  ‘group’

Documented arguments not in \usage in Rd file 'hrm.1w.0f.Rd':
  ‘factor1’

Documented arguments not in \usage in Rd file 'hrm.2w.2f.Rd':
  ‘factor’

Documented arguments not in \usage in Rd file 'hrm.mv.1w.1f.Rd':
  ‘H’ ‘text’

Documented arguments not in \usage in Rd file 'hrm.mv.internal.Rd':
  ‘alpha’ ‘H’ ‘text’

Documented arguments not in \usage in Rd file 'hrm.test.1.none.Rd':
  ‘factor1’ ‘factor2’

Documented arguments not in \usage in Rd file 'hrm.test.1.one.Rd':
  ‘group’ ‘factor2’

Documented arguments not in \usage in Rd file 'hrm.test.2.one.Rd':
  ‘factor2’

Documented arguments not in \usage in Rd file 'hrm.test.2.two.Rd':
  ‘group’

Documented arguments not in \usage in Rd file 'hrm.test.3.three.Rd':
  ‘group’

Documented arguments not in \usage in Rd file 'hrm.test.4.four.Rd':
  ‘group’

Documented arguments not in \usage in Rd file 'hrm.test.5.five.Rd':
  ‘group’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘quantreg’
  All declared Imports should be used.
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    data   7.1Mb
'LazyData' is specified without a 'data' directory
File ‘hsphase/libs/hsphase.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘recipes’ ‘tune’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘igraph’
  All declared Imports should be used.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   1.8Mb
    doc    2.3Mb
    help   1.1Mb
checkRd: (-1) simplePostToHost.Rd:14: Escaped LaTeX specials: \&
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
File ‘humaniformat/libs/humaniformat.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘hurricaneexposuredata’
Namespace in Imports field not imported from: ‘mapproj’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘R6’ ‘xml2’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
  ‘colourpicker’ ‘shiny’ ‘wordcloud2’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 1 marked UTF-8 string
Package suggested but not available for checking: ‘microViz’
Package suggested but not available for checking: ‘nhdplusTools’
Running examples in ‘hydroloom-Ex.R’ failed
The error most likely occurred in:

> ### Name: index_points_to_waterbodies
> ### Title: Index Points to Waterbodies
> ### Aliases: index_points_to_waterbodies
> 
> ### ** Examples
> 
> 
> source(system.file("extdata/sample_data.R", package = "nhdplusTools"))
Error in source(system.file("extdata/sample_data.R", package = "nhdplusTools")) : 
  empty file/url name
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘advanced_network.Rmd’ using rmarkdown
--- finished re-building ‘advanced_network.Rmd’

--- re-building ‘flow-table.Rmd’ using rmarkdown

Quitting from lines 12-32 [setup] (flow-table.Rmd)
Error: processing vignette 'flow-table.Rmd' failed with diagnostics:
there is no package called 'nhdplusTools'
--- failed re-building ‘flow-table.Rmd’

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

--- re-building ‘non-dendritic.Rmd’ using rmarkdown
--- finished re-building ‘non-dendritic.Rmd’

SUMMARY: processing the following file failed:
  ‘flow-table.Rmd’

Error: Vignette re-building failed.
Execution halted
Invalid package aliases in Rd file 'HydroMe-package.Rd':
  ‘HydroMe2-package’
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    extdata   5.5Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    extdata   4.8Mb
'LazyData' is specified without a 'data' directory
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    extdata   5.8Mb
Package suggested but not available for checking: ‘flowCore’
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    doc   6.4Mb
checkRd: (-1) palettes.Rd:25: Escaped LaTeX specials: \#
Documented arguments not in \usage in Rd file 'read.txt.Witec.Rd':
  ‘nwl’ ‘remove.zerospc’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Imports includes 22 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Namespace in Imports field not imported from: ‘raster’
  All declared Imports should be used.
Found the following files/directories:
  ‘pulse-PKdhtXMmr18n’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package vignette with \VignetteEngine{} not specifying an engine package:
  ‘index.Rmd’
Engines should be specified as \VignetteEngine{PKG::ENG}.
Note: found 38558 marked UTF-8 strings
Note: found 1058038 marked UTF-8 strings
Specified C++11: please drop specification unless essential
Note: found 1 marked UTF-8 string
Note: found 359 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
File ‘ibmcraftr/libs/ibmcraftr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package suggested but not available for checking: ‘SparkR’
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   6.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 356712 marked UTF-8 strings
Package suggested but not available for checking: ‘icd’
Note: found 55 marked UTF-8 strings
Undeclared package ‘tibble’ in Rd xrefs
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
checkRd: (-1) ICEscale.Rd:53: Escaped LaTeX specials: \^
checkRd: (-1) dpwdg.Rd:14: Escaped LaTeX specials: \$
checkRd: (-1) dpwdg.Rd:15: Escaped LaTeX specials: \$
Imports includes 26 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Namespaces in Imports field not imported from:
  ‘digest’ ‘purrr’ ‘tidyverse’
  All declared Imports should be used.
Note: found 10 marked UTF-8 strings
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Undeclared packages ‘mlogit’, ‘logitr’ in Rd xrefs
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘rggobi’
'LazyData' is specified without a 'data' directory
Undeclared package ‘tibble’ in Rd xrefs
Undeclared packages ‘sfsmisc’, ‘RColorBrewer’, ‘hexbin’ in Rd xrefs
Namespace in Imports field not imported from: ‘kableExtra’
  All declared Imports should be used.
Note: found 4 marked UTF-8 strings
File ‘ieeeround/libs/ieeeround.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Note: found 366 marked UTF-8 strings
Imports includes 31 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Note: found 40 marked UTF-8 strings
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
Package suggested but not available for checking: ‘IFCdata’
File ‘IFP/libs/IFP.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘kableExtra’ ‘knitr’ ‘xtable’
  All declared Imports should be used.
Note: found 160 marked UTF-8 strings
Package required but not available: ‘arrow’

Imports includes 31 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    doc    1.2Mb
    help   1.9Mb
    libs   3.6Mb
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    dlib-19.20   9.5Mb
Undeclared packages ‘bmp’, ‘jpeg’, ‘png’, ‘tiff’ in Rd xrefs
Documented arguments not in \usage in Rd file 'dot-compl.Rd':
  ‘imgfile’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘tesseract’
installed size is 16.3Mb
  sub-directories of 1Mb or more:
    data      1.4Mb
    doc       5.2Mb
    extdata   1.1Mb
    include   3.0Mb
    libs      4.9Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Note: found 2 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
checkRd: (-1) immer_proc_data.Rd:77: Lost braces
    77 | \code{A}{design matrix}
       |         ^
checkRd: (-1) immer_proc_data.Rd:78: Lost braces
    78 | \code{itemtable2}{Processed item table}
       |                  ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘accdata’
Documented arguments not in \usage in Rd file 'new_impactr_peaks.Rd':
  ‘acc_signal:’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘data.table’ ‘dplyr’ ‘haven’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘pscl’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘lme4’ ‘reshape2’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
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}
       |                                                                       ^
Note: found 2 marked UTF-8 strings
Specified C++11: please drop specification unless essential
Undeclared package ‘minfi’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Note: found 151 marked UTF-8 strings
Namespace in Imports field not imported from: ‘svglite’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
checkRd: (-1) school23.Rd:30: Escaped LaTeX specials: \&
checkRd: (-1) school23.Rd:35: Escaped LaTeX specials: \&
Problems with news in ‘NEWS.md’:
No news entries found.
Package which this enhances but not available for checking: ‘gurobi’
File ‘infotheo/libs/infotheo.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following files/directories:
  ‘c.txt’ ‘rho.txt’ ‘sta.txt’ ‘topo.txt’
'LazyData' is specified without a 'data' directory
File ‘INLAspacetime/libs/INLAspacetime.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   4.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Imports includes 25 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    INSPECTumours (development version)
File ‘INSPIRE/libs/INSPIRE.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Malformed Title field: should not end in a period.
Namespace in Imports field not imported from: ‘splines2’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘Error_Estimation_Response_1.tiff’ ‘Error_Estimation_Response_2.tiff’
  ‘Error_Estimation_Response_3.tiff’
Undeclared packages ‘quantreg’, ‘effects’, ‘Hmisc’, ‘rockchalk’, ‘pequod’ in Rd xrefs
Specified C++11: please drop specification unless essential
Undeclared package ‘colorspace’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘moonBook’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘curl’ ‘readxl’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Auto-generated content requiring editing in Rd file 'IntervalSurgeon-package.Rd':
  \seealso: ‘Optional links to other man pages’
  \examples: ‘## Optional simple examples of the most important functions ...’
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    doc  10.0Mb
Undeclared package ‘DT’ in Rd xrefs
Specified C++11: please drop specification unless essential
Argument items with no description in Rd file 'selectRuleRRF.Rd':
  ‘target’
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Note: found 12106 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Undeclared packages ‘nlstools’, ‘lme4’ in Rd xrefs
Namespaces in Imports field not imported from:
  ‘fdrtool’ ‘nimble’
  All declared Imports should be used.
Package suggested but not available for checking: ‘surveyspec’
Undeclared package ‘plotly’ in Rd xrefs
Note: found 102 marked UTF-8 strings
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Note: found 1475 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
File ‘iotools/libs/iotools.so’:
  Found non-API calls to R: ‘R_GetConnection’, ‘R_ReadConnection’,
    ‘R_WriteConnection’
File ‘iotools/libs/iotools.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

Compiled code should not call non-API entry points in R.
It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘expm’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘gmodels’ ‘lmtest’ ‘testthat’ ‘tidyverse’ ‘zoo’
  All declared Imports should be used.
Note: found 46 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Undeclared package ‘Rpadrino’ in Rd xrefs
Invalid package aliases in Rd file 'iprior_package.Rd':
  ‘iprior_package-package’
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘seqinr’
  All declared Imports should be used.
Argument items with no description in Rd file 'mrbayes.Rd':
  ‘unlink’ ‘constraint’
Argument items with no description in Rd file 'mrbayes.lset.Rd':
  ‘partition’
Argument items with no description in Rd file 'multistate.Rd':
  ‘model’
File ‘iRafNet/libs/iRafNet.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘Rdpack’ ‘glmnet’
  All declared Imports should be used.
checkRd: (-1) constrained.Rd:49: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 1 marked UTF-8 string
Specified C++11: please drop specification unless essential
checkRd: (-1) bp.coeff.raw.Rd:5: Escaped LaTeX specials: \&
checkRd: (-1) bp.coeff.raw.Rd:41: Escaped LaTeX specials: \&
checkRd: (-1) bp.coeff.raw.Rd:53: Escaped LaTeX specials: \&
checkRd: (-1) fleiss.kappa.raw.Rd:52: Escaped LaTeX specials: \&
checkRd: (-1) landis.koch.bf.Rd:14: Escaped LaTeX specials: \&
checkRd: (-1) landis.koch.bf.Rd:17: Escaped LaTeX specials: \&
checkRd: (-1) ir_to_transmittance.Rd:49: Escaped LaTeX specials: \&
Undeclared package ‘irr’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in Rd file 'print.cat_output.Rd':
  ‘object’

Documented arguments not in \usage in Rd file 'sub-subset-Itempool-numeric-missing-method.Rd':
  ‘...’

Documented arguments not in \usage in Rd file 'sub-subset-Response_set-numeric-missing-method.Rd':
  ‘...’

Documented arguments not in \usage in Rd file 'sub-subset-Testlet-numeric-missing-method.Rd':
  ‘...’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
S3 methods shown with full name in Rd file 'print.Item.Rd':
  ‘print.Item’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Note: found 117 marked UTF-8 strings
Package suggested but not available for checking: ‘xcms’
'LazyData' is specified without a 'data' directory
Note: found 12 marked UTF-8 strings
Note: found 104 marked UTF-8 strings
File ‘isingLenzMC/libs/isingLenzMC.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Undeclared package ‘Unicode’ in Rd xrefs
Note: found 7479 marked UTF-8 strings
Namespace in Imports field not imported from: ‘rmarkdown’
  All declared Imports should be used.
Note: found 12 marked UTF-8 strings
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
Undeclared package ‘multtest’ in Rd xrefs
Package vignette without corresponding tangle output:
  ‘IsoGene.Rnw’
checkRd: (-1) ISOpureS1.model_optimize.kappa.kappa_deriv_loglikelihood.Rd:9: Escaped LaTeX specials: \$
checkRd: (-1) ISOpureS1.model_optimize.kappa.kappa_deriv_loglikelihood.Rd:14: Escaped LaTeX specials: \$
checkRd: (-1) ISOpureS1.model_optimize.kappa.kappa_loglikelihood.Rd:11: Escaped LaTeX specials: \$
checkRd: (-1) ISOpureS2.model_optimize.kappa.kappa_deriv_loglikelihood.Rd:11: Escaped LaTeX specials: \$
checkRd: (-1) ISOpureS2.model_optimize.kappa.kappa_loglikelihood.Rd:11: Escaped LaTeX specials: \$
Specified C++14: please drop specification unless essential
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    data   1.9Mb
    doc    2.3Mb
    libs   4.5Mb
Namespace in Imports field not imported from: ‘rstantools’
  All declared Imports should be used.
checkRd: (-1) run_mcmc.Rd:61: Lost braces; missing escapes or markup?
    61 |   object of class \code{networkModelStanfit} and {mcmc.list}, which still
       |                                                  ^
GNU make is a SystemRequirements.
Undeclared package ‘surveillance’ in Rd xrefs
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   5.1Mb
Namespace in Imports field not imported from: ‘curl’
  All declared Imports should be used.
Note: found 87 marked UTF-8 strings
Note: found 1 marked UTF-8 string
Namespace in Imports field not imported from: ‘readr’
  All declared Imports should be used.
Found the following files/directories:
  ‘RMTplot.pdf’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Undeclared package ‘AER’ in Rd xrefs
Package suggested but not available for checking: ‘gurobi’
Note: found 58 marked UTF-8 strings
Package suggested but not available for checking: ‘locClass’
Packages suggested but not available for checking: 'gurobi', 'cplexAPI'
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Invalid package aliases in Rd file 'ivprobit-package.Rd':
  ‘ivProbit-package’
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘dplyr’ ‘magrittr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
  ‘fBasics’ ‘reshape’ ‘tidyr’ ‘utils’
  All declared Imports should be used.
Note: found 2261 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Note: found 1 marked UTF-8 string
Note: found 1984 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘grid’ ‘mcmcplots’ ‘tidyverse’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Found the following Makefile(s) with an include directive with a pathname using R_HOME:
  src/jvm-w32/Makefile
Even though not recommended, variable R_HOME may contain spaces.
Makefile directives use space as a separator and there is no portable
way to quote/escape the space in Make rules and directives.  However,
one can and should quote pathnames when passed from Makefile to the
shell, and this can be done specifically when invoking Make recursively.
It is therefore recommended to use the Make '-f' option to include files
in directories specified using R_HOME.  This option can be specified
multiple times to include multiple Makefiles.  Note that 'Makeconf' is
included automatically into top-level makefile of a package.
More information can be found in 'Writing R Extensions'.
File ‘JavaGD/libs/JavaGD.so’:
  Found ‘__sprintf_chk’, possibly from ‘sprintf’ (C)
    Object: ‘jGDtalk.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘GA’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    htmlwidgets   5.7Mb
Namespace in Imports field not imported from: ‘ids’
  All declared Imports should be used.
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    doc    3.2Mb
    libs   3.9Mb
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    extdata   5.5Mb
Note: found 87 marked UTF-8 strings
Specified C++11: please drop specification unless essential
Note: found 16726 marked UTF-8 strings
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Imports includes 23 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    R      3.9Mb
    i18n   6.5Mb
Namespaces in Imports field not imported from:
  ‘BayesFactor’ ‘GGally’ ‘GPArotation’ ‘MASS’ ‘PMCMR’ ‘R6’ ‘ROCR’
  ‘afex’ ‘car’ ‘dplyr’ ‘emmeans’ ‘ggrepel’ ‘ggridges’ ‘lavaan’
  ‘multcomp’ ‘mvnormtest’ ‘nnet’ ‘psych’ ‘vcd’ ‘vcdExtra’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Package which this enhances but not available for checking: ‘remMap’
Documented arguments not in \usage in Rd file 'paste_coef.Rd':
  ‘parlemts’

Documented arguments not in \usage in Rd file 'paste_linpred.Rd':
  ‘parlemts’ ‘matname’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/data/gannet/ripley/R/packages/tests-clang/journalabbr.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘doParallel’
  All declared Imports should be used.
Note: found 925830 marked UTF-8 strings
Note: found 176 marked UTF-8 strings
Undeclared package ‘later’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Imports includes 31 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    examples      2.9Mb
    htmlwidgets   1.1Mb
    www           2.7Mb
Note: found 17 marked UTF-8 strings
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    pre-release juicr (2017 - 2021)
Undeclared package ‘ggplot2’ in Rd xrefs
Namespaces in Imports field not imported from:
  ‘Superpower’ ‘pwr’ ‘shinydashboard’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 111752 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
File ‘kappalab/libs/kappalab.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘gifski’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘base’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘EQL’ ‘univariateML’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
prepare_Rd: NEWS.Rd:58: Dropping empty section ‘kelvin INITIAL VERSION 1.0-0 (2012-05-30)’
'LazyData' is specified without a 'data' directory
File ‘Kendall/libs/Kendall.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘lme4’ ‘metafor’ ‘nlme’
  All declared Imports should be used.
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    doc    3.6Mb
    help   7.0Mb
checkRd: (-1) image_load.Rd:20: Lost braces
    20 | \item{color_mode}{One of {\code{"grayscale"}, \code{"rgb"}, \code{"rgba"}}.
       |                          ^
checkRd: (-1) k_placeholder.Rd:19: Lost braces
    19 | \item{ndim}{Number of axes of the tensor. At least one of {\code{shape}, \code{ndim}}
       |                                                           ^
checkRd: (-1) metric_auc.Rd:40: Lost braces; missing escapes or markup?
    40 | to {-epsilon, 1+epsilon} for a small positive epsilon value will be
       |    ^
Namespace in Imports field not imported from: ‘mvtnorm’
  All declared Imports should be used.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
File ‘KERE/libs/KERE.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
File ‘KernSmoothIRT/libs/KernSmoothIRT.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
S3 methods shown with full name in Rd file 'bw.abram.temp.Rd':
  ‘bw.abram.temp’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Minor Changes
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘splines’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘RcppProgress’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc       3.2Mb
    extdata   1.2Mb
Namespaces in Imports field not imported from:
  ‘Biostrings’ ‘Rsamtools’ ‘rtracklayer’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘fitdistrplus’ ‘plotly’
  All declared Imports should be used.
Package vignettes without corresponding tangle output:
  ‘kinship_code_details.Rmd’
  ‘pedigree.Rmd’
'LazyData' is specified without a 'data' directory
File ‘kknn/libs/kknn.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package which this enhances but not available for checking: ‘rkward’
Note: found 8 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘RGeostats’
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘SnowballC’ ‘stringi’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Undeclared package ‘kml3d’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘Killed after ’
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘FNN’ ‘caret’ ‘datasets’ ‘dplyr’ ‘e1071’ ‘psycho’ ‘rhandsontable’
  ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 9 marked Latin-1 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘mice’ ‘tibble’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Packages suggested but not available for checking:
  'koRpus.lang.de', 'koRpus.lang.es', 'koRpus.lang.fr',
  'koRpus.lang.it', 'koRpus.lang.nl', 'koRpus.lang.pt',
  'koRpus.lang.ru'

Package which this enhances but not available for checking: ‘rkward’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘tibble’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
File ‘kriging/libs/kriging.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘KSEA Bar Plot.tiff’ ‘KSEA Kinase Scores.csv’
  ‘KSEA.Merged.Heatmap.png’ ‘Kinase-Substrate Links.csv’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘RUnit’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘robustbase’
  All declared Imports should be used.
Undeclared package ‘fso’ in Rd xrefs
File ‘labdsv/libs/labdsv.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Undeclared packages ‘carData’, ‘factoextra’, ‘labstatR’ in Rd xrefs
Found the following files/directories:
  ‘MYSLID.csv’ ‘tabelle.csv’
Namespace in Imports field not imported from: ‘stringr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    data   8.3Mb
Undeclared package ‘spdep’ in Rd xrefs
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   5.6Mb
Undeclared package ‘plyr’ in Rd xrefs
Undeclared package ‘gsl’ in Rd xrefs
GNU make is a SystemRequirements.
Undeclared package ‘raster’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) LaplaceApproximation.Rd:485: Escaped LaTeX specials: \&
checkRd: (-1) LossMatrix.Rd:115: Escaped LaTeX specials: \&
checkRd: (-1) LossMatrix.Rd:117: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
Note: found 6 marked UTF-8 strings
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Undeclared package ‘glmnet’ in Rd xrefs
File ‘LassoNet/libs/LassoNet.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘lassoshooting/libs/lassoshooting.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Undeclared package ‘ggplot2’ in Rd xrefs
checkRd: (-1) LKrig.MLE.Rd:114: Escaped LaTeX specials: \$ \$
checkRd: (-1) LKrig.MLE.Rd:115: Escaped LaTeX specials: \$
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    doc   6.4Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘doParallel’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Undeclared package ‘gridExtra’ in Rd xrefs
Skipping checking math rendering: package 'V8' unavailable
Found the following files/directories:
  ‘temp.float.csv’ ‘temp.result.athena.csv’
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    libs   8.7Mb
Packages suggested but not available for checking: 'xcms', 'MSnbase'
Found export directive that requires package ‘methods’:
  ‘exportClasses’
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains ‘methods’.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘cli’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Imports includes 28 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Namespaces in Imports field not imported from:
  ‘DT’ ‘SnowballC’ ‘chinese.misc’ ‘dplyr’ ‘factoextra’ ‘glasso’
  ‘highcharter’ ‘htmlwidgets’ ‘ldatuning’ ‘qgraph’ ‘quanteda’ ‘rvest’
  ‘shinyBS’ ‘shinyWidgets’ ‘shinyalert’ ‘shinybusy’ ‘shinycssloaders’
  ‘shinydashboard’ ‘shinyjs’ ‘stringr’ ‘textmineR’ ‘textplot’ ‘tidyr’
  ‘topicmodels’
  All declared Imports should be used.
Documented arguments not in \usage in Rd file 'dot-choose_best_subjects.Rd':
  ‘best’ ‘candidate’

Documented arguments not in \usage in Rd file 'dot-normalize_props.Rd':
  ‘keep_all_items’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Argument items with no description in Rd file 'top.topic.words.Rd':
  ‘alpha’
File ‘lda/libs/lda.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Imports includes 25 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Namespaces in Imports field not imported from:
  ‘DT’ ‘SnowballC’ ‘beepr’ ‘broom’ ‘chinese.misc’ ‘dplyr’ ‘highcharter’
  ‘htmlwidgets’ ‘ldatuning’ ‘parallel’ ‘plotly’ ‘purrr’ ‘quanteda’
  ‘shinyBS’ ‘shinyWidgets’ ‘shinyalert’ ‘shinycssloaders’ ‘shinyjs’
  ‘stringr’ ‘textmineR’ ‘tidyr’ ‘tidytext’ ‘topicmodels’
  All declared Imports should be used.
Undeclared package ‘tm’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘devtools’ ‘reticulate’ ‘tensorflow’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
Note: found 75 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘htmlwidgets’ ‘jsonlite’ ‘sf’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    light.interception.voxels() - This function create the Fraction absorbed incident light
    light.interception.raster() - Create a raster of Fraction absorbed incident light
    light.incident.voxels() - This function create the Fraction incident light
    light.incident.raster() - Create a raster of the Fraction incident light