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) may_require_permanent_cache.Rd:14: Lost braces; missing escapes or markup?
    14 | warning if not, but since {R.cache} version \verb{0.15.0} (release date
       |                           ^
checkRd: (-1) may_require_permanent_cache.Rd:17: Lost braces; missing escapes or markup?
    17 | if someone updates the R package {precommit} but not the hook revisions.
       |                                  ^
checkRd: (-1) update_rev_in_config.Rd:5: Lost braces; missing escapes or markup?
     5 | \title{Updates the hook version ref of {precommit} in a \code{.pre-commit-config} file}
       |                                        ^
Documented arguments not in \usage in Rd file 'local_test_setup.Rd':
  ‘use_precommmit’

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 ‘testthat.R’ [133s/183s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(precommit)
  > test_check("precommit")
  [ FAIL 1 | WARN 1 | SKIP 5 | PASS 152 ]
  
  ══ Skipped tests (5) ═══════════════════════════════════════════════════════════
  • !is_windows() is TRUE (1): 'test-exec.R:19:3'
  • On CRAN (3): 'test-config.R:15:3', 'test-setup.R:88:3', 'test-zzz.R:2:3'
  • not_conda() is TRUE (1): 'test-hooks-regex-exclude.R:2:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-hook-roxygenize.R:168:3'): warns if there is any other warning ──
  `roxygenize_with_cache(list(getwd()), dirs = dirs_R.cache("roxygenize"))` did not produce any warnings.
  
  [ FAIL 1 | WARN 1 | SKIP 5 | PASS 152 ]
  Error: Test failures
  Execution halted
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 ?
checkRd: (-1) dev_data.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dev_data.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dev_data.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dev_data.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gusto.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gusto.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gusto.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gusto.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gusto.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) val_data.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) val_data.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) val_data.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) val_data.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) val_data.Rd:14: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
checkRd: (-1) preference-package.Rd:48-49: Lost braces in \itemize; meant \describe ?
checkRd: (-1) preference-package.Rd:50-51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) preference-package.Rd:52-53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) preference-package.Rd:58-60: Lost braces in \itemize; meant \describe ?
checkRd: (-1) preference-package.Rd:61-63: Lost braces in \itemize; meant \describe ?
checkRd: (-1) preference-package.Rd:68-69: Lost braces in \itemize; meant \describe ?
checkRd: (-1) preference-package.Rd:70-71: Lost braces in \itemize; meant \describe ?
checkRd: (-1) preference-package.Rd:72-73: Lost braces in \itemize; meant \describe ?
checkRd: (-1) preference-package.Rd:78-79: Lost braces in \itemize; meant \describe ?
checkRd: (-1) preference-package.Rd:80-81: Lost braces in \itemize; meant \describe ?
checkRd: (-1) preference.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) preference.Rd:22-23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) preference.Rd:24-25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) preference.Rd:26-27: Lost braces in \itemize; meant \describe ?
'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
checkRd: (-1) rebuild.Rd:18: Lost braces in \itemize; \value handles \item{}{} directly
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
checkRd: (-1) parse_issue_events.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) parse_issue_events.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) parse_issue_events.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) parse_issue_events.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) parse_issue_events.Rd:28: Lost braces in \itemize; meant \describe ?
Documented arguments not in \usage in Rd file 'validate_inputs.Rd':
  ‘required_vars’

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: ‘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}.}
       |                                                           ^
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in Rd file 'bitAND.Rd':
  ‘a’ ‘b’

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) 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) read.sample.Rd:37: Lost braces; missing escapes or markup?
    37 | \code{2*0xffff} = {131070} bytes (= samples) as per ProTracker standards.
       |                   ^
Package suggested but not available for checking: ‘GOSemSim’
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’
Documented arguments not in \usage in Rd file 'dot-marxan_data_reader.Rd':
  ‘parameter’

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) 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’
Documented arguments not in \usage in Rd file 'estimateDeltaLOH.PairedPSCBS.Rd':
  ‘scale’

Documented arguments not in \usage in Rd file 'getLocusData.AbstractCBS.Rd':
  ‘splitters’

Documented arguments not in \usage in Rd file 'getSegments.AbstractCBS.Rd':
  ‘simplify’ ‘splitters’

Documented arguments not in \usage in Rd file 'mergeTwoSegments.AbstractCBS.Rd':
  ‘left’ ‘update’ ‘verbose’

Documented arguments not in \usage in Rd file 'plotTracks.PairedPSCBS.Rd':
  ‘x’ ‘tracks’ ‘scatter’ ‘calls’ ‘pch’ ‘col’ ‘cex’ ‘changepoints’
  ‘grid’ ‘quantiles’ ‘xlim’ ‘Clim’ ‘Blim’ ‘xScale’ ‘add’ ‘subplots’
  ‘verbose’

Documented arguments not in \usage in Rd file 'updateMeansTogether.AbstractCBS.Rd':
  ‘idxList’ ‘verbose’

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 significant warnings:
  util.c:13:9: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/pscl.Rcheck/00install.out’ for details.
* used C compiler: ‘Debian clang version 17.0.6 (3)’
checkRd: (-1) partycodes.Rd:15-16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) partycodes.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) presidentialElections.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) presidentialElections.Rd:15: Lost braces
    15 |     \item{\item{demVote}}{numeric, percent of the vote for president won by the
       |                ^
checkRd: (-1) presidentialElections.Rd:15-16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) presidentialElections.Rd:17: Lost braces
    17 |     \item{\item{year}}{numeric, integer}
       |                ^
checkRd: (-1) presidentialElections.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) presidentialElections.Rd:18: Lost braces
    18 |     \item{\item{south}}{logical, \code{TRUE} if state is one of the 11 states
       |                ^
checkRd: (-1) presidentialElections.Rd:18-19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) unionDensity.Rd:15-17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) unionDensity.Rd:18-20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) unionDensity.Rd:21-22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) unionDensity.Rd:23-29: Lost braces in \itemize; meant \describe ?
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
Running examples in ‘psidread-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: psid_read
> ### Title: Read PSID data from the packaged data file or customized data
> ###   file
> ### Aliases: psid_read
> 
> ### ** Examples
> 
> # Example 1: Read from multiple package data files (Whole procedure)
> psid_varlist = c(" hh_age || [13]ER53017 [17]ER66017",
+                             " p_age || [13]ER34204")
> str_df <- psid_str(varlist = psid_varlist,
+                    type = "separated")
> # Below is the file path for the package test data, set this to your own directory
> exdir <- system.file(package = "psidread","extdata")
> indir <- system.file(package = "psidread","extdata")
> psid_unzip(indir = indir,
+            exdir = exdir,
+            zipped = TRUE,
+            type = "package",
+            filename = NA)
Error in utils::unzip(zipfile = file.path(indir, list_tozip[i]), exdir = file.path(indir,  : 
  cannot open file '/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/psidread/extdata/fam2013er/FAM2013ER_codebook.pdf': Read-only file system
Calls: psid_unzip -> <Anonymous>
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘my-vignette.Rmd’ using rmarkdown

Quitting from lines 163-170 [unnamed-chunk-6] (my-vignette.Rmd)
Error: processing vignette 'my-vignette.Rmd' failed with diagnostics:
cannot open file '/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/psidread/extdata/fam2013er/FAM2013ER_codebook.pdf': Read-only file system
--- failed re-building ‘my-vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
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.
Invalid package aliases in Rd file 'package-ptf.Rd':
  ‘package-ptf-package’
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 ?
Documented arguments not in \usage in Rd file 'assert_correct_attributes.Rd':
  ‘expected_colnames’

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

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

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) 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
'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 'PVAClone-package.Rd':
  ‘PVA-package’ ‘pva-package’ ‘Pva-package’
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: \&
Documented arguments not in \usage in Rd file 'http_was_redirected.Rd':
  ‘response’

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

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

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

Documented arguments not in \usage in Rd file 'str_pad.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
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
Documented arguments not in \usage in Rd file 'get_names_MV.Rd':
  ‘path_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.
'LazyData' is specified without a 'data' directory
Objects in \usage without \alias in Rd file 'Qest-internal.rd':
  ‘expit’ ‘logit’ ‘pmax0’ ‘num.fun’ ‘format.perc’ ‘Ltau’ ‘minabs’
  ‘invJ’ ‘tensorX’ ‘buildTau’ ‘callwtau’ ‘callQ’ ‘start.Qest’
  ‘start.Qest.family’ ‘rq.fit.br2’ ‘Qest.sgs.internal’
  ‘Qest.gs.internal’ ‘Qest.gs’ ‘Qest.newton’ ‘Qlm.bfun’ ‘start.Qlm’
  ‘scalevars.Qlm’ ‘descalecoef.Qlm’ ‘Qlm.sgs.internal’
  ‘Qlm.gs.internal’ ‘Qlm.gs’ ‘Qlm.newton’ ‘plfcox’ ‘scalevars.Qcoxph’
  ‘descalecoef.Qcoxph’ ‘check.singularities’ ‘starting.points.Qcox’
  ‘adjust.coef’ ‘agsurv.Qcoxph’ ‘coxsurv.fit.Qcoxph’ ‘seg.lm.fit1’ ‘gs’
  ‘myg’ ‘dlist’ ‘omega’ ‘choose_eps’ ‘derQtheta’ ‘der2Qtheta’ ‘intA’
  ‘findp’ ‘findAp’ ‘A_beta_fun’ ‘A_gamma_fun’ ‘A_beta_beta_fun’
  ‘A_gamma_gamma_mix_fun’ ‘A_gamma_gamma_fun’ ‘A_beta_gamma_fun’
  ‘coxBB’ ‘derQtheta.gamma’ ‘der2Qtheta.gamma’ ‘findAp.gamma’
  ‘QestGamma.ee.u’ ‘QestGamma.ee.c’ ‘QestGamma.ee.ct’ ‘tau.pois’
  ‘ppoisC’ ‘dpoisC’ ‘qpoisC.955’ ‘qpoisC.me’ ‘qpoisC.bisec’ ‘qpoisC’
  ‘derQtheta.pois’ ‘der2Qtheta.pois’ ‘findp.pois’ ‘findAp.pois’
  ‘QestPois.ee.u’ ‘QestUnif.ee.u’ ‘QestNorm.ee.u’ ‘QestNorm.ee.c’
  ‘QestNorm.ee.ct’ ‘Qest.ee.u’ ‘Qest.ee.c’ ‘Qest.ee.ct’ ‘QCox.ee.c’
  ‘QCox.ee.ct’ ‘Qlm.ee.u’ ‘Qest.covar’ ‘Qcox.covar’ ‘Qlm.covar’ ‘Loss’
  ‘coxLoss’ ‘qlmLoss’

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 'Qest-internal.rd':
  ‘format.perc’

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
'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}.}
       |                                                                  ^
checkRd: (-1) piqr.Rd:114: Lost braces; missing escapes or markup?
   114 |   \code{y} is always {0}. See example 5 in \sQuote{Examples}.
       |                      ^
Objects in \usage without \alias in Rd file 'qrcmNP-internal.Rd':
  ‘Q’ ‘funQ1’ ‘check.fun’ ‘boot’ ‘predBeta’ ‘grad3’ ‘grad2’ ‘num.int’
  ‘integr’ ‘bisec’ ‘Bfun’ ‘bfun’ ‘funGrad’ ‘Fun’ ‘armijo’ ‘check.in.2’
  ‘check.out.2’ ‘piqr.newton’ ‘piqr.ee’ ‘pciqr.ee’ ‘pctiqr.ee’
  ‘plotCoef’ ‘nonzeroCoef’ ‘cov.theta.2’ ‘plot.piqr2’
  ‘divide.et.impera.2’ ‘print.niqr’ ‘print.summary.niqr’ ‘print.piqr’
  ‘print.summary.piqr’ ‘terms.piqr’ ‘coef.piqr’ ‘model.matrix.piqr’
  ‘nobs.piqr’
Assignments in \usage in Rd file 'qrcmNP-internal.Rd':
  start.theta.niqr <- function(fun, x0, X, y, control = list()) piqr.internal(mf, 
      cl, formula.p, tol = 1e-06, maxit = 100, s, segno = 1, lambda = 0, 
      check = FALSE, A, st.theta = FALSE, theta0)

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 'qrcmNP-internal.Rd':
  ‘plot.piqr2’

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.
Objects in \usage without \alias in Rd file 'qrcm-internal.Rd':
  ‘check.in.iqr’ ‘check.in0.iqrL’ ‘check.in.iqrL’ ‘check.out’
  ‘start.iqr’ ‘start.iqrL’ ‘ctiqr.internal’ ‘iqrL.internal’ ‘iqrL.fit’
  ‘iqr.ee’ ‘ciqr.ee’ ‘ctiqr.ee’ ‘iobjfun’ ‘iobjfun.ct’ ‘cov.fun.iqr’
  ‘iqrL.ee’ ‘cov.fun.iqrL’ ‘iqr.newton’ ‘divide.et.impera’
  ‘iqrL.newton’ ‘pmax0’ ‘maxind’ ‘num.fun’ ‘make.bfun’ ‘apply_bfun’
  ‘p.bisec’ ‘p.bisec.internal’ ‘slp.basis’ ‘is.slp’ ‘safesolve’
  ‘iqr.waldtest’ ‘extract.p’ ‘pred.beta’ ‘km’ ‘alpha’ ‘test.unif.ct’
  ‘findagoodestimator’ ‘quickpred’ ‘trans’ ‘alpha.bisec’
  ‘alpha.bisec.out’ ‘ks’ ‘print.iqr’ ‘print.summary.iqr’ ‘terms.iqr’
  ‘model.matrix.iqr’ ‘vcov.iqr’ ‘nobs.iqr’ ‘predict.iqrL.internal’
  ‘print.iqrL’ ‘print.summary.iqrL’ ‘terms.iqrL’ ‘model.matrix.iqrL’
  ‘vcov.iqrL’ ‘nobs.iqrL’ ‘qc.penalty’ ‘fixqc’ ‘print.qc.iqr’

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 'qrcm-internal.Rd':
  ‘predict.iqrL.internal’

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) 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 ?
Documented arguments not in \usage in Rd file 'export_responses_filedownload.Rd':
  ‘requestID’

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 ‘testthat.R’ [222s/249s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  > library(QuantBondCurves)
  > 
  > test_check("QuantBondCurves")
  [ FAIL 1 | WARN 0 | SKIP 8 | PASS 174 ]
  
  ══ Skipped tests (8) ═══════════════════════════════════════════════════════════
  • On CRAN (2): 'test-curvefunctions.R:77:3', 'test-curvefunctions.R:88:3'
  • Test is for plotting curves (2): 'test-CurveCalibration.R:242:3',
    'test-CurveCalibration.R:341:3'
  • Test is for plotting the forward curve (1): 'test-curvefunctions.R:35:3'
  • Test is for plotting the spot constant curve (1):
    'test-curvefunctions.R:137:3'
  • Test is for plotting the spot linear curve (1): 'test-curvefunctions.R:109:3'
  • Test is to construct the plot of basis curve (1):
    'test-bondValuation.R:700:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-generalFunctions.R:263:3'): Introducing the input of coupon dates also works fine ──
  coupons(...) has length 1, not length 2.
  
  [ FAIL 1 | WARN 0 | SKIP 8 | PASS 174 ]
  Error: Test failures
  Execution halted
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.
Documented arguments not in \usage in Rd file 'wordcloud_comparison.Rd':
  ‘random.color’ ‘ordered.colors’

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 ?
Specified C++11: please drop specification unless essential
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’
checkRd: (-1) runMLwiN.Rd:83: Lost braces; missing escapes or markup?
    83 | behaviour when creating contrast variables. If code {FALSE} (default) factor
       |                                                     ^
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
Package vignette without corresponding tangle output:
  ‘rainbow.Rnw’
'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 ?
Documented arguments not in \usage in Rd file 'print.ramchoiceRevealAtte.Rd':
  ‘object’

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

Documented arguments not in \usage in Rd file 'print.ramchoiceRevealPrefModel.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.
'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
Auto-generated content requiring editing in Rd file 'RApiDatetime-package.Rd':
  \references: ‘This optional section can contain literature or other refere...’
  \seealso: ‘Optional links to other man pages’
  \examples: ‘# Optional simple examples of the most important functions’
'LazyData' is specified without a 'data' directory
'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’
checkRd: (-1) amount.target.Rd:34: Lost braces
    34 | code{numeric} vector.
       |     ^
checkRd: (-1) space.held.Rd:26: Lost braces
    26 | code{matrix} object.
       |     ^
Objects in \usage without \alias in Rd file 'cache.Rd':
  ‘\S4method{cache}{RapData,character,ANY}’
  ‘\S4method{cache}{RapData,character,missing}’
  ‘\S4method{cache}{RapResults,character,ANY}’
  ‘\S4method{cache}{RapResults,character,missing}’

Objects in \usage without \alias in Rd file 'is.cached.Rd':
  ‘\S4method{is.cached}{RapData,character}’
  ‘\S4method{is.cached}{RapResults,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
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.}
       |                                                                                           ^
checkRd: (-1) PipelineResult.Rd:195: Lost braces
   195 | \item{\code{...}}{passed to code{link{pipeline_read}}}
       |                                 ^
checkRd: (-1) PipelineResult.Rd:195: Lost braces
   195 | \item{\code{...}}{passed to code{link{pipeline_read}}}
       |                                      ^
'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
Found the following significant warnings:
  /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/BH/include/boost/math/tools/config.hpp:23:6: warning: "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" [-W#warnings]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/rbscCI.Rcheck/00install.out’ for details.
* used C++ compiler: ‘Debian clang version 17.0.6 (3)’
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 ?
S3 methods shown with full name in Rd file 'export.default.Rd':
  ‘export.default’

S3 methods shown with full name in Rd file 'export.listpoly.Rd':
  ‘export.listpoly’

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.
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) Rcmdr.Utilities.Rd:477: Lost braces
   477 |   code{TRUE}.}
       |       ^
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’
Auto-generated content requiring editing in Rd file 'RcppAnnoy-package.Rd':
  \examples: ‘# Optional simple examples of the most important functions’
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
Documented arguments not in \usage in Rd file 'h_opt_density_res.Rd':
  ‘x’ ‘dgp_F1’ ‘dgp_Fp1’ ‘f_low’ ‘f_up’

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
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘devAll’
Documented arguments not in \usage in Rd file 'favicon.Rd':
  ‘file’

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) 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 ?
Package suggested but not available for checking: ‘GOSemSim’
'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
checkRd: (-1) MA.estimates.Rd:108-109: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) MA.estimates.Rd:109-114: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) MA.estimates.Rd:110-111: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) MA.estimates.Rd:111-112: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) MA.estimates.Rd:112: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) MA.estimates.Rd:113: Lost braces
   113 | \item{Design Effect}{The design effect of the RDS} \item{s.e.}{standard error}
       |      ^
checkRd: (-1) MA.estimates.Rd:113: Lost braces
   113 | \item{Design Effect}{The design effect of the RDS} \item{s.e.}{standard error}
       |                     ^
checkRd: (-1) MA.estimates.Rd:113: Lost braces
   113 | \item{Design Effect}{The design effect of the RDS} \item{s.e.}{standard error}
       |                                                         ^
checkRd: (-1) MA.estimates.Rd:113: Lost braces
   113 | \item{Design Effect}{The design effect of the RDS} \item{s.e.}{standard error}
       |                                                               ^
checkRd: (-1) MA.estimates.Rd:114: Lost braces
   114 | \item{n}{count of the number of sample values with that value of the trait} } }
       |      ^
checkRd: (-1) MA.estimates.Rd:114: Lost braces
   114 | \item{n}{count of the number of sample values with that value of the trait} } }
       |         ^
checkRd: (-1) MA.estimates.Rd:190: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MA.estimates.Rd:191: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rds.interval.estimate.Rd:89: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rds.interval.estimate.Rd:90: Lost braces in \itemize; meant \describe ?
Package suggested but not available for checking: ‘DIDmultiplegt’
Missing or unexported object: ‘CausalQueries::strategy_statements’
Running examples in ‘rdss-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: process_tracing_estimator
> ### Title: Process tracing estimator
> ### Aliases: process_tracing_estimator
> 
> ### ** Examples
> 
> 
> process_tracing_estimator(
+   CausalQueries::make_model("X -> Y"),
+   "Y[X=1] > Y[X=0]",
+   data.frame(X=1, Y = 1),
+   "X-Y")
Loading required namespace: CausalQueries
Error: 'strategy_statements' is not an exported object from 'namespace:CausalQueries'
Execution halted
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) extractHPCConstants.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) extractHPCConstants.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) extractHPCConstants.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) readBrukerFlexDir.Rd:46: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) readBrukerFlexDir.Rd:47: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) readBrukerFlexDir.Rd:48: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) readBrukerFlexFile.Rd:42: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) readBrukerFlexFile.Rd:43: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) readBrukerFlexFile.Rd:44: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) readBrukerFlexFile.Rd:45: Lost braces in \itemize; \value handles \item{}{} directly
Documented arguments not in \usage in Rd file 'readAcquFile.Rd':
  ‘file’

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) 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}).}
       |                                                                                                                                                                                                                                      ^
Documented arguments not in \usage in Rd file 'rearrr_fn_.Rd':
  ‘overwrite’

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

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) 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.
       |                            ^
checkRd: (-1) fieldCastingFunctions.Rd:73-75: Lost braces
    73 | {date_, datetime_, datetime_seconds_, time_mm_ss, time_hh_mm_ss, time, float,
       | ^
checkRd: (-1) recordsTypedMethods.Rd:121-123: Lost braces
   121 | {date_, datetime_, datetime_seconds_, time_mm_ss, time_hh_mm_ss, time, float,
       | ^
checkRd: (-1) recordsTypedMethods.Rd:143: Lost braces; missing escapes or markup?
   143 | HTML and UNICODE raw label and scanning for units={"UNITS"} in description}
       |                                                   ^
'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}.)
       |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  ^
checkRd: (-1) app_server.Rd:10: Lost braces; missing escapes or markup?
    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)}
       | ^
checkRd: (-1) reparto_div.Rd:37: Lost braces; missing escapes or markup?
    37 | The set of divisors is formed by the odd numbers, that is {1,3,..,2n+1}.
       |                                                           ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) plconfint.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plconfint.Rd:31-32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plconfint.Rd:33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plconfint.Rd:34-37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plconfint.Rd:95-98: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plconfint.Rd:99-101: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plconfint.Rd:102: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plconfint.Rd:103-104: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.inference.Rd:64-67: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.inference.Rd:68-70: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.inference.Rd:71: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.inference.Rd:72-73: Lost braces in \itemize; meant \describe ?
checkRd: (-1) termtable.Rd:49: Lost braces; missing escapes or markup?
    49 |   --- {F}{or t for objects of class \code{lm, lmrob} and \code{glm}
       |       ^
checkRd: (-1) termtable.Rd:49-50: Lost braces
    49 |   --- {F}{or t for objects of class \code{lm, lmrob} and \code{glm}
       |          ^
checkRd: (-1) termtable.Rd:51: Lost braces; missing escapes or markup?
    51 |   --- {Chi-squared}{for other \code{glm}s and \code{survreg}}\cr
       |       ^
checkRd: (-1) termtable.Rd:51: Lost braces
    51 |   --- {Chi-squared}{for other \code{glm}s and \code{survreg}}\cr
       |                    ^
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
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) LS.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'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{
       |            ^
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
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    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:238-243: Lost braces in \itemize; \value handles \item{}{} directly
Found the following files/directories:
  ‘PackageCites.bib’
'LazyData' is specified without a 'data' directory
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No news entries found.
checkRd: (-1) repo_build.Rd:44-47: Lost braces
    44 | ## chunk "item 1" {
       |                   ^
checkRd: (-1) repo_dependencies.Rd:48: Lost braces in \itemize; meant \describe ?
checkRd: (-1) repo_dependencies.Rd:49-50: Lost braces in \itemize; meant \describe ?
checkRd: (-1) repo_dependencies.Rd:51-53: Lost braces in \itemize; meant \describe ?
Packages suggested but not available for checking:
  'clusterProfiler', 'enrichplot'
Running examples in ‘ReporterScore-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: KO_enrich
> ### Title: Perform enrichment analysis
> ### Aliases: KO_enrich KO_fisher as.enrich_res KO_gsea
> 
> ### ** Examples
> 
> ## use `enricher` from the `clusterProfiler` package.
> data("reporter_score_res")
> enrich_res <- KO_enrich(reporter_score_res)
clusterProfiler: this package haven't install, should install?
yes/no(y/n)?
Error in pcutils::lib_ps("clusterProfiler", library = FALSE) : 
  exit, because 'clusterProfiler' need to install
Calls: KO_enrich -> <Anonymous>
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) 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
Documented arguments not in \usage in Rd file 'gaussian_process_cv.Rd':
  ‘ncomp’

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

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

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

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

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.
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) resistance.Rd:52: Lost braces
    52 |     \item B. Bollob\'{a}s, 1998.  \emph{Modern Graph Theory}.  Springer.
       |                      ^
checkRd: (-1) calc_MO2.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) calc_MO2.Rd:31: Lost braces in \itemize; meant \describe ?
Documented arguments not in \usage in Rd file 'get.V.Rd':
  ‘ct.lst’

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
Re-building vignettes had CPU time 3.2 times elapsed time
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
Rd files without \alias:
  ‘retry-package.Rd’
'LazyData' is specified without a 'data' directory
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
checkRd: (-1) fs_search.Rd:76: Lost braces
    76 | \\code{\link{fs_auth}} \code{\link{fs_browse}}
       |       ^
checkRd: (-1) GenericDataFile.Rd:87-88: Lost braces in \itemize; meant \describe ?
checkRd: (-1) GenericDataFile.Rd:89: Lost braces in \itemize; meant \describe ?
checkRd: (-1) GenericDataFile.Rd:90: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) GenericDataFile.Rd:92: Lost braces in \itemize; meant \describe ?
Documented arguments not in \usage in Rd file 'compareChecksum.GenericDataFile.Rd':
  ‘verbose’

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

Documented arguments not in \usage in Rd file 'dsApplyInPairs.GenericDataFileSet.Rd':
  ‘ds’

Documented arguments not in \usage in Rd file 'fromFile.GenericDataFile.Rd':
  ‘unknown’

Documented arguments not in \usage in Rd file 'gzip.GenericDataFile.Rd':
  ‘verbose’

Documented arguments not in \usage in Rd file 'readChecksum.ChecksumFile.Rd':
  ‘verbose’

Documented arguments not in \usage in Rd file 'writeChecksum.GenericDataFile.Rd':
  ‘verbose’

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) 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")) {
       |                                                   ^
Package suggested but not available for checking: ‘rgdal’
checkRd: (-1) Ghana_2021_school_attendance.Rd:75: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Ghana_2021_school_attendance_geometry.Rd:75: Lost braces in \itemize; meant \describe ?
'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
Documented arguments not in \usage in Rd file 'dimnames.AbstractFileArray.Rd':
  ‘...’

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

Documented arguments not in \usage in Rd file 'readContiguousValues.AbstractFileArray.Rd':
  ‘length’

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
Package vignette without corresponding tangle output:
  ‘rich_introduction.Rmd’
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
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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
Documented arguments not in \usage in Rd file 'inner_t_index_calculation.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.
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)
Documented arguments not in \usage in Rd file 'rJava-internal.Rd':
  ‘r.convertor’

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.
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-clang/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
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Invalid package aliases in Rd file 'rkt-package.Rd':
  ‘tkt-package’
'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 : {}}"}
       |                  ^
Found the following significant warnings:
  ../inst/include/internal/dists.hpp:158:35: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/Rnanoflann.Rcheck/00install.out’ for details.
* used C++ compiler: ‘Debian clang version 17.0.6 (3)’
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’
checkRd: (-1) PlotWindProfile.Rd:69: Lost braces in \itemize; meant \describe ?
checkRd: (-1) PlotWindProfile.Rd:70: Lost braces in \itemize; meant \describe ?
checkRd: (-1) PlotWindProfile.Rd:71: Lost braces in \itemize; meant \describe ?
checkRd: (-1) PlotWindProfile.Rd:72: Lost braces in \itemize; meant \describe ?
checkRd: (-1) PlotWindProfile.Rd:73: Lost braces in \itemize; meant \describe ?
checkRd: (-1) PlotWindProfile.Rd:74: Lost braces in \itemize; meant \describe ?
checkRd: (-1) PlotWindProfile.Rd:75: Lost braces in \itemize; meant \describe ?
checkRd: (-1) PlotWindProfile.Rd:76: Lost braces in \itemize; meant \describe ?
checkRd: (-1) PlotWindProfile.Rd:77: Lost braces in \itemize; meant \describe ?
checkRd: (-1) PlotWindProfile.Rd:78: Lost braces in \itemize; meant \describe ?
checkRd: (-1) PlotWindProfile.Rd:79: Lost braces in \itemize; meant \describe ?
checkRd: (-1) PlotWindProfile.Rd:80: Lost braces in \itemize; meant \describe ?
checkRd: (-1) PlotWindProfile.Rd:81: Lost braces in \itemize; meant \describe ?
checkRd: (-1) PlotWindProfile.Rd:82: Lost braces in \itemize; meant \describe ?
checkRd: (-1) PlotWindProfile.Rd:83: Lost braces in \itemize; meant \describe ?
Documented arguments not in \usage in Rd file 'SanitizeURL.Rd':
  ‘bad.str’

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) 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
Invalid package aliases in Rd file '0RobRDA-package.Rd':
  ‘RobRDA-package’
'LazyData' is specified without a 'data' directory
checkRd: (-1) cubinf.summaries.Rd:46: Lost braces
    46 | The class "lm" functions \code{effects}, \code{alias}, \code{add1}, \code{drop1}, code{kappa},
       |                                                                                       ^
Running examples in ‘robcbi-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: QQline
> ### Title: Add a theoretical QQ-line in a plot
> ### Aliases: QQline
> ### Keywords: stats
> 
> ### ** Examples
> 
> library(robcbi)
> data(Finney)
> Vol  <- Finney$Vol; Rate <- Finney$Rate; Resp <- Finney$Resp
> lVol <-log(Vol); lRate <- log(Rate)
> z.cub <- glm(Resp~lVol+lRate,family=binomial,method="cubinf", ufact=3.2)
Floating point exception
Specified C++11: please drop specification unless essential
Package vignette without corresponding tangle output:
  ‘robflreg.Rnw’
Documented arguments not in \usage in Rd file 'createITPSplineResult.Rd':
  ‘measure’

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) 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
Documented arguments not in \usage in Rd file 'Sample.rgasp.Rd':
  ‘interval_data’

Objects in \usage without \alias in Rd file 'neg_log_marginal_post_approx_ref_ppgasp.Rd':
  ‘neg_log_marginal_post_approx_ref’

Objects in \usage without \alias in Rd file 'separable_multi_kernel.Rd':
  ‘separable_kernel’

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) 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
Argument items with no description in Rd file 'choose.test.Rd':
  ‘Xpaired’ ‘Ypaired’ ‘Xextra’ ‘Yextra’ ‘mc.rep’
Argument items with no description in Rd file 'multinom.test.Rd':
  ‘X’ ‘Y’ ‘alternative’ ‘correct’ ‘perm’ ‘mc.rep’ ‘method’ ‘verbose’
  ‘mode’ ‘useC’
Argument items with no description in Rd file 'mw.mw.2.perm.Rd':
  ‘X’ ‘Y’ ‘Xprime’ ‘Yprime’ ‘.corr’ ‘mc.rep’ ‘alternative’ ‘verbose’
Argument items with no description in Rd file 'pm.wilcox.test.Rd':
  ‘Xpaired’ ‘Ypaired’ ‘Xextra’ ‘Yextra’ ‘alternative’ ‘verbose’
Argument items with no description in Rd file 'sim.partially.matched.Rd':
  ‘meanRatio’ ‘sdRatio’ ‘within.sd’ ‘type’ ‘hyp’
Argument items with no description in Rd file 'wmw.paired.replicates.test.Rd':
  ‘X’ ‘Y’ ‘alternative’ ‘correct’ ‘perm’ ‘mc.rep’ ‘method’ ‘verbose’
  ‘mode’ ‘useC’
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
Package suggested but not available for checking: ‘rENA’
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:70: Lost braces; missing escapes or markup?
    70 | This function creates an R Markdown template from a {preregr}
       |                                                     ^
checkRd: (-1) rmd_templates.Rd:72: Lost braces; missing escapes or markup?
    72 | Sheet holding the (pre)registration form specification (in {preregr}
       |                                                            ^
checkRd: (-1) rmd_templates.Rd:76: Lost braces; missing escapes or markup?
    76 | specification, or a loaded or imported {preregr} (pre)registration form.
       |                                        ^
Unknown package ‘rENA’ in Rd xrefs
'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
Documented arguments not in \usage in Rd file 'add_matches_columns.Rd':
  ‘Matches’

Documented arguments not in \usage in Rd file 'run_checks_two.Rd':
  ‘lookback’ ‘standard_deviaion’ ‘match_on’ ‘model_type’

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

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.
Auto-generated content requiring editing in Rd file 'roloc-package.Rd':
  \references: ‘~~ Literature or other references for background information ~~’
  \seealso: ‘~~ Optional links to other man pages, e.g. ~~’
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
Documented arguments not in \usage in Rd file 'DOLLAR.Class.Rd':
  ‘...’

Documented arguments not in \usage in Rd file 'DOLLARLT_-.Class.Rd':
  ‘...’

Documented arguments not in \usage in Rd file 'getMethods.Class.Rd':
  ‘unqiue’

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 significant warnings:
  /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/BH/include/boost/math/tools/config.hpp:23:6: warning: "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" [-W#warnings]
  /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/BH/include/boost/multiprecision/detail/standalone_config.hpp:36:7: warning: "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" [-W#warnings]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/rootWishart.Rcheck/00install.out’ for details.
* used C compiler: ‘Debian clang version 17.0.6 (3)’
* used C++ compiler: ‘Debian clang version 17.0.6 (3)’
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
'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
checkRd: (-1) FS.DAAR.heuristic.RST.Rd:20: Lost braces
    20 | code{decision.table}. It usually corresponds to \code{attr(decision.table, "desc.attrs")}.}
       |     ^
checkRd: (-1) RoughSetData.Rd:19: Lost braces; missing escapes or markup?
    19 | \item Diploma: it has the following values: {"MBA", "MSc", "MCE"}.
       |                                             ^
checkRd: (-1) RoughSetData.Rd:20: Lost braces; missing escapes or markup?
    20 | \item Exprience: it has the following values: {"High", "Low", "Medium"}.
       |                                               ^
checkRd: (-1) RoughSetData.Rd:21: Lost braces; missing escapes or markup?
    21 | \item French: it has the following values: {"Yes", "No"}.
       |                                            ^
checkRd: (-1) RoughSetData.Rd:22: Lost braces; missing escapes or markup?
    22 | \item Reference: it has the following values: {"Excellent", "Good", "Neutral"}.
       |                                               ^
checkRd: (-1) RoughSetData.Rd:23: Lost braces; missing escapes or markup?
    23 | \item Decision: it is a decision attribute that contains the following values: {"Accept", "Reject"}.
       |                                                                                ^
checkRd: (-1) RoughSetData.Rd:87: Lost braces; missing escapes or markup?
    87 | \item class: it is nominal decision attribute that has values: {1, 2, 3}.
       |                                                                ^
Invalid package aliases in Rd file 'A.Introduction-RoughSets.Rd':
  ‘A.Introduction-RoughSets-package’
Invalid package aliases in Rd file 'B.Introduction-FuzzyRoughSets.Rd':
  ‘B.Introduction-FuzzyRoughSets-package’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) getAvailablePlotTypes.Rd:30: Lost braces; missing escapes or markup?
    30 | Returns a list if \code{option} is either \code{capnum} or {numcap}
       |                                                            ^
checkRd: (-1) getRawData.Rd:39-41: Lost braces
    39 | if (event == TRUE) {\cr
       |                    ^
checkRd: (-1) getRawData.Rd:41-43: Lost braces
    41 | } else if (dropoutEvent == TRUE) {\cr
       |                                  ^
checkRd: (-1) getRawData.Rd:43-45: Lost braces
    43 | } else {\cr
       |        ^
checkRd: (-1) getSimulationSurvival.Rd:339-341: Lost braces
   339 | if (event == TRUE) {\cr
       |                    ^
checkRd: (-1) getSimulationSurvival.Rd:341-343: Lost braces
   341 | } else if (dropoutEvent == TRUE) {\cr
       |                                  ^
checkRd: (-1) getSimulationSurvival.Rd:343-345: Lost braces
   343 | } else {\cr
       |        ^
checkRd: (-1) readDataset.Rd:22: Lost braces
    22 | \item{...}{Further arguments to be passed to code{\link[utils]{read.table}}.}
       |                                                  ^
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
Package vignette without corresponding tangle output:
  ‘RPPanalyzer.rnw’
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
Specified C++11: please drop specification unless essential
checkRd: (-1) RprobitB_normalization.Rd:85: Lost braces; missing escapes or markup?
    85 | \item For level normalization, {RprobitB} takes utility differences with
       |                                ^
checkRd: (-1) RprobitB_normalization.Rd:87: Lost braces; missing escapes or markup?
    87 | For the ordered model where only one utility is modeled, {RprobitB}
       |                                                          ^
checkRd: (-1) as_cov_names.Rd:22: Lost braces; missing escapes or markup?
    22 | In {RprobitB}, alternative specific covariates must be named in the format
       |    ^
checkRd: (-1) update_s.Rd:30: Lost braces; missing escapes or markup?
    30 | Note that in {RprobitB}, \eqn{\delta_1=\dots=\delta_C}. This restriction is necessary because the class number \eqn{C} can change.
       |              ^
'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) impseq.Rd:29: Lost braces
    29 |     \emph{Computational Biology and Chemistry}, bold{31},  320--327.
       |                                                     ^
checkRd: (-1) impseqrob.Rd:39: Lost braces
    39 |     \emph{Computational Biology and Chemistry}, bold{31},  320--327.
       |                                                     ^
Documented arguments not in \usage in Rd file 'rrcov-utils.Rd':
  ‘tol’ ‘sv’ ‘n’ ‘p’

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) 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 ?
Package suggested but not available for checking: ‘Rphylopars’
checkRd: (-1) ordinate.Rd:151-153: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ordinate.Rd:154-160: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ordinate.Rd:161-170: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pairwise.Rd:82-90: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pairwise.Rd:91-97: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pairwise.Rd:98-105: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pairwise.Rd:106-115: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pairwise.Rd:146: Lost braces
   146 |  In previous versions of pairwise, code{\link{summary.pairwise}} had three 
       |                                        ^
checkRd: (-1) summary.pairwise.Rd:45-53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) summary.pairwise.Rd:54-60: Lost braces in \itemize; meant \describe ?
checkRd: (-1) summary.pairwise.Rd:61-68: Lost braces in \itemize; meant \describe ?
checkRd: (-1) summary.pairwise.Rd:69-81: Lost braces in \itemize; meant \describe ?
checkRd: (-1) summary.pairwise.Rd:88: Lost braces
    88 |  In previous versions of pairwise, code{\link{summary.pairwise}} had three 
       |                                        ^
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file '000-LB-.RspDocument.Rd':
  ‘...’

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

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

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

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

Documented arguments not in \usage in Rd file 'buildNonSweaveVignettes.Rd':
  ‘path’ ‘pattern’

Documented arguments not in \usage in Rd file 'exprToCode.RspSourceCodeFactory.Rd':
  ‘expr’

Documented arguments not in \usage in Rd file 'getContent.RspText.Rd':
  ‘unescaped’

Documented arguments not in \usage in Rd file 'toSourceCode.RspSourceCodeFactory.Rd':
  ‘expr’

Documented arguments not in \usage in Rd file 'trim.RspDocument.Rd':
  ‘envir’

Documented arguments not in \usage in Rd file 'writeResponse.RspResponse.Rd':
  ‘collapse’ ‘sep’

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) makedata.Rd:35: Lost braces; missing escapes or markup?
    35 |         {e = (1-h)*N(0, ve) + h*N(0, ve.contam)}.}
       |         ^
Package vignette without corresponding tangle output:
  ‘rsae.Rmd’
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
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-clang/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
Found the following significant warnings:
  siena07internals.cpp:418:9: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
  siena07utilities.cpp:118:9: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
  model/variables/BehaviorVariable.cpp:990:43: warning: format specifies type 'unsigned int' but the argument has type 'Effect *' [-Wformat]
  model/variables/BehaviorVariable.cpp:994:42: warning: format specifies type 'unsigned int' but the argument has type 'Effect *' [-Wformat]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/RSiena.Rcheck/00install.out’ for details.
* used C++ compiler: ‘Debian clang version 17.0.6 (3)’
Documented arguments not in \usage in Rd file 'ApiRequest.Rd':
  ‘report.description’

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

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
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
Running ‘tinytest.R’ [0s/1s]
Running the tests in ‘tests/tinytest.R’ failed.
Complete output:
  > tmp_user_dir <- tempdir()
  > Sys.setenv(RSPM_USER_DIR=tmp_user_dir)
  > 
  > if (requireNamespace("tinytest", quietly=TRUE)) {
  +   home <- identical(Sys.getenv("CI"), "true")
  +   tinytest::test_package("rspm", at_home=home)
  + }
   You are using 'tinytest::' to express test expectations.
   The results from these tests are not collected. Found the following occurrences:
   > test_integration.R#002: tinytest::expect_match 
   Remove the 'tinytest::' prefix to register the test results.FALSE
  
  test_integration.R............    0 tests    
  test_integration.R............    1 tests [0;32mOK[0m 
  test_integration.R............    2 tests [0;32mOK[0m 
  test_integration.R............    2 tests [0;32mOK[0m 
  test_integration.R............    3 tests [0;32mOK[0m Error: please, install the following required utilities: apt-file
  Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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"}
       |                   ^
checkRd: (-1) rstanarm-datasets.Rd:81: Lost braces; missing escapes or markup?
    81 | \item \code{age} {in years}
       |                  ^
checkRd: (-1) rstanarm-datasets.Rd:82: Lost braces; missing escapes or markup?
    82 | \item \code{albumin} {serum albumin (g/dl)}
       |                      ^
checkRd: (-1) rstanarm-datasets.Rd:83: Lost braces; missing escapes or markup?
    83 | \item \code{logBili} {logarithm of serum bilirubin}
       |                      ^
checkRd: (-1) rstanarm-datasets.Rd:84: Lost braces; missing escapes or markup?
    84 | \item \code{death} {indicator of death at endpoint} 
       |                    ^
checkRd: (-1) rstanarm-datasets.Rd:85-86: Lost braces
    85 | \item \code{futimeYears} {time (in years) between baseline and  
       |                          ^
checkRd: (-1) rstanarm-datasets.Rd:87: Lost braces; missing escapes or markup?
    87 | \item \code{id} {numeric ID unique to each individual}
       |                 ^
checkRd: (-1) rstanarm-datasets.Rd:88: Lost braces; missing escapes or markup?
    88 | \item \code{platelet} {platelet count}
       |                       ^
checkRd: (-1) rstanarm-datasets.Rd:89: Lost braces; missing escapes or markup?
    89 | \item \code{sex} {gender (m = male, f = female)}
       |                  ^
checkRd: (-1) rstanarm-datasets.Rd:90-91: Lost braces
    90 | \item \code{status} {status at endpoint (0 = censored, 
       |                     ^
checkRd: (-1) rstanarm-datasets.Rd:92-93: Lost braces
    92 | \item \code{trt} {binary treatment code (0 = placebo, 1 = 
       |                  ^
checkRd: (-1) rstanarm-datasets.Rd:94-95: Lost braces
    94 | \item \code{year} {time (in years) of the longitudinal measurements,
       |                   ^
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
checkRd: (-1) rstan_create_package.Rd:33: Lost braces; missing escapes or markup?
    33 | \code{TRUE}. If so, a file `R/{pkgname}-package.R`` is added to the package with
       |                               ^
'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’
Documented arguments not in \usage in Rd file 'calculate.var.np.Rd':
  ‘sone’ ‘szero’ ‘yone’ ‘yzero’

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.
checkRd: (-1) datasheet.Rd:153-155: Lost braces in \itemize; meant \describe ?
checkRd: (-1) datasheet.Rd:156-157: Lost braces in \itemize; meant \describe ?
checkRd: (-1) datasheet.Rd:158-159: Lost braces in \itemize; meant \describe ?
checkRd: (-1) datasheet.Rd:162: Lost braces in \itemize; meant \describe ?
checkRd: (-1) datasheet.Rd:163-164: Lost braces in \itemize; meant \describe ?
checkRd: (-1) datasheet.Rd:166-167: Lost braces in \itemize; meant \describe ?
checkRd: (-1) datasheet.Rd:169-170: Lost braces in \itemize; meant \describe ?
checkRd: (-1) project.Rd:50: Lost braces in \itemize; meant \describe ?
checkRd: (-1) project.Rd:51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) project.Rd:52-53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) scenario.Rd:62: Lost braces in \itemize; meant \describe ?
checkRd: (-1) scenario.Rd:64: Lost braces in \itemize; meant \describe ?
checkRd: (-1) scenario.Rd:66: Lost braces in \itemize; meant \describe ?
checkRd: (-1) scenario.Rd:68-69: Lost braces in \itemize; meant \describe ?
checkRd: (-1) scenario.Rd:71-74: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ssimLibrary.Rd:86-87: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ssimLibrary.Rd:88-89: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ssimLibrary.Rd:90-93: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ssimLibrary.Rd:94-96: Lost braces in \itemize; meant \describe ?
'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’
Package unavailable to check Rd xrefs: ‘cmdstanr’
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
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in Rd file 'tidy_pi_traces.Rd':
  ‘mix_indiv_tib’

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
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
       |                                                                    ^
Documented arguments not in \usage in Rd file 'MEM_MIDAS_lr_pred_no_skew.Rd':
  ‘daily_ret’

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) 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) }
       |                                                                                   ^
Package required but not available: ‘clusterProfiler’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package 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’
'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.
       |                                                                                                                                                                                                                                                                                            ^
Found the following significant warnings:
  F_MAIN_CAM.cpp:159:10: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  F_MAIN_CAM_Concentration.cpp:194:10: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  F_MAIN_fSAN.cpp:141:10: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  F_MAIN_fiSAN.cpp:143:10: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  F_MAIN_fiSAN_Concentration.cpp:184:10: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/SANvi.Rcheck/00install.out’ for details.
* used C++ compiler: ‘Debian clang version 17.0.6 (3)’
'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’
'library' or 'require' call to ‘progress’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' 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
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
checkRd: (-1) sassy.Rd:25-26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sassy.Rd:27-28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sassy.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sassy.Rd:30-31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sassy.Rd:32-33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sassy.Rd:34: Lost braces in \itemize; meant \describe ?
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.}
       |         ^
Package suggested but not available for checking: ‘rgdal’
'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
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
checkRd: (-1) shape.constrained.smooth.terms.Rd:11-14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) shape.constrained.smooth.terms.Rd:16-18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) shape.constrained.smooth.terms.Rd:20-21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) shape.constrained.smooth.terms.Rd:23-24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) shape.constrained.smooth.terms.Rd:26-29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) shape.constrained.smooth.terms.Rd:31-33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) shape.constrained.smooth.terms.Rd:35-38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) shape.constrained.smooth.terms.Rd:40-41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) shape.constrained.smooth.terms.Rd:54-55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) shape.constrained.smooth.terms.Rd:57-58: Lost braces in \itemize; meant \describe ?
checkRd: (-1) shape.constrained.smooth.terms.Rd:60-61: Lost braces in \itemize; meant \describe ?
checkRd: (-1) shape.constrained.smooth.terms.Rd:63-64: Lost braces in \itemize; meant \describe ?
checkRd: (-1) shape.constrained.smooth.terms.Rd:66-67: Lost braces in \itemize; meant \describe ?
checkRd: (-1) shape.constrained.smooth.terms.Rd:69-70: Lost braces in \itemize; meant \describe ?
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}}
       |       ^
'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
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
Packages suggested but not available for checking: 'GOSemSim', 'rrvgo'
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'sceasy', 'SeuratDisk', 'SeuratWrappers'
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
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.
Package suggested but not available for checking: ‘simplifyEnrichment’
'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
Packages suggested but not available for checking:
  'clusterProfiler', 'enrichplot'
'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.
Packages suggested but not available for checking: 'rgdal', 'rgeos'
Packages suggested but not available for checking: 'maptools', 'rgdal'
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
checkRd: (-1) errors.Rd:180: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) errors.Rd:181: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) errors.Rd:182: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) errors.Rd:183: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) errors.Rd:184: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) errors.Rd:185: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) errors.Rd:186: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) errors.Rd:187: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) errors.Rd:188: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) errors.Rd:189: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) errors.Rd:190: Lost braces in \itemize; \value handles \item{}{} directly
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"}.}
       |                                                                                                                                   ^
Package required but not available: ‘msa’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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:
  'flowMerge', 'flowClust', 'flowCore'
Packages unavailable to check Rd xrefs: ‘flowClust’, ‘flowMerge’
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
checkRd: (-1) SEMrun.Rd:57: Lost braces; missing escapes or markup?
    57 | \code{start = 0.1} generally performs well with {-1, 0, 1} weights.}
       |                                                 ^
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
Running examples in ‘SenTinMixt-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Mixt.fit.init
> ### Title: Initialization for the EM-based algorithms
> ### Aliases: Mixt.fit.init
> 
> ### ** Examples
> 
> set.seed(1234)
> n <- 50
> k <- 2
> Pi <- c(0.5, 0.5)
> mu <- matrix(c(0, 0, 4, 5), 2, 2)
> cov.model <- "EEE"
> lambda <- c(0.5, 0.5)
> delta <- c(0.7, 0.7)
> gamma <- c(2.62, 2.62)
> theta <- c(0.1, 0.1)
> density <- "MSEN"
> data <- rMixt(n, k, Pi, mu, cov.model, lambda, delta, gamma, theta, density)
> 
> X <- data$X
> nstartR <- 1
> init.par <- Mixt.fit.init(X, k, density, nstartR)
Warning in socketConnection(port = port, server = TRUE, blocking = TRUE,  :
  port 11132 cannot be opened
Error in socketConnection(port = port, server = TRUE, blocking = TRUE,  : 
  cannot open the connection
Calls: Mixt.fit.init ... <Anonymous> -> makeSOCKcluster -> newSOCKnode -> socketConnection
Execution halted
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
Found the following significant warnings:
  D_optimal.cpp:54:18: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  QIC.cpp:53:18: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  getMH.cpp:53:18: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/seqest.Rcheck/00install.out’ for details.
* used C++ compiler: ‘Debian clang version 17.0.6 (3)’
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
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/sgd.Rcheck/00install.out’ for details.
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},
       |                                          ^
Invalid package aliases in Rd file 'package_sgmodel.Rd':
  ‘package_sgmodel-package’
'LazyData' is specified without a 'data' directory
'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.}
       |                            ^
checkRd: (-1) plot_multiclass_obs_pred.Rd:23: Lost braces; missing escapes or markup?
    23 | {tidymodels} results for a multi-class classification model.
       | ^
checkRd: (-1) plot_multiclass_pred_factorcol.Rd:43: Lost braces; missing escapes or markup?
    43 | {tidymodels} results for a multi-class classification model.
       | ^
checkRd: (-1) plot_multiclass_pred_numcol.Rd:43: Lost braces; missing escapes or markup?
    43 | on {tidymodels} results for a multi-class classification model.
       |    ^
checkRd: (-1) plot_numeric_obs_pred.Rd:27: Lost braces; missing escapes or markup?
    27 | {tidymodels} results for a regression model.
       | ^
checkRd: (-1) plot_numeric_res_factorcol.Rd:36: Lost braces; missing escapes or markup?
    36 | {tidymodels} results for a regression model.
       | ^
checkRd: (-1) plot_numeric_res_numcol.Rd:36: Lost braces; missing escapes or markup?
    36 | {tidymodels} results for a regression model.
       | ^
checkRd: (-1) plot_numeric_res_pred.Rd:25: Lost braces; missing escapes or markup?
    25 | {tidymodels} results for a regression model.
       | ^
checkRd: (-1) plot_twoclass_obs_pred.Rd:25: Lost braces; missing escapes or markup?
    25 | {tidymodels} results for a two-class classification model.
       | ^
checkRd: (-1) plot_twoclass_pred_factorcol.Rd:46: Lost braces; missing escapes or markup?
    46 | {tidymodels} results for a two-class classification model.
       | ^
checkRd: (-1) plot_twoclass_pred_numcol.Rd:46: Lost braces; missing escapes or markup?
    46 | on {tidymodels} results for a two-class classification model.
       |    ^
Documented arguments not in \usage in Rd file 'shiny_models.Rd':
  ‘original_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.
'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
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    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
Packages suggested but not available for checking: 'ggseqlogo', 'qlcMatrix'
Unknown package ‘ggseqlogo’ in Rd xrefs
checkRd: (-1) add_k_mer_state.Rd:33: Lost braces in \itemize; \value handles \item{}{} directly
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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Found the following files/directories:
  ‘ExportFigtree1.tre’
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    64 | \item x_{l,i}, local variable l,
       |         ^
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    70 | \item d_{r,i} the distance between the center of pixel r and the observation at site i.
       |         ^
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    51 |     \item \code{dist = "binomial"} is drawn from eqn{Bin(XB, XB(1-XB))}
       |                                                     ^
Specified C++11: please drop specification unless essential
Argument items with no description in Rd file 'estThetaRow.Rd':
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'LazyData' is specified without a 'data' directory
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    69 | \code{dfptsde1d} {gives the density estimate of fpt.}
       |                  ^
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    70 | \code{fptsde1d} {generates random of fpt.}
       |                 ^
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    75 | \code{dfptsde2d} {gives the kernel density approximation for fpt.}
       |                  ^
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    76 | \code{fptsde2d} {generates random of fpt.}
       |                 ^
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    77 | \code{dfptsde3d} {gives the marginal kernel density approximation for fpt.}
       |                  ^
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    78 | \code{fptsde3d} {generates random of fpt.}
       |                 ^
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    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)}.}
       |               ^
'LazyData' is specified without a 'data' directory
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    25 | convert_xlsx_to_csv<-function(xlsx_file){
       |                                         ^
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    33 |   for (i in Sheetnames) {
       |                         ^
'LazyData' is specified without a 'data' directory
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  ‘database.csv’ ‘output.csv’ ‘output_clst.csv’
Specified C++11: please drop specification unless essential
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GNU make is a SystemRequirements.
Documented arguments not in \usage in Rd file 'make_kernel_dist.Rd':
  ‘Umax’

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:
  ‘res_mutation.tsv’ ‘res_mutationCounts.txt’
  ‘res_processContribution.txt’ ‘res_processes.txt’
Packages suggested but not available for checking: 'Rcgmin', 'Rvmmin'
Unknown packages ‘Rvmmin’, ‘Rcgmin’ in Rd xrefs
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    93 | {FD(h[i](t)) = (exp(g(x[j]) - g(x[l])) - 1) * 100}
       | ^
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Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    simpleCache [0.0.1]
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'rgdal', 'rgeos'
Documented arguments not in \usage in Rd file 'interval_labels.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.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Auto-generated content requiring editing in Rd file 'SimplifyStats-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...’
checkRd: (-1) cross.Rd:11: Lost braces
    11 | \item{x}{\code{\link{Pop-class}} or code{\link{Colony-class}} or \code{\link{MultiColony-class}},
       |                                         ^
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘fg_step_tab_pp’
Invalid package aliases in Rd file 'SimReg-package.Rd':
  ‘SimReg3-package’
Documented arguments not in \usage in Rd file 'sim_founderRVstatus.Rd':
  ‘intro_RV’

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) SimDataDist-class.Rd:28: Lost braces in \itemize; meant \describe ?
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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.
       |                                                                                                                         ^
checkRd: (-1) exportData.Rd:7: Lost braces
     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.
       |                                                                                                                                 ^
Package suggested but not available for checking: ‘INLA’
Specified C++14: please drop specification unless essential
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    Version (Date)
'LazyData' is specified without a 'data' directory
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    67 |  \code{within.SD} to be extremely small (e.g., $1 * 10^{-7}$) and all corresponding correlations in matrix
       |                                                        ^
checkRd: (-1) add_bold.Rd:15: Lost braces; missing escapes or markup?
    15 | For example, in latex it would take "2" and output "{\\bf 2}"; in html
       |                                                     ^
checkRd: (-1) NAP.Rd:109: Lost braces
   109 | bounds for P{X<Y}, based on two independent samples. \emph{The Annals of
       |             ^
Specified C++11: please drop specification unless essential
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checkRd: (-1) sim.bdh.age.Rd:67: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) sim.bdh.taxa.ssa.Rd:70: Lost braces in \itemize; meant \describe ?
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No news entries found.
'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
checkRd: (-1) sitar-package.Rd:27: Lost braces; missing escapes or markup?
    27 | individual curves, adjusted for {abcd} to lie on top of (i.e. be
       |                                 ^
checkRd: (-1) sitar.Rd:110: Lost braces; missing escapes or markup?
   110 | \code{\link{nlme}}) (default {nlmeControl(returnObject = TRUE)}).}
       |                              ^
checkRd: (-1) rawCCD.Rd:20: Lost braces; missing escapes or markup?
    20 |   \item{distr.type}{school district type (constructed for illustration purposes; (values={"A", "B", "C", "D"})).}
       |                                                                                          ^
checkRd: (-1) selectMatch.Rd:61: Lost braces; missing escapes or markup?
    61 | \item{replacementUnitsFilename}{character; csv filename for saving {unit:replacement} directory when writeOut == TRUE; default = "replacementUnits.csv"}
       |                                                                    ^
checkRd: (-1) selectMatch.Rd:63: Lost braces; missing escapes or markup?
    63 | \item{subUnitTableFilename}{character; csv filename for saving {unit:replacement} directory when writeOut == TRUE; default = "subUnitTable.csv"}
       |                                                                ^
checkRd: (-1) selectMatch.Rd:66: Lost braces; missing escapes or markup?
    66 | list with: 1) table of the form: {selected unit i: (unit i replacements)}, 2) table of the form: {potential unit i:(unit i sub-units)}, 3) balance diagnostics.
       |                                  ^
checkRd: (-1) selectMatch.Rd:66: Lost braces; missing escapes or markup?
    66 | list with: 1) table of the form: {selected unit i: (unit i replacements)}, 2) table of the form: {potential unit i:(unit i sub-units)}, 3) balance diagnostics.
       |                                                                                                  ^
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) OU_14.Rd:15: Lost braces in \itemize; meant \describe ?
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'LazyData' is specified without a 'data' directory
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checkRd: (-1) grow.dbhinc.hgtinc.Rd:29: Lost braces; missing escapes or markup?
    29 |   {dbh.inc.mm } {DBH increment in mm}
       |   ^
checkRd: (-1) grow.dbhinc.hgtinc.Rd:29: Lost braces; missing escapes or markup?
    29 |   {dbh.inc.mm } {DBH increment in mm}
       |                 ^
checkRd: (-1) grow.dbhinc.hgtinc.Rd:30: Lost braces; missing escapes or markup?
    30 |   {hgt.inc.dm } {Height increment in dm}
       |   ^
checkRd: (-1) grow.dbhinc.hgtinc.Rd:30: Lost braces; missing escapes or markup?
    30 |   {hgt.inc.dm } {Height increment in dm}
       |                 ^
Argument items with no description in Rd file 'management.prob.Rd':
  ‘...’
Argument items with no description in Rd file 'mng.tree.removal.Rd':
  ‘\dots’
Argument items with no description in Rd file 'prep.common.vars.fun.Rd':
  ‘\dots’
Argument items with no description in Rd file 'recr.BBG2008.Rd':
  ‘common.vars’
checkRd: (-1) ss.cc.Rd:44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ss.ci.Rd:26: Lost braces
    26 | \item{alpha}{The eqn{\\alpha} error used to compute the \eqn{100*(1-\\alpha)\%} confidence interval}
       |                     ^
checkRd: (-1) ss.rr.Rd:84: Lost braces; missing escapes or markup?
    84 | $MS_{factor}/MS_{interaction}$, e.g. in appendix A of AIAG MSA manual, 
       |     ^
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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.
       |                                        ^
Package vignette without corresponding tangle output:
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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 which this enhances but not available for checking: ‘kmndirs’
Unavailable namespace imported from by a ':::' call: ‘kmndirs’
  See the note in ?`:::` about the use of this operator.
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘texPreview’
Unknown package ‘texPreview’ in Rd xrefs
Specified C++11: please drop specification unless essential
checkRd: (-1) outliers.hdts.Rd:44: Lost braces; missing escapes or markup?
    44 |   \item I.cov.rob - The matrix (V'GnV)^{-1} used to compute the statistics to detect the idiosyncratic outliers.
       |                                        ^
'LazyData' is specified without a 'data' directory
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checkRd: (-1) ex0723.Rd:29: Escaped LaTeX specials: \&
checkRd: (-1) ex0915.Rd:25: Escaped LaTeX specials: \&
checkRd: (-1) ex1515.Rd:4: Escaped LaTeX specials: \&
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  ‘chapter03-HortonMosaic.Rnw’
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  ‘chapter05-HortonMosaic.Rnw’
  ‘chapter06-HortonMosaic.Rnw’
  ‘chapter07-HortonMosaic.Rnw’
  ‘chapter08-HortonMosaic.Rnw’
  ‘chapter09-HortonMosaic.Rnw’
  ‘chapter10-HortonMosaic.Rnw’
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  ‘chapter13-HortonMosaic.Rnw’
Engines should be specified as \VignetteEngine{PKG::ENG}.
Package vignettes without corresponding tangle output:
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  ‘chapter02-HortonMosaic.Rnw’
  ‘chapter03-HortonMosaic.Rnw’
  ‘chapter04-HortonMosaic.Rnw’
  ‘chapter05-HortonMosaic.Rnw’
  ‘chapter06-HortonMosaic.Rnw’
  ‘chapter07-HortonMosaic.Rnw’
  ‘chapter08-HortonMosaic.Rnw’
  ‘chapter09-HortonMosaic.Rnw’
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  ‘chapter11-HortonMosaic.Rnw’
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  ‘chapter02-HortonMosaic.Rnw’
  ‘chapter03-HortonMosaic.Rnw’
  ‘chapter04-HortonMosaic.Rnw’
  ‘chapter05-HortonMosaic.Rnw’
  ‘chapter06-HortonMosaic.Rnw’
  ‘chapter07-HortonMosaic.Rnw’
  ‘chapter08-HortonMosaic.Rnw’
  ‘chapter09-HortonMosaic.Rnw’
  ‘chapter10-HortonMosaic.Rnw’
  ‘chapter11-HortonMosaic.Rnw’
  ‘chapter12-HortonMosaic.Rnw’
  ‘chapter13-HortonMosaic.Rnw’
Engines should be specified as \VignetteEngine{PKG::ENG}.
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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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checkRd: (-1) morsescales.Rd:15: Lost braces in \itemize; meant \describe ?
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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.
       |                                                                                                                                                                                                                                                                                                                                                        ^
checkRd: (-1) bcmds.Rd:111: Lost braces; missing escapes or markup?
   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 
       |                  ^
checkRd: (-1) aggrtab.Rd:24: Lost braces; missing escapes or markup?
    24 | D = {D[[j]]} of marginal tables/cubes of A spesified by the list d = d{[[j]]} generated 
       |     ^
checkRd: (-1) aggrtab.Rd:24: Lost braces
    24 | D = {D[[j]]} of marginal tables/cubes of A spesified by the list d = d{[[j]]} generated 
       |                                                                       ^
checkRd: (-1) makeroundtabs.Rd:31: Lost braces
    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
       |                  ^
Package suggested but not available for checking: ‘gurobi’
Auto-generated content requiring editing in Rd file 'smallstuff-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...’
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘rgdal’
'LazyData' is specified without a 'data' directory
Package vignettes without corresponding tangle output:
  ‘DTR.Rmd’
  ‘SST.Rmd’
Unknown package ‘InformationValue’ in Rd xrefs
checkRd: (-1) cities_lon_lat.Rd:6: Lost braces
     6 | A subset of world.cities{maps}. Extracted in order to shink number of dependencies. 
       |                         ^
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'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.
checkRd: (-1) customerRetentionDemographics.Rd:10: Escaped LaTeX specials: \$
checkRd: (-1) customerRetentionDemographics.Rd:11: Escaped LaTeX specials: \$ \$
checkRd: (-1) customerRetentionDemographics.Rd:12: Escaped LaTeX specials: \$ \$
checkRd: (-1) customerRetentionDemographics.Rd:13: Escaped LaTeX specials: \$ \$
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checkRd: (-1) trlong.Rd:17: Lost braces
    17 |     \item{\code{resp}}{a factor indicating the transport mode choice, and \code{B} denotes taking the bus, code{D} denotes driving one's own vehicle, \code{F} denotes getting a ride with a friend, \code{O} denotes other, and \code{W} denotes walking}
       |                                                                                                                ^
checkRd: (-1) smdi_diagnose.Rd:49: Lost braces; missing escapes or markup?
    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
       |            ^
checkRd: (-1) smdocker_log.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) smdocker_log.Rd:35-37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) smdocker_log.Rd:38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) smdocker_log.Rd:16: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) smdocker_log.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) smdocker_log.Rd:19: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
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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},...}
       |                                                  ^
checkRd: (-1) SimModel1.Rd:21: Lost braces; missing escapes or markup?
    21 | \item{beta}{the \eqn{\beta} matrix, iqx+ip*ik, y_{1,t-1},y_{1,t-2},...,y_{2,t-1},y_{2,t-2},...}
       |                                                            ^
checkRd: (-1) SimModel1.Rd:21: Lost braces; missing escapes or markup?
    21 | \item{beta}{the \eqn{\beta} matrix, iqx+ip*ik, y_{1,t-1},y_{1,t-2},...,y_{2,t-1},y_{2,t-2},...}
       |                                                                          ^
checkRd: (-1) SimModel1.Rd:21: Lost braces; missing escapes or markup?
    21 | \item{beta}{the \eqn{\beta} matrix, iqx+ip*ik, y_{1,t-1},y_{1,t-2},...,y_{2,t-1},y_{2,t-2},...}
       |                                                                                    ^
checkRd: (-1) SimModel2.Rd:19: Lost braces; missing escapes or markup?
    19 | \item{beta_0}{the initial beta, iqx+ip*ik, y_{1,t-1},y_{1,t-2},...,y_{2,t-1},y_{2,t-2},....}
       |                                              ^
checkRd: (-1) SimModel2.Rd:19: Lost braces; missing escapes or markup?
    19 | \item{beta_0}{the initial beta, iqx+ip*ik, y_{1,t-1},y_{1,t-2},...,y_{2,t-1},y_{2,t-2},....}
       |                                                        ^
checkRd: (-1) SimModel2.Rd:19: Lost braces; missing escapes or markup?
    19 | \item{beta_0}{the initial beta, iqx+ip*ik, y_{1,t-1},y_{1,t-2},...,y_{2,t-1},y_{2,t-2},....}
       |                                                                      ^
checkRd: (-1) SimModel2.Rd:19: Lost braces; missing escapes or markup?
    19 | \item{beta_0}{the initial beta, iqx+ip*ik, y_{1,t-1},y_{1,t-2},...,y_{2,t-1},y_{2,t-2},....}
       |                                                                                ^
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) fit_spm.Rd:73: Lost braces; missing escapes or markup?
    73 | algorithm to be used. For details, see {optim}.}
       |                                        ^
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    76 | the optimization algorithm to be used. For details, see {optim}.}
       |                                                         ^
checkRd: (-1) fit_spm.Rd:101: Lost braces; missing escapes or markup?
   101 | the control parameters from the {optim} function through the argument
       |                                 ^
Documented arguments not in \usage in Rd file 'aux_cs.Rd':
  ‘dists’

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

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

Documented arguments not in \usage in Rd file 'aux_mat.Rd':
  ‘mat_list1’ ‘mat_list2’ ‘x’ ‘y’ ‘return_single’

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

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

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

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

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
Invalid package aliases in Rd file 'SMLE-package.Rd':
  ‘smle-package’
Specified C++11: please drop specification unless essential
checkRd: (-1) SMMA.Rd:115: Lost braces
   115 |  is the empirical explained variance from \cite{Meinshausen and B{u}hlmann, 2015}.  See \cite{Lund et al., 2020} for more details and references.
       |                                                                  ^
checkRd: (-1) SMMA.Rd:170: Lost braces
   170 | Meinshausen, N and P. B{u}hlmann (2015). Maximin effects in inhomogeneous large-scale data.
       |                        ^
Specified C++11: please drop specification unless essential
checkRd: (-1) estimMk.Rd:44: Lost braces; missing escapes or markup?
    44 | estimMk returns the transition probability matrix of size (S^{k})xS (with S = length(E)) 
       |                                                              ^
Specified C++11: please drop specification unless essential
checkRd: (-1) getKernel.Rd:25-26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) getKernel.Rd:27-28: Lost braces in \itemize; \value handles \item{}{} directly
Auto-generated content requiring editing in Rd file 'smoke-package.Rd':
  \details: ‘...the package, including the most important ~~ ~~ functions ~~’
checkRd: (-1) getGlobalOptimum.Rd:16: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) getGlobalOptimum.Rd:17: Lost braces in \itemize; \value handles \item{}{} directly
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checkRd: (-1) getLocalOptimum.Rd:16: Lost braces in \itemize; \value handles \item{}{} directly
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    10 | or code{smoof_multi_objective_function}. Both single- and multi-objective functions share the following attributes.
       |        ^
'LazyData' is specified without a 'data' directory
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    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) sm.rm.Rd:50-54: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) sm.rm.Rd:60-63: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sm.rm.Rd:64-67: Lost braces in \itemize; meant \describe ?
Objects in \usage without \alias in Rd file 'sm-internal.Rd':
  ‘sm.check.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.
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
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    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,
       |                                                      ^
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    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
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 ?
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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
       |                                     ^
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    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 ?
checkRd: (-1) superClass.Rd:92-93: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) superClass.Rd:94: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) superClass.Rd:95-96: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) trainSOM.Rd:40: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) trainSOM.Rd:41: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) trainSOM.Rd:42-44: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) trainSOM.Rd:45-47: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) trainSOM.Rd:48: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) trainSOM.Rd:49-50: Lost braces in \itemize; \value handles \item{}{} directly
Package vignettes with \VignetteEngine{} not specifying an engine package:
  ‘a-doc-SOMbrero-package.Rmd’
  ‘c-doc-numericSOM.Rmd’
  ‘d-doc-korrespSOM.Rmd’
  ‘e-doc-relationalSOM.Rmd’
Engines should be specified as \VignetteEngine{PKG::ENG}.
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
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checkRd: (-1) findFn.Rd:126-130: Lost braces in \itemize; \value handles \item{}{} directly
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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
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’.
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’.
Found the following significant warnings:
  lacov.cpp:56:13: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  lacov.cpp:89:13: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  lacov.cpp:126:13: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  stkmat.cpp:27:13: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  stkmat.cpp:52:13: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  stkmat.cpp:77:13: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/SpaceTimeBSS.Rcheck/00install.out’ for details.
* used C++ compiler: ‘Debian clang version 17.0.6 (3)’
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
Documented arguments not in \usage in Rd file 'logit.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.
'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
Argument items with no description in Rd file 'binarizer.Rd':
  ‘\dots’
Found the following significant warnings:
  /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/BH/include/boost/math/tools/config.hpp:23:6: warning: "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" [-W#warnings]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/spatialwidget.Rcheck/00install.out’ for details.
* used C++ compiler: ‘Debian clang version 17.0.6 (3)’
Specified C++11: 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.
'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 ?
checkRd: (-1) xshewhartrunsrules.arl.Rd:39-40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) xshewhartrunsrules.arl.Rd:41-42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) xshewhartrunsrules.arl.Rd:43-44: Lost braces in \itemize; meant \describe ?
Package suggested but not available for checking: ‘spDataLarge’
Documented arguments not in \usage in Rd file 'hazard.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.
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
Documented arguments not in \usage in Rd file 'grapes-matches-grapes.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) FitAkdParameters.Rd:23: Lost braces; missing escapes or markup?
    23 |       p(y|ens) = 1 / K * sum {dnorm(y, z.i, s)} \cr
       |                              ^
checkRd: (-1) australia.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) australia.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) australia.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) australia.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) australia.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) SpectraInTime-class.Rd:66: Lost braces
    66 | \item{colors}{colorblind friendly palettes are used from the de \code{\link[viridis]{viridis_pal}} choice between code{"A"} (magna),
       |                                                                                                                       ^
checkRd: (-1) SpectraInTime-class.Rd:67: Lost braces
    67 | code{"B"} (inferno),  \code{"C"} (plasma) and \code{"D"} the default viridis color palette}
       |     ^
checkRd: (-1) addPreprocessingStep.Rd:17: Lost braces
    17 | code{\link{SpectraInTime-class}}
       |     ^
checkRd: (-1) baselineCorrect.Rd:24: Lost braces
    24 | \item{degree}{numeric value, degree of the polynomial used only if \code{method} is code{'modpolyfit'}}
       |                                                                                         ^
checkRd: (-1) scatterCorrect.Rd:19: Lost braces
    19 | \item{referenceSpectra}{the reference spectra when not derived from the current data, defaults to code{NULL} when \code{referenceMethod} is used 
       |                                                                                                       ^
checkRd: (-1) spectralIntegration.Rd:19: Lost braces
    19 | \item{smoothingValue}{numeric value between 0 and 1, amount of code{\link[stats]{lowess}}-smoothing,
       |                                                                    ^
Documented arguments not in \usage in Rd file 'changeDevSettings.Rd':
  ‘defaultsSettings’

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

Documented arguments not in \usage in Rd file 'convertListToS4.Rd':
  ‘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.
checkRd: (-1) image.plot.Rd:78: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘cooltools’
Unknown package ‘cooltools’ in Rd xrefs
Specified C++11: please drop specification unless essential
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’
checkRd: (-1) moment_empirical_var.Rd:15: Lost braces; missing escapes or markup?
    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
checkRd: (-1) cylinder.counts.Rd:61-62: Lost braces
    61 | nucleotide, so that \code{a.c} represents the set {\code{aac}, \code{acc}, 
       |                                                   ^
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘cooltools’
checkRd: (-1) adaptIntegrateSpherePolar.Rd:14: Lost braces
    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’
Specified C++11: please drop specification unless essential
checkRd: (-1) BVCfit.Rd:71: Lost braces in \itemize; meant \describe ?
checkRd: (-1) BVCfit.Rd:72: Lost braces in \itemize; meant \describe ?
checkRd: (-1) BVCfit.Rd:73: Lost braces in \itemize; meant \describe ?
checkRd: (-1) BVCfit.Rd:74: Lost braces in \itemize; meant \describe ?
checkRd: (-1) BVCfit.Rd:75: Lost braces in \itemize; meant \describe ?
checkRd: (-1) BVCfit.Rd:76: Lost braces in \itemize; meant \describe ?
checkRd: (-1) PimaIndiansDiabetes_long.Rd:14: Escaped LaTeX specials: \^
checkRd: (-1) PimaIndiansDiabetes_wide.Rd:16: Escaped LaTeX specials: \^
checkRd: (-1) cartesian_to_xy.Rd:21: Lost braces; missing escapes or markup?
    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
checkRd: (-1) speedtestdata.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) speedtestdata.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) speedtestdata.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) speedtestdata.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) speedtestdata.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) speedtestdata.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ds_aat.Rd:16: Lost braces
    16 | \doi{10.1111/add.14071}{Boffo et al., 2018}. Participants were presented stimuli from a "test"
       |                        ^
checkRd: (-1) ds_gng.Rd:16: Lost braces
    16 | described in detail in \doi{10.1016/j.tate.2019.102887}{Hedge, Powell, and Sumner (2018)}. 
       |                                                        ^
checkRd: (-1) ds_iat.Rd:19: Lost braces
    19 | \doi{10.1016/j.tate.2019.102887}{Abacioglu and colleagues (2019)}. 
       |                                 ^
checkRd: (-1) ds_rapi.Rd:15: Lost braces
    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
checkRd: (-1) gbmidwcv.Rd:118: Lost braces
   118 | rfcv{randomForest} and gbm
       |     ^
checkRd: (-1) gbmokgbmidwcv.Rd:108: Lost braces
   108 | variable and anisotropy parameters. see notes vgm{gstat} for details.
       |                                                  ^
Specified C++11: please drop specification unless essential
checkRd: (-1) spnn-package.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) spnn-package.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) spnn-package.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) spnn-package.Rd:18: Lost braces in \itemize; meant \describe ?
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
checkRd: (-1) hockey_goaltenders_restricted_area.Rd:38: Lost braces; missing escapes or markup?
    38 | "has_trapezoid" key in the \code{rink_params} passed to geom_{league}
       |                                                              ^
Documented arguments not in \usage in Rd file 'basketball_center_circle_fill.Rd':
  ‘linethickness’

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

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

Documented arguments not in \usage in Rd file 'curling_features_set_colors.Rd':
  ‘sheet’ ‘ring_1’ ‘ring_2’ ‘ring_3’

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

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

Documented arguments not in \usage in Rd file 'hockey_features_set_colors.Rd':
  ‘boards_color’ ‘center_line_color’ ‘blue_line_color’
  ‘goal_line_color’ ‘goalkeepers_restricted_area_color’
  ‘goal_crease_outline_color’ ‘goal_crease_fill_color’
  ‘referee_crease_color’ ‘center_faceoff_spot_color’
  ‘faceoff_spot_outer_ring_color’ ‘faceoff_spot_fill_color’
  ‘center_faceoff_circle_color’ ‘non_center_faceoff_circle_color’
  ‘faceoff_line_color’ ‘goal_color’ ‘goal_fill_color’

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

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

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) 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
checkRd: (-1) shpdata1.Rd:7: Lost braces
     7 | \format{An object of class /code{"list"}.}
       |                                 ^
checkRd: (-1) shypEstFun.Rd:52: Escaped LaTeX specials: \$
checkRd: (-1) shypEstFun.Rd:54: Escaped LaTeX specials: \$
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
       |                                            ^
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
       |                                                         ^
checkRd: (-1) sncFun.02110.Rd:27: Lost braces
    27 | The function is Eq. Table 1-B in insertRef{Streck.2020}{spsh}
       |                                           ^
checkRd: (-1) sncFun.02110.Rd:27: Lost braces
    27 | The function is Eq. Table 1-B 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}
       |                                            ^
checkRd: (-1) sncFun.04110.Rd:27: Lost braces
    27 | The function is Eq. Table 1-A  in insertRef{Streck.2020}{spsh}
       |                                                         ^
checkRd: (-1) impactspsur.Rd:42: Lost braces; missing escapes or markup?
    42 | and a matching \code{Qres} list attribute if {Q} was given.
       |                                              ^
checkRd: (-1) spsur3sls.Rd:158: Lost braces; missing escapes or markup?
   158 |   the matrix of regressors, of order \emph{(Nxp_{g})}. Moreover, 
       |                                                 ^
checkRd: (-1) spsurgs3sls.Rd:67: Lost braces; missing escapes or markup?
    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.
checkRd: (-1) spsOption.Rd:29: Lost braces; missing escapes or markup?
    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
       |                              ^
checkRd: (-1) spsOption.Rd:29: Lost braces; missing escapes or markup?
    29 | Some functions in {spsUtil}, {spsComps} and {systempPipeShiny} will behave
       |                                             ^
checkRd: (-1) predict.spT.Rd:36: Lost braces
    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
checkRd: (-1) vol.m3.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) vol.m3.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) vol.m3.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sqldf.Rd:248: Lost braces
   248 | and code{port} arguments of sqldf.
       |         ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) fpiter.Rd:55-58: Lost braces
    55 |     \code{tol}{ - a small, positive scalar that determines when iterations 
       |               ^
checkRd: (-1) fpiter.Rd:60-61: Lost braces
    60 |     \code{maxiter}{ - an integer denoting the maximum limit on the number of 
       |                   ^
checkRd: (-1) fpiter.Rd:63-65: Lost braces
    63 |     \code{trace}{ - a logical variable denoting whether some of the intermediate 
       |                 ^
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).
       |                                                     ^
Documented arguments not in \usage in Rd file 'sraAutoregTimeseries.Rd':
  ‘logs2’

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) plot.SRCS.Rd:48-50: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.SRCS.Rd:51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.SRCS.Rd:52-53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.SRCS.Rd:54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.SRCS.Rd:55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.SRCS.Rd:56-58: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.SRCS.Rd:59-60: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.SRCS.Rd:61-62: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.SRCS.Rd:63-64: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.SRCS.Rd:65-66: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.SRCS.Rd:72-73: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.SRCS.Rd:74-75: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.SRCS.Rd:76: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.SRCS.Rd:77-79: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.SRCS.Rd:80-81: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.SRCS.Rd:82: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.SRCS.Rd:87-88: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.SRCS.Rd:89: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.SRCS.Rd:143-144: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.SRCS.Rd:145: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.SRCS.Rd:146-148: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.SRCS.Rd:149: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
checkRd: (-1) ssaBSS-package.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ssaBSS-package.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ssaBSS-package.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ssaBSS-package.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ssaBSS-package.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sscor.Rd:33: Lost braces; missing escapes or markup?
    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
Specified C++11: please drop specification unless essential
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 ?
checkRd: (-1) new.distance.Rd:31-32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) new.distance.Rd:33-34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) new.distance.Rd:35-36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) new.distance.Rd:37-38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) new.distance.Rd:39-40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sensitivity.plot.Rd:30-33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sensitivity.plot.Rd:34-35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sensitivity.plot.Rd:36-37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sensitivity.plot.Rd:38-40: Lost braces in \itemize; meant \describe ?
'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) 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
       |                                      ^
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
       |                                                ^
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'namesMultiple.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.
checkRd: (-1) SRanalysis.Rd:100: Lost braces
   100 |   P. B{\"u}hlmann (2019). Stabilizing Variable Selection and
       |       ^
checkRd: (-1) StabilizedRegression.Rd:109: Lost braces
   109 |   P. B{\"u}hlmann (2019). Stabilizing Variable Selection and
       |       ^
'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) stabsel_parameters.Rd:42: Lost braces
    42 |     always use code{"none"}.}
       |                    ^
checkRd: (-1) stabsel_stabsel.Rd:25: Lost braces
    25 |     always use code{"none"}.}
       |                    ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) stackExample.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) stackExample.Rd:11: Lost braces in \itemize; meant \describe ?
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.
Documented arguments not in \usage in Rd file 'which_class.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.
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}.
       |                                                                                                    ^
Invalid package aliases in Rd file 'statcheck-package.Rd':
  ‘{statcheck}-package’
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.IBDprob.Rd:45-46: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.IBDprob.Rd:47-48: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.IBDprob.Rd:49-50: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.IBDprob.Rd:51-52: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.IBDprob.Rd:53-54: Lost braces in \itemize; meant \describe ?
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 ?
Documented arguments not in \usage in Rd file 'estEffsCPP.Rd':
  ‘y’ ‘w’ ‘x’ ‘ncores’

Documented arguments not in \usage in Rd file 'updateFA.Rd':
  ‘Y’ ‘WStart’ ‘m’ ‘PStart’

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: ‘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’
'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: \&
checkRd: (-1) keypoints.Rd:35-36: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) keypoints.Rd:37-39: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) keypoints.Rd:40-44: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) keypoints.Rd:45-48: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) keypoints.Rd:49-50: Lost braces in \enumerate; meant \describe ?
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
checkRd: (-1) Medellin.Rd:8: Lost braces
     8 | This dataset represents the spatio-temporal locations of traffic accidents in an area near the pontifical bolivarian university in Medell\'{i}n (Colombia) during 2016. The entire data were published in the OpenData portal of Medell\'{i}n Town Hall at https://www.medellin.gov.co/geomedellin/index.hyg.
       |                                                                                                                                            ^
checkRd: (-1) Medellin.Rd:8: Lost braces
     8 | This dataset represents the spatio-temporal locations of traffic accidents in an area near the pontifical bolivarian university in Medell\'{i}n (Colombia) during 2016. The entire data were published in the OpenData portal of Medell\'{i}n Town Hall at https://www.medellin.gov.co/geomedellin/index.hyg.
       |                                                                                                                                                                                                                                          ^
'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.
'LazyData' is specified without a 'data' directory
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
Auto-generated content requiring editing in Rd file 'strategicplayers-package.Rd':
  \details: ‘...o use the package, including the most important functions ~~’
  \references: ‘~~ Literature or other references for background information ~~’
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
Package suggested but not available for checking: ‘rgeos’
Specified C++11: please drop specification unless essential
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
       |                                                ^
'LazyData' is specified without a 'data' directory
'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.
       |   ^
checkRd: (-1) SP2001.Rd:3: Escaped LaTeX specials: \&
checkRd: (-1) SP2001.Rd:5: Escaped LaTeX specials: \&
checkRd: (-1) SP2001.Rd:12: Escaped LaTeX specials: \&
checkRd: (-1) breakpoints.Rd:223: Lost braces
   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 ?
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘maptools’
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}.}
       |                                ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) fp19.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fp19.Rd:12-13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fp19.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fp19.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fp19.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fp19.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fp19.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fp19.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fp19.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fp19.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fp19.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fp19.Rd:23-24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fp19.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) suggests.Rd:14: Lost braces; missing escapes or markup?
    14 | {suggests} aims to make that workflow as minimal and painless as possible,
       | ^
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
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:[];}`}
       |                                                                                                     ^
checkRd: (-1) sund2b.Rd:22: Lost braces; missing escapes or markup?
    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 ~~’
Specified C++11: please drop specification unless essential
checkRd: (-1) plot.supc.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) BiclustSet-class.Rd:19: Lost braces
    19 |     \item{\code{Number}:}{code{"numeric"}, number of biclusters in the set}
       |                               ^
checkRd: (-1) plot.Rd:42: Lost braces; missing escapes or markup?
    42 |  \item{color.off}{color code; specifying the color for set(s) which are "{absent}" for an intersection.}
       |                                                                          ^
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘extraTrees’
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
       |                              ^
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
       |                                       ^
checkRd: (-1) SL.cforest.Rd:5: Lost braces; missing escapes or markup?
     5 | \title{cforest {party}}
       |                ^
Unknown package ‘extraTrees’ in Rd xrefs
Package suggested but not available for checking: ‘extraTrees’
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in Rd file 'check_package.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.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘apollo’
Specified C++11: please drop specification unless essential
checkRd: (-1) getFittedProbs.Rd:6-8: Lost braces
     6 | getFittedValues <- function(object) {
       |                                     ^
checkRd: (-1) getFittedProbs.Rd:14-16: Lost braces
    14 | getFittedValues <- function(object) {
       |                                     ^
surfaceSimulate : phytransform: no visible global function definition
  for ‘rescale’
Undefined global functions or variables:
  rescale
'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: ‘INLA’
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘treeshap’
'LazyData' is specified without a 'data' directory
checkRd: (-1) svyquantile.Rd:58: Lost braces; missing escapes or markup?
    58 | quantile interval; \code{"hf1"} to {"hf9"} are weighted analogues of
       |                                    ^
Package suggested but not available for checking: ‘gurobi’
Specified C++11: please drop specification unless essential
Packages suggested but not available for checking:
  'survHEinla', 'survHEhmc', 'INLA'
checkRd: (-1) tprob.Rd:138: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tprob.Rd:139: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tprob.Rd:140: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tprob.Rd:141: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tprob.Rd:142: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tprob.Rd:143: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tprob.Rd:144: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tprob.Rd:145: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tprob.Rd:146: Lost braces in \itemize; meant \describe ?
Package suggested but not available for checking: ‘distr6’
checkRd: (-1) set_seed.Rd:19: Lost braces; missing escapes or markup?
    19 | using \link{set.seed} as usual but also in {numpy} and {torch} via {reticulate}.
       |                                            ^
checkRd: (-1) set_seed.Rd:19: Lost braces; missing escapes or markup?
    19 | using \link{set.seed} as usual but also in {numpy} and {torch} via {reticulate}.
       |                                                        ^
checkRd: (-1) set_seed.Rd:19: Lost braces; missing escapes or markup?
    19 | using \link{set.seed} as usual but also in {numpy} and {torch} via {reticulate}.
       |                                                                    ^
Unknown package ‘distr6’ in Rd xrefs
checkRd: (-1) coxph_mpl_dc.Rd:24: Lost braces; missing escapes or markup?
    24 | \item{mpl_h0t}{MPL estimates of the baseline hazard for T, i.e. h_{0T}(x_i)}
       |                                                                   ^
checkRd: (-1) coxph_mpl_dc.Rd:25: Lost braces; missing escapes or markup?
    25 | \item{mpl_h0c}{MPL estimates of the baseline hazard for C, i.e. h_{0C}(x_i)}
       |                                                                   ^
checkRd: (-1) coxph_mpl_dc.Rd:26: Lost braces; missing escapes or markup?
    26 | \item{mpl_H0t}{MPL estimates of the baseline cumulative hazard for T, i.e. H_{0T}(x_i)}
       |                                                                              ^
checkRd: (-1) coxph_mpl_dc.Rd:27: Lost braces; missing escapes or markup?
    27 | \item{mpl_H0c}{MPL estimates of the baseline cumulative hazard for C, i.e. H_{0c}(x_i)}
       |                                                                              ^
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    28 | \item{mpl_S0t}{MPL estimates of the baseline survival for T, i.e. S_{0T}(x_i)}
       |                                                                     ^
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    29 | \item{mpl_S0c}{MPL estimates of the baseline survival for C, i.e. S_{0C}(x_i)}
       |                                                                     ^
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    14 |     \item{\code{outcome}}{outcome: code{censor}, \code{thymic
       |                                        ^
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    57 |  \item{newname = cumtdc(y,x, init)}{ Similar to tdc, except that the event
       |       ^
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    57 |  \item{newname = cumtdc(y,x, init)}{ Similar to tdc, except that the event
       |                                    ^
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    62 |  \item{newname = event(y,x)}{ Mark an event at time y.
       |       ^
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    62 |  \item{newname = event(y,x)}{ Mark an event at time y.
       |                             ^
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    66 |  \item{newname = cumevent(y,x)}{ Cumulative events}.
       |       ^
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    66 |  \item{newname = cumevent(y,x)}{ Cumulative events}.
       |                                ^
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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},
       |                                                                      ^
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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.
       |                                                         ^
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    37 | Both SciViews-K and {svKomodo} should be considered archived items. I keep
       |                     ^
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    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,
       |                   ^
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    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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    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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Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Additional functions and data sets
    Amendments to functions
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Problems with news in ‘NEWS.md’:
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    pre-release switchboard (2020 - 2021)
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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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    14 | \code{n} x 4 matrix of coordinates consisting of {lat or y, lon or x} pairs for each each site
       |                                                  ^
Invalid package aliases in Rd file 'syncrng-package.Rd':
  ‘syncrng-package’
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    28 | before plotting {ex: \code{trans = c(s = "exp", d = "exp")}}/}
       |                 ^
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Found the following files/directories:
  ‘test.csv’
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Documented arguments not in \usage in Rd file 'table_params_circle.Rd':
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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.
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    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
       |                                       ^
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    33 | and error = 0.45, then \code{form} = "{estimate} ({error})" will return
       |                                                   ^
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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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    68 | \\code{yvarlabels = list(race = "Race/ethnicity", age_yrs = "Age (years)")}.}
       |       ^
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    67 | \\code{yvarlabels = list(race = "Race/ethnicity", age_yrs = "Age (years)")}.}
       |       ^
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    38 |  '{{ip ip_address}} [{{date access_date}}]...'.
       |   ^
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    38 |  '{{ip ip_address}} [{{date access_date}}]...'.
       |                      ^
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Problems with news in ‘NEWS.md’:
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Specified C++11: please drop specification unless essential
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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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   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.
       |                                                                                   ^
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    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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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.
'LazyData' is specified without a 'data' directory
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    24 | \item{na.rm}{logical code{TRUE/FALSE}. Remove NAs from the dataset. Defaults
       |                          ^
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    24 | \item{na.rm}{logical code{TRUE/FALSE}. Remove NAs from the dataset. Defaults
       |                          ^
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    35 | \item{C1.map}{An \code{p1} by \code{k} matrix of 0/1 values, indicating for each of the \code{p1} covariates in \code{C1} whether to consider its potential effects on the values of each of the \code{k} sources (e.g., if position \code{i,j} in \code{C1.map} is 1 then the potential effect of the \code{i}-th covariate in \code{C1} on the {j}-th source will be considered). If \code{C1.map == NULL} then effects for all covariates in \code{C1} will be considered in each of the sources. Note that \code{C1.map} is available only if \code{constrain_mu == TRUE}.}
       |                                                                                                                                                                                                                                                                                                                                                  ^
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Malformed Description field: should contain one or more complete sentences.
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Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/TDA.Rcheck/00install.out’ for details.
Specified C++11: please drop specification unless essential
Package required but not available: ‘TDA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/BH/include/boost/math/tools/config.hpp:23:6: warning: "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" [-W#warnings]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/teachingApps.Rcheck/00install.out’ for details.
* used C++ compiler: ‘Debian clang version 17.0.6 (3)’
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    66 | code{link{create_logo}}
       |     ^
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    66 | code{link{create_logo}}
       |          ^
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    68 | code{link{add_logo}}
       |     ^
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    68 | code{link{add_logo}}
       |          ^
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    32 | link{squaredError}
       |     ^
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    72 | \item{las}{numeric in {0,1,2,3}; the style of the axis labels. See \code{\link[graphics]{par}}.}
       |                       ^
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    27 | \item{las}{numeric in {0,1,2,3}; the style of the axis labels. See: \code{\link[graphics]{par}}}
       |                       ^
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Perhaps the ‘VignetteBuilder’ information is missing from the
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    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 }.
       |                               ^
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   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.}
       |                                                                                                             ^
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    18 | code{\link[ergm:blocks-ergmConstraint]{blocks}} constraints and
       |     ^
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     9 | code{discordance_fraction} of proposed toggles being made on the set of discordant dyads,
       |     ^
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    19 | \item{lsf}{objective function with limit state function in form of function(x) {x[1]+x[2]...}}
       |                                                                                ^
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    23 | \item{lsf}{objective function with limit state function in form of function(x) {x[1]+x[2]...}}
       |                                                                                ^
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    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
checkRd: (-1) lognormConstCVCI.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) normConstCVCI.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) normConstCVCI.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) normConstCVCI.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) testassay.Rd:32: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) testassay.Rd:33: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) testassay.Rd:34: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) testassay.Rd:35: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) testassay.Rd:36: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) testassay.Rd:37: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) testassay.Rd:38: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) testassay.Rd:39: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) testassay.Rd:40: Lost braces in \itemize; \value handles \item{}{} directly
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
'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.}
       |  ^
Specified C++11: please drop specification unless essential
checkRd: (-1) DivideFile.Rd:16: Lost braces
    16 | \item{document}{A character vector that includes \emph{every line} from \\begin{document} to the first \\end\{document\}} }
       |                                                                                ^
Documented arguments not in \usage in Rd file 'CompileLatexDir.Rd':
  ‘engine:’ ‘compile.dir:’

Documented arguments not in \usage in Rd file 'GetLayerSampleIndexes.Rd':
  ‘NamesOfListToSample’ ‘isRandomized’

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) 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}}
       |                                                    ^
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.
Rd file 'textEmbedReduce.Rd':
  \usage lines wider than 90 characters:
         "https://raw.githubusercontent.com/adithya8/ContextualEmbeddingDR/master/models/fb20/scalar.csv",
         "https://raw.githubusercontent.com/adithya8/ContextualEmbeddingDR/master/models/fb20/rpca_roberta_768_D_20.csv"

These lines will be truncated in the PDF manual.
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
       |                           ^
Objects in \usage without \alias in Rd file 'timeSeries.Rd':
  ‘tbind.timeSeries’

Objects in \usage without \alias in Rd file 'tis.Rd':
  ‘tfstart.tis’

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) 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: \&
checkRd: (-1) Kinship.Rd:23: Escaped LaTeX specials: \&
checkRd: (-1) T2func.Rd:44: Escaped LaTeX specials: \&
checkRd: (-1) T2funcrep.Rd:44: Escaped LaTeX specials: \&
checkRd: (-1) T3dimensionalityplot.Rd:18: Escaped LaTeX specials: \&
checkRd: (-1) T3func.Rd:43: Escaped LaTeX specials: \&
checkRd: (-1) T3func.Rd:44: Escaped LaTeX specials: \&
checkRd: (-1) T3funcrep.Rd:43: Escaped LaTeX specials: \&
checkRd: (-1) T3funcrep.Rd:44: Escaped LaTeX specials: \&
checkRd: (-1) TV.Rd:26: Escaped LaTeX specials: \& \& \&
checkRd: (-1) TV.Rd:30: Escaped LaTeX specials: \&
checkRd: (-1) TV.Rd:31: Escaped LaTeX specials: \&
checkRd: (-1) TV.Rd:32: Escaped LaTeX specials: \&
checkRd: (-1) TV.Rd:33: Escaped LaTeX specials: \&
checkRd: (-1) pcamean.Rd:33: Escaped LaTeX specials: \&
checkRd: (-1) threewayanova.Rd:24: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) 01-dataObjects.Rd:18-19: Lost braces
    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
checkRd: (-1) to_survey.Rd:25: Lost braces
    25 | Currently the only option is code{"rep_weights"}/.}
       |                                  ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'gate_interactive_chr_int.Rd':
  ‘gate_list’

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

Documented arguments not in \usage in Rd file 'gate_programmatic_chr_int.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.
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]+}
       |                                                 ^
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in Rd file 'deprecated-se.Rd':
  ‘expand_cols’

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

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 '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’
Auto-generated content requiring editing in Rd file 'timeperiodsR-package.Rd':
  \details: ‘...o use the package, including the most important functions ~~’
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
Package required but not available: ‘clusterProfiler’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'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
Package suggested but not available for checking: ‘RClickhouse’
Unknown package ‘RClickhouse’ in Rd xrefs
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
Specified C++14: please drop specification unless essential
checkRd: (-1) pmvn.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pmvn.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pmvn.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pmvt.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pmvt.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pmvt.Rd:25: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
checkRd: (-1) tv_episode_changes.Rd:29: Lost braces; missing escapes or markup?
    29 | This method is used in conjunction with the /tv/{id}/changes method. This method uses the episode_id value found in the change entries.
       |                                                 ^
checkRd: (-1) tv_season_changes.Rd:29: Lost braces; missing escapes or markup?
    29 | This method is used in conjunction with the /tv/{id}/changes method. This method uses the season_id value found in the change entries.
       |                                                 ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) estimateQ.Rd:22: Lost braces
    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.}
       |                                                                        ^
checkRd: (-1) tmle.Sl.dbarts2.Rd:26: Lost braces
    26 | \item{id}{id}{id to group observations, not used}
       |              ^
checkRd: (-1) tmle.Sl.dbarts2.Rd:51: Lost braces
    51 | {object}{an object of type tmle.SL.dbarts2 used internally by \code{Super Learner}}
       |         ^
checkRd: (-1) pvalEffectPlot.Rd:90: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pvalEffectPlot.Rd:91: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pvalEffectPlot.Rd:92: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pvalEffectPlot.Rd:93: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pvalEffectPlot.Rd:94: Lost braces in \itemize; meant \describe ?
Invalid package aliases in Rd file 'tm.plugin.alceste-package.Rd':
  ‘tm.plugin.europresse-package’
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'Rcampdf', 'tm.lexicon.GeneralInquirer'
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'TNRS_core.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.
Specified C++11: please drop specification unless essential
Packages required but not available: 'clusterProfiler', 'enrichplot'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) jsonStr.Rd:5: Lost braces; missing escapes or markup?
     5 | \title{Format data as a JSON object (like this: {"x": "120"}).}
       |                                                 ^
checkRd: (-1) jsonStr.Rd:18: Lost braces; missing escapes or markup?
    18 | Format data as a JSON object (like this: {"x": "120"}).
       |                                          ^
checkRd: (-1) fixed_width_no_modeling.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) fixed_width_no_modeling.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) fixed_width_no_modeling.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Data.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Data.Rd:11: Lost braces in \itemize; meant \describe ?
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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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Packages suggested but not available for checking:
  'RGtk2', 'gWidgets2RGtk2'
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    21 | \doi{10.1021/acs.est.7b01613}{Blackwell et al., 2017}.
       |                              ^
Documented arguments not in \usage in Rd file 'createLink.Rd':
  ‘hits’

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
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    33 | {param}. Supply as a named list, where the element name is the parameter.}
       | ^
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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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Unknown package ‘moveVis’ in Rd xrefs
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Argument items with no description in Rd file 'abrams.Rd':
  ‘prior’ ‘change’
Argument items with no description in Rd file 'absoluteIncreaseALL.Rd':
  ‘storedev’ ‘\dots’
Argument items with no description in Rd file 'boundaryLineALL.Rd':
  ‘\dots’
Argument items with no description in Rd file 'growthAveragingALL.Rd':
  ‘\dots’
Argument items with no description in Rd file 'plotFirstYears.Rd':
  ‘\dots’
Argument items with no description in Rd file 'plotRelease.Rd':
  ‘\dots’
Argument items with no description in Rd file 'splechtnaALL.Rd':
  ‘\dots’
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    46 | "Found {trans("file", .n = n_files)} in {trans("directory", .n = n_dirs)}".
       |        ^
checkRd: (-1) trans.Rd:46: Lost braces; missing escapes or markup?
    46 | "Found {trans("file", .n = n_files)} in {trans("directory", .n = n_dirs)}".
       |                                         ^
Specified C++11: please drop specification unless essential
Objects in \usage without \alias in Rd file 'transport-internal.Rd':
  ‘gif.generate’ ‘plot_pgrid_wpp’

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: ‘fwelnet’
'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:
  'Eunomia', 'CohortGenerator', 'CirceR', 'Capr'
checkRd: (-1) trtsel.Rd:69: Lost braces; missing escapes or markup?
    69 | numeric with two values {0,1} and gaussian(link = "identity") otherwise.
       |                         ^
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    75 | such as `{CG}` indicating either a C or G, which is not supported by any R interpreter,
       |          ^
Documented arguments not in \usage in Rd file 'clean_data.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.
checkRd: (-1) dcc.Rd:227: Escaped LaTeX specials: \&
checkRd: (-1) seascorr.Rd:128: Escaped LaTeX specials: \&
Documented arguments not in \usage in Rd file 'correct_continuous.Rd':
  ‘x’

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

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

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

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

Documented arguments not in \usage in Rd file 'truncate_input.Rd':
  ‘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.
checkRd: (-1) HiC2Tree.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
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Package suggested but not available for checking: ‘TreeDistData’
Specified C++11: please drop specification unless essential
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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 ...’
Specified C++11: please drop specification unless essential
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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}).}
       |                  ^
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GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) coef.tridim_transformation.Rd:31: Lost braces
    31 | If summary=TRUE, a data.frame with columns "dv{index}" with mean for each dependent
       |                                               ^
checkRd: (-1) coef.tridim_transformation.Rd:32: Lost braces
    32 | variable plus optional quantiles columns with names "dv{index}_{quantile}".
       |                                                        ^
checkRd: (-1) coef.tridim_transformation.Rd:32: Lost braces; missing escapes or markup?
    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
       |                                               ^
checkRd: (-1) predict.tridim_transformation.Rd:25: Lost braces
    25 | variable plus optional quantiles columns with names "dv{index}_{quantile}".
       |                                                        ^
checkRd: (-1) predict.tridim_transformation.Rd:25: Lost braces; missing escapes or markup?
    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
       |                  ^
checkRd: (-1) variable_summary.Rd:19: Lost braces; missing escapes or markup?
    19 | "{var_name}_{prob}" columns for each probability.
       |  ^
checkRd: (-1) variable_summary.Rd:19: Lost braces; missing escapes or markup?
    19 | "{var_name}_{prob}" columns for each probability.
       |             ^
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
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'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
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
  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.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘log2console’
checkRd: (-1) summary.armasubsets.Rd:16: Lost braces
    16 | \item{matrix.logical}{With matrix=TRUE, the matrix is logical TRUE/FALSE or string "*"/code{" "}}
       |                                                                                            ^
checkRd: (-1) tsBSS-package.Rd:23: Lost braces in \itemize; meant \describe ?
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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.
       |                      ^
checkRd: (-1) diss.AR.PIC.Rd:31: Lost braces; missing escapes or markup?
    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.
       |                      ^
Documented arguments not in \usage in Rd file 'dvinecopula_objective.Rd':
  ‘udata’

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

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
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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}.
       |                         ^
checkRd: (-1) regime.Rd:26: Lost braces; missing escapes or markup?
    26 | \item{discretize}{logical (default TRUE) whether the series are discretized to {1,2}, 
       |                                                                                ^
Objects in \usage without \alias in Rd file 'nlar.struct.Rd':
  ‘getNUsed’

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
S3 methods shown with full name in Rd file 'tsibble-vctrs.Rd':
  ‘vec_ptype2.tbl_ts’ ‘vec_cast.tbl_ts’ ‘vec_cast.yearmonth’
  ‘vec_ptype2.yearmonth’ ‘vec_cast.yearquarter’
  ‘vec_ptype2.yearquarter’ ‘vec_cast.yearweek’ ‘vec_ptype2.yearweek’

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
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Invalid package aliases in Rd file 'tsoutliers-package.Rd':
  ‘tsouliers-package’
'LazyData' is specified without a 'data' directory
checkRd: (-1) repr_dwt.Rd:28: Lost braces; missing escapes or markup?
    28 | The final representation has length equal to floor(n / 2^{level}), where n is a length of original time series.
       |                                                          ^
'LazyData' is specified without a 'data' directory
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checkRd: (-1) FULLoption.Rd:180: Lost braces; missing escapes or markup?
   180 |  (see the function {selectdirectory} more more informations)
       |                    ^
checkRd: (-1) fixdata.Rd:18: Lost braces; missing escapes or markup?
    18 | fixdata() call the function fix() that act on the rawdata base. The fix() function itself call the function edit() from the package {utils}
       |                                                                                                                                     ^
Invalid package aliases in Rd file 'TTAinterface-package.Rd':
  ‘TTAinterface-package’
'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
Package vignette with \VignetteEngine{} not specifying an engine package:
  ‘turner_introduction.Rnw’
Engines should be specified as \VignetteEngine{PKG::ENG}.
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Specified C++11: please drop specification unless essential
checkRd: (-1) tweedie-internal.Rd:74: Lost braces
    74 | 	doi{10.1093/biomet/74.2.221}
       |            ^
Specified C++11: please drop specification unless essential
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'LazyData' is specified without a 'data' directory
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checkRd: (-1) fit_stm.Rd:25: Lost braces
    25 | \item{xcov}{Either a \[stats]{formula} with an empty left-hand side specifying external covariates
       |                              ^
'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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    30 | \item{threshold_estimate_explanatory}{Point estimate of d_{0}}
       |                                                           ^
checkRd: (-1) threshold_estimate_ir.Rd:31: Lost braces; missing escapes or markup?
    31 | \item{threshold_estimate_response}{Estimate of f(d_{0}), which may not be 
       |                                                    ^
checkRd: (-1) twoway.Rd:66: Lost braces
    66 | code{\link{twoway.formula}}, code{\link[stats]{medpolish}}
       |     ^
checkRd: (-1) twoway.Rd:66: Lost braces
    66 | code{\link{twoway.formula}}, code{\link[stats]{medpolish}}
       |                                  ^
Package which this enhances but not available for checking: ‘sl3’
checkRd: (-1) est_g_exp.Rd:55: Lost braces; missing escapes or markup?
    55 |  {A - delta}, {A + delta}, and {A + 2 * delta}).
       |  ^
checkRd: (-1) est_g_exp.Rd:55: Lost braces; missing escapes or markup?
    55 |  {A - delta}, {A + delta}, and {A + 2 * delta}).
       |               ^
checkRd: (-1) est_g_exp.Rd:55: Lost braces; missing escapes or markup?
    55 |  {A - delta}, {A + delta}, and {A + 2 * delta}).
       |                                ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) cambodia.Rd:47: Lost braces
    47 | (\doi{10.1371/journal.pmed.1000253}{10.1371/journal.pmed.1000253})
       |                                    ^
checkRd: (-1) microdata.Rd:33: Lost braces
    33 | (\doi{10.1371/journal.pmed.1000253}{10.1371/journal.pmed.1000253})
       |                                    ^
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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)))})
       |                         ^
GNU make is a SystemRequirements.
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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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Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    uktrans_get is fixed when start_date is used (#2)
    Extra layer of of NULL returns to fail gracefully with an informative message.
    Removed travis & appveyor and using gh_actions instead.
    Using gh-pages to create the pkgdown website.
    Create an app as vignette page to search with the help of uklr.
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  ‘U’ ‘relabel_technique’ ‘w’ ‘X’ ‘distCriterion’ ‘K’ ‘GDM’
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  ‘X’ ‘K’ ‘distancemetric’ ‘iter.max’ ‘nstart’ ‘algorithm’ ‘trace’
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  ‘ref’ ‘input’ ‘technique’ ‘X’ ‘distCriterion’
Documented arguments not in \usage in Rd file 'sqrtm.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.
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  ‘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.
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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
       |              ^
Documented arguments not in \usage in Rd file 'use_course_details.Rd':
  ‘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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  ‘trascriptsTable’

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

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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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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    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
       |             ^
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    25 | data.frame of observations with additional column #' code{COVER_PERC}
       |                                                          ^
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    27 | author{Florian Jansen #' email{florian.jansen@uni-rostock.de} }
       |       ^
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    27 | author{Florian Jansen #' email{florian.jansen@uni-rostock.de} }
       |                               ^
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    26 | Journal of vegetation science, 21(6), 1179-1186. @url{http://dx.doi.org/10.1111/j.1654-1103.2010.01209.x}
       |                                                      ^
S3 methods shown with full name in Rd file 'syntab.Rd':
  ‘print.syntab’

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.
Documented arguments not in \usage in Rd file 'vein-deprecated.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.
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    51 | S = dbar/sqrt(2*pi*se_{d}(0)/N),
       |                       ^
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
       |                                                                                                                              ^
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:79: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fit.vfp.Rd:80: Lost braces in \itemize; meant \describe ?
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   597 |   Changes relating to the code{lss} argument have very important
       |                               ^
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    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.}
       |                    ^
Documented arguments not in \usage in Rd file 'boxplot_VICI.Rd':
  ‘res_2plot’

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) show_query.Rd:27: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) vietnamcode.Rd:28: Lost braces in \itemize; meant \describe ?
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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:52: Lost braces in \itemize; meant \describe ?
checkRd: (-1) viridis.Rd:53: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) viridis.map.Rd:13-14: Lost braces in \itemize; meant \describe ?
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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 ?
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checkRd: (-1) ViSiElse.Rd:105-106: Lost braces in \itemize; meant \describe ?
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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 ?
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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
Found the following significant warnings:
  /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/BH/include/boost/math/tools/config.hpp:23:6: warning: "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" [-W#warnings]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/vlad.Rcheck/00install.out’ for details.
* used C++ compiler: ‘Debian clang version 17.0.6 (3)’
Specified C++11: please drop specification unless essential
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’
Documented arguments not in \usage in Rd file 'cpp_vol2bird_version.Rd':
  ‘path’

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

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
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 ?
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checkRd: (-1) Data-Examples.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
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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 ?
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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 ?
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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
Documented arguments not in \usage in Rd file 'get.wal.mipmap.heights.Rd':
  ‘height_mm’

Documented arguments not in \usage in Rd file 'get.wal.mipmap.widths.Rd':
  ‘width_mm’

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) dyad.Rd:6: Lost braces; missing escapes or markup?
     6 | Returns a vector of integers $2^j+1,...,2^{j+1}$.
       |                                           ^
checkRd: (-1) dyad.Rd:19: Lost braces; missing escapes or markup?
    19 | Returns a vector of integers $2^j+1,...,2^{j+1}$.
       |                                           ^
checkRd: (-1) dyadjk.Rd:20: Lost braces; missing escapes or markup?
    20 | of the wavelet coefficient $w_{j,k}$ in a vector of wavelet 
       |                               ^
Documented arguments not in \usage in Rd file 'WaveDjF.Rd':
  ‘y_fft’

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.
Auto-generated content requiring editing in Rd file 'maxithresh.Rd':
  \details: ‘~~ If necessary, more details than the description above ~~’
  \arguments: data: ‘~~Describe \code{data} here~~’
  \arguments: g: ‘~~Describe \code{g} here~~’
  \arguments: L: ‘~~Describe \code{L} here~~’
  \arguments: F: ‘~~Describe \code{F} here~~’
  \arguments: eta: ‘~~Describe \code{eta} here~~’
'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
Error(s) in re-building vignettes:
  ...
--- re-building ‘multi-scale-assessment.Rmd’ using rmarkdown

Quitting from lines 121-126 [unnamed-chunk-8] (multi-scale-assessment.Rmd)
Error: processing vignette 'multi-scale-assessment.Rmd' failed with diagnostics:
Cannot open "/tmp/RtmpsowPqy"; The source could be corrupt or not supported. See `st_drivers()` for a list of supported formats.
--- failed re-building ‘multi-scale-assessment.Rmd’

--- re-building ‘residual-autocorrelation.Rmd’ using rmarkdown
--- finished re-building ‘residual-autocorrelation.Rmd’

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

SUMMARY: processing the following file failed:
  ‘multi-scale-assessment.Rmd’

Error: Vignette re-building failed.
Execution halted
checkRd: (-1) plot_wbaconmv.Rd:23: Lost braces
    23 |     \item{pch}{plot character of outliers, code{[integer]} (default:
       |                                                ^
Invalid package aliases in Rd file 'wce-package.Rd':
  ‘wce-package’
'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
Documented arguments not in \usage in Rd file 'remove_empty.Rd':
  ‘quiet’

Documented arguments not in \usage in Rd file 'undoHistory.Rd':
  ‘class’ ‘btn_class’ ‘back_text’ ‘fwd_text’ ‘back_title’ ‘fwd_title’
  ‘back_icon’ ‘fwd_icon’

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) get.deriv.smooth.hist.Rd:5: Lost braces; missing escapes or markup?
     5 | \title{Gets $n^{th}$ derivative of smoothed histogram}
       |                ^
Package suggested but not available for checking: ‘rgdal’
Documented arguments not in \usage in Rd file 'displayDataTable.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
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’
Running examples in ‘wikkitidy-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: xtools_page
> ### Title: Access page-level statistics from the XTools Page API endpoint
> ### Aliases: xtools_page get_xtools_page_info get_xtools_page_prose
> ###   get_xtools_page_links get_xtools_page_top_editors
> ###   get_xtools_page_assessment
> 
> ### ** Examples
> 
> # Get basic statistics about Erich Auerbach on German Wikipedia
> auerbach <- get_xtools_page_info("Erich Auerbach", language = "de")
Error in `purrr::pmap()`:
ℹ In index: 1.
Caused by error in `_fn`:
! Failed to perform HTTP request.
Caused by error in `curl::curl_fetch_memory()`:
! Timeout was reached: [xtools.wmflabs.org] Resolving timed out after 10000 milliseconds
Backtrace:
     ▆
  1. ├─wikkitidy::get_xtools_page_info("Erich Auerbach", language = "de")
  2. │ └─wikkitidy:::get_rest_resource(...)
  3. │   └─purrr::pmap(params, get_one, .progress = T)
  4. │     └─purrr:::pmap_("list", .l, .f, ..., .progress = .progress)
  5. │       ├─purrr:::with_indexed_errors(...)
  6. │       │ └─base::withCallingHandlers(...)
  7. │       ├─purrr:::call_with_cleanup(...)
  8. │       └─purrr (local) .f(...)
  9. └─httr2 (local) `_fn`(`_out`)
 10.   └─base::tryCatch(...)
 11.     └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 12.       └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 13.         └─value[[3L]](cond)
Execution halted
'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
checkRd: (-1) predict_race.Rd:132: Lost braces in \itemize; meant \describe ?
checkRd: (-1) predict_race.Rd:133: Lost braces in \itemize; meant \describe ?
checkRd: (-1) predict_race.Rd:134: Lost braces in \itemize; meant \describe ?
checkRd: (-1) predict_race.Rd:135: Lost braces in \itemize; meant \describe ?
checkRd: (-1) predict_race.Rd:136: Lost braces in \itemize; meant \describe ?
Documented arguments not in \usage in Rd file 'sample_me.Rd':
  ‘middle_name’ ‘M_rs’ ‘M_rf’ ‘M_rm’ ‘alpha’ ‘me_race’

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
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 ?
'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.
checkRd: (-1) read_nm_model.Rd:34: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) read_nm_model.Rd:35: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) read_nm_model.Rd:36-39: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) read_nm_model.Rd:40: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) read_nm_model.Rd:41: Lost braces in \itemize; \value handles \item{}{} directly
Documented arguments not in \usage in Rd file 'check_problem.Rd':
  ‘xpdb’

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) xts.Rd:39: Lost braces
    39 |   \item{tclass}{ time class to use for the index. See code{\link{tclass}}. }
       |                                                           ^
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
checkRd: (-1) brier_survival.Rd:21: Lost braces; missing escapes or markup?
    21 | predicting with {censored} model. This should be an unquoted column name
       |                 ^
checkRd: (-1) brier_survival_integrated.Rd:27: Lost braces; missing escapes or markup?
    27 | predicting with {censored} model. This should be an unquoted column name
       |                 ^
checkRd: (-1) roc_curve_survival.Rd:18: Lost braces; missing escapes or markup?
    18 | predicting with {censored} model. This should be an unquoted column name
       |                 ^
'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
checkRd: (-1) abclass.Rd:133: Lost braces; missing escapes or markup?
   133 |     \code{abclass.control()} returns an object of class {abclass.control}
       |                                                         ^
checkRd: (-1) supclass.Rd:109: Lost braces; missing escapes or markup?
   109 | to solve the equivalent linear programming problem via the package {Rglpk}.
       |                                                                    ^
checkRd: (-1) supclass.Rd:110: Lost braces; missing escapes or markup?
   110 | It is recommended to use a recent version of {GLPK}.
       |                                              ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) abess.Rd:260: Lost braces in \itemize; meant \describe ?
checkRd: (-1) abess.Rd:261: Lost braces in \itemize; meant \describe ?
checkRd: (-1) abess.Rd:262: Lost braces in \itemize; meant \describe ?
checkRd: (-1) abess.Rd:263: Lost braces in \itemize; meant \describe ?
checkRd: (-1) coef.abesspca.Rd:16: Lost braces; missing escapes or markup?
    16 | This parameter is omitted if {sparse.type = "kpc"}.}
       |                              ^
checkRd: (-1) coef.abesspca.Rd:22: Lost braces; missing escapes or markup?
    22 | This parameter is omitted if {sparse.type = "fpc"}.}
       |                              ^
checkRd: (-1) generate.data.Rd:51: Lost braces
    51 | code{cortype = 3} denotes the constant structure,
       |     ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) get_ex_data.Rd:31-32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) get_ex_data.Rd:33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) get_ex_data.Rd:34-35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) get_ex_data.Rd:36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tidy_results.Rd:28-29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tidy_results.Rd:30: 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
checkRd: (-1) bind_tweets.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bind_tweets.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) accelimp.Rd:15: Lost braces
    15 | \item[]{...}
       |        ^
Found the following files/directories:
  ‘acceldata2.RData’
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’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) overstallwoods.Rd:184-185: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) overstallwoods.Rd:186-187: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) overstallwoods.Rd:188-189: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) overstallwoods.Rd:190-191: 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
Documented arguments not in \usage in Rd file 'fitSnpNmfArray.Rd':
  ‘maxIter’ ‘acc’

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) Ehrenfest.Rd:19: Lost braces
    19 | In this experiment there are i balls in Urn I, and remaining 2n-i balls in Urn II. Then at any instance, the probability of selecting a ball from Urn I and placing it in Urn II is i/2n, and the other way of placing a ball from Urn II to Urn I is (2n-i)/2n. At each instant we let the number i of balls in the Urn I to be the state of the system. Thus, the state space is S = { 0, 1, 2, \ldots, 2n }. Then we can pass from state i only to either of the states i-1 or i+1.
       |                                                                                                                                                                                                                                                                                                                                                                                        ^
checkRd: (-1) Ehrenfest.Rd:20: Lost braces
    20 | Here, S = {0, 1, \ldots, 2n}. 
       |           ^
Problems with news in ‘NEWS.md’:
No news entries found.
Problems with news in ‘NEWS.md’:
No news entries found.
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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘Example.jpeg’
checkRd: (-1) est_S_Plus_Plus_MethodA.Rd:31: Lost braces; missing escapes or markup?
    31 |   \item{trt_diff}{Estimate of treatment difference for S_{++} using Method A}
       |                                                          ^
checkRd: (-1) est_S_Plus_Plus_MethodB.Rd:31: Lost braces; missing escapes or markup?
    31 |   \item{trt_diff}{Estimate of treatment difference for S_{++} using Method B}
       |                                                          ^
checkRd: (-1) est_S_Star_Plus_MethodA.Rd:29: Lost braces; missing escapes or markup?
    29 |   \item{trt_diff}{Estimate of treatment difference for S_{++} using Method A}
       |                                                          ^
checkRd: (-1) est_S_Star_Plus_MethodB.Rd:29: Lost braces; missing escapes or markup?
    29 |   \item{trt_diff}{Estimate of treatment difference for S_{*+} using Method B}
       |                                                          ^
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) adana.Rd:25: Lost braces; missing escapes or markup?
    25 |   \item{gatype}{Type of GA. \itemize{\item{"gga": generational GA}  \item{"ssga": steady state GA} } {Default value is "gga"}}
       |                                                                                                      ^
checkRd: (-1) adana.Rd:26: Lost braces; missing escapes or markup?
    26 |   \item{objective}{Type of optimization. \itemize{\item{"min": minimization}  \item{"max": maximization} } {Default value is "max"}}
       |                                                                                                            ^
checkRd: (-1) adana.Rd:34: Lost braces; missing escapes or markup?
    34 |                  {Default value is "initbin"}}
       |                  ^
checkRd: (-1) adana.Rd:56: Lost braces; missing escapes or markup?
    56 |                \itemize{\item{"integer"}  \item{"real"} } {Default value is "real"}}
       |                                                           ^
checkRd: (-1) adana.Rd:185: Lost braces; missing escapes or markup?
   185 |     {Default value is "w"}
       |     ^
'LazyData' is specified without a 'data' directory
Invalid package aliases in Rd file 'AdaptGauss-package.Rd':
  ‘MultiModal-package’
checkRd: (-1) aslm-methods.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) aslm-methods.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) aslm-methods.Rd:13: Lost braces in \itemize; meant \describe ?
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’
Specified C++11: please drop specification unless essential
Unknown packages ‘HI’, ‘MHadaptive’ in Rd xrefs
checkRd: (-1) adapt.Rd:46: Lost braces
    46 | \item{qvals}{a vector of values in [0, 1]U{Inf}. Q-values. See Details}
       |                                           ^
checkRd: (-1) corr_lfdr.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) corr_lfdr.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) corr_lfdr.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) corr_lfdr.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) corr_lfdr.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ctgm_lfdr.Rd:32: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ctgm_lfdr.Rd:33: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) plot_2d.Rd:40: Lost braces; missing escapes or markup?
    40 | \code{plot_2d_lfdr} gives the contour plot of local FDR estimates when all p-values are equal to \code{targetp}. It is recommended to run \code{plot_2d_lfdr} for multiple \code{targetp}'s ranging from {0.001, 0.005, 0.01, 0.05}.
       |                                                                                                                                                                                                          ^
checkRd: (-1) SVMDECON.Rd:23: Lost braces; missing escapes or markup?
    23 | and the best result from three values of v = {0.25, 0.5, 0.75}
       |                                              ^
checkRd: (-1) ada.Rd:171: Escaped LaTeX specials: \&
Running ‘testthat.R’ [2s/4s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  > library(adbi)
  > 
  > test_check("adbi")
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 9 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-show.R:23:3'): show methods print ──────────────────────────────
  <adbc_error_child_count_not_zero/simpleError/error/condition>
  Error in `adbcdrivermanager::adbc_connection_release(conn@connection)`: <adbcsqlite_connection/adbc_connection/adbc_xptr> has 1 unreleased child object
  Backtrace:
       ▆
    1. ├─testthat::expect_warning(dbDisconnect(con, force = TRUE)) at test-show.R:23:3
    2. │ └─testthat:::quasi_capture(...)
    3. │   ├─testthat (local) .capture(...)
    4. │   │ └─base::withCallingHandlers(...)
    5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
    6. ├─DBI::dbDisconnect(con, force = TRUE)
    7. └─adbi::dbDisconnect(con, force = TRUE)
    8.   └─adbi (local) .local(conn, ...)
    9.     └─adbcdrivermanager::adbc_connection_release(conn@connection)
   10.       └─adbcdrivermanager:::stop_for_nonzero_child_count(connection)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 9 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) additive.Rd:140: Lost braces
   140 | \item{gamma}{Increase this beyond 1 to produce smoother models. \code{gamma} multiplies the effective degrees of freedom in the GCV or UBRE/AIC. code{n/gamma} can be viewed as an effective sample size in the GCV score, and this also enables it to be used with REML/ML. Ignored with P-RE/ML or the \code{efs} optimizer. }
       |                                                                                                                                                      ^
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
checkRd: (-1) varipart.Rd:19: Lost braces
    19 | \item{type}{a character specifying the algorithm which should be used to adjust R-squared (either \code{"simulated"} or \ code{"parametric"}).}
       |                                                                                                                               ^
checkRd: (-1) adeoptions.Rd:21-23: Lost braces
    21 |   \code{epsilon}{  the smallest significant distance between two points
       |                 ^
checkRd: (-1) adeoptions.Rd:25-27: Lost braces
    25 |   \code{shortprint}{  logical.  Defines whether special \code{show}
       |                    ^
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.
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
checkRd: (-1) med.groups.Rd:20: Lost braces; missing escapes or markup?
    20 | medication groups using the construction \emph{"{NAME}"}.
       |                                                 ^
checkRd: (-1) med.groups.Rd:26: Lost braces; missing escapes or markup?
    26 | Another example is "NotVita" defined as "(!{Vitamines})", which selects all
       |                                            ^
Package vignette without corresponding tangle output:
  ‘adivGuide.Rnw’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) Amatdual.Rd:15: Lost braces
    15 |   \item{removelist}{a vector of indices into env{X} of the lifted coefficients during the transform (in the order of removal). }
       |                                                 ^
checkRd: (-1) fwtnp.Rd:30: Lost braces
    30 | 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. 
       |                                                                           ^
'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
'LazyData' is specified without a 'data' directory
checkRd: (-1) count_cases.Rd:49: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) count_cases.Rd:50: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) count_cases.Rd:51: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) count_cases.Rd:52: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) count_cases.Rd:53: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) enrich.Rd:75: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) enrich.Rd:76: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) enrich.Rd:77: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) enrich.Rd:78: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) enrich.Rd:83: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) enrich.Rd:84: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) enrich.Rd:85: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) enrich.Rd:86: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) enrich.Rd:87: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) enrich.Rd:88: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) fitaep.Rd:14: Lost braces
    14 | \item A sequence of goodness-of-fit measures consist of Akaike Information Criterion (\code{AIC}), Consistent Akaike Information Criterion (\code{CAIC}), Bayesian Information Criterion (\code{BIC}), Hannan-Quinn information criterion (\code{HQIC}), Anderson-Darling (\code{AD}), Cram\'{e}er-von Misses (\code{CVM}), Kolmogorov-Smirnov (\code{KS}), and log-likelihood (\code{log-likelihood}) statistics.
       |                                                                                                                                                                                                                                                                                              ^
Found the following files/directories:
  ‘table_AeRobiology’
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) estimate.affinity.matrix.Rd:31: Lost braces; missing escapes or markup?
    31 | than \code{Y}, then those variables that appear in \code{X} but no in {Y}
       |                                                                       ^
checkRd: (-1) estimate.affinity.matrix.lowrank.Rd:36: Lost braces; missing escapes or markup?
    36 | \code{Y}, then those variables that appear in \code{X} but no in {Y} should
       |                                                                  ^
checkRd: (-1) show.correlations.Rd:47: Lost braces
    47 | code{ndims} dimensions. Defaults to all dimensions unless the latter are
       |     ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) gini.w.Rd:20: Lost braces; missing escapes or markup?
    20 | where \eqn{x_i,x_j} are incomes of individuals \eqn{i} and {j}, respectively, \eqn{n} is the number of individuals, \eqn{\mu_w} is the mean income. The Gini coefficient ranges between 1 (perfect equality) and 1 (perfect inequality).
       |                                                            ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) getNetworkGridLayout.Rd:6-11: Lost braces
     6 | getCoordinatesFromVertexId2<-function(AFMImage, vId) {
       |                                                      ^
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
Package suggested but not available for checking: ‘rgdal’
checkRd: (-1) battese.survey.Rd:42: Lost braces
    42 |   emph{Journal of the American Statistical Association}, 83, 28-36.
       |       ^
checkRd: (-1) butron.maize.Rd:49: Lost braces
    49 |   Butron, A and Velasco, P and Ord{\'a}s, A and Malvar, RA (2004).
       |                                   ^
Package which this enhances but not available for checking: ‘asreml’
Specified C++11: please drop specification unless essential
checkRd: (-1) h2o_train.Rd:108: Lost braces
   108 | \item{mtries}{Number of variables randomly sampled as candidates at each split. If set to -1, defaults to sqrt{p} for
       |                                                                                                               ^
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
'LazyData' is specified without a 'data' directory
checkRd: (-1) AEHMLE.Rd:42-45: Lost braces
    42 | \item{basehaz}{: {baseline hazard structure including baseline
       |                  ^
checkRd: (-1) AHMLE.Rd:41-43: Lost braces
    41 | \item{basehaz}{: {baseline hazard structure including baseline
       |                  ^
checkRd: (-1) CalOptimalDecision.Rd:45: Lost braces; missing escapes or markup?
    45 | A \code{data.frame} of (1) the probability that the optimal decision for each observation being d in {0,1,...,k}, (2) expected utility of binary version of judge's decision (g_d), (3) expected utility of binary DMF recommendation, and (4) the difference between (2) and (3). If \code{include.utility.diff.mcmc = TRUE}, returns a list of such \code{data.frame} and a \code{data.frame} that includes the result for mean and quantile of \code{Utility.diff.control.mcmc} and \code{Utility.diff.treated.mcmc} across mcmc samples.
       |                                                                                                      ^
checkRd: (-1) aimPlot.Rd:39: Lost braces; missing escapes or markup?
    39 |  \item \code{Variable} {1st column: The various aims to be completed}
       |                        ^
checkRd: (-1) aimPlot.Rd:40: Lost braces; missing escapes or markup?
    40 |  \item \code{Percentage} {2nd column: The percentage of completeness}
       |                          ^
Invalid package aliases in Rd file 'aire.zmvm-deprecated.Rd':
  ‘aire.zmvm-deprecated-package’
checkRd: (-1) CreateInputsPert.Rd:65: Lost braces
    65 | \emph{InputsPert}{[list] object of class \emph{InputsModel} containing the ensembles of perturbed model inputs required to perform data assimilation:}
       |                  ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) monitor_combine.Rd:14: Lost braces
    14 | \item{...}{Any number of valid emph{mts_monitor} objects or a list of objects.}
       |                                    ^
checkRd: (-1) monitor_leaflet.Rd:60: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) monitor_leaflet.Rd:61: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) monitor_leaflet.Rd:62: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) monitor_leaflet.Rd:63: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) monitor_nowcast.Rd:32: Lost braces; missing escapes or markup?
    32 | \item{\code{pm}}: {hours = 12, weight = 0.5}
       |                   ^
checkRd: (-1) monitor_nowcast.Rd:33: Lost braces; missing escapes or markup?
    33 | \item{\code{pmAsian}}: {hours = 3, weight = 0.1}
       |                        ^
checkRd: (-1) monitor_nowcast.Rd:34: Lost braces; missing escapes or markup?
    34 | \item{\code{ozone}}: {hours = 8, weight = NA}
       |                      ^
checkRd: (-1) monitor_replaceValues.Rd:12: Lost braces
    12 | \item{filter}{\R{R} expression used to identify values for replacement.}
       |                 ^
checkRd: (-1) get_airnow_area.Rd:25: Lost braces; missing escapes or markup?
    25 | \item{parameters}{Parameter(s) to return data for. Choices are PM_{2.5}
       |                                                                   ^
Found the following files/directories:
  ‘stuve.pdf’
'LazyData' is specified without a 'data' directory
checkRd: (-1) plot.dke.fun.Rd:33: Lost braces; missing escapes or markup?
    33 |   \item{las}{ Numeric in {0,1,2,3}; the style of axis labels. 
       |                          ^
checkRd: (-1) interpp.Rd:119: Lost braces
   119 |   If \code{linear} is \\code{TRUE}, linear
       |                             ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) buildPhylipLineage.Rd:61: Lost braces; missing escapes or markup?
    61 |                                      names with the format {"Inferred1", "Inferred2", ...}.
       |                                                            ^
checkRd: (-1) ALF.Rd:47: Escaped LaTeX specials: \&
checkRd: (-1) APEXMS.Rd:14: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) APEXMS.Rd:15: Lost braces in \enumerate; meant \describe ?
'LazyData' is specified without a 'data' directory
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
checkRd: (-1) amDataset.Rd:28: Lost braces
    28 | 		A code{matrix} or \code{data.frame} containing samples in rows and alleles in columns.\cr
       |                       ^
checkRd: (-1) ASBT.Rd:36-37: Lost braces
    36 | \item{method}{Method for aggregating across categories: {"none", "max",
       |                                                         ^
checkRd: (-1) Aggregator.Rd:26: Lost braces; missing escapes or markup?
    26 | {"none", "max", "sum"}. Default: "none".}
       | ^
checkRd: (-1) DGP.Rd:72: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DGP.Rd:73: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DGP.Rd:74: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DGP.Rd:75: Lost braces in \itemize; meant \describe ?
checkRd: (-1) OLS.Rd:17: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) OLS.Rd:18: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) OLS.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) OLS.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) allestimates.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) allestimates.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) allestimates.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) allestimates.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) compare_cohorts.Rd:35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) compare_cohorts.Rd:36: Lost braces in \itemize; meant \describe ?
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'gs.Rd':
  ‘x’ ‘parallel’

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) UN1.Rd:16: Escaped LaTeX specials: \$
checkRd: (-1) rateprof.Rd:64: Escaped LaTeX specials: \&
Malformed Title field: should not end in a period.
checkRd: (-1) 6_ci.reg.Rd:23: Lost braces
    23 | Interval Estimation of E{Y_h}
       |                         ^
Argument items with no description in Rd file 'MLS.Rd':
  ‘MSE1’
'LazyData' is specified without a 'data' directory
checkRd: (-1) altopt.ic.Rd:63: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) altopt.ic.Rd:64: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) altopt.ic.Rd:65: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) altopt.ic.Rd:66: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) altopt.ic.Rd:67: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) altopt.ic.Rd:68: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) altopt.ic.Rd:69: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) altopt.rc.Rd:60: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) altopt.rc.Rd:61: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) altopt.rc.Rd:62: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) altopt.rc.Rd:63: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) altopt.rc.Rd:64: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) altopt.rc.Rd:65: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) altopt.rc.Rd:66: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) convertCoord.Rd:32: Lost braces
    32 | Please check here{https://lbs.amap.com/faq/account/key/72}}
       |                  ^
checkRd: (-1) convertCoord.individual.Rd:33: Lost braces
    33 | Please check here{https://lbs.amap.com/faq/account/key/72}}
       |                  ^
checkRd: (-1) getCoord.Rd:39: Lost braces
    39 | Please check here{https://lbs.amap.com/faq/account/key/72}}
       |                  ^
checkRd: (-1) getCoord.individual.Rd:39: Lost braces
    39 | here{https://lbs.amap.com/faq/account/key/72}}
       |     ^
checkRd: (-1) getLocation.Rd:60: Lost braces; missing escapes or markup?
    60 | {https://lbs.amap.com/faq/account/key/72}}
       | ^
checkRd: (-1) getLocation.individual.Rd:60: Lost braces
    60 | Please check here{https://lbs.amap.com/faq/account/key/72}}
       |                  ^
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.
'LazyData' is specified without a 'data' directory
checkRd: (-1) aMNLFA.prune.Rd:15: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) aMNLFA.prune.Rd:16: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) aMNLFA.prune.Rd:17: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) aMNLFA.prune.Rd:18: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) aMNLFA.prune.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) aMNLFA.prune.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) aMNLFA.prune.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) aMNLFA.prune.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
checkRd: (-1) AmpliconDuo-package.Rd:37-39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) AmpliconDuo-package.Rd:40-42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) AmpliconDuo-package.Rd:43-46: Lost braces in \itemize; meant \describe ?
checkRd: (-1) AmpliconDuo-package.Rd:47-49: Lost braces in \itemize; meant \describe ?
checkRd: (-1) AmpliconDuo-package.Rd:50-52: Lost braces in \itemize; meant \describe ?
checkRd: (-1) AmpliconDuo-package.Rd:53-55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) AmpliconDuo-package.Rd:56-58: Lost braces in \itemize; meant \describe ?
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
'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: \~
checkRd: (-1) EKF_1d_interp_joint.Rd:55: Lost braces; missing escapes or markup?
    55 | Prior 1x1 covariance matrix for predicting x_t from x_{t-1}.
       |                                                       ^
checkRd: (-1) EKF_interp_joint.Rd:65: Lost braces; missing escapes or markup?
    65 | Prior 2x2 covariance matrix for predicting x_t from x_{t-1}.
       |                                                       ^
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) animate.Rd:625-627: Lost braces
   625 | group = function(...) {
       |                       ^
Documented arguments not in \usage in Rd file 'crawl_interpolation.Rd':
  ‘pt.colors’

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
checkRd: (-1) concat.Rd:35: Lost braces; missing escapes or markup?
    35 | \item{index_unique}{Whether to make the index unique by using the keys. If provided, this is the delimeter between "{orig_idx}{index_unique}{key}". When \code{NULL}, the original indices are kept.}
       |                                                                                                                     ^
checkRd: (-1) concat.Rd:35: Lost braces
    35 | \item{index_unique}{Whether to make the index unique by using the keys. If provided, this is the delimeter between "{orig_idx}{index_unique}{key}". When \code{NULL}, the original indices are kept.}
       |                                                                                                                               ^
checkRd: (-1) concat.Rd:35: Lost braces
    35 | \item{index_unique}{Whether to make the index unique by using the keys. If provided, this is the delimeter between "{orig_idx}{index_unique}{key}". When \code{NULL}, the original indices are kept.}
       |                                                                                                                                             ^
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: \_ \_
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) aggregatate_mc_all.Rd:40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) aggregatate_mc_all.Rd:41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) aggregatate_mc_all.Rd:42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) PS-methods.Rd:61: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) PS-methods.Rd:62: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) PS-methods.Rd:63: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) PS-methods.Rd:64: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) PS-methods.Rd:65-67: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Sim-Functions.Rd:126: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Sim-Functions.Rd:127-129: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Sim-Functions.Rd:135: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Sim-Functions.Rd:136-137: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Sim-Functions.Rd:138-140: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Sim-Functions.Rd:141-143: 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
Specified C++11: please drop specification unless essential
checkRd: (-1) gof.Rd:32: Lost braces
    32 | Assuming that the data length is \eqn{N} and the number of the parameters in the model is \eqn{p}, eqn{D} and eqn{X^2} are compared to a chi-squared distribution with \eqn{N-p} degrees of freedom.
       |                                                                                                       ^
checkRd: (-1) gof.Rd:32: Lost braces
    32 | Assuming that the data length is \eqn{N} and the number of the parameters in the model is \eqn{p}, eqn{D} and eqn{X^2} are compared to a chi-squared distribution with \eqn{N-p} degrees of freedom.
       |                                                                                                                  ^
checkRd: (-1) iccbin.Rd:23: Lost braces
    23 |   \item{m}{A vector of the numbers of successes (proportions are eqn{y = m / n}).}
       |                                                                     ^
checkRd: (-1) varbin.Rd:22: Lost braces
    22 |   \item{m}{A vector of the numbers of successes (proportions are eqn{y = m / n}).}
       |                                                                     ^
Documented arguments not in \usage in Rd file 'alternate.sol3.Rd':
  ‘lambda0’

Documented arguments not in \usage in Rd file 'check.group.Rd':
  ‘k’

Documented arguments not in \usage in Rd file 'getrow3.Rd':
  ‘lambda0’

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.
Specified C++11: please drop specification unless essential
Argument items with no description in Rd file 'apci.Rd':
  ‘\dots’
Argument items with no description in Rd file 'apci.bar.Rd':
  ‘\dots’
Argument items with no description in Rd file 'apci.plot.Rd':
  ‘\dots’
Argument items with no description in Rd file 'apci.plot.heatmap.Rd':
  ‘\dots’
Argument items with no description in Rd file 'apci.plot.hexagram.Rd':
  ‘first_age’ ‘first_period’ ‘interval’ ‘first_age_isoline’
  ‘first_period_isoline’ ‘isoline_interval’ ‘line_width’ ‘line_color’
  ‘label_size’ ‘label_color’ ‘scale_units’ ‘wrap_cohort_labels’
  ‘quantile’
Argument items with no description in Rd file 'apci.plot.raw.Rd':
  ‘\dots’
Argument items with no description in Rd file 'cohortdeviation.Rd':
  ‘\dots’
Argument items with no description in Rd file 'compute_xcoordinate.Rd':
  ‘p’
Argument items with no description in Rd file 'compute_ycoordinate.Rd':
  ‘p’ ‘a’
Argument items with no description in Rd file 'maineffect.Rd':
  ‘\dots’
Argument items with no description in Rd file 'temp_model.Rd':
  ‘\dots’
Argument items with no description in Rd file 'tests.Rd':
  ‘\dots’
checkRd: (-1) apc.indiv.est.model.Rd:142: Lost braces
   142 | For model testing: \code{\link{apc.indiv.model.table}}, code{\link{apc.indiv.compare.direct}}, \code{\link{waldtest}}, \code{\link{linearHypothesis}}
       |                                                             ^
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
checkRd: (-1) aphylo-class.Rd:28: Lost braces; missing escapes or markup?
    28 | \item{tip.type, node.type}{Integer vectors with values {0,1}. 0 denotes duplication node and 1 speciation node. This is used in \link{LogLike}.}
       |                                                        ^
checkRd: (-1) raphylo.Rd:33: Lost braces; missing escapes or markup?
    33 | \item{tip.type, node.type}{Integer vectors with values {0,1}. 0 denotes duplication node and 1 speciation node. This is used in \link{LogLike}.}
       |                                                        ^
checkRd: (-1) sim_fun_on_tree.Rd:24: Lost braces; missing escapes or markup?
    24 | \item{tip.type, node.type}{Integer vectors with values {0,1}. 0 denotes duplication node and 1 speciation node. This is used in \link{LogLike}.}
       |                                                        ^
checkRd: (-1) predict_adjust.Rd:77: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) predict_adjust.Rd:78: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) predict_adjust.Rd:79: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) predict_adjust.Rd:80: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) print.predict_adjust.Rd:32: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) print.predict_adjust.Rd:33: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) print.predict_adjust.Rd:34: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) print.predict_adjust.Rd:35: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) iconplot.Rd:172: Lost braces
   172 |     the height of the area containing the panels and a margin of size code{100 * 0.1} 
       |                                                                           ^
Found the following calls to attach():
File ‘apollo/R/apollo_attach.R’:
  attach(as.list(apollo_beta), warn.conflicts = FALSE)
  attach(database, warn.conflicts = FALSE)
  attach(draws, warn.conflicts = FALSE)
  attach(randcoeff, warn.conflicts = FALSE)
  attach(lcpars, warn.conflicts = FALSE)
See section ‘Good practice’ in ‘?attach’.
checkRd: (-1) apple_apps.Rd:22: Lost braces; missing escapes or markup?
    22 | with a corresponding ID that can be used in {appler} functions.
       |                                             ^
checkRd: (-1) get_apple_reviews.Rd:38: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get_apple_reviews.Rd:39: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get_apple_reviews.Rd:40: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get_apple_reviews.Rd:41: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get_apple_reviews.Rd:42: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get_apple_reviews.Rd:43: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get_apple_reviews.Rd:44: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) itunes_artists.Rd:22: Lost braces; missing escapes or markup?
    22 | a corresponding ID that can be used in {appler} functions.
       |                                        ^
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
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’
checkRd: (-1) isolate.signal.Rd:79-81: Lost braces in \itemize; meant \describe ?
checkRd: (-1) isolate.signal.Rd:82-86: Lost braces in \itemize; meant \describe ?
checkRd: (-1) isolate.signal.Rd:87-94: Lost braces in \itemize; meant \describe ?
checkRd: (-1) calcEto.Rd:63-64: Lost braces
    63 | \code{ET.Daily:} {daily estimations of reference crop evapotranspiration
       |                  ^
checkRd: (-1) calcEto.Rd:66-67: Lost braces
    66 | \code{Ra.Daily:} {daily estimations of extraterristrial radiation
       |                  ^
checkRd: (-1) calcEto.Rd:69-70: Lost braces
    69 | \code{Slope.Daily:} {daily estimations of slope of vapour pressure curve
       |                     ^
checkRd: (-1) calcEto.Rd:72: Lost braces; missing escapes or markup?
    72 | \code{ET.type:} {type of the estimation obtained}
       |                 ^
checkRd: (-1) getages.Rd:11: Lost braces; missing escapes or markup?
    11 | containing the amalgamated $^{40}$Ar$^*$/$^{39}$Ar$_K$-ratios and
       |                              ^
checkRd: (-1) getages.Rd:11: Lost braces; missing escapes or markup?
    11 | containing the amalgamated $^{40}$Ar$^*$/$^{39}$Ar$_K$-ratios and
       |                                            ^
Package suggested but not available for checking: ‘arcgisbinding’
checkRd: (-1) MultiPhasesTransition.Rd:23: Lost braces
    23 | code{position_minimum}.}
       |     ^
checkRd: (-1) find_closer_points.Rd:41: Lost braces
    41 |   \item rows_closer_matrix, a matrix with ]code{npoints} rows  which are closer to each archetype
       |                                                ^
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘TDA’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) estimate_t0.Rd:41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) estimate_t0.Rd:42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) estimate_t0.Rd:43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fitArCo.Rd:73: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fitArCo.Rd:74: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fitArCo.Rd:75: Lost braces in \itemize; meant \describe ?
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’.
Argument items with no description in Rd file 'dynamac_pkg_bounds_test.Rd':
  ‘obs’ ‘fstat’ ‘tstat’ ‘case’ ‘k’
checkRd: (-1) recm.Rd:55: Lost braces; missing escapes or markup?
    55 | {In all cases,} \eqn{x_{j,t-1}} {in} \eqn{ECT} {is replaced by} \eqn{x_{j,t} \;\;\;\;\; \forall \;\; q_{j} = 0}
       | ^
checkRd: (-1) recm.Rd:55: Lost braces; missing escapes or markup?
    55 | {In all cases,} \eqn{x_{j,t-1}} {in} \eqn{ECT} {is replaced by} \eqn{x_{j,t} \;\;\;\;\; \forall \;\; q_{j} = 0}
       |                                 ^
checkRd: (-1) recm.Rd:55: Lost braces; missing escapes or markup?
    55 | {In all cases,} \eqn{x_{j,t-1}} {in} \eqn{ECT} {is replaced by} \eqn{x_{j,t} \;\;\;\;\; \forall \;\; q_{j} = 0}
       |                                                ^
checkRd: (-1) uecm.Rd:76: Lost braces; missing escapes or markup?
    76 |   {In addition,} \eqn{x_{j,t-1}} {and} \eqn{\Delta x_{j,t}} {cancel out
       |   ^
checkRd: (-1) uecm.Rd:76: Lost braces; missing escapes or markup?
    76 |   {In addition,} \eqn{x_{j,t-1}} {and} \eqn{\Delta x_{j,t}} {cancel out
       |                                  ^
checkRd: (-1) uecm.Rd:76-77: Lost braces
    76 |   {In addition,} \eqn{x_{j,t-1}} {and} \eqn{\Delta x_{j,t}} {cancel out
       |                                                             ^
'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
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) CnPlm.Rd:83-84: Lost braces in \itemize; meant \describe ?
checkRd: (-1) SnpPlm.Rd:65-66: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getAlleleProbePairs.AffymetrixCdfFile.Rd:41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getAlleleProbePairs.AffymetrixCdfFile.Rd:42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getAlleleProbePairs3.AffymetrixCdfFile.Rd:41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getAlleleProbePairs3.AffymetrixCdfFile.Rd:42: Lost braces in \itemize; meant \describe ?
Documented arguments not in \usage in Rd file 'allocateFromCdf.AromaUnitTabularBinaryFile.Rd':
  ‘path’ ‘tags’ ‘footer’

Documented arguments not in \usage in Rd file 'byChipType.DChipSnpInformation.Rd':
  ‘rootPath’ ‘pattern’ ‘verbose’

Documented arguments not in \usage in Rd file 'byChipType.UgpGenomeInformation.Rd':
  ‘version’

Documented arguments not in \usage in Rd file 'calculateResidualSet.FirmaModel.Rd':
  ‘verbose’

Documented arguments not in \usage in Rd file 'findByChipType.AromaChipTypeAnnotationFile.Rd':
  ‘chipType’ ‘tags’

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

Documented arguments not in \usage in Rd file 'getCellIndices.ExonChipEffectFile.Rd':
  ‘units’

Documented arguments not in \usage in Rd file 'getImage.AffymetrixCelFile.Rd':
  ‘palette’

Documented arguments not in \usage in Rd file 'getOutputDataSet.Transform.Rd':
  ‘force’

Documented arguments not in \usage in Rd file 'getUnitTypes.AffymetrixCdfFile.Rd':
  ‘map’

Documented arguments not in \usage in Rd file 'plotMvsX.AffymetrixCelFile.Rd':
  ‘xlim’ ‘xlab’

Documented arguments not in \usage in Rd file 'process.BackgroundCorrection.Rd':
  ‘force’ ‘verbose’

Documented arguments not in \usage in Rd file 'readUnits.CnagCfhFile.Rd':
  ‘cdf’

Documented arguments not in \usage in Rd file 'setArrays.ArrayExplorer.Rd':
  ‘arrays’

Documented arguments not in \usage in Rd file 'setRestructor.AffymetrixCdfFile.Rd':
  ‘units’

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

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 'fitOne.MultiSourceCopyNumberNormalization.Rd':
  ‘name’

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:
  'sfit', 'expectile', 'HaarSeg', 'mpcbs'
checkRd: (-1) colBinnedSmoothing.matrix.Rd:64: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) colBinnedSmoothing.matrix.Rd:65: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) colBinnedSmoothing.matrix.Rd:66-67: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) colBinnedSmoothing.matrix.Rd:68: Lost braces in \itemize; \value handles \item{}{} directly
Documented arguments not in \usage in Rd file 'fit.CopyNumberSegmentationModel.Rd':
  ‘chromosome’

Documented arguments not in \usage in Rd file 'getPath.Explorer.Rd':
  ‘create’

Documented arguments not in \usage in Rd file 'process.AromaTransform.Rd':
  ‘force’ ‘verbose’

Documented arguments not in \usage in Rd file 'process.ChromosomeExplorer.Rd':
  ‘chromosome’

Documented arguments not in \usage in Rd file 'process.Explorer.Rd':
  ‘arrays’ ‘verbose’

Documented arguments not in \usage in Rd file 'setArrays.Explorer.Rd':
  ‘arrays’

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) ars.Rd:27: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) ars.Rd:28: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) ars.Rd:29: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) ars.Rd:30: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) ars.Rd:31: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) ars.Rd:32: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) ars.Rd:36: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) ars.Rd:37: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) ars.Rd:38: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) ars.Rd:39: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) breast_cancer_clean_features.Rd:45: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'RweaveAsciiSetup.Rd':
  ‘stylepath’

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

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

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

Documented arguments not in \usage in Rd file 'RweaveT2t.Rd':
  ‘stylepath’

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

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) convertAlgoPerfToWideFormat.Rd:28: Lost braces
    28 | code{NA} means the performance value is not available, possibly because the algorithm run was aborted.
       |     ^
checkRd: (-1) parseASScenario.Rd:40: Lost braces
    40 |   code{NA} means the cost is not available, possibly because the feature computation was aborted.
       |       ^
checkRd: (-1) parseASScenario.Rd:47: Lost braces
    47 |   code{NA} means the cost is not available, possibly because the feature computation was aborted.
       |       ^
checkRd: (-1) parseASScenario.Rd:55: Lost braces
    55 |   code{NA} means the feature is not available, possibly because the feature computation was aborted.
       |       ^
checkRd: (-1) parseASScenario.Rd:62: Lost braces
    62 |   code{NA} means the feature is not available, possibly because the feature computation was aborted.
       |       ^
Package which this enhances but not available for checking: ‘asreml’
checkRd: (-1) G.tuneup.Rd:81-88: Lost braces in \itemize; meant \describe ?
checkRd: (-1) G.tuneup.Rd:89-91: Lost braces in \itemize; meant \describe ?
checkRd: (-1) G.tuneup.Rd:92-95: Lost braces in \itemize; meant \describe ?
checkRd: (-1) snp.pruning.Rd:75: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) snp.pruning.Rd:76: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) synthetic.cross.Rd:103-108: Lost braces
   103 | \item{If \code{na.action = "expected"},
       |      ^
Documented arguments not in \usage in Rd file 'check.args_.Rd':
  ‘rename_’ ‘arg.update_’

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) assert.Rd:12: Lost braces; missing escapes or markup?
    12 | \item{msg}{A character string containing the error message to display if any of the conditions are not met. The string can include the placeholder {failed_expressions} to insert a list of the failed expressions. The string can also include {?s} and {?is/are} to insert the correct pluralization for the list of failed expressions.}
       |                                                                                                                                                    ^
checkRd: (-1) assert.Rd:12: Lost braces; missing escapes or markup?
    12 | \item{msg}{A character string containing the error message to display if any of the conditions are not met. The string can include the placeholder {failed_expressions} to insert a list of the failed expressions. The string can also include {?s} and {?is/are} to insert the correct pluralization for the list of failed expressions.}
       |                                                                                                                                                                                                                                                 ^
checkRd: (-1) assert.Rd:12: Lost braces; missing escapes or markup?
    12 | \item{msg}{A character string containing the error message to display if any of the conditions are not met. The string can include the placeholder {failed_expressions} to insert a list of the failed expressions. The string can also include {?s} and {?is/are} to insert the correct pluralization for the list of failed expressions.}
       |                                                                                                                                                                                                                                                          ^
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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) plot.AssetPricing.Rd:199-200: Lost braces
   199 |   yakka. (Note that \code{flap} stands for dQuote{function list
       |                                                  ^
Package suggested but not available for checking: ‘asteRiskData’
Specified C++11: please drop specification unless essential
checkRd: (-1) readOEM.Rd:34: Lost braces
    34 |   always, the identifier has the format YYYY-NNNP{PP}, where YYYY is the year
       |                                                  ^
checkRd: (-1) readOEM.Rd:36: Lost braces
    36 |   during year YYYY and P{PP} is a part specifier comprising 1 to 3 capital letters
       |                         ^
checkRd: (-1) readOEM.Rd:74-75: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) readOEM.Rd:76-79: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) readOEM.Rd:80-86: Lost braces in \itemize; \value handles \item{}{} directly
GNU make is a SystemRequirements.
checkRd: (-1) gen.Rd:36: Lost braces; missing escapes or markup?
    36 | `gen({...}) returns an \link{iteror}.
       |      ^
checkRd: (-1) ataCoKriging.Rd:52: Lost braces; missing escapes or markup?
    52 | only one contrained condition for all points and all variables, \\sum_{i=1}^n\\lambda_i +\\sum_{j=1}^m\\beta_j =1, assuming expected means of variables known and constant with the study area.
       |                                                                       ^
checkRd: (-1) ataCoKriging.Rd:52: Lost braces; missing escapes or markup?
    52 | only one contrained condition for all points and all variables, \\sum_{i=1}^n\\lambda_i +\\sum_{j=1}^m\\beta_j =1, assuming expected means of variables known and constant with the study area.
       |                                                                                                ^
checkRd: (-1) simulation_dgp.Rd:14: Lost braces; missing escapes or markup?
    14 | \item{x_discrete}{TRUE if the distribution of the covariate is uniform on {-3.0, -2.9, ..., 3.0} and
       |                                                                           ^
checkRd: (-1) simulation_dgp.Rd:23: Lost braces
    23 | \item{att_oracle}{the sample analog of E[D{Y(1) - Y(0)}|D=1]}
       |                                           ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Unknown package ‘snpar’ in Rd xrefs
checkRd: (-1) att_from_rmds.Rd:42: Lost braces; missing escapes or markup?
    42 | {knitr} and {rmarkdown} are added by default to allow building the vignettes
       | ^
checkRd: (-1) att_from_rmds.Rd:42: Lost braces; missing escapes or markup?
    42 | {knitr} and {rmarkdown} are added by default to allow building the vignettes
       |             ^
checkRd: (-1) create_renv_for_dev.Rd:6: Lost braces; missing escapes or markup?
     6 | \title{Create reproducible environments for your R projects with {renv}}
       |                                                                  ^
checkRd: (-1) create_renv_for_dev.Rd:60: Lost braces; missing escapes or markup?
    60 | Indeed, although packages like {attachment} or {pkgload} must be installed to develop,
       |                                ^
checkRd: (-1) create_renv_for_dev.Rd:60: Lost braces; missing escapes or markup?
    60 | Indeed, although packages like {attachment} or {pkgload} must be installed to develop,
       |                                                ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) audioSample.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) audioSample.Rd:21: Lost braces in \itemize; meant \describe ?
File ‘audio/libs/audio.so’:
  Found non-API call to R: ‘R_checkActivity’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'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.
Re-building vignettes had CPU time 3.3 times elapsed time
checkRd: (-1) get_candidate_covariates.Rd:50: Lost braces
    50 | \item \code{covars_data}   {The \code{data.frame} that is filtered out of \code{df} with only the selected \code{covars}}. The values of the
       |                            ^
checkRd: (-1) get_candidate_covariates.Rd:53: Lost braces
    53 | \item \code{patientIds}   {The list of patient ids present in the original input \code{df}. This is exactly the same as the input \code{patientIdVector}}
       |                           ^
checkRd: (-1) get_prioritised_covariates.Rd:40: Lost braces
    40 | \item \code{multiplicative_bias}{The absolute log of the multiplicative bias term for each of the auto-selected prioritised covariates}
       |                                 ^
checkRd: (-1) get_recurrence_covariates.Rd:34: Lost braces
    34 | \item \code{patientIds}   {The list of patient ids present in the original input \code{df}. This is exactly the same as the input \code{patientIdVector}}
       |                           ^
'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
checkRd: (-1) autonewsmd.Rd:197: Lost braces
   197 | Defaults to `"^v(\\d+\\.){2}\\d+(\\.\\d+)?$"` to identify patterns of
       |                          ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) Autoplotprotein-package.Rd:27: Lost braces
    27 | code{\link{help}}
       |     ^
checkRd: (-1) Autoplotprotein.Rd:25: Lost braces
    25 | code{\link{help}}
       |     ^
checkRd: (-1) data.Rd:22: Lost braces
    22 | code{\link{help}}
       |     ^
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) plotsite.Rd:30: Lost braces
    30 | code{\link{help}}
       |     ^
checkRd: (-1) site_data.Rd:30: Lost braces
    30 | code{\link{help}}
       |     ^
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) noauto_scorecard.Rd:20: Lost braces; missing escapes or markup?
    20 | \item{fit}{See glm {stats}.}
       |                    ^
checkRd: (-1) noauto_scorecard2.Rd:21: Lost braces; missing escapes or markup?
    21 | \item{fit}{See glm {stats}.}
       |                    ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) avar_mo_cpp.Rd:15: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) avar_mo_cpp.Rd:16: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) avar_mo_cpp.Rd:17: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) avar_to_cpp.Rd:15: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) avar_to_cpp.Rd:16: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) avar_to_cpp.Rd:17: Lost braces in \itemize; \value handles \item{}{} directly
'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
checkRd: (-1) FI.ZI.Rd:15-17: Lost braces
    15 | {'poisson','geometric','nb','bb','bnb','normal','halfnormal','lognormal','exponential',
       | ^
checkRd: (-1) kstest.A.Rd:18-21: Lost braces
    18 | \item{dist}{The distribution used as the null hypothesis. Can be one of {'poisson', 'geometric',
       |                                                                         ^
checkRd: (-1) kstest.B.Rd:18-21: Lost braces
    18 | \item{dist}{The distribution used as the null hypothesis. Can be one of {'poisson', 'geometric',
       |                                                                         ^
checkRd: (-1) new.mle.Rd:29-30: Lost braces
    29 |  be one of {'poisson', 'geometric', 'nb', 'nb1', 'bb', 'bb1', 'bnb', 'bnb1', 'normal', 'halfnormal',
       |            ^
checkRd: (-1) sample.h1.Rd:15: Lost braces; missing escapes or markup?
    15 | \item{dist}{The corresponding standard distribution. Can be one of {'poisson', 'geometric','nb','bb', 'bnb','normal', 'lognormal', 'halfnormal','exponential'}, which corresponds to Poisson, geometric, negative binomial, beta binomial, beta negative binomial, normal, log normal, hal fnormal, and exponential distributions respectively.}
       |                                                                    ^
checkRd: (-1) sample.zi1.Rd:15: Lost braces; missing escapes or markup?
    15 | \item{dist}{The corresponding standard distribution. Can be one of {'poisson', 'geometric','nb','bb', 'bnb','normal', 'lognormal', 'halfnormal','exponential'}, which corresponds to Poisson, geometric, negative binomial, beta binomial, beta negative binomial, normal, log normal, hal fnormal, and exponential distributions respectively.}
       |                                                                    ^
checkRd: (-1) zih.mle.Rd:32-33: Lost braces
    32 | of {'poisson.zihmle', 'geometric.zihmle', 'nb.zihmle', 'nb1.zihmle', 'bb.zihmle', 'bb1.zihmle',
       |    ^
checkRd: (-1) cosmos_mongo.Rd:21: Lost braces; missing escapes or markup?
    21 | \item{host}{For \code{cosmos_mongo_endpoint}, the URL of the Cosmos DB MongoDB endpoint. Usually of the form "https://{account-name}.mongo.cosmos.azure.com:443/".}
       |                                                                                                                       ^
Package suggested but not available for checking: ‘lixoftConnectors’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'write.narrative.Rd':
  ‘trials:’

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.
'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
Specified C++11: please drop specification unless essential
checkRd: (-1) contour.angmcmc.Rd:48: Lost braces; missing escapes or markup?
    48 | Ignored if {show.data == FALSE}.}
       |            ^
checkRd: (-1) contour.angmcmc.Rd:51: Lost braces; missing escapes or markup?
    51 | Ignored if {show.data == FALSE}.}
       |            ^
checkRd: (-1) fit_incremental_angmix.Rd:104: Lost braces; missing escapes or markup?
   104 | \item{alpha}{significance level used in the test H_{0K}: expected log predictive density (elpd) for the fitted model with  K components >= elpd for the fitted model
       |                                                    ^
checkRd: (-1) fit_incremental_angmix.Rd:148: Lost braces; missing escapes or markup?
   148 | H_{0K}: expected log predictive density (elpd) for the fitted model with  K components >= elpd for the fitted model
       |   ^
checkRd: (-1) fit_incremental_angmix.Rd:163: Lost braces; missing escapes or markup?
   163 | The incremental fitting stops if  H_{0K} cannot be rejected
       |                                     ^
Specified C++11: please drop specification unless essential
checkRd: (-1) null_dispersion_field_distribution.Rd:34: Lost braces
    34 |          random values it uses the function code{\link[bamm]{permute_pam}}
       |                                                 ^
Package suggested but not available for checking: ‘fdpbandsdata’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) barcode.Rd:52: Escaped LaTeX specials: \&
checkRd: (-1) barcoding.spe.identify2.Rd:27: Lost braces; missing escapes or markup?
    27 | read.dna() from package {ape} was used to obtain DNAbin object for unaligned non-coding barcodes.
       |                         ^
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/bartBMA.Rcheck/00install.out’ for details.
* used C++ compiler: ‘g++-13 (Debian 13.2.0-9) 13.2.0’
Specified C++11: please drop specification unless essential
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    61 |     Argument to code{\link{hist}}.
       |                     ^
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Auto-generated content requiring editing in Rd file 'BartMixVs-package.Rd':
  \seealso: ‘Optional links to other man pages’
  \examples: ‘\dontrun{      ## Optional simple examples of the most impor...’
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    30 | the {dplyr}'s verbs and thus use it in local memory completely.
       |     ^
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    52 | Writes a remote table to disk that was called via {bdplyr}.
       |                                                   ^
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     5 | \title{Compatibility with {dplyr} verbs without using SQL language}
       |                           ^
Package suggested but not available for checking: ‘rgdal’
'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
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   659 | `function(v, cell) { if(isTRUE(v>0.8)) return("green") }`.\cr
       |                    ^
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   151 | The CSS style rule, e.g. { text-align: center; color: red; }
       |                          ^
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   172 | The CSS style rule, e.g. cell { text-align: center; color: red; }
       |                               ^
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   209 | The CSS style rule, e.g. { text-align: center; color: red; }
       |                          ^
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   232 | The CSS style rule, e.g. cell { text-align: center; color: red; }
       |                               ^
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    23 | code{(4)} the number of
       |     ^
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    14 |   \item{\code{algo.id} [\code{character(1)}]:}{algo.id}{Algorithm ID.}
       |                                                        ^
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    13 | \item{ids}{[code{integer}]\cr
       |                 ^
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    13 | \item{ids}{[code{integer}]\cr
       |                 ^
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    28 | Default is dQuote{<name of registry>_files} in current working directory.}
       |                  ^
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    41 |  \item{namespaces}{code{character} with required packages to load via \code{\link[base]{requireNamespace}}.}
       |                        ^
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    31 | Algorithms are functions which get the code{data} part as well as the problem instance (the return value of the
       |                                            ^
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    51 | When {penalty="elastic net"} (default), the elastic net penalty is adopted. If {penalty="lasso"}, the lasso penalty is used.
       |      ^
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    51 | When {penalty="elastic net"} (default), the elastic net penalty is adopted. If {penalty="lasso"}, the lasso penalty is used.
       |                                                                                ^
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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.
       |      ^
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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.
       |                                                                                                                          ^
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    55 | When {robust=TRUE} (default), the distribution of \eqn{\epsilon_{i}} is defined as a Laplace distribution with density
       |      ^
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    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.
       |                                                                                     ^
GNU make is a SystemRequirements.
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    32 | plot{...} functions are generated programmatically so the function calls in
       |     ^
Invalid package aliases in Rd file 'bayesANOVA-package.Rd':
  ‘bayesANOVA-package’
'LazyData' is specified without a 'data' directory
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Problems with news in ‘NEWS.md’:
No news entries found.
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'LazyData' is specified without a 'data' directory
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    48 | doi{10.1002/jae.3950090208} Griffiths, W.E., Hill, R.C., and Judge, G.G. (1993).
       |    ^
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    30 | variables. It was observed that there are only ten sets of values for the first three explanatory variables, so these sets served as conditions for controlled distillation. These conditions are listed in the variable \ code {batch}.
       |                                                                                                                                                                                                                                 ^
GNU make is a SystemRequirements.
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    91 | \item{$H_n1 }{ Bayesian prediction of volatilities and co-volatilities for y_{n+1}.}
       |                                                                              ^
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    92 | \item{$R_n1 }{ Bayesian prediction of coditional correlation for y_{n+1}.}
       |                                                                    ^
GNU make is a SystemRequirements.
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No news entries found.
'LazyData' is specified without a 'data' directory
checkRd: (-1) GroupSingleVoxelFETS.Rd:53: Lost braces
    53 | online trajectories related to the state parameter, the simulated BOLD responses, \mjseqn{\hat{Y}}{ascii}.
       |                                                                                                   ^
'LazyData' is specified without a 'data' directory
Package vignettes with \VignetteEngine{} not specifying an engine package:
  ‘compare_lme4.Rmd’
  ‘index.Rmd’
  ‘odds_probs.Rmd’
  ‘priors.Rmd’
Engines should be specified as \VignetteEngine{PKG::ENG}.
Package suggested but not available for checking: ‘INLA’
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
checkRd: (-1) gMLE.bb.Rd:18: Lost braces
    18 |   \item{optim.method}{optimization method in \code{optim()}{stats}.}
       |                                                            ^
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
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    69 | the initial values for parameters in models. For example, inits<-function(){list(alpha=0,beta=0,c=0,var1=0.5,r=1,lamda=0.01)}.
       |                                                                            ^
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
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    18 |   \item{X         }{ If call \code{bayeslm} with matrices input \code{x} and {y} but not formula, pass new matrix to predict here. See example for details.}
       |                                                                              ^
GNU make is a SystemRequirements.
Problems with news in ‘NEWS.md’:
No news entries found.
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   172 |    code{\link[stats]{formula}} interface instead, a regressor matrix may
       |        ^
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    71 | the plots are saved into directory {sim.dir}/predictions/migTrajectories.}
       |                                    ^
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    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.
       |                                                                                                                                                      ^
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checkRd: (-1) pulse_of_the_nation.Rd:10: Escaped LaTeX specials: \$
GNU make is a SystemRequirements.
Argument items with no description in Rd file 'hmmeantemp.Rd':
  ‘dat’
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Found the following significant warnings:
  mbart.cpp:406:18: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘ivs’ {aka ‘long unsigned int’} [-Wformat=]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/BayesTree.Rcheck/00install.out’ for details.
* used C++ compiler: ‘g++-13 (Debian 13.2.0-9) 13.2.0’
checkRd: (-1) bart.Rd:271: Escaped LaTeX specials: \_
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
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    11 | Runs a \bold{Shiny} application. This function normally does not return; interrupt bold{R} to stop the application (usually by pressing Ctrl+C or Esc).
       |                                                                                        ^
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GNU make is a SystemRequirements.
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
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    18 | discrepancy measure T(bm{y}, bm{Theta}) with following steps
       |                         ^
checkRd: (-1) BayesT.Rd:18: Lost braces
    18 | discrepancy measure T(bm{y}, bm{Theta}) with following steps
       |                                ^
checkRd: (-1) goftype1.Rd:4: Lost braces
     4 | \description{The goodness-of-fit (GOF) measures consist of Anderson-Darling (\code{AD}) and Cram\'{e}er-von Misses (\code{CVM}) statistics for progressive type-I interval censoring scheme are given, respectively, by
       |                                                                                                   ^
Found the following files/directories:
  ‘fabiabreast.txt’
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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.
'LazyData' is specified without a 'data' directory
checkRd: (-1) BchronDensity.Rd:47: Lost braces in \itemize; \value handles \item{}{} directly
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    34 | itemize{
       |        ^
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    32 | `code{\link{GetVT}}`.   Otherwise, any column (e.g. \code{"Depth"}) in the 
       |      ^
checkRd: (-1) WindowSweep.Rd:36: Lost braces
    36 | \code{T.mid}  from the output of the `code{\link{GetVT}}`.}
       |                                           ^
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) gene_s.Rd:17: Lost braces; missing escapes or markup?
    17 | giving the virus access to the cell and thus facilitating the COVID-19 disease. The gene sequence is mapped to the alphabet {0,1,2,3} via the obvious map A->0, C->1, G->2, T->3.
       |                                                                                                                             ^
checkRd: (-1) sars_cov_2.Rd:16: Lost braces; missing escapes or markup?
    16 | It consists of n = 29903 base pairs. The gene sequence is mapped to the alphabet {0,1,2,3} via the obvious map A->0, C->1, G->2, T->3.
       |                                                                                  ^
Running examples in ‘bdchecks-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: DC_countryMismatch
> ### Title: Data check countryMismatch Check if given country match given
> ###   country code.
> ### Aliases: DC_countryMismatch
> 
> ### ** Examples
> 
> performDC(DC = DC_countryMismatch, DATA = bdchecks::dataBats)
Loading required package: rgbif
Error in eval(parse(text = dependencies[j])) : 
  object 'isocodes' not found
Calls: performDC -> performDC -> assign -> eval -> eval
Execution halted
Running ‘testthat.R’ [3s/6s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(bdchecks)
  > 
  > test_check("bdchecks")
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 5 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('tests_all.R:10:5'): summary_DC ──────────────────────────────────────
  Error in `eval(parse(text = dependencies[j]))`: object 'isocodes' not found
  Backtrace:
      ▆
   1. ├─testthat::expect_warning(performDataCheck(dataBats)) at tests_all.R:10:5
   2. │ └─testthat:::quasi_capture(...)
   3. │   ├─testthat (local) .capture(...)
   4. │   │ └─base::withCallingHandlers(...)
   5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
   6. └─bdchecks::performDataCheck(dataBats)
   7.   ├─bdchecks::performDC(DCcurrent, data)
   8.   └─bdchecks::performDC(DCcurrent, data)
  ── Error ('tests_all.R:41:5'): performDataCheck ────────────────────────────────
  Error in `eval(parse(text = dependencies[j]))`: object 'isocodes' not found
  Backtrace:
      ▆
   1. ├─testthat::expect_warning(bdchecks::performDataCheck(dataBats)) at tests_all.R:41:5
   2. │ └─testthat:::quasi_capture(...)
   3. │   ├─testthat (local) .capture(...)
   4. │   │ └─base::withCallingHandlers(...)
   5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
   6. └─bdchecks::performDataCheck(dataBats)
   7.   ├─bdchecks::performDC(DCcurrent, data)
   8.   └─bdchecks::performDC(DCcurrent, data)
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 5 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) bde.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bde.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bde.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bde.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bde.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bde.Rd:35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bde.Rd:36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bde.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bde.Rd:42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bde.Rd:47: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bde.Rd:48: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bde.Rd:49: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bde.Rd:54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bde.Rd:55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bde.Rd:56: 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
Found the following files/directories:
  ‘dump.txt’
Argument items with no description in Rd file 'bdw.Rd':
  ‘\dots’
Argument items with no description in Rd file 'plot.bdw.Rd':
  ‘\dots’
Argument items with no description in Rd file 'summary.bdw.Rd':
  ‘\dots’
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘beast_plot_toy.pdf’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
checkRd: (-1) excess.Rd:20: Lost braces
    20 |       \link{dea}, \link{dea.direct}, link{sdea}, and \link{mea}. }
       |                                          ^
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
checkRd: (-1) sockeye.Rd:13-14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sockeye.Rd:15-16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) stagnant.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) stagnant.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) hill.Rd:39: Lost braces; missing escapes or markup?
    39 | \code{a} in {0, 1, 2} (see details))}
       |             ^
checkRd: (-1) read_ambi.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) read_ambi.Rd:23-24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) read_iti.Rd:39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) read_iti.Rd:40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) read_iti.Rd:41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) read_iti.Rd:42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) read_taxa.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) read_taxa.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) read_taxa.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) read_taxa.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) read_twn.Rd:36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) read_twn.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) read_twn.Rd:38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) read_twn.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) read_twn.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) read_twn.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) read_twn.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) headtail.Rd:28: Lost braces
    28 | Tries to find good methods of combining the two results according to {code{class(x)}}.
       |                                                                      ^
checkRd: (-1) headtail.Rd:28: Lost braces
    28 | Tries to find good methods of combining the two results according to {code{class(x)}}.
       |                                                                           ^
checkRd: (-1) logAxis.Rd:47: Lost braces; missing escapes or markup?
    47 | \item{expr}{Expression drawing over the ablines, like (points(x,y). Can be code within {braces}.}
       |                                                                                        ^
checkRd: (-1) smallPlot.Rd:26: Lost braces; missing escapes or markup?
    26 | \item{expr}{expression creating a plot. Can be code within {braces}.}
       |                                                            ^
Specified C++11: please drop specification unless essential
checkRd: (-1) gen.data.Rd:42: Lost braces
    42 | code{cortype = 2} denotes the constant structure, where the \eqn{(i,j)} entry of covariance
       |     ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
checkRd: (-1) BETSsearch.Rd:56: Lost braces
    56 |        \item{To exclude whole expressions from the search, surround them with code{' '} and insert a \code{~} before each of them.
       |                                                                                   ^
checkRd: (-1) dummy.Rd:23: Lost braces; missing escapes or markup?
    23 | \item{date}{a \code{list}. The periods for which the dummy must be set to one. Periods must be represented as {integer vectors}, as described for \code{start} and \code{end}.}
       |                                                                                                               ^
checkRd: (-1) dummy.Rd:25: Lost braces; missing escapes or markup?
    25 | \item{from}{An \code{integer vector} The starting period of a sequence of perids for which the dummy must be set to one. Periods must be represented as {integer vectors}, as described for \code{start} and \code{end}.}
       |                                                                                                                                                         ^
checkRd: (-1) dummy.Rd:27: Lost braces; missing escapes or markup?
    27 | \item{to}{The ending period of a sequence of perids for which the dummy must be set to one. Periods must be represented as {integer vectors}, as described for \code{start} and \code{end}.}
       |                                                                                                                            ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) bdp_dw_bayes_factor_k1.Rd:5: Lost braces; missing escapes or markup?
     5 | \title{Estimating the Bayes factor of hypothesis {k1 = 1}.}
       |                                                  ^
checkRd: (-1) bdp_dw_bayes_factor_k1.Rd:19: Lost braces; missing escapes or markup?
    19 | Estimating the Bayes factor of hypothesis {k1 = 1}.
       |                                           ^
checkRd: (-1) local_moving_FT_zigzag.Rd:14: Lost braces; missing escapes or markup?
    14 | \item{thinning_factor}{Selected from {1, 2, 3}.}
       |                                      ^
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.
checkRd: (-1) bggCollection.Rd:63-64: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bggCollection.Rd:65-67: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bggCollection.Rd:68-69: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bggCollection.Rd:70-73: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bggCollection.Rd:74-76: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bggCollection.Rd:77-80: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bggGames.Rd:68-69: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bggGames.Rd:70-72: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bggSearch.Rd:66-67: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bggSearch.Rd:68-71: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bggSearch.Rd:72-73: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
checkRd: (-1) bgmm-package.Rd:23: Escaped LaTeX specials: \&
checkRd: (-1) sp_bgsmtr.Rd:42: Lost braces; missing escapes or markup?
    42 | \item{c.star}{The threshold for computing posterior tail probabilities p_{ij} for Bayesian FDR as defined in Section 3.2 of  Song, Ge et al.(2019). If not specified the default is to set this threshold as the minimum posterior standard deviation, where the minimum is taken over all regression coefficients in the model.}
       |                                                                          ^
GNU make is a SystemRequirements.
checkRd: (-1) dotPlot.Rd:56: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
checkRd: (-1) fmridata.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fmridata.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fmridata.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fmridata.Rd:21: Lost braces in \itemize; meant \describe ?
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’
checkRd: (-1) module_calibrationfile_server.Rd:19: Lost braces; missing escapes or markup?
    19 | expression: input_re = reactive({input})}
       |                                 ^
checkRd: (-1) module_correctedplots_server.Rd:19: Lost braces; missing escapes or markup?
    19 | expression: input_re = reactive({input})}
       |                                 ^
checkRd: (-1) module_correctedstats_server.Rd:19: Lost braces; missing escapes or markup?
    19 | expression: input_re = reactive({input})}
       |                                 ^
checkRd: (-1) module_fileupload_server.Rd:19: Lost braces; missing escapes or markup?
    19 | expression: input_re = reactive({input})}
       |                                 ^
checkRd: (-1) module_info_server.Rd:19: Lost braces; missing escapes or markup?
    19 | expression: input_re = reactive({input})}
       |                                 ^
checkRd: (-1) module_log_server.Rd:19: Lost braces; missing escapes or markup?
    19 | expression: input_re = reactive({input})}
       |                                 ^
checkRd: (-1) module_modelselection_server.Rd:19: Lost braces; missing escapes or markup?
    19 | expression: input_re = reactive({input})}
       |                                 ^
checkRd: (-1) module_plotting_server.Rd:19: Lost braces; missing escapes or markup?
    19 | expression: input_re = reactive({input})}
       |                                 ^
checkRd: (-1) module_results_server.Rd:19: Lost braces; missing escapes or markup?
    19 | expression: input_re = reactive({input})}
       |                                 ^
checkRd: (-1) module_settings_server.Rd:19: Lost braces; missing escapes or markup?
    19 | expression: input_re = reactive({input})}
       |                                 ^
checkRd: (-1) module_statistics_server.Rd:19: Lost braces; missing escapes or markup?
    19 | expression: input_re = reactive({input})}
       |                                 ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) Jeffreysbs.Rd:17: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
checkRd: (-1) BiDimRegression.Rd:29: Lost braces; missing escapes or markup?
    29 | \item \code{euclidean.df1, affine.df1} -  degrees of freedom of the nominator used for the F-statistics propagated by Nakaya (1997); df1 = p-2, with p is the number of elements  needed to calculate the referring model: p=4 for the Euclidean and p=6 for the affine geometry {Nakaya, 1997, Table 1}.
       |                                                                                                                                                                                                                                                                                  ^
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘lavaan.survey’
Unknown package ‘lavaan.survey’ in Rd xrefs
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’
Invalid package aliases in Rd file 'package_bigdist.Rd':
  ‘package_bigdist-package’
Package suggested but not available for checking: ‘INLA’
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’.
Specified C++14: please drop specification unless essential
checkRd: (-1) bdm.ptsne.Rd:47: Lost braces; missing escapes or markup?
    47 | By default the algorithm is structured in \eqn{\sqrt{n}} epochs of \eqn{\sqrt{z}} iterations each, where \var{n} is the dataset size and \var{z} is the thread-size (\eqn{z=n*layers/threads}). The running time of the algorithm is then determined by \eqn{epochs*iters*t_i+ epochs*t_e} where \var{t_{i}} is the running time of a single iteration and \var{t_{e}} is the inter-epoch running time.
       |                                                                                                                                                                                                                                                                                                         ^
checkRd: (-1) bdm.ptsne.Rd:47: Lost braces; missing escapes or markup?
    47 | By default the algorithm is structured in \eqn{\sqrt{n}} epochs of \eqn{\sqrt{z}} iterations each, where \var{n} is the dataset size and \var{z} is the thread-size (\eqn{z=n*layers/threads}). The running time of the algorithm is then determined by \eqn{epochs*iters*t_i+ epochs*t_e} where \var{t_{i}} is the running time of a single iteration and \var{t_{e}} is the inter-epoch running time.
       |                                                                                                                                                                                                                                                                                                                                                                   ^
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘rrelaxiv’
checkRd: (-1) pQF.Rd:30: Lost braces; missing escapes or markup?
    30 | When \code{M} is not square, a randomised estimator for the trace of \code{crossprod(M)^2} is used. This is the sample size. When \code{M} is of \code{"matrixfree"} and does not include the trace of {crossprod(M)} as a component, this sample size will also be used to compute that. See Hutchinson reference. }
       |                                                                                                                                                                                                        ^
checkRd: (-1) bqr_upload_data.Rd:112: Lost braces
   112 | url{https://cloud.google.com/bigquery/loading-data-post-request}
       |    ^
'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) FBM-class.Rd:97: Lost braces; missing escapes or markup?
    97 | to be used by package {bigmemory}.
       |                       ^
checkRd: (-1) FBM-class.Rd:99: Lost braces; missing escapes or markup?
    99 | to be used by package {bigmemory}.
       |                       ^
checkRd: (-1) big_read.Rd:57: Lost braces; missing escapes or markup?
    57 | Read a file as a Filebacked Big Matrix by using package {bigreadr}.
       |                                                         ^
Specified C++11: please drop specification unless essential
checkRd: (-1) VARXFit.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) VARXFit.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) VARXFit.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) VARXFit.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) VARXFit.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) VARXFit.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) VARXLagCons.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) VARXLagCons.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
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
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
'LazyData' is specified without a 'data' directory
checkRd: (-1) binom.confint.Rd:28-29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) binom.confint.Rd:30-31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) binom.confint.Rd:32-37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) binom.confint.Rd:38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) binom.confint.Rd:39-40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) binom.confint.Rd:41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) binom.confint.Rd:42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) binom.confint.Rd:43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) binom.confint.Rd:44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) binom.confint.Rd:45: 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.
Specified C++11: please drop specification unless essential
checkRd: (-1) aa.index.Rd:14: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) aa.index.Rd:15: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) aa.index.Rd:16: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) aa.index.Rd:17: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) aa.index.Rd:18: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) aa.index.Rd:19: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) aa.index.Rd:20-23: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) aa.index.Rd:24: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) example.data.Rd:33-37: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) example.data.Rd:38-39: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) example.data.Rd:40-41: Lost braces in \enumerate; meant \describe ?
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) CalcROC.Rd:47: Lost braces
    47 | The accuracy of the classifier is the mean value of dQuote{(optSn, optSp)} for two-class problem and the mean value of \dQuote{(optSn, optSp,optS3)} for three-class problem.
       |                                                           ^
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.
checkRd: (-1) ringApply.Rd:9: Lost braces; missing escapes or markup?
     9 |   \item{lv}{{numeric} position, or {character} name, of an
       |                                    ^
checkRd: (-1) calc_ed.Rd:14: Lost braces; missing escapes or markup?
    14 | of groups or less than \code{a}. Both \code{a} and {b} must have the the same 
       |                                                    ^
checkRd: (-1) calc_pi.Rd:14: Lost braces; missing escapes or markup?
    14 | of groups or less than \code{a}. Both \code{a} and {b} must have the the same 
       |                                                    ^
checkRd: (-1) calc_si.Rd:14: Lost braces; missing escapes or markup?
    14 | of groups or less than \code{a}. Both \code{a} and {b} must have the the same 
       |                                                    ^
checkRd: (-1) cluster_reg_exp.Rd:15: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) cluster_reg_exp.Rd:16: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) cluster_reg_exp.Rd:17: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) cluster_reg_exp.Rd:18: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
checkRd: (-1) ROC.Rd:55: Lost braces in \enumerate; \value handles \item{}{} directly
checkRd: (-1) ROC.Rd:56: Lost braces in \enumerate; \value handles \item{}{} directly
checkRd: (-1) ROC.Rd:57: Lost braces in \enumerate; \value handles \item{}{} directly
checkRd: (-1) ROC.Rd:58: Lost braces in \enumerate; \value handles \item{}{} directly
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.
checkRd: (-1) simulation.Rd:52-54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulation.Rd:55-57: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulation.Rd:58-59: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulation.Rd:60-62: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulation.Rd:63: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulation.Rd:64: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulation.Rd:65: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dynamic_omes.Rd:45: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dynamic_omes.Rd:46: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dynamic_omes.Rd:47: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dynamic_omes.Rd:48: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dynamic_omes.Rd:49: Lost braces in \itemize; meant \describe ?
checkRd: (-1) elsc.Rd:39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) elsc.Rd:40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) elsc.Rd:41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) entropy.Rd:35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) entropy.Rd:36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) entropy.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mcbasc.Rd:36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mcbasc.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mcbasc.Rd:38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mcbasc.Rd:39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mcbasc.Rd:40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mcbasc.Rd:41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) omes.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) omes.Rd:38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) omes.Rd:39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) omes.Rd:40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) omes.Rd:41: Lost braces in \itemize; meant \describe ?
Invalid package aliases in Rd file 'bios2cor-package.Rd':
  ‘bios2cor-package’
checkRd: (-1) mmds.2D.multi.Rd:118: Lost braces
   118 |   a numeric value in inches indicating the height of graph outfile. Default differs by outfile.type. The resolution for tiff and png figures is 150 dpi. See \code{pdf}, code{tiff}, \code{png}, \code{postscript}.
       |                                                                                                                                                                              ^
checkRd: (-1) mmds.2D.plot.Rd:134: Lost braces
   134 |   a numeric value in inches indicating the height of graph outfile. Default differs by outfile.type. The resolution for tiff and png figures is 150 dpi. See \code{pdf}, code{tiff}, \code{png}, \code{postscript}.
       |                                                                                                                                                                              ^
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) tocher.Rd:13: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
checkRd: (-1) keypos.rd:27: Lost braces
    27 |   an integer vector of the same length as code{x} containing positions relativ to code{sort(unique(x), na.last=FALSE)}
       |                                               ^
checkRd: (-1) keypos.rd:27: Lost braces
    27 |   an integer vector of the same length as code{x} containing positions relativ to code{sort(unique(x), na.last=FALSE)}
       |                                                                                       ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Argument items with no description in Rd file 'ONA_compiled.Rd':
  ‘ATN’
Argument items with no description in Rd file 'export.dyadic.Rd':
  ‘blauObj’
Package suggested but not available for checking: ‘cmdstanr’
GNU make is a SystemRequirements.
checkRd: (-1) posteriorFeasibility.Rd:25: Escaped LaTeX specials: \#
checkRd: (-1) sp500Returns.Rd:4: Escaped LaTeX specials: \&
checkRd: (-1) RLdata500.Rd:8: Lost braces
     8 | A data frame with five variables: \code{fname_c1},\code{lname_c1},  \code{by}, code{bm}, \code{bd}.
       |                                                                                    ^
checkRd: (-1) identity.RLdata500.Rd:15: Lost braces
    15 | format A vector that contains the code{id}
       |                                       ^
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) durban.Rd:16: Lost braces; missing escapes or markup?
    16 | This data set was obtained from the durban.rowcol {agridat} example in package 'agridat' 
       |                                                   ^
checkRd: (-1) fraction.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) fraction.Rd:31-32: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) fraction.Rd:33: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimate_density.Rd:25: Lost braces; missing escapes or markup?
    25 | evenly spaced points between \code{min} and {max}.
       |                                             ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) bluebike.Rd:17: Lost braces
    17 | \item{\code{import_month_data}}\cr {Takes in numeric year/month values and imports data from \href{https://www.bluebikes.com/system-data}{Blue Bikes System Data} for the specified time}
       |                                    ^
checkRd: (-1) bluebike.Rd:18: Lost braces; missing escapes or markup?
    18 | \item{\code{station_distance}}\cr {Returns stations with distance in ascending order given the user's current location}
       |                                   ^
checkRd: (-1) bluebike.Rd:19: Lost braces; missing escapes or markup?
    19 | \item{\code{station_radius}}\cr {Plots the position of the stations within walking distance (500 m), and present the basic information about the stations via leaflet}
       |                                 ^
checkRd: (-1) bluebike.Rd:20: Lost braces; missing escapes or markup?
    20 | \item{\code{trip_distance}}\cr {Computes the geographical distance between the start and end stations}
       |                                ^
checkRd: (-1) bluebike.Rd:25: Lost braces; missing escapes or markup?
    25 | \item{\code{trip_history_sample}} \cr {A sample of 1000 trip data entries from February 2022}
       |                                       ^
checkRd: (-1) bluebike.Rd:26: Lost braces; missing escapes or markup?
    26 | \item{\code{station_data}} \cr {A dataset that includes identification, position, and other basic information about bluebike stations}
       |                                ^
Specified C++11: please drop specification unless essential
checkRd: (-1) dot-pred_array_to_df.Rd:20: Lost braces; missing escapes or markup?
    20 | Helper function for as.data.frame.{fitted, forecast}. Converts predictive array to data.frame.
       |                                   ^
GNU make is a SystemRequirements.
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.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
checkRd: (-1) BMRMM.Rd:92: Lost braces in \itemize; meant \describe ?
checkRd: (-1) BMRMM.Rd:93-94: Lost braces in \itemize; meant \describe ?
checkRd: (-1) BMRMM.Rd:95-98: Lost braces in \itemize; meant \describe ?
checkRd: (-1) summary.BMRMM.Rd:38-41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) summary.BMRMM.Rd:44-53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) BMSC_pareto_k_table.Rd:54-56: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) BMSC_pareto_k_table.Rd:57-59: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) BMSC_pareto_k_table.Rd:60-63: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) BMSC_pareto_k_table.Rd:64-66: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) BMSC_pareto_k_table.Rd:67-71: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) BMSC_pareto_k_table.Rd:72-74: Lost braces in \itemize; \value handles \item{}{} directly
Package suggested but not available for checking: ‘INLA’
GNU make is a SystemRequirements.
checkRd: (-1) autoplot.tsregime.Rd:20: Lost braces
    20 | Graph for the stochastic processes of the object \ dQuote {\ code {tsregime}} for: Output process and if they exist for: Threshold process and Covariates process. In the case that there are missing data, a red line is drawn at the indicated time.
       |                                                           ^
checkRd: (-1) autoplot.tsregime.Rd:20: Lost braces; missing escapes or markup?
    20 | Graph for the stochastic processes of the object \ dQuote {\ code {tsregime}} for: Output process and if they exist for: Threshold process and Covariates process. In the case that there are missing data, a red line is drawn at the indicated time.
       |                                                                   ^
checkRd: (-1) MvInv.Rd:23-35: Lost braces
    23 | function(eps, u = 0.5, alpha = 1, kappa = 1, gama = 1 / 2, N = 3001) {
       |                                                                      ^
checkRd: (-1) dt_.Rd:19-21: Lost braces
    19 | function(x, df, mean, sd) {
       |                           ^
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) strength.viewer.Rd:148: Lost braces in \itemize; meant \describe ?
checkRd: (-1) strength.viewer.Rd:149: Lost braces in \itemize; meant \describe ?
checkRd: (-1) strength.viewer.Rd:150: Lost braces in \itemize; meant \describe ?
checkRd: (-1) strength.viewer.Rd:151: Lost braces in \itemize; meant \describe ?
checkRd: (-1) strength.viewer.Rd:152: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
checkRd: (-1) boa.chain.collapse.Rd:20: Lost braces
    20 | \seealso{ code{\link{boa.chain.reset}}, code{\link{boa.chain.subset}} }
       |               ^
checkRd: (-1) boa.chain.collapse.Rd:20: Lost braces
    20 | \seealso{ code{\link{boa.chain.reset}}, code{\link{boa.chain.subset}} }
       |                                             ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) refAnnots.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) refAnnots.Rd:11-12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) untreatedAnnots.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) untreatedAnnots.Rd:11-12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) untreatedAnnots.Rd:13-14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Extractor.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Extractor.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Extractor.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Extractor.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Extractor.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Extractor.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Extractor.Rd:19: Lost braces in \itemize; meant \describe ?
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
checkRd: (-1) select_Uc.Rd:16: Lost braces
    16 | function /code{ppBS_srs()}.
       |               ^
checkRd: (-1) bootSVD.Rd:13: Lost braces; missing escapes or markup?
    13 | \item{Y}{initial data sample, which can be either a matrix or a \code{\link{ff}} matrix. \code{Y} can be either tall (\eqn{p} by \eqn{n}) or wide (\eqn{n} by \eqn{p}). If \code{Y} is entered and \code{V}, \code{d} and \code{U} (see definitions below) are not entered, then \code{bootSVD} will also compute the SVD of \code{Y}. In this case where the SVD is computed, \code{bootSVD} will assume that the larger dimension of \code{Y} is \eqn{p}, and the smaller dimension of code {Y} is \eqn{n} (i.e. \code{bootSVD} assumes that (\eqn{p>n}). This assumption can be overriden by manually entering \code{V}, \code{U} and \code{d}.\cr
       |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               ^
Documented arguments not in \usage in Rd file 'check_inputs.Rd':
  ‘h_rs’

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

Documented arguments not in \usage in Rd file 'path.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.
Specified C++11: please drop specification unless essential
checkRd: (-1) bp_rats.Rd:41: Escaped LaTeX specials: \&
checkRd: (-1) bp_sv.Rd:75: Lost braces; missing escapes or markup?
    75 | $$SV = sqrt(sum(x_{i+1} - x_i)^2/n-1)$$
       |                   ^
checkRd: (-1) bp_sv.Rd:80: Lost braces; missing escapes or markup?
    80 | $$SD = sqrt(sum(x_{i+1} - xbar)^2/n-1)$$
       |                   ^
checkRd: (-1) sv.Rd:78: Lost braces; missing escapes or markup?
    78 | $$SV = sqrt(sum(x_{i+1} - x_i)^2/n-1)$$
       |                   ^
checkRd: (-1) sv.Rd:82: Lost braces; missing escapes or markup?
    82 | $$SD = sqrt(sum(x_{i+1} - xbar)^2/n-1)$$
       |                   ^
checkRd: (-1) little.ana.bc.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) little.ana.bc.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) little.ana.bc.Rd:16-17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) little.ana.bc.Rd:22-27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) little.ana.bc.Rd:32-33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) little.ana.bc.Rd:34: Lost braces in \itemize; meant \describe ?
Packages suggested but not available for checking: 'RGtk2', 'cairoDevice'
checkRd: (-1) utils.Rd:58: Lost braces in \itemize; meant \describe ?
checkRd: (-1) utils.Rd:59: Lost braces in \itemize; meant \describe ?
checkRd: (-1) utils.Rd:60: Lost braces in \itemize; meant \describe ?
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.
'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) breakfast.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) breakfast.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) breakfast.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) breakfast.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) breakfast.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) breakfast.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) breakfast.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) breakfast.Rd:33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) breakfast.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) breakfast.Rd:35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) breakfast.Rd:36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) breakfast.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) breakfast.Rd:43: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) breakfast.Rd:44: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) breakfast.Rd:46: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) breakfast.Rd:47: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) breakfast.Rd:48: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) breakfast.Rd:49: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) breakfast.Rd:50: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) model.lp.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) model.lp.Rd:24: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
checkRd: (-1) t50_bluck_coward.Rd:15: Lost braces; missing escapes or markup?
    15 | Time where value is 1/2 of the maximum, i.e. t_{50} or t_{1/2} in minutes; 
       |                                                ^
checkRd: (-1) t50_bluck_coward.Rd:15: Lost braces; missing escapes or markup?
    15 | Time where value is 1/2 of the maximum, i.e. t_{50} or t_{1/2} in minutes; 
       |                                                          ^
checkRd: (-1) t50_bluck_coward.Rd:16: Lost braces; missing escapes or markup?
    16 | in the publication by Bluck et al, the parameter is called t_{1/2(in)}.
       |                                                              ^
GNU make is a SystemRequirements.
Documented arguments not in \usage in Rd file 'availability.int.Rd':
  ‘v.set’ ‘dir.set’

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 'subset.int.Rd':
  ‘subset.int’

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) brglm.Rd:173: Lost braces in \itemize; meant \describe ?
checkRd: (-1) brglm.Rd:174: Lost braces in \itemize; meant \describe ?
checkRd: (-1) brglm.Rd:175-176: Lost braces in \itemize; meant \describe ?
checkRd: (-1) brglm.Rd:177-178: Lost braces in \itemize; meant \describe ?
checkRd: (-1) brglm.Rd:179-180: Lost braces in \itemize; meant \describe ?
checkRd: (-1) brglm.Rd:181-182: Lost braces in \itemize; meant \describe ?
checkRd: (-1) brglm.Rd:183-184: Lost braces in \itemize; meant \describe ?
checkRd: (-1) profile.brglm.Rd:54-55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) profile.brglm.Rd:56: Lost braces in \itemize; meant \describe ?
checkRd: (-1) profile.brglm.Rd:57: Lost braces in \itemize; meant \describe ?
checkRd: (-1) profile.brglm.Rd:58: Lost braces in \itemize; meant \describe ?
checkRd: (-1) printHands.Rd:40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) printHands.Rd:41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) printHands.Rd:42: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) assertall.Rd:45: Lost braces in \itemize; meant \describe ?
checkRd: (-1) assertall.Rd:46: Lost braces in \itemize; meant \describe ?
checkRd: (-1) assertall.Rd:47: Lost braces in \itemize; meant \describe ?
checkRd: (-1) assertall.Rd:48: Lost braces in \itemize; meant \describe ?
checkRd: (-1) brmsmargins.Rd:129: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) brmsmargins.Rd:130: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) brmsmargins.Rd:131: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) brmsmargins.Rd:132: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) builders.Rd:50: Lost braces in \itemize; meant \describe ?
checkRd: (-1) builders.Rd:51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) builders.Rd:52: Lost braces in \itemize; meant \describe ?
checkRd: (-1) builders.Rd:53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) builders.Rd:54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) builders.Rd:55: Lost braces in \itemize; meant \describe ?
Package suggested but not available for checking: ‘cmdstanr’
checkRd: (-1) gp.Rd:93-99: Lost braces in \itemize; meant \describe ?
checkRd: (-1) select_helpers.Rd:43: Lost braces; missing escapes or markup?
    43 | Set of functions to supplement the {tidyselect} set of
       |                                    ^
Package suggested but not available for checking: ‘glmmADMB’
checkRd: (-1) tidy.varFunc.Rd:26-27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tidy.varFunc.Rd:28-30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tidy.varFunc.Rd:31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tidy.varFunc.Rd:32-33: Lost braces in \itemize; meant \describe ?
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'.
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'table.Rd':
  ‘headTitles’

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) bsaqdpm.Rd:166: Lost braces
   166 | MacEachern, S. N. and M{\"u}ller, P. (1998) Estimating mixture of Dirichlet process models.
       |                        ^
checkRd: (-1) bsardpm.Rd:165: Lost braces
   165 | MacEachern, S. N. and M{\"u}ller, P. (1998) Estimating mixture of Dirichlet process models.
       |                        ^
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’
checkRd: (-1) bscontrol.Rd:39: Lost braces; missing escapes or markup?
    39 | \item{opt.solver}{a character string in the set {'enum', 'enum_c', 'gurobi', 'cplex', 'lpSolve', 'greedy'} indicating the optimization solver to be used in the program. The choice of 'cplex' requires the package \code{cplexAPI}, 'gurobi' requires the package \code{gurobi}, and 'lpSolve' requires the package \code{lpSolve}. These solver options are only available in the full version at \url{https://github.com/profyliu/bsnsing/}. The default (and the best) is 'enum_c'.}
       |                                                 ^
checkRd: (-1) bscontrol.Rd:45: Lost braces; missing escapes or markup?
    45 | \item{opt.model}{a character string in the set {'gini','error'} indicating the optimization model to solve in the program. The default is 'gini'. The 'error' option is not available in the current version.}
       |                                                ^
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    51 | {splines::bs()}, {splines2::bSpline()}
       |                  ^
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    37 | {bsc}, {par2bsp}
       |        ^
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   192 | Users can create their own statistics for use with the code{gof} methods. To
       |                                                            ^
Package suggested but not available for checking: ‘gvcm.cat’
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Unknown package ‘gvcm.cat’ in Rd xrefs
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    42 | function. If {sizeBreaks} vector is supplied then this will be ignored and
       |              ^
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    96 | function. If {sizeBreaks} vector is supplied then this will be ignored and
       |              ^
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   117 | \code{unitBase}. This will be supplied to pretty function. If {sizeBreaks} is
       |                                                               ^
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checkRd: (-1) kink_estimator.Rd:60: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
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  ‘.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.
'LazyData' is specified without a 'data' directory
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   144 | To export the classification of each pair set the argument code{keep.pairScore} to \code{TRUE} and call the function \code{getPairScore} on the result of the \code{BuyseTest} function. \cr \cr \cr
       |                                                                ^
Documented arguments not in \usage in Rd file 'calcIntegralSurv2_cpp.Rd':
  ‘dsurvival’

Documented arguments not in \usage in Rd file 'dot-calcIntegralCif_cpp.Rd':
  ‘cif’ ‘CIF_t’

Documented arguments not in \usage in Rd file 'validFCTs.Rd':
  ‘super.classes’

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:
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Malformed Description field: should contain one or more complete sentences.
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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checkRd: (-1) calcUnique.Rd:24: Lost braces
    24 | functions, and often the /code{cut()} function are relatively slow when working with tens of millions of rows or more.
       |                               ^
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    19 | \item{y}{response variable (in {0,1}).}
       |                                ^
Documented arguments not in \usage in Rd file 'get_result.Rd':
  ‘out’

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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    18 | B{\"o}hning, D.  and Schlattmann, P. and Lindsay, B. (1992). \dQuote{Computer-Assisted Analysis of Mixtures (C.A.MAN): Statistical Algorithms}. \emph{Biometrics}. \bold{48}, 283--303.
       |  ^
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     5 | Hepatitis B data from Schlattmann and B{\"o}hning (1993).
       |                                        ^
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    19 | Schlattmann, P. and B{\"o}hning, D. (1993). \dQuote{Mixture models and disease mapping}. \emph{Statistics in Medicine}. \bold{12}, 1943--1950.
       |                      ^
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   117 | D. B{\"o}hning, P. Schlattmann, B.G. Lindsay: C.A.MAN - Computer Assisted
       |     ^
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    19 | Schelp, F., P. Vivatanasept, P. Sitaputra, S. Sornmani, P. Pongpaew, N. Vudhivai, S. Egormaiphol, and D. B{\"o}hning.  \dQuote{Relationship of the morbidity of under-fives to anthropometric measurements and community health intervention.} \emph{Trop Med Parasitol}, 1990, 41(2), 121--126.
       |                                                                                                           ^
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   112 | Stop recording images with {camcorder}.
       |                            ^
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    35 | \item{resolution}{Resolution of the geographic data. {cancensus} will download simplified geometries by default. For lower level geometries like DB or DA this will be very close to the high resolution data.
       |                                                      ^
Argument items with no description in Rd file 'makeEventHistory.Rd':
  ‘type’
Argument items with no description in Rd file 'plotSeqCount.Rd':
  ‘segColors’
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  ‘MDA231_tree.pdf’
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    31 |      {RRD = ln(N_1/N_2)}
       |      ^
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    34 |      {PDI = (N_1/(N_1 + N_2))-0.5}
       |      ^
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    33 |   \item{Length of tip branch lengths (TIPS)}{Length of tip branch lengths (TIPS)}{Unlike UEH, this measure does not use the unique paths to each tips on the \strong{subtree} and instead gives the sum of the unique branches leading to the tips on the \strong{complete tree}.}
       |                                                                                  ^
'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:
    captr .1.4
    captr .1.3
    captr .1.2
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checkRd: (-1) zipcode.Rd:14: Lost braces; missing escapes or markup?
    14 | This is a dataset from the archived/orphaned {zipcode} package.
       |                                              ^
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    96 |     \item code{train} now removes duplicate models in the tuning grid. Duplicates could occur for models with discrete parameters.
       |               ^
checkRd: (-1) calibration.Rd:46: Lost braces; missing escapes or markup?
    46 | formula. This argument is not used for \code{xyplot.calibration}. For {ggplot.calibration}, \code{data}
       |                                                                       ^
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    13 | The exit status code{R CMD build}, invisibly.
       |                     ^
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
checkRd: (-1) compareCoefs.Rd:30: Lost braces
    30 | \item{pvals}{If code{TRUE} (the default is \code{FALSE}), print two-sided p-values
       |                     ^
checkRd: (-1) mcPlots.Rd:38: Lost braces; missing escapes or markup?
    38 |   axis.  To plot against a factor, you need to specify the full name of one of the indicator variables that define the factor.  For example, for a factor called \code{type} with levels \code{A}, \code{B} and {C}, using the usual drop-first level parameterization of the factor, the regressors for \code{type} would be \code{typeB} or \code{typeC}.  Similarly, to plot against the regressor \code{log(X4)}, you must specify \code{"log((X4)"}, not \code{"X4"}.
       |                                                                                                                                                                                                                 ^
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   137 | For  \code{style="filled"} several subarguments modify the appearance of the region:  code{alpha} is a number between 0 and 1 that specifies opacity with defualt 0.15, \code{border}, \code{TRUE} or \code{FALSE} specifies a border for the envelope, and \code{vertical} either \code{TRUE} or \code{FALSE}, modifies the behavior of the envelope at the edges of the graph.
       |                                                                                           ^
GNU make is a SystemRequirements.
Package vignettes without corresponding tangle output:
  ‘competingRisk.Rmd’
  ‘customizingpopTime.Rmd’
  ‘plotabsRisk.Rmd’
  ‘plotsmoothHazard.Rmd’
  ‘popTime.Rmd’
  ‘smoothHazard.Rmd’
'LazyData' is specified without a 'data' directory
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Invalid package aliases in Rd file 'EcoLinkPredict.Rd':
  ‘EcoLinkPredict-package’
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Documented arguments not in \usage in Rd file 'validate_cover_cats.Rd':
  ‘cats_target’

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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    13 | assessors, \code{J} products, code{M} attributes where CATA data have values 
       |                                   ^
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    12 | assessors, \code{J} products, code{M} attributes where CATA data have values 
       |                                   ^
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    12 | assessors, \code{J} products, code{M} attributes where CATA data have values 
       |                                   ^
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  ‘count-insolvency.Rnw’
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  ‘loglinear-birth.Rnw’
  ‘loglinear-leukoplakia.Rnw’
  ‘modbin-dust.Rnw’
  ‘modbin-foodstamp.Rnw’
  ‘modbin-unemployment1.Rnw’
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  ‘multinomial-addiction1.Rnw’
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  ‘multinomial-party1.Rnw’
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  ‘ordinal-retinopathy1.Rnw’
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    73 | Y = X_0 Beta_0^T + X_1 Beta_1^T + Z Gamma^T + E Sigma^{1/2},
       |                                                       ^
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   130 | \code{x1, x2, x3, \dots}- {input to the model, there must be one column
       |                           ^
Documented arguments not in \usage in Rd file 'add_catmaply_slider.Rd':
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Documented arguments not in \usage in Rd file 'add_catmaply_traces.Rd':
  ‘categorical_col’

Documented arguments not in \usage in Rd file 'catmaply_annotations.Rd':
  ‘fig’ ‘text_font_color’

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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Found the following files/directories:
  ‘catmapdata.fixed.effects.plot.pdf’ ‘catmapdata.funnel.plot.pdf’
  ‘catmapdata.output.txt’ ‘catmapdata.random.effects.plot.pdf’
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    79 |      Meteorol. Soc. textbf{30} 291-303. 
       |                           ^
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'LazyData' is specified without a 'data' directory
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GNU make is a SystemRequirements.
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    71 |   \item{states.samples}{(\code{niter}- \code{burn}) draws from p(alpha_t | Y_{1:T}).}
       |                                                                              ^
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    61 |   \item{states.samples}{(\code{niter}- \code{burn}) draws from p(alpha_t | Y_{1:T}).}
       |                                                                              ^
GNU make is a SystemRequirements.
Package vignette with \VignetteEngine{} not specifying an engine package:
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checkRd: (-1) cbc_design.Rd:160: Lost braces; missing escapes or markup?
   160 | see \code{?DoE.base::fac.design} as well as the JSS article on the {DoE.base}
       |                                                                    ^
checkRd: (-1) cbc_design.Rd:174: Lost braces; missing escapes or markup?
   174 | well as the JSS article on the {DoE.base} package (Grömping, 2018).
       |                                ^
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   197 | {idefix} package (Traets et al, 2020).
       | ^
checkRd: (-1) cbc_power.Rd:70: Lost braces; missing escapes or markup?
    70 | estimation. See the {logitr} documentation for details about other
       |                     ^
GNU make is a SystemRequirements.
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checkRd: (-1) CUR.Rd:25: Lost braces; missing escapes or markup?
    25 | The number of low-dimension of C (J1 < {N,M}).
       |                                        ^
checkRd: (-1) CUR.Rd:29: Lost braces; missing escapes or markup?
    29 | The number of low-dimension of R (J2 < {N,M}).
       |                                        ^
checkRd: (-1) CX.Rd:23: Lost braces; missing escapes or markup?
    23 | The number of low-dimension (J < {N,M}).
       |                                  ^
'LazyData' is specified without a 'data' directory
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  ‘hotcold.csv’
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checkRd: (-1) cdnet.Rd:91: Lost braces in \itemize; meant \describe ?
checkRd: (-1) cdnet.Rd:92: Lost braces in \itemize; meant \describe ?
checkRd: (-1) cdnet.Rd:93: Lost braces in \itemize; meant \describe ?
Problems with news in ‘NEWS.md’:
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Specified C++11: please drop specification unless essential
Packages which this enhances but not available for checking:
  'CirceR', 'Capr'
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    57 | \code{RU}: {Referent units}
       |            ^
checkRd: (-1) data.dtmr.Rd:59: Lost braces; missing escapes or markup?
    59 | \code{PI}: {Partitioning and iterating attribute}
       |            ^
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    61 | \code{APP}: {Appropriateness attribute}
       |             ^
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    63 | \code{MC}: {Multiplicative Comparison attribute}
       |            ^
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    62 | Note, that a more simple bound constraint method is used. Instead of the Transformation T_{a,b}(x) 
       |                                                                                           ^
Documented arguments not in \usage in Rd file 'buildModel.Rd':
  ‘x’ ‘y’

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

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

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:
  ‘figure01ceg.pdf’ ‘figure02ceg.pdf’ ‘staged.tree.graph.pdf’
  ‘stratified-event-tree-plot.pdf’
Documented arguments not in \usage in Rd file 'evaluate_rule.Rd':
  ‘class’

Documented arguments not in \usage in Rd file 'tree_leaf_nodes.Rd':
  ‘classes.’ ‘invert.’

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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checkRd: (-1) rMMSN.contour.Rd:20: Lost braces
    20 |  is an object resultant from the code{\link{fit.FMMSNC}} function.
       |                                      ^
Auto-generated content requiring editing in Rd file 'CensMFM-package.Rd':
  \details: ‘...o use the package, including the most important functions ~~’
Unexported objects imported by ':::' calls:
  ‘copula:::dCdu’ ‘copula:::fitCopStart’
  See the note in ?`:::` about the use of this operator.
Package suggested but not available for checking: ‘aorsf’
Documented arguments not in \usage in Rd file 'blackboost_train.Rd':
  ‘x’ ‘y’

Documented arguments not in \usage in Rd file 'survival_prob_mboost.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.
Running examples in ‘censored-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: aorsf_internal
> ### Title: Internal helper function for aorsf objects
> ### Aliases: aorsf_internal survival_prob_orsf
> ### Keywords: internal
> 
> ### ** Examples
> 
> library(aorsf)
Error in library(aorsf) : there is no package called ‘aorsf’
Execution halted
checkRd: (-1) listCensusApis.Rd:10: Lost braces; missing escapes or markup?
    10 | Scrapes {https://api.census.gov/data.json} and returns a dataframe
       |         ^
checkRd: (-1) call_api_once.Rd:36: Lost braces
    36 | A code{data.frame} with the requested variables at the requested
       |       ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) centroid.Rd:22: Lost braces; missing escapes or markup?
    22 | Centroid value C_{cen}(v) for node v defined as:
       |                  ^
checkRd: (-1) clusterrank.Rd:23: Lost braces; missing escapes or markup?
    23 | where the term f(c_{i}) accounts for the effect of i's local clustering and the term '+1' results from the contribution of \eqn{j}{j} itself. \cr
       |                    ^
Argument items with no description in Rd file 'centralplot.Rd':
  ‘alpha’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) cequre.Rd:31: Lost braces; missing escapes or markup?
    31 |   {epsi}^{# regression coefficients} times the initial value,
       |   ^
checkRd: (-1) cequre.Rd:31: Lost braces; missing escapes or markup?
    31 |   {epsi}^{# regression coefficients} times the initial value,
       |          ^
checkRd: (-1) cities.Rd:8: Lost braces; missing escapes or markup?
     8 | Dataset from package {maps}.
       |                      ^
Specified C++11: please drop specification unless essential
checkRd: (-1) performParallelNLMERun.Rd:22: Lost braces
    22 | \item{partialJob}{is /code{TRUE} if it is not required to stop the job
       |                           ^
checkRd: (-1) performParallelNLMERun.Rd:25: Lost braces
    25 | \item{allowIntermediateResults}{is /code{TRUE} if intermediate results
       |                                         ^
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
'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.
checkRd: (-1) cfc.tbasis.Rd:23: Lost braces
    23 | Assuming one-dimensional \code{p1} and \code{p2} for clarity, the algorithm calculates cumulative incidence function for cuase 1 using a recursive formula: \code{ci1[n+1] = ci1[n] + dci1[n]}, where \code{dci1[n] = 0.5*(p2[n] + p2[n+1])*(p1[n] - p1[n+1])}. The increment in cumulative incidence function for cause 2 is similarly calculated, \code{dci2[n] = 0.5*(p1[n] + p1[n+1])*(p2[n] - p2[n+1])}. These equations guarantee that \code{dci1[n] + dci2[n] = p1[n]*p2[n] - p1[n+1]*p2[n+1]}. Event-free probability is simply calculated as code{efp[n] = p1[n]*p2[n]}. Taken together, this numerical integration ensures that \code{efp[n+1] - efp[n] + dci1[n] + dci2[n] = 0}.
       |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           ^
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) CGGP_internal_calcpw.Rd:22: Lost braces; missing escapes or markup?
    22 | Predictive weights are Sigma^{-1}*y in standard GP.
       |                              ^
S3 methods shown with full name in Rd file 'select.cglasso.Rd':
  ‘select.cglasso’

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) comparisonsTable.cgOneFactorFit.Rd:47: Lost braces
    47 | 	call (see {\dots } section below.)
       |                   ^
checkRd: (-1) InfluenceMap.Rd:54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) InfluenceMap.Rd:55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) InfluenceMap.Rd:56: Lost braces in \itemize; meant \describe ?
checkRd: (-1) InfluenceMap.Rd:57: Lost braces in \itemize; meant \describe ?
Objects in \usage without \alias in Rd file 'influence-methods.Rd':
  ‘influence’

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) ftse100.Rd:8: Lost braces; missing escapes or markup?
     8 |  This dataset gives the daily returns (c_{t+1}/c_t -1) of the UK FTSE 100 index from 2nd April 1984 until the 13th September 2012.
       |                                          ^
checkRd: (-1) Hausdorff.dist.Rd:10: Lost braces; missing escapes or markup?
    10 | \item{vec1}{A \code{integer} vector forms a subset of {1, 2, ..., n}.}
       |                                                       ^
checkRd: (-1) Hausdorff.dist.Rd:12: Lost braces; missing escapes or markup?
    12 | \item{vec2}{A \code{integer} vector forms a subset of {1, 2, ..., n}.}
       |                                                       ^
checkRd: (-1) online.univar.multi.Rd:47-57: Lost braces
    47 | online.univar.one2 = function(y_vec, gamma, tau_gamma, ...){
       |                                                            ^
checkRd: (-1) online.univar.multi.Rd:50-55: Lost braces
    50 |   while(FLAG == 0 & t <= length(y_vec)){
       |                                        ^
checkRd: (-1) online.univar.multi.Rd:71-89: Lost braces
    71 | online.univar.one3 = function(y_vec, tau_vec, ...){
       |                                                   ^
checkRd: (-1) online.univar.multi.Rd:72-74: Lost braces
    72 |   if(length(y_vec) != length(tau_vec)){
       |                                       ^
checkRd: (-1) online.univar.multi.Rd:77-87: Lost braces
    77 |   while(FLAG == 0 & t <= length(y_vec)){
       |                                        ^
checkRd: (-1) online.univar.multi.Rd:81-86: Lost braces
    81 |     while(j < J & FLAG == 0){
       |                             ^
Invalid package aliases in Rd file 'jumpointsVar-package.Rd':
  ‘jumpointsVar-package’
Objects in \usage without \alias in Rd file 'jumpointsVar-internal.Rd':
  ‘seg.lm.fit0.gamma’ ‘max.rss’ ‘print.jumpointsVar’

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 'jumpointsVar-internal.Rd':
  ‘max.rss’

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

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) cql.Rd:28: Lost braces; missing escapes or markup?
    28 | {X} \code{<x_var>, <(x_facet)>}: \tab\tab\tab\tab  X-axis variable. May include a second categorical\cr
       | ^
checkRd: (-1) cql.Rd:30: Lost braces; missing escapes or markup?
    30 | {Y} \code{<y_var>}: \tab\tab\tab\tab Y-axis variable. *Not used for \code{hist}.\cr
       | ^
checkRd: (-1) cql.Rd:38: Lost braces; missing escapes or markup?
    38 | {Y_label} \code{'<ylab>'}: \tab\tab\tab\tab  Y-axis custom label. Defaults to <y_var>\cr
       | ^
checkRd: (-1) cql.Rd:39: Lost braces; missing escapes or markup?
    39 | {Legend} \code{'<legend>'}: \tab\tab\tab\tab  Legend custom label. Defaults to <x_category>\cr
       | ^
checkRd: (-1) cql.Rd:40: Lost braces; missing escapes or markup?
    40 | {Colorset} \code{'<clist>'}: \tab\tab\tab\tab  Custom set of colors for <x_category> levels.\cr
       | ^
checkRd: (-1) cql.Rd:42: Lost braces; missing escapes or markup?
    42 | {AggFunc} \code{'<func>'}: \tab\tab\tab\tab Summary function for \code{bar} type.\cr
       | ^
checkRd: (-1) cql.Rd:45: Lost braces; missing escapes or markup?
    45 | {Fit} \code{'<show_se>'}: \tab\tab\tab\tab Valid types: \code{true|false}. Fit quadratic line.\cr
       | ^
checkRd: (-1) cql.Rd:47: Lost braces; missing escapes or markup?
    47 | {ConfInt} \code{'<interval>'}: \tab\tab\tab\tab  Show error bars. Value is confidence interval value. E.g. '.95'
       | ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) create_unit_tests.Rd:17: Lost braces; missing escapes or markup?
    17 | Create `{testthat}` test cases for the code.
       |         ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) as.data.frame.checkglobals.Rd:43: Lost braces; missing escapes or markup?
    43 | \item \code{type}, the type of the detected entity, either \code{"global"} or {"import"}.
       |                                                                               ^
checkRd: (-1) as.matrix.checkglobals.Rd:32: Lost braces; missing escapes or markup?
    32 | \item \code{type}, the type of the detected entity, either \code{"global"} or {"import"}.
       |                                                                               ^
Package suggested but not available for checking: ‘darts’
checkRd: (-1) LoadCollection.Rd:7: Lost braces
     7 | for loading and saving code{CommunityCollection} objects to text files.
       |                            ^
checkRd: (-1) ShortestPaths.Rd:25: Lost braces
    25 | \references{Williams, R.J. and Berlow, E.L. and Dunne, J.A. and Barab{\'a}si, 
       |                                                                      ^
checkRd: (-1) YthanEstuary.Rd:19: Lost braces
    19 | Read G., St\"{o}hr S., Walter T.C., Costello M.J. Editors. (2012) World 
       |              ^
checkRd: (-1) calc_metrics.Rd:22-25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) calc_metrics.Rd:26-29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) calc_metrics.Rd:30-33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) calc_metrics.Rd:34-37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) calc_metrics.Rd:38-44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) calc_metrics.Rd:45-48: Lost braces in \itemize; meant \describe ?
checkRd: (-1) calc_metrics.Rd:49-52: Lost braces in \itemize; meant \describe ?
checkRd: (-1) calc_metrics.Rd:53-55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) calc_metrics.Rd:56-58: Lost braces in \itemize; meant \describe ?
checkRd: (-1) calc_metrics.Rd:59-61: Lost braces in \itemize; meant \describe ?
checkRd: (-1) calc_metrics.Rd:62-64: Lost braces in \itemize; meant \describe ?
checkRd: (-1) files2SpectraObject.Rd:142: Lost braces
   142 | (in code{matrix2SpectraObject}) is done one at
       |         ^
checkRd: (-1) check4Gaps.Rd:31: Lost braces; missing escapes or markup?
    31 | Also a plot if {y} is provided.  In the event there are no gaps found,
       |                ^
Documented arguments not in \usage in Rd file 'dot-chkArgs.Rd':
  ‘mode.’

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: ‘countreg’
'LazyData' is specified without a 'data' directory
checkRd: (-1) C316.amp.Rd:28-32: Lost braces
    28 |     40 x {
       |          ^
checkRd: (-1) C317.amp.Rd:28-32: Lost braces
    28 |     40 x {
       |          ^
checkRd: (-1) C60.amp.Rd:63-67: Lost braces
    63 |     40 x {
       |          ^
Invalid package aliases in Rd file 'ChIPtest-package.Rd':
  ‘ChIPtest_1.0-package’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘cmdstanr’
Package unavailable to check Rd xrefs: ‘cmdstanr’
checkRd: (-1) logB.to.OBIGT.Rd:39: Lost braces
    39 | To avoid overfitting, only the first three parameters (code{G}, \code{S}, and \code{c1}) are used by default.
       |                                                            ^
checkRd: (-1) util.fasta.Rd:39: Lost braces; missing escapes or markup?
    39 | If {id} is not given, and a UniProt FASTA header is detected (regular expression \code{"\\|......\\|.*_"}), information there (accession, name, organism) is split into the \code{protein}, \code{abbrv}, and {organism} columns of the resulting data frame.
       |    ^
checkRd: (-1) util.fasta.Rd:39: Lost braces; missing escapes or markup?
    39 | If {id} is not given, and a UniProt FASTA header is detected (regular expression \code{"\\|......\\|.*_"}), information there (accession, name, organism) is split into the \code{protein}, \code{abbrv}, and {organism} columns of the resulting data frame.
       |                                                                                                                                                                                                               ^
Problems with news in ‘NEWS.md’:
No news entries found.
Objects in \usage without \alias in Rd file 'choplump-internal.Rd':
  ‘chooseMatrix’

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 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’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) chunker-methods.Rd:63: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) chunker-methods.Rd:64: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) chunker-methods.Rd:69: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) chunker-methods.Rd:70: Lost braces in \enumerate; meant \describe ?
Documented arguments not in \usage in Rd file 'SearchEmptyClusters.Rd':
  ‘oldcluster’ ‘SSminvec’

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) ec.datalag.Rd:5: Lost braces; missing escapes or markup?
     5 | \title{prepares Dy y_1 Dy_1 ... Dy_{nlag-1} for estimation}
       |                                    ^
checkRd: (-1) ec.datalag.Rd:15: Lost braces
    15 | ymat contains the folloiwing columns {Dy y_1 Dy_1 ... Dy_{nlag-1}}
       |                                      ^
checkRd: (-1) ec.datalag.Rd:15: Lost braces; missing escapes or markup?
    15 | ymat contains the folloiwing columns {Dy y_1 Dy_1 ... Dy_{nlag-1}}
       |                                                          ^
checkRd: (-1) lagn.Rd:21: Lost braces; missing escapes or markup?
    21 |              REM: alternative to "lead-lag" {dplyr} which applies to vector y
       |                                             ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘userfriendlyscience’
checkRd: (-1) CIplot.Rd:58: Lost braces; missing escapes or markup?
    58 | \item{las}{numeric in {0,1,2,3}; the style of axis labels.
       |                       ^
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
checkRd: (-1) rstable.Rd:42: Lost braces
    42 | Lo\"{g}ae\"{v}e, M. (1977). Probability Theory I. (fourth edition) Springer-Verlag, New York.
       |     ^
checkRd: (-1) rstable.Rd:42: Lost braces
    42 | Lo\"{g}ae\"{v}e, M. (1977). Probability Theory I. (fourth edition) Springer-Verlag, New York.
       |            ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) doseFind.Rd:63: Lost braces in \itemize; meant \describe ?
checkRd: (-1) doseFind.Rd:64: Lost braces in \itemize; meant \describe ?
checkRd: (-1) doseFind.Rd:50: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) doseFind.Rd:51: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) doseFind.Rd:52: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) doseFind.Rd:53: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) quickInverse.Rd:56: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) quickInverse.Rd:57: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) quickInverse.Rd:58: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) quickIsotone.Rd:44: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) quickIsotone.Rd:45: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) quickIsotone.Rd:46: Lost braces in \itemize; \value handles \item{}{} directly
Specified C++11: please drop specification unless essential
checkRd: (-1) data_generator.Rd:93: Lost braces; missing escapes or markup?
    93 |   \item{estimand_mean}{List of means of the FULL, S_{++}, S_{*+} and
       |                                                     ^
checkRd: (-1) data_generator.Rd:93: Lost braces; missing escapes or markup?
    93 |   \item{estimand_mean}{List of means of the FULL, S_{++}, S_{*+} and
       |                                                             ^
checkRd: (-1) data_generator.Rd:95: Lost braces; missing escapes or markup?
    95 |   \item{estimand_sd}{List of standard deviations of the FULL, S_{++}, S_{*+}
       |                                                                 ^
checkRd: (-1) data_generator.Rd:95: Lost braces; missing escapes or markup?
    95 |   \item{estimand_sd}{List of standard deviations of the FULL, S_{++}, S_{*+}
       |                                                                         ^
checkRd: (-1) data_generator_loop.Rd:96: Lost braces; missing escapes or markup?
    96 |   \item{estimand_mean}{List of means of the FULL, S_{++}, S_{*+} and
       |                                                     ^
checkRd: (-1) data_generator_loop.Rd:96: Lost braces; missing escapes or markup?
    96 |   \item{estimand_mean}{List of means of the FULL, S_{++}, S_{*+} and
       |                                                             ^
checkRd: (-1) data_generator_loop.Rd:98: Lost braces; missing escapes or markup?
    98 |   \item{estimand_sd}{List of standard deviations of the FULL, S_{++},
       |                                                                 ^
checkRd: (-1) data_generator_loop.Rd:99: Lost braces; missing escapes or markup?
    99 |   S_{*+} and PP estimands}
       |     ^
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) ciu.ggplot.col.Rd:41: Lost braces; missing escapes or markup?
    41 | \item{ind.inputs}{Indices of input features to explain (the set {i} in CIU
       |                                                                 ^
checkRd: (-1) ciu.meta.explain.Rd:27: Lost braces; missing escapes or markup?
    27 | \item{ind.inputs}{Indices of input features to explain (the set {i} in CIU
       |                                                                 ^
checkRd: (-1) ciu.meta.result.new.Rd:30: Lost braces; missing escapes or markup?
    30 | \item{ind.inputs}{Indices of input features to explain (the set {i} in CIU
       |                                                                 ^
checkRd: (-1) ciu.textual.Rd:38: Lost braces; missing escapes or markup?
    38 | \item{ind.inputs}{Indices of input features to explain (the set {i} in CIU
       |                                                                 ^
'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) get_langs.Rd:13: Lost braces
    13 | character vector listing all the languages that tag API call supports. See \code{\link{tag_images}} and code{\link{tag_image_urls}}
       |                                                                                                             ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) cd01-0-distanceMatrix.Rd:37-39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) cd01-0-distanceMatrix.Rd:40-43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) cd01-0-distanceMatrix.Rd:44-46: Lost braces in \itemize; meant \describe ?
checkRd: (-1) cd01-0-distanceMatrix.Rd:47-48: Lost braces in \itemize; meant \describe ?
checkRd: (-1) cd01-0-distanceMatrix.Rd:49-50: Lost braces in \itemize; meant \describe ?
checkRd: (-1) cd01-0-distanceMatrix.Rd:51-52: Lost braces in \itemize; meant \describe ?
checkRd: (-1) cd02-1-cluster3.Rd:25: Lost braces
    25 |   Kevin R. Coombes email{krc@silicovore.com}
       |                         ^
checkRd: (-1) cd03-0-ClusterTest-class.Rd:70: Lost braces
    70 |   Kevin R. Coombes email{krc@silicovore.com}
       |                         ^
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) clean.Rd:136: Lost braces in \itemize; meant \describe ?
checkRd: (-1) clean.Rd:137: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) clean.Rd:142: 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
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
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) cf_save_kml.Rd:68: Lost braces
    68 | \code{\link{cf_find_station}} and code{vignette("choose-station")} for
       |                                       ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) clinsig.Rd:129: Lost braces
   129 |  be calculated with the measures specified in samp{mct} and samp{disp},
       |                                                   ^
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   129 |  be calculated with the measures specified in samp{mct} and samp{disp},
       |                                                                 ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) print.clogitL1.Rd:21: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) print.clogitL1.Rd:23: Lost braces in \itemize; meant \describe ?
Problems with news in ‘NEWS.md’:
No news entries found.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
checkRd: (-1) cb_participant_count.Rd:13: Lost braces
    13 | \item{query}{A phenotype query defined using the code{\link{phenotype}} function and logic operators (see example below)}
       |                                                      ^
checkRd: (-1) phenotype.Rd:10: Lost braces
    10 | \item{id}{A single phenotype id. Possible phenotyoes can be explored using the code{\link{cb_search_phenotypes}} function}
       |                                                                                    ^
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.
checkRd: (-1) clr.Rd:24: Lost braces
    24 | the sense that its Karhunen-Lo\`{e}ve decomposition has qx terms only.}
       |                                 ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) impute_covariance_matrix.Rd:74-79: Lost braces in \itemize; meant \describe ?
checkRd: (-1) impute_covariance_matrix.Rd:80-87: Lost braces in \itemize; meant \describe ?
checkRd: (-1) impute_covariance_matrix.Rd:88-98: 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) estimate_H_fractions.Rd:5: Lost braces; missing escapes or markup?
     5 | \title{Estimates |H_i|/|H_{i+1}| for the first r rows}
       |                           ^
Documented arguments not in \usage in Rd file 'auxiliary_functions.Rd':
  ‘edelist’

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.
Objects in \usage without \alias in Rd file 'clustEff-internal.Rd':
  ‘.get_ave_sil_width’ ‘.get_withinSS’ ‘print.clustEff’
  ‘print.summary.clustEff’ ‘print.fpcac’ ‘print.summary.fpcac’

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:
  ‘clusterhap_reports’
Specified C++11: please drop specification unless essential
checkRd: (-1) HTKmeans.Rd:62: Lost braces
    62 | \item{centers }{A matrix of cluster centres.}
       |      ^
checkRd: (-1) HTKmeans.Rd:62: Lost braces
    62 | \item{centers }{A matrix of cluster centres.}
       |                ^
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    63 | \item{cluster }{A vector of integers (from 1:\code{k}) indicating the cluster to which each point is allocated.}
       |      ^
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    63 | \item{cluster }{A vector of integers (from 1:\code{k}) indicating the cluster to which each point is allocated.}
       |                ^
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    64 | \item{itnb }{The number of iterations executed until convergence}
       |      ^
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    64 | \item{itnb }{The number of iterations executed until convergence}
       |             ^
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    65 | \item{converged }{Whether the algorithm stopped by converging or through reaching the maximum number of itertions.}
       |      ^
checkRd: (-1) HTKmeans.Rd:65: Lost braces
    65 | \item{converged }{Whether the algorithm stopped by converging or through reaching the maximum number of itertions.}
       |                  ^
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.
'LazyData' is specified without a 'data' directory
checkRd: (-1) cluster.Gen.rd:82: Lost braces
    82 | Steinley, D., Henson, R. (2005), \emph{OCLUS: an analytic method for generating clusters with known overlap}, "Journal of Classification", vol. 22, 221-250. Available at: \\doi{10.1007/s00357-005-0015-6}.
       |                                                                                                                                                                                 ^
checkRd: (-1) index.DB.rd:23: Lost braces; missing escapes or markup?
    23 | \item{R}{R matrix $(S_r+S_s)/d_{rs}$}
       |                                ^
checkRd: (-1) index.GAP.rd:12: Lost braces; missing escapes or markup?
    12 | "pc" - generate the reference variables from a uniform distribution over a box aligned with the principal components of the data. In detail, if $X=\{x_{ij}\}$  is our   n x m data matrix, assume that the columns have mean 0 and compute the singular value decomposition $X=UDV^T$. We transform via $X'=XV$ and then draw uniform features Z'  over the ranges of the columns of X' , as in method a) above. Finally we back-transform via $Z=Z'V^T$   to give reference data Z 
       |                                                                                                                                                        ^
checkRd: (-1) pattern.GDM1.rd:77: Lost braces
    77 | Jajuga, K., Walesiak, M., Bak, A. (2003), \emph{On the general distance measure}, In: M. Schwaiger, O. Opitz (Eds.), Exploratory data analysis in empirical research, Springer-Verlag, Berlin, Heidelberg, 104-109. Available at: doi{10.1007/978-3-642-55721-7_12}.
       |                                                                                                                                                                                                                                      ^
checkRd: (-1) dtmvnom.Rd:30: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) CMAPSS.Rd:10: Lost braces
    10 | \item \code{train}{ a list of class "hhsmm.data" as the train dataset}
       |                   ^
checkRd: (-1) CMAPSS.Rd:11: Lost braces
    11 | \item \code{test}{ a list of class "hhsmm.data" as the test dataset}
       |                  ^
checkRd: (-1) CMAPSS.Rd:12: Lost braces
    12 | \item \code{subsets}{ a matrix containig the number of units in each subset of the CMAPSS data set (FD001-FD004) for the train and test datasets}
       |                     ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) cmb.search.Rd:50: Lost braces; missing escapes or markup?
    50 |   \item{order}{applied conditioning order {length p}}
       |                                           ^
checkRd: (-1) gp.realize.Rd:20: Lost braces; missing escapes or markup?
    20 | The list \code{l.v} is created by \code{makedistlist()} from a {n x p} design matrix on which to generate the unconditional GP realization.  The correlation parameters take on values in \code{(0,1)} and use the Gaussian correlation model, calculated as \code{rho^d(xi,xj)^2}.  This helper function is used to create the demonstration data used in the example for \code{calibrate()}.
       |                                                                ^
'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) bvp.Rd:24: Lost braces
    24 | differential equations.  The code{midptivp} method solves initial
       |                                  ^
checkRd: (-1) ivp.Rd:38: Lost braces
    38 | differential equations.  The code{midptivp} method solves initial
       |                                  ^
checkRd: (-1) ivpsys.Rd:29: Lost braces
    29 | differential equations.  The code{midptivp} method solves initial
       |                                  ^
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: \#
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘tobit1’
'LazyData' is specified without a 'data' directory
checkRd: (-1) cnlt.reg.Rd:43: Lost braces
    43 | \emph{Technometrics}, bold{60} (1), 48-60, DOI 10.1080/00401706.2017.1281846.\cr\cr
       |                           ^
checkRd: (-1) fwtnppermC.Rd:35: Lost braces
    35 | Given \eqn{n} points on a line, \env{x}, each with a corresponding env{f} value this function computes
       |                                                                       ^
Specified C++11: please drop specification unless essential
checkRd: (-1) conversion.Rd:66-67: Lost braces in \itemize; meant \describe ?
checkRd: (-1) conversion.Rd:68-69: Lost braces in \itemize; meant \describe ?
checkRd: (-1) conversion.Rd:70-72: Lost braces in \itemize; meant \describe ?
checkRd: (-1) conversion.Rd:72-74: Lost braces in \itemize; meant \describe ?
checkRd: (-1) conversion.Rd:75-76: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tools.Rd:103-104: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tools.Rd:105-106: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tools.Rd:107-109: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tools.Rd:109-111: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tools.Rd:112-113: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
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’
Documented arguments not in \usage in Rd file 'lb_calculation.Rd':
  ‘qu.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.
'LazyData' is specified without a 'data' directory
checkRd: (-1) drqssbc.Rd:83: Escaped LaTeX specials: \&
checkRd: (-1) qbsks.Rd:81: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘rkward’
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’
checkRd: (-1) educFM.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) educFM.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) educFM.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) educFM.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) educFM.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) educFM.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) educFM.Rd:28: Lost braces in \itemize; meant \describe ?
Package suggested but not available for checking: ‘userfriendlyscience’
checkRd: (-1) cb_add_col_attributes.Rd:41-51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) cb_add_col_attributes.Rd:52-61: Lost braces in \itemize; meant \describe ?
checkRd: (-1) cb_add_col_attributes.Rd:62-95: Lost braces in \itemize; meant \describe ?
checkRd: (-1) cb_add_col_attributes.Rd:96-131: Lost braces in \itemize; meant \describe ?
checkRd: (-1) cb_add_col_attributes.Rd:132-141: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) asVarName.Rd:26-27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) asVarName.Rd:28-30: Lost braces in \itemize; meant \describe ?
Found the following files/directories:
  ‘foo.R’ ‘foo.html’
Package suggested but not available for checking: ‘bvpSolve’
'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) kprime.Rd:36: Lost braces; missing escapes or markup?
    36 | kprime is a {p,d,q} set of functions that compute the K-prime distribution. This distribution has many applications,
       |             ^
checkRd: (-1) lsecond.Rd:37: Lost braces; missing escapes or markup?
    37 | lsecond are {p,d,q} functions that compute the Lambda-second (L") distribution. This
       |             ^
checkRd: (-1) pilsecond.Rd:39: Lost braces; missing escapes or markup?
    39 | pilsecond are {p,d,q} functions that compute the prior-informed Lambda-second (L") distribution. This
       |               ^
Package suggested but not available for checking: ‘CodelistGenerator’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) getHistList.Rd:32: Lost braces; missing escapes or markup?
    32 | ({FALSE})? If a bin is empty, the center of the bin is returned as the
       |  ^
checkRd: (-1) imageClusterPipeline.Rd:82: Lost braces; missing escapes or markup?
    82 | of the bin ({FALSE})? If a bin is empty, the center of the bin is returned
       |             ^
'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
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) colour_values.Rd:143: Lost braces in \itemize; meant \describe ?
checkRd: (-1) colour_values.Rd:144: Lost braces in \itemize; meant \describe ?
checkRd: (-1) colour_values_rgb.Rd:143: Lost braces in \itemize; meant \describe ?
checkRd: (-1) colour_values_rgb.Rd:144: Lost braces in \itemize; meant \describe ?
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.
Malformed Description field: should contain one or more complete sentences.
checkRd: (-1) xsimplex.Rd:6: Lost braces; missing escapes or markup?
     6 |              Generates all points on a {p,n} simplex lattice (i.e. a p-part
       |                                        ^
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) sum_every_n.Rd:15: Lost braces; missing escapes or markup?
    15 | \code{sum_every_n} returns a vector of sums of every \code{n}^{th} element of the vector \code{x}.
       |                                                               ^
checkRd: (-1) sum_every_n1.Rd:15: Lost braces; missing escapes or markup?
    15 | \code{sum_every_n1} returns a vector of sums of every \code{n}^{th} element of the vector \code{x}, plus 1.
       |                                                                ^
Argument items with no description in Rd file 'summary.CommunityClimateInput.Rd':
  ‘object’ ‘\dots’
Argument items with no description in Rd file 'summary.CommunityClimateStatistics.Rd':
  ‘object’ ‘\dots’
Found the following files/directories:
  ‘cometExactTest_plot.pdf’
checkRd: (-1) calcHbExSteady.Rd:57-103: Lost braces
    57 | Returns a data.frame with the following columns \cr{
       |                                                    ^
checkRd: (-1) calcIso7933.Rd:71-100: Lost braces
    71 | \code{calcISO7933} returns a data.frame with the following items: \cr{
       |                                                                      ^
checkRd: (-1) calcdTNZ.Rd:53-57: Lost braces
    53 | \code{calcdTNZ} returns a dataframe with the columns dTNZ, dTNZTs, dTNZTa. Thereby \cr{
       |                                                                                       ^
Objects in \usage without \alias in Rd file 'comf-internal.Rd':
  ‘calcet’

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) BMD.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) BMD.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
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checkRd: (-1) BMD.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
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checkRd: (-1) add.risk.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
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checkRd: (-1) comire.gibbs.Rd:66: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) comire.gibbs.Rd:67-68: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) comire.gibbs.Rd:69: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) comire.gibbs.Rd:70: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) comire.gibbs.Rd:71: Lost braces in \itemize; \value handles \item{}{} directly
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checkRd: (-1) comire.gibbs.Rd:73: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) comire.gibbs.Rd:74: Lost braces in \itemize; \value handles \item{}{} directly
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checkRd: (-1) comire.gibbs.Rd:76: Lost braces in \itemize; \value handles \item{}{} directly
Specified C++11: please drop specification unless essential
checkRd: (-1) count_pairs.Rd:19-20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) count_pairs.Rd:21-22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) count_pairs.Rd:23-24: Lost braces in \itemize; \value handles \item{}{} directly
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    36 | {0, 1}.
       | ^
checkRd: (-1) score_log_semiparam.Rd:40: Lost braces; missing escapes or markup?
    40 | values in {0, 1}.
       |           ^
checkRd: (-1) sort_pairs.Rd:18: Lost braces in \itemize; \value handles \item{}{} directly
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checkRd: (-1) sort_pairs.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sort_pairs.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
Specified C++11: please drop specification unless essential
checkRd: (-1) hmm.Rd:47-55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) hmm.Rd:56-62: Lost braces in \itemize; meant \describe ?
checkRd: (-1) hmm.Rd:63-70: Lost braces in \itemize; meant \describe ?
checkRd: (-1) hmm.Rd:71-74: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) hmm.Rd:79-84: Lost braces in \itemize; meant \describe ?
checkRd: (-1) hmm.Rd:85-89: Lost braces in \itemize; meant \describe ?
checkRd: (-1) hmm.Rd:95-103: Lost braces in \itemize; meant \describe ?
checkRd: (-1) hmm.Rd:104-107: Lost braces in \itemize; meant \describe ?
checkRd: (-1) hmm.Rd:108-111: Lost braces in \itemize; meant \describe ?
checkRd: (-1) hmm.Rd:112-118: Lost braces in \itemize; meant \describe ?
checkRd: (-1) hmm.Rd:119-129: Lost braces in \itemize; meant \describe ?
checkRd: (-1) hmm.Rd:130-133: Lost braces in \itemize; meant \describe ?
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘CAM’
checkRd: (-1) ARE_tte.Rd:36: Lost braces; missing escapes or markup?
    36 | \item{case}{integer parameter in {1,2,3,4}
       |                                  ^
checkRd: (-1) effectsize_tte.Rd:37: Lost braces; missing escapes or markup?
    37 | \item{case}{integer parameter in {1,2,3,4}
       |                                  ^
checkRd: (-1) plot_tte.Rd:37: Lost braces; missing escapes or markup?
    37 | \item{case}{integer parameter in {1,2,3,4}
       |                                  ^
checkRd: (-1) samplesize_tte.Rd:39: Lost braces; missing escapes or markup?
    39 | \item{case}{integer parameter in {1,2,3,4}
       |                                  ^
checkRd: (-1) simula_tte.Rd:35: Lost braces; missing escapes or markup?
    35 | \item{case}{integer parameter in {1,2,3,4}
       |                                  ^
checkRd: (-1) surv_tte.Rd:36: Lost braces; missing escapes or markup?
    36 | \item{case}{integer parameter in {1,2,3,4}
       |                                  ^
Documented arguments not in \usage in Rd file 'CopulaSelection.Rd':
  ‘rhoType’

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) glass.Rd:10: Lost braces
    10 | \item{item}{factor}{200 levels - which item the measurements came from}
       |                    ^
checkRd: (-1) glass.Rd:11-12: Lost braces
    11 | \item{fragment}{factor}{4 levels - which of the four fragments from each item the observations were made
       |                        ^
checkRd: (-1) glass.Rd:13: Lost braces
    13 | \item{logNaO}{numeric}{log of sodium concentration to oxygen concentration}
       |                       ^
checkRd: (-1) glass.Rd:14: Lost braces
    14 | \item{logMgO}{numeric}{log of magnesium concentration to oxygen concentration}
       |                       ^
checkRd: (-1) glass.Rd:15: Lost braces
    15 | \item{logAlO}{numeric}{log of aluminium concentration to oxygen concentration}
       |                       ^
checkRd: (-1) glass.Rd:16: Lost braces
    16 | \item{logSiO}{numeric}{log of silicon concentration to oxygen concentration}
       |                       ^
checkRd: (-1) glass.Rd:17: Lost braces
    17 | \item{logKO}{numeric}{log of potassium concentration to oxygen concentration}
       |                      ^
checkRd: (-1) glass.Rd:18: Lost braces
    18 | \item{logCaO}{numeric}{log of calcium concentration to oxygen concentration}
       |                       ^
checkRd: (-1) glass.Rd:19: Lost braces
    19 | \item{logFeO}{numeric}{log of iron concentration to oxygen concentration}
       |                       ^
checkRd: (-1) atomdeps.Rd:9: Lost braces
     9 |  \item{"tangle"}: {Dihedral angle defined by atoms A-B-C-D as described below. \code{NA}'s represent the free side chain dihedral angles \emph{chi} for that amino acid.}
       |                   ^
checkRd: (-1) atomdeps.Rd:10: Lost braces; missing escapes or markup?
    10 |  \item{"names"}: {The component atoms of the amino acid side chain.  Represents atom D in the dihedral.}
       |                  ^
checkRd: (-1) atomdeps.Rd:11: Lost braces; missing escapes or markup?
    11 |  \item{"matx"}: {The names of atoms A,B,C in the dihedral, with rows corresponding to the atoms in "names".}
       |                 ^
checkRd: (-1) atomdeps.Rd:12: Lost braces; missing escapes or markup?
    12 |  \item{"bangle"}: {Planar bond angle formed between B-C-D}
       |                   ^
checkRd: (-1) atomdeps.Rd:13: Lost braces; missing escapes or markup?
    13 |  \item{"blength"}: {Bond length between C-D}
       |                    ^
checkRd: (-1) keener.Rd:82: Lost braces; missing escapes or markup?
    82 | a_{ij} = (S_ij + 1) / (S_ij + S_ji + 2). This step should make comparing
       |   ^
Rd files without \alias:
  ‘CompoundEvents-package.Rd’
'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
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...’
checkRd: (-1) concstats_hhi.Rd:13: Lost braces; missing escapes or markup?
    13 | value is required. Ranges from {0, 1} and often used for comparison over
       |                                ^
checkRd: (-1) KCI.Rd:44: Lost braces
    44 |  \item \code{testStatistic} the statistic Tr(K_{(ddot{(Y)}|X)} * K_{(E|X)})
       |                                                ^
checkRd: (-1) KCI.Rd:44: Lost braces
    44 |  \item \code{testStatistic} the statistic Tr(K_{(ddot{(Y)}|X)} * K_{(E|X)})
       |                                                      ^
checkRd: (-1) KCI.Rd:44: Lost braces; missing escapes or markup?
    44 |  \item \code{testStatistic} the statistic Tr(K_{(ddot{(Y)}|X)} * K_{(E|X)})
       |                                                                    ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) babies.Rd:35: 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) mya.Rd:18: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mya.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mya.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mya.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mya.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
'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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) coversim.Rd:103: Lost braces; missing escapes or markup?
   103 | \item{xlas}{numeric in {0, 1, 2, 3} specifying the style of axis labels (see \code{las} in \code{\link{par}},
       |                        ^
checkRd: (-1) coversim.Rd:106: Lost braces; missing escapes or markup?
   106 | \item{ylas}{numeric in {0, 1, 2, 3} specifying the style of axis labels (see \code{las} in \code{\link{par}},
       |                        ^
checkRd: (-1) crplot.Rd:77: Lost braces; missing escapes or markup?
    77 | \item{xlas}{numeric in {0, 1, 2, 3} specifying the style of axis labels (see \code{las} in \code{\link{par}}).}
       |                        ^
checkRd: (-1) crplot.Rd:79: Lost braces; missing escapes or markup?
    79 | \item{ylas}{numeric in {0, 1, 2, 3} specifying the style of axis labels (see \code{las} in \code{\link{par}}).}
       |                        ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) binary_class_cm.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) binary_class_cm.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) binary_class_cm.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) binary_class_cm.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) multi_class_cm.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) multi_class_cm.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) multi_class_cm.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) multi_class_cm.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
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
checkRd: (-1) NetStats.Rd:15: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) NetStats.Rd:16: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) NetStats.Rd:17: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) NetStats.Rd:18: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) NetStats.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) NetStats.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) NetStats.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) NetStats.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) NetStats.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) generate_network.Rd:35: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) generate_network.Rd:36: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) generate_network.Rd:37: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) generate_network.Rd:38: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) generate_network.Rd:39: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) generate_network.Rd:40: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) generate_network.Rd:41: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) generate_network.Rd:42: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) generate_network.Rd:43: Lost braces in \itemize; \value handles \item{}{} directly
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
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'conosPanel', 'p2data'
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in Rd file 'checkCountsWholeNumbers.Rd':
  ‘aggregated.samples’

Documented arguments not in \usage in Rd file 'getGlobalClusterMarkers.Rd':
  ‘min.percent.samples.expression’

Documented arguments not in \usage in Rd file 'getPercentGlobalClusters.Rd':
  ‘min.cell.count.per.samples’

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) Univranks.Rd:69: Lost braces; missing escapes or markup?
    69 | To obtain the preference rankings from the paired comparisons the procedure has been the following: the first row of the raw data is [1  3  2   1   2   1  1  2  1   1   1   2   1    1   2]. London is preferred to Paris, St. Gallen, Barcelona Stockholm (LP, LM, LSg, LB and LSt are always equal to 1), and there is no preference between London and Milan (they are tied); Milan is preferred to Paris (PM = 2), St. Gallen, Barcelona and Stockholm; and so on. The first ordering is then <{L M} Sg St B P> corresponding to a ranking [1,5,1,2,4,3], where the columns indicate L  P  M Sg  B St.  
       |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     ^
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
checkRd: (-1) getConvexHull.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getConvexHull.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getConvexHull.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) cf_grid.Rd:38: Lost braces; missing escapes or markup?
    38 | heat.colors, terrain.colors, topo.colors, and function(x) {gray((1:x)/x)}.}
       |                                                           ^
checkRd: (-1) cf_highdim.Rd:58: Lost braces; missing escapes or markup?
    58 | heat.colors, terrain.colors, topo.colors, and function(x) {gray((1:x)/x)}.}
       |                                                           ^
checkRd: (-1) gcf_grid.Rd:51: Lost braces; missing escapes or markup?
    51 | heat.colors, terrain.colors, topo.colors, and function(x) {gray((1:x)/x)}.}
       |                                                           ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) set_seed.Rd:15: Lost braces
    15 | a code{\link{DISTRIBUTION}} object of the same class
       |       ^
Documented arguments not in \usage in Rd file 'print_table.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
'LazyData' is specified without a 'data' directory
checkRd: (-1) CovrgPlot.Rd:28: Lost braces; missing escapes or markup?
    28 | \item{plotCI}{a vector of up to 4 numbers out of the set {1,2,3,4}, corresponding to which
       |                                                          ^
Specified C++11: please drop specification unless essential
Invalid package aliases in Rd file 'coopProductGame-package.Rd':
  ‘coopProducGame-package’
checkRd: (-1) copCAR.Rd:40: Lost braces
    40 |        item{\code{maxit}}{the maximum number of iterations to be used by \code{\link{optim}} when optimizing the objective function. Defaults to \code{1000}.}
       |            ^
checkRd: (-1) copCAR.Rd:40: Lost braces
    40 |        item{\code{maxit}}{the maximum number of iterations to be used by \code{\link{optim}} when optimizing the objective function. Defaults to \code{1000}.}
       |                          ^
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}
       |                                                                              ^
checkRd: (-1) ComputeCope.Rd:50: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ComputeCope.Rd:52: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ComputeCope.Rd:53: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ComputeCope.Rd:54-56: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ComputeCope.Rd:57-61: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) DrawContour.Rd:5: Lost braces; missing escapes or markup?
     5 | \title{Draws the contour {f=c}.}
       |                          ^
checkRd: (-1) DrawContour.Rd:20: Lost braces; missing escapes or markup?
    20 | Draws the contour {f=c}.
       |                   ^
checkRd: (-1) cope.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) cope.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) cope.Rd:33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) cope.Rd:35: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
checkRd: (-1) cdtamodel.Rd:15-19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) cdtamodel.Rd:20-21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) cdtamodel.Rd:22-23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) cdtamodel.Rd:24-25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) cdtamodel.Rd:26-31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) cdtamodel.Rd:32-33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) cdtamodel.Rd:34-35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) cdtamodel.Rd:36-38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) cdtamodel.Rd:39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) cdtamodel.Rd:40-41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) cdtamodel.Rd:42-44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) cdtamodel.Rd:45-46: Lost braces in \itemize; meant \describe ?
checkRd: (-1) cdtamodel.Rd:47: Lost braces in \itemize; meant \describe ?
checkRd: (-1) cdtamodel.Rd:48: Lost braces in \itemize; meant \describe ?
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
'LazyData' is specified without a 'data' directory
checkRd: (-1) CopulaREMADA.Rd:17: Lost braces; missing escapes or markup?
    17 | {gl$nodes} and weights {gl$weights}.
       | ^
checkRd: (-1) CopulaREMADA.Rd:17: Lost braces; missing escapes or markup?
    17 | {gl$nodes} and weights {gl$weights}.
       |                        ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) getSurface.Rd:22: Lost braces
    22 | value \code{getSurface} shortens the output of \code{conv} to remove artificial surface layers. The output is thus a subset of the input, and identical in structure to the /code{conv} output.
       |                                                                                                                                                                                  ^
checkRd: (-1) cvGen.Rd:29: Lost braces
    29 | The function code{gatherFromList} returns a list with components containing elements of the same name.
       |                  ^
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) CorMID.Rd:54: Lost braces; missing escapes or markup?
    54 |  individual compound containing 2 carbons and observe a vector of {978,22,0}.
       |                                                                   ^
checkRd: (-1) CorMID.Rd:58: Lost braces; missing escapes or markup?
    58 |  The equivalent corMID vector would be {1,0,0}, indicating that the non-labeled
       |                                        ^
checkRd: (-1) carstats.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) carstats.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) carstats.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) carstats.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) carstats.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) carstats.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) carstats.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) carstats.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) carstats.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) titanic.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) titanic.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) titanic.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) titanic.Rd:14: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
checkRd: (-1) get_policy_scores.Rd:63: Lost braces
    63 | \code{low_estimate}\\code{high_estimate} columns. The \code{SD_estimate} column has the standard deviation of the
       |                          ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) jointprobs.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) jointprobs.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) jointprobs.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) jointprobs.Rd:21: Lost braces; missing escapes or markup?
    21 | \eqn{K+1} categories the arrays will have either \eqn{K+1} or {K} dimensions, depending on whether 
       |                                                               ^
checkRd: (-1) multinom.gen.Rd:46: Lost braces
    46 | For a \emph{K}-variate multinomial, the matrix{m} should have \emph{K-1} columns
       |                                               ^
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) HeartAttack.Rd:25: Lost braces
    25 | \references{Saporta, G. (1990) Probabilit\'{e}s analyse des donn\'{e}es et statistique. Paris,\'{E}ditions technip}
       |                                            ^
checkRd: (-1) HeartAttack.Rd:25: Lost braces
    25 | \references{Saporta, G. (1990) Probabilit\'{e}s analyse des donn\'{e}es et statistique. Paris,\'{E}ditions technip}
       |                                                                   ^
checkRd: (-1) HeartAttack.Rd:25: Lost braces
    25 | \references{Saporta, G. (1990) Probabilit\'{e}s analyse des donn\'{e}es et statistique. Paris,\'{E}ditions technip}
       |                                                                                                 ^
checkRd: (-1) cosmoFns-package.Rd:34: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
checkRd: (-1) summary_fitlist.Rd:15: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) summary_fitlist.Rd:16: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) summary_fitlist.Rd:17: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) summary_fitlist.Rd:18: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) summary_fitlist.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) fasttrakg.Rd:18: Lost braces
    18 |     \item{\code{killip}}{Killip level of cardiac event severity (1-4)age75}{1= Age>75; 0=Age<=75}
       |                                                                            ^
'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:
  ‘covfefe_inauguration.txt’
'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
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) gen_data.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gen_data.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gen_data.Rd:23-24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) plot.coxr.Rd:36: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) plot.coxr.Rd:37: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) plot.coxr.Rd:38-39: Lost braces in \itemize; \value handles \item{}{} directly
Specified C++11: please drop specification unless essential
checkRd: (-1) coxph.RT.Rd:57: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) coxph.RT.Rd:58: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) coxph.RT.Rd:59-71: 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) Sample.data.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Sample.data.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Sample.data.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Sample.data.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Sample.data.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Sample.data.Rd:21: Lost braces in \itemize; meant \describe ?
Package suggested but not available for checking: ‘BEST’
Specified C++14: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
checkRd: (-1) sharedat.Rd:23: Lost braces
    23 | \doi{10.7910/DVN/YXMQZM}{Harvard dataverse}
       |                         ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) update_PACKAGES.Rd:35: Lost braces; missing escapes or markup?
    35 |     Type of packages: currently source \file{.tar.{gz,bz2,xz}} archives,
       |                                                   ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) crwPredict.Rd:54-68: Lost braces
    54 | \item("predTime"){
       |                  ^
checkRd: (-1) crwPredict.Rd:59: Lost braces
    59 |  no longer the default (see \item{return.type}). If the original data were 
       |                                  ^
checkRd: (-1) make_style.Rd:51: Lost braces
    51 | The style (the code{...} argument) can be anything of the
       |                    ^
'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) normFit.Rd:39: Lost braces; missing escapes or markup?
    39 | {analytes}}
       | ^
checkRd: (-1) normPred.Rd:27: Lost braces
    27 | ode{standards}, \code{analytes}}
       |    ^
checkRd: (-1) DualEndpointOld-class.Rd:21: Lost braces; missing escapes or markup?
    21 | contain a vector with elements \code{a} and {b} for the inverse-gamma prior
       |                                             ^
checkRd: (-1) DualEndpointRW-class.Rd:39: Lost braces; missing escapes or markup?
    39 | contain a vector with elements \code{a} and {b} for the inverse-gamma prior
       |                                             ^
checkRd: (-1) simulate-DualResponsesSamplesDesign-method.Rd:45: Lost braces
    45 | \item{trueNu}{(not with code{\linkS4class{EffFlexi}}) the precision, the inverse of the 
       |                             ^
checkRd: (-1) simulate-DualResponsesSamplesDesign-method.Rd:48: Lost braces
    48 | \item{trueSigma2}{(only with code{\linkS4class{EffFlexi}}) the true variance of the efficacy 
       |                                  ^
checkRd: (-1) simulate-DualResponsesSamplesDesign-method.Rd:51: Lost braces
    51 | \item{trueSigma2betaW}{(only with code{\linkS4class{EffFlexi}}) the true variance for the 
       |                                       ^
Documented arguments not in \usage in Rd file 'pinvGamma.Rd':
  ‘logical;’

Documented arguments not in \usage in Rd file 'qinvGamma.Rd':
  ‘logical;’

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:
  ‘crop.eps’ ‘crop.pdf’ ‘crop.png’ ‘crop.ps’
'LazyData' is specified without a 'data' directory
checkRd: (-1) confRegCCR.Rd:24: Lost braces; missing escapes or markup?
    24 | of interest, beta_{0r}, and the remaining ones are the constrained MLEs given beta_{0r}.}
       |                   ^
checkRd: (-1) confRegCCR.Rd:24: Lost braces; missing escapes or markup?
    24 | of interest, beta_{0r}, and the remaining ones are the constrained MLEs given beta_{0r}.}
       |                                                                                    ^
checkRd: (-1) confRegCCR.Rd:27: Lost braces; missing escapes or markup?
    27 | beta_{0r} in \code{paramVals}, which are those of interest, usually the ones
       |      ^
checkRd: (-1) confRegUCRandUCCR.Rd:24: Lost braces; missing escapes or markup?
    24 | of interest, beta_{0r}, and the remaining ones are the unconstrained MLEs given beta_{0r}.}
       |                   ^
checkRd: (-1) confRegUCRandUCCR.Rd:24: Lost braces; missing escapes or markup?
    24 | of interest, beta_{0r}, and the remaining ones are the unconstrained MLEs given beta_{0r}.}
       |                                                                                      ^
checkRd: (-1) confRegUCRandUCCR.Rd:27: Lost braces; missing escapes or markup?
    27 | beta_{0r} in \code{paramVals}, which are those of interest, usually the ones
       |      ^
Package suggested but not available for checking: ‘INLA’
checkRd: (-1) cruts-package.Rd:21: Lost braces
    21 | section{Dependencies}{
       |        ^
checkRd: (-1) cruts-package.Rd:21-24: Lost braces
    21 | section{Dependencies}{
       |                      ^
checkRd: (-1) cruts-package.Rd:26: Lost braces
    26 | section{Citation}{
       |        ^
checkRd: (-1) cruts-package.Rd:26-28: Lost braces
    26 | section{Citation}{
       |                  ^
checkRd: (-1) cruts-package.Rd:30-32: Lost braces
    30 | references{
       |           ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) calculate_cell_volume.Rd:16: Lost braces; missing escapes or markup?
    16 | V A real number. The volume (in angstroms^3 or angstroms^{-3})
       |                                                          ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) calculateEffects.Rd:24: Lost braces; missing escapes or markup?
    24 | equals (I-B)^{-1}Gamma. The indirect effect equals the difference between
       |              ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) ch_tr_sign.Rd:15: Lost braces; missing escapes or markup?
    15 | {x} {an array of indices 1, 2, 3}
       |     ^
checkRd: (-1) ch_tr_signif.Rd:15: Lost braces; missing escapes or markup?
    15 | {x} {an array of indices 1 and 2, where 1 is NS and 2 is significant}
       |     ^
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.
checkRd: (-1) csvy.Rd:58: Lost braces in \itemize; meant \describe ?
checkRd: (-1) csvy.Rd:59: Lost braces in \itemize; meant \describe ?
checkRd: (-1) csvy.Rd:60: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) mcmc.fmove.Rd:81: Lost braces; missing escapes or markup?
    81 |   beta ~ N( 0 , tau^2 * QQ^{-1} )
       |                            ^
'LazyData' is specified without a 'data' directory
Objects in \usage without \alias in Rd file 'ctqr-internal.Rd':
  ‘findagoodestimator’ ‘safe.pch’ ‘quickpred’ ‘check.in.ctqr’ ‘start’
  ‘ee.u’ ‘ee.cens’ ‘ee.cens.trunc’ ‘ee.icens’ ‘qr.gs’ ‘nobs.ctqr’
  ‘vcov.ctqr’ ‘coef.ctqr’ ‘print.ctqr’ ‘summary.ctqr’
  ‘print.summary.ctqr’ ‘firstep.ct’ ‘firstep.ic’ ‘asy.qr.ct’
  ‘asy.qr.ic’ ‘safesolve’ ‘regularize_corr’

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 'ctqr-internal.Rd':
  ‘qr.gs’

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
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘Hello.csv’
checkRd: (-1) cubintegrate.Rd:67: Lost braces; missing escapes or markup?
    67 | evaluated} - {returnCode}{the actual integer return code
       |              ^
checkRd: (-1) cubintegrate.Rd:67-69: Lost braces
    67 | evaluated} - {returnCode}{the actual integer return code
       |                          ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) chi2cub1cov.Rd:18-19: Lost braces
    18 | \item{gama}{gama}{Vector of parameters for the feeling component, with length equal to 2
       |                  ^
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.
'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
'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: \_ \_ \_
checkRd: (-1) bandingEst.Rd:21: Lost braces; missing escapes or markup?
    21 | that are far removed from one another. The {i, j} entry of the estimated
       |                                            ^
checkRd: (-1) bandingEst.Rd:22: Lost braces; missing escapes or markup?
    22 | covariance matrix will be zero if the absolute value of {i - j} is greater
       |                                                         ^
checkRd: (-1) taperingEst.Rd:29: Lost braces; missing escapes or markup?
    29 | \code{abs(i - j) <= k / 2}, then entry {i, j} in the weight matrix is equal
       |                                        ^
checkRd: (-1) taperingEst.Rd:30: Lost braces; missing escapes or markup?
    30 | to 1. If \code{k / 2 < abs(i - j) < k}, then entry {i, j} is equal to
       |                                                    ^
checkRd: (-1) taperingEst.Rd:31: Lost braces; missing escapes or markup?
    31 | \code{2 - 2 * abs(i - j) / k}. Otherwise, entry {i, j} is equal to 0.
       |                                                 ^
Documented arguments not in \usage in Rd file 'cvRiskPlot.Rd':
  ‘estimator’

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

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: ‘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
checkRd: (-1) render_toc.Rd:49: Lost braces; missing escapes or markup?
    49 |     ```{r echo=FALSE}
       |        ^
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:
  'gurobi', 'rcbc'
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) fit.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fit.Rd:38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fit.Rd:39: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
checkRd: (-1) CytofTree.Rd:47-48: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) CytofTree.Rd:49: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) CytofTree.Rd:50: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) CytofTree.Rd:51-52: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) CytofTree.Rd:53: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) CytofTree.Rd:54: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) CytomeTree.Rd:33-34: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) CytomeTree.Rd:35: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) CytomeTree.Rd:36: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) CytomeTree.Rd:37-38: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) RetrievePops.Rd:20-21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) RetrievePops.Rd:22-23: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
checkRd: (-1) czso_get_catalogue.Rd:14: Lost braces; missing escapes or markup?
    14 | \item the \code{spatial} columns contains an IRI ending in the pattern {unit_type}/{unit_code}.
       |                                                                        ^
checkRd: (-1) czso_get_catalogue.Rd:14: Lost braces; missing escapes or markup?
    14 | \item the \code{spatial} columns contains an IRI ending in the pattern {unit_type}/{unit_code}.
       |                                                                                    ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'tree.filter.Rd':
  ‘nodeList’

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) 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 ?
checkRd: (-1) bestsetNoise.Rd:128-129: Lost braces
   128 |   \code{tcrit}{For each model, the minimum of the absolute values of
       |               ^
checkRd: (-1) bestsetNoise.Rd:130: Lost braces
   130 |   \code{regsubsets_obj}{The object returned by the call to \code{regsubsets}.}
       |                        ^
checkRd: (-1) plotSimScat.Rd:30: Lost braces; missing escapes or markup?
    30 | Specify \code{points} or {residuals}.
       |                          ^
checkRd: (-1) print.sumry.glm.Rd:34: Lost braces; missing escapes or markup?
    34 |   \item{show.iter}{\code{NULL} or {integer}. If \code{NULL}, or if
       |                                   ^
checkRd: (-1) fpiter.Rd:55-58: Lost braces
    55 |     \code{tol}{  A small, positive scalar that determines when iterations
       |               ^
checkRd: (-1) fpiter.Rd:60-61: Lost braces
    60 |     \code{maxiter}{  An integer denoting the maximum limit on the number of
       |                   ^
checkRd: (-1) fpiter.Rd:63-65: Lost braces
    63 |     \code{trace}{  A logical variable denoting whether some of the intermediate
       |                 ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) formatScientificTeX.Rd:33: Lost braces; missing escapes or markup?
    33 | function will return  " 3.0\\\\times 10^{2}"
       |                                         ^
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
Invalid package aliases in Rd file 'dap-package.Rd':
  ‘dap-package’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) gl.filter.maf.Rd:7: Lost braces; missing escapes or markup?
     7 |  {adegenet} object}
       |  ^
checkRd: (-1) gl.pcoa.Rd:68: Lost braces; missing escapes or markup?
    68 | The function is essentially a wrapper for glPca {adegenet} or pcoa \{ape\}
       |                                                 ^
checkRd: (-1) gl.play.history.Rd:17: Lost braces
    17 | code{x2@other$history[c(1,4,5)]}). [optional].}
       |     ^
checkRd: (-1) utils.jackknife.Rd:49: Lost braces
    49 | bold{Note} that when n is very small, jackknife resampling is not recommended.
       |     ^
checkRd: (-1) utils.jackknife.Rd:51: Lost braces
    51 | Parallel computation is implemented. The argument code{n.cores} indicates the 
       |                                                       ^
GNU make is a SystemRequirements.
checkRd: (-1) StartEnd.Rd:31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) StartEnd.Rd:32: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) processFlow.Rd:14: Lost braces
    14 | \item{roundDigits}{Integer. If NA, numerics are not rounded before comparison. If /code{roundDigits} is specified, numerics are 
       |                                                                                        ^
checkRd: (-1) processFlow.Rd:15: Lost braces
    15 | rounded to /code{roundDigits} decimal places using \link[base]{round}.}
       |                 ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) data_edit.Rd:137: Lost braces
   137 | code{data_edit} is a shiny application built on \code{rhandsontable} that is
       |     ^
Documented arguments not in \usage in Rd file 'plotDataExplorer.single.Rd':
  ‘obj’

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) number_of_rows.Rd:30-32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) number_of_rows.Rd:33-37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) schema_methods.Rd:38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) schema_methods.Rd:39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) schema_methods.Rd:40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) schema_methods.Rd:41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) schema_source.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) schema_source.Rd:31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) special_simulation.Rd:37-39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) special_simulation.Rd:40-43: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
checkRd: (-1) defaultFactorSummaries.Rd:29: Lost braces
    29 | code{\link{variableType}}, \code{\link{countMissing}}, \code{\link{uniqueValues}},
       |     ^
Found the following files/directories:
  ‘my new data set.rds’
'LazyData' is specified without a 'data' directory
checkRd: (-1) build_date_factor.Rd:15: Lost braces; missing escapes or markup?
    15 | Map a vector of dates to a factor at one of these levels {"yearmonth", "yearquarter", "quarter", "month"}
       |                                                          ^
checkRd: (-1) build_date_factor.Rd:12: Lost braces; missing escapes or markup?
    12 | \item{type}{One of {"year", "yearquarter", "yearmonth", "quarter", "month"}}
       |                    ^
checkRd: (-1) defaultFactorSummaries.Rd:29: Lost braces
    29 | code{\link{variableType}}, \code{\link{countMissing}}, \code{\link{uniqueValues}},
       |     ^
checkRd: (-1) readNWISuse.Rd:21: Lost braces
    21 | numeric (id), or code{NULL}, which will
       |                      ^
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
checkRd: (-1) is_datelife_query.Rd:17: Lost braces; missing escapes or markup?
    17 | First, that \code{input} is of class {datelifeQuery}.
       |                                      ^
Package suggested but not available for checking: ‘SASxport’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) plot.mleBb.Rd:48: Lost braces
    48 |   \ code{size} is extracted from argument \code{x}.
       |         ^
checkRd: (-1) value_missing_table.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) value_missing_table.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) CI_mc.Rd:10: Lost braces; missing escapes or markup?
    10 | \item{i}{the row index of the interest entry X_{i,j}}
       |                                                ^
checkRd: (-1) CI_mc.Rd:12: Lost braces; missing escapes or markup?
    12 | \item{j}{the row index of the interest entry X_{i,j}}
       |                                                ^
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) Velocity.Rd:9: Lost braces; missing escapes or markup?
     9 | \item{probs}{the weight of each value {-1,0,1}. They define the probability that each of them will be picked}
       |                                       ^
checkRd: (-1) cte_times_vel_cpp.Rd:14: Lost braces; missing escapes or markup?
    14 | \item{abs_op}{the final number of {1,-1} operations}
       |                                   ^
checkRd: (-1) natVelocity.Rd:15: Lost braces; missing escapes or markup?
    15 | \item{probs}{the weight of each value {-1,0,1}. They define the probability that each of them will be picked}
       |                                       ^
checkRd: (-1) nat_cte_times_vel_cpp.Rd:16: Lost braces; missing escapes or markup?
    16 | \item{abs_op}{the final number of {1,-1} operations}
       |                                   ^
checkRd: (-1) nat_vel_plus_vel_cpp.Rd:18: Lost braces; missing escapes or markup?
    18 | \item{abs_op1}{the number of {1,-1} operations in the first velocity}
       |                              ^
checkRd: (-1) nat_vel_plus_vel_cpp.Rd:20: Lost braces; missing escapes or markup?
    20 | \item{abs_op2}{the number of {1,-1} operations in the second velocity}
       |                              ^
checkRd: (-1) randomize_vl_cpp.Rd:12: Lost braces; missing escapes or markup?
    12 | \item{probs}{the probabilities of each value in the set {-1,0,1}}
       |                                                         ^
checkRd: (-1) vel_plus_vel_cpp.Rd:14: Lost braces; missing escapes or markup?
    14 | \item{abs_op}{the final number of {1,-1} operations}
       |                                   ^
S3 methods shown with full name in Rd file 'dbglm-internal.Rd':
  ‘dbglm.iteration’

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
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.
checkRd: (-1) data.Rd:11: Lost braces
    11 | \doi{10.1007/s40258-021-00647-3}{DOI}
       |                                 ^
Problems with news in ‘NEWS.md’:
No news entries found.
Package suggested but not available for checking: ‘INLA’
checkRd: (-1) CalcStatClusterGivenCenter.Rd:36: Lost braces; missing escapes or markup?
    36 | This can be "glm" for generalized linear models (\link{glm} {stats}),
       |                                                             ^
checkRd: (-1) CalcStatClusterGivenCenter.Rd:37: Lost braces; missing escapes or markup?
    37 | "glmer" for generalized linear mixed model (\link{glmer} {lme4}),
       |                                                          ^
checkRd: (-1) CalcStatsAllClusters.Rd:49: Lost braces; missing escapes or markup?
    49 | This can be "glm" for generalized linear models (\link{glm} {stats}),
       |                                                             ^
checkRd: (-1) CalcStatsAllClusters.Rd:50: Lost braces; missing escapes or markup?
    50 | "glmer" for generalized linear mixed model (\link{glmer} {lme4}),
       |                                                          ^
checkRd: (-1) DetectClustersModel.Rd:60: Lost braces; missing escapes or markup?
    60 | This can be "glm" for generalized linear models (\link{glm} {stats}),
       |                                                             ^
checkRd: (-1) DetectClustersModel.Rd:61: Lost braces; missing escapes or markup?
    61 | "glmer" for generalized linear mixed model (\link{glmer} {lme4}),
       |                                                          ^
checkRd: (-1) glmAndZIP.iscluster.Rd:34: Lost braces; missing escapes or markup?
    34 | This can be "glm" for generalized linear models (\link{glm} {stats}),
       |                                                             ^
checkRd: (-1) glmAndZIP.iscluster.Rd:35: Lost braces; missing escapes or markup?
    35 | "glmer" for generalized linear mixed model (\link{glmer} {lme4}),
       |                                                          ^
checkRd: (-1) DCluster.Rd:67: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DCluster.Rd:68: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DCluster.Rd:69: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DCluster.Rd:134: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DCluster.Rd:136: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DCluster.Rd:138: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DCluster.Rd:140: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DCluster.Rd:142: 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
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
checkRd: (-1) kernel.assign.Rd:27: Lost braces; missing escapes or markup?
    27 |  {q = [0, 1]}. Kernels are of the Müller-Wang type ("MW"), Müller type ("M")
       |  ^
checkRd: (-1) dNMF.Rd:76: Lost braces; missing escapes or markup?
    76 | The number of low-dimension (J < {N, M}, Default: 3)
       |                                  ^
checkRd: (-1) dNMF.Rd:103: Lost braces; missing escapes or markup?
   103 |   U : A matrix which has N-rows and J-columns (J < {N, M}).
       |                                                    ^
checkRd: (-1) dNMF.Rd:104: Lost braces; missing escapes or markup?
   104 |   V : A matrix which has M-rows and J-columns (J < {N, M}).
       |                                                    ^
checkRd: (-1) dPLS.Rd:53: Lost braces; missing escapes or markup?
    53 | The number of low-dimension (J < {N, M}, Default: 3)
       |                                  ^
checkRd: (-1) dPLS.Rd:74: Lost braces; missing escapes or markup?
    74 |   U : A matrix which has N-rows and J-columns (J < {N, M}).
       |                                                    ^
checkRd: (-1) dPLS.Rd:75: Lost braces; missing escapes or markup?
    75 |   V : A matrix which has M-rows and J-columns (J < {N, M}).
       |                                                    ^
checkRd: (-1) dSVD.Rd:60: Lost braces; missing escapes or markup?
    60 | The number of low-dimension (J < {N, M}, Default: 3)
       |                                  ^
checkRd: (-1) dSVD.Rd:81: Lost braces; missing escapes or markup?
    81 |   U : A matrix which has N-rows and J-columns (J < {N, M}).
       |                                                    ^
checkRd: (-1) dSVD.Rd:82: Lost braces; missing escapes or markup?
    82 |   V : A matrix which has M-rows and J-columns (J < {N, M}).
       |                                                    ^
Specified C++11: please drop specification unless essential
checkRd: (-1) detectAgeInterval.Rd:10: Lost braces
    10 | \item{Dat}{a \code{data.frame} containing a column called \code{Age}, or code{age}.}
       |                                                                              ^
checkRd: (-1) detectSex.Rd:10: Lost braces
    10 | \item{Dat}{a \code{data.frame} containing a column called \code{Sex}, or code{sex}.}
       |                                                                              ^
checkRd: (-1) ggbgetAgesFit.Rd:28: Lost braces
    28 | code{\link{ggbChooseAges}}
       |     ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) plot.ddpcr_plate.Rd:136-137: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.ddpcr_plate.Rd:138-139: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.ddpcr_plate.Rd:140-141: Lost braces in \itemize; meant \describe ?
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
checkRd: (-1) ddsPLS.Rd:81: Lost braces; missing escapes or markup?
    81 |   \item \code{$U_star}: Loadings for \code{X} in original base: $U_star=U(P'U)^{-1}$.
       |                                                                                ^
checkRd: (-1) modelddsPLSCpp_Rcpp.Rd:38: Lost braces; missing escapes or markup?
    38 |   \item \code{$U_star}: Loadings for \code{X} in original base: $U_star=U(P'U)^{-1}$.
       |                                                                                ^
checkRd: (-1) predict.ddsPLS.Rd:89-91: Lost braces in \itemize; meant \describe ?
checkRd: (-1) predict.ddsPLS.Rd:92-93: Lost braces in \itemize; meant \describe ?
checkRd: (-1) predict.ddsPLS.Rd:43: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) predict.ddsPLS.Rd:44-45: Lost braces in \itemize; \value handles \item{}{} directly
'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
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.
checkRd: (-1) deconv.Rd:85: Lost braces; missing escapes or markup?
    85 |     \code{tg}, std. error of \eqn{g}, \eqn{G} (the cdf of {g}),
       |                                                           ^
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) deepNN-package.Rd:18: Lost braces
    18 | section{Dependencies}{
       |        ^
checkRd: (-1) deepNN-package.Rd:18-21: Lost braces
    18 | section{Dependencies}{
       |                      ^
checkRd: (-1) deepNN-package.Rd:23: Lost braces
    23 | section{Citation}{
       |        ^
checkRd: (-1) deepNN-package.Rd:23-25: Lost braces
    23 | section{Citation}{
       |                  ^
checkRd: (-1) deepNN-package.Rd:27-38: Lost braces
    27 | references{
       |           ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) defm_terms.Rd:69: Lost braces; missing escapes or markup?
    69 | \item Intercept effect: {...} No transition, only including the current state.
       |                         ^
checkRd: (-1) defm_terms.Rd:70: Lost braces; missing escapes or markup?
    70 | \item Transition effect: {...} > {...} Includes current and previous states.
       |                          ^
checkRd: (-1) defm_terms.Rd:70: Lost braces; missing escapes or markup?
    70 | \item Transition effect: {...} > {...} Includes current and previous states.
       |                                  ^
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in Rd file 'degreenet-internal.Rd':
  ‘range’ ‘lims’
Objects in \usage without \alias in Rd file 'degreenet-internal.Rd':
  ‘bootstrapyule’

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) deltaPlot.Rd:28: Lost braces
    28 |  \item{purify}{logical: should item purification be performed? (Default is code{FALSE}). See \bold{Details}.}
       |                                                                                ^
Found the following files/directories:
  ‘res.pdf’ ‘res1.jpg’
'LazyData' is specified without a 'data' directory
checkRd: (-1) deming.Rd:71: Lost braces
    71 | on whether the code{cv} option is TRUE or FALSE, respectively.
       |                    ^
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’
checkRd: (-1) pval_shapiro.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pval_shapiro.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pval_shapiro.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pval_shapiro.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pval_shapiro.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) kin.Rd:49-50: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) kin.Rd:51-52: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) kin.Rd:53-61: Lost braces
    53 | {\itemize{
       | ^
checkRd: (-1) kin.Rd:54: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) kin.Rd:55: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) kin.Rd:56: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) kin.Rd:57: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) kin.Rd:58: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) kin.Rd:59: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) kin2sex.Rd:56-57: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) kin2sex.Rd:58: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) kin2sex.Rd:59-67: Lost braces
    59 | {\itemize{
       | ^
checkRd: (-1) kin2sex.Rd:60: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) kin2sex.Rd:61: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) kin2sex.Rd:62: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) kin2sex.Rd:63: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) kin2sex.Rd:64: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) kin2sex.Rd:65: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
checkRd: (-1) scramb.Rd:44: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
checkRd: (-1) conifersIP.Rd:9: Lost braces; missing escapes or markup?
     9 | \code{conifersIP} {has following variables:}
       |                   ^
checkRd: (-1) conifersIP.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) conifersIP.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) conifersIP.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) conifersIP.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) conifersIP.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sync.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sync.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sync.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sync.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sync.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sync.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sync.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly
Documented arguments not in \usage in Rd file 'boot_f_cor.Rd':
  ‘fun’

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

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) DendSer.Rd:50: Escaped LaTeX specials: \&
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Rd files without \alias:
  ‘densityClust-package.Rd’
'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: ‘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’
checkRd: (-1) responses.Rd:68: Lost braces
    68 | 	response.  See code{\link{makeDepmix}} for an example of how to use
       |                            ^
checkRd: (-1) crs.Rd:34: Lost braces; missing escapes or markup?
    34 | system, crs) of DeponsRaster and DeponsTrack objects. For {sp} objects the
       |                                                           ^
Specified C++11: please drop specification unless essential
checkRd: (-1) barriers.Rd:127: Escaped LaTeX specials: \$
checkRd: (-1) Deriv.Rd:33: Lost braces
    33 | guessed either from\ code{names(formals(f))} (if \code{f} is a function)
       |                          ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) weighted.cor2.Rd:7: Lost braces; missing escapes or markup?
     7 | Computes a matrix of weighted correlations between the columns of \code{x} and the columns of {y}. This can be Pearson, Spearman or Kendall correlation.
       |                                                                                               ^
checkRd: (-1) weighted.cov2.Rd:7: Lost braces; missing escapes or markup?
     7 | Computes a matrix of weighted covariances between the columns of \code{x} and the columns of {y}.
       |                                                                                              ^
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’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘RDCOMClient’
checkRd: (-1) alpha.split.Rd:21: Lost braces; missing escapes or markup?
    21 | \item{r}{vector for the proportion for each sub-population, r_1 is 1, r_i>r_{i+1}}
       |                                                                             ^
checkRd: (-1) designCTPB.Rd:25: Lost braces; missing escapes or markup?
    25 | \item{r_set}{the matrix of proportion for each sub-population, r_1 is 1, r_i>r_{i+1}}
       |                                                                                ^
checkRd: (-1) phat.Rd:21: Lost braces; missing escapes or markup?
    21 | \item{r}{vector for the proportion for each sub-population, r_1is 1, r_i>r_{i+1}}
       |                                                                            ^
Package which this enhances but not available for checking: ‘gurobi’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) detour-shiny.Rd:26: Lost braces; missing escapes or markup?
    26 | \item{expr}{an expression that generates a {detourr} widget}
       |                                            ^
checkRd: (-1) show_sage.Rd:80: Lost braces; missing escapes or markup?
    80 | supported using {crosstalk}. The set of interactive controls available are:
       |                 ^
checkRd: (-1) show_scatter.Rd:67: Lost braces; missing escapes or markup?
    67 | supported using {crosstalk}. The set of interactive controls available are:
       |                 ^
checkRd: (-1) show_scatter_internal.Rd:65: Lost braces; missing escapes or markup?
    65 | supported using {crosstalk}. The set of interactive controls available are:
       |                 ^
checkRd: (-1) show_slice.Rd:76: Lost braces; missing escapes or markup?
    76 | supported using {crosstalk}. The set of interactive controls available are:
       |                 ^
checkRd: (-1) tour_aes.Rd:11: Lost braces; missing escapes or markup?
    11 | Variables are evaluated using {tidyselect} syntax.}
       |                               ^
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
'LazyData' is specified without a 'data' directory
Package required but not available: ‘signatureSearch’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Specified C++11: please drop specification unless essential
checkRd: (-1) mtaBin_next.Rd:27: Lost braces
    27 |   \item{s_1}{A function depending on the number of patients included used for adaptive randomization in plateau determination, only used if the estimation method chosen is "MTA-RA". The default function is function(n_cur,n){0.2}.}
       |                                                                                                                                                                                                                                ^
checkRd: (-1) mtaBin_sim.Rd:30: Lost braces
    30 |   \item{s_1}{A function depending on the number of patients included used for adaptive randomization in plateau determination, only used if the estimation method chosen is "MTA-RA". The default function is function(n_cur){0.2}.}
       |                                                                                                                                                                                                                              ^
'LazyData' is specified without a 'data' directory
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
checkRd: (-1) AIC.dglars.Rd:47: Lost braces
    47 | \item{comp}{the measures of model complexity used to compute the measure of goodness-of-fit. It is equal to \code{npar} when code{complexity = "df"};}
       |                                                                                                                                  ^
checkRd: (-1) dglars.Rd:258: Lost braces
   258 | 		\item{\code{7}}{maximum number of solution points ('code{np}') reached.}
       |                                                                         ^
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) dHSIC-package.Rd:32: Lost braces
    32 |   Gretton, A., K. Fukumizu, C. H. Teo, L. Song, B. Sch{\"o}lkopf and
       |                                                       ^
checkRd: (-1) dHSIC-package.Rd:36: Lost braces
    36 |   Pfister, N., P. B{\"u}hlmann, B. Sch{\"o}lkopf and J. Peters (2017).
       |                    ^
checkRd: (-1) dHSIC-package.Rd:36: Lost braces
    36 |   Pfister, N., P. B{\"u}hlmann, B. Sch{\"o}lkopf and J. Peters (2017).
       |                                       ^
checkRd: (-1) dhsic.Rd:84: Lost braces
    84 |   Gretton, A., K. Fukumizu, C. H. Teo, L. Song, B. Sch{\"o}lkopf and
       |                                                       ^
checkRd: (-1) dhsic.Rd:88: Lost braces
    88 |   Pfister, N., P. B{\"u}hlmann, B. Sch{\"o}lkopf and J. Peters (2017).
       |                    ^
checkRd: (-1) dhsic.Rd:88: Lost braces
    88 |   Pfister, N., P. B{\"u}hlmann, B. Sch{\"o}lkopf and J. Peters (2017).
       |                                       ^
checkRd: (-1) dhsic.test.Rd:124: Lost braces
   124 |   Gretton, A., K. Fukumizu, C. H. Teo, L. Song, B. Sch{\"o}lkopf and
       |                                                       ^
checkRd: (-1) dhsic.test.Rd:128: Lost braces
   128 |   Pfister, N., P. B{\"u}hlmann, B. Sch{\"o}lkopf and J. Peters (2017).
       |                    ^
checkRd: (-1) dhsic.test.Rd:128: Lost braces
   128 |   Pfister, N., P. B{\"u}hlmann, B. Sch{\"o}lkopf and J. Peters (2017).
       |                                       ^
checkRd: (-1) grViz.Rd:44: Lost braces
    44 | pkg{htmlwidgets}.
       |    ^
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.
Package suggested but not available for checking: ‘mixedClust’
checkRd: (-1) DIconvex.Rd:40: Lost braces; missing escapes or markup?
    40 |  {Paul Schneider <paul.schneider@usi.ch>}{}
       |  ^
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checkRd: (-1) define.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) define.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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checkRd: (-1) did_imputation.Rd:74: Lost braces; missing escapes or markup?
    74 | form average treatment effects for groups of {it}.
       |                                              ^
'LazyData' is specified without a 'data' directory
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checkRd: (-1) sensitivitySamplerManual-DPMech-function-numeric-numeric-numeric-method.Rd:25: Lost braces
    25 | \item{k}{order statistic index in {1,...,\code{m}}.}
       |                                   ^
checkRd: (-1) sensitivitySamplerManual-DPMechNumeric-function-numeric-numeric-numeric-method.Rd:25: Lost braces
    25 | \item{k}{order statistic index in {1,...,\code{m}}.}
       |                                   ^
checkRd: (-1) sensitivitySamplerManual.Rd:22: Lost braces
    22 | \item{k}{order statistic index in {1,...,\code{m}}.}
       |                                   ^
'LazyData' is specified without a 'data' directory
'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’
checkRd: (-1) simulate_diff_tables.Rd:72: Lost braces; missing escapes or markup?
    72 |   {The Sharma-Song test} {\code{\link[DiffXTables]{sharma.song.test}}}
       |   ^
checkRd: (-1) simulate_diff_tables.Rd:74: Lost braces; missing escapes or markup?
    74 |   {The comparative chi-squared test} {\code{\link[DiffXTables]{cp.chisq.test}}}
       |   ^
checkRd: (-1) simulate_diff_tables.Rd:76: Lost braces; missing escapes or markup?
    76 |   {The heterogeneity test} {\code{\link[DiffXTables]{heterogeneity.test}}}
       |   ^
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   185 |  \code{\link[deltaPlotR]{deltaPlot}}, code{\link[deltaPlotR]{diagPlot}}, \code{\link{dichoDif}}
       |                                           ^
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checkRd: (-1) DIME.Rd:272: Lost braces; missing escapes or markup?
   272 | \item{name}{the name of the model {"GNG", "iNUDGE","NUDGE"} where
       |                                   ^
checkRd: (-1) DRR-class.Rd:79: Lost braces; missing escapes or markup?
    79 | n^{1/3} up to sacrificing some accuracy, for details see
       |   ^
Specified C++11: please drop specification unless essential
checkRd: (-1) restart_session.Rd:11: Lost braces
    11 | 'RStudio', use \code{startup}{restart} instead.
       |                              ^
Package suggested but not available for checking: ‘rrelaxiv’
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'LazyData' is specified without a 'data' directory
checkRd: (-1) TempDisaggDGP.Rd:79: Escaped LaTeX specials: \&
checkRd: (-1) disaggregate.Rd:56: Escaped LaTeX specials: \&
Package suggested but not available for checking: ‘INLA’
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
checkRd: (-1) app_server.Rd:10: Lost braces; missing escapes or markup?
    10 | \item{input, output, session}{Internal parameters for `{shiny}`.
       |                                                        ^
Specified C++11: please drop specification unless essential
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Package suggested but not available for checking: ‘discreteMTP’
Unknown package ‘discreteMTP’ in Rd xrefs
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) mc_attitudes.Rd:52: Lost braces
    52 | P\'{a}ez, A. (2013). Mapping travelers’ attitudes: does space matter?. Journal of Transport Geography, 26, 117-125. (https://doi.org/10.1016/j.jtrangeo.2012.09.002)
       |    ^
checkRd: (-1) mc_commute.csv.Rd:49: Lost braces
    49 | Whalen, K. E., P\'{a}ez, A., & Carrasco, J. A. (2013). Mode choice of university students commuting to school and the role of active travel. Journal of Transport Geography, 31, 132-142. (https://doi.org/10.1016/j.jtrangeo.2013.06.008)
       |                   ^
checkRd: (-1) mc_commute_long.Rd:74: Lost braces
    74 | Whalen, K. E., P\'{a}ez, A., & Carrasco, J. A. (2013). Mode choice of university students commuting to school and the role of active travel. Journal of Transport Geography, 31, 132-142. (https://doi.org/10.1016/j.jtrangeo.2013.06.008)
       |                   ^
checkRd: (-1) mc_commute_wide.Rd:87: Lost braces
    87 | Whalen, K. E., P\'{a}ez, A., & Carrasco, J. A. (2013). Mode choice of university students commuting to school and the role of active travel. Journal of Transport Geography, 31, 132-142. (https://doi.org/10.1016/j.jtrangeo.2013.06.008)
       |                   ^
checkRd: (-1) mc_modality.Rd:50: Lost braces
    50 | Lavery, T., P\'{a}ez, A., & Kanaroglou, P.S. (2013). Driving out of choices: An investigation of transport modality in a university sample. Transportation Research Part A: Policy and Practice, 57:37-46 (https://doi.org/10.1016/j.tra.2013.09.010)
       |                ^
checkRd: (-1) cIndex.Rd:32: Lost braces; missing escapes or markup?
    32 | [a_{q-1}, a_q) are available.
       |    ^
checkRd: (-1) cIndexCompRisks.Rd:31: Lost braces; missing escapes or markup?
    31 | [a_{q-1}, a_q) are available.
       |    ^
checkRd: (-1) dataCensoring.Rd:78: Escaped LaTeX specials: \&
checkRd: (-1) dataLong.Rd:170: Escaped LaTeX specials: \&
checkRd: (-1) dataLongCompRisksTimeDep.Rd:130: Escaped LaTeX specials: \&
checkRd: (-1) dataLongMultiSpell.Rd:123: Escaped LaTeX specials: \&
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    23 | a_2), ..., [a_{q-1}, a_q), [a_q, Inf).
       |               ^
checkRd: (-1) estMargProbCompRisks.Rd:24: Lost braces; missing escapes or markup?
    24 | a_2), ..., [a_{q-1}, a_q), [a_q, Inf).
       |               ^
checkRd: (-1) estSurv.Rd:23: Lost braces; missing escapes or markup?
    23 | a_2), ..., [a_{q-1}, a_q), [a_q, Inf).
       |               ^
checkRd: (-1) estSurvCompRisks.Rd:24: Lost braces; missing escapes or markup?
    24 | a_2), ..., [a_{q-1}, a_q), [a_q, Inf).
       |               ^
checkRd: (-1) lifeTable.Rd:21: Lost braces; missing escapes or markup?
    21 | [a_0, a_1), [a_1, a_2), ..., [a_{q-1}, a_q) ("character vector")}
       |                                 ^
Package which this enhances but not available for checking: ‘INLA’
'LazyData' is specified without a 'data' directory
checkRd: (-1) csv_to_disk.frame.Rd:56: Lost braces; missing escapes or markup?
    56 | strings, and you are encouraged to use {fasttime} to convert the strings to
       |                                        ^
checkRd: (-1) purrr_as_mapper.Rd:10: Lost braces; missing escapes or markup?
    10 | \item{.f}{a normal function or purrr syntax function i.e. `~{ ...code...}`}
       |                                                             ^
checkRd: (-1) mess.Rd:28: Lost braces
    28 | Elith J., M. Kearney M., and S. Phillips, 2010. The art of modelling range-shifting species. \doi{10.1111/j.2041-210X.2010.00036.x}{Methods in Ecology and Evolution 1:330-342}.
       |                                                                                                                                    ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) store_in_DB.Rd:89: Lost braces
    89 | link{read_from_DB} function. Those parameters define rows and columns that will be returned.
       |     ^
checkRd: (-1) unite_two_DF.Rd:46: Lost braces; missing escapes or markup?
    46 | \code{data1.shared.var} and {data2.shared.var} must contain unique values within its own data frame.
       |                             ^
'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: \&
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) dapply.Rd:27-30: Lost braces
    27 | udf <- function(x){
       |                   ^
Documented arguments not in \usage in Rd file 'internals.Rd':
  ‘namestoGather’ ‘namestoGatherNS’

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) autoplot.distribution.Rd:18: Lost braces; missing escapes or markup?
    18 | the {ggdist} package to produce your own distribution plots. You can learn
       |     ^
checkRd: (-1) autoplot.distribution.Rd:19: Lost braces; missing escapes or markup?
    19 | more about how this plot can be produced using {ggdist} here:
       |                                                ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) Exponential.Rd:31: Lost braces
    31 | \strong{Support}: {x in [0, \eqn{\infty})}
       |                   ^
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checkRd: (-1) moranTest.Rd:37: Lost braces; missing escapes or markup?
    37 |   {M(theta)=-(log(y_1-y_0)+log(y_2-y_1)+...+log(y_m-y_m-1))}
       |   ^
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'distrMod', 'ROptEst'

Package which this enhances but not available for checking: ‘RobAStBase’
Unknown packages ‘distrMod’, ‘RobAStBase’ in Rd xrefs
Assignments in \usage in Rd file 'internalGenerics.Rd':
  x <- samplesize(object, value)

Documented arguments not in \usage in Rd file 'internals.Rd':
  ‘DClass’
Objects in \usage without \alias in Rd file 'internals.Rd':
  ‘.consolidategaps’ ‘.List’

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 ‘distr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Binom-class
> ### Title: Class "Binom"
> ### Aliases: Binom-class Binom initialize,Binom-method
> ### Keywords: distribution
> 
> ### ** Examples
> 
> B <- Binom(prob=0.5,size=1) # B is a binomial distribution with prob=0.5 and size=1.
> r(B)(1) # # one random number generated from this distribution, e.g. 1
[1] 0
> d(B)(1) # Density of this distribution is  0.5 for x=1.
[1] 0.5
> p(B)(0.4) # Probability that x<0.4 is 0.5.
[1] 0.5
> q(B)(.1) # x=0 is the smallest value x such that p(B)(x)>=0.1.
[1] 0
> ## in RStudio or Jupyter IRKernel, use q.l(.)(.) instead of q(.)(.)
> size(B) # size of this distribution is 1.
[1] 1
> size(B) <- 2 # size of this distribution is now 2.
> C <- Binom(prob = 0.5, size = 1) # C is a binomial distribution with prob=0.5 and size=1.
> D <- Binom(prob = 0.6, size = 1) # D is a binomial distribution with prob=0.6 and size=1.
> E <- B + C # E is a binomial distribution with prob=0.5 and size=3.
> F <- B + D # F is an object of class LatticeDistribution.
Warning in .local(.Object, ...) : you have to specify slot r at least
Error in h(simpleError(msg, call)) : 
  error in evaluating the argument 'object' in selecting a method for function 'prob': unable to find an inherited method for function ‘r’ for signature ‘object = "numeric"’
Calls: + ... initialize -> initialize -> .local -> table -> r -> <Anonymous>
Execution halted
'LazyData' is specified without a 'data' directory
checkRd: (-1) fadlad.Rd:30: Lost braces
    30 | \item{diffbin}{\code{(logical)}: Difference-based duration for discreet time (only applicabble to cases when \code{bin} is provided). If set to \code{TRUE}, single-interval taxa will \code{0} durations. Setting this argument to \code{FALSE} will add code{1} to the durations of all taxa.}
       |                                                                                                                                                                                                                                                               ^
checkRd: (-1) slice.Rd:27: Lost braces
    27 | Due to stratigraphic constraints, we can only process deep time data, when it is sliced to discrete bins. It is suggested that you do this separately for most of your analyses. This function is also used by the code{\link{divDyn}} function when \code{age} entries are provided.
       |                                                                                                                                                                                                                        ^
checkRd: (-1) tabinate.Rd:31: Lost braces
    31 | Setting both \code{bin} If \code{bin=NULL} and code{tax=NULL}, will run \code{FUN} on the entire dataset (no effect). Providing either \code{bin} or \code{tax} and keeping the other \code{NULL} will iterate \code{FUN} for every \code{bin} or \code{tax} entry (whichever is presented).
       |                                                    ^
checkRd: (-1) diveMove-internal.Rd:180-181: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) diveMove-internal.Rd:183: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) diveMove-internal.Rd:185-186: Lost braces in \itemize; \value handles \item{}{} directly
Objects in \usage without \alias in Rd file 'diveMove-internal.Rd':
  ‘.diveMatches’

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: ‘BOLTSSIRR’
Package suggested but not available for checking: ‘rgdal’
'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:
    Changes to previous versions
    Minor changes
    Fixes
    Previous Versions
Invalid package aliases in Rd file 'dmaiIntro.Rd':
  ‘dmaiIntro-package’
'LazyData' is specified without a 'data' directory
checkRd: (-1) dma.Rd:47: Lost braces; missing escapes or markup?
    47 | When y_t is controlled, only y_{t-delay-1} and before 
       |                                ^
checkRd: (-1) dma.Rd:64: Lost braces; missing escapes or markup?
    64 | 		 estimate of theta_{j-1} for model k at t}
       |                                    ^
checkRd: (-1) dma.Rd:66: Lost braces; missing escapes or markup?
    66 | 		 variance of theta_{j-1} for model k at t}
       |                                    ^
checkRd: (-1) dma.Rd:68: Lost braces; missing escapes or markup?
    68 | 		 estimate of theta_{j-1} at t}
       |                                    ^
checkRd: (-1) dma.Rd:70: Lost braces; missing escapes or markup?
    70 | 		 variance of thetahat_{j-1} at t}
       |                                       ^
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’
checkRd: (-1) dca.Rd:24: Lost braces; missing escapes or markup?
    24 | \eqn{neglinks_{ij} = 1} means chunklet \code{i} and chunklet {j}
       |                                                              ^
checkRd: (-1) dca.Rd:26: Lost braces; missing escapes or markup?
    26 | \eqn{neglinks_{ij} = 0} means chunklet \code{i} and chunklet {j}
       |                                                              ^
checkRd: (-1) rca.Rd:57: Lost braces; missing escapes or markup?
    57 |       e.g. {1, 3, 7} and {4, 6}, might belong to the
       |            ^
checkRd: (-1) rca.Rd:57: Lost braces; missing escapes or markup?
    57 |       e.g. {1, 3, 7} and {4, 6}, might belong to the
       |                          ^
checkRd: (-1) scale_color_dMod.Rd:10: Lost braces
    10 | \item{...}{arguments goint to code{scale_color_manual()}}
       |                                   ^
checkRd: (-1) scale_fill_dMod.Rd:10: Lost braces
    10 | \item{...}{arguments goint to code{scale_color_manual()}}
       |                                   ^
checkRd: (-1) trust.Rd:103: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) trust.Rd:104: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) trust.Rd:105: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) trust.Rd:106: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) trust.Rd:107-108: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) trust.Rd:109-110: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) trust.Rd:111-112: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) trust.Rd:113-114: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) trust.Rd:115-122: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) trust.Rd:123-126: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) trust.Rd:127: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) trust.Rd:128-131: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) trust.Rd:132-133: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) trust.Rd:134-135: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) trust.Rd:136-138: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) trust.Rd:139-141: Lost braces in \itemize; \value handles \item{}{} directly
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) outliers.ranking.Rd:142: Lost braces; missing escapes or markup?
   142 |   max ( 0, ( |g_{y,i}| - |g_{x,i}| ) / ( |g_{y,i}| + |g_{x,i}| ) ),
       |                 ^
checkRd: (-1) outliers.ranking.Rd:142: Lost braces; missing escapes or markup?
   142 |   max ( 0, ( |g_{y,i}| - |g_{x,i}| ) / ( |g_{y,i}| + |g_{x,i}| ) ),
       |                             ^
checkRd: (-1) outliers.ranking.Rd:142: Lost braces; missing escapes or markup?
   142 |   max ( 0, ( |g_{y,i}| - |g_{x,i}| ) / ( |g_{y,i}| + |g_{x,i}| ) ),
       |                                             ^
checkRd: (-1) outliers.ranking.Rd:142: Lost braces; missing escapes or markup?
   142 |   max ( 0, ( |g_{y,i}| - |g_{x,i}| ) / ( |g_{y,i}| + |g_{x,i}| ) ),
       |                                                         ^
checkRd: (-1) outliers.ranking.Rd:143: Lost braces; missing escapes or markup?
   143 |   where g_{y,i} and g_{x,i} are the two groups involved in the merge at
       |           ^
checkRd: (-1) outliers.ranking.Rd:143: Lost braces; missing escapes or markup?
   143 |   where g_{y,i} and g_{x,i} are the two groups involved in the merge at
       |                       ^
checkRd: (-1) outliers.ranking.Rd:144: Lost braces; missing escapes or markup?
   144 |   step i, and g_{x,i} is the group which X belongs to. Note that if X
       |                 ^
checkRd: (-1) setCPT.O.Rd:85: Lost braces; missing escapes or markup?
    85 | statespace {0,1,2}, which this is *not* checked anywhere. Thus, if
       |            ^
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.
'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) 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’
checkRd: (-1) beetle.Rd:13: Lost braces; missing escapes or markup?
    13 |     \item{\code{x}}{dose (log base 10 CS2mgl^{-1})}
       |                                              ^
Documented arguments not in \usage in Rd file 'concDict.Rd':
  ‘text’

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
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
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
       |                 ^
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    23 | \item{id_col}{Specify column of the code{sf} \code{data.frame} object which
       |                                         ^
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    85 | \item{id_col}{For \code{sf}-formatted data only: Specify column of the code{sf}
       |                                                                            ^
GNU make is a SystemRequirements.
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    96 |       URL{http://www.jstatsoft.org/v32/i07/}.
       |          ^
'LazyData' is specified without a 'data' directory
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     5 | \title{Tell {reticulate} to use Python Conda version available on Domino Data Lab.}
       |             ^
Found the following calls to attach():
File ‘doParallel/R/doParallel.R’:
  attach(exportEnv)
See section ‘Good practice’ in ‘?attach’.
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    56 | You can increase it by including a {timeout=n} argument value.
       |                                    ^
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    54 | You can increase it by including a {timeout=n} argument value.
       |                                    ^
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    New features
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Package suggested but not available for checking: ‘gurobi’
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File ‘doSNOW/R/doSNOW.R’:
  attach(exportEnv)
See section ‘Good practice’ in ‘?attach’.
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  ‘myfile.ps’ ‘myfile.svg’
Unknown package ‘broomExtra’ in Rd xrefs
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    20 |   \item{D1}{Randomize the intial value if |mu_h-mu_{h+1}|>D1}
       |                                                    ^
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    21 |   \item{D2}{Randomize the intial value if |sigma_h-sigma_{h+1}|>D2}
       |                                                          ^
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    20 |   \item{D1}{Randomize the intial value if |mu_h-mu_{h+1}|>D1}
       |                                                    ^
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    21 |   \item{D2}{Randomize the intial value if |sigma_h-sigma_{h+1}|>D2}
       |                                                          ^
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    20 |   \item{D1}{Randomize the intial value if |mu_h-mu_{h+1}|>D1}
       |                                                    ^
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    21 |   \item{D2}{Randomize the intial value if |sigma_h-sigma_{h+1}|>D2}
       |                                                          ^
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     9 | \item{occupancies}{Either a data frame containing two columns or an object of class \code{"upgrain"} from the \code{\link{upgrain}} function. If using a data frame the first column must be the grain sizes (cell area in squared units e.g. km^{2}). The second column is the proportion of occupancies at each grain size.}
       |                                                                                                                                                                                                                                                  ^
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    13 | \item{new.areas}{vector of grain sizes (in squared units e.g. km^{2}) for which area of occupancy will be predicted.}
       |                                                                  ^
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    13 | \item{new.areas}{vector of grain sizes as cell area (in same units as cell.width but squared e.g. km^{2}) at fine scales for model prediction.}
       |                                                                                                      ^
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    10 | \item{new.areas}{vector of grain sizes (in squared units e.g. km^{2}) for which area of occupancy will be predicted.}
       |                                                                  ^
'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’.
'LazyData' is specified without a 'data' directory
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    19 | expression: input_re = reactive({input})}
       |                                 ^
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    19 | expression: input_re = reactive({input})}
       |                                 ^
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    19 | expression: input_re = reactive({input})}
       |                                 ^
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    19 | expression: input_re = reactive({input})}
       |                                 ^
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    19 | expression: input_re = reactive({input})}
       |                                 ^
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    19 | expression: input_re = reactive({input})}
       |                                 ^
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    19 | expression: input_re = reactive({input})}
       |                                 ^
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    19 | expression: input_re = reactive({input})}
       |                                 ^
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    19 | expression: input_re = reactive({input})}
       |                                 ^
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No news entries found.
'LazyData' is specified without a 'data' directory
'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’
'LazyData' is specified without a 'data' directory
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    43 |   emph{Generalized Linear Models}, 
       |       ^
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    18 |     \item{\code{GR}}{a numeric vector: germination rates in d^{-1}}
       |                                                               ^
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    16 |     \item{\code{GR}}{a numeric vector: germination rates in d^{-1}}
       |                                                               ^
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    34 | This function allows values other than {0, 1, -1} for \code{alpha} and \code{delta} but
       |                                        ^
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    35 | This function allows values other than {0, 1, -1} for \code{alpha} and \code{delta} but
       |                                        ^
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    11 | code{\link[DrDimont]{compute_correlation_matrices}}}
       |     ^
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    53 | a dose returns the plot of pr(trt_dose - trt_{reference_dose} | data).}
       |                                              ^
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    70 | a dose returns the plot of pr(trt_dose - trt_{reference_dose} | data).}
       |                                              ^
Specified C++11: please drop specification unless essential
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GNU make is a SystemRequirements.
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No news entries found.
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'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘CodelistGenerator’
Error(s) in re-building vignettes:
  ...
--- re-building ‘addIndications-example.Rmd’ using rmarkdown
trying URL 'https://example-data.ohdsi.dev/GiBleed.zip'
Content type 'application/zip' length 6754786 bytes (6.4 MB)
==================================================
downloaded 6.4 MB


Quitting from lines 38-54 [setup ] (addIndications-example.Rmd)
Error: processing vignette 'addIndications-example.Rmd' failed with diagnostics:
there is no package called 'CodelistGenerator'
--- failed re-building ‘addIndications-example.Rmd’

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

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

Quitting from lines 23-38 [setup] (introCreateCohort.Rmd)
Error: processing vignette 'introCreateCohort.Rmd' failed with diagnostics:
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--- failed re-building ‘introCreateCohort.Rmd’

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

Quitting from lines 112-124 [unnamed-chunk-6] (routePatternDose.Rmd)
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--- failed re-building ‘routePatternDose.Rmd’

Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
Warning: Database is garbage-collected, use dbDisconnect(con, shutdown=TRUE) or duckdb::duckdb_shutdown(drv) to avoid this.
SUMMARY: processing the following files failed:
  ‘addIndications-example.Rmd’ ‘introCreateCohort.Rmd’
  ‘routePatternDose.Rmd’

Error: Vignette re-building failed.
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'LazyData' is specified without a 'data' directory
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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.
checkRd: (-1) read_mnist.Rd:24-25: Lost braces
    24 | \item{keep.files}{A logical. If \code{TRUE} the downloaded files will be saved in \code{destdir}. If \code{FALSE} the entire directory is erased. This argument is ignored if \code{download} is \code{FALSE}.){
       |                                                                                                                                                                                                                ^
Specified C++11: please drop specification unless essential
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checkRd: (-1) dsm_varprop.Rd:67: Lost braces
    67 | parameter uncertainty. See Wood, Pya & S{\"a}fken (2016) for more
       |                                         ^
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   100 | Wood, S.N., Pya, N. and S{\"a}fken, B. (2016) Smoothing parameter and model
       |                          ^
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'LazyData' is specified without a 'data' directory
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    24 |   - PPV = 1 / {1 + (1 / pi - 1) / pDLR}
       |               ^
checkRd: (-1) pv.prev.Rd:25: Lost braces; missing escapes or markup?
    25 |   - NPV = 1 / {1 + (1 / (1 / pi - 1)) / nDLR}. 
       |               ^
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    22 |   \item{error}{ Numeric value. Maximum pointwise error when estimating the density associated to X (f) in two consecutive steps. If this is missing, it is $1e{-06}$.}
       |                                                                                                                                                               ^
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    21 |    \item{error}{ Numeric value. Maximum pointwise error when estimating the density associated to X (f) in two consecutive steps. If this is missing, it is $1e{-06}$.}
       |                                                                                                                                                                ^
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    24 |   \item{error}{ Numeric value. Maximum pointwise error when estimating the density associated to X (f) in two consecutive steps. If this is missing, it is $1e{-06}$.}
       |                                                                                                                                                               ^
Specified C++11: please drop specification unless essential
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   105 |   argument \code{what}.  For code{"["} the cutted object.
       |                                  ^
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    64 | The empiric model is specified as F(d, beta) = d^{exp(beta)}. The logistic model is
       |                                                  ^
'LazyData' is specified without a 'data' directory
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    29 | {.subgroup} for the subgroup column name and \{.name\} for the subgroup
       | ^
checkRd: (-1) p_count_subgroup.Rd:29: Lost braces; missing escapes or markup?
    29 | {.subgroup} for the subgroup column name and \{.name\} for the subgroup
       | ^
GNU make is a SystemRequirements.
checkRd: (-1) DTWUMI_1gap_imputation.Rd:33: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) DTWUMI_1gap_imputation.Rd:34: Lost braces in \itemize; \value handles \item{}{} directly
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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.
'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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'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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    27 |      For example, the order {a, b, c} implies that a > b, a  > c, and b > c.
       |                             ^
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   107 |   For \code{coef} a new \R{XXc} field is created so as not to trample
       |                           ^
'LazyData' is specified without a 'data' directory
Invalid package aliases in Rd file 'dynConfiR-package.Rd':
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    57 | By default, sampled from {-1, 1} with probabilities {.25, .75}.
       |                          ^
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    57 | By default, sampled from {-1, 1} with probabilities {.25, .75}.
       |                                                     ^
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    19 | \item{log_style}{is a {crayon::style()} that will colorize
       |                       ^
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    22 | \item{msg_style}{is a {crayon::style()} style that will gray scale the
       |                       ^
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    22 | \item{"sysname"} : {The operating system name.}
       |                    ^
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    23 | \item{"release"} : {The OS release.}
       |                    ^
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    24 | \item{"version"} : {The OS version.}
       |                    ^
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    25 | \item{"nodename"} : {A name by which the machine is known on the network (if any).}
       |                     ^
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    26 | \item{"machine"} : {A concise description of the hardware, often the CPU type.}
       |                    ^
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    27 | \item{"login"} : {The user's login name, or "unknown" if it cannot be ascertained.}
       |                  ^
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    28 | \item{"user"} : {The name of the real user ID, or "unknown" if it cannot be ascertained.}
       |                 ^
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    29 | \item{"r-ver"} : {R Version in (major).(minor) format.}
       |                  ^
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checkRd: (-1) WBC-measurements-data.Rd:30: Escaped LaTeX specials: \&
checkRd: (-1) WBC-measurements-data.Rd:40: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
checkRd: (-1) dynsim.Rd:48: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dynsim.Rd:49: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dynsim.Rd:50-51: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dynsim.Rd:52: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dynsim.Rd:53-54: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dynsim.Rd:55-56: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dynsim.Rd:57-58: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dynsim.Rd:59-60: Lost braces in \itemize; \value handles \item{}{} directly
Specified C++11: please drop specification unless essential
checkRd: (-1) monitor_long_1d.Rd:33: Lost braces
    33 | If \code{side="upward"}{apply control charts that aim to detect upward shifts.} \cr
       |                        ^
checkRd: (-1) monitor_long_1d.Rd:34: Lost braces
    34 | If \code{side="downward"}{apply control charts that aim to detect downward shifts.} \cr
       |                          ^
checkRd: (-1) monitor_long_1d.Rd:35: Lost braces
    35 | If \code{side="both"}{apply control charts that aim to detect shifts in both sides}}
       |                      ^
checkRd: (-1) monitor_long_1d.Rd:38: Lost braces
    38 | If \code{chart="CUSUM"}{apply CUSUM charts.} \cr
       |                        ^
checkRd: (-1) monitor_long_1d.Rd:39: Lost braces
    39 | If \code{chart="EWMA"}{apply EWMA charts.}}
       |                       ^
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
checkRd: (-1) AM.Rd:95-98: Lost braces in \itemize; meant \describe ?
checkRd: (-1) AM.Rd:99-102: Lost braces in \itemize; meant \describe ?
checkRd: (-1) AM.Rd:103: Lost braces in \itemize; meant \describe ?
checkRd: (-1) AM.Rd:123-125: Lost braces in \itemize; meant \describe ?
checkRd: (-1) AM.Rd:126-133: Lost braces in \itemize; meant \describe ?
checkRd: (-1) AM.Rd:134-135: Lost braces in \itemize; meant \describe ?
checkRd: (-1) AM.Rd:136-137: Lost braces in \itemize; meant \describe ?
checkRd: (-1) AM.Rd:163-165: Lost braces in \itemize; meant \describe ?
checkRd: (-1) AM.Rd:166-173: Lost braces in \itemize; meant \describe ?
checkRd: (-1) AM.Rd:174-176: Lost braces in \itemize; meant \describe ?
checkRd: (-1) AM.Rd:177-178: Lost braces in \itemize; meant \describe ?
checkRd: (-1) AM.Rd:179-180: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MHLS.Rd:48-51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MHLS.Rd:52: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MHLS.Rd:53-54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MHLS.Rd:55-56: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MHLS.Rd:75: Lost braces; missing escapes or markup?
    75 | From the initial values, \code{B0} and {S0}, \code{\link{MHLS}} draws \code{beta} and \code{subgrad} samples.
       |                                        ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) plot.earlyR.Rd:34-46: Lost braces
    34 | if (require(incidence)) {
       |                         ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) surrogates_ews.Rd:31: Lost braces
    31 | \item{span}{parameter that controls the degree of smoothing (numeric between 0 and 100, Default 25). see more on loess{stats}}
       |                                                                                                                       ^
checkRd: (-1) surrogates_ews.Rd:33: Lost braces
    33 | \item{degree}{the degree of polynomial to be used for when loess fitting is applied, normally 1 or 2 (Default). see more on loess{stats}}
       |                                                                                                                                  ^
checkRd: (-1) varmod.Rd:99-101: Lost braces in \itemize; meant \describe ?
checkRd: (-1) varmod.Rd:102-104: Lost braces in \itemize; meant \describe ?
checkRd: (-1) varmod.Rd:105-108: Lost braces in \itemize; meant \describe ?
checkRd: (-1) varmod.Rd:109-112: 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
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’
checkRd: (-1) ArrayToNc.Rd:30-38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ArrayToNc.Rd:39-50: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ArrayToNc.Rd:51-76: 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 which this enhances but not available for checking: ‘gurobi’
checkRd: (-1) write_spss.Rd:31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) write_spss.Rd:32-33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) write_spss.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) write_spss.Rd:35-40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) write_spss.Rd:45: Lost braces in \itemize; meant \describe ?
checkRd: (-1) write_spss.Rd:46: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
checkRd: (-1) OCC1950.Rd:64: Lost braces
    64 |     \doi{10.18128/D010.V10.0}{IPUMS USA: Version 10.0 [dataset]. Minneapolis, MN: IPUMS}. 
       |                              ^
checkRd: (-1) Oil.Rd:45: Lost braces
    45 |       code{pt-pt-1} on a constant
       |           ^
checkRd: (-1) breaches.Rd:70-74: Lost braces
    70 |     \code{breach_end}{
       |                      ^
checkRd: (-1) breaches.Rd:75-78: Lost braces
    75 |     \code{year}{
       |                ^
checkRd: (-1) nuclearWeaponStates.Rd:82-92: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nuclearWeaponStates.Rd:93-103: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nuclearWeaponStates.Rd:104-127: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nuclearWeaponStates.Rd:128-140: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nuclearWeaponStates.Rd:141-150: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nuclearWeaponStates.Rd:151-161: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nuclearWeaponStates.Rd:162-172: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nuclearWeaponStates.Rd:173-191: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nuclearWeaponStates.Rd:192-219: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
checkRd: (-1) BoxCox.Rd:266-269: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) BoxCox.Rd:270-275: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) BoxCox.Rd:276-284: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) BoxCox.Rd:285-293: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Newdata.Rd:88-91: Lost braces
    88 |   {replace \code{newDat[, x2]}:  
       |   ^
checkRd: (-1) interpPairs.Rd:120: Lost braces
   120 |     environment / list to use with code{object},
       |                                        ^
checkRd: (-1) matchQuote.Rd:72-74: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) matchQuote.Rd:75-80: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) matchQuote.Rd:81-88: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) matchQuote.Rd:89-94: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simulate.bic.glm.Rd:81-91: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulate.bic.glm.Rd:92-103: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulate.bic.glm.Rd:104-108: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulate.glm.Rd:79-83: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulate.glm.Rd:84-95: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulate.glm.Rd:96-100: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
checkRd: (-1) e_pictorial.Rd:57-58: Lost braces in \itemize; meant \describe ?
checkRd: (-1) e_pictorial.Rd:60: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nesting.Rd:48: Lost braces
    48 | `{itemStyle: {color: 'red', fontBold: 'bold'}}`.
       |  ^
checkRd: (-1) nesting.Rd:48: Lost braces; missing escapes or markup?
    48 | `{itemStyle: {color: 'red', fontBold: 'bold'}}`.
       |              ^
checkRd: (-1) nesting.Rd:51: Lost braces; missing escapes or markup?
    51 | `{symbolSize: 4}`.
       |  ^
Argument items with no description in Rd file 'e.cluster.decision.Rd':
  ‘reg_data’ ‘log.lambda’
Argument items with no description in Rd file 'e.cluster.dendrogram.Rd':
  ‘echelon.obj’ ‘n.sim’ ‘cluster.legend.pos’ ‘cluster_reg’ ‘p_rank’
  ‘para’
Argument items with no description in Rd file 'e.cluster.map.Rd':
  ‘x’ ‘c_separates’ ‘locs’ ‘coo’ ‘rin’ ‘p_rank’ ‘cluster_reg’ ‘n.sim’
  ‘cluster.type’
Argument items with no description in Rd file 'e.dendrogram.Rd':
  ‘peaks’ ‘locs’ ‘x’ ‘separates’ ‘c_separates’ ‘number’ ‘parents’
  ‘pare_locs’ ‘progeny’ ‘symbols’ ‘col.symbols’ ‘cex.symbols’ ‘lwd’
  ‘col’ ‘ens’ ‘adj.ens’ ‘col.ens’ ‘cex.ens’ ‘limb’
Argument items with no description in Rd file 'e.dendrogram.axis.Rd':
  ‘main’ ‘ylab’ ‘yaxes’ ‘ylim’ ‘xaxes’ ‘xdper’ ‘dmai’ ‘peaks’ ‘x’
Argument items with no description in Rd file 'e.main.Rd':
  ‘x’ ‘rin’ ‘T’
Argument items with no description in Rd file 'e.monte.bin.Rd':
  ‘rin’ ‘cas’ ‘pop’ ‘n.sim’ ‘K’ ‘cluster.type’
Argument items with no description in Rd file 'e.monte.poi.Rd':
  ‘rin’ ‘cas’ ‘pop’ ‘ex’ ‘n.sim’ ‘K’ ‘cluster.type’
Argument items with no description in Rd file 'e.profile.Rd':
  ‘peaks’ ‘parents’ ‘separates’
Argument items with no description in Rd file 'e.scan.Rd':
  ‘x’ ‘locs’ ‘peaks’ ‘c_separates’ ‘parents’ ‘K’
Argument items with no description in Rd file 'e.scan.pop.Rd':
  ‘x’ ‘locs’ ‘peaks’ ‘c_separates’ ‘parents’ ‘K’ ‘pop’
Argument items with no description in Rd file 'nlimb.Rd':
  ‘x’ ‘k2’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) ecolRxC.Rd:161-166: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ecolRxC.Rd:167-175: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ecolRxC.Rd:176-178: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ecolRxC.Rd:179-185: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ecolRxC.Rd:186-192: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ecolRxC.Rd:193-201: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ecolRxC.Rd:202-208: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ecolRxC.Rd:209-216: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ecolRxC.Rd:217-221: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
Package vignette without corresponding tangle output:
  ‘ecoreg-guide.Rnw’
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
checkRd: (-1) transformFitness.Rd:25: Lost braces; missing escapes or markup?
    25 | minimization (most others). This function computes a factor from {-1, 1} for
       |                                                                  ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) sd_map.Rd:33-34: Lost braces
    33 | the map. \itemize{ \item{\code{elem} {displays elementary and unified
       |                                      ^
checkRd: (-1) sd_map.Rd:34: Lost braces; missing escapes or markup?
    34 | districts}} \item{\code{secon} {displays secondary and unified districts}}}
       |                                ^
checkRd: (-1) read.edf.Rd:30: Lost braces
    30 | Kemp B., V\"{a}rri, A., Rosa, A.C., Nielsen, K.D. and Gade, J. (1992).
       |             ^
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    TODO:
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) parseMix.Rd:15: Lost braces
    15 | list with categorical expression (\code{cat}), which is normalized,  a numerical expression (code{nums}) 
       |                                                                                                  ^
checkRd: (-1) parseMix.Rd:16: Lost braces
    16 | and a negated version of this  expression (code{negNums})
       |                                                ^
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
checkRd: (-1) edm2psd.Rd:10: Lost braces; missing escapes or markup?
    10 | \item{D}{A matrix in the set D_{n}^{-}.}
       |                                ^
checkRd: (-1) edm2psd.Rd:10: Lost braces; missing escapes or markup?
    10 | \item{D}{A matrix in the set D_{n}^{-}.}
       |                                    ^
checkRd: (-1) items_ordered_eclsk_atl.Rd:23: Lost braces; missing escapes or markup?
    23 | \item \code{P4SRS10}: Keep working at something until {he/she} is finished?
       |                                                       ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) eesim.Rd:148-151: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) eesim.Rd:152-155: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) eesim.Rd:156-158: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘lavaan.survey’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘eval_test_LG_ROC.pdf’ ‘test.pdf’
Package suggested but not available for checking: ‘eggCountsExtra’
GNU make is a SystemRequirements.
Documented arguments not in \usage in Rd file 'rotate_to_equilibrium.Rd':
  ‘xy_may’

Documented arguments not in \usage in Rd file 'wide.dyads.to.edgelist.Rd':
  ‘fist.var’

Documented arguments not in \usage in Rd file 'wide.to.long.Rd':
  ‘last.col’ ‘ego.vars’

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) Constants.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Constants.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Constants.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) boxConcMonth.Rd:24: Lost braces; missing escapes or markup?
    24 | \item{las}{numeric in {0,1,2,3}; the style of axis labels, see ?par}
       |                       ^
checkRd: (-1) boxQTwice.Rd:28: Lost braces; missing escapes or markup?
    28 | \item{las}{numeric in {0,1,2,3}; the style of axis labels, see ?par}
       |                       ^
checkRd: (-1) boxResidMonth.Rd:17: Lost braces; missing escapes or markup?
    17 | \item{las}{numeric in {0,1,2,3}; the style of axis labels}
       |                       ^
Invalid package aliases in Rd file 'HOF-package.Rd':
  ‘HOF-package’
Problems with news in ‘NEWS.md’:
No news entries found.
Specified C++11: please drop specification unless essential
Specified C++14: please drop specification unless essential
checkRd: (-1) colBoxplot4.Rd:14: Lost braces; missing escapes or markup?
    14 | \item{id}{Internal parameters for {shiny}.}
       |                                   ^
checkRd: (-1) elaborator_server.Rd:10: Lost braces; missing escapes or markup?
    10 | \item{id, input, output, session}{Internal parameters for {shiny}.}
       |                                                           ^
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
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
checkRd: (-1) fit_mean.Rd:54: Lost braces
    54 | \code{t_optims}{optimal parametrizations}
       |                ^
checkRd: (-1) fit_mean.Rd:55: Lost braces
    55 | \code{G_optims}{optimal rotations}
       |                ^
checkRd: (-1) fit_mean.Rd:56: Lost braces
    56 | \code{b_optims}{optimal scalings}
       |                ^
checkRd: (-1) fit_mean.Rd:57: Lost braces
    57 | \code{n_optims}{optimal re-normalization}
       |                ^
checkRd: (-1) fit_mean.Rd:58: Lost braces
    58 | \code{n_iter}{number of iterations until convergence}
       |              ^
checkRd: (-1) docs_delete_by_query.Rd:47: Lost braces; missing escapes or markup?
    47 | as a document at .tasks/task/${taskId}. This is yours to keep or remove
       |                               ^
checkRd: (-1) docs_update_by_query.Rd:48: Lost braces; missing escapes or markup?
    48 | as a document at .tasks/task/${taskId}. This is yours to keep or remove
       |                               ^
'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: \_
'LazyData' is specified without a 'data' directory
checkRd: (-1) electData.Rd:16: Lost braces; missing escapes or markup?
    16 | Variables: \code{id}  = {identification number},
       |                         ^
checkRd: (-1) electData.Rd:17: Lost braces; missing escapes or markup?
    17 | \code{state} = {state}, \code{age} = age in years on a shifted scale (current age minus 70),
       |                ^
checkRd: (-1) summary.elect.Rd:25: Lost braces; missing escapes or markup?
    25 |  TRUE for output on start-state totals e_{r.} (for \code{S}>0)
       |                                          ^
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) prepareInitsLM.Rd:21-23: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) elliptic-package.Rd:92: Lost braces
    92 |     J. Kotus and M. Urb\'{a}nski 2003.  \emph{Hausdorff dimension and Hausdorff
       |                          ^
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) elo.run.Rd:80: Lost braces
    80 | \code{\link{score}}, \link{elo.run.helpers}{elo.run helpers}, \code{\link{elo.calc}},
       |                                            ^
GNU make is a SystemRequirements.
checkRd: (-1) Emas.Rd:55: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Emas.Rd:56: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Emas.Rd:57: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Emas.Rd:58: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Emas.Rd:59: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Emas.Rd:60: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Emas.Rd:61: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Emas.Rd:62: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Emas.Rd:63: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Emas.Rd:64: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) NEWS.Rd:194: Lost braces; missing escapes or markup?
   194 | 	    \item added {d,r}betabinom
       |                         ^
Found the following significant warnings:
  emd-rubner.c:810:20: warning: ‘minI’ is used uninitialized [-Wuninitialized]
  emd-rubner.c:810:26: warning: ‘minJ’ is used uninitialized [-Wuninitialized]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/emdist.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-13 (Debian 13.2.0-9) 13.2.0’
License stub is invalid DCF.
Specified C++11: please drop specification unless essential
checkRd: (-1) minimize.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) minimize.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) minimize.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) minimize.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) minimize.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) minimize.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) minimize.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) minimize.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) minimize.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) minimize.Rd:31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) minimize.Rd:32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) minimize.Rd:33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) EmiStatR-methods.Rd:86: Lost braces; missing escapes or markup?
    86 | execute {EmiStatR} function
       |         ^
checkRd: (-1) input-class.Rd:136: Lost braces; missing escapes or markup?
   136 |     \item{EmiStatR}{\code{signature(x = "input")}: execute {EmiStatR} function }
       |                                                            ^
'LazyData' is specified without a 'data' directory
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/EMMIXgene.Rcheck/00install.out’ for details.
* used C++ compiler: ‘g++-13 (Debian 13.2.0-9) 13.2.0’
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’.
checkRd: (-1) macacaModels.Rd:9: Lost braces in \itemize; meant \describe ?
checkRd: (-1) macacaModels.Rd:10-11: Lost braces in \itemize; meant \describe ?
Found the following significant warnings:
  bitstring.h:28:54: warning: format ‘%i’ expects argument of type ‘int’, but argument 2 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/emoa.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-13 (Debian 13.2.0-9) 13.2.0’
checkRd: (-1) medal.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) medal.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) medal.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) WRegTest.Rd:43: Lost braces
    43 | For ordinary least squares estimator, \code{psifun} should be the identity function psifun <- function(t){t}.
       |                                                                                                          ^
Specified C++11: please drop specification unless essential
checkRd: (-1) em.Rd:25: Lost braces
    25 |  \code{terms} the code{terms} object used.
       |                       ^
checkRd: (-1) em.clogit.Rd:65: Lost braces
    65 |  \code{terms} the code{terms} object used.
       |                       ^
checkRd: (-1) em.default.Rd:65: Lost braces
    65 |  \code{terms} the code{terms} object used.
       |                       ^
checkRd: (-1) em.fitdist.Rd:49: Lost braces
    49 |  \code{terms} the code{terms} object used.
       |                       ^
checkRd: (-1) em.glmerMod.Rd:50: Lost braces
    50 |  \code{terms} the code{terms} object used.
       |                       ^
checkRd: (-1) em.panelmodel.Rd:49: Lost braces
    49 |  \code{terms} the code{terms} object used.
       |                       ^
checkRd: (-1) EMSC.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) EMSC.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) EMSC.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) EMSC.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) droso.Rd:8: Lost braces; missing escapes or markup?
     8 | The dataset contains 400 true donor sites, 400 false donor sites and 50 false sites as test set. Each sequence is of 40 nucleotides long. The conserved di-nucleotides GT are present at $21^{st}$ and $22^{nd}$ positions respectively.
       |                                                                                                                                                                                              ^
checkRd: (-1) droso.Rd:8: Lost braces; missing escapes or markup?
     8 | The dataset contains 400 true donor sites, 400 false donor sites and 50 false sites as test set. Each sequence is of 40 nucleotides long. The conserved di-nucleotides GT are present at $21^{st}$ and $22^{nd}$ positions respectively.
       |                                                                                                                                                                                                            ^
checkRd: (-1) encode.character.Rd:22: Escaped LaTeX specials: \~
'LazyData' is specified without a 'data' directory
Rd files without \alias:
  ‘enc-package.Rd’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘file.path(temp_dir, gp2.csv)’
checkRd: (-1) enetLTS-package.Rd:41: Lost braces; missing escapes or markup?
    41 |   \code{family="binomial"} should be a factor with two levels which is coded as \code{0} and {1}.
       |                                                                                              ^
checkRd: (-1) CTN.Rd:22: Lost braces; missing escapes or markup?
    22 | less memory. Genetic data consists of nucleotide data {A,T,C,G} and are usually saved
       |                                                       ^
checkRd: (-1) ALL.Regression.Config-class.Rd:39: Lost braces
    39 |     \item{code{shrinkage}:}{Object of class \code{"numeric"}, defining the shrinkage parameter applied to each tree in expansion.}
       |               ^
Package vignette with \VignetteEngine{} not specifying an engine package:
  ‘ensurer.Rmd’
Engines should be specified as \VignetteEngine{PKG::ENG}.
checkRd: (-1) entropy.Dirichlet.Rd:65: Lost braces in \itemize; meant \describe ?
checkRd: (-1) entropy.Dirichlet.Rd:66: Lost braces in \itemize; meant \describe ?
checkRd: (-1) entropy.Dirichlet.Rd:67: Lost braces in \itemize; meant \describe ?
checkRd: (-1) entropy.Dirichlet.Rd:68: Lost braces in \itemize; meant \describe ?
checkRd: (-1) entropy.Dirichlet.Rd:69: Lost braces in \itemize; meant \describe ?
checkRd: (-1) entropy.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) entropy.Rd:35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) entropy.Rd:36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) entropy.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) entropy.Rd:38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) entropy.Rd:39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) entropy.Rd:40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) entropy.Rd:41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) entropy.Rd:42: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'div_plot.Rd':
  ‘plot_cols’

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

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) HIdermal.Rd:35: Lost braces; missing escapes or markup?
    35 | AD {EnviroPRA}
       |    ^
checkRd: (-1) HIinhal.Rd:32: Lost braces; missing escapes or markup?
    32 | AIR {EnviroPRA}
       |     ^
checkRd: (-1) RISKdermal.Rd:34: Lost braces; missing escapes or markup?
    34 | AD {EnviroPRA}
       |    ^
Auto-generated content requiring editing in Rd file 'EnviroPRA-package.Rd':
  \details: ‘...o use the package, including the most important functions ~~’
checkRd: (-1) metrics.Rd:124: Lost braces
   124 | Avg = 0.5 (sum | P_i - Q_i| + max{ | P_i - Q_i |})
       |                                  ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) Olympic.NH4.df.Rd:35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Olympic.NH4.df.Rd:36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Olympic.NH4.df.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Olympic.NH4.df.Rd:38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Olympic.NH4.df.Rd:39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Olympic.NH4.df.Rd:40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Olympic.NH4.df.Rd:41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Olympic.NH4.df.Rd:42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) eqpois.Rd:200: Lost braces
   200 |   \code{\link{epois}}, \link[stats]{Poisson}, code{\link{estimate.object}}.
       |                                                   ^
checkRd: (-1) plotPredIntLnormAltSimultaneousTestPowerCurve.Rd:77: Lost braces
    77 |   positive integer between \code{1} and code{r} specifying the number of future 
       |                                             ^
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘Net1-fromR.inp’
checkRd: (-1) misClustRate.Rd:18: Lost braces; missing escapes or markup?
    18 | Compute the empirical MCR, assuming that #{cluster} = #{block},
       |                                           ^
checkRd: (-1) misClustRate.Rd:18: Lost braces; missing escapes or markup?
    18 | Compute the empirical MCR, assuming that #{cluster} = #{block},
       |                                                        ^
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’.
checkRd: (-1) risk.display.rd:98: Escaped LaTeX specials: \$
checkRd: (-1) estimate_R.Rd:59-62: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimate_R.Rd:64-65: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimate_R.Rd:67-68: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimate_R.Rd:70-72: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimate_R.Rd:74: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimate_R.Rd:76-77: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimate_R.Rd:79-80: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimate_R.Rd:82: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimate_R.Rd:84-86: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) wallinga_teunis.Rd:48-51: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) wallinga_teunis.Rd:51-52: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) wallinga_teunis.Rd:53-54: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) wallinga_teunis.Rd:54-55: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) wallinga_teunis.Rd:55-56: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) wallinga_teunis.Rd:56-58: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) wallinga_teunis.Rd:58-59: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) EpiForsk-package.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) EpiForsk-package.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) EpiForsk-package.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) EpiForsk-package.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) EpiForsk-package.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) charlson_score.Rd:65-68: Lost braces in \itemize; meant \describe ?
checkRd: (-1) charlson_score.Rd:69-73: Lost braces in \itemize; meant \describe ?
checkRd: (-1) charlson_score.Rd:74-77: Lost braces in \itemize; meant \describe ?
Package suggested but not available for checking: ‘epidict’
Documented arguments not in \usage in Rd file 'dots_to_charlist.Rd':
  ‘call’ ‘...’

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) runSim.Rd:111: Lost braces
   111 | \ifelse{html}{\out{<i>r</i><sub>1</sub> = 1}}{{\eqn{r_1 = 1}}{r_1 = 1}} while the individual with the lowest phenotypic value
       |                                                              ^
checkRd: (-1) runSim.Rd:112: Lost braces
   112 | is given the rank \ifelse{html}{\out{<i>r<sub>n</sub></i> = <i>n</i>}}{{\eqn{r_n = n}}{r_n = n}}), the probability of an individual
       |                                                                                       ^
checkRd: (-1) runSim.Rd:120-122: Lost braces
   120 | }{
       |  ^
GNU make is a SystemRequirements.
checkRd: (-1) LCa.fit.Rd:151: Lost braces
   151 |   \code{pi} (\code{p}eriod code{i}nteraction) refers to \eqn{b_p(a)}{b_p(a)}
       |                                ^
checkRd: (-1) lls.Rd:30: Lost braces
    30 | code{name},
       |     ^
checkRd: (-1) lls.Rd:31: Lost braces
    31 | code{mode},
       |     ^
checkRd: (-1) lls.Rd:32: Lost braces
    32 | code{class} and
       |     ^
checkRd: (-1) lls.Rd:33: Lost braces
    33 | code{size} and one row per object in the workspace (if \code{pos=1}).
       |     ^
checkRd: (-1) plotCIF.Rd:79: Lost braces
    79 | \author{Esa L{\"a}{\"a}r{\"a}, \email{esa.laara@oulu.fi}
       |              ^
checkRd: (-1) plotCIF.Rd:79: Lost braces
    79 | \author{Esa L{\"a}{\"a}r{\"a}, \email{esa.laara@oulu.fi}
       |                   ^
checkRd: (-1) plotCIF.Rd:79: Lost braces
    79 | \author{Esa L{\"a}{\"a}r{\"a}, \email{esa.laara@oulu.fi}
       |                         ^
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.
checkRd: (-1) getAgeGender.Rd:52: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getAgeGender.Rd:53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getAgeGender.Rd:54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getAgeGender.Rd:55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getMap.Rd:44-45: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getMap.Rd:46-48: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getMap.Rd:49-51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getSeason.Rd:55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getSeason.Rd:56: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getSeason.Rd:57: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getSeason.Rd:58: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getTableByMS.Rd:59: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getTableByMS.Rd:60: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getTableByMS.Rd:61-62: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getTrend.Rd:55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getTrend.Rd:56: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotAgeGender.Rd:45: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotAgeGender.Rd:46: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotAgeGender.Rd:47: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotSeasonality.Rd:42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotSeasonality.Rd:43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotSeasonality.Rd:44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotSeasonality.Rd:45: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotTS12MAvg.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotTS12MAvg.Rd:28: Lost braces in \itemize; meant \describe ?
'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’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Invalid package aliases in Rd file 'equateMultiple-package.Rd':
  ‘EquateMultiple-package’
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) Tm.Rd:46-48: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Tm.Rd:49-51: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Tm.Rd:52-54: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Tm.Rd:55-57: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Tm.Rd:58-60: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) fitpot.Rd:36-39: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) fitpot.Rd:40-42: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) fitpot.Rd:43-46: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) fitpot.Rd:47-49: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) thrselect.Rd:54-56: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) thrselect.Rd:57-59: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) thrselect.Rd:60-62: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) thrselect.Rd:63-65: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) thrselect.Rd:66-68: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) thrselect.Rd:69-71: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) thrselect.Rd:72-74: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) thrselect.Rd:75-77: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) evReturn.Rd:34: Lost braces
    34 |   \item{daEst }{  data used to estimate the market model for the last firm as specified in code{firm}.}
       |                                                                                                ^
checkRd: (-1) evRisk.Rd:19: Lost braces
    19 |   \item{daEst }{  data used to estimate CAPM for the last firm as specified in code{firm}.}
       |                                                                                    ^
checkRd: (-1) Lazega.Rd:58: Lost braces; missing escapes or markup?
    58 | \item{\code{friendship}}{(logical) whether \eqn{i} considers {j} a friend outside of work.}
       |                                                              ^
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.
checkRd: (-1) ergm.rank-package.Rd:42: Lost braces
    42 | 1100-1128. c("\\Sexpr[results=rd,stage=build]{tools:::Rd_expr_doi(\"#1\")}",
       |                                              ^
checkRd: (-1) ifa.Rd:16: Lost braces; missing escapes or markup?
    16 | If Sigma has the q-factor decomposition Sigma=diag(Psi)+BB', then Sigma^{-1} 
       |                                                                         ^
checkRd: (-1) ifa.Rd:17: Lost braces; missing escapes or markup?
    17 | has the corresponding q-factor decomposition Sigma^{-1}=diag(phi)(I-theta theta')diag(phi), where theta is a mxq matrix and phi the vector of 
       |                                                    ^
checkRd: (-1) ifa.Rd:21: Lost braces; missing escapes or markup?
    21 | \item{iSB}{m x q matrix (diag(Psi)+BB')^{-1}B.}
       |                                         ^
checkRd: (-1) isqrtfa.Rd:15: Lost braces; missing escapes or markup?
    15 | If Sigma has the q-factor decomposition Sigma=diag(Psi)+BB', then the function returns a matrix Omega such that Sigma^{-1} = Omega Omega'. Equivalently,
       |                                                                                                                       ^
checkRd: (-1) best_distribution.Rd:33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) best_distribution.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) best_distribution.Rd:35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) best_distribution.Rd:36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) best_distribution.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) best_distribution.Rd:38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) best_distribution.Rd:39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sort_distributions.Rd:36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sort_distributions.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sort_distributions.Rd:38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sort_distributions.Rd:39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sort_distributions.Rd:40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sort_distributions.Rd:41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sort_distributions.Rd:42: Lost braces in \itemize; meant \describe ?
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’
checkRd: (-1) enp.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) enp.Rd:31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) evolat.Rd:49: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) evolat.Rd:50: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) psns.Rd:37: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) psns.Rd:38: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
checkRd: (-1) festRidge.Rd:80: Lost braces; missing escapes or markup?
    80 | \item{XtXlamIinv}{explicit value of (X'X + diag(penalty))^{-1}.  Useful
       |                                                           ^
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checkRd: (-1) recovered.Rd:11: Lost braces in \itemize; meant \describe ?
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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    12 | \item{orden}{Es un valor numérico que representa el orden del momento central (orden = {1,2,3,4,...})}
       |                                                                                        ^
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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
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checkRd: (-1) integration.Rd:39: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) maxlogLreg.Rd:138: Lost braces; missing escapes or markup?
   138 | $j^{th}$ for all the observations.
       |    ^
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   136 |   uses the {C++} code implemented using the \pkg{Rcpp} package,
       |            ^
checkRd: (-1) etas.Rd:142: Lost braces; missing escapes or markup?
   142 |   {C++} code carries out the computations.
       |   ^
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.
checkRd: (-1) ETC-package.Rd:28-29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ETC-package.Rd:30-31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ETC-package.Rd:32: Lost braces in \itemize; meant \describe ?
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 required but not available: ‘TDA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
Documented arguments not in \usage in Rd file 'poly_clip.Rd':
  ‘x’ ‘y’

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

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

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

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) FuzzyCluster.Rd:15: Lost braces; missing escapes or markup?
    15 | A list of cluster labels and a R object of class "fcm {ppclust}"
       |                                                       ^
checkRd: (-1) pamCluster.Rd:15: Lost braces; missing escapes or markup?
    15 | A list of cluster labels and a R object of class "pam {cluster}"
       |                                                       ^
checkRd: (-1) dist.evaluate.core.Rd:26: Lost braces; missing escapes or markup?
    26 | the \code{names} column in {data} as labels. If \code{NULL} (default),
       |                            ^
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    23 |   L'intensit\'{e} maximale des pr\'{e}cipitations en Belgique.
       |               ^
checkRd: (-1) uccle.Rd:23: Lost braces
    23 |   L'intensit\'{e} maximale des pr\'{e}cipitations en Belgique.
       |                                    ^
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    24 |   \emph{Inst. Royal M\'{e}t\'{e}or. Belgique, B} \bold{86}.
       |                        ^
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    24 |   \emph{Inst. Royal M\'{e}t\'{e}or. Belgique, B} \bold{86}.
       |                              ^
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
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) colplot.Rd:52: Lost braces
    52 | \item{legend}{should a legend be added? Defaults to code{FALSE}}
       |                                                         ^
checkRd: (-1) colplot.Rd:56: Lost braces
    56 | \item{legend.pretty}{logical: should the legend values produced by \[base]{pretty}? Othewrwise they are exact. Defaults to \code{TRUE}}
       |                                                                           ^
checkRd: (-1) calculateGLR.Rd:43: Escaped LaTeX specials: \&
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     5 |   Conducts a generalized likelihood ratio test testing whether {\eqn{\beta \in}  (-\code{c},\code{c})}. Covariates can be accommodated.
       |                                                                ^
checkRd: (-1) glr.Rd:34: Lost braces
    34 |   This is a similar function to the main function \code{evian}. Instead of testing H0: \eqn{\beta}=0, it tests for whether H0:{\eqn{\beta \in} (-\code{c},\code{c})}.
       |                                                                                                                               ^
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   183 |  \item {nlumgammagpd} and {proflumgammagpd} - \code{c(mgshape, mgscale, mgweight[1:(M-1)], sigmau, xi)}
       |                           ^
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   181 |  \item {nlumgammagpdcon} and {proflumgammagpdcon} - \code{c(mgshape, mgscale, mgweight[1:(M-1)], xi)}
       |                              ^
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    87 | code{\link[evmix:kernels]{kd*}}  and \code{\link[evmix:kernels]{kp*}} give the
       |     ^
Found the following files/directories:
  ‘sample .nwk’
checkRd: (-1) ShapeDist.Rd:18: Lost braces; missing escapes or markup?
    18 | Procrustes distance provides a measure of coincidence of two point sets {xi} and {yi}, i=1..N. For this purpose the variance of point deviations is calculated at the optimal superposition of the sets. It allows to characterize the shape proximity of a given simplex to shape of a reference one.
       |                                                                         ^
checkRd: (-1) ShapeDist.Rd:18: Lost braces; missing escapes or markup?
    18 | Procrustes distance provides a measure of coincidence of two point sets {xi} and {yi}, i=1..N. For this purpose the variance of point deviations is calculated at the optimal superposition of the sets. It allows to characterize the shape proximity of a given simplex to shape of a reference one.
       |                                                                                  ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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checkRd: (-1) stop_rule.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'borrOrderingInternal.Rd':
  ‘n.cntrl’

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++14: please drop specification unless essential
Package suggested but not available for checking: ‘ExactData’
checkRd: (-1) exams2sakai.Rd:152: Escaped LaTeX specials: \&
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'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
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
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: \&
checkRd: (-1) ccF.Rd:42: Lost braces
    42 | CALI\'{N}SKI, T.; CORSTEN, L. C. A. Clustering
       |       ^
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    41 | CALI\'{N}SKI, T.; CORSTEN, L. C. A. Clustering
       |       ^
Argument items with no description in Rd file 'plot.expectreg.Rd':
  ‘\dots’
Argument items with no description in Rd file 'update.expectreg.Rd':
  ‘\dots’
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
checkRd: (-1) get_wcs_limit.Rd:55: Lost braces; missing escapes or markup?
    55 |   difference(s) between \code{rl} and {sl}, if \code{xform[2] != "no"} on
       |                                       ^
checkRd: (-1) get_wcs_limit.Rd:58: Lost braces; missing escapes or markup?
    58 |   difference(s) between \code{rl} and {sl} on the original scale.}
       |                                       ^
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
checkRd: (-1) MatIn.Rd:6: Lost braces
     6 | Computation of aggregation matrices for generalized interactions that are used in code{\link{extRC}} to estimate extended RC models.
       |                                                                                       ^
checkRd: (-1) plot.Rd:5: Lost braces
     5 | \description{It plots the output of code{\link{extRC}} function for a vector of lambda values.}
       |                                         ^
checkRd: (-1) print.Rd:5: Lost braces
     5 | \description{Given the output of code{\link{extRC}} function, it is written in a readable form.}
       |                                      ^
checkRd: (-1) summary.Rd:5: Lost braces
     5 | \description{Summary method for the output of code{\link{extRC}} function.}
       |                                                   ^
Argument items with no description in Rd file 'fbvpot.Rd':
  ‘cutoff’
checkRd: (-1) outlierPlot.Rd:30: Escaped LaTeX specials: \$
checkRd: (-1) outlierPlot.Rd:32: Escaped LaTeX specials: \$
Documented arguments not in \usage in Rd file 'getQQLimit.Rd':
  ‘N’ ‘rho’

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: ‘exuberdata’
checkRd: (-1) read_edf.Rd:32: Lost braces
    32 | code{TRUE}}
       |     ^
checkRd: (-1) read_edf.Rd:35: Lost braces
    35 | code{TRUE}}
       |     ^
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Functions and objects (details)
checkRd: (-1) va.Rd:80: Lost braces
    80 | \doi{10.1016/s0002-9394(02)01825-1}{Beck et al.}, and
       |                                    ^
checkRd: (-1) codePasses.Rd:64: Escaped LaTeX specials: \#
'LazyData' is specified without a 'data' directory
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checkRd: (-1) EEzGP_fit.Rd:51: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) EEzGP_predict.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) EEzGP_predict.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) EzGP_fit.Rd:50: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) EzGP_fit.Rd:51: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) EzGP_predict.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) EzGP_predict.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) LEzGP_fit.Rd:59: Lost braces in \itemize; \value handles \item{}{} directly
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checkRd: (-1) ez-package.Rd:33: 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
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) getStuffForDIC.Rd:49: Lost braces
    49 | 	The information criteria are saved to the \code{informationCriteria_map_model.txt} file in the code{outputFolder}. 
       |                                                                                                            ^
Argument items with no description in Rd file 'complete.log.likelihood_Sj.Rd':
  ‘z’
Auto-generated content requiring editing in Rd file 'getStuffForDIC.Rd':
  \details: ‘If necessary, more details than the description above’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) fmCov.Rd:37: Lost braces; missing escapes or markup?
    37 | where, \code{alpha(i)} is the intercept, \code{f(t)} is a {K x 1} vector of 
       |                                                           ^
checkRd: (-1) plot.ffm.Rd:82: Lost braces; missing escapes or markup?
    82 | \item{las}{one of {0, 1, 2, 3} to set the direction of axis labels, same as
       |                   ^
checkRd: (-1) summary.ffm.Rd:39: Lost braces; missing escapes or markup?
    39 | Returned object is of class {summary.ffm}.
       |                             ^
checkRd: (-1) fviz_nbclust.Rd:75: Lost braces; missing escapes or markup?
    75 | (2001) proposed: "the smallest k such that gap(k) >= gap(k+1) - s_{k+1}". 
       |                                                                   ^
checkRd: (-1) fviz_nbclust.Rd:77: Lost braces; missing escapes or markup?
    77 | SE.factor*s_{k+1}" where SE.factor is a numeric value which can be 1
       |             ^
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    minor changes
Auto-generated content requiring editing in Rd file 'procrustes_switching.Rd':
  \details: ‘If necessary, more details than the description above.’
Auto-generated content requiring editing in Rd file 'rsp_exact.Rd':
  \details: ‘If necessary, more details than the description above.’
Auto-generated content requiring editing in Rd file 'rsp_full_sa.Rd':
  \details: ‘If necessary, more details than the description above.’
Auto-generated content requiring editing in Rd file 'rsp_partial_sa.Rd':
  \details: ‘If necessary, more details than the description above.’
Auto-generated content requiring editing in Rd file 'weighted_procrustes_switching.Rd':
  \details: ‘If necessary, more details than the description above.’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) FADPclust.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) FADPclust.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
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checkRd: (-1) FADPclust.Rd:33: Lost braces in \itemize; \value handles \item{}{} directly
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checkRd: (-1) happy.Rd:14: Lost braces
    14 |                  code{Pretty happy} <  \code{Very happy}}
       |                      ^
checkRd: (-1) fra_sf.Rd:22: Lost braces; missing escapes or markup?
    22 | A map of France as {sf} object. Can be used as dataset or for maps
       |                    ^
Documented arguments not in \usage in Rd file 'dot-get_default_sign_size.Rd':
  ‘outcome_type’

Documented arguments not in \usage in Rd file 'dot-get_iteration_data.Rd':
  ‘file_dir’

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

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) Multistate.Rd:16: Lost braces
    16 | item{S}{the multistate survival function (S) and multistate transition probabilities (P)}
       |     ^
checkRd: (-1) Multistate.Rd:16: Lost braces
    16 | item{S}{the multistate survival function (S) and multistate transition probabilities (P)}
       |        ^
checkRd: (-1) Multistate.Rd:17: Lost braces
    17 | item{mslt}{other measures of the multistate life table: person-years (L); expectation at birth of sojourn times in the various states (e0); expectation at age x of the remaining expected sojourn times in the various states: population-based measures (e.p); expectation at age x of the remaining expected sojourn times in the various states: status-based measures (e.p)}
       |     ^
checkRd: (-1) Multistate.Rd:17: Lost braces
    17 | item{mslt}{other measures of the multistate life table: person-years (L); expectation at birth of sojourn times in the various states (e0); expectation at age x of the remaining expected sojourn times in the various states: population-based measures (e.p); expectation at age x of the remaining expected sojourn times in the various states: status-based measures (e.p)}
       |           ^
Specified C++11: please drop specification unless essential
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checkRd: (-1) pi0FAMT.Rd:18: Lost braces
    18 | \code{pi0}{The estimated proportion \code{pi0} of null hypotheses.}}
       |           ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) download_faostat_bulk.Rd:49: Lost braces in \itemize; meant \describe ?
checkRd: (-1) download_faostat_bulk.Rd:50: Lost braces in \itemize; meant \describe ?
checkRd: (-1) download_faostat_bulk.Rd:51-55: Lost braces in \itemize; meant \describe ?
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.
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
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
checkRd: (-1) icevision_IAAAffine.Rd:50: Lost braces; missing escapes or markup?
    50 | via affine transformations. Note: This class introduce interpolation artifacts to mask if it has values other than {0;1}
       |                                                                                                                    ^
checkRd: (-1) icevision_IAAPerspective.Rd:30: Lost braces; missing escapes or markup?
    30 | Note: This class introduce interpolation artifacts to mask if it has values other than {0;1}
       |                                                                                        ^
checkRd: (-1) icevision_IAAPiecewiseAffine.Rd:42: Lost braces; missing escapes or markup?
    42 | via affine transformations. Note: This class introduce interpolation artifacts to mask if it has values other than {0;1}
       |                                                                                                                    ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘bcp’
Error(s) in re-building vignettes:
  ...
--- re-building ‘comparison-packages.Rmd’ using rmarkdown

Quitting from lines 261-262 [univariate-mean-change-bcp] (comparison-packages.Rmd)
Error: processing vignette 'comparison-packages.Rmd' failed with diagnostics:
there is no package called 'bcp'
--- failed re-building ‘comparison-packages.Rmd’

--- re-building ‘comparison-pelt.Rmd’ using rmarkdown
--- finished re-building ‘comparison-pelt.Rmd’

--- re-building ‘examples-advanced.Rmd’ using rmarkdown
--- finished re-building ‘examples-advanced.Rmd’

--- re-building ‘examples-introductory.Rmd’ using rmarkdown
--- finished re-building ‘examples-introductory.Rmd’

SUMMARY: processing the following file failed:
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Error: Vignette re-building failed.
Execution halted
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
Specified C++11: please drop specification unless essential
checkRd: (-1) show.fgasp.Rd:13: Lost braces
    13 | Function to print the code{fgasp} object. 
       |                           ^
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
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: ‘coxKM’
checkRd: (-1) KITdesign.Rd:36: Lost braces; missing escapes or markup?
    36 |  \item{trait}{One of {'c','d','s',NULL} indicating the type
       |                      ^
checkRd: (-1) KITkernel.Rd:51: Lost braces; missing escapes or markup?
    51 |  \item{trait}{One of {'c','d','s',NULL} indicating the type
       |                      ^
checkRd: (-1) geno.Rd:19: Lost braces; missing escapes or markup?
    19 |                 Must be one of {'ibs', 'linear', 'quadratic'}.
       |                                ^
checkRd: (-1) geno.Rd:31: Lost braces; missing escapes or markup?
    31 |                      {'add', 'dom', 'rec'} indicating additive,
       |                      ^
checkRd: (-1) nongeno.Rd:14: Lost braces; missing escapes or markup?
    14 |                 Must be one of {'interactive', 'linear', 'quadratic'}.
       |                                ^
checkRd: (-1) eigen_compute_single_entry_of_diagonal_matrix.Rd:17: Lost braces; missing escapes or markup?
    17 | The value of m^{-1}_{j,j}
       |                ^
checkRd: (-1) eigen_compute_single_entry_of_diagonal_matrix.Rd:17: Lost braces; missing escapes or markup?
    17 | The value of m^{-1}_{j,j}
       |                     ^
'LazyData' is specified without a 'data' directory
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/fastlogranktest.Rcheck/00install.out’ for details.
* used C++ compiler: ‘g++-13 (Debian 13.2.0-9) 13.2.0’
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) FastPCS-package.Rd:29: Escaped LaTeX specials: \&
checkRd: (-1) FastPCS.Rd:24: Lost braces
    24 | item{best}{The index of the observations with outlyingness smaller than the rejection threshold after C-steps are taken.}
       |     ^
checkRd: (-1) FastPCS.Rd:24: Lost braces
    24 | item{best}{The index of the observations with outlyingness smaller than the rejection threshold after C-steps are taken.}
       |           ^
checkRd: (-1) FastPCS.Rd:104: Escaped LaTeX specials: \&
Rd files without \alias:
  ‘FastPCS-package.Rd’
Specified C++11: please drop specification unless essential
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’
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 ?
.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
'LazyData' is specified without a 'data' directory
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.
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘NNLM’
GNU make is a SystemRequirements.
checkRd: (-1) Error-Classes.Rd:107-119: Lost braces
   107 |   \item \code{do_verbose(response, template)} {
       |                                               ^
checkRd: (-1) Error.Rd:33-45: Lost braces
    33 |   \item \code{do(response, mssg)} {
       |                                   ^
checkRd: (-1) fh_bounds.Rd:14: Lost braces
    14 | \item{params1}{Arguments to pass to the r{dist} function for distribution 1}
       |                                          ^
checkRd: (-1) fh_bounds.Rd:16: Lost braces
    16 | \item{params2}{Arguments to pass to the r{dist} function for distribution 2}
       |                                          ^
checkRd: (-1) FBN.histogramMaxima.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FBN.histogramMaxima.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FBN.histogramMaxima.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FBN.histogramMaxima.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FBN.kmeans.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FBN.kmeans.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FBN.kmeans.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FBN.kmeans.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FBNormalization.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FBNormalization.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FBNormalization.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FBNormalization.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FBNormalization.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FBNormalization.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FBNormalization.Rd:35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FBNormalization.Rd:36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FBNormalization.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FBNormalization.Rd:38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FBNormalization.Rd:39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FBNormalization.Rd:40: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
checkRd: (-1) fbad_copy_ad.Rd:25: Lost braces; missing escapes or markup?
    25 | \item{status_option}{(string) enum {ACTIVE, PAUSED, INHERITED_FROM_SOURCE}}
       |                                    ^
checkRd: (-1) fbad_copy_ad.Rd:27: Lost braces; missing escapes or markup?
    27 | \item{rename_strategy}{(string) enum {DEEP_RENAME, ONLY_TOP_LEVEL_RENAME, NO_RENAME}}
       |                                      ^
checkRd: (-1) fbad_copy_adset.Rd:34: Lost braces; missing escapes or markup?
    34 | \item{status_option}{(string) enum {ACTIVE, PAUSED, INHERITED_FROM_SOURCE}}
       |                                    ^
checkRd: (-1) fbad_copy_adset.Rd:36: Lost braces; missing escapes or markup?
    36 | \item{rename_strategy}{(string) enum {DEEP_RENAME, ONLY_TOP_LEVEL_RENAME, NO_RENAME}}
       |                                      ^
checkRd: (-1) fbad_copy_campaign.Rd:31: Lost braces; missing escapes or markup?
    31 | \item{status_option}{(string) enum {ACTIVE, PAUSED, INHERITED_FROM_SOURCE}}
       |                                    ^
checkRd: (-1) fbad_copy_campaign.Rd:33: Lost braces; missing escapes or markup?
    33 | \item{rename_strategy}{(string) enum {DEEP_RENAME, ONLY_TOP_LEVEL_RENAME, NO_RENAME}}
       |                                      ^
checkRd: (-1) plot.fbroc.conf.Rd:5: Lost braces
     5 | \title{Plots function for object of class{fbroc.conf}}
       |                                          ^
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
Found the following files/directories:
  ‘test2delete.txt’ ‘test2delete2_values.txt’ ‘test2delete_values.txt’
checkRd: (-1) fcr-package.Rd:15: Lost braces; missing escapes or markup?
    15 | Let $y_{ij}$ denote some outcome measured at
       |        ^
checkRd: (-1) fcr-package.Rd:16: Lost braces; missing escapes or markup?
    16 | $t_{ij}$ on the functional domain (e.g. time) for subject $i$ at observation
       |    ^
checkRd: (-1) fcr-package.Rd:29: Lost braces; missing escapes or markup?
    29 | Initially, a model is fit without $b_i(t_{ij})$. Using the residuals from this initial fit,
       |                                          ^
checkRd: (-1) fcr.Rd:13: Lost braces; missing escapes or markup?
    13 | The formula should only include terms not associated with the random function intercept b_i(t_{ij}). See Examples.}
       |                                                                                               ^
checkRd: (-1) fcs.Rd:36: Lost braces; missing escapes or markup?
    36 | The argument nPoints must be smaller than the total number of temporal observations N, it is recommended to set nPoints = 2^n, with n = {2, ..., infinity}.
       |                                                                                                                                         ^
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘.Rprofile’
Unexported object imported by a ':::' call: ‘fdapace:::interp2lin’
  See the note in ?`:::` about the use of this operator.
checkRd: (-1) simulation_model9.Rd:47: Lost braces; missing escapes or markup?
    47 | \item{ci}{A vector of 2 values containing $c_{1i}$ and $c_{2i}$ in the contamination
       |                                              ^
checkRd: (-1) simulation_model9.Rd:47: Lost braces; missing escapes or markup?
    47 | \item{ci}{A vector of 2 values containing $c_{1i}$ and $c_{2i}$ in the contamination
       |                                                           ^
checkRd: (-1) MakeGPFunctionalData.Rd:33: Lost braces; missing escapes or markup?
    33 | Y: X(t_{j}), Yn: noisy observations
       |        ^
checkRd: (-1) NormCurvToArea.Rd:20: Lost braces
    20 | Normalise a curve such that \\int{yNew}dx = area (according to trapezoid integration)
       |                                  ^
checkRd: (-1) NormCurvToArea.Rd:17: Lost braces
    17 | yNew values of curve at times x such that [\\int{yNew}dx = area]
       |                                                 ^
GNU make is a SystemRequirements.
Argument items with no description in Rd file 'getbasispenalty.Rd':
  ‘Lfdobj’
checkRd: (-1) NASAtemp.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) NASAtemp.Rd:15: Lost braces in \itemize; meant \describe ?
Specified C++11: please drop specification unless essential
checkRd: (-1) plot.dma.Rd:46: Lost braces; missing escapes or markup?
    46 | If {x} comes from estimation of Dynamic Model Selection (DMS) or Median Probability Model (MED), after executing \code{plot} the User is asked to choose
       |    ^
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘vert.txt’
checkRd: (-1) p.fdr.Rd:30: Lost braces
    30 | \item{adjust.method}{A string used to identify the p-value and false discovery rate adjustment method. Defaults to \code{BH}. Options are \code{BH}, \code{BY}, code{Bon},\code{Holm}, \code{Hoch}, and \code{Sidak}.}
       |                                                                                                                                                                     ^
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
checkRd: (-1) mutlicol_terminator.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mutlicol_terminator.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mutlicol_terminator.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mutlicol_terminator.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rfeTerminator.Rd:42: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rfeTerminator.Rd:43: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rfeTerminator.Rd:44: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rfeTerminator.Rd:45: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
checkRd: (-1) morse.Rd:40: Escaped LaTeX specials: \#
checkRd: (-1) noRegMin.Rd:23: Escaped LaTeX specials: \#
checkRd: (-1) noRegMin.Rd:24: Escaped LaTeX specials: \#
checkRd: (-1) regMin.Rd:24: Escaped LaTeX specials: \#
Specified C++11: please drop specification unless essential
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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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
Documented arguments not in \usage in Rd file 'recode_subquad.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.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) contemParametros.Rd:19: Lost braces
    19 | \item{exclui3pontos}{verify por ... ? in f<-function(a, ...){ }}
       |                                                             ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) fhir_cast.Rd:28: Lost braces; missing escapes or markup?
    28 | with {.} as a separator, e.g. \code{code.coding.system}. These names are produced automatically by \code{\link[=fhir_crack]{fhir_crack()}}
       |      ^
Package suggested but not available for checking: ‘MicrobeDS’
checkRd: (-1) FORTRAN.internal.Rd:50: Lost braces
    50 | \item{evlpoly}{evaluates a univariate polynomial. See code{fields.evlpoly}}
       |                                                           ^
checkRd: (-1) FORTRAN.internal.Rd:51: Lost braces
    51 | \item{evlpoly2}{ evaluates a multivariate polynomial. See code{fields.evlpoly2}}
       |                                                               ^
checkRd: (-1) registeredC.Rd:77: Lost braces
    77 | \item{addToDiagC}{ adds diagonal elements to a matrix. See code{mKrig}.}
       |                                                                ^
checkRd: (-1) sim.Krig.Rd:200-221: Lost braces
   200 | \code{simLocal.spatialProcess}{This function is
       |                               ^
checkRd: (-1) tim.colors.Rd:96: Lost braces
    96 | \item{\dots}{Additional plotting arguments to code{image.plot}}
       |                                                   ^
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
'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: ‘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: \&
checkRd: (-1) fun-igraph_financial.Rd:34: Lost braces; missing escapes or markup?
    34 | The same result for both \code{igraph} and {igraph_financial} objects
       |                                            ^
checkRd: (-1) igraph_E_iterators.Rd:31: Lost braces; missing escapes or markup?
    31 | The same result for both \code{igraph} and {igraph_financial} objects
       |                                            ^
checkRd: (-1) igraph_v_iterators.Rd:29: Lost braces; missing escapes or markup?
    29 | The same result for both \code{igraph} and {igraph_financial} objects
       |                                            ^
checkRd: (-1) plot_igraph-methods.Rd:22: Lost braces
    22 | Methods to extend code{igraph}'s plotting functions to \code{igraph_financial} objects
       |                       ^
checkRd: (-1) plot_igraph-methods.Rd:19: Lost braces; missing escapes or markup?
    19 | For both \code{igraph} and {igraph_financial} objects, returns NULL invisibly. It is called to print the graph to any R device. (see method and \href{https://rdrr.io/cran/igraph/man/plot.igraph.html}{igraph::plot.igraph})
       |                            ^
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Specified C++11: please drop specification unless essential
checkRd: (-1) FiSh-package.Rd:19: Lost braces
    19 | \doi{10.3389/feart.2020.00255}{Frontiers in Earth Science, 8:255}.
       |                               ^
checkRd: (-1) FiSh-package.Rd:32: Lost braces
    32 | \doi{10.3389/feart.2020.00255}{Frontiers in Earth Science, 8:255}.
       |                               ^
checkRd: (-1) SEP_FIM.Rd:46: Lost braces
    46 | \doi{10.3389/feart.2020.00255}{Frontiers in Earth Science, 8:255}.
       |                               ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'plot_data_type.Rd':
  ‘client_id’ ‘client_secret’ ‘refresh_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) fitConic.Rd:66-73: Lost braces
    66 | \code{parA }{vector of the six "ABCDEF" coefficients
       |             ^
checkRd: (-1) fitConic.Rd:67: Lost braces
    67 | \code{RSS }{'root sum square' figure of merit describing the relative fit quality}
       |            ^
checkRd: (-1) fitConic.Rd:68: Lost braces
    68 | \code{iters }{number of iterations at convergence}
       |              ^
checkRd: (-1) fitConic.Rd:69-71: Lost braces
    69 | \code{exitCode }{1 means ellipse, 2 means hyperbola, 3 means parabola.
       |                 ^
checkRd: (-1) rotateA.Rd:59: Lost braces; missing escapes or markup?
    59 | For \code{xyrot} {a Nx2 array of the x,y coordinates of the rotated data set. }
       |                  ^
checkRd: (-1) fitmixEM.Rd:51: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'nCDunnett', 'reliaR', 'STAR'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘fivethirtyeightdata’
checkRd: (-1) food_world_cup.Rd:70: Lost braces in \itemize; meant \describe ?
checkRd: (-1) food_world_cup.Rd:71: Lost braces in \itemize; meant \describe ?
checkRd: (-1) food_world_cup.Rd:72: Lost braces in \itemize; meant \describe ?
checkRd: (-1) food_world_cup.Rd:73: Lost braces in \itemize; meant \describe ?
checkRd: (-1) food_world_cup.Rd:74: Lost braces in \itemize; meant \describe ?
checkRd: (-1) food_world_cup.Rd:75: Lost braces in \itemize; meant \describe ?
Package unavailable to check Rd xrefs: ‘fivethirtyeightdata’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) distribution_vector.Rd:14: Lost braces; missing escapes or markup?
    14 | All standard distributions from {stats} package are covered. For a list
       |                                 ^
'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) convertInitDesignToGrid.Rd:11: Lost braces; missing escapes or markup?
    11 | The initial design, consisting of \code{d + 1} columns ({d} dimensions and
       |                                                         ^
Specified C++11: please drop specification unless essential
checkRd: (-1) ModelMixHMM-class.Rd:31: Lost braces; missing escapes or markup?
    31 |         \code{smoothed} of class {StatMixHMM}).
       |                                  ^
checkRd: (-1) ModelMixHMMR-class.Rd:31: Lost braces; missing escapes or markup?
    31 |         \code{smoothed} of class {StatMixHMMR}).
       |                                  ^
checkRd: (-1) summary.flamcv.rd:8: Lost braces
     8 | This function summarizes a call to code{\link{flamCV}} and identifies the tuning parameter chosen by cross-validation.
       |                                        ^
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
checkRd: (-1) flashClust.Rd:92: Escaped LaTeX specials: \&
checkRd: (-1) flashlight.Rd:53: Lost braces; missing escapes or markup?
    53 | like those in package {MetricsWeighted}.}
       |                       ^
checkRd: (-1) grouped_stats.Rd:49: Lost braces; missing escapes or markup?
    49 | {MetricsWeighted}.}
       | ^
checkRd: (-1) plot_counts.Rd:45: Lost braces; missing escapes or markup?
    45 | Experimental. Uses package {ggpubr} to rearrange the figure.
       |                            ^
'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: \&
checkRd: (-1) flex_dashboard.Rd:96: Lost braces; missing escapes or markup?
    96 | the `{.storyboard}` attribute to individual pages rather than using the
       |      ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) fmp.Rd:45: Lost braces; missing escapes or markup?
    45 | If k = 0: (xi_1, ..., x_{C_i - 1}, omega)
       |                         ^
checkRd: (-1) fmp.Rd:47: Lost braces; missing escapes or markup?
    47 | If k = 1: (xi_1, ..., x_{C_i - 1}, omega, alpha1, tau1)
       |                         ^
checkRd: (-1) fmp.Rd:49: Lost braces; missing escapes or markup?
    49 | If k = 2: (xi_1, ..., x_{C_i - 1}, omega, alpha1, tau1, alpha2, tau2)
       |                         ^
GNU make is a SystemRequirements.
checkRd: (-1) bootci.fmsm.Rd:24: Lost braces
    24 | \item{fn}{Function to bootstrap the results of.  It must have an argument named `code{x} giving a fitted flexsurv model object.  This may return a value with any format, e.g. list, matrix or vector, as long as it can be converted to a numeric vector with \code{unlist}.   See the example below.}
       |                                                                                      ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) flow_embed.Rd:30: Lost braces; missing escapes or markup?
    30 | \item Don't forget to add {flow} to Suggests in your DESCRIPTION file.
       |                           ^
checkRd: (-1) flowdata.Rd:10: Lost braces; missing escapes or markup?
    10 | \item{Flow}{Water flow, in m^{3}/s}
       |                              ^
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   110 | \strong{Behaviour:}{
       |                    ^
checkRd: (-1) to_flowdef.Rd:111-115: Lost braces
   111 | {
       | ^
Malformed Description field: should contain one or more complete sentences.
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Found the following files/directories:
  ‘flux.CH4.txt’
'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
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'LazyData' is specified without a 'data' directory
checkRd: (-1) FMP.Rd:30: Lost braces; missing escapes or markup?
    30 | \eqn{m(\theta) = b_0 + b_1 \theta + b_2 \theta^2 + b_3 \theta^3}. Acceptable values of k = {0,1,2,3}. According to 
       |                                                                                            ^
checkRd: (-1) autoFMradio.Rd:46: Lost braces; missing escapes or markup?
    46 | Step 1 (regularized correlation matrix estimation) is performed using the \code{X}, \code{t}, and {fold} arguments.
       |                                                                                                   ^
'LazyData' is specified without a 'data' directory
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    40 |   \code{dEstable}{ gives the density function;}
       |                  ^
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    41 |   \code{pEstable}{ gives the distribution function or its complement;}
       |                  ^
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    42 |   \code{qEstable}{ gives quantiles;}
       |                  ^
checkRd: (-1) Estable.Rd:43-56: Lost braces
    43 |   \code{tailsEstable}{ returns a list with the following components
       |                      ^
checkRd: (-1) FMstable.Rd:50: Lost braces
    50 |   \code{dFMstable}{ gives the density function;}
       |                   ^
checkRd: (-1) FMstable.Rd:51: Lost braces
    51 |   \code{pFMstable}{ gives the distribution function or its complement;}
       |                   ^
checkRd: (-1) FMstable.Rd:52: Lost braces
    52 |   \code{qFMstable}{ gives quantiles;}
       |                   ^
checkRd: (-1) FMstable.Rd:53-66: Lost braces
    53 |   \code{tailsFMstable}{  returns a list with the following components
       |                       ^
Documented arguments not in \usage in Rd file 'hl.factor.number.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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) cran_details.Rd:69-70: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) navbar_page.Rd:38: Lost braces in \itemize; meant \describe ?
'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
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) foreca.Rd:77: Lost braces in \itemize; \value handles \item{}{} directly
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checkRd: (-1) foreca.Rd:93: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) initialize_weightvector.Rd:53-54: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) initialize_weightvector.Rd:56: Lost braces in \itemize; meant \describe ?
checkRd: (-1) initialize_weightvector.Rd:57: Lost braces in \itemize; meant \describe ?
checkRd: (-1) initialize_weightvector.Rd:58: Lost braces in \itemize; meant \describe ?
checkRd: (-1) initialize_weightvector.Rd:59: Lost braces in \itemize; meant \describe ?
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) errorMetricFunctions.Rd:48: Lost braces
    48 | 	The metric MdAE is obtained using code{type = "AE"} and  \code{statistic = "Md"}
       |                                               ^
'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)
checkRd: (-1) species_bw.Rd:23: Lost braces
    23 | between trees." \doi{10.1371/journal.pone.0229930}{PLOS One 15: e0229930}.
       |                                                   ^
'LazyData' is specified without a 'data' directory
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checkRd: (-1) process_pcl.Rd:28: Lost braces; missing escapes or markup?
    28 | \item{pavd}{logical input to include Plant Area Volume Density Plot from {plot_pavd},
       |                                                                          ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) depth.Rd:17: Lost braces; missing escapes or markup?
    17 |   \item {file} : {filename}
       |                  ^
checkRd: (-1) depth.Rd:18: Lost braces; missing escapes or markup?
    18 |   \item {z_depth} : {measured focus range depth (z)}}
       |                     ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) correlations.Rd:97: Lost braces
    97 |           for same named columns of \code{k.tree.plot} in code{\link{simulations}} \sQuote{Value}.
       |                                                               ^
checkRd: (-1) FGf.Rd:15: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) FGf.Rd:16: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) FGf.Rd:17: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) FGf.Rd:18: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) FGf.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) FourgameteP.Rd:20: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) FourgameteP.Rd:23: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) FourgameteP.Rd:33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FourgameteP.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FourgameteP.Rd:35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FourgameteP.Rd:36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FourgameteP.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FourgameteP.Rd:38: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) plot_lines.Rd:66: Lost braces
    66 | moderator. By default it is equal to \8code{c(19, 17, 15, 8, 5, 4, 3, 1)}.}
       |                                            ^
checkRd: (-1) Fpop.Rd:8: Lost braces; missing escapes or markup?
     8 | sum_{i=1}^n (x_i-m_i)^2 + lambda * sum_{i=1}^{n-1} I(m_i !=
       |     ^
checkRd: (-1) Fpop.Rd:8: Lost braces; missing escapes or markup?
     8 | sum_{i=1}^n (x_i-m_i)^2 + lambda * sum_{i=1}^{n-1} I(m_i !=
       |                                        ^
checkRd: (-1) Fpop.Rd:8: Lost braces; missing escapes or markup?
     8 | sum_{i=1}^n (x_i-m_i)^2 + lambda * sum_{i=1}^{n-1} I(m_i !=
       |                                              ^
checkRd: (-1) Fpop.Rd:9: Lost braces; missing escapes or markup?
     9 | m_{i+1}), where the indicator function I counts the number of
       |   ^
Package suggested but not available for checking: ‘bcp’
Package suggested but not available for checking: ‘RandomFields’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) emfrail_control.Rd:49: Lost braces in \itemize; meant \describe ?
checkRd: (-1) emfrail_control.Rd:50: Lost braces in \itemize; meant \describe ?
checkRd: (-1) emfrail_control.Rd:51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) emfrail_control.Rd:52: Lost braces in \itemize; meant \describe ?
checkRd: (-1) emfrail_control.Rd:53-54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) emfrail_control.Rd:55-57: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) MultiAsset.Rd:26: Escaped LaTeX specials: \&
checkRd: (-1) summary.frbs.Rd:32: Lost braces
    32 |                           \code{"GAUSSIAN"}, code{"TRIANGLE"}, \code{"TRAPEZOID"}, \code{"SIGMOID"}, and \code{"BELL"}.
       |                                                  ^
checkRd: (-1) summary.frbs.Rd:60: Lost braces; missing escapes or markup?
    60 |          {4.0, 0.23, 0.43, 0.53, 0.73} on its column. It means that the label a.2 of variable v.1 
       |          ^
checkRd: (-1) grade.Rd:57: Lost braces
    57 |   \code{freealg} object comprising terms of grade code{n}.
       |                                                       ^
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in Rd file 'assert.surface.Rd':
  ‘surf’

Documented arguments not in \usage in Rd file 'check.dtype.for.data.Rd':
  ‘silent’

Documented arguments not in \usage in Rd file 'fread3.Rd':
  ‘filehandle:’

Documented arguments not in \usage in Rd file 'fwrite3.Rd':
  ‘filehandle:’ ‘data:’

Documented arguments not in \usage in Rd file 'polygon.soup.to.indexed.mesh.Rd':
  ‘face_vertex_coords’

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 '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
checkRd: (-1) maximin.Rd:197: Lost braces
   197 | Meinshausen, N and P. B{u}hlmann (2015). Maximin effects in inhomogeneous large-scale data.
       |                        ^
checkRd: (-1) adminlte_color.Rd:64: Lost braces; missing escapes or markup?
    64 |  defaults colors in {shinydashboard}.
       |                     ^
checkRd: (-1) adminlte_global.Rd:21: Lost braces; missing escapes or markup?
    21 |  global settings in {shinydashboard}.
       |                     ^
checkRd: (-1) adminlte_sidebar.Rd:61: Lost braces; missing escapes or markup?
    61 |  the sidebar in {shinydashboard}.
       |                 ^
checkRd: (-1) search_vars_adminlte2.Rd:15: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) search_vars_adminlte2.Rd:16: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) search_vars_bs.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) search_vars_bs.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) search_vars_bs4dash.Rd:17: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) search_vars_bs4dash.Rd:18: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) search_vars_bs4dash.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'dggrids', 'INLA'
'LazyData' is specified without a 'data' directory
checkRd: (-1) export.Rd:60: Lost braces; missing escapes or markup?
    60 | magick image instance or named list, depending on the value of 'img_only'. If the latter, the list contains the fields 'rev_vl', 'rev_cb', and 'rev_ex', which are the return values of the functions \code{vislayout.from.coloredmeshes}, \code{coloredmesh.plot.colorbar.separate}, and {combine.colorbar.with.brainview.image}, respectively.
       |                                                                                                                                                                                                                                                                                           ^
checkRd: (-1) vis.export.from.coloredmeshes.Rd:57: Lost braces; missing escapes or markup?
    57 | magick image instance or named list, depending on the value of 'img_only'. If the latter, the list contains the fields 'rev_vl', 'rev_cb', and 'rev_ex', which are the return values of the functions \code{vislayout.from.coloredmeshes}, \code{coloredmesh.plot.colorbar.separate}, and {combine.colorbar.with.brainview.image}, respectively.
       |                                                                                                                                                                                                                                                                                           ^
Documented arguments not in \usage in Rd file 'draw.colorbar.Rd':
  ‘coloredmesh’

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

Documented arguments not in \usage in Rd file 'surf.sphere.spatialfilter.Rd':
  ‘gaussian_weight’

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:
  'extraTrees', 'foba', 'nodeHarvest', 'obliqueRF', 'relaxo', 'rrlda'
Argument items with no description in Rd file 'fsdam.Rd':
  ‘verbose’ ‘which’
checkRd: (-1) FSelector-package.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FSelector-package.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FSelector-package.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FSelector-package.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) relief.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) relief.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dot-information_gain.Rd:43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dot-information_gain.Rd:44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) information_gain.Rd:44: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) information_gain.Rd:45: Lost braces in \itemize; \value handles \item{}{} directly
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’
checkRd: (-1) report.Rd:18: Lost braces; missing escapes or markup?
    18 | 	\item{las}{numeric in {0,1,2,3}; the style of axis labels (see \code{\link{par}}).}
       |                               ^
Specified C++11: please drop specification unless essential
checkRd: (-1) fsl_cluster.Rd:76: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) fsl_cluster.Rd:77: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) fsl_cluster.Rd:78: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) fsl_cluster.Rd:79: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) fsl_cluster.Rd:80: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) fsl_cluster.Rd:81: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) fsl_cluster.Rd:82: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) fsl_cluster.Rd:83: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rpi_orient.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rpi_orient.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rpi_orient.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) fsEnsemble.Rd:17-22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fsEnsemble.Rd:23-25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fsMTS.Rd:25-34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fsMTS.Rd:27: Lost braces
    27 |  \item{\strong{"distance"}}{ - distance-based feature selection.
       |       ^
checkRd: (-1) fsMTS.Rd:27-31: Lost braces
    27 |  \item{\strong{"distance"}}{ - distance-based feature selection.
       |                            ^
checkRd: (-1) fsMTS.Rd:32: Lost braces
    32 |  \item{\strong{"CCF"}}{ - cross-correlation-based. The method returns values of Pearson's correlation coefficient between every MTS component
       |       ^
checkRd: (-1) fsMTS.Rd:32-33: Lost braces
    32 |  \item{\strong{"CCF"}}{ - cross-correlation-based. The method returns values of Pearson's correlation coefficient between every MTS component
       |                       ^
checkRd: (-1) fsMTS.Rd:35-38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fsMTS.Rd:39-43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fsMTS.Rd:44-47: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fsMTS.Rd:48-52: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fsMTS.Rd:53-54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fsMTS.Rd:70-72: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fsMTS.Rd:73-75: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fsMTS.Rd:76-78: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fsSimilarity.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fsSimilarity.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fsSimilarity.Rd:30: Lost braces in \itemize; meant \describe ?
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
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) T_stationary.Rd:40: Lost braces
    40 | A. Aue, G. Rice, O. S\"{o}nmez (2018) "Detecting and dating structural breaks in functional data without dimension reduction", \emph{Journal of the Royal Statistical Society: Series B}, \bold{80}(3), 509-529.
       |                        ^
checkRd: (-1) facf.Rd:24: Lost braces
    24 | L. Horv\'{a}th, G. Rice and S. Whipple (2016) Adaptive bandwidth selection in the long run covariance estimator of functional time series, \emph{Computational Statistics and Data Analysis}, \bold{100}, 676-693.
       |          ^
checkRd: (-1) farforecast.Rd:43: Lost braces
    43 | J. Klepsch, C. Kl\"{u}ppelberg and T. Wei (2017) "Prediction of functional ARMA processes with an application to traffic data", \emph{Econometrics and Statistics}, \bold{1}, 128-149.
       |                    ^
checkRd: (-1) fplsr.Rd:122: Lost braces
   122 | M. Febrero-Bande, P. Galeano, W. Gonz\'{a}lez-Manteiga (2017), "Functional principal component regression and functional partial least-squares regression: An overview and a comparative study", \emph{International Statistical Review}, \bold{85}(1), 61-83.
       |                                        ^
Package vignette without corresponding tangle output:
  ‘ftsa.Rnw’
checkRd: (-1) Spec_compare_localize_freq.Rd:49: Escaped LaTeX specials: \&
checkRd: (-1) Spec_compare_localize_freq.Rd:52: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) control_charts_sof_pc.Rd:39: Lost braces
    39 | and code{y},
       |         ^
Malformed Description field: should contain one or more complete sentences.
Objects in \usage without \alias in Rd file 'funData-constructor.Rd':
  ‘funData’

Objects in \usage without \alias in Rd file 'irregFunData-constructor.Rd':
  ‘irregFunData’

Objects in \usage without \alias in Rd file 'multiFunData-constructor.Rd':
  ‘multiFunData’

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.funData.Rd':
  ‘plot.funData’

S3 methods shown with full name in Rd file 'plot.irregFunData.Rd':
  ‘plot.irregFunData’

S3 methods shown with full name in Rd file 'plot.multiFunData.Rd':
  ‘plot.multiFunData’

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) SchmidLeiman.Rd:142: Lost braces
   142 |   \item{strong{HeywoodFlag}}(Integer) An integer indicating whether one or more 
       |               ^
checkRd: (-1) summary.monte.Rd:34: Lost braces in \enumerate; \value handles \item{}{} directly
checkRd: (-1) summary.monte.Rd:35: Lost braces in \enumerate; \value handles \item{}{} directly
checkRd: (-1) summary.monte.Rd:36: Lost braces in \enumerate; \value handles \item{}{} directly
checkRd: (-1) summary.monte.Rd:38: Lost braces in \enumerate; \value handles \item{}{} directly
checkRd: (-1) summary.monte.Rd:39: Lost braces in \enumerate; \value handles \item{}{} directly
checkRd: (-1) summary.monte.Rd:40: Lost braces in \enumerate; \value handles \item{}{} directly
checkRd: (-1) summary.monte.Rd:41: Lost braces in \enumerate; \value handles \item{}{} directly
checkRd: (-1) summary.monte.Rd:42: Lost braces in \enumerate; \value handles \item{}{} directly
checkRd: (-1) summary.monte.Rd:43: Lost braces in \enumerate; \value handles \item{}{} directly
checkRd: (-1) summary.monte.Rd:44: Lost braces in \enumerate; \value handles \item{}{} directly
checkRd: (-1) summary.monte.Rd:45: Lost braces in \enumerate; \value handles \item{}{} directly
checkRd: (-1) summary.monte.Rd:46: Lost braces in \enumerate; \value handles \item{}{} directly
checkRd: (-1) summary.monte.Rd:47: Lost braces in \enumerate; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
checkRd: (-1) plot.fd.Rd:69-71: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.fd.Rd:72-77: Lost braces in \itemize; meant \describe ?
checkRd: (-1) funnel_plot.Rd:50: Lost braces in \itemize; meant \describe ?
checkRd: (-1) funnel_plot.Rd:51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) funnel_plot.Rd:52: Lost braces in \itemize; meant \describe ?
checkRd: (-1) funnel_plot.Rd:53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) funnel_plot.Rd:54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) funnel_plot.Rd:55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) funnel_plot.Rd:56: Lost braces in \itemize; meant \describe ?
checkRd: (-1) funnel_plot.Rd:57: Lost braces in \itemize; meant \describe ?
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) bpp.Rd:31: Lost braces
    31 | The BPP algorithm calculates the sum{K=0,k, 1/(b^K) * FracSum} , where FracSum is defined by the sum(M=1,m, A[M]/(m*K + M)^s) .  This means that the number of elements of \code{A} must equal \code{m}. Zero values are legal and are used to reject fractions not wanted in the inner sum. 
       |                                     ^
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
checkRd: (-1) misspellings.Rd:18: Lost braces
    18 | This is a code{tbl_df} mapping misspellings of their words, compiled by
       |               ^
checkRd: (-1) trapezoidalApproximation-methods.Rd:49: Lost braces; missing escapes or markup?
    49 | For example, if Val(A) < EV_{1/3}(A) or Val(A) > EV_{2/3}(A),
       |                             ^
checkRd: (-1) trapezoidalApproximation-methods.Rd:49: Lost braces; missing escapes or markup?
    49 | For example, if Val(A) < EV_{1/3}(A) or Val(A) > EV_{2/3}(A),
       |                                                     ^
checkRd: (-1) genmf.Rd:26: Lost braces; missing escapes or markup?
    26 | \item 'gbellmf' is c(\code{a, b, c}), where \code{a} denotes the width, \code{b} is usually positive and {c} locates the center of the curve.
       |                                                                                                          ^
checkRd: (-1) multTSA.Rd:40: Lost braces
    40 | deprecated argument; link{type} should now be used instead, although (at least for the timebeing) this argument will still be accepted (with Favourability=TRUE internally resulting in type="F") for back-compatibility.
       |                          ^
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) GAabbreviate.Rd:53: Lost braces; missing escapes or markup?
    53 | where \eqn{I} represents a user-specified fixed item cost, \eqn{k} represents the number of items retained by the GA (in any given iteration), \eqn{s} is the number of subscales in the measure, \eqn{w_i} are the weights (by default {w_i = 1} for any \eqn{i}) associated with each subscale (if there are any subsets to be retained), and \eqn{R_i^2} is the amount of variance in the ith subscale that can be explained by a linear combination of individual item scores. Adjusting the value of \eqn{I} low or high yields longer or shorter measures respectively. When the cost of each individual item retained in each generation outweighs the cost of a loss in explained variance, the GA yields a relatively brief measure. When the cost is low, the GA yields a relatively longer measure maximizing explained variance (Yarkoni, 2010).  
       |                                                                                                                                                                                                                                         ^