checkRd: (-1) Produc.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Produc.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Produc.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Produc.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Produc.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Produc.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Produc.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Produc.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Produc.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Produc.Rd:22: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
checkRd: (-1) NKI-breast-cancer-clinical-data.Rd:26: Escaped LaTeX specials: \&
checkRd: (-1) NKI-breast-cancer-clinical-data.Rd:33: Escaped LaTeX specials: \&
checkRd: (-1) NKI-breast-cancer-clinical-data.Rd:37: Escaped LaTeX specials: \&
checkRd: (-1) WBC-follow-up-data.Rd:13: Escaped LaTeX specials: \&
checkRd: (-1) WBC-follow-up-data.Rd:14: Escaped LaTeX specials: \&
checkRd: (-1) WBC-follow-up-data.Rd:26: Escaped LaTeX specials: \&
checkRd: (-1) WBC-follow-up-data.Rd:31: Escaped LaTeX specials: \&
checkRd: (-1) WBC-follow-up-data.Rd:41: Escaped LaTeX specials: \&
checkRd: (-1) WBC-measurements-data.Rd:13: Escaped LaTeX specials: \&
checkRd: (-1) WBC-measurements-data.Rd:14: Escaped LaTeX specials: \&
checkRd: (-1) WBC-measurements-data.Rd:25: Escaped LaTeX specials: \&
checkRd: (-1) WBC-measurements-data.Rd:30: Escaped LaTeX specials: \&
checkRd: (-1) WBC-measurements-data.Rd:40: Escaped LaTeX specials: \&
'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’
'LazyData' is specified without a 'data' directory
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
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 13.2.0-7) 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
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 13.2.0-7) 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.}
       |               ^
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
Package suggested but not available for checking: ‘RStoolbox’
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’
checkRd: (-1) addLegend.Rd:98: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) addLegend.Rd:99: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) addLegend.Rd:100: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) addLegend.Rd:101: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gridMetrics.Rd:39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gridMetrics.Rd:40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gridMetrics.Rd:41-42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gridMetrics.Rd:49-51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gridMetrics.Rd:53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gridMetrics.Rd:54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gridMetrics.Rd:55-56: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gridMetrics.Rd:60: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gridMetrics.Rd:62: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gridMetrics.Rd:63: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gridMetrics.Rd:64-65: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gridMetrics.Rd:66: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gridMetrics.Rd:67: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gridMetrics.Rd:68: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gridMetrics.Rd:69: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gridMetrics.Rd:73: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gridMetrics.Rd:74-75: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gridMetrics.Rd:76-77: Lost braces in \itemize; meant \describe ?
'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\")}",
       |                                              ^
Found the following significant warnings:
  wtedgetree.c:288:23: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘double’ [-Wformat=]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ergm.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-13 (Debian 13.2.0-7) 13.2.0’
Documented arguments not in \usage in Rd file 'call.ErgmTerm.Rd':
  ‘A’

Objects in \usage without \alias in Rd file 'ergm-defunct.Rd':
  ‘sociality’

Documented arguments not in \usage in Rd file 'ergm-deprecated.Rd':
  ‘fname’ ‘varnames’ ‘vartypes’ ‘defaultvalues’ ‘required’
  ‘nw.bipartiteflag’ ‘requirement’ ‘extramessage’ ‘nw.directedflag’ ‘m’
  ‘response’ ‘new’ ‘from.new’ ‘model’ ‘proposal’ ‘eta0’ ‘control’
  ‘verbose’ ‘update.nws’ ‘Clist’ ‘prev.run’ ‘burnin’ ‘samplesize’
  ‘interval’ ‘maxedges’ ‘attrname’ ‘label’ ‘coord’ ‘jitter’ ‘thresh’
  ‘usearrows’ ‘mode’ ‘displayisolates’ ‘interactive’ ‘xlab’ ‘ylab’
  ‘xlim’ ‘ylim’ ‘pad’ ‘label.pad’ ‘displaylabels’ ‘boxed.labels’
  ‘label.pos’ ‘label.bg’ ‘vertex.sides’ ‘vertex.rot’ ‘arrowhead.cex’
  ‘label.cex’ ‘loop.cex’ ‘vertex.cex’ ‘edge.col’ ‘label.col’
  ‘vertex.col’ ‘label.border’ ‘vertex.border’ ‘edge.lty’ ‘label.lty’
  ‘vertex.lty’ ‘edge.lwd’ ‘label.lwd’ ‘edge.len’ ‘edge.curve’
  ‘edge.steps’ ‘loop.steps’ ‘object.scale’ ‘uselen’ ‘usecurve’
  ‘suppress.axes’ ‘vertices.last’ ‘layout.par’ ‘cex.main’ ‘cex.sub’
  ‘seed’ ‘latent.control’ ‘colornames’ ‘latent’ ‘preserve.eattr’

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

Documented arguments not in \usage in Rd file 'nodal_attributes-API.Rd':
  ‘l’

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

Functions with \usage entries need to have the appropriate \alias
entries, and all their 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) 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
       |                                                           ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) USA_state_N.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) USA_state_N.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) confirmed.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) confirmed.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) death.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) death.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) recovered.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) recovered.Rd:11: 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
Specified C++11: please drop specification unless essential
checkRd: (-1) momento.central.Rd:12: Lost braces; missing escapes or markup?
    12 | \item{orden}{Es un valor numérico que representa el orden del momento central (orden = {1,2,3,4,...})}
       |                                                                                        ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) aic.Rd:25: Escaped LaTeX specials: \&
checkRd: (-1) aic.Rd:29: Escaped LaTeX specials: \&
checkRd: (-1) ictab.Rd:56: Escaped LaTeX specials: \&
checkRd: (-1) ictab.Rd:60: Escaped LaTeX specials: \&
checkRd: (-1) ictab.Rd:64: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) integration.Rd:37-38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) integration.Rd:39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) integration.Rd:40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) integration.Rd:41-42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) loess.options.Rd:25-26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) loess.options.Rd:27-28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) maxlogLreg.Rd:138: Lost braces; missing escapes or markup?
   138 | $j^{th}$ for all the observations.
       |    ^
Specified C++11: please drop specification unless essential
checkRd: (-1) lm_lin.Rd:99: Lost braces
    99 | and \code{scaled_center}{the means of each of the covariates used for centering them}
       |                         ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) etas.Rd:136: Lost braces; missing escapes or markup?
   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’.
checkRd: (-1) data_cls.Rd:24: Lost braces
    24 | \item Graphs: Erd\"{o}s-R\'{e}nyi graphs with connection probability 0.10 for
       |                    ^
checkRd: (-1) data_cls.Rd:24: Lost braces
    24 | \item Graphs: Erd\"{o}s-R\'{e}nyi graphs with connection probability 0.10 for
       |                            ^
checkRd: (-1) data_reg.Rd:21: Lost braces
    21 | \item Graphs: Erd\"{o}s-R\'{e}nyi graphs with connection probability given by
       |                    ^
checkRd: (-1) data_reg.Rd:21: Lost braces
    21 | \item Graphs: Erd\"{o}s-R\'{e}nyi graphs with connection probability given by
       |                            ^
'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),
       |                            ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) uccle.Rd:23: Lost braces
    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.
       |                                    ^
checkRd: (-1) uccle.Rd:24: Lost braces
    24 |   \emph{Inst. Royal M\'{e}t\'{e}or. Belgique, B} \bold{86}.
       |                        ^
checkRd: (-1) uccle.Rd:24: Lost braces
    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: \&
checkRd: (-1) glr.Rd:5: Lost braces
     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})}.
       |                                                                                                                               ^
checkRd: (-1) Snoring.Rd:21: Escaped LaTeX specials: \&
checkRd: (-1) fmgammagpd.Rd:183: Lost braces; missing escapes or markup?
   183 |  \item {nlumgammagpd} and {proflumgammagpd} - \code{c(mgshape, mgscale, mgweight[1:(M-1)], sigmau, xi)}
       |                           ^
checkRd: (-1) fmgammagpdcon.Rd:181: Lost braces; missing escapes or markup?
   181 |  \item {nlumgammagpdcon} and {proflumgammagpdcon} - \code{c(mgshape, mgscale, mgweight[1:(M-1)], xi)}
       |                              ^
checkRd: (-1) kernels.Rd:87: Lost braces
    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
checkRd: (-1) stop_rule.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) stop_rule.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) stop_rule.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
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: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Unknown package ‘iptools’ in Rd xrefs
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
Found the following significant warnings:
  error.c:45:23: warning: format ‘%s’ expects argument of type ‘char *’, but argument 3 has type ‘int’ [-Wformat=]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ExomeDepth.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-13 (Debian 13.2.0-7) 13.2.0’
* used C++ compiler: ‘g++-13 (Debian 13.2.0-7) 13.2.0’
Error: package or namespace load failed for ‘ExomeDepth’:
 .onLoad failed in loadNamespace() for 'Rsamtools', details:
  call: h(simpleError(msg, call))
  error: error in evaluating the argument 'x' in selecting a method for function 'levels': class should be either a character-string name or a class definition
Call sequence:
6: stop(msg, call. = FALSE, domain = NA)
5: value[[3L]](cond)
4: tryCatchOne(expr, names, parentenv, handlers[[1L]])
3: tryCatchList(expr, classes, parentenv, handlers)
2: tryCatch({
       attr(package, "LibPath") <- which.lib.loc
       ns <- loadNamespace(package, lib.loc)
       env <- attachNamespace(ns, pos = pos, deps, exclude, include.only)
   }, error = function(e) {
       P <- if (!is.null(cc <- conditionCall(e))) 
           paste(" in", deparse(cc)[1L])
       else ""
       msg <- gettextf("package or namespace load failed for %s%s:\n %s", 
           sQuote(package), P, conditionMessage(e))
       if (logical.return && !quietly) 
           mess
Execution halted
'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
       |       ^
checkRd: (-1) ccF.Rd:41: Lost braces
    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) make_exvadec.Rd:21: Lost braces
    21 | (e.g., \code{"USA"}, code{"NAFTA"}, etc.). The default \code{"all"}
       |                          ^
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
checkRd: (-1) EEzGP_fit.Rd:50: Lost braces in \itemize; \value handles \item{}{} directly
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
checkRd: (-1) LEzGP_fit.Rd:60: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) LLF_gradients.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) LLF_gradients.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
checkRd: (-1) ez-package.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ez-package.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ez-package.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ez-package.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ez-package.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ez-package.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ez-package.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ez-package.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ez-package.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ez-package.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ez-package.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ez-package.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ez-package.Rd:32: Lost braces in \itemize; meant \describe ?
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
checkRd: (-1) FADPclust.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) FADPclust.Rd:31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) FADPclust.Rd:32: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) FADPclust.Rd:33: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) FADPclust.Rd:34: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) FADPclust.Rd:35: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) FADPclust.Rd:36: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) FADPclust.Rd:37: Lost braces in \itemize; \value handles \item{}{} directly
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
'LazyData' is specified without a 'data' directory
checkRd: (-1) pi0FAMT.Rd:18: Lost braces
    18 | \code{pi0}{The estimated proportion \code{pi0} of null hypotheses.}}
       |           ^
Found the following significant warnings:
  ezprof.c:55:38: warning: format ‘%f’ expects argument of type ‘double’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=]
  ezprof.c:57:38: warning: format ‘%f’ expects argument of type ‘double’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/fanc.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-13 (Debian 13.2.0-7) 13.2.0’
'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
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
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’
Specified C++11: please drop specification unless essential
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]
       |                                                 ^
Found the following significant warnings:
  Density_Estimation/Source/../../Skeletons/Include/../../Density_Estimation/Include/Data_Problem_imp.h:174:24: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘std::vector<Point<2>, std::allocator<Point<2> > >::size_type’ {aka ‘long unsigned int’} [-Wformat=]
  Density_Estimation/Source/../../Skeletons/Include/../../Density_Estimation/Include/Data_Problem_imp.h:174:24: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘std::vector<Point<3>, std::allocator<Point<3> > >::size_type’ {aka ‘long unsigned int’} [-Wformat=]
  FPCA/Source/Mixed_FE_FPCA.cpp:290:251: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘__gnu_cxx::__alloc_traits<std::allocator<double>, double>::value_type’ {aka ‘double’} [-Wformat=]
  Inference/Source/Inference_Data.cpp:271:21: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘long int’ [-Wformat=]
  C_Libraries/triangle.c:1426:9: warning: too many arguments for format [-Wformat-extra-args]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/fdaPDE.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-13 (Debian 13.2.0-7) 13.2.0’
* used C++ compiler: ‘g++-13 (Debian 13.2.0-7) 13.2.0’
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
Specified C++11: please drop specification unless essential
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.
Found the following significant warnings:
  fftw.c:112:34: warning: format ‘%x’ expects argument of type ‘unsigned int’, but argument 2 has type ‘double (*)[2]’ [-Wformat=]
  fftw.c:113:34: warning: format ‘%x’ expects argument of type ‘unsigned int’, but argument 2 has type ‘double (*)[2]’ [-Wformat=]
  fftw.c:114:34: warning: format ‘%x’ expects argument of type ‘unsigned int’, but argument 2 has type ‘fftw_plan’ {aka ‘struct fftw_plan_s *’} [-Wformat=]
  fftw.c:115:34: warning: format ‘%x’ expects argument of type ‘unsigned int’, but argument 2 has type ‘fftw_plan’ {aka ‘struct fftw_plan_s *’} [-Wformat=]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/fftw.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-13 (Debian 13.2.0-7) 13.2.0’
'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()}}
       |      ^
Specified C++11: please drop specification unless essential
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: \&
Found the following significant warnings:
  finite_moment_test.cpp:412:22: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated: use braced initialiser list instead [-Wdeprecated-declarations]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/finity.Rcheck/00install.out’ for details.
* used C++ compiler: ‘g++-13 (Debian 13.2.0-7) 13.2.0’
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: \&
checkRd: (-1) fitDist.Rd:47: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fitDist.Rd:48: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fitDist.Rd:49: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fitDist.Rd:50: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fitDist.Rd:51-52: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fitDist.Rd:53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fitZIDist.Rd:52: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fitZIDist.Rd:53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fitZIDist.Rd:54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fitZIDist.Rd:55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fitZIDist.Rd:56: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fitZIDist.Rd:57-58: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fitZIDist.Rd:59: Lost braces in \itemize; meant \describe ?
checkRd: (-1) readData.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) readData.Rd:25-27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) readData.Rd:28-30: Lost braces in \itemize; \value handles \item{}{} directly
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}
       |                              ^
checkRd: (-1) to_flow.Rd:110-117: Lost braces
   110 | \strong{Behaviour:}{
       |                    ^
checkRd: (-1) to_flowdef.Rd:111-115: Lost braces
   111 | {
       | ^
Malformed Description field: should contain one or more complete sentences.
Found the following significant warnings:
  FLSAGeneral.cc:248:66: warning: format ‘%d’ expects argument of type ‘int’, but argument 5 has type ‘std::set<int>::size_type’ {aka ‘long unsigned int’} [-Wformat=]
  FLSAGeneral.cc:248:70: warning: format ‘%d’ expects argument of type ‘int’, but argument 6 has type ‘std::set<int>::size_type’ {aka ‘long unsigned int’} [-Wformat=]
  FLSAGeneral.cc:280:63: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘long unsigned int’ [-Wformat=]
  FLSAGeneral.cc:369:62: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘std::set<int>::size_type’ {aka ‘long unsigned int’} [-Wformat=]
  FLSAGeneral.cc:369:65: warning: format ‘%d’ expects argument of type ‘int’, but argument 5 has type ‘std::set<int>::size_type’ {aka ‘long unsigned int’} [-Wformat=]
  MaxFlowGraph.cc:560:43: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘__gnu_cxx::__normal_iterator<std::vector<MaxFlowEdge>*, std::vector<std::vector<MaxFlowEdge> > >::difference_type’ {aka ‘long int’} [-Wformat=]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/flsa.Rcheck/00install.out’ for details.
* used C++ compiler: ‘g++-13 (Debian 13.2.0-7) 13.2.0’
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
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) FMP.Rd:30: Lost braces; missing escapes or markup?
    30 | \eqn{m(\theta) = b_0 + b_1 \theta + b_2 \theta^2 + b_3 \theta^3}. Acceptable values of k = {0,1,2,3}. According to 
       |                                                                                            ^
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
checkRd: (-1) GompertzMakeham.Rd:13: Lost braces
    13 |  \item{A}{The parameter A of the Gompertz-Makeham model u(t)=A*exp{B*t}+C.}
       |                                                                   ^
checkRd: (-1) GompertzMakeham.Rd:14: Lost braces
    14 |  \item{B}{The parameter B of the Gompertz-Makeham model u(t)=A*exp{B*t}+C.}
       |                                                                   ^
checkRd: (-1) GompertzMakeham.Rd:15: Lost braces
    15 |  \item{C}{The parameter C of the Gompertz-Makeham model u(t)=A*exp{B*t}+C.}
       |                                                                   ^
checkRd: (-1) truemedian.Rd:6: Lost braces; missing escapes or markup?
     6 |   exactly same.  For example, median of {3, 3, 4, 4, 4} will be 4.
       |                                         ^
checkRd: (-1) truemedian.Rd:9-10: Lost braces
     9 |   the previous data can be treated as rounded values of {2.75, 3.25,
       |                                                         ^
checkRd: (-1) truemedian.Rd:10: Lost braces; missing escapes or markup?
    10 |   11/3, 4, 13/3}.  From this viewpoint, true median of {3, 3, 4, 4, 4}
       |                                                        ^
checkRd: (-1) Estable.Rd:40: Lost braces
    40 |   \code{dEstable}{ gives the density function;}
       |                  ^
checkRd: (-1) Estable.Rd:41: Lost braces
    41 |   \code{pEstable}{ gives the distribution function or its complement;}
       |                  ^
checkRd: (-1) Estable.Rd:42: Lost braces
    42 |   \code{qEstable}{ gives quantiles;}
       |                  ^
checkRd: (-1) Estable.Rd:43-56: Lost braces
    43 |   \code{tailsEstable}{ returns a list with the following components
       |                      ^
checkRd: (-1) FMstable.Rd:50: Lost braces
    50 |   \code{dFMstable}{ gives the density function;}
       |                   ^
checkRd: (-1) FMstable.Rd:51: Lost braces
    51 |   \code{pFMstable}{ gives the distribution function or its complement;}
       |                   ^
checkRd: (-1) FMstable.Rd:52: Lost braces
    52 |   \code{qFMstable}{ gives quantiles;}
       |                   ^
checkRd: (-1) FMstable.Rd:53-66: Lost braces
    53 |   \code{tailsFMstable}{  returns a list with the following components
       |                       ^
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.
Found the following significant warnings:
  ANN.cpp:173:23: warning: too many arguments for format [-Wformat-extra-args]
  ANN.cpp:181:26: warning: too many arguments for format [-Wformat-extra-args]
  KNN_cover_tree.cpp:103:18: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wformat=]
  KNN_cover_tree.cpp:156:18: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘std::vector<Id_dist>::size_type’ {aka ‘long unsigned int’} [-Wformat=]
  KNN_cover_tree.cpp:221:20: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘std::vector<Id_dist>::size_type’ {aka ‘long unsigned int’} [-Wformat=]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/FNN.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-13 (Debian 13.2.0-7) 13.2.0’
* used C++ compiler: ‘g++-13 (Debian 13.2.0-7) 13.2.0’
'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 ?
checkRd: (-1) cran_details.Rd:72: Lost braces in \itemize; meant \describe ?
checkRd: (-1) cran_details.Rd:74-77: Lost braces in \itemize; meant \describe ?
checkRd: (-1) cran_results.Rd:64-65: Lost braces in \itemize; meant \describe ?
checkRd: (-1) cran_results.Rd:67: Lost braces in \itemize; meant \describe ?
checkRd: (-1) cran_results.Rd:69-72: Lost braces in \itemize; meant \describe ?
checkRd: (-1) navbar_page.Rd:36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) navbar_page.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) navbar_page.Rd:38: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
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
checkRd: (-1) foreca.Rd:78-80: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) foreca.Rd:81-83: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) foreca.Rd:84-87: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) foreca.Rd:88-90: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) foreca.Rd:91-92: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) foreca.Rd:93: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) initialize_weightvector.Rd:53-54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) initialize_weightvector.Rd:55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) initialize_weightvector.Rd:56: Lost braces in \itemize; meant \describe ?
checkRd: (-1) initialize_weightvector.Rd:57: Lost braces in \itemize; meant \describe ?
checkRd: (-1) initialize_weightvector.Rd:58: Lost braces in \itemize; meant \describe ?
checkRd: (-1) initialize_weightvector.Rd:59: Lost braces in \itemize; meant \describe ?
checkRd: (-1) initialize_weightvector.Rd:60-61: Lost braces in \itemize; meant \describe ?
checkRd: (-1) initialize_weightvector.Rd:62: Lost braces in \itemize; meant \describe ?
checkRd: (-1) initialize_weightvector.Rd:63: Lost braces in \itemize; meant \describe ?
checkRd: (-1) initialize_weightvector.Rd:64-65: Lost braces in \itemize; meant \describe ?
'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
checkRd: (-1) forest_theme.Rd:161: Lost braces in \itemize; meant \describe ?
checkRd: (-1) forest_theme.Rd:162: Lost braces in \itemize; meant \describe ?
checkRd: (-1) forest_theme.Rd:163: Lost braces in \itemize; meant \describe ?
checkRd: (-1) forest_theme.Rd:164: Lost braces in \itemize; meant \describe ?
checkRd: (-1) forest_theme.Rd:165: Lost braces in \itemize; meant \describe ?
checkRd: (-1) forest_theme.Rd:166: Lost braces in \itemize; meant \describe ?
checkRd: (-1) forest_theme.Rd:167: Lost braces in \itemize; meant \describe ?
checkRd: (-1) forest_theme.Rd:168: Lost braces in \itemize; meant \describe ?
checkRd: (-1) forest_theme.Rd:169: Lost braces in \itemize; meant \describe ?
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 ?
checkRd: (-1) FourgameteP.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FourgameteP.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FourgameteP.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FourgameteP.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FourgameteP.Rd:32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FourgameteP.Rd:33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FourgameteP.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FourgameteP.Rd:35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FourgameteP.Rd:36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FourgameteP.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FourgameteP.Rd:38: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) plot_lines.Rd:66: Lost braces
    66 | moderator. By default it is equal to \8code{c(19, 17, 15, 8, 5, 4, 3, 1)}.}
       |                                            ^
checkRd: (-1) Fpop.Rd:8: Lost braces; missing escapes or markup?
     8 | sum_{i=1}^n (x_i-m_i)^2 + lambda * sum_{i=1}^{n-1} I(m_i !=
       |     ^
checkRd: (-1) Fpop.Rd:8: Lost braces; missing escapes or markup?
     8 | sum_{i=1}^n (x_i-m_i)^2 + lambda * sum_{i=1}^{n-1} I(m_i !=
       |                                        ^
checkRd: (-1) Fpop.Rd:8: Lost braces; missing escapes or markup?
     8 | sum_{i=1}^n (x_i-m_i)^2 + lambda * sum_{i=1}^{n-1} I(m_i !=
       |                                              ^
checkRd: (-1) Fpop.Rd:9: Lost braces; missing escapes or markup?
     9 | m_{i+1}), where the indicator function I counts the number of
       |   ^
Package suggested but not available for checking: ‘RandomFields’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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}.
       |                                                       ^
checkRd: (-1) print.Rd:14: Lost braces
    14 |   \item{latex}{Boolean, with code{TRUE} meaning to print latex-friendly
       |                                  ^
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.
       |                                        ^
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’
Documented arguments not in \usage in Rd file 'loggedOutput.Rd':
  ‘future’

Functions with \usage entries need to have the appropriate \alias
entries, and all their 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) plan.Rd:59-62: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plan.Rd:63-67: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plan.Rd:68-74: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plan.Rd:75-80: Lost braces in \itemize; meant \describe ?
Documented arguments not in \usage in Rd file 'mandelbrot.Rd':
  ‘Z’ ‘xmid’ ‘ymid’ ‘side’ ‘resolution’ ‘maxIter’ ‘tau’

Functions with \usage entries need to have the appropriate \alias
entries, and all their 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) 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).  
       |                                                                                                                                                                                                                                         ^
Invalid package aliases in Rd file 'GAabbreviate-internal.Rd':
  ‘GAabbreviation-package’
checkRd: (-1) cpp_multinomial_gaga.Rd:44: Lost braces; missing escapes or markup?
    44 | Coefficient matrix with K-1 columns beta_1,...,beta_{K-1} where K is the class number.
       |                                                     ^
checkRd: (-1) multinomial_GAGA.Rd:44: Lost braces; missing escapes or markup?
    44 | Coefficient matrix with K-1 columns beta_1,...,beta_{K-1} where K is the class number.
       |                                                     ^
checkRd: (-1) min_hpd_inc_area_df.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) min_hpd_inc_area_df.Rd:21-22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) min_hpd_inc_area_df.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) vza_mean_and_var_rasters.Rd:20: Lost braces
    20 | of the paper on Wilson's warbler, this function computes $tilde{T}^{(mu)}$ (returned as
       |                                                                ^
checkRd: (-1) vza_mean_and_var_rasters.Rd:20: Lost braces; missing escapes or markup?
    20 | of the paper on Wilson's warbler, this function computes $tilde{T}^{(mu)}$ (returned as
       |                                                                    ^
checkRd: (-1) vza_mean_and_var_rasters.Rd:21: Lost braces; missing escapes or markup?
    21 | list component \code{mean.raster}) and $R^{(sigma^2)}$ (returned as list component
       |                                           ^
checkRd: (-1) QTLmarkers.Rd:30: Lost braces
    30 | (\doi{10.1093/jas/sky382}{PubMed})
       |                          ^
checkRd: (-1) QTLwindows.Rd:31: Lost braces
    31 | (\doi{10.1093/jas/sky382}{PubMed})
       |                          ^
Documented arguments not in \usage in Rd file 'splitQTL_comment.Rd':
  ‘output_qtls’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
checkRd: (-1) stabsel.mboostLSS.Rd:44: Lost braces
    44 |     always use code{"none"}.}
       |                    ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) naref.Rd:13: Lost braces
    13 | \details{ For every \code{factor} or \code{character} column in \code{x}, \code{naref} sets \code{NA} as the reference level for a \code{factor} variable. Columns coded as \code{character} class are first converted to factors via \R{factor(x)}.  If \code{impute=TRUE} then the numeric columns are converted to two columns, one appended \code{.x} that contains imputed values and another appended \code{.miss} which is a binary variable indicating whether the original value was missing.  Numeric columns are returned without change if \code{impute=FALSE} or if they do not contain any missing values.  
       |                                                                                                                                                                                                                                         ^
checkRd: (-1) plotNN.Rd:20: Lost braces
    20 |   \item{nid}{logical value indicating if neural interpretation diagram is plotted, default is  code{TRUE}}
       |                                                                                                    ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) LGAclaims.Rd:30: Escaped LaTeX specials: \_
checkRd: (-1) LGAclaims.Rd:34: Escaped LaTeX specials: \_
checkRd: (-1) LGAclaims.Rd:35: Escaped LaTeX specials: \_
checkRd: (-1) LGAclaims.Rd:36: Escaped LaTeX specials: \_
checkRd: (-1) brownfat.Rd:35: Lost braces
    35 | \references{ Routhier-Labadie, A., Ouellet, V.,  Bellemare, W., Richard, D., Lakhal-Chaieb, L., Turcotte, E., and Carpentier, A. C. (2011), Outdoor Temperature, Age, Sex, Body Mass Index, and Diabetic Status Determine the Prevalence, Mass, and Glucose-Uptake Activity of 18{F}-{FDG}-Detected {BAT} in Humans.\emph{The Journal of Clinical Endocrinology and Metabolism}, 	Volume \bold{96}, number 1, pp 192-199.
       |                                                                                                                                                                                                                                                                                  ^
checkRd: (-1) pc.Rd:17: Lost braces
    17 | The functions \code{gamlss.pcr()} and \code{gamlss.pc()} are supporting functions. The  are not intended to be called directly by users. The function \code{gamlss.pc()} is using the linear model function \code{lm()} to fit the first principal components while the function code{gamlss.pcr()} uses \code{fitPCR()}.
       |                                                                                                                                                                                                                                                                                      ^
checkRd: (-1) term.plotZadj.Rd:6: Lost braces
     6 |  \ This is a wrapper to function \code{\link[gamlss]{term.plot}}. code{term.plotZadj} produces term plots for a specified parameter from a    
       |                                                                       ^
Invalid package aliases in Rd file 'gamlss.mx.package.Rd':
  ‘gamlss.mix-package’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) GSE.Test.Main.Rd:23: Escaped LaTeX specials: \_
checkRd: (-1) Gapfill.Rd:66-68: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Gapfill.Rd:69-70: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Gapfill.Rd:71-77: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Gapfill.Rd:72: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Gapfill.Rd:73: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Gapfill.Rd:74: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Gapfill.Rd:75: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Gapfill.Rd:78: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ndvi.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ndvi.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ndvi.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ndvi.Rd:13: Lost braces in \itemize; meant \describe ?
Documented arguments not in \usage in Rd file 'as.gapdata.Rd':
  ‘labels_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.
Specified C++14: please drop specification unless essential
':::' call which should be '::': ‘graphics:::grid’
  See the note in ?`:::` about the use of this operator.
checkRd: (-1) gaControl.Rd:20-27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gaControl.Rd:28-35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gaControl.Rd:36-43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gaControl.Rd:45: Lost braces in \itemize; meant \describe ?
checkRd: (-1) glag.Rd:7: Lost braces; missing escapes or markup?
     7 | Similar to the \code{\link{lag}} function from the \code{stats} package, but \code{glag} enables padding (e.g. {NA}s or 0s) of the lost entries. Contrary to the \code{\link{lag}} function in the stats package, however, the default in \code{glag} is to pad (with \code{NA}s). The \code{glag} is particularly suited for \code{\link{zoo}} objects, since their indexing is retained
       |                                                                                                                ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) read.ctable.Rd:19: Lost braces; missing escapes or markup?
    19 | a integer scalar which is the index ({icol,irow}) of {row,col}-header
       |                                      ^
checkRd: (-1) read.ctable.Rd:19: Lost braces; missing escapes or markup?
    19 | a integer scalar which is the index ({icol,irow}) of {row,col}-header
       |                                                      ^
checkRd: (-1) read.ctable.Rd:29: Lost braces; missing escapes or markup?
    29 | output array, {row,col}.names are not necessary \code{dimnames[[1]]} and
       |               ^
checkRd: (-1) simulate_gastempt.Rd:30: Lost braces; missing escapes or markup?
    30 | \item{tempt_mean, tempt_std}{Mean and between record standard deviation of parameter $t_{empt}$, typically in minutes.}
       |                                                                                         ^
GNU make is a SystemRequirements.
Documented arguments not in \usage in Rd file 'lrr_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) summary.GauPro.Rd:5-35: Lost braces
     5 | \title{if (F) {
       |               ^
checkRd: (-1) summary.GauPro.Rd:20-22: Lost braces
    20 |   #' if (requireNamespace("MASS", quietly = TRUE)) {
       |                                                    ^
checkRd: (-1) summary.GauPro.Rd:24-34: Lost braces
    24 |   plot.GauPro <- function(x,  ...) {
       |                                    ^
checkRd: (-1) summary.GauPro.Rd:26-28: Lost braces
    26 |     # if (x$D == 1) {
       |                     ^
checkRd: (-1) summary.GauPro.Rd:28-30: Lost braces
    28 |     # } else if (x$D == 2) {
       |                            ^
checkRd: (-1) summary.GauPro.Rd:30-33: Lost braces
    30 |     # } else {
       |              ^
checkRd: (-1) summary.GauPro.Rd:49-79: Lost braces
    49 | if (F) {
       |        ^
checkRd: (-1) summary.GauPro.Rd:64-66: Lost braces
    64 |   #' if (requireNamespace("MASS", quietly = TRUE)) {
       |                                                    ^
checkRd: (-1) summary.GauPro.Rd:68-78: Lost braces
    68 |   plot.GauPro <- function(x,  ...) {
       |                                    ^
checkRd: (-1) summary.GauPro.Rd:70-72: Lost braces
    70 |     # if (x$D == 1) {
       |                     ^
checkRd: (-1) summary.GauPro.Rd:72-74: Lost braces
    72 |     # } else if (x$D == 2) {
       |                            ^
checkRd: (-1) summary.GauPro.Rd:74-77: Lost braces
    74 |     # } else {
       |              ^
checkRd: (-1) Sim.Markov.Chain.Rd:14: Lost braces; missing escapes or markup?
    14 | \item{eta0}{inital value in {1,...,r}.}
       |                             ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) CompoundDensPlot.Rd:18: Lost braces
    18 |   \item{shape1, scale ,shape2, shape3}{numeric; positive parameters of the GB2 distribution. On the plot they are denotes as \code{a}, code{b}, \code{p}, \code{q} and \code{pl0} respectively.}
       |                                                                                                                                            ^
checkRd: (-1) CompoundVarest.Rd:58: Lost braces
    58 | \code{scoreU.cgb2} returns a \eqn{N \times (L-1)} matrix of scores <code{U}.
       |                                                                         ^
checkRd: (-1) Fisk.Rd:26: Lost braces
    26 | \value{\code{fisk} and \code{fiskh} return vectors of length 4 containing the estimated parameters \eqn{a}, eqn{b}, as well as \eqn{p=1} and \eqn{q=1}. 
       |                                                                                                                ^
checkRd: (-1) MLfullGB2.Rd:23: Lost braces
    23 |   \item{method}{numeric; the method to be used by \code{optim}. By default, code{method = }1 and the used method is BFGS. If \code{method = }2, method L-BFGS-B is used.}
       |                                                                                 ^
checkRd: (-1) MLprofGB2.Rd:16: Lost braces
    16 |   \item{method}{numeric; the method to be used by \code{optim}. By default, code{method = }1 and the used method is BFGS. If \code{method = }2, method L-BFGS-B is used.}
       |                                                                                 ^
checkRd: (-1) gbfs.Rd:26-27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gbfs.Rd:28-29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gbfs.Rd:41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gbfs.Rd:42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gbfs.Rd:43-44: Lost braces in \itemize; meant \describe ?
Specified C++11: please drop specification unless essential
Found the following files/directories:
  ‘checkdata.csv’ ‘gbmforest.sas’
checkRd: (-1) gbm.auto.Rd:208: Lost braces; missing escapes or markup?
   208 | \item Error in if (n.trees > x$n.trees) { : argument is of length zero}. LR or BF probably too low
       |                                         ^
Found the following significant warnings:
  node_categorical.cpp:42:16: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘long unsigned int’ [-Wformat=]
  node_categorical.cpp:45:19: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘long unsigned int’ [-Wformat=]
  node_categorical.cpp:52:16: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘long unsigned int’ [-Wformat=]
  node_categorical.cpp:55:19: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘long unsigned int’ [-Wformat=]
  node_continuous.cpp:37:16: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘long unsigned int’ [-Wformat=]
  node_continuous.cpp:43:16: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘long unsigned int’ [-Wformat=]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/gbm.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-13 (Debian 13.2.0-7) 13.2.0’
* used C++ compiler: ‘g++-13 (Debian 13.2.0-7) 13.2.0’
checkRd: (-1) gbm.Rd:85: Lost braces; missing escapes or markup?
    85 | targets {0,1} are expected for \code{map} and \code{mrr}. For \code{ndcg}
       |         ^
checkRd: (-1) gbm.Rd:319: Lost braces
   319 | url{https://dl.acm.org/citation.cfm?id=1354603}.
       |    ^
checkRd: (-1) gbm.fit.Rd:96: Lost braces; missing escapes or markup?
    96 | targets {0,1} are expected for \code{map} and \code{mrr}. For \code{ndcg}
       |         ^
checkRd: (-1) gbm.fit.Rd:215: Lost braces
   215 | url{https://dl.acm.org/citation.cfm?id=1354603}.
       |    ^
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
checkRd: (-1) fitgbd.Rd:29: Escaped LaTeX specials: \&
checkRd: (-1) fitgld.Rd:30: Escaped LaTeX specials: \&
checkRd: (-1) gb.Rd:28: Escaped LaTeX specials: \&
checkRd: (-1) gbd.Rd:37: Escaped LaTeX specials: \&
checkRd: (-1) gld.Rd:36: Escaped LaTeX specials: \&
Package in Depends field not imported from: ‘tools’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Unexported objects imported by ':::' calls:
  ‘tools:::.Rd_get_argument_names’ ‘tools:::RdTags’ ‘tools:::fetchRdDB’
  See the note in ?`:::` about the use of this operator.
checkRd: (-1) estprops.Rd:40: Escaped LaTeX specials: \&
Documented arguments not in \usage in Rd file 'align_peaks.Rd':
  ‘gc_peak_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.
Package suggested but not available for checking: ‘gputools’
Package suggested but not available for checking: ‘paleofire’
'LazyData' is specified without a 'data' directory
checkRd: (-1) listInverseBlocks.Rd:5: Lost braces; missing escapes or markup?
     5 | \title{List all the inverse matrices of the leading sub-matrix of P=Sigma^{-1}
       |                                                                           ^
checkRd: (-1) listInverseBlocks.Rd:17: Lost braces; missing escapes or markup?
    17 | List all the inverse matrices of the leading sub-matrix of P=Sigma^{-1}
       |                                                                    ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) matern.cormat.Rd:17: Lost braces; missing escapes or markup?
    17 | value of the shape parameter of the Matern correlation class. The default {alpha = 0.5} corresponds to an exponential correlation model. 
       |                                                                           ^
checkRd: (-1) gconsensus.Rd:48-54: Lost braces
    48 | {\code{display.signif.digits} an integer representing the number of significant digits to be obtained in the adaptative approach of the Monte Carlo simulation,
       | ^
Specified C++11: please drop specification unless essential
checkRd: (-1) GCTF.Rd:56: Lost braces; missing escapes or markup?
    56 |   U : A matrix which has N-rows and J-columns (J < {N, M}).
       |                                                    ^
checkRd: (-1) GCTF.Rd:57: Lost braces; missing escapes or markup?
    57 |   V : A matrix which has M-rows and J-columns (J < {N, M}).
       |                                                    ^
checkRd: (-1) GCTF.Rd:58: Lost braces; missing escapes or markup?
    58 |   J : The number of dimension (J < {N, M}).
       |                                    ^
checkRd: (-1) nearblack.Rd:30: Lost braces
    30 | code{infile=}, indicating that the input file should be
       |     ^
Found the following calls to attach():
File ‘g.data/R/g.data.attach.R’:
  attach(NULL, pos, basename(dir))
See section ‘Good practice’ in ‘?attach’.
checkRd: (-1) is.what.Rd:23-24: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) is.what.Rd:25: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) is.what.Rd:26-27: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) GMSCDM.Rd:25: Lost braces; missing escapes or markup?
    25 | representing restricted GMS-DINA and GMS-DINO models where delta_{jm1} are equal for all strategies. Note that only a single model can be used
       |                                                                  ^
Specified C++11: please drop specification unless essential
checkRd: (-1) GDSARM.Rd:7: Lost braces
     7 | Cand{\`e}s, E. and Tao, T. (2007). The Dantzig selector: Statistical estimation when p is much
       |     ^
checkRd: (-1) GDSARM.Rd:10: Lost braces
    10 | Dopico-Garc{\' i}a, M.S., Valentao, P., Guerra, L., Andrade, P. B., and Seabra, R. M. (2007).
       |            ^
checkRd: (-1) GDS_givencols.Rd:7: Lost braces
     7 | Cand{\`e}s, E. and Tao, T. (2007). The Dantzig selector: Statistical estimation when p is much
       |     ^
checkRd: (-1) GDS_givencols.Rd:10: Lost braces
    10 | Dopico-Garc{\' i}a, M.S., Valentao, P., Guerra, L., Andrade, P. B., and Seabra, R. M. (2007).
       |            ^
checkRd: (-1) dantzig.delta.Rd:7: Lost braces
     7 | Cand{\`e}s, E. and Tao, T. (2007). The Dantzig selector: Statistical estimation when p is much
       |     ^
checkRd: (-1) dantzigS.Rd:7: Lost braces
     7 | Cand{\`e}s, E. and Tao, T. (2007). The Dantzig selector: Statistical estimation when p is much
       |     ^
checkRd: (-1) dataCompoundExt.Rd:6: Lost braces
     6 | \title{Compound Extraction experiment of Dopico-Garc{\' i}a et al. (2007)}
       |                                                     ^
checkRd: (-1) dataCompoundExt.Rd:35: Lost braces
    35 | An analytical experiment conducted by Dopico-Garc{\' i}a et al. (2007) to
       |                                                  ^
checkRd: (-1) dataCompoundExt.Rd:22: Lost braces
    22 | Dopico-Garc{\' i}a, M.S., Valentao, P., Guerra, L., Andrade, P. B., and Seabra, R. M. (2007).
       |            ^
Package suggested but not available for checking: ‘gdxrrw’
'LazyData' is specified without a 'data' directory
Objects in \usage without \alias in Rd file 'geepack-internal.Rd':
  ‘genZcor’

Functions with \usage entries need to have the appropriate \alias
entries, and all their 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) dental.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dental.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dental.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dental.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dental.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dental.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) seizure.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) seizure.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) seizure.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) seizure.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) seizure.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) seizure.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) seizure.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) geexex.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) geexex.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) geexex.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) geexex.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) geexex.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) geexex.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) geexex.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) geexex.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) geexex.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gelnet.logreg.obj.Rd:17: Lost braces; missing escapes or markup?
    17 | \item{y}{n-by-1 binary response vector sampled from {0,1}}
       |                                                     ^
checkRd: (-1) ReadGem.Rd:55: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ReadGem.Rd:56: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ReadGem.Rd:57: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ReadGem.Rd:58: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ReadGem.Rd:61: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ReadGem.Rd:62: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ReadGem.Rd:63: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ReadGem.Rd:64: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ReadGem.Rd:65: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ReadGem.Rd:66: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ReadGem.Rd:67: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ReadGem.Rd:68: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ReadGem.Rd:69: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ReadGem.Rd:70: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ReadGem.Rd:73: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ReadGem.Rd:74: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ReadGem.Rd:75: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ReadGem.Rd:76: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ReadGem.Rd:77: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ReadGem.Rd:78: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ReadGem.Rd:79-80: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ReadGem.Rd:81-82: Lost braces in \itemize; \value handles \item{}{} directly
Auto-generated content requiring editing in Rd file 'gemlog-package.Rd':
  \details: ‘...the package, including the most important ~~ ~~ functions ~~’
'LazyData' is specified without a 'data' directory
checkRd: (-1) parkinson.Rd:9: Lost braces in \itemize; meant \describe ?
checkRd: (-1) parkinson.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) parkinson.Rd:11: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Invalid package aliases in Rd file 'GenBinom-package.Rd':
  ‘GenbinomApps-package’
Package suggested but not available for checking: ‘genderdata’
Documented arguments not in \usage in Rd file 'CirDisp.Rd':
  ‘x’

Documented arguments not in \usage in Rd file 'CirKurt.Rd':
  ‘x’ ‘na.rm’

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

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

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

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

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

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

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

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

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
checkRd: (-1) kde2dplot.Rd:32: Lost braces
    32 | \item{...}{additional params for contour see code{\link[graphics]{contour}}}
       |                                                  ^
checkRd: (-1) plotTL.Rd:13: Lost braces
    13 | \item{start}{Start of Data to plot. Passed to get.intervals, see code{\link[GENEAread]{get.intervals}}}
       |                                                                      ^
checkRd: (-1) positionals.Rd:21: Lost braces
    21 | \item{...}{Arguements passed to code{\link[GENEAread]{get.intervals}}}
       |                                     ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) GeneF-internal.Rd:40: Lost braces; missing escapes or markup?
    40 | \author{Yinglei Lai {ylai@gwu.edu}}
       |                     ^
checkRd: (-1) flexorhtest.Rd:57: Lost braces; missing escapes or markup?
    57 | \author{Yinglei Lai {ylai@gwu.edu}}
       |                     ^
checkRd: (-1) flexorhtest.pvalue.Rd:57: Lost braces; missing escapes or markup?
    57 | \author{Yinglei Lai {ylai@gwu.edu}}
       |                     ^
Package suggested but not available for checking: ‘maptools’
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Documented arguments not in \usage in Rd file 'generalizedwendland-internal.Rd':
  ‘numint.abstol (default: 1e-3)’ ‘numint.reltol (default: 1e-3)’
  ‘numint.qag_key (default: 0)’ ‘numint.subintervals (default: 0)’
  ‘interp.method (default: 'none')’ ‘interp.num_support (default: 0)’
  ‘cov.reparameterize (default: TRUE)’ ‘cov.eps (default:
  .Machine$double.eps^0.5)’ ‘cov.d_value (default: 2)’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) cpm.Rd:70: Lost braces; missing escapes or markup?
    70 | covariates included in \code{formula_l} or {formula_s} (required).}
       |                                            ^
checkRd: (-1) LD.Rd:37-46: Lost braces in \itemize; meant \describe ?
checkRd: (-1) LD.Rd:47-64: Lost braces in \itemize; meant \describe ?
checkRd: (-1) LD.Rd:66-73: Lost braces in \itemize; meant \describe ?
checkRd: (-1) LD.Rd:78-79: Lost braces in \itemize; meant \describe ?
checkRd: (-1) LD.Rd:80-81: Lost braces in \itemize; meant \describe ?
checkRd: (-1) LD.Rd:82-83: Lost braces in \itemize; meant \describe ?
checkRd: (-1) LD.Rd:84-85: Lost braces in \itemize; meant \describe ?
checkRd: (-1) LD.Rd:86-87: Lost braces in \itemize; meant \describe ?
checkRd: (-1) diseq.Rd:48-58: Lost braces in \itemize; meant \describe ?
checkRd: (-1) diseq.Rd:59-76: Lost braces in \itemize; meant \describe ?
checkRd: (-1) diseq.Rd:78-87: Lost braces in \itemize; meant \describe ?
checkRd: (-1) diseq.Rd:93-94: Lost braces in \itemize; meant \describe ?
checkRd: (-1) diseq.Rd:95-96: Lost braces in \itemize; meant \describe ?
checkRd: (-1) diseq.Rd:97-98: Lost braces in \itemize; meant \describe ?
checkRd: (-1) diseq.Rd:124: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) diseq.Rd:125: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) diseq.Rd:126-128: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) diseq.Rd:129: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) set_synapse_credentials.Rd:27: Lost braces; missing escapes or markup?
    27 | (see {https://genie-bpc.github.io/genieBPC/}{README 'Data Access and Authentication'} for details).
       |      ^
checkRd: (-1) set_synapse_credentials.Rd:27: Lost braces
    27 | (see {https://genie-bpc.github.io/genieBPC/}{README 'Data Access and Authentication'} for details).
       |                                             ^
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
checkRd: (-1) GLgen-class.Rd:21: Lost braces
    21 |     \item{depth}{\code{signature(x = "GLgen")}}{ Gives the depth of the genealogy. }
       |                                                ^
checkRd: (-1) GLgen-class.Rd:22: Lost braces
    22 |     \item{length}{\code{signature(x = "GLgen")}}{ Gives the number of individuals in the genealogy. }
       |                                                 ^
Invalid package aliases in Rd file 'GenlibR-package.Rd':
  ‘GenlibR-package’
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
checkRd: (-1) simulate_admixture.Rd:36: Lost braces
    36 | \code{location}{ location of the marker under selection (in Morgan) }
       |                ^
checkRd: (-1) simulate_ancestry.Rd:49: Lost braces
    49 | \code{location}{ location of the marker under selection (in Morgan) }
       |                ^
checkRd: (-1) simulate_ancestry_migration.Rd:59: Lost braces
    59 | \code{location}{ location of the marker under selection (in Morgan) }
       |                ^
checkRd: (-1) simulate_sequence.Rd:51: Lost braces
    51 | \code{location}{ location of the marker under selection (in Morgan) }
       |                ^
checkRd: (-1) simulate_sequence_migration.Rd:58: Lost braces
    58 | \code{location}{ location of the marker under selection (in Morgan) }
       |                ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) barto.Rd:15-18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) barto.Rd:19-22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) barto.Rd:23-26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) chrY_subseg.Rd:16-17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) chrY_subseg.Rd:18-19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mauve_bbone.Rd:16-17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mauve_bbone.Rd:18-19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) three_genes.Rd:17-18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) three_genes.Rd:19-20: Lost braces in \itemize; meant \describe ?
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
checkRd: (-1) cfunc.new.Rd:57: Lost braces in \itemize; meant \describe ?
checkRd: (-1) cfunc.new.Rd:58-59: Lost braces in \itemize; meant \describe ?
checkRd: (-1) cfunc.new.Rd:60-61: Lost braces in \itemize; meant \describe ?
checkRd: (-1) cfunc.new.Rd:62: Lost braces in \itemize; meant \describe ?
checkRd: (-1) cfunc.new.Rd:63-64: Lost braces in \itemize; meant \describe ?
checkRd: (-1) cfunc.new.Rd:65: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gensvm.grid.Rd:125: Lost braces
   125 | "Kernels in GenSVM" in the code{ink{gensvm-package}} page for more info.}
       |                                ^
checkRd: (-1) gensvm.grid.Rd:125: Lost braces
   125 | "Kernels in GenSVM" in the code{ink{gensvm-package}} page for more info.}
       |                                    ^
checkRd: (-1) gensvm.grid.Rd:127: Lost braces
   127 | GenSVM" in the code{ink{gensvm-package}} page for more info.}
       |                    ^
checkRd: (-1) gensvm.grid.Rd:127: Lost braces
   127 | GenSVM" in the code{ink{gensvm-package}} page for more info.}
       |                        ^
checkRd: (-1) gensvm.grid.Rd:129: Lost braces
   129 | section "Kernels in GenSVM" in the code{ink{gensvm-package}} page for more 
       |                                        ^
checkRd: (-1) gensvm.grid.Rd:129: Lost braces
   129 | section "Kernels in GenSVM" in the code{ink{gensvm-package}} page for more 
       |                                            ^
checkRd: (-1) read_comparable_areas.Rd:38: Lost braces
    38 | \doi{10.1590/0101-416147182phe}{Philipp Ehrl}, and translated
       |                                ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) geodist.Rd:59: Lost braces
    59 | code{sf::st_dist()} function.
       |     ^
checkRd: (-1) geodist_vec.Rd:65: Lost braces
    65 | code{sf::st_dist()} function.
       |     ^
checkRd: (-1) georange.Rd:36: Lost braces
    36 | code{sf::st_dist()} function.
       |     ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) calvaria.Rd:8: Lost braces; missing escapes or markup?
     8 | A named list containing \code{x} {a vector containing the ages}
       |                                  ^
checkRd: (-1) calvaria.Rd:9: Lost braces; missing escapes or markup?
     9 |   \code{y} {a matrix where each column is a preshape.} The 23rd, 101st,
       |            ^
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
Documented arguments not in \usage in Rd file 'variables_query-method.Rd':
  ‘variables’

Functions with \usage entries need to have the appropriate \alias
entries, and all their 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: ‘geomarocdata’
'LazyData' is specified without a 'data' directory
checkRd: (-1) GMLVerticalCRS.Rd:39: Lost braces
    39 | \item{\code{verticalDatum}}{[code{GMLVerticalDatum}]}
       |                                  ^
checkRd: (-1) GSWorkspaceManager.Rd:131: Lost braces; missing escapes or markup?
   131 |    with the URI being "http://{workspaceName}. If the URI is specified, the method
       |                               ^
checkRd: (-1) GSWorkspaceManager.Rd:157: Lost braces; missing escapes or markup?
   157 |    with the URI being "http://{workspaceName}. If the URI is specified, the method
       |                               ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘RandomFields’

Package which this enhances but not available for checking: ‘INLA’
Unknown package ‘RandomFields’ in Rd xrefs
Malformed Description field: should contain one or more complete sentences.
Found the following calls to data() loading into the global environment:
File ‘geotools/R/zzz.R’:
  data(fr_geo_rad)
See section ‘Good practice’ in ‘?data’.
checkRd: (-1) getvalues.brick.at.depth.Rd:50: Lost braces
    50 | code{\link{vertical.aggregate.brick.within.depth}}
       |     ^
checkRd: (-1) write.vectorized.variable.in.string.Rd:15: Lost braces
    15 | \item{l}{a code{list} object contained the variables (scalars, vectors or Rasters) which will be written in a string each.}
       |                ^
Package suggested but not available for checking: ‘rgdal’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) gesso.cv.Rd:46: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gesso.cv.Rd:47: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gesso.cv.Rd:48: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gesso.cv.Rd:49: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gesso.cv.Rd:50: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gestMultiple.Rd:80: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gestMultiple.Rd:81-83: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gestMultiple.Rd:84-86: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gestMultiple.Rd:87-90: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gestSingle.Rd:74: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gestSingle.Rd:75-78: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gestSingle.Rd:79-80: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gestSingle.Rd:81-84: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
checkRd: (-1) residual.Rd:23: Lost braces; missing escapes or markup?
    23 | Subtract the theoretical function S_{H_0} or the mean of the functions
       |                                     ^
checkRd: (-1) vargaugeiis.Rd:22: Lost braces
    22 | \details{The function computes the variance of the Gauge (false-positive rate of outliers in impulse indicator saturation) for a given level of significance of selection (\code{t.pval}) and sample size ({\code{T}) based on Jiao and Pretis (2019). This is an auxilliary function used within the \code{\link{outliertest}} function.}}
       |                                                                                                                                                                                                            ^
Package suggested but not available for checking: ‘RGtk2’
checkRd: (-1) QANOVA.Rd:62: Lost braces in \itemize; meant \describe ?
checkRd: (-1) QANOVA.Rd:63: Lost braces in \itemize; meant \describe ?
checkRd: (-1) QANOVA.Rd:64-66: Lost braces in \itemize; meant \describe ?
checkRd: (-1) QANOVA.Rd:67: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
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) gfonts.Rd:8: Lost braces; missing escapes or markup?
     8 | Download Google fonts and generate CSS to use in {rmarkdown} documents and
       |                                                  ^
checkRd: (-1) gfonts.Rd:9: Lost braces; missing escapes or markup?
     9 | {shiny} applications. Some popular fonts are included and ready to use.
       | ^
checkRd: (-1) use_pkg_gfont.Rd:5: Lost braces; missing escapes or markup?
     5 | \title{Use a Google Font included in {gfonts}}
       |                                      ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'attract_by_distance.Rd':
  ‘prop_start’ ‘prop_end’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) dag.Rd:17: Lost braces
    17 | A convenience wrapper for dagitty::dagitty("dag{...}")
       |                                                ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) dendro_data.Rd:107-108: Lost braces
   107 | line segments, labels or leaf labels use: \itemize{ \item{\code{\link[=segment]{segment()}}}: {the
       |                                                                                               ^
checkRd: (-1) dendro_data.Rd:108: Lost braces; missing escapes or markup?
   108 | line segment data} \item{\code{\link[=label]{label()}}}: {the text for each end segment}
       |                                                          ^
checkRd: (-1) dendro_data.Rd:109: Lost braces; missing escapes or markup?
   109 | \item{\code{\link[=leaf_label]{leaf_label()}}}: {the leaf labels of a tree diagram} }
       |                                                 ^
checkRd: (-1) ggdendro-package.Rd:35: Lost braces; missing escapes or markup?
    35 | \item{\code{\link[=segment]{segment()}}}: {the line segment data}
       |                                           ^
checkRd: (-1) ggdendro-package.Rd:36: Lost braces; missing escapes or markup?
    36 | \item{\code{\link[=label]{label()}}}: {the text for each end segment}
       |                                       ^
checkRd: (-1) ggdendro-package.Rd:37: Lost braces; missing escapes or markup?
    37 | \item{\code{\link[=leaf_label]{leaf_label()}}}: {the leaf labels of a tree diagram}
       |                                                 ^
Documented arguments not in \usage in Rd file 'labels.rpart.Rd':
  ‘pretty:’

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

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

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) gg_lm.Rd:44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gg_lm.Rd:45: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gg_lm.Rd:46: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gg_lm.Rd:47: Lost braces in \itemize; meant \describe ?
checkRd: (-1) half_normal.Rd:46: Lost braces in \itemize; meant \describe ?
checkRd: (-1) half_normal.Rd:47-48: Lost braces in \itemize; meant \describe ?
checkRd: (-1) half_normal.Rd:49-51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) half_normal.Rd:52-53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) half_normal.Rd:54-55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) half_normal.Rd:56: Lost braces in \itemize; meant \describe ?
checkRd: (-1) half_normal.Rd:57-61: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pareto_plot.Rd:40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pareto_plot.Rd:41-42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pareto_plot.Rd:43-45: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pareto_plot.Rd:46-47: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pareto_plot.Rd:48-49: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pareto_plot.Rd:50: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pareto_plot.Rd:51-55: Lost braces in \itemize; meant \describe ?
Found the following assignments to the global environment:
File ‘ggExtra/R/ggMarginalGadget.R’:
  assign(plotname, eval(parse(text = origPlot)), envir = .GlobalEnv)
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'interpolateDataFrame.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) render_context.Rd:42: Lost braces; missing escapes or markup?
    42 | \item{xmin, ymin, xmax, ymax}{Boundaries of the area in pixels. {0,0} is the
       |                                                                 ^
'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
Specified C++11: please drop specification unless essential
checkRd: (-1) boot_eip.Rd:50: Escaped LaTeX specials: \&
checkRd: (-1) constrained.Rd:93: Escaped LaTeX specials: \&
checkRd: (-1) constrained.Rd:37: Escaped LaTeX specials: \&
':::' call which should be '::': ‘scales:::censor’
  See the note in ?`:::` about the use of this operator.
Unexported object imported by a ':::' call: ‘productplots:::bound’
  See the note in ?`:::` about the use of this operator.
Argument items with no description in Rd file 'isADMG.Rd':
  ‘amat’
Argument items with no description in Rd file 'isAG.Rd':
  ‘amat’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) raster_bathymetry.Rd:30: Lost braces
    30 | \item{warp}{Logical indicating whether the resulting grid should be resampled to a new CRS if \code{proj.out} != code{proj.bathy} using the \code{\link[stars]{st_warp}} function. A time-consuming operation, but necessary when CRS changes in raster bathymetries. Not required if the next step is to vectorise the bathymetry.}
       |                                                                                                                      ^
Invalid package aliases in Rd file 'package-ggparallel.Rd':
  ‘package-ggparallel-package’
'LazyData' is specified without a 'data' directory
checkRd: (-1) geom_from_path.Rd:79: Lost braces in \itemize; meant \describe ?
checkRd: (-1) geom_from_path.Rd:80: Lost braces in \itemize; meant \describe ?
checkRd: (-1) geom_from_path.Rd:81: Lost braces in \itemize; meant \describe ?
checkRd: (-1) geom_from_path.Rd:82: Lost braces in \itemize; meant \describe ?
checkRd: (-1) geom_from_path.Rd:83: Lost braces in \itemize; meant \describe ?
checkRd: (-1) geom_from_path.Rd:84: Lost braces in \itemize; meant \describe ?
checkRd: (-1) geom_from_path.Rd:85: Lost braces in \itemize; meant \describe ?
checkRd: (-1) geom_from_path.Rd:86: Lost braces in \itemize; meant \describe ?
checkRd: (-1) geom_from_path.Rd:87-90: Lost braces in \itemize; meant \describe ?
checkRd: (-1) geom_from_path.Rd:91-94: Lost braces in \itemize; meant \describe ?
checkRd: (-1) geom_lines.Rd:77: Lost braces in \itemize; meant \describe ?
checkRd: (-1) geom_lines.Rd:78: Lost braces in \itemize; meant \describe ?
checkRd: (-1) geom_lines.Rd:79: Lost braces in \itemize; meant \describe ?
checkRd: (-1) geom_lines.Rd:80: Lost braces in \itemize; meant \describe ?
checkRd: (-1) geom_lines.Rd:81: Lost braces in \itemize; meant \describe ?
checkRd: (-1) geom_lines.Rd:82: Lost braces in \itemize; meant \describe ?
checkRd: (-1) geom_lines.Rd:83: Lost braces in \itemize; meant \describe ?
checkRd: (-1) scale_pattern_alpha_continuous.Rd:24-45: Lost braces
    24 | if (require("ggplot2")) {
       |                         ^
checkRd: (-1) pcp_scale.Rd:50: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pcp_scale.Rd:51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pcp_scale.Rd:52: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pcp_scale.Rd:53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pcp_scale.Rd:54-55: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘lixoftConnectors’
'LazyData' is specified without a 'data' directory
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  ‘x’ ‘y’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
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    80 | Adopted from the geom_violinhalf() source code from the {see} package
       |                                                         ^
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    28 | James T. Robinson, Helga Thorvaldsd\'{o}ttir, Wendy Winckler,
       |                                      ^
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    * Changes all data options to .data to decrease possibility of column naming overlap
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    21 | \Sexpr[results=rd,stage=build]{ggtern:::rd_theme()}
       | ^
Documented arguments not in \usage in Rd file 'ggplot_gtable.Rd':
  ‘plot’

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

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Win CRAN check results - R Windows
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    33 |   {chisq_i = sum( (O_iz - E_iz)^2 / E_iz; z = 0, ..., C ), }
       |   ^
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    27 |   GUM-based probabilities just constrain alpha to a unit vector of length {I}
       |                                                                           ^
Documented arguments not in \usage in Rd file 'add_scale.Rd':
  ‘domain’

Documented arguments not in \usage in Rd file 'bin_vector.Rd':
  ‘width’ ‘origin’ ‘closed’ ‘pad’

Functions with \usage entries need to have the appropriate \alias
entries, and all their 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
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
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Found the following files/directories:
  ‘Pictures_analyzed’ ‘cutoff_vals’ ‘cutoff_vals1’ ‘gina_cran.JPG’
Unknown package ‘IC2’ in Rd xrefs
Specified C++11: please drop specification unless essential
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'LazyData' is specified without a 'data' directory
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    27 |   \item{\code{y}}{n by S matrix updated with censored {values} substituted for
       |                                                       ^
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    32 | Missing times in the data occur where there are gaps in \code{timeCol} column of \code{xdata} and the initial time \code{0} for each sequence.  New versions of the data have \code{NA} (\code{xdata}) or prior values with appropriate weight (\code{ydata}).  Missing times are filled in \code{xdata, ydata, edata}, including a time \code{0} which serves as a prior mean for \code{ydata} for time code{1}.  The group and time indices in columns \code{groupCol} and \code{timeCol} of \code{xdata} reference the time for a given time series.  Missing values in the columns \code{groupVars} of \code{xdata} are filled automatically filled in.  This assumes that values for these variables are fixed for the group.  If \code{FILLMEANS}, the missing  values in \code{ydata} are filled with means for the group and given a low weight specified in \code{missingEffort}.
       |                                                                                                                                                                                                                                                                                                                                                                                                              ^
Problems with news in ‘NEWS.md’:
No news entries found.
Specified C++11: please drop specification unless essential
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    60 |   \code{gpd} uses GPD parameterisation, see {van Staden and Loots (2009)}
       |                                             ^
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    14 |   {\eqn{\lambda_1}{lambda 1} location parameter}
       |   ^
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    15 |   {\eqn{\lambda_2}{lambda 2} - scale parameter}
       |   ^
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    16 |   {\eqn{\lambda_3}{lambda 3} - first shape parameter}
       |   ^
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    17 |   {\eqn{\lambda_4}{lambda 4} - second shape parameter}
       |   ^
Package suggested but not available for checking: ‘mlr3proba’
Argument items with no description in Rd file 'GLD.lm.full.surv.Rd':
  ‘maxit’
Argument items with no description in Rd file 'GLD.lm.surv.Rd':
  ‘maxit’
Documented arguments not in \usage in Rd file 'getBeta.Rd':
  ‘thetaConrol’

Functions with \usage entries need to have the appropriate \alias
entries, and all their 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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    16 |         \item Now \code{AICc == Inf} when {n <= p + 1}.
       |                                           ^
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     5 | \title{Plot method for a fitted code{glmcat} model object}
       |                                     ^
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     5 | \title{Print method for a fitted code{glmcat} model object}
       |                                      ^
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    34 | \item{method}{NULL or character vector of length 0, 1 or 2; may be code{"LRT"} or \code{"Rao"} or \code{c("LRT", "Rao")} to compute specified P-values.
       |                                                                        ^
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     4 | \description{Section 4.1.2 of the refence below descries a simulation study with data generated from a probit mixed model with six fixed effects parameters and a bivariate random effects vector having a 2 by 2 symmetric positive definite covariance matrix. The function simulates a data set from this model with 2500 groups and the number of observation in each group being a random draw from {20,21,...,30}.}
       |                                                                                                                                                                                                                                                                                                                                                                                                          ^
GNU make is a SystemRequirements.
checkRd: (-1) glmm.hp.Rd:56: Lost braces; missing escapes or markup?
    56 | {Kim Nimon} \email{kim.nimon@gmail.com}
       | ^
GNU make is a SystemRequirements.
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    10 | \code{TRUE} or {FALSE} depending on availability of OpenMP
       |                ^
Documented arguments not in \usage in Rd file 'glmpathcr-internal.Rd':
  ‘fit’

Functions with \usage entries need to have the appropriate \alias
entries, and all their 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) ccancer.Rd:16: Lost braces
    16 |                          a factor with levels either \\code{F} (female) or code{M} (male)}
       |                                                            ^
checkRd: (-1) ccancer.Rd:16: Lost braces
    16 |                          a factor with levels either \\code{F} (female) or code{M} (male)}
       |                                                                                ^
checkRd: (-1) galapagos.Rd:4: Lost braces
     4 | \title{{Gal\'{a}pagos} Island species data}
       |              ^
checkRd: (-1) galapagos.Rd:6: Lost braces
     6 |   The number of species on the {Gal\'{a}pagos} Islands
       |                                ^
checkRd: (-1) galapagos.Rd:6: Lost braces
     6 |   The number of species on the {Gal\'{a}pagos} Islands
       |                                      ^
checkRd: (-1) galapagos.Rd:40: Lost braces
    40 |    {Gal\'{a}pagos} (the endemics). 
       |    ^
checkRd: (-1) galapagos.Rd:40: Lost braces
    40 |    {Gal\'{a}pagos} (the endemics). 
       |          ^
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    44 |   Species number and endemism: The {Gal\'{a}pagos} Archipelago revisited.
       |                                          ^
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    14 |   \item{object}{A fitted model object, of class \code{glm}, \code{lm} or code{glm.nb}}
       |                                                                              ^
checkRd: (-1) getfit.Rd:26: Escaped LaTeX specials: \&
checkRd: (-1) glmulti-class.Rd:26: Escaped LaTeX specials: \&
checkRd: (-1) glmulti-methods.Rd:14: Lost braces
    14 | code{glmulti} finds what are the \code{n} best models (the confidence set of models) among all possible models (the candidate set, as specified by the user).
       |     ^
checkRd: (-1) glmulti.Rd:99: Escaped LaTeX specials: \&
checkRd: (-1) summary.glmulti.Rd:72: Escaped LaTeX specials: \&
Malformed Description field: should contain one or more complete sentences.
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    35 |   Returns the current scale factor $r_{ii}$ for row \code{i} of the specified
       |                                       ^
checkRd: (-1) getSjjGLPK.Rd:35: Lost braces; missing escapes or markup?
    35 |   Returns the current scale factor $s_{jj}$ for column \code{j} of the
       |                                       ^
checkRd: (-1) setRiiGLPK.Rd:28: Lost braces; missing escapes or markup?
    28 |     Scale factor $r_{ii}$.
       |                     ^
checkRd: (-1) setSjjGLPK.Rd:28: Lost braces; missing escapes or markup?
    28 |     Scale factor $s_{jj}$.
       |                     ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) rtheta.Rd:50-76: Lost braces in \itemize; meant \describe ?
Documented arguments not in \usage in Rd file 'fun.svd_1.Rd':
  ‘X’

Documented arguments not in \usage in Rd file 'fun.svd_2.Rd':
  ‘X’

Documented arguments not in \usage in Rd file 'fun.svd_3.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
checkRd: (-1) Maf.data.frame.Rd:65: Lost braces
    65 | the lag distance to take. \%For other options see code{getEmpVariogramSlice}.}
       |                                                       ^
checkRd: (-1) NGSAustralia.Rd:114: Lost braces; missing escapes or markup?
   114 | \item{MRB}{obtained from simplifying the major crustal boundaries of {Korsch2015a, Korsch2015b}}
       |                                                                      ^
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
checkRd: (-1) ATEgel.Rd:24: Lost braces
    24 | \item{g}{A formula as \code{y~z}, where code{y} is the response and
       |                                             ^
checkRd: (-1) plotRectangle3D.Rd:27: Lost braces; missing escapes or markup?
    27 | The rectangle is defined by {x|a <= x <= b} where a is the minimum values and
       |                             ^
'LazyData' is specified without a 'data' directory
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checkRd: (-1) logLik.joint.Rd:21: Lost braces; missing escapes or markup?
    21 | \code{AIC} and {BIC} which are the Akaike or Bayes information criterion evaluated at either
       |                ^
checkRd: (-1) GNE.ceq.Rd:50: Lost braces
    50 | (KKT) system denoted by \eqn{H(z)=0}, for \eqn{z \in \Omega} where eqn{z} is formed by the players strategy 
       |                                                                       ^
checkRd: (-1) GNE.nseq.Rd:76: Lost braces
    76 | (KKT) system denoted by \eqn{\Phi(z)=0}{Phi(z)=0}, where eqn{z} is formed by the players strategy 
       |                                                             ^
'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) filter_tf_idf.Rd:43: Lost braces
    43 | Bettina Gr\"{u}n, Kurt Hornik, and Tyler Rinker <tyler.rinker@gmail.com>.
       |             ^
'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
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checkRd: (-1) BVDWSTOXX.Rd:15: Escaped LaTeX specials: \&
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checkRd: (-1) create_golem.Rd:30: Lost braces; missing escapes or markup?
    30 | \item{package_name}{Package name to use. By default, {golem} uses
       |                                                      ^
checkRd: (-1) fill_desc.Rd:42: Lost braces; missing escapes or markup?
    42 | The {desc} object, invisibly.
       |     ^
checkRd: (-1) get_sysreqs.Rd:23: Lost braces; missing escapes or markup?
    23 | {dockerfiler}.
       | ^
checkRd: (-1) golem_opts.Rd:80: Lost braces; missing escapes or markup?
    80 | \item{config_file}{path to the {golem} config file}
       |                                ^
checkRd: (-1) install_dev_deps.Rd:5: Lost braces; missing escapes or markup?
     5 | \title{Install {golem} dev dependencies}
       |                ^
checkRd: (-1) project_hook.Rd:13: Lost braces; missing escapes or markup?
    13 | \item{package_name}{Package name to use. By default, {golem} uses
       |                                                      ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Rd files without \alias:
  ‘goodpractice-package.Rd’
Package suggested but not available for checking: ‘ganalytics’
Documented arguments not in \usage in Rd file 'doHttrRequest.Rd':
  ‘session’ ‘params’

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

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
checkRd: (-1) GitHubEventsConfig.Rd:16: Lost braces; missing escapes or markup?
    16 | \item{x}{The repository in format {owner}/{repo} e.g. MarkEdmondson1234/googleCloudRunner}
       |                                   ^
checkRd: (-1) GitHubEventsConfig.Rd:16: Lost braces; missing escapes or markup?
    16 | \item{x}{The repository in format {owner}/{repo} e.g. MarkEdmondson1234/googleCloudRunner}
       |                                           ^
checkRd: (-1) cr_buildstep_targets.Rd:27: Lost braces
    27 | \item{id}{The id of the buildstep.  In link{cr_buildstep_targets_multi} this is used along with \code{waitFor} to determine the order of execution}
       |                                            ^
checkRd: (-1) cr_setup_service.Rd:21: Lost braces; missing escapes or markup?
    21 | \item{account_email}{The service account email e.g. \code{accountId@projectid.iam.gserviceaccount.com} or {12345678@cloudbuild.gserviceaccount.com}}
       |                                                                                                           ^
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'LazyData' is specified without a 'data' directory
checkRd: (-1) google_find_place.Rd:67: Lost braces in \itemize; meant \describe ?
checkRd: (-1) google_find_place.Rd:68: Lost braces in \itemize; meant \describe ?
checkRd: (-1) google_find_place.Rd:69: Lost braces in \itemize; meant \describe ?
checkRd: (-1) google_map.Rd:54: Lost braces; missing escapes or markup?
    54 | of `{sf}` objects).}
       |     ^
checkRd: (-1) compute_lower_bound_1tree.Rd:31: Lost braces; missing escapes or markup?
    31 | instance from vertex 1.  Internally, it creates the graph Kn-{v1}
       |                                                              ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Documented arguments not in \usage in Rd file 'estimate_noise_nn.Rd':
  ‘n_thread’

Functions with \usage entries need to have the appropriate \alias
entries, and all their 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: ‘gvcm.cat’
Specified C++11: please drop specification unless essential
Unknown package ‘gvcm.cat’ in Rd xrefs
checkRd: (-1) solve_game.Rd:86: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) solve_game.Rd:87: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) solve_game.Rd:88: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) solve_game.Rd:89: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) solve_game.Rd:90: Lost braces in \itemize; \value handles \item{}{} directly
Package suggested but not available for checking: ‘maptools’
checkRd: (-1) exponential_spacetime.Rd:18: Lost braces; missing escapes or markup?
    18 | Each row of locs is a point in R^{d+1}. The first \code{d} columns
       |                                  ^
checkRd: (-1) matern_spacetime.Rd:18: Lost braces; missing escapes or markup?
    18 | Each row of locs is a point in R^{d+1}. The first \code{d} columns
       |                                  ^
checkRd: (-1) order_coordinate.Rd:15: Lost braces; missing escapes or markup?
    15 | \item{coordinate}{integer or vector of integers in {1,...,d}. If a single integer,
       |                                                    ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) barplot2.Rd:219: Escaped LaTeX specials: \_
checkRd: (-1) colorpanel.Rd:31: Escaped LaTeX specials: \#
checkRd: (-1) qqnorm.aov.Rd:33: Escaped LaTeX specials: \&
checkRd: (-1) venn.Rd:21: Lost braces
    21 |     in code{data} not in this list will be ignored. Use \code{NA} to
       |            ^
checkRd: (-1) venn.Rd:59: Escaped LaTeX specials: \_
Specified C++11: please drop specification unless essential
checkRd: (-1) Auxil.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Auxil.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Auxil.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Auxil.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Fit.Rd:39: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Fit.Rd:40: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Fit.Rd:41: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Fit.Rd:42: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Fit.Rd:43: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Predict.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Predict.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Predict.Rd:23: 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) order_coordinate.Rd:15: Lost braces; missing escapes or markup?
    15 | \item{coordinate}{integer or vector of integers in {1,...,d}. If a single integer,
       |                                                    ^
'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) grade-package.Rd:51-54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) grade-package.Rd:55-57: Lost braces in \itemize; meant \describe ?
checkRd: (-1) grade-package.Rd:58-71: Lost braces in \itemize; meant \describe ?
checkRd: (-1) grade-package.Rd:72-74: Lost braces in \itemize; meant \describe ?
checkRd: (-1) grade-package.Rd:75-78: Lost braces in \itemize; meant \describe ?
checkRd: (-1) grade-package.Rd:79-81: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘monocle’
Package unavailable to check Rd xrefs: ‘monocle’
checkRd: (-1) Granger.inference.difference.Rd:65: Lost braces; missing escapes or markup?
    65 | 	least one root larger than one) on bootstrapped \verb{x} and {y}.
       |                                                                      ^
checkRd: (-1) Granger.inference.difference.Rd:68: Lost braces; missing escapes or markup?
    68 | 	least one root larger than one) on bootstrapped \verb{x} and {z}.
       |                                                                      ^
checkRd: (-1) Granger.inference.difference.Rd:71: Lost braces; missing escapes or markup?
    71 | 	least one root larger than one) on bootstrapped \verb{x}, \verb{y} and {z}.
       |                                                                                ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) corrApp.Rd:40: Escaped LaTeX specials: \&
checkRd: (-1) crdApp.Rd:46: Escaped LaTeX specials: \&
checkRd: (-1) descApp.Rd:55: Escaped LaTeX specials: \&
checkRd: (-1) layoutApp.Rd:50: Escaped LaTeX specials: \&
checkRd: (-1) rbdApp.Rd:46: Escaped LaTeX specials: \&
checkRd: (-1) ttApp.Rd:43: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'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
Argument items with no description in Rd file 'HistPCA.Rd':
  ‘ggplot’
Specified C++11: please drop specification unless essential
checkRd: (-1) term_names.Rd:19: Lost braces; missing escapes or markup?
    19 | \item{object}{a fitted GAM object or an {mgcv} smooth object}
       |                                         ^
Specified C++11: please drop specification unless essential
checkRd: (-1) MinimiseEPL.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MinimiseEPL.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MinimiseEPL.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MinimiseEPL.Rd:20: Lost braces in \itemize; meant \describe ?
GNU make is a SystemRequirements.
Documented arguments not in \usage in Rd file 'prCaSetRownames.Rd':
  ‘rownames.fn’

Documented arguments not in \usage in Rd file 'prClearPCAclass.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) covFun.Rd:89-90: Lost braces in \itemize; meant \describe ?
checkRd: (-1) covFun.Rd:91-92: Lost braces in \itemize; meant \describe ?
checkRd: (-1) covFun.Rd:93-95: Lost braces in \itemize; meant \describe ?
checkRd: (-1) covFun.Rd:96-97: Lost braces in \itemize; meant \describe ?
checkRd: (-1) covFun.Rd:98-99: Lost braces in \itemize; meant \describe ?
checkRd: (-1) covFun.Rd:100-103: Lost braces in \itemize; meant \describe ?
checkRd: (-1) covFun.Rd:104-106: Lost braces in \itemize; meant \describe ?
checkRd: (-1) covFun.Rd:107-109: Lost braces in \itemize; meant \describe ?
checkRd: (-1) covFun.Rd:110-111: Lost braces in \itemize; meant \describe ?
checkRd: (-1) covFun.Rd:112-113: Lost braces in \itemize; meant \describe ?
checkRd: (-1) covFun.Rd:114-115: Lost braces in \itemize; meant \describe ?
checkRd: (-1) covFun.Rd:116-117: Lost braces in \itemize; meant \describe ?
checkRd: (-1) GREMLINS.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) GREMLINS.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) GREMLINS.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) GREMLINS.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) GREMLINS.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) GREMLINS.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) GREMLINS.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) GREMLINS.Rd:23: Lost braces in \itemize; meant \describe ?
accrualReport: multiple local function definitions for ‘gg’ with
  different formal arguments
checkRd: (-1) setgreportOption.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) setgreportOption.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) setgreportOption.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) setgreportOption.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) setgreportOption.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) setgreportOption.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) setgreportOption.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) setgreportOption.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) setgreportOption.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) setgreportOption.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) setgreportOption.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) setgreportOption.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) setgreportOption.Rd:24: Lost braces
    24 | \item{code{figpos}:}{LaTeX figure environment position; default is \code{"htb!"}}
       |           ^
checkRd: (-1) setgreportOption.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) setgreportOption.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) setgreportOption.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) setgreportOption.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) setgreportOption.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) setgreportOption.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) iterate_matrix.Rd:32-33: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) iterate_matrix.Rd:34-36: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) iterate_matrix.Rd:37-38: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) iterate_matrix.Rd:39-41: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) iterate_matrix.Rd:42-44: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) inference.Rd:123-124: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) inference.Rd:125-126: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) inference.Rd:127: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) inference.Rd:128-130: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) inference.Rd:131-132: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) BCNormal.Rd:60: Lost braces; missing escapes or markup?
    60 | f(y) = y^{lambda-1} 1/sqrt(2 pi) exp(-((y^lambda-1)/lambda -mu)^2 / (2 sigma^2))
       |          ^
checkRd: (-1) cramer.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) cramer.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) cramer.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) cramer.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mcor.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mcor.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mcor.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mcor.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mcor.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rmcb.Rd:38: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rmcb.Rd:39: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rmcb.Rd:40: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rmcb.Rd:41-42: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rmcb.Rd:43-44: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rmcb.Rd:45-46: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rmcb.Rd:47: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rmcb.Rd:48: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rmcb.Rd:49: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rmcb.Rd:50: Lost braces in \itemize; \value handles \item{}{} directly
GNU make is a SystemRequirements.
Malformed Description field: should contain one or more complete sentences.
checkRd: (-1) estimate.gridCopula.Rd:53-62: Lost braces
    53 | {@misc{https://doi.org/10.48550/arxiv.2010.15709,
       |       ^
Specified C++14: please drop specification unless essential
Specified C++11: please drop specification unless essential
checkRd: (-1) NEWS.Rd:669: Lost braces; missing escapes or markup?
   669 |     parameters are rounded so they belong to one of {0, 0.5, 1}. (Simon)
       |                                                     ^
checkRd: (-1) gradients.Rd:96-99: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gradients.Rd:100-103: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gradients.Rd:104-107: Lost braces in \itemize; meant \describe ?
Specified C++11: please drop specification unless essential
checkRd: (-1) testadd.Rd:34: Lost braces; missing escapes or markup?
    34 | Let M0 be the model and e={u,v} be an edge and let M1 be
       |                           ^
'LazyData' is specified without a 'data' directory
S3 methods shown with full name in Rd file 'groc.fit.Rd':
  ‘groc.fit’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) predict.Rd:30: Lost braces
    30 | resp. code{'exponential'} or \code{'no_lag'} for \code{fit_easylinear}.}
       |           ^
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Invalid package aliases in Rd file 'fit_grp.Rd':
  ‘grplasso-package’
checkRd: (-1) Birthwt.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Birthwt.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Birthwt.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Birthwt.Rd:21-22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Birthwt.Rd:26-28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Birthwt.Rd:29-31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Birthwt.Rd:32-33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Birthwt.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Birthwt.Rd:35-37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Birthwt.Rd:38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Birthwt.Rd:39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Birthwt.Rd:40-43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Lung.Rd:14-16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Lung.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Lung.Rd:18-19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Lung.Rd:23-24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Lung.Rd:25-27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Lung.Rd:28-30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Lung.Rd:31-33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Lung.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Lung.Rd:36-38: Lost braces in \itemize; meant \describe ?
Found the following files/directories:
  ‘p1_20up-vs-p2_25up_in_str1.txt’ ‘p1_20up-vs-p2_25up_in_str2.txt’
  ‘p2_25up-vs-p1_20up_in_str1.txt’ ‘p2_25up-vs-p1_20up_in_str2.txt’
  ‘s0_20up.txt’ ‘s0_30up.txt’ ‘s0_f2up.txt’ ‘strs.vec_01mx.txt’
  ‘strs.vec_02mx.txt’ ‘strs.vec_03mx.txt’ ‘strs.vec_04mx.txt’
  ‘strs.vec_05mx.txt’ ‘strs.vec_06mx.txt’ ‘strs.vec_30up.txt’
  ‘strs.vec_50up.txt’ ‘strs.vec_f2up.txt’ ‘uni_p1_20up-p2_25up.txt’
checkRd: (-1) matches.Rd:33: Lost braces; missing escapes or markup?
    33 | be set to an index value of \code{length+1}.  If {indexes=FALSE}, they will
       |                                                  ^
checkRd: (-1) runGRM.Rd:24: Lost braces
    24 |    from \code{\link{mirt}} or code{\linkS4class{lavaan}} from from
       |                                   ^
checkRd: (-1) GRS.Powerfunc.Rd:22: Lost braces
    22 | {Power: }{Matrix of power values plotted}
       |          ^
checkRd: (-1) fmddisc.Rd:23: Escaped LaTeX specials: \_
checkRd: (-1) schuster.Rd:46: Escaped LaTeX specials: \_
checkRd: (-1) schuster.Rd:54: Escaped LaTeX specials: \&
Found the following files/directories:
  ‘FMD mag discontinuities_disc.png’ ‘FMD mag
  discontinuities_disc1.res’ ‘FMD mag discontinuities_disc2.res’
  ‘IDYLLWILD_bvmed.png’ ‘IDYLLWILD_fig.png’ ‘Schuster's
  diagram_schu.png’ ‘hour.res’
checkRd: (-1) qdb.p.correct.Rd:14: Lost braces; missing escapes or markup?
    14 | \item{refpts}{a numeric vector used as a reference point to determine the correct side of the \code{qdb} for classifying \code{x}. The \code{length(refpts)} should be equal to {ncol(x)}. Default to \code{colMeans(x)}. }
       |                                                                                                                                                                                 ^
Objects in \usage without \alias in Rd file 'GSA.internal.Rd':
  ‘est.s0’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Invalid package aliases in Rd file 'gsb-package.Rd':
  ‘gsb-package’
checkRd: (-1) crossval.Rd:54: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) crossval.Rd:55: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) crossval.Rd:56: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) crossval.Rd:57: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) crossval.Rd:58: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) crossval.Rd:59: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gsbm_mcgd.Rd:57: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gsbm_mcgd.Rd:58: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gsbm_mcgd.Rd:59: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gsbm_mcgd.Rd:60: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gsbm_mcgd.Rd:61: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gsbm_mcgd.Rd:62: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gsbm_mcgd_parallel.Rd:57: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gsbm_mcgd_parallel.Rd:58: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gsbm_mcgd_parallel.Rd:59: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gsbm_mcgd_parallel.Rd:60: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gsbm_mcgd_parallel.Rd:61: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gsbm_mcgd_parallel.Rd:62: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) besselap.Rd:58: Lost braces
    58 | Thomas Sailer, email{t.sailer@alumni.ethz.ch}.\cr Conversion to R by
       |                     ^
checkRd: (-1) diric.Rd:25: Lost braces; missing escapes or markup?
    25 | evaluated at the elements of the input array {x}.
       |                                              ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) lisiecki2005.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) lisiecki2005.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) lisiecki2005.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) spratt2016.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) spratt2016.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) spratt2016.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) spratt2016.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) spratt2016.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) spratt2016.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) spratt2016.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) spratt2016.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) spratt2016.Rd:29: Lost braces in \itemize; meant \describe ?
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
checkRd: (-1) geneSelection.Rd:71: Lost braces; missing escapes or markup?
    71 | performs the vector magnitude in the [L_{p}] norm (as well as k powers
       |                                         ^
checkRd: (-1) lp_norm_k_powers_surv.Rd:35: Lost braces; missing escapes or markup?
    35 | the vector magnitude in the [L_{p}] norm (as well
       |                                ^
checkRd: (-1) jura.Rd:29: Lost braces; missing escapes or markup?
    29 | 	\item{Cd}{ mg cadmium kg^{-1} topsoil }
       |                                  ^
checkRd: (-1) jura.Rd:30: Lost braces; missing escapes or markup?
    30 | 	\item{Co}{ mg cobalt kg^{-1} topsoil }
       |                                 ^
checkRd: (-1) jura.Rd:31: Lost braces; missing escapes or markup?
    31 | 	\item{Cr}{ mg chromium kg^{-1} topsoil }
       |                                   ^
checkRd: (-1) jura.Rd:32: Lost braces; missing escapes or markup?
    32 | 	\item{Cu}{ mg copper kg^{-1} topsoil }
       |                                 ^
checkRd: (-1) jura.Rd:33: Lost braces; missing escapes or markup?
    33 | 	\item{Ni}{ mg nickel kg^{-1} topsoil }
       |                                 ^
checkRd: (-1) jura.Rd:34: Lost braces; missing escapes or markup?
    34 | 	\item{Pb}{ mg lead kg^{-1} topsoil }
       |                               ^
checkRd: (-1) jura.Rd:35: Lost braces; missing escapes or markup?
    35 | 	\item{Zn}{ mg zinc kg^{-1} topsoil }
       |                               ^
checkRd: (-1) variogramST.Rd:49: Lost braces; missing escapes or markup?
    49 |   time lag $t$, the pseudo cross variogram $(Z_i(s)-Z_{i+t}(s+h))^2$ is averaged over all time 
       |                                                       ^
checkRd: (-1) variogramST.Rd:50: Lost braces; missing escapes or markup?
    50 |   lagged observation sets $Z_i$ and $Z_{i+t}$ available (weighted by the number of pairs involved).
       |                                        ^
Specified C++11: please drop specification unless essential
checkRd: (-1) artset1987.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tumor.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tumor.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tumor.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gte.Rd:98: Lost braces; missing escapes or markup?
    98 | \code{left} and {right} for illustrative purpose), one would need a third variable (\code{status}) taking the value 0 
       |                 ^
checkRd: (-1) as_flex_table.Rd:24: Lost braces; missing escapes or markup?
    24 | A {flextable} object
       |   ^
checkRd: (-1) as_hux_table.Rd:37: Lost braces; missing escapes or markup?
    37 | A {huxtable} object
       |   ^
checkRd: (-1) as_kable_extra.Rd:42: Lost braces; missing escapes or markup?
    42 | and {kableExtra}; \code{as_kable_extra()} supports arguments in \code{knitr::kable()}.
       |     ^
checkRd: (-1) as_kable_extra.Rd:37: Lost braces; missing escapes or markup?
    37 | A {kableExtra} table
       |   ^
checkRd: (-1) select_helpers.Rd:53: Lost braces; missing escapes or markup?
    53 | Set of functions to supplement the {tidyselect} set of
       |                                    ^
checkRd: (-1) tbl_summary.Rd:91: Lost braces; missing escapes or markup?
    91 | from the \\{tidyselect\\} package and \\{gtsummary\\} package are available to
       |            ^
checkRd: (-1) tbl_summary.Rd:91: Lost braces; missing escapes or markup?
    91 | from the \\{tidyselect\\} package and \\{gtsummary\\} package are available to
       |                                         ^
checkRd: (-1) tbl_svysummary.Rd:183: Lost braces; missing escapes or markup?
   183 | from the \\{tidyselect\\} package and \\{gtsummary\\} package are available to
       |            ^
checkRd: (-1) tbl_svysummary.Rd:183: Lost braces; missing escapes or markup?
   183 | from the \\{tidyselect\\} package and \\{gtsummary\\} package are available to
       |                                         ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) PLSSVD.Rd:24: Lost braces; missing escapes or markup?
    24 | The number of low-dimension (k < {N, M, L}, Default: .minDim(X, Y))
       |                                  ^
checkRd: (-1) guidedPLS.Rd:33: Lost braces; missing escapes or markup?
    33 | The number of low-dimension (k < {N, M, L, O}, Default: .minDim(X1, X2, Y1, Y2))
       |                                  ^
checkRd: (-1) sPLSDA.Rd:24: Lost braces; missing escapes or markup?
    24 | The number of low-dimension (k < {N, M, L}, Default: .minDim(X, Y))
       |                                  ^
checkRd: (-1) guild_merge.Rd:38: Lost braces; missing escapes or markup?
    38 |     \item{\code{summary_name}}{Name used for the run summary. Use '${run_id}' in the name to include the run ID.}
       |                                                                     ^
checkRd: (-1) guild_merge_cli.Rd:88: Lost braces; missing escapes or markup?
    88 | \item{summary_name}{Name used for the run summary. Use '${run_id}' in the name to include the run ID.}
       |                                                          ^
Found the following files/directories:
  ‘RRprof.out’
checkRd: (-1) gumbel.Rd:65: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gumbel.Rd:66: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gumbel.Rd:67: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gumbel.Rd:73: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gumbel.Rd:74: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gumbel.Rd:75: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
checkRd: (-1) esSim.Rd:81: Lost braces; missing escapes or markup?
    81 | \eqn{83} SNPs are in cluster {-}, \eqn{714} SNPs are in cluster \eqn{0},
       |                              ^
checkRd: (-1) esSimDiffPriors.Rd:91: Lost braces; missing escapes or markup?
    91 | \eqn{64} SNPs are in cluster {-}, \eqn{708} SNPs are in cluster \eqn{0},
       |                              ^
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) get_Basin.Rd:19: Lost braces; missing escapes or markup?
    19 | looking at {nhdplusTools} as that has a lot of functionality and better documentation.
       |            ^
checkRd: (-1) get_basin_interactively.Rd:35: Lost braces; missing escapes or markup?
    35 | shiny app. It uses the {elevatr} package for DEM and {whitebox} package to delineate the watershed.
       |                        ^
checkRd: (-1) get_basin_interactively.Rd:35: Lost braces; missing escapes or markup?
    35 | shiny app. It uses the {elevatr} package for DEM and {whitebox} package to delineate the watershed.
       |                                                      ^
checkRd: (-1) gWidgets2tcltk-undocumented.Rd:285: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gWidgets2tcltk-undocumented.Rd:286-293: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gWidgets2tcltk-undocumented.Rd:378: Lost braces
   378 | \item{visible}{logical. If code{TRUE} window is drawn when
       |                                ^
'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: ‘rgeos’
Found the following files/directories:
  ‘testdata1.txt’ ‘testdata2.txt’ ‘testdata3.txt’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) h2o.cut.Rd:39: Lost braces
    39 | \item{right}{/code{Logical}, indicating if the intervals should be closed on the right (opened on the left) or vice
       |                   ^
checkRd: (-1) h2o.gam.Rd:95: Lost braces
    95 | {{'c1'},{'c2','c3'},{'c4'},...}}
       | ^
checkRd: (-1) h2o.gam.Rd:95: Lost braces; missing escapes or markup?
    95 | {{'c1'},{'c2','c3'},{'c4'},...}}
       |         ^
checkRd: (-1) h2o.gam.Rd:95: Lost braces; missing escapes or markup?
    95 | {{'c1'},{'c2','c3'},{'c4'},...}}
       |                     ^
checkRd: (-1) h2o.randomForest.Rd:160: Lost braces
   160 | \item{mtries}{Number of variables randomly sampled as candidates at each split. If set to -1, defaults to sqrt{p} for
       |                                                                                                               ^
checkRd: (-1) h2o.upliftRandomForest.Rd:86: Lost braces
    86 | \item{mtries}{Number of variables randomly sampled as candidates at each split. If set to -1, defaults to sqrt{p} for
       |                                                                                                               ^
checkRd: (-1) row_to_tree_assignment.H2OModel.Rd:37: Lost braces; missing escapes or markup?
    37 | Where 1 in the tree_{number} cols means row is used in the tree and 0 means that row is not used.
       |                     ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘.ga.breed’ ‘.ga.fitness’ ‘.ga.init’ ‘.ga.mutate’ ‘.ga.step’
  ‘.ga.weight’
'LazyData' is specified without a 'data' directory
Invalid package aliases in Rd file 'modeling-package.Rd':
  ‘modeling-package’
checkRd: (-1) HWAlr.Rd:25: Escaped LaTeX specials: \&
checkRd: (-1) HWAlrPlot.Rd:25: Escaped LaTeX specials: \&
checkRd: (-1) HWClr.Rd:23: Escaped LaTeX specials: \&
checkRd: (-1) HWClrPlot.Rd:25: Escaped LaTeX specials: \&
checkRd: (-1) HWIlr.Rd:30: Escaped LaTeX specials: \&
checkRd: (-1) HWPerm.Rd:37: Lost braces
    37 | Ziegler, A. & K\"{o}nig, I.R. (2006) A statistical approach to genetic
       |                  ^
checkRd: (-1) HWf.Rd:25: Escaped LaTeX specials: \&
Found the following significant warnings:
  HARDataCreationC.cpp:43:31: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated: use braced initialiser list instead [-Wdeprecated-declarations]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/HARModel.Rcheck/00install.out’ for details.
* used C++ compiler: ‘g++-13 (Debian 13.2.0-7) 13.2.0’
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
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Specified C++14: please drop specification unless essential
GNU make is a SystemRequirements.
checkRd: (-1) deff.sigma.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) deff.sigma.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) deff.sigma.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) deff.sigma.Rd:31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) deff.sigma.Rd:32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) deff.sigma.Rd:33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) deff.sigma.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) deff.sigma.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
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) phenowheat.Rd:18: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) phenowheat.Rd:19: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) hdda.Rd:121-123: Lost braces in \itemize; meant \describe ?
checkRd: (-1) hdda.Rd:124-127: Lost braces in \itemize; meant \describe ?
checkRd: (-1) hdda.Rd:128-132: Lost braces in \itemize; meant \describe ?
checkRd: (-1) hddc.Rd:162-164: Lost braces in \itemize; meant \describe ?
checkRd: (-1) hddc.Rd:165-168: Lost braces in \itemize; meant \describe ?
Found the following significant warnings:
  datatype_export.c:67:13: warning: ISO C does not support the 'I' printf flag [-Wformat=]
  datatype_export.c:67:22: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘hid_t’ {aka ‘long int’} [-Wformat=]
  convert.c:261:63: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘R_xlen_t’ {aka ‘long int’} [-Wformat=]
  convert.c:261:76: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘R_xlen_t’ {aka ‘long int’} [-Wformat=]
  Wrapper_manual_H5T.c:76:57: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘long long int’ [-Wformat=]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/hdf5r.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-13 (Debian 13.2.0-7) 13.2.0’
checkRd: (-1) H5File-class.Rd:202: Lost braces; missing escapes or markup?
   202 | \item{robj}{An R-object to take as a template for creating the dataset. Either \code{robj} or both \code{dtype} and {space}
       |                                                                                                                     ^
checkRd: (-1) H5Group-class.Rd:138: Lost braces; missing escapes or markup?
   138 | \item{robj}{An R-object to take as a template for creating the dataset. Either \code{robj} or both \code{dtype} and {space}
       |                                                                                                                     ^
checkRd: (-1) H5P_factory.Rd:5: Lost braces
     5 | \title{Create an \\code{\\link{H5P}} out of an id}
       |                        ^
checkRd: (-1) H5P_factory.Rd:5: Lost braces
     5 | \title{Create an \\code{\\link{H5P}} out of an id}
       |                               ^
checkRd: (-1) H5P_factory.Rd:16: Lost braces
    16 | Create an \\code{\\link{H5P}} out of an id
       |                 ^
checkRd: (-1) H5P_factory.Rd:16: Lost braces
    16 | Create an \\code{\\link{H5P}} out of an id
       |                        ^
checkRd: (-1) H5P_factory.Rd:13: Lost braces
    13 | An object of class \\code{\\link{H5P}}
       |                          ^
checkRd: (-1) H5P_factory.Rd:13: Lost braces
    13 | An object of class \\code{\\link{H5P}}
       |                                 ^
checkRd: (-1) args_regularity_evaluation.Rd:21: Lost braces
    21 | \code{needs_reshuffle}, code{reshuffle}, \code{result_dims_pre_shuffle}, \code{result_dims_post_shuffle}, \code{max_dims}
       |                             ^
Documented arguments not in \usage in Rd file 'check_arg_for_hyperslab_func.Rd':
  ‘cur_arg’

Documented arguments not in \usage in Rd file 'extract_dim.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
checkRd: (-1) lasso.proj.Rd:62: Lost braces; missing escapes or markup?
    62 |     indicated using an index vector with entries in {1,...,p} or a list thereof.}
       |                                                     ^
checkRd: (-1) lambdaCalculation.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) lambdaCalculation.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) lambdaCalculation.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) lambdaCalculation.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) lambdaCalculation.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rlasso.Rd:51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rlasso.Rd:52: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rlasso.Rd:53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rlasso.Rd:54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rlasso.Rd:55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fit_aenet.Rd:34: Lost braces; missing escapes or markup?
    34 | default is {FALSE}. To enable parallel tuning, load the
       |            ^
checkRd: (-1) fit_enet.Rd:33: Lost braces; missing escapes or markup?
    33 | default is {FALSE}. To enable parallel tuning, load the
       |            ^
checkRd: (-1) fit_flasso.Rd:46: Lost braces; missing escapes or markup?
    46 | default is {FALSE}. To enable parallel tuning, load the
       |            ^
checkRd: (-1) fit_mcp.Rd:38: Lost braces; missing escapes or markup?
    38 | default is {FALSE}. To enable parallel tuning, load the
       |            ^
checkRd: (-1) fit_mnet.Rd:41: Lost braces; missing escapes or markup?
    41 | default is {FALSE}. To enable parallel tuning, load the
       |            ^
checkRd: (-1) fit_scad.Rd:38: Lost braces; missing escapes or markup?
    38 | default is {FALSE}. To enable parallel tuning, load the
       |            ^
checkRd: (-1) fit_snet.Rd:41: Lost braces; missing escapes or markup?
    41 | default is {FALSE}. To enable parallel tuning, load the
       |            ^
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
checkRd: (-1) colByValue.Rd:20: Lost braces; missing escapes or markup?
    20 | \item{las}{numeric in {0,1,2,3}; the style of axis labels.}
       |                       ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) heatmaply.Rd:282: Lost braces
   282 | row and column dendrograms. The default uses stats{reorder.dendrogram}}
       |                                                   ^
checkRd: (-1) heatmapr.Rd:93: Lost braces
    93 | \item{reorderfun}{function(d, w) of dendrogram and weights for reordering the row and column dendrograms. The default uses stats{reorder.dendrogram}}
       |                                                                                                                                 ^
checkRd: (-1) is.plotly.Rd:16: Lost braces
    16 | Helpful for the plot_method in link{heatmaply}.
       |                                    ^
Specified C++11: please drop specification unless essential
checkRd: (-1) category.Rd:117-118: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) category.Rd:119-120: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) category.Rd:121: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) category.Rd:122-123: Lost braces in \enumerate; meant \describe ?
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'compute_counts.Rd':
  ‘init’ ‘inflow’

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

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

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

Documented arguments not in \usage in Rd file 'get_state_value_names.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
checkRd: (-1) duplicated_packages.Rd:19-22: Lost braces
    19 | if (nrow(li) != 0) {\cr
       |                    ^
checkRd: (-1) newcompassRose.Rd:54: Lost braces; missing escapes or markup?
    54 | modified from Jim Lemon; See compassRose {sp}
       |                                          ^
checkRd: (-1) newmap.scale.Rd:51: Lost braces; missing escapes or markup?
    51 | See map.scale {maps}
       |               ^
checkRd: (-1) symmetricize.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) symmetricize.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) symmetricize.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) symmetricize.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) symmetricize.Rd:22: Lost braces in \itemize; meant \describe ?
Specified C++11: please drop specification unless essential
checkRd: (-1) heplot.Rd:356: Lost braces
   356 | c("\\Sexpr[results=rd,stage=build]{tools:::Rd_expr_doi(\"#1\")}",
       |                                   ^
checkRd: (-1) heplots-package.Rd:76: Lost braces
    76 | c("\\Sexpr[results=rd,stage=build]{tools:::Rd_expr_doi(\"#1\")}",
       |                                   ^
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  MHproposal.c:24:49: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘long unsigned int’ [-Wformat=]
  MHproposal.c:37:54: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘long unsigned int’ [-Wformat=]
  changestats.c:1465:38: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘long unsigned int’ [-Wformat=]
  changestats.c:1517:34: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘long unsigned int’ [-Wformat=]
  h_ergm.c:1910:84: warning: format ‘%i’ expects a matching ‘int’ argument [-Wformat=]
  model.c:57:58: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘long unsigned int’ [-Wformat=]
  model.c:68:58: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘long unsigned int’ [-Wformat=]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/hergm.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-13 (Debian 13.2.0-7) 13.2.0’
* used C++ compiler: ‘g++-13 (Debian 13.2.0-7) 13.2.0’
checkRd: (-1) marker_h2.Rd:92: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) marker_h2.Rd:93: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) marker_h2.Rd:94: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) marker_h2.Rd:95: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) marker_h2.Rd:96-97: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) marker_h2.Rd:98: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) marker_h2.Rd:99: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) marker_h2_means.Rd:94: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) marker_h2_means.Rd:95: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) marker_h2_means.Rd:96: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) marker_h2_means.Rd:97: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) marker_h2_means.Rd:98-99: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) marker_h2_means.Rd:100: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) marker_h2_means.Rd:101: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) marker_h2_means.Rd:102: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) repeatability.Rd:38: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) repeatability.Rd:39: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) repeatability.Rd:40: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) repeatability.Rd:41-43: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) repeatability.Rd:44: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) repeatability.Rd:45: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) glm.hermite.Rd:46-48: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) glm.hermite.Rd:49-51: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) glm.hermite.Rd:52-54: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) glm.hermite.Rd:55-58: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) glm.hermite.Rd:59-60: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) glm.hermite.Rd:61-65: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) glm.hermite.Rd:66-67: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) glm.hermite.Rd:68-69: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) phermite.Rd:38: Lost braces; missing escapes or markup?
    38 |   {b} and \code{m} to be lower (or greater) than \code{q}.
       |   ^
GNU make is a SystemRequirements.
checkRd: (-1) hero.Rd:67-68: Lost braces
    67 | then \code{\link[pbapply]{pblapply}} is used. If code{package ==
       |                                                      ^
checkRd: (-1) hero.Rd:69: Lost braces
    69 | code{package == "Rmpi"}, then \code{\link[Rmpi]{mpi.applyLB}} is used.}
       |     ^
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in Rd file 'check.Rd':
  ‘inner_class’

Functions with \usage entries need to have the appropriate \alias
entries, and all their 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) mleHetGP.Rd:57: Lost braces; missing escapes or markup?
    57 | Level \code{2} gives more details. Level {3} additionaly displays all details about initialization of hyperparameters.
       |                                          ^
checkRd: (-1) mleHetTP.Rd:61: Lost braces; missing escapes or markup?
    61 | Level \code{2} gives more details. Level {3} additionaly displays all details about initialization of hyperparameters.
       |                                          ^
checkRd: (-1) mleHomTP.Rd:76: Lost braces; missing escapes or markup?
    76 | \item \code{nit_opt}, \code{msg}: \code{counts} and {msg} returned by \code{\link[stats]{optim}}
       |                                                     ^
checkRd: (-1) predictPair.Rd:20: Lost braces; missing escapes or markup?
    20 | A number in the set {-1, 0, 1}, where 1 means row1 is predicted to
       |                     ^
checkRd: (-1) predictPairInternal.Rd:18: Lost braces; missing escapes or markup?
    18 | A number in the set {-1, 0, 1}, where 1 means row1 is predicted to
       |                     ^
checkRd: (-1) search_repo_logo.Rd:25: Lost braces; missing escapes or markup?
    25 | look for, separated by |. {pkg_name} Can be used as a placeholder for
       |                           ^
Documented arguments not in \usage in Rd file 'check_known_repos.Rd':
  ‘known_packages’

Functions with \usage entries need to have the appropriate \alias
entries, and all their 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) ohio.Rd:104: Escaped LaTeX specials: \&
checkRd: (-1) ohio.Rd:105: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  rcpp_internals.cpp:65:34: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘Rcpp::traits::storage_type<14>::type’ {aka ‘double’} [-Wformat=]
  rcpp_internals.cpp:65:55: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘Rcpp::traits::storage_type<14>::type’ {aka ‘double’} [-Wformat=]
  rcpp_internals.cpp:65:80: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘Rcpp::traits::storage_type<14>::type’ {aka ‘double’} [-Wformat=]
  rcpp_internals.cpp:65:100: warning: format ‘%d’ expects argument of type ‘int’, but argument 5 has type ‘Rcpp::traits::storage_type<14>::type’ {aka ‘double’} [-Wformat=]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/HHG.Rcheck/00install.out’ for details.
* used C++ compiler: ‘g++-13 (Debian 13.2.0-7) 13.2.0’
Specified C++11: please drop specification unless essential
checkRd: (-1) hhg.univariate.nulltable.from.mstats.Rd:46: Lost braces
    46 |   \code{m.stats}{The input \code{m.stats} if \code{keep.simulation.data=TRUE}} 
       |                 ^
checkRd: (-1) hhg.univariate.nulltable.from.mstats.Rd:48: Lost braces
    48 |   \code{univariate.object}{A useful format of the null tables for computing p-values efficiently.}. 
       |                           ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) likertWeighted47.Rd:97: Lost braces; missing escapes or markup?
    97 |   used with \code{as.percent=TRUE}, the i^{th} stacked bar is 100\% wide
       |                                           ^
S3 methods shown with full name in Rd file 'HH-defunct.Rd':
  ‘anova.mean’ ‘print.glht.mmc.multicomp’ ‘coef.arima.HH’ ‘glht.mmc’
  ‘plot.odds.ratio’ ‘persp.plane’ ‘persp.floor’ ‘persp.back.wall.x’
  ‘persp.back.wall.y’ ‘persp.setup’ ‘plot.hov’ ‘plot.hov.bf’
  ‘plot.matchMMC’ ‘seqplot.forecast’

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 'residual.plots.lattice.Rd':
  ‘X’
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) read.VCF.Rd:21: Lost braces
    21 | Reads a \url{https://samtools.github.io/hts-specs/}{Variant Call Format (VCF)} file into a BED object,
       |                                                    ^
checkRd: (-1) hierNet.Rd:28: Lost braces; missing escapes or markup?
    28 |     terms, th_{jj}X_j^2, in the model.  Default TRUE.}
       |               ^
checkRd: (-1) hierNet.logistic.Rd:30: Lost braces; missing escapes or markup?
    30 |     terms, th_{jj}X_j^2, in the model.  Default TRUE.}  
       |               ^
checkRd: (-1) hierNet.logistic.Rd:63: Lost braces
    63 | \seealso{\link{predict.hierNet.logistic},link{hierNet.logistic.path}}
       |                                              ^
checkRd: (-1) hierNet.logistic.path.Rd:39: Lost braces; missing escapes or markup?
    39 |   terms, th_{jj}X_j^2, in the model.  Default TRUE.}
       |             ^
checkRd: (-1) hierNet.path.Rd:38: Lost braces; missing escapes or markup?
    38 |   terms, th_{jj}X_j^2, in the model.  Default TRUE.}
       |             ^
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘INLA’
checkRd: (-1) normplate.Rd:35: Lost braces
    35 |   Normalization method to be applied. Currenlty implemented methods include C-score (\eqn{cscore}), B-score (\eqn{bscore}), Z-score (eqn{zscore}) and no normalization (\eqn{raw}).
       |                                                                                                                                         ^
Argument items with no description in Rd file 'qcplate.Rd':
  ‘dat’
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘colorfulVennPlot’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rgdal’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Auto-generated content requiring editing in Rd file 'HistDAWass-package.Rd':
  \details: ‘...o use the package, including the most important functions ~~’
Invalid package aliases in Rd file 'histogram-package.Rd':
  ‘histogramtools-package’
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘trackr’
Package which this enhances but not available for checking: ‘HadoopStreaming’
Specified C++11: please drop specification unless essential
checkRd: (-1) hlt.Rd:64: Lost braces in \itemize; meant \describe ?
checkRd: (-1) hlt.Rd:65: Lost braces in \itemize; meant \describe ?
checkRd: (-1) hlt.Rd:66: Lost braces in \itemize; meant \describe ?
checkRd: (-1) hlt.Rd:67: Lost braces in \itemize; meant \describe ?
checkRd: (-1) hlt.Rd:68: Lost braces in \itemize; meant \describe ?
checkRd: (-1) hlt.Rd:77-78: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hlt.Rd:79: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hlt.Rd:80-81: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hlt.Rd:82: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hlt.Rd:83: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hltsim.Rd:31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hltsim.Rd:32: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hltsim.Rd:33: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hltsim.Rd:34: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hltsim.Rd:35: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hltsim.Rd:36: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hltsim.Rd:37: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hltsim.Rd:38: Lost braces in \itemize; \value handles \item{}{} directly
Specified C++11: please drop specification unless essential
html_describe_con: multiple local function definitions for ‘g’ with
  different formal arguments
checkRd: (-1) summaryP.Rd:29: Lost braces
    29 | 	\code{Hmisc::dotchartpl} with code{plotly} if \code{marginVal} is
       |                                           ^
checkRd: (-1) SimMarkovChain.Rd:18: Lost braces; missing escapes or markup?
    18 | starting from a state eta0 or the uniform distribution on {1,..., r}
       |                                                           ^
Documented arguments not in \usage in Rd file 'bootstrapfun.Rd':
  ‘DoF’ ‘n_sample’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
checkRd: (-1) nafracCalc.Rd:45: Lost braces
    45 |   as if code{y} were not of class \code{"multipleHmmDataSets"}.
       |             ^
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) hmmm.model.Rd:45: Lost braces; missing escapes or markup?
    45 | with categories k_1, k_2, the joint frequencies y = {y_ij}, where i=1,...,k_1, j=1,...,k_2, 
       |                                                     ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) disc42.Rd:28: Escaped LaTeX specials: \&
checkRd: (-1) discrimination.Rd:31: Escaped LaTeX specials: \&
checkRd: (-1) sampleMcmc.Rd:93: Lost braces; missing escapes or markup?
    93 |   disable some of them, by adding a \code{$UPDATER_NAME=FALSE} pair to the {updater} argument. Another usage of
       |                                                                            ^
Auto-generated content requiring editing in Rd file 'HMVD-package.Rd':
  \details: ‘...o use the package, including the most important functions ~~’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘glmmADMB’
Invalid package aliases in Rd file 'hoardeR-package.Rd':
  ‘R/hoardeR-package’
checkRd: (-1) HOasso.Rd:43: Lost braces; missing escapes or markup?
    43 | Arguments \code{x} and {y} are \code{character} objects and can assume values   \code{"sout"}, \code{"dout"}, \code{"lout"}, \code{"sin"}, \code{"din"}, \code{"lin"} representing the out-strength, out-degree, out-log-strength, in-strength, in-degree, and in-log-strength respectively.
       |                        ^
Argument items with no description in Rd file 'bid2.Rd':
  ‘numattable1’ ‘playerseats1’ ‘blinds1’ ‘dealer1’ ‘b3’ ‘b4’ ‘round1’
  ‘ntable1’ ‘decision1’
Argument items with no description in Rd file 'calcwin1.Rd':
  ‘numattable1’ ‘playerseats1’ ‘b3’ ‘b7’
Argument items with no description in Rd file 'mycount1.Rd':
  ‘x’
Argument items with no description in Rd file 'mygraphics1.Rd':
  ‘numattable1’ ‘playerseats1’ ‘chips1’ ‘blinds1’ ‘dealer1’ ‘b3’ ‘b4’
  ‘b5’ ‘b6’ ‘b7’ ‘chips2’ ‘ntable1’ ‘myfast1’ ‘chipstart1’ ‘name1’
  ‘lowercut1’
Argument items with no description in Rd file 'nothing1.Rd':
  ‘x’
Argument items with no description in Rd file 'onepair1.Rd':
  ‘x’
Argument items with no description in Rd file 'straight1.Rd':
  ‘x’
Argument items with no description in Rd file 'straightdraw1.Rd':
  ‘x’
Argument items with no description in Rd file 'strflsh1.Rd':
  ‘x’ ‘y’
Argument items with no description in Rd file 'trip1.Rd':
  ‘x’
Argument items with no description in Rd file 'twopair1.Rd':
  ‘x’
Argument items with no description in Rd file 'writebets1.Rd':
  ‘b9’ ‘y1’ ‘numattable1’ ‘b3’ ‘playerseats1’ ‘chips1’ ‘chips2’ ‘over1’
  ‘myfast1’ ‘name1’
Specified C++11: please drop specification unless essential
checkRd: (-1) hopit.control.Rd:46: Lost braces in \itemize; meant \describe ?
checkRd: (-1) hopit.control.Rd:47: Lost braces in \itemize; meant \describe ?
checkRd: (-1) hopit.control.Rd:48: Lost braces in \itemize; meant \describe ?
checkRd: (-1) hopit.control.Rd:49: Lost braces in \itemize; meant \describe ?
checkRd: (-1) hopit.control.Rd:50: Lost braces in \itemize; meant \describe ?
Documented arguments not in \usage in Rd file 'plot.hopitCP.Rd':
  ‘plotf’

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

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

Functions with \usage entries need to have the appropriate \alias
entries, and all their 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) hd.ord.Rd:43: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hd.ord.Rd:44: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hd.ord.Rd:45: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hd.ord.Rd:46: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hd.ord.Rd:47: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hd.ord.Rd:48: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hd.ord.Rd:49: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hd.ord.Rd:50: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hd.ord.Rd:51: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hd.ord.Rd:52: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hd.ord.Rd:53: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hd.ord.Rd:54: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hd.ord.Rd:55: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hd.ord.Rd:56: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hot.deck.Rd:39: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hot.deck.Rd:40: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hot.deck.Rd:41: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hot.deck.Rd:42: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hot.deck.Rd:43: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hot.deck.Rd:44: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) HPLB.Rd:33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) HPLB.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) HPLB.Rd:35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) HPLB.Rd:36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) HPLB.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) HPLB.Rd:38: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
Rd files without \alias:
  ‘hpoPlot-package.Rd’
Packages suggested but not available for checking: 'RGtk2', 'cairoDevice'
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in Rd file 'dot-E3.Rd':
  ‘i’ ‘M’

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
checkRd: (-1) genotypes.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) genotypes.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) map.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) map.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) map.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pedigree.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pedigree.Rd:13: Lost braces in \itemize; meant \describe ?
Argument items with no description in Rd file 'imageplot.Rd':
  ‘\dots’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Argument items with no description in Rd file 'FramedHTML.Rd':
  ‘DiagnosticsPath’
checkRd: (-1) BD_shift.Rd:67-73: Lost braces in \itemize; meant \describe ?
checkRd: (-1) BD_shift.Rd:74-77: Lost braces in \itemize; meant \describe ?
checkRd: (-1) BD_shift.Rd:78-82: Lost braces in \itemize; meant \describe ?
checkRd: (-1) BD_shift.Rd:83-87: Lost braces in \itemize; meant \describe ?
checkRd: (-1) data-physeq_rep3.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) data-physeq_rep3.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) data-physeq_rep3.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) data-physeq_rep3.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) data-physeq_rep3.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) data-physeq_rep3.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) heavy_SIP.Rd:69-71: Lost braces in \itemize; meant \describe ?
checkRd: (-1) heavy_SIP.Rd:72-75: Lost braces in \itemize; meant \describe ?
checkRd: (-1) heavy_SIP.Rd:76-79: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simplePostToHost.Rd:14: Escaped LaTeX specials: \&
Documented arguments not in \usage in Rd file 'as-redactor.Rd':
  ‘expr’

Functions with \usage entries need to have the appropriate \alias
entries, and all their 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
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'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.
       |                                                           ^
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘hurricaneexposuredata’
'LazyData' is specified without a 'data' directory
checkRd: (-1) simgl.Rd:50: Lost braces; missing escapes or markup?
    50 | Uses the {updog} R package for simulating read counts and generating
       |          ^
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
checkRd: (-1) ws_download.Rd:31: Lost braces; missing escapes or markup?
    31 | (while using the {hwsdr} package for HWSD v2.0).
       |                  ^
Package suggested but not available for checking: ‘microViz’
Invalid package aliases in Rd file 'HydroMe-package.Rd':
  ‘HydroMe2-package’
'LazyData' is specified without a 'data' directory
checkRd: (-1) extractPeriod.Rd:57: Lost braces
    57 | NOTE: all the dates in the datalist should follow the format in ?as.Date{base}.
       |                                                                         ^
checkRd: (-1) Ops.hyper2.Rd:48: Lost braces; missing escapes or markup?
    48 |   Idiom \code{H1-H1} returns {H1 + (-1)*H2}, useful for investigating
       |                              ^
checkRd: (-1) eurodance.Rd:37: Lost braces
    37 |     2009---{Wikipedia}{,} The Free Encyclopedia}, 2018,
       |                       ^
checkRd: (-1) eurovision.Rd:45: Lost braces
    45 |     2009---{Wikipedia}{,} The Free Encyclopedia}, 2018,
       |                       ^
checkRd: (-1) formula1.Rd:56: Lost braces
    56 |     Championship---{Wikipedia}{,} The Free Encyclopedia}, 2018.
       |                               ^
checkRd: (-1) pentathlon.Rd:30: Lost braces
    30 |     Summer Olympics - Men's}.  {Wikipedia}{,} The Free Encyclopedia,
       |                                           ^
Package suggested but not available for checking: ‘rgeos’
checkRd: (-1) extractreplace.Rd:36: Lost braces
    36 | \code{[[} and code{[[<-} accept indexing with logical matrix or a n by 2
       |                   ^
checkRd: (-1) palettes.Rd:25: Escaped LaTeX specials: \#
Documented arguments not in \usage in Rd file 'read.txt.Witec.Rd':
  ‘nwl’ ‘remove.zerospc’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
checkRd: (-1) hypervolume_set.Rd:42: Lost braces; missing escapes or markup?
    42 | By default, the function uses \code{check.memory=TRUE} which will provide an estimate of the computational cost of the set operations. The function should then be re-run with {check_memory=FALSE} if the cost is acceptable. This algorithm's memory and time cost scale quadratically with the number of input points, so large datasets can have disproportionately high costs. This error-checking is intended to prevent the user from large accidental memory allocation. 
       |                                                                                                                                                                                ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) IATData.Rd:24: Lost braces; missing escapes or markup?
    24 | Dan Martin {dpmartin42@gmail.com}
       |            ^
Objects in \usage without \alias in Rd file 'btibgen.Rd':
  ‘ibdgen’

Functions with \usage entries need to have the appropriate \alias
entries, and all their 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 'pairSum.Rd':
  ‘cov1’ ‘cov2’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘SparkR’
Specified C++11: please drop specification unless essential
checkRd: (-1) EW_popIMD_14.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) EW_popIMD_14.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) setServerLogLevel.Rd:20: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) setServerLogLevel.Rd:21: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) setServerLogLevel.Rd:22: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) setServerLogLevel.Rd:23: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) setServerLogLevel.Rd:24: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) betaS1lr.Rd:28: Lost braces; missing escapes or markup?
    28 |  \item{Rm1U}{matrix R^{-1}U (see reference).}
       |                       ^
checkRd: (-1) lrsmoother.Rd:32: Lost braces; missing escapes or markup?
    32 |   R^{-1}U (see reference) and \link{smoothCon} for the definition of smoothobject}
       |     ^
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'GetCustomKmerCounts.Rd':
  ‘custom.range’

Documented arguments not in \usage in Rd file 'GetMutationLoadsFromStrelkaIDVCFs.Rd':
  ‘list.of.vcfs’

Documented arguments not in \usage in Rd file 'GetMutationLoadsFromStrelkaSBSVCFs.Rd':
  ‘split.vcfs’

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

Documented arguments not in \usage in Rd file 'PlotPPMToPdf.Rd':
  ‘list.of.pwm’

Documented arguments not in \usage in Rd file 'ReadStrelkaSBSVCF.Rd':
  ‘suppress.discarded.variants.warnings’

Documented arguments not in \usage in Rd file 'ReadVCF.Rd':
  ‘num.of.cores’

Functions with \usage entries need to have the appropriate \alias
entries, and all their 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_p.Rd:29: Lost braces; missing escapes or markup?
    29 | \item A numeric p_norm, giving the factor between p_{gs} and phi_{0gs} (see paper for details).
       |                                                     ^
checkRd: (-1) get_p.Rd:29: Lost braces; missing escapes or markup?
    29 | \item A numeric p_norm, giving the factor between p_{gs} and phi_{0gs} (see paper for details).
       |                                                                  ^
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: ‘icd’
checkRd: (-1) ICEscale.Rd:53: Escaped LaTeX specials: \^
checkRd: (-1) dpwdg.Rd:14: Escaped LaTeX specials: \$
checkRd: (-1) dpwdg.Rd:15: Escaped LaTeX specials: \$
Found the following significant warnings:
  icenReg_files/basicUtilities.cpp:589:69: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wformat=]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/icenReg.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-13 (Debian 13.2.0-7) 13.2.0’
* used C++ compiler: ‘g++-13 (Debian 13.2.0-7) 13.2.0’
checkRd: (-1) getFitEsts.Rd:27: Lost braces; missing escapes or markup?
    27 | If \code{p} is provided, will return the estimated F^{-1}(p | x). If \code{q} is provided, 
       |                                                      ^
checkRd: (-1) Bpa.Rd:39-40: Lost braces
    39 | stocks. \doi{10.17895/ices.pub.3036}{\emph{ICES Advice
       |                                     ^
checkRd: (-1) Fpa.Rd:42-43: Lost braces
    42 | stocks. \doi{10.17895/ices.pub.3036}{\emph{ICES Advice
       |                                     ^
checkRd: (-1) icesRound.Rd:64-65: Lost braces
    64 | \doi{10.17895/ices.pub.3038}{\emph{ICES Advice Technical
       |                             ^
checkRd: (-1) mohn.Rd:71-72: Lost braces
    71 | \doi{10.17895/ices.pub.5997}{\emph{ICES Scientific Reports
       |                             ^
Specified C++11: please drop specification unless essential
checkRd: (-1) ic.ranks.Rd:46: Lost braces; missing escapes or markup?
    46 | \item{n_adjust}{an integer-valued entry for advanced control over the lower- or upper-bound algorithms. When the "adjustL" parameter is TRUE, the new value of n_adjust is chosen automatically as the best adjustment on the lower affine bound of the chi-square quantiles according to the data. If adjustU is TRUE, then n_adjust contains the point at which the upper affine bound is tangent on the chi-square quantiles. Possible values {1,...,n-1}. If both adjustL and adjustU variables are left FALSE, then the default choice is that the lower affine bound passes between the chi-square quantiles at 1 and n-1 degrees of freedom, and the upper affine bound is tangent on n-1.}
       |                                                                                                                                                                                                                                                                                                                                                                                                                                                  ^
Specified C++11: please drop specification unless essential
checkRd: (-1) data.Rd:7: Lost braces in \itemize; meant \describe ?
checkRd: (-1) data.Rd:8: Lost braces in \itemize; meant \describe ?
checkRd: (-1) data.Rd:9: 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: ‘rggobi’
'LazyData' is specified without a 'data' directory
Objects in \usage without \alias in Rd file 'pkg-internal.Rd':
  ‘iplotMain’ ‘segments.circle’ ‘griddat’

Functions with \usage entries need to have the appropriate \alias
entries, and all their 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 'pkg-internal.Rd':
  ‘plot.page’

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: ‘IFCdata’
'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) simHawkes1a.Rd:35: Lost braces; missing escapes or markup?
    35 | distribution; 'd${dis}' gives the density function \eqn{g(\cdot)}.}
       |                  ^
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) lab.qcs.Rd:24: Lost braces
    24 | It develops an object of \code{lab.qcs}-code{link{class}} to perform statistical quality control.
       |                                             ^
checkRd: (-1) lab.qcs.Rd:24: Lost braces
    24 | It develops an object of \code{lab.qcs}-code{link{class}} to perform statistical quality control.
       |                                                  ^
checkRd: (-1) define_target_function.Rd:41: Lost braces; missing escapes or markup?
    41 | be done either as a single vector of values (e.g. `function(x) { ... }`), or individual inputs for each parameter
       |                                                                ^
checkRd: (-1) define_target_function.Rd:42: Lost braces; missing escapes or markup?
    42 | (e.g. `function(x1, x2) { ... }`). If a single vector is used, all parameters will be passed to the target function as
       |                         ^
checkRd: (-1) image_contour_detector.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) image_contour_detector.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) image_contour_detector.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
Specified C++11: please drop specification unless essential
checkRd: (-1) fitSpline.Rd:109: Lost braces
   109 |        \code{response} and it will have the same order of code{x} as \code{data}. 
       |                                                               ^
checkRd: (-1) image_fhog.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) image_fhog.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) image_fhog.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) image_fhog.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) image_fhog.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) image_fhog.Rd:31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) image_surf.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) image_surf.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) image_surf.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) image_surf.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) image_surf.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) image_surf.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) image_surf.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) image_surf.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
Documented arguments not in \usage in Rd file 'dot-compl.Rd':
  ‘imgfile’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
checkRd: (-1) image_line_segment_detector.Rd:65: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) image_line_segment_detector.Rd:66-72: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) image_line_segment_detector.Rd:73-76: Lost braces in \itemize; \value handles \item{}{} directly
Specified C++11: please drop specification unless essential
checkRd: (-1) distance_transform.Rd:14: Lost braces; missing escapes or markup?
    14 | \item{metric}{Type of metric. Can be <tt>{ 0=Chebyshev | 1=Manhattan | 2=Euclidean | 3=Squared-euclidean }</tt>.}
       |                                          ^
checkRd: (-1) warp.Rd:14: Lost braces; missing escapes or markup?
    14 | \item{mode}{Can be { 0=backward-absolute | 1=backward-relative | 2=forward-absolute | 3=forward-relative }}
       |                    ^
checkRd: (-1) warp.Rd:16: Lost braces; missing escapes or markup?
    16 | \item{interpolation}{Can be <tt>{ 0=nearest | 1=linear | 2=cubic }</tt>.}
       |                                 ^
checkRd: (-1) warp.Rd:18: Lost braces; missing escapes or markup?
    18 | \item{boundary_conditions}{Boundary conditions. Can be <tt>{ 0=dirichlet | 1=neumann | 2=periodic }</tt>.}
       |                                                            ^
checkRd: (-1) imagesToKerasInput.Rd:23: Lost braces
    23 | \item{grayscale}{logical. Defines color channels of images: 1 if code{TRUE}, 3 if \code{FALSE}.}
       |                                                                      ^
'LazyData' is specified without a 'data' directory
Invalid package aliases in Rd file 'image-package.Rd':
  ‘image-package’
Specified C++11: please drop specification unless essential
checkRd: (-1) oversample.Rd:23-24: Lost braces
    23 | minority examples and majority ones, that is, the quotient {size of
       |                                                            ^
checkRd: (-1) oversample.Rd:24: Lost braces; missing escapes or markup?
    24 | minority class}/{size of majority class}. There are methods, such as
       |                 ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) plot.FeatureEffects.Rd:32: Lost braces; missing escapes or markup?
    32 | In contrast to other plot methods in {iml}, for FeatureEffects the returned
       |                                      ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) immer_proc_data.Rd:77: Lost braces
    77 | \code{A}{design matrix}
       |         ^
checkRd: (-1) immer_proc_data.Rd:78: Lost braces
    78 | \code{itemtable2}{Processed item table}
       |                  ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) stringCSSRule.Rd:22: Lost braces
    22 | using the {{placeholder}} convention.
       |           ^
checkRd: (-1) stringTemplate.Rd:23: Lost braces
    23 | placeholders are marked using the {{placeholder}} convention.
       |                                   ^
checkRd: (-1) stringTemplate.Rd:12: Lost braces
    12 | {{placeholder}} format.}
       | ^
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘accdata’
Documented arguments not in \usage in Rd file 'new_impactr_peaks.Rd':
  ‘acc_signal:’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
checkRd: (-1) impala_unnest.Rd:22-25: Lost braces
    22 | \describe{\code{impala_unnest()}}{ unnests a
       |                                  ^
'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) imptree_params.Rd:26-27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) imptree_params.Rd:28-29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) imptree_params.Rd:30-31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) predict.imptree.Rd:42: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) predict.imptree.Rd:43: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) predict.imptree.Rd:44: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) predict.imptree.Rd:45-46: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) predict.imptree.Rd:47-48: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) predict.imptree.Rd:49: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) predict.imptree.Rd:50: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) predict.imptree.Rd:51: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
Rd files without \alias:
  ‘imputeYn-package.Rd’
checkRd: (-1) kmpp.Rd:27: Lost braces
    27 |   \item{call}{a string containing the matched function call that generates this sQuote{inaparc} object.}
       |                                                                                       ^
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
checkRd: (-1) incidence.Rd:172: Lost braces; missing escapes or markup?
   172 | using the pattern "{n} {W} weeks" where "{W}" represents the weekday in an
       |                    ^
checkRd: (-1) incidence.Rd:172: Lost braces; missing escapes or markup?
   172 | using the pattern "{n} {W} weeks" where "{W}" represents the weekday in an
       |                        ^
checkRd: (-1) incidence.Rd:172: Lost braces; missing escapes or markup?
   172 | using the pattern "{n} {W} weeks" where "{W}" represents the weekday in an
       |                                          ^
checkRd: (-1) incidence.Rd:173: Lost braces; missing escapes or markup?
   173 | English or current locale and "{n}" represents the duration, but this can be
       |                                ^
checkRd: (-1) make_likelihood_matrix.Rd:16: Lost braces; missing escapes or markup?
    16 | This function creates a matrix such that P[t, s] = P(C = t | I = s) = theta_{t-s} for s <= t and 0 otherwise.
       |                                                                             ^
checkRd: (-1) IndexComp.Rd:69: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) IndexComp.Rd:70: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) IndexComp.Rd:71: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) IndexComp.Rd:72: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) IndexComp.Rd:73: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) IndexComp.Rd:74: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) IndexComp.Rd:78: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) IndexComp.Rd:79: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) IndexComp.Rd:80: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) IndexComp.Rd:81: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
checkRd: (-1) process_stats.Rd:11: Lost braces; missing escapes or markup?
    11 | the {janitor} package}
       |     ^
checkRd: (-1) theme_industRial.Rd:40: Lost braces; missing escapes or markup?
    40 | adapted from the package {cowplot} by Claus O.Wilke and reflects the principles
       |                          ^
checkRd: (-1) theme_industRial.Rd:45: Lost braces; missing escapes or markup?
    45 | It basically combines the half open theme with a grid background from {cowplot}
       |                                                                       ^
checkRd: (-1) vaccinesim.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) vaccinesim.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) vaccinesim.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) vaccinesim.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) vaccinesim.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) vaccinesim.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) voters.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) voters.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) voters.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) voters.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) voters.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) voters.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) voters.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) voters.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) voters.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) shade_confidence_interval.Rd:33: Lost braces; missing escapes or markup?
    33 | \item{...}{Other arguments passed along to \\{ggplot2\\} functions.}
       |                                              ^
checkRd: (-1) shade_confidence_interval.Rd:36: Lost braces; missing escapes or markup?
    36 | If added to an existing {infer} visualization, a \\{ggplot2\\}
       |                         ^
checkRd: (-1) shade_confidence_interval.Rd:36: Lost braces; missing escapes or markup?
    36 | If added to an existing {infer} visualization, a \\{ggplot2\\}
       |                                                    ^
checkRd: (-1) shade_p_value.Rd:31: Lost braces; missing escapes or markup?
    31 | \item{...}{Other arguments passed along to \\{ggplot2\\} functions.
       |                                              ^
checkRd: (-1) shade_p_value.Rd:35: Lost braces; missing escapes or markup?
    35 | If added to an existing {infer} visualization, a \\{ggplot2\\}
       |                         ^
checkRd: (-1) shade_p_value.Rd:35: Lost braces; missing escapes or markup?
    35 | If added to an existing {infer} visualization, a \\{ggplot2\\}
       |                                                    ^
checkRd: (-1) t_stat.Rd:46: Lost braces; missing escapes or markup?
    46 | \item{...}{Pass in arguments to \\{infer\\} functions.}
       |                                   ^
checkRd: (-1) visualize.Rd:30: Lost braces; missing escapes or markup?
    30 | \item{...}{Other arguments passed along to \\{ggplot2\\} functions.}
       |                                              ^
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) school23.Rd:30: Escaped LaTeX specials: \&
checkRd: (-1) school23.Rd:35: Escaped LaTeX specials: \&
Problems with news in ‘NEWS.md’:
No news entries found.
Package which this enhances but not available for checking: ‘gurobi’
Found the following files/directories:
  ‘c.txt’ ‘rho.txt’ ‘sta.txt’ ‘topo.txt’
checkRd: (-1) write_workflow.Rd:8: Lost braces
     8 | code{write_workflow} writes a workflow script for inference. Beyond possibly saving some typing, this suggests what may be a reasonably good starting workflow. One should not expect to control all options of the workflow through the \code{write_workflow} arguments.
       |     ^
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
Package suggested but not available for checking: ‘INLA’
Package suggested but not available for checking: ‘INLA’
Package suggested but not available for checking: ‘INLA’
checkRd: (-1) ar2precision.Rd:19: Lost braces; missing escapes or markup?
    19 | considering the specification stated in {details}.
       |                                         ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    INSPECTumours (development version)
checkRd: (-1) ask.user.yn.question.Rd:44: Lost braces; missing escapes or markup?
    44 | menu in the {utils} package, yesno in the {devtools} package.
       |             ^
checkRd: (-1) ask.user.yn.question.Rd:44: Lost braces; missing escapes or markup?
    44 | menu in the {utils} package, yesno in the {devtools} package.
       |                                           ^
checkRd: (-1) install.FFmpeg.Rd:25: Lost braces; missing escapes or markup?
    25 | This function is useful for saveVideo() in the {animation} package.
       |                                                ^
checkRd: (-1) install.SWFTools.Rd:27: Lost braces; missing escapes or markup?
    27 | This function is useful for saveSWF() in the {animation} package.
       |                                              ^
checkRd: (-1) os.shutdown.Rd:25: Lost braces; missing escapes or markup?
    25 | This function is a modified version of Yihui's shutdown function from the {fun} package.
       |                                                                           ^
Package suggested but not available for checking: ‘cmdstanr’
Malformed Title field: should not end in a period.
checkRd: (-1) model_performance.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) model_performance.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) model_performance.Rd:23: Lost braces in \itemize; meant \describe ?
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘Error_Estimation_Response_1.tiff’ ‘Error_Estimation_Response_2.tiff’
  ‘Error_Estimation_Response_3.tiff’
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
'LazyData' is specified without a 'data' directory
checkRd: (-1) remit.Rd:32: Lost braces
    32 | A data set to replicate the findings of Escrib\`{a}-Folch,
       |                                                 ^
checkRd: (-1) remit.Rd:38: Lost braces
    38 | Escrib\`{a}-Folch, A., Meseguer, C. and Wright, J. (2018), Remittances and Protest in Dictatorships. American Journal of Political Science, 62: 889-904. \doi{10.1111/ajps.12382}
       |         ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) interval-internal.Rd:40: Lost braces
    40 | \item{dqfunc}{function, density of the results of the quantile function, e.g., function(x){dnorm(qnorm(x))} (used for 'general' scores, 
       |                                                                                           ^
Auto-generated content requiring editing in Rd file 'IntervalSurgeon-package.Rd':
  \seealso: ‘Optional links to other man pages’
  \examples: ‘## Optional simple examples of the most important functions ...’
Specified C++11: please drop specification unless essential
checkRd: (-1) decompose_volume.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) decompose_volume.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) decompose_volume.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) decompose_volume.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) fit_volume.Rd:44: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) fit_volume.Rd:45: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) fit_volume.Rd:46: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) fit_volume.Rd:47: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) forecast_volume.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) forecast_volume.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) forecast_volume.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) forecast_volume.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) generate_plots.Rd:15: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) generate_plots.Rd:16: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) generate_plots.Rd:17: Lost braces in \itemize; \value handles \item{}{} directly
Argument items with no description in Rd file 'selectRuleRRF.Rd':
  ‘target’
checkRd: (-1) twonn.Rd:113: Lost braces
   113 | \item{\code{method = "bayes"}}{the output contains the {(1 + \code{alpha}) / 2}
       |                                                        ^
checkRd: (-1) twonn.Rd:114: Lost braces
   114 | and {(1 - \code{alpha}) / 2}
       |     ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) intRvals-package.Rd:60: Lost braces
    60 | B\'{e}dard, J. & Gauthier, G. 1986. Assessment of faecal output in geese. Journal of Applied Ecology, 23, 77-90.
       |    ^
checkRd: (-1) partition.Rd:64: Lost braces
    64 | Bates, D., M\"{a}chler, M., Bolker, B.M. & Walker, S.C. (2015). Fitting linear mixed-effects models using lme4. Journal of Statistical Software, 67, 1-48.
       |               ^
Package suggested but not available for checking: ‘INLA’
Package unavailable to check Rd xrefs: ‘INLA’
Specified C++11: please drop specification unless essential
checkRd: (-1) cox_cure_net.Rd:132: Lost braces
   132 | \code{surv_lambda} (or code{cure_lambda}) that produces all-zero
       |                            ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) computeAvgTotCost.Rd:42: Lost braces
    42 |  \item{\code{number_year_values}: the number of costs per year included}
       |       ^
checkRd: (-1) rawAvgCost-deprecated.Rd:95: Lost braces
    95 |  \item{\code{number_year_values}: the number of yearly costs included}
       |       ^
Documented arguments not in \usage in Rd file 'rawAvgCost-deprecated.Rd':
  ‘cost.transf’ ‘in.millions’ ‘confidence.interval’ ‘minimum.year’
  ‘maximum.year’ ‘final.year’ ‘incomplete.year.threshold’
  ‘incomplete.year.weights’ ‘gam.k’ ‘mars.nprune’ ‘...’

Functions with \usage entries need to have the appropriate \alias
entries, and all their 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) Inventorymodel-package.Rd:34: Lost braces
    34 | M.G. Fiestras-Janeiro, I. García-Jurado, A. Meca, M.A. Mosquera (2015). Cooperation on capacitated inventory situations with fixed holding costs. emph{European Journal of Operational Research}, \bold{241}(3), 719--726.
       |                                                                                                                                                       ^
Package suggested but not available for checking: ‘surveyspec’
checkRd: (-1) f.influence.Rd:25: Lost braces; missing escapes or markup?
    25 | where F is the field of influence, k is order of influence, l_{ij} is the ith row and jth column element of the Leontief Inverse and -s indicates the sth element has been removed.
       |                                                               ^
Specified C++11: please drop specification unless essential
checkRd: (-1) IOHproblem.Rd:31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) IOHproblem.Rd:32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) IOHproblem.Rd:33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) IOHproblem.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) IOHproblem.Rd:35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) IOHproblem.Rd:36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) IOHproblem.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) IOHproblem.Rd:38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) IOHproblem.Rd:39-40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) IOHproblem.Rd:44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) IOHproblem.Rd:45: Lost braces in \itemize; meant \describe ?
checkRd: (-1) IOHproblem.Rd:46-48: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) aiPux.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) aiPux.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) aiPux.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) aiPux.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) aiPux.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) aiPux.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) aiPuxComposite.Rd:34: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) aiPuxComposite.Rd:35: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) aiPuxComposite.Rd:36: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) aiPuxComposite.Rd:37: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) aiPuxComposite.Rd:38: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) aiPuxComposite.Rd:39: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dls2007.Rd:19: Lost braces
    19 | impact. emph{Journal of Applied Psychology}, 92(5), 1380.
       |             ^
checkRd: (-1) paretoXX.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) paretoXX.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) paretoXX.Rd:22-23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) paretoXY.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) paretoXY.Rd:30-31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) paretoXY.Rd:32-33: Lost braces in \itemize; \value handles \item{}{} directly
Documented arguments not in \usage in Rd file 'chars_collapse.Rd':
  ‘collapse’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
File ‘iotools/libs/iotools.so’:
  Found non-API calls to R: ‘R_GetConnection’, ‘R_ReadConnection’,
    ‘R_WriteConnection’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) check_convergence.Rd:47: Lost braces
    47 | \code{conv_plot}: code{ipm} invisibly.
       |                       ^
checkRd: (-1) init_ipm.Rd:50-51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) init_ipm.Rd:52-53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) init_ipm.Rd:57: Lost braces in \itemize; meant \describe ?
checkRd: (-1) init_ipm.Rd:58: Lost braces in \itemize; meant \describe ?
checkRd: (-1) init_ipm.Rd:62: Lost braces in \itemize; meant \describe ?
checkRd: (-1) init_ipm.Rd:63-65: Lost braces in \itemize; meant \describe ?
checkRd: (-1) init_ipm.Rd:70-74: Lost braces in \itemize; meant \describe ?
checkRd: (-1) init_ipm.Rd:75-78: Lost braces in \itemize; meant \describe ?
checkRd: (-1) make_ipm.Rd:276: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) make_ipm.Rd:277-281: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) make_ipm.Rd:282-286: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) make_ipm.Rd:287-291: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) make_ipm.Rd:292-293: Lost braces in \itemize; \value handles \item{}{} directly
Found the following significant warnings:
  templates/Rip-bsearch-template.c:889:18: warning: too many arguments for format [-Wformat-extra-args]
  Rip-match.c:467:13: warning: too many arguments for format [-Wformat-extra-args]
  Rip-match.c:1125:15: warning: too many arguments for format [-Wformat-extra-args]
  Rip-match.c:1173:13: warning: too many arguments for format [-Wformat-extra-args]
  Rip-match.c:1407:15: warning: too many arguments for format [-Wformat-extra-args]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/IP.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-13 (Debian 13.2.0-7) 13.2.0’
Invalid package aliases in Rd file 'iprior_package.Rd':
  ‘iprior_package-package’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) gblocks.Rd:30: Lost braces; missing escapes or markup?
    30 | the number of selected positions, i.e. are {more conservative}. Defaults to
       |                                            ^
Argument items with no description in Rd file 'mrbayes.Rd':
  ‘unlink’ ‘constraint’
Argument items with no description in Rd file 'mrbayes.lset.Rd':
  ‘partition’
Argument items with no description in Rd file 'multistate.Rd':
  ‘model’
checkRd: (-1) monty.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) monty.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) monty.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) irboost.Rd:62: Lost braces; missing escapes or markup?
    62 |   \item \code{weight_update_log} a matrix of \code{nobs} row by {iter}      column of observation weights in each iteration of the IRCO algorithm
       |                                                                 ^
checkRd: (-1) irboost.Rd:64: Lost braces
    64 |   \item\code{loss_log}{sum of loss value of the composite function \code{cfun(dfun)} in each IRCO iteration. Note, \code{cfun} requires \code{dfun} non-negative in some cases. Thus some \code{dfun} needs attentions. For instance, with \code{dfun="reg:gamma"}, the loss value is defined gamma-nloglik - (1+log(min(y))). The second term is introduced such that the loss value is non-negative. In fact, gamma-nloglik=y/ypre + log(ypre) in the \code{xgboost}, where ypre is the mean prediction value, can be negative. It can be derived that for fixed \code{y}, the minimum value of gamma-nloglik is achived at ypre=y, or 1+log(y). Thus, among all \code{y} values, the minimum of gamma-nloglik is 1+log(min(y)).}
       |                       ^
checkRd: (-1) irboost_aft.Rd:46: Lost braces; missing escapes or markup?
    46 |   \item \code{weight_update_log} a matrix of \code{nobs} row by {iter} column of observation weights in each iteration of the IRCO algorithm
       |                                                                 ^
checkRd: (-1) constrained.Rd:49: 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
checkRd: (-1) createBssUrl.Rd:28: Lost braces
    28 |     \code{constraint}{ a character string containing value constraints }
       |                      ^
checkRd: (-1) createBssUrl.Rd:29: Lost braces
    29 |     \code{url}{ optional url of the BSS measurements service }
       |               ^
checkRd: (-1) getGeneralValueMetrics.Rd:28: Lost braces
    28 |       \code{constraint}{ a character string containing value constraints }
       |                        ^
checkRd: (-1) getGeneralValueMetrics.Rd:29: Lost braces
    29 |       \code{url}{ optional url of the MUSTANG measurements service} 
       |                 ^
checkRd: (-1) getMustangMetrics.Rd:28: Lost braces
    28 |      \code{constraint}{ a character string containing value constraints }
       |                       ^
checkRd: (-1) getMustangMetrics.Rd:29: Lost braces
    29 |      \code{url}{ optional url of the MUSTANG measurements service }
       |                ^
checkRd: (-1) getTimeseries.Rd:30: Lost braces
    30 |      \code{processing}{optional character string with processing commands }
       |                       ^
checkRd: (-1) mergeTraces.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mergeTraces.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) psdStatistics.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) psdStatistics.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) psdStatistics.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) psdStatistics.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) psdStatistics.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) psdStatistics.Rd:31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) psdStatistics.Rd:32: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) psdStatistics.Rd:33: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) psdStatistics.Rd:34: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) psdStatistics.Rd:35: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) psdStatistics.Rd:36: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) psdStatistics.Rd:37: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) psdStatistics.Rd:38: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) partial_eigen.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) partial_eigen.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) prcomp_irlba.Rd:41-44: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) prcomp_irlba.Rd:45-46: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) prcomp_irlba.Rd:47-50: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) prcomp_irlba.Rd:51: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ssvd.Rd:52: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ssvd.Rd:53: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ssvd.Rd:54: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ssvd.Rd:55: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ssvd.Rd:56: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ssvd.Rd:57: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ssvd.Rd:58: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ssvd.Rd:59: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) bp.coeff.raw.Rd:5: Escaped LaTeX specials: \&
checkRd: (-1) bp.coeff.raw.Rd:41: Escaped LaTeX specials: \&
checkRd: (-1) bp.coeff.raw.Rd:53: Escaped LaTeX specials: \&
checkRd: (-1) fleiss.kappa.raw.Rd:52: Escaped LaTeX specials: \&
checkRd: (-1) landis.koch.bf.Rd:14: Escaped LaTeX specials: \&
checkRd: (-1) landis.koch.bf.Rd:17: Escaped LaTeX specials: \&
checkRd: (-1) ir_to_transmittance.Rd:49: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
checkRd: (-1) est_mg.Rd:284: Lost braces
   284 | item parameter estimates across the groups in the code{\link{est_mg}} function.
       |                                                       ^
checkRd: (-1) llike_score.Rd:22: Lost braces
    22 | function. See \code{\link{est_irt}}, \code{\link{irtfit}}, \\code{\link{info}},
       |                                                                  ^
Specified C++11: please drop specification unless essential
checkRd: (-1) Response-class.Rd:33: Lost braces
    33 | responses. For example, code{misc = list(item_role = c("O", "O", "O","F"))}
       |                             ^
checkRd: (-1) ks.Rd:38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ks.Rd:39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ks.Rd:40-41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ks.Rd:42-44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ks.Rd:62: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ks.Rd:63-65: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ks.Rd:66-67: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ks.Rd:68-69: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ks.Rd:70: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) plot.cat_output.Rd:36-37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.cat_output.Rd:38-39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.cat_output.Rd:40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) response.Rd:39: Lost braces
    39 | responses. For example, code{misc = list(item_role = c("O", "O", "O","F"))}
       |                             ^
Documented arguments not in \usage in Rd file 'print.cat_output.Rd':
  ‘object’

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

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

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

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

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) analyseISE.Rd:66: Lost braces; missing escapes or markup?
    66 | 	False positive rate used for detection threshold (not output) to calculate LOD(alpha, beta) {only returned if SN = NA}
       |                                                                                                     ^
checkRd: (-1) analyseISE.Rd:69: Lost braces; missing escapes or markup?
    69 | 	False negative rate used to calculate LOD(alpha, beta) {only returned if SN = NA}
       |                                                                ^
checkRd: (-1) describeISE.Rd:71: Lost braces; missing escapes or markup?
    71 | 	False positive rate used for detection threshold (not output) to calculate LOD(alpha, beta) {only returned if SN = NA}
       |                                                                                                     ^
checkRd: (-1) describeISE.Rd:74: Lost braces; missing escapes or markup?
    74 | 	False negative rate used to calculate LOD(alpha, beta) {only returned if SN = NA}
       |                                                                ^
Objects in \usage without \alias in Rd file 'islasso-internal.Rd':
  ‘modelX’ ‘.checkinput’ ‘.startpoint’ ‘.islasso’
  ‘checkinput.islasso.path’ ‘startpoint.islasso.path’
  ‘islasso.path.fit.glm’ ‘islasso.path.fitter2’ ‘interpolate’ ‘makeHyp’
  ‘printHyp’ ‘cislasso’ ‘ci.fitted.islasso’

Functions with \usage entries need to have the appropriate \alias
entries, and all their 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
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in Rd file 'dot-assignmentMaker.Rd':
  ‘.precip_raster’ ‘.precip_SD_raster’

Functions with \usage entries need to have the appropriate \alias
entries, and all their 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) CLM.Rd:30: Lost braces
    30 | item{tau0}{the mean circular Kendall Tau of the initial order with the data.}
       |     ^
checkRd: (-1) CLM.Rd:30: Lost braces
    30 | item{tau0}{the mean circular Kendall Tau of the initial order with the data.}
       |           ^
checkRd: (-1) ISOpureS1.model_optimize.kappa.kappa_deriv_loglikelihood.Rd:9: Escaped LaTeX specials: \$
checkRd: (-1) ISOpureS1.model_optimize.kappa.kappa_deriv_loglikelihood.Rd:14: Escaped LaTeX specials: \$
checkRd: (-1) ISOpureS1.model_optimize.kappa.kappa_loglikelihood.Rd:11: Escaped LaTeX specials: \$
checkRd: (-1) ISOpureS2.model_optimize.kappa.kappa_deriv_loglikelihood.Rd:11: Escaped LaTeX specials: \$
checkRd: (-1) ISOpureS2.model_optimize.kappa.kappa_loglikelihood.Rd:11: Escaped LaTeX specials: \$
Specified C++14: please drop specification unless essential
checkRd: (-1) run_mcmc.Rd:61: Lost braces; missing escapes or markup?
    61 |   object of class \code{networkModelStanfit} and {mcmc.list}, which still
       |                                                  ^
GNU make is a SystemRequirements.
checkRd: (-1) is_israd_database.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) is_israd_database.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) is_israd_database.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) is_israd_database.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) is_israd_database.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) is_israd_database.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) is_israd_database.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) is_israd_database.Rd:26: Lost braces in \itemize; meant \describe ?
Found the following files/directories:
  ‘RMTplot.pdf’
checkRd: (-1) secretin.Rd:17: Lost braces
    17 |       {\code{a}: 1st sample};
       |       ^
checkRd: (-1) secretin.Rd:18: Lost braces
    18 |       {\code{b}: 2nd sample}.}
       |       ^
checkRd: (-1) secretin.Rd:20: Lost braces
    20 |       {\code{20+}: 20 minutes or longer since injection};
       |       ^
checkRd: (-1) secretin.Rd:21: Lost braces
    21 |       {\code{pre}: before injection.}}
       |       ^
checkRd: (-1) secretin.Rd:23: Lost braces
    23 |       {\code{20}:  20 minutes since injection};
       |       ^
checkRd: (-1) secretin.Rd:24: Lost braces
    24 |       {\code{30+}: 30 minutes or longer since injection};
       |       ^
checkRd: (-1) secretin.Rd:25: Lost braces
    25 |       {\code{pre}: before injection.  }}
       |       ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘gurobi’
Package suggested but not available for checking: ‘locClass’
Packages suggested but not available for checking: 'gurobi', 'cplexAPI'
checkRd: (-1) sTsls.Rd:17: Lost braces; missing escapes or markup?
    17 | \item{pi}{the matrix E[XZ']E[ZZ']^{-1}}
       |                                   ^
checkRd: (-1) sTslsSplines.Rd:20: Lost braces; missing escapes or markup?
    20 | \item{pi}{matrix, corresponds to E[XZ']E[ZZ']^{-1}, the first stage
       |                                               ^
Invalid package aliases in Rd file 'ivprobit-package.Rd':
  ‘ivProbit-package’
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) jaccard.test.Rd:41: Lost braces; missing escapes or markup?
    41 | The {bootstrap} method uses resampling with replacement binary vectors to compute a p-value (see optional arguments).
       |     ^
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Rd files without \alias:
  ‘jackknifeKME-package.Rd’
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Found the following Makefile(s) with an include directive with a pathname using R_HOME:
  src/jvm-w32/Makefile
Even though not recommended, variable R_HOME may contain spaces.
Makefile directives use space as a separator and there is no portable
way to quote/escape the space in Make rules and directives.  However,
one can and should quote pathnames when passed from Makefile to the
shell, and this can be done specifically when invoking Make recursively.
It is therefore recommended to use the Make '-f' option to include files
in directories specified using R_HOME.  This option can be specified
multiple times to include multiple Makefiles.  Note that 'Makeconf' is
included automatically into top-level makefile of a package.
More information can be found in 'Writing R Extensions'.
File ‘JavaGD/libs/JavaGD.so’:
  Found ‘__sprintf_chk’, possibly from ‘sprintf’ (C)
    Object: ‘jGDtalk.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
checkRd: (-1) model_fairness.Rd:116-118: Lost braces in \itemize; meant \describe ?
checkRd: (-1) model_fairness.Rd:119-121: Lost braces in \itemize; meant \describe ?
checkRd: (-1) model_fairness.Rd:122-123: Lost braces in \itemize; meant \describe ?
checkRd: (-1) model_fairness.Rd:124-126: Lost braces in \itemize; meant \describe ?
checkRd: (-1) model_fairness.Rd:127-129: Lost braces in \itemize; meant \describe ?
checkRd: (-1) model_fairness.Rd:130-132: Lost braces in \itemize; meant \describe ?
checkRd: (-1) model_fairness.Rd:133-135: Lost braces in \itemize; meant \describe ?
checkRd: (-1) model_fairness.Rd:136-137: Lost braces in \itemize; meant \describe ?
checkRd: (-1) model_fairness.Rd:138-139: Lost braces in \itemize; meant \describe ?
GNU make is a SystemRequirements.
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
checkRd: (-1) data_timeinv.Rd:14: Lost braces; missing escapes or markup?
    14 | \item{X5}{categorical covariate taking values from {1, 2, 3, 4, 5}; time-invariant}
       |                                                    ^
checkRd: (-1) data_timeinv.Rd:18: Lost braces; missing escapes or markup?
    18 | \item{g}{true latent class identifier {1, 2, 3, 4}, which is determined by 
       |                                       ^
checkRd: (-1) data_timevar.Rd:15: Lost braces; missing escapes or markup?
    15 | \item{X5}{categorical covariate taking values from {1, 2, 3, 4, 5}; time-varying}
       |                                                    ^
checkRd: (-1) data_timevar.Rd:20: Lost braces; missing escapes or markup?
    20 | \item{g}{true latent class identifier {1, 2, 3, 4}, which is determined by 
       |                                       ^
checkRd: (-1) jointLPM.Rd:298: Lost braces; missing escapes or markup?
   298 | following transformation b_1 + b_2*I_1(Y(t)) + ... + b_{n+2}*I_{n+1}(Y(t)),
       |                                                        ^
checkRd: (-1) jointLPM.Rd:298: Lost braces; missing escapes or markup?
   298 | following transformation b_1 + b_2*I_1(Y(t)) + ... + b_{n+2}*I_{n+1}(Y(t)),
       |                                                                ^
checkRd: (-1) jointLPM.Rd:299: Lost braces; missing escapes or markup?
   299 | where I_1,...,I_{n+1} is the basis of quadratic I-splines. To constraint the
       |                 ^
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
checkRd: (-1) jmdem.control.Rd:42: Lost braces; missing escapes or markup?
    42 |     The control argument of \code{jmdem} is by default passed to the control argument of {jmdem.fit}, which uses its elements as arguments to {jmdem.control}: the latter provides defaults and sanity checking.
       |                                                                                          ^
checkRd: (-1) jmdem.control.Rd:42: Lost braces; missing escapes or markup?
    42 |     The control argument of \code{jmdem} is by default passed to the control argument of {jmdem.fit}, which uses its elements as arguments to {jmdem.control}: the latter provides defaults and sanity checking.
       |                                                                                                                                               ^
'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
Specified C++11: please drop specification unless essential
Package which this enhances but not available for checking: ‘remMap’
checkRd: (-1) JointAIObject.Rd:72: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) JointAIObject.Rd:73: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) JointAIObject.Rd:74: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) JointAIObject.Rd:75: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) JointAIObject.Rd:76: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) JointAIObject.Rd:77: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) JointAIObject.Rd:78-79: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) model_imp.Rd:579: Lost braces
   579 | code{D_main} (for multi-level models) and
       |     ^
Documented arguments not in \usage in Rd file 'paste_coef.Rd':
  ‘parlemts’

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

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) jrt.Rd:45-46: Lost braces
    45 | \item{Difference models (more or less constrained versions of the
       |      ^
checkRd: (-1) jrt.Rd:54-55: Lost braces
    54 |  \item{Divide-by-total models (more or less constrained versions of the
       |       ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) jSDM_binomial_probit_long_format.Rd:45: Lost braces
    45 | \code{species} \tab numeric or character eqn{n_{obs}}{n_obs}-length vector indicating the species observed, \cr 
       |                                             ^
checkRd: (-1) jSDM_binomial_probit_long_format.Rd:45: Lost braces; missing escapes or markup?
    45 | \code{species} \tab numeric or character eqn{n_{obs}}{n_obs}-length vector indicating the species observed, \cr 
       |                                                ^
checkRd: (-1) jSDM_binomial_probit_long_format.Rd:45: Lost braces
    45 | \code{species} \tab numeric or character eqn{n_{obs}}{n_obs}-length vector indicating the species observed, \cr 
       |                                                      ^
checkRd: (-1) compute_indirect_effect_for.Rd:47: Lost braces; missing escapes or markup?
    47 | Thanks to the returned values of \eqn{a}{a} and {b}{b} (\eqn{b_51}{b_51}
       |                                                 ^
checkRd: (-1) compute_indirect_effect_for.Rd:47: Lost braces
    47 | Thanks to the returned values of \eqn{a}{a} and {b}{b} (\eqn{b_51}{b_51}
       |                                                    ^
checkRd: (-1) mdt_simple.Rd:64: Lost braces; missing escapes or markup?
    64 | through {M} (see Models section).
       |         ^
checkRd: (-1) mdt_within.Rd:76: Lost braces; missing escapes or markup?
    76 | through {M} (see Models section).
       |         ^
checkRd: (-1) mdt_within_wide.Rd:73: Lost braces; missing escapes or markup?
    73 | through {M} (see Models section).
       |         ^
'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) export_summs.Rd:26: Lost braces; missing escapes or markup?
    26 | Default: "({std.error})"}
       |            ^
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    pre-release juicr (2017 - 2021)
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
Rd files without \alias:
  ‘karaoke-package.Rd’
Found the following files/directories:
  ‘song.wav’ ‘song4karaoke.wav’
checkRd: (-1) get.fit.Rd:46: Lost braces in \itemize; meant \describe ?
checkRd: (-1) get.fit.Rd:47: Lost braces in \itemize; meant \describe ?
checkRd: (-1) get.fit.Rd:48-49: Lost braces in \itemize; meant \describe ?
checkRd: (-1) get.fit.Rd:50-51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) get.fit.Rd:52-54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) get.fit.Rd:55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) get.fit.Rd:56: Lost braces in \itemize; meant \describe ?
checkRd: (-1) get.fit.Rd:57-60: Lost braces in \itemize; meant \describe ?
checkRd: (-1) get.fit.Rd:61-62: Lost braces in \itemize; meant \describe ?
checkRd: (-1) get.fit.Rd:63-64: Lost braces in \itemize; meant \describe ?
checkRd: (-1) get.fit.Rd:70: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get.fit.Rd:71: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get.fit.Rd:72: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get.fit.Rd:73: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get.fit.Rd:74: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get.fit.Rd:75: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get.fit.Rd:76: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get.fit.Rd:77: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get.fit.Rd:78: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get.fit.Rd:79: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get.fit.Rd:80: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get.sim.trajectories.Rd:66: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get.sim.trajectories.Rd:67: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) kdist.Rd:14: Lost braces; missing escapes or markup?
    14 | The {kdist} functions dk, pk, qk and rk, calculates the K-distribution
       |     ^
'LazyData' is specified without a 'data' directory
prepare_Rd: NEWS.Rd:58: Dropping empty section ‘kelvin INITIAL VERSION 1.0-0 (2012-05-30)’
'LazyData' is specified without a 'data' directory
checkRd: (-1) image_load.Rd:20: Lost braces
    20 | \item{color_mode}{One of {\code{"grayscale"}, \code{"rgb"}, \code{"rgba"}}.
       |                          ^
checkRd: (-1) k_placeholder.Rd:19: Lost braces
    19 | \item{ndim}{Number of axes of the tensor. At least one of {\code{shape}, \code{ndim}}
       |                                                           ^
checkRd: (-1) metric_auc.Rd:40: Lost braces; missing escapes or markup?
    40 | to {-epsilon, 1+epsilon} for a small positive epsilon value will be
       |    ^
checkRd: (-1) checkGrad.Rd:73-75: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) checkGrad.Rd:77-79: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) checkGrad.Rd:81-85: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) plot.gp.Rd:48: Lost braces; missing escapes or markup?
    48 |     A subset of {1, 2, 3} indicating which figures to plot (see
       |                 ^
checkRd: (-1) prinKrige.Rd:21-26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) prinKrige.Rd:27-32: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) prinKrige.Rd:33-37: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simulate.gp.Rd:104-105: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simulate.gp.Rd:106: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simulate.gp.Rd:107: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simulate.gp.Rd:108: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simulate.gp.Rd:109-110: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simulate.gp.Rd:110: Lost braces in \itemize; \value handles \item{}{} directly
Argument items with no description in Rd file 'covQualNested.Rd':
  ‘covBet’
checkRd: (-1) kernelFactory.Rd:21: Lost braces; missing escapes or markup?
    21 | \item{method}{Can be one of the following: POLynomial kernel function (\code{pol}), LINear kernel function (\code{lin}), Radial Basis kernel Function \code{rbf}), random choice (random={pol, lin, rbf}) (\code{random}), burn- in choice of best function (burn={pol, lin, rbf }) (\code{burn}). Use \code{random} or \code{burn} if you don't know in advance which kernel function is best.}
       |                                                                                                                                                                                          ^
checkRd: (-1) kernelFactory.Rd:21: Lost braces; missing escapes or markup?
    21 | \item{method}{Can be one of the following: POLynomial kernel function (\code{pol}), LINear kernel function (\code{lin}), Radial Basis kernel Function \code{rbf}), random choice (random={pol, lin, rbf}) (\code{random}), burn- in choice of best function (burn={pol, lin, rbf }) (\code{burn}). Use \code{random} or \code{burn} if you don't know in advance which kernel function is best.}
       |                                                                                                                                                                                                                                                                   ^
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) ipop-class.Rd:28: Lost braces
    28 |   \item{primal}{Object of class \code{ipop}}{Return the primal of the problem}
       |                                             ^
checkRd: (-1) ipop-class.Rd:29: Lost braces
    29 |   \item{dual}{Object of class \code{ipop}}{Return the dual of the problem}
       |                                           ^
checkRd: (-1) ipop-class.Rd:30: Lost braces
    30 |   \item{how}{Object of class \code{ipop}}{Return information on convergence}
       |                                          ^
checkRd: (-1) compute_all_tests.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) compute_all_tests.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) compute_all_tests.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) compute_all_tests.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) compute_all_tests.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) compute_all_tests.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) compute_all_tests.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) compute_all_tests.Rd:58: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) compute_all_tests.Rd:59: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) compute_all_tests.Rd:60: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) compute_all_tests.Rd:61: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) compute_all_tests.Rd:62: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) compute_all_tests.Rd:64: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) compute_all_tests.Rd:65-66: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sim_SCR_data.Rd:43: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sim_SCR_data.Rd:44: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sim_SCR_data.Rd:45: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sim_SCR_data.Rd:46: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sim_SCR_data.Rd:47: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sim_SCR_data.Rd:48: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sim_SCR_data.Rd:49: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) subjOCCDIF.Rd:23: Lost braces
    23 | the scale on which to evaluate each subject. \code{stype = "ObsScore"} uses the subject's total score. \code{stype = "Theta"} uses the subject's rank on the \code{thetadist} scale. \code{stype = "ThetaML"} uses the maximum likelihood estimate for the subject on the \code{thetadist} scale. code{stype = "ScoreML"} uses the maximum likelihood estimate for the subject on the overall test score scale.
       |                                                                                                                                                                                                                                                                                                       ^
S3 methods shown with full name in Rd file 'bw.abram.temp.Rd':
  ‘bw.abram.temp’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Documented arguments not in \usage in Rd file 'calc_PGtheta_R.Rd':
  ‘model’ ‘iter’

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

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

Functions with \usage entries need to have the appropriate \alias
entries, and all their 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) useKeys.Rd:13: Lost braces; missing escapes or markup?
    13 | This function adds the {keys} dependencies to your application
       |                        ^
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Minor Changes
checkRd: (-1) kfda.Rd:26: Lost braces
    26 |  \item{kpca.train}{An object of class "kpca". It has results of \code{kpca} function. (see{\code{\link[kernlab]{kpca}}} (in package \pkg{kernlab}))}
       |                                                                                           ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) kfino_plot.Rd:52: Lost braces; missing escapes or markup?
    52 |        plus the OK values. Prediction corresponds to E[X_{t} | Y_{1...t}] 
       |                                                          ^
checkRd: (-1) kfino_plot.Rd:52: Lost braces; missing escapes or markup?
    52 |        plus the OK values. Prediction corresponds to E[X_{t} | Y_{1...t}] 
       |                                                                  ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) mount_appdata.Rd:10: Lost braces; missing escapes or markup?
    10 | \item{x}{An object of class \code{KinPairData} or {KinPairSimulation}}
       |                                                   ^
checkRd: (-1) plot.pedigree.Rd:119: Lost braces; missing escapes or markup?
   119 |         {sum(x- mean(p))^2/(k^a)}
       |         ^
checkRd: (-1) Kira-package.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Kira-package.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Kira-package.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Kira-package.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) kissmig.Rd:32: Lost braces
    32 | migration in species distribution models (\doi{10.1111/ecog.00930}{Nobis and Normand 2014}).
       |                                                                   ^
checkRd: (-1) kissmig.Rd:86: Lost braces
    86 | \item{\doi{10.1111/ecog.00930}{Nobis MP and Normand S (2014)} KISSMig - a simple model for R to account for
       |                               ^
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘rkward’
checkRd: (-1) klausuR.answ-class.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) klausuR.answ-class.Rd:18-22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) klausuR.answ-class.Rd:23-24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) klausuR.answ-class.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) klausuR.answ-class.Rd:35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) klausuR.answ-class.Rd:36-37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) klausur.Rd:107-109: Lost braces in \itemize; meant \describe ?
checkRd: (-1) klausur.Rd:110-111: Lost braces in \itemize; meant \describe ?
checkRd: (-1) klausur.Rd:112-113: Lost braces in \itemize; meant \describe ?
checkRd: (-1) klausur.Rd:114-116: Lost braces in \itemize; meant \describe ?
checkRd: (-1) klausur.Rd:117-118: Lost braces in \itemize; meant \describe ?
checkRd: (-1) klausur.Rd:119-120: Lost braces in \itemize; meant \describe ?
checkRd: (-1) klausur.Rd:121-123: Lost braces in \itemize; meant \describe ?
checkRd: (-1) klausur.Rd:124-126: Lost braces in \itemize; meant \describe ?
checkRd: (-1) klausur.Rd:147: Lost braces in \itemize; meant \describe ?
checkRd: (-1) klausur.Rd:148: Lost braces in \itemize; meant \describe ?
checkRd: (-1) klausur.Rd:149: Lost braces in \itemize; meant \describe ?
checkRd: (-1) klausur.Rd:150: Lost braces in \itemize; meant \describe ?
checkRd: (-1) klausur.Rd:151: Lost braces in \itemize; meant \describe ?
checkRd: (-1) klausur.Rd:152-155: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) plotkmc.Rd:21: Lost braces; missing escapes or markup?
    21 |     list of two functions,flist=list( f1=function( x ) { x } ,f2=function( x ) { x^2 } )  
       |                                                        ^
checkRd: (-1) plotkmc.Rd:21: Lost braces; missing escapes or markup?
    21 |     list of two functions,flist=list( f1=function( x ) { x } ,f2=function( x ) { x^2 } )  
       |                                                                                ^
checkRd: (-1) Kmedians.Rd:17: Lost braces
    17 | \item{method}{The selected method for the K-medians algorithm. Can be \code{'Offline'} (default), code{'Semi-Online'} or \code{'Online'}.}
       |                                                                                                       ^
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) sampl.mcmc.Rd:20: Lost braces; missing escapes or markup?
    20 | a matrix of {0, 1} with each row representing a sample
       |             ^
S3 methods shown with full name in Rd file 'unlist.constr.Rd':
  ‘unlist.constr’

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
Package suggested but not available for checking: ‘maptools’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘Killed after ’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) knockoff.Rd:22-24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) knockoff.Rd:25-27: Lost braces in \itemize; meant \describe ?
Invalid package aliases in Rd file 'knotR-package.Rd':
  ‘knot-package’
checkRd: (-1) MapPolygon.Rd:20: Lost braces
    20 |   \item{shape}{If the estimators in the function link[KnowBR]{KnowBPolygon} were calculated using an external shape file, it is necessary to indicate the file in this argument. It is not necessary to select any polygon within the file, just to load the whole shape file.}
       |                                                              ^
checkRd: (-1) SurveyQ.Rd:26: Lost braces
    26 |   \item{shape}{If the estimators in the function link[KnowBR]{KnowBPolygon} were calculated using an external shape file, it is necessary to indicate the file in this argument. It is not necessary to select any polygon within the file, just to load the whole shape file.}
       |                                                              ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) kobotools_kpi_data.Rd:30: Lost braces; missing escapes or markup?
    30 | `kobotools_kpi_data` is a wrapper for kobotoolbox API `https://[URL]/api/v2/assets/{assetid}/data/`
       |                                                                                    ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'koRpus.lang.de', 'koRpus.lang.es', 'koRpus.lang.fr',
  'koRpus.lang.it', 'koRpus.lang.nl', 'koRpus.lang.pt',
  'koRpus.lang.ru'

Package which this enhances but not available for checking: ‘rkward’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) hsic.perm.Rd:36: Lost braces; missing escapes or markup?
    36 | Let x and y be two samples of length n. Gram matrices K and L are defined as: \eqn{K_{i,j} = \exp\frac{(x_i-x_j)^2}{\sigma^2}}{K_{i,j} =exp((x_i-x_j)^2/sig^2)} and \eqn{L_{i,j} = \exp\frac{(y_i-y_j)^2}{\sigma^2}}{L_{i,j} =exp((y_i-y_j)^2/sig^2)}. \eqn{H_{i,j} = \delta_{i,j} - \frac{1}{n}}{H_{i,j} = \delta_{i,j} - 1/n}. Let \eqn{A=HKH} and \eqn{B=HLH}, then \eqn{HSIC(x,y)=\frac{1}{n^2}Tr(AB)}{HSIC(x,y)=Tr(AB)/n^2}. Permutation test permutes y p times to get \eqn{y_{(p)}} and calculates HSIC(x,y_{(p)}). \eqn{pval = \frac{1(HSIC(x,y)>HSIC(x,y_{(p)}))}{p}}{(HSIC(x,y)>HSIC(x,y_{(p)}))/p}.
       |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) kpmt.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) kpmt.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) kpmt.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) kpmt.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) kpmt.Rd:46: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) kpmt.Rd:47: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) kpmt.Rd:48: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) kpmt.Rd:49: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) kpmt.Rd:50: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) kpmt.Rd:51: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) kpmt.Rd:52: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
checkRd: (-1) compose.Rd:13: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) compose.Rd:14: Lost braces in \enumerate; meant \describe ?
'LazyData' is specified without a 'data' directory
checkRd: (-1) EGIparallel.Rd:60: Lost braces; missing escapes or markup?
    60 | Finally, one can control the field {optim.option} in order to decide how to optimize the sampling criterion.
       |                                    ^
checkRd: (-1) max_sur_parallel.Rd:29: Lost braces; missing escapes or markup?
    29 | Finally, one can control the field {optim.option} in order to decide how to optimize the sampling criterion. 
       |                                    ^
checkRd: (-1) max_timse_parallel.Rd:30: Lost braces; missing escapes or markup?
    30 | Finally, one can control the field {optim.option} in order to decide how to optimize the sampling criterion. 
       |                                    ^
checkRd: (-1) max_vorob_parallel.Rd:30: Lost braces; missing escapes or markup?
    30 | Finally, one can control the field {optim.option} in order to decide how to optimize the sampling criterion.
       |                                    ^
checkRd: (-1) print_uncertainty_nd.Rd:72: Lost braces
    72 | Optional argument. When set to code{NULL} (default) the function performs the projections on plans spanned by each pair (i,j) of dimension. Otherwise, the argument is an array of size 2 corresponding to the dimensions spanning the (only) plan on which the projection is performed.
       |                                    ^
checkRd: (-1) Predict_kernel_Ridge_MM.Rd:45: Lost braces; missing escapes or markup?
    45 |   and alpha_train is the BLUP of alpha for the model, i.e. alpha_train=Cov(alpha,Y_train)*Var(Y_train)^{-1}*(Y_train - E[Y_train]) }
       |                                                                                                        ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) ks_test_stat.Rd:14: Lost braces
    14 | are valid. See /code{LcKS} for accepted functions.}
       |                     ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘KSEA Bar Plot.tiff’ ‘KSEA Kinase Scores.csv’
  ‘KSEA.Merged.Heatmap.png’ ‘Kinase-Substrate Links.csv’
Package suggested but not available for checking: ‘FactoClass’
'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) GenSyntheticLogistic.Rd:46: Lost braces; missing escapes or markup?
    46 | 3) Every coordinate yi of the outcome vector y exists in {-1, 1}^n is sampled 
       |                                                          ^
checkRd: (-1) L0Learn-package.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) L0Learn-package.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) L0Learn-package.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) L0Learn-package.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) L0Learn-package.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) L0Learn-package.Rd:25: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
checkRd: (-1) CreateDataSet.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) CreateDataSet.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) CreateDataSet.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) FindElement.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) FindElement.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) FindNbrClusters.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) FindNbrClusters.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) FindStructure.Rd:15: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) FindStructure.Rd:16: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) l1_spectralclustering.Rd:32: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) l1_spectralclustering.Rd:33: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) l1_spectralclustering.Rd:34: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) l1_spectralclustering.Rd:35: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) predict.l2boost.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) predict.l2boost.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) predict.l2boost.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) predict.l2boost.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) predict.l2boost.Rd:31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) predict.l2boost.Rd:32: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) reconcile.Rd:26: Lost braces
    26 | refer to as the sQuote{comm} data.frame.  The other data.frame contains all the
       |                       ^
checkRd: (-1) ln_quantile_value.Rd:44: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ln_quantile_value.Rd:45: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ln_quantile_value.Rd:46: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ln_quantile_value.Rd:47: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ln_quantile_value.Rd:48: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ln_quantile_value.Rd:49: Lost braces in \itemize; \value handles \item{}{} directly
Found the following files/directories:
  ‘MYSLID.csv’ ‘tabelle.csv’
'LazyData' is specified without a 'data' directory
checkRd: (-1) laf_open.Rd:10: Lost braces; missing escapes or markup?
    10 | \item{model}{a {data model}, such as one returned by \link{read_dm} or
       |                ^
checkRd: (-1) conn.Rd:300: Lost braces
   300 | Soranno et al. (2017) \doi{10.1093/gigascience/gix101}{Gigascience 6:12}
       |                                                       ^
checkRd: (-1) lakes_limno.Rd:36: Lost braces
    36 | Soranno et al. (2017) \doi{10.1093/gigascience/gix101}{Gigascience 6:12}
       |                                                       ^
checkRd: (-1) lambda.r-package.Rd:71-74: Lost braces
    71 | x \%g\% y \%:=\% {
       |                  ^
GNU make is a SystemRequirements.
checkRd: (-1) GenerateData.Rd:35-36: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) GenerateData.Rd:37-38: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) GenerateData.Rd:39-40: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) GenerateData.Rd:41-42: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) GenerateData.Rd:43-44: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) GenerateData.Rd:45: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) landmix.estimator.Rd:59-65: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) landmix.estimator.Rd:67-74: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) DOS.Rd:34: Lost braces; missing escapes or markup?
    34 | 	Band-specific sensor $G_{rescale}$ (gain). Require either gain and offset or Grescale and Brescale to convert DN to radiance.
       |                                 ^
checkRd: (-1) DOS.Rd:37: Lost braces; missing escapes or markup?
    37 | 	Band-specific sensor $B_{rescale}$ (bias). Require either gain and offset or Grescale and Brescale to convert DN to radiance.
       |                                 ^
'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) LML.Rd:43: Lost braces
    43 |     is specified only with the \code{GD}, code{HME}, or \code{NSIS}
       |                                               ^
checkRd: (-1) LaplaceApproximation.Rd:485: Escaped LaTeX specials: \&
checkRd: (-1) LossMatrix.Rd:115: Escaped LaTeX specials: \&
checkRd: (-1) LossMatrix.Rd:117: Escaped LaTeX specials: \&
checkRd: (-1) MISS.Rd:106: Lost braces
   106 |   code{Fit$Imp}. In the presence of numerous missing values, say more
       |       ^
checkRd: (-1) Matrices.Rd:316: Lost braces
   316 |   Gauss-Hermite quadrature rules. A grid of order eqn{K} provides an
       |                                                      ^
checkRd: (-1) PMC.Rd:214: Lost braces
   214 |   item{nu}{This is the degrees of freedom parameter \eqn{\nu}{nu} for
       |       ^
checkRd: (-1) PMC.Rd:214-215: Lost braces
   214 |   item{nu}{This is the degrees of freedom parameter \eqn{\nu}{nu} for
       |           ^
checkRd: (-1) caterpillar.plot.Rd:15: Lost braces
    15 |     code{demonoid.hpc}, \code{iterquad}, \code{laplace}, \code{pmc},
       |         ^
Specified C++11: please drop specification unless essential
checkRd: (-1) LA_LHDC.Rd:62: Lost braces; missing escapes or markup?
    62 | \item{i}{A positive integer, which stands for the i^{th} row of \code{X}.}
       |                                                     ^
checkRd: (-1) LA_LHDC.Rd:64: Lost braces; missing escapes or markup?
    64 | \item{j}{A positive integer, which stands for the j^{th} column (or row) of \code{X}, and it should be within [1,ncol(X)] (or [1,nrow(X)]).}
       |                                                     ^
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: ‘ergm.userterms’
checkRd: (-1) simulate.ergmm.Rd:35: Escaped LaTeX specials: \$
checkRd: (-1) simulate.ergmm.Rd:36: Escaped LaTeX specials: \$
Unknown package ‘ergm.userterms’ in Rd xrefs
GNU make is a SystemRequirements.
Running examples in ‘latexpdf-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: tex2pdf
> ### Title: Convert TEX to PDF
> ### Aliases: tex2pdf
> 
> ### ** Examples
> 
> file <- file.path(tempdir(),'test.tex')
> writeLines(as.ltable(head(Theoph)), file)
> tex2pdf(file)
arguments 'show.output.on.console', 'minimized' and 'invisible' are for Windows only
This is pdfTeX, Version 3.141592653-2.6-1.40.25 (TeX Live 2023/Debian) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode
(/home/hornik/tmp/scratch/RtmpYAoMzR/test_doc.tex
LaTeX2e <2023-11-01>
L3 programming layer <2023-11-09>
(/usr/share/texlive/texmf-dist/tex/latex/base/article.cls
Document Class: article 2023/05/17 v1.4n Standard LaTeX document class
(/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo))
(/usr/share/texlive/texmf-dist/tex/latex/xcolor/xcolor.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/color.cfg)

Package xcolor Warning: Package option `usenames' is obsolete and ignored on in
put line 266.


! LaTeX Error: Unknown option 'dvispnames' for package xcolor.

For immediate help type H <return>.
 ...                                              
                                                  
l.266 \edef
           \Gin@driver{\Gin@driver}
? No pages of output.
Transcript written on /home/hornik/tmp/scratch/RtmpYAoMzR/test_doc.log.
Error in as.pdf.document(as.document(x, ...), stem = stem, ...) : 
  could not make /home/hornik/tmp/scratch/RtmpYAoMzR/test_doc.pdf
Calls: tex2pdf -> as.pdf.character -> as.pdf -> as.pdf.document
Execution halted
Package suggested but not available for checking: ‘akmedoids’
Unknown package ‘akmedoids’ in Rd xrefs
Objects in \usage without \alias in Rd file 'latrend-generics.Rd':
  ‘nClusters’ ‘clusterProportions’ ‘clusterTrajectories’ ‘compose’
  ‘converged’ ‘externalMetric’ ‘estimationTime’ ‘fit’
  ‘fittedTrajectories’ ‘getArgumentDefaults’ ‘getArgumentExclusions’
  ‘getLabel’ ‘getLcMethod’ ‘getName’ ‘getShortName’ ‘idVariable’
  ‘metric’ ‘plotFittedTrajectories’ ‘plotClusterTrajectories’ ‘postFit’
  ‘postprob’ ‘predictAssignments’ ‘predictForCluster’ ‘predictPostprob’
  ‘prepareData’ ‘preFit’ ‘qqPlot’ ‘responseVariable’ ‘strip’
  ‘timeVariable’ ‘trajectoryAssignments’ ‘validate’

Functions with \usage entries need to have the appropriate \alias
entries, and all their 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) LKrig.MLE.Rd:114: Escaped LaTeX specials: \$ \$
checkRd: (-1) LKrig.MLE.Rd:115: Escaped LaTeX specials: \$
checkRd: (-1) VignetteExamples.Rd:25: Lost braces; missing escapes or markup?
    25 |  See Section 4 in the {LatticeKrig Vignette} for the use of these data.
       |                       ^
checkRd: (-1) lav_model.Rd:22: Lost braces
    22 | \item{x}{Numeric.}{A vector containing the values of all the free model parameters.}
       |                   ^
checkRd: (-1) lav_partable.Rd:118: Lost braces
   118 | \item{warn}{Logical. If code{TRUE}, a warning is produced when duplicated
       |                             ^
checkRd: (-1) lav_partable.Rd:120: Lost braces
   120 | \item{add}{A named list.}{A single row of a parameter table as a named list.}
       |                          ^
checkRd: (-1) parameterEstimates.Rd:78: Lost braces
    78 | name of the endogenous variable, while the code{op} column contains \code{r2},
       |                                                ^
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'moments2.Rd':
  ‘...’

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

Documented arguments not in \usage in Rd file 'vcov2-internal.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
'LazyData' is specified without a 'data' directory
Found the following calls to attach():
File ‘lazyData/R/requireData.R’:
  attach(NULL, pos = pos, name = searchDataName)
See section ‘Good practice’ in ‘?attach’.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) univ.Rd:35: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) univ.Rd:36: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) univ.Rd:37: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) univ.Rd:38: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) univ.Rd:39: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) univ.Rd:40: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) univ.Rd:41: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) univ.Rd:42: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) univ.Rd:43: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) univ.Rd:44: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) univ.Rd:45: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) univ.Rd:46: Lost braces in \enumerate; meant \describe ?
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘temp.float.csv’ ‘temp.result.athena.csv’
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) set_param.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) set_param.Rd:24-30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) set_param.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) set_param.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) set_param.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) set_param.Rd:31-32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) set_param.Rd:33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) set_param.Rd:34: Lost braces in \itemize; meant \describe ?
Documented arguments not in \usage in Rd file 'dot-choose_best_subjects.Rd':
  ‘best’ ‘candidate’

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

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Argument items with no description in Rd file 'top.topic.words.Rd':
  ‘alpha’
checkRd: (-1) TS_diagnostics_plot.Rd:19: Lost braces
    19 | \item{interactive}{\code{logical} input, should be code{TRUE} unless
       |                                                        ^
checkRd: (-1) plot.TS_fit.Rd:29: Lost braces
    29 | \item{interactive}{\code{logical} input, should be code{TRUE} unless
       |                                                        ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) model.Rd:14: Lost braces
    14 | An already trained ML model (including trainData & testData) with the "lm" method using the default data from the package, to be used in the predict example{, and potentially by the user for further predictions}.
       |                                                                                                                                                             ^
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
checkRd: (-1) dynamicMapLayerOptions.Rd:23: Lost braces; missing escapes or markup?
    23 | \item{layerDefs}{A string representing a query to run against the service before the image is rendered. This can be a string like "3:STATE_NAME="Kansas"" or an object mapping different queries to specific layers {3:"STATE_NAME="Kansas"", 2:"POP2007>25000"}.}
       |                                                                                                                                                                                                                     ^
checkRd: (-1) featureLayerOptions.Rd:35: Lost braces; missing escapes or markup?
    35 | Can be an object like {start:"startTime", end:"endTime"} or a string like "created".}
       |                       ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) search-options.Rd:23: Lost braces; missing escapes or markup?
    23 | \item{url}{url for search by ajax request, ex: "search.php?q={s}". Can be function that returns string for dynamic parameter setting.}
       |                                                              ^
'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:
    light.interception.voxels() - This function create the Fraction absorbed incident light
    light.interception.raster() - Create a raster of Fraction absorbed incident light
    light.incident.voxels() - This function create the Fraction incident light
    light.incident.raster() - Create a raster of the Fraction incident light
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) subnet.simulation.Rd:33: Lost braces
    33 |     probability function used for picking attachment point in iterative construction of subnetworks. defaults to preferential attachment based on node degree. To disable preferential attachment, use prob_function=function(degs){rep(1/length(degs),length(degs))}
       |                                                                                                                                                                                                                                    ^
Invalid package aliases in Rd file 'LEANR-package.Rd':
  ‘LEAN-package’
checkRd: (-1) IPODFUN.Rd:18: Lost braces; missing escapes or markup?
    18 |   \item{H}{an N by N projection matrix X(X'X)^{-1}X' }
       |                                               ^
checkRd: (-1) leaps.Rd:38: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
checkRd: (-1) clusterDistance.Rd:28-29: Lost braces
    28 | \code{approach} indicates the algorithm used to get the value. \code{distance} indicates the distance used to get the value. Possible values: {\code{'MAX'},
       |                                                                                                                                               ^
checkRd: (-1) clusterDistance.details.Rd:28-29: Lost braces
    28 | \code{approach} indicates the algorithm used to get the value. \code{distance} indicates the distance used to get the value. Possible values: {\code{'MAX'},
       |                                                                                                                                               ^
checkRd: (-1) clusterDistanceByApproach.Rd:24-25: Lost braces
    24 | \code{approach} indicates the algorithm used to get the value. Possible values: {\code{'MAX'},
       |                                                                                 ^
checkRd: (-1) clusterDistanceByApproach.details.Rd:24-25: Lost braces
    24 | \code{approach} indicates the algorithm used to get the value. Possible values: {\code{'MAX'},
       |                                                                                 ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) S2mu.Rd:18: Lost braces; missing escapes or markup?
    18 | \code{S2mu} computes a estimation of the variance, given a sample {x} with known population mean (denoted by \code{mu}).
       |                                                                   ^
checkRd: (-1) sample.quantile.Rd:20: Lost braces; missing escapes or markup?
    20 | \code{sample.quantile} computes a estimation of different quantiles, given a sample {x}, using order statistics.
       |                                                                                     ^
Invalid package aliases in Rd file 'learnn.Rd':
  ‘learnn-package’
Documented arguments not in \usage in Rd file 'backward_step.Rd':
  ‘empty_start_dataset’ ‘fit’ ‘...’

Documented arguments not in \usage in Rd file 'backward_step_IM.Rd':
  ‘empty_start_dataset’ ‘fit’ ‘...’

Documented arguments not in \usage in Rd file 'forward_step.Rd':
  ‘empty_start_dataset’ ‘fit’ ‘...’

Documented arguments not in \usage in Rd file 'forward_step_IM.Rd':
  ‘empty_start_dataset’ ‘fit’ ‘...’

Functions with \usage entries need to have the appropriate \alias
entries, and all their 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
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘maptools’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) controlBFGS.Rd:42: Lost braces; missing escapes or markup?
    42 | \item{stepSize}{Initial stepSize of the outer iteration (theta_{k+1} = theta_k + stepSize * Stepdirection)}
       |                                                                ^
checkRd: (-1) controlGlmnet.Rd:48: Lost braces; missing escapes or markup?
    48 | (theta_{k+1} = theta_k + stepSize * Stepdirection)}
       |        ^
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'get_generic.Rd':
  ‘mismatch’

Functions with \usage entries need to have the appropriate \alias
entries, and all their 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) hash_sentiment_slangsd.Rd:28-37: Lost braces
    28 | article{DBLP:journals/corr/Wu-etal16,
       |        ^
checkRd: (-1) hash_sentiment_slangsd.Rd:29: Lost braces; missing escapes or markup?
    29 |   author    = {Liang Wu and Fred Morstatter and Huan Liu},
       |               ^
checkRd: (-1) hash_sentiment_slangsd.Rd:30-31: Lost braces
    30 |   title     = {SlangSD: Building and Using a Sentiment Dictionary of Slang 
       |               ^
checkRd: (-1) hash_sentiment_slangsd.Rd:32: Lost braces; missing escapes or markup?
    32 |   journal   = {CoRR},
       |               ^
checkRd: (-1) hash_sentiment_slangsd.Rd:33: Lost braces; missing escapes or markup?
    33 |   volume    = {abs/1608.05129},
       |               ^
checkRd: (-1) hash_sentiment_slangsd.Rd:34: Lost braces; missing escapes or markup?
    34 |   year      = {2016},
       |               ^
checkRd: (-1) hash_sentiment_slangsd.Rd:35: Lost braces; missing escapes or markup?
    35 |   url       = {http://arxiv.org/abs/1608.05129},
       |               ^
checkRd: (-1) hash_sentiment_slangsd.Rd:36: Lost braces; missing escapes or markup?
    36 |   timestamp = {Wed, 17 Aug 2016 23:32:57 GMT}
       |               ^
checkRd: (-1) sw_python.Rd:32: Lost braces; missing escapes or markup?
    32 | * Neither the name of the {organization} nor the names of its
       |                           ^
Found the following significant warnings:
  utils.c:34:68: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘mybigint_t’ {aka ‘long int’} [-Wformat=]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/lfe.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-13 (Debian 13.2.0-7) 13.2.0’
Specified C++11: please drop specification unless essential
checkRd: (-1) flowunit.Rd:30: Lost braces; missing escapes or markup?
    30 | Usually flow units are of dimension $L^3 T^{-1}$. Currently a length $l$ can be on of \code{c("metre", "cm", "centimetre" "litre")}, whereas time $T$ can be one in \code{c("days", "hours", "mins", "secs")}, possibly abbreviated. The numerator of the fraction (everything before the literal \code{"/"}) is interpreted as the length (superscripts like \code{"^3"} are discarded), the denominator as time. E.g. valid units would be \code{"cm^3/s"}, \code{"m^3/day"} or \code{"litre/sec"}.
       |                                            ^
checkRd: (-1) seasindex.Rd:30: Lost braces
    30 | Laaha, G. and Bl{\"o}schl, G. (2006), Seasonality indices for regionalizing
       |                 ^
checkRd: (-1) seasindex.Rd:34: Lost braces
    34 | Mitteilungen, Inst. f{\"u}r Wasserbau u. Ingenieurhydrologie,
       |                      ^
checkRd: (-1) seasratio.Rd:31: Lost braces
    31 | Laaha, G. and Bl{\"o}schl, G. (2006), Seasonality indices for regionalizing low flows. Hydrol. Process., 20
       |                 ^
checkRd: (-1) prior_to_num.Rd:13: Lost braces; missing escapes or markup?
    13 |   {'uniform', 'normal', 'student-t', 'gamma', 'inv-gamma', 'log-normal'}
       |   ^
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) dij.Rd:12: Lost braces; missing escapes or markup?
    12 | \item{i}{A positive integer, which stands for the i^{th} row of \code{X}.}
       |                                                     ^
checkRd: (-1) dij.Rd:14: Lost braces; missing escapes or markup?
    14 | \item{j}{A positive integer, which stands for the j^{th} row of \code{X}. Both \code{i} and \code{j} should be in [1,nrow(X)] and they should not be equal to each other.}
       |                                                     ^
checkRd: (-1) exchange.Rd:12: Lost braces; missing escapes or markup?
    12 | \item{j}{A positive integer, which stands for the j^{th} column (or row) of \code{X}, and it should be within [1,ncol(X)] (or [1,nrow(X)]).}
       |                                                     ^
Specified C++11: please drop specification unless essential
checkRd: (-1) isingdata.Rd:14: Lost braces; missing escapes or markup?
    14 |     \item{X}{a 5000-by-100 matrix, each entry is in {-1,1}.}
       |                                                     ^
checkRd: (-1) predict.lb.Rd:16: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
checkRd: (-1) libstable4u-package.Rd:16: Lost braces; missing escapes or markup?
    16 | \item Fast and accurate evaluation of the quantile function (CDF^{-1}).
       |                                                                  ^
Packages suggested but not available for checking:
  'gWidgets', 'gWidgetsRGtk2', 'RGtk2'
checkRd: (-1) lx_list_lights.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) lx_list_lights.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) lx_list_lights.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) lx_list_lights.Rd:27: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) likelihood_calculation.Rd:24: Lost braces
    24 | For eqn{i = 1\dots N} independent observations in a vector \var{X}, with individual observations \eqn{x_i}{xi}, and a set of parameter values \eqn{\theta}:
       |        ^
checkRd: (-1) simulated_annealing_algorithm.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulated_annealing_algorithm.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulated_annealing_algorithm.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulated_annealing_algorithm.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulated_annealing_algorithm.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulated_annealing_algorithm.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulated_annealing_algorithm.Rd:27: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
checkRd: (-1) LIMEcoli.Rd:125: Escaped LaTeX specials: \_
checkRd: (-1) Read.Rd:88: Escaped LaTeX specials: \#
checkRd: (-1) Read.Rd:92: Escaped LaTeX specials: \#
checkRd: (-1) Read.Rd:98: Escaped LaTeX specials: \#
checkRd: (-1) Read.Rd:104: Escaped LaTeX specials: \#
checkRd: (-1) Read.Rd:105: Escaped LaTeX specials: \# \#
checkRd: (-1) Read.Rd:106: Escaped LaTeX specials: \# \#
checkRd: (-1) Read.Rd:107: Escaped LaTeX specials: \#
checkRd: (-1) Read.Rd:108: Escaped LaTeX specials: \#
checkRd: (-1) Read.Rd:109: Escaped LaTeX specials: \#
checkRd: (-1) Read.Rd:110: Escaped LaTeX specials: \#
checkRd: (-1) Read.Rd:111: Escaped LaTeX specials: \# \#
checkRd: (-1) Read.Rd:112: Escaped LaTeX specials: \# \#
checkRd: (-1) Read.Rd:113: Escaped LaTeX specials: \#
checkRd: (-1) Read.Rd:114: Escaped LaTeX specials: \# \#
Specified C++11: please drop specification unless essential
S3 methods shown with full name in Rd file 'BIC.threshold.Rd':
  ‘BIC.threshold’

S3 methods shown with full name in Rd file 'BIC.threshold.ggm.Rd':
  ‘BIC.threshold.ggm’

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) glottolog.Rd:34: Lost braces
    34 | Hammarstr{\"o}m, Harald and Forkel, Robert and Haspelmath, Martin and Bank, Sebastian. 2023.
       |          ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) solveLP.Rd:119: Escaped LaTeX specials: \&
Documented arguments not in \usage in Rd file 'MassAcylCer.Rd':
  ‘glccer’

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

Documented arguments not in \usage in Rd file 'findMS2precursor.Rd':
  ‘minint’ ‘maxint’

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

Functions with \usage entries need to have the appropriate \alias
entries, and all their 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) ld_build_html_site.Rd:41: Lost braces
    41 | directory specified by `rmd_dir`. Note that this is an {{rmarkdown}}
       |                                                        ^
checkRd: (-1) ld_create_doc.Rd:29: Lost braces
    29 | directory specified by `rmd_dir`. Note that this is an {{rmarkdown}}
       |                                                        ^
Documented arguments not in \usage in Rd file 'get_variable.Rd':
  ‘x’ ‘name’ ‘mustExist’ ‘create’

Functions with \usage entries need to have the appropriate \alias
entries, and all their 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:
  combine.c:664:43: warning: format ‘%g’ expects argument of type ‘double’, but argument 2 has type ‘int’ [-Wformat=]
  combine.c:664:15: warning: too many arguments for format [-Wformat-extra-args]
  subroutines.c:57:15: warning: too many arguments for format [-Wformat-extra-args]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/list.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-13 (Debian 13.2.0-7) 13.2.0’
'LazyData' is specified without a 'data' directory
checkRd: (-1) lit.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) lit.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) lit.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) lit_plink.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) lit_plink.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) lit_plink.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) is_natural_number.Rd:17: Lost braces; missing escapes or markup?
    17 | Test for natural numbers according to ISO 80000-2, that is the set  {0, 1, 2, ...}
       |                                                                     ^
checkRd: (-1) lstats.liu.Rd:41: Escaped LaTeX specials: \&
checkRd: (-1) vcov.liu.Rd:20: Lost braces
    20 | A list of matrix of estimated covariances in the linear Liu regression model for scalar or vector biasing parameter \code{d}{d} is produced. Each list element has row and column names corresponding to the parameter names given by the \code{coef(mod)}. List items are named correspond to values of biasing parameter \eqn{d}{d}.}
       |                                                                                                                             ^
checkRd: (-1) MHDI.Rd:23: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) relLik.Rd:16: Lost braces
    16 | \item{AIC(x), BIC(x) }{The \code{AIC} or ]code{BIC} value of the first model object.}
       |                                               ^
checkRd: (-1) relLik.Rd:17: Lost braces
    17 | \item{AIC(y), BIC(y) }{The \code{AIC} or ]code{BIC} value of the second model object.}
       |                                               ^
checkRd: (-1) bootstrap_pvals.Rd:78: Lost braces; missing escapes or markup?
    78 | $(n_{extreme} + 1) / (B + 1)$.
       |     ^
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
checkRd: (-1) par2qua2lo.Rd:31: Lost braces
    31 | Alternatively, the returned value could be a weighting function for subsequent calls as \code{wfunc} to \code{par2qua2lo} (see \bold{Examples}). This alternative operation is triggered by setting \code{wfunc} to an arbitrary character string, and internally the contents of \code{xlo1} and \code{xlo2}, which themselves have to be called as named arguments, are recombined. This means that the \code{xin} and code{xout} are recombined, into their respective samples. Each data point is then categorized with probability zero for the \code{xlo1} values and probability unity for the \code{xlo2} values. A logistic regression is fit using logit-link function for a binomial family using a generalized linear model. The binomial (0 or 1) is regressed as a function of the plotting positions of a sample composed of \code{xlo1} and \code{xlo2}. The coefficients of the regression are extracted, and a function created to predict the probability of event \dQuote{\code{xlo2}}. The \code{attributes} of the computed value inside the function store the coefficients, the regression model, and potentially useful for graphical review, a \code{data.frame} of the data used for the regression. This sounds more complicated than it really is (see source code and \bold{Examples}).
       |                                                                                                                                                                                                                                                                                                                                                                                                                              ^
Specified C++11: please drop specification unless essential
checkRd: (-1) cauchypoly.Rd:39: Escaped LaTeX specials: \_ \_ \_
checkRd: (-1) cauchypoly.Rd:40: Escaped LaTeX specials: \_
checkRd: (-1) normpoly.Rd:38: Escaped LaTeX specials: \_ \_ \_
checkRd: (-1) normpoly.Rd:39: Escaped LaTeX specials: \_
checkRd: (-1) lmomPi-Package.Rd:9: Lost braces
     9 | {\code{\link{cdf}}}{: generic distribution function;  }  
       |                    ^
checkRd: (-1) lmomPi-Package.Rd:10: Lost braces
    10 | {\code{\link{qua}}}{: generic quantile function;  } 
       |                    ^
checkRd: (-1) lmomPi-Package.Rd:11: Lost braces
    11 | {\code{\link{pel}}}{: fitting of probability distribution function through L-moments. }
       |                    ^
checkRd: (-1) lmomPi-Package.Rd:27: Lost braces; missing escapes or markup?
    27 | The function  \code{\link{spi.cdf}()} is compared against \code{SPEI::spi()} in SPEI package (\url{https://cran.r-project.org/package=SPEI}). The differences in SPI extimation have order of magnitude averagely about 10^{-8},  due to  the different fitting methods implemented in the two packages. 
       |                                                                                                                                                                                                                            ^
checkRd: (-1) vcov.Rd:20: Lost braces
    20 | A list of matrix of estimated covariances in the linear ridge regression model for scalar or vector biasing parameter \code{K}{K} is produced. Each list element has row and column names corresponding to the parameter names given by the \code{coef(mod)}. List items are named correspond to values of biasing parameter \eqn{K}{K}.}
       |                                                                                                                               ^
Specified C++11: please drop specification unless essential
checkRd: (-1) lmSubsets-package.Rd:48: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘tTestTable.rda’
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Author
    Maintainer
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) mte_tilde_at.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mte_tilde_at.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mte_tilde_at.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mte_tilde_at.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mte_tilde_at.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
checkRd: (-1) Rvarlacf.Rd:104: Lost braces
   104 | 	eqn{(2s+1)^{-2}} (this was the default in versions prior to
       |            ^
checkRd: (-1) Rvarlacf.Rd:104: Lost braces; missing escapes or markup?
   104 | 	eqn{(2s+1)^{-2}} (this was the default in versions prior to
       |                    ^
checkRd: (-1) FootballBrain.Rd:15: Lost braces; missing escapes or markup?
    15 |     { } \tab {or \code{FBConcuss}=football player with concussion history} \cr
       |     ^
checkRd: (-1) HappyPlanetIndex.Rd:14: Lost braces; missing escapes or markup?
    14 |     { } \tab {\code{5}=South Asia, \code{6}=East Asia, \code{7}=former Communist countries}\cr
       |     ^
checkRd: (-1) RockandRoll2012.Rd:17: Lost braces; missing escapes or markup?
    17 |     { } \tab {\code{Lifetime Achievement}, \code{Sideman}} \cr
       |     ^
checkRd: (-1) RockandRoll2015.Rd:17: Lost braces; missing escapes or markup?
    17 |     { } \tab {\code{Lifetime Achievement}, \code{Sideman}} \cr
       |     ^
checkRd: (-1) StudentSurvey.Rd:12: Lost braces; missing escapes or markup?
    12 |     \item{\code{Sex}}{code {F}=female or \code{M}=male}
       |                            ^
checkRd: (-1) SynchronizedMovement.Rd:16: Lost braces; missing escapes or markup?
    16 |     { } \tab {for High/Low Synchronization + High/Low Exertion}\cr
       |     ^
checkRd: (-1) TrafficFlow.Rd:25: Escaped LaTeX specials: \#
Invalid package aliases in Rd file 'Lock5Data-package.Rd':
  ‘Lock5Data-package’
Specified C++11: please drop specification unless essential
Argument items with no description in Rd file 'spec.emb.Rd':
  ‘A’
checkRd: (-1) analysis.Rd:61-62: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) analysis.Rd:63-64: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) analysis.Rd:65-66: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) analysis.Rd:67-68: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) analysis.Rd:69: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
Argument items with no description in Rd file 'dlogitnorm.Rd':
  ‘sigma’
Argument items with no description in Rd file 'invlogit.Rd':
  ‘q’ ‘\dots’
Argument items with no description in Rd file 'logit.Rd':
  ‘p’ ‘\dots’
Argument items with no description in Rd file 'plogitnorm.Rd':
  ‘sigma’ ‘\dots’
Argument items with no description in Rd file 'qlogitnorm.Rd':
  ‘sigma’ ‘\dots’
Argument items with no description in Rd file 'twCoefLogitnorm.Rd':
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     6 | \title{Simulated SP dataset of mode choice (from the {apollo} package).}
       |                                                      ^
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     6 | \title{Stated preference data for the choice of electricity suppliers (from {mlogit} package)}
       |                                                                             ^
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    24 | using the following R packages: {logitr}, {mixl}, {mlogit}, {gmnl}, and
       |                                 ^
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    24 | using the following R packages: {logitr}, {mixl}, {mlogit}, {gmnl}, and
       |                                           ^
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    24 | using the following R packages: {logitr}, {mixl}, {mlogit}, {gmnl}, and
       |                                                   ^
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    24 | using the following R packages: {logitr}, {mixl}, {mlogit}, {gmnl}, and
       |                                                             ^
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    25 | {apollo}. The run times are exported from the Google colab notebook here:
       | ^
Specified C++11: please drop specification unless essential
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    33 | The function \code{logdensity} computes kernel density estimates (KDE) of strictly positive distributions by performing the KDE in the log domain and then transforming the result back again. The syntax and function structure is largely borrowed from the function \code{density} in package {stats}.
       |                                                                                                                                                                                                                                                                                                  ^
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    33 | The function \code{logdensity_fft} computes kernel density estimates (KDE) of strictly positive distributions by performing the KDE via fast fourier transform utilizing the \code{fft} function. The syntax and function structure is largely borrowed from the function \code{density} in package {stats}.
       |                                                                                                                                                                                                                                                                                                     ^
'LazyData' is specified without a 'data' directory
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Argument items with no description in Rd file 'levopt.Rd':
  ‘x’ ‘alpha’ ‘fmax’ ‘tm’
Argument items with no description in Rd file 'pershow.Rd':
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  ‘alist’
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  ‘exportMethods’
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains ‘methods’.
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    96 |   J.E. Rossouw, J.P.D. Plessis, A.J.S. Benad\'{e}, P.C.J. Jordaan, 
       |                                               ^
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    97 |   J.P. Kotz\'{e}, P.L. Jooste, and J.J. Ferreira (1983)
       |              ^
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    30 | when 'code{labels = FALSE}, the default \code{active} is  \code{-1}; and when \code{labels} is a vector of length equal
       |           ^
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Auto-generated content requiring editing in Rd file 'LoopAnalyst-package.Rd':
  \details: ‘...the package, including the most important ~~ ~~ functions ~~’
Found the following files/directories:
  ‘Model_1.cm’ ‘dambacher.dot’ ‘levins.dot’
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'importance_sampling.array.Rd':
  ‘is_method’

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Documented arguments not in \usage in Rd file 'importance_sampling.matrix.Rd':
  ‘is_method’

Functions with \usage entries need to have the appropriate \alias
entries, and all their 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: ‘scio’
Malformed Description field: should contain one or more complete sentences.
checkRd: (-1) gyr.Rd:35: Lost braces
    35 |   on \sQuote{Deriving relativistic momentum and energy: {I}{I}.
       |                                                            ^
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    16 | \item{q}{A number between \code{0} and \code{1}. The quantile of the distribution of $lambda_{QUT}$ to take.}
       |                                                                                              ^
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    25 | the value of $lambda_{QUT}$ to use in LoRI.
       |                      ^
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    34 | \code{\link{align.missing}},code{\link{MissingGeoMorph}}
       |                                 ^
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    37 | \code{\link{align.missing}}, \{code{\link{MissingGeoMorph}}
       |                                    ^
Argument items with no description in Rd file 'LotkasXX.Rd':
  ‘Table’
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'LazyData' is specified without a 'data' directory
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Argument items with no description in Rd file 'followx.Rd':
  ‘Xi’ ‘x0’ ‘h’ ‘t0’ ‘iter’ ‘way’ ‘weights’ ‘pen’ ‘phi’
  ‘lasteigenvector’ ‘rho0’ ‘boundary’ ‘convergence.at’ ‘cross’
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    70 | Regime 1 = (1-\eqn{F(z_{t-1})})*y_{(t-p)}, \cr
       |                                   ^
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    71 | Regime 2 = \eqn{F(z_{t-1})}*y_{(t-p)}.}
       |                               ^
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   128 | \item{fz}{A vector containing the values of the transition function F(z_{t-1}).}
       |                                                                         ^
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    84 | Regime 1 = (1-\eqn{F(z_{t-1})})*y_{(t-p)}, \cr
       |                                   ^
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    85 | Regime 2 = \eqn{F(z_{t-1})}*y_{(t-p)}.}
       |                               ^
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   129 | \item{fz}{A vector, containing the values of the transition function F(z_{t-1}).}
       |                                                                          ^
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   103 | Regime 1 = (1-\eqn{F(z_{t-1})})*y_{(t-p)}, \cr
       |                                   ^
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   104 | Regime 2 = \eqn{F(z_{t-1})}*y_{(t-p)}.
       |                               ^
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    76 | \author{Christian E. Galarza <\email{cgalarza88@gmail.com}>, {Luis Benites} <\email{lsanchez@ime.usp.br}> and
       |                                                              ^
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    66 | \author{Christian E. Galarza <\email{cgalarza88@gmail.com}>, {Luis Benites} <\email{lsanchez@ime.usp.br}> and
       |                                                              ^
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    70 | \author{Christian E. Galarza <\email{chedgala@espol.edu.ec}>, {Marcelo Bourguignon} <\email{m.p.bourguignon@gmail.com}> and
       |                                                               ^
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    86 | \author{Christian E. Galarza <\email{cgalarza88@gmail.com}>, {Luis Benites} <\email{lsanchez@ime.usp.br}> and
       |                                                              ^
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    98 | \author{Christian E. Galarza <\email{cgalarza88@gmail.com}>, {Luis Benites} <\email{lsanchez@ime.usp.br}> and
       |                                                              ^
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    22 | \author{Christian E. Galarza <\email{cgalarza88@gmail.com}>, {Luis Benites} <\email{lsanchez@ime.usp.br}> and 
       |                                                              ^
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    83 | \author{Christian E. Galarza <\email{cgalarza88@gmail.com}>, {Luis Benites} <\email{lsanchez@ime.usp.br}> and
       |                                                              ^
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   112 | \code{"rows"} and code{"columns"}.}
       |                       ^
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    27 |  code{\link{ACSPlan-class}}, 
       |      ^
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    38 | code{\link{arima.sim}} 
       |     ^
Specified C++11: please drop specification unless essential
checkRd: (-1) Upload_to_db.Rd:43: Lost braces
    43 | lucas]{Connect_to_db}
       |       ^
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Documented arguments not in \usage in Rd file 'setlogdata.Rd':
  ‘logdata’

Functions with \usage entries need to have the appropriate \alias
entries, and all their 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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  ‘test’
checkRd: (-1) LVGP_fit.Rd:47: Lost braces in \itemize; \value handles \item{}{} directly
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    21 | Data are sampled from the modified math function based on the first example in the paper listed in code{references}.
       |                                                                                                        ^
Specified C++11: please drop specification unless essential
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    11 | \item{response}{N by J matrix containing {0,1,...,M-1} responses, where N is the number of respondents and J is the number of items.}
       |                                          ^
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    15 | Returns an error condition of class{error_column_not_found}.
       |                                    ^
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    18 | Returns an error condition of class{error_no_method_for_class}.
       |                                    ^
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    13 | Returns an error condition of class{error_package_not_installed}.
       |                                    ^
Package suggested but not available for checking: ‘depth’
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   101 | determines whether the width of the box for letter value LV(i) should be proportional to i (linear), proportional to $2^{-i}$ (height), or  whether
       |                                                                                                                         ^
checkRd: (-1) geom_lv.Rd:102: Lost braces; missing escapes or markup?
   102 | the area of the box should be proportional to $2^{-i}$ (area).}
       |                                                  ^
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    26 | v: \tab speed (m.s^{-1})\cr
       |                    ^
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checkRd: (-1) examinee-class.Rd:61: Lost braces; missing escapes or markup?
    61 | \item{\code{routing_based_on}}{a vector containing the routing was based on \code{estimated_theta_by_phase} or {estimated_theta_by_test} at each module position.}
       |                                                                                                                ^
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    23 | \item{x, y}{original two sample raw data, code{x}:"Control", \code{y}: "Case".}
       |                                               ^
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    26 | specified by \code{t}. code{n0}:"Control", \code{n1}: "Case".}
       |                            ^
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    50 | Wrapping all code{mable} fit of regression models in one function.
       |                  ^
checkRd: (-1) maple.dr.Rd:23: Lost braces
    23 | \item{x, y}{original two sample raw data, code{x}:"Control", \code{y}: "Case".}
       |                                               ^
checkRd: (-1) maple.dr.group.Rd:27: Lost braces
    27 | specified by \code{t}. code{n0}:"Control", \code{n1}: "Case".}
       |                            ^
checkRd: (-1) mada-data.Rd:45: Lost braces
    45 | Kriston, L., H{\"o}elzel, L., Weiser, A., Berner, M., & Haerter, M. (2008).\dQuote{ Meta-analysis: Are 3
       |               ^
GNU make is a SystemRequirements.
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    49 | If {rel} is missing \code{to} refers to the aggregation target dimension name.}
       |    ^
checkRd: (-1) toolGetMapping.Rd:18: Lost braces
    18 | and rda (which needs to have the data stored with the object name "data"!). Use code{\link{toolConvertMapping}}
       |                                                                                     ^
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Packages suggested but not available for checking: 'lpjmlkit', 'quitte'
'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’.
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    45 |     this defaults to \code{1:L}, where code{L} is the number of categories.
       |                                            ^
Argument items with no description in Rd file 'plot.magree.Rd':
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Argument items with no description in Rd file 'print.summary.magree.Rd':
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Argument items with no description in Rd file 'summary.magree.Rd':
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Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
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    21 | 	\item{gr}{A function to return the gradient for the \dQuote{nlminb}, \dQuote{BFGS}, \dQuote{CG} and {L-BFGS-B} methods.  If it is \sQuote{NULL}, a finite-difference approximation will be used. For the \dQuote{SANN} method it specifies a function to generate a new candidate point.  If it is \sQuote{NULL} a default Gaussian Markov kernel is used.}
       |                                                                                                             ^
checkRd: (-1) Robda-methods.Rd:69: Lost braces
    69 | \seealso{\code{\link{lda}}, \code{\link{qda}}, \code{\link{snda}}, \code{\linkS4class{IData}}, \code{\linkS4class{RobEstControl}},code{\link{ConfMat}} }
       |                                                                                                                                       ^
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Package unavailable to check Rd xrefs: ‘INLA’
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    34 | email{noahsilverman@ucla.edu}
       |      ^
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    11 | the following child folders: {repo_base}/bin/ and {repo_base}/src/. A
       |                              ^
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    11 | the following child folders: {repo_base}/bin/ and {repo_base}/src/. A
       |                                                   ^
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    11 | the following child folders: {repo_base}/bin/ and {repo_base}/src/. A
       |                              ^
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    11 | the following child folders: {repo_base}/bin/ and {repo_base}/src/. A
       |                                                   ^
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    37 |       An object of class \\code{\link[Mangrove]{MangrovePed}}
       |                                ^
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checkRd: (-1) EEGwide.Rd:30-33: Lost braces
    30 |   if(requireNamespace("ggplot2")){ 
       |                                  ^
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    19 | \eqn{0} means there exists no path for node \eqn{i} and {j}.
       |                                                         ^
Specified C++11: please drop specification unless essential
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    27 | is a URL template, i.e. a string containing '{x}' and '{y}', it loads terrain tiles on demand
       |                                              ^
checkRd: (-1) add_terrain.Rd:27: Lost braces; missing escapes or markup?
    27 | is a URL template, i.e. a string containing '{x}' and '{y}', it loads terrain tiles on demand
       |                                                        ^
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Bug Fixes
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    77 |     \code{chisq.pval.thres}{threshold used to perform the segregation tests}
       |                            ^
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    78 |     \code{chisq.pval}{p-values associated with the performed segregation tests}
       |                      ^
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    18 | \code{'marker'}{filter out markers based on their percentage of missing data (default)}
       |                ^
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    19 | \code{'individual'}{filter out individuals based on their percentage of missing data}
       |                    ^
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
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    53 | When {sparse=TRUE} (default), spike--and--slab priors are imposed to identify important main and interaction effects. If {sparse=FALSE}, Laplacian shrinkage will be used.
       |      ^
checkRd: (-1) marble.Rd:53: Lost braces; missing escapes or markup?
    53 | When {sparse=TRUE} (default), spike--and--slab priors are imposed to identify important main and interaction effects. If {sparse=FALSE}, Laplacian shrinkage will be used.
       |                                                                                                                          ^
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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.
       |                                                                                     ^
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    29 | \code{\link{quickfit}}, code{\link{locator}}
       |                             ^
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    14 | 1. \code{\link{estimate_shift}} {Estimate a range shift process.}
       |                                 ^
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    16 | 2. \code{\link{simulate_shift}} {Simulate a range shift process.}
       |                                 ^
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    18 | 3. \code{\link{plot.shiftfit}} {Visualize a range shift process.}
       |                                ^
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    20 | 4. \code{\link{test_rangeshift}} {Test whether a range shift occurred.}
       |                                  ^
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    22 | 5. \code{\link{test_return}} {Test whether a migration was a return migration.}
       |                              ^
checkRd: (-1) marcher-package.Rd:24: Lost braces; missing escapes or markup?
    24 | 6. \code{\link{test_stopover}} {Test whether a stopover occurred during a migration.}
       |                                ^
checkRd: (-1) quickfit.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) quickfit.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) test_rangeshift.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) test_rangeshift.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) test_rangeshift.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) test_rangeshift.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Interpolation-class.Rd:41: Escaped LaTeX specials: \#
checkRd: (-1) MareyMap-class.Rd:85: Escaped LaTeX specials: \_
checkRd: (-1) MareyMap-methods.Rd:11: Escaped LaTeX specials: \_ \_ \_ \_
checkRd: (-1) MareyMap-methods.Rd:12: Escaped LaTeX specials: \_
checkRd: (-1) SpeciesMaps-methods.Rd:11: Escaped LaTeX specials: \_
checkRd: (-1) interpolation-methods.Rd:13: Escaped LaTeX specials: \_
Argument items with no description in Rd file 'bias.factor.Rd':
  ‘RRud’ ‘RReu’ ‘rr’ ‘s2’
'LazyData' is specified without a 'data' directory
checkRd: (-1) mma.Rd:67: Escaped LaTeX specials: \&
checkRd: (-1) residuals.rsm.Rd:74: Escaped LaTeX specials: \&
checkRd: (-1) marima.Rd:28: Lost braces; missing escapes or markup?
    28 | ( if(is.ts(DATA)) { DATA <- as.matrix(data.frame(DATA)) } and a message
       |                   ^
checkRd: (-1) marima.Rd:223: Escaped LaTeX specials: \&
checkRd: (-1) markdownInput.Rd:17: Lost braces
    17 | \item{inputId}{The code{input} slot that will be used to access the value.}
       |                        ^
checkRd: (-1) markdownInput.Rd:35: Lost braces in \enumerate; \value handles \item{}{} directly
checkRd: (-1) markdownInput.Rd:36: Lost braces in \enumerate; \value handles \item{}{} directly
checkRd: (-1) markdownInput.Rd:81-82: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) markdownInput.Rd:84-86: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) markdownInput.Rd:89-90: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) moduleMarkdownInput.Rd:64-65: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) moduleMarkdownInput.Rd:67-69: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) moduleMarkdownInput.Rd:72-73: Lost braces in \enumerate; meant \describe ?
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Packages required but not available: 'CausalImpact', 'bsts'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'mark_my_dir.Rd':
  ‘mark_file’

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

Documented arguments not in \usage in Rd file 'read_assignment_yml.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.
checkRd: (-1) markovchainFit.Rd:31: Lost braces; missing escapes or markup?
    31 | \item{stringchar}{It can be a {n x n} matrix or a character vector or a list}
       |                               ^
checkRd: (-1) markovchainFit.Rd:39: Lost braces; missing escapes or markup?
    39 | \item{data}{It can be a character vector or a {n x n} matrix or a {n x n} data frame or a list}
       |                                               ^
checkRd: (-1) markovchainFit.Rd:39: Lost braces; missing escapes or markup?
    39 | \item{data}{It can be a character vector or a {n x n} matrix or a {n x n} data frame or a list}
       |                                                                   ^
checkRd: (-1) markovchainFit.Rd:61: Lost braces; missing escapes or markup?
    61 | {k x k} where k is the number of states in the chain and the values
       | ^
GNU make is a SystemRequirements.
checkRd: (-1) Markovchart.Rd:154: Lost braces
   154 | If either \code{h} or \code{k} have length greater than 1, then the \code{G-value} (weighted average of average cost and cost standard deviation) is calculated for all given values without optimisation. The value of the function in this case is a data frame of class code{Markov_grid} with \code{length(h)*length(k)} number of rows and three columns for \code{h}, \code{k} and the \code{G-value}.
       |                                                                                                                                                                                                                                                                                ^
checkRd: (-1) marqLevAlg-package.Rd:14: Lost braces; missing escapes or markup?
    14 | (GH^{-1}G).
       |     ^
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘marssTMB’
Objects in \usage without \alias in Rd file 'utility_functions.Rd':
  ‘fully.spec.x’ ‘marssMODEL.to.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.
'LazyData' is specified without a 'data' directory
checkRd: (-1) focalCompare.Rd:14: Lost braces
    14 | \item{fun}{The function fun should take multiple numbers, and return a single number. For example mean, modal, min or max. It should also accept a na.rm argument (or ignore it, e.g. as one of the 'dots' arguments. For example, length will fail, but function(x, ...){na.omit(length(x))} works. (Specifications from `raster::focal`)}
       |                                                                                                                                                                                                                                                                          ^
checkRd: (-1) hr_levels.Rd:9-12: Lost braces
     9 | kernelBiweight <- function(x, mean = 0, sd = 1) {
       |                                                 ^
checkRd: (-1) hr_levels.Rd:33-36: Lost braces
    33 | kernelCosine <- function(x, mean = 0, sd = 1) {
       |                                               ^
checkRd: (-1) hr_levels.Rd:41-44: Lost braces
    41 | kernelEpanechnikov <- function(x, mean = 0, sd = 1) {
       |                                                     ^
checkRd: (-1) hr_levels.Rd:58-61: Lost braces
    58 | kernelOptCosine <- function(x, mean = 0, sd = 1) {
       |                                                  ^
checkRd: (-1) hr_levels.Rd:65-68: Lost braces
    65 | kernelRectangular <- function(x, mean = 0, sd = 1) {
       |                                                    ^
checkRd: (-1) hr_levels.Rd:72-75: Lost braces
    72 | kernelSquaredCosine <- function(x, mean = 0, sd = 1) {
       |                                                      ^
checkRd: (-1) hr_levels.Rd:79-82: Lost braces
    79 | kernelTriangular <- function(x, mean = 0, sd = 1) {
       |                                                   ^
checkRd: (-1) hr_levels.Rd:86-89: Lost braces
    86 | kernelTricube <- function(x, mean = 0, sd = 1) {
       |                                                ^
checkRd: (-1) hr_levels.Rd:93-96: Lost braces
    93 | kernelTriweight <- function(x, mean = 0, sd = 1) {
       |                                                  ^
checkRd: (-1) hr_levels.Rd:100-103: Lost braces
   100 | kernelUniform <- function(x, mean = 0, sd = 1) {
       |                                                ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) CF2004.Rd:8: Lost braces; missing escapes or markup?
     8 |   \item{X2}{an optional second variable with same length as \code{X}, should the equation be multiple (see Details) {in mm}}
       |                                                                                                                     ^
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Invalid package aliases in Rd file 'NewPackage-package.Rd':
  ‘NewPackage-package’
Auto-generated content requiring editing in Rd file 'NewPackage-package.Rd':
  \references: ‘This optional section can contain literature or other refere...’
  \seealso: ‘Optional links to other man pages’
  \examples: ‘\dontrun{      ## Optional simple examples of the most impor...’
Package suggested but not available for checking: ‘gurobi’
checkRd: (-1) Rand.index.Rd:22: Lost braces; missing escapes or markup?
    22 | The two vectors \code{x} and \code{y} must have equal length. Given a set \eqn{S} and two partitions \eqn{X} and \eqn{Y} of \eqn{S}, the Rand index is the proportion of pairs of elements in \eqn{S} (out of all pairs) that are either concordant in both \eqn{X} and \eqn{Y} (i.e., they belong to the same member of \eqn{X} and to the same member of \eqn{Y}) or discordant (i.e., not concordant) in both \eqn{X} and {Y}.  
       |                                                                                                                                                                                                                                                                                                                                                                                                                              ^
checkRd: (-1) predict.matchFeat.Rd:21: Lost braces
    21 | The function \code{predict.matchFeat} finds the best matching for new feature vectors relative to an existing set of cluster/class centers. If code{object} results from a call to \code{\link{match.gaussmix}}, the same function is used for prediction (with fixed mean vectors and covariance matrices). In other cases, the function \code{\link{match.template}} is used for prediction. 
       |                                                                                                                                                    ^
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘gurobi’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rrelaxiv’
checkRd: (-1) matchMulti-package.Rd:75: Lost braces
    75 | c("\\Sexpr[results=rd,stage=build]{tools:::Rd_package_author(\"#1\")}",
       |                                   ^
checkRd: (-1) matchMulti-package.Rd:79: Lost braces
    79 | c("\\Sexpr[results=rd,stage=build]{tools:::Rd_package_maintainer(\"#1\")}",
       |                                   ^
checkRd: (-1) Match.Rd:90: Lost braces; missing escapes or markup?
    90 | expression in braces. For example, the condition "{[ab]*}" is equivalent
       |                                                   ^
checkRd: (-1) size_t-class.Rd:6: Escaped LaTeX specials: \_
checkRd: (-1) vectors3d.Rd:86: Lost braces
    86 | \code{\link{arrows3d}}, code{\link[rgl]{texts3d}}, code{\link[rgl]{rgl.material}}
       |                             ^
checkRd: (-1) vectors3d.Rd:86: Lost braces
    86 | \code{\link{arrows3d}}, code{\link[rgl]{texts3d}}, code{\link[rgl]{rgl.material}}
       |                                                        ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) MatrixCorrelation.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MatrixCorrelation.Rd:18-19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MatrixCorrelation.Rd:20-21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MatrixCorrelation.Rd:22-23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MatrixCorrelation.Rd:24-25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MatrixCorrelation.Rd:26-27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MatrixCorrelation.Rd:28-29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) RV.Rd:61-62: Lost braces in \itemize; meant \describe ?
checkRd: (-1) RV.Rd:63-64: Lost braces in \itemize; meant \describe ?
checkRd: (-1) RV.Rd:65-66: Lost braces in \itemize; meant \describe ?
checkRd: (-1) RV.Rd:67-68: Lost braces in \itemize; meant \describe ?
checkRd: (-1) allCorrelations.Rd:63: Lost braces in \itemize; meant \describe ?
checkRd: (-1) allCorrelations.Rd:64-65: Lost braces in \itemize; meant \describe ?
checkRd: (-1) allCorrelations.Rd:66-67: Lost braces in \itemize; meant \describe ?
checkRd: (-1) allCorrelations.Rd:68-69: Lost braces in \itemize; meant \describe ?
checkRd: (-1) allCorrelations.Rd:70-71: Lost braces in \itemize; meant \describe ?
checkRd: (-1) allCorrelations.Rd:72-73: Lost braces in \itemize; meant \describe ?
checkRd: (-1) allCorrelations.Rd:74-75: Lost braces in \itemize; meant \describe ?
checkRd: (-1) r1.Rd:71: Lost braces in \itemize; meant \describe ?
checkRd: (-1) r1.Rd:72: Lost braces in \itemize; meant \describe ?
checkRd: (-1) r1.Rd:73: Lost braces in \itemize; meant \describe ?
checkRd: (-1) r1.Rd:74: Lost braces in \itemize; meant \describe ?
checkRd: (-1) r1.Rd:75: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Matrix_eQTL_main.Rd:31: Lost braces; missing escapes or markup?
    31 |     {genepos} in the call of \code{Matrix_eQTL_main} function.
       |     ^
checkRd: (-1) Matrix_eQTL_main.Rd:35: Lost braces; missing escapes or markup?
    35 |     the data frames \code{snpspos} and {genepos}.
       |                                        ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘utilities.R’
checkRd: (-1) MaxentVariableSelection-package.Rd:46: Lost braces; missing escapes or markup?
    46 | \tab Tyberghein L, Verbruggen H, Pauly K, Troupin C, Mineur F and {De Clerck}, O (2012)\cr
       |                                                                   ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found export directive that requires package ‘methods’:
  ‘exportClasses’
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains ‘methods’.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘map_5.png’ ‘maze_5.html’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) findDescendingTrans.Rd:29: Lost braces
    29 |    Foster, S.D., Hosack, G.R., J. Monk, Lawrence, E., Barrett, N.S., Williams, A. and Przeslawski, P. (2020) Spatially-Balanced Designs for Transect-Based Surveys. Methods in Ecology and Evolution. emph{11}: 95--105
       |                                                                                                                                                                                                           ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) SIGMAS.Rd:17: Lost braces; missing escapes or markup?
    17 | Sigmahat =  (Y^{T} Y)/n;
       |                ^
checkRd: (-1) SIGMAS.Rd:18: Lost braces; missing escapes or markup?
    18 | Sigmahat_fit = (Y^{T}  P_fx  Y)/n;
       |                   ^
checkRd: (-1) matpower.Rd:17: Lost braces; missing escapes or markup?
    17 | The function computes M^{power} for a symmetric matrix M. }
       |                         ^
checkRd: (-1) satisfaction.Rd:28: Lost braces
    28 | Della Valle E (2010) Della Valle E 2010 Analisi Multidimensionale dei Dati: la Qualit\'{a} del Lavoro nelle Cooperative Sociali. 
       |                                                                                        ^
checkRd: (-1) satisfaction.Rd:29: Lost braces
    29 | Unpublished thesis, Seconda Universit\'{a}  degli Studi di Napoli, Capua Italy.
       |                                        ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Auto-generated content requiring editing in Rd file 'mccca-package.Rd':
  \references: ‘This optional section can contain literature or other refere...’
  \seealso: ‘Optional links to other man pages’
  \examples: ‘\dontrun{      ## Optional simple examples of the most impor...’
'LazyData' is specified without a 'data' directory
checkRd: (-1) mc.lnOR.Rd:7: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
checkRd: (-1) MCbound.precalc1.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MCbound.precalc1.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MCbound.precalc1.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MCbound.precalc1.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MCbound.precalc1.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MCbound.precalc1.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MCbound.precalc1.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MCbound.precalc1.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MCbound.precalc1.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MCbound.precalc1.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MCbound.precalc1.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MCbound.precalc1.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MCtest.Rd:39: Escaped LaTeX specials: \#
checkRd: (-1) MCtest.Rd:40: Escaped LaTeX specials: \#
Specified C++14: please drop specification unless essential
Specified C++11: please drop specification unless essential
Found the following significant warnings:
  cHDPHSMMnegbin.cc:570:28: warning: too many arguments for format [-Wformat-extra-args]
  cHMMpanelRE.cc:406:16: warning: too many arguments for format [-Wformat-extra-args]
  cHMMpanelRE.cc:407:16: warning: too many arguments for format [-Wformat-extra-args]
  cHMMpanelRE.cc:408:16: warning: too many arguments for format [-Wformat-extra-args]
  cHMMpanelRE.cc:409:16: warning: too many arguments for format [-Wformat-extra-args]
  cHMMpanelRE.cc:410:16: warning: too many arguments for format [-Wformat-extra-args]
  cMCMCoprobitChange.cc:49:13: warning: too many arguments for format [-Wformat-extra-args]
  cMCMCpaircompare2d.cc:448:15: warning: too many arguments for format [-Wformat-extra-args]
  cMCMCpaircompare2d.cc:449:15: warning: too many arguments for format [-Wformat-extra-args]
  cMCMCpaircompare2d.cc:450:15: warning: too many arguments for format [-Wformat-extra-args]
  cMCMCpaircompare2dDP.cc:765:25: warning: too many arguments for format [-Wformat-extra-args]
  cMCMCpaircompare2dDP.cc:766:25: warning: too many arguments for format [-Wformat-extra-args]
  cMCMCpaircompare2dDP.cc:767:25: warning: too many arguments for format [-Wformat-extra-args]
  cMCMCprobitres.cc:147:13: warning: too many arguments for format [-Wformat-extra-args]
  cMCMCprobitres.cc:148:13: warning: too many arguments for format [-Wformat-extra-args]
  cSSVSquantreg.cc:262:24: warning: format ‘%f’ expects argument of type ‘double’, but argument 2 has type ‘int’ [-Wformat=]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/MCMCpack.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-13 (Debian 13.2.0-7) 13.2.0’
* used C++ compiler: ‘g++-13 (Debian 13.2.0-7) 13.2.0’
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
Specified C++11: please drop specification unless essential
checkRd: (-1) ess.Rd:14: Lost braces
    14 | \code{g} should take a vector input only. Ifcode{g} is \code{NULL}, \code{g} is set to be identity, which is estimation
       |                                                 ^
Package suggested but not available for checking: ‘cmdstanr’
Found the following significant warnings:
  nsga2.c:300:13: warning: format ‘%i’ expects argument of type ‘int’, but argument 2 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
  nsga2.c:300:13: warning: format ‘%i’ expects argument of type ‘int’, but argument 3 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
  nsga2.c:306:13: warning: format ‘%i’ expects argument of type ‘int’, but argument 2 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
  nsga2.c:306:13: warning: format ‘%i’ expects argument of type ‘int’, but argument 3 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
  nsga2.c:336:15: warning: format ‘%i’ expects argument of type ‘int’, but argument 2 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
  nsga2.c:336:15: warning: format ‘%i’ expects argument of type ‘int’, but argument 3 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
  nsga2.c:342:15: warning: format ‘%i’ expects argument of type ‘int’, but argument 2 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
  nsga2.c:342:15: warning: format ‘%i’ expects argument of type ‘int’, but argument 3 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/mco.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-13 (Debian 13.2.0-7) 13.2.0’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'geom_cp_density.Rd':
  ‘include’

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

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

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) eigp.Rd:34: Escaped LaTeX specials: \&
checkRd: (-1) imcdiag.Rd:50: Escaped LaTeX specials: \&
checkRd: (-1) imcdiag.Rd:52: Escaped LaTeX specials: \&
checkRd: (-1) mc.plot.Rd:23: Escaped LaTeX specials: \&
checkRd: (-1) mc.plot.Rd:25: Escaped LaTeX specials: \&
checkRd: (-1) mctest.Rd:39: Escaped LaTeX specials: \&
checkRd: (-1) mctest.Rd:41: Escaped LaTeX specials: \&
checkRd: (-1) omcdiag.Rd:39: Escaped LaTeX specials: \&
checkRd: (-1) omcdiag.Rd:41: Escaped LaTeX specials: \&
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Initial version.
checkRd: (-1) mcvis.Rd:32: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mcvis.Rd:33: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mcvis.Rd:34: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) pBED.Rd:34: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) get_mdgc.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) get_mdgc.Rd:35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) get_mdgc.Rd:36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) get_mdgc.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) normalizeWithMA.Rd:19: Lost braces
    19 | 	\item{expGroup}{ a \code{vector} of experimental grouping variable such as plate. The length of code{expGroup} must be same as the number of rows of \code{mD}.}
       |                                                                                                             ^
Package suggested but not available for checking: ‘RGtk2’
'LazyData' is specified without a 'data' directory
checkRd: (-1) data.mb.Rd:76: Lost braces
    76 | level-1 variables code{y}, \code{x} and the level-2 variable \code{w}.
       |                       ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) mdp_example_forest.Rd:36: Lost braces; missing escapes or markup?
    36 | Let {1, ... S} be the states of the forest. the Sth state being the oldest.
       |     ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) Elections.Rd:8: Lost braces
     8 | An object of class \\code{tbl_df} (inherits from \\code{tbl}, \\code{data.frame}) 
       |                          ^
checkRd: (-1) Elections.Rd:8: Lost braces
     8 | An object of class \\code{tbl_df} (inherits from \\code{tbl}, \\code{data.frame}) 
       |                                                        ^
checkRd: (-1) Elections.Rd:8: Lost braces
     8 | An object of class \\code{tbl_df} (inherits from \\code{tbl}, \\code{data.frame}) 
       |                                                                     ^
checkRd: (-1) Violations.Rd:39-45: Lost braces
    39 | {
       | ^
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘MethylCapSig’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘cmdstanr’
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) bhm.mcmc.Rd:37: Lost braces; missing escapes or markup?
    37 |   where \eqn{N_{ij}} denotes the number of times that the error profile \eqn{i} is cited on a report from hospital {j} and \eqn{y_{ij}} is the corresponding number of times that profile \eqn{i} in hospital \eqn{j} was reported with harm.
       |                                                                                                                    ^
checkRd: (-1) strings-internal.Rd:14: Lost braces
    14 | code{stringPlaceExact}: find location of string, using exact match
       |     ^
checkRd: (-1) strings-internal.Rd:17: Lost braces
    17 | code{stringPlaceFuzzy}: find location of string, using partial match
       |     ^
checkRd: (-1) strings-internal.Rd:19: Lost braces
    19 | code{stringPlace}: find location of string, generic
       |     ^
checkRd: (-1) strings-internal.Rd:21: Lost braces
    21 | code{checkFuzzy}: check for "close" string matches
       |     ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) MED.Rd:25: Lost braces
    25 | The vector of treatment assignments of length \eqn{n}. Must be coded as \eqn{\{0,1} {{0,1}}.
       |                                                                                     ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) medScan.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) medScan.Rd:24-26: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘Data_Correlation.txt’ ‘correlation_FDR_table.txt’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) mgLandscape.Rd:79: Lost braces
    79 | A code{$summary} table giving the results of the variation partitioning.  The following table
       |       ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) Soybean.Rd:15: Escaped LaTeX specials: \#
checkRd: (-1) Soybean.Rd:33: Escaped LaTeX specials: \#
'LazyData' is specified without a 'data' directory
checkRd: (-1) Mercator-class.Rd:91-92: Lost braces
    91 |     \item{barplot{height, main = '', sub = NULL, border = NA, space =
       |                  ^
checkRd: (-1) Mercator-class.Rd:109-112: Lost braces
   109 |     \item{hist:}{\code{signature(object = "Mercator")}}{
       |                                                        ^
checkRd: (-1) Mercator-class.Rd:113-116: Lost braces
   113 |     \item{summary:}{\code{signature(object = "Mercator")}}{
       |                                                           ^
checkRd: (-1) Mercator-class.Rd:117-119: Lost braces
   117 |     \item{dim:}{\code{signature(object = "Mercator")}}{
       |                                                       ^
checkRd: (-1) Mercator-class.Rd:120-122: Lost braces
   120 |     \item{[:}{\code{signature(object = "Mercator")}}{
       |                                                     ^
checkRd: (-1) threshLGF.Rd:21: Lost braces; missing escapes or markup?
    21 |   \item{object}{An object of class {BinaryMatrix}
       |                                    ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) findFormFuns.Rd:26: Lost braces
    26 | term specified as \code{I(x^2)}, we were returning the mean of x{^2} not the
       |                                                                 ^
Documented arguments not in \usage in Rd file 'buildModelMatrix.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.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) expand.Rd:28: Lost braces; missing escapes or markup?
    28 | approximate dates (annotated with '..', '{ , }', 'XX' or '~').
       |                                          ^
Package suggested but not available for checking: ‘INLA’
'LazyData' is specified without a 'data' directory
checkRd: (-1) CVLasoelacox.Rd:68-69: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) CVLasoelacox.Rd:70-71: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) CVLasoelacox.Rd:72: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) CVLasoelacox.Rd:73: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) CVLasoelacox.Rd:74-76: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) CVLasoelacox.Rd:77-79: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) CVLasoelacox.Rd:80-81: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) CVLasoelacox.Rd:82-85: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) CVLasoelacox.Rd:86-87: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get_sort_var.Rd:14: Lost braces
    14 | * `"{{index}}"` : This means to use the index of rows/items
       |     ^
checkRd: (-1) get_sort_var.Rd:15: Lost braces
    15 | * `"{{name}}"`  : This means to use row/item names.
       |     ^
checkRd: (-1) get_sort_var.Rd:16: Lost braces
    16 | * `"{{value}}"` : This means to use the values in vectors or lists. Lists}
       |     ^
checkRd: (-1) lookup_tax_data.Rd:57: Lost braces
    57 | * `"{{index}}"` : This means to use the index of rows/items
       |     ^
checkRd: (-1) lookup_tax_data.Rd:58: Lost braces
    58 | * `"{{name}}"`  : This means to use row/item names.
       |     ^
checkRd: (-1) lookup_tax_data.Rd:59: Lost braces
    59 | * `"{{value}}"` : This means to use the values in vectors or lists. Lists
       |     ^
checkRd: (-1) parse_tax_data.Rd:82: Lost braces
    82 | following: * For tables, the names of columns can be used. * `"{{index}}"` : This means to use
       |                                                                ^
checkRd: (-1) parse_tax_data.Rd:83: Lost braces
    83 | the index of rows/items * `"{{name}}"`  : This means to use row/item names. * `"{{value}}"` :
       |                             ^
checkRd: (-1) parse_tax_data.Rd:83: Lost braces
    83 | the index of rows/items * `"{{name}}"`  : This means to use row/item names. * `"{{value}}"` :
       |                                                                                 ^
Invalid package aliases in Rd file 'taxa-package.Rd':
  ‘taxa-package’
Documented arguments not in \usage in Rd file 'limited_print.Rd':
  ‘trunc’

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

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

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘cycHumanBloodData.csv’ ‘cycHumanBloodDesign.csv’
  ‘cycMouseLiverProtein.txt’ ‘cycMouseLiverRNA.csv’ ‘cycSimu4h2d.csv’
  ‘cycYeastCycle.csv’ ‘example’
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'ClusterMF-deprecated.Rd':
  ‘formula’ ‘data’ ‘vi’ ‘study’ ‘whichweights’ ‘num.trees’ ‘mtry’
  ‘method’ ‘tau2’

Functions with \usage entries need to have the appropriate \alias
entries, and all their 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: 'Rcgmin', 'Rvmmin'
checkRd: (-1) conv.wald.Rd:109: Lost braces; missing escapes or markup?
   109 |       Note that the back-calculated sampling variance for study 2 is not identical in these two examples, because the CI bounds and p-value are rounded to two decimal places, which introduces some inaccuracies. Also, if both (\code{ci.lb}, \code{ci.ub}) and either \code{zval} or {pval} is available for a study, then the back-calculation of \mjseqn{v_i} via the confidence interval is preferred.
       |                                                                                                                                                                                                                                                                                         ^
Unknown packages ‘Rcgmin’, ‘Rvmmin’ in Rd xrefs
checkRd: (-1) datagenerator.Rd:17: Lost braces; missing escapes or markup?
    17 | Returns data frame with \code{n*K} rows (if \code{n} is a scalar), or \code{sum(n)} rows (if \code{n} is a \code{K}-element vector). The data frame contains columns "y", "x1", \dots, "x_{p-1}" and "group" if \code{family="gaussian"}, \code{"binomial"} or \code{"poisson"}; or contains columns "time", "status", "x1", \dots, "x_{p-1}" and "group" if \code{family="cox"}.
       |                                                                                                                                                                                           ^
checkRd: (-1) datagenerator.Rd:17: Lost braces; missing escapes or markup?
    17 | Returns data frame with \code{n*K} rows (if \code{n} is a scalar), or \code{sum(n)} rows (if \code{n} is a \code{K}-element vector). The data frame contains columns "y", "x1", \dots, "x_{p-1}" and "group" if \code{family="gaussian"}, \code{"binomial"} or \code{"poisson"}; or contains columns "time", "status", "x1", \dots, "x_{p-1}" and "group" if \code{family="cox"}.
       |                                                                                                                                                                                                                                                                                                                                        ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) asympVar_LinReg.Rd:52: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) asympVar_LinReg.Rd:53: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) asympVar_LinReg.Rd:54: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) asympVar_LinReg.Rd:55: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) asympVar_LinReg.Rd:56: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) asympVar_LogReg.Rd:55: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) asympVar_LogReg.Rd:56: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) asympVar_LogReg.Rd:57: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) asympVar_LogReg.Rd:58: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) asympVar_LogReg.Rd:59: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get_gamma_EB.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get_gamma_EB.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get_gamma_EB.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
checkRd: (-1) rland.graph.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rland.graph.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rland.graph.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rland.graph.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rland.graph.Rd:31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rland.graph.Rd:32: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rland.graph.Rd:33-34: Lost braces in \itemize; \value handles \item{}{} directly
Specified C++11: please drop specification unless essential
checkRd: (-1) metaplot.Rd:33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) metaplot.Rd:35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) metaplot.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) metaplot.Rd:39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) metaplot.Rd:41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) metaplot.Rd:43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) metaplot.Rd:45: Lost braces in \itemize; meant \describe ?
checkRd: (-1) metaplot.Rd:47: Lost braces in \itemize; meant \describe ?
checkRd: (-1) metaplot.Rd:49: Lost braces in \itemize; meant \describe ?
checkRd: (-1) metaplot.Rd:51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) metaplot.Rd:53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) metaplot.Rd:55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) metaplot.Rd:57: Lost braces in \itemize; meant \describe ?
checkRd: (-1) metaplot.Rd:59: Lost braces in \itemize; meant \describe ?
checkRd: (-1) metaplot.Rd:61: Lost braces in \itemize; meant \describe ?
checkRd: (-1) metaplot.Rd:63: Lost braces in \itemize; meant \describe ?
checkRd: (-1) metaplot.Rd:65: Lost braces in \itemize; meant \describe ?
checkRd: (-1) metaplot.Rd:71: Lost braces in \itemize; meant \describe ?
checkRd: (-1) metaplot.Rd:72: Lost braces in \itemize; meant \describe ?
checkRd: (-1) metaplot.Rd:73: Lost braces in \itemize; meant \describe ?
checkRd: (-1) metaplot.Rd:74: Lost braces in \itemize; meant \describe ?
Documented arguments not in \usage in Rd file 'plot.metaplot_gtable.Rd':
  ‘y’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) funnel.meta.Rd:105: Lost braces
   105 | \code{"invse"}, code{"size"}, code{"invsqrtsize"}, or
       |                     ^
checkRd: (-1) funnel.meta.Rd:105: Lost braces
   105 | \code{"invse"}, code{"size"}, code{"invsqrtsize"}, or
       |                                   ^
checkRd: (-1) funnel.meta.Rd:106: Lost braces
   106 | code{"ess"}.}
       |     ^
checkRd: (-1) param.Rd:29: Lost braces
    29 | T. Strub, S. Giuliano, T. Ye, et al. (2011) Essential role of microphthalmia transcription factor for DNA replication, mitosis and genomic stability in melanoma. emph{Oncogene} \bold{30}:2319-32.
       |                                                                                                                                                                       ^
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
checkRd: (-1) cardiac.Rd:15: Escaped LaTeX specials: \&
checkRd: (-1) plvol.Rd:14: Escaped LaTeX specials: \&
checkRd: (-1) sbp.Rd:16: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘MetProc_output.pdf’ ‘sample_removed.csv’ ‘sample_retained.csv’
Package suggested but not available for checking: ‘INLA’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Argument items with no description in Rd file 'predict.mfp.Rd':
  ‘safe’
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  matrix.c:144:17: warning: too many arguments for format [-Wformat-extra-args]
  misc.c:31:25: warning: format ‘%d’ 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/mgcv.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-13 (Debian 13.2.0-7) 13.2.0’
checkRd: (-1) summarize_stats_CSV.Rd:81: Lost braces; missing escapes or markup?
    81 | {stage}\emph{Mean}(patchNum).csv and {stage}\emph{Quantile}(quantNum)_(patchNum).csv.
       | ^
checkRd: (-1) summarize_stats_CSV.Rd:81: Lost braces; missing escapes or markup?
    81 | {stage}\emph{Mean}(patchNum).csv and {stage}\emph{Quantile}(quantNum)_(patchNum).csv.
       |                                      ^
checkRd: (-1) summarize_stats_CSV_decoupled.Rd:84: Lost braces; missing escapes or markup?
    84 | {stage}\emph{Mean}(patchNum).csv and {stage}\emph{Quantile}(quantNum)_(patchNum).csv.
       | ^
checkRd: (-1) summarize_stats_CSV_decoupled.Rd:84: Lost braces; missing escapes or markup?
    84 | {stage}\emph{Mean}(patchNum).csv and {stage}\emph{Quantile}(quantNum)_(patchNum).csv.
       |                                      ^
checkRd: (-1) calcQuantiles.Rd:52: Lost braces; missing escapes or markup?
    52 | {M/F}\emph{Mean}(patchNum).csv and {M/F}\emph{Quantile}(quantNum)_(patchNum).csv.
       | ^
checkRd: (-1) calcQuantiles.Rd:52: Lost braces; missing escapes or markup?
    52 | {M/F}\emph{Mean}(patchNum).csv and {M/F}\emph{Quantile}(quantNum)_(patchNum).csv.
       |                                    ^
checkRd: (-1) mgm.Rd:75: Lost braces; missing escapes or markup?
    75 | If \code{binarySign = TRUE}, a sign for the interaction within binary nodes and between binary and continuous nodes is provided in the output. Note that in this case the two categories of the binary variables have to be coded in {0,1}. This is to ensure that the interpretation of the sign is unambigous: a positive sign of a parameter means that increasing the associated predictor results in a higher probability for category 1.
       |                                                                                                                                                                                                                                      ^
checkRd: (-1) mvar.Rd:75: Lost braces; missing escapes or markup?
    75 | If \code{binarySign = TRUE}, a sign for the interaction within binary nodes and between binary and continuous nodes is provided in the output. Note that in this case the two categories of the binary variables have to be coded in {0,1}. This is to ensure that the interpretation of the sign is unambigous: a positive sign of a parameter means that increasing the associated predictor results in a higher probability for category 1.
       |                                                                                                                                                                                                                                      ^
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Invalid package aliases in Rd file 'Rpackage-package.Rd':
  ‘Rpackage-package’
Auto-generated content requiring editing in Rd file 'Rpackage-package.Rd':
  \references: ‘This optional section can contain literature or other refere...’
  \seealso: ‘Optional links to other man pages’
  \examples: ‘\dontrun{      ## Optional simple examples of the most impor...’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘structSSI’
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
S3 methods shown with full name in Rd file 'complete.miceadds.Rd':
  ‘complete.mids.nmi’ ‘complete.mids.1chain’

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.
Specified C++11: please drop specification unless essential
checkRd: (-1) VIF.Rd:47: Lost braces; missing escapes or markup?
    47 | vif_corrected = vif_basic^{(1/(2*df))}
       |                           ^
checkRd: (-1) ampute.Rd:143: Lost braces
   143 | we refer to \doi{10.1177/0049124118799376}{Schouten and Vink, 2018}.
       |                                           ^
checkRd: (-1) ampute.Rd:188: Lost braces
   188 | \doi{10.1080/00949655.2018.1491577}{Schouten, Lugtig and Vink, 2018}.
       |                                    ^
checkRd: (-1) ampute.Rd:223: Lost braces
   223 | Schouten, R.M. and Vink, G. (2018){The Dance of the Mechanisms: How Observed Information Influences the Validity of Missingness Assumptions}.
       |                                   ^
checkRd: (-1) mice.Rd:348: Lost braces; missing escapes or markup?
   348 | The \pkg{mice} software was published in the {Journal of Statistical Software} (Van Buuren and Groothuis-Oudshoorn, 2011). \doi{10.18637/jss.v045.i03}
       |                                              ^
checkRd: (-1) mice.impute.pmm.Rd:87: Lost braces; missing escapes or markup?
    87 | \item{Construct \eqn{n_0} sets \eqn{Z_j}, each containing \eqn{d} candidate donors, from Y_{obs} such that \eqn{\sum_d\dot\eta(i,j)} is minimum for all \eqn{j=1,\dots,n_0}. Break ties randomly.}
       |                                                                                            ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) linda.Rd:106: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) linda.Rd:107: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) linda.Rd:108: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) linda.Rd:109: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) linda.Rd:110: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) linda.Rd:111: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) linda.Rd:112: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) linda.Rd:113-114: Lost braces in \itemize; \value handles \item{}{} directly
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘microcontax.data’
Package unavailable to check Rd xrefs: ‘microcontax.data’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) NEWS.Rd:56: Lost braces; missing escapes or markup?
    56 |       \item Fix to CRS strings for stale sp data objects included with the package.  This was done in anticipation of updates to sp and rgdal.  This affects the \code{USstates}, \code{WSA3}, and {OrEcoLevel3} data objects used in the examples and the \code{txeco} data object used in the vignette.
       |                                                                                                                                                                                                    ^
Specified C++11: please drop specification unless essential
checkRd: (-1) addSchemes.Rd:13: Lost braces
    13 | \item{extraSchemes}{array of schemes to add, see code{\link{SetOfSchemes-class}}}
       |                                                      ^
checkRd: (-1) pkCurveStat.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pkCurveStat.Rd:31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pkCurveStat.Rd:32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rankObject.Rd:33-36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rankObject.Rd:37: Lost braces in \itemize; meant \describe ?
Documented arguments not in \usage in Rd file 'changeDevSettings.Rd':
  ‘defaultsSettings’

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

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
checkRd: (-1) readFastq.Rd:62: Lost braces
    62 | code{\link{readFasta}}.
       |     ^
checkRd: (-1) RNGStream.Rd:29: Lost braces
    29 | item{open}{function to use the current seed}
       |     ^
checkRd: (-1) RNGStream.Rd:29: Lost braces
    29 | item{open}{function to use the current seed}
       |           ^
checkRd: (-1) RNGStream.Rd:30: Lost braces
    30 | item{close}{function to make the current seed equal to .Random.seed}
       |     ^
checkRd: (-1) RNGStream.Rd:30: Lost braces
    30 | item{close}{function to make the current seed equal to .Random.seed}
       |            ^
checkRd: (-1) RNGStream.Rd:31: Lost braces
    31 | item{resetStream}{function to move back to start of stream}
       |     ^
checkRd: (-1) RNGStream.Rd:31: Lost braces
    31 | item{resetStream}{function to move back to start of stream}
       |                  ^
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    32 | item{resetSubStream}{function to move back to start of sub-stream}
       |     ^
checkRd: (-1) RNGStream.Rd:32: Lost braces
    32 | item{resetSubStream}{function to move back to start of sub-stream}
       |                     ^
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    33 | item{nextSubStream}{function to move to next sub-stream}
       |     ^
checkRd: (-1) RNGStream.Rd:33: Lost braces
    33 | item{nextSubStream}{function to move to next sub-stream}
       |                    ^
checkRd: (-1) RNGStream.Rd:34: Lost braces
    34 | item{nextStream}{function to move to next stream}
       |     ^
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    34 | item{nextStream}{function to move to next stream}
       |                 ^
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    73 | Be aware that this is only an approximation since this formula belongs to a time-homogeneuous Markov model and not to the more flexible time-inhomogeneuous Markov model (as used by MicSim). Thus, here for the time interval covered by $p_{ij}$ a time-homogeneuous Markov model is assumed. Many users may have annual transition probabilities at hand, i.e., \eqn{t=1}. 
       |                                                                                                                                                                                                                                              ^
Argument items with no description in Rd file 'micSimParallel.Rd':
  ‘transitionMatrix’ ‘absStates’ ‘varInitStates’ ‘initStatesProb’
  ‘fixInitStates’ ‘maxAge’ ‘simHorizon’ ‘fertTr’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Auto-generated content requiring editing in Rd file 'MIDASwrappeR-package.Rd':
  \references: ‘This optional section can contain literature or other refere...’
  \seealso: ‘Optional links to other man pages’
  \examples: ‘## Optional simple examples of the most important functions ...’
Package suggested but not available for checking: ‘midfielddata’
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'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
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    58 | \item{two vectors containing the cutpoints for each variable : \emph{cutpoints1} corresponds to /emph{myDist1}, /emph{cutpoints2} corresponds to /emph{myDist2}.}
       |                                                                                                      ^
checkRd: (-1) discretizeMutual.Rd:58: Lost braces
    58 | \item{two vectors containing the cutpoints for each variable : \emph{cutpoints1} corresponds to /emph{myDist1}, /emph{cutpoints2} corresponds to /emph{myDist2}.}
       |                                                                                                                      ^
checkRd: (-1) discretizeMutual.Rd:58: Lost braces
    58 | \item{two vectors containing the cutpoints for each variable : \emph{cutpoints1} corresponds to /emph{myDist1}, /emph{cutpoints2} corresponds to /emph{myDist2}.}
       |                                                                                                                                                       ^
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    62 | \item{if $emph{plot} == TRUE, a plot object (requires ggplot2 and gridExtra).}
       |               ^
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   426 | \link{MIIVsem}{miivs}
       |               ^
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    60 | Zena Lapp, {zenalapp@umich.edu}
       |            ^
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    62 | Kelly Sovacool, {sovacool@umich.edu}
       |                 ^
checkRd: (-1) create_grouped_k_multifolds.Rd:30: Lost braces; missing escapes or markup?
    30 | Zena Lapp, {zenalapp@umich.edu}
       |            ^
checkRd: (-1) get_partition_indices.Rd:58: Lost braces; missing escapes or markup?
    58 | Kelly Sovacool, {sovacool@umich.edu}
       |                 ^
checkRd: (-1) set_hparams_glmnet.Rd:16: Lost braces; missing escapes or markup?
    16 | Zena Lapp, {zenalapp@umich.edu}
       |            ^
Package suggested but not available for checking: ‘gurobi’
Specified C++11: please drop specification unless essential
checkRd: (-1) milr.Rd:45: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) milr.Rd:46-47: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) milr.Rd:48: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) milr.Rd:49: Lost braces in \itemize; \value handles \item{}{} directly
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    14 |   \item{BROADBND}{Cellular data plan for a smartphone or other mobile device}{1 yes 2 no}
       |                                                                              ^
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    21 |   \item{MHP}{Mobile home costs}{$, yearly}
       |                                ^
Documented arguments not in \usage in Rd file 'getvol.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
'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 significant warnings:
  subfunc.cpp:322:20: warning: ‘arma::mat_injector<arma::Mat<eT> > arma::Mat<eT>::operator<<(eT) [with eT = double]’ is deprecated: use braced initialiser list instead [-Wdeprecated-declarations]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/minimaxdesign.Rcheck/00install.out’ for details.
* used C++ compiler: ‘g++-13 (Debian 13.2.0-7) 13.2.0’
':::' call which should be '::': ‘parallel:::detectCores’
  See the note in ?`:::` about the use of this operator.
'LazyData' is specified without a 'data' directory
checkRd: (-1) gof.estimates.Rd:59-62: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) vcov.mipfp.Rd:63-66: Lost braces in \itemize; meant \describe ?
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GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
checkRd: (-1) sumKeepAttr.Rd:19: Lost braces
    19 |       (only relevant if code{x} has only one element).}
       |                             ^
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    47 | of \code{nlambda} and code{lambda.min.ratio}. Default is NULL}
       |                           ^
checkRd: (-1) cv.saenet.Rd:55: Lost braces
    55 | of \code{nlambda} and code{lambda.min.ratio}. Default is NULL}
       |                           ^
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    45 | of \code{nlambda} and code{lambda.min.ratio}. Default is NULL}
       |                           ^
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    53 | of \code{nlambda} and code{lambda.min.ratio}. Default is NULL}
       |                           ^
Documented arguments not in \usage in Rd file 'logAdd.Rd':
  ‘x’ ‘y’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Argument items with no description in Rd file 'randomizationTest.Rd':
  ‘R’
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    14 | plausible value in turn; with code{rewrite=FALSE} a new data set is
       |                                   ^
Specified C++11: please drop specification unless essential
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    64 |   code{\link{mixAR}},
       |       ^
Documented arguments not in \usage in Rd file 'mixAR-internal.Rd':
  ‘p’ ‘value’ ‘tau’ ‘etk’ ‘parscore’ ‘sigma’ ‘logpdf’

Functions with \usage entries need to have the appropriate \alias
entries, and all their 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 'rigaussian.Rd':
  ‘mu’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
checkRd: (-1) mixedBayes.Rd:65: Lost braces; missing escapes or markup?
    65 | When {structure="group"}, group-level selection will be conducted on \eqn{||\gamma_{3l}||_{2}}. If {structure="individual"}, individual-level selection will be conducted on each \eqn{\gamma_{3lq}}, (\eqn{q=1,\ldots,m}).
       |      ^
checkRd: (-1) mixedBayes.Rd:65: Lost braces; missing escapes or markup?
    65 | When {structure="group"}, group-level selection will be conducted on \eqn{||\gamma_{3l}||_{2}}. If {structure="individual"}, individual-level selection will be conducted on each \eqn{\gamma_{3lq}}, (\eqn{q=1,\ldots,m}).
       |                                                                                                    ^
checkRd: (-1) mixedBayes.Rd:67: Lost braces; missing escapes or markup?
    67 | When {slope=TRUE} (default), random intercept and slope model will be used as the mixed effects model.
       |      ^
checkRd: (-1) mixedBayes.Rd:69: Lost braces; missing escapes or markup?
    69 | When {sparse=TRUE} (default), spike--and--slab priors are imposed on individual and/or group levels to identify important main and interaction effects. Otherwise, Laplacian shrinkage will be used.
       |      ^
checkRd: (-1) mixedBayes.Rd:71: Lost braces; missing escapes or markup?
    71 | When {robust=TRUE} (default), the distribution of \eqn{\epsilon_{ij}} is defined as a Laplace distribution with density.
       |      ^
checkRd: (-1) mixedBayes.Rd:75: Lost braces; missing escapes or markup?
    75 | }, (\eqn{i=1,\dots,n,j=1,\dots,k }), which leads to a Bayesian formulation of quantile regression. If {robust=FALSE}, \eqn{\epsilon_{ij}} follows a normal distribution.
       |                                                                                                       ^
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
checkRd: (-1) SimCopulaSeries.Rd:16: Lost braces; missing escapes or markup?
    16 | \item{param}{extra copula parameter: for "fgm",  param in {2,3,...} is the dimension of the copula; for "t", param = nu}
       |                                                           ^
Documented arguments not in \usage in Rd file 'Sn_A.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.
checkRd: (-1) SLD.Rd:20: Escaped LaTeX specials: \&
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    35 |   \code{t * 1} and \code{B} is of dimension{t * N}. Ideally, \code{fun.sim}()
       |                                            ^
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checkRd: (-1) FindVariableFeaturesMix.Rd:33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FindVariableFeaturesMix.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FindVariableFeaturesMix.Rd:35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FindVariableFeaturesMix.Rd:36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FindVariableFeaturesMix.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FindVariableFeaturesMix.Rd:38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FindVariableFeaturesMix.Rd:39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FindVariableFeaturesMix.Rd:52: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FindVariableFeaturesMix.Rd:53: Lost braces in \itemize; meant \describe ?
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Bug Fix
    Update Vignettes
    Function Optimizing
    New Functions
    Vignette
    Optimization
    Fix Bugs
    Add New Function
    Update Description Files
    Fix bugs
    New .R files
    Update Old .R files
checkRd: (-1) combine.kernels.Rd:50-51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) combine.kernels.Rd:52-54: Lost braces
    52 |   \item \code{"full-UMKL"}{: computes a kernel that minimizes the distortion 
       |                           ^
checkRd: (-1) combine.kernels.Rd:55-56: Lost braces
    55 |   \item \code{"sparse-UMKL"}{: a sparse variant of the \code{"full-UMKL"} 
       |                             ^
checkRd: (-1) combine.kernels.Rd:36: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) combine.kernels.Rd:37-39: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) combine.kernels.Rd:40-41: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) kernel.pca.Rd:18: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) kernel.pca.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) kernel.pca.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) kernel.pca.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) kernel.pca.Rd:22-23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) kernel.pca.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) kernel.pca.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
Auto-generated content requiring editing in Rd file 'mixl-package.Rd':
  \references: ‘This optional section can contain literature or other refere...’
  \seealso: ‘Optional links to other man pages’
Specified C++11: please drop specification unless essential
checkRd: (-1) mixmeta-package.Rd:115: Escaped LaTeX specials: \&
checkRd: (-1) mixmeta.ml.Rd:56: Escaped LaTeX specials: \&
checkRd: (-1) ml.igls.Rd:62: Escaped LaTeX specials: \&
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checkRd: (-1) print.selectEM.Rd:18: Lost braces
    18 | The function \code{print.selectEM} is the print method for the class{selectEM}, which is the output
       |                                                                     ^
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Specified C++11: please drop specification unless essential
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'LazyData' is specified without a 'data' directory
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     9 |       (2) All x-coordinates of R1',..,Rn' are distinct, and take values in {1,..,2n}.
       |                                                                            ^
checkRd: (-1) real2canon.rd:10: Lost braces; missing escapes or markup?
    10 |       (3) All y-coordinates of R1',..,Rn' are distinct, and take values in {1,..,2n}.
       |                                                                            ^
checkRd: (-1) gp.list.Rd:16: Escaped LaTeX specials: \#
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No news entries found.
'LazyData' is specified without a 'data' directory
checkRd: (-1) MLGL.Rd:43: Lost braces; missing escapes or markup?
    43 | \item{y}{vector of size n. If loss = "logit", elements of y must be in {-1,1}}
       |                                                                        ^
checkRd: (-1) cv.MLGL.Rd:25: Lost braces; missing escapes or markup?
    25 | \item{y}{vector of size n. If loss = "logit", elements of y must be in {-1,1}}
       |                                                                        ^
checkRd: (-1) overlapgglasso.Rd:26: Lost braces; missing escapes or markup?
    26 | \item{y}{vector of size n. If loss = "logit", elements of y must be in {-1,1}}
       |                                                                        ^
checkRd: (-1) stability.MLGL.Rd:25: Lost braces; missing escapes or markup?
    25 | \item{y}{vector of size n. If loss = "logit", elements of y must be in {-1,1}}
       |                                                                        ^
checkRd: (-1) mlim.Rd:58: Lost braces
    58 |              Note that code{"XGB"} is only available in Mac OS and Linux. moreover,
       |                            ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) refBasedCts.Rd:44: Lost braces
    44 | using reference based imputation as proposed by \doi{10.1080/10543406.2013.834911}{Carpenter et al (2013)}. This approach
       |                                                                                   ^
Packages suggested but not available for checking:
  'ueadata1', 'ueadata2', 'ueadata3', 'ueadata4', 'ueadata5',
  'ueadata6', 'ueadata7', 'ueadata8'
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    19 |   \item{BMI}{Body mass index given by the formula (frac{kg}{meters^2}.}
       |                                                        ^
checkRd: (-1) hdp.Rd:19: Lost braces
    19 |   \item{BMI}{Body mass index given by the formula (frac{kg}{meters^2}.}
       |                                                            ^
checkRd: (-1) groupdiff_tau.Rd:23: Lost braces
    23 | \code{groupdiff_tau()} computes \eqn{min(x/y, y/x)}, i.e. the smallest symmetric ratio between \eqn{x} and eqn{y}
       |                                                                                                               ^
Documented arguments not in \usage in Rd file 'cpoTemplate.Rd':
  ‘affect.names’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
checkRd: (-1) MBOMultiObjResult.Rd:8: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) setMBOControlMultiObj.Rd:119-120: Lost braces
   119 | Notes in Computer Science, ISBN 978-3-642-37139-4, pp. 756{770,
       |                                                           ^
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checkRd: (-1) aggregations.Rd:50-54: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
Argument items with no description in Rd file 'mlVARsim0.Rd':
  ‘nPerson’ ‘nNode’ ‘nTime’ ‘sparsity’ ‘parRange’ ‘propPositive’
  ‘diagPositive’ ‘diagIncluded’ ‘sdRange’ ‘shrinkFactor’
  ‘residualStyle’ ‘residualShared’ ‘residualSDrange’ ‘verbose’
checkRd: (-1) simpopmlx.Rd:21: Lost braces; missing escapes or markup?
    21 | \item{fim}{the Fisher Information Matrix estimated by Monolix. fim={"sa", "lin"} (default="sa")}
       |                                                                    ^
Problems with news in ‘NEWS.md’:
No news entries found.
Found the following files/directories:
  ‘MM2S_Predictions_Heatmap.pdf’ ‘MM2S_Predictions_StackedBarplot.pdf’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) get_mean_sd_hour.Rd:20: Lost braces
    20 | A function for calcualting the average timing of variables (in this case the M10 and L5).  Find the average timing mu that min{ sum { min[ (tind_i - mu)^2, (1440 + mu - tind_i )^2 ]}}
       |                                                                                                                               ^
checkRd: (-1) get_mean_sd_hour.Rd:20: Lost braces; missing escapes or markup?
    20 | A function for calcualting the average timing of variables (in this case the M10 and L5).  Find the average timing mu that min{ sum { min[ (tind_i - mu)^2, (1440 + mu - tind_i )^2 ]}}
       |                                                                                                                                     ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) MMD_attr.Rd:62: Lost braces; missing escapes or markup?
    62 | \item Probability of attribution of each unknown individual to each source $p_{u,s}$
       |                                                                               ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) mmeln.Rd:69: Lost braces; missing escapes or markup?
    69 |   \item{obj$M}{Number of total observations sum_{i=1}^N(pi)}
       |                                                 ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) average.fit.models.Rd:6: Lost braces; missing escapes or markup?
     6 | These function takes the output of pgls.iter and uses its list of objects { model fits, optimzations (e.g.AICc)} and performs a weighted average on the ctoefficients estimated in the former by weighting by the latter. The parameters can also optionally be converted to binary by specifying "binary=FALSE" or just running the alias wraper function for assessing evidence of variable importance (Burnham & Anderson 2000).
       |                                                                           ^
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
checkRd: (-1) k2d.Rd:26: Lost braces
    26 | d_ND(x,y) = sqrt{ k(x,x) - 2k(x,y) + k(y,y)}.
       |                 ^
checkRd: (-1) k2d.Rd:34: Lost braces
    34 | d_n(x,y) = 1 - k(x,y)/sqrt{ k(x,x)k(y,y)},
       |                           ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) association.Rd:82: Lost braces in \itemize; meant \describe ?
checkRd: (-1) association.Rd:83: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) association.Rd:88: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) association.Rd:96: Lost braces in \itemize; meant \describe ?
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) rMNB.Rd:23: Lost braces; missing escapes or markup?
    23 | It simulates a multivariate response variable, Y_{ij}, that is jth measurement
       |                                                  ^
Rd files without \alias:
  ‘mnlfa-package.Rd’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) mom.mtruncnorm.Rd:35: Lost braces
    35 |   \item{cum}{a logical value; if  code{TRUE}  (default value), cumulants 
       |                                       ^
checkRd: (-1) mom.mtruncnorm.Rd:43: Lost braces; missing escapes or markup?
    43 | The maximal value of {d} is \code{20}. If this threshold is exceeded, \code{NA}s
       |                      ^
checkRd: (-1) mt.Rd:110: Lost braces
   110 |   and code{tvpack}, downloaded in 2005 and again in 2007 from his webpage, 
       |           ^
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Packages suggested but not available for checking: 'optiSel', 'alstructure'

Packages which this enhances but not available for checking:
  'miraculix', 'RandomFieldsUtils', 'MoBPSmaps'
checkRd: (-1) creating.phenotypic.transform.Rd:20: Lost braces
    20 | trafo <- function(x){ return(x^2)}
       |                     ^
'LazyData' is specified without a 'data' directory
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checkRd: (-1) lientz.Rd:46: Lost braces in \itemize; \value handles \item{}{} directly
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checkRd: (-1) vieu.Rd:56: Escaped LaTeX specials: \&
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'LazyData' is specified without a 'data' directory
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Specified C++11: please drop specification unless essential
checkRd: (-1) model.importance.plot.Rd:139: Lost braces
   139 | For binary CF models, if{importance.type = 2}, function uses AUC-based variables importances as described by Janitza et al. (2012). Here, the area under the curve instead of the accuracy is used to calculate the importance of each variable. This AUC-based variable importance measure is more robust towards class imbalance. 
       |                         ^
Documented arguments not in \usage in Rd file 'check_augment_data_specification.Rd':
  ‘strict’

Functions with \usage entries need to have the appropriate \alias
entries, and all their 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) geom_categorical_model.Rd:75: Lost braces; missing escapes or markup?
    75 | the {ggplot2} package, but provides functionality that \code{geom_smooth()}
       |     ^
checkRd: (-1) geom_parallel_slopes.Rd:85: Lost braces; missing escapes or markup?
    85 | {ggplot2} grouping aesthetics: \code{group}, \code{color}, \code{fill},
       | ^
checkRd: (-1) geom_parallel_slopes.Rd:87: Lost braces; missing escapes or markup?
    87 | {ggplot2} package, but provides functionality that \code{geom_smooth()}
       | ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Warning: no function found corresponding to methods exports from ‘moko’ for: ‘show’

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file.
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) CHECKSUCCESS.Rd:44: Escaped LaTeX specials: \&
checkRd: (-1) bfnormmix.Rd:53: Lost braces; missing escapes or markup?
    53 |   d(mu,Sigma)= [prod_{j<l} (mu_j-mu_l)' A (mu_j-mu_l)]
       |                      ^
checkRd: (-1) bfnormmix.Rd:55: Lost braces; missing escapes or markup?
    55 |   and A is the average of Sigma_1^{-1},...,Sigma_k^{-1}. Note that
       |                                   ^
checkRd: (-1) bfnormmix.Rd:55: Lost braces; missing escapes or markup?
    55 |   and A is the average of Sigma_1^{-1},...,Sigma_k^{-1}. Note that
       |                                                    ^
checkRd: (-1) localnulltest.Rd:89: Lost braces; missing escapes or markup?
    89 |   y[i]= beta_0(z[i]) + sum_{j=1}^p beta_j(z[i], x[i]) + e[i]
       |                            ^
checkRd: (-1) msPriorSpec-class.Rd:141: Lost braces; missing escapes or markup?
   141 |   p_z(delta; tau)= prod_j N(delta_j; 0, (tau/p_j)) (X_j'X_j)^{-1})
       |                                                              ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) year-methods.Rd:76: Lost braces; missing escapes or markup?
    76 | \code{month} returns the month \code{numeric} {1, ..., 12}.
       |                                               ^
Argument items with no description in Rd file 'as.difftime.rd':
  ‘tim’ ‘format’
'LazyData' is specified without a 'data' directory
checkRd: (-1) TemplateList-class.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) TemplateList-class.Rd:30: Lost braces in \itemize; meant \describe ?
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    21 | The distance between two observations {i} and {j} of a circular variable {q}
       |                                       ^
checkRd: (-1) circ_dist.Rd:21: Lost braces; missing escapes or markup?
    21 | The distance between two observations {i} and {j} of a circular variable {q}
       |                                               ^
checkRd: (-1) circ_dist.Rd:21: Lost braces; missing escapes or markup?
    21 | The distance between two observations {i} and {j} of a circular variable {q}
       |                                                                          ^
checkRd: (-1) legacy.Rd:27: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) morphemepiece_cache_dir.Rd:17-19: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) morphemepiece_cache_dir.Rd:22-24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.LCx.Rd:34: Lost braces
    34 | \\code{LCx} class. It plots the survival probability as a function of concentration.
       |       ^
checkRd: (-1) mortaar_life_table.Rd:7: Lost braces; missing escapes or markup?
     7 | \title{{mortaar_life_table} and {mortaar_life_table_list}}
       |                                 ^
checkRd: (-1) MortalityLaw.Rd:79-81: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) MortalityLaw.Rd:82-84: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) MortalityLaw.Rd:85-86: Lost braces in \enumerate; meant \describe ?
'LazyData' is specified without a 'data' directory
checkRd: (-1) ssvdEN_sol_path.Rd:58: Lost braces; missing escapes or markup?
    58 | \item{tol}{Convergence is determined when ||U_j - U_{j-1}||_F < tol,
       |                                                     ^
checkRd: (-1) ssvdEN_sol_path_par.Rd:59: Lost braces; missing escapes or markup?
    59 | \item{tol}{Convergence is determined when ||U_j - U_{j-1}||_F < tol,
       |                                                     ^
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in Rd file 'create_barrier_cs.Rd':
  ‘fields’

Functions with \usage entries need to have the appropriate \alias
entries, and all their 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) brownian.motion.variance.dyn.Rd:39: Lost braces
    39 | 	\link{brownian.bridge.dyn}, link{dynBGBvariance}
       |                                         ^
Package suggested but not available for checking: ‘corpus.useR.2008.abstracts’
Specified C++11: please drop specification unless essential
checkRd: (-1) thresh.est.Rd:16: Lost braces
    16 |   Calculates the stimulus level(s) for a probit model of a psychometric function for given levels of performance.  For a more general version, see \link[MASS]{dose.p} in pkg{MASS}.
       |                                                                                                                                                                              ^
checkRd: (-1) genotype_data.Rd:7: Escaped LaTeX specials: \_
checkRd: (-1) genotype_data.Rd:18: Escaped LaTeX specials: \_
checkRd: (-1) phenotype_data.Rd:15: Escaped LaTeX specials: \_
Rd files without \alias:
  ‘MPLikelihoodWB-package.Rd’
checkRd: (-1) glmfence.Rd:21: Lost braces; missing escapes or markup?
    21 | is performed where the boundary is cstar*hat(sigma)_{M,tildeM}.}
       |                                                     ^
checkRd: (-1) lmfence.Rd:21: Lost braces; missing escapes or markup?
    21 | is performed where the boundary is cstar*hat(sigma)_{M,tildeM}.}
       |                                                     ^
Documented arguments not in \usage in Rd file 'addHeaderToSavedata.Rd':
  ‘director’

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

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

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

Functions with \usage entries need to have the appropriate \alias
entries, and all their 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) apc.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) apc.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) apc.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
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checkRd: (-1) mpn.Rd:28-29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mpn.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mpn.Rd:31-35: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mpn.Rd:36-40: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mpn.Rd:41: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mpn.Rd:42: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mpn.Rd:43: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mpn.Rd:44: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mpn.Rd:45: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
checkRd: (-1) get.mpt.fia.Rd:60: Lost braces
    60 | \item{lnconst}{When inequality constraints are present, \code{lnconst} serves as an adjustment of code{lnInt}. It estimates the logarithm of the proportion of parameter space [0,1]^S that satisfies those inequality constraints, and the log integral term is given by \code{lnInt+lnconst}.
       |                                                                                                       ^
checkRd: (-1) prediction.plot.Rd:38: Lost braces
    38 | The labels on the x-axis. Default is \code{Tree 1} to code{Tree n}.
       |                                                           ^
'LazyData' is specified without a 'data' directory
Objects in \usage without \alias in Rd file 'Mqrcm-internal.Rd':
  ‘check.in’ ‘check.out’ ‘start.theta’ ‘iMqr.internal’ ‘cov.theta’
  ‘iobjfun’ ‘sortH’ ‘isigma’ ‘iMqr.newton’ ‘num.fun’ ‘make.bfun’
  ‘apply_bfun’ ‘p.bisec’ ‘slp.basis’ ‘is.slp’ ‘iqr.waldtest’
  ‘extract.p’ ‘pred.beta’ ‘print.iMqr’ ‘print.summary.iMqr’
  ‘terms.iMqr’ ‘model.matrix.iMqr’ ‘vcov.iMqr’ ‘nobs.iMqr’

Functions with \usage entries need to have the appropriate \alias
entries, and all their 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) F.huggins.estim.Rd:199: Escaped LaTeX specials: \$ \$
checkRd: (-1) F.huggins.estim.Rd:205: Escaped LaTeX specials: \$
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checkRd: (-1) lines.cjs.Rd:15: Escaped LaTeX specials: \$
checkRd: (-1) mvmr_egger_rjags.Rd:51-59: Lost braces
    51 | if (requireNamespace("rjags", quietly = TRUE)) {
       |                                                ^
GNU make is a SystemRequirements.
Auto-generated content requiring editing in Rd file 'mrbsizer-package.Rd':
  \references: ‘This optional section can contain literature or other refere...’
  \seealso: ‘Optional links to other man pages’
  \examples: ‘\dontrun{      ## Optional simple examples of the most impor...’
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'rgdal', 'rgeos'
checkRd: (-1) MultiManhattan.Rd:33: Lost braces; missing escapes or markup?
    33 | 	\item{LogTimes}{Magnification of {-log10(P-value)}; the default is
       |                                          ^
checkRd: (-1) MultiManhattan.Rd:35: Lost braces; missing escapes or markup?
    35 |     \item{LODTimes}{Magnification of {LOD score}; the default is 1.2.}
       |                                      ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) bmi.bmi.Rd:14: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) bmi.bmi.Rd:15: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) bmi.bmi.Rd:16: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) bmi.sbp.Rd:14: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) bmi.sbp.Rd:15: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) bmi.sbp.Rd:16: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) data_binary.Rd:10: Lost braces; missing escapes or markup?
    10 |            log E(Y_{t+1} | A_t = 0, I_t = 1) = alpha_0 + alpha_1 * time / total_T
       |                    ^
checkRd: (-1) aenet.Rd:64: Lost braces; missing escapes or markup?
    64 | default is {FALSE}. To enable parallel tuning, load the
       |            ^
checkRd: (-1) amnet.Rd:59: Lost braces; missing escapes or markup?
    59 | default is {FALSE}. To enable parallel tuning, load the
       |            ^
checkRd: (-1) asnet.Rd:59: Lost braces; missing escapes or markup?
    59 | default is {FALSE}. To enable parallel tuning, load the
       |            ^
checkRd: (-1) msaenet.Rd:80: Lost braces; missing escapes or markup?
    80 | default is {FALSE}. To enable parallel tuning, load the
       |            ^
checkRd: (-1) msamnet.Rd:74: Lost braces; missing escapes or markup?
    74 | default is {FALSE}. To enable parallel tuning, load the
       |            ^
checkRd: (-1) msasnet.Rd:74: Lost braces; missing escapes or markup?
    74 | default is {FALSE}. To enable parallel tuning, load the
       |            ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) msa-package.Rd:17: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) msa-package.Rd:19: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) msa-package.Rd:21: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) msa.Rd:65: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) msa.Rd:67: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) msa.Rd:69: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) msa.Rd:42: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) msa.Rd:43: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) msa.Rd:44: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) msa.Rd:45: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) msa.Rd:47: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) msa.Rd:48: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) summary.msa.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) summary.msa.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) summary.msa.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) summary.msa.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) summary.msa.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) summary.msa.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) summary.msa.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) n.Rd:46: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) n.Rd:47-48: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) n.Rd:49-50: Lost braces in \itemize; \value handles \item{}{} directly
Specified C++11: please drop specification unless essential
checkRd: (-1) SignalProcessing.Rd:42: Lost braces; missing escapes or markup?
    42 |   \item{calibrateIntensity_method}{a \code{character} indicating the intensities calibration method used (\code{"TIC"} method by default).  This calibration method can be remplaced by \code{"PQN"} or {"median"}.See \code{calibrateIntensity-methods} of the \code{MALDIquant} R package for details.}
       |                                                                                                                                                                                                         ^
'LazyData' is specified without a 'data' directory
Argument items with no description in Rd file 'msda.Rd':
  ‘sml’
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'CalcMPDynamics.Rd':
  ‘M_ageArray’ ‘TAC_f’ ‘E_f’ ‘SizeLim_f’ ‘FinF’ ‘Spat_targ’
  ‘CAL_binsmid’ ‘Linf’ ‘Len_age’ ‘maxage’ ‘nareas’ ‘Asize’ ‘nCALbins’
  ‘qs’ ‘qvar’ ‘qinc’

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

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

Documented arguments not in \usage in Rd file 'qestMICE.Rd':
  ‘mod’ ‘plusgroup.’ ‘WtC’

Functions with \usage entries need to have the appropriate \alias
entries, and all their 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:
  ‘test.txt’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘Acceleration.pdf’ ‘File1.pdf’ ‘Forecast.pdf’ ‘Series.pdf’
  ‘Velocity.pdf’
checkRd: (-1) ml_g.Rd:47: Escaped LaTeX specials: \&
Argument items with no description in Rd file 'DAGOSTINO.Rd':
  ‘data’
Argument items with no description in Rd file 'HZ.test.Rd':
  ‘data’
Argument items with no description in Rd file 'MardiaTest.Rd':
  ‘data’
Argument items with no description in Rd file 'Royston.test.Rd':
  ‘data’
Argument items with no description in Rd file 'gen.var.Rd':
  ‘\dots’
Argument items with no description in Rd file 'larg.ellip.Rd':
  ‘n’ ‘box’ ‘add’ ‘xlim’ ‘ylim’ ‘zlim’ ‘xlab’ ‘ylab’ ‘zlab’ ‘col’
  ‘alpha’ ‘\dots’
Argument items with no description in Rd file 'prism.Rd':
  ‘add’
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
checkRd: (-1) ms_sev.Rd:31: Escaped LaTeX specials: \_
Invalid package aliases in Rd file 'ms_sev-package.Rd':
  ‘ms_sev-package’
Found the following significant warnings:
  PF.cpp:44:43: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘long int’ [-Wformat=]
  laplace.cpp:519:24: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘long unsigned int’ [-Wformat=]
  laplace.cpp:559:24: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘long unsigned int’ [-Wformat=]
  laplace.cpp:559:29: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘long unsigned int’ [-Wformat=]
  laplace.cpp:628:24: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘long unsigned int’ [-Wformat=]
  laplace.cpp:630:24: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘long unsigned int’ [-Wformat=]
  problem_data.cpp:60:21: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘long int’ [-Wformat=]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/mssm.Rcheck/00install.out’ for details.
* used C++ compiler: ‘g++-13 (Debian 13.2.0-7) 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
checkRd: (-1) multivar_joint_shannon_entropy.Rd:20: Lost braces
    20 |     {\code{table.variables}, \code{table.class}}.
       |     ^
checkRd: (-1) total_correlation.Rd:20: Lost braces
    20 |     {\code{table.variables}, \code{table.class}}.
       |     ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) time_plot_event.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) time_plot_event.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) time_plot_event.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) time_plot_event.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) time_plot_event.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) time_plot_event.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) time_plot_event.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) time_plot_event.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) time_plot_interval.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) time_plot_interval.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) time_plot_interval.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) time_plot_interval.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) time_plot_interval.Rd:23: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
S3 methods shown with full name in Rd file 'data.visualisation.Rd':
  ‘lda.plot.wrap.1’

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) mkjnw.Rd:3: Escaped LaTeX specials: \&
checkRd: (-1) mkjnw.Rd:6: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) coef.mdf.Rd:17: Lost braces; missing escapes or markup?
    17 |   \item{type}{: Argument that controls the type of parameters to be returned. If \code{type="persons"} (default), a vector with the person parameters is returned. When \code{type="items"} then a vector with the item ranks obtained by the MUDFOLD item selection algorithm is returned. If {type="all"} then a list with both person and item coefficients is returned to the user.
       |                                                                                                                                                                                                                                                                                                ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in Rd file 'plotBoxes.Rd':
  ‘lwd’ ‘T.base’ ‘font.family’ ‘fig’ ‘mar’

Documented arguments not in \usage in Rd file 'plotLetters.Rd':
  ‘width’ ‘lwd’ ‘label.groups’ ‘T.base’ ‘orientation’

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

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
checkRd: (-1) MultEq-package.Rd:26-27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MultEq-package.Rd:28-29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MultEq-package.Rd:30: Lost braces in \itemize; meant \describe ?
'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
checkRd: (-1) dbivCMP.Rd:14: Lost braces; missing escapes or markup?
    14 | \item{bivprob}{Bivariate probabilities, {p00, p01, p10, p11}.}
       |                                         ^
checkRd: (-1) PPCA.Rd:35: Lost braces
    35 | Returns an object of class 'pcaRes.'  See documentation in the package code{\link[pcaMethods:pcaMethods]{ pcaMethods}}
       |                                                                            ^
Documented arguments not in \usage in Rd file 'Trace.Rd':
  ‘x’

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

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

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

Documented arguments not in \usage in Rd file 'select_initial_Iter.Rd':
  ‘X’ ‘parametrs’

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

Documented arguments not in \usage in Rd file 'similarity_noncum.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.
Package suggested but not available for checking: ‘cmdstanr’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
checkRd: (-1) LayerMeasures.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) LayerMeasures.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) LayerMeasures.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Plot.Rd:38: Lost braces; missing escapes or markup?
    38 | \item{vertex.shape}{Symbol to use for nodes, corresponding to the parameter {pch} of the R \code{points} function.  This can either
       |                                                                             ^
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
checkRd: (-1) heck2017.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) heck2017.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) heck2017.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) heck2017.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) hilbig2014.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) hilbig2014.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) hilbig2014.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nirt_to_Ab.Rd:32-33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nirt_to_Ab.Rd:34-35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nirt_to_Ab.Rd:36-38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) strategy_multiattribute.Rd:29-32: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) strategy_multiattribute.Rd:33: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) strategy_multiattribute.Rd:34: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) strategy_multiattribute.Rd:35: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) strategy_multiattribute.Rd:36: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) swop5.Rd:21: Lost braces; missing escapes or markup?
    21 | for all 10 paired comparisons of 5 choice elements {a,b,c,d,e} in a
       |                                                    ^
Package suggested but not available for checking: ‘rrelaxiv’
checkRd: (-1) mPhen.defineOptions.Rd:4: Escaped LaTeX specials: \$
GNU make is a SystemRequirements.
checkRd: (-1) nullestimation.Rd:17: Lost braces; missing escapes or markup?
    17 |           \code{U}        \tab The common latent space vectors. U in R^{n x d}\cr
       |                                                                        ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) biomasse.Rd:30: Lost braces
    30 | Makowski, D., Jeuffroy, M.-H., Gu\'{e}rif, M., 2004 Bayesian methods for
       |                                    ^
checkRd: (-1) climat.Rd:20: Lost braces
    20 | Makowski, D., Jeuffroy, M.-H., Gu\'{e}rif, M., 2004 Bayesian methods for
       |                                    ^
checkRd: (-1) simulmodel.Rd:15: Lost braces
    15 |   \item{\dots}{... }{possible fixed parameters of the R-function}
       |                     ^
checkRd: (-1) Distancia.Rd:148: Lost braces
   148 | /code{/link{dist}/}
       |      ^
checkRd: (-1) Distancia.Rd:148: Lost braces
   148 | /code{/link{dist}/}
       |            ^
checkRd: (-1) HeatPlot.Rd:81: Lost braces
    81 | /code{/link{Distancia}/} ,/code{/link{Dendrograma}/}, /code{/link{heatplot}/}
       |      ^
checkRd: (-1) HeatPlot.Rd:81: Lost braces
    81 | /code{/link{Distancia}/} ,/code{/link{Dendrograma}/}, /code{/link{heatplot}/}
       |            ^
checkRd: (-1) HeatPlot.Rd:81: Lost braces
    81 | /code{/link{Distancia}/} ,/code{/link{Dendrograma}/}, /code{/link{heatplot}/}
       |                                ^
checkRd: (-1) HeatPlot.Rd:81: Lost braces
    81 | /code{/link{Distancia}/} ,/code{/link{Dendrograma}/}, /code{/link{heatplot}/}
       |                                      ^
checkRd: (-1) HeatPlot.Rd:81: Lost braces
    81 | /code{/link{Distancia}/} ,/code{/link{Dendrograma}/}, /code{/link{heatplot}/}
       |                                                            ^
checkRd: (-1) HeatPlot.Rd:81: Lost braces
    81 | /code{/link{Distancia}/} ,/code{/link{Dendrograma}/}, /code{/link{heatplot}/}
       |                                                                  ^
checkRd: (-1) Normatiza.Rd:55: Lost braces
    55 | /code{/link{dist}/}
       |      ^
checkRd: (-1) Normatiza.Rd:55: Lost braces
    55 | /code{/link{dist}/}
       |            ^
checkRd: (-1) SummaryDistancia.Rd:98: Lost braces
    98 | /code{/link{dist}/}
       |      ^
checkRd: (-1) SummaryDistancia.Rd:98: Lost braces
    98 | /code{/link{dist}/}
       |            ^
Specified C++11: please drop specification unless essential
checkRd: (-1) durante.Rd:60-61: Lost braces
    60 | in their study, \doi{10.1177/0956797612466416}{\emph{The
       |                                               ^
checkRd: (-1) hurricane.Rd:34: Lost braces
    34 | in their study, \doi{10.1073/pnas.1402786111}{\emph{Female hurricanes are deadlier than male hurricanes}}.
       |                                              ^
checkRd: (-1) userlogs.Rd:33: Lost braces
    33 | \doi{10.1145/2470654.2481359}{Evaluating the Efficiency of Physical Visualizations}
       |                              ^
Specified C++11: please drop specification unless essential
checkRd: (-1) metricUnfolding.Rd:69-70: Lost braces in \itemize; meant \describe ?
checkRd: (-1) metricUnfolding.Rd:71-72: Lost braces in \itemize; meant \describe ?
checkRd: (-1) metricUnfolding.Rd:73-74: Lost braces in \itemize; meant \describe ?
checkRd: (-1) metricUnfolding.Rd:75-79: Lost braces in \itemize; meant \describe ?
checkRd: (-1) metricUnfolding.Rd:80-86: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotLociHC.Rd:55: Lost braces; missing escapes or markup?
    55 | If \code{value} is one of {0.2,0.4,0.6,0.8,1,2,3,4,5,6,7,8,9,10}
       |                           ^
Documented arguments not in \usage in Rd file 'check_mnsl.Rd':
  ‘fix’

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

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) cv.glm1path.Rd:74: Lost braces
    74 | \code{\link{glm1path}}, \\code{\link{glm1}}, \code{\link{glm}}, \code{\link{family}}
       |                               ^
checkRd: (-1) hurricane.Rd:47-48: Lost braces
    47 | \doi{10.1073/pnas.1402786111}{Female hurricanes are
       |                              ^
checkRd: (-1) hurricane.Rd:55: Lost braces
    55 | \doi{10.1038/s41562-020-0912-z}{Specification curve analysis}
       |                                ^
checkRd: (-1) soccer.Rd:67: Lost braces; missing escapes or markup?
    67 | {rater1} and {rater2}, and the 5-point scale values were
       | ^
checkRd: (-1) soccer.Rd:67: Lost braces; missing escapes or markup?
    67 | {rater1} and {rater2}, and the 5-point scale values were
       |              ^
checkRd: (-1) bal.Rd:156: Escaped LaTeX specials: \&
checkRd: (-1) MVNtestchar-package.Rd:16-17: Lost braces; missing escapes or markup?
    16 | {Provides a test of multivariate normality of a sample which does not require estimation of the nuisance parameters, the mean      vector and covariance matrix.  Rather, a sequence of transformations removes these nuisance parameters, resulting in a set of    sample matrices that are positive definite.  If, and only if the original data is multivariate normal, these matrices are       uniformly distributed on the space of positive definite matrices in the unit hyper-rectangle.  The package performs a goodness    of fit test of this hypothesis. In addition to the test, functions in the package give visualizations of the  support region    of positive definite matrices for p equals 2.
       | ^
checkRd: (-1) pkb.Rd:14: Escaped LaTeX specials: \# \# \#
checkRd: (-1) dmvss.Rd:92: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dmvss.Rd:93: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dmvss.Rd:94: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dmvss.Rd:95: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dmvss.Rd:96: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pmvss.Rd:97: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pmvss.Rd:98: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pmvss.Rd:99: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pmvss.Rd:100: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pmvss.Rd:101: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) bbc.Rd:39: Lost braces
    39 | The "nbdev.mxm" (negative binomial deviance) is missing. For more information on these see \code{\link{cv.ses}}. bold{Note} that they come with "".
       |                                                                                                                      ^
checkRd: (-1) cv.fbed.lmm.reg.Rd:32: Lost braces; missing escapes or markup?
    32 | The folds of the data to use (a list generated by the function generateCVRuns {TunePareto}). If NULL the folds are created internally with the same function.
       |                                                                               ^
checkRd: (-1) cv.gomp.Rd:29: Lost braces; missing escapes or markup?
    29 | The folds of the data to use (a list generated by the function generateCVRuns {TunePareto}). If NULL the folds are created internally with the same function.
       |                                                                               ^
checkRd: (-1) cv.ses.Rd:94: Lost braces; missing escapes or markup?
    94 | The folds of the data to use (a list generated by the function generateCVRuns {TunePareto}). If NULL the folds are created internally with the same function.
       |                                                                               ^
Package suggested but not available for checking: ‘rTubeDB’
Package unavailable to check Rd xrefs: ‘rTubeDB’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) mzipmed_data.Rd:22: Lost braces; missing escapes or markup?
    22 | @source {Simulated to serve as an example}
       |         ^
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
checkRd: (-1) PipeOpMice.Rd:33: Lost braces; missing escapes or markup?
    33 | set of methods to chose. Avalible methods {"pmm", "midastouch", "sample", "cart", "rf"} Default 'pmm'. If seted on NULL this methods are used predictive mean matching (numeric data) logreg, logistic regression imputation (binary data, factor with 2 levels) polyreg, polytomous regression imputation for unordered categorical data (factor > 2 levels) polr, proportional odds model for (ordered, > 2 levels).
       |                                           ^
checkRd: (-1) M36NT2PM.dat.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) M36NT2PM.dat.Rd:38: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
checkRd: (-1) DSIVdata.Rd:15-23: Lost braces
    15 | for(i in 1:50){
       |               ^
checkRd: (-1) DSIVdata.Rd:17-21: Lost braces
    17 |   for(j in 1:50){
       |                 ^
checkRd: (-1) DSIVdata.Rd:31-39: Lost braces
    31 | for(i in 1:20){
       |               ^
checkRd: (-1) DSIVdata.Rd:33-37: Lost braces
    33 |   for(j in 1:20){
       |                 ^
checkRd: (-1) DSLIVEdata.Rd:10-18: Lost braces
    10 | for(i in 1:200){
       |                ^
checkRd: (-1) DSLIVEdata.Rd:12-16: Lost braces
    12 |   for(j in 1:200){
       |                  ^
checkRd: (-1) DSLIVEdata.Rd:26-34: Lost braces
    26 | for(i in 1:20){
       |               ^
checkRd: (-1) DSLIVEdata.Rd:28-32: Lost braces
    28 |   for(j in 1:20){
       |                 ^
checkRd: (-1) DSLIVEdata.Rd:50-54: Lost braces
    50 | for(kk in 1:length(p)){
       |                       ^
Package suggested but not available for checking: ‘re2r’
Argument items with no description in Rd file 'check_subject_pattern.Rd':
  ‘subject.vec’ ‘pattern’
Argument items with no description in Rd file 'names_or_error.Rd':
  ‘pattern’
Argument items with no description in Rd file 'only_captures.Rd':
  ‘match.mat’ ‘pattern’
Argument items with no description in Rd file 'stop_for_names.Rd':
  ‘pattern’
checkRd: (-1) drop_name_crossref.Rd:49: Lost braces; missing escapes or markup?
    49 | Takes one or several dois and extracts information from Crossref, then processes them into visual citations with \code{\link{drop_name}}. Requires {rcrossref} > v1.1, see README for further details.
       |                                                                                                                                                    ^
checkRd: (-1) mcar_test.Rd:28: Lost braces; missing escapes or markup?
    28 | Code is adapted from LittleMCAR() in the now-orphaned {BaylorEdPsych}
       |                                                       ^
checkRd: (-1) mcar_test.Rd:31: Lost braces; missing escapes or markup?
    31 | using Maximum likelihood estimation from {norm}.
       |                                          ^
Specified C++11: please drop specification unless essential
checkRd: (-1) nanoperiod.Rd:268: Lost braces
   268 | possible to use the binary operator `code{+}`. Instead the
       |                                          ^
checkRd: (-1) fod.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fod.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fod.Rd:14: Lost braces in \itemize; meant \describe ?
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘spatialClust’
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Version (2018-01-22)
    Version  (2017-08-22)
    Version
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘gurobi’
Packages suggested but not available for checking:
  'rgeos', 'rgdal', 'maptools'
checkRd: (-1) classify_occ.Rd:134-136: Lost braces in \itemize; meant \describe ?
checkRd: (-1) classify_occ.Rd:137-138: Lost braces in \itemize; meant \describe ?
checkRd: (-1) classify_occ.Rd:139-140: Lost braces in \itemize; meant \describe ?
checkRd: (-1) classify_occ.Rd:141-142: Lost braces in \itemize; meant \describe ?
checkRd: (-1) classify_occ.Rd:143-144: Lost braces in \itemize; meant \describe ?
checkRd: (-1) classify_occ.Rd:145: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Invalid package aliases in Rd file 'NBBttest-package.Rd':
  ‘NBBtatest-package’
checkRd: (-1) NbClust.Rd:50: Lost braces; missing escapes or markup?
    50 |       \item \bold{Average} : The distance \eqn{D_{ij}}{D_ij} between two clusters \eqn{C_{i}}{C_i} and \eqn{C_{j}}{C_j} is the mean of the distances between the pair of points {x} and {y}, where \eqn{x \in C_{i}, y \in C_{j}}{x in C_i, y in C_j}.
       |                                                                                                                                                                                 ^
checkRd: (-1) NbClust.Rd:50: Lost braces; missing escapes or markup?
    50 |       \item \bold{Average} : The distance \eqn{D_{ij}}{D_ij} between two clusters \eqn{C_{i}}{C_i} and \eqn{C_{j}}{C_j} is the mean of the distances between the pair of points {x} and {y}, where \eqn{x \in C_{i}, y \in C_{j}}{x in C_i, y in C_j}.
       |                                                                                                                                                                                         ^
checkRd: (-1) nbconvert.Rd:49: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) nbconvert.Rd:50: Lost braces in \enumerate; meant \describe ?
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Documented arguments not in \usage in Rd file 'Moth.Rd':
  ‘delta.ident’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) ncpen.Rd:108: Lost braces; missing escapes or markup?
   108 |   \item{gamma}{extra shrinkage parameter for \code{classo} and {sridge} only.}
       |                                                                ^
checkRd: (-1) ncpen.reg.Rd:109: Lost braces; missing escapes or markup?
   109 |   \item{gamma}{extra shrinkage parameter for \code{classo} and {sridge} only.}
       |                                                                ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) cv.ncvreg.Rd:153: Lost braces
   153 | c("\\Sexpr[results=rd]{tools:::Rd_expr_doi(\"#1\")}",
       |                       ^
checkRd: (-1) ncvreg.Rd:207: Lost braces
   207 | c("\\Sexpr[results=rd]{tools:::Rd_expr_doi(\"#1\")}",
       |                       ^
checkRd: (-1) ncvsurv.Rd:178: Lost braces
   178 | \strong{5}: 232-253.  c("\\Sexpr[results=rd]{tools:::Rd_expr_doi(\"#1\")}",
       |                                             ^
checkRd: (-1) ncvsurv.Rd:184: Lost braces
   184 | c("\\Sexpr[results=rd]{tools:::Rd_expr_doi(\"#1\")}",
       |                       ^
checkRd: (-1) plot.cv.ncvreg.Rd:81: Lost braces
    81 | c("\\Sexpr[results=rd]{tools:::Rd_expr_doi(\"#1\")}",
       |                       ^
checkRd: (-1) plot.ncvreg.Rd:40: Lost braces
    40 | c("\\Sexpr[results=rd]{tools:::Rd_expr_doi(\"#1\")}",
       |                       ^
checkRd: (-1) predict.ncvreg.Rd:92: Lost braces
    92 | c("\\Sexpr[results=rd]{tools:::Rd_expr_doi(\"#1\")}",
       |                       ^
checkRd: (-1) predict.ncvsurv.Rd:88: Lost braces
    88 | \strong{5}: 232-253.  c("\\Sexpr[results=rd]{tools:::Rd_expr_doi(\"#1\")}",
       |                                             ^
checkRd: (-1) summary.cv.ncvreg.Rd:64: Lost braces
    64 | c("\\Sexpr[results=rd]{tools:::Rd_expr_doi(\"#1\")}",
       |                       ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) norm_tests.Rd:69: Lost braces
    69 | Anderson-Darling test." See url{https://github.com/Lakens/perfect-t-test} for
       |                                ^
checkRd: (-1) t_neat.Rd:243: Lost braces
   243 | Anderson-Darling test." See url{https://github.com/Lakens/perfect-t-test} for
       |                                ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) color_palette.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) color_palette.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) color_palette.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) color_palette.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) color_palette.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) color_palette.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) color_palette.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) color_palette.Rd:29: Lost braces in \itemize; meant \describe ?
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
checkRd: (-1) GSS.Rd:17: Lost braces
    17 | code{2016}.}
       |     ^
checkRd: (-1) partial_correlation.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) partial_correlation.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) partial_correlation.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) partial_correlation.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) chaingibbs.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) chaingibbs.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) chaingibbs.Rd:30: Lost braces in \itemize; meant \describe ?
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
':::' call which should be '::': ‘lhs:::maximinLHS’
  See the note in ?`:::` about the use of this operator.
checkRd: (-1) exportToTSPlibFormat.Rd:32: Escaped LaTeX specials: \_
checkRd: (-1) exportToTSPlibFormat.Rd:32: Escaped LaTeX specials: \_ \_
checkRd: (-1) makeNetwork.Rd:31: Escaped LaTeX specials: \_
'LazyData' is specified without a 'data' directory
checkRd: (-1) lawdata.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) lawdata.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) lawdata.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) lawdata.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) lawdata.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) lawdata.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) lawdata.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) lawdata.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) PVmodule.Rd:27: Lost braces; missing escapes or markup?
    27 | In the resulting netSEM model, time was used as a proxy for damp heat exposure stress (S) variable and $P_{max}$ (maximum power generated by the modules) was used as the performance level response ($R$) variable, several mechanistic variables ($M$) were obtained through chemical evaluation methods, including FTIR and TGA  on EVA encapsulant. 
       |                                                                                                           ^
checkRd: (-1) netSEMp1.Rd:55: Lost braces
    55 | For example, in the quadratic functional form y ~ b0 + b1x + b2x^2, the three P-values correspond two those of \\hat{b0}, \\hat{b1} and \\hat{b2}, respectively. 
       |                                                                                                                     ^
checkRd: (-1) netSEMp1.Rd:55: Lost braces
    55 | For example, in the quadratic functional form y ~ b0 + b1x + b2x^2, the three P-values correspond two those of \\hat{b0}, \\hat{b1} and \\hat{b2}, respectively. 
       |                                                                                                                                ^
checkRd: (-1) netSEMp1.Rd:55: Lost braces
    55 | For example, in the quadratic functional form y ~ b0 + b1x + b2x^2, the three P-values correspond two those of \\hat{b0}, \\hat{b1} and \\hat{b2}, respectively. 
       |                                                                                                                                              ^
checkRd: (-1) spec_clust.Rd:33: Lost braces; missing escapes or markup?
    33 | A label vector of size n x 1 with elements in {1,2,...,K}
       |                                               ^
checkRd: (-1) nettskjema_get_data.Rd:64-65: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nettskjema_get_data.Rd:66-67: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nettskjema_get_data.Rd:68-69: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nettskjema_token2renviron.Rd:32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nettskjema_token2renviron.Rd:33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nettskjema_token2renviron.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nettskjema_write_codebook.Rd:44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nettskjema_write_codebook.Rd:45: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rc.plot.ideogram.Rd:20: Lost braces; missing escapes or markup?
    20 |  \item{las}{numeric in {0,1,2,3}; the style of chromosome labels. 0, always parallel to the track [default]; 1, always horizontal; 2, always perpendicular to the track; 3, always vertical.}
       |                        ^
checkRd: (-1) NetworkChange.Rd:163: Escaped LaTeX specials: \&
checkRd: (-1) NetworkChangeRobust.Rd:144: Escaped LaTeX specials: \&
checkRd: (-1) NetworkStatic.Rd:142: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
checkRd: (-1) harry_potter.Rd:44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) harry_potter.Rd:45: Lost braces in \itemize; meant \describe ?
checkRd: (-1) harry_potter.Rd:46: Lost braces in \itemize; meant \describe ?
checkRd: (-1) harry_potter.Rd:47-48: Lost braces in \itemize; meant \describe ?
checkRd: (-1) harry_potter.Rd:49: Lost braces in \itemize; meant \describe ?
checkRd: (-1) vanDeBunt_students.Rd:46: Lost braces in \itemize; meant \describe ?
checkRd: (-1) vanDeBunt_students.Rd:47: Lost braces in \itemize; meant \describe ?
checkRd: (-1) vanDeBunt_students.Rd:48: Lost braces in \itemize; meant \describe ?
checkRd: (-1) vanDeBunt_students.Rd:49: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nodeLogic.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nodeLogic.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nodeLogic.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nodeLogic.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nodeLogic.Rd:32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nodeLogic.Rd:33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nodeLogic.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nodeLogic.Rd:35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nodeLogic.Rd:36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nodeLogic.Rd:41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nodeLogic.Rd:42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nodeLogic.Rd:43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nodeLogic.Rd:44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nodeLogic.Rd:45: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nodeLogic.Rd:46: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘map.png’ ‘maze.html’
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
checkRd: (-1) networktree.Rd:56: Lost braces; missing escapes or markup?
    56 | with a matrix response {y}. \code{x1} and \code{x2} are used as
       |                        ^
checkRd: (-1) SensMatPlot.Rd:21: Lost braces; missing escapes or markup?
    21 | \item{output}{\code{numeric} or {character} specifying the output neuron or output name to be plotted.
       |                                 ^
checkRd: (-1) SensitivityPlots.Rd:28: Lost braces; missing escapes or markup?
    28 | \item{output}{\code{numeric} or {character} specifying the output neuron or output name to be plotted.
       |                                 ^
checkRd: (-1) syntheticdata.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) syntheticdata.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) syntheticdata.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) syntheticdata.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) syntheticdata.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) syntheticdata.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) syntheticdata.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) syntheticdata.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) syntheticdata.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) syntheticdata.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) syntheticdata.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) syntheticdata.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) syntheticdata.Rd:32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) syntheticdata.Rd:33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) syntheticdata.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) syntheticdata.Rd:35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) orient_rpi.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) orient_rpi.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) orient_rpi.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'ANTsR', 'ITKR', 'extrantsr', 'MNITemplate', 'RAVEL', 'neurodata'
checkRd: (-1) 03-MixOf3Beta-class.Rd:35: Lost braces; missing escapes or markup?
    35 |       parameters \code{L} and {M} (in that order).}
       |                               ^
checkRd: (-1) load_schedules.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) load_schedules.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) load_schedules.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) load_schedules.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) load_schedules.Rd:31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) load_schedules.Rd:60: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) load_schedules.Rd:61: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) load_schedules.Rd:62: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) load_schedules.Rd:63: Lost braces in \itemize; \value handles \item{}{} directly
Specified C++14: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) NHANES.Rd:278: Lost braces
   278 | \code{AgeFirstMarij}{Age participant first tried marijuana. Reported for participants aged 18 to 59 years.}
       |                     ^
checkRd: (-1) get_huc.Rd:25: Lost braces
    25 | See /link{download_nhdplusv2} for documentation of that dataset.}
       |          ^
checkRd: (-1) get_huc12.Rd:15: Lost braces
    15 | See /link{download_nhdplusv2} for documentation of that dataset.}
       |          ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) init.theta.MSAR.Rd:56: Lost braces
    56 | with \eqn{Z} the covariate and eqn{d_Z} its dimension (number of covariates)
       |                                   ^
checkRd: (-1) test.model.MSAR.Rd:47: Lost braces
    47 | 	Marginal distribution: {\deqn{ S = \int_{-\infty}^{\infty} \left| F_n(x)-F(x) \right| dx} } 
       |                                ^
checkRd: (-1) test.model.MSAR.Rd:49: Lost braces
    49 | 	Marginal distribution, based on Anderson Darling statistic: {\deqn{ S = \int_{-\infty}^{\infty} \left| \frac{F_n(x)-F(x)}{F(x)(1-F(x))} \right| dx} } 
       |                                                                     ^
checkRd: (-1) test.model.MSAR.Rd:51: Lost braces
    51 | 		Correlation function: {\deqn{ S = \int_0^L\left|C_n(l)-C(l)\right|dl} } 
       |                                       ^
Invalid package aliases in Rd file 'NH-MSAR-package.Rd':
  ‘NH-MSAR-package’
Argument items with no description in Rd file 'ENu_graph.Rd':
  ‘N.s.data’
Argument items with no description in Rd file 'Estep.MSAR.VM.Rd':
  ‘verbose’
Auto-generated content requiring editing in Rd file 'NH-MSAR-package.Rd':
  \details: ‘...the package, including the most important ~~ ~~ functions ~~’
Argument items with no description in Rd file 'init.theta.MSAR.Rd':
  ‘\dots’
Argument items with no description in Rd file 'init.theta.MSAR.VM.Rd':
  ‘\dots’
checkRd: (-1) graphresU.fun.Rd:72: Escaped LaTeX specials: \&
checkRd: (-1) bootstrap_param_est.Rd:52: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bootstrap_param_est.Rd:53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bootstrap_param_est.Rd:54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) get_emission.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) get_emission.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) get_emission.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) impute.Rd:51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) impute.Rd:52: Lost braces in \itemize; meant \describe ?
checkRd: (-1) impute.Rd:53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) impute_ref.Rd:54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) impute_ref.Rd:55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) impute_ref.Rd:56: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sim_data.Rd:42: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sim_data.Rd:43: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sim_data.Rd:44: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
checkRd: (-1) postPredSPD.Rd:53: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) postPredSPD.Rd:54: Lost braces in \itemize; \value handles \item{}{} directly
Found the following significant warnings:
  RcppUtils.cpp:237:72: warning: unknown conversion type character '>' in format [-Wformat=]
  RcppUtils.cpp:273:73: warning: unknown conversion type character '>' in format [-Wformat=]
  ../include/nimble/Utils.h:64:80: warning: format '%s' expects argument of type 'char*', but argument 2 has type 'SEXP' {aka 'SEXPREC*'} [-Wformat=]
  ../include/nimble/Utils.h:65:89: warning: format '%s' expects argument of type 'char*', but argument 3 has type 'SEXP' {aka 'SEXPREC*'} [-Wformat=]
  ../include/nimble/Utils.h:66:98: warning: format '%d' expects argument of type 'int', but argument 4 has type 'std::vector<int>::size_type' {aka 'long unsigned int'} [-Wformat=]
  ../include/nimble/Utils.h:65:89: warning: format '%s' expects argument of type 'char*', but argument 2 has type 'SEXP' {aka 'SEXPREC*'} [-Wformat=]
  Utils.cpp:66:26: warning: zero-length gnu_printf format string [-Wformat-zero-length]
  RcppUtils.cpp:237:72: warning: unknown conversion type character ‘>’ in format [-Wformat=]
  RcppUtils.cpp:273:73: warning: unknown conversion type character ‘>’ in format [-Wformat=]
  ../inst/include/nimble/Utils.h:64:80: warning: format ‘%s’ expects argument of type ‘char*’, but argument 2 has type ‘SEXP’ {aka ‘SEXPREC*’} [-Wformat=]
  ../inst/include/nimble/Utils.h:65:89: warning: format ‘%s’ expects argument of type ‘char*’, but argument 3 has type ‘SEXP’ {aka ‘SEXPREC*’} [-Wformat=]
  ../inst/include/nimble/Utils.h:66:98: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wformat=]
  ../inst/include/nimble/Utils.h:65:89: warning: format ‘%s’ expects argument of type ‘char*’, but argument 2 has type ‘SEXP’ {aka ‘SEXPREC*’} [-Wformat=]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/nimble.Rcheck/00install.out’ for details.
* used C++ compiler: ‘g++-13 (Debian 13.2.0-7) 13.2.0’
checkRd: (-1) buildIteratedFilter2.Rd:105: Lost braces
   105 | Ionides, E.L., D. Nguyen, Y. Atchad{\'e}, S. Stoev, and A.A. King (2015). Inference for dynamic and latent variable models via iterated, perturbed Bayes maps. \emph{Proceedings of the National Academy of Sciences}, 112(3), 719-724.
       |                                    ^
Package which this enhances but not available for checking: ‘jpndistrict’
Malformed Description field: should contain one or more complete sentences.
Objects in \usage without \alias in Rd file 'internalRK.Rd':
  ‘brkCalc’ ‘findPowerR’

Functions with \usage entries need to have the appropriate \alias
entries, and all their 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) mcrPlot.Rd:42-44: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mcrPlot.Rd:45-47: 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++11: please drop specification unless essential
Packages suggested but not available for checking: 'Rvmmin', 'Rcgmin'
Specified C++11: please drop specification unless essential
checkRd: (-1) dot-make_long_data.Rd:44: Lost braces; missing escapes or markup?
    44 | training sample), psi (the value of this observations Psihat(P_{n,B_n}^0)),
       |                                                                ^
checkRd: (-1) dot-make_long_data_nested_cv.Rd:49: Lost braces; missing escapes or markup?
    49 | training sample), psi (the value of this observations Psihat(P_{n,B_n}^0)),
       |                                                                ^
checkRd: (-1) Dmean.Rd:62: Escaped LaTeX specials: \&
checkRd: (-1) Dvar.Rd:63: Escaped LaTeX specials: \&
Documented arguments not in \usage in Rd file 'nldoc_write_nldoc.Rd':
  ‘number_ections’

Functions with \usage entries need to have the appropriate \alias
entries, and all their 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) anova.Rd:19: Lost braces
    19 |   Returns an object of class code{anova}.  These objects represent
       |                                  ^
checkRd: (-1) fwtnpperm.Rd:34: Lost braces
    34 | Given \eqn{n} points on a line, \env{input}, each with a corresponding env{f} value this algorithm computes a lifting transform of the (\env{input},\env{f}) data. If lengths are inputted (\env{inputtype="lengths"}), then the gridpoints are taken to be the left endpoints of the intervals defined by the lengths inputted. 
       |                                                                           ^
checkRd: (-1) check_input_event_times.Rd:16-17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) check_input_event_times.Rd:18-19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) check_time_unit.Rd:12-13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) check_time_unit.Rd:14-15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) default_params_doc.Rd:30-31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) default_params_doc.Rd:32-33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nltt_diff_exact_brts.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nltt_diff_exact_brts.Rd:31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nltt_diff_exact_brts.Rd:36-37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nltt_diff_exact_brts.Rd:38-39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nltt_diff_exact_extinct.Rd:31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nltt_diff_exact_extinct.Rd:32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nltt_diff_exact_extinct.Rd:37-38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nltt_diff_exact_extinct.Rd:39-40: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
Package suggested but not available for checking: ‘mail’
checkRd: (-1) rnmf.Rd:262: Lost braces
   262 |   code{rnmf(min(ncol(W), nrow(H)), ..., W=W, H=H)}.
       |       ^
Documented arguments not in \usage in Rd file 'ccSpec.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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  logistf.c:118:58: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘long int’ [-Wformat=]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/nncc.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-13 (Debian 13.2.0-7) 13.2.0’
Invalid package aliases in Rd file 'logistf-package.Rd':
  ‘logistf-package’ ‘{logistf}-package’
'LazyData' is specified without a 'data' directory
checkRd: (-1) Wmat.Rd:28: Lost braces
    28 | \eqn{w_{ij}=I(} point eqn{j} is a NN of point \eqn{i))} i.e. \eqn{w_{ij}=1} if point \eqn{j} is a NN of point \eqn{i} and 0 otherwise.
       |                          ^
checkRd: (-1) Wmat.Rd:23: Lost braces
    23 | The incidence matrix \eqn{W=(w_ij)} where \eqn{w_{ij}=I(} point eqn{j} is a NN of point \eqn{i))},
       |                                                                    ^
checkRd: (-1) funsQandR.Rd:29: Lost braces
    29 | \code{Rval}{the \eqn{R} value, the number of reflexive NNs}
       |            ^
checkRd: (-1) rself.ref.Rd:55: Lost braces; missing escapes or markup?
    55 | \eqn{X_i \stackrel{iid}{\sim} BVN(CM(S_1),I_{2x})} where \eqn{CM(S_1)} is the center of mass of \eqn{S_1} and I_{2x} is a \eqn{2 \times 2} matrix with diagonals
       |                                                                                                                 ^
checkRd: (-1) rself.ref.Rd:61: Lost braces; missing escapes or markup?
    61 | \eqn{Y_j \stackrel{iid}{\sim} BVN(CM(S_2),I_{2y})} where \eqn{CM(S_1)} is the center of mass of \eqn{S_1} and I_{2y} is a \eqn{2 \times 2} matrix with diagonals
       |                                                                                                                 ^
checkRd: (-1) sharedNNmc.Rd:27: Lost braces
    27 | \code{Rval}{the \eqn{R} value, the number of reflexive NNs}
       |            ^
checkRd: (-1) swamptrees.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) swamptrees.Rd:38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) swamptrees.Rd:39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) swamptrees.Rd:40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) swamptrees.Rd:41: Lost braces in \itemize; meant \describe ?
GNU make is a SystemRequirements.
checkRd: (-1) ROCplots.Rd:35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ROCplots.Rd:36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ROCplots.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ROCplots.Rd:38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ROCplots.Rd:39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ROCplots.Rd:40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) GabrielNMF.Rd:23: Lost braces; missing escapes or markup?
    23 | The number of low-dimension (J < {N, M}).
       |                                  ^
checkRd: (-1) NMF.Rd:71: Lost braces; missing escapes or markup?
    71 | The number of low-dimension (J < {N, M}). If a numerical vector is specified
       |                                  ^
checkRd: (-1) NMF.Rd:119: Lost braces; missing escapes or markup?
   119 |   U : A matrix which has N-rows and J-columns (J < {N, M}).
       |                                                    ^
checkRd: (-1) NMF.Rd:120: Lost braces; missing escapes or markup?
   120 |   V : A matrix which has M-rows and J-columns (J < {N, M}).
       |                                                    ^
checkRd: (-1) NMF.Rd:121: Lost braces; missing escapes or markup?
   121 |   J : The number of dimension (J < {N, M}).
       |                                    ^
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘hurricaneexposuredata’
checkRd: (-1) match_forecast_county.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) match_forecast_county.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) match_forecast_county.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) parse_damage.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) parse_damage.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) parse_damage.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) parse_damage.Rd:29: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) dbConnect-AthenaDriver-method.Rd:108-110: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dbConnect-AthenaDriver-method.Rd:111-113: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dbConnect-AthenaDriver-method.Rd:114-117: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dbConnect-AthenaDriver-method.Rd:118-120: 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: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulatePop.Rd:40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulatePop.Rd:41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulatePop.Rd:42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulatePop.Rd:43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulatePop.Rd:44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulatePop.Rd:45: Lost braces in \itemize; meant \describe ?
checkRd: (-1) imp_int_an.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) imp_int_an.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.ndmodel.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.ndmodel.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.ndmodel.Rd:18: Lost braces in \itemize; meant \describe ?
Auto-generated content requiring editing in Rd file 'noise-package.Rd':
  \details: ‘...the package, including the most important ~~ ~~ functions ~~’
'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 'get_max_stat.Rd':
  ‘statfunc’

Functions with \usage entries need to have the appropriate \alias
entries, and all their 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) systemPSN.Rd:23: Lost braces
    23 | If psn is not available system{base} is used.
       |                               ^
checkRd: (-1) vpcfig.Rd:91: Lost braces
    91 | The fy and fx arguments can be used to alter the scale of data plotted. For example, using fy=function(y){log(y+1)}
       |                                                                                                          ^
Documented arguments not in \usage in Rd file 'StatQQVPC.Rd':
  ‘mapping’ ‘data’ ‘geom’ ‘position’ ‘na.rm’ ‘show.legend’
  ‘inherit.aes’ ‘...’

Documented arguments not in \usage in Rd file 'StatQQnorm.Rd':
  ‘mapping’ ‘data’ ‘geom’ ‘position’ ‘na.rm’ ‘show.legend’
  ‘inherit.aes’ ‘...’

Documented arguments not in \usage in Rd file 'StatQQrefline.Rd':
  ‘mapping’ ‘data’ ‘geom’ ‘position’ ‘na.rm’ ‘show.legend’
  ‘inherit.aes’ ‘...’

Documented arguments not in \usage in Rd file 'covload.sub.table.Rd':
  ‘nrows’

Functions with \usage entries need to have the appropriate \alias
entries, and all their 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) set.data.Rd:14: Lost braces; missing escapes or markup?
    14 |   \item{shape}{either \code{wide} or {long}. Default \code{wide}. See Details.}
       |                                      ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) mle_parameters.Rd:36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mle_parameters.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mle_parameters.Rd:38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mle_parameters.Rd:39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mle_parameters.Rd:40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mle_parameters.Rd:41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mle_parameters.Rd:42: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
Auto-generated content requiring editing in Rd file 'nose-package.Rd':
  \details: ‘...the package, including the most important ~~ ~~ functions ~~’
checkRd: (-1) parseFunction.Rd:38: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) parseFunction.Rd:39: Lost braces in \itemize; \value handles \item{}{} directly
Documented arguments not in \usage in Rd file 'FunctionSanityChecks.Rd':
  ‘structure’

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

Documented arguments not in \usage in Rd file 'nosoiSimConstructor.Rd':
  ‘pres.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
'LazyData' is specified without a 'data' directory
checkRd: (-1) Lcm.Rd:75: Lost braces
    75 |     \item{\code{GetTrace()}:}{retrieve all traced iterations. Returns a list with all the parameters set using the method SetTrace(). See description of snapshot{reference} method for a description of the parameters.  }
       |                                                                                                                                                                  ^
Specified C++11: please drop specification unless essential
checkRd: (-1) plot.regression.circular.Rd:35: Lost braces
    35 |               code{plot.type="circle"} and \code{x} is the output of \code{\link{kern.reg.circ.lin}}) or to \code{\link{lines3d}} (if \code{plot.type="circle"})
       |                   ^
checkRd: (-1) npde-package.Rd:24: Lost braces
    24 | Mentr{\'e}. Metrics for external model evaluation with an application to the
       |      ^
checkRd: (-1) npdeData.Rd:77: Lost braces
    77 | Mentr{\'e}. Metrics for external model evaluation with an application to the
       |      ^
Documented arguments not in \usage in Rd file 'read.Rd':
  ‘dots’

Functions with \usage entries need to have the appropriate \alias
entries, and all their 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) DiscHazRateAuxFunctions.Rd:46: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DiscHazRateAuxFunctions.Rd:47: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DiscHazRateAuxFunctions.Rd:48: Lost braces in \itemize; meant \describe ?
checkRd: (-1) n2pwr.NPH.Rd:59-61: Lost braces
    59 | Default: function(x) {
       |                      ^
checkRd: (-1) pwr2n.NPH.Rd:60-62: Lost braces
    60 | Default: function(x) {
       |                      ^
checkRd: (-1) prepareplot.Rd:64: Escaped LaTeX specials: \#
checkRd: (-1) prepareplot.Rd:68: Escaped LaTeX specials: \#
checkRd: (-1) nplr.Rd:48-51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nplr.Rd:52-55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nplr.Rd:56-59: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nplr.Rd:70: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nplr.Rd:71: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nplr.Rd:72: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nplr.Rd:73: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nplr.Rd:74: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nplr.Rd:75: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nplr.Rd:76: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nplr.Rd:77: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nplr.Rd:78: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nplr.Rd:79: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nplr.Rd:80: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nplr.Rd:81: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nplr.Rd:82: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nppbib.Rd:28: Escaped LaTeX specials: \#
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.
Documented arguments not in \usage in Rd file 'Create_P.Rd':
  ‘y_zx_dependent’

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

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) np.reg.test.Rd:148: Lost braces
   148 | ter Braak, C. J. F. (1992). Permutation versus bootstrap significance tests in multiple regression and ANOVA. In K. H. J\"{o}ckel, G. Rothe, & W. Sendler (Eds.), Bootstrapping and related techniques. lecture notes in economics and mathematical systems, vol 376 (pp. 79-86). Springer.
       |                                                                                                                           ^
checkRd: (-1) nptest-package.Rd:73: Lost braces
    73 | ter Braak, C. J. F. (1992). Permutation versus bootstrap significance tests in multiple regression and ANOVA. In K. H. J\"{o}ckel, G. Rothe, & W. Sendler (Eds.), Bootstrapping and related techniques. lecture notes in economics and mathematical systems, vol 376 (pp. 79-86). Springer.
       |                                                                                                                           ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) NSAE.Rd:14: Lost braces; missing escapes or markup?
    14 | {Maintainer}: Saurav Guha \email{saurav.iasri@gmail.com}
       | ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) NScluster-package.Rd:30-34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) NScluster-package.Rd:35-43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) NScluster-package.Rd:44-48: Lost braces in \itemize; meant \describe ?
checkRd: (-1) NScluster-package.Rd:49-53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mple.cppm.Rd:44-66: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mple.cppm.Rd:69-110: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mple.cppm.Rd:113-155: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sim.cppm.Rd:36-87: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sim.cppm.Rd:90-120: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sim.cppm.Rd:123-148: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sim.cppm.Rd:151-192: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sim.cppm.Rd:195-211: Lost braces in \itemize; meant \describe ?
checkRd: (-1) svr.df.Rd:13: Lost braces
    13 | \item{z}{the vector of zi = min{Xi, Yi}}
       |                                ^
checkRd: (-1) MSM.fit.Rd:21: Lost braces
    21 | \code{MSM.fit} returns an object of class code{MSM.lm} or \code{MSM.glm}, depending on the input model.
       |                                               ^
checkRd: (-1) SMC.Smooth.Rd:25: Lost braces; missing escapes or markup?
    25 | observation at current time step. It should return {xx} (the samples xt) and
       |                                                    ^
checkRd: (-1) SMC.Smooth.Rd:26: Lost braces; missing escapes or markup?
    26 | {logww} (their corresponding log weight).}
       | ^
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
checkRd: (-1) get_exp_likelihoods.Rd:17: Lost braces; missing escapes or markup?
    17 | \item{exp_counts}{dataframe Single-cell expression counts {CHROM, seg, cnv_state, gene, Y_obs, lambda_ref}}
       |                                                           ^
Documented arguments not in \usage in Rd file 'exp_hclust.Rd':
  ‘df_allele’

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

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
GNU make is a SystemRequirements.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  nro_train.cpp:79:15: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wformat=]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/Numero.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-13 (Debian 13.2.0-7) 13.2.0’
* used C++ compiler: ‘g++-13 (Debian 13.2.0-7) 13.2.0’
Specified C++11: please drop specification unless essential
checkRd: (-1) numero.clean.Rd:38: Lost braces
    38 | The frequency of missing values (against /code{na.freq}) is tested first
       |                                               ^
checkRd: (-1) numero.plot.Rd:55: Lost braces
    55 | code{\link{numero.evaluate}()} or similar.
       |     ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) xyz2R.Rd:31: Lost braces
    31 |    \item Finally, code{T} is rotated an angle \code{z} about its NEWEST z-axis.
       |                       ^
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) oplsda.Rd:28-29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) oplsda.Rd:30-32: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) oplsda.Rd:33-35: Lost braces in \itemize; \value handles \item{}{} directly
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checkRd: (-1) plsda.Rd:38: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) plsda.Rd:39: Lost braces
    39 | \item{code{PRESS}}{The residual sum of squares for the samples which were not used to fit the model}
       |           ^
checkRd: (-1) plsda.Rd:39: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) plsda.Rd:40: Lost braces
    40 | \item{code{Q2}}{quality of  cross-validation}}
       |           ^
checkRd: (-1) plsda.Rd:40: Lost braces in \itemize; \value handles \item{}{} directly
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) OBMb.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) OBMb.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) OBMb.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) OBMb.Rd:31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) OBMb.Rd:32: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) OBMb.Rd:33: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) ChangepointDetector.Rd:93: Lost braces; missing escapes or markup?
    93 | \code{'sparse'}, then only (S^{diag}, S^{off,d})
       |                               ^
checkRd: (-1) ChangepointDetector.Rd:93: Lost braces; missing escapes or markup?
    93 | \code{'sparse'}, then only (S^{diag}, S^{off,d})
       |                                         ^
checkRd: (-1) ChangepointDetector.Rd:94: Lost braces; missing escapes or markup?
    94 | and (S^{diag}, S^{off,s}) are included in \code{stat} respectively.);
       |        ^
checkRd: (-1) ChangepointDetector.Rd:94: Lost braces; missing escapes or markup?
    94 | and (S^{diag}, S^{off,s}) are included in \code{stat} respectively.);
       |                  ^
checkRd: (-1) mapping.Rd:197-199: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mapping.Rd:200-202: Lost braces in \itemize; \value handles \item{}{} directly
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checkRd: (-1) mapping.Rd:213-215: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mapping.Rd:216-218: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mapping.Rd:219-221: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mapping.Rd:226-228: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mapping.Rd:229-231: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mapping.Rd:236-238: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mapping.Rd:239-241: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mapping.Rd:246-247: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mapping.Rd:248-250: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mapping.Rd:251-252: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mapping.Rd:253-254: Lost braces in \itemize; \value handles \item{}{} directly
Argument items with no description in Rd file 'plot.comphat.Rd':
  ‘\dots’
checkRd: (-1) onlineCPD.Rd:35: Lost braces
    35 |  function(x, lambda){const_hazard(x, lambda=100)}
       |                     ^
checkRd: (-1) ocsApiUserProvisioningManager.Rd:87: Lost braces
    87 |  \item{code{addToGroup(userid, groupid)}}{
       |            ^
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) plot.ODEmorris.Rd:62-63: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.ODEmorris.Rd:64-65: Lost braces in \itemize; meant \describe ?
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) formula.oglmx.Rd:49: Lost braces
    49 |   \code{\link{oglmx}}, code{\link[lmtest]{lrtest}}, code{\link{formula}}.
       |                            ^
checkRd: (-1) formula.oglmx.Rd:49: Lost braces
    49 |   \code{\link{oglmx}}, code{\link[lmtest]{lrtest}}, code{\link{formula}}.
       |                                                         ^
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in ‘oldbailey-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: find_trials
> ### Title: Find Old Bailey Trials
> ### Aliases: find_trials
> 
> ### ** Examples
> 
> # Return a dataframe with 5 trials.
> trials <- find_trials(n_results = 5)
Error: lexical error: invalid char in json text.
                                       <!doctype html><html lang="en">
                     (right here) ------^
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) dot-discoveryRequest.Rd:15-16: Lost braces
    15 | \item{service}{One of {"locations", "deployments", "deviceCategories", "devices",
       |                       ^
checkRd: (-1) dot-discoveryRequest.Rd:18: Lost braces; missing escapes or markup?
    18 | \item{method}{One of {"get", "getTree"}}
       |                      ^
checkRd: (-1) dot-saveAsFile.Rd:19: Lost braces; missing escapes or markup?
    19 | (numeric) Result code from {0: done, -1: error, -2: fileExists}
       |                            ^
Package suggested but not available for checking: ‘cmdstanr’
checkRd: (-1) summary.blrm_trial.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) summary.blrm_trial.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) summary.blrm_trial.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) summary.blrm_trial.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) summary.blrm_trial.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) summary.blrm_trial.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) summary.blrm_trial.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) summary.blrm_trial.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) summary.blrm_trial.Rd:28-29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) summary.blrm_trial.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) summary.blrm_trial.Rd:31-33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) summary.blrm_trial.Rd:34: Lost braces in \itemize; meant \describe ?
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
checkRd: (-1) oncotree.fit.Rd:63: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) oncotree.fit.Rd:64: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) oncotree.fit.Rd:65: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) oncotree.fit.Rd:66: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) oncotree.fit.Rd:67: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rgdal’
checkRd: (-1) one_sample.Rd:40: Lost braces; missing escapes or markup?
    40 | In two sided or one sided interval estimation of \code{sigma^2} of one normal sample, {side} is a parameter used to control whether to compute two sided or one sided interval estimation. When computing the one sided upper limit, input \code{side = -1}; when computing the one sided lower limit, input \code{side = 1}; when computing the two sided limits, input \code{side = 0} (default).
       |                                                                                       ^
Rd files without \alias:
  ‘ontologyPlot-package.Rd’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
License stub is invalid DCF.
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
checkRd: (-1) GeoJson.Rd:16: Lost braces
    16 | As GeoJSON is defined in \url{https://datatracker.ietf.org/doc/html/rfc7946}{RFC7946} the coordinate reference system is
       |                                                                             ^
S3 methods shown with full name in Rd file 'unary_ops.Rd':
  ‘log10.ProcessNode’ ‘log10.ProcessGraphParameter’

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
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘openNLPmodels.en’
Documented arguments not in \usage in Rd file 'clique_color_pals.Rd':
  ‘aplha’

Functions with \usage entries need to have the appropriate \alias
entries, and all their 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) constructD.Rd:18: Lost braces
    18 | values for code{"columns"} and \code{"rows"}).}
       |                ^
checkRd: (-1) indexConflict2.Rd:43: Lost braces; missing escapes or markup?
    43 |                { Z_max x Z_mdn - Z_min <= crit }.
       |                ^
checkRd: (-1) indexConflict2.Rd:46: Lost braces; missing escapes or markup?
    46 |                { Z_min - Z_max x Z_mdn <= crit }.
       |                ^
checkRd: (-1) indexConflict2.Rd:56: Lost braces; missing escapes or markup?
    56 |        { a x Z_max x Z_mdn =< crit/a + Z_min}. This shows that a bigger value of \code{a}
       |        ^
checkRd: (-1) perturbate.Rd:18: Lost braces; missing escapes or markup?
    18 | range. Usually {-1, 1} are reasonable settings}
       |                ^
checkRd: (-1) settings.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) settings.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) settings.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) settings.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) settings.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) settings.Rd:28: Lost braces in \itemize; meant \describe ?
Documented arguments not in \usage in Rd file 'bertinBase.Rd':
  ‘x’ ‘ratings’ ‘trim’

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

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

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

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

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

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Packages suggested but not available for checking: 'maptools', 'rgeos'
checkRd: (-1) codeVA.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) codeVA.Rd:32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) codeVA.Rd:33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) codeVA.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) codeVA.Rd:58: Lost braces in \itemize; meant \describe ?
checkRd: (-1) interVA_train.Rd:32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) loss.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) loss.Rd:25-26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) loss.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) loss.Rd:32-33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) loss.Rd:34-35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mixture-opera.Rd:79: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mixture-opera.Rd:80: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mixture-opera.Rd:81: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mixture-opera.Rd:82: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mixture-opera.Rd:83: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mixture-opera.Rd:84: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mixture-opera.Rd:85: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.mixture.Rd:33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.mixture.Rd:34: Lost braces in \itemize; meant \describe ?
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) word_imp.Rd:14: Lost braces
    14 | number of individual records. An \code{n} x code{2} dataframe can
       |                                                 ^
checkRd: (-1) MonteCarlo.Rd:23: Lost braces
    23 | N is computed from \code{p} length. M is code{10^4} by default.
       |                                              ^
Package suggested but not available for checking: ‘gurobi’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘Graph_layout_Doptbd_trtE’
Malformed Title field: should not end in a period.
checkRd: (-1) optimal_holdout_size.Rd:30: Lost braces; missing escapes or markup?
    30 | List/data frame of dimension (number of evaluations) x (4 + n_par) containing input data and results. Columns \code{size} and \code{cost} are optimal holdout size and cost at this size respectively. Parameters N, k1, theta.1, theta.2,...,theta.{n_par} are input data.
       |                                                                                                                                                                                                                                                     ^
checkRd: (-1) drawdesign.Rd:39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) drawdesign.Rd:40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) drawdesign.Rd:41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) drawdesign.Rd:42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) drawdesign.Rd:43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) drawdesign.Rd:44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) lorenz.Rd:82: Lost braces; missing escapes or markup?
    82 | L_i = sum_{j=1}^{i} x_j * n_j / sum_{j=1}^{n} x_j * n_j.
       |           ^
checkRd: (-1) lorenz.Rd:82: Lost braces; missing escapes or markup?
    82 | L_i = sum_{j=1}^{i} x_j * n_j / sum_{j=1}^{n} x_j * n_j.
       |                 ^
checkRd: (-1) lorenz.Rd:82: Lost braces; missing escapes or markup?
    82 | L_i = sum_{j=1}^{i} x_j * n_j / sum_{j=1}^{n} x_j * n_j.
       |                                     ^
checkRd: (-1) lorenz.Rd:82: Lost braces; missing escapes or markup?
    82 | L_i = sum_{j=1}^{i} x_j * n_j / sum_{j=1}^{n} x_j * n_j.
       |                                           ^
checkRd: (-1) lorenz.Rd:83: Lost braces; missing escapes or markup?
    83 | where x_i are indexed in non-decreasing order (x_i <= x_{i+1}).
       |                                                         ^
checkRd: (-1) gnu_style.Rd:24: Lost braces
    24 | [GNU Command Line Standards]{http://www.gnu.org/prep/standards/standards.html}
       |                             ^
Package which this enhances but not available for checking: ‘gurobi’
'LazyData' is specified without a 'data' directory
checkRd: (-1) calc_n_from_c.Rd:5: Lost braces; missing escapes or markup?
     5 | \title{Helper function to calculate other n's given n_{1,T} and allocation ratios}
       |                                                       ^
checkRd: (-1) calc_n_from_c.Rd:15: Lost braces; missing escapes or markup?
    15 | Helper function to calculate other n's given n_{1,T} and allocation ratios
       |                                                ^
checkRd: (-1) optimum_allocation.Rd:28: Lost braces; missing escapes or markup?
    28 | each sampled unit. If \code{data} holds \code{sd_h} and {N_h}, the
       |                                                         ^
checkRd: (-1) sample_strata.Rd:48: Lost braces; missing escapes or markup?
    48 | returns {data} as a dataframe with a new column named
       |         ^
'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’.
Package suggested but not available for checking: ‘rrelaxiv’
Found the following files/directories:
  ‘Graph_layout_Doptrcd_trtE’
Package suggested but not available for checking: ‘gurobi’
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Argument items with no description in Rd file 'dsevdist.Rd':
  ‘x’ ‘sevdist’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) internal.Rd:26-27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) internal.Rd:29-31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) internal.Rd:33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) internal.Rd:35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) internal.Rd:37-38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) internal.Rd:40-41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) internal.Rd:43-44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) internal.Rd:46: Lost braces in \itemize; meant \describe ?
checkRd: (-1) internal.Rd:48: Lost braces in \itemize; meant \describe ?
checkRd: (-1) internal.Rd:50: Lost braces in \itemize; meant \describe ?
checkRd: (-1) internal.Rd:52: Lost braces in \itemize; meant \describe ?
checkRd: (-1) internal.Rd:54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) internal.Rd:56-57: Lost braces in \itemize; meant \describe ?
checkRd: (-1) internal.Rd:59-60: Lost braces in \itemize; meant \describe ?
checkRd: (-1) internal.Rd:62-63: Lost braces in \itemize; meant \describe ?
checkRd: (-1) internal.Rd:65-66: Lost braces in \itemize; meant \describe ?
checkRd: (-1) internal.Rd:68: Lost braces in \itemize; meant \describe ?
checkRd: (-1) internal.Rd:70: Lost braces in \itemize; meant \describe ?
Specified C++11: please drop specification unless essential
checkRd: (-1) minK.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) minK.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) minK.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) lra-ord.Rd:54: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) lra-ord.Rd:55-56: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) lra-ord.Rd:57-58: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) lra-ord.Rd:59: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) lra-ord.Rd:60: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
checkRd: (-1) orf.Rd:74: Lost braces
    74 | matrix of covariates \code{X} and a vector of outcomes 'code{Y} to the \code{orf}
       |                                                             ^
Found the following files/directories:
  ‘cluster of fitted mean data.eps’ ‘cluster of fitted mean data.txt’
  ‘cluster of raw data.txt’
checkRd: (-1) distsumlpmin.Rd:69: Lost braces
    69 |   \code{Véase}{Vease} \enc{también}{tambien} \code{\link{distsummin}}, \code{\link{orloca.es-package}}, \code{\link{loca.p}} y \code{\link{distsum}}.
       |               ^
checkRd: (-1) distsummin.Rd:80: Lost braces
    80 | \code{Véase}{Vease} \enc{también}{tambien} \code{\link{orloca.es-package}}, \code{\link{loca.p}} y \code{\link{distsum}}.
       |             ^
Documented arguments not in \usage in Rd file 'distsuml2.Rd':
  ‘partial’

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

Functions with \usage entries need to have the appropriate \alias
entries, and all their 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) hillEquation.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hillEquation.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hillEquation.Rd:30-31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hillEquation.Rd:31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hillEquation.Rd:32: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hillEquation.Rd:33: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hillEquation.Rd:34: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hillEquation.Rd:35: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) qiba.Rd:81-83: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) qiba.Rd:84-85: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) qiba.Rd:86-87: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) qiba.Rd:88-90: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) qiba.Rd:91-93: Lost braces in \itemize; \value handles \item{}{} directly
Documented arguments not in \usage in Rd file 'dosepred.Rd':
  ‘w’

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

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

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
checkRd: (-1) polynomial.derivatives.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) polynomial.derivatives.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) polynomial.derivatives.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) polynomial.integrals.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) polynomial.integrals.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) polynomial.integrals.Rd:21: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) oscar.Rd:44: Lost braces; missing escapes or markup?
    44 | \item{print}{Level of verbosity in Fortran (may not be visible on all terminals); should be an integer between {range, range}, Default: 3}
       |                                                                                                                ^
checkRd: (-1) oscar.control.Rd:41: Lost braces; missing escapes or markup?
    41 | \item{start}{Starting point generation method, see vignettes for details; should be an integer between {range,range}, Default: 2}
       |                                                                                                        ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) RLum.OSL_decomposition.Rd:90-91: Lost braces
    90 | \item \link{optimise_OSLintervals}: {Approximates the optimal integration intervals. Uses the global
       |                                     ^
checkRd: (-1) RLum.OSL_decomposition.Rd:92-94: Lost braces
    92 | \item \link{decompose_OSLcurve}: {Calculates component intensities for \strong{all} \code{record_type} measurements.
       |                                  ^
checkRd: (-1) fit_OSLcurve.Rd:97: Lost braces; missing escapes or markup?
    97 | fitting with the \emph{RSS_{K-1}} value of the previous fitting and calculates
       |                            ^
'LazyData' is specified without a 'data' directory
Rd files without \alias:
  ‘otp-package.Rd’
'LazyData' is specified without a 'data' directory
checkRd: (-1) otp_create_surface.Rd:33: Lost braces; missing escapes or markup?
    33 | The file will be named surface_{id}.tiff, with {id} replaced by the OTP id assigned
       |                                ^
checkRd: (-1) otp_create_surface.Rd:33: Lost braces; missing escapes or markup?
    33 | The file will be named surface_{id}.tiff, with {id} replaced by the OTP id assigned
       |                                                ^
checkRd: (-1) imput_cov.Rd:79: Lost braces
    79 | \item van Buuren, S., Groothuis-Oudshoorn, K. (2011). mice: Multivariate Imputation by Chained Equations in R. Journal of Statistical Software, 45(3), 1–67. url{https://www.jstatsoft.org/v45/i03/}
       |                                                                                                                                                                 ^
checkRd: (-1) indiv_grp_closest.Rd:47: Lost braces; missing escapes or markup?
    47 | The function \code{indiv_grp_closest} is an intermediate function used in the implementation of an algorithm called {OUTCOME} (and its enrichment {R-OUTCOME}, see the reference (2) for more details) dedicated to the solving of recoding problems in data fusion using Optimal Transportation theory.
       |                                                                                                                     ^
checkRd: (-1) indiv_grp_closest.Rd:47: Lost braces; missing escapes or markup?
    47 | The function \code{indiv_grp_closest} is an intermediate function used in the implementation of an algorithm called {OUTCOME} (and its enrichment {R-OUTCOME}, see the reference (2) for more details) dedicated to the solving of recoding problems in data fusion using Optimal Transportation theory.
       |                                                                                                                                                   ^
checkRd: (-1) merge_dbs.Rd:179: Lost braces
   179 | \item van Buuren, S., Groothuis-Oudshoorn, K. (2011). mice: Multivariate Imputation by Chained Equations in R. Journal of Statistical Software, 45(3), 1–67. url{https://www.jstatsoft.org/v45/i03/}
       |                                                                                                                                                                 ^
Specified C++11: please drop specification unless essential
checkRd: (-1) fmat.Rd:15: Lost braces; missing escapes or markup?
    15 | \item outcome: codes {I, P, R, NC, O, UH, UO, eUH, eUO, NE}
       |                      ^
checkRd: (-1) fmat.Rd:24: Lost braces; missing escapes or markup?
    24 | The input parameters given by the user are {I, P, R, NC, O, UH, UO} and
       |                                            ^
checkRd: (-1) fmat.Rd:25: Lost braces; missing escapes or markup?
    25 | the parameter 'e'. The parameter e is multiplied by {UH, UO} internally so as to
       |                                                     ^
checkRd: (-1) fmat.Rd:26: Lost braces; missing escapes or markup?
    26 | produce {eUH, eUO}.
       |         ^
checkRd: (-1) middleearth.Rd:14: Lost braces; missing escapes or markup?
    14 | \item \strong{code:} one of the outcome codes {I, P, R, NC, O, UH, UO, UH, UO, NE}
       |                                               ^
Specified C++11: please drop specification unless essential
checkRd: (-1) BFGS_lpdf.Rd:37: Lost braces
    37 | A wrapper for code{\link{BFGS_std}} that is useful for easily calling 
       |                   ^
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) lint_package.Rd:20: Lost braces
    20 | code{\link[lintr:lint_package]{lintr::lint_package}} where we hardcode the
       |     ^
checkRd: (-1) provide_news_rd.Rd:22: Lost braces
    22 | Christian Vonderach uses the index thus wants file{inst/NEWS.rd} to
       |                                                   ^
checkRd: (-1) provide_news_rd.Rd:23: Lost braces
    23 | automatically be in sync with file{./NEWS.md}.
       |                                   ^
Invalid package aliases in Rd file 'packagetracker.Rd':
  ‘packagetracker-package’
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'prediction_regression.Rd':
  ‘dataset’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Changes
'LazyData' is specified without a 'data' directory
checkRd: (-1) residuals_paco.Rd:10: Escaped LaTeX specials: \$
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) pagoo.Rd:107-110: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pagoo.Rd:112-115: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pagoo.Rd:117-119: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pagoo.Rd:121-125: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pagoo.Rd:127-129: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pagoo.Rd:131-133: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pagoo.Rd:135: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pagoo.Rd:137-138: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pagoo.Rd:140-141: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pagoo.Rd:143-146: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pagoo.Rd:148-149: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pagoo.Rd:151-152: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pagoo.Rd:154-157: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pagoo.Rd:159-160: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pagoo.Rd:162-163: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pagoo.Rd:165-167: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pagoo.Rd:169-170: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pagoo.Rd:172-173: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
checkRd: (-1) MICS2014Ch.Rd:296: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) MICS2014Ch.Rd:297: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) MICS2014HH.Rd:214: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) MICS2014HH.Rd:215: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) MICS2014HL.Rd:109: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) MICS2014HL.Rd:110: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) MICS2014Wm.Rd:336: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) MICS2014Wm.Rd:337: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) PakPMICS2018bh.Rd:88: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) PakPMICS2018bh.Rd:89: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) PakPMICS2018fs.Rd:308: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) PakPMICS2018fs.Rd:309: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) PakPMICS2018hh.Rd:362: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) PakPMICS2018hh.Rd:363: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) PakPMICS2018mm.Rd:69: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) PakPMICS2018mm.Rd:70: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) PakPMICS2018mn.Rd:243: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) PakPMICS2018mn.Rd:244: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) PakPMICS2018bh.Rd:90: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) PakPMICS2018ch.Rd:454: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) PakPMICS2018fs.Rd:310: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) PakPMICS2018hh.Rd:364: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) PakPMICS2018hl.Rd:132: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) PakPMICS2018mm.Rd:71: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) PakPMICS2018mn.Rd:245: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) PakPMICS2018wm.Rd:448: Lost braces in \enumerate; meant \describe ?
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘CorShrink’
Documented arguments not in \usage in Rd file 'other.Rd':
  ‘trial’

Functions with \usage entries need to have the appropriate \alias
entries, and all their 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) branchClasses.Rd:15: Lost braces; missing escapes or markup?
    15 | \item{whichExtant}{A logical vector with length equal to number of tips in the tree. A {TRUE} value indicates
       |                                                                                        ^
checkRd: (-1) minCharChange.Rd:134: Lost braces; missing escapes or markup?
   134 | an identical name in function \code{phyDat} in package {phangorn}.
       |                                                        ^
checkRd: (-1) resolveTreeChar.Rd:98: Lost braces; missing escapes or markup?
    98 | an identical name in function \code{phyDat} in package {phangorn}.
       |                                                        ^
checkRd: (-1) simFossilRecord.Rd:44: Lost braces
    44 | since its origination time is code{D},
       |                                   ^
checkRd: (-1) as_ped.Rd:91: Lost braces
    91 | variables that were used to create the PED object (code{data}).}
       |                                                        ^
Documented arguments not in \usage in Rd file 'dplyr_verbs.Rd':
  ‘funs’ ‘.dots’ ‘keep_attributes’

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

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

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
checkRd: (-1) checkSoundscapeInput.Rd:40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) checkSoundscapeInput.Rd:41-42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) checkSoundscapeInput.Rd:43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) checkSoundscapeInput.Rd:44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotPSD.Rd:77: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotPSD.Rd:78-79: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotPSD.Rd:80-81: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotPSD.Rd:82-85: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotPSD.Rd:86-89: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
checkRd: (-1) Pandoc.convert.Rd:42: Lost braces
    42 | Calling John MacFarlane's great program to convert specified file (see \code{f} parameter below) or character vector {see \code{text} paramater} to other formats like \code{HTML}, \code{pdf}, \code{docx}, \code{odt} etc.
       |                                                                                                                      ^
checkRd: (-1) btsdemo.Rd:22: Escaped LaTeX specials: \_
checkRd: (-1) btsdemo.Rd:23: Escaped LaTeX specials: \_
checkRd: (-1) btsdemo.Rd:24: Escaped LaTeX specials: \_
checkRd: (-1) btsdemo.Rd:25: Escaped LaTeX specials: \_
checkRd: (-1) btsdemo.Rd:26: Escaped LaTeX specials: \_
checkRd: (-1) btsdemo.Rd:30: Escaped LaTeX specials: \_
Specified C++11: please drop specification unless essential
checkRd: (-1) panelsummary.Rd:112: Lost braces; missing escapes or markup?
   112 | \item `"{exp(estimate) * std.error}"
       |         ^
checkRd: (-1) panelsummary_raw.Rd:90: Lost braces; missing escapes or markup?
    90 | \item `"{exp(estimate) * std.error}"
       |         ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) hvidovre.Rd:11: Lost braces
    11 |     \item{\code{roof_tile}}{a numeric vector, roof_tile}{dummy, roof made out of tiles =1}
       |                                                         ^
checkRd: (-1) hvidovre.Rd:25: Lost braces
    25 |     \item{\code{railways}}{a numeric vector, railways}{distance to nearest railway in meters}
       |                                                       ^
checkRd: (-1) hvidovre.Rd:26: Lost braces
    26 |     \item{\code{nature_SLD}}{a numeric vector, nature_SLD}{distance to nearest nature area in meters}
       |                                                           ^
checkRd: (-1) apa_print.htest.Rd:58: Lost braces
    58 | [here]{https://github.com/crsh/papaja/issues} (please include
       |       ^
checkRd: (-1) init_apa_results.Rd:15-16: Lost braces
    15 | \item{\code{full_result}}{A (named list of) character strings comprised of \code{estimate} and \verb{statistic`` for each factor.\} \\item\{}table`}{A data frame containing all results; can, for example, be passed to \code{\link[=apa_table]{apa_table()}}.
       |                                                                                                                                                     ^
checkRd: (-1) agreement.Rd:52: Lost braces in \itemize; meant \describe ?
checkRd: (-1) agreement.Rd:53-54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) agreement.Rd:55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) agreement.Rd:56: Lost braces in \itemize; meant \describe ?
checkRd: (-1) agreement.Rd:57: Lost braces in \itemize; meant \describe ?
checkRd: (-1) agreement.Rd:58: Lost braces in \itemize; meant \describe ?
checkRd: (-1) papciUI.Rd:33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) papciUI.Rd:34-35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) papciUI.Rd:36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) papciUI.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) papciUI.Rd:38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) papciUI.Rd:39: Lost braces in \itemize; meant \describe ?
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in Rd file 'getOption2.Rd':
  ‘envvar’

Functions with \usage entries need to have the appropriate \alias
entries, and all their 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) getParamNr.Rd:15: Lost braces
    15 | Default is code{FALSE}.}
       |                ^
checkRd: (-1) getRequirements.Rd:16: Lost braces
    16 | code{TRUE}.}
       |     ^
checkRd: (-1) sampleValue.Rd:15: Lost braces; missing escapes or markup?
    15 | Default is code {FALSE}.}
       |                 ^
checkRd: (-1) sampleValues.Rd:18: Lost braces; missing escapes or markup?
    18 | Default is code {FALSE}.}
       |                 ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) returns.Rd:21: Lost braces; missing escapes or markup?
    21 |   \item{...}{Other options including {type} which refers to the
       |                                      ^
Malformed Description field: should contain one or more complete sentences.
checkRd: (-1) Code.Rd:68: Lost braces
    68 | ([base]{character})
       |        ^
checkRd: (-1) printMessage.Rd:10: Lost braces
    10 | \item{notPermitted}{([base]{data.frame})}
       |                            ^
checkRd: (-1) printMessage.Rd:12: Lost braces
    12 | \item{versionCheck}{([base]{data.frame})}
       |                            ^
checkRd: (-1) PPS.fit.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) PPS.fit.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) PPS.fit.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) PPS.fit.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) PPS.fit.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) PPS.fit.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) forbes400.Rd:8: Lost braces in \itemize; meant \describe ?
checkRd: (-1) forbes400.Rd:9: Lost braces in \itemize; meant \describe ?
checkRd: (-1) turkey.Rd:8: Lost braces in \itemize; meant \describe ?
checkRd: (-1) turkey.Rd:9: Lost braces in \itemize; meant \describe ?
checkRd: (-1) turkey.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) turkey.Rd:11: Lost braces in \itemize; meant \describe ?
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘rgdal’
Documented arguments not in \usage in Rd file 'expect_missing_argument.Rd':
  ‘message’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
checkRd: (-1) summary.parsec.Rd:13-14: Lost braces in \itemize; meant \describe ?
Specified C++14: please drop specification unless essential
checkRd: (-1) convert_notes.Rd:36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) convert_notes.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) convert_notes.Rd:38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) convert_notes.Rd:39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) convert_notes.Rd:40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) convert_notes.Rd:41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) convert_notes.Rd:42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) convert_notes.Rd:43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) convert_notes.Rd:44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) convert_notes.Rd:45: Lost braces in \itemize; meant \describe ?
checkRd: (-1) convert_notes.Rd:46: Lost braces in \itemize; meant \describe ?
checkRd: (-1) load_notes.Rd:71: Lost braces in \itemize; meant \describe ?
checkRd: (-1) load_notes.Rd:72: Lost braces in \itemize; meant \describe ?
checkRd: (-1) load_notes.Rd:73: Lost braces in \itemize; meant \describe ?
checkRd: (-1) load_notes.Rd:74: Lost braces in \itemize; meant \describe ?
checkRd: (-1) load_notes.Rd:75: Lost braces in \itemize; meant \describe ?
checkRd: (-1) load_notes.Rd:76: Lost braces in \itemize; meant \describe ?
checkRd: (-1) load_notes.Rd:77: Lost braces in \itemize; meant \describe ?
checkRd: (-1) load_notes.Rd:78: Lost braces in \itemize; meant \describe ?
checkRd: (-1) load_notes.Rd:79: Lost braces in \itemize; meant \describe ?
checkRd: (-1) load_notes.Rd:80: 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
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in Rd file 'as_partition.Rd':
  ‘.partition_step’

Functions with \usage entries need to have the appropriate \alias
entries, and all their 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:
  ‘co2’ ‘co2.1’ ‘co2.2’ ‘co2s.1’ ‘co2s.2’ ‘ctm.1’ ‘ctm.2’ ‘m’ ‘m.1’
  ‘m.2’ ‘test’ ‘test.1’ ‘test.2’ ‘testa.1’ ‘testa.2’ ‘xfile.1’
  ‘xfile.2’
Documented arguments not in \usage in Rd file 'fixvar_of_red_mod.Rd':
  ‘data’

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

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
checkRd: (-1) parse_iso8601_matrix.Rd:15: Lost braces
    15 | \code{yearweek} and code{weakday}.
       |                         ^
S3 methods shown with full name in Rd file 'vec_cast.partial_time.Rd':
  ‘vec_cast.partial_time’

S3 methods shown with full name in Rd file 'vec_cast.timespan.Rd':
  ‘vec_cast.timespan’

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.
Specified C++11: please drop specification unless essential
checkRd: (-1) PAS-package.Rd:30: Lost braces
    30 |     {\code{bin model}}{\cr Zhiqiu Hu, Zhiquan Wang, and Shizhong Xu (2012) An infinitesimal model for quantitative trait genomic value prediction. PloS ONE 7: e41336.}
       |                       ^
checkRd: (-1) regul.Rd:52: Escaped LaTeX specials: \# \# \#
checkRd: (-1) regul.Rd:52: Escaped LaTeX specials: \#
checkRd: (-1) as_config.Rd:32: Lost braces; missing escapes or markup?
    32 | with `{config}` package, which requires existence of default key.
       |       ^
checkRd: (-1) as_config.Rd:28: Lost braces; missing escapes or markup?
    28 | list compatible with `{config}` package
       |                       ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) get_gene_sets_list.Rd:32: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get_gene_sets_list.Rd:33: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get_kegg_gsets.Rd:15: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get_kegg_gsets.Rd:16: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get_mgsigdb_gsets.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get_mgsigdb_gsets.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get_reactome_gsets.Rd:12: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get_reactome_gsets.Rd:13: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gset_list_from_gmt.Rd:16: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gset_list_from_gmt.Rd:17: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) plotHeat.Rd:113: Lost braces
   113 | code{\link[patternize]{patPCA}}, as 'one' when visualizing single image or as 'multi' for multi
       |     ^
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Argument items with no description in Rd file 'markbouts.acclist.Rd':
  ‘extreme’
S3 methods shown with full name in Rd file 'ped.Rd':
  ‘ped.markerNames’

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) pbd_loglik.Rd:31: Lost braces
    31 |     \code{pars2[1]} {set the conditioning on non-extinction of the clade (1) or not (0) \cr \cr}
       |                     ^
checkRd: (-1) pbd_loglik.Rd:32: Lost braces
    32 |     \code{pars2[2]} {sets whether the likelihood is for the branching times (0) or the phylogeny (1) \cr \cr}
       |                     ^
checkRd: (-1) pbd_loglik.Rd:33: Lost braces
    33 |     \code{pars2[3]} {sets whether the first element of the branching times is the stem (1) or the crown (2) age \cr \cr}
       |                     ^
checkRd: (-1) pbd_loglik.Rd:34: Lost braces
    34 |     \code{pars2[4]} {sets whether the parameters and likelihood should be shown on screen (1) or not (0) \cr \cr}
       |                     ^
checkRd: (-1) pbd_loglik.Rd:35: Lost braces
    35 |     \code{pars2[5]} {sets which method should be used in the ode-solver. Default is 'lsoda'. See package deSolve for details. \cr \cr}
       |                     ^
checkRd: (-1) pbd_loglik.Rd:36: Lost braces
    36 |     \code{pars2[6]}{Sets the lower bound of the number of species on which conditioning should be done when cond = 2. Set this to 0 when conditioning should be done on precisely the number of species (default)\cr \cr}
       |                    ^
checkRd: (-1) pbd_loglik.Rd:37: Lost braces
    37 |     \code{pars2[7]}{Sets the upper bound of the number of species on which conditioning should be done when cond = 2. Set this to 0 when conditioning should be done on precisely the number of species (default)\cr \cr}  
       |                    ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  PBSddesolve.c:221:23: warning: too many arguments for format [-Wformat-extra-args]
  ddeq.c:307:85: warning: format ‘%d’ expects argument of type ‘int’, but argument 5 has type ‘long int’ [-Wformat=]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/PBSddesolve.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-13 (Debian 13.2.0-7) 13.2.0’
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
checkRd: (-1) addBgKnowledge.Rd:26: Lost braces; missing escapes or markup?
    26 | If \code{x} and \code{y} are not specified (or empty vectors) this function simply completes the orientation rules from Meek (1995). If \code{x} and \code{y} are vectors of length k, k>1, this function tries to add \code{x[i] -> y[i]} to the adjacency matrix amat and complete the orientation rules from Meek (1995) for every i in {1,...,k} (see Algorithm 1 in Perkovic et. al, 2017). 
       |                                                                                                                                                                                                                                                                                                                                            ^
checkRd: (-1) adjustment.Rd:33: Lost braces; missing escapes or markup?
    33 | is returned that consists of all (possible) ancestors of \code{x} and {y},
       |                                                                       ^
checkRd: (-1) fci.Rd:70: Lost braces
    70 |     and the size of Possible-D-SEP(\code{x})\ {\code{x},\code{y}} is
       |                                               ^
checkRd: (-1) fci.Rd:154: Lost braces; missing escapes or markup?
   154 |   and \code{y} if and only if variables {x} and {y} are conditionally dependent
       |                                         ^
checkRd: (-1) fci.Rd:154: Lost braces; missing escapes or markup?
   154 |   and \code{y} if and only if variables {x} and {y} are conditionally dependent
       |                                                 ^
checkRd: (-1) pdsep.Rd:61: Lost braces
    61 |     and the size of Possible-D-SEP(x,G)\ {\code{x},\code{y}}, is
       |                                          ^
checkRd: (-1) rfci.Rd:117: Lost braces; missing escapes or markup?
   117 |   given all subsets of sepset(d,c) \ {f1,f2 }. If we do not find any
       |                                      ^
checkRd: (-1) twoby2Calibrate.Rd:84: Lost braces in \itemize; meant \describe ?
checkRd: (-1) twoby2Calibrate.Rd:85-86: Lost braces in \itemize; meant \describe ?
checkRd: (-1) twoby2Calibrate.Rd:87-92: Lost braces in \itemize; meant \describe ?
checkRd: (-1) twoby2Calibrate.Rd:97-100: Lost braces in \itemize; meant \describe ?
checkRd: (-1) twoby2Calibrate.Rd:101-103: Lost braces in \itemize; meant \describe ?
checkRd: (-1) twoby2Calibrate.Rd:104-107: Lost braces in \itemize; meant \describe ?
checkRd: (-1) twoby2Calibrate.Rd:108-110: Lost braces in \itemize; meant \describe ?
checkRd: (-1) twoby2Calibrate.Rd:111-116: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) IarcPEset2pnt.std.tri.Rd:34: Lost braces
    34 | \eqn{I(}\code{p} is in U_{x in \code{S}} \eqn{N_{PE}(x,r))}
       |                          ^
checkRd: (-1) IarcPEset2pnt.tri.Rd:35: Lost braces
    35 | I(\code{p} is in U_{x in \code{S}} N_{PE}(x,r)),
       |                    ^
checkRd: (-1) IarcPEset2pnt.tri.Rd:35: Lost braces; missing escapes or markup?
    35 | I(\code{p} is in U_{x in \code{S}} N_{PE}(x,r)),
       |                                      ^
checkRd: (-1) IarcPEtetra.Rd:32: Lost braces; missing escapes or markup?
    32 | returns 0 otherwise, where N_{PE}(x,r) is the PE proximity region for point \eqn{x} with the expansion parameter \eqn{r \ge 1}.
       |                              ^
checkRd: (-1) swamptrees.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) swamptrees.Rd:38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) swamptrees.Rd:39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) swamptrees.Rd:40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) swamptrees.Rd:41: Lost braces in \itemize; meant \describe ?
GNU make is a SystemRequirements.
Objects in \usage without \alias in Rd file 'pch-internal.Rd':
  ‘CumSum’ ‘myapply’ ‘makebreaks.ct’ ‘makebreaks.ic’ ‘pois.loglik’
  ‘icpch.loglik’ ‘convert.Surv’ ‘break.y’ ‘pois.fit’ ‘pch.fit.ct’
  ‘pch.fit.ic’ ‘newton’ ‘cleanlambda’ ‘predF.pch’ ‘predQ.pch’ ‘sim.pch’
  ‘build.splinex’ ‘predict.splinex’ ‘logLik.pch’ ‘nobs.pch’ ‘vcov.pch’
  ‘coef.pch’ ‘print.pch’ ‘summary.pch’ ‘print.summary.pch’

Functions with \usage entries need to have the appropriate \alias
entries, and all their 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) PCM_ABC.Rd:106: Lost braces in \itemize; meant \describe ?
checkRd: (-1) PCM_ABC.Rd:108-109: Lost braces in \itemize; meant \describe ?
checkRd: (-1) PCM_ABC.Rd:114: Lost braces in \itemize; meant \describe ?
checkRd: (-1) PCM_ABC.Rd:115: Lost braces in \itemize; meant \describe ?
checkRd: (-1) PCM_ABC.Rd:117: Lost braces in \itemize; meant \describe ?
checkRd: (-1) PCM_ABC.Rd:205-207: Lost braces in \itemize; meant \describe ?
checkRd: (-1) PCM_ABC.Rd:208-211: Lost braces in \itemize; meant \describe ?
checkRd: (-1) PCM_ABC.Rd:212-216: Lost braces in \itemize; meant \describe ?
checkRd: (-1) PCM_ABC.Rd:221-224: Lost braces in \itemize; meant \describe ?
checkRd: (-1) PCM_ABC.Rd:225-228: Lost braces in \itemize; meant \describe ?
checkRd: (-1) PCM_ABC.Rd:229-231: Lost braces in \itemize; meant \describe ?
checkRd: (-1) PCM_ABC.Rd:232: Lost braces in \itemize; meant \describe ?
checkRd: (-1) PCM_ABC.Rd:233: Lost braces in \itemize; meant \describe ?
checkRd: (-1) PCM_ABC.Rd:234: Lost braces in \itemize; meant \describe ?
checkRd: (-1) PCM_ABC.Rd:235: Lost braces in \itemize; meant \describe ?
checkRd: (-1) PCM_ABC.Rd:236: Lost braces in \itemize; meant \describe ?
checkRd: (-1) PCM_ABC.Rd:237: Lost braces in \itemize; meant \describe ?
checkRd: (-1) PCM_ABC.Rd:238: Lost braces in \itemize; meant \describe ?
checkRd: (-1) PCM_ABC.Rd:239: Lost braces in \itemize; meant \describe ?
checkRd: (-1) PCM_ABC.Rd:240: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulate_phylproc.Rd:56: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulate_phylproc.Rd:58-59: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulate_phylproc.Rd:64: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulate_phylproc.Rd:65: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulate_phylproc.Rd:67: Lost braces in \itemize; meant \describe ?
Specified C++11: please drop specification unless essential
checkRd: (-1) MiniBenchmarkRvsCpp.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MiniBenchmarkRvsCpp.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MiniBenchmarkRvsCpp.Rd:18: Lost braces in \itemize; meant \describe ?
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
checkRd: (-1) pcoxtimecv.Rd:51: Lost braces; missing escapes or markup?
    51 | \item{foldids}{an optional sequence of values between \code{1} and {nfolds} specifying what fold each observation is in. This is important when comparing performance across models. If specified, \code{nfolds} can be missing.}
       |                                                                    ^
checkRd: (-1) pcoxtimecv.Rd:89: Lost braces
    89 | If more than one \code{alphas} is specified, say code{(0.2, 0.5, 1)}, the \code{pcoxtimecv} will search (experimental) for optimal values for alpha with respect to the corresponding lambda values. In this case, optimal alpha and lambda sequence will be returned, i.e., the \code{(alphas, lambdas)} pair that corresponds to the lowest predicted cross-validated error (likelihood deviance).
       |                                                      ^
checkRd: (-1) simtdc.Rd:67: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simtdc.Rd:69: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simtdc.Rd:70: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simtdc.Rd:71: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simtdc.Rd:72: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simtdc.Rd:73: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simtdc.Rd:74: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simtdc.Rd:76: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simtdc.Rd:77: Lost braces in \itemize; \value handles \item{}{} directly
Documented arguments not in \usage in Rd file 'getResponse.Rd':
  ‘model’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
checkRd: (-1) getPCRAData.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getPCRAData.Rd:29: Lost braces in \itemize; meant \describe ?
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
checkRd: (-1) get_cols.Rd:12: Lost braces; missing escapes or markup?
    12 | \item{pal}{col1~3; or a vector of colors, you can get from here too.{RColorBrewer::brewer.pal(5,"Set2")} {ggsci::pal_aaas()(5)}}
       |                                                                     ^
checkRd: (-1) get_cols.Rd:12: Lost braces; missing escapes or markup?
    12 | \item{pal}{col1~3; or a vector of colors, you can get from here too.{RColorBrewer::brewer.pal(5,"Set2")} {ggsci::pal_aaas()(5)}}
       |                                                                                                          ^
checkRd: (-1) my_circo.Rd:20: Lost braces; missing escapes or markup?
    20 | \item{pal}{a vector of colors, you can get from here too.{RColorBrewer::brewer.pal(5,"Set2")} {ggsci::pal_aaas()(5)}}
       |                                                          ^
checkRd: (-1) my_circo.Rd:20: Lost braces; missing escapes or markup?
    20 | \item{pal}{a vector of colors, you can get from here too.{RColorBrewer::brewer.pal(5,"Set2")} {ggsci::pal_aaas()(5)}}
       |                                                                                               ^
checkRd: (-1) pcvpcr.Rd:42: Lost braces; missing escapes or markup?
    42 | set {X, y} and cross-validation.
       |     ^
checkRd: (-1) pcvpls.Rd:42: Lost braces; missing escapes or markup?
    42 | set {X, y} and cross-validation.
       |     ^
Objects in \usage without \alias in Rd file 'ODACATH.estimate.Rd':
  ‘ODACAT.estimate’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Package suggested but not available for checking: ‘PythonInR’
checkRd: (-1) keyword_directory.Rd:48: Lost braces
    48 | Default pattern is "\\p{WHITE_SPACE}{3,}" which can be interpreted as: 
       |                        ^
checkRd: (-1) keyword_directory.Rd:48: Lost braces
    48 | Default pattern is "\\p{WHITE_SPACE}{3,}" which can be interpreted as: 
       |                                     ^
checkRd: (-1) keyword_search.Rd:59: Lost braces
    59 | Default pattern is "\\p{WHITE_SPACE}{3,}" which can be interpreted as: 
       |                        ^
checkRd: (-1) keyword_search.Rd:59: Lost braces
    59 | Default pattern is "\\p{WHITE_SPACE}{3,}" which can be interpreted as: 
       |                                     ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) get_training_data.Rd:6-14: Lost braces
     6 | where <- function(name, env = parent.frame()) {
       |                                               ^
checkRd: (-1) get_training_data.Rd:7-9: Lost braces
     7 |   if (identical(env, emptyenv())) {
       |                                   ^
checkRd: (-1) get_training_data.Rd:9-11: Lost braces
     9 |   } else if (exists(name, envir = env, inherits = FALSE)) {
       |                                                           ^
checkRd: (-1) get_training_data.Rd:11-13: Lost braces
    11 |   } else {
       |          ^
checkRd: (-1) get_training_data.Rd:20-28: Lost braces
    20 | where <- function(name, env = parent.frame()) {
       |                                               ^
checkRd: (-1) get_training_data.Rd:21-23: Lost braces
    21 |   if (identical(env, emptyenv())) {
       |                                   ^
checkRd: (-1) get_training_data.Rd:23-25: Lost braces
    23 |   } else if (exists(name, envir = env, inherits = FALSE)) {
       |                                                           ^
checkRd: (-1) get_training_data.Rd:25-27: Lost braces
    25 |   } else {
       |          ^
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) pdkMeans.Rd:63: Lost braces
    63 | \cite{C18}{pdSpecEst} for more details. Note that this comes at the cost of increased computation time in comparison to one
       |           ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) embedded.blocks.Rd:39: Lost braces
    39 | \item{miv.threshold}{MIV (marginal information value) entrance threshold applicable only for code{"stepMIV"} method.
       |                                                                                                  ^
checkRd: (-1) embedded.blocks.Rd:44: Lost braces
    44 | \item{m.ch.p.val}{Significance level of p-value for marginal chi-square test applicable only for code{"stepMIV"} method.
       |                                                                                                      ^
checkRd: (-1) ensemble.blocks.Rd:39: Lost braces
    39 | \item{miv.threshold}{MIV (marginal information value) entrance threshold applicable only for code{"stepMIV"} method.
       |                                                                                                  ^
checkRd: (-1) ensemble.blocks.Rd:44: Lost braces
    44 | \item{m.ch.p.val}{Significance level of p-value for marginal chi-square test applicable only for code{"stepMIV"} method.
       |                                                                                                      ^
checkRd: (-1) staged.blocks.Rd:39: Lost braces
    39 | \item{miv.threshold}{MIV (marginal information value) entrance threshold applicable only for code{"stepMIV"} method.
       |                                                                                                  ^
checkRd: (-1) staged.blocks.Rd:44: Lost braces
    44 | \item{m.ch.p.val}{Significance level of p-value for marginal chi-square test applicable only for code{"stepMIV"} method.
       |                                                                                                      ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) Peacock.test-package.Rd:28: Escaped LaTeX specials: \_
'LazyData' is specified without a 'data' directory
Argument items with no description in Rd file 'PoissonLoss.Rd':
  ‘count’ ‘seg.mean’ ‘weight’
Argument items with no description in Rd file 'getPath.Rd':
  ‘A’
Argument items with no description in Rd file 'PoissonLoss.Rd':
  ‘count’ ‘seg.mean’ ‘weight’
Argument items with no description in Rd file 'featureMatrixJoint.Rd':
  ‘profile.list’
Specified C++11: please drop specification unless essential
Argument items with no description in Rd file 'PoissonLoss.Rd':
  ‘count’ ‘seg.mean’ ‘weight’
Argument items with no description in Rd file 'oracleModelComplexity.Rd':
  ‘bases’ ‘segments’
checkRd: (-1) est_norm.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) est_norm.Rd:23-24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) est_norm.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) est_norm.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) est_norm.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) example.geno.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) example.geno.Rd:25-26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) example.geno.Rd:27-28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) example.geno.Rd:33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) example.geno.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) example.geno.Rd:35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) example.geno.Rd:36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) example.geno.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) example.geno.Rd:38-40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) example.geno.Rd:41-45: Lost braces in \itemize; meant \describe ?
checkRd: (-1) example.geno.Rd:49: Lost braces in \itemize; meant \describe ?
checkRd: (-1) example.geno.Rd:50: Lost braces in \itemize; meant \describe ?
checkRd: (-1) example.geno.Rd:55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) example.geno.Rd:56-57: Lost braces in \itemize; meant \describe ?
checkRd: (-1) example.geno.Rd:58-59: Lost braces in \itemize; meant \describe ?
checkRd: (-1) example.geno.Rd:60-61: Lost braces in \itemize; meant \describe ?
S3 methods shown with full name in Rd file 'format.relation.Rd':
  ‘format.relation’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
checkRd: (-1) pedigree_ll_terms.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pedigree_ll_terms.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pedigree_ll_terms.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pedigree_ll_terms.Rd:19-20: Lost braces in \itemize; meant \describe ?
Package suggested but not available for checking: ‘georob’
checkRd: (-1) variogramGuess.Rd:94: Lost braces
    94 | Method \code{"b"} was proposed by \doi{10.1016/0098-3004(95)00095-X}{Jian et al. (1996)} and
       |                                                                     ^
checkRd: (-1) variogramGuess.Rd:98: Lost braces
    98 | \doi{10.1016/j.cageo.2008.10.011}{Hiemstra et al. (2009)}.
       |                                  ^
checkRd: (-1) variogramGuess.Rd:100: Lost braces
   100 | Method \code{"d"} was developed by \doi{10.1007/s11004-012-9434-1}{Desassis & Renard (2012)}.
       |                                                                   ^
GNU make is a SystemRequirements.
checkRd: (-1) 5.1.pems.plots.Rd:212: Lost braces; missing escapes or markup?
   212 |   (Logical or character) For {WatsonPlot}, how to 
       |                              ^
checkRd: (-1) 5.1.pems.plots.Rd:221: Lost braces; missing escapes or markup?
   221 |   (numeric) For {WatsonPlot}, pre-set plot types: 
       |                 ^
checkRd: (-1) 6.2.check.functions.Rd:189: Lost braces
   189 |   If a parent function is identified as \code{fun.name} and the check case (code{input}, 
       |                                                                                 ^
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    89 |   code{\link{common.calculations}} for further details.
       |       ^
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    90 |   emissions calculation methods. It accepts an input code{conc} which it checks and passes 
       |                                                          ^
checkRd: (-1) 8.1.tidyverse.tools.Rd:139: Lost braces
   139 |    (\code{pems}, code{data.frame}, etc) to 
       |                      ^
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    81 | max_b { b' Sigma_bet b  - lambda*d*sum(abs(b)) } s.t. ||b||^2 <= 1
       |       ^
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    88 | max_b { b' Sigma_bet b - lambda*d*sum(abs(b)) - lambda2*d*sum(abs(bj -
       |       ^
Specified C++11: please drop specification unless essential
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checkRd: (-1) my.bspline.Rd:38: Escaped LaTeX specials: \$ \$ \$
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    53 | is not 2^{p} but the number of unique models `visited' by the 
       |          ^
Argument items with no description in Rd file 'lmres.Rd':
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Argument items with no description in Rd file 'simpleSlope.Rd':
  ‘\dots’
Argument items with no description in Rd file 'summary.lmres.Rd':
  ‘\dots’
Specified C++11: please drop specification unless essential
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Package suggested but not available for checking: ‘DMwR’
checkRd: (-1) classificationMetrics.Rd:85: Lost braces; missing escapes or markup?
    85 |   will use some extra notation, namely: TP = #{p == + & t == +} ; FP =
       |                                               ^
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    86 |   #{p == + & t == -} ; TN = #{p == - & t == -}; FN = #{p == - & t == +}
       |    ^
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    86 |   #{p == + & t == -} ; TN = #{p == - & t == -}; FN = #{p == - & t == +}
       |                              ^
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    86 |   #{p == + & t == -} ; TN = #{p == - & t == -}; FN = #{p == - & t == +}
       |                                                       ^
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    87 |   ; P = #{t == +} ; N = #{t == -}; Finally, for some descriptions
       |          ^
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    87 |   ; P = #{t == +} ; N = #{t == -}; Finally, for some descriptions
       |                          ^
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Documented arguments not in \usage in Rd file 'allTrees.Rd':
  ‘dist’

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

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

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
checkRd: (-1) jackal.Rd:32: Escaped LaTeX specials: \&
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Invalid package aliases in Rd file 'perspective-package.Rd':
  ‘perspective-package’
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Fixed issues
'LazyData' is specified without a 'data' directory
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    15 | A code{\link{marked_petrinet}}
       |       ^
'LazyData' is specified without a 'data' directory
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     5 | \title{Loads the variant_numth variant, and then fills buf with {0, 1, 2, NA}
       |                                                                 ^
checkRd: (-1) ReadIntList.Rd:17: Lost braces; missing escapes or markup?
    17 | correspond to variant_subset, and values are in {0, 1, 2, NA} indicating
       |                                                 ^
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Unknown packages ‘maptools’, ‘rgdal’ in Rd xrefs
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'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
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   100 | "Result": {
       |           ^
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   105 | "BacteriaLysed": {
       |                  ^
Specified C++11: please drop specification unless essential
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    19 | A \code{plotly} {htmlwidget} with rose plots for locomotor activity.
       |                 ^
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    19 | #' @return A \code{plotly} {htmlwidget} with rose plots for sleep data.
       |                            ^
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    84 | identified {see (3) above}, if this point is a saddle then the manifolds are
       |            ^
Found the following files/directories:
  ‘test.pdf’
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'process_season.Rd':
  ‘d’ ‘options_season’

Functions with \usage entries need to have the appropriate \alias
entries, and all their 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) connectedSets.Rd:27: Escaped LaTeX specials: \_ \_
checkRd: (-1) connectedSets.Rd:29: Escaped LaTeX specials: \_ \_
checkRd: (-1) connectedSets.Rd:31: Escaped LaTeX specials: \_ \_
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Auto-generated content requiring editing in Rd file 'phm-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) read_cid_spectravue_csv.Rd:46: Lost braces
    46 | function code{range()} will return range of wavelengths expressed in
       |              ^
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    78 |   \code{tz = UTC} and {time.shift.min = 120} to convert times to UTC. This
       |                       ^
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    18 |   Irradiance was in the range 10 to 15 W m$^{-2}$.
       |                                             ^
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    87 |   \item \code{theta} The ncol{counts} by K matrix of estimated
       |                              ^
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    89 |   \item \code{omega} The nrow{counts} by K matrix of estimated
       |                              ^
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    51 | the output ({out$DiscardedGenes}).}
       |             ^
Package suggested but not available for checking: ‘INLA’
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    11 | code{l2df}: convert list to data.frame
       |     ^
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    14 | code{convertTZ}: force a new timezone on datetime
       |     ^
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    16 | code{createTime}: create datetime variable
       |     ^
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    18 | code{addDayIndex}: create ID_day variable from timestamp
       |     ^
'LazyData' is specified without a 'data' directory
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checkRd: (-1) traitgram.Rd:14: Escaped LaTeX specials: \$
checkRd: (-1) utility.Rd:37: Escaped LaTeX specials: \$ \$
Specified C++11: please drop specification unless essential
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checkRd: (-1) game_systems.Rd:106: Lost braces
   106 | \item{playing_cards_expansion}{A piecepack with the standard dQuote{French} playing card suits.
       |                                                                    ^
Specified C++11: please drop specification unless essential
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'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘pinnacle.API’
checkRd: (-1) pinp.Rd:60: Lost braces; missing escapes or markup?
    60 |   {current date}"}
       |   ^
Specified C++11: please drop specification unless essential
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Invalid package aliases in Rd file 'pipegs.Rd':
  ‘pipegs-package’
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Documented arguments not in \usage in Rd file 'TungUbRF.Rd':
  ‘feature_num_tree’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) get_pixels.Rd:27-29: Lost braces
    27 | if (interactive()) {
       |                    ^
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'LazyData' is specified without a 'data' directory
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checkRd: (-1) build_reference.Rd:157: Lost braces; missing escapes or markup?
   157 | a top-level \code{icons} directory. This should contain {.png} files that are
       |                                                         ^
Documented arguments not in \usage in Rd file 'make_pgk_cache_subdir_for_all_relative_files.Rd':
  ‘relative_filenames’

Functions with \usage entries need to have the appropriate \alias
entries, and all their 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) write.pkgbib.Rd:44: Lost braces; missing escapes or markup?
    44 | The Old version of this function {write.bib} has now been integrated
       |                                  ^
'LazyData' is specified without a 'data' directory
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checkRd: (-1) pkgstats.Rd:17: Lost braces in \enumerate; \value handles \item{}{} directly
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checkRd: (-1) pk.calc.sparse_auc.Rd:49: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) sparse_auc_weight_linear.Rd:28: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) time_calc.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
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    27 | item j. For example, in the ranking \\{1\\} > \\{3, 4\\} > \\{2\\},
       |                                       ^
checkRd: (-1) adjacency.Rd:27: Lost braces; missing escapes or markup?
    27 | item j. For example, in the ranking \\{1\\} > \\{3, 4\\} > \\{2\\},
       |                                                 ^
checkRd: (-1) adjacency.Rd:27: Lost braces; missing escapes or markup?
    27 | item j. For example, in the ranking \\{1\\} > \\{3, 4\\} > \\{2\\},
       |                                                              ^
checkRd: (-1) rankings.Rd:127: Lost braces; missing escapes or markup?
   127 | rank skipped. For example {1, 0, 2, 1}, ranks the first and fourth items in
       |                           ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) 01-TCGA-ESCA-data.Rd:47: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) 01-TCGA-ESCA-data.Rd:48: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) 01-TCGA-ESCA-data.Rd:49-51: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) 01-TCGA-ESCA-data.Rd:52-55: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) 01-TCGA-ESCA-data.Rd:56-58: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) 01-TCGA-ESCA-data.Rd:59-62: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) 01-TCGA-ESCA-data.Rd:63-64: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) 02-fitCoxModel.Rd:87: Lost braces; missing escapes or markup?
    87 |   returns the value on which it was invoked. The {summary} method
       |                                                  ^
Found the following files/directories:
  ‘P2Run.csv’ ‘P2Run.html’ ‘P2Run.png’
checkRd: (-1) one_design.Rd:125-126: Lost braces
   125 | function serves for the purpose of spot-testing for any pre-specified {n,
       |                                                                       ^
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
checkRd: (-1) plgraphics-internal.Rd:19: Lost braces
    19 |     \item{RNAMES}{code{row.names} if \code{x} is a matrix or data.frame,
       |                       ^
checkRd: (-1) check_hwe.Rd:103: Lost braces; missing escapes or markup?
   103 | {'ALL', 'AFF', 'UNAFF', 'ALL(QT)', 'ALL(NP)'}), A1 (Allele 1; usually minor),
       | ^
checkRd: (-1) trichoptera.Rd:10: Lost braces
    10 | \code{Abundance}{a 49 x 17 matrix of abundancies/counts (49 trapping nights and 17 trichoptera species)}
       |                 ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) delta2a.Rd:21: Lost braces; missing escapes or markup?
    21 | delta_k = log(a_k - a_{k+1})
       |                       ^
checkRd: (-1) ordprob.mple.Rd:29: Lost braces
    29 | logical. If code{TRUE} all the q variable are assumed to have the same mean.
       |                 ^
checkRd: (-1) colors.Rd:43: Lost braces; missing escapes or markup?
    43 |     To combine transparency with lighting or shading, pass argument {alpha} 
       |                                                                     ^
checkRd: (-1) trans3D.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
checkRd: (-1) add_bars.Rd:15: Lost braces
    15 | When \\code{y0} is not specified, the lowest value of the y-axis is used.}
       |            ^
checkRd: (-1) add_bars.Rd:24: Lost braces
    24 | \\code{\\link[graphics]{par}}.}
       |       ^
checkRd: (-1) add_bars.Rd:24: Lost braces
    24 | \\code{\\link[graphics]{par}}.}
       |                        ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) plotluck.Rd:129: Lost braces
   129 |  in factors are are shown as a special factor level code{"?"}. They can be
       |                                                         ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) domain_data.Rd:29: Lost braces
    29 | code{\link{help}}
       |     ^
checkRd: (-1) length_data.Rd:32: Lost braces
    32 | code{\link{help}}
       |     ^
checkRd: (-1) plotdomain.Rd:30: Lost braces
    30 | code{\link{help}}
       |     ^
checkRd: (-1) plotmutagensis.Rd:30: Lost braces
    30 | code{\link{help}}
       |     ^
checkRd: (-1) plotprotein-package.Rd:20: Lost braces
    20 | code{\link{help}}
       |     ^
checkRd: (-1) plotprotein.Rd:30: Lost braces
    30 | code{\link{help}}
       |     ^
checkRd: (-1) plotsite.Rd:30: Lost braces
    30 | code{\link{help}}
       |     ^
checkRd: (-1) site_data.Rd:30: Lost braces
    30 | code{\link{help}}
       |     ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) spls.cv.Rd:70-72: Lost braces
    70 | \item{scale.X}{aa}{boolean value indicating whether the data matrices 
       |                   ^
checkRd: (-1) spls.stab.Rd:65-67: Lost braces
    65 | \item{scale.X}{aa}{boolean value indicating whether the data matrices 
       |                   ^
Invalid package aliases in Rd file 'plsgenomics-deprecated.Rd':
  ‘plsgenomics-deprecated-package’
Invalid package aliases in Rd file 'plsgenomics-internal.Rd':
  ‘plsgenomics-internal-package’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) plu_more.Rd:16: Lost braces; missing escapes or markup?
    16 | Additional arguments are replaced with "{n} more".
       |                                         ^
Found the following significant warnings:
  FLSAGeneral.cc:240:66: warning: format ‘%d’ expects argument of type ‘int’, but argument 5 has type ‘std::set<int>::size_type’ {aka ‘long unsigned int’} [-Wformat=]
  FLSAGeneral.cc:240:70: warning: format ‘%d’ expects argument of type ‘int’, but argument 6 has type ‘std::set<int>::size_type’ {aka ‘long unsigned int’} [-Wformat=]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/PMA.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-13 (Debian 13.2.0-7) 13.2.0’
* used C++ compiler: ‘g++-13 (Debian 13.2.0-7) 13.2.0’
Package suggested but not available for checking: ‘pmartRdata’
checkRd: (-1) PMCMR-deprecated.Rd:36: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) PMCMR-deprecated.Rd:37: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) PMCMR-deprecated.Rd:38: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) PMCMR-deprecated.Rd:39-40: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) PMCMR-deprecated.Rd:41: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
checkRd: (-1) pmledecon.Rd:113: Lost braces; missing escapes or markup?
   113 |     likelihood less than $10^{-10}$ are replaced by $10^{-10}$.
       |                              ^
checkRd: (-1) pmledecon.Rd:113: Lost braces; missing escapes or markup?
   113 |     likelihood less than $10^{-10}$ are replaced by $10^{-10}$.
       |                                                         ^
checkRd: (-1) ahp.Rd:16: Lost braces; missing escapes or markup?
    16 | an ``A'' matrix. It should be a square matrix with diagonal values equal 1 and $a_{ij} = 1/a_{ij}$.
       |                                                                                   ^
checkRd: (-1) ahp.Rd:16: Lost braces; missing escapes or markup?
    16 | an ``A'' matrix. It should be a square matrix with diagonal values equal 1 and $a_{ij} = 1/a_{ij}$.
       |                                                                                              ^
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'sample_store.Rd':
  ‘subjects_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.
checkRd: (-1) plot_scm.Rd:106: Lost braces; missing escapes or markup?
   106 | \item{lookupDF}{A data frame containing a lookup table for node labels. By default, {plot_scm} will use the PSN model names. If a lookup table containing the fields `Model` and `Alias` is provided, model names in `Model` will be replaced in the output plots by mtaching labels in `Alias`.}
       |                                                                                     ^
checkRd: (-1) rnm.Rd:56: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rnm.Rd:57: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rnm.Rd:58: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rnm.Rd:59: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rnm.Rd:60: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rnm.Rd:61: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rnm.Rd:62: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rnm.Rd:63: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rnm.Rd:64: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rnm.Rd:65: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rnm.Rd:66: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rnm.Rd:67: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rnm.Rd:68: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rnm.Rd:69: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rnm.Rd:70: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rnm.Rd:71: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
Package unavailable to check Rd xrefs: ‘INLA’
checkRd: (-1) estimate.functional.Rd:34: Lost braces; missing escapes or markup?
    34 | \item{bw}{function describing bandwidth selection (see ?gmm for alternatives). Standard is that the bandwidth depends on the sample length $T$ by $m(T)=T^{1/5}$.}
       |                                                                                                                                                           ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) pois.fe.robust.Rd:47: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pois.fe.robust.Rd:48: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pois.fe.robust.Rd:49: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pois.fe.robust.Rd:50-51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pois.fe.robust.Rd:66: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pois.fe.robust.Rd:67: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pois.fe.robust.Rd:68-69: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) carcinoma.Rd:8: Escaped LaTeX specials: \&
checkRd: (-1) poLCA.Rd:63: Escaped LaTeX specials: \&
checkRd: (-1) poLCA.Rd:69: Escaped LaTeX specials: \&
checkRd: (-1) nuisance_functions.Rd:18-19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) policy.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) policy_data.Rd:124-125: Lost braces in \itemize; meant \describe ?
checkRd: (-1) policy_data.Rd:126: Lost braces in \itemize; meant \describe ?
checkRd: (-1) policy_data.Rd:127-128: Lost braces in \itemize; meant \describe ?
checkRd: (-1) policy_data.Rd:129: Lost braces in \itemize; meant \describe ?
checkRd: (-1) policy_data.Rd:130: Lost braces in \itemize; meant \describe ?
checkRd: (-1) policy_data.Rd:131: Lost braces in \itemize; meant \describe ?
checkRd: (-1) policy_data.Rd:132: Lost braces in \itemize; meant \describe ?
checkRd: (-1) policy_eval.Rd:193: Lost braces in \itemize; meant \describe ?
checkRd: (-1) policy_eval.Rd:194: Lost braces in \itemize; meant \describe ?
checkRd: (-1) policy_eval.Rd:195: Lost braces in \itemize; meant \describe ?
checkRd: (-1) policy_eval.Rd:196-197: Lost braces in \itemize; meant \describe ?
checkRd: (-1) policy_eval.Rd:198: Lost braces in \itemize; meant \describe ?
checkRd: (-1) policy_eval.Rd:199: Lost braces in \itemize; meant \describe ?
checkRd: (-1) policy_learn.Rd:129: Lost braces in \itemize; meant \describe ?
checkRd: (-1) policy_learn.Rd:130: Lost braces in \itemize; meant \describe ?
checkRd: (-1) policy_learn.Rd:131: Lost braces in \itemize; meant \describe ?
checkRd: (-1) policy_learn.Rd:132-133: Lost braces in \itemize; meant \describe ?
checkRd: (-1) policy_learn.Rd:134: Lost braces in \itemize; meant \describe ?
Package suggested but not available for checking: ‘pollimetrydata’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) inputData.Rd:94: Lost braces
    94 | recommend using either \sQuote{code{.}} (a period) or
       |                                    ^
checkRd: (-1) inputData.Rd:95: Lost braces
    95 | \sQuote{code{_}} (an underscore) rather than a space.
       |             ^
checkRd: (-1) preprocessData.Rd:81: Lost braces
    81 | recommend using either \sQuote{code{.}} (a period) or
       |                                    ^
checkRd: (-1) preprocessData.Rd:82: Lost braces
    82 | \sQuote{code{_}} (an underscore) rather than a space.
       |             ^
checkRd: (-1) stat_quantile_prob.Rd:14: Lost braces; missing escapes or markup?
    14 | Number {25, 50, 75}
       |        ^
Specified C++11: please drop specification unless essential
checkRd: (-1) calculateDIC.Rd:30-31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) calculateDIC.Rd:32-33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) polySegratioMM-package.Rd:70-72: Lost braces in \itemize; meant \describe ?
Found the following files/directories:
  ‘test-data.R’ ‘test-inits.R’ ‘test.bug’ ‘test.cmd’
checkRd: (-1) MLM_Model.Rd:31: Lost braces; missing escapes or markup?
    31 |   the weight vectors \bold{{w}^{i}} corresponds to class \eqn{i}{i}.
       |                                ^
checkRd: (-1) MLM_Model.Rd:33: Lost braces; missing escapes or markup?
    33 | We set \eqn{{\bold{{w}}^{h}} = 0} and the parameters to be learned are the weight vectors \bold{{w}^{i}}
       |                                                                                                     ^
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Found export directive that requires package ‘methods’:
  ‘exportClasses’
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains ‘methods’.
checkRd: (-1) Kendall.Rd:12-13: Lost braces
    12 | \item{rates}{a}{matrix or dataframe with four columns: Rate identifier, Year,
       |                ^
checkRd: (-1) Kendall.Rd:15: Lost braces
    15 | \item{grades}{number}{of different levels of means and variances to try, default is 1000}
       |                      ^
checkRd: (-1) Kendall.Rd:17-18: Lost braces
    17 | \item{maxvar}{maximum}{variance to search over, default is 0.20. The maximum
       |                       ^
checkRd: (-1) Kendall.Rd:20: Lost braces
    20 | \item{minvar}{minimum}{variance to search, default is 0.00001}
       |                       ^
checkRd: (-1) Kendall.Rd:22: Lost braces
    22 | \item{maxmean}{maximum}{limit on the mean values to search, default 1}
       |                        ^
checkRd: (-1) Kendall.Rd:24: Lost braces
    24 | \item{minmean}{minimum}{limit on the mean values to search, default 0.01}
       |                        ^
checkRd: (-1) Kendall.Rd:73: Escaped LaTeX specials: \&
checkRd: (-1) countCDFxt.Rd:63: Escaped LaTeX specials: \&
checkRd: (-1) plot.tfam.Rd:17: Lost braces
    17 | objects created using code{tfam_inertia}.}
       |                           ^
checkRd: (-1) popdemo-package.Rd:32: Lost braces
    32 |        code{\link{inertia}} measures asymptotic population density relative to stable
       |            ^
checkRd: (-1) tfa_inertia.Rd:33: Lost braces
    33 | item{inertia}{inertias of perturbed matrices}
       |     ^
checkRd: (-1) tfa_inertia.Rd:33: Lost braces
    33 | item{inertia}{inertias of perturbed matrices}
       |              ^
checkRd: (-1) survmean.Rd:83: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) survmean.Rd:84: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) survmean.Rd:85: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) survmean.Rd:86-88: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) cutoff_predictor.Rd:27: Lost braces
    27 |   \doi{10.5281/zenodo.17424}{DOI: 10.5281/zenodo.17424}. 
       |                             ^
checkRd: (-1) filter_stats.Rd:64: Lost braces
    64 |   \doi{10.5281/zenodo.17424}{DOI: 10.5281/zenodo.17424}
       |                             ^
checkRd: (-1) ia.Rd:105: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ia.Rd:106-108: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ia.Rd:109: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ia.Rd:110-112: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ia.Rd:118: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ia.Rd:119-121: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mlg.Rd:125-126: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mlg.Rd:126-128: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mlg.Rd:128-130: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mlg.Rd:102-104: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mlg.Rd:104-106: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mlg.Rd:106-107: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) plot_filter_stats.Rd:37: Lost braces
    37 |   \doi{10.5281/zenodo.17424}{DOI: 10.5281/zenodo.17424}
       |                             ^
Documented arguments not in \usage in Rd file 'genclone-method.Rd':
  ‘gen’ ‘loc’ ‘treatOther’ ‘quiet’

Functions with \usage entries need to have the appropriate \alias
entries, and all their 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
Missing link or links in Rd file 'pop.predict.Rd':
  ‘rrBLUP’

Missing link or links in Rd file 'x.val.Rd':
  ‘rrBLUP’

See section 'Cross-references' in the 'Writing R Extensions' manual.
Package suggested but not available for checking: ‘ragt2ridges’
Unknown package ‘ragt2ridges’ in Rd xrefs
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
checkRd: (-1) tradelist-class.Rd:91: Escaped LaTeX specials: \$
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
Specified C++11: please drop specification unless essential
checkRd: (-1) summary.POUMM.Rd:28: Lost braces; missing escapes or markup?
    28 | \item{stats}{a named list of functions of the form function(par) { number },
       |                                                                  ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) coalesce_xy.Rd:22: Lost braces; missing escapes or markup?
    22 | the \code{conflict} argument of {powerjoin}'s join functions. \code{coalesce_xy()} is
       |                                 ^
checkRd: (-1) power_left_join.Rd:67: Lost braces; missing escapes or markup?
    67 | \item{by}{As in {dplyr}, but extended so user can supply a formula or a list
       |                 ^
checkRd: (-1) power_left_join.Rd:79: Lost braces; missing escapes or markup?
    79 | \item{keep}{A boolean for compatibility with {dplyr}, or a value among "left",
       |                                              ^
checkRd: (-1) preprocess_inputs.Rd:37: Lost braces; missing escapes or markup?
    37 | only be used in the \code{x} and \code{y} arguments of {powerjoin} join functions. No
       |                                                        ^
checkRd: (-1) equal.ordered.Rd:27: Lost braces; missing escapes or markup?
    27 | A vector of values for one in {kappa, N, power} that is not supplied by the user.
       |                               ^
checkRd: (-1) equal.ordered.cov.Rd:33: Lost braces; missing escapes or markup?
    33 | A vector of values for one in {kappa, N, power} that is not supplied by the user.
       |                               ^
checkRd: (-1) equal.unordered.Rd:27: Lost braces; missing escapes or markup?
    27 | A vector of values for one in {kappa, N, power} that is not supplied by the user.
       |                               ^
checkRd: (-1) equal.unordered.cov.Rd:33: Lost braces; missing escapes or markup?
    33 | A vector of values for one in {kappa, N, power} that is not supplied by the user.
       |                               ^
checkRd: (-1) unequal.ordered.Rd:30: Lost braces; missing escapes or markup?
    30 | A vector of values for one in {kappa, N, power} that is not supplied by the user.
       |                               ^
checkRd: (-1) unequal.ordered.cov.Rd:36: Lost braces; missing escapes or markup?
    36 | A vector of values for one in {kappa, N, power} that is not supplied by the user.
       |                               ^
checkRd: (-1) unequal.unordered.Rd:30: Lost braces; missing escapes or markup?
    30 | A vector of values for one in {kappa, N, power} that is not supplied by the user.
       |                               ^
checkRd: (-1) unequal.unordered.cov.Rd:36: Lost braces; missing escapes or markup?
    36 | A vector of values for one in {kappa, N, power} that is not supplied by the user.
       |                               ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) bira2.Rd:91: Escaped LaTeX specials: \&
checkRd: (-1) bira2.Rd:144: Escaped LaTeX specials: \&
checkRd: (-1) bira2.Rd:146: Escaped LaTeX specials: \&
checkRd: (-1) bira2.Rd:148: Escaped LaTeX specials: \&
checkRd: (-1) bira2.Rd:150: Escaped LaTeX specials: \&
checkRd: (-1) cra2.Rd:126: Escaped LaTeX specials: \&
checkRd: (-1) cra2.Rd:219: Escaped LaTeX specials: \&
checkRd: (-1) cra2.Rd:221: Escaped LaTeX specials: \&
checkRd: (-1) cra2.Rd:223: Escaped LaTeX specials: \&
checkRd: (-1) cra2.Rd:225: Escaped LaTeX specials: \&
checkRd: (-1) cra2.Rd:227: Escaped LaTeX specials: \&
checkRd: (-1) cra2.Rd:229: Escaped LaTeX specials: \&
checkRd: (-1) cra2.Rd:231: Escaped LaTeX specials: \&
checkRd: (-1) cra2.Rd:233: Escaped LaTeX specials: \&
checkRd: (-1) cra2.Rd:235: Escaped LaTeX specials: \&
checkRd: (-1) cra2.Rd:237: Escaped LaTeX specials: \&
checkRd: (-1) cra3.Rd:301: Escaped LaTeX specials: \&
checkRd: (-1) cra3.Rd:303: Escaped LaTeX specials: \&
checkRd: (-1) cra3.Rd:305: Escaped LaTeX specials: \&
checkRd: (-1) cra3.Rd:307: Escaped LaTeX specials: \&
checkRd: (-1) cra3.Rd:309: Escaped LaTeX specials: \&
checkRd: (-1) med_pn.Rd:129: Escaped LaTeX specials: \&
Objects in \usage without \alias in Rd file 'ppmlasso-internal.Rd':
  ‘spatRes’

Functions with \usage entries need to have the appropriate \alias
entries, and all their 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) ccp_ppm.Rd:26: Lost braces; missing escapes or markup?
    26 | \item{model}{Determines of model fit is such that there are p_{it}s (model=1) or
       |                                                               ^
checkRd: (-1) curve_ppmx.Rd:145: Lost braces; missing escapes or markup?
   145 | \item sig2 - a matrix of dimension (T, N) containing MCMC iterates associated with each subjects variance parameter (sigma2*_{c_i})
       |                                                                                                                              ^
checkRd: (-1) gaussian_ppmx.Rd:143: Lost braces; missing escapes or markup?
   143 | \item mu - a matrix  of dimension (T, N) containing MCMC iterates associated with each subjects mean parameter (mu*_{c_i}).
       |                                                                                                                     ^
checkRd: (-1) gaussian_ppmx.Rd:145: Lost braces; missing escapes or markup?
   145 | \item sig2 - a matrix of dimension (T, N) containing MCMC iterates associated with each subjects variance parameter (sigma2*_{c_i})
       |                                                                                                                              ^
checkRd: (-1) ordinal_ppmx.Rd:145: Lost braces; missing escapes or markup?
   145 | \item mu - a matrix  of dimension (T, N) containing MCMC iterates associated with each subjects mean parameter (mu*_{c_i}).
       |                                                                                                                     ^
checkRd: (-1) ordinal_ppmx.Rd:147: Lost braces; missing escapes or markup?
   147 | \item sig2 - a matrix of dimension (T, N) containing MCMC iterates associated with each sujbects variance parameter (sigma2*_{c_i})
       |                                                                                                                              ^
'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
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
checkRd: (-1) pqrBayes.Rd:58: Lost braces; missing escapes or markup?
    58 | When {sparse=TRUE} (default), spike--and--slab priors are adopted. Otherwise, Laplacian shrinkage will be used.
       |      ^
checkRd: (-1) pqrBayes.Rd:62: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pqrBayes.Rd:63: Lost braces in \itemize; meant \describe ?
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) PRDA.Rd:8: Lost braces; missing escapes or markup?
     8 | Given an hypothetical value of effect size, {PRDA} performs a prospective
       |                                             ^
checkRd: (-1) PRDA.Rd:22: Lost braces; missing escapes or markup?
    22 | In {PRDA} there are two main functions:
       |    ^
checkRd: (-1) PRDA.Rd:51: Lost braces; missing escapes or markup?
    51 | Alternatively, {PRDA} allows users to specify a distribution of plausible
       |                ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) 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.
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 ?
Found the following significant warnings:
  ./include/MCMC/sampler.h:241:55: warning: format ‘%i’ expects argument of type ‘int’, but argument 2 has type ‘uint_fast32_t’ {aka ‘long unsigned int’} [-Wformat=]
  postProcess.cpp:57:51: warning: format ‘%i’ expects argument of type ‘int’, but argument 2 has type ‘long unsigned int’ [-Wformat=]
  postProcess.cpp:102:43: warning: format ‘%i’ expects argument of type ‘int’, but argument 2 has type ‘long unsigned int’ [-Wformat=]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/PReMiuM.Rcheck/00install.out’ for details.
* used C++ compiler: ‘g++-13 (Debian 13.2.0-7) 13.2.0’
'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.
       |                   ^
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.
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
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) read.clipboard.Rd:62: Lost braces
    62 | \details{A typical session of R might involve data stored in text files, generated online, etc. Although it is easy to just read from a file (particularly if using \code{\link{read.file}}, an alternative is to use one's local system to copy from the file to the clipboard and then read from the clipboard  \code{\link{read.clipboard}}. This is  very convenient (and somewhat more intuitive to the naive user). This is particularly convenient when copying from a text book or article and just moving a section of text into R.)  However, copying from a file and then reading the clipboard is hard to automate in a script.  Thus, code{\link{read.file}} will read from a file.
       |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        ^
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
Found the following significant warnings:
  bounded_reg.cpp:33:25: warning: ‘std::ostream& arma::arma_cerr_stream(std::ostream*) [with T = char; std::ostream = std::basic_ostream<char>]’ is deprecated: this function does nothing; instead use ARMA_CERR_STREAM or ARMA_WARN_LEVEL; see documentation [-Wdeprecated-declarations]
  elastic_net.cpp:35:25: warning: ‘std::ostream& arma::arma_cerr_stream(std::ostream*) [with T = char; std::ostream = std::basic_ostream<char>]’ is deprecated: this function does nothing; instead use ARMA_CERR_STREAM or ARMA_WARN_LEVEL; see documentation [-Wdeprecated-declarations]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/quadrupen.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-13 (Debian 13.2.0-7) 13.2.0’
* used C++ compiler: ‘g++-13 (Debian 13.2.0-7) 13.2.0’
checkRd: (-1) bounded.reg.Rd:90-95: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bounded.reg.Rd:97-98: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bounded.reg.Rd:100-102: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bounded.reg.Rd:104-106: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bounded.reg.Rd:108-111: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bounded.reg.Rd:113-115: Lost braces in \itemize; meant \describe ?
checkRd: (-1) elastic.net.Rd:92-97: Lost braces in \itemize; meant \describe ?
checkRd: (-1) elastic.net.Rd:99-100: Lost braces in \itemize; meant \describe ?
checkRd: (-1) elastic.net.Rd:102-103: Lost braces in \itemize; meant \describe ?
checkRd: (-1) elastic.net.Rd:105-107: Lost braces in \itemize; meant \describe ?
checkRd: (-1) elastic.net.Rd:109-112: Lost braces in \itemize; meant \describe ?
checkRd: (-1) elastic.net.Rd:114-119: Lost braces in \itemize; meant \describe ?
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.
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 ?
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
'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.
Found the following significant warnings:
  cdotree.cpp:33:23: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
  cdotree.cpp:33:32: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
  cdotree.cpp:57:23: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
  cdotree.cpp:57:30: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
  cdotree.cpp:57:39: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
  cmbrt.cpp:149:21: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
  cmbrt.cpp:161:29: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 2 has type ‘int’ [-Wformat=]
  cmbrt.cpp:170:31: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
  cpsambrt.cpp:188:21: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
  cpsambrt.cpp:208:29: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 2 has type ‘int’ [-Wformat=]
  cpsambrt.cpp:222:31: warning: format ‘%d’ 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/rbart.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-13 (Debian 13.2.0-7) 13.2.0’
* used C++ compiler: ‘g++-13 (Debian 13.2.0-7) 13.2.0’
Specified C++11: please drop specification unless essential
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
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.
Found the following significant warnings:
  ../inst/include/Rcpp/iostream/Rstreambuf.h:53:20: warning: field precision specifier ‘.*’ expects argument of type ‘int’, but argument 2 has type ‘std::streamsize’ {aka ‘long int’} [-Wformat=]
  ../inst/include/Rcpp/iostream/Rstreambuf.h:57:21: warning: field precision specifier ‘.*’ expects argument of type ‘int’, but argument 2 has type ‘std::streamsize’ {aka ‘long int’} [-Wformat=]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/Rcpp.Rcheck/00install.out’ for details.
* used C++ compiler: ‘g++-13 (Debian 13.2.0-7) 13.2.0’
checkRd: (-1) getRcppVersion.Rd:22: Lost braces; missing escapes or markup?
    22 | {DESCRIPTION}, this version does get incremented more easily
       | ^
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
'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.
checkRd: (-1) DecisionTree.Rd:513: Lost braces; missing escapes or markup?
   513 | \item{\code{by}}{One of {"path", "strategy", "run"}. If "path", the table has
       |                         ^
checkRd: (-1) Graph.Rd:303: Lost braces
   303 | cell is {\code{FALSE}, \code{TRUE}}.}
       |         ^
checkRd: (-1) SemiMarkovModel.Rd:39: Lost braces; missing escapes or markup?
    39 | nodes {A,B} representing the transition probabilities from A to B and 
       |       ^
'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 ?
'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’
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.
'LazyData' is specified without a 'data' directory
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}
       |                                                   ^
Found the following files/directories:
  ‘Filled.RData’ ‘cleaned.RData’ ‘days’ ‘gridded’
'LazyData' is specified without a 'data' directory
checkRd: (-1) redist.calc.frontier.size.Rd:15: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) redist.calc.frontier.size.Rd:16: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) redist.calc.frontier.size.Rd:17: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) redist.calc.frontier.size.Rd:18: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) redist.crsg.Rd:49-50: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) redist.crsg.Rd:51-52: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) redist.crsg.Rd:53-54: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) redist.rsg.Rd:39-40: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) redist.rsg.Rd:41-42: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) redist.rsg.Rd:43-44: Lost braces in \itemize; \value handles \item{}{} directly
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)}
       | ^
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    37 | The set of divisors is formed by the odd numbers, that is {1,3,..,2n+1}.
       |                                                           ^
'LazyData' is specified without a 'data' directory
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    49 |   --- {F}{or t for objects of class \code{lm, lmrob} and \code{glm}
       |       ^
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    49 |   --- {F}{or t for objects of class \code{lm, lmrob} and \code{glm}
       |          ^
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    51 |   --- {Chi-squared}{for other \code{glm}s and \code{survreg}}\cr
       |       ^
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    51 |   --- {Chi-squared}{for other \code{glm}s and \code{survreg}}\cr
       |                    ^
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   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
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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) ena.plot.group.Rd:44: Escaped LaTeX specials: \$
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    17 | /enumerated{
       |            ^
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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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    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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checkRd: (-1) repo_build.Rd:44-47: Lost braces
    44 | ## chunk "item 1" {
       |                   ^
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checkRd: (-1) repo_dependencies.Rd:51-53: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) NCBirths2004.Rd:16: Lost braces
    16 |     \item{\code{Smoker}}{Mother a smoker? code{No}, \code{Yes}}
       |                                               ^
checkRd: (-1) ExpandProbs.Rd:35: Lost braces; missing escapes or markup?
    35 |      {z_probs2 sqrt((n-1)/n) = t_probs,n-1}
       |      ^
'LazyData' is specified without a 'data' directory
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: \_
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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
checkRd: (-1) harmonize_values.Rd:44: Lost braces; missing escapes or markup?
    44 | \item{perl}{Use perl-like regex? Defaults to {FALSE}.}
       |                                              ^
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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 ?
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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"}.}
       |                   ^
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    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: \$
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'LazyData' is specified without a 'data' directory
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    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}}
       |       ^
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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.
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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}}
       |                                             ^
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    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: 
       |          ^
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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
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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
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    64 | \code{facetMincount={#}} to exclude facets with a count less than {#}}
       |                                                                   ^
checkRd: (-1) name_lookup.Rd:114: Lost braces; missing escapes or markup?
   114 | facetMincount={#} to exclude facets with a count less than {#}, e.g.
       |               ^
checkRd: (-1) name_lookup.Rd:114: Lost braces; missing escapes or markup?
   114 | facetMincount={#} to exclude facets with a count less than {#}, e.g.
       |                                                            ^
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
       |                                                                                                                                               ^
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No news entries found.
checkRd: (-1) gd_region.Rd:13: Lost braces; missing escapes or markup?
    13 | \item{x}{either a WKT string (character), a {terra} SpatRaster(Collection)/SpatVector(Collection)/SpatExtent, an {sf} object, an {sp} Spatial* object or a {raster} RasterLayer/RasterStack.}
       |                                             ^
checkRd: (-1) gd_region.Rd:13: Lost braces; missing escapes or markup?
    13 | \item{x}{either a WKT string (character), a {terra} SpatRaster(Collection)/SpatVector(Collection)/SpatExtent, an {sf} object, an {sp} Spatial* object or a {raster} RasterLayer/RasterStack.}
       |                                                                                                                  ^
checkRd: (-1) gd_region.Rd:13: Lost braces; missing escapes or markup?
    13 | \item{x}{either a WKT string (character), a {terra} SpatRaster(Collection)/SpatVector(Collection)/SpatExtent, an {sf} object, an {sp} Spatial* object or a {raster} RasterLayer/RasterStack.}
       |                                                                                                                                  ^
checkRd: (-1) gd_region.Rd:13: Lost braces; missing escapes or markup?
    13 | \item{x}{either a WKT string (character), a {terra} SpatRaster(Collection)/SpatVector(Collection)/SpatExtent, an {sf} object, an {sp} Spatial* object or a {raster} RasterLayer/RasterStack.}
       |                                                                                                                                                            ^
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 ?
Found the following significant warnings:
  Rglpk_read_file.c:215:26: warning: format ‘%c’ expects argument of type ‘int’, but argument 2 has type ‘char *’ [-Wformat=]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/Rglpk.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-13 (Debian 13.2.0-7) 13.2.0’
'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
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: \&
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Specified C++11: please drop specification unless essential
checkRd: (-1) iex.chart.Rd:23: Lost braces; missing escapes or markup?
    23 | r takes only of of the values accepted IN API request. {"5y", "2y", "1y", "ytd", "6m", "3m", "1m", "1d"}
       |                                                        ^
checkRd: (-1) descrip.Rd:122: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) descrip.Rd:123: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) descrip.Rd:124-125: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) descrip.Rd:126-128: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) descrip.Rd:129-133: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) descrip.Rd:134-135: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) descrip.Rd:136-138: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) descrip.Rd:139-140: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) descrip.Rd:141-144: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) descrip.Rd:145-146: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) descrip.Rd:147: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) descrip.Rd:148: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) descrip.Rd:149: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) correct_sign.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) correct_sign.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
File ‘RInside/libs/RInside.so’:
  Found ‘srand’, possibly from ‘srand’ (C)
    Object: ‘RInside.o’
File ‘RInside/libs/RInside.so’:
  Found non-API calls to R: ‘R_CStackLimit’, ‘R_CleanTempDir’,
    ‘R_DefParams’, ‘R_ReplDLLinit’, ‘R_RunExitFinalizers’,
    ‘R_SetParams’, ‘R_SignalHandlers’, ‘R_TempDir’, ‘Rf_endEmbeddedR’,
    ‘Rf_initEmbeddedR’, ‘run_Rmainloop’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
checkRd: (-1) ipc_get_analyses.Rd:46: Lost braces; missing escapes or markup?
    46 | available on the \strong{analyses/{id}/{period}} advanced API endpoint,
       |                                   ^
checkRd: (-1) ipc_get_analyses.Rd:46: Lost braces; missing escapes or markup?
    46 | available on the \strong{analyses/{id}/{period}} advanced API endpoint,
       |                                        ^
checkRd: (-1) ipc_get_areas.Rd:50: Lost braces; missing escapes or markup?
    50 | and period, available on the \strong{areas/{id}/{period}} advanced API endpoint,
       |                                            ^
checkRd: (-1) ipc_get_areas.Rd:50: Lost braces; missing escapes or markup?
    50 | and period, available on the \strong{areas/{id}/{period}} advanced API endpoint,
       |                                                 ^
checkRd: (-1) ipc_get_icons.Rd:49: Lost braces; missing escapes or markup?
    49 | and period, available on the \strong{types/{id}/{period}} advanced API endpoint,
       |                                            ^
checkRd: (-1) ipc_get_icons.Rd:49: Lost braces; missing escapes or markup?
    49 | and period, available on the \strong{types/{id}/{period}} advanced API endpoint,
       |                                                 ^
checkRd: (-1) ipc_get_points.Rd:47: Lost braces; missing escapes or markup?
    47 | and period, available on the \strong{types/{id}/{period}} advanced API endpoint,
       |                                            ^
checkRd: (-1) ipc_get_points.Rd:47: Lost braces; missing escapes or markup?
    47 | and period, available on the \strong{types/{id}/{period}} advanced API endpoint,
       |                                                 ^
checkRd: (-1) ipc_get_population.Rd:49: Lost braces; missing escapes or markup?
    49 | analysis, available on the \strong{types/{id}} advanced API endpoint,
       |                                          ^
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) pkg_ref.Rd:74-93: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pkg_ref.Rd:77: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pkg_ref.Rd:78-80: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pkg_ref.Rd:81-91: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pkg_ref.Rd:84-85: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pkg_ref.Rd:86-87: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pkg_ref.Rd:88-89: Lost braces in \itemize; meant \describe ?
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.}
       |                              ^
checkRd: (-1) iidCox.Rd:91: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) iidCox.Rd:92: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) iidCox.Rd:93: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) iidCox.Rd:94: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) iidCox.Rd:95: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) iidCox.Rd:96: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) iidCox.Rd:97: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) iidCox.Rd:98: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) plotCalibration.Rd:53-56: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotCalibration.Rd:57-61: Lost braces
    57 | \item{\code{"nne"}}: {The observed proportion at predicted risk value 'p' is obtained based
       |                      ^
checkRd: (-1) plotCalibration.Rd:65-67: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotCalibration.Rd:68-71: Lost braces in \itemize; meant \describe ?
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-gcc/Work/build/Packages/rJava/libs/rJava.so’:
  Found ‘_exit’, possibly from ‘_exit’ (C)
  Found ‘stderr’, possibly from ‘stderr’ (C)
  Found ‘stdout’, possibly from ‘stdout’ (C)
File ‘rJava/libs/rJava.so’:
  Found non-API calls to R: ‘R_CStackLimit’, ‘R_CStackStart’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Specified C++11: please drop specification unless essential
License stub is invalid DCF.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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 : {}}"}
       |                  ^
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
checkRd: (-1) internal_plots.Rd:193-203: Lost braces
   193 | \code{.cexscale}{rescales the point sizes of the points to be plotted;
       |                 ^
checkRd: (-1) internal_plots.Rd:204: Lost braces
   204 | \code{.getDimsTD}{returns the number of different coordinates to be plotted.}
       |                  ^
checkRd: (-1) internal_plots.Rd:205-207: Lost braces
   205 | \code{.producePanelFirstS}{for each graphical panel inserts
       |                           ^
checkRd: (-1) internal_plots.Rd:208-209: Lost braces
   208 | \code{.getX.vec}{produces the x-grid (on original scale) for each of the panels
       |                 ^
checkRd: (-1) internal_plots.Rd:211-212: Lost braces
   211 | \code{.getXlimYlim}{produces panel-wise \code{xlim} and \code{ylim} arguments
       |                    ^
checkRd: (-1) internal_plots.Rd:213: Lost braces
   213 | \code{.prepareTitles}{produces the titles for the panels}
       |                      ^
checkRd: (-1) internal_plots.Rd:214: Lost braces
   214 | \code{.getToDraw}{computes which panels are to be drawn}
       |                  ^
checkRd: (-1) internal_plots.Rd:215-216: Lost braces
   215 | \code{.preparePanelFirstLast}{prepares the \code{panel.first} and \code{panel.last}
       |                              ^
Documented arguments not in \usage in Rd file 'internal_plots.Rd':
  ‘panelFirst’

Documented arguments not in \usage in Rd file 'internals.Rd':
  ‘L2fam’
Objects in \usage without \alias in Rd file 'internals.Rd':
  ‘.evalListRec’ ‘.filterEargsWEargList’

Functions with \usage entries need to have the appropriate \alias
entries, and all their 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 ‘RobAStBase-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: RobAStBase-package
> ### Title: Robust Asymptotic Statistics
> ### Aliases: RobAStBase-package RobAStBase
> ### Keywords: package
> 
> ### ** Examples
> 
> library(RobAStBase)
> ## some L2 differentiable parametric family from package distrMod, e.g.
> B <- BinomFamily(size = 25, prob = 0.25) 
Warning in .local(.Object, ...) : you have to specify slot r at least
Error: unable to find an inherited method for function ‘r’ for signature ‘object = "numeric"’
Execution halted
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},
       |                                                                                       ^
Specified C++11: please drop specification unless essential
checkRd: (-1) GEV-class.Rd:27: Lost braces
    27 | point (if eqn{s > 0}).
       |              ^
Documented arguments not in \usage in Rd file 'internal-interpolate.Rd':
  ‘upRad.s’
Objects in \usage without \alias in Rd file 'internal-interpolate.Rd':
  ‘.getPsi.wL’ ‘.getPsi.P’

Objects in \usage without \alias in Rd file 'rescaleFunction-methods.Rd':
  ‘rescaleFunction’

Functions with \usage entries need to have the appropriate \alias
entries, and all their 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 '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) weighted_median_line.Rd:34: Lost braces; missing escapes or markup?
    34 |                     {m([y - m(y, w)][x - m(x, w)], w) / m([x - m(x, w)]^2, w).}
       |                     ^
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
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.
       |                                        ^
'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
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}".}
       |                                                                                                                                                                                                                                                                                                                                                               ^
Running examples in ‘ROptEstOld-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: BinomFamily
> ### Title: Generating function for Binomial families
> ### Aliases: BinomFamily
> ### Keywords: models
> 
> ### ** Examples
> 
> (B1 <- BinomFamily(size = 25, prob = 0.25))
Warning in .local(.Object, ...) : you have to specify slot r at least
Error: unable to find an inherited method for function ‘r’ for signature ‘object = "numeric"’
Execution halted
checkRd: (-1) internal-interpolate.Rd:160: Lost braces
   160 |   \code{.saveGridToCSV}{\code{invisible(NULL)}. }
       |                        ^
checkRd: (-1) internal-interpolate.Rd:162-164: Lost braces
   162 |   \code{.readGridFromCSV}{ a list with the read-in items, i.e.,
       |                          ^
checkRd: (-1) internal-interpolate.Rd:166: Lost braces
   166 |   \code{.generateInterpGrid}{\code{invisible(NULL)}. }
       |                             ^
Documented arguments not in \usage in Rd file 'internal-interpolate.Rd':
  ‘upRad.s’ ‘withSmooth’
Assignments in \usage in Rd file 'internal-interpolate.Rd':
  .readGridFromCSV <- function(fromFileCSV) .generateInterpGrid(thGrid, 
      PFam, toFileCSV = "temp.csv", getFun = .getLMGrid, ..., modifyfct, 
      nameInSysdata, GridFileName, withPrint = TRUE, len = 13)

Objects in \usage without \alias in Rd file 'internalRobestHelpers.Rd':
  ‘.constructArg.list’ ‘.fix.in.defaults’ ‘.pretreat’ ‘.check.eps’
  ‘.isOKsteps’ ‘.isOKfsCor’

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

Objects in \usage without \alias in Rd file 'internals.Rd':
  ‘.isVirginW’

Functions with \usage entries need to have the appropriate \alias
entries, and all their 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 ‘ROptEst-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: RMXEOMSEMBREOBRE
> ### Title: Optimally robust estimation: RMXE, OMSE, MBRE, and OBRE
> ### Aliases: RMXEstimator OMSEstimator OBREstimator MBREstimator
> ### Keywords: robust
> 
> ### ** Examples
> 
> #############################
> ## 1. Binomial data
> #############################
> ## generate a sample of contaminated data
> set.seed(123)
> ind <- rbinom(100, size=1, prob=0.05)
> x <- rbinom(100, size=25, prob=(1-ind)*0.25 + ind*0.9)
> 
> ## ML-estimate
> MLE.bin <- MLEstimator(x, BinomFamily(size = 25))
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 'startPar': unable to find an inherited method for function ‘r’ for signature ‘object = "numeric"’
Calls: MLEstimator ... initialize -> initialize -> .local -> table -> r -> <Anonymous>
Execution halted
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
Specified C++11: please drop specification unless essential
'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.
Found the following significant warnings:
  phylopars_rcpp.cpp:125:26: warning: ‘void arma::set_cerr_stream(const std::ostream&)’ is deprecated: this function does nothing; instead use ARMA_CERR_STREAM or ARMA_WARN_LEVEL; see documentation [-Wdeprecated-declarations]
  phylopars_rcpp.cpp:144:26: warning: ‘void arma::set_cerr_stream(const std::ostream&)’ is deprecated: this function does nothing; instead use ARMA_CERR_STREAM or ARMA_WARN_LEVEL; see documentation [-Wdeprecated-declarations]
  phylopars_rcpp.cpp:179:26: warning: ‘void arma::set_cerr_stream(const std::ostream&)’ is deprecated: this function does nothing; instead use ARMA_CERR_STREAM or ARMA_WARN_LEVEL; see documentation [-Wdeprecated-declarations]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/Rphylopars.Rcheck/00install.out’ for details.
* used C++ compiler: ‘g++-13 (Debian 13.2.0-7) 13.2.0’
checkRd: (-1) simtraits.Rd:7: Lost braces
     7 | Simulates traits for code{phylopars} estimation.
       |                          ^
Argument items with no description in Rd file 'anova.phylopars.lm.Rd':
  ‘\dots’
Argument items with no description in Rd file 'logLik.phylopars.Rd':
  ‘\dots’
Argument items with no description in Rd file 'logLik.phylopars.lm.Rd':
  ‘\dots’
Argument items with no description in Rd file 'print.SSC.Rd':
  ‘\dots’
Argument items with no description in Rd file 'print.phylopars.Rd':
  ‘\dots’
Argument items with no description in Rd file 'print.phylopars.lm.Rd':
  ‘\dots’
Argument items with no description in Rd file 'summary.phylopars.Rd':
  ‘\dots’
Argument items with no description in Rd file 'summary.phylopars.lm.Rd':
  ‘\dots’
'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
Found the following significant warnings:
  RS-pgsql-copy.c:305:44: warning: format ‘%s’ expects argument of type ‘char *’, but argument 2 has type ‘int’ [-Wformat=]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/RPostgreSQL.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-13 (Debian 13.2.0-7) 13.2.0’
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 ?
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)}.}
       |         ^
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-gcc/Work/build/Packages/Rserve/libs/Rserve.so’:
  Found ‘exit’, possibly from ‘exit’ (C)
  Found ‘rand’, possibly from ‘rand’ (C)
  Found ‘random’, possibly from ‘random’ (C)
  Found ‘srandom’, possibly from ‘srandom’ (C)
  Found ‘stderr’, possibly from ‘stderr’ (C)
File ‘Rserve/libs/Rserve.so’:
  Found non-API calls to R: ‘R_Consolefile’, ‘R_InputHandlers’,
    ‘R_Outputfile’, ‘R_TempDir’, ‘R_Visible’, ‘addInputHandler’,
    ‘ptr_R_Busy’, ‘ptr_R_ClearerrConsole’, ‘ptr_R_FlushConsole’,
    ‘ptr_R_ReadConsole’, ‘ptr_R_ResetConsole’, ‘ptr_R_ShowMessage’,
    ‘ptr_R_WriteConsole’, ‘ptr_R_WriteConsoleEx’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  model/variables/BehaviorVariable.cpp:990:55: warning: format ‘%x’ expects argument of type ‘unsigned int’, but argument 3 has type ‘siena::Effect*’ [-Wformat=]
  model/variables/BehaviorVariable.cpp:994:54: warning: format ‘%x’ expects argument of type ‘unsigned int’, but argument 3 has type ‘siena::Effect*’ [-Wformat=]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/RSiena.Rcheck/00install.out’ for details.
* used C++ compiler: ‘g++-13 (Debian 13.2.0-7) 13.2.0’
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
'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.
Found the following significant warnings:
  ../inst/include/rstan/io/r_ostream.hpp:48:20: warning: field precision specifier ‘.*’ expects argument of type ‘int’, but argument 2 has type ‘std::streamsize’ {aka ‘long int’} [-Wformat=]
  ../inst/include/rstan/io/r_ostream.hpp:71:21: warning: field precision specifier ‘.*’ expects argument of type ‘int’, but argument 2 has type ‘std::streamsize’ {aka ‘long int’} [-Wformat=]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/rstan.Rcheck/00install.out’ for details.
* used C++ compiler: ‘g++-13 (Debian 13.2.0-7) 13.2.0’
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’
checkRd: (-1) article.Rd:414: Lost braces
   414 | \verb{https://uk.sagepub.com/sites/default/files/sage_latex_template_4.zip}{class}.
       |                                                                            ^
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})}
       |     ^
Specified C++11: please drop specification unless essential
Found the following significant warnings:
  triangle.c:1428:9: warning: too many arguments for format [-Wformat-extra-args]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/RTriangle.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-13 (Debian 13.2.0-7) 13.2.0’
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) }
       |                                                                                   ^
'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) plotprofmle.Rd:20: Lost braces
    20 | \item{code{signature(object="profile.mle2")}}{The preferred invocation for these methods.}
       |           ^
checkRd: (-1) plotprofmle.Rd:21: Lost braces
    21 | \item{code{signature(object="mle2")}}{A convenience wrapper that calls \code{profile} on the mle2 object and runs the former method.}
       |           ^
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.
       |                                                                                                                                                                                                                                                                                            ^
'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
'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 ?
checkRd: (-1) simulation.Rd:42-44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulation.Rd:45-47: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulation.Rd:48-49: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulation.Rd:50-52: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulation.Rd:53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulation.Rd:54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulation.Rd:55: 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
checkRd: (-1) session_details.Rd:17: Lost braces; missing escapes or markup?
    17 | authenticated file downloads by appending josso={'jossoSessionId'} to the 
       |                                                 ^
Documented arguments not in \usage in Rd file 'item_rm_recursive.Rd':
  ‘sb_id’

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

Documented arguments not in \usage in Rd file 'session_expired.Rd':
  ‘sb_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.
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
'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.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
S3 methods shown with full name in Rd file 'plot.Rd':
  ‘plot.discretization’

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

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

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
checkRd: (-1) reduce_dimensionality.Rd:19: Lost braces
    19 | \item{ndim}{the maximum dimension of the space which the data are to be represented in; must be in {1, 2, \ldots, n-1}.}
       |                                                                                                    ^
checkRd: (-1) ti_scorpius.Rd:18: Lost braces; missing escapes or markup?
    18 | \item{distance_method}{A character string indicating which correlationcoefficient (or covariance) is to be computed. One of "pearson", "spearman" (default), or "cosine". Domain: {spearman, pearson, cosine}. Default: spearman. Format: character.}
       |                                                                                                                                                                                   ^
checkRd: (-1) ti_scorpius.Rd:30: Lost braces; missing escapes or markup?
    30 | \item{smoother}{\code{principal_curve} parameter; choice of smoother. Domain: {smooth_spline, lowess, periodic_lowess}. Default: smooth_spline. Format: character.}
       |                                                                               ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) simulateSNPs.Rd:46: Escaped LaTeX specials: \& \& \&
checkRd: (-1) simulateSNPs.Rd:80: Escaped LaTeX specials: \& \& \&
checkRd: (-1) scriptloc.Rd:5: Lost braces; missing escapes or markup?
     5 | \title{Get location of script in a fashion analagous to ${BASH_SOURCE[0]}}
       |                                                          ^
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
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 ?
Found the following significant warnings:
  Suda2.h:772:68: warning: format ‘%f’ expects argument of type ‘double’, but argument 3 has type ‘int’ [-Wformat=]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/sdcMicro.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-13 (Debian 13.2.0-7) 13.2.0’
* used C++ compiler: ‘g++-13 (Debian 13.2.0-7) 13.2.0’
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"}.}
       |                                                                                                                                   ^
checkRd: (-1) Gmixt_simultanee.Rd:21: Lost braces
    21 | { \\sum{p=1 -> P} log( \\pi{p} f( y{ij} ; \\theta{p} ) ) }
       | ^
checkRd: (-1) Gmixt_simultanee.Rd:21: Lost braces
    21 | { \\sum{p=1 -> P} log( \\pi{p} f( y{ij} ; \\theta{p} ) ) }
       |        ^
checkRd: (-1) Gmixt_simultanee.Rd:21: Lost braces
    21 | { \\sum{p=1 -> P} log( \\pi{p} f( y{ij} ; \\theta{p} ) ) }
       |                            ^
checkRd: (-1) Gmixt_simultanee.Rd:21: Lost braces
    21 | { \\sum{p=1 -> P} log( \\pi{p} f( y{ij} ; \\theta{p} ) ) }
       |                                    ^
checkRd: (-1) Gmixt_simultanee.Rd:21: Lost braces
    21 | { \\sum{p=1 -> P} log( \\pi{p} f( y{ij} ; \\theta{p} ) ) }
       |                                                  ^
checkRd: (-1) segclust2d.Rd:37: Lost braces
    37 | Patin, R., Etienne, M. P., Lebarbier, E., Chamaill{\'e}-Jammes, S., 
       |                                                   ^
Packages suggested but not available for checking: 'spgrass6', 'rgdal'
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
checkRd: (-1) SVbound.Rd:26: Lost braces; missing escapes or markup?
    26 | \item{RR_UY_T1}{Input value. The sensitivity parameter RR_{UY|T=1}. Must be
       |                                                           ^
checkRd: (-1) SVbound.Rd:29: Lost braces; missing escapes or markup?
    29 | \item{RR_UY_T0}{Input value. The sensitivity parameter RR_{UY|T=0}. Must be
       |                                                           ^
checkRd: (-1) SVbound.Rd:32: Lost braces; missing escapes or markup?
    32 | \item{RR_SU_T1}{Input value. The sensitivity parameter RR_{SU|T=1}. Must be
       |                                                           ^
checkRd: (-1) SVbound.Rd:35: Lost braces; missing escapes or markup?
    35 | \item{RR_SU_T0}{Input value. The sensitivity parameter RR_{SU|T=0}. Must be
       |                                                           ^
checkRd: (-1) SVbound.Rd:38: Lost braces; missing escapes or markup?
    38 | \item{RR_UY_S1}{Input value. The sensitivity parameter RR_{UY|S=1}. Must be
       |                                                           ^
checkRd: (-1) SVbound.Rd:41: Lost braces; missing escapes or markup?
    41 | \item{RR_TU_S1}{Input value. The sensitivity parameter RR_{TU|S=1}. Must be
       |                                                           ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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
checkRd: (-1) PAVranking.Rd:77-79: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) PAVranking.Rd:80-82: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) PAVranking.Rd:83-85: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) PAVranking.Rd:86-87: Lost braces in \itemize; \value handles \item{}{} directly
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
checkRd: (-1) sendmail_options.Rd:32-35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sendmail_options.Rd:36-37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sendmail_options.Rd:38-39: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
checkRd: (-1) match_dataphy.Rd:37-38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) match_dataphy.Rd:39-41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) match_dataphy.Rd:42-44: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Auto-generated content requiring editing in Rd file 'seqCBS-package.Rd':
  \details: ‘...the package, including the most important ~~ ~~ functions ~~’
Specified C++14: please drop specification unless essential
checkRd: (-1) process,HybridSequenceClassifier-method.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) process,HybridSequenceClassifier-method.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) process,HybridSequenceClassifier-method.Rd:32: Lost braces in \itemize; \value handles \item{}{} directly
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) SeqDesignInference.Rd:319: Lost braces; missing escapes or markup?
   319 | (a) difference in means estimator i.e. [ybar_T - ybar_C +/- t_{alpha/2, n_T + n_C - 2} s_{ybar_T - ybar_C}] or
       |                                                               ^
checkRd: (-1) SeqDesignInference.Rd:319: Lost braces; missing escapes or markup?
   319 | (a) difference in means estimator i.e. [ybar_T - ybar_C +/- t_{alpha/2, n_T + n_C - 2} s_{ybar_T - ybar_C}] or
       |                                                                                          ^
checkRd: (-1) SeqDesignInference.Rd:320: Lost braces; missing escapes or markup?
   320 | (b) the OLS estimator i.e. [beta_hat_T +/- t_{alpha/2, n + p - 2} s_{beta_hat_T}]
       |                                              ^
checkRd: (-1) SeqDesignInference.Rd:320: Lost braces; missing escapes or markup?
   320 | (b) the OLS estimator i.e. [beta_hat_T +/- t_{alpha/2, n + p - 2} s_{beta_hat_T}]
       |                                                                     ^
Found the following files/directories:
  ‘assocpointpair_result.csv’ ‘foundereffectfinder_result.csv’
  ‘getfreqs_result.csv’ ‘getfreqs_result.png’ ‘orPlot.pdf1_1.pdf’
  ‘orPlot.pdf2_1.pdf’ ‘orPlot.pdf3_1.pdf’ ‘orPlot.pdf4_1.pdf’
  ‘orPlot.pdf5_1.pdf’ ‘orPlot.pdf6_1.pdf’ ‘orPlot.pdf7_1.pdf’
  ‘orPlot.pdf8_1.pdf’ ‘q-values_result.csv’ ‘rewritetuple_result.csv’
  ‘tartan_plot.pdf’ ‘vispair_plot.pdf’ ‘vispairfeat_plot.pdf’
  ‘volcano_plot.pdf’
checkRd: (-1) poisthin.Rd:82-83: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) poisthin.Rd:84-85: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) poisthin.Rd:86: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) poisthin.Rd:87-88: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Argument items with no description in Rd file 'sequential.design.Rd':
  ‘\dots’
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) SEset_to_network.Rd:50: Escaped LaTeX specials: \&
checkRd: (-1) network_to_SEset.Rd:72: Escaped LaTeX specials: \&
checkRd: (-1) network_to_path.Rd:50: Escaped LaTeX specials: \&
checkRd: (-1) path_to_network.Rd:29: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘BPCells’
Packages suggested but not available for checking:
  'BPCells', 'monocle', 'presto'
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) kernels.Rd:28: Lost braces; missing escapes or markup?
    28 | \item \code{guassian}: K(z) = (2pi)^{1/2} * exp(-z^2/2)
       |                                     ^
Documented arguments not in \usage in Rd file 'jc_clc_perm_impl.Rd':
  ‘a’

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

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

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
checkRd: (-1) spatial_morphers.Rd:112: Lost braces
   112 | geospatial features as object of class code{\link[sf]{sf}} or
       |                                            ^
checkRd: (-1) st_relate.Rd:19: Lost braces; missing escapes or markup?
    19 | In case \code{pattern} is not given, \code{st_relate} returns a dense \code{character} matrix; element [i,j] has nine characters, referring to the DE9-IM relationship between x[i] and y[j], encoded as IxIy,IxBy,IxEy,BxIy,BxBy,BxEy,ExIy,ExBy,ExEy where I refers to interior, B to boundary, and E to exterior, and e.g. BxIy the dimensionality of the intersection of the the boundary of x[i] and the interior of y[j], which is one of {0,1,2,F}, digits denoting dimensionality, F denoting not intersecting. When \code{pattern} is given, a dense logical matrix or sparse index list returned with matches to the given pattern; see \link{st_intersection} for a description of the returned matrix or list. See also \url{https://en.wikipedia.org/wiki/DE-9IM} for further explanation.
       |                                                                                                                                                                                                                                                                                                                                                                                                                                                ^
Found the following significant warnings:
  c_functions.c:279:32: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘long long int’ [-Wformat=]
  c_functions.c:288:35: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘long long int’ [-Wformat=]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/SFSI.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-13 (Debian 13.2.0-7) 13.2.0’
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
Specified C++11: please drop specification unless essential
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},
       |                                          ^
checkRd: (-1) sgl_predict.Rd:38-49: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sgl_predict.Rd:40-43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sgl_predict.Rd:42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sgl_predict.Rd:44-47: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sgl_predict.Rd:46: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sgl_predict.Rd:50-61: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sgl_predict.Rd:52-55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sgl_predict.Rd:54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sgl_predict.Rd:56-59: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sgl_predict.Rd:58: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sgl_subsampling.Rd:73-84: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sgl_subsampling.Rd:75-78: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sgl_subsampling.Rd:77: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sgl_subsampling.Rd:79-82: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sgl_subsampling.Rd:81: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sgl_subsampling.Rd:85-96: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sgl_subsampling.Rd:87-90: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sgl_subsampling.Rd:89: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sgl_subsampling.Rd:91-94: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sgl_subsampling.Rd:93: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sgl_subsampling.Rd:105: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sgl_subsampling.Rd:106: Lost braces in \itemize; meant \describe ?
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
'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
checkRd: (-1) checkbox.Rd:54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) checkbox.Rd:55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) checkbox.Rd:56: Lost braces in \itemize; meant \describe ?
checkRd: (-1) multiple_checkbox.Rd:56: Lost braces in \itemize; meant \describe ?
checkRd: (-1) multiple_checkbox.Rd:57: Lost braces in \itemize; meant \describe ?
checkRd: (-1) multiple_checkbox.Rd:58: Lost braces in \itemize; meant \describe ?
checkRd: (-1) search_selection_api.Rd:27-70: Lost braces
    27 | if (interactive()) {
       |                    ^
checkRd: (-1) search_selection_api.Rd:33-42: Lost braces
    33 |    ui <- function() {
       |                     ^
checkRd: (-1) search_selection_api.Rd:44-67: Lost braces
    44 |   server <- shinyServer(function(input, output, session) {
       |                                                          ^
checkRd: (-1) search_selection_api.Rd:46-58: Lost braces
    46 |    search_api <- function(gapminder, q) {
       |                                         ^
checkRd: (-1) search_selection_api.Rd:47-49: Lost braces
    47 |      has_matching <- function(field) {
       |                                      ^
checkRd: (-1) text_input.Rd:50: Lost braces in \itemize; meant \describe ?
checkRd: (-1) text_input.Rd:51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) text_input.Rd:52: Lost braces in \itemize; meant \describe ?
checkRd: (-1) text_input.Rd:53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) text_input.Rd:54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) text_input.Rd:55: 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:
  ‘.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 ?
checkRd: (-1) pickerOptions.Rd:81: Lost braces; missing escapes or markup?
    81 | \item{noneResultsText}{The text displayed when a search doesn't return any results. Type: string; Default: 'No results matched {0}'.}
       |                                                                                                                                ^
checkRd: (-1) setBackgroundColor.Rd:25: Lost braces; missing escapes or markup?
    25 | \item{shinydashboard}{Set to \code{TRUE} if in a {shinydasboard} application.}
       |                                                  ^
checkRd: (-1) setBackgroundImage.Rd:13: Lost braces; missing escapes or markup?
    13 | \item{shinydashboard}{Set to \code{TRUE} if in a {shinydasboard} application.}
       |                                                  ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) MrBayes.Rd:24: Lost braces
    24 | \item{contype}{A character string; the type of consensus tree calculated from the posterior distribution of trees}{either "halfcompat" (majority-rule consensus tree) or "allcombat" (strict consensus tree)}
       |                                                                                                                   ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) shutterplot.Rd:59: Lost braces; missing escapes or markup?
    59 | \item{las}{numeric in {0,1,2,3}; the style of axis labels.'
       |                       ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) pop.dist.Rd:41: Lost braces; missing escapes or markup?
    41 | where \emph{dist(i,j)} represents the distance between populations \emph{i} and \emph{j}, \emph{m} and \emph{n} are the number of sequences in populations \emph{i} and \emph{j}, respectively, and \emph{dist(H_{ki},H_{lj})} is the distance between the \emph{k-th} sequence found in population \emph{i} and the \emph{l-th} sequence found in population \emph{j}. 
       |                                                                                                                                                                                                                  ^
checkRd: (-1) pop.dist.Rd:41: Lost braces; missing escapes or markup?
    41 | where \emph{dist(i,j)} represents the distance between populations \emph{i} and \emph{j}, \emph{m} and \emph{n} are the number of sequences in populations \emph{i} and \emph{j}, respectively, and \emph{dist(H_{ki},H_{lj})} is the distance between the \emph{k-th} sequence found in population \emph{i} and the \emph{l-th} sequence found in population \emph{j}. 
       |                                                                                                                                                                                                                         ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) drr.Rd:36: Lost braces; missing escapes or markup?
    36 |   \code{drr} {is Rosin - Rammler probability density function}\cr
       |              ^
checkRd: (-1) drr.Rd:37: Lost braces; missing escapes or markup?
    37 |   \code{urr} {is Rosin - Rammler cumulative distribution function (CDF) representing undersize mass fraction}\cr
       |              ^
checkRd: (-1) drr.Rd:38: Lost braces
    38 |   \code{orr} {is Rosin - Rammler complementary CDF representing oversize mass fraction ie. relative remainder on the sieve with the mesh size \code{x}}\cr
       |              ^
Specified C++11: please drop specification unless essential
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
checkRd: (-1) add_k_mer_state.Rd:34: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) add_k_mer_state.Rd:35: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) add_k_mer_state.Rd:36: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) duration_viterbi.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) duration_viterbi.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) duration_viterbi.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) duration_viterbi.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) sig.Rd:35: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sig.Rd:36: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sig_report.Rd:41: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sig_report.Rd:42: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sig_report.Rd:43: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sig_report.Rd:44: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sig_report.Rd:45-46: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sig_report.Rd:47: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sig_report.Rd:48: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sig_report.Rd:49-50: Lost braces in \itemize; \value handles \item{}{} directly